3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
34 /* separate the items from eachother */
41 /* doesnt get processed in javahelp */
50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.3">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>
99 <td><div align="left">
102 <li><!-- JAL-2643 -->Pressing tab after updating the colour threshold text field doesn't trigger an update to the alignment view</li>
103 <li><!-- JAL-2682 -->Race condition when parsing sequence ID strings in parallel</li>
104 <li><!-- JAL-2608 -->Overview windows are also closed when alignment window is closed</li>
108 <li><!-- JAL-2777 -->Structures with whitespace chainCode cannot be viewed in Chimera</li>
109 <li><!-- JAL-2728 -->Protein annotation panel too high in CDS/Protein view
111 <li><!-- JAL-2757 -->Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs
113 <li><!-- JAL-2253 -->Slow EnsemblGenome ID lookup</li>
114 <li><!-- JAL-2739 -->Hidden column marker in last column not rendered when switching back from Wrapped to normal view</li>
115 <li><!-- JAL-2768 -->Annotation display corrupted when scrolling right in unwapped alignment view</li>
116 <li><!-- JAL-2542 -->Existing features on subsequence incorrectly relocated when full sequence retrieved from database</li>
117 <li><!-- JAL-2733 -->Last reported memory still shown when Desktop->Show Memory is unticked (OSX only)</li>
118 <li><!-- JAL-2658 -->Amend Features dialog doesn't allow features of same type and group to be selected for amending</li>
119 <li><!-- JAL-2524 -->Jalview becomes sluggish in wide alignments when hidden columns are present</li>
120 <li><!-- JAL-2392 -->Jalview freezes when loading and displaying several structures</li>
121 <li><!-- JAL-2732 -->Black outlines left after resizing or moving a window</li>
122 <li><!-- JAL-1900,JAL-1625 -->Unable to minimise windows within the Jalview desktop on OSX</li>
124 <strong><em>Applet</em></strong><br/>
126 <li><!-- JAL-2687 -->Concurrent modification exception when closing alignment panel</li>
131 <td width="60" nowrap>
133 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
134 <em>2/10/2017</em></strong>
137 <td><div align="left">
138 <em>New features in Jalview Desktop</em>
141 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
143 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
147 <td><div align="left">
151 <td width="60" nowrap>
153 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
154 <em>7/9/2017</em></strong>
157 <td><div align="left">
161 <!-- JAL-2588 -->Show gaps in overview window by colouring
162 in grey (sequences used to be coloured grey, and gaps were
166 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
170 <!-- JAL-2587 -->Overview updates immediately on increase
171 in size and progress bar shown as higher resolution
172 overview is recalculated
177 <td><div align="left">
181 <!-- JAL-2664 -->Overview window redraws every hidden
182 column region row by row
185 <!-- JAL-2681 -->duplicate protein sequences shown after
186 retrieving Ensembl crossrefs for sequences from Uniprot
189 <!-- JAL-2603 -->Overview window throws NPE if show boxes
190 format setting is unticked
193 <!-- JAL-2610 -->Groups are coloured wrongly in overview
194 if group has show boxes format setting unticked
197 <!-- JAL-2672,JAL-2665 -->Redraw problems when
198 autoscrolling whilst dragging current selection group to
199 include sequences and columns not currently displayed
202 <!-- JAL-2691 -->Not all chains are mapped when multimeric
203 assemblies are imported via CIF file
206 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
207 displayed when threshold or conservation colouring is also
211 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
215 <!-- JAL-2673 -->Jalview continues to scroll after
216 dragging a selected region off the visible region of the
220 <!-- JAL-2724 -->Cannot apply annotation based
221 colourscheme to all groups in a view
224 <!-- JAL-2511 -->IDs don't line up with sequences
225 initially after font size change using the Font chooser or
232 <td width="60" nowrap>
234 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
237 <td><div align="left">
238 <em>Calculations</em>
242 <!-- JAL-1933 -->Occupancy annotation row shows number of
243 ungapped positions in each column of the alignment.
246 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
247 a calculation dialog box
250 <!-- JAL-2379 -->Revised implementation of PCA for speed
251 and memory efficiency (~30x faster)
254 <!-- JAL-2403 -->Revised implementation of sequence
255 similarity scores as used by Tree, PCA, Shading Consensus
256 and other calculations
259 <!-- JAL-2416 -->Score matrices are stored as resource
260 files within the Jalview codebase
263 <!-- JAL-2500 -->Trees computed on Sequence Feature
264 Similarity may have different topology due to increased
271 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
272 model for alignments and groups
275 <!-- JAL-384 -->Custom shading schemes created via groovy
282 <!-- JAL-2526 -->Efficiency improvements for interacting
283 with alignment and overview windows
286 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
290 <!-- JAL-2388 -->Hidden columns and sequences can be
294 <!-- JAL-2611 -->Click-drag in visible area allows fine
295 adjustment of visible position
299 <em>Data import/export</em>
302 <!-- JAL-2535 -->Posterior probability annotation from
303 Stockholm files imported as sequence associated annotation
306 <!-- JAL-2507 -->More robust per-sequence positional
307 annotation input/output via stockholm flatfile
310 <!-- JAL-2533 -->Sequence names don't include file
311 extension when importing structure files without embedded
312 names or PDB accessions
315 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
316 format sequence substitution matrices
319 <em>User Interface</em>
322 <!-- JAL-2447 --> Experimental Features Checkbox in
323 Desktop's Tools menu to hide or show untested features in
327 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
328 via Overview or sequence motif search operations
331 <!-- JAL-2547 -->Amend sequence features dialog box can be
332 opened by double clicking gaps within sequence feature
336 <!-- JAL-1476 -->Status bar message shown when not enough
337 aligned positions were available to create a 3D structure
341 <em>3D Structure</em>
344 <!-- JAL-2430 -->Hidden regions in alignment views are not
345 coloured in linked structure views
348 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
349 file-based command exchange
352 <!-- JAL-2375 -->Structure chooser automatically shows
353 Cached Structures rather than querying the PDBe if
354 structures are already available for sequences
357 <!-- JAL-2520 -->Structures imported via URL are cached in
358 the Jalview project rather than downloaded again when the
362 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
363 to transfer Chimera's structure attributes as Jalview
364 features, and vice-versa (<strong>Experimental
368 <em>Web Services</em>
371 <!-- JAL-2549 -->Updated JABAWS client to v2.2
374 <!-- JAL-2335 -->Filter non-standard amino acids and
375 nucleotides when submitting to AACon and other MSA
379 <!-- JAL-2316, -->URLs for viewing database
380 cross-references provided by identifiers.org and the
388 <!-- JAL-2344 -->FileFormatI interface for describing and
389 identifying file formats (instead of String constants)
392 <!-- JAL-2228 -->FeatureCounter script refactored for
393 efficiency when counting all displayed features (not
394 backwards compatible with 2.10.1)
397 <em>Example files</em>
400 <!-- JAL-2631 -->Graduated feature colour style example
401 included in the example feature file
404 <em>Documentation</em>
407 <!-- JAL-2339 -->Release notes reformatted for readability
408 with the built-in Java help viewer
411 <!-- JAL-1644 -->Find documentation updated with 'search
412 sequence description' option
418 <!-- JAL-2485, -->External service integration tests for
419 Uniprot REST Free Text Search Client
422 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
425 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
430 <td><div align="left">
431 <em>Calculations</em>
434 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
435 matrix - C->R should be '-3'<br />Old matrix restored
436 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
438 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
439 Jalview's treatment of gaps in PCA and substitution matrix
440 based Tree calculations.<br /> <br />In earlier versions
441 of Jalview, gaps matching gaps were penalised, and gaps
442 matching non-gaps penalised even more. In the PCA
443 calculation, gaps were actually treated as non-gaps - so
444 different costs were applied, which meant Jalview's PCAs
445 were different to those produced by SeqSpace.<br />Jalview
446 now treats gaps in the same way as SeqSpace (ie it scores
447 them as 0). <br /> <br />Enter the following in the
448 Groovy console to restore pre-2.10.2 behaviour:<br />
449 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
450 // for 2.10.1 mode <br />
451 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
452 // to restore 2.10.2 mode <br /> <br /> <em>Note:
453 these settings will affect all subsequent tree and PCA
454 calculations (not recommended)</em></li>
456 <!-- JAL-2424 -->Fixed off-by-one bug that affected
457 scaling of branch lengths for trees computed using
458 Sequence Feature Similarity.
461 <!-- JAL-2377 -->PCA calculation could hang when
462 generating output report when working with highly
466 <!-- JAL-2544 --> Sort by features includes features to
467 right of selected region when gaps present on right-hand
471 <em>User Interface</em>
474 <!-- JAL-2346 -->Reopening Colour by annotation dialog
475 doesn't reselect a specific sequence's associated
476 annotation after it was used for colouring a view
479 <!-- JAL-2419 -->Current selection lost if popup menu
480 opened on a region of alignment without groups
483 <!-- JAL-2374 -->Popup menu not always shown for regions
484 of an alignment with overlapping groups
487 <!-- JAL-2310 -->Finder double counts if both a sequence's
488 name and description match
491 <!-- JAL-2370 -->Hiding column selection containing two
492 hidden regions results in incorrect hidden regions
495 <!-- JAL-2386 -->'Apply to all groups' setting when
496 changing colour does not apply Conservation slider value
500 <!-- JAL-2373 -->Percentage identity and conservation menu
501 items do not show a tick or allow shading to be disabled
504 <!-- JAL-2385 -->Conservation shading or PID threshold
505 lost when base colourscheme changed if slider not visible
508 <!-- JAL-2547 -->Sequence features shown in tooltip for
509 gaps before start of features
512 <!-- JAL-2623 -->Graduated feature colour threshold not
513 restored to UI when feature colour is edited
516 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
517 a time when scrolling vertically in wrapped mode.
520 <!-- JAL-2630 -->Structure and alignment overview update
521 as graduate feature colour settings are modified via the
525 <!-- JAL-2034 -->Overview window doesn't always update
526 when a group defined on the alignment is resized
529 <!-- JAL-2605 -->Mouseovers on left/right scale region in
530 wrapped view result in positional status updates
534 <!-- JAL-2563 -->Status bar doesn't show position for
535 ambiguous amino acid and nucleotide symbols
538 <!-- JAL-2602 -->Copy consensus sequence failed if
539 alignment included gapped columns
542 <!-- JAL-2473 -->Minimum size set for Jalview windows so
543 widgets don't permanently disappear
546 <!-- JAL-2503 -->Cannot select or filter quantitative
547 annotation that are shown only as column labels (e.g.
548 T-Coffee column reliability scores)
551 <!-- JAL-2594 -->Exception thrown if trying to create a
552 sequence feature on gaps only
555 <!-- JAL-2504 -->Features created with 'New feature'
556 button from a Find inherit previously defined feature type
557 rather than the Find query string
560 <!-- JAL-2423 -->incorrect title in output window when
561 exporting tree calculated in Jalview
564 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
565 and then revealing them reorders sequences on the
569 <!-- JAL-964 -->Group panel in sequence feature settings
570 doesn't update to reflect available set of groups after
571 interactively adding or modifying features
574 <!-- JAL-2225 -->Sequence Database chooser unusable on
578 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
579 only excluded gaps in current sequence and ignored
586 <!-- JAL-2421 -->Overview window visible region moves
587 erratically when hidden rows or columns are present
590 <!-- JAL-2362 -->Per-residue colourschemes applied via the
591 Structure Viewer's colour menu don't correspond to
595 <!-- JAL-2405 -->Protein specific colours only offered in
596 colour and group colour menu for protein alignments
599 <!-- JAL-2385 -->Colour threshold slider doesn't update to
600 reflect currently selected view or group's shading
604 <!-- JAL-2624 -->Feature colour thresholds not respected
605 when rendered on overview and structures when opacity at
609 <!-- JAL-2589 -->User defined gap colour not shown in
610 overview when features overlaid on alignment
613 <em>Data import/export</em>
616 <!-- JAL-2576 -->Very large alignments take a long time to
620 <!-- JAL-2507 -->Per-sequence RNA secondary structures
621 added after a sequence was imported are not written to
625 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
626 when importing RNA secondary structure via Stockholm
629 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
630 not shown in correct direction for simple pseudoknots
633 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
634 with lightGray or darkGray via features file (but can
638 <!-- JAL-2383 -->Above PID colour threshold not recovered
639 when alignment view imported from project
642 <!-- JAL-2520,JAL-2465 -->No mappings generated between
643 structure and sequences extracted from structure files
644 imported via URL and viewed in Jmol
647 <!-- JAL-2520 -->Structures loaded via URL are saved in
648 Jalview Projects rather than fetched via URL again when
649 the project is loaded and the structure viewed
652 <em>Web Services</em>
655 <!-- JAL-2519 -->EnsemblGenomes example failing after
656 release of Ensembl v.88
659 <!-- JAL-2366 -->Proxy server address and port always
660 appear enabled in Preferences->Connections
663 <!-- JAL-2461 -->DAS registry not found exceptions
664 removed from console output
667 <!-- JAL-2582 -->Cannot retrieve protein products from
668 Ensembl by Peptide ID
671 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
672 created from SIFTs, and spurious 'Couldn't open structure
673 in Chimera' errors raised after April 2017 update (problem
674 due to 'null' string rather than empty string used for
675 residues with no corresponding PDB mapping).
