3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.3">2.10.3</a><br />
74 <em>14/11/2017</em></strong>
77 <td><div align="left">
81 <!-- JAL-2446 -->Faster and more efficient management and
82 rendering of sequence features
85 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
86 429 rate limit request hander
89 <!-- JAL-2773 -->Structure views don't get updated unless
90 their colours have changed
92 <li><!-- JAL-2495 -->All linked sequences are highlighted for a structure mousover (Jmol) or selection (Chimera)</li>
93 <li><!-- JAL-2790 -->'Cancel' button in progress bar for JABAWS AACon, RNAAliFold and Disorder prediction jobs
96 <li><!-- JAL-2617 -->Stop codons are excluded in CDS/Protein view from Ensembl locus cross-references</li>
97 <li><!-- JAL-2685 -->Start/End limits are shown in Pairwise Alignment report</li>
101 <li>Groovy interpreter updated to 2.4.12</li>
102 <li>Example groovy script for generating a matrix of percent identity scores for current alignment.</li>
104 <em>Testing and Deployment</em>
105 <ul><li><!-- JAL-2727 -->Test to catch memory leaks in Jalview UI</li></ul>
108 <td><div align="left">
111 <li><!-- JAL-2643 -->Pressing tab after updating the colour threshold text field doesn't trigger an update to the alignment view</li>
112 <li><!-- JAL-2682 -->Race condition when parsing sequence ID strings in parallel</li>
113 <li><!-- JAL-2608 -->Overview windows are also closed when alignment window is closed</li>
114 <li><!-- JAL-2548 -->Export of features doesn't always respect group visibility</li>
118 <li><!-- JAL-2777 -->Structures with whitespace chainCode cannot be viewed in Chimera</li>
119 <li><!-- JAL-2728 -->Protein annotation panel too high in CDS/Protein view
121 <li><!-- JAL-2757 -->Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs
123 <li><!-- JAL-2253 -->Slow EnsemblGenome ID lookup</li>
124 <li><!-- JAL-2529 -->Revised Ensembl REST API CDNA query</li>
125 <li><!-- JAL-2739 -->Hidden column marker in last column not rendered when switching back from Wrapped to normal view</li>
126 <li><!-- JAL-2768 -->Annotation display corrupted when scrolling right in unwapped alignment view</li>
127 <li><!-- JAL-2542 -->Existing features on subsequence incorrectly relocated when full sequence retrieved from database</li>
128 <li><!-- JAL-2733 -->Last reported memory still shown when Desktop->Show Memory is unticked (OSX only)</li>
129 <li><!-- JAL-2658 -->Amend Features dialog doesn't allow features of same type and group to be selected for amending</li>
130 <li><!-- JAL-2524 -->Jalview becomes sluggish in wide alignments when hidden columns are present</li>
131 <li><!-- JAL-2392 -->Jalview freezes when loading and displaying several structures</li>
132 <li><!-- JAL-2732 -->Black outlines left after resizing or moving a window</li>
133 <li><!-- JAL-1900,JAL-1625 -->Unable to minimise windows within the Jalview desktop on OSX</li>
134 <li><!-- JAL-2667 -->Mouse wheel doesn't scroll vertically when in wrapped alignment mode</li>
135 <li><!-- JAL-2636 -->Scale mark not shown when close to right hand end of alignment</li>
136 <li><!-- JAL-2684 -->Pairwise alignment only aligns selected regions of each selected sequence</li>
137 <li><!-- JAL-2973 -->Alignment ruler height set incorrectly after canceling the Alignment Window's Font dialog</li>
138 <li><!-- JAL-2036 -->Show cross-references not enabled after restoring project until a new view is created</li>
139 <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>
140 <li><!-- JAL-2775 -->Overview redraws whole window when box position is adjusted</li>
141 <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>
143 <strong><em>Applet</em></strong><br/>
145 <li><!-- JAL-2687 -->Concurrent modification exception when closing alignment panel</li>
147 <strong><em>BioJSON</em></strong><br/>
150 <!-- JAL-2546 -->BioJSON export does not preserve non-positional features
153 <strong>Known Java 9 Issues</strong>
155 <li><!-- JAL-2902 -->Groovy Console very slow to open and is
156 not responsive when entering characters (Webstart, Java 9.01,
160 <strong>New Known Issues</strong>
162 <li><!-- JAL- --></li>
168 <td width="60" nowrap>
170 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
171 <em>2/10/2017</em></strong>
174 <td><div align="left">
175 <em>New features in Jalview Desktop</em>
178 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
180 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
184 <td><div align="left">
188 <td width="60" nowrap>
190 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
191 <em>7/9/2017</em></strong>
194 <td><div align="left">
198 <!-- JAL-2588 -->Show gaps in overview window by colouring
199 in grey (sequences used to be coloured grey, and gaps were
203 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
207 <!-- JAL-2587 -->Overview updates immediately on increase
208 in size and progress bar shown as higher resolution
209 overview is recalculated
214 <td><div align="left">
218 <!-- JAL-2664 -->Overview window redraws every hidden
219 column region row by row
222 <!-- JAL-2681 -->duplicate protein sequences shown after
223 retrieving Ensembl crossrefs for sequences from Uniprot
226 <!-- JAL-2603 -->Overview window throws NPE if show boxes
227 format setting is unticked
230 <!-- JAL-2610 -->Groups are coloured wrongly in overview
231 if group has show boxes format setting unticked
234 <!-- JAL-2672,JAL-2665 -->Redraw problems when
235 autoscrolling whilst dragging current selection group to
236 include sequences and columns not currently displayed
239 <!-- JAL-2691 -->Not all chains are mapped when multimeric
240 assemblies are imported via CIF file
243 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
244 displayed when threshold or conservation colouring is also
248 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
252 <!-- JAL-2673 -->Jalview continues to scroll after
253 dragging a selected region off the visible region of the
257 <!-- JAL-2724 -->Cannot apply annotation based
258 colourscheme to all groups in a view
261 <!-- JAL-2511 -->IDs don't line up with sequences
262 initially after font size change using the Font chooser or
269 <td width="60" nowrap>
271 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
274 <td><div align="left">
275 <em>Calculations</em>
279 <!-- JAL-1933 -->Occupancy annotation row shows number of
280 ungapped positions in each column of the alignment.
283 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
284 a calculation dialog box
287 <!-- JAL-2379 -->Revised implementation of PCA for speed
288 and memory efficiency (~30x faster)
291 <!-- JAL-2403 -->Revised implementation of sequence
292 similarity scores as used by Tree, PCA, Shading Consensus
293 and other calculations
296 <!-- JAL-2416 -->Score matrices are stored as resource
297 files within the Jalview codebase
300 <!-- JAL-2500 -->Trees computed on Sequence Feature
301 Similarity may have different topology due to increased
308 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
309 model for alignments and groups
312 <!-- JAL-384 -->Custom shading schemes created via groovy
319 <!-- JAL-2526 -->Efficiency improvements for interacting
320 with alignment and overview windows
323 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
327 <!-- JAL-2388 -->Hidden columns and sequences can be
331 <!-- JAL-2611 -->Click-drag in visible area allows fine
332 adjustment of visible position
336 <em>Data import/export</em>
339 <!-- JAL-2535 -->Posterior probability annotation from
340 Stockholm files imported as sequence associated annotation
343 <!-- JAL-2507 -->More robust per-sequence positional
344 annotation input/output via stockholm flatfile
347 <!-- JAL-2533 -->Sequence names don't include file
348 extension when importing structure files without embedded
349 names or PDB accessions
352 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
353 format sequence substitution matrices
356 <em>User Interface</em>
359 <!-- JAL-2447 --> Experimental Features Checkbox in
360 Desktop's Tools menu to hide or show untested features in
364 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
365 via Overview or sequence motif search operations
368 <!-- JAL-2547 -->Amend sequence features dialog box can be
369 opened by double clicking gaps within sequence feature
373 <!-- JAL-1476 -->Status bar message shown when not enough
374 aligned positions were available to create a 3D structure
378 <em>3D Structure</em>
381 <!-- JAL-2430 -->Hidden regions in alignment views are not
382 coloured in linked structure views
385 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
386 file-based command exchange
389 <!-- JAL-2375 -->Structure chooser automatically shows
390 Cached Structures rather than querying the PDBe if
391 structures are already available for sequences
394 <!-- JAL-2520 -->Structures imported via URL are cached in
395 the Jalview project rather than downloaded again when the
399 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
400 to transfer Chimera's structure attributes as Jalview
401 features, and vice-versa (<strong>Experimental
405 <em>Web Services</em>
408 <!-- JAL-2549 -->Updated JABAWS client to v2.2
411 <!-- JAL-2335 -->Filter non-standard amino acids and
412 nucleotides when submitting to AACon and other MSA
416 <!-- JAL-2316, -->URLs for viewing database
417 cross-references provided by identifiers.org and the
425 <!-- JAL-2344 -->FileFormatI interface for describing and
426 identifying file formats (instead of String constants)
429 <!-- JAL-2228 -->FeatureCounter script refactored for
430 efficiency when counting all displayed features (not
431 backwards compatible with 2.10.1)
434 <em>Example files</em>
437 <!-- JAL-2631 -->Graduated feature colour style example
438 included in the example feature file
441 <em>Documentation</em>
444 <!-- JAL-2339 -->Release notes reformatted for readability
445 with the built-in Java help viewer
448 <!-- JAL-1644 -->Find documentation updated with 'search
449 sequence description' option
455 <!-- JAL-2485, -->External service integration tests for
456 Uniprot REST Free Text Search Client
459 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
462 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
467 <td><div align="left">
468 <em>Calculations</em>
471 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
472 matrix - C->R should be '-3'<br />Old matrix restored
473 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
475 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
476 Jalview's treatment of gaps in PCA and substitution matrix
477 based Tree calculations.<br /> <br />In earlier versions
478 of Jalview, gaps matching gaps were penalised, and gaps
479 matching non-gaps penalised even more. In the PCA
480 calculation, gaps were actually treated as non-gaps - so
481 different costs were applied, which meant Jalview's PCAs
482 were different to those produced by SeqSpace.<br />Jalview
483 now treats gaps in the same way as SeqSpace (ie it scores
484 them as 0). <br /> <br />Enter the following in the
485 Groovy console to restore pre-2.10.2 behaviour:<br />
486 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
487 // for 2.10.1 mode <br />
488 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
489 // to restore 2.10.2 mode <br /> <br /> <em>Note:
490 these settings will affect all subsequent tree and PCA
491 calculations (not recommended)</em></li>
493 <!-- JAL-2424 -->Fixed off-by-one bug that affected
494 scaling of branch lengths for trees computed using
495 Sequence Feature Similarity.
498 <!-- JAL-2377 -->PCA calculation could hang when
499 generating output report when working with highly
503 <!-- JAL-2544 --> Sort by features includes features to
504 right of selected region when gaps present on right-hand
508 <em>User Interface</em>
511 <!-- JAL-2346 -->Reopening Colour by annotation dialog
512 doesn't reselect a specific sequence's associated
513 annotation after it was used for colouring a view
516 <!-- JAL-2419 -->Current selection lost if popup menu
517 opened on a region of alignment without groups
520 <!-- JAL-2374 -->Popup menu not always shown for regions
521 of an alignment with overlapping groups
524 <!-- JAL-2310 -->Finder double counts if both a sequence's
525 name and description match
528 <!-- JAL-2370 -->Hiding column selection containing two
529 hidden regions results in incorrect hidden regions
532 <!-- JAL-2386 -->'Apply to all groups' setting when
533 changing colour does not apply Conservation slider value
537 <!-- JAL-2373 -->Percentage identity and conservation menu
538 items do not show a tick or allow shading to be disabled
541 <!-- JAL-2385 -->Conservation shading or PID threshold
542 lost when base colourscheme changed if slider not visible
545 <!-- JAL-2547 -->Sequence features shown in tooltip for
546 gaps before start of features
549 <!-- JAL-2623 -->Graduated feature colour threshold not
550 restored to UI when feature colour is edited
553 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
554 a time when scrolling vertically in wrapped mode.
