3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
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27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.3">2.10.3</a><br />
74 <em>14/11/2017</em></strong>
77 <td><div align="left">
81 <!-- JAL-2446 -->Faster and more efficient management and
82 rendering of sequence features
85 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
86 429 rate limit request hander
89 <!-- JAL-2773 -->Structure views don't get updated unless
90 their colours have changed
92 <li><!-- JAL-2495 -->All linked sequences are highlighted for a structure mousover (Jmol) or selection (Chimera)</li>
93 <li><!-- JAL-2790 -->'Cancel' button in progress bar for JABAWS AACon, RNAAliFold and Disorder prediction jobs
96 <li><!-- JAL-2617 -->Stop codons are excluded in CDS/Protein view from Ensembl locus cross-references</li>
97 <li><!-- JAL-2685 -->Start/End limits are shown in Pairwise Alignment report</li>
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>
123 <li><!-- JAL-2777 -->Structures with whitespace chainCode cannot be viewed in Chimera</li>
124 <li><!-- JAL-2728 -->Protein annotation panel too high in CDS/Protein view
126 <li><!-- JAL-2757 -->Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs
128 <li><!-- JAL-2253 -->Slow EnsemblGenome ID lookup</li>
129 <li><!-- JAL-2529 -->Revised Ensembl REST API CDNA query</li>
130 <li><!-- JAL-2739 -->Hidden column marker in last column not rendered when switching back from Wrapped to normal view</li>
131 <li><!-- JAL-2768 -->Annotation display corrupted when scrolling right in unwapped alignment view</li>
132 <li><!-- JAL-2542 -->Existing features on subsequence incorrectly relocated when full sequence retrieved from database</li>
133 <li><!-- JAL-2733 -->Last reported memory still shown when Desktop->Show Memory is unticked (OSX only)</li>
134 <li><!-- JAL-2658 -->Amend Features dialog doesn't allow features of same type and group to be selected for amending</li>
135 <li><!-- JAL-2524 -->Jalview becomes sluggish in wide alignments when hidden columns are present</li>
136 <li><!-- JAL-2392 -->Jalview freezes when loading and displaying several structures</li>
137 <li><!-- JAL-2732 -->Black outlines left after resizing or moving a window</li>
138 <li><!-- JAL-1900,JAL-1625 -->Unable to minimise windows within the Jalview desktop on OSX</li>
139 <li><!-- JAL-2667 -->Mouse wheel doesn't scroll vertically when in wrapped alignment mode</li>
140 <li><!-- JAL-2636 -->Scale mark not shown when close to right hand end of alignment</li>
141 <li><!-- JAL-2684 -->Pairwise alignment only aligns selected regions of each selected sequence</li>
142 <li><!-- JAL-2973 -->Alignment ruler height set incorrectly after canceling the Alignment Window's Font dialog</li>
143 <li><!-- JAL-2036 -->Show cross-references not enabled after restoring project until a new view is created</li>
144 <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>
145 <li><!-- JAL-2775 -->Overview redraws whole window when box position is adjusted</li>
146 <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 <strong><em>Applet</em></strong><br/>
150 <li><!-- JAL-2687 -->Concurrent modification exception when closing alignment panel</li>
152 <strong><em>BioJSON</em></strong><br/>
155 <!-- JAL-2546 -->BioJSON export does not preserve non-positional features
158 <strong>Known Java 9 Issues</strong>
160 <li><!-- JAL-2902 -->Groovy Console very slow to open and is
161 not responsive when entering characters (Webstart, Java 9.01,
165 <strong>New Known Issues</strong>
167 <li><!-- JAL- --></li>
173 <td width="60" nowrap>
175 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
176 <em>2/10/2017</em></strong>
179 <td><div align="left">
180 <em>New features in Jalview Desktop</em>
183 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
185 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
189 <td><div align="left">
193 <td width="60" nowrap>
195 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
196 <em>7/9/2017</em></strong>
199 <td><div align="left">
203 <!-- JAL-2588 -->Show gaps in overview window by colouring
204 in grey (sequences used to be coloured grey, and gaps were
208 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
212 <!-- JAL-2587 -->Overview updates immediately on increase
213 in size and progress bar shown as higher resolution
214 overview is recalculated
219 <td><div align="left">
223 <!-- JAL-2664 -->Overview window redraws every hidden
224 column region row by row
227 <!-- JAL-2681 -->duplicate protein sequences shown after
228 retrieving Ensembl crossrefs for sequences from Uniprot
231 <!-- JAL-2603 -->Overview window throws NPE if show boxes
232 format setting is unticked
235 <!-- JAL-2610 -->Groups are coloured wrongly in overview
236 if group has show boxes format setting unticked
239 <!-- JAL-2672,JAL-2665 -->Redraw problems when
240 autoscrolling whilst dragging current selection group to
241 include sequences and columns not currently displayed
244 <!-- JAL-2691 -->Not all chains are mapped when multimeric
245 assemblies are imported via CIF file
248 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
249 displayed when threshold or conservation colouring is also
253 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
257 <!-- JAL-2673 -->Jalview continues to scroll after
258 dragging a selected region off the visible region of the
262 <!-- JAL-2724 -->Cannot apply annotation based
263 colourscheme to all groups in a view
266 <!-- JAL-2511 -->IDs don't line up with sequences
267 initially after font size change using the Font chooser or
274 <td width="60" nowrap>
276 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
279 <td><div align="left">
280 <em>Calculations</em>
284 <!-- JAL-1933 -->Occupancy annotation row shows number of
285 ungapped positions in each column of the alignment.
288 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
289 a calculation dialog box
292 <!-- JAL-2379 -->Revised implementation of PCA for speed
293 and memory efficiency (~30x faster)
296 <!-- JAL-2403 -->Revised implementation of sequence
297 similarity scores as used by Tree, PCA, Shading Consensus
298 and other calculations
301 <!-- JAL-2416 -->Score matrices are stored as resource
302 files within the Jalview codebase
305 <!-- JAL-2500 -->Trees computed on Sequence Feature
306 Similarity may have different topology due to increased
313 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
314 model for alignments and groups
317 <!-- JAL-384 -->Custom shading schemes created via groovy
324 <!-- JAL-2526 -->Efficiency improvements for interacting
325 with alignment and overview windows
328 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
332 <!-- JAL-2388 -->Hidden columns and sequences can be
336 <!-- JAL-2611 -->Click-drag in visible area allows fine
337 adjustment of visible position
341 <em>Data import/export</em>
344 <!-- JAL-2535 -->Posterior probability annotation from
345 Stockholm files imported as sequence associated annotation
348 <!-- JAL-2507 -->More robust per-sequence positional
349 annotation input/output via stockholm flatfile
352 <!-- JAL-2533 -->Sequence names don't include file
353 extension when importing structure files without embedded
354 names or PDB accessions
357 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
358 format sequence substitution matrices
361 <em>User Interface</em>
364 <!-- JAL-2447 --> Experimental Features Checkbox in
365 Desktop's Tools menu to hide or show untested features in
369 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
370 via Overview or sequence motif search operations
373 <!-- JAL-2547 -->Amend sequence features dialog box can be
374 opened by double clicking gaps within sequence feature
378 <!-- JAL-1476 -->Status bar message shown when not enough
379 aligned positions were available to create a 3D structure
383 <em>3D Structure</em>
386 <!-- JAL-2430 -->Hidden regions in alignment views are not
387 coloured in linked structure views
390 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
391 file-based command exchange
394 <!-- JAL-2375 -->Structure chooser automatically shows
395 Cached Structures rather than querying the PDBe if
396 structures are already available for sequences
399 <!-- JAL-2520 -->Structures imported via URL are cached in
400 the Jalview project rather than downloaded again when the
404 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
405 to transfer Chimera's structure attributes as Jalview
406 features, and vice-versa (<strong>Experimental
410 <em>Web Services</em>
413 <!-- JAL-2549 -->Updated JABAWS client to v2.2
416 <!-- JAL-2335 -->Filter non-standard amino acids and
417 nucleotides when submitting to AACon and other MSA
421 <!-- JAL-2316, -->URLs for viewing database
422 cross-references provided by identifiers.org and the
430 <!-- JAL-2344 -->FileFormatI interface for describing and
431 identifying file formats (instead of String constants)
434 <!-- JAL-2228 -->FeatureCounter script refactored for
435 efficiency when counting all displayed features (not
436 backwards compatible with 2.10.1)
439 <em>Example files</em>
442 <!-- JAL-2631 -->Graduated feature colour style example
443 included in the example feature file
446 <em>Documentation</em>
449 <!-- JAL-2339 -->Release notes reformatted for readability
450 with the built-in Java help viewer
453 <!-- JAL-1644 -->Find documentation updated with 'search
454 sequence description' option
460 <!-- JAL-2485, -->External service integration tests for
461 Uniprot REST Free Text Search Client
464 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
467 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
472 <td><div align="left">
473 <em>Calculations</em>
476 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
477 matrix - C->R should be '-3'<br />Old matrix restored
478 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
480 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
481 Jalview's treatment of gaps in PCA and substitution matrix
482 based Tree calculations.<br /> <br />In earlier versions
483 of Jalview, gaps matching gaps were penalised, and gaps
484 matching non-gaps penalised even more. In the PCA
485 calculation, gaps were actually treated as non-gaps - so
486 different costs were applied, which meant Jalview's PCAs
487 were different to those produced by SeqSpace.<br />Jalview
488 now treats gaps in the same way as SeqSpace (ie it scores
489 them as 0). <br /> <br />Enter the following in the
490 Groovy console to restore pre-2.10.2 behaviour:<br />
491 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
492 // for 2.10.1 mode <br />
493 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
494 // to restore 2.10.2 mode <br /> <br /> <em>Note:
495 these settings will affect all subsequent tree and PCA
496 calculations (not recommended)</em></li>
498 <!-- JAL-2424 -->Fixed off-by-one bug that affected
499 scaling of branch lengths for trees computed using
500 Sequence Feature Similarity.
503 <!-- JAL-2377 -->PCA calculation could hang when
504 generating output report when working with highly
508 <!-- JAL-2544 --> Sort by features includes features to
509 right of selected region when gaps present on right-hand
513 <em>User Interface</em>
516 <!-- JAL-2346 -->Reopening Colour by annotation dialog
517 doesn't reselect a specific sequence's associated
518 annotation after it was used for colouring a view
521 <!-- JAL-2419 -->Current selection lost if popup menu
522 opened on a region of alignment without groups
525 <!-- JAL-2374 -->Popup menu not always shown for regions
526 of an alignment with overlapping groups
529 <!-- JAL-2310 -->Finder double counts if both a sequence's
530 name and description match
533 <!-- JAL-2370 -->Hiding column selection containing two
534 hidden regions results in incorrect hidden regions
537 <!-- JAL-2386 -->'Apply to all groups' setting when
538 changing colour does not apply Conservation slider value
542 <!-- JAL-2373 -->Percentage identity and conservation menu
543 items do not show a tick or allow shading to be disabled
546 <!-- JAL-2385 -->Conservation shading or PID threshold
547 lost when base colourscheme changed if slider not visible
550 <!-- JAL-2547 -->Sequence features shown in tooltip for
551 gaps before start of features
554 <!-- JAL-2623 -->Graduated feature colour threshold not
555 restored to UI when feature colour is edited
558 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
559 a time when scrolling vertically in wrapped mode.
562 <!-- JAL-2630 -->Structure and alignment overview update
563 as graduate feature colour settings are modified via the
567 <!-- JAL-2034 -->Overview window doesn't always update
568 when a group defined on the alignment is resized
571 <!-- JAL-2605 -->Mouseovers on left/right scale region in
572 wrapped view result in positional status updates
576 <!-- JAL-2563 -->Status bar doesn't show position for
577 ambiguous amino acid and nucleotide symbols
580 <!-- JAL-2602 -->Copy consensus sequence failed if
581 alignment included gapped columns
584 <!-- JAL-2473 -->Minimum size set for Jalview windows so
585 widgets don't permanently disappear
588 <!-- JAL-2503 -->Cannot select or filter quantitative
589 annotation that are shown only as column labels (e.g.
