3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.3">2.10.3</a><br />
74 <em>10/10/2017</em></strong>
77 <td><div align="left">
81 <!-- JAL-2446 -->Faster and more efficient management and
82 rendering of sequence features
85 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
86 429 rate limit request hander
89 <!-- JAL-2773 -->Structure views don't get updated unless
90 their colours have changed
93 <ul><li>Example groovy script for generating a matrix of percent identity scores for current alignment.</li></ul>
95 <td><div align="left">
98 <li><!-- JAL-2777 -->Structures with whitespace chainCode cannot be viewed in Chimera</li>
99 <li><!-- JAL-2728 -->Protein annotation panel too high in CDS/Protein view
101 <li><!-- JAL-2757 -->Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs
103 <li><!-- JAL-2253 -->Slow EnsemblGenome ID lookup</li>
104 <li><!-- JAL-2682 -->Race condition when parsing sequence ID strings in parallel</li>
105 <li><!-- JAL-2739 -->Hidden column marker in last column not rendered when switching back from Wrapped to normal view</li>
106 <li><!-- JAL-2768 -->Annotation display corrupted when scrolling right in unwapped alignment view</li>
107 <li><!-- JAL-2542 -->Existing features on subsequence incorrectly relocated when full sequence retrieved from database</li>
108 <li><!-- JAL-2608 -->Overview windows are also closed when alignment window is closed</li>
109 <li><!-- JAL-2733 -->Last reported memory still shown when Desktop->Show Memory is unticked (OSX only)</li>
110 <li><!-- JAL-2658 -->Amend Features dialog doesn't allow features of same type and group to be selected for amending</li>
111 <li><!-- JAL-2524 -->Jalview becomes sluggish in wide alignments when hidden columns are present</li>
113 <strong><em>Applet</em></strong><br/>
115 <li><!-- JAL-2687 -->Concurrent modification exception when closing alignment panel</li>
120 <td width="60" nowrap>
122 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
123 <em>2/10/2017</em></strong>
126 <td><div align="left">
127 <em>New features in Jalview Desktop</em>
130 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
132 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
136 <td><div align="left">
140 <td width="60" nowrap>
142 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
143 <em>7/9/2017</em></strong>
146 <td><div align="left">
150 <!-- JAL-2588 -->Show gaps in overview window by colouring
151 in grey (sequences used to be coloured grey, and gaps were
155 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
159 <!-- JAL-2587 -->Overview updates immediately on increase
160 in size and progress bar shown as higher resolution
161 overview is recalculated
166 <td><div align="left">
170 <!-- JAL-2664 -->Overview window redraws every hidden
171 column region row by row
174 <!-- JAL-2681 -->duplicate protein sequences shown after
175 retrieving Ensembl crossrefs for sequences from Uniprot
178 <!-- JAL-2603 -->Overview window throws NPE if show boxes
179 format setting is unticked
182 <!-- JAL-2610 -->Groups are coloured wrongly in overview
183 if group has show boxes format setting unticked
186 <!-- JAL-2672,JAL-2665 -->Redraw problems when
187 autoscrolling whilst dragging current selection group to
188 include sequences and columns not currently displayed
191 <!-- JAL-2691 -->Not all chains are mapped when multimeric
192 assemblies are imported via CIF file
195 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
196 displayed when threshold or conservation colouring is also
200 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
204 <!-- JAL-2673 -->Jalview continues to scroll after
205 dragging a selected region off the visible region of the
209 <!-- JAL-2724 -->Cannot apply annotation based
210 colourscheme to all groups in a view
213 <!-- JAL-2511 -->IDs don't line up with sequences
214 initially after font size change using the Font chooser or
221 <td width="60" nowrap>
223 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
226 <td><div align="left">
227 <em>Calculations</em>
231 <!-- JAL-1933 -->Occupancy annotation row shows number of
232 ungapped positions in each column of the alignment.
235 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
236 a calculation dialog box
239 <!-- JAL-2379 -->Revised implementation of PCA for speed
240 and memory efficiency (~30x faster)
243 <!-- JAL-2403 -->Revised implementation of sequence
244 similarity scores as used by Tree, PCA, Shading Consensus
245 and other calculations
248 <!-- JAL-2416 -->Score matrices are stored as resource
249 files within the Jalview codebase
252 <!-- JAL-2500 -->Trees computed on Sequence Feature
253 Similarity may have different topology due to increased
260 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
261 model for alignments and groups
264 <!-- JAL-384 -->Custom shading schemes created via groovy
271 <!-- JAL-2526 -->Efficiency improvements for interacting
272 with alignment and overview windows
275 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
279 <!-- JAL-2388 -->Hidden columns and sequences can be
283 <!-- JAL-2611 -->Click-drag in visible area allows fine
284 adjustment of visible position
288 <em>Data import/export</em>
291 <!-- JAL-2535 -->Posterior probability annotation from
292 Stockholm files imported as sequence associated annotation
295 <!-- JAL-2507 -->More robust per-sequence positional
296 annotation input/output via stockholm flatfile
299 <!-- JAL-2533 -->Sequence names don't include file
300 extension when importing structure files without embedded
301 names or PDB accessions
304 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
305 format sequence substitution matrices
308 <em>User Interface</em>
311 <!-- JAL-2447 --> Experimental Features Checkbox in
312 Desktop's Tools menu to hide or show untested features in
316 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
317 via Overview or sequence motif search operations
320 <!-- JAL-2547 -->Amend sequence features dialog box can be
321 opened by double clicking gaps within sequence feature
325 <!-- JAL-1476 -->Status bar message shown when not enough
326 aligned positions were available to create a 3D structure
330 <em>3D Structure</em>
333 <!-- JAL-2430 -->Hidden regions in alignment views are not
334 coloured in linked structure views
337 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
338 file-based command exchange
341 <!-- JAL-2375 -->Structure chooser automatically shows
342 Cached Structures rather than querying the PDBe if
343 structures are already available for sequences
346 <!-- JAL-2520 -->Structures imported via URL are cached in
347 the Jalview project rather than downloaded again when the
351 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
352 to transfer Chimera's structure attributes as Jalview
353 features, and vice-versa (<strong>Experimental
357 <em>Web Services</em>
360 <!-- JAL-2549 -->Updated JABAWS client to v2.2
363 <!-- JAL-2335 -->Filter non-standard amino acids and
364 nucleotides when submitting to AACon and other MSA
368 <!-- JAL-2316, -->URLs for viewing database
369 cross-references provided by identifiers.org and the
377 <!-- JAL-2344 -->FileFormatI interface for describing and
378 identifying file formats (instead of String constants)
381 <!-- JAL-2228 -->FeatureCounter script refactored for
382 efficiency when counting all displayed features (not
383 backwards compatible with 2.10.1)
386 <em>Example files</em>
389 <!-- JAL-2631 -->Graduated feature colour style example
390 included in the example feature file
393 <em>Documentation</em>
396 <!-- JAL-2339 -->Release notes reformatted for readability
397 with the built-in Java help viewer
400 <!-- JAL-1644 -->Find documentation updated with 'search
401 sequence description' option
407 <!-- JAL-2485, -->External service integration tests for
408 Uniprot REST Free Text Search Client
411 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
414 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
419 <td><div align="left">
420 <em>Calculations</em>
423 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
424 matrix - C->R should be '-3'<br />Old matrix restored
425 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
427 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
428 Jalview's treatment of gaps in PCA and substitution matrix
429 based Tree calculations.<br /> <br />In earlier versions
430 of Jalview, gaps matching gaps were penalised, and gaps
431 matching non-gaps penalised even more. In the PCA
432 calculation, gaps were actually treated as non-gaps - so
433 different costs were applied, which meant Jalview's PCAs
434 were different to those produced by SeqSpace.<br />Jalview
435 now treats gaps in the same way as SeqSpace (ie it scores
436 them as 0). <br /> <br />Enter the following in the
437 Groovy console to restore pre-2.10.2 behaviour:<br />
438 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
439 // for 2.10.1 mode <br />
440 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
441 // to restore 2.10.2 mode <br /> <br /> <em>Note:
442 these settings will affect all subsequent tree and PCA
443 calculations (not recommended)</em></li>
445 <!-- JAL-2424 -->Fixed off-by-one bug that affected
446 scaling of branch lengths for trees computed using
447 Sequence Feature Similarity.
450 <!-- JAL-2377 -->PCA calculation could hang when
451 generating output report when working with highly
455 <!-- JAL-2544 --> Sort by features includes features to
456 right of selected region when gaps present on right-hand
460 <em>User Interface</em>
463 <!-- JAL-2346 -->Reopening Colour by annotation dialog
464 doesn't reselect a specific sequence's associated
465 annotation after it was used for colouring a view
468 <!-- JAL-2419 -->Current selection lost if popup menu
469 opened on a region of alignment without groups
472 <!-- JAL-2374 -->Popup menu not always shown for regions
473 of an alignment with overlapping groups
476 <!-- JAL-2310 -->Finder double counts if both a sequence's
477 name and description match
480 <!-- JAL-2370 -->Hiding column selection containing two
481 hidden regions results in incorrect hidden regions
484 <!-- JAL-2386 -->'Apply to all groups' setting when
485 changing colour does not apply Conservation slider value
489 <!-- JAL-2373 -->Percentage identity and conservation menu
490 items do not show a tick or allow shading to be disabled
493 <!-- JAL-2385 -->Conservation shading or PID threshold
494 lost when base colourscheme changed if slider not visible
497 <!-- JAL-2547 -->Sequence features shown in tooltip for
498 gaps before start of features
501 <!-- JAL-2623 -->Graduated feature colour threshold not
502 restored to UI when feature colour is edited
505 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
506 a time when scrolling vertically in wrapped mode.
509 <!-- JAL-2630 -->Structure and alignment overview update
510 as graduate feature colour settings are modified via the
514 <!-- JAL-2034 -->Overview window doesn't always update
515 when a group defined on the alignment is resized
518 <!-- JAL-2605 -->Mouseovers on left/right scale region in
519 wrapped view result in positional status updates
523 <!-- JAL-2563 -->Status bar doesn't show position for
524 ambiguous amino acid and nucleotide symbols
527 <!-- JAL-2602 -->Copy consensus sequence failed if
528 alignment included gapped columns
531 <!-- JAL-2473 -->Minimum size set for Jalview windows so
532 widgets don't permanently disappear
535 <!-- JAL-2503 -->Cannot select or filter quantitative
536 annotation that are shown only as column labels (e.g.
537 T-Coffee column reliability scores)
540 <!-- JAL-2594 -->Exception thrown if trying to create a
541 sequence feature on gaps only
544 <!-- JAL-2504 -->Features created with 'New feature'
545 button from a Find inherit previously defined feature type
546 rather than the Find query string
549 <!-- JAL-2423 -->incorrect title in output window when
550 exporting tree calculated in Jalview
553 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
554 and then revealing them reorders sequences on the
558 <!-- JAL-964 -->Group panel in sequence feature settings
559 doesn't update to reflect available set of groups after
560 interactively adding or modifying features
563 <!-- JAL-2225 -->Sequence Database chooser unusable on
567 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
568 only excluded gaps in current sequence and ignored
575 <!-- JAL-2421 -->Overview window visible region moves
576 erratically when hidden rows or columns are present
579 <!-- JAL-2362 -->Per-residue colourschemes applied via the
580 Structure Viewer's colour menu don't correspond to
584 <!-- JAL-2405 -->Protein specific colours only offered in
585 colour and group colour menu for protein alignments
588 <!-- JAL-2385 -->Colour threshold slider doesn't update to
589 reflect currently selected view or group's shading
593 <!-- JAL-2624 -->Feature colour thresholds not respected
594 when rendered on overview and structures when opacity at
598 <!-- JAL-2589 -->User defined gap colour not shown in
599 overview when features overlaid on alignment
602 <em>Data import/export</em>
605 <!-- JAL-2576 -->Very large alignments take a long time to
609 <!-- JAL-2507 -->Per-sequence RNA secondary structures
610 added after a sequence was imported are not written to
614 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
615 when importing RNA secondary structure via Stockholm
618 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
619 not shown in correct direction for simple pseudoknots
622 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
623 with lightGray or darkGray via features file (but can
627 <!-- JAL-2383 -->Above PID colour threshold not recovered
628 when alignment view imported from project
631 <!-- JAL-2520,JAL-2465 -->No mappings generated between
632 structure and sequences extracted from structure files
633 imported via URL and viewed in Jmol
636 <!-- JAL-2520 -->Structures loaded via URL are saved in
637 Jalview Projects rather than fetched via URL again when
638 the project is loaded and the structure viewed
641 <em>Web Services</em>
644 <!-- JAL-2519 -->EnsemblGenomes example failing after
645 release of Ensembl v.88
648 <!-- JAL-2366 -->Proxy server address and port always
649 appear enabled in Preferences->Connections
652 <!-- JAL-2461 -->DAS registry not found exceptions
653 removed from console output
656 <!-- JAL-2582 -->Cannot retrieve protein products from
657 Ensembl by Peptide ID
660 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
661 created from SIFTs, and spurious 'Couldn't open structure
662 in Chimera' errors raised after April 2017 update (problem
663 due to 'null' string rather than empty string used for
664 residues with no corresponding PDB mapping).
