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)
94 <ul><li>Example groovy script for generating a matrix of percent identity scores for current alignment.</li></ul>
96 <td><div align="left">
99 <li><!-- JAL-2643 -->Pressing tab after updating the colour threshold text field doesn't trigger an update to the alignment view</li>
100 <li><!-- JAL-2682 -->Race condition when parsing sequence ID strings in parallel</li>
101 <li><!-- JAL-2608 -->Overview windows are also closed when alignment window is closed</li>
105 <li><!-- JAL-2777 -->Structures with whitespace chainCode cannot be viewed in Chimera</li>
106 <li><!-- JAL-2728 -->Protein annotation panel too high in CDS/Protein view
108 <li><!-- JAL-2757 -->Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs
110 <li><!-- JAL-2253 -->Slow EnsemblGenome ID lookup</li>
111 <li><!-- JAL-2739 -->Hidden column marker in last column not rendered when switching back from Wrapped to normal view</li>
112 <li><!-- JAL-2768 -->Annotation display corrupted when scrolling right in unwapped alignment view</li>
113 <li><!-- JAL-2542 -->Existing features on subsequence incorrectly relocated when full sequence retrieved from database</li>
114 <li><!-- JAL-2733 -->Last reported memory still shown when Desktop->Show Memory is unticked (OSX only)</li>
115 <li><!-- JAL-2658 -->Amend Features dialog doesn't allow features of same type and group to be selected for amending</li>
116 <li><!-- JAL-2524 -->Jalview becomes sluggish in wide alignments when hidden columns are present</li>
118 <strong><em>Applet</em></strong><br/>
120 <li><!-- JAL-2687 -->Concurrent modification exception when closing alignment panel</li>
125 <td width="60" nowrap>
127 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
128 <em>2/10/2017</em></strong>
131 <td><div align="left">
132 <em>New features in Jalview Desktop</em>
135 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
137 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
141 <td><div align="left">
145 <td width="60" nowrap>
147 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
148 <em>7/9/2017</em></strong>
151 <td><div align="left">
155 <!-- JAL-2588 -->Show gaps in overview window by colouring
156 in grey (sequences used to be coloured grey, and gaps were
160 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
164 <!-- JAL-2587 -->Overview updates immediately on increase
165 in size and progress bar shown as higher resolution
166 overview is recalculated
171 <td><div align="left">
175 <!-- JAL-2664 -->Overview window redraws every hidden
176 column region row by row
179 <!-- JAL-2681 -->duplicate protein sequences shown after
180 retrieving Ensembl crossrefs for sequences from Uniprot
183 <!-- JAL-2603 -->Overview window throws NPE if show boxes
184 format setting is unticked
187 <!-- JAL-2610 -->Groups are coloured wrongly in overview
188 if group has show boxes format setting unticked
191 <!-- JAL-2672,JAL-2665 -->Redraw problems when
192 autoscrolling whilst dragging current selection group to
193 include sequences and columns not currently displayed
196 <!-- JAL-2691 -->Not all chains are mapped when multimeric
197 assemblies are imported via CIF file
200 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
201 displayed when threshold or conservation colouring is also
205 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
209 <!-- JAL-2673 -->Jalview continues to scroll after
210 dragging a selected region off the visible region of the
214 <!-- JAL-2724 -->Cannot apply annotation based
215 colourscheme to all groups in a view
218 <!-- JAL-2511 -->IDs don't line up with sequences
219 initially after font size change using the Font chooser or
226 <td width="60" nowrap>
228 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
231 <td><div align="left">
232 <em>Calculations</em>
236 <!-- JAL-1933 -->Occupancy annotation row shows number of
237 ungapped positions in each column of the alignment.
240 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
241 a calculation dialog box
244 <!-- JAL-2379 -->Revised implementation of PCA for speed
245 and memory efficiency (~30x faster)
248 <!-- JAL-2403 -->Revised implementation of sequence
249 similarity scores as used by Tree, PCA, Shading Consensus
250 and other calculations
253 <!-- JAL-2416 -->Score matrices are stored as resource
254 files within the Jalview codebase
257 <!-- JAL-2500 -->Trees computed on Sequence Feature
258 Similarity may have different topology due to increased
265 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
266 model for alignments and groups
269 <!-- JAL-384 -->Custom shading schemes created via groovy
276 <!-- JAL-2526 -->Efficiency improvements for interacting
277 with alignment and overview windows
280 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
284 <!-- JAL-2388 -->Hidden columns and sequences can be
288 <!-- JAL-2611 -->Click-drag in visible area allows fine
289 adjustment of visible position
293 <em>Data import/export</em>
296 <!-- JAL-2535 -->Posterior probability annotation from
297 Stockholm files imported as sequence associated annotation
300 <!-- JAL-2507 -->More robust per-sequence positional
301 annotation input/output via stockholm flatfile
304 <!-- JAL-2533 -->Sequence names don't include file
305 extension when importing structure files without embedded
306 names or PDB accessions
309 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
310 format sequence substitution matrices
313 <em>User Interface</em>
316 <!-- JAL-2447 --> Experimental Features Checkbox in
317 Desktop's Tools menu to hide or show untested features in
321 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
322 via Overview or sequence motif search operations
325 <!-- JAL-2547 -->Amend sequence features dialog box can be
326 opened by double clicking gaps within sequence feature
330 <!-- JAL-1476 -->Status bar message shown when not enough
331 aligned positions were available to create a 3D structure
335 <em>3D Structure</em>
338 <!-- JAL-2430 -->Hidden regions in alignment views are not
339 coloured in linked structure views
342 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
343 file-based command exchange
346 <!-- JAL-2375 -->Structure chooser automatically shows
347 Cached Structures rather than querying the PDBe if
348 structures are already available for sequences
351 <!-- JAL-2520 -->Structures imported via URL are cached in
352 the Jalview project rather than downloaded again when the
356 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
357 to transfer Chimera's structure attributes as Jalview
358 features, and vice-versa (<strong>Experimental
362 <em>Web Services</em>
365 <!-- JAL-2549 -->Updated JABAWS client to v2.2
368 <!-- JAL-2335 -->Filter non-standard amino acids and
369 nucleotides when submitting to AACon and other MSA
373 <!-- JAL-2316, -->URLs for viewing database
374 cross-references provided by identifiers.org and the
382 <!-- JAL-2344 -->FileFormatI interface for describing and
383 identifying file formats (instead of String constants)
386 <!-- JAL-2228 -->FeatureCounter script refactored for
387 efficiency when counting all displayed features (not
388 backwards compatible with 2.10.1)
391 <em>Example files</em>
394 <!-- JAL-2631 -->Graduated feature colour style example
395 included in the example feature file
398 <em>Documentation</em>
401 <!-- JAL-2339 -->Release notes reformatted for readability
402 with the built-in Java help viewer
405 <!-- JAL-1644 -->Find documentation updated with 'search
406 sequence description' option
412 <!-- JAL-2485, -->External service integration tests for
413 Uniprot REST Free Text Search Client
416 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
419 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
424 <td><div align="left">
425 <em>Calculations</em>
428 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
429 matrix - C->R should be '-3'<br />Old matrix restored
430 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
432 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
433 Jalview's treatment of gaps in PCA and substitution matrix
434 based Tree calculations.<br /> <br />In earlier versions
435 of Jalview, gaps matching gaps were penalised, and gaps
436 matching non-gaps penalised even more. In the PCA
437 calculation, gaps were actually treated as non-gaps - so
438 different costs were applied, which meant Jalview's PCAs
439 were different to those produced by SeqSpace.<br />Jalview
440 now treats gaps in the same way as SeqSpace (ie it scores
441 them as 0). <br /> <br />Enter the following in the
442 Groovy console to restore pre-2.10.2 behaviour:<br />
443 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
444 // for 2.10.1 mode <br />
445 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
446 // to restore 2.10.2 mode <br /> <br /> <em>Note:
447 these settings will affect all subsequent tree and PCA
448 calculations (not recommended)</em></li>
450 <!-- JAL-2424 -->Fixed off-by-one bug that affected
451 scaling of branch lengths for trees computed using
452 Sequence Feature Similarity.
455 <!-- JAL-2377 -->PCA calculation could hang when
456 generating output report when working with highly
460 <!-- JAL-2544 --> Sort by features includes features to
461 right of selected region when gaps present on right-hand
465 <em>User Interface</em>
468 <!-- JAL-2346 -->Reopening Colour by annotation dialog
469 doesn't reselect a specific sequence's associated
470 annotation after it was used for colouring a view
473 <!-- JAL-2419 -->Current selection lost if popup menu
474 opened on a region of alignment without groups
477 <!-- JAL-2374 -->Popup menu not always shown for regions
478 of an alignment with overlapping groups
481 <!-- JAL-2310 -->Finder double counts if both a sequence's
482 name and description match
485 <!-- JAL-2370 -->Hiding column selection containing two
486 hidden regions results in incorrect hidden regions
489 <!-- JAL-2386 -->'Apply to all groups' setting when
490 changing colour does not apply Conservation slider value
494 <!-- JAL-2373 -->Percentage identity and conservation menu
495 items do not show a tick or allow shading to be disabled
498 <!-- JAL-2385 -->Conservation shading or PID threshold
499 lost when base colourscheme changed if slider not visible
502 <!-- JAL-2547 -->Sequence features shown in tooltip for
503 gaps before start of features
506 <!-- JAL-2623 -->Graduated feature colour threshold not
507 restored to UI when feature colour is edited
510 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
511 a time when scrolling vertically in wrapped mode.
514 <!-- JAL-2630 -->Structure and alignment overview update
515 as graduate feature colour settings are modified via the
519 <!-- JAL-2034 -->Overview window doesn't always update
520 when a group defined on the alignment is resized
523 <!-- JAL-2605 -->Mouseovers on left/right scale region in
524 wrapped view result in positional status updates
528 <!-- JAL-2563 -->Status bar doesn't show position for
529 ambiguous amino acid and nucleotide symbols
532 <!-- JAL-2602 -->Copy consensus sequence failed if
533 alignment included gapped columns
536 <!-- JAL-2473 -->Minimum size set for Jalview windows so
537 widgets don't permanently disappear
540 <!-- JAL-2503 -->Cannot select or filter quantitative
541 annotation that are shown only as column labels (e.g.
542 T-Coffee column reliability scores)
545 <!-- JAL-2594 -->Exception thrown if trying to create a
546 sequence feature on gaps only
549 <!-- JAL-2504 -->Features created with 'New feature'
550 button from a Find inherit previously defined feature type
551 rather than the Find query string
554 <!-- JAL-2423 -->incorrect title in output window when
555 exporting tree calculated in Jalview
558 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
559 and then revealing them reorders sequences on the
563 <!-- JAL-964 -->Group panel in sequence feature settings
564 doesn't update to reflect available set of groups after
565 interactively adding or modifying features
568 <!-- JAL-2225 -->Sequence Database chooser unusable on
572 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
573 only excluded gaps in current sequence and ignored
580 <!-- JAL-2421 -->Overview window visible region moves
581 erratically when hidden rows or columns are present
584 <!-- JAL-2362 -->Per-residue colourschemes applied via the
585 Structure Viewer's colour menu don't correspond to
589 <!-- JAL-2405 -->Protein specific colours only offered in
590 colour and group colour menu for protein alignments
593 <!-- JAL-2385 -->Colour threshold slider doesn't update to
594 reflect currently selected view or group's shading
598 <!-- JAL-2624 -->Feature colour thresholds not respected
599 when rendered on overview and structures when opacity at
603 <!-- JAL-2589 -->User defined gap colour not shown in
604 overview when features overlaid on alignment
607 <em>Data import/export</em>
610 <!-- JAL-2576 -->Very large alignments take a long time to
614 <!-- JAL-2507 -->Per-sequence RNA secondary structures
615 added after a sequence was imported are not written to
619 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
620 when importing RNA secondary structure via Stockholm
623 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
624 not shown in correct direction for simple pseudoknots
627 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
628 with lightGray or darkGray via features file (but can
632 <!-- JAL-2383 -->Above PID colour threshold not recovered
633 when alignment view imported from project
636 <!-- JAL-2520,JAL-2465 -->No mappings generated between
637 structure and sequences extracted from structure files
638 imported via URL and viewed in Jmol
641 <!-- JAL-2520 -->Structures loaded via URL are saved in
642 Jalview Projects rather than fetched via URL again when
643 the project is loaded and the structure viewed
646 <em>Web Services</em>
649 <!-- JAL-2519 -->EnsemblGenomes example failing after
650 release of Ensembl v.88
653 <!-- JAL-2366 -->Proxy server address and port always
654 appear enabled in Preferences->Connections
657 <!-- JAL-2461 -->DAS registry not found exceptions
658 removed from console output
661 <!-- JAL-2582 -->Cannot retrieve protein products from
662 Ensembl by Peptide ID
665 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
666 created from SIFTs, and spurious 'Couldn't open structure
667 in Chimera' errors raised after April 2017 update (problem
668 due to 'null' string rather than empty string used for
669 residues with no corresponding PDB mapping).
