3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.3">2.10.3</a><br />
74 <em>17/11/2017</em></strong>
77 <td><div align="left">
81 <!-- JAL-2446 -->Faster and more efficient management and
82 rendering of sequence features
85 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
86 429 rate limit request hander
89 <!-- JAL-2773 -->Structure views don't get updated unless
90 their colours have changed
92 <li><!-- JAL-2495 -->All linked sequences are highlighted for a structure mousover (Jmol) or selection (Chimera)</li>
93 <li><!-- JAL-2790 -->'Cancel' button in progress bar for JABAWS AACon, RNAAliFold and Disorder prediction jobs
96 <li><!-- JAL-2617 -->Stop codons are excluded in CDS/Protein view from Ensembl locus cross-references</li>
97 <li><!-- JAL-2685 -->Start/End limits are shown in Pairwise Alignment report</li>
98 <li><!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch' feature can be disabled</li>
99 <li><!-- JAL-2810 -->Retrieve IDs tab added for UniProt and PDB easier retrieval of sequences for lists of IDs</li>
100 <li><!-- JAL-2758 -->Short names for sequences retrieved from Uniprot</li>
104 <li>Groovy interpreter updated to 2.4.12</li>
105 <li>Example groovy script for generating a matrix of percent identity scores for current alignment.</li>
107 <em>Testing and Deployment</em>
109 <li><!-- JAL-2727 -->Test to catch memory leaks in Jalview UI</li>
113 <td><div align="left">
116 <li><!-- JAL-2643 -->Pressing tab after updating the colour threshold text field doesn't trigger an update to the alignment view</li>
117 <li><!-- JAL-2682 -->Race condition when parsing sequence ID strings in parallel</li>
118 <li><!-- JAL-2608 -->Overview windows are also closed when alignment window is closed</li>
119 <li><!-- JAL-2548 -->Export of features doesn't always respect group visibility</li>
120 <li><!-- JAL-2831 -->Jumping from column 1 to column 100,000 takes a long time in Cursor mode</li>
124 <li><!-- JAL-2777 -->Structures with whitespace chainCode cannot be viewed in Chimera</li>
125 <li><!-- JAL-2728 -->Protein annotation panel too high in CDS/Protein view
127 <li><!-- JAL-2757 -->Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs
129 <li><!-- JAL-2253 -->Slow EnsemblGenome ID lookup</li>
130 <li><!-- JAL-2529 -->Revised Ensembl REST API CDNA query</li>
131 <li><!-- JAL-2739 -->Hidden column marker in last column not rendered when switching back from Wrapped to normal view</li>
132 <li><!-- JAL-2768 -->Annotation display corrupted when scrolling right in unwapped alignment view</li>
133 <li><!-- JAL-2542 -->Existing features on subsequence incorrectly relocated when full sequence retrieved from database</li>
134 <li><!-- JAL-2733 -->Last reported memory still shown when Desktop->Show Memory is unticked (OSX only)</li>
135 <li><!-- JAL-2658 -->Amend Features dialog doesn't allow features of same type and group to be selected for amending</li>
136 <li><!-- JAL-2524 -->Jalview becomes sluggish in wide alignments when hidden columns are present</li>
137 <li><!-- JAL-2392 -->Jalview freezes when loading and displaying several structures</li>
138 <li><!-- JAL-2732 -->Black outlines left after resizing or moving a window</li>
139 <li><!-- JAL-1900,JAL-1625 -->Unable to minimise windows within the Jalview desktop on OSX</li>
140 <li><!-- JAL-2667 -->Mouse wheel doesn't scroll vertically when in wrapped alignment mode</li>
141 <li><!-- JAL-2636 -->Scale mark not shown when close to right hand end of alignment</li>
142 <li><!-- JAL-2684 -->Pairwise alignment of selected regions of each selected sequence do not have correct start/end positions</li>
143 <li><!-- JAL-2973 -->Alignment ruler height set incorrectly after canceling the Alignment Window's Font dialog</li>
144 <li><!-- JAL-2036 -->Show cross-references not enabled after restoring project until a new view is created</li>
145 <li><!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in URL links appears when only default EMBL-EBI link is configured (since 2.10.2b2)</li>
146 <li><!-- JAL-2775 -->Overview redraws whole window when box position is adjusted</li>
147 <li><!-- JAL-2225 -->Structure viewer doesn't map all chains in a multi-chain structure when viewing alignment involving more than one chain (since 2.10)</li>
148 <li><!-- JAL-2811 -->Double residue highlights in cursor mode if new selection moves alignment window</li>
149 <li><!-- JAL-2837,JAL-2840 -->Alignment vanishes when using arrow key in cursor mode to pass hidden column marker</li>
151 <strong><em>Applet</em></strong><br/>
153 <li><!-- JAL-2687 -->Concurrent modification exception when closing alignment panel</li>
155 <strong><em>BioJSON</em></strong><br/>
158 <!-- JAL-2546 -->BioJSON export does not preserve non-positional features
161 <strong>Known Java 9 Issues</strong>
163 <li><!-- JAL-2902 -->Groovy Console very slow to open and is
164 not responsive when entering characters (Webstart, Java 9.01,
168 <strong>New Known Issues</strong>
170 <li><!-- JAL-2541 -->Delete/Cut selection doesn't relocate sequence features correctly (for many previous versions of Jalview)</li>
171 <li><!-- JAL-2841 -->Cursor mode unexpectedly scrolls when using cursor in wrapped panel other than top</li>
172 <li><!-- JAL-2791 -->Select columns containing feature ignores graduated colour threshold</li>
178 <td width="60" nowrap>
180 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
181 <em>2/10/2017</em></strong>
184 <td><div align="left">
185 <em>New features in Jalview Desktop</em>
188 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
190 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
194 <td><div align="left">
198 <td width="60" nowrap>
200 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
201 <em>7/9/2017</em></strong>
204 <td><div align="left">
208 <!-- JAL-2588 -->Show gaps in overview window by colouring
209 in grey (sequences used to be coloured grey, and gaps were
213 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
217 <!-- JAL-2587 -->Overview updates immediately on increase
218 in size and progress bar shown as higher resolution
219 overview is recalculated
224 <td><div align="left">
228 <!-- JAL-2664 -->Overview window redraws every hidden
229 column region row by row
232 <!-- JAL-2681 -->duplicate protein sequences shown after
233 retrieving Ensembl crossrefs for sequences from Uniprot
236 <!-- JAL-2603 -->Overview window throws NPE if show boxes
237 format setting is unticked
240 <!-- JAL-2610 -->Groups are coloured wrongly in overview
241 if group has show boxes format setting unticked
244 <!-- JAL-2672,JAL-2665 -->Redraw problems when
245 autoscrolling whilst dragging current selection group to
246 include sequences and columns not currently displayed
249 <!-- JAL-2691 -->Not all chains are mapped when multimeric
250 assemblies are imported via CIF file
253 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
254 displayed when threshold or conservation colouring is also
258 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
262 <!-- JAL-2673 -->Jalview continues to scroll after
263 dragging a selected region off the visible region of the
267 <!-- JAL-2724 -->Cannot apply annotation based
268 colourscheme to all groups in a view
271 <!-- JAL-2511 -->IDs don't line up with sequences
272 initially after font size change using the Font chooser or
279 <td width="60" nowrap>
281 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
284 <td><div align="left">
285 <em>Calculations</em>
289 <!-- JAL-1933 -->Occupancy annotation row shows number of
290 ungapped positions in each column of the alignment.
293 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
294 a calculation dialog box
297 <!-- JAL-2379 -->Revised implementation of PCA for speed
298 and memory efficiency (~30x faster)
301 <!-- JAL-2403 -->Revised implementation of sequence
302 similarity scores as used by Tree, PCA, Shading Consensus
303 and other calculations
306 <!-- JAL-2416 -->Score matrices are stored as resource
307 files within the Jalview codebase
310 <!-- JAL-2500 -->Trees computed on Sequence Feature
311 Similarity may have different topology due to increased
318 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
319 model for alignments and groups
322 <!-- JAL-384 -->Custom shading schemes created via groovy
329 <!-- JAL-2526 -->Efficiency improvements for interacting
330 with alignment and overview windows
333 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
337 <!-- JAL-2388 -->Hidden columns and sequences can be
341 <!-- JAL-2611 -->Click-drag in visible area allows fine
342 adjustment of visible position
346 <em>Data import/export</em>
349 <!-- JAL-2535 -->Posterior probability annotation from
350 Stockholm files imported as sequence associated annotation
353 <!-- JAL-2507 -->More robust per-sequence positional
354 annotation input/output via stockholm flatfile
357 <!-- JAL-2533 -->Sequence names don't include file
358 extension when importing structure files without embedded
359 names or PDB accessions
362 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
363 format sequence substitution matrices
366 <em>User Interface</em>
369 <!-- JAL-2447 --> Experimental Features Checkbox in
370 Desktop's Tools menu to hide or show untested features in
374 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
375 via Overview or sequence motif search operations
378 <!-- JAL-2547 -->Amend sequence features dialog box can be
379 opened by double clicking gaps within sequence feature
383 <!-- JAL-1476 -->Status bar message shown when not enough
384 aligned positions were available to create a 3D structure
388 <em>3D Structure</em>
391 <!-- JAL-2430 -->Hidden regions in alignment views are not
392 coloured in linked structure views
395 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
396 file-based command exchange
399 <!-- JAL-2375 -->Structure chooser automatically shows
400 Cached Structures rather than querying the PDBe if
401 structures are already available for sequences
404 <!-- JAL-2520 -->Structures imported via URL are cached in
405 the Jalview project rather than downloaded again when the
409 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
410 to transfer Chimera's structure attributes as Jalview
411 features, and vice-versa (<strong>Experimental
415 <em>Web Services</em>
418 <!-- JAL-2549 -->Updated JABAWS client to v2.2
421 <!-- JAL-2335 -->Filter non-standard amino acids and
422 nucleotides when submitting to AACon and other MSA
426 <!-- JAL-2316, -->URLs for viewing database
427 cross-references provided by identifiers.org and the
435 <!-- JAL-2344 -->FileFormatI interface for describing and
436 identifying file formats (instead of String constants)
439 <!-- JAL-2228 -->FeatureCounter script refactored for
440 efficiency when counting all displayed features (not
441 backwards compatible with 2.10.1)
444 <em>Example files</em>
447 <!-- JAL-2631 -->Graduated feature colour style example
448 included in the example feature file
451 <em>Documentation</em>
454 <!-- JAL-2339 -->Release notes reformatted for readability
455 with the built-in Java help viewer
458 <!-- JAL-1644 -->Find documentation updated with 'search
459 sequence description' option
465 <!-- JAL-2485, -->External service integration tests for
466 Uniprot REST Free Text Search Client
469 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
472 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
477 <td><div align="left">
478 <em>Calculations</em>
481 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
482 matrix - C->R should be '-3'<br />Old matrix restored
483 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
485 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
486 Jalview's treatment of gaps in PCA and substitution matrix
487 based Tree calculations.<br /> <br />In earlier versions
488 of Jalview, gaps matching gaps were penalised, and gaps
489 matching non-gaps penalised even more. In the PCA
490 calculation, gaps were actually treated as non-gaps - so
491 different costs were applied, which meant Jalview's PCAs
492 were different to those produced by SeqSpace.<br />Jalview
493 now treats gaps in the same way as SeqSpace (ie it scores
494 them as 0). <br /> <br />Enter the following in the
495 Groovy console to restore pre-2.10.2 behaviour:<br />
496 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
497 // for 2.10.1 mode <br />
498 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
499 // to restore 2.10.2 mode <br /> <br /> <em>Note:
500 these settings will affect all subsequent tree and PCA
501 calculations (not recommended)</em></li>
503 <!-- JAL-2424 -->Fixed off-by-one bug that affected
504 scaling of branch lengths for trees computed using
505 Sequence Feature Similarity.
508 <!-- JAL-2377 -->PCA calculation could hang when
509 generating output report when working with highly
513 <!-- JAL-2544 --> Sort by features includes features to
514 right of selected region when gaps present on right-hand
518 <em>User Interface</em>
521 <!-- JAL-2346 -->Reopening Colour by annotation dialog
522 doesn't reselect a specific sequence's associated
523 annotation after it was used for colouring a view
526 <!-- JAL-2419 -->Current selection lost if popup menu
527 opened on a region of alignment without groups
530 <!-- JAL-2374 -->Popup menu not always shown for regions
531 of an alignment with overlapping groups
534 <!-- JAL-2310 -->Finder double counts if both a sequence's
535 name and description match
538 <!-- JAL-2370 -->Hiding column selection containing two
539 hidden regions results in incorrect hidden regions
542 <!-- JAL-2386 -->'Apply to all groups' setting when
543 changing colour does not apply Conservation slider value
547 <!-- JAL-2373 -->Percentage identity and conservation menu
548 items do not show a tick or allow shading to be disabled
551 <!-- JAL-2385 -->Conservation shading or PID threshold
552 lost when base colourscheme changed if slider not visible
555 <!-- JAL-2547 -->Sequence features shown in tooltip for
556 gaps before start of features
559 <!-- JAL-2623 -->Graduated feature colour threshold not
560 restored to UI when feature colour is edited
563 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
564 a time when scrolling vertically in wrapped mode.
