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.2.10.4">2.10.4</a><br /> <em>27/02/2018</em></strong>
76 <td><div align="left">
80 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence ID and annotation area margins can be click-dragged to adjust them.</li>
82 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and Ensembl services
87 <td><div align="left">
90 <!-- JAL-2778 -->Slow redraw when Overview panel shown overlapping alignment panel
93 <!-- JAL-2666 -->Linked scrolling via protein horizontal scroll bar doesn't work for some CDS/Protein views
100 <td width="60" nowrap>
102 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
105 <td><div align="left">
106 <ul><li>Updated Certum Codesigning Certificate
107 (Valid till 30th November 2018)</li></ul></div></td>
108 <td><div align="left">
111 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
112 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
113 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
114 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
115 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
116 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
117 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
123 <td width="60" nowrap>
125 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
128 <td><div align="left">
132 <!-- JAL-2446 -->Faster and more efficient management and
133 rendering of sequence features
136 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
137 429 rate limit request hander
140 <!-- JAL-2773 -->Structure views don't get updated unless
141 their colours have changed
144 <!-- JAL-2495 -->All linked sequences are highlighted for
145 a structure mousover (Jmol) or selection (Chimera)
148 <!-- JAL-2790 -->'Cancel' button in progress bar for
149 JABAWS AACon, RNAAliFold and Disorder prediction jobs
152 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
153 view from Ensembl locus cross-references
156 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
160 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
161 feature can be disabled
164 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
165 PDB easier retrieval of sequences for lists of IDs
168 <!-- JAL-2758 -->Short names for sequences retrieved from
174 <li>Groovy interpreter updated to 2.4.12</li>
175 <li>Example groovy script for generating a matrix of
176 percent identity scores for current alignment.</li>
178 <em>Testing and Deployment</em>
181 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
185 <td><div align="left">
189 <!-- JAL-2643 -->Pressing tab after updating the colour
190 threshold text field doesn't trigger an update to the
194 <!-- JAL-2682 -->Race condition when parsing sequence ID
198 <!-- JAL-2608 -->Overview windows are also closed when
199 alignment window is closed
202 <!-- JAL-2548 -->Export of features doesn't always respect
206 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
207 takes a long time in Cursor mode
213 <!-- JAL-2777 -->Structures with whitespace chainCode
214 cannot be viewed in Chimera
217 <!-- JAL-2728 -->Protein annotation panel too high in
221 <!-- JAL-2757 -->Can't edit the query after the server
222 error warning icon is shown in Uniprot and PDB Free Text
226 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
229 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
232 <!-- JAL-2739 -->Hidden column marker in last column not
233 rendered when switching back from Wrapped to normal view
236 <!-- JAL-2768 -->Annotation display corrupted when
237 scrolling right in unwapped alignment view
240 <!-- JAL-2542 -->Existing features on subsequence
241 incorrectly relocated when full sequence retrieved from
245 <!-- JAL-2733 -->Last reported memory still shown when
246 Desktop->Show Memory is unticked (OSX only)
249 <!-- JAL-2658 -->Amend Features dialog doesn't allow
250 features of same type and group to be selected for
254 <!-- JAL-2524 -->Jalview becomes sluggish in wide
255 alignments when hidden columns are present
258 <!-- JAL-2392 -->Jalview freezes when loading and
259 displaying several structures
262 <!-- JAL-2732 -->Black outlines left after resizing or
266 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
267 within the Jalview desktop on OSX
270 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
271 when in wrapped alignment mode
274 <!-- JAL-2636 -->Scale mark not shown when close to right
275 hand end of alignment
278 <!-- JAL-2684 -->Pairwise alignment of selected regions of
279 each selected sequence do not have correct start/end
283 <!-- JAL-2793 -->Alignment ruler height set incorrectly
284 after canceling the Alignment Window's Font dialog
287 <!-- JAL-2036 -->Show cross-references not enabled after
288 restoring project until a new view is created
291 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
292 URL links appears when only default EMBL-EBI link is
293 configured (since 2.10.2b2)
296 <!-- JAL-2775 -->Overview redraws whole window when box
300 <!-- JAL-2225 -->Structure viewer doesn't map all chains
301 in a multi-chain structure when viewing alignment
302 involving more than one chain (since 2.10)
305 <!-- JAL-2811 -->Double residue highlights in cursor mode
306 if new selection moves alignment window
309 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
310 arrow key in cursor mode to pass hidden column marker
313 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
314 that produces correctly annotated transcripts and products
317 <!-- JAL-2776 -->Toggling a feature group after first time
318 doesn't update associated structure view
321 <em>Applet</em><br />
324 <!-- JAL-2687 -->Concurrent modification exception when
325 closing alignment panel
328 <em>BioJSON</em><br />
331 <!-- JAL-2546 -->BioJSON export does not preserve
332 non-positional features
335 <em>New Known Issues</em>
338 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
339 sequence features correctly (for many previous versions of
343 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
344 using cursor in wrapped panel other than top
347 <!-- JAL-2791 -->Select columns containing feature ignores
348 graduated colour threshold
351 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
352 always preserve numbering and sequence features
355 <em>Known Java 9 Issues</em>
358 <!-- JAL-2902 -->Groovy Console very slow to open and is
359 not responsive when entering characters (Webstart, Java
366 <td width="60" nowrap>
368 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
369 <em>2/10/2017</em></strong>
372 <td><div align="left">
373 <em>New features in Jalview Desktop</em>
376 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
378 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
382 <td><div align="left">
386 <td width="60" nowrap>
388 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
389 <em>7/9/2017</em></strong>
392 <td><div align="left">
396 <!-- JAL-2588 -->Show gaps in overview window by colouring
397 in grey (sequences used to be coloured grey, and gaps were
401 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
405 <!-- JAL-2587 -->Overview updates immediately on increase
406 in size and progress bar shown as higher resolution
407 overview is recalculated
412 <td><div align="left">
416 <!-- JAL-2664 -->Overview window redraws every hidden
417 column region row by row
420 <!-- JAL-2681 -->duplicate protein sequences shown after
421 retrieving Ensembl crossrefs for sequences from Uniprot
424 <!-- JAL-2603 -->Overview window throws NPE if show boxes
425 format setting is unticked
428 <!-- JAL-2610 -->Groups are coloured wrongly in overview
429 if group has show boxes format setting unticked
432 <!-- JAL-2672,JAL-2665 -->Redraw problems when
433 autoscrolling whilst dragging current selection group to
434 include sequences and columns not currently displayed
437 <!-- JAL-2691 -->Not all chains are mapped when multimeric
438 assemblies are imported via CIF file
441 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
442 displayed when threshold or conservation colouring is also
446 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
450 <!-- JAL-2673 -->Jalview continues to scroll after
451 dragging a selected region off the visible region of the
455 <!-- JAL-2724 -->Cannot apply annotation based
456 colourscheme to all groups in a view
459 <!-- JAL-2511 -->IDs don't line up with sequences
460 initially after font size change using the Font chooser or
467 <td width="60" nowrap>
469 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
472 <td><div align="left">
473 <em>Calculations</em>
477 <!-- JAL-1933 -->Occupancy annotation row shows number of
478 ungapped positions in each column of the alignment.
481 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
482 a calculation dialog box
485 <!-- JAL-2379 -->Revised implementation of PCA for speed
486 and memory efficiency (~30x faster)
489 <!-- JAL-2403 -->Revised implementation of sequence
490 similarity scores as used by Tree, PCA, Shading Consensus
491 and other calculations
494 <!-- JAL-2416 -->Score matrices are stored as resource
495 files within the Jalview codebase
498 <!-- JAL-2500 -->Trees computed on Sequence Feature
499 Similarity may have different topology due to increased
506 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
507 model for alignments and groups
510 <!-- JAL-384 -->Custom shading schemes created via groovy
517 <!-- JAL-2526 -->Efficiency improvements for interacting
518 with alignment and overview windows
521 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
525 <!-- JAL-2388 -->Hidden columns and sequences can be
529 <!-- JAL-2611 -->Click-drag in visible area allows fine
530 adjustment of visible position
534 <em>Data import/export</em>
537 <!-- JAL-2535 -->Posterior probability annotation from
538 Stockholm files imported as sequence associated annotation
541 <!-- JAL-2507 -->More robust per-sequence positional
542 annotation input/output via stockholm flatfile
545 <!-- JAL-2533 -->Sequence names don't include file
546 extension when importing structure files without embedded
547 names or PDB accessions
550 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
551 format sequence substitution matrices
554 <em>User Interface</em>
557 <!-- JAL-2447 --> Experimental Features Checkbox in
558 Desktop's Tools menu to hide or show untested features in
562 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
563 via Overview or sequence motif search operations
566 <!-- JAL-2547 -->Amend sequence features dialog box can be
567 opened by double clicking gaps within sequence feature
571 <!-- JAL-1476 -->Status bar message shown when not enough
572 aligned positions were available to create a 3D structure
576 <em>3D Structure</em>
579 <!-- JAL-2430 -->Hidden regions in alignment views are not
580 coloured in linked structure views
583 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
584 file-based command exchange
587 <!-- JAL-2375 -->Structure chooser automatically shows
588 Cached Structures rather than querying the PDBe if
589 structures are already available for sequences
592 <!-- JAL-2520 -->Structures imported via URL are cached in
593 the Jalview project rather than downloaded again when the
597 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
598 to transfer Chimera's structure attributes as Jalview
599 features, and vice-versa (<strong>Experimental
603 <em>Web Services</em>
606 <!-- JAL-2549 -->Updated JABAWS client to v2.2
609 <!-- JAL-2335 -->Filter non-standard amino acids and
610 nucleotides when submitting to AACon and other MSA
614 <!-- JAL-2316, -->URLs for viewing database
615 cross-references provided by identifiers.org and the
623 <!-- JAL-2344 -->FileFormatI interface for describing and
624 identifying file formats (instead of String constants)
627 <!-- JAL-2228 -->FeatureCounter script refactored for
628 efficiency when counting all displayed features (not
629 backwards compatible with 2.10.1)
632 <em>Example files</em>
635 <!-- JAL-2631 -->Graduated feature colour style example
636 included in the example feature file
639 <em>Documentation</em>
642 <!-- JAL-2339 -->Release notes reformatted for readability
643 with the built-in Java help viewer
646 <!-- JAL-1644 -->Find documentation updated with 'search
647 sequence description' option
653 <!-- JAL-2485, -->External service integration tests for
654 Uniprot REST Free Text Search Client
657 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
660 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
665 <td><div align="left">
666 <em>Calculations</em>
669 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
670 matrix - C->R should be '-3'<br />Old matrix restored
671 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
673 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
674 Jalview's treatment of gaps in PCA and substitution matrix
675 based Tree calculations.<br /> <br />In earlier versions
676 of Jalview, gaps matching gaps were penalised, and gaps
677 matching non-gaps penalised even more. In the PCA
678 calculation, gaps were actually treated as non-gaps - so
679 different costs were applied, which meant Jalview's PCAs
680 were different to those produced by SeqSpace.<br />Jalview
681 now treats gaps in the same way as SeqSpace (ie it scores
682 them as 0). <br /> <br />Enter the following in the
683 Groovy console to restore pre-2.10.2 behaviour:<br />
684 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
685 // for 2.10.1 mode <br />
686 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
687 // to restore 2.10.2 mode <br /> <br /> <em>Note:
688 these settings will affect all subsequent tree and PCA
689 calculations (not recommended)</em></li>
691 <!-- JAL-2424 -->Fixed off-by-one bug that affected
692 scaling of branch lengths for trees computed using
693 Sequence Feature Similarity.
696 <!-- JAL-2377 -->PCA calculation could hang when
697 generating output report when working with highly
701 <!-- JAL-2544 --> Sort by features includes features to
702 right of selected region when gaps present on right-hand
706 <em>User Interface</em>
709 <!-- JAL-2346 -->Reopening Colour by annotation dialog
710 doesn't reselect a specific sequence's associated
711 annotation after it was used for colouring a view
714 <!-- JAL-2419 -->Current selection lost if popup menu
715 opened on a region of alignment without groups
718 <!-- JAL-2374 -->Popup menu not always shown for regions
719 of an alignment with overlapping groups
722 <!-- JAL-2310 -->Finder double counts if both a sequence's
723 name and description match
726 <!-- JAL-2370 -->Hiding column selection containing two
727 hidden regions results in incorrect hidden regions
730 <!-- JAL-2386 -->'Apply to all groups' setting when
731 changing colour does not apply Conservation slider value
735 <!-- JAL-2373 -->Percentage identity and conservation menu
736 items do not show a tick or allow shading to be disabled
739 <!-- JAL-2385 -->Conservation shading or PID threshold
740 lost when base colourscheme changed if slider not visible
743 <!-- JAL-2547 -->Sequence features shown in tooltip for
744 gaps before start of features
747 <!-- JAL-2623 -->Graduated feature colour threshold not
748 restored to UI when feature colour is edited
751 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
752 a time when scrolling vertically in wrapped mode.