672 <em>Application UI</em>
675 <!-- JAL-2361 -->User Defined Colours not added to Colour
679 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
680 case' residues (button in colourscheme editor debugged and
681 new documentation and tooltips added)
684 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
685 doesn't restore group-specific text colour thresholds
688 <!-- JAL-2243 -->Feature settings panel does not update as
689 new features are added to alignment
692 <!-- JAL-2532 -->Cancel in feature settings reverts
693 changes to feature colours via the Amend features dialog
696 <!-- JAL-2506 -->Null pointer exception when attempting to
697 edit graduated feature colour via amend features dialog
701 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
702 selection menu changes colours of alignment views
705 <!-- JAL-2426 -->Spurious exceptions in console raised
706 from alignment calculation workers after alignment has
710 <!-- JAL-1608 -->Typo in selection popup menu - Create
711 groups now 'Create Group'
714 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
715 Create/Undefine group doesn't always work
718 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
719 shown again after pressing 'Cancel'
722 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
723 adjusts start position in wrap mode
726 <!-- JAL-2563 -->Status bar doesn't show positions for
727 ambiguous amino acids
730 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
731 CDS/Protein view after CDS sequences added for aligned
735 <!-- JAL-2592 -->User defined colourschemes called 'User
736 Defined' don't appear in Colours menu
742 <!-- JAL-2468 -->Switching between Nucleotide and Protein
743 score models doesn't always result in an updated PCA plot
746 <!-- JAL-2442 -->Features not rendered as transparent on
747 overview or linked structure view
750 <!-- JAL-2372 -->Colour group by conservation doesn't
754 <!-- JAL-2517 -->Hitting Cancel after applying
755 user-defined colourscheme doesn't restore original
762 <!-- JAL-2314 -->Unit test failure:
763 jalview.ws.jabaws.RNAStructExportImport setup fails
766 <!-- JAL-2307 -->Unit test failure:
767 jalview.ws.sifts.SiftsClientTest due to compatibility
768 problems with deep array comparison equality asserts in
769 successive versions of TestNG
772 <!-- JAL-2479 -->Relocated StructureChooserTest and
773 ParameterUtilsTest Unit tests to Network suite
776 <em>New Known Issues</em>
779 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
780 phase after a sequence motif find operation
783 <!-- JAL-2550 -->Importing annotation file with rows
784 containing just upper and lower case letters are
785 interpreted as WUSS RNA secondary structure symbols
788 <!-- JAL-2590 -->Cannot load and display Newick trees
789 reliably from eggnog Ortholog database
792 <!-- JAL-2468 -->Status bar shows 'Marked x columns
793 containing features of type Highlight' when 'B' is pressed
794 to mark columns containing highlighted regions.
797 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
798 doesn't always add secondary structure annotation.
803 <td width="60" nowrap>
805 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
808 <td><div align="left">
812 <!-- JAL-98 -->Improved memory usage: sparse arrays used
813 for all consensus calculations
816 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
819 <li>Updated Jalview's Certum code signing certificate
825 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
826 set of database cross-references, sorted alphabetically
829 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
830 from database cross references. Users with custom links
831 will receive a <a href="webServices/urllinks.html#warning">warning
832 dialog</a> asking them to update their preferences.
835 <!-- JAL-2287-->Cancel button and escape listener on
836 dialog warning user about disconnecting Jalview from a
840 <!-- JAL-2320-->Jalview's Chimera control window closes if
841 the Chimera it is connected to is shut down
844 <!-- JAL-1738-->New keystroke (B) and Select highlighted
845 columns menu item to mark columns containing highlighted
846 regions (e.g. from structure selections or results of a
850 <!-- JAL-2284-->Command line option for batch-generation
851 of HTML pages rendering alignment data with the BioJS
861 <!-- JAL-2286 -->Columns with more than one modal residue
862 are not coloured or thresholded according to percent
863 identity (first observed in Jalview 2.8.2)
866 <!-- JAL-2301 -->Threonine incorrectly reported as not
870 <!-- JAL-2318 -->Updates to documentation pages (above PID
871 threshold, amino acid properties)
874 <!-- JAL-2292 -->Lower case residues in sequences are not
875 reported as mapped to residues in a structure file in the
879 <!--JAL-2324 -->Identical features with non-numeric scores
880 could be added multiple times to a sequence
883 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
884 bond features shown as two highlighted residues rather
885 than a range in linked structure views, and treated
886 correctly when selecting and computing trees from features
889 <!-- JAL-2281-->Custom URL links for database
890 cross-references are matched to database name regardless
898 <!-- JAL-2282-->Custom URL links for specific database
899 names without regular expressions also offer links from
903 <!-- JAL-2315-->Removing a single configured link in the
904 URL links pane in Connections preferences doesn't actually
905 update Jalview configuration
908 <!-- JAL-2272-->CTRL-Click on a selected region to open
909 the alignment area popup menu doesn't work on El-Capitan
912 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
913 files with similarly named sequences if dropped onto the
917 <!-- JAL-2312 -->Additional mappings are shown for PDB
918 entries where more chains exist in the PDB accession than
919 are reported in the SIFTS file
922 <!-- JAL-2317-->Certain structures do not get mapped to
923 the structure view when displayed with Chimera
926 <!-- JAL-2317-->No chains shown in the Chimera view
927 panel's View->Show Chains submenu
930 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
931 work for wrapped alignment views
934 <!--JAL-2197 -->Rename UI components for running JPred
935 predictions from 'JNet' to 'JPred'
938 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
939 corrupted when annotation panel vertical scroll is not at
943 <!--JAL-2332 -->Attempting to view structure for Hen
944 lysozyme results in a PDB Client error dialog box
947 <!-- JAL-2319 -->Structure View's mapping report switched
948 ranges for PDB and sequence for SIFTS
951 SIFTS 'Not_Observed' residues mapped to non-existant
955 <!-- <em>New Known Issues</em>
962 <td width="60" nowrap>
964 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
965 <em>25/10/2016</em></strong>
968 <td><em>Application</em>
970 <li>3D Structure chooser opens with 'Cached structures'
971 view if structures already loaded</li>
972 <li>Progress bar reports models as they are loaded to
979 <li>Colour by conservation always enabled and no tick
980 shown in menu when BLOSUM or PID shading applied</li>
981 <li>FER1_ARATH and FER2_ARATH labels were switched in
982 example sequences/projects/trees</li>
986 <li>Jalview projects with views of local PDB structure
987 files saved on Windows cannot be opened on OSX</li>
988 <li>Multiple structure views can be opened and superposed
989 without timeout for structures with multiple models or
990 multiple sequences in alignment</li>
991 <li>Cannot import or associated local PDB files without a
992 PDB ID HEADER line</li>
993 <li>RMSD is not output in Jmol console when superposition
995 <li>Drag and drop of URL from Browser fails for Linux and
996 OSX versions earlier than El Capitan</li>
997 <li>ENA client ignores invalid content from ENA server</li>
998 <li>Exceptions are not raised in console when ENA client
999 attempts to fetch non-existent IDs via Fetch DB Refs UI
1001 <li>Exceptions are not raised in console when a new view
1002 is created on the alignment</li>
1003 <li>OSX right-click fixed for group selections: CMD-click
1004 to insert/remove gaps in groups and CTRL-click to open group
1007 <em>Build and deployment</em>
1009 <li>URL link checker now copes with multi-line anchor
1012 <em>New Known Issues</em>
1014 <li>Drag and drop from URL links in browsers do not work
1021 <td width="60" nowrap>
1022 <div align="center">
1023 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1026 <td><em>General</em>
1029 <!-- JAL-2124 -->Updated Spanish translations.
1032 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1033 for importing structure data to Jalview. Enables mmCIF and
1037 <!-- JAL-192 --->Alignment ruler shows positions relative to
1041 <!-- JAL-2202 -->Position/residue shown in status bar when
1042 mousing over sequence associated annotation
1045 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1049 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1050 '()', canonical '[]' and invalid '{}' base pair populations
1054 <!-- JAL-2092 -->Feature settings popup menu options for
1055 showing or hiding columns containing a feature
1058 <!-- JAL-1557 -->Edit selected group by double clicking on
1059 group and sequence associated annotation labels
1062 <!-- JAL-2236 -->Sequence name added to annotation label in
1063 select/hide columns by annotation and colour by annotation
1067 </ul> <em>Application</em>
1070 <!-- JAL-2050-->Automatically hide introns when opening a
1071 gene/transcript view
1074 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1078 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1079 structure mappings with the EMBL-EBI PDBe SIFTS database
1082 <!-- JAL-2079 -->Updated download sites used for Rfam and
1083 Pfam sources to xfam.org
1086 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1089 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1090 over sequences in Jalview
1093 <!-- JAL-2027-->Support for reverse-complement coding
1094 regions in ENA and EMBL
1097 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1098 for record retrieval via ENA rest API
1101 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1105 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1106 groovy script execution
1109 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1110 alignment window's Calculate menu
1113 <!-- JAL-1812 -->Allow groovy scripts that call
1114 Jalview.getAlignFrames() to run in headless mode
1117 <!-- JAL-2068 -->Support for creating new alignment
1118 calculation workers from groovy scripts
1121 <!-- JAL-1369 --->Store/restore reference sequence in
1125 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1126 associations are now saved/restored from project
1129 <!-- JAL-1993 -->Database selection dialog always shown
1130 before sequence fetcher is opened
1133 <!-- JAL-2183 -->Double click on an entry in Jalview's
1134 database chooser opens a sequence fetcher
1137 <!-- JAL-1563 -->Free-text search client for UniProt using
1138 the UniProt REST API
1141 <!-- JAL-2168 -->-nonews command line parameter to prevent
1142 the news reader opening
1145 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1146 querying stored in preferences
1149 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1153 <!-- JAL-1977-->Tooltips shown on database chooser
1156 <!-- JAL-391 -->Reverse complement function in calculate
1157 menu for nucleotide sequences
1160 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1161 and feature counts preserves alignment ordering (and
1162 debugged for complex feature sets).
1165 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1166 viewing structures with Jalview 2.10
1169 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1170 genome, transcript CCDS and gene ids via the Ensembl and
1171 Ensembl Genomes REST API
1174 <!-- JAL-2049 -->Protein sequence variant annotation
1175 computed for 'sequence_variant' annotation on CDS regions
1179 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1183 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1184 Ref Fetcher fails to match, or otherwise updates sequence
1185 data from external database records.
1188 <!-- JAL-2154 -->Revised Jalview Project format for
1189 efficient recovery of sequence coding and alignment
1190 annotation relationships.
