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>
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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
92 <li><!-- JAL-2495 -->All linked sequences are highlighted for a structure mousover (Jmol) or selection (Chimera)</li>
93 <li><!-- JAL-2790 -->'Cancel' button in progress bar for JABAWS AACon, RNAAliFold and Disorder prediction jobs
96 <li><!-- JAL-2617 -->Stop codons are excluded in CDS/Protein view from Ensembl locus cross-references</li>
98 <ul><li>Example groovy script for generating a matrix of percent identity scores for current alignment.</li></ul>
99 <em>Testing and Deployment</em>
100 <ul><li><!-- JAL-2727 -->Test to catch memory leaks in Jalview UI</li></ul>
103 <td><div align="left">
106 <li><!-- JAL-2643 -->Pressing tab after updating the colour threshold text field doesn't trigger an update to the alignment view</li>
107 <li><!-- JAL-2682 -->Race condition when parsing sequence ID strings in parallel</li>
108 <li><!-- JAL-2608 -->Overview windows are also closed when alignment window is closed</li>
112 <li><!-- JAL-2777 -->Structures with whitespace chainCode cannot be viewed in Chimera</li>
113 <li><!-- JAL-2728 -->Protein annotation panel too high in CDS/Protein view
115 <li><!-- JAL-2757 -->Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs
117 <li><!-- JAL-2253 -->Slow EnsemblGenome ID lookup</li>
118 <li><!-- JAL-2739 -->Hidden column marker in last column not rendered when switching back from Wrapped to normal view</li>
119 <li><!-- JAL-2768 -->Annotation display corrupted when scrolling right in unwapped alignment view</li>
120 <li><!-- JAL-2542 -->Existing features on subsequence incorrectly relocated when full sequence retrieved from database</li>
121 <li><!-- JAL-2733 -->Last reported memory still shown when Desktop->Show Memory is unticked (OSX only)</li>
122 <li><!-- JAL-2658 -->Amend Features dialog doesn't allow features of same type and group to be selected for amending</li>
123 <li><!-- JAL-2524 -->Jalview becomes sluggish in wide alignments when hidden columns are present</li>
124 <li><!-- JAL-2392 -->Jalview freezes when loading and displaying several structures</li>
125 <li><!-- JAL-2732 -->Black outlines left after resizing or moving a window</li>
126 <li><!-- JAL-1900,JAL-1625 -->Unable to minimise windows within the Jalview desktop on OSX</li>
127 <li><!-- JAL-2667 -->Mouse wheel doesn't scroll vertically when in wrapped alignment mode</li>
128 <li><!-- JAL-2636 -->Scale mark not shown when close to right hand end of alignment</li>
130 <strong><em>Applet</em></strong><br/>
132 <li><!-- JAL-2687 -->Concurrent modification exception when closing alignment panel</li>
138 <td width="60" nowrap>
140 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
141 <em>2/10/2017</em></strong>
144 <td><div align="left">
145 <em>New features in Jalview Desktop</em>
148 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
150 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
154 <td><div align="left">
158 <td width="60" nowrap>
160 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
161 <em>7/9/2017</em></strong>
164 <td><div align="left">
168 <!-- JAL-2588 -->Show gaps in overview window by colouring
169 in grey (sequences used to be coloured grey, and gaps were
173 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
177 <!-- JAL-2587 -->Overview updates immediately on increase
178 in size and progress bar shown as higher resolution
179 overview is recalculated
184 <td><div align="left">
188 <!-- JAL-2664 -->Overview window redraws every hidden
189 column region row by row
192 <!-- JAL-2681 -->duplicate protein sequences shown after
193 retrieving Ensembl crossrefs for sequences from Uniprot
196 <!-- JAL-2603 -->Overview window throws NPE if show boxes
197 format setting is unticked
200 <!-- JAL-2610 -->Groups are coloured wrongly in overview
201 if group has show boxes format setting unticked
204 <!-- JAL-2672,JAL-2665 -->Redraw problems when
205 autoscrolling whilst dragging current selection group to
206 include sequences and columns not currently displayed
209 <!-- JAL-2691 -->Not all chains are mapped when multimeric
210 assemblies are imported via CIF file
213 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
214 displayed when threshold or conservation colouring is also
218 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
222 <!-- JAL-2673 -->Jalview continues to scroll after
223 dragging a selected region off the visible region of the
227 <!-- JAL-2724 -->Cannot apply annotation based
228 colourscheme to all groups in a view
231 <!-- JAL-2511 -->IDs don't line up with sequences
232 initially after font size change using the Font chooser or
239 <td width="60" nowrap>
241 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
244 <td><div align="left">
245 <em>Calculations</em>
249 <!-- JAL-1933 -->Occupancy annotation row shows number of
250 ungapped positions in each column of the alignment.
253 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
254 a calculation dialog box
257 <!-- JAL-2379 -->Revised implementation of PCA for speed
258 and memory efficiency (~30x faster)
261 <!-- JAL-2403 -->Revised implementation of sequence
262 similarity scores as used by Tree, PCA, Shading Consensus
263 and other calculations
266 <!-- JAL-2416 -->Score matrices are stored as resource
267 files within the Jalview codebase
270 <!-- JAL-2500 -->Trees computed on Sequence Feature
271 Similarity may have different topology due to increased
278 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
279 model for alignments and groups
282 <!-- JAL-384 -->Custom shading schemes created via groovy
289 <!-- JAL-2526 -->Efficiency improvements for interacting
290 with alignment and overview windows
293 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
297 <!-- JAL-2388 -->Hidden columns and sequences can be
301 <!-- JAL-2611 -->Click-drag in visible area allows fine
302 adjustment of visible position
306 <em>Data import/export</em>
309 <!-- JAL-2535 -->Posterior probability annotation from
310 Stockholm files imported as sequence associated annotation
313 <!-- JAL-2507 -->More robust per-sequence positional
314 annotation input/output via stockholm flatfile
317 <!-- JAL-2533 -->Sequence names don't include file
318 extension when importing structure files without embedded
319 names or PDB accessions
322 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
323 format sequence substitution matrices
326 <em>User Interface</em>
329 <!-- JAL-2447 --> Experimental Features Checkbox in
330 Desktop's Tools menu to hide or show untested features in
334 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
335 via Overview or sequence motif search operations
338 <!-- JAL-2547 -->Amend sequence features dialog box can be
339 opened by double clicking gaps within sequence feature
343 <!-- JAL-1476 -->Status bar message shown when not enough
344 aligned positions were available to create a 3D structure
348 <em>3D Structure</em>
351 <!-- JAL-2430 -->Hidden regions in alignment views are not
352 coloured in linked structure views
355 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
356 file-based command exchange
359 <!-- JAL-2375 -->Structure chooser automatically shows
360 Cached Structures rather than querying the PDBe if
361 structures are already available for sequences
364 <!-- JAL-2520 -->Structures imported via URL are cached in
365 the Jalview project rather than downloaded again when the
369 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
370 to transfer Chimera's structure attributes as Jalview
371 features, and vice-versa (<strong>Experimental
375 <em>Web Services</em>
378 <!-- JAL-2549 -->Updated JABAWS client to v2.2
381 <!-- JAL-2335 -->Filter non-standard amino acids and
382 nucleotides when submitting to AACon and other MSA
386 <!-- JAL-2316, -->URLs for viewing database
387 cross-references provided by identifiers.org and the
395 <!-- JAL-2344 -->FileFormatI interface for describing and
396 identifying file formats (instead of String constants)
399 <!-- JAL-2228 -->FeatureCounter script refactored for
400 efficiency when counting all displayed features (not
401 backwards compatible with 2.10.1)
404 <em>Example files</em>
407 <!-- JAL-2631 -->Graduated feature colour style example
408 included in the example feature file
411 <em>Documentation</em>
414 <!-- JAL-2339 -->Release notes reformatted for readability
415 with the built-in Java help viewer
418 <!-- JAL-1644 -->Find documentation updated with 'search
419 sequence description' option
425 <!-- JAL-2485, -->External service integration tests for
426 Uniprot REST Free Text Search Client
429 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
432 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
437 <td><div align="left">
438 <em>Calculations</em>
441 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
442 matrix - C->R should be '-3'<br />Old matrix restored
443 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
445 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
446 Jalview's treatment of gaps in PCA and substitution matrix
447 based Tree calculations.<br /> <br />In earlier versions
448 of Jalview, gaps matching gaps were penalised, and gaps
449 matching non-gaps penalised even more. In the PCA
450 calculation, gaps were actually treated as non-gaps - so
451 different costs were applied, which meant Jalview's PCAs
452 were different to those produced by SeqSpace.<br />Jalview
453 now treats gaps in the same way as SeqSpace (ie it scores
454 them as 0). <br /> <br />Enter the following in the
455 Groovy console to restore pre-2.10.2 behaviour:<br />
456 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
457 // for 2.10.1 mode <br />
458 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
459 // to restore 2.10.2 mode <br /> <br /> <em>Note:
460 these settings will affect all subsequent tree and PCA
461 calculations (not recommended)</em></li>
463 <!-- JAL-2424 -->Fixed off-by-one bug that affected
464 scaling of branch lengths for trees computed using
465 Sequence Feature Similarity.
468 <!-- JAL-2377 -->PCA calculation could hang when
469 generating output report when working with highly
473 <!-- JAL-2544 --> Sort by features includes features to
474 right of selected region when gaps present on right-hand
478 <em>User Interface</em>
481 <!-- JAL-2346 -->Reopening Colour by annotation dialog
482 doesn't reselect a specific sequence's associated
483 annotation after it was used for colouring a view
486 <!-- JAL-2419 -->Current selection lost if popup menu
487 opened on a region of alignment without groups
490 <!-- JAL-2374 -->Popup menu not always shown for regions
491 of an alignment with overlapping groups
494 <!-- JAL-2310 -->Finder double counts if both a sequence's
495 name and description match
498 <!-- JAL-2370 -->Hiding column selection containing two
499 hidden regions results in incorrect hidden regions
502 <!-- JAL-2386 -->'Apply to all groups' setting when
503 changing colour does not apply Conservation slider value
507 <!-- JAL-2373 -->Percentage identity and conservation menu
508 items do not show a tick or allow shading to be disabled
511 <!-- JAL-2385 -->Conservation shading or PID threshold
512 lost when base colourscheme changed if slider not visible
515 <!-- JAL-2547 -->Sequence features shown in tooltip for
516 gaps before start of features
519 <!-- JAL-2623 -->Graduated feature colour threshold not
520 restored to UI when feature colour is edited
523 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
524 a time when scrolling vertically in wrapped mode.
527 <!-- JAL-2630 -->Structure and alignment overview update
528 as graduate feature colour settings are modified via the
532 <!-- JAL-2034 -->Overview window doesn't always update
533 when a group defined on the alignment is resized
536 <!-- JAL-2605 -->Mouseovers on left/right scale region in
537 wrapped view result in positional status updates
541 <!-- JAL-2563 -->Status bar doesn't show position for
542 ambiguous amino acid and nucleotide symbols
545 <!-- JAL-2602 -->Copy consensus sequence failed if
546 alignment included gapped columns
549 <!-- JAL-2473 -->Minimum size set for Jalview windows so
550 widgets don't permanently disappear
553 <!-- JAL-2503 -->Cannot select or filter quantitative
554 annotation that are shown only as column labels (e.g.
