3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
34 /* separate the items from eachother */
41 /* doesnt get processed in javahelp */
50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>1/05/2018</em></strong>
76 <td><div align="left">
80 <!-- JAL-1847 JAL-2944 -->Structure Chooser controls to
81 control superposition of multiple structures and open
82 structures in existing views
85 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
86 ID and annotation area margins can be click-dragged to
90 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
94 <!-- JAL-2759 -->Improved performance for large alignments
95 and lots of hidden columns
100 <td><div align="left">
103 <!-- JAL-2778 -->Slow redraw when Overview panel shown
104 overlapping alignment panel
107 <!-- JAL-2666 -->Linked scrolling via protein horizontal
108 scroll bar doesn't work for some CDS/Protein views
111 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
112 Java 1.8u153 onwards and Java 1.9u4+.
115 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
116 columns in annotation row
119 <!-- JAL-2913 -->Preferences panel's ID Width control is
120 honored in interactive and batch mode
126 <!-- JAL-2926 -->Copy consensus sequence option in applet
127 should copy the group consensus when popup is opened on it
134 <td width="60" nowrap>
136 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
139 <td><div align="left">
140 <ul><li>Updated Certum Codesigning Certificate
141 (Valid till 30th November 2018)</li></ul></div></td>
142 <td><div align="left">
145 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
146 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
147 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
148 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
149 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
150 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
151 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
157 <td width="60" nowrap>
159 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
162 <td><div align="left">
166 <!-- JAL-2446 -->Faster and more efficient management and
167 rendering of sequence features
170 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
171 429 rate limit request hander
174 <!-- JAL-2773 -->Structure views don't get updated unless
175 their colours have changed
178 <!-- JAL-2495 -->All linked sequences are highlighted for
179 a structure mousover (Jmol) or selection (Chimera)
182 <!-- JAL-2790 -->'Cancel' button in progress bar for
183 JABAWS AACon, RNAAliFold and Disorder prediction jobs
186 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
187 view from Ensembl locus cross-references
190 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
194 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
195 feature can be disabled
198 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
199 PDB easier retrieval of sequences for lists of IDs
202 <!-- JAL-2758 -->Short names for sequences retrieved from
208 <li>Groovy interpreter updated to 2.4.12</li>
209 <li>Example groovy script for generating a matrix of
210 percent identity scores for current alignment.</li>
212 <em>Testing and Deployment</em>
215 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
219 <td><div align="left">
223 <!-- JAL-2643 -->Pressing tab after updating the colour
224 threshold text field doesn't trigger an update to the
228 <!-- JAL-2682 -->Race condition when parsing sequence ID
232 <!-- JAL-2608 -->Overview windows are also closed when
233 alignment window is closed
236 <!-- JAL-2548 -->Export of features doesn't always respect
240 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
241 takes a long time in Cursor mode
247 <!-- JAL-2777 -->Structures with whitespace chainCode
248 cannot be viewed in Chimera
251 <!-- JAL-2728 -->Protein annotation panel too high in
255 <!-- JAL-2757 -->Can't edit the query after the server
256 error warning icon is shown in Uniprot and PDB Free Text
260 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
263 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
266 <!-- JAL-2739 -->Hidden column marker in last column not
267 rendered when switching back from Wrapped to normal view
270 <!-- JAL-2768 -->Annotation display corrupted when
271 scrolling right in unwapped alignment view
274 <!-- JAL-2542 -->Existing features on subsequence
275 incorrectly relocated when full sequence retrieved from
279 <!-- JAL-2733 -->Last reported memory still shown when
280 Desktop->Show Memory is unticked (OSX only)
283 <!-- JAL-2658 -->Amend Features dialog doesn't allow
284 features of same type and group to be selected for
288 <!-- JAL-2524 -->Jalview becomes sluggish in wide