557 <!-- JAL-2630 -->Structure and alignment overview update
558 as graduate feature colour settings are modified via the
562 <!-- JAL-2034 -->Overview window doesn't always update
563 when a group defined on the alignment is resized
566 <!-- JAL-2605 -->Mouseovers on left/right scale region in
567 wrapped view result in positional status updates
571 <!-- JAL-2563 -->Status bar doesn't show position for
572 ambiguous amino acid and nucleotide symbols
575 <!-- JAL-2602 -->Copy consensus sequence failed if
576 alignment included gapped columns
579 <!-- JAL-2473 -->Minimum size set for Jalview windows so
580 widgets don't permanently disappear
583 <!-- JAL-2503 -->Cannot select or filter quantitative
584 annotation that are shown only as column labels (e.g.
585 T-Coffee column reliability scores)
588 <!-- JAL-2594 -->Exception thrown if trying to create a
589 sequence feature on gaps only
592 <!-- JAL-2504 -->Features created with 'New feature'
593 button from a Find inherit previously defined feature type
594 rather than the Find query string
597 <!-- JAL-2423 -->incorrect title in output window when
598 exporting tree calculated in Jalview
601 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
602 and then revealing them reorders sequences on the
606 <!-- JAL-964 -->Group panel in sequence feature settings
607 doesn't update to reflect available set of groups after
608 interactively adding or modifying features
611 <!-- JAL-2225 -->Sequence Database chooser unusable on
615 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
616 only excluded gaps in current sequence and ignored
623 <!-- JAL-2421 -->Overview window visible region moves
624 erratically when hidden rows or columns are present
627 <!-- JAL-2362 -->Per-residue colourschemes applied via the
628 Structure Viewer's colour menu don't correspond to
632 <!-- JAL-2405 -->Protein specific colours only offered in
633 colour and group colour menu for protein alignments
636 <!-- JAL-2385 -->Colour threshold slider doesn't update to
637 reflect currently selected view or group's shading
641 <!-- JAL-2624 -->Feature colour thresholds not respected
642 when rendered on overview and structures when opacity at
646 <!-- JAL-2589 -->User defined gap colour not shown in
647 overview when features overlaid on alignment
650 <em>Data import/export</em>
653 <!-- JAL-2576 -->Very large alignments take a long time to
657 <!-- JAL-2507 -->Per-sequence RNA secondary structures
658 added after a sequence was imported are not written to
662 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
663 when importing RNA secondary structure via Stockholm
666 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
667 not shown in correct direction for simple pseudoknots
670 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
671 with lightGray or darkGray via features file (but can
675 <!-- JAL-2383 -->Above PID colour threshold not recovered
676 when alignment view imported from project
679 <!-- JAL-2520,JAL-2465 -->No mappings generated between
680 structure and sequences extracted from structure files
681 imported via URL and viewed in Jmol
684 <!-- JAL-2520 -->Structures loaded via URL are saved in
685 Jalview Projects rather than fetched via URL again when
686 the project is loaded and the structure viewed
689 <em>Web Services</em>
692 <!-- JAL-2519 -->EnsemblGenomes example failing after
693 release of Ensembl v.88
696 <!-- JAL-2366 -->Proxy server address and port always
697 appear enabled in Preferences->Connections
700 <!-- JAL-2461 -->DAS registry not found exceptions
701 removed from console output
704 <!-- JAL-2582 -->Cannot retrieve protein products from
705 Ensembl by Peptide ID
708 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
709 created from SIFTs, and spurious 'Couldn't open structure
710 in Chimera' errors raised after April 2017 update (problem
711 due to 'null' string rather than empty string used for
712 residues with no corresponding PDB mapping).
715 <em>Application UI</em>
718 <!-- JAL-2361 -->User Defined Colours not added to Colour
722 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
723 case' residues (button in colourscheme editor debugged and
724 new documentation and tooltips added)
727 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
728 doesn't restore group-specific text colour thresholds
731 <!-- JAL-2243 -->Feature settings panel does not update as
732 new features are added to alignment
735 <!-- JAL-2532 -->Cancel in feature settings reverts
736 changes to feature colours via the Amend features dialog
739 <!-- JAL-2506 -->Null pointer exception when attempting to
740 edit graduated feature colour via amend features dialog
744 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
745 selection menu changes colours of alignment views
748 <!-- JAL-2426 -->Spurious exceptions in console raised
749 from alignment calculation workers after alignment has
753 <!-- JAL-1608 -->Typo in selection popup menu - Create
754 groups now 'Create Group'
757 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
758 Create/Undefine group doesn't always work
761 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
762 shown again after pressing 'Cancel'
765 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
766 adjusts start position in wrap mode
769 <!-- JAL-2563 -->Status bar doesn't show positions for
770 ambiguous amino acids
773 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
774 CDS/Protein view after CDS sequences added for aligned
778 <!-- JAL-2592 -->User defined colourschemes called 'User
779 Defined' don't appear in Colours menu
785 <!-- JAL-2468 -->Switching between Nucleotide and Protein
786 score models doesn't always result in an updated PCA plot
789 <!-- JAL-2442 -->Features not rendered as transparent on
790 overview or linked structure view
793 <!-- JAL-2372 -->Colour group by conservation doesn't
797 <!-- JAL-2517 -->Hitting Cancel after applying
798 user-defined colourscheme doesn't restore original
805 <!-- JAL-2314 -->Unit test failure:
806 jalview.ws.jabaws.RNAStructExportImport setup fails
809 <!-- JAL-2307 -->Unit test failure:
810 jalview.ws.sifts.SiftsClientTest due to compatibility
811 problems with deep array comparison equality asserts in
812 successive versions of TestNG
815 <!-- JAL-2479 -->Relocated StructureChooserTest and
816 ParameterUtilsTest Unit tests to Network suite
819 <em>New Known Issues</em>
822 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
823 phase after a sequence motif find operation
826 <!-- JAL-2550 -->Importing annotation file with rows
827 containing just upper and lower case letters are
828 interpreted as WUSS RNA secondary structure symbols
831 <!-- JAL-2590 -->Cannot load and display Newick trees
832 reliably from eggnog Ortholog database
835 <!-- JAL-2468 -->Status bar shows 'Marked x columns
836 containing features of type Highlight' when 'B' is pressed
837 to mark columns containing highlighted regions.
840 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
841 doesn't always add secondary structure annotation.
846 <td width="60" nowrap>
848 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
851 <td><div align="left">
855 <!-- JAL-98 -->Improved memory usage: sparse arrays used
856 for all consensus calculations
859 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
862 <li>Updated Jalview's Certum code signing certificate
868 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
869 set of database cross-references, sorted alphabetically
872 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
873 from database cross references. Users with custom links
874 will receive a <a href="webServices/urllinks.html#warning">warning
875 dialog</a> asking them to update their preferences.
878 <!-- JAL-2287-->Cancel button and escape listener on
879 dialog warning user about disconnecting Jalview from a
883 <!-- JAL-2320-->Jalview's Chimera control window closes if
884 the Chimera it is connected to is shut down
887 <!-- JAL-1738-->New keystroke (B) and Select highlighted
888 columns menu item to mark columns containing highlighted
889 regions (e.g. from structure selections or results of a
893 <!-- JAL-2284-->Command line option for batch-generation
894 of HTML pages rendering alignment data with the BioJS
904 <!-- JAL-2286 -->Columns with more than one modal residue
905 are not coloured or thresholded according to percent
906 identity (first observed in Jalview 2.8.2)
909 <!-- JAL-2301 -->Threonine incorrectly reported as not
913 <!-- JAL-2318 -->Updates to documentation pages (above PID
914 threshold, amino acid properties)
917 <!-- JAL-2292 -->Lower case residues in sequences are not
918 reported as mapped to residues in a structure file in the
922 <!--JAL-2324 -->Identical features with non-numeric scores
923 could be added multiple times to a sequence
926 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
927 bond features shown as two highlighted residues rather
928 than a range in linked structure views, and treated
929 correctly when selecting and computing trees from features
932 <!-- JAL-2281-->Custom URL links for database
933 cross-references are matched to database name regardless
941 <!-- JAL-2282-->Custom URL links for specific database
942 names without regular expressions also offer links from
946 <!-- JAL-2315-->Removing a single configured link in the
947 URL links pane in Connections preferences doesn't actually
948 update Jalview configuration
951 <!-- JAL-2272-->CTRL-Click on a selected region to open
952 the alignment area popup menu doesn't work on El-Capitan
955 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
956 files with similarly named sequences if dropped onto the
960 <!-- JAL-2312 -->Additional mappings are shown for PDB
961 entries where more chains exist in the PDB accession than
962 are reported in the SIFTS file
965 <!-- JAL-2317-->Certain structures do not get mapped to
966 the structure view when displayed with Chimera
969 <!-- JAL-2317-->No chains shown in the Chimera view
970 panel's View->Show Chains submenu
973 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
974 work for wrapped alignment views
977 <!--JAL-2197 -->Rename UI components for running JPred
978 predictions from 'JNet' to 'JPred'
981 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
982 corrupted when annotation panel vertical scroll is not at
986 <!--JAL-2332 -->Attempting to view structure for Hen
987 lysozyme results in a PDB Client error dialog box
990 <!-- JAL-2319 -->Structure View's mapping report switched
991 ranges for PDB and sequence for SIFTS
994 SIFTS 'Not_Observed' residues mapped to non-existant
998 <!-- <em>New Known Issues</em>
1005 <td width="60" nowrap>
1006 <div align="center">
1007 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1008 <em>25/10/2016</em></strong>
1011 <td><em>Application</em>
1013 <li>3D Structure chooser opens with 'Cached structures'
1014 view if structures already loaded</li>
1015 <li>Progress bar reports models as they are loaded to
1016 structure views</li>
1022 <li>Colour by conservation always enabled and no tick
1023 shown in menu when BLOSUM or PID shading applied</li>
1024 <li>FER1_ARATH and FER2_ARATH labels were switched in
1025 example sequences/projects/trees</li>
1027 <em>Application</em>
1029 <li>Jalview projects with views of local PDB structure
1030 files saved on Windows cannot be opened on OSX</li>
1031 <li>Multiple structure views can be opened and superposed
1032 without timeout for structures with multiple models or
1033 multiple sequences in alignment</li>
1034 <li>Cannot import or associated local PDB files without a
1035 PDB ID HEADER line</li>
1036 <li>RMSD is not output in Jmol console when superposition
1038 <li>Drag and drop of URL from Browser fails for Linux and
1039 OSX versions earlier than El Capitan</li>
1040 <li>ENA client ignores invalid content from ENA server</li>
1041 <li>Exceptions are not raised in console when ENA client
1042 attempts to fetch non-existent IDs via Fetch DB Refs UI
1044 <li>Exceptions are not raised in console when a new view
1045 is created on the alignment</li>
1046 <li>OSX right-click fixed for group selections: CMD-click
1047 to insert/remove gaps in groups and CTRL-click to open group
1050 <em>Build and deployment</em>
1052 <li>URL link checker now copes with multi-line anchor
1055 <em>New Known Issues</em>
1057 <li>Drag and drop from URL links in browsers do not work
1064 <td width="60" nowrap>
1065 <div align="center">
1066 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1069 <td><em>General</em>
1072 <!-- JAL-2124 -->Updated Spanish translations.
1075 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1076 for importing structure data to Jalview. Enables mmCIF and
1080 <!-- JAL-192 --->Alignment ruler shows positions relative to
1084 <!-- JAL-2202 -->Position/residue shown in status bar when
1085 mousing over sequence associated annotation
1088 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1092 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1093 '()', canonical '[]' and invalid '{}' base pair populations
1097 <!-- JAL-2092 -->Feature settings popup menu options for
1098 showing or hiding columns containing a feature
1101 <!-- JAL-1557 -->Edit selected group by double clicking on
1102 group and sequence associated annotation labels
1105 <!-- JAL-2236 -->Sequence name added to annotation label in
1106 select/hide columns by annotation and colour by annotation
1110 </ul> <em>Application</em>
1113 <!-- JAL-2050-->Automatically hide introns when opening a
1114 gene/transcript view
1117 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1121 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1122 structure mappings with the EMBL-EBI PDBe SIFTS database
1125 <!-- JAL-2079 -->Updated download sites used for Rfam and
1126 Pfam sources to xfam.org
1129 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1132 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1133 over sequences in Jalview
1136 <!-- JAL-2027-->Support for reverse-complement coding
1137 regions in ENA and EMBL
1140 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1141 for record retrieval via ENA rest API
1144 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1148 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1149 groovy script execution
1152 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1153 alignment window's Calculate menu
1156 <!-- JAL-1812 -->Allow groovy scripts that call
1157 Jalview.getAlignFrames() to run in headless mode
1160 <!-- JAL-2068 -->Support for creating new alignment
1161 calculation workers from groovy scripts
1164 <!-- JAL-1369 --->Store/restore reference sequence in
1168 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1169 associations are now saved/restored from project
1172 <!-- JAL-1993 -->Database selection dialog always shown
1173 before sequence fetcher is opened
1176 <!-- JAL-2183 -->Double click on an entry in Jalview's
1177 database chooser opens a sequence fetcher
1180 <!-- JAL-1563 -->Free-text search client for UniProt using
1181 the UniProt REST API
1184 <!-- JAL-2168 -->-nonews command line parameter to prevent
1185 the news reader opening
1188 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1189 querying stored in preferences
1192 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1196 <!-- JAL-1977-->Tooltips shown on database chooser
1199 <!-- JAL-391 -->Reverse complement function in calculate
1200 menu for nucleotide sequences
1203 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1204 and feature counts preserves alignment ordering (and
1205 debugged for complex feature sets).
