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
97 <ul><li>Example groovy script for generating a matrix of percent identity scores for current alignment.</li></ul>
98 <em>Testing and Deployment</em>
99 <ul><li><!-- JAL-2727 -->Test to catch memory leaks in Jalview UI</li></ul>
101 <td><div align="left">
104 <li><!-- JAL-2643 -->Pressing tab after updating the colour threshold text field doesn't trigger an update to the alignment view</li>
105 <li><!-- JAL-2682 -->Race condition when parsing sequence ID strings in parallel</li>
106 <li><!-- JAL-2608 -->Overview windows are also closed when alignment window is closed</li>
107 <li><!-- JAL-2742 -->Analysis (tree, pca, etc) of a selected region starting after a hidden column can include the last hidden column</li>
111 <li><!-- JAL-2777 -->Structures with whitespace chainCode cannot be viewed in Chimera</li>
112 <li><!-- JAL-2728 -->Protein annotation panel too high in CDS/Protein view
114 <li><!-- JAL-2757 -->Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs
116 <li><!-- JAL-2253 -->Slow EnsemblGenome ID lookup</li>
117 <li><!-- JAL-2739 -->Hidden column marker in last column not rendered when switching back from Wrapped to normal view</li>
118 <li><!-- JAL-2768 -->Annotation display corrupted when scrolling right in unwapped alignment view</li>
119 <li><!-- JAL-2542 -->Existing features on subsequence incorrectly relocated when full sequence retrieved from database</li>
120 <li><!-- JAL-2733 -->Last reported memory still shown when Desktop->Show Memory is unticked (OSX only)</li>
121 <li><!-- JAL-2658 -->Amend Features dialog doesn't allow features of same type and group to be selected for amending</li>
122 <li><!-- JAL-2524 -->Jalview becomes sluggish in wide alignments when hidden columns are present</li>
123 <li><!-- JAL-2392 -->Jalview freezes when loading and displaying several structures</li>
124 <li><!-- JAL-2732 -->Black outlines left after resizing or moving a window</li>
125 <li><!-- JAL-1900,JAL-1625 -->Unable to minimise windows within the Jalview desktop on OSX</li>
127 <strong><em>Applet</em></strong><br/>
129 <li><!-- JAL-2687 -->Concurrent modification exception when closing alignment panel</li>
134 <td width="60" nowrap>
136 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
137 <em>2/10/2017</em></strong>
140 <td><div align="left">
141 <em>New features in Jalview Desktop</em>
144 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
146 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
150 <td><div align="left">
154 <td width="60" nowrap>
156 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
157 <em>7/9/2017</em></strong>
160 <td><div align="left">
164 <!-- JAL-2588 -->Show gaps in overview window by colouring
165 in grey (sequences used to be coloured grey, and gaps were
169 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
173 <!-- JAL-2587 -->Overview updates immediately on increase
174 in size and progress bar shown as higher resolution
175 overview is recalculated
180 <td><div align="left">
184 <!-- JAL-2664 -->Overview window redraws every hidden
185 column region row by row
188 <!-- JAL-2681 -->duplicate protein sequences shown after
189 retrieving Ensembl crossrefs for sequences from Uniprot
192 <!-- JAL-2603 -->Overview window throws NPE if show boxes
193 format setting is unticked
196 <!-- JAL-2610 -->Groups are coloured wrongly in overview
197 if group has show boxes format setting unticked
200 <!-- JAL-2672,JAL-2665 -->Redraw problems when
201 autoscrolling whilst dragging current selection group to
202 include sequences and columns not currently displayed
205 <!-- JAL-2691 -->Not all chains are mapped when multimeric
206 assemblies are imported via CIF file
209 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
210 displayed when threshold or conservation colouring is also
214 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
218 <!-- JAL-2673 -->Jalview continues to scroll after
219 dragging a selected region off the visible region of the
223 <!-- JAL-2724 -->Cannot apply annotation based
224 colourscheme to all groups in a view
227 <!-- JAL-2511 -->IDs don't line up with sequences
228 initially after font size change using the Font chooser or
235 <td width="60" nowrap>
237 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
240 <td><div align="left">
241 <em>Calculations</em>
245 <!-- JAL-1933 -->Occupancy annotation row shows number of
246 ungapped positions in each column of the alignment.
249 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
250 a calculation dialog box
253 <!-- JAL-2379 -->Revised implementation of PCA for speed
254 and memory efficiency (~30x faster)
257 <!-- JAL-2403 -->Revised implementation of sequence
258 similarity scores as used by Tree, PCA, Shading Consensus
259 and other calculations
262 <!-- JAL-2416 -->Score matrices are stored as resource
263 files within the Jalview codebase
266 <!-- JAL-2500 -->Trees computed on Sequence Feature
267 Similarity may have different topology due to increased
274 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
275 model for alignments and groups
278 <!-- JAL-384 -->Custom shading schemes created via groovy
285 <!-- JAL-2526 -->Efficiency improvements for interacting
286 with alignment and overview windows
289 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
293 <!-- JAL-2388 -->Hidden columns and sequences can be
297 <!-- JAL-2611 -->Click-drag in visible area allows fine
298 adjustment of visible position
302 <em>Data import/export</em>
305 <!-- JAL-2535 -->Posterior probability annotation from
306 Stockholm files imported as sequence associated annotation
309 <!-- JAL-2507 -->More robust per-sequence positional
310 annotation input/output via stockholm flatfile
313 <!-- JAL-2533 -->Sequence names don't include file
314 extension when importing structure files without embedded
315 names or PDB accessions
318 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
319 format sequence substitution matrices
322 <em>User Interface</em>
325 <!-- JAL-2447 --> Experimental Features Checkbox in
326 Desktop's Tools menu to hide or show untested features in
330 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
331 via Overview or sequence motif search operations
334 <!-- JAL-2547 -->Amend sequence features dialog box can be
335 opened by double clicking gaps within sequence feature
339 <!-- JAL-1476 -->Status bar message shown when not enough
340 aligned positions were available to create a 3D structure
344 <em>3D Structure</em>
347 <!-- JAL-2430 -->Hidden regions in alignment views are not
348 coloured in linked structure views
351 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
352 file-based command exchange
355 <!-- JAL-2375 -->Structure chooser automatically shows
356 Cached Structures rather than querying the PDBe if
357 structures are already available for sequences
360 <!-- JAL-2520 -->Structures imported via URL are cached in
361 the Jalview project rather than downloaded again when the
365 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
366 to transfer Chimera's structure attributes as Jalview
367 features, and vice-versa (<strong>Experimental
371 <em>Web Services</em>
374 <!-- JAL-2549 -->Updated JABAWS client to v2.2
377 <!-- JAL-2335 -->Filter non-standard amino acids and
378 nucleotides when submitting to AACon and other MSA
382 <!-- JAL-2316, -->URLs for viewing database
383 cross-references provided by identifiers.org and the
391 <!-- JAL-2344 -->FileFormatI interface for describing and
392 identifying file formats (instead of String constants)
395 <!-- JAL-2228 -->FeatureCounter script refactored for
396 efficiency when counting all displayed features (not
397 backwards compatible with 2.10.1)
400 <em>Example files</em>
403 <!-- JAL-2631 -->Graduated feature colour style example
404 included in the example feature file
407 <em>Documentation</em>
410 <!-- JAL-2339 -->Release notes reformatted for readability
411 with the built-in Java help viewer
414 <!-- JAL-1644 -->Find documentation updated with 'search
415 sequence description' option
421 <!-- JAL-2485, -->External service integration tests for
422 Uniprot REST Free Text Search Client
425 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
428 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
433 <td><div align="left">
434 <em>Calculations</em>
437 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
438 matrix - C->R should be '-3'<br />Old matrix restored
439 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
441 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
442 Jalview's treatment of gaps in PCA and substitution matrix
443 based Tree calculations.<br /> <br />In earlier versions
444 of Jalview, gaps matching gaps were penalised, and gaps
445 matching non-gaps penalised even more. In the PCA
446 calculation, gaps were actually treated as non-gaps - so
447 different costs were applied, which meant Jalview's PCAs
448 were different to those produced by SeqSpace.<br />Jalview
449 now treats gaps in the same way as SeqSpace (ie it scores
450 them as 0). <br /> <br />Enter the following in the
451 Groovy console to restore pre-2.10.2 behaviour:<br />
452 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
453 // for 2.10.1 mode <br />
454 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
455 // to restore 2.10.2 mode <br /> <br /> <em>Note:
456 these settings will affect all subsequent tree and PCA
457 calculations (not recommended)</em></li>
459 <!-- JAL-2424 -->Fixed off-by-one bug that affected
460 scaling of branch lengths for trees computed using
461 Sequence Feature Similarity.
464 <!-- JAL-2377 -->PCA calculation could hang when
465 generating output report when working with highly
469 <!-- JAL-2544 --> Sort by features includes features to
470 right of selected region when gaps present on right-hand
474 <em>User Interface</em>
477 <!-- JAL-2346 -->Reopening Colour by annotation dialog
478 doesn't reselect a specific sequence's associated
479 annotation after it was used for colouring a view
482 <!-- JAL-2419 -->Current selection lost if popup menu
483 opened on a region of alignment without groups
486 <!-- JAL-2374 -->Popup menu not always shown for regions
487 of an alignment with overlapping groups
490 <!-- JAL-2310 -->Finder double counts if both a sequence's
491 name and description match
494 <!-- JAL-2370 -->Hiding column selection containing two
495 hidden regions results in incorrect hidden regions
498 <!-- JAL-2386 -->'Apply to all groups' setting when
499 changing colour does not apply Conservation slider value
503 <!-- JAL-2373 -->Percentage identity and conservation menu
504 items do not show a tick or allow shading to be disabled
507 <!-- JAL-2385 -->Conservation shading or PID threshold
508 lost when base colourscheme changed if slider not visible
511 <!-- JAL-2547 -->Sequence features shown in tooltip for
512 gaps before start of features
515 <!-- JAL-2623 -->Graduated feature colour threshold not
516 restored to UI when feature colour is edited
519 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
520 a time when scrolling vertically in wrapped mode.
523 <!-- JAL-2630 -->Structure and alignment overview update
524 as graduate feature colour settings are modified via the
528 <!-- JAL-2034 -->Overview window doesn't always update
529 when a group defined on the alignment is resized
532 <!-- JAL-2605 -->Mouseovers on left/right scale region in
533 wrapped view result in positional status updates
537 <!-- JAL-2563 -->Status bar doesn't show position for
538 ambiguous amino acid and nucleotide symbols
541 <!-- JAL-2602 -->Copy consensus sequence failed if
542 alignment included gapped columns
545 <!-- JAL-2473 -->Minimum size set for Jalview windows so
546 widgets don't permanently disappear
549 <!-- JAL-2503 -->Cannot select or filter quantitative
550 annotation that are shown only as column labels (e.g.
