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>14/11/2017</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>
99 <ul><li>Example groovy script for generating a matrix of percent identity scores for current alignment.</li></ul>
100 <em>Testing and Deployment</em>
101 <ul><li><!-- JAL-2727 -->Test to catch memory leaks in Jalview UI</li></ul>
104 <td><div align="left">
107 <li><!-- JAL-2643 -->Pressing tab after updating the colour threshold text field doesn't trigger an update to the alignment view</li>
108 <li><!-- JAL-2682 -->Race condition when parsing sequence ID strings in parallel</li>
109 <li><!-- JAL-2608 -->Overview windows are also closed when alignment window is closed</li>
110 <li><!-- JAL-2548 -->Export of features doesn't always respect group visibility</li>
114 <li><!-- JAL-2777 -->Structures with whitespace chainCode cannot be viewed in Chimera</li>
115 <li><!-- JAL-2728 -->Protein annotation panel too high in CDS/Protein view
117 <li><!-- JAL-2757 -->Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs
119 <li><!-- JAL-2253 -->Slow EnsemblGenome ID lookup</li>
120 <li><!-- JAL-2529 -->Revised Ensembl REST API CDNA query</li>
121 <li><!-- JAL-2739 -->Hidden column marker in last column not rendered when switching back from Wrapped to normal view</li>
122 <li><!-- JAL-2768 -->Annotation display corrupted when scrolling right in unwapped alignment view</li>
123 <li><!-- JAL-2542 -->Existing features on subsequence incorrectly relocated when full sequence retrieved from database</li>
124 <li><!-- JAL-2733 -->Last reported memory still shown when Desktop->Show Memory is unticked (OSX only)</li>
125 <li><!-- JAL-2658 -->Amend Features dialog doesn't allow features of same type and group to be selected for amending</li>
126 <li><!-- JAL-2524 -->Jalview becomes sluggish in wide alignments when hidden columns are present</li>
127 <li><!-- JAL-2392 -->Jalview freezes when loading and displaying several structures</li>
128 <li><!-- JAL-2732 -->Black outlines left after resizing or moving a window</li>
129 <li><!-- JAL-1900,JAL-1625 -->Unable to minimise windows within the Jalview desktop on OSX</li>
130 <li><!-- JAL-2667 -->Mouse wheel doesn't scroll vertically when in wrapped alignment mode</li>
131 <li><!-- JAL-2636 -->Scale mark not shown when close to right hand end of alignment</li>
132 <li><!-- JAL-2684 -->Pairwise alignment only aligns selected regions of each selected sequence</li>
133 <li><!-- JAL-2973 -->Alignment ruler height set incorrectly after canceling the Alignment Window's Font dialog</li>
134 <li><!-- JAL-2036 -->Show cross-references not enabled after restoring project until a new view is created</li>
135 <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>
136 <li><!-- JAL-2775 -->Overview redraws whole window when box position is adjusted</li>
137 <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>
139 <strong><em>Applet</em></strong><br/>
141 <li><!-- JAL-2687 -->Concurrent modification exception when closing alignment panel</li>
143 <strong><em>BioJSON</em></strong><br/>
146 <!-- JAL-2546 -->BioJSON export does not preserve non-positional features
153 <td width="60" nowrap>
155 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
156 <em>2/10/2017</em></strong>
159 <td><div align="left">
160 <em>New features in Jalview Desktop</em>
163 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
165 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
169 <td><div align="left">
173 <td width="60" nowrap>
175 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
176 <em>7/9/2017</em></strong>
179 <td><div align="left">
183 <!-- JAL-2588 -->Show gaps in overview window by colouring
184 in grey (sequences used to be coloured grey, and gaps were
188 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
192 <!-- JAL-2587 -->Overview updates immediately on increase
193 in size and progress bar shown as higher resolution
194 overview is recalculated
199 <td><div align="left">
203 <!-- JAL-2664 -->Overview window redraws every hidden
204 column region row by row
207 <!-- JAL-2681 -->duplicate protein sequences shown after
208 retrieving Ensembl crossrefs for sequences from Uniprot
211 <!-- JAL-2603 -->Overview window throws NPE if show boxes
212 format setting is unticked
215 <!-- JAL-2610 -->Groups are coloured wrongly in overview
216 if group has show boxes format setting unticked
219 <!-- JAL-2672,JAL-2665 -->Redraw problems when
220 autoscrolling whilst dragging current selection group to
221 include sequences and columns not currently displayed
224 <!-- JAL-2691 -->Not all chains are mapped when multimeric
225 assemblies are imported via CIF file
228 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
229 displayed when threshold or conservation colouring is also
233 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
237 <!-- JAL-2673 -->Jalview continues to scroll after
238 dragging a selected region off the visible region of the
242 <!-- JAL-2724 -->Cannot apply annotation based
243 colourscheme to all groups in a view
246 <!-- JAL-2511 -->IDs don't line up with sequences
247 initially after font size change using the Font chooser or
254 <td width="60" nowrap>
256 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
259 <td><div align="left">
260 <em>Calculations</em>
264 <!-- JAL-1933 -->Occupancy annotation row shows number of
265 ungapped positions in each column of the alignment.
268 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
269 a calculation dialog box
272 <!-- JAL-2379 -->Revised implementation of PCA for speed
273 and memory efficiency (~30x faster)
276 <!-- JAL-2403 -->Revised implementation of sequence
277 similarity scores as used by Tree, PCA, Shading Consensus
278 and other calculations
281 <!-- JAL-2416 -->Score matrices are stored as resource
282 files within the Jalview codebase
285 <!-- JAL-2500 -->Trees computed on Sequence Feature
286 Similarity may have different topology due to increased
293 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
294 model for alignments and groups
297 <!-- JAL-384 -->Custom shading schemes created via groovy
304 <!-- JAL-2526 -->Efficiency improvements for interacting
305 with alignment and overview windows
308 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
312 <!-- JAL-2388 -->Hidden columns and sequences can be
316 <!-- JAL-2611 -->Click-drag in visible area allows fine
317 adjustment of visible position
321 <em>Data import/export</em>
324 <!-- JAL-2535 -->Posterior probability annotation from
325 Stockholm files imported as sequence associated annotation
328 <!-- JAL-2507 -->More robust per-sequence positional
329 annotation input/output via stockholm flatfile
332 <!-- JAL-2533 -->Sequence names don't include file
333 extension when importing structure files without embedded
334 names or PDB accessions
337 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
338 format sequence substitution matrices
341 <em>User Interface</em>
344 <!-- JAL-2447 --> Experimental Features Checkbox in
345 Desktop's Tools menu to hide or show untested features in
349 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
350 via Overview or sequence motif search operations
353 <!-- JAL-2547 -->Amend sequence features dialog box can be
354 opened by double clicking gaps within sequence feature
358 <!-- JAL-1476 -->Status bar message shown when not enough
359 aligned positions were available to create a 3D structure
363 <em>3D Structure</em>
366 <!-- JAL-2430 -->Hidden regions in alignment views are not
367 coloured in linked structure views
370 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
371 file-based command exchange
374 <!-- JAL-2375 -->Structure chooser automatically shows
375 Cached Structures rather than querying the PDBe if
376 structures are already available for sequences
379 <!-- JAL-2520 -->Structures imported via URL are cached in
380 the Jalview project rather than downloaded again when the
384 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
385 to transfer Chimera's structure attributes as Jalview
386 features, and vice-versa (<strong>Experimental
390 <em>Web Services</em>
393 <!-- JAL-2549 -->Updated JABAWS client to v2.2
396 <!-- JAL-2335 -->Filter non-standard amino acids and
397 nucleotides when submitting to AACon and other MSA
401 <!-- JAL-2316, -->URLs for viewing database
402 cross-references provided by identifiers.org and the
410 <!-- JAL-2344 -->FileFormatI interface for describing and
411 identifying file formats (instead of String constants)
414 <!-- JAL-2228 -->FeatureCounter script refactored for
415 efficiency when counting all displayed features (not
416 backwards compatible with 2.10.1)
419 <em>Example files</em>
422 <!-- JAL-2631 -->Graduated feature colour style example
423 included in the example feature file
426 <em>Documentation</em>
429 <!-- JAL-2339 -->Release notes reformatted for readability
430 with the built-in Java help viewer
433 <!-- JAL-1644 -->Find documentation updated with 'search
434 sequence description' option
440 <!-- JAL-2485, -->External service integration tests for
441 Uniprot REST Free Text Search Client
444 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
447 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
452 <td><div align="left">
453 <em>Calculations</em>
456 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
457 matrix - C->R should be '-3'<br />Old matrix restored
458 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
460 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
461 Jalview's treatment of gaps in PCA and substitution matrix
462 based Tree calculations.<br /> <br />In earlier versions
463 of Jalview, gaps matching gaps were penalised, and gaps
464 matching non-gaps penalised even more. In the PCA
465 calculation, gaps were actually treated as non-gaps - so
466 different costs were applied, which meant Jalview's PCAs
467 were different to those produced by SeqSpace.<br />Jalview
468 now treats gaps in the same way as SeqSpace (ie it scores
469 them as 0). <br /> <br />Enter the following in the
470 Groovy console to restore pre-2.10.2 behaviour:<br />
471 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
472 // for 2.10.1 mode <br />
473 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
474 // to restore 2.10.2 mode <br /> <br /> <em>Note:
475 these settings will affect all subsequent tree and PCA
476 calculations (not recommended)</em></li>
478 <!-- JAL-2424 -->Fixed off-by-one bug that affected
479 scaling of branch lengths for trees computed using
480 Sequence Feature Similarity.
483 <!-- JAL-2377 -->PCA calculation could hang when
484 generating output report when working with highly
488 <!-- JAL-2544 --> Sort by features includes features to
489 right of selected region when gaps present on right-hand
493 <em>User Interface</em>
496 <!-- JAL-2346 -->Reopening Colour by annotation dialog
497 doesn't reselect a specific sequence's associated
498 annotation after it was used for colouring a view
501 <!-- JAL-2419 -->Current selection lost if popup menu
502 opened on a region of alignment without groups
505 <!-- JAL-2374 -->Popup menu not always shown for regions
506 of an alignment with overlapping groups
509 <!-- JAL-2310 -->Finder double counts if both a sequence's
510 name and description match
513 <!-- JAL-2370 -->Hiding column selection containing two
514 hidden regions results in incorrect hidden regions
517 <!-- JAL-2386 -->'Apply to all groups' setting when
518 changing colour does not apply Conservation slider value
522 <!-- JAL-2373 -->Percentage identity and conservation menu
523 items do not show a tick or allow shading to be disabled
526 <!-- JAL-2385 -->Conservation shading or PID threshold
527 lost when base colourscheme changed if slider not visible
530 <!-- JAL-2547 -->Sequence features shown in tooltip for
531 gaps before start of features
534 <!-- JAL-2623 -->Graduated feature colour threshold not
535 restored to UI when feature colour is edited
538 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
539 a time when scrolling vertically in wrapped mode.
542 <!-- JAL-2630 -->Structure and alignment overview update
543 as graduate feature colour settings are modified via the
547 <!-- JAL-2034 -->Overview window doesn't always update
548 when a group defined on the alignment is resized
551 <!-- JAL-2605 -->Mouseovers on left/right scale region in
552 wrapped view result in positional status updates
556 <!-- JAL-2563 -->Status bar doesn't show position for
557 ambiguous amino acid and nucleotide symbols
560 <!-- JAL-2602 -->Copy consensus sequence failed if
561 alignment included gapped columns
564 <!-- JAL-2473 -->Minimum size set for Jalview windows so
565 widgets don't permanently disappear
568 <!-- JAL-2503 -->Cannot select or filter quantitative
569 annotation that are shown only as column labels (e.g.
