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
98 <!-- JAL-2593 -->Improved performance when rendering lots
104 <td><div align="left">
107 <!-- JAL-2778 -->Slow redraw when Overview panel shown
108 overlapping alignment panel
111 <!-- JAL-2666 -->Linked scrolling via protein horizontal
112 scroll bar doesn't work for some CDS/Protein views
115 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
116 Java 1.8u153 onwards and Java 1.9u4+.
119 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
120 columns in annotation row
123 <!-- JAL-2913 -->Preferences panel's ID Width control is
124 honored in interactive and batch mode
127 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
128 for structures added to existing Jmol view
131 <!-- JAL-2223 -->'View Mappings' includes duplicate
132 entries after importing project with multiple views
135 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
136 protein sequences via SIFTS from associated PDB entries
137 with negative residue numbers or missing residues fails
140 <!-- JAL-2952 -->Exception when shading sequence with negative
141 Temperature Factor values from annotated PDB files (e.g.
142 as generated by CONSURF)
145 <!-- JAL-2954 -->Selecting columns from highlighted regions
146 very slow for alignments with large numbers of sequences
148 <li><em>New Defects</em>
151 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
152 structures for protein subsequence (if 'Trim Retrieved
153 Sequences' enabled) or Ensembl isoforms (Workaround in
154 2.10.4 is to fail back to N&W mapping)
161 <!-- JAL-2926 -->Copy consensus sequence option in applet
162 should copy the group consensus when popup is opened on it
170 <td width="60" nowrap>
172 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
175 <td><div align="left">
176 <ul><li>Updated Certum Codesigning Certificate
177 (Valid till 30th November 2018)</li></ul></div></td>
178 <td><div align="left">
181 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
182 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
183 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
184 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
185 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
186 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
187 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
193 <td width="60" nowrap>
195 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
198 <td><div align="left">
202 <!-- JAL-2446 -->Faster and more efficient management and
203 rendering of sequence features
206 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
207 429 rate limit request hander
210 <!-- JAL-2773 -->Structure views don't get updated unless
211 their colours have changed
214 <!-- JAL-2495 -->All linked sequences are highlighted for
215 a structure mousover (Jmol) or selection (Chimera)
218 <!-- JAL-2790 -->'Cancel' button in progress bar for
219 JABAWS AACon, RNAAliFold and Disorder prediction jobs
222 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
223 view from Ensembl locus cross-references
226 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
230 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
231 feature can be disabled
234 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
235 PDB easier retrieval of sequences for lists of IDs
238 <!-- JAL-2758 -->Short names for sequences retrieved from
244 <li>Groovy interpreter updated to 2.4.12</li>
245 <li>Example groovy script for generating a matrix of
246 percent identity scores for current alignment.</li>
248 <em>Testing and Deployment</em>
251 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
255 <td><div align="left">
259 <!-- JAL-2643 -->Pressing tab after updating the colour
260 threshold text field doesn't trigger an update to the
264 <!-- JAL-2682 -->Race condition when parsing sequence ID
268 <!-- JAL-2608 -->Overview windows are also closed when
269 alignment window is closed
272 <!-- JAL-2548 -->Export of features doesn't always respect
276 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
277 takes a long time in Cursor mode
283 <!-- JAL-2777 -->Structures with whitespace chainCode
284 cannot be viewed in Chimera
287 <!-- JAL-2728 -->Protein annotation panel too high in
291 <!-- JAL-2757 -->Can't edit the query after the server
292 error warning icon is shown in Uniprot and PDB Free Text
296 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
299 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
302 <!-- JAL-2739 -->Hidden column marker in last column not
303 rendered when switching back from Wrapped to normal view
306 <!-- JAL-2768 -->Annotation display corrupted when
307 scrolling right in unwapped alignment view
310 <!-- JAL-2542 -->Existing features on subsequence
311 incorrectly relocated when full sequence retrieved from
315 <!-- JAL-2733 -->Last reported memory still shown when
316 Desktop->Show Memory is unticked (OSX only)
319 <!-- JAL-2658 -->Amend Features dialog doesn't allow
320 features of same type and group to be selected for
324 <!-- JAL-2524 -->Jalview becomes sluggish in wide
325 alignments when hidden columns are present
328 <!-- JAL-2392 -->Jalview freezes when loading and
329 displaying several structures
332 <!-- JAL-2732 -->Black outlines left after resizing or
336 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
337 within the Jalview desktop on OSX
340 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
341 when in wrapped alignment mode
344 <!-- JAL-2636 -->Scale mark not shown when close to right
345 hand end of alignment
348 <!-- JAL-2684 -->Pairwise alignment of selected regions of
349 each selected sequence do not have correct start/end
353 <!-- JAL-2793 -->Alignment ruler height set incorrectly
354 after canceling the Alignment Window's Font dialog
357 <!-- JAL-2036 -->Show cross-references not enabled after
358 restoring project until a new view is created
361 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
362 URL links appears when only default EMBL-EBI link is
363 configured (since 2.10.2b2)
366 <!-- JAL-2775 -->Overview redraws whole window when box
370 <!-- JAL-2225 -->Structure viewer doesn't map all chains
371 in a multi-chain structure when viewing alignment
372 involving more than one chain (since 2.10)
375 <!-- JAL-2811 -->Double residue highlights in cursor mode
376 if new selection moves alignment window
379 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
380 arrow key in cursor mode to pass hidden column marker
383 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
384 that produces correctly annotated transcripts and products
387 <!-- JAL-2776 -->Toggling a feature group after first time
388 doesn't update associated structure view
391 <em>Applet</em><br />
394 <!-- JAL-2687 -->Concurrent modification exception when
395 closing alignment panel
398 <em>BioJSON</em><br />
401 <!-- JAL-2546 -->BioJSON export does not preserve
402 non-positional features
405 <em>New Known Issues</em>
408 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
409 sequence features correctly (for many previous versions of
413 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
414 using cursor in wrapped panel other than top
417 <!-- JAL-2791 -->Select columns containing feature ignores
418 graduated colour threshold
421 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
422 always preserve numbering and sequence features
425 <em>Known Java 9 Issues</em>
428 <!-- JAL-2902 -->Groovy Console very slow to open and is
429 not responsive when entering characters (Webstart, Java
436 <td width="60" nowrap>
438 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
439 <em>2/10/2017</em></strong>
442 <td><div align="left">
443 <em>New features in Jalview Desktop</em>
446 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
448 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
452 <td><div align="left">
456 <td width="60" nowrap>
458 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
459 <em>7/9/2017</em></strong>
462 <td><div align="left">
466 <!-- JAL-2588 -->Show gaps in overview window by colouring
467 in grey (sequences used to be coloured grey, and gaps were
471 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
475 <!-- JAL-2587 -->Overview updates immediately on increase
476 in size and progress bar shown as higher resolution
477 overview is recalculated
482 <td><div align="left">
486 <!-- JAL-2664 -->Overview window redraws every hidden
487 column region row by row
490 <!-- JAL-2681 -->duplicate protein sequences shown after
491 retrieving Ensembl crossrefs for sequences from Uniprot
494 <!-- JAL-2603 -->Overview window throws NPE if show boxes
495 format setting is unticked
498 <!-- JAL-2610 -->Groups are coloured wrongly in overview
499 if group has show boxes format setting unticked
502 <!-- JAL-2672,JAL-2665 -->Redraw problems when
503 autoscrolling whilst dragging current selection group to
504 include sequences and columns not currently displayed
507 <!-- JAL-2691 -->Not all chains are mapped when multimeric
508 assemblies are imported via CIF file
511 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
512 displayed when threshold or conservation colouring is also
516 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
520 <!-- JAL-2673 -->Jalview continues to scroll after
521 dragging a selected region off the visible region of the
525 <!-- JAL-2724 -->Cannot apply annotation based
526 colourscheme to all groups in a view
529 <!-- JAL-2511 -->IDs don't line up with sequences
530 initially after font size change using the Font chooser or
537 <td width="60" nowrap>
539 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
542 <td><div align="left">
543 <em>Calculations</em>
547 <!-- JAL-1933 -->Occupancy annotation row shows number of
548 ungapped positions in each column of the alignment.
551 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
552 a calculation dialog box
555 <!-- JAL-2379 -->Revised implementation of PCA for speed
556 and memory efficiency (~30x faster)
559 <!-- JAL-2403 -->Revised implementation of sequence
560 similarity scores as used by Tree, PCA, Shading Consensus
561 and other calculations
564 <!-- JAL-2416 -->Score matrices are stored as resource
565 files within the Jalview codebase
568 <!-- JAL-2500 -->Trees computed on Sequence Feature
569 Similarity may have different topology due to increased
576 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
577 model for alignments and groups
580 <!-- JAL-384 -->Custom shading schemes created via groovy
587 <!-- JAL-2526 -->Efficiency improvements for interacting
588 with alignment and overview windows
591 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
595 <!-- JAL-2388 -->Hidden columns and sequences can be
599 <!-- JAL-2611 -->Click-drag in visible area allows fine
600 adjustment of visible position
604 <em>Data import/export</em>
607 <!-- JAL-2535 -->Posterior probability annotation from
608 Stockholm files imported as sequence associated annotation
611 <!-- JAL-2507 -->More robust per-sequence positional
612 annotation input/output via stockholm flatfile
615 <!-- JAL-2533 -->Sequence names don't include file
616 extension when importing structure files without embedded
617 names or PDB accessions
620 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
621 format sequence substitution matrices
624 <em>User Interface</em>
627 <!-- JAL-2447 --> Experimental Features Checkbox in
628 Desktop's Tools menu to hide or show untested features in
632 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
633 via Overview or sequence motif search operations
636 <!-- JAL-2547 -->Amend sequence features dialog box can be
637 opened by double clicking gaps within sequence feature
641 <!-- JAL-1476 -->Status bar message shown when not enough
642 aligned positions were available to create a 3D structure
646 <em>3D Structure</em>
649 <!-- JAL-2430 -->Hidden regions in alignment views are not
650 coloured in linked structure views
653 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
654 file-based command exchange
657 <!-- JAL-2375 -->Structure chooser automatically shows
658 Cached Structures rather than querying the PDBe if
659 structures are already available for sequences
662 <!-- JAL-2520 -->Structures imported via URL are cached in
663 the Jalview project rather than downloaded again when the
667 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
668 to transfer Chimera's structure attributes as Jalview
669 features, and vice-versa (<strong>Experimental
673 <em>Web Services</em>
676 <!-- JAL-2549 -->Updated JABAWS client to v2.2
679 <!-- JAL-2335 -->Filter non-standard amino acids and
680 nucleotides when submitting to AACon and other MSA
684 <!-- JAL-2316, -->URLs for viewing database
685 cross-references provided by identifiers.org and the
693 <!-- JAL-2344 -->FileFormatI interface for describing and
694 identifying file formats (instead of String constants)
697 <!-- JAL-2228 -->FeatureCounter script refactored for
698 efficiency when counting all displayed features (not
699 backwards compatible with 2.10.1)
702 <em>Example files</em>
705 <!-- JAL-2631 -->Graduated feature colour style example
706 included in the example feature file
709 <em>Documentation</em>
712 <!-- JAL-2339 -->Release notes reformatted for readability
713 with the built-in Java help viewer
716 <!-- JAL-1644 -->Find documentation updated with 'search
717 sequence description' option
723 <!-- JAL-2485, -->External service integration tests for
724 Uniprot REST Free Text Search Client
727 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
730 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
735 <td><div align="left">
736 <em>Calculations</em>
739 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
740 matrix - C->R should be '-3'<br />Old matrix restored
741 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
743 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
744 Jalview's treatment of gaps in PCA and substitution matrix
745 based Tree calculations.<br /> <br />In earlier versions
746 of Jalview, gaps matching gaps were penalised, and gaps
747 matching non-gaps penalised even more. In the PCA
748 calculation, gaps were actually treated as non-gaps - so
749 different costs were applied, which meant Jalview's PCAs
750 were different to those produced by SeqSpace.<br />Jalview
751 now treats gaps in the same way as SeqSpace (ie it scores
752 them as 0). <br /> <br />Enter the following in the
753 Groovy console to restore pre-2.10.2 behaviour:<br />
754 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
755 // for 2.10.1 mode <br />
756 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
757 // to restore 2.10.2 mode <br /> <br /> <em>Note:
758 these settings will affect all subsequent tree and PCA
759 calculations (not recommended)</em></li>
761 <!-- JAL-2424 -->Fixed off-by-one bug that affected
762 scaling of branch lengths for trees computed using
763 Sequence Feature Similarity.
766 <!-- JAL-2377 -->PCA calculation could hang when
767 generating output report when working with highly
771 <!-- JAL-2544 --> Sort by features includes features to
772 right of selected region when gaps present on right-hand
776 <em>User Interface</em>
779 <!-- JAL-2346 -->Reopening Colour by annotation dialog
780 doesn't reselect a specific sequence's associated
781 annotation after it was used for colouring a view
784 <!-- JAL-2419 -->Current selection lost if popup menu
785 opened on a region of alignment without groups
788 <!-- JAL-2374 -->Popup menu not always shown for regions
789 of an alignment with overlapping groups
792 <!-- JAL-2310 -->Finder double counts if both a sequence's
793 name and description match
796 <!-- JAL-2370 -->Hiding column selection containing two
797 hidden regions results in incorrect hidden regions
800 <!-- JAL-2386 -->'Apply to all groups' setting when
801 changing colour does not apply Conservation slider value
805 <!-- JAL-2373 -->Percentage identity and conservation menu
806 items do not show a tick or allow shading to be disabled
809 <!-- JAL-2385 -->Conservation shading or PID threshold
810 lost when base colourscheme changed if slider not visible
813 <!-- JAL-2547 -->Sequence features shown in tooltip for
814 gaps before start of features
817 <!-- JAL-2623 -->Graduated feature colour threshold not
818 restored to UI when feature colour is edited
821 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
822 a time when scrolling vertically in wrapped mode.