1192 </ul> <!-- <em>Applet</em>
1203 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1207 <!-- JAL-2018-->Export features in Jalview format (again)
1208 includes graduated colourschemes
1211 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1212 working with big alignments and lots of hidden columns
1215 <!-- JAL-2053-->Hidden column markers not always rendered
1216 at right of alignment window
1219 <!-- JAL-2067 -->Tidied up links in help file table of
1223 <!-- JAL-2072 -->Feature based tree calculation not shown
1227 <!-- JAL-2075 -->Hidden columns ignored during feature
1228 based tree calculation
1231 <!-- JAL-2065 -->Alignment view stops updating when show
1232 unconserved enabled for group on alignment
1235 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1239 <!-- JAL-2146 -->Alignment column in status incorrectly
1240 shown as "Sequence position" when mousing over
1244 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1245 hidden columns present
1248 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1249 user created annotation added to alignment
1252 <!-- JAL-1841 -->RNA Structure consensus only computed for
1253 '()' base pair annotation
1256 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1257 in zero scores for all base pairs in RNA Structure
1261 <!-- JAL-2174-->Extend selection with columns containing
1265 <!-- JAL-2275 -->Pfam format writer puts extra space at
1266 beginning of sequence
1269 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1273 <!-- JAL-2238 -->Cannot create groups on an alignment from
1274 from a tree when t-coffee scores are shown
1277 <!-- JAL-1836,1967 -->Cannot import and view PDB
1278 structures with chains containing negative resnums (4q4h)
1281 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1285 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1286 to Clustal, PIR and PileUp output
1289 <!-- JAL-2008 -->Reordering sequence features that are
1290 not visible causes alignment window to repaint
1293 <!-- JAL-2006 -->Threshold sliders don't work in
1294 graduated colour and colour by annotation row for e-value
1295 scores associated with features and annotation rows
1298 <!-- JAL-1797 -->amino acid physicochemical conservation
1299 calculation should be case independent
1302 <!-- JAL-2173 -->Remove annotation also updates hidden
1306 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1307 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1308 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1311 <!-- JAL-2065 -->Null pointer exceptions and redraw
1312 problems when reference sequence defined and 'show
1313 non-conserved' enabled
1316 <!-- JAL-1306 -->Quality and Conservation are now shown on
1317 load even when Consensus calculation is disabled
1320 <!-- JAL-1932 -->Remove right on penultimate column of
1321 alignment does nothing
1324 <em>Application</em>
1327 <!-- JAL-1552-->URLs and links can't be imported by
1328 drag'n'drop on OSX when launched via webstart (note - not
1329 yet fixed for El Capitan)
1332 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1333 output when running on non-gb/us i18n platforms
1336 <!-- JAL-1944 -->Error thrown when exporting a view with
1337 hidden sequences as flat-file alignment
1340 <!-- JAL-2030-->InstallAnywhere distribution fails when
1344 <!-- JAL-2080-->Jalview very slow to launch via webstart
1345 (also hotfix for 2.9.0b2)
1348 <!-- JAL-2085 -->Cannot save project when view has a
1349 reference sequence defined
1352 <!-- JAL-1011 -->Columns are suddenly selected in other
1353 alignments and views when revealing hidden columns
1356 <!-- JAL-1989 -->Hide columns not mirrored in complement
1357 view in a cDNA/Protein splitframe
1360 <!-- JAL-1369 -->Cannot save/restore representative
1361 sequence from project when only one sequence is
1365 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1366 in Structure Chooser
1369 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1370 structure consensus didn't refresh annotation panel
1373 <!-- JAL-1962 -->View mapping in structure view shows
1374 mappings between sequence and all chains in a PDB file
1377 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1378 dialogs format columns correctly, don't display array
1379 data, sort columns according to type
1382 <!-- JAL-1975 -->Export complete shown after destination
1383 file chooser is cancelled during an image export
1386 <!-- JAL-2025 -->Error when querying PDB Service with
1387 sequence name containing special characters
1390 <!-- JAL-2024 -->Manual PDB structure querying should be
1394 <!-- JAL-2104 -->Large tooltips with broken HTML
1395 formatting don't wrap
1398 <!-- JAL-1128 -->Figures exported from wrapped view are
1399 truncated so L looks like I in consensus annotation
1402 <!-- JAL-2003 -->Export features should only export the
1403 currently displayed features for the current selection or
1407 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1408 after fetching cross-references, and restoring from
1412 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1413 followed in the structure viewer
1416 <!-- JAL-2163 -->Titles for individual alignments in
1417 splitframe not restored from project
1420 <!-- JAL-2145 -->missing autocalculated annotation at
1421 trailing end of protein alignment in transcript/product
1422 splitview when pad-gaps not enabled by default
1425 <!-- JAL-1797 -->amino acid physicochemical conservation
1429 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1430 article has been read (reopened issue due to
1431 internationalisation problems)
1434 <!-- JAL-1960 -->Only offer PDB structures in structure
1435 viewer based on sequence name, PDB and UniProt
1440 <!-- JAL-1976 -->No progress bar shown during export of
1444 <!-- JAL-2213 -->Structures not always superimposed after
1445 multiple structures are shown for one or more sequences.
1448 <!-- JAL-1370 -->Reference sequence characters should not
1449 be replaced with '.' when 'Show unconserved' format option
1453 <!-- JAL-1823 -->Cannot specify chain code when entering
1454 specific PDB id for sequence
1457 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1458 'Export hidden sequences' is enabled, but 'export hidden
1459 columns' is disabled.
1462 <!--JAL-2026-->Best Quality option in structure chooser
1463 selects lowest rather than highest resolution structures
1467 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1468 to sequence mapping in 'View Mappings' report
1471 <!-- JAL-2284 -->Unable to read old Jalview projects that
1472 contain non-XML data added after Jalvew wrote project.
1475 <!-- JAL-2118 -->Newly created annotation row reorders
1476 after clicking on it to create new annotation for a
1480 <!-- JAL-1980 -->Null Pointer Exception raised when
1481 pressing Add on an orphaned cut'n'paste window.
1483 <!-- may exclude, this is an external service stability issue JAL-1941
1484 -- > RNA 3D structure not added via DSSR service</li> -->
1489 <!-- JAL-2151 -->Incorrect columns are selected when
1490 hidden columns present before start of sequence
1493 <!-- JAL-1986 -->Missing dependencies on applet pages
1497 <!-- JAL-1947 -->Overview pixel size changes when
1498 sequences are hidden in applet
1501 <!-- JAL-1996 -->Updated instructions for applet
1502 deployment on examples pages.
1509 <td width="60" nowrap>
1510 <div align="center">
1511 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1512 <em>16/10/2015</em></strong>
1515 <td><em>General</em>
1517 <li>Time stamps for signed Jalview application and applet
1522 <em>Application</em>
1524 <li>Duplicate group consensus and conservation rows
1525 shown when tree is partitioned</li>
1526 <li>Erratic behaviour when tree partitions made with
1527 multiple cDNA/Protein split views</li>
1533 <td width="60" nowrap>
1534 <div align="center">
1535 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1536 <em>8/10/2015</em></strong>
1539 <td><em>General</em>
1541 <li>Updated Spanish translations of localized text for
1543 </ul> <em>Application</em>
1545 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1546 <li>Signed OSX InstallAnywhere installer<br></li>
1547 <li>Support for per-sequence based annotations in BioJSON</li>
1548 </ul> <em>Applet</em>
1550 <li>Split frame example added to applet examples page</li>
1551 </ul> <em>Build and Deployment</em>
1554 <!-- JAL-1888 -->New ant target for running Jalview's test
1562 <li>Mapping of cDNA to protein in split frames
1563 incorrect when sequence start > 1</li>
1564 <li>Broken images in filter column by annotation dialog
1566 <li>Feature colours not parsed from features file</li>
1567 <li>Exceptions and incomplete link URLs recovered when
1568 loading a features file containing HTML tags in feature
1572 <em>Application</em>
1574 <li>Annotations corrupted after BioJS export and
1576 <li>Incorrect sequence limits after Fetch DB References
1577 with 'trim retrieved sequences'</li>
1578 <li>Incorrect warning about deleting all data when
1579 deleting selected columns</li>
1580 <li>Patch to build system for shipping properly signed
1581 JNLP templates for webstart launch</li>
1582 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1583 unreleased structures for download or viewing</li>
1584 <li>Tab/space/return keystroke operation of EMBL-PDBe
1585 fetcher/viewer dialogs works correctly</li>
1586 <li>Disabled 'minimise' button on Jalview windows
1587 running on OSX to workaround redraw hang bug</li>
1588 <li>Split cDNA/Protein view position and geometry not
1589 recovered from jalview project</li>
1590 <li>Initial enabled/disabled state of annotation menu
1591 sorter 'show autocalculated first/last' corresponds to
1593 <li>Restoring of Clustal, RNA Helices and T-Coffee
1594 color schemes from BioJSON</li>
1598 <li>Reorder sequences mirrored in cDNA/Protein split
1600 <li>Applet with Jmol examples not loading correctly</li>
1606 <td><div align="center">
1607 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1609 <td><em>General</em>
1611 <li>Linked visualisation and analysis of DNA and Protein
1614 <li>Translated cDNA alignments shown as split protein
1615 and DNA alignment views</li>
1616 <li>Codon consensus annotation for linked protein and
1617 cDNA alignment views</li>
1618 <li>Link cDNA or Protein product sequences by loading
1619 them onto Protein or cDNA alignments</li>
1620 <li>Reconstruct linked cDNA alignment from aligned
1621 protein sequences</li>
1624 <li>Jmol integration updated to Jmol v14.2.14</li>
1625 <li>Import and export of Jalview alignment views as <a
1626 href="features/bioJsonFormat.html">BioJSON</a></li>
1627 <li>New alignment annotation file statements for
1628 reference sequences and marking hidden columns</li>
1629 <li>Reference sequence based alignment shading to
1630 highlight variation</li>
1631 <li>Select or hide columns according to alignment
1633 <li>Find option for locating sequences by description</li>
1634 <li>Conserved physicochemical properties shown in amino
1635 acid conservation row</li>
1636 <li>Alignments can be sorted by number of RNA helices</li>
1637 </ul> <em>Application</em>
1639 <li>New cDNA/Protein analysis capabilities
1641 <li>Get Cross-References should open a Split Frame
1642 view with cDNA/Protein</li>
1643 <li>Detect when nucleotide sequences and protein
1644 sequences are placed in the same alignment</li>
1645 <li>Split cDNA/Protein views are saved in Jalview
1650 <li>Use REST API to talk to Chimera</li>
1651 <li>Selected regions in Chimera are highlighted in linked
1652 Jalview windows</li>
1654 <li>VARNA RNA viewer updated to v3.93</li>
1655 <li>VARNA views are saved in Jalview Projects</li>
1656 <li>Pseudoknots displayed as Jalview RNA annotation can
1657 be shown in VARNA</li>
1659 <li>Make groups for selection uses marked columns as well
1660 as the active selected region</li>
1662 <li>Calculate UPGMA and NJ trees using sequence feature
1664 <li>New Export options
1666 <li>New Export Settings dialog to control hidden
1667 region export in flat file generation</li>
1669 <li>Export alignment views for display with the <a
1670 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1672 <li>Export scrollable SVG in HTML page</li>
1673 <li>Optional embedding of BioJSON data when exporting
1674 alignment figures to HTML</li>
1676 <li>3D structure retrieval and display
1678 <li>Free text and structured queries with the PDBe
1680 <li>PDBe Search API based discovery and selection of
1681 PDB structures for a sequence set</li>
1685 <li>JPred4 employed for protein secondary structure
1687 <li>Hide Insertions menu option to hide unaligned columns
1688 for one or a group of sequences</li>
1689 <li>Automatically hide insertions in alignments imported
1690 from the JPred4 web server</li>
1691 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1692 system on OSX<br />LGPL libraries courtesy of <a
1693 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1695 <li>changed 'View nucleotide structure' submenu to 'View
1696 VARNA 2D Structure'</li>
1697 <li>change "View protein structure" menu option to "3D
1700 </ul> <em>Applet</em>
1702 <li>New layout for applet example pages</li>
1703 <li>New parameters to enable SplitFrame view
1704 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1705 <li>New example demonstrating linked viewing of cDNA and
1706 Protein alignments</li>
1707 </ul> <em>Development and deployment</em>
1709 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1710 <li>Include installation type and git revision in build
1711 properties and console log output</li>
1712 <li>Jalview Github organisation, and new github site for
1713 storing BioJsMSA Templates</li>
1714 <li>Jalview's unit tests now managed with TestNG</li>
1717 <!-- <em>General</em>
1719 </ul> --> <!-- issues resolved --> <em>Application</em>
1721 <li>Escape should close any open find dialogs</li>
1722 <li>Typo in select-by-features status report</li>
1723 <li>Consensus RNA secondary secondary structure
1724 predictions are not highlighted in amber</li>
1725 <li>Missing gap character in v2.7 example file means
1726 alignment appears unaligned when pad-gaps is not enabled</li>
1727 <li>First switch to RNA Helices colouring doesn't colour
1728 associated structure views</li>
1729 <li>ID width preference option is greyed out when auto
1730 width checkbox not enabled</li>
1731 <li>Stopped a warning dialog from being shown when
1732 creating user defined colours</li>
1733 <li>'View Mapping' in structure viewer shows sequence
1734 mappings for just that viewer's sequences</li>
1735 <li>Workaround for superposing PDB files containing
1736 multiple models in Chimera</li>
1737 <li>Report sequence position in status bar when hovering
1738 over Jmol structure</li>