590 T-Coffee column reliability scores)
593 <!-- JAL-2594 -->Exception thrown if trying to create a
594 sequence feature on gaps only
597 <!-- JAL-2504 -->Features created with 'New feature'
598 button from a Find inherit previously defined feature type
599 rather than the Find query string
602 <!-- JAL-2423 -->incorrect title in output window when
603 exporting tree calculated in Jalview
606 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
607 and then revealing them reorders sequences on the
611 <!-- JAL-964 -->Group panel in sequence feature settings
612 doesn't update to reflect available set of groups after
613 interactively adding or modifying features
616 <!-- JAL-2225 -->Sequence Database chooser unusable on
620 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
621 only excluded gaps in current sequence and ignored
628 <!-- JAL-2421 -->Overview window visible region moves
629 erratically when hidden rows or columns are present
632 <!-- JAL-2362 -->Per-residue colourschemes applied via the
633 Structure Viewer's colour menu don't correspond to
637 <!-- JAL-2405 -->Protein specific colours only offered in
638 colour and group colour menu for protein alignments
641 <!-- JAL-2385 -->Colour threshold slider doesn't update to
642 reflect currently selected view or group's shading
646 <!-- JAL-2624 -->Feature colour thresholds not respected
647 when rendered on overview and structures when opacity at
651 <!-- JAL-2589 -->User defined gap colour not shown in
652 overview when features overlaid on alignment
655 <em>Data import/export</em>
658 <!-- JAL-2576 -->Very large alignments take a long time to
662 <!-- JAL-2507 -->Per-sequence RNA secondary structures
663 added after a sequence was imported are not written to
667 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
668 when importing RNA secondary structure via Stockholm
671 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
672 not shown in correct direction for simple pseudoknots
675 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
676 with lightGray or darkGray via features file (but can
680 <!-- JAL-2383 -->Above PID colour threshold not recovered
681 when alignment view imported from project
684 <!-- JAL-2520,JAL-2465 -->No mappings generated between
685 structure and sequences extracted from structure files
686 imported via URL and viewed in Jmol
689 <!-- JAL-2520 -->Structures loaded via URL are saved in
690 Jalview Projects rather than fetched via URL again when
691 the project is loaded and the structure viewed
694 <em>Web Services</em>
697 <!-- JAL-2519 -->EnsemblGenomes example failing after
698 release of Ensembl v.88
701 <!-- JAL-2366 -->Proxy server address and port always
702 appear enabled in Preferences->Connections
705 <!-- JAL-2461 -->DAS registry not found exceptions
706 removed from console output
709 <!-- JAL-2582 -->Cannot retrieve protein products from
710 Ensembl by Peptide ID
713 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
714 created from SIFTs, and spurious 'Couldn't open structure
715 in Chimera' errors raised after April 2017 update (problem
716 due to 'null' string rather than empty string used for
717 residues with no corresponding PDB mapping).
720 <em>Application UI</em>
723 <!-- JAL-2361 -->User Defined Colours not added to Colour
727 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
728 case' residues (button in colourscheme editor debugged and
729 new documentation and tooltips added)
732 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
733 doesn't restore group-specific text colour thresholds
736 <!-- JAL-2243 -->Feature settings panel does not update as
737 new features are added to alignment
740 <!-- JAL-2532 -->Cancel in feature settings reverts
741 changes to feature colours via the Amend features dialog
744 <!-- JAL-2506 -->Null pointer exception when attempting to
745 edit graduated feature colour via amend features dialog
749 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
750 selection menu changes colours of alignment views
753 <!-- JAL-2426 -->Spurious exceptions in console raised
754 from alignment calculation workers after alignment has
758 <!-- JAL-1608 -->Typo in selection popup menu - Create
759 groups now 'Create Group'
762 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
763 Create/Undefine group doesn't always work
766 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
767 shown again after pressing 'Cancel'
770 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
771 adjusts start position in wrap mode
774 <!-- JAL-2563 -->Status bar doesn't show positions for
775 ambiguous amino acids
778 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
779 CDS/Protein view after CDS sequences added for aligned
783 <!-- JAL-2592 -->User defined colourschemes called 'User
784 Defined' don't appear in Colours menu
790 <!-- JAL-2468 -->Switching between Nucleotide and Protein
791 score models doesn't always result in an updated PCA plot
794 <!-- JAL-2442 -->Features not rendered as transparent on
795 overview or linked structure view
798 <!-- JAL-2372 -->Colour group by conservation doesn't
802 <!-- JAL-2517 -->Hitting Cancel after applying
803 user-defined colourscheme doesn't restore original
810 <!-- JAL-2314 -->Unit test failure:
811 jalview.ws.jabaws.RNAStructExportImport setup fails
814 <!-- JAL-2307 -->Unit test failure:
815 jalview.ws.sifts.SiftsClientTest due to compatibility
816 problems with deep array comparison equality asserts in
817 successive versions of TestNG
820 <!-- JAL-2479 -->Relocated StructureChooserTest and
821 ParameterUtilsTest Unit tests to Network suite
824 <em>New Known Issues</em>
827 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
828 phase after a sequence motif find operation
831 <!-- JAL-2550 -->Importing annotation file with rows
832 containing just upper and lower case letters are
833 interpreted as WUSS RNA secondary structure symbols
836 <!-- JAL-2590 -->Cannot load and display Newick trees
837 reliably from eggnog Ortholog database
840 <!-- JAL-2468 -->Status bar shows 'Marked x columns
841 containing features of type Highlight' when 'B' is pressed
842 to mark columns containing highlighted regions.
845 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
846 doesn't always add secondary structure annotation.
851 <td width="60" nowrap>
853 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
856 <td><div align="left">
860 <!-- JAL-98 -->Improved memory usage: sparse arrays used
861 for all consensus calculations
864 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
867 <li>Updated Jalview's Certum code signing certificate
873 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
874 set of database cross-references, sorted alphabetically
877 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
878 from database cross references. Users with custom links
879 will receive a <a href="webServices/urllinks.html#warning">warning
880 dialog</a> asking them to update their preferences.
883 <!-- JAL-2287-->Cancel button and escape listener on
884 dialog warning user about disconnecting Jalview from a
888 <!-- JAL-2320-->Jalview's Chimera control window closes if
889 the Chimera it is connected to is shut down
892 <!-- JAL-1738-->New keystroke (B) and Select highlighted
893 columns menu item to mark columns containing highlighted
894 regions (e.g. from structure selections or results of a
898 <!-- JAL-2284-->Command line option for batch-generation
899 of HTML pages rendering alignment data with the BioJS
909 <!-- JAL-2286 -->Columns with more than one modal residue
910 are not coloured or thresholded according to percent
911 identity (first observed in Jalview 2.8.2)
914 <!-- JAL-2301 -->Threonine incorrectly reported as not
918 <!-- JAL-2318 -->Updates to documentation pages (above PID
919 threshold, amino acid properties)
922 <!-- JAL-2292 -->Lower case residues in sequences are not
923 reported as mapped to residues in a structure file in the
927 <!--JAL-2324 -->Identical features with non-numeric scores
928 could be added multiple times to a sequence
931 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
932 bond features shown as two highlighted residues rather
933 than a range in linked structure views, and treated
934 correctly when selecting and computing trees from features
937 <!-- JAL-2281-->Custom URL links for database
938 cross-references are matched to database name regardless
946 <!-- JAL-2282-->Custom URL links for specific database
947 names without regular expressions also offer links from
951 <!-- JAL-2315-->Removing a single configured link in the
952 URL links pane in Connections preferences doesn't actually
953 update Jalview configuration
956 <!-- JAL-2272-->CTRL-Click on a selected region to open
957 the alignment area popup menu doesn't work on El-Capitan
960 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
961 files with similarly named sequences if dropped onto the
965 <!-- JAL-2312 -->Additional mappings are shown for PDB
966 entries where more chains exist in the PDB accession than
967 are reported in the SIFTS file
970 <!-- JAL-2317-->Certain structures do not get mapped to
971 the structure view when displayed with Chimera
974 <!-- JAL-2317-->No chains shown in the Chimera view
975 panel's View->Show Chains submenu
978 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
979 work for wrapped alignment views
982 <!--JAL-2197 -->Rename UI components for running JPred
983 predictions from 'JNet' to 'JPred'
986 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
987 corrupted when annotation panel vertical scroll is not at
991 <!--JAL-2332 -->Attempting to view structure for Hen
992 lysozyme results in a PDB Client error dialog box
995 <!-- JAL-2319 -->Structure View's mapping report switched
996 ranges for PDB and sequence for SIFTS
999 SIFTS 'Not_Observed' residues mapped to non-existant
1003 <!-- <em>New Known Issues</em>
1010 <td width="60" nowrap>
1011 <div align="center">
1012 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1013 <em>25/10/2016</em></strong>
1016 <td><em>Application</em>
1018 <li>3D Structure chooser opens with 'Cached structures'
1019 view if structures already loaded</li>
1020 <li>Progress bar reports models as they are loaded to
1021 structure views</li>
1027 <li>Colour by conservation always enabled and no tick
1028 shown in menu when BLOSUM or PID shading applied</li>
1029 <li>FER1_ARATH and FER2_ARATH labels were switched in
1030 example sequences/projects/trees</li>
1032 <em>Application</em>
1034 <li>Jalview projects with views of local PDB structure
1035 files saved on Windows cannot be opened on OSX</li>
1036 <li>Multiple structure views can be opened and superposed
1037 without timeout for structures with multiple models or
1038 multiple sequences in alignment</li>
1039 <li>Cannot import or associated local PDB files without a
1040 PDB ID HEADER line</li>
1041 <li>RMSD is not output in Jmol console when superposition
1043 <li>Drag and drop of URL from Browser fails for Linux and
1044 OSX versions earlier than El Capitan</li>
1045 <li>ENA client ignores invalid content from ENA server</li>
1046 <li>Exceptions are not raised in console when ENA client
1047 attempts to fetch non-existent IDs via Fetch DB Refs UI
1049 <li>Exceptions are not raised in console when a new view
1050 is created on the alignment</li>
1051 <li>OSX right-click fixed for group selections: CMD-click
1052 to insert/remove gaps in groups and CTRL-click to open group
1055 <em>Build and deployment</em>
1057 <li>URL link checker now copes with multi-line anchor
1060 <em>New Known Issues</em>
1062 <li>Drag and drop from URL links in browsers do not work
1069 <td width="60" nowrap>
1070 <div align="center">
1071 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1074 <td><em>General</em>
1077 <!-- JAL-2124 -->Updated Spanish translations.
1080 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1081 for importing structure data to Jalview. Enables mmCIF and
1085 <!-- JAL-192 --->Alignment ruler shows positions relative to
1089 <!-- JAL-2202 -->Position/residue shown in status bar when
1090 mousing over sequence associated annotation
1093 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1097 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1098 '()', canonical '[]' and invalid '{}' base pair populations
1102 <!-- JAL-2092 -->Feature settings popup menu options for
1103 showing or hiding columns containing a feature
1106 <!-- JAL-1557 -->Edit selected group by double clicking on
1107 group and sequence associated annotation labels
1110 <!-- JAL-2236 -->Sequence name added to annotation label in
1111 select/hide columns by annotation and colour by annotation
1115 </ul> <em>Application</em>
1118 <!-- JAL-2050-->Automatically hide introns when opening a
1119 gene/transcript view
1122 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1126 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1127 structure mappings with the EMBL-EBI PDBe SIFTS database
1130 <!-- JAL-2079 -->Updated download sites used for Rfam and
1131 Pfam sources to xfam.org
1134 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1137 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1138 over sequences in Jalview
1141 <!-- JAL-2027-->Support for reverse-complement coding
1142 regions in ENA and EMBL
1145 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1146 for record retrieval via ENA rest API
1149 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1153 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1154 groovy script execution
1157 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1158 alignment window's Calculate menu
1161 <!-- JAL-1812 -->Allow groovy scripts that call
1162 Jalview.getAlignFrames() to run in headless mode
1165 <!-- JAL-2068 -->Support for creating new alignment
1166 calculation workers from groovy scripts
1169 <!-- JAL-1369 --->Store/restore reference sequence in
1173 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1174 associations are now saved/restored from project
1177 <!-- JAL-1993 -->Database selection dialog always shown
1178 before sequence fetcher is opened
1181 <!-- JAL-2183 -->Double click on an entry in Jalview's
1182 database chooser opens a sequence fetcher
1185 <!-- JAL-1563 -->Free-text search client for UniProt using
1186 the UniProt REST API
1189 <!-- JAL-2168 -->-nonews command line parameter to prevent
1190 the news reader opening
1193 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1194 querying stored in preferences
1197 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1201 <!-- JAL-1977-->Tooltips shown on database chooser
1204 <!-- JAL-391 -->Reverse complement function in calculate
1205 menu for nucleotide sequences
1208 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1209 and feature counts preserves alignment ordering (and
1210 debugged for complex feature sets).
