3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.3">2.10.3</a><br />
74 <em>17/11/2017</em></strong>
77 <td><div align="left">
81 <!-- JAL-2446 -->Faster and more efficient management and
82 rendering of sequence features
85 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
86 429 rate limit request hander
89 <!-- JAL-2773 -->Structure views don't get updated unless
90 their colours have changed
92 <li><!-- JAL-2495 -->All linked sequences are highlighted for a structure mousover (Jmol) or selection (Chimera)</li>
93 <li><!-- JAL-2790 -->'Cancel' button in progress bar for JABAWS AACon, RNAAliFold and Disorder prediction jobs
96 <li><!-- JAL-2617 -->Stop codons are excluded in CDS/Protein view from Ensembl locus cross-references</li>
97 <li><!-- JAL-2685 -->Start/End limits are shown in Pairwise Alignment report</li>
98 <li><!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch' feature can be disabled</li>
99 <li><!-- JAL-2810 -->Retrieve IDs tab added for UniProt and PDB easier retrieval of sequences for lists of IDs</li>
100 <li><!-- JAL-2758 -->Short names for sequences retrieved from Uniprot</li>
104 <li>Groovy interpreter updated to 2.4.12</li>
105 <li>Example groovy script for generating a matrix of percent identity scores for current alignment.</li>
107 <em>Testing and Deployment</em>
109 <li><!-- JAL-2727 -->Test to catch memory leaks in Jalview UI</li>
113 <td><div align="left">
116 <li><!-- JAL-2643 -->Pressing tab after updating the colour threshold text field doesn't trigger an update to the alignment view</li>
117 <li><!-- JAL-2682 -->Race condition when parsing sequence ID strings in parallel</li>
118 <li><!-- JAL-2608 -->Overview windows are also closed when alignment window is closed</li>
119 <li><!-- JAL-2548 -->Export of features doesn't always respect group visibility</li>
120 <li><!-- JAL-2831 -->Jumping from column 1 to column 100,000 takes a long time in Keyboard mode</li>
124 <li><!-- JAL-2777 -->Structures with whitespace chainCode cannot be viewed in Chimera</li>
125 <li><!-- JAL-2728 -->Protein annotation panel too high in CDS/Protein view
127 <li><!-- JAL-2757 -->Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs
129 <li><!-- JAL-2253 -->Slow EnsemblGenome ID lookup</li>
130 <li><!-- JAL-2529 -->Revised Ensembl REST API CDNA query</li>
131 <li><!-- JAL-2739 -->Hidden column marker in last column not rendered when switching back from Wrapped to normal view</li>
132 <li><!-- JAL-2768 -->Annotation display corrupted when scrolling right in unwapped alignment view</li>
133 <li><!-- JAL-2542 -->Existing features on subsequence incorrectly relocated when full sequence retrieved from database</li>
134 <li><!-- JAL-2733 -->Last reported memory still shown when Desktop->Show Memory is unticked (OSX only)</li>
135 <li><!-- JAL-2658 -->Amend Features dialog doesn't allow features of same type and group to be selected for amending</li>
136 <li><!-- JAL-2524 -->Jalview becomes sluggish in wide alignments when hidden columns are present</li>
137 <li><!-- JAL-2392 -->Jalview freezes when loading and displaying several structures</li>
138 <li><!-- JAL-2732 -->Black outlines left after resizing or moving a window</li>
139 <li><!-- JAL-1900,JAL-1625 -->Unable to minimise windows within the Jalview desktop on OSX</li>
140 <li><!-- JAL-2667 -->Mouse wheel doesn't scroll vertically when in wrapped alignment mode</li>
141 <li><!-- JAL-2636 -->Scale mark not shown when close to right hand end of alignment</li>
142 <li><!-- JAL-2684 -->Pairwise alignment only aligns selected regions of each selected sequence</li>
143 <li><!-- JAL-2973 -->Alignment ruler height set incorrectly after canceling the Alignment Window's Font dialog</li>
144 <li><!-- JAL-2036 -->Show cross-references not enabled after restoring project until a new view is created</li>
145 <li><!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in URL links appears when only default EMBL-EBI link is configured (since 2.10.2b2)</li>
146 <li><!-- JAL-2775 -->Overview redraws whole window when box position is adjusted</li>
147 <li><!-- JAL-2225 -->Structure viewer doesn't map all chains in a multi-chain structure when viewing alignment involving more than one chain (since 2.10)</li>
149 <strong><em>Applet</em></strong><br/>
151 <li><!-- JAL-2687 -->Concurrent modification exception when closing alignment panel</li>
153 <strong><em>BioJSON</em></strong><br/>
156 <!-- JAL-2546 -->BioJSON export does not preserve non-positional features
159 <strong>Known Java 9 Issues</strong>
161 <li><!-- JAL-2902 -->Groovy Console very slow to open and is
162 not responsive when entering characters (Webstart, Java 9.01,
166 <strong>New Known Issues</strong>
168 <li><!-- JAL- --></li>
174 <td width="60" nowrap>
176 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
177 <em>2/10/2017</em></strong>
180 <td><div align="left">
181 <em>New features in Jalview Desktop</em>
184 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
186 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
190 <td><div align="left">
194 <td width="60" nowrap>
196 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
197 <em>7/9/2017</em></strong>
200 <td><div align="left">
204 <!-- JAL-2588 -->Show gaps in overview window by colouring
205 in grey (sequences used to be coloured grey, and gaps were
209 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
213 <!-- JAL-2587 -->Overview updates immediately on increase
214 in size and progress bar shown as higher resolution
215 overview is recalculated
220 <td><div align="left">
224 <!-- JAL-2664 -->Overview window redraws every hidden
225 column region row by row
228 <!-- JAL-2681 -->duplicate protein sequences shown after
229 retrieving Ensembl crossrefs for sequences from Uniprot
232 <!-- JAL-2603 -->Overview window throws NPE if show boxes
233 format setting is unticked
236 <!-- JAL-2610 -->Groups are coloured wrongly in overview
237 if group has show boxes format setting unticked
240 <!-- JAL-2672,JAL-2665 -->Redraw problems when
241 autoscrolling whilst dragging current selection group to
242 include sequences and columns not currently displayed
245 <!-- JAL-2691 -->Not all chains are mapped when multimeric
246 assemblies are imported via CIF file
249 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
250 displayed when threshold or conservation colouring is also
254 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
258 <!-- JAL-2673 -->Jalview continues to scroll after
259 dragging a selected region off the visible region of the
263 <!-- JAL-2724 -->Cannot apply annotation based
264 colourscheme to all groups in a view
267 <!-- JAL-2511 -->IDs don't line up with sequences
268 initially after font size change using the Font chooser or
275 <td width="60" nowrap>
277 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
280 <td><div align="left">
281 <em>Calculations</em>
285 <!-- JAL-1933 -->Occupancy annotation row shows number of
286 ungapped positions in each column of the alignment.
289 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
290 a calculation dialog box
293 <!-- JAL-2379 -->Revised implementation of PCA for speed
294 and memory efficiency (~30x faster)
297 <!-- JAL-2403 -->Revised implementation of sequence
298 similarity scores as used by Tree, PCA, Shading Consensus
299 and other calculations
302 <!-- JAL-2416 -->Score matrices are stored as resource
303 files within the Jalview codebase
306 <!-- JAL-2500 -->Trees computed on Sequence Feature
307 Similarity may have different topology due to increased
314 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
315 model for alignments and groups
318 <!-- JAL-384 -->Custom shading schemes created via groovy
325 <!-- JAL-2526 -->Efficiency improvements for interacting
326 with alignment and overview windows
329 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
333 <!-- JAL-2388 -->Hidden columns and sequences can be
337 <!-- JAL-2611 -->Click-drag in visible area allows fine
338 adjustment of visible position
342 <em>Data import/export</em>
345 <!-- JAL-2535 -->Posterior probability annotation from
346 Stockholm files imported as sequence associated annotation
349 <!-- JAL-2507 -->More robust per-sequence positional
350 annotation input/output via stockholm flatfile
353 <!-- JAL-2533 -->Sequence names don't include file
354 extension when importing structure files without embedded
355 names or PDB accessions
358 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
359 format sequence substitution matrices
362 <em>User Interface</em>
365 <!-- JAL-2447 --> Experimental Features Checkbox in
366 Desktop's Tools menu to hide or show untested features in
370 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
371 via Overview or sequence motif search operations
374 <!-- JAL-2547 -->Amend sequence features dialog box can be
375 opened by double clicking gaps within sequence feature
379 <!-- JAL-1476 -->Status bar message shown when not enough
380 aligned positions were available to create a 3D structure
384 <em>3D Structure</em>
387 <!-- JAL-2430 -->Hidden regions in alignment views are not
388 coloured in linked structure views
391 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
392 file-based command exchange
395 <!-- JAL-2375 -->Structure chooser automatically shows
396 Cached Structures rather than querying the PDBe if
397 structures are already available for sequences
400 <!-- JAL-2520 -->Structures imported via URL are cached in
401 the Jalview project rather than downloaded again when the
405 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
406 to transfer Chimera's structure attributes as Jalview
407 features, and vice-versa (<strong>Experimental
411 <em>Web Services</em>
414 <!-- JAL-2549 -->Updated JABAWS client to v2.2
417 <!-- JAL-2335 -->Filter non-standard amino acids and
418 nucleotides when submitting to AACon and other MSA
422 <!-- JAL-2316, -->URLs for viewing database
423 cross-references provided by identifiers.org and the
431 <!-- JAL-2344 -->FileFormatI interface for describing and
432 identifying file formats (instead of String constants)
435 <!-- JAL-2228 -->FeatureCounter script refactored for
436 efficiency when counting all displayed features (not
437 backwards compatible with 2.10.1)
440 <em>Example files</em>
443 <!-- JAL-2631 -->Graduated feature colour style example
444 included in the example feature file
447 <em>Documentation</em>
450 <!-- JAL-2339 -->Release notes reformatted for readability
451 with the built-in Java help viewer
454 <!-- JAL-1644 -->Find documentation updated with 'search
455 sequence description' option
461 <!-- JAL-2485, -->External service integration tests for
462 Uniprot REST Free Text Search Client
465 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
468 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
473 <td><div align="left">
474 <em>Calculations</em>
477 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
478 matrix - C->R should be '-3'<br />Old matrix restored
479 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
481 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
482 Jalview's treatment of gaps in PCA and substitution matrix
483 based Tree calculations.<br /> <br />In earlier versions
484 of Jalview, gaps matching gaps were penalised, and gaps
485 matching non-gaps penalised even more. In the PCA
486 calculation, gaps were actually treated as non-gaps - so
487 different costs were applied, which meant Jalview's PCAs
488 were different to those produced by SeqSpace.<br />Jalview
489 now treats gaps in the same way as SeqSpace (ie it scores
490 them as 0). <br /> <br />Enter the following in the
491 Groovy console to restore pre-2.10.2 behaviour:<br />
492 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
493 // for 2.10.1 mode <br />
494 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
495 // to restore 2.10.2 mode <br /> <br /> <em>Note:
496 these settings will affect all subsequent tree and PCA
497 calculations (not recommended)</em></li>
499 <!-- JAL-2424 -->Fixed off-by-one bug that affected
500 scaling of branch lengths for trees computed using
501 Sequence Feature Similarity.
504 <!-- JAL-2377 -->PCA calculation could hang when
505 generating output report when working with highly
509 <!-- JAL-2544 --> Sort by features includes features to
510 right of selected region when gaps present on right-hand
514 <em>User Interface</em>
517 <!-- JAL-2346 -->Reopening Colour by annotation dialog
518 doesn't reselect a specific sequence's associated
519 annotation after it was used for colouring a view
522 <!-- JAL-2419 -->Current selection lost if popup menu
523 opened on a region of alignment without groups
526 <!-- JAL-2374 -->Popup menu not always shown for regions
527 of an alignment with overlapping groups
530 <!-- JAL-2310 -->Finder double counts if both a sequence's
531 name and description match
534 <!-- JAL-2370 -->Hiding column selection containing two
535 hidden regions results in incorrect hidden regions
538 <!-- JAL-2386 -->'Apply to all groups' setting when
539 changing colour does not apply Conservation slider value
543 <!-- JAL-2373 -->Percentage identity and conservation menu
544 items do not show a tick or allow shading to be disabled
547 <!-- JAL-2385 -->Conservation shading or PID threshold
548 lost when base colourscheme changed if slider not visible
551 <!-- JAL-2547 -->Sequence features shown in tooltip for
552 gaps before start of features
555 <!-- JAL-2623 -->Graduated feature colour threshold not
556 restored to UI when feature colour is edited
559 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
560 a time when scrolling vertically in wrapped mode.
