3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.3">2.10.3</a><br />
74 <em>17/11/2017</em></strong>
77 <td><div align="left">
81 <!-- JAL-2446 -->Faster and more efficient management and
82 rendering of sequence features
85 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
86 429 rate limit request hander
89 <!-- JAL-2773 -->Structure views don't get updated unless
90 their colours have changed
92 <li><!-- JAL-2495 -->All linked sequences are highlighted for a structure mousover (Jmol) or selection (Chimera)</li>
93 <li><!-- JAL-2790 -->'Cancel' button in progress bar for JABAWS AACon, RNAAliFold and Disorder prediction jobs
96 <li><!-- JAL-2617 -->Stop codons are excluded in CDS/Protein view from Ensembl locus cross-references</li>
97 <li><!-- JAL-2685 -->Start/End limits are shown in Pairwise Alignment report</li>
98 <li><!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch' feature can be disabled</li>
99 <li><!-- JAL-2810 -->Retrieve IDs tab added for UniProt and PDB easier retrieval of sequences for lists of IDs</li>
100 <li><!-- JAL-2758 -->Short names for sequences retrieved from Uniprot</li>
104 <li>Groovy interpreter updated to 2.4.12</li>
105 <li>Example groovy script for generating a matrix of percent identity scores for current alignment.</li>
107 <em>Testing and Deployment</em>
109 <li><!-- JAL-2727 -->Test to catch memory leaks in Jalview UI</li>
113 <td><div align="left">
116 <li><!-- JAL-2643 -->Pressing tab after updating the colour threshold text field doesn't trigger an update to the alignment view</li>
117 <li><!-- JAL-2682 -->Race condition when parsing sequence ID strings in parallel</li>
118 <li><!-- JAL-2608 -->Overview windows are also closed when alignment window is closed</li>
119 <li><!-- JAL-2548 -->Export of features doesn't always respect group visibility</li>
120 <li><!-- JAL-2831 -->Jumping from column 1 to column 100,000 takes a long time in Cursor mode</li>
124 <li><!-- JAL-2777 -->Structures with whitespace chainCode cannot be viewed in Chimera</li>
125 <li><!-- JAL-2728 -->Protein annotation panel too high in CDS/Protein view
127 <li><!-- JAL-2757 -->Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs
129 <li><!-- JAL-2253 -->Slow EnsemblGenome ID lookup</li>
130 <li><!-- JAL-2529 -->Revised Ensembl REST API CDNA query</li>
131 <li><!-- JAL-2739 -->Hidden column marker in last column not rendered when switching back from Wrapped to normal view</li>
132 <li><!-- JAL-2768 -->Annotation display corrupted when scrolling right in unwapped alignment view</li>
133 <li><!-- JAL-2542 -->Existing features on subsequence incorrectly relocated when full sequence retrieved from database</li>
134 <li><!-- JAL-2733 -->Last reported memory still shown when Desktop->Show Memory is unticked (OSX only)</li>
135 <li><!-- JAL-2658 -->Amend Features dialog doesn't allow features of same type and group to be selected for amending</li>
136 <li><!-- JAL-2524 -->Jalview becomes sluggish in wide alignments when hidden columns are present</li>
137 <li><!-- JAL-2392 -->Jalview freezes when loading and displaying several structures</li>
138 <li><!-- JAL-2732 -->Black outlines left after resizing or moving a window</li>
139 <li><!-- JAL-1900,JAL-1625 -->Unable to minimise windows within the Jalview desktop on OSX</li>
140 <li><!-- JAL-2667 -->Mouse wheel doesn't scroll vertically when in wrapped alignment mode</li>
141 <li><!-- JAL-2636 -->Scale mark not shown when close to right hand end of alignment</li>
142 <li><!-- JAL-2684 -->Pairwise alignment 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>
148 <li><!-- JAL-2811 -->Double residue highlights in cursor mode if new selection moves alignment window</li>
150 <strong><em>Applet</em></strong><br/>
152 <li><!-- JAL-2687 -->Concurrent modification exception when closing alignment panel</li>
154 <strong><em>BioJSON</em></strong><br/>
157 <!-- JAL-2546 -->BioJSON export does not preserve non-positional features
160 <strong>Known Java 9 Issues</strong>
162 <li><!-- JAL-2902 -->Groovy Console very slow to open and is
163 not responsive when entering characters (Webstart, Java 9.01,
167 <strong>New Known Issues</strong>
169 <li><!-- JAL- --></li>
175 <td width="60" nowrap>
177 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
178 <em>2/10/2017</em></strong>
181 <td><div align="left">
182 <em>New features in Jalview Desktop</em>
185 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
187 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
191 <td><div align="left">
195 <td width="60" nowrap>
197 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
198 <em>7/9/2017</em></strong>
201 <td><div align="left">
205 <!-- JAL-2588 -->Show gaps in overview window by colouring
206 in grey (sequences used to be coloured grey, and gaps were
210 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
214 <!-- JAL-2587 -->Overview updates immediately on increase
215 in size and progress bar shown as higher resolution
216 overview is recalculated
221 <td><div align="left">
225 <!-- JAL-2664 -->Overview window redraws every hidden
226 column region row by row
229 <!-- JAL-2681 -->duplicate protein sequences shown after
230 retrieving Ensembl crossrefs for sequences from Uniprot
233 <!-- JAL-2603 -->Overview window throws NPE if show boxes
234 format setting is unticked
237 <!-- JAL-2610 -->Groups are coloured wrongly in overview
238 if group has show boxes format setting unticked
241 <!-- JAL-2672,JAL-2665 -->Redraw problems when
242 autoscrolling whilst dragging current selection group to
243 include sequences and columns not currently displayed
246 <!-- JAL-2691 -->Not all chains are mapped when multimeric
247 assemblies are imported via CIF file
250 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
251 displayed when threshold or conservation colouring is also
255 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
259 <!-- JAL-2673 -->Jalview continues to scroll after
260 dragging a selected region off the visible region of the
264 <!-- JAL-2724 -->Cannot apply annotation based
265 colourscheme to all groups in a view
268 <!-- JAL-2511 -->IDs don't line up with sequences
269 initially after font size change using the Font chooser or
276 <td width="60" nowrap>
278 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
281 <td><div align="left">
282 <em>Calculations</em>
286 <!-- JAL-1933 -->Occupancy annotation row shows number of
287 ungapped positions in each column of the alignment.
290 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
291 a calculation dialog box
294 <!-- JAL-2379 -->Revised implementation of PCA for speed
295 and memory efficiency (~30x faster)
298 <!-- JAL-2403 -->Revised implementation of sequence
299 similarity scores as used by Tree, PCA, Shading Consensus
300 and other calculations
303 <!-- JAL-2416 -->Score matrices are stored as resource
304 files within the Jalview codebase
307 <!-- JAL-2500 -->Trees computed on Sequence Feature
308 Similarity may have different topology due to increased
315 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
316 model for alignments and groups
319 <!-- JAL-384 -->Custom shading schemes created via groovy
326 <!-- JAL-2526 -->Efficiency improvements for interacting
327 with alignment and overview windows
330 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
334 <!-- JAL-2388 -->Hidden columns and sequences can be
338 <!-- JAL-2611 -->Click-drag in visible area allows fine
339 adjustment of visible position
343 <em>Data import/export</em>
346 <!-- JAL-2535 -->Posterior probability annotation from
347 Stockholm files imported as sequence associated annotation
350 <!-- JAL-2507 -->More robust per-sequence positional
351 annotation input/output via stockholm flatfile
354 <!-- JAL-2533 -->Sequence names don't include file
355 extension when importing structure files without embedded
356 names or PDB accessions
359 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
360 format sequence substitution matrices
363 <em>User Interface</em>
366 <!-- JAL-2447 --> Experimental Features Checkbox in
367 Desktop's Tools menu to hide or show untested features in
371 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
372 via Overview or sequence motif search operations
375 <!-- JAL-2547 -->Amend sequence features dialog box can be
376 opened by double clicking gaps within sequence feature
380 <!-- JAL-1476 -->Status bar message shown when not enough
381 aligned positions were available to create a 3D structure
385 <em>3D Structure</em>
388 <!-- JAL-2430 -->Hidden regions in alignment views are not
389 coloured in linked structure views
392 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
393 file-based command exchange
396 <!-- JAL-2375 -->Structure chooser automatically shows
397 Cached Structures rather than querying the PDBe if
398 structures are already available for sequences
401 <!-- JAL-2520 -->Structures imported via URL are cached in
402 the Jalview project rather than downloaded again when the
406 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
407 to transfer Chimera's structure attributes as Jalview
408 features, and vice-versa (<strong>Experimental
412 <em>Web Services</em>
415 <!-- JAL-2549 -->Updated JABAWS client to v2.2
418 <!-- JAL-2335 -->Filter non-standard amino acids and
419 nucleotides when submitting to AACon and other MSA
423 <!-- JAL-2316, -->URLs for viewing database
424 cross-references provided by identifiers.org and the
432 <!-- JAL-2344 -->FileFormatI interface for describing and
433 identifying file formats (instead of String constants)
436 <!-- JAL-2228 -->FeatureCounter script refactored for
437 efficiency when counting all displayed features (not
438 backwards compatible with 2.10.1)
441 <em>Example files</em>
444 <!-- JAL-2631 -->Graduated feature colour style example
445 included in the example feature file
448 <em>Documentation</em>
451 <!-- JAL-2339 -->Release notes reformatted for readability
452 with the built-in Java help viewer
455 <!-- JAL-1644 -->Find documentation updated with 'search
456 sequence description' option
462 <!-- JAL-2485, -->External service integration tests for
463 Uniprot REST Free Text Search Client
466 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
469 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
474 <td><div align="left">
475 <em>Calculations</em>
478 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
479 matrix - C->R should be '-3'<br />Old matrix restored
480 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
482 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
483 Jalview's treatment of gaps in PCA and substitution matrix
484 based Tree calculations.<br /> <br />In earlier versions
485 of Jalview, gaps matching gaps were penalised, and gaps
486 matching non-gaps penalised even more. In the PCA
487 calculation, gaps were actually treated as non-gaps - so
488 different costs were applied, which meant Jalview's PCAs
489 were different to those produced by SeqSpace.<br />Jalview
490 now treats gaps in the same way as SeqSpace (ie it scores
491 them as 0). <br /> <br />Enter the following in the
492 Groovy console to restore pre-2.10.2 behaviour:<br />
493 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
494 // for 2.10.1 mode <br />
495 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
496 // to restore 2.10.2 mode <br /> <br /> <em>Note:
497 these settings will affect all subsequent tree and PCA
498 calculations (not recommended)</em></li>
500 <!-- JAL-2424 -->Fixed off-by-one bug that affected
501 scaling of branch lengths for trees computed using
502 Sequence Feature Similarity.
505 <!-- JAL-2377 -->PCA calculation could hang when
506 generating output report when working with highly
510 <!-- JAL-2544 --> Sort by features includes features to
511 right of selected region when gaps present on right-hand
515 <em>User Interface</em>
518 <!-- JAL-2346 -->Reopening Colour by annotation dialog
519 doesn't reselect a specific sequence's associated
520 annotation after it was used for colouring a view
523 <!-- JAL-2419 -->Current selection lost if popup menu
524 opened on a region of alignment without groups
527 <!-- JAL-2374 -->Popup menu not always shown for regions
528 of an alignment with overlapping groups
531 <!-- JAL-2310 -->Finder double counts if both a sequence's
532 name and description match
535 <!-- JAL-2370 -->Hiding column selection containing two
536 hidden regions results in incorrect hidden regions
539 <!-- JAL-2386 -->'Apply to all groups' setting when
540 changing colour does not apply Conservation slider value
544 <!-- JAL-2373 -->Percentage identity and conservation menu
545 items do not show a tick or allow shading to be disabled
548 <!-- JAL-2385 -->Conservation shading or PID threshold
549 lost when base colourscheme changed if slider not visible
552 <!-- JAL-2547 -->Sequence features shown in tooltip for
553 gaps before start of features
556 <!-- JAL-2623 -->Graduated feature colour threshold not
557 restored to UI when feature colour is edited
560 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
561 a time when scrolling vertically in wrapped mode.