755 <!-- JAL-2630 -->Structure and alignment overview update
756 as graduate feature colour settings are modified via the
760 <!-- JAL-2034 -->Overview window doesn't always update
761 when a group defined on the alignment is resized
764 <!-- JAL-2605 -->Mouseovers on left/right scale region in
765 wrapped view result in positional status updates
769 <!-- JAL-2563 -->Status bar doesn't show position for
770 ambiguous amino acid and nucleotide symbols
773 <!-- JAL-2602 -->Copy consensus sequence failed if
774 alignment included gapped columns
777 <!-- JAL-2473 -->Minimum size set for Jalview windows so
778 widgets don't permanently disappear
781 <!-- JAL-2503 -->Cannot select or filter quantitative
782 annotation that are shown only as column labels (e.g.
783 T-Coffee column reliability scores)
786 <!-- JAL-2594 -->Exception thrown if trying to create a
787 sequence feature on gaps only
790 <!-- JAL-2504 -->Features created with 'New feature'
791 button from a Find inherit previously defined feature type
792 rather than the Find query string
795 <!-- JAL-2423 -->incorrect title in output window when
796 exporting tree calculated in Jalview
799 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
800 and then revealing them reorders sequences on the
804 <!-- JAL-964 -->Group panel in sequence feature settings
805 doesn't update to reflect available set of groups after
806 interactively adding or modifying features
809 <!-- JAL-2225 -->Sequence Database chooser unusable on
813 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
814 only excluded gaps in current sequence and ignored
821 <!-- JAL-2421 -->Overview window visible region moves
822 erratically when hidden rows or columns are present
825 <!-- JAL-2362 -->Per-residue colourschemes applied via the
826 Structure Viewer's colour menu don't correspond to
830 <!-- JAL-2405 -->Protein specific colours only offered in
831 colour and group colour menu for protein alignments
834 <!-- JAL-2385 -->Colour threshold slider doesn't update to
835 reflect currently selected view or group's shading
839 <!-- JAL-2624 -->Feature colour thresholds not respected
840 when rendered on overview and structures when opacity at
844 <!-- JAL-2589 -->User defined gap colour not shown in
845 overview when features overlaid on alignment
848 <em>Data import/export</em>
851 <!-- JAL-2576 -->Very large alignments take a long time to
855 <!-- JAL-2507 -->Per-sequence RNA secondary structures
856 added after a sequence was imported are not written to
860 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
861 when importing RNA secondary structure via Stockholm
864 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
865 not shown in correct direction for simple pseudoknots
868 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
869 with lightGray or darkGray via features file (but can
873 <!-- JAL-2383 -->Above PID colour threshold not recovered
874 when alignment view imported from project
877 <!-- JAL-2520,JAL-2465 -->No mappings generated between
878 structure and sequences extracted from structure files
879 imported via URL and viewed in Jmol
882 <!-- JAL-2520 -->Structures loaded via URL are saved in
883 Jalview Projects rather than fetched via URL again when
884 the project is loaded and the structure viewed
887 <em>Web Services</em>
890 <!-- JAL-2519 -->EnsemblGenomes example failing after
891 release of Ensembl v.88
894 <!-- JAL-2366 -->Proxy server address and port always
895 appear enabled in Preferences->Connections
898 <!-- JAL-2461 -->DAS registry not found exceptions
899 removed from console output
902 <!-- JAL-2582 -->Cannot retrieve protein products from
903 Ensembl by Peptide ID
906 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
907 created from SIFTs, and spurious 'Couldn't open structure
908 in Chimera' errors raised after April 2017 update (problem
909 due to 'null' string rather than empty string used for
910 residues with no corresponding PDB mapping).
913 <em>Application UI</em>
916 <!-- JAL-2361 -->User Defined Colours not added to Colour
920 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
921 case' residues (button in colourscheme editor debugged and
922 new documentation and tooltips added)
925 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
926 doesn't restore group-specific text colour thresholds
929 <!-- JAL-2243 -->Feature settings panel does not update as
930 new features are added to alignment
933 <!-- JAL-2532 -->Cancel in feature settings reverts
934 changes to feature colours via the Amend features dialog
937 <!-- JAL-2506 -->Null pointer exception when attempting to
938 edit graduated feature colour via amend features dialog
942 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
943 selection menu changes colours of alignment views
946 <!-- JAL-2426 -->Spurious exceptions in console raised
947 from alignment calculation workers after alignment has
951 <!-- JAL-1608 -->Typo in selection popup menu - Create
952 groups now 'Create Group'
955 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
956 Create/Undefine group doesn't always work
959 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
960 shown again after pressing 'Cancel'
963 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
964 adjusts start position in wrap mode
967 <!-- JAL-2563 -->Status bar doesn't show positions for
968 ambiguous amino acids
971 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
972 CDS/Protein view after CDS sequences added for aligned
976 <!-- JAL-2592 -->User defined colourschemes called 'User
977 Defined' don't appear in Colours menu
983 <!-- JAL-2468 -->Switching between Nucleotide and Protein
984 score models doesn't always result in an updated PCA plot
987 <!-- JAL-2442 -->Features not rendered as transparent on
988 overview or linked structure view
991 <!-- JAL-2372 -->Colour group by conservation doesn't
995 <!-- JAL-2517 -->Hitting Cancel after applying
996 user-defined colourscheme doesn't restore original
1003 <!-- JAL-2314 -->Unit test failure:
1004 jalview.ws.jabaws.RNAStructExportImport setup fails
1007 <!-- JAL-2307 -->Unit test failure:
1008 jalview.ws.sifts.SiftsClientTest due to compatibility
1009 problems with deep array comparison equality asserts in
1010 successive versions of TestNG
1013 <!-- JAL-2479 -->Relocated StructureChooserTest and
1014 ParameterUtilsTest Unit tests to Network suite
1017 <em>New Known Issues</em>
1020 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1021 phase after a sequence motif find operation
1024 <!-- JAL-2550 -->Importing annotation file with rows
1025 containing just upper and lower case letters are
1026 interpreted as WUSS RNA secondary structure symbols
1029 <!-- JAL-2590 -->Cannot load and display Newick trees
1030 reliably from eggnog Ortholog database
1033 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1034 containing features of type Highlight' when 'B' is pressed
1035 to mark columns containing highlighted regions.
1038 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1039 doesn't always add secondary structure annotation.
1044 <td width="60" nowrap>
1045 <div align="center">
1046 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1049 <td><div align="left">
1053 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1054 for all consensus calculations
1057 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1060 <li>Updated Jalview's Certum code signing certificate
1063 <em>Application</em>
1066 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1067 set of database cross-references, sorted alphabetically
1070 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1071 from database cross references. Users with custom links
1072 will receive a <a href="webServices/urllinks.html#warning">warning
1073 dialog</a> asking them to update their preferences.
1076 <!-- JAL-2287-->Cancel button and escape listener on
1077 dialog warning user about disconnecting Jalview from a
1081 <!-- JAL-2320-->Jalview's Chimera control window closes if
1082 the Chimera it is connected to is shut down
1085 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1086 columns menu item to mark columns containing highlighted
1087 regions (e.g. from structure selections or results of a
1091 <!-- JAL-2284-->Command line option for batch-generation
1092 of HTML pages rendering alignment data with the BioJS
1102 <!-- JAL-2286 -->Columns with more than one modal residue
1103 are not coloured or thresholded according to percent
1104 identity (first observed in Jalview 2.8.2)
1107 <!-- JAL-2301 -->Threonine incorrectly reported as not
1111 <!-- JAL-2318 -->Updates to documentation pages (above PID
1112 threshold, amino acid properties)
1115 <!-- JAL-2292 -->Lower case residues in sequences are not
1116 reported as mapped to residues in a structure file in the
1120 <!--JAL-2324 -->Identical features with non-numeric scores
1121 could be added multiple times to a sequence
1124 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1125 bond features shown as two highlighted residues rather
1126 than a range in linked structure views, and treated
1127 correctly when selecting and computing trees from features
1130 <!-- JAL-2281-->Custom URL links for database
1131 cross-references are matched to database name regardless
1136 <em>Application</em>
1139 <!-- JAL-2282-->Custom URL links for specific database
1140 names without regular expressions also offer links from
1144 <!-- JAL-2315-->Removing a single configured link in the
1145 URL links pane in Connections preferences doesn't actually
1146 update Jalview configuration
1149 <!-- JAL-2272-->CTRL-Click on a selected region to open
1150 the alignment area popup menu doesn't work on El-Capitan
1153 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1154 files with similarly named sequences if dropped onto the
1158 <!-- JAL-2312 -->Additional mappings are shown for PDB
1159 entries where more chains exist in the PDB accession than
1160 are reported in the SIFTS file
1163 <!-- JAL-2317-->Certain structures do not get mapped to
1164 the structure view when displayed with Chimera
1167 <!-- JAL-2317-->No chains shown in the Chimera view
1168 panel's View->Show Chains submenu
1171 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1172 work for wrapped alignment views
1175 <!--JAL-2197 -->Rename UI components for running JPred
1176 predictions from 'JNet' to 'JPred'
1179 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1180 corrupted when annotation panel vertical scroll is not at
1181 first annotation row
1184 <!--JAL-2332 -->Attempting to view structure for Hen
1185 lysozyme results in a PDB Client error dialog box
1188 <!-- JAL-2319 -->Structure View's mapping report switched
1189 ranges for PDB and sequence for SIFTS
1192 SIFTS 'Not_Observed' residues mapped to non-existant
1196 <!-- <em>New Known Issues</em>
1203 <td width="60" nowrap>
1204 <div align="center">
1205 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1206 <em>25/10/2016</em></strong>
1209 <td><em>Application</em>
1211 <li>3D Structure chooser opens with 'Cached structures'
1212 view if structures already loaded</li>
1213 <li>Progress bar reports models as they are loaded to
1214 structure views</li>
1220 <li>Colour by conservation always enabled and no tick
1221 shown in menu when BLOSUM or PID shading applied</li>
1222 <li>FER1_ARATH and FER2_ARATH labels were switched in
1223 example sequences/projects/trees</li>
1225 <em>Application</em>
1227 <li>Jalview projects with views of local PDB structure
1228 files saved on Windows cannot be opened on OSX</li>
1229 <li>Multiple structure views can be opened and superposed
1230 without timeout for structures with multiple models or
1231 multiple sequences in alignment</li>
1232 <li>Cannot import or associated local PDB files without a
1233 PDB ID HEADER line</li>
1234 <li>RMSD is not output in Jmol console when superposition
1236 <li>Drag and drop of URL from Browser fails for Linux and
1237 OSX versions earlier than El Capitan</li>
1238 <li>ENA client ignores invalid content from ENA server</li>
1239 <li>Exceptions are not raised in console when ENA client
1240 attempts to fetch non-existent IDs via Fetch DB Refs UI
1242 <li>Exceptions are not raised in console when a new view
1243 is created on the alignment</li>
1244 <li>OSX right-click fixed for group selections: CMD-click
1245 to insert/remove gaps in groups and CTRL-click to open group
1248 <em>Build and deployment</em>
1250 <li>URL link checker now copes with multi-line anchor
1253 <em>New Known Issues</em>
1255 <li>Drag and drop from URL links in browsers do not work
1262 <td width="60" nowrap>
1263 <div align="center">
1264 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1267 <td><em>General</em>
1270 <!-- JAL-2124 -->Updated Spanish translations.
