3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
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27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>1/05/2018</em></strong>
76 <td><div align="left">
80 <!-- JAL-1847 JAL-2944 -->Structure Chooser controls to
81 control superposition of multiple structures and open
82 structures in existing views
85 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
86 ID and annotation area margins can be click-dragged to
90 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
94 <!-- JAL-2759 -->Improved performance for large alignments
95 and lots of hidden columns
100 <td><div align="left">
103 <!-- JAL-2778 -->Slow redraw when Overview panel shown
104 overlapping alignment panel
107 <!-- JAL-2666 -->Linked scrolling via protein horizontal
108 scroll bar doesn't work for some CDS/Protein views
111 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
112 Java 1.8u153 onwards and Java 1.9u4+.
115 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
116 columns in annotation row
119 <!-- JAL-2913 -->Preferences panel's ID Width control is
120 honored in interactive and batch mode
123 <!-- JAL-2223 -->'View Mappings' includes duplicate
124 entries after importing project with multiple views
127 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
128 protein sequences via SIFTS from associated PDB entries
129 with negative residue numbers or missing residues fails
131 <li><em>New Defects</em>
134 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
135 structures for protein subsequence (if 'Trim Retrieved
136 Sequences' enabled) or Ensembl isoforms (Workaround in
137 2.10.4 is to fail back to N&W mapping)
144 <!-- JAL-2926 -->Copy consensus sequence option in applet
145 should copy the group consensus when popup is opened on it
153 <td width="60" nowrap>
155 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
158 <td><div align="left">
159 <ul><li>Updated Certum Codesigning Certificate
160 (Valid till 30th November 2018)</li></ul></div></td>
161 <td><div align="left">
164 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
165 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
166 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
167 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
168 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
169 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
170 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
176 <td width="60" nowrap>
178 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
181 <td><div align="left">
185 <!-- JAL-2446 -->Faster and more efficient management and
186 rendering of sequence features
189 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
190 429 rate limit request hander
193 <!-- JAL-2773 -->Structure views don't get updated unless
194 their colours have changed
197 <!-- JAL-2495 -->All linked sequences are highlighted for
198 a structure mousover (Jmol) or selection (Chimera)
201 <!-- JAL-2790 -->'Cancel' button in progress bar for
202 JABAWS AACon, RNAAliFold and Disorder prediction jobs
205 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
206 view from Ensembl locus cross-references
209 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
213 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
214 feature can be disabled
217 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
218 PDB easier retrieval of sequences for lists of IDs
221 <!-- JAL-2758 -->Short names for sequences retrieved from
227 <li>Groovy interpreter updated to 2.4.12</li>
228 <li>Example groovy script for generating a matrix of
229 percent identity scores for current alignment.</li>
231 <em>Testing and Deployment</em>
234 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
238 <td><div align="left">
242 <!-- JAL-2643 -->Pressing tab after updating the colour
243 threshold text field doesn't trigger an update to the
247 <!-- JAL-2682 -->Race condition when parsing sequence ID
251 <!-- JAL-2608 -->Overview windows are also closed when
252 alignment window is closed
255 <!-- JAL-2548 -->Export of features doesn't always respect
259 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
260 takes a long time in Cursor mode
266 <!-- JAL-2777 -->Structures with whitespace chainCode
267 cannot be viewed in Chimera
270 <!-- JAL-2728 -->Protein annotation panel too high in
274 <!-- JAL-2757 -->Can't edit the query after the server
275 error warning icon is shown in Uniprot and PDB Free Text
279 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
282 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
285 <!-- JAL-2739 -->Hidden column marker in last column not
286 rendered when switching back from Wrapped to normal view
289 <!-- JAL-2768 -->Annotation display corrupted when
290 scrolling right in unwapped alignment view
293 <!-- JAL-2542 -->Existing features on subsequence
294 incorrectly relocated when full sequence retrieved from
298 <!-- JAL-2733 -->Last reported memory still shown when
299 Desktop->Show Memory is unticked (OSX only)
302 <!-- JAL-2658 -->Amend Features dialog doesn't allow
303 features of same type and group to be selected for
307 <!-- JAL-2524 -->Jalview becomes sluggish in wide
308 alignments when hidden columns are present
311 <!-- JAL-2392 -->Jalview freezes when loading and
312 displaying several structures
315 <!-- JAL-2732 -->Black outlines left after resizing or
319 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
320 within the Jalview desktop on OSX
323 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
324 when in wrapped alignment mode
327 <!-- JAL-2636 -->Scale mark not shown when close to right
328 hand end of alignment
331 <!-- JAL-2684 -->Pairwise alignment of selected regions of
332 each selected sequence do not have correct start/end
336 <!-- JAL-2793 -->Alignment ruler height set incorrectly
337 after canceling the Alignment Window's Font dialog
340 <!-- JAL-2036 -->Show cross-references not enabled after
341 restoring project until a new view is created
344 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
345 URL links appears when only default EMBL-EBI link is
346 configured (since 2.10.2b2)
349 <!-- JAL-2775 -->Overview redraws whole window when box
353 <!-- JAL-2225 -->Structure viewer doesn't map all chains
354 in a multi-chain structure when viewing alignment
355 involving more than one chain (since 2.10)
358 <!-- JAL-2811 -->Double residue highlights in cursor mode
359 if new selection moves alignment window
362 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
363 arrow key in cursor mode to pass hidden column marker
366 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
367 that produces correctly annotated transcripts and products
370 <!-- JAL-2776 -->Toggling a feature group after first time
371 doesn't update associated structure view
374 <em>Applet</em><br />
377 <!-- JAL-2687 -->Concurrent modification exception when
378 closing alignment panel
381 <em>BioJSON</em><br />
384 <!-- JAL-2546 -->BioJSON export does not preserve
385 non-positional features
388 <em>New Known Issues</em>
391 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
392 sequence features correctly (for many previous versions of
396 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
397 using cursor in wrapped panel other than top
400 <!-- JAL-2791 -->Select columns containing feature ignores
401 graduated colour threshold
404 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
405 always preserve numbering and sequence features
408 <em>Known Java 9 Issues</em>
411 <!-- JAL-2902 -->Groovy Console very slow to open and is
412 not responsive when entering characters (Webstart, Java
419 <td width="60" nowrap>
421 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
422 <em>2/10/2017</em></strong>
425 <td><div align="left">
426 <em>New features in Jalview Desktop</em>
429 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
431 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
435 <td><div align="left">
439 <td width="60" nowrap>
441 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
442 <em>7/9/2017</em></strong>
445 <td><div align="left">
449 <!-- JAL-2588 -->Show gaps in overview window by colouring
450 in grey (sequences used to be coloured grey, and gaps were
454 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
458 <!-- JAL-2587 -->Overview updates immediately on increase
459 in size and progress bar shown as higher resolution
460 overview is recalculated
465 <td><div align="left">
469 <!-- JAL-2664 -->Overview window redraws every hidden
470 column region row by row
473 <!-- JAL-2681 -->duplicate protein sequences shown after
474 retrieving Ensembl crossrefs for sequences from Uniprot
477 <!-- JAL-2603 -->Overview window throws NPE if show boxes
478 format setting is unticked
481 <!-- JAL-2610 -->Groups are coloured wrongly in overview
482 if group has show boxes format setting unticked
485 <!-- JAL-2672,JAL-2665 -->Redraw problems when
486 autoscrolling whilst dragging current selection group to
487 include sequences and columns not currently displayed
490 <!-- JAL-2691 -->Not all chains are mapped when multimeric
491 assemblies are imported via CIF file
494 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
495 displayed when threshold or conservation colouring is also
499 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
503 <!-- JAL-2673 -->Jalview continues to scroll after
504 dragging a selected region off the visible region of the
508 <!-- JAL-2724 -->Cannot apply annotation based
509 colourscheme to all groups in a view
512 <!-- JAL-2511 -->IDs don't line up with sequences
513 initially after font size change using the Font chooser or
520 <td width="60" nowrap>
522 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
525 <td><div align="left">
526 <em>Calculations</em>
530 <!-- JAL-1933 -->Occupancy annotation row shows number of
531 ungapped positions in each column of the alignment.
534 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
535 a calculation dialog box
538 <!-- JAL-2379 -->Revised implementation of PCA for speed
539 and memory efficiency (~30x faster)
542 <!-- JAL-2403 -->Revised implementation of sequence
543 similarity scores as used by Tree, PCA, Shading Consensus
544 and other calculations
547 <!-- JAL-2416 -->Score matrices are stored as resource
548 files within the Jalview codebase
551 <!-- JAL-2500 -->Trees computed on Sequence Feature
552 Similarity may have different topology due to increased
559 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
560 model for alignments and groups
563 <!-- JAL-384 -->Custom shading schemes created via groovy
570 <!-- JAL-2526 -->Efficiency improvements for interacting
571 with alignment and overview windows
574 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
578 <!-- JAL-2388 -->Hidden columns and sequences can be
582 <!-- JAL-2611 -->Click-drag in visible area allows fine
583 adjustment of visible position
587 <em>Data import/export</em>
590 <!-- JAL-2535 -->Posterior probability annotation from
591 Stockholm files imported as sequence associated annotation
594 <!-- JAL-2507 -->More robust per-sequence positional
595 annotation input/output via stockholm flatfile
598 <!-- JAL-2533 -->Sequence names don't include file
599 extension when importing structure files without embedded
600 names or PDB accessions
603 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
604 format sequence substitution matrices
607 <em>User Interface</em>
610 <!-- JAL-2447 --> Experimental Features Checkbox in
611 Desktop's Tools menu to hide or show untested features in
615 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
616 via Overview or sequence motif search operations
619 <!-- JAL-2547 -->Amend sequence features dialog box can be
620 opened by double clicking gaps within sequence feature
624 <!-- JAL-1476 -->Status bar message shown when not enough
625 aligned positions were available to create a 3D structure
629 <em>3D Structure</em>
632 <!-- JAL-2430 -->Hidden regions in alignment views are not
633 coloured in linked structure views
636 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
637 file-based command exchange
640 <!-- JAL-2375 -->Structure chooser automatically shows
641 Cached Structures rather than querying the PDBe if
642 structures are already available for sequences
645 <!-- JAL-2520 -->Structures imported via URL are cached in
646 the Jalview project rather than downloaded again when the
650 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
651 to transfer Chimera's structure attributes as Jalview
652 features, and vice-versa (<strong>Experimental
656 <em>Web Services</em>
659 <!-- JAL-2549 -->Updated JABAWS client to v2.2
662 <!-- JAL-2335 -->Filter non-standard amino acids and
663 nucleotides when submitting to AACon and other MSA
667 <!-- JAL-2316, -->URLs for viewing database
668 cross-references provided by identifiers.org and the
676 <!-- JAL-2344 -->FileFormatI interface for describing and
677 identifying file formats (instead of String constants)
680 <!-- JAL-2228 -->FeatureCounter script refactored for
681 efficiency when counting all displayed features (not
682 backwards compatible with 2.10.1)
685 <em>Example files</em>
688 <!-- JAL-2631 -->Graduated feature colour style example
689 included in the example feature file
692 <em>Documentation</em>
695 <!-- JAL-2339 -->Release notes reformatted for readability
696 with the built-in Java help viewer
699 <!-- JAL-1644 -->Find documentation updated with 'search
700 sequence description' option
706 <!-- JAL-2485, -->External service integration tests for
707 Uniprot REST Free Text Search Client
710 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
713 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
718 <td><div align="left">
719 <em>Calculations</em>
722 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
723 matrix - C->R should be '-3'<br />Old matrix restored
724 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
726 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
727 Jalview's treatment of gaps in PCA and substitution matrix
728 based Tree calculations.<br /> <br />In earlier versions
729 of Jalview, gaps matching gaps were penalised, and gaps
730 matching non-gaps penalised even more. In the PCA
731 calculation, gaps were actually treated as non-gaps - so
732 different costs were applied, which meant Jalview's PCAs
733 were different to those produced by SeqSpace.<br />Jalview
734 now treats gaps in the same way as SeqSpace (ie it scores
735 them as 0). <br /> <br />Enter the following in the
736 Groovy console to restore pre-2.10.2 behaviour:<br />
737 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
738 // for 2.10.1 mode <br />
739 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
740 // to restore 2.10.2 mode <br /> <br /> <em>Note:
741 these settings will affect all subsequent tree and PCA
742 calculations (not recommended)</em></li>
744 <!-- JAL-2424 -->Fixed off-by-one bug that affected
745 scaling of branch lengths for trees computed using
746 Sequence Feature Similarity.
749 <!-- JAL-2377 -->PCA calculation could hang when
750 generating output report when working with highly
754 <!-- JAL-2544 --> Sort by features includes features to
755 right of selected region when gaps present on right-hand
759 <em>User Interface</em>
762 <!-- JAL-2346 -->Reopening Colour by annotation dialog
763 doesn't reselect a specific sequence's associated
764 annotation after it was used for colouring a view
767 <!-- JAL-2419 -->Current selection lost if popup menu
768 opened on a region of alignment without groups
771 <!-- JAL-2374 -->Popup menu not always shown for regions
772 of an alignment with overlapping groups
775 <!-- JAL-2310 -->Finder double counts if both a sequence's
776 name and description match
779 <!-- JAL-2370 -->Hiding column selection containing two
780 hidden regions results in incorrect hidden regions
783 <!-- JAL-2386 -->'Apply to all groups' setting when
784 changing colour does not apply Conservation slider value
788 <!-- JAL-2373 -->Percentage identity and conservation menu
789 items do not show a tick or allow shading to be disabled
792 <!-- JAL-2385 -->Conservation shading or PID threshold
793 lost when base colourscheme changed if slider not visible
796 <!-- JAL-2547 -->Sequence features shown in tooltip for
797 gaps before start of features
800 <!-- JAL-2623 -->Graduated feature colour threshold not
801 restored to UI when feature colour is edited
804 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
805 a time when scrolling vertically in wrapped mode.