1213 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1214 viewing structures with Jalview 2.10
1217 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1218 genome, transcript CCDS and gene ids via the Ensembl and
1219 Ensembl Genomes REST API
1222 <!-- JAL-2049 -->Protein sequence variant annotation
1223 computed for 'sequence_variant' annotation on CDS regions
1227 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1231 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1232 Ref Fetcher fails to match, or otherwise updates sequence
1233 data from external database records.
1236 <!-- JAL-2154 -->Revised Jalview Project format for
1237 efficient recovery of sequence coding and alignment
1238 annotation relationships.
1240 </ul> <!-- <em>Applet</em>
1251 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1255 <!-- JAL-2018-->Export features in Jalview format (again)
1256 includes graduated colourschemes
1259 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1260 working with big alignments and lots of hidden columns
1263 <!-- JAL-2053-->Hidden column markers not always rendered
1264 at right of alignment window
1267 <!-- JAL-2067 -->Tidied up links in help file table of
1271 <!-- JAL-2072 -->Feature based tree calculation not shown
1275 <!-- JAL-2075 -->Hidden columns ignored during feature
1276 based tree calculation
1279 <!-- JAL-2065 -->Alignment view stops updating when show
1280 unconserved enabled for group on alignment
1283 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1287 <!-- JAL-2146 -->Alignment column in status incorrectly
1288 shown as "Sequence position" when mousing over
1292 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1293 hidden columns present
1296 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1297 user created annotation added to alignment
1300 <!-- JAL-1841 -->RNA Structure consensus only computed for
1301 '()' base pair annotation
1304 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1305 in zero scores for all base pairs in RNA Structure
1309 <!-- JAL-2174-->Extend selection with columns containing
1313 <!-- JAL-2275 -->Pfam format writer puts extra space at
1314 beginning of sequence
1317 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1321 <!-- JAL-2238 -->Cannot create groups on an alignment from
1322 from a tree when t-coffee scores are shown
1325 <!-- JAL-1836,1967 -->Cannot import and view PDB
1326 structures with chains containing negative resnums (4q4h)
1329 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1333 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1334 to Clustal, PIR and PileUp output
1337 <!-- JAL-2008 -->Reordering sequence features that are
1338 not visible causes alignment window to repaint
1341 <!-- JAL-2006 -->Threshold sliders don't work in
1342 graduated colour and colour by annotation row for e-value
1343 scores associated with features and annotation rows
1346 <!-- JAL-1797 -->amino acid physicochemical conservation
1347 calculation should be case independent
1350 <!-- JAL-2173 -->Remove annotation also updates hidden
1354 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1355 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1356 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1359 <!-- JAL-2065 -->Null pointer exceptions and redraw
1360 problems when reference sequence defined and 'show
1361 non-conserved' enabled
1364 <!-- JAL-1306 -->Quality and Conservation are now shown on
1365 load even when Consensus calculation is disabled
1368 <!-- JAL-1932 -->Remove right on penultimate column of
1369 alignment does nothing
1372 <em>Application</em>
1375 <!-- JAL-1552-->URLs and links can't be imported by
1376 drag'n'drop on OSX when launched via webstart (note - not
1377 yet fixed for El Capitan)
1380 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1381 output when running on non-gb/us i18n platforms
1384 <!-- JAL-1944 -->Error thrown when exporting a view with
1385 hidden sequences as flat-file alignment
1388 <!-- JAL-2030-->InstallAnywhere distribution fails when
1392 <!-- JAL-2080-->Jalview very slow to launch via webstart
1393 (also hotfix for 2.9.0b2)
1396 <!-- JAL-2085 -->Cannot save project when view has a
1397 reference sequence defined
1400 <!-- JAL-1011 -->Columns are suddenly selected in other
1401 alignments and views when revealing hidden columns
1404 <!-- JAL-1989 -->Hide columns not mirrored in complement
1405 view in a cDNA/Protein splitframe
1408 <!-- JAL-1369 -->Cannot save/restore representative
1409 sequence from project when only one sequence is
1413 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1414 in Structure Chooser
1417 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1418 structure consensus didn't refresh annotation panel
1421 <!-- JAL-1962 -->View mapping in structure view shows
1422 mappings between sequence and all chains in a PDB file
1425 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1426 dialogs format columns correctly, don't display array
1427 data, sort columns according to type
1430 <!-- JAL-1975 -->Export complete shown after destination
1431 file chooser is cancelled during an image export
1434 <!-- JAL-2025 -->Error when querying PDB Service with
1435 sequence name containing special characters
1438 <!-- JAL-2024 -->Manual PDB structure querying should be
1442 <!-- JAL-2104 -->Large tooltips with broken HTML
1443 formatting don't wrap
1446 <!-- JAL-1128 -->Figures exported from wrapped view are
1447 truncated so L looks like I in consensus annotation
1450 <!-- JAL-2003 -->Export features should only export the
1451 currently displayed features for the current selection or
1455 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1456 after fetching cross-references, and restoring from
1460 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1461 followed in the structure viewer
1464 <!-- JAL-2163 -->Titles for individual alignments in
1465 splitframe not restored from project
1468 <!-- JAL-2145 -->missing autocalculated annotation at
1469 trailing end of protein alignment in transcript/product
1470 splitview when pad-gaps not enabled by default
1473 <!-- JAL-1797 -->amino acid physicochemical conservation
1477 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1478 article has been read (reopened issue due to
1479 internationalisation problems)
1482 <!-- JAL-1960 -->Only offer PDB structures in structure
1483 viewer based on sequence name, PDB and UniProt
1488 <!-- JAL-1976 -->No progress bar shown during export of
1492 <!-- JAL-2213 -->Structures not always superimposed after
1493 multiple structures are shown for one or more sequences.
1496 <!-- JAL-1370 -->Reference sequence characters should not
1497 be replaced with '.' when 'Show unconserved' format option
1501 <!-- JAL-1823 -->Cannot specify chain code when entering
1502 specific PDB id for sequence
1505 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1506 'Export hidden sequences' is enabled, but 'export hidden
1507 columns' is disabled.
1510 <!--JAL-2026-->Best Quality option in structure chooser
1511 selects lowest rather than highest resolution structures
1515 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1516 to sequence mapping in 'View Mappings' report
1519 <!-- JAL-2284 -->Unable to read old Jalview projects that
1520 contain non-XML data added after Jalvew wrote project.
1523 <!-- JAL-2118 -->Newly created annotation row reorders
1524 after clicking on it to create new annotation for a
1528 <!-- JAL-1980 -->Null Pointer Exception raised when
1529 pressing Add on an orphaned cut'n'paste window.
1531 <!-- may exclude, this is an external service stability issue JAL-1941
1532 -- > RNA 3D structure not added via DSSR service</li> -->
1537 <!-- JAL-2151 -->Incorrect columns are selected when
1538 hidden columns present before start of sequence
1541 <!-- JAL-1986 -->Missing dependencies on applet pages
1545 <!-- JAL-1947 -->Overview pixel size changes when
1546 sequences are hidden in applet
1549 <!-- JAL-1996 -->Updated instructions for applet
1550 deployment on examples pages.
1557 <td width="60" nowrap>
1558 <div align="center">
1559 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1560 <em>16/10/2015</em></strong>
1563 <td><em>General</em>
1565 <li>Time stamps for signed Jalview application and applet
1570 <em>Application</em>
1572 <li>Duplicate group consensus and conservation rows
1573 shown when tree is partitioned</li>
1574 <li>Erratic behaviour when tree partitions made with
1575 multiple cDNA/Protein split views</li>
1581 <td width="60" nowrap>
1582 <div align="center">
1583 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1584 <em>8/10/2015</em></strong>
1587 <td><em>General</em>
1589 <li>Updated Spanish translations of localized text for
1591 </ul> <em>Application</em>
1593 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1594 <li>Signed OSX InstallAnywhere installer<br></li>
1595 <li>Support for per-sequence based annotations in BioJSON</li>
1596 </ul> <em>Applet</em>
1598 <li>Split frame example added to applet examples page</li>
1599 </ul> <em>Build and Deployment</em>
1602 <!-- JAL-1888 -->New ant target for running Jalview's test
1610 <li>Mapping of cDNA to protein in split frames
1611 incorrect when sequence start > 1</li>
1612 <li>Broken images in filter column by annotation dialog
1614 <li>Feature colours not parsed from features file</li>
1615 <li>Exceptions and incomplete link URLs recovered when
1616 loading a features file containing HTML tags in feature
1620 <em>Application</em>
1622 <li>Annotations corrupted after BioJS export and
1624 <li>Incorrect sequence limits after Fetch DB References
1625 with 'trim retrieved sequences'</li>
1626 <li>Incorrect warning about deleting all data when
1627 deleting selected columns</li>
1628 <li>Patch to build system for shipping properly signed
1629 JNLP templates for webstart launch</li>
1630 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1631 unreleased structures for download or viewing</li>
1632 <li>Tab/space/return keystroke operation of EMBL-PDBe
1633 fetcher/viewer dialogs works correctly</li>
1634 <li>Disabled 'minimise' button on Jalview windows
1635 running on OSX to workaround redraw hang bug</li>
1636 <li>Split cDNA/Protein view position and geometry not
1637 recovered from jalview project</li>
1638 <li>Initial enabled/disabled state of annotation menu
1639 sorter 'show autocalculated first/last' corresponds to
1641 <li>Restoring of Clustal, RNA Helices and T-Coffee
1642 color schemes from BioJSON</li>
1646 <li>Reorder sequences mirrored in cDNA/Protein split
1648 <li>Applet with Jmol examples not loading correctly</li>
1654 <td><div align="center">
1655 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1657 <td><em>General</em>
1659 <li>Linked visualisation and analysis of DNA and Protein
1662 <li>Translated cDNA alignments shown as split protein
1663 and DNA alignment views</li>
1664 <li>Codon consensus annotation for linked protein and
1665 cDNA alignment views</li>
1666 <li>Link cDNA or Protein product sequences by loading
1667 them onto Protein or cDNA alignments</li>
1668 <li>Reconstruct linked cDNA alignment from aligned
1669 protein sequences</li>
1672 <li>Jmol integration updated to Jmol v14.2.14</li>
1673 <li>Import and export of Jalview alignment views as <a
1674 href="features/bioJsonFormat.html">BioJSON</a></li>
1675 <li>New alignment annotation file statements for
1676 reference sequences and marking hidden columns</li>
1677 <li>Reference sequence based alignment shading to
1678 highlight variation</li>
1679 <li>Select or hide columns according to alignment
1681 <li>Find option for locating sequences by description</li>
1682 <li>Conserved physicochemical properties shown in amino
1683 acid conservation row</li>
1684 <li>Alignments can be sorted by number of RNA helices</li>
1685 </ul> <em>Application</em>
1687 <li>New cDNA/Protein analysis capabilities
1689 <li>Get Cross-References should open a Split Frame
1690 view with cDNA/Protein</li>
1691 <li>Detect when nucleotide sequences and protein
1692 sequences are placed in the same alignment</li>
1693 <li>Split cDNA/Protein views are saved in Jalview
1698 <li>Use REST API to talk to Chimera</li>
1699 <li>Selected regions in Chimera are highlighted in linked
1700 Jalview windows</li>
1702 <li>VARNA RNA viewer updated to v3.93</li>
1703 <li>VARNA views are saved in Jalview Projects</li>
1704 <li>Pseudoknots displayed as Jalview RNA annotation can
1705 be shown in VARNA</li>
1707 <li>Make groups for selection uses marked columns as well
1708 as the active selected region</li>
1710 <li>Calculate UPGMA and NJ trees using sequence feature
1712 <li>New Export options
1714 <li>New Export Settings dialog to control hidden
1715 region export in flat file generation</li>
1717 <li>Export alignment views for display with the <a
