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.2.10.3b1">2.10.3b1</a><br /> <em>5/12/2017</em></strong>
76 <td><div align="left">
79 <td><div align="left">
81 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
82 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
83 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
89 <td width="60" nowrap>
91 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
94 <td><div align="left">
98 <!-- JAL-2446 -->Faster and more efficient management and
99 rendering of sequence features
102 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
103 429 rate limit request hander
106 <!-- JAL-2773 -->Structure views don't get updated unless
107 their colours have changed
110 <!-- JAL-2495 -->All linked sequences are highlighted for
111 a structure mousover (Jmol) or selection (Chimera)
114 <!-- JAL-2790 -->'Cancel' button in progress bar for
115 JABAWS AACon, RNAAliFold and Disorder prediction jobs
118 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
119 view from Ensembl locus cross-references
122 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
126 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
127 feature can be disabled
130 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
131 PDB easier retrieval of sequences for lists of IDs
134 <!-- JAL-2758 -->Short names for sequences retrieved from
140 <li>Groovy interpreter updated to 2.4.12</li>
141 <li>Example groovy script for generating a matrix of
142 percent identity scores for current alignment.</li>
144 <em>Testing and Deployment</em>
147 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
151 <td><div align="left">
155 <!-- JAL-2643 -->Pressing tab after updating the colour
156 threshold text field doesn't trigger an update to the
160 <!-- JAL-2682 -->Race condition when parsing sequence ID
164 <!-- JAL-2608 -->Overview windows are also closed when
165 alignment window is closed
168 <!-- JAL-2548 -->Export of features doesn't always respect
172 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
173 takes a long time in Cursor mode
179 <!-- JAL-2777 -->Structures with whitespace chainCode
180 cannot be viewed in Chimera
183 <!-- JAL-2728 -->Protein annotation panel too high in
187 <!-- JAL-2757 -->Can't edit the query after the server
188 error warning icon is shown in Uniprot and PDB Free Text
192 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
195 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
198 <!-- JAL-2739 -->Hidden column marker in last column not
199 rendered when switching back from Wrapped to normal view
202 <!-- JAL-2768 -->Annotation display corrupted when
203 scrolling right in unwapped alignment view
206 <!-- JAL-2542 -->Existing features on subsequence
207 incorrectly relocated when full sequence retrieved from
211 <!-- JAL-2733 -->Last reported memory still shown when
212 Desktop->Show Memory is unticked (OSX only)
215 <!-- JAL-2658 -->Amend Features dialog doesn't allow
216 features of same type and group to be selected for
220 <!-- JAL-2524 -->Jalview becomes sluggish in wide
221 alignments when hidden columns are present
224 <!-- JAL-2392 -->Jalview freezes when loading and
225 displaying several structures
228 <!-- JAL-2732 -->Black outlines left after resizing or
232 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
233 within the Jalview desktop on OSX
236 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
237 when in wrapped alignment mode
240 <!-- JAL-2636 -->Scale mark not shown when close to right
241 hand end of alignment
244 <!-- JAL-2684 -->Pairwise alignment of selected regions of
245 each selected sequence do not have correct start/end
249 <!-- JAL-2793 -->Alignment ruler height set incorrectly
250 after canceling the Alignment Window's Font dialog
253 <!-- JAL-2036 -->Show cross-references not enabled after
254 restoring project until a new view is created
257 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
258 URL links appears when only default EMBL-EBI link is
259 configured (since 2.10.2b2)
262 <!-- JAL-2775 -->Overview redraws whole window when box
266 <!-- JAL-2225 -->Structure viewer doesn't map all chains
267 in a multi-chain structure when viewing alignment
268 involving more than one chain (since 2.10)
271 <!-- JAL-2811 -->Double residue highlights in cursor mode
272 if new selection moves alignment window
275 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
276 arrow key in cursor mode to pass hidden column marker
279 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
280 that produces correctly annotated transcripts and products
283 <!-- JAL-2776 -->Toggling a feature group after first time
284 doesn't update associated structure view
287 <em>Applet</em><br />
290 <!-- JAL-2687 -->Concurrent modification exception when
291 closing alignment panel
294 <em>BioJSON</em><br />
297 <!-- JAL-2546 -->BioJSON export does not preserve
298 non-positional features
301 <em>New Known Issues</em>
304 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
305 sequence features correctly (for many previous versions of
309 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
310 using cursor in wrapped panel other than top
313 <!-- JAL-2791 -->Select columns containing feature ignores
314 graduated colour threshold
317 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
318 always preserve numbering and sequence features
321 <em>Known Java 9 Issues</em>
324 <!-- JAL-2902 -->Groovy Console very slow to open and is
325 not responsive when entering characters (Webstart, Java
332 <td width="60" nowrap>
334 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
335 <em>2/10/2017</em></strong>
338 <td><div align="left">
339 <em>New features in Jalview Desktop</em>
342 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
344 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
348 <td><div align="left">
352 <td width="60" nowrap>
354 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
355 <em>7/9/2017</em></strong>
358 <td><div align="left">
362 <!-- JAL-2588 -->Show gaps in overview window by colouring
363 in grey (sequences used to be coloured grey, and gaps were
367 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
371 <!-- JAL-2587 -->Overview updates immediately on increase
372 in size and progress bar shown as higher resolution
373 overview is recalculated
378 <td><div align="left">
382 <!-- JAL-2664 -->Overview window redraws every hidden
383 column region row by row
386 <!-- JAL-2681 -->duplicate protein sequences shown after
387 retrieving Ensembl crossrefs for sequences from Uniprot
390 <!-- JAL-2603 -->Overview window throws NPE if show boxes
391 format setting is unticked
394 <!-- JAL-2610 -->Groups are coloured wrongly in overview
395 if group has show boxes format setting unticked
398 <!-- JAL-2672,JAL-2665 -->Redraw problems when
399 autoscrolling whilst dragging current selection group to
400 include sequences and columns not currently displayed
403 <!-- JAL-2691 -->Not all chains are mapped when multimeric
404 assemblies are imported via CIF file
407 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
408 displayed when threshold or conservation colouring is also
412 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
416 <!-- JAL-2673 -->Jalview continues to scroll after
417 dragging a selected region off the visible region of the
421 <!-- JAL-2724 -->Cannot apply annotation based
422 colourscheme to all groups in a view
425 <!-- JAL-2511 -->IDs don't line up with sequences
426 initially after font size change using the Font chooser or
433 <td width="60" nowrap>
435 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
438 <td><div align="left">
439 <em>Calculations</em>
443 <!-- JAL-1933 -->Occupancy annotation row shows number of
444 ungapped positions in each column of the alignment.
447 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
448 a calculation dialog box
451 <!-- JAL-2379 -->Revised implementation of PCA for speed
452 and memory efficiency (~30x faster)
455 <!-- JAL-2403 -->Revised implementation of sequence
456 similarity scores as used by Tree, PCA, Shading Consensus
457 and other calculations
460 <!-- JAL-2416 -->Score matrices are stored as resource
461 files within the Jalview codebase
464 <!-- JAL-2500 -->Trees computed on Sequence Feature
465 Similarity may have different topology due to increased
472 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
473 model for alignments and groups
476 <!-- JAL-384 -->Custom shading schemes created via groovy
483 <!-- JAL-2526 -->Efficiency improvements for interacting
484 with alignment and overview windows
487 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
491 <!-- JAL-2388 -->Hidden columns and sequences can be
495 <!-- JAL-2611 -->Click-drag in visible area allows fine
496 adjustment of visible position
500 <em>Data import/export</em>
503 <!-- JAL-2535 -->Posterior probability annotation from
504 Stockholm files imported as sequence associated annotation
507 <!-- JAL-2507 -->More robust per-sequence positional
508 annotation input/output via stockholm flatfile
511 <!-- JAL-2533 -->Sequence names don't include file
512 extension when importing structure files without embedded
513 names or PDB accessions
516 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
517 format sequence substitution matrices
520 <em>User Interface</em>
523 <!-- JAL-2447 --> Experimental Features Checkbox in
524 Desktop's Tools menu to hide or show untested features in
528 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
529 via Overview or sequence motif search operations
532 <!-- JAL-2547 -->Amend sequence features dialog box can be
533 opened by double clicking gaps within sequence feature
537 <!-- JAL-1476 -->Status bar message shown when not enough
538 aligned positions were available to create a 3D structure
542 <em>3D Structure</em>
545 <!-- JAL-2430 -->Hidden regions in alignment views are not
546 coloured in linked structure views
549 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
550 file-based command exchange
553 <!-- JAL-2375 -->Structure chooser automatically shows
554 Cached Structures rather than querying the PDBe if
555 structures are already available for sequences
558 <!-- JAL-2520 -->Structures imported via URL are cached in
559 the Jalview project rather than downloaded again when the
563 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
564 to transfer Chimera's structure attributes as Jalview
565 features, and vice-versa (<strong>Experimental
569 <em>Web Services</em>
572 <!-- JAL-2549 -->Updated JABAWS client to v2.2
575 <!-- JAL-2335 -->Filter non-standard amino acids and
576 nucleotides when submitting to AACon and other MSA
580 <!-- JAL-2316, -->URLs for viewing database
581 cross-references provided by identifiers.org and the
589 <!-- JAL-2344 -->FileFormatI interface for describing and
590 identifying file formats (instead of String constants)
593 <!-- JAL-2228 -->FeatureCounter script refactored for
594 efficiency when counting all displayed features (not
595 backwards compatible with 2.10.1)
598 <em>Example files</em>
601 <!-- JAL-2631 -->Graduated feature colour style example
602 included in the example feature file
605 <em>Documentation</em>
608 <!-- JAL-2339 -->Release notes reformatted for readability
609 with the built-in Java help viewer
612 <!-- JAL-1644 -->Find documentation updated with 'search
613 sequence description' option
619 <!-- JAL-2485, -->External service integration tests for
620 Uniprot REST Free Text Search Client
623 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
626 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
631 <td><div align="left">
632 <em>Calculations</em>
635 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
636 matrix - C->R should be '-3'<br />Old matrix restored
637 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
639 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
640 Jalview's treatment of gaps in PCA and substitution matrix
641 based Tree calculations.<br /> <br />In earlier versions
642 of Jalview, gaps matching gaps were penalised, and gaps
643 matching non-gaps penalised even more. In the PCA
644 calculation, gaps were actually treated as non-gaps - so
645 different costs were applied, which meant Jalview's PCAs
646 were different to those produced by SeqSpace.<br />Jalview
647 now treats gaps in the same way as SeqSpace (ie it scores
648 them as 0). <br /> <br />Enter the following in the
649 Groovy console to restore pre-2.10.2 behaviour:<br />
650 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
651 // for 2.10.1 mode <br />
652 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
653 // to restore 2.10.2 mode <br /> <br /> <em>Note:
654 these settings will affect all subsequent tree and PCA
655 calculations (not recommended)</em></li>
657 <!-- JAL-2424 -->Fixed off-by-one bug that affected
658 scaling of branch lengths for trees computed using
659 Sequence Feature Similarity.
662 <!-- JAL-2377 -->PCA calculation could hang when
663 generating output report when working with highly
667 <!-- JAL-2544 --> Sort by features includes features to
668 right of selected region when gaps present on right-hand
672 <em>User Interface</em>
675 <!-- JAL-2346 -->Reopening Colour by annotation dialog
676 doesn't reselect a specific sequence's associated
677 annotation after it was used for colouring a view
680 <!-- JAL-2419 -->Current selection lost if popup menu
681 opened on a region of alignment without groups
684 <!-- JAL-2374 -->Popup menu not always shown for regions
685 of an alignment with overlapping groups
688 <!-- JAL-2310 -->Finder double counts if both a sequence's
689 name and description match
692 <!-- JAL-2370 -->Hiding column selection containing two
693 hidden regions results in incorrect hidden regions
696 <!-- JAL-2386 -->'Apply to all groups' setting when
697 changing colour does not apply Conservation slider value
701 <!-- JAL-2373 -->Percentage identity and conservation menu
702 items do not show a tick or allow shading to be disabled
705 <!-- JAL-2385 -->Conservation shading or PID threshold
706 lost when base colourscheme changed if slider not visible
709 <!-- JAL-2547 -->Sequence features shown in tooltip for
710 gaps before start of features
713 <!-- JAL-2623 -->Graduated feature colour threshold not
714 restored to UI when feature colour is edited
717 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
718 a time when scrolling vertically in wrapped mode.