567 <!-- JAL-2630 -->Structure and alignment overview update
568 as graduate feature colour settings are modified via the
572 <!-- JAL-2034 -->Overview window doesn't always update
573 when a group defined on the alignment is resized
576 <!-- JAL-2605 -->Mouseovers on left/right scale region in
577 wrapped view result in positional status updates
581 <!-- JAL-2563 -->Status bar doesn't show position for
582 ambiguous amino acid and nucleotide symbols
585 <!-- JAL-2602 -->Copy consensus sequence failed if
586 alignment included gapped columns
589 <!-- JAL-2473 -->Minimum size set for Jalview windows so
590 widgets don't permanently disappear
593 <!-- JAL-2503 -->Cannot select or filter quantitative
594 annotation that are shown only as column labels (e.g.
595 T-Coffee column reliability scores)
598 <!-- JAL-2594 -->Exception thrown if trying to create a
599 sequence feature on gaps only
602 <!-- JAL-2504 -->Features created with 'New feature'
603 button from a Find inherit previously defined feature type
604 rather than the Find query string
607 <!-- JAL-2423 -->incorrect title in output window when
608 exporting tree calculated in Jalview
611 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
612 and then revealing them reorders sequences on the
616 <!-- JAL-964 -->Group panel in sequence feature settings
617 doesn't update to reflect available set of groups after
618 interactively adding or modifying features
621 <!-- JAL-2225 -->Sequence Database chooser unusable on
625 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
626 only excluded gaps in current sequence and ignored
633 <!-- JAL-2421 -->Overview window visible region moves
634 erratically when hidden rows or columns are present
637 <!-- JAL-2362 -->Per-residue colourschemes applied via the
638 Structure Viewer's colour menu don't correspond to
642 <!-- JAL-2405 -->Protein specific colours only offered in
643 colour and group colour menu for protein alignments
646 <!-- JAL-2385 -->Colour threshold slider doesn't update to
647 reflect currently selected view or group's shading
651 <!-- JAL-2624 -->Feature colour thresholds not respected
652 when rendered on overview and structures when opacity at
656 <!-- JAL-2589 -->User defined gap colour not shown in
657 overview when features overlaid on alignment
660 <em>Data import/export</em>
663 <!-- JAL-2576 -->Very large alignments take a long time to
667 <!-- JAL-2507 -->Per-sequence RNA secondary structures
668 added after a sequence was imported are not written to
672 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
673 when importing RNA secondary structure via Stockholm
676 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
677 not shown in correct direction for simple pseudoknots
680 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
681 with lightGray or darkGray via features file (but can
685 <!-- JAL-2383 -->Above PID colour threshold not recovered
686 when alignment view imported from project
689 <!-- JAL-2520,JAL-2465 -->No mappings generated between
690 structure and sequences extracted from structure files
691 imported via URL and viewed in Jmol
694 <!-- JAL-2520 -->Structures loaded via URL are saved in
695 Jalview Projects rather than fetched via URL again when
696 the project is loaded and the structure viewed
699 <em>Web Services</em>
702 <!-- JAL-2519 -->EnsemblGenomes example failing after
703 release of Ensembl v.88
706 <!-- JAL-2366 -->Proxy server address and port always
707 appear enabled in Preferences->Connections
710 <!-- JAL-2461 -->DAS registry not found exceptions
711 removed from console output
714 <!-- JAL-2582 -->Cannot retrieve protein products from
715 Ensembl by Peptide ID
718 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
719 created from SIFTs, and spurious 'Couldn't open structure
720 in Chimera' errors raised after April 2017 update (problem
721 due to 'null' string rather than empty string used for
722 residues with no corresponding PDB mapping).
725 <em>Application UI</em>
728 <!-- JAL-2361 -->User Defined Colours not added to Colour
732 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
733 case' residues (button in colourscheme editor debugged and
734 new documentation and tooltips added)
737 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
738 doesn't restore group-specific text colour thresholds
741 <!-- JAL-2243 -->Feature settings panel does not update as
742 new features are added to alignment
745 <!-- JAL-2532 -->Cancel in feature settings reverts
746 changes to feature colours via the Amend features dialog
749 <!-- JAL-2506 -->Null pointer exception when attempting to
750 edit graduated feature colour via amend features dialog
754 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
755 selection menu changes colours of alignment views
758 <!-- JAL-2426 -->Spurious exceptions in console raised
759 from alignment calculation workers after alignment has
763 <!-- JAL-1608 -->Typo in selection popup menu - Create
764 groups now 'Create Group'
767 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
768 Create/Undefine group doesn't always work
771 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
772 shown again after pressing 'Cancel'
775 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
776 adjusts start position in wrap mode
779 <!-- JAL-2563 -->Status bar doesn't show positions for
780 ambiguous amino acids
783 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
784 CDS/Protein view after CDS sequences added for aligned
788 <!-- JAL-2592 -->User defined colourschemes called 'User
789 Defined' don't appear in Colours menu
795 <!-- JAL-2468 -->Switching between Nucleotide and Protein
796 score models doesn't always result in an updated PCA plot
799 <!-- JAL-2442 -->Features not rendered as transparent on
800 overview or linked structure view
803 <!-- JAL-2372 -->Colour group by conservation doesn't
807 <!-- JAL-2517 -->Hitting Cancel after applying
808 user-defined colourscheme doesn't restore original
815 <!-- JAL-2314 -->Unit test failure:
816 jalview.ws.jabaws.RNAStructExportImport setup fails
819 <!-- JAL-2307 -->Unit test failure:
820 jalview.ws.sifts.SiftsClientTest due to compatibility
821 problems with deep array comparison equality asserts in
822 successive versions of TestNG
825 <!-- JAL-2479 -->Relocated StructureChooserTest and
826 ParameterUtilsTest Unit tests to Network suite
829 <em>New Known Issues</em>
832 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
833 phase after a sequence motif find operation
836 <!-- JAL-2550 -->Importing annotation file with rows
837 containing just upper and lower case letters are
838 interpreted as WUSS RNA secondary structure symbols
841 <!-- JAL-2590 -->Cannot load and display Newick trees
842 reliably from eggnog Ortholog database
845 <!-- JAL-2468 -->Status bar shows 'Marked x columns
846 containing features of type Highlight' when 'B' is pressed
847 to mark columns containing highlighted regions.
850 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
851 doesn't always add secondary structure annotation.
856 <td width="60" nowrap>
858 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
861 <td><div align="left">
865 <!-- JAL-98 -->Improved memory usage: sparse arrays used
866 for all consensus calculations
869 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
872 <li>Updated Jalview's Certum code signing certificate
878 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
879 set of database cross-references, sorted alphabetically
882 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
883 from database cross references. Users with custom links
884 will receive a <a href="webServices/urllinks.html#warning">warning
885 dialog</a> asking them to update their preferences.
888 <!-- JAL-2287-->Cancel button and escape listener on
889 dialog warning user about disconnecting Jalview from a
893 <!-- JAL-2320-->Jalview's Chimera control window closes if
894 the Chimera it is connected to is shut down
897 <!-- JAL-1738-->New keystroke (B) and Select highlighted
898 columns menu item to mark columns containing highlighted
899 regions (e.g. from structure selections or results of a
903 <!-- JAL-2284-->Command line option for batch-generation
904 of HTML pages rendering alignment data with the BioJS
914 <!-- JAL-2286 -->Columns with more than one modal residue
915 are not coloured or thresholded according to percent
916 identity (first observed in Jalview 2.8.2)
919 <!-- JAL-2301 -->Threonine incorrectly reported as not
923 <!-- JAL-2318 -->Updates to documentation pages (above PID
924 threshold, amino acid properties)
927 <!-- JAL-2292 -->Lower case residues in sequences are not
928 reported as mapped to residues in a structure file in the
932 <!--JAL-2324 -->Identical features with non-numeric scores
933 could be added multiple times to a sequence
936 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
937 bond features shown as two highlighted residues rather
938 than a range in linked structure views, and treated
939 correctly when selecting and computing trees from features
942 <!-- JAL-2281-->Custom URL links for database
943 cross-references are matched to database name regardless
951 <!-- JAL-2282-->Custom URL links for specific database
952 names without regular expressions also offer links from
956 <!-- JAL-2315-->Removing a single configured link in the
957 URL links pane in Connections preferences doesn't actually
958 update Jalview configuration
961 <!-- JAL-2272-->CTRL-Click on a selected region to open
962 the alignment area popup menu doesn't work on El-Capitan
965 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
966 files with similarly named sequences if dropped onto the
970 <!-- JAL-2312 -->Additional mappings are shown for PDB
971 entries where more chains exist in the PDB accession than
972 are reported in the SIFTS file
975 <!-- JAL-2317-->Certain structures do not get mapped to
976 the structure view when displayed with Chimera
979 <!-- JAL-2317-->No chains shown in the Chimera view
980 panel's View->Show Chains submenu
983 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
984 work for wrapped alignment views
987 <!--JAL-2197 -->Rename UI components for running JPred
988 predictions from 'JNet' to 'JPred'
991 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
992 corrupted when annotation panel vertical scroll is not at
996 <!--JAL-2332 -->Attempting to view structure for Hen
997 lysozyme results in a PDB Client error dialog box
1000 <!-- JAL-2319 -->Structure View's mapping report switched
1001 ranges for PDB and sequence for SIFTS
1004 SIFTS 'Not_Observed' residues mapped to non-existant
1008 <!-- <em>New Known Issues</em>
1015 <td width="60" nowrap>
1016 <div align="center">
1017 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1018 <em>25/10/2016</em></strong>
1021 <td><em>Application</em>
1023 <li>3D Structure chooser opens with 'Cached structures'
1024 view if structures already loaded</li>
1025 <li>Progress bar reports models as they are loaded to
1026 structure views</li>
1032 <li>Colour by conservation always enabled and no tick
1033 shown in menu when BLOSUM or PID shading applied</li>
1034 <li>FER1_ARATH and FER2_ARATH labels were switched in
1035 example sequences/projects/trees</li>
1037 <em>Application</em>
1039 <li>Jalview projects with views of local PDB structure
1040 files saved on Windows cannot be opened on OSX</li>
1041 <li>Multiple structure views can be opened and superposed
1042 without timeout for structures with multiple models or
1043 multiple sequences in alignment</li>
1044 <li>Cannot import or associated local PDB files without a
1045 PDB ID HEADER line</li>
1046 <li>RMSD is not output in Jmol console when superposition
1048 <li>Drag and drop of URL from Browser fails for Linux and
1049 OSX versions earlier than El Capitan</li>
1050 <li>ENA client ignores invalid content from ENA server</li>
1051 <li>Exceptions are not raised in console when ENA client
1052 attempts to fetch non-existent IDs via Fetch DB Refs UI
1054 <li>Exceptions are not raised in console when a new view
1055 is created on the alignment</li>
1056 <li>OSX right-click fixed for group selections: CMD-click
1057 to insert/remove gaps in groups and CTRL-click to open group
1060 <em>Build and deployment</em>
1062 <li>URL link checker now copes with multi-line anchor
1065 <em>New Known Issues</em>
1067 <li>Drag and drop from URL links in browsers do not work
1074 <td width="60" nowrap>
1075 <div align="center">
1076 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1079 <td><em>General</em>
1082 <!-- JAL-2124 -->Updated Spanish translations.