1273 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1274 for importing structure data to Jalview. Enables mmCIF and
1278 <!-- JAL-192 --->Alignment ruler shows positions relative to
1282 <!-- JAL-2202 -->Position/residue shown in status bar when
1283 mousing over sequence associated annotation
1286 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1290 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1291 '()', canonical '[]' and invalid '{}' base pair populations
1295 <!-- JAL-2092 -->Feature settings popup menu options for
1296 showing or hiding columns containing a feature
1299 <!-- JAL-1557 -->Edit selected group by double clicking on
1300 group and sequence associated annotation labels
1303 <!-- JAL-2236 -->Sequence name added to annotation label in
1304 select/hide columns by annotation and colour by annotation
1308 </ul> <em>Application</em>
1311 <!-- JAL-2050-->Automatically hide introns when opening a
1312 gene/transcript view
1315 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1319 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1320 structure mappings with the EMBL-EBI PDBe SIFTS database
1323 <!-- JAL-2079 -->Updated download sites used for Rfam and
1324 Pfam sources to xfam.org
1327 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1330 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1331 over sequences in Jalview
1334 <!-- JAL-2027-->Support for reverse-complement coding
1335 regions in ENA and EMBL
1338 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1339 for record retrieval via ENA rest API
1342 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1346 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1347 groovy script execution
1350 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1351 alignment window's Calculate menu
1354 <!-- JAL-1812 -->Allow groovy scripts that call
1355 Jalview.getAlignFrames() to run in headless mode
1358 <!-- JAL-2068 -->Support for creating new alignment
1359 calculation workers from groovy scripts
1362 <!-- JAL-1369 --->Store/restore reference sequence in
1366 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1367 associations are now saved/restored from project
1370 <!-- JAL-1993 -->Database selection dialog always shown
1371 before sequence fetcher is opened
1374 <!-- JAL-2183 -->Double click on an entry in Jalview's
1375 database chooser opens a sequence fetcher
1378 <!-- JAL-1563 -->Free-text search client for UniProt using
1379 the UniProt REST API
1382 <!-- JAL-2168 -->-nonews command line parameter to prevent
1383 the news reader opening
1386 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1387 querying stored in preferences
1390 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1394 <!-- JAL-1977-->Tooltips shown on database chooser
1397 <!-- JAL-391 -->Reverse complement function in calculate
1398 menu for nucleotide sequences
1401 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1402 and feature counts preserves alignment ordering (and
1403 debugged for complex feature sets).
1406 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1407 viewing structures with Jalview 2.10
1410 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1411 genome, transcript CCDS and gene ids via the Ensembl and
1412 Ensembl Genomes REST API
1415 <!-- JAL-2049 -->Protein sequence variant annotation
1416 computed for 'sequence_variant' annotation on CDS regions
1420 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1424 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1425 Ref Fetcher fails to match, or otherwise updates sequence
1426 data from external database records.
1429 <!-- JAL-2154 -->Revised Jalview Project format for
1430 efficient recovery of sequence coding and alignment
1431 annotation relationships.
1433 </ul> <!-- <em>Applet</em>
1444 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1448 <!-- JAL-2018-->Export features in Jalview format (again)
1449 includes graduated colourschemes
1452 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1453 working with big alignments and lots of hidden columns
1456 <!-- JAL-2053-->Hidden column markers not always rendered
1457 at right of alignment window
1460 <!-- JAL-2067 -->Tidied up links in help file table of
1464 <!-- JAL-2072 -->Feature based tree calculation not shown
1468 <!-- JAL-2075 -->Hidden columns ignored during feature
1469 based tree calculation
1472 <!-- JAL-2065 -->Alignment view stops updating when show
1473 unconserved enabled for group on alignment
1476 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1480 <!-- JAL-2146 -->Alignment column in status incorrectly
1481 shown as "Sequence position" when mousing over
1485 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1486 hidden columns present
1489 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1490 user created annotation added to alignment
1493 <!-- JAL-1841 -->RNA Structure consensus only computed for
1494 '()' base pair annotation
1497 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1498 in zero scores for all base pairs in RNA Structure
1502 <!-- JAL-2174-->Extend selection with columns containing
1506 <!-- JAL-2275 -->Pfam format writer puts extra space at
1507 beginning of sequence
1510 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1514 <!-- JAL-2238 -->Cannot create groups on an alignment from
1515 from a tree when t-coffee scores are shown
1518 <!-- JAL-1836,1967 -->Cannot import and view PDB
1519 structures with chains containing negative resnums (4q4h)
1522 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1526 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1527 to Clustal, PIR and PileUp output
1530 <!-- JAL-2008 -->Reordering sequence features that are
1531 not visible causes alignment window to repaint
1534 <!-- JAL-2006 -->Threshold sliders don't work in
1535 graduated colour and colour by annotation row for e-value
1536 scores associated with features and annotation rows
1539 <!-- JAL-1797 -->amino acid physicochemical conservation
1540 calculation should be case independent
1543 <!-- JAL-2173 -->Remove annotation also updates hidden
1547 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1548 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1549 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1552 <!-- JAL-2065 -->Null pointer exceptions and redraw
1553 problems when reference sequence defined and 'show
1554 non-conserved' enabled
1557 <!-- JAL-1306 -->Quality and Conservation are now shown on
1558 load even when Consensus calculation is disabled
1561 <!-- JAL-1932 -->Remove right on penultimate column of
1562 alignment does nothing
1565 <em>Application</em>
1568 <!-- JAL-1552-->URLs and links can't be imported by
1569 drag'n'drop on OSX when launched via webstart (note - not
1570 yet fixed for El Capitan)
1573 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1574 output when running on non-gb/us i18n platforms
1577 <!-- JAL-1944 -->Error thrown when exporting a view with
1578 hidden sequences as flat-file alignment
1581 <!-- JAL-2030-->InstallAnywhere distribution fails when
1585 <!-- JAL-2080-->Jalview very slow to launch via webstart
1586 (also hotfix for 2.9.0b2)
1589 <!-- JAL-2085 -->Cannot save project when view has a
1590 reference sequence defined
1593 <!-- JAL-1011 -->Columns are suddenly selected in other
1594 alignments and views when revealing hidden columns
1597 <!-- JAL-1989 -->Hide columns not mirrored in complement
1598 view in a cDNA/Protein splitframe
1601 <!-- JAL-1369 -->Cannot save/restore representative
1602 sequence from project when only one sequence is
1606 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1607 in Structure Chooser
1610 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1611 structure consensus didn't refresh annotation panel
1614 <!-- JAL-1962 -->View mapping in structure view shows
1615 mappings between sequence and all chains in a PDB file
1618 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1619 dialogs format columns correctly, don't display array
1620 data, sort columns according to type
1623 <!-- JAL-1975 -->Export complete shown after destination
1624 file chooser is cancelled during an image export
1627 <!-- JAL-2025 -->Error when querying PDB Service with
1628 sequence name containing special characters
1631 <!-- JAL-2024 -->Manual PDB structure querying should be
1635 <!-- JAL-2104 -->Large tooltips with broken HTML
1636 formatting don't wrap
1639 <!-- JAL-1128 -->Figures exported from wrapped view are
1640 truncated so L looks like I in consensus annotation
1643 <!-- JAL-2003 -->Export features should only export the
1644 currently displayed features for the current selection or
1648 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1649 after fetching cross-references, and restoring from
1653 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1654 followed in the structure viewer
1657 <!-- JAL-2163 -->Titles for individual alignments in
1658 splitframe not restored from project
1661 <!-- JAL-2145 -->missing autocalculated annotation at
1662 trailing end of protein alignment in transcript/product
1663 splitview when pad-gaps not enabled by default
1666 <!-- JAL-1797 -->amino acid physicochemical conservation
1670 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1671 article has been read (reopened issue due to
1672 internationalisation problems)
1675 <!-- JAL-1960 -->Only offer PDB structures in structure
1676 viewer based on sequence name, PDB and UniProt
1681 <!-- JAL-1976 -->No progress bar shown during export of
1685 <!-- JAL-2213 -->Structures not always superimposed after
1686 multiple structures are shown for one or more sequences.
1689 <!-- JAL-1370 -->Reference sequence characters should not
1690 be replaced with '.' when 'Show unconserved' format option
1694 <!-- JAL-1823 -->Cannot specify chain code when entering
1695 specific PDB id for sequence
1698 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1699 'Export hidden sequences' is enabled, but 'export hidden
1700 columns' is disabled.
1703 <!--JAL-2026-->Best Quality option in structure chooser
1704 selects lowest rather than highest resolution structures
1708 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1709 to sequence mapping in 'View Mappings' report
1712 <!-- JAL-2284 -->Unable to read old Jalview projects that
1713 contain non-XML data added after Jalvew wrote project.
1716 <!-- JAL-2118 -->Newly created annotation row reorders
1717 after clicking on it to create new annotation for a
1721 <!-- JAL-1980 -->Null Pointer Exception raised when
1722 pressing Add on an orphaned cut'n'paste window.
1724 <!-- may exclude, this is an external service stability issue JAL-1941
1725 -- > RNA 3D structure not added via DSSR service</li> -->
1730 <!-- JAL-2151 -->Incorrect columns are selected when
1731 hidden columns present before start of sequence
1734 <!-- JAL-1986 -->Missing dependencies on applet pages
1738 <!-- JAL-1947 -->Overview pixel size changes when
1739 sequences are hidden in applet
1742 <!-- JAL-1996 -->Updated instructions for applet
1743 deployment on examples pages.