678 <em>Application UI</em>
681 <!-- JAL-2361 -->User Defined Colours not added to Colour
685 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
686 case' residues (button in colourscheme editor debugged and
687 new documentation and tooltips added)
690 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
691 doesn't restore group-specific text colour thresholds
694 <!-- JAL-2243 -->Feature settings panel does not update as
695 new features are added to alignment
698 <!-- JAL-2532 -->Cancel in feature settings reverts
699 changes to feature colours via the Amend features dialog
702 <!-- JAL-2506 -->Null pointer exception when attempting to
703 edit graduated feature colour via amend features dialog
707 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
708 selection menu changes colours of alignment views
711 <!-- JAL-2426 -->Spurious exceptions in console raised
712 from alignment calculation workers after alignment has
716 <!-- JAL-1608 -->Typo in selection popup menu - Create
717 groups now 'Create Group'
720 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
721 Create/Undefine group doesn't always work
724 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
725 shown again after pressing 'Cancel'
728 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
729 adjusts start position in wrap mode
732 <!-- JAL-2563 -->Status bar doesn't show positions for
733 ambiguous amino acids
736 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
737 CDS/Protein view after CDS sequences added for aligned
741 <!-- JAL-2592 -->User defined colourschemes called 'User
742 Defined' don't appear in Colours menu
748 <!-- JAL-2468 -->Switching between Nucleotide and Protein
749 score models doesn't always result in an updated PCA plot
752 <!-- JAL-2442 -->Features not rendered as transparent on
753 overview or linked structure view
756 <!-- JAL-2372 -->Colour group by conservation doesn't
760 <!-- JAL-2517 -->Hitting Cancel after applying
761 user-defined colourscheme doesn't restore original
768 <!-- JAL-2314 -->Unit test failure:
769 jalview.ws.jabaws.RNAStructExportImport setup fails
772 <!-- JAL-2307 -->Unit test failure:
773 jalview.ws.sifts.SiftsClientTest due to compatibility
774 problems with deep array comparison equality asserts in
775 successive versions of TestNG
778 <!-- JAL-2479 -->Relocated StructureChooserTest and
779 ParameterUtilsTest Unit tests to Network suite
782 <em>New Known Issues</em>
785 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
786 phase after a sequence motif find operation
789 <!-- JAL-2550 -->Importing annotation file with rows
790 containing just upper and lower case letters are
791 interpreted as WUSS RNA secondary structure symbols
794 <!-- JAL-2590 -->Cannot load and display Newick trees
795 reliably from eggnog Ortholog database
798 <!-- JAL-2468 -->Status bar shows 'Marked x columns
799 containing features of type Highlight' when 'B' is pressed
800 to mark columns containing highlighted regions.
803 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
804 doesn't always add secondary structure annotation.
809 <td width="60" nowrap>
811 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
814 <td><div align="left">
818 <!-- JAL-98 -->Improved memory usage: sparse arrays used
819 for all consensus calculations
822 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
825 <li>Updated Jalview's Certum code signing certificate
831 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
832 set of database cross-references, sorted alphabetically
835 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
836 from database cross references. Users with custom links
837 will receive a <a href="webServices/urllinks.html#warning">warning
838 dialog</a> asking them to update their preferences.
841 <!-- JAL-2287-->Cancel button and escape listener on
842 dialog warning user about disconnecting Jalview from a
846 <!-- JAL-2320-->Jalview's Chimera control window closes if
847 the Chimera it is connected to is shut down
850 <!-- JAL-1738-->New keystroke (B) and Select highlighted
851 columns menu item to mark columns containing highlighted
852 regions (e.g. from structure selections or results of a
856 <!-- JAL-2284-->Command line option for batch-generation
857 of HTML pages rendering alignment data with the BioJS
867 <!-- JAL-2286 -->Columns with more than one modal residue
868 are not coloured or thresholded according to percent
869 identity (first observed in Jalview 2.8.2)
872 <!-- JAL-2301 -->Threonine incorrectly reported as not
876 <!-- JAL-2318 -->Updates to documentation pages (above PID
877 threshold, amino acid properties)
880 <!-- JAL-2292 -->Lower case residues in sequences are not
881 reported as mapped to residues in a structure file in the
885 <!--JAL-2324 -->Identical features with non-numeric scores
886 could be added multiple times to a sequence
889 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
890 bond features shown as two highlighted residues rather
891 than a range in linked structure views, and treated
892 correctly when selecting and computing trees from features
895 <!-- JAL-2281-->Custom URL links for database
896 cross-references are matched to database name regardless
904 <!-- JAL-2282-->Custom URL links for specific database
905 names without regular expressions also offer links from
909 <!-- JAL-2315-->Removing a single configured link in the
910 URL links pane in Connections preferences doesn't actually
911 update Jalview configuration
914 <!-- JAL-2272-->CTRL-Click on a selected region to open
915 the alignment area popup menu doesn't work on El-Capitan
918 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
919 files with similarly named sequences if dropped onto the
923 <!-- JAL-2312 -->Additional mappings are shown for PDB
924 entries where more chains exist in the PDB accession than
925 are reported in the SIFTS file
928 <!-- JAL-2317-->Certain structures do not get mapped to
929 the structure view when displayed with Chimera
932 <!-- JAL-2317-->No chains shown in the Chimera view
933 panel's View->Show Chains submenu
936 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
937 work for wrapped alignment views
940 <!--JAL-2197 -->Rename UI components for running JPred
941 predictions from 'JNet' to 'JPred'
944 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
945 corrupted when annotation panel vertical scroll is not at
949 <!--JAL-2332 -->Attempting to view structure for Hen
950 lysozyme results in a PDB Client error dialog box
953 <!-- JAL-2319 -->Structure View's mapping report switched
954 ranges for PDB and sequence for SIFTS
957 SIFTS 'Not_Observed' residues mapped to non-existant
961 <!-- <em>New Known Issues</em>
968 <td width="60" nowrap>
970 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
971 <em>25/10/2016</em></strong>
974 <td><em>Application</em>
976 <li>3D Structure chooser opens with 'Cached structures'
977 view if structures already loaded</li>
978 <li>Progress bar reports models as they are loaded to
985 <li>Colour by conservation always enabled and no tick
986 shown in menu when BLOSUM or PID shading applied</li>
987 <li>FER1_ARATH and FER2_ARATH labels were switched in
988 example sequences/projects/trees</li>
992 <li>Jalview projects with views of local PDB structure
993 files saved on Windows cannot be opened on OSX</li>
994 <li>Multiple structure views can be opened and superposed
995 without timeout for structures with multiple models or
996 multiple sequences in alignment</li>
997 <li>Cannot import or associated local PDB files without a
998 PDB ID HEADER line</li>
999 <li>RMSD is not output in Jmol console when superposition
1001 <li>Drag and drop of URL from Browser fails for Linux and
1002 OSX versions earlier than El Capitan</li>
1003 <li>ENA client ignores invalid content from ENA server</li>
1004 <li>Exceptions are not raised in console when ENA client
1005 attempts to fetch non-existent IDs via Fetch DB Refs UI
1007 <li>Exceptions are not raised in console when a new view
1008 is created on the alignment</li>
1009 <li>OSX right-click fixed for group selections: CMD-click
1010 to insert/remove gaps in groups and CTRL-click to open group
1013 <em>Build and deployment</em>
1015 <li>URL link checker now copes with multi-line anchor
1018 <em>New Known Issues</em>
1020 <li>Drag and drop from URL links in browsers do not work
1027 <td width="60" nowrap>
1028 <div align="center">
1029 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1032 <td><em>General</em>
1035 <!-- JAL-2124 -->Updated Spanish translations.
1038 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1039 for importing structure data to Jalview. Enables mmCIF and
1043 <!-- JAL-192 --->Alignment ruler shows positions relative to
1047 <!-- JAL-2202 -->Position/residue shown in status bar when
1048 mousing over sequence associated annotation
1051 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1055 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1056 '()', canonical '[]' and invalid '{}' base pair populations
1060 <!-- JAL-2092 -->Feature settings popup menu options for
1061 showing or hiding columns containing a feature
1064 <!-- JAL-1557 -->Edit selected group by double clicking on
1065 group and sequence associated annotation labels
1068 <!-- JAL-2236 -->Sequence name added to annotation label in
1069 select/hide columns by annotation and colour by annotation
1073 </ul> <em>Application</em>
1076 <!-- JAL-2050-->Automatically hide introns when opening a
1077 gene/transcript view
1080 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1084 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1085 structure mappings with the EMBL-EBI PDBe SIFTS database
1088 <!-- JAL-2079 -->Updated download sites used for Rfam and
1089 Pfam sources to xfam.org
1092 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1095 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1096 over sequences in Jalview
1099 <!-- JAL-2027-->Support for reverse-complement coding
1100 regions in ENA and EMBL
1103 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1104 for record retrieval via ENA rest API
1107 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1111 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1112 groovy script execution
1115 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1116 alignment window's Calculate menu
1119 <!-- JAL-1812 -->Allow groovy scripts that call
1120 Jalview.getAlignFrames() to run in headless mode
1123 <!-- JAL-2068 -->Support for creating new alignment
1124 calculation workers from groovy scripts
1127 <!-- JAL-1369 --->Store/restore reference sequence in
1131 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1132 associations are now saved/restored from project
1135 <!-- JAL-1993 -->Database selection dialog always shown
1136 before sequence fetcher is opened
1139 <!-- JAL-2183 -->Double click on an entry in Jalview's
1140 database chooser opens a sequence fetcher
1143 <!-- JAL-1563 -->Free-text search client for UniProt using
1144 the UniProt REST API
1147 <!-- JAL-2168 -->-nonews command line parameter to prevent
1148 the news reader opening
1151 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1152 querying stored in preferences
1155 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1159 <!-- JAL-1977-->Tooltips shown on database chooser
1162 <!-- JAL-391 -->Reverse complement function in calculate
1163 menu for nucleotide sequences
1166 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1167 and feature counts preserves alignment ordering (and
1168 debugged for complex feature sets).
1171 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1172 viewing structures with Jalview 2.10
1175 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1176 genome, transcript CCDS and gene ids via the Ensembl and
1177 Ensembl Genomes REST API
1180 <!-- JAL-2049 -->Protein sequence variant annotation
1181 computed for 'sequence_variant' annotation on CDS regions
1185 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1189 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1190 Ref Fetcher fails to match, or otherwise updates sequence
1191 data from external database records.
1194 <!-- JAL-2154 -->Revised Jalview Project format for
1195 efficient recovery of sequence coding and alignment
1196 annotation relationships.