564 <!-- JAL-2630 -->Structure and alignment overview update
565 as graduate feature colour settings are modified via the
569 <!-- JAL-2034 -->Overview window doesn't always update
570 when a group defined on the alignment is resized
573 <!-- JAL-2605 -->Mouseovers on left/right scale region in
574 wrapped view result in positional status updates
578 <!-- JAL-2563 -->Status bar doesn't show position for
579 ambiguous amino acid and nucleotide symbols
582 <!-- JAL-2602 -->Copy consensus sequence failed if
583 alignment included gapped columns
586 <!-- JAL-2473 -->Minimum size set for Jalview windows so
587 widgets don't permanently disappear
590 <!-- JAL-2503 -->Cannot select or filter quantitative
591 annotation that are shown only as column labels (e.g.
592 T-Coffee column reliability scores)
595 <!-- JAL-2594 -->Exception thrown if trying to create a
596 sequence feature on gaps only
599 <!-- JAL-2504 -->Features created with 'New feature'
600 button from a Find inherit previously defined feature type
601 rather than the Find query string
604 <!-- JAL-2423 -->incorrect title in output window when
605 exporting tree calculated in Jalview
608 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
609 and then revealing them reorders sequences on the
613 <!-- JAL-964 -->Group panel in sequence feature settings
614 doesn't update to reflect available set of groups after
615 interactively adding or modifying features
618 <!-- JAL-2225 -->Sequence Database chooser unusable on
622 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
623 only excluded gaps in current sequence and ignored
630 <!-- JAL-2421 -->Overview window visible region moves
631 erratically when hidden rows or columns are present
634 <!-- JAL-2362 -->Per-residue colourschemes applied via the
635 Structure Viewer's colour menu don't correspond to
639 <!-- JAL-2405 -->Protein specific colours only offered in
640 colour and group colour menu for protein alignments
643 <!-- JAL-2385 -->Colour threshold slider doesn't update to
644 reflect currently selected view or group's shading
648 <!-- JAL-2624 -->Feature colour thresholds not respected
649 when rendered on overview and structures when opacity at
653 <!-- JAL-2589 -->User defined gap colour not shown in
654 overview when features overlaid on alignment
657 <em>Data import/export</em>
660 <!-- JAL-2576 -->Very large alignments take a long time to
664 <!-- JAL-2507 -->Per-sequence RNA secondary structures
665 added after a sequence was imported are not written to
669 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
670 when importing RNA secondary structure via Stockholm
673 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
674 not shown in correct direction for simple pseudoknots
677 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
678 with lightGray or darkGray via features file (but can
682 <!-- JAL-2383 -->Above PID colour threshold not recovered
683 when alignment view imported from project
686 <!-- JAL-2520,JAL-2465 -->No mappings generated between
687 structure and sequences extracted from structure files
688 imported via URL and viewed in Jmol
691 <!-- JAL-2520 -->Structures loaded via URL are saved in
692 Jalview Projects rather than fetched via URL again when
693 the project is loaded and the structure viewed
696 <em>Web Services</em>
699 <!-- JAL-2519 -->EnsemblGenomes example failing after
700 release of Ensembl v.88
703 <!-- JAL-2366 -->Proxy server address and port always
704 appear enabled in Preferences->Connections
707 <!-- JAL-2461 -->DAS registry not found exceptions
708 removed from console output
711 <!-- JAL-2582 -->Cannot retrieve protein products from
712 Ensembl by Peptide ID
715 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
716 created from SIFTs, and spurious 'Couldn't open structure
717 in Chimera' errors raised after April 2017 update (problem
718 due to 'null' string rather than empty string used for
719 residues with no corresponding PDB mapping).
722 <em>Application UI</em>
725 <!-- JAL-2361 -->User Defined Colours not added to Colour
729 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
730 case' residues (button in colourscheme editor debugged and
731 new documentation and tooltips added)
734 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
735 doesn't restore group-specific text colour thresholds
738 <!-- JAL-2243 -->Feature settings panel does not update as
739 new features are added to alignment
742 <!-- JAL-2532 -->Cancel in feature settings reverts
743 changes to feature colours via the Amend features dialog
746 <!-- JAL-2506 -->Null pointer exception when attempting to
747 edit graduated feature colour via amend features dialog
751 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
752 selection menu changes colours of alignment views
755 <!-- JAL-2426 -->Spurious exceptions in console raised
756 from alignment calculation workers after alignment has
760 <!-- JAL-1608 -->Typo in selection popup menu - Create
761 groups now 'Create Group'
764 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
765 Create/Undefine group doesn't always work
768 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
769 shown again after pressing 'Cancel'
772 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
773 adjusts start position in wrap mode
776 <!-- JAL-2563 -->Status bar doesn't show positions for
777 ambiguous amino acids
780 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
781 CDS/Protein view after CDS sequences added for aligned
785 <!-- JAL-2592 -->User defined colourschemes called 'User
786 Defined' don't appear in Colours menu
792 <!-- JAL-2468 -->Switching between Nucleotide and Protein
793 score models doesn't always result in an updated PCA plot
796 <!-- JAL-2442 -->Features not rendered as transparent on
797 overview or linked structure view
800 <!-- JAL-2372 -->Colour group by conservation doesn't
804 <!-- JAL-2517 -->Hitting Cancel after applying
805 user-defined colourscheme doesn't restore original
812 <!-- JAL-2314 -->Unit test failure:
813 jalview.ws.jabaws.RNAStructExportImport setup fails
816 <!-- JAL-2307 -->Unit test failure:
817 jalview.ws.sifts.SiftsClientTest due to compatibility
818 problems with deep array comparison equality asserts in
819 successive versions of TestNG
822 <!-- JAL-2479 -->Relocated StructureChooserTest and
823 ParameterUtilsTest Unit tests to Network suite
826 <em>New Known Issues</em>
829 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
830 phase after a sequence motif find operation
833 <!-- JAL-2550 -->Importing annotation file with rows
834 containing just upper and lower case letters are
835 interpreted as WUSS RNA secondary structure symbols
838 <!-- JAL-2590 -->Cannot load and display Newick trees
839 reliably from eggnog Ortholog database
842 <!-- JAL-2468 -->Status bar shows 'Marked x columns
843 containing features of type Highlight' when 'B' is pressed
844 to mark columns containing highlighted regions.
847 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
848 doesn't always add secondary structure annotation.
853 <td width="60" nowrap>
855 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
858 <td><div align="left">
862 <!-- JAL-98 -->Improved memory usage: sparse arrays used
863 for all consensus calculations
866 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
869 <li>Updated Jalview's Certum code signing certificate
875 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
876 set of database cross-references, sorted alphabetically
879 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
880 from database cross references. Users with custom links
881 will receive a <a href="webServices/urllinks.html#warning">warning
882 dialog</a> asking them to update their preferences.
885 <!-- JAL-2287-->Cancel button and escape listener on
886 dialog warning user about disconnecting Jalview from a
890 <!-- JAL-2320-->Jalview's Chimera control window closes if
891 the Chimera it is connected to is shut down
894 <!-- JAL-1738-->New keystroke (B) and Select highlighted
895 columns menu item to mark columns containing highlighted
896 regions (e.g. from structure selections or results of a
900 <!-- JAL-2284-->Command line option for batch-generation
901 of HTML pages rendering alignment data with the BioJS
911 <!-- JAL-2286 -->Columns with more than one modal residue
912 are not coloured or thresholded according to percent
913 identity (first observed in Jalview 2.8.2)
916 <!-- JAL-2301 -->Threonine incorrectly reported as not
920 <!-- JAL-2318 -->Updates to documentation pages (above PID
921 threshold, amino acid properties)
924 <!-- JAL-2292 -->Lower case residues in sequences are not
925 reported as mapped to residues in a structure file in the
929 <!--JAL-2324 -->Identical features with non-numeric scores
930 could be added multiple times to a sequence
933 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
934 bond features shown as two highlighted residues rather
935 than a range in linked structure views, and treated
936 correctly when selecting and computing trees from features
939 <!-- JAL-2281-->Custom URL links for database
940 cross-references are matched to database name regardless
948 <!-- JAL-2282-->Custom URL links for specific database
949 names without regular expressions also offer links from
953 <!-- JAL-2315-->Removing a single configured link in the
954 URL links pane in Connections preferences doesn't actually
955 update Jalview configuration
958 <!-- JAL-2272-->CTRL-Click on a selected region to open
959 the alignment area popup menu doesn't work on El-Capitan
962 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
963 files with similarly named sequences if dropped onto the
967 <!-- JAL-2312 -->Additional mappings are shown for PDB
968 entries where more chains exist in the PDB accession than
969 are reported in the SIFTS file
972 <!-- JAL-2317-->Certain structures do not get mapped to
973 the structure view when displayed with Chimera
976 <!-- JAL-2317-->No chains shown in the Chimera view
977 panel's View->Show Chains submenu
980 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
981 work for wrapped alignment views
984 <!--JAL-2197 -->Rename UI components for running JPred
985 predictions from 'JNet' to 'JPred'
988 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
989 corrupted when annotation panel vertical scroll is not at
993 <!--JAL-2332 -->Attempting to view structure for Hen
994 lysozyme results in a PDB Client error dialog box
997 <!-- JAL-2319 -->Structure View's mapping report switched
998 ranges for PDB and sequence for SIFTS
1001 SIFTS 'Not_Observed' residues mapped to non-existant
1005 <!-- <em>New Known Issues</em>
1012 <td width="60" nowrap>
1013 <div align="center">
1014 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1015 <em>25/10/2016</em></strong>
1018 <td><em>Application</em>
1020 <li>3D Structure chooser opens with 'Cached structures'
1021 view if structures already loaded</li>
1022 <li>Progress bar reports models as they are loaded to
1023 structure views</li>
1029 <li>Colour by conservation always enabled and no tick
1030 shown in menu when BLOSUM or PID shading applied</li>
1031 <li>FER1_ARATH and FER2_ARATH labels were switched in
1032 example sequences/projects/trees</li>
1034 <em>Application</em>
1036 <li>Jalview projects with views of local PDB structure
1037 files saved on Windows cannot be opened on OSX</li>
1038 <li>Multiple structure views can be opened and superposed
1039 without timeout for structures with multiple models or
1040 multiple sequences in alignment</li>
1041 <li>Cannot import or associated local PDB files without a
1042 PDB ID HEADER line</li>
1043 <li>RMSD is not output in Jmol console when superposition
1045 <li>Drag and drop of URL from Browser fails for Linux and
1046 OSX versions earlier than El Capitan</li>
1047 <li>ENA client ignores invalid content from ENA server</li>
1048 <li>Exceptions are not raised in console when ENA client
1049 attempts to fetch non-existent IDs via Fetch DB Refs UI
1051 <li>Exceptions are not raised in console when a new view
1052 is created on the alignment</li>
1053 <li>OSX right-click fixed for group selections: CMD-click
1054 to insert/remove gaps in groups and CTRL-click to open group
1057 <em>Build and deployment</em>
1059 <li>URL link checker now copes with multi-line anchor
1062 <em>New Known Issues</em>
1064 <li>Drag and drop from URL links in browsers do not work
1071 <td width="60" nowrap>
1072 <div align="center">
1073 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1076 <td><em>General</em>
1079 <!-- JAL-2124 -->Updated Spanish translations.
1082 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1083 for importing structure data to Jalview. Enables mmCIF and
1087 <!-- JAL-192 --->Alignment ruler shows positions relative to
1091 <!-- JAL-2202 -->Position/residue shown in status bar when
1092 mousing over sequence associated annotation
1095 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1099 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1100 '()', canonical '[]' and invalid '{}' base pair populations
1104 <!-- JAL-2092 -->Feature settings popup menu options for
1105 showing or hiding columns containing a feature
1108 <!-- JAL-1557 -->Edit selected group by double clicking on
1109 group and sequence associated annotation labels
1112 <!-- JAL-2236 -->Sequence name added to annotation label in
1113 select/hide columns by annotation and colour by annotation
1117 </ul> <em>Application</em>
1120 <!-- JAL-2050-->Automatically hide introns when opening a
1121 gene/transcript view
1124 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1128 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1129 structure mappings with the EMBL-EBI PDBe SIFTS database
1132 <!-- JAL-2079 -->Updated download sites used for Rfam and
1133 Pfam sources to xfam.org
1136 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1139 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1140 over sequences in Jalview
1143 <!-- JAL-2027-->Support for reverse-complement coding
1144 regions in ENA and EMBL
1147 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1148 for record retrieval via ENA rest API
1151 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1155 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1156 groovy script execution
1159 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1160 alignment window's Calculate menu
1163 <!-- JAL-1812 -->Allow groovy scripts that call
1164 Jalview.getAlignFrames() to run in headless mode
1167 <!-- JAL-2068 -->Support for creating new alignment
1168 calculation workers from groovy scripts
1171 <!-- JAL-1369 --->Store/restore reference sequence in
1175 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1176 associations are now saved/restored from project
1179 <!-- JAL-1993 -->Database selection dialog always shown
1180 before sequence fetcher is opened
1183 <!-- JAL-2183 -->Double click on an entry in Jalview's
1184 database chooser opens a sequence fetcher
1187 <!-- JAL-1563 -->Free-text search client for UniProt using
1188 the UniProt REST API
1191 <!-- JAL-2168 -->-nonews command line parameter to prevent
1192 the news reader opening
1195 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1196 querying stored in preferences
1199 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1203 <!-- JAL-1977-->Tooltips shown on database chooser
1206 <!-- JAL-391 -->Reverse complement function in calculate
1207 menu for nucleotide sequences
1210 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1211 and feature counts preserves alignment ordering (and
1212 debugged for complex feature sets).