570 T-Coffee column reliability scores)
573 <!-- JAL-2594 -->Exception thrown if trying to create a
574 sequence feature on gaps only
577 <!-- JAL-2504 -->Features created with 'New feature'
578 button from a Find inherit previously defined feature type
579 rather than the Find query string
582 <!-- JAL-2423 -->incorrect title in output window when
583 exporting tree calculated in Jalview
586 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
587 and then revealing them reorders sequences on the
591 <!-- JAL-964 -->Group panel in sequence feature settings
592 doesn't update to reflect available set of groups after
593 interactively adding or modifying features
596 <!-- JAL-2225 -->Sequence Database chooser unusable on
600 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
601 only excluded gaps in current sequence and ignored
608 <!-- JAL-2421 -->Overview window visible region moves
609 erratically when hidden rows or columns are present
612 <!-- JAL-2362 -->Per-residue colourschemes applied via the
613 Structure Viewer's colour menu don't correspond to
617 <!-- JAL-2405 -->Protein specific colours only offered in
618 colour and group colour menu for protein alignments
621 <!-- JAL-2385 -->Colour threshold slider doesn't update to
622 reflect currently selected view or group's shading
626 <!-- JAL-2624 -->Feature colour thresholds not respected
627 when rendered on overview and structures when opacity at
631 <!-- JAL-2589 -->User defined gap colour not shown in
632 overview when features overlaid on alignment
635 <em>Data import/export</em>
638 <!-- JAL-2576 -->Very large alignments take a long time to
642 <!-- JAL-2507 -->Per-sequence RNA secondary structures
643 added after a sequence was imported are not written to
647 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
648 when importing RNA secondary structure via Stockholm
651 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
652 not shown in correct direction for simple pseudoknots
655 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
656 with lightGray or darkGray via features file (but can
660 <!-- JAL-2383 -->Above PID colour threshold not recovered
661 when alignment view imported from project
664 <!-- JAL-2520,JAL-2465 -->No mappings generated between
665 structure and sequences extracted from structure files
666 imported via URL and viewed in Jmol
669 <!-- JAL-2520 -->Structures loaded via URL are saved in
670 Jalview Projects rather than fetched via URL again when
671 the project is loaded and the structure viewed
674 <em>Web Services</em>
677 <!-- JAL-2519 -->EnsemblGenomes example failing after
678 release of Ensembl v.88
681 <!-- JAL-2366 -->Proxy server address and port always
682 appear enabled in Preferences->Connections
685 <!-- JAL-2461 -->DAS registry not found exceptions
686 removed from console output
689 <!-- JAL-2582 -->Cannot retrieve protein products from
690 Ensembl by Peptide ID
693 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
694 created from SIFTs, and spurious 'Couldn't open structure
695 in Chimera' errors raised after April 2017 update (problem
696 due to 'null' string rather than empty string used for
697 residues with no corresponding PDB mapping).
700 <em>Application UI</em>
703 <!-- JAL-2361 -->User Defined Colours not added to Colour
707 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
708 case' residues (button in colourscheme editor debugged and
709 new documentation and tooltips added)
712 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
713 doesn't restore group-specific text colour thresholds
716 <!-- JAL-2243 -->Feature settings panel does not update as
717 new features are added to alignment
720 <!-- JAL-2532 -->Cancel in feature settings reverts
721 changes to feature colours via the Amend features dialog
724 <!-- JAL-2506 -->Null pointer exception when attempting to
725 edit graduated feature colour via amend features dialog
729 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
730 selection menu changes colours of alignment views
733 <!-- JAL-2426 -->Spurious exceptions in console raised
734 from alignment calculation workers after alignment has
738 <!-- JAL-1608 -->Typo in selection popup menu - Create
739 groups now 'Create Group'
742 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
743 Create/Undefine group doesn't always work
746 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
747 shown again after pressing 'Cancel'
750 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
751 adjusts start position in wrap mode
754 <!-- JAL-2563 -->Status bar doesn't show positions for
755 ambiguous amino acids
758 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
759 CDS/Protein view after CDS sequences added for aligned
763 <!-- JAL-2592 -->User defined colourschemes called 'User
764 Defined' don't appear in Colours menu
770 <!-- JAL-2468 -->Switching between Nucleotide and Protein
771 score models doesn't always result in an updated PCA plot
774 <!-- JAL-2442 -->Features not rendered as transparent on
775 overview or linked structure view
778 <!-- JAL-2372 -->Colour group by conservation doesn't
782 <!-- JAL-2517 -->Hitting Cancel after applying
783 user-defined colourscheme doesn't restore original
790 <!-- JAL-2314 -->Unit test failure:
791 jalview.ws.jabaws.RNAStructExportImport setup fails
794 <!-- JAL-2307 -->Unit test failure:
795 jalview.ws.sifts.SiftsClientTest due to compatibility
796 problems with deep array comparison equality asserts in
797 successive versions of TestNG
800 <!-- JAL-2479 -->Relocated StructureChooserTest and
801 ParameterUtilsTest Unit tests to Network suite
804 <em>New Known Issues</em>
807 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
808 phase after a sequence motif find operation
811 <!-- JAL-2550 -->Importing annotation file with rows
812 containing just upper and lower case letters are
813 interpreted as WUSS RNA secondary structure symbols
816 <!-- JAL-2590 -->Cannot load and display Newick trees
817 reliably from eggnog Ortholog database
820 <!-- JAL-2468 -->Status bar shows 'Marked x columns
821 containing features of type Highlight' when 'B' is pressed
822 to mark columns containing highlighted regions.
825 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
826 doesn't always add secondary structure annotation.
831 <td width="60" nowrap>
833 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
836 <td><div align="left">
840 <!-- JAL-98 -->Improved memory usage: sparse arrays used
841 for all consensus calculations
844 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
847 <li>Updated Jalview's Certum code signing certificate
853 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
854 set of database cross-references, sorted alphabetically
857 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
858 from database cross references. Users with custom links
859 will receive a <a href="webServices/urllinks.html#warning">warning
860 dialog</a> asking them to update their preferences.
863 <!-- JAL-2287-->Cancel button and escape listener on
864 dialog warning user about disconnecting Jalview from a
868 <!-- JAL-2320-->Jalview's Chimera control window closes if
869 the Chimera it is connected to is shut down
872 <!-- JAL-1738-->New keystroke (B) and Select highlighted
873 columns menu item to mark columns containing highlighted
874 regions (e.g. from structure selections or results of a
878 <!-- JAL-2284-->Command line option for batch-generation
879 of HTML pages rendering alignment data with the BioJS
889 <!-- JAL-2286 -->Columns with more than one modal residue
890 are not coloured or thresholded according to percent
891 identity (first observed in Jalview 2.8.2)
894 <!-- JAL-2301 -->Threonine incorrectly reported as not
898 <!-- JAL-2318 -->Updates to documentation pages (above PID
899 threshold, amino acid properties)
902 <!-- JAL-2292 -->Lower case residues in sequences are not
903 reported as mapped to residues in a structure file in the
907 <!--JAL-2324 -->Identical features with non-numeric scores
908 could be added multiple times to a sequence
911 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
912 bond features shown as two highlighted residues rather
913 than a range in linked structure views, and treated
914 correctly when selecting and computing trees from features
917 <!-- JAL-2281-->Custom URL links for database
918 cross-references are matched to database name regardless
926 <!-- JAL-2282-->Custom URL links for specific database
927 names without regular expressions also offer links from
931 <!-- JAL-2315-->Removing a single configured link in the
932 URL links pane in Connections preferences doesn't actually
933 update Jalview configuration
936 <!-- JAL-2272-->CTRL-Click on a selected region to open
937 the alignment area popup menu doesn't work on El-Capitan
940 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
941 files with similarly named sequences if dropped onto the
945 <!-- JAL-2312 -->Additional mappings are shown for PDB
946 entries where more chains exist in the PDB accession than
947 are reported in the SIFTS file
950 <!-- JAL-2317-->Certain structures do not get mapped to
951 the structure view when displayed with Chimera
954 <!-- JAL-2317-->No chains shown in the Chimera view
955 panel's View->Show Chains submenu
958 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
959 work for wrapped alignment views
962 <!--JAL-2197 -->Rename UI components for running JPred
963 predictions from 'JNet' to 'JPred'
966 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
967 corrupted when annotation panel vertical scroll is not at
971 <!--JAL-2332 -->Attempting to view structure for Hen
972 lysozyme results in a PDB Client error dialog box
975 <!-- JAL-2319 -->Structure View's mapping report switched
976 ranges for PDB and sequence for SIFTS
979 SIFTS 'Not_Observed' residues mapped to non-existant
983 <!-- <em>New Known Issues</em>
990 <td width="60" nowrap>
992 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
993 <em>25/10/2016</em></strong>
996 <td><em>Application</em>
998 <li>3D Structure chooser opens with 'Cached structures'
999 view if structures already loaded</li>
1000 <li>Progress bar reports models as they are loaded to
1001 structure views</li>
1007 <li>Colour by conservation always enabled and no tick
1008 shown in menu when BLOSUM or PID shading applied</li>
1009 <li>FER1_ARATH and FER2_ARATH labels were switched in
1010 example sequences/projects/trees</li>
1012 <em>Application</em>
1014 <li>Jalview projects with views of local PDB structure
1015 files saved on Windows cannot be opened on OSX</li>
1016 <li>Multiple structure views can be opened and superposed
1017 without timeout for structures with multiple models or
1018 multiple sequences in alignment</li>
1019 <li>Cannot import or associated local PDB files without a
1020 PDB ID HEADER line</li>
1021 <li>RMSD is not output in Jmol console when superposition
1023 <li>Drag and drop of URL from Browser fails for Linux and
1024 OSX versions earlier than El Capitan</li>
1025 <li>ENA client ignores invalid content from ENA server</li>
1026 <li>Exceptions are not raised in console when ENA client
1027 attempts to fetch non-existent IDs via Fetch DB Refs UI
1029 <li>Exceptions are not raised in console when a new view
1030 is created on the alignment</li>
1031 <li>OSX right-click fixed for group selections: CMD-click
1032 to insert/remove gaps in groups and CTRL-click to open group
1035 <em>Build and deployment</em>
1037 <li>URL link checker now copes with multi-line anchor
1040 <em>New Known Issues</em>
1042 <li>Drag and drop from URL links in browsers do not work
1049 <td width="60" nowrap>
1050 <div align="center">
1051 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1054 <td><em>General</em>
1057 <!-- JAL-2124 -->Updated Spanish translations.
1060 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1061 for importing structure data to Jalview. Enables mmCIF and
1065 <!-- JAL-192 --->Alignment ruler shows positions relative to
1069 <!-- JAL-2202 -->Position/residue shown in status bar when
1070 mousing over sequence associated annotation
1073 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1077 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1078 '()', canonical '[]' and invalid '{}' base pair populations
1082 <!-- JAL-2092 -->Feature settings popup menu options for
1083 showing or hiding columns containing a feature
1086 <!-- JAL-1557 -->Edit selected group by double clicking on
1087 group and sequence associated annotation labels
1090 <!-- JAL-2236 -->Sequence name added to annotation label in
1091 select/hide columns by annotation and colour by annotation
1095 </ul> <em>Application</em>
1098 <!-- JAL-2050-->Automatically hide introns when opening a
1099 gene/transcript view
1102 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1106 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1107 structure mappings with the EMBL-EBI PDBe SIFTS database
1110 <!-- JAL-2079 -->Updated download sites used for Rfam and
1111 Pfam sources to xfam.org
1114 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1117 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1118 over sequences in Jalview
1121 <!-- JAL-2027-->Support for reverse-complement coding
1122 regions in ENA and EMBL
1125 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1126 for record retrieval via ENA rest API
1129 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1133 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1134 groovy script execution
1137 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1138 alignment window's Calculate menu
1141 <!-- JAL-1812 -->Allow groovy scripts that call
1142 Jalview.getAlignFrames() to run in headless mode
1145 <!-- JAL-2068 -->Support for creating new alignment
1146 calculation workers from groovy scripts
1149 <!-- JAL-1369 --->Store/restore reference sequence in
1153 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1154 associations are now saved/restored from project
1157 <!-- JAL-1993 -->Database selection dialog always shown
1158 before sequence fetcher is opened
1161 <!-- JAL-2183 -->Double click on an entry in Jalview's
1162 database chooser opens a sequence fetcher
1165 <!-- JAL-1563 -->Free-text search client for UniProt using
1166 the UniProt REST API
1169 <!-- JAL-2168 -->-nonews command line parameter to prevent
1170 the news reader opening
1173 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1174 querying stored in preferences
1177 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1181 <!-- JAL-1977-->Tooltips shown on database chooser
1184 <!-- JAL-391 -->Reverse complement function in calculate
1185 menu for nucleotide sequences
1188 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1189 and feature counts preserves alignment ordering (and
1190 debugged for complex feature sets).
