3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
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27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.3">2.10.3</a><br />
74 <em>10/10/2017</em></strong>
77 <td><div align="left">
81 <!-- JAL-2446 -->Faster and more efficient management and
82 rendering of sequence features
85 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
86 429 rate limit request hander
89 <!-- JAL-2773 -->Structure views don't get updated unless
90 their colours have changed
92 <li><!-- JAL-2495 -->All linked sequences are highlighted for a structure mousover (Jmol) or selection (Chimera)</li>
93 <li><!-- JAL-2790 -->'Cancel' button in progress bar for JABAWS AACon, RNAAliFold and Disorder prediction jobs
97 <ul><li>Example groovy script for generating a matrix of percent identity scores for current alignment.</li></ul>
98 <em>Testing and Deployment</em>
99 <ul><li><!-- JAL-2727 -->Test to catch memory leaks in Jalview UI</li></ul>
101 <td><div align="left">
104 <li><!-- JAL-2643 -->Pressing tab after updating the colour threshold text field doesn't trigger an update to the alignment view</li>
105 <li><!-- JAL-2682 -->Race condition when parsing sequence ID strings in parallel</li>
106 <li><!-- JAL-2608 -->Overview windows are also closed when alignment window is closed</li>
110 <li><!-- JAL-2777 -->Structures with whitespace chainCode cannot be viewed in Chimera</li>
111 <li><!-- JAL-2728 -->Protein annotation panel too high in CDS/Protein view
113 <li><!-- JAL-2757 -->Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs
115 <li><!-- JAL-2253 -->Slow EnsemblGenome ID lookup</li>
116 <li><!-- JAL-2739 -->Hidden column marker in last column not rendered when switching back from Wrapped to normal view</li>
117 <li><!-- JAL-2768 -->Annotation display corrupted when scrolling right in unwapped alignment view</li>
118 <li><!-- JAL-2542 -->Existing features on subsequence incorrectly relocated when full sequence retrieved from database</li>
119 <li><!-- JAL-2733 -->Last reported memory still shown when Desktop->Show Memory is unticked (OSX only)</li>
120 <li><!-- JAL-2658 -->Amend Features dialog doesn't allow features of same type and group to be selected for amending</li>
121 <li><!-- JAL-2524 -->Jalview becomes sluggish in wide alignments when hidden columns are present</li>
122 <li><!-- JAL-2392 -->Jalview freezes when loading and displaying several structures</li>
123 <li><!-- JAL-2732 -->Black outlines left after resizing or moving a window</li>
124 <li><!-- JAL-1900,JAL-1625 -->Unable to minimise windows within the Jalview desktop on OSX</li>
126 <strong><em>Applet</em></strong><br/>
128 <li><!-- JAL-2687 -->Concurrent modification exception when closing alignment panel</li>
133 <td width="60" nowrap>
135 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
136 <em>2/10/2017</em></strong>
139 <td><div align="left">
140 <em>New features in Jalview Desktop</em>
143 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
145 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
149 <td><div align="left">
153 <td width="60" nowrap>
155 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
156 <em>7/9/2017</em></strong>
159 <td><div align="left">
163 <!-- JAL-2588 -->Show gaps in overview window by colouring
164 in grey (sequences used to be coloured grey, and gaps were
168 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
172 <!-- JAL-2587 -->Overview updates immediately on increase
173 in size and progress bar shown as higher resolution
174 overview is recalculated
179 <td><div align="left">
183 <!-- JAL-2664 -->Overview window redraws every hidden
184 column region row by row
187 <!-- JAL-2681 -->duplicate protein sequences shown after
188 retrieving Ensembl crossrefs for sequences from Uniprot
191 <!-- JAL-2603 -->Overview window throws NPE if show boxes
192 format setting is unticked
195 <!-- JAL-2610 -->Groups are coloured wrongly in overview
196 if group has show boxes format setting unticked
199 <!-- JAL-2672,JAL-2665 -->Redraw problems when
200 autoscrolling whilst dragging current selection group to
201 include sequences and columns not currently displayed
204 <!-- JAL-2691 -->Not all chains are mapped when multimeric
205 assemblies are imported via CIF file
208 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
209 displayed when threshold or conservation colouring is also
213 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
217 <!-- JAL-2673 -->Jalview continues to scroll after
218 dragging a selected region off the visible region of the
222 <!-- JAL-2724 -->Cannot apply annotation based
223 colourscheme to all groups in a view
226 <!-- JAL-2511 -->IDs don't line up with sequences
227 initially after font size change using the Font chooser or
234 <td width="60" nowrap>
236 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
239 <td><div align="left">
240 <em>Calculations</em>
244 <!-- JAL-1933 -->Occupancy annotation row shows number of
245 ungapped positions in each column of the alignment.
248 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
249 a calculation dialog box
252 <!-- JAL-2379 -->Revised implementation of PCA for speed
253 and memory efficiency (~30x faster)
256 <!-- JAL-2403 -->Revised implementation of sequence
257 similarity scores as used by Tree, PCA, Shading Consensus
258 and other calculations
261 <!-- JAL-2416 -->Score matrices are stored as resource
262 files within the Jalview codebase
265 <!-- JAL-2500 -->Trees computed on Sequence Feature
266 Similarity may have different topology due to increased
273 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
274 model for alignments and groups
277 <!-- JAL-384 -->Custom shading schemes created via groovy
284 <!-- JAL-2526 -->Efficiency improvements for interacting
285 with alignment and overview windows
288 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
292 <!-- JAL-2388 -->Hidden columns and sequences can be
296 <!-- JAL-2611 -->Click-drag in visible area allows fine
297 adjustment of visible position
301 <em>Data import/export</em>
304 <!-- JAL-2535 -->Posterior probability annotation from
305 Stockholm files imported as sequence associated annotation
308 <!-- JAL-2507 -->More robust per-sequence positional
309 annotation input/output via stockholm flatfile
312 <!-- JAL-2533 -->Sequence names don't include file
313 extension when importing structure files without embedded
314 names or PDB accessions
317 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
318 format sequence substitution matrices
321 <em>User Interface</em>
324 <!-- JAL-2447 --> Experimental Features Checkbox in
325 Desktop's Tools menu to hide or show untested features in
329 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
330 via Overview or sequence motif search operations
333 <!-- JAL-2547 -->Amend sequence features dialog box can be
334 opened by double clicking gaps within sequence feature
338 <!-- JAL-1476 -->Status bar message shown when not enough
339 aligned positions were available to create a 3D structure
343 <em>3D Structure</em>
346 <!-- JAL-2430 -->Hidden regions in alignment views are not
347 coloured in linked structure views
350 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
351 file-based command exchange
354 <!-- JAL-2375 -->Structure chooser automatically shows
355 Cached Structures rather than querying the PDBe if
356 structures are already available for sequences
359 <!-- JAL-2520 -->Structures imported via URL are cached in
360 the Jalview project rather than downloaded again when the
364 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
365 to transfer Chimera's structure attributes as Jalview
366 features, and vice-versa (<strong>Experimental
370 <em>Web Services</em>
373 <!-- JAL-2549 -->Updated JABAWS client to v2.2
376 <!-- JAL-2335 -->Filter non-standard amino acids and
377 nucleotides when submitting to AACon and other MSA
381 <!-- JAL-2316, -->URLs for viewing database
382 cross-references provided by identifiers.org and the
390 <!-- JAL-2344 -->FileFormatI interface for describing and
391 identifying file formats (instead of String constants)
394 <!-- JAL-2228 -->FeatureCounter script refactored for
395 efficiency when counting all displayed features (not
396 backwards compatible with 2.10.1)
399 <em>Example files</em>
402 <!-- JAL-2631 -->Graduated feature colour style example
403 included in the example feature file
406 <em>Documentation</em>
409 <!-- JAL-2339 -->Release notes reformatted for readability
410 with the built-in Java help viewer
413 <!-- JAL-1644 -->Find documentation updated with 'search
414 sequence description' option
420 <!-- JAL-2485, -->External service integration tests for
421 Uniprot REST Free Text Search Client
424 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
427 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
432 <td><div align="left">
433 <em>Calculations</em>
436 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
437 matrix - C->R should be '-3'<br />Old matrix restored
438 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
440 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
441 Jalview's treatment of gaps in PCA and substitution matrix
442 based Tree calculations.<br /> <br />In earlier versions
443 of Jalview, gaps matching gaps were penalised, and gaps
444 matching non-gaps penalised even more. In the PCA
445 calculation, gaps were actually treated as non-gaps - so
446 different costs were applied, which meant Jalview's PCAs
447 were different to those produced by SeqSpace.<br />Jalview
448 now treats gaps in the same way as SeqSpace (ie it scores
449 them as 0). <br /> <br />Enter the following in the
450 Groovy console to restore pre-2.10.2 behaviour:<br />
451 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
452 // for 2.10.1 mode <br />
453 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
454 // to restore 2.10.2 mode <br /> <br /> <em>Note:
455 these settings will affect all subsequent tree and PCA
456 calculations (not recommended)</em></li>
458 <!-- JAL-2424 -->Fixed off-by-one bug that affected
459 scaling of branch lengths for trees computed using
460 Sequence Feature Similarity.
463 <!-- JAL-2377 -->PCA calculation could hang when
464 generating output report when working with highly
468 <!-- JAL-2544 --> Sort by features includes features to
469 right of selected region when gaps present on right-hand
473 <em>User Interface</em>
476 <!-- JAL-2346 -->Reopening Colour by annotation dialog
477 doesn't reselect a specific sequence's associated
478 annotation after it was used for colouring a view
481 <!-- JAL-2419 -->Current selection lost if popup menu
482 opened on a region of alignment without groups
485 <!-- JAL-2374 -->Popup menu not always shown for regions
486 of an alignment with overlapping groups
489 <!-- JAL-2310 -->Finder double counts if both a sequence's
490 name and description match
493 <!-- JAL-2370 -->Hiding column selection containing two
494 hidden regions results in incorrect hidden regions
497 <!-- JAL-2386 -->'Apply to all groups' setting when
498 changing colour does not apply Conservation slider value
502 <!-- JAL-2373 -->Percentage identity and conservation menu
503 items do not show a tick or allow shading to be disabled
506 <!-- JAL-2385 -->Conservation shading or PID threshold
507 lost when base colourscheme changed if slider not visible
510 <!-- JAL-2547 -->Sequence features shown in tooltip for
511 gaps before start of features
514 <!-- JAL-2623 -->Graduated feature colour threshold not
515 restored to UI when feature colour is edited
518 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
519 a time when scrolling vertically in wrapped mode.
522 <!-- JAL-2630 -->Structure and alignment overview update
523 as graduate feature colour settings are modified via the
527 <!-- JAL-2034 -->Overview window doesn't always update
528 when a group defined on the alignment is resized
531 <!-- JAL-2605 -->Mouseovers on left/right scale region in
532 wrapped view result in positional status updates
536 <!-- JAL-2563 -->Status bar doesn't show position for
537 ambiguous amino acid and nucleotide symbols
540 <!-- JAL-2602 -->Copy consensus sequence failed if
541 alignment included gapped columns
544 <!-- JAL-2473 -->Minimum size set for Jalview windows so
545 widgets don't permanently disappear
548 <!-- JAL-2503 -->Cannot select or filter quantitative
549 annotation that are shown only as column labels (e.g.