1215 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1216 viewing structures with Jalview 2.10
1219 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1220 genome, transcript CCDS and gene ids via the Ensembl and
1221 Ensembl Genomes REST API
1224 <!-- JAL-2049 -->Protein sequence variant annotation
1225 computed for 'sequence_variant' annotation on CDS regions
1229 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1233 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1234 Ref Fetcher fails to match, or otherwise updates sequence
1235 data from external database records.
1238 <!-- JAL-2154 -->Revised Jalview Project format for
1239 efficient recovery of sequence coding and alignment
1240 annotation relationships.
1242 </ul> <!-- <em>Applet</em>
1253 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1257 <!-- JAL-2018-->Export features in Jalview format (again)
1258 includes graduated colourschemes
1261 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1262 working with big alignments and lots of hidden columns
1265 <!-- JAL-2053-->Hidden column markers not always rendered
1266 at right of alignment window
1269 <!-- JAL-2067 -->Tidied up links in help file table of
1273 <!-- JAL-2072 -->Feature based tree calculation not shown
1277 <!-- JAL-2075 -->Hidden columns ignored during feature
1278 based tree calculation
1281 <!-- JAL-2065 -->Alignment view stops updating when show
1282 unconserved enabled for group on alignment
1285 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1289 <!-- JAL-2146 -->Alignment column in status incorrectly
1290 shown as "Sequence position" when mousing over
1294 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1295 hidden columns present
1298 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1299 user created annotation added to alignment
1302 <!-- JAL-1841 -->RNA Structure consensus only computed for
1303 '()' base pair annotation
1306 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1307 in zero scores for all base pairs in RNA Structure
1311 <!-- JAL-2174-->Extend selection with columns containing
1315 <!-- JAL-2275 -->Pfam format writer puts extra space at
1316 beginning of sequence
1319 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1323 <!-- JAL-2238 -->Cannot create groups on an alignment from
1324 from a tree when t-coffee scores are shown
1327 <!-- JAL-1836,1967 -->Cannot import and view PDB
1328 structures with chains containing negative resnums (4q4h)
1331 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1335 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1336 to Clustal, PIR and PileUp output
1339 <!-- JAL-2008 -->Reordering sequence features that are
1340 not visible causes alignment window to repaint
1343 <!-- JAL-2006 -->Threshold sliders don't work in
1344 graduated colour and colour by annotation row for e-value
1345 scores associated with features and annotation rows
1348 <!-- JAL-1797 -->amino acid physicochemical conservation
1349 calculation should be case independent
1352 <!-- JAL-2173 -->Remove annotation also updates hidden
1356 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1357 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1358 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1361 <!-- JAL-2065 -->Null pointer exceptions and redraw
1362 problems when reference sequence defined and 'show
1363 non-conserved' enabled
1366 <!-- JAL-1306 -->Quality and Conservation are now shown on
1367 load even when Consensus calculation is disabled
1370 <!-- JAL-1932 -->Remove right on penultimate column of
1371 alignment does nothing
1374 <em>Application</em>
1377 <!-- JAL-1552-->URLs and links can't be imported by
1378 drag'n'drop on OSX when launched via webstart (note - not
1379 yet fixed for El Capitan)
1382 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1383 output when running on non-gb/us i18n platforms
1386 <!-- JAL-1944 -->Error thrown when exporting a view with
1387 hidden sequences as flat-file alignment
1390 <!-- JAL-2030-->InstallAnywhere distribution fails when
1394 <!-- JAL-2080-->Jalview very slow to launch via webstart
1395 (also hotfix for 2.9.0b2)
1398 <!-- JAL-2085 -->Cannot save project when view has a
1399 reference sequence defined
1402 <!-- JAL-1011 -->Columns are suddenly selected in other
1403 alignments and views when revealing hidden columns
1406 <!-- JAL-1989 -->Hide columns not mirrored in complement
1407 view in a cDNA/Protein splitframe
1410 <!-- JAL-1369 -->Cannot save/restore representative
1411 sequence from project when only one sequence is
1415 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1416 in Structure Chooser
1419 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1420 structure consensus didn't refresh annotation panel
1423 <!-- JAL-1962 -->View mapping in structure view shows
1424 mappings between sequence and all chains in a PDB file
1427 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1428 dialogs format columns correctly, don't display array
1429 data, sort columns according to type
1432 <!-- JAL-1975 -->Export complete shown after destination
1433 file chooser is cancelled during an image export
1436 <!-- JAL-2025 -->Error when querying PDB Service with
1437 sequence name containing special characters
1440 <!-- JAL-2024 -->Manual PDB structure querying should be
1444 <!-- JAL-2104 -->Large tooltips with broken HTML
1445 formatting don't wrap
1448 <!-- JAL-1128 -->Figures exported from wrapped view are
1449 truncated so L looks like I in consensus annotation
1452 <!-- JAL-2003 -->Export features should only export the
1453 currently displayed features for the current selection or
1457 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1458 after fetching cross-references, and restoring from
1462 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1463 followed in the structure viewer
1466 <!-- JAL-2163 -->Titles for individual alignments in
1467 splitframe not restored from project
1470 <!-- JAL-2145 -->missing autocalculated annotation at
1471 trailing end of protein alignment in transcript/product
1472 splitview when pad-gaps not enabled by default
1475 <!-- JAL-1797 -->amino acid physicochemical conservation
1479 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1480 article has been read (reopened issue due to
1481 internationalisation problems)
1484 <!-- JAL-1960 -->Only offer PDB structures in structure
1485 viewer based on sequence name, PDB and UniProt
1490 <!-- JAL-1976 -->No progress bar shown during export of
1494 <!-- JAL-2213 -->Structures not always superimposed after
1495 multiple structures are shown for one or more sequences.
1498 <!-- JAL-1370 -->Reference sequence characters should not
1499 be replaced with '.' when 'Show unconserved' format option
1503 <!-- JAL-1823 -->Cannot specify chain code when entering
1504 specific PDB id for sequence
1507 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1508 'Export hidden sequences' is enabled, but 'export hidden
1509 columns' is disabled.
1512 <!--JAL-2026-->Best Quality option in structure chooser
1513 selects lowest rather than highest resolution structures
1517 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1518 to sequence mapping in 'View Mappings' report
1521 <!-- JAL-2284 -->Unable to read old Jalview projects that
1522 contain non-XML data added after Jalvew wrote project.
1525 <!-- JAL-2118 -->Newly created annotation row reorders
1526 after clicking on it to create new annotation for a
1530 <!-- JAL-1980 -->Null Pointer Exception raised when
1531 pressing Add on an orphaned cut'n'paste window.
1533 <!-- may exclude, this is an external service stability issue JAL-1941
1534 -- > RNA 3D structure not added via DSSR service</li> -->
1539 <!-- JAL-2151 -->Incorrect columns are selected when
1540 hidden columns present before start of sequence
1543 <!-- JAL-1986 -->Missing dependencies on applet pages
1547 <!-- JAL-1947 -->Overview pixel size changes when
1548 sequences are hidden in applet
1551 <!-- JAL-1996 -->Updated instructions for applet
1552 deployment on examples pages.
1559 <td width="60" nowrap>
1560 <div align="center">
1561 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1562 <em>16/10/2015</em></strong>
1565 <td><em>General</em>
1567 <li>Time stamps for signed Jalview application and applet
1572 <em>Application</em>
1574 <li>Duplicate group consensus and conservation rows
1575 shown when tree is partitioned</li>
1576 <li>Erratic behaviour when tree partitions made with
1577 multiple cDNA/Protein split views</li>
1583 <td width="60" nowrap>
1584 <div align="center">
1585 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1586 <em>8/10/2015</em></strong>
1589 <td><em>General</em>
1591 <li>Updated Spanish translations of localized text for
1593 </ul> <em>Application</em>
1595 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1596 <li>Signed OSX InstallAnywhere installer<br></li>
1597 <li>Support for per-sequence based annotations in BioJSON</li>
1598 </ul> <em>Applet</em>
1600 <li>Split frame example added to applet examples page</li>
1601 </ul> <em>Build and Deployment</em>
1604 <!-- JAL-1888 -->New ant target for running Jalview's test
1612 <li>Mapping of cDNA to protein in split frames
1613 incorrect when sequence start > 1</li>
1614 <li>Broken images in filter column by annotation dialog
1616 <li>Feature colours not parsed from features file</li>
1617 <li>Exceptions and incomplete link URLs recovered when
1618 loading a features file containing HTML tags in feature
1622 <em>Application</em>
1624 <li>Annotations corrupted after BioJS export and
1626 <li>Incorrect sequence limits after Fetch DB References
1627 with 'trim retrieved sequences'</li>
1628 <li>Incorrect warning about deleting all data when
1629 deleting selected columns</li>
1630 <li>Patch to build system for shipping properly signed
1631 JNLP templates for webstart launch</li>
1632 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1633 unreleased structures for download or viewing</li>
1634 <li>Tab/space/return keystroke operation of EMBL-PDBe
1635 fetcher/viewer dialogs works correctly</li>
1636 <li>Disabled 'minimise' button on Jalview windows
1637 running on OSX to workaround redraw hang bug</li>
1638 <li>Split cDNA/Protein view position and geometry not
1639 recovered from jalview project</li>
1640 <li>Initial enabled/disabled state of annotation menu
1641 sorter 'show autocalculated first/last' corresponds to
1643 <li>Restoring of Clustal, RNA Helices and T-Coffee
1644 color schemes from BioJSON</li>
1648 <li>Reorder sequences mirrored in cDNA/Protein split
1650 <li>Applet with Jmol examples not loading correctly</li>
1656 <td><div align="center">
1657 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1659 <td><em>General</em>
1661 <li>Linked visualisation and analysis of DNA and Protein
1664 <li>Translated cDNA alignments shown as split protein
1665 and DNA alignment views</li>
1666 <li>Codon consensus annotation for linked protein and
1667 cDNA alignment views</li>
1668 <li>Link cDNA or Protein product sequences by loading
1669 them onto Protein or cDNA alignments</li>
1670 <li>Reconstruct linked cDNA alignment from aligned
1671 protein sequences</li>
1674 <li>Jmol integration updated to Jmol v14.2.14</li>
1675 <li>Import and export of Jalview alignment views as <a
1676 href="features/bioJsonFormat.html">BioJSON</a></li>
1677 <li>New alignment annotation file statements for
1678 reference sequences and marking hidden columns</li>
1679 <li>Reference sequence based alignment shading to
1680 highlight variation</li>
1681 <li>Select or hide columns according to alignment
1683 <li>Find option for locating sequences by description</li>
1684 <li>Conserved physicochemical properties shown in amino
1685 acid conservation row</li>
1686 <li>Alignments can be sorted by number of RNA helices</li>
1687 </ul> <em>Application</em>
1689 <li>New cDNA/Protein analysis capabilities
1691 <li>Get Cross-References should open a Split Frame
1692 view with cDNA/Protein</li>
1693 <li>Detect when nucleotide sequences and protein
1694 sequences are placed in the same alignment</li>
1695 <li>Split cDNA/Protein views are saved in Jalview
1700 <li>Use REST API to talk to Chimera</li>
1701 <li>Selected regions in Chimera are highlighted in linked
1702 Jalview windows</li>
1704 <li>VARNA RNA viewer updated to v3.93</li>
1705 <li>VARNA views are saved in Jalview Projects</li>
1706 <li>Pseudoknots displayed as Jalview RNA annotation can
1707 be shown in VARNA</li>
1709 <li>Make groups for selection uses marked columns as well
1710 as the active selected region</li>
1712 <li>Calculate UPGMA and NJ trees using sequence feature
1714 <li>New Export options
1716 <li>New Export Settings dialog to control hidden
1717 region export in flat file generation</li>
1719 <li>Export alignment views for display with the <a