667 <em>Application UI</em>
670 <!-- JAL-2361 -->User Defined Colours not added to Colour
674 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
675 case' residues (button in colourscheme editor debugged and
676 new documentation and tooltips added)
679 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
680 doesn't restore group-specific text colour thresholds
683 <!-- JAL-2243 -->Feature settings panel does not update as
684 new features are added to alignment
687 <!-- JAL-2532 -->Cancel in feature settings reverts
688 changes to feature colours via the Amend features dialog
691 <!-- JAL-2506 -->Null pointer exception when attempting to
692 edit graduated feature colour via amend features dialog
696 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
697 selection menu changes colours of alignment views
700 <!-- JAL-2426 -->Spurious exceptions in console raised
701 from alignment calculation workers after alignment has
705 <!-- JAL-1608 -->Typo in selection popup menu - Create
706 groups now 'Create Group'
709 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
710 Create/Undefine group doesn't always work
713 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
714 shown again after pressing 'Cancel'
717 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
718 adjusts start position in wrap mode
721 <!-- JAL-2563 -->Status bar doesn't show positions for
722 ambiguous amino acids
725 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
726 CDS/Protein view after CDS sequences added for aligned
730 <!-- JAL-2592 -->User defined colourschemes called 'User
731 Defined' don't appear in Colours menu
737 <!-- JAL-2468 -->Switching between Nucleotide and Protein
738 score models doesn't always result in an updated PCA plot
741 <!-- JAL-2442 -->Features not rendered as transparent on
742 overview or linked structure view
745 <!-- JAL-2372 -->Colour group by conservation doesn't
749 <!-- JAL-2517 -->Hitting Cancel after applying
750 user-defined colourscheme doesn't restore original
757 <!-- JAL-2314 -->Unit test failure:
758 jalview.ws.jabaws.RNAStructExportImport setup fails
761 <!-- JAL-2307 -->Unit test failure:
762 jalview.ws.sifts.SiftsClientTest due to compatibility
763 problems with deep array comparison equality asserts in
764 successive versions of TestNG
767 <!-- JAL-2479 -->Relocated StructureChooserTest and
768 ParameterUtilsTest Unit tests to Network suite
771 <em>New Known Issues</em>
774 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
775 phase after a sequence motif find operation
778 <!-- JAL-2550 -->Importing annotation file with rows
779 containing just upper and lower case letters are
780 interpreted as WUSS RNA secondary structure symbols
783 <!-- JAL-2590 -->Cannot load and display Newick trees
784 reliably from eggnog Ortholog database
787 <!-- JAL-2468 -->Status bar shows 'Marked x columns
788 containing features of type Highlight' when 'B' is pressed
789 to mark columns containing highlighted regions.
792 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
793 doesn't always add secondary structure annotation.
798 <td width="60" nowrap>
800 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
803 <td><div align="left">
807 <!-- JAL-98 -->Improved memory usage: sparse arrays used
808 for all consensus calculations
811 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
814 <li>Updated Jalview's Certum code signing certificate
820 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
821 set of database cross-references, sorted alphabetically
824 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
825 from database cross references. Users with custom links
826 will receive a <a href="webServices/urllinks.html#warning">warning
827 dialog</a> asking them to update their preferences.
830 <!-- JAL-2287-->Cancel button and escape listener on
831 dialog warning user about disconnecting Jalview from a
835 <!-- JAL-2320-->Jalview's Chimera control window closes if
836 the Chimera it is connected to is shut down
839 <!-- JAL-1738-->New keystroke (B) and Select highlighted
840 columns menu item to mark columns containing highlighted
841 regions (e.g. from structure selections or results of a
845 <!-- JAL-2284-->Command line option for batch-generation
846 of HTML pages rendering alignment data with the BioJS
856 <!-- JAL-2286 -->Columns with more than one modal residue
857 are not coloured or thresholded according to percent
858 identity (first observed in Jalview 2.8.2)
861 <!-- JAL-2301 -->Threonine incorrectly reported as not
865 <!-- JAL-2318 -->Updates to documentation pages (above PID
866 threshold, amino acid properties)
869 <!-- JAL-2292 -->Lower case residues in sequences are not
870 reported as mapped to residues in a structure file in the
874 <!--JAL-2324 -->Identical features with non-numeric scores
875 could be added multiple times to a sequence
878 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
879 bond features shown as two highlighted residues rather
880 than a range in linked structure views, and treated
881 correctly when selecting and computing trees from features
884 <!-- JAL-2281-->Custom URL links for database
885 cross-references are matched to database name regardless
893 <!-- JAL-2282-->Custom URL links for specific database
894 names without regular expressions also offer links from
898 <!-- JAL-2315-->Removing a single configured link in the
899 URL links pane in Connections preferences doesn't actually
900 update Jalview configuration
903 <!-- JAL-2272-->CTRL-Click on a selected region to open
904 the alignment area popup menu doesn't work on El-Capitan
907 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
908 files with similarly named sequences if dropped onto the
912 <!-- JAL-2312 -->Additional mappings are shown for PDB
913 entries where more chains exist in the PDB accession than
914 are reported in the SIFTS file
917 <!-- JAL-2317-->Certain structures do not get mapped to
918 the structure view when displayed with Chimera
921 <!-- JAL-2317-->No chains shown in the Chimera view
922 panel's View->Show Chains submenu
925 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
926 work for wrapped alignment views
929 <!--JAL-2197 -->Rename UI components for running JPred
930 predictions from 'JNet' to 'JPred'
933 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
934 corrupted when annotation panel vertical scroll is not at
938 <!--JAL-2332 -->Attempting to view structure for Hen
939 lysozyme results in a PDB Client error dialog box
942 <!-- JAL-2319 -->Structure View's mapping report switched
943 ranges for PDB and sequence for SIFTS
946 SIFTS 'Not_Observed' residues mapped to non-existant
950 <!-- <em>New Known Issues</em>
957 <td width="60" nowrap>
959 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
960 <em>25/10/2016</em></strong>
963 <td><em>Application</em>
965 <li>3D Structure chooser opens with 'Cached structures'
966 view if structures already loaded</li>
967 <li>Progress bar reports models as they are loaded to
974 <li>Colour by conservation always enabled and no tick
975 shown in menu when BLOSUM or PID shading applied</li>
976 <li>FER1_ARATH and FER2_ARATH labels were switched in
977 example sequences/projects/trees</li>
981 <li>Jalview projects with views of local PDB structure
982 files saved on Windows cannot be opened on OSX</li>
983 <li>Multiple structure views can be opened and superposed
984 without timeout for structures with multiple models or
985 multiple sequences in alignment</li>
986 <li>Cannot import or associated local PDB files without a
987 PDB ID HEADER line</li>
988 <li>RMSD is not output in Jmol console when superposition
990 <li>Drag and drop of URL from Browser fails for Linux and
991 OSX versions earlier than El Capitan</li>
992 <li>ENA client ignores invalid content from ENA server</li>
993 <li>Exceptions are not raised in console when ENA client
994 attempts to fetch non-existent IDs via Fetch DB Refs UI
996 <li>Exceptions are not raised in console when a new view
997 is created on the alignment</li>
998 <li>OSX right-click fixed for group selections: CMD-click
999 to insert/remove gaps in groups and CTRL-click to open group
1002 <em>Build and deployment</em>
1004 <li>URL link checker now copes with multi-line anchor
1007 <em>New Known Issues</em>
1009 <li>Drag and drop from URL links in browsers do not work
1016 <td width="60" nowrap>
1017 <div align="center">
1018 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1021 <td><em>General</em>
1024 <!-- JAL-2124 -->Updated Spanish translations.
1027 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1028 for importing structure data to Jalview. Enables mmCIF and
1032 <!-- JAL-192 --->Alignment ruler shows positions relative to
1036 <!-- JAL-2202 -->Position/residue shown in status bar when
1037 mousing over sequence associated annotation
1040 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1044 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1045 '()', canonical '[]' and invalid '{}' base pair populations
1049 <!-- JAL-2092 -->Feature settings popup menu options for
1050 showing or hiding columns containing a feature
1053 <!-- JAL-1557 -->Edit selected group by double clicking on
1054 group and sequence associated annotation labels
1057 <!-- JAL-2236 -->Sequence name added to annotation label in
1058 select/hide columns by annotation and colour by annotation
1062 </ul> <em>Application</em>
1065 <!-- JAL-2050-->Automatically hide introns when opening a
1066 gene/transcript view
1069 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1073 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1074 structure mappings with the EMBL-EBI PDBe SIFTS database
1077 <!-- JAL-2079 -->Updated download sites used for Rfam and
1078 Pfam sources to xfam.org
1081 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1084 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1085 over sequences in Jalview
1088 <!-- JAL-2027-->Support for reverse-complement coding
1089 regions in ENA and EMBL
1092 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1093 for record retrieval via ENA rest API
1096 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1100 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1101 groovy script execution
1104 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1105 alignment window's Calculate menu
1108 <!-- JAL-1812 -->Allow groovy scripts that call
1109 Jalview.getAlignFrames() to run in headless mode
1112 <!-- JAL-2068 -->Support for creating new alignment
1113 calculation workers from groovy scripts
1116 <!-- JAL-1369 --->Store/restore reference sequence in
1120 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1121 associations are now saved/restored from project
1124 <!-- JAL-1993 -->Database selection dialog always shown
1125 before sequence fetcher is opened
1128 <!-- JAL-2183 -->Double click on an entry in Jalview's
1129 database chooser opens a sequence fetcher
1132 <!-- JAL-1563 -->Free-text search client for UniProt using
1133 the UniProt REST API
1136 <!-- JAL-2168 -->-nonews command line parameter to prevent
1137 the news reader opening
1140 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1141 querying stored in preferences
1144 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1148 <!-- JAL-1977-->Tooltips shown on database chooser
1151 <!-- JAL-391 -->Reverse complement function in calculate
1152 menu for nucleotide sequences
1155 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1156 and feature counts preserves alignment ordering (and
1157 debugged for complex feature sets).
1160 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1161 viewing structures with Jalview 2.10
1164 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1165 genome, transcript CCDS and gene ids via the Ensembl and
1166 Ensembl Genomes REST API
1169 <!-- JAL-2049 -->Protein sequence variant annotation
1170 computed for 'sequence_variant' annotation on CDS regions
1174 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1178 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1179 Ref Fetcher fails to match, or otherwise updates sequence
1180 data from external database records.
1183 <!-- JAL-2154 -->Revised Jalview Project format for
1184 efficient recovery of sequence coding and alignment
1185 annotation relationships.