550 T-Coffee column reliability scores)
553 <!-- JAL-2594 -->Exception thrown if trying to create a
554 sequence feature on gaps only
557 <!-- JAL-2504 -->Features created with 'New feature'
558 button from a Find inherit previously defined feature type
559 rather than the Find query string
562 <!-- JAL-2423 -->incorrect title in output window when
563 exporting tree calculated in Jalview
566 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
567 and then revealing them reorders sequences on the
571 <!-- JAL-964 -->Group panel in sequence feature settings
572 doesn't update to reflect available set of groups after
573 interactively adding or modifying features
576 <!-- JAL-2225 -->Sequence Database chooser unusable on
580 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
581 only excluded gaps in current sequence and ignored
588 <!-- JAL-2421 -->Overview window visible region moves
589 erratically when hidden rows or columns are present
592 <!-- JAL-2362 -->Per-residue colourschemes applied via the
593 Structure Viewer's colour menu don't correspond to
597 <!-- JAL-2405 -->Protein specific colours only offered in
598 colour and group colour menu for protein alignments
601 <!-- JAL-2385 -->Colour threshold slider doesn't update to
602 reflect currently selected view or group's shading
606 <!-- JAL-2624 -->Feature colour thresholds not respected
607 when rendered on overview and structures when opacity at
611 <!-- JAL-2589 -->User defined gap colour not shown in
612 overview when features overlaid on alignment
615 <em>Data import/export</em>
618 <!-- JAL-2576 -->Very large alignments take a long time to
622 <!-- JAL-2507 -->Per-sequence RNA secondary structures
623 added after a sequence was imported are not written to
627 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
628 when importing RNA secondary structure via Stockholm
631 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
632 not shown in correct direction for simple pseudoknots
635 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
636 with lightGray or darkGray via features file (but can
640 <!-- JAL-2383 -->Above PID colour threshold not recovered
641 when alignment view imported from project
644 <!-- JAL-2520,JAL-2465 -->No mappings generated between
645 structure and sequences extracted from structure files
646 imported via URL and viewed in Jmol
649 <!-- JAL-2520 -->Structures loaded via URL are saved in
650 Jalview Projects rather than fetched via URL again when
651 the project is loaded and the structure viewed
654 <em>Web Services</em>
657 <!-- JAL-2519 -->EnsemblGenomes example failing after
658 release of Ensembl v.88
661 <!-- JAL-2366 -->Proxy server address and port always
662 appear enabled in Preferences->Connections
665 <!-- JAL-2461 -->DAS registry not found exceptions
666 removed from console output
669 <!-- JAL-2582 -->Cannot retrieve protein products from
670 Ensembl by Peptide ID
673 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
674 created from SIFTs, and spurious 'Couldn't open structure
675 in Chimera' errors raised after April 2017 update (problem
676 due to 'null' string rather than empty string used for
677 residues with no corresponding PDB mapping).
680 <em>Application UI</em>
683 <!-- JAL-2361 -->User Defined Colours not added to Colour
687 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
688 case' residues (button in colourscheme editor debugged and
689 new documentation and tooltips added)
692 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
693 doesn't restore group-specific text colour thresholds
696 <!-- JAL-2243 -->Feature settings panel does not update as
697 new features are added to alignment
700 <!-- JAL-2532 -->Cancel in feature settings reverts
701 changes to feature colours via the Amend features dialog
704 <!-- JAL-2506 -->Null pointer exception when attempting to
705 edit graduated feature colour via amend features dialog
709 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
710 selection menu changes colours of alignment views
713 <!-- JAL-2426 -->Spurious exceptions in console raised
714 from alignment calculation workers after alignment has
718 <!-- JAL-1608 -->Typo in selection popup menu - Create
719 groups now 'Create Group'
722 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
723 Create/Undefine group doesn't always work
726 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
727 shown again after pressing 'Cancel'
730 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
731 adjusts start position in wrap mode
734 <!-- JAL-2563 -->Status bar doesn't show positions for
735 ambiguous amino acids
738 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
739 CDS/Protein view after CDS sequences added for aligned
743 <!-- JAL-2592 -->User defined colourschemes called 'User
744 Defined' don't appear in Colours menu
750 <!-- JAL-2468 -->Switching between Nucleotide and Protein
751 score models doesn't always result in an updated PCA plot
754 <!-- JAL-2442 -->Features not rendered as transparent on
755 overview or linked structure view
758 <!-- JAL-2372 -->Colour group by conservation doesn't
762 <!-- JAL-2517 -->Hitting Cancel after applying
763 user-defined colourscheme doesn't restore original
770 <!-- JAL-2314 -->Unit test failure:
771 jalview.ws.jabaws.RNAStructExportImport setup fails
774 <!-- JAL-2307 -->Unit test failure:
775 jalview.ws.sifts.SiftsClientTest due to compatibility
776 problems with deep array comparison equality asserts in
777 successive versions of TestNG
780 <!-- JAL-2479 -->Relocated StructureChooserTest and
781 ParameterUtilsTest Unit tests to Network suite
784 <em>New Known Issues</em>
787 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
788 phase after a sequence motif find operation
791 <!-- JAL-2550 -->Importing annotation file with rows
792 containing just upper and lower case letters are
793 interpreted as WUSS RNA secondary structure symbols
796 <!-- JAL-2590 -->Cannot load and display Newick trees
797 reliably from eggnog Ortholog database
800 <!-- JAL-2468 -->Status bar shows 'Marked x columns
801 containing features of type Highlight' when 'B' is pressed
802 to mark columns containing highlighted regions.
805 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
806 doesn't always add secondary structure annotation.
811 <td width="60" nowrap>
813 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
816 <td><div align="left">
820 <!-- JAL-98 -->Improved memory usage: sparse arrays used
821 for all consensus calculations
824 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
827 <li>Updated Jalview's Certum code signing certificate
833 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
834 set of database cross-references, sorted alphabetically
837 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
838 from database cross references. Users with custom links
839 will receive a <a href="webServices/urllinks.html#warning">warning
840 dialog</a> asking them to update their preferences.
843 <!-- JAL-2287-->Cancel button and escape listener on
844 dialog warning user about disconnecting Jalview from a
848 <!-- JAL-2320-->Jalview's Chimera control window closes if
849 the Chimera it is connected to is shut down
852 <!-- JAL-1738-->New keystroke (B) and Select highlighted
853 columns menu item to mark columns containing highlighted
854 regions (e.g. from structure selections or results of a
858 <!-- JAL-2284-->Command line option for batch-generation
859 of HTML pages rendering alignment data with the BioJS
869 <!-- JAL-2286 -->Columns with more than one modal residue
870 are not coloured or thresholded according to percent
871 identity (first observed in Jalview 2.8.2)
874 <!-- JAL-2301 -->Threonine incorrectly reported as not
878 <!-- JAL-2318 -->Updates to documentation pages (above PID
879 threshold, amino acid properties)
882 <!-- JAL-2292 -->Lower case residues in sequences are not
883 reported as mapped to residues in a structure file in the
887 <!--JAL-2324 -->Identical features with non-numeric scores
888 could be added multiple times to a sequence
891 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
892 bond features shown as two highlighted residues rather
893 than a range in linked structure views, and treated
894 correctly when selecting and computing trees from features
897 <!-- JAL-2281-->Custom URL links for database
898 cross-references are matched to database name regardless
906 <!-- JAL-2282-->Custom URL links for specific database
907 names without regular expressions also offer links from
911 <!-- JAL-2315-->Removing a single configured link in the
912 URL links pane in Connections preferences doesn't actually
913 update Jalview configuration
916 <!-- JAL-2272-->CTRL-Click on a selected region to open
917 the alignment area popup menu doesn't work on El-Capitan
920 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
921 files with similarly named sequences if dropped onto the
925 <!-- JAL-2312 -->Additional mappings are shown for PDB
926 entries where more chains exist in the PDB accession than
927 are reported in the SIFTS file
930 <!-- JAL-2317-->Certain structures do not get mapped to
931 the structure view when displayed with Chimera
934 <!-- JAL-2317-->No chains shown in the Chimera view
935 panel's View->Show Chains submenu
938 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
939 work for wrapped alignment views
942 <!--JAL-2197 -->Rename UI components for running JPred
943 predictions from 'JNet' to 'JPred'
946 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
947 corrupted when annotation panel vertical scroll is not at
951 <!--JAL-2332 -->Attempting to view structure for Hen
952 lysozyme results in a PDB Client error dialog box
955 <!-- JAL-2319 -->Structure View's mapping report switched
956 ranges for PDB and sequence for SIFTS
959 SIFTS 'Not_Observed' residues mapped to non-existant
963 <!-- <em>New Known Issues</em>
970 <td width="60" nowrap>
972 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
973 <em>25/10/2016</em></strong>
976 <td><em>Application</em>
978 <li>3D Structure chooser opens with 'Cached structures'
979 view if structures already loaded</li>
980 <li>Progress bar reports models as they are loaded to
987 <li>Colour by conservation always enabled and no tick
988 shown in menu when BLOSUM or PID shading applied</li>
989 <li>FER1_ARATH and FER2_ARATH labels were switched in
990 example sequences/projects/trees</li>
994 <li>Jalview projects with views of local PDB structure
995 files saved on Windows cannot be opened on OSX</li>
996 <li>Multiple structure views can be opened and superposed
997 without timeout for structures with multiple models or
998 multiple sequences in alignment</li>
999 <li>Cannot import or associated local PDB files without a
1000 PDB ID HEADER line</li>
1001 <li>RMSD is not output in Jmol console when superposition
1003 <li>Drag and drop of URL from Browser fails for Linux and
1004 OSX versions earlier than El Capitan</li>
1005 <li>ENA client ignores invalid content from ENA server</li>
1006 <li>Exceptions are not raised in console when ENA client
1007 attempts to fetch non-existent IDs via Fetch DB Refs UI
1009 <li>Exceptions are not raised in console when a new view
1010 is created on the alignment</li>
1011 <li>OSX right-click fixed for group selections: CMD-click
1012 to insert/remove gaps in groups and CTRL-click to open group
1015 <em>Build and deployment</em>
1017 <li>URL link checker now copes with multi-line anchor
1020 <em>New Known Issues</em>
1022 <li>Drag and drop from URL links in browsers do not work
1029 <td width="60" nowrap>
1030 <div align="center">
1031 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1034 <td><em>General</em>
1037 <!-- JAL-2124 -->Updated Spanish translations.
1040 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1041 for importing structure data to Jalview. Enables mmCIF and
1045 <!-- JAL-192 --->Alignment ruler shows positions relative to
1049 <!-- JAL-2202 -->Position/residue shown in status bar when
1050 mousing over sequence associated annotation
1053 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1057 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1058 '()', canonical '[]' and invalid '{}' base pair populations
1062 <!-- JAL-2092 -->Feature settings popup menu options for
1063 showing or hiding columns containing a feature
1066 <!-- JAL-1557 -->Edit selected group by double clicking on
1067 group and sequence associated annotation labels
1070 <!-- JAL-2236 -->Sequence name added to annotation label in
1071 select/hide columns by annotation and colour by annotation
1075 </ul> <em>Application</em>
1078 <!-- JAL-2050-->Automatically hide introns when opening a
1079 gene/transcript view
1082 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1086 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1087 structure mappings with the EMBL-EBI PDBe SIFTS database
1090 <!-- JAL-2079 -->Updated download sites used for Rfam and
1091 Pfam sources to xfam.org
1094 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1097 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1098 over sequences in Jalview
1101 <!-- JAL-2027-->Support for reverse-complement coding
1102 regions in ENA and EMBL
1105 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1106 for record retrieval via ENA rest API
1109 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1113 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1114 groovy script execution
1117 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1118 alignment window's Calculate menu
1121 <!-- JAL-1812 -->Allow groovy scripts that call
1122 Jalview.getAlignFrames() to run in headless mode
1125 <!-- JAL-2068 -->Support for creating new alignment
1126 calculation workers from groovy scripts
1129 <!-- JAL-1369 --->Store/restore reference sequence in
1133 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1134 associations are now saved/restored from project
1137 <!-- JAL-1993 -->Database selection dialog always shown
1138 before sequence fetcher is opened
1141 <!-- JAL-2183 -->Double click on an entry in Jalview's
1142 database chooser opens a sequence fetcher
1145 <!-- JAL-1563 -->Free-text search client for UniProt using
1146 the UniProt REST API
1149 <!-- JAL-2168 -->-nonews command line parameter to prevent
1150 the news reader opening
1153 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1154 querying stored in preferences
1157 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1161 <!-- JAL-1977-->Tooltips shown on database chooser
1164 <!-- JAL-391 -->Reverse complement function in calculate
1165 menu for nucleotide sequences
1168 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1169 and feature counts preserves alignment ordering (and
1170 debugged for complex feature sets).