1198 </ul> <!-- <em>Applet</em>
1209 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1213 <!-- JAL-2018-->Export features in Jalview format (again)
1214 includes graduated colourschemes
1217 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1218 working with big alignments and lots of hidden columns
1221 <!-- JAL-2053-->Hidden column markers not always rendered
1222 at right of alignment window
1225 <!-- JAL-2067 -->Tidied up links in help file table of
1229 <!-- JAL-2072 -->Feature based tree calculation not shown
1233 <!-- JAL-2075 -->Hidden columns ignored during feature
1234 based tree calculation
1237 <!-- JAL-2065 -->Alignment view stops updating when show
1238 unconserved enabled for group on alignment
1241 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1245 <!-- JAL-2146 -->Alignment column in status incorrectly
1246 shown as "Sequence position" when mousing over
1250 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1251 hidden columns present
1254 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1255 user created annotation added to alignment
1258 <!-- JAL-1841 -->RNA Structure consensus only computed for
1259 '()' base pair annotation
1262 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1263 in zero scores for all base pairs in RNA Structure
1267 <!-- JAL-2174-->Extend selection with columns containing
1271 <!-- JAL-2275 -->Pfam format writer puts extra space at
1272 beginning of sequence
1275 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1279 <!-- JAL-2238 -->Cannot create groups on an alignment from
1280 from a tree when t-coffee scores are shown
1283 <!-- JAL-1836,1967 -->Cannot import and view PDB
1284 structures with chains containing negative resnums (4q4h)
1287 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1291 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1292 to Clustal, PIR and PileUp output
1295 <!-- JAL-2008 -->Reordering sequence features that are
1296 not visible causes alignment window to repaint
1299 <!-- JAL-2006 -->Threshold sliders don't work in
1300 graduated colour and colour by annotation row for e-value
1301 scores associated with features and annotation rows
1304 <!-- JAL-1797 -->amino acid physicochemical conservation
1305 calculation should be case independent
1308 <!-- JAL-2173 -->Remove annotation also updates hidden
1312 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1313 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1314 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1317 <!-- JAL-2065 -->Null pointer exceptions and redraw
1318 problems when reference sequence defined and 'show
1319 non-conserved' enabled
1322 <!-- JAL-1306 -->Quality and Conservation are now shown on
1323 load even when Consensus calculation is disabled
1326 <!-- JAL-1932 -->Remove right on penultimate column of
1327 alignment does nothing
1330 <em>Application</em>
1333 <!-- JAL-1552-->URLs and links can't be imported by
1334 drag'n'drop on OSX when launched via webstart (note - not
1335 yet fixed for El Capitan)
1338 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1339 output when running on non-gb/us i18n platforms
1342 <!-- JAL-1944 -->Error thrown when exporting a view with
1343 hidden sequences as flat-file alignment
1346 <!-- JAL-2030-->InstallAnywhere distribution fails when
1350 <!-- JAL-2080-->Jalview very slow to launch via webstart
1351 (also hotfix for 2.9.0b2)
1354 <!-- JAL-2085 -->Cannot save project when view has a
1355 reference sequence defined
1358 <!-- JAL-1011 -->Columns are suddenly selected in other
1359 alignments and views when revealing hidden columns
1362 <!-- JAL-1989 -->Hide columns not mirrored in complement
1363 view in a cDNA/Protein splitframe
1366 <!-- JAL-1369 -->Cannot save/restore representative
1367 sequence from project when only one sequence is
1371 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1372 in Structure Chooser
1375 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1376 structure consensus didn't refresh annotation panel
1379 <!-- JAL-1962 -->View mapping in structure view shows
1380 mappings between sequence and all chains in a PDB file
1383 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1384 dialogs format columns correctly, don't display array
1385 data, sort columns according to type
1388 <!-- JAL-1975 -->Export complete shown after destination
1389 file chooser is cancelled during an image export
1392 <!-- JAL-2025 -->Error when querying PDB Service with
1393 sequence name containing special characters
1396 <!-- JAL-2024 -->Manual PDB structure querying should be
1400 <!-- JAL-2104 -->Large tooltips with broken HTML
1401 formatting don't wrap
1404 <!-- JAL-1128 -->Figures exported from wrapped view are
1405 truncated so L looks like I in consensus annotation
1408 <!-- JAL-2003 -->Export features should only export the
1409 currently displayed features for the current selection or
1413 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1414 after fetching cross-references, and restoring from
1418 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1419 followed in the structure viewer
1422 <!-- JAL-2163 -->Titles for individual alignments in
1423 splitframe not restored from project
1426 <!-- JAL-2145 -->missing autocalculated annotation at
1427 trailing end of protein alignment in transcript/product
1428 splitview when pad-gaps not enabled by default
1431 <!-- JAL-1797 -->amino acid physicochemical conservation
1435 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1436 article has been read (reopened issue due to
1437 internationalisation problems)
1440 <!-- JAL-1960 -->Only offer PDB structures in structure
1441 viewer based on sequence name, PDB and UniProt
1446 <!-- JAL-1976 -->No progress bar shown during export of
1450 <!-- JAL-2213 -->Structures not always superimposed after
1451 multiple structures are shown for one or more sequences.
1454 <!-- JAL-1370 -->Reference sequence characters should not
1455 be replaced with '.' when 'Show unconserved' format option
1459 <!-- JAL-1823 -->Cannot specify chain code when entering
1460 specific PDB id for sequence
1463 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1464 'Export hidden sequences' is enabled, but 'export hidden
1465 columns' is disabled.
1468 <!--JAL-2026-->Best Quality option in structure chooser
1469 selects lowest rather than highest resolution structures
1473 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1474 to sequence mapping in 'View Mappings' report
1477 <!-- JAL-2284 -->Unable to read old Jalview projects that
1478 contain non-XML data added after Jalvew wrote project.
1481 <!-- JAL-2118 -->Newly created annotation row reorders
1482 after clicking on it to create new annotation for a
1486 <!-- JAL-1980 -->Null Pointer Exception raised when
1487 pressing Add on an orphaned cut'n'paste window.
1489 <!-- may exclude, this is an external service stability issue JAL-1941
1490 -- > RNA 3D structure not added via DSSR service</li> -->
1495 <!-- JAL-2151 -->Incorrect columns are selected when
1496 hidden columns present before start of sequence
1499 <!-- JAL-1986 -->Missing dependencies on applet pages
1503 <!-- JAL-1947 -->Overview pixel size changes when
1504 sequences are hidden in applet
1507 <!-- JAL-1996 -->Updated instructions for applet
1508 deployment on examples pages.
1515 <td width="60" nowrap>
1516 <div align="center">
1517 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1518 <em>16/10/2015</em></strong>
1521 <td><em>General</em>
1523 <li>Time stamps for signed Jalview application and applet
1528 <em>Application</em>
1530 <li>Duplicate group consensus and conservation rows
1531 shown when tree is partitioned</li>
1532 <li>Erratic behaviour when tree partitions made with
1533 multiple cDNA/Protein split views</li>
1539 <td width="60" nowrap>
1540 <div align="center">
1541 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1542 <em>8/10/2015</em></strong>
1545 <td><em>General</em>
1547 <li>Updated Spanish translations of localized text for
1549 </ul> <em>Application</em>
1551 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1552 <li>Signed OSX InstallAnywhere installer<br></li>
1553 <li>Support for per-sequence based annotations in BioJSON</li>
1554 </ul> <em>Applet</em>
1556 <li>Split frame example added to applet examples page</li>
1557 </ul> <em>Build and Deployment</em>
1560 <!-- JAL-1888 -->New ant target for running Jalview's test
1568 <li>Mapping of cDNA to protein in split frames
1569 incorrect when sequence start > 1</li>
1570 <li>Broken images in filter column by annotation dialog
1572 <li>Feature colours not parsed from features file</li>
1573 <li>Exceptions and incomplete link URLs recovered when
1574 loading a features file containing HTML tags in feature
1578 <em>Application</em>
1580 <li>Annotations corrupted after BioJS export and
1582 <li>Incorrect sequence limits after Fetch DB References
1583 with 'trim retrieved sequences'</li>
1584 <li>Incorrect warning about deleting all data when
1585 deleting selected columns</li>
1586 <li>Patch to build system for shipping properly signed
1587 JNLP templates for webstart launch</li>
1588 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1589 unreleased structures for download or viewing</li>
1590 <li>Tab/space/return keystroke operation of EMBL-PDBe
1591 fetcher/viewer dialogs works correctly</li>
1592 <li>Disabled 'minimise' button on Jalview windows
1593 running on OSX to workaround redraw hang bug</li>
1594 <li>Split cDNA/Protein view position and geometry not
1595 recovered from jalview project</li>
1596 <li>Initial enabled/disabled state of annotation menu
1597 sorter 'show autocalculated first/last' corresponds to
1599 <li>Restoring of Clustal, RNA Helices and T-Coffee
1600 color schemes from BioJSON</li>
1604 <li>Reorder sequences mirrored in cDNA/Protein split
1606 <li>Applet with Jmol examples not loading correctly</li>
1612 <td><div align="center">
1613 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1615 <td><em>General</em>
1617 <li>Linked visualisation and analysis of DNA and Protein
1620 <li>Translated cDNA alignments shown as split protein
1621 and DNA alignment views</li>
1622 <li>Codon consensus annotation for linked protein and
1623 cDNA alignment views</li>
1624 <li>Link cDNA or Protein product sequences by loading
1625 them onto Protein or cDNA alignments</li>
1626 <li>Reconstruct linked cDNA alignment from aligned
1627 protein sequences</li>
1630 <li>Jmol integration updated to Jmol v14.2.14</li>
1631 <li>Import and export of Jalview alignment views as <a
1632 href="features/bioJsonFormat.html">BioJSON</a></li>
1633 <li>New alignment annotation file statements for
1634 reference sequences and marking hidden columns</li>
1635 <li>Reference sequence based alignment shading to
1636 highlight variation</li>
1637 <li>Select or hide columns according to alignment
1639 <li>Find option for locating sequences by description</li>
1640 <li>Conserved physicochemical properties shown in amino
1641 acid conservation row</li>
1642 <li>Alignments can be sorted by number of RNA helices</li>
1643 </ul> <em>Application</em>
1645 <li>New cDNA/Protein analysis capabilities
1647 <li>Get Cross-References should open a Split Frame
1648 view with cDNA/Protein</li>
1649 <li>Detect when nucleotide sequences and protein
1650 sequences are placed in the same alignment</li>
1651 <li>Split cDNA/Protein views are saved in Jalview
1656 <li>Use REST API to talk to Chimera</li>
1657 <li>Selected regions in Chimera are highlighted in linked
1658 Jalview windows</li>
1660 <li>VARNA RNA viewer updated to v3.93</li>
1661 <li>VARNA views are saved in Jalview Projects</li>
1662 <li>Pseudoknots displayed as Jalview RNA annotation can
1663 be shown in VARNA</li>
1665 <li>Make groups for selection uses marked columns as well
1666 as the active selected region</li>
1668 <li>Calculate UPGMA and NJ trees using sequence feature
1670 <li>New Export options
1672 <li>New Export Settings dialog to control hidden
1673 region export in flat file generation</li>
1675 <li>Export alignment views for display with the <a
1676 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1678 <li>Export scrollable SVG in HTML page</li>
1679 <li>Optional embedding of BioJSON data when exporting
1680 alignment figures to HTML</li>
1682 <li>3D structure retrieval and display
1684 <li>Free text and structured queries with the PDBe
1686 <li>PDBe Search API based discovery and selection of
1687 PDB structures for a sequence set</li>
1691 <li>JPred4 employed for protein secondary structure
1693 <li>Hide Insertions menu option to hide unaligned columns
1694 for one or a group of sequences</li>
1695 <li>Automatically hide insertions in alignments imported
1696 from the JPred4 web server</li>
1697 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1698 system on OSX<br />LGPL libraries courtesy of <a
1699 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1701 <li>changed 'View nucleotide structure' submenu to 'View
1702 VARNA 2D Structure'</li>
1703 <li>change "View protein structure" menu option to "3D
1706 </ul> <em>Applet</em>
1708 <li>New layout for applet example pages</li>
1709 <li>New parameters to enable SplitFrame view
1710 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1711 <li>New example demonstrating linked viewing of cDNA and
1712 Protein alignments</li>
1713 </ul> <em>Development and deployment</em>
1715 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1716 <li>Include installation type and git revision in build
1717 properties and console log output</li>
1718 <li>Jalview Github organisation, and new github site for
1719 storing BioJsMSA Templates</li>
1720 <li>Jalview's unit tests now managed with TestNG</li>
1723 <!-- <em>General</em>
1725 </ul> --> <!-- issues resolved --> <em>Application</em>
1727 <li>Escape should close any open find dialogs</li>
1728 <li>Typo in select-by-features status report</li>
1729 <li>Consensus RNA secondary secondary structure
1730 predictions are not highlighted in amber</li>
1731 <li>Missing gap character in v2.7 example file means
1732 alignment appears unaligned when pad-gaps is not enabled</li>
1733 <li>First switch to RNA Helices colouring doesn't colour
1734 associated structure views</li>
1735 <li>ID width preference option is greyed out when auto
1736 width checkbox not enabled</li>
1737 <li>Stopped a warning dialog from being shown when
1738 creating user defined colours</li>
1739 <li>'View Mapping' in structure viewer shows sequence
1740 mappings for just that viewer's sequences</li>
1741 <li>Workaround for superposing PDB files containing
1742 multiple models in Chimera</li>
1743 <li>Report sequence position in status bar when hovering
1744 over Jmol structure</li>