289 alignments when hidden columns are present
292 <!-- JAL-2392 -->Jalview freezes when loading and
293 displaying several structures
296 <!-- JAL-2732 -->Black outlines left after resizing or
300 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
301 within the Jalview desktop on OSX
304 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
305 when in wrapped alignment mode
308 <!-- JAL-2636 -->Scale mark not shown when close to right
309 hand end of alignment
312 <!-- JAL-2684 -->Pairwise alignment of selected regions of
313 each selected sequence do not have correct start/end
317 <!-- JAL-2793 -->Alignment ruler height set incorrectly
318 after canceling the Alignment Window's Font dialog
321 <!-- JAL-2036 -->Show cross-references not enabled after
322 restoring project until a new view is created
325 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
326 URL links appears when only default EMBL-EBI link is
327 configured (since 2.10.2b2)
330 <!-- JAL-2775 -->Overview redraws whole window when box
334 <!-- JAL-2225 -->Structure viewer doesn't map all chains
335 in a multi-chain structure when viewing alignment
336 involving more than one chain (since 2.10)
339 <!-- JAL-2811 -->Double residue highlights in cursor mode
340 if new selection moves alignment window
343 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
344 arrow key in cursor mode to pass hidden column marker
347 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
348 that produces correctly annotated transcripts and products
351 <!-- JAL-2776 -->Toggling a feature group after first time
352 doesn't update associated structure view
355 <em>Applet</em><br />
358 <!-- JAL-2687 -->Concurrent modification exception when
359 closing alignment panel
362 <em>BioJSON</em><br />
365 <!-- JAL-2546 -->BioJSON export does not preserve
366 non-positional features
369 <em>New Known Issues</em>
372 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
373 sequence features correctly (for many previous versions of
377 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
378 using cursor in wrapped panel other than top
381 <!-- JAL-2791 -->Select columns containing feature ignores
382 graduated colour threshold
385 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
386 always preserve numbering and sequence features
389 <em>Known Java 9 Issues</em>
392 <!-- JAL-2902 -->Groovy Console very slow to open and is
393 not responsive when entering characters (Webstart, Java
400 <td width="60" nowrap>
402 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
403 <em>2/10/2017</em></strong>
406 <td><div align="left">
407 <em>New features in Jalview Desktop</em>
410 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
412 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
416 <td><div align="left">
420 <td width="60" nowrap>
422 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
423 <em>7/9/2017</em></strong>
426 <td><div align="left">
430 <!-- JAL-2588 -->Show gaps in overview window by colouring
431 in grey (sequences used to be coloured grey, and gaps were
435 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
439 <!-- JAL-2587 -->Overview updates immediately on increase
440 in size and progress bar shown as higher resolution
441 overview is recalculated
446 <td><div align="left">
450 <!-- JAL-2664 -->Overview window redraws every hidden
451 column region row by row
454 <!-- JAL-2681 -->duplicate protein sequences shown after
455 retrieving Ensembl crossrefs for sequences from Uniprot
458 <!-- JAL-2603 -->Overview window throws NPE if show boxes
459 format setting is unticked
462 <!-- JAL-2610 -->Groups are coloured wrongly in overview
463 if group has show boxes format setting unticked
466 <!-- JAL-2672,JAL-2665 -->Redraw problems when
467 autoscrolling whilst dragging current selection group to
468 include sequences and columns not currently displayed
471 <!-- JAL-2691 -->Not all chains are mapped when multimeric
472 assemblies are imported via CIF file
475 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
476 displayed when threshold or conservation colouring is also
480 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
484 <!-- JAL-2673 -->Jalview continues to scroll after
485 dragging a selected region off the visible region of the
489 <!-- JAL-2724 -->Cannot apply annotation based
490 colourscheme to all groups in a view
493 <!-- JAL-2511 -->IDs don't line up with sequences
494 initially after font size change using the Font chooser or
501 <td width="60" nowrap>
503 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
506 <td><div align="left">
507 <em>Calculations</em>
511 <!-- JAL-1933 -->Occupancy annotation row shows number of
512 ungapped positions in each column of the alignment.