825 <!-- JAL-2630 -->Structure and alignment overview update
826 as graduate feature colour settings are modified via the
830 <!-- JAL-2034 -->Overview window doesn't always update
831 when a group defined on the alignment is resized
834 <!-- JAL-2605 -->Mouseovers on left/right scale region in
835 wrapped view result in positional status updates
839 <!-- JAL-2563 -->Status bar doesn't show position for
840 ambiguous amino acid and nucleotide symbols
843 <!-- JAL-2602 -->Copy consensus sequence failed if
844 alignment included gapped columns
847 <!-- JAL-2473 -->Minimum size set for Jalview windows so
848 widgets don't permanently disappear
851 <!-- JAL-2503 -->Cannot select or filter quantitative
852 annotation that are shown only as column labels (e.g.
853 T-Coffee column reliability scores)
856 <!-- JAL-2594 -->Exception thrown if trying to create a
857 sequence feature on gaps only
860 <!-- JAL-2504 -->Features created with 'New feature'
861 button from a Find inherit previously defined feature type
862 rather than the Find query string
865 <!-- JAL-2423 -->incorrect title in output window when
866 exporting tree calculated in Jalview
869 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
870 and then revealing them reorders sequences on the
874 <!-- JAL-964 -->Group panel in sequence feature settings
875 doesn't update to reflect available set of groups after
876 interactively adding or modifying features
879 <!-- JAL-2225 -->Sequence Database chooser unusable on
883 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
884 only excluded gaps in current sequence and ignored
891 <!-- JAL-2421 -->Overview window visible region moves
892 erratically when hidden rows or columns are present
895 <!-- JAL-2362 -->Per-residue colourschemes applied via the
896 Structure Viewer's colour menu don't correspond to
900 <!-- JAL-2405 -->Protein specific colours only offered in
901 colour and group colour menu for protein alignments
904 <!-- JAL-2385 -->Colour threshold slider doesn't update to
905 reflect currently selected view or group's shading
909 <!-- JAL-2624 -->Feature colour thresholds not respected
910 when rendered on overview and structures when opacity at
914 <!-- JAL-2589 -->User defined gap colour not shown in
915 overview when features overlaid on alignment
918 <em>Data import/export</em>
921 <!-- JAL-2576 -->Very large alignments take a long time to
925 <!-- JAL-2507 -->Per-sequence RNA secondary structures
926 added after a sequence was imported are not written to
930 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
931 when importing RNA secondary structure via Stockholm
934 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
935 not shown in correct direction for simple pseudoknots
938 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
939 with lightGray or darkGray via features file (but can
943 <!-- JAL-2383 -->Above PID colour threshold not recovered
944 when alignment view imported from project
947 <!-- JAL-2520,JAL-2465 -->No mappings generated between
948 structure and sequences extracted from structure files
949 imported via URL and viewed in Jmol
952 <!-- JAL-2520 -->Structures loaded via URL are saved in
953 Jalview Projects rather than fetched via URL again when
954 the project is loaded and the structure viewed
957 <em>Web Services</em>
960 <!-- JAL-2519 -->EnsemblGenomes example failing after
961 release of Ensembl v.88
964 <!-- JAL-2366 -->Proxy server address and port always
965 appear enabled in Preferences->Connections
968 <!-- JAL-2461 -->DAS registry not found exceptions
969 removed from console output
972 <!-- JAL-2582 -->Cannot retrieve protein products from
973 Ensembl by Peptide ID
976 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
977 created from SIFTs, and spurious 'Couldn't open structure
978 in Chimera' errors raised after April 2017 update (problem
979 due to 'null' string rather than empty string used for
980 residues with no corresponding PDB mapping).
983 <em>Application UI</em>
986 <!-- JAL-2361 -->User Defined Colours not added to Colour
990 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
991 case' residues (button in colourscheme editor debugged and
992 new documentation and tooltips added)
995 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
996 doesn't restore group-specific text colour thresholds
999 <!-- JAL-2243 -->Feature settings panel does not update as
1000 new features are added to alignment
1003 <!-- JAL-2532 -->Cancel in feature settings reverts
1004 changes to feature colours via the Amend features dialog
1007 <!-- JAL-2506 -->Null pointer exception when attempting to
1008 edit graduated feature colour via amend features dialog
1012 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1013 selection menu changes colours of alignment views
1016 <!-- JAL-2426 -->Spurious exceptions in console raised
1017 from alignment calculation workers after alignment has
1021 <!-- JAL-1608 -->Typo in selection popup menu - Create
1022 groups now 'Create Group'
1025 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1026 Create/Undefine group doesn't always work
1029 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1030 shown again after pressing 'Cancel'
1033 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1034 adjusts start position in wrap mode
1037 <!-- JAL-2563 -->Status bar doesn't show positions for
1038 ambiguous amino acids
1041 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1042 CDS/Protein view after CDS sequences added for aligned
1046 <!-- JAL-2592 -->User defined colourschemes called 'User
1047 Defined' don't appear in Colours menu
1053 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1054 score models doesn't always result in an updated PCA plot
1057 <!-- JAL-2442 -->Features not rendered as transparent on
1058 overview or linked structure view
1061 <!-- JAL-2372 -->Colour group by conservation doesn't
1065 <!-- JAL-2517 -->Hitting Cancel after applying
1066 user-defined colourscheme doesn't restore original
1073 <!-- JAL-2314 -->Unit test failure:
1074 jalview.ws.jabaws.RNAStructExportImport setup fails
1077 <!-- JAL-2307 -->Unit test failure:
1078 jalview.ws.sifts.SiftsClientTest due to compatibility
1079 problems with deep array comparison equality asserts in
1080 successive versions of TestNG
1083 <!-- JAL-2479 -->Relocated StructureChooserTest and
1084 ParameterUtilsTest Unit tests to Network suite
1087 <em>New Known Issues</em>
1090 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1091 phase after a sequence motif find operation
1094 <!-- JAL-2550 -->Importing annotation file with rows
1095 containing just upper and lower case letters are
1096 interpreted as WUSS RNA secondary structure symbols
1099 <!-- JAL-2590 -->Cannot load and display Newick trees
1100 reliably from eggnog Ortholog database
1103 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1104 containing features of type Highlight' when 'B' is pressed
1105 to mark columns containing highlighted regions.
1108 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1109 doesn't always add secondary structure annotation.
1114 <td width="60" nowrap>
1115 <div align="center">
1116 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1119 <td><div align="left">
1123 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1124 for all consensus calculations
1127 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1130 <li>Updated Jalview's Certum code signing certificate
1133 <em>Application</em>
1136 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1137 set of database cross-references, sorted alphabetically
1140 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1141 from database cross references. Users with custom links
1142 will receive a <a href="webServices/urllinks.html#warning">warning
1143 dialog</a> asking them to update their preferences.
1146 <!-- JAL-2287-->Cancel button and escape listener on
1147 dialog warning user about disconnecting Jalview from a
1151 <!-- JAL-2320-->Jalview's Chimera control window closes if
1152 the Chimera it is connected to is shut down
1155 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1156 columns menu item to mark columns containing highlighted
1157 regions (e.g. from structure selections or results of a
1161 <!-- JAL-2284-->Command line option for batch-generation
1162 of HTML pages rendering alignment data with the BioJS
1172 <!-- JAL-2286 -->Columns with more than one modal residue
1173 are not coloured or thresholded according to percent
1174 identity (first observed in Jalview 2.8.2)
1177 <!-- JAL-2301 -->Threonine incorrectly reported as not
1181 <!-- JAL-2318 -->Updates to documentation pages (above PID
1182 threshold, amino acid properties)
1185 <!-- JAL-2292 -->Lower case residues in sequences are not
1186 reported as mapped to residues in a structure file in the
1190 <!--JAL-2324 -->Identical features with non-numeric scores
1191 could be added multiple times to a sequence
1194 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1195 bond features shown as two highlighted residues rather
1196 than a range in linked structure views, and treated
1197 correctly when selecting and computing trees from features
1200 <!-- JAL-2281-->Custom URL links for database
1201 cross-references are matched to database name regardless
1206 <em>Application</em>
1209 <!-- JAL-2282-->Custom URL links for specific database
1210 names without regular expressions also offer links from
1214 <!-- JAL-2315-->Removing a single configured link in the
1215 URL links pane in Connections preferences doesn't actually
1216 update Jalview configuration
1219 <!-- JAL-2272-->CTRL-Click on a selected region to open
1220 the alignment area popup menu doesn't work on El-Capitan
1223 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1224 files with similarly named sequences if dropped onto the
1228 <!-- JAL-2312 -->Additional mappings are shown for PDB
1229 entries where more chains exist in the PDB accession than
1230 are reported in the SIFTS file
1233 <!-- JAL-2317-->Certain structures do not get mapped to
1234 the structure view when displayed with Chimera
1237 <!-- JAL-2317-->No chains shown in the Chimera view
1238 panel's View->Show Chains submenu
1241 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1242 work for wrapped alignment views
1245 <!--JAL-2197 -->Rename UI components for running JPred
1246 predictions from 'JNet' to 'JPred'
1249 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1250 corrupted when annotation panel vertical scroll is not at
1251 first annotation row
1254 <!--JAL-2332 -->Attempting to view structure for Hen
1255 lysozyme results in a PDB Client error dialog box
1258 <!-- JAL-2319 -->Structure View's mapping report switched
1259 ranges for PDB and sequence for SIFTS
1262 SIFTS 'Not_Observed' residues mapped to non-existant
1266 <!-- <em>New Known Issues</em>
1273 <td width="60" nowrap>
1274 <div align="center">
1275 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1276 <em>25/10/2016</em></strong>
1279 <td><em>Application</em>
1281 <li>3D Structure chooser opens with 'Cached structures'
1282 view if structures already loaded</li>
1283 <li>Progress bar reports models as they are loaded to
1284 structure views</li>
1290 <li>Colour by conservation always enabled and no tick
1291 shown in menu when BLOSUM or PID shading applied</li>
1292 <li>FER1_ARATH and FER2_ARATH labels were switched in
1293 example sequences/projects/trees</li>
1295 <em>Application</em>
1297 <li>Jalview projects with views of local PDB structure
1298 files saved on Windows cannot be opened on OSX</li>
1299 <li>Multiple structure views can be opened and superposed
1300 without timeout for structures with multiple models or
1301 multiple sequences in alignment</li>
1302 <li>Cannot import or associated local PDB files without a
1303 PDB ID HEADER line</li>
1304 <li>RMSD is not output in Jmol console when superposition
1306 <li>Drag and drop of URL from Browser fails for Linux and
1307 OSX versions earlier than El Capitan</li>
1308 <li>ENA client ignores invalid content from ENA server</li>
1309 <li>Exceptions are not raised in console when ENA client
1310 attempts to fetch non-existent IDs via Fetch DB Refs UI
1312 <li>Exceptions are not raised in console when a new view
1313 is created on the alignment</li>
1314 <li>OSX right-click fixed for group selections: CMD-click
1315 to insert/remove gaps in groups and CTRL-click to open group
1318 <em>Build and deployment</em>
1320 <li>URL link checker now copes with multi-line anchor
1323 <em>New Known Issues</em>
1325 <li>Drag and drop from URL links in browsers do not work
1332 <td width="60" nowrap>
1333 <div align="center">
1334 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1337 <td><em>General</em>
1340 <!-- JAL-2124 -->Updated Spanish translations.