721 <!-- JAL-2630 -->Structure and alignment overview update
722 as graduate feature colour settings are modified via the
726 <!-- JAL-2034 -->Overview window doesn't always update
727 when a group defined on the alignment is resized
730 <!-- JAL-2605 -->Mouseovers on left/right scale region in
731 wrapped view result in positional status updates
735 <!-- JAL-2563 -->Status bar doesn't show position for
736 ambiguous amino acid and nucleotide symbols
739 <!-- JAL-2602 -->Copy consensus sequence failed if
740 alignment included gapped columns
743 <!-- JAL-2473 -->Minimum size set for Jalview windows so
744 widgets don't permanently disappear
747 <!-- JAL-2503 -->Cannot select or filter quantitative
748 annotation that are shown only as column labels (e.g.
749 T-Coffee column reliability scores)
752 <!-- JAL-2594 -->Exception thrown if trying to create a
753 sequence feature on gaps only
756 <!-- JAL-2504 -->Features created with 'New feature'
757 button from a Find inherit previously defined feature type
758 rather than the Find query string
761 <!-- JAL-2423 -->incorrect title in output window when
762 exporting tree calculated in Jalview
765 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
766 and then revealing them reorders sequences on the
770 <!-- JAL-964 -->Group panel in sequence feature settings
771 doesn't update to reflect available set of groups after
772 interactively adding or modifying features
775 <!-- JAL-2225 -->Sequence Database chooser unusable on
779 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
780 only excluded gaps in current sequence and ignored
787 <!-- JAL-2421 -->Overview window visible region moves
788 erratically when hidden rows or columns are present
791 <!-- JAL-2362 -->Per-residue colourschemes applied via the
792 Structure Viewer's colour menu don't correspond to
796 <!-- JAL-2405 -->Protein specific colours only offered in
797 colour and group colour menu for protein alignments
800 <!-- JAL-2385 -->Colour threshold slider doesn't update to
801 reflect currently selected view or group's shading
805 <!-- JAL-2624 -->Feature colour thresholds not respected
806 when rendered on overview and structures when opacity at
810 <!-- JAL-2589 -->User defined gap colour not shown in
811 overview when features overlaid on alignment
814 <em>Data import/export</em>
817 <!-- JAL-2576 -->Very large alignments take a long time to
821 <!-- JAL-2507 -->Per-sequence RNA secondary structures
822 added after a sequence was imported are not written to
826 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
827 when importing RNA secondary structure via Stockholm
830 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
831 not shown in correct direction for simple pseudoknots
834 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
835 with lightGray or darkGray via features file (but can
839 <!-- JAL-2383 -->Above PID colour threshold not recovered
840 when alignment view imported from project
843 <!-- JAL-2520,JAL-2465 -->No mappings generated between
844 structure and sequences extracted from structure files
845 imported via URL and viewed in Jmol
848 <!-- JAL-2520 -->Structures loaded via URL are saved in
849 Jalview Projects rather than fetched via URL again when
850 the project is loaded and the structure viewed
853 <em>Web Services</em>
856 <!-- JAL-2519 -->EnsemblGenomes example failing after
857 release of Ensembl v.88
860 <!-- JAL-2366 -->Proxy server address and port always
861 appear enabled in Preferences->Connections
864 <!-- JAL-2461 -->DAS registry not found exceptions
865 removed from console output
868 <!-- JAL-2582 -->Cannot retrieve protein products from
869 Ensembl by Peptide ID
872 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
873 created from SIFTs, and spurious 'Couldn't open structure
874 in Chimera' errors raised after April 2017 update (problem
875 due to 'null' string rather than empty string used for
876 residues with no corresponding PDB mapping).
879 <em>Application UI</em>
882 <!-- JAL-2361 -->User Defined Colours not added to Colour
886 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
887 case' residues (button in colourscheme editor debugged and
888 new documentation and tooltips added)
891 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
892 doesn't restore group-specific text colour thresholds
895 <!-- JAL-2243 -->Feature settings panel does not update as
896 new features are added to alignment
899 <!-- JAL-2532 -->Cancel in feature settings reverts
900 changes to feature colours via the Amend features dialog
903 <!-- JAL-2506 -->Null pointer exception when attempting to
904 edit graduated feature colour via amend features dialog
908 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
909 selection menu changes colours of alignment views
912 <!-- JAL-2426 -->Spurious exceptions in console raised
913 from alignment calculation workers after alignment has
917 <!-- JAL-1608 -->Typo in selection popup menu - Create
918 groups now 'Create Group'
921 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
922 Create/Undefine group doesn't always work
925 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
926 shown again after pressing 'Cancel'
929 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
930 adjusts start position in wrap mode
933 <!-- JAL-2563 -->Status bar doesn't show positions for
934 ambiguous amino acids
937 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
938 CDS/Protein view after CDS sequences added for aligned
942 <!-- JAL-2592 -->User defined colourschemes called 'User
943 Defined' don't appear in Colours menu
949 <!-- JAL-2468 -->Switching between Nucleotide and Protein
950 score models doesn't always result in an updated PCA plot
953 <!-- JAL-2442 -->Features not rendered as transparent on
954 overview or linked structure view
957 <!-- JAL-2372 -->Colour group by conservation doesn't
961 <!-- JAL-2517 -->Hitting Cancel after applying
962 user-defined colourscheme doesn't restore original
969 <!-- JAL-2314 -->Unit test failure:
970 jalview.ws.jabaws.RNAStructExportImport setup fails
973 <!-- JAL-2307 -->Unit test failure:
974 jalview.ws.sifts.SiftsClientTest due to compatibility
975 problems with deep array comparison equality asserts in
976 successive versions of TestNG
979 <!-- JAL-2479 -->Relocated StructureChooserTest and
980 ParameterUtilsTest Unit tests to Network suite
983 <em>New Known Issues</em>
986 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
987 phase after a sequence motif find operation
990 <!-- JAL-2550 -->Importing annotation file with rows
991 containing just upper and lower case letters are
992 interpreted as WUSS RNA secondary structure symbols
995 <!-- JAL-2590 -->Cannot load and display Newick trees
996 reliably from eggnog Ortholog database
999 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1000 containing features of type Highlight' when 'B' is pressed
1001 to mark columns containing highlighted regions.
1004 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1005 doesn't always add secondary structure annotation.
1010 <td width="60" nowrap>
1011 <div align="center">
1012 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1015 <td><div align="left">
1019 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1020 for all consensus calculations
1023 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1026 <li>Updated Jalview's Certum code signing certificate
1029 <em>Application</em>
1032 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1033 set of database cross-references, sorted alphabetically
1036 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1037 from database cross references. Users with custom links
1038 will receive a <a href="webServices/urllinks.html#warning">warning
1039 dialog</a> asking them to update their preferences.
1042 <!-- JAL-2287-->Cancel button and escape listener on
1043 dialog warning user about disconnecting Jalview from a
1047 <!-- JAL-2320-->Jalview's Chimera control window closes if
1048 the Chimera it is connected to is shut down
1051 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1052 columns menu item to mark columns containing highlighted
1053 regions (e.g. from structure selections or results of a
1057 <!-- JAL-2284-->Command line option for batch-generation
1058 of HTML pages rendering alignment data with the BioJS
1068 <!-- JAL-2286 -->Columns with more than one modal residue
1069 are not coloured or thresholded according to percent
1070 identity (first observed in Jalview 2.8.2)
1073 <!-- JAL-2301 -->Threonine incorrectly reported as not
1077 <!-- JAL-2318 -->Updates to documentation pages (above PID
1078 threshold, amino acid properties)
1081 <!-- JAL-2292 -->Lower case residues in sequences are not
1082 reported as mapped to residues in a structure file in the
1086 <!--JAL-2324 -->Identical features with non-numeric scores
1087 could be added multiple times to a sequence
1090 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1091 bond features shown as two highlighted residues rather
1092 than a range in linked structure views, and treated
1093 correctly when selecting and computing trees from features
1096 <!-- JAL-2281-->Custom URL links for database
1097 cross-references are matched to database name regardless
1102 <em>Application</em>
1105 <!-- JAL-2282-->Custom URL links for specific database
1106 names without regular expressions also offer links from
1110 <!-- JAL-2315-->Removing a single configured link in the
1111 URL links pane in Connections preferences doesn't actually
1112 update Jalview configuration
1115 <!-- JAL-2272-->CTRL-Click on a selected region to open
1116 the alignment area popup menu doesn't work on El-Capitan
1119 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1120 files with similarly named sequences if dropped onto the
1124 <!-- JAL-2312 -->Additional mappings are shown for PDB
1125 entries where more chains exist in the PDB accession than
1126 are reported in the SIFTS file
1129 <!-- JAL-2317-->Certain structures do not get mapped to
1130 the structure view when displayed with Chimera
1133 <!-- JAL-2317-->No chains shown in the Chimera view
1134 panel's View->Show Chains submenu
1137 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1138 work for wrapped alignment views
1141 <!--JAL-2197 -->Rename UI components for running JPred
1142 predictions from 'JNet' to 'JPred'
1145 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1146 corrupted when annotation panel vertical scroll is not at
1147 first annotation row
1150 <!--JAL-2332 -->Attempting to view structure for Hen
1151 lysozyme results in a PDB Client error dialog box
1154 <!-- JAL-2319 -->Structure View's mapping report switched
1155 ranges for PDB and sequence for SIFTS
1158 SIFTS 'Not_Observed' residues mapped to non-existant
1162 <!-- <em>New Known Issues</em>
1169 <td width="60" nowrap>
1170 <div align="center">
1171 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1172 <em>25/10/2016</em></strong>
1175 <td><em>Application</em>
1177 <li>3D Structure chooser opens with 'Cached structures'
1178 view if structures already loaded</li>
1179 <li>Progress bar reports models as they are loaded to
1180 structure views</li>
1186 <li>Colour by conservation always enabled and no tick
1187 shown in menu when BLOSUM or PID shading applied</li>
1188 <li>FER1_ARATH and FER2_ARATH labels were switched in
1189 example sequences/projects/trees</li>
1191 <em>Application</em>
1193 <li>Jalview projects with views of local PDB structure
1194 files saved on Windows cannot be opened on OSX</li>
1195 <li>Multiple structure views can be opened and superposed
1196 without timeout for structures with multiple models or
1197 multiple sequences in alignment</li>
1198 <li>Cannot import or associated local PDB files without a
1199 PDB ID HEADER line</li>
1200 <li>RMSD is not output in Jmol console when superposition
1202 <li>Drag and drop of URL from Browser fails for Linux and
1203 OSX versions earlier than El Capitan</li>
1204 <li>ENA client ignores invalid content from ENA server</li>
1205 <li>Exceptions are not raised in console when ENA client
1206 attempts to fetch non-existent IDs via Fetch DB Refs UI
1208 <li>Exceptions are not raised in console when a new view
1209 is created on the alignment</li>
1210 <li>OSX right-click fixed for group selections: CMD-click
1211 to insert/remove gaps in groups and CTRL-click to open group
1214 <em>Build and deployment</em>
1216 <li>URL link checker now copes with multi-line anchor
1219 <em>New Known Issues</em>
1221 <li>Drag and drop from URL links in browsers do not work
1228 <td width="60" nowrap>
1229 <div align="center">
1230 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1233 <td><em>General</em>
1236 <!-- JAL-2124 -->Updated Spanish translations.