1720 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1722 <li>Export scrollable SVG in HTML page</li>
1723 <li>Optional embedding of BioJSON data when exporting
1724 alignment figures to HTML</li>
1726 <li>3D structure retrieval and display
1728 <li>Free text and structured queries with the PDBe
1730 <li>PDBe Search API based discovery and selection of
1731 PDB structures for a sequence set</li>
1735 <li>JPred4 employed for protein secondary structure
1737 <li>Hide Insertions menu option to hide unaligned columns
1738 for one or a group of sequences</li>
1739 <li>Automatically hide insertions in alignments imported
1740 from the JPred4 web server</li>
1741 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1742 system on OSX<br />LGPL libraries courtesy of <a
1743 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1745 <li>changed 'View nucleotide structure' submenu to 'View
1746 VARNA 2D Structure'</li>
1747 <li>change "View protein structure" menu option to "3D
1750 </ul> <em>Applet</em>
1752 <li>New layout for applet example pages</li>
1753 <li>New parameters to enable SplitFrame view
1754 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1755 <li>New example demonstrating linked viewing of cDNA and
1756 Protein alignments</li>
1757 </ul> <em>Development and deployment</em>
1759 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1760 <li>Include installation type and git revision in build
1761 properties and console log output</li>
1762 <li>Jalview Github organisation, and new github site for
1763 storing BioJsMSA Templates</li>
1764 <li>Jalview's unit tests now managed with TestNG</li>
1767 <!-- <em>General</em>
1769 </ul> --> <!-- issues resolved --> <em>Application</em>
1771 <li>Escape should close any open find dialogs</li>
1772 <li>Typo in select-by-features status report</li>
1773 <li>Consensus RNA secondary secondary structure
1774 predictions are not highlighted in amber</li>
1775 <li>Missing gap character in v2.7 example file means
1776 alignment appears unaligned when pad-gaps is not enabled</li>
1777 <li>First switch to RNA Helices colouring doesn't colour
1778 associated structure views</li>
1779 <li>ID width preference option is greyed out when auto
1780 width checkbox not enabled</li>
1781 <li>Stopped a warning dialog from being shown when
1782 creating user defined colours</li>
1783 <li>'View Mapping' in structure viewer shows sequence
1784 mappings for just that viewer's sequences</li>
1785 <li>Workaround for superposing PDB files containing
1786 multiple models in Chimera</li>
1787 <li>Report sequence position in status bar when hovering
1788 over Jmol structure</li>
1789 <li>Cannot output gaps as '.' symbols with Selection ->
1790 output to text box</li>
1791 <li>Flat file exports of alignments with hidden columns
1792 have incorrect sequence start/end</li>
1793 <li>'Aligning' a second chain to a Chimera structure from
1795 <li>Colour schemes applied to structure viewers don't
1796 work for nucleotide</li>
1797 <li>Loading/cut'n'pasting an empty or invalid file leads
1798 to a grey/invisible alignment window</li>
1799 <li>Exported Jpred annotation from a sequence region
1800 imports to different position</li>
1801 <li>Space at beginning of sequence feature tooltips shown
1802 on some platforms</li>
1803 <li>Chimera viewer 'View | Show Chain' menu is not
1805 <li>'New View' fails with a Null Pointer Exception in
1806 console if Chimera has been opened</li>
1807 <li>Mouseover to Chimera not working</li>
1808 <li>Miscellaneous ENA XML feature qualifiers not
1810 <li>NPE in annotation renderer after 'Extract Scores'</li>
1811 <li>If two structures in one Chimera window, mouseover of
1812 either sequence shows on first structure</li>
1813 <li>'Show annotations' options should not make
1814 non-positional annotations visible</li>
1815 <li>Subsequence secondary structure annotation not shown
1816 in right place after 'view flanking regions'</li>
1817 <li>File Save As type unset when current file format is
1819 <li>Save as '.jar' option removed for saving Jalview
1821 <li>Colour by Sequence colouring in Chimera more
1823 <li>Cannot 'add reference annotation' for a sequence in
1824 several views on same alignment</li>
1825 <li>Cannot show linked products for EMBL / ENA records</li>
1826 <li>Jalview's tooltip wraps long texts containing no
1828 </ul> <em>Applet</em>
1830 <li>Jmol to JalviewLite mouseover/link not working</li>
1831 <li>JalviewLite can't import sequences with ID
1832 descriptions containing angle brackets</li>
1833 </ul> <em>General</em>
1835 <li>Cannot export and reimport RNA secondary structure
1836 via jalview annotation file</li>
1837 <li>Random helix colour palette for colour by annotation
1838 with RNA secondary structure</li>
1839 <li>Mouseover to cDNA from STOP residue in protein
1840 translation doesn't work.</li>
1841 <li>hints when using the select by annotation dialog box</li>
1842 <li>Jmol alignment incorrect if PDB file has alternate CA
1844 <li>FontChooser message dialog appears to hang after
1845 choosing 1pt font</li>
1846 <li>Peptide secondary structure incorrectly imported from
1847 annotation file when annotation display text includes 'e' or
1849 <li>Cannot set colour of new feature type whilst creating
1851 <li>cDNA translation alignment should not be sequence
1852 order dependent</li>
1853 <li>'Show unconserved' doesn't work for lower case
1855 <li>Nucleotide ambiguity codes involving R not recognised</li>
1856 </ul> <em>Deployment and Documentation</em>
1858 <li>Applet example pages appear different to the rest of
1859 www.jalview.org</li>
1860 </ul> <em>Application Known issues</em>
1862 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1863 <li>Misleading message appears after trying to delete
1865 <li>Jalview icon not shown in dock after InstallAnywhere
1866 version launches</li>
1867 <li>Fetching EMBL reference for an RNA sequence results
1868 fails with a sequence mismatch</li>
1869 <li>Corrupted or unreadable alignment display when
1870 scrolling alignment to right</li>
1871 <li>ArrayIndexOutOfBoundsException thrown when remove
1872 empty columns called on alignment with ragged gapped ends</li>
1873 <li>auto calculated alignment annotation rows do not get
1874 placed above or below non-autocalculated rows</li>
1875 <li>Jalview dekstop becomes sluggish at full screen in
1876 ultra-high resolution</li>
1877 <li>Cannot disable consensus calculation independently of
1878 quality and conservation</li>
1879 <li>Mouseover highlighting between cDNA and protein can
1880 become sluggish with more than one splitframe shown</li>
1881 </ul> <em>Applet Known Issues</em>
1883 <li>Core PDB parsing code requires Jmol</li>
1884 <li>Sequence canvas panel goes white when alignment
1885 window is being resized</li>
1891 <td><div align="center">
1892 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1894 <td><em>General</em>
1896 <li>Updated Java code signing certificate donated by
1898 <li>Features and annotation preserved when performing
1899 pairwise alignment</li>
1900 <li>RNA pseudoknot annotation can be
1901 imported/exported/displayed</li>
1902 <li>'colour by annotation' can colour by RNA and
1903 protein secondary structure</li>
1904 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1905 post-hoc with 2.9 release</em>)
1908 </ul> <em>Application</em>
1910 <li>Extract and display secondary structure for sequences
1911 with 3D structures</li>
1912 <li>Support for parsing RNAML</li>
1913 <li>Annotations menu for layout
1915 <li>sort sequence annotation rows by alignment</li>
1916 <li>place sequence annotation above/below alignment
1919 <li>Output in Stockholm format</li>
1920 <li>Internationalisation: improved Spanish (es)
1922 <li>Structure viewer preferences tab</li>
1923 <li>Disorder and Secondary Structure annotation tracks
1924 shared between alignments</li>
1925 <li>UCSF Chimera launch and linked highlighting from
1927 <li>Show/hide all sequence associated annotation rows for
1928 all or current selection</li>
1929 <li>disorder and secondary structure predictions
1930 available as dataset annotation</li>
1931 <li>Per-sequence rna helices colouring</li>
1934 <li>Sequence database accessions imported when fetching
1935 alignments from Rfam</li>
1936 <li>update VARNA version to 3.91</li>
1938 <li>New groovy scripts for exporting aligned positions,
1939 conservation values, and calculating sum of pairs scores.</li>
1940 <li>Command line argument to set default JABAWS server</li>
1941 <li>include installation type in build properties and
1942 console log output</li>
1943 <li>Updated Jalview project format to preserve dataset
1947 <!-- issues resolved --> <em>Application</em>
1949 <li>Distinguish alignment and sequence associated RNA
1950 structure in structure->view->VARNA</li>
1951 <li>Raise dialog box if user deletes all sequences in an
1953 <li>Pressing F1 results in documentation opening twice</li>
1954 <li>Sequence feature tooltip is wrapped</li>
1955 <li>Double click on sequence associated annotation
1956 selects only first column</li>
1957 <li>Redundancy removal doesn't result in unlinked
1958 leaves shown in tree</li>
1959 <li>Undos after several redundancy removals don't undo
1961 <li>Hide sequence doesn't hide associated annotation</li>
1962 <li>User defined colours dialog box too big to fit on
1963 screen and buttons not visible</li>
1964 <li>author list isn't updated if already written to
1965 Jalview properties</li>
1966 <li>Popup menu won't open after retrieving sequence
1968 <li>File open window for associate PDB doesn't open</li>
1969 <li>Left-then-right click on a sequence id opens a
1970 browser search window</li>
1971 <li>Cannot open sequence feature shading/sort popup menu
1972 in feature settings dialog</li>
1973 <li>better tooltip placement for some areas of Jalview
1975 <li>Allow addition of JABAWS Server which doesn't
1976 pass validation</li>
1977 <li>Web services parameters dialog box is too large to
1979 <li>Muscle nucleotide alignment preset obscured by
1981 <li>JABAWS preset submenus don't contain newly
1982 defined user preset</li>
1983 <li>MSA web services warns user if they were launched
1984 with invalid input</li>
1985 <li>Jalview cannot contact DAS Registy when running on
1988 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1989 'Superpose with' submenu not shown when new view
1993 </ul> <!-- <em>Applet</em>
1995 </ul> <em>General</em>
1997 </ul>--> <em>Deployment and Documentation</em>
1999 <li>2G and 1G options in launchApp have no effect on
2000 memory allocation</li>
2001 <li>launchApp service doesn't automatically open
2002 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2004 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2005 InstallAnywhere reports cannot find valid JVM when Java
2006 1.7_055 is available
2008 </ul> <em>Application Known issues</em>
2011 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2012 corrupted or unreadable alignment display when scrolling
2016 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2017 retrieval fails but progress bar continues for DAS retrieval
2018 with large number of ID
2021 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2022 flatfile output of visible region has incorrect sequence
2026 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2027 rna structure consensus doesn't update when secondary
2028 structure tracks are rearranged
2031 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2032 invalid rna structure positional highlighting does not
2033 highlight position of invalid base pairs
2036 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2037 out of memory errors are not raised when saving Jalview
2038 project from alignment window file menu
2041 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2042 Switching to RNA Helices colouring doesn't propagate to
2046 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2047 colour by RNA Helices not enabled when user created
2048 annotation added to alignment
2051 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2052 Jalview icon not shown on dock in Mountain Lion/Webstart
2054 </ul> <em>Applet Known Issues</em>
2057 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2058 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2061 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2062 Jalview and Jmol example not compatible with IE9
2065 <li>Sort by annotation score doesn't reverse order
2071 <td><div align="center">
2072 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2075 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2078 <li>Internationalisation of user interface (usually
2079 called i18n support) and translation for Spanish locale</li>
2080 <li>Define/Undefine group on current selection with
2081 Ctrl-G/Shift Ctrl-G</li>