551 T-Coffee column reliability scores)
554 <!-- JAL-2594 -->Exception thrown if trying to create a
555 sequence feature on gaps only
558 <!-- JAL-2504 -->Features created with 'New feature'
559 button from a Find inherit previously defined feature type
560 rather than the Find query string
563 <!-- JAL-2423 -->incorrect title in output window when
564 exporting tree calculated in Jalview
567 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
568 and then revealing them reorders sequences on the
572 <!-- JAL-964 -->Group panel in sequence feature settings
573 doesn't update to reflect available set of groups after
574 interactively adding or modifying features
577 <!-- JAL-2225 -->Sequence Database chooser unusable on
581 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
582 only excluded gaps in current sequence and ignored
589 <!-- JAL-2421 -->Overview window visible region moves
590 erratically when hidden rows or columns are present
593 <!-- JAL-2362 -->Per-residue colourschemes applied via the
594 Structure Viewer's colour menu don't correspond to
598 <!-- JAL-2405 -->Protein specific colours only offered in
599 colour and group colour menu for protein alignments
602 <!-- JAL-2385 -->Colour threshold slider doesn't update to
603 reflect currently selected view or group's shading
607 <!-- JAL-2624 -->Feature colour thresholds not respected
608 when rendered on overview and structures when opacity at
612 <!-- JAL-2589 -->User defined gap colour not shown in
613 overview when features overlaid on alignment
616 <em>Data import/export</em>
619 <!-- JAL-2576 -->Very large alignments take a long time to
623 <!-- JAL-2507 -->Per-sequence RNA secondary structures
624 added after a sequence was imported are not written to
628 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
629 when importing RNA secondary structure via Stockholm
632 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
633 not shown in correct direction for simple pseudoknots
636 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
637 with lightGray or darkGray via features file (but can
641 <!-- JAL-2383 -->Above PID colour threshold not recovered
642 when alignment view imported from project
645 <!-- JAL-2520,JAL-2465 -->No mappings generated between
646 structure and sequences extracted from structure files
647 imported via URL and viewed in Jmol
650 <!-- JAL-2520 -->Structures loaded via URL are saved in
651 Jalview Projects rather than fetched via URL again when
652 the project is loaded and the structure viewed
655 <em>Web Services</em>
658 <!-- JAL-2519 -->EnsemblGenomes example failing after
659 release of Ensembl v.88
662 <!-- JAL-2366 -->Proxy server address and port always
663 appear enabled in Preferences->Connections
666 <!-- JAL-2461 -->DAS registry not found exceptions
667 removed from console output
670 <!-- JAL-2582 -->Cannot retrieve protein products from
671 Ensembl by Peptide ID
674 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
675 created from SIFTs, and spurious 'Couldn't open structure
676 in Chimera' errors raised after April 2017 update (problem
677 due to 'null' string rather than empty string used for
678 residues with no corresponding PDB mapping).
681 <em>Application UI</em>
684 <!-- JAL-2361 -->User Defined Colours not added to Colour
688 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
689 case' residues (button in colourscheme editor debugged and
690 new documentation and tooltips added)
693 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
694 doesn't restore group-specific text colour thresholds
697 <!-- JAL-2243 -->Feature settings panel does not update as
698 new features are added to alignment
701 <!-- JAL-2532 -->Cancel in feature settings reverts
702 changes to feature colours via the Amend features dialog
705 <!-- JAL-2506 -->Null pointer exception when attempting to
706 edit graduated feature colour via amend features dialog
710 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
711 selection menu changes colours of alignment views
714 <!-- JAL-2426 -->Spurious exceptions in console raised
715 from alignment calculation workers after alignment has
719 <!-- JAL-1608 -->Typo in selection popup menu - Create
720 groups now 'Create Group'
723 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
724 Create/Undefine group doesn't always work
727 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
728 shown again after pressing 'Cancel'
731 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
732 adjusts start position in wrap mode
735 <!-- JAL-2563 -->Status bar doesn't show positions for
736 ambiguous amino acids
739 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
740 CDS/Protein view after CDS sequences added for aligned
744 <!-- JAL-2592 -->User defined colourschemes called 'User
745 Defined' don't appear in Colours menu
751 <!-- JAL-2468 -->Switching between Nucleotide and Protein
752 score models doesn't always result in an updated PCA plot
755 <!-- JAL-2442 -->Features not rendered as transparent on
756 overview or linked structure view
759 <!-- JAL-2372 -->Colour group by conservation doesn't
763 <!-- JAL-2517 -->Hitting Cancel after applying
764 user-defined colourscheme doesn't restore original
771 <!-- JAL-2314 -->Unit test failure:
772 jalview.ws.jabaws.RNAStructExportImport setup fails
775 <!-- JAL-2307 -->Unit test failure:
776 jalview.ws.sifts.SiftsClientTest due to compatibility
777 problems with deep array comparison equality asserts in
778 successive versions of TestNG
781 <!-- JAL-2479 -->Relocated StructureChooserTest and
782 ParameterUtilsTest Unit tests to Network suite
785 <em>New Known Issues</em>
788 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
789 phase after a sequence motif find operation
792 <!-- JAL-2550 -->Importing annotation file with rows
793 containing just upper and lower case letters are
794 interpreted as WUSS RNA secondary structure symbols
797 <!-- JAL-2590 -->Cannot load and display Newick trees
798 reliably from eggnog Ortholog database
801 <!-- JAL-2468 -->Status bar shows 'Marked x columns
802 containing features of type Highlight' when 'B' is pressed
803 to mark columns containing highlighted regions.
806 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
807 doesn't always add secondary structure annotation.
812 <td width="60" nowrap>
814 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
817 <td><div align="left">
821 <!-- JAL-98 -->Improved memory usage: sparse arrays used
822 for all consensus calculations
825 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
828 <li>Updated Jalview's Certum code signing certificate
834 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
835 set of database cross-references, sorted alphabetically
838 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
839 from database cross references. Users with custom links
840 will receive a <a href="webServices/urllinks.html#warning">warning
841 dialog</a> asking them to update their preferences.
844 <!-- JAL-2287-->Cancel button and escape listener on
845 dialog warning user about disconnecting Jalview from a
849 <!-- JAL-2320-->Jalview's Chimera control window closes if
850 the Chimera it is connected to is shut down
853 <!-- JAL-1738-->New keystroke (B) and Select highlighted
854 columns menu item to mark columns containing highlighted
855 regions (e.g. from structure selections or results of a
859 <!-- JAL-2284-->Command line option for batch-generation
860 of HTML pages rendering alignment data with the BioJS
870 <!-- JAL-2286 -->Columns with more than one modal residue
871 are not coloured or thresholded according to percent
872 identity (first observed in Jalview 2.8.2)
875 <!-- JAL-2301 -->Threonine incorrectly reported as not
879 <!-- JAL-2318 -->Updates to documentation pages (above PID
880 threshold, amino acid properties)
883 <!-- JAL-2292 -->Lower case residues in sequences are not
884 reported as mapped to residues in a structure file in the
888 <!--JAL-2324 -->Identical features with non-numeric scores
889 could be added multiple times to a sequence
892 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
893 bond features shown as two highlighted residues rather
894 than a range in linked structure views, and treated
895 correctly when selecting and computing trees from features
898 <!-- JAL-2281-->Custom URL links for database
899 cross-references are matched to database name regardless
907 <!-- JAL-2282-->Custom URL links for specific database
908 names without regular expressions also offer links from
912 <!-- JAL-2315-->Removing a single configured link in the
913 URL links pane in Connections preferences doesn't actually
914 update Jalview configuration
917 <!-- JAL-2272-->CTRL-Click on a selected region to open
918 the alignment area popup menu doesn't work on El-Capitan
921 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
922 files with similarly named sequences if dropped onto the
926 <!-- JAL-2312 -->Additional mappings are shown for PDB
927 entries where more chains exist in the PDB accession than
928 are reported in the SIFTS file
931 <!-- JAL-2317-->Certain structures do not get mapped to
932 the structure view when displayed with Chimera
935 <!-- JAL-2317-->No chains shown in the Chimera view
936 panel's View->Show Chains submenu
939 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
940 work for wrapped alignment views
943 <!--JAL-2197 -->Rename UI components for running JPred
944 predictions from 'JNet' to 'JPred'
947 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
948 corrupted when annotation panel vertical scroll is not at
952 <!--JAL-2332 -->Attempting to view structure for Hen
953 lysozyme results in a PDB Client error dialog box
956 <!-- JAL-2319 -->Structure View's mapping report switched
957 ranges for PDB and sequence for SIFTS
960 SIFTS 'Not_Observed' residues mapped to non-existant
964 <!-- <em>New Known Issues</em>
971 <td width="60" nowrap>
973 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
974 <em>25/10/2016</em></strong>
977 <td><em>Application</em>
979 <li>3D Structure chooser opens with 'Cached structures'
980 view if structures already loaded</li>
981 <li>Progress bar reports models as they are loaded to
988 <li>Colour by conservation always enabled and no tick
989 shown in menu when BLOSUM or PID shading applied</li>
990 <li>FER1_ARATH and FER2_ARATH labels were switched in
991 example sequences/projects/trees</li>
995 <li>Jalview projects with views of local PDB structure
996 files saved on Windows cannot be opened on OSX</li>
997 <li>Multiple structure views can be opened and superposed
998 without timeout for structures with multiple models or
999 multiple sequences in alignment</li>
1000 <li>Cannot import or associated local PDB files without a
1001 PDB ID HEADER line</li>
1002 <li>RMSD is not output in Jmol console when superposition
1004 <li>Drag and drop of URL from Browser fails for Linux and
1005 OSX versions earlier than El Capitan</li>
1006 <li>ENA client ignores invalid content from ENA server</li>
1007 <li>Exceptions are not raised in console when ENA client
1008 attempts to fetch non-existent IDs via Fetch DB Refs UI
1010 <li>Exceptions are not raised in console when a new view
1011 is created on the alignment</li>
1012 <li>OSX right-click fixed for group selections: CMD-click
1013 to insert/remove gaps in groups and CTRL-click to open group
1016 <em>Build and deployment</em>
1018 <li>URL link checker now copes with multi-line anchor
1021 <em>New Known Issues</em>
1023 <li>Drag and drop from URL links in browsers do not work
1030 <td width="60" nowrap>
1031 <div align="center">
1032 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1035 <td><em>General</em>
1038 <!-- JAL-2124 -->Updated Spanish translations.
1041 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1042 for importing structure data to Jalview. Enables mmCIF and
1046 <!-- JAL-192 --->Alignment ruler shows positions relative to
1050 <!-- JAL-2202 -->Position/residue shown in status bar when
1051 mousing over sequence associated annotation
1054 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1058 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1059 '()', canonical '[]' and invalid '{}' base pair populations
1063 <!-- JAL-2092 -->Feature settings popup menu options for
1064 showing or hiding columns containing a feature
1067 <!-- JAL-1557 -->Edit selected group by double clicking on
1068 group and sequence associated annotation labels
1071 <!-- JAL-2236 -->Sequence name added to annotation label in
1072 select/hide columns by annotation and colour by annotation
1076 </ul> <em>Application</em>
1079 <!-- JAL-2050-->Automatically hide introns when opening a
1080 gene/transcript view
1083 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1087 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1088 structure mappings with the EMBL-EBI PDBe SIFTS database
1091 <!-- JAL-2079 -->Updated download sites used for Rfam and
1092 Pfam sources to xfam.org
1095 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1098 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1099 over sequences in Jalview
1102 <!-- JAL-2027-->Support for reverse-complement coding
1103 regions in ENA and EMBL
1106 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1107 for record retrieval via ENA rest API
1110 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1114 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1115 groovy script execution
1118 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1119 alignment window's Calculate menu
1122 <!-- JAL-1812 -->Allow groovy scripts that call
1123 Jalview.getAlignFrames() to run in headless mode
1126 <!-- JAL-2068 -->Support for creating new alignment
1127 calculation workers from groovy scripts
1130 <!-- JAL-1369 --->Store/restore reference sequence in
1134 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1135 associations are now saved/restored from project
1138 <!-- JAL-1993 -->Database selection dialog always shown
1139 before sequence fetcher is opened
1142 <!-- JAL-2183 -->Double click on an entry in Jalview's
1143 database chooser opens a sequence fetcher
1146 <!-- JAL-1563 -->Free-text search client for UniProt using
1147 the UniProt REST API
1150 <!-- JAL-2168 -->-nonews command line parameter to prevent
1151 the news reader opening
1154 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1155 querying stored in preferences
1158 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1162 <!-- JAL-1977-->Tooltips shown on database chooser
1165 <!-- JAL-391 -->Reverse complement function in calculate
1166 menu for nucleotide sequences
1169 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1170 and feature counts preserves alignment ordering (and
1171 debugged for complex feature sets).
1174 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1175 viewing structures with Jalview 2.10
1178 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1179 genome, transcript CCDS and gene ids via the Ensembl and
1180 Ensembl Genomes REST API
1183 <!-- JAL-2049 -->Protein sequence variant annotation
1184 computed for 'sequence_variant' annotation on CDS regions
1188 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1192 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1193 Ref Fetcher fails to match, or otherwise updates sequence
1194 data from external database records.