1343 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1344 for importing structure data to Jalview. Enables mmCIF and
1348 <!-- JAL-192 --->Alignment ruler shows positions relative to
1352 <!-- JAL-2202 -->Position/residue shown in status bar when
1353 mousing over sequence associated annotation
1356 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1360 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1361 '()', canonical '[]' and invalid '{}' base pair populations
1365 <!-- JAL-2092 -->Feature settings popup menu options for
1366 showing or hiding columns containing a feature
1369 <!-- JAL-1557 -->Edit selected group by double clicking on
1370 group and sequence associated annotation labels
1373 <!-- JAL-2236 -->Sequence name added to annotation label in
1374 select/hide columns by annotation and colour by annotation
1378 </ul> <em>Application</em>
1381 <!-- JAL-2050-->Automatically hide introns when opening a
1382 gene/transcript view
1385 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1389 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1390 structure mappings with the EMBL-EBI PDBe SIFTS database
1393 <!-- JAL-2079 -->Updated download sites used for Rfam and
1394 Pfam sources to xfam.org
1397 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1400 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1401 over sequences in Jalview
1404 <!-- JAL-2027-->Support for reverse-complement coding
1405 regions in ENA and EMBL
1408 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1409 for record retrieval via ENA rest API
1412 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1416 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1417 groovy script execution
1420 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1421 alignment window's Calculate menu
1424 <!-- JAL-1812 -->Allow groovy scripts that call
1425 Jalview.getAlignFrames() to run in headless mode
1428 <!-- JAL-2068 -->Support for creating new alignment
1429 calculation workers from groovy scripts
1432 <!-- JAL-1369 --->Store/restore reference sequence in
1436 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1437 associations are now saved/restored from project
1440 <!-- JAL-1993 -->Database selection dialog always shown
1441 before sequence fetcher is opened
1444 <!-- JAL-2183 -->Double click on an entry in Jalview's
1445 database chooser opens a sequence fetcher
1448 <!-- JAL-1563 -->Free-text search client for UniProt using
1449 the UniProt REST API
1452 <!-- JAL-2168 -->-nonews command line parameter to prevent
1453 the news reader opening
1456 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1457 querying stored in preferences
1460 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1464 <!-- JAL-1977-->Tooltips shown on database chooser
1467 <!-- JAL-391 -->Reverse complement function in calculate
1468 menu for nucleotide sequences
1471 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1472 and feature counts preserves alignment ordering (and
1473 debugged for complex feature sets).
1476 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1477 viewing structures with Jalview 2.10
1480 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1481 genome, transcript CCDS and gene ids via the Ensembl and
1482 Ensembl Genomes REST API
1485 <!-- JAL-2049 -->Protein sequence variant annotation
1486 computed for 'sequence_variant' annotation on CDS regions
1490 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1494 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1495 Ref Fetcher fails to match, or otherwise updates sequence
1496 data from external database records.
1499 <!-- JAL-2154 -->Revised Jalview Project format for
1500 efficient recovery of sequence coding and alignment
1501 annotation relationships.
1503 </ul> <!-- <em>Applet</em>
1514 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1518 <!-- JAL-2018-->Export features in Jalview format (again)
1519 includes graduated colourschemes
1522 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1523 working with big alignments and lots of hidden columns
1526 <!-- JAL-2053-->Hidden column markers not always rendered
1527 at right of alignment window
1530 <!-- JAL-2067 -->Tidied up links in help file table of
1534 <!-- JAL-2072 -->Feature based tree calculation not shown
1538 <!-- JAL-2075 -->Hidden columns ignored during feature
1539 based tree calculation
1542 <!-- JAL-2065 -->Alignment view stops updating when show
1543 unconserved enabled for group on alignment
1546 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1550 <!-- JAL-2146 -->Alignment column in status incorrectly
1551 shown as "Sequence position" when mousing over
1555 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1556 hidden columns present
1559 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1560 user created annotation added to alignment
1563 <!-- JAL-1841 -->RNA Structure consensus only computed for
1564 '()' base pair annotation
1567 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1568 in zero scores for all base pairs in RNA Structure
1572 <!-- JAL-2174-->Extend selection with columns containing
1576 <!-- JAL-2275 -->Pfam format writer puts extra space at
1577 beginning of sequence
1580 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1584 <!-- JAL-2238 -->Cannot create groups on an alignment from
1585 from a tree when t-coffee scores are shown
1588 <!-- JAL-1836,1967 -->Cannot import and view PDB
1589 structures with chains containing negative resnums (4q4h)
1592 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1596 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1597 to Clustal, PIR and PileUp output
1600 <!-- JAL-2008 -->Reordering sequence features that are
1601 not visible causes alignment window to repaint
1604 <!-- JAL-2006 -->Threshold sliders don't work in
1605 graduated colour and colour by annotation row for e-value
1606 scores associated with features and annotation rows
1609 <!-- JAL-1797 -->amino acid physicochemical conservation
1610 calculation should be case independent
1613 <!-- JAL-2173 -->Remove annotation also updates hidden
1617 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1618 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1619 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1622 <!-- JAL-2065 -->Null pointer exceptions and redraw
1623 problems when reference sequence defined and 'show
1624 non-conserved' enabled
1627 <!-- JAL-1306 -->Quality and Conservation are now shown on
1628 load even when Consensus calculation is disabled
1631 <!-- JAL-1932 -->Remove right on penultimate column of
1632 alignment does nothing
1635 <em>Application</em>
1638 <!-- JAL-1552-->URLs and links can't be imported by
1639 drag'n'drop on OSX when launched via webstart (note - not
1640 yet fixed for El Capitan)
1643 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1644 output when running on non-gb/us i18n platforms
1647 <!-- JAL-1944 -->Error thrown when exporting a view with
1648 hidden sequences as flat-file alignment
1651 <!-- JAL-2030-->InstallAnywhere distribution fails when
1655 <!-- JAL-2080-->Jalview very slow to launch via webstart
1656 (also hotfix for 2.9.0b2)
1659 <!-- JAL-2085 -->Cannot save project when view has a
1660 reference sequence defined
1663 <!-- JAL-1011 -->Columns are suddenly selected in other
1664 alignments and views when revealing hidden columns
1667 <!-- JAL-1989 -->Hide columns not mirrored in complement
1668 view in a cDNA/Protein splitframe
1671 <!-- JAL-1369 -->Cannot save/restore representative
1672 sequence from project when only one sequence is
1676 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1677 in Structure Chooser
1680 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1681 structure consensus didn't refresh annotation panel
1684 <!-- JAL-1962 -->View mapping in structure view shows
1685 mappings between sequence and all chains in a PDB file
1688 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1689 dialogs format columns correctly, don't display array
1690 data, sort columns according to type
1693 <!-- JAL-1975 -->Export complete shown after destination
1694 file chooser is cancelled during an image export
1697 <!-- JAL-2025 -->Error when querying PDB Service with
1698 sequence name containing special characters
1701 <!-- JAL-2024 -->Manual PDB structure querying should be
1705 <!-- JAL-2104 -->Large tooltips with broken HTML
1706 formatting don't wrap
1709 <!-- JAL-1128 -->Figures exported from wrapped view are
1710 truncated so L looks like I in consensus annotation
1713 <!-- JAL-2003 -->Export features should only export the
1714 currently displayed features for the current selection or
1718 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1719 after fetching cross-references, and restoring from
1723 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1724 followed in the structure viewer
1727 <!-- JAL-2163 -->Titles for individual alignments in
1728 splitframe not restored from project
1731 <!-- JAL-2145 -->missing autocalculated annotation at
1732 trailing end of protein alignment in transcript/product
1733 splitview when pad-gaps not enabled by default
1736 <!-- JAL-1797 -->amino acid physicochemical conservation
1740 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1741 article has been read (reopened issue due to
1742 internationalisation problems)
1745 <!-- JAL-1960 -->Only offer PDB structures in structure
1746 viewer based on sequence name, PDB and UniProt
1751 <!-- JAL-1976 -->No progress bar shown during export of
1755 <!-- JAL-2213 -->Structures not always superimposed after
1756 multiple structures are shown for one or more sequences.
1759 <!-- JAL-1370 -->Reference sequence characters should not
1760 be replaced with '.' when 'Show unconserved' format option
1764 <!-- JAL-1823 -->Cannot specify chain code when entering
1765 specific PDB id for sequence
1768 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1769 'Export hidden sequences' is enabled, but 'export hidden
1770 columns' is disabled.
1773 <!--JAL-2026-->Best Quality option in structure chooser
1774 selects lowest rather than highest resolution structures
1778 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1779 to sequence mapping in 'View Mappings' report
1782 <!-- JAL-2284 -->Unable to read old Jalview projects that
1783 contain non-XML data added after Jalvew wrote project.
1786 <!-- JAL-2118 -->Newly created annotation row reorders
1787 after clicking on it to create new annotation for a
1791 <!-- JAL-1980 -->Null Pointer Exception raised when
1792 pressing Add on an orphaned cut'n'paste window.
1794 <!-- may exclude, this is an external service stability issue JAL-1941
1795 -- > RNA 3D structure not added via DSSR service</li> -->
1800 <!-- JAL-2151 -->Incorrect columns are selected when
1801 hidden columns present before start of sequence
1804 <!-- JAL-1986 -->Missing dependencies on applet pages
1808 <!-- JAL-1947 -->Overview pixel size changes when
1809 sequences are hidden in applet
1812 <!-- JAL-1996 -->Updated instructions for applet
1813 deployment on examples pages.