563 <!-- JAL-2630 -->Structure and alignment overview update
564 as graduate feature colour settings are modified via the
568 <!-- JAL-2034 -->Overview window doesn't always update
569 when a group defined on the alignment is resized
572 <!-- JAL-2605 -->Mouseovers on left/right scale region in
573 wrapped view result in positional status updates
577 <!-- JAL-2563 -->Status bar doesn't show position for
578 ambiguous amino acid and nucleotide symbols
581 <!-- JAL-2602 -->Copy consensus sequence failed if
582 alignment included gapped columns
585 <!-- JAL-2473 -->Minimum size set for Jalview windows so
586 widgets don't permanently disappear
589 <!-- JAL-2503 -->Cannot select or filter quantitative
590 annotation that are shown only as column labels (e.g.
591 T-Coffee column reliability scores)
594 <!-- JAL-2594 -->Exception thrown if trying to create a
595 sequence feature on gaps only
598 <!-- JAL-2504 -->Features created with 'New feature'
599 button from a Find inherit previously defined feature type
600 rather than the Find query string
603 <!-- JAL-2423 -->incorrect title in output window when
604 exporting tree calculated in Jalview
607 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
608 and then revealing them reorders sequences on the
612 <!-- JAL-964 -->Group panel in sequence feature settings
613 doesn't update to reflect available set of groups after
614 interactively adding or modifying features
617 <!-- JAL-2225 -->Sequence Database chooser unusable on
621 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
622 only excluded gaps in current sequence and ignored
629 <!-- JAL-2421 -->Overview window visible region moves
630 erratically when hidden rows or columns are present
633 <!-- JAL-2362 -->Per-residue colourschemes applied via the
634 Structure Viewer's colour menu don't correspond to
638 <!-- JAL-2405 -->Protein specific colours only offered in
639 colour and group colour menu for protein alignments
642 <!-- JAL-2385 -->Colour threshold slider doesn't update to
643 reflect currently selected view or group's shading
647 <!-- JAL-2624 -->Feature colour thresholds not respected
648 when rendered on overview and structures when opacity at
652 <!-- JAL-2589 -->User defined gap colour not shown in
653 overview when features overlaid on alignment
656 <em>Data import/export</em>
659 <!-- JAL-2576 -->Very large alignments take a long time to
663 <!-- JAL-2507 -->Per-sequence RNA secondary structures
664 added after a sequence was imported are not written to
668 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
669 when importing RNA secondary structure via Stockholm
672 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
673 not shown in correct direction for simple pseudoknots
676 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
677 with lightGray or darkGray via features file (but can
681 <!-- JAL-2383 -->Above PID colour threshold not recovered
682 when alignment view imported from project
685 <!-- JAL-2520,JAL-2465 -->No mappings generated between
686 structure and sequences extracted from structure files
687 imported via URL and viewed in Jmol
690 <!-- JAL-2520 -->Structures loaded via URL are saved in
691 Jalview Projects rather than fetched via URL again when
692 the project is loaded and the structure viewed
695 <em>Web Services</em>
698 <!-- JAL-2519 -->EnsemblGenomes example failing after
699 release of Ensembl v.88
702 <!-- JAL-2366 -->Proxy server address and port always
703 appear enabled in Preferences->Connections
706 <!-- JAL-2461 -->DAS registry not found exceptions
707 removed from console output
710 <!-- JAL-2582 -->Cannot retrieve protein products from
711 Ensembl by Peptide ID
714 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
715 created from SIFTs, and spurious 'Couldn't open structure
716 in Chimera' errors raised after April 2017 update (problem
717 due to 'null' string rather than empty string used for
718 residues with no corresponding PDB mapping).
721 <em>Application UI</em>
724 <!-- JAL-2361 -->User Defined Colours not added to Colour
728 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
729 case' residues (button in colourscheme editor debugged and
730 new documentation and tooltips added)
733 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
734 doesn't restore group-specific text colour thresholds
737 <!-- JAL-2243 -->Feature settings panel does not update as
738 new features are added to alignment
741 <!-- JAL-2532 -->Cancel in feature settings reverts
742 changes to feature colours via the Amend features dialog
745 <!-- JAL-2506 -->Null pointer exception when attempting to
746 edit graduated feature colour via amend features dialog
750 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
751 selection menu changes colours of alignment views
754 <!-- JAL-2426 -->Spurious exceptions in console raised
755 from alignment calculation workers after alignment has
759 <!-- JAL-1608 -->Typo in selection popup menu - Create
760 groups now 'Create Group'
763 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
764 Create/Undefine group doesn't always work
767 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
768 shown again after pressing 'Cancel'
771 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
772 adjusts start position in wrap mode
775 <!-- JAL-2563 -->Status bar doesn't show positions for
776 ambiguous amino acids
779 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
780 CDS/Protein view after CDS sequences added for aligned
784 <!-- JAL-2592 -->User defined colourschemes called 'User
785 Defined' don't appear in Colours menu
791 <!-- JAL-2468 -->Switching between Nucleotide and Protein
792 score models doesn't always result in an updated PCA plot
795 <!-- JAL-2442 -->Features not rendered as transparent on
796 overview or linked structure view
799 <!-- JAL-2372 -->Colour group by conservation doesn't
803 <!-- JAL-2517 -->Hitting Cancel after applying
804 user-defined colourscheme doesn't restore original
811 <!-- JAL-2314 -->Unit test failure:
812 jalview.ws.jabaws.RNAStructExportImport setup fails
815 <!-- JAL-2307 -->Unit test failure:
816 jalview.ws.sifts.SiftsClientTest due to compatibility
817 problems with deep array comparison equality asserts in
818 successive versions of TestNG
821 <!-- JAL-2479 -->Relocated StructureChooserTest and
822 ParameterUtilsTest Unit tests to Network suite
825 <em>New Known Issues</em>
828 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
829 phase after a sequence motif find operation
832 <!-- JAL-2550 -->Importing annotation file with rows
833 containing just upper and lower case letters are
834 interpreted as WUSS RNA secondary structure symbols
837 <!-- JAL-2590 -->Cannot load and display Newick trees
838 reliably from eggnog Ortholog database
841 <!-- JAL-2468 -->Status bar shows 'Marked x columns
842 containing features of type Highlight' when 'B' is pressed
843 to mark columns containing highlighted regions.
846 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
847 doesn't always add secondary structure annotation.
852 <td width="60" nowrap>
854 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
857 <td><div align="left">
861 <!-- JAL-98 -->Improved memory usage: sparse arrays used
862 for all consensus calculations
865 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
868 <li>Updated Jalview's Certum code signing certificate
874 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
875 set of database cross-references, sorted alphabetically
878 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
879 from database cross references. Users with custom links
880 will receive a <a href="webServices/urllinks.html#warning">warning
881 dialog</a> asking them to update their preferences.
884 <!-- JAL-2287-->Cancel button and escape listener on
885 dialog warning user about disconnecting Jalview from a
889 <!-- JAL-2320-->Jalview's Chimera control window closes if
890 the Chimera it is connected to is shut down
893 <!-- JAL-1738-->New keystroke (B) and Select highlighted
894 columns menu item to mark columns containing highlighted
895 regions (e.g. from structure selections or results of a
899 <!-- JAL-2284-->Command line option for batch-generation
900 of HTML pages rendering alignment data with the BioJS
910 <!-- JAL-2286 -->Columns with more than one modal residue
911 are not coloured or thresholded according to percent
912 identity (first observed in Jalview 2.8.2)
915 <!-- JAL-2301 -->Threonine incorrectly reported as not
919 <!-- JAL-2318 -->Updates to documentation pages (above PID
920 threshold, amino acid properties)
923 <!-- JAL-2292 -->Lower case residues in sequences are not
924 reported as mapped to residues in a structure file in the
928 <!--JAL-2324 -->Identical features with non-numeric scores
929 could be added multiple times to a sequence
932 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
933 bond features shown as two highlighted residues rather
934 than a range in linked structure views, and treated
935 correctly when selecting and computing trees from features
938 <!-- JAL-2281-->Custom URL links for database
939 cross-references are matched to database name regardless
947 <!-- JAL-2282-->Custom URL links for specific database
948 names without regular expressions also offer links from
952 <!-- JAL-2315-->Removing a single configured link in the
953 URL links pane in Connections preferences doesn't actually
954 update Jalview configuration
957 <!-- JAL-2272-->CTRL-Click on a selected region to open
958 the alignment area popup menu doesn't work on El-Capitan
961 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
962 files with similarly named sequences if dropped onto the
966 <!-- JAL-2312 -->Additional mappings are shown for PDB
967 entries where more chains exist in the PDB accession than
968 are reported in the SIFTS file
971 <!-- JAL-2317-->Certain structures do not get mapped to
972 the structure view when displayed with Chimera
975 <!-- JAL-2317-->No chains shown in the Chimera view
976 panel's View->Show Chains submenu
979 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
980 work for wrapped alignment views
983 <!--JAL-2197 -->Rename UI components for running JPred
984 predictions from 'JNet' to 'JPred'
987 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
988 corrupted when annotation panel vertical scroll is not at
992 <!--JAL-2332 -->Attempting to view structure for Hen
993 lysozyme results in a PDB Client error dialog box
996 <!-- JAL-2319 -->Structure View's mapping report switched
997 ranges for PDB and sequence for SIFTS
1000 SIFTS 'Not_Observed' residues mapped to non-existant
1004 <!-- <em>New Known Issues</em>
1011 <td width="60" nowrap>
1012 <div align="center">
1013 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1014 <em>25/10/2016</em></strong>
1017 <td><em>Application</em>
1019 <li>3D Structure chooser opens with 'Cached structures'
1020 view if structures already loaded</li>
1021 <li>Progress bar reports models as they are loaded to
1022 structure views</li>
1028 <li>Colour by conservation always enabled and no tick
1029 shown in menu when BLOSUM or PID shading applied</li>
1030 <li>FER1_ARATH and FER2_ARATH labels were switched in
1031 example sequences/projects/trees</li>
1033 <em>Application</em>
1035 <li>Jalview projects with views of local PDB structure
1036 files saved on Windows cannot be opened on OSX</li>
1037 <li>Multiple structure views can be opened and superposed
1038 without timeout for structures with multiple models or
1039 multiple sequences in alignment</li>
1040 <li>Cannot import or associated local PDB files without a
1041 PDB ID HEADER line</li>
1042 <li>RMSD is not output in Jmol console when superposition
1044 <li>Drag and drop of URL from Browser fails for Linux and
1045 OSX versions earlier than El Capitan</li>
1046 <li>ENA client ignores invalid content from ENA server</li>
1047 <li>Exceptions are not raised in console when ENA client
1048 attempts to fetch non-existent IDs via Fetch DB Refs UI
1050 <li>Exceptions are not raised in console when a new view
1051 is created on the alignment</li>
1052 <li>OSX right-click fixed for group selections: CMD-click
1053 to insert/remove gaps in groups and CTRL-click to open group
1056 <em>Build and deployment</em>
1058 <li>URL link checker now copes with multi-line anchor
1061 <em>New Known Issues</em>
1063 <li>Drag and drop from URL links in browsers do not work
1070 <td width="60" nowrap>
1071 <div align="center">
1072 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1075 <td><em>General</em>
1078 <!-- JAL-2124 -->Updated Spanish translations.
