3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.3">2.10.3</a><br />
74 <em>10/10/2017</em></strong>
77 <td><div align="left">
81 <!-- JAL-2446 -->Faster and more efficient management and
82 rendering of sequence features
85 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
86 429 rate limit request hander
89 <!-- JAL-2773 -->Structure views don't get updated unless
90 their colours have changed
92 <li><!-- JAL-2495 -->All linked sequences are highlighted for a structure mousover (Jmol) or selection (Chimera)</li>
93 <li><!-- JAL-2790 -->'Cancel' button in progress bar for JABAWS AACon, RNAAliFold and Disorder prediction jobs
97 <ul><li>Example groovy script for generating a matrix of percent identity scores for current alignment.</li></ul>
98 <em>Testing and Deployment</em>
99 <ul><li><!-- JAL-2727 -->Test to catch memory leaks in Jalview UI</li></ul>
102 <td><div align="left">
105 <li><!-- JAL-2643 -->Pressing tab after updating the colour threshold text field doesn't trigger an update to the alignment view</li>
106 <li><!-- JAL-2682 -->Race condition when parsing sequence ID strings in parallel</li>
107 <li><!-- JAL-2608 -->Overview windows are also closed when alignment window is closed</li>
111 <li><!-- JAL-2777 -->Structures with whitespace chainCode cannot be viewed in Chimera</li>
112 <li><!-- JAL-2728 -->Protein annotation panel too high in CDS/Protein view
114 <li><!-- JAL-2757 -->Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs
116 <li><!-- JAL-2253 -->Slow EnsemblGenome ID lookup</li>
117 <li><!-- JAL-2739 -->Hidden column marker in last column not rendered when switching back from Wrapped to normal view</li>
118 <li><!-- JAL-2768 -->Annotation display corrupted when scrolling right in unwapped alignment view</li>
119 <li><!-- JAL-2542 -->Existing features on subsequence incorrectly relocated when full sequence retrieved from database</li>
120 <li><!-- JAL-2733 -->Last reported memory still shown when Desktop->Show Memory is unticked (OSX only)</li>
121 <li><!-- JAL-2658 -->Amend Features dialog doesn't allow features of same type and group to be selected for amending</li>
122 <li><!-- JAL-2524 -->Jalview becomes sluggish in wide alignments when hidden columns are present</li>
123 <li><!-- JAL-2392 -->Jalview freezes when loading and displaying several structures</li>
124 <li><!-- JAL-2732 -->Black outlines left after resizing or moving a window</li>
125 <li><!-- JAL-1900,JAL-1625 -->Unable to minimise windows within the Jalview desktop on OSX</li>
126 <li><!-- JAL-2667 -->Mouse wheel doesn't scroll vertically when in wrapped alignment mode</li>
127 <li><!-- JAL-2636 -->Scale mark not shown when close to right hand end of alignment</li>
129 <strong><em>Applet</em></strong><br/>
131 <li><!-- JAL-2687 -->Concurrent modification exception when closing alignment panel</li>
137 <td width="60" nowrap>
139 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
140 <em>2/10/2017</em></strong>
143 <td><div align="left">
144 <em>New features in Jalview Desktop</em>
147 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
149 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
153 <td><div align="left">
157 <td width="60" nowrap>
159 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
160 <em>7/9/2017</em></strong>
163 <td><div align="left">
167 <!-- JAL-2588 -->Show gaps in overview window by colouring
168 in grey (sequences used to be coloured grey, and gaps were
172 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
176 <!-- JAL-2587 -->Overview updates immediately on increase
177 in size and progress bar shown as higher resolution
178 overview is recalculated
183 <td><div align="left">
187 <!-- JAL-2664 -->Overview window redraws every hidden
188 column region row by row
191 <!-- JAL-2681 -->duplicate protein sequences shown after
192 retrieving Ensembl crossrefs for sequences from Uniprot
195 <!-- JAL-2603 -->Overview window throws NPE if show boxes
196 format setting is unticked
199 <!-- JAL-2610 -->Groups are coloured wrongly in overview
200 if group has show boxes format setting unticked
203 <!-- JAL-2672,JAL-2665 -->Redraw problems when
204 autoscrolling whilst dragging current selection group to
205 include sequences and columns not currently displayed
208 <!-- JAL-2691 -->Not all chains are mapped when multimeric
209 assemblies are imported via CIF file
212 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
213 displayed when threshold or conservation colouring is also
217 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
221 <!-- JAL-2673 -->Jalview continues to scroll after
222 dragging a selected region off the visible region of the
226 <!-- JAL-2724 -->Cannot apply annotation based
227 colourscheme to all groups in a view
230 <!-- JAL-2511 -->IDs don't line up with sequences
231 initially after font size change using the Font chooser or
238 <td width="60" nowrap>
240 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
243 <td><div align="left">
244 <em>Calculations</em>
248 <!-- JAL-1933 -->Occupancy annotation row shows number of
249 ungapped positions in each column of the alignment.
252 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
253 a calculation dialog box
256 <!-- JAL-2379 -->Revised implementation of PCA for speed
257 and memory efficiency (~30x faster)
260 <!-- JAL-2403 -->Revised implementation of sequence
261 similarity scores as used by Tree, PCA, Shading Consensus
262 and other calculations
265 <!-- JAL-2416 -->Score matrices are stored as resource
266 files within the Jalview codebase
269 <!-- JAL-2500 -->Trees computed on Sequence Feature
270 Similarity may have different topology due to increased
277 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
278 model for alignments and groups
281 <!-- JAL-384 -->Custom shading schemes created via groovy
288 <!-- JAL-2526 -->Efficiency improvements for interacting
289 with alignment and overview windows
292 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
296 <!-- JAL-2388 -->Hidden columns and sequences can be
300 <!-- JAL-2611 -->Click-drag in visible area allows fine
301 adjustment of visible position
305 <em>Data import/export</em>
308 <!-- JAL-2535 -->Posterior probability annotation from
309 Stockholm files imported as sequence associated annotation
312 <!-- JAL-2507 -->More robust per-sequence positional
313 annotation input/output via stockholm flatfile
316 <!-- JAL-2533 -->Sequence names don't include file
317 extension when importing structure files without embedded
318 names or PDB accessions
321 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
322 format sequence substitution matrices
325 <em>User Interface</em>
328 <!-- JAL-2447 --> Experimental Features Checkbox in
329 Desktop's Tools menu to hide or show untested features in
333 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
334 via Overview or sequence motif search operations
337 <!-- JAL-2547 -->Amend sequence features dialog box can be
338 opened by double clicking gaps within sequence feature
342 <!-- JAL-1476 -->Status bar message shown when not enough
343 aligned positions were available to create a 3D structure
347 <em>3D Structure</em>
350 <!-- JAL-2430 -->Hidden regions in alignment views are not
351 coloured in linked structure views
354 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
355 file-based command exchange
358 <!-- JAL-2375 -->Structure chooser automatically shows
359 Cached Structures rather than querying the PDBe if
360 structures are already available for sequences
363 <!-- JAL-2520 -->Structures imported via URL are cached in
364 the Jalview project rather than downloaded again when the
368 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
369 to transfer Chimera's structure attributes as Jalview
370 features, and vice-versa (<strong>Experimental
374 <em>Web Services</em>
377 <!-- JAL-2549 -->Updated JABAWS client to v2.2
380 <!-- JAL-2335 -->Filter non-standard amino acids and
381 nucleotides when submitting to AACon and other MSA
385 <!-- JAL-2316, -->URLs for viewing database
386 cross-references provided by identifiers.org and the
394 <!-- JAL-2344 -->FileFormatI interface for describing and
395 identifying file formats (instead of String constants)
398 <!-- JAL-2228 -->FeatureCounter script refactored for
399 efficiency when counting all displayed features (not
400 backwards compatible with 2.10.1)
403 <em>Example files</em>
406 <!-- JAL-2631 -->Graduated feature colour style example
407 included in the example feature file
410 <em>Documentation</em>
413 <!-- JAL-2339 -->Release notes reformatted for readability
414 with the built-in Java help viewer
417 <!-- JAL-1644 -->Find documentation updated with 'search
418 sequence description' option
424 <!-- JAL-2485, -->External service integration tests for
425 Uniprot REST Free Text Search Client
428 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
431 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
436 <td><div align="left">
437 <em>Calculations</em>
440 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
441 matrix - C->R should be '-3'<br />Old matrix restored
442 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
444 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
445 Jalview's treatment of gaps in PCA and substitution matrix
446 based Tree calculations.<br /> <br />In earlier versions
447 of Jalview, gaps matching gaps were penalised, and gaps
448 matching non-gaps penalised even more. In the PCA
449 calculation, gaps were actually treated as non-gaps - so
450 different costs were applied, which meant Jalview's PCAs
451 were different to those produced by SeqSpace.<br />Jalview
452 now treats gaps in the same way as SeqSpace (ie it scores
453 them as 0). <br /> <br />Enter the following in the
454 Groovy console to restore pre-2.10.2 behaviour:<br />
455 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
456 // for 2.10.1 mode <br />
457 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
458 // to restore 2.10.2 mode <br /> <br /> <em>Note:
459 these settings will affect all subsequent tree and PCA
460 calculations (not recommended)</em></li>
462 <!-- JAL-2424 -->Fixed off-by-one bug that affected
463 scaling of branch lengths for trees computed using
464 Sequence Feature Similarity.
467 <!-- JAL-2377 -->PCA calculation could hang when
468 generating output report when working with highly
472 <!-- JAL-2544 --> Sort by features includes features to
473 right of selected region when gaps present on right-hand
477 <em>User Interface</em>
480 <!-- JAL-2346 -->Reopening Colour by annotation dialog
481 doesn't reselect a specific sequence's associated
482 annotation after it was used for colouring a view
485 <!-- JAL-2419 -->Current selection lost if popup menu
486 opened on a region of alignment without groups
489 <!-- JAL-2374 -->Popup menu not always shown for regions
490 of an alignment with overlapping groups
493 <!-- JAL-2310 -->Finder double counts if both a sequence's
494 name and description match
497 <!-- JAL-2370 -->Hiding column selection containing two
498 hidden regions results in incorrect hidden regions
501 <!-- JAL-2386 -->'Apply to all groups' setting when
502 changing colour does not apply Conservation slider value
506 <!-- JAL-2373 -->Percentage identity and conservation menu
507 items do not show a tick or allow shading to be disabled
510 <!-- JAL-2385 -->Conservation shading or PID threshold
511 lost when base colourscheme changed if slider not visible
514 <!-- JAL-2547 -->Sequence features shown in tooltip for
515 gaps before start of features
518 <!-- JAL-2623 -->Graduated feature colour threshold not
519 restored to UI when feature colour is edited
522 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
523 a time when scrolling vertically in wrapped mode.
526 <!-- JAL-2630 -->Structure and alignment overview update
527 as graduate feature colour settings are modified via the
531 <!-- JAL-2034 -->Overview window doesn't always update
532 when a group defined on the alignment is resized
535 <!-- JAL-2605 -->Mouseovers on left/right scale region in
536 wrapped view result in positional status updates
540 <!-- JAL-2563 -->Status bar doesn't show position for
541 ambiguous amino acid and nucleotide symbols
544 <!-- JAL-2602 -->Copy consensus sequence failed if
545 alignment included gapped columns
548 <!-- JAL-2473 -->Minimum size set for Jalview windows so
549 widgets don't permanently disappear
552 <!-- JAL-2503 -->Cannot select or filter quantitative
553 annotation that are shown only as column labels (e.g.