1197 <!-- JAL-2154 -->Revised Jalview Project format for
1198 efficient recovery of sequence coding and alignment
1199 annotation relationships.
1201 </ul> <!-- <em>Applet</em>
1212 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1216 <!-- JAL-2018-->Export features in Jalview format (again)
1217 includes graduated colourschemes
1220 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1221 working with big alignments and lots of hidden columns
1224 <!-- JAL-2053-->Hidden column markers not always rendered
1225 at right of alignment window
1228 <!-- JAL-2067 -->Tidied up links in help file table of
1232 <!-- JAL-2072 -->Feature based tree calculation not shown
1236 <!-- JAL-2075 -->Hidden columns ignored during feature
1237 based tree calculation
1240 <!-- JAL-2065 -->Alignment view stops updating when show
1241 unconserved enabled for group on alignment
1244 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1248 <!-- JAL-2146 -->Alignment column in status incorrectly
1249 shown as "Sequence position" when mousing over
1253 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1254 hidden columns present
1257 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1258 user created annotation added to alignment
1261 <!-- JAL-1841 -->RNA Structure consensus only computed for
1262 '()' base pair annotation
1265 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1266 in zero scores for all base pairs in RNA Structure
1270 <!-- JAL-2174-->Extend selection with columns containing
1274 <!-- JAL-2275 -->Pfam format writer puts extra space at
1275 beginning of sequence
1278 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1282 <!-- JAL-2238 -->Cannot create groups on an alignment from
1283 from a tree when t-coffee scores are shown
1286 <!-- JAL-1836,1967 -->Cannot import and view PDB
1287 structures with chains containing negative resnums (4q4h)
1290 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1294 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1295 to Clustal, PIR and PileUp output
1298 <!-- JAL-2008 -->Reordering sequence features that are
1299 not visible causes alignment window to repaint
1302 <!-- JAL-2006 -->Threshold sliders don't work in
1303 graduated colour and colour by annotation row for e-value
1304 scores associated with features and annotation rows
1307 <!-- JAL-1797 -->amino acid physicochemical conservation
1308 calculation should be case independent
1311 <!-- JAL-2173 -->Remove annotation also updates hidden
1315 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1316 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1317 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1320 <!-- JAL-2065 -->Null pointer exceptions and redraw
1321 problems when reference sequence defined and 'show
1322 non-conserved' enabled
1325 <!-- JAL-1306 -->Quality and Conservation are now shown on
1326 load even when Consensus calculation is disabled
1329 <!-- JAL-1932 -->Remove right on penultimate column of
1330 alignment does nothing
1333 <em>Application</em>
1336 <!-- JAL-1552-->URLs and links can't be imported by
1337 drag'n'drop on OSX when launched via webstart (note - not
1338 yet fixed for El Capitan)
1341 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1342 output when running on non-gb/us i18n platforms
1345 <!-- JAL-1944 -->Error thrown when exporting a view with
1346 hidden sequences as flat-file alignment
1349 <!-- JAL-2030-->InstallAnywhere distribution fails when
1353 <!-- JAL-2080-->Jalview very slow to launch via webstart
1354 (also hotfix for 2.9.0b2)
1357 <!-- JAL-2085 -->Cannot save project when view has a
1358 reference sequence defined
1361 <!-- JAL-1011 -->Columns are suddenly selected in other
1362 alignments and views when revealing hidden columns
1365 <!-- JAL-1989 -->Hide columns not mirrored in complement
1366 view in a cDNA/Protein splitframe
1369 <!-- JAL-1369 -->Cannot save/restore representative
1370 sequence from project when only one sequence is
1374 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1375 in Structure Chooser
1378 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1379 structure consensus didn't refresh annotation panel
1382 <!-- JAL-1962 -->View mapping in structure view shows
1383 mappings between sequence and all chains in a PDB file
1386 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1387 dialogs format columns correctly, don't display array
1388 data, sort columns according to type
1391 <!-- JAL-1975 -->Export complete shown after destination
1392 file chooser is cancelled during an image export
1395 <!-- JAL-2025 -->Error when querying PDB Service with
1396 sequence name containing special characters
1399 <!-- JAL-2024 -->Manual PDB structure querying should be
1403 <!-- JAL-2104 -->Large tooltips with broken HTML
1404 formatting don't wrap
1407 <!-- JAL-1128 -->Figures exported from wrapped view are
1408 truncated so L looks like I in consensus annotation
1411 <!-- JAL-2003 -->Export features should only export the
1412 currently displayed features for the current selection or
1416 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1417 after fetching cross-references, and restoring from
1421 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1422 followed in the structure viewer
1425 <!-- JAL-2163 -->Titles for individual alignments in
1426 splitframe not restored from project
1429 <!-- JAL-2145 -->missing autocalculated annotation at
1430 trailing end of protein alignment in transcript/product
1431 splitview when pad-gaps not enabled by default
1434 <!-- JAL-1797 -->amino acid physicochemical conservation
1438 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1439 article has been read (reopened issue due to
1440 internationalisation problems)
1443 <!-- JAL-1960 -->Only offer PDB structures in structure
1444 viewer based on sequence name, PDB and UniProt
1449 <!-- JAL-1976 -->No progress bar shown during export of
1453 <!-- JAL-2213 -->Structures not always superimposed after
1454 multiple structures are shown for one or more sequences.
1457 <!-- JAL-1370 -->Reference sequence characters should not
1458 be replaced with '.' when 'Show unconserved' format option
1462 <!-- JAL-1823 -->Cannot specify chain code when entering
1463 specific PDB id for sequence
1466 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1467 'Export hidden sequences' is enabled, but 'export hidden
1468 columns' is disabled.
1471 <!--JAL-2026-->Best Quality option in structure chooser
1472 selects lowest rather than highest resolution structures
1476 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1477 to sequence mapping in 'View Mappings' report
1480 <!-- JAL-2284 -->Unable to read old Jalview projects that
1481 contain non-XML data added after Jalvew wrote project.
1484 <!-- JAL-2118 -->Newly created annotation row reorders
1485 after clicking on it to create new annotation for a
1489 <!-- JAL-1980 -->Null Pointer Exception raised when
1490 pressing Add on an orphaned cut'n'paste window.
1492 <!-- may exclude, this is an external service stability issue JAL-1941
1493 -- > RNA 3D structure not added via DSSR service</li> -->
1498 <!-- JAL-2151 -->Incorrect columns are selected when
1499 hidden columns present before start of sequence
1502 <!-- JAL-1986 -->Missing dependencies on applet pages
1506 <!-- JAL-1947 -->Overview pixel size changes when
1507 sequences are hidden in applet
1510 <!-- JAL-1996 -->Updated instructions for applet
1511 deployment on examples pages.
1518 <td width="60" nowrap>
1519 <div align="center">
1520 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1521 <em>16/10/2015</em></strong>
1524 <td><em>General</em>
1526 <li>Time stamps for signed Jalview application and applet
1531 <em>Application</em>
1533 <li>Duplicate group consensus and conservation rows
1534 shown when tree is partitioned</li>
1535 <li>Erratic behaviour when tree partitions made with
1536 multiple cDNA/Protein split views</li>
1542 <td width="60" nowrap>
1543 <div align="center">
1544 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1545 <em>8/10/2015</em></strong>
1548 <td><em>General</em>
1550 <li>Updated Spanish translations of localized text for
1552 </ul> <em>Application</em>
1554 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1555 <li>Signed OSX InstallAnywhere installer<br></li>
1556 <li>Support for per-sequence based annotations in BioJSON</li>
1557 </ul> <em>Applet</em>
1559 <li>Split frame example added to applet examples page</li>
1560 </ul> <em>Build and Deployment</em>
1563 <!-- JAL-1888 -->New ant target for running Jalview's test
1571 <li>Mapping of cDNA to protein in split frames
1572 incorrect when sequence start > 1</li>
1573 <li>Broken images in filter column by annotation dialog
1575 <li>Feature colours not parsed from features file</li>
1576 <li>Exceptions and incomplete link URLs recovered when
1577 loading a features file containing HTML tags in feature
1581 <em>Application</em>
1583 <li>Annotations corrupted after BioJS export and
1585 <li>Incorrect sequence limits after Fetch DB References
1586 with 'trim retrieved sequences'</li>
1587 <li>Incorrect warning about deleting all data when
1588 deleting selected columns</li>
1589 <li>Patch to build system for shipping properly signed
1590 JNLP templates for webstart launch</li>
1591 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1592 unreleased structures for download or viewing</li>
1593 <li>Tab/space/return keystroke operation of EMBL-PDBe
1594 fetcher/viewer dialogs works correctly</li>
1595 <li>Disabled 'minimise' button on Jalview windows
1596 running on OSX to workaround redraw hang bug</li>
1597 <li>Split cDNA/Protein view position and geometry not
1598 recovered from jalview project</li>
1599 <li>Initial enabled/disabled state of annotation menu
1600 sorter 'show autocalculated first/last' corresponds to
1602 <li>Restoring of Clustal, RNA Helices and T-Coffee
1603 color schemes from BioJSON</li>
1607 <li>Reorder sequences mirrored in cDNA/Protein split
1609 <li>Applet with Jmol examples not loading correctly</li>
1615 <td><div align="center">
1616 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1618 <td><em>General</em>
1620 <li>Linked visualisation and analysis of DNA and Protein
1623 <li>Translated cDNA alignments shown as split protein
1624 and DNA alignment views</li>
1625 <li>Codon consensus annotation for linked protein and
1626 cDNA alignment views</li>
1627 <li>Link cDNA or Protein product sequences by loading
1628 them onto Protein or cDNA alignments</li>
1629 <li>Reconstruct linked cDNA alignment from aligned
1630 protein sequences</li>
1633 <li>Jmol integration updated to Jmol v14.2.14</li>
1634 <li>Import and export of Jalview alignment views as <a
1635 href="features/bioJsonFormat.html">BioJSON</a></li>
1636 <li>New alignment annotation file statements for
1637 reference sequences and marking hidden columns</li>
1638 <li>Reference sequence based alignment shading to
1639 highlight variation</li>
1640 <li>Select or hide columns according to alignment
1642 <li>Find option for locating sequences by description</li>
1643 <li>Conserved physicochemical properties shown in amino
1644 acid conservation row</li>
1645 <li>Alignments can be sorted by number of RNA helices</li>
1646 </ul> <em>Application</em>
1648 <li>New cDNA/Protein analysis capabilities
1650 <li>Get Cross-References should open a Split Frame
1651 view with cDNA/Protein</li>
1652 <li>Detect when nucleotide sequences and protein
1653 sequences are placed in the same alignment</li>
1654 <li>Split cDNA/Protein views are saved in Jalview
1659 <li>Use REST API to talk to Chimera</li>
1660 <li>Selected regions in Chimera are highlighted in linked
1661 Jalview windows</li>
1663 <li>VARNA RNA viewer updated to v3.93</li>
1664 <li>VARNA views are saved in Jalview Projects</li>
1665 <li>Pseudoknots displayed as Jalview RNA annotation can
1666 be shown in VARNA</li>
1668 <li>Make groups for selection uses marked columns as well
1669 as the active selected region</li>
1671 <li>Calculate UPGMA and NJ trees using sequence feature
1673 <li>New Export options
1675 <li>New Export Settings dialog to control hidden
1676 region export in flat file generation</li>
1678 <li>Export alignment views for display with the <a
1679 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1681 <li>Export scrollable SVG in HTML page</li>
1682 <li>Optional embedding of BioJSON data when exporting
1683 alignment figures to HTML</li>
1685 <li>3D structure retrieval and display
1687 <li>Free text and structured queries with the PDBe
1689 <li>PDBe Search API based discovery and selection of
1690 PDB structures for a sequence set</li>
1694 <li>JPred4 employed for protein secondary structure
1696 <li>Hide Insertions menu option to hide unaligned columns
1697 for one or a group of sequences</li>
1698 <li>Automatically hide insertions in alignments imported
1699 from the JPred4 web server</li>
1700 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1701 system on OSX<br />LGPL libraries courtesy of <a
1702 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1704 <li>changed 'View nucleotide structure' submenu to 'View
1705 VARNA 2D Structure'</li>
1706 <li>change "View protein structure" menu option to "3D
1709 </ul> <em>Applet</em>
1711 <li>New layout for applet example pages</li>
1712 <li>New parameters to enable SplitFrame view
1713 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1714 <li>New example demonstrating linked viewing of cDNA and
1715 Protein alignments</li>
1716 </ul> <em>Development and deployment</em>
1718 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1719 <li>Include installation type and git revision in build
1720 properties and console log output</li>
1721 <li>Jalview Github organisation, and new github site for
1722 storing BioJsMSA Templates</li>
1723 <li>Jalview's unit tests now managed with TestNG</li>
1726 <!-- <em>General</em>
1728 </ul> --> <!-- issues resolved --> <em>Application</em>
1730 <li>Escape should close any open find dialogs</li>
1731 <li>Typo in select-by-features status report</li>
1732 <li>Consensus RNA secondary secondary structure
1733 predictions are not highlighted in amber</li>
1734 <li>Missing gap character in v2.7 example file means
1735 alignment appears unaligned when pad-gaps is not enabled</li>
1736 <li>First switch to RNA Helices colouring doesn't colour
1737 associated structure views</li>
1738 <li>ID width preference option is greyed out when auto
1739 width checkbox not enabled</li>
1740 <li>Stopped a warning dialog from being shown when
1741 creating user defined colours</li>
1742 <li>'View Mapping' in structure viewer shows sequence
1743 mappings for just that viewer's sequences</li>
1744 <li>Workaround for superposing PDB files containing
1745 multiple models in Chimera</li>
1746 <li>Report sequence position in status bar when hovering