808 <!-- JAL-2630 -->Structure and alignment overview update
809 as graduate feature colour settings are modified via the
813 <!-- JAL-2034 -->Overview window doesn't always update
814 when a group defined on the alignment is resized
817 <!-- JAL-2605 -->Mouseovers on left/right scale region in
818 wrapped view result in positional status updates
822 <!-- JAL-2563 -->Status bar doesn't show position for
823 ambiguous amino acid and nucleotide symbols
826 <!-- JAL-2602 -->Copy consensus sequence failed if
827 alignment included gapped columns
830 <!-- JAL-2473 -->Minimum size set for Jalview windows so
831 widgets don't permanently disappear
834 <!-- JAL-2503 -->Cannot select or filter quantitative
835 annotation that are shown only as column labels (e.g.
836 T-Coffee column reliability scores)
839 <!-- JAL-2594 -->Exception thrown if trying to create a
840 sequence feature on gaps only
843 <!-- JAL-2504 -->Features created with 'New feature'
844 button from a Find inherit previously defined feature type
845 rather than the Find query string
848 <!-- JAL-2423 -->incorrect title in output window when
849 exporting tree calculated in Jalview
852 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
853 and then revealing them reorders sequences on the
857 <!-- JAL-964 -->Group panel in sequence feature settings
858 doesn't update to reflect available set of groups after
859 interactively adding or modifying features
862 <!-- JAL-2225 -->Sequence Database chooser unusable on
866 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
867 only excluded gaps in current sequence and ignored
874 <!-- JAL-2421 -->Overview window visible region moves
875 erratically when hidden rows or columns are present
878 <!-- JAL-2362 -->Per-residue colourschemes applied via the
879 Structure Viewer's colour menu don't correspond to
883 <!-- JAL-2405 -->Protein specific colours only offered in
884 colour and group colour menu for protein alignments
887 <!-- JAL-2385 -->Colour threshold slider doesn't update to
888 reflect currently selected view or group's shading
892 <!-- JAL-2624 -->Feature colour thresholds not respected
893 when rendered on overview and structures when opacity at
897 <!-- JAL-2589 -->User defined gap colour not shown in
898 overview when features overlaid on alignment
901 <em>Data import/export</em>
904 <!-- JAL-2576 -->Very large alignments take a long time to
908 <!-- JAL-2507 -->Per-sequence RNA secondary structures
909 added after a sequence was imported are not written to
913 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
914 when importing RNA secondary structure via Stockholm
917 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
918 not shown in correct direction for simple pseudoknots
921 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
922 with lightGray or darkGray via features file (but can
926 <!-- JAL-2383 -->Above PID colour threshold not recovered
927 when alignment view imported from project
930 <!-- JAL-2520,JAL-2465 -->No mappings generated between
931 structure and sequences extracted from structure files
932 imported via URL and viewed in Jmol
935 <!-- JAL-2520 -->Structures loaded via URL are saved in
936 Jalview Projects rather than fetched via URL again when
937 the project is loaded and the structure viewed
940 <em>Web Services</em>
943 <!-- JAL-2519 -->EnsemblGenomes example failing after
944 release of Ensembl v.88
947 <!-- JAL-2366 -->Proxy server address and port always
948 appear enabled in Preferences->Connections
951 <!-- JAL-2461 -->DAS registry not found exceptions
952 removed from console output
955 <!-- JAL-2582 -->Cannot retrieve protein products from
956 Ensembl by Peptide ID
959 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
960 created from SIFTs, and spurious 'Couldn't open structure
961 in Chimera' errors raised after April 2017 update (problem
962 due to 'null' string rather than empty string used for
963 residues with no corresponding PDB mapping).
966 <em>Application UI</em>
969 <!-- JAL-2361 -->User Defined Colours not added to Colour
973 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
974 case' residues (button in colourscheme editor debugged and
975 new documentation and tooltips added)
978 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
979 doesn't restore group-specific text colour thresholds
982 <!-- JAL-2243 -->Feature settings panel does not update as
983 new features are added to alignment
986 <!-- JAL-2532 -->Cancel in feature settings reverts
987 changes to feature colours via the Amend features dialog
990 <!-- JAL-2506 -->Null pointer exception when attempting to
991 edit graduated feature colour via amend features dialog
995 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
996 selection menu changes colours of alignment views
999 <!-- JAL-2426 -->Spurious exceptions in console raised
1000 from alignment calculation workers after alignment has
1004 <!-- JAL-1608 -->Typo in selection popup menu - Create
1005 groups now 'Create Group'
1008 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1009 Create/Undefine group doesn't always work
1012 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1013 shown again after pressing 'Cancel'
1016 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1017 adjusts start position in wrap mode
1020 <!-- JAL-2563 -->Status bar doesn't show positions for
1021 ambiguous amino acids
1024 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1025 CDS/Protein view after CDS sequences added for aligned
1029 <!-- JAL-2592 -->User defined colourschemes called 'User
1030 Defined' don't appear in Colours menu
1036 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1037 score models doesn't always result in an updated PCA plot
1040 <!-- JAL-2442 -->Features not rendered as transparent on
1041 overview or linked structure view
1044 <!-- JAL-2372 -->Colour group by conservation doesn't
1048 <!-- JAL-2517 -->Hitting Cancel after applying
1049 user-defined colourscheme doesn't restore original
1056 <!-- JAL-2314 -->Unit test failure:
1057 jalview.ws.jabaws.RNAStructExportImport setup fails
1060 <!-- JAL-2307 -->Unit test failure:
1061 jalview.ws.sifts.SiftsClientTest due to compatibility
1062 problems with deep array comparison equality asserts in
1063 successive versions of TestNG
1066 <!-- JAL-2479 -->Relocated StructureChooserTest and
1067 ParameterUtilsTest Unit tests to Network suite
1070 <em>New Known Issues</em>
1073 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1074 phase after a sequence motif find operation
1077 <!-- JAL-2550 -->Importing annotation file with rows
1078 containing just upper and lower case letters are
1079 interpreted as WUSS RNA secondary structure symbols
1082 <!-- JAL-2590 -->Cannot load and display Newick trees
1083 reliably from eggnog Ortholog database
1086 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1087 containing features of type Highlight' when 'B' is pressed
1088 to mark columns containing highlighted regions.
1091 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1092 doesn't always add secondary structure annotation.
1097 <td width="60" nowrap>
1098 <div align="center">
1099 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1102 <td><div align="left">
1106 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1107 for all consensus calculations
1110 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1113 <li>Updated Jalview's Certum code signing certificate
1116 <em>Application</em>
1119 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1120 set of database cross-references, sorted alphabetically
1123 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1124 from database cross references. Users with custom links
1125 will receive a <a href="webServices/urllinks.html#warning">warning
1126 dialog</a> asking them to update their preferences.
1129 <!-- JAL-2287-->Cancel button and escape listener on
1130 dialog warning user about disconnecting Jalview from a
1134 <!-- JAL-2320-->Jalview's Chimera control window closes if
1135 the Chimera it is connected to is shut down
1138 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1139 columns menu item to mark columns containing highlighted
1140 regions (e.g. from structure selections or results of a
1144 <!-- JAL-2284-->Command line option for batch-generation
1145 of HTML pages rendering alignment data with the BioJS
1155 <!-- JAL-2286 -->Columns with more than one modal residue
1156 are not coloured or thresholded according to percent
1157 identity (first observed in Jalview 2.8.2)
1160 <!-- JAL-2301 -->Threonine incorrectly reported as not
1164 <!-- JAL-2318 -->Updates to documentation pages (above PID
1165 threshold, amino acid properties)
1168 <!-- JAL-2292 -->Lower case residues in sequences are not
1169 reported as mapped to residues in a structure file in the
1173 <!--JAL-2324 -->Identical features with non-numeric scores
1174 could be added multiple times to a sequence
1177 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1178 bond features shown as two highlighted residues rather
1179 than a range in linked structure views, and treated
1180 correctly when selecting and computing trees from features
1183 <!-- JAL-2281-->Custom URL links for database
1184 cross-references are matched to database name regardless
1189 <em>Application</em>
1192 <!-- JAL-2282-->Custom URL links for specific database
1193 names without regular expressions also offer links from
1197 <!-- JAL-2315-->Removing a single configured link in the
1198 URL links pane in Connections preferences doesn't actually
1199 update Jalview configuration
1202 <!-- JAL-2272-->CTRL-Click on a selected region to open
1203 the alignment area popup menu doesn't work on El-Capitan
1206 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1207 files with similarly named sequences if dropped onto the
1211 <!-- JAL-2312 -->Additional mappings are shown for PDB
1212 entries where more chains exist in the PDB accession than
1213 are reported in the SIFTS file
1216 <!-- JAL-2317-->Certain structures do not get mapped to
1217 the structure view when displayed with Chimera
1220 <!-- JAL-2317-->No chains shown in the Chimera view
1221 panel's View->Show Chains submenu
1224 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1225 work for wrapped alignment views
1228 <!--JAL-2197 -->Rename UI components for running JPred
1229 predictions from 'JNet' to 'JPred'
1232 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1233 corrupted when annotation panel vertical scroll is not at
1234 first annotation row
1237 <!--JAL-2332 -->Attempting to view structure for Hen
1238 lysozyme results in a PDB Client error dialog box
1241 <!-- JAL-2319 -->Structure View's mapping report switched
1242 ranges for PDB and sequence for SIFTS
1245 SIFTS 'Not_Observed' residues mapped to non-existant
1249 <!-- <em>New Known Issues</em>
1256 <td width="60" nowrap>
1257 <div align="center">
1258 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1259 <em>25/10/2016</em></strong>
1262 <td><em>Application</em>
1264 <li>3D Structure chooser opens with 'Cached structures'
1265 view if structures already loaded</li>
1266 <li>Progress bar reports models as they are loaded to
1267 structure views</li>
1273 <li>Colour by conservation always enabled and no tick
1274 shown in menu when BLOSUM or PID shading applied</li>
1275 <li>FER1_ARATH and FER2_ARATH labels were switched in
1276 example sequences/projects/trees</li>
1278 <em>Application</em>
1280 <li>Jalview projects with views of local PDB structure
1281 files saved on Windows cannot be opened on OSX</li>
1282 <li>Multiple structure views can be opened and superposed
1283 without timeout for structures with multiple models or
1284 multiple sequences in alignment</li>
1285 <li>Cannot import or associated local PDB files without a
1286 PDB ID HEADER line</li>
1287 <li>RMSD is not output in Jmol console when superposition
1289 <li>Drag and drop of URL from Browser fails for Linux and
1290 OSX versions earlier than El Capitan</li>
1291 <li>ENA client ignores invalid content from ENA server</li>
1292 <li>Exceptions are not raised in console when ENA client
1293 attempts to fetch non-existent IDs via Fetch DB Refs UI
1295 <li>Exceptions are not raised in console when a new view
1296 is created on the alignment</li>
1297 <li>OSX right-click fixed for group selections: CMD-click
1298 to insert/remove gaps in groups and CTRL-click to open group
1301 <em>Build and deployment</em>
1303 <li>URL link checker now copes with multi-line anchor
1306 <em>New Known Issues</em>
1308 <li>Drag and drop from URL links in browsers do not work
1315 <td width="60" nowrap>
1316 <div align="center">
1317 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1320 <td><em>General</em>
1323 <!-- JAL-2124 -->Updated Spanish translations.