515 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
516 a calculation dialog box
519 <!-- JAL-2379 -->Revised implementation of PCA for speed
520 and memory efficiency (~30x faster)
523 <!-- JAL-2403 -->Revised implementation of sequence
524 similarity scores as used by Tree, PCA, Shading Consensus
525 and other calculations
528 <!-- JAL-2416 -->Score matrices are stored as resource
529 files within the Jalview codebase
532 <!-- JAL-2500 -->Trees computed on Sequence Feature
533 Similarity may have different topology due to increased
540 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
541 model for alignments and groups
544 <!-- JAL-384 -->Custom shading schemes created via groovy
551 <!-- JAL-2526 -->Efficiency improvements for interacting
552 with alignment and overview windows
555 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
559 <!-- JAL-2388 -->Hidden columns and sequences can be
563 <!-- JAL-2611 -->Click-drag in visible area allows fine
564 adjustment of visible position
568 <em>Data import/export</em>
571 <!-- JAL-2535 -->Posterior probability annotation from
572 Stockholm files imported as sequence associated annotation
575 <!-- JAL-2507 -->More robust per-sequence positional
576 annotation input/output via stockholm flatfile
579 <!-- JAL-2533 -->Sequence names don't include file
580 extension when importing structure files without embedded
581 names or PDB accessions
584 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
585 format sequence substitution matrices
588 <em>User Interface</em>
591 <!-- JAL-2447 --> Experimental Features Checkbox in
592 Desktop's Tools menu to hide or show untested features in
596 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
597 via Overview or sequence motif search operations
600 <!-- JAL-2547 -->Amend sequence features dialog box can be
601 opened by double clicking gaps within sequence feature
605 <!-- JAL-1476 -->Status bar message shown when not enough
606 aligned positions were available to create a 3D structure
610 <em>3D Structure</em>
613 <!-- JAL-2430 -->Hidden regions in alignment views are not
614 coloured in linked structure views
617 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
618 file-based command exchange
621 <!-- JAL-2375 -->Structure chooser automatically shows
622 Cached Structures rather than querying the PDBe if
623 structures are already available for sequences
626 <!-- JAL-2520 -->Structures imported via URL are cached in
627 the Jalview project rather than downloaded again when the
631 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
632 to transfer Chimera's structure attributes as Jalview
633 features, and vice-versa (<strong>Experimental
637 <em>Web Services</em>
640 <!-- JAL-2549 -->Updated JABAWS client to v2.2
643 <!-- JAL-2335 -->Filter non-standard amino acids and
644 nucleotides when submitting to AACon and other MSA
648 <!-- JAL-2316, -->URLs for viewing database
649 cross-references provided by identifiers.org and the
657 <!-- JAL-2344 -->FileFormatI interface for describing and
658 identifying file formats (instead of String constants)
661 <!-- JAL-2228 -->FeatureCounter script refactored for
662 efficiency when counting all displayed features (not
663 backwards compatible with 2.10.1)
666 <em>Example files</em>
669 <!-- JAL-2631 -->Graduated feature colour style example
670 included in the example feature file
673 <em>Documentation</em>
676 <!-- JAL-2339 -->Release notes reformatted for readability
677 with the built-in Java help viewer
680 <!-- JAL-1644 -->Find documentation updated with 'search
681 sequence description' option
687 <!-- JAL-2485, -->External service integration tests for
688 Uniprot REST Free Text Search Client
691 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
694 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
699 <td><div align="left">
700 <em>Calculations</em>
703 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
704 matrix - C->R should be '-3'<br />Old matrix restored
705 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
707 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
708 Jalview's treatment of gaps in PCA and substitution matrix
709 based Tree calculations.<br /> <br />In earlier versions
710 of Jalview, gaps matching gaps were penalised, and gaps
711 matching non-gaps penalised even more. In the PCA
712 calculation, gaps were actually treated as non-gaps - so
713 different costs were applied, which meant Jalview's PCAs
714 were different to those produced by SeqSpace.<br />Jalview
715 now treats gaps in the same way as SeqSpace (ie it scores
716 them as 0). <br /> <br />Enter the following in the
717 Groovy console to restore pre-2.10.2 behaviour:<br />
718 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
719 // for 2.10.1 mode <br />
720 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
721 // to restore 2.10.2 mode <br /> <br /> <em>Note:
722 these settings will affect all subsequent tree and PCA
723 calculations (not recommended)</em></li>
725 <!-- JAL-2424 -->Fixed off-by-one bug that affected
726 scaling of branch lengths for trees computed using
727 Sequence Feature Similarity.
730 <!-- JAL-2377 -->PCA calculation could hang when
731 generating output report when working with highly
735 <!-- JAL-2544 --> Sort by features includes features to
736 right of selected region when gaps present on right-hand
740 <em>User Interface</em>
743 <!-- JAL-2346 -->Reopening Colour by annotation dialog
744 doesn't reselect a specific sequence's associated
745 annotation after it was used for colouring a view
748 <!-- JAL-2419 -->Current selection lost if popup menu
749 opened on a region of alignment without groups
752 <!-- JAL-2374 -->Popup menu not always shown for regions
753 of an alignment with overlapping groups
756 <!-- JAL-2310 -->Finder double counts if both a sequence's
757 name and description match
760 <!-- JAL-2370 -->Hiding column selection containing two
761 hidden regions results in incorrect hidden regions
764 <!-- JAL-2386 -->'Apply to all groups' setting when
765 changing colour does not apply Conservation slider value
769 <!-- JAL-2373 -->Percentage identity and conservation menu
770 items do not show a tick or allow shading to be disabled
773 <!-- JAL-2385 -->Conservation shading or PID threshold
774 lost when base colourscheme changed if slider not visible
777 <!-- JAL-2547 -->Sequence features shown in tooltip for
778 gaps before start of features
781 <!-- JAL-2623 -->Graduated feature colour threshold not
782 restored to UI when feature colour is edited
785 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
786 a time when scrolling vertically in wrapped mode.
789 <!-- JAL-2630 -->Structure and alignment overview update
790 as graduate feature colour settings are modified via the
794 <!-- JAL-2034 -->Overview window doesn't always update
795 when a group defined on the alignment is resized
798 <!-- JAL-2605 -->Mouseovers on left/right scale region in
799 wrapped view result in positional status updates
803 <!-- JAL-2563 -->Status bar doesn't show position for
804 ambiguous amino acid and nucleotide symbols
807 <!-- JAL-2602 -->Copy consensus sequence failed if
808 alignment included gapped columns
811 <!-- JAL-2473 -->Minimum size set for Jalview windows so
812 widgets don't permanently disappear
815 <!-- JAL-2503 -->Cannot select or filter quantitative
816 annotation that are shown only as column labels (e.g.
817 T-Coffee column reliability scores)
820 <!-- JAL-2594 -->Exception thrown if trying to create a
821 sequence feature on gaps only
824 <!-- JAL-2504 -->Features created with 'New feature'
825 button from a Find inherit previously defined feature type
826 rather than the Find query string
829 <!-- JAL-2423 -->incorrect title in output window when
830 exporting tree calculated in Jalview
833 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
834 and then revealing them reorders sequences on the
838 <!-- JAL-964 -->Group panel in sequence feature settings
839 doesn't update to reflect available set of groups after
840 interactively adding or modifying features
843 <!-- JAL-2225 -->Sequence Database chooser unusable on
847 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
848 only excluded gaps in current sequence and ignored
855 <!-- JAL-2421 -->Overview window visible region moves
856 erratically when hidden rows or columns are present
859 <!-- JAL-2362 -->Per-residue colourschemes applied via the
860 Structure Viewer's colour menu don't correspond to
864 <!-- JAL-2405 -->Protein specific colours only offered in
865 colour and group colour menu for protein alignments
868 <!-- JAL-2385 -->Colour threshold slider doesn't update to
869 reflect currently selected view or group's shading
873 <!-- JAL-2624 -->Feature colour thresholds not respected
874 when rendered on overview and structures when opacity at
878 <!-- JAL-2589 -->User defined gap colour not shown in
879 overview when features overlaid on alignment
882 <em>Data import/export</em>
885 <!-- JAL-2576 -->Very large alignments take a long time to
889 <!-- JAL-2507 -->Per-sequence RNA secondary structures
890 added after a sequence was imported are not written to
894 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
895 when importing RNA secondary structure via Stockholm
898 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
899 not shown in correct direction for simple pseudoknots
902 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
903 with lightGray or darkGray via features file (but can
907 <!-- JAL-2383 -->Above PID colour threshold not recovered
908 when alignment view imported from project
911 <!-- JAL-2520,JAL-2465 -->No mappings generated between
912 structure and sequences extracted from structure files
913 imported via URL and viewed in Jmol
916 <!-- JAL-2520 -->Structures loaded via URL are saved in
917 Jalview Projects rather than fetched via URL again when
918 the project is loaded and the structure viewed
921 <em>Web Services</em>
924 <!-- JAL-2519 -->EnsemblGenomes example failing after
925 release of Ensembl v.88
928 <!-- JAL-2366 -->Proxy server address and port always
929 appear enabled in Preferences->Connections
932 <!-- JAL-2461 -->DAS registry not found exceptions
933 removed from console output
936 <!-- JAL-2582 -->Cannot retrieve protein products from
937 Ensembl by Peptide ID
940 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
941 created from SIFTs, and spurious 'Couldn't open structure
942 in Chimera' errors raised after April 2017 update (problem
943 due to 'null' string rather than empty string used for
944 residues with no corresponding PDB mapping).