1081 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1082 for importing structure data to Jalview. Enables mmCIF and
1086 <!-- JAL-192 --->Alignment ruler shows positions relative to
1090 <!-- JAL-2202 -->Position/residue shown in status bar when
1091 mousing over sequence associated annotation
1094 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1098 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1099 '()', canonical '[]' and invalid '{}' base pair populations
1103 <!-- JAL-2092 -->Feature settings popup menu options for
1104 showing or hiding columns containing a feature
1107 <!-- JAL-1557 -->Edit selected group by double clicking on
1108 group and sequence associated annotation labels
1111 <!-- JAL-2236 -->Sequence name added to annotation label in
1112 select/hide columns by annotation and colour by annotation
1116 </ul> <em>Application</em>
1119 <!-- JAL-2050-->Automatically hide introns when opening a
1120 gene/transcript view
1123 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1127 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1128 structure mappings with the EMBL-EBI PDBe SIFTS database
1131 <!-- JAL-2079 -->Updated download sites used for Rfam and
1132 Pfam sources to xfam.org
1135 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1138 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1139 over sequences in Jalview
1142 <!-- JAL-2027-->Support for reverse-complement coding
1143 regions in ENA and EMBL
1146 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1147 for record retrieval via ENA rest API
1150 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1154 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1155 groovy script execution
1158 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1159 alignment window's Calculate menu
1162 <!-- JAL-1812 -->Allow groovy scripts that call
1163 Jalview.getAlignFrames() to run in headless mode
1166 <!-- JAL-2068 -->Support for creating new alignment
1167 calculation workers from groovy scripts
1170 <!-- JAL-1369 --->Store/restore reference sequence in
1174 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1175 associations are now saved/restored from project
1178 <!-- JAL-1993 -->Database selection dialog always shown
1179 before sequence fetcher is opened
1182 <!-- JAL-2183 -->Double click on an entry in Jalview's
1183 database chooser opens a sequence fetcher
1186 <!-- JAL-1563 -->Free-text search client for UniProt using
1187 the UniProt REST API
1190 <!-- JAL-2168 -->-nonews command line parameter to prevent
1191 the news reader opening
1194 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1195 querying stored in preferences
1198 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1202 <!-- JAL-1977-->Tooltips shown on database chooser
1205 <!-- JAL-391 -->Reverse complement function in calculate
1206 menu for nucleotide sequences
1209 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1210 and feature counts preserves alignment ordering (and
1211 debugged for complex feature sets).
1214 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1215 viewing structures with Jalview 2.10
1218 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1219 genome, transcript CCDS and gene ids via the Ensembl and
1220 Ensembl Genomes REST API
1223 <!-- JAL-2049 -->Protein sequence variant annotation
1224 computed for 'sequence_variant' annotation on CDS regions
1228 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1232 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1233 Ref Fetcher fails to match, or otherwise updates sequence
1234 data from external database records.
1237 <!-- JAL-2154 -->Revised Jalview Project format for
1238 efficient recovery of sequence coding and alignment
1239 annotation relationships.
1241 </ul> <!-- <em>Applet</em>
1252 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1256 <!-- JAL-2018-->Export features in Jalview format (again)
1257 includes graduated colourschemes
1260 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1261 working with big alignments and lots of hidden columns
1264 <!-- JAL-2053-->Hidden column markers not always rendered
1265 at right of alignment window
1268 <!-- JAL-2067 -->Tidied up links in help file table of
1272 <!-- JAL-2072 -->Feature based tree calculation not shown
1276 <!-- JAL-2075 -->Hidden columns ignored during feature
1277 based tree calculation
1280 <!-- JAL-2065 -->Alignment view stops updating when show
1281 unconserved enabled for group on alignment
1284 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1288 <!-- JAL-2146 -->Alignment column in status incorrectly
1289 shown as "Sequence position" when mousing over
1293 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1294 hidden columns present
1297 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1298 user created annotation added to alignment
1301 <!-- JAL-1841 -->RNA Structure consensus only computed for
1302 '()' base pair annotation
1305 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1306 in zero scores for all base pairs in RNA Structure
1310 <!-- JAL-2174-->Extend selection with columns containing
1314 <!-- JAL-2275 -->Pfam format writer puts extra space at
1315 beginning of sequence
1318 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1322 <!-- JAL-2238 -->Cannot create groups on an alignment from
1323 from a tree when t-coffee scores are shown
1326 <!-- JAL-1836,1967 -->Cannot import and view PDB
1327 structures with chains containing negative resnums (4q4h)
1330 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1334 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1335 to Clustal, PIR and PileUp output
1338 <!-- JAL-2008 -->Reordering sequence features that are
1339 not visible causes alignment window to repaint
1342 <!-- JAL-2006 -->Threshold sliders don't work in
1343 graduated colour and colour by annotation row for e-value
1344 scores associated with features and annotation rows
1347 <!-- JAL-1797 -->amino acid physicochemical conservation
1348 calculation should be case independent
1351 <!-- JAL-2173 -->Remove annotation also updates hidden
1355 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1356 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1357 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1360 <!-- JAL-2065 -->Null pointer exceptions and redraw
1361 problems when reference sequence defined and 'show
1362 non-conserved' enabled
1365 <!-- JAL-1306 -->Quality and Conservation are now shown on
1366 load even when Consensus calculation is disabled
1369 <!-- JAL-1932 -->Remove right on penultimate column of
1370 alignment does nothing
1373 <em>Application</em>
1376 <!-- JAL-1552-->URLs and links can't be imported by
1377 drag'n'drop on OSX when launched via webstart (note - not
1378 yet fixed for El Capitan)
1381 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1382 output when running on non-gb/us i18n platforms
1385 <!-- JAL-1944 -->Error thrown when exporting a view with
1386 hidden sequences as flat-file alignment
1389 <!-- JAL-2030-->InstallAnywhere distribution fails when
1393 <!-- JAL-2080-->Jalview very slow to launch via webstart
1394 (also hotfix for 2.9.0b2)
1397 <!-- JAL-2085 -->Cannot save project when view has a
1398 reference sequence defined
1401 <!-- JAL-1011 -->Columns are suddenly selected in other
1402 alignments and views when revealing hidden columns
1405 <!-- JAL-1989 -->Hide columns not mirrored in complement
1406 view in a cDNA/Protein splitframe
1409 <!-- JAL-1369 -->Cannot save/restore representative
1410 sequence from project when only one sequence is
1414 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1415 in Structure Chooser
1418 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1419 structure consensus didn't refresh annotation panel
1422 <!-- JAL-1962 -->View mapping in structure view shows
1423 mappings between sequence and all chains in a PDB file
1426 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1427 dialogs format columns correctly, don't display array
1428 data, sort columns according to type
1431 <!-- JAL-1975 -->Export complete shown after destination
1432 file chooser is cancelled during an image export
1435 <!-- JAL-2025 -->Error when querying PDB Service with
1436 sequence name containing special characters
1439 <!-- JAL-2024 -->Manual PDB structure querying should be
1443 <!-- JAL-2104 -->Large tooltips with broken HTML
1444 formatting don't wrap
1447 <!-- JAL-1128 -->Figures exported from wrapped view are
1448 truncated so L looks like I in consensus annotation
1451 <!-- JAL-2003 -->Export features should only export the
1452 currently displayed features for the current selection or
1456 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1457 after fetching cross-references, and restoring from
1461 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1462 followed in the structure viewer
1465 <!-- JAL-2163 -->Titles for individual alignments in
1466 splitframe not restored from project
1469 <!-- JAL-2145 -->missing autocalculated annotation at
1470 trailing end of protein alignment in transcript/product
1471 splitview when pad-gaps not enabled by default
1474 <!-- JAL-1797 -->amino acid physicochemical conservation
1478 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1479 article has been read (reopened issue due to
1480 internationalisation problems)
1483 <!-- JAL-1960 -->Only offer PDB structures in structure
1484 viewer based on sequence name, PDB and UniProt
1489 <!-- JAL-1976 -->No progress bar shown during export of
1493 <!-- JAL-2213 -->Structures not always superimposed after
1494 multiple structures are shown for one or more sequences.
1497 <!-- JAL-1370 -->Reference sequence characters should not
1498 be replaced with '.' when 'Show unconserved' format option
1502 <!-- JAL-1823 -->Cannot specify chain code when entering
1503 specific PDB id for sequence
1506 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1507 'Export hidden sequences' is enabled, but 'export hidden
1508 columns' is disabled.
1511 <!--JAL-2026-->Best Quality option in structure chooser
1512 selects lowest rather than highest resolution structures
1516 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1517 to sequence mapping in 'View Mappings' report
1520 <!-- JAL-2284 -->Unable to read old Jalview projects that
1521 contain non-XML data added after Jalvew wrote project.
1524 <!-- JAL-2118 -->Newly created annotation row reorders
1525 after clicking on it to create new annotation for a
1529 <!-- JAL-1980 -->Null Pointer Exception raised when
1530 pressing Add on an orphaned cut'n'paste window.
1532 <!-- may exclude, this is an external service stability issue JAL-1941
1533 -- > RNA 3D structure not added via DSSR service</li> -->
1538 <!-- JAL-2151 -->Incorrect columns are selected when
1539 hidden columns present before start of sequence
1542 <!-- JAL-1986 -->Missing dependencies on applet pages
1546 <!-- JAL-1947 -->Overview pixel size changes when
1547 sequences are hidden in applet
1550 <!-- JAL-1996 -->Updated instructions for applet
1551 deployment on examples pages.
1558 <td width="60" nowrap>
1559 <div align="center">
1560 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1561 <em>16/10/2015</em></strong>
1564 <td><em>General</em>
1566 <li>Time stamps for signed Jalview application and applet
1571 <em>Application</em>
1573 <li>Duplicate group consensus and conservation rows
1574 shown when tree is partitioned</li>
1575 <li>Erratic behaviour when tree partitions made with
1576 multiple cDNA/Protein split views</li>
1582 <td width="60" nowrap>
1583 <div align="center">
1584 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1585 <em>8/10/2015</em></strong>
1588 <td><em>General</em>
1590 <li>Updated Spanish translations of localized text for
1592 </ul> <em>Application</em>
1594 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1595 <li>Signed OSX InstallAnywhere installer<br></li>
1596 <li>Support for per-sequence based annotations in BioJSON</li>
1597 </ul> <em>Applet</em>
1599 <li>Split frame example added to applet examples page</li>
1600 </ul> <em>Build and Deployment</em>
1603 <!-- JAL-1888 -->New ant target for running Jalview's test
1611 <li>Mapping of cDNA to protein in split frames
1612 incorrect when sequence start > 1</li>
1613 <li>Broken images in filter column by annotation dialog
1615 <li>Feature colours not parsed from features file</li>
1616 <li>Exceptions and incomplete link URLs recovered when
1617 loading a features file containing HTML tags in feature
1621 <em>Application</em>
1623 <li>Annotations corrupted after BioJS export and
1625 <li>Incorrect sequence limits after Fetch DB References
1626 with 'trim retrieved sequences'</li>
1627 <li>Incorrect warning about deleting all data when
1628 deleting selected columns</li>
1629 <li>Patch to build system for shipping properly signed
1630 JNLP templates for webstart launch</li>
1631 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1632 unreleased structures for download or viewing</li>
1633 <li>Tab/space/return keystroke operation of EMBL-PDBe
1634 fetcher/viewer dialogs works correctly</li>
1635 <li>Disabled 'minimise' button on Jalview windows
1636 running on OSX to workaround redraw hang bug</li>
1637 <li>Split cDNA/Protein view position and geometry not
1638 recovered from jalview project</li>