1747 over Jmol structure</li>
1748 <li>Cannot output gaps as '.' symbols with Selection ->
1749 output to text box</li>
1750 <li>Flat file exports of alignments with hidden columns
1751 have incorrect sequence start/end</li>
1752 <li>'Aligning' a second chain to a Chimera structure from
1754 <li>Colour schemes applied to structure viewers don't
1755 work for nucleotide</li>
1756 <li>Loading/cut'n'pasting an empty or invalid file leads
1757 to a grey/invisible alignment window</li>
1758 <li>Exported Jpred annotation from a sequence region
1759 imports to different position</li>
1760 <li>Space at beginning of sequence feature tooltips shown
1761 on some platforms</li>
1762 <li>Chimera viewer 'View | Show Chain' menu is not
1764 <li>'New View' fails with a Null Pointer Exception in
1765 console if Chimera has been opened</li>
1766 <li>Mouseover to Chimera not working</li>
1767 <li>Miscellaneous ENA XML feature qualifiers not
1769 <li>NPE in annotation renderer after 'Extract Scores'</li>
1770 <li>If two structures in one Chimera window, mouseover of
1771 either sequence shows on first structure</li>
1772 <li>'Show annotations' options should not make
1773 non-positional annotations visible</li>
1774 <li>Subsequence secondary structure annotation not shown
1775 in right place after 'view flanking regions'</li>
1776 <li>File Save As type unset when current file format is
1778 <li>Save as '.jar' option removed for saving Jalview
1780 <li>Colour by Sequence colouring in Chimera more
1782 <li>Cannot 'add reference annotation' for a sequence in
1783 several views on same alignment</li>
1784 <li>Cannot show linked products for EMBL / ENA records</li>
1785 <li>Jalview's tooltip wraps long texts containing no
1787 </ul> <em>Applet</em>
1789 <li>Jmol to JalviewLite mouseover/link not working</li>
1790 <li>JalviewLite can't import sequences with ID
1791 descriptions containing angle brackets</li>
1792 </ul> <em>General</em>
1794 <li>Cannot export and reimport RNA secondary structure
1795 via jalview annotation file</li>
1796 <li>Random helix colour palette for colour by annotation
1797 with RNA secondary structure</li>
1798 <li>Mouseover to cDNA from STOP residue in protein
1799 translation doesn't work.</li>
1800 <li>hints when using the select by annotation dialog box</li>
1801 <li>Jmol alignment incorrect if PDB file has alternate CA
1803 <li>FontChooser message dialog appears to hang after
1804 choosing 1pt font</li>
1805 <li>Peptide secondary structure incorrectly imported from
1806 annotation file when annotation display text includes 'e' or
1808 <li>Cannot set colour of new feature type whilst creating
1810 <li>cDNA translation alignment should not be sequence
1811 order dependent</li>
1812 <li>'Show unconserved' doesn't work for lower case
1814 <li>Nucleotide ambiguity codes involving R not recognised</li>
1815 </ul> <em>Deployment and Documentation</em>
1817 <li>Applet example pages appear different to the rest of
1818 www.jalview.org</li>
1819 </ul> <em>Application Known issues</em>
1821 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1822 <li>Misleading message appears after trying to delete
1824 <li>Jalview icon not shown in dock after InstallAnywhere
1825 version launches</li>
1826 <li>Fetching EMBL reference for an RNA sequence results
1827 fails with a sequence mismatch</li>
1828 <li>Corrupted or unreadable alignment display when
1829 scrolling alignment to right</li>
1830 <li>ArrayIndexOutOfBoundsException thrown when remove
1831 empty columns called on alignment with ragged gapped ends</li>
1832 <li>auto calculated alignment annotation rows do not get
1833 placed above or below non-autocalculated rows</li>
1834 <li>Jalview dekstop becomes sluggish at full screen in
1835 ultra-high resolution</li>
1836 <li>Cannot disable consensus calculation independently of
1837 quality and conservation</li>
1838 <li>Mouseover highlighting between cDNA and protein can
1839 become sluggish with more than one splitframe shown</li>
1840 </ul> <em>Applet Known Issues</em>
1842 <li>Core PDB parsing code requires Jmol</li>
1843 <li>Sequence canvas panel goes white when alignment
1844 window is being resized</li>
1850 <td><div align="center">
1851 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1853 <td><em>General</em>
1855 <li>Updated Java code signing certificate donated by
1857 <li>Features and annotation preserved when performing
1858 pairwise alignment</li>
1859 <li>RNA pseudoknot annotation can be
1860 imported/exported/displayed</li>
1861 <li>'colour by annotation' can colour by RNA and
1862 protein secondary structure</li>
1863 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1864 post-hoc with 2.9 release</em>)
1867 </ul> <em>Application</em>
1869 <li>Extract and display secondary structure for sequences
1870 with 3D structures</li>
1871 <li>Support for parsing RNAML</li>
1872 <li>Annotations menu for layout
1874 <li>sort sequence annotation rows by alignment</li>
1875 <li>place sequence annotation above/below alignment
1878 <li>Output in Stockholm format</li>
1879 <li>Internationalisation: improved Spanish (es)
1881 <li>Structure viewer preferences tab</li>
1882 <li>Disorder and Secondary Structure annotation tracks
1883 shared between alignments</li>
1884 <li>UCSF Chimera launch and linked highlighting from
1886 <li>Show/hide all sequence associated annotation rows for
1887 all or current selection</li>
1888 <li>disorder and secondary structure predictions
1889 available as dataset annotation</li>
1890 <li>Per-sequence rna helices colouring</li>
1893 <li>Sequence database accessions imported when fetching
1894 alignments from Rfam</li>
1895 <li>update VARNA version to 3.91</li>
1897 <li>New groovy scripts for exporting aligned positions,
1898 conservation values, and calculating sum of pairs scores.</li>
1899 <li>Command line argument to set default JABAWS server</li>
1900 <li>include installation type in build properties and
1901 console log output</li>
1902 <li>Updated Jalview project format to preserve dataset
1906 <!-- issues resolved --> <em>Application</em>
1908 <li>Distinguish alignment and sequence associated RNA
1909 structure in structure->view->VARNA</li>
1910 <li>Raise dialog box if user deletes all sequences in an
1912 <li>Pressing F1 results in documentation opening twice</li>
1913 <li>Sequence feature tooltip is wrapped</li>
1914 <li>Double click on sequence associated annotation
1915 selects only first column</li>
1916 <li>Redundancy removal doesn't result in unlinked
1917 leaves shown in tree</li>
1918 <li>Undos after several redundancy removals don't undo
1920 <li>Hide sequence doesn't hide associated annotation</li>
1921 <li>User defined colours dialog box too big to fit on
1922 screen and buttons not visible</li>
1923 <li>author list isn't updated if already written to
1924 Jalview properties</li>
1925 <li>Popup menu won't open after retrieving sequence
1927 <li>File open window for associate PDB doesn't open</li>
1928 <li>Left-then-right click on a sequence id opens a
1929 browser search window</li>
1930 <li>Cannot open sequence feature shading/sort popup menu
1931 in feature settings dialog</li>
1932 <li>better tooltip placement for some areas of Jalview
1934 <li>Allow addition of JABAWS Server which doesn't
1935 pass validation</li>
1936 <li>Web services parameters dialog box is too large to
1938 <li>Muscle nucleotide alignment preset obscured by
1940 <li>JABAWS preset submenus don't contain newly
1941 defined user preset</li>
1942 <li>MSA web services warns user if they were launched
1943 with invalid input</li>
1944 <li>Jalview cannot contact DAS Registy when running on
1947 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1948 'Superpose with' submenu not shown when new view
1952 </ul> <!-- <em>Applet</em>
1954 </ul> <em>General</em>
1956 </ul>--> <em>Deployment and Documentation</em>
1958 <li>2G and 1G options in launchApp have no effect on
1959 memory allocation</li>
1960 <li>launchApp service doesn't automatically open
1961 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1963 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1964 InstallAnywhere reports cannot find valid JVM when Java
1965 1.7_055 is available
1967 </ul> <em>Application Known issues</em>
1970 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1971 corrupted or unreadable alignment display when scrolling
1975 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1976 retrieval fails but progress bar continues for DAS retrieval
1977 with large number of ID
1980 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1981 flatfile output of visible region has incorrect sequence
1985 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1986 rna structure consensus doesn't update when secondary
1987 structure tracks are rearranged
1990 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1991 invalid rna structure positional highlighting does not
1992 highlight position of invalid base pairs
1995 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1996 out of memory errors are not raised when saving Jalview
1997 project from alignment window file menu
2000 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2001 Switching to RNA Helices colouring doesn't propagate to
2005 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2006 colour by RNA Helices not enabled when user created
2007 annotation added to alignment
2010 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2011 Jalview icon not shown on dock in Mountain Lion/Webstart
2013 </ul> <em>Applet Known Issues</em>
2016 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2017 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2020 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2021 Jalview and Jmol example not compatible with IE9
2024 <li>Sort by annotation score doesn't reverse order
2030 <td><div align="center">
2031 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2034 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2037 <li>Internationalisation of user interface (usually
2038 called i18n support) and translation for Spanish locale</li>
2039 <li>Define/Undefine group on current selection with
2040 Ctrl-G/Shift Ctrl-G</li>
2041 <li>Improved group creation/removal options in
2042 alignment/sequence Popup menu</li>
2043 <li>Sensible precision for symbol distribution
2044 percentages shown in logo tooltip.</li>
2045 <li>Annotation panel height set according to amount of
2046 annotation when alignment first opened</li>
2047 </ul> <em>Application</em>
2049 <li>Interactive consensus RNA secondary structure
2050 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2051 <li>Select columns containing particular features from
2052 Feature Settings dialog</li>
2053 <li>View all 'representative' PDB structures for selected
2055 <li>Update Jalview project format:
2057 <li>New file extension for Jalview projects '.jvp'</li>
2058 <li>Preserve sequence and annotation dataset (to
2059 store secondary structure annotation,etc)</li>
2060 <li>Per group and alignment annotation and RNA helix
2064 <li>New similarity measures for PCA and Tree calculation
2066 <li>Experimental support for retrieval and viewing of
2067 flanking regions for an alignment</li>
2071 <!-- issues resolved --> <em>Application</em>
2073 <li>logo keeps spinning and status remains at queued or
2074 running after job is cancelled</li>
2075 <li>cannot export features from alignments imported from
2076 Jalview/VAMSAS projects</li>
2077 <li>Buggy slider for web service parameters that take
2079 <li>Newly created RNA secondary structure line doesn't
2080 have 'display all symbols' flag set</li>
2081 <li>T-COFFEE alignment score shading scheme and other
2082 annotation shading not saved in Jalview project</li>
2083 <li>Local file cannot be loaded in freshly downloaded
2085 <li>Jalview icon not shown on dock in Mountain
2087 <li>Load file from desktop file browser fails</li>
2088 <li>Occasional NPE thrown when calculating large trees</li>
2089 <li>Cannot reorder or slide sequences after dragging an
2090 alignment onto desktop</li>
2091 <li>Colour by annotation dialog throws NPE after using
2092 'extract scores' function</li>
2093 <li>Loading/cut'n'pasting an empty file leads to a grey
2094 alignment window</li>
2095 <li>Disorder thresholds rendered incorrectly after
2096 performing IUPred disorder prediction</li>
2097 <li>Multiple group annotated consensus rows shown when
2098 changing 'normalise logo' display setting</li>
2099 <li>Find shows blank dialog after 'finished searching' if
2100 nothing matches query</li>
2101 <li>Null Pointer Exceptions raised when sorting by
2102 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2104 <li>Errors in Jmol console when structures in alignment
2105 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2107 <li>Not all working JABAWS services are shown in
2109 <li>JAVAWS version of Jalview fails to launch with
2110 'invalid literal/length code'</li>
2111 <li>Annotation/RNA Helix colourschemes cannot be applied
2112 to alignment with groups (actually fixed in 2.8.0b1)</li>
2113 <li>RNA Helices and T-Coffee Scores available as default
2116 </ul> <em>Applet</em>
2118 <li>Remove group option is shown even when selection is
2120 <li>Apply to all groups ticked but colourscheme changes
2121 don't affect groups</li>
2122 <li>Documented RNA Helices and T-Coffee Scores as valid
2123 colourscheme name</li>
2124 <li>Annotation labels drawn on sequence IDs when
2125 Annotation panel is not displayed</li>
2126 <li>Increased font size for dropdown menus on OSX and
2127 embedded windows</li>
2128 </ul> <em>Other</em>
2130 <li>Consensus sequence for alignments/groups with a
2131 single sequence were not calculated</li>
2132 <li>annotation files that contain only groups imported as
2133 annotation and junk sequences</li>
2134 <li>Fasta files with sequences containing '*' incorrectly
2135 recognised as PFAM or BLC</li>
2136 <li>conservation/PID slider apply all groups option
2137 doesn't affect background (2.8.0b1)
2139 <li>redundancy highlighting is erratic at 0% and 100%</li>
2140 <li>Remove gapped columns fails for sequences with ragged
2142 <li>AMSA annotation row with leading spaces is not
2143 registered correctly on import</li>
2144 <li>Jalview crashes when selecting PCA analysis for
2145 certain alignments</li>
2146 <li>Opening the colour by annotation dialog for an
2147 existing annotation based 'use original colours'
2148 colourscheme loses original colours setting</li>
2153 <td><div align="center">
2154 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2155 <em>30/1/2014</em></strong>
2159 <li>Trusted certificates for JalviewLite applet and
2160 Jalview Desktop application<br />Certificate was donated by
2161 <a href="https://www.certum.eu">Certum</a> to the Jalview
2162 open source project).