1208 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1209 viewing structures with Jalview 2.10
1212 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1213 genome, transcript CCDS and gene ids via the Ensembl and
1214 Ensembl Genomes REST API
1217 <!-- JAL-2049 -->Protein sequence variant annotation
1218 computed for 'sequence_variant' annotation on CDS regions
1222 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1226 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1227 Ref Fetcher fails to match, or otherwise updates sequence
1228 data from external database records.
1231 <!-- JAL-2154 -->Revised Jalview Project format for
1232 efficient recovery of sequence coding and alignment
1233 annotation relationships.
1235 </ul> <!-- <em>Applet</em>
1246 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1250 <!-- JAL-2018-->Export features in Jalview format (again)
1251 includes graduated colourschemes
1254 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1255 working with big alignments and lots of hidden columns
1258 <!-- JAL-2053-->Hidden column markers not always rendered
1259 at right of alignment window
1262 <!-- JAL-2067 -->Tidied up links in help file table of
1266 <!-- JAL-2072 -->Feature based tree calculation not shown
1270 <!-- JAL-2075 -->Hidden columns ignored during feature
1271 based tree calculation
1274 <!-- JAL-2065 -->Alignment view stops updating when show
1275 unconserved enabled for group on alignment
1278 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1282 <!-- JAL-2146 -->Alignment column in status incorrectly
1283 shown as "Sequence position" when mousing over
1287 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1288 hidden columns present
1291 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1292 user created annotation added to alignment
1295 <!-- JAL-1841 -->RNA Structure consensus only computed for
1296 '()' base pair annotation
1299 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1300 in zero scores for all base pairs in RNA Structure
1304 <!-- JAL-2174-->Extend selection with columns containing
1308 <!-- JAL-2275 -->Pfam format writer puts extra space at
1309 beginning of sequence
1312 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1316 <!-- JAL-2238 -->Cannot create groups on an alignment from
1317 from a tree when t-coffee scores are shown
1320 <!-- JAL-1836,1967 -->Cannot import and view PDB
1321 structures with chains containing negative resnums (4q4h)
1324 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1328 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1329 to Clustal, PIR and PileUp output
1332 <!-- JAL-2008 -->Reordering sequence features that are
1333 not visible causes alignment window to repaint
1336 <!-- JAL-2006 -->Threshold sliders don't work in
1337 graduated colour and colour by annotation row for e-value
1338 scores associated with features and annotation rows
1341 <!-- JAL-1797 -->amino acid physicochemical conservation
1342 calculation should be case independent
1345 <!-- JAL-2173 -->Remove annotation also updates hidden
1349 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1350 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1351 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1354 <!-- JAL-2065 -->Null pointer exceptions and redraw
1355 problems when reference sequence defined and 'show
1356 non-conserved' enabled
1359 <!-- JAL-1306 -->Quality and Conservation are now shown on
1360 load even when Consensus calculation is disabled
1363 <!-- JAL-1932 -->Remove right on penultimate column of
1364 alignment does nothing
1367 <em>Application</em>
1370 <!-- JAL-1552-->URLs and links can't be imported by
1371 drag'n'drop on OSX when launched via webstart (note - not
1372 yet fixed for El Capitan)
1375 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1376 output when running on non-gb/us i18n platforms
1379 <!-- JAL-1944 -->Error thrown when exporting a view with
1380 hidden sequences as flat-file alignment
1383 <!-- JAL-2030-->InstallAnywhere distribution fails when
1387 <!-- JAL-2080-->Jalview very slow to launch via webstart
1388 (also hotfix for 2.9.0b2)
1391 <!-- JAL-2085 -->Cannot save project when view has a
1392 reference sequence defined
1395 <!-- JAL-1011 -->Columns are suddenly selected in other
1396 alignments and views when revealing hidden columns
1399 <!-- JAL-1989 -->Hide columns not mirrored in complement
1400 view in a cDNA/Protein splitframe
1403 <!-- JAL-1369 -->Cannot save/restore representative
1404 sequence from project when only one sequence is
1408 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1409 in Structure Chooser
1412 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1413 structure consensus didn't refresh annotation panel
1416 <!-- JAL-1962 -->View mapping in structure view shows
1417 mappings between sequence and all chains in a PDB file
1420 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1421 dialogs format columns correctly, don't display array
1422 data, sort columns according to type
1425 <!-- JAL-1975 -->Export complete shown after destination
1426 file chooser is cancelled during an image export
1429 <!-- JAL-2025 -->Error when querying PDB Service with
1430 sequence name containing special characters
1433 <!-- JAL-2024 -->Manual PDB structure querying should be
1437 <!-- JAL-2104 -->Large tooltips with broken HTML
1438 formatting don't wrap
1441 <!-- JAL-1128 -->Figures exported from wrapped view are
1442 truncated so L looks like I in consensus annotation
1445 <!-- JAL-2003 -->Export features should only export the
1446 currently displayed features for the current selection or
1450 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1451 after fetching cross-references, and restoring from
1455 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1456 followed in the structure viewer
1459 <!-- JAL-2163 -->Titles for individual alignments in
1460 splitframe not restored from project
1463 <!-- JAL-2145 -->missing autocalculated annotation at
1464 trailing end of protein alignment in transcript/product
1465 splitview when pad-gaps not enabled by default
1468 <!-- JAL-1797 -->amino acid physicochemical conservation
1472 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1473 article has been read (reopened issue due to
1474 internationalisation problems)
1477 <!-- JAL-1960 -->Only offer PDB structures in structure
1478 viewer based on sequence name, PDB and UniProt
1483 <!-- JAL-1976 -->No progress bar shown during export of
1487 <!-- JAL-2213 -->Structures not always superimposed after
1488 multiple structures are shown for one or more sequences.
1491 <!-- JAL-1370 -->Reference sequence characters should not
1492 be replaced with '.' when 'Show unconserved' format option
1496 <!-- JAL-1823 -->Cannot specify chain code when entering
1497 specific PDB id for sequence
1500 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1501 'Export hidden sequences' is enabled, but 'export hidden
1502 columns' is disabled.
1505 <!--JAL-2026-->Best Quality option in structure chooser
1506 selects lowest rather than highest resolution structures
1510 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1511 to sequence mapping in 'View Mappings' report
1514 <!-- JAL-2284 -->Unable to read old Jalview projects that
1515 contain non-XML data added after Jalvew wrote project.
1518 <!-- JAL-2118 -->Newly created annotation row reorders
1519 after clicking on it to create new annotation for a
1523 <!-- JAL-1980 -->Null Pointer Exception raised when
1524 pressing Add on an orphaned cut'n'paste window.
1526 <!-- may exclude, this is an external service stability issue JAL-1941
1527 -- > RNA 3D structure not added via DSSR service</li> -->
1532 <!-- JAL-2151 -->Incorrect columns are selected when
1533 hidden columns present before start of sequence
1536 <!-- JAL-1986 -->Missing dependencies on applet pages
1540 <!-- JAL-1947 -->Overview pixel size changes when
1541 sequences are hidden in applet
1544 <!-- JAL-1996 -->Updated instructions for applet
1545 deployment on examples pages.
1552 <td width="60" nowrap>
1553 <div align="center">
1554 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1555 <em>16/10/2015</em></strong>
1558 <td><em>General</em>
1560 <li>Time stamps for signed Jalview application and applet
1565 <em>Application</em>
1567 <li>Duplicate group consensus and conservation rows
1568 shown when tree is partitioned</li>
1569 <li>Erratic behaviour when tree partitions made with
1570 multiple cDNA/Protein split views</li>
1576 <td width="60" nowrap>
1577 <div align="center">
1578 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1579 <em>8/10/2015</em></strong>
1582 <td><em>General</em>
1584 <li>Updated Spanish translations of localized text for
1586 </ul> <em>Application</em>
1588 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1589 <li>Signed OSX InstallAnywhere installer<br></li>
1590 <li>Support for per-sequence based annotations in BioJSON</li>
1591 </ul> <em>Applet</em>
1593 <li>Split frame example added to applet examples page</li>
1594 </ul> <em>Build and Deployment</em>
1597 <!-- JAL-1888 -->New ant target for running Jalview's test
1605 <li>Mapping of cDNA to protein in split frames
1606 incorrect when sequence start > 1</li>
1607 <li>Broken images in filter column by annotation dialog
1609 <li>Feature colours not parsed from features file</li>
1610 <li>Exceptions and incomplete link URLs recovered when
1611 loading a features file containing HTML tags in feature
1615 <em>Application</em>
1617 <li>Annotations corrupted after BioJS export and
1619 <li>Incorrect sequence limits after Fetch DB References
1620 with 'trim retrieved sequences'</li>
1621 <li>Incorrect warning about deleting all data when
1622 deleting selected columns</li>
1623 <li>Patch to build system for shipping properly signed
1624 JNLP templates for webstart launch</li>
1625 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1626 unreleased structures for download or viewing</li>
1627 <li>Tab/space/return keystroke operation of EMBL-PDBe
1628 fetcher/viewer dialogs works correctly</li>
1629 <li>Disabled 'minimise' button on Jalview windows
1630 running on OSX to workaround redraw hang bug</li>
1631 <li>Split cDNA/Protein view position and geometry not
1632 recovered from jalview project</li>
1633 <li>Initial enabled/disabled state of annotation menu
1634 sorter 'show autocalculated first/last' corresponds to
1636 <li>Restoring of Clustal, RNA Helices and T-Coffee
1637 color schemes from BioJSON</li>
1641 <li>Reorder sequences mirrored in cDNA/Protein split
1643 <li>Applet with Jmol examples not loading correctly</li>
1649 <td><div align="center">
1650 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1652 <td><em>General</em>
1654 <li>Linked visualisation and analysis of DNA and Protein
1657 <li>Translated cDNA alignments shown as split protein
1658 and DNA alignment views</li>
1659 <li>Codon consensus annotation for linked protein and
1660 cDNA alignment views</li>
1661 <li>Link cDNA or Protein product sequences by loading
1662 them onto Protein or cDNA alignments</li>
1663 <li>Reconstruct linked cDNA alignment from aligned
1664 protein sequences</li>
1667 <li>Jmol integration updated to Jmol v14.2.14</li>
1668 <li>Import and export of Jalview alignment views as <a
1669 href="features/bioJsonFormat.html">BioJSON</a></li>
1670 <li>New alignment annotation file statements for
1671 reference sequences and marking hidden columns</li>
1672 <li>Reference sequence based alignment shading to
1673 highlight variation</li>
1674 <li>Select or hide columns according to alignment
1676 <li>Find option for locating sequences by description</li>
1677 <li>Conserved physicochemical properties shown in amino
1678 acid conservation row</li>
1679 <li>Alignments can be sorted by number of RNA helices</li>
1680 </ul> <em>Application</em>
1682 <li>New cDNA/Protein analysis capabilities
1684 <li>Get Cross-References should open a Split Frame
1685 view with cDNA/Protein</li>
1686 <li>Detect when nucleotide sequences and protein
1687 sequences are placed in the same alignment</li>
1688 <li>Split cDNA/Protein views are saved in Jalview
1693 <li>Use REST API to talk to Chimera</li>
1694 <li>Selected regions in Chimera are highlighted in linked
1695 Jalview windows</li>
1697 <li>VARNA RNA viewer updated to v3.93</li>
1698 <li>VARNA views are saved in Jalview Projects</li>
1699 <li>Pseudoknots displayed as Jalview RNA annotation can
1700 be shown in VARNA</li>
1702 <li>Make groups for selection uses marked columns as well
1703 as the active selected region</li>
1705 <li>Calculate UPGMA and NJ trees using sequence feature
1707 <li>New Export options
1709 <li>New Export Settings dialog to control hidden
1710 region export in flat file generation</li>
1712 <li>Export alignment views for display with the <a