1639 <li>Initial enabled/disabled state of annotation menu
1640 sorter 'show autocalculated first/last' corresponds to
1642 <li>Restoring of Clustal, RNA Helices and T-Coffee
1643 color schemes from BioJSON</li>
1647 <li>Reorder sequences mirrored in cDNA/Protein split
1649 <li>Applet with Jmol examples not loading correctly</li>
1655 <td><div align="center">
1656 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1658 <td><em>General</em>
1660 <li>Linked visualisation and analysis of DNA and Protein
1663 <li>Translated cDNA alignments shown as split protein
1664 and DNA alignment views</li>
1665 <li>Codon consensus annotation for linked protein and
1666 cDNA alignment views</li>
1667 <li>Link cDNA or Protein product sequences by loading
1668 them onto Protein or cDNA alignments</li>
1669 <li>Reconstruct linked cDNA alignment from aligned
1670 protein sequences</li>
1673 <li>Jmol integration updated to Jmol v14.2.14</li>
1674 <li>Import and export of Jalview alignment views as <a
1675 href="features/bioJsonFormat.html">BioJSON</a></li>
1676 <li>New alignment annotation file statements for
1677 reference sequences and marking hidden columns</li>
1678 <li>Reference sequence based alignment shading to
1679 highlight variation</li>
1680 <li>Select or hide columns according to alignment
1682 <li>Find option for locating sequences by description</li>
1683 <li>Conserved physicochemical properties shown in amino
1684 acid conservation row</li>
1685 <li>Alignments can be sorted by number of RNA helices</li>
1686 </ul> <em>Application</em>
1688 <li>New cDNA/Protein analysis capabilities
1690 <li>Get Cross-References should open a Split Frame
1691 view with cDNA/Protein</li>
1692 <li>Detect when nucleotide sequences and protein
1693 sequences are placed in the same alignment</li>
1694 <li>Split cDNA/Protein views are saved in Jalview
1699 <li>Use REST API to talk to Chimera</li>
1700 <li>Selected regions in Chimera are highlighted in linked
1701 Jalview windows</li>
1703 <li>VARNA RNA viewer updated to v3.93</li>
1704 <li>VARNA views are saved in Jalview Projects</li>
1705 <li>Pseudoknots displayed as Jalview RNA annotation can
1706 be shown in VARNA</li>
1708 <li>Make groups for selection uses marked columns as well
1709 as the active selected region</li>
1711 <li>Calculate UPGMA and NJ trees using sequence feature
1713 <li>New Export options
1715 <li>New Export Settings dialog to control hidden
1716 region export in flat file generation</li>
1718 <li>Export alignment views for display with the <a
1719 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1721 <li>Export scrollable SVG in HTML page</li>
1722 <li>Optional embedding of BioJSON data when exporting
1723 alignment figures to HTML</li>
1725 <li>3D structure retrieval and display
1727 <li>Free text and structured queries with the PDBe
1729 <li>PDBe Search API based discovery and selection of
1730 PDB structures for a sequence set</li>
1734 <li>JPred4 employed for protein secondary structure
1736 <li>Hide Insertions menu option to hide unaligned columns
1737 for one or a group of sequences</li>
1738 <li>Automatically hide insertions in alignments imported
1739 from the JPred4 web server</li>
1740 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1741 system on OSX<br />LGPL libraries courtesy of <a
1742 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1744 <li>changed 'View nucleotide structure' submenu to 'View
1745 VARNA 2D Structure'</li>
1746 <li>change "View protein structure" menu option to "3D
1749 </ul> <em>Applet</em>
1751 <li>New layout for applet example pages</li>
1752 <li>New parameters to enable SplitFrame view
1753 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1754 <li>New example demonstrating linked viewing of cDNA and
1755 Protein alignments</li>
1756 </ul> <em>Development and deployment</em>
1758 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1759 <li>Include installation type and git revision in build
1760 properties and console log output</li>
1761 <li>Jalview Github organisation, and new github site for
1762 storing BioJsMSA Templates</li>
1763 <li>Jalview's unit tests now managed with TestNG</li>
1766 <!-- <em>General</em>
1768 </ul> --> <!-- issues resolved --> <em>Application</em>
1770 <li>Escape should close any open find dialogs</li>
1771 <li>Typo in select-by-features status report</li>
1772 <li>Consensus RNA secondary secondary structure
1773 predictions are not highlighted in amber</li>
1774 <li>Missing gap character in v2.7 example file means
1775 alignment appears unaligned when pad-gaps is not enabled</li>
1776 <li>First switch to RNA Helices colouring doesn't colour
1777 associated structure views</li>
1778 <li>ID width preference option is greyed out when auto
1779 width checkbox not enabled</li>
1780 <li>Stopped a warning dialog from being shown when
1781 creating user defined colours</li>
1782 <li>'View Mapping' in structure viewer shows sequence
1783 mappings for just that viewer's sequences</li>
1784 <li>Workaround for superposing PDB files containing
1785 multiple models in Chimera</li>
1786 <li>Report sequence position in status bar when hovering
1787 over Jmol structure</li>
1788 <li>Cannot output gaps as '.' symbols with Selection ->
1789 output to text box</li>
1790 <li>Flat file exports of alignments with hidden columns
1791 have incorrect sequence start/end</li>
1792 <li>'Aligning' a second chain to a Chimera structure from
1794 <li>Colour schemes applied to structure viewers don't
1795 work for nucleotide</li>
1796 <li>Loading/cut'n'pasting an empty or invalid file leads
1797 to a grey/invisible alignment window</li>
1798 <li>Exported Jpred annotation from a sequence region
1799 imports to different position</li>
1800 <li>Space at beginning of sequence feature tooltips shown
1801 on some platforms</li>
1802 <li>Chimera viewer 'View | Show Chain' menu is not
1804 <li>'New View' fails with a Null Pointer Exception in
1805 console if Chimera has been opened</li>
1806 <li>Mouseover to Chimera not working</li>
1807 <li>Miscellaneous ENA XML feature qualifiers not
1809 <li>NPE in annotation renderer after 'Extract Scores'</li>
1810 <li>If two structures in one Chimera window, mouseover of
1811 either sequence shows on first structure</li>
1812 <li>'Show annotations' options should not make
1813 non-positional annotations visible</li>
1814 <li>Subsequence secondary structure annotation not shown
1815 in right place after 'view flanking regions'</li>
1816 <li>File Save As type unset when current file format is
1818 <li>Save as '.jar' option removed for saving Jalview
1820 <li>Colour by Sequence colouring in Chimera more
1822 <li>Cannot 'add reference annotation' for a sequence in
1823 several views on same alignment</li>
1824 <li>Cannot show linked products for EMBL / ENA records</li>
1825 <li>Jalview's tooltip wraps long texts containing no
1827 </ul> <em>Applet</em>
1829 <li>Jmol to JalviewLite mouseover/link not working</li>
1830 <li>JalviewLite can't import sequences with ID
1831 descriptions containing angle brackets</li>
1832 </ul> <em>General</em>
1834 <li>Cannot export and reimport RNA secondary structure
1835 via jalview annotation file</li>
1836 <li>Random helix colour palette for colour by annotation
1837 with RNA secondary structure</li>
1838 <li>Mouseover to cDNA from STOP residue in protein
1839 translation doesn't work.</li>
1840 <li>hints when using the select by annotation dialog box</li>
1841 <li>Jmol alignment incorrect if PDB file has alternate CA
1843 <li>FontChooser message dialog appears to hang after
1844 choosing 1pt font</li>
1845 <li>Peptide secondary structure incorrectly imported from
1846 annotation file when annotation display text includes 'e' or
1848 <li>Cannot set colour of new feature type whilst creating
1850 <li>cDNA translation alignment should not be sequence
1851 order dependent</li>
1852 <li>'Show unconserved' doesn't work for lower case
1854 <li>Nucleotide ambiguity codes involving R not recognised</li>
1855 </ul> <em>Deployment and Documentation</em>
1857 <li>Applet example pages appear different to the rest of
1858 www.jalview.org</li>
1859 </ul> <em>Application Known issues</em>
1861 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1862 <li>Misleading message appears after trying to delete
1864 <li>Jalview icon not shown in dock after InstallAnywhere
1865 version launches</li>
1866 <li>Fetching EMBL reference for an RNA sequence results
1867 fails with a sequence mismatch</li>
1868 <li>Corrupted or unreadable alignment display when
1869 scrolling alignment to right</li>
1870 <li>ArrayIndexOutOfBoundsException thrown when remove
1871 empty columns called on alignment with ragged gapped ends</li>
1872 <li>auto calculated alignment annotation rows do not get
1873 placed above or below non-autocalculated rows</li>
1874 <li>Jalview dekstop becomes sluggish at full screen in
1875 ultra-high resolution</li>
1876 <li>Cannot disable consensus calculation independently of
1877 quality and conservation</li>
1878 <li>Mouseover highlighting between cDNA and protein can
1879 become sluggish with more than one splitframe shown</li>
1880 </ul> <em>Applet Known Issues</em>
1882 <li>Core PDB parsing code requires Jmol</li>
1883 <li>Sequence canvas panel goes white when alignment
1884 window is being resized</li>
1890 <td><div align="center">
1891 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1893 <td><em>General</em>
1895 <li>Updated Java code signing certificate donated by
1897 <li>Features and annotation preserved when performing
1898 pairwise alignment</li>
1899 <li>RNA pseudoknot annotation can be
1900 imported/exported/displayed</li>
1901 <li>'colour by annotation' can colour by RNA and
1902 protein secondary structure</li>
1903 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1904 post-hoc with 2.9 release</em>)
1907 </ul> <em>Application</em>
1909 <li>Extract and display secondary structure for sequences
1910 with 3D structures</li>
1911 <li>Support for parsing RNAML</li>
1912 <li>Annotations menu for layout
1914 <li>sort sequence annotation rows by alignment</li>
1915 <li>place sequence annotation above/below alignment
1918 <li>Output in Stockholm format</li>
1919 <li>Internationalisation: improved Spanish (es)
1921 <li>Structure viewer preferences tab</li>
1922 <li>Disorder and Secondary Structure annotation tracks
1923 shared between alignments</li>
1924 <li>UCSF Chimera launch and linked highlighting from
1926 <li>Show/hide all sequence associated annotation rows for
1927 all or current selection</li>
1928 <li>disorder and secondary structure predictions
1929 available as dataset annotation</li>
1930 <li>Per-sequence rna helices colouring</li>
1933 <li>Sequence database accessions imported when fetching
1934 alignments from Rfam</li>
1935 <li>update VARNA version to 3.91</li>
1937 <li>New groovy scripts for exporting aligned positions,
1938 conservation values, and calculating sum of pairs scores.</li>
1939 <li>Command line argument to set default JABAWS server</li>
1940 <li>include installation type in build properties and
1941 console log output</li>
1942 <li>Updated Jalview project format to preserve dataset
1946 <!-- issues resolved --> <em>Application</em>
1948 <li>Distinguish alignment and sequence associated RNA
1949 structure in structure->view->VARNA</li>
1950 <li>Raise dialog box if user deletes all sequences in an
1952 <li>Pressing F1 results in documentation opening twice</li>
1953 <li>Sequence feature tooltip is wrapped</li>
1954 <li>Double click on sequence associated annotation
1955 selects only first column</li>
1956 <li>Redundancy removal doesn't result in unlinked
1957 leaves shown in tree</li>
1958 <li>Undos after several redundancy removals don't undo
1960 <li>Hide sequence doesn't hide associated annotation</li>
1961 <li>User defined colours dialog box too big to fit on
1962 screen and buttons not visible</li>
1963 <li>author list isn't updated if already written to
1964 Jalview properties</li>
1965 <li>Popup menu won't open after retrieving sequence
1967 <li>File open window for associate PDB doesn't open</li>
1968 <li>Left-then-right click on a sequence id opens a
1969 browser search window</li>
1970 <li>Cannot open sequence feature shading/sort popup menu
1971 in feature settings dialog</li>
1972 <li>better tooltip placement for some areas of Jalview
1974 <li>Allow addition of JABAWS Server which doesn't
1975 pass validation</li>
1976 <li>Web services parameters dialog box is too large to
1978 <li>Muscle nucleotide alignment preset obscured by
1980 <li>JABAWS preset submenus don't contain newly
1981 defined user preset</li>
1982 <li>MSA web services warns user if they were launched
1983 with invalid input</li>
1984 <li>Jalview cannot contact DAS Registy when running on
1987 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1988 'Superpose with' submenu not shown when new view
1992 </ul> <!-- <em>Applet</em>
1994 </ul> <em>General</em>
1996 </ul>--> <em>Deployment and Documentation</em>
1998 <li>2G and 1G options in launchApp have no effect on
1999 memory allocation</li>
2000 <li>launchApp service doesn't automatically open
2001 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2003 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2004 InstallAnywhere reports cannot find valid JVM when Java