1820 <td width="60" nowrap>
1821 <div align="center">
1822 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1823 <em>16/10/2015</em></strong>
1826 <td><em>General</em>
1828 <li>Time stamps for signed Jalview application and applet
1833 <em>Application</em>
1835 <li>Duplicate group consensus and conservation rows
1836 shown when tree is partitioned</li>
1837 <li>Erratic behaviour when tree partitions made with
1838 multiple cDNA/Protein split views</li>
1844 <td width="60" nowrap>
1845 <div align="center">
1846 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1847 <em>8/10/2015</em></strong>
1850 <td><em>General</em>
1852 <li>Updated Spanish translations of localized text for
1854 </ul> <em>Application</em>
1856 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1857 <li>Signed OSX InstallAnywhere installer<br></li>
1858 <li>Support for per-sequence based annotations in BioJSON</li>
1859 </ul> <em>Applet</em>
1861 <li>Split frame example added to applet examples page</li>
1862 </ul> <em>Build and Deployment</em>
1865 <!-- JAL-1888 -->New ant target for running Jalview's test
1873 <li>Mapping of cDNA to protein in split frames
1874 incorrect when sequence start > 1</li>
1875 <li>Broken images in filter column by annotation dialog
1877 <li>Feature colours not parsed from features file</li>
1878 <li>Exceptions and incomplete link URLs recovered when
1879 loading a features file containing HTML tags in feature
1883 <em>Application</em>
1885 <li>Annotations corrupted after BioJS export and
1887 <li>Incorrect sequence limits after Fetch DB References
1888 with 'trim retrieved sequences'</li>
1889 <li>Incorrect warning about deleting all data when
1890 deleting selected columns</li>
1891 <li>Patch to build system for shipping properly signed
1892 JNLP templates for webstart launch</li>
1893 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1894 unreleased structures for download or viewing</li>
1895 <li>Tab/space/return keystroke operation of EMBL-PDBe
1896 fetcher/viewer dialogs works correctly</li>
1897 <li>Disabled 'minimise' button on Jalview windows
1898 running on OSX to workaround redraw hang bug</li>
1899 <li>Split cDNA/Protein view position and geometry not
1900 recovered from jalview project</li>
1901 <li>Initial enabled/disabled state of annotation menu
1902 sorter 'show autocalculated first/last' corresponds to
1904 <li>Restoring of Clustal, RNA Helices and T-Coffee
1905 color schemes from BioJSON</li>
1909 <li>Reorder sequences mirrored in cDNA/Protein split
1911 <li>Applet with Jmol examples not loading correctly</li>
1917 <td><div align="center">
1918 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1920 <td><em>General</em>
1922 <li>Linked visualisation and analysis of DNA and Protein
1925 <li>Translated cDNA alignments shown as split protein
1926 and DNA alignment views</li>
1927 <li>Codon consensus annotation for linked protein and
1928 cDNA alignment views</li>
1929 <li>Link cDNA or Protein product sequences by loading
1930 them onto Protein or cDNA alignments</li>
1931 <li>Reconstruct linked cDNA alignment from aligned
1932 protein sequences</li>
1935 <li>Jmol integration updated to Jmol v14.2.14</li>
1936 <li>Import and export of Jalview alignment views as <a
1937 href="features/bioJsonFormat.html">BioJSON</a></li>
1938 <li>New alignment annotation file statements for
1939 reference sequences and marking hidden columns</li>
1940 <li>Reference sequence based alignment shading to
1941 highlight variation</li>
1942 <li>Select or hide columns according to alignment
1944 <li>Find option for locating sequences by description</li>
1945 <li>Conserved physicochemical properties shown in amino
1946 acid conservation row</li>
1947 <li>Alignments can be sorted by number of RNA helices</li>
1948 </ul> <em>Application</em>
1950 <li>New cDNA/Protein analysis capabilities
1952 <li>Get Cross-References should open a Split Frame
1953 view with cDNA/Protein</li>
1954 <li>Detect when nucleotide sequences and protein
1955 sequences are placed in the same alignment</li>
1956 <li>Split cDNA/Protein views are saved in Jalview
1961 <li>Use REST API to talk to Chimera</li>
1962 <li>Selected regions in Chimera are highlighted in linked
1963 Jalview windows</li>
1965 <li>VARNA RNA viewer updated to v3.93</li>
1966 <li>VARNA views are saved in Jalview Projects</li>
1967 <li>Pseudoknots displayed as Jalview RNA annotation can
1968 be shown in VARNA</li>
1970 <li>Make groups for selection uses marked columns as well
1971 as the active selected region</li>
1973 <li>Calculate UPGMA and NJ trees using sequence feature
1975 <li>New Export options
1977 <li>New Export Settings dialog to control hidden
1978 region export in flat file generation</li>
1980 <li>Export alignment views for display with the <a
1981 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1983 <li>Export scrollable SVG in HTML page</li>
1984 <li>Optional embedding of BioJSON data when exporting
1985 alignment figures to HTML</li>
1987 <li>3D structure retrieval and display
1989 <li>Free text and structured queries with the PDBe
1991 <li>PDBe Search API based discovery and selection of
1992 PDB structures for a sequence set</li>
1996 <li>JPred4 employed for protein secondary structure
1998 <li>Hide Insertions menu option to hide unaligned columns
1999 for one or a group of sequences</li>
2000 <li>Automatically hide insertions in alignments imported
2001 from the JPred4 web server</li>
2002 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2003 system on OSX<br />LGPL libraries courtesy of <a
2004 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2006 <li>changed 'View nucleotide structure' submenu to 'View
2007 VARNA 2D Structure'</li>
2008 <li>change "View protein structure" menu option to "3D
2011 </ul> <em>Applet</em>
2013 <li>New layout for applet example pages</li>
2014 <li>New parameters to enable SplitFrame view
2015 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2016 <li>New example demonstrating linked viewing of cDNA and
2017 Protein alignments</li>
2018 </ul> <em>Development and deployment</em>
2020 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2021 <li>Include installation type and git revision in build
2022 properties and console log output</li>
2023 <li>Jalview Github organisation, and new github site for
2024 storing BioJsMSA Templates</li>
2025 <li>Jalview's unit tests now managed with TestNG</li>
2028 <!-- <em>General</em>
2030 </ul> --> <!-- issues resolved --> <em>Application</em>
2032 <li>Escape should close any open find dialogs</li>
2033 <li>Typo in select-by-features status report</li>
2034 <li>Consensus RNA secondary secondary structure
2035 predictions are not highlighted in amber</li>
2036 <li>Missing gap character in v2.7 example file means
2037 alignment appears unaligned when pad-gaps is not enabled</li>
2038 <li>First switch to RNA Helices colouring doesn't colour
2039 associated structure views</li>
2040 <li>ID width preference option is greyed out when auto
2041 width checkbox not enabled</li>
2042 <li>Stopped a warning dialog from being shown when
2043 creating user defined colours</li>
2044 <li>'View Mapping' in structure viewer shows sequence
2045 mappings for just that viewer's sequences</li>
2046 <li>Workaround for superposing PDB files containing
2047 multiple models in Chimera</li>
2048 <li>Report sequence position in status bar when hovering
2049 over Jmol structure</li>
2050 <li>Cannot output gaps as '.' symbols with Selection ->
2051 output to text box</li>
2052 <li>Flat file exports of alignments with hidden columns
2053 have incorrect sequence start/end</li>
2054 <li>'Aligning' a second chain to a Chimera structure from
2056 <li>Colour schemes applied to structure viewers don't
2057 work for nucleotide</li>
2058 <li>Loading/cut'n'pasting an empty or invalid file leads
2059 to a grey/invisible alignment window</li>
2060 <li>Exported Jpred annotation from a sequence region
2061 imports to different position</li>
2062 <li>Space at beginning of sequence feature tooltips shown
2063 on some platforms</li>
2064 <li>Chimera viewer 'View | Show Chain' menu is not
2066 <li>'New View' fails with a Null Pointer Exception in
2067 console if Chimera has been opened</li>
2068 <li>Mouseover to Chimera not working</li>
2069 <li>Miscellaneous ENA XML feature qualifiers not
2071 <li>NPE in annotation renderer after 'Extract Scores'</li>
2072 <li>If two structures in one Chimera window, mouseover of
2073 either sequence shows on first structure</li>
2074 <li>'Show annotations' options should not make
2075 non-positional annotations visible</li>
2076 <li>Subsequence secondary structure annotation not shown
2077 in right place after 'view flanking regions'</li>
2078 <li>File Save As type unset when current file format is
2080 <li>Save as '.jar' option removed for saving Jalview
2082 <li>Colour by Sequence colouring in Chimera more
2084 <li>Cannot 'add reference annotation' for a sequence in
2085 several views on same alignment</li>
2086 <li>Cannot show linked products for EMBL / ENA records</li>
2087 <li>Jalview's tooltip wraps long texts containing no
2089 </ul> <em>Applet</em>
2091 <li>Jmol to JalviewLite mouseover/link not working</li>
2092 <li>JalviewLite can't import sequences with ID
2093 descriptions containing angle brackets</li>
2094 </ul> <em>General</em>
2096 <li>Cannot export and reimport RNA secondary structure
2097 via jalview annotation file</li>
2098 <li>Random helix colour palette for colour by annotation
2099 with RNA secondary structure</li>
2100 <li>Mouseover to cDNA from STOP residue in protein
2101 translation doesn't work.</li>
2102 <li>hints when using the select by annotation dialog box</li>
2103 <li>Jmol alignment incorrect if PDB file has alternate CA
2105 <li>FontChooser message dialog appears to hang after
2106 choosing 1pt font</li>
2107 <li>Peptide secondary structure incorrectly imported from
2108 annotation file when annotation display text includes 'e' or
2110 <li>Cannot set colour of new feature type whilst creating
2112 <li>cDNA translation alignment should not be sequence
2113 order dependent</li>
2114 <li>'Show unconserved' doesn't work for lower case
2116 <li>Nucleotide ambiguity codes involving R not recognised</li>
2117 </ul> <em>Deployment and Documentation</em>
2119 <li>Applet example pages appear different to the rest of
2120 www.jalview.org</li>
2121 </ul> <em>Application Known issues</em>
2123 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2124 <li>Misleading message appears after trying to delete
2126 <li>Jalview icon not shown in dock after InstallAnywhere
2127 version launches</li>
2128 <li>Fetching EMBL reference for an RNA sequence results
2129 fails with a sequence mismatch</li>
2130 <li>Corrupted or unreadable alignment display when
2131 scrolling alignment to right</li>
2132 <li>ArrayIndexOutOfBoundsException thrown when remove
2133 empty columns called on alignment with ragged gapped ends</li>
2134 <li>auto calculated alignment annotation rows do not get
2135 placed above or below non-autocalculated rows</li>
2136 <li>Jalview dekstop becomes sluggish at full screen in
2137 ultra-high resolution</li>
2138 <li>Cannot disable consensus calculation independently of
2139 quality and conservation</li>
2140 <li>Mouseover highlighting between cDNA and protein can
2141 become sluggish with more than one splitframe shown</li>
2142 </ul> <em>Applet Known Issues</em>
2144 <li>Core PDB parsing code requires Jmol</li>
2145 <li>Sequence canvas panel goes white when alignment
2146 window is being resized</li>
2152 <td><div align="center">
2153 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2155 <td><em>General</em>
2157 <li>Updated Java code signing certificate donated by
2159 <li>Features and annotation preserved when performing
2160 pairwise alignment</li>
2161 <li>RNA pseudoknot annotation can be
2162 imported/exported/displayed</li>
2163 <li>'colour by annotation' can colour by RNA and
2164 protein secondary structure</li>
2165 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2166 post-hoc with 2.9 release</em>)
2169 </ul> <em>Application</em>
2171 <li>Extract and display secondary structure for sequences
2172 with 3D structures</li>
2173 <li>Support for parsing RNAML</li>
2174 <li>Annotations menu for layout
2176 <li>sort sequence annotation rows by alignment</li>
2177 <li>place sequence annotation above/below alignment
2180 <li>Output in Stockholm format</li>
2181 <li>Internationalisation: improved Spanish (es)
2183 <li>Structure viewer preferences tab</li>
2184 <li>Disorder and Secondary Structure annotation tracks
2185 shared between alignments</li>
2186 <li>UCSF Chimera launch and linked highlighting from
2188 <li>Show/hide all sequence associated annotation rows for
2189 all or current selection</li>
2190 <li>disorder and secondary structure predictions
2191 available as dataset annotation</li>
2192 <li>Per-sequence rna helices colouring</li>
2195 <li>Sequence database accessions imported when fetching
2196 alignments from Rfam</li>
2197 <li>update VARNA version to 3.91</li>
2199 <li>New groovy scripts for exporting aligned positions,
2200 conservation values, and calculating sum of pairs scores.</li>
2201 <li>Command line argument to set default JABAWS server</li>
2202 <li>include installation type in build properties and
2203 console log output</li>
2204 <li>Updated Jalview project format to preserve dataset
2208 <!-- issues resolved --> <em>Application</em>
2210 <li>Distinguish alignment and sequence associated RNA
2211 structure in structure->view->VARNA</li>
2212 <li>Raise dialog box if user deletes all sequences in an
2214 <li>Pressing F1 results in documentation opening twice</li>
2215 <li>Sequence feature tooltip is wrapped</li>
2216 <li>Double click on sequence associated annotation