555 T-Coffee column reliability scores)
558 <!-- JAL-2594 -->Exception thrown if trying to create a
559 sequence feature on gaps only
562 <!-- JAL-2504 -->Features created with 'New feature'
563 button from a Find inherit previously defined feature type
564 rather than the Find query string
567 <!-- JAL-2423 -->incorrect title in output window when
568 exporting tree calculated in Jalview
571 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
572 and then revealing them reorders sequences on the
576 <!-- JAL-964 -->Group panel in sequence feature settings
577 doesn't update to reflect available set of groups after
578 interactively adding or modifying features
581 <!-- JAL-2225 -->Sequence Database chooser unusable on
585 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
586 only excluded gaps in current sequence and ignored
593 <!-- JAL-2421 -->Overview window visible region moves
594 erratically when hidden rows or columns are present
597 <!-- JAL-2362 -->Per-residue colourschemes applied via the
598 Structure Viewer's colour menu don't correspond to
602 <!-- JAL-2405 -->Protein specific colours only offered in
603 colour and group colour menu for protein alignments
606 <!-- JAL-2385 -->Colour threshold slider doesn't update to
607 reflect currently selected view or group's shading
611 <!-- JAL-2624 -->Feature colour thresholds not respected
612 when rendered on overview and structures when opacity at
616 <!-- JAL-2589 -->User defined gap colour not shown in
617 overview when features overlaid on alignment
620 <em>Data import/export</em>
623 <!-- JAL-2576 -->Very large alignments take a long time to
627 <!-- JAL-2507 -->Per-sequence RNA secondary structures
628 added after a sequence was imported are not written to
632 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
633 when importing RNA secondary structure via Stockholm
636 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
637 not shown in correct direction for simple pseudoknots
640 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
641 with lightGray or darkGray via features file (but can
645 <!-- JAL-2383 -->Above PID colour threshold not recovered
646 when alignment view imported from project
649 <!-- JAL-2520,JAL-2465 -->No mappings generated between
650 structure and sequences extracted from structure files
651 imported via URL and viewed in Jmol
654 <!-- JAL-2520 -->Structures loaded via URL are saved in
655 Jalview Projects rather than fetched via URL again when
656 the project is loaded and the structure viewed
659 <em>Web Services</em>
662 <!-- JAL-2519 -->EnsemblGenomes example failing after
663 release of Ensembl v.88
666 <!-- JAL-2366 -->Proxy server address and port always
667 appear enabled in Preferences->Connections
670 <!-- JAL-2461 -->DAS registry not found exceptions
671 removed from console output
674 <!-- JAL-2582 -->Cannot retrieve protein products from
675 Ensembl by Peptide ID
678 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
679 created from SIFTs, and spurious 'Couldn't open structure
680 in Chimera' errors raised after April 2017 update (problem
681 due to 'null' string rather than empty string used for
682 residues with no corresponding PDB mapping).
685 <em>Application UI</em>
688 <!-- JAL-2361 -->User Defined Colours not added to Colour
692 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
693 case' residues (button in colourscheme editor debugged and
694 new documentation and tooltips added)
697 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
698 doesn't restore group-specific text colour thresholds
701 <!-- JAL-2243 -->Feature settings panel does not update as
702 new features are added to alignment
705 <!-- JAL-2532 -->Cancel in feature settings reverts
706 changes to feature colours via the Amend features dialog
709 <!-- JAL-2506 -->Null pointer exception when attempting to
710 edit graduated feature colour via amend features dialog
714 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
715 selection menu changes colours of alignment views
718 <!-- JAL-2426 -->Spurious exceptions in console raised
719 from alignment calculation workers after alignment has
723 <!-- JAL-1608 -->Typo in selection popup menu - Create
724 groups now 'Create Group'
727 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
728 Create/Undefine group doesn't always work
731 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
732 shown again after pressing 'Cancel'
735 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
736 adjusts start position in wrap mode
739 <!-- JAL-2563 -->Status bar doesn't show positions for
740 ambiguous amino acids
743 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
744 CDS/Protein view after CDS sequences added for aligned
748 <!-- JAL-2592 -->User defined colourschemes called 'User
749 Defined' don't appear in Colours menu
755 <!-- JAL-2468 -->Switching between Nucleotide and Protein
756 score models doesn't always result in an updated PCA plot
759 <!-- JAL-2442 -->Features not rendered as transparent on
760 overview or linked structure view
763 <!-- JAL-2372 -->Colour group by conservation doesn't
767 <!-- JAL-2517 -->Hitting Cancel after applying
768 user-defined colourscheme doesn't restore original
775 <!-- JAL-2314 -->Unit test failure:
776 jalview.ws.jabaws.RNAStructExportImport setup fails
779 <!-- JAL-2307 -->Unit test failure:
780 jalview.ws.sifts.SiftsClientTest due to compatibility
781 problems with deep array comparison equality asserts in
782 successive versions of TestNG
785 <!-- JAL-2479 -->Relocated StructureChooserTest and
786 ParameterUtilsTest Unit tests to Network suite
789 <em>New Known Issues</em>
792 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
793 phase after a sequence motif find operation
796 <!-- JAL-2550 -->Importing annotation file with rows
797 containing just upper and lower case letters are
798 interpreted as WUSS RNA secondary structure symbols
801 <!-- JAL-2590 -->Cannot load and display Newick trees
802 reliably from eggnog Ortholog database
805 <!-- JAL-2468 -->Status bar shows 'Marked x columns
806 containing features of type Highlight' when 'B' is pressed
807 to mark columns containing highlighted regions.
810 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
811 doesn't always add secondary structure annotation.
816 <td width="60" nowrap>
818 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
821 <td><div align="left">
825 <!-- JAL-98 -->Improved memory usage: sparse arrays used
826 for all consensus calculations
829 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
832 <li>Updated Jalview's Certum code signing certificate
838 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
839 set of database cross-references, sorted alphabetically
842 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
843 from database cross references. Users with custom links
844 will receive a <a href="webServices/urllinks.html#warning">warning
845 dialog</a> asking them to update their preferences.
848 <!-- JAL-2287-->Cancel button and escape listener on
849 dialog warning user about disconnecting Jalview from a
853 <!-- JAL-2320-->Jalview's Chimera control window closes if
854 the Chimera it is connected to is shut down
857 <!-- JAL-1738-->New keystroke (B) and Select highlighted
858 columns menu item to mark columns containing highlighted
859 regions (e.g. from structure selections or results of a
863 <!-- JAL-2284-->Command line option for batch-generation
864 of HTML pages rendering alignment data with the BioJS
874 <!-- JAL-2286 -->Columns with more than one modal residue
875 are not coloured or thresholded according to percent
876 identity (first observed in Jalview 2.8.2)
879 <!-- JAL-2301 -->Threonine incorrectly reported as not
883 <!-- JAL-2318 -->Updates to documentation pages (above PID
884 threshold, amino acid properties)
887 <!-- JAL-2292 -->Lower case residues in sequences are not
888 reported as mapped to residues in a structure file in the
892 <!--JAL-2324 -->Identical features with non-numeric scores
893 could be added multiple times to a sequence
896 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
897 bond features shown as two highlighted residues rather
898 than a range in linked structure views, and treated
899 correctly when selecting and computing trees from features
902 <!-- JAL-2281-->Custom URL links for database
903 cross-references are matched to database name regardless
911 <!-- JAL-2282-->Custom URL links for specific database
912 names without regular expressions also offer links from
916 <!-- JAL-2315-->Removing a single configured link in the
917 URL links pane in Connections preferences doesn't actually
918 update Jalview configuration
921 <!-- JAL-2272-->CTRL-Click on a selected region to open
922 the alignment area popup menu doesn't work on El-Capitan
925 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
926 files with similarly named sequences if dropped onto the
930 <!-- JAL-2312 -->Additional mappings are shown for PDB
931 entries where more chains exist in the PDB accession than
932 are reported in the SIFTS file
935 <!-- JAL-2317-->Certain structures do not get mapped to
936 the structure view when displayed with Chimera
939 <!-- JAL-2317-->No chains shown in the Chimera view
940 panel's View->Show Chains submenu
943 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
944 work for wrapped alignment views
947 <!--JAL-2197 -->Rename UI components for running JPred
948 predictions from 'JNet' to 'JPred'
951 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
952 corrupted when annotation panel vertical scroll is not at
956 <!--JAL-2332 -->Attempting to view structure for Hen
957 lysozyme results in a PDB Client error dialog box
960 <!-- JAL-2319 -->Structure View's mapping report switched
961 ranges for PDB and sequence for SIFTS
964 SIFTS 'Not_Observed' residues mapped to non-existant
968 <!-- <em>New Known Issues</em>
975 <td width="60" nowrap>
977 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
978 <em>25/10/2016</em></strong>
981 <td><em>Application</em>
983 <li>3D Structure chooser opens with 'Cached structures'
984 view if structures already loaded</li>
985 <li>Progress bar reports models as they are loaded to
992 <li>Colour by conservation always enabled and no tick
993 shown in menu when BLOSUM or PID shading applied</li>
994 <li>FER1_ARATH and FER2_ARATH labels were switched in
995 example sequences/projects/trees</li>
999 <li>Jalview projects with views of local PDB structure
1000 files saved on Windows cannot be opened on OSX</li>
1001 <li>Multiple structure views can be opened and superposed
1002 without timeout for structures with multiple models or
1003 multiple sequences in alignment</li>
1004 <li>Cannot import or associated local PDB files without a
1005 PDB ID HEADER line</li>
1006 <li>RMSD is not output in Jmol console when superposition
1008 <li>Drag and drop of URL from Browser fails for Linux and
1009 OSX versions earlier than El Capitan</li>
1010 <li>ENA client ignores invalid content from ENA server</li>
1011 <li>Exceptions are not raised in console when ENA client
1012 attempts to fetch non-existent IDs via Fetch DB Refs UI
1014 <li>Exceptions are not raised in console when a new view
1015 is created on the alignment</li>
1016 <li>OSX right-click fixed for group selections: CMD-click
1017 to insert/remove gaps in groups and CTRL-click to open group
1020 <em>Build and deployment</em>
1022 <li>URL link checker now copes with multi-line anchor
1025 <em>New Known Issues</em>
1027 <li>Drag and drop from URL links in browsers do not work
1034 <td width="60" nowrap>
1035 <div align="center">
1036 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1039 <td><em>General</em>
1042 <!-- JAL-2124 -->Updated Spanish translations.
1045 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1046 for importing structure data to Jalview. Enables mmCIF and
1050 <!-- JAL-192 --->Alignment ruler shows positions relative to
1054 <!-- JAL-2202 -->Position/residue shown in status bar when
1055 mousing over sequence associated annotation
1058 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1062 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1063 '()', canonical '[]' and invalid '{}' base pair populations
1067 <!-- JAL-2092 -->Feature settings popup menu options for
1068 showing or hiding columns containing a feature
1071 <!-- JAL-1557 -->Edit selected group by double clicking on
1072 group and sequence associated annotation labels
1075 <!-- JAL-2236 -->Sequence name added to annotation label in
1076 select/hide columns by annotation and colour by annotation
1080 </ul> <em>Application</em>
1083 <!-- JAL-2050-->Automatically hide introns when opening a
1084 gene/transcript view
1087 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1091 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1092 structure mappings with the EMBL-EBI PDBe SIFTS database
1095 <!-- JAL-2079 -->Updated download sites used for Rfam and
1096 Pfam sources to xfam.org
1099 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1102 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1103 over sequences in Jalview
1106 <!-- JAL-2027-->Support for reverse-complement coding
1107 regions in ENA and EMBL
1110 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1111 for record retrieval via ENA rest API
1114 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1118 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1119 groovy script execution
1122 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1123 alignment window's Calculate menu
1126 <!-- JAL-1812 -->Allow groovy scripts that call
1127 Jalview.getAlignFrames() to run in headless mode
1130 <!-- JAL-2068 -->Support for creating new alignment
1131 calculation workers from groovy scripts
1134 <!-- JAL-1369 --->Store/restore reference sequence in
1138 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1139 associations are now saved/restored from project
1142 <!-- JAL-1993 -->Database selection dialog always shown
1143 before sequence fetcher is opened
1146 <!-- JAL-2183 -->Double click on an entry in Jalview's
1147 database chooser opens a sequence fetcher
1150 <!-- JAL-1563 -->Free-text search client for UniProt using
1151 the UniProt REST API
1154 <!-- JAL-2168 -->-nonews command line parameter to prevent
1155 the news reader opening
1158 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1159 querying stored in preferences
1162 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1166 <!-- JAL-1977-->Tooltips shown on database chooser
1169 <!-- JAL-391 -->Reverse complement function in calculate
1170 menu for nucleotide sequences
1173 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1174 and feature counts preserves alignment ordering (and
1175 debugged for complex feature sets).