1718 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1720 <li>Export scrollable SVG in HTML page</li>
1721 <li>Optional embedding of BioJSON data when exporting
1722 alignment figures to HTML</li>
1724 <li>3D structure retrieval and display
1726 <li>Free text and structured queries with the PDBe
1728 <li>PDBe Search API based discovery and selection of
1729 PDB structures for a sequence set</li>
1733 <li>JPred4 employed for protein secondary structure
1735 <li>Hide Insertions menu option to hide unaligned columns
1736 for one or a group of sequences</li>
1737 <li>Automatically hide insertions in alignments imported
1738 from the JPred4 web server</li>
1739 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1740 system on OSX<br />LGPL libraries courtesy of <a
1741 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1743 <li>changed 'View nucleotide structure' submenu to 'View
1744 VARNA 2D Structure'</li>
1745 <li>change "View protein structure" menu option to "3D
1748 </ul> <em>Applet</em>
1750 <li>New layout for applet example pages</li>
1751 <li>New parameters to enable SplitFrame view
1752 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1753 <li>New example demonstrating linked viewing of cDNA and
1754 Protein alignments</li>
1755 </ul> <em>Development and deployment</em>
1757 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1758 <li>Include installation type and git revision in build
1759 properties and console log output</li>
1760 <li>Jalview Github organisation, and new github site for
1761 storing BioJsMSA Templates</li>
1762 <li>Jalview's unit tests now managed with TestNG</li>
1765 <!-- <em>General</em>
1767 </ul> --> <!-- issues resolved --> <em>Application</em>
1769 <li>Escape should close any open find dialogs</li>
1770 <li>Typo in select-by-features status report</li>
1771 <li>Consensus RNA secondary secondary structure
1772 predictions are not highlighted in amber</li>
1773 <li>Missing gap character in v2.7 example file means
1774 alignment appears unaligned when pad-gaps is not enabled</li>
1775 <li>First switch to RNA Helices colouring doesn't colour
1776 associated structure views</li>
1777 <li>ID width preference option is greyed out when auto
1778 width checkbox not enabled</li>
1779 <li>Stopped a warning dialog from being shown when
1780 creating user defined colours</li>
1781 <li>'View Mapping' in structure viewer shows sequence
1782 mappings for just that viewer's sequences</li>
1783 <li>Workaround for superposing PDB files containing
1784 multiple models in Chimera</li>
1785 <li>Report sequence position in status bar when hovering
1786 over Jmol structure</li>
1787 <li>Cannot output gaps as '.' symbols with Selection ->
1788 output to text box</li>
1789 <li>Flat file exports of alignments with hidden columns
1790 have incorrect sequence start/end</li>
1791 <li>'Aligning' a second chain to a Chimera structure from
1793 <li>Colour schemes applied to structure viewers don't
1794 work for nucleotide</li>
1795 <li>Loading/cut'n'pasting an empty or invalid file leads
1796 to a grey/invisible alignment window</li>
1797 <li>Exported Jpred annotation from a sequence region
1798 imports to different position</li>
1799 <li>Space at beginning of sequence feature tooltips shown
1800 on some platforms</li>
1801 <li>Chimera viewer 'View | Show Chain' menu is not
1803 <li>'New View' fails with a Null Pointer Exception in
1804 console if Chimera has been opened</li>
1805 <li>Mouseover to Chimera not working</li>
1806 <li>Miscellaneous ENA XML feature qualifiers not
1808 <li>NPE in annotation renderer after 'Extract Scores'</li>
1809 <li>If two structures in one Chimera window, mouseover of
1810 either sequence shows on first structure</li>
1811 <li>'Show annotations' options should not make
1812 non-positional annotations visible</li>
1813 <li>Subsequence secondary structure annotation not shown
1814 in right place after 'view flanking regions'</li>
1815 <li>File Save As type unset when current file format is
1817 <li>Save as '.jar' option removed for saving Jalview
1819 <li>Colour by Sequence colouring in Chimera more
1821 <li>Cannot 'add reference annotation' for a sequence in
1822 several views on same alignment</li>
1823 <li>Cannot show linked products for EMBL / ENA records</li>
1824 <li>Jalview's tooltip wraps long texts containing no
1826 </ul> <em>Applet</em>
1828 <li>Jmol to JalviewLite mouseover/link not working</li>
1829 <li>JalviewLite can't import sequences with ID
1830 descriptions containing angle brackets</li>
1831 </ul> <em>General</em>
1833 <li>Cannot export and reimport RNA secondary structure
1834 via jalview annotation file</li>
1835 <li>Random helix colour palette for colour by annotation
1836 with RNA secondary structure</li>
1837 <li>Mouseover to cDNA from STOP residue in protein
1838 translation doesn't work.</li>
1839 <li>hints when using the select by annotation dialog box</li>
1840 <li>Jmol alignment incorrect if PDB file has alternate CA
1842 <li>FontChooser message dialog appears to hang after
1843 choosing 1pt font</li>
1844 <li>Peptide secondary structure incorrectly imported from
1845 annotation file when annotation display text includes 'e' or
1847 <li>Cannot set colour of new feature type whilst creating
1849 <li>cDNA translation alignment should not be sequence
1850 order dependent</li>
1851 <li>'Show unconserved' doesn't work for lower case
1853 <li>Nucleotide ambiguity codes involving R not recognised</li>
1854 </ul> <em>Deployment and Documentation</em>
1856 <li>Applet example pages appear different to the rest of
1857 www.jalview.org</li>
1858 </ul> <em>Application Known issues</em>
1860 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1861 <li>Misleading message appears after trying to delete
1863 <li>Jalview icon not shown in dock after InstallAnywhere
1864 version launches</li>
1865 <li>Fetching EMBL reference for an RNA sequence results
1866 fails with a sequence mismatch</li>
1867 <li>Corrupted or unreadable alignment display when
1868 scrolling alignment to right</li>
1869 <li>ArrayIndexOutOfBoundsException thrown when remove
1870 empty columns called on alignment with ragged gapped ends</li>
1871 <li>auto calculated alignment annotation rows do not get
1872 placed above or below non-autocalculated rows</li>
1873 <li>Jalview dekstop becomes sluggish at full screen in
1874 ultra-high resolution</li>
1875 <li>Cannot disable consensus calculation independently of
1876 quality and conservation</li>
1877 <li>Mouseover highlighting between cDNA and protein can
1878 become sluggish with more than one splitframe shown</li>
1879 </ul> <em>Applet Known Issues</em>
1881 <li>Core PDB parsing code requires Jmol</li>
1882 <li>Sequence canvas panel goes white when alignment
1883 window is being resized</li>
1889 <td><div align="center">
1890 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1892 <td><em>General</em>
1894 <li>Updated Java code signing certificate donated by
1896 <li>Features and annotation preserved when performing
1897 pairwise alignment</li>
1898 <li>RNA pseudoknot annotation can be
1899 imported/exported/displayed</li>
1900 <li>'colour by annotation' can colour by RNA and
1901 protein secondary structure</li>
1902 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1903 post-hoc with 2.9 release</em>)
1906 </ul> <em>Application</em>
1908 <li>Extract and display secondary structure for sequences
1909 with 3D structures</li>
1910 <li>Support for parsing RNAML</li>
1911 <li>Annotations menu for layout
1913 <li>sort sequence annotation rows by alignment</li>
1914 <li>place sequence annotation above/below alignment
1917 <li>Output in Stockholm format</li>
1918 <li>Internationalisation: improved Spanish (es)
1920 <li>Structure viewer preferences tab</li>
1921 <li>Disorder and Secondary Structure annotation tracks
1922 shared between alignments</li>
1923 <li>UCSF Chimera launch and linked highlighting from
1925 <li>Show/hide all sequence associated annotation rows for
1926 all or current selection</li>
1927 <li>disorder and secondary structure predictions
1928 available as dataset annotation</li>
1929 <li>Per-sequence rna helices colouring</li>
1932 <li>Sequence database accessions imported when fetching
1933 alignments from Rfam</li>
1934 <li>update VARNA version to 3.91</li>
1936 <li>New groovy scripts for exporting aligned positions,
1937 conservation values, and calculating sum of pairs scores.</li>
1938 <li>Command line argument to set default JABAWS server</li>
1939 <li>include installation type in build properties and
1940 console log output</li>
1941 <li>Updated Jalview project format to preserve dataset
1945 <!-- issues resolved --> <em>Application</em>
1947 <li>Distinguish alignment and sequence associated RNA
1948 structure in structure->view->VARNA</li>
1949 <li>Raise dialog box if user deletes all sequences in an
1951 <li>Pressing F1 results in documentation opening twice</li>
1952 <li>Sequence feature tooltip is wrapped</li>
1953 <li>Double click on sequence associated annotation
1954 selects only first column</li>
1955 <li>Redundancy removal doesn't result in unlinked
1956 leaves shown in tree</li>
1957 <li>Undos after several redundancy removals don't undo
1959 <li>Hide sequence doesn't hide associated annotation</li>
1960 <li>User defined colours dialog box too big to fit on
1961 screen and buttons not visible</li>
1962 <li>author list isn't updated if already written to
1963 Jalview properties</li>
1964 <li>Popup menu won't open after retrieving sequence
1966 <li>File open window for associate PDB doesn't open</li>
1967 <li>Left-then-right click on a sequence id opens a
1968 browser search window</li>
1969 <li>Cannot open sequence feature shading/sort popup menu
1970 in feature settings dialog</li>
1971 <li>better tooltip placement for some areas of Jalview
1973 <li>Allow addition of JABAWS Server which doesn't
1974 pass validation</li>
1975 <li>Web services parameters dialog box is too large to
1977 <li>Muscle nucleotide alignment preset obscured by
1979 <li>JABAWS preset submenus don't contain newly
1980 defined user preset</li>
1981 <li>MSA web services warns user if they were launched
1982 with invalid input</li>
1983 <li>Jalview cannot contact DAS Registy when running on
1986 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1987 'Superpose with' submenu not shown when new view
1991 </ul> <!-- <em>Applet</em>
1993 </ul> <em>General</em>
1995 </ul>--> <em>Deployment and Documentation</em>
1997 <li>2G and 1G options in launchApp have no effect on
1998 memory allocation</li>
1999 <li>launchApp service doesn't automatically open
2000 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2002 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2003 InstallAnywhere reports cannot find valid JVM when Java
2004 1.7_055 is available
2006 </ul> <em>Application Known issues</em>
2009 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2010 corrupted or unreadable alignment display when scrolling
2014 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2015 retrieval fails but progress bar continues for DAS retrieval
2016 with large number of ID
2019 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2020 flatfile output of visible region has incorrect sequence
2024 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2025 rna structure consensus doesn't update when secondary
2026 structure tracks are rearranged
2029 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2030 invalid rna structure positional highlighting does not
2031 highlight position of invalid base pairs
2034 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2035 out of memory errors are not raised when saving Jalview
2036 project from alignment window file menu
2039 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2040 Switching to RNA Helices colouring doesn't propagate to
2044 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2045 colour by RNA Helices not enabled when user created
2046 annotation added to alignment
2049 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2050 Jalview icon not shown on dock in Mountain Lion/Webstart
2052 </ul> <em>Applet Known Issues</em>
2055 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2056 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2059 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2060 Jalview and Jmol example not compatible with IE9
2063 <li>Sort by annotation score doesn't reverse order
2069 <td><div align="center">
2070 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2073 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2076 <li>Internationalisation of user interface (usually
2077 called i18n support) and translation for Spanish locale</li>
2078 <li>Define/Undefine group on current selection with
2079 Ctrl-G/Shift Ctrl-G</li>