2217 selects only first column</li>
2218 <li>Redundancy removal doesn't result in unlinked
2219 leaves shown in tree</li>
2220 <li>Undos after several redundancy removals don't undo
2222 <li>Hide sequence doesn't hide associated annotation</li>
2223 <li>User defined colours dialog box too big to fit on
2224 screen and buttons not visible</li>
2225 <li>author list isn't updated if already written to
2226 Jalview properties</li>
2227 <li>Popup menu won't open after retrieving sequence
2229 <li>File open window for associate PDB doesn't open</li>
2230 <li>Left-then-right click on a sequence id opens a
2231 browser search window</li>
2232 <li>Cannot open sequence feature shading/sort popup menu
2233 in feature settings dialog</li>
2234 <li>better tooltip placement for some areas of Jalview
2236 <li>Allow addition of JABAWS Server which doesn't
2237 pass validation</li>
2238 <li>Web services parameters dialog box is too large to
2240 <li>Muscle nucleotide alignment preset obscured by
2242 <li>JABAWS preset submenus don't contain newly
2243 defined user preset</li>
2244 <li>MSA web services warns user if they were launched
2245 with invalid input</li>
2246 <li>Jalview cannot contact DAS Registy when running on
2249 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2250 'Superpose with' submenu not shown when new view
2254 </ul> <!-- <em>Applet</em>
2256 </ul> <em>General</em>
2258 </ul>--> <em>Deployment and Documentation</em>
2260 <li>2G and 1G options in launchApp have no effect on
2261 memory allocation</li>
2262 <li>launchApp service doesn't automatically open
2263 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2265 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2266 InstallAnywhere reports cannot find valid JVM when Java
2267 1.7_055 is available
2269 </ul> <em>Application Known issues</em>
2272 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2273 corrupted or unreadable alignment display when scrolling
2277 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2278 retrieval fails but progress bar continues for DAS retrieval
2279 with large number of ID
2282 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2283 flatfile output of visible region has incorrect sequence
2287 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2288 rna structure consensus doesn't update when secondary
2289 structure tracks are rearranged
2292 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2293 invalid rna structure positional highlighting does not
2294 highlight position of invalid base pairs
2297 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2298 out of memory errors are not raised when saving Jalview
2299 project from alignment window file menu
2302 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2303 Switching to RNA Helices colouring doesn't propagate to
2307 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2308 colour by RNA Helices not enabled when user created
2309 annotation added to alignment
2312 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2313 Jalview icon not shown on dock in Mountain Lion/Webstart
2315 </ul> <em>Applet Known Issues</em>
2318 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2319 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2322 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2323 Jalview and Jmol example not compatible with IE9
2326 <li>Sort by annotation score doesn't reverse order
2332 <td><div align="center">
2333 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2336 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2339 <li>Internationalisation of user interface (usually
2340 called i18n support) and translation for Spanish locale</li>
2341 <li>Define/Undefine group on current selection with
2342 Ctrl-G/Shift Ctrl-G</li>
2343 <li>Improved group creation/removal options in
2344 alignment/sequence Popup menu</li>
2345 <li>Sensible precision for symbol distribution
2346 percentages shown in logo tooltip.</li>
2347 <li>Annotation panel height set according to amount of
2348 annotation when alignment first opened</li>
2349 </ul> <em>Application</em>
2351 <li>Interactive consensus RNA secondary structure
2352 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2353 <li>Select columns containing particular features from
2354 Feature Settings dialog</li>
2355 <li>View all 'representative' PDB structures for selected
2357 <li>Update Jalview project format:
2359 <li>New file extension for Jalview projects '.jvp'</li>
2360 <li>Preserve sequence and annotation dataset (to
2361 store secondary structure annotation,etc)</li>
2362 <li>Per group and alignment annotation and RNA helix
2366 <li>New similarity measures for PCA and Tree calculation
2368 <li>Experimental support for retrieval and viewing of
2369 flanking regions for an alignment</li>
2373 <!-- issues resolved --> <em>Application</em>
2375 <li>logo keeps spinning and status remains at queued or
2376 running after job is cancelled</li>
2377 <li>cannot export features from alignments imported from
2378 Jalview/VAMSAS projects</li>
2379 <li>Buggy slider for web service parameters that take
2381 <li>Newly created RNA secondary structure line doesn't
2382 have 'display all symbols' flag set</li>
2383 <li>T-COFFEE alignment score shading scheme and other
2384 annotation shading not saved in Jalview project</li>
2385 <li>Local file cannot be loaded in freshly downloaded
2387 <li>Jalview icon not shown on dock in Mountain
2389 <li>Load file from desktop file browser fails</li>
2390 <li>Occasional NPE thrown when calculating large trees</li>
2391 <li>Cannot reorder or slide sequences after dragging an
2392 alignment onto desktop</li>
2393 <li>Colour by annotation dialog throws NPE after using
2394 'extract scores' function</li>
2395 <li>Loading/cut'n'pasting an empty file leads to a grey
2396 alignment window</li>
2397 <li>Disorder thresholds rendered incorrectly after
2398 performing IUPred disorder prediction</li>
2399 <li>Multiple group annotated consensus rows shown when
2400 changing 'normalise logo' display setting</li>
2401 <li>Find shows blank dialog after 'finished searching' if
2402 nothing matches query</li>
2403 <li>Null Pointer Exceptions raised when sorting by
2404 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2406 <li>Errors in Jmol console when structures in alignment
2407 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2409 <li>Not all working JABAWS services are shown in
2411 <li>JAVAWS version of Jalview fails to launch with
2412 'invalid literal/length code'</li>
2413 <li>Annotation/RNA Helix colourschemes cannot be applied
2414 to alignment with groups (actually fixed in 2.8.0b1)</li>
2415 <li>RNA Helices and T-Coffee Scores available as default
2418 </ul> <em>Applet</em>
2420 <li>Remove group option is shown even when selection is
2422 <li>Apply to all groups ticked but colourscheme changes
2423 don't affect groups</li>
2424 <li>Documented RNA Helices and T-Coffee Scores as valid
2425 colourscheme name</li>
2426 <li>Annotation labels drawn on sequence IDs when
2427 Annotation panel is not displayed</li>
2428 <li>Increased font size for dropdown menus on OSX and
2429 embedded windows</li>
2430 </ul> <em>Other</em>
2432 <li>Consensus sequence for alignments/groups with a
2433 single sequence were not calculated</li>
2434 <li>annotation files that contain only groups imported as
2435 annotation and junk sequences</li>
2436 <li>Fasta files with sequences containing '*' incorrectly
2437 recognised as PFAM or BLC</li>
2438 <li>conservation/PID slider apply all groups option
2439 doesn't affect background (2.8.0b1)
2441 <li>redundancy highlighting is erratic at 0% and 100%</li>
2442 <li>Remove gapped columns fails for sequences with ragged
2444 <li>AMSA annotation row with leading spaces is not
2445 registered correctly on import</li>
2446 <li>Jalview crashes when selecting PCA analysis for
2447 certain alignments</li>
2448 <li>Opening the colour by annotation dialog for an
2449 existing annotation based 'use original colours'
2450 colourscheme loses original colours setting</li>
2455 <td><div align="center">
2456 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2457 <em>30/1/2014</em></strong>
2461 <li>Trusted certificates for JalviewLite applet and
2462 Jalview Desktop application<br />Certificate was donated by
2463 <a href="https://www.certum.eu">Certum</a> to the Jalview
2464 open source project).
2466 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2467 <li>Output in Stockholm format</li>
2468 <li>Allow import of data from gzipped files</li>
2469 <li>Export/import group and sequence associated line
2470 graph thresholds</li>
2471 <li>Nucleotide substitution matrix that supports RNA and
2472 ambiguity codes</li>
2473 <li>Allow disorder predictions to be made on the current
2474 selection (or visible selection) in the same way that JPred
2476 <li>Groovy scripting for headless Jalview operation</li>
2477 </ul> <em>Other improvements</em>
2479 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2480 <li>COMBINE statement uses current SEQUENCE_REF and
2481 GROUP_REF scope to group annotation rows</li>
2482 <li>Support '' style escaping of quotes in Newick
2484 <li>Group options for JABAWS service by command line name</li>
2485 <li>Empty tooltip shown for JABA service options with a
2486 link but no description</li>
2487 <li>Select primary source when selecting authority in
2488 database fetcher GUI</li>
2489 <li>Add .mfa to FASTA file extensions recognised by
2491 <li>Annotation label tooltip text wrap</li>
2496 <li>Slow scrolling when lots of annotation rows are
2498 <li>Lots of NPE (and slowness) after creating RNA
2499 secondary structure annotation line</li>
2500 <li>Sequence database accessions not imported when
2501 fetching alignments from Rfam</li>
2502 <li>Incorrect SHMR submission for sequences with
2504 <li>View all structures does not always superpose
2506 <li>Option widgets in service parameters not updated to
2507 reflect user or preset settings</li>
2508 <li>Null pointer exceptions for some services without
2509 presets or adjustable parameters</li>
2510 <li>Discover PDB IDs entry in structure menu doesn't
2511 discover PDB xRefs</li>
2512 <li>Exception encountered while trying to retrieve
2513 features with DAS</li>
2514 <li>Lowest value in annotation row isn't coloured
2515 when colour by annotation (per sequence) is coloured</li>
2516 <li>Keyboard mode P jumps to start of gapped region when
2517 residue follows a gap</li>
2518 <li>Jalview appears to hang importing an alignment with
2519 Wrap as default or after enabling Wrap</li>
2520 <li>'Right click to add annotations' message
2521 shown in wrap mode when no annotations present</li>
2522 <li>Disorder predictions fail with NPE if no automatic
2523 annotation already exists on alignment</li>
2524 <li>oninit javascript function should be called after
2525 initialisation completes</li>
2526 <li>Remove redundancy after disorder prediction corrupts
2527 alignment window display</li>
2528 <li>Example annotation file in documentation is invalid</li>
2529 <li>Grouped line graph annotation rows are not exported
2530 to annotation file</li>
2531 <li>Multi-harmony analysis cannot be run when only two
2533 <li>Cannot create multiple groups of line graphs with
2534 several 'combine' statements in annotation file</li>
2535 <li>Pressing return several times causes Number Format
2536 exceptions in keyboard mode</li>
2537 <li>Multi-harmony (SHMMR) method doesn't submit
2538 correct partitions for input data</li>
2539 <li>Translation from DNA to Amino Acids fails</li>
2540 <li>Jalview fail to load newick tree with quoted label</li>
2541 <li>--headless flag isn't understood</li>
2542 <li>ClassCastException when generating EPS in headless
2544 <li>Adjusting sequence-associated shading threshold only
2545 changes one row's threshold</li>
2546 <li>Preferences and Feature settings panel panel
2547 doesn't open</li>
2548 <li>hide consensus histogram also hides conservation and
2549 quality histograms</li>
2554 <td><div align="center">
2555 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2557 <td><em>Application</em>
2559 <li>Support for JABAWS 2.0 Services (AACon alignment
2560 conservation, protein disorder and Clustal Omega)</li>
2561 <li>JABAWS server status indicator in Web Services
2563 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2564 in Jalview alignment window</li>
2565 <li>Updated Jalview build and deploy framework for OSX
2566 mountain lion, windows 7, and 8</li>
2567 <li>Nucleotide substitution matrix for PCA that supports
2568 RNA and ambiguity codes</li>
2570 <li>Improved sequence database retrieval GUI</li>
2571 <li>Support fetching and database reference look up
2572 against multiple DAS sources (Fetch all from in 'fetch db
2574 <li>Jalview project improvements
2576 <li>Store and retrieve the 'belowAlignment'
2577 flag for annotation</li>
2578 <li>calcId attribute to group annotation rows on the
2580 <li>Store AACon calculation settings for a view in
2581 Jalview project</li>
2585 <li>horizontal scrolling gesture support</li>
2586 <li>Visual progress indicator when PCA calculation is
2588 <li>Simpler JABA web services menus</li>
2589 <li>visual indication that web service results are still
2590 being retrieved from server</li>
2591 <li>Serialise the dialogs that are shown when Jalview
2592 starts up for first time</li>
2593 <li>Jalview user agent string for interacting with HTTP
2595 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2597 <li>Examples directory and Groovy library included in
2598 InstallAnywhere distribution</li>
2599 </ul> <em>Applet</em>
2601 <li>RNA alignment and secondary structure annotation
2602 visualization applet example</li>
2603 </ul> <em>General</em>