1085 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1086 for importing structure data to Jalview. Enables mmCIF and
1090 <!-- JAL-192 --->Alignment ruler shows positions relative to
1094 <!-- JAL-2202 -->Position/residue shown in status bar when
1095 mousing over sequence associated annotation
1098 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1102 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1103 '()', canonical '[]' and invalid '{}' base pair populations
1107 <!-- JAL-2092 -->Feature settings popup menu options for
1108 showing or hiding columns containing a feature
1111 <!-- JAL-1557 -->Edit selected group by double clicking on
1112 group and sequence associated annotation labels
1115 <!-- JAL-2236 -->Sequence name added to annotation label in
1116 select/hide columns by annotation and colour by annotation
1120 </ul> <em>Application</em>
1123 <!-- JAL-2050-->Automatically hide introns when opening a
1124 gene/transcript view
1127 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1131 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1132 structure mappings with the EMBL-EBI PDBe SIFTS database
1135 <!-- JAL-2079 -->Updated download sites used for Rfam and
1136 Pfam sources to xfam.org
1139 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1142 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1143 over sequences in Jalview
1146 <!-- JAL-2027-->Support for reverse-complement coding
1147 regions in ENA and EMBL
1150 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1151 for record retrieval via ENA rest API
1154 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1158 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1159 groovy script execution
1162 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1163 alignment window's Calculate menu
1166 <!-- JAL-1812 -->Allow groovy scripts that call
1167 Jalview.getAlignFrames() to run in headless mode
1170 <!-- JAL-2068 -->Support for creating new alignment
1171 calculation workers from groovy scripts
1174 <!-- JAL-1369 --->Store/restore reference sequence in
1178 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1179 associations are now saved/restored from project
1182 <!-- JAL-1993 -->Database selection dialog always shown
1183 before sequence fetcher is opened
1186 <!-- JAL-2183 -->Double click on an entry in Jalview's
1187 database chooser opens a sequence fetcher
1190 <!-- JAL-1563 -->Free-text search client for UniProt using
1191 the UniProt REST API
1194 <!-- JAL-2168 -->-nonews command line parameter to prevent
1195 the news reader opening
1198 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1199 querying stored in preferences
1202 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1206 <!-- JAL-1977-->Tooltips shown on database chooser
1209 <!-- JAL-391 -->Reverse complement function in calculate
1210 menu for nucleotide sequences
1213 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1214 and feature counts preserves alignment ordering (and
1215 debugged for complex feature sets).
1218 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1219 viewing structures with Jalview 2.10
1222 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1223 genome, transcript CCDS and gene ids via the Ensembl and
1224 Ensembl Genomes REST API
1227 <!-- JAL-2049 -->Protein sequence variant annotation
1228 computed for 'sequence_variant' annotation on CDS regions
1232 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1236 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1237 Ref Fetcher fails to match, or otherwise updates sequence
1238 data from external database records.
1241 <!-- JAL-2154 -->Revised Jalview Project format for
1242 efficient recovery of sequence coding and alignment
1243 annotation relationships.
1245 </ul> <!-- <em>Applet</em>
1256 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1260 <!-- JAL-2018-->Export features in Jalview format (again)
1261 includes graduated colourschemes
1264 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1265 working with big alignments and lots of hidden columns
1268 <!-- JAL-2053-->Hidden column markers not always rendered
1269 at right of alignment window
1272 <!-- JAL-2067 -->Tidied up links in help file table of
1276 <!-- JAL-2072 -->Feature based tree calculation not shown
1280 <!-- JAL-2075 -->Hidden columns ignored during feature
1281 based tree calculation
1284 <!-- JAL-2065 -->Alignment view stops updating when show
1285 unconserved enabled for group on alignment
1288 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1292 <!-- JAL-2146 -->Alignment column in status incorrectly
1293 shown as "Sequence position" when mousing over
1297 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1298 hidden columns present
1301 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1302 user created annotation added to alignment
1305 <!-- JAL-1841 -->RNA Structure consensus only computed for
1306 '()' base pair annotation
1309 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1310 in zero scores for all base pairs in RNA Structure
1314 <!-- JAL-2174-->Extend selection with columns containing
1318 <!-- JAL-2275 -->Pfam format writer puts extra space at
1319 beginning of sequence
1322 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1326 <!-- JAL-2238 -->Cannot create groups on an alignment from
1327 from a tree when t-coffee scores are shown
1330 <!-- JAL-1836,1967 -->Cannot import and view PDB
1331 structures with chains containing negative resnums (4q4h)
1334 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1338 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1339 to Clustal, PIR and PileUp output
1342 <!-- JAL-2008 -->Reordering sequence features that are
1343 not visible causes alignment window to repaint
1346 <!-- JAL-2006 -->Threshold sliders don't work in
1347 graduated colour and colour by annotation row for e-value
1348 scores associated with features and annotation rows
1351 <!-- JAL-1797 -->amino acid physicochemical conservation
1352 calculation should be case independent
1355 <!-- JAL-2173 -->Remove annotation also updates hidden
1359 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1360 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1361 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1364 <!-- JAL-2065 -->Null pointer exceptions and redraw
1365 problems when reference sequence defined and 'show
1366 non-conserved' enabled
1369 <!-- JAL-1306 -->Quality and Conservation are now shown on
1370 load even when Consensus calculation is disabled
1373 <!-- JAL-1932 -->Remove right on penultimate column of
1374 alignment does nothing
1377 <em>Application</em>
1380 <!-- JAL-1552-->URLs and links can't be imported by
1381 drag'n'drop on OSX when launched via webstart (note - not
1382 yet fixed for El Capitan)
1385 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1386 output when running on non-gb/us i18n platforms
1389 <!-- JAL-1944 -->Error thrown when exporting a view with
1390 hidden sequences as flat-file alignment
1393 <!-- JAL-2030-->InstallAnywhere distribution fails when
1397 <!-- JAL-2080-->Jalview very slow to launch via webstart
1398 (also hotfix for 2.9.0b2)
1401 <!-- JAL-2085 -->Cannot save project when view has a
1402 reference sequence defined
1405 <!-- JAL-1011 -->Columns are suddenly selected in other
1406 alignments and views when revealing hidden columns
1409 <!-- JAL-1989 -->Hide columns not mirrored in complement
1410 view in a cDNA/Protein splitframe
1413 <!-- JAL-1369 -->Cannot save/restore representative
1414 sequence from project when only one sequence is
1418 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1419 in Structure Chooser
1422 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1423 structure consensus didn't refresh annotation panel
1426 <!-- JAL-1962 -->View mapping in structure view shows
1427 mappings between sequence and all chains in a PDB file
1430 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1431 dialogs format columns correctly, don't display array
1432 data, sort columns according to type
1435 <!-- JAL-1975 -->Export complete shown after destination
1436 file chooser is cancelled during an image export
1439 <!-- JAL-2025 -->Error when querying PDB Service with
1440 sequence name containing special characters
1443 <!-- JAL-2024 -->Manual PDB structure querying should be
1447 <!-- JAL-2104 -->Large tooltips with broken HTML
1448 formatting don't wrap
1451 <!-- JAL-1128 -->Figures exported from wrapped view are
1452 truncated so L looks like I in consensus annotation
1455 <!-- JAL-2003 -->Export features should only export the
1456 currently displayed features for the current selection or
1460 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1461 after fetching cross-references, and restoring from
1465 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1466 followed in the structure viewer
1469 <!-- JAL-2163 -->Titles for individual alignments in
1470 splitframe not restored from project
1473 <!-- JAL-2145 -->missing autocalculated annotation at
1474 trailing end of protein alignment in transcript/product
1475 splitview when pad-gaps not enabled by default
1478 <!-- JAL-1797 -->amino acid physicochemical conservation
1482 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1483 article has been read (reopened issue due to
1484 internationalisation problems)
1487 <!-- JAL-1960 -->Only offer PDB structures in structure
1488 viewer based on sequence name, PDB and UniProt
1493 <!-- JAL-1976 -->No progress bar shown during export of
1497 <!-- JAL-2213 -->Structures not always superimposed after
1498 multiple structures are shown for one or more sequences.
1501 <!-- JAL-1370 -->Reference sequence characters should not
1502 be replaced with '.' when 'Show unconserved' format option
1506 <!-- JAL-1823 -->Cannot specify chain code when entering
1507 specific PDB id for sequence
1510 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1511 'Export hidden sequences' is enabled, but 'export hidden
1512 columns' is disabled.
1515 <!--JAL-2026-->Best Quality option in structure chooser
1516 selects lowest rather than highest resolution structures
1520 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1521 to sequence mapping in 'View Mappings' report
1524 <!-- JAL-2284 -->Unable to read old Jalview projects that
1525 contain non-XML data added after Jalvew wrote project.
1528 <!-- JAL-2118 -->Newly created annotation row reorders
1529 after clicking on it to create new annotation for a
1533 <!-- JAL-1980 -->Null Pointer Exception raised when
1534 pressing Add on an orphaned cut'n'paste window.
1536 <!-- may exclude, this is an external service stability issue JAL-1941
1537 -- > RNA 3D structure not added via DSSR service</li> -->
1542 <!-- JAL-2151 -->Incorrect columns are selected when
1543 hidden columns present before start of sequence
1546 <!-- JAL-1986 -->Missing dependencies on applet pages
1550 <!-- JAL-1947 -->Overview pixel size changes when
1551 sequences are hidden in applet
1554 <!-- JAL-1996 -->Updated instructions for applet
1555 deployment on examples pages.