1745 <li>Cannot output gaps as '.' symbols with Selection ->
1746 output to text box</li>
1747 <li>Flat file exports of alignments with hidden columns
1748 have incorrect sequence start/end</li>
1749 <li>'Aligning' a second chain to a Chimera structure from
1751 <li>Colour schemes applied to structure viewers don't
1752 work for nucleotide</li>
1753 <li>Loading/cut'n'pasting an empty or invalid file leads
1754 to a grey/invisible alignment window</li>
1755 <li>Exported Jpred annotation from a sequence region
1756 imports to different position</li>
1757 <li>Space at beginning of sequence feature tooltips shown
1758 on some platforms</li>
1759 <li>Chimera viewer 'View | Show Chain' menu is not
1761 <li>'New View' fails with a Null Pointer Exception in
1762 console if Chimera has been opened</li>
1763 <li>Mouseover to Chimera not working</li>
1764 <li>Miscellaneous ENA XML feature qualifiers not
1766 <li>NPE in annotation renderer after 'Extract Scores'</li>
1767 <li>If two structures in one Chimera window, mouseover of
1768 either sequence shows on first structure</li>
1769 <li>'Show annotations' options should not make
1770 non-positional annotations visible</li>
1771 <li>Subsequence secondary structure annotation not shown
1772 in right place after 'view flanking regions'</li>
1773 <li>File Save As type unset when current file format is
1775 <li>Save as '.jar' option removed for saving Jalview
1777 <li>Colour by Sequence colouring in Chimera more
1779 <li>Cannot 'add reference annotation' for a sequence in
1780 several views on same alignment</li>
1781 <li>Cannot show linked products for EMBL / ENA records</li>
1782 <li>Jalview's tooltip wraps long texts containing no
1784 </ul> <em>Applet</em>
1786 <li>Jmol to JalviewLite mouseover/link not working</li>
1787 <li>JalviewLite can't import sequences with ID
1788 descriptions containing angle brackets</li>
1789 </ul> <em>General</em>
1791 <li>Cannot export and reimport RNA secondary structure
1792 via jalview annotation file</li>
1793 <li>Random helix colour palette for colour by annotation
1794 with RNA secondary structure</li>
1795 <li>Mouseover to cDNA from STOP residue in protein
1796 translation doesn't work.</li>
1797 <li>hints when using the select by annotation dialog box</li>
1798 <li>Jmol alignment incorrect if PDB file has alternate CA
1800 <li>FontChooser message dialog appears to hang after
1801 choosing 1pt font</li>
1802 <li>Peptide secondary structure incorrectly imported from
1803 annotation file when annotation display text includes 'e' or
1805 <li>Cannot set colour of new feature type whilst creating
1807 <li>cDNA translation alignment should not be sequence
1808 order dependent</li>
1809 <li>'Show unconserved' doesn't work for lower case
1811 <li>Nucleotide ambiguity codes involving R not recognised</li>
1812 </ul> <em>Deployment and Documentation</em>
1814 <li>Applet example pages appear different to the rest of
1815 www.jalview.org</li>
1816 </ul> <em>Application Known issues</em>
1818 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1819 <li>Misleading message appears after trying to delete
1821 <li>Jalview icon not shown in dock after InstallAnywhere
1822 version launches</li>
1823 <li>Fetching EMBL reference for an RNA sequence results
1824 fails with a sequence mismatch</li>
1825 <li>Corrupted or unreadable alignment display when
1826 scrolling alignment to right</li>
1827 <li>ArrayIndexOutOfBoundsException thrown when remove
1828 empty columns called on alignment with ragged gapped ends</li>
1829 <li>auto calculated alignment annotation rows do not get
1830 placed above or below non-autocalculated rows</li>
1831 <li>Jalview dekstop becomes sluggish at full screen in
1832 ultra-high resolution</li>
1833 <li>Cannot disable consensus calculation independently of
1834 quality and conservation</li>
1835 <li>Mouseover highlighting between cDNA and protein can
1836 become sluggish with more than one splitframe shown</li>
1837 </ul> <em>Applet Known Issues</em>
1839 <li>Core PDB parsing code requires Jmol</li>
1840 <li>Sequence canvas panel goes white when alignment
1841 window is being resized</li>
1847 <td><div align="center">
1848 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1850 <td><em>General</em>
1852 <li>Updated Java code signing certificate donated by
1854 <li>Features and annotation preserved when performing
1855 pairwise alignment</li>
1856 <li>RNA pseudoknot annotation can be
1857 imported/exported/displayed</li>
1858 <li>'colour by annotation' can colour by RNA and
1859 protein secondary structure</li>
1860 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1861 post-hoc with 2.9 release</em>)
1864 </ul> <em>Application</em>
1866 <li>Extract and display secondary structure for sequences
1867 with 3D structures</li>
1868 <li>Support for parsing RNAML</li>
1869 <li>Annotations menu for layout
1871 <li>sort sequence annotation rows by alignment</li>
1872 <li>place sequence annotation above/below alignment
1875 <li>Output in Stockholm format</li>
1876 <li>Internationalisation: improved Spanish (es)
1878 <li>Structure viewer preferences tab</li>
1879 <li>Disorder and Secondary Structure annotation tracks
1880 shared between alignments</li>
1881 <li>UCSF Chimera launch and linked highlighting from
1883 <li>Show/hide all sequence associated annotation rows for
1884 all or current selection</li>
1885 <li>disorder and secondary structure predictions
1886 available as dataset annotation</li>
1887 <li>Per-sequence rna helices colouring</li>
1890 <li>Sequence database accessions imported when fetching
1891 alignments from Rfam</li>
1892 <li>update VARNA version to 3.91</li>
1894 <li>New groovy scripts for exporting aligned positions,
1895 conservation values, and calculating sum of pairs scores.</li>
1896 <li>Command line argument to set default JABAWS server</li>
1897 <li>include installation type in build properties and
1898 console log output</li>
1899 <li>Updated Jalview project format to preserve dataset
1903 <!-- issues resolved --> <em>Application</em>
1905 <li>Distinguish alignment and sequence associated RNA
1906 structure in structure->view->VARNA</li>
1907 <li>Raise dialog box if user deletes all sequences in an
1909 <li>Pressing F1 results in documentation opening twice</li>
1910 <li>Sequence feature tooltip is wrapped</li>
1911 <li>Double click on sequence associated annotation
1912 selects only first column</li>
1913 <li>Redundancy removal doesn't result in unlinked
1914 leaves shown in tree</li>
1915 <li>Undos after several redundancy removals don't undo
1917 <li>Hide sequence doesn't hide associated annotation</li>
1918 <li>User defined colours dialog box too big to fit on
1919 screen and buttons not visible</li>
1920 <li>author list isn't updated if already written to
1921 Jalview properties</li>
1922 <li>Popup menu won't open after retrieving sequence
1924 <li>File open window for associate PDB doesn't open</li>
1925 <li>Left-then-right click on a sequence id opens a
1926 browser search window</li>
1927 <li>Cannot open sequence feature shading/sort popup menu
1928 in feature settings dialog</li>
1929 <li>better tooltip placement for some areas of Jalview
1931 <li>Allow addition of JABAWS Server which doesn't
1932 pass validation</li>
1933 <li>Web services parameters dialog box is too large to
1935 <li>Muscle nucleotide alignment preset obscured by
1937 <li>JABAWS preset submenus don't contain newly
1938 defined user preset</li>
1939 <li>MSA web services warns user if they were launched
1940 with invalid input</li>
1941 <li>Jalview cannot contact DAS Registy when running on
1944 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1945 'Superpose with' submenu not shown when new view
1949 </ul> <!-- <em>Applet</em>
1951 </ul> <em>General</em>
1953 </ul>--> <em>Deployment and Documentation</em>
1955 <li>2G and 1G options in launchApp have no effect on
1956 memory allocation</li>
1957 <li>launchApp service doesn't automatically open
1958 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1960 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1961 InstallAnywhere reports cannot find valid JVM when Java
1962 1.7_055 is available
1964 </ul> <em>Application Known issues</em>
1967 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1968 corrupted or unreadable alignment display when scrolling
1972 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1973 retrieval fails but progress bar continues for DAS retrieval
1974 with large number of ID
1977 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1978 flatfile output of visible region has incorrect sequence
1982 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1983 rna structure consensus doesn't update when secondary
1984 structure tracks are rearranged
1987 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1988 invalid rna structure positional highlighting does not
1989 highlight position of invalid base pairs
1992 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1993 out of memory errors are not raised when saving Jalview
1994 project from alignment window file menu
1997 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1998 Switching to RNA Helices colouring doesn't propagate to
2002 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2003 colour by RNA Helices not enabled when user created
2004 annotation added to alignment
2007 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2008 Jalview icon not shown on dock in Mountain Lion/Webstart
2010 </ul> <em>Applet Known Issues</em>
2013 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2014 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2017 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2018 Jalview and Jmol example not compatible with IE9
2021 <li>Sort by annotation score doesn't reverse order
2027 <td><div align="center">
2028 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2031 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2034 <li>Internationalisation of user interface (usually
2035 called i18n support) and translation for Spanish locale</li>
2036 <li>Define/Undefine group on current selection with
2037 Ctrl-G/Shift Ctrl-G</li>
2038 <li>Improved group creation/removal options in
2039 alignment/sequence Popup menu</li>
2040 <li>Sensible precision for symbol distribution
2041 percentages shown in logo tooltip.</li>
2042 <li>Annotation panel height set according to amount of
2043 annotation when alignment first opened</li>
2044 </ul> <em>Application</em>
2046 <li>Interactive consensus RNA secondary structure
2047 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2048 <li>Select columns containing particular features from
2049 Feature Settings dialog</li>
2050 <li>View all 'representative' PDB structures for selected
2052 <li>Update Jalview project format:
2054 <li>New file extension for Jalview projects '.jvp'</li>
2055 <li>Preserve sequence and annotation dataset (to
2056 store secondary structure annotation,etc)</li>
2057 <li>Per group and alignment annotation and RNA helix
2061 <li>New similarity measures for PCA and Tree calculation
2063 <li>Experimental support for retrieval and viewing of
2064 flanking regions for an alignment</li>
2068 <!-- issues resolved --> <em>Application</em>
2070 <li>logo keeps spinning and status remains at queued or
2071 running after job is cancelled</li>
2072 <li>cannot export features from alignments imported from
2073 Jalview/VAMSAS projects</li>
2074 <li>Buggy slider for web service parameters that take
2076 <li>Newly created RNA secondary structure line doesn't
2077 have 'display all symbols' flag set</li>
2078 <li>T-COFFEE alignment score shading scheme and other
2079 annotation shading not saved in Jalview project</li>
2080 <li>Local file cannot be loaded in freshly downloaded
2082 <li>Jalview icon not shown on dock in Mountain
2084 <li>Load file from desktop file browser fails</li>
2085 <li>Occasional NPE thrown when calculating large trees</li>
2086 <li>Cannot reorder or slide sequences after dragging an
2087 alignment onto desktop</li>
2088 <li>Colour by annotation dialog throws NPE after using
2089 'extract scores' function</li>
2090 <li>Loading/cut'n'pasting an empty file leads to a grey
2091 alignment window</li>
2092 <li>Disorder thresholds rendered incorrectly after
2093 performing IUPred disorder prediction</li>
2094 <li>Multiple group annotated consensus rows shown when
2095 changing 'normalise logo' display setting</li>
2096 <li>Find shows blank dialog after 'finished searching' if
2097 nothing matches query</li>
2098 <li>Null Pointer Exceptions raised when sorting by
2099 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2101 <li>Errors in Jmol console when structures in alignment
2102 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2104 <li>Not all working JABAWS services are shown in
2106 <li>JAVAWS version of Jalview fails to launch with
2107 'invalid literal/length code'</li>
2108 <li>Annotation/RNA Helix colourschemes cannot be applied
2109 to alignment with groups (actually fixed in 2.8.0b1)</li>
2110 <li>RNA Helices and T-Coffee Scores available as default
2113 </ul> <em>Applet</em>
2115 <li>Remove group option is shown even when selection is
2117 <li>Apply to all groups ticked but colourscheme changes
2118 don't affect groups</li>
2119 <li>Documented RNA Helices and T-Coffee Scores as valid
2120 colourscheme name</li>
2121 <li>Annotation labels drawn on sequence IDs when
2122 Annotation panel is not displayed</li>
2123 <li>Increased font size for dropdown menus on OSX and
2124 embedded windows</li>
2125 </ul> <em>Other</em>
2127 <li>Consensus sequence for alignments/groups with a
2128 single sequence were not calculated</li>
2129 <li>annotation files that contain only groups imported as
2130 annotation and junk sequences</li>
2131 <li>Fasta files with sequences containing '*' incorrectly
2132 recognised as PFAM or BLC</li>
2133 <li>conservation/PID slider apply all groups option
2134 doesn't affect background (2.8.0b1)
2136 <li>redundancy highlighting is erratic at 0% and 100%</li>
2137 <li>Remove gapped columns fails for sequences with ragged
2139 <li>AMSA annotation row with leading spaces is not
2140 registered correctly on import</li>
2141 <li>Jalview crashes when selecting PCA analysis for
2142 certain alignments</li>
2143 <li>Opening the colour by annotation dialog for an
2144 existing annotation based 'use original colours'
2145 colourscheme loses original colours setting</li>
2150 <td><div align="center">
2151 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2152 <em>30/1/2014</em></strong>
2156 <li>Trusted certificates for JalviewLite applet and
2157 Jalview Desktop application<br />Certificate was donated by
2158 <a href="https://www.certum.eu">Certum</a> to the Jalview
2159 open source project).