1187 </ul> <!-- <em>Applet</em>
1198 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1202 <!-- JAL-2018-->Export features in Jalview format (again)
1203 includes graduated colourschemes
1206 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1207 working with big alignments and lots of hidden columns
1210 <!-- JAL-2053-->Hidden column markers not always rendered
1211 at right of alignment window
1214 <!-- JAL-2067 -->Tidied up links in help file table of
1218 <!-- JAL-2072 -->Feature based tree calculation not shown
1222 <!-- JAL-2075 -->Hidden columns ignored during feature
1223 based tree calculation
1226 <!-- JAL-2065 -->Alignment view stops updating when show
1227 unconserved enabled for group on alignment
1230 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1234 <!-- JAL-2146 -->Alignment column in status incorrectly
1235 shown as "Sequence position" when mousing over
1239 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1240 hidden columns present
1243 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1244 user created annotation added to alignment
1247 <!-- JAL-1841 -->RNA Structure consensus only computed for
1248 '()' base pair annotation
1251 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1252 in zero scores for all base pairs in RNA Structure
1256 <!-- JAL-2174-->Extend selection with columns containing
1260 <!-- JAL-2275 -->Pfam format writer puts extra space at
1261 beginning of sequence
1264 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1268 <!-- JAL-2238 -->Cannot create groups on an alignment from
1269 from a tree when t-coffee scores are shown
1272 <!-- JAL-1836,1967 -->Cannot import and view PDB
1273 structures with chains containing negative resnums (4q4h)
1276 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1280 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1281 to Clustal, PIR and PileUp output
1284 <!-- JAL-2008 -->Reordering sequence features that are
1285 not visible causes alignment window to repaint
1288 <!-- JAL-2006 -->Threshold sliders don't work in
1289 graduated colour and colour by annotation row for e-value
1290 scores associated with features and annotation rows
1293 <!-- JAL-1797 -->amino acid physicochemical conservation
1294 calculation should be case independent
1297 <!-- JAL-2173 -->Remove annotation also updates hidden
1301 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1302 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1303 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1306 <!-- JAL-2065 -->Null pointer exceptions and redraw
1307 problems when reference sequence defined and 'show
1308 non-conserved' enabled
1311 <!-- JAL-1306 -->Quality and Conservation are now shown on
1312 load even when Consensus calculation is disabled
1315 <!-- JAL-1932 -->Remove right on penultimate column of
1316 alignment does nothing
1319 <em>Application</em>
1322 <!-- JAL-1552-->URLs and links can't be imported by
1323 drag'n'drop on OSX when launched via webstart (note - not
1324 yet fixed for El Capitan)
1327 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1328 output when running on non-gb/us i18n platforms
1331 <!-- JAL-1944 -->Error thrown when exporting a view with
1332 hidden sequences as flat-file alignment
1335 <!-- JAL-2030-->InstallAnywhere distribution fails when
1339 <!-- JAL-2080-->Jalview very slow to launch via webstart
1340 (also hotfix for 2.9.0b2)
1343 <!-- JAL-2085 -->Cannot save project when view has a
1344 reference sequence defined
1347 <!-- JAL-1011 -->Columns are suddenly selected in other
1348 alignments and views when revealing hidden columns
1351 <!-- JAL-1989 -->Hide columns not mirrored in complement
1352 view in a cDNA/Protein splitframe
1355 <!-- JAL-1369 -->Cannot save/restore representative
1356 sequence from project when only one sequence is
1360 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1361 in Structure Chooser
1364 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1365 structure consensus didn't refresh annotation panel
1368 <!-- JAL-1962 -->View mapping in structure view shows
1369 mappings between sequence and all chains in a PDB file
1372 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1373 dialogs format columns correctly, don't display array
1374 data, sort columns according to type
1377 <!-- JAL-1975 -->Export complete shown after destination
1378 file chooser is cancelled during an image export
1381 <!-- JAL-2025 -->Error when querying PDB Service with
1382 sequence name containing special characters
1385 <!-- JAL-2024 -->Manual PDB structure querying should be
1389 <!-- JAL-2104 -->Large tooltips with broken HTML
1390 formatting don't wrap
1393 <!-- JAL-1128 -->Figures exported from wrapped view are
1394 truncated so L looks like I in consensus annotation
1397 <!-- JAL-2003 -->Export features should only export the
1398 currently displayed features for the current selection or
1402 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1403 after fetching cross-references, and restoring from
1407 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1408 followed in the structure viewer
1411 <!-- JAL-2163 -->Titles for individual alignments in
1412 splitframe not restored from project
1415 <!-- JAL-2145 -->missing autocalculated annotation at
1416 trailing end of protein alignment in transcript/product
1417 splitview when pad-gaps not enabled by default
1420 <!-- JAL-1797 -->amino acid physicochemical conservation
1424 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1425 article has been read (reopened issue due to
1426 internationalisation problems)
1429 <!-- JAL-1960 -->Only offer PDB structures in structure
1430 viewer based on sequence name, PDB and UniProt
1435 <!-- JAL-1976 -->No progress bar shown during export of
1439 <!-- JAL-2213 -->Structures not always superimposed after
1440 multiple structures are shown for one or more sequences.
1443 <!-- JAL-1370 -->Reference sequence characters should not
1444 be replaced with '.' when 'Show unconserved' format option
1448 <!-- JAL-1823 -->Cannot specify chain code when entering
1449 specific PDB id for sequence
1452 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1453 'Export hidden sequences' is enabled, but 'export hidden
1454 columns' is disabled.
1457 <!--JAL-2026-->Best Quality option in structure chooser
1458 selects lowest rather than highest resolution structures
1462 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1463 to sequence mapping in 'View Mappings' report
1466 <!-- JAL-2284 -->Unable to read old Jalview projects that
1467 contain non-XML data added after Jalvew wrote project.
1470 <!-- JAL-2118 -->Newly created annotation row reorders
1471 after clicking on it to create new annotation for a
1475 <!-- JAL-1980 -->Null Pointer Exception raised when
1476 pressing Add on an orphaned cut'n'paste window.
1478 <!-- may exclude, this is an external service stability issue JAL-1941
1479 -- > RNA 3D structure not added via DSSR service</li> -->
1484 <!-- JAL-2151 -->Incorrect columns are selected when
1485 hidden columns present before start of sequence
1488 <!-- JAL-1986 -->Missing dependencies on applet pages
1492 <!-- JAL-1947 -->Overview pixel size changes when
1493 sequences are hidden in applet
1496 <!-- JAL-1996 -->Updated instructions for applet
1497 deployment on examples pages.
1504 <td width="60" nowrap>
1505 <div align="center">
1506 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1507 <em>16/10/2015</em></strong>
1510 <td><em>General</em>
1512 <li>Time stamps for signed Jalview application and applet
1517 <em>Application</em>
1519 <li>Duplicate group consensus and conservation rows
1520 shown when tree is partitioned</li>
1521 <li>Erratic behaviour when tree partitions made with
1522 multiple cDNA/Protein split views</li>
1528 <td width="60" nowrap>
1529 <div align="center">
1530 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1531 <em>8/10/2015</em></strong>
1534 <td><em>General</em>
1536 <li>Updated Spanish translations of localized text for
1538 </ul> <em>Application</em>
1540 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1541 <li>Signed OSX InstallAnywhere installer<br></li>
1542 <li>Support for per-sequence based annotations in BioJSON</li>
1543 </ul> <em>Applet</em>
1545 <li>Split frame example added to applet examples page</li>
1546 </ul> <em>Build and Deployment</em>
1549 <!-- JAL-1888 -->New ant target for running Jalview's test
1557 <li>Mapping of cDNA to protein in split frames
1558 incorrect when sequence start > 1</li>
1559 <li>Broken images in filter column by annotation dialog
1561 <li>Feature colours not parsed from features file</li>
1562 <li>Exceptions and incomplete link URLs recovered when
1563 loading a features file containing HTML tags in feature
1567 <em>Application</em>
1569 <li>Annotations corrupted after BioJS export and
1571 <li>Incorrect sequence limits after Fetch DB References
1572 with 'trim retrieved sequences'</li>
1573 <li>Incorrect warning about deleting all data when
1574 deleting selected columns</li>
1575 <li>Patch to build system for shipping properly signed
1576 JNLP templates for webstart launch</li>
1577 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1578 unreleased structures for download or viewing</li>
1579 <li>Tab/space/return keystroke operation of EMBL-PDBe
1580 fetcher/viewer dialogs works correctly</li>
1581 <li>Disabled 'minimise' button on Jalview windows
1582 running on OSX to workaround redraw hang bug</li>
1583 <li>Split cDNA/Protein view position and geometry not
1584 recovered from jalview project</li>
1585 <li>Initial enabled/disabled state of annotation menu
1586 sorter 'show autocalculated first/last' corresponds to
1588 <li>Restoring of Clustal, RNA Helices and T-Coffee
1589 color schemes from BioJSON</li>
1593 <li>Reorder sequences mirrored in cDNA/Protein split
1595 <li>Applet with Jmol examples not loading correctly</li>
1601 <td><div align="center">
1602 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1604 <td><em>General</em>
1606 <li>Linked visualisation and analysis of DNA and Protein
1609 <li>Translated cDNA alignments shown as split protein
1610 and DNA alignment views</li>
1611 <li>Codon consensus annotation for linked protein and
1612 cDNA alignment views</li>
1613 <li>Link cDNA or Protein product sequences by loading
1614 them onto Protein or cDNA alignments</li>
1615 <li>Reconstruct linked cDNA alignment from aligned
1616 protein sequences</li>
1619 <li>Jmol integration updated to Jmol v14.2.14</li>
1620 <li>Import and export of Jalview alignment views as <a
1621 href="features/bioJsonFormat.html">BioJSON</a></li>
1622 <li>New alignment annotation file statements for
1623 reference sequences and marking hidden columns</li>
1624 <li>Reference sequence based alignment shading to
1625 highlight variation</li>
1626 <li>Select or hide columns according to alignment
1628 <li>Find option for locating sequences by description</li>
1629 <li>Conserved physicochemical properties shown in amino
1630 acid conservation row</li>
1631 <li>Alignments can be sorted by number of RNA helices</li>
1632 </ul> <em>Application</em>
1634 <li>New cDNA/Protein analysis capabilities
1636 <li>Get Cross-References should open a Split Frame
1637 view with cDNA/Protein</li>
1638 <li>Detect when nucleotide sequences and protein
1639 sequences are placed in the same alignment</li>
1640 <li>Split cDNA/Protein views are saved in Jalview
1645 <li>Use REST API to talk to Chimera</li>
1646 <li>Selected regions in Chimera are highlighted in linked
1647 Jalview windows</li>
1649 <li>VARNA RNA viewer updated to v3.93</li>
1650 <li>VARNA views are saved in Jalview Projects</li>
1651 <li>Pseudoknots displayed as Jalview RNA annotation can
1652 be shown in VARNA</li>
1654 <li>Make groups for selection uses marked columns as well
1655 as the active selected region</li>
1657 <li>Calculate UPGMA and NJ trees using sequence feature
1659 <li>New Export options
1661 <li>New Export Settings dialog to control hidden
1662 region export in flat file generation</li>
1664 <li>Export alignment views for display with the <a
1665 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1667 <li>Export scrollable SVG in HTML page</li>
1668 <li>Optional embedding of BioJSON data when exporting
1669 alignment figures to HTML</li>
1671 <li>3D structure retrieval and display
1673 <li>Free text and structured queries with the PDBe
1675 <li>PDBe Search API based discovery and selection of
1676 PDB structures for a sequence set</li>
1680 <li>JPred4 employed for protein secondary structure
1682 <li>Hide Insertions menu option to hide unaligned columns
1683 for one or a group of sequences</li>
1684 <li>Automatically hide insertions in alignments imported
1685 from the JPred4 web server</li>
1686 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1687 system on OSX<br />LGPL libraries courtesy of <a
1688 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1690 <li>changed 'View nucleotide structure' submenu to 'View
1691 VARNA 2D Structure'</li>
1692 <li>change "View protein structure" menu option to "3D
1695 </ul> <em>Applet</em>
1697 <li>New layout for applet example pages</li>
1698 <li>New parameters to enable SplitFrame view
1699 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1700 <li>New example demonstrating linked viewing of cDNA and
1701 Protein alignments</li>
1702 </ul> <em>Development and deployment</em>
1704 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1705 <li>Include installation type and git revision in build
1706 properties and console log output</li>
1707 <li>Jalview Github organisation, and new github site for
1708 storing BioJsMSA Templates</li>
1709 <li>Jalview's unit tests now managed with TestNG</li>
1712 <!-- <em>General</em>
1714 </ul> --> <!-- issues resolved --> <em>Application</em>
1716 <li>Escape should close any open find dialogs</li>
1717 <li>Typo in select-by-features status report</li>
1718 <li>Consensus RNA secondary secondary structure
1719 predictions are not highlighted in amber</li>
1720 <li>Missing gap character in v2.7 example file means
1721 alignment appears unaligned when pad-gaps is not enabled</li>
1722 <li>First switch to RNA Helices colouring doesn't colour
1723 associated structure views</li>
1724 <li>ID width preference option is greyed out when auto
1725 width checkbox not enabled</li>
1726 <li>Stopped a warning dialog from being shown when
1727 creating user defined colours</li>
1728 <li>'View Mapping' in structure viewer shows sequence
1729 mappings for just that viewer's sequences</li>
1730 <li>Workaround for superposing PDB files containing
1731 multiple models in Chimera</li>
1732 <li>Report sequence position in status bar when hovering
1733 over Jmol structure</li>