1562 <td width="60" nowrap>
1563 <div align="center">
1564 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1565 <em>16/10/2015</em></strong>
1568 <td><em>General</em>
1570 <li>Time stamps for signed Jalview application and applet
1575 <em>Application</em>
1577 <li>Duplicate group consensus and conservation rows
1578 shown when tree is partitioned</li>
1579 <li>Erratic behaviour when tree partitions made with
1580 multiple cDNA/Protein split views</li>
1586 <td width="60" nowrap>
1587 <div align="center">
1588 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1589 <em>8/10/2015</em></strong>
1592 <td><em>General</em>
1594 <li>Updated Spanish translations of localized text for
1596 </ul> <em>Application</em>
1598 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1599 <li>Signed OSX InstallAnywhere installer<br></li>
1600 <li>Support for per-sequence based annotations in BioJSON</li>
1601 </ul> <em>Applet</em>
1603 <li>Split frame example added to applet examples page</li>
1604 </ul> <em>Build and Deployment</em>
1607 <!-- JAL-1888 -->New ant target for running Jalview's test
1615 <li>Mapping of cDNA to protein in split frames
1616 incorrect when sequence start > 1</li>
1617 <li>Broken images in filter column by annotation dialog
1619 <li>Feature colours not parsed from features file</li>
1620 <li>Exceptions and incomplete link URLs recovered when
1621 loading a features file containing HTML tags in feature
1625 <em>Application</em>
1627 <li>Annotations corrupted after BioJS export and
1629 <li>Incorrect sequence limits after Fetch DB References
1630 with 'trim retrieved sequences'</li>
1631 <li>Incorrect warning about deleting all data when
1632 deleting selected columns</li>
1633 <li>Patch to build system for shipping properly signed
1634 JNLP templates for webstart launch</li>
1635 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1636 unreleased structures for download or viewing</li>
1637 <li>Tab/space/return keystroke operation of EMBL-PDBe
1638 fetcher/viewer dialogs works correctly</li>
1639 <li>Disabled 'minimise' button on Jalview windows
1640 running on OSX to workaround redraw hang bug</li>
1641 <li>Split cDNA/Protein view position and geometry not
1642 recovered from jalview project</li>
1643 <li>Initial enabled/disabled state of annotation menu
1644 sorter 'show autocalculated first/last' corresponds to
1646 <li>Restoring of Clustal, RNA Helices and T-Coffee
1647 color schemes from BioJSON</li>
1651 <li>Reorder sequences mirrored in cDNA/Protein split
1653 <li>Applet with Jmol examples not loading correctly</li>
1659 <td><div align="center">
1660 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1662 <td><em>General</em>
1664 <li>Linked visualisation and analysis of DNA and Protein
1667 <li>Translated cDNA alignments shown as split protein
1668 and DNA alignment views</li>
1669 <li>Codon consensus annotation for linked protein and
1670 cDNA alignment views</li>
1671 <li>Link cDNA or Protein product sequences by loading
1672 them onto Protein or cDNA alignments</li>
1673 <li>Reconstruct linked cDNA alignment from aligned
1674 protein sequences</li>
1677 <li>Jmol integration updated to Jmol v14.2.14</li>
1678 <li>Import and export of Jalview alignment views as <a
1679 href="features/bioJsonFormat.html">BioJSON</a></li>
1680 <li>New alignment annotation file statements for
1681 reference sequences and marking hidden columns</li>
1682 <li>Reference sequence based alignment shading to
1683 highlight variation</li>
1684 <li>Select or hide columns according to alignment
1686 <li>Find option for locating sequences by description</li>
1687 <li>Conserved physicochemical properties shown in amino
1688 acid conservation row</li>
1689 <li>Alignments can be sorted by number of RNA helices</li>
1690 </ul> <em>Application</em>
1692 <li>New cDNA/Protein analysis capabilities
1694 <li>Get Cross-References should open a Split Frame
1695 view with cDNA/Protein</li>
1696 <li>Detect when nucleotide sequences and protein
1697 sequences are placed in the same alignment</li>
1698 <li>Split cDNA/Protein views are saved in Jalview
1703 <li>Use REST API to talk to Chimera</li>
1704 <li>Selected regions in Chimera are highlighted in linked
1705 Jalview windows</li>
1707 <li>VARNA RNA viewer updated to v3.93</li>
1708 <li>VARNA views are saved in Jalview Projects</li>
1709 <li>Pseudoknots displayed as Jalview RNA annotation can
1710 be shown in VARNA</li>
1712 <li>Make groups for selection uses marked columns as well
1713 as the active selected region</li>
1715 <li>Calculate UPGMA and NJ trees using sequence feature
1717 <li>New Export options
1719 <li>New Export Settings dialog to control hidden
1720 region export in flat file generation</li>
1722 <li>Export alignment views for display with the <a
1723 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1725 <li>Export scrollable SVG in HTML page</li>
1726 <li>Optional embedding of BioJSON data when exporting
1727 alignment figures to HTML</li>
1729 <li>3D structure retrieval and display
1731 <li>Free text and structured queries with the PDBe
1733 <li>PDBe Search API based discovery and selection of
1734 PDB structures for a sequence set</li>
1738 <li>JPred4 employed for protein secondary structure
1740 <li>Hide Insertions menu option to hide unaligned columns
1741 for one or a group of sequences</li>
1742 <li>Automatically hide insertions in alignments imported
1743 from the JPred4 web server</li>
1744 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1745 system on OSX<br />LGPL libraries courtesy of <a
1746 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1748 <li>changed 'View nucleotide structure' submenu to 'View
1749 VARNA 2D Structure'</li>
1750 <li>change "View protein structure" menu option to "3D
1753 </ul> <em>Applet</em>
1755 <li>New layout for applet example pages</li>
1756 <li>New parameters to enable SplitFrame view
1757 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1758 <li>New example demonstrating linked viewing of cDNA and
1759 Protein alignments</li>
1760 </ul> <em>Development and deployment</em>
1762 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1763 <li>Include installation type and git revision in build
1764 properties and console log output</li>
1765 <li>Jalview Github organisation, and new github site for
1766 storing BioJsMSA Templates</li>
1767 <li>Jalview's unit tests now managed with TestNG</li>
1770 <!-- <em>General</em>
1772 </ul> --> <!-- issues resolved --> <em>Application</em>
1774 <li>Escape should close any open find dialogs</li>
1775 <li>Typo in select-by-features status report</li>
1776 <li>Consensus RNA secondary secondary structure
1777 predictions are not highlighted in amber</li>
1778 <li>Missing gap character in v2.7 example file means
1779 alignment appears unaligned when pad-gaps is not enabled</li>
1780 <li>First switch to RNA Helices colouring doesn't colour
1781 associated structure views</li>
1782 <li>ID width preference option is greyed out when auto
1783 width checkbox not enabled</li>
1784 <li>Stopped a warning dialog from being shown when
1785 creating user defined colours</li>
1786 <li>'View Mapping' in structure viewer shows sequence
1787 mappings for just that viewer's sequences</li>
1788 <li>Workaround for superposing PDB files containing
1789 multiple models in Chimera</li>
1790 <li>Report sequence position in status bar when hovering
1791 over Jmol structure</li>
1792 <li>Cannot output gaps as '.' symbols with Selection ->
1793 output to text box</li>
1794 <li>Flat file exports of alignments with hidden columns
1795 have incorrect sequence start/end</li>
1796 <li>'Aligning' a second chain to a Chimera structure from
1798 <li>Colour schemes applied to structure viewers don't
1799 work for nucleotide</li>
1800 <li>Loading/cut'n'pasting an empty or invalid file leads
1801 to a grey/invisible alignment window</li>
1802 <li>Exported Jpred annotation from a sequence region
1803 imports to different position</li>
1804 <li>Space at beginning of sequence feature tooltips shown
1805 on some platforms</li>
1806 <li>Chimera viewer 'View | Show Chain' menu is not
1808 <li>'New View' fails with a Null Pointer Exception in
1809 console if Chimera has been opened</li>
1810 <li>Mouseover to Chimera not working</li>
1811 <li>Miscellaneous ENA XML feature qualifiers not
1813 <li>NPE in annotation renderer after 'Extract Scores'</li>
1814 <li>If two structures in one Chimera window, mouseover of
1815 either sequence shows on first structure</li>
1816 <li>'Show annotations' options should not make
1817 non-positional annotations visible</li>
1818 <li>Subsequence secondary structure annotation not shown
1819 in right place after 'view flanking regions'</li>
1820 <li>File Save As type unset when current file format is
1822 <li>Save as '.jar' option removed for saving Jalview
1824 <li>Colour by Sequence colouring in Chimera more
1826 <li>Cannot 'add reference annotation' for a sequence in
1827 several views on same alignment</li>
1828 <li>Cannot show linked products for EMBL / ENA records</li>
1829 <li>Jalview's tooltip wraps long texts containing no
1831 </ul> <em>Applet</em>
1833 <li>Jmol to JalviewLite mouseover/link not working</li>
1834 <li>JalviewLite can't import sequences with ID
1835 descriptions containing angle brackets</li>
1836 </ul> <em>General</em>
1838 <li>Cannot export and reimport RNA secondary structure
1839 via jalview annotation file</li>
1840 <li>Random helix colour palette for colour by annotation
1841 with RNA secondary structure</li>
1842 <li>Mouseover to cDNA from STOP residue in protein
1843 translation doesn't work.</li>
1844 <li>hints when using the select by annotation dialog box</li>
1845 <li>Jmol alignment incorrect if PDB file has alternate CA
1847 <li>FontChooser message dialog appears to hang after
1848 choosing 1pt font</li>
1849 <li>Peptide secondary structure incorrectly imported from
1850 annotation file when annotation display text includes 'e' or
1852 <li>Cannot set colour of new feature type whilst creating
1854 <li>cDNA translation alignment should not be sequence
1855 order dependent</li>
1856 <li>'Show unconserved' doesn't work for lower case
1858 <li>Nucleotide ambiguity codes involving R not recognised</li>
1859 </ul> <em>Deployment and Documentation</em>
1861 <li>Applet example pages appear different to the rest of
1862 www.jalview.org</li>
1863 </ul> <em>Application Known issues</em>
1865 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1866 <li>Misleading message appears after trying to delete
1868 <li>Jalview icon not shown in dock after InstallAnywhere
1869 version launches</li>
1870 <li>Fetching EMBL reference for an RNA sequence results
1871 fails with a sequence mismatch</li>
1872 <li>Corrupted or unreadable alignment display when
1873 scrolling alignment to right</li>
1874 <li>ArrayIndexOutOfBoundsException thrown when remove
1875 empty columns called on alignment with ragged gapped ends</li>
1876 <li>auto calculated alignment annotation rows do not get
1877 placed above or below non-autocalculated rows</li>
1878 <li>Jalview dekstop becomes sluggish at full screen in
1879 ultra-high resolution</li>
1880 <li>Cannot disable consensus calculation independently of
1881 quality and conservation</li>
1882 <li>Mouseover highlighting between cDNA and protein can
1883 become sluggish with more than one splitframe shown</li>
1884 </ul> <em>Applet Known Issues</em>
1886 <li>Core PDB parsing code requires Jmol</li>
1887 <li>Sequence canvas panel goes white when alignment
1888 window is being resized</li>
1894 <td><div align="center">
1895 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1897 <td><em>General</em>
1899 <li>Updated Java code signing certificate donated by
1901 <li>Features and annotation preserved when performing
1902 pairwise alignment</li>
1903 <li>RNA pseudoknot annotation can be
1904 imported/exported/displayed</li>
1905 <li>'colour by annotation' can colour by RNA and
1906 protein secondary structure</li>
1907 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1908 post-hoc with 2.9 release</em>)
1911 </ul> <em>Application</em>
1913 <li>Extract and display secondary structure for sequences
1914 with 3D structures</li>
1915 <li>Support for parsing RNAML</li>
1916 <li>Annotations menu for layout
1918 <li>sort sequence annotation rows by alignment</li>
1919 <li>place sequence annotation above/below alignment
1922 <li>Output in Stockholm format</li>
1923 <li>Internationalisation: improved Spanish (es)
1925 <li>Structure viewer preferences tab</li>
1926 <li>Disorder and Secondary Structure annotation tracks
1927 shared between alignments</li>
1928 <li>UCSF Chimera launch and linked highlighting from
1930 <li>Show/hide all sequence associated annotation rows for
1931 all or current selection</li>
1932 <li>disorder and secondary structure predictions
1933 available as dataset annotation</li>
1934 <li>Per-sequence rna helices colouring</li>
1937 <li>Sequence database accessions imported when fetching
1938 alignments from Rfam</li>
1939 <li>update VARNA version to 3.91</li>
1941 <li>New groovy scripts for exporting aligned positions,
1942 conservation values, and calculating sum of pairs scores.</li>
1943 <li>Command line argument to set default JABAWS server</li>
1944 <li>include installation type in build properties and
1945 console log output</li>
1946 <li>Updated Jalview project format to preserve dataset
1950 <!-- issues resolved --> <em>Application</em>
1952 <li>Distinguish alignment and sequence associated RNA
1953 structure in structure->view->VARNA</li>
1954 <li>Raise dialog box if user deletes all sequences in an
1956 <li>Pressing F1 results in documentation opening twice</li>
1957 <li>Sequence feature tooltip is wrapped</li>
1958 <li>Double click on sequence associated annotation