554 T-Coffee column reliability scores)
557 <!-- JAL-2594 -->Exception thrown if trying to create a
558 sequence feature on gaps only
561 <!-- JAL-2504 -->Features created with 'New feature'
562 button from a Find inherit previously defined feature type
563 rather than the Find query string
566 <!-- JAL-2423 -->incorrect title in output window when
567 exporting tree calculated in Jalview
570 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
571 and then revealing them reorders sequences on the
575 <!-- JAL-964 -->Group panel in sequence feature settings
576 doesn't update to reflect available set of groups after
577 interactively adding or modifying features
580 <!-- JAL-2225 -->Sequence Database chooser unusable on
584 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
585 only excluded gaps in current sequence and ignored
592 <!-- JAL-2421 -->Overview window visible region moves
593 erratically when hidden rows or columns are present
596 <!-- JAL-2362 -->Per-residue colourschemes applied via the
597 Structure Viewer's colour menu don't correspond to
601 <!-- JAL-2405 -->Protein specific colours only offered in
602 colour and group colour menu for protein alignments
605 <!-- JAL-2385 -->Colour threshold slider doesn't update to
606 reflect currently selected view or group's shading
610 <!-- JAL-2624 -->Feature colour thresholds not respected
611 when rendered on overview and structures when opacity at
615 <!-- JAL-2589 -->User defined gap colour not shown in
616 overview when features overlaid on alignment
619 <em>Data import/export</em>
622 <!-- JAL-2576 -->Very large alignments take a long time to
626 <!-- JAL-2507 -->Per-sequence RNA secondary structures
627 added after a sequence was imported are not written to
631 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
632 when importing RNA secondary structure via Stockholm
635 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
636 not shown in correct direction for simple pseudoknots
639 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
640 with lightGray or darkGray via features file (but can
644 <!-- JAL-2383 -->Above PID colour threshold not recovered
645 when alignment view imported from project
648 <!-- JAL-2520,JAL-2465 -->No mappings generated between
649 structure and sequences extracted from structure files
650 imported via URL and viewed in Jmol
653 <!-- JAL-2520 -->Structures loaded via URL are saved in
654 Jalview Projects rather than fetched via URL again when
655 the project is loaded and the structure viewed
658 <em>Web Services</em>
661 <!-- JAL-2519 -->EnsemblGenomes example failing after
662 release of Ensembl v.88
665 <!-- JAL-2366 -->Proxy server address and port always
666 appear enabled in Preferences->Connections
669 <!-- JAL-2461 -->DAS registry not found exceptions
670 removed from console output
673 <!-- JAL-2582 -->Cannot retrieve protein products from
674 Ensembl by Peptide ID
677 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
678 created from SIFTs, and spurious 'Couldn't open structure
679 in Chimera' errors raised after April 2017 update (problem
680 due to 'null' string rather than empty string used for
681 residues with no corresponding PDB mapping).
684 <em>Application UI</em>
687 <!-- JAL-2361 -->User Defined Colours not added to Colour
691 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
692 case' residues (button in colourscheme editor debugged and
693 new documentation and tooltips added)
696 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
697 doesn't restore group-specific text colour thresholds
700 <!-- JAL-2243 -->Feature settings panel does not update as
701 new features are added to alignment
704 <!-- JAL-2532 -->Cancel in feature settings reverts
705 changes to feature colours via the Amend features dialog
708 <!-- JAL-2506 -->Null pointer exception when attempting to
709 edit graduated feature colour via amend features dialog
713 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
714 selection menu changes colours of alignment views
717 <!-- JAL-2426 -->Spurious exceptions in console raised
718 from alignment calculation workers after alignment has
722 <!-- JAL-1608 -->Typo in selection popup menu - Create
723 groups now 'Create Group'
726 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
727 Create/Undefine group doesn't always work
730 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
731 shown again after pressing 'Cancel'
734 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
735 adjusts start position in wrap mode
738 <!-- JAL-2563 -->Status bar doesn't show positions for
739 ambiguous amino acids
742 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
743 CDS/Protein view after CDS sequences added for aligned
747 <!-- JAL-2592 -->User defined colourschemes called 'User
748 Defined' don't appear in Colours menu
754 <!-- JAL-2468 -->Switching between Nucleotide and Protein
755 score models doesn't always result in an updated PCA plot
758 <!-- JAL-2442 -->Features not rendered as transparent on
759 overview or linked structure view
762 <!-- JAL-2372 -->Colour group by conservation doesn't
766 <!-- JAL-2517 -->Hitting Cancel after applying
767 user-defined colourscheme doesn't restore original
774 <!-- JAL-2314 -->Unit test failure:
775 jalview.ws.jabaws.RNAStructExportImport setup fails
778 <!-- JAL-2307 -->Unit test failure:
779 jalview.ws.sifts.SiftsClientTest due to compatibility
780 problems with deep array comparison equality asserts in
781 successive versions of TestNG
784 <!-- JAL-2479 -->Relocated StructureChooserTest and
785 ParameterUtilsTest Unit tests to Network suite
788 <em>New Known Issues</em>
791 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
792 phase after a sequence motif find operation
795 <!-- JAL-2550 -->Importing annotation file with rows
796 containing just upper and lower case letters are
797 interpreted as WUSS RNA secondary structure symbols
800 <!-- JAL-2590 -->Cannot load and display Newick trees
801 reliably from eggnog Ortholog database
804 <!-- JAL-2468 -->Status bar shows 'Marked x columns
805 containing features of type Highlight' when 'B' is pressed
806 to mark columns containing highlighted regions.
809 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
810 doesn't always add secondary structure annotation.
815 <td width="60" nowrap>
817 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
820 <td><div align="left">
824 <!-- JAL-98 -->Improved memory usage: sparse arrays used
825 for all consensus calculations
828 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
831 <li>Updated Jalview's Certum code signing certificate
837 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
838 set of database cross-references, sorted alphabetically
841 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
842 from database cross references. Users with custom links
843 will receive a <a href="webServices/urllinks.html#warning">warning
844 dialog</a> asking them to update their preferences.
847 <!-- JAL-2287-->Cancel button and escape listener on
848 dialog warning user about disconnecting Jalview from a
852 <!-- JAL-2320-->Jalview's Chimera control window closes if
853 the Chimera it is connected to is shut down
856 <!-- JAL-1738-->New keystroke (B) and Select highlighted
857 columns menu item to mark columns containing highlighted
858 regions (e.g. from structure selections or results of a
862 <!-- JAL-2284-->Command line option for batch-generation
863 of HTML pages rendering alignment data with the BioJS
873 <!-- JAL-2286 -->Columns with more than one modal residue
874 are not coloured or thresholded according to percent
875 identity (first observed in Jalview 2.8.2)
878 <!-- JAL-2301 -->Threonine incorrectly reported as not
882 <!-- JAL-2318 -->Updates to documentation pages (above PID
883 threshold, amino acid properties)
886 <!-- JAL-2292 -->Lower case residues in sequences are not
887 reported as mapped to residues in a structure file in the
891 <!--JAL-2324 -->Identical features with non-numeric scores
892 could be added multiple times to a sequence
895 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
896 bond features shown as two highlighted residues rather
897 than a range in linked structure views, and treated
898 correctly when selecting and computing trees from features
901 <!-- JAL-2281-->Custom URL links for database
902 cross-references are matched to database name regardless
910 <!-- JAL-2282-->Custom URL links for specific database
911 names without regular expressions also offer links from
915 <!-- JAL-2315-->Removing a single configured link in the
916 URL links pane in Connections preferences doesn't actually
917 update Jalview configuration
920 <!-- JAL-2272-->CTRL-Click on a selected region to open
921 the alignment area popup menu doesn't work on El-Capitan
924 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
925 files with similarly named sequences if dropped onto the
929 <!-- JAL-2312 -->Additional mappings are shown for PDB
930 entries where more chains exist in the PDB accession than
931 are reported in the SIFTS file
934 <!-- JAL-2317-->Certain structures do not get mapped to
935 the structure view when displayed with Chimera
938 <!-- JAL-2317-->No chains shown in the Chimera view
939 panel's View->Show Chains submenu
942 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
943 work for wrapped alignment views
946 <!--JAL-2197 -->Rename UI components for running JPred
947 predictions from 'JNet' to 'JPred'
950 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
951 corrupted when annotation panel vertical scroll is not at
955 <!--JAL-2332 -->Attempting to view structure for Hen
956 lysozyme results in a PDB Client error dialog box
959 <!-- JAL-2319 -->Structure View's mapping report switched
960 ranges for PDB and sequence for SIFTS
963 SIFTS 'Not_Observed' residues mapped to non-existant
967 <!-- <em>New Known Issues</em>
974 <td width="60" nowrap>
976 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
977 <em>25/10/2016</em></strong>
980 <td><em>Application</em>
982 <li>3D Structure chooser opens with 'Cached structures'
983 view if structures already loaded</li>
984 <li>Progress bar reports models as they are loaded to
991 <li>Colour by conservation always enabled and no tick
992 shown in menu when BLOSUM or PID shading applied</li>
993 <li>FER1_ARATH and FER2_ARATH labels were switched in
994 example sequences/projects/trees</li>
998 <li>Jalview projects with views of local PDB structure
999 files saved on Windows cannot be opened on OSX</li>
1000 <li>Multiple structure views can be opened and superposed
1001 without timeout for structures with multiple models or
1002 multiple sequences in alignment</li>
1003 <li>Cannot import or associated local PDB files without a
1004 PDB ID HEADER line</li>
1005 <li>RMSD is not output in Jmol console when superposition
1007 <li>Drag and drop of URL from Browser fails for Linux and
1008 OSX versions earlier than El Capitan</li>
1009 <li>ENA client ignores invalid content from ENA server</li>
1010 <li>Exceptions are not raised in console when ENA client
1011 attempts to fetch non-existent IDs via Fetch DB Refs UI
1013 <li>Exceptions are not raised in console when a new view
1014 is created on the alignment</li>
1015 <li>OSX right-click fixed for group selections: CMD-click
1016 to insert/remove gaps in groups and CTRL-click to open group
1019 <em>Build and deployment</em>
1021 <li>URL link checker now copes with multi-line anchor
1024 <em>New Known Issues</em>
1026 <li>Drag and drop from URL links in browsers do not work
1033 <td width="60" nowrap>
1034 <div align="center">
1035 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1038 <td><em>General</em>
1041 <!-- JAL-2124 -->Updated Spanish translations.
1044 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1045 for importing structure data to Jalview. Enables mmCIF and
1049 <!-- JAL-192 --->Alignment ruler shows positions relative to
1053 <!-- JAL-2202 -->Position/residue shown in status bar when
1054 mousing over sequence associated annotation
1057 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1061 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1062 '()', canonical '[]' and invalid '{}' base pair populations
1066 <!-- JAL-2092 -->Feature settings popup menu options for
1067 showing or hiding columns containing a feature
1070 <!-- JAL-1557 -->Edit selected group by double clicking on
1071 group and sequence associated annotation labels
1074 <!-- JAL-2236 -->Sequence name added to annotation label in
1075 select/hide columns by annotation and colour by annotation
1079 </ul> <em>Application</em>
1082 <!-- JAL-2050-->Automatically hide introns when opening a
1083 gene/transcript view
1086 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1090 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1091 structure mappings with the EMBL-EBI PDBe SIFTS database
1094 <!-- JAL-2079 -->Updated download sites used for Rfam and
1095 Pfam sources to xfam.org
1098 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1101 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1102 over sequences in Jalview
1105 <!-- JAL-2027-->Support for reverse-complement coding
1106 regions in ENA and EMBL
1109 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1110 for record retrieval via ENA rest API
1113 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1117 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1118 groovy script execution
1121 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1122 alignment window's Calculate menu
1125 <!-- JAL-1812 -->Allow groovy scripts that call
1126 Jalview.getAlignFrames() to run in headless mode
1129 <!-- JAL-2068 -->Support for creating new alignment
1130 calculation workers from groovy scripts
1133 <!-- JAL-1369 --->Store/restore reference sequence in
1137 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1138 associations are now saved/restored from project
1141 <!-- JAL-1993 -->Database selection dialog always shown
1142 before sequence fetcher is opened
1145 <!-- JAL-2183 -->Double click on an entry in Jalview's
1146 database chooser opens a sequence fetcher
1149 <!-- JAL-1563 -->Free-text search client for UniProt using
1150 the UniProt REST API
1153 <!-- JAL-2168 -->-nonews command line parameter to prevent
1154 the news reader opening
1157 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1158 querying stored in preferences
1161 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1165 <!-- JAL-1977-->Tooltips shown on database chooser
1168 <!-- JAL-391 -->Reverse complement function in calculate
1169 menu for nucleotide sequences
1172 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1173 and feature counts preserves alignment ordering (and
1174 debugged for complex feature sets).