2082 <li>Improved group creation/removal options in
2083 alignment/sequence Popup menu</li>
2084 <li>Sensible precision for symbol distribution
2085 percentages shown in logo tooltip.</li>
2086 <li>Annotation panel height set according to amount of
2087 annotation when alignment first opened</li>
2088 </ul> <em>Application</em>
2090 <li>Interactive consensus RNA secondary structure
2091 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2092 <li>Select columns containing particular features from
2093 Feature Settings dialog</li>
2094 <li>View all 'representative' PDB structures for selected
2096 <li>Update Jalview project format:
2098 <li>New file extension for Jalview projects '.jvp'</li>
2099 <li>Preserve sequence and annotation dataset (to
2100 store secondary structure annotation,etc)</li>
2101 <li>Per group and alignment annotation and RNA helix
2105 <li>New similarity measures for PCA and Tree calculation
2107 <li>Experimental support for retrieval and viewing of
2108 flanking regions for an alignment</li>
2112 <!-- issues resolved --> <em>Application</em>
2114 <li>logo keeps spinning and status remains at queued or
2115 running after job is cancelled</li>
2116 <li>cannot export features from alignments imported from
2117 Jalview/VAMSAS projects</li>
2118 <li>Buggy slider for web service parameters that take
2120 <li>Newly created RNA secondary structure line doesn't
2121 have 'display all symbols' flag set</li>
2122 <li>T-COFFEE alignment score shading scheme and other
2123 annotation shading not saved in Jalview project</li>
2124 <li>Local file cannot be loaded in freshly downloaded
2126 <li>Jalview icon not shown on dock in Mountain
2128 <li>Load file from desktop file browser fails</li>
2129 <li>Occasional NPE thrown when calculating large trees</li>
2130 <li>Cannot reorder or slide sequences after dragging an
2131 alignment onto desktop</li>
2132 <li>Colour by annotation dialog throws NPE after using
2133 'extract scores' function</li>
2134 <li>Loading/cut'n'pasting an empty file leads to a grey
2135 alignment window</li>
2136 <li>Disorder thresholds rendered incorrectly after
2137 performing IUPred disorder prediction</li>
2138 <li>Multiple group annotated consensus rows shown when
2139 changing 'normalise logo' display setting</li>
2140 <li>Find shows blank dialog after 'finished searching' if
2141 nothing matches query</li>
2142 <li>Null Pointer Exceptions raised when sorting by
2143 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2145 <li>Errors in Jmol console when structures in alignment
2146 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2148 <li>Not all working JABAWS services are shown in
2150 <li>JAVAWS version of Jalview fails to launch with
2151 'invalid literal/length code'</li>
2152 <li>Annotation/RNA Helix colourschemes cannot be applied
2153 to alignment with groups (actually fixed in 2.8.0b1)</li>
2154 <li>RNA Helices and T-Coffee Scores available as default
2157 </ul> <em>Applet</em>
2159 <li>Remove group option is shown even when selection is
2161 <li>Apply to all groups ticked but colourscheme changes
2162 don't affect groups</li>
2163 <li>Documented RNA Helices and T-Coffee Scores as valid
2164 colourscheme name</li>
2165 <li>Annotation labels drawn on sequence IDs when
2166 Annotation panel is not displayed</li>
2167 <li>Increased font size for dropdown menus on OSX and
2168 embedded windows</li>
2169 </ul> <em>Other</em>
2171 <li>Consensus sequence for alignments/groups with a
2172 single sequence were not calculated</li>
2173 <li>annotation files that contain only groups imported as
2174 annotation and junk sequences</li>
2175 <li>Fasta files with sequences containing '*' incorrectly
2176 recognised as PFAM or BLC</li>
2177 <li>conservation/PID slider apply all groups option
2178 doesn't affect background (2.8.0b1)
2180 <li>redundancy highlighting is erratic at 0% and 100%</li>
2181 <li>Remove gapped columns fails for sequences with ragged
2183 <li>AMSA annotation row with leading spaces is not
2184 registered correctly on import</li>
2185 <li>Jalview crashes when selecting PCA analysis for
2186 certain alignments</li>
2187 <li>Opening the colour by annotation dialog for an
2188 existing annotation based 'use original colours'
2189 colourscheme loses original colours setting</li>
2194 <td><div align="center">
2195 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2196 <em>30/1/2014</em></strong>
2200 <li>Trusted certificates for JalviewLite applet and
2201 Jalview Desktop application<br />Certificate was donated by
2202 <a href="https://www.certum.eu">Certum</a> to the Jalview
2203 open source project).
2205 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2206 <li>Output in Stockholm format</li>
2207 <li>Allow import of data from gzipped files</li>
2208 <li>Export/import group and sequence associated line
2209 graph thresholds</li>
2210 <li>Nucleotide substitution matrix that supports RNA and
2211 ambiguity codes</li>
2212 <li>Allow disorder predictions to be made on the current
2213 selection (or visible selection) in the same way that JPred
2215 <li>Groovy scripting for headless Jalview operation</li>
2216 </ul> <em>Other improvements</em>
2218 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2219 <li>COMBINE statement uses current SEQUENCE_REF and
2220 GROUP_REF scope to group annotation rows</li>
2221 <li>Support '' style escaping of quotes in Newick
2223 <li>Group options for JABAWS service by command line name</li>
2224 <li>Empty tooltip shown for JABA service options with a
2225 link but no description</li>
2226 <li>Select primary source when selecting authority in
2227 database fetcher GUI</li>
2228 <li>Add .mfa to FASTA file extensions recognised by
2230 <li>Annotation label tooltip text wrap</li>
2235 <li>Slow scrolling when lots of annotation rows are
2237 <li>Lots of NPE (and slowness) after creating RNA
2238 secondary structure annotation line</li>
2239 <li>Sequence database accessions not imported when
2240 fetching alignments from Rfam</li>
2241 <li>Incorrect SHMR submission for sequences with
2243 <li>View all structures does not always superpose
2245 <li>Option widgets in service parameters not updated to
2246 reflect user or preset settings</li>
2247 <li>Null pointer exceptions for some services without
2248 presets or adjustable parameters</li>
2249 <li>Discover PDB IDs entry in structure menu doesn't
2250 discover PDB xRefs</li>
2251 <li>Exception encountered while trying to retrieve
2252 features with DAS</li>
2253 <li>Lowest value in annotation row isn't coloured
2254 when colour by annotation (per sequence) is coloured</li>
2255 <li>Keyboard mode P jumps to start of gapped region when
2256 residue follows a gap</li>
2257 <li>Jalview appears to hang importing an alignment with
2258 Wrap as default or after enabling Wrap</li>
2259 <li>'Right click to add annotations' message
2260 shown in wrap mode when no annotations present</li>
2261 <li>Disorder predictions fail with NPE if no automatic
2262 annotation already exists on alignment</li>
2263 <li>oninit javascript function should be called after
2264 initialisation completes</li>
2265 <li>Remove redundancy after disorder prediction corrupts
2266 alignment window display</li>
2267 <li>Example annotation file in documentation is invalid</li>
2268 <li>Grouped line graph annotation rows are not exported
2269 to annotation file</li>
2270 <li>Multi-harmony analysis cannot be run when only two
2272 <li>Cannot create multiple groups of line graphs with
2273 several 'combine' statements in annotation file</li>
2274 <li>Pressing return several times causes Number Format
2275 exceptions in keyboard mode</li>
2276 <li>Multi-harmony (SHMMR) method doesn't submit
2277 correct partitions for input data</li>
2278 <li>Translation from DNA to Amino Acids fails</li>
2279 <li>Jalview fail to load newick tree with quoted label</li>
2280 <li>--headless flag isn't understood</li>
2281 <li>ClassCastException when generating EPS in headless
2283 <li>Adjusting sequence-associated shading threshold only
2284 changes one row's threshold</li>
2285 <li>Preferences and Feature settings panel panel
2286 doesn't open</li>
2287 <li>hide consensus histogram also hides conservation and
2288 quality histograms</li>
2293 <td><div align="center">
2294 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2296 <td><em>Application</em>
2298 <li>Support for JABAWS 2.0 Services (AACon alignment
2299 conservation, protein disorder and Clustal Omega)</li>
2300 <li>JABAWS server status indicator in Web Services
2302 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2303 in Jalview alignment window</li>
2304 <li>Updated Jalview build and deploy framework for OSX
2305 mountain lion, windows 7, and 8</li>
2306 <li>Nucleotide substitution matrix for PCA that supports
2307 RNA and ambiguity codes</li>
2309 <li>Improved sequence database retrieval GUI</li>
2310 <li>Support fetching and database reference look up
2311 against multiple DAS sources (Fetch all from in 'fetch db
2313 <li>Jalview project improvements
2315 <li>Store and retrieve the 'belowAlignment'
2316 flag for annotation</li>
2317 <li>calcId attribute to group annotation rows on the
2319 <li>Store AACon calculation settings for a view in
2320 Jalview project</li>
2324 <li>horizontal scrolling gesture support</li>
2325 <li>Visual progress indicator when PCA calculation is
2327 <li>Simpler JABA web services menus</li>
2328 <li>visual indication that web service results are still
2329 being retrieved from server</li>
2330 <li>Serialise the dialogs that are shown when Jalview
2331 starts up for first time</li>
2332 <li>Jalview user agent string for interacting with HTTP
2334 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2336 <li>Examples directory and Groovy library included in
2337 InstallAnywhere distribution</li>
2338 </ul> <em>Applet</em>
2340 <li>RNA alignment and secondary structure annotation
2341 visualization applet example</li>
2342 </ul> <em>General</em>
2344 <li>Normalise option for consensus sequence logo</li>
2345 <li>Reset button in PCA window to return dimensions to
2347 <li>Allow seqspace or Jalview variant of alignment PCA
2349 <li>PCA with either nucleic acid and protein substitution
2351 <li>Allow windows containing HTML reports to be exported
2353 <li>Interactive display and editing of RNA secondary
2354 structure contacts</li>
2355 <li>RNA Helix Alignment Colouring</li>
2356 <li>RNA base pair logo consensus</li>
2357 <li>Parse sequence associated secondary structure
2358 information in Stockholm files</li>
2359 <li>HTML Export database accessions and annotation
2360 information presented in tooltip for sequences</li>
2361 <li>Import secondary structure from LOCARNA clustalw
2362 style RNA alignment files</li>
2363 <li>import and visualise T-COFFEE quality scores for an
2365 <li>'colour by annotation' per sequence option to
2366 shade each sequence according to its associated alignment
2368 <li>New Jalview Logo</li>
2369 </ul> <em>Documentation and Development</em>
2371 <li>documentation for score matrices used in Jalview</li>
2372 <li>New Website!</li>
2374 <td><em>Application</em>
2376 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2377 wsdbfetch REST service</li>
2378 <li>Stop windows being moved outside desktop on OSX</li>
2379 <li>Filetype associations not installed for webstart
2381 <li>Jalview does not always retrieve progress of a JABAWS
2382 job execution in full once it is complete</li>
2383 <li>revise SHMR RSBS definition to ensure alignment is
2384 uploaded via ali_file parameter</li>
2385 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2386 <li>View all structures superposed fails with exception</li>
2387 <li>Jnet job queues forever if a very short sequence is
2388 submitted for prediction</li>
2389 <li>Cut and paste menu not opened when mouse clicked on
2391 <li>Putting fractional value into integer text box in
2392 alignment parameter dialog causes Jalview to hang</li>
2393 <li>Structure view highlighting doesn't work on
2395 <li>View all structures fails with exception shown in
2397 <li>Characters in filename associated with PDBEntry not
2398 escaped in a platform independent way</li>
2399 <li>Jalview desktop fails to launch with exception when
2401 <li>Tree calculation reports 'you must have 2 or more
2402 sequences selected' when selection is empty</li>
2403 <li>Jalview desktop fails to launch with jar signature
2404 failure when java web start temporary file caching is
2406 <li>DAS Sequence retrieval with range qualification
2407 results in sequence xref which includes range qualification</li>
2408 <li>Errors during processing of command line arguments
2409 cause progress bar (JAL-898) to be removed</li>
2410 <li>Replace comma for semi-colon option not disabled for
2411 DAS sources in sequence fetcher</li>