1713 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1715 <li>Export scrollable SVG in HTML page</li>
1716 <li>Optional embedding of BioJSON data when exporting
1717 alignment figures to HTML</li>
1719 <li>3D structure retrieval and display
1721 <li>Free text and structured queries with the PDBe
1723 <li>PDBe Search API based discovery and selection of
1724 PDB structures for a sequence set</li>
1728 <li>JPred4 employed for protein secondary structure
1730 <li>Hide Insertions menu option to hide unaligned columns
1731 for one or a group of sequences</li>
1732 <li>Automatically hide insertions in alignments imported
1733 from the JPred4 web server</li>
1734 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1735 system on OSX<br />LGPL libraries courtesy of <a
1736 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1738 <li>changed 'View nucleotide structure' submenu to 'View
1739 VARNA 2D Structure'</li>
1740 <li>change "View protein structure" menu option to "3D
1743 </ul> <em>Applet</em>
1745 <li>New layout for applet example pages</li>
1746 <li>New parameters to enable SplitFrame view
1747 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1748 <li>New example demonstrating linked viewing of cDNA and
1749 Protein alignments</li>
1750 </ul> <em>Development and deployment</em>
1752 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1753 <li>Include installation type and git revision in build
1754 properties and console log output</li>
1755 <li>Jalview Github organisation, and new github site for
1756 storing BioJsMSA Templates</li>
1757 <li>Jalview's unit tests now managed with TestNG</li>
1760 <!-- <em>General</em>
1762 </ul> --> <!-- issues resolved --> <em>Application</em>
1764 <li>Escape should close any open find dialogs</li>
1765 <li>Typo in select-by-features status report</li>
1766 <li>Consensus RNA secondary secondary structure
1767 predictions are not highlighted in amber</li>
1768 <li>Missing gap character in v2.7 example file means
1769 alignment appears unaligned when pad-gaps is not enabled</li>
1770 <li>First switch to RNA Helices colouring doesn't colour
1771 associated structure views</li>
1772 <li>ID width preference option is greyed out when auto
1773 width checkbox not enabled</li>
1774 <li>Stopped a warning dialog from being shown when
1775 creating user defined colours</li>
1776 <li>'View Mapping' in structure viewer shows sequence
1777 mappings for just that viewer's sequences</li>
1778 <li>Workaround for superposing PDB files containing
1779 multiple models in Chimera</li>
1780 <li>Report sequence position in status bar when hovering
1781 over Jmol structure</li>
1782 <li>Cannot output gaps as '.' symbols with Selection ->
1783 output to text box</li>
1784 <li>Flat file exports of alignments with hidden columns
1785 have incorrect sequence start/end</li>
1786 <li>'Aligning' a second chain to a Chimera structure from
1788 <li>Colour schemes applied to structure viewers don't
1789 work for nucleotide</li>
1790 <li>Loading/cut'n'pasting an empty or invalid file leads
1791 to a grey/invisible alignment window</li>
1792 <li>Exported Jpred annotation from a sequence region
1793 imports to different position</li>
1794 <li>Space at beginning of sequence feature tooltips shown
1795 on some platforms</li>
1796 <li>Chimera viewer 'View | Show Chain' menu is not
1798 <li>'New View' fails with a Null Pointer Exception in
1799 console if Chimera has been opened</li>
1800 <li>Mouseover to Chimera not working</li>
1801 <li>Miscellaneous ENA XML feature qualifiers not
1803 <li>NPE in annotation renderer after 'Extract Scores'</li>
1804 <li>If two structures in one Chimera window, mouseover of
1805 either sequence shows on first structure</li>
1806 <li>'Show annotations' options should not make
1807 non-positional annotations visible</li>
1808 <li>Subsequence secondary structure annotation not shown
1809 in right place after 'view flanking regions'</li>
1810 <li>File Save As type unset when current file format is
1812 <li>Save as '.jar' option removed for saving Jalview
1814 <li>Colour by Sequence colouring in Chimera more
1816 <li>Cannot 'add reference annotation' for a sequence in
1817 several views on same alignment</li>
1818 <li>Cannot show linked products for EMBL / ENA records</li>
1819 <li>Jalview's tooltip wraps long texts containing no
1821 </ul> <em>Applet</em>
1823 <li>Jmol to JalviewLite mouseover/link not working</li>
1824 <li>JalviewLite can't import sequences with ID
1825 descriptions containing angle brackets</li>
1826 </ul> <em>General</em>
1828 <li>Cannot export and reimport RNA secondary structure
1829 via jalview annotation file</li>
1830 <li>Random helix colour palette for colour by annotation
1831 with RNA secondary structure</li>
1832 <li>Mouseover to cDNA from STOP residue in protein
1833 translation doesn't work.</li>
1834 <li>hints when using the select by annotation dialog box</li>
1835 <li>Jmol alignment incorrect if PDB file has alternate CA
1837 <li>FontChooser message dialog appears to hang after
1838 choosing 1pt font</li>
1839 <li>Peptide secondary structure incorrectly imported from
1840 annotation file when annotation display text includes 'e' or
1842 <li>Cannot set colour of new feature type whilst creating
1844 <li>cDNA translation alignment should not be sequence
1845 order dependent</li>
1846 <li>'Show unconserved' doesn't work for lower case
1848 <li>Nucleotide ambiguity codes involving R not recognised</li>
1849 </ul> <em>Deployment and Documentation</em>
1851 <li>Applet example pages appear different to the rest of
1852 www.jalview.org</li>
1853 </ul> <em>Application Known issues</em>
1855 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1856 <li>Misleading message appears after trying to delete
1858 <li>Jalview icon not shown in dock after InstallAnywhere
1859 version launches</li>
1860 <li>Fetching EMBL reference for an RNA sequence results
1861 fails with a sequence mismatch</li>
1862 <li>Corrupted or unreadable alignment display when
1863 scrolling alignment to right</li>
1864 <li>ArrayIndexOutOfBoundsException thrown when remove
1865 empty columns called on alignment with ragged gapped ends</li>
1866 <li>auto calculated alignment annotation rows do not get
1867 placed above or below non-autocalculated rows</li>
1868 <li>Jalview dekstop becomes sluggish at full screen in
1869 ultra-high resolution</li>
1870 <li>Cannot disable consensus calculation independently of
1871 quality and conservation</li>
1872 <li>Mouseover highlighting between cDNA and protein can
1873 become sluggish with more than one splitframe shown</li>
1874 </ul> <em>Applet Known Issues</em>
1876 <li>Core PDB parsing code requires Jmol</li>
1877 <li>Sequence canvas panel goes white when alignment
1878 window is being resized</li>
1884 <td><div align="center">
1885 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1887 <td><em>General</em>
1889 <li>Updated Java code signing certificate donated by
1891 <li>Features and annotation preserved when performing
1892 pairwise alignment</li>
1893 <li>RNA pseudoknot annotation can be
1894 imported/exported/displayed</li>
1895 <li>'colour by annotation' can colour by RNA and
1896 protein secondary structure</li>
1897 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1898 post-hoc with 2.9 release</em>)
1901 </ul> <em>Application</em>
1903 <li>Extract and display secondary structure for sequences
1904 with 3D structures</li>
1905 <li>Support for parsing RNAML</li>
1906 <li>Annotations menu for layout
1908 <li>sort sequence annotation rows by alignment</li>
1909 <li>place sequence annotation above/below alignment
1912 <li>Output in Stockholm format</li>
1913 <li>Internationalisation: improved Spanish (es)
1915 <li>Structure viewer preferences tab</li>
1916 <li>Disorder and Secondary Structure annotation tracks
1917 shared between alignments</li>
1918 <li>UCSF Chimera launch and linked highlighting from
1920 <li>Show/hide all sequence associated annotation rows for
1921 all or current selection</li>
1922 <li>disorder and secondary structure predictions
1923 available as dataset annotation</li>
1924 <li>Per-sequence rna helices colouring</li>
1927 <li>Sequence database accessions imported when fetching
1928 alignments from Rfam</li>
1929 <li>update VARNA version to 3.91</li>
1931 <li>New groovy scripts for exporting aligned positions,
1932 conservation values, and calculating sum of pairs scores.</li>
1933 <li>Command line argument to set default JABAWS server</li>
1934 <li>include installation type in build properties and
1935 console log output</li>
1936 <li>Updated Jalview project format to preserve dataset
1940 <!-- issues resolved --> <em>Application</em>
1942 <li>Distinguish alignment and sequence associated RNA
1943 structure in structure->view->VARNA</li>
1944 <li>Raise dialog box if user deletes all sequences in an
1946 <li>Pressing F1 results in documentation opening twice</li>
1947 <li>Sequence feature tooltip is wrapped</li>
1948 <li>Double click on sequence associated annotation
1949 selects only first column</li>
1950 <li>Redundancy removal doesn't result in unlinked
1951 leaves shown in tree</li>
1952 <li>Undos after several redundancy removals don't undo
1954 <li>Hide sequence doesn't hide associated annotation</li>
1955 <li>User defined colours dialog box too big to fit on
1956 screen and buttons not visible</li>
1957 <li>author list isn't updated if already written to
1958 Jalview properties</li>
1959 <li>Popup menu won't open after retrieving sequence
1961 <li>File open window for associate PDB doesn't open</li>
1962 <li>Left-then-right click on a sequence id opens a
1963 browser search window</li>
1964 <li>Cannot open sequence feature shading/sort popup menu
1965 in feature settings dialog</li>
1966 <li>better tooltip placement for some areas of Jalview
1968 <li>Allow addition of JABAWS Server which doesn't
1969 pass validation</li>
1970 <li>Web services parameters dialog box is too large to
1972 <li>Muscle nucleotide alignment preset obscured by
1974 <li>JABAWS preset submenus don't contain newly
1975 defined user preset</li>
1976 <li>MSA web services warns user if they were launched
1977 with invalid input</li>
1978 <li>Jalview cannot contact DAS Registy when running on
1981 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1982 'Superpose with' submenu not shown when new view
1986 </ul> <!-- <em>Applet</em>
1988 </ul> <em>General</em>
1990 </ul>--> <em>Deployment and Documentation</em>
1992 <li>2G and 1G options in launchApp have no effect on
1993 memory allocation</li>
1994 <li>launchApp service doesn't automatically open
1995 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1997 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1998 InstallAnywhere reports cannot find valid JVM when Java
1999 1.7_055 is available
2001 </ul> <em>Application Known issues</em>
2004 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2005 corrupted or unreadable alignment display when scrolling
2009 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2010 retrieval fails but progress bar continues for DAS retrieval
2011 with large number of ID
2014 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2015 flatfile output of visible region has incorrect sequence
2019 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2020 rna structure consensus doesn't update when secondary
2021 structure tracks are rearranged
2024 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2025 invalid rna structure positional highlighting does not
2026 highlight position of invalid base pairs
2029 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2030 out of memory errors are not raised when saving Jalview
2031 project from alignment window file menu
2034 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2035 Switching to RNA Helices colouring doesn't propagate to
2039 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2040 colour by RNA Helices not enabled when user created
2041 annotation added to alignment
2044 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2045 Jalview icon not shown on dock in Mountain Lion/Webstart
2047 </ul> <em>Applet Known Issues</em>
2050 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2051 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2054 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2055 Jalview and Jmol example not compatible with IE9
2058 <li>Sort by annotation score doesn't reverse order
2064 <td><div align="center">
2065 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2068 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2071 <li>Internationalisation of user interface (usually
2072 called i18n support) and translation for Spanish locale</li>
2073 <li>Define/Undefine group on current selection with
2074 Ctrl-G/Shift Ctrl-G</li>