1239 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1240 for importing structure data to Jalview. Enables mmCIF and
1244 <!-- JAL-192 --->Alignment ruler shows positions relative to
1248 <!-- JAL-2202 -->Position/residue shown in status bar when
1249 mousing over sequence associated annotation
1252 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1256 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1257 '()', canonical '[]' and invalid '{}' base pair populations
1261 <!-- JAL-2092 -->Feature settings popup menu options for
1262 showing or hiding columns containing a feature
1265 <!-- JAL-1557 -->Edit selected group by double clicking on
1266 group and sequence associated annotation labels
1269 <!-- JAL-2236 -->Sequence name added to annotation label in
1270 select/hide columns by annotation and colour by annotation
1274 </ul> <em>Application</em>
1277 <!-- JAL-2050-->Automatically hide introns when opening a
1278 gene/transcript view
1281 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1285 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1286 structure mappings with the EMBL-EBI PDBe SIFTS database
1289 <!-- JAL-2079 -->Updated download sites used for Rfam and
1290 Pfam sources to xfam.org
1293 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1296 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1297 over sequences in Jalview
1300 <!-- JAL-2027-->Support for reverse-complement coding
1301 regions in ENA and EMBL
1304 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1305 for record retrieval via ENA rest API
1308 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1312 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1313 groovy script execution
1316 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1317 alignment window's Calculate menu
1320 <!-- JAL-1812 -->Allow groovy scripts that call
1321 Jalview.getAlignFrames() to run in headless mode
1324 <!-- JAL-2068 -->Support for creating new alignment
1325 calculation workers from groovy scripts
1328 <!-- JAL-1369 --->Store/restore reference sequence in
1332 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1333 associations are now saved/restored from project
1336 <!-- JAL-1993 -->Database selection dialog always shown
1337 before sequence fetcher is opened
1340 <!-- JAL-2183 -->Double click on an entry in Jalview's
1341 database chooser opens a sequence fetcher
1344 <!-- JAL-1563 -->Free-text search client for UniProt using
1345 the UniProt REST API
1348 <!-- JAL-2168 -->-nonews command line parameter to prevent
1349 the news reader opening
1352 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1353 querying stored in preferences
1356 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1360 <!-- JAL-1977-->Tooltips shown on database chooser
1363 <!-- JAL-391 -->Reverse complement function in calculate
1364 menu for nucleotide sequences
1367 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1368 and feature counts preserves alignment ordering (and
1369 debugged for complex feature sets).
1372 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1373 viewing structures with Jalview 2.10
1376 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1377 genome, transcript CCDS and gene ids via the Ensembl and
1378 Ensembl Genomes REST API
1381 <!-- JAL-2049 -->Protein sequence variant annotation
1382 computed for 'sequence_variant' annotation on CDS regions
1386 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1390 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1391 Ref Fetcher fails to match, or otherwise updates sequence
1392 data from external database records.
1395 <!-- JAL-2154 -->Revised Jalview Project format for
1396 efficient recovery of sequence coding and alignment
1397 annotation relationships.
1399 </ul> <!-- <em>Applet</em>
1410 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1414 <!-- JAL-2018-->Export features in Jalview format (again)
1415 includes graduated colourschemes
1418 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1419 working with big alignments and lots of hidden columns
1422 <!-- JAL-2053-->Hidden column markers not always rendered
1423 at right of alignment window
1426 <!-- JAL-2067 -->Tidied up links in help file table of
1430 <!-- JAL-2072 -->Feature based tree calculation not shown
1434 <!-- JAL-2075 -->Hidden columns ignored during feature
1435 based tree calculation
1438 <!-- JAL-2065 -->Alignment view stops updating when show
1439 unconserved enabled for group on alignment
1442 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1446 <!-- JAL-2146 -->Alignment column in status incorrectly
1447 shown as "Sequence position" when mousing over
1451 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1452 hidden columns present
1455 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1456 user created annotation added to alignment
1459 <!-- JAL-1841 -->RNA Structure consensus only computed for
1460 '()' base pair annotation
1463 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1464 in zero scores for all base pairs in RNA Structure
1468 <!-- JAL-2174-->Extend selection with columns containing
1472 <!-- JAL-2275 -->Pfam format writer puts extra space at
1473 beginning of sequence
1476 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1480 <!-- JAL-2238 -->Cannot create groups on an alignment from
1481 from a tree when t-coffee scores are shown
1484 <!-- JAL-1836,1967 -->Cannot import and view PDB
1485 structures with chains containing negative resnums (4q4h)
1488 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1492 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1493 to Clustal, PIR and PileUp output
1496 <!-- JAL-2008 -->Reordering sequence features that are
1497 not visible causes alignment window to repaint
1500 <!-- JAL-2006 -->Threshold sliders don't work in
1501 graduated colour and colour by annotation row for e-value
1502 scores associated with features and annotation rows
1505 <!-- JAL-1797 -->amino acid physicochemical conservation
1506 calculation should be case independent
1509 <!-- JAL-2173 -->Remove annotation also updates hidden
1513 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1514 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1515 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1518 <!-- JAL-2065 -->Null pointer exceptions and redraw
1519 problems when reference sequence defined and 'show
1520 non-conserved' enabled
1523 <!-- JAL-1306 -->Quality and Conservation are now shown on
1524 load even when Consensus calculation is disabled
1527 <!-- JAL-1932 -->Remove right on penultimate column of
1528 alignment does nothing
1531 <em>Application</em>
1534 <!-- JAL-1552-->URLs and links can't be imported by
1535 drag'n'drop on OSX when launched via webstart (note - not
1536 yet fixed for El Capitan)
1539 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1540 output when running on non-gb/us i18n platforms
1543 <!-- JAL-1944 -->Error thrown when exporting a view with
1544 hidden sequences as flat-file alignment
1547 <!-- JAL-2030-->InstallAnywhere distribution fails when
1551 <!-- JAL-2080-->Jalview very slow to launch via webstart
1552 (also hotfix for 2.9.0b2)
1555 <!-- JAL-2085 -->Cannot save project when view has a
1556 reference sequence defined
1559 <!-- JAL-1011 -->Columns are suddenly selected in other
1560 alignments and views when revealing hidden columns
1563 <!-- JAL-1989 -->Hide columns not mirrored in complement
1564 view in a cDNA/Protein splitframe
1567 <!-- JAL-1369 -->Cannot save/restore representative
1568 sequence from project when only one sequence is
1572 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1573 in Structure Chooser
1576 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1577 structure consensus didn't refresh annotation panel
1580 <!-- JAL-1962 -->View mapping in structure view shows
1581 mappings between sequence and all chains in a PDB file
1584 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1585 dialogs format columns correctly, don't display array
1586 data, sort columns according to type
1589 <!-- JAL-1975 -->Export complete shown after destination
1590 file chooser is cancelled during an image export
1593 <!-- JAL-2025 -->Error when querying PDB Service with
1594 sequence name containing special characters
1597 <!-- JAL-2024 -->Manual PDB structure querying should be
1601 <!-- JAL-2104 -->Large tooltips with broken HTML
1602 formatting don't wrap
1605 <!-- JAL-1128 -->Figures exported from wrapped view are
1606 truncated so L looks like I in consensus annotation
1609 <!-- JAL-2003 -->Export features should only export the
1610 currently displayed features for the current selection or
1614 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1615 after fetching cross-references, and restoring from
1619 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1620 followed in the structure viewer
1623 <!-- JAL-2163 -->Titles for individual alignments in
1624 splitframe not restored from project
1627 <!-- JAL-2145 -->missing autocalculated annotation at
1628 trailing end of protein alignment in transcript/product
1629 splitview when pad-gaps not enabled by default
1632 <!-- JAL-1797 -->amino acid physicochemical conservation
1636 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1637 article has been read (reopened issue due to
1638 internationalisation problems)
1641 <!-- JAL-1960 -->Only offer PDB structures in structure
1642 viewer based on sequence name, PDB and UniProt
1647 <!-- JAL-1976 -->No progress bar shown during export of
1651 <!-- JAL-2213 -->Structures not always superimposed after
1652 multiple structures are shown for one or more sequences.
1655 <!-- JAL-1370 -->Reference sequence characters should not
1656 be replaced with '.' when 'Show unconserved' format option
1660 <!-- JAL-1823 -->Cannot specify chain code when entering
1661 specific PDB id for sequence
1664 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1665 'Export hidden sequences' is enabled, but 'export hidden
1666 columns' is disabled.
1669 <!--JAL-2026-->Best Quality option in structure chooser
1670 selects lowest rather than highest resolution structures
1674 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1675 to sequence mapping in 'View Mappings' report
1678 <!-- JAL-2284 -->Unable to read old Jalview projects that
1679 contain non-XML data added after Jalvew wrote project.
1682 <!-- JAL-2118 -->Newly created annotation row reorders
1683 after clicking on it to create new annotation for a
1687 <!-- JAL-1980 -->Null Pointer Exception raised when
1688 pressing Add on an orphaned cut'n'paste window.
1690 <!-- may exclude, this is an external service stability issue JAL-1941
1691 -- > RNA 3D structure not added via DSSR service</li> -->
1696 <!-- JAL-2151 -->Incorrect columns are selected when
1697 hidden columns present before start of sequence
1700 <!-- JAL-1986 -->Missing dependencies on applet pages
1704 <!-- JAL-1947 -->Overview pixel size changes when
1705 sequences are hidden in applet
1708 <!-- JAL-1996 -->Updated instructions for applet
1709 deployment on examples pages.
1716 <td width="60" nowrap>
1717 <div align="center">
1718 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1719 <em>16/10/2015</em></strong>
1722 <td><em>General</em>
1724 <li>Time stamps for signed Jalview application and applet
1729 <em>Application</em>
1731 <li>Duplicate group consensus and conservation rows
1732 shown when tree is partitioned</li>
1733 <li>Erratic behaviour when tree partitions made with
1734 multiple cDNA/Protein split views</li>
1740 <td width="60" nowrap>
1741 <div align="center">
1742 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1743 <em>8/10/2015</em></strong>
1746 <td><em>General</em>
1748 <li>Updated Spanish translations of localized text for
1750 </ul> <em>Application</em>
1752 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1753 <li>Signed OSX InstallAnywhere installer<br></li>
1754 <li>Support for per-sequence based annotations in BioJSON</li>
1755 </ul> <em>Applet</em>
1757 <li>Split frame example added to applet examples page</li>
1758 </ul> <em>Build and Deployment</em>
1761 <!-- JAL-1888 -->New ant target for running Jalview's test
1769 <li>Mapping of cDNA to protein in split frames
1770 incorrect when sequence start > 1</li>
1771 <li>Broken images in filter column by annotation dialog
1773 <li>Feature colours not parsed from features file</li>
1774 <li>Exceptions and incomplete link URLs recovered when
1775 loading a features file containing HTML tags in feature
1779 <em>Application</em>
1781 <li>Annotations corrupted after BioJS export and
1783 <li>Incorrect sequence limits after Fetch DB References
1784 with 'trim retrieved sequences'</li>
1785 <li>Incorrect warning about deleting all data when
1786 deleting selected columns</li>
1787 <li>Patch to build system for shipping properly signed
1788 JNLP templates for webstart launch</li>
1789 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1790 unreleased structures for download or viewing</li>
1791 <li>Tab/space/return keystroke operation of EMBL-PDBe
1792 fetcher/viewer dialogs works correctly</li>
1793 <li>Disabled 'minimise' button on Jalview windows
1794 running on OSX to workaround redraw hang bug</li>
1795 <li>Split cDNA/Protein view position and geometry not
1796 recovered from jalview project</li>