1750 <td width="60" nowrap>
1751 <div align="center">
1752 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1753 <em>16/10/2015</em></strong>
1756 <td><em>General</em>
1758 <li>Time stamps for signed Jalview application and applet
1763 <em>Application</em>
1765 <li>Duplicate group consensus and conservation rows
1766 shown when tree is partitioned</li>
1767 <li>Erratic behaviour when tree partitions made with
1768 multiple cDNA/Protein split views</li>
1774 <td width="60" nowrap>
1775 <div align="center">
1776 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1777 <em>8/10/2015</em></strong>
1780 <td><em>General</em>
1782 <li>Updated Spanish translations of localized text for
1784 </ul> <em>Application</em>
1786 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1787 <li>Signed OSX InstallAnywhere installer<br></li>
1788 <li>Support for per-sequence based annotations in BioJSON</li>
1789 </ul> <em>Applet</em>
1791 <li>Split frame example added to applet examples page</li>
1792 </ul> <em>Build and Deployment</em>
1795 <!-- JAL-1888 -->New ant target for running Jalview's test
1803 <li>Mapping of cDNA to protein in split frames
1804 incorrect when sequence start > 1</li>
1805 <li>Broken images in filter column by annotation dialog
1807 <li>Feature colours not parsed from features file</li>
1808 <li>Exceptions and incomplete link URLs recovered when
1809 loading a features file containing HTML tags in feature
1813 <em>Application</em>
1815 <li>Annotations corrupted after BioJS export and
1817 <li>Incorrect sequence limits after Fetch DB References
1818 with 'trim retrieved sequences'</li>
1819 <li>Incorrect warning about deleting all data when
1820 deleting selected columns</li>
1821 <li>Patch to build system for shipping properly signed
1822 JNLP templates for webstart launch</li>
1823 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1824 unreleased structures for download or viewing</li>
1825 <li>Tab/space/return keystroke operation of EMBL-PDBe
1826 fetcher/viewer dialogs works correctly</li>
1827 <li>Disabled 'minimise' button on Jalview windows
1828 running on OSX to workaround redraw hang bug</li>
1829 <li>Split cDNA/Protein view position and geometry not
1830 recovered from jalview project</li>
1831 <li>Initial enabled/disabled state of annotation menu
1832 sorter 'show autocalculated first/last' corresponds to
1834 <li>Restoring of Clustal, RNA Helices and T-Coffee
1835 color schemes from BioJSON</li>
1839 <li>Reorder sequences mirrored in cDNA/Protein split
1841 <li>Applet with Jmol examples not loading correctly</li>
1847 <td><div align="center">
1848 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1850 <td><em>General</em>
1852 <li>Linked visualisation and analysis of DNA and Protein
1855 <li>Translated cDNA alignments shown as split protein
1856 and DNA alignment views</li>
1857 <li>Codon consensus annotation for linked protein and
1858 cDNA alignment views</li>
1859 <li>Link cDNA or Protein product sequences by loading
1860 them onto Protein or cDNA alignments</li>
1861 <li>Reconstruct linked cDNA alignment from aligned
1862 protein sequences</li>
1865 <li>Jmol integration updated to Jmol v14.2.14</li>
1866 <li>Import and export of Jalview alignment views as <a
1867 href="features/bioJsonFormat.html">BioJSON</a></li>
1868 <li>New alignment annotation file statements for
1869 reference sequences and marking hidden columns</li>
1870 <li>Reference sequence based alignment shading to
1871 highlight variation</li>
1872 <li>Select or hide columns according to alignment
1874 <li>Find option for locating sequences by description</li>
1875 <li>Conserved physicochemical properties shown in amino
1876 acid conservation row</li>
1877 <li>Alignments can be sorted by number of RNA helices</li>
1878 </ul> <em>Application</em>
1880 <li>New cDNA/Protein analysis capabilities
1882 <li>Get Cross-References should open a Split Frame
1883 view with cDNA/Protein</li>
1884 <li>Detect when nucleotide sequences and protein
1885 sequences are placed in the same alignment</li>
1886 <li>Split cDNA/Protein views are saved in Jalview
1891 <li>Use REST API to talk to Chimera</li>
1892 <li>Selected regions in Chimera are highlighted in linked
1893 Jalview windows</li>
1895 <li>VARNA RNA viewer updated to v3.93</li>
1896 <li>VARNA views are saved in Jalview Projects</li>
1897 <li>Pseudoknots displayed as Jalview RNA annotation can
1898 be shown in VARNA</li>
1900 <li>Make groups for selection uses marked columns as well
1901 as the active selected region</li>
1903 <li>Calculate UPGMA and NJ trees using sequence feature
1905 <li>New Export options
1907 <li>New Export Settings dialog to control hidden
1908 region export in flat file generation</li>
1910 <li>Export alignment views for display with the <a
1911 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1913 <li>Export scrollable SVG in HTML page</li>
1914 <li>Optional embedding of BioJSON data when exporting
1915 alignment figures to HTML</li>
1917 <li>3D structure retrieval and display
1919 <li>Free text and structured queries with the PDBe
1921 <li>PDBe Search API based discovery and selection of
1922 PDB structures for a sequence set</li>
1926 <li>JPred4 employed for protein secondary structure
1928 <li>Hide Insertions menu option to hide unaligned columns
1929 for one or a group of sequences</li>
1930 <li>Automatically hide insertions in alignments imported
1931 from the JPred4 web server</li>
1932 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1933 system on OSX<br />LGPL libraries courtesy of <a
1934 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1936 <li>changed 'View nucleotide structure' submenu to 'View
1937 VARNA 2D Structure'</li>
1938 <li>change "View protein structure" menu option to "3D
1941 </ul> <em>Applet</em>
1943 <li>New layout for applet example pages</li>
1944 <li>New parameters to enable SplitFrame view
1945 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1946 <li>New example demonstrating linked viewing of cDNA and
1947 Protein alignments</li>
1948 </ul> <em>Development and deployment</em>
1950 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1951 <li>Include installation type and git revision in build
1952 properties and console log output</li>
1953 <li>Jalview Github organisation, and new github site for
1954 storing BioJsMSA Templates</li>
1955 <li>Jalview's unit tests now managed with TestNG</li>
1958 <!-- <em>General</em>
1960 </ul> --> <!-- issues resolved --> <em>Application</em>
1962 <li>Escape should close any open find dialogs</li>
1963 <li>Typo in select-by-features status report</li>
1964 <li>Consensus RNA secondary secondary structure
1965 predictions are not highlighted in amber</li>
1966 <li>Missing gap character in v2.7 example file means
1967 alignment appears unaligned when pad-gaps is not enabled</li>
1968 <li>First switch to RNA Helices colouring doesn't colour
1969 associated structure views</li>
1970 <li>ID width preference option is greyed out when auto
1971 width checkbox not enabled</li>
1972 <li>Stopped a warning dialog from being shown when
1973 creating user defined colours</li>
1974 <li>'View Mapping' in structure viewer shows sequence
1975 mappings for just that viewer's sequences</li>
1976 <li>Workaround for superposing PDB files containing
1977 multiple models in Chimera</li>
1978 <li>Report sequence position in status bar when hovering
1979 over Jmol structure</li>
1980 <li>Cannot output gaps as '.' symbols with Selection ->
1981 output to text box</li>
1982 <li>Flat file exports of alignments with hidden columns
1983 have incorrect sequence start/end</li>
1984 <li>'Aligning' a second chain to a Chimera structure from
1986 <li>Colour schemes applied to structure viewers don't
1987 work for nucleotide</li>
1988 <li>Loading/cut'n'pasting an empty or invalid file leads
1989 to a grey/invisible alignment window</li>
1990 <li>Exported Jpred annotation from a sequence region
1991 imports to different position</li>
1992 <li>Space at beginning of sequence feature tooltips shown
1993 on some platforms</li>
1994 <li>Chimera viewer 'View | Show Chain' menu is not
1996 <li>'New View' fails with a Null Pointer Exception in
1997 console if Chimera has been opened</li>
1998 <li>Mouseover to Chimera not working</li>
1999 <li>Miscellaneous ENA XML feature qualifiers not
2001 <li>NPE in annotation renderer after 'Extract Scores'</li>
2002 <li>If two structures in one Chimera window, mouseover of
2003 either sequence shows on first structure</li>
2004 <li>'Show annotations' options should not make
2005 non-positional annotations visible</li>
2006 <li>Subsequence secondary structure annotation not shown
2007 in right place after 'view flanking regions'</li>
2008 <li>File Save As type unset when current file format is
2010 <li>Save as '.jar' option removed for saving Jalview
2012 <li>Colour by Sequence colouring in Chimera more
2014 <li>Cannot 'add reference annotation' for a sequence in
2015 several views on same alignment</li>
2016 <li>Cannot show linked products for EMBL / ENA records</li>
2017 <li>Jalview's tooltip wraps long texts containing no
2019 </ul> <em>Applet</em>
2021 <li>Jmol to JalviewLite mouseover/link not working</li>
2022 <li>JalviewLite can't import sequences with ID
2023 descriptions containing angle brackets</li>
2024 </ul> <em>General</em>
2026 <li>Cannot export and reimport RNA secondary structure
2027 via jalview annotation file</li>
2028 <li>Random helix colour palette for colour by annotation
2029 with RNA secondary structure</li>
2030 <li>Mouseover to cDNA from STOP residue in protein
2031 translation doesn't work.</li>
2032 <li>hints when using the select by annotation dialog box</li>
2033 <li>Jmol alignment incorrect if PDB file has alternate CA
2035 <li>FontChooser message dialog appears to hang after
2036 choosing 1pt font</li>
2037 <li>Peptide secondary structure incorrectly imported from
2038 annotation file when annotation display text includes 'e' or
2040 <li>Cannot set colour of new feature type whilst creating
2042 <li>cDNA translation alignment should not be sequence
2043 order dependent</li>
2044 <li>'Show unconserved' doesn't work for lower case
2046 <li>Nucleotide ambiguity codes involving R not recognised</li>
2047 </ul> <em>Deployment and Documentation</em>
2049 <li>Applet example pages appear different to the rest of
2050 www.jalview.org</li>
2051 </ul> <em>Application Known issues</em>
2053 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2054 <li>Misleading message appears after trying to delete
2056 <li>Jalview icon not shown in dock after InstallAnywhere
2057 version launches</li>
2058 <li>Fetching EMBL reference for an RNA sequence results
2059 fails with a sequence mismatch</li>
2060 <li>Corrupted or unreadable alignment display when
2061 scrolling alignment to right</li>
2062 <li>ArrayIndexOutOfBoundsException thrown when remove
2063 empty columns called on alignment with ragged gapped ends</li>
2064 <li>auto calculated alignment annotation rows do not get
2065 placed above or below non-autocalculated rows</li>
2066 <li>Jalview dekstop becomes sluggish at full screen in
2067 ultra-high resolution</li>
2068 <li>Cannot disable consensus calculation independently of
2069 quality and conservation</li>
2070 <li>Mouseover highlighting between cDNA and protein can
2071 become sluggish with more than one splitframe shown</li>
2072 </ul> <em>Applet Known Issues</em>
2074 <li>Core PDB parsing code requires Jmol</li>
2075 <li>Sequence canvas panel goes white when alignment
2076 window is being resized</li>
2082 <td><div align="center">
2083 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2085 <td><em>General</em>
2087 <li>Updated Java code signing certificate donated by
2089 <li>Features and annotation preserved when performing
2090 pairwise alignment</li>
2091 <li>RNA pseudoknot annotation can be
2092 imported/exported/displayed</li>
2093 <li>'colour by annotation' can colour by RNA and
2094 protein secondary structure</li>
2095 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2096 post-hoc with 2.9 release</em>)
2099 </ul> <em>Application</em>
2101 <li>Extract and display secondary structure for sequences
2102 with 3D structures</li>
2103 <li>Support for parsing RNAML</li>
2104 <li>Annotations menu for layout
2106 <li>sort sequence annotation rows by alignment</li>
2107 <li>place sequence annotation above/below alignment
2110 <li>Output in Stockholm format</li>
2111 <li>Internationalisation: improved Spanish (es)
2113 <li>Structure viewer preferences tab</li>
2114 <li>Disorder and Secondary Structure annotation tracks
2115 shared between alignments</li>
2116 <li>UCSF Chimera launch and linked highlighting from
2118 <li>Show/hide all sequence associated annotation rows for
2119 all or current selection</li>
2120 <li>disorder and secondary structure predictions
2121 available as dataset annotation</li>
2122 <li>Per-sequence rna helices colouring</li>
2125 <li>Sequence database accessions imported when fetching
2126 alignments from Rfam</li>
2127 <li>update VARNA version to 3.91</li>
2129 <li>New groovy scripts for exporting aligned positions,
2130 conservation values, and calculating sum of pairs scores.</li>
2131 <li>Command line argument to set default JABAWS server</li>
2132 <li>include installation type in build properties and
2133 console log output</li>
2134 <li>Updated Jalview project format to preserve dataset
2138 <!-- issues resolved --> <em>Application</em>
2140 <li>Distinguish alignment and sequence associated RNA
2141 structure in structure->view->VARNA</li>
2142 <li>Raise dialog box if user deletes all sequences in an
2144 <li>Pressing F1 results in documentation opening twice</li>
2145 <li>Sequence feature tooltip is wrapped</li>
2146 <li>Double click on sequence associated annotation