2075 <li>Improved group creation/removal options in
2076 alignment/sequence Popup menu</li>
2077 <li>Sensible precision for symbol distribution
2078 percentages shown in logo tooltip.</li>
2079 <li>Annotation panel height set according to amount of
2080 annotation when alignment first opened</li>
2081 </ul> <em>Application</em>
2083 <li>Interactive consensus RNA secondary structure
2084 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2085 <li>Select columns containing particular features from
2086 Feature Settings dialog</li>
2087 <li>View all 'representative' PDB structures for selected
2089 <li>Update Jalview project format:
2091 <li>New file extension for Jalview projects '.jvp'</li>
2092 <li>Preserve sequence and annotation dataset (to
2093 store secondary structure annotation,etc)</li>
2094 <li>Per group and alignment annotation and RNA helix
2098 <li>New similarity measures for PCA and Tree calculation
2100 <li>Experimental support for retrieval and viewing of
2101 flanking regions for an alignment</li>
2105 <!-- issues resolved --> <em>Application</em>
2107 <li>logo keeps spinning and status remains at queued or
2108 running after job is cancelled</li>
2109 <li>cannot export features from alignments imported from
2110 Jalview/VAMSAS projects</li>
2111 <li>Buggy slider for web service parameters that take
2113 <li>Newly created RNA secondary structure line doesn't
2114 have 'display all symbols' flag set</li>
2115 <li>T-COFFEE alignment score shading scheme and other
2116 annotation shading not saved in Jalview project</li>
2117 <li>Local file cannot be loaded in freshly downloaded
2119 <li>Jalview icon not shown on dock in Mountain
2121 <li>Load file from desktop file browser fails</li>
2122 <li>Occasional NPE thrown when calculating large trees</li>
2123 <li>Cannot reorder or slide sequences after dragging an
2124 alignment onto desktop</li>
2125 <li>Colour by annotation dialog throws NPE after using
2126 'extract scores' function</li>
2127 <li>Loading/cut'n'pasting an empty file leads to a grey
2128 alignment window</li>
2129 <li>Disorder thresholds rendered incorrectly after
2130 performing IUPred disorder prediction</li>
2131 <li>Multiple group annotated consensus rows shown when
2132 changing 'normalise logo' display setting</li>
2133 <li>Find shows blank dialog after 'finished searching' if
2134 nothing matches query</li>
2135 <li>Null Pointer Exceptions raised when sorting by
2136 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2138 <li>Errors in Jmol console when structures in alignment
2139 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2141 <li>Not all working JABAWS services are shown in
2143 <li>JAVAWS version of Jalview fails to launch with
2144 'invalid literal/length code'</li>
2145 <li>Annotation/RNA Helix colourschemes cannot be applied
2146 to alignment with groups (actually fixed in 2.8.0b1)</li>
2147 <li>RNA Helices and T-Coffee Scores available as default
2150 </ul> <em>Applet</em>
2152 <li>Remove group option is shown even when selection is
2154 <li>Apply to all groups ticked but colourscheme changes
2155 don't affect groups</li>
2156 <li>Documented RNA Helices and T-Coffee Scores as valid
2157 colourscheme name</li>
2158 <li>Annotation labels drawn on sequence IDs when
2159 Annotation panel is not displayed</li>
2160 <li>Increased font size for dropdown menus on OSX and
2161 embedded windows</li>
2162 </ul> <em>Other</em>
2164 <li>Consensus sequence for alignments/groups with a
2165 single sequence were not calculated</li>
2166 <li>annotation files that contain only groups imported as
2167 annotation and junk sequences</li>
2168 <li>Fasta files with sequences containing '*' incorrectly
2169 recognised as PFAM or BLC</li>
2170 <li>conservation/PID slider apply all groups option
2171 doesn't affect background (2.8.0b1)
2173 <li>redundancy highlighting is erratic at 0% and 100%</li>
2174 <li>Remove gapped columns fails for sequences with ragged
2176 <li>AMSA annotation row with leading spaces is not
2177 registered correctly on import</li>
2178 <li>Jalview crashes when selecting PCA analysis for
2179 certain alignments</li>
2180 <li>Opening the colour by annotation dialog for an
2181 existing annotation based 'use original colours'
2182 colourscheme loses original colours setting</li>
2187 <td><div align="center">
2188 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2189 <em>30/1/2014</em></strong>
2193 <li>Trusted certificates for JalviewLite applet and
2194 Jalview Desktop application<br />Certificate was donated by
2195 <a href="https://www.certum.eu">Certum</a> to the Jalview
2196 open source project).
2198 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2199 <li>Output in Stockholm format</li>
2200 <li>Allow import of data from gzipped files</li>
2201 <li>Export/import group and sequence associated line
2202 graph thresholds</li>
2203 <li>Nucleotide substitution matrix that supports RNA and
2204 ambiguity codes</li>
2205 <li>Allow disorder predictions to be made on the current
2206 selection (or visible selection) in the same way that JPred
2208 <li>Groovy scripting for headless Jalview operation</li>
2209 </ul> <em>Other improvements</em>
2211 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2212 <li>COMBINE statement uses current SEQUENCE_REF and
2213 GROUP_REF scope to group annotation rows</li>
2214 <li>Support '' style escaping of quotes in Newick
2216 <li>Group options for JABAWS service by command line name</li>
2217 <li>Empty tooltip shown for JABA service options with a
2218 link but no description</li>
2219 <li>Select primary source when selecting authority in
2220 database fetcher GUI</li>
2221 <li>Add .mfa to FASTA file extensions recognised by
2223 <li>Annotation label tooltip text wrap</li>
2228 <li>Slow scrolling when lots of annotation rows are
2230 <li>Lots of NPE (and slowness) after creating RNA
2231 secondary structure annotation line</li>
2232 <li>Sequence database accessions not imported when
2233 fetching alignments from Rfam</li>
2234 <li>Incorrect SHMR submission for sequences with
2236 <li>View all structures does not always superpose
2238 <li>Option widgets in service parameters not updated to
2239 reflect user or preset settings</li>
2240 <li>Null pointer exceptions for some services without
2241 presets or adjustable parameters</li>
2242 <li>Discover PDB IDs entry in structure menu doesn't
2243 discover PDB xRefs</li>
2244 <li>Exception encountered while trying to retrieve
2245 features with DAS</li>
2246 <li>Lowest value in annotation row isn't coloured
2247 when colour by annotation (per sequence) is coloured</li>
2248 <li>Keyboard mode P jumps to start of gapped region when
2249 residue follows a gap</li>
2250 <li>Jalview appears to hang importing an alignment with
2251 Wrap as default or after enabling Wrap</li>
2252 <li>'Right click to add annotations' message
2253 shown in wrap mode when no annotations present</li>
2254 <li>Disorder predictions fail with NPE if no automatic
2255 annotation already exists on alignment</li>
2256 <li>oninit javascript function should be called after
2257 initialisation completes</li>
2258 <li>Remove redundancy after disorder prediction corrupts
2259 alignment window display</li>
2260 <li>Example annotation file in documentation is invalid</li>
2261 <li>Grouped line graph annotation rows are not exported
2262 to annotation file</li>
2263 <li>Multi-harmony analysis cannot be run when only two
2265 <li>Cannot create multiple groups of line graphs with
2266 several 'combine' statements in annotation file</li>
2267 <li>Pressing return several times causes Number Format
2268 exceptions in keyboard mode</li>
2269 <li>Multi-harmony (SHMMR) method doesn't submit
2270 correct partitions for input data</li>
2271 <li>Translation from DNA to Amino Acids fails</li>
2272 <li>Jalview fail to load newick tree with quoted label</li>
2273 <li>--headless flag isn't understood</li>
2274 <li>ClassCastException when generating EPS in headless
2276 <li>Adjusting sequence-associated shading threshold only
2277 changes one row's threshold</li>
2278 <li>Preferences and Feature settings panel panel
2279 doesn't open</li>
2280 <li>hide consensus histogram also hides conservation and
2281 quality histograms</li>
2286 <td><div align="center">
2287 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2289 <td><em>Application</em>
2291 <li>Support for JABAWS 2.0 Services (AACon alignment
2292 conservation, protein disorder and Clustal Omega)</li>
2293 <li>JABAWS server status indicator in Web Services
2295 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2296 in Jalview alignment window</li>
2297 <li>Updated Jalview build and deploy framework for OSX
2298 mountain lion, windows 7, and 8</li>
2299 <li>Nucleotide substitution matrix for PCA that supports
2300 RNA and ambiguity codes</li>
2302 <li>Improved sequence database retrieval GUI</li>
2303 <li>Support fetching and database reference look up
2304 against multiple DAS sources (Fetch all from in 'fetch db
2306 <li>Jalview project improvements
2308 <li>Store and retrieve the 'belowAlignment'
2309 flag for annotation</li>
2310 <li>calcId attribute to group annotation rows on the
2312 <li>Store AACon calculation settings for a view in
2313 Jalview project</li>
2317 <li>horizontal scrolling gesture support</li>
2318 <li>Visual progress indicator when PCA calculation is
2320 <li>Simpler JABA web services menus</li>
2321 <li>visual indication that web service results are still
2322 being retrieved from server</li>
2323 <li>Serialise the dialogs that are shown when Jalview
2324 starts up for first time</li>
2325 <li>Jalview user agent string for interacting with HTTP
2327 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2329 <li>Examples directory and Groovy library included in
2330 InstallAnywhere distribution</li>
2331 </ul> <em>Applet</em>
2333 <li>RNA alignment and secondary structure annotation
2334 visualization applet example</li>
2335 </ul> <em>General</em>
2337 <li>Normalise option for consensus sequence logo</li>
2338 <li>Reset button in PCA window to return dimensions to
2340 <li>Allow seqspace or Jalview variant of alignment PCA
2342 <li>PCA with either nucleic acid and protein substitution
2344 <li>Allow windows containing HTML reports to be exported
2346 <li>Interactive display and editing of RNA secondary
2347 structure contacts</li>
2348 <li>RNA Helix Alignment Colouring</li>
2349 <li>RNA base pair logo consensus</li>
2350 <li>Parse sequence associated secondary structure
2351 information in Stockholm files</li>
2352 <li>HTML Export database accessions and annotation
2353 information presented in tooltip for sequences</li>
2354 <li>Import secondary structure from LOCARNA clustalw
2355 style RNA alignment files</li>
2356 <li>import and visualise T-COFFEE quality scores for an
2358 <li>'colour by annotation' per sequence option to
2359 shade each sequence according to its associated alignment
2361 <li>New Jalview Logo</li>
2362 </ul> <em>Documentation and Development</em>
2364 <li>documentation for score matrices used in Jalview</li>
2365 <li>New Website!</li>
2367 <td><em>Application</em>
2369 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2370 wsdbfetch REST service</li>
2371 <li>Stop windows being moved outside desktop on OSX</li>
2372 <li>Filetype associations not installed for webstart
2374 <li>Jalview does not always retrieve progress of a JABAWS
2375 job execution in full once it is complete</li>
2376 <li>revise SHMR RSBS definition to ensure alignment is
2377 uploaded via ali_file parameter</li>
2378 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2379 <li>View all structures superposed fails with exception</li>
2380 <li>Jnet job queues forever if a very short sequence is
2381 submitted for prediction</li>
2382 <li>Cut and paste menu not opened when mouse clicked on
2384 <li>Putting fractional value into integer text box in
2385 alignment parameter dialog causes Jalview to hang</li>
2386 <li>Structure view highlighting doesn't work on
2388 <li>View all structures fails with exception shown in
2390 <li>Characters in filename associated with PDBEntry not
2391 escaped in a platform independent way</li>
2392 <li>Jalview desktop fails to launch with exception when
2394 <li>Tree calculation reports 'you must have 2 or more
2395 sequences selected' when selection is empty</li>
2396 <li>Jalview desktop fails to launch with jar signature
2397 failure when java web start temporary file caching is
2399 <li>DAS Sequence retrieval with range qualification
2400 results in sequence xref which includes range qualification</li>
2401 <li>Errors during processing of command line arguments
2402 cause progress bar (JAL-898) to be removed</li>
2403 <li>Replace comma for semi-colon option not disabled for
2404 DAS sources in sequence fetcher</li>