2412 <li>Cannot close news reader when JABAWS server warning
2413 dialog is shown</li>
2414 <li>Option widgets not updated to reflect user settings</li>
2415 <li>Edited sequence not submitted to web service</li>
2416 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2417 <li>InstallAnywhere installer doesn't unpack and run
2418 on OSX Mountain Lion</li>
2419 <li>Annotation panel not given a scroll bar when
2420 sequences with alignment annotation are pasted into the
2422 <li>Sequence associated annotation rows not associated
2423 when loaded from Jalview project</li>
2424 <li>Browser launch fails with NPE on java 1.7</li>
2425 <li>JABAWS alignment marked as finished when job was
2426 cancelled or job failed due to invalid input</li>
2427 <li>NPE with v2.7 example when clicking on Tree
2428 associated with all views</li>
2429 <li>Exceptions when copy/paste sequences with grouped
2430 annotation rows to new window</li>
2431 </ul> <em>Applet</em>
2433 <li>Sequence features are momentarily displayed before
2434 they are hidden using hidefeaturegroups applet parameter</li>
2435 <li>loading features via javascript API automatically
2436 enables feature display</li>
2437 <li>scrollToColumnIn javascript API method doesn't
2439 </ul> <em>General</em>
2441 <li>Redundancy removal fails for rna alignment</li>
2442 <li>PCA calculation fails when sequence has been selected
2443 and then deselected</li>
2444 <li>PCA window shows grey box when first opened on OSX</li>
2445 <li>Letters coloured pink in sequence logo when alignment
2446 coloured with clustalx</li>
2447 <li>Choosing fonts without letter symbols defined causes
2448 exceptions and redraw errors</li>
2449 <li>Initial PCA plot view is not same as manually
2450 reconfigured view</li>
2451 <li>Grouped annotation graph label has incorrect line
2453 <li>Grouped annotation graph label display is corrupted
2454 for lots of labels</li>
2459 <div align="center">
2460 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2463 <td><em>Application</em>
2465 <li>Jalview Desktop News Reader</li>
2466 <li>Tweaked default layout of web services menu</li>
2467 <li>View/alignment association menu to enable user to
2468 easily specify which alignment a multi-structure view takes
2469 its colours/correspondences from</li>
2470 <li>Allow properties file location to be specified as URL</li>
2471 <li>Extend Jalview project to preserve associations
2472 between many alignment views and a single Jmol display</li>
2473 <li>Store annotation row height in Jalview project file</li>
2474 <li>Annotation row column label formatting attributes
2475 stored in project file</li>
2476 <li>Annotation row order for auto-calculated annotation
2477 rows preserved in Jalview project file</li>
2478 <li>Visual progress indication when Jalview state is
2479 saved using Desktop window menu</li>
2480 <li>Visual indication that command line arguments are
2481 still being processed</li>
2482 <li>Groovy script execution from URL</li>
2483 <li>Colour by annotation default min and max colours in
2485 <li>Automatically associate PDB files dragged onto an
2486 alignment with sequences that have high similarity and
2488 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2489 <li>'view structures' option to open many
2490 structures in same window</li>
2491 <li>Sort associated views menu option for tree panel</li>
2492 <li>Group all JABA and non-JABA services for a particular
2493 analysis function in its own submenu</li>
2494 </ul> <em>Applet</em>
2496 <li>Userdefined and autogenerated annotation rows for
2498 <li>Adjustment of alignment annotation pane height</li>
2499 <li>Annotation scrollbar for annotation panel</li>
2500 <li>Drag to reorder annotation rows in annotation panel</li>
2501 <li>'automaticScrolling' parameter</li>
2502 <li>Allow sequences with partial ID string matches to be
2503 annotated from GFF/Jalview features files</li>
2504 <li>Sequence logo annotation row in applet</li>
2505 <li>Absolute paths relative to host server in applet
2506 parameters are treated as such</li>
2507 <li>New in the JalviewLite javascript API:
2509 <li>JalviewLite.js javascript library</li>
2510 <li>Javascript callbacks for
2512 <li>Applet initialisation</li>
2513 <li>Sequence/alignment mouse-overs and selections</li>
2516 <li>scrollTo row and column alignment scrolling
2518 <li>Select sequence/alignment regions from javascript</li>
2519 <li>javascript structure viewer harness to pass
2520 messages between Jmol and Jalview when running as
2521 distinct applets</li>
2522 <li>sortBy method</li>
2523 <li>Set of applet and application examples shipped
2524 with documentation</li>
2525 <li>New example to demonstrate JalviewLite and Jmol
2526 javascript message exchange</li>
2528 </ul> <em>General</em>
2530 <li>Enable Jmol displays to be associated with multiple
2531 multiple alignments</li>
2532 <li>Option to automatically sort alignment with new tree</li>
2533 <li>User configurable link to enable redirects to a
2534 www.Jalview.org mirror</li>
2535 <li>Jmol colours option for Jmol displays</li>
2536 <li>Configurable newline string when writing alignment
2537 and other flat files</li>
2538 <li>Allow alignment annotation description lines to
2539 contain html tags</li>
2540 </ul> <em>Documentation and Development</em>
2542 <li>Add groovy test harness for bulk load testing to
2544 <li>Groovy script to load and align a set of sequences
2545 using a web service before displaying the result in the
2546 Jalview desktop</li>
2547 <li>Restructured javascript and applet api documentation</li>
2548 <li>Ant target to publish example html files with applet
2550 <li>Netbeans project for building Jalview from source</li>
2551 <li>ant task to create online javadoc for Jalview source</li>
2553 <td><em>Application</em>
2555 <li>User defined colourscheme throws exception when
2556 current built in colourscheme is saved as new scheme</li>
2557 <li>AlignFrame->Save in application pops up save
2558 dialog for valid filename/format</li>
2559 <li>Cannot view associated structure for UniProt sequence</li>
2560 <li>PDB file association breaks for UniProt sequence
2562 <li>Associate PDB from file dialog does not tell you
2563 which sequence is to be associated with the file</li>
2564 <li>Find All raises null pointer exception when query
2565 only matches sequence IDs</li>
2566 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2567 <li>Jalview project with Jmol views created with Jalview
2568 2.4 cannot be loaded</li>
2569 <li>Filetype associations not installed for webstart
2571 <li>Two or more chains in a single PDB file associated
2572 with sequences in different alignments do not get coloured
2573 by their associated sequence</li>
2574 <li>Visibility status of autocalculated annotation row
2575 not preserved when project is loaded</li>
2576 <li>Annotation row height and visibility attributes not
2577 stored in Jalview project</li>
2578 <li>Tree bootstraps are not preserved when saved as a
2579 Jalview project</li>
2580 <li>Envision2 workflow tooltips are corrupted</li>
2581 <li>Enabling show group conservation also enables colour
2582 by conservation</li>
2583 <li>Duplicate group associated conservation or consensus
2584 created on new view</li>
2585 <li>Annotation scrollbar not displayed after 'show
2586 all hidden annotation rows' option selected</li>
2587 <li>Alignment quality not updated after alignment
2588 annotation row is hidden then shown</li>
2589 <li>Preserve colouring of structures coloured by
2590 sequences in pre Jalview 2.7 projects</li>
2591 <li>Web service job parameter dialog is not laid out
2593 <li>Web services menu not refreshed after 'reset
2594 services' button is pressed in preferences</li>
2595 <li>Annotation off by one in Jalview v2_3 example project</li>
2596 <li>Structures imported from file and saved in project
2597 get name like jalview_pdb1234.txt when reloaded</li>
2598 <li>Jalview does not always retrieve progress of a JABAWS
2599 job execution in full once it is complete</li>
2600 </ul> <em>Applet</em>
2602 <li>Alignment height set incorrectly when lots of
2603 annotation rows are displayed</li>
2604 <li>Relative URLs in feature HTML text not resolved to
2606 <li>View follows highlighting does not work for positions
2608 <li><= shown as = in tooltip</li>
2609 <li>Export features raises exception when no features
2611 <li>Separator string used for serialising lists of IDs
2612 for javascript api is modified when separator string
2613 provided as parameter</li>
2614 <li>Null pointer exception when selecting tree leaves for
2615 alignment with no existing selection</li>
2616 <li>Relative URLs for datasources assumed to be relative
2617 to applet's codebase</li>
2618 <li>Status bar not updated after finished searching and
2619 search wraps around to first result</li>
2620 <li>StructureSelectionManager instance shared between
2621 several Jalview applets causes race conditions and memory
2623 <li>Hover tooltip and mouseover of position on structure
2624 not sent from Jmol in applet</li>
2625 <li>Certain sequences of javascript method calls to
2626 applet API fatally hang browser</li>
2627 </ul> <em>General</em>
2629 <li>View follows structure mouseover scrolls beyond
2630 position with wrapped view and hidden regions</li>
2631 <li>Find sequence position moves to wrong residue
2632 with/without hidden columns</li>
2633 <li>Sequence length given in alignment properties window
2635 <li>InvalidNumberFormat exceptions thrown when trying to
2636 import PDB like structure files</li>
2637 <li>Positional search results are only highlighted
2638 between user-supplied sequence start/end bounds</li>
2639 <li>End attribute of sequence is not validated</li>
2640 <li>Find dialog only finds first sequence containing a
2641 given sequence position</li>
2642 <li>Sequence numbering not preserved in MSF alignment
2644 <li>Jalview PDB file reader does not extract sequence
2645 from nucleotide chains correctly</li>
2646 <li>Structure colours not updated when tree partition
2647 changed in alignment</li>
2648 <li>Sequence associated secondary structure not correctly
2649 parsed in interleaved stockholm</li>
2650 <li>Colour by annotation dialog does not restore current
2652 <li>Hiding (nearly) all sequences doesn't work
2654 <li>Sequences containing lowercase letters are not
2655 properly associated with their pdb files</li>
2656 </ul> <em>Documentation and Development</em>
2658 <li>schemas/JalviewWsParamSet.xsd corrupted by
2659 ApplyCopyright tool</li>
2664 <div align="center">
2665 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2668 <td><em>Application</em>
2670 <li>New warning dialog when the Jalview Desktop cannot
2671 contact web services</li>
2672 <li>JABA service parameters for a preset are shown in
2673 service job window</li>
2674 <li>JABA Service menu entries reworded</li>
2678 <li>Modeller PIR IO broken - cannot correctly import a
2679 pir file emitted by Jalview</li>
2680 <li>Existing feature settings transferred to new
2681 alignment view created from cut'n'paste</li>
2682 <li>Improved test for mixed amino/nucleotide chains when
2683 parsing PDB files</li>
2684 <li>Consensus and conservation annotation rows
2685 occasionally become blank for all new windows</li>
2686 <li>Exception raised when right clicking above sequences
2687 in wrapped view mode</li>
2688 </ul> <em>Application</em>
2690 <li>multiple multiply aligned structure views cause cpu
2691 usage to hit 100% and computer to hang</li>
2692 <li>Web Service parameter layout breaks for long user
2693 parameter names</li>
2694 <li>Jaba service discovery hangs desktop if Jaba server
2701 <div align="center">
2702 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2705 <td><em>Application</em>
2707 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2708 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2711 <li>Web Services preference tab</li>
2712 <li>Analysis parameters dialog box and user defined
2714 <li>Improved speed and layout of Envision2 service menu</li>
2715 <li>Superpose structures using associated sequence
2717 <li>Export coordinates and projection as CSV from PCA
2719 </ul> <em>Applet</em>
2721 <li>enable javascript: execution by the applet via the
2722 link out mechanism</li>
2723 </ul> <em>Other</em>
2725 <li>Updated the Jmol Jalview interface to work with Jmol
2727 <li>The Jalview Desktop and JalviewLite applet now
2728 require Java 1.5</li>
2729 <li>Allow Jalview feature colour specification for GFF
2730 sequence annotation files</li>
2731 <li>New 'colour by label' keword in Jalview feature file
2732 type colour specification</li>
2733 <li>New Jalview Desktop Groovy API method that allows a
2734 script to check if it being run in an interactive session or
2735 in a batch operation from the Jalview command line</li>
2739 <li>clustalx colourscheme colours Ds preferentially when