2080 <li>Improved group creation/removal options in
2081 alignment/sequence Popup menu</li>
2082 <li>Sensible precision for symbol distribution
2083 percentages shown in logo tooltip.</li>
2084 <li>Annotation panel height set according to amount of
2085 annotation when alignment first opened</li>
2086 </ul> <em>Application</em>
2088 <li>Interactive consensus RNA secondary structure
2089 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2090 <li>Select columns containing particular features from
2091 Feature Settings dialog</li>
2092 <li>View all 'representative' PDB structures for selected
2094 <li>Update Jalview project format:
2096 <li>New file extension for Jalview projects '.jvp'</li>
2097 <li>Preserve sequence and annotation dataset (to
2098 store secondary structure annotation,etc)</li>
2099 <li>Per group and alignment annotation and RNA helix
2103 <li>New similarity measures for PCA and Tree calculation
2105 <li>Experimental support for retrieval and viewing of
2106 flanking regions for an alignment</li>
2110 <!-- issues resolved --> <em>Application</em>
2112 <li>logo keeps spinning and status remains at queued or
2113 running after job is cancelled</li>
2114 <li>cannot export features from alignments imported from
2115 Jalview/VAMSAS projects</li>
2116 <li>Buggy slider for web service parameters that take
2118 <li>Newly created RNA secondary structure line doesn't
2119 have 'display all symbols' flag set</li>
2120 <li>T-COFFEE alignment score shading scheme and other
2121 annotation shading not saved in Jalview project</li>
2122 <li>Local file cannot be loaded in freshly downloaded
2124 <li>Jalview icon not shown on dock in Mountain
2126 <li>Load file from desktop file browser fails</li>
2127 <li>Occasional NPE thrown when calculating large trees</li>
2128 <li>Cannot reorder or slide sequences after dragging an
2129 alignment onto desktop</li>
2130 <li>Colour by annotation dialog throws NPE after using
2131 'extract scores' function</li>
2132 <li>Loading/cut'n'pasting an empty file leads to a grey
2133 alignment window</li>
2134 <li>Disorder thresholds rendered incorrectly after
2135 performing IUPred disorder prediction</li>
2136 <li>Multiple group annotated consensus rows shown when
2137 changing 'normalise logo' display setting</li>
2138 <li>Find shows blank dialog after 'finished searching' if
2139 nothing matches query</li>
2140 <li>Null Pointer Exceptions raised when sorting by
2141 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2143 <li>Errors in Jmol console when structures in alignment
2144 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2146 <li>Not all working JABAWS services are shown in
2148 <li>JAVAWS version of Jalview fails to launch with
2149 'invalid literal/length code'</li>
2150 <li>Annotation/RNA Helix colourschemes cannot be applied
2151 to alignment with groups (actually fixed in 2.8.0b1)</li>
2152 <li>RNA Helices and T-Coffee Scores available as default
2155 </ul> <em>Applet</em>
2157 <li>Remove group option is shown even when selection is
2159 <li>Apply to all groups ticked but colourscheme changes
2160 don't affect groups</li>
2161 <li>Documented RNA Helices and T-Coffee Scores as valid
2162 colourscheme name</li>
2163 <li>Annotation labels drawn on sequence IDs when
2164 Annotation panel is not displayed</li>
2165 <li>Increased font size for dropdown menus on OSX and
2166 embedded windows</li>
2167 </ul> <em>Other</em>
2169 <li>Consensus sequence for alignments/groups with a
2170 single sequence were not calculated</li>
2171 <li>annotation files that contain only groups imported as
2172 annotation and junk sequences</li>
2173 <li>Fasta files with sequences containing '*' incorrectly
2174 recognised as PFAM or BLC</li>
2175 <li>conservation/PID slider apply all groups option
2176 doesn't affect background (2.8.0b1)
2178 <li>redundancy highlighting is erratic at 0% and 100%</li>
2179 <li>Remove gapped columns fails for sequences with ragged
2181 <li>AMSA annotation row with leading spaces is not
2182 registered correctly on import</li>
2183 <li>Jalview crashes when selecting PCA analysis for
2184 certain alignments</li>
2185 <li>Opening the colour by annotation dialog for an
2186 existing annotation based 'use original colours'
2187 colourscheme loses original colours setting</li>
2192 <td><div align="center">
2193 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2194 <em>30/1/2014</em></strong>
2198 <li>Trusted certificates for JalviewLite applet and
2199 Jalview Desktop application<br />Certificate was donated by
2200 <a href="https://www.certum.eu">Certum</a> to the Jalview
2201 open source project).
2203 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2204 <li>Output in Stockholm format</li>
2205 <li>Allow import of data from gzipped files</li>
2206 <li>Export/import group and sequence associated line
2207 graph thresholds</li>
2208 <li>Nucleotide substitution matrix that supports RNA and
2209 ambiguity codes</li>
2210 <li>Allow disorder predictions to be made on the current
2211 selection (or visible selection) in the same way that JPred
2213 <li>Groovy scripting for headless Jalview operation</li>
2214 </ul> <em>Other improvements</em>
2216 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2217 <li>COMBINE statement uses current SEQUENCE_REF and
2218 GROUP_REF scope to group annotation rows</li>
2219 <li>Support '' style escaping of quotes in Newick
2221 <li>Group options for JABAWS service by command line name</li>
2222 <li>Empty tooltip shown for JABA service options with a
2223 link but no description</li>
2224 <li>Select primary source when selecting authority in
2225 database fetcher GUI</li>
2226 <li>Add .mfa to FASTA file extensions recognised by
2228 <li>Annotation label tooltip text wrap</li>
2233 <li>Slow scrolling when lots of annotation rows are
2235 <li>Lots of NPE (and slowness) after creating RNA
2236 secondary structure annotation line</li>
2237 <li>Sequence database accessions not imported when
2238 fetching alignments from Rfam</li>
2239 <li>Incorrect SHMR submission for sequences with
2241 <li>View all structures does not always superpose
2243 <li>Option widgets in service parameters not updated to
2244 reflect user or preset settings</li>
2245 <li>Null pointer exceptions for some services without
2246 presets or adjustable parameters</li>
2247 <li>Discover PDB IDs entry in structure menu doesn't
2248 discover PDB xRefs</li>
2249 <li>Exception encountered while trying to retrieve
2250 features with DAS</li>
2251 <li>Lowest value in annotation row isn't coloured
2252 when colour by annotation (per sequence) is coloured</li>
2253 <li>Keyboard mode P jumps to start of gapped region when
2254 residue follows a gap</li>
2255 <li>Jalview appears to hang importing an alignment with
2256 Wrap as default or after enabling Wrap</li>
2257 <li>'Right click to add annotations' message
2258 shown in wrap mode when no annotations present</li>
2259 <li>Disorder predictions fail with NPE if no automatic
2260 annotation already exists on alignment</li>
2261 <li>oninit javascript function should be called after
2262 initialisation completes</li>
2263 <li>Remove redundancy after disorder prediction corrupts
2264 alignment window display</li>
2265 <li>Example annotation file in documentation is invalid</li>
2266 <li>Grouped line graph annotation rows are not exported
2267 to annotation file</li>
2268 <li>Multi-harmony analysis cannot be run when only two
2270 <li>Cannot create multiple groups of line graphs with
2271 several 'combine' statements in annotation file</li>
2272 <li>Pressing return several times causes Number Format
2273 exceptions in keyboard mode</li>
2274 <li>Multi-harmony (SHMMR) method doesn't submit
2275 correct partitions for input data</li>
2276 <li>Translation from DNA to Amino Acids fails</li>
2277 <li>Jalview fail to load newick tree with quoted label</li>
2278 <li>--headless flag isn't understood</li>
2279 <li>ClassCastException when generating EPS in headless
2281 <li>Adjusting sequence-associated shading threshold only
2282 changes one row's threshold</li>
2283 <li>Preferences and Feature settings panel panel
2284 doesn't open</li>
2285 <li>hide consensus histogram also hides conservation and
2286 quality histograms</li>
2291 <td><div align="center">
2292 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2294 <td><em>Application</em>
2296 <li>Support for JABAWS 2.0 Services (AACon alignment
2297 conservation, protein disorder and Clustal Omega)</li>
2298 <li>JABAWS server status indicator in Web Services
2300 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2301 in Jalview alignment window</li>
2302 <li>Updated Jalview build and deploy framework for OSX
2303 mountain lion, windows 7, and 8</li>
2304 <li>Nucleotide substitution matrix for PCA that supports
2305 RNA and ambiguity codes</li>
2307 <li>Improved sequence database retrieval GUI</li>
2308 <li>Support fetching and database reference look up
2309 against multiple DAS sources (Fetch all from in 'fetch db
2311 <li>Jalview project improvements
2313 <li>Store and retrieve the 'belowAlignment'
2314 flag for annotation</li>
2315 <li>calcId attribute to group annotation rows on the
2317 <li>Store AACon calculation settings for a view in
2318 Jalview project</li>
2322 <li>horizontal scrolling gesture support</li>
2323 <li>Visual progress indicator when PCA calculation is
2325 <li>Simpler JABA web services menus</li>
2326 <li>visual indication that web service results are still
2327 being retrieved from server</li>
2328 <li>Serialise the dialogs that are shown when Jalview
2329 starts up for first time</li>
2330 <li>Jalview user agent string for interacting with HTTP
2332 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2334 <li>Examples directory and Groovy library included in
2335 InstallAnywhere distribution</li>
2336 </ul> <em>Applet</em>
2338 <li>RNA alignment and secondary structure annotation
2339 visualization applet example</li>
2340 </ul> <em>General</em>
2342 <li>Normalise option for consensus sequence logo</li>
2343 <li>Reset button in PCA window to return dimensions to
2345 <li>Allow seqspace or Jalview variant of alignment PCA
2347 <li>PCA with either nucleic acid and protein substitution
2349 <li>Allow windows containing HTML reports to be exported
2351 <li>Interactive display and editing of RNA secondary
2352 structure contacts</li>
2353 <li>RNA Helix Alignment Colouring</li>
2354 <li>RNA base pair logo consensus</li>
2355 <li>Parse sequence associated secondary structure
2356 information in Stockholm files</li>
2357 <li>HTML Export database accessions and annotation
2358 information presented in tooltip for sequences</li>
2359 <li>Import secondary structure from LOCARNA clustalw
2360 style RNA alignment files</li>
2361 <li>import and visualise T-COFFEE quality scores for an
2363 <li>'colour by annotation' per sequence option to
2364 shade each sequence according to its associated alignment
2366 <li>New Jalview Logo</li>
2367 </ul> <em>Documentation and Development</em>
2369 <li>documentation for score matrices used in Jalview</li>
2370 <li>New Website!</li>
2372 <td><em>Application</em>
2374 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2375 wsdbfetch REST service</li>
2376 <li>Stop windows being moved outside desktop on OSX</li>
2377 <li>Filetype associations not installed for webstart
2379 <li>Jalview does not always retrieve progress of a JABAWS
2380 job execution in full once it is complete</li>
2381 <li>revise SHMR RSBS definition to ensure alignment is
2382 uploaded via ali_file parameter</li>
2383 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2384 <li>View all structures superposed fails with exception</li>
2385 <li>Jnet job queues forever if a very short sequence is
2386 submitted for prediction</li>
2387 <li>Cut and paste menu not opened when mouse clicked on
2389 <li>Putting fractional value into integer text box in
2390 alignment parameter dialog causes Jalview to hang</li>
2391 <li>Structure view highlighting doesn't work on
2393 <li>View all structures fails with exception shown in
2395 <li>Characters in filename associated with PDBEntry not
2396 escaped in a platform independent way</li>
2397 <li>Jalview desktop fails to launch with exception when
2399 <li>Tree calculation reports 'you must have 2 or more
2400 sequences selected' when selection is empty</li>
2401 <li>Jalview desktop fails to launch with jar signature
2402 failure when java web start temporary file caching is
2404 <li>DAS Sequence retrieval with range qualification
2405 results in sequence xref which includes range qualification</li>
2406 <li>Errors during processing of command line arguments
2407 cause progress bar (JAL-898) to be removed</li>
2408 <li>Replace comma for semi-colon option not disabled for
2409 DAS sources in sequence fetcher</li>