1173 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1174 viewing structures with Jalview 2.10
1177 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1178 genome, transcript CCDS and gene ids via the Ensembl and
1179 Ensembl Genomes REST API
1182 <!-- JAL-2049 -->Protein sequence variant annotation
1183 computed for 'sequence_variant' annotation on CDS regions
1187 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1191 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1192 Ref Fetcher fails to match, or otherwise updates sequence
1193 data from external database records.
1196 <!-- JAL-2154 -->Revised Jalview Project format for
1197 efficient recovery of sequence coding and alignment
1198 annotation relationships.
1200 </ul> <!-- <em>Applet</em>
1211 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1215 <!-- JAL-2018-->Export features in Jalview format (again)
1216 includes graduated colourschemes
1219 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1220 working with big alignments and lots of hidden columns
1223 <!-- JAL-2053-->Hidden column markers not always rendered
1224 at right of alignment window
1227 <!-- JAL-2067 -->Tidied up links in help file table of
1231 <!-- JAL-2072 -->Feature based tree calculation not shown
1235 <!-- JAL-2075 -->Hidden columns ignored during feature
1236 based tree calculation
1239 <!-- JAL-2065 -->Alignment view stops updating when show
1240 unconserved enabled for group on alignment
1243 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1247 <!-- JAL-2146 -->Alignment column in status incorrectly
1248 shown as "Sequence position" when mousing over
1252 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1253 hidden columns present
1256 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1257 user created annotation added to alignment
1260 <!-- JAL-1841 -->RNA Structure consensus only computed for
1261 '()' base pair annotation
1264 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1265 in zero scores for all base pairs in RNA Structure
1269 <!-- JAL-2174-->Extend selection with columns containing
1273 <!-- JAL-2275 -->Pfam format writer puts extra space at
1274 beginning of sequence
1277 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1281 <!-- JAL-2238 -->Cannot create groups on an alignment from
1282 from a tree when t-coffee scores are shown
1285 <!-- JAL-1836,1967 -->Cannot import and view PDB
1286 structures with chains containing negative resnums (4q4h)
1289 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1293 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1294 to Clustal, PIR and PileUp output
1297 <!-- JAL-2008 -->Reordering sequence features that are
1298 not visible causes alignment window to repaint
1301 <!-- JAL-2006 -->Threshold sliders don't work in
1302 graduated colour and colour by annotation row for e-value
1303 scores associated with features and annotation rows
1306 <!-- JAL-1797 -->amino acid physicochemical conservation
1307 calculation should be case independent
1310 <!-- JAL-2173 -->Remove annotation also updates hidden
1314 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1315 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1316 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1319 <!-- JAL-2065 -->Null pointer exceptions and redraw
1320 problems when reference sequence defined and 'show
1321 non-conserved' enabled
1324 <!-- JAL-1306 -->Quality and Conservation are now shown on
1325 load even when Consensus calculation is disabled
1328 <!-- JAL-1932 -->Remove right on penultimate column of
1329 alignment does nothing
1332 <em>Application</em>
1335 <!-- JAL-1552-->URLs and links can't be imported by
1336 drag'n'drop on OSX when launched via webstart (note - not
1337 yet fixed for El Capitan)
1340 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1341 output when running on non-gb/us i18n platforms
1344 <!-- JAL-1944 -->Error thrown when exporting a view with
1345 hidden sequences as flat-file alignment
1348 <!-- JAL-2030-->InstallAnywhere distribution fails when
1352 <!-- JAL-2080-->Jalview very slow to launch via webstart
1353 (also hotfix for 2.9.0b2)
1356 <!-- JAL-2085 -->Cannot save project when view has a
1357 reference sequence defined
1360 <!-- JAL-1011 -->Columns are suddenly selected in other
1361 alignments and views when revealing hidden columns
1364 <!-- JAL-1989 -->Hide columns not mirrored in complement
1365 view in a cDNA/Protein splitframe
1368 <!-- JAL-1369 -->Cannot save/restore representative
1369 sequence from project when only one sequence is
1373 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1374 in Structure Chooser
1377 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1378 structure consensus didn't refresh annotation panel
1381 <!-- JAL-1962 -->View mapping in structure view shows
1382 mappings between sequence and all chains in a PDB file
1385 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1386 dialogs format columns correctly, don't display array
1387 data, sort columns according to type
1390 <!-- JAL-1975 -->Export complete shown after destination
1391 file chooser is cancelled during an image export
1394 <!-- JAL-2025 -->Error when querying PDB Service with
1395 sequence name containing special characters
1398 <!-- JAL-2024 -->Manual PDB structure querying should be
1402 <!-- JAL-2104 -->Large tooltips with broken HTML
1403 formatting don't wrap
1406 <!-- JAL-1128 -->Figures exported from wrapped view are
1407 truncated so L looks like I in consensus annotation
1410 <!-- JAL-2003 -->Export features should only export the
1411 currently displayed features for the current selection or
1415 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1416 after fetching cross-references, and restoring from
1420 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1421 followed in the structure viewer
1424 <!-- JAL-2163 -->Titles for individual alignments in
1425 splitframe not restored from project
1428 <!-- JAL-2145 -->missing autocalculated annotation at
1429 trailing end of protein alignment in transcript/product
1430 splitview when pad-gaps not enabled by default
1433 <!-- JAL-1797 -->amino acid physicochemical conservation
1437 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1438 article has been read (reopened issue due to
1439 internationalisation problems)
1442 <!-- JAL-1960 -->Only offer PDB structures in structure
1443 viewer based on sequence name, PDB and UniProt
1448 <!-- JAL-1976 -->No progress bar shown during export of
1452 <!-- JAL-2213 -->Structures not always superimposed after
1453 multiple structures are shown for one or more sequences.
1456 <!-- JAL-1370 -->Reference sequence characters should not
1457 be replaced with '.' when 'Show unconserved' format option
1461 <!-- JAL-1823 -->Cannot specify chain code when entering
1462 specific PDB id for sequence
1465 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1466 'Export hidden sequences' is enabled, but 'export hidden
1467 columns' is disabled.
1470 <!--JAL-2026-->Best Quality option in structure chooser
1471 selects lowest rather than highest resolution structures
1475 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1476 to sequence mapping in 'View Mappings' report
1479 <!-- JAL-2284 -->Unable to read old Jalview projects that
1480 contain non-XML data added after Jalvew wrote project.
1483 <!-- JAL-2118 -->Newly created annotation row reorders
1484 after clicking on it to create new annotation for a
1488 <!-- JAL-1980 -->Null Pointer Exception raised when
1489 pressing Add on an orphaned cut'n'paste window.
1491 <!-- may exclude, this is an external service stability issue JAL-1941
1492 -- > RNA 3D structure not added via DSSR service</li> -->
1497 <!-- JAL-2151 -->Incorrect columns are selected when
1498 hidden columns present before start of sequence
1501 <!-- JAL-1986 -->Missing dependencies on applet pages
1505 <!-- JAL-1947 -->Overview pixel size changes when
1506 sequences are hidden in applet
1509 <!-- JAL-1996 -->Updated instructions for applet
1510 deployment on examples pages.
1517 <td width="60" nowrap>
1518 <div align="center">
1519 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1520 <em>16/10/2015</em></strong>
1523 <td><em>General</em>
1525 <li>Time stamps for signed Jalview application and applet
1530 <em>Application</em>
1532 <li>Duplicate group consensus and conservation rows
1533 shown when tree is partitioned</li>
1534 <li>Erratic behaviour when tree partitions made with
1535 multiple cDNA/Protein split views</li>
1541 <td width="60" nowrap>
1542 <div align="center">
1543 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1544 <em>8/10/2015</em></strong>
1547 <td><em>General</em>
1549 <li>Updated Spanish translations of localized text for
1551 </ul> <em>Application</em>
1553 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1554 <li>Signed OSX InstallAnywhere installer<br></li>
1555 <li>Support for per-sequence based annotations in BioJSON</li>
1556 </ul> <em>Applet</em>
1558 <li>Split frame example added to applet examples page</li>
1559 </ul> <em>Build and Deployment</em>
1562 <!-- JAL-1888 -->New ant target for running Jalview's test
1570 <li>Mapping of cDNA to protein in split frames
1571 incorrect when sequence start > 1</li>
1572 <li>Broken images in filter column by annotation dialog
1574 <li>Feature colours not parsed from features file</li>
1575 <li>Exceptions and incomplete link URLs recovered when
1576 loading a features file containing HTML tags in feature
1580 <em>Application</em>
1582 <li>Annotations corrupted after BioJS export and
1584 <li>Incorrect sequence limits after Fetch DB References
1585 with 'trim retrieved sequences'</li>
1586 <li>Incorrect warning about deleting all data when
1587 deleting selected columns</li>
1588 <li>Patch to build system for shipping properly signed
1589 JNLP templates for webstart launch</li>
1590 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1591 unreleased structures for download or viewing</li>
1592 <li>Tab/space/return keystroke operation of EMBL-PDBe
1593 fetcher/viewer dialogs works correctly</li>
1594 <li>Disabled 'minimise' button on Jalview windows
1595 running on OSX to workaround redraw hang bug</li>
1596 <li>Split cDNA/Protein view position and geometry not
1597 recovered from jalview project</li>
1598 <li>Initial enabled/disabled state of annotation menu
1599 sorter 'show autocalculated first/last' corresponds to
1601 <li>Restoring of Clustal, RNA Helices and T-Coffee
1602 color schemes from BioJSON</li>
1606 <li>Reorder sequences mirrored in cDNA/Protein split
1608 <li>Applet with Jmol examples not loading correctly</li>
1614 <td><div align="center">
1615 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1617 <td><em>General</em>
1619 <li>Linked visualisation and analysis of DNA and Protein
1622 <li>Translated cDNA alignments shown as split protein
1623 and DNA alignment views</li>
1624 <li>Codon consensus annotation for linked protein and
1625 cDNA alignment views</li>
1626 <li>Link cDNA or Protein product sequences by loading
1627 them onto Protein or cDNA alignments</li>
1628 <li>Reconstruct linked cDNA alignment from aligned
1629 protein sequences</li>
1632 <li>Jmol integration updated to Jmol v14.2.14</li>
1633 <li>Import and export of Jalview alignment views as <a
1634 href="features/bioJsonFormat.html">BioJSON</a></li>
1635 <li>New alignment annotation file statements for
1636 reference sequences and marking hidden columns</li>
1637 <li>Reference sequence based alignment shading to
1638 highlight variation</li>
1639 <li>Select or hide columns according to alignment
1641 <li>Find option for locating sequences by description</li>
1642 <li>Conserved physicochemical properties shown in amino
1643 acid conservation row</li>
1644 <li>Alignments can be sorted by number of RNA helices</li>
1645 </ul> <em>Application</em>
1647 <li>New cDNA/Protein analysis capabilities
1649 <li>Get Cross-References should open a Split Frame
1650 view with cDNA/Protein</li>
1651 <li>Detect when nucleotide sequences and protein
1652 sequences are placed in the same alignment</li>
1653 <li>Split cDNA/Protein views are saved in Jalview
1658 <li>Use REST API to talk to Chimera</li>
1659 <li>Selected regions in Chimera are highlighted in linked
1660 Jalview windows</li>
1662 <li>VARNA RNA viewer updated to v3.93</li>
1663 <li>VARNA views are saved in Jalview Projects</li>
1664 <li>Pseudoknots displayed as Jalview RNA annotation can
1665 be shown in VARNA</li>
1667 <li>Make groups for selection uses marked columns as well
1668 as the active selected region</li>
1670 <li>Calculate UPGMA and NJ trees using sequence feature
1672 <li>New Export options
1674 <li>New Export Settings dialog to control hidden
1675 region export in flat file generation</li>
1677 <li>Export alignment views for display with the <a
1678 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1680 <li>Export scrollable SVG in HTML page</li>
1681 <li>Optional embedding of BioJSON data when exporting
1682 alignment figures to HTML</li>
1684 <li>3D structure retrieval and display
1686 <li>Free text and structured queries with the PDBe
1688 <li>PDBe Search API based discovery and selection of
1689 PDB structures for a sequence set</li>
1693 <li>JPred4 employed for protein secondary structure
1695 <li>Hide Insertions menu option to hide unaligned columns
1696 for one or a group of sequences</li>
1697 <li>Automatically hide insertions in alignments imported
1698 from the JPred4 web server</li>
1699 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1700 system on OSX<br />LGPL libraries courtesy of <a
1701 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1703 <li>changed 'View nucleotide structure' submenu to 'View
1704 VARNA 2D Structure'</li>
1705 <li>change "View protein structure" menu option to "3D
1708 </ul> <em>Applet</em>
1710 <li>New layout for applet example pages</li>
1711 <li>New parameters to enable SplitFrame view
1712 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1713 <li>New example demonstrating linked viewing of cDNA and
1714 Protein alignments</li>
1715 </ul> <em>Development and deployment</em>
1717 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1718 <li>Include installation type and git revision in build
1719 properties and console log output</li>
1720 <li>Jalview Github organisation, and new github site for
1721 storing BioJsMSA Templates</li>
1722 <li>Jalview's unit tests now managed with TestNG</li>
1725 <!-- <em>General</em>
1727 </ul> --> <!-- issues resolved --> <em>Application</em>
1729 <li>Escape should close any open find dialogs</li>
1730 <li>Typo in select-by-features status report</li>
1731 <li>Consensus RNA secondary secondary structure
1732 predictions are not highlighted in amber</li>
1733 <li>Missing gap character in v2.7 example file means
1734 alignment appears unaligned when pad-gaps is not enabled</li>
1735 <li>First switch to RNA Helices colouring doesn't colour
1736 associated structure views</li>
1737 <li>ID width preference option is greyed out when auto
1738 width checkbox not enabled</li>
1739 <li>Stopped a warning dialog from being shown when