2740 both D+E are present in over 50% of the column</li>
2741 </ul> <em>Application</em>
2743 <li>typo in AlignmentFrame->View->Hide->all but
2744 selected Regions menu item</li>
2745 <li>sequence fetcher replaces ',' for ';' when the ',' is
2746 part of a valid accession ID</li>
2747 <li>fatal OOM if object retrieved by sequence fetcher
2748 runs out of memory</li>
2749 <li>unhandled Out of Memory Error when viewing pca
2750 analysis results</li>
2751 <li>InstallAnywhere builds fail to launch on OS X java
2752 10.5 update 4 (due to apple Java 1.6 update)</li>
2753 <li>Installanywhere Jalview silently fails to launch</li>
2754 </ul> <em>Applet</em>
2756 <li>Jalview.getFeatureGroups() raises an
2757 ArrayIndexOutOfBoundsException if no feature groups are
2764 <div align="center">
2765 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2771 <li>Alignment prettyprinter doesn't cope with long
2773 <li>clustalx colourscheme colours Ds preferentially when
2774 both D+E are present in over 50% of the column</li>
2775 <li>nucleic acid structures retrieved from PDB do not
2776 import correctly</li>
2777 <li>More columns get selected than were clicked on when a
2778 number of columns are hidden</li>
2779 <li>annotation label popup menu not providing correct
2780 add/hide/show options when rows are hidden or none are
2782 <li>Stockholm format shown in list of readable formats,
2783 and parser copes better with alignments from RFAM.</li>
2784 <li>CSV output of consensus only includes the percentage
2785 of all symbols if sequence logo display is enabled</li>
2787 </ul> <em>Applet</em>
2789 <li>annotation panel disappears when annotation is
2791 </ul> <em>Application</em>
2793 <li>Alignment view not redrawn properly when new
2794 alignment opened where annotation panel is visible but no
2795 annotations are present on alignment</li>
2796 <li>pasted region containing hidden columns is
2797 incorrectly displayed in new alignment window</li>
2798 <li>Jalview slow to complete operations when stdout is
2799 flooded (fix is to close the Jalview console)</li>
2800 <li>typo in AlignmentFrame->View->Hide->all but
2801 selected Rregions menu item.</li>
2802 <li>inconsistent group submenu and Format submenu entry
2803 'Un' or 'Non'conserved</li>
2804 <li>Sequence feature settings are being shared by
2805 multiple distinct alignments</li>
2806 <li>group annotation not recreated when tree partition is
2808 <li>double click on group annotation to select sequences
2809 does not propagate to associated trees</li>
2810 <li>Mac OSX specific issues:
2812 <li>exception raised when mouse clicked on desktop
2813 window background</li>
2814 <li>Desktop menu placed on menu bar and application
2815 name set correctly</li>
2816 <li>sequence feature settings not wide enough for the
2817 save feature colourscheme button</li>
2826 <div align="center">
2827 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2830 <td><em>New Capabilities</em>
2832 <li>URL links generated from description line for
2833 regular-expression based URL links (applet and application)
2835 <li>Non-positional feature URL links are shown in link
2837 <li>Linked viewing of nucleic acid sequences and
2839 <li>Automatic Scrolling option in View menu to display
2840 the currently highlighted region of an alignment.</li>
2841 <li>Order an alignment by sequence length, or using the
2842 average score or total feature count for each sequence.</li>
2843 <li>Shading features by score or associated description</li>
2844 <li>Subdivide alignment and groups based on identity of
2845 selected subsequence (Make Groups from Selection).</li>
2846 <li>New hide/show options including Shift+Control+H to
2847 hide everything but the currently selected region.</li>
2848 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2849 </ul> <em>Application</em>
2851 <li>Fetch DB References capabilities and UI expanded to
2852 support retrieval from DAS sequence sources</li>
2853 <li>Local DAS Sequence sources can be added via the
2854 command line or via the Add local source dialog box.</li>
2855 <li>DAS Dbref and DbxRef feature types are parsed as
2856 database references and protein_name is parsed as
2857 description line (BioSapiens terms).</li>
2858 <li>Enable or disable non-positional feature and database
2859 references in sequence ID tooltip from View menu in
2861 <!-- <li>New hidden columns and rows and representatives capabilities
2862 in annotations file (in progress - not yet fully implemented)</li> -->
2863 <li>Group-associated consensus, sequence logos and
2864 conservation plots</li>
2865 <li>Symbol distributions for each column can be exported
2866 and visualized as sequence logos</li>
2867 <li>Optionally scale multi-character column labels to fit
2868 within each column of annotation row<!-- todo for applet -->
2870 <li>Optional automatic sort of associated alignment view
2871 when a new tree is opened.</li>
2872 <li>Jalview Java Console</li>
2873 <li>Better placement of desktop window when moving
2874 between different screens.</li>
2875 <li>New preference items for sequence ID tooltip and
2876 consensus annotation</li>
2877 <li>Client to submit sequences and IDs to Envision2
2879 <li><em>Vamsas Capabilities</em>
2881 <li>Improved VAMSAS synchronization (Jalview archive
2882 used to preserve views, structures, and tree display
2884 <li>Import of vamsas documents from disk or URL via
2886 <li>Sharing of selected regions between views and
2887 with other VAMSAS applications (Experimental feature!)</li>
2888 <li>Updated API to VAMSAS version 0.2</li>
2890 </ul> <em>Applet</em>
2892 <li>Middle button resizes annotation row height</li>
2895 <li>sortByTree (true/false) - automatically sort the
2896 associated alignment view by the tree when a new tree is
2898 <li>showTreeBootstraps (true/false) - show or hide
2899 branch bootstraps (default is to show them if available)</li>
2900 <li>showTreeDistances (true/false) - show or hide
2901 branch lengths (default is to show them if available)</li>
2902 <li>showUnlinkedTreeNodes (true/false) - indicate if
2903 unassociated nodes should be highlighted in the tree
2905 <li>heightScale and widthScale (1.0 or more) -
2906 increase the height or width of a cell in the alignment
2907 grid relative to the current font size.</li>
2910 <li>Non-positional features displayed in sequence ID
2912 </ul> <em>Other</em>
2914 <li>Features format: graduated colour definitions and
2915 specification of feature scores</li>
2916 <li>Alignment Annotations format: new keywords for group
2917 associated annotation (GROUP_REF) and annotation row display
2918 properties (ROW_PROPERTIES)</li>
2919 <li>XML formats extended to support graduated feature
2920 colourschemes, group associated annotation, and profile
2921 visualization settings.</li></td>
2924 <li>Source field in GFF files parsed as feature source
2925 rather than description</li>
2926 <li>Non-positional features are now included in sequence
2927 feature and gff files (controlled via non-positional feature
2928 visibility in tooltip).</li>
2929 <li>URL links generated for all feature links (bugfix)</li>
2930 <li>Added URL embedding instructions to features file
2932 <li>Codons containing ambiguous nucleotides translated as
2933 'X' in peptide product</li>
2934 <li>Match case switch in find dialog box works for both
2935 sequence ID and sequence string and query strings do not
2936 have to be in upper case to match case-insensitively.</li>
2937 <li>AMSA files only contain first column of
2938 multi-character column annotation labels</li>
2939 <li>Jalview Annotation File generation/parsing consistent
2940 with documentation (e.g. Stockholm annotation can be
2941 exported and re-imported)</li>
2942 <li>PDB files without embedded PDB IDs given a friendly
2944 <li>Find incrementally searches ID string matches as well
2945 as subsequence matches, and correctly reports total number
2949 <li>Better handling of exceptions during sequence
2951 <li>Dasobert generated non-positional feature URL
2952 link text excludes the start_end suffix</li>
2953 <li>DAS feature and source retrieval buttons disabled
2954 when fetch or registry operations in progress.</li>
2955 <li>PDB files retrieved from URLs are cached properly</li>
2956 <li>Sequence description lines properly shared via
2958 <li>Sequence fetcher fetches multiple records for all
2960 <li>Ensured that command line das feature retrieval
2961 completes before alignment figures are generated.</li>
2962 <li>Reduced time taken when opening file browser for
2964 <li>isAligned check prior to calculating tree, PCA or
2965 submitting an MSA to JNet now excludes hidden sequences.</li>
2966 <li>User defined group colours properly recovered
2967 from Jalview projects.</li>
2976 <div align="center">
2977 <strong>2.4.0.b2</strong><br> 28/10/2009
2982 <li>Experimental support for google analytics usage
2984 <li>Jalview privacy settings (user preferences and docs).</li>
2989 <li>Race condition in applet preventing startup in
2991 <li>Exception when feature created from selection beyond
2992 length of sequence.</li>
2993 <li>Allow synthetic PDB files to be imported gracefully</li>
2994 <li>Sequence associated annotation rows associate with
2995 all sequences with a given id</li>
2996 <li>Find function matches case-insensitively for sequence
2997 ID string searches</li>
2998 <li>Non-standard characters do not cause pairwise
2999 alignment to fail with exception</li>
3000 </ul> <em>Application Issues</em>
3002 <li>Sequences are now validated against EMBL database</li>
3003 <li>Sequence fetcher fetches multiple records for all
3005 </ul> <em>InstallAnywhere Issues</em>
3007 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3008 issue with installAnywhere mechanism)</li>
3009 <li>Command line launching of JARs from InstallAnywhere
3010 version (java class versioning error fixed)</li>
3017 <div align="center">
3018 <strong>2.4</strong><br> 27/8/2008
3021 <td><em>User Interface</em>
3023 <li>Linked highlighting of codon and amino acid from
3024 translation and protein products</li>
3025 <li>Linked highlighting of structure associated with
3026 residue mapping to codon position</li>
3027 <li>Sequence Fetcher provides example accession numbers
3028 and 'clear' button</li>
3029 <li>MemoryMonitor added as an option under Desktop's
3031 <li>Extract score function to parse whitespace separated
3032 numeric data in description line</li>
3033 <li>Column labels in alignment annotation can be centred.</li>
3034 <li>Tooltip for sequence associated annotation give name
3036 </ul> <em>Web Services and URL fetching</em>
3038 <li>JPred3 web service</li>
3039 <li>Prototype sequence search client (no public services
3041 <li>Fetch either seed alignment or full alignment from
3043 <li>URL Links created for matching database cross
3044 references as well as sequence ID</li>
3045 <li>URL Links can be created using regular-expressions</li>
3046 </ul> <em>Sequence Database Connectivity</em>
3048 <li>Retrieval of cross-referenced sequences from other
3050 <li>Generalised database reference retrieval and
3051 validation to all fetchable databases</li>
3052 <li>Fetch sequences from DAS sources supporting the
3053 sequence command</li>
3054 </ul> <em>Import and Export</em>
3055 <li>export annotation rows as CSV for spreadsheet import</li>
3056 <li>Jalview projects record alignment dataset associations,
3057 EMBL products, and cDNA sequence mappings</li>
3058 <li>Sequence Group colour can be specified in Annotation
3060 <li>Ad-hoc colouring of group in Annotation File using RGB
3061 triplet as name of colourscheme</li>
3062 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3064 <li>treenode binding for VAMSAS tree exchange</li>
3065 <li>local editing and update of sequences in VAMSAS
3066 alignments (experimental)</li>
3067 <li>Create new or select existing session to join</li>
3068 <li>load and save of vamsas documents</li>
3069 </ul> <em>Application command line</em>
3071 <li>-tree parameter to open trees (introduced for passing
3073 <li>-fetchfrom command line argument to specify nicknames
3074 of DAS servers to query for alignment features</li>
3075 <li>-dasserver command line argument to add new servers
3076 that are also automatically queried for features</li>
3077 <li>-groovy command line argument executes a given groovy
3078 script after all input data has been loaded and parsed</li>
3079 </ul> <em>Applet-Application data exchange</em>
3081 <li>Trees passed as applet parameters can be passed to
3082 application (when using "View in full
3083 application")</li>
3084 </ul> <em>Applet Parameters</em>
3086 <li>feature group display control parameter</li>
3087 <li>debug parameter</li>
3088 <li>showbutton parameter</li>
3089 </ul> <em>Applet API methods</em>
3091 <li>newView public method</li>