1959 selects only first column</li>
1960 <li>Redundancy removal doesn't result in unlinked
1961 leaves shown in tree</li>
1962 <li>Undos after several redundancy removals don't undo
1964 <li>Hide sequence doesn't hide associated annotation</li>
1965 <li>User defined colours dialog box too big to fit on
1966 screen and buttons not visible</li>
1967 <li>author list isn't updated if already written to
1968 Jalview properties</li>
1969 <li>Popup menu won't open after retrieving sequence
1971 <li>File open window for associate PDB doesn't open</li>
1972 <li>Left-then-right click on a sequence id opens a
1973 browser search window</li>
1974 <li>Cannot open sequence feature shading/sort popup menu
1975 in feature settings dialog</li>
1976 <li>better tooltip placement for some areas of Jalview
1978 <li>Allow addition of JABAWS Server which doesn't
1979 pass validation</li>
1980 <li>Web services parameters dialog box is too large to
1982 <li>Muscle nucleotide alignment preset obscured by
1984 <li>JABAWS preset submenus don't contain newly
1985 defined user preset</li>
1986 <li>MSA web services warns user if they were launched
1987 with invalid input</li>
1988 <li>Jalview cannot contact DAS Registy when running on
1991 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1992 'Superpose with' submenu not shown when new view
1996 </ul> <!-- <em>Applet</em>
1998 </ul> <em>General</em>
2000 </ul>--> <em>Deployment and Documentation</em>
2002 <li>2G and 1G options in launchApp have no effect on
2003 memory allocation</li>
2004 <li>launchApp service doesn't automatically open
2005 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2007 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2008 InstallAnywhere reports cannot find valid JVM when Java
2009 1.7_055 is available
2011 </ul> <em>Application Known issues</em>
2014 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2015 corrupted or unreadable alignment display when scrolling
2019 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2020 retrieval fails but progress bar continues for DAS retrieval
2021 with large number of ID
2024 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2025 flatfile output of visible region has incorrect sequence
2029 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2030 rna structure consensus doesn't update when secondary
2031 structure tracks are rearranged
2034 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2035 invalid rna structure positional highlighting does not
2036 highlight position of invalid base pairs
2039 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2040 out of memory errors are not raised when saving Jalview
2041 project from alignment window file menu
2044 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2045 Switching to RNA Helices colouring doesn't propagate to
2049 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2050 colour by RNA Helices not enabled when user created
2051 annotation added to alignment
2054 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2055 Jalview icon not shown on dock in Mountain Lion/Webstart
2057 </ul> <em>Applet Known Issues</em>
2060 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2061 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2064 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2065 Jalview and Jmol example not compatible with IE9
2068 <li>Sort by annotation score doesn't reverse order
2074 <td><div align="center">
2075 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2078 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2081 <li>Internationalisation of user interface (usually
2082 called i18n support) and translation for Spanish locale</li>
2083 <li>Define/Undefine group on current selection with
2084 Ctrl-G/Shift Ctrl-G</li>
2085 <li>Improved group creation/removal options in
2086 alignment/sequence Popup menu</li>
2087 <li>Sensible precision for symbol distribution
2088 percentages shown in logo tooltip.</li>
2089 <li>Annotation panel height set according to amount of
2090 annotation when alignment first opened</li>
2091 </ul> <em>Application</em>
2093 <li>Interactive consensus RNA secondary structure
2094 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2095 <li>Select columns containing particular features from
2096 Feature Settings dialog</li>
2097 <li>View all 'representative' PDB structures for selected
2099 <li>Update Jalview project format:
2101 <li>New file extension for Jalview projects '.jvp'</li>
2102 <li>Preserve sequence and annotation dataset (to
2103 store secondary structure annotation,etc)</li>
2104 <li>Per group and alignment annotation and RNA helix
2108 <li>New similarity measures for PCA and Tree calculation
2110 <li>Experimental support for retrieval and viewing of
2111 flanking regions for an alignment</li>
2115 <!-- issues resolved --> <em>Application</em>
2117 <li>logo keeps spinning and status remains at queued or
2118 running after job is cancelled</li>
2119 <li>cannot export features from alignments imported from
2120 Jalview/VAMSAS projects</li>
2121 <li>Buggy slider for web service parameters that take
2123 <li>Newly created RNA secondary structure line doesn't
2124 have 'display all symbols' flag set</li>
2125 <li>T-COFFEE alignment score shading scheme and other
2126 annotation shading not saved in Jalview project</li>
2127 <li>Local file cannot be loaded in freshly downloaded
2129 <li>Jalview icon not shown on dock in Mountain
2131 <li>Load file from desktop file browser fails</li>
2132 <li>Occasional NPE thrown when calculating large trees</li>
2133 <li>Cannot reorder or slide sequences after dragging an
2134 alignment onto desktop</li>
2135 <li>Colour by annotation dialog throws NPE after using
2136 'extract scores' function</li>
2137 <li>Loading/cut'n'pasting an empty file leads to a grey
2138 alignment window</li>
2139 <li>Disorder thresholds rendered incorrectly after
2140 performing IUPred disorder prediction</li>
2141 <li>Multiple group annotated consensus rows shown when
2142 changing 'normalise logo' display setting</li>
2143 <li>Find shows blank dialog after 'finished searching' if
2144 nothing matches query</li>
2145 <li>Null Pointer Exceptions raised when sorting by
2146 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2148 <li>Errors in Jmol console when structures in alignment
2149 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2151 <li>Not all working JABAWS services are shown in
2153 <li>JAVAWS version of Jalview fails to launch with
2154 'invalid literal/length code'</li>
2155 <li>Annotation/RNA Helix colourschemes cannot be applied
2156 to alignment with groups (actually fixed in 2.8.0b1)</li>
2157 <li>RNA Helices and T-Coffee Scores available as default
2160 </ul> <em>Applet</em>
2162 <li>Remove group option is shown even when selection is
2164 <li>Apply to all groups ticked but colourscheme changes
2165 don't affect groups</li>
2166 <li>Documented RNA Helices and T-Coffee Scores as valid
2167 colourscheme name</li>
2168 <li>Annotation labels drawn on sequence IDs when
2169 Annotation panel is not displayed</li>
2170 <li>Increased font size for dropdown menus on OSX and
2171 embedded windows</li>
2172 </ul> <em>Other</em>
2174 <li>Consensus sequence for alignments/groups with a
2175 single sequence were not calculated</li>
2176 <li>annotation files that contain only groups imported as
2177 annotation and junk sequences</li>
2178 <li>Fasta files with sequences containing '*' incorrectly
2179 recognised as PFAM or BLC</li>
2180 <li>conservation/PID slider apply all groups option
2181 doesn't affect background (2.8.0b1)
2183 <li>redundancy highlighting is erratic at 0% and 100%</li>
2184 <li>Remove gapped columns fails for sequences with ragged
2186 <li>AMSA annotation row with leading spaces is not
2187 registered correctly on import</li>
2188 <li>Jalview crashes when selecting PCA analysis for
2189 certain alignments</li>
2190 <li>Opening the colour by annotation dialog for an
2191 existing annotation based 'use original colours'
2192 colourscheme loses original colours setting</li>
2197 <td><div align="center">
2198 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2199 <em>30/1/2014</em></strong>
2203 <li>Trusted certificates for JalviewLite applet and
2204 Jalview Desktop application<br />Certificate was donated by
2205 <a href="https://www.certum.eu">Certum</a> to the Jalview
2206 open source project).
2208 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2209 <li>Output in Stockholm format</li>
2210 <li>Allow import of data from gzipped files</li>
2211 <li>Export/import group and sequence associated line
2212 graph thresholds</li>
2213 <li>Nucleotide substitution matrix that supports RNA and
2214 ambiguity codes</li>
2215 <li>Allow disorder predictions to be made on the current
2216 selection (or visible selection) in the same way that JPred
2218 <li>Groovy scripting for headless Jalview operation</li>
2219 </ul> <em>Other improvements</em>
2221 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2222 <li>COMBINE statement uses current SEQUENCE_REF and
2223 GROUP_REF scope to group annotation rows</li>
2224 <li>Support '' style escaping of quotes in Newick
2226 <li>Group options for JABAWS service by command line name</li>
2227 <li>Empty tooltip shown for JABA service options with a
2228 link but no description</li>
2229 <li>Select primary source when selecting authority in
2230 database fetcher GUI</li>
2231 <li>Add .mfa to FASTA file extensions recognised by
2233 <li>Annotation label tooltip text wrap</li>
2238 <li>Slow scrolling when lots of annotation rows are
2240 <li>Lots of NPE (and slowness) after creating RNA
2241 secondary structure annotation line</li>
2242 <li>Sequence database accessions not imported when
2243 fetching alignments from Rfam</li>
2244 <li>Incorrect SHMR submission for sequences with
2246 <li>View all structures does not always superpose
2248 <li>Option widgets in service parameters not updated to
2249 reflect user or preset settings</li>
2250 <li>Null pointer exceptions for some services without
2251 presets or adjustable parameters</li>
2252 <li>Discover PDB IDs entry in structure menu doesn't
2253 discover PDB xRefs</li>
2254 <li>Exception encountered while trying to retrieve
2255 features with DAS</li>
2256 <li>Lowest value in annotation row isn't coloured
2257 when colour by annotation (per sequence) is coloured</li>
2258 <li>Keyboard mode P jumps to start of gapped region when
2259 residue follows a gap</li>
2260 <li>Jalview appears to hang importing an alignment with
2261 Wrap as default or after enabling Wrap</li>
2262 <li>'Right click to add annotations' message
2263 shown in wrap mode when no annotations present</li>
2264 <li>Disorder predictions fail with NPE if no automatic
2265 annotation already exists on alignment</li>
2266 <li>oninit javascript function should be called after
2267 initialisation completes</li>
2268 <li>Remove redundancy after disorder prediction corrupts
2269 alignment window display</li>
2270 <li>Example annotation file in documentation is invalid</li>
2271 <li>Grouped line graph annotation rows are not exported
2272 to annotation file</li>
2273 <li>Multi-harmony analysis cannot be run when only two
2275 <li>Cannot create multiple groups of line graphs with
2276 several 'combine' statements in annotation file</li>
2277 <li>Pressing return several times causes Number Format
2278 exceptions in keyboard mode</li>
2279 <li>Multi-harmony (SHMMR) method doesn't submit
2280 correct partitions for input data</li>
2281 <li>Translation from DNA to Amino Acids fails</li>
2282 <li>Jalview fail to load newick tree with quoted label</li>
2283 <li>--headless flag isn't understood</li>
2284 <li>ClassCastException when generating EPS in headless
2286 <li>Adjusting sequence-associated shading threshold only
2287 changes one row's threshold</li>
2288 <li>Preferences and Feature settings panel panel
2289 doesn't open</li>
2290 <li>hide consensus histogram also hides conservation and
2291 quality histograms</li>
2296 <td><div align="center">
2297 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2299 <td><em>Application</em>
2301 <li>Support for JABAWS 2.0 Services (AACon alignment
2302 conservation, protein disorder and Clustal Omega)</li>
2303 <li>JABAWS server status indicator in Web Services
2305 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2306 in Jalview alignment window</li>
2307 <li>Updated Jalview build and deploy framework for OSX
2308 mountain lion, windows 7, and 8</li>
2309 <li>Nucleotide substitution matrix for PCA that supports
2310 RNA and ambiguity codes</li>
2312 <li>Improved sequence database retrieval GUI</li>
2313 <li>Support fetching and database reference look up
2314 against multiple DAS sources (Fetch all from in 'fetch db
2316 <li>Jalview project improvements
2318 <li>Store and retrieve the 'belowAlignment'
2319 flag for annotation</li>
2320 <li>calcId attribute to group annotation rows on the
2322 <li>Store AACon calculation settings for a view in
2323 Jalview project</li>
2327 <li>horizontal scrolling gesture support</li>
2328 <li>Visual progress indicator when PCA calculation is
2330 <li>Simpler JABA web services menus</li>
2331 <li>visual indication that web service results are still
2332 being retrieved from server</li>
2333 <li>Serialise the dialogs that are shown when Jalview
2334 starts up for first time</li>
2335 <li>Jalview user agent string for interacting with HTTP
2337 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2339 <li>Examples directory and Groovy library included in
2340 InstallAnywhere distribution</li>
2341 </ul> <em>Applet</em>
2343 <li>RNA alignment and secondary structure annotation
2344 visualization applet example</li>
2345 </ul> <em>General</em>