1740 creating user defined colours</li>
1741 <li>'View Mapping' in structure viewer shows sequence
1742 mappings for just that viewer's sequences</li>
1743 <li>Workaround for superposing PDB files containing
1744 multiple models in Chimera</li>
1745 <li>Report sequence position in status bar when hovering
1746 over Jmol structure</li>
1747 <li>Cannot output gaps as '.' symbols with Selection ->
1748 output to text box</li>
1749 <li>Flat file exports of alignments with hidden columns
1750 have incorrect sequence start/end</li>
1751 <li>'Aligning' a second chain to a Chimera structure from
1753 <li>Colour schemes applied to structure viewers don't
1754 work for nucleotide</li>
1755 <li>Loading/cut'n'pasting an empty or invalid file leads
1756 to a grey/invisible alignment window</li>
1757 <li>Exported Jpred annotation from a sequence region
1758 imports to different position</li>
1759 <li>Space at beginning of sequence feature tooltips shown
1760 on some platforms</li>
1761 <li>Chimera viewer 'View | Show Chain' menu is not
1763 <li>'New View' fails with a Null Pointer Exception in
1764 console if Chimera has been opened</li>
1765 <li>Mouseover to Chimera not working</li>
1766 <li>Miscellaneous ENA XML feature qualifiers not
1768 <li>NPE in annotation renderer after 'Extract Scores'</li>
1769 <li>If two structures in one Chimera window, mouseover of
1770 either sequence shows on first structure</li>
1771 <li>'Show annotations' options should not make
1772 non-positional annotations visible</li>
1773 <li>Subsequence secondary structure annotation not shown
1774 in right place after 'view flanking regions'</li>
1775 <li>File Save As type unset when current file format is
1777 <li>Save as '.jar' option removed for saving Jalview
1779 <li>Colour by Sequence colouring in Chimera more
1781 <li>Cannot 'add reference annotation' for a sequence in
1782 several views on same alignment</li>
1783 <li>Cannot show linked products for EMBL / ENA records</li>
1784 <li>Jalview's tooltip wraps long texts containing no
1786 </ul> <em>Applet</em>
1788 <li>Jmol to JalviewLite mouseover/link not working</li>
1789 <li>JalviewLite can't import sequences with ID
1790 descriptions containing angle brackets</li>
1791 </ul> <em>General</em>
1793 <li>Cannot export and reimport RNA secondary structure
1794 via jalview annotation file</li>
1795 <li>Random helix colour palette for colour by annotation
1796 with RNA secondary structure</li>
1797 <li>Mouseover to cDNA from STOP residue in protein
1798 translation doesn't work.</li>
1799 <li>hints when using the select by annotation dialog box</li>
1800 <li>Jmol alignment incorrect if PDB file has alternate CA
1802 <li>FontChooser message dialog appears to hang after
1803 choosing 1pt font</li>
1804 <li>Peptide secondary structure incorrectly imported from
1805 annotation file when annotation display text includes 'e' or
1807 <li>Cannot set colour of new feature type whilst creating
1809 <li>cDNA translation alignment should not be sequence
1810 order dependent</li>
1811 <li>'Show unconserved' doesn't work for lower case
1813 <li>Nucleotide ambiguity codes involving R not recognised</li>
1814 </ul> <em>Deployment and Documentation</em>
1816 <li>Applet example pages appear different to the rest of
1817 www.jalview.org</li>
1818 </ul> <em>Application Known issues</em>
1820 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1821 <li>Misleading message appears after trying to delete
1823 <li>Jalview icon not shown in dock after InstallAnywhere
1824 version launches</li>
1825 <li>Fetching EMBL reference for an RNA sequence results
1826 fails with a sequence mismatch</li>
1827 <li>Corrupted or unreadable alignment display when
1828 scrolling alignment to right</li>
1829 <li>ArrayIndexOutOfBoundsException thrown when remove
1830 empty columns called on alignment with ragged gapped ends</li>
1831 <li>auto calculated alignment annotation rows do not get
1832 placed above or below non-autocalculated rows</li>
1833 <li>Jalview dekstop becomes sluggish at full screen in
1834 ultra-high resolution</li>
1835 <li>Cannot disable consensus calculation independently of
1836 quality and conservation</li>
1837 <li>Mouseover highlighting between cDNA and protein can
1838 become sluggish with more than one splitframe shown</li>
1839 </ul> <em>Applet Known Issues</em>
1841 <li>Core PDB parsing code requires Jmol</li>
1842 <li>Sequence canvas panel goes white when alignment
1843 window is being resized</li>
1849 <td><div align="center">
1850 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1852 <td><em>General</em>
1854 <li>Updated Java code signing certificate donated by
1856 <li>Features and annotation preserved when performing
1857 pairwise alignment</li>
1858 <li>RNA pseudoknot annotation can be
1859 imported/exported/displayed</li>
1860 <li>'colour by annotation' can colour by RNA and
1861 protein secondary structure</li>
1862 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1863 post-hoc with 2.9 release</em>)
1866 </ul> <em>Application</em>
1868 <li>Extract and display secondary structure for sequences
1869 with 3D structures</li>
1870 <li>Support for parsing RNAML</li>
1871 <li>Annotations menu for layout
1873 <li>sort sequence annotation rows by alignment</li>
1874 <li>place sequence annotation above/below alignment
1877 <li>Output in Stockholm format</li>
1878 <li>Internationalisation: improved Spanish (es)
1880 <li>Structure viewer preferences tab</li>
1881 <li>Disorder and Secondary Structure annotation tracks
1882 shared between alignments</li>
1883 <li>UCSF Chimera launch and linked highlighting from
1885 <li>Show/hide all sequence associated annotation rows for
1886 all or current selection</li>
1887 <li>disorder and secondary structure predictions
1888 available as dataset annotation</li>
1889 <li>Per-sequence rna helices colouring</li>
1892 <li>Sequence database accessions imported when fetching
1893 alignments from Rfam</li>
1894 <li>update VARNA version to 3.91</li>
1896 <li>New groovy scripts for exporting aligned positions,
1897 conservation values, and calculating sum of pairs scores.</li>
1898 <li>Command line argument to set default JABAWS server</li>
1899 <li>include installation type in build properties and
1900 console log output</li>
1901 <li>Updated Jalview project format to preserve dataset
1905 <!-- issues resolved --> <em>Application</em>
1907 <li>Distinguish alignment and sequence associated RNA
1908 structure in structure->view->VARNA</li>
1909 <li>Raise dialog box if user deletes all sequences in an
1911 <li>Pressing F1 results in documentation opening twice</li>
1912 <li>Sequence feature tooltip is wrapped</li>
1913 <li>Double click on sequence associated annotation
1914 selects only first column</li>
1915 <li>Redundancy removal doesn't result in unlinked
1916 leaves shown in tree</li>
1917 <li>Undos after several redundancy removals don't undo
1919 <li>Hide sequence doesn't hide associated annotation</li>
1920 <li>User defined colours dialog box too big to fit on
1921 screen and buttons not visible</li>
1922 <li>author list isn't updated if already written to
1923 Jalview properties</li>
1924 <li>Popup menu won't open after retrieving sequence
1926 <li>File open window for associate PDB doesn't open</li>
1927 <li>Left-then-right click on a sequence id opens a
1928 browser search window</li>
1929 <li>Cannot open sequence feature shading/sort popup menu
1930 in feature settings dialog</li>
1931 <li>better tooltip placement for some areas of Jalview
1933 <li>Allow addition of JABAWS Server which doesn't
1934 pass validation</li>
1935 <li>Web services parameters dialog box is too large to
1937 <li>Muscle nucleotide alignment preset obscured by
1939 <li>JABAWS preset submenus don't contain newly
1940 defined user preset</li>
1941 <li>MSA web services warns user if they were launched
1942 with invalid input</li>
1943 <li>Jalview cannot contact DAS Registy when running on
1946 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1947 'Superpose with' submenu not shown when new view
1951 </ul> <!-- <em>Applet</em>
1953 </ul> <em>General</em>
1955 </ul>--> <em>Deployment and Documentation</em>
1957 <li>2G and 1G options in launchApp have no effect on
1958 memory allocation</li>
1959 <li>launchApp service doesn't automatically open
1960 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1962 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1963 InstallAnywhere reports cannot find valid JVM when Java
1964 1.7_055 is available
1966 </ul> <em>Application Known issues</em>
1969 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1970 corrupted or unreadable alignment display when scrolling
1974 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1975 retrieval fails but progress bar continues for DAS retrieval
1976 with large number of ID
1979 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1980 flatfile output of visible region has incorrect sequence
1984 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1985 rna structure consensus doesn't update when secondary
1986 structure tracks are rearranged
1989 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1990 invalid rna structure positional highlighting does not
1991 highlight position of invalid base pairs
1994 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1995 out of memory errors are not raised when saving Jalview
1996 project from alignment window file menu
1999 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2000 Switching to RNA Helices colouring doesn't propagate to
2004 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2005 colour by RNA Helices not enabled when user created
2006 annotation added to alignment
2009 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2010 Jalview icon not shown on dock in Mountain Lion/Webstart
2012 </ul> <em>Applet Known Issues</em>
2015 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2016 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2019 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2020 Jalview and Jmol example not compatible with IE9
2023 <li>Sort by annotation score doesn't reverse order
2029 <td><div align="center">
2030 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2033 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2036 <li>Internationalisation of user interface (usually
2037 called i18n support) and translation for Spanish locale</li>
2038 <li>Define/Undefine group on current selection with
2039 Ctrl-G/Shift Ctrl-G</li>
2040 <li>Improved group creation/removal options in
2041 alignment/sequence Popup menu</li>
2042 <li>Sensible precision for symbol distribution
2043 percentages shown in logo tooltip.</li>
2044 <li>Annotation panel height set according to amount of
2045 annotation when alignment first opened</li>
2046 </ul> <em>Application</em>
2048 <li>Interactive consensus RNA secondary structure
2049 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2050 <li>Select columns containing particular features from
2051 Feature Settings dialog</li>
2052 <li>View all 'representative' PDB structures for selected
2054 <li>Update Jalview project format:
2056 <li>New file extension for Jalview projects '.jvp'</li>
2057 <li>Preserve sequence and annotation dataset (to
2058 store secondary structure annotation,etc)</li>
2059 <li>Per group and alignment annotation and RNA helix
2063 <li>New similarity measures for PCA and Tree calculation
2065 <li>Experimental support for retrieval and viewing of
2066 flanking regions for an alignment</li>
2070 <!-- issues resolved --> <em>Application</em>
2072 <li>logo keeps spinning and status remains at queued or
2073 running after job is cancelled</li>
2074 <li>cannot export features from alignments imported from
2075 Jalview/VAMSAS projects</li>
2076 <li>Buggy slider for web service parameters that take
2078 <li>Newly created RNA secondary structure line doesn't
2079 have 'display all symbols' flag set</li>
2080 <li>T-COFFEE alignment score shading scheme and other
2081 annotation shading not saved in Jalview project</li>
2082 <li>Local file cannot be loaded in freshly downloaded
2084 <li>Jalview icon not shown on dock in Mountain
2086 <li>Load file from desktop file browser fails</li>
2087 <li>Occasional NPE thrown when calculating large trees</li>
2088 <li>Cannot reorder or slide sequences after dragging an
2089 alignment onto desktop</li>
2090 <li>Colour by annotation dialog throws NPE after using
2091 'extract scores' function</li>
2092 <li>Loading/cut'n'pasting an empty file leads to a grey
2093 alignment window</li>
2094 <li>Disorder thresholds rendered incorrectly after
2095 performing IUPred disorder prediction</li>
2096 <li>Multiple group annotated consensus rows shown when
2097 changing 'normalise logo' display setting</li>
2098 <li>Find shows blank dialog after 'finished searching' if
2099 nothing matches query</li>
2100 <li>Null Pointer Exceptions raised when sorting by
2101 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2103 <li>Errors in Jmol console when structures in alignment
2104 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2106 <li>Not all working JABAWS services are shown in
2108 <li>JAVAWS version of Jalview fails to launch with
2109 'invalid literal/length code'</li>
2110 <li>Annotation/RNA Helix colourschemes cannot be applied
2111 to alignment with groups (actually fixed in 2.8.0b1)</li>
2112 <li>RNA Helices and T-Coffee Scores available as default
2115 </ul> <em>Applet</em>
2117 <li>Remove group option is shown even when selection is
2119 <li>Apply to all groups ticked but colourscheme changes
2120 don't affect groups</li>
2121 <li>Documented RNA Helices and T-Coffee Scores as valid
2122 colourscheme name</li>
2123 <li>Annotation labels drawn on sequence IDs when
2124 Annotation panel is not displayed</li>
2125 <li>Increased font size for dropdown menus on OSX and
2126 embedded windows</li>
2127 </ul> <em>Other</em>
2129 <li>Consensus sequence for alignments/groups with a
2130 single sequence were not calculated</li>
2131 <li>annotation files that contain only groups imported as
2132 annotation and junk sequences</li>
2133 <li>Fasta files with sequences containing '*' incorrectly
2134 recognised as PFAM or BLC</li>
2135 <li>conservation/PID slider apply all groups option
2136 doesn't affect background (2.8.0b1)
2138 <li>redundancy highlighting is erratic at 0% and 100%</li>
2139 <li>Remove gapped columns fails for sequences with ragged
2141 <li>AMSA annotation row with leading spaces is not
2142 registered correctly on import</li>
2143 <li>Jalview crashes when selecting PCA analysis for
2144 certain alignments</li>
2145 <li>Opening the colour by annotation dialog for an
2146 existing annotation based 'use original colours'
2147 colourscheme loses original colours setting</li>
2152 <td><div align="center">
2153 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2154 <em>30/1/2014</em></strong>
2158 <li>Trusted certificates for JalviewLite applet and
2159 Jalview Desktop application<br />Certificate was donated by
2160 <a href="https://www.certum.eu">Certum</a> to the Jalview
2161 open source project).