2161 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2162 <li>Output in Stockholm format</li>
2163 <li>Allow import of data from gzipped files</li>
2164 <li>Export/import group and sequence associated line
2165 graph thresholds</li>
2166 <li>Nucleotide substitution matrix that supports RNA and
2167 ambiguity codes</li>
2168 <li>Allow disorder predictions to be made on the current
2169 selection (or visible selection) in the same way that JPred
2171 <li>Groovy scripting for headless Jalview operation</li>
2172 </ul> <em>Other improvements</em>
2174 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2175 <li>COMBINE statement uses current SEQUENCE_REF and
2176 GROUP_REF scope to group annotation rows</li>
2177 <li>Support '' style escaping of quotes in Newick
2179 <li>Group options for JABAWS service by command line name</li>
2180 <li>Empty tooltip shown for JABA service options with a
2181 link but no description</li>
2182 <li>Select primary source when selecting authority in
2183 database fetcher GUI</li>
2184 <li>Add .mfa to FASTA file extensions recognised by
2186 <li>Annotation label tooltip text wrap</li>
2191 <li>Slow scrolling when lots of annotation rows are
2193 <li>Lots of NPE (and slowness) after creating RNA
2194 secondary structure annotation line</li>
2195 <li>Sequence database accessions not imported when
2196 fetching alignments from Rfam</li>
2197 <li>Incorrect SHMR submission for sequences with
2199 <li>View all structures does not always superpose
2201 <li>Option widgets in service parameters not updated to
2202 reflect user or preset settings</li>
2203 <li>Null pointer exceptions for some services without
2204 presets or adjustable parameters</li>
2205 <li>Discover PDB IDs entry in structure menu doesn't
2206 discover PDB xRefs</li>
2207 <li>Exception encountered while trying to retrieve
2208 features with DAS</li>
2209 <li>Lowest value in annotation row isn't coloured
2210 when colour by annotation (per sequence) is coloured</li>
2211 <li>Keyboard mode P jumps to start of gapped region when
2212 residue follows a gap</li>
2213 <li>Jalview appears to hang importing an alignment with
2214 Wrap as default or after enabling Wrap</li>
2215 <li>'Right click to add annotations' message
2216 shown in wrap mode when no annotations present</li>
2217 <li>Disorder predictions fail with NPE if no automatic
2218 annotation already exists on alignment</li>
2219 <li>oninit javascript function should be called after
2220 initialisation completes</li>
2221 <li>Remove redundancy after disorder prediction corrupts
2222 alignment window display</li>
2223 <li>Example annotation file in documentation is invalid</li>
2224 <li>Grouped line graph annotation rows are not exported
2225 to annotation file</li>
2226 <li>Multi-harmony analysis cannot be run when only two
2228 <li>Cannot create multiple groups of line graphs with
2229 several 'combine' statements in annotation file</li>
2230 <li>Pressing return several times causes Number Format
2231 exceptions in keyboard mode</li>
2232 <li>Multi-harmony (SHMMR) method doesn't submit
2233 correct partitions for input data</li>
2234 <li>Translation from DNA to Amino Acids fails</li>
2235 <li>Jalview fail to load newick tree with quoted label</li>
2236 <li>--headless flag isn't understood</li>
2237 <li>ClassCastException when generating EPS in headless
2239 <li>Adjusting sequence-associated shading threshold only
2240 changes one row's threshold</li>
2241 <li>Preferences and Feature settings panel panel
2242 doesn't open</li>
2243 <li>hide consensus histogram also hides conservation and
2244 quality histograms</li>
2249 <td><div align="center">
2250 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2252 <td><em>Application</em>
2254 <li>Support for JABAWS 2.0 Services (AACon alignment
2255 conservation, protein disorder and Clustal Omega)</li>
2256 <li>JABAWS server status indicator in Web Services
2258 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2259 in Jalview alignment window</li>
2260 <li>Updated Jalview build and deploy framework for OSX
2261 mountain lion, windows 7, and 8</li>
2262 <li>Nucleotide substitution matrix for PCA that supports
2263 RNA and ambiguity codes</li>
2265 <li>Improved sequence database retrieval GUI</li>
2266 <li>Support fetching and database reference look up
2267 against multiple DAS sources (Fetch all from in 'fetch db
2269 <li>Jalview project improvements
2271 <li>Store and retrieve the 'belowAlignment'
2272 flag for annotation</li>
2273 <li>calcId attribute to group annotation rows on the
2275 <li>Store AACon calculation settings for a view in
2276 Jalview project</li>
2280 <li>horizontal scrolling gesture support</li>
2281 <li>Visual progress indicator when PCA calculation is
2283 <li>Simpler JABA web services menus</li>
2284 <li>visual indication that web service results are still
2285 being retrieved from server</li>
2286 <li>Serialise the dialogs that are shown when Jalview
2287 starts up for first time</li>
2288 <li>Jalview user agent string for interacting with HTTP
2290 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2292 <li>Examples directory and Groovy library included in
2293 InstallAnywhere distribution</li>
2294 </ul> <em>Applet</em>
2296 <li>RNA alignment and secondary structure annotation
2297 visualization applet example</li>
2298 </ul> <em>General</em>
2300 <li>Normalise option for consensus sequence logo</li>
2301 <li>Reset button in PCA window to return dimensions to
2303 <li>Allow seqspace or Jalview variant of alignment PCA
2305 <li>PCA with either nucleic acid and protein substitution
2307 <li>Allow windows containing HTML reports to be exported
2309 <li>Interactive display and editing of RNA secondary
2310 structure contacts</li>
2311 <li>RNA Helix Alignment Colouring</li>
2312 <li>RNA base pair logo consensus</li>
2313 <li>Parse sequence associated secondary structure
2314 information in Stockholm files</li>
2315 <li>HTML Export database accessions and annotation
2316 information presented in tooltip for sequences</li>
2317 <li>Import secondary structure from LOCARNA clustalw
2318 style RNA alignment files</li>
2319 <li>import and visualise T-COFFEE quality scores for an
2321 <li>'colour by annotation' per sequence option to
2322 shade each sequence according to its associated alignment
2324 <li>New Jalview Logo</li>
2325 </ul> <em>Documentation and Development</em>
2327 <li>documentation for score matrices used in Jalview</li>
2328 <li>New Website!</li>
2330 <td><em>Application</em>
2332 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2333 wsdbfetch REST service</li>
2334 <li>Stop windows being moved outside desktop on OSX</li>
2335 <li>Filetype associations not installed for webstart
2337 <li>Jalview does not always retrieve progress of a JABAWS
2338 job execution in full once it is complete</li>
2339 <li>revise SHMR RSBS definition to ensure alignment is
2340 uploaded via ali_file parameter</li>
2341 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2342 <li>View all structures superposed fails with exception</li>
2343 <li>Jnet job queues forever if a very short sequence is
2344 submitted for prediction</li>
2345 <li>Cut and paste menu not opened when mouse clicked on
2347 <li>Putting fractional value into integer text box in
2348 alignment parameter dialog causes Jalview to hang</li>
2349 <li>Structure view highlighting doesn't work on
2351 <li>View all structures fails with exception shown in
2353 <li>Characters in filename associated with PDBEntry not
2354 escaped in a platform independent way</li>
2355 <li>Jalview desktop fails to launch with exception when
2357 <li>Tree calculation reports 'you must have 2 or more
2358 sequences selected' when selection is empty</li>
2359 <li>Jalview desktop fails to launch with jar signature
2360 failure when java web start temporary file caching is
2362 <li>DAS Sequence retrieval with range qualification
2363 results in sequence xref which includes range qualification</li>
2364 <li>Errors during processing of command line arguments
2365 cause progress bar (JAL-898) to be removed</li>
2366 <li>Replace comma for semi-colon option not disabled for
2367 DAS sources in sequence fetcher</li>
2368 <li>Cannot close news reader when JABAWS server warning
2369 dialog is shown</li>
2370 <li>Option widgets not updated to reflect user settings</li>
2371 <li>Edited sequence not submitted to web service</li>
2372 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2373 <li>InstallAnywhere installer doesn't unpack and run
2374 on OSX Mountain Lion</li>
2375 <li>Annotation panel not given a scroll bar when
2376 sequences with alignment annotation are pasted into the
2378 <li>Sequence associated annotation rows not associated
2379 when loaded from Jalview project</li>
2380 <li>Browser launch fails with NPE on java 1.7</li>
2381 <li>JABAWS alignment marked as finished when job was
2382 cancelled or job failed due to invalid input</li>
2383 <li>NPE with v2.7 example when clicking on Tree
2384 associated with all views</li>
2385 <li>Exceptions when copy/paste sequences with grouped
2386 annotation rows to new window</li>
2387 </ul> <em>Applet</em>
2389 <li>Sequence features are momentarily displayed before
2390 they are hidden using hidefeaturegroups applet parameter</li>
2391 <li>loading features via javascript API automatically
2392 enables feature display</li>
2393 <li>scrollToColumnIn javascript API method doesn't
2395 </ul> <em>General</em>
2397 <li>Redundancy removal fails for rna alignment</li>
2398 <li>PCA calculation fails when sequence has been selected
2399 and then deselected</li>
2400 <li>PCA window shows grey box when first opened on OSX</li>
2401 <li>Letters coloured pink in sequence logo when alignment
2402 coloured with clustalx</li>
2403 <li>Choosing fonts without letter symbols defined causes
2404 exceptions and redraw errors</li>
2405 <li>Initial PCA plot view is not same as manually
2406 reconfigured view</li>
2407 <li>Grouped annotation graph label has incorrect line
2409 <li>Grouped annotation graph label display is corrupted
2410 for lots of labels</li>
2415 <div align="center">
2416 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2419 <td><em>Application</em>
2421 <li>Jalview Desktop News Reader</li>
2422 <li>Tweaked default layout of web services menu</li>
2423 <li>View/alignment association menu to enable user to
2424 easily specify which alignment a multi-structure view takes
2425 its colours/correspondences from</li>
2426 <li>Allow properties file location to be specified as URL</li>
2427 <li>Extend Jalview project to preserve associations
2428 between many alignment views and a single Jmol display</li>
2429 <li>Store annotation row height in Jalview project file</li>
2430 <li>Annotation row column label formatting attributes
2431 stored in project file</li>
2432 <li>Annotation row order for auto-calculated annotation
2433 rows preserved in Jalview project file</li>
2434 <li>Visual progress indication when Jalview state is
2435 saved using Desktop window menu</li>
2436 <li>Visual indication that command line arguments are
2437 still being processed</li>
2438 <li>Groovy script execution from URL</li>
2439 <li>Colour by annotation default min and max colours in
2441 <li>Automatically associate PDB files dragged onto an
2442 alignment with sequences that have high similarity and
2444 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2445 <li>'view structures' option to open many
2446 structures in same window</li>
2447 <li>Sort associated views menu option for tree panel</li>
2448 <li>Group all JABA and non-JABA services for a particular
2449 analysis function in its own submenu</li>