1797 <li>Initial enabled/disabled state of annotation menu
1798 sorter 'show autocalculated first/last' corresponds to
1800 <li>Restoring of Clustal, RNA Helices and T-Coffee
1801 color schemes from BioJSON</li>
1805 <li>Reorder sequences mirrored in cDNA/Protein split
1807 <li>Applet with Jmol examples not loading correctly</li>
1813 <td><div align="center">
1814 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1816 <td><em>General</em>
1818 <li>Linked visualisation and analysis of DNA and Protein
1821 <li>Translated cDNA alignments shown as split protein
1822 and DNA alignment views</li>
1823 <li>Codon consensus annotation for linked protein and
1824 cDNA alignment views</li>
1825 <li>Link cDNA or Protein product sequences by loading
1826 them onto Protein or cDNA alignments</li>
1827 <li>Reconstruct linked cDNA alignment from aligned
1828 protein sequences</li>
1831 <li>Jmol integration updated to Jmol v14.2.14</li>
1832 <li>Import and export of Jalview alignment views as <a
1833 href="features/bioJsonFormat.html">BioJSON</a></li>
1834 <li>New alignment annotation file statements for
1835 reference sequences and marking hidden columns</li>
1836 <li>Reference sequence based alignment shading to
1837 highlight variation</li>
1838 <li>Select or hide columns according to alignment
1840 <li>Find option for locating sequences by description</li>
1841 <li>Conserved physicochemical properties shown in amino
1842 acid conservation row</li>
1843 <li>Alignments can be sorted by number of RNA helices</li>
1844 </ul> <em>Application</em>
1846 <li>New cDNA/Protein analysis capabilities
1848 <li>Get Cross-References should open a Split Frame
1849 view with cDNA/Protein</li>
1850 <li>Detect when nucleotide sequences and protein
1851 sequences are placed in the same alignment</li>
1852 <li>Split cDNA/Protein views are saved in Jalview
1857 <li>Use REST API to talk to Chimera</li>
1858 <li>Selected regions in Chimera are highlighted in linked
1859 Jalview windows</li>
1861 <li>VARNA RNA viewer updated to v3.93</li>
1862 <li>VARNA views are saved in Jalview Projects</li>
1863 <li>Pseudoknots displayed as Jalview RNA annotation can
1864 be shown in VARNA</li>
1866 <li>Make groups for selection uses marked columns as well
1867 as the active selected region</li>
1869 <li>Calculate UPGMA and NJ trees using sequence feature
1871 <li>New Export options
1873 <li>New Export Settings dialog to control hidden
1874 region export in flat file generation</li>
1876 <li>Export alignment views for display with the <a
1877 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1879 <li>Export scrollable SVG in HTML page</li>
1880 <li>Optional embedding of BioJSON data when exporting
1881 alignment figures to HTML</li>
1883 <li>3D structure retrieval and display
1885 <li>Free text and structured queries with the PDBe
1887 <li>PDBe Search API based discovery and selection of
1888 PDB structures for a sequence set</li>
1892 <li>JPred4 employed for protein secondary structure
1894 <li>Hide Insertions menu option to hide unaligned columns
1895 for one or a group of sequences</li>
1896 <li>Automatically hide insertions in alignments imported
1897 from the JPred4 web server</li>
1898 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1899 system on OSX<br />LGPL libraries courtesy of <a
1900 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1902 <li>changed 'View nucleotide structure' submenu to 'View
1903 VARNA 2D Structure'</li>
1904 <li>change "View protein structure" menu option to "3D
1907 </ul> <em>Applet</em>
1909 <li>New layout for applet example pages</li>
1910 <li>New parameters to enable SplitFrame view
1911 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1912 <li>New example demonstrating linked viewing of cDNA and
1913 Protein alignments</li>
1914 </ul> <em>Development and deployment</em>
1916 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1917 <li>Include installation type and git revision in build
1918 properties and console log output</li>
1919 <li>Jalview Github organisation, and new github site for
1920 storing BioJsMSA Templates</li>
1921 <li>Jalview's unit tests now managed with TestNG</li>
1924 <!-- <em>General</em>
1926 </ul> --> <!-- issues resolved --> <em>Application</em>
1928 <li>Escape should close any open find dialogs</li>
1929 <li>Typo in select-by-features status report</li>
1930 <li>Consensus RNA secondary secondary structure
1931 predictions are not highlighted in amber</li>
1932 <li>Missing gap character in v2.7 example file means
1933 alignment appears unaligned when pad-gaps is not enabled</li>
1934 <li>First switch to RNA Helices colouring doesn't colour
1935 associated structure views</li>
1936 <li>ID width preference option is greyed out when auto
1937 width checkbox not enabled</li>
1938 <li>Stopped a warning dialog from being shown when
1939 creating user defined colours</li>
1940 <li>'View Mapping' in structure viewer shows sequence
1941 mappings for just that viewer's sequences</li>
1942 <li>Workaround for superposing PDB files containing
1943 multiple models in Chimera</li>
1944 <li>Report sequence position in status bar when hovering
1945 over Jmol structure</li>
1946 <li>Cannot output gaps as '.' symbols with Selection ->
1947 output to text box</li>
1948 <li>Flat file exports of alignments with hidden columns
1949 have incorrect sequence start/end</li>
1950 <li>'Aligning' a second chain to a Chimera structure from
1952 <li>Colour schemes applied to structure viewers don't
1953 work for nucleotide</li>
1954 <li>Loading/cut'n'pasting an empty or invalid file leads
1955 to a grey/invisible alignment window</li>
1956 <li>Exported Jpred annotation from a sequence region
1957 imports to different position</li>
1958 <li>Space at beginning of sequence feature tooltips shown
1959 on some platforms</li>
1960 <li>Chimera viewer 'View | Show Chain' menu is not
1962 <li>'New View' fails with a Null Pointer Exception in
1963 console if Chimera has been opened</li>
1964 <li>Mouseover to Chimera not working</li>
1965 <li>Miscellaneous ENA XML feature qualifiers not
1967 <li>NPE in annotation renderer after 'Extract Scores'</li>
1968 <li>If two structures in one Chimera window, mouseover of
1969 either sequence shows on first structure</li>
1970 <li>'Show annotations' options should not make
1971 non-positional annotations visible</li>
1972 <li>Subsequence secondary structure annotation not shown
1973 in right place after 'view flanking regions'</li>
1974 <li>File Save As type unset when current file format is
1976 <li>Save as '.jar' option removed for saving Jalview
1978 <li>Colour by Sequence colouring in Chimera more
1980 <li>Cannot 'add reference annotation' for a sequence in
1981 several views on same alignment</li>
1982 <li>Cannot show linked products for EMBL / ENA records</li>
1983 <li>Jalview's tooltip wraps long texts containing no
1985 </ul> <em>Applet</em>
1987 <li>Jmol to JalviewLite mouseover/link not working</li>
1988 <li>JalviewLite can't import sequences with ID
1989 descriptions containing angle brackets</li>
1990 </ul> <em>General</em>
1992 <li>Cannot export and reimport RNA secondary structure
1993 via jalview annotation file</li>
1994 <li>Random helix colour palette for colour by annotation
1995 with RNA secondary structure</li>
1996 <li>Mouseover to cDNA from STOP residue in protein
1997 translation doesn't work.</li>
1998 <li>hints when using the select by annotation dialog box</li>
1999 <li>Jmol alignment incorrect if PDB file has alternate CA
2001 <li>FontChooser message dialog appears to hang after
2002 choosing 1pt font</li>
2003 <li>Peptide secondary structure incorrectly imported from
2004 annotation file when annotation display text includes 'e' or
2006 <li>Cannot set colour of new feature type whilst creating
2008 <li>cDNA translation alignment should not be sequence
2009 order dependent</li>
2010 <li>'Show unconserved' doesn't work for lower case
2012 <li>Nucleotide ambiguity codes involving R not recognised</li>
2013 </ul> <em>Deployment and Documentation</em>
2015 <li>Applet example pages appear different to the rest of
2016 www.jalview.org</li>
2017 </ul> <em>Application Known issues</em>
2019 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2020 <li>Misleading message appears after trying to delete
2022 <li>Jalview icon not shown in dock after InstallAnywhere
2023 version launches</li>
2024 <li>Fetching EMBL reference for an RNA sequence results
2025 fails with a sequence mismatch</li>
2026 <li>Corrupted or unreadable alignment display when
2027 scrolling alignment to right</li>
2028 <li>ArrayIndexOutOfBoundsException thrown when remove
2029 empty columns called on alignment with ragged gapped ends</li>
2030 <li>auto calculated alignment annotation rows do not get
2031 placed above or below non-autocalculated rows</li>
2032 <li>Jalview dekstop becomes sluggish at full screen in
2033 ultra-high resolution</li>
2034 <li>Cannot disable consensus calculation independently of
2035 quality and conservation</li>
2036 <li>Mouseover highlighting between cDNA and protein can
2037 become sluggish with more than one splitframe shown</li>
2038 </ul> <em>Applet Known Issues</em>
2040 <li>Core PDB parsing code requires Jmol</li>
2041 <li>Sequence canvas panel goes white when alignment
2042 window is being resized</li>
2048 <td><div align="center">
2049 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2051 <td><em>General</em>
2053 <li>Updated Java code signing certificate donated by
2055 <li>Features and annotation preserved when performing
2056 pairwise alignment</li>
2057 <li>RNA pseudoknot annotation can be
2058 imported/exported/displayed</li>
2059 <li>'colour by annotation' can colour by RNA and
2060 protein secondary structure</li>
2061 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2062 post-hoc with 2.9 release</em>)
2065 </ul> <em>Application</em>
2067 <li>Extract and display secondary structure for sequences
2068 with 3D structures</li>
2069 <li>Support for parsing RNAML</li>
2070 <li>Annotations menu for layout
2072 <li>sort sequence annotation rows by alignment</li>
2073 <li>place sequence annotation above/below alignment
2076 <li>Output in Stockholm format</li>
2077 <li>Internationalisation: improved Spanish (es)
2079 <li>Structure viewer preferences tab</li>
2080 <li>Disorder and Secondary Structure annotation tracks
2081 shared between alignments</li>
2082 <li>UCSF Chimera launch and linked highlighting from
2084 <li>Show/hide all sequence associated annotation rows for
2085 all or current selection</li>
2086 <li>disorder and secondary structure predictions
2087 available as dataset annotation</li>
2088 <li>Per-sequence rna helices colouring</li>
2091 <li>Sequence database accessions imported when fetching
2092 alignments from Rfam</li>
2093 <li>update VARNA version to 3.91</li>
2095 <li>New groovy scripts for exporting aligned positions,
2096 conservation values, and calculating sum of pairs scores.</li>
2097 <li>Command line argument to set default JABAWS server</li>
2098 <li>include installation type in build properties and
2099 console log output</li>
2100 <li>Updated Jalview project format to preserve dataset
2104 <!-- issues resolved --> <em>Application</em>
2106 <li>Distinguish alignment and sequence associated RNA
2107 structure in structure->view->VARNA</li>
2108 <li>Raise dialog box if user deletes all sequences in an
2110 <li>Pressing F1 results in documentation opening twice</li>
2111 <li>Sequence feature tooltip is wrapped</li>
2112 <li>Double click on sequence associated annotation
2113 selects only first column</li>
2114 <li>Redundancy removal doesn't result in unlinked
2115 leaves shown in tree</li>
2116 <li>Undos after several redundancy removals don't undo
2118 <li>Hide sequence doesn't hide associated annotation</li>
2119 <li>User defined colours dialog box too big to fit on
2120 screen and buttons not visible</li>
2121 <li>author list isn't updated if already written to
2122 Jalview properties</li>
2123 <li>Popup menu won't open after retrieving sequence
2125 <li>File open window for associate PDB doesn't open</li>
2126 <li>Left-then-right click on a sequence id opens a
2127 browser search window</li>
2128 <li>Cannot open sequence feature shading/sort popup menu
2129 in feature settings dialog</li>
2130 <li>better tooltip placement for some areas of Jalview
2132 <li>Allow addition of JABAWS Server which doesn't
2133 pass validation</li>
2134 <li>Web services parameters dialog box is too large to
2136 <li>Muscle nucleotide alignment preset obscured by
2138 <li>JABAWS preset submenus don't contain newly
2139 defined user preset</li>
2140 <li>MSA web services warns user if they were launched
2141 with invalid input</li>
2142 <li>Jalview cannot contact DAS Registy when running on
2145 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2146 'Superpose with' submenu not shown when new view
2150 </ul> <!-- <em>Applet</em>
2152 </ul> <em>General</em>
2154 </ul>--> <em>Deployment and Documentation</em>
2156 <li>2G and 1G options in launchApp have no effect on
2157 memory allocation</li>
2158 <li>launchApp service doesn't automatically open
2159 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2161 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2162 InstallAnywhere reports cannot find valid JVM when Java