1734 <li>Cannot output gaps as '.' symbols with Selection ->
1735 output to text box</li>
1736 <li>Flat file exports of alignments with hidden columns
1737 have incorrect sequence start/end</li>
1738 <li>'Aligning' a second chain to a Chimera structure from
1740 <li>Colour schemes applied to structure viewers don't
1741 work for nucleotide</li>
1742 <li>Loading/cut'n'pasting an empty or invalid file leads
1743 to a grey/invisible alignment window</li>
1744 <li>Exported Jpred annotation from a sequence region
1745 imports to different position</li>
1746 <li>Space at beginning of sequence feature tooltips shown
1747 on some platforms</li>
1748 <li>Chimera viewer 'View | Show Chain' menu is not
1750 <li>'New View' fails with a Null Pointer Exception in
1751 console if Chimera has been opened</li>
1752 <li>Mouseover to Chimera not working</li>
1753 <li>Miscellaneous ENA XML feature qualifiers not
1755 <li>NPE in annotation renderer after 'Extract Scores'</li>
1756 <li>If two structures in one Chimera window, mouseover of
1757 either sequence shows on first structure</li>
1758 <li>'Show annotations' options should not make
1759 non-positional annotations visible</li>
1760 <li>Subsequence secondary structure annotation not shown
1761 in right place after 'view flanking regions'</li>
1762 <li>File Save As type unset when current file format is
1764 <li>Save as '.jar' option removed for saving Jalview
1766 <li>Colour by Sequence colouring in Chimera more
1768 <li>Cannot 'add reference annotation' for a sequence in
1769 several views on same alignment</li>
1770 <li>Cannot show linked products for EMBL / ENA records</li>
1771 <li>Jalview's tooltip wraps long texts containing no
1773 </ul> <em>Applet</em>
1775 <li>Jmol to JalviewLite mouseover/link not working</li>
1776 <li>JalviewLite can't import sequences with ID
1777 descriptions containing angle brackets</li>
1778 </ul> <em>General</em>
1780 <li>Cannot export and reimport RNA secondary structure
1781 via jalview annotation file</li>
1782 <li>Random helix colour palette for colour by annotation
1783 with RNA secondary structure</li>
1784 <li>Mouseover to cDNA from STOP residue in protein
1785 translation doesn't work.</li>
1786 <li>hints when using the select by annotation dialog box</li>
1787 <li>Jmol alignment incorrect if PDB file has alternate CA
1789 <li>FontChooser message dialog appears to hang after
1790 choosing 1pt font</li>
1791 <li>Peptide secondary structure incorrectly imported from
1792 annotation file when annotation display text includes 'e' or
1794 <li>Cannot set colour of new feature type whilst creating
1796 <li>cDNA translation alignment should not be sequence
1797 order dependent</li>
1798 <li>'Show unconserved' doesn't work for lower case
1800 <li>Nucleotide ambiguity codes involving R not recognised</li>
1801 </ul> <em>Deployment and Documentation</em>
1803 <li>Applet example pages appear different to the rest of
1804 www.jalview.org</li>
1805 </ul> <em>Application Known issues</em>
1807 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1808 <li>Misleading message appears after trying to delete
1810 <li>Jalview icon not shown in dock after InstallAnywhere
1811 version launches</li>
1812 <li>Fetching EMBL reference for an RNA sequence results
1813 fails with a sequence mismatch</li>
1814 <li>Corrupted or unreadable alignment display when
1815 scrolling alignment to right</li>
1816 <li>ArrayIndexOutOfBoundsException thrown when remove
1817 empty columns called on alignment with ragged gapped ends</li>
1818 <li>auto calculated alignment annotation rows do not get
1819 placed above or below non-autocalculated rows</li>
1820 <li>Jalview dekstop becomes sluggish at full screen in
1821 ultra-high resolution</li>
1822 <li>Cannot disable consensus calculation independently of
1823 quality and conservation</li>
1824 <li>Mouseover highlighting between cDNA and protein can
1825 become sluggish with more than one splitframe shown</li>
1826 </ul> <em>Applet Known Issues</em>
1828 <li>Core PDB parsing code requires Jmol</li>
1829 <li>Sequence canvas panel goes white when alignment
1830 window is being resized</li>
1836 <td><div align="center">
1837 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1839 <td><em>General</em>
1841 <li>Updated Java code signing certificate donated by
1843 <li>Features and annotation preserved when performing
1844 pairwise alignment</li>
1845 <li>RNA pseudoknot annotation can be
1846 imported/exported/displayed</li>
1847 <li>'colour by annotation' can colour by RNA and
1848 protein secondary structure</li>
1849 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1850 post-hoc with 2.9 release</em>)
1853 </ul> <em>Application</em>
1855 <li>Extract and display secondary structure for sequences
1856 with 3D structures</li>
1857 <li>Support for parsing RNAML</li>
1858 <li>Annotations menu for layout
1860 <li>sort sequence annotation rows by alignment</li>
1861 <li>place sequence annotation above/below alignment
1864 <li>Output in Stockholm format</li>
1865 <li>Internationalisation: improved Spanish (es)
1867 <li>Structure viewer preferences tab</li>
1868 <li>Disorder and Secondary Structure annotation tracks
1869 shared between alignments</li>
1870 <li>UCSF Chimera launch and linked highlighting from
1872 <li>Show/hide all sequence associated annotation rows for
1873 all or current selection</li>
1874 <li>disorder and secondary structure predictions
1875 available as dataset annotation</li>
1876 <li>Per-sequence rna helices colouring</li>
1879 <li>Sequence database accessions imported when fetching
1880 alignments from Rfam</li>
1881 <li>update VARNA version to 3.91</li>
1883 <li>New groovy scripts for exporting aligned positions,
1884 conservation values, and calculating sum of pairs scores.</li>
1885 <li>Command line argument to set default JABAWS server</li>
1886 <li>include installation type in build properties and
1887 console log output</li>
1888 <li>Updated Jalview project format to preserve dataset
1892 <!-- issues resolved --> <em>Application</em>
1894 <li>Distinguish alignment and sequence associated RNA
1895 structure in structure->view->VARNA</li>
1896 <li>Raise dialog box if user deletes all sequences in an
1898 <li>Pressing F1 results in documentation opening twice</li>
1899 <li>Sequence feature tooltip is wrapped</li>
1900 <li>Double click on sequence associated annotation
1901 selects only first column</li>
1902 <li>Redundancy removal doesn't result in unlinked
1903 leaves shown in tree</li>
1904 <li>Undos after several redundancy removals don't undo
1906 <li>Hide sequence doesn't hide associated annotation</li>
1907 <li>User defined colours dialog box too big to fit on
1908 screen and buttons not visible</li>
1909 <li>author list isn't updated if already written to
1910 Jalview properties</li>
1911 <li>Popup menu won't open after retrieving sequence
1913 <li>File open window for associate PDB doesn't open</li>
1914 <li>Left-then-right click on a sequence id opens a
1915 browser search window</li>
1916 <li>Cannot open sequence feature shading/sort popup menu
1917 in feature settings dialog</li>
1918 <li>better tooltip placement for some areas of Jalview
1920 <li>Allow addition of JABAWS Server which doesn't
1921 pass validation</li>
1922 <li>Web services parameters dialog box is too large to
1924 <li>Muscle nucleotide alignment preset obscured by
1926 <li>JABAWS preset submenus don't contain newly
1927 defined user preset</li>
1928 <li>MSA web services warns user if they were launched
1929 with invalid input</li>
1930 <li>Jalview cannot contact DAS Registy when running on
1933 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1934 'Superpose with' submenu not shown when new view
1938 </ul> <!-- <em>Applet</em>
1940 </ul> <em>General</em>
1942 </ul>--> <em>Deployment and Documentation</em>
1944 <li>2G and 1G options in launchApp have no effect on
1945 memory allocation</li>
1946 <li>launchApp service doesn't automatically open
1947 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1949 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1950 InstallAnywhere reports cannot find valid JVM when Java
1951 1.7_055 is available
1953 </ul> <em>Application Known issues</em>
1956 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1957 corrupted or unreadable alignment display when scrolling
1961 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1962 retrieval fails but progress bar continues for DAS retrieval
1963 with large number of ID
1966 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1967 flatfile output of visible region has incorrect sequence
1971 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1972 rna structure consensus doesn't update when secondary
1973 structure tracks are rearranged
1976 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1977 invalid rna structure positional highlighting does not
1978 highlight position of invalid base pairs
1981 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1982 out of memory errors are not raised when saving Jalview
1983 project from alignment window file menu
1986 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1987 Switching to RNA Helices colouring doesn't propagate to
1991 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1992 colour by RNA Helices not enabled when user created
1993 annotation added to alignment
1996 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1997 Jalview icon not shown on dock in Mountain Lion/Webstart
1999 </ul> <em>Applet Known Issues</em>
2002 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2003 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2006 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2007 Jalview and Jmol example not compatible with IE9
2010 <li>Sort by annotation score doesn't reverse order
2016 <td><div align="center">
2017 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2020 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2023 <li>Internationalisation of user interface (usually
2024 called i18n support) and translation for Spanish locale</li>
2025 <li>Define/Undefine group on current selection with
2026 Ctrl-G/Shift Ctrl-G</li>
2027 <li>Improved group creation/removal options in
2028 alignment/sequence Popup menu</li>
2029 <li>Sensible precision for symbol distribution
2030 percentages shown in logo tooltip.</li>
2031 <li>Annotation panel height set according to amount of
2032 annotation when alignment first opened</li>
2033 </ul> <em>Application</em>
2035 <li>Interactive consensus RNA secondary structure
2036 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2037 <li>Select columns containing particular features from
2038 Feature Settings dialog</li>
2039 <li>View all 'representative' PDB structures for selected
2041 <li>Update Jalview project format:
2043 <li>New file extension for Jalview projects '.jvp'</li>
2044 <li>Preserve sequence and annotation dataset (to
2045 store secondary structure annotation,etc)</li>
2046 <li>Per group and alignment annotation and RNA helix
2050 <li>New similarity measures for PCA and Tree calculation
2052 <li>Experimental support for retrieval and viewing of
2053 flanking regions for an alignment</li>
2057 <!-- issues resolved --> <em>Application</em>
2059 <li>logo keeps spinning and status remains at queued or
2060 running after job is cancelled</li>
2061 <li>cannot export features from alignments imported from
2062 Jalview/VAMSAS projects</li>
2063 <li>Buggy slider for web service parameters that take
2065 <li>Newly created RNA secondary structure line doesn't
2066 have 'display all symbols' flag set</li>
2067 <li>T-COFFEE alignment score shading scheme and other
2068 annotation shading not saved in Jalview project</li>
2069 <li>Local file cannot be loaded in freshly downloaded
2071 <li>Jalview icon not shown on dock in Mountain
2073 <li>Load file from desktop file browser fails</li>
2074 <li>Occasional NPE thrown when calculating large trees</li>
2075 <li>Cannot reorder or slide sequences after dragging an
2076 alignment onto desktop</li>
2077 <li>Colour by annotation dialog throws NPE after using
2078 'extract scores' function</li>
2079 <li>Loading/cut'n'pasting an empty file leads to a grey
2080 alignment window</li>
2081 <li>Disorder thresholds rendered incorrectly after
2082 performing IUPred disorder prediction</li>
2083 <li>Multiple group annotated consensus rows shown when
2084 changing 'normalise logo' display setting</li>
2085 <li>Find shows blank dialog after 'finished searching' if
2086 nothing matches query</li>
2087 <li>Null Pointer Exceptions raised when sorting by
2088 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2090 <li>Errors in Jmol console when structures in alignment
2091 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2093 <li>Not all working JABAWS services are shown in
2095 <li>JAVAWS version of Jalview fails to launch with
2096 'invalid literal/length code'</li>
2097 <li>Annotation/RNA Helix colourschemes cannot be applied
2098 to alignment with groups (actually fixed in 2.8.0b1)</li>
2099 <li>RNA Helices and T-Coffee Scores available as default
2102 </ul> <em>Applet</em>
2104 <li>Remove group option is shown even when selection is
2106 <li>Apply to all groups ticked but colourscheme changes
2107 don't affect groups</li>
2108 <li>Documented RNA Helices and T-Coffee Scores as valid
2109 colourscheme name</li>
2110 <li>Annotation labels drawn on sequence IDs when
2111 Annotation panel is not displayed</li>
2112 <li>Increased font size for dropdown menus on OSX and
2113 embedded windows</li>
2114 </ul> <em>Other</em>
2116 <li>Consensus sequence for alignments/groups with a
2117 single sequence were not calculated</li>
2118 <li>annotation files that contain only groups imported as
2119 annotation and junk sequences</li>
2120 <li>Fasta files with sequences containing '*' incorrectly
2121 recognised as PFAM or BLC</li>
2122 <li>conservation/PID slider apply all groups option
2123 doesn't affect background (2.8.0b1)
2125 <li>redundancy highlighting is erratic at 0% and 100%</li>
2126 <li>Remove gapped columns fails for sequences with ragged
2128 <li>AMSA annotation row with leading spaces is not
2129 registered correctly on import</li>
2130 <li>Jalview crashes when selecting PCA analysis for
2131 certain alignments</li>
2132 <li>Opening the colour by annotation dialog for an
2133 existing annotation based 'use original colours'
2134 colourscheme loses original colours setting</li>
2139 <td><div align="center">
2140 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2141 <em>30/1/2014</em></strong>
2145 <li>Trusted certificates for JalviewLite applet and
2146 Jalview Desktop application<br />Certificate was donated by
2147 <a href="https://www.certum.eu">Certum</a> to the Jalview
2148 open source project).