1739 <li>Cannot output gaps as '.' symbols with Selection ->
1740 output to text box</li>
1741 <li>Flat file exports of alignments with hidden columns
1742 have incorrect sequence start/end</li>
1743 <li>'Aligning' a second chain to a Chimera structure from
1745 <li>Colour schemes applied to structure viewers don't
1746 work for nucleotide</li>
1747 <li>Loading/cut'n'pasting an empty or invalid file leads
1748 to a grey/invisible alignment window</li>
1749 <li>Exported Jpred annotation from a sequence region
1750 imports to different position</li>
1751 <li>Space at beginning of sequence feature tooltips shown
1752 on some platforms</li>
1753 <li>Chimera viewer 'View | Show Chain' menu is not
1755 <li>'New View' fails with a Null Pointer Exception in
1756 console if Chimera has been opened</li>
1757 <li>Mouseover to Chimera not working</li>
1758 <li>Miscellaneous ENA XML feature qualifiers not
1760 <li>NPE in annotation renderer after 'Extract Scores'</li>
1761 <li>If two structures in one Chimera window, mouseover of
1762 either sequence shows on first structure</li>
1763 <li>'Show annotations' options should not make
1764 non-positional annotations visible</li>
1765 <li>Subsequence secondary structure annotation not shown
1766 in right place after 'view flanking regions'</li>
1767 <li>File Save As type unset when current file format is
1769 <li>Save as '.jar' option removed for saving Jalview
1771 <li>Colour by Sequence colouring in Chimera more
1773 <li>Cannot 'add reference annotation' for a sequence in
1774 several views on same alignment</li>
1775 <li>Cannot show linked products for EMBL / ENA records</li>
1776 <li>Jalview's tooltip wraps long texts containing no
1778 </ul> <em>Applet</em>
1780 <li>Jmol to JalviewLite mouseover/link not working</li>
1781 <li>JalviewLite can't import sequences with ID
1782 descriptions containing angle brackets</li>
1783 </ul> <em>General</em>
1785 <li>Cannot export and reimport RNA secondary structure
1786 via jalview annotation file</li>
1787 <li>Random helix colour palette for colour by annotation
1788 with RNA secondary structure</li>
1789 <li>Mouseover to cDNA from STOP residue in protein
1790 translation doesn't work.</li>
1791 <li>hints when using the select by annotation dialog box</li>
1792 <li>Jmol alignment incorrect if PDB file has alternate CA
1794 <li>FontChooser message dialog appears to hang after
1795 choosing 1pt font</li>
1796 <li>Peptide secondary structure incorrectly imported from
1797 annotation file when annotation display text includes 'e' or
1799 <li>Cannot set colour of new feature type whilst creating
1801 <li>cDNA translation alignment should not be sequence
1802 order dependent</li>
1803 <li>'Show unconserved' doesn't work for lower case
1805 <li>Nucleotide ambiguity codes involving R not recognised</li>
1806 </ul> <em>Deployment and Documentation</em>
1808 <li>Applet example pages appear different to the rest of
1809 www.jalview.org</li>
1810 </ul> <em>Application Known issues</em>
1812 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1813 <li>Misleading message appears after trying to delete
1815 <li>Jalview icon not shown in dock after InstallAnywhere
1816 version launches</li>
1817 <li>Fetching EMBL reference for an RNA sequence results
1818 fails with a sequence mismatch</li>
1819 <li>Corrupted or unreadable alignment display when
1820 scrolling alignment to right</li>
1821 <li>ArrayIndexOutOfBoundsException thrown when remove
1822 empty columns called on alignment with ragged gapped ends</li>
1823 <li>auto calculated alignment annotation rows do not get
1824 placed above or below non-autocalculated rows</li>
1825 <li>Jalview dekstop becomes sluggish at full screen in
1826 ultra-high resolution</li>
1827 <li>Cannot disable consensus calculation independently of
1828 quality and conservation</li>
1829 <li>Mouseover highlighting between cDNA and protein can
1830 become sluggish with more than one splitframe shown</li>
1831 </ul> <em>Applet Known Issues</em>
1833 <li>Core PDB parsing code requires Jmol</li>
1834 <li>Sequence canvas panel goes white when alignment
1835 window is being resized</li>
1841 <td><div align="center">
1842 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1844 <td><em>General</em>
1846 <li>Updated Java code signing certificate donated by
1848 <li>Features and annotation preserved when performing
1849 pairwise alignment</li>
1850 <li>RNA pseudoknot annotation can be
1851 imported/exported/displayed</li>
1852 <li>'colour by annotation' can colour by RNA and
1853 protein secondary structure</li>
1854 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1855 post-hoc with 2.9 release</em>)
1858 </ul> <em>Application</em>
1860 <li>Extract and display secondary structure for sequences
1861 with 3D structures</li>
1862 <li>Support for parsing RNAML</li>
1863 <li>Annotations menu for layout
1865 <li>sort sequence annotation rows by alignment</li>
1866 <li>place sequence annotation above/below alignment
1869 <li>Output in Stockholm format</li>
1870 <li>Internationalisation: improved Spanish (es)
1872 <li>Structure viewer preferences tab</li>
1873 <li>Disorder and Secondary Structure annotation tracks
1874 shared between alignments</li>
1875 <li>UCSF Chimera launch and linked highlighting from
1877 <li>Show/hide all sequence associated annotation rows for
1878 all or current selection</li>
1879 <li>disorder and secondary structure predictions
1880 available as dataset annotation</li>
1881 <li>Per-sequence rna helices colouring</li>
1884 <li>Sequence database accessions imported when fetching
1885 alignments from Rfam</li>
1886 <li>update VARNA version to 3.91</li>
1888 <li>New groovy scripts for exporting aligned positions,
1889 conservation values, and calculating sum of pairs scores.</li>
1890 <li>Command line argument to set default JABAWS server</li>
1891 <li>include installation type in build properties and
1892 console log output</li>
1893 <li>Updated Jalview project format to preserve dataset
1897 <!-- issues resolved --> <em>Application</em>
1899 <li>Distinguish alignment and sequence associated RNA
1900 structure in structure->view->VARNA</li>
1901 <li>Raise dialog box if user deletes all sequences in an
1903 <li>Pressing F1 results in documentation opening twice</li>
1904 <li>Sequence feature tooltip is wrapped</li>
1905 <li>Double click on sequence associated annotation
1906 selects only first column</li>
1907 <li>Redundancy removal doesn't result in unlinked
1908 leaves shown in tree</li>
1909 <li>Undos after several redundancy removals don't undo
1911 <li>Hide sequence doesn't hide associated annotation</li>
1912 <li>User defined colours dialog box too big to fit on
1913 screen and buttons not visible</li>
1914 <li>author list isn't updated if already written to
1915 Jalview properties</li>
1916 <li>Popup menu won't open after retrieving sequence
1918 <li>File open window for associate PDB doesn't open</li>
1919 <li>Left-then-right click on a sequence id opens a
1920 browser search window</li>
1921 <li>Cannot open sequence feature shading/sort popup menu
1922 in feature settings dialog</li>
1923 <li>better tooltip placement for some areas of Jalview
1925 <li>Allow addition of JABAWS Server which doesn't
1926 pass validation</li>
1927 <li>Web services parameters dialog box is too large to
1929 <li>Muscle nucleotide alignment preset obscured by
1931 <li>JABAWS preset submenus don't contain newly
1932 defined user preset</li>
1933 <li>MSA web services warns user if they were launched
1934 with invalid input</li>
1935 <li>Jalview cannot contact DAS Registy when running on
1938 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1939 'Superpose with' submenu not shown when new view
1943 </ul> <!-- <em>Applet</em>
1945 </ul> <em>General</em>
1947 </ul>--> <em>Deployment and Documentation</em>
1949 <li>2G and 1G options in launchApp have no effect on
1950 memory allocation</li>
1951 <li>launchApp service doesn't automatically open
1952 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1954 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1955 InstallAnywhere reports cannot find valid JVM when Java
1956 1.7_055 is available
1958 </ul> <em>Application Known issues</em>
1961 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1962 corrupted or unreadable alignment display when scrolling
1966 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1967 retrieval fails but progress bar continues for DAS retrieval
1968 with large number of ID
1971 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1972 flatfile output of visible region has incorrect sequence
1976 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1977 rna structure consensus doesn't update when secondary
1978 structure tracks are rearranged
1981 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1982 invalid rna structure positional highlighting does not
1983 highlight position of invalid base pairs
1986 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1987 out of memory errors are not raised when saving Jalview
1988 project from alignment window file menu
1991 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1992 Switching to RNA Helices colouring doesn't propagate to
1996 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1997 colour by RNA Helices not enabled when user created
1998 annotation added to alignment
2001 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2002 Jalview icon not shown on dock in Mountain Lion/Webstart
2004 </ul> <em>Applet Known Issues</em>
2007 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2008 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2011 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2012 Jalview and Jmol example not compatible with IE9
2015 <li>Sort by annotation score doesn't reverse order
2021 <td><div align="center">
2022 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2025 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2028 <li>Internationalisation of user interface (usually
2029 called i18n support) and translation for Spanish locale</li>
2030 <li>Define/Undefine group on current selection with
2031 Ctrl-G/Shift Ctrl-G</li>
2032 <li>Improved group creation/removal options in
2033 alignment/sequence Popup menu</li>
2034 <li>Sensible precision for symbol distribution
2035 percentages shown in logo tooltip.</li>
2036 <li>Annotation panel height set according to amount of
2037 annotation when alignment first opened</li>
2038 </ul> <em>Application</em>
2040 <li>Interactive consensus RNA secondary structure
2041 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2042 <li>Select columns containing particular features from
2043 Feature Settings dialog</li>
2044 <li>View all 'representative' PDB structures for selected
2046 <li>Update Jalview project format:
2048 <li>New file extension for Jalview projects '.jvp'</li>
2049 <li>Preserve sequence and annotation dataset (to
2050 store secondary structure annotation,etc)</li>
2051 <li>Per group and alignment annotation and RNA helix
2055 <li>New similarity measures for PCA and Tree calculation
2057 <li>Experimental support for retrieval and viewing of
2058 flanking regions for an alignment</li>
2062 <!-- issues resolved --> <em>Application</em>
2064 <li>logo keeps spinning and status remains at queued or
2065 running after job is cancelled</li>
2066 <li>cannot export features from alignments imported from
2067 Jalview/VAMSAS projects</li>
2068 <li>Buggy slider for web service parameters that take
2070 <li>Newly created RNA secondary structure line doesn't
2071 have 'display all symbols' flag set</li>
2072 <li>T-COFFEE alignment score shading scheme and other
2073 annotation shading not saved in Jalview project</li>
2074 <li>Local file cannot be loaded in freshly downloaded
2076 <li>Jalview icon not shown on dock in Mountain
2078 <li>Load file from desktop file browser fails</li>
2079 <li>Occasional NPE thrown when calculating large trees</li>
2080 <li>Cannot reorder or slide sequences after dragging an
2081 alignment onto desktop</li>
2082 <li>Colour by annotation dialog throws NPE after using
2083 'extract scores' function</li>
2084 <li>Loading/cut'n'pasting an empty file leads to a grey
2085 alignment window</li>
2086 <li>Disorder thresholds rendered incorrectly after
2087 performing IUPred disorder prediction</li>
2088 <li>Multiple group annotated consensus rows shown when
2089 changing 'normalise logo' display setting</li>
2090 <li>Find shows blank dialog after 'finished searching' if
2091 nothing matches query</li>
2092 <li>Null Pointer Exceptions raised when sorting by
2093 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2095 <li>Errors in Jmol console when structures in alignment
2096 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2098 <li>Not all working JABAWS services are shown in
2100 <li>JAVAWS version of Jalview fails to launch with
2101 'invalid literal/length code'</li>
2102 <li>Annotation/RNA Helix colourschemes cannot be applied
2103 to alignment with groups (actually fixed in 2.8.0b1)</li>
2104 <li>RNA Helices and T-Coffee Scores available as default
2107 </ul> <em>Applet</em>
2109 <li>Remove group option is shown even when selection is
2111 <li>Apply to all groups ticked but colourscheme changes
2112 don't affect groups</li>
2113 <li>Documented RNA Helices and T-Coffee Scores as valid
2114 colourscheme name</li>
2115 <li>Annotation labels drawn on sequence IDs when
2116 Annotation panel is not displayed</li>
2117 <li>Increased font size for dropdown menus on OSX and
2118 embedded windows</li>
2119 </ul> <em>Other</em>
2121 <li>Consensus sequence for alignments/groups with a
2122 single sequence were not calculated</li>
2123 <li>annotation files that contain only groups imported as
2124 annotation and junk sequences</li>
2125 <li>Fasta files with sequences containing '*' incorrectly
2126 recognised as PFAM or BLC</li>
2127 <li>conservation/PID slider apply all groups option
2128 doesn't affect background (2.8.0b1)
2130 <li>redundancy highlighting is erratic at 0% and 100%</li>
2131 <li>Remove gapped columns fails for sequences with ragged
2133 <li>AMSA annotation row with leading spaces is not
2134 registered correctly on import</li>
2135 <li>Jalview crashes when selecting PCA analysis for
2136 certain alignments</li>
2137 <li>Opening the colour by annotation dialog for an
2138 existing annotation based 'use original colours'
2139 colourscheme loses original colours setting</li>
2144 <td><div align="center">
2145 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2146 <em>30/1/2014</em></strong>
2150 <li>Trusted certificates for JalviewLite applet and
2151 Jalview Desktop application<br />Certificate was donated by
2152 <a href="https://www.certum.eu">Certum</a> to the Jalview
2153 open source project).