2405 <li>Cannot close news reader when JABAWS server warning
2406 dialog is shown</li>
2407 <li>Option widgets not updated to reflect user settings</li>
2408 <li>Edited sequence not submitted to web service</li>
2409 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2410 <li>InstallAnywhere installer doesn't unpack and run
2411 on OSX Mountain Lion</li>
2412 <li>Annotation panel not given a scroll bar when
2413 sequences with alignment annotation are pasted into the
2415 <li>Sequence associated annotation rows not associated
2416 when loaded from Jalview project</li>
2417 <li>Browser launch fails with NPE on java 1.7</li>
2418 <li>JABAWS alignment marked as finished when job was
2419 cancelled or job failed due to invalid input</li>
2420 <li>NPE with v2.7 example when clicking on Tree
2421 associated with all views</li>
2422 <li>Exceptions when copy/paste sequences with grouped
2423 annotation rows to new window</li>
2424 </ul> <em>Applet</em>
2426 <li>Sequence features are momentarily displayed before
2427 they are hidden using hidefeaturegroups applet parameter</li>
2428 <li>loading features via javascript API automatically
2429 enables feature display</li>
2430 <li>scrollToColumnIn javascript API method doesn't
2432 </ul> <em>General</em>
2434 <li>Redundancy removal fails for rna alignment</li>
2435 <li>PCA calculation fails when sequence has been selected
2436 and then deselected</li>
2437 <li>PCA window shows grey box when first opened on OSX</li>
2438 <li>Letters coloured pink in sequence logo when alignment
2439 coloured with clustalx</li>
2440 <li>Choosing fonts without letter symbols defined causes
2441 exceptions and redraw errors</li>
2442 <li>Initial PCA plot view is not same as manually
2443 reconfigured view</li>
2444 <li>Grouped annotation graph label has incorrect line
2446 <li>Grouped annotation graph label display is corrupted
2447 for lots of labels</li>
2452 <div align="center">
2453 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2456 <td><em>Application</em>
2458 <li>Jalview Desktop News Reader</li>
2459 <li>Tweaked default layout of web services menu</li>
2460 <li>View/alignment association menu to enable user to
2461 easily specify which alignment a multi-structure view takes
2462 its colours/correspondences from</li>
2463 <li>Allow properties file location to be specified as URL</li>
2464 <li>Extend Jalview project to preserve associations
2465 between many alignment views and a single Jmol display</li>
2466 <li>Store annotation row height in Jalview project file</li>
2467 <li>Annotation row column label formatting attributes
2468 stored in project file</li>
2469 <li>Annotation row order for auto-calculated annotation
2470 rows preserved in Jalview project file</li>
2471 <li>Visual progress indication when Jalview state is
2472 saved using Desktop window menu</li>
2473 <li>Visual indication that command line arguments are
2474 still being processed</li>
2475 <li>Groovy script execution from URL</li>
2476 <li>Colour by annotation default min and max colours in
2478 <li>Automatically associate PDB files dragged onto an
2479 alignment with sequences that have high similarity and
2481 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2482 <li>'view structures' option to open many
2483 structures in same window</li>
2484 <li>Sort associated views menu option for tree panel</li>
2485 <li>Group all JABA and non-JABA services for a particular
2486 analysis function in its own submenu</li>
2487 </ul> <em>Applet</em>
2489 <li>Userdefined and autogenerated annotation rows for
2491 <li>Adjustment of alignment annotation pane height</li>
2492 <li>Annotation scrollbar for annotation panel</li>
2493 <li>Drag to reorder annotation rows in annotation panel</li>
2494 <li>'automaticScrolling' parameter</li>
2495 <li>Allow sequences with partial ID string matches to be
2496 annotated from GFF/Jalview features files</li>
2497 <li>Sequence logo annotation row in applet</li>
2498 <li>Absolute paths relative to host server in applet
2499 parameters are treated as such</li>
2500 <li>New in the JalviewLite javascript API:
2502 <li>JalviewLite.js javascript library</li>
2503 <li>Javascript callbacks for
2505 <li>Applet initialisation</li>
2506 <li>Sequence/alignment mouse-overs and selections</li>
2509 <li>scrollTo row and column alignment scrolling
2511 <li>Select sequence/alignment regions from javascript</li>
2512 <li>javascript structure viewer harness to pass
2513 messages between Jmol and Jalview when running as
2514 distinct applets</li>
2515 <li>sortBy method</li>
2516 <li>Set of applet and application examples shipped
2517 with documentation</li>
2518 <li>New example to demonstrate JalviewLite and Jmol
2519 javascript message exchange</li>
2521 </ul> <em>General</em>
2523 <li>Enable Jmol displays to be associated with multiple
2524 multiple alignments</li>
2525 <li>Option to automatically sort alignment with new tree</li>
2526 <li>User configurable link to enable redirects to a
2527 www.Jalview.org mirror</li>
2528 <li>Jmol colours option for Jmol displays</li>
2529 <li>Configurable newline string when writing alignment
2530 and other flat files</li>
2531 <li>Allow alignment annotation description lines to
2532 contain html tags</li>
2533 </ul> <em>Documentation and Development</em>
2535 <li>Add groovy test harness for bulk load testing to
2537 <li>Groovy script to load and align a set of sequences
2538 using a web service before displaying the result in the
2539 Jalview desktop</li>
2540 <li>Restructured javascript and applet api documentation</li>
2541 <li>Ant target to publish example html files with applet
2543 <li>Netbeans project for building Jalview from source</li>
2544 <li>ant task to create online javadoc for Jalview source</li>
2546 <td><em>Application</em>
2548 <li>User defined colourscheme throws exception when
2549 current built in colourscheme is saved as new scheme</li>
2550 <li>AlignFrame->Save in application pops up save
2551 dialog for valid filename/format</li>
2552 <li>Cannot view associated structure for UniProt sequence</li>
2553 <li>PDB file association breaks for UniProt sequence
2555 <li>Associate PDB from file dialog does not tell you
2556 which sequence is to be associated with the file</li>
2557 <li>Find All raises null pointer exception when query
2558 only matches sequence IDs</li>
2559 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2560 <li>Jalview project with Jmol views created with Jalview
2561 2.4 cannot be loaded</li>
2562 <li>Filetype associations not installed for webstart
2564 <li>Two or more chains in a single PDB file associated
2565 with sequences in different alignments do not get coloured
2566 by their associated sequence</li>
2567 <li>Visibility status of autocalculated annotation row
2568 not preserved when project is loaded</li>
2569 <li>Annotation row height and visibility attributes not
2570 stored in Jalview project</li>
2571 <li>Tree bootstraps are not preserved when saved as a
2572 Jalview project</li>
2573 <li>Envision2 workflow tooltips are corrupted</li>
2574 <li>Enabling show group conservation also enables colour
2575 by conservation</li>
2576 <li>Duplicate group associated conservation or consensus
2577 created on new view</li>
2578 <li>Annotation scrollbar not displayed after 'show
2579 all hidden annotation rows' option selected</li>
2580 <li>Alignment quality not updated after alignment
2581 annotation row is hidden then shown</li>
2582 <li>Preserve colouring of structures coloured by
2583 sequences in pre Jalview 2.7 projects</li>
2584 <li>Web service job parameter dialog is not laid out
2586 <li>Web services menu not refreshed after 'reset
2587 services' button is pressed in preferences</li>
2588 <li>Annotation off by one in Jalview v2_3 example project</li>
2589 <li>Structures imported from file and saved in project
2590 get name like jalview_pdb1234.txt when reloaded</li>
2591 <li>Jalview does not always retrieve progress of a JABAWS
2592 job execution in full once it is complete</li>
2593 </ul> <em>Applet</em>
2595 <li>Alignment height set incorrectly when lots of
2596 annotation rows are displayed</li>
2597 <li>Relative URLs in feature HTML text not resolved to
2599 <li>View follows highlighting does not work for positions
2601 <li><= shown as = in tooltip</li>
2602 <li>Export features raises exception when no features
2604 <li>Separator string used for serialising lists of IDs
2605 for javascript api is modified when separator string
2606 provided as parameter</li>
2607 <li>Null pointer exception when selecting tree leaves for
2608 alignment with no existing selection</li>
2609 <li>Relative URLs for datasources assumed to be relative
2610 to applet's codebase</li>
2611 <li>Status bar not updated after finished searching and
2612 search wraps around to first result</li>
2613 <li>StructureSelectionManager instance shared between
2614 several Jalview applets causes race conditions and memory
2616 <li>Hover tooltip and mouseover of position on structure
2617 not sent from Jmol in applet</li>
2618 <li>Certain sequences of javascript method calls to
2619 applet API fatally hang browser</li>
2620 </ul> <em>General</em>
2622 <li>View follows structure mouseover scrolls beyond
2623 position with wrapped view and hidden regions</li>
2624 <li>Find sequence position moves to wrong residue
2625 with/without hidden columns</li>
2626 <li>Sequence length given in alignment properties window
2628 <li>InvalidNumberFormat exceptions thrown when trying to
2629 import PDB like structure files</li>
2630 <li>Positional search results are only highlighted
2631 between user-supplied sequence start/end bounds</li>
2632 <li>End attribute of sequence is not validated</li>
2633 <li>Find dialog only finds first sequence containing a
2634 given sequence position</li>
2635 <li>Sequence numbering not preserved in MSF alignment
2637 <li>Jalview PDB file reader does not extract sequence
2638 from nucleotide chains correctly</li>
2639 <li>Structure colours not updated when tree partition
2640 changed in alignment</li>
2641 <li>Sequence associated secondary structure not correctly
2642 parsed in interleaved stockholm</li>
2643 <li>Colour by annotation dialog does not restore current
2645 <li>Hiding (nearly) all sequences doesn't work
2647 <li>Sequences containing lowercase letters are not
2648 properly associated with their pdb files</li>
2649 </ul> <em>Documentation and Development</em>
2651 <li>schemas/JalviewWsParamSet.xsd corrupted by
2652 ApplyCopyright tool</li>
2657 <div align="center">
2658 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2661 <td><em>Application</em>
2663 <li>New warning dialog when the Jalview Desktop cannot
2664 contact web services</li>
2665 <li>JABA service parameters for a preset are shown in
2666 service job window</li>
2667 <li>JABA Service menu entries reworded</li>
2671 <li>Modeller PIR IO broken - cannot correctly import a
2672 pir file emitted by Jalview</li>
2673 <li>Existing feature settings transferred to new
2674 alignment view created from cut'n'paste</li>
2675 <li>Improved test for mixed amino/nucleotide chains when
2676 parsing PDB files</li>
2677 <li>Consensus and conservation annotation rows
2678 occasionally become blank for all new windows</li>
2679 <li>Exception raised when right clicking above sequences
2680 in wrapped view mode</li>
2681 </ul> <em>Application</em>
2683 <li>multiple multiply aligned structure views cause cpu
2684 usage to hit 100% and computer to hang</li>
2685 <li>Web Service parameter layout breaks for long user
2686 parameter names</li>
2687 <li>Jaba service discovery hangs desktop if Jaba server
2694 <div align="center">
2695 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2698 <td><em>Application</em>
2700 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2701 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2704 <li>Web Services preference tab</li>
2705 <li>Analysis parameters dialog box and user defined
2707 <li>Improved speed and layout of Envision2 service menu</li>
2708 <li>Superpose structures using associated sequence
2710 <li>Export coordinates and projection as CSV from PCA
2712 </ul> <em>Applet</em>
2714 <li>enable javascript: execution by the applet via the
2715 link out mechanism</li>
2716 </ul> <em>Other</em>
2718 <li>Updated the Jmol Jalview interface to work with Jmol
2720 <li>The Jalview Desktop and JalviewLite applet now
2721 require Java 1.5</li>
2722 <li>Allow Jalview feature colour specification for GFF
2723 sequence annotation files</li>
2724 <li>New 'colour by label' keword in Jalview feature file
2725 type colour specification</li>
2726 <li>New Jalview Desktop Groovy API method that allows a
2727 script to check if it being run in an interactive session or
2728 in a batch operation from the Jalview command line</li>
2732 <li>clustalx colourscheme colours Ds preferentially when