2150 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2151 <li>Output in Stockholm format</li>
2152 <li>Allow import of data from gzipped files</li>
2153 <li>Export/import group and sequence associated line
2154 graph thresholds</li>
2155 <li>Nucleotide substitution matrix that supports RNA and
2156 ambiguity codes</li>
2157 <li>Allow disorder predictions to be made on the current
2158 selection (or visible selection) in the same way that JPred
2160 <li>Groovy scripting for headless Jalview operation</li>
2161 </ul> <em>Other improvements</em>
2163 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2164 <li>COMBINE statement uses current SEQUENCE_REF and
2165 GROUP_REF scope to group annotation rows</li>
2166 <li>Support '' style escaping of quotes in Newick
2168 <li>Group options for JABAWS service by command line name</li>
2169 <li>Empty tooltip shown for JABA service options with a
2170 link but no description</li>
2171 <li>Select primary source when selecting authority in
2172 database fetcher GUI</li>
2173 <li>Add .mfa to FASTA file extensions recognised by
2175 <li>Annotation label tooltip text wrap</li>
2180 <li>Slow scrolling when lots of annotation rows are
2182 <li>Lots of NPE (and slowness) after creating RNA
2183 secondary structure annotation line</li>
2184 <li>Sequence database accessions not imported when
2185 fetching alignments from Rfam</li>
2186 <li>Incorrect SHMR submission for sequences with
2188 <li>View all structures does not always superpose
2190 <li>Option widgets in service parameters not updated to
2191 reflect user or preset settings</li>
2192 <li>Null pointer exceptions for some services without
2193 presets or adjustable parameters</li>
2194 <li>Discover PDB IDs entry in structure menu doesn't
2195 discover PDB xRefs</li>
2196 <li>Exception encountered while trying to retrieve
2197 features with DAS</li>
2198 <li>Lowest value in annotation row isn't coloured
2199 when colour by annotation (per sequence) is coloured</li>
2200 <li>Keyboard mode P jumps to start of gapped region when
2201 residue follows a gap</li>
2202 <li>Jalview appears to hang importing an alignment with
2203 Wrap as default or after enabling Wrap</li>
2204 <li>'Right click to add annotations' message
2205 shown in wrap mode when no annotations present</li>
2206 <li>Disorder predictions fail with NPE if no automatic
2207 annotation already exists on alignment</li>
2208 <li>oninit javascript function should be called after
2209 initialisation completes</li>
2210 <li>Remove redundancy after disorder prediction corrupts
2211 alignment window display</li>
2212 <li>Example annotation file in documentation is invalid</li>
2213 <li>Grouped line graph annotation rows are not exported
2214 to annotation file</li>
2215 <li>Multi-harmony analysis cannot be run when only two
2217 <li>Cannot create multiple groups of line graphs with
2218 several 'combine' statements in annotation file</li>
2219 <li>Pressing return several times causes Number Format
2220 exceptions in keyboard mode</li>
2221 <li>Multi-harmony (SHMMR) method doesn't submit
2222 correct partitions for input data</li>
2223 <li>Translation from DNA to Amino Acids fails</li>
2224 <li>Jalview fail to load newick tree with quoted label</li>
2225 <li>--headless flag isn't understood</li>
2226 <li>ClassCastException when generating EPS in headless
2228 <li>Adjusting sequence-associated shading threshold only
2229 changes one row's threshold</li>
2230 <li>Preferences and Feature settings panel panel
2231 doesn't open</li>
2232 <li>hide consensus histogram also hides conservation and
2233 quality histograms</li>
2238 <td><div align="center">
2239 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2241 <td><em>Application</em>
2243 <li>Support for JABAWS 2.0 Services (AACon alignment
2244 conservation, protein disorder and Clustal Omega)</li>
2245 <li>JABAWS server status indicator in Web Services
2247 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2248 in Jalview alignment window</li>
2249 <li>Updated Jalview build and deploy framework for OSX
2250 mountain lion, windows 7, and 8</li>
2251 <li>Nucleotide substitution matrix for PCA that supports
2252 RNA and ambiguity codes</li>
2254 <li>Improved sequence database retrieval GUI</li>
2255 <li>Support fetching and database reference look up
2256 against multiple DAS sources (Fetch all from in 'fetch db
2258 <li>Jalview project improvements
2260 <li>Store and retrieve the 'belowAlignment'
2261 flag for annotation</li>
2262 <li>calcId attribute to group annotation rows on the
2264 <li>Store AACon calculation settings for a view in
2265 Jalview project</li>
2269 <li>horizontal scrolling gesture support</li>
2270 <li>Visual progress indicator when PCA calculation is
2272 <li>Simpler JABA web services menus</li>
2273 <li>visual indication that web service results are still
2274 being retrieved from server</li>
2275 <li>Serialise the dialogs that are shown when Jalview
2276 starts up for first time</li>
2277 <li>Jalview user agent string for interacting with HTTP
2279 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2281 <li>Examples directory and Groovy library included in
2282 InstallAnywhere distribution</li>
2283 </ul> <em>Applet</em>
2285 <li>RNA alignment and secondary structure annotation
2286 visualization applet example</li>
2287 </ul> <em>General</em>
2289 <li>Normalise option for consensus sequence logo</li>
2290 <li>Reset button in PCA window to return dimensions to
2292 <li>Allow seqspace or Jalview variant of alignment PCA
2294 <li>PCA with either nucleic acid and protein substitution
2296 <li>Allow windows containing HTML reports to be exported
2298 <li>Interactive display and editing of RNA secondary
2299 structure contacts</li>
2300 <li>RNA Helix Alignment Colouring</li>
2301 <li>RNA base pair logo consensus</li>
2302 <li>Parse sequence associated secondary structure
2303 information in Stockholm files</li>
2304 <li>HTML Export database accessions and annotation
2305 information presented in tooltip for sequences</li>
2306 <li>Import secondary structure from LOCARNA clustalw
2307 style RNA alignment files</li>
2308 <li>import and visualise T-COFFEE quality scores for an
2310 <li>'colour by annotation' per sequence option to
2311 shade each sequence according to its associated alignment
2313 <li>New Jalview Logo</li>
2314 </ul> <em>Documentation and Development</em>
2316 <li>documentation for score matrices used in Jalview</li>
2317 <li>New Website!</li>
2319 <td><em>Application</em>
2321 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2322 wsdbfetch REST service</li>
2323 <li>Stop windows being moved outside desktop on OSX</li>
2324 <li>Filetype associations not installed for webstart
2326 <li>Jalview does not always retrieve progress of a JABAWS
2327 job execution in full once it is complete</li>
2328 <li>revise SHMR RSBS definition to ensure alignment is
2329 uploaded via ali_file parameter</li>
2330 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2331 <li>View all structures superposed fails with exception</li>
2332 <li>Jnet job queues forever if a very short sequence is
2333 submitted for prediction</li>
2334 <li>Cut and paste menu not opened when mouse clicked on
2336 <li>Putting fractional value into integer text box in
2337 alignment parameter dialog causes Jalview to hang</li>
2338 <li>Structure view highlighting doesn't work on
2340 <li>View all structures fails with exception shown in
2342 <li>Characters in filename associated with PDBEntry not
2343 escaped in a platform independent way</li>
2344 <li>Jalview desktop fails to launch with exception when
2346 <li>Tree calculation reports 'you must have 2 or more
2347 sequences selected' when selection is empty</li>
2348 <li>Jalview desktop fails to launch with jar signature
2349 failure when java web start temporary file caching is
2351 <li>DAS Sequence retrieval with range qualification
2352 results in sequence xref which includes range qualification</li>
2353 <li>Errors during processing of command line arguments
2354 cause progress bar (JAL-898) to be removed</li>
2355 <li>Replace comma for semi-colon option not disabled for
2356 DAS sources in sequence fetcher</li>
2357 <li>Cannot close news reader when JABAWS server warning
2358 dialog is shown</li>
2359 <li>Option widgets not updated to reflect user settings</li>
2360 <li>Edited sequence not submitted to web service</li>
2361 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2362 <li>InstallAnywhere installer doesn't unpack and run
2363 on OSX Mountain Lion</li>
2364 <li>Annotation panel not given a scroll bar when
2365 sequences with alignment annotation are pasted into the
2367 <li>Sequence associated annotation rows not associated
2368 when loaded from Jalview project</li>
2369 <li>Browser launch fails with NPE on java 1.7</li>
2370 <li>JABAWS alignment marked as finished when job was
2371 cancelled or job failed due to invalid input</li>
2372 <li>NPE with v2.7 example when clicking on Tree
2373 associated with all views</li>
2374 <li>Exceptions when copy/paste sequences with grouped
2375 annotation rows to new window</li>
2376 </ul> <em>Applet</em>
2378 <li>Sequence features are momentarily displayed before
2379 they are hidden using hidefeaturegroups applet parameter</li>
2380 <li>loading features via javascript API automatically
2381 enables feature display</li>
2382 <li>scrollToColumnIn javascript API method doesn't
2384 </ul> <em>General</em>
2386 <li>Redundancy removal fails for rna alignment</li>
2387 <li>PCA calculation fails when sequence has been selected
2388 and then deselected</li>
2389 <li>PCA window shows grey box when first opened on OSX</li>
2390 <li>Letters coloured pink in sequence logo when alignment
2391 coloured with clustalx</li>
2392 <li>Choosing fonts without letter symbols defined causes
2393 exceptions and redraw errors</li>
2394 <li>Initial PCA plot view is not same as manually
2395 reconfigured view</li>
2396 <li>Grouped annotation graph label has incorrect line
2398 <li>Grouped annotation graph label display is corrupted
2399 for lots of labels</li>
2404 <div align="center">
2405 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2408 <td><em>Application</em>
2410 <li>Jalview Desktop News Reader</li>
2411 <li>Tweaked default layout of web services menu</li>
2412 <li>View/alignment association menu to enable user to
2413 easily specify which alignment a multi-structure view takes
2414 its colours/correspondences from</li>
2415 <li>Allow properties file location to be specified as URL</li>
2416 <li>Extend Jalview project to preserve associations
2417 between many alignment views and a single Jmol display</li>
2418 <li>Store annotation row height in Jalview project file</li>
2419 <li>Annotation row column label formatting attributes
2420 stored in project file</li>
2421 <li>Annotation row order for auto-calculated annotation
2422 rows preserved in Jalview project file</li>
2423 <li>Visual progress indication when Jalview state is
2424 saved using Desktop window menu</li>
2425 <li>Visual indication that command line arguments are
2426 still being processed</li>
2427 <li>Groovy script execution from URL</li>
2428 <li>Colour by annotation default min and max colours in
2430 <li>Automatically associate PDB files dragged onto an
2431 alignment with sequences that have high similarity and
2433 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2434 <li>'view structures' option to open many
2435 structures in same window</li>
2436 <li>Sort associated views menu option for tree panel</li>
2437 <li>Group all JABA and non-JABA services for a particular
2438 analysis function in its own submenu</li>