2155 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2156 <li>Output in Stockholm format</li>
2157 <li>Allow import of data from gzipped files</li>
2158 <li>Export/import group and sequence associated line
2159 graph thresholds</li>
2160 <li>Nucleotide substitution matrix that supports RNA and
2161 ambiguity codes</li>
2162 <li>Allow disorder predictions to be made on the current
2163 selection (or visible selection) in the same way that JPred
2165 <li>Groovy scripting for headless Jalview operation</li>
2166 </ul> <em>Other improvements</em>
2168 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2169 <li>COMBINE statement uses current SEQUENCE_REF and
2170 GROUP_REF scope to group annotation rows</li>
2171 <li>Support '' style escaping of quotes in Newick
2173 <li>Group options for JABAWS service by command line name</li>
2174 <li>Empty tooltip shown for JABA service options with a
2175 link but no description</li>
2176 <li>Select primary source when selecting authority in
2177 database fetcher GUI</li>
2178 <li>Add .mfa to FASTA file extensions recognised by
2180 <li>Annotation label tooltip text wrap</li>
2185 <li>Slow scrolling when lots of annotation rows are
2187 <li>Lots of NPE (and slowness) after creating RNA
2188 secondary structure annotation line</li>
2189 <li>Sequence database accessions not imported when
2190 fetching alignments from Rfam</li>
2191 <li>Incorrect SHMR submission for sequences with
2193 <li>View all structures does not always superpose
2195 <li>Option widgets in service parameters not updated to
2196 reflect user or preset settings</li>
2197 <li>Null pointer exceptions for some services without
2198 presets or adjustable parameters</li>
2199 <li>Discover PDB IDs entry in structure menu doesn't
2200 discover PDB xRefs</li>
2201 <li>Exception encountered while trying to retrieve
2202 features with DAS</li>
2203 <li>Lowest value in annotation row isn't coloured
2204 when colour by annotation (per sequence) is coloured</li>
2205 <li>Keyboard mode P jumps to start of gapped region when
2206 residue follows a gap</li>
2207 <li>Jalview appears to hang importing an alignment with
2208 Wrap as default or after enabling Wrap</li>
2209 <li>'Right click to add annotations' message
2210 shown in wrap mode when no annotations present</li>
2211 <li>Disorder predictions fail with NPE if no automatic
2212 annotation already exists on alignment</li>
2213 <li>oninit javascript function should be called after
2214 initialisation completes</li>
2215 <li>Remove redundancy after disorder prediction corrupts
2216 alignment window display</li>
2217 <li>Example annotation file in documentation is invalid</li>
2218 <li>Grouped line graph annotation rows are not exported
2219 to annotation file</li>
2220 <li>Multi-harmony analysis cannot be run when only two
2222 <li>Cannot create multiple groups of line graphs with
2223 several 'combine' statements in annotation file</li>
2224 <li>Pressing return several times causes Number Format
2225 exceptions in keyboard mode</li>
2226 <li>Multi-harmony (SHMMR) method doesn't submit
2227 correct partitions for input data</li>
2228 <li>Translation from DNA to Amino Acids fails</li>
2229 <li>Jalview fail to load newick tree with quoted label</li>
2230 <li>--headless flag isn't understood</li>
2231 <li>ClassCastException when generating EPS in headless
2233 <li>Adjusting sequence-associated shading threshold only
2234 changes one row's threshold</li>
2235 <li>Preferences and Feature settings panel panel
2236 doesn't open</li>
2237 <li>hide consensus histogram also hides conservation and
2238 quality histograms</li>
2243 <td><div align="center">
2244 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2246 <td><em>Application</em>
2248 <li>Support for JABAWS 2.0 Services (AACon alignment
2249 conservation, protein disorder and Clustal Omega)</li>
2250 <li>JABAWS server status indicator in Web Services
2252 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2253 in Jalview alignment window</li>
2254 <li>Updated Jalview build and deploy framework for OSX
2255 mountain lion, windows 7, and 8</li>
2256 <li>Nucleotide substitution matrix for PCA that supports
2257 RNA and ambiguity codes</li>
2259 <li>Improved sequence database retrieval GUI</li>
2260 <li>Support fetching and database reference look up
2261 against multiple DAS sources (Fetch all from in 'fetch db
2263 <li>Jalview project improvements
2265 <li>Store and retrieve the 'belowAlignment'
2266 flag for annotation</li>
2267 <li>calcId attribute to group annotation rows on the
2269 <li>Store AACon calculation settings for a view in
2270 Jalview project</li>
2274 <li>horizontal scrolling gesture support</li>
2275 <li>Visual progress indicator when PCA calculation is
2277 <li>Simpler JABA web services menus</li>
2278 <li>visual indication that web service results are still
2279 being retrieved from server</li>
2280 <li>Serialise the dialogs that are shown when Jalview
2281 starts up for first time</li>
2282 <li>Jalview user agent string for interacting with HTTP
2284 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2286 <li>Examples directory and Groovy library included in
2287 InstallAnywhere distribution</li>
2288 </ul> <em>Applet</em>
2290 <li>RNA alignment and secondary structure annotation
2291 visualization applet example</li>
2292 </ul> <em>General</em>
2294 <li>Normalise option for consensus sequence logo</li>
2295 <li>Reset button in PCA window to return dimensions to
2297 <li>Allow seqspace or Jalview variant of alignment PCA
2299 <li>PCA with either nucleic acid and protein substitution
2301 <li>Allow windows containing HTML reports to be exported
2303 <li>Interactive display and editing of RNA secondary
2304 structure contacts</li>
2305 <li>RNA Helix Alignment Colouring</li>
2306 <li>RNA base pair logo consensus</li>
2307 <li>Parse sequence associated secondary structure
2308 information in Stockholm files</li>
2309 <li>HTML Export database accessions and annotation
2310 information presented in tooltip for sequences</li>
2311 <li>Import secondary structure from LOCARNA clustalw
2312 style RNA alignment files</li>
2313 <li>import and visualise T-COFFEE quality scores for an
2315 <li>'colour by annotation' per sequence option to
2316 shade each sequence according to its associated alignment
2318 <li>New Jalview Logo</li>
2319 </ul> <em>Documentation and Development</em>
2321 <li>documentation for score matrices used in Jalview</li>
2322 <li>New Website!</li>
2324 <td><em>Application</em>
2326 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2327 wsdbfetch REST service</li>
2328 <li>Stop windows being moved outside desktop on OSX</li>
2329 <li>Filetype associations not installed for webstart
2331 <li>Jalview does not always retrieve progress of a JABAWS
2332 job execution in full once it is complete</li>
2333 <li>revise SHMR RSBS definition to ensure alignment is
2334 uploaded via ali_file parameter</li>
2335 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2336 <li>View all structures superposed fails with exception</li>
2337 <li>Jnet job queues forever if a very short sequence is
2338 submitted for prediction</li>
2339 <li>Cut and paste menu not opened when mouse clicked on
2341 <li>Putting fractional value into integer text box in
2342 alignment parameter dialog causes Jalview to hang</li>
2343 <li>Structure view highlighting doesn't work on
2345 <li>View all structures fails with exception shown in
2347 <li>Characters in filename associated with PDBEntry not
2348 escaped in a platform independent way</li>
2349 <li>Jalview desktop fails to launch with exception when
2351 <li>Tree calculation reports 'you must have 2 or more
2352 sequences selected' when selection is empty</li>
2353 <li>Jalview desktop fails to launch with jar signature
2354 failure when java web start temporary file caching is
2356 <li>DAS Sequence retrieval with range qualification
2357 results in sequence xref which includes range qualification</li>
2358 <li>Errors during processing of command line arguments
2359 cause progress bar (JAL-898) to be removed</li>
2360 <li>Replace comma for semi-colon option not disabled for
2361 DAS sources in sequence fetcher</li>
2362 <li>Cannot close news reader when JABAWS server warning
2363 dialog is shown</li>
2364 <li>Option widgets not updated to reflect user settings</li>
2365 <li>Edited sequence not submitted to web service</li>
2366 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2367 <li>InstallAnywhere installer doesn't unpack and run
2368 on OSX Mountain Lion</li>
2369 <li>Annotation panel not given a scroll bar when
2370 sequences with alignment annotation are pasted into the
2372 <li>Sequence associated annotation rows not associated
2373 when loaded from Jalview project</li>
2374 <li>Browser launch fails with NPE on java 1.7</li>
2375 <li>JABAWS alignment marked as finished when job was
2376 cancelled or job failed due to invalid input</li>
2377 <li>NPE with v2.7 example when clicking on Tree
2378 associated with all views</li>
2379 <li>Exceptions when copy/paste sequences with grouped
2380 annotation rows to new window</li>
2381 </ul> <em>Applet</em>
2383 <li>Sequence features are momentarily displayed before
2384 they are hidden using hidefeaturegroups applet parameter</li>
2385 <li>loading features via javascript API automatically
2386 enables feature display</li>
2387 <li>scrollToColumnIn javascript API method doesn't
2389 </ul> <em>General</em>
2391 <li>Redundancy removal fails for rna alignment</li>
2392 <li>PCA calculation fails when sequence has been selected
2393 and then deselected</li>
2394 <li>PCA window shows grey box when first opened on OSX</li>
2395 <li>Letters coloured pink in sequence logo when alignment
2396 coloured with clustalx</li>
2397 <li>Choosing fonts without letter symbols defined causes
2398 exceptions and redraw errors</li>
2399 <li>Initial PCA plot view is not same as manually
2400 reconfigured view</li>
2401 <li>Grouped annotation graph label has incorrect line
2403 <li>Grouped annotation graph label display is corrupted
2404 for lots of labels</li>
2409 <div align="center">
2410 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2413 <td><em>Application</em>
2415 <li>Jalview Desktop News Reader</li>
2416 <li>Tweaked default layout of web services menu</li>
2417 <li>View/alignment association menu to enable user to
2418 easily specify which alignment a multi-structure view takes
2419 its colours/correspondences from</li>
2420 <li>Allow properties file location to be specified as URL</li>
2421 <li>Extend Jalview project to preserve associations
2422 between many alignment views and a single Jmol display</li>
2423 <li>Store annotation row height in Jalview project file</li>
2424 <li>Annotation row column label formatting attributes
2425 stored in project file</li>
2426 <li>Annotation row order for auto-calculated annotation
2427 rows preserved in Jalview project file</li>
2428 <li>Visual progress indication when Jalview state is
2429 saved using Desktop window menu</li>
2430 <li>Visual indication that command line arguments are
2431 still being processed</li>
2432 <li>Groovy script execution from URL</li>
2433 <li>Colour by annotation default min and max colours in
2435 <li>Automatically associate PDB files dragged onto an
2436 alignment with sequences that have high similarity and
2438 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2439 <li>'view structures' option to open many
2440 structures in same window</li>
2441 <li>Sort associated views menu option for tree panel</li>
2442 <li>Group all JABA and non-JABA services for a particular
2443 analysis function in its own submenu</li>