2147 selects only first column</li>
2148 <li>Redundancy removal doesn't result in unlinked
2149 leaves shown in tree</li>
2150 <li>Undos after several redundancy removals don't undo
2152 <li>Hide sequence doesn't hide associated annotation</li>
2153 <li>User defined colours dialog box too big to fit on
2154 screen and buttons not visible</li>
2155 <li>author list isn't updated if already written to
2156 Jalview properties</li>
2157 <li>Popup menu won't open after retrieving sequence
2159 <li>File open window for associate PDB doesn't open</li>
2160 <li>Left-then-right click on a sequence id opens a
2161 browser search window</li>
2162 <li>Cannot open sequence feature shading/sort popup menu
2163 in feature settings dialog</li>
2164 <li>better tooltip placement for some areas of Jalview
2166 <li>Allow addition of JABAWS Server which doesn't
2167 pass validation</li>
2168 <li>Web services parameters dialog box is too large to
2170 <li>Muscle nucleotide alignment preset obscured by
2172 <li>JABAWS preset submenus don't contain newly
2173 defined user preset</li>
2174 <li>MSA web services warns user if they were launched
2175 with invalid input</li>
2176 <li>Jalview cannot contact DAS Registy when running on
2179 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2180 'Superpose with' submenu not shown when new view
2184 </ul> <!-- <em>Applet</em>
2186 </ul> <em>General</em>
2188 </ul>--> <em>Deployment and Documentation</em>
2190 <li>2G and 1G options in launchApp have no effect on
2191 memory allocation</li>
2192 <li>launchApp service doesn't automatically open
2193 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2195 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2196 InstallAnywhere reports cannot find valid JVM when Java
2197 1.7_055 is available
2199 </ul> <em>Application Known issues</em>
2202 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2203 corrupted or unreadable alignment display when scrolling
2207 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2208 retrieval fails but progress bar continues for DAS retrieval
2209 with large number of ID
2212 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2213 flatfile output of visible region has incorrect sequence
2217 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2218 rna structure consensus doesn't update when secondary
2219 structure tracks are rearranged
2222 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2223 invalid rna structure positional highlighting does not
2224 highlight position of invalid base pairs
2227 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2228 out of memory errors are not raised when saving Jalview
2229 project from alignment window file menu
2232 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2233 Switching to RNA Helices colouring doesn't propagate to
2237 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2238 colour by RNA Helices not enabled when user created
2239 annotation added to alignment
2242 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2243 Jalview icon not shown on dock in Mountain Lion/Webstart
2245 </ul> <em>Applet Known Issues</em>
2248 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2249 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2252 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2253 Jalview and Jmol example not compatible with IE9
2256 <li>Sort by annotation score doesn't reverse order
2262 <td><div align="center">
2263 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2266 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2269 <li>Internationalisation of user interface (usually
2270 called i18n support) and translation for Spanish locale</li>
2271 <li>Define/Undefine group on current selection with
2272 Ctrl-G/Shift Ctrl-G</li>
2273 <li>Improved group creation/removal options in
2274 alignment/sequence Popup menu</li>
2275 <li>Sensible precision for symbol distribution
2276 percentages shown in logo tooltip.</li>
2277 <li>Annotation panel height set according to amount of
2278 annotation when alignment first opened</li>
2279 </ul> <em>Application</em>
2281 <li>Interactive consensus RNA secondary structure
2282 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2283 <li>Select columns containing particular features from
2284 Feature Settings dialog</li>
2285 <li>View all 'representative' PDB structures for selected
2287 <li>Update Jalview project format:
2289 <li>New file extension for Jalview projects '.jvp'</li>
2290 <li>Preserve sequence and annotation dataset (to
2291 store secondary structure annotation,etc)</li>
2292 <li>Per group and alignment annotation and RNA helix
2296 <li>New similarity measures for PCA and Tree calculation
2298 <li>Experimental support for retrieval and viewing of
2299 flanking regions for an alignment</li>
2303 <!-- issues resolved --> <em>Application</em>
2305 <li>logo keeps spinning and status remains at queued or
2306 running after job is cancelled</li>
2307 <li>cannot export features from alignments imported from
2308 Jalview/VAMSAS projects</li>
2309 <li>Buggy slider for web service parameters that take
2311 <li>Newly created RNA secondary structure line doesn't
2312 have 'display all symbols' flag set</li>
2313 <li>T-COFFEE alignment score shading scheme and other
2314 annotation shading not saved in Jalview project</li>
2315 <li>Local file cannot be loaded in freshly downloaded
2317 <li>Jalview icon not shown on dock in Mountain
2319 <li>Load file from desktop file browser fails</li>
2320 <li>Occasional NPE thrown when calculating large trees</li>
2321 <li>Cannot reorder or slide sequences after dragging an
2322 alignment onto desktop</li>
2323 <li>Colour by annotation dialog throws NPE after using
2324 'extract scores' function</li>
2325 <li>Loading/cut'n'pasting an empty file leads to a grey
2326 alignment window</li>
2327 <li>Disorder thresholds rendered incorrectly after
2328 performing IUPred disorder prediction</li>
2329 <li>Multiple group annotated consensus rows shown when
2330 changing 'normalise logo' display setting</li>
2331 <li>Find shows blank dialog after 'finished searching' if
2332 nothing matches query</li>
2333 <li>Null Pointer Exceptions raised when sorting by
2334 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2336 <li>Errors in Jmol console when structures in alignment
2337 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2339 <li>Not all working JABAWS services are shown in
2341 <li>JAVAWS version of Jalview fails to launch with
2342 'invalid literal/length code'</li>
2343 <li>Annotation/RNA Helix colourschemes cannot be applied
2344 to alignment with groups (actually fixed in 2.8.0b1)</li>
2345 <li>RNA Helices and T-Coffee Scores available as default
2348 </ul> <em>Applet</em>
2350 <li>Remove group option is shown even when selection is
2352 <li>Apply to all groups ticked but colourscheme changes
2353 don't affect groups</li>
2354 <li>Documented RNA Helices and T-Coffee Scores as valid
2355 colourscheme name</li>
2356 <li>Annotation labels drawn on sequence IDs when
2357 Annotation panel is not displayed</li>
2358 <li>Increased font size for dropdown menus on OSX and
2359 embedded windows</li>
2360 </ul> <em>Other</em>
2362 <li>Consensus sequence for alignments/groups with a
2363 single sequence were not calculated</li>
2364 <li>annotation files that contain only groups imported as
2365 annotation and junk sequences</li>
2366 <li>Fasta files with sequences containing '*' incorrectly
2367 recognised as PFAM or BLC</li>
2368 <li>conservation/PID slider apply all groups option
2369 doesn't affect background (2.8.0b1)
2371 <li>redundancy highlighting is erratic at 0% and 100%</li>
2372 <li>Remove gapped columns fails for sequences with ragged
2374 <li>AMSA annotation row with leading spaces is not
2375 registered correctly on import</li>
2376 <li>Jalview crashes when selecting PCA analysis for
2377 certain alignments</li>
2378 <li>Opening the colour by annotation dialog for an
2379 existing annotation based 'use original colours'
2380 colourscheme loses original colours setting</li>
2385 <td><div align="center">
2386 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2387 <em>30/1/2014</em></strong>
2391 <li>Trusted certificates for JalviewLite applet and
2392 Jalview Desktop application<br />Certificate was donated by
2393 <a href="https://www.certum.eu">Certum</a> to the Jalview
2394 open source project).
2396 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2397 <li>Output in Stockholm format</li>
2398 <li>Allow import of data from gzipped files</li>
2399 <li>Export/import group and sequence associated line
2400 graph thresholds</li>
2401 <li>Nucleotide substitution matrix that supports RNA and
2402 ambiguity codes</li>
2403 <li>Allow disorder predictions to be made on the current
2404 selection (or visible selection) in the same way that JPred
2406 <li>Groovy scripting for headless Jalview operation</li>
2407 </ul> <em>Other improvements</em>
2409 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2410 <li>COMBINE statement uses current SEQUENCE_REF and
2411 GROUP_REF scope to group annotation rows</li>
2412 <li>Support '' style escaping of quotes in Newick
2414 <li>Group options for JABAWS service by command line name</li>
2415 <li>Empty tooltip shown for JABA service options with a
2416 link but no description</li>
2417 <li>Select primary source when selecting authority in
2418 database fetcher GUI</li>
2419 <li>Add .mfa to FASTA file extensions recognised by
2421 <li>Annotation label tooltip text wrap</li>
2426 <li>Slow scrolling when lots of annotation rows are
2428 <li>Lots of NPE (and slowness) after creating RNA
2429 secondary structure annotation line</li>
2430 <li>Sequence database accessions not imported when
2431 fetching alignments from Rfam</li>
2432 <li>Incorrect SHMR submission for sequences with
2434 <li>View all structures does not always superpose
2436 <li>Option widgets in service parameters not updated to
2437 reflect user or preset settings</li>
2438 <li>Null pointer exceptions for some services without
2439 presets or adjustable parameters</li>
2440 <li>Discover PDB IDs entry in structure menu doesn't
2441 discover PDB xRefs</li>
2442 <li>Exception encountered while trying to retrieve
2443 features with DAS</li>
2444 <li>Lowest value in annotation row isn't coloured
2445 when colour by annotation (per sequence) is coloured</li>
2446 <li>Keyboard mode P jumps to start of gapped region when
2447 residue follows a gap</li>
2448 <li>Jalview appears to hang importing an alignment with
2449 Wrap as default or after enabling Wrap</li>
2450 <li>'Right click to add annotations' message
2451 shown in wrap mode when no annotations present</li>
2452 <li>Disorder predictions fail with NPE if no automatic
2453 annotation already exists on alignment</li>
2454 <li>oninit javascript function should be called after
2455 initialisation completes</li>
2456 <li>Remove redundancy after disorder prediction corrupts
2457 alignment window display</li>
2458 <li>Example annotation file in documentation is invalid</li>
2459 <li>Grouped line graph annotation rows are not exported
2460 to annotation file</li>
2461 <li>Multi-harmony analysis cannot be run when only two
2463 <li>Cannot create multiple groups of line graphs with
2464 several 'combine' statements in annotation file</li>
2465 <li>Pressing return several times causes Number Format
2466 exceptions in keyboard mode</li>
2467 <li>Multi-harmony (SHMMR) method doesn't submit
2468 correct partitions for input data</li>
2469 <li>Translation from DNA to Amino Acids fails</li>
2470 <li>Jalview fail to load newick tree with quoted label</li>
2471 <li>--headless flag isn't understood</li>
2472 <li>ClassCastException when generating EPS in headless
2474 <li>Adjusting sequence-associated shading threshold only
2475 changes one row's threshold</li>
2476 <li>Preferences and Feature settings panel panel
2477 doesn't open</li>
2478 <li>hide consensus histogram also hides conservation and
2479 quality histograms</li>
2484 <td><div align="center">
2485 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2487 <td><em>Application</em>
2489 <li>Support for JABAWS 2.0 Services (AACon alignment
2490 conservation, protein disorder and Clustal Omega)</li>
2491 <li>JABAWS server status indicator in Web Services
2493 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2494 in Jalview alignment window</li>
2495 <li>Updated Jalview build and deploy framework for OSX
2496 mountain lion, windows 7, and 8</li>
2497 <li>Nucleotide substitution matrix for PCA that supports
2498 RNA and ambiguity codes</li>
2500 <li>Improved sequence database retrieval GUI</li>
2501 <li>Support fetching and database reference look up
2502 against multiple DAS sources (Fetch all from in 'fetch db
2504 <li>Jalview project improvements
2506 <li>Store and retrieve the 'belowAlignment'
2507 flag for annotation</li>
2508 <li>calcId attribute to group annotation rows on the
2510 <li>Store AACon calculation settings for a view in
2511 Jalview project</li>
2515 <li>horizontal scrolling gesture support</li>
2516 <li>Visual progress indicator when PCA calculation is
2518 <li>Simpler JABA web services menus</li>
2519 <li>visual indication that web service results are still
2520 being retrieved from server</li>
2521 <li>Serialise the dialogs that are shown when Jalview
2522 starts up for first time</li>
2523 <li>Jalview user agent string for interacting with HTTP
2525 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2527 <li>Examples directory and Groovy library included in
2528 InstallAnywhere distribution</li>
2529 </ul> <em>Applet</em>
2531 <li>RNA alignment and secondary structure annotation
2532 visualization applet example</li>
2533 </ul> <em>General</em>