2439 </ul> <em>Applet</em>
2441 <li>Userdefined and autogenerated annotation rows for
2443 <li>Adjustment of alignment annotation pane height</li>
2444 <li>Annotation scrollbar for annotation panel</li>
2445 <li>Drag to reorder annotation rows in annotation panel</li>
2446 <li>'automaticScrolling' parameter</li>
2447 <li>Allow sequences with partial ID string matches to be
2448 annotated from GFF/Jalview features files</li>
2449 <li>Sequence logo annotation row in applet</li>
2450 <li>Absolute paths relative to host server in applet
2451 parameters are treated as such</li>
2452 <li>New in the JalviewLite javascript API:
2454 <li>JalviewLite.js javascript library</li>
2455 <li>Javascript callbacks for
2457 <li>Applet initialisation</li>
2458 <li>Sequence/alignment mouse-overs and selections</li>
2461 <li>scrollTo row and column alignment scrolling
2463 <li>Select sequence/alignment regions from javascript</li>
2464 <li>javascript structure viewer harness to pass
2465 messages between Jmol and Jalview when running as
2466 distinct applets</li>
2467 <li>sortBy method</li>
2468 <li>Set of applet and application examples shipped
2469 with documentation</li>
2470 <li>New example to demonstrate JalviewLite and Jmol
2471 javascript message exchange</li>
2473 </ul> <em>General</em>
2475 <li>Enable Jmol displays to be associated with multiple
2476 multiple alignments</li>
2477 <li>Option to automatically sort alignment with new tree</li>
2478 <li>User configurable link to enable redirects to a
2479 www.Jalview.org mirror</li>
2480 <li>Jmol colours option for Jmol displays</li>
2481 <li>Configurable newline string when writing alignment
2482 and other flat files</li>
2483 <li>Allow alignment annotation description lines to
2484 contain html tags</li>
2485 </ul> <em>Documentation and Development</em>
2487 <li>Add groovy test harness for bulk load testing to
2489 <li>Groovy script to load and align a set of sequences
2490 using a web service before displaying the result in the
2491 Jalview desktop</li>
2492 <li>Restructured javascript and applet api documentation</li>
2493 <li>Ant target to publish example html files with applet
2495 <li>Netbeans project for building Jalview from source</li>
2496 <li>ant task to create online javadoc for Jalview source</li>
2498 <td><em>Application</em>
2500 <li>User defined colourscheme throws exception when
2501 current built in colourscheme is saved as new scheme</li>
2502 <li>AlignFrame->Save in application pops up save
2503 dialog for valid filename/format</li>
2504 <li>Cannot view associated structure for UniProt sequence</li>
2505 <li>PDB file association breaks for UniProt sequence
2507 <li>Associate PDB from file dialog does not tell you
2508 which sequence is to be associated with the file</li>
2509 <li>Find All raises null pointer exception when query
2510 only matches sequence IDs</li>
2511 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2512 <li>Jalview project with Jmol views created with Jalview
2513 2.4 cannot be loaded</li>
2514 <li>Filetype associations not installed for webstart
2516 <li>Two or more chains in a single PDB file associated
2517 with sequences in different alignments do not get coloured
2518 by their associated sequence</li>
2519 <li>Visibility status of autocalculated annotation row
2520 not preserved when project is loaded</li>
2521 <li>Annotation row height and visibility attributes not
2522 stored in Jalview project</li>
2523 <li>Tree bootstraps are not preserved when saved as a
2524 Jalview project</li>
2525 <li>Envision2 workflow tooltips are corrupted</li>
2526 <li>Enabling show group conservation also enables colour
2527 by conservation</li>
2528 <li>Duplicate group associated conservation or consensus
2529 created on new view</li>
2530 <li>Annotation scrollbar not displayed after 'show
2531 all hidden annotation rows' option selected</li>
2532 <li>Alignment quality not updated after alignment
2533 annotation row is hidden then shown</li>
2534 <li>Preserve colouring of structures coloured by
2535 sequences in pre Jalview 2.7 projects</li>
2536 <li>Web service job parameter dialog is not laid out
2538 <li>Web services menu not refreshed after 'reset
2539 services' button is pressed in preferences</li>
2540 <li>Annotation off by one in Jalview v2_3 example project</li>
2541 <li>Structures imported from file and saved in project
2542 get name like jalview_pdb1234.txt when reloaded</li>
2543 <li>Jalview does not always retrieve progress of a JABAWS
2544 job execution in full once it is complete</li>
2545 </ul> <em>Applet</em>
2547 <li>Alignment height set incorrectly when lots of
2548 annotation rows are displayed</li>
2549 <li>Relative URLs in feature HTML text not resolved to
2551 <li>View follows highlighting does not work for positions
2553 <li><= shown as = in tooltip</li>
2554 <li>Export features raises exception when no features
2556 <li>Separator string used for serialising lists of IDs
2557 for javascript api is modified when separator string
2558 provided as parameter</li>
2559 <li>Null pointer exception when selecting tree leaves for
2560 alignment with no existing selection</li>
2561 <li>Relative URLs for datasources assumed to be relative
2562 to applet's codebase</li>
2563 <li>Status bar not updated after finished searching and
2564 search wraps around to first result</li>
2565 <li>StructureSelectionManager instance shared between
2566 several Jalview applets causes race conditions and memory
2568 <li>Hover tooltip and mouseover of position on structure
2569 not sent from Jmol in applet</li>
2570 <li>Certain sequences of javascript method calls to
2571 applet API fatally hang browser</li>
2572 </ul> <em>General</em>
2574 <li>View follows structure mouseover scrolls beyond
2575 position with wrapped view and hidden regions</li>
2576 <li>Find sequence position moves to wrong residue
2577 with/without hidden columns</li>
2578 <li>Sequence length given in alignment properties window
2580 <li>InvalidNumberFormat exceptions thrown when trying to
2581 import PDB like structure files</li>
2582 <li>Positional search results are only highlighted
2583 between user-supplied sequence start/end bounds</li>
2584 <li>End attribute of sequence is not validated</li>
2585 <li>Find dialog only finds first sequence containing a
2586 given sequence position</li>
2587 <li>Sequence numbering not preserved in MSF alignment
2589 <li>Jalview PDB file reader does not extract sequence
2590 from nucleotide chains correctly</li>
2591 <li>Structure colours not updated when tree partition
2592 changed in alignment</li>
2593 <li>Sequence associated secondary structure not correctly
2594 parsed in interleaved stockholm</li>
2595 <li>Colour by annotation dialog does not restore current
2597 <li>Hiding (nearly) all sequences doesn't work
2599 <li>Sequences containing lowercase letters are not
2600 properly associated with their pdb files</li>
2601 </ul> <em>Documentation and Development</em>
2603 <li>schemas/JalviewWsParamSet.xsd corrupted by
2604 ApplyCopyright tool</li>
2609 <div align="center">
2610 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2613 <td><em>Application</em>
2615 <li>New warning dialog when the Jalview Desktop cannot
2616 contact web services</li>
2617 <li>JABA service parameters for a preset are shown in
2618 service job window</li>
2619 <li>JABA Service menu entries reworded</li>
2623 <li>Modeller PIR IO broken - cannot correctly import a
2624 pir file emitted by Jalview</li>
2625 <li>Existing feature settings transferred to new
2626 alignment view created from cut'n'paste</li>
2627 <li>Improved test for mixed amino/nucleotide chains when
2628 parsing PDB files</li>
2629 <li>Consensus and conservation annotation rows
2630 occasionally become blank for all new windows</li>
2631 <li>Exception raised when right clicking above sequences
2632 in wrapped view mode</li>
2633 </ul> <em>Application</em>
2635 <li>multiple multiply aligned structure views cause cpu
2636 usage to hit 100% and computer to hang</li>
2637 <li>Web Service parameter layout breaks for long user
2638 parameter names</li>
2639 <li>Jaba service discovery hangs desktop if Jaba server
2646 <div align="center">
2647 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2650 <td><em>Application</em>
2652 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2653 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2656 <li>Web Services preference tab</li>
2657 <li>Analysis parameters dialog box and user defined
2659 <li>Improved speed and layout of Envision2 service menu</li>
2660 <li>Superpose structures using associated sequence
2662 <li>Export coordinates and projection as CSV from PCA
2664 </ul> <em>Applet</em>
2666 <li>enable javascript: execution by the applet via the
2667 link out mechanism</li>
2668 </ul> <em>Other</em>
2670 <li>Updated the Jmol Jalview interface to work with Jmol
2672 <li>The Jalview Desktop and JalviewLite applet now
2673 require Java 1.5</li>
2674 <li>Allow Jalview feature colour specification for GFF
2675 sequence annotation files</li>
2676 <li>New 'colour by label' keword in Jalview feature file
2677 type colour specification</li>
2678 <li>New Jalview Desktop Groovy API method that allows a
2679 script to check if it being run in an interactive session or
2680 in a batch operation from the Jalview command line</li>
2684 <li>clustalx colourscheme colours Ds preferentially when
2685 both D+E are present in over 50% of the column</li>
2686 </ul> <em>Application</em>
2688 <li>typo in AlignmentFrame->View->Hide->all but
2689 selected Regions menu item</li>
2690 <li>sequence fetcher replaces ',' for ';' when the ',' is
2691 part of a valid accession ID</li>
2692 <li>fatal OOM if object retrieved by sequence fetcher
2693 runs out of memory</li>
2694 <li>unhandled Out of Memory Error when viewing pca
2695 analysis results</li>
2696 <li>InstallAnywhere builds fail to launch on OS X java
2697 10.5 update 4 (due to apple Java 1.6 update)</li>
2698 <li>Installanywhere Jalview silently fails to launch</li>
2699 </ul> <em>Applet</em>
2701 <li>Jalview.getFeatureGroups() raises an
2702 ArrayIndexOutOfBoundsException if no feature groups are
2709 <div align="center">
2710 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2716 <li>Alignment prettyprinter doesn't cope with long
2718 <li>clustalx colourscheme colours Ds preferentially when
2719 both D+E are present in over 50% of the column</li>
2720 <li>nucleic acid structures retrieved from PDB do not
2721 import correctly</li>
2722 <li>More columns get selected than were clicked on when a
2723 number of columns are hidden</li>
2724 <li>annotation label popup menu not providing correct
2725 add/hide/show options when rows are hidden or none are
2727 <li>Stockholm format shown in list of readable formats,
2728 and parser copes better with alignments from RFAM.</li>
2729 <li>CSV output of consensus only includes the percentage
2730 of all symbols if sequence logo display is enabled</li>
2732 </ul> <em>Applet</em>
2734 <li>annotation panel disappears when annotation is
2736 </ul> <em>Application</em>
2738 <li>Alignment view not redrawn properly when new
2739 alignment opened where annotation panel is visible but no
2740 annotations are present on alignment</li>
2741 <li>pasted region containing hidden columns is
2742 incorrectly displayed in new alignment window</li>
2743 <li>Jalview slow to complete operations when stdout is
2744 flooded (fix is to close the Jalview console)</li>
2745 <li>typo in AlignmentFrame->View->Hide->all but
2746 selected Rregions menu item.</li>
2747 <li>inconsistent group submenu and Format submenu entry
2748 'Un' or 'Non'conserved</li>
2749 <li>Sequence feature settings are being shared by