2444 </ul> <em>Applet</em>
2446 <li>Userdefined and autogenerated annotation rows for
2448 <li>Adjustment of alignment annotation pane height</li>
2449 <li>Annotation scrollbar for annotation panel</li>
2450 <li>Drag to reorder annotation rows in annotation panel</li>
2451 <li>'automaticScrolling' parameter</li>
2452 <li>Allow sequences with partial ID string matches to be
2453 annotated from GFF/Jalview features files</li>
2454 <li>Sequence logo annotation row in applet</li>
2455 <li>Absolute paths relative to host server in applet
2456 parameters are treated as such</li>
2457 <li>New in the JalviewLite javascript API:
2459 <li>JalviewLite.js javascript library</li>
2460 <li>Javascript callbacks for
2462 <li>Applet initialisation</li>
2463 <li>Sequence/alignment mouse-overs and selections</li>
2466 <li>scrollTo row and column alignment scrolling
2468 <li>Select sequence/alignment regions from javascript</li>
2469 <li>javascript structure viewer harness to pass
2470 messages between Jmol and Jalview when running as
2471 distinct applets</li>
2472 <li>sortBy method</li>
2473 <li>Set of applet and application examples shipped
2474 with documentation</li>
2475 <li>New example to demonstrate JalviewLite and Jmol
2476 javascript message exchange</li>
2478 </ul> <em>General</em>
2480 <li>Enable Jmol displays to be associated with multiple
2481 multiple alignments</li>
2482 <li>Option to automatically sort alignment with new tree</li>
2483 <li>User configurable link to enable redirects to a
2484 www.Jalview.org mirror</li>
2485 <li>Jmol colours option for Jmol displays</li>
2486 <li>Configurable newline string when writing alignment
2487 and other flat files</li>
2488 <li>Allow alignment annotation description lines to
2489 contain html tags</li>
2490 </ul> <em>Documentation and Development</em>
2492 <li>Add groovy test harness for bulk load testing to
2494 <li>Groovy script to load and align a set of sequences
2495 using a web service before displaying the result in the
2496 Jalview desktop</li>
2497 <li>Restructured javascript and applet api documentation</li>
2498 <li>Ant target to publish example html files with applet
2500 <li>Netbeans project for building Jalview from source</li>
2501 <li>ant task to create online javadoc for Jalview source</li>
2503 <td><em>Application</em>
2505 <li>User defined colourscheme throws exception when
2506 current built in colourscheme is saved as new scheme</li>
2507 <li>AlignFrame->Save in application pops up save
2508 dialog for valid filename/format</li>
2509 <li>Cannot view associated structure for UniProt sequence</li>
2510 <li>PDB file association breaks for UniProt sequence
2512 <li>Associate PDB from file dialog does not tell you
2513 which sequence is to be associated with the file</li>
2514 <li>Find All raises null pointer exception when query
2515 only matches sequence IDs</li>
2516 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2517 <li>Jalview project with Jmol views created with Jalview
2518 2.4 cannot be loaded</li>
2519 <li>Filetype associations not installed for webstart
2521 <li>Two or more chains in a single PDB file associated
2522 with sequences in different alignments do not get coloured
2523 by their associated sequence</li>
2524 <li>Visibility status of autocalculated annotation row
2525 not preserved when project is loaded</li>
2526 <li>Annotation row height and visibility attributes not
2527 stored in Jalview project</li>
2528 <li>Tree bootstraps are not preserved when saved as a
2529 Jalview project</li>
2530 <li>Envision2 workflow tooltips are corrupted</li>
2531 <li>Enabling show group conservation also enables colour
2532 by conservation</li>
2533 <li>Duplicate group associated conservation or consensus
2534 created on new view</li>
2535 <li>Annotation scrollbar not displayed after 'show
2536 all hidden annotation rows' option selected</li>
2537 <li>Alignment quality not updated after alignment
2538 annotation row is hidden then shown</li>
2539 <li>Preserve colouring of structures coloured by
2540 sequences in pre Jalview 2.7 projects</li>
2541 <li>Web service job parameter dialog is not laid out
2543 <li>Web services menu not refreshed after 'reset
2544 services' button is pressed in preferences</li>
2545 <li>Annotation off by one in Jalview v2_3 example project</li>
2546 <li>Structures imported from file and saved in project
2547 get name like jalview_pdb1234.txt when reloaded</li>
2548 <li>Jalview does not always retrieve progress of a JABAWS
2549 job execution in full once it is complete</li>
2550 </ul> <em>Applet</em>
2552 <li>Alignment height set incorrectly when lots of
2553 annotation rows are displayed</li>
2554 <li>Relative URLs in feature HTML text not resolved to
2556 <li>View follows highlighting does not work for positions
2558 <li><= shown as = in tooltip</li>
2559 <li>Export features raises exception when no features
2561 <li>Separator string used for serialising lists of IDs
2562 for javascript api is modified when separator string
2563 provided as parameter</li>
2564 <li>Null pointer exception when selecting tree leaves for
2565 alignment with no existing selection</li>
2566 <li>Relative URLs for datasources assumed to be relative
2567 to applet's codebase</li>
2568 <li>Status bar not updated after finished searching and
2569 search wraps around to first result</li>
2570 <li>StructureSelectionManager instance shared between
2571 several Jalview applets causes race conditions and memory
2573 <li>Hover tooltip and mouseover of position on structure
2574 not sent from Jmol in applet</li>
2575 <li>Certain sequences of javascript method calls to
2576 applet API fatally hang browser</li>
2577 </ul> <em>General</em>
2579 <li>View follows structure mouseover scrolls beyond
2580 position with wrapped view and hidden regions</li>
2581 <li>Find sequence position moves to wrong residue
2582 with/without hidden columns</li>
2583 <li>Sequence length given in alignment properties window
2585 <li>InvalidNumberFormat exceptions thrown when trying to
2586 import PDB like structure files</li>
2587 <li>Positional search results are only highlighted
2588 between user-supplied sequence start/end bounds</li>
2589 <li>End attribute of sequence is not validated</li>
2590 <li>Find dialog only finds first sequence containing a
2591 given sequence position</li>
2592 <li>Sequence numbering not preserved in MSF alignment
2594 <li>Jalview PDB file reader does not extract sequence
2595 from nucleotide chains correctly</li>
2596 <li>Structure colours not updated when tree partition
2597 changed in alignment</li>
2598 <li>Sequence associated secondary structure not correctly
2599 parsed in interleaved stockholm</li>
2600 <li>Colour by annotation dialog does not restore current
2602 <li>Hiding (nearly) all sequences doesn't work
2604 <li>Sequences containing lowercase letters are not
2605 properly associated with their pdb files</li>
2606 </ul> <em>Documentation and Development</em>
2608 <li>schemas/JalviewWsParamSet.xsd corrupted by
2609 ApplyCopyright tool</li>
2614 <div align="center">
2615 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2618 <td><em>Application</em>
2620 <li>New warning dialog when the Jalview Desktop cannot
2621 contact web services</li>
2622 <li>JABA service parameters for a preset are shown in
2623 service job window</li>
2624 <li>JABA Service menu entries reworded</li>
2628 <li>Modeller PIR IO broken - cannot correctly import a
2629 pir file emitted by Jalview</li>
2630 <li>Existing feature settings transferred to new
2631 alignment view created from cut'n'paste</li>
2632 <li>Improved test for mixed amino/nucleotide chains when
2633 parsing PDB files</li>
2634 <li>Consensus and conservation annotation rows
2635 occasionally become blank for all new windows</li>
2636 <li>Exception raised when right clicking above sequences
2637 in wrapped view mode</li>
2638 </ul> <em>Application</em>
2640 <li>multiple multiply aligned structure views cause cpu
2641 usage to hit 100% and computer to hang</li>
2642 <li>Web Service parameter layout breaks for long user
2643 parameter names</li>
2644 <li>Jaba service discovery hangs desktop if Jaba server
2651 <div align="center">
2652 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2655 <td><em>Application</em>
2657 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2658 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2661 <li>Web Services preference tab</li>
2662 <li>Analysis parameters dialog box and user defined
2664 <li>Improved speed and layout of Envision2 service menu</li>
2665 <li>Superpose structures using associated sequence
2667 <li>Export coordinates and projection as CSV from PCA
2669 </ul> <em>Applet</em>
2671 <li>enable javascript: execution by the applet via the
2672 link out mechanism</li>
2673 </ul> <em>Other</em>
2675 <li>Updated the Jmol Jalview interface to work with Jmol
2677 <li>The Jalview Desktop and JalviewLite applet now
2678 require Java 1.5</li>
2679 <li>Allow Jalview feature colour specification for GFF
2680 sequence annotation files</li>
2681 <li>New 'colour by label' keword in Jalview feature file
2682 type colour specification</li>
2683 <li>New Jalview Desktop Groovy API method that allows a
2684 script to check if it being run in an interactive session or
2685 in a batch operation from the Jalview command line</li>
2689 <li>clustalx colourscheme colours Ds preferentially when
2690 both D+E are present in over 50% of the column</li>
2691 </ul> <em>Application</em>
2693 <li>typo in AlignmentFrame->View->Hide->all but
2694 selected Regions menu item</li>
2695 <li>sequence fetcher replaces ',' for ';' when the ',' is
2696 part of a valid accession ID</li>
2697 <li>fatal OOM if object retrieved by sequence fetcher
2698 runs out of memory</li>
2699 <li>unhandled Out of Memory Error when viewing pca
2700 analysis results</li>
2701 <li>InstallAnywhere builds fail to launch on OS X java
2702 10.5 update 4 (due to apple Java 1.6 update)</li>
2703 <li>Installanywhere Jalview silently fails to launch</li>
2704 </ul> <em>Applet</em>
2706 <li>Jalview.getFeatureGroups() raises an
2707 ArrayIndexOutOfBoundsException if no feature groups are
2714 <div align="center">
2715 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2721 <li>Alignment prettyprinter doesn't cope with long
2723 <li>clustalx colourscheme colours Ds preferentially when
2724 both D+E are present in over 50% of the column</li>
2725 <li>nucleic acid structures retrieved from PDB do not
2726 import correctly</li>
2727 <li>More columns get selected than were clicked on when a
2728 number of columns are hidden</li>
2729 <li>annotation label popup menu not providing correct
2730 add/hide/show options when rows are hidden or none are
2732 <li>Stockholm format shown in list of readable formats,
2733 and parser copes better with alignments from RFAM.</li>
2734 <li>CSV output of consensus only includes the percentage
2735 of all symbols if sequence logo display is enabled</li>
2737 </ul> <em>Applet</em>
2739 <li>annotation panel disappears when annotation is
2741 </ul> <em>Application</em>
2743 <li>Alignment view not redrawn properly when new
2744 alignment opened where annotation panel is visible but no
2745 annotations are present on alignment</li>
2746 <li>pasted region containing hidden columns is
2747 incorrectly displayed in new alignment window</li>
2748 <li>Jalview slow to complete operations when stdout is
2749 flooded (fix is to close the Jalview console)</li>
2750 <li>typo in AlignmentFrame->View->Hide->all but
2751 selected Rregions menu item.</li>
2752 <li>inconsistent group submenu and Format submenu entry
2753 'Un' or 'Non'conserved</li>
2754 <li>Sequence feature settings are being shared by