1178 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1179 viewing structures with Jalview 2.10
1182 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1183 genome, transcript CCDS and gene ids via the Ensembl and
1184 Ensembl Genomes REST API
1187 <!-- JAL-2049 -->Protein sequence variant annotation
1188 computed for 'sequence_variant' annotation on CDS regions
1192 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1196 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1197 Ref Fetcher fails to match, or otherwise updates sequence
1198 data from external database records.
1201 <!-- JAL-2154 -->Revised Jalview Project format for
1202 efficient recovery of sequence coding and alignment
1203 annotation relationships.
1205 </ul> <!-- <em>Applet</em>
1216 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1220 <!-- JAL-2018-->Export features in Jalview format (again)
1221 includes graduated colourschemes
1224 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1225 working with big alignments and lots of hidden columns
1228 <!-- JAL-2053-->Hidden column markers not always rendered
1229 at right of alignment window
1232 <!-- JAL-2067 -->Tidied up links in help file table of
1236 <!-- JAL-2072 -->Feature based tree calculation not shown
1240 <!-- JAL-2075 -->Hidden columns ignored during feature
1241 based tree calculation
1244 <!-- JAL-2065 -->Alignment view stops updating when show
1245 unconserved enabled for group on alignment
1248 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1252 <!-- JAL-2146 -->Alignment column in status incorrectly
1253 shown as "Sequence position" when mousing over
1257 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1258 hidden columns present
1261 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1262 user created annotation added to alignment
1265 <!-- JAL-1841 -->RNA Structure consensus only computed for
1266 '()' base pair annotation
1269 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1270 in zero scores for all base pairs in RNA Structure
1274 <!-- JAL-2174-->Extend selection with columns containing
1278 <!-- JAL-2275 -->Pfam format writer puts extra space at
1279 beginning of sequence
1282 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1286 <!-- JAL-2238 -->Cannot create groups on an alignment from
1287 from a tree when t-coffee scores are shown
1290 <!-- JAL-1836,1967 -->Cannot import and view PDB
1291 structures with chains containing negative resnums (4q4h)
1294 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1298 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1299 to Clustal, PIR and PileUp output
1302 <!-- JAL-2008 -->Reordering sequence features that are
1303 not visible causes alignment window to repaint
1306 <!-- JAL-2006 -->Threshold sliders don't work in
1307 graduated colour and colour by annotation row for e-value
1308 scores associated with features and annotation rows
1311 <!-- JAL-1797 -->amino acid physicochemical conservation
1312 calculation should be case independent
1315 <!-- JAL-2173 -->Remove annotation also updates hidden
1319 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1320 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1321 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1324 <!-- JAL-2065 -->Null pointer exceptions and redraw
1325 problems when reference sequence defined and 'show
1326 non-conserved' enabled
1329 <!-- JAL-1306 -->Quality and Conservation are now shown on
1330 load even when Consensus calculation is disabled
1333 <!-- JAL-1932 -->Remove right on penultimate column of
1334 alignment does nothing
1337 <em>Application</em>
1340 <!-- JAL-1552-->URLs and links can't be imported by
1341 drag'n'drop on OSX when launched via webstart (note - not
1342 yet fixed for El Capitan)
1345 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1346 output when running on non-gb/us i18n platforms
1349 <!-- JAL-1944 -->Error thrown when exporting a view with
1350 hidden sequences as flat-file alignment
1353 <!-- JAL-2030-->InstallAnywhere distribution fails when
1357 <!-- JAL-2080-->Jalview very slow to launch via webstart
1358 (also hotfix for 2.9.0b2)
1361 <!-- JAL-2085 -->Cannot save project when view has a
1362 reference sequence defined
1365 <!-- JAL-1011 -->Columns are suddenly selected in other
1366 alignments and views when revealing hidden columns
1369 <!-- JAL-1989 -->Hide columns not mirrored in complement
1370 view in a cDNA/Protein splitframe
1373 <!-- JAL-1369 -->Cannot save/restore representative
1374 sequence from project when only one sequence is
1378 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1379 in Structure Chooser
1382 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1383 structure consensus didn't refresh annotation panel
1386 <!-- JAL-1962 -->View mapping in structure view shows
1387 mappings between sequence and all chains in a PDB file
1390 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1391 dialogs format columns correctly, don't display array
1392 data, sort columns according to type
1395 <!-- JAL-1975 -->Export complete shown after destination
1396 file chooser is cancelled during an image export
1399 <!-- JAL-2025 -->Error when querying PDB Service with
1400 sequence name containing special characters
1403 <!-- JAL-2024 -->Manual PDB structure querying should be
1407 <!-- JAL-2104 -->Large tooltips with broken HTML
1408 formatting don't wrap
1411 <!-- JAL-1128 -->Figures exported from wrapped view are
1412 truncated so L looks like I in consensus annotation
1415 <!-- JAL-2003 -->Export features should only export the
1416 currently displayed features for the current selection or
1420 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1421 after fetching cross-references, and restoring from
1425 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1426 followed in the structure viewer
1429 <!-- JAL-2163 -->Titles for individual alignments in
1430 splitframe not restored from project
1433 <!-- JAL-2145 -->missing autocalculated annotation at
1434 trailing end of protein alignment in transcript/product
1435 splitview when pad-gaps not enabled by default
1438 <!-- JAL-1797 -->amino acid physicochemical conservation
1442 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1443 article has been read (reopened issue due to
1444 internationalisation problems)
1447 <!-- JAL-1960 -->Only offer PDB structures in structure
1448 viewer based on sequence name, PDB and UniProt
1453 <!-- JAL-1976 -->No progress bar shown during export of
1457 <!-- JAL-2213 -->Structures not always superimposed after
1458 multiple structures are shown for one or more sequences.
1461 <!-- JAL-1370 -->Reference sequence characters should not
1462 be replaced with '.' when 'Show unconserved' format option
1466 <!-- JAL-1823 -->Cannot specify chain code when entering
1467 specific PDB id for sequence
1470 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1471 'Export hidden sequences' is enabled, but 'export hidden
1472 columns' is disabled.
1475 <!--JAL-2026-->Best Quality option in structure chooser
1476 selects lowest rather than highest resolution structures
1480 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1481 to sequence mapping in 'View Mappings' report
1484 <!-- JAL-2284 -->Unable to read old Jalview projects that
1485 contain non-XML data added after Jalvew wrote project.
1488 <!-- JAL-2118 -->Newly created annotation row reorders
1489 after clicking on it to create new annotation for a
1493 <!-- JAL-1980 -->Null Pointer Exception raised when
1494 pressing Add on an orphaned cut'n'paste window.
1496 <!-- may exclude, this is an external service stability issue JAL-1941
1497 -- > RNA 3D structure not added via DSSR service</li> -->
1502 <!-- JAL-2151 -->Incorrect columns are selected when
1503 hidden columns present before start of sequence
1506 <!-- JAL-1986 -->Missing dependencies on applet pages
1510 <!-- JAL-1947 -->Overview pixel size changes when
1511 sequences are hidden in applet
1514 <!-- JAL-1996 -->Updated instructions for applet
1515 deployment on examples pages.
1522 <td width="60" nowrap>
1523 <div align="center">
1524 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1525 <em>16/10/2015</em></strong>
1528 <td><em>General</em>
1530 <li>Time stamps for signed Jalview application and applet
1535 <em>Application</em>
1537 <li>Duplicate group consensus and conservation rows
1538 shown when tree is partitioned</li>
1539 <li>Erratic behaviour when tree partitions made with
1540 multiple cDNA/Protein split views</li>
1546 <td width="60" nowrap>
1547 <div align="center">
1548 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1549 <em>8/10/2015</em></strong>
1552 <td><em>General</em>
1554 <li>Updated Spanish translations of localized text for
1556 </ul> <em>Application</em>
1558 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1559 <li>Signed OSX InstallAnywhere installer<br></li>
1560 <li>Support for per-sequence based annotations in BioJSON</li>
1561 </ul> <em>Applet</em>
1563 <li>Split frame example added to applet examples page</li>
1564 </ul> <em>Build and Deployment</em>
1567 <!-- JAL-1888 -->New ant target for running Jalview's test
1575 <li>Mapping of cDNA to protein in split frames
1576 incorrect when sequence start > 1</li>
1577 <li>Broken images in filter column by annotation dialog
1579 <li>Feature colours not parsed from features file</li>
1580 <li>Exceptions and incomplete link URLs recovered when
1581 loading a features file containing HTML tags in feature
1585 <em>Application</em>
1587 <li>Annotations corrupted after BioJS export and
1589 <li>Incorrect sequence limits after Fetch DB References
1590 with 'trim retrieved sequences'</li>
1591 <li>Incorrect warning about deleting all data when
1592 deleting selected columns</li>
1593 <li>Patch to build system for shipping properly signed
1594 JNLP templates for webstart launch</li>
1595 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1596 unreleased structures for download or viewing</li>
1597 <li>Tab/space/return keystroke operation of EMBL-PDBe
1598 fetcher/viewer dialogs works correctly</li>
1599 <li>Disabled 'minimise' button on Jalview windows
1600 running on OSX to workaround redraw hang bug</li>
1601 <li>Split cDNA/Protein view position and geometry not
1602 recovered from jalview project</li>
1603 <li>Initial enabled/disabled state of annotation menu
1604 sorter 'show autocalculated first/last' corresponds to
1606 <li>Restoring of Clustal, RNA Helices and T-Coffee
1607 color schemes from BioJSON</li>
1611 <li>Reorder sequences mirrored in cDNA/Protein split
1613 <li>Applet with Jmol examples not loading correctly</li>
1619 <td><div align="center">
1620 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1622 <td><em>General</em>
1624 <li>Linked visualisation and analysis of DNA and Protein
1627 <li>Translated cDNA alignments shown as split protein
1628 and DNA alignment views</li>
1629 <li>Codon consensus annotation for linked protein and
1630 cDNA alignment views</li>
1631 <li>Link cDNA or Protein product sequences by loading
1632 them onto Protein or cDNA alignments</li>
1633 <li>Reconstruct linked cDNA alignment from aligned
1634 protein sequences</li>
1637 <li>Jmol integration updated to Jmol v14.2.14</li>
1638 <li>Import and export of Jalview alignment views as <a
1639 href="features/bioJsonFormat.html">BioJSON</a></li>
1640 <li>New alignment annotation file statements for
1641 reference sequences and marking hidden columns</li>
1642 <li>Reference sequence based alignment shading to
1643 highlight variation</li>
1644 <li>Select or hide columns according to alignment
1646 <li>Find option for locating sequences by description</li>
1647 <li>Conserved physicochemical properties shown in amino
1648 acid conservation row</li>
1649 <li>Alignments can be sorted by number of RNA helices</li>
1650 </ul> <em>Application</em>
1652 <li>New cDNA/Protein analysis capabilities
1654 <li>Get Cross-References should open a Split Frame
1655 view with cDNA/Protein</li>
1656 <li>Detect when nucleotide sequences and protein
1657 sequences are placed in the same alignment</li>
1658 <li>Split cDNA/Protein views are saved in Jalview
1663 <li>Use REST API to talk to Chimera</li>
1664 <li>Selected regions in Chimera are highlighted in linked
1665 Jalview windows</li>
1667 <li>VARNA RNA viewer updated to v3.93</li>
1668 <li>VARNA views are saved in Jalview Projects</li>
1669 <li>Pseudoknots displayed as Jalview RNA annotation can
1670 be shown in VARNA</li>
1672 <li>Make groups for selection uses marked columns as well
1673 as the active selected region</li>
1675 <li>Calculate UPGMA and NJ trees using sequence feature
1677 <li>New Export options
1679 <li>New Export Settings dialog to control hidden
1680 region export in flat file generation</li>
1682 <li>Export alignment views for display with the <a
1683 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1685 <li>Export scrollable SVG in HTML page</li>
1686 <li>Optional embedding of BioJSON data when exporting
1687 alignment figures to HTML</li>
1689 <li>3D structure retrieval and display
1691 <li>Free text and structured queries with the PDBe
1693 <li>PDBe Search API based discovery and selection of
1694 PDB structures for a sequence set</li>
1698 <li>JPred4 employed for protein secondary structure
1700 <li>Hide Insertions menu option to hide unaligned columns
1701 for one or a group of sequences</li>
1702 <li>Automatically hide insertions in alignments imported
1703 from the JPred4 web server</li>
1704 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1705 system on OSX<br />LGPL libraries courtesy of <a
1706 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1708 <li>changed 'View nucleotide structure' submenu to 'View
1709 VARNA 2D Structure'</li>
1710 <li>change "View protein structure" menu option to "3D
1713 </ul> <em>Applet</em>
1715 <li>New layout for applet example pages</li>
1716 <li>New parameters to enable SplitFrame view
1717 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1718 <li>New example demonstrating linked viewing of cDNA and
1719 Protein alignments</li>
1720 </ul> <em>Development and deployment</em>
1722 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1723 <li>Include installation type and git revision in build
1724 properties and console log output</li>
1725 <li>Jalview Github organisation, and new github site for
1726 storing BioJsMSA Templates</li>
1727 <li>Jalview's unit tests now managed with TestNG</li>
1730 <!-- <em>General</em>
1732 </ul> --> <!-- issues resolved --> <em>Application</em>
1734 <li>Escape should close any open find dialogs</li>
1735 <li>Typo in select-by-features status report</li>
1736 <li>Consensus RNA secondary secondary structure
1737 predictions are not highlighted in amber</li>
1738 <li>Missing gap character in v2.7 example file means
1739 alignment appears unaligned when pad-gaps is not enabled</li>
1740 <li>First switch to RNA Helices colouring doesn't colour
1741 associated structure views</li>
1742 <li>ID width preference option is greyed out when auto
1743 width checkbox not enabled</li>
1744 <li>Stopped a warning dialog from being shown when