2750 multiple distinct alignments</li>
2751 <li>group annotation not recreated when tree partition is
2753 <li>double click on group annotation to select sequences
2754 does not propagate to associated trees</li>
2755 <li>Mac OSX specific issues:
2757 <li>exception raised when mouse clicked on desktop
2758 window background</li>
2759 <li>Desktop menu placed on menu bar and application
2760 name set correctly</li>
2761 <li>sequence feature settings not wide enough for the
2762 save feature colourscheme button</li>
2771 <div align="center">
2772 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2775 <td><em>New Capabilities</em>
2777 <li>URL links generated from description line for
2778 regular-expression based URL links (applet and application)
2780 <li>Non-positional feature URL links are shown in link
2782 <li>Linked viewing of nucleic acid sequences and
2784 <li>Automatic Scrolling option in View menu to display
2785 the currently highlighted region of an alignment.</li>
2786 <li>Order an alignment by sequence length, or using the
2787 average score or total feature count for each sequence.</li>
2788 <li>Shading features by score or associated description</li>
2789 <li>Subdivide alignment and groups based on identity of
2790 selected subsequence (Make Groups from Selection).</li>
2791 <li>New hide/show options including Shift+Control+H to
2792 hide everything but the currently selected region.</li>
2793 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2794 </ul> <em>Application</em>
2796 <li>Fetch DB References capabilities and UI expanded to
2797 support retrieval from DAS sequence sources</li>
2798 <li>Local DAS Sequence sources can be added via the
2799 command line or via the Add local source dialog box.</li>
2800 <li>DAS Dbref and DbxRef feature types are parsed as
2801 database references and protein_name is parsed as
2802 description line (BioSapiens terms).</li>
2803 <li>Enable or disable non-positional feature and database
2804 references in sequence ID tooltip from View menu in
2806 <!-- <li>New hidden columns and rows and representatives capabilities
2807 in annotations file (in progress - not yet fully implemented)</li> -->
2808 <li>Group-associated consensus, sequence logos and
2809 conservation plots</li>
2810 <li>Symbol distributions for each column can be exported
2811 and visualized as sequence logos</li>
2812 <li>Optionally scale multi-character column labels to fit
2813 within each column of annotation row<!-- todo for applet -->
2815 <li>Optional automatic sort of associated alignment view
2816 when a new tree is opened.</li>
2817 <li>Jalview Java Console</li>
2818 <li>Better placement of desktop window when moving
2819 between different screens.</li>
2820 <li>New preference items for sequence ID tooltip and
2821 consensus annotation</li>
2822 <li>Client to submit sequences and IDs to Envision2
2824 <li><em>Vamsas Capabilities</em>
2826 <li>Improved VAMSAS synchronization (Jalview archive
2827 used to preserve views, structures, and tree display
2829 <li>Import of vamsas documents from disk or URL via
2831 <li>Sharing of selected regions between views and
2832 with other VAMSAS applications (Experimental feature!)</li>
2833 <li>Updated API to VAMSAS version 0.2</li>
2835 </ul> <em>Applet</em>
2837 <li>Middle button resizes annotation row height</li>
2840 <li>sortByTree (true/false) - automatically sort the
2841 associated alignment view by the tree when a new tree is
2843 <li>showTreeBootstraps (true/false) - show or hide
2844 branch bootstraps (default is to show them if available)</li>
2845 <li>showTreeDistances (true/false) - show or hide
2846 branch lengths (default is to show them if available)</li>
2847 <li>showUnlinkedTreeNodes (true/false) - indicate if
2848 unassociated nodes should be highlighted in the tree
2850 <li>heightScale and widthScale (1.0 or more) -
2851 increase the height or width of a cell in the alignment
2852 grid relative to the current font size.</li>
2855 <li>Non-positional features displayed in sequence ID
2857 </ul> <em>Other</em>
2859 <li>Features format: graduated colour definitions and
2860 specification of feature scores</li>
2861 <li>Alignment Annotations format: new keywords for group
2862 associated annotation (GROUP_REF) and annotation row display
2863 properties (ROW_PROPERTIES)</li>
2864 <li>XML formats extended to support graduated feature
2865 colourschemes, group associated annotation, and profile
2866 visualization settings.</li></td>
2869 <li>Source field in GFF files parsed as feature source
2870 rather than description</li>
2871 <li>Non-positional features are now included in sequence
2872 feature and gff files (controlled via non-positional feature
2873 visibility in tooltip).</li>
2874 <li>URL links generated for all feature links (bugfix)</li>
2875 <li>Added URL embedding instructions to features file
2877 <li>Codons containing ambiguous nucleotides translated as
2878 'X' in peptide product</li>
2879 <li>Match case switch in find dialog box works for both
2880 sequence ID and sequence string and query strings do not
2881 have to be in upper case to match case-insensitively.</li>
2882 <li>AMSA files only contain first column of
2883 multi-character column annotation labels</li>
2884 <li>Jalview Annotation File generation/parsing consistent
2885 with documentation (e.g. Stockholm annotation can be
2886 exported and re-imported)</li>
2887 <li>PDB files without embedded PDB IDs given a friendly
2889 <li>Find incrementally searches ID string matches as well
2890 as subsequence matches, and correctly reports total number
2894 <li>Better handling of exceptions during sequence
2896 <li>Dasobert generated non-positional feature URL
2897 link text excludes the start_end suffix</li>
2898 <li>DAS feature and source retrieval buttons disabled
2899 when fetch or registry operations in progress.</li>
2900 <li>PDB files retrieved from URLs are cached properly</li>
2901 <li>Sequence description lines properly shared via
2903 <li>Sequence fetcher fetches multiple records for all
2905 <li>Ensured that command line das feature retrieval
2906 completes before alignment figures are generated.</li>
2907 <li>Reduced time taken when opening file browser for
2909 <li>isAligned check prior to calculating tree, PCA or
2910 submitting an MSA to JNet now excludes hidden sequences.</li>
2911 <li>User defined group colours properly recovered
2912 from Jalview projects.</li>
2921 <div align="center">
2922 <strong>2.4.0.b2</strong><br> 28/10/2009
2927 <li>Experimental support for google analytics usage
2929 <li>Jalview privacy settings (user preferences and docs).</li>
2934 <li>Race condition in applet preventing startup in
2936 <li>Exception when feature created from selection beyond
2937 length of sequence.</li>
2938 <li>Allow synthetic PDB files to be imported gracefully</li>
2939 <li>Sequence associated annotation rows associate with
2940 all sequences with a given id</li>
2941 <li>Find function matches case-insensitively for sequence
2942 ID string searches</li>
2943 <li>Non-standard characters do not cause pairwise
2944 alignment to fail with exception</li>
2945 </ul> <em>Application Issues</em>
2947 <li>Sequences are now validated against EMBL database</li>
2948 <li>Sequence fetcher fetches multiple records for all
2950 </ul> <em>InstallAnywhere Issues</em>
2952 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2953 issue with installAnywhere mechanism)</li>
2954 <li>Command line launching of JARs from InstallAnywhere
2955 version (java class versioning error fixed)</li>
2962 <div align="center">
2963 <strong>2.4</strong><br> 27/8/2008
2966 <td><em>User Interface</em>
2968 <li>Linked highlighting of codon and amino acid from
2969 translation and protein products</li>
2970 <li>Linked highlighting of structure associated with
2971 residue mapping to codon position</li>
2972 <li>Sequence Fetcher provides example accession numbers
2973 and 'clear' button</li>
2974 <li>MemoryMonitor added as an option under Desktop's
2976 <li>Extract score function to parse whitespace separated
2977 numeric data in description line</li>
2978 <li>Column labels in alignment annotation can be centred.</li>
2979 <li>Tooltip for sequence associated annotation give name
2981 </ul> <em>Web Services and URL fetching</em>
2983 <li>JPred3 web service</li>
2984 <li>Prototype sequence search client (no public services
2986 <li>Fetch either seed alignment or full alignment from
2988 <li>URL Links created for matching database cross
2989 references as well as sequence ID</li>
2990 <li>URL Links can be created using regular-expressions</li>
2991 </ul> <em>Sequence Database Connectivity</em>
2993 <li>Retrieval of cross-referenced sequences from other
2995 <li>Generalised database reference retrieval and
2996 validation to all fetchable databases</li>
2997 <li>Fetch sequences from DAS sources supporting the
2998 sequence command</li>
2999 </ul> <em>Import and Export</em>
3000 <li>export annotation rows as CSV for spreadsheet import</li>
3001 <li>Jalview projects record alignment dataset associations,
3002 EMBL products, and cDNA sequence mappings</li>
3003 <li>Sequence Group colour can be specified in Annotation
3005 <li>Ad-hoc colouring of group in Annotation File using RGB
3006 triplet as name of colourscheme</li>
3007 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3009 <li>treenode binding for VAMSAS tree exchange</li>
3010 <li>local editing and update of sequences in VAMSAS
3011 alignments (experimental)</li>
3012 <li>Create new or select existing session to join</li>
3013 <li>load and save of vamsas documents</li>
3014 </ul> <em>Application command line</em>
3016 <li>-tree parameter to open trees (introduced for passing
3018 <li>-fetchfrom command line argument to specify nicknames
3019 of DAS servers to query for alignment features</li>
3020 <li>-dasserver command line argument to add new servers
3021 that are also automatically queried for features</li>
3022 <li>-groovy command line argument executes a given groovy
3023 script after all input data has been loaded and parsed</li>
3024 </ul> <em>Applet-Application data exchange</em>
3026 <li>Trees passed as applet parameters can be passed to
3027 application (when using "View in full
3028 application")</li>
3029 </ul> <em>Applet Parameters</em>
3031 <li>feature group display control parameter</li>
3032 <li>debug parameter</li>
3033 <li>showbutton parameter</li>
3034 </ul> <em>Applet API methods</em>
3036 <li>newView public method</li>
3037 <li>Window (current view) specific get/set public methods</li>
3038 <li>Feature display control methods</li>
3039 <li>get list of currently selected sequences</li>
3040 </ul> <em>New Jalview distribution features</em>
3042 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3043 <li>RELEASE file gives build properties for the latest
3044 Jalview release.</li>
3045 <li>Java 1.1 Applet build made easier and donotobfuscate
3046 property controls execution of obfuscator</li>
3047 <li>Build target for generating source distribution</li>
3048 <li>Debug flag for javacc</li>
3049 <li>.jalview_properties file is documented (slightly) in
3050 jalview.bin.Cache</li>
3051 <li>Continuous Build Integration for stable and
3052 development version of Application, Applet and source
3057 <li>selected region output includes visible annotations
3058 (for certain formats)</li>
3059 <li>edit label/displaychar contains existing label/char
3061 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3062 <li>shorter peptide product names from EMBL records</li>
3063 <li>Newick string generator makes compact representations</li>