2005 1.7_055 is available
2007 </ul> <em>Application Known issues</em>
2010 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2011 corrupted or unreadable alignment display when scrolling
2015 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2016 retrieval fails but progress bar continues for DAS retrieval
2017 with large number of ID
2020 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2021 flatfile output of visible region has incorrect sequence
2025 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2026 rna structure consensus doesn't update when secondary
2027 structure tracks are rearranged
2030 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2031 invalid rna structure positional highlighting does not
2032 highlight position of invalid base pairs
2035 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2036 out of memory errors are not raised when saving Jalview
2037 project from alignment window file menu
2040 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2041 Switching to RNA Helices colouring doesn't propagate to
2045 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2046 colour by RNA Helices not enabled when user created
2047 annotation added to alignment
2050 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2051 Jalview icon not shown on dock in Mountain Lion/Webstart
2053 </ul> <em>Applet Known Issues</em>
2056 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2057 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2060 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2061 Jalview and Jmol example not compatible with IE9
2064 <li>Sort by annotation score doesn't reverse order
2070 <td><div align="center">
2071 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2074 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2077 <li>Internationalisation of user interface (usually
2078 called i18n support) and translation for Spanish locale</li>
2079 <li>Define/Undefine group on current selection with
2080 Ctrl-G/Shift Ctrl-G</li>
2081 <li>Improved group creation/removal options in
2082 alignment/sequence Popup menu</li>
2083 <li>Sensible precision for symbol distribution
2084 percentages shown in logo tooltip.</li>
2085 <li>Annotation panel height set according to amount of
2086 annotation when alignment first opened</li>
2087 </ul> <em>Application</em>
2089 <li>Interactive consensus RNA secondary structure
2090 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2091 <li>Select columns containing particular features from
2092 Feature Settings dialog</li>
2093 <li>View all 'representative' PDB structures for selected
2095 <li>Update Jalview project format:
2097 <li>New file extension for Jalview projects '.jvp'</li>
2098 <li>Preserve sequence and annotation dataset (to
2099 store secondary structure annotation,etc)</li>
2100 <li>Per group and alignment annotation and RNA helix
2104 <li>New similarity measures for PCA and Tree calculation
2106 <li>Experimental support for retrieval and viewing of
2107 flanking regions for an alignment</li>
2111 <!-- issues resolved --> <em>Application</em>
2113 <li>logo keeps spinning and status remains at queued or
2114 running after job is cancelled</li>
2115 <li>cannot export features from alignments imported from
2116 Jalview/VAMSAS projects</li>
2117 <li>Buggy slider for web service parameters that take
2119 <li>Newly created RNA secondary structure line doesn't
2120 have 'display all symbols' flag set</li>
2121 <li>T-COFFEE alignment score shading scheme and other
2122 annotation shading not saved in Jalview project</li>
2123 <li>Local file cannot be loaded in freshly downloaded
2125 <li>Jalview icon not shown on dock in Mountain
2127 <li>Load file from desktop file browser fails</li>
2128 <li>Occasional NPE thrown when calculating large trees</li>
2129 <li>Cannot reorder or slide sequences after dragging an
2130 alignment onto desktop</li>
2131 <li>Colour by annotation dialog throws NPE after using
2132 'extract scores' function</li>
2133 <li>Loading/cut'n'pasting an empty file leads to a grey
2134 alignment window</li>
2135 <li>Disorder thresholds rendered incorrectly after
2136 performing IUPred disorder prediction</li>
2137 <li>Multiple group annotated consensus rows shown when
2138 changing 'normalise logo' display setting</li>
2139 <li>Find shows blank dialog after 'finished searching' if
2140 nothing matches query</li>
2141 <li>Null Pointer Exceptions raised when sorting by
2142 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2144 <li>Errors in Jmol console when structures in alignment
2145 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2147 <li>Not all working JABAWS services are shown in
2149 <li>JAVAWS version of Jalview fails to launch with
2150 'invalid literal/length code'</li>
2151 <li>Annotation/RNA Helix colourschemes cannot be applied
2152 to alignment with groups (actually fixed in 2.8.0b1)</li>
2153 <li>RNA Helices and T-Coffee Scores available as default
2156 </ul> <em>Applet</em>
2158 <li>Remove group option is shown even when selection is
2160 <li>Apply to all groups ticked but colourscheme changes
2161 don't affect groups</li>
2162 <li>Documented RNA Helices and T-Coffee Scores as valid
2163 colourscheme name</li>
2164 <li>Annotation labels drawn on sequence IDs when
2165 Annotation panel is not displayed</li>
2166 <li>Increased font size for dropdown menus on OSX and
2167 embedded windows</li>
2168 </ul> <em>Other</em>
2170 <li>Consensus sequence for alignments/groups with a
2171 single sequence were not calculated</li>
2172 <li>annotation files that contain only groups imported as
2173 annotation and junk sequences</li>
2174 <li>Fasta files with sequences containing '*' incorrectly
2175 recognised as PFAM or BLC</li>
2176 <li>conservation/PID slider apply all groups option
2177 doesn't affect background (2.8.0b1)
2179 <li>redundancy highlighting is erratic at 0% and 100%</li>
2180 <li>Remove gapped columns fails for sequences with ragged
2182 <li>AMSA annotation row with leading spaces is not
2183 registered correctly on import</li>
2184 <li>Jalview crashes when selecting PCA analysis for
2185 certain alignments</li>
2186 <li>Opening the colour by annotation dialog for an
2187 existing annotation based 'use original colours'
2188 colourscheme loses original colours setting</li>
2193 <td><div align="center">
2194 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2195 <em>30/1/2014</em></strong>
2199 <li>Trusted certificates for JalviewLite applet and
2200 Jalview Desktop application<br />Certificate was donated by
2201 <a href="https://www.certum.eu">Certum</a> to the Jalview
2202 open source project).
2204 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2205 <li>Output in Stockholm format</li>
2206 <li>Allow import of data from gzipped files</li>
2207 <li>Export/import group and sequence associated line
2208 graph thresholds</li>
2209 <li>Nucleotide substitution matrix that supports RNA and
2210 ambiguity codes</li>
2211 <li>Allow disorder predictions to be made on the current
2212 selection (or visible selection) in the same way that JPred
2214 <li>Groovy scripting for headless Jalview operation</li>
2215 </ul> <em>Other improvements</em>
2217 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2218 <li>COMBINE statement uses current SEQUENCE_REF and
2219 GROUP_REF scope to group annotation rows</li>
2220 <li>Support '' style escaping of quotes in Newick
2222 <li>Group options for JABAWS service by command line name</li>
2223 <li>Empty tooltip shown for JABA service options with a
2224 link but no description</li>
2225 <li>Select primary source when selecting authority in
2226 database fetcher GUI</li>
2227 <li>Add .mfa to FASTA file extensions recognised by
2229 <li>Annotation label tooltip text wrap</li>
2234 <li>Slow scrolling when lots of annotation rows are
2236 <li>Lots of NPE (and slowness) after creating RNA
2237 secondary structure annotation line</li>
2238 <li>Sequence database accessions not imported when
2239 fetching alignments from Rfam</li>
2240 <li>Incorrect SHMR submission for sequences with
2242 <li>View all structures does not always superpose
2244 <li>Option widgets in service parameters not updated to
2245 reflect user or preset settings</li>
2246 <li>Null pointer exceptions for some services without
2247 presets or adjustable parameters</li>
2248 <li>Discover PDB IDs entry in structure menu doesn't
2249 discover PDB xRefs</li>
2250 <li>Exception encountered while trying to retrieve
2251 features with DAS</li>
2252 <li>Lowest value in annotation row isn't coloured
2253 when colour by annotation (per sequence) is coloured</li>
2254 <li>Keyboard mode P jumps to start of gapped region when
2255 residue follows a gap</li>
2256 <li>Jalview appears to hang importing an alignment with
2257 Wrap as default or after enabling Wrap</li>
2258 <li>'Right click to add annotations' message
2259 shown in wrap mode when no annotations present</li>
2260 <li>Disorder predictions fail with NPE if no automatic
2261 annotation already exists on alignment</li>
2262 <li>oninit javascript function should be called after
2263 initialisation completes</li>
2264 <li>Remove redundancy after disorder prediction corrupts
2265 alignment window display</li>
2266 <li>Example annotation file in documentation is invalid</li>
2267 <li>Grouped line graph annotation rows are not exported
2268 to annotation file</li>
2269 <li>Multi-harmony analysis cannot be run when only two
2271 <li>Cannot create multiple groups of line graphs with
2272 several 'combine' statements in annotation file</li>
2273 <li>Pressing return several times causes Number Format
2274 exceptions in keyboard mode</li>
2275 <li>Multi-harmony (SHMMR) method doesn't submit
2276 correct partitions for input data</li>
2277 <li>Translation from DNA to Amino Acids fails</li>
2278 <li>Jalview fail to load newick tree with quoted label</li>
2279 <li>--headless flag isn't understood</li>
2280 <li>ClassCastException when generating EPS in headless
2282 <li>Adjusting sequence-associated shading threshold only
2283 changes one row's threshold</li>
2284 <li>Preferences and Feature settings panel panel
2285 doesn't open</li>
2286 <li>hide consensus histogram also hides conservation and
2287 quality histograms</li>
2292 <td><div align="center">
2293 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2295 <td><em>Application</em>
2297 <li>Support for JABAWS 2.0 Services (AACon alignment
2298 conservation, protein disorder and Clustal Omega)</li>
2299 <li>JABAWS server status indicator in Web Services
2301 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2302 in Jalview alignment window</li>
2303 <li>Updated Jalview build and deploy framework for OSX
2304 mountain lion, windows 7, and 8</li>
2305 <li>Nucleotide substitution matrix for PCA that supports
2306 RNA and ambiguity codes</li>
2308 <li>Improved sequence database retrieval GUI</li>
2309 <li>Support fetching and database reference look up
2310 against multiple DAS sources (Fetch all from in 'fetch db
2312 <li>Jalview project improvements
2314 <li>Store and retrieve the 'belowAlignment'
2315 flag for annotation</li>
2316 <li>calcId attribute to group annotation rows on the
2318 <li>Store AACon calculation settings for a view in
2319 Jalview project</li>
2323 <li>horizontal scrolling gesture support</li>
2324 <li>Visual progress indicator when PCA calculation is
2326 <li>Simpler JABA web services menus</li>
2327 <li>visual indication that web service results are still
2328 being retrieved from server</li>
2329 <li>Serialise the dialogs that are shown when Jalview
2330 starts up for first time</li>
2331 <li>Jalview user agent string for interacting with HTTP
2333 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2335 <li>Examples directory and Groovy library included in
2336 InstallAnywhere distribution</li>
2337 </ul> <em>Applet</em>
2339 <li>RNA alignment and secondary structure annotation
2340 visualization applet example</li>
2341 </ul> <em>General</em>
2343 <li>Normalise option for consensus sequence logo</li>
2344 <li>Reset button in PCA window to return dimensions to
2346 <li>Allow seqspace or Jalview variant of alignment PCA
2348 <li>PCA with either nucleic acid and protein substitution
2350 <li>Allow windows containing HTML reports to be exported
2352 <li>Interactive display and editing of RNA secondary
2353 structure contacts</li>
2354 <li>RNA Helix Alignment Colouring</li>
2355 <li>RNA base pair logo consensus</li>
2356 <li>Parse sequence associated secondary structure
2357 information in Stockholm files</li>
2358 <li>HTML Export database accessions and annotation
2359 information presented in tooltip for sequences</li>
2360 <li>Import secondary structure from LOCARNA clustalw
2361 style RNA alignment files</li>
2362 <li>import and visualise T-COFFEE quality scores for an
2364 <li>'colour by annotation' per sequence option to
2365 shade each sequence according to its associated alignment
2367 <li>New Jalview Logo</li>
2368 </ul> <em>Documentation and Development</em>
2370 <li>documentation for score matrices used in Jalview</li>
2371 <li>New Website!</li>
2373 <td><em>Application</em>
2375 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2376 wsdbfetch REST service</li>
2377 <li>Stop windows being moved outside desktop on OSX</li>