2535 <li>Normalise option for consensus sequence logo</li>
2536 <li>Reset button in PCA window to return dimensions to
2538 <li>Allow seqspace or Jalview variant of alignment PCA
2540 <li>PCA with either nucleic acid and protein substitution
2542 <li>Allow windows containing HTML reports to be exported
2544 <li>Interactive display and editing of RNA secondary
2545 structure contacts</li>
2546 <li>RNA Helix Alignment Colouring</li>
2547 <li>RNA base pair logo consensus</li>
2548 <li>Parse sequence associated secondary structure
2549 information in Stockholm files</li>
2550 <li>HTML Export database accessions and annotation
2551 information presented in tooltip for sequences</li>
2552 <li>Import secondary structure from LOCARNA clustalw
2553 style RNA alignment files</li>
2554 <li>import and visualise T-COFFEE quality scores for an
2556 <li>'colour by annotation' per sequence option to
2557 shade each sequence according to its associated alignment
2559 <li>New Jalview Logo</li>
2560 </ul> <em>Documentation and Development</em>
2562 <li>documentation for score matrices used in Jalview</li>
2563 <li>New Website!</li>
2565 <td><em>Application</em>
2567 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2568 wsdbfetch REST service</li>
2569 <li>Stop windows being moved outside desktop on OSX</li>
2570 <li>Filetype associations not installed for webstart
2572 <li>Jalview does not always retrieve progress of a JABAWS
2573 job execution in full once it is complete</li>
2574 <li>revise SHMR RSBS definition to ensure alignment is
2575 uploaded via ali_file parameter</li>
2576 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2577 <li>View all structures superposed fails with exception</li>
2578 <li>Jnet job queues forever if a very short sequence is
2579 submitted for prediction</li>
2580 <li>Cut and paste menu not opened when mouse clicked on
2582 <li>Putting fractional value into integer text box in
2583 alignment parameter dialog causes Jalview to hang</li>
2584 <li>Structure view highlighting doesn't work on
2586 <li>View all structures fails with exception shown in
2588 <li>Characters in filename associated with PDBEntry not
2589 escaped in a platform independent way</li>
2590 <li>Jalview desktop fails to launch with exception when
2592 <li>Tree calculation reports 'you must have 2 or more
2593 sequences selected' when selection is empty</li>
2594 <li>Jalview desktop fails to launch with jar signature
2595 failure when java web start temporary file caching is
2597 <li>DAS Sequence retrieval with range qualification
2598 results in sequence xref which includes range qualification</li>
2599 <li>Errors during processing of command line arguments
2600 cause progress bar (JAL-898) to be removed</li>
2601 <li>Replace comma for semi-colon option not disabled for
2602 DAS sources in sequence fetcher</li>
2603 <li>Cannot close news reader when JABAWS server warning
2604 dialog is shown</li>
2605 <li>Option widgets not updated to reflect user settings</li>
2606 <li>Edited sequence not submitted to web service</li>
2607 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2608 <li>InstallAnywhere installer doesn't unpack and run
2609 on OSX Mountain Lion</li>
2610 <li>Annotation panel not given a scroll bar when
2611 sequences with alignment annotation are pasted into the
2613 <li>Sequence associated annotation rows not associated
2614 when loaded from Jalview project</li>
2615 <li>Browser launch fails with NPE on java 1.7</li>
2616 <li>JABAWS alignment marked as finished when job was
2617 cancelled or job failed due to invalid input</li>
2618 <li>NPE with v2.7 example when clicking on Tree
2619 associated with all views</li>
2620 <li>Exceptions when copy/paste sequences with grouped
2621 annotation rows to new window</li>
2622 </ul> <em>Applet</em>
2624 <li>Sequence features are momentarily displayed before
2625 they are hidden using hidefeaturegroups applet parameter</li>
2626 <li>loading features via javascript API automatically
2627 enables feature display</li>
2628 <li>scrollToColumnIn javascript API method doesn't
2630 </ul> <em>General</em>
2632 <li>Redundancy removal fails for rna alignment</li>
2633 <li>PCA calculation fails when sequence has been selected
2634 and then deselected</li>
2635 <li>PCA window shows grey box when first opened on OSX</li>
2636 <li>Letters coloured pink in sequence logo when alignment
2637 coloured with clustalx</li>
2638 <li>Choosing fonts without letter symbols defined causes
2639 exceptions and redraw errors</li>
2640 <li>Initial PCA plot view is not same as manually
2641 reconfigured view</li>
2642 <li>Grouped annotation graph label has incorrect line
2644 <li>Grouped annotation graph label display is corrupted
2645 for lots of labels</li>
2650 <div align="center">
2651 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2654 <td><em>Application</em>
2656 <li>Jalview Desktop News Reader</li>
2657 <li>Tweaked default layout of web services menu</li>
2658 <li>View/alignment association menu to enable user to
2659 easily specify which alignment a multi-structure view takes
2660 its colours/correspondences from</li>
2661 <li>Allow properties file location to be specified as URL</li>
2662 <li>Extend Jalview project to preserve associations
2663 between many alignment views and a single Jmol display</li>
2664 <li>Store annotation row height in Jalview project file</li>
2665 <li>Annotation row column label formatting attributes
2666 stored in project file</li>
2667 <li>Annotation row order for auto-calculated annotation
2668 rows preserved in Jalview project file</li>
2669 <li>Visual progress indication when Jalview state is
2670 saved using Desktop window menu</li>
2671 <li>Visual indication that command line arguments are
2672 still being processed</li>
2673 <li>Groovy script execution from URL</li>
2674 <li>Colour by annotation default min and max colours in
2676 <li>Automatically associate PDB files dragged onto an
2677 alignment with sequences that have high similarity and
2679 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2680 <li>'view structures' option to open many
2681 structures in same window</li>
2682 <li>Sort associated views menu option for tree panel</li>
2683 <li>Group all JABA and non-JABA services for a particular
2684 analysis function in its own submenu</li>
2685 </ul> <em>Applet</em>
2687 <li>Userdefined and autogenerated annotation rows for
2689 <li>Adjustment of alignment annotation pane height</li>
2690 <li>Annotation scrollbar for annotation panel</li>
2691 <li>Drag to reorder annotation rows in annotation panel</li>
2692 <li>'automaticScrolling' parameter</li>
2693 <li>Allow sequences with partial ID string matches to be
2694 annotated from GFF/Jalview features files</li>
2695 <li>Sequence logo annotation row in applet</li>
2696 <li>Absolute paths relative to host server in applet
2697 parameters are treated as such</li>
2698 <li>New in the JalviewLite javascript API:
2700 <li>JalviewLite.js javascript library</li>
2701 <li>Javascript callbacks for
2703 <li>Applet initialisation</li>
2704 <li>Sequence/alignment mouse-overs and selections</li>
2707 <li>scrollTo row and column alignment scrolling
2709 <li>Select sequence/alignment regions from javascript</li>
2710 <li>javascript structure viewer harness to pass
2711 messages between Jmol and Jalview when running as
2712 distinct applets</li>
2713 <li>sortBy method</li>
2714 <li>Set of applet and application examples shipped
2715 with documentation</li>
2716 <li>New example to demonstrate JalviewLite and Jmol
2717 javascript message exchange</li>
2719 </ul> <em>General</em>
2721 <li>Enable Jmol displays to be associated with multiple
2722 multiple alignments</li>
2723 <li>Option to automatically sort alignment with new tree</li>
2724 <li>User configurable link to enable redirects to a
2725 www.Jalview.org mirror</li>
2726 <li>Jmol colours option for Jmol displays</li>
2727 <li>Configurable newline string when writing alignment
2728 and other flat files</li>
2729 <li>Allow alignment annotation description lines to
2730 contain html tags</li>
2731 </ul> <em>Documentation and Development</em>
2733 <li>Add groovy test harness for bulk load testing to
2735 <li>Groovy script to load and align a set of sequences
2736 using a web service before displaying the result in the
2737 Jalview desktop</li>
2738 <li>Restructured javascript and applet api documentation</li>
2739 <li>Ant target to publish example html files with applet
2741 <li>Netbeans project for building Jalview from source</li>
2742 <li>ant task to create online javadoc for Jalview source</li>
2744 <td><em>Application</em>
2746 <li>User defined colourscheme throws exception when
2747 current built in colourscheme is saved as new scheme</li>
2748 <li>AlignFrame->Save in application pops up save
2749 dialog for valid filename/format</li>
2750 <li>Cannot view associated structure for UniProt sequence</li>
2751 <li>PDB file association breaks for UniProt sequence
2753 <li>Associate PDB from file dialog does not tell you
2754 which sequence is to be associated with the file</li>
2755 <li>Find All raises null pointer exception when query
2756 only matches sequence IDs</li>
2757 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2758 <li>Jalview project with Jmol views created with Jalview
2759 2.4 cannot be loaded</li>
2760 <li>Filetype associations not installed for webstart
2762 <li>Two or more chains in a single PDB file associated
2763 with sequences in different alignments do not get coloured
2764 by their associated sequence</li>
2765 <li>Visibility status of autocalculated annotation row
2766 not preserved when project is loaded</li>
2767 <li>Annotation row height and visibility attributes not
2768 stored in Jalview project</li>
2769 <li>Tree bootstraps are not preserved when saved as a
2770 Jalview project</li>
2771 <li>Envision2 workflow tooltips are corrupted</li>
2772 <li>Enabling show group conservation also enables colour
2773 by conservation</li>
2774 <li>Duplicate group associated conservation or consensus
2775 created on new view</li>
2776 <li>Annotation scrollbar not displayed after 'show
2777 all hidden annotation rows' option selected</li>
2778 <li>Alignment quality not updated after alignment
2779 annotation row is hidden then shown</li>
2780 <li>Preserve colouring of structures coloured by
2781 sequences in pre Jalview 2.7 projects</li>
2782 <li>Web service job parameter dialog is not laid out
2784 <li>Web services menu not refreshed after 'reset
2785 services' button is pressed in preferences</li>
2786 <li>Annotation off by one in Jalview v2_3 example project</li>
2787 <li>Structures imported from file and saved in project
2788 get name like jalview_pdb1234.txt when reloaded</li>
2789 <li>Jalview does not always retrieve progress of a JABAWS
2790 job execution in full once it is complete</li>
2791 </ul> <em>Applet</em>
2793 <li>Alignment height set incorrectly when lots of
2794 annotation rows are displayed</li>
2795 <li>Relative URLs in feature HTML text not resolved to
2797 <li>View follows highlighting does not work for positions
2799 <li><= shown as = in tooltip</li>
2800 <li>Export features raises exception when no features
2802 <li>Separator string used for serialising lists of IDs
2803 for javascript api is modified when separator string
2804 provided as parameter</li>
2805 <li>Null pointer exception when selecting tree leaves for
2806 alignment with no existing selection</li>
2807 <li>Relative URLs for datasources assumed to be relative
2808 to applet's codebase</li>
2809 <li>Status bar not updated after finished searching and
2810 search wraps around to first result</li>
2811 <li>StructureSelectionManager instance shared between
2812 several Jalview applets causes race conditions and memory
2814 <li>Hover tooltip and mouseover of position on structure
2815 not sent from Jmol in applet</li>
2816 <li>Certain sequences of javascript method calls to
2817 applet API fatally hang browser</li>
2818 </ul> <em>General</em>
2820 <li>View follows structure mouseover scrolls beyond
2821 position with wrapped view and hidden regions</li>
2822 <li>Find sequence position moves to wrong residue
2823 with/without hidden columns</li>
2824 <li>Sequence length given in alignment properties window
2826 <li>InvalidNumberFormat exceptions thrown when trying to
2827 import PDB like structure files</li>
2828 <li>Positional search results are only highlighted
2829 between user-supplied sequence start/end bounds</li>
2830 <li>End attribute of sequence is not validated</li>
2831 <li>Find dialog only finds first sequence containing a
2832 given sequence position</li>
2833 <li>Sequence numbering not preserved in MSF alignment
2835 <li>Jalview PDB file reader does not extract sequence
2836 from nucleotide chains correctly</li>
2837 <li>Structure colours not updated when tree partition
2838 changed in alignment</li>
2839 <li>Sequence associated secondary structure not correctly
2840 parsed in interleaved stockholm</li>
2841 <li>Colour by annotation dialog does not restore current
2843 <li>Hiding (nearly) all sequences doesn't work
2845 <li>Sequences containing lowercase letters are not
2846 properly associated with their pdb files</li>
2847 </ul> <em>Documentation and Development</em>
2849 <li>schemas/JalviewWsParamSet.xsd corrupted by
2850 ApplyCopyright tool</li>
2855 <div align="center">
2856 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2859 <td><em>Application</em>
2861 <li>New warning dialog when the Jalview Desktop cannot
2862 contact web services</li>
2863 <li>JABA service parameters for a preset are shown in
2864 service job window</li>
2865 <li>JABA Service menu entries reworded</li>
2869 <li>Modeller PIR IO broken - cannot correctly import a
2870 pir file emitted by Jalview</li>