2450 </ul> <em>Applet</em>
2452 <li>Userdefined and autogenerated annotation rows for
2454 <li>Adjustment of alignment annotation pane height</li>
2455 <li>Annotation scrollbar for annotation panel</li>
2456 <li>Drag to reorder annotation rows in annotation panel</li>
2457 <li>'automaticScrolling' parameter</li>
2458 <li>Allow sequences with partial ID string matches to be
2459 annotated from GFF/Jalview features files</li>
2460 <li>Sequence logo annotation row in applet</li>
2461 <li>Absolute paths relative to host server in applet
2462 parameters are treated as such</li>
2463 <li>New in the JalviewLite javascript API:
2465 <li>JalviewLite.js javascript library</li>
2466 <li>Javascript callbacks for
2468 <li>Applet initialisation</li>
2469 <li>Sequence/alignment mouse-overs and selections</li>
2472 <li>scrollTo row and column alignment scrolling
2474 <li>Select sequence/alignment regions from javascript</li>
2475 <li>javascript structure viewer harness to pass
2476 messages between Jmol and Jalview when running as
2477 distinct applets</li>
2478 <li>sortBy method</li>
2479 <li>Set of applet and application examples shipped
2480 with documentation</li>
2481 <li>New example to demonstrate JalviewLite and Jmol
2482 javascript message exchange</li>
2484 </ul> <em>General</em>
2486 <li>Enable Jmol displays to be associated with multiple
2487 multiple alignments</li>
2488 <li>Option to automatically sort alignment with new tree</li>
2489 <li>User configurable link to enable redirects to a
2490 www.Jalview.org mirror</li>
2491 <li>Jmol colours option for Jmol displays</li>
2492 <li>Configurable newline string when writing alignment
2493 and other flat files</li>
2494 <li>Allow alignment annotation description lines to
2495 contain html tags</li>
2496 </ul> <em>Documentation and Development</em>
2498 <li>Add groovy test harness for bulk load testing to
2500 <li>Groovy script to load and align a set of sequences
2501 using a web service before displaying the result in the
2502 Jalview desktop</li>
2503 <li>Restructured javascript and applet api documentation</li>
2504 <li>Ant target to publish example html files with applet
2506 <li>Netbeans project for building Jalview from source</li>
2507 <li>ant task to create online javadoc for Jalview source</li>
2509 <td><em>Application</em>
2511 <li>User defined colourscheme throws exception when
2512 current built in colourscheme is saved as new scheme</li>
2513 <li>AlignFrame->Save in application pops up save
2514 dialog for valid filename/format</li>
2515 <li>Cannot view associated structure for UniProt sequence</li>
2516 <li>PDB file association breaks for UniProt sequence
2518 <li>Associate PDB from file dialog does not tell you
2519 which sequence is to be associated with the file</li>
2520 <li>Find All raises null pointer exception when query
2521 only matches sequence IDs</li>
2522 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2523 <li>Jalview project with Jmol views created with Jalview
2524 2.4 cannot be loaded</li>
2525 <li>Filetype associations not installed for webstart
2527 <li>Two or more chains in a single PDB file associated
2528 with sequences in different alignments do not get coloured
2529 by their associated sequence</li>
2530 <li>Visibility status of autocalculated annotation row
2531 not preserved when project is loaded</li>
2532 <li>Annotation row height and visibility attributes not
2533 stored in Jalview project</li>
2534 <li>Tree bootstraps are not preserved when saved as a
2535 Jalview project</li>
2536 <li>Envision2 workflow tooltips are corrupted</li>
2537 <li>Enabling show group conservation also enables colour
2538 by conservation</li>
2539 <li>Duplicate group associated conservation or consensus
2540 created on new view</li>
2541 <li>Annotation scrollbar not displayed after 'show
2542 all hidden annotation rows' option selected</li>
2543 <li>Alignment quality not updated after alignment
2544 annotation row is hidden then shown</li>
2545 <li>Preserve colouring of structures coloured by
2546 sequences in pre Jalview 2.7 projects</li>
2547 <li>Web service job parameter dialog is not laid out
2549 <li>Web services menu not refreshed after 'reset
2550 services' button is pressed in preferences</li>
2551 <li>Annotation off by one in Jalview v2_3 example project</li>
2552 <li>Structures imported from file and saved in project
2553 get name like jalview_pdb1234.txt when reloaded</li>
2554 <li>Jalview does not always retrieve progress of a JABAWS
2555 job execution in full once it is complete</li>
2556 </ul> <em>Applet</em>
2558 <li>Alignment height set incorrectly when lots of
2559 annotation rows are displayed</li>
2560 <li>Relative URLs in feature HTML text not resolved to
2562 <li>View follows highlighting does not work for positions
2564 <li><= shown as = in tooltip</li>
2565 <li>Export features raises exception when no features
2567 <li>Separator string used for serialising lists of IDs
2568 for javascript api is modified when separator string
2569 provided as parameter</li>
2570 <li>Null pointer exception when selecting tree leaves for
2571 alignment with no existing selection</li>
2572 <li>Relative URLs for datasources assumed to be relative
2573 to applet's codebase</li>
2574 <li>Status bar not updated after finished searching and
2575 search wraps around to first result</li>
2576 <li>StructureSelectionManager instance shared between
2577 several Jalview applets causes race conditions and memory
2579 <li>Hover tooltip and mouseover of position on structure
2580 not sent from Jmol in applet</li>
2581 <li>Certain sequences of javascript method calls to
2582 applet API fatally hang browser</li>
2583 </ul> <em>General</em>
2585 <li>View follows structure mouseover scrolls beyond
2586 position with wrapped view and hidden regions</li>
2587 <li>Find sequence position moves to wrong residue
2588 with/without hidden columns</li>
2589 <li>Sequence length given in alignment properties window
2591 <li>InvalidNumberFormat exceptions thrown when trying to
2592 import PDB like structure files</li>
2593 <li>Positional search results are only highlighted
2594 between user-supplied sequence start/end bounds</li>
2595 <li>End attribute of sequence is not validated</li>
2596 <li>Find dialog only finds first sequence containing a
2597 given sequence position</li>
2598 <li>Sequence numbering not preserved in MSF alignment
2600 <li>Jalview PDB file reader does not extract sequence
2601 from nucleotide chains correctly</li>
2602 <li>Structure colours not updated when tree partition
2603 changed in alignment</li>
2604 <li>Sequence associated secondary structure not correctly
2605 parsed in interleaved stockholm</li>
2606 <li>Colour by annotation dialog does not restore current
2608 <li>Hiding (nearly) all sequences doesn't work
2610 <li>Sequences containing lowercase letters are not
2611 properly associated with their pdb files</li>
2612 </ul> <em>Documentation and Development</em>
2614 <li>schemas/JalviewWsParamSet.xsd corrupted by
2615 ApplyCopyright tool</li>
2620 <div align="center">
2621 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2624 <td><em>Application</em>
2626 <li>New warning dialog when the Jalview Desktop cannot
2627 contact web services</li>
2628 <li>JABA service parameters for a preset are shown in
2629 service job window</li>
2630 <li>JABA Service menu entries reworded</li>
2634 <li>Modeller PIR IO broken - cannot correctly import a
2635 pir file emitted by Jalview</li>
2636 <li>Existing feature settings transferred to new
2637 alignment view created from cut'n'paste</li>
2638 <li>Improved test for mixed amino/nucleotide chains when
2639 parsing PDB files</li>
2640 <li>Consensus and conservation annotation rows
2641 occasionally become blank for all new windows</li>
2642 <li>Exception raised when right clicking above sequences
2643 in wrapped view mode</li>
2644 </ul> <em>Application</em>
2646 <li>multiple multiply aligned structure views cause cpu
2647 usage to hit 100% and computer to hang</li>
2648 <li>Web Service parameter layout breaks for long user
2649 parameter names</li>
2650 <li>Jaba service discovery hangs desktop if Jaba server
2657 <div align="center">
2658 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2661 <td><em>Application</em>
2663 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2664 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2667 <li>Web Services preference tab</li>
2668 <li>Analysis parameters dialog box and user defined
2670 <li>Improved speed and layout of Envision2 service menu</li>
2671 <li>Superpose structures using associated sequence
2673 <li>Export coordinates and projection as CSV from PCA
2675 </ul> <em>Applet</em>
2677 <li>enable javascript: execution by the applet via the
2678 link out mechanism</li>
2679 </ul> <em>Other</em>
2681 <li>Updated the Jmol Jalview interface to work with Jmol
2683 <li>The Jalview Desktop and JalviewLite applet now
2684 require Java 1.5</li>
2685 <li>Allow Jalview feature colour specification for GFF
2686 sequence annotation files</li>
2687 <li>New 'colour by label' keword in Jalview feature file
2688 type colour specification</li>
2689 <li>New Jalview Desktop Groovy API method that allows a
2690 script to check if it being run in an interactive session or
2691 in a batch operation from the Jalview command line</li>
2695 <li>clustalx colourscheme colours Ds preferentially when
2696 both D+E are present in over 50% of the column</li>
2697 </ul> <em>Application</em>
2699 <li>typo in AlignmentFrame->View->Hide->all but
2700 selected Regions menu item</li>
2701 <li>sequence fetcher replaces ',' for ';' when the ',' is
2702 part of a valid accession ID</li>
2703 <li>fatal OOM if object retrieved by sequence fetcher
2704 runs out of memory</li>
2705 <li>unhandled Out of Memory Error when viewing pca
2706 analysis results</li>
2707 <li>InstallAnywhere builds fail to launch on OS X java
2708 10.5 update 4 (due to apple Java 1.6 update)</li>
2709 <li>Installanywhere Jalview silently fails to launch</li>
2710 </ul> <em>Applet</em>
2712 <li>Jalview.getFeatureGroups() raises an
2713 ArrayIndexOutOfBoundsException if no feature groups are
2720 <div align="center">
2721 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2727 <li>Alignment prettyprinter doesn't cope with long
2729 <li>clustalx colourscheme colours Ds preferentially when
2730 both D+E are present in over 50% of the column</li>
2731 <li>nucleic acid structures retrieved from PDB do not
2732 import correctly</li>
2733 <li>More columns get selected than were clicked on when a
2734 number of columns are hidden</li>
2735 <li>annotation label popup menu not providing correct
2736 add/hide/show options when rows are hidden or none are
2738 <li>Stockholm format shown in list of readable formats,
2739 and parser copes better with alignments from RFAM.</li>
2740 <li>CSV output of consensus only includes the percentage
2741 of all symbols if sequence logo display is enabled</li>
2743 </ul> <em>Applet</em>
2745 <li>annotation panel disappears when annotation is
2747 </ul> <em>Application</em>
2749 <li>Alignment view not redrawn properly when new
2750 alignment opened where annotation panel is visible but no
2751 annotations are present on alignment</li>
2752 <li>pasted region containing hidden columns is
2753 incorrectly displayed in new alignment window</li>
2754 <li>Jalview slow to complete operations when stdout is
2755 flooded (fix is to close the Jalview console)</li>
2756 <li>typo in AlignmentFrame->View->Hide->all but
2757 selected Rregions menu item.</li>
2758 <li>inconsistent group submenu and Format submenu entry
2759 'Un' or 'Non'conserved</li>
2760 <li>Sequence feature settings are being shared by