2163 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2164 <li>Output in Stockholm format</li>
2165 <li>Allow import of data from gzipped files</li>
2166 <li>Export/import group and sequence associated line
2167 graph thresholds</li>
2168 <li>Nucleotide substitution matrix that supports RNA and
2169 ambiguity codes</li>
2170 <li>Allow disorder predictions to be made on the current
2171 selection (or visible selection) in the same way that JPred
2173 <li>Groovy scripting for headless Jalview operation</li>
2174 </ul> <em>Other improvements</em>
2176 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2177 <li>COMBINE statement uses current SEQUENCE_REF and
2178 GROUP_REF scope to group annotation rows</li>
2179 <li>Support '' style escaping of quotes in Newick
2181 <li>Group options for JABAWS service by command line name</li>
2182 <li>Empty tooltip shown for JABA service options with a
2183 link but no description</li>
2184 <li>Select primary source when selecting authority in
2185 database fetcher GUI</li>
2186 <li>Add .mfa to FASTA file extensions recognised by
2188 <li>Annotation label tooltip text wrap</li>
2193 <li>Slow scrolling when lots of annotation rows are
2195 <li>Lots of NPE (and slowness) after creating RNA
2196 secondary structure annotation line</li>
2197 <li>Sequence database accessions not imported when
2198 fetching alignments from Rfam</li>
2199 <li>Incorrect SHMR submission for sequences with
2201 <li>View all structures does not always superpose
2203 <li>Option widgets in service parameters not updated to
2204 reflect user or preset settings</li>
2205 <li>Null pointer exceptions for some services without
2206 presets or adjustable parameters</li>
2207 <li>Discover PDB IDs entry in structure menu doesn't
2208 discover PDB xRefs</li>
2209 <li>Exception encountered while trying to retrieve
2210 features with DAS</li>
2211 <li>Lowest value in annotation row isn't coloured
2212 when colour by annotation (per sequence) is coloured</li>
2213 <li>Keyboard mode P jumps to start of gapped region when
2214 residue follows a gap</li>
2215 <li>Jalview appears to hang importing an alignment with
2216 Wrap as default or after enabling Wrap</li>
2217 <li>'Right click to add annotations' message
2218 shown in wrap mode when no annotations present</li>
2219 <li>Disorder predictions fail with NPE if no automatic
2220 annotation already exists on alignment</li>
2221 <li>oninit javascript function should be called after
2222 initialisation completes</li>
2223 <li>Remove redundancy after disorder prediction corrupts
2224 alignment window display</li>
2225 <li>Example annotation file in documentation is invalid</li>
2226 <li>Grouped line graph annotation rows are not exported
2227 to annotation file</li>
2228 <li>Multi-harmony analysis cannot be run when only two
2230 <li>Cannot create multiple groups of line graphs with
2231 several 'combine' statements in annotation file</li>
2232 <li>Pressing return several times causes Number Format
2233 exceptions in keyboard mode</li>
2234 <li>Multi-harmony (SHMMR) method doesn't submit
2235 correct partitions for input data</li>
2236 <li>Translation from DNA to Amino Acids fails</li>
2237 <li>Jalview fail to load newick tree with quoted label</li>
2238 <li>--headless flag isn't understood</li>
2239 <li>ClassCastException when generating EPS in headless
2241 <li>Adjusting sequence-associated shading threshold only
2242 changes one row's threshold</li>
2243 <li>Preferences and Feature settings panel panel
2244 doesn't open</li>
2245 <li>hide consensus histogram also hides conservation and
2246 quality histograms</li>
2251 <td><div align="center">
2252 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2254 <td><em>Application</em>
2256 <li>Support for JABAWS 2.0 Services (AACon alignment
2257 conservation, protein disorder and Clustal Omega)</li>
2258 <li>JABAWS server status indicator in Web Services
2260 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2261 in Jalview alignment window</li>
2262 <li>Updated Jalview build and deploy framework for OSX
2263 mountain lion, windows 7, and 8</li>
2264 <li>Nucleotide substitution matrix for PCA that supports
2265 RNA and ambiguity codes</li>
2267 <li>Improved sequence database retrieval GUI</li>
2268 <li>Support fetching and database reference look up
2269 against multiple DAS sources (Fetch all from in 'fetch db
2271 <li>Jalview project improvements
2273 <li>Store and retrieve the 'belowAlignment'
2274 flag for annotation</li>
2275 <li>calcId attribute to group annotation rows on the
2277 <li>Store AACon calculation settings for a view in
2278 Jalview project</li>
2282 <li>horizontal scrolling gesture support</li>
2283 <li>Visual progress indicator when PCA calculation is
2285 <li>Simpler JABA web services menus</li>
2286 <li>visual indication that web service results are still
2287 being retrieved from server</li>
2288 <li>Serialise the dialogs that are shown when Jalview
2289 starts up for first time</li>
2290 <li>Jalview user agent string for interacting with HTTP
2292 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2294 <li>Examples directory and Groovy library included in
2295 InstallAnywhere distribution</li>
2296 </ul> <em>Applet</em>
2298 <li>RNA alignment and secondary structure annotation
2299 visualization applet example</li>
2300 </ul> <em>General</em>
2302 <li>Normalise option for consensus sequence logo</li>
2303 <li>Reset button in PCA window to return dimensions to
2305 <li>Allow seqspace or Jalview variant of alignment PCA
2307 <li>PCA with either nucleic acid and protein substitution
2309 <li>Allow windows containing HTML reports to be exported
2311 <li>Interactive display and editing of RNA secondary
2312 structure contacts</li>
2313 <li>RNA Helix Alignment Colouring</li>
2314 <li>RNA base pair logo consensus</li>
2315 <li>Parse sequence associated secondary structure
2316 information in Stockholm files</li>
2317 <li>HTML Export database accessions and annotation
2318 information presented in tooltip for sequences</li>
2319 <li>Import secondary structure from LOCARNA clustalw
2320 style RNA alignment files</li>
2321 <li>import and visualise T-COFFEE quality scores for an
2323 <li>'colour by annotation' per sequence option to
2324 shade each sequence according to its associated alignment
2326 <li>New Jalview Logo</li>
2327 </ul> <em>Documentation and Development</em>
2329 <li>documentation for score matrices used in Jalview</li>
2330 <li>New Website!</li>
2332 <td><em>Application</em>
2334 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2335 wsdbfetch REST service</li>
2336 <li>Stop windows being moved outside desktop on OSX</li>
2337 <li>Filetype associations not installed for webstart
2339 <li>Jalview does not always retrieve progress of a JABAWS
2340 job execution in full once it is complete</li>
2341 <li>revise SHMR RSBS definition to ensure alignment is
2342 uploaded via ali_file parameter</li>
2343 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2344 <li>View all structures superposed fails with exception</li>
2345 <li>Jnet job queues forever if a very short sequence is
2346 submitted for prediction</li>
2347 <li>Cut and paste menu not opened when mouse clicked on
2349 <li>Putting fractional value into integer text box in
2350 alignment parameter dialog causes Jalview to hang</li>
2351 <li>Structure view highlighting doesn't work on
2353 <li>View all structures fails with exception shown in
2355 <li>Characters in filename associated with PDBEntry not
2356 escaped in a platform independent way</li>
2357 <li>Jalview desktop fails to launch with exception when
2359 <li>Tree calculation reports 'you must have 2 or more
2360 sequences selected' when selection is empty</li>
2361 <li>Jalview desktop fails to launch with jar signature
2362 failure when java web start temporary file caching is
2364 <li>DAS Sequence retrieval with range qualification
2365 results in sequence xref which includes range qualification</li>
2366 <li>Errors during processing of command line arguments
2367 cause progress bar (JAL-898) to be removed</li>
2368 <li>Replace comma for semi-colon option not disabled for
2369 DAS sources in sequence fetcher</li>
2370 <li>Cannot close news reader when JABAWS server warning
2371 dialog is shown</li>
2372 <li>Option widgets not updated to reflect user settings</li>
2373 <li>Edited sequence not submitted to web service</li>
2374 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2375 <li>InstallAnywhere installer doesn't unpack and run
2376 on OSX Mountain Lion</li>
2377 <li>Annotation panel not given a scroll bar when
2378 sequences with alignment annotation are pasted into the
2380 <li>Sequence associated annotation rows not associated
2381 when loaded from Jalview project</li>
2382 <li>Browser launch fails with NPE on java 1.7</li>
2383 <li>JABAWS alignment marked as finished when job was
2384 cancelled or job failed due to invalid input</li>
2385 <li>NPE with v2.7 example when clicking on Tree
2386 associated with all views</li>
2387 <li>Exceptions when copy/paste sequences with grouped
2388 annotation rows to new window</li>
2389 </ul> <em>Applet</em>
2391 <li>Sequence features are momentarily displayed before
2392 they are hidden using hidefeaturegroups applet parameter</li>
2393 <li>loading features via javascript API automatically
2394 enables feature display</li>
2395 <li>scrollToColumnIn javascript API method doesn't
2397 </ul> <em>General</em>
2399 <li>Redundancy removal fails for rna alignment</li>
2400 <li>PCA calculation fails when sequence has been selected
2401 and then deselected</li>
2402 <li>PCA window shows grey box when first opened on OSX</li>
2403 <li>Letters coloured pink in sequence logo when alignment
2404 coloured with clustalx</li>
2405 <li>Choosing fonts without letter symbols defined causes
2406 exceptions and redraw errors</li>
2407 <li>Initial PCA plot view is not same as manually
2408 reconfigured view</li>
2409 <li>Grouped annotation graph label has incorrect line
2411 <li>Grouped annotation graph label display is corrupted
2412 for lots of labels</li>
2417 <div align="center">
2418 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2421 <td><em>Application</em>
2423 <li>Jalview Desktop News Reader</li>
2424 <li>Tweaked default layout of web services menu</li>
2425 <li>View/alignment association menu to enable user to
2426 easily specify which alignment a multi-structure view takes
2427 its colours/correspondences from</li>
2428 <li>Allow properties file location to be specified as URL</li>
2429 <li>Extend Jalview project to preserve associations
2430 between many alignment views and a single Jmol display</li>
2431 <li>Store annotation row height in Jalview project file</li>
2432 <li>Annotation row column label formatting attributes
2433 stored in project file</li>
2434 <li>Annotation row order for auto-calculated annotation
2435 rows preserved in Jalview project file</li>
2436 <li>Visual progress indication when Jalview state is
2437 saved using Desktop window menu</li>
2438 <li>Visual indication that command line arguments are
2439 still being processed</li>
2440 <li>Groovy script execution from URL</li>
2441 <li>Colour by annotation default min and max colours in
2443 <li>Automatically associate PDB files dragged onto an
2444 alignment with sequences that have high similarity and
2446 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2447 <li>'view structures' option to open many
2448 structures in same window</li>
2449 <li>Sort associated views menu option for tree panel</li>
2450 <li>Group all JABA and non-JABA services for a particular
2451 analysis function in its own submenu</li>