2347 <li>Normalise option for consensus sequence logo</li>
2348 <li>Reset button in PCA window to return dimensions to
2350 <li>Allow seqspace or Jalview variant of alignment PCA
2352 <li>PCA with either nucleic acid and protein substitution
2354 <li>Allow windows containing HTML reports to be exported
2356 <li>Interactive display and editing of RNA secondary
2357 structure contacts</li>
2358 <li>RNA Helix Alignment Colouring</li>
2359 <li>RNA base pair logo consensus</li>
2360 <li>Parse sequence associated secondary structure
2361 information in Stockholm files</li>
2362 <li>HTML Export database accessions and annotation
2363 information presented in tooltip for sequences</li>
2364 <li>Import secondary structure from LOCARNA clustalw
2365 style RNA alignment files</li>
2366 <li>import and visualise T-COFFEE quality scores for an
2368 <li>'colour by annotation' per sequence option to
2369 shade each sequence according to its associated alignment
2371 <li>New Jalview Logo</li>
2372 </ul> <em>Documentation and Development</em>
2374 <li>documentation for score matrices used in Jalview</li>
2375 <li>New Website!</li>
2377 <td><em>Application</em>
2379 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2380 wsdbfetch REST service</li>
2381 <li>Stop windows being moved outside desktop on OSX</li>
2382 <li>Filetype associations not installed for webstart
2384 <li>Jalview does not always retrieve progress of a JABAWS
2385 job execution in full once it is complete</li>
2386 <li>revise SHMR RSBS definition to ensure alignment is
2387 uploaded via ali_file parameter</li>
2388 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2389 <li>View all structures superposed fails with exception</li>
2390 <li>Jnet job queues forever if a very short sequence is
2391 submitted for prediction</li>
2392 <li>Cut and paste menu not opened when mouse clicked on
2394 <li>Putting fractional value into integer text box in
2395 alignment parameter dialog causes Jalview to hang</li>
2396 <li>Structure view highlighting doesn't work on
2398 <li>View all structures fails with exception shown in
2400 <li>Characters in filename associated with PDBEntry not
2401 escaped in a platform independent way</li>
2402 <li>Jalview desktop fails to launch with exception when
2404 <li>Tree calculation reports 'you must have 2 or more
2405 sequences selected' when selection is empty</li>
2406 <li>Jalview desktop fails to launch with jar signature
2407 failure when java web start temporary file caching is
2409 <li>DAS Sequence retrieval with range qualification
2410 results in sequence xref which includes range qualification</li>
2411 <li>Errors during processing of command line arguments
2412 cause progress bar (JAL-898) to be removed</li>
2413 <li>Replace comma for semi-colon option not disabled for
2414 DAS sources in sequence fetcher</li>
2415 <li>Cannot close news reader when JABAWS server warning
2416 dialog is shown</li>
2417 <li>Option widgets not updated to reflect user settings</li>
2418 <li>Edited sequence not submitted to web service</li>
2419 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2420 <li>InstallAnywhere installer doesn't unpack and run
2421 on OSX Mountain Lion</li>
2422 <li>Annotation panel not given a scroll bar when
2423 sequences with alignment annotation are pasted into the
2425 <li>Sequence associated annotation rows not associated
2426 when loaded from Jalview project</li>
2427 <li>Browser launch fails with NPE on java 1.7</li>
2428 <li>JABAWS alignment marked as finished when job was
2429 cancelled or job failed due to invalid input</li>
2430 <li>NPE with v2.7 example when clicking on Tree
2431 associated with all views</li>
2432 <li>Exceptions when copy/paste sequences with grouped
2433 annotation rows to new window</li>
2434 </ul> <em>Applet</em>
2436 <li>Sequence features are momentarily displayed before
2437 they are hidden using hidefeaturegroups applet parameter</li>
2438 <li>loading features via javascript API automatically
2439 enables feature display</li>
2440 <li>scrollToColumnIn javascript API method doesn't
2442 </ul> <em>General</em>
2444 <li>Redundancy removal fails for rna alignment</li>
2445 <li>PCA calculation fails when sequence has been selected
2446 and then deselected</li>
2447 <li>PCA window shows grey box when first opened on OSX</li>
2448 <li>Letters coloured pink in sequence logo when alignment
2449 coloured with clustalx</li>
2450 <li>Choosing fonts without letter symbols defined causes
2451 exceptions and redraw errors</li>
2452 <li>Initial PCA plot view is not same as manually
2453 reconfigured view</li>
2454 <li>Grouped annotation graph label has incorrect line
2456 <li>Grouped annotation graph label display is corrupted
2457 for lots of labels</li>
2462 <div align="center">
2463 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2466 <td><em>Application</em>
2468 <li>Jalview Desktop News Reader</li>
2469 <li>Tweaked default layout of web services menu</li>
2470 <li>View/alignment association menu to enable user to
2471 easily specify which alignment a multi-structure view takes
2472 its colours/correspondences from</li>
2473 <li>Allow properties file location to be specified as URL</li>
2474 <li>Extend Jalview project to preserve associations
2475 between many alignment views and a single Jmol display</li>
2476 <li>Store annotation row height in Jalview project file</li>
2477 <li>Annotation row column label formatting attributes
2478 stored in project file</li>
2479 <li>Annotation row order for auto-calculated annotation
2480 rows preserved in Jalview project file</li>
2481 <li>Visual progress indication when Jalview state is
2482 saved using Desktop window menu</li>
2483 <li>Visual indication that command line arguments are
2484 still being processed</li>
2485 <li>Groovy script execution from URL</li>
2486 <li>Colour by annotation default min and max colours in
2488 <li>Automatically associate PDB files dragged onto an
2489 alignment with sequences that have high similarity and
2491 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2492 <li>'view structures' option to open many
2493 structures in same window</li>
2494 <li>Sort associated views menu option for tree panel</li>
2495 <li>Group all JABA and non-JABA services for a particular
2496 analysis function in its own submenu</li>
2497 </ul> <em>Applet</em>
2499 <li>Userdefined and autogenerated annotation rows for
2501 <li>Adjustment of alignment annotation pane height</li>
2502 <li>Annotation scrollbar for annotation panel</li>
2503 <li>Drag to reorder annotation rows in annotation panel</li>
2504 <li>'automaticScrolling' parameter</li>
2505 <li>Allow sequences with partial ID string matches to be
2506 annotated from GFF/Jalview features files</li>
2507 <li>Sequence logo annotation row in applet</li>
2508 <li>Absolute paths relative to host server in applet
2509 parameters are treated as such</li>
2510 <li>New in the JalviewLite javascript API:
2512 <li>JalviewLite.js javascript library</li>
2513 <li>Javascript callbacks for
2515 <li>Applet initialisation</li>
2516 <li>Sequence/alignment mouse-overs and selections</li>
2519 <li>scrollTo row and column alignment scrolling
2521 <li>Select sequence/alignment regions from javascript</li>
2522 <li>javascript structure viewer harness to pass
2523 messages between Jmol and Jalview when running as
2524 distinct applets</li>
2525 <li>sortBy method</li>
2526 <li>Set of applet and application examples shipped
2527 with documentation</li>
2528 <li>New example to demonstrate JalviewLite and Jmol
2529 javascript message exchange</li>
2531 </ul> <em>General</em>
2533 <li>Enable Jmol displays to be associated with multiple
2534 multiple alignments</li>
2535 <li>Option to automatically sort alignment with new tree</li>
2536 <li>User configurable link to enable redirects to a
2537 www.Jalview.org mirror</li>
2538 <li>Jmol colours option for Jmol displays</li>
2539 <li>Configurable newline string when writing alignment
2540 and other flat files</li>
2541 <li>Allow alignment annotation description lines to
2542 contain html tags</li>
2543 </ul> <em>Documentation and Development</em>
2545 <li>Add groovy test harness for bulk load testing to
2547 <li>Groovy script to load and align a set of sequences
2548 using a web service before displaying the result in the
2549 Jalview desktop</li>
2550 <li>Restructured javascript and applet api documentation</li>
2551 <li>Ant target to publish example html files with applet
2553 <li>Netbeans project for building Jalview from source</li>
2554 <li>ant task to create online javadoc for Jalview source</li>
2556 <td><em>Application</em>
2558 <li>User defined colourscheme throws exception when
2559 current built in colourscheme is saved as new scheme</li>
2560 <li>AlignFrame->Save in application pops up save
2561 dialog for valid filename/format</li>
2562 <li>Cannot view associated structure for UniProt sequence</li>
2563 <li>PDB file association breaks for UniProt sequence
2565 <li>Associate PDB from file dialog does not tell you
2566 which sequence is to be associated with the file</li>
2567 <li>Find All raises null pointer exception when query
2568 only matches sequence IDs</li>
2569 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2570 <li>Jalview project with Jmol views created with Jalview
2571 2.4 cannot be loaded</li>
2572 <li>Filetype associations not installed for webstart
2574 <li>Two or more chains in a single PDB file associated
2575 with sequences in different alignments do not get coloured
2576 by their associated sequence</li>
2577 <li>Visibility status of autocalculated annotation row
2578 not preserved when project is loaded</li>
2579 <li>Annotation row height and visibility attributes not
2580 stored in Jalview project</li>
2581 <li>Tree bootstraps are not preserved when saved as a
2582 Jalview project</li>
2583 <li>Envision2 workflow tooltips are corrupted</li>
2584 <li>Enabling show group conservation also enables colour
2585 by conservation</li>
2586 <li>Duplicate group associated conservation or consensus
2587 created on new view</li>
2588 <li>Annotation scrollbar not displayed after 'show
2589 all hidden annotation rows' option selected</li>
2590 <li>Alignment quality not updated after alignment
2591 annotation row is hidden then shown</li>
2592 <li>Preserve colouring of structures coloured by
2593 sequences in pre Jalview 2.7 projects</li>
2594 <li>Web service job parameter dialog is not laid out
2596 <li>Web services menu not refreshed after 'reset
2597 services' button is pressed in preferences</li>
2598 <li>Annotation off by one in Jalview v2_3 example project</li>
2599 <li>Structures imported from file and saved in project
2600 get name like jalview_pdb1234.txt when reloaded</li>
2601 <li>Jalview does not always retrieve progress of a JABAWS
2602 job execution in full once it is complete</li>
2603 </ul> <em>Applet</em>
2605 <li>Alignment height set incorrectly when lots of
2606 annotation rows are displayed</li>
2607 <li>Relative URLs in feature HTML text not resolved to
2609 <li>View follows highlighting does not work for positions
2611 <li><= shown as = in tooltip</li>
2612 <li>Export features raises exception when no features
2614 <li>Separator string used for serialising lists of IDs
2615 for javascript api is modified when separator string
2616 provided as parameter</li>
2617 <li>Null pointer exception when selecting tree leaves for
2618 alignment with no existing selection</li>
2619 <li>Relative URLs for datasources assumed to be relative
2620 to applet's codebase</li>
2621 <li>Status bar not updated after finished searching and
2622 search wraps around to first result</li>
2623 <li>StructureSelectionManager instance shared between
2624 several Jalview applets causes race conditions and memory
2626 <li>Hover tooltip and mouseover of position on structure
2627 not sent from Jmol in applet</li>
2628 <li>Certain sequences of javascript method calls to
2629 applet API fatally hang browser</li>
2630 </ul> <em>General</em>
2632 <li>View follows structure mouseover scrolls beyond
2633 position with wrapped view and hidden regions</li>
2634 <li>Find sequence position moves to wrong residue
2635 with/without hidden columns</li>
2636 <li>Sequence length given in alignment properties window
2638 <li>InvalidNumberFormat exceptions thrown when trying to
2639 import PDB like structure files</li>
2640 <li>Positional search results are only highlighted
2641 between user-supplied sequence start/end bounds</li>
2642 <li>End attribute of sequence is not validated</li>
2643 <li>Find dialog only finds first sequence containing a
2644 given sequence position</li>
2645 <li>Sequence numbering not preserved in MSF alignment
2647 <li>Jalview PDB file reader does not extract sequence
2648 from nucleotide chains correctly</li>
2649 <li>Structure colours not updated when tree partition
2650 changed in alignment</li>
2651 <li>Sequence associated secondary structure not correctly
2652 parsed in interleaved stockholm</li>
2653 <li>Colour by annotation dialog does not restore current
2655 <li>Hiding (nearly) all sequences doesn't work
2657 <li>Sequences containing lowercase letters are not
2658 properly associated with their pdb files</li>
2659 </ul> <em>Documentation and Development</em>
2661 <li>schemas/JalviewWsParamSet.xsd corrupted by
2662 ApplyCopyright tool</li>
2667 <div align="center">
2668 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2671 <td><em>Application</em>
2673 <li>New warning dialog when the Jalview Desktop cannot
2674 contact web services</li>
2675 <li>JABA service parameters for a preset are shown in
2676 service job window</li>
2677 <li>JABA Service menu entries reworded</li>
2681 <li>Modeller PIR IO broken - cannot correctly import a
2682 pir file emitted by Jalview</li>