2871 <li>Existing feature settings transferred to new
2872 alignment view created from cut'n'paste</li>
2873 <li>Improved test for mixed amino/nucleotide chains when
2874 parsing PDB files</li>
2875 <li>Consensus and conservation annotation rows
2876 occasionally become blank for all new windows</li>
2877 <li>Exception raised when right clicking above sequences
2878 in wrapped view mode</li>
2879 </ul> <em>Application</em>
2881 <li>multiple multiply aligned structure views cause cpu
2882 usage to hit 100% and computer to hang</li>
2883 <li>Web Service parameter layout breaks for long user
2884 parameter names</li>
2885 <li>Jaba service discovery hangs desktop if Jaba server
2892 <div align="center">
2893 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2896 <td><em>Application</em>
2898 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2899 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2902 <li>Web Services preference tab</li>
2903 <li>Analysis parameters dialog box and user defined
2905 <li>Improved speed and layout of Envision2 service menu</li>
2906 <li>Superpose structures using associated sequence
2908 <li>Export coordinates and projection as CSV from PCA
2910 </ul> <em>Applet</em>
2912 <li>enable javascript: execution by the applet via the
2913 link out mechanism</li>
2914 </ul> <em>Other</em>
2916 <li>Updated the Jmol Jalview interface to work with Jmol
2918 <li>The Jalview Desktop and JalviewLite applet now
2919 require Java 1.5</li>
2920 <li>Allow Jalview feature colour specification for GFF
2921 sequence annotation files</li>
2922 <li>New 'colour by label' keword in Jalview feature file
2923 type colour specification</li>
2924 <li>New Jalview Desktop Groovy API method that allows a
2925 script to check if it being run in an interactive session or
2926 in a batch operation from the Jalview command line</li>
2930 <li>clustalx colourscheme colours Ds preferentially when
2931 both D+E are present in over 50% of the column</li>
2932 </ul> <em>Application</em>
2934 <li>typo in AlignmentFrame->View->Hide->all but
2935 selected Regions menu item</li>
2936 <li>sequence fetcher replaces ',' for ';' when the ',' is
2937 part of a valid accession ID</li>
2938 <li>fatal OOM if object retrieved by sequence fetcher
2939 runs out of memory</li>
2940 <li>unhandled Out of Memory Error when viewing pca
2941 analysis results</li>
2942 <li>InstallAnywhere builds fail to launch on OS X java
2943 10.5 update 4 (due to apple Java 1.6 update)</li>
2944 <li>Installanywhere Jalview silently fails to launch</li>
2945 </ul> <em>Applet</em>
2947 <li>Jalview.getFeatureGroups() raises an
2948 ArrayIndexOutOfBoundsException if no feature groups are
2955 <div align="center">
2956 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2962 <li>Alignment prettyprinter doesn't cope with long
2964 <li>clustalx colourscheme colours Ds preferentially when
2965 both D+E are present in over 50% of the column</li>
2966 <li>nucleic acid structures retrieved from PDB do not
2967 import correctly</li>
2968 <li>More columns get selected than were clicked on when a
2969 number of columns are hidden</li>
2970 <li>annotation label popup menu not providing correct
2971 add/hide/show options when rows are hidden or none are
2973 <li>Stockholm format shown in list of readable formats,
2974 and parser copes better with alignments from RFAM.</li>
2975 <li>CSV output of consensus only includes the percentage
2976 of all symbols if sequence logo display is enabled</li>
2978 </ul> <em>Applet</em>
2980 <li>annotation panel disappears when annotation is
2982 </ul> <em>Application</em>
2984 <li>Alignment view not redrawn properly when new
2985 alignment opened where annotation panel is visible but no
2986 annotations are present on alignment</li>
2987 <li>pasted region containing hidden columns is
2988 incorrectly displayed in new alignment window</li>
2989 <li>Jalview slow to complete operations when stdout is
2990 flooded (fix is to close the Jalview console)</li>
2991 <li>typo in AlignmentFrame->View->Hide->all but
2992 selected Rregions menu item.</li>
2993 <li>inconsistent group submenu and Format submenu entry
2994 'Un' or 'Non'conserved</li>
2995 <li>Sequence feature settings are being shared by
2996 multiple distinct alignments</li>
2997 <li>group annotation not recreated when tree partition is
2999 <li>double click on group annotation to select sequences
3000 does not propagate to associated trees</li>
3001 <li>Mac OSX specific issues:
3003 <li>exception raised when mouse clicked on desktop
3004 window background</li>
3005 <li>Desktop menu placed on menu bar and application
3006 name set correctly</li>
3007 <li>sequence feature settings not wide enough for the
3008 save feature colourscheme button</li>
3017 <div align="center">
3018 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3021 <td><em>New Capabilities</em>
3023 <li>URL links generated from description line for
3024 regular-expression based URL links (applet and application)
3026 <li>Non-positional feature URL links are shown in link
3028 <li>Linked viewing of nucleic acid sequences and
3030 <li>Automatic Scrolling option in View menu to display
3031 the currently highlighted region of an alignment.</li>
3032 <li>Order an alignment by sequence length, or using the
3033 average score or total feature count for each sequence.</li>
3034 <li>Shading features by score or associated description</li>
3035 <li>Subdivide alignment and groups based on identity of
3036 selected subsequence (Make Groups from Selection).</li>
3037 <li>New hide/show options including Shift+Control+H to
3038 hide everything but the currently selected region.</li>
3039 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3040 </ul> <em>Application</em>
3042 <li>Fetch DB References capabilities and UI expanded to
3043 support retrieval from DAS sequence sources</li>
3044 <li>Local DAS Sequence sources can be added via the
3045 command line or via the Add local source dialog box.</li>
3046 <li>DAS Dbref and DbxRef feature types are parsed as
3047 database references and protein_name is parsed as
3048 description line (BioSapiens terms).</li>
3049 <li>Enable or disable non-positional feature and database
3050 references in sequence ID tooltip from View menu in
3052 <!-- <li>New hidden columns and rows and representatives capabilities
3053 in annotations file (in progress - not yet fully implemented)</li> -->
3054 <li>Group-associated consensus, sequence logos and
3055 conservation plots</li>
3056 <li>Symbol distributions for each column can be exported
3057 and visualized as sequence logos</li>
3058 <li>Optionally scale multi-character column labels to fit
3059 within each column of annotation row<!-- todo for applet -->
3061 <li>Optional automatic sort of associated alignment view
3062 when a new tree is opened.</li>
3063 <li>Jalview Java Console</li>
3064 <li>Better placement of desktop window when moving
3065 between different screens.</li>
3066 <li>New preference items for sequence ID tooltip and
3067 consensus annotation</li>
3068 <li>Client to submit sequences and IDs to Envision2
3070 <li><em>Vamsas Capabilities</em>
3072 <li>Improved VAMSAS synchronization (Jalview archive
3073 used to preserve views, structures, and tree display
3075 <li>Import of vamsas documents from disk or URL via
3077 <li>Sharing of selected regions between views and
3078 with other VAMSAS applications (Experimental feature!)</li>
3079 <li>Updated API to VAMSAS version 0.2</li>
3081 </ul> <em>Applet</em>
3083 <li>Middle button resizes annotation row height</li>
3086 <li>sortByTree (true/false) - automatically sort the
3087 associated alignment view by the tree when a new tree is
3089 <li>showTreeBootstraps (true/false) - show or hide
3090 branch bootstraps (default is to show them if available)</li>
3091 <li>showTreeDistances (true/false) - show or hide
3092 branch lengths (default is to show them if available)</li>
3093 <li>showUnlinkedTreeNodes (true/false) - indicate if
3094 unassociated nodes should be highlighted in the tree
3096 <li>heightScale and widthScale (1.0 or more) -
3097 increase the height or width of a cell in the alignment
3098 grid relative to the current font size.</li>
3101 <li>Non-positional features displayed in sequence ID
3103 </ul> <em>Other</em>
3105 <li>Features format: graduated colour definitions and
3106 specification of feature scores</li>
3107 <li>Alignment Annotations format: new keywords for group
3108 associated annotation (GROUP_REF) and annotation row display
3109 properties (ROW_PROPERTIES)</li>
3110 <li>XML formats extended to support graduated feature
3111 colourschemes, group associated annotation, and profile
3112 visualization settings.</li></td>
3115 <li>Source field in GFF files parsed as feature source
3116 rather than description</li>
3117 <li>Non-positional features are now included in sequence
3118 feature and gff files (controlled via non-positional feature
3119 visibility in tooltip).</li>
3120 <li>URL links generated for all feature links (bugfix)</li>
3121 <li>Added URL embedding instructions to features file
3123 <li>Codons containing ambiguous nucleotides translated as
3124 'X' in peptide product</li>
3125 <li>Match case switch in find dialog box works for both
3126 sequence ID and sequence string and query strings do not
3127 have to be in upper case to match case-insensitively.</li>
3128 <li>AMSA files only contain first column of
3129 multi-character column annotation labels</li>
3130 <li>Jalview Annotation File generation/parsing consistent
3131 with documentation (e.g. Stockholm annotation can be
3132 exported and re-imported)</li>
3133 <li>PDB files without embedded PDB IDs given a friendly
3135 <li>Find incrementally searches ID string matches as well
3136 as subsequence matches, and correctly reports total number
3140 <li>Better handling of exceptions during sequence
3142 <li>Dasobert generated non-positional feature URL
3143 link text excludes the start_end suffix</li>
3144 <li>DAS feature and source retrieval buttons disabled
3145 when fetch or registry operations in progress.</li>
3146 <li>PDB files retrieved from URLs are cached properly</li>
3147 <li>Sequence description lines properly shared via
3149 <li>Sequence fetcher fetches multiple records for all
3151 <li>Ensured that command line das feature retrieval
3152 completes before alignment figures are generated.</li>
3153 <li>Reduced time taken when opening file browser for
3155 <li>isAligned check prior to calculating tree, PCA or
3156 submitting an MSA to JNet now excludes hidden sequences.</li>
3157 <li>User defined group colours properly recovered
3158 from Jalview projects.</li>
3167 <div align="center">
3168 <strong>2.4.0.b2</strong><br> 28/10/2009
3173 <li>Experimental support for google analytics usage
3175 <li>Jalview privacy settings (user preferences and docs).</li>
3180 <li>Race condition in applet preventing startup in
3182 <li>Exception when feature created from selection beyond
3183 length of sequence.</li>
3184 <li>Allow synthetic PDB files to be imported gracefully</li>
3185 <li>Sequence associated annotation rows associate with
3186 all sequences with a given id</li>
3187 <li>Find function matches case-insensitively for sequence
3188 ID string searches</li>
3189 <li>Non-standard characters do not cause pairwise
3190 alignment to fail with exception</li>
3191 </ul> <em>Application Issues</em>
3193 <li>Sequences are now validated against EMBL database</li>
3194 <li>Sequence fetcher fetches multiple records for all
3196 </ul> <em>InstallAnywhere Issues</em>
3198 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3199 issue with installAnywhere mechanism)</li>
3200 <li>Command line launching of JARs from InstallAnywhere
3201 version (java class versioning error fixed)</li>
3208 <div align="center">
3209 <strong>2.4</strong><br> 27/8/2008
3212 <td><em>User Interface</em>
3214 <li>Linked highlighting of codon and amino acid from
3215 translation and protein products</li>
3216 <li>Linked highlighting of structure associated with
3217 residue mapping to codon position</li>
3218 <li>Sequence Fetcher provides example accession numbers
3219 and 'clear' button</li>
3220 <li>MemoryMonitor added as an option under Desktop's
3222 <li>Extract score function to parse whitespace separated
3223 numeric data in description line</li>
3224 <li>Column labels in alignment annotation can be centred.</li>
3225 <li>Tooltip for sequence associated annotation give name
3227 </ul> <em>Web Services and URL fetching</em>
3229 <li>JPred3 web service</li>
3230 <li>Prototype sequence search client (no public services
3232 <li>Fetch either seed alignment or full alignment from
3234 <li>URL Links created for matching database cross
3235 references as well as sequence ID</li>
3236 <li>URL Links can be created using regular-expressions</li>
3237 </ul> <em>Sequence Database Connectivity</em>
3239 <li>Retrieval of cross-referenced sequences from other
3241 <li>Generalised database reference retrieval and
3242 validation to all fetchable databases</li>
3243 <li>Fetch sequences from DAS sources supporting the
3244 sequence command</li>
3245 </ul> <em>Import and Export</em>
3246 <li>export annotation rows as CSV for spreadsheet import</li>
3247 <li>Jalview projects record alignment dataset associations,
3248 EMBL products, and cDNA sequence mappings</li>
3249 <li>Sequence Group colour can be specified in Annotation
3251 <li>Ad-hoc colouring of group in Annotation File using RGB
3252 triplet as name of colourscheme</li>
3253 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3255 <li>treenode binding for VAMSAS tree exchange</li>
3256 <li>local editing and update of sequences in VAMSAS
3257 alignments (experimental)</li>
3258 <li>Create new or select existing session to join</li>