2755 multiple distinct alignments</li>
2756 <li>group annotation not recreated when tree partition is
2758 <li>double click on group annotation to select sequences
2759 does not propagate to associated trees</li>
2760 <li>Mac OSX specific issues:
2762 <li>exception raised when mouse clicked on desktop
2763 window background</li>
2764 <li>Desktop menu placed on menu bar and application
2765 name set correctly</li>
2766 <li>sequence feature settings not wide enough for the
2767 save feature colourscheme button</li>
2776 <div align="center">
2777 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2780 <td><em>New Capabilities</em>
2782 <li>URL links generated from description line for
2783 regular-expression based URL links (applet and application)
2785 <li>Non-positional feature URL links are shown in link
2787 <li>Linked viewing of nucleic acid sequences and
2789 <li>Automatic Scrolling option in View menu to display
2790 the currently highlighted region of an alignment.</li>
2791 <li>Order an alignment by sequence length, or using the
2792 average score or total feature count for each sequence.</li>
2793 <li>Shading features by score or associated description</li>
2794 <li>Subdivide alignment and groups based on identity of
2795 selected subsequence (Make Groups from Selection).</li>
2796 <li>New hide/show options including Shift+Control+H to
2797 hide everything but the currently selected region.</li>
2798 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2799 </ul> <em>Application</em>
2801 <li>Fetch DB References capabilities and UI expanded to
2802 support retrieval from DAS sequence sources</li>
2803 <li>Local DAS Sequence sources can be added via the
2804 command line or via the Add local source dialog box.</li>
2805 <li>DAS Dbref and DbxRef feature types are parsed as
2806 database references and protein_name is parsed as
2807 description line (BioSapiens terms).</li>
2808 <li>Enable or disable non-positional feature and database
2809 references in sequence ID tooltip from View menu in
2811 <!-- <li>New hidden columns and rows and representatives capabilities
2812 in annotations file (in progress - not yet fully implemented)</li> -->
2813 <li>Group-associated consensus, sequence logos and
2814 conservation plots</li>
2815 <li>Symbol distributions for each column can be exported
2816 and visualized as sequence logos</li>
2817 <li>Optionally scale multi-character column labels to fit
2818 within each column of annotation row<!-- todo for applet -->
2820 <li>Optional automatic sort of associated alignment view
2821 when a new tree is opened.</li>
2822 <li>Jalview Java Console</li>
2823 <li>Better placement of desktop window when moving
2824 between different screens.</li>
2825 <li>New preference items for sequence ID tooltip and
2826 consensus annotation</li>
2827 <li>Client to submit sequences and IDs to Envision2
2829 <li><em>Vamsas Capabilities</em>
2831 <li>Improved VAMSAS synchronization (Jalview archive
2832 used to preserve views, structures, and tree display
2834 <li>Import of vamsas documents from disk or URL via
2836 <li>Sharing of selected regions between views and
2837 with other VAMSAS applications (Experimental feature!)</li>
2838 <li>Updated API to VAMSAS version 0.2</li>
2840 </ul> <em>Applet</em>
2842 <li>Middle button resizes annotation row height</li>
2845 <li>sortByTree (true/false) - automatically sort the
2846 associated alignment view by the tree when a new tree is
2848 <li>showTreeBootstraps (true/false) - show or hide
2849 branch bootstraps (default is to show them if available)</li>
2850 <li>showTreeDistances (true/false) - show or hide
2851 branch lengths (default is to show them if available)</li>
2852 <li>showUnlinkedTreeNodes (true/false) - indicate if
2853 unassociated nodes should be highlighted in the tree
2855 <li>heightScale and widthScale (1.0 or more) -
2856 increase the height or width of a cell in the alignment
2857 grid relative to the current font size.</li>
2860 <li>Non-positional features displayed in sequence ID
2862 </ul> <em>Other</em>
2864 <li>Features format: graduated colour definitions and
2865 specification of feature scores</li>
2866 <li>Alignment Annotations format: new keywords for group
2867 associated annotation (GROUP_REF) and annotation row display
2868 properties (ROW_PROPERTIES)</li>
2869 <li>XML formats extended to support graduated feature
2870 colourschemes, group associated annotation, and profile
2871 visualization settings.</li></td>
2874 <li>Source field in GFF files parsed as feature source
2875 rather than description</li>
2876 <li>Non-positional features are now included in sequence
2877 feature and gff files (controlled via non-positional feature
2878 visibility in tooltip).</li>
2879 <li>URL links generated for all feature links (bugfix)</li>
2880 <li>Added URL embedding instructions to features file
2882 <li>Codons containing ambiguous nucleotides translated as
2883 'X' in peptide product</li>
2884 <li>Match case switch in find dialog box works for both
2885 sequence ID and sequence string and query strings do not
2886 have to be in upper case to match case-insensitively.</li>
2887 <li>AMSA files only contain first column of
2888 multi-character column annotation labels</li>
2889 <li>Jalview Annotation File generation/parsing consistent
2890 with documentation (e.g. Stockholm annotation can be
2891 exported and re-imported)</li>
2892 <li>PDB files without embedded PDB IDs given a friendly
2894 <li>Find incrementally searches ID string matches as well
2895 as subsequence matches, and correctly reports total number
2899 <li>Better handling of exceptions during sequence
2901 <li>Dasobert generated non-positional feature URL
2902 link text excludes the start_end suffix</li>
2903 <li>DAS feature and source retrieval buttons disabled
2904 when fetch or registry operations in progress.</li>
2905 <li>PDB files retrieved from URLs are cached properly</li>
2906 <li>Sequence description lines properly shared via
2908 <li>Sequence fetcher fetches multiple records for all
2910 <li>Ensured that command line das feature retrieval
2911 completes before alignment figures are generated.</li>
2912 <li>Reduced time taken when opening file browser for
2914 <li>isAligned check prior to calculating tree, PCA or
2915 submitting an MSA to JNet now excludes hidden sequences.</li>
2916 <li>User defined group colours properly recovered
2917 from Jalview projects.</li>
2926 <div align="center">
2927 <strong>2.4.0.b2</strong><br> 28/10/2009
2932 <li>Experimental support for google analytics usage
2934 <li>Jalview privacy settings (user preferences and docs).</li>
2939 <li>Race condition in applet preventing startup in
2941 <li>Exception when feature created from selection beyond
2942 length of sequence.</li>
2943 <li>Allow synthetic PDB files to be imported gracefully</li>
2944 <li>Sequence associated annotation rows associate with
2945 all sequences with a given id</li>
2946 <li>Find function matches case-insensitively for sequence
2947 ID string searches</li>
2948 <li>Non-standard characters do not cause pairwise
2949 alignment to fail with exception</li>
2950 </ul> <em>Application Issues</em>
2952 <li>Sequences are now validated against EMBL database</li>
2953 <li>Sequence fetcher fetches multiple records for all
2955 </ul> <em>InstallAnywhere Issues</em>
2957 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2958 issue with installAnywhere mechanism)</li>
2959 <li>Command line launching of JARs from InstallAnywhere
2960 version (java class versioning error fixed)</li>
2967 <div align="center">
2968 <strong>2.4</strong><br> 27/8/2008
2971 <td><em>User Interface</em>
2973 <li>Linked highlighting of codon and amino acid from
2974 translation and protein products</li>
2975 <li>Linked highlighting of structure associated with
2976 residue mapping to codon position</li>
2977 <li>Sequence Fetcher provides example accession numbers
2978 and 'clear' button</li>
2979 <li>MemoryMonitor added as an option under Desktop's
2981 <li>Extract score function to parse whitespace separated
2982 numeric data in description line</li>
2983 <li>Column labels in alignment annotation can be centred.</li>
2984 <li>Tooltip for sequence associated annotation give name
2986 </ul> <em>Web Services and URL fetching</em>
2988 <li>JPred3 web service</li>
2989 <li>Prototype sequence search client (no public services
2991 <li>Fetch either seed alignment or full alignment from
2993 <li>URL Links created for matching database cross
2994 references as well as sequence ID</li>
2995 <li>URL Links can be created using regular-expressions</li>
2996 </ul> <em>Sequence Database Connectivity</em>
2998 <li>Retrieval of cross-referenced sequences from other
3000 <li>Generalised database reference retrieval and
3001 validation to all fetchable databases</li>
3002 <li>Fetch sequences from DAS sources supporting the
3003 sequence command</li>
3004 </ul> <em>Import and Export</em>
3005 <li>export annotation rows as CSV for spreadsheet import</li>
3006 <li>Jalview projects record alignment dataset associations,
3007 EMBL products, and cDNA sequence mappings</li>
3008 <li>Sequence Group colour can be specified in Annotation
3010 <li>Ad-hoc colouring of group in Annotation File using RGB
3011 triplet as name of colourscheme</li>
3012 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3014 <li>treenode binding for VAMSAS tree exchange</li>
3015 <li>local editing and update of sequences in VAMSAS
3016 alignments (experimental)</li>
3017 <li>Create new or select existing session to join</li>
3018 <li>load and save of vamsas documents</li>
3019 </ul> <em>Application command line</em>
3021 <li>-tree parameter to open trees (introduced for passing
3023 <li>-fetchfrom command line argument to specify nicknames
3024 of DAS servers to query for alignment features</li>
3025 <li>-dasserver command line argument to add new servers
3026 that are also automatically queried for features</li>
3027 <li>-groovy command line argument executes a given groovy
3028 script after all input data has been loaded and parsed</li>
3029 </ul> <em>Applet-Application data exchange</em>
3031 <li>Trees passed as applet parameters can be passed to
3032 application (when using "View in full
3033 application")</li>
3034 </ul> <em>Applet Parameters</em>
3036 <li>feature group display control parameter</li>
3037 <li>debug parameter</li>
3038 <li>showbutton parameter</li>
3039 </ul> <em>Applet API methods</em>
3041 <li>newView public method</li>
3042 <li>Window (current view) specific get/set public methods</li>
3043 <li>Feature display control methods</li>
3044 <li>get list of currently selected sequences</li>
3045 </ul> <em>New Jalview distribution features</em>
3047 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3048 <li>RELEASE file gives build properties for the latest
3049 Jalview release.</li>
3050 <li>Java 1.1 Applet build made easier and donotobfuscate
3051 property controls execution of obfuscator</li>
3052 <li>Build target for generating source distribution</li>
3053 <li>Debug flag for javacc</li>
3054 <li>.jalview_properties file is documented (slightly) in
3055 jalview.bin.Cache</li>
3056 <li>Continuous Build Integration for stable and
3057 development version of Application, Applet and source
3062 <li>selected region output includes visible annotations
3063 (for certain formats)</li>
3064 <li>edit label/displaychar contains existing label/char
3066 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3067 <li>shorter peptide product names from EMBL records</li>
3068 <li>Newick string generator makes compact representations</li>