2683 <li>Existing feature settings transferred to new
2684 alignment view created from cut'n'paste</li>
2685 <li>Improved test for mixed amino/nucleotide chains when
2686 parsing PDB files</li>
2687 <li>Consensus and conservation annotation rows
2688 occasionally become blank for all new windows</li>
2689 <li>Exception raised when right clicking above sequences
2690 in wrapped view mode</li>
2691 </ul> <em>Application</em>
2693 <li>multiple multiply aligned structure views cause cpu
2694 usage to hit 100% and computer to hang</li>
2695 <li>Web Service parameter layout breaks for long user
2696 parameter names</li>
2697 <li>Jaba service discovery hangs desktop if Jaba server
2704 <div align="center">
2705 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2708 <td><em>Application</em>
2710 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2711 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2714 <li>Web Services preference tab</li>
2715 <li>Analysis parameters dialog box and user defined
2717 <li>Improved speed and layout of Envision2 service menu</li>
2718 <li>Superpose structures using associated sequence
2720 <li>Export coordinates and projection as CSV from PCA
2722 </ul> <em>Applet</em>
2724 <li>enable javascript: execution by the applet via the
2725 link out mechanism</li>
2726 </ul> <em>Other</em>
2728 <li>Updated the Jmol Jalview interface to work with Jmol
2730 <li>The Jalview Desktop and JalviewLite applet now
2731 require Java 1.5</li>
2732 <li>Allow Jalview feature colour specification for GFF
2733 sequence annotation files</li>
2734 <li>New 'colour by label' keword in Jalview feature file
2735 type colour specification</li>
2736 <li>New Jalview Desktop Groovy API method that allows a
2737 script to check if it being run in an interactive session or
2738 in a batch operation from the Jalview command line</li>
2742 <li>clustalx colourscheme colours Ds preferentially when
2743 both D+E are present in over 50% of the column</li>
2744 </ul> <em>Application</em>
2746 <li>typo in AlignmentFrame->View->Hide->all but
2747 selected Regions menu item</li>
2748 <li>sequence fetcher replaces ',' for ';' when the ',' is
2749 part of a valid accession ID</li>
2750 <li>fatal OOM if object retrieved by sequence fetcher
2751 runs out of memory</li>
2752 <li>unhandled Out of Memory Error when viewing pca
2753 analysis results</li>
2754 <li>InstallAnywhere builds fail to launch on OS X java
2755 10.5 update 4 (due to apple Java 1.6 update)</li>
2756 <li>Installanywhere Jalview silently fails to launch</li>
2757 </ul> <em>Applet</em>
2759 <li>Jalview.getFeatureGroups() raises an
2760 ArrayIndexOutOfBoundsException if no feature groups are
2767 <div align="center">
2768 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2774 <li>Alignment prettyprinter doesn't cope with long
2776 <li>clustalx colourscheme colours Ds preferentially when
2777 both D+E are present in over 50% of the column</li>
2778 <li>nucleic acid structures retrieved from PDB do not
2779 import correctly</li>
2780 <li>More columns get selected than were clicked on when a
2781 number of columns are hidden</li>
2782 <li>annotation label popup menu not providing correct
2783 add/hide/show options when rows are hidden or none are
2785 <li>Stockholm format shown in list of readable formats,
2786 and parser copes better with alignments from RFAM.</li>
2787 <li>CSV output of consensus only includes the percentage
2788 of all symbols if sequence logo display is enabled</li>
2790 </ul> <em>Applet</em>
2792 <li>annotation panel disappears when annotation is
2794 </ul> <em>Application</em>
2796 <li>Alignment view not redrawn properly when new
2797 alignment opened where annotation panel is visible but no
2798 annotations are present on alignment</li>
2799 <li>pasted region containing hidden columns is
2800 incorrectly displayed in new alignment window</li>
2801 <li>Jalview slow to complete operations when stdout is
2802 flooded (fix is to close the Jalview console)</li>
2803 <li>typo in AlignmentFrame->View->Hide->all but
2804 selected Rregions menu item.</li>
2805 <li>inconsistent group submenu and Format submenu entry
2806 'Un' or 'Non'conserved</li>
2807 <li>Sequence feature settings are being shared by
2808 multiple distinct alignments</li>
2809 <li>group annotation not recreated when tree partition is
2811 <li>double click on group annotation to select sequences
2812 does not propagate to associated trees</li>
2813 <li>Mac OSX specific issues:
2815 <li>exception raised when mouse clicked on desktop
2816 window background</li>
2817 <li>Desktop menu placed on menu bar and application
2818 name set correctly</li>
2819 <li>sequence feature settings not wide enough for the
2820 save feature colourscheme button</li>
2829 <div align="center">
2830 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2833 <td><em>New Capabilities</em>
2835 <li>URL links generated from description line for
2836 regular-expression based URL links (applet and application)
2838 <li>Non-positional feature URL links are shown in link
2840 <li>Linked viewing of nucleic acid sequences and
2842 <li>Automatic Scrolling option in View menu to display
2843 the currently highlighted region of an alignment.</li>
2844 <li>Order an alignment by sequence length, or using the
2845 average score or total feature count for each sequence.</li>
2846 <li>Shading features by score or associated description</li>
2847 <li>Subdivide alignment and groups based on identity of
2848 selected subsequence (Make Groups from Selection).</li>
2849 <li>New hide/show options including Shift+Control+H to
2850 hide everything but the currently selected region.</li>
2851 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2852 </ul> <em>Application</em>
2854 <li>Fetch DB References capabilities and UI expanded to
2855 support retrieval from DAS sequence sources</li>
2856 <li>Local DAS Sequence sources can be added via the
2857 command line or via the Add local source dialog box.</li>
2858 <li>DAS Dbref and DbxRef feature types are parsed as
2859 database references and protein_name is parsed as
2860 description line (BioSapiens terms).</li>
2861 <li>Enable or disable non-positional feature and database
2862 references in sequence ID tooltip from View menu in
2864 <!-- <li>New hidden columns and rows and representatives capabilities
2865 in annotations file (in progress - not yet fully implemented)</li> -->
2866 <li>Group-associated consensus, sequence logos and
2867 conservation plots</li>
2868 <li>Symbol distributions for each column can be exported
2869 and visualized as sequence logos</li>
2870 <li>Optionally scale multi-character column labels to fit
2871 within each column of annotation row<!-- todo for applet -->
2873 <li>Optional automatic sort of associated alignment view
2874 when a new tree is opened.</li>
2875 <li>Jalview Java Console</li>
2876 <li>Better placement of desktop window when moving
2877 between different screens.</li>
2878 <li>New preference items for sequence ID tooltip and
2879 consensus annotation</li>
2880 <li>Client to submit sequences and IDs to Envision2
2882 <li><em>Vamsas Capabilities</em>
2884 <li>Improved VAMSAS synchronization (Jalview archive
2885 used to preserve views, structures, and tree display
2887 <li>Import of vamsas documents from disk or URL via
2889 <li>Sharing of selected regions between views and
2890 with other VAMSAS applications (Experimental feature!)</li>
2891 <li>Updated API to VAMSAS version 0.2</li>
2893 </ul> <em>Applet</em>
2895 <li>Middle button resizes annotation row height</li>
2898 <li>sortByTree (true/false) - automatically sort the
2899 associated alignment view by the tree when a new tree is
2901 <li>showTreeBootstraps (true/false) - show or hide
2902 branch bootstraps (default is to show them if available)</li>
2903 <li>showTreeDistances (true/false) - show or hide
2904 branch lengths (default is to show them if available)</li>
2905 <li>showUnlinkedTreeNodes (true/false) - indicate if
2906 unassociated nodes should be highlighted in the tree
2908 <li>heightScale and widthScale (1.0 or more) -
2909 increase the height or width of a cell in the alignment
2910 grid relative to the current font size.</li>
2913 <li>Non-positional features displayed in sequence ID
2915 </ul> <em>Other</em>
2917 <li>Features format: graduated colour definitions and
2918 specification of feature scores</li>
2919 <li>Alignment Annotations format: new keywords for group
2920 associated annotation (GROUP_REF) and annotation row display
2921 properties (ROW_PROPERTIES)</li>
2922 <li>XML formats extended to support graduated feature
2923 colourschemes, group associated annotation, and profile
2924 visualization settings.</li></td>
2927 <li>Source field in GFF files parsed as feature source
2928 rather than description</li>
2929 <li>Non-positional features are now included in sequence
2930 feature and gff files (controlled via non-positional feature
2931 visibility in tooltip).</li>
2932 <li>URL links generated for all feature links (bugfix)</li>
2933 <li>Added URL embedding instructions to features file
2935 <li>Codons containing ambiguous nucleotides translated as
2936 'X' in peptide product</li>
2937 <li>Match case switch in find dialog box works for both
2938 sequence ID and sequence string and query strings do not
2939 have to be in upper case to match case-insensitively.</li>
2940 <li>AMSA files only contain first column of
2941 multi-character column annotation labels</li>
2942 <li>Jalview Annotation File generation/parsing consistent
2943 with documentation (e.g. Stockholm annotation can be
2944 exported and re-imported)</li>
2945 <li>PDB files without embedded PDB IDs given a friendly
2947 <li>Find incrementally searches ID string matches as well
2948 as subsequence matches, and correctly reports total number
2952 <li>Better handling of exceptions during sequence
2954 <li>Dasobert generated non-positional feature URL
2955 link text excludes the start_end suffix</li>
2956 <li>DAS feature and source retrieval buttons disabled
2957 when fetch or registry operations in progress.</li>
2958 <li>PDB files retrieved from URLs are cached properly</li>
2959 <li>Sequence description lines properly shared via
2961 <li>Sequence fetcher fetches multiple records for all
2963 <li>Ensured that command line das feature retrieval
2964 completes before alignment figures are generated.</li>
2965 <li>Reduced time taken when opening file browser for
2967 <li>isAligned check prior to calculating tree, PCA or
2968 submitting an MSA to JNet now excludes hidden sequences.</li>
2969 <li>User defined group colours properly recovered
2970 from Jalview projects.</li>
2979 <div align="center">
2980 <strong>2.4.0.b2</strong><br> 28/10/2009
2985 <li>Experimental support for google analytics usage
2987 <li>Jalview privacy settings (user preferences and docs).</li>
2992 <li>Race condition in applet preventing startup in
2994 <li>Exception when feature created from selection beyond
2995 length of sequence.</li>
2996 <li>Allow synthetic PDB files to be imported gracefully</li>
2997 <li>Sequence associated annotation rows associate with
2998 all sequences with a given id</li>
2999 <li>Find function matches case-insensitively for sequence
3000 ID string searches</li>
3001 <li>Non-standard characters do not cause pairwise
3002 alignment to fail with exception</li>
3003 </ul> <em>Application Issues</em>
3005 <li>Sequences are now validated against EMBL database</li>
3006 <li>Sequence fetcher fetches multiple records for all
3008 </ul> <em>InstallAnywhere Issues</em>
3010 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3011 issue with installAnywhere mechanism)</li>
3012 <li>Command line launching of JARs from InstallAnywhere
3013 version (java class versioning error fixed)</li>
3020 <div align="center">
3021 <strong>2.4</strong><br> 27/8/2008
3024 <td><em>User Interface</em>
3026 <li>Linked highlighting of codon and amino acid from
3027 translation and protein products</li>
3028 <li>Linked highlighting of structure associated with
3029 residue mapping to codon position</li>
3030 <li>Sequence Fetcher provides example accession numbers
3031 and 'clear' button</li>
3032 <li>MemoryMonitor added as an option under Desktop's
3034 <li>Extract score function to parse whitespace separated
3035 numeric data in description line</li>
3036 <li>Column labels in alignment annotation can be centred.</li>
3037 <li>Tooltip for sequence associated annotation give name
3039 </ul> <em>Web Services and URL fetching</em>
3041 <li>JPred3 web service</li>
3042 <li>Prototype sequence search client (no public services
3044 <li>Fetch either seed alignment or full alignment from
3046 <li>URL Links created for matching database cross
3047 references as well as sequence ID</li>
3048 <li>URL Links can be created using regular-expressions</li>
3049 </ul> <em>Sequence Database Connectivity</em>
3051 <li>Retrieval of cross-referenced sequences from other
3053 <li>Generalised database reference retrieval and
3054 validation to all fetchable databases</li>
3055 <li>Fetch sequences from DAS sources supporting the
3056 sequence command</li>
3057 </ul> <em>Import and Export</em>
3058 <li>export annotation rows as CSV for spreadsheet import</li>
3059 <li>Jalview projects record alignment dataset associations,
3060 EMBL products, and cDNA sequence mappings</li>
3061 <li>Sequence Group colour can be specified in Annotation
3063 <li>Ad-hoc colouring of group in Annotation File using RGB
3064 triplet as name of colourscheme</li>
3065 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3067 <li>treenode binding for VAMSAS tree exchange</li>
3068 <li>local editing and update of sequences in VAMSAS
3069 alignments (experimental)</li>
3070 <li>Create new or select existing session to join</li>