1326 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1327 for importing structure data to Jalview. Enables mmCIF and
1331 <!-- JAL-192 --->Alignment ruler shows positions relative to
1335 <!-- JAL-2202 -->Position/residue shown in status bar when
1336 mousing over sequence associated annotation
1339 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1343 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1344 '()', canonical '[]' and invalid '{}' base pair populations
1348 <!-- JAL-2092 -->Feature settings popup menu options for
1349 showing or hiding columns containing a feature
1352 <!-- JAL-1557 -->Edit selected group by double clicking on
1353 group and sequence associated annotation labels
1356 <!-- JAL-2236 -->Sequence name added to annotation label in
1357 select/hide columns by annotation and colour by annotation
1361 </ul> <em>Application</em>
1364 <!-- JAL-2050-->Automatically hide introns when opening a
1365 gene/transcript view
1368 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1372 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1373 structure mappings with the EMBL-EBI PDBe SIFTS database
1376 <!-- JAL-2079 -->Updated download sites used for Rfam and
1377 Pfam sources to xfam.org
1380 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1383 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1384 over sequences in Jalview
1387 <!-- JAL-2027-->Support for reverse-complement coding
1388 regions in ENA and EMBL
1391 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1392 for record retrieval via ENA rest API
1395 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1399 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1400 groovy script execution
1403 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1404 alignment window's Calculate menu
1407 <!-- JAL-1812 -->Allow groovy scripts that call
1408 Jalview.getAlignFrames() to run in headless mode
1411 <!-- JAL-2068 -->Support for creating new alignment
1412 calculation workers from groovy scripts
1415 <!-- JAL-1369 --->Store/restore reference sequence in
1419 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1420 associations are now saved/restored from project
1423 <!-- JAL-1993 -->Database selection dialog always shown
1424 before sequence fetcher is opened
1427 <!-- JAL-2183 -->Double click on an entry in Jalview's
1428 database chooser opens a sequence fetcher
1431 <!-- JAL-1563 -->Free-text search client for UniProt using
1432 the UniProt REST API
1435 <!-- JAL-2168 -->-nonews command line parameter to prevent
1436 the news reader opening
1439 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1440 querying stored in preferences
1443 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1447 <!-- JAL-1977-->Tooltips shown on database chooser
1450 <!-- JAL-391 -->Reverse complement function in calculate
1451 menu for nucleotide sequences
1454 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1455 and feature counts preserves alignment ordering (and
1456 debugged for complex feature sets).
1459 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1460 viewing structures with Jalview 2.10
1463 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1464 genome, transcript CCDS and gene ids via the Ensembl and
1465 Ensembl Genomes REST API
1468 <!-- JAL-2049 -->Protein sequence variant annotation
1469 computed for 'sequence_variant' annotation on CDS regions
1473 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1477 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1478 Ref Fetcher fails to match, or otherwise updates sequence
1479 data from external database records.
1482 <!-- JAL-2154 -->Revised Jalview Project format for
1483 efficient recovery of sequence coding and alignment
1484 annotation relationships.
1486 </ul> <!-- <em>Applet</em>
1497 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1501 <!-- JAL-2018-->Export features in Jalview format (again)
1502 includes graduated colourschemes
1505 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1506 working with big alignments and lots of hidden columns
1509 <!-- JAL-2053-->Hidden column markers not always rendered
1510 at right of alignment window
1513 <!-- JAL-2067 -->Tidied up links in help file table of
1517 <!-- JAL-2072 -->Feature based tree calculation not shown
1521 <!-- JAL-2075 -->Hidden columns ignored during feature
1522 based tree calculation
1525 <!-- JAL-2065 -->Alignment view stops updating when show
1526 unconserved enabled for group on alignment
1529 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1533 <!-- JAL-2146 -->Alignment column in status incorrectly
1534 shown as "Sequence position" when mousing over
1538 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1539 hidden columns present
1542 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1543 user created annotation added to alignment
1546 <!-- JAL-1841 -->RNA Structure consensus only computed for
1547 '()' base pair annotation
1550 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1551 in zero scores for all base pairs in RNA Structure
1555 <!-- JAL-2174-->Extend selection with columns containing
1559 <!-- JAL-2275 -->Pfam format writer puts extra space at
1560 beginning of sequence
1563 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1567 <!-- JAL-2238 -->Cannot create groups on an alignment from
1568 from a tree when t-coffee scores are shown
1571 <!-- JAL-1836,1967 -->Cannot import and view PDB
1572 structures with chains containing negative resnums (4q4h)
1575 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1579 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1580 to Clustal, PIR and PileUp output
1583 <!-- JAL-2008 -->Reordering sequence features that are
1584 not visible causes alignment window to repaint
1587 <!-- JAL-2006 -->Threshold sliders don't work in
1588 graduated colour and colour by annotation row for e-value
1589 scores associated with features and annotation rows
1592 <!-- JAL-1797 -->amino acid physicochemical conservation
1593 calculation should be case independent
1596 <!-- JAL-2173 -->Remove annotation also updates hidden
1600 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1601 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1602 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1605 <!-- JAL-2065 -->Null pointer exceptions and redraw
1606 problems when reference sequence defined and 'show
1607 non-conserved' enabled
1610 <!-- JAL-1306 -->Quality and Conservation are now shown on
1611 load even when Consensus calculation is disabled
1614 <!-- JAL-1932 -->Remove right on penultimate column of
1615 alignment does nothing
1618 <em>Application</em>
1621 <!-- JAL-1552-->URLs and links can't be imported by
1622 drag'n'drop on OSX when launched via webstart (note - not
1623 yet fixed for El Capitan)
1626 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1627 output when running on non-gb/us i18n platforms
1630 <!-- JAL-1944 -->Error thrown when exporting a view with
1631 hidden sequences as flat-file alignment
1634 <!-- JAL-2030-->InstallAnywhere distribution fails when
1638 <!-- JAL-2080-->Jalview very slow to launch via webstart
1639 (also hotfix for 2.9.0b2)
1642 <!-- JAL-2085 -->Cannot save project when view has a
1643 reference sequence defined
1646 <!-- JAL-1011 -->Columns are suddenly selected in other
1647 alignments and views when revealing hidden columns
1650 <!-- JAL-1989 -->Hide columns not mirrored in complement
1651 view in a cDNA/Protein splitframe
1654 <!-- JAL-1369 -->Cannot save/restore representative
1655 sequence from project when only one sequence is
1659 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1660 in Structure Chooser
1663 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1664 structure consensus didn't refresh annotation panel
1667 <!-- JAL-1962 -->View mapping in structure view shows
1668 mappings between sequence and all chains in a PDB file
1671 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1672 dialogs format columns correctly, don't display array
1673 data, sort columns according to type
1676 <!-- JAL-1975 -->Export complete shown after destination
1677 file chooser is cancelled during an image export
1680 <!-- JAL-2025 -->Error when querying PDB Service with
1681 sequence name containing special characters
1684 <!-- JAL-2024 -->Manual PDB structure querying should be
1688 <!-- JAL-2104 -->Large tooltips with broken HTML
1689 formatting don't wrap
1692 <!-- JAL-1128 -->Figures exported from wrapped view are
1693 truncated so L looks like I in consensus annotation
1696 <!-- JAL-2003 -->Export features should only export the
1697 currently displayed features for the current selection or
1701 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1702 after fetching cross-references, and restoring from
1706 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1707 followed in the structure viewer
1710 <!-- JAL-2163 -->Titles for individual alignments in
1711 splitframe not restored from project
1714 <!-- JAL-2145 -->missing autocalculated annotation at
1715 trailing end of protein alignment in transcript/product
1716 splitview when pad-gaps not enabled by default
1719 <!-- JAL-1797 -->amino acid physicochemical conservation
1723 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1724 article has been read (reopened issue due to
1725 internationalisation problems)
1728 <!-- JAL-1960 -->Only offer PDB structures in structure
1729 viewer based on sequence name, PDB and UniProt
1734 <!-- JAL-1976 -->No progress bar shown during export of
1738 <!-- JAL-2213 -->Structures not always superimposed after
1739 multiple structures are shown for one or more sequences.
1742 <!-- JAL-1370 -->Reference sequence characters should not
1743 be replaced with '.' when 'Show unconserved' format option
1747 <!-- JAL-1823 -->Cannot specify chain code when entering
1748 specific PDB id for sequence
1751 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1752 'Export hidden sequences' is enabled, but 'export hidden
1753 columns' is disabled.
1756 <!--JAL-2026-->Best Quality option in structure chooser
1757 selects lowest rather than highest resolution structures
1761 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1762 to sequence mapping in 'View Mappings' report
1765 <!-- JAL-2284 -->Unable to read old Jalview projects that
1766 contain non-XML data added after Jalvew wrote project.
1769 <!-- JAL-2118 -->Newly created annotation row reorders
1770 after clicking on it to create new annotation for a
1774 <!-- JAL-1980 -->Null Pointer Exception raised when
1775 pressing Add on an orphaned cut'n'paste window.
1777 <!-- may exclude, this is an external service stability issue JAL-1941
1778 -- > RNA 3D structure not added via DSSR service</li> -->
1783 <!-- JAL-2151 -->Incorrect columns are selected when
1784 hidden columns present before start of sequence
1787 <!-- JAL-1986 -->Missing dependencies on applet pages
1791 <!-- JAL-1947 -->Overview pixel size changes when
1792 sequences are hidden in applet
1795 <!-- JAL-1996 -->Updated instructions for applet
1796 deployment on examples pages.