2163 1.7_055 is available
2165 </ul> <em>Application Known issues</em>
2168 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2169 corrupted or unreadable alignment display when scrolling
2173 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2174 retrieval fails but progress bar continues for DAS retrieval
2175 with large number of ID
2178 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2179 flatfile output of visible region has incorrect sequence
2183 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2184 rna structure consensus doesn't update when secondary
2185 structure tracks are rearranged
2188 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2189 invalid rna structure positional highlighting does not
2190 highlight position of invalid base pairs
2193 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2194 out of memory errors are not raised when saving Jalview
2195 project from alignment window file menu
2198 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2199 Switching to RNA Helices colouring doesn't propagate to
2203 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2204 colour by RNA Helices not enabled when user created
2205 annotation added to alignment
2208 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2209 Jalview icon not shown on dock in Mountain Lion/Webstart
2211 </ul> <em>Applet Known Issues</em>
2214 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2215 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2218 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2219 Jalview and Jmol example not compatible with IE9
2222 <li>Sort by annotation score doesn't reverse order
2228 <td><div align="center">
2229 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2232 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2235 <li>Internationalisation of user interface (usually
2236 called i18n support) and translation for Spanish locale</li>
2237 <li>Define/Undefine group on current selection with
2238 Ctrl-G/Shift Ctrl-G</li>
2239 <li>Improved group creation/removal options in
2240 alignment/sequence Popup menu</li>
2241 <li>Sensible precision for symbol distribution
2242 percentages shown in logo tooltip.</li>
2243 <li>Annotation panel height set according to amount of
2244 annotation when alignment first opened</li>
2245 </ul> <em>Application</em>
2247 <li>Interactive consensus RNA secondary structure
2248 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2249 <li>Select columns containing particular features from
2250 Feature Settings dialog</li>
2251 <li>View all 'representative' PDB structures for selected
2253 <li>Update Jalview project format:
2255 <li>New file extension for Jalview projects '.jvp'</li>
2256 <li>Preserve sequence and annotation dataset (to
2257 store secondary structure annotation,etc)</li>
2258 <li>Per group and alignment annotation and RNA helix
2262 <li>New similarity measures for PCA and Tree calculation
2264 <li>Experimental support for retrieval and viewing of
2265 flanking regions for an alignment</li>
2269 <!-- issues resolved --> <em>Application</em>
2271 <li>logo keeps spinning and status remains at queued or
2272 running after job is cancelled</li>
2273 <li>cannot export features from alignments imported from
2274 Jalview/VAMSAS projects</li>
2275 <li>Buggy slider for web service parameters that take
2277 <li>Newly created RNA secondary structure line doesn't
2278 have 'display all symbols' flag set</li>
2279 <li>T-COFFEE alignment score shading scheme and other
2280 annotation shading not saved in Jalview project</li>
2281 <li>Local file cannot be loaded in freshly downloaded
2283 <li>Jalview icon not shown on dock in Mountain
2285 <li>Load file from desktop file browser fails</li>
2286 <li>Occasional NPE thrown when calculating large trees</li>
2287 <li>Cannot reorder or slide sequences after dragging an
2288 alignment onto desktop</li>
2289 <li>Colour by annotation dialog throws NPE after using
2290 'extract scores' function</li>
2291 <li>Loading/cut'n'pasting an empty file leads to a grey
2292 alignment window</li>
2293 <li>Disorder thresholds rendered incorrectly after
2294 performing IUPred disorder prediction</li>
2295 <li>Multiple group annotated consensus rows shown when
2296 changing 'normalise logo' display setting</li>
2297 <li>Find shows blank dialog after 'finished searching' if
2298 nothing matches query</li>
2299 <li>Null Pointer Exceptions raised when sorting by
2300 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2302 <li>Errors in Jmol console when structures in alignment
2303 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2305 <li>Not all working JABAWS services are shown in
2307 <li>JAVAWS version of Jalview fails to launch with
2308 'invalid literal/length code'</li>
2309 <li>Annotation/RNA Helix colourschemes cannot be applied
2310 to alignment with groups (actually fixed in 2.8.0b1)</li>
2311 <li>RNA Helices and T-Coffee Scores available as default
2314 </ul> <em>Applet</em>
2316 <li>Remove group option is shown even when selection is
2318 <li>Apply to all groups ticked but colourscheme changes
2319 don't affect groups</li>
2320 <li>Documented RNA Helices and T-Coffee Scores as valid
2321 colourscheme name</li>
2322 <li>Annotation labels drawn on sequence IDs when
2323 Annotation panel is not displayed</li>
2324 <li>Increased font size for dropdown menus on OSX and
2325 embedded windows</li>
2326 </ul> <em>Other</em>
2328 <li>Consensus sequence for alignments/groups with a
2329 single sequence were not calculated</li>
2330 <li>annotation files that contain only groups imported as
2331 annotation and junk sequences</li>
2332 <li>Fasta files with sequences containing '*' incorrectly
2333 recognised as PFAM or BLC</li>
2334 <li>conservation/PID slider apply all groups option
2335 doesn't affect background (2.8.0b1)
2337 <li>redundancy highlighting is erratic at 0% and 100%</li>
2338 <li>Remove gapped columns fails for sequences with ragged
2340 <li>AMSA annotation row with leading spaces is not
2341 registered correctly on import</li>
2342 <li>Jalview crashes when selecting PCA analysis for
2343 certain alignments</li>
2344 <li>Opening the colour by annotation dialog for an
2345 existing annotation based 'use original colours'
2346 colourscheme loses original colours setting</li>
2351 <td><div align="center">
2352 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2353 <em>30/1/2014</em></strong>
2357 <li>Trusted certificates for JalviewLite applet and
2358 Jalview Desktop application<br />Certificate was donated by
2359 <a href="https://www.certum.eu">Certum</a> to the Jalview
2360 open source project).
2362 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2363 <li>Output in Stockholm format</li>
2364 <li>Allow import of data from gzipped files</li>
2365 <li>Export/import group and sequence associated line
2366 graph thresholds</li>
2367 <li>Nucleotide substitution matrix that supports RNA and
2368 ambiguity codes</li>
2369 <li>Allow disorder predictions to be made on the current
2370 selection (or visible selection) in the same way that JPred
2372 <li>Groovy scripting for headless Jalview operation</li>
2373 </ul> <em>Other improvements</em>
2375 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2376 <li>COMBINE statement uses current SEQUENCE_REF and
2377 GROUP_REF scope to group annotation rows</li>
2378 <li>Support '' style escaping of quotes in Newick
2380 <li>Group options for JABAWS service by command line name</li>
2381 <li>Empty tooltip shown for JABA service options with a
2382 link but no description</li>
2383 <li>Select primary source when selecting authority in
2384 database fetcher GUI</li>
2385 <li>Add .mfa to FASTA file extensions recognised by
2387 <li>Annotation label tooltip text wrap</li>
2392 <li>Slow scrolling when lots of annotation rows are
2394 <li>Lots of NPE (and slowness) after creating RNA
2395 secondary structure annotation line</li>
2396 <li>Sequence database accessions not imported when
2397 fetching alignments from Rfam</li>
2398 <li>Incorrect SHMR submission for sequences with
2400 <li>View all structures does not always superpose
2402 <li>Option widgets in service parameters not updated to
2403 reflect user or preset settings</li>
2404 <li>Null pointer exceptions for some services without
2405 presets or adjustable parameters</li>
2406 <li>Discover PDB IDs entry in structure menu doesn't
2407 discover PDB xRefs</li>
2408 <li>Exception encountered while trying to retrieve
2409 features with DAS</li>
2410 <li>Lowest value in annotation row isn't coloured
2411 when colour by annotation (per sequence) is coloured</li>
2412 <li>Keyboard mode P jumps to start of gapped region when
2413 residue follows a gap</li>
2414 <li>Jalview appears to hang importing an alignment with
2415 Wrap as default or after enabling Wrap</li>
2416 <li>'Right click to add annotations' message
2417 shown in wrap mode when no annotations present</li>
2418 <li>Disorder predictions fail with NPE if no automatic
2419 annotation already exists on alignment</li>
2420 <li>oninit javascript function should be called after
2421 initialisation completes</li>
2422 <li>Remove redundancy after disorder prediction corrupts
2423 alignment window display</li>
2424 <li>Example annotation file in documentation is invalid</li>
2425 <li>Grouped line graph annotation rows are not exported
2426 to annotation file</li>
2427 <li>Multi-harmony analysis cannot be run when only two
2429 <li>Cannot create multiple groups of line graphs with
2430 several 'combine' statements in annotation file</li>
2431 <li>Pressing return several times causes Number Format
2432 exceptions in keyboard mode</li>
2433 <li>Multi-harmony (SHMMR) method doesn't submit
2434 correct partitions for input data</li>
2435 <li>Translation from DNA to Amino Acids fails</li>
2436 <li>Jalview fail to load newick tree with quoted label</li>
2437 <li>--headless flag isn't understood</li>
2438 <li>ClassCastException when generating EPS in headless
2440 <li>Adjusting sequence-associated shading threshold only
2441 changes one row's threshold</li>
2442 <li>Preferences and Feature settings panel panel
2443 doesn't open</li>
2444 <li>hide consensus histogram also hides conservation and
2445 quality histograms</li>
2450 <td><div align="center">
2451 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2453 <td><em>Application</em>
2455 <li>Support for JABAWS 2.0 Services (AACon alignment
2456 conservation, protein disorder and Clustal Omega)</li>
2457 <li>JABAWS server status indicator in Web Services
2459 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2460 in Jalview alignment window</li>
2461 <li>Updated Jalview build and deploy framework for OSX
2462 mountain lion, windows 7, and 8</li>
2463 <li>Nucleotide substitution matrix for PCA that supports
2464 RNA and ambiguity codes</li>
2466 <li>Improved sequence database retrieval GUI</li>
2467 <li>Support fetching and database reference look up
2468 against multiple DAS sources (Fetch all from in 'fetch db
2470 <li>Jalview project improvements
2472 <li>Store and retrieve the 'belowAlignment'
2473 flag for annotation</li>
2474 <li>calcId attribute to group annotation rows on the
2476 <li>Store AACon calculation settings for a view in
2477 Jalview project</li>
2481 <li>horizontal scrolling gesture support</li>
2482 <li>Visual progress indicator when PCA calculation is
2484 <li>Simpler JABA web services menus</li>
2485 <li>visual indication that web service results are still
2486 being retrieved from server</li>
2487 <li>Serialise the dialogs that are shown when Jalview
2488 starts up for first time</li>
2489 <li>Jalview user agent string for interacting with HTTP
2491 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2493 <li>Examples directory and Groovy library included in
2494 InstallAnywhere distribution</li>
2495 </ul> <em>Applet</em>
2497 <li>RNA alignment and secondary structure annotation
2498 visualization applet example</li>
2499 </ul> <em>General</em>
2501 <li>Normalise option for consensus sequence logo</li>
2502 <li>Reset button in PCA window to return dimensions to
2504 <li>Allow seqspace or Jalview variant of alignment PCA
2506 <li>PCA with either nucleic acid and protein substitution
2508 <li>Allow windows containing HTML reports to be exported
2510 <li>Interactive display and editing of RNA secondary
2511 structure contacts</li>
2512 <li>RNA Helix Alignment Colouring</li>
2513 <li>RNA base pair logo consensus</li>
2514 <li>Parse sequence associated secondary structure
2515 information in Stockholm files</li>
2516 <li>HTML Export database accessions and annotation
2517 information presented in tooltip for sequences</li>
2518 <li>Import secondary structure from LOCARNA clustalw
2519 style RNA alignment files</li>
2520 <li>import and visualise T-COFFEE quality scores for an
2522 <li>'colour by annotation' per sequence option to
2523 shade each sequence according to its associated alignment
2525 <li>New Jalview Logo</li>
2526 </ul> <em>Documentation and Development</em>
2528 <li>documentation for score matrices used in Jalview</li>
2529 <li>New Website!</li>
2531 <td><em>Application</em>
2533 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2534 wsdbfetch REST service</li>
2535 <li>Stop windows being moved outside desktop on OSX</li>