2452 </ul> <em>Applet</em>
2454 <li>Userdefined and autogenerated annotation rows for
2456 <li>Adjustment of alignment annotation pane height</li>
2457 <li>Annotation scrollbar for annotation panel</li>
2458 <li>Drag to reorder annotation rows in annotation panel</li>
2459 <li>'automaticScrolling' parameter</li>
2460 <li>Allow sequences with partial ID string matches to be
2461 annotated from GFF/Jalview features files</li>
2462 <li>Sequence logo annotation row in applet</li>
2463 <li>Absolute paths relative to host server in applet
2464 parameters are treated as such</li>
2465 <li>New in the JalviewLite javascript API:
2467 <li>JalviewLite.js javascript library</li>
2468 <li>Javascript callbacks for
2470 <li>Applet initialisation</li>
2471 <li>Sequence/alignment mouse-overs and selections</li>
2474 <li>scrollTo row and column alignment scrolling
2476 <li>Select sequence/alignment regions from javascript</li>
2477 <li>javascript structure viewer harness to pass
2478 messages between Jmol and Jalview when running as
2479 distinct applets</li>
2480 <li>sortBy method</li>
2481 <li>Set of applet and application examples shipped
2482 with documentation</li>
2483 <li>New example to demonstrate JalviewLite and Jmol
2484 javascript message exchange</li>
2486 </ul> <em>General</em>
2488 <li>Enable Jmol displays to be associated with multiple
2489 multiple alignments</li>
2490 <li>Option to automatically sort alignment with new tree</li>
2491 <li>User configurable link to enable redirects to a
2492 www.Jalview.org mirror</li>
2493 <li>Jmol colours option for Jmol displays</li>
2494 <li>Configurable newline string when writing alignment
2495 and other flat files</li>
2496 <li>Allow alignment annotation description lines to
2497 contain html tags</li>
2498 </ul> <em>Documentation and Development</em>
2500 <li>Add groovy test harness for bulk load testing to
2502 <li>Groovy script to load and align a set of sequences
2503 using a web service before displaying the result in the
2504 Jalview desktop</li>
2505 <li>Restructured javascript and applet api documentation</li>
2506 <li>Ant target to publish example html files with applet
2508 <li>Netbeans project for building Jalview from source</li>
2509 <li>ant task to create online javadoc for Jalview source</li>
2511 <td><em>Application</em>
2513 <li>User defined colourscheme throws exception when
2514 current built in colourscheme is saved as new scheme</li>
2515 <li>AlignFrame->Save in application pops up save
2516 dialog for valid filename/format</li>
2517 <li>Cannot view associated structure for UniProt sequence</li>
2518 <li>PDB file association breaks for UniProt sequence
2520 <li>Associate PDB from file dialog does not tell you
2521 which sequence is to be associated with the file</li>
2522 <li>Find All raises null pointer exception when query
2523 only matches sequence IDs</li>
2524 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2525 <li>Jalview project with Jmol views created with Jalview
2526 2.4 cannot be loaded</li>
2527 <li>Filetype associations not installed for webstart
2529 <li>Two or more chains in a single PDB file associated
2530 with sequences in different alignments do not get coloured
2531 by their associated sequence</li>
2532 <li>Visibility status of autocalculated annotation row
2533 not preserved when project is loaded</li>
2534 <li>Annotation row height and visibility attributes not
2535 stored in Jalview project</li>
2536 <li>Tree bootstraps are not preserved when saved as a
2537 Jalview project</li>
2538 <li>Envision2 workflow tooltips are corrupted</li>
2539 <li>Enabling show group conservation also enables colour
2540 by conservation</li>
2541 <li>Duplicate group associated conservation or consensus
2542 created on new view</li>
2543 <li>Annotation scrollbar not displayed after 'show
2544 all hidden annotation rows' option selected</li>
2545 <li>Alignment quality not updated after alignment
2546 annotation row is hidden then shown</li>
2547 <li>Preserve colouring of structures coloured by
2548 sequences in pre Jalview 2.7 projects</li>
2549 <li>Web service job parameter dialog is not laid out
2551 <li>Web services menu not refreshed after 'reset
2552 services' button is pressed in preferences</li>
2553 <li>Annotation off by one in Jalview v2_3 example project</li>
2554 <li>Structures imported from file and saved in project
2555 get name like jalview_pdb1234.txt when reloaded</li>
2556 <li>Jalview does not always retrieve progress of a JABAWS
2557 job execution in full once it is complete</li>
2558 </ul> <em>Applet</em>
2560 <li>Alignment height set incorrectly when lots of
2561 annotation rows are displayed</li>
2562 <li>Relative URLs in feature HTML text not resolved to
2564 <li>View follows highlighting does not work for positions
2566 <li><= shown as = in tooltip</li>
2567 <li>Export features raises exception when no features
2569 <li>Separator string used for serialising lists of IDs
2570 for javascript api is modified when separator string
2571 provided as parameter</li>
2572 <li>Null pointer exception when selecting tree leaves for
2573 alignment with no existing selection</li>
2574 <li>Relative URLs for datasources assumed to be relative
2575 to applet's codebase</li>
2576 <li>Status bar not updated after finished searching and
2577 search wraps around to first result</li>
2578 <li>StructureSelectionManager instance shared between
2579 several Jalview applets causes race conditions and memory
2581 <li>Hover tooltip and mouseover of position on structure
2582 not sent from Jmol in applet</li>
2583 <li>Certain sequences of javascript method calls to
2584 applet API fatally hang browser</li>
2585 </ul> <em>General</em>
2587 <li>View follows structure mouseover scrolls beyond
2588 position with wrapped view and hidden regions</li>
2589 <li>Find sequence position moves to wrong residue
2590 with/without hidden columns</li>
2591 <li>Sequence length given in alignment properties window
2593 <li>InvalidNumberFormat exceptions thrown when trying to
2594 import PDB like structure files</li>
2595 <li>Positional search results are only highlighted
2596 between user-supplied sequence start/end bounds</li>
2597 <li>End attribute of sequence is not validated</li>
2598 <li>Find dialog only finds first sequence containing a
2599 given sequence position</li>
2600 <li>Sequence numbering not preserved in MSF alignment
2602 <li>Jalview PDB file reader does not extract sequence
2603 from nucleotide chains correctly</li>
2604 <li>Structure colours not updated when tree partition
2605 changed in alignment</li>
2606 <li>Sequence associated secondary structure not correctly
2607 parsed in interleaved stockholm</li>
2608 <li>Colour by annotation dialog does not restore current
2610 <li>Hiding (nearly) all sequences doesn't work
2612 <li>Sequences containing lowercase letters are not
2613 properly associated with their pdb files</li>
2614 </ul> <em>Documentation and Development</em>
2616 <li>schemas/JalviewWsParamSet.xsd corrupted by
2617 ApplyCopyright tool</li>
2622 <div align="center">
2623 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2626 <td><em>Application</em>
2628 <li>New warning dialog when the Jalview Desktop cannot
2629 contact web services</li>
2630 <li>JABA service parameters for a preset are shown in
2631 service job window</li>
2632 <li>JABA Service menu entries reworded</li>
2636 <li>Modeller PIR IO broken - cannot correctly import a
2637 pir file emitted by Jalview</li>
2638 <li>Existing feature settings transferred to new
2639 alignment view created from cut'n'paste</li>
2640 <li>Improved test for mixed amino/nucleotide chains when
2641 parsing PDB files</li>
2642 <li>Consensus and conservation annotation rows
2643 occasionally become blank for all new windows</li>
2644 <li>Exception raised when right clicking above sequences
2645 in wrapped view mode</li>
2646 </ul> <em>Application</em>
2648 <li>multiple multiply aligned structure views cause cpu
2649 usage to hit 100% and computer to hang</li>
2650 <li>Web Service parameter layout breaks for long user
2651 parameter names</li>
2652 <li>Jaba service discovery hangs desktop if Jaba server
2659 <div align="center">
2660 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2663 <td><em>Application</em>
2665 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2666 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2669 <li>Web Services preference tab</li>
2670 <li>Analysis parameters dialog box and user defined
2672 <li>Improved speed and layout of Envision2 service menu</li>
2673 <li>Superpose structures using associated sequence
2675 <li>Export coordinates and projection as CSV from PCA
2677 </ul> <em>Applet</em>
2679 <li>enable javascript: execution by the applet via the
2680 link out mechanism</li>
2681 </ul> <em>Other</em>
2683 <li>Updated the Jmol Jalview interface to work with Jmol
2685 <li>The Jalview Desktop and JalviewLite applet now
2686 require Java 1.5</li>
2687 <li>Allow Jalview feature colour specification for GFF
2688 sequence annotation files</li>
2689 <li>New 'colour by label' keword in Jalview feature file
2690 type colour specification</li>
2691 <li>New Jalview Desktop Groovy API method that allows a
2692 script to check if it being run in an interactive session or
2693 in a batch operation from the Jalview command line</li>
2697 <li>clustalx colourscheme colours Ds preferentially when
2698 both D+E are present in over 50% of the column</li>
2699 </ul> <em>Application</em>
2701 <li>typo in AlignmentFrame->View->Hide->all but
2702 selected Regions menu item</li>
2703 <li>sequence fetcher replaces ',' for ';' when the ',' is
2704 part of a valid accession ID</li>
2705 <li>fatal OOM if object retrieved by sequence fetcher
2706 runs out of memory</li>
2707 <li>unhandled Out of Memory Error when viewing pca
2708 analysis results</li>
2709 <li>InstallAnywhere builds fail to launch on OS X java
2710 10.5 update 4 (due to apple Java 1.6 update)</li>
2711 <li>Installanywhere Jalview silently fails to launch</li>
2712 </ul> <em>Applet</em>
2714 <li>Jalview.getFeatureGroups() raises an
2715 ArrayIndexOutOfBoundsException if no feature groups are
2722 <div align="center">
2723 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2729 <li>Alignment prettyprinter doesn't cope with long
2731 <li>clustalx colourscheme colours Ds preferentially when
2732 both D+E are present in over 50% of the column</li>
2733 <li>nucleic acid structures retrieved from PDB do not
2734 import correctly</li>
2735 <li>More columns get selected than were clicked on when a
2736 number of columns are hidden</li>
2737 <li>annotation label popup menu not providing correct
2738 add/hide/show options when rows are hidden or none are
2740 <li>Stockholm format shown in list of readable formats,
2741 and parser copes better with alignments from RFAM.</li>
2742 <li>CSV output of consensus only includes the percentage
2743 of all symbols if sequence logo display is enabled</li>
2745 </ul> <em>Applet</em>
2747 <li>annotation panel disappears when annotation is
2749 </ul> <em>Application</em>
2751 <li>Alignment view not redrawn properly when new
2752 alignment opened where annotation panel is visible but no
2753 annotations are present on alignment</li>
2754 <li>pasted region containing hidden columns is
2755 incorrectly displayed in new alignment window</li>
2756 <li>Jalview slow to complete operations when stdout is
2757 flooded (fix is to close the Jalview console)</li>
2758 <li>typo in AlignmentFrame->View->Hide->all but
2759 selected Rregions menu item.</li>
2760 <li>inconsistent group submenu and Format submenu entry
2761 'Un' or 'Non'conserved</li>
2762 <li>Sequence feature settings are being shared by