3064 <li>bootstrap values parsed correctly for tree files with
3066 <li>pathological filechooser bug avoided by not allowing
3067 filenames containing a ':'</li>
3068 <li>Fixed exception when parsing GFF files containing
3069 global sequence features</li>
3070 <li>Alignment datasets are finalized only when number of
3071 references from alignment sequences goes to zero</li>
3072 <li>Close of tree branch colour box without colour
3073 selection causes cascading exceptions</li>
3074 <li>occasional negative imgwidth exceptions</li>
3075 <li>better reporting of non-fatal warnings to user when
3076 file parsing fails.</li>
3077 <li>Save works when Jalview project is default format</li>
3078 <li>Save as dialog opened if current alignment format is
3079 not a valid output format</li>
3080 <li>UniProt canonical names introduced for both das and
3082 <li>Histidine should be midblue (not pink!) in Zappo</li>
3083 <li>error messages passed up and output when data read
3085 <li>edit undo recovers previous dataset sequence when
3086 sequence is edited</li>
3087 <li>allow PDB files without pdb ID HEADER lines (like
3088 those generated by MODELLER) to be read in properly</li>
3089 <li>allow reading of JPred concise files as a normal
3091 <li>Stockholm annotation parsing and alignment properties
3092 import fixed for PFAM records</li>
3093 <li>Structure view windows have correct name in Desktop
3095 <li>annotation consisting of sequence associated scores
3096 can be read and written correctly to annotation file</li>
3097 <li>Aligned cDNA translation to aligned peptide works
3099 <li>Fixed display of hidden sequence markers and
3100 non-italic font for representatives in Applet</li>
3101 <li>Applet Menus are always embedded in applet window on
3103 <li>Newly shown features appear at top of stack (in
3105 <li>Annotations added via parameter not drawn properly
3106 due to null pointer exceptions</li>
3107 <li>Secondary structure lines are drawn starting from
3108 first column of alignment</li>
3109 <li>UniProt XML import updated for new schema release in
3111 <li>Sequence feature to sequence ID match for Features
3112 file is case-insensitive</li>
3113 <li>Sequence features read from Features file appended to
3114 all sequences with matching IDs</li>
3115 <li>PDB structure coloured correctly for associated views
3116 containing a sub-sequence</li>
3117 <li>PDB files can be retrieved by applet from Jar files</li>
3118 <li>feature and annotation file applet parameters
3119 referring to different directories are retrieved correctly</li>
3120 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3121 <li>Fixed application hang whilst waiting for
3122 splash-screen version check to complete</li>
3123 <li>Applet properly URLencodes input parameter values
3124 when passing them to the launchApp service</li>
3125 <li>display name and local features preserved in results
3126 retrieved from web service</li>
3127 <li>Visual delay indication for sequence retrieval and
3128 sequence fetcher initialisation</li>
3129 <li>updated Application to use DAS 1.53e version of
3130 dasobert DAS client</li>
3131 <li>Re-instated Full AMSA support and .amsa file
3133 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3141 <div align="center">
3142 <strong>2.3</strong><br> 9/5/07
3147 <li>Jmol 11.0.2 integration</li>
3148 <li>PDB views stored in Jalview XML files</li>
3149 <li>Slide sequences</li>
3150 <li>Edit sequence in place</li>
3151 <li>EMBL CDS features</li>
3152 <li>DAS Feature mapping</li>
3153 <li>Feature ordering</li>
3154 <li>Alignment Properties</li>
3155 <li>Annotation Scores</li>
3156 <li>Sort by scores</li>
3157 <li>Feature/annotation editing in applet</li>
3162 <li>Headless state operation in 2.2.1</li>
3163 <li>Incorrect and unstable DNA pairwise alignment</li>
3164 <li>Cut and paste of sequences with annotation</li>
3165 <li>Feature group display state in XML</li>
3166 <li>Feature ordering in XML</li>
3167 <li>blc file iteration selection using filename # suffix</li>
3168 <li>Stockholm alignment properties</li>
3169 <li>Stockhom alignment secondary structure annotation</li>
3170 <li>2.2.1 applet had no feature transparency</li>
3171 <li>Number pad keys can be used in cursor mode</li>
3172 <li>Structure Viewer mirror image resolved</li>
3179 <div align="center">
3180 <strong>2.2.1</strong><br> 12/2/07
3185 <li>Non standard characters can be read and displayed
3186 <li>Annotations/Features can be imported/exported to the
3188 <li>Applet allows editing of sequence/annotation/group
3189 name & description
3190 <li>Preference setting to display sequence name in
3192 <li>Annotation file format extended to allow
3193 Sequence_groups to be defined
3194 <li>Default opening of alignment overview panel can be
3195 specified in preferences
3196 <li>PDB residue numbering annotation added to associated
3202 <li>Applet crash under certain Linux OS with Java 1.6
3204 <li>Annotation file export / import bugs fixed
3205 <li>PNG / EPS image output bugs fixed
3211 <div align="center">
3212 <strong>2.2</strong><br> 27/11/06
3217 <li>Multiple views on alignment
3218 <li>Sequence feature editing
3219 <li>"Reload" alignment
3220 <li>"Save" to current filename
3221 <li>Background dependent text colour
3222 <li>Right align sequence ids
3223 <li>User-defined lower case residue colours
3226 <li>Menu item accelerator keys
3227 <li>Control-V pastes to current alignment
3228 <li>Cancel button for DAS Feature Fetching
3229 <li>PCA and PDB Viewers zoom via mouse roller
3230 <li>User-defined sub-tree colours and sub-tree selection
3232 <li>'New Window' button on the 'Output to Text box'
3237 <li>New memory efficient Undo/Redo System
3238 <li>Optimised symbol lookups and conservation/consensus
3240 <li>Region Conservation/Consensus recalculated after
3242 <li>Fixed Remove Empty Columns Bug (empty columns at end
3244 <li>Slowed DAS Feature Fetching for increased robustness.
3246 <li>Made angle brackets in ASCII feature descriptions
3248 <li>Re-instated Zoom function for PCA
3249 <li>Sequence descriptions conserved in web service
3251 <li>UniProt ID discoverer uses any word separated by
3253 <li>WsDbFetch query/result association resolved
3254 <li>Tree leaf to sequence mapping improved
3255 <li>Smooth fonts switch moved to FontChooser dialog box.
3262 <div align="center">
3263 <strong>2.1.1</strong><br> 12/9/06
3268 <li>Copy consensus sequence to clipboard</li>
3273 <li>Image output - rightmost residues are rendered if
3274 sequence id panel has been resized</li>
3275 <li>Image output - all offscreen group boundaries are
3277 <li>Annotation files with sequence references - all
3278 elements in file are relative to sequence position</li>
3279 <li>Mac Applet users can use Alt key for group editing</li>
3285 <div align="center">
3286 <strong>2.1</strong><br> 22/8/06
3291 <li>MAFFT Multiple Alignment in default Web Service list</li>
3292 <li>DAS Feature fetching</li>
3293 <li>Hide sequences and columns</li>
3294 <li>Export Annotations and Features</li>
3295 <li>GFF file reading / writing</li>
3296 <li>Associate structures with sequences from local PDB
3298 <li>Add sequences to exisiting alignment</li>
3299 <li>Recently opened files / URL lists</li>
3300 <li>Applet can launch the full application</li>
3301 <li>Applet has transparency for features (Java 1.2
3303 <li>Applet has user defined colours parameter</li>
3304 <li>Applet can load sequences from parameter
3305 "sequence<em>x</em>"
3311 <li>Redundancy Panel reinstalled in the Applet</li>
3312 <li>Monospaced font - EPS / rescaling bug fixed</li>
3313 <li>Annotation files with sequence references bug fixed</li>
3319 <div align="center">
3320 <strong>2.08.1</strong><br> 2/5/06
3325 <li>Change case of selected region from Popup menu</li>
3326 <li>Choose to match case when searching</li>
3327 <li>Middle mouse button and mouse movement can compress /
3328 expand the visible width and height of the alignment</li>
3333 <li>Annotation Panel displays complete JNet results</li>
3339 <div align="center">
3340 <strong>2.08b</strong><br> 18/4/06
3346 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3347 <li>Righthand label on wrapped alignments shows correct
3354 <div align="center">
3355 <strong>2.08</strong><br> 10/4/06
3360 <li>Editing can be locked to the selection area</li>
3361 <li>Keyboard editing</li>
3362 <li>Create sequence features from searches</li>
3363 <li>Precalculated annotations can be loaded onto
3365 <li>Features file allows grouping of features</li>
3366 <li>Annotation Colouring scheme added</li>
3367 <li>Smooth fonts off by default - Faster rendering</li>
3368 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3373 <li>Drag & Drop fixed on Linux</li>
3374 <li>Jalview Archive file faster to load/save, sequence
3375 descriptions saved.</li>
3381 <div align="center">
3382 <strong>2.07</strong><br> 12/12/05
3387 <li>PDB Structure Viewer enhanced</li>
3388 <li>Sequence Feature retrieval and display enhanced</li>
3389 <li>Choose to output sequence start-end after sequence
3390 name for file output</li>
3391 <li>Sequence Fetcher WSDBFetch@EBI</li>
3392 <li>Applet can read feature files, PDB files and can be
3393 used for HTML form input</li>
3398 <li>HTML output writes groups and features</li>
3399 <li>Group editing is Control and mouse click</li>
3400 <li>File IO bugs</li>
3406 <div align="center">
3407 <strong>2.06</strong><br> 28/9/05
3412 <li>View annotations in wrapped mode</li>
3413 <li>More options for PCA viewer</li>
3418 <li>GUI bugs resolved</li>
3419 <li>Runs with -nodisplay from command line</li>
3425 <div align="center">
3426 <strong>2.05b</strong><br> 15/9/05
3431 <li>Choose EPS export as lineart or text</li>
3432 <li>Jar files are executable</li>
3433 <li>Can read in Uracil - maps to unknown residue</li>
3438 <li>Known OutOfMemory errors give warning message</li>
3439 <li>Overview window calculated more efficiently</li>
3440 <li>Several GUI bugs resolved</li>
3446 <div align="center">
3447 <strong>2.05</strong><br> 30/8/05
3452 <li>Edit and annotate in "Wrapped" view</li>
3457 <li>Several GUI bugs resolved</li>
3463 <div align="center">
3464 <strong>2.04</strong><br> 24/8/05
3469 <li>Hold down mouse wheel & scroll to change font
3475 <li>Improved JPred client reliability</li>
3476 <li>Improved loading of Jalview files</li>
3482 <div align="center">
3483 <strong>2.03</strong><br> 18/8/05
3488 <li>Set Proxy server name and port in preferences</li>
3489 <li>Multiple URL links from sequence ids</li>
3490 <li>User Defined Colours can have a scheme name and added
3492 <li>Choose to ignore gaps in consensus calculation</li>
3493 <li>Unix users can set default web browser</li>
3494 <li>Runs without GUI for batch processing</li>
3495 <li>Dynamically generated Web Service Menus</li>
3500 <li>InstallAnywhere download for Sparc Solaris</li>
3506 <div align="center">
3507 <strong>2.02</strong><br> 18/7/05
3513 <li>Copy & Paste order of sequences maintains
3514 alignment order.</li>
3520 <div align="center">
3521 <strong>2.01</strong><br> 12/7/05
3526 <li>Use delete key for deleting selection.</li>
3527 <li>Use Mouse wheel to scroll sequences.</li>
3528 <li>Help file updated to describe how to add alignment
3530 <li>Version and build date written to build properties
3532 <li>InstallAnywhere installation will check for updates
3533 at launch of Jalview.</li>
3538 <li>Delete gaps bug fixed.</li>
3539 <li>FileChooser sorts columns.</li>
3540 <li>Can remove groups one by one.</li>
3541 <li>Filechooser icons installed.</li>
3542 <li>Finder ignores return character when searching.
3543 Return key will initiate a search.<br>
3550 <div align="center">
3551 <strong>2.0</strong><br> 20/6/05
3556 <li>New codebase</li>