2164 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2165 <li>Output in Stockholm format</li>
2166 <li>Allow import of data from gzipped files</li>
2167 <li>Export/import group and sequence associated line
2168 graph thresholds</li>
2169 <li>Nucleotide substitution matrix that supports RNA and
2170 ambiguity codes</li>
2171 <li>Allow disorder predictions to be made on the current
2172 selection (or visible selection) in the same way that JPred
2174 <li>Groovy scripting for headless Jalview operation</li>
2175 </ul> <em>Other improvements</em>
2177 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2178 <li>COMBINE statement uses current SEQUENCE_REF and
2179 GROUP_REF scope to group annotation rows</li>
2180 <li>Support '' style escaping of quotes in Newick
2182 <li>Group options for JABAWS service by command line name</li>
2183 <li>Empty tooltip shown for JABA service options with a
2184 link but no description</li>
2185 <li>Select primary source when selecting authority in
2186 database fetcher GUI</li>
2187 <li>Add .mfa to FASTA file extensions recognised by
2189 <li>Annotation label tooltip text wrap</li>
2194 <li>Slow scrolling when lots of annotation rows are
2196 <li>Lots of NPE (and slowness) after creating RNA
2197 secondary structure annotation line</li>
2198 <li>Sequence database accessions not imported when
2199 fetching alignments from Rfam</li>
2200 <li>Incorrect SHMR submission for sequences with
2202 <li>View all structures does not always superpose
2204 <li>Option widgets in service parameters not updated to
2205 reflect user or preset settings</li>
2206 <li>Null pointer exceptions for some services without
2207 presets or adjustable parameters</li>
2208 <li>Discover PDB IDs entry in structure menu doesn't
2209 discover PDB xRefs</li>
2210 <li>Exception encountered while trying to retrieve
2211 features with DAS</li>
2212 <li>Lowest value in annotation row isn't coloured
2213 when colour by annotation (per sequence) is coloured</li>
2214 <li>Keyboard mode P jumps to start of gapped region when
2215 residue follows a gap</li>
2216 <li>Jalview appears to hang importing an alignment with
2217 Wrap as default or after enabling Wrap</li>
2218 <li>'Right click to add annotations' message
2219 shown in wrap mode when no annotations present</li>
2220 <li>Disorder predictions fail with NPE if no automatic
2221 annotation already exists on alignment</li>
2222 <li>oninit javascript function should be called after
2223 initialisation completes</li>
2224 <li>Remove redundancy after disorder prediction corrupts
2225 alignment window display</li>
2226 <li>Example annotation file in documentation is invalid</li>
2227 <li>Grouped line graph annotation rows are not exported
2228 to annotation file</li>
2229 <li>Multi-harmony analysis cannot be run when only two
2231 <li>Cannot create multiple groups of line graphs with
2232 several 'combine' statements in annotation file</li>
2233 <li>Pressing return several times causes Number Format
2234 exceptions in keyboard mode</li>
2235 <li>Multi-harmony (SHMMR) method doesn't submit
2236 correct partitions for input data</li>
2237 <li>Translation from DNA to Amino Acids fails</li>
2238 <li>Jalview fail to load newick tree with quoted label</li>
2239 <li>--headless flag isn't understood</li>
2240 <li>ClassCastException when generating EPS in headless
2242 <li>Adjusting sequence-associated shading threshold only
2243 changes one row's threshold</li>
2244 <li>Preferences and Feature settings panel panel
2245 doesn't open</li>
2246 <li>hide consensus histogram also hides conservation and
2247 quality histograms</li>
2252 <td><div align="center">
2253 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2255 <td><em>Application</em>
2257 <li>Support for JABAWS 2.0 Services (AACon alignment
2258 conservation, protein disorder and Clustal Omega)</li>
2259 <li>JABAWS server status indicator in Web Services
2261 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2262 in Jalview alignment window</li>
2263 <li>Updated Jalview build and deploy framework for OSX
2264 mountain lion, windows 7, and 8</li>
2265 <li>Nucleotide substitution matrix for PCA that supports
2266 RNA and ambiguity codes</li>
2268 <li>Improved sequence database retrieval GUI</li>
2269 <li>Support fetching and database reference look up
2270 against multiple DAS sources (Fetch all from in 'fetch db
2272 <li>Jalview project improvements
2274 <li>Store and retrieve the 'belowAlignment'
2275 flag for annotation</li>
2276 <li>calcId attribute to group annotation rows on the
2278 <li>Store AACon calculation settings for a view in
2279 Jalview project</li>
2283 <li>horizontal scrolling gesture support</li>
2284 <li>Visual progress indicator when PCA calculation is
2286 <li>Simpler JABA web services menus</li>
2287 <li>visual indication that web service results are still
2288 being retrieved from server</li>
2289 <li>Serialise the dialogs that are shown when Jalview
2290 starts up for first time</li>
2291 <li>Jalview user agent string for interacting with HTTP
2293 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2295 <li>Examples directory and Groovy library included in
2296 InstallAnywhere distribution</li>
2297 </ul> <em>Applet</em>
2299 <li>RNA alignment and secondary structure annotation
2300 visualization applet example</li>
2301 </ul> <em>General</em>
2303 <li>Normalise option for consensus sequence logo</li>
2304 <li>Reset button in PCA window to return dimensions to
2306 <li>Allow seqspace or Jalview variant of alignment PCA
2308 <li>PCA with either nucleic acid and protein substitution
2310 <li>Allow windows containing HTML reports to be exported
2312 <li>Interactive display and editing of RNA secondary
2313 structure contacts</li>
2314 <li>RNA Helix Alignment Colouring</li>
2315 <li>RNA base pair logo consensus</li>
2316 <li>Parse sequence associated secondary structure
2317 information in Stockholm files</li>
2318 <li>HTML Export database accessions and annotation
2319 information presented in tooltip for sequences</li>
2320 <li>Import secondary structure from LOCARNA clustalw
2321 style RNA alignment files</li>
2322 <li>import and visualise T-COFFEE quality scores for an
2324 <li>'colour by annotation' per sequence option to
2325 shade each sequence according to its associated alignment
2327 <li>New Jalview Logo</li>
2328 </ul> <em>Documentation and Development</em>
2330 <li>documentation for score matrices used in Jalview</li>
2331 <li>New Website!</li>
2333 <td><em>Application</em>
2335 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2336 wsdbfetch REST service</li>
2337 <li>Stop windows being moved outside desktop on OSX</li>
2338 <li>Filetype associations not installed for webstart
2340 <li>Jalview does not always retrieve progress of a JABAWS
2341 job execution in full once it is complete</li>
2342 <li>revise SHMR RSBS definition to ensure alignment is
2343 uploaded via ali_file parameter</li>
2344 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2345 <li>View all structures superposed fails with exception</li>
2346 <li>Jnet job queues forever if a very short sequence is
2347 submitted for prediction</li>
2348 <li>Cut and paste menu not opened when mouse clicked on
2350 <li>Putting fractional value into integer text box in
2351 alignment parameter dialog causes Jalview to hang</li>
2352 <li>Structure view highlighting doesn't work on
2354 <li>View all structures fails with exception shown in
2356 <li>Characters in filename associated with PDBEntry not
2357 escaped in a platform independent way</li>
2358 <li>Jalview desktop fails to launch with exception when
2360 <li>Tree calculation reports 'you must have 2 or more
2361 sequences selected' when selection is empty</li>
2362 <li>Jalview desktop fails to launch with jar signature
2363 failure when java web start temporary file caching is
2365 <li>DAS Sequence retrieval with range qualification
2366 results in sequence xref which includes range qualification</li>
2367 <li>Errors during processing of command line arguments
2368 cause progress bar (JAL-898) to be removed</li>
2369 <li>Replace comma for semi-colon option not disabled for
2370 DAS sources in sequence fetcher</li>
2371 <li>Cannot close news reader when JABAWS server warning
2372 dialog is shown</li>
2373 <li>Option widgets not updated to reflect user settings</li>
2374 <li>Edited sequence not submitted to web service</li>
2375 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2376 <li>InstallAnywhere installer doesn't unpack and run
2377 on OSX Mountain Lion</li>
2378 <li>Annotation panel not given a scroll bar when
2379 sequences with alignment annotation are pasted into the
2381 <li>Sequence associated annotation rows not associated
2382 when loaded from Jalview project</li>
2383 <li>Browser launch fails with NPE on java 1.7</li>
2384 <li>JABAWS alignment marked as finished when job was
2385 cancelled or job failed due to invalid input</li>
2386 <li>NPE with v2.7 example when clicking on Tree
2387 associated with all views</li>
2388 <li>Exceptions when copy/paste sequences with grouped
2389 annotation rows to new window</li>
2390 </ul> <em>Applet</em>
2392 <li>Sequence features are momentarily displayed before
2393 they are hidden using hidefeaturegroups applet parameter</li>
2394 <li>loading features via javascript API automatically
2395 enables feature display</li>
2396 <li>scrollToColumnIn javascript API method doesn't
2398 </ul> <em>General</em>
2400 <li>Redundancy removal fails for rna alignment</li>
2401 <li>PCA calculation fails when sequence has been selected
2402 and then deselected</li>
2403 <li>PCA window shows grey box when first opened on OSX</li>
2404 <li>Letters coloured pink in sequence logo when alignment
2405 coloured with clustalx</li>
2406 <li>Choosing fonts without letter symbols defined causes
2407 exceptions and redraw errors</li>
2408 <li>Initial PCA plot view is not same as manually
2409 reconfigured view</li>
2410 <li>Grouped annotation graph label has incorrect line
2412 <li>Grouped annotation graph label display is corrupted
2413 for lots of labels</li>
2418 <div align="center">
2419 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2422 <td><em>Application</em>
2424 <li>Jalview Desktop News Reader</li>
2425 <li>Tweaked default layout of web services menu</li>
2426 <li>View/alignment association menu to enable user to
2427 easily specify which alignment a multi-structure view takes
2428 its colours/correspondences from</li>
2429 <li>Allow properties file location to be specified as URL</li>
2430 <li>Extend Jalview project to preserve associations
2431 between many alignment views and a single Jmol display</li>
2432 <li>Store annotation row height in Jalview project file</li>
2433 <li>Annotation row column label formatting attributes
2434 stored in project file</li>
2435 <li>Annotation row order for auto-calculated annotation
2436 rows preserved in Jalview project file</li>
2437 <li>Visual progress indication when Jalview state is
2438 saved using Desktop window menu</li>
2439 <li>Visual indication that command line arguments are
2440 still being processed</li>
2441 <li>Groovy script execution from URL</li>
2442 <li>Colour by annotation default min and max colours in
2444 <li>Automatically associate PDB files dragged onto an
2445 alignment with sequences that have high similarity and
2447 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2448 <li>'view structures' option to open many
2449 structures in same window</li>
2450 <li>Sort associated views menu option for tree panel</li>
2451 <li>Group all JABA and non-JABA services for a particular
2452 analysis function in its own submenu</li>