2763 multiple distinct alignments</li>
2764 <li>group annotation not recreated when tree partition is
2766 <li>double click on group annotation to select sequences
2767 does not propagate to associated trees</li>
2768 <li>Mac OSX specific issues:
2770 <li>exception raised when mouse clicked on desktop
2771 window background</li>
2772 <li>Desktop menu placed on menu bar and application
2773 name set correctly</li>
2774 <li>sequence feature settings not wide enough for the
2775 save feature colourscheme button</li>
2784 <div align="center">
2785 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2788 <td><em>New Capabilities</em>
2790 <li>URL links generated from description line for
2791 regular-expression based URL links (applet and application)
2793 <li>Non-positional feature URL links are shown in link
2795 <li>Linked viewing of nucleic acid sequences and
2797 <li>Automatic Scrolling option in View menu to display
2798 the currently highlighted region of an alignment.</li>
2799 <li>Order an alignment by sequence length, or using the
2800 average score or total feature count for each sequence.</li>
2801 <li>Shading features by score or associated description</li>
2802 <li>Subdivide alignment and groups based on identity of
2803 selected subsequence (Make Groups from Selection).</li>
2804 <li>New hide/show options including Shift+Control+H to
2805 hide everything but the currently selected region.</li>
2806 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2807 </ul> <em>Application</em>
2809 <li>Fetch DB References capabilities and UI expanded to
2810 support retrieval from DAS sequence sources</li>
2811 <li>Local DAS Sequence sources can be added via the
2812 command line or via the Add local source dialog box.</li>
2813 <li>DAS Dbref and DbxRef feature types are parsed as
2814 database references and protein_name is parsed as
2815 description line (BioSapiens terms).</li>
2816 <li>Enable or disable non-positional feature and database
2817 references in sequence ID tooltip from View menu in
2819 <!-- <li>New hidden columns and rows and representatives capabilities
2820 in annotations file (in progress - not yet fully implemented)</li> -->
2821 <li>Group-associated consensus, sequence logos and
2822 conservation plots</li>
2823 <li>Symbol distributions for each column can be exported
2824 and visualized as sequence logos</li>
2825 <li>Optionally scale multi-character column labels to fit
2826 within each column of annotation row<!-- todo for applet -->
2828 <li>Optional automatic sort of associated alignment view
2829 when a new tree is opened.</li>
2830 <li>Jalview Java Console</li>
2831 <li>Better placement of desktop window when moving
2832 between different screens.</li>
2833 <li>New preference items for sequence ID tooltip and
2834 consensus annotation</li>
2835 <li>Client to submit sequences and IDs to Envision2
2837 <li><em>Vamsas Capabilities</em>
2839 <li>Improved VAMSAS synchronization (Jalview archive
2840 used to preserve views, structures, and tree display
2842 <li>Import of vamsas documents from disk or URL via
2844 <li>Sharing of selected regions between views and
2845 with other VAMSAS applications (Experimental feature!)</li>
2846 <li>Updated API to VAMSAS version 0.2</li>
2848 </ul> <em>Applet</em>
2850 <li>Middle button resizes annotation row height</li>
2853 <li>sortByTree (true/false) - automatically sort the
2854 associated alignment view by the tree when a new tree is
2856 <li>showTreeBootstraps (true/false) - show or hide
2857 branch bootstraps (default is to show them if available)</li>
2858 <li>showTreeDistances (true/false) - show or hide
2859 branch lengths (default is to show them if available)</li>
2860 <li>showUnlinkedTreeNodes (true/false) - indicate if
2861 unassociated nodes should be highlighted in the tree
2863 <li>heightScale and widthScale (1.0 or more) -
2864 increase the height or width of a cell in the alignment
2865 grid relative to the current font size.</li>
2868 <li>Non-positional features displayed in sequence ID
2870 </ul> <em>Other</em>
2872 <li>Features format: graduated colour definitions and
2873 specification of feature scores</li>
2874 <li>Alignment Annotations format: new keywords for group
2875 associated annotation (GROUP_REF) and annotation row display
2876 properties (ROW_PROPERTIES)</li>
2877 <li>XML formats extended to support graduated feature
2878 colourschemes, group associated annotation, and profile
2879 visualization settings.</li></td>
2882 <li>Source field in GFF files parsed as feature source
2883 rather than description</li>
2884 <li>Non-positional features are now included in sequence
2885 feature and gff files (controlled via non-positional feature
2886 visibility in tooltip).</li>
2887 <li>URL links generated for all feature links (bugfix)</li>
2888 <li>Added URL embedding instructions to features file
2890 <li>Codons containing ambiguous nucleotides translated as
2891 'X' in peptide product</li>
2892 <li>Match case switch in find dialog box works for both
2893 sequence ID and sequence string and query strings do not
2894 have to be in upper case to match case-insensitively.</li>
2895 <li>AMSA files only contain first column of
2896 multi-character column annotation labels</li>
2897 <li>Jalview Annotation File generation/parsing consistent
2898 with documentation (e.g. Stockholm annotation can be
2899 exported and re-imported)</li>
2900 <li>PDB files without embedded PDB IDs given a friendly
2902 <li>Find incrementally searches ID string matches as well
2903 as subsequence matches, and correctly reports total number
2907 <li>Better handling of exceptions during sequence
2909 <li>Dasobert generated non-positional feature URL
2910 link text excludes the start_end suffix</li>
2911 <li>DAS feature and source retrieval buttons disabled
2912 when fetch or registry operations in progress.</li>
2913 <li>PDB files retrieved from URLs are cached properly</li>
2914 <li>Sequence description lines properly shared via
2916 <li>Sequence fetcher fetches multiple records for all
2918 <li>Ensured that command line das feature retrieval
2919 completes before alignment figures are generated.</li>
2920 <li>Reduced time taken when opening file browser for
2922 <li>isAligned check prior to calculating tree, PCA or
2923 submitting an MSA to JNet now excludes hidden sequences.</li>
2924 <li>User defined group colours properly recovered
2925 from Jalview projects.</li>
2934 <div align="center">
2935 <strong>2.4.0.b2</strong><br> 28/10/2009
2940 <li>Experimental support for google analytics usage
2942 <li>Jalview privacy settings (user preferences and docs).</li>
2947 <li>Race condition in applet preventing startup in
2949 <li>Exception when feature created from selection beyond
2950 length of sequence.</li>
2951 <li>Allow synthetic PDB files to be imported gracefully</li>
2952 <li>Sequence associated annotation rows associate with
2953 all sequences with a given id</li>
2954 <li>Find function matches case-insensitively for sequence
2955 ID string searches</li>
2956 <li>Non-standard characters do not cause pairwise
2957 alignment to fail with exception</li>
2958 </ul> <em>Application Issues</em>
2960 <li>Sequences are now validated against EMBL database</li>
2961 <li>Sequence fetcher fetches multiple records for all
2963 </ul> <em>InstallAnywhere Issues</em>
2965 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2966 issue with installAnywhere mechanism)</li>
2967 <li>Command line launching of JARs from InstallAnywhere
2968 version (java class versioning error fixed)</li>
2975 <div align="center">
2976 <strong>2.4</strong><br> 27/8/2008
2979 <td><em>User Interface</em>
2981 <li>Linked highlighting of codon and amino acid from
2982 translation and protein products</li>
2983 <li>Linked highlighting of structure associated with
2984 residue mapping to codon position</li>
2985 <li>Sequence Fetcher provides example accession numbers
2986 and 'clear' button</li>
2987 <li>MemoryMonitor added as an option under Desktop's
2989 <li>Extract score function to parse whitespace separated
2990 numeric data in description line</li>
2991 <li>Column labels in alignment annotation can be centred.</li>
2992 <li>Tooltip for sequence associated annotation give name
2994 </ul> <em>Web Services and URL fetching</em>
2996 <li>JPred3 web service</li>
2997 <li>Prototype sequence search client (no public services
2999 <li>Fetch either seed alignment or full alignment from
3001 <li>URL Links created for matching database cross
3002 references as well as sequence ID</li>
3003 <li>URL Links can be created using regular-expressions</li>
3004 </ul> <em>Sequence Database Connectivity</em>
3006 <li>Retrieval of cross-referenced sequences from other
3008 <li>Generalised database reference retrieval and
3009 validation to all fetchable databases</li>
3010 <li>Fetch sequences from DAS sources supporting the
3011 sequence command</li>
3012 </ul> <em>Import and Export</em>
3013 <li>export annotation rows as CSV for spreadsheet import</li>
3014 <li>Jalview projects record alignment dataset associations,
3015 EMBL products, and cDNA sequence mappings</li>
3016 <li>Sequence Group colour can be specified in Annotation
3018 <li>Ad-hoc colouring of group in Annotation File using RGB
3019 triplet as name of colourscheme</li>
3020 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3022 <li>treenode binding for VAMSAS tree exchange</li>
3023 <li>local editing and update of sequences in VAMSAS
3024 alignments (experimental)</li>
3025 <li>Create new or select existing session to join</li>
3026 <li>load and save of vamsas documents</li>
3027 </ul> <em>Application command line</em>
3029 <li>-tree parameter to open trees (introduced for passing
3031 <li>-fetchfrom command line argument to specify nicknames
3032 of DAS servers to query for alignment features</li>
3033 <li>-dasserver command line argument to add new servers
3034 that are also automatically queried for features</li>
3035 <li>-groovy command line argument executes a given groovy
3036 script after all input data has been loaded and parsed</li>
3037 </ul> <em>Applet-Application data exchange</em>
3039 <li>Trees passed as applet parameters can be passed to
3040 application (when using "View in full
3041 application")</li>
3042 </ul> <em>Applet Parameters</em>
3044 <li>feature group display control parameter</li>
3045 <li>debug parameter</li>
3046 <li>showbutton parameter</li>
3047 </ul> <em>Applet API methods</em>
3049 <li>newView public method</li>
3050 <li>Window (current view) specific get/set public methods</li>
3051 <li>Feature display control methods</li>
3052 <li>get list of currently selected sequences</li>
3053 </ul> <em>New Jalview distribution features</em>
3055 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3056 <li>RELEASE file gives build properties for the latest
3057 Jalview release.</li>
3058 <li>Java 1.1 Applet build made easier and donotobfuscate
3059 property controls execution of obfuscator</li>
3060 <li>Build target for generating source distribution</li>
3061 <li>Debug flag for javacc</li>
3062 <li>.jalview_properties file is documented (slightly) in
3063 jalview.bin.Cache</li>
3064 <li>Continuous Build Integration for stable and
3065 development version of Application, Applet and source
3070 <li>selected region output includes visible annotations
3071 (for certain formats)</li>
3072 <li>edit label/displaychar contains existing label/char
3074 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3075 <li>shorter peptide product names from EMBL records</li>
3076 <li>Newick string generator makes compact representations</li>