1177 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1178 viewing structures with Jalview 2.10
1181 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1182 genome, transcript CCDS and gene ids via the Ensembl and
1183 Ensembl Genomes REST API
1186 <!-- JAL-2049 -->Protein sequence variant annotation
1187 computed for 'sequence_variant' annotation on CDS regions
1191 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1195 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1196 Ref Fetcher fails to match, or otherwise updates sequence
1197 data from external database records.
1200 <!-- JAL-2154 -->Revised Jalview Project format for
1201 efficient recovery of sequence coding and alignment
1202 annotation relationships.
1204 </ul> <!-- <em>Applet</em>
1215 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1219 <!-- JAL-2018-->Export features in Jalview format (again)
1220 includes graduated colourschemes
1223 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1224 working with big alignments and lots of hidden columns
1227 <!-- JAL-2053-->Hidden column markers not always rendered
1228 at right of alignment window
1231 <!-- JAL-2067 -->Tidied up links in help file table of
1235 <!-- JAL-2072 -->Feature based tree calculation not shown
1239 <!-- JAL-2075 -->Hidden columns ignored during feature
1240 based tree calculation
1243 <!-- JAL-2065 -->Alignment view stops updating when show
1244 unconserved enabled for group on alignment
1247 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1251 <!-- JAL-2146 -->Alignment column in status incorrectly
1252 shown as "Sequence position" when mousing over
1256 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1257 hidden columns present
1260 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1261 user created annotation added to alignment
1264 <!-- JAL-1841 -->RNA Structure consensus only computed for
1265 '()' base pair annotation
1268 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1269 in zero scores for all base pairs in RNA Structure
1273 <!-- JAL-2174-->Extend selection with columns containing
1277 <!-- JAL-2275 -->Pfam format writer puts extra space at
1278 beginning of sequence
1281 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1285 <!-- JAL-2238 -->Cannot create groups on an alignment from
1286 from a tree when t-coffee scores are shown
1289 <!-- JAL-1836,1967 -->Cannot import and view PDB
1290 structures with chains containing negative resnums (4q4h)
1293 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1297 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1298 to Clustal, PIR and PileUp output
1301 <!-- JAL-2008 -->Reordering sequence features that are
1302 not visible causes alignment window to repaint
1305 <!-- JAL-2006 -->Threshold sliders don't work in
1306 graduated colour and colour by annotation row for e-value
1307 scores associated with features and annotation rows
1310 <!-- JAL-1797 -->amino acid physicochemical conservation
1311 calculation should be case independent
1314 <!-- JAL-2173 -->Remove annotation also updates hidden
1318 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1319 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1320 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1323 <!-- JAL-2065 -->Null pointer exceptions and redraw
1324 problems when reference sequence defined and 'show
1325 non-conserved' enabled
1328 <!-- JAL-1306 -->Quality and Conservation are now shown on
1329 load even when Consensus calculation is disabled
1332 <!-- JAL-1932 -->Remove right on penultimate column of
1333 alignment does nothing
1336 <em>Application</em>
1339 <!-- JAL-1552-->URLs and links can't be imported by
1340 drag'n'drop on OSX when launched via webstart (note - not
1341 yet fixed for El Capitan)
1344 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1345 output when running on non-gb/us i18n platforms
1348 <!-- JAL-1944 -->Error thrown when exporting a view with
1349 hidden sequences as flat-file alignment
1352 <!-- JAL-2030-->InstallAnywhere distribution fails when
1356 <!-- JAL-2080-->Jalview very slow to launch via webstart
1357 (also hotfix for 2.9.0b2)
1360 <!-- JAL-2085 -->Cannot save project when view has a
1361 reference sequence defined
1364 <!-- JAL-1011 -->Columns are suddenly selected in other
1365 alignments and views when revealing hidden columns
1368 <!-- JAL-1989 -->Hide columns not mirrored in complement
1369 view in a cDNA/Protein splitframe
1372 <!-- JAL-1369 -->Cannot save/restore representative
1373 sequence from project when only one sequence is
1377 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1378 in Structure Chooser
1381 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1382 structure consensus didn't refresh annotation panel
1385 <!-- JAL-1962 -->View mapping in structure view shows
1386 mappings between sequence and all chains in a PDB file
1389 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1390 dialogs format columns correctly, don't display array
1391 data, sort columns according to type
1394 <!-- JAL-1975 -->Export complete shown after destination
1395 file chooser is cancelled during an image export
1398 <!-- JAL-2025 -->Error when querying PDB Service with
1399 sequence name containing special characters
1402 <!-- JAL-2024 -->Manual PDB structure querying should be
1406 <!-- JAL-2104 -->Large tooltips with broken HTML
1407 formatting don't wrap
1410 <!-- JAL-1128 -->Figures exported from wrapped view are
1411 truncated so L looks like I in consensus annotation
1414 <!-- JAL-2003 -->Export features should only export the
1415 currently displayed features for the current selection or
1419 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1420 after fetching cross-references, and restoring from
1424 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1425 followed in the structure viewer
1428 <!-- JAL-2163 -->Titles for individual alignments in
1429 splitframe not restored from project
1432 <!-- JAL-2145 -->missing autocalculated annotation at
1433 trailing end of protein alignment in transcript/product
1434 splitview when pad-gaps not enabled by default
1437 <!-- JAL-1797 -->amino acid physicochemical conservation
1441 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1442 article has been read (reopened issue due to
1443 internationalisation problems)
1446 <!-- JAL-1960 -->Only offer PDB structures in structure
1447 viewer based on sequence name, PDB and UniProt
1452 <!-- JAL-1976 -->No progress bar shown during export of
1456 <!-- JAL-2213 -->Structures not always superimposed after
1457 multiple structures are shown for one or more sequences.
1460 <!-- JAL-1370 -->Reference sequence characters should not
1461 be replaced with '.' when 'Show unconserved' format option
1465 <!-- JAL-1823 -->Cannot specify chain code when entering
1466 specific PDB id for sequence
1469 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1470 'Export hidden sequences' is enabled, but 'export hidden
1471 columns' is disabled.
1474 <!--JAL-2026-->Best Quality option in structure chooser
1475 selects lowest rather than highest resolution structures
1479 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1480 to sequence mapping in 'View Mappings' report
1483 <!-- JAL-2284 -->Unable to read old Jalview projects that
1484 contain non-XML data added after Jalvew wrote project.
1487 <!-- JAL-2118 -->Newly created annotation row reorders
1488 after clicking on it to create new annotation for a
1492 <!-- JAL-1980 -->Null Pointer Exception raised when
1493 pressing Add on an orphaned cut'n'paste window.
1495 <!-- may exclude, this is an external service stability issue JAL-1941
1496 -- > RNA 3D structure not added via DSSR service</li> -->
1501 <!-- JAL-2151 -->Incorrect columns are selected when
1502 hidden columns present before start of sequence
1505 <!-- JAL-1986 -->Missing dependencies on applet pages
1509 <!-- JAL-1947 -->Overview pixel size changes when
1510 sequences are hidden in applet
1513 <!-- JAL-1996 -->Updated instructions for applet
1514 deployment on examples pages.
1521 <td width="60" nowrap>
1522 <div align="center">
1523 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1524 <em>16/10/2015</em></strong>
1527 <td><em>General</em>
1529 <li>Time stamps for signed Jalview application and applet
1534 <em>Application</em>
1536 <li>Duplicate group consensus and conservation rows
1537 shown when tree is partitioned</li>
1538 <li>Erratic behaviour when tree partitions made with
1539 multiple cDNA/Protein split views</li>
1545 <td width="60" nowrap>
1546 <div align="center">
1547 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1548 <em>8/10/2015</em></strong>
1551 <td><em>General</em>
1553 <li>Updated Spanish translations of localized text for
1555 </ul> <em>Application</em>
1557 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1558 <li>Signed OSX InstallAnywhere installer<br></li>
1559 <li>Support for per-sequence based annotations in BioJSON</li>
1560 </ul> <em>Applet</em>
1562 <li>Split frame example added to applet examples page</li>
1563 </ul> <em>Build and Deployment</em>
1566 <!-- JAL-1888 -->New ant target for running Jalview's test
1574 <li>Mapping of cDNA to protein in split frames
1575 incorrect when sequence start > 1</li>
1576 <li>Broken images in filter column by annotation dialog
1578 <li>Feature colours not parsed from features file</li>
1579 <li>Exceptions and incomplete link URLs recovered when
1580 loading a features file containing HTML tags in feature
1584 <em>Application</em>
1586 <li>Annotations corrupted after BioJS export and
1588 <li>Incorrect sequence limits after Fetch DB References
1589 with 'trim retrieved sequences'</li>
1590 <li>Incorrect warning about deleting all data when
1591 deleting selected columns</li>
1592 <li>Patch to build system for shipping properly signed
1593 JNLP templates for webstart launch</li>
1594 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1595 unreleased structures for download or viewing</li>
1596 <li>Tab/space/return keystroke operation of EMBL-PDBe
1597 fetcher/viewer dialogs works correctly</li>
1598 <li>Disabled 'minimise' button on Jalview windows
1599 running on OSX to workaround redraw hang bug</li>
1600 <li>Split cDNA/Protein view position and geometry not
1601 recovered from jalview project</li>
1602 <li>Initial enabled/disabled state of annotation menu
1603 sorter 'show autocalculated first/last' corresponds to
1605 <li>Restoring of Clustal, RNA Helices and T-Coffee
1606 color schemes from BioJSON</li>
1610 <li>Reorder sequences mirrored in cDNA/Protein split
1612 <li>Applet with Jmol examples not loading correctly</li>
1618 <td><div align="center">
1619 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1621 <td><em>General</em>
1623 <li>Linked visualisation and analysis of DNA and Protein
1626 <li>Translated cDNA alignments shown as split protein
1627 and DNA alignment views</li>
1628 <li>Codon consensus annotation for linked protein and
1629 cDNA alignment views</li>
1630 <li>Link cDNA or Protein product sequences by loading
1631 them onto Protein or cDNA alignments</li>
1632 <li>Reconstruct linked cDNA alignment from aligned
1633 protein sequences</li>
1636 <li>Jmol integration updated to Jmol v14.2.14</li>
1637 <li>Import and export of Jalview alignment views as <a
1638 href="features/bioJsonFormat.html">BioJSON</a></li>
1639 <li>New alignment annotation file statements for
1640 reference sequences and marking hidden columns</li>
1641 <li>Reference sequence based alignment shading to
1642 highlight variation</li>
1643 <li>Select or hide columns according to alignment
1645 <li>Find option for locating sequences by description</li>
1646 <li>Conserved physicochemical properties shown in amino
1647 acid conservation row</li>
1648 <li>Alignments can be sorted by number of RNA helices</li>
1649 </ul> <em>Application</em>
1651 <li>New cDNA/Protein analysis capabilities
1653 <li>Get Cross-References should open a Split Frame
1654 view with cDNA/Protein</li>
1655 <li>Detect when nucleotide sequences and protein
1656 sequences are placed in the same alignment</li>
1657 <li>Split cDNA/Protein views are saved in Jalview
1662 <li>Use REST API to talk to Chimera</li>
1663 <li>Selected regions in Chimera are highlighted in linked
1664 Jalview windows</li>
1666 <li>VARNA RNA viewer updated to v3.93</li>
1667 <li>VARNA views are saved in Jalview Projects</li>
1668 <li>Pseudoknots displayed as Jalview RNA annotation can
1669 be shown in VARNA</li>
1671 <li>Make groups for selection uses marked columns as well
1672 as the active selected region</li>
1674 <li>Calculate UPGMA and NJ trees using sequence feature
1676 <li>New Export options
1678 <li>New Export Settings dialog to control hidden
1679 region export in flat file generation</li>
1681 <li>Export alignment views for display with the <a
1682 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1684 <li>Export scrollable SVG in HTML page</li>
1685 <li>Optional embedding of BioJSON data when exporting
1686 alignment figures to HTML</li>
1688 <li>3D structure retrieval and display
1690 <li>Free text and structured queries with the PDBe
1692 <li>PDBe Search API based discovery and selection of
1693 PDB structures for a sequence set</li>
1697 <li>JPred4 employed for protein secondary structure
1699 <li>Hide Insertions menu option to hide unaligned columns
1700 for one or a group of sequences</li>
1701 <li>Automatically hide insertions in alignments imported
1702 from the JPred4 web server</li>
1703 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1704 system on OSX<br />LGPL libraries courtesy of <a
1705 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1707 <li>changed 'View nucleotide structure' submenu to 'View
1708 VARNA 2D Structure'</li>
1709 <li>change "View protein structure" menu option to "3D
1712 </ul> <em>Applet</em>
1714 <li>New layout for applet example pages</li>
1715 <li>New parameters to enable SplitFrame view
1716 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1717 <li>New example demonstrating linked viewing of cDNA and
1718 Protein alignments</li>
1719 </ul> <em>Development and deployment</em>
1721 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1722 <li>Include installation type and git revision in build
1723 properties and console log output</li>
1724 <li>Jalview Github organisation, and new github site for
1725 storing BioJsMSA Templates</li>
1726 <li>Jalview's unit tests now managed with TestNG</li>
1729 <!-- <em>General</em>
1731 </ul> --> <!-- issues resolved --> <em>Application</em>
1733 <li>Escape should close any open find dialogs</li>
1734 <li>Typo in select-by-features status report</li>
1735 <li>Consensus RNA secondary secondary structure
1736 predictions are not highlighted in amber</li>
1737 <li>Missing gap character in v2.7 example file means
1738 alignment appears unaligned when pad-gaps is not enabled</li>
1739 <li>First switch to RNA Helices colouring doesn't colour
1740 associated structure views</li>
1741 <li>ID width preference option is greyed out when auto
1742 width checkbox not enabled</li>
1743 <li>Stopped a warning dialog from being shown when