3071 <li>load and save of vamsas documents</li>
3072 </ul> <em>Application command line</em>
3074 <li>-tree parameter to open trees (introduced for passing
3076 <li>-fetchfrom command line argument to specify nicknames
3077 of DAS servers to query for alignment features</li>
3078 <li>-dasserver command line argument to add new servers
3079 that are also automatically queried for features</li>
3080 <li>-groovy command line argument executes a given groovy
3081 script after all input data has been loaded and parsed</li>
3082 </ul> <em>Applet-Application data exchange</em>
3084 <li>Trees passed as applet parameters can be passed to
3085 application (when using "View in full
3086 application")</li>
3087 </ul> <em>Applet Parameters</em>
3089 <li>feature group display control parameter</li>
3090 <li>debug parameter</li>
3091 <li>showbutton parameter</li>
3092 </ul> <em>Applet API methods</em>
3094 <li>newView public method</li>
3095 <li>Window (current view) specific get/set public methods</li>
3096 <li>Feature display control methods</li>
3097 <li>get list of currently selected sequences</li>
3098 </ul> <em>New Jalview distribution features</em>
3100 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3101 <li>RELEASE file gives build properties for the latest
3102 Jalview release.</li>
3103 <li>Java 1.1 Applet build made easier and donotobfuscate
3104 property controls execution of obfuscator</li>
3105 <li>Build target for generating source distribution</li>
3106 <li>Debug flag for javacc</li>
3107 <li>.jalview_properties file is documented (slightly) in
3108 jalview.bin.Cache</li>
3109 <li>Continuous Build Integration for stable and
3110 development version of Application, Applet and source
3115 <li>selected region output includes visible annotations
3116 (for certain formats)</li>
3117 <li>edit label/displaychar contains existing label/char
3119 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3120 <li>shorter peptide product names from EMBL records</li>
3121 <li>Newick string generator makes compact representations</li>
3122 <li>bootstrap values parsed correctly for tree files with
3124 <li>pathological filechooser bug avoided by not allowing
3125 filenames containing a ':'</li>
3126 <li>Fixed exception when parsing GFF files containing
3127 global sequence features</li>
3128 <li>Alignment datasets are finalized only when number of
3129 references from alignment sequences goes to zero</li>
3130 <li>Close of tree branch colour box without colour
3131 selection causes cascading exceptions</li>
3132 <li>occasional negative imgwidth exceptions</li>
3133 <li>better reporting of non-fatal warnings to user when
3134 file parsing fails.</li>
3135 <li>Save works when Jalview project is default format</li>
3136 <li>Save as dialog opened if current alignment format is
3137 not a valid output format</li>
3138 <li>UniProt canonical names introduced for both das and
3140 <li>Histidine should be midblue (not pink!) in Zappo</li>
3141 <li>error messages passed up and output when data read
3143 <li>edit undo recovers previous dataset sequence when
3144 sequence is edited</li>
3145 <li>allow PDB files without pdb ID HEADER lines (like
3146 those generated by MODELLER) to be read in properly</li>
3147 <li>allow reading of JPred concise files as a normal
3149 <li>Stockholm annotation parsing and alignment properties
3150 import fixed for PFAM records</li>
3151 <li>Structure view windows have correct name in Desktop
3153 <li>annotation consisting of sequence associated scores
3154 can be read and written correctly to annotation file</li>
3155 <li>Aligned cDNA translation to aligned peptide works
3157 <li>Fixed display of hidden sequence markers and
3158 non-italic font for representatives in Applet</li>
3159 <li>Applet Menus are always embedded in applet window on
3161 <li>Newly shown features appear at top of stack (in
3163 <li>Annotations added via parameter not drawn properly
3164 due to null pointer exceptions</li>
3165 <li>Secondary structure lines are drawn starting from
3166 first column of alignment</li>
3167 <li>UniProt XML import updated for new schema release in
3169 <li>Sequence feature to sequence ID match for Features
3170 file is case-insensitive</li>
3171 <li>Sequence features read from Features file appended to
3172 all sequences with matching IDs</li>
3173 <li>PDB structure coloured correctly for associated views
3174 containing a sub-sequence</li>
3175 <li>PDB files can be retrieved by applet from Jar files</li>
3176 <li>feature and annotation file applet parameters
3177 referring to different directories are retrieved correctly</li>
3178 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3179 <li>Fixed application hang whilst waiting for
3180 splash-screen version check to complete</li>
3181 <li>Applet properly URLencodes input parameter values
3182 when passing them to the launchApp service</li>
3183 <li>display name and local features preserved in results
3184 retrieved from web service</li>
3185 <li>Visual delay indication for sequence retrieval and
3186 sequence fetcher initialisation</li>
3187 <li>updated Application to use DAS 1.53e version of
3188 dasobert DAS client</li>
3189 <li>Re-instated Full AMSA support and .amsa file
3191 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3199 <div align="center">
3200 <strong>2.3</strong><br> 9/5/07
3205 <li>Jmol 11.0.2 integration</li>
3206 <li>PDB views stored in Jalview XML files</li>
3207 <li>Slide sequences</li>
3208 <li>Edit sequence in place</li>
3209 <li>EMBL CDS features</li>
3210 <li>DAS Feature mapping</li>
3211 <li>Feature ordering</li>
3212 <li>Alignment Properties</li>
3213 <li>Annotation Scores</li>
3214 <li>Sort by scores</li>
3215 <li>Feature/annotation editing in applet</li>
3220 <li>Headless state operation in 2.2.1</li>
3221 <li>Incorrect and unstable DNA pairwise alignment</li>
3222 <li>Cut and paste of sequences with annotation</li>
3223 <li>Feature group display state in XML</li>
3224 <li>Feature ordering in XML</li>
3225 <li>blc file iteration selection using filename # suffix</li>
3226 <li>Stockholm alignment properties</li>
3227 <li>Stockhom alignment secondary structure annotation</li>
3228 <li>2.2.1 applet had no feature transparency</li>
3229 <li>Number pad keys can be used in cursor mode</li>
3230 <li>Structure Viewer mirror image resolved</li>
3237 <div align="center">
3238 <strong>2.2.1</strong><br> 12/2/07
3243 <li>Non standard characters can be read and displayed
3244 <li>Annotations/Features can be imported/exported to the
3246 <li>Applet allows editing of sequence/annotation/group
3247 name & description
3248 <li>Preference setting to display sequence name in
3250 <li>Annotation file format extended to allow
3251 Sequence_groups to be defined
3252 <li>Default opening of alignment overview panel can be
3253 specified in preferences
3254 <li>PDB residue numbering annotation added to associated
3260 <li>Applet crash under certain Linux OS with Java 1.6
3262 <li>Annotation file export / import bugs fixed
3263 <li>PNG / EPS image output bugs fixed
3269 <div align="center">
3270 <strong>2.2</strong><br> 27/11/06
3275 <li>Multiple views on alignment
3276 <li>Sequence feature editing
3277 <li>"Reload" alignment
3278 <li>"Save" to current filename
3279 <li>Background dependent text colour
3280 <li>Right align sequence ids
3281 <li>User-defined lower case residue colours
3284 <li>Menu item accelerator keys
3285 <li>Control-V pastes to current alignment
3286 <li>Cancel button for DAS Feature Fetching
3287 <li>PCA and PDB Viewers zoom via mouse roller
3288 <li>User-defined sub-tree colours and sub-tree selection
3290 <li>'New Window' button on the 'Output to Text box'
3295 <li>New memory efficient Undo/Redo System
3296 <li>Optimised symbol lookups and conservation/consensus
3298 <li>Region Conservation/Consensus recalculated after
3300 <li>Fixed Remove Empty Columns Bug (empty columns at end
3302 <li>Slowed DAS Feature Fetching for increased robustness.
3304 <li>Made angle brackets in ASCII feature descriptions
3306 <li>Re-instated Zoom function for PCA
3307 <li>Sequence descriptions conserved in web service
3309 <li>UniProt ID discoverer uses any word separated by
3311 <li>WsDbFetch query/result association resolved
3312 <li>Tree leaf to sequence mapping improved
3313 <li>Smooth fonts switch moved to FontChooser dialog box.
3320 <div align="center">
3321 <strong>2.1.1</strong><br> 12/9/06
3326 <li>Copy consensus sequence to clipboard</li>
3331 <li>Image output - rightmost residues are rendered if
3332 sequence id panel has been resized</li>
3333 <li>Image output - all offscreen group boundaries are
3335 <li>Annotation files with sequence references - all
3336 elements in file are relative to sequence position</li>
3337 <li>Mac Applet users can use Alt key for group editing</li>
3343 <div align="center">
3344 <strong>2.1</strong><br> 22/8/06
3349 <li>MAFFT Multiple Alignment in default Web Service list</li>
3350 <li>DAS Feature fetching</li>
3351 <li>Hide sequences and columns</li>
3352 <li>Export Annotations and Features</li>
3353 <li>GFF file reading / writing</li>
3354 <li>Associate structures with sequences from local PDB
3356 <li>Add sequences to exisiting alignment</li>
3357 <li>Recently opened files / URL lists</li>
3358 <li>Applet can launch the full application</li>
3359 <li>Applet has transparency for features (Java 1.2
3361 <li>Applet has user defined colours parameter</li>
3362 <li>Applet can load sequences from parameter
3363 "sequence<em>x</em>"
3369 <li>Redundancy Panel reinstalled in the Applet</li>
3370 <li>Monospaced font - EPS / rescaling bug fixed</li>
3371 <li>Annotation files with sequence references bug fixed</li>
3377 <div align="center">
3378 <strong>2.08.1</strong><br> 2/5/06
3383 <li>Change case of selected region from Popup menu</li>
3384 <li>Choose to match case when searching</li>
3385 <li>Middle mouse button and mouse movement can compress /
3386 expand the visible width and height of the alignment</li>
3391 <li>Annotation Panel displays complete JNet results</li>
3397 <div align="center">
3398 <strong>2.08b</strong><br> 18/4/06
3404 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3405 <li>Righthand label on wrapped alignments shows correct
3412 <div align="center">
3413 <strong>2.08</strong><br> 10/4/06
3418 <li>Editing can be locked to the selection area</li>
3419 <li>Keyboard editing</li>
3420 <li>Create sequence features from searches</li>
3421 <li>Precalculated annotations can be loaded onto
3423 <li>Features file allows grouping of features</li>
3424 <li>Annotation Colouring scheme added</li>
3425 <li>Smooth fonts off by default - Faster rendering</li>
3426 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3431 <li>Drag & Drop fixed on Linux</li>
3432 <li>Jalview Archive file faster to load/save, sequence
3433 descriptions saved.</li>
3439 <div align="center">
3440 <strong>2.07</strong><br> 12/12/05
3445 <li>PDB Structure Viewer enhanced</li>
3446 <li>Sequence Feature retrieval and display enhanced</li>
3447 <li>Choose to output sequence start-end after sequence
3448 name for file output</li>
3449 <li>Sequence Fetcher WSDBFetch@EBI</li>
3450 <li>Applet can read feature files, PDB files and can be
3451 used for HTML form input</li>
3456 <li>HTML output writes groups and features</li>
3457 <li>Group editing is Control and mouse click</li>
3458 <li>File IO bugs</li>
3464 <div align="center">
3465 <strong>2.06</strong><br> 28/9/05
3470 <li>View annotations in wrapped mode</li>
3471 <li>More options for PCA viewer</li>
3476 <li>GUI bugs resolved</li>
3477 <li>Runs with -nodisplay from command line</li>
3483 <div align="center">
3484 <strong>2.05b</strong><br> 15/9/05
3489 <li>Choose EPS export as lineart or text</li>
3490 <li>Jar files are executable</li>
3491 <li>Can read in Uracil - maps to unknown residue</li>
3496 <li>Known OutOfMemory errors give warning message</li>
3497 <li>Overview window calculated more efficiently</li>
3498 <li>Several GUI bugs resolved</li>
3504 <div align="center">
3505 <strong>2.05</strong><br> 30/8/05
3510 <li>Edit and annotate in "Wrapped" view</li>
3515 <li>Several GUI bugs resolved</li>
3521 <div align="center">
3522 <strong>2.04</strong><br> 24/8/05
3527 <li>Hold down mouse wheel & scroll to change font
3533 <li>Improved JPred client reliability</li>
3534 <li>Improved loading of Jalview files</li>
3540 <div align="center">
3541 <strong>2.03</strong><br> 18/8/05
3546 <li>Set Proxy server name and port in preferences</li>
3547 <li>Multiple URL links from sequence ids</li>
3548 <li>User Defined Colours can have a scheme name and added
3550 <li>Choose to ignore gaps in consensus calculation</li>
3551 <li>Unix users can set default web browser</li>
3552 <li>Runs without GUI for batch processing</li>
3553 <li>Dynamically generated Web Service Menus</li>
3558 <li>InstallAnywhere download for Sparc Solaris</li>
3564 <div align="center">
3565 <strong>2.02</strong><br> 18/7/05
3571 <li>Copy & Paste order of sequences maintains
3572 alignment order.</li>
3578 <div align="center">
3579 <strong>2.01</strong><br> 12/7/05
3584 <li>Use delete key for deleting selection.</li>
3585 <li>Use Mouse wheel to scroll sequences.</li>
3586 <li>Help file updated to describe how to add alignment
3588 <li>Version and build date written to build properties
3590 <li>InstallAnywhere installation will check for updates
3591 at launch of Jalview.</li>
3596 <li>Delete gaps bug fixed.</li>
3597 <li>FileChooser sorts columns.</li>
3598 <li>Can remove groups one by one.</li>
3599 <li>Filechooser icons installed.</li>
3600 <li>Finder ignores return character when searching.
3601 Return key will initiate a search.<br>
3608 <div align="center">
3609 <strong>2.0</strong><br> 20/6/05
3614 <li>New codebase</li>