1193 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1194 viewing structures with Jalview 2.10
1197 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1198 genome, transcript CCDS and gene ids via the Ensembl and
1199 Ensembl Genomes REST API
1202 <!-- JAL-2049 -->Protein sequence variant annotation
1203 computed for 'sequence_variant' annotation on CDS regions
1207 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1211 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1212 Ref Fetcher fails to match, or otherwise updates sequence
1213 data from external database records.
1216 <!-- JAL-2154 -->Revised Jalview Project format for
1217 efficient recovery of sequence coding and alignment
1218 annotation relationships.
1220 </ul> <!-- <em>Applet</em>
1231 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1235 <!-- JAL-2018-->Export features in Jalview format (again)
1236 includes graduated colourschemes
1239 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1240 working with big alignments and lots of hidden columns
1243 <!-- JAL-2053-->Hidden column markers not always rendered
1244 at right of alignment window
1247 <!-- JAL-2067 -->Tidied up links in help file table of
1251 <!-- JAL-2072 -->Feature based tree calculation not shown
1255 <!-- JAL-2075 -->Hidden columns ignored during feature
1256 based tree calculation
1259 <!-- JAL-2065 -->Alignment view stops updating when show
1260 unconserved enabled for group on alignment
1263 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1267 <!-- JAL-2146 -->Alignment column in status incorrectly
1268 shown as "Sequence position" when mousing over
1272 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1273 hidden columns present
1276 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1277 user created annotation added to alignment
1280 <!-- JAL-1841 -->RNA Structure consensus only computed for
1281 '()' base pair annotation
1284 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1285 in zero scores for all base pairs in RNA Structure
1289 <!-- JAL-2174-->Extend selection with columns containing
1293 <!-- JAL-2275 -->Pfam format writer puts extra space at
1294 beginning of sequence
1297 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1301 <!-- JAL-2238 -->Cannot create groups on an alignment from
1302 from a tree when t-coffee scores are shown
1305 <!-- JAL-1836,1967 -->Cannot import and view PDB
1306 structures with chains containing negative resnums (4q4h)
1309 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1313 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1314 to Clustal, PIR and PileUp output
1317 <!-- JAL-2008 -->Reordering sequence features that are
1318 not visible causes alignment window to repaint
1321 <!-- JAL-2006 -->Threshold sliders don't work in
1322 graduated colour and colour by annotation row for e-value
1323 scores associated with features and annotation rows
1326 <!-- JAL-1797 -->amino acid physicochemical conservation
1327 calculation should be case independent
1330 <!-- JAL-2173 -->Remove annotation also updates hidden
1334 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1335 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1336 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1339 <!-- JAL-2065 -->Null pointer exceptions and redraw
1340 problems when reference sequence defined and 'show
1341 non-conserved' enabled
1344 <!-- JAL-1306 -->Quality and Conservation are now shown on
1345 load even when Consensus calculation is disabled
1348 <!-- JAL-1932 -->Remove right on penultimate column of
1349 alignment does nothing
1352 <em>Application</em>
1355 <!-- JAL-1552-->URLs and links can't be imported by
1356 drag'n'drop on OSX when launched via webstart (note - not
1357 yet fixed for El Capitan)
1360 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1361 output when running on non-gb/us i18n platforms
1364 <!-- JAL-1944 -->Error thrown when exporting a view with
1365 hidden sequences as flat-file alignment
1368 <!-- JAL-2030-->InstallAnywhere distribution fails when
1372 <!-- JAL-2080-->Jalview very slow to launch via webstart
1373 (also hotfix for 2.9.0b2)
1376 <!-- JAL-2085 -->Cannot save project when view has a
1377 reference sequence defined
1380 <!-- JAL-1011 -->Columns are suddenly selected in other
1381 alignments and views when revealing hidden columns
1384 <!-- JAL-1989 -->Hide columns not mirrored in complement
1385 view in a cDNA/Protein splitframe
1388 <!-- JAL-1369 -->Cannot save/restore representative
1389 sequence from project when only one sequence is
1393 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1394 in Structure Chooser
1397 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1398 structure consensus didn't refresh annotation panel
1401 <!-- JAL-1962 -->View mapping in structure view shows
1402 mappings between sequence and all chains in a PDB file
1405 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1406 dialogs format columns correctly, don't display array
1407 data, sort columns according to type
1410 <!-- JAL-1975 -->Export complete shown after destination
1411 file chooser is cancelled during an image export
1414 <!-- JAL-2025 -->Error when querying PDB Service with
1415 sequence name containing special characters
1418 <!-- JAL-2024 -->Manual PDB structure querying should be
1422 <!-- JAL-2104 -->Large tooltips with broken HTML
1423 formatting don't wrap
1426 <!-- JAL-1128 -->Figures exported from wrapped view are
1427 truncated so L looks like I in consensus annotation
1430 <!-- JAL-2003 -->Export features should only export the
1431 currently displayed features for the current selection or
1435 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1436 after fetching cross-references, and restoring from
1440 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1441 followed in the structure viewer
1444 <!-- JAL-2163 -->Titles for individual alignments in
1445 splitframe not restored from project
1448 <!-- JAL-2145 -->missing autocalculated annotation at
1449 trailing end of protein alignment in transcript/product
1450 splitview when pad-gaps not enabled by default
1453 <!-- JAL-1797 -->amino acid physicochemical conservation
1457 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1458 article has been read (reopened issue due to
1459 internationalisation problems)
1462 <!-- JAL-1960 -->Only offer PDB structures in structure
1463 viewer based on sequence name, PDB and UniProt
1468 <!-- JAL-1976 -->No progress bar shown during export of
1472 <!-- JAL-2213 -->Structures not always superimposed after
1473 multiple structures are shown for one or more sequences.
1476 <!-- JAL-1370 -->Reference sequence characters should not
1477 be replaced with '.' when 'Show unconserved' format option
1481 <!-- JAL-1823 -->Cannot specify chain code when entering
1482 specific PDB id for sequence
1485 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1486 'Export hidden sequences' is enabled, but 'export hidden
1487 columns' is disabled.
1490 <!--JAL-2026-->Best Quality option in structure chooser
1491 selects lowest rather than highest resolution structures
1495 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1496 to sequence mapping in 'View Mappings' report
1499 <!-- JAL-2284 -->Unable to read old Jalview projects that
1500 contain non-XML data added after Jalvew wrote project.
1503 <!-- JAL-2118 -->Newly created annotation row reorders
1504 after clicking on it to create new annotation for a
1508 <!-- JAL-1980 -->Null Pointer Exception raised when
1509 pressing Add on an orphaned cut'n'paste window.
1511 <!-- may exclude, this is an external service stability issue JAL-1941
1512 -- > RNA 3D structure not added via DSSR service</li> -->
1517 <!-- JAL-2151 -->Incorrect columns are selected when
1518 hidden columns present before start of sequence
1521 <!-- JAL-1986 -->Missing dependencies on applet pages
1525 <!-- JAL-1947 -->Overview pixel size changes when
1526 sequences are hidden in applet
1529 <!-- JAL-1996 -->Updated instructions for applet
1530 deployment on examples pages.
1537 <td width="60" nowrap>
1538 <div align="center">
1539 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1540 <em>16/10/2015</em></strong>
1543 <td><em>General</em>
1545 <li>Time stamps for signed Jalview application and applet
1550 <em>Application</em>
1552 <li>Duplicate group consensus and conservation rows
1553 shown when tree is partitioned</li>
1554 <li>Erratic behaviour when tree partitions made with
1555 multiple cDNA/Protein split views</li>
1561 <td width="60" nowrap>
1562 <div align="center">
1563 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1564 <em>8/10/2015</em></strong>
1567 <td><em>General</em>
1569 <li>Updated Spanish translations of localized text for
1571 </ul> <em>Application</em>
1573 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1574 <li>Signed OSX InstallAnywhere installer<br></li>
1575 <li>Support for per-sequence based annotations in BioJSON</li>
1576 </ul> <em>Applet</em>
1578 <li>Split frame example added to applet examples page</li>
1579 </ul> <em>Build and Deployment</em>
1582 <!-- JAL-1888 -->New ant target for running Jalview's test
1590 <li>Mapping of cDNA to protein in split frames
1591 incorrect when sequence start > 1</li>
1592 <li>Broken images in filter column by annotation dialog
1594 <li>Feature colours not parsed from features file</li>
1595 <li>Exceptions and incomplete link URLs recovered when
1596 loading a features file containing HTML tags in feature
1600 <em>Application</em>
1602 <li>Annotations corrupted after BioJS export and
1604 <li>Incorrect sequence limits after Fetch DB References
1605 with 'trim retrieved sequences'</li>
1606 <li>Incorrect warning about deleting all data when
1607 deleting selected columns</li>
1608 <li>Patch to build system for shipping properly signed
1609 JNLP templates for webstart launch</li>
1610 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1611 unreleased structures for download or viewing</li>
1612 <li>Tab/space/return keystroke operation of EMBL-PDBe
1613 fetcher/viewer dialogs works correctly</li>
1614 <li>Disabled 'minimise' button on Jalview windows
1615 running on OSX to workaround redraw hang bug</li>
1616 <li>Split cDNA/Protein view position and geometry not
1617 recovered from jalview project</li>
1618 <li>Initial enabled/disabled state of annotation menu
1619 sorter 'show autocalculated first/last' corresponds to
1621 <li>Restoring of Clustal, RNA Helices and T-Coffee
1622 color schemes from BioJSON</li>
1626 <li>Reorder sequences mirrored in cDNA/Protein split
1628 <li>Applet with Jmol examples not loading correctly</li>
1634 <td><div align="center">
1635 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1637 <td><em>General</em>
1639 <li>Linked visualisation and analysis of DNA and Protein
1642 <li>Translated cDNA alignments shown as split protein
1643 and DNA alignment views</li>
1644 <li>Codon consensus annotation for linked protein and
1645 cDNA alignment views</li>
1646 <li>Link cDNA or Protein product sequences by loading
1647 them onto Protein or cDNA alignments</li>
1648 <li>Reconstruct linked cDNA alignment from aligned
1649 protein sequences</li>
1652 <li>Jmol integration updated to Jmol v14.2.14</li>
1653 <li>Import and export of Jalview alignment views as <a
1654 href="features/bioJsonFormat.html">BioJSON</a></li>
1655 <li>New alignment annotation file statements for
1656 reference sequences and marking hidden columns</li>
1657 <li>Reference sequence based alignment shading to
1658 highlight variation</li>
1659 <li>Select or hide columns according to alignment
1661 <li>Find option for locating sequences by description</li>
1662 <li>Conserved physicochemical properties shown in amino
1663 acid conservation row</li>
1664 <li>Alignments can be sorted by number of RNA helices</li>
1665 </ul> <em>Application</em>
1667 <li>New cDNA/Protein analysis capabilities
1669 <li>Get Cross-References should open a Split Frame
1670 view with cDNA/Protein</li>
1671 <li>Detect when nucleotide sequences and protein
1672 sequences are placed in the same alignment</li>
1673 <li>Split cDNA/Protein views are saved in Jalview
1678 <li>Use REST API to talk to Chimera</li>
1679 <li>Selected regions in Chimera are highlighted in linked
1680 Jalview windows</li>
1682 <li>VARNA RNA viewer updated to v3.93</li>
1683 <li>VARNA views are saved in Jalview Projects</li>
1684 <li>Pseudoknots displayed as Jalview RNA annotation can
1685 be shown in VARNA</li>
1687 <li>Make groups for selection uses marked columns as well
1688 as the active selected region</li>
1690 <li>Calculate UPGMA and NJ trees using sequence feature
1692 <li>New Export options
1694 <li>New Export Settings dialog to control hidden
1695 region export in flat file generation</li>
1697 <li>Export alignment views for display with the <a