1745 creating user defined colours</li>
1746 <li>'View Mapping' in structure viewer shows sequence
1747 mappings for just that viewer's sequences</li>
1748 <li>Workaround for superposing PDB files containing
1749 multiple models in Chimera</li>
1750 <li>Report sequence position in status bar when hovering
1751 over Jmol structure</li>
1752 <li>Cannot output gaps as '.' symbols with Selection ->
1753 output to text box</li>
1754 <li>Flat file exports of alignments with hidden columns
1755 have incorrect sequence start/end</li>
1756 <li>'Aligning' a second chain to a Chimera structure from
1758 <li>Colour schemes applied to structure viewers don't
1759 work for nucleotide</li>
1760 <li>Loading/cut'n'pasting an empty or invalid file leads
1761 to a grey/invisible alignment window</li>
1762 <li>Exported Jpred annotation from a sequence region
1763 imports to different position</li>
1764 <li>Space at beginning of sequence feature tooltips shown
1765 on some platforms</li>
1766 <li>Chimera viewer 'View | Show Chain' menu is not
1768 <li>'New View' fails with a Null Pointer Exception in
1769 console if Chimera has been opened</li>
1770 <li>Mouseover to Chimera not working</li>
1771 <li>Miscellaneous ENA XML feature qualifiers not
1773 <li>NPE in annotation renderer after 'Extract Scores'</li>
1774 <li>If two structures in one Chimera window, mouseover of
1775 either sequence shows on first structure</li>
1776 <li>'Show annotations' options should not make
1777 non-positional annotations visible</li>
1778 <li>Subsequence secondary structure annotation not shown
1779 in right place after 'view flanking regions'</li>
1780 <li>File Save As type unset when current file format is
1782 <li>Save as '.jar' option removed for saving Jalview
1784 <li>Colour by Sequence colouring in Chimera more
1786 <li>Cannot 'add reference annotation' for a sequence in
1787 several views on same alignment</li>
1788 <li>Cannot show linked products for EMBL / ENA records</li>
1789 <li>Jalview's tooltip wraps long texts containing no
1791 </ul> <em>Applet</em>
1793 <li>Jmol to JalviewLite mouseover/link not working</li>
1794 <li>JalviewLite can't import sequences with ID
1795 descriptions containing angle brackets</li>
1796 </ul> <em>General</em>
1798 <li>Cannot export and reimport RNA secondary structure
1799 via jalview annotation file</li>
1800 <li>Random helix colour palette for colour by annotation
1801 with RNA secondary structure</li>
1802 <li>Mouseover to cDNA from STOP residue in protein
1803 translation doesn't work.</li>
1804 <li>hints when using the select by annotation dialog box</li>
1805 <li>Jmol alignment incorrect if PDB file has alternate CA
1807 <li>FontChooser message dialog appears to hang after
1808 choosing 1pt font</li>
1809 <li>Peptide secondary structure incorrectly imported from
1810 annotation file when annotation display text includes 'e' or
1812 <li>Cannot set colour of new feature type whilst creating
1814 <li>cDNA translation alignment should not be sequence
1815 order dependent</li>
1816 <li>'Show unconserved' doesn't work for lower case
1818 <li>Nucleotide ambiguity codes involving R not recognised</li>
1819 </ul> <em>Deployment and Documentation</em>
1821 <li>Applet example pages appear different to the rest of
1822 www.jalview.org</li>
1823 </ul> <em>Application Known issues</em>
1825 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1826 <li>Misleading message appears after trying to delete
1828 <li>Jalview icon not shown in dock after InstallAnywhere
1829 version launches</li>
1830 <li>Fetching EMBL reference for an RNA sequence results
1831 fails with a sequence mismatch</li>
1832 <li>Corrupted or unreadable alignment display when
1833 scrolling alignment to right</li>
1834 <li>ArrayIndexOutOfBoundsException thrown when remove
1835 empty columns called on alignment with ragged gapped ends</li>
1836 <li>auto calculated alignment annotation rows do not get
1837 placed above or below non-autocalculated rows</li>
1838 <li>Jalview dekstop becomes sluggish at full screen in
1839 ultra-high resolution</li>
1840 <li>Cannot disable consensus calculation independently of
1841 quality and conservation</li>
1842 <li>Mouseover highlighting between cDNA and protein can
1843 become sluggish with more than one splitframe shown</li>
1844 </ul> <em>Applet Known Issues</em>
1846 <li>Core PDB parsing code requires Jmol</li>
1847 <li>Sequence canvas panel goes white when alignment
1848 window is being resized</li>
1854 <td><div align="center">
1855 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1857 <td><em>General</em>
1859 <li>Updated Java code signing certificate donated by
1861 <li>Features and annotation preserved when performing
1862 pairwise alignment</li>
1863 <li>RNA pseudoknot annotation can be
1864 imported/exported/displayed</li>
1865 <li>'colour by annotation' can colour by RNA and
1866 protein secondary structure</li>
1867 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1868 post-hoc with 2.9 release</em>)
1871 </ul> <em>Application</em>
1873 <li>Extract and display secondary structure for sequences
1874 with 3D structures</li>
1875 <li>Support for parsing RNAML</li>
1876 <li>Annotations menu for layout
1878 <li>sort sequence annotation rows by alignment</li>
1879 <li>place sequence annotation above/below alignment
1882 <li>Output in Stockholm format</li>
1883 <li>Internationalisation: improved Spanish (es)
1885 <li>Structure viewer preferences tab</li>
1886 <li>Disorder and Secondary Structure annotation tracks
1887 shared between alignments</li>
1888 <li>UCSF Chimera launch and linked highlighting from
1890 <li>Show/hide all sequence associated annotation rows for
1891 all or current selection</li>
1892 <li>disorder and secondary structure predictions
1893 available as dataset annotation</li>
1894 <li>Per-sequence rna helices colouring</li>
1897 <li>Sequence database accessions imported when fetching
1898 alignments from Rfam</li>
1899 <li>update VARNA version to 3.91</li>
1901 <li>New groovy scripts for exporting aligned positions,
1902 conservation values, and calculating sum of pairs scores.</li>
1903 <li>Command line argument to set default JABAWS server</li>
1904 <li>include installation type in build properties and
1905 console log output</li>
1906 <li>Updated Jalview project format to preserve dataset
1910 <!-- issues resolved --> <em>Application</em>
1912 <li>Distinguish alignment and sequence associated RNA
1913 structure in structure->view->VARNA</li>
1914 <li>Raise dialog box if user deletes all sequences in an
1916 <li>Pressing F1 results in documentation opening twice</li>
1917 <li>Sequence feature tooltip is wrapped</li>
1918 <li>Double click on sequence associated annotation
1919 selects only first column</li>
1920 <li>Redundancy removal doesn't result in unlinked
1921 leaves shown in tree</li>
1922 <li>Undos after several redundancy removals don't undo
1924 <li>Hide sequence doesn't hide associated annotation</li>
1925 <li>User defined colours dialog box too big to fit on
1926 screen and buttons not visible</li>
1927 <li>author list isn't updated if already written to
1928 Jalview properties</li>
1929 <li>Popup menu won't open after retrieving sequence
1931 <li>File open window for associate PDB doesn't open</li>
1932 <li>Left-then-right click on a sequence id opens a
1933 browser search window</li>
1934 <li>Cannot open sequence feature shading/sort popup menu
1935 in feature settings dialog</li>
1936 <li>better tooltip placement for some areas of Jalview
1938 <li>Allow addition of JABAWS Server which doesn't
1939 pass validation</li>
1940 <li>Web services parameters dialog box is too large to
1942 <li>Muscle nucleotide alignment preset obscured by
1944 <li>JABAWS preset submenus don't contain newly
1945 defined user preset</li>
1946 <li>MSA web services warns user if they were launched
1947 with invalid input</li>
1948 <li>Jalview cannot contact DAS Registy when running on
1951 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1952 'Superpose with' submenu not shown when new view
1956 </ul> <!-- <em>Applet</em>
1958 </ul> <em>General</em>
1960 </ul>--> <em>Deployment and Documentation</em>
1962 <li>2G and 1G options in launchApp have no effect on
1963 memory allocation</li>
1964 <li>launchApp service doesn't automatically open
1965 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1967 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1968 InstallAnywhere reports cannot find valid JVM when Java
1969 1.7_055 is available
1971 </ul> <em>Application Known issues</em>
1974 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1975 corrupted or unreadable alignment display when scrolling
1979 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1980 retrieval fails but progress bar continues for DAS retrieval
1981 with large number of ID
1984 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1985 flatfile output of visible region has incorrect sequence
1989 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1990 rna structure consensus doesn't update when secondary
1991 structure tracks are rearranged
1994 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1995 invalid rna structure positional highlighting does not
1996 highlight position of invalid base pairs
1999 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2000 out of memory errors are not raised when saving Jalview
2001 project from alignment window file menu
2004 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2005 Switching to RNA Helices colouring doesn't propagate to
2009 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2010 colour by RNA Helices not enabled when user created
2011 annotation added to alignment
2014 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2015 Jalview icon not shown on dock in Mountain Lion/Webstart
2017 </ul> <em>Applet Known Issues</em>
2020 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2021 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2024 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2025 Jalview and Jmol example not compatible with IE9
2028 <li>Sort by annotation score doesn't reverse order
2034 <td><div align="center">
2035 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2038 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2041 <li>Internationalisation of user interface (usually
2042 called i18n support) and translation for Spanish locale</li>
2043 <li>Define/Undefine group on current selection with
2044 Ctrl-G/Shift Ctrl-G</li>
2045 <li>Improved group creation/removal options in
2046 alignment/sequence Popup menu</li>
2047 <li>Sensible precision for symbol distribution
2048 percentages shown in logo tooltip.</li>
2049 <li>Annotation panel height set according to amount of
2050 annotation when alignment first opened</li>
2051 </ul> <em>Application</em>
2053 <li>Interactive consensus RNA secondary structure
2054 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2055 <li>Select columns containing particular features from
2056 Feature Settings dialog</li>
2057 <li>View all 'representative' PDB structures for selected
2059 <li>Update Jalview project format:
2061 <li>New file extension for Jalview projects '.jvp'</li>
2062 <li>Preserve sequence and annotation dataset (to
2063 store secondary structure annotation,etc)</li>
2064 <li>Per group and alignment annotation and RNA helix
2068 <li>New similarity measures for PCA and Tree calculation
2070 <li>Experimental support for retrieval and viewing of
2071 flanking regions for an alignment</li>
2075 <!-- issues resolved --> <em>Application</em>
2077 <li>logo keeps spinning and status remains at queued or
2078 running after job is cancelled</li>
2079 <li>cannot export features from alignments imported from
2080 Jalview/VAMSAS projects</li>
2081 <li>Buggy slider for web service parameters that take
2083 <li>Newly created RNA secondary structure line doesn't
2084 have 'display all symbols' flag set</li>
2085 <li>T-COFFEE alignment score shading scheme and other
2086 annotation shading not saved in Jalview project</li>
2087 <li>Local file cannot be loaded in freshly downloaded
2089 <li>Jalview icon not shown on dock in Mountain
2091 <li>Load file from desktop file browser fails</li>
2092 <li>Occasional NPE thrown when calculating large trees</li>
2093 <li>Cannot reorder or slide sequences after dragging an
2094 alignment onto desktop</li>
2095 <li>Colour by annotation dialog throws NPE after using
2096 'extract scores' function</li>
2097 <li>Loading/cut'n'pasting an empty file leads to a grey
2098 alignment window</li>
2099 <li>Disorder thresholds rendered incorrectly after
2100 performing IUPred disorder prediction</li>
2101 <li>Multiple group annotated consensus rows shown when
2102 changing 'normalise logo' display setting</li>
2103 <li>Find shows blank dialog after 'finished searching' if
2104 nothing matches query</li>
2105 <li>Null Pointer Exceptions raised when sorting by
2106 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2108 <li>Errors in Jmol console when structures in alignment
2109 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2111 <li>Not all working JABAWS services are shown in
2113 <li>JAVAWS version of Jalview fails to launch with
2114 'invalid literal/length code'</li>
2115 <li>Annotation/RNA Helix colourschemes cannot be applied
2116 to alignment with groups (actually fixed in 2.8.0b1)</li>
2117 <li>RNA Helices and T-Coffee Scores available as default
2120 </ul> <em>Applet</em>
2122 <li>Remove group option is shown even when selection is
2124 <li>Apply to all groups ticked but colourscheme changes
2125 don't affect groups</li>
2126 <li>Documented RNA Helices and T-Coffee Scores as valid
2127 colourscheme name</li>
2128 <li>Annotation labels drawn on sequence IDs when
2129 Annotation panel is not displayed</li>
2130 <li>Increased font size for dropdown menus on OSX and
2131 embedded windows</li>
2132 </ul> <em>Other</em>
2134 <li>Consensus sequence for alignments/groups with a
2135 single sequence were not calculated</li>
2136 <li>annotation files that contain only groups imported as
2137 annotation and junk sequences</li>
2138 <li>Fasta files with sequences containing '*' incorrectly
2139 recognised as PFAM or BLC</li>
2140 <li>conservation/PID slider apply all groups option
2141 doesn't affect background (2.8.0b1)
2143 <li>redundancy highlighting is erratic at 0% and 100%</li>
2144 <li>Remove gapped columns fails for sequences with ragged
2146 <li>AMSA annotation row with leading spaces is not
2147 registered correctly on import</li>
2148 <li>Jalview crashes when selecting PCA analysis for
2149 certain alignments</li>
2150 <li>Opening the colour by annotation dialog for an
2151 existing annotation based 'use original colours'
2152 colourscheme loses original colours setting</li>
2157 <td><div align="center">
2158 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2159 <em>30/1/2014</em></strong>
2163 <li>Trusted certificates for JalviewLite applet and
2164 Jalview Desktop application<br />Certificate was donated by
2165 <a href="https://www.certum.eu">Certum</a> to the Jalview
2166 open source project).