2605 <li>Normalise option for consensus sequence logo</li>
2606 <li>Reset button in PCA window to return dimensions to
2608 <li>Allow seqspace or Jalview variant of alignment PCA
2610 <li>PCA with either nucleic acid and protein substitution
2612 <li>Allow windows containing HTML reports to be exported
2614 <li>Interactive display and editing of RNA secondary
2615 structure contacts</li>
2616 <li>RNA Helix Alignment Colouring</li>
2617 <li>RNA base pair logo consensus</li>
2618 <li>Parse sequence associated secondary structure
2619 information in Stockholm files</li>
2620 <li>HTML Export database accessions and annotation
2621 information presented in tooltip for sequences</li>
2622 <li>Import secondary structure from LOCARNA clustalw
2623 style RNA alignment files</li>
2624 <li>import and visualise T-COFFEE quality scores for an
2626 <li>'colour by annotation' per sequence option to
2627 shade each sequence according to its associated alignment
2629 <li>New Jalview Logo</li>
2630 </ul> <em>Documentation and Development</em>
2632 <li>documentation for score matrices used in Jalview</li>
2633 <li>New Website!</li>
2635 <td><em>Application</em>
2637 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2638 wsdbfetch REST service</li>
2639 <li>Stop windows being moved outside desktop on OSX</li>
2640 <li>Filetype associations not installed for webstart
2642 <li>Jalview does not always retrieve progress of a JABAWS
2643 job execution in full once it is complete</li>
2644 <li>revise SHMR RSBS definition to ensure alignment is
2645 uploaded via ali_file parameter</li>
2646 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2647 <li>View all structures superposed fails with exception</li>
2648 <li>Jnet job queues forever if a very short sequence is
2649 submitted for prediction</li>
2650 <li>Cut and paste menu not opened when mouse clicked on
2652 <li>Putting fractional value into integer text box in
2653 alignment parameter dialog causes Jalview to hang</li>
2654 <li>Structure view highlighting doesn't work on
2656 <li>View all structures fails with exception shown in
2658 <li>Characters in filename associated with PDBEntry not
2659 escaped in a platform independent way</li>
2660 <li>Jalview desktop fails to launch with exception when
2662 <li>Tree calculation reports 'you must have 2 or more
2663 sequences selected' when selection is empty</li>
2664 <li>Jalview desktop fails to launch with jar signature
2665 failure when java web start temporary file caching is
2667 <li>DAS Sequence retrieval with range qualification
2668 results in sequence xref which includes range qualification</li>
2669 <li>Errors during processing of command line arguments
2670 cause progress bar (JAL-898) to be removed</li>
2671 <li>Replace comma for semi-colon option not disabled for
2672 DAS sources in sequence fetcher</li>
2673 <li>Cannot close news reader when JABAWS server warning
2674 dialog is shown</li>
2675 <li>Option widgets not updated to reflect user settings</li>
2676 <li>Edited sequence not submitted to web service</li>
2677 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2678 <li>InstallAnywhere installer doesn't unpack and run
2679 on OSX Mountain Lion</li>
2680 <li>Annotation panel not given a scroll bar when
2681 sequences with alignment annotation are pasted into the
2683 <li>Sequence associated annotation rows not associated
2684 when loaded from Jalview project</li>
2685 <li>Browser launch fails with NPE on java 1.7</li>
2686 <li>JABAWS alignment marked as finished when job was
2687 cancelled or job failed due to invalid input</li>
2688 <li>NPE with v2.7 example when clicking on Tree
2689 associated with all views</li>
2690 <li>Exceptions when copy/paste sequences with grouped
2691 annotation rows to new window</li>
2692 </ul> <em>Applet</em>
2694 <li>Sequence features are momentarily displayed before
2695 they are hidden using hidefeaturegroups applet parameter</li>
2696 <li>loading features via javascript API automatically
2697 enables feature display</li>
2698 <li>scrollToColumnIn javascript API method doesn't
2700 </ul> <em>General</em>
2702 <li>Redundancy removal fails for rna alignment</li>
2703 <li>PCA calculation fails when sequence has been selected
2704 and then deselected</li>
2705 <li>PCA window shows grey box when first opened on OSX</li>
2706 <li>Letters coloured pink in sequence logo when alignment
2707 coloured with clustalx</li>
2708 <li>Choosing fonts without letter symbols defined causes
2709 exceptions and redraw errors</li>
2710 <li>Initial PCA plot view is not same as manually
2711 reconfigured view</li>
2712 <li>Grouped annotation graph label has incorrect line
2714 <li>Grouped annotation graph label display is corrupted
2715 for lots of labels</li>
2720 <div align="center">
2721 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2724 <td><em>Application</em>
2726 <li>Jalview Desktop News Reader</li>
2727 <li>Tweaked default layout of web services menu</li>
2728 <li>View/alignment association menu to enable user to
2729 easily specify which alignment a multi-structure view takes
2730 its colours/correspondences from</li>
2731 <li>Allow properties file location to be specified as URL</li>
2732 <li>Extend Jalview project to preserve associations
2733 between many alignment views and a single Jmol display</li>
2734 <li>Store annotation row height in Jalview project file</li>
2735 <li>Annotation row column label formatting attributes
2736 stored in project file</li>
2737 <li>Annotation row order for auto-calculated annotation
2738 rows preserved in Jalview project file</li>
2739 <li>Visual progress indication when Jalview state is
2740 saved using Desktop window menu</li>
2741 <li>Visual indication that command line arguments are
2742 still being processed</li>
2743 <li>Groovy script execution from URL</li>
2744 <li>Colour by annotation default min and max colours in
2746 <li>Automatically associate PDB files dragged onto an
2747 alignment with sequences that have high similarity and
2749 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2750 <li>'view structures' option to open many
2751 structures in same window</li>
2752 <li>Sort associated views menu option for tree panel</li>
2753 <li>Group all JABA and non-JABA services for a particular
2754 analysis function in its own submenu</li>
2755 </ul> <em>Applet</em>
2757 <li>Userdefined and autogenerated annotation rows for
2759 <li>Adjustment of alignment annotation pane height</li>
2760 <li>Annotation scrollbar for annotation panel</li>
2761 <li>Drag to reorder annotation rows in annotation panel</li>
2762 <li>'automaticScrolling' parameter</li>
2763 <li>Allow sequences with partial ID string matches to be
2764 annotated from GFF/Jalview features files</li>
2765 <li>Sequence logo annotation row in applet</li>
2766 <li>Absolute paths relative to host server in applet
2767 parameters are treated as such</li>
2768 <li>New in the JalviewLite javascript API:
2770 <li>JalviewLite.js javascript library</li>
2771 <li>Javascript callbacks for
2773 <li>Applet initialisation</li>
2774 <li>Sequence/alignment mouse-overs and selections</li>
2777 <li>scrollTo row and column alignment scrolling
2779 <li>Select sequence/alignment regions from javascript</li>
2780 <li>javascript structure viewer harness to pass
2781 messages between Jmol and Jalview when running as
2782 distinct applets</li>
2783 <li>sortBy method</li>
2784 <li>Set of applet and application examples shipped
2785 with documentation</li>
2786 <li>New example to demonstrate JalviewLite and Jmol
2787 javascript message exchange</li>
2789 </ul> <em>General</em>
2791 <li>Enable Jmol displays to be associated with multiple
2792 multiple alignments</li>
2793 <li>Option to automatically sort alignment with new tree</li>
2794 <li>User configurable link to enable redirects to a
2795 www.Jalview.org mirror</li>
2796 <li>Jmol colours option for Jmol displays</li>
2797 <li>Configurable newline string when writing alignment
2798 and other flat files</li>
2799 <li>Allow alignment annotation description lines to
2800 contain html tags</li>
2801 </ul> <em>Documentation and Development</em>
2803 <li>Add groovy test harness for bulk load testing to
2805 <li>Groovy script to load and align a set of sequences
2806 using a web service before displaying the result in the
2807 Jalview desktop</li>
2808 <li>Restructured javascript and applet api documentation</li>
2809 <li>Ant target to publish example html files with applet
2811 <li>Netbeans project for building Jalview from source</li>
2812 <li>ant task to create online javadoc for Jalview source</li>
2814 <td><em>Application</em>
2816 <li>User defined colourscheme throws exception when
2817 current built in colourscheme is saved as new scheme</li>
2818 <li>AlignFrame->Save in application pops up save
2819 dialog for valid filename/format</li>
2820 <li>Cannot view associated structure for UniProt sequence</li>
2821 <li>PDB file association breaks for UniProt sequence
2823 <li>Associate PDB from file dialog does not tell you
2824 which sequence is to be associated with the file</li>
2825 <li>Find All raises null pointer exception when query
2826 only matches sequence IDs</li>
2827 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2828 <li>Jalview project with Jmol views created with Jalview
2829 2.4 cannot be loaded</li>
2830 <li>Filetype associations not installed for webstart
2832 <li>Two or more chains in a single PDB file associated
2833 with sequences in different alignments do not get coloured
2834 by their associated sequence</li>
2835 <li>Visibility status of autocalculated annotation row
2836 not preserved when project is loaded</li>
2837 <li>Annotation row height and visibility attributes not
2838 stored in Jalview project</li>
2839 <li>Tree bootstraps are not preserved when saved as a
2840 Jalview project</li>
2841 <li>Envision2 workflow tooltips are corrupted</li>
2842 <li>Enabling show group conservation also enables colour
2843 by conservation</li>
2844 <li>Duplicate group associated conservation or consensus
2845 created on new view</li>
2846 <li>Annotation scrollbar not displayed after 'show
2847 all hidden annotation rows' option selected</li>
2848 <li>Alignment quality not updated after alignment
2849 annotation row is hidden then shown</li>
2850 <li>Preserve colouring of structures coloured by
2851 sequences in pre Jalview 2.7 projects</li>
2852 <li>Web service job parameter dialog is not laid out
2854 <li>Web services menu not refreshed after 'reset
2855 services' button is pressed in preferences</li>
2856 <li>Annotation off by one in Jalview v2_3 example project</li>
2857 <li>Structures imported from file and saved in project
2858 get name like jalview_pdb1234.txt when reloaded</li>
2859 <li>Jalview does not always retrieve progress of a JABAWS
2860 job execution in full once it is complete</li>
2861 </ul> <em>Applet</em>
2863 <li>Alignment height set incorrectly when lots of
2864 annotation rows are displayed</li>
2865 <li>Relative URLs in feature HTML text not resolved to
2867 <li>View follows highlighting does not work for positions
2869 <li><= shown as = in tooltip</li>
2870 <li>Export features raises exception when no features
2872 <li>Separator string used for serialising lists of IDs
2873 for javascript api is modified when separator string
2874 provided as parameter</li>
2875 <li>Null pointer exception when selecting tree leaves for
2876 alignment with no existing selection</li>
2877 <li>Relative URLs for datasources assumed to be relative
2878 to applet's codebase</li>
2879 <li>Status bar not updated after finished searching and
2880 search wraps around to first result</li>
2881 <li>StructureSelectionManager instance shared between
2882 several Jalview applets causes race conditions and memory
2884 <li>Hover tooltip and mouseover of position on structure
2885 not sent from Jmol in applet</li>
2886 <li>Certain sequences of javascript method calls to
2887 applet API fatally hang browser</li>
2888 </ul> <em>General</em>
2890 <li>View follows structure mouseover scrolls beyond
2891 position with wrapped view and hidden regions</li>
2892 <li>Find sequence position moves to wrong residue
2893 with/without hidden columns</li>
2894 <li>Sequence length given in alignment properties window
2896 <li>InvalidNumberFormat exceptions thrown when trying to
2897 import PDB like structure files</li>
2898 <li>Positional search results are only highlighted
2899 between user-supplied sequence start/end bounds</li>
2900 <li>End attribute of sequence is not validated</li>
2901 <li>Find dialog only finds first sequence containing a
2902 given sequence position</li>
2903 <li>Sequence numbering not preserved in MSF alignment
2905 <li>Jalview PDB file reader does not extract sequence
2906 from nucleotide chains correctly</li>
2907 <li>Structure colours not updated when tree partition
2908 changed in alignment</li>
2909 <li>Sequence associated secondary structure not correctly
2910 parsed in interleaved stockholm</li>
2911 <li>Colour by annotation dialog does not restore current
2913 <li>Hiding (nearly) all sequences doesn't work
2915 <li>Sequences containing lowercase letters are not
2916 properly associated with their pdb files</li>
2917 </ul> <em>Documentation and Development</em>
2919 <li>schemas/JalviewWsParamSet.xsd corrupted by
2920 ApplyCopyright tool</li>
2925 <div align="center">
2926 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2929 <td><em>Application</em>
2931 <li>New warning dialog when the Jalview Desktop cannot
2932 contact web services</li>
2933 <li>JABA service parameters for a preset are shown in
2934 service job window</li>
2935 <li>JABA Service menu entries reworded</li>
2939 <li>Modeller PIR IO broken - cannot correctly import a
2940 pir file emitted by Jalview</li>