2733 both D+E are present in over 50% of the column</li>
2734 </ul> <em>Application</em>
2736 <li>typo in AlignmentFrame->View->Hide->all but
2737 selected Regions menu item</li>
2738 <li>sequence fetcher replaces ',' for ';' when the ',' is
2739 part of a valid accession ID</li>
2740 <li>fatal OOM if object retrieved by sequence fetcher
2741 runs out of memory</li>
2742 <li>unhandled Out of Memory Error when viewing pca
2743 analysis results</li>
2744 <li>InstallAnywhere builds fail to launch on OS X java
2745 10.5 update 4 (due to apple Java 1.6 update)</li>
2746 <li>Installanywhere Jalview silently fails to launch</li>
2747 </ul> <em>Applet</em>
2749 <li>Jalview.getFeatureGroups() raises an
2750 ArrayIndexOutOfBoundsException if no feature groups are
2757 <div align="center">
2758 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2764 <li>Alignment prettyprinter doesn't cope with long
2766 <li>clustalx colourscheme colours Ds preferentially when
2767 both D+E are present in over 50% of the column</li>
2768 <li>nucleic acid structures retrieved from PDB do not
2769 import correctly</li>
2770 <li>More columns get selected than were clicked on when a
2771 number of columns are hidden</li>
2772 <li>annotation label popup menu not providing correct
2773 add/hide/show options when rows are hidden or none are
2775 <li>Stockholm format shown in list of readable formats,
2776 and parser copes better with alignments from RFAM.</li>
2777 <li>CSV output of consensus only includes the percentage
2778 of all symbols if sequence logo display is enabled</li>
2780 </ul> <em>Applet</em>
2782 <li>annotation panel disappears when annotation is
2784 </ul> <em>Application</em>
2786 <li>Alignment view not redrawn properly when new
2787 alignment opened where annotation panel is visible but no
2788 annotations are present on alignment</li>
2789 <li>pasted region containing hidden columns is
2790 incorrectly displayed in new alignment window</li>
2791 <li>Jalview slow to complete operations when stdout is
2792 flooded (fix is to close the Jalview console)</li>
2793 <li>typo in AlignmentFrame->View->Hide->all but
2794 selected Rregions menu item.</li>
2795 <li>inconsistent group submenu and Format submenu entry
2796 'Un' or 'Non'conserved</li>
2797 <li>Sequence feature settings are being shared by
2798 multiple distinct alignments</li>
2799 <li>group annotation not recreated when tree partition is
2801 <li>double click on group annotation to select sequences
2802 does not propagate to associated trees</li>
2803 <li>Mac OSX specific issues:
2805 <li>exception raised when mouse clicked on desktop
2806 window background</li>
2807 <li>Desktop menu placed on menu bar and application
2808 name set correctly</li>
2809 <li>sequence feature settings not wide enough for the
2810 save feature colourscheme button</li>
2819 <div align="center">
2820 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2823 <td><em>New Capabilities</em>
2825 <li>URL links generated from description line for
2826 regular-expression based URL links (applet and application)
2828 <li>Non-positional feature URL links are shown in link
2830 <li>Linked viewing of nucleic acid sequences and
2832 <li>Automatic Scrolling option in View menu to display
2833 the currently highlighted region of an alignment.</li>
2834 <li>Order an alignment by sequence length, or using the
2835 average score or total feature count for each sequence.</li>
2836 <li>Shading features by score or associated description</li>
2837 <li>Subdivide alignment and groups based on identity of
2838 selected subsequence (Make Groups from Selection).</li>
2839 <li>New hide/show options including Shift+Control+H to
2840 hide everything but the currently selected region.</li>
2841 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2842 </ul> <em>Application</em>
2844 <li>Fetch DB References capabilities and UI expanded to
2845 support retrieval from DAS sequence sources</li>
2846 <li>Local DAS Sequence sources can be added via the
2847 command line or via the Add local source dialog box.</li>
2848 <li>DAS Dbref and DbxRef feature types are parsed as
2849 database references and protein_name is parsed as
2850 description line (BioSapiens terms).</li>
2851 <li>Enable or disable non-positional feature and database
2852 references in sequence ID tooltip from View menu in
2854 <!-- <li>New hidden columns and rows and representatives capabilities
2855 in annotations file (in progress - not yet fully implemented)</li> -->
2856 <li>Group-associated consensus, sequence logos and
2857 conservation plots</li>
2858 <li>Symbol distributions for each column can be exported
2859 and visualized as sequence logos</li>
2860 <li>Optionally scale multi-character column labels to fit
2861 within each column of annotation row<!-- todo for applet -->
2863 <li>Optional automatic sort of associated alignment view
2864 when a new tree is opened.</li>
2865 <li>Jalview Java Console</li>
2866 <li>Better placement of desktop window when moving
2867 between different screens.</li>
2868 <li>New preference items for sequence ID tooltip and
2869 consensus annotation</li>
2870 <li>Client to submit sequences and IDs to Envision2
2872 <li><em>Vamsas Capabilities</em>
2874 <li>Improved VAMSAS synchronization (Jalview archive
2875 used to preserve views, structures, and tree display
2877 <li>Import of vamsas documents from disk or URL via
2879 <li>Sharing of selected regions between views and
2880 with other VAMSAS applications (Experimental feature!)</li>
2881 <li>Updated API to VAMSAS version 0.2</li>
2883 </ul> <em>Applet</em>
2885 <li>Middle button resizes annotation row height</li>
2888 <li>sortByTree (true/false) - automatically sort the
2889 associated alignment view by the tree when a new tree is
2891 <li>showTreeBootstraps (true/false) - show or hide
2892 branch bootstraps (default is to show them if available)</li>
2893 <li>showTreeDistances (true/false) - show or hide
2894 branch lengths (default is to show them if available)</li>
2895 <li>showUnlinkedTreeNodes (true/false) - indicate if
2896 unassociated nodes should be highlighted in the tree
2898 <li>heightScale and widthScale (1.0 or more) -
2899 increase the height or width of a cell in the alignment
2900 grid relative to the current font size.</li>
2903 <li>Non-positional features displayed in sequence ID
2905 </ul> <em>Other</em>
2907 <li>Features format: graduated colour definitions and
2908 specification of feature scores</li>
2909 <li>Alignment Annotations format: new keywords for group
2910 associated annotation (GROUP_REF) and annotation row display
2911 properties (ROW_PROPERTIES)</li>
2912 <li>XML formats extended to support graduated feature
2913 colourschemes, group associated annotation, and profile
2914 visualization settings.</li></td>
2917 <li>Source field in GFF files parsed as feature source
2918 rather than description</li>
2919 <li>Non-positional features are now included in sequence
2920 feature and gff files (controlled via non-positional feature
2921 visibility in tooltip).</li>
2922 <li>URL links generated for all feature links (bugfix)</li>
2923 <li>Added URL embedding instructions to features file
2925 <li>Codons containing ambiguous nucleotides translated as
2926 'X' in peptide product</li>
2927 <li>Match case switch in find dialog box works for both
2928 sequence ID and sequence string and query strings do not
2929 have to be in upper case to match case-insensitively.</li>
2930 <li>AMSA files only contain first column of
2931 multi-character column annotation labels</li>
2932 <li>Jalview Annotation File generation/parsing consistent
2933 with documentation (e.g. Stockholm annotation can be
2934 exported and re-imported)</li>
2935 <li>PDB files without embedded PDB IDs given a friendly
2937 <li>Find incrementally searches ID string matches as well
2938 as subsequence matches, and correctly reports total number
2942 <li>Better handling of exceptions during sequence
2944 <li>Dasobert generated non-positional feature URL
2945 link text excludes the start_end suffix</li>
2946 <li>DAS feature and source retrieval buttons disabled
2947 when fetch or registry operations in progress.</li>
2948 <li>PDB files retrieved from URLs are cached properly</li>
2949 <li>Sequence description lines properly shared via
2951 <li>Sequence fetcher fetches multiple records for all
2953 <li>Ensured that command line das feature retrieval
2954 completes before alignment figures are generated.</li>
2955 <li>Reduced time taken when opening file browser for
2957 <li>isAligned check prior to calculating tree, PCA or
2958 submitting an MSA to JNet now excludes hidden sequences.</li>
2959 <li>User defined group colours properly recovered
2960 from Jalview projects.</li>
2969 <div align="center">
2970 <strong>2.4.0.b2</strong><br> 28/10/2009
2975 <li>Experimental support for google analytics usage
2977 <li>Jalview privacy settings (user preferences and docs).</li>
2982 <li>Race condition in applet preventing startup in
2984 <li>Exception when feature created from selection beyond
2985 length of sequence.</li>
2986 <li>Allow synthetic PDB files to be imported gracefully</li>
2987 <li>Sequence associated annotation rows associate with
2988 all sequences with a given id</li>
2989 <li>Find function matches case-insensitively for sequence
2990 ID string searches</li>
2991 <li>Non-standard characters do not cause pairwise
2992 alignment to fail with exception</li>
2993 </ul> <em>Application Issues</em>
2995 <li>Sequences are now validated against EMBL database</li>
2996 <li>Sequence fetcher fetches multiple records for all
2998 </ul> <em>InstallAnywhere Issues</em>
3000 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3001 issue with installAnywhere mechanism)</li>
3002 <li>Command line launching of JARs from InstallAnywhere
3003 version (java class versioning error fixed)</li>
3010 <div align="center">
3011 <strong>2.4</strong><br> 27/8/2008
3014 <td><em>User Interface</em>
3016 <li>Linked highlighting of codon and amino acid from
3017 translation and protein products</li>
3018 <li>Linked highlighting of structure associated with
3019 residue mapping to codon position</li>
3020 <li>Sequence Fetcher provides example accession numbers
3021 and 'clear' button</li>
3022 <li>MemoryMonitor added as an option under Desktop's
3024 <li>Extract score function to parse whitespace separated
3025 numeric data in description line</li>
3026 <li>Column labels in alignment annotation can be centred.</li>
3027 <li>Tooltip for sequence associated annotation give name
3029 </ul> <em>Web Services and URL fetching</em>
3031 <li>JPred3 web service</li>
3032 <li>Prototype sequence search client (no public services
3034 <li>Fetch either seed alignment or full alignment from
3036 <li>URL Links created for matching database cross
3037 references as well as sequence ID</li>
3038 <li>URL Links can be created using regular-expressions</li>
3039 </ul> <em>Sequence Database Connectivity</em>
3041 <li>Retrieval of cross-referenced sequences from other
3043 <li>Generalised database reference retrieval and
3044 validation to all fetchable databases</li>
3045 <li>Fetch sequences from DAS sources supporting the
3046 sequence command</li>
3047 </ul> <em>Import and Export</em>
3048 <li>export annotation rows as CSV for spreadsheet import</li>
3049 <li>Jalview projects record alignment dataset associations,
3050 EMBL products, and cDNA sequence mappings</li>
3051 <li>Sequence Group colour can be specified in Annotation
3053 <li>Ad-hoc colouring of group in Annotation File using RGB
3054 triplet as name of colourscheme</li>
3055 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3057 <li>treenode binding for VAMSAS tree exchange</li>
3058 <li>local editing and update of sequences in VAMSAS
3059 alignments (experimental)</li>
3060 <li>Create new or select existing session to join</li>
3061 <li>load and save of vamsas documents</li>
3062 </ul> <em>Application command line</em>
3064 <li>-tree parameter to open trees (introduced for passing
3066 <li>-fetchfrom command line argument to specify nicknames
3067 of DAS servers to query for alignment features</li>
3068 <li>-dasserver command line argument to add new servers
3069 that are also automatically queried for features</li>
3070 <li>-groovy command line argument executes a given groovy
3071 script after all input data has been loaded and parsed</li>
3072 </ul> <em>Applet-Application data exchange</em>
3074 <li>Trees passed as applet parameters can be passed to
3075 application (when using "View in full
3076 application")</li>
3077 </ul> <em>Applet Parameters</em>
3079 <li>feature group display control parameter</li>
3080 <li>debug parameter</li>
3081 <li>showbutton parameter</li>
3082 </ul> <em>Applet API methods</em>
3084 <li>newView public method</li>