2453 </ul> <em>Applet</em>
2455 <li>Userdefined and autogenerated annotation rows for
2457 <li>Adjustment of alignment annotation pane height</li>
2458 <li>Annotation scrollbar for annotation panel</li>
2459 <li>Drag to reorder annotation rows in annotation panel</li>
2460 <li>'automaticScrolling' parameter</li>
2461 <li>Allow sequences with partial ID string matches to be
2462 annotated from GFF/Jalview features files</li>
2463 <li>Sequence logo annotation row in applet</li>
2464 <li>Absolute paths relative to host server in applet
2465 parameters are treated as such</li>
2466 <li>New in the JalviewLite javascript API:
2468 <li>JalviewLite.js javascript library</li>
2469 <li>Javascript callbacks for
2471 <li>Applet initialisation</li>
2472 <li>Sequence/alignment mouse-overs and selections</li>
2475 <li>scrollTo row and column alignment scrolling
2477 <li>Select sequence/alignment regions from javascript</li>
2478 <li>javascript structure viewer harness to pass
2479 messages between Jmol and Jalview when running as
2480 distinct applets</li>
2481 <li>sortBy method</li>
2482 <li>Set of applet and application examples shipped
2483 with documentation</li>
2484 <li>New example to demonstrate JalviewLite and Jmol
2485 javascript message exchange</li>
2487 </ul> <em>General</em>
2489 <li>Enable Jmol displays to be associated with multiple
2490 multiple alignments</li>
2491 <li>Option to automatically sort alignment with new tree</li>
2492 <li>User configurable link to enable redirects to a
2493 www.Jalview.org mirror</li>
2494 <li>Jmol colours option for Jmol displays</li>
2495 <li>Configurable newline string when writing alignment
2496 and other flat files</li>
2497 <li>Allow alignment annotation description lines to
2498 contain html tags</li>
2499 </ul> <em>Documentation and Development</em>
2501 <li>Add groovy test harness for bulk load testing to
2503 <li>Groovy script to load and align a set of sequences
2504 using a web service before displaying the result in the
2505 Jalview desktop</li>
2506 <li>Restructured javascript and applet api documentation</li>
2507 <li>Ant target to publish example html files with applet
2509 <li>Netbeans project for building Jalview from source</li>
2510 <li>ant task to create online javadoc for Jalview source</li>
2512 <td><em>Application</em>
2514 <li>User defined colourscheme throws exception when
2515 current built in colourscheme is saved as new scheme</li>
2516 <li>AlignFrame->Save in application pops up save
2517 dialog for valid filename/format</li>
2518 <li>Cannot view associated structure for UniProt sequence</li>
2519 <li>PDB file association breaks for UniProt sequence
2521 <li>Associate PDB from file dialog does not tell you
2522 which sequence is to be associated with the file</li>
2523 <li>Find All raises null pointer exception when query
2524 only matches sequence IDs</li>
2525 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2526 <li>Jalview project with Jmol views created with Jalview
2527 2.4 cannot be loaded</li>
2528 <li>Filetype associations not installed for webstart
2530 <li>Two or more chains in a single PDB file associated
2531 with sequences in different alignments do not get coloured
2532 by their associated sequence</li>
2533 <li>Visibility status of autocalculated annotation row
2534 not preserved when project is loaded</li>
2535 <li>Annotation row height and visibility attributes not
2536 stored in Jalview project</li>
2537 <li>Tree bootstraps are not preserved when saved as a
2538 Jalview project</li>
2539 <li>Envision2 workflow tooltips are corrupted</li>
2540 <li>Enabling show group conservation also enables colour
2541 by conservation</li>
2542 <li>Duplicate group associated conservation or consensus
2543 created on new view</li>
2544 <li>Annotation scrollbar not displayed after 'show
2545 all hidden annotation rows' option selected</li>
2546 <li>Alignment quality not updated after alignment
2547 annotation row is hidden then shown</li>
2548 <li>Preserve colouring of structures coloured by
2549 sequences in pre Jalview 2.7 projects</li>
2550 <li>Web service job parameter dialog is not laid out
2552 <li>Web services menu not refreshed after 'reset
2553 services' button is pressed in preferences</li>
2554 <li>Annotation off by one in Jalview v2_3 example project</li>
2555 <li>Structures imported from file and saved in project
2556 get name like jalview_pdb1234.txt when reloaded</li>
2557 <li>Jalview does not always retrieve progress of a JABAWS
2558 job execution in full once it is complete</li>
2559 </ul> <em>Applet</em>
2561 <li>Alignment height set incorrectly when lots of
2562 annotation rows are displayed</li>
2563 <li>Relative URLs in feature HTML text not resolved to
2565 <li>View follows highlighting does not work for positions
2567 <li><= shown as = in tooltip</li>
2568 <li>Export features raises exception when no features
2570 <li>Separator string used for serialising lists of IDs
2571 for javascript api is modified when separator string
2572 provided as parameter</li>
2573 <li>Null pointer exception when selecting tree leaves for
2574 alignment with no existing selection</li>
2575 <li>Relative URLs for datasources assumed to be relative
2576 to applet's codebase</li>
2577 <li>Status bar not updated after finished searching and
2578 search wraps around to first result</li>
2579 <li>StructureSelectionManager instance shared between
2580 several Jalview applets causes race conditions and memory
2582 <li>Hover tooltip and mouseover of position on structure
2583 not sent from Jmol in applet</li>
2584 <li>Certain sequences of javascript method calls to
2585 applet API fatally hang browser</li>
2586 </ul> <em>General</em>
2588 <li>View follows structure mouseover scrolls beyond
2589 position with wrapped view and hidden regions</li>
2590 <li>Find sequence position moves to wrong residue
2591 with/without hidden columns</li>
2592 <li>Sequence length given in alignment properties window
2594 <li>InvalidNumberFormat exceptions thrown when trying to
2595 import PDB like structure files</li>
2596 <li>Positional search results are only highlighted
2597 between user-supplied sequence start/end bounds</li>
2598 <li>End attribute of sequence is not validated</li>
2599 <li>Find dialog only finds first sequence containing a
2600 given sequence position</li>
2601 <li>Sequence numbering not preserved in MSF alignment
2603 <li>Jalview PDB file reader does not extract sequence
2604 from nucleotide chains correctly</li>
2605 <li>Structure colours not updated when tree partition
2606 changed in alignment</li>
2607 <li>Sequence associated secondary structure not correctly
2608 parsed in interleaved stockholm</li>
2609 <li>Colour by annotation dialog does not restore current
2611 <li>Hiding (nearly) all sequences doesn't work
2613 <li>Sequences containing lowercase letters are not
2614 properly associated with their pdb files</li>
2615 </ul> <em>Documentation and Development</em>
2617 <li>schemas/JalviewWsParamSet.xsd corrupted by
2618 ApplyCopyright tool</li>
2623 <div align="center">
2624 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2627 <td><em>Application</em>
2629 <li>New warning dialog when the Jalview Desktop cannot
2630 contact web services</li>
2631 <li>JABA service parameters for a preset are shown in
2632 service job window</li>
2633 <li>JABA Service menu entries reworded</li>
2637 <li>Modeller PIR IO broken - cannot correctly import a
2638 pir file emitted by Jalview</li>
2639 <li>Existing feature settings transferred to new
2640 alignment view created from cut'n'paste</li>
2641 <li>Improved test for mixed amino/nucleotide chains when
2642 parsing PDB files</li>
2643 <li>Consensus and conservation annotation rows
2644 occasionally become blank for all new windows</li>
2645 <li>Exception raised when right clicking above sequences
2646 in wrapped view mode</li>
2647 </ul> <em>Application</em>
2649 <li>multiple multiply aligned structure views cause cpu
2650 usage to hit 100% and computer to hang</li>
2651 <li>Web Service parameter layout breaks for long user
2652 parameter names</li>
2653 <li>Jaba service discovery hangs desktop if Jaba server
2660 <div align="center">
2661 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2664 <td><em>Application</em>
2666 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2667 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2670 <li>Web Services preference tab</li>
2671 <li>Analysis parameters dialog box and user defined
2673 <li>Improved speed and layout of Envision2 service menu</li>
2674 <li>Superpose structures using associated sequence
2676 <li>Export coordinates and projection as CSV from PCA
2678 </ul> <em>Applet</em>
2680 <li>enable javascript: execution by the applet via the
2681 link out mechanism</li>
2682 </ul> <em>Other</em>
2684 <li>Updated the Jmol Jalview interface to work with Jmol
2686 <li>The Jalview Desktop and JalviewLite applet now
2687 require Java 1.5</li>
2688 <li>Allow Jalview feature colour specification for GFF
2689 sequence annotation files</li>
2690 <li>New 'colour by label' keword in Jalview feature file
2691 type colour specification</li>
2692 <li>New Jalview Desktop Groovy API method that allows a
2693 script to check if it being run in an interactive session or
2694 in a batch operation from the Jalview command line</li>
2698 <li>clustalx colourscheme colours Ds preferentially when
2699 both D+E are present in over 50% of the column</li>
2700 </ul> <em>Application</em>
2702 <li>typo in AlignmentFrame->View->Hide->all but
2703 selected Regions menu item</li>
2704 <li>sequence fetcher replaces ',' for ';' when the ',' is
2705 part of a valid accession ID</li>
2706 <li>fatal OOM if object retrieved by sequence fetcher
2707 runs out of memory</li>
2708 <li>unhandled Out of Memory Error when viewing pca
2709 analysis results</li>
2710 <li>InstallAnywhere builds fail to launch on OS X java
2711 10.5 update 4 (due to apple Java 1.6 update)</li>
2712 <li>Installanywhere Jalview silently fails to launch</li>
2713 </ul> <em>Applet</em>
2715 <li>Jalview.getFeatureGroups() raises an
2716 ArrayIndexOutOfBoundsException if no feature groups are
2723 <div align="center">
2724 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2730 <li>Alignment prettyprinter doesn't cope with long
2732 <li>clustalx colourscheme colours Ds preferentially when
2733 both D+E are present in over 50% of the column</li>
2734 <li>nucleic acid structures retrieved from PDB do not
2735 import correctly</li>
2736 <li>More columns get selected than were clicked on when a
2737 number of columns are hidden</li>
2738 <li>annotation label popup menu not providing correct
2739 add/hide/show options when rows are hidden or none are
2741 <li>Stockholm format shown in list of readable formats,
2742 and parser copes better with alignments from RFAM.</li>
2743 <li>CSV output of consensus only includes the percentage
2744 of all symbols if sequence logo display is enabled</li>
2746 </ul> <em>Applet</em>
2748 <li>annotation panel disappears when annotation is
2750 </ul> <em>Application</em>
2752 <li>Alignment view not redrawn properly when new
2753 alignment opened where annotation panel is visible but no
2754 annotations are present on alignment</li>
2755 <li>pasted region containing hidden columns is
2756 incorrectly displayed in new alignment window</li>
2757 <li>Jalview slow to complete operations when stdout is
2758 flooded (fix is to close the Jalview console)</li>
2759 <li>typo in AlignmentFrame->View->Hide->all but
2760 selected Rregions menu item.</li>
2761 <li>inconsistent group submenu and Format submenu entry
2762 'Un' or 'Non'conserved</li>
2763 <li>Sequence feature settings are being shared by