2761 multiple distinct alignments</li>
2762 <li>group annotation not recreated when tree partition is
2764 <li>double click on group annotation to select sequences
2765 does not propagate to associated trees</li>
2766 <li>Mac OSX specific issues:
2768 <li>exception raised when mouse clicked on desktop
2769 window background</li>
2770 <li>Desktop menu placed on menu bar and application
2771 name set correctly</li>
2772 <li>sequence feature settings not wide enough for the
2773 save feature colourscheme button</li>
2782 <div align="center">
2783 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2786 <td><em>New Capabilities</em>
2788 <li>URL links generated from description line for
2789 regular-expression based URL links (applet and application)
2791 <li>Non-positional feature URL links are shown in link
2793 <li>Linked viewing of nucleic acid sequences and
2795 <li>Automatic Scrolling option in View menu to display
2796 the currently highlighted region of an alignment.</li>
2797 <li>Order an alignment by sequence length, or using the
2798 average score or total feature count for each sequence.</li>
2799 <li>Shading features by score or associated description</li>
2800 <li>Subdivide alignment and groups based on identity of
2801 selected subsequence (Make Groups from Selection).</li>
2802 <li>New hide/show options including Shift+Control+H to
2803 hide everything but the currently selected region.</li>
2804 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2805 </ul> <em>Application</em>
2807 <li>Fetch DB References capabilities and UI expanded to
2808 support retrieval from DAS sequence sources</li>
2809 <li>Local DAS Sequence sources can be added via the
2810 command line or via the Add local source dialog box.</li>
2811 <li>DAS Dbref and DbxRef feature types are parsed as
2812 database references and protein_name is parsed as
2813 description line (BioSapiens terms).</li>
2814 <li>Enable or disable non-positional feature and database
2815 references in sequence ID tooltip from View menu in
2817 <!-- <li>New hidden columns and rows and representatives capabilities
2818 in annotations file (in progress - not yet fully implemented)</li> -->
2819 <li>Group-associated consensus, sequence logos and
2820 conservation plots</li>
2821 <li>Symbol distributions for each column can be exported
2822 and visualized as sequence logos</li>
2823 <li>Optionally scale multi-character column labels to fit
2824 within each column of annotation row<!-- todo for applet -->
2826 <li>Optional automatic sort of associated alignment view
2827 when a new tree is opened.</li>
2828 <li>Jalview Java Console</li>
2829 <li>Better placement of desktop window when moving
2830 between different screens.</li>
2831 <li>New preference items for sequence ID tooltip and
2832 consensus annotation</li>
2833 <li>Client to submit sequences and IDs to Envision2
2835 <li><em>Vamsas Capabilities</em>
2837 <li>Improved VAMSAS synchronization (Jalview archive
2838 used to preserve views, structures, and tree display
2840 <li>Import of vamsas documents from disk or URL via
2842 <li>Sharing of selected regions between views and
2843 with other VAMSAS applications (Experimental feature!)</li>
2844 <li>Updated API to VAMSAS version 0.2</li>
2846 </ul> <em>Applet</em>
2848 <li>Middle button resizes annotation row height</li>
2851 <li>sortByTree (true/false) - automatically sort the
2852 associated alignment view by the tree when a new tree is
2854 <li>showTreeBootstraps (true/false) - show or hide
2855 branch bootstraps (default is to show them if available)</li>
2856 <li>showTreeDistances (true/false) - show or hide
2857 branch lengths (default is to show them if available)</li>
2858 <li>showUnlinkedTreeNodes (true/false) - indicate if
2859 unassociated nodes should be highlighted in the tree
2861 <li>heightScale and widthScale (1.0 or more) -
2862 increase the height or width of a cell in the alignment
2863 grid relative to the current font size.</li>
2866 <li>Non-positional features displayed in sequence ID
2868 </ul> <em>Other</em>
2870 <li>Features format: graduated colour definitions and
2871 specification of feature scores</li>
2872 <li>Alignment Annotations format: new keywords for group
2873 associated annotation (GROUP_REF) and annotation row display
2874 properties (ROW_PROPERTIES)</li>
2875 <li>XML formats extended to support graduated feature
2876 colourschemes, group associated annotation, and profile
2877 visualization settings.</li></td>
2880 <li>Source field in GFF files parsed as feature source
2881 rather than description</li>
2882 <li>Non-positional features are now included in sequence
2883 feature and gff files (controlled via non-positional feature
2884 visibility in tooltip).</li>
2885 <li>URL links generated for all feature links (bugfix)</li>
2886 <li>Added URL embedding instructions to features file
2888 <li>Codons containing ambiguous nucleotides translated as
2889 'X' in peptide product</li>
2890 <li>Match case switch in find dialog box works for both
2891 sequence ID and sequence string and query strings do not
2892 have to be in upper case to match case-insensitively.</li>
2893 <li>AMSA files only contain first column of
2894 multi-character column annotation labels</li>
2895 <li>Jalview Annotation File generation/parsing consistent
2896 with documentation (e.g. Stockholm annotation can be
2897 exported and re-imported)</li>
2898 <li>PDB files without embedded PDB IDs given a friendly
2900 <li>Find incrementally searches ID string matches as well
2901 as subsequence matches, and correctly reports total number
2905 <li>Better handling of exceptions during sequence
2907 <li>Dasobert generated non-positional feature URL
2908 link text excludes the start_end suffix</li>
2909 <li>DAS feature and source retrieval buttons disabled
2910 when fetch or registry operations in progress.</li>
2911 <li>PDB files retrieved from URLs are cached properly</li>
2912 <li>Sequence description lines properly shared via
2914 <li>Sequence fetcher fetches multiple records for all
2916 <li>Ensured that command line das feature retrieval
2917 completes before alignment figures are generated.</li>
2918 <li>Reduced time taken when opening file browser for
2920 <li>isAligned check prior to calculating tree, PCA or
2921 submitting an MSA to JNet now excludes hidden sequences.</li>
2922 <li>User defined group colours properly recovered
2923 from Jalview projects.</li>
2932 <div align="center">
2933 <strong>2.4.0.b2</strong><br> 28/10/2009
2938 <li>Experimental support for google analytics usage
2940 <li>Jalview privacy settings (user preferences and docs).</li>
2945 <li>Race condition in applet preventing startup in
2947 <li>Exception when feature created from selection beyond
2948 length of sequence.</li>
2949 <li>Allow synthetic PDB files to be imported gracefully</li>
2950 <li>Sequence associated annotation rows associate with
2951 all sequences with a given id</li>
2952 <li>Find function matches case-insensitively for sequence
2953 ID string searches</li>
2954 <li>Non-standard characters do not cause pairwise
2955 alignment to fail with exception</li>
2956 </ul> <em>Application Issues</em>
2958 <li>Sequences are now validated against EMBL database</li>
2959 <li>Sequence fetcher fetches multiple records for all
2961 </ul> <em>InstallAnywhere Issues</em>
2963 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2964 issue with installAnywhere mechanism)</li>
2965 <li>Command line launching of JARs from InstallAnywhere
2966 version (java class versioning error fixed)</li>
2973 <div align="center">
2974 <strong>2.4</strong><br> 27/8/2008
2977 <td><em>User Interface</em>
2979 <li>Linked highlighting of codon and amino acid from
2980 translation and protein products</li>
2981 <li>Linked highlighting of structure associated with
2982 residue mapping to codon position</li>
2983 <li>Sequence Fetcher provides example accession numbers
2984 and 'clear' button</li>
2985 <li>MemoryMonitor added as an option under Desktop's
2987 <li>Extract score function to parse whitespace separated
2988 numeric data in description line</li>
2989 <li>Column labels in alignment annotation can be centred.</li>
2990 <li>Tooltip for sequence associated annotation give name
2992 </ul> <em>Web Services and URL fetching</em>
2994 <li>JPred3 web service</li>
2995 <li>Prototype sequence search client (no public services
2997 <li>Fetch either seed alignment or full alignment from
2999 <li>URL Links created for matching database cross
3000 references as well as sequence ID</li>
3001 <li>URL Links can be created using regular-expressions</li>
3002 </ul> <em>Sequence Database Connectivity</em>
3004 <li>Retrieval of cross-referenced sequences from other
3006 <li>Generalised database reference retrieval and
3007 validation to all fetchable databases</li>
3008 <li>Fetch sequences from DAS sources supporting the
3009 sequence command</li>
3010 </ul> <em>Import and Export</em>
3011 <li>export annotation rows as CSV for spreadsheet import</li>
3012 <li>Jalview projects record alignment dataset associations,
3013 EMBL products, and cDNA sequence mappings</li>
3014 <li>Sequence Group colour can be specified in Annotation
3016 <li>Ad-hoc colouring of group in Annotation File using RGB
3017 triplet as name of colourscheme</li>
3018 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3020 <li>treenode binding for VAMSAS tree exchange</li>
3021 <li>local editing and update of sequences in VAMSAS
3022 alignments (experimental)</li>
3023 <li>Create new or select existing session to join</li>
3024 <li>load and save of vamsas documents</li>
3025 </ul> <em>Application command line</em>
3027 <li>-tree parameter to open trees (introduced for passing
3029 <li>-fetchfrom command line argument to specify nicknames
3030 of DAS servers to query for alignment features</li>
3031 <li>-dasserver command line argument to add new servers
3032 that are also automatically queried for features</li>
3033 <li>-groovy command line argument executes a given groovy
3034 script after all input data has been loaded and parsed</li>
3035 </ul> <em>Applet-Application data exchange</em>
3037 <li>Trees passed as applet parameters can be passed to
3038 application (when using "View in full
3039 application")</li>
3040 </ul> <em>Applet Parameters</em>
3042 <li>feature group display control parameter</li>
3043 <li>debug parameter</li>
3044 <li>showbutton parameter</li>
3045 </ul> <em>Applet API methods</em>
3047 <li>newView public method</li>
3048 <li>Window (current view) specific get/set public methods</li>
3049 <li>Feature display control methods</li>
3050 <li>get list of currently selected sequences</li>
3051 </ul> <em>New Jalview distribution features</em>
3053 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3054 <li>RELEASE file gives build properties for the latest
3055 Jalview release.</li>
3056 <li>Java 1.1 Applet build made easier and donotobfuscate
3057 property controls execution of obfuscator</li>
3058 <li>Build target for generating source distribution</li>
3059 <li>Debug flag for javacc</li>
3060 <li>.jalview_properties file is documented (slightly) in
3061 jalview.bin.Cache</li>
3062 <li>Continuous Build Integration for stable and
3063 development version of Application, Applet and source
3068 <li>selected region output includes visible annotations
3069 (for certain formats)</li>
3070 <li>edit label/displaychar contains existing label/char
3072 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3073 <li>shorter peptide product names from EMBL records</li>
3074 <li>Newick string generator makes compact representations</li>