1803 <td width="60" nowrap>
1804 <div align="center">
1805 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1806 <em>16/10/2015</em></strong>
1809 <td><em>General</em>
1811 <li>Time stamps for signed Jalview application and applet
1816 <em>Application</em>
1818 <li>Duplicate group consensus and conservation rows
1819 shown when tree is partitioned</li>
1820 <li>Erratic behaviour when tree partitions made with
1821 multiple cDNA/Protein split views</li>
1827 <td width="60" nowrap>
1828 <div align="center">
1829 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1830 <em>8/10/2015</em></strong>
1833 <td><em>General</em>
1835 <li>Updated Spanish translations of localized text for
1837 </ul> <em>Application</em>
1839 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1840 <li>Signed OSX InstallAnywhere installer<br></li>
1841 <li>Support for per-sequence based annotations in BioJSON</li>
1842 </ul> <em>Applet</em>
1844 <li>Split frame example added to applet examples page</li>
1845 </ul> <em>Build and Deployment</em>
1848 <!-- JAL-1888 -->New ant target for running Jalview's test
1856 <li>Mapping of cDNA to protein in split frames
1857 incorrect when sequence start > 1</li>
1858 <li>Broken images in filter column by annotation dialog
1860 <li>Feature colours not parsed from features file</li>
1861 <li>Exceptions and incomplete link URLs recovered when
1862 loading a features file containing HTML tags in feature
1866 <em>Application</em>
1868 <li>Annotations corrupted after BioJS export and
1870 <li>Incorrect sequence limits after Fetch DB References
1871 with 'trim retrieved sequences'</li>
1872 <li>Incorrect warning about deleting all data when
1873 deleting selected columns</li>
1874 <li>Patch to build system for shipping properly signed
1875 JNLP templates for webstart launch</li>
1876 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1877 unreleased structures for download or viewing</li>
1878 <li>Tab/space/return keystroke operation of EMBL-PDBe
1879 fetcher/viewer dialogs works correctly</li>
1880 <li>Disabled 'minimise' button on Jalview windows
1881 running on OSX to workaround redraw hang bug</li>
1882 <li>Split cDNA/Protein view position and geometry not
1883 recovered from jalview project</li>
1884 <li>Initial enabled/disabled state of annotation menu
1885 sorter 'show autocalculated first/last' corresponds to
1887 <li>Restoring of Clustal, RNA Helices and T-Coffee
1888 color schemes from BioJSON</li>
1892 <li>Reorder sequences mirrored in cDNA/Protein split
1894 <li>Applet with Jmol examples not loading correctly</li>
1900 <td><div align="center">
1901 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1903 <td><em>General</em>
1905 <li>Linked visualisation and analysis of DNA and Protein
1908 <li>Translated cDNA alignments shown as split protein
1909 and DNA alignment views</li>
1910 <li>Codon consensus annotation for linked protein and
1911 cDNA alignment views</li>
1912 <li>Link cDNA or Protein product sequences by loading
1913 them onto Protein or cDNA alignments</li>
1914 <li>Reconstruct linked cDNA alignment from aligned
1915 protein sequences</li>
1918 <li>Jmol integration updated to Jmol v14.2.14</li>
1919 <li>Import and export of Jalview alignment views as <a
1920 href="features/bioJsonFormat.html">BioJSON</a></li>
1921 <li>New alignment annotation file statements for
1922 reference sequences and marking hidden columns</li>
1923 <li>Reference sequence based alignment shading to
1924 highlight variation</li>
1925 <li>Select or hide columns according to alignment
1927 <li>Find option for locating sequences by description</li>
1928 <li>Conserved physicochemical properties shown in amino
1929 acid conservation row</li>
1930 <li>Alignments can be sorted by number of RNA helices</li>
1931 </ul> <em>Application</em>
1933 <li>New cDNA/Protein analysis capabilities
1935 <li>Get Cross-References should open a Split Frame
1936 view with cDNA/Protein</li>
1937 <li>Detect when nucleotide sequences and protein
1938 sequences are placed in the same alignment</li>
1939 <li>Split cDNA/Protein views are saved in Jalview
1944 <li>Use REST API to talk to Chimera</li>
1945 <li>Selected regions in Chimera are highlighted in linked
1946 Jalview windows</li>
1948 <li>VARNA RNA viewer updated to v3.93</li>
1949 <li>VARNA views are saved in Jalview Projects</li>
1950 <li>Pseudoknots displayed as Jalview RNA annotation can
1951 be shown in VARNA</li>
1953 <li>Make groups for selection uses marked columns as well
1954 as the active selected region</li>
1956 <li>Calculate UPGMA and NJ trees using sequence feature
1958 <li>New Export options
1960 <li>New Export Settings dialog to control hidden
1961 region export in flat file generation</li>
1963 <li>Export alignment views for display with the <a
1964 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1966 <li>Export scrollable SVG in HTML page</li>
1967 <li>Optional embedding of BioJSON data when exporting
1968 alignment figures to HTML</li>
1970 <li>3D structure retrieval and display
1972 <li>Free text and structured queries with the PDBe
1974 <li>PDBe Search API based discovery and selection of
1975 PDB structures for a sequence set</li>
1979 <li>JPred4 employed for protein secondary structure
1981 <li>Hide Insertions menu option to hide unaligned columns
1982 for one or a group of sequences</li>
1983 <li>Automatically hide insertions in alignments imported
1984 from the JPred4 web server</li>
1985 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1986 system on OSX<br />LGPL libraries courtesy of <a
1987 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1989 <li>changed 'View nucleotide structure' submenu to 'View
1990 VARNA 2D Structure'</li>
1991 <li>change "View protein structure" menu option to "3D
1994 </ul> <em>Applet</em>
1996 <li>New layout for applet example pages</li>
1997 <li>New parameters to enable SplitFrame view
1998 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1999 <li>New example demonstrating linked viewing of cDNA and
2000 Protein alignments</li>
2001 </ul> <em>Development and deployment</em>
2003 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2004 <li>Include installation type and git revision in build
2005 properties and console log output</li>
2006 <li>Jalview Github organisation, and new github site for
2007 storing BioJsMSA Templates</li>
2008 <li>Jalview's unit tests now managed with TestNG</li>
2011 <!-- <em>General</em>
2013 </ul> --> <!-- issues resolved --> <em>Application</em>
2015 <li>Escape should close any open find dialogs</li>
2016 <li>Typo in select-by-features status report</li>
2017 <li>Consensus RNA secondary secondary structure
2018 predictions are not highlighted in amber</li>
2019 <li>Missing gap character in v2.7 example file means
2020 alignment appears unaligned when pad-gaps is not enabled</li>
2021 <li>First switch to RNA Helices colouring doesn't colour
2022 associated structure views</li>
2023 <li>ID width preference option is greyed out when auto
2024 width checkbox not enabled</li>
2025 <li>Stopped a warning dialog from being shown when
2026 creating user defined colours</li>
2027 <li>'View Mapping' in structure viewer shows sequence
2028 mappings for just that viewer's sequences</li>
2029 <li>Workaround for superposing PDB files containing
2030 multiple models in Chimera</li>
2031 <li>Report sequence position in status bar when hovering
2032 over Jmol structure</li>
2033 <li>Cannot output gaps as '.' symbols with Selection ->
2034 output to text box</li>
2035 <li>Flat file exports of alignments with hidden columns
2036 have incorrect sequence start/end</li>
2037 <li>'Aligning' a second chain to a Chimera structure from
2039 <li>Colour schemes applied to structure viewers don't
2040 work for nucleotide</li>
2041 <li>Loading/cut'n'pasting an empty or invalid file leads
2042 to a grey/invisible alignment window</li>
2043 <li>Exported Jpred annotation from a sequence region
2044 imports to different position</li>
2045 <li>Space at beginning of sequence feature tooltips shown
2046 on some platforms</li>
2047 <li>Chimera viewer 'View | Show Chain' menu is not
2049 <li>'New View' fails with a Null Pointer Exception in
2050 console if Chimera has been opened</li>
2051 <li>Mouseover to Chimera not working</li>
2052 <li>Miscellaneous ENA XML feature qualifiers not
2054 <li>NPE in annotation renderer after 'Extract Scores'</li>
2055 <li>If two structures in one Chimera window, mouseover of
2056 either sequence shows on first structure</li>
2057 <li>'Show annotations' options should not make
2058 non-positional annotations visible</li>
2059 <li>Subsequence secondary structure annotation not shown
2060 in right place after 'view flanking regions'</li>
2061 <li>File Save As type unset when current file format is
2063 <li>Save as '.jar' option removed for saving Jalview
2065 <li>Colour by Sequence colouring in Chimera more
2067 <li>Cannot 'add reference annotation' for a sequence in
2068 several views on same alignment</li>
2069 <li>Cannot show linked products for EMBL / ENA records</li>
2070 <li>Jalview's tooltip wraps long texts containing no
2072 </ul> <em>Applet</em>
2074 <li>Jmol to JalviewLite mouseover/link not working</li>
2075 <li>JalviewLite can't import sequences with ID
2076 descriptions containing angle brackets</li>
2077 </ul> <em>General</em>
2079 <li>Cannot export and reimport RNA secondary structure
2080 via jalview annotation file</li>
2081 <li>Random helix colour palette for colour by annotation
2082 with RNA secondary structure</li>
2083 <li>Mouseover to cDNA from STOP residue in protein
2084 translation doesn't work.</li>
2085 <li>hints when using the select by annotation dialog box</li>
2086 <li>Jmol alignment incorrect if PDB file has alternate CA
2088 <li>FontChooser message dialog appears to hang after
2089 choosing 1pt font</li>
2090 <li>Peptide secondary structure incorrectly imported from
2091 annotation file when annotation display text includes 'e' or
2093 <li>Cannot set colour of new feature type whilst creating
2095 <li>cDNA translation alignment should not be sequence
2096 order dependent</li>
2097 <li>'Show unconserved' doesn't work for lower case
2099 <li>Nucleotide ambiguity codes involving R not recognised</li>
2100 </ul> <em>Deployment and Documentation</em>
2102 <li>Applet example pages appear different to the rest of
2103 www.jalview.org</li>
2104 </ul> <em>Application Known issues</em>
2106 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2107 <li>Misleading message appears after trying to delete
2109 <li>Jalview icon not shown in dock after InstallAnywhere
2110 version launches</li>
2111 <li>Fetching EMBL reference for an RNA sequence results
2112 fails with a sequence mismatch</li>
2113 <li>Corrupted or unreadable alignment display when
2114 scrolling alignment to right</li>
2115 <li>ArrayIndexOutOfBoundsException thrown when remove
2116 empty columns called on alignment with ragged gapped ends</li>
2117 <li>auto calculated alignment annotation rows do not get
2118 placed above or below non-autocalculated rows</li>
2119 <li>Jalview dekstop becomes sluggish at full screen in
2120 ultra-high resolution</li>
2121 <li>Cannot disable consensus calculation independently of
2122 quality and conservation</li>
2123 <li>Mouseover highlighting between cDNA and protein can
2124 become sluggish with more than one splitframe shown</li>
2125 </ul> <em>Applet Known Issues</em>
2127 <li>Core PDB parsing code requires Jmol</li>
2128 <li>Sequence canvas panel goes white when alignment
2129 window is being resized</li>
2135 <td><div align="center">
2136 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2138 <td><em>General</em>
2140 <li>Updated Java code signing certificate donated by
2142 <li>Features and annotation preserved when performing
2143 pairwise alignment</li>
2144 <li>RNA pseudoknot annotation can be
2145 imported/exported/displayed</li>
2146 <li>'colour by annotation' can colour by RNA and
2147 protein secondary structure</li>
2148 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2149 post-hoc with 2.9 release</em>)
2152 </ul> <em>Application</em>
2154 <li>Extract and display secondary structure for sequences
2155 with 3D structures</li>
2156 <li>Support for parsing RNAML</li>
2157 <li>Annotations menu for layout
2159 <li>sort sequence annotation rows by alignment</li>
2160 <li>place sequence annotation above/below alignment
2163 <li>Output in Stockholm format</li>
2164 <li>Internationalisation: improved Spanish (es)
2166 <li>Structure viewer preferences tab</li>
2167 <li>Disorder and Secondary Structure annotation tracks
2168 shared between alignments</li>
2169 <li>UCSF Chimera launch and linked highlighting from
2171 <li>Show/hide all sequence associated annotation rows for
2172 all or current selection</li>
2173 <li>disorder and secondary structure predictions
2174 available as dataset annotation</li>
2175 <li>Per-sequence rna helices colouring</li>
2178 <li>Sequence database accessions imported when fetching
2179 alignments from Rfam</li>
2180 <li>update VARNA version to 3.91</li>
2182 <li>New groovy scripts for exporting aligned positions,
2183 conservation values, and calculating sum of pairs scores.</li>
2184 <li>Command line argument to set default JABAWS server</li>
2185 <li>include installation type in build properties and
2186 console log output</li>
2187 <li>Updated Jalview project format to preserve dataset
2191 <!-- issues resolved --> <em>Application</em>
2193 <li>Distinguish alignment and sequence associated RNA
2194 structure in structure->view->VARNA</li>
2195 <li>Raise dialog box if user deletes all sequences in an
2197 <li>Pressing F1 results in documentation opening twice</li>
2198 <li>Sequence feature tooltip is wrapped</li>
2199 <li>Double click on sequence associated annotation