3092 <li>Window (current view) specific get/set public methods</li>
3093 <li>Feature display control methods</li>
3094 <li>get list of currently selected sequences</li>
3095 </ul> <em>New Jalview distribution features</em>
3097 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3098 <li>RELEASE file gives build properties for the latest
3099 Jalview release.</li>
3100 <li>Java 1.1 Applet build made easier and donotobfuscate
3101 property controls execution of obfuscator</li>
3102 <li>Build target for generating source distribution</li>
3103 <li>Debug flag for javacc</li>
3104 <li>.jalview_properties file is documented (slightly) in
3105 jalview.bin.Cache</li>
3106 <li>Continuous Build Integration for stable and
3107 development version of Application, Applet and source
3112 <li>selected region output includes visible annotations
3113 (for certain formats)</li>
3114 <li>edit label/displaychar contains existing label/char
3116 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3117 <li>shorter peptide product names from EMBL records</li>
3118 <li>Newick string generator makes compact representations</li>
3119 <li>bootstrap values parsed correctly for tree files with
3121 <li>pathological filechooser bug avoided by not allowing
3122 filenames containing a ':'</li>
3123 <li>Fixed exception when parsing GFF files containing
3124 global sequence features</li>
3125 <li>Alignment datasets are finalized only when number of
3126 references from alignment sequences goes to zero</li>
3127 <li>Close of tree branch colour box without colour
3128 selection causes cascading exceptions</li>
3129 <li>occasional negative imgwidth exceptions</li>
3130 <li>better reporting of non-fatal warnings to user when
3131 file parsing fails.</li>
3132 <li>Save works when Jalview project is default format</li>
3133 <li>Save as dialog opened if current alignment format is
3134 not a valid output format</li>
3135 <li>UniProt canonical names introduced for both das and
3137 <li>Histidine should be midblue (not pink!) in Zappo</li>
3138 <li>error messages passed up and output when data read
3140 <li>edit undo recovers previous dataset sequence when
3141 sequence is edited</li>
3142 <li>allow PDB files without pdb ID HEADER lines (like
3143 those generated by MODELLER) to be read in properly</li>
3144 <li>allow reading of JPred concise files as a normal
3146 <li>Stockholm annotation parsing and alignment properties
3147 import fixed for PFAM records</li>
3148 <li>Structure view windows have correct name in Desktop
3150 <li>annotation consisting of sequence associated scores
3151 can be read and written correctly to annotation file</li>
3152 <li>Aligned cDNA translation to aligned peptide works
3154 <li>Fixed display of hidden sequence markers and
3155 non-italic font for representatives in Applet</li>
3156 <li>Applet Menus are always embedded in applet window on
3158 <li>Newly shown features appear at top of stack (in
3160 <li>Annotations added via parameter not drawn properly
3161 due to null pointer exceptions</li>
3162 <li>Secondary structure lines are drawn starting from
3163 first column of alignment</li>
3164 <li>UniProt XML import updated for new schema release in
3166 <li>Sequence feature to sequence ID match for Features
3167 file is case-insensitive</li>
3168 <li>Sequence features read from Features file appended to
3169 all sequences with matching IDs</li>
3170 <li>PDB structure coloured correctly for associated views
3171 containing a sub-sequence</li>
3172 <li>PDB files can be retrieved by applet from Jar files</li>
3173 <li>feature and annotation file applet parameters
3174 referring to different directories are retrieved correctly</li>
3175 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3176 <li>Fixed application hang whilst waiting for
3177 splash-screen version check to complete</li>
3178 <li>Applet properly URLencodes input parameter values
3179 when passing them to the launchApp service</li>
3180 <li>display name and local features preserved in results
3181 retrieved from web service</li>
3182 <li>Visual delay indication for sequence retrieval and
3183 sequence fetcher initialisation</li>
3184 <li>updated Application to use DAS 1.53e version of
3185 dasobert DAS client</li>
3186 <li>Re-instated Full AMSA support and .amsa file
3188 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3196 <div align="center">
3197 <strong>2.3</strong><br> 9/5/07
3202 <li>Jmol 11.0.2 integration</li>
3203 <li>PDB views stored in Jalview XML files</li>
3204 <li>Slide sequences</li>
3205 <li>Edit sequence in place</li>
3206 <li>EMBL CDS features</li>
3207 <li>DAS Feature mapping</li>
3208 <li>Feature ordering</li>
3209 <li>Alignment Properties</li>
3210 <li>Annotation Scores</li>
3211 <li>Sort by scores</li>
3212 <li>Feature/annotation editing in applet</li>
3217 <li>Headless state operation in 2.2.1</li>
3218 <li>Incorrect and unstable DNA pairwise alignment</li>
3219 <li>Cut and paste of sequences with annotation</li>
3220 <li>Feature group display state in XML</li>
3221 <li>Feature ordering in XML</li>
3222 <li>blc file iteration selection using filename # suffix</li>
3223 <li>Stockholm alignment properties</li>
3224 <li>Stockhom alignment secondary structure annotation</li>
3225 <li>2.2.1 applet had no feature transparency</li>
3226 <li>Number pad keys can be used in cursor mode</li>
3227 <li>Structure Viewer mirror image resolved</li>
3234 <div align="center">
3235 <strong>2.2.1</strong><br> 12/2/07
3240 <li>Non standard characters can be read and displayed
3241 <li>Annotations/Features can be imported/exported to the
3243 <li>Applet allows editing of sequence/annotation/group
3244 name & description
3245 <li>Preference setting to display sequence name in
3247 <li>Annotation file format extended to allow
3248 Sequence_groups to be defined
3249 <li>Default opening of alignment overview panel can be
3250 specified in preferences
3251 <li>PDB residue numbering annotation added to associated
3257 <li>Applet crash under certain Linux OS with Java 1.6
3259 <li>Annotation file export / import bugs fixed
3260 <li>PNG / EPS image output bugs fixed
3266 <div align="center">
3267 <strong>2.2</strong><br> 27/11/06
3272 <li>Multiple views on alignment
3273 <li>Sequence feature editing
3274 <li>"Reload" alignment
3275 <li>"Save" to current filename
3276 <li>Background dependent text colour
3277 <li>Right align sequence ids
3278 <li>User-defined lower case residue colours
3281 <li>Menu item accelerator keys
3282 <li>Control-V pastes to current alignment
3283 <li>Cancel button for DAS Feature Fetching
3284 <li>PCA and PDB Viewers zoom via mouse roller
3285 <li>User-defined sub-tree colours and sub-tree selection
3287 <li>'New Window' button on the 'Output to Text box'
3292 <li>New memory efficient Undo/Redo System
3293 <li>Optimised symbol lookups and conservation/consensus
3295 <li>Region Conservation/Consensus recalculated after
3297 <li>Fixed Remove Empty Columns Bug (empty columns at end
3299 <li>Slowed DAS Feature Fetching for increased robustness.
3301 <li>Made angle brackets in ASCII feature descriptions
3303 <li>Re-instated Zoom function for PCA
3304 <li>Sequence descriptions conserved in web service
3306 <li>UniProt ID discoverer uses any word separated by
3308 <li>WsDbFetch query/result association resolved
3309 <li>Tree leaf to sequence mapping improved
3310 <li>Smooth fonts switch moved to FontChooser dialog box.
3317 <div align="center">
3318 <strong>2.1.1</strong><br> 12/9/06
3323 <li>Copy consensus sequence to clipboard</li>
3328 <li>Image output - rightmost residues are rendered if
3329 sequence id panel has been resized</li>
3330 <li>Image output - all offscreen group boundaries are
3332 <li>Annotation files with sequence references - all
3333 elements in file are relative to sequence position</li>
3334 <li>Mac Applet users can use Alt key for group editing</li>
3340 <div align="center">
3341 <strong>2.1</strong><br> 22/8/06
3346 <li>MAFFT Multiple Alignment in default Web Service list</li>
3347 <li>DAS Feature fetching</li>
3348 <li>Hide sequences and columns</li>
3349 <li>Export Annotations and Features</li>
3350 <li>GFF file reading / writing</li>
3351 <li>Associate structures with sequences from local PDB
3353 <li>Add sequences to exisiting alignment</li>
3354 <li>Recently opened files / URL lists</li>
3355 <li>Applet can launch the full application</li>
3356 <li>Applet has transparency for features (Java 1.2
3358 <li>Applet has user defined colours parameter</li>
3359 <li>Applet can load sequences from parameter
3360 "sequence<em>x</em>"
3366 <li>Redundancy Panel reinstalled in the Applet</li>
3367 <li>Monospaced font - EPS / rescaling bug fixed</li>
3368 <li>Annotation files with sequence references bug fixed</li>
3374 <div align="center">
3375 <strong>2.08.1</strong><br> 2/5/06
3380 <li>Change case of selected region from Popup menu</li>
3381 <li>Choose to match case when searching</li>
3382 <li>Middle mouse button and mouse movement can compress /
3383 expand the visible width and height of the alignment</li>
3388 <li>Annotation Panel displays complete JNet results</li>
3394 <div align="center">
3395 <strong>2.08b</strong><br> 18/4/06
3401 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3402 <li>Righthand label on wrapped alignments shows correct
3409 <div align="center">
3410 <strong>2.08</strong><br> 10/4/06
3415 <li>Editing can be locked to the selection area</li>
3416 <li>Keyboard editing</li>
3417 <li>Create sequence features from searches</li>
3418 <li>Precalculated annotations can be loaded onto
3420 <li>Features file allows grouping of features</li>
3421 <li>Annotation Colouring scheme added</li>
3422 <li>Smooth fonts off by default - Faster rendering</li>
3423 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3428 <li>Drag & Drop fixed on Linux</li>
3429 <li>Jalview Archive file faster to load/save, sequence
3430 descriptions saved.</li>
3436 <div align="center">
3437 <strong>2.07</strong><br> 12/12/05
3442 <li>PDB Structure Viewer enhanced</li>
3443 <li>Sequence Feature retrieval and display enhanced</li>
3444 <li>Choose to output sequence start-end after sequence
3445 name for file output</li>
3446 <li>Sequence Fetcher WSDBFetch@EBI</li>
3447 <li>Applet can read feature files, PDB files and can be
3448 used for HTML form input</li>
3453 <li>HTML output writes groups and features</li>
3454 <li>Group editing is Control and mouse click</li>
3455 <li>File IO bugs</li>
3461 <div align="center">
3462 <strong>2.06</strong><br> 28/9/05
3467 <li>View annotations in wrapped mode</li>
3468 <li>More options for PCA viewer</li>
3473 <li>GUI bugs resolved</li>
3474 <li>Runs with -nodisplay from command line</li>
3480 <div align="center">
3481 <strong>2.05b</strong><br> 15/9/05
3486 <li>Choose EPS export as lineart or text</li>
3487 <li>Jar files are executable</li>
3488 <li>Can read in Uracil - maps to unknown residue</li>
3493 <li>Known OutOfMemory errors give warning message</li>
3494 <li>Overview window calculated more efficiently</li>
3495 <li>Several GUI bugs resolved</li>
3501 <div align="center">
3502 <strong>2.05</strong><br> 30/8/05
3507 <li>Edit and annotate in "Wrapped" view</li>
3512 <li>Several GUI bugs resolved</li>
3518 <div align="center">
3519 <strong>2.04</strong><br> 24/8/05
3524 <li>Hold down mouse wheel & scroll to change font
3530 <li>Improved JPred client reliability</li>
3531 <li>Improved loading of Jalview files</li>
3537 <div align="center">
3538 <strong>2.03</strong><br> 18/8/05
3543 <li>Set Proxy server name and port in preferences</li>
3544 <li>Multiple URL links from sequence ids</li>
3545 <li>User Defined Colours can have a scheme name and added
3547 <li>Choose to ignore gaps in consensus calculation</li>
3548 <li>Unix users can set default web browser</li>
3549 <li>Runs without GUI for batch processing</li>
3550 <li>Dynamically generated Web Service Menus</li>
3555 <li>InstallAnywhere download for Sparc Solaris</li>
3561 <div align="center">
3562 <strong>2.02</strong><br> 18/7/05
3568 <li>Copy & Paste order of sequences maintains
3569 alignment order.</li>
3575 <div align="center">
3576 <strong>2.01</strong><br> 12/7/05
3581 <li>Use delete key for deleting selection.</li>
3582 <li>Use Mouse wheel to scroll sequences.</li>
3583 <li>Help file updated to describe how to add alignment
3585 <li>Version and build date written to build properties
3587 <li>InstallAnywhere installation will check for updates
3588 at launch of Jalview.</li>
3593 <li>Delete gaps bug fixed.</li>
3594 <li>FileChooser sorts columns.</li>
3595 <li>Can remove groups one by one.</li>
3596 <li>Filechooser icons installed.</li>
3597 <li>Finder ignores return character when searching.
3598 Return key will initiate a search.<br>
3605 <div align="center">
3606 <strong>2.0</strong><br> 20/6/05
3611 <li>New codebase</li>