1744 creating user defined colours</li>
1745 <li>'View Mapping' in structure viewer shows sequence
1746 mappings for just that viewer's sequences</li>
1747 <li>Workaround for superposing PDB files containing
1748 multiple models in Chimera</li>
1749 <li>Report sequence position in status bar when hovering
1750 over Jmol structure</li>
1751 <li>Cannot output gaps as '.' symbols with Selection ->
1752 output to text box</li>
1753 <li>Flat file exports of alignments with hidden columns
1754 have incorrect sequence start/end</li>
1755 <li>'Aligning' a second chain to a Chimera structure from
1757 <li>Colour schemes applied to structure viewers don't
1758 work for nucleotide</li>
1759 <li>Loading/cut'n'pasting an empty or invalid file leads
1760 to a grey/invisible alignment window</li>
1761 <li>Exported Jpred annotation from a sequence region
1762 imports to different position</li>
1763 <li>Space at beginning of sequence feature tooltips shown
1764 on some platforms</li>
1765 <li>Chimera viewer 'View | Show Chain' menu is not
1767 <li>'New View' fails with a Null Pointer Exception in
1768 console if Chimera has been opened</li>
1769 <li>Mouseover to Chimera not working</li>
1770 <li>Miscellaneous ENA XML feature qualifiers not
1772 <li>NPE in annotation renderer after 'Extract Scores'</li>
1773 <li>If two structures in one Chimera window, mouseover of
1774 either sequence shows on first structure</li>
1775 <li>'Show annotations' options should not make
1776 non-positional annotations visible</li>
1777 <li>Subsequence secondary structure annotation not shown
1778 in right place after 'view flanking regions'</li>
1779 <li>File Save As type unset when current file format is
1781 <li>Save as '.jar' option removed for saving Jalview
1783 <li>Colour by Sequence colouring in Chimera more
1785 <li>Cannot 'add reference annotation' for a sequence in
1786 several views on same alignment</li>
1787 <li>Cannot show linked products for EMBL / ENA records</li>
1788 <li>Jalview's tooltip wraps long texts containing no
1790 </ul> <em>Applet</em>
1792 <li>Jmol to JalviewLite mouseover/link not working</li>
1793 <li>JalviewLite can't import sequences with ID
1794 descriptions containing angle brackets</li>
1795 </ul> <em>General</em>
1797 <li>Cannot export and reimport RNA secondary structure
1798 via jalview annotation file</li>
1799 <li>Random helix colour palette for colour by annotation
1800 with RNA secondary structure</li>
1801 <li>Mouseover to cDNA from STOP residue in protein
1802 translation doesn't work.</li>
1803 <li>hints when using the select by annotation dialog box</li>
1804 <li>Jmol alignment incorrect if PDB file has alternate CA
1806 <li>FontChooser message dialog appears to hang after
1807 choosing 1pt font</li>
1808 <li>Peptide secondary structure incorrectly imported from
1809 annotation file when annotation display text includes 'e' or
1811 <li>Cannot set colour of new feature type whilst creating
1813 <li>cDNA translation alignment should not be sequence
1814 order dependent</li>
1815 <li>'Show unconserved' doesn't work for lower case
1817 <li>Nucleotide ambiguity codes involving R not recognised</li>
1818 </ul> <em>Deployment and Documentation</em>
1820 <li>Applet example pages appear different to the rest of
1821 www.jalview.org</li>
1822 </ul> <em>Application Known issues</em>
1824 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1825 <li>Misleading message appears after trying to delete
1827 <li>Jalview icon not shown in dock after InstallAnywhere
1828 version launches</li>
1829 <li>Fetching EMBL reference for an RNA sequence results
1830 fails with a sequence mismatch</li>
1831 <li>Corrupted or unreadable alignment display when
1832 scrolling alignment to right</li>
1833 <li>ArrayIndexOutOfBoundsException thrown when remove
1834 empty columns called on alignment with ragged gapped ends</li>
1835 <li>auto calculated alignment annotation rows do not get
1836 placed above or below non-autocalculated rows</li>
1837 <li>Jalview dekstop becomes sluggish at full screen in
1838 ultra-high resolution</li>
1839 <li>Cannot disable consensus calculation independently of
1840 quality and conservation</li>
1841 <li>Mouseover highlighting between cDNA and protein can
1842 become sluggish with more than one splitframe shown</li>
1843 </ul> <em>Applet Known Issues</em>
1845 <li>Core PDB parsing code requires Jmol</li>
1846 <li>Sequence canvas panel goes white when alignment
1847 window is being resized</li>
1853 <td><div align="center">
1854 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1856 <td><em>General</em>
1858 <li>Updated Java code signing certificate donated by
1860 <li>Features and annotation preserved when performing
1861 pairwise alignment</li>
1862 <li>RNA pseudoknot annotation can be
1863 imported/exported/displayed</li>
1864 <li>'colour by annotation' can colour by RNA and
1865 protein secondary structure</li>
1866 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1867 post-hoc with 2.9 release</em>)
1870 </ul> <em>Application</em>
1872 <li>Extract and display secondary structure for sequences
1873 with 3D structures</li>
1874 <li>Support for parsing RNAML</li>
1875 <li>Annotations menu for layout
1877 <li>sort sequence annotation rows by alignment</li>
1878 <li>place sequence annotation above/below alignment
1881 <li>Output in Stockholm format</li>
1882 <li>Internationalisation: improved Spanish (es)
1884 <li>Structure viewer preferences tab</li>
1885 <li>Disorder and Secondary Structure annotation tracks
1886 shared between alignments</li>
1887 <li>UCSF Chimera launch and linked highlighting from
1889 <li>Show/hide all sequence associated annotation rows for
1890 all or current selection</li>
1891 <li>disorder and secondary structure predictions
1892 available as dataset annotation</li>
1893 <li>Per-sequence rna helices colouring</li>
1896 <li>Sequence database accessions imported when fetching
1897 alignments from Rfam</li>
1898 <li>update VARNA version to 3.91</li>
1900 <li>New groovy scripts for exporting aligned positions,
1901 conservation values, and calculating sum of pairs scores.</li>
1902 <li>Command line argument to set default JABAWS server</li>
1903 <li>include installation type in build properties and
1904 console log output</li>
1905 <li>Updated Jalview project format to preserve dataset
1909 <!-- issues resolved --> <em>Application</em>
1911 <li>Distinguish alignment and sequence associated RNA
1912 structure in structure->view->VARNA</li>
1913 <li>Raise dialog box if user deletes all sequences in an
1915 <li>Pressing F1 results in documentation opening twice</li>
1916 <li>Sequence feature tooltip is wrapped</li>
1917 <li>Double click on sequence associated annotation
1918 selects only first column</li>
1919 <li>Redundancy removal doesn't result in unlinked
1920 leaves shown in tree</li>
1921 <li>Undos after several redundancy removals don't undo
1923 <li>Hide sequence doesn't hide associated annotation</li>
1924 <li>User defined colours dialog box too big to fit on
1925 screen and buttons not visible</li>
1926 <li>author list isn't updated if already written to
1927 Jalview properties</li>
1928 <li>Popup menu won't open after retrieving sequence
1930 <li>File open window for associate PDB doesn't open</li>
1931 <li>Left-then-right click on a sequence id opens a
1932 browser search window</li>
1933 <li>Cannot open sequence feature shading/sort popup menu
1934 in feature settings dialog</li>
1935 <li>better tooltip placement for some areas of Jalview
1937 <li>Allow addition of JABAWS Server which doesn't
1938 pass validation</li>
1939 <li>Web services parameters dialog box is too large to
1941 <li>Muscle nucleotide alignment preset obscured by
1943 <li>JABAWS preset submenus don't contain newly
1944 defined user preset</li>
1945 <li>MSA web services warns user if they were launched
1946 with invalid input</li>
1947 <li>Jalview cannot contact DAS Registy when running on
1950 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1951 'Superpose with' submenu not shown when new view
1955 </ul> <!-- <em>Applet</em>
1957 </ul> <em>General</em>
1959 </ul>--> <em>Deployment and Documentation</em>
1961 <li>2G and 1G options in launchApp have no effect on
1962 memory allocation</li>
1963 <li>launchApp service doesn't automatically open
1964 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1966 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1967 InstallAnywhere reports cannot find valid JVM when Java
1968 1.7_055 is available
1970 </ul> <em>Application Known issues</em>
1973 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1974 corrupted or unreadable alignment display when scrolling
1978 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1979 retrieval fails but progress bar continues for DAS retrieval
1980 with large number of ID
1983 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1984 flatfile output of visible region has incorrect sequence
1988 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1989 rna structure consensus doesn't update when secondary
1990 structure tracks are rearranged
1993 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1994 invalid rna structure positional highlighting does not
1995 highlight position of invalid base pairs
1998 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1999 out of memory errors are not raised when saving Jalview
2000 project from alignment window file menu
2003 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2004 Switching to RNA Helices colouring doesn't propagate to
2008 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2009 colour by RNA Helices not enabled when user created
2010 annotation added to alignment
2013 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2014 Jalview icon not shown on dock in Mountain Lion/Webstart
2016 </ul> <em>Applet Known Issues</em>
2019 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2020 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2023 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2024 Jalview and Jmol example not compatible with IE9
2027 <li>Sort by annotation score doesn't reverse order
2033 <td><div align="center">
2034 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2037 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2040 <li>Internationalisation of user interface (usually
2041 called i18n support) and translation for Spanish locale</li>
2042 <li>Define/Undefine group on current selection with
2043 Ctrl-G/Shift Ctrl-G</li>
2044 <li>Improved group creation/removal options in
2045 alignment/sequence Popup menu</li>
2046 <li>Sensible precision for symbol distribution
2047 percentages shown in logo tooltip.</li>
2048 <li>Annotation panel height set according to amount of
2049 annotation when alignment first opened</li>
2050 </ul> <em>Application</em>
2052 <li>Interactive consensus RNA secondary structure
2053 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2054 <li>Select columns containing particular features from
2055 Feature Settings dialog</li>
2056 <li>View all 'representative' PDB structures for selected
2058 <li>Update Jalview project format:
2060 <li>New file extension for Jalview projects '.jvp'</li>
2061 <li>Preserve sequence and annotation dataset (to
2062 store secondary structure annotation,etc)</li>
2063 <li>Per group and alignment annotation and RNA helix
2067 <li>New similarity measures for PCA and Tree calculation
2069 <li>Experimental support for retrieval and viewing of
2070 flanking regions for an alignment</li>
2074 <!-- issues resolved --> <em>Application</em>
2076 <li>logo keeps spinning and status remains at queued or
2077 running after job is cancelled</li>
2078 <li>cannot export features from alignments imported from
2079 Jalview/VAMSAS projects</li>
2080 <li>Buggy slider for web service parameters that take
2082 <li>Newly created RNA secondary structure line doesn't
2083 have 'display all symbols' flag set</li>
2084 <li>T-COFFEE alignment score shading scheme and other
2085 annotation shading not saved in Jalview project</li>
2086 <li>Local file cannot be loaded in freshly downloaded
2088 <li>Jalview icon not shown on dock in Mountain
2090 <li>Load file from desktop file browser fails</li>
2091 <li>Occasional NPE thrown when calculating large trees</li>
2092 <li>Cannot reorder or slide sequences after dragging an
2093 alignment onto desktop</li>
2094 <li>Colour by annotation dialog throws NPE after using
2095 'extract scores' function</li>
2096 <li>Loading/cut'n'pasting an empty file leads to a grey
2097 alignment window</li>
2098 <li>Disorder thresholds rendered incorrectly after
2099 performing IUPred disorder prediction</li>
2100 <li>Multiple group annotated consensus rows shown when
2101 changing 'normalise logo' display setting</li>
2102 <li>Find shows blank dialog after 'finished searching' if
2103 nothing matches query</li>
2104 <li>Null Pointer Exceptions raised when sorting by
2105 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2107 <li>Errors in Jmol console when structures in alignment
2108 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2110 <li>Not all working JABAWS services are shown in
2112 <li>JAVAWS version of Jalview fails to launch with
2113 'invalid literal/length code'</li>
2114 <li>Annotation/RNA Helix colourschemes cannot be applied
2115 to alignment with groups (actually fixed in 2.8.0b1)</li>
2116 <li>RNA Helices and T-Coffee Scores available as default
2119 </ul> <em>Applet</em>
2121 <li>Remove group option is shown even when selection is
2123 <li>Apply to all groups ticked but colourscheme changes
2124 don't affect groups</li>
2125 <li>Documented RNA Helices and T-Coffee Scores as valid
2126 colourscheme name</li>
2127 <li>Annotation labels drawn on sequence IDs when
2128 Annotation panel is not displayed</li>
2129 <li>Increased font size for dropdown menus on OSX and
2130 embedded windows</li>
2131 </ul> <em>Other</em>
2133 <li>Consensus sequence for alignments/groups with a
2134 single sequence were not calculated</li>
2135 <li>annotation files that contain only groups imported as
2136 annotation and junk sequences</li>
2137 <li>Fasta files with sequences containing '*' incorrectly
2138 recognised as PFAM or BLC</li>
2139 <li>conservation/PID slider apply all groups option
2140 doesn't affect background (2.8.0b1)
2142 <li>redundancy highlighting is erratic at 0% and 100%</li>
2143 <li>Remove gapped columns fails for sequences with ragged
2145 <li>AMSA annotation row with leading spaces is not
2146 registered correctly on import</li>
2147 <li>Jalview crashes when selecting PCA analysis for
2148 certain alignments</li>
2149 <li>Opening the colour by annotation dialog for an
2150 existing annotation based 'use original colours'
2151 colourscheme loses original colours setting</li>
2156 <td><div align="center">
2157 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2158 <em>30/1/2014</em></strong>
2162 <li>Trusted certificates for JalviewLite applet and
2163 Jalview Desktop application<br />Certificate was donated by
2164 <a href="https://www.certum.eu">Certum</a> to the Jalview
2165 open source project).