2536 <li>Filetype associations not installed for webstart
2538 <li>Jalview does not always retrieve progress of a JABAWS
2539 job execution in full once it is complete</li>
2540 <li>revise SHMR RSBS definition to ensure alignment is
2541 uploaded via ali_file parameter</li>
2542 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2543 <li>View all structures superposed fails with exception</li>
2544 <li>Jnet job queues forever if a very short sequence is
2545 submitted for prediction</li>
2546 <li>Cut and paste menu not opened when mouse clicked on
2548 <li>Putting fractional value into integer text box in
2549 alignment parameter dialog causes Jalview to hang</li>
2550 <li>Structure view highlighting doesn't work on
2552 <li>View all structures fails with exception shown in
2554 <li>Characters in filename associated with PDBEntry not
2555 escaped in a platform independent way</li>
2556 <li>Jalview desktop fails to launch with exception when
2558 <li>Tree calculation reports 'you must have 2 or more
2559 sequences selected' when selection is empty</li>
2560 <li>Jalview desktop fails to launch with jar signature
2561 failure when java web start temporary file caching is
2563 <li>DAS Sequence retrieval with range qualification
2564 results in sequence xref which includes range qualification</li>
2565 <li>Errors during processing of command line arguments
2566 cause progress bar (JAL-898) to be removed</li>
2567 <li>Replace comma for semi-colon option not disabled for
2568 DAS sources in sequence fetcher</li>
2569 <li>Cannot close news reader when JABAWS server warning
2570 dialog is shown</li>
2571 <li>Option widgets not updated to reflect user settings</li>
2572 <li>Edited sequence not submitted to web service</li>
2573 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2574 <li>InstallAnywhere installer doesn't unpack and run
2575 on OSX Mountain Lion</li>
2576 <li>Annotation panel not given a scroll bar when
2577 sequences with alignment annotation are pasted into the
2579 <li>Sequence associated annotation rows not associated
2580 when loaded from Jalview project</li>
2581 <li>Browser launch fails with NPE on java 1.7</li>
2582 <li>JABAWS alignment marked as finished when job was
2583 cancelled or job failed due to invalid input</li>
2584 <li>NPE with v2.7 example when clicking on Tree
2585 associated with all views</li>
2586 <li>Exceptions when copy/paste sequences with grouped
2587 annotation rows to new window</li>
2588 </ul> <em>Applet</em>
2590 <li>Sequence features are momentarily displayed before
2591 they are hidden using hidefeaturegroups applet parameter</li>
2592 <li>loading features via javascript API automatically
2593 enables feature display</li>
2594 <li>scrollToColumnIn javascript API method doesn't
2596 </ul> <em>General</em>
2598 <li>Redundancy removal fails for rna alignment</li>
2599 <li>PCA calculation fails when sequence has been selected
2600 and then deselected</li>
2601 <li>PCA window shows grey box when first opened on OSX</li>
2602 <li>Letters coloured pink in sequence logo when alignment
2603 coloured with clustalx</li>
2604 <li>Choosing fonts without letter symbols defined causes
2605 exceptions and redraw errors</li>
2606 <li>Initial PCA plot view is not same as manually
2607 reconfigured view</li>
2608 <li>Grouped annotation graph label has incorrect line
2610 <li>Grouped annotation graph label display is corrupted
2611 for lots of labels</li>
2616 <div align="center">
2617 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2620 <td><em>Application</em>
2622 <li>Jalview Desktop News Reader</li>
2623 <li>Tweaked default layout of web services menu</li>
2624 <li>View/alignment association menu to enable user to
2625 easily specify which alignment a multi-structure view takes
2626 its colours/correspondences from</li>
2627 <li>Allow properties file location to be specified as URL</li>
2628 <li>Extend Jalview project to preserve associations
2629 between many alignment views and a single Jmol display</li>
2630 <li>Store annotation row height in Jalview project file</li>
2631 <li>Annotation row column label formatting attributes
2632 stored in project file</li>
2633 <li>Annotation row order for auto-calculated annotation
2634 rows preserved in Jalview project file</li>
2635 <li>Visual progress indication when Jalview state is
2636 saved using Desktop window menu</li>
2637 <li>Visual indication that command line arguments are
2638 still being processed</li>
2639 <li>Groovy script execution from URL</li>
2640 <li>Colour by annotation default min and max colours in
2642 <li>Automatically associate PDB files dragged onto an
2643 alignment with sequences that have high similarity and
2645 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2646 <li>'view structures' option to open many
2647 structures in same window</li>
2648 <li>Sort associated views menu option for tree panel</li>
2649 <li>Group all JABA and non-JABA services for a particular
2650 analysis function in its own submenu</li>
2651 </ul> <em>Applet</em>
2653 <li>Userdefined and autogenerated annotation rows for
2655 <li>Adjustment of alignment annotation pane height</li>
2656 <li>Annotation scrollbar for annotation panel</li>
2657 <li>Drag to reorder annotation rows in annotation panel</li>
2658 <li>'automaticScrolling' parameter</li>
2659 <li>Allow sequences with partial ID string matches to be
2660 annotated from GFF/Jalview features files</li>
2661 <li>Sequence logo annotation row in applet</li>
2662 <li>Absolute paths relative to host server in applet
2663 parameters are treated as such</li>
2664 <li>New in the JalviewLite javascript API:
2666 <li>JalviewLite.js javascript library</li>
2667 <li>Javascript callbacks for
2669 <li>Applet initialisation</li>
2670 <li>Sequence/alignment mouse-overs and selections</li>
2673 <li>scrollTo row and column alignment scrolling
2675 <li>Select sequence/alignment regions from javascript</li>
2676 <li>javascript structure viewer harness to pass
2677 messages between Jmol and Jalview when running as
2678 distinct applets</li>
2679 <li>sortBy method</li>
2680 <li>Set of applet and application examples shipped
2681 with documentation</li>
2682 <li>New example to demonstrate JalviewLite and Jmol
2683 javascript message exchange</li>
2685 </ul> <em>General</em>
2687 <li>Enable Jmol displays to be associated with multiple
2688 multiple alignments</li>
2689 <li>Option to automatically sort alignment with new tree</li>
2690 <li>User configurable link to enable redirects to a
2691 www.Jalview.org mirror</li>
2692 <li>Jmol colours option for Jmol displays</li>
2693 <li>Configurable newline string when writing alignment
2694 and other flat files</li>
2695 <li>Allow alignment annotation description lines to
2696 contain html tags</li>
2697 </ul> <em>Documentation and Development</em>
2699 <li>Add groovy test harness for bulk load testing to
2701 <li>Groovy script to load and align a set of sequences
2702 using a web service before displaying the result in the
2703 Jalview desktop</li>
2704 <li>Restructured javascript and applet api documentation</li>
2705 <li>Ant target to publish example html files with applet
2707 <li>Netbeans project for building Jalview from source</li>
2708 <li>ant task to create online javadoc for Jalview source</li>
2710 <td><em>Application</em>
2712 <li>User defined colourscheme throws exception when
2713 current built in colourscheme is saved as new scheme</li>
2714 <li>AlignFrame->Save in application pops up save
2715 dialog for valid filename/format</li>
2716 <li>Cannot view associated structure for UniProt sequence</li>
2717 <li>PDB file association breaks for UniProt sequence
2719 <li>Associate PDB from file dialog does not tell you
2720 which sequence is to be associated with the file</li>
2721 <li>Find All raises null pointer exception when query
2722 only matches sequence IDs</li>
2723 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2724 <li>Jalview project with Jmol views created with Jalview
2725 2.4 cannot be loaded</li>
2726 <li>Filetype associations not installed for webstart
2728 <li>Two or more chains in a single PDB file associated
2729 with sequences in different alignments do not get coloured
2730 by their associated sequence</li>
2731 <li>Visibility status of autocalculated annotation row
2732 not preserved when project is loaded</li>
2733 <li>Annotation row height and visibility attributes not
2734 stored in Jalview project</li>
2735 <li>Tree bootstraps are not preserved when saved as a
2736 Jalview project</li>
2737 <li>Envision2 workflow tooltips are corrupted</li>
2738 <li>Enabling show group conservation also enables colour
2739 by conservation</li>
2740 <li>Duplicate group associated conservation or consensus
2741 created on new view</li>
2742 <li>Annotation scrollbar not displayed after 'show
2743 all hidden annotation rows' option selected</li>
2744 <li>Alignment quality not updated after alignment
2745 annotation row is hidden then shown</li>
2746 <li>Preserve colouring of structures coloured by
2747 sequences in pre Jalview 2.7 projects</li>
2748 <li>Web service job parameter dialog is not laid out
2750 <li>Web services menu not refreshed after 'reset
2751 services' button is pressed in preferences</li>
2752 <li>Annotation off by one in Jalview v2_3 example project</li>
2753 <li>Structures imported from file and saved in project
2754 get name like jalview_pdb1234.txt when reloaded</li>
2755 <li>Jalview does not always retrieve progress of a JABAWS
2756 job execution in full once it is complete</li>
2757 </ul> <em>Applet</em>
2759 <li>Alignment height set incorrectly when lots of
2760 annotation rows are displayed</li>
2761 <li>Relative URLs in feature HTML text not resolved to
2763 <li>View follows highlighting does not work for positions
2765 <li><= shown as = in tooltip</li>
2766 <li>Export features raises exception when no features
2768 <li>Separator string used for serialising lists of IDs
2769 for javascript api is modified when separator string
2770 provided as parameter</li>
2771 <li>Null pointer exception when selecting tree leaves for
2772 alignment with no existing selection</li>
2773 <li>Relative URLs for datasources assumed to be relative
2774 to applet's codebase</li>
2775 <li>Status bar not updated after finished searching and
2776 search wraps around to first result</li>
2777 <li>StructureSelectionManager instance shared between
2778 several Jalview applets causes race conditions and memory
2780 <li>Hover tooltip and mouseover of position on structure
2781 not sent from Jmol in applet</li>
2782 <li>Certain sequences of javascript method calls to
2783 applet API fatally hang browser</li>
2784 </ul> <em>General</em>
2786 <li>View follows structure mouseover scrolls beyond
2787 position with wrapped view and hidden regions</li>
2788 <li>Find sequence position moves to wrong residue
2789 with/without hidden columns</li>
2790 <li>Sequence length given in alignment properties window
2792 <li>InvalidNumberFormat exceptions thrown when trying to
2793 import PDB like structure files</li>
2794 <li>Positional search results are only highlighted
2795 between user-supplied sequence start/end bounds</li>
2796 <li>End attribute of sequence is not validated</li>
2797 <li>Find dialog only finds first sequence containing a
2798 given sequence position</li>
2799 <li>Sequence numbering not preserved in MSF alignment
2801 <li>Jalview PDB file reader does not extract sequence
2802 from nucleotide chains correctly</li>
2803 <li>Structure colours not updated when tree partition
2804 changed in alignment</li>
2805 <li>Sequence associated secondary structure not correctly
2806 parsed in interleaved stockholm</li>
2807 <li>Colour by annotation dialog does not restore current
2809 <li>Hiding (nearly) all sequences doesn't work
2811 <li>Sequences containing lowercase letters are not
2812 properly associated with their pdb files</li>
2813 </ul> <em>Documentation and Development</em>
2815 <li>schemas/JalviewWsParamSet.xsd corrupted by
2816 ApplyCopyright tool</li>
2821 <div align="center">
2822 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2825 <td><em>Application</em>
2827 <li>New warning dialog when the Jalview Desktop cannot
2828 contact web services</li>
2829 <li>JABA service parameters for a preset are shown in
2830 service job window</li>
2831 <li>JABA Service menu entries reworded</li>
2835 <li>Modeller PIR IO broken - cannot correctly import a
2836 pir file emitted by Jalview</li>
2837 <li>Existing feature settings transferred to new
2838 alignment view created from cut'n'paste</li>
2839 <li>Improved test for mixed amino/nucleotide chains when
2840 parsing PDB files</li>
2841 <li>Consensus and conservation annotation rows
2842 occasionally become blank for all new windows</li>
2843 <li>Exception raised when right clicking above sequences
2844 in wrapped view mode</li>
2845 </ul> <em>Application</em>
2847 <li>multiple multiply aligned structure views cause cpu
2848 usage to hit 100% and computer to hang</li>
2849 <li>Web Service parameter layout breaks for long user
2850 parameter names</li>
2851 <li>Jaba service discovery hangs desktop if Jaba server
2858 <div align="center">
2859 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2862 <td><em>Application</em>
2864 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2865 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2868 <li>Web Services preference tab</li>