2941 <li>Existing feature settings transferred to new
2942 alignment view created from cut'n'paste</li>
2943 <li>Improved test for mixed amino/nucleotide chains when
2944 parsing PDB files</li>
2945 <li>Consensus and conservation annotation rows
2946 occasionally become blank for all new windows</li>
2947 <li>Exception raised when right clicking above sequences
2948 in wrapped view mode</li>
2949 </ul> <em>Application</em>
2951 <li>multiple multiply aligned structure views cause cpu
2952 usage to hit 100% and computer to hang</li>
2953 <li>Web Service parameter layout breaks for long user
2954 parameter names</li>
2955 <li>Jaba service discovery hangs desktop if Jaba server
2962 <div align="center">
2963 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2966 <td><em>Application</em>
2968 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2969 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2972 <li>Web Services preference tab</li>
2973 <li>Analysis parameters dialog box and user defined
2975 <li>Improved speed and layout of Envision2 service menu</li>
2976 <li>Superpose structures using associated sequence
2978 <li>Export coordinates and projection as CSV from PCA
2980 </ul> <em>Applet</em>
2982 <li>enable javascript: execution by the applet via the
2983 link out mechanism</li>
2984 </ul> <em>Other</em>
2986 <li>Updated the Jmol Jalview interface to work with Jmol
2988 <li>The Jalview Desktop and JalviewLite applet now
2989 require Java 1.5</li>
2990 <li>Allow Jalview feature colour specification for GFF
2991 sequence annotation files</li>
2992 <li>New 'colour by label' keword in Jalview feature file
2993 type colour specification</li>
2994 <li>New Jalview Desktop Groovy API method that allows a
2995 script to check if it being run in an interactive session or
2996 in a batch operation from the Jalview command line</li>
3000 <li>clustalx colourscheme colours Ds preferentially when
3001 both D+E are present in over 50% of the column</li>
3002 </ul> <em>Application</em>
3004 <li>typo in AlignmentFrame->View->Hide->all but
3005 selected Regions menu item</li>
3006 <li>sequence fetcher replaces ',' for ';' when the ',' is
3007 part of a valid accession ID</li>
3008 <li>fatal OOM if object retrieved by sequence fetcher
3009 runs out of memory</li>
3010 <li>unhandled Out of Memory Error when viewing pca
3011 analysis results</li>
3012 <li>InstallAnywhere builds fail to launch on OS X java
3013 10.5 update 4 (due to apple Java 1.6 update)</li>
3014 <li>Installanywhere Jalview silently fails to launch</li>
3015 </ul> <em>Applet</em>
3017 <li>Jalview.getFeatureGroups() raises an
3018 ArrayIndexOutOfBoundsException if no feature groups are
3025 <div align="center">
3026 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3032 <li>Alignment prettyprinter doesn't cope with long
3034 <li>clustalx colourscheme colours Ds preferentially when
3035 both D+E are present in over 50% of the column</li>
3036 <li>nucleic acid structures retrieved from PDB do not
3037 import correctly</li>
3038 <li>More columns get selected than were clicked on when a
3039 number of columns are hidden</li>
3040 <li>annotation label popup menu not providing correct
3041 add/hide/show options when rows are hidden or none are
3043 <li>Stockholm format shown in list of readable formats,
3044 and parser copes better with alignments from RFAM.</li>
3045 <li>CSV output of consensus only includes the percentage
3046 of all symbols if sequence logo display is enabled</li>
3048 </ul> <em>Applet</em>
3050 <li>annotation panel disappears when annotation is
3052 </ul> <em>Application</em>
3054 <li>Alignment view not redrawn properly when new
3055 alignment opened where annotation panel is visible but no
3056 annotations are present on alignment</li>
3057 <li>pasted region containing hidden columns is
3058 incorrectly displayed in new alignment window</li>
3059 <li>Jalview slow to complete operations when stdout is
3060 flooded (fix is to close the Jalview console)</li>
3061 <li>typo in AlignmentFrame->View->Hide->all but
3062 selected Rregions menu item.</li>
3063 <li>inconsistent group submenu and Format submenu entry
3064 'Un' or 'Non'conserved</li>
3065 <li>Sequence feature settings are being shared by
3066 multiple distinct alignments</li>
3067 <li>group annotation not recreated when tree partition is
3069 <li>double click on group annotation to select sequences
3070 does not propagate to associated trees</li>
3071 <li>Mac OSX specific issues:
3073 <li>exception raised when mouse clicked on desktop
3074 window background</li>
3075 <li>Desktop menu placed on menu bar and application
3076 name set correctly</li>
3077 <li>sequence feature settings not wide enough for the
3078 save feature colourscheme button</li>
3087 <div align="center">
3088 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3091 <td><em>New Capabilities</em>
3093 <li>URL links generated from description line for
3094 regular-expression based URL links (applet and application)
3096 <li>Non-positional feature URL links are shown in link
3098 <li>Linked viewing of nucleic acid sequences and
3100 <li>Automatic Scrolling option in View menu to display
3101 the currently highlighted region of an alignment.</li>
3102 <li>Order an alignment by sequence length, or using the
3103 average score or total feature count for each sequence.</li>
3104 <li>Shading features by score or associated description</li>
3105 <li>Subdivide alignment and groups based on identity of
3106 selected subsequence (Make Groups from Selection).</li>
3107 <li>New hide/show options including Shift+Control+H to
3108 hide everything but the currently selected region.</li>
3109 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3110 </ul> <em>Application</em>
3112 <li>Fetch DB References capabilities and UI expanded to
3113 support retrieval from DAS sequence sources</li>
3114 <li>Local DAS Sequence sources can be added via the
3115 command line or via the Add local source dialog box.</li>
3116 <li>DAS Dbref and DbxRef feature types are parsed as
3117 database references and protein_name is parsed as
3118 description line (BioSapiens terms).</li>
3119 <li>Enable or disable non-positional feature and database
3120 references in sequence ID tooltip from View menu in
3122 <!-- <li>New hidden columns and rows and representatives capabilities
3123 in annotations file (in progress - not yet fully implemented)</li> -->
3124 <li>Group-associated consensus, sequence logos and
3125 conservation plots</li>
3126 <li>Symbol distributions for each column can be exported
3127 and visualized as sequence logos</li>
3128 <li>Optionally scale multi-character column labels to fit
3129 within each column of annotation row<!-- todo for applet -->
3131 <li>Optional automatic sort of associated alignment view
3132 when a new tree is opened.</li>
3133 <li>Jalview Java Console</li>
3134 <li>Better placement of desktop window when moving
3135 between different screens.</li>
3136 <li>New preference items for sequence ID tooltip and
3137 consensus annotation</li>
3138 <li>Client to submit sequences and IDs to Envision2
3140 <li><em>Vamsas Capabilities</em>
3142 <li>Improved VAMSAS synchronization (Jalview archive
3143 used to preserve views, structures, and tree display
3145 <li>Import of vamsas documents from disk or URL via
3147 <li>Sharing of selected regions between views and
3148 with other VAMSAS applications (Experimental feature!)</li>
3149 <li>Updated API to VAMSAS version 0.2</li>
3151 </ul> <em>Applet</em>
3153 <li>Middle button resizes annotation row height</li>
3156 <li>sortByTree (true/false) - automatically sort the
3157 associated alignment view by the tree when a new tree is
3159 <li>showTreeBootstraps (true/false) - show or hide
3160 branch bootstraps (default is to show them if available)</li>
3161 <li>showTreeDistances (true/false) - show or hide
3162 branch lengths (default is to show them if available)</li>
3163 <li>showUnlinkedTreeNodes (true/false) - indicate if
3164 unassociated nodes should be highlighted in the tree
3166 <li>heightScale and widthScale (1.0 or more) -
3167 increase the height or width of a cell in the alignment
3168 grid relative to the current font size.</li>
3171 <li>Non-positional features displayed in sequence ID
3173 </ul> <em>Other</em>
3175 <li>Features format: graduated colour definitions and
3176 specification of feature scores</li>
3177 <li>Alignment Annotations format: new keywords for group
3178 associated annotation (GROUP_REF) and annotation row display
3179 properties (ROW_PROPERTIES)</li>
3180 <li>XML formats extended to support graduated feature
3181 colourschemes, group associated annotation, and profile
3182 visualization settings.</li></td>
3185 <li>Source field in GFF files parsed as feature source
3186 rather than description</li>
3187 <li>Non-positional features are now included in sequence
3188 feature and gff files (controlled via non-positional feature
3189 visibility in tooltip).</li>
3190 <li>URL links generated for all feature links (bugfix)</li>
3191 <li>Added URL embedding instructions to features file
3193 <li>Codons containing ambiguous nucleotides translated as
3194 'X' in peptide product</li>
3195 <li>Match case switch in find dialog box works for both
3196 sequence ID and sequence string and query strings do not
3197 have to be in upper case to match case-insensitively.</li>
3198 <li>AMSA files only contain first column of
3199 multi-character column annotation labels</li>
3200 <li>Jalview Annotation File generation/parsing consistent
3201 with documentation (e.g. Stockholm annotation can be
3202 exported and re-imported)</li>
3203 <li>PDB files without embedded PDB IDs given a friendly
3205 <li>Find incrementally searches ID string matches as well
3206 as subsequence matches, and correctly reports total number
3210 <li>Better handling of exceptions during sequence
3212 <li>Dasobert generated non-positional feature URL
3213 link text excludes the start_end suffix</li>
3214 <li>DAS feature and source retrieval buttons disabled
3215 when fetch or registry operations in progress.</li>
3216 <li>PDB files retrieved from URLs are cached properly</li>
3217 <li>Sequence description lines properly shared via
3219 <li>Sequence fetcher fetches multiple records for all
3221 <li>Ensured that command line das feature retrieval
3222 completes before alignment figures are generated.</li>
3223 <li>Reduced time taken when opening file browser for
3225 <li>isAligned check prior to calculating tree, PCA or
3226 submitting an MSA to JNet now excludes hidden sequences.</li>
3227 <li>User defined group colours properly recovered
3228 from Jalview projects.</li>
3237 <div align="center">
3238 <strong>2.4.0.b2</strong><br> 28/10/2009
3243 <li>Experimental support for google analytics usage
3245 <li>Jalview privacy settings (user preferences and docs).</li>
3250 <li>Race condition in applet preventing startup in
3252 <li>Exception when feature created from selection beyond
3253 length of sequence.</li>
3254 <li>Allow synthetic PDB files to be imported gracefully</li>
3255 <li>Sequence associated annotation rows associate with
3256 all sequences with a given id</li>
3257 <li>Find function matches case-insensitively for sequence
3258 ID string searches</li>
3259 <li>Non-standard characters do not cause pairwise
3260 alignment to fail with exception</li>
3261 </ul> <em>Application Issues</em>
3263 <li>Sequences are now validated against EMBL database</li>
3264 <li>Sequence fetcher fetches multiple records for all
3266 </ul> <em>InstallAnywhere Issues</em>
3268 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3269 issue with installAnywhere mechanism)</li>
3270 <li>Command line launching of JARs from InstallAnywhere
3271 version (java class versioning error fixed)</li>
3278 <div align="center">
3279 <strong>2.4</strong><br> 27/8/2008
3282 <td><em>User Interface</em>
3284 <li>Linked highlighting of codon and amino acid from
3285 translation and protein products</li>
3286 <li>Linked highlighting of structure associated with
3287 residue mapping to codon position</li>
3288 <li>Sequence Fetcher provides example accession numbers
3289 and 'clear' button</li>
3290 <li>MemoryMonitor added as an option under Desktop's
3292 <li>Extract score function to parse whitespace separated
3293 numeric data in description line</li>
3294 <li>Column labels in alignment annotation can be centred.</li>
3295 <li>Tooltip for sequence associated annotation give name
3297 </ul> <em>Web Services and URL fetching</em>
3299 <li>JPred3 web service</li>
3300 <li>Prototype sequence search client (no public services
3302 <li>Fetch either seed alignment or full alignment from
3304 <li>URL Links created for matching database cross
3305 references as well as sequence ID</li>
3306 <li>URL Links can be created using regular-expressions</li>
3307 </ul> <em>Sequence Database Connectivity</em>
3309 <li>Retrieval of cross-referenced sequences from other
3311 <li>Generalised database reference retrieval and
3312 validation to all fetchable databases</li>
3313 <li>Fetch sequences from DAS sources supporting the
3314 sequence command</li>
3315 </ul> <em>Import and Export</em>
3316 <li>export annotation rows as CSV for spreadsheet import</li>
3317 <li>Jalview projects record alignment dataset associations,
3318 EMBL products, and cDNA sequence mappings</li>
3319 <li>Sequence Group colour can be specified in Annotation
3321 <li>Ad-hoc colouring of group in Annotation File using RGB
3322 triplet as name of colourscheme</li>
3323 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3325 <li>treenode binding for VAMSAS tree exchange</li>
3326 <li>local editing and update of sequences in VAMSAS
3327 alignments (experimental)</li>
3328 <li>Create new or select existing session to join</li>