2168 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2169 <li>Output in Stockholm format</li>
2170 <li>Allow import of data from gzipped files</li>
2171 <li>Export/import group and sequence associated line
2172 graph thresholds</li>
2173 <li>Nucleotide substitution matrix that supports RNA and
2174 ambiguity codes</li>
2175 <li>Allow disorder predictions to be made on the current
2176 selection (or visible selection) in the same way that JPred
2178 <li>Groovy scripting for headless Jalview operation</li>
2179 </ul> <em>Other improvements</em>
2181 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2182 <li>COMBINE statement uses current SEQUENCE_REF and
2183 GROUP_REF scope to group annotation rows</li>
2184 <li>Support '' style escaping of quotes in Newick
2186 <li>Group options for JABAWS service by command line name</li>
2187 <li>Empty tooltip shown for JABA service options with a
2188 link but no description</li>
2189 <li>Select primary source when selecting authority in
2190 database fetcher GUI</li>
2191 <li>Add .mfa to FASTA file extensions recognised by
2193 <li>Annotation label tooltip text wrap</li>
2198 <li>Slow scrolling when lots of annotation rows are
2200 <li>Lots of NPE (and slowness) after creating RNA
2201 secondary structure annotation line</li>
2202 <li>Sequence database accessions not imported when
2203 fetching alignments from Rfam</li>
2204 <li>Incorrect SHMR submission for sequences with
2206 <li>View all structures does not always superpose
2208 <li>Option widgets in service parameters not updated to
2209 reflect user or preset settings</li>
2210 <li>Null pointer exceptions for some services without
2211 presets or adjustable parameters</li>
2212 <li>Discover PDB IDs entry in structure menu doesn't
2213 discover PDB xRefs</li>
2214 <li>Exception encountered while trying to retrieve
2215 features with DAS</li>
2216 <li>Lowest value in annotation row isn't coloured
2217 when colour by annotation (per sequence) is coloured</li>
2218 <li>Keyboard mode P jumps to start of gapped region when
2219 residue follows a gap</li>
2220 <li>Jalview appears to hang importing an alignment with
2221 Wrap as default or after enabling Wrap</li>
2222 <li>'Right click to add annotations' message
2223 shown in wrap mode when no annotations present</li>
2224 <li>Disorder predictions fail with NPE if no automatic
2225 annotation already exists on alignment</li>
2226 <li>oninit javascript function should be called after
2227 initialisation completes</li>
2228 <li>Remove redundancy after disorder prediction corrupts
2229 alignment window display</li>
2230 <li>Example annotation file in documentation is invalid</li>
2231 <li>Grouped line graph annotation rows are not exported
2232 to annotation file</li>
2233 <li>Multi-harmony analysis cannot be run when only two
2235 <li>Cannot create multiple groups of line graphs with
2236 several 'combine' statements in annotation file</li>
2237 <li>Pressing return several times causes Number Format
2238 exceptions in keyboard mode</li>
2239 <li>Multi-harmony (SHMMR) method doesn't submit
2240 correct partitions for input data</li>
2241 <li>Translation from DNA to Amino Acids fails</li>
2242 <li>Jalview fail to load newick tree with quoted label</li>
2243 <li>--headless flag isn't understood</li>
2244 <li>ClassCastException when generating EPS in headless
2246 <li>Adjusting sequence-associated shading threshold only
2247 changes one row's threshold</li>
2248 <li>Preferences and Feature settings panel panel
2249 doesn't open</li>
2250 <li>hide consensus histogram also hides conservation and
2251 quality histograms</li>
2256 <td><div align="center">
2257 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2259 <td><em>Application</em>
2261 <li>Support for JABAWS 2.0 Services (AACon alignment
2262 conservation, protein disorder and Clustal Omega)</li>
2263 <li>JABAWS server status indicator in Web Services
2265 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2266 in Jalview alignment window</li>
2267 <li>Updated Jalview build and deploy framework for OSX
2268 mountain lion, windows 7, and 8</li>
2269 <li>Nucleotide substitution matrix for PCA that supports
2270 RNA and ambiguity codes</li>
2272 <li>Improved sequence database retrieval GUI</li>
2273 <li>Support fetching and database reference look up
2274 against multiple DAS sources (Fetch all from in 'fetch db
2276 <li>Jalview project improvements
2278 <li>Store and retrieve the 'belowAlignment'
2279 flag for annotation</li>
2280 <li>calcId attribute to group annotation rows on the
2282 <li>Store AACon calculation settings for a view in
2283 Jalview project</li>
2287 <li>horizontal scrolling gesture support</li>
2288 <li>Visual progress indicator when PCA calculation is
2290 <li>Simpler JABA web services menus</li>
2291 <li>visual indication that web service results are still
2292 being retrieved from server</li>
2293 <li>Serialise the dialogs that are shown when Jalview
2294 starts up for first time</li>
2295 <li>Jalview user agent string for interacting with HTTP
2297 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2299 <li>Examples directory and Groovy library included in
2300 InstallAnywhere distribution</li>
2301 </ul> <em>Applet</em>
2303 <li>RNA alignment and secondary structure annotation
2304 visualization applet example</li>
2305 </ul> <em>General</em>
2307 <li>Normalise option for consensus sequence logo</li>
2308 <li>Reset button in PCA window to return dimensions to
2310 <li>Allow seqspace or Jalview variant of alignment PCA
2312 <li>PCA with either nucleic acid and protein substitution
2314 <li>Allow windows containing HTML reports to be exported
2316 <li>Interactive display and editing of RNA secondary
2317 structure contacts</li>
2318 <li>RNA Helix Alignment Colouring</li>
2319 <li>RNA base pair logo consensus</li>
2320 <li>Parse sequence associated secondary structure
2321 information in Stockholm files</li>
2322 <li>HTML Export database accessions and annotation
2323 information presented in tooltip for sequences</li>
2324 <li>Import secondary structure from LOCARNA clustalw
2325 style RNA alignment files</li>
2326 <li>import and visualise T-COFFEE quality scores for an
2328 <li>'colour by annotation' per sequence option to
2329 shade each sequence according to its associated alignment
2331 <li>New Jalview Logo</li>
2332 </ul> <em>Documentation and Development</em>
2334 <li>documentation for score matrices used in Jalview</li>
2335 <li>New Website!</li>
2337 <td><em>Application</em>
2339 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2340 wsdbfetch REST service</li>
2341 <li>Stop windows being moved outside desktop on OSX</li>
2342 <li>Filetype associations not installed for webstart
2344 <li>Jalview does not always retrieve progress of a JABAWS
2345 job execution in full once it is complete</li>
2346 <li>revise SHMR RSBS definition to ensure alignment is
2347 uploaded via ali_file parameter</li>
2348 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2349 <li>View all structures superposed fails with exception</li>
2350 <li>Jnet job queues forever if a very short sequence is
2351 submitted for prediction</li>
2352 <li>Cut and paste menu not opened when mouse clicked on
2354 <li>Putting fractional value into integer text box in
2355 alignment parameter dialog causes Jalview to hang</li>
2356 <li>Structure view highlighting doesn't work on
2358 <li>View all structures fails with exception shown in
2360 <li>Characters in filename associated with PDBEntry not
2361 escaped in a platform independent way</li>
2362 <li>Jalview desktop fails to launch with exception when
2364 <li>Tree calculation reports 'you must have 2 or more
2365 sequences selected' when selection is empty</li>
2366 <li>Jalview desktop fails to launch with jar signature
2367 failure when java web start temporary file caching is
2369 <li>DAS Sequence retrieval with range qualification
2370 results in sequence xref which includes range qualification</li>
2371 <li>Errors during processing of command line arguments
2372 cause progress bar (JAL-898) to be removed</li>
2373 <li>Replace comma for semi-colon option not disabled for
2374 DAS sources in sequence fetcher</li>
2375 <li>Cannot close news reader when JABAWS server warning
2376 dialog is shown</li>
2377 <li>Option widgets not updated to reflect user settings</li>
2378 <li>Edited sequence not submitted to web service</li>
2379 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2380 <li>InstallAnywhere installer doesn't unpack and run
2381 on OSX Mountain Lion</li>
2382 <li>Annotation panel not given a scroll bar when
2383 sequences with alignment annotation are pasted into the
2385 <li>Sequence associated annotation rows not associated
2386 when loaded from Jalview project</li>
2387 <li>Browser launch fails with NPE on java 1.7</li>
2388 <li>JABAWS alignment marked as finished when job was
2389 cancelled or job failed due to invalid input</li>
2390 <li>NPE with v2.7 example when clicking on Tree
2391 associated with all views</li>
2392 <li>Exceptions when copy/paste sequences with grouped
2393 annotation rows to new window</li>
2394 </ul> <em>Applet</em>
2396 <li>Sequence features are momentarily displayed before
2397 they are hidden using hidefeaturegroups applet parameter</li>
2398 <li>loading features via javascript API automatically
2399 enables feature display</li>
2400 <li>scrollToColumnIn javascript API method doesn't
2402 </ul> <em>General</em>
2404 <li>Redundancy removal fails for rna alignment</li>
2405 <li>PCA calculation fails when sequence has been selected
2406 and then deselected</li>
2407 <li>PCA window shows grey box when first opened on OSX</li>
2408 <li>Letters coloured pink in sequence logo when alignment
2409 coloured with clustalx</li>
2410 <li>Choosing fonts without letter symbols defined causes
2411 exceptions and redraw errors</li>
2412 <li>Initial PCA plot view is not same as manually
2413 reconfigured view</li>
2414 <li>Grouped annotation graph label has incorrect line
2416 <li>Grouped annotation graph label display is corrupted
2417 for lots of labels</li>
2422 <div align="center">
2423 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2426 <td><em>Application</em>
2428 <li>Jalview Desktop News Reader</li>
2429 <li>Tweaked default layout of web services menu</li>
2430 <li>View/alignment association menu to enable user to
2431 easily specify which alignment a multi-structure view takes
2432 its colours/correspondences from</li>
2433 <li>Allow properties file location to be specified as URL</li>
2434 <li>Extend Jalview project to preserve associations
2435 between many alignment views and a single Jmol display</li>
2436 <li>Store annotation row height in Jalview project file</li>
2437 <li>Annotation row column label formatting attributes
2438 stored in project file</li>
2439 <li>Annotation row order for auto-calculated annotation
2440 rows preserved in Jalview project file</li>
2441 <li>Visual progress indication when Jalview state is
2442 saved using Desktop window menu</li>
2443 <li>Visual indication that command line arguments are
2444 still being processed</li>
2445 <li>Groovy script execution from URL</li>
2446 <li>Colour by annotation default min and max colours in
2448 <li>Automatically associate PDB files dragged onto an
2449 alignment with sequences that have high similarity and
2451 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2452 <li>'view structures' option to open many
2453 structures in same window</li>
2454 <li>Sort associated views menu option for tree panel</li>
2455 <li>Group all JABA and non-JABA services for a particular
2456 analysis function in its own submenu</li>