2764 multiple distinct alignments</li>
2765 <li>group annotation not recreated when tree partition is
2767 <li>double click on group annotation to select sequences
2768 does not propagate to associated trees</li>
2769 <li>Mac OSX specific issues:
2771 <li>exception raised when mouse clicked on desktop
2772 window background</li>
2773 <li>Desktop menu placed on menu bar and application
2774 name set correctly</li>
2775 <li>sequence feature settings not wide enough for the
2776 save feature colourscheme button</li>
2785 <div align="center">
2786 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2789 <td><em>New Capabilities</em>
2791 <li>URL links generated from description line for
2792 regular-expression based URL links (applet and application)
2794 <li>Non-positional feature URL links are shown in link
2796 <li>Linked viewing of nucleic acid sequences and
2798 <li>Automatic Scrolling option in View menu to display
2799 the currently highlighted region of an alignment.</li>
2800 <li>Order an alignment by sequence length, or using the
2801 average score or total feature count for each sequence.</li>
2802 <li>Shading features by score or associated description</li>
2803 <li>Subdivide alignment and groups based on identity of
2804 selected subsequence (Make Groups from Selection).</li>
2805 <li>New hide/show options including Shift+Control+H to
2806 hide everything but the currently selected region.</li>
2807 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2808 </ul> <em>Application</em>
2810 <li>Fetch DB References capabilities and UI expanded to
2811 support retrieval from DAS sequence sources</li>
2812 <li>Local DAS Sequence sources can be added via the
2813 command line or via the Add local source dialog box.</li>
2814 <li>DAS Dbref and DbxRef feature types are parsed as
2815 database references and protein_name is parsed as
2816 description line (BioSapiens terms).</li>
2817 <li>Enable or disable non-positional feature and database
2818 references in sequence ID tooltip from View menu in
2820 <!-- <li>New hidden columns and rows and representatives capabilities
2821 in annotations file (in progress - not yet fully implemented)</li> -->
2822 <li>Group-associated consensus, sequence logos and
2823 conservation plots</li>
2824 <li>Symbol distributions for each column can be exported
2825 and visualized as sequence logos</li>
2826 <li>Optionally scale multi-character column labels to fit
2827 within each column of annotation row<!-- todo for applet -->
2829 <li>Optional automatic sort of associated alignment view
2830 when a new tree is opened.</li>
2831 <li>Jalview Java Console</li>
2832 <li>Better placement of desktop window when moving
2833 between different screens.</li>
2834 <li>New preference items for sequence ID tooltip and
2835 consensus annotation</li>
2836 <li>Client to submit sequences and IDs to Envision2
2838 <li><em>Vamsas Capabilities</em>
2840 <li>Improved VAMSAS synchronization (Jalview archive
2841 used to preserve views, structures, and tree display
2843 <li>Import of vamsas documents from disk or URL via
2845 <li>Sharing of selected regions between views and
2846 with other VAMSAS applications (Experimental feature!)</li>
2847 <li>Updated API to VAMSAS version 0.2</li>
2849 </ul> <em>Applet</em>
2851 <li>Middle button resizes annotation row height</li>
2854 <li>sortByTree (true/false) - automatically sort the
2855 associated alignment view by the tree when a new tree is
2857 <li>showTreeBootstraps (true/false) - show or hide
2858 branch bootstraps (default is to show them if available)</li>
2859 <li>showTreeDistances (true/false) - show or hide
2860 branch lengths (default is to show them if available)</li>
2861 <li>showUnlinkedTreeNodes (true/false) - indicate if
2862 unassociated nodes should be highlighted in the tree
2864 <li>heightScale and widthScale (1.0 or more) -
2865 increase the height or width of a cell in the alignment
2866 grid relative to the current font size.</li>
2869 <li>Non-positional features displayed in sequence ID
2871 </ul> <em>Other</em>
2873 <li>Features format: graduated colour definitions and
2874 specification of feature scores</li>
2875 <li>Alignment Annotations format: new keywords for group
2876 associated annotation (GROUP_REF) and annotation row display
2877 properties (ROW_PROPERTIES)</li>
2878 <li>XML formats extended to support graduated feature
2879 colourschemes, group associated annotation, and profile
2880 visualization settings.</li></td>
2883 <li>Source field in GFF files parsed as feature source
2884 rather than description</li>
2885 <li>Non-positional features are now included in sequence
2886 feature and gff files (controlled via non-positional feature
2887 visibility in tooltip).</li>
2888 <li>URL links generated for all feature links (bugfix)</li>
2889 <li>Added URL embedding instructions to features file
2891 <li>Codons containing ambiguous nucleotides translated as
2892 'X' in peptide product</li>
2893 <li>Match case switch in find dialog box works for both
2894 sequence ID and sequence string and query strings do not
2895 have to be in upper case to match case-insensitively.</li>
2896 <li>AMSA files only contain first column of
2897 multi-character column annotation labels</li>
2898 <li>Jalview Annotation File generation/parsing consistent
2899 with documentation (e.g. Stockholm annotation can be
2900 exported and re-imported)</li>
2901 <li>PDB files without embedded PDB IDs given a friendly
2903 <li>Find incrementally searches ID string matches as well
2904 as subsequence matches, and correctly reports total number
2908 <li>Better handling of exceptions during sequence
2910 <li>Dasobert generated non-positional feature URL
2911 link text excludes the start_end suffix</li>
2912 <li>DAS feature and source retrieval buttons disabled
2913 when fetch or registry operations in progress.</li>
2914 <li>PDB files retrieved from URLs are cached properly</li>
2915 <li>Sequence description lines properly shared via
2917 <li>Sequence fetcher fetches multiple records for all
2919 <li>Ensured that command line das feature retrieval
2920 completes before alignment figures are generated.</li>
2921 <li>Reduced time taken when opening file browser for
2923 <li>isAligned check prior to calculating tree, PCA or
2924 submitting an MSA to JNet now excludes hidden sequences.</li>
2925 <li>User defined group colours properly recovered
2926 from Jalview projects.</li>
2935 <div align="center">
2936 <strong>2.4.0.b2</strong><br> 28/10/2009
2941 <li>Experimental support for google analytics usage
2943 <li>Jalview privacy settings (user preferences and docs).</li>
2948 <li>Race condition in applet preventing startup in
2950 <li>Exception when feature created from selection beyond
2951 length of sequence.</li>
2952 <li>Allow synthetic PDB files to be imported gracefully</li>
2953 <li>Sequence associated annotation rows associate with
2954 all sequences with a given id</li>
2955 <li>Find function matches case-insensitively for sequence
2956 ID string searches</li>
2957 <li>Non-standard characters do not cause pairwise
2958 alignment to fail with exception</li>
2959 </ul> <em>Application Issues</em>
2961 <li>Sequences are now validated against EMBL database</li>
2962 <li>Sequence fetcher fetches multiple records for all
2964 </ul> <em>InstallAnywhere Issues</em>
2966 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2967 issue with installAnywhere mechanism)</li>
2968 <li>Command line launching of JARs from InstallAnywhere
2969 version (java class versioning error fixed)</li>
2976 <div align="center">
2977 <strong>2.4</strong><br> 27/8/2008
2980 <td><em>User Interface</em>
2982 <li>Linked highlighting of codon and amino acid from
2983 translation and protein products</li>
2984 <li>Linked highlighting of structure associated with
2985 residue mapping to codon position</li>
2986 <li>Sequence Fetcher provides example accession numbers
2987 and 'clear' button</li>
2988 <li>MemoryMonitor added as an option under Desktop's
2990 <li>Extract score function to parse whitespace separated
2991 numeric data in description line</li>
2992 <li>Column labels in alignment annotation can be centred.</li>
2993 <li>Tooltip for sequence associated annotation give name
2995 </ul> <em>Web Services and URL fetching</em>
2997 <li>JPred3 web service</li>
2998 <li>Prototype sequence search client (no public services
3000 <li>Fetch either seed alignment or full alignment from
3002 <li>URL Links created for matching database cross
3003 references as well as sequence ID</li>
3004 <li>URL Links can be created using regular-expressions</li>
3005 </ul> <em>Sequence Database Connectivity</em>
3007 <li>Retrieval of cross-referenced sequences from other
3009 <li>Generalised database reference retrieval and
3010 validation to all fetchable databases</li>
3011 <li>Fetch sequences from DAS sources supporting the
3012 sequence command</li>
3013 </ul> <em>Import and Export</em>
3014 <li>export annotation rows as CSV for spreadsheet import</li>
3015 <li>Jalview projects record alignment dataset associations,
3016 EMBL products, and cDNA sequence mappings</li>
3017 <li>Sequence Group colour can be specified in Annotation
3019 <li>Ad-hoc colouring of group in Annotation File using RGB
3020 triplet as name of colourscheme</li>
3021 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3023 <li>treenode binding for VAMSAS tree exchange</li>
3024 <li>local editing and update of sequences in VAMSAS
3025 alignments (experimental)</li>
3026 <li>Create new or select existing session to join</li>
3027 <li>load and save of vamsas documents</li>
3028 </ul> <em>Application command line</em>
3030 <li>-tree parameter to open trees (introduced for passing
3032 <li>-fetchfrom command line argument to specify nicknames
3033 of DAS servers to query for alignment features</li>
3034 <li>-dasserver command line argument to add new servers
3035 that are also automatically queried for features</li>
3036 <li>-groovy command line argument executes a given groovy
3037 script after all input data has been loaded and parsed</li>
3038 </ul> <em>Applet-Application data exchange</em>
3040 <li>Trees passed as applet parameters can be passed to
3041 application (when using "View in full
3042 application")</li>
3043 </ul> <em>Applet Parameters</em>
3045 <li>feature group display control parameter</li>
3046 <li>debug parameter</li>
3047 <li>showbutton parameter</li>
3048 </ul> <em>Applet API methods</em>
3050 <li>newView public method</li>
3051 <li>Window (current view) specific get/set public methods</li>
3052 <li>Feature display control methods</li>
3053 <li>get list of currently selected sequences</li>
3054 </ul> <em>New Jalview distribution features</em>
3056 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3057 <li>RELEASE file gives build properties for the latest
3058 Jalview release.</li>
3059 <li>Java 1.1 Applet build made easier and donotobfuscate
3060 property controls execution of obfuscator</li>
3061 <li>Build target for generating source distribution</li>
3062 <li>Debug flag for javacc</li>
3063 <li>.jalview_properties file is documented (slightly) in
3064 jalview.bin.Cache</li>
3065 <li>Continuous Build Integration for stable and
3066 development version of Application, Applet and source
3071 <li>selected region output includes visible annotations
3072 (for certain formats)</li>
3073 <li>edit label/displaychar contains existing label/char
3075 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3076 <li>shorter peptide product names from EMBL records</li>
3077 <li>Newick string generator makes compact representations</li>