2378 <li>Filetype associations not installed for webstart
2380 <li>Jalview does not always retrieve progress of a JABAWS
2381 job execution in full once it is complete</li>
2382 <li>revise SHMR RSBS definition to ensure alignment is
2383 uploaded via ali_file parameter</li>
2384 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2385 <li>View all structures superposed fails with exception</li>
2386 <li>Jnet job queues forever if a very short sequence is
2387 submitted for prediction</li>
2388 <li>Cut and paste menu not opened when mouse clicked on
2390 <li>Putting fractional value into integer text box in
2391 alignment parameter dialog causes Jalview to hang</li>
2392 <li>Structure view highlighting doesn't work on
2394 <li>View all structures fails with exception shown in
2396 <li>Characters in filename associated with PDBEntry not
2397 escaped in a platform independent way</li>
2398 <li>Jalview desktop fails to launch with exception when
2400 <li>Tree calculation reports 'you must have 2 or more
2401 sequences selected' when selection is empty</li>
2402 <li>Jalview desktop fails to launch with jar signature
2403 failure when java web start temporary file caching is
2405 <li>DAS Sequence retrieval with range qualification
2406 results in sequence xref which includes range qualification</li>
2407 <li>Errors during processing of command line arguments
2408 cause progress bar (JAL-898) to be removed</li>
2409 <li>Replace comma for semi-colon option not disabled for
2410 DAS sources in sequence fetcher</li>
2411 <li>Cannot close news reader when JABAWS server warning
2412 dialog is shown</li>
2413 <li>Option widgets not updated to reflect user settings</li>
2414 <li>Edited sequence not submitted to web service</li>
2415 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2416 <li>InstallAnywhere installer doesn't unpack and run
2417 on OSX Mountain Lion</li>
2418 <li>Annotation panel not given a scroll bar when
2419 sequences with alignment annotation are pasted into the
2421 <li>Sequence associated annotation rows not associated
2422 when loaded from Jalview project</li>
2423 <li>Browser launch fails with NPE on java 1.7</li>
2424 <li>JABAWS alignment marked as finished when job was
2425 cancelled or job failed due to invalid input</li>
2426 <li>NPE with v2.7 example when clicking on Tree
2427 associated with all views</li>
2428 <li>Exceptions when copy/paste sequences with grouped
2429 annotation rows to new window</li>
2430 </ul> <em>Applet</em>
2432 <li>Sequence features are momentarily displayed before
2433 they are hidden using hidefeaturegroups applet parameter</li>
2434 <li>loading features via javascript API automatically
2435 enables feature display</li>
2436 <li>scrollToColumnIn javascript API method doesn't
2438 </ul> <em>General</em>
2440 <li>Redundancy removal fails for rna alignment</li>
2441 <li>PCA calculation fails when sequence has been selected
2442 and then deselected</li>
2443 <li>PCA window shows grey box when first opened on OSX</li>
2444 <li>Letters coloured pink in sequence logo when alignment
2445 coloured with clustalx</li>
2446 <li>Choosing fonts without letter symbols defined causes
2447 exceptions and redraw errors</li>
2448 <li>Initial PCA plot view is not same as manually
2449 reconfigured view</li>
2450 <li>Grouped annotation graph label has incorrect line
2452 <li>Grouped annotation graph label display is corrupted
2453 for lots of labels</li>
2458 <div align="center">
2459 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2462 <td><em>Application</em>
2464 <li>Jalview Desktop News Reader</li>
2465 <li>Tweaked default layout of web services menu</li>
2466 <li>View/alignment association menu to enable user to
2467 easily specify which alignment a multi-structure view takes
2468 its colours/correspondences from</li>
2469 <li>Allow properties file location to be specified as URL</li>
2470 <li>Extend Jalview project to preserve associations
2471 between many alignment views and a single Jmol display</li>
2472 <li>Store annotation row height in Jalview project file</li>
2473 <li>Annotation row column label formatting attributes
2474 stored in project file</li>
2475 <li>Annotation row order for auto-calculated annotation
2476 rows preserved in Jalview project file</li>
2477 <li>Visual progress indication when Jalview state is
2478 saved using Desktop window menu</li>
2479 <li>Visual indication that command line arguments are
2480 still being processed</li>
2481 <li>Groovy script execution from URL</li>
2482 <li>Colour by annotation default min and max colours in
2484 <li>Automatically associate PDB files dragged onto an
2485 alignment with sequences that have high similarity and
2487 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2488 <li>'view structures' option to open many
2489 structures in same window</li>
2490 <li>Sort associated views menu option for tree panel</li>
2491 <li>Group all JABA and non-JABA services for a particular
2492 analysis function in its own submenu</li>
2493 </ul> <em>Applet</em>
2495 <li>Userdefined and autogenerated annotation rows for
2497 <li>Adjustment of alignment annotation pane height</li>
2498 <li>Annotation scrollbar for annotation panel</li>
2499 <li>Drag to reorder annotation rows in annotation panel</li>
2500 <li>'automaticScrolling' parameter</li>
2501 <li>Allow sequences with partial ID string matches to be
2502 annotated from GFF/Jalview features files</li>
2503 <li>Sequence logo annotation row in applet</li>
2504 <li>Absolute paths relative to host server in applet
2505 parameters are treated as such</li>
2506 <li>New in the JalviewLite javascript API:
2508 <li>JalviewLite.js javascript library</li>
2509 <li>Javascript callbacks for
2511 <li>Applet initialisation</li>
2512 <li>Sequence/alignment mouse-overs and selections</li>
2515 <li>scrollTo row and column alignment scrolling
2517 <li>Select sequence/alignment regions from javascript</li>
2518 <li>javascript structure viewer harness to pass
2519 messages between Jmol and Jalview when running as
2520 distinct applets</li>
2521 <li>sortBy method</li>
2522 <li>Set of applet and application examples shipped
2523 with documentation</li>
2524 <li>New example to demonstrate JalviewLite and Jmol
2525 javascript message exchange</li>
2527 </ul> <em>General</em>
2529 <li>Enable Jmol displays to be associated with multiple
2530 multiple alignments</li>
2531 <li>Option to automatically sort alignment with new tree</li>
2532 <li>User configurable link to enable redirects to a
2533 www.Jalview.org mirror</li>
2534 <li>Jmol colours option for Jmol displays</li>
2535 <li>Configurable newline string when writing alignment
2536 and other flat files</li>
2537 <li>Allow alignment annotation description lines to
2538 contain html tags</li>
2539 </ul> <em>Documentation and Development</em>
2541 <li>Add groovy test harness for bulk load testing to
2543 <li>Groovy script to load and align a set of sequences
2544 using a web service before displaying the result in the
2545 Jalview desktop</li>
2546 <li>Restructured javascript and applet api documentation</li>
2547 <li>Ant target to publish example html files with applet
2549 <li>Netbeans project for building Jalview from source</li>
2550 <li>ant task to create online javadoc for Jalview source</li>
2552 <td><em>Application</em>
2554 <li>User defined colourscheme throws exception when
2555 current built in colourscheme is saved as new scheme</li>
2556 <li>AlignFrame->Save in application pops up save
2557 dialog for valid filename/format</li>
2558 <li>Cannot view associated structure for UniProt sequence</li>
2559 <li>PDB file association breaks for UniProt sequence
2561 <li>Associate PDB from file dialog does not tell you
2562 which sequence is to be associated with the file</li>
2563 <li>Find All raises null pointer exception when query
2564 only matches sequence IDs</li>
2565 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2566 <li>Jalview project with Jmol views created with Jalview
2567 2.4 cannot be loaded</li>
2568 <li>Filetype associations not installed for webstart
2570 <li>Two or more chains in a single PDB file associated
2571 with sequences in different alignments do not get coloured
2572 by their associated sequence</li>
2573 <li>Visibility status of autocalculated annotation row
2574 not preserved when project is loaded</li>
2575 <li>Annotation row height and visibility attributes not
2576 stored in Jalview project</li>
2577 <li>Tree bootstraps are not preserved when saved as a
2578 Jalview project</li>
2579 <li>Envision2 workflow tooltips are corrupted</li>
2580 <li>Enabling show group conservation also enables colour
2581 by conservation</li>
2582 <li>Duplicate group associated conservation or consensus
2583 created on new view</li>
2584 <li>Annotation scrollbar not displayed after 'show
2585 all hidden annotation rows' option selected</li>
2586 <li>Alignment quality not updated after alignment
2587 annotation row is hidden then shown</li>
2588 <li>Preserve colouring of structures coloured by
2589 sequences in pre Jalview 2.7 projects</li>
2590 <li>Web service job parameter dialog is not laid out
2592 <li>Web services menu not refreshed after 'reset
2593 services' button is pressed in preferences</li>
2594 <li>Annotation off by one in Jalview v2_3 example project</li>
2595 <li>Structures imported from file and saved in project
2596 get name like jalview_pdb1234.txt when reloaded</li>
2597 <li>Jalview does not always retrieve progress of a JABAWS
2598 job execution in full once it is complete</li>
2599 </ul> <em>Applet</em>
2601 <li>Alignment height set incorrectly when lots of
2602 annotation rows are displayed</li>
2603 <li>Relative URLs in feature HTML text not resolved to
2605 <li>View follows highlighting does not work for positions
2607 <li><= shown as = in tooltip</li>
2608 <li>Export features raises exception when no features
2610 <li>Separator string used for serialising lists of IDs
2611 for javascript api is modified when separator string
2612 provided as parameter</li>
2613 <li>Null pointer exception when selecting tree leaves for
2614 alignment with no existing selection</li>
2615 <li>Relative URLs for datasources assumed to be relative
2616 to applet's codebase</li>
2617 <li>Status bar not updated after finished searching and
2618 search wraps around to first result</li>
2619 <li>StructureSelectionManager instance shared between
2620 several Jalview applets causes race conditions and memory
2622 <li>Hover tooltip and mouseover of position on structure
2623 not sent from Jmol in applet</li>
2624 <li>Certain sequences of javascript method calls to
2625 applet API fatally hang browser</li>
2626 </ul> <em>General</em>
2628 <li>View follows structure mouseover scrolls beyond
2629 position with wrapped view and hidden regions</li>
2630 <li>Find sequence position moves to wrong residue
2631 with/without hidden columns</li>
2632 <li>Sequence length given in alignment properties window
2634 <li>InvalidNumberFormat exceptions thrown when trying to
2635 import PDB like structure files</li>
2636 <li>Positional search results are only highlighted
2637 between user-supplied sequence start/end bounds</li>
2638 <li>End attribute of sequence is not validated</li>
2639 <li>Find dialog only finds first sequence containing a
2640 given sequence position</li>
2641 <li>Sequence numbering not preserved in MSF alignment
2643 <li>Jalview PDB file reader does not extract sequence
2644 from nucleotide chains correctly</li>
2645 <li>Structure colours not updated when tree partition
2646 changed in alignment</li>
2647 <li>Sequence associated secondary structure not correctly
2648 parsed in interleaved stockholm</li>
2649 <li>Colour by annotation dialog does not restore current
2651 <li>Hiding (nearly) all sequences doesn't work
2653 <li>Sequences containing lowercase letters are not
2654 properly associated with their pdb files</li>
2655 </ul> <em>Documentation and Development</em>
2657 <li>schemas/JalviewWsParamSet.xsd corrupted by
2658 ApplyCopyright tool</li>
2663 <div align="center">
2664 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2667 <td><em>Application</em>
2669 <li>New warning dialog when the Jalview Desktop cannot
2670 contact web services</li>
2671 <li>JABA service parameters for a preset are shown in
2672 service job window</li>
2673 <li>JABA Service menu entries reworded</li>
2677 <li>Modeller PIR IO broken - cannot correctly import a
2678 pir file emitted by Jalview</li>
2679 <li>Existing feature settings transferred to new
2680 alignment view created from cut'n'paste</li>
2681 <li>Improved test for mixed amino/nucleotide chains when
2682 parsing PDB files</li>
2683 <li>Consensus and conservation annotation rows
2684 occasionally become blank for all new windows</li>
2685 <li>Exception raised when right clicking above sequences
2686 in wrapped view mode</li>
2687 </ul> <em>Application</em>
2689 <li>multiple multiply aligned structure views cause cpu
2690 usage to hit 100% and computer to hang</li>
2691 <li>Web Service parameter layout breaks for long user
2692 parameter names</li>
2693 <li>Jaba service discovery hangs desktop if Jaba server
2700 <div align="center">
2701 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2704 <td><em>Application</em>
2706 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2707 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2710 <li>Web Services preference tab</li>