2200 selects only first column</li>
2201 <li>Redundancy removal doesn't result in unlinked
2202 leaves shown in tree</li>
2203 <li>Undos after several redundancy removals don't undo
2205 <li>Hide sequence doesn't hide associated annotation</li>
2206 <li>User defined colours dialog box too big to fit on
2207 screen and buttons not visible</li>
2208 <li>author list isn't updated if already written to
2209 Jalview properties</li>
2210 <li>Popup menu won't open after retrieving sequence
2212 <li>File open window for associate PDB doesn't open</li>
2213 <li>Left-then-right click on a sequence id opens a
2214 browser search window</li>
2215 <li>Cannot open sequence feature shading/sort popup menu
2216 in feature settings dialog</li>
2217 <li>better tooltip placement for some areas of Jalview
2219 <li>Allow addition of JABAWS Server which doesn't
2220 pass validation</li>
2221 <li>Web services parameters dialog box is too large to
2223 <li>Muscle nucleotide alignment preset obscured by
2225 <li>JABAWS preset submenus don't contain newly
2226 defined user preset</li>
2227 <li>MSA web services warns user if they were launched
2228 with invalid input</li>
2229 <li>Jalview cannot contact DAS Registy when running on
2232 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2233 'Superpose with' submenu not shown when new view
2237 </ul> <!-- <em>Applet</em>
2239 </ul> <em>General</em>
2241 </ul>--> <em>Deployment and Documentation</em>
2243 <li>2G and 1G options in launchApp have no effect on
2244 memory allocation</li>
2245 <li>launchApp service doesn't automatically open
2246 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2248 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2249 InstallAnywhere reports cannot find valid JVM when Java
2250 1.7_055 is available
2252 </ul> <em>Application Known issues</em>
2255 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2256 corrupted or unreadable alignment display when scrolling
2260 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2261 retrieval fails but progress bar continues for DAS retrieval
2262 with large number of ID
2265 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2266 flatfile output of visible region has incorrect sequence
2270 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2271 rna structure consensus doesn't update when secondary
2272 structure tracks are rearranged
2275 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2276 invalid rna structure positional highlighting does not
2277 highlight position of invalid base pairs
2280 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2281 out of memory errors are not raised when saving Jalview
2282 project from alignment window file menu
2285 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2286 Switching to RNA Helices colouring doesn't propagate to
2290 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2291 colour by RNA Helices not enabled when user created
2292 annotation added to alignment
2295 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2296 Jalview icon not shown on dock in Mountain Lion/Webstart
2298 </ul> <em>Applet Known Issues</em>
2301 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2302 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2305 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2306 Jalview and Jmol example not compatible with IE9
2309 <li>Sort by annotation score doesn't reverse order
2315 <td><div align="center">
2316 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2319 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2322 <li>Internationalisation of user interface (usually
2323 called i18n support) and translation for Spanish locale</li>
2324 <li>Define/Undefine group on current selection with
2325 Ctrl-G/Shift Ctrl-G</li>
2326 <li>Improved group creation/removal options in
2327 alignment/sequence Popup menu</li>
2328 <li>Sensible precision for symbol distribution
2329 percentages shown in logo tooltip.</li>
2330 <li>Annotation panel height set according to amount of
2331 annotation when alignment first opened</li>
2332 </ul> <em>Application</em>
2334 <li>Interactive consensus RNA secondary structure
2335 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2336 <li>Select columns containing particular features from
2337 Feature Settings dialog</li>
2338 <li>View all 'representative' PDB structures for selected
2340 <li>Update Jalview project format:
2342 <li>New file extension for Jalview projects '.jvp'</li>
2343 <li>Preserve sequence and annotation dataset (to
2344 store secondary structure annotation,etc)</li>
2345 <li>Per group and alignment annotation and RNA helix
2349 <li>New similarity measures for PCA and Tree calculation
2351 <li>Experimental support for retrieval and viewing of
2352 flanking regions for an alignment</li>
2356 <!-- issues resolved --> <em>Application</em>
2358 <li>logo keeps spinning and status remains at queued or
2359 running after job is cancelled</li>
2360 <li>cannot export features from alignments imported from
2361 Jalview/VAMSAS projects</li>
2362 <li>Buggy slider for web service parameters that take
2364 <li>Newly created RNA secondary structure line doesn't
2365 have 'display all symbols' flag set</li>
2366 <li>T-COFFEE alignment score shading scheme and other
2367 annotation shading not saved in Jalview project</li>
2368 <li>Local file cannot be loaded in freshly downloaded
2370 <li>Jalview icon not shown on dock in Mountain
2372 <li>Load file from desktop file browser fails</li>
2373 <li>Occasional NPE thrown when calculating large trees</li>
2374 <li>Cannot reorder or slide sequences after dragging an
2375 alignment onto desktop</li>
2376 <li>Colour by annotation dialog throws NPE after using
2377 'extract scores' function</li>
2378 <li>Loading/cut'n'pasting an empty file leads to a grey
2379 alignment window</li>
2380 <li>Disorder thresholds rendered incorrectly after
2381 performing IUPred disorder prediction</li>
2382 <li>Multiple group annotated consensus rows shown when
2383 changing 'normalise logo' display setting</li>
2384 <li>Find shows blank dialog after 'finished searching' if
2385 nothing matches query</li>
2386 <li>Null Pointer Exceptions raised when sorting by
2387 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2389 <li>Errors in Jmol console when structures in alignment
2390 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2392 <li>Not all working JABAWS services are shown in
2394 <li>JAVAWS version of Jalview fails to launch with
2395 'invalid literal/length code'</li>
2396 <li>Annotation/RNA Helix colourschemes cannot be applied
2397 to alignment with groups (actually fixed in 2.8.0b1)</li>
2398 <li>RNA Helices and T-Coffee Scores available as default
2401 </ul> <em>Applet</em>
2403 <li>Remove group option is shown even when selection is
2405 <li>Apply to all groups ticked but colourscheme changes
2406 don't affect groups</li>
2407 <li>Documented RNA Helices and T-Coffee Scores as valid
2408 colourscheme name</li>
2409 <li>Annotation labels drawn on sequence IDs when
2410 Annotation panel is not displayed</li>
2411 <li>Increased font size for dropdown menus on OSX and
2412 embedded windows</li>
2413 </ul> <em>Other</em>
2415 <li>Consensus sequence for alignments/groups with a
2416 single sequence were not calculated</li>
2417 <li>annotation files that contain only groups imported as
2418 annotation and junk sequences</li>
2419 <li>Fasta files with sequences containing '*' incorrectly
2420 recognised as PFAM or BLC</li>
2421 <li>conservation/PID slider apply all groups option
2422 doesn't affect background (2.8.0b1)
2424 <li>redundancy highlighting is erratic at 0% and 100%</li>
2425 <li>Remove gapped columns fails for sequences with ragged
2427 <li>AMSA annotation row with leading spaces is not
2428 registered correctly on import</li>
2429 <li>Jalview crashes when selecting PCA analysis for
2430 certain alignments</li>
2431 <li>Opening the colour by annotation dialog for an
2432 existing annotation based 'use original colours'
2433 colourscheme loses original colours setting</li>
2438 <td><div align="center">
2439 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2440 <em>30/1/2014</em></strong>
2444 <li>Trusted certificates for JalviewLite applet and
2445 Jalview Desktop application<br />Certificate was donated by
2446 <a href="https://www.certum.eu">Certum</a> to the Jalview
2447 open source project).
2449 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2450 <li>Output in Stockholm format</li>
2451 <li>Allow import of data from gzipped files</li>
2452 <li>Export/import group and sequence associated line
2453 graph thresholds</li>
2454 <li>Nucleotide substitution matrix that supports RNA and
2455 ambiguity codes</li>
2456 <li>Allow disorder predictions to be made on the current
2457 selection (or visible selection) in the same way that JPred
2459 <li>Groovy scripting for headless Jalview operation</li>
2460 </ul> <em>Other improvements</em>
2462 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2463 <li>COMBINE statement uses current SEQUENCE_REF and
2464 GROUP_REF scope to group annotation rows</li>
2465 <li>Support '' style escaping of quotes in Newick
2467 <li>Group options for JABAWS service by command line name</li>
2468 <li>Empty tooltip shown for JABA service options with a
2469 link but no description</li>
2470 <li>Select primary source when selecting authority in
2471 database fetcher GUI</li>
2472 <li>Add .mfa to FASTA file extensions recognised by
2474 <li>Annotation label tooltip text wrap</li>
2479 <li>Slow scrolling when lots of annotation rows are
2481 <li>Lots of NPE (and slowness) after creating RNA
2482 secondary structure annotation line</li>
2483 <li>Sequence database accessions not imported when
2484 fetching alignments from Rfam</li>
2485 <li>Incorrect SHMR submission for sequences with
2487 <li>View all structures does not always superpose
2489 <li>Option widgets in service parameters not updated to
2490 reflect user or preset settings</li>
2491 <li>Null pointer exceptions for some services without
2492 presets or adjustable parameters</li>
2493 <li>Discover PDB IDs entry in structure menu doesn't
2494 discover PDB xRefs</li>
2495 <li>Exception encountered while trying to retrieve
2496 features with DAS</li>
2497 <li>Lowest value in annotation row isn't coloured
2498 when colour by annotation (per sequence) is coloured</li>
2499 <li>Keyboard mode P jumps to start of gapped region when
2500 residue follows a gap</li>
2501 <li>Jalview appears to hang importing an alignment with
2502 Wrap as default or after enabling Wrap</li>
2503 <li>'Right click to add annotations' message
2504 shown in wrap mode when no annotations present</li>
2505 <li>Disorder predictions fail with NPE if no automatic
2506 annotation already exists on alignment</li>
2507 <li>oninit javascript function should be called after
2508 initialisation completes</li>
2509 <li>Remove redundancy after disorder prediction corrupts
2510 alignment window display</li>
2511 <li>Example annotation file in documentation is invalid</li>
2512 <li>Grouped line graph annotation rows are not exported
2513 to annotation file</li>
2514 <li>Multi-harmony analysis cannot be run when only two
2516 <li>Cannot create multiple groups of line graphs with
2517 several 'combine' statements in annotation file</li>
2518 <li>Pressing return several times causes Number Format
2519 exceptions in keyboard mode</li>
2520 <li>Multi-harmony (SHMMR) method doesn't submit
2521 correct partitions for input data</li>
2522 <li>Translation from DNA to Amino Acids fails</li>
2523 <li>Jalview fail to load newick tree with quoted label</li>
2524 <li>--headless flag isn't understood</li>
2525 <li>ClassCastException when generating EPS in headless
2527 <li>Adjusting sequence-associated shading threshold only
2528 changes one row's threshold</li>
2529 <li>Preferences and Feature settings panel panel
2530 doesn't open</li>
2531 <li>hide consensus histogram also hides conservation and
2532 quality histograms</li>
2537 <td><div align="center">
2538 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2540 <td><em>Application</em>
2542 <li>Support for JABAWS 2.0 Services (AACon alignment
2543 conservation, protein disorder and Clustal Omega)</li>
2544 <li>JABAWS server status indicator in Web Services
2546 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2547 in Jalview alignment window</li>
2548 <li>Updated Jalview build and deploy framework for OSX
2549 mountain lion, windows 7, and 8</li>
2550 <li>Nucleotide substitution matrix for PCA that supports
2551 RNA and ambiguity codes</li>
2553 <li>Improved sequence database retrieval GUI</li>
2554 <li>Support fetching and database reference look up
2555 against multiple DAS sources (Fetch all from in 'fetch db
2557 <li>Jalview project improvements
2559 <li>Store and retrieve the 'belowAlignment'
2560 flag for annotation</li>
2561 <li>calcId attribute to group annotation rows on the
2563 <li>Store AACon calculation settings for a view in
2564 Jalview project</li>
2568 <li>horizontal scrolling gesture support</li>
2569 <li>Visual progress indicator when PCA calculation is
2571 <li>Simpler JABA web services menus</li>
2572 <li>visual indication that web service results are still
2573 being retrieved from server</li>
2574 <li>Serialise the dialogs that are shown when Jalview
2575 starts up for first time</li>
2576 <li>Jalview user agent string for interacting with HTTP
2578 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2580 <li>Examples directory and Groovy library included in
2581 InstallAnywhere distribution</li>
2582 </ul> <em>Applet</em>
2584 <li>RNA alignment and secondary structure annotation
2585 visualization applet example</li>
2586 </ul> <em>General</em>