2167 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2168 <li>Output in Stockholm format</li>
2169 <li>Allow import of data from gzipped files</li>
2170 <li>Export/import group and sequence associated line
2171 graph thresholds</li>
2172 <li>Nucleotide substitution matrix that supports RNA and
2173 ambiguity codes</li>
2174 <li>Allow disorder predictions to be made on the current
2175 selection (or visible selection) in the same way that JPred
2177 <li>Groovy scripting for headless Jalview operation</li>
2178 </ul> <em>Other improvements</em>
2180 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2181 <li>COMBINE statement uses current SEQUENCE_REF and
2182 GROUP_REF scope to group annotation rows</li>
2183 <li>Support '' style escaping of quotes in Newick
2185 <li>Group options for JABAWS service by command line name</li>
2186 <li>Empty tooltip shown for JABA service options with a
2187 link but no description</li>
2188 <li>Select primary source when selecting authority in
2189 database fetcher GUI</li>
2190 <li>Add .mfa to FASTA file extensions recognised by
2192 <li>Annotation label tooltip text wrap</li>
2197 <li>Slow scrolling when lots of annotation rows are
2199 <li>Lots of NPE (and slowness) after creating RNA
2200 secondary structure annotation line</li>
2201 <li>Sequence database accessions not imported when
2202 fetching alignments from Rfam</li>
2203 <li>Incorrect SHMR submission for sequences with
2205 <li>View all structures does not always superpose
2207 <li>Option widgets in service parameters not updated to
2208 reflect user or preset settings</li>
2209 <li>Null pointer exceptions for some services without
2210 presets or adjustable parameters</li>
2211 <li>Discover PDB IDs entry in structure menu doesn't
2212 discover PDB xRefs</li>
2213 <li>Exception encountered while trying to retrieve
2214 features with DAS</li>
2215 <li>Lowest value in annotation row isn't coloured
2216 when colour by annotation (per sequence) is coloured</li>
2217 <li>Keyboard mode P jumps to start of gapped region when
2218 residue follows a gap</li>
2219 <li>Jalview appears to hang importing an alignment with
2220 Wrap as default or after enabling Wrap</li>
2221 <li>'Right click to add annotations' message
2222 shown in wrap mode when no annotations present</li>
2223 <li>Disorder predictions fail with NPE if no automatic
2224 annotation already exists on alignment</li>
2225 <li>oninit javascript function should be called after
2226 initialisation completes</li>
2227 <li>Remove redundancy after disorder prediction corrupts
2228 alignment window display</li>
2229 <li>Example annotation file in documentation is invalid</li>
2230 <li>Grouped line graph annotation rows are not exported
2231 to annotation file</li>
2232 <li>Multi-harmony analysis cannot be run when only two
2234 <li>Cannot create multiple groups of line graphs with
2235 several 'combine' statements in annotation file</li>
2236 <li>Pressing return several times causes Number Format
2237 exceptions in keyboard mode</li>
2238 <li>Multi-harmony (SHMMR) method doesn't submit
2239 correct partitions for input data</li>
2240 <li>Translation from DNA to Amino Acids fails</li>
2241 <li>Jalview fail to load newick tree with quoted label</li>
2242 <li>--headless flag isn't understood</li>
2243 <li>ClassCastException when generating EPS in headless
2245 <li>Adjusting sequence-associated shading threshold only
2246 changes one row's threshold</li>
2247 <li>Preferences and Feature settings panel panel
2248 doesn't open</li>
2249 <li>hide consensus histogram also hides conservation and
2250 quality histograms</li>
2255 <td><div align="center">
2256 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2258 <td><em>Application</em>
2260 <li>Support for JABAWS 2.0 Services (AACon alignment
2261 conservation, protein disorder and Clustal Omega)</li>
2262 <li>JABAWS server status indicator in Web Services
2264 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2265 in Jalview alignment window</li>
2266 <li>Updated Jalview build and deploy framework for OSX
2267 mountain lion, windows 7, and 8</li>
2268 <li>Nucleotide substitution matrix for PCA that supports
2269 RNA and ambiguity codes</li>
2271 <li>Improved sequence database retrieval GUI</li>
2272 <li>Support fetching and database reference look up
2273 against multiple DAS sources (Fetch all from in 'fetch db
2275 <li>Jalview project improvements
2277 <li>Store and retrieve the 'belowAlignment'
2278 flag for annotation</li>
2279 <li>calcId attribute to group annotation rows on the
2281 <li>Store AACon calculation settings for a view in
2282 Jalview project</li>
2286 <li>horizontal scrolling gesture support</li>
2287 <li>Visual progress indicator when PCA calculation is
2289 <li>Simpler JABA web services menus</li>
2290 <li>visual indication that web service results are still
2291 being retrieved from server</li>
2292 <li>Serialise the dialogs that are shown when Jalview
2293 starts up for first time</li>
2294 <li>Jalview user agent string for interacting with HTTP
2296 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2298 <li>Examples directory and Groovy library included in
2299 InstallAnywhere distribution</li>
2300 </ul> <em>Applet</em>
2302 <li>RNA alignment and secondary structure annotation
2303 visualization applet example</li>
2304 </ul> <em>General</em>
2306 <li>Normalise option for consensus sequence logo</li>
2307 <li>Reset button in PCA window to return dimensions to
2309 <li>Allow seqspace or Jalview variant of alignment PCA
2311 <li>PCA with either nucleic acid and protein substitution
2313 <li>Allow windows containing HTML reports to be exported
2315 <li>Interactive display and editing of RNA secondary
2316 structure contacts</li>
2317 <li>RNA Helix Alignment Colouring</li>
2318 <li>RNA base pair logo consensus</li>
2319 <li>Parse sequence associated secondary structure
2320 information in Stockholm files</li>
2321 <li>HTML Export database accessions and annotation
2322 information presented in tooltip for sequences</li>
2323 <li>Import secondary structure from LOCARNA clustalw
2324 style RNA alignment files</li>
2325 <li>import and visualise T-COFFEE quality scores for an
2327 <li>'colour by annotation' per sequence option to
2328 shade each sequence according to its associated alignment
2330 <li>New Jalview Logo</li>
2331 </ul> <em>Documentation and Development</em>
2333 <li>documentation for score matrices used in Jalview</li>
2334 <li>New Website!</li>
2336 <td><em>Application</em>
2338 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2339 wsdbfetch REST service</li>
2340 <li>Stop windows being moved outside desktop on OSX</li>
2341 <li>Filetype associations not installed for webstart
2343 <li>Jalview does not always retrieve progress of a JABAWS
2344 job execution in full once it is complete</li>
2345 <li>revise SHMR RSBS definition to ensure alignment is
2346 uploaded via ali_file parameter</li>
2347 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2348 <li>View all structures superposed fails with exception</li>
2349 <li>Jnet job queues forever if a very short sequence is
2350 submitted for prediction</li>
2351 <li>Cut and paste menu not opened when mouse clicked on
2353 <li>Putting fractional value into integer text box in
2354 alignment parameter dialog causes Jalview to hang</li>
2355 <li>Structure view highlighting doesn't work on
2357 <li>View all structures fails with exception shown in
2359 <li>Characters in filename associated with PDBEntry not
2360 escaped in a platform independent way</li>
2361 <li>Jalview desktop fails to launch with exception when
2363 <li>Tree calculation reports 'you must have 2 or more
2364 sequences selected' when selection is empty</li>
2365 <li>Jalview desktop fails to launch with jar signature
2366 failure when java web start temporary file caching is
2368 <li>DAS Sequence retrieval with range qualification
2369 results in sequence xref which includes range qualification</li>
2370 <li>Errors during processing of command line arguments
2371 cause progress bar (JAL-898) to be removed</li>
2372 <li>Replace comma for semi-colon option not disabled for
2373 DAS sources in sequence fetcher</li>
2374 <li>Cannot close news reader when JABAWS server warning
2375 dialog is shown</li>
2376 <li>Option widgets not updated to reflect user settings</li>
2377 <li>Edited sequence not submitted to web service</li>
2378 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2379 <li>InstallAnywhere installer doesn't unpack and run
2380 on OSX Mountain Lion</li>
2381 <li>Annotation panel not given a scroll bar when
2382 sequences with alignment annotation are pasted into the
2384 <li>Sequence associated annotation rows not associated
2385 when loaded from Jalview project</li>
2386 <li>Browser launch fails with NPE on java 1.7</li>
2387 <li>JABAWS alignment marked as finished when job was
2388 cancelled or job failed due to invalid input</li>
2389 <li>NPE with v2.7 example when clicking on Tree
2390 associated with all views</li>
2391 <li>Exceptions when copy/paste sequences with grouped
2392 annotation rows to new window</li>
2393 </ul> <em>Applet</em>
2395 <li>Sequence features are momentarily displayed before
2396 they are hidden using hidefeaturegroups applet parameter</li>
2397 <li>loading features via javascript API automatically
2398 enables feature display</li>
2399 <li>scrollToColumnIn javascript API method doesn't
2401 </ul> <em>General</em>
2403 <li>Redundancy removal fails for rna alignment</li>
2404 <li>PCA calculation fails when sequence has been selected
2405 and then deselected</li>
2406 <li>PCA window shows grey box when first opened on OSX</li>
2407 <li>Letters coloured pink in sequence logo when alignment
2408 coloured with clustalx</li>
2409 <li>Choosing fonts without letter symbols defined causes
2410 exceptions and redraw errors</li>
2411 <li>Initial PCA plot view is not same as manually
2412 reconfigured view</li>
2413 <li>Grouped annotation graph label has incorrect line
2415 <li>Grouped annotation graph label display is corrupted
2416 for lots of labels</li>
2421 <div align="center">
2422 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2425 <td><em>Application</em>
2427 <li>Jalview Desktop News Reader</li>
2428 <li>Tweaked default layout of web services menu</li>
2429 <li>View/alignment association menu to enable user to
2430 easily specify which alignment a multi-structure view takes
2431 its colours/correspondences from</li>
2432 <li>Allow properties file location to be specified as URL</li>
2433 <li>Extend Jalview project to preserve associations
2434 between many alignment views and a single Jmol display</li>
2435 <li>Store annotation row height in Jalview project file</li>
2436 <li>Annotation row column label formatting attributes
2437 stored in project file</li>
2438 <li>Annotation row order for auto-calculated annotation
2439 rows preserved in Jalview project file</li>
2440 <li>Visual progress indication when Jalview state is
2441 saved using Desktop window menu</li>
2442 <li>Visual indication that command line arguments are
2443 still being processed</li>
2444 <li>Groovy script execution from URL</li>
2445 <li>Colour by annotation default min and max colours in
2447 <li>Automatically associate PDB files dragged onto an
2448 alignment with sequences that have high similarity and
2450 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2451 <li>'view structures' option to open many
2452 structures in same window</li>
2453 <li>Sort associated views menu option for tree panel</li>
2454 <li>Group all JABA and non-JABA services for a particular
2455 analysis function in its own submenu</li>