1698 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1700 <li>Export scrollable SVG in HTML page</li>
1701 <li>Optional embedding of BioJSON data when exporting
1702 alignment figures to HTML</li>
1704 <li>3D structure retrieval and display
1706 <li>Free text and structured queries with the PDBe
1708 <li>PDBe Search API based discovery and selection of
1709 PDB structures for a sequence set</li>
1713 <li>JPred4 employed for protein secondary structure
1715 <li>Hide Insertions menu option to hide unaligned columns
1716 for one or a group of sequences</li>
1717 <li>Automatically hide insertions in alignments imported
1718 from the JPred4 web server</li>
1719 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1720 system on OSX<br />LGPL libraries courtesy of <a
1721 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1723 <li>changed 'View nucleotide structure' submenu to 'View
1724 VARNA 2D Structure'</li>
1725 <li>change "View protein structure" menu option to "3D
1728 </ul> <em>Applet</em>
1730 <li>New layout for applet example pages</li>
1731 <li>New parameters to enable SplitFrame view
1732 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1733 <li>New example demonstrating linked viewing of cDNA and
1734 Protein alignments</li>
1735 </ul> <em>Development and deployment</em>
1737 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1738 <li>Include installation type and git revision in build
1739 properties and console log output</li>
1740 <li>Jalview Github organisation, and new github site for
1741 storing BioJsMSA Templates</li>
1742 <li>Jalview's unit tests now managed with TestNG</li>
1745 <!-- <em>General</em>
1747 </ul> --> <!-- issues resolved --> <em>Application</em>
1749 <li>Escape should close any open find dialogs</li>
1750 <li>Typo in select-by-features status report</li>
1751 <li>Consensus RNA secondary secondary structure
1752 predictions are not highlighted in amber</li>
1753 <li>Missing gap character in v2.7 example file means
1754 alignment appears unaligned when pad-gaps is not enabled</li>
1755 <li>First switch to RNA Helices colouring doesn't colour
1756 associated structure views</li>
1757 <li>ID width preference option is greyed out when auto
1758 width checkbox not enabled</li>
1759 <li>Stopped a warning dialog from being shown when
1760 creating user defined colours</li>
1761 <li>'View Mapping' in structure viewer shows sequence
1762 mappings for just that viewer's sequences</li>
1763 <li>Workaround for superposing PDB files containing
1764 multiple models in Chimera</li>
1765 <li>Report sequence position in status bar when hovering
1766 over Jmol structure</li>
1767 <li>Cannot output gaps as '.' symbols with Selection ->
1768 output to text box</li>
1769 <li>Flat file exports of alignments with hidden columns
1770 have incorrect sequence start/end</li>
1771 <li>'Aligning' a second chain to a Chimera structure from
1773 <li>Colour schemes applied to structure viewers don't
1774 work for nucleotide</li>
1775 <li>Loading/cut'n'pasting an empty or invalid file leads
1776 to a grey/invisible alignment window</li>
1777 <li>Exported Jpred annotation from a sequence region
1778 imports to different position</li>
1779 <li>Space at beginning of sequence feature tooltips shown
1780 on some platforms</li>
1781 <li>Chimera viewer 'View | Show Chain' menu is not
1783 <li>'New View' fails with a Null Pointer Exception in
1784 console if Chimera has been opened</li>
1785 <li>Mouseover to Chimera not working</li>
1786 <li>Miscellaneous ENA XML feature qualifiers not
1788 <li>NPE in annotation renderer after 'Extract Scores'</li>
1789 <li>If two structures in one Chimera window, mouseover of
1790 either sequence shows on first structure</li>
1791 <li>'Show annotations' options should not make
1792 non-positional annotations visible</li>
1793 <li>Subsequence secondary structure annotation not shown
1794 in right place after 'view flanking regions'</li>
1795 <li>File Save As type unset when current file format is
1797 <li>Save as '.jar' option removed for saving Jalview
1799 <li>Colour by Sequence colouring in Chimera more
1801 <li>Cannot 'add reference annotation' for a sequence in
1802 several views on same alignment</li>
1803 <li>Cannot show linked products for EMBL / ENA records</li>
1804 <li>Jalview's tooltip wraps long texts containing no
1806 </ul> <em>Applet</em>
1808 <li>Jmol to JalviewLite mouseover/link not working</li>
1809 <li>JalviewLite can't import sequences with ID
1810 descriptions containing angle brackets</li>
1811 </ul> <em>General</em>
1813 <li>Cannot export and reimport RNA secondary structure
1814 via jalview annotation file</li>
1815 <li>Random helix colour palette for colour by annotation
1816 with RNA secondary structure</li>
1817 <li>Mouseover to cDNA from STOP residue in protein
1818 translation doesn't work.</li>
1819 <li>hints when using the select by annotation dialog box</li>
1820 <li>Jmol alignment incorrect if PDB file has alternate CA
1822 <li>FontChooser message dialog appears to hang after
1823 choosing 1pt font</li>
1824 <li>Peptide secondary structure incorrectly imported from
1825 annotation file when annotation display text includes 'e' or
1827 <li>Cannot set colour of new feature type whilst creating
1829 <li>cDNA translation alignment should not be sequence
1830 order dependent</li>
1831 <li>'Show unconserved' doesn't work for lower case
1833 <li>Nucleotide ambiguity codes involving R not recognised</li>
1834 </ul> <em>Deployment and Documentation</em>
1836 <li>Applet example pages appear different to the rest of
1837 www.jalview.org</li>
1838 </ul> <em>Application Known issues</em>
1840 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1841 <li>Misleading message appears after trying to delete
1843 <li>Jalview icon not shown in dock after InstallAnywhere
1844 version launches</li>
1845 <li>Fetching EMBL reference for an RNA sequence results
1846 fails with a sequence mismatch</li>
1847 <li>Corrupted or unreadable alignment display when
1848 scrolling alignment to right</li>
1849 <li>ArrayIndexOutOfBoundsException thrown when remove
1850 empty columns called on alignment with ragged gapped ends</li>
1851 <li>auto calculated alignment annotation rows do not get
1852 placed above or below non-autocalculated rows</li>
1853 <li>Jalview dekstop becomes sluggish at full screen in
1854 ultra-high resolution</li>
1855 <li>Cannot disable consensus calculation independently of
1856 quality and conservation</li>
1857 <li>Mouseover highlighting between cDNA and protein can
1858 become sluggish with more than one splitframe shown</li>
1859 </ul> <em>Applet Known Issues</em>
1861 <li>Core PDB parsing code requires Jmol</li>
1862 <li>Sequence canvas panel goes white when alignment
1863 window is being resized</li>
1869 <td><div align="center">
1870 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1872 <td><em>General</em>
1874 <li>Updated Java code signing certificate donated by
1876 <li>Features and annotation preserved when performing
1877 pairwise alignment</li>
1878 <li>RNA pseudoknot annotation can be
1879 imported/exported/displayed</li>
1880 <li>'colour by annotation' can colour by RNA and
1881 protein secondary structure</li>
1882 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1883 post-hoc with 2.9 release</em>)
1886 </ul> <em>Application</em>
1888 <li>Extract and display secondary structure for sequences
1889 with 3D structures</li>
1890 <li>Support for parsing RNAML</li>
1891 <li>Annotations menu for layout
1893 <li>sort sequence annotation rows by alignment</li>
1894 <li>place sequence annotation above/below alignment
1897 <li>Output in Stockholm format</li>
1898 <li>Internationalisation: improved Spanish (es)
1900 <li>Structure viewer preferences tab</li>
1901 <li>Disorder and Secondary Structure annotation tracks
1902 shared between alignments</li>
1903 <li>UCSF Chimera launch and linked highlighting from
1905 <li>Show/hide all sequence associated annotation rows for
1906 all or current selection</li>
1907 <li>disorder and secondary structure predictions
1908 available as dataset annotation</li>
1909 <li>Per-sequence rna helices colouring</li>
1912 <li>Sequence database accessions imported when fetching
1913 alignments from Rfam</li>
1914 <li>update VARNA version to 3.91</li>
1916 <li>New groovy scripts for exporting aligned positions,
1917 conservation values, and calculating sum of pairs scores.</li>
1918 <li>Command line argument to set default JABAWS server</li>
1919 <li>include installation type in build properties and
1920 console log output</li>
1921 <li>Updated Jalview project format to preserve dataset
1925 <!-- issues resolved --> <em>Application</em>
1927 <li>Distinguish alignment and sequence associated RNA
1928 structure in structure->view->VARNA</li>
1929 <li>Raise dialog box if user deletes all sequences in an
1931 <li>Pressing F1 results in documentation opening twice</li>
1932 <li>Sequence feature tooltip is wrapped</li>
1933 <li>Double click on sequence associated annotation
1934 selects only first column</li>
1935 <li>Redundancy removal doesn't result in unlinked
1936 leaves shown in tree</li>
1937 <li>Undos after several redundancy removals don't undo
1939 <li>Hide sequence doesn't hide associated annotation</li>
1940 <li>User defined colours dialog box too big to fit on
1941 screen and buttons not visible</li>
1942 <li>author list isn't updated if already written to
1943 Jalview properties</li>
1944 <li>Popup menu won't open after retrieving sequence
1946 <li>File open window for associate PDB doesn't open</li>
1947 <li>Left-then-right click on a sequence id opens a
1948 browser search window</li>
1949 <li>Cannot open sequence feature shading/sort popup menu
1950 in feature settings dialog</li>
1951 <li>better tooltip placement for some areas of Jalview
1953 <li>Allow addition of JABAWS Server which doesn't
1954 pass validation</li>
1955 <li>Web services parameters dialog box is too large to
1957 <li>Muscle nucleotide alignment preset obscured by
1959 <li>JABAWS preset submenus don't contain newly
1960 defined user preset</li>
1961 <li>MSA web services warns user if they were launched
1962 with invalid input</li>
1963 <li>Jalview cannot contact DAS Registy when running on
1966 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1967 'Superpose with' submenu not shown when new view
1971 </ul> <!-- <em>Applet</em>
1973 </ul> <em>General</em>
1975 </ul>--> <em>Deployment and Documentation</em>
1977 <li>2G and 1G options in launchApp have no effect on
1978 memory allocation</li>
1979 <li>launchApp service doesn't automatically open
1980 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1982 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1983 InstallAnywhere reports cannot find valid JVM when Java
1984 1.7_055 is available
1986 </ul> <em>Application Known issues</em>
1989 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1990 corrupted or unreadable alignment display when scrolling
1994 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1995 retrieval fails but progress bar continues for DAS retrieval
1996 with large number of ID
1999 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2000 flatfile output of visible region has incorrect sequence
2004 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2005 rna structure consensus doesn't update when secondary
2006 structure tracks are rearranged
2009 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2010 invalid rna structure positional highlighting does not
2011 highlight position of invalid base pairs
2014 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2015 out of memory errors are not raised when saving Jalview
2016 project from alignment window file menu
2019 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2020 Switching to RNA Helices colouring doesn't propagate to
2024 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2025 colour by RNA Helices not enabled when user created
2026 annotation added to alignment
2029 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2030 Jalview icon not shown on dock in Mountain Lion/Webstart
2032 </ul> <em>Applet Known Issues</em>
2035 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2036 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2039 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2040 Jalview and Jmol example not compatible with IE9
2043 <li>Sort by annotation score doesn't reverse order
2049 <td><div align="center">
2050 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2053 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2056 <li>Internationalisation of user interface (usually
2057 called i18n support) and translation for Spanish locale</li>
2058 <li>Define/Undefine group on current selection with
2059 Ctrl-G/Shift Ctrl-G</li>