3078 <li>bootstrap values parsed correctly for tree files with
3080 <li>pathological filechooser bug avoided by not allowing
3081 filenames containing a ':'</li>
3082 <li>Fixed exception when parsing GFF files containing
3083 global sequence features</li>
3084 <li>Alignment datasets are finalized only when number of
3085 references from alignment sequences goes to zero</li>
3086 <li>Close of tree branch colour box without colour
3087 selection causes cascading exceptions</li>
3088 <li>occasional negative imgwidth exceptions</li>
3089 <li>better reporting of non-fatal warnings to user when
3090 file parsing fails.</li>
3091 <li>Save works when Jalview project is default format</li>
3092 <li>Save as dialog opened if current alignment format is
3093 not a valid output format</li>
3094 <li>UniProt canonical names introduced for both das and
3096 <li>Histidine should be midblue (not pink!) in Zappo</li>
3097 <li>error messages passed up and output when data read
3099 <li>edit undo recovers previous dataset sequence when
3100 sequence is edited</li>
3101 <li>allow PDB files without pdb ID HEADER lines (like
3102 those generated by MODELLER) to be read in properly</li>
3103 <li>allow reading of JPred concise files as a normal
3105 <li>Stockholm annotation parsing and alignment properties
3106 import fixed for PFAM records</li>
3107 <li>Structure view windows have correct name in Desktop
3109 <li>annotation consisting of sequence associated scores
3110 can be read and written correctly to annotation file</li>
3111 <li>Aligned cDNA translation to aligned peptide works
3113 <li>Fixed display of hidden sequence markers and
3114 non-italic font for representatives in Applet</li>
3115 <li>Applet Menus are always embedded in applet window on
3117 <li>Newly shown features appear at top of stack (in
3119 <li>Annotations added via parameter not drawn properly
3120 due to null pointer exceptions</li>
3121 <li>Secondary structure lines are drawn starting from
3122 first column of alignment</li>
3123 <li>UniProt XML import updated for new schema release in
3125 <li>Sequence feature to sequence ID match for Features
3126 file is case-insensitive</li>
3127 <li>Sequence features read from Features file appended to
3128 all sequences with matching IDs</li>
3129 <li>PDB structure coloured correctly for associated views
3130 containing a sub-sequence</li>
3131 <li>PDB files can be retrieved by applet from Jar files</li>
3132 <li>feature and annotation file applet parameters
3133 referring to different directories are retrieved correctly</li>
3134 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3135 <li>Fixed application hang whilst waiting for
3136 splash-screen version check to complete</li>
3137 <li>Applet properly URLencodes input parameter values
3138 when passing them to the launchApp service</li>
3139 <li>display name and local features preserved in results
3140 retrieved from web service</li>
3141 <li>Visual delay indication for sequence retrieval and
3142 sequence fetcher initialisation</li>
3143 <li>updated Application to use DAS 1.53e version of
3144 dasobert DAS client</li>
3145 <li>Re-instated Full AMSA support and .amsa file
3147 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3155 <div align="center">
3156 <strong>2.3</strong><br> 9/5/07
3161 <li>Jmol 11.0.2 integration</li>
3162 <li>PDB views stored in Jalview XML files</li>
3163 <li>Slide sequences</li>
3164 <li>Edit sequence in place</li>
3165 <li>EMBL CDS features</li>
3166 <li>DAS Feature mapping</li>
3167 <li>Feature ordering</li>
3168 <li>Alignment Properties</li>
3169 <li>Annotation Scores</li>
3170 <li>Sort by scores</li>
3171 <li>Feature/annotation editing in applet</li>
3176 <li>Headless state operation in 2.2.1</li>
3177 <li>Incorrect and unstable DNA pairwise alignment</li>
3178 <li>Cut and paste of sequences with annotation</li>
3179 <li>Feature group display state in XML</li>
3180 <li>Feature ordering in XML</li>
3181 <li>blc file iteration selection using filename # suffix</li>
3182 <li>Stockholm alignment properties</li>
3183 <li>Stockhom alignment secondary structure annotation</li>
3184 <li>2.2.1 applet had no feature transparency</li>
3185 <li>Number pad keys can be used in cursor mode</li>
3186 <li>Structure Viewer mirror image resolved</li>
3193 <div align="center">
3194 <strong>2.2.1</strong><br> 12/2/07
3199 <li>Non standard characters can be read and displayed
3200 <li>Annotations/Features can be imported/exported to the
3202 <li>Applet allows editing of sequence/annotation/group
3203 name & description
3204 <li>Preference setting to display sequence name in
3206 <li>Annotation file format extended to allow
3207 Sequence_groups to be defined
3208 <li>Default opening of alignment overview panel can be
3209 specified in preferences
3210 <li>PDB residue numbering annotation added to associated
3216 <li>Applet crash under certain Linux OS with Java 1.6
3218 <li>Annotation file export / import bugs fixed
3219 <li>PNG / EPS image output bugs fixed
3225 <div align="center">
3226 <strong>2.2</strong><br> 27/11/06
3231 <li>Multiple views on alignment
3232 <li>Sequence feature editing
3233 <li>"Reload" alignment
3234 <li>"Save" to current filename
3235 <li>Background dependent text colour
3236 <li>Right align sequence ids
3237 <li>User-defined lower case residue colours
3240 <li>Menu item accelerator keys
3241 <li>Control-V pastes to current alignment
3242 <li>Cancel button for DAS Feature Fetching
3243 <li>PCA and PDB Viewers zoom via mouse roller
3244 <li>User-defined sub-tree colours and sub-tree selection
3246 <li>'New Window' button on the 'Output to Text box'
3251 <li>New memory efficient Undo/Redo System
3252 <li>Optimised symbol lookups and conservation/consensus
3254 <li>Region Conservation/Consensus recalculated after
3256 <li>Fixed Remove Empty Columns Bug (empty columns at end
3258 <li>Slowed DAS Feature Fetching for increased robustness.
3260 <li>Made angle brackets in ASCII feature descriptions
3262 <li>Re-instated Zoom function for PCA
3263 <li>Sequence descriptions conserved in web service
3265 <li>UniProt ID discoverer uses any word separated by
3267 <li>WsDbFetch query/result association resolved
3268 <li>Tree leaf to sequence mapping improved
3269 <li>Smooth fonts switch moved to FontChooser dialog box.
3276 <div align="center">
3277 <strong>2.1.1</strong><br> 12/9/06
3282 <li>Copy consensus sequence to clipboard</li>
3287 <li>Image output - rightmost residues are rendered if
3288 sequence id panel has been resized</li>
3289 <li>Image output - all offscreen group boundaries are
3291 <li>Annotation files with sequence references - all
3292 elements in file are relative to sequence position</li>
3293 <li>Mac Applet users can use Alt key for group editing</li>
3299 <div align="center">
3300 <strong>2.1</strong><br> 22/8/06
3305 <li>MAFFT Multiple Alignment in default Web Service list</li>
3306 <li>DAS Feature fetching</li>
3307 <li>Hide sequences and columns</li>
3308 <li>Export Annotations and Features</li>
3309 <li>GFF file reading / writing</li>
3310 <li>Associate structures with sequences from local PDB
3312 <li>Add sequences to exisiting alignment</li>
3313 <li>Recently opened files / URL lists</li>
3314 <li>Applet can launch the full application</li>
3315 <li>Applet has transparency for features (Java 1.2
3317 <li>Applet has user defined colours parameter</li>
3318 <li>Applet can load sequences from parameter
3319 "sequence<em>x</em>"
3325 <li>Redundancy Panel reinstalled in the Applet</li>
3326 <li>Monospaced font - EPS / rescaling bug fixed</li>
3327 <li>Annotation files with sequence references bug fixed</li>
3333 <div align="center">
3334 <strong>2.08.1</strong><br> 2/5/06
3339 <li>Change case of selected region from Popup menu</li>
3340 <li>Choose to match case when searching</li>
3341 <li>Middle mouse button and mouse movement can compress /
3342 expand the visible width and height of the alignment</li>
3347 <li>Annotation Panel displays complete JNet results</li>
3353 <div align="center">
3354 <strong>2.08b</strong><br> 18/4/06
3360 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3361 <li>Righthand label on wrapped alignments shows correct
3368 <div align="center">
3369 <strong>2.08</strong><br> 10/4/06
3374 <li>Editing can be locked to the selection area</li>
3375 <li>Keyboard editing</li>
3376 <li>Create sequence features from searches</li>
3377 <li>Precalculated annotations can be loaded onto
3379 <li>Features file allows grouping of features</li>
3380 <li>Annotation Colouring scheme added</li>
3381 <li>Smooth fonts off by default - Faster rendering</li>
3382 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3387 <li>Drag & Drop fixed on Linux</li>
3388 <li>Jalview Archive file faster to load/save, sequence
3389 descriptions saved.</li>
3395 <div align="center">
3396 <strong>2.07</strong><br> 12/12/05
3401 <li>PDB Structure Viewer enhanced</li>
3402 <li>Sequence Feature retrieval and display enhanced</li>
3403 <li>Choose to output sequence start-end after sequence
3404 name for file output</li>
3405 <li>Sequence Fetcher WSDBFetch@EBI</li>
3406 <li>Applet can read feature files, PDB files and can be
3407 used for HTML form input</li>
3412 <li>HTML output writes groups and features</li>
3413 <li>Group editing is Control and mouse click</li>
3414 <li>File IO bugs</li>
3420 <div align="center">
3421 <strong>2.06</strong><br> 28/9/05
3426 <li>View annotations in wrapped mode</li>
3427 <li>More options for PCA viewer</li>
3432 <li>GUI bugs resolved</li>
3433 <li>Runs with -nodisplay from command line</li>
3439 <div align="center">
3440 <strong>2.05b</strong><br> 15/9/05
3445 <li>Choose EPS export as lineart or text</li>
3446 <li>Jar files are executable</li>
3447 <li>Can read in Uracil - maps to unknown residue</li>
3452 <li>Known OutOfMemory errors give warning message</li>
3453 <li>Overview window calculated more efficiently</li>
3454 <li>Several GUI bugs resolved</li>
3460 <div align="center">
3461 <strong>2.05</strong><br> 30/8/05
3466 <li>Edit and annotate in "Wrapped" view</li>
3471 <li>Several GUI bugs resolved</li>
3477 <div align="center">
3478 <strong>2.04</strong><br> 24/8/05
3483 <li>Hold down mouse wheel & scroll to change font
3489 <li>Improved JPred client reliability</li>
3490 <li>Improved loading of Jalview files</li>
3496 <div align="center">
3497 <strong>2.03</strong><br> 18/8/05
3502 <li>Set Proxy server name and port in preferences</li>
3503 <li>Multiple URL links from sequence ids</li>
3504 <li>User Defined Colours can have a scheme name and added
3506 <li>Choose to ignore gaps in consensus calculation</li>
3507 <li>Unix users can set default web browser</li>
3508 <li>Runs without GUI for batch processing</li>
3509 <li>Dynamically generated Web Service Menus</li>
3514 <li>InstallAnywhere download for Sparc Solaris</li>
3520 <div align="center">
3521 <strong>2.02</strong><br> 18/7/05
3527 <li>Copy & Paste order of sequences maintains
3528 alignment order.</li>
3534 <div align="center">
3535 <strong>2.01</strong><br> 12/7/05
3540 <li>Use delete key for deleting selection.</li>
3541 <li>Use Mouse wheel to scroll sequences.</li>
3542 <li>Help file updated to describe how to add alignment
3544 <li>Version and build date written to build properties
3546 <li>InstallAnywhere installation will check for updates
3547 at launch of Jalview.</li>
3552 <li>Delete gaps bug fixed.</li>
3553 <li>FileChooser sorts columns.</li>
3554 <li>Can remove groups one by one.</li>
3555 <li>Filechooser icons installed.</li>
3556 <li>Finder ignores return character when searching.
3557 Return key will initiate a search.<br>
3564 <div align="center">
3565 <strong>2.0</strong><br> 20/6/05
3570 <li>New codebase</li>