3259 <li>load and save of vamsas documents</li>
3260 </ul> <em>Application command line</em>
3262 <li>-tree parameter to open trees (introduced for passing
3264 <li>-fetchfrom command line argument to specify nicknames
3265 of DAS servers to query for alignment features</li>
3266 <li>-dasserver command line argument to add new servers
3267 that are also automatically queried for features</li>
3268 <li>-groovy command line argument executes a given groovy
3269 script after all input data has been loaded and parsed</li>
3270 </ul> <em>Applet-Application data exchange</em>
3272 <li>Trees passed as applet parameters can be passed to
3273 application (when using "View in full
3274 application")</li>
3275 </ul> <em>Applet Parameters</em>
3277 <li>feature group display control parameter</li>
3278 <li>debug parameter</li>
3279 <li>showbutton parameter</li>
3280 </ul> <em>Applet API methods</em>
3282 <li>newView public method</li>
3283 <li>Window (current view) specific get/set public methods</li>
3284 <li>Feature display control methods</li>
3285 <li>get list of currently selected sequences</li>
3286 </ul> <em>New Jalview distribution features</em>
3288 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3289 <li>RELEASE file gives build properties for the latest
3290 Jalview release.</li>
3291 <li>Java 1.1 Applet build made easier and donotobfuscate
3292 property controls execution of obfuscator</li>
3293 <li>Build target for generating source distribution</li>
3294 <li>Debug flag for javacc</li>
3295 <li>.jalview_properties file is documented (slightly) in
3296 jalview.bin.Cache</li>
3297 <li>Continuous Build Integration for stable and
3298 development version of Application, Applet and source
3303 <li>selected region output includes visible annotations
3304 (for certain formats)</li>
3305 <li>edit label/displaychar contains existing label/char
3307 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3308 <li>shorter peptide product names from EMBL records</li>
3309 <li>Newick string generator makes compact representations</li>
3310 <li>bootstrap values parsed correctly for tree files with
3312 <li>pathological filechooser bug avoided by not allowing
3313 filenames containing a ':'</li>
3314 <li>Fixed exception when parsing GFF files containing
3315 global sequence features</li>
3316 <li>Alignment datasets are finalized only when number of
3317 references from alignment sequences goes to zero</li>
3318 <li>Close of tree branch colour box without colour
3319 selection causes cascading exceptions</li>
3320 <li>occasional negative imgwidth exceptions</li>
3321 <li>better reporting of non-fatal warnings to user when
3322 file parsing fails.</li>
3323 <li>Save works when Jalview project is default format</li>
3324 <li>Save as dialog opened if current alignment format is
3325 not a valid output format</li>
3326 <li>UniProt canonical names introduced for both das and
3328 <li>Histidine should be midblue (not pink!) in Zappo</li>
3329 <li>error messages passed up and output when data read
3331 <li>edit undo recovers previous dataset sequence when
3332 sequence is edited</li>
3333 <li>allow PDB files without pdb ID HEADER lines (like
3334 those generated by MODELLER) to be read in properly</li>
3335 <li>allow reading of JPred concise files as a normal
3337 <li>Stockholm annotation parsing and alignment properties
3338 import fixed for PFAM records</li>
3339 <li>Structure view windows have correct name in Desktop
3341 <li>annotation consisting of sequence associated scores
3342 can be read and written correctly to annotation file</li>
3343 <li>Aligned cDNA translation to aligned peptide works
3345 <li>Fixed display of hidden sequence markers and
3346 non-italic font for representatives in Applet</li>
3347 <li>Applet Menus are always embedded in applet window on
3349 <li>Newly shown features appear at top of stack (in
3351 <li>Annotations added via parameter not drawn properly
3352 due to null pointer exceptions</li>
3353 <li>Secondary structure lines are drawn starting from
3354 first column of alignment</li>
3355 <li>UniProt XML import updated for new schema release in
3357 <li>Sequence feature to sequence ID match for Features
3358 file is case-insensitive</li>
3359 <li>Sequence features read from Features file appended to
3360 all sequences with matching IDs</li>
3361 <li>PDB structure coloured correctly for associated views
3362 containing a sub-sequence</li>
3363 <li>PDB files can be retrieved by applet from Jar files</li>
3364 <li>feature and annotation file applet parameters
3365 referring to different directories are retrieved correctly</li>
3366 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3367 <li>Fixed application hang whilst waiting for
3368 splash-screen version check to complete</li>
3369 <li>Applet properly URLencodes input parameter values
3370 when passing them to the launchApp service</li>
3371 <li>display name and local features preserved in results
3372 retrieved from web service</li>
3373 <li>Visual delay indication for sequence retrieval and
3374 sequence fetcher initialisation</li>
3375 <li>updated Application to use DAS 1.53e version of
3376 dasobert DAS client</li>
3377 <li>Re-instated Full AMSA support and .amsa file
3379 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3387 <div align="center">
3388 <strong>2.3</strong><br> 9/5/07
3393 <li>Jmol 11.0.2 integration</li>
3394 <li>PDB views stored in Jalview XML files</li>
3395 <li>Slide sequences</li>
3396 <li>Edit sequence in place</li>
3397 <li>EMBL CDS features</li>
3398 <li>DAS Feature mapping</li>
3399 <li>Feature ordering</li>
3400 <li>Alignment Properties</li>
3401 <li>Annotation Scores</li>
3402 <li>Sort by scores</li>
3403 <li>Feature/annotation editing in applet</li>
3408 <li>Headless state operation in 2.2.1</li>
3409 <li>Incorrect and unstable DNA pairwise alignment</li>
3410 <li>Cut and paste of sequences with annotation</li>
3411 <li>Feature group display state in XML</li>
3412 <li>Feature ordering in XML</li>
3413 <li>blc file iteration selection using filename # suffix</li>
3414 <li>Stockholm alignment properties</li>
3415 <li>Stockhom alignment secondary structure annotation</li>
3416 <li>2.2.1 applet had no feature transparency</li>
3417 <li>Number pad keys can be used in cursor mode</li>
3418 <li>Structure Viewer mirror image resolved</li>
3425 <div align="center">
3426 <strong>2.2.1</strong><br> 12/2/07
3431 <li>Non standard characters can be read and displayed
3432 <li>Annotations/Features can be imported/exported to the
3434 <li>Applet allows editing of sequence/annotation/group
3435 name & description
3436 <li>Preference setting to display sequence name in
3438 <li>Annotation file format extended to allow
3439 Sequence_groups to be defined
3440 <li>Default opening of alignment overview panel can be
3441 specified in preferences
3442 <li>PDB residue numbering annotation added to associated
3448 <li>Applet crash under certain Linux OS with Java 1.6
3450 <li>Annotation file export / import bugs fixed
3451 <li>PNG / EPS image output bugs fixed
3457 <div align="center">
3458 <strong>2.2</strong><br> 27/11/06
3463 <li>Multiple views on alignment
3464 <li>Sequence feature editing
3465 <li>"Reload" alignment
3466 <li>"Save" to current filename
3467 <li>Background dependent text colour
3468 <li>Right align sequence ids
3469 <li>User-defined lower case residue colours
3472 <li>Menu item accelerator keys
3473 <li>Control-V pastes to current alignment
3474 <li>Cancel button for DAS Feature Fetching
3475 <li>PCA and PDB Viewers zoom via mouse roller
3476 <li>User-defined sub-tree colours and sub-tree selection
3478 <li>'New Window' button on the 'Output to Text box'
3483 <li>New memory efficient Undo/Redo System
3484 <li>Optimised symbol lookups and conservation/consensus
3486 <li>Region Conservation/Consensus recalculated after
3488 <li>Fixed Remove Empty Columns Bug (empty columns at end
3490 <li>Slowed DAS Feature Fetching for increased robustness.
3492 <li>Made angle brackets in ASCII feature descriptions
3494 <li>Re-instated Zoom function for PCA
3495 <li>Sequence descriptions conserved in web service
3497 <li>UniProt ID discoverer uses any word separated by
3499 <li>WsDbFetch query/result association resolved
3500 <li>Tree leaf to sequence mapping improved
3501 <li>Smooth fonts switch moved to FontChooser dialog box.
3508 <div align="center">
3509 <strong>2.1.1</strong><br> 12/9/06
3514 <li>Copy consensus sequence to clipboard</li>
3519 <li>Image output - rightmost residues are rendered if
3520 sequence id panel has been resized</li>
3521 <li>Image output - all offscreen group boundaries are
3523 <li>Annotation files with sequence references - all
3524 elements in file are relative to sequence position</li>
3525 <li>Mac Applet users can use Alt key for group editing</li>
3531 <div align="center">
3532 <strong>2.1</strong><br> 22/8/06
3537 <li>MAFFT Multiple Alignment in default Web Service list</li>
3538 <li>DAS Feature fetching</li>
3539 <li>Hide sequences and columns</li>
3540 <li>Export Annotations and Features</li>
3541 <li>GFF file reading / writing</li>
3542 <li>Associate structures with sequences from local PDB
3544 <li>Add sequences to exisiting alignment</li>
3545 <li>Recently opened files / URL lists</li>
3546 <li>Applet can launch the full application</li>
3547 <li>Applet has transparency for features (Java 1.2
3549 <li>Applet has user defined colours parameter</li>
3550 <li>Applet can load sequences from parameter
3551 "sequence<em>x</em>"
3557 <li>Redundancy Panel reinstalled in the Applet</li>
3558 <li>Monospaced font - EPS / rescaling bug fixed</li>
3559 <li>Annotation files with sequence references bug fixed</li>
3565 <div align="center">
3566 <strong>2.08.1</strong><br> 2/5/06
3571 <li>Change case of selected region from Popup menu</li>
3572 <li>Choose to match case when searching</li>
3573 <li>Middle mouse button and mouse movement can compress /
3574 expand the visible width and height of the alignment</li>
3579 <li>Annotation Panel displays complete JNet results</li>
3585 <div align="center">
3586 <strong>2.08b</strong><br> 18/4/06
3592 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3593 <li>Righthand label on wrapped alignments shows correct
3600 <div align="center">
3601 <strong>2.08</strong><br> 10/4/06
3606 <li>Editing can be locked to the selection area</li>
3607 <li>Keyboard editing</li>
3608 <li>Create sequence features from searches</li>
3609 <li>Precalculated annotations can be loaded onto
3611 <li>Features file allows grouping of features</li>
3612 <li>Annotation Colouring scheme added</li>
3613 <li>Smooth fonts off by default - Faster rendering</li>
3614 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3619 <li>Drag & Drop fixed on Linux</li>
3620 <li>Jalview Archive file faster to load/save, sequence
3621 descriptions saved.</li>
3627 <div align="center">
3628 <strong>2.07</strong><br> 12/12/05
3633 <li>PDB Structure Viewer enhanced</li>
3634 <li>Sequence Feature retrieval and display enhanced</li>
3635 <li>Choose to output sequence start-end after sequence
3636 name for file output</li>
3637 <li>Sequence Fetcher WSDBFetch@EBI</li>
3638 <li>Applet can read feature files, PDB files and can be
3639 used for HTML form input</li>
3644 <li>HTML output writes groups and features</li>
3645 <li>Group editing is Control and mouse click</li>
3646 <li>File IO bugs</li>
3652 <div align="center">
3653 <strong>2.06</strong><br> 28/9/05
3658 <li>View annotations in wrapped mode</li>
3659 <li>More options for PCA viewer</li>
3664 <li>GUI bugs resolved</li>
3665 <li>Runs with -nodisplay from command line</li>
3671 <div align="center">
3672 <strong>2.05b</strong><br> 15/9/05
3677 <li>Choose EPS export as lineart or text</li>
3678 <li>Jar files are executable</li>
3679 <li>Can read in Uracil - maps to unknown residue</li>
3684 <li>Known OutOfMemory errors give warning message</li>
3685 <li>Overview window calculated more efficiently</li>
3686 <li>Several GUI bugs resolved</li>
3692 <div align="center">
3693 <strong>2.05</strong><br> 30/8/05
3698 <li>Edit and annotate in "Wrapped" view</li>
3703 <li>Several GUI bugs resolved</li>
3709 <div align="center">
3710 <strong>2.04</strong><br> 24/8/05
3715 <li>Hold down mouse wheel & scroll to change font
3721 <li>Improved JPred client reliability</li>
3722 <li>Improved loading of Jalview files</li>
3728 <div align="center">
3729 <strong>2.03</strong><br> 18/8/05
3734 <li>Set Proxy server name and port in preferences</li>
3735 <li>Multiple URL links from sequence ids</li>
3736 <li>User Defined Colours can have a scheme name and added
3738 <li>Choose to ignore gaps in consensus calculation</li>
3739 <li>Unix users can set default web browser</li>
3740 <li>Runs without GUI for batch processing</li>
3741 <li>Dynamically generated Web Service Menus</li>
3746 <li>InstallAnywhere download for Sparc Solaris</li>
3752 <div align="center">
3753 <strong>2.02</strong><br> 18/7/05
3759 <li>Copy & Paste order of sequences maintains
3760 alignment order.</li>
3766 <div align="center">
3767 <strong>2.01</strong><br> 12/7/05
3772 <li>Use delete key for deleting selection.</li>
3773 <li>Use Mouse wheel to scroll sequences.</li>
3774 <li>Help file updated to describe how to add alignment
3776 <li>Version and build date written to build properties
3778 <li>InstallAnywhere installation will check for updates
3779 at launch of Jalview.</li>
3784 <li>Delete gaps bug fixed.</li>
3785 <li>FileChooser sorts columns.</li>
3786 <li>Can remove groups one by one.</li>
3787 <li>Filechooser icons installed.</li>
3788 <li>Finder ignores return character when searching.
3789 Return key will initiate a search.<br>
3796 <div align="center">
3797 <strong>2.0</strong><br> 20/6/05
3802 <li>New codebase</li>