3077 <li>bootstrap values parsed correctly for tree files with
3079 <li>pathological filechooser bug avoided by not allowing
3080 filenames containing a ':'</li>
3081 <li>Fixed exception when parsing GFF files containing
3082 global sequence features</li>
3083 <li>Alignment datasets are finalized only when number of
3084 references from alignment sequences goes to zero</li>
3085 <li>Close of tree branch colour box without colour
3086 selection causes cascading exceptions</li>
3087 <li>occasional negative imgwidth exceptions</li>
3088 <li>better reporting of non-fatal warnings to user when
3089 file parsing fails.</li>
3090 <li>Save works when Jalview project is default format</li>
3091 <li>Save as dialog opened if current alignment format is
3092 not a valid output format</li>
3093 <li>UniProt canonical names introduced for both das and
3095 <li>Histidine should be midblue (not pink!) in Zappo</li>
3096 <li>error messages passed up and output when data read
3098 <li>edit undo recovers previous dataset sequence when
3099 sequence is edited</li>
3100 <li>allow PDB files without pdb ID HEADER lines (like
3101 those generated by MODELLER) to be read in properly</li>
3102 <li>allow reading of JPred concise files as a normal
3104 <li>Stockholm annotation parsing and alignment properties
3105 import fixed for PFAM records</li>
3106 <li>Structure view windows have correct name in Desktop
3108 <li>annotation consisting of sequence associated scores
3109 can be read and written correctly to annotation file</li>
3110 <li>Aligned cDNA translation to aligned peptide works
3112 <li>Fixed display of hidden sequence markers and
3113 non-italic font for representatives in Applet</li>
3114 <li>Applet Menus are always embedded in applet window on
3116 <li>Newly shown features appear at top of stack (in
3118 <li>Annotations added via parameter not drawn properly
3119 due to null pointer exceptions</li>
3120 <li>Secondary structure lines are drawn starting from
3121 first column of alignment</li>
3122 <li>UniProt XML import updated for new schema release in
3124 <li>Sequence feature to sequence ID match for Features
3125 file is case-insensitive</li>
3126 <li>Sequence features read from Features file appended to
3127 all sequences with matching IDs</li>
3128 <li>PDB structure coloured correctly for associated views
3129 containing a sub-sequence</li>
3130 <li>PDB files can be retrieved by applet from Jar files</li>
3131 <li>feature and annotation file applet parameters
3132 referring to different directories are retrieved correctly</li>
3133 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3134 <li>Fixed application hang whilst waiting for
3135 splash-screen version check to complete</li>
3136 <li>Applet properly URLencodes input parameter values
3137 when passing them to the launchApp service</li>
3138 <li>display name and local features preserved in results
3139 retrieved from web service</li>
3140 <li>Visual delay indication for sequence retrieval and
3141 sequence fetcher initialisation</li>
3142 <li>updated Application to use DAS 1.53e version of
3143 dasobert DAS client</li>
3144 <li>Re-instated Full AMSA support and .amsa file
3146 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3154 <div align="center">
3155 <strong>2.3</strong><br> 9/5/07
3160 <li>Jmol 11.0.2 integration</li>
3161 <li>PDB views stored in Jalview XML files</li>
3162 <li>Slide sequences</li>
3163 <li>Edit sequence in place</li>
3164 <li>EMBL CDS features</li>
3165 <li>DAS Feature mapping</li>
3166 <li>Feature ordering</li>
3167 <li>Alignment Properties</li>
3168 <li>Annotation Scores</li>
3169 <li>Sort by scores</li>
3170 <li>Feature/annotation editing in applet</li>
3175 <li>Headless state operation in 2.2.1</li>
3176 <li>Incorrect and unstable DNA pairwise alignment</li>
3177 <li>Cut and paste of sequences with annotation</li>
3178 <li>Feature group display state in XML</li>
3179 <li>Feature ordering in XML</li>
3180 <li>blc file iteration selection using filename # suffix</li>
3181 <li>Stockholm alignment properties</li>
3182 <li>Stockhom alignment secondary structure annotation</li>
3183 <li>2.2.1 applet had no feature transparency</li>
3184 <li>Number pad keys can be used in cursor mode</li>
3185 <li>Structure Viewer mirror image resolved</li>
3192 <div align="center">
3193 <strong>2.2.1</strong><br> 12/2/07
3198 <li>Non standard characters can be read and displayed
3199 <li>Annotations/Features can be imported/exported to the
3201 <li>Applet allows editing of sequence/annotation/group
3202 name & description
3203 <li>Preference setting to display sequence name in
3205 <li>Annotation file format extended to allow
3206 Sequence_groups to be defined
3207 <li>Default opening of alignment overview panel can be
3208 specified in preferences
3209 <li>PDB residue numbering annotation added to associated
3215 <li>Applet crash under certain Linux OS with Java 1.6
3217 <li>Annotation file export / import bugs fixed
3218 <li>PNG / EPS image output bugs fixed
3224 <div align="center">
3225 <strong>2.2</strong><br> 27/11/06
3230 <li>Multiple views on alignment
3231 <li>Sequence feature editing
3232 <li>"Reload" alignment
3233 <li>"Save" to current filename
3234 <li>Background dependent text colour
3235 <li>Right align sequence ids
3236 <li>User-defined lower case residue colours
3239 <li>Menu item accelerator keys
3240 <li>Control-V pastes to current alignment
3241 <li>Cancel button for DAS Feature Fetching
3242 <li>PCA and PDB Viewers zoom via mouse roller
3243 <li>User-defined sub-tree colours and sub-tree selection
3245 <li>'New Window' button on the 'Output to Text box'
3250 <li>New memory efficient Undo/Redo System
3251 <li>Optimised symbol lookups and conservation/consensus
3253 <li>Region Conservation/Consensus recalculated after
3255 <li>Fixed Remove Empty Columns Bug (empty columns at end
3257 <li>Slowed DAS Feature Fetching for increased robustness.
3259 <li>Made angle brackets in ASCII feature descriptions
3261 <li>Re-instated Zoom function for PCA
3262 <li>Sequence descriptions conserved in web service
3264 <li>UniProt ID discoverer uses any word separated by
3266 <li>WsDbFetch query/result association resolved
3267 <li>Tree leaf to sequence mapping improved
3268 <li>Smooth fonts switch moved to FontChooser dialog box.
3275 <div align="center">
3276 <strong>2.1.1</strong><br> 12/9/06
3281 <li>Copy consensus sequence to clipboard</li>
3286 <li>Image output - rightmost residues are rendered if
3287 sequence id panel has been resized</li>
3288 <li>Image output - all offscreen group boundaries are
3290 <li>Annotation files with sequence references - all
3291 elements in file are relative to sequence position</li>
3292 <li>Mac Applet users can use Alt key for group editing</li>
3298 <div align="center">
3299 <strong>2.1</strong><br> 22/8/06
3304 <li>MAFFT Multiple Alignment in default Web Service list</li>
3305 <li>DAS Feature fetching</li>
3306 <li>Hide sequences and columns</li>
3307 <li>Export Annotations and Features</li>
3308 <li>GFF file reading / writing</li>
3309 <li>Associate structures with sequences from local PDB
3311 <li>Add sequences to exisiting alignment</li>
3312 <li>Recently opened files / URL lists</li>
3313 <li>Applet can launch the full application</li>
3314 <li>Applet has transparency for features (Java 1.2
3316 <li>Applet has user defined colours parameter</li>
3317 <li>Applet can load sequences from parameter
3318 "sequence<em>x</em>"
3324 <li>Redundancy Panel reinstalled in the Applet</li>
3325 <li>Monospaced font - EPS / rescaling bug fixed</li>
3326 <li>Annotation files with sequence references bug fixed</li>
3332 <div align="center">
3333 <strong>2.08.1</strong><br> 2/5/06
3338 <li>Change case of selected region from Popup menu</li>
3339 <li>Choose to match case when searching</li>
3340 <li>Middle mouse button and mouse movement can compress /
3341 expand the visible width and height of the alignment</li>
3346 <li>Annotation Panel displays complete JNet results</li>
3352 <div align="center">
3353 <strong>2.08b</strong><br> 18/4/06
3359 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3360 <li>Righthand label on wrapped alignments shows correct
3367 <div align="center">
3368 <strong>2.08</strong><br> 10/4/06
3373 <li>Editing can be locked to the selection area</li>
3374 <li>Keyboard editing</li>
3375 <li>Create sequence features from searches</li>
3376 <li>Precalculated annotations can be loaded onto
3378 <li>Features file allows grouping of features</li>
3379 <li>Annotation Colouring scheme added</li>
3380 <li>Smooth fonts off by default - Faster rendering</li>
3381 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3386 <li>Drag & Drop fixed on Linux</li>
3387 <li>Jalview Archive file faster to load/save, sequence
3388 descriptions saved.</li>
3394 <div align="center">
3395 <strong>2.07</strong><br> 12/12/05
3400 <li>PDB Structure Viewer enhanced</li>
3401 <li>Sequence Feature retrieval and display enhanced</li>
3402 <li>Choose to output sequence start-end after sequence
3403 name for file output</li>
3404 <li>Sequence Fetcher WSDBFetch@EBI</li>
3405 <li>Applet can read feature files, PDB files and can be
3406 used for HTML form input</li>
3411 <li>HTML output writes groups and features</li>
3412 <li>Group editing is Control and mouse click</li>
3413 <li>File IO bugs</li>
3419 <div align="center">
3420 <strong>2.06</strong><br> 28/9/05
3425 <li>View annotations in wrapped mode</li>
3426 <li>More options for PCA viewer</li>
3431 <li>GUI bugs resolved</li>
3432 <li>Runs with -nodisplay from command line</li>
3438 <div align="center">
3439 <strong>2.05b</strong><br> 15/9/05
3444 <li>Choose EPS export as lineart or text</li>
3445 <li>Jar files are executable</li>
3446 <li>Can read in Uracil - maps to unknown residue</li>
3451 <li>Known OutOfMemory errors give warning message</li>
3452 <li>Overview window calculated more efficiently</li>
3453 <li>Several GUI bugs resolved</li>
3459 <div align="center">
3460 <strong>2.05</strong><br> 30/8/05
3465 <li>Edit and annotate in "Wrapped" view</li>
3470 <li>Several GUI bugs resolved</li>
3476 <div align="center">
3477 <strong>2.04</strong><br> 24/8/05
3482 <li>Hold down mouse wheel & scroll to change font
3488 <li>Improved JPred client reliability</li>
3489 <li>Improved loading of Jalview files</li>
3495 <div align="center">
3496 <strong>2.03</strong><br> 18/8/05
3501 <li>Set Proxy server name and port in preferences</li>
3502 <li>Multiple URL links from sequence ids</li>
3503 <li>User Defined Colours can have a scheme name and added
3505 <li>Choose to ignore gaps in consensus calculation</li>
3506 <li>Unix users can set default web browser</li>
3507 <li>Runs without GUI for batch processing</li>
3508 <li>Dynamically generated Web Service Menus</li>
3513 <li>InstallAnywhere download for Sparc Solaris</li>
3519 <div align="center">
3520 <strong>2.02</strong><br> 18/7/05
3526 <li>Copy & Paste order of sequences maintains
3527 alignment order.</li>
3533 <div align="center">
3534 <strong>2.01</strong><br> 12/7/05
3539 <li>Use delete key for deleting selection.</li>
3540 <li>Use Mouse wheel to scroll sequences.</li>
3541 <li>Help file updated to describe how to add alignment
3543 <li>Version and build date written to build properties
3545 <li>InstallAnywhere installation will check for updates
3546 at launch of Jalview.</li>
3551 <li>Delete gaps bug fixed.</li>
3552 <li>FileChooser sorts columns.</li>
3553 <li>Can remove groups one by one.</li>
3554 <li>Filechooser icons installed.</li>
3555 <li>Finder ignores return character when searching.
3556 Return key will initiate a search.<br>
3563 <div align="center">
3564 <strong>2.0</strong><br> 20/6/05
3569 <li>New codebase</li>