2711 <li>Analysis parameters dialog box and user defined
2713 <li>Improved speed and layout of Envision2 service menu</li>
2714 <li>Superpose structures using associated sequence
2716 <li>Export coordinates and projection as CSV from PCA
2718 </ul> <em>Applet</em>
2720 <li>enable javascript: execution by the applet via the
2721 link out mechanism</li>
2722 </ul> <em>Other</em>
2724 <li>Updated the Jmol Jalview interface to work with Jmol
2726 <li>The Jalview Desktop and JalviewLite applet now
2727 require Java 1.5</li>
2728 <li>Allow Jalview feature colour specification for GFF
2729 sequence annotation files</li>
2730 <li>New 'colour by label' keword in Jalview feature file
2731 type colour specification</li>
2732 <li>New Jalview Desktop Groovy API method that allows a
2733 script to check if it being run in an interactive session or
2734 in a batch operation from the Jalview command line</li>
2738 <li>clustalx colourscheme colours Ds preferentially when
2739 both D+E are present in over 50% of the column</li>
2740 </ul> <em>Application</em>
2742 <li>typo in AlignmentFrame->View->Hide->all but
2743 selected Regions menu item</li>
2744 <li>sequence fetcher replaces ',' for ';' when the ',' is
2745 part of a valid accession ID</li>
2746 <li>fatal OOM if object retrieved by sequence fetcher
2747 runs out of memory</li>
2748 <li>unhandled Out of Memory Error when viewing pca
2749 analysis results</li>
2750 <li>InstallAnywhere builds fail to launch on OS X java
2751 10.5 update 4 (due to apple Java 1.6 update)</li>
2752 <li>Installanywhere Jalview silently fails to launch</li>
2753 </ul> <em>Applet</em>
2755 <li>Jalview.getFeatureGroups() raises an
2756 ArrayIndexOutOfBoundsException if no feature groups are
2763 <div align="center">
2764 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2770 <li>Alignment prettyprinter doesn't cope with long
2772 <li>clustalx colourscheme colours Ds preferentially when
2773 both D+E are present in over 50% of the column</li>
2774 <li>nucleic acid structures retrieved from PDB do not
2775 import correctly</li>
2776 <li>More columns get selected than were clicked on when a
2777 number of columns are hidden</li>
2778 <li>annotation label popup menu not providing correct
2779 add/hide/show options when rows are hidden or none are
2781 <li>Stockholm format shown in list of readable formats,
2782 and parser copes better with alignments from RFAM.</li>
2783 <li>CSV output of consensus only includes the percentage
2784 of all symbols if sequence logo display is enabled</li>
2786 </ul> <em>Applet</em>
2788 <li>annotation panel disappears when annotation is
2790 </ul> <em>Application</em>
2792 <li>Alignment view not redrawn properly when new
2793 alignment opened where annotation panel is visible but no
2794 annotations are present on alignment</li>
2795 <li>pasted region containing hidden columns is
2796 incorrectly displayed in new alignment window</li>
2797 <li>Jalview slow to complete operations when stdout is
2798 flooded (fix is to close the Jalview console)</li>
2799 <li>typo in AlignmentFrame->View->Hide->all but
2800 selected Rregions menu item.</li>
2801 <li>inconsistent group submenu and Format submenu entry
2802 'Un' or 'Non'conserved</li>
2803 <li>Sequence feature settings are being shared by
2804 multiple distinct alignments</li>
2805 <li>group annotation not recreated when tree partition is
2807 <li>double click on group annotation to select sequences
2808 does not propagate to associated trees</li>
2809 <li>Mac OSX specific issues:
2811 <li>exception raised when mouse clicked on desktop
2812 window background</li>
2813 <li>Desktop menu placed on menu bar and application
2814 name set correctly</li>
2815 <li>sequence feature settings not wide enough for the
2816 save feature colourscheme button</li>
2825 <div align="center">
2826 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2829 <td><em>New Capabilities</em>
2831 <li>URL links generated from description line for
2832 regular-expression based URL links (applet and application)
2834 <li>Non-positional feature URL links are shown in link
2836 <li>Linked viewing of nucleic acid sequences and
2838 <li>Automatic Scrolling option in View menu to display
2839 the currently highlighted region of an alignment.</li>
2840 <li>Order an alignment by sequence length, or using the
2841 average score or total feature count for each sequence.</li>
2842 <li>Shading features by score or associated description</li>
2843 <li>Subdivide alignment and groups based on identity of
2844 selected subsequence (Make Groups from Selection).</li>
2845 <li>New hide/show options including Shift+Control+H to
2846 hide everything but the currently selected region.</li>
2847 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2848 </ul> <em>Application</em>
2850 <li>Fetch DB References capabilities and UI expanded to
2851 support retrieval from DAS sequence sources</li>
2852 <li>Local DAS Sequence sources can be added via the
2853 command line or via the Add local source dialog box.</li>
2854 <li>DAS Dbref and DbxRef feature types are parsed as
2855 database references and protein_name is parsed as
2856 description line (BioSapiens terms).</li>
2857 <li>Enable or disable non-positional feature and database
2858 references in sequence ID tooltip from View menu in
2860 <!-- <li>New hidden columns and rows and representatives capabilities
2861 in annotations file (in progress - not yet fully implemented)</li> -->
2862 <li>Group-associated consensus, sequence logos and
2863 conservation plots</li>
2864 <li>Symbol distributions for each column can be exported
2865 and visualized as sequence logos</li>
2866 <li>Optionally scale multi-character column labels to fit
2867 within each column of annotation row<!-- todo for applet -->
2869 <li>Optional automatic sort of associated alignment view
2870 when a new tree is opened.</li>
2871 <li>Jalview Java Console</li>
2872 <li>Better placement of desktop window when moving
2873 between different screens.</li>
2874 <li>New preference items for sequence ID tooltip and
2875 consensus annotation</li>
2876 <li>Client to submit sequences and IDs to Envision2
2878 <li><em>Vamsas Capabilities</em>
2880 <li>Improved VAMSAS synchronization (Jalview archive
2881 used to preserve views, structures, and tree display
2883 <li>Import of vamsas documents from disk or URL via
2885 <li>Sharing of selected regions between views and
2886 with other VAMSAS applications (Experimental feature!)</li>
2887 <li>Updated API to VAMSAS version 0.2</li>
2889 </ul> <em>Applet</em>
2891 <li>Middle button resizes annotation row height</li>
2894 <li>sortByTree (true/false) - automatically sort the
2895 associated alignment view by the tree when a new tree is
2897 <li>showTreeBootstraps (true/false) - show or hide
2898 branch bootstraps (default is to show them if available)</li>
2899 <li>showTreeDistances (true/false) - show or hide
2900 branch lengths (default is to show them if available)</li>
2901 <li>showUnlinkedTreeNodes (true/false) - indicate if
2902 unassociated nodes should be highlighted in the tree
2904 <li>heightScale and widthScale (1.0 or more) -
2905 increase the height or width of a cell in the alignment
2906 grid relative to the current font size.</li>
2909 <li>Non-positional features displayed in sequence ID
2911 </ul> <em>Other</em>
2913 <li>Features format: graduated colour definitions and
2914 specification of feature scores</li>
2915 <li>Alignment Annotations format: new keywords for group
2916 associated annotation (GROUP_REF) and annotation row display
2917 properties (ROW_PROPERTIES)</li>
2918 <li>XML formats extended to support graduated feature
2919 colourschemes, group associated annotation, and profile
2920 visualization settings.</li></td>
2923 <li>Source field in GFF files parsed as feature source
2924 rather than description</li>
2925 <li>Non-positional features are now included in sequence
2926 feature and gff files (controlled via non-positional feature
2927 visibility in tooltip).</li>
2928 <li>URL links generated for all feature links (bugfix)</li>
2929 <li>Added URL embedding instructions to features file
2931 <li>Codons containing ambiguous nucleotides translated as
2932 'X' in peptide product</li>
2933 <li>Match case switch in find dialog box works for both
2934 sequence ID and sequence string and query strings do not
2935 have to be in upper case to match case-insensitively.</li>
2936 <li>AMSA files only contain first column of
2937 multi-character column annotation labels</li>
2938 <li>Jalview Annotation File generation/parsing consistent
2939 with documentation (e.g. Stockholm annotation can be
2940 exported and re-imported)</li>
2941 <li>PDB files without embedded PDB IDs given a friendly
2943 <li>Find incrementally searches ID string matches as well
2944 as subsequence matches, and correctly reports total number
2948 <li>Better handling of exceptions during sequence
2950 <li>Dasobert generated non-positional feature URL
2951 link text excludes the start_end suffix</li>
2952 <li>DAS feature and source retrieval buttons disabled
2953 when fetch or registry operations in progress.</li>
2954 <li>PDB files retrieved from URLs are cached properly</li>
2955 <li>Sequence description lines properly shared via
2957 <li>Sequence fetcher fetches multiple records for all
2959 <li>Ensured that command line das feature retrieval
2960 completes before alignment figures are generated.</li>
2961 <li>Reduced time taken when opening file browser for
2963 <li>isAligned check prior to calculating tree, PCA or
2964 submitting an MSA to JNet now excludes hidden sequences.</li>
2965 <li>User defined group colours properly recovered
2966 from Jalview projects.</li>
2975 <div align="center">
2976 <strong>2.4.0.b2</strong><br> 28/10/2009
2981 <li>Experimental support for google analytics usage
2983 <li>Jalview privacy settings (user preferences and docs).</li>
2988 <li>Race condition in applet preventing startup in
2990 <li>Exception when feature created from selection beyond
2991 length of sequence.</li>
2992 <li>Allow synthetic PDB files to be imported gracefully</li>
2993 <li>Sequence associated annotation rows associate with
2994 all sequences with a given id</li>
2995 <li>Find function matches case-insensitively for sequence
2996 ID string searches</li>
2997 <li>Non-standard characters do not cause pairwise
2998 alignment to fail with exception</li>
2999 </ul> <em>Application Issues</em>
3001 <li>Sequences are now validated against EMBL database</li>
3002 <li>Sequence fetcher fetches multiple records for all
3004 </ul> <em>InstallAnywhere Issues</em>
3006 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3007 issue with installAnywhere mechanism)</li>
3008 <li>Command line launching of JARs from InstallAnywhere
3009 version (java class versioning error fixed)</li>
3016 <div align="center">
3017 <strong>2.4</strong><br> 27/8/2008
3020 <td><em>User Interface</em>
3022 <li>Linked highlighting of codon and amino acid from
3023 translation and protein products</li>
3024 <li>Linked highlighting of structure associated with
3025 residue mapping to codon position</li>
3026 <li>Sequence Fetcher provides example accession numbers
3027 and 'clear' button</li>
3028 <li>MemoryMonitor added as an option under Desktop's
3030 <li>Extract score function to parse whitespace separated
3031 numeric data in description line</li>
3032 <li>Column labels in alignment annotation can be centred.</li>
3033 <li>Tooltip for sequence associated annotation give name
3035 </ul> <em>Web Services and URL fetching</em>
3037 <li>JPred3 web service</li>
3038 <li>Prototype sequence search client (no public services
3040 <li>Fetch either seed alignment or full alignment from
3042 <li>URL Links created for matching database cross
3043 references as well as sequence ID</li>
3044 <li>URL Links can be created using regular-expressions</li>
3045 </ul> <em>Sequence Database Connectivity</em>
3047 <li>Retrieval of cross-referenced sequences from other
3049 <li>Generalised database reference retrieval and
3050 validation to all fetchable databases</li>
3051 <li>Fetch sequences from DAS sources supporting the
3052 sequence command</li>
3053 </ul> <em>Import and Export</em>
3054 <li>export annotation rows as CSV for spreadsheet import</li>
3055 <li>Jalview projects record alignment dataset associations,
3056 EMBL products, and cDNA sequence mappings</li>
3057 <li>Sequence Group colour can be specified in Annotation
3059 <li>Ad-hoc colouring of group in Annotation File using RGB
3060 triplet as name of colourscheme</li>
3061 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3063 <li>treenode binding for VAMSAS tree exchange</li>
3064 <li>local editing and update of sequences in VAMSAS
3065 alignments (experimental)</li>
3066 <li>Create new or select existing session to join</li>
3067 <li>load and save of vamsas documents</li>
3068 </ul> <em>Application command line</em>
3070 <li>-tree parameter to open trees (introduced for passing
3072 <li>-fetchfrom command line argument to specify nicknames
3073 of DAS servers to query for alignment features</li>
3074 <li>-dasserver command line argument to add new servers
3075 that are also automatically queried for features</li>