2456 </ul> <em>Applet</em>
2458 <li>Userdefined and autogenerated annotation rows for
2460 <li>Adjustment of alignment annotation pane height</li>
2461 <li>Annotation scrollbar for annotation panel</li>
2462 <li>Drag to reorder annotation rows in annotation panel</li>
2463 <li>'automaticScrolling' parameter</li>
2464 <li>Allow sequences with partial ID string matches to be
2465 annotated from GFF/Jalview features files</li>
2466 <li>Sequence logo annotation row in applet</li>
2467 <li>Absolute paths relative to host server in applet
2468 parameters are treated as such</li>
2469 <li>New in the JalviewLite javascript API:
2471 <li>JalviewLite.js javascript library</li>
2472 <li>Javascript callbacks for
2474 <li>Applet initialisation</li>
2475 <li>Sequence/alignment mouse-overs and selections</li>
2478 <li>scrollTo row and column alignment scrolling
2480 <li>Select sequence/alignment regions from javascript</li>
2481 <li>javascript structure viewer harness to pass
2482 messages between Jmol and Jalview when running as
2483 distinct applets</li>
2484 <li>sortBy method</li>
2485 <li>Set of applet and application examples shipped
2486 with documentation</li>
2487 <li>New example to demonstrate JalviewLite and Jmol
2488 javascript message exchange</li>
2490 </ul> <em>General</em>
2492 <li>Enable Jmol displays to be associated with multiple
2493 multiple alignments</li>
2494 <li>Option to automatically sort alignment with new tree</li>
2495 <li>User configurable link to enable redirects to a
2496 www.Jalview.org mirror</li>
2497 <li>Jmol colours option for Jmol displays</li>
2498 <li>Configurable newline string when writing alignment
2499 and other flat files</li>
2500 <li>Allow alignment annotation description lines to
2501 contain html tags</li>
2502 </ul> <em>Documentation and Development</em>
2504 <li>Add groovy test harness for bulk load testing to
2506 <li>Groovy script to load and align a set of sequences
2507 using a web service before displaying the result in the
2508 Jalview desktop</li>
2509 <li>Restructured javascript and applet api documentation</li>
2510 <li>Ant target to publish example html files with applet
2512 <li>Netbeans project for building Jalview from source</li>
2513 <li>ant task to create online javadoc for Jalview source</li>
2515 <td><em>Application</em>
2517 <li>User defined colourscheme throws exception when
2518 current built in colourscheme is saved as new scheme</li>
2519 <li>AlignFrame->Save in application pops up save
2520 dialog for valid filename/format</li>
2521 <li>Cannot view associated structure for UniProt sequence</li>
2522 <li>PDB file association breaks for UniProt sequence
2524 <li>Associate PDB from file dialog does not tell you
2525 which sequence is to be associated with the file</li>
2526 <li>Find All raises null pointer exception when query
2527 only matches sequence IDs</li>
2528 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2529 <li>Jalview project with Jmol views created with Jalview
2530 2.4 cannot be loaded</li>
2531 <li>Filetype associations not installed for webstart
2533 <li>Two or more chains in a single PDB file associated
2534 with sequences in different alignments do not get coloured
2535 by their associated sequence</li>
2536 <li>Visibility status of autocalculated annotation row
2537 not preserved when project is loaded</li>
2538 <li>Annotation row height and visibility attributes not
2539 stored in Jalview project</li>
2540 <li>Tree bootstraps are not preserved when saved as a
2541 Jalview project</li>
2542 <li>Envision2 workflow tooltips are corrupted</li>
2543 <li>Enabling show group conservation also enables colour
2544 by conservation</li>
2545 <li>Duplicate group associated conservation or consensus
2546 created on new view</li>
2547 <li>Annotation scrollbar not displayed after 'show
2548 all hidden annotation rows' option selected</li>
2549 <li>Alignment quality not updated after alignment
2550 annotation row is hidden then shown</li>
2551 <li>Preserve colouring of structures coloured by
2552 sequences in pre Jalview 2.7 projects</li>
2553 <li>Web service job parameter dialog is not laid out
2555 <li>Web services menu not refreshed after 'reset
2556 services' button is pressed in preferences</li>
2557 <li>Annotation off by one in Jalview v2_3 example project</li>
2558 <li>Structures imported from file and saved in project
2559 get name like jalview_pdb1234.txt when reloaded</li>
2560 <li>Jalview does not always retrieve progress of a JABAWS
2561 job execution in full once it is complete</li>
2562 </ul> <em>Applet</em>
2564 <li>Alignment height set incorrectly when lots of
2565 annotation rows are displayed</li>
2566 <li>Relative URLs in feature HTML text not resolved to
2568 <li>View follows highlighting does not work for positions
2570 <li><= shown as = in tooltip</li>
2571 <li>Export features raises exception when no features
2573 <li>Separator string used for serialising lists of IDs
2574 for javascript api is modified when separator string
2575 provided as parameter</li>
2576 <li>Null pointer exception when selecting tree leaves for
2577 alignment with no existing selection</li>
2578 <li>Relative URLs for datasources assumed to be relative
2579 to applet's codebase</li>
2580 <li>Status bar not updated after finished searching and
2581 search wraps around to first result</li>
2582 <li>StructureSelectionManager instance shared between
2583 several Jalview applets causes race conditions and memory
2585 <li>Hover tooltip and mouseover of position on structure
2586 not sent from Jmol in applet</li>
2587 <li>Certain sequences of javascript method calls to
2588 applet API fatally hang browser</li>
2589 </ul> <em>General</em>
2591 <li>View follows structure mouseover scrolls beyond
2592 position with wrapped view and hidden regions</li>
2593 <li>Find sequence position moves to wrong residue
2594 with/without hidden columns</li>
2595 <li>Sequence length given in alignment properties window
2597 <li>InvalidNumberFormat exceptions thrown when trying to
2598 import PDB like structure files</li>
2599 <li>Positional search results are only highlighted
2600 between user-supplied sequence start/end bounds</li>
2601 <li>End attribute of sequence is not validated</li>
2602 <li>Find dialog only finds first sequence containing a
2603 given sequence position</li>
2604 <li>Sequence numbering not preserved in MSF alignment
2606 <li>Jalview PDB file reader does not extract sequence
2607 from nucleotide chains correctly</li>
2608 <li>Structure colours not updated when tree partition
2609 changed in alignment</li>
2610 <li>Sequence associated secondary structure not correctly
2611 parsed in interleaved stockholm</li>
2612 <li>Colour by annotation dialog does not restore current
2614 <li>Hiding (nearly) all sequences doesn't work
2616 <li>Sequences containing lowercase letters are not
2617 properly associated with their pdb files</li>
2618 </ul> <em>Documentation and Development</em>
2620 <li>schemas/JalviewWsParamSet.xsd corrupted by
2621 ApplyCopyright tool</li>
2626 <div align="center">
2627 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2630 <td><em>Application</em>
2632 <li>New warning dialog when the Jalview Desktop cannot
2633 contact web services</li>
2634 <li>JABA service parameters for a preset are shown in
2635 service job window</li>
2636 <li>JABA Service menu entries reworded</li>
2640 <li>Modeller PIR IO broken - cannot correctly import a
2641 pir file emitted by Jalview</li>
2642 <li>Existing feature settings transferred to new
2643 alignment view created from cut'n'paste</li>
2644 <li>Improved test for mixed amino/nucleotide chains when
2645 parsing PDB files</li>
2646 <li>Consensus and conservation annotation rows
2647 occasionally become blank for all new windows</li>
2648 <li>Exception raised when right clicking above sequences
2649 in wrapped view mode</li>
2650 </ul> <em>Application</em>
2652 <li>multiple multiply aligned structure views cause cpu
2653 usage to hit 100% and computer to hang</li>
2654 <li>Web Service parameter layout breaks for long user
2655 parameter names</li>
2656 <li>Jaba service discovery hangs desktop if Jaba server
2663 <div align="center">
2664 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2667 <td><em>Application</em>
2669 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2670 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2673 <li>Web Services preference tab</li>
2674 <li>Analysis parameters dialog box and user defined
2676 <li>Improved speed and layout of Envision2 service menu</li>
2677 <li>Superpose structures using associated sequence
2679 <li>Export coordinates and projection as CSV from PCA
2681 </ul> <em>Applet</em>
2683 <li>enable javascript: execution by the applet via the
2684 link out mechanism</li>
2685 </ul> <em>Other</em>
2687 <li>Updated the Jmol Jalview interface to work with Jmol
2689 <li>The Jalview Desktop and JalviewLite applet now
2690 require Java 1.5</li>
2691 <li>Allow Jalview feature colour specification for GFF
2692 sequence annotation files</li>
2693 <li>New 'colour by label' keword in Jalview feature file
2694 type colour specification</li>
2695 <li>New Jalview Desktop Groovy API method that allows a
2696 script to check if it being run in an interactive session or
2697 in a batch operation from the Jalview command line</li>
2701 <li>clustalx colourscheme colours Ds preferentially when
2702 both D+E are present in over 50% of the column</li>
2703 </ul> <em>Application</em>
2705 <li>typo in AlignmentFrame->View->Hide->all but
2706 selected Regions menu item</li>
2707 <li>sequence fetcher replaces ',' for ';' when the ',' is
2708 part of a valid accession ID</li>
2709 <li>fatal OOM if object retrieved by sequence fetcher
2710 runs out of memory</li>
2711 <li>unhandled Out of Memory Error when viewing pca
2712 analysis results</li>
2713 <li>InstallAnywhere builds fail to launch on OS X java
2714 10.5 update 4 (due to apple Java 1.6 update)</li>
2715 <li>Installanywhere Jalview silently fails to launch</li>
2716 </ul> <em>Applet</em>
2718 <li>Jalview.getFeatureGroups() raises an
2719 ArrayIndexOutOfBoundsException if no feature groups are
2726 <div align="center">
2727 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2733 <li>Alignment prettyprinter doesn't cope with long
2735 <li>clustalx colourscheme colours Ds preferentially when
2736 both D+E are present in over 50% of the column</li>
2737 <li>nucleic acid structures retrieved from PDB do not
2738 import correctly</li>
2739 <li>More columns get selected than were clicked on when a
2740 number of columns are hidden</li>
2741 <li>annotation label popup menu not providing correct
2742 add/hide/show options when rows are hidden or none are
2744 <li>Stockholm format shown in list of readable formats,
2745 and parser copes better with alignments from RFAM.</li>
2746 <li>CSV output of consensus only includes the percentage
2747 of all symbols if sequence logo display is enabled</li>
2749 </ul> <em>Applet</em>
2751 <li>annotation panel disappears when annotation is
2753 </ul> <em>Application</em>
2755 <li>Alignment view not redrawn properly when new
2756 alignment opened where annotation panel is visible but no
2757 annotations are present on alignment</li>
2758 <li>pasted region containing hidden columns is
2759 incorrectly displayed in new alignment window</li>
2760 <li>Jalview slow to complete operations when stdout is
2761 flooded (fix is to close the Jalview console)</li>
2762 <li>typo in AlignmentFrame->View->Hide->all but
2763 selected Rregions menu item.</li>
2764 <li>inconsistent group submenu and Format submenu entry
2765 'Un' or 'Non'conserved</li>
2766 <li>Sequence feature settings are being shared by