2410 <li>Cannot close news reader when JABAWS server warning
2411 dialog is shown</li>
2412 <li>Option widgets not updated to reflect user settings</li>
2413 <li>Edited sequence not submitted to web service</li>
2414 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2415 <li>InstallAnywhere installer doesn't unpack and run
2416 on OSX Mountain Lion</li>
2417 <li>Annotation panel not given a scroll bar when
2418 sequences with alignment annotation are pasted into the
2420 <li>Sequence associated annotation rows not associated
2421 when loaded from Jalview project</li>
2422 <li>Browser launch fails with NPE on java 1.7</li>
2423 <li>JABAWS alignment marked as finished when job was
2424 cancelled or job failed due to invalid input</li>
2425 <li>NPE with v2.7 example when clicking on Tree
2426 associated with all views</li>
2427 <li>Exceptions when copy/paste sequences with grouped
2428 annotation rows to new window</li>
2429 </ul> <em>Applet</em>
2431 <li>Sequence features are momentarily displayed before
2432 they are hidden using hidefeaturegroups applet parameter</li>
2433 <li>loading features via javascript API automatically
2434 enables feature display</li>
2435 <li>scrollToColumnIn javascript API method doesn't
2437 </ul> <em>General</em>
2439 <li>Redundancy removal fails for rna alignment</li>
2440 <li>PCA calculation fails when sequence has been selected
2441 and then deselected</li>
2442 <li>PCA window shows grey box when first opened on OSX</li>
2443 <li>Letters coloured pink in sequence logo when alignment
2444 coloured with clustalx</li>
2445 <li>Choosing fonts without letter symbols defined causes
2446 exceptions and redraw errors</li>
2447 <li>Initial PCA plot view is not same as manually
2448 reconfigured view</li>
2449 <li>Grouped annotation graph label has incorrect line
2451 <li>Grouped annotation graph label display is corrupted
2452 for lots of labels</li>
2457 <div align="center">
2458 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2461 <td><em>Application</em>
2463 <li>Jalview Desktop News Reader</li>
2464 <li>Tweaked default layout of web services menu</li>
2465 <li>View/alignment association menu to enable user to
2466 easily specify which alignment a multi-structure view takes
2467 its colours/correspondences from</li>
2468 <li>Allow properties file location to be specified as URL</li>
2469 <li>Extend Jalview project to preserve associations
2470 between many alignment views and a single Jmol display</li>
2471 <li>Store annotation row height in Jalview project file</li>
2472 <li>Annotation row column label formatting attributes
2473 stored in project file</li>
2474 <li>Annotation row order for auto-calculated annotation
2475 rows preserved in Jalview project file</li>
2476 <li>Visual progress indication when Jalview state is
2477 saved using Desktop window menu</li>
2478 <li>Visual indication that command line arguments are
2479 still being processed</li>
2480 <li>Groovy script execution from URL</li>
2481 <li>Colour by annotation default min and max colours in
2483 <li>Automatically associate PDB files dragged onto an
2484 alignment with sequences that have high similarity and
2486 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2487 <li>'view structures' option to open many
2488 structures in same window</li>
2489 <li>Sort associated views menu option for tree panel</li>
2490 <li>Group all JABA and non-JABA services for a particular
2491 analysis function in its own submenu</li>
2492 </ul> <em>Applet</em>
2494 <li>Userdefined and autogenerated annotation rows for
2496 <li>Adjustment of alignment annotation pane height</li>
2497 <li>Annotation scrollbar for annotation panel</li>
2498 <li>Drag to reorder annotation rows in annotation panel</li>
2499 <li>'automaticScrolling' parameter</li>
2500 <li>Allow sequences with partial ID string matches to be
2501 annotated from GFF/Jalview features files</li>
2502 <li>Sequence logo annotation row in applet</li>
2503 <li>Absolute paths relative to host server in applet
2504 parameters are treated as such</li>
2505 <li>New in the JalviewLite javascript API:
2507 <li>JalviewLite.js javascript library</li>
2508 <li>Javascript callbacks for
2510 <li>Applet initialisation</li>
2511 <li>Sequence/alignment mouse-overs and selections</li>
2514 <li>scrollTo row and column alignment scrolling
2516 <li>Select sequence/alignment regions from javascript</li>
2517 <li>javascript structure viewer harness to pass
2518 messages between Jmol and Jalview when running as
2519 distinct applets</li>
2520 <li>sortBy method</li>
2521 <li>Set of applet and application examples shipped
2522 with documentation</li>
2523 <li>New example to demonstrate JalviewLite and Jmol
2524 javascript message exchange</li>
2526 </ul> <em>General</em>
2528 <li>Enable Jmol displays to be associated with multiple
2529 multiple alignments</li>
2530 <li>Option to automatically sort alignment with new tree</li>
2531 <li>User configurable link to enable redirects to a
2532 www.Jalview.org mirror</li>
2533 <li>Jmol colours option for Jmol displays</li>
2534 <li>Configurable newline string when writing alignment
2535 and other flat files</li>
2536 <li>Allow alignment annotation description lines to
2537 contain html tags</li>
2538 </ul> <em>Documentation and Development</em>
2540 <li>Add groovy test harness for bulk load testing to
2542 <li>Groovy script to load and align a set of sequences
2543 using a web service before displaying the result in the
2544 Jalview desktop</li>
2545 <li>Restructured javascript and applet api documentation</li>
2546 <li>Ant target to publish example html files with applet
2548 <li>Netbeans project for building Jalview from source</li>
2549 <li>ant task to create online javadoc for Jalview source</li>
2551 <td><em>Application</em>
2553 <li>User defined colourscheme throws exception when
2554 current built in colourscheme is saved as new scheme</li>
2555 <li>AlignFrame->Save in application pops up save
2556 dialog for valid filename/format</li>
2557 <li>Cannot view associated structure for UniProt sequence</li>
2558 <li>PDB file association breaks for UniProt sequence
2560 <li>Associate PDB from file dialog does not tell you
2561 which sequence is to be associated with the file</li>
2562 <li>Find All raises null pointer exception when query
2563 only matches sequence IDs</li>
2564 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2565 <li>Jalview project with Jmol views created with Jalview
2566 2.4 cannot be loaded</li>
2567 <li>Filetype associations not installed for webstart
2569 <li>Two or more chains in a single PDB file associated
2570 with sequences in different alignments do not get coloured
2571 by their associated sequence</li>
2572 <li>Visibility status of autocalculated annotation row
2573 not preserved when project is loaded</li>
2574 <li>Annotation row height and visibility attributes not
2575 stored in Jalview project</li>
2576 <li>Tree bootstraps are not preserved when saved as a
2577 Jalview project</li>
2578 <li>Envision2 workflow tooltips are corrupted</li>
2579 <li>Enabling show group conservation also enables colour
2580 by conservation</li>
2581 <li>Duplicate group associated conservation or consensus
2582 created on new view</li>
2583 <li>Annotation scrollbar not displayed after 'show
2584 all hidden annotation rows' option selected</li>
2585 <li>Alignment quality not updated after alignment
2586 annotation row is hidden then shown</li>
2587 <li>Preserve colouring of structures coloured by
2588 sequences in pre Jalview 2.7 projects</li>
2589 <li>Web service job parameter dialog is not laid out
2591 <li>Web services menu not refreshed after 'reset
2592 services' button is pressed in preferences</li>
2593 <li>Annotation off by one in Jalview v2_3 example project</li>
2594 <li>Structures imported from file and saved in project
2595 get name like jalview_pdb1234.txt when reloaded</li>
2596 <li>Jalview does not always retrieve progress of a JABAWS
2597 job execution in full once it is complete</li>
2598 </ul> <em>Applet</em>
2600 <li>Alignment height set incorrectly when lots of
2601 annotation rows are displayed</li>
2602 <li>Relative URLs in feature HTML text not resolved to
2604 <li>View follows highlighting does not work for positions
2606 <li><= shown as = in tooltip</li>
2607 <li>Export features raises exception when no features
2609 <li>Separator string used for serialising lists of IDs
2610 for javascript api is modified when separator string
2611 provided as parameter</li>
2612 <li>Null pointer exception when selecting tree leaves for
2613 alignment with no existing selection</li>
2614 <li>Relative URLs for datasources assumed to be relative
2615 to applet's codebase</li>
2616 <li>Status bar not updated after finished searching and
2617 search wraps around to first result</li>
2618 <li>StructureSelectionManager instance shared between
2619 several Jalview applets causes race conditions and memory
2621 <li>Hover tooltip and mouseover of position on structure
2622 not sent from Jmol in applet</li>
2623 <li>Certain sequences of javascript method calls to
2624 applet API fatally hang browser</li>
2625 </ul> <em>General</em>
2627 <li>View follows structure mouseover scrolls beyond
2628 position with wrapped view and hidden regions</li>
2629 <li>Find sequence position moves to wrong residue
2630 with/without hidden columns</li>
2631 <li>Sequence length given in alignment properties window
2633 <li>InvalidNumberFormat exceptions thrown when trying to
2634 import PDB like structure files</li>
2635 <li>Positional search results are only highlighted
2636 between user-supplied sequence start/end bounds</li>
2637 <li>End attribute of sequence is not validated</li>
2638 <li>Find dialog only finds first sequence containing a
2639 given sequence position</li>
2640 <li>Sequence numbering not preserved in MSF alignment
2642 <li>Jalview PDB file reader does not extract sequence
2643 from nucleotide chains correctly</li>
2644 <li>Structure colours not updated when tree partition
2645 changed in alignment</li>
2646 <li>Sequence associated secondary structure not correctly
2647 parsed in interleaved stockholm</li>
2648 <li>Colour by annotation dialog does not restore current
2650 <li>Hiding (nearly) all sequences doesn't work
2652 <li>Sequences containing lowercase letters are not
2653 properly associated with their pdb files</li>
2654 </ul> <em>Documentation and Development</em>
2656 <li>schemas/JalviewWsParamSet.xsd corrupted by
2657 ApplyCopyright tool</li>
2662 <div align="center">
2663 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2666 <td><em>Application</em>
2668 <li>New warning dialog when the Jalview Desktop cannot
2669 contact web services</li>
2670 <li>JABA service parameters for a preset are shown in
2671 service job window</li>
2672 <li>JABA Service menu entries reworded</li>
2676 <li>Modeller PIR IO broken - cannot correctly import a
2677 pir file emitted by Jalview</li>
2678 <li>Existing feature settings transferred to new
2679 alignment view created from cut'n'paste</li>
2680 <li>Improved test for mixed amino/nucleotide chains when
2681 parsing PDB files</li>
2682 <li>Consensus and conservation annotation rows
2683 occasionally become blank for all new windows</li>
2684 <li>Exception raised when right clicking above sequences
2685 in wrapped view mode</li>
2686 </ul> <em>Application</em>
2688 <li>multiple multiply aligned structure views cause cpu
2689 usage to hit 100% and computer to hang</li>
2690 <li>Web Service parameter layout breaks for long user
2691 parameter names</li>
2692 <li>Jaba service discovery hangs desktop if Jaba server
2699 <div align="center">
2700 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2703 <td><em>Application</em>
2705 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2706 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2709 <li>Web Services preference tab</li>
2710 <li>Analysis parameters dialog box and user defined
2712 <li>Improved speed and layout of Envision2 service menu</li>
2713 <li>Superpose structures using associated sequence
2715 <li>Export coordinates and projection as CSV from PCA
2717 </ul> <em>Applet</em>
2719 <li>enable javascript: execution by the applet via the
2720 link out mechanism</li>
2721 </ul> <em>Other</em>
2723 <li>Updated the Jmol Jalview interface to work with Jmol
2725 <li>The Jalview Desktop and JalviewLite applet now
2726 require Java 1.5</li>
2727 <li>Allow Jalview feature colour specification for GFF
2728 sequence annotation files</li>
2729 <li>New 'colour by label' keword in Jalview feature file
2730 type colour specification</li>
2731 <li>New Jalview Desktop Groovy API method that allows a
2732 script to check if it being run in an interactive session or
2733 in a batch operation from the Jalview command line</li>
2737 <li>clustalx colourscheme colours Ds preferentially when