2060 <li>Improved group creation/removal options in
2061 alignment/sequence Popup menu</li>
2062 <li>Sensible precision for symbol distribution
2063 percentages shown in logo tooltip.</li>
2064 <li>Annotation panel height set according to amount of
2065 annotation when alignment first opened</li>
2066 </ul> <em>Application</em>
2068 <li>Interactive consensus RNA secondary structure
2069 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2070 <li>Select columns containing particular features from
2071 Feature Settings dialog</li>
2072 <li>View all 'representative' PDB structures for selected
2074 <li>Update Jalview project format:
2076 <li>New file extension for Jalview projects '.jvp'</li>
2077 <li>Preserve sequence and annotation dataset (to
2078 store secondary structure annotation,etc)</li>
2079 <li>Per group and alignment annotation and RNA helix
2083 <li>New similarity measures for PCA and Tree calculation
2085 <li>Experimental support for retrieval and viewing of
2086 flanking regions for an alignment</li>
2090 <!-- issues resolved --> <em>Application</em>
2092 <li>logo keeps spinning and status remains at queued or
2093 running after job is cancelled</li>
2094 <li>cannot export features from alignments imported from
2095 Jalview/VAMSAS projects</li>
2096 <li>Buggy slider for web service parameters that take
2098 <li>Newly created RNA secondary structure line doesn't
2099 have 'display all symbols' flag set</li>
2100 <li>T-COFFEE alignment score shading scheme and other
2101 annotation shading not saved in Jalview project</li>
2102 <li>Local file cannot be loaded in freshly downloaded
2104 <li>Jalview icon not shown on dock in Mountain
2106 <li>Load file from desktop file browser fails</li>
2107 <li>Occasional NPE thrown when calculating large trees</li>
2108 <li>Cannot reorder or slide sequences after dragging an
2109 alignment onto desktop</li>
2110 <li>Colour by annotation dialog throws NPE after using
2111 'extract scores' function</li>
2112 <li>Loading/cut'n'pasting an empty file leads to a grey
2113 alignment window</li>
2114 <li>Disorder thresholds rendered incorrectly after
2115 performing IUPred disorder prediction</li>
2116 <li>Multiple group annotated consensus rows shown when
2117 changing 'normalise logo' display setting</li>
2118 <li>Find shows blank dialog after 'finished searching' if
2119 nothing matches query</li>
2120 <li>Null Pointer Exceptions raised when sorting by
2121 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2123 <li>Errors in Jmol console when structures in alignment
2124 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2126 <li>Not all working JABAWS services are shown in
2128 <li>JAVAWS version of Jalview fails to launch with
2129 'invalid literal/length code'</li>
2130 <li>Annotation/RNA Helix colourschemes cannot be applied
2131 to alignment with groups (actually fixed in 2.8.0b1)</li>
2132 <li>RNA Helices and T-Coffee Scores available as default
2135 </ul> <em>Applet</em>
2137 <li>Remove group option is shown even when selection is
2139 <li>Apply to all groups ticked but colourscheme changes
2140 don't affect groups</li>
2141 <li>Documented RNA Helices and T-Coffee Scores as valid
2142 colourscheme name</li>
2143 <li>Annotation labels drawn on sequence IDs when
2144 Annotation panel is not displayed</li>
2145 <li>Increased font size for dropdown menus on OSX and
2146 embedded windows</li>
2147 </ul> <em>Other</em>
2149 <li>Consensus sequence for alignments/groups with a
2150 single sequence were not calculated</li>
2151 <li>annotation files that contain only groups imported as
2152 annotation and junk sequences</li>
2153 <li>Fasta files with sequences containing '*' incorrectly
2154 recognised as PFAM or BLC</li>
2155 <li>conservation/PID slider apply all groups option
2156 doesn't affect background (2.8.0b1)
2158 <li>redundancy highlighting is erratic at 0% and 100%</li>
2159 <li>Remove gapped columns fails for sequences with ragged
2161 <li>AMSA annotation row with leading spaces is not
2162 registered correctly on import</li>
2163 <li>Jalview crashes when selecting PCA analysis for
2164 certain alignments</li>
2165 <li>Opening the colour by annotation dialog for an
2166 existing annotation based 'use original colours'
2167 colourscheme loses original colours setting</li>
2172 <td><div align="center">
2173 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2174 <em>30/1/2014</em></strong>
2178 <li>Trusted certificates for JalviewLite applet and
2179 Jalview Desktop application<br />Certificate was donated by
2180 <a href="https://www.certum.eu">Certum</a> to the Jalview
2181 open source project).
2183 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2184 <li>Output in Stockholm format</li>
2185 <li>Allow import of data from gzipped files</li>
2186 <li>Export/import group and sequence associated line
2187 graph thresholds</li>
2188 <li>Nucleotide substitution matrix that supports RNA and
2189 ambiguity codes</li>
2190 <li>Allow disorder predictions to be made on the current
2191 selection (or visible selection) in the same way that JPred
2193 <li>Groovy scripting for headless Jalview operation</li>
2194 </ul> <em>Other improvements</em>
2196 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2197 <li>COMBINE statement uses current SEQUENCE_REF and
2198 GROUP_REF scope to group annotation rows</li>
2199 <li>Support '' style escaping of quotes in Newick
2201 <li>Group options for JABAWS service by command line name</li>
2202 <li>Empty tooltip shown for JABA service options with a
2203 link but no description</li>
2204 <li>Select primary source when selecting authority in
2205 database fetcher GUI</li>
2206 <li>Add .mfa to FASTA file extensions recognised by
2208 <li>Annotation label tooltip text wrap</li>
2213 <li>Slow scrolling when lots of annotation rows are
2215 <li>Lots of NPE (and slowness) after creating RNA
2216 secondary structure annotation line</li>
2217 <li>Sequence database accessions not imported when
2218 fetching alignments from Rfam</li>
2219 <li>Incorrect SHMR submission for sequences with
2221 <li>View all structures does not always superpose
2223 <li>Option widgets in service parameters not updated to
2224 reflect user or preset settings</li>
2225 <li>Null pointer exceptions for some services without
2226 presets or adjustable parameters</li>
2227 <li>Discover PDB IDs entry in structure menu doesn't
2228 discover PDB xRefs</li>
2229 <li>Exception encountered while trying to retrieve
2230 features with DAS</li>
2231 <li>Lowest value in annotation row isn't coloured
2232 when colour by annotation (per sequence) is coloured</li>
2233 <li>Keyboard mode P jumps to start of gapped region when
2234 residue follows a gap</li>
2235 <li>Jalview appears to hang importing an alignment with
2236 Wrap as default or after enabling Wrap</li>
2237 <li>'Right click to add annotations' message
2238 shown in wrap mode when no annotations present</li>
2239 <li>Disorder predictions fail with NPE if no automatic
2240 annotation already exists on alignment</li>
2241 <li>oninit javascript function should be called after
2242 initialisation completes</li>
2243 <li>Remove redundancy after disorder prediction corrupts
2244 alignment window display</li>
2245 <li>Example annotation file in documentation is invalid</li>
2246 <li>Grouped line graph annotation rows are not exported
2247 to annotation file</li>
2248 <li>Multi-harmony analysis cannot be run when only two
2250 <li>Cannot create multiple groups of line graphs with
2251 several 'combine' statements in annotation file</li>
2252 <li>Pressing return several times causes Number Format
2253 exceptions in keyboard mode</li>
2254 <li>Multi-harmony (SHMMR) method doesn't submit
2255 correct partitions for input data</li>
2256 <li>Translation from DNA to Amino Acids fails</li>
2257 <li>Jalview fail to load newick tree with quoted label</li>
2258 <li>--headless flag isn't understood</li>
2259 <li>ClassCastException when generating EPS in headless
2261 <li>Adjusting sequence-associated shading threshold only
2262 changes one row's threshold</li>
2263 <li>Preferences and Feature settings panel panel
2264 doesn't open</li>
2265 <li>hide consensus histogram also hides conservation and
2266 quality histograms</li>
2271 <td><div align="center">
2272 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2274 <td><em>Application</em>
2276 <li>Support for JABAWS 2.0 Services (AACon alignment
2277 conservation, protein disorder and Clustal Omega)</li>
2278 <li>JABAWS server status indicator in Web Services
2280 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2281 in Jalview alignment window</li>
2282 <li>Updated Jalview build and deploy framework for OSX
2283 mountain lion, windows 7, and 8</li>
2284 <li>Nucleotide substitution matrix for PCA that supports
2285 RNA and ambiguity codes</li>
2287 <li>Improved sequence database retrieval GUI</li>
2288 <li>Support fetching and database reference look up
2289 against multiple DAS sources (Fetch all from in 'fetch db
2291 <li>Jalview project improvements
2293 <li>Store and retrieve the 'belowAlignment'
2294 flag for annotation</li>
2295 <li>calcId attribute to group annotation rows on the
2297 <li>Store AACon calculation settings for a view in
2298 Jalview project</li>
2302 <li>horizontal scrolling gesture support</li>
2303 <li>Visual progress indicator when PCA calculation is
2305 <li>Simpler JABA web services menus</li>
2306 <li>visual indication that web service results are still
2307 being retrieved from server</li>
2308 <li>Serialise the dialogs that are shown when Jalview
2309 starts up for first time</li>
2310 <li>Jalview user agent string for interacting with HTTP
2312 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2314 <li>Examples directory and Groovy library included in
2315 InstallAnywhere distribution</li>
2316 </ul> <em>Applet</em>
2318 <li>RNA alignment and secondary structure annotation
2319 visualization applet example</li>
2320 </ul> <em>General</em>
2322 <li>Normalise option for consensus sequence logo</li>
2323 <li>Reset button in PCA window to return dimensions to
2325 <li>Allow seqspace or Jalview variant of alignment PCA
2327 <li>PCA with either nucleic acid and protein substitution
2329 <li>Allow windows containing HTML reports to be exported
2331 <li>Interactive display and editing of RNA secondary
2332 structure contacts</li>
2333 <li>RNA Helix Alignment Colouring</li>
2334 <li>RNA base pair logo consensus</li>
2335 <li>Parse sequence associated secondary structure
2336 information in Stockholm files</li>
2337 <li>HTML Export database accessions and annotation
2338 information presented in tooltip for sequences</li>
2339 <li>Import secondary structure from LOCARNA clustalw
2340 style RNA alignment files</li>
2341 <li>import and visualise T-COFFEE quality scores for an
2343 <li>'colour by annotation' per sequence option to
2344 shade each sequence according to its associated alignment
2346 <li>New Jalview Logo</li>
2347 </ul> <em>Documentation and Development</em>
2349 <li>documentation for score matrices used in Jalview</li>
2350 <li>New Website!</li>
2352 <td><em>Application</em>
2354 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2355 wsdbfetch REST service</li>
2356 <li>Stop windows being moved outside desktop on OSX</li>
2357 <li>Filetype associations not installed for webstart
2359 <li>Jalview does not always retrieve progress of a JABAWS
2360 job execution in full once it is complete</li>
2361 <li>revise SHMR RSBS definition to ensure alignment is
2362 uploaded via ali_file parameter</li>
2363 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2364 <li>View all structures superposed fails with exception</li>
2365 <li>Jnet job queues forever if a very short sequence is
2366 submitted for prediction</li>
2367 <li>Cut and paste menu not opened when mouse clicked on
2369 <li>Putting fractional value into integer text box in
2370 alignment parameter dialog causes Jalview to hang</li>
2371 <li>Structure view highlighting doesn't work on
2373 <li>View all structures fails with exception shown in
2375 <li>Characters in filename associated with PDBEntry not
2376 escaped in a platform independent way</li>
2377 <li>Jalview desktop fails to launch with exception when
2379 <li>Tree calculation reports 'you must have 2 or more
2380 sequences selected' when selection is empty</li>
2381 <li>Jalview desktop fails to launch with jar signature
2382 failure when java web start temporary file caching is
2384 <li>DAS Sequence retrieval with range qualification
2385 results in sequence xref which includes range qualification</li>
2386 <li>Errors during processing of command line arguments
2387 cause progress bar (JAL-898) to be removed</li>
2388 <li>Replace comma for semi-colon option not disabled for
2389 DAS sources in sequence fetcher</li>