2767 multiple distinct alignments</li>
2768 <li>group annotation not recreated when tree partition is
2770 <li>double click on group annotation to select sequences
2771 does not propagate to associated trees</li>
2772 <li>Mac OSX specific issues:
2774 <li>exception raised when mouse clicked on desktop
2775 window background</li>
2776 <li>Desktop menu placed on menu bar and application
2777 name set correctly</li>
2778 <li>sequence feature settings not wide enough for the
2779 save feature colourscheme button</li>
2788 <div align="center">
2789 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2792 <td><em>New Capabilities</em>
2794 <li>URL links generated from description line for
2795 regular-expression based URL links (applet and application)
2797 <li>Non-positional feature URL links are shown in link
2799 <li>Linked viewing of nucleic acid sequences and
2801 <li>Automatic Scrolling option in View menu to display
2802 the currently highlighted region of an alignment.</li>
2803 <li>Order an alignment by sequence length, or using the
2804 average score or total feature count for each sequence.</li>
2805 <li>Shading features by score or associated description</li>
2806 <li>Subdivide alignment and groups based on identity of
2807 selected subsequence (Make Groups from Selection).</li>
2808 <li>New hide/show options including Shift+Control+H to
2809 hide everything but the currently selected region.</li>
2810 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2811 </ul> <em>Application</em>
2813 <li>Fetch DB References capabilities and UI expanded to
2814 support retrieval from DAS sequence sources</li>
2815 <li>Local DAS Sequence sources can be added via the
2816 command line or via the Add local source dialog box.</li>
2817 <li>DAS Dbref and DbxRef feature types are parsed as
2818 database references and protein_name is parsed as
2819 description line (BioSapiens terms).</li>
2820 <li>Enable or disable non-positional feature and database
2821 references in sequence ID tooltip from View menu in
2823 <!-- <li>New hidden columns and rows and representatives capabilities
2824 in annotations file (in progress - not yet fully implemented)</li> -->
2825 <li>Group-associated consensus, sequence logos and
2826 conservation plots</li>
2827 <li>Symbol distributions for each column can be exported
2828 and visualized as sequence logos</li>
2829 <li>Optionally scale multi-character column labels to fit
2830 within each column of annotation row<!-- todo for applet -->
2832 <li>Optional automatic sort of associated alignment view
2833 when a new tree is opened.</li>
2834 <li>Jalview Java Console</li>
2835 <li>Better placement of desktop window when moving
2836 between different screens.</li>
2837 <li>New preference items for sequence ID tooltip and
2838 consensus annotation</li>
2839 <li>Client to submit sequences and IDs to Envision2
2841 <li><em>Vamsas Capabilities</em>
2843 <li>Improved VAMSAS synchronization (Jalview archive
2844 used to preserve views, structures, and tree display
2846 <li>Import of vamsas documents from disk or URL via
2848 <li>Sharing of selected regions between views and
2849 with other VAMSAS applications (Experimental feature!)</li>
2850 <li>Updated API to VAMSAS version 0.2</li>
2852 </ul> <em>Applet</em>
2854 <li>Middle button resizes annotation row height</li>
2857 <li>sortByTree (true/false) - automatically sort the
2858 associated alignment view by the tree when a new tree is
2860 <li>showTreeBootstraps (true/false) - show or hide
2861 branch bootstraps (default is to show them if available)</li>
2862 <li>showTreeDistances (true/false) - show or hide
2863 branch lengths (default is to show them if available)</li>
2864 <li>showUnlinkedTreeNodes (true/false) - indicate if
2865 unassociated nodes should be highlighted in the tree
2867 <li>heightScale and widthScale (1.0 or more) -
2868 increase the height or width of a cell in the alignment
2869 grid relative to the current font size.</li>
2872 <li>Non-positional features displayed in sequence ID
2874 </ul> <em>Other</em>
2876 <li>Features format: graduated colour definitions and
2877 specification of feature scores</li>
2878 <li>Alignment Annotations format: new keywords for group
2879 associated annotation (GROUP_REF) and annotation row display
2880 properties (ROW_PROPERTIES)</li>
2881 <li>XML formats extended to support graduated feature
2882 colourschemes, group associated annotation, and profile
2883 visualization settings.</li></td>
2886 <li>Source field in GFF files parsed as feature source
2887 rather than description</li>
2888 <li>Non-positional features are now included in sequence
2889 feature and gff files (controlled via non-positional feature
2890 visibility in tooltip).</li>
2891 <li>URL links generated for all feature links (bugfix)</li>
2892 <li>Added URL embedding instructions to features file
2894 <li>Codons containing ambiguous nucleotides translated as
2895 'X' in peptide product</li>
2896 <li>Match case switch in find dialog box works for both
2897 sequence ID and sequence string and query strings do not
2898 have to be in upper case to match case-insensitively.</li>
2899 <li>AMSA files only contain first column of
2900 multi-character column annotation labels</li>
2901 <li>Jalview Annotation File generation/parsing consistent
2902 with documentation (e.g. Stockholm annotation can be
2903 exported and re-imported)</li>
2904 <li>PDB files without embedded PDB IDs given a friendly
2906 <li>Find incrementally searches ID string matches as well
2907 as subsequence matches, and correctly reports total number
2911 <li>Better handling of exceptions during sequence
2913 <li>Dasobert generated non-positional feature URL
2914 link text excludes the start_end suffix</li>
2915 <li>DAS feature and source retrieval buttons disabled
2916 when fetch or registry operations in progress.</li>
2917 <li>PDB files retrieved from URLs are cached properly</li>
2918 <li>Sequence description lines properly shared via
2920 <li>Sequence fetcher fetches multiple records for all
2922 <li>Ensured that command line das feature retrieval
2923 completes before alignment figures are generated.</li>
2924 <li>Reduced time taken when opening file browser for
2926 <li>isAligned check prior to calculating tree, PCA or
2927 submitting an MSA to JNet now excludes hidden sequences.</li>
2928 <li>User defined group colours properly recovered
2929 from Jalview projects.</li>
2938 <div align="center">
2939 <strong>2.4.0.b2</strong><br> 28/10/2009
2944 <li>Experimental support for google analytics usage
2946 <li>Jalview privacy settings (user preferences and docs).</li>
2951 <li>Race condition in applet preventing startup in
2953 <li>Exception when feature created from selection beyond
2954 length of sequence.</li>
2955 <li>Allow synthetic PDB files to be imported gracefully</li>
2956 <li>Sequence associated annotation rows associate with
2957 all sequences with a given id</li>
2958 <li>Find function matches case-insensitively for sequence
2959 ID string searches</li>
2960 <li>Non-standard characters do not cause pairwise
2961 alignment to fail with exception</li>
2962 </ul> <em>Application Issues</em>
2964 <li>Sequences are now validated against EMBL database</li>
2965 <li>Sequence fetcher fetches multiple records for all
2967 </ul> <em>InstallAnywhere Issues</em>
2969 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2970 issue with installAnywhere mechanism)</li>
2971 <li>Command line launching of JARs from InstallAnywhere
2972 version (java class versioning error fixed)</li>
2979 <div align="center">
2980 <strong>2.4</strong><br> 27/8/2008
2983 <td><em>User Interface</em>
2985 <li>Linked highlighting of codon and amino acid from
2986 translation and protein products</li>
2987 <li>Linked highlighting of structure associated with
2988 residue mapping to codon position</li>
2989 <li>Sequence Fetcher provides example accession numbers
2990 and 'clear' button</li>
2991 <li>MemoryMonitor added as an option under Desktop's
2993 <li>Extract score function to parse whitespace separated
2994 numeric data in description line</li>
2995 <li>Column labels in alignment annotation can be centred.</li>
2996 <li>Tooltip for sequence associated annotation give name
2998 </ul> <em>Web Services and URL fetching</em>
3000 <li>JPred3 web service</li>
3001 <li>Prototype sequence search client (no public services
3003 <li>Fetch either seed alignment or full alignment from
3005 <li>URL Links created for matching database cross
3006 references as well as sequence ID</li>
3007 <li>URL Links can be created using regular-expressions</li>
3008 </ul> <em>Sequence Database Connectivity</em>
3010 <li>Retrieval of cross-referenced sequences from other
3012 <li>Generalised database reference retrieval and
3013 validation to all fetchable databases</li>
3014 <li>Fetch sequences from DAS sources supporting the
3015 sequence command</li>
3016 </ul> <em>Import and Export</em>
3017 <li>export annotation rows as CSV for spreadsheet import</li>
3018 <li>Jalview projects record alignment dataset associations,
3019 EMBL products, and cDNA sequence mappings</li>
3020 <li>Sequence Group colour can be specified in Annotation
3022 <li>Ad-hoc colouring of group in Annotation File using RGB
3023 triplet as name of colourscheme</li>
3024 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3026 <li>treenode binding for VAMSAS tree exchange</li>
3027 <li>local editing and update of sequences in VAMSAS
3028 alignments (experimental)</li>
3029 <li>Create new or select existing session to join</li>
3030 <li>load and save of vamsas documents</li>
3031 </ul> <em>Application command line</em>
3033 <li>-tree parameter to open trees (introduced for passing
3035 <li>-fetchfrom command line argument to specify nicknames
3036 of DAS servers to query for alignment features</li>
3037 <li>-dasserver command line argument to add new servers
3038 that are also automatically queried for features</li>
3039 <li>-groovy command line argument executes a given groovy
3040 script after all input data has been loaded and parsed</li>
3041 </ul> <em>Applet-Application data exchange</em>
3043 <li>Trees passed as applet parameters can be passed to
3044 application (when using "View in full
3045 application")</li>
3046 </ul> <em>Applet Parameters</em>
3048 <li>feature group display control parameter</li>
3049 <li>debug parameter</li>
3050 <li>showbutton parameter</li>
3051 </ul> <em>Applet API methods</em>
3053 <li>newView public method</li>
3054 <li>Window (current view) specific get/set public methods</li>
3055 <li>Feature display control methods</li>
3056 <li>get list of currently selected sequences</li>
3057 </ul> <em>New Jalview distribution features</em>
3059 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3060 <li>RELEASE file gives build properties for the latest
3061 Jalview release.</li>
3062 <li>Java 1.1 Applet build made easier and donotobfuscate
3063 property controls execution of obfuscator</li>
3064 <li>Build target for generating source distribution</li>
3065 <li>Debug flag for javacc</li>
3066 <li>.jalview_properties file is documented (slightly) in
3067 jalview.bin.Cache</li>
3068 <li>Continuous Build Integration for stable and
3069 development version of Application, Applet and source
3074 <li>selected region output includes visible annotations
3075 (for certain formats)</li>
3076 <li>edit label/displaychar contains existing label/char
3078 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3079 <li>shorter peptide product names from EMBL records</li>
3080 <li>Newick string generator makes compact representations</li>