3329 <li>load and save of vamsas documents</li>
3330 </ul> <em>Application command line</em>
3332 <li>-tree parameter to open trees (introduced for passing
3334 <li>-fetchfrom command line argument to specify nicknames
3335 of DAS servers to query for alignment features</li>
3336 <li>-dasserver command line argument to add new servers
3337 that are also automatically queried for features</li>
3338 <li>-groovy command line argument executes a given groovy
3339 script after all input data has been loaded and parsed</li>
3340 </ul> <em>Applet-Application data exchange</em>
3342 <li>Trees passed as applet parameters can be passed to
3343 application (when using "View in full
3344 application")</li>
3345 </ul> <em>Applet Parameters</em>
3347 <li>feature group display control parameter</li>
3348 <li>debug parameter</li>
3349 <li>showbutton parameter</li>
3350 </ul> <em>Applet API methods</em>
3352 <li>newView public method</li>
3353 <li>Window (current view) specific get/set public methods</li>
3354 <li>Feature display control methods</li>
3355 <li>get list of currently selected sequences</li>
3356 </ul> <em>New Jalview distribution features</em>
3358 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3359 <li>RELEASE file gives build properties for the latest
3360 Jalview release.</li>
3361 <li>Java 1.1 Applet build made easier and donotobfuscate
3362 property controls execution of obfuscator</li>
3363 <li>Build target for generating source distribution</li>
3364 <li>Debug flag for javacc</li>
3365 <li>.jalview_properties file is documented (slightly) in
3366 jalview.bin.Cache</li>
3367 <li>Continuous Build Integration for stable and
3368 development version of Application, Applet and source
3373 <li>selected region output includes visible annotations
3374 (for certain formats)</li>
3375 <li>edit label/displaychar contains existing label/char
3377 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3378 <li>shorter peptide product names from EMBL records</li>
3379 <li>Newick string generator makes compact representations</li>
3380 <li>bootstrap values parsed correctly for tree files with
3382 <li>pathological filechooser bug avoided by not allowing
3383 filenames containing a ':'</li>
3384 <li>Fixed exception when parsing GFF files containing
3385 global sequence features</li>
3386 <li>Alignment datasets are finalized only when number of
3387 references from alignment sequences goes to zero</li>
3388 <li>Close of tree branch colour box without colour
3389 selection causes cascading exceptions</li>
3390 <li>occasional negative imgwidth exceptions</li>
3391 <li>better reporting of non-fatal warnings to user when
3392 file parsing fails.</li>
3393 <li>Save works when Jalview project is default format</li>
3394 <li>Save as dialog opened if current alignment format is
3395 not a valid output format</li>
3396 <li>UniProt canonical names introduced for both das and
3398 <li>Histidine should be midblue (not pink!) in Zappo</li>
3399 <li>error messages passed up and output when data read
3401 <li>edit undo recovers previous dataset sequence when
3402 sequence is edited</li>
3403 <li>allow PDB files without pdb ID HEADER lines (like
3404 those generated by MODELLER) to be read in properly</li>
3405 <li>allow reading of JPred concise files as a normal
3407 <li>Stockholm annotation parsing and alignment properties
3408 import fixed for PFAM records</li>
3409 <li>Structure view windows have correct name in Desktop
3411 <li>annotation consisting of sequence associated scores
3412 can be read and written correctly to annotation file</li>
3413 <li>Aligned cDNA translation to aligned peptide works
3415 <li>Fixed display of hidden sequence markers and
3416 non-italic font for representatives in Applet</li>
3417 <li>Applet Menus are always embedded in applet window on
3419 <li>Newly shown features appear at top of stack (in
3421 <li>Annotations added via parameter not drawn properly
3422 due to null pointer exceptions</li>
3423 <li>Secondary structure lines are drawn starting from
3424 first column of alignment</li>
3425 <li>UniProt XML import updated for new schema release in
3427 <li>Sequence feature to sequence ID match for Features
3428 file is case-insensitive</li>
3429 <li>Sequence features read from Features file appended to
3430 all sequences with matching IDs</li>
3431 <li>PDB structure coloured correctly for associated views
3432 containing a sub-sequence</li>
3433 <li>PDB files can be retrieved by applet from Jar files</li>
3434 <li>feature and annotation file applet parameters
3435 referring to different directories are retrieved correctly</li>
3436 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3437 <li>Fixed application hang whilst waiting for
3438 splash-screen version check to complete</li>
3439 <li>Applet properly URLencodes input parameter values
3440 when passing them to the launchApp service</li>
3441 <li>display name and local features preserved in results
3442 retrieved from web service</li>
3443 <li>Visual delay indication for sequence retrieval and
3444 sequence fetcher initialisation</li>
3445 <li>updated Application to use DAS 1.53e version of
3446 dasobert DAS client</li>
3447 <li>Re-instated Full AMSA support and .amsa file
3449 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3457 <div align="center">
3458 <strong>2.3</strong><br> 9/5/07
3463 <li>Jmol 11.0.2 integration</li>
3464 <li>PDB views stored in Jalview XML files</li>
3465 <li>Slide sequences</li>
3466 <li>Edit sequence in place</li>
3467 <li>EMBL CDS features</li>
3468 <li>DAS Feature mapping</li>
3469 <li>Feature ordering</li>
3470 <li>Alignment Properties</li>
3471 <li>Annotation Scores</li>
3472 <li>Sort by scores</li>
3473 <li>Feature/annotation editing in applet</li>
3478 <li>Headless state operation in 2.2.1</li>
3479 <li>Incorrect and unstable DNA pairwise alignment</li>
3480 <li>Cut and paste of sequences with annotation</li>
3481 <li>Feature group display state in XML</li>
3482 <li>Feature ordering in XML</li>
3483 <li>blc file iteration selection using filename # suffix</li>
3484 <li>Stockholm alignment properties</li>
3485 <li>Stockhom alignment secondary structure annotation</li>
3486 <li>2.2.1 applet had no feature transparency</li>
3487 <li>Number pad keys can be used in cursor mode</li>
3488 <li>Structure Viewer mirror image resolved</li>
3495 <div align="center">
3496 <strong>2.2.1</strong><br> 12/2/07
3501 <li>Non standard characters can be read and displayed
3502 <li>Annotations/Features can be imported/exported to the
3504 <li>Applet allows editing of sequence/annotation/group
3505 name & description
3506 <li>Preference setting to display sequence name in
3508 <li>Annotation file format extended to allow
3509 Sequence_groups to be defined
3510 <li>Default opening of alignment overview panel can be
3511 specified in preferences
3512 <li>PDB residue numbering annotation added to associated
3518 <li>Applet crash under certain Linux OS with Java 1.6
3520 <li>Annotation file export / import bugs fixed
3521 <li>PNG / EPS image output bugs fixed
3527 <div align="center">
3528 <strong>2.2</strong><br> 27/11/06
3533 <li>Multiple views on alignment
3534 <li>Sequence feature editing
3535 <li>"Reload" alignment
3536 <li>"Save" to current filename
3537 <li>Background dependent text colour
3538 <li>Right align sequence ids
3539 <li>User-defined lower case residue colours
3542 <li>Menu item accelerator keys
3543 <li>Control-V pastes to current alignment
3544 <li>Cancel button for DAS Feature Fetching
3545 <li>PCA and PDB Viewers zoom via mouse roller
3546 <li>User-defined sub-tree colours and sub-tree selection
3548 <li>'New Window' button on the 'Output to Text box'
3553 <li>New memory efficient Undo/Redo System
3554 <li>Optimised symbol lookups and conservation/consensus
3556 <li>Region Conservation/Consensus recalculated after
3558 <li>Fixed Remove Empty Columns Bug (empty columns at end
3560 <li>Slowed DAS Feature Fetching for increased robustness.
3562 <li>Made angle brackets in ASCII feature descriptions
3564 <li>Re-instated Zoom function for PCA
3565 <li>Sequence descriptions conserved in web service
3567 <li>UniProt ID discoverer uses any word separated by
3569 <li>WsDbFetch query/result association resolved
3570 <li>Tree leaf to sequence mapping improved
3571 <li>Smooth fonts switch moved to FontChooser dialog box.
3578 <div align="center">
3579 <strong>2.1.1</strong><br> 12/9/06
3584 <li>Copy consensus sequence to clipboard</li>
3589 <li>Image output - rightmost residues are rendered if
3590 sequence id panel has been resized</li>
3591 <li>Image output - all offscreen group boundaries are
3593 <li>Annotation files with sequence references - all
3594 elements in file are relative to sequence position</li>
3595 <li>Mac Applet users can use Alt key for group editing</li>
3601 <div align="center">
3602 <strong>2.1</strong><br> 22/8/06
3607 <li>MAFFT Multiple Alignment in default Web Service list</li>
3608 <li>DAS Feature fetching</li>
3609 <li>Hide sequences and columns</li>
3610 <li>Export Annotations and Features</li>
3611 <li>GFF file reading / writing</li>
3612 <li>Associate structures with sequences from local PDB
3614 <li>Add sequences to exisiting alignment</li>
3615 <li>Recently opened files / URL lists</li>
3616 <li>Applet can launch the full application</li>
3617 <li>Applet has transparency for features (Java 1.2
3619 <li>Applet has user defined colours parameter</li>
3620 <li>Applet can load sequences from parameter
3621 "sequence<em>x</em>"
3627 <li>Redundancy Panel reinstalled in the Applet</li>
3628 <li>Monospaced font - EPS / rescaling bug fixed</li>
3629 <li>Annotation files with sequence references bug fixed</li>
3635 <div align="center">
3636 <strong>2.08.1</strong><br> 2/5/06
3641 <li>Change case of selected region from Popup menu</li>
3642 <li>Choose to match case when searching</li>
3643 <li>Middle mouse button and mouse movement can compress /
3644 expand the visible width and height of the alignment</li>
3649 <li>Annotation Panel displays complete JNet results</li>
3655 <div align="center">
3656 <strong>2.08b</strong><br> 18/4/06
3662 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3663 <li>Righthand label on wrapped alignments shows correct
3670 <div align="center">
3671 <strong>2.08</strong><br> 10/4/06
3676 <li>Editing can be locked to the selection area</li>
3677 <li>Keyboard editing</li>
3678 <li>Create sequence features from searches</li>
3679 <li>Precalculated annotations can be loaded onto
3681 <li>Features file allows grouping of features</li>
3682 <li>Annotation Colouring scheme added</li>
3683 <li>Smooth fonts off by default - Faster rendering</li>
3684 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3689 <li>Drag & Drop fixed on Linux</li>
3690 <li>Jalview Archive file faster to load/save, sequence
3691 descriptions saved.</li>
3697 <div align="center">
3698 <strong>2.07</strong><br> 12/12/05
3703 <li>PDB Structure Viewer enhanced</li>
3704 <li>Sequence Feature retrieval and display enhanced</li>
3705 <li>Choose to output sequence start-end after sequence
3706 name for file output</li>
3707 <li>Sequence Fetcher WSDBFetch@EBI</li>
3708 <li>Applet can read feature files, PDB files and can be
3709 used for HTML form input</li>
3714 <li>HTML output writes groups and features</li>
3715 <li>Group editing is Control and mouse click</li>
3716 <li>File IO bugs</li>
3722 <div align="center">
3723 <strong>2.06</strong><br> 28/9/05
3728 <li>View annotations in wrapped mode</li>
3729 <li>More options for PCA viewer</li>
3734 <li>GUI bugs resolved</li>
3735 <li>Runs with -nodisplay from command line</li>
3741 <div align="center">
3742 <strong>2.05b</strong><br> 15/9/05
3747 <li>Choose EPS export as lineart or text</li>
3748 <li>Jar files are executable</li>
3749 <li>Can read in Uracil - maps to unknown residue</li>
3754 <li>Known OutOfMemory errors give warning message</li>
3755 <li>Overview window calculated more efficiently</li>
3756 <li>Several GUI bugs resolved</li>
3762 <div align="center">
3763 <strong>2.05</strong><br> 30/8/05
3768 <li>Edit and annotate in "Wrapped" view</li>
3773 <li>Several GUI bugs resolved</li>
3779 <div align="center">
3780 <strong>2.04</strong><br> 24/8/05
3785 <li>Hold down mouse wheel & scroll to change font
3791 <li>Improved JPred client reliability</li>
3792 <li>Improved loading of Jalview files</li>
3798 <div align="center">
3799 <strong>2.03</strong><br> 18/8/05
3804 <li>Set Proxy server name and port in preferences</li>
3805 <li>Multiple URL links from sequence ids</li>
3806 <li>User Defined Colours can have a scheme name and added
3808 <li>Choose to ignore gaps in consensus calculation</li>
3809 <li>Unix users can set default web browser</li>
3810 <li>Runs without GUI for batch processing</li>
3811 <li>Dynamically generated Web Service Menus</li>
3816 <li>InstallAnywhere download for Sparc Solaris</li>
3822 <div align="center">
3823 <strong>2.02</strong><br> 18/7/05
3829 <li>Copy & Paste order of sequences maintains
3830 alignment order.</li>
3836 <div align="center">
3837 <strong>2.01</strong><br> 12/7/05
3842 <li>Use delete key for deleting selection.</li>
3843 <li>Use Mouse wheel to scroll sequences.</li>
3844 <li>Help file updated to describe how to add alignment
3846 <li>Version and build date written to build properties
3848 <li>InstallAnywhere installation will check for updates
3849 at launch of Jalview.</li>
3854 <li>Delete gaps bug fixed.</li>
3855 <li>FileChooser sorts columns.</li>
3856 <li>Can remove groups one by one.</li>
3857 <li>Filechooser icons installed.</li>
3858 <li>Finder ignores return character when searching.
3859 Return key will initiate a search.<br>
3866 <div align="center">
3867 <strong>2.0</strong><br> 20/6/05
3872 <li>New codebase</li>