2869 <li>Analysis parameters dialog box and user defined
2871 <li>Improved speed and layout of Envision2 service menu</li>
2872 <li>Superpose structures using associated sequence
2874 <li>Export coordinates and projection as CSV from PCA
2876 </ul> <em>Applet</em>
2878 <li>enable javascript: execution by the applet via the
2879 link out mechanism</li>
2880 </ul> <em>Other</em>
2882 <li>Updated the Jmol Jalview interface to work with Jmol
2884 <li>The Jalview Desktop and JalviewLite applet now
2885 require Java 1.5</li>
2886 <li>Allow Jalview feature colour specification for GFF
2887 sequence annotation files</li>
2888 <li>New 'colour by label' keword in Jalview feature file
2889 type colour specification</li>
2890 <li>New Jalview Desktop Groovy API method that allows a
2891 script to check if it being run in an interactive session or
2892 in a batch operation from the Jalview command line</li>
2896 <li>clustalx colourscheme colours Ds preferentially when
2897 both D+E are present in over 50% of the column</li>
2898 </ul> <em>Application</em>
2900 <li>typo in AlignmentFrame->View->Hide->all but
2901 selected Regions menu item</li>
2902 <li>sequence fetcher replaces ',' for ';' when the ',' is
2903 part of a valid accession ID</li>
2904 <li>fatal OOM if object retrieved by sequence fetcher
2905 runs out of memory</li>
2906 <li>unhandled Out of Memory Error when viewing pca
2907 analysis results</li>
2908 <li>InstallAnywhere builds fail to launch on OS X java
2909 10.5 update 4 (due to apple Java 1.6 update)</li>
2910 <li>Installanywhere Jalview silently fails to launch</li>
2911 </ul> <em>Applet</em>
2913 <li>Jalview.getFeatureGroups() raises an
2914 ArrayIndexOutOfBoundsException if no feature groups are
2921 <div align="center">
2922 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2928 <li>Alignment prettyprinter doesn't cope with long
2930 <li>clustalx colourscheme colours Ds preferentially when
2931 both D+E are present in over 50% of the column</li>
2932 <li>nucleic acid structures retrieved from PDB do not
2933 import correctly</li>
2934 <li>More columns get selected than were clicked on when a
2935 number of columns are hidden</li>
2936 <li>annotation label popup menu not providing correct
2937 add/hide/show options when rows are hidden or none are
2939 <li>Stockholm format shown in list of readable formats,
2940 and parser copes better with alignments from RFAM.</li>
2941 <li>CSV output of consensus only includes the percentage
2942 of all symbols if sequence logo display is enabled</li>
2944 </ul> <em>Applet</em>
2946 <li>annotation panel disappears when annotation is
2948 </ul> <em>Application</em>
2950 <li>Alignment view not redrawn properly when new
2951 alignment opened where annotation panel is visible but no
2952 annotations are present on alignment</li>
2953 <li>pasted region containing hidden columns is
2954 incorrectly displayed in new alignment window</li>
2955 <li>Jalview slow to complete operations when stdout is
2956 flooded (fix is to close the Jalview console)</li>
2957 <li>typo in AlignmentFrame->View->Hide->all but
2958 selected Rregions menu item.</li>
2959 <li>inconsistent group submenu and Format submenu entry
2960 'Un' or 'Non'conserved</li>
2961 <li>Sequence feature settings are being shared by
2962 multiple distinct alignments</li>
2963 <li>group annotation not recreated when tree partition is
2965 <li>double click on group annotation to select sequences
2966 does not propagate to associated trees</li>
2967 <li>Mac OSX specific issues:
2969 <li>exception raised when mouse clicked on desktop
2970 window background</li>
2971 <li>Desktop menu placed on menu bar and application
2972 name set correctly</li>
2973 <li>sequence feature settings not wide enough for the
2974 save feature colourscheme button</li>
2983 <div align="center">
2984 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2987 <td><em>New Capabilities</em>
2989 <li>URL links generated from description line for
2990 regular-expression based URL links (applet and application)
2992 <li>Non-positional feature URL links are shown in link
2994 <li>Linked viewing of nucleic acid sequences and
2996 <li>Automatic Scrolling option in View menu to display
2997 the currently highlighted region of an alignment.</li>
2998 <li>Order an alignment by sequence length, or using the
2999 average score or total feature count for each sequence.</li>
3000 <li>Shading features by score or associated description</li>
3001 <li>Subdivide alignment and groups based on identity of
3002 selected subsequence (Make Groups from Selection).</li>
3003 <li>New hide/show options including Shift+Control+H to
3004 hide everything but the currently selected region.</li>
3005 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3006 </ul> <em>Application</em>
3008 <li>Fetch DB References capabilities and UI expanded to
3009 support retrieval from DAS sequence sources</li>
3010 <li>Local DAS Sequence sources can be added via the
3011 command line or via the Add local source dialog box.</li>
3012 <li>DAS Dbref and DbxRef feature types are parsed as
3013 database references and protein_name is parsed as
3014 description line (BioSapiens terms).</li>
3015 <li>Enable or disable non-positional feature and database
3016 references in sequence ID tooltip from View menu in
3018 <!-- <li>New hidden columns and rows and representatives capabilities
3019 in annotations file (in progress - not yet fully implemented)</li> -->
3020 <li>Group-associated consensus, sequence logos and
3021 conservation plots</li>
3022 <li>Symbol distributions for each column can be exported
3023 and visualized as sequence logos</li>
3024 <li>Optionally scale multi-character column labels to fit
3025 within each column of annotation row<!-- todo for applet -->
3027 <li>Optional automatic sort of associated alignment view
3028 when a new tree is opened.</li>
3029 <li>Jalview Java Console</li>
3030 <li>Better placement of desktop window when moving
3031 between different screens.</li>
3032 <li>New preference items for sequence ID tooltip and
3033 consensus annotation</li>
3034 <li>Client to submit sequences and IDs to Envision2
3036 <li><em>Vamsas Capabilities</em>
3038 <li>Improved VAMSAS synchronization (Jalview archive
3039 used to preserve views, structures, and tree display
3041 <li>Import of vamsas documents from disk or URL via
3043 <li>Sharing of selected regions between views and
3044 with other VAMSAS applications (Experimental feature!)</li>
3045 <li>Updated API to VAMSAS version 0.2</li>
3047 </ul> <em>Applet</em>
3049 <li>Middle button resizes annotation row height</li>
3052 <li>sortByTree (true/false) - automatically sort the
3053 associated alignment view by the tree when a new tree is
3055 <li>showTreeBootstraps (true/false) - show or hide
3056 branch bootstraps (default is to show them if available)</li>
3057 <li>showTreeDistances (true/false) - show or hide
3058 branch lengths (default is to show them if available)</li>
3059 <li>showUnlinkedTreeNodes (true/false) - indicate if
3060 unassociated nodes should be highlighted in the tree
3062 <li>heightScale and widthScale (1.0 or more) -
3063 increase the height or width of a cell in the alignment
3064 grid relative to the current font size.</li>
3067 <li>Non-positional features displayed in sequence ID
3069 </ul> <em>Other</em>
3071 <li>Features format: graduated colour definitions and
3072 specification of feature scores</li>
3073 <li>Alignment Annotations format: new keywords for group
3074 associated annotation (GROUP_REF) and annotation row display
3075 properties (ROW_PROPERTIES)</li>
3076 <li>XML formats extended to support graduated feature
3077 colourschemes, group associated annotation, and profile
3078 visualization settings.</li></td>
3081 <li>Source field in GFF files parsed as feature source
3082 rather than description</li>
3083 <li>Non-positional features are now included in sequence
3084 feature and gff files (controlled via non-positional feature
3085 visibility in tooltip).</li>
3086 <li>URL links generated for all feature links (bugfix)</li>
3087 <li>Added URL embedding instructions to features file
3089 <li>Codons containing ambiguous nucleotides translated as
3090 'X' in peptide product</li>
3091 <li>Match case switch in find dialog box works for both
3092 sequence ID and sequence string and query strings do not
3093 have to be in upper case to match case-insensitively.</li>
3094 <li>AMSA files only contain first column of
3095 multi-character column annotation labels</li>
3096 <li>Jalview Annotation File generation/parsing consistent
3097 with documentation (e.g. Stockholm annotation can be
3098 exported and re-imported)</li>
3099 <li>PDB files without embedded PDB IDs given a friendly
3101 <li>Find incrementally searches ID string matches as well
3102 as subsequence matches, and correctly reports total number
3106 <li>Better handling of exceptions during sequence
3108 <li>Dasobert generated non-positional feature URL
3109 link text excludes the start_end suffix</li>
3110 <li>DAS feature and source retrieval buttons disabled
3111 when fetch or registry operations in progress.</li>
3112 <li>PDB files retrieved from URLs are cached properly</li>
3113 <li>Sequence description lines properly shared via
3115 <li>Sequence fetcher fetches multiple records for all
3117 <li>Ensured that command line das feature retrieval
3118 completes before alignment figures are generated.</li>
3119 <li>Reduced time taken when opening file browser for
3121 <li>isAligned check prior to calculating tree, PCA or
3122 submitting an MSA to JNet now excludes hidden sequences.</li>
3123 <li>User defined group colours properly recovered
3124 from Jalview projects.</li>
3133 <div align="center">
3134 <strong>2.4.0.b2</strong><br> 28/10/2009
3139 <li>Experimental support for google analytics usage
3141 <li>Jalview privacy settings (user preferences and docs).</li>
3146 <li>Race condition in applet preventing startup in
3148 <li>Exception when feature created from selection beyond
3149 length of sequence.</li>
3150 <li>Allow synthetic PDB files to be imported gracefully</li>
3151 <li>Sequence associated annotation rows associate with
3152 all sequences with a given id</li>
3153 <li>Find function matches case-insensitively for sequence
3154 ID string searches</li>
3155 <li>Non-standard characters do not cause pairwise
3156 alignment to fail with exception</li>
3157 </ul> <em>Application Issues</em>
3159 <li>Sequences are now validated against EMBL database</li>
3160 <li>Sequence fetcher fetches multiple records for all
3162 </ul> <em>InstallAnywhere Issues</em>
3164 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3165 issue with installAnywhere mechanism)</li>
3166 <li>Command line launching of JARs from InstallAnywhere
3167 version (java class versioning error fixed)</li>
3174 <div align="center">
3175 <strong>2.4</strong><br> 27/8/2008
3178 <td><em>User Interface</em>
3180 <li>Linked highlighting of codon and amino acid from
3181 translation and protein products</li>
3182 <li>Linked highlighting of structure associated with
3183 residue mapping to codon position</li>
3184 <li>Sequence Fetcher provides example accession numbers
3185 and 'clear' button</li>
3186 <li>MemoryMonitor added as an option under Desktop's
3188 <li>Extract score function to parse whitespace separated
3189 numeric data in description line</li>
3190 <li>Column labels in alignment annotation can be centred.</li>
3191 <li>Tooltip for sequence associated annotation give name
3193 </ul> <em>Web Services and URL fetching</em>
3195 <li>JPred3 web service</li>
3196 <li>Prototype sequence search client (no public services
3198 <li>Fetch either seed alignment or full alignment from
3200 <li>URL Links created for matching database cross
3201 references as well as sequence ID</li>
3202 <li>URL Links can be created using regular-expressions</li>
3203 </ul> <em>Sequence Database Connectivity</em>
3205 <li>Retrieval of cross-referenced sequences from other
3207 <li>Generalised database reference retrieval and
3208 validation to all fetchable databases</li>
3209 <li>Fetch sequences from DAS sources supporting the
3210 sequence command</li>
3211 </ul> <em>Import and Export</em>
3212 <li>export annotation rows as CSV for spreadsheet import</li>
3213 <li>Jalview projects record alignment dataset associations,
3214 EMBL products, and cDNA sequence mappings</li>
3215 <li>Sequence Group colour can be specified in Annotation
3217 <li>Ad-hoc colouring of group in Annotation File using RGB
3218 triplet as name of colourscheme</li>
3219 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3221 <li>treenode binding for VAMSAS tree exchange</li>
3222 <li>local editing and update of sequences in VAMSAS
3223 alignments (experimental)</li>
3224 <li>Create new or select existing session to join</li>
3225 <li>load and save of vamsas documents</li>
3226 </ul> <em>Application command line</em>
3228 <li>-tree parameter to open trees (introduced for passing
3230 <li>-fetchfrom command line argument to specify nicknames
3231 of DAS servers to query for alignment features</li>
3232 <li>-dasserver command line argument to add new servers
3233 that are also automatically queried for features</li>