2588 <li>Normalise option for consensus sequence logo</li>
2589 <li>Reset button in PCA window to return dimensions to
2591 <li>Allow seqspace or Jalview variant of alignment PCA
2593 <li>PCA with either nucleic acid and protein substitution
2595 <li>Allow windows containing HTML reports to be exported
2597 <li>Interactive display and editing of RNA secondary
2598 structure contacts</li>
2599 <li>RNA Helix Alignment Colouring</li>
2600 <li>RNA base pair logo consensus</li>
2601 <li>Parse sequence associated secondary structure
2602 information in Stockholm files</li>
2603 <li>HTML Export database accessions and annotation
2604 information presented in tooltip for sequences</li>
2605 <li>Import secondary structure from LOCARNA clustalw
2606 style RNA alignment files</li>
2607 <li>import and visualise T-COFFEE quality scores for an
2609 <li>'colour by annotation' per sequence option to
2610 shade each sequence according to its associated alignment
2612 <li>New Jalview Logo</li>
2613 </ul> <em>Documentation and Development</em>
2615 <li>documentation for score matrices used in Jalview</li>
2616 <li>New Website!</li>
2618 <td><em>Application</em>
2620 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2621 wsdbfetch REST service</li>
2622 <li>Stop windows being moved outside desktop on OSX</li>
2623 <li>Filetype associations not installed for webstart
2625 <li>Jalview does not always retrieve progress of a JABAWS
2626 job execution in full once it is complete</li>
2627 <li>revise SHMR RSBS definition to ensure alignment is
2628 uploaded via ali_file parameter</li>
2629 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2630 <li>View all structures superposed fails with exception</li>
2631 <li>Jnet job queues forever if a very short sequence is
2632 submitted for prediction</li>
2633 <li>Cut and paste menu not opened when mouse clicked on
2635 <li>Putting fractional value into integer text box in
2636 alignment parameter dialog causes Jalview to hang</li>
2637 <li>Structure view highlighting doesn't work on
2639 <li>View all structures fails with exception shown in
2641 <li>Characters in filename associated with PDBEntry not
2642 escaped in a platform independent way</li>
2643 <li>Jalview desktop fails to launch with exception when
2645 <li>Tree calculation reports 'you must have 2 or more
2646 sequences selected' when selection is empty</li>
2647 <li>Jalview desktop fails to launch with jar signature
2648 failure when java web start temporary file caching is
2650 <li>DAS Sequence retrieval with range qualification
2651 results in sequence xref which includes range qualification</li>
2652 <li>Errors during processing of command line arguments
2653 cause progress bar (JAL-898) to be removed</li>
2654 <li>Replace comma for semi-colon option not disabled for
2655 DAS sources in sequence fetcher</li>
2656 <li>Cannot close news reader when JABAWS server warning
2657 dialog is shown</li>
2658 <li>Option widgets not updated to reflect user settings</li>
2659 <li>Edited sequence not submitted to web service</li>
2660 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2661 <li>InstallAnywhere installer doesn't unpack and run
2662 on OSX Mountain Lion</li>
2663 <li>Annotation panel not given a scroll bar when
2664 sequences with alignment annotation are pasted into the
2666 <li>Sequence associated annotation rows not associated
2667 when loaded from Jalview project</li>
2668 <li>Browser launch fails with NPE on java 1.7</li>
2669 <li>JABAWS alignment marked as finished when job was
2670 cancelled or job failed due to invalid input</li>
2671 <li>NPE with v2.7 example when clicking on Tree
2672 associated with all views</li>
2673 <li>Exceptions when copy/paste sequences with grouped
2674 annotation rows to new window</li>
2675 </ul> <em>Applet</em>
2677 <li>Sequence features are momentarily displayed before
2678 they are hidden using hidefeaturegroups applet parameter</li>
2679 <li>loading features via javascript API automatically
2680 enables feature display</li>
2681 <li>scrollToColumnIn javascript API method doesn't
2683 </ul> <em>General</em>
2685 <li>Redundancy removal fails for rna alignment</li>
2686 <li>PCA calculation fails when sequence has been selected
2687 and then deselected</li>
2688 <li>PCA window shows grey box when first opened on OSX</li>
2689 <li>Letters coloured pink in sequence logo when alignment
2690 coloured with clustalx</li>
2691 <li>Choosing fonts without letter symbols defined causes
2692 exceptions and redraw errors</li>
2693 <li>Initial PCA plot view is not same as manually
2694 reconfigured view</li>
2695 <li>Grouped annotation graph label has incorrect line
2697 <li>Grouped annotation graph label display is corrupted
2698 for lots of labels</li>
2703 <div align="center">
2704 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2707 <td><em>Application</em>
2709 <li>Jalview Desktop News Reader</li>
2710 <li>Tweaked default layout of web services menu</li>
2711 <li>View/alignment association menu to enable user to
2712 easily specify which alignment a multi-structure view takes
2713 its colours/correspondences from</li>
2714 <li>Allow properties file location to be specified as URL</li>
2715 <li>Extend Jalview project to preserve associations
2716 between many alignment views and a single Jmol display</li>
2717 <li>Store annotation row height in Jalview project file</li>
2718 <li>Annotation row column label formatting attributes
2719 stored in project file</li>
2720 <li>Annotation row order for auto-calculated annotation
2721 rows preserved in Jalview project file</li>
2722 <li>Visual progress indication when Jalview state is
2723 saved using Desktop window menu</li>
2724 <li>Visual indication that command line arguments are
2725 still being processed</li>
2726 <li>Groovy script execution from URL</li>
2727 <li>Colour by annotation default min and max colours in
2729 <li>Automatically associate PDB files dragged onto an
2730 alignment with sequences that have high similarity and
2732 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2733 <li>'view structures' option to open many
2734 structures in same window</li>
2735 <li>Sort associated views menu option for tree panel</li>
2736 <li>Group all JABA and non-JABA services for a particular
2737 analysis function in its own submenu</li>
2738 </ul> <em>Applet</em>
2740 <li>Userdefined and autogenerated annotation rows for
2742 <li>Adjustment of alignment annotation pane height</li>
2743 <li>Annotation scrollbar for annotation panel</li>
2744 <li>Drag to reorder annotation rows in annotation panel</li>
2745 <li>'automaticScrolling' parameter</li>
2746 <li>Allow sequences with partial ID string matches to be
2747 annotated from GFF/Jalview features files</li>
2748 <li>Sequence logo annotation row in applet</li>
2749 <li>Absolute paths relative to host server in applet
2750 parameters are treated as such</li>
2751 <li>New in the JalviewLite javascript API:
2753 <li>JalviewLite.js javascript library</li>
2754 <li>Javascript callbacks for
2756 <li>Applet initialisation</li>
2757 <li>Sequence/alignment mouse-overs and selections</li>
2760 <li>scrollTo row and column alignment scrolling
2762 <li>Select sequence/alignment regions from javascript</li>
2763 <li>javascript structure viewer harness to pass
2764 messages between Jmol and Jalview when running as
2765 distinct applets</li>
2766 <li>sortBy method</li>
2767 <li>Set of applet and application examples shipped
2768 with documentation</li>
2769 <li>New example to demonstrate JalviewLite and Jmol
2770 javascript message exchange</li>
2772 </ul> <em>General</em>
2774 <li>Enable Jmol displays to be associated with multiple
2775 multiple alignments</li>
2776 <li>Option to automatically sort alignment with new tree</li>
2777 <li>User configurable link to enable redirects to a
2778 www.Jalview.org mirror</li>
2779 <li>Jmol colours option for Jmol displays</li>
2780 <li>Configurable newline string when writing alignment
2781 and other flat files</li>
2782 <li>Allow alignment annotation description lines to
2783 contain html tags</li>
2784 </ul> <em>Documentation and Development</em>
2786 <li>Add groovy test harness for bulk load testing to
2788 <li>Groovy script to load and align a set of sequences
2789 using a web service before displaying the result in the
2790 Jalview desktop</li>
2791 <li>Restructured javascript and applet api documentation</li>
2792 <li>Ant target to publish example html files with applet
2794 <li>Netbeans project for building Jalview from source</li>
2795 <li>ant task to create online javadoc for Jalview source</li>
2797 <td><em>Application</em>
2799 <li>User defined colourscheme throws exception when
2800 current built in colourscheme is saved as new scheme</li>
2801 <li>AlignFrame->Save in application pops up save
2802 dialog for valid filename/format</li>
2803 <li>Cannot view associated structure for UniProt sequence</li>
2804 <li>PDB file association breaks for UniProt sequence
2806 <li>Associate PDB from file dialog does not tell you
2807 which sequence is to be associated with the file</li>
2808 <li>Find All raises null pointer exception when query
2809 only matches sequence IDs</li>
2810 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2811 <li>Jalview project with Jmol views created with Jalview
2812 2.4 cannot be loaded</li>
2813 <li>Filetype associations not installed for webstart
2815 <li>Two or more chains in a single PDB file associated
2816 with sequences in different alignments do not get coloured
2817 by their associated sequence</li>
2818 <li>Visibility status of autocalculated annotation row
2819 not preserved when project is loaded</li>
2820 <li>Annotation row height and visibility attributes not
2821 stored in Jalview project</li>
2822 <li>Tree bootstraps are not preserved when saved as a
2823 Jalview project</li>
2824 <li>Envision2 workflow tooltips are corrupted</li>
2825 <li>Enabling show group conservation also enables colour
2826 by conservation</li>
2827 <li>Duplicate group associated conservation or consensus
2828 created on new view</li>
2829 <li>Annotation scrollbar not displayed after 'show
2830 all hidden annotation rows' option selected</li>
2831 <li>Alignment quality not updated after alignment
2832 annotation row is hidden then shown</li>
2833 <li>Preserve colouring of structures coloured by
2834 sequences in pre Jalview 2.7 projects</li>
2835 <li>Web service job parameter dialog is not laid out
2837 <li>Web services menu not refreshed after 'reset
2838 services' button is pressed in preferences</li>
2839 <li>Annotation off by one in Jalview v2_3 example project</li>
2840 <li>Structures imported from file and saved in project
2841 get name like jalview_pdb1234.txt when reloaded</li>
2842 <li>Jalview does not always retrieve progress of a JABAWS
2843 job execution in full once it is complete</li>
2844 </ul> <em>Applet</em>
2846 <li>Alignment height set incorrectly when lots of
2847 annotation rows are displayed</li>
2848 <li>Relative URLs in feature HTML text not resolved to
2850 <li>View follows highlighting does not work for positions
2852 <li><= shown as = in tooltip</li>
2853 <li>Export features raises exception when no features
2855 <li>Separator string used for serialising lists of IDs
2856 for javascript api is modified when separator string
2857 provided as parameter</li>
2858 <li>Null pointer exception when selecting tree leaves for
2859 alignment with no existing selection</li>
2860 <li>Relative URLs for datasources assumed to be relative
2861 to applet's codebase</li>
2862 <li>Status bar not updated after finished searching and
2863 search wraps around to first result</li>
2864 <li>StructureSelectionManager instance shared between
2865 several Jalview applets causes race conditions and memory
2867 <li>Hover tooltip and mouseover of position on structure
2868 not sent from Jmol in applet</li>
2869 <li>Certain sequences of javascript method calls to
2870 applet API fatally hang browser</li>
2871 </ul> <em>General</em>
2873 <li>View follows structure mouseover scrolls beyond
2874 position with wrapped view and hidden regions</li>
2875 <li>Find sequence position moves to wrong residue
2876 with/without hidden columns</li>
2877 <li>Sequence length given in alignment properties window
2879 <li>InvalidNumberFormat exceptions thrown when trying to
2880 import PDB like structure files</li>
2881 <li>Positional search results are only highlighted
2882 between user-supplied sequence start/end bounds</li>
2883 <li>End attribute of sequence is not validated</li>
2884 <li>Find dialog only finds first sequence containing a
2885 given sequence position</li>
2886 <li>Sequence numbering not preserved in MSF alignment
2888 <li>Jalview PDB file reader does not extract sequence
2889 from nucleotide chains correctly</li>
2890 <li>Structure colours not updated when tree partition
2891 changed in alignment</li>
2892 <li>Sequence associated secondary structure not correctly
2893 parsed in interleaved stockholm</li>
2894 <li>Colour by annotation dialog does not restore current
2896 <li>Hiding (nearly) all sequences doesn't work
2898 <li>Sequences containing lowercase letters are not
2899 properly associated with their pdb files</li>
2900 </ul> <em>Documentation and Development</em>
2902 <li>schemas/JalviewWsParamSet.xsd corrupted by
2903 ApplyCopyright tool</li>
2908 <div align="center">
2909 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2912 <td><em>Application</em>
2914 <li>New warning dialog when the Jalview Desktop cannot
2915 contact web services</li>
2916 <li>JABA service parameters for a preset are shown in
2917 service job window</li>
2918 <li>JABA Service menu entries reworded</li>
2922 <li>Modeller PIR IO broken - cannot correctly import a
2923 pir file emitted by Jalview</li>