2457 </ul> <em>Applet</em>
2459 <li>Userdefined and autogenerated annotation rows for
2461 <li>Adjustment of alignment annotation pane height</li>
2462 <li>Annotation scrollbar for annotation panel</li>
2463 <li>Drag to reorder annotation rows in annotation panel</li>
2464 <li>'automaticScrolling' parameter</li>
2465 <li>Allow sequences with partial ID string matches to be
2466 annotated from GFF/Jalview features files</li>
2467 <li>Sequence logo annotation row in applet</li>
2468 <li>Absolute paths relative to host server in applet
2469 parameters are treated as such</li>
2470 <li>New in the JalviewLite javascript API:
2472 <li>JalviewLite.js javascript library</li>
2473 <li>Javascript callbacks for
2475 <li>Applet initialisation</li>
2476 <li>Sequence/alignment mouse-overs and selections</li>
2479 <li>scrollTo row and column alignment scrolling
2481 <li>Select sequence/alignment regions from javascript</li>
2482 <li>javascript structure viewer harness to pass
2483 messages between Jmol and Jalview when running as
2484 distinct applets</li>
2485 <li>sortBy method</li>
2486 <li>Set of applet and application examples shipped
2487 with documentation</li>
2488 <li>New example to demonstrate JalviewLite and Jmol
2489 javascript message exchange</li>
2491 </ul> <em>General</em>
2493 <li>Enable Jmol displays to be associated with multiple
2494 multiple alignments</li>
2495 <li>Option to automatically sort alignment with new tree</li>
2496 <li>User configurable link to enable redirects to a
2497 www.Jalview.org mirror</li>
2498 <li>Jmol colours option for Jmol displays</li>
2499 <li>Configurable newline string when writing alignment
2500 and other flat files</li>
2501 <li>Allow alignment annotation description lines to
2502 contain html tags</li>
2503 </ul> <em>Documentation and Development</em>
2505 <li>Add groovy test harness for bulk load testing to
2507 <li>Groovy script to load and align a set of sequences
2508 using a web service before displaying the result in the
2509 Jalview desktop</li>
2510 <li>Restructured javascript and applet api documentation</li>
2511 <li>Ant target to publish example html files with applet
2513 <li>Netbeans project for building Jalview from source</li>
2514 <li>ant task to create online javadoc for Jalview source</li>
2516 <td><em>Application</em>
2518 <li>User defined colourscheme throws exception when
2519 current built in colourscheme is saved as new scheme</li>
2520 <li>AlignFrame->Save in application pops up save
2521 dialog for valid filename/format</li>
2522 <li>Cannot view associated structure for UniProt sequence</li>
2523 <li>PDB file association breaks for UniProt sequence
2525 <li>Associate PDB from file dialog does not tell you
2526 which sequence is to be associated with the file</li>
2527 <li>Find All raises null pointer exception when query
2528 only matches sequence IDs</li>
2529 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2530 <li>Jalview project with Jmol views created with Jalview
2531 2.4 cannot be loaded</li>
2532 <li>Filetype associations not installed for webstart
2534 <li>Two or more chains in a single PDB file associated
2535 with sequences in different alignments do not get coloured
2536 by their associated sequence</li>
2537 <li>Visibility status of autocalculated annotation row
2538 not preserved when project is loaded</li>
2539 <li>Annotation row height and visibility attributes not
2540 stored in Jalview project</li>
2541 <li>Tree bootstraps are not preserved when saved as a
2542 Jalview project</li>
2543 <li>Envision2 workflow tooltips are corrupted</li>
2544 <li>Enabling show group conservation also enables colour
2545 by conservation</li>
2546 <li>Duplicate group associated conservation or consensus
2547 created on new view</li>
2548 <li>Annotation scrollbar not displayed after 'show
2549 all hidden annotation rows' option selected</li>
2550 <li>Alignment quality not updated after alignment
2551 annotation row is hidden then shown</li>
2552 <li>Preserve colouring of structures coloured by
2553 sequences in pre Jalview 2.7 projects</li>
2554 <li>Web service job parameter dialog is not laid out
2556 <li>Web services menu not refreshed after 'reset
2557 services' button is pressed in preferences</li>
2558 <li>Annotation off by one in Jalview v2_3 example project</li>
2559 <li>Structures imported from file and saved in project
2560 get name like jalview_pdb1234.txt when reloaded</li>
2561 <li>Jalview does not always retrieve progress of a JABAWS
2562 job execution in full once it is complete</li>
2563 </ul> <em>Applet</em>
2565 <li>Alignment height set incorrectly when lots of
2566 annotation rows are displayed</li>
2567 <li>Relative URLs in feature HTML text not resolved to
2569 <li>View follows highlighting does not work for positions
2571 <li><= shown as = in tooltip</li>
2572 <li>Export features raises exception when no features
2574 <li>Separator string used for serialising lists of IDs
2575 for javascript api is modified when separator string
2576 provided as parameter</li>
2577 <li>Null pointer exception when selecting tree leaves for
2578 alignment with no existing selection</li>
2579 <li>Relative URLs for datasources assumed to be relative
2580 to applet's codebase</li>
2581 <li>Status bar not updated after finished searching and
2582 search wraps around to first result</li>
2583 <li>StructureSelectionManager instance shared between
2584 several Jalview applets causes race conditions and memory
2586 <li>Hover tooltip and mouseover of position on structure
2587 not sent from Jmol in applet</li>
2588 <li>Certain sequences of javascript method calls to
2589 applet API fatally hang browser</li>
2590 </ul> <em>General</em>
2592 <li>View follows structure mouseover scrolls beyond
2593 position with wrapped view and hidden regions</li>
2594 <li>Find sequence position moves to wrong residue
2595 with/without hidden columns</li>
2596 <li>Sequence length given in alignment properties window
2598 <li>InvalidNumberFormat exceptions thrown when trying to
2599 import PDB like structure files</li>
2600 <li>Positional search results are only highlighted
2601 between user-supplied sequence start/end bounds</li>
2602 <li>End attribute of sequence is not validated</li>
2603 <li>Find dialog only finds first sequence containing a
2604 given sequence position</li>
2605 <li>Sequence numbering not preserved in MSF alignment
2607 <li>Jalview PDB file reader does not extract sequence
2608 from nucleotide chains correctly</li>
2609 <li>Structure colours not updated when tree partition
2610 changed in alignment</li>
2611 <li>Sequence associated secondary structure not correctly
2612 parsed in interleaved stockholm</li>
2613 <li>Colour by annotation dialog does not restore current
2615 <li>Hiding (nearly) all sequences doesn't work
2617 <li>Sequences containing lowercase letters are not
2618 properly associated with their pdb files</li>
2619 </ul> <em>Documentation and Development</em>
2621 <li>schemas/JalviewWsParamSet.xsd corrupted by
2622 ApplyCopyright tool</li>
2627 <div align="center">
2628 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2631 <td><em>Application</em>
2633 <li>New warning dialog when the Jalview Desktop cannot
2634 contact web services</li>
2635 <li>JABA service parameters for a preset are shown in
2636 service job window</li>
2637 <li>JABA Service menu entries reworded</li>
2641 <li>Modeller PIR IO broken - cannot correctly import a
2642 pir file emitted by Jalview</li>
2643 <li>Existing feature settings transferred to new
2644 alignment view created from cut'n'paste</li>
2645 <li>Improved test for mixed amino/nucleotide chains when
2646 parsing PDB files</li>
2647 <li>Consensus and conservation annotation rows
2648 occasionally become blank for all new windows</li>
2649 <li>Exception raised when right clicking above sequences
2650 in wrapped view mode</li>
2651 </ul> <em>Application</em>
2653 <li>multiple multiply aligned structure views cause cpu
2654 usage to hit 100% and computer to hang</li>
2655 <li>Web Service parameter layout breaks for long user
2656 parameter names</li>
2657 <li>Jaba service discovery hangs desktop if Jaba server
2664 <div align="center">
2665 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2668 <td><em>Application</em>
2670 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2671 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2674 <li>Web Services preference tab</li>
2675 <li>Analysis parameters dialog box and user defined
2677 <li>Improved speed and layout of Envision2 service menu</li>
2678 <li>Superpose structures using associated sequence
2680 <li>Export coordinates and projection as CSV from PCA
2682 </ul> <em>Applet</em>
2684 <li>enable javascript: execution by the applet via the
2685 link out mechanism</li>
2686 </ul> <em>Other</em>
2688 <li>Updated the Jmol Jalview interface to work with Jmol
2690 <li>The Jalview Desktop and JalviewLite applet now
2691 require Java 1.5</li>
2692 <li>Allow Jalview feature colour specification for GFF
2693 sequence annotation files</li>
2694 <li>New 'colour by label' keword in Jalview feature file
2695 type colour specification</li>
2696 <li>New Jalview Desktop Groovy API method that allows a
2697 script to check if it being run in an interactive session or
2698 in a batch operation from the Jalview command line</li>
2702 <li>clustalx colourscheme colours Ds preferentially when
2703 both D+E are present in over 50% of the column</li>
2704 </ul> <em>Application</em>
2706 <li>typo in AlignmentFrame->View->Hide->all but
2707 selected Regions menu item</li>
2708 <li>sequence fetcher replaces ',' for ';' when the ',' is
2709 part of a valid accession ID</li>
2710 <li>fatal OOM if object retrieved by sequence fetcher
2711 runs out of memory</li>
2712 <li>unhandled Out of Memory Error when viewing pca
2713 analysis results</li>
2714 <li>InstallAnywhere builds fail to launch on OS X java
2715 10.5 update 4 (due to apple Java 1.6 update)</li>
2716 <li>Installanywhere Jalview silently fails to launch</li>
2717 </ul> <em>Applet</em>
2719 <li>Jalview.getFeatureGroups() raises an
2720 ArrayIndexOutOfBoundsException if no feature groups are
2727 <div align="center">
2728 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2734 <li>Alignment prettyprinter doesn't cope with long
2736 <li>clustalx colourscheme colours Ds preferentially when
2737 both D+E are present in over 50% of the column</li>
2738 <li>nucleic acid structures retrieved from PDB do not
2739 import correctly</li>
2740 <li>More columns get selected than were clicked on when a
2741 number of columns are hidden</li>
2742 <li>annotation label popup menu not providing correct
2743 add/hide/show options when rows are hidden or none are
2745 <li>Stockholm format shown in list of readable formats,
2746 and parser copes better with alignments from RFAM.</li>
2747 <li>CSV output of consensus only includes the percentage
2748 of all symbols if sequence logo display is enabled</li>
2750 </ul> <em>Applet</em>
2752 <li>annotation panel disappears when annotation is
2754 </ul> <em>Application</em>
2756 <li>Alignment view not redrawn properly when new
2757 alignment opened where annotation panel is visible but no
2758 annotations are present on alignment</li>
2759 <li>pasted region containing hidden columns is
2760 incorrectly displayed in new alignment window</li>
2761 <li>Jalview slow to complete operations when stdout is
2762 flooded (fix is to close the Jalview console)</li>
2763 <li>typo in AlignmentFrame->View->Hide->all but
2764 selected Rregions menu item.</li>
2765 <li>inconsistent group submenu and Format submenu entry
2766 'Un' or 'Non'conserved</li>
2767 <li>Sequence feature settings are being shared by