3234 <li>-groovy command line argument executes a given groovy
3235 script after all input data has been loaded and parsed</li>
3236 </ul> <em>Applet-Application data exchange</em>
3238 <li>Trees passed as applet parameters can be passed to
3239 application (when using "View in full
3240 application")</li>
3241 </ul> <em>Applet Parameters</em>
3243 <li>feature group display control parameter</li>
3244 <li>debug parameter</li>
3245 <li>showbutton parameter</li>
3246 </ul> <em>Applet API methods</em>
3248 <li>newView public method</li>
3249 <li>Window (current view) specific get/set public methods</li>
3250 <li>Feature display control methods</li>
3251 <li>get list of currently selected sequences</li>
3252 </ul> <em>New Jalview distribution features</em>
3254 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3255 <li>RELEASE file gives build properties for the latest
3256 Jalview release.</li>
3257 <li>Java 1.1 Applet build made easier and donotobfuscate
3258 property controls execution of obfuscator</li>
3259 <li>Build target for generating source distribution</li>
3260 <li>Debug flag for javacc</li>
3261 <li>.jalview_properties file is documented (slightly) in
3262 jalview.bin.Cache</li>
3263 <li>Continuous Build Integration for stable and
3264 development version of Application, Applet and source
3269 <li>selected region output includes visible annotations
3270 (for certain formats)</li>
3271 <li>edit label/displaychar contains existing label/char
3273 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3274 <li>shorter peptide product names from EMBL records</li>
3275 <li>Newick string generator makes compact representations</li>
3276 <li>bootstrap values parsed correctly for tree files with
3278 <li>pathological filechooser bug avoided by not allowing
3279 filenames containing a ':'</li>
3280 <li>Fixed exception when parsing GFF files containing
3281 global sequence features</li>
3282 <li>Alignment datasets are finalized only when number of
3283 references from alignment sequences goes to zero</li>
3284 <li>Close of tree branch colour box without colour
3285 selection causes cascading exceptions</li>
3286 <li>occasional negative imgwidth exceptions</li>
3287 <li>better reporting of non-fatal warnings to user when
3288 file parsing fails.</li>
3289 <li>Save works when Jalview project is default format</li>
3290 <li>Save as dialog opened if current alignment format is
3291 not a valid output format</li>
3292 <li>UniProt canonical names introduced for both das and
3294 <li>Histidine should be midblue (not pink!) in Zappo</li>
3295 <li>error messages passed up and output when data read
3297 <li>edit undo recovers previous dataset sequence when
3298 sequence is edited</li>
3299 <li>allow PDB files without pdb ID HEADER lines (like
3300 those generated by MODELLER) to be read in properly</li>
3301 <li>allow reading of JPred concise files as a normal
3303 <li>Stockholm annotation parsing and alignment properties
3304 import fixed for PFAM records</li>
3305 <li>Structure view windows have correct name in Desktop
3307 <li>annotation consisting of sequence associated scores
3308 can be read and written correctly to annotation file</li>
3309 <li>Aligned cDNA translation to aligned peptide works
3311 <li>Fixed display of hidden sequence markers and
3312 non-italic font for representatives in Applet</li>
3313 <li>Applet Menus are always embedded in applet window on
3315 <li>Newly shown features appear at top of stack (in
3317 <li>Annotations added via parameter not drawn properly
3318 due to null pointer exceptions</li>
3319 <li>Secondary structure lines are drawn starting from
3320 first column of alignment</li>
3321 <li>UniProt XML import updated for new schema release in
3323 <li>Sequence feature to sequence ID match for Features
3324 file is case-insensitive</li>
3325 <li>Sequence features read from Features file appended to
3326 all sequences with matching IDs</li>
3327 <li>PDB structure coloured correctly for associated views
3328 containing a sub-sequence</li>
3329 <li>PDB files can be retrieved by applet from Jar files</li>
3330 <li>feature and annotation file applet parameters
3331 referring to different directories are retrieved correctly</li>
3332 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3333 <li>Fixed application hang whilst waiting for
3334 splash-screen version check to complete</li>
3335 <li>Applet properly URLencodes input parameter values
3336 when passing them to the launchApp service</li>
3337 <li>display name and local features preserved in results
3338 retrieved from web service</li>
3339 <li>Visual delay indication for sequence retrieval and
3340 sequence fetcher initialisation</li>
3341 <li>updated Application to use DAS 1.53e version of
3342 dasobert DAS client</li>
3343 <li>Re-instated Full AMSA support and .amsa file
3345 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3353 <div align="center">
3354 <strong>2.3</strong><br> 9/5/07
3359 <li>Jmol 11.0.2 integration</li>
3360 <li>PDB views stored in Jalview XML files</li>
3361 <li>Slide sequences</li>
3362 <li>Edit sequence in place</li>
3363 <li>EMBL CDS features</li>
3364 <li>DAS Feature mapping</li>
3365 <li>Feature ordering</li>
3366 <li>Alignment Properties</li>
3367 <li>Annotation Scores</li>
3368 <li>Sort by scores</li>
3369 <li>Feature/annotation editing in applet</li>
3374 <li>Headless state operation in 2.2.1</li>
3375 <li>Incorrect and unstable DNA pairwise alignment</li>
3376 <li>Cut and paste of sequences with annotation</li>
3377 <li>Feature group display state in XML</li>
3378 <li>Feature ordering in XML</li>
3379 <li>blc file iteration selection using filename # suffix</li>
3380 <li>Stockholm alignment properties</li>
3381 <li>Stockhom alignment secondary structure annotation</li>
3382 <li>2.2.1 applet had no feature transparency</li>
3383 <li>Number pad keys can be used in cursor mode</li>
3384 <li>Structure Viewer mirror image resolved</li>
3391 <div align="center">
3392 <strong>2.2.1</strong><br> 12/2/07
3397 <li>Non standard characters can be read and displayed
3398 <li>Annotations/Features can be imported/exported to the
3400 <li>Applet allows editing of sequence/annotation/group
3401 name & description
3402 <li>Preference setting to display sequence name in
3404 <li>Annotation file format extended to allow
3405 Sequence_groups to be defined
3406 <li>Default opening of alignment overview panel can be
3407 specified in preferences
3408 <li>PDB residue numbering annotation added to associated
3414 <li>Applet crash under certain Linux OS with Java 1.6
3416 <li>Annotation file export / import bugs fixed
3417 <li>PNG / EPS image output bugs fixed
3423 <div align="center">
3424 <strong>2.2</strong><br> 27/11/06
3429 <li>Multiple views on alignment
3430 <li>Sequence feature editing
3431 <li>"Reload" alignment
3432 <li>"Save" to current filename
3433 <li>Background dependent text colour
3434 <li>Right align sequence ids
3435 <li>User-defined lower case residue colours
3438 <li>Menu item accelerator keys
3439 <li>Control-V pastes to current alignment
3440 <li>Cancel button for DAS Feature Fetching
3441 <li>PCA and PDB Viewers zoom via mouse roller
3442 <li>User-defined sub-tree colours and sub-tree selection
3444 <li>'New Window' button on the 'Output to Text box'
3449 <li>New memory efficient Undo/Redo System
3450 <li>Optimised symbol lookups and conservation/consensus
3452 <li>Region Conservation/Consensus recalculated after
3454 <li>Fixed Remove Empty Columns Bug (empty columns at end
3456 <li>Slowed DAS Feature Fetching for increased robustness.
3458 <li>Made angle brackets in ASCII feature descriptions
3460 <li>Re-instated Zoom function for PCA
3461 <li>Sequence descriptions conserved in web service
3463 <li>UniProt ID discoverer uses any word separated by
3465 <li>WsDbFetch query/result association resolved
3466 <li>Tree leaf to sequence mapping improved
3467 <li>Smooth fonts switch moved to FontChooser dialog box.
3474 <div align="center">
3475 <strong>2.1.1</strong><br> 12/9/06
3480 <li>Copy consensus sequence to clipboard</li>
3485 <li>Image output - rightmost residues are rendered if
3486 sequence id panel has been resized</li>
3487 <li>Image output - all offscreen group boundaries are
3489 <li>Annotation files with sequence references - all
3490 elements in file are relative to sequence position</li>
3491 <li>Mac Applet users can use Alt key for group editing</li>
3497 <div align="center">
3498 <strong>2.1</strong><br> 22/8/06
3503 <li>MAFFT Multiple Alignment in default Web Service list</li>
3504 <li>DAS Feature fetching</li>
3505 <li>Hide sequences and columns</li>
3506 <li>Export Annotations and Features</li>
3507 <li>GFF file reading / writing</li>
3508 <li>Associate structures with sequences from local PDB
3510 <li>Add sequences to exisiting alignment</li>
3511 <li>Recently opened files / URL lists</li>
3512 <li>Applet can launch the full application</li>
3513 <li>Applet has transparency for features (Java 1.2
3515 <li>Applet has user defined colours parameter</li>
3516 <li>Applet can load sequences from parameter
3517 "sequence<em>x</em>"
3523 <li>Redundancy Panel reinstalled in the Applet</li>
3524 <li>Monospaced font - EPS / rescaling bug fixed</li>
3525 <li>Annotation files with sequence references bug fixed</li>
3531 <div align="center">
3532 <strong>2.08.1</strong><br> 2/5/06
3537 <li>Change case of selected region from Popup menu</li>
3538 <li>Choose to match case when searching</li>
3539 <li>Middle mouse button and mouse movement can compress /
3540 expand the visible width and height of the alignment</li>
3545 <li>Annotation Panel displays complete JNet results</li>
3551 <div align="center">
3552 <strong>2.08b</strong><br> 18/4/06
3558 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3559 <li>Righthand label on wrapped alignments shows correct
3566 <div align="center">
3567 <strong>2.08</strong><br> 10/4/06
3572 <li>Editing can be locked to the selection area</li>
3573 <li>Keyboard editing</li>
3574 <li>Create sequence features from searches</li>
3575 <li>Precalculated annotations can be loaded onto
3577 <li>Features file allows grouping of features</li>
3578 <li>Annotation Colouring scheme added</li>
3579 <li>Smooth fonts off by default - Faster rendering</li>
3580 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3585 <li>Drag & Drop fixed on Linux</li>
3586 <li>Jalview Archive file faster to load/save, sequence
3587 descriptions saved.</li>
3593 <div align="center">
3594 <strong>2.07</strong><br> 12/12/05
3599 <li>PDB Structure Viewer enhanced</li>
3600 <li>Sequence Feature retrieval and display enhanced</li>
3601 <li>Choose to output sequence start-end after sequence
3602 name for file output</li>
3603 <li>Sequence Fetcher WSDBFetch@EBI</li>
3604 <li>Applet can read feature files, PDB files and can be
3605 used for HTML form input</li>
3610 <li>HTML output writes groups and features</li>
3611 <li>Group editing is Control and mouse click</li>
3612 <li>File IO bugs</li>
3618 <div align="center">
3619 <strong>2.06</strong><br> 28/9/05
3624 <li>View annotations in wrapped mode</li>
3625 <li>More options for PCA viewer</li>
3630 <li>GUI bugs resolved</li>
3631 <li>Runs with -nodisplay from command line</li>
3637 <div align="center">
3638 <strong>2.05b</strong><br> 15/9/05
3643 <li>Choose EPS export as lineart or text</li>
3644 <li>Jar files are executable</li>
3645 <li>Can read in Uracil - maps to unknown residue</li>
3650 <li>Known OutOfMemory errors give warning message</li>
3651 <li>Overview window calculated more efficiently</li>
3652 <li>Several GUI bugs resolved</li>
3658 <div align="center">
3659 <strong>2.05</strong><br> 30/8/05
3664 <li>Edit and annotate in "Wrapped" view</li>
3669 <li>Several GUI bugs resolved</li>
3675 <div align="center">
3676 <strong>2.04</strong><br> 24/8/05
3681 <li>Hold down mouse wheel & scroll to change font
3687 <li>Improved JPred client reliability</li>
3688 <li>Improved loading of Jalview files</li>
3694 <div align="center">
3695 <strong>2.03</strong><br> 18/8/05
3700 <li>Set Proxy server name and port in preferences</li>
3701 <li>Multiple URL links from sequence ids</li>
3702 <li>User Defined Colours can have a scheme name and added
3704 <li>Choose to ignore gaps in consensus calculation</li>
3705 <li>Unix users can set default web browser</li>
3706 <li>Runs without GUI for batch processing</li>
3707 <li>Dynamically generated Web Service Menus</li>
3712 <li>InstallAnywhere download for Sparc Solaris</li>
3718 <div align="center">
3719 <strong>2.02</strong><br> 18/7/05
3725 <li>Copy & Paste order of sequences maintains
3726 alignment order.</li>
3732 <div align="center">
3733 <strong>2.01</strong><br> 12/7/05
3738 <li>Use delete key for deleting selection.</li>
3739 <li>Use Mouse wheel to scroll sequences.</li>
3740 <li>Help file updated to describe how to add alignment
3742 <li>Version and build date written to build properties
3744 <li>InstallAnywhere installation will check for updates
3745 at launch of Jalview.</li>
3750 <li>Delete gaps bug fixed.</li>
3751 <li>FileChooser sorts columns.</li>
3752 <li>Can remove groups one by one.</li>
3753 <li>Filechooser icons installed.</li>
3754 <li>Finder ignores return character when searching.
3755 Return key will initiate a search.<br>
3762 <div align="center">
3763 <strong>2.0</strong><br> 20/6/05
3768 <li>New codebase</li>