2924 <li>Existing feature settings transferred to new
2925 alignment view created from cut'n'paste</li>
2926 <li>Improved test for mixed amino/nucleotide chains when
2927 parsing PDB files</li>
2928 <li>Consensus and conservation annotation rows
2929 occasionally become blank for all new windows</li>
2930 <li>Exception raised when right clicking above sequences
2931 in wrapped view mode</li>
2932 </ul> <em>Application</em>
2934 <li>multiple multiply aligned structure views cause cpu
2935 usage to hit 100% and computer to hang</li>
2936 <li>Web Service parameter layout breaks for long user
2937 parameter names</li>
2938 <li>Jaba service discovery hangs desktop if Jaba server
2945 <div align="center">
2946 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2949 <td><em>Application</em>
2951 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2952 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2955 <li>Web Services preference tab</li>
2956 <li>Analysis parameters dialog box and user defined
2958 <li>Improved speed and layout of Envision2 service menu</li>
2959 <li>Superpose structures using associated sequence
2961 <li>Export coordinates and projection as CSV from PCA
2963 </ul> <em>Applet</em>
2965 <li>enable javascript: execution by the applet via the
2966 link out mechanism</li>
2967 </ul> <em>Other</em>
2969 <li>Updated the Jmol Jalview interface to work with Jmol
2971 <li>The Jalview Desktop and JalviewLite applet now
2972 require Java 1.5</li>
2973 <li>Allow Jalview feature colour specification for GFF
2974 sequence annotation files</li>
2975 <li>New 'colour by label' keword in Jalview feature file
2976 type colour specification</li>
2977 <li>New Jalview Desktop Groovy API method that allows a
2978 script to check if it being run in an interactive session or
2979 in a batch operation from the Jalview command line</li>
2983 <li>clustalx colourscheme colours Ds preferentially when
2984 both D+E are present in over 50% of the column</li>
2985 </ul> <em>Application</em>
2987 <li>typo in AlignmentFrame->View->Hide->all but
2988 selected Regions menu item</li>
2989 <li>sequence fetcher replaces ',' for ';' when the ',' is
2990 part of a valid accession ID</li>
2991 <li>fatal OOM if object retrieved by sequence fetcher
2992 runs out of memory</li>
2993 <li>unhandled Out of Memory Error when viewing pca
2994 analysis results</li>
2995 <li>InstallAnywhere builds fail to launch on OS X java
2996 10.5 update 4 (due to apple Java 1.6 update)</li>
2997 <li>Installanywhere Jalview silently fails to launch</li>
2998 </ul> <em>Applet</em>
3000 <li>Jalview.getFeatureGroups() raises an
3001 ArrayIndexOutOfBoundsException if no feature groups are
3008 <div align="center">
3009 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3015 <li>Alignment prettyprinter doesn't cope with long
3017 <li>clustalx colourscheme colours Ds preferentially when
3018 both D+E are present in over 50% of the column</li>
3019 <li>nucleic acid structures retrieved from PDB do not
3020 import correctly</li>
3021 <li>More columns get selected than were clicked on when a
3022 number of columns are hidden</li>
3023 <li>annotation label popup menu not providing correct
3024 add/hide/show options when rows are hidden or none are
3026 <li>Stockholm format shown in list of readable formats,
3027 and parser copes better with alignments from RFAM.</li>
3028 <li>CSV output of consensus only includes the percentage
3029 of all symbols if sequence logo display is enabled</li>
3031 </ul> <em>Applet</em>
3033 <li>annotation panel disappears when annotation is
3035 </ul> <em>Application</em>
3037 <li>Alignment view not redrawn properly when new
3038 alignment opened where annotation panel is visible but no
3039 annotations are present on alignment</li>
3040 <li>pasted region containing hidden columns is
3041 incorrectly displayed in new alignment window</li>
3042 <li>Jalview slow to complete operations when stdout is
3043 flooded (fix is to close the Jalview console)</li>
3044 <li>typo in AlignmentFrame->View->Hide->all but
3045 selected Rregions menu item.</li>
3046 <li>inconsistent group submenu and Format submenu entry
3047 'Un' or 'Non'conserved</li>
3048 <li>Sequence feature settings are being shared by
3049 multiple distinct alignments</li>
3050 <li>group annotation not recreated when tree partition is
3052 <li>double click on group annotation to select sequences
3053 does not propagate to associated trees</li>
3054 <li>Mac OSX specific issues:
3056 <li>exception raised when mouse clicked on desktop
3057 window background</li>
3058 <li>Desktop menu placed on menu bar and application
3059 name set correctly</li>
3060 <li>sequence feature settings not wide enough for the
3061 save feature colourscheme button</li>
3070 <div align="center">
3071 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3074 <td><em>New Capabilities</em>
3076 <li>URL links generated from description line for
3077 regular-expression based URL links (applet and application)
3079 <li>Non-positional feature URL links are shown in link
3081 <li>Linked viewing of nucleic acid sequences and
3083 <li>Automatic Scrolling option in View menu to display
3084 the currently highlighted region of an alignment.</li>
3085 <li>Order an alignment by sequence length, or using the
3086 average score or total feature count for each sequence.</li>
3087 <li>Shading features by score or associated description</li>
3088 <li>Subdivide alignment and groups based on identity of
3089 selected subsequence (Make Groups from Selection).</li>
3090 <li>New hide/show options including Shift+Control+H to
3091 hide everything but the currently selected region.</li>
3092 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3093 </ul> <em>Application</em>
3095 <li>Fetch DB References capabilities and UI expanded to
3096 support retrieval from DAS sequence sources</li>
3097 <li>Local DAS Sequence sources can be added via the
3098 command line or via the Add local source dialog box.</li>
3099 <li>DAS Dbref and DbxRef feature types are parsed as
3100 database references and protein_name is parsed as
3101 description line (BioSapiens terms).</li>
3102 <li>Enable or disable non-positional feature and database
3103 references in sequence ID tooltip from View menu in
3105 <!-- <li>New hidden columns and rows and representatives capabilities
3106 in annotations file (in progress - not yet fully implemented)</li> -->
3107 <li>Group-associated consensus, sequence logos and
3108 conservation plots</li>
3109 <li>Symbol distributions for each column can be exported
3110 and visualized as sequence logos</li>
3111 <li>Optionally scale multi-character column labels to fit
3112 within each column of annotation row<!-- todo for applet -->
3114 <li>Optional automatic sort of associated alignment view
3115 when a new tree is opened.</li>
3116 <li>Jalview Java Console</li>
3117 <li>Better placement of desktop window when moving
3118 between different screens.</li>
3119 <li>New preference items for sequence ID tooltip and
3120 consensus annotation</li>
3121 <li>Client to submit sequences and IDs to Envision2
3123 <li><em>Vamsas Capabilities</em>
3125 <li>Improved VAMSAS synchronization (Jalview archive
3126 used to preserve views, structures, and tree display
3128 <li>Import of vamsas documents from disk or URL via
3130 <li>Sharing of selected regions between views and
3131 with other VAMSAS applications (Experimental feature!)</li>
3132 <li>Updated API to VAMSAS version 0.2</li>
3134 </ul> <em>Applet</em>
3136 <li>Middle button resizes annotation row height</li>
3139 <li>sortByTree (true/false) - automatically sort the
3140 associated alignment view by the tree when a new tree is
3142 <li>showTreeBootstraps (true/false) - show or hide
3143 branch bootstraps (default is to show them if available)</li>
3144 <li>showTreeDistances (true/false) - show or hide
3145 branch lengths (default is to show them if available)</li>
3146 <li>showUnlinkedTreeNodes (true/false) - indicate if
3147 unassociated nodes should be highlighted in the tree
3149 <li>heightScale and widthScale (1.0 or more) -
3150 increase the height or width of a cell in the alignment
3151 grid relative to the current font size.</li>
3154 <li>Non-positional features displayed in sequence ID
3156 </ul> <em>Other</em>
3158 <li>Features format: graduated colour definitions and
3159 specification of feature scores</li>
3160 <li>Alignment Annotations format: new keywords for group
3161 associated annotation (GROUP_REF) and annotation row display
3162 properties (ROW_PROPERTIES)</li>
3163 <li>XML formats extended to support graduated feature
3164 colourschemes, group associated annotation, and profile
3165 visualization settings.</li></td>
3168 <li>Source field in GFF files parsed as feature source
3169 rather than description</li>
3170 <li>Non-positional features are now included in sequence
3171 feature and gff files (controlled via non-positional feature
3172 visibility in tooltip).</li>
3173 <li>URL links generated for all feature links (bugfix)</li>
3174 <li>Added URL embedding instructions to features file
3176 <li>Codons containing ambiguous nucleotides translated as
3177 'X' in peptide product</li>
3178 <li>Match case switch in find dialog box works for both
3179 sequence ID and sequence string and query strings do not
3180 have to be in upper case to match case-insensitively.</li>
3181 <li>AMSA files only contain first column of
3182 multi-character column annotation labels</li>
3183 <li>Jalview Annotation File generation/parsing consistent
3184 with documentation (e.g. Stockholm annotation can be
3185 exported and re-imported)</li>
3186 <li>PDB files without embedded PDB IDs given a friendly
3188 <li>Find incrementally searches ID string matches as well
3189 as subsequence matches, and correctly reports total number
3193 <li>Better handling of exceptions during sequence
3195 <li>Dasobert generated non-positional feature URL
3196 link text excludes the start_end suffix</li>
3197 <li>DAS feature and source retrieval buttons disabled
3198 when fetch or registry operations in progress.</li>
3199 <li>PDB files retrieved from URLs are cached properly</li>
3200 <li>Sequence description lines properly shared via
3202 <li>Sequence fetcher fetches multiple records for all
3204 <li>Ensured that command line das feature retrieval
3205 completes before alignment figures are generated.</li>
3206 <li>Reduced time taken when opening file browser for
3208 <li>isAligned check prior to calculating tree, PCA or
3209 submitting an MSA to JNet now excludes hidden sequences.</li>
3210 <li>User defined group colours properly recovered
3211 from Jalview projects.</li>
3220 <div align="center">
3221 <strong>2.4.0.b2</strong><br> 28/10/2009
3226 <li>Experimental support for google analytics usage
3228 <li>Jalview privacy settings (user preferences and docs).</li>
3233 <li>Race condition in applet preventing startup in
3235 <li>Exception when feature created from selection beyond
3236 length of sequence.</li>
3237 <li>Allow synthetic PDB files to be imported gracefully</li>
3238 <li>Sequence associated annotation rows associate with
3239 all sequences with a given id</li>
3240 <li>Find function matches case-insensitively for sequence
3241 ID string searches</li>
3242 <li>Non-standard characters do not cause pairwise
3243 alignment to fail with exception</li>
3244 </ul> <em>Application Issues</em>
3246 <li>Sequences are now validated against EMBL database</li>
3247 <li>Sequence fetcher fetches multiple records for all
3249 </ul> <em>InstallAnywhere Issues</em>
3251 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3252 issue with installAnywhere mechanism)</li>
3253 <li>Command line launching of JARs from InstallAnywhere
3254 version (java class versioning error fixed)</li>
3261 <div align="center">
3262 <strong>2.4</strong><br> 27/8/2008
3265 <td><em>User Interface</em>
3267 <li>Linked highlighting of codon and amino acid from
3268 translation and protein products</li>
3269 <li>Linked highlighting of structure associated with
3270 residue mapping to codon position</li>
3271 <li>Sequence Fetcher provides example accession numbers
3272 and 'clear' button</li>
3273 <li>MemoryMonitor added as an option under Desktop's
3275 <li>Extract score function to parse whitespace separated
3276 numeric data in description line</li>
3277 <li>Column labels in alignment annotation can be centred.</li>
3278 <li>Tooltip for sequence associated annotation give name
3280 </ul> <em>Web Services and URL fetching</em>
3282 <li>JPred3 web service</li>
3283 <li>Prototype sequence search client (no public services
3285 <li>Fetch either seed alignment or full alignment from
3287 <li>URL Links created for matching database cross
3288 references as well as sequence ID</li>
3289 <li>URL Links can be created using regular-expressions</li>
3290 </ul> <em>Sequence Database Connectivity</em>
3292 <li>Retrieval of cross-referenced sequences from other
3294 <li>Generalised database reference retrieval and
3295 validation to all fetchable databases</li>
3296 <li>Fetch sequences from DAS sources supporting the
3297 sequence command</li>
3298 </ul> <em>Import and Export</em>
3299 <li>export annotation rows as CSV for spreadsheet import</li>
3300 <li>Jalview projects record alignment dataset associations,
3301 EMBL products, and cDNA sequence mappings</li>
3302 <li>Sequence Group colour can be specified in Annotation
3304 <li>Ad-hoc colouring of group in Annotation File using RGB
3305 triplet as name of colourscheme</li>
3306 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3308 <li>treenode binding for VAMSAS tree exchange</li>
3309 <li>local editing and update of sequences in VAMSAS
3310 alignments (experimental)</li>
3311 <li>Create new or select existing session to join</li>