2738 both D+E are present in over 50% of the column</li>
2739 </ul> <em>Application</em>
2741 <li>typo in AlignmentFrame->View->Hide->all but
2742 selected Regions menu item</li>
2743 <li>sequence fetcher replaces ',' for ';' when the ',' is
2744 part of a valid accession ID</li>
2745 <li>fatal OOM if object retrieved by sequence fetcher
2746 runs out of memory</li>
2747 <li>unhandled Out of Memory Error when viewing pca
2748 analysis results</li>
2749 <li>InstallAnywhere builds fail to launch on OS X java
2750 10.5 update 4 (due to apple Java 1.6 update)</li>
2751 <li>Installanywhere Jalview silently fails to launch</li>
2752 </ul> <em>Applet</em>
2754 <li>Jalview.getFeatureGroups() raises an
2755 ArrayIndexOutOfBoundsException if no feature groups are
2762 <div align="center">
2763 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2769 <li>Alignment prettyprinter doesn't cope with long
2771 <li>clustalx colourscheme colours Ds preferentially when
2772 both D+E are present in over 50% of the column</li>
2773 <li>nucleic acid structures retrieved from PDB do not
2774 import correctly</li>
2775 <li>More columns get selected than were clicked on when a
2776 number of columns are hidden</li>
2777 <li>annotation label popup menu not providing correct
2778 add/hide/show options when rows are hidden or none are
2780 <li>Stockholm format shown in list of readable formats,
2781 and parser copes better with alignments from RFAM.</li>
2782 <li>CSV output of consensus only includes the percentage
2783 of all symbols if sequence logo display is enabled</li>
2785 </ul> <em>Applet</em>
2787 <li>annotation panel disappears when annotation is
2789 </ul> <em>Application</em>
2791 <li>Alignment view not redrawn properly when new
2792 alignment opened where annotation panel is visible but no
2793 annotations are present on alignment</li>
2794 <li>pasted region containing hidden columns is
2795 incorrectly displayed in new alignment window</li>
2796 <li>Jalview slow to complete operations when stdout is
2797 flooded (fix is to close the Jalview console)</li>
2798 <li>typo in AlignmentFrame->View->Hide->all but
2799 selected Rregions menu item.</li>
2800 <li>inconsistent group submenu and Format submenu entry
2801 'Un' or 'Non'conserved</li>
2802 <li>Sequence feature settings are being shared by
2803 multiple distinct alignments</li>
2804 <li>group annotation not recreated when tree partition is
2806 <li>double click on group annotation to select sequences
2807 does not propagate to associated trees</li>
2808 <li>Mac OSX specific issues:
2810 <li>exception raised when mouse clicked on desktop
2811 window background</li>
2812 <li>Desktop menu placed on menu bar and application
2813 name set correctly</li>
2814 <li>sequence feature settings not wide enough for the
2815 save feature colourscheme button</li>
2824 <div align="center">
2825 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2828 <td><em>New Capabilities</em>
2830 <li>URL links generated from description line for
2831 regular-expression based URL links (applet and application)
2833 <li>Non-positional feature URL links are shown in link
2835 <li>Linked viewing of nucleic acid sequences and
2837 <li>Automatic Scrolling option in View menu to display
2838 the currently highlighted region of an alignment.</li>
2839 <li>Order an alignment by sequence length, or using the
2840 average score or total feature count for each sequence.</li>
2841 <li>Shading features by score or associated description</li>
2842 <li>Subdivide alignment and groups based on identity of
2843 selected subsequence (Make Groups from Selection).</li>
2844 <li>New hide/show options including Shift+Control+H to
2845 hide everything but the currently selected region.</li>
2846 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2847 </ul> <em>Application</em>
2849 <li>Fetch DB References capabilities and UI expanded to
2850 support retrieval from DAS sequence sources</li>
2851 <li>Local DAS Sequence sources can be added via the
2852 command line or via the Add local source dialog box.</li>
2853 <li>DAS Dbref and DbxRef feature types are parsed as
2854 database references and protein_name is parsed as
2855 description line (BioSapiens terms).</li>
2856 <li>Enable or disable non-positional feature and database
2857 references in sequence ID tooltip from View menu in
2859 <!-- <li>New hidden columns and rows and representatives capabilities
2860 in annotations file (in progress - not yet fully implemented)</li> -->
2861 <li>Group-associated consensus, sequence logos and
2862 conservation plots</li>
2863 <li>Symbol distributions for each column can be exported
2864 and visualized as sequence logos</li>
2865 <li>Optionally scale multi-character column labels to fit
2866 within each column of annotation row<!-- todo for applet -->
2868 <li>Optional automatic sort of associated alignment view
2869 when a new tree is opened.</li>
2870 <li>Jalview Java Console</li>
2871 <li>Better placement of desktop window when moving
2872 between different screens.</li>
2873 <li>New preference items for sequence ID tooltip and
2874 consensus annotation</li>
2875 <li>Client to submit sequences and IDs to Envision2
2877 <li><em>Vamsas Capabilities</em>
2879 <li>Improved VAMSAS synchronization (Jalview archive
2880 used to preserve views, structures, and tree display
2882 <li>Import of vamsas documents from disk or URL via
2884 <li>Sharing of selected regions between views and
2885 with other VAMSAS applications (Experimental feature!)</li>
2886 <li>Updated API to VAMSAS version 0.2</li>
2888 </ul> <em>Applet</em>
2890 <li>Middle button resizes annotation row height</li>
2893 <li>sortByTree (true/false) - automatically sort the
2894 associated alignment view by the tree when a new tree is
2896 <li>showTreeBootstraps (true/false) - show or hide
2897 branch bootstraps (default is to show them if available)</li>
2898 <li>showTreeDistances (true/false) - show or hide
2899 branch lengths (default is to show them if available)</li>
2900 <li>showUnlinkedTreeNodes (true/false) - indicate if
2901 unassociated nodes should be highlighted in the tree
2903 <li>heightScale and widthScale (1.0 or more) -
2904 increase the height or width of a cell in the alignment
2905 grid relative to the current font size.</li>
2908 <li>Non-positional features displayed in sequence ID
2910 </ul> <em>Other</em>
2912 <li>Features format: graduated colour definitions and
2913 specification of feature scores</li>
2914 <li>Alignment Annotations format: new keywords for group
2915 associated annotation (GROUP_REF) and annotation row display
2916 properties (ROW_PROPERTIES)</li>
2917 <li>XML formats extended to support graduated feature
2918 colourschemes, group associated annotation, and profile
2919 visualization settings.</li></td>
2922 <li>Source field in GFF files parsed as feature source
2923 rather than description</li>
2924 <li>Non-positional features are now included in sequence
2925 feature and gff files (controlled via non-positional feature
2926 visibility in tooltip).</li>
2927 <li>URL links generated for all feature links (bugfix)</li>
2928 <li>Added URL embedding instructions to features file
2930 <li>Codons containing ambiguous nucleotides translated as
2931 'X' in peptide product</li>
2932 <li>Match case switch in find dialog box works for both
2933 sequence ID and sequence string and query strings do not
2934 have to be in upper case to match case-insensitively.</li>
2935 <li>AMSA files only contain first column of
2936 multi-character column annotation labels</li>
2937 <li>Jalview Annotation File generation/parsing consistent
2938 with documentation (e.g. Stockholm annotation can be
2939 exported and re-imported)</li>
2940 <li>PDB files without embedded PDB IDs given a friendly
2942 <li>Find incrementally searches ID string matches as well
2943 as subsequence matches, and correctly reports total number
2947 <li>Better handling of exceptions during sequence
2949 <li>Dasobert generated non-positional feature URL
2950 link text excludes the start_end suffix</li>
2951 <li>DAS feature and source retrieval buttons disabled
2952 when fetch or registry operations in progress.</li>
2953 <li>PDB files retrieved from URLs are cached properly</li>
2954 <li>Sequence description lines properly shared via
2956 <li>Sequence fetcher fetches multiple records for all
2958 <li>Ensured that command line das feature retrieval
2959 completes before alignment figures are generated.</li>
2960 <li>Reduced time taken when opening file browser for
2962 <li>isAligned check prior to calculating tree, PCA or
2963 submitting an MSA to JNet now excludes hidden sequences.</li>
2964 <li>User defined group colours properly recovered
2965 from Jalview projects.</li>
2974 <div align="center">
2975 <strong>2.4.0.b2</strong><br> 28/10/2009
2980 <li>Experimental support for google analytics usage
2982 <li>Jalview privacy settings (user preferences and docs).</li>
2987 <li>Race condition in applet preventing startup in
2989 <li>Exception when feature created from selection beyond
2990 length of sequence.</li>
2991 <li>Allow synthetic PDB files to be imported gracefully</li>
2992 <li>Sequence associated annotation rows associate with
2993 all sequences with a given id</li>
2994 <li>Find function matches case-insensitively for sequence
2995 ID string searches</li>
2996 <li>Non-standard characters do not cause pairwise
2997 alignment to fail with exception</li>
2998 </ul> <em>Application Issues</em>
3000 <li>Sequences are now validated against EMBL database</li>
3001 <li>Sequence fetcher fetches multiple records for all
3003 </ul> <em>InstallAnywhere Issues</em>
3005 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3006 issue with installAnywhere mechanism)</li>
3007 <li>Command line launching of JARs from InstallAnywhere
3008 version (java class versioning error fixed)</li>
3015 <div align="center">
3016 <strong>2.4</strong><br> 27/8/2008
3019 <td><em>User Interface</em>
3021 <li>Linked highlighting of codon and amino acid from
3022 translation and protein products</li>
3023 <li>Linked highlighting of structure associated with
3024 residue mapping to codon position</li>
3025 <li>Sequence Fetcher provides example accession numbers
3026 and 'clear' button</li>
3027 <li>MemoryMonitor added as an option under Desktop's
3029 <li>Extract score function to parse whitespace separated
3030 numeric data in description line</li>
3031 <li>Column labels in alignment annotation can be centred.</li>
3032 <li>Tooltip for sequence associated annotation give name
3034 </ul> <em>Web Services and URL fetching</em>
3036 <li>JPred3 web service</li>
3037 <li>Prototype sequence search client (no public services
3039 <li>Fetch either seed alignment or full alignment from
3041 <li>URL Links created for matching database cross
3042 references as well as sequence ID</li>
3043 <li>URL Links can be created using regular-expressions</li>
3044 </ul> <em>Sequence Database Connectivity</em>
3046 <li>Retrieval of cross-referenced sequences from other
3048 <li>Generalised database reference retrieval and
3049 validation to all fetchable databases</li>
3050 <li>Fetch sequences from DAS sources supporting the
3051 sequence command</li>
3052 </ul> <em>Import and Export</em>
3053 <li>export annotation rows as CSV for spreadsheet import</li>
3054 <li>Jalview projects record alignment dataset associations,
3055 EMBL products, and cDNA sequence mappings</li>
3056 <li>Sequence Group colour can be specified in Annotation
3058 <li>Ad-hoc colouring of group in Annotation File using RGB
3059 triplet as name of colourscheme</li>
3060 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3062 <li>treenode binding for VAMSAS tree exchange</li>
3063 <li>local editing and update of sequences in VAMSAS
3064 alignments (experimental)</li>
3065 <li>Create new or select existing session to join</li>
3066 <li>load and save of vamsas documents</li>
3067 </ul> <em>Application command line</em>
3069 <li>-tree parameter to open trees (introduced for passing
3071 <li>-fetchfrom command line argument to specify nicknames
3072 of DAS servers to query for alignment features</li>
3073 <li>-dasserver command line argument to add new servers
3074 that are also automatically queried for features</li>
3075 <li>-groovy command line argument executes a given groovy
3076 script after all input data has been loaded and parsed</li>
3077 </ul> <em>Applet-Application data exchange</em>
3079 <li>Trees passed as applet parameters can be passed to
3080 application (when using "View in full
3081 application")</li>
3082 </ul> <em>Applet Parameters</em>
3084 <li>feature group display control parameter</li>
3085 <li>debug parameter</li>
3086 <li>showbutton parameter</li>
3087 </ul> <em>Applet API methods</em>
3089 <li>newView public method</li>