2390 <li>Cannot close news reader when JABAWS server warning
2391 dialog is shown</li>
2392 <li>Option widgets not updated to reflect user settings</li>
2393 <li>Edited sequence not submitted to web service</li>
2394 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2395 <li>InstallAnywhere installer doesn't unpack and run
2396 on OSX Mountain Lion</li>
2397 <li>Annotation panel not given a scroll bar when
2398 sequences with alignment annotation are pasted into the
2400 <li>Sequence associated annotation rows not associated
2401 when loaded from Jalview project</li>
2402 <li>Browser launch fails with NPE on java 1.7</li>
2403 <li>JABAWS alignment marked as finished when job was
2404 cancelled or job failed due to invalid input</li>
2405 <li>NPE with v2.7 example when clicking on Tree
2406 associated with all views</li>
2407 <li>Exceptions when copy/paste sequences with grouped
2408 annotation rows to new window</li>
2409 </ul> <em>Applet</em>
2411 <li>Sequence features are momentarily displayed before
2412 they are hidden using hidefeaturegroups applet parameter</li>
2413 <li>loading features via javascript API automatically
2414 enables feature display</li>
2415 <li>scrollToColumnIn javascript API method doesn't
2417 </ul> <em>General</em>
2419 <li>Redundancy removal fails for rna alignment</li>
2420 <li>PCA calculation fails when sequence has been selected
2421 and then deselected</li>
2422 <li>PCA window shows grey box when first opened on OSX</li>
2423 <li>Letters coloured pink in sequence logo when alignment
2424 coloured with clustalx</li>
2425 <li>Choosing fonts without letter symbols defined causes
2426 exceptions and redraw errors</li>
2427 <li>Initial PCA plot view is not same as manually
2428 reconfigured view</li>
2429 <li>Grouped annotation graph label has incorrect line
2431 <li>Grouped annotation graph label display is corrupted
2432 for lots of labels</li>
2437 <div align="center">
2438 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2441 <td><em>Application</em>
2443 <li>Jalview Desktop News Reader</li>
2444 <li>Tweaked default layout of web services menu</li>
2445 <li>View/alignment association menu to enable user to
2446 easily specify which alignment a multi-structure view takes
2447 its colours/correspondences from</li>
2448 <li>Allow properties file location to be specified as URL</li>
2449 <li>Extend Jalview project to preserve associations
2450 between many alignment views and a single Jmol display</li>
2451 <li>Store annotation row height in Jalview project file</li>
2452 <li>Annotation row column label formatting attributes
2453 stored in project file</li>
2454 <li>Annotation row order for auto-calculated annotation
2455 rows preserved in Jalview project file</li>
2456 <li>Visual progress indication when Jalview state is
2457 saved using Desktop window menu</li>
2458 <li>Visual indication that command line arguments are
2459 still being processed</li>
2460 <li>Groovy script execution from URL</li>
2461 <li>Colour by annotation default min and max colours in
2463 <li>Automatically associate PDB files dragged onto an
2464 alignment with sequences that have high similarity and
2466 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2467 <li>'view structures' option to open many
2468 structures in same window</li>
2469 <li>Sort associated views menu option for tree panel</li>
2470 <li>Group all JABA and non-JABA services for a particular
2471 analysis function in its own submenu</li>
2472 </ul> <em>Applet</em>
2474 <li>Userdefined and autogenerated annotation rows for
2476 <li>Adjustment of alignment annotation pane height</li>
2477 <li>Annotation scrollbar for annotation panel</li>
2478 <li>Drag to reorder annotation rows in annotation panel</li>
2479 <li>'automaticScrolling' parameter</li>
2480 <li>Allow sequences with partial ID string matches to be
2481 annotated from GFF/Jalview features files</li>
2482 <li>Sequence logo annotation row in applet</li>
2483 <li>Absolute paths relative to host server in applet
2484 parameters are treated as such</li>
2485 <li>New in the JalviewLite javascript API:
2487 <li>JalviewLite.js javascript library</li>
2488 <li>Javascript callbacks for
2490 <li>Applet initialisation</li>
2491 <li>Sequence/alignment mouse-overs and selections</li>
2494 <li>scrollTo row and column alignment scrolling
2496 <li>Select sequence/alignment regions from javascript</li>
2497 <li>javascript structure viewer harness to pass
2498 messages between Jmol and Jalview when running as
2499 distinct applets</li>
2500 <li>sortBy method</li>
2501 <li>Set of applet and application examples shipped
2502 with documentation</li>
2503 <li>New example to demonstrate JalviewLite and Jmol
2504 javascript message exchange</li>
2506 </ul> <em>General</em>
2508 <li>Enable Jmol displays to be associated with multiple
2509 multiple alignments</li>
2510 <li>Option to automatically sort alignment with new tree</li>
2511 <li>User configurable link to enable redirects to a
2512 www.Jalview.org mirror</li>
2513 <li>Jmol colours option for Jmol displays</li>
2514 <li>Configurable newline string when writing alignment
2515 and other flat files</li>
2516 <li>Allow alignment annotation description lines to
2517 contain html tags</li>
2518 </ul> <em>Documentation and Development</em>
2520 <li>Add groovy test harness for bulk load testing to
2522 <li>Groovy script to load and align a set of sequences
2523 using a web service before displaying the result in the
2524 Jalview desktop</li>
2525 <li>Restructured javascript and applet api documentation</li>
2526 <li>Ant target to publish example html files with applet
2528 <li>Netbeans project for building Jalview from source</li>
2529 <li>ant task to create online javadoc for Jalview source</li>
2531 <td><em>Application</em>
2533 <li>User defined colourscheme throws exception when
2534 current built in colourscheme is saved as new scheme</li>
2535 <li>AlignFrame->Save in application pops up save
2536 dialog for valid filename/format</li>
2537 <li>Cannot view associated structure for UniProt sequence</li>
2538 <li>PDB file association breaks for UniProt sequence
2540 <li>Associate PDB from file dialog does not tell you
2541 which sequence is to be associated with the file</li>
2542 <li>Find All raises null pointer exception when query
2543 only matches sequence IDs</li>
2544 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2545 <li>Jalview project with Jmol views created with Jalview
2546 2.4 cannot be loaded</li>
2547 <li>Filetype associations not installed for webstart
2549 <li>Two or more chains in a single PDB file associated
2550 with sequences in different alignments do not get coloured
2551 by their associated sequence</li>
2552 <li>Visibility status of autocalculated annotation row
2553 not preserved when project is loaded</li>
2554 <li>Annotation row height and visibility attributes not
2555 stored in Jalview project</li>
2556 <li>Tree bootstraps are not preserved when saved as a
2557 Jalview project</li>
2558 <li>Envision2 workflow tooltips are corrupted</li>
2559 <li>Enabling show group conservation also enables colour
2560 by conservation</li>
2561 <li>Duplicate group associated conservation or consensus
2562 created on new view</li>
2563 <li>Annotation scrollbar not displayed after 'show
2564 all hidden annotation rows' option selected</li>
2565 <li>Alignment quality not updated after alignment
2566 annotation row is hidden then shown</li>
2567 <li>Preserve colouring of structures coloured by
2568 sequences in pre Jalview 2.7 projects</li>
2569 <li>Web service job parameter dialog is not laid out
2571 <li>Web services menu not refreshed after 'reset
2572 services' button is pressed in preferences</li>
2573 <li>Annotation off by one in Jalview v2_3 example project</li>
2574 <li>Structures imported from file and saved in project
2575 get name like jalview_pdb1234.txt when reloaded</li>
2576 <li>Jalview does not always retrieve progress of a JABAWS
2577 job execution in full once it is complete</li>
2578 </ul> <em>Applet</em>
2580 <li>Alignment height set incorrectly when lots of
2581 annotation rows are displayed</li>
2582 <li>Relative URLs in feature HTML text not resolved to
2584 <li>View follows highlighting does not work for positions
2586 <li><= shown as = in tooltip</li>
2587 <li>Export features raises exception when no features
2589 <li>Separator string used for serialising lists of IDs
2590 for javascript api is modified when separator string
2591 provided as parameter</li>
2592 <li>Null pointer exception when selecting tree leaves for
2593 alignment with no existing selection</li>
2594 <li>Relative URLs for datasources assumed to be relative
2595 to applet's codebase</li>
2596 <li>Status bar not updated after finished searching and
2597 search wraps around to first result</li>
2598 <li>StructureSelectionManager instance shared between
2599 several Jalview applets causes race conditions and memory
2601 <li>Hover tooltip and mouseover of position on structure
2602 not sent from Jmol in applet</li>
2603 <li>Certain sequences of javascript method calls to
2604 applet API fatally hang browser</li>
2605 </ul> <em>General</em>
2607 <li>View follows structure mouseover scrolls beyond
2608 position with wrapped view and hidden regions</li>
2609 <li>Find sequence position moves to wrong residue
2610 with/without hidden columns</li>
2611 <li>Sequence length given in alignment properties window
2613 <li>InvalidNumberFormat exceptions thrown when trying to
2614 import PDB like structure files</li>
2615 <li>Positional search results are only highlighted
2616 between user-supplied sequence start/end bounds</li>
2617 <li>End attribute of sequence is not validated</li>
2618 <li>Find dialog only finds first sequence containing a
2619 given sequence position</li>
2620 <li>Sequence numbering not preserved in MSF alignment
2622 <li>Jalview PDB file reader does not extract sequence
2623 from nucleotide chains correctly</li>
2624 <li>Structure colours not updated when tree partition
2625 changed in alignment</li>
2626 <li>Sequence associated secondary structure not correctly
2627 parsed in interleaved stockholm</li>
2628 <li>Colour by annotation dialog does not restore current
2630 <li>Hiding (nearly) all sequences doesn't work
2632 <li>Sequences containing lowercase letters are not
2633 properly associated with their pdb files</li>
2634 </ul> <em>Documentation and Development</em>
2636 <li>schemas/JalviewWsParamSet.xsd corrupted by
2637 ApplyCopyright tool</li>
2642 <div align="center">
2643 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2646 <td><em>Application</em>
2648 <li>New warning dialog when the Jalview Desktop cannot
2649 contact web services</li>
2650 <li>JABA service parameters for a preset are shown in
2651 service job window</li>
2652 <li>JABA Service menu entries reworded</li>
2656 <li>Modeller PIR IO broken - cannot correctly import a
2657 pir file emitted by Jalview</li>
2658 <li>Existing feature settings transferred to new
2659 alignment view created from cut'n'paste</li>
2660 <li>Improved test for mixed amino/nucleotide chains when
2661 parsing PDB files</li>
2662 <li>Consensus and conservation annotation rows
2663 occasionally become blank for all new windows</li>
2664 <li>Exception raised when right clicking above sequences
2665 in wrapped view mode</li>
2666 </ul> <em>Application</em>
2668 <li>multiple multiply aligned structure views cause cpu
2669 usage to hit 100% and computer to hang</li>
2670 <li>Web Service parameter layout breaks for long user
2671 parameter names</li>
2672 <li>Jaba service discovery hangs desktop if Jaba server
2679 <div align="center">
2680 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2683 <td><em>Application</em>
2685 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2686 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2689 <li>Web Services preference tab</li>
2690 <li>Analysis parameters dialog box and user defined
2692 <li>Improved speed and layout of Envision2 service menu</li>
2693 <li>Superpose structures using associated sequence
2695 <li>Export coordinates and projection as CSV from PCA
2697 </ul> <em>Applet</em>
2699 <li>enable javascript: execution by the applet via the
2700 link out mechanism</li>
2701 </ul> <em>Other</em>
2703 <li>Updated the Jmol Jalview interface to work with Jmol
2705 <li>The Jalview Desktop and JalviewLite applet now
2706 require Java 1.5</li>
2707 <li>Allow Jalview feature colour specification for GFF
2708 sequence annotation files</li>
2709 <li>New 'colour by label' keword in Jalview feature file
2710 type colour specification</li>
2711 <li>New Jalview Desktop Groovy API method that allows a
2712 script to check if it being run in an interactive session or
2713 in a batch operation from the Jalview command line</li>
2717 <li>clustalx colourscheme colours Ds preferentially when