3076 <li>-groovy command line argument executes a given groovy
3077 script after all input data has been loaded and parsed</li>
3078 </ul> <em>Applet-Application data exchange</em>
3080 <li>Trees passed as applet parameters can be passed to
3081 application (when using "View in full
3082 application")</li>
3083 </ul> <em>Applet Parameters</em>
3085 <li>feature group display control parameter</li>
3086 <li>debug parameter</li>
3087 <li>showbutton parameter</li>
3088 </ul> <em>Applet API methods</em>
3090 <li>newView public method</li>
3091 <li>Window (current view) specific get/set public methods</li>
3092 <li>Feature display control methods</li>
3093 <li>get list of currently selected sequences</li>
3094 </ul> <em>New Jalview distribution features</em>
3096 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3097 <li>RELEASE file gives build properties for the latest
3098 Jalview release.</li>
3099 <li>Java 1.1 Applet build made easier and donotobfuscate
3100 property controls execution of obfuscator</li>
3101 <li>Build target for generating source distribution</li>
3102 <li>Debug flag for javacc</li>
3103 <li>.jalview_properties file is documented (slightly) in
3104 jalview.bin.Cache</li>
3105 <li>Continuous Build Integration for stable and
3106 development version of Application, Applet and source
3111 <li>selected region output includes visible annotations
3112 (for certain formats)</li>
3113 <li>edit label/displaychar contains existing label/char
3115 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3116 <li>shorter peptide product names from EMBL records</li>
3117 <li>Newick string generator makes compact representations</li>
3118 <li>bootstrap values parsed correctly for tree files with
3120 <li>pathological filechooser bug avoided by not allowing
3121 filenames containing a ':'</li>
3122 <li>Fixed exception when parsing GFF files containing
3123 global sequence features</li>
3124 <li>Alignment datasets are finalized only when number of
3125 references from alignment sequences goes to zero</li>
3126 <li>Close of tree branch colour box without colour
3127 selection causes cascading exceptions</li>
3128 <li>occasional negative imgwidth exceptions</li>
3129 <li>better reporting of non-fatal warnings to user when
3130 file parsing fails.</li>
3131 <li>Save works when Jalview project is default format</li>
3132 <li>Save as dialog opened if current alignment format is
3133 not a valid output format</li>
3134 <li>UniProt canonical names introduced for both das and
3136 <li>Histidine should be midblue (not pink!) in Zappo</li>
3137 <li>error messages passed up and output when data read
3139 <li>edit undo recovers previous dataset sequence when
3140 sequence is edited</li>
3141 <li>allow PDB files without pdb ID HEADER lines (like
3142 those generated by MODELLER) to be read in properly</li>
3143 <li>allow reading of JPred concise files as a normal
3145 <li>Stockholm annotation parsing and alignment properties
3146 import fixed for PFAM records</li>
3147 <li>Structure view windows have correct name in Desktop
3149 <li>annotation consisting of sequence associated scores
3150 can be read and written correctly to annotation file</li>
3151 <li>Aligned cDNA translation to aligned peptide works
3153 <li>Fixed display of hidden sequence markers and
3154 non-italic font for representatives in Applet</li>
3155 <li>Applet Menus are always embedded in applet window on
3157 <li>Newly shown features appear at top of stack (in
3159 <li>Annotations added via parameter not drawn properly
3160 due to null pointer exceptions</li>
3161 <li>Secondary structure lines are drawn starting from
3162 first column of alignment</li>
3163 <li>UniProt XML import updated for new schema release in
3165 <li>Sequence feature to sequence ID match for Features
3166 file is case-insensitive</li>
3167 <li>Sequence features read from Features file appended to
3168 all sequences with matching IDs</li>
3169 <li>PDB structure coloured correctly for associated views
3170 containing a sub-sequence</li>
3171 <li>PDB files can be retrieved by applet from Jar files</li>
3172 <li>feature and annotation file applet parameters
3173 referring to different directories are retrieved correctly</li>
3174 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3175 <li>Fixed application hang whilst waiting for
3176 splash-screen version check to complete</li>
3177 <li>Applet properly URLencodes input parameter values
3178 when passing them to the launchApp service</li>
3179 <li>display name and local features preserved in results
3180 retrieved from web service</li>
3181 <li>Visual delay indication for sequence retrieval and
3182 sequence fetcher initialisation</li>
3183 <li>updated Application to use DAS 1.53e version of
3184 dasobert DAS client</li>
3185 <li>Re-instated Full AMSA support and .amsa file
3187 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3195 <div align="center">
3196 <strong>2.3</strong><br> 9/5/07
3201 <li>Jmol 11.0.2 integration</li>
3202 <li>PDB views stored in Jalview XML files</li>
3203 <li>Slide sequences</li>
3204 <li>Edit sequence in place</li>
3205 <li>EMBL CDS features</li>
3206 <li>DAS Feature mapping</li>
3207 <li>Feature ordering</li>
3208 <li>Alignment Properties</li>
3209 <li>Annotation Scores</li>
3210 <li>Sort by scores</li>
3211 <li>Feature/annotation editing in applet</li>
3216 <li>Headless state operation in 2.2.1</li>
3217 <li>Incorrect and unstable DNA pairwise alignment</li>
3218 <li>Cut and paste of sequences with annotation</li>
3219 <li>Feature group display state in XML</li>
3220 <li>Feature ordering in XML</li>
3221 <li>blc file iteration selection using filename # suffix</li>
3222 <li>Stockholm alignment properties</li>
3223 <li>Stockhom alignment secondary structure annotation</li>
3224 <li>2.2.1 applet had no feature transparency</li>
3225 <li>Number pad keys can be used in cursor mode</li>
3226 <li>Structure Viewer mirror image resolved</li>
3233 <div align="center">
3234 <strong>2.2.1</strong><br> 12/2/07
3239 <li>Non standard characters can be read and displayed
3240 <li>Annotations/Features can be imported/exported to the
3242 <li>Applet allows editing of sequence/annotation/group
3243 name & description
3244 <li>Preference setting to display sequence name in
3246 <li>Annotation file format extended to allow
3247 Sequence_groups to be defined
3248 <li>Default opening of alignment overview panel can be
3249 specified in preferences
3250 <li>PDB residue numbering annotation added to associated
3256 <li>Applet crash under certain Linux OS with Java 1.6
3258 <li>Annotation file export / import bugs fixed
3259 <li>PNG / EPS image output bugs fixed
3265 <div align="center">
3266 <strong>2.2</strong><br> 27/11/06
3271 <li>Multiple views on alignment
3272 <li>Sequence feature editing
3273 <li>"Reload" alignment
3274 <li>"Save" to current filename
3275 <li>Background dependent text colour
3276 <li>Right align sequence ids
3277 <li>User-defined lower case residue colours
3280 <li>Menu item accelerator keys
3281 <li>Control-V pastes to current alignment
3282 <li>Cancel button for DAS Feature Fetching
3283 <li>PCA and PDB Viewers zoom via mouse roller
3284 <li>User-defined sub-tree colours and sub-tree selection
3286 <li>'New Window' button on the 'Output to Text box'
3291 <li>New memory efficient Undo/Redo System
3292 <li>Optimised symbol lookups and conservation/consensus
3294 <li>Region Conservation/Consensus recalculated after
3296 <li>Fixed Remove Empty Columns Bug (empty columns at end
3298 <li>Slowed DAS Feature Fetching for increased robustness.
3300 <li>Made angle brackets in ASCII feature descriptions
3302 <li>Re-instated Zoom function for PCA
3303 <li>Sequence descriptions conserved in web service
3305 <li>UniProt ID discoverer uses any word separated by
3307 <li>WsDbFetch query/result association resolved
3308 <li>Tree leaf to sequence mapping improved
3309 <li>Smooth fonts switch moved to FontChooser dialog box.
3316 <div align="center">
3317 <strong>2.1.1</strong><br> 12/9/06
3322 <li>Copy consensus sequence to clipboard</li>
3327 <li>Image output - rightmost residues are rendered if
3328 sequence id panel has been resized</li>
3329 <li>Image output - all offscreen group boundaries are
3331 <li>Annotation files with sequence references - all
3332 elements in file are relative to sequence position</li>
3333 <li>Mac Applet users can use Alt key for group editing</li>
3339 <div align="center">
3340 <strong>2.1</strong><br> 22/8/06
3345 <li>MAFFT Multiple Alignment in default Web Service list</li>
3346 <li>DAS Feature fetching</li>
3347 <li>Hide sequences and columns</li>
3348 <li>Export Annotations and Features</li>
3349 <li>GFF file reading / writing</li>
3350 <li>Associate structures with sequences from local PDB
3352 <li>Add sequences to exisiting alignment</li>
3353 <li>Recently opened files / URL lists</li>
3354 <li>Applet can launch the full application</li>
3355 <li>Applet has transparency for features (Java 1.2
3357 <li>Applet has user defined colours parameter</li>
3358 <li>Applet can load sequences from parameter
3359 "sequence<em>x</em>"
3365 <li>Redundancy Panel reinstalled in the Applet</li>
3366 <li>Monospaced font - EPS / rescaling bug fixed</li>
3367 <li>Annotation files with sequence references bug fixed</li>
3373 <div align="center">
3374 <strong>2.08.1</strong><br> 2/5/06
3379 <li>Change case of selected region from Popup menu</li>
3380 <li>Choose to match case when searching</li>
3381 <li>Middle mouse button and mouse movement can compress /
3382 expand the visible width and height of the alignment</li>
3387 <li>Annotation Panel displays complete JNet results</li>
3393 <div align="center">
3394 <strong>2.08b</strong><br> 18/4/06
3400 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3401 <li>Righthand label on wrapped alignments shows correct
3408 <div align="center">
3409 <strong>2.08</strong><br> 10/4/06
3414 <li>Editing can be locked to the selection area</li>
3415 <li>Keyboard editing</li>
3416 <li>Create sequence features from searches</li>
3417 <li>Precalculated annotations can be loaded onto
3419 <li>Features file allows grouping of features</li>
3420 <li>Annotation Colouring scheme added</li>
3421 <li>Smooth fonts off by default - Faster rendering</li>
3422 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3427 <li>Drag & Drop fixed on Linux</li>
3428 <li>Jalview Archive file faster to load/save, sequence
3429 descriptions saved.</li>
3435 <div align="center">
3436 <strong>2.07</strong><br> 12/12/05
3441 <li>PDB Structure Viewer enhanced</li>
3442 <li>Sequence Feature retrieval and display enhanced</li>
3443 <li>Choose to output sequence start-end after sequence
3444 name for file output</li>
3445 <li>Sequence Fetcher WSDBFetch@EBI</li>
3446 <li>Applet can read feature files, PDB files and can be
3447 used for HTML form input</li>
3452 <li>HTML output writes groups and features</li>
3453 <li>Group editing is Control and mouse click</li>
3454 <li>File IO bugs</li>
3460 <div align="center">
3461 <strong>2.06</strong><br> 28/9/05
3466 <li>View annotations in wrapped mode</li>
3467 <li>More options for PCA viewer</li>
3472 <li>GUI bugs resolved</li>
3473 <li>Runs with -nodisplay from command line</li>
3479 <div align="center">
3480 <strong>2.05b</strong><br> 15/9/05
3485 <li>Choose EPS export as lineart or text</li>
3486 <li>Jar files are executable</li>
3487 <li>Can read in Uracil - maps to unknown residue</li>
3492 <li>Known OutOfMemory errors give warning message</li>
3493 <li>Overview window calculated more efficiently</li>
3494 <li>Several GUI bugs resolved</li>
3500 <div align="center">
3501 <strong>2.05</strong><br> 30/8/05
3506 <li>Edit and annotate in "Wrapped" view</li>
3511 <li>Several GUI bugs resolved</li>
3517 <div align="center">
3518 <strong>2.04</strong><br> 24/8/05
3523 <li>Hold down mouse wheel & scroll to change font
3529 <li>Improved JPred client reliability</li>
3530 <li>Improved loading of Jalview files</li>
3536 <div align="center">
3537 <strong>2.03</strong><br> 18/8/05
3542 <li>Set Proxy server name and port in preferences</li>
3543 <li>Multiple URL links from sequence ids</li>
3544 <li>User Defined Colours can have a scheme name and added
3546 <li>Choose to ignore gaps in consensus calculation</li>
3547 <li>Unix users can set default web browser</li>
3548 <li>Runs without GUI for batch processing</li>
3549 <li>Dynamically generated Web Service Menus</li>
3554 <li>InstallAnywhere download for Sparc Solaris</li>
3560 <div align="center">
3561 <strong>2.02</strong><br> 18/7/05
3567 <li>Copy & Paste order of sequences maintains
3568 alignment order.</li>
3574 <div align="center">
3575 <strong>2.01</strong><br> 12/7/05
3580 <li>Use delete key for deleting selection.</li>
3581 <li>Use Mouse wheel to scroll sequences.</li>
3582 <li>Help file updated to describe how to add alignment
3584 <li>Version and build date written to build properties
3586 <li>InstallAnywhere installation will check for updates
3587 at launch of Jalview.</li>
3592 <li>Delete gaps bug fixed.</li>
3593 <li>FileChooser sorts columns.</li>
3594 <li>Can remove groups one by one.</li>
3595 <li>Filechooser icons installed.</li>
3596 <li>Finder ignores return character when searching.
3597 Return key will initiate a search.<br>
3604 <div align="center">
3605 <strong>2.0</strong><br> 20/6/05
3610 <li>New codebase</li>