3075 <li>bootstrap values parsed correctly for tree files with
3077 <li>pathological filechooser bug avoided by not allowing
3078 filenames containing a ':'</li>
3079 <li>Fixed exception when parsing GFF files containing
3080 global sequence features</li>
3081 <li>Alignment datasets are finalized only when number of
3082 references from alignment sequences goes to zero</li>
3083 <li>Close of tree branch colour box without colour
3084 selection causes cascading exceptions</li>
3085 <li>occasional negative imgwidth exceptions</li>
3086 <li>better reporting of non-fatal warnings to user when
3087 file parsing fails.</li>
3088 <li>Save works when Jalview project is default format</li>
3089 <li>Save as dialog opened if current alignment format is
3090 not a valid output format</li>
3091 <li>UniProt canonical names introduced for both das and
3093 <li>Histidine should be midblue (not pink!) in Zappo</li>
3094 <li>error messages passed up and output when data read
3096 <li>edit undo recovers previous dataset sequence when
3097 sequence is edited</li>
3098 <li>allow PDB files without pdb ID HEADER lines (like
3099 those generated by MODELLER) to be read in properly</li>
3100 <li>allow reading of JPred concise files as a normal
3102 <li>Stockholm annotation parsing and alignment properties
3103 import fixed for PFAM records</li>
3104 <li>Structure view windows have correct name in Desktop
3106 <li>annotation consisting of sequence associated scores
3107 can be read and written correctly to annotation file</li>
3108 <li>Aligned cDNA translation to aligned peptide works
3110 <li>Fixed display of hidden sequence markers and
3111 non-italic font for representatives in Applet</li>
3112 <li>Applet Menus are always embedded in applet window on
3114 <li>Newly shown features appear at top of stack (in
3116 <li>Annotations added via parameter not drawn properly
3117 due to null pointer exceptions</li>
3118 <li>Secondary structure lines are drawn starting from
3119 first column of alignment</li>
3120 <li>UniProt XML import updated for new schema release in
3122 <li>Sequence feature to sequence ID match for Features
3123 file is case-insensitive</li>
3124 <li>Sequence features read from Features file appended to
3125 all sequences with matching IDs</li>
3126 <li>PDB structure coloured correctly for associated views
3127 containing a sub-sequence</li>
3128 <li>PDB files can be retrieved by applet from Jar files</li>
3129 <li>feature and annotation file applet parameters
3130 referring to different directories are retrieved correctly</li>
3131 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3132 <li>Fixed application hang whilst waiting for
3133 splash-screen version check to complete</li>
3134 <li>Applet properly URLencodes input parameter values
3135 when passing them to the launchApp service</li>
3136 <li>display name and local features preserved in results
3137 retrieved from web service</li>
3138 <li>Visual delay indication for sequence retrieval and
3139 sequence fetcher initialisation</li>
3140 <li>updated Application to use DAS 1.53e version of
3141 dasobert DAS client</li>
3142 <li>Re-instated Full AMSA support and .amsa file
3144 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3152 <div align="center">
3153 <strong>2.3</strong><br> 9/5/07
3158 <li>Jmol 11.0.2 integration</li>
3159 <li>PDB views stored in Jalview XML files</li>
3160 <li>Slide sequences</li>
3161 <li>Edit sequence in place</li>
3162 <li>EMBL CDS features</li>
3163 <li>DAS Feature mapping</li>
3164 <li>Feature ordering</li>
3165 <li>Alignment Properties</li>
3166 <li>Annotation Scores</li>
3167 <li>Sort by scores</li>
3168 <li>Feature/annotation editing in applet</li>
3173 <li>Headless state operation in 2.2.1</li>
3174 <li>Incorrect and unstable DNA pairwise alignment</li>
3175 <li>Cut and paste of sequences with annotation</li>
3176 <li>Feature group display state in XML</li>
3177 <li>Feature ordering in XML</li>
3178 <li>blc file iteration selection using filename # suffix</li>
3179 <li>Stockholm alignment properties</li>
3180 <li>Stockhom alignment secondary structure annotation</li>
3181 <li>2.2.1 applet had no feature transparency</li>
3182 <li>Number pad keys can be used in cursor mode</li>
3183 <li>Structure Viewer mirror image resolved</li>
3190 <div align="center">
3191 <strong>2.2.1</strong><br> 12/2/07
3196 <li>Non standard characters can be read and displayed
3197 <li>Annotations/Features can be imported/exported to the
3199 <li>Applet allows editing of sequence/annotation/group
3200 name & description
3201 <li>Preference setting to display sequence name in
3203 <li>Annotation file format extended to allow
3204 Sequence_groups to be defined
3205 <li>Default opening of alignment overview panel can be
3206 specified in preferences
3207 <li>PDB residue numbering annotation added to associated
3213 <li>Applet crash under certain Linux OS with Java 1.6
3215 <li>Annotation file export / import bugs fixed
3216 <li>PNG / EPS image output bugs fixed
3222 <div align="center">
3223 <strong>2.2</strong><br> 27/11/06
3228 <li>Multiple views on alignment
3229 <li>Sequence feature editing
3230 <li>"Reload" alignment
3231 <li>"Save" to current filename
3232 <li>Background dependent text colour
3233 <li>Right align sequence ids
3234 <li>User-defined lower case residue colours
3237 <li>Menu item accelerator keys
3238 <li>Control-V pastes to current alignment
3239 <li>Cancel button for DAS Feature Fetching
3240 <li>PCA and PDB Viewers zoom via mouse roller
3241 <li>User-defined sub-tree colours and sub-tree selection
3243 <li>'New Window' button on the 'Output to Text box'
3248 <li>New memory efficient Undo/Redo System
3249 <li>Optimised symbol lookups and conservation/consensus
3251 <li>Region Conservation/Consensus recalculated after
3253 <li>Fixed Remove Empty Columns Bug (empty columns at end
3255 <li>Slowed DAS Feature Fetching for increased robustness.
3257 <li>Made angle brackets in ASCII feature descriptions
3259 <li>Re-instated Zoom function for PCA
3260 <li>Sequence descriptions conserved in web service
3262 <li>UniProt ID discoverer uses any word separated by
3264 <li>WsDbFetch query/result association resolved
3265 <li>Tree leaf to sequence mapping improved
3266 <li>Smooth fonts switch moved to FontChooser dialog box.
3273 <div align="center">
3274 <strong>2.1.1</strong><br> 12/9/06
3279 <li>Copy consensus sequence to clipboard</li>
3284 <li>Image output - rightmost residues are rendered if
3285 sequence id panel has been resized</li>
3286 <li>Image output - all offscreen group boundaries are
3288 <li>Annotation files with sequence references - all
3289 elements in file are relative to sequence position</li>
3290 <li>Mac Applet users can use Alt key for group editing</li>
3296 <div align="center">
3297 <strong>2.1</strong><br> 22/8/06
3302 <li>MAFFT Multiple Alignment in default Web Service list</li>
3303 <li>DAS Feature fetching</li>
3304 <li>Hide sequences and columns</li>
3305 <li>Export Annotations and Features</li>
3306 <li>GFF file reading / writing</li>
3307 <li>Associate structures with sequences from local PDB
3309 <li>Add sequences to exisiting alignment</li>
3310 <li>Recently opened files / URL lists</li>
3311 <li>Applet can launch the full application</li>
3312 <li>Applet has transparency for features (Java 1.2
3314 <li>Applet has user defined colours parameter</li>
3315 <li>Applet can load sequences from parameter
3316 "sequence<em>x</em>"
3322 <li>Redundancy Panel reinstalled in the Applet</li>
3323 <li>Monospaced font - EPS / rescaling bug fixed</li>
3324 <li>Annotation files with sequence references bug fixed</li>
3330 <div align="center">
3331 <strong>2.08.1</strong><br> 2/5/06
3336 <li>Change case of selected region from Popup menu</li>
3337 <li>Choose to match case when searching</li>
3338 <li>Middle mouse button and mouse movement can compress /
3339 expand the visible width and height of the alignment</li>
3344 <li>Annotation Panel displays complete JNet results</li>
3350 <div align="center">
3351 <strong>2.08b</strong><br> 18/4/06
3357 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3358 <li>Righthand label on wrapped alignments shows correct
3365 <div align="center">
3366 <strong>2.08</strong><br> 10/4/06
3371 <li>Editing can be locked to the selection area</li>
3372 <li>Keyboard editing</li>
3373 <li>Create sequence features from searches</li>
3374 <li>Precalculated annotations can be loaded onto
3376 <li>Features file allows grouping of features</li>
3377 <li>Annotation Colouring scheme added</li>
3378 <li>Smooth fonts off by default - Faster rendering</li>
3379 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3384 <li>Drag & Drop fixed on Linux</li>
3385 <li>Jalview Archive file faster to load/save, sequence
3386 descriptions saved.</li>
3392 <div align="center">
3393 <strong>2.07</strong><br> 12/12/05
3398 <li>PDB Structure Viewer enhanced</li>
3399 <li>Sequence Feature retrieval and display enhanced</li>
3400 <li>Choose to output sequence start-end after sequence
3401 name for file output</li>
3402 <li>Sequence Fetcher WSDBFetch@EBI</li>
3403 <li>Applet can read feature files, PDB files and can be
3404 used for HTML form input</li>
3409 <li>HTML output writes groups and features</li>
3410 <li>Group editing is Control and mouse click</li>
3411 <li>File IO bugs</li>
3417 <div align="center">
3418 <strong>2.06</strong><br> 28/9/05
3423 <li>View annotations in wrapped mode</li>
3424 <li>More options for PCA viewer</li>
3429 <li>GUI bugs resolved</li>
3430 <li>Runs with -nodisplay from command line</li>
3436 <div align="center">
3437 <strong>2.05b</strong><br> 15/9/05
3442 <li>Choose EPS export as lineart or text</li>
3443 <li>Jar files are executable</li>
3444 <li>Can read in Uracil - maps to unknown residue</li>
3449 <li>Known OutOfMemory errors give warning message</li>
3450 <li>Overview window calculated more efficiently</li>
3451 <li>Several GUI bugs resolved</li>
3457 <div align="center">
3458 <strong>2.05</strong><br> 30/8/05
3463 <li>Edit and annotate in "Wrapped" view</li>
3468 <li>Several GUI bugs resolved</li>
3474 <div align="center">
3475 <strong>2.04</strong><br> 24/8/05
3480 <li>Hold down mouse wheel & scroll to change font
3486 <li>Improved JPred client reliability</li>
3487 <li>Improved loading of Jalview files</li>
3493 <div align="center">
3494 <strong>2.03</strong><br> 18/8/05
3499 <li>Set Proxy server name and port in preferences</li>
3500 <li>Multiple URL links from sequence ids</li>
3501 <li>User Defined Colours can have a scheme name and added
3503 <li>Choose to ignore gaps in consensus calculation</li>
3504 <li>Unix users can set default web browser</li>
3505 <li>Runs without GUI for batch processing</li>
3506 <li>Dynamically generated Web Service Menus</li>
3511 <li>InstallAnywhere download for Sparc Solaris</li>
3517 <div align="center">
3518 <strong>2.02</strong><br> 18/7/05
3524 <li>Copy & Paste order of sequences maintains
3525 alignment order.</li>
3531 <div align="center">
3532 <strong>2.01</strong><br> 12/7/05
3537 <li>Use delete key for deleting selection.</li>
3538 <li>Use Mouse wheel to scroll sequences.</li>
3539 <li>Help file updated to describe how to add alignment
3541 <li>Version and build date written to build properties
3543 <li>InstallAnywhere installation will check for updates
3544 at launch of Jalview.</li>
3549 <li>Delete gaps bug fixed.</li>
3550 <li>FileChooser sorts columns.</li>
3551 <li>Can remove groups one by one.</li>
3552 <li>Filechooser icons installed.</li>
3553 <li>Finder ignores return character when searching.
3554 Return key will initiate a search.<br>
3561 <div align="center">
3562 <strong>2.0</strong><br> 20/6/05
3567 <li>New codebase</li>