2718 both D+E are present in over 50% of the column</li>
2719 </ul> <em>Application</em>
2721 <li>typo in AlignmentFrame->View->Hide->all but
2722 selected Regions menu item</li>
2723 <li>sequence fetcher replaces ',' for ';' when the ',' is
2724 part of a valid accession ID</li>
2725 <li>fatal OOM if object retrieved by sequence fetcher
2726 runs out of memory</li>
2727 <li>unhandled Out of Memory Error when viewing pca
2728 analysis results</li>
2729 <li>InstallAnywhere builds fail to launch on OS X java
2730 10.5 update 4 (due to apple Java 1.6 update)</li>
2731 <li>Installanywhere Jalview silently fails to launch</li>
2732 </ul> <em>Applet</em>
2734 <li>Jalview.getFeatureGroups() raises an
2735 ArrayIndexOutOfBoundsException if no feature groups are
2742 <div align="center">
2743 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2749 <li>Alignment prettyprinter doesn't cope with long
2751 <li>clustalx colourscheme colours Ds preferentially when
2752 both D+E are present in over 50% of the column</li>
2753 <li>nucleic acid structures retrieved from PDB do not
2754 import correctly</li>
2755 <li>More columns get selected than were clicked on when a
2756 number of columns are hidden</li>
2757 <li>annotation label popup menu not providing correct
2758 add/hide/show options when rows are hidden or none are
2760 <li>Stockholm format shown in list of readable formats,
2761 and parser copes better with alignments from RFAM.</li>
2762 <li>CSV output of consensus only includes the percentage
2763 of all symbols if sequence logo display is enabled</li>
2765 </ul> <em>Applet</em>
2767 <li>annotation panel disappears when annotation is
2769 </ul> <em>Application</em>
2771 <li>Alignment view not redrawn properly when new
2772 alignment opened where annotation panel is visible but no
2773 annotations are present on alignment</li>
2774 <li>pasted region containing hidden columns is
2775 incorrectly displayed in new alignment window</li>
2776 <li>Jalview slow to complete operations when stdout is
2777 flooded (fix is to close the Jalview console)</li>
2778 <li>typo in AlignmentFrame->View->Hide->all but
2779 selected Rregions menu item.</li>
2780 <li>inconsistent group submenu and Format submenu entry
2781 'Un' or 'Non'conserved</li>
2782 <li>Sequence feature settings are being shared by
2783 multiple distinct alignments</li>
2784 <li>group annotation not recreated when tree partition is
2786 <li>double click on group annotation to select sequences
2787 does not propagate to associated trees</li>
2788 <li>Mac OSX specific issues:
2790 <li>exception raised when mouse clicked on desktop
2791 window background</li>
2792 <li>Desktop menu placed on menu bar and application
2793 name set correctly</li>
2794 <li>sequence feature settings not wide enough for the
2795 save feature colourscheme button</li>
2804 <div align="center">
2805 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2808 <td><em>New Capabilities</em>
2810 <li>URL links generated from description line for
2811 regular-expression based URL links (applet and application)
2813 <li>Non-positional feature URL links are shown in link
2815 <li>Linked viewing of nucleic acid sequences and
2817 <li>Automatic Scrolling option in View menu to display
2818 the currently highlighted region of an alignment.</li>
2819 <li>Order an alignment by sequence length, or using the
2820 average score or total feature count for each sequence.</li>
2821 <li>Shading features by score or associated description</li>
2822 <li>Subdivide alignment and groups based on identity of
2823 selected subsequence (Make Groups from Selection).</li>
2824 <li>New hide/show options including Shift+Control+H to
2825 hide everything but the currently selected region.</li>
2826 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2827 </ul> <em>Application</em>
2829 <li>Fetch DB References capabilities and UI expanded to
2830 support retrieval from DAS sequence sources</li>
2831 <li>Local DAS Sequence sources can be added via the
2832 command line or via the Add local source dialog box.</li>
2833 <li>DAS Dbref and DbxRef feature types are parsed as
2834 database references and protein_name is parsed as
2835 description line (BioSapiens terms).</li>
2836 <li>Enable or disable non-positional feature and database
2837 references in sequence ID tooltip from View menu in
2839 <!-- <li>New hidden columns and rows and representatives capabilities
2840 in annotations file (in progress - not yet fully implemented)</li> -->
2841 <li>Group-associated consensus, sequence logos and
2842 conservation plots</li>
2843 <li>Symbol distributions for each column can be exported
2844 and visualized as sequence logos</li>
2845 <li>Optionally scale multi-character column labels to fit
2846 within each column of annotation row<!-- todo for applet -->
2848 <li>Optional automatic sort of associated alignment view
2849 when a new tree is opened.</li>
2850 <li>Jalview Java Console</li>
2851 <li>Better placement of desktop window when moving
2852 between different screens.</li>
2853 <li>New preference items for sequence ID tooltip and
2854 consensus annotation</li>
2855 <li>Client to submit sequences and IDs to Envision2
2857 <li><em>Vamsas Capabilities</em>
2859 <li>Improved VAMSAS synchronization (Jalview archive
2860 used to preserve views, structures, and tree display
2862 <li>Import of vamsas documents from disk or URL via
2864 <li>Sharing of selected regions between views and
2865 with other VAMSAS applications (Experimental feature!)</li>
2866 <li>Updated API to VAMSAS version 0.2</li>
2868 </ul> <em>Applet</em>
2870 <li>Middle button resizes annotation row height</li>
2873 <li>sortByTree (true/false) - automatically sort the
2874 associated alignment view by the tree when a new tree is
2876 <li>showTreeBootstraps (true/false) - show or hide
2877 branch bootstraps (default is to show them if available)</li>
2878 <li>showTreeDistances (true/false) - show or hide
2879 branch lengths (default is to show them if available)</li>
2880 <li>showUnlinkedTreeNodes (true/false) - indicate if
2881 unassociated nodes should be highlighted in the tree
2883 <li>heightScale and widthScale (1.0 or more) -
2884 increase the height or width of a cell in the alignment
2885 grid relative to the current font size.</li>
2888 <li>Non-positional features displayed in sequence ID
2890 </ul> <em>Other</em>
2892 <li>Features format: graduated colour definitions and
2893 specification of feature scores</li>
2894 <li>Alignment Annotations format: new keywords for group
2895 associated annotation (GROUP_REF) and annotation row display
2896 properties (ROW_PROPERTIES)</li>
2897 <li>XML formats extended to support graduated feature
2898 colourschemes, group associated annotation, and profile
2899 visualization settings.</li></td>
2902 <li>Source field in GFF files parsed as feature source
2903 rather than description</li>
2904 <li>Non-positional features are now included in sequence
2905 feature and gff files (controlled via non-positional feature
2906 visibility in tooltip).</li>
2907 <li>URL links generated for all feature links (bugfix)</li>
2908 <li>Added URL embedding instructions to features file
2910 <li>Codons containing ambiguous nucleotides translated as
2911 'X' in peptide product</li>
2912 <li>Match case switch in find dialog box works for both
2913 sequence ID and sequence string and query strings do not
2914 have to be in upper case to match case-insensitively.</li>
2915 <li>AMSA files only contain first column of
2916 multi-character column annotation labels</li>
2917 <li>Jalview Annotation File generation/parsing consistent
2918 with documentation (e.g. Stockholm annotation can be
2919 exported and re-imported)</li>
2920 <li>PDB files without embedded PDB IDs given a friendly
2922 <li>Find incrementally searches ID string matches as well
2923 as subsequence matches, and correctly reports total number
2927 <li>Better handling of exceptions during sequence
2929 <li>Dasobert generated non-positional feature URL
2930 link text excludes the start_end suffix</li>
2931 <li>DAS feature and source retrieval buttons disabled
2932 when fetch or registry operations in progress.</li>
2933 <li>PDB files retrieved from URLs are cached properly</li>
2934 <li>Sequence description lines properly shared via
2936 <li>Sequence fetcher fetches multiple records for all
2938 <li>Ensured that command line das feature retrieval
2939 completes before alignment figures are generated.</li>
2940 <li>Reduced time taken when opening file browser for
2942 <li>isAligned check prior to calculating tree, PCA or
2943 submitting an MSA to JNet now excludes hidden sequences.</li>
2944 <li>User defined group colours properly recovered
2945 from Jalview projects.</li>
2954 <div align="center">
2955 <strong>2.4.0.b2</strong><br> 28/10/2009
2960 <li>Experimental support for google analytics usage
2962 <li>Jalview privacy settings (user preferences and docs).</li>
2967 <li>Race condition in applet preventing startup in
2969 <li>Exception when feature created from selection beyond
2970 length of sequence.</li>
2971 <li>Allow synthetic PDB files to be imported gracefully</li>
2972 <li>Sequence associated annotation rows associate with
2973 all sequences with a given id</li>
2974 <li>Find function matches case-insensitively for sequence
2975 ID string searches</li>
2976 <li>Non-standard characters do not cause pairwise
2977 alignment to fail with exception</li>
2978 </ul> <em>Application Issues</em>
2980 <li>Sequences are now validated against EMBL database</li>
2981 <li>Sequence fetcher fetches multiple records for all
2983 </ul> <em>InstallAnywhere Issues</em>
2985 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2986 issue with installAnywhere mechanism)</li>
2987 <li>Command line launching of JARs from InstallAnywhere
2988 version (java class versioning error fixed)</li>
2995 <div align="center">
2996 <strong>2.4</strong><br> 27/8/2008
2999 <td><em>User Interface</em>
3001 <li>Linked highlighting of codon and amino acid from
3002 translation and protein products</li>
3003 <li>Linked highlighting of structure associated with
3004 residue mapping to codon position</li>
3005 <li>Sequence Fetcher provides example accession numbers
3006 and 'clear' button</li>
3007 <li>MemoryMonitor added as an option under Desktop's
3009 <li>Extract score function to parse whitespace separated
3010 numeric data in description line</li>
3011 <li>Column labels in alignment annotation can be centred.</li>
3012 <li>Tooltip for sequence associated annotation give name
3014 </ul> <em>Web Services and URL fetching</em>
3016 <li>JPred3 web service</li>
3017 <li>Prototype sequence search client (no public services
3019 <li>Fetch either seed alignment or full alignment from
3021 <li>URL Links created for matching database cross
3022 references as well as sequence ID</li>
3023 <li>URL Links can be created using regular-expressions</li>
3024 </ul> <em>Sequence Database Connectivity</em>
3026 <li>Retrieval of cross-referenced sequences from other
3028 <li>Generalised database reference retrieval and
3029 validation to all fetchable databases</li>
3030 <li>Fetch sequences from DAS sources supporting the
3031 sequence command</li>
3032 </ul> <em>Import and Export</em>
3033 <li>export annotation rows as CSV for spreadsheet import</li>
3034 <li>Jalview projects record alignment dataset associations,
3035 EMBL products, and cDNA sequence mappings</li>
3036 <li>Sequence Group colour can be specified in Annotation
3038 <li>Ad-hoc colouring of group in Annotation File using RGB
3039 triplet as name of colourscheme</li>
3040 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3042 <li>treenode binding for VAMSAS tree exchange</li>
3043 <li>local editing and update of sequences in VAMSAS
3044 alignments (experimental)</li>
3045 <li>Create new or select existing session to join</li>
3046 <li>load and save of vamsas documents</li>
3047 </ul> <em>Application command line</em>
3049 <li>-tree parameter to open trees (introduced for passing
3051 <li>-fetchfrom command line argument to specify nicknames
3052 of DAS servers to query for alignment features</li>
3053 <li>-dasserver command line argument to add new servers
3054 that are also automatically queried for features</li>
3055 <li>-groovy command line argument executes a given groovy
3056 script after all input data has been loaded and parsed</li>
3057 </ul> <em>Applet-Application data exchange</em>
3059 <li>Trees passed as applet parameters can be passed to
3060 application (when using "View in full
3061 application")</li>
3062 </ul> <em>Applet Parameters</em>
3064 <li>feature group display control parameter</li>
3065 <li>debug parameter</li>
3066 <li>showbutton parameter</li>
3067 </ul> <em>Applet API methods</em>
3069 <li>newView public method</li>