3069 <li>bootstrap values parsed correctly for tree files with
3071 <li>pathological filechooser bug avoided by not allowing
3072 filenames containing a ':'</li>
3073 <li>Fixed exception when parsing GFF files containing
3074 global sequence features</li>
3075 <li>Alignment datasets are finalized only when number of
3076 references from alignment sequences goes to zero</li>
3077 <li>Close of tree branch colour box without colour
3078 selection causes cascading exceptions</li>
3079 <li>occasional negative imgwidth exceptions</li>
3080 <li>better reporting of non-fatal warnings to user when
3081 file parsing fails.</li>
3082 <li>Save works when Jalview project is default format</li>
3083 <li>Save as dialog opened if current alignment format is
3084 not a valid output format</li>
3085 <li>UniProt canonical names introduced for both das and
3087 <li>Histidine should be midblue (not pink!) in Zappo</li>
3088 <li>error messages passed up and output when data read
3090 <li>edit undo recovers previous dataset sequence when
3091 sequence is edited</li>
3092 <li>allow PDB files without pdb ID HEADER lines (like
3093 those generated by MODELLER) to be read in properly</li>
3094 <li>allow reading of JPred concise files as a normal
3096 <li>Stockholm annotation parsing and alignment properties
3097 import fixed for PFAM records</li>
3098 <li>Structure view windows have correct name in Desktop
3100 <li>annotation consisting of sequence associated scores
3101 can be read and written correctly to annotation file</li>
3102 <li>Aligned cDNA translation to aligned peptide works
3104 <li>Fixed display of hidden sequence markers and
3105 non-italic font for representatives in Applet</li>
3106 <li>Applet Menus are always embedded in applet window on
3108 <li>Newly shown features appear at top of stack (in
3110 <li>Annotations added via parameter not drawn properly
3111 due to null pointer exceptions</li>
3112 <li>Secondary structure lines are drawn starting from
3113 first column of alignment</li>
3114 <li>UniProt XML import updated for new schema release in
3116 <li>Sequence feature to sequence ID match for Features
3117 file is case-insensitive</li>
3118 <li>Sequence features read from Features file appended to
3119 all sequences with matching IDs</li>
3120 <li>PDB structure coloured correctly for associated views
3121 containing a sub-sequence</li>
3122 <li>PDB files can be retrieved by applet from Jar files</li>
3123 <li>feature and annotation file applet parameters
3124 referring to different directories are retrieved correctly</li>
3125 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3126 <li>Fixed application hang whilst waiting for
3127 splash-screen version check to complete</li>
3128 <li>Applet properly URLencodes input parameter values
3129 when passing them to the launchApp service</li>
3130 <li>display name and local features preserved in results
3131 retrieved from web service</li>
3132 <li>Visual delay indication for sequence retrieval and
3133 sequence fetcher initialisation</li>
3134 <li>updated Application to use DAS 1.53e version of
3135 dasobert DAS client</li>
3136 <li>Re-instated Full AMSA support and .amsa file
3138 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3146 <div align="center">
3147 <strong>2.3</strong><br> 9/5/07
3152 <li>Jmol 11.0.2 integration</li>
3153 <li>PDB views stored in Jalview XML files</li>
3154 <li>Slide sequences</li>
3155 <li>Edit sequence in place</li>
3156 <li>EMBL CDS features</li>
3157 <li>DAS Feature mapping</li>
3158 <li>Feature ordering</li>
3159 <li>Alignment Properties</li>
3160 <li>Annotation Scores</li>
3161 <li>Sort by scores</li>
3162 <li>Feature/annotation editing in applet</li>
3167 <li>Headless state operation in 2.2.1</li>
3168 <li>Incorrect and unstable DNA pairwise alignment</li>
3169 <li>Cut and paste of sequences with annotation</li>
3170 <li>Feature group display state in XML</li>
3171 <li>Feature ordering in XML</li>
3172 <li>blc file iteration selection using filename # suffix</li>
3173 <li>Stockholm alignment properties</li>
3174 <li>Stockhom alignment secondary structure annotation</li>
3175 <li>2.2.1 applet had no feature transparency</li>
3176 <li>Number pad keys can be used in cursor mode</li>
3177 <li>Structure Viewer mirror image resolved</li>
3184 <div align="center">
3185 <strong>2.2.1</strong><br> 12/2/07
3190 <li>Non standard characters can be read and displayed
3191 <li>Annotations/Features can be imported/exported to the
3193 <li>Applet allows editing of sequence/annotation/group
3194 name & description
3195 <li>Preference setting to display sequence name in
3197 <li>Annotation file format extended to allow
3198 Sequence_groups to be defined
3199 <li>Default opening of alignment overview panel can be
3200 specified in preferences
3201 <li>PDB residue numbering annotation added to associated
3207 <li>Applet crash under certain Linux OS with Java 1.6
3209 <li>Annotation file export / import bugs fixed
3210 <li>PNG / EPS image output bugs fixed
3216 <div align="center">
3217 <strong>2.2</strong><br> 27/11/06
3222 <li>Multiple views on alignment
3223 <li>Sequence feature editing
3224 <li>"Reload" alignment
3225 <li>"Save" to current filename
3226 <li>Background dependent text colour
3227 <li>Right align sequence ids
3228 <li>User-defined lower case residue colours
3231 <li>Menu item accelerator keys
3232 <li>Control-V pastes to current alignment
3233 <li>Cancel button for DAS Feature Fetching
3234 <li>PCA and PDB Viewers zoom via mouse roller
3235 <li>User-defined sub-tree colours and sub-tree selection
3237 <li>'New Window' button on the 'Output to Text box'
3242 <li>New memory efficient Undo/Redo System
3243 <li>Optimised symbol lookups and conservation/consensus
3245 <li>Region Conservation/Consensus recalculated after
3247 <li>Fixed Remove Empty Columns Bug (empty columns at end
3249 <li>Slowed DAS Feature Fetching for increased robustness.
3251 <li>Made angle brackets in ASCII feature descriptions
3253 <li>Re-instated Zoom function for PCA
3254 <li>Sequence descriptions conserved in web service
3256 <li>UniProt ID discoverer uses any word separated by
3258 <li>WsDbFetch query/result association resolved
3259 <li>Tree leaf to sequence mapping improved
3260 <li>Smooth fonts switch moved to FontChooser dialog box.
3267 <div align="center">
3268 <strong>2.1.1</strong><br> 12/9/06
3273 <li>Copy consensus sequence to clipboard</li>
3278 <li>Image output - rightmost residues are rendered if
3279 sequence id panel has been resized</li>
3280 <li>Image output - all offscreen group boundaries are
3282 <li>Annotation files with sequence references - all
3283 elements in file are relative to sequence position</li>
3284 <li>Mac Applet users can use Alt key for group editing</li>
3290 <div align="center">
3291 <strong>2.1</strong><br> 22/8/06
3296 <li>MAFFT Multiple Alignment in default Web Service list</li>
3297 <li>DAS Feature fetching</li>
3298 <li>Hide sequences and columns</li>
3299 <li>Export Annotations and Features</li>
3300 <li>GFF file reading / writing</li>
3301 <li>Associate structures with sequences from local PDB
3303 <li>Add sequences to exisiting alignment</li>
3304 <li>Recently opened files / URL lists</li>
3305 <li>Applet can launch the full application</li>
3306 <li>Applet has transparency for features (Java 1.2
3308 <li>Applet has user defined colours parameter</li>
3309 <li>Applet can load sequences from parameter
3310 "sequence<em>x</em>"
3316 <li>Redundancy Panel reinstalled in the Applet</li>
3317 <li>Monospaced font - EPS / rescaling bug fixed</li>
3318 <li>Annotation files with sequence references bug fixed</li>
3324 <div align="center">
3325 <strong>2.08.1</strong><br> 2/5/06
3330 <li>Change case of selected region from Popup menu</li>
3331 <li>Choose to match case when searching</li>
3332 <li>Middle mouse button and mouse movement can compress /
3333 expand the visible width and height of the alignment</li>
3338 <li>Annotation Panel displays complete JNet results</li>
3344 <div align="center">
3345 <strong>2.08b</strong><br> 18/4/06
3351 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3352 <li>Righthand label on wrapped alignments shows correct
3359 <div align="center">
3360 <strong>2.08</strong><br> 10/4/06
3365 <li>Editing can be locked to the selection area</li>
3366 <li>Keyboard editing</li>
3367 <li>Create sequence features from searches</li>
3368 <li>Precalculated annotations can be loaded onto
3370 <li>Features file allows grouping of features</li>
3371 <li>Annotation Colouring scheme added</li>
3372 <li>Smooth fonts off by default - Faster rendering</li>
3373 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3378 <li>Drag & Drop fixed on Linux</li>
3379 <li>Jalview Archive file faster to load/save, sequence
3380 descriptions saved.</li>
3386 <div align="center">
3387 <strong>2.07</strong><br> 12/12/05
3392 <li>PDB Structure Viewer enhanced</li>
3393 <li>Sequence Feature retrieval and display enhanced</li>
3394 <li>Choose to output sequence start-end after sequence
3395 name for file output</li>
3396 <li>Sequence Fetcher WSDBFetch@EBI</li>
3397 <li>Applet can read feature files, PDB files and can be
3398 used for HTML form input</li>
3403 <li>HTML output writes groups and features</li>
3404 <li>Group editing is Control and mouse click</li>
3405 <li>File IO bugs</li>
3411 <div align="center">
3412 <strong>2.06</strong><br> 28/9/05
3417 <li>View annotations in wrapped mode</li>
3418 <li>More options for PCA viewer</li>
3423 <li>GUI bugs resolved</li>
3424 <li>Runs with -nodisplay from command line</li>
3430 <div align="center">
3431 <strong>2.05b</strong><br> 15/9/05
3436 <li>Choose EPS export as lineart or text</li>
3437 <li>Jar files are executable</li>
3438 <li>Can read in Uracil - maps to unknown residue</li>
3443 <li>Known OutOfMemory errors give warning message</li>
3444 <li>Overview window calculated more efficiently</li>
3445 <li>Several GUI bugs resolved</li>
3451 <div align="center">
3452 <strong>2.05</strong><br> 30/8/05
3457 <li>Edit and annotate in "Wrapped" view</li>
3462 <li>Several GUI bugs resolved</li>
3468 <div align="center">
3469 <strong>2.04</strong><br> 24/8/05
3474 <li>Hold down mouse wheel & scroll to change font
3480 <li>Improved JPred client reliability</li>
3481 <li>Improved loading of Jalview files</li>
3487 <div align="center">
3488 <strong>2.03</strong><br> 18/8/05
3493 <li>Set Proxy server name and port in preferences</li>
3494 <li>Multiple URL links from sequence ids</li>
3495 <li>User Defined Colours can have a scheme name and added
3497 <li>Choose to ignore gaps in consensus calculation</li>
3498 <li>Unix users can set default web browser</li>
3499 <li>Runs without GUI for batch processing</li>
3500 <li>Dynamically generated Web Service Menus</li>
3505 <li>InstallAnywhere download for Sparc Solaris</li>
3511 <div align="center">
3512 <strong>2.02</strong><br> 18/7/05
3518 <li>Copy & Paste order of sequences maintains
3519 alignment order.</li>
3525 <div align="center">
3526 <strong>2.01</strong><br> 12/7/05
3531 <li>Use delete key for deleting selection.</li>
3532 <li>Use Mouse wheel to scroll sequences.</li>
3533 <li>Help file updated to describe how to add alignment
3535 <li>Version and build date written to build properties
3537 <li>InstallAnywhere installation will check for updates
3538 at launch of Jalview.</li>
3543 <li>Delete gaps bug fixed.</li>
3544 <li>FileChooser sorts columns.</li>
3545 <li>Can remove groups one by one.</li>
3546 <li>Filechooser icons installed.</li>
3547 <li>Finder ignores return character when searching.
3548 Return key will initiate a search.<br>
3555 <div align="center">
3556 <strong>2.0</strong><br> 20/6/05
3561 <li>New codebase</li>