2768 multiple distinct alignments</li>
2769 <li>group annotation not recreated when tree partition is
2771 <li>double click on group annotation to select sequences
2772 does not propagate to associated trees</li>
2773 <li>Mac OSX specific issues:
2775 <li>exception raised when mouse clicked on desktop
2776 window background</li>
2777 <li>Desktop menu placed on menu bar and application
2778 name set correctly</li>
2779 <li>sequence feature settings not wide enough for the
2780 save feature colourscheme button</li>
2789 <div align="center">
2790 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2793 <td><em>New Capabilities</em>
2795 <li>URL links generated from description line for
2796 regular-expression based URL links (applet and application)
2798 <li>Non-positional feature URL links are shown in link
2800 <li>Linked viewing of nucleic acid sequences and
2802 <li>Automatic Scrolling option in View menu to display
2803 the currently highlighted region of an alignment.</li>
2804 <li>Order an alignment by sequence length, or using the
2805 average score or total feature count for each sequence.</li>
2806 <li>Shading features by score or associated description</li>
2807 <li>Subdivide alignment and groups based on identity of
2808 selected subsequence (Make Groups from Selection).</li>
2809 <li>New hide/show options including Shift+Control+H to
2810 hide everything but the currently selected region.</li>
2811 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2812 </ul> <em>Application</em>
2814 <li>Fetch DB References capabilities and UI expanded to
2815 support retrieval from DAS sequence sources</li>
2816 <li>Local DAS Sequence sources can be added via the
2817 command line or via the Add local source dialog box.</li>
2818 <li>DAS Dbref and DbxRef feature types are parsed as
2819 database references and protein_name is parsed as
2820 description line (BioSapiens terms).</li>
2821 <li>Enable or disable non-positional feature and database
2822 references in sequence ID tooltip from View menu in
2824 <!-- <li>New hidden columns and rows and representatives capabilities
2825 in annotations file (in progress - not yet fully implemented)</li> -->
2826 <li>Group-associated consensus, sequence logos and
2827 conservation plots</li>
2828 <li>Symbol distributions for each column can be exported
2829 and visualized as sequence logos</li>
2830 <li>Optionally scale multi-character column labels to fit
2831 within each column of annotation row<!-- todo for applet -->
2833 <li>Optional automatic sort of associated alignment view
2834 when a new tree is opened.</li>
2835 <li>Jalview Java Console</li>
2836 <li>Better placement of desktop window when moving
2837 between different screens.</li>
2838 <li>New preference items for sequence ID tooltip and
2839 consensus annotation</li>
2840 <li>Client to submit sequences and IDs to Envision2
2842 <li><em>Vamsas Capabilities</em>
2844 <li>Improved VAMSAS synchronization (Jalview archive
2845 used to preserve views, structures, and tree display
2847 <li>Import of vamsas documents from disk or URL via
2849 <li>Sharing of selected regions between views and
2850 with other VAMSAS applications (Experimental feature!)</li>
2851 <li>Updated API to VAMSAS version 0.2</li>
2853 </ul> <em>Applet</em>
2855 <li>Middle button resizes annotation row height</li>
2858 <li>sortByTree (true/false) - automatically sort the
2859 associated alignment view by the tree when a new tree is
2861 <li>showTreeBootstraps (true/false) - show or hide
2862 branch bootstraps (default is to show them if available)</li>
2863 <li>showTreeDistances (true/false) - show or hide
2864 branch lengths (default is to show them if available)</li>
2865 <li>showUnlinkedTreeNodes (true/false) - indicate if
2866 unassociated nodes should be highlighted in the tree
2868 <li>heightScale and widthScale (1.0 or more) -
2869 increase the height or width of a cell in the alignment
2870 grid relative to the current font size.</li>
2873 <li>Non-positional features displayed in sequence ID
2875 </ul> <em>Other</em>
2877 <li>Features format: graduated colour definitions and
2878 specification of feature scores</li>
2879 <li>Alignment Annotations format: new keywords for group
2880 associated annotation (GROUP_REF) and annotation row display
2881 properties (ROW_PROPERTIES)</li>
2882 <li>XML formats extended to support graduated feature
2883 colourschemes, group associated annotation, and profile
2884 visualization settings.</li></td>
2887 <li>Source field in GFF files parsed as feature source
2888 rather than description</li>
2889 <li>Non-positional features are now included in sequence
2890 feature and gff files (controlled via non-positional feature
2891 visibility in tooltip).</li>
2892 <li>URL links generated for all feature links (bugfix)</li>
2893 <li>Added URL embedding instructions to features file
2895 <li>Codons containing ambiguous nucleotides translated as
2896 'X' in peptide product</li>
2897 <li>Match case switch in find dialog box works for both
2898 sequence ID and sequence string and query strings do not
2899 have to be in upper case to match case-insensitively.</li>
2900 <li>AMSA files only contain first column of
2901 multi-character column annotation labels</li>
2902 <li>Jalview Annotation File generation/parsing consistent
2903 with documentation (e.g. Stockholm annotation can be
2904 exported and re-imported)</li>
2905 <li>PDB files without embedded PDB IDs given a friendly
2907 <li>Find incrementally searches ID string matches as well
2908 as subsequence matches, and correctly reports total number
2912 <li>Better handling of exceptions during sequence
2914 <li>Dasobert generated non-positional feature URL
2915 link text excludes the start_end suffix</li>
2916 <li>DAS feature and source retrieval buttons disabled
2917 when fetch or registry operations in progress.</li>
2918 <li>PDB files retrieved from URLs are cached properly</li>
2919 <li>Sequence description lines properly shared via
2921 <li>Sequence fetcher fetches multiple records for all
2923 <li>Ensured that command line das feature retrieval
2924 completes before alignment figures are generated.</li>
2925 <li>Reduced time taken when opening file browser for
2927 <li>isAligned check prior to calculating tree, PCA or
2928 submitting an MSA to JNet now excludes hidden sequences.</li>
2929 <li>User defined group colours properly recovered
2930 from Jalview projects.</li>
2939 <div align="center">
2940 <strong>2.4.0.b2</strong><br> 28/10/2009
2945 <li>Experimental support for google analytics usage
2947 <li>Jalview privacy settings (user preferences and docs).</li>
2952 <li>Race condition in applet preventing startup in
2954 <li>Exception when feature created from selection beyond
2955 length of sequence.</li>
2956 <li>Allow synthetic PDB files to be imported gracefully</li>
2957 <li>Sequence associated annotation rows associate with
2958 all sequences with a given id</li>
2959 <li>Find function matches case-insensitively for sequence
2960 ID string searches</li>
2961 <li>Non-standard characters do not cause pairwise
2962 alignment to fail with exception</li>
2963 </ul> <em>Application Issues</em>
2965 <li>Sequences are now validated against EMBL database</li>
2966 <li>Sequence fetcher fetches multiple records for all
2968 </ul> <em>InstallAnywhere Issues</em>
2970 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2971 issue with installAnywhere mechanism)</li>
2972 <li>Command line launching of JARs from InstallAnywhere
2973 version (java class versioning error fixed)</li>
2980 <div align="center">
2981 <strong>2.4</strong><br> 27/8/2008
2984 <td><em>User Interface</em>
2986 <li>Linked highlighting of codon and amino acid from
2987 translation and protein products</li>
2988 <li>Linked highlighting of structure associated with
2989 residue mapping to codon position</li>
2990 <li>Sequence Fetcher provides example accession numbers
2991 and 'clear' button</li>
2992 <li>MemoryMonitor added as an option under Desktop's
2994 <li>Extract score function to parse whitespace separated
2995 numeric data in description line</li>
2996 <li>Column labels in alignment annotation can be centred.</li>
2997 <li>Tooltip for sequence associated annotation give name
2999 </ul> <em>Web Services and URL fetching</em>
3001 <li>JPred3 web service</li>
3002 <li>Prototype sequence search client (no public services
3004 <li>Fetch either seed alignment or full alignment from
3006 <li>URL Links created for matching database cross
3007 references as well as sequence ID</li>
3008 <li>URL Links can be created using regular-expressions</li>
3009 </ul> <em>Sequence Database Connectivity</em>
3011 <li>Retrieval of cross-referenced sequences from other
3013 <li>Generalised database reference retrieval and
3014 validation to all fetchable databases</li>
3015 <li>Fetch sequences from DAS sources supporting the
3016 sequence command</li>
3017 </ul> <em>Import and Export</em>
3018 <li>export annotation rows as CSV for spreadsheet import</li>
3019 <li>Jalview projects record alignment dataset associations,
3020 EMBL products, and cDNA sequence mappings</li>
3021 <li>Sequence Group colour can be specified in Annotation
3023 <li>Ad-hoc colouring of group in Annotation File using RGB
3024 triplet as name of colourscheme</li>
3025 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3027 <li>treenode binding for VAMSAS tree exchange</li>
3028 <li>local editing and update of sequences in VAMSAS
3029 alignments (experimental)</li>
3030 <li>Create new or select existing session to join</li>
3031 <li>load and save of vamsas documents</li>
3032 </ul> <em>Application command line</em>
3034 <li>-tree parameter to open trees (introduced for passing
3036 <li>-fetchfrom command line argument to specify nicknames
3037 of DAS servers to query for alignment features</li>
3038 <li>-dasserver command line argument to add new servers
3039 that are also automatically queried for features</li>
3040 <li>-groovy command line argument executes a given groovy
3041 script after all input data has been loaded and parsed</li>
3042 </ul> <em>Applet-Application data exchange</em>
3044 <li>Trees passed as applet parameters can be passed to
3045 application (when using "View in full
3046 application")</li>
3047 </ul> <em>Applet Parameters</em>
3049 <li>feature group display control parameter</li>
3050 <li>debug parameter</li>
3051 <li>showbutton parameter</li>
3052 </ul> <em>Applet API methods</em>
3054 <li>newView public method</li>
3055 <li>Window (current view) specific get/set public methods</li>
3056 <li>Feature display control methods</li>
3057 <li>get list of currently selected sequences</li>
3058 </ul> <em>New Jalview distribution features</em>
3060 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3061 <li>RELEASE file gives build properties for the latest
3062 Jalview release.</li>
3063 <li>Java 1.1 Applet build made easier and donotobfuscate
3064 property controls execution of obfuscator</li>
3065 <li>Build target for generating source distribution</li>
3066 <li>Debug flag for javacc</li>
3067 <li>.jalview_properties file is documented (slightly) in
3068 jalview.bin.Cache</li>
3069 <li>Continuous Build Integration for stable and
3070 development version of Application, Applet and source
3075 <li>selected region output includes visible annotations
3076 (for certain formats)</li>
3077 <li>edit label/displaychar contains existing label/char
3079 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3080 <li>shorter peptide product names from EMBL records</li>
3081 <li>Newick string generator makes compact representations</li>