3081 <li>bootstrap values parsed correctly for tree files with
3083 <li>pathological filechooser bug avoided by not allowing
3084 filenames containing a ':'</li>
3085 <li>Fixed exception when parsing GFF files containing
3086 global sequence features</li>
3087 <li>Alignment datasets are finalized only when number of
3088 references from alignment sequences goes to zero</li>
3089 <li>Close of tree branch colour box without colour
3090 selection causes cascading exceptions</li>
3091 <li>occasional negative imgwidth exceptions</li>
3092 <li>better reporting of non-fatal warnings to user when
3093 file parsing fails.</li>
3094 <li>Save works when Jalview project is default format</li>
3095 <li>Save as dialog opened if current alignment format is
3096 not a valid output format</li>
3097 <li>UniProt canonical names introduced for both das and
3099 <li>Histidine should be midblue (not pink!) in Zappo</li>
3100 <li>error messages passed up and output when data read
3102 <li>edit undo recovers previous dataset sequence when
3103 sequence is edited</li>
3104 <li>allow PDB files without pdb ID HEADER lines (like
3105 those generated by MODELLER) to be read in properly</li>
3106 <li>allow reading of JPred concise files as a normal
3108 <li>Stockholm annotation parsing and alignment properties
3109 import fixed for PFAM records</li>
3110 <li>Structure view windows have correct name in Desktop
3112 <li>annotation consisting of sequence associated scores
3113 can be read and written correctly to annotation file</li>
3114 <li>Aligned cDNA translation to aligned peptide works
3116 <li>Fixed display of hidden sequence markers and
3117 non-italic font for representatives in Applet</li>
3118 <li>Applet Menus are always embedded in applet window on
3120 <li>Newly shown features appear at top of stack (in
3122 <li>Annotations added via parameter not drawn properly
3123 due to null pointer exceptions</li>
3124 <li>Secondary structure lines are drawn starting from
3125 first column of alignment</li>
3126 <li>UniProt XML import updated for new schema release in
3128 <li>Sequence feature to sequence ID match for Features
3129 file is case-insensitive</li>
3130 <li>Sequence features read from Features file appended to
3131 all sequences with matching IDs</li>
3132 <li>PDB structure coloured correctly for associated views
3133 containing a sub-sequence</li>
3134 <li>PDB files can be retrieved by applet from Jar files</li>
3135 <li>feature and annotation file applet parameters
3136 referring to different directories are retrieved correctly</li>
3137 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3138 <li>Fixed application hang whilst waiting for
3139 splash-screen version check to complete</li>
3140 <li>Applet properly URLencodes input parameter values
3141 when passing them to the launchApp service</li>
3142 <li>display name and local features preserved in results
3143 retrieved from web service</li>
3144 <li>Visual delay indication for sequence retrieval and
3145 sequence fetcher initialisation</li>
3146 <li>updated Application to use DAS 1.53e version of
3147 dasobert DAS client</li>
3148 <li>Re-instated Full AMSA support and .amsa file
3150 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3158 <div align="center">
3159 <strong>2.3</strong><br> 9/5/07
3164 <li>Jmol 11.0.2 integration</li>
3165 <li>PDB views stored in Jalview XML files</li>
3166 <li>Slide sequences</li>
3167 <li>Edit sequence in place</li>
3168 <li>EMBL CDS features</li>
3169 <li>DAS Feature mapping</li>
3170 <li>Feature ordering</li>
3171 <li>Alignment Properties</li>
3172 <li>Annotation Scores</li>
3173 <li>Sort by scores</li>
3174 <li>Feature/annotation editing in applet</li>
3179 <li>Headless state operation in 2.2.1</li>
3180 <li>Incorrect and unstable DNA pairwise alignment</li>
3181 <li>Cut and paste of sequences with annotation</li>
3182 <li>Feature group display state in XML</li>
3183 <li>Feature ordering in XML</li>
3184 <li>blc file iteration selection using filename # suffix</li>
3185 <li>Stockholm alignment properties</li>
3186 <li>Stockhom alignment secondary structure annotation</li>
3187 <li>2.2.1 applet had no feature transparency</li>
3188 <li>Number pad keys can be used in cursor mode</li>
3189 <li>Structure Viewer mirror image resolved</li>
3196 <div align="center">
3197 <strong>2.2.1</strong><br> 12/2/07
3202 <li>Non standard characters can be read and displayed
3203 <li>Annotations/Features can be imported/exported to the
3205 <li>Applet allows editing of sequence/annotation/group
3206 name & description
3207 <li>Preference setting to display sequence name in
3209 <li>Annotation file format extended to allow
3210 Sequence_groups to be defined
3211 <li>Default opening of alignment overview panel can be
3212 specified in preferences
3213 <li>PDB residue numbering annotation added to associated
3219 <li>Applet crash under certain Linux OS with Java 1.6
3221 <li>Annotation file export / import bugs fixed
3222 <li>PNG / EPS image output bugs fixed
3228 <div align="center">
3229 <strong>2.2</strong><br> 27/11/06
3234 <li>Multiple views on alignment
3235 <li>Sequence feature editing
3236 <li>"Reload" alignment
3237 <li>"Save" to current filename
3238 <li>Background dependent text colour
3239 <li>Right align sequence ids
3240 <li>User-defined lower case residue colours
3243 <li>Menu item accelerator keys
3244 <li>Control-V pastes to current alignment
3245 <li>Cancel button for DAS Feature Fetching
3246 <li>PCA and PDB Viewers zoom via mouse roller
3247 <li>User-defined sub-tree colours and sub-tree selection
3249 <li>'New Window' button on the 'Output to Text box'
3254 <li>New memory efficient Undo/Redo System
3255 <li>Optimised symbol lookups and conservation/consensus
3257 <li>Region Conservation/Consensus recalculated after
3259 <li>Fixed Remove Empty Columns Bug (empty columns at end
3261 <li>Slowed DAS Feature Fetching for increased robustness.
3263 <li>Made angle brackets in ASCII feature descriptions
3265 <li>Re-instated Zoom function for PCA
3266 <li>Sequence descriptions conserved in web service
3268 <li>UniProt ID discoverer uses any word separated by
3270 <li>WsDbFetch query/result association resolved
3271 <li>Tree leaf to sequence mapping improved
3272 <li>Smooth fonts switch moved to FontChooser dialog box.
3279 <div align="center">
3280 <strong>2.1.1</strong><br> 12/9/06
3285 <li>Copy consensus sequence to clipboard</li>
3290 <li>Image output - rightmost residues are rendered if
3291 sequence id panel has been resized</li>
3292 <li>Image output - all offscreen group boundaries are
3294 <li>Annotation files with sequence references - all
3295 elements in file are relative to sequence position</li>
3296 <li>Mac Applet users can use Alt key for group editing</li>
3302 <div align="center">
3303 <strong>2.1</strong><br> 22/8/06
3308 <li>MAFFT Multiple Alignment in default Web Service list</li>
3309 <li>DAS Feature fetching</li>
3310 <li>Hide sequences and columns</li>
3311 <li>Export Annotations and Features</li>
3312 <li>GFF file reading / writing</li>
3313 <li>Associate structures with sequences from local PDB
3315 <li>Add sequences to exisiting alignment</li>
3316 <li>Recently opened files / URL lists</li>
3317 <li>Applet can launch the full application</li>
3318 <li>Applet has transparency for features (Java 1.2
3320 <li>Applet has user defined colours parameter</li>
3321 <li>Applet can load sequences from parameter
3322 "sequence<em>x</em>"
3328 <li>Redundancy Panel reinstalled in the Applet</li>
3329 <li>Monospaced font - EPS / rescaling bug fixed</li>
3330 <li>Annotation files with sequence references bug fixed</li>
3336 <div align="center">
3337 <strong>2.08.1</strong><br> 2/5/06
3342 <li>Change case of selected region from Popup menu</li>
3343 <li>Choose to match case when searching</li>
3344 <li>Middle mouse button and mouse movement can compress /
3345 expand the visible width and height of the alignment</li>
3350 <li>Annotation Panel displays complete JNet results</li>
3356 <div align="center">
3357 <strong>2.08b</strong><br> 18/4/06
3363 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3364 <li>Righthand label on wrapped alignments shows correct
3371 <div align="center">
3372 <strong>2.08</strong><br> 10/4/06
3377 <li>Editing can be locked to the selection area</li>
3378 <li>Keyboard editing</li>
3379 <li>Create sequence features from searches</li>
3380 <li>Precalculated annotations can be loaded onto
3382 <li>Features file allows grouping of features</li>
3383 <li>Annotation Colouring scheme added</li>
3384 <li>Smooth fonts off by default - Faster rendering</li>
3385 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3390 <li>Drag & Drop fixed on Linux</li>
3391 <li>Jalview Archive file faster to load/save, sequence
3392 descriptions saved.</li>
3398 <div align="center">
3399 <strong>2.07</strong><br> 12/12/05
3404 <li>PDB Structure Viewer enhanced</li>
3405 <li>Sequence Feature retrieval and display enhanced</li>
3406 <li>Choose to output sequence start-end after sequence
3407 name for file output</li>
3408 <li>Sequence Fetcher WSDBFetch@EBI</li>
3409 <li>Applet can read feature files, PDB files and can be
3410 used for HTML form input</li>
3415 <li>HTML output writes groups and features</li>
3416 <li>Group editing is Control and mouse click</li>
3417 <li>File IO bugs</li>
3423 <div align="center">
3424 <strong>2.06</strong><br> 28/9/05
3429 <li>View annotations in wrapped mode</li>
3430 <li>More options for PCA viewer</li>
3435 <li>GUI bugs resolved</li>
3436 <li>Runs with -nodisplay from command line</li>
3442 <div align="center">
3443 <strong>2.05b</strong><br> 15/9/05
3448 <li>Choose EPS export as lineart or text</li>
3449 <li>Jar files are executable</li>
3450 <li>Can read in Uracil - maps to unknown residue</li>
3455 <li>Known OutOfMemory errors give warning message</li>
3456 <li>Overview window calculated more efficiently</li>
3457 <li>Several GUI bugs resolved</li>
3463 <div align="center">
3464 <strong>2.05</strong><br> 30/8/05
3469 <li>Edit and annotate in "Wrapped" view</li>
3474 <li>Several GUI bugs resolved</li>
3480 <div align="center">
3481 <strong>2.04</strong><br> 24/8/05
3486 <li>Hold down mouse wheel & scroll to change font
3492 <li>Improved JPred client reliability</li>
3493 <li>Improved loading of Jalview files</li>
3499 <div align="center">
3500 <strong>2.03</strong><br> 18/8/05
3505 <li>Set Proxy server name and port in preferences</li>
3506 <li>Multiple URL links from sequence ids</li>
3507 <li>User Defined Colours can have a scheme name and added
3509 <li>Choose to ignore gaps in consensus calculation</li>
3510 <li>Unix users can set default web browser</li>
3511 <li>Runs without GUI for batch processing</li>
3512 <li>Dynamically generated Web Service Menus</li>
3517 <li>InstallAnywhere download for Sparc Solaris</li>
3523 <div align="center">
3524 <strong>2.02</strong><br> 18/7/05
3530 <li>Copy & Paste order of sequences maintains
3531 alignment order.</li>
3537 <div align="center">
3538 <strong>2.01</strong><br> 12/7/05
3543 <li>Use delete key for deleting selection.</li>
3544 <li>Use Mouse wheel to scroll sequences.</li>
3545 <li>Help file updated to describe how to add alignment
3547 <li>Version and build date written to build properties
3549 <li>InstallAnywhere installation will check for updates
3550 at launch of Jalview.</li>
3555 <li>Delete gaps bug fixed.</li>
3556 <li>FileChooser sorts columns.</li>
3557 <li>Can remove groups one by one.</li>
3558 <li>Filechooser icons installed.</li>
3559 <li>Finder ignores return character when searching.
3560 Return key will initiate a search.<br>
3567 <div align="center">
3568 <strong>2.0</strong><br> 20/6/05
3573 <li>New codebase</li>