3085 <li>Window (current view) specific get/set public methods</li>
3086 <li>Feature display control methods</li>
3087 <li>get list of currently selected sequences</li>
3088 </ul> <em>New Jalview distribution features</em>
3090 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3091 <li>RELEASE file gives build properties for the latest
3092 Jalview release.</li>
3093 <li>Java 1.1 Applet build made easier and donotobfuscate
3094 property controls execution of obfuscator</li>
3095 <li>Build target for generating source distribution</li>
3096 <li>Debug flag for javacc</li>
3097 <li>.jalview_properties file is documented (slightly) in
3098 jalview.bin.Cache</li>
3099 <li>Continuous Build Integration for stable and
3100 development version of Application, Applet and source
3105 <li>selected region output includes visible annotations
3106 (for certain formats)</li>
3107 <li>edit label/displaychar contains existing label/char
3109 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3110 <li>shorter peptide product names from EMBL records</li>
3111 <li>Newick string generator makes compact representations</li>
3112 <li>bootstrap values parsed correctly for tree files with
3114 <li>pathological filechooser bug avoided by not allowing
3115 filenames containing a ':'</li>
3116 <li>Fixed exception when parsing GFF files containing
3117 global sequence features</li>
3118 <li>Alignment datasets are finalized only when number of
3119 references from alignment sequences goes to zero</li>
3120 <li>Close of tree branch colour box without colour
3121 selection causes cascading exceptions</li>
3122 <li>occasional negative imgwidth exceptions</li>
3123 <li>better reporting of non-fatal warnings to user when
3124 file parsing fails.</li>
3125 <li>Save works when Jalview project is default format</li>
3126 <li>Save as dialog opened if current alignment format is
3127 not a valid output format</li>
3128 <li>UniProt canonical names introduced for both das and
3130 <li>Histidine should be midblue (not pink!) in Zappo</li>
3131 <li>error messages passed up and output when data read
3133 <li>edit undo recovers previous dataset sequence when
3134 sequence is edited</li>
3135 <li>allow PDB files without pdb ID HEADER lines (like
3136 those generated by MODELLER) to be read in properly</li>
3137 <li>allow reading of JPred concise files as a normal
3139 <li>Stockholm annotation parsing and alignment properties
3140 import fixed for PFAM records</li>
3141 <li>Structure view windows have correct name in Desktop
3143 <li>annotation consisting of sequence associated scores
3144 can be read and written correctly to annotation file</li>
3145 <li>Aligned cDNA translation to aligned peptide works
3147 <li>Fixed display of hidden sequence markers and
3148 non-italic font for representatives in Applet</li>
3149 <li>Applet Menus are always embedded in applet window on
3151 <li>Newly shown features appear at top of stack (in
3153 <li>Annotations added via parameter not drawn properly
3154 due to null pointer exceptions</li>
3155 <li>Secondary structure lines are drawn starting from
3156 first column of alignment</li>
3157 <li>UniProt XML import updated for new schema release in
3159 <li>Sequence feature to sequence ID match for Features
3160 file is case-insensitive</li>
3161 <li>Sequence features read from Features file appended to
3162 all sequences with matching IDs</li>
3163 <li>PDB structure coloured correctly for associated views
3164 containing a sub-sequence</li>
3165 <li>PDB files can be retrieved by applet from Jar files</li>
3166 <li>feature and annotation file applet parameters
3167 referring to different directories are retrieved correctly</li>
3168 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3169 <li>Fixed application hang whilst waiting for
3170 splash-screen version check to complete</li>
3171 <li>Applet properly URLencodes input parameter values
3172 when passing them to the launchApp service</li>
3173 <li>display name and local features preserved in results
3174 retrieved from web service</li>
3175 <li>Visual delay indication for sequence retrieval and
3176 sequence fetcher initialisation</li>
3177 <li>updated Application to use DAS 1.53e version of
3178 dasobert DAS client</li>
3179 <li>Re-instated Full AMSA support and .amsa file
3181 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3189 <div align="center">
3190 <strong>2.3</strong><br> 9/5/07
3195 <li>Jmol 11.0.2 integration</li>
3196 <li>PDB views stored in Jalview XML files</li>
3197 <li>Slide sequences</li>
3198 <li>Edit sequence in place</li>
3199 <li>EMBL CDS features</li>
3200 <li>DAS Feature mapping</li>
3201 <li>Feature ordering</li>
3202 <li>Alignment Properties</li>
3203 <li>Annotation Scores</li>
3204 <li>Sort by scores</li>
3205 <li>Feature/annotation editing in applet</li>
3210 <li>Headless state operation in 2.2.1</li>
3211 <li>Incorrect and unstable DNA pairwise alignment</li>
3212 <li>Cut and paste of sequences with annotation</li>
3213 <li>Feature group display state in XML</li>
3214 <li>Feature ordering in XML</li>
3215 <li>blc file iteration selection using filename # suffix</li>
3216 <li>Stockholm alignment properties</li>
3217 <li>Stockhom alignment secondary structure annotation</li>
3218 <li>2.2.1 applet had no feature transparency</li>
3219 <li>Number pad keys can be used in cursor mode</li>
3220 <li>Structure Viewer mirror image resolved</li>
3227 <div align="center">
3228 <strong>2.2.1</strong><br> 12/2/07
3233 <li>Non standard characters can be read and displayed
3234 <li>Annotations/Features can be imported/exported to the
3236 <li>Applet allows editing of sequence/annotation/group
3237 name & description
3238 <li>Preference setting to display sequence name in
3240 <li>Annotation file format extended to allow
3241 Sequence_groups to be defined
3242 <li>Default opening of alignment overview panel can be
3243 specified in preferences
3244 <li>PDB residue numbering annotation added to associated
3250 <li>Applet crash under certain Linux OS with Java 1.6
3252 <li>Annotation file export / import bugs fixed
3253 <li>PNG / EPS image output bugs fixed
3259 <div align="center">
3260 <strong>2.2</strong><br> 27/11/06
3265 <li>Multiple views on alignment
3266 <li>Sequence feature editing
3267 <li>"Reload" alignment
3268 <li>"Save" to current filename
3269 <li>Background dependent text colour
3270 <li>Right align sequence ids
3271 <li>User-defined lower case residue colours
3274 <li>Menu item accelerator keys
3275 <li>Control-V pastes to current alignment
3276 <li>Cancel button for DAS Feature Fetching
3277 <li>PCA and PDB Viewers zoom via mouse roller
3278 <li>User-defined sub-tree colours and sub-tree selection
3280 <li>'New Window' button on the 'Output to Text box'
3285 <li>New memory efficient Undo/Redo System
3286 <li>Optimised symbol lookups and conservation/consensus
3288 <li>Region Conservation/Consensus recalculated after
3290 <li>Fixed Remove Empty Columns Bug (empty columns at end
3292 <li>Slowed DAS Feature Fetching for increased robustness.
3294 <li>Made angle brackets in ASCII feature descriptions
3296 <li>Re-instated Zoom function for PCA
3297 <li>Sequence descriptions conserved in web service
3299 <li>UniProt ID discoverer uses any word separated by
3301 <li>WsDbFetch query/result association resolved
3302 <li>Tree leaf to sequence mapping improved
3303 <li>Smooth fonts switch moved to FontChooser dialog box.
3310 <div align="center">
3311 <strong>2.1.1</strong><br> 12/9/06
3316 <li>Copy consensus sequence to clipboard</li>
3321 <li>Image output - rightmost residues are rendered if
3322 sequence id panel has been resized</li>
3323 <li>Image output - all offscreen group boundaries are
3325 <li>Annotation files with sequence references - all
3326 elements in file are relative to sequence position</li>
3327 <li>Mac Applet users can use Alt key for group editing</li>
3333 <div align="center">
3334 <strong>2.1</strong><br> 22/8/06
3339 <li>MAFFT Multiple Alignment in default Web Service list</li>
3340 <li>DAS Feature fetching</li>
3341 <li>Hide sequences and columns</li>
3342 <li>Export Annotations and Features</li>
3343 <li>GFF file reading / writing</li>
3344 <li>Associate structures with sequences from local PDB
3346 <li>Add sequences to exisiting alignment</li>
3347 <li>Recently opened files / URL lists</li>
3348 <li>Applet can launch the full application</li>
3349 <li>Applet has transparency for features (Java 1.2
3351 <li>Applet has user defined colours parameter</li>
3352 <li>Applet can load sequences from parameter
3353 "sequence<em>x</em>"
3359 <li>Redundancy Panel reinstalled in the Applet</li>
3360 <li>Monospaced font - EPS / rescaling bug fixed</li>
3361 <li>Annotation files with sequence references bug fixed</li>
3367 <div align="center">
3368 <strong>2.08.1</strong><br> 2/5/06
3373 <li>Change case of selected region from Popup menu</li>
3374 <li>Choose to match case when searching</li>
3375 <li>Middle mouse button and mouse movement can compress /
3376 expand the visible width and height of the alignment</li>
3381 <li>Annotation Panel displays complete JNet results</li>
3387 <div align="center">
3388 <strong>2.08b</strong><br> 18/4/06
3394 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3395 <li>Righthand label on wrapped alignments shows correct
3402 <div align="center">
3403 <strong>2.08</strong><br> 10/4/06
3408 <li>Editing can be locked to the selection area</li>
3409 <li>Keyboard editing</li>
3410 <li>Create sequence features from searches</li>
3411 <li>Precalculated annotations can be loaded onto
3413 <li>Features file allows grouping of features</li>
3414 <li>Annotation Colouring scheme added</li>
3415 <li>Smooth fonts off by default - Faster rendering</li>
3416 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3421 <li>Drag & Drop fixed on Linux</li>
3422 <li>Jalview Archive file faster to load/save, sequence
3423 descriptions saved.</li>
3429 <div align="center">
3430 <strong>2.07</strong><br> 12/12/05
3435 <li>PDB Structure Viewer enhanced</li>
3436 <li>Sequence Feature retrieval and display enhanced</li>
3437 <li>Choose to output sequence start-end after sequence
3438 name for file output</li>
3439 <li>Sequence Fetcher WSDBFetch@EBI</li>
3440 <li>Applet can read feature files, PDB files and can be
3441 used for HTML form input</li>
3446 <li>HTML output writes groups and features</li>
3447 <li>Group editing is Control and mouse click</li>
3448 <li>File IO bugs</li>
3454 <div align="center">
3455 <strong>2.06</strong><br> 28/9/05
3460 <li>View annotations in wrapped mode</li>
3461 <li>More options for PCA viewer</li>
3466 <li>GUI bugs resolved</li>
3467 <li>Runs with -nodisplay from command line</li>
3473 <div align="center">
3474 <strong>2.05b</strong><br> 15/9/05
3479 <li>Choose EPS export as lineart or text</li>
3480 <li>Jar files are executable</li>
3481 <li>Can read in Uracil - maps to unknown residue</li>
3486 <li>Known OutOfMemory errors give warning message</li>
3487 <li>Overview window calculated more efficiently</li>
3488 <li>Several GUI bugs resolved</li>
3494 <div align="center">
3495 <strong>2.05</strong><br> 30/8/05
3500 <li>Edit and annotate in "Wrapped" view</li>
3505 <li>Several GUI bugs resolved</li>
3511 <div align="center">
3512 <strong>2.04</strong><br> 24/8/05
3517 <li>Hold down mouse wheel & scroll to change font
3523 <li>Improved JPred client reliability</li>
3524 <li>Improved loading of Jalview files</li>
3530 <div align="center">
3531 <strong>2.03</strong><br> 18/8/05
3536 <li>Set Proxy server name and port in preferences</li>
3537 <li>Multiple URL links from sequence ids</li>
3538 <li>User Defined Colours can have a scheme name and added
3540 <li>Choose to ignore gaps in consensus calculation</li>
3541 <li>Unix users can set default web browser</li>
3542 <li>Runs without GUI for batch processing</li>
3543 <li>Dynamically generated Web Service Menus</li>
3548 <li>InstallAnywhere download for Sparc Solaris</li>
3554 <div align="center">
3555 <strong>2.02</strong><br> 18/7/05
3561 <li>Copy & Paste order of sequences maintains
3562 alignment order.</li>
3568 <div align="center">
3569 <strong>2.01</strong><br> 12/7/05
3574 <li>Use delete key for deleting selection.</li>
3575 <li>Use Mouse wheel to scroll sequences.</li>
3576 <li>Help file updated to describe how to add alignment
3578 <li>Version and build date written to build properties
3580 <li>InstallAnywhere installation will check for updates
3581 at launch of Jalview.</li>
3586 <li>Delete gaps bug fixed.</li>
3587 <li>FileChooser sorts columns.</li>
3588 <li>Can remove groups one by one.</li>
3589 <li>Filechooser icons installed.</li>
3590 <li>Finder ignores return character when searching.
3591 Return key will initiate a search.<br>
3598 <div align="center">
3599 <strong>2.0</strong><br> 20/6/05
3604 <li>New codebase</li>