3090 <li>Window (current view) specific get/set public methods</li>
3091 <li>Feature display control methods</li>
3092 <li>get list of currently selected sequences</li>
3093 </ul> <em>New Jalview distribution features</em>
3095 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3096 <li>RELEASE file gives build properties for the latest
3097 Jalview release.</li>
3098 <li>Java 1.1 Applet build made easier and donotobfuscate
3099 property controls execution of obfuscator</li>
3100 <li>Build target for generating source distribution</li>
3101 <li>Debug flag for javacc</li>
3102 <li>.jalview_properties file is documented (slightly) in
3103 jalview.bin.Cache</li>
3104 <li>Continuous Build Integration for stable and
3105 development version of Application, Applet and source
3110 <li>selected region output includes visible annotations
3111 (for certain formats)</li>
3112 <li>edit label/displaychar contains existing label/char
3114 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3115 <li>shorter peptide product names from EMBL records</li>
3116 <li>Newick string generator makes compact representations</li>
3117 <li>bootstrap values parsed correctly for tree files with
3119 <li>pathological filechooser bug avoided by not allowing
3120 filenames containing a ':'</li>
3121 <li>Fixed exception when parsing GFF files containing
3122 global sequence features</li>
3123 <li>Alignment datasets are finalized only when number of
3124 references from alignment sequences goes to zero</li>
3125 <li>Close of tree branch colour box without colour
3126 selection causes cascading exceptions</li>
3127 <li>occasional negative imgwidth exceptions</li>
3128 <li>better reporting of non-fatal warnings to user when
3129 file parsing fails.</li>
3130 <li>Save works when Jalview project is default format</li>
3131 <li>Save as dialog opened if current alignment format is
3132 not a valid output format</li>
3133 <li>UniProt canonical names introduced for both das and
3135 <li>Histidine should be midblue (not pink!) in Zappo</li>
3136 <li>error messages passed up and output when data read
3138 <li>edit undo recovers previous dataset sequence when
3139 sequence is edited</li>
3140 <li>allow PDB files without pdb ID HEADER lines (like
3141 those generated by MODELLER) to be read in properly</li>
3142 <li>allow reading of JPred concise files as a normal
3144 <li>Stockholm annotation parsing and alignment properties
3145 import fixed for PFAM records</li>
3146 <li>Structure view windows have correct name in Desktop
3148 <li>annotation consisting of sequence associated scores
3149 can be read and written correctly to annotation file</li>
3150 <li>Aligned cDNA translation to aligned peptide works
3152 <li>Fixed display of hidden sequence markers and
3153 non-italic font for representatives in Applet</li>
3154 <li>Applet Menus are always embedded in applet window on
3156 <li>Newly shown features appear at top of stack (in
3158 <li>Annotations added via parameter not drawn properly
3159 due to null pointer exceptions</li>
3160 <li>Secondary structure lines are drawn starting from
3161 first column of alignment</li>
3162 <li>UniProt XML import updated for new schema release in
3164 <li>Sequence feature to sequence ID match for Features
3165 file is case-insensitive</li>
3166 <li>Sequence features read from Features file appended to
3167 all sequences with matching IDs</li>
3168 <li>PDB structure coloured correctly for associated views
3169 containing a sub-sequence</li>
3170 <li>PDB files can be retrieved by applet from Jar files</li>
3171 <li>feature and annotation file applet parameters
3172 referring to different directories are retrieved correctly</li>
3173 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3174 <li>Fixed application hang whilst waiting for
3175 splash-screen version check to complete</li>
3176 <li>Applet properly URLencodes input parameter values
3177 when passing them to the launchApp service</li>
3178 <li>display name and local features preserved in results
3179 retrieved from web service</li>
3180 <li>Visual delay indication for sequence retrieval and
3181 sequence fetcher initialisation</li>
3182 <li>updated Application to use DAS 1.53e version of
3183 dasobert DAS client</li>
3184 <li>Re-instated Full AMSA support and .amsa file
3186 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3194 <div align="center">
3195 <strong>2.3</strong><br> 9/5/07
3200 <li>Jmol 11.0.2 integration</li>
3201 <li>PDB views stored in Jalview XML files</li>
3202 <li>Slide sequences</li>
3203 <li>Edit sequence in place</li>
3204 <li>EMBL CDS features</li>
3205 <li>DAS Feature mapping</li>
3206 <li>Feature ordering</li>
3207 <li>Alignment Properties</li>
3208 <li>Annotation Scores</li>
3209 <li>Sort by scores</li>
3210 <li>Feature/annotation editing in applet</li>
3215 <li>Headless state operation in 2.2.1</li>
3216 <li>Incorrect and unstable DNA pairwise alignment</li>
3217 <li>Cut and paste of sequences with annotation</li>
3218 <li>Feature group display state in XML</li>
3219 <li>Feature ordering in XML</li>
3220 <li>blc file iteration selection using filename # suffix</li>
3221 <li>Stockholm alignment properties</li>
3222 <li>Stockhom alignment secondary structure annotation</li>
3223 <li>2.2.1 applet had no feature transparency</li>
3224 <li>Number pad keys can be used in cursor mode</li>
3225 <li>Structure Viewer mirror image resolved</li>
3232 <div align="center">
3233 <strong>2.2.1</strong><br> 12/2/07
3238 <li>Non standard characters can be read and displayed
3239 <li>Annotations/Features can be imported/exported to the
3241 <li>Applet allows editing of sequence/annotation/group
3242 name & description
3243 <li>Preference setting to display sequence name in
3245 <li>Annotation file format extended to allow
3246 Sequence_groups to be defined
3247 <li>Default opening of alignment overview panel can be
3248 specified in preferences
3249 <li>PDB residue numbering annotation added to associated
3255 <li>Applet crash under certain Linux OS with Java 1.6
3257 <li>Annotation file export / import bugs fixed
3258 <li>PNG / EPS image output bugs fixed
3264 <div align="center">
3265 <strong>2.2</strong><br> 27/11/06
3270 <li>Multiple views on alignment
3271 <li>Sequence feature editing
3272 <li>"Reload" alignment
3273 <li>"Save" to current filename
3274 <li>Background dependent text colour
3275 <li>Right align sequence ids
3276 <li>User-defined lower case residue colours
3279 <li>Menu item accelerator keys
3280 <li>Control-V pastes to current alignment
3281 <li>Cancel button for DAS Feature Fetching
3282 <li>PCA and PDB Viewers zoom via mouse roller
3283 <li>User-defined sub-tree colours and sub-tree selection
3285 <li>'New Window' button on the 'Output to Text box'
3290 <li>New memory efficient Undo/Redo System
3291 <li>Optimised symbol lookups and conservation/consensus
3293 <li>Region Conservation/Consensus recalculated after
3295 <li>Fixed Remove Empty Columns Bug (empty columns at end
3297 <li>Slowed DAS Feature Fetching for increased robustness.
3299 <li>Made angle brackets in ASCII feature descriptions
3301 <li>Re-instated Zoom function for PCA
3302 <li>Sequence descriptions conserved in web service
3304 <li>UniProt ID discoverer uses any word separated by
3306 <li>WsDbFetch query/result association resolved
3307 <li>Tree leaf to sequence mapping improved
3308 <li>Smooth fonts switch moved to FontChooser dialog box.
3315 <div align="center">
3316 <strong>2.1.1</strong><br> 12/9/06
3321 <li>Copy consensus sequence to clipboard</li>
3326 <li>Image output - rightmost residues are rendered if
3327 sequence id panel has been resized</li>
3328 <li>Image output - all offscreen group boundaries are
3330 <li>Annotation files with sequence references - all
3331 elements in file are relative to sequence position</li>
3332 <li>Mac Applet users can use Alt key for group editing</li>
3338 <div align="center">
3339 <strong>2.1</strong><br> 22/8/06
3344 <li>MAFFT Multiple Alignment in default Web Service list</li>
3345 <li>DAS Feature fetching</li>
3346 <li>Hide sequences and columns</li>
3347 <li>Export Annotations and Features</li>
3348 <li>GFF file reading / writing</li>
3349 <li>Associate structures with sequences from local PDB
3351 <li>Add sequences to exisiting alignment</li>
3352 <li>Recently opened files / URL lists</li>
3353 <li>Applet can launch the full application</li>
3354 <li>Applet has transparency for features (Java 1.2
3356 <li>Applet has user defined colours parameter</li>
3357 <li>Applet can load sequences from parameter
3358 "sequence<em>x</em>"
3364 <li>Redundancy Panel reinstalled in the Applet</li>
3365 <li>Monospaced font - EPS / rescaling bug fixed</li>
3366 <li>Annotation files with sequence references bug fixed</li>
3372 <div align="center">
3373 <strong>2.08.1</strong><br> 2/5/06
3378 <li>Change case of selected region from Popup menu</li>
3379 <li>Choose to match case when searching</li>
3380 <li>Middle mouse button and mouse movement can compress /
3381 expand the visible width and height of the alignment</li>
3386 <li>Annotation Panel displays complete JNet results</li>
3392 <div align="center">
3393 <strong>2.08b</strong><br> 18/4/06
3399 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3400 <li>Righthand label on wrapped alignments shows correct
3407 <div align="center">
3408 <strong>2.08</strong><br> 10/4/06
3413 <li>Editing can be locked to the selection area</li>
3414 <li>Keyboard editing</li>
3415 <li>Create sequence features from searches</li>
3416 <li>Precalculated annotations can be loaded onto
3418 <li>Features file allows grouping of features</li>
3419 <li>Annotation Colouring scheme added</li>
3420 <li>Smooth fonts off by default - Faster rendering</li>
3421 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3426 <li>Drag & Drop fixed on Linux</li>
3427 <li>Jalview Archive file faster to load/save, sequence
3428 descriptions saved.</li>
3434 <div align="center">
3435 <strong>2.07</strong><br> 12/12/05
3440 <li>PDB Structure Viewer enhanced</li>
3441 <li>Sequence Feature retrieval and display enhanced</li>
3442 <li>Choose to output sequence start-end after sequence
3443 name for file output</li>
3444 <li>Sequence Fetcher WSDBFetch@EBI</li>
3445 <li>Applet can read feature files, PDB files and can be
3446 used for HTML form input</li>
3451 <li>HTML output writes groups and features</li>
3452 <li>Group editing is Control and mouse click</li>
3453 <li>File IO bugs</li>
3459 <div align="center">
3460 <strong>2.06</strong><br> 28/9/05
3465 <li>View annotations in wrapped mode</li>
3466 <li>More options for PCA viewer</li>
3471 <li>GUI bugs resolved</li>
3472 <li>Runs with -nodisplay from command line</li>
3478 <div align="center">
3479 <strong>2.05b</strong><br> 15/9/05
3484 <li>Choose EPS export as lineart or text</li>
3485 <li>Jar files are executable</li>
3486 <li>Can read in Uracil - maps to unknown residue</li>
3491 <li>Known OutOfMemory errors give warning message</li>
3492 <li>Overview window calculated more efficiently</li>
3493 <li>Several GUI bugs resolved</li>
3499 <div align="center">
3500 <strong>2.05</strong><br> 30/8/05
3505 <li>Edit and annotate in "Wrapped" view</li>
3510 <li>Several GUI bugs resolved</li>
3516 <div align="center">
3517 <strong>2.04</strong><br> 24/8/05
3522 <li>Hold down mouse wheel & scroll to change font
3528 <li>Improved JPred client reliability</li>
3529 <li>Improved loading of Jalview files</li>
3535 <div align="center">
3536 <strong>2.03</strong><br> 18/8/05
3541 <li>Set Proxy server name and port in preferences</li>
3542 <li>Multiple URL links from sequence ids</li>
3543 <li>User Defined Colours can have a scheme name and added
3545 <li>Choose to ignore gaps in consensus calculation</li>
3546 <li>Unix users can set default web browser</li>
3547 <li>Runs without GUI for batch processing</li>
3548 <li>Dynamically generated Web Service Menus</li>
3553 <li>InstallAnywhere download for Sparc Solaris</li>
3559 <div align="center">
3560 <strong>2.02</strong><br> 18/7/05
3566 <li>Copy & Paste order of sequences maintains
3567 alignment order.</li>
3573 <div align="center">
3574 <strong>2.01</strong><br> 12/7/05
3579 <li>Use delete key for deleting selection.</li>
3580 <li>Use Mouse wheel to scroll sequences.</li>
3581 <li>Help file updated to describe how to add alignment
3583 <li>Version and build date written to build properties
3585 <li>InstallAnywhere installation will check for updates
3586 at launch of Jalview.</li>
3591 <li>Delete gaps bug fixed.</li>
3592 <li>FileChooser sorts columns.</li>
3593 <li>Can remove groups one by one.</li>
3594 <li>Filechooser icons installed.</li>
3595 <li>Finder ignores return character when searching.
3596 Return key will initiate a search.<br>
3603 <div align="center">
3604 <strong>2.0</strong><br> 20/6/05
3609 <li>New codebase</li>