3082 <li>bootstrap values parsed correctly for tree files with
3084 <li>pathological filechooser bug avoided by not allowing
3085 filenames containing a ':'</li>
3086 <li>Fixed exception when parsing GFF files containing
3087 global sequence features</li>
3088 <li>Alignment datasets are finalized only when number of
3089 references from alignment sequences goes to zero</li>
3090 <li>Close of tree branch colour box without colour
3091 selection causes cascading exceptions</li>
3092 <li>occasional negative imgwidth exceptions</li>
3093 <li>better reporting of non-fatal warnings to user when
3094 file parsing fails.</li>
3095 <li>Save works when Jalview project is default format</li>
3096 <li>Save as dialog opened if current alignment format is
3097 not a valid output format</li>
3098 <li>UniProt canonical names introduced for both das and
3100 <li>Histidine should be midblue (not pink!) in Zappo</li>
3101 <li>error messages passed up and output when data read
3103 <li>edit undo recovers previous dataset sequence when
3104 sequence is edited</li>
3105 <li>allow PDB files without pdb ID HEADER lines (like
3106 those generated by MODELLER) to be read in properly</li>
3107 <li>allow reading of JPred concise files as a normal
3109 <li>Stockholm annotation parsing and alignment properties
3110 import fixed for PFAM records</li>
3111 <li>Structure view windows have correct name in Desktop
3113 <li>annotation consisting of sequence associated scores
3114 can be read and written correctly to annotation file</li>
3115 <li>Aligned cDNA translation to aligned peptide works
3117 <li>Fixed display of hidden sequence markers and
3118 non-italic font for representatives in Applet</li>
3119 <li>Applet Menus are always embedded in applet window on
3121 <li>Newly shown features appear at top of stack (in
3123 <li>Annotations added via parameter not drawn properly
3124 due to null pointer exceptions</li>
3125 <li>Secondary structure lines are drawn starting from
3126 first column of alignment</li>
3127 <li>UniProt XML import updated for new schema release in
3129 <li>Sequence feature to sequence ID match for Features
3130 file is case-insensitive</li>
3131 <li>Sequence features read from Features file appended to
3132 all sequences with matching IDs</li>
3133 <li>PDB structure coloured correctly for associated views
3134 containing a sub-sequence</li>
3135 <li>PDB files can be retrieved by applet from Jar files</li>
3136 <li>feature and annotation file applet parameters
3137 referring to different directories are retrieved correctly</li>
3138 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3139 <li>Fixed application hang whilst waiting for
3140 splash-screen version check to complete</li>
3141 <li>Applet properly URLencodes input parameter values
3142 when passing them to the launchApp service</li>
3143 <li>display name and local features preserved in results
3144 retrieved from web service</li>
3145 <li>Visual delay indication for sequence retrieval and
3146 sequence fetcher initialisation</li>
3147 <li>updated Application to use DAS 1.53e version of
3148 dasobert DAS client</li>
3149 <li>Re-instated Full AMSA support and .amsa file
3151 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3159 <div align="center">
3160 <strong>2.3</strong><br> 9/5/07
3165 <li>Jmol 11.0.2 integration</li>
3166 <li>PDB views stored in Jalview XML files</li>
3167 <li>Slide sequences</li>
3168 <li>Edit sequence in place</li>
3169 <li>EMBL CDS features</li>
3170 <li>DAS Feature mapping</li>
3171 <li>Feature ordering</li>
3172 <li>Alignment Properties</li>
3173 <li>Annotation Scores</li>
3174 <li>Sort by scores</li>
3175 <li>Feature/annotation editing in applet</li>
3180 <li>Headless state operation in 2.2.1</li>
3181 <li>Incorrect and unstable DNA pairwise alignment</li>
3182 <li>Cut and paste of sequences with annotation</li>
3183 <li>Feature group display state in XML</li>
3184 <li>Feature ordering in XML</li>
3185 <li>blc file iteration selection using filename # suffix</li>
3186 <li>Stockholm alignment properties</li>
3187 <li>Stockhom alignment secondary structure annotation</li>
3188 <li>2.2.1 applet had no feature transparency</li>
3189 <li>Number pad keys can be used in cursor mode</li>
3190 <li>Structure Viewer mirror image resolved</li>
3197 <div align="center">
3198 <strong>2.2.1</strong><br> 12/2/07
3203 <li>Non standard characters can be read and displayed
3204 <li>Annotations/Features can be imported/exported to the
3206 <li>Applet allows editing of sequence/annotation/group
3207 name & description
3208 <li>Preference setting to display sequence name in
3210 <li>Annotation file format extended to allow
3211 Sequence_groups to be defined
3212 <li>Default opening of alignment overview panel can be
3213 specified in preferences
3214 <li>PDB residue numbering annotation added to associated
3220 <li>Applet crash under certain Linux OS with Java 1.6
3222 <li>Annotation file export / import bugs fixed
3223 <li>PNG / EPS image output bugs fixed
3229 <div align="center">
3230 <strong>2.2</strong><br> 27/11/06
3235 <li>Multiple views on alignment
3236 <li>Sequence feature editing
3237 <li>"Reload" alignment
3238 <li>"Save" to current filename
3239 <li>Background dependent text colour
3240 <li>Right align sequence ids
3241 <li>User-defined lower case residue colours
3244 <li>Menu item accelerator keys
3245 <li>Control-V pastes to current alignment
3246 <li>Cancel button for DAS Feature Fetching
3247 <li>PCA and PDB Viewers zoom via mouse roller
3248 <li>User-defined sub-tree colours and sub-tree selection
3250 <li>'New Window' button on the 'Output to Text box'
3255 <li>New memory efficient Undo/Redo System
3256 <li>Optimised symbol lookups and conservation/consensus
3258 <li>Region Conservation/Consensus recalculated after
3260 <li>Fixed Remove Empty Columns Bug (empty columns at end
3262 <li>Slowed DAS Feature Fetching for increased robustness.
3264 <li>Made angle brackets in ASCII feature descriptions
3266 <li>Re-instated Zoom function for PCA
3267 <li>Sequence descriptions conserved in web service
3269 <li>UniProt ID discoverer uses any word separated by
3271 <li>WsDbFetch query/result association resolved
3272 <li>Tree leaf to sequence mapping improved
3273 <li>Smooth fonts switch moved to FontChooser dialog box.
3280 <div align="center">
3281 <strong>2.1.1</strong><br> 12/9/06
3286 <li>Copy consensus sequence to clipboard</li>
3291 <li>Image output - rightmost residues are rendered if
3292 sequence id panel has been resized</li>
3293 <li>Image output - all offscreen group boundaries are
3295 <li>Annotation files with sequence references - all
3296 elements in file are relative to sequence position</li>
3297 <li>Mac Applet users can use Alt key for group editing</li>
3303 <div align="center">
3304 <strong>2.1</strong><br> 22/8/06
3309 <li>MAFFT Multiple Alignment in default Web Service list</li>
3310 <li>DAS Feature fetching</li>
3311 <li>Hide sequences and columns</li>
3312 <li>Export Annotations and Features</li>
3313 <li>GFF file reading / writing</li>
3314 <li>Associate structures with sequences from local PDB
3316 <li>Add sequences to exisiting alignment</li>
3317 <li>Recently opened files / URL lists</li>
3318 <li>Applet can launch the full application</li>
3319 <li>Applet has transparency for features (Java 1.2
3321 <li>Applet has user defined colours parameter</li>
3322 <li>Applet can load sequences from parameter
3323 "sequence<em>x</em>"
3329 <li>Redundancy Panel reinstalled in the Applet</li>
3330 <li>Monospaced font - EPS / rescaling bug fixed</li>
3331 <li>Annotation files with sequence references bug fixed</li>
3337 <div align="center">
3338 <strong>2.08.1</strong><br> 2/5/06
3343 <li>Change case of selected region from Popup menu</li>
3344 <li>Choose to match case when searching</li>
3345 <li>Middle mouse button and mouse movement can compress /
3346 expand the visible width and height of the alignment</li>
3351 <li>Annotation Panel displays complete JNet results</li>
3357 <div align="center">
3358 <strong>2.08b</strong><br> 18/4/06
3364 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3365 <li>Righthand label on wrapped alignments shows correct
3372 <div align="center">
3373 <strong>2.08</strong><br> 10/4/06
3378 <li>Editing can be locked to the selection area</li>
3379 <li>Keyboard editing</li>
3380 <li>Create sequence features from searches</li>
3381 <li>Precalculated annotations can be loaded onto
3383 <li>Features file allows grouping of features</li>
3384 <li>Annotation Colouring scheme added</li>
3385 <li>Smooth fonts off by default - Faster rendering</li>
3386 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3391 <li>Drag & Drop fixed on Linux</li>
3392 <li>Jalview Archive file faster to load/save, sequence
3393 descriptions saved.</li>
3399 <div align="center">
3400 <strong>2.07</strong><br> 12/12/05
3405 <li>PDB Structure Viewer enhanced</li>
3406 <li>Sequence Feature retrieval and display enhanced</li>
3407 <li>Choose to output sequence start-end after sequence
3408 name for file output</li>
3409 <li>Sequence Fetcher WSDBFetch@EBI</li>
3410 <li>Applet can read feature files, PDB files and can be
3411 used for HTML form input</li>
3416 <li>HTML output writes groups and features</li>
3417 <li>Group editing is Control and mouse click</li>
3418 <li>File IO bugs</li>
3424 <div align="center">
3425 <strong>2.06</strong><br> 28/9/05
3430 <li>View annotations in wrapped mode</li>
3431 <li>More options for PCA viewer</li>
3436 <li>GUI bugs resolved</li>
3437 <li>Runs with -nodisplay from command line</li>
3443 <div align="center">
3444 <strong>2.05b</strong><br> 15/9/05
3449 <li>Choose EPS export as lineart or text</li>
3450 <li>Jar files are executable</li>
3451 <li>Can read in Uracil - maps to unknown residue</li>
3456 <li>Known OutOfMemory errors give warning message</li>
3457 <li>Overview window calculated more efficiently</li>
3458 <li>Several GUI bugs resolved</li>
3464 <div align="center">
3465 <strong>2.05</strong><br> 30/8/05
3470 <li>Edit and annotate in "Wrapped" view</li>
3475 <li>Several GUI bugs resolved</li>
3481 <div align="center">
3482 <strong>2.04</strong><br> 24/8/05
3487 <li>Hold down mouse wheel & scroll to change font
3493 <li>Improved JPred client reliability</li>
3494 <li>Improved loading of Jalview files</li>
3500 <div align="center">
3501 <strong>2.03</strong><br> 18/8/05
3506 <li>Set Proxy server name and port in preferences</li>
3507 <li>Multiple URL links from sequence ids</li>
3508 <li>User Defined Colours can have a scheme name and added
3510 <li>Choose to ignore gaps in consensus calculation</li>
3511 <li>Unix users can set default web browser</li>
3512 <li>Runs without GUI for batch processing</li>
3513 <li>Dynamically generated Web Service Menus</li>
3518 <li>InstallAnywhere download for Sparc Solaris</li>
3524 <div align="center">
3525 <strong>2.02</strong><br> 18/7/05
3531 <li>Copy & Paste order of sequences maintains
3532 alignment order.</li>
3538 <div align="center">
3539 <strong>2.01</strong><br> 12/7/05
3544 <li>Use delete key for deleting selection.</li>
3545 <li>Use Mouse wheel to scroll sequences.</li>
3546 <li>Help file updated to describe how to add alignment
3548 <li>Version and build date written to build properties
3550 <li>InstallAnywhere installation will check for updates
3551 at launch of Jalview.</li>
3556 <li>Delete gaps bug fixed.</li>
3557 <li>FileChooser sorts columns.</li>
3558 <li>Can remove groups one by one.</li>
3559 <li>Filechooser icons installed.</li>
3560 <li>Finder ignores return character when searching.
3561 Return key will initiate a search.<br>
3568 <div align="center">
3569 <strong>2.0</strong><br> 20/6/05
3574 <li>New codebase</li>