3312 <li>load and save of vamsas documents</li>
3313 </ul> <em>Application command line</em>
3315 <li>-tree parameter to open trees (introduced for passing
3317 <li>-fetchfrom command line argument to specify nicknames
3318 of DAS servers to query for alignment features</li>
3319 <li>-dasserver command line argument to add new servers
3320 that are also automatically queried for features</li>
3321 <li>-groovy command line argument executes a given groovy
3322 script after all input data has been loaded and parsed</li>
3323 </ul> <em>Applet-Application data exchange</em>
3325 <li>Trees passed as applet parameters can be passed to
3326 application (when using "View in full
3327 application")</li>
3328 </ul> <em>Applet Parameters</em>
3330 <li>feature group display control parameter</li>
3331 <li>debug parameter</li>
3332 <li>showbutton parameter</li>
3333 </ul> <em>Applet API methods</em>
3335 <li>newView public method</li>
3336 <li>Window (current view) specific get/set public methods</li>
3337 <li>Feature display control methods</li>
3338 <li>get list of currently selected sequences</li>
3339 </ul> <em>New Jalview distribution features</em>
3341 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3342 <li>RELEASE file gives build properties for the latest
3343 Jalview release.</li>
3344 <li>Java 1.1 Applet build made easier and donotobfuscate
3345 property controls execution of obfuscator</li>
3346 <li>Build target for generating source distribution</li>
3347 <li>Debug flag for javacc</li>
3348 <li>.jalview_properties file is documented (slightly) in
3349 jalview.bin.Cache</li>
3350 <li>Continuous Build Integration for stable and
3351 development version of Application, Applet and source
3356 <li>selected region output includes visible annotations
3357 (for certain formats)</li>
3358 <li>edit label/displaychar contains existing label/char
3360 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3361 <li>shorter peptide product names from EMBL records</li>
3362 <li>Newick string generator makes compact representations</li>
3363 <li>bootstrap values parsed correctly for tree files with
3365 <li>pathological filechooser bug avoided by not allowing
3366 filenames containing a ':'</li>
3367 <li>Fixed exception when parsing GFF files containing
3368 global sequence features</li>
3369 <li>Alignment datasets are finalized only when number of
3370 references from alignment sequences goes to zero</li>
3371 <li>Close of tree branch colour box without colour
3372 selection causes cascading exceptions</li>
3373 <li>occasional negative imgwidth exceptions</li>
3374 <li>better reporting of non-fatal warnings to user when
3375 file parsing fails.</li>
3376 <li>Save works when Jalview project is default format</li>
3377 <li>Save as dialog opened if current alignment format is
3378 not a valid output format</li>
3379 <li>UniProt canonical names introduced for both das and
3381 <li>Histidine should be midblue (not pink!) in Zappo</li>
3382 <li>error messages passed up and output when data read
3384 <li>edit undo recovers previous dataset sequence when
3385 sequence is edited</li>
3386 <li>allow PDB files without pdb ID HEADER lines (like
3387 those generated by MODELLER) to be read in properly</li>
3388 <li>allow reading of JPred concise files as a normal
3390 <li>Stockholm annotation parsing and alignment properties
3391 import fixed for PFAM records</li>
3392 <li>Structure view windows have correct name in Desktop
3394 <li>annotation consisting of sequence associated scores
3395 can be read and written correctly to annotation file</li>
3396 <li>Aligned cDNA translation to aligned peptide works
3398 <li>Fixed display of hidden sequence markers and
3399 non-italic font for representatives in Applet</li>
3400 <li>Applet Menus are always embedded in applet window on
3402 <li>Newly shown features appear at top of stack (in
3404 <li>Annotations added via parameter not drawn properly
3405 due to null pointer exceptions</li>
3406 <li>Secondary structure lines are drawn starting from
3407 first column of alignment</li>
3408 <li>UniProt XML import updated for new schema release in
3410 <li>Sequence feature to sequence ID match for Features
3411 file is case-insensitive</li>
3412 <li>Sequence features read from Features file appended to
3413 all sequences with matching IDs</li>
3414 <li>PDB structure coloured correctly for associated views
3415 containing a sub-sequence</li>
3416 <li>PDB files can be retrieved by applet from Jar files</li>
3417 <li>feature and annotation file applet parameters
3418 referring to different directories are retrieved correctly</li>
3419 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3420 <li>Fixed application hang whilst waiting for
3421 splash-screen version check to complete</li>
3422 <li>Applet properly URLencodes input parameter values
3423 when passing them to the launchApp service</li>
3424 <li>display name and local features preserved in results
3425 retrieved from web service</li>
3426 <li>Visual delay indication for sequence retrieval and
3427 sequence fetcher initialisation</li>
3428 <li>updated Application to use DAS 1.53e version of
3429 dasobert DAS client</li>
3430 <li>Re-instated Full AMSA support and .amsa file
3432 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3440 <div align="center">
3441 <strong>2.3</strong><br> 9/5/07
3446 <li>Jmol 11.0.2 integration</li>
3447 <li>PDB views stored in Jalview XML files</li>
3448 <li>Slide sequences</li>
3449 <li>Edit sequence in place</li>
3450 <li>EMBL CDS features</li>
3451 <li>DAS Feature mapping</li>
3452 <li>Feature ordering</li>
3453 <li>Alignment Properties</li>
3454 <li>Annotation Scores</li>
3455 <li>Sort by scores</li>
3456 <li>Feature/annotation editing in applet</li>
3461 <li>Headless state operation in 2.2.1</li>
3462 <li>Incorrect and unstable DNA pairwise alignment</li>
3463 <li>Cut and paste of sequences with annotation</li>
3464 <li>Feature group display state in XML</li>
3465 <li>Feature ordering in XML</li>
3466 <li>blc file iteration selection using filename # suffix</li>
3467 <li>Stockholm alignment properties</li>
3468 <li>Stockhom alignment secondary structure annotation</li>
3469 <li>2.2.1 applet had no feature transparency</li>
3470 <li>Number pad keys can be used in cursor mode</li>
3471 <li>Structure Viewer mirror image resolved</li>
3478 <div align="center">
3479 <strong>2.2.1</strong><br> 12/2/07
3484 <li>Non standard characters can be read and displayed
3485 <li>Annotations/Features can be imported/exported to the
3487 <li>Applet allows editing of sequence/annotation/group
3488 name & description
3489 <li>Preference setting to display sequence name in
3491 <li>Annotation file format extended to allow
3492 Sequence_groups to be defined
3493 <li>Default opening of alignment overview panel can be
3494 specified in preferences
3495 <li>PDB residue numbering annotation added to associated
3501 <li>Applet crash under certain Linux OS with Java 1.6
3503 <li>Annotation file export / import bugs fixed
3504 <li>PNG / EPS image output bugs fixed
3510 <div align="center">
3511 <strong>2.2</strong><br> 27/11/06
3516 <li>Multiple views on alignment
3517 <li>Sequence feature editing
3518 <li>"Reload" alignment
3519 <li>"Save" to current filename
3520 <li>Background dependent text colour
3521 <li>Right align sequence ids
3522 <li>User-defined lower case residue colours
3525 <li>Menu item accelerator keys
3526 <li>Control-V pastes to current alignment
3527 <li>Cancel button for DAS Feature Fetching
3528 <li>PCA and PDB Viewers zoom via mouse roller
3529 <li>User-defined sub-tree colours and sub-tree selection
3531 <li>'New Window' button on the 'Output to Text box'
3536 <li>New memory efficient Undo/Redo System
3537 <li>Optimised symbol lookups and conservation/consensus
3539 <li>Region Conservation/Consensus recalculated after
3541 <li>Fixed Remove Empty Columns Bug (empty columns at end
3543 <li>Slowed DAS Feature Fetching for increased robustness.
3545 <li>Made angle brackets in ASCII feature descriptions
3547 <li>Re-instated Zoom function for PCA
3548 <li>Sequence descriptions conserved in web service
3550 <li>UniProt ID discoverer uses any word separated by
3552 <li>WsDbFetch query/result association resolved
3553 <li>Tree leaf to sequence mapping improved
3554 <li>Smooth fonts switch moved to FontChooser dialog box.
3561 <div align="center">
3562 <strong>2.1.1</strong><br> 12/9/06
3567 <li>Copy consensus sequence to clipboard</li>
3572 <li>Image output - rightmost residues are rendered if
3573 sequence id panel has been resized</li>
3574 <li>Image output - all offscreen group boundaries are
3576 <li>Annotation files with sequence references - all
3577 elements in file are relative to sequence position</li>
3578 <li>Mac Applet users can use Alt key for group editing</li>
3584 <div align="center">
3585 <strong>2.1</strong><br> 22/8/06
3590 <li>MAFFT Multiple Alignment in default Web Service list</li>
3591 <li>DAS Feature fetching</li>
3592 <li>Hide sequences and columns</li>
3593 <li>Export Annotations and Features</li>
3594 <li>GFF file reading / writing</li>
3595 <li>Associate structures with sequences from local PDB
3597 <li>Add sequences to exisiting alignment</li>
3598 <li>Recently opened files / URL lists</li>
3599 <li>Applet can launch the full application</li>
3600 <li>Applet has transparency for features (Java 1.2
3602 <li>Applet has user defined colours parameter</li>
3603 <li>Applet can load sequences from parameter
3604 "sequence<em>x</em>"
3610 <li>Redundancy Panel reinstalled in the Applet</li>
3611 <li>Monospaced font - EPS / rescaling bug fixed</li>
3612 <li>Annotation files with sequence references bug fixed</li>
3618 <div align="center">
3619 <strong>2.08.1</strong><br> 2/5/06
3624 <li>Change case of selected region from Popup menu</li>
3625 <li>Choose to match case when searching</li>
3626 <li>Middle mouse button and mouse movement can compress /
3627 expand the visible width and height of the alignment</li>
3632 <li>Annotation Panel displays complete JNet results</li>
3638 <div align="center">
3639 <strong>2.08b</strong><br> 18/4/06
3645 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3646 <li>Righthand label on wrapped alignments shows correct
3653 <div align="center">
3654 <strong>2.08</strong><br> 10/4/06
3659 <li>Editing can be locked to the selection area</li>
3660 <li>Keyboard editing</li>
3661 <li>Create sequence features from searches</li>
3662 <li>Precalculated annotations can be loaded onto
3664 <li>Features file allows grouping of features</li>
3665 <li>Annotation Colouring scheme added</li>
3666 <li>Smooth fonts off by default - Faster rendering</li>
3667 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3672 <li>Drag & Drop fixed on Linux</li>
3673 <li>Jalview Archive file faster to load/save, sequence
3674 descriptions saved.</li>
3680 <div align="center">
3681 <strong>2.07</strong><br> 12/12/05
3686 <li>PDB Structure Viewer enhanced</li>
3687 <li>Sequence Feature retrieval and display enhanced</li>
3688 <li>Choose to output sequence start-end after sequence
3689 name for file output</li>
3690 <li>Sequence Fetcher WSDBFetch@EBI</li>
3691 <li>Applet can read feature files, PDB files and can be
3692 used for HTML form input</li>
3697 <li>HTML output writes groups and features</li>
3698 <li>Group editing is Control and mouse click</li>
3699 <li>File IO bugs</li>
3705 <div align="center">
3706 <strong>2.06</strong><br> 28/9/05
3711 <li>View annotations in wrapped mode</li>
3712 <li>More options for PCA viewer</li>
3717 <li>GUI bugs resolved</li>
3718 <li>Runs with -nodisplay from command line</li>
3724 <div align="center">
3725 <strong>2.05b</strong><br> 15/9/05
3730 <li>Choose EPS export as lineart or text</li>
3731 <li>Jar files are executable</li>
3732 <li>Can read in Uracil - maps to unknown residue</li>
3737 <li>Known OutOfMemory errors give warning message</li>
3738 <li>Overview window calculated more efficiently</li>
3739 <li>Several GUI bugs resolved</li>
3745 <div align="center">
3746 <strong>2.05</strong><br> 30/8/05
3751 <li>Edit and annotate in "Wrapped" view</li>
3756 <li>Several GUI bugs resolved</li>
3762 <div align="center">
3763 <strong>2.04</strong><br> 24/8/05
3768 <li>Hold down mouse wheel & scroll to change font
3774 <li>Improved JPred client reliability</li>
3775 <li>Improved loading of Jalview files</li>
3781 <div align="center">
3782 <strong>2.03</strong><br> 18/8/05
3787 <li>Set Proxy server name and port in preferences</li>
3788 <li>Multiple URL links from sequence ids</li>
3789 <li>User Defined Colours can have a scheme name and added
3791 <li>Choose to ignore gaps in consensus calculation</li>
3792 <li>Unix users can set default web browser</li>
3793 <li>Runs without GUI for batch processing</li>
3794 <li>Dynamically generated Web Service Menus</li>
3799 <li>InstallAnywhere download for Sparc Solaris</li>
3805 <div align="center">
3806 <strong>2.02</strong><br> 18/7/05
3812 <li>Copy & Paste order of sequences maintains
3813 alignment order.</li>
3819 <div align="center">
3820 <strong>2.01</strong><br> 12/7/05
3825 <li>Use delete key for deleting selection.</li>
3826 <li>Use Mouse wheel to scroll sequences.</li>
3827 <li>Help file updated to describe how to add alignment
3829 <li>Version and build date written to build properties
3831 <li>InstallAnywhere installation will check for updates
3832 at launch of Jalview.</li>
3837 <li>Delete gaps bug fixed.</li>
3838 <li>FileChooser sorts columns.</li>
3839 <li>Can remove groups one by one.</li>
3840 <li>Filechooser icons installed.</li>
3841 <li>Finder ignores return character when searching.
3842 Return key will initiate a search.<br>
3849 <div align="center">
3850 <strong>2.0</strong><br> 20/6/05
3855 <li>New codebase</li>