3070 <li>Window (current view) specific get/set public methods</li>
3071 <li>Feature display control methods</li>
3072 <li>get list of currently selected sequences</li>
3073 </ul> <em>New Jalview distribution features</em>
3075 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3076 <li>RELEASE file gives build properties for the latest
3077 Jalview release.</li>
3078 <li>Java 1.1 Applet build made easier and donotobfuscate
3079 property controls execution of obfuscator</li>
3080 <li>Build target for generating source distribution</li>
3081 <li>Debug flag for javacc</li>
3082 <li>.jalview_properties file is documented (slightly) in
3083 jalview.bin.Cache</li>
3084 <li>Continuous Build Integration for stable and
3085 development version of Application, Applet and source
3090 <li>selected region output includes visible annotations
3091 (for certain formats)</li>
3092 <li>edit label/displaychar contains existing label/char
3094 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3095 <li>shorter peptide product names from EMBL records</li>
3096 <li>Newick string generator makes compact representations</li>
3097 <li>bootstrap values parsed correctly for tree files with
3099 <li>pathological filechooser bug avoided by not allowing
3100 filenames containing a ':'</li>
3101 <li>Fixed exception when parsing GFF files containing
3102 global sequence features</li>
3103 <li>Alignment datasets are finalized only when number of
3104 references from alignment sequences goes to zero</li>
3105 <li>Close of tree branch colour box without colour
3106 selection causes cascading exceptions</li>
3107 <li>occasional negative imgwidth exceptions</li>
3108 <li>better reporting of non-fatal warnings to user when
3109 file parsing fails.</li>
3110 <li>Save works when Jalview project is default format</li>
3111 <li>Save as dialog opened if current alignment format is
3112 not a valid output format</li>
3113 <li>UniProt canonical names introduced for both das and
3115 <li>Histidine should be midblue (not pink!) in Zappo</li>
3116 <li>error messages passed up and output when data read
3118 <li>edit undo recovers previous dataset sequence when
3119 sequence is edited</li>
3120 <li>allow PDB files without pdb ID HEADER lines (like
3121 those generated by MODELLER) to be read in properly</li>
3122 <li>allow reading of JPred concise files as a normal
3124 <li>Stockholm annotation parsing and alignment properties
3125 import fixed for PFAM records</li>
3126 <li>Structure view windows have correct name in Desktop
3128 <li>annotation consisting of sequence associated scores
3129 can be read and written correctly to annotation file</li>
3130 <li>Aligned cDNA translation to aligned peptide works
3132 <li>Fixed display of hidden sequence markers and
3133 non-italic font for representatives in Applet</li>
3134 <li>Applet Menus are always embedded in applet window on
3136 <li>Newly shown features appear at top of stack (in
3138 <li>Annotations added via parameter not drawn properly
3139 due to null pointer exceptions</li>
3140 <li>Secondary structure lines are drawn starting from
3141 first column of alignment</li>
3142 <li>UniProt XML import updated for new schema release in
3144 <li>Sequence feature to sequence ID match for Features
3145 file is case-insensitive</li>
3146 <li>Sequence features read from Features file appended to
3147 all sequences with matching IDs</li>
3148 <li>PDB structure coloured correctly for associated views
3149 containing a sub-sequence</li>
3150 <li>PDB files can be retrieved by applet from Jar files</li>
3151 <li>feature and annotation file applet parameters
3152 referring to different directories are retrieved correctly</li>
3153 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3154 <li>Fixed application hang whilst waiting for
3155 splash-screen version check to complete</li>
3156 <li>Applet properly URLencodes input parameter values
3157 when passing them to the launchApp service</li>
3158 <li>display name and local features preserved in results
3159 retrieved from web service</li>
3160 <li>Visual delay indication for sequence retrieval and
3161 sequence fetcher initialisation</li>
3162 <li>updated Application to use DAS 1.53e version of
3163 dasobert DAS client</li>
3164 <li>Re-instated Full AMSA support and .amsa file
3166 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3174 <div align="center">
3175 <strong>2.3</strong><br> 9/5/07
3180 <li>Jmol 11.0.2 integration</li>
3181 <li>PDB views stored in Jalview XML files</li>
3182 <li>Slide sequences</li>
3183 <li>Edit sequence in place</li>
3184 <li>EMBL CDS features</li>
3185 <li>DAS Feature mapping</li>
3186 <li>Feature ordering</li>
3187 <li>Alignment Properties</li>
3188 <li>Annotation Scores</li>
3189 <li>Sort by scores</li>
3190 <li>Feature/annotation editing in applet</li>
3195 <li>Headless state operation in 2.2.1</li>
3196 <li>Incorrect and unstable DNA pairwise alignment</li>
3197 <li>Cut and paste of sequences with annotation</li>
3198 <li>Feature group display state in XML</li>
3199 <li>Feature ordering in XML</li>
3200 <li>blc file iteration selection using filename # suffix</li>
3201 <li>Stockholm alignment properties</li>
3202 <li>Stockhom alignment secondary structure annotation</li>
3203 <li>2.2.1 applet had no feature transparency</li>
3204 <li>Number pad keys can be used in cursor mode</li>
3205 <li>Structure Viewer mirror image resolved</li>
3212 <div align="center">
3213 <strong>2.2.1</strong><br> 12/2/07
3218 <li>Non standard characters can be read and displayed
3219 <li>Annotations/Features can be imported/exported to the
3221 <li>Applet allows editing of sequence/annotation/group
3222 name & description
3223 <li>Preference setting to display sequence name in
3225 <li>Annotation file format extended to allow
3226 Sequence_groups to be defined
3227 <li>Default opening of alignment overview panel can be
3228 specified in preferences
3229 <li>PDB residue numbering annotation added to associated
3235 <li>Applet crash under certain Linux OS with Java 1.6
3237 <li>Annotation file export / import bugs fixed
3238 <li>PNG / EPS image output bugs fixed
3244 <div align="center">
3245 <strong>2.2</strong><br> 27/11/06
3250 <li>Multiple views on alignment
3251 <li>Sequence feature editing
3252 <li>"Reload" alignment
3253 <li>"Save" to current filename
3254 <li>Background dependent text colour
3255 <li>Right align sequence ids
3256 <li>User-defined lower case residue colours
3259 <li>Menu item accelerator keys
3260 <li>Control-V pastes to current alignment
3261 <li>Cancel button for DAS Feature Fetching
3262 <li>PCA and PDB Viewers zoom via mouse roller
3263 <li>User-defined sub-tree colours and sub-tree selection
3265 <li>'New Window' button on the 'Output to Text box'
3270 <li>New memory efficient Undo/Redo System
3271 <li>Optimised symbol lookups and conservation/consensus
3273 <li>Region Conservation/Consensus recalculated after
3275 <li>Fixed Remove Empty Columns Bug (empty columns at end
3277 <li>Slowed DAS Feature Fetching for increased robustness.
3279 <li>Made angle brackets in ASCII feature descriptions
3281 <li>Re-instated Zoom function for PCA
3282 <li>Sequence descriptions conserved in web service
3284 <li>UniProt ID discoverer uses any word separated by
3286 <li>WsDbFetch query/result association resolved
3287 <li>Tree leaf to sequence mapping improved
3288 <li>Smooth fonts switch moved to FontChooser dialog box.
3295 <div align="center">
3296 <strong>2.1.1</strong><br> 12/9/06
3301 <li>Copy consensus sequence to clipboard</li>
3306 <li>Image output - rightmost residues are rendered if
3307 sequence id panel has been resized</li>
3308 <li>Image output - all offscreen group boundaries are
3310 <li>Annotation files with sequence references - all
3311 elements in file are relative to sequence position</li>
3312 <li>Mac Applet users can use Alt key for group editing</li>
3318 <div align="center">
3319 <strong>2.1</strong><br> 22/8/06
3324 <li>MAFFT Multiple Alignment in default Web Service list</li>
3325 <li>DAS Feature fetching</li>
3326 <li>Hide sequences and columns</li>
3327 <li>Export Annotations and Features</li>
3328 <li>GFF file reading / writing</li>
3329 <li>Associate structures with sequences from local PDB
3331 <li>Add sequences to exisiting alignment</li>
3332 <li>Recently opened files / URL lists</li>
3333 <li>Applet can launch the full application</li>
3334 <li>Applet has transparency for features (Java 1.2
3336 <li>Applet has user defined colours parameter</li>
3337 <li>Applet can load sequences from parameter
3338 "sequence<em>x</em>"
3344 <li>Redundancy Panel reinstalled in the Applet</li>
3345 <li>Monospaced font - EPS / rescaling bug fixed</li>
3346 <li>Annotation files with sequence references bug fixed</li>
3352 <div align="center">
3353 <strong>2.08.1</strong><br> 2/5/06
3358 <li>Change case of selected region from Popup menu</li>
3359 <li>Choose to match case when searching</li>
3360 <li>Middle mouse button and mouse movement can compress /
3361 expand the visible width and height of the alignment</li>
3366 <li>Annotation Panel displays complete JNet results</li>
3372 <div align="center">
3373 <strong>2.08b</strong><br> 18/4/06
3379 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3380 <li>Righthand label on wrapped alignments shows correct
3387 <div align="center">
3388 <strong>2.08</strong><br> 10/4/06
3393 <li>Editing can be locked to the selection area</li>
3394 <li>Keyboard editing</li>
3395 <li>Create sequence features from searches</li>
3396 <li>Precalculated annotations can be loaded onto
3398 <li>Features file allows grouping of features</li>
3399 <li>Annotation Colouring scheme added</li>
3400 <li>Smooth fonts off by default - Faster rendering</li>
3401 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3406 <li>Drag & Drop fixed on Linux</li>
3407 <li>Jalview Archive file faster to load/save, sequence
3408 descriptions saved.</li>
3414 <div align="center">
3415 <strong>2.07</strong><br> 12/12/05
3420 <li>PDB Structure Viewer enhanced</li>
3421 <li>Sequence Feature retrieval and display enhanced</li>
3422 <li>Choose to output sequence start-end after sequence
3423 name for file output</li>
3424 <li>Sequence Fetcher WSDBFetch@EBI</li>
3425 <li>Applet can read feature files, PDB files and can be
3426 used for HTML form input</li>
3431 <li>HTML output writes groups and features</li>
3432 <li>Group editing is Control and mouse click</li>
3433 <li>File IO bugs</li>
3439 <div align="center">
3440 <strong>2.06</strong><br> 28/9/05
3445 <li>View annotations in wrapped mode</li>
3446 <li>More options for PCA viewer</li>
3451 <li>GUI bugs resolved</li>
3452 <li>Runs with -nodisplay from command line</li>
3458 <div align="center">
3459 <strong>2.05b</strong><br> 15/9/05
3464 <li>Choose EPS export as lineart or text</li>
3465 <li>Jar files are executable</li>
3466 <li>Can read in Uracil - maps to unknown residue</li>
3471 <li>Known OutOfMemory errors give warning message</li>
3472 <li>Overview window calculated more efficiently</li>
3473 <li>Several GUI bugs resolved</li>
3479 <div align="center">
3480 <strong>2.05</strong><br> 30/8/05
3485 <li>Edit and annotate in "Wrapped" view</li>
3490 <li>Several GUI bugs resolved</li>
3496 <div align="center">
3497 <strong>2.04</strong><br> 24/8/05
3502 <li>Hold down mouse wheel & scroll to change font
3508 <li>Improved JPred client reliability</li>
3509 <li>Improved loading of Jalview files</li>
3515 <div align="center">
3516 <strong>2.03</strong><br> 18/8/05
3521 <li>Set Proxy server name and port in preferences</li>
3522 <li>Multiple URL links from sequence ids</li>
3523 <li>User Defined Colours can have a scheme name and added
3525 <li>Choose to ignore gaps in consensus calculation</li>
3526 <li>Unix users can set default web browser</li>
3527 <li>Runs without GUI for batch processing</li>
3528 <li>Dynamically generated Web Service Menus</li>
3533 <li>InstallAnywhere download for Sparc Solaris</li>
3539 <div align="center">
3540 <strong>2.02</strong><br> 18/7/05
3546 <li>Copy & Paste order of sequences maintains
3547 alignment order.</li>
3553 <div align="center">
3554 <strong>2.01</strong><br> 12/7/05
3559 <li>Use delete key for deleting selection.</li>
3560 <li>Use Mouse wheel to scroll sequences.</li>
3561 <li>Help file updated to describe how to add alignment
3563 <li>Version and build date written to build properties
3565 <li>InstallAnywhere installation will check for updates
3566 at launch of Jalview.</li>
3571 <li>Delete gaps bug fixed.</li>
3572 <li>FileChooser sorts columns.</li>
3573 <li>Can remove groups one by one.</li>
3574 <li>Filechooser icons installed.</li>
3575 <li>Finder ignores return character when searching.
3576 Return key will initiate a search.<br>
3583 <div align="center">
3584 <strong>2.0</strong><br> 20/6/05
3589 <li>New codebase</li>