947 <em>Application UI</em>
950 <!-- JAL-2361 -->User Defined Colours not added to Colour
954 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
955 case' residues (button in colourscheme editor debugged and
956 new documentation and tooltips added)
959 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
960 doesn't restore group-specific text colour thresholds
963 <!-- JAL-2243 -->Feature settings panel does not update as
964 new features are added to alignment
967 <!-- JAL-2532 -->Cancel in feature settings reverts
968 changes to feature colours via the Amend features dialog
971 <!-- JAL-2506 -->Null pointer exception when attempting to
972 edit graduated feature colour via amend features dialog
976 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
977 selection menu changes colours of alignment views
980 <!-- JAL-2426 -->Spurious exceptions in console raised
981 from alignment calculation workers after alignment has
985 <!-- JAL-1608 -->Typo in selection popup menu - Create
986 groups now 'Create Group'
989 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
990 Create/Undefine group doesn't always work
993 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
994 shown again after pressing 'Cancel'
997 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
998 adjusts start position in wrap mode
1001 <!-- JAL-2563 -->Status bar doesn't show positions for
1002 ambiguous amino acids
1005 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1006 CDS/Protein view after CDS sequences added for aligned
1010 <!-- JAL-2592 -->User defined colourschemes called 'User
1011 Defined' don't appear in Colours menu
1017 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1018 score models doesn't always result in an updated PCA plot
1021 <!-- JAL-2442 -->Features not rendered as transparent on
1022 overview or linked structure view
1025 <!-- JAL-2372 -->Colour group by conservation doesn't
1029 <!-- JAL-2517 -->Hitting Cancel after applying
1030 user-defined colourscheme doesn't restore original
1037 <!-- JAL-2314 -->Unit test failure:
1038 jalview.ws.jabaws.RNAStructExportImport setup fails
1041 <!-- JAL-2307 -->Unit test failure:
1042 jalview.ws.sifts.SiftsClientTest due to compatibility
1043 problems with deep array comparison equality asserts in
1044 successive versions of TestNG
1047 <!-- JAL-2479 -->Relocated StructureChooserTest and
1048 ParameterUtilsTest Unit tests to Network suite
1051 <em>New Known Issues</em>
1054 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1055 phase after a sequence motif find operation
1058 <!-- JAL-2550 -->Importing annotation file with rows
1059 containing just upper and lower case letters are
1060 interpreted as WUSS RNA secondary structure symbols
1063 <!-- JAL-2590 -->Cannot load and display Newick trees
1064 reliably from eggnog Ortholog database
1067 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1068 containing features of type Highlight' when 'B' is pressed
1069 to mark columns containing highlighted regions.
1072 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1073 doesn't always add secondary structure annotation.
1078 <td width="60" nowrap>
1079 <div align="center">
1080 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1083 <td><div align="left">
1087 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1088 for all consensus calculations
1091 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1094 <li>Updated Jalview's Certum code signing certificate
1097 <em>Application</em>
1100 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1101 set of database cross-references, sorted alphabetically
1104 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1105 from database cross references. Users with custom links
1106 will receive a <a href="webServices/urllinks.html#warning">warning
1107 dialog</a> asking them to update their preferences.
1110 <!-- JAL-2287-->Cancel button and escape listener on
1111 dialog warning user about disconnecting Jalview from a
1115 <!-- JAL-2320-->Jalview's Chimera control window closes if
1116 the Chimera it is connected to is shut down
1119 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1120 columns menu item to mark columns containing highlighted
1121 regions (e.g. from structure selections or results of a
1125 <!-- JAL-2284-->Command line option for batch-generation
1126 of HTML pages rendering alignment data with the BioJS
1136 <!-- JAL-2286 -->Columns with more than one modal residue
1137 are not coloured or thresholded according to percent
1138 identity (first observed in Jalview 2.8.2)
1141 <!-- JAL-2301 -->Threonine incorrectly reported as not
1145 <!-- JAL-2318 -->Updates to documentation pages (above PID
1146 threshold, amino acid properties)
1149 <!-- JAL-2292 -->Lower case residues in sequences are not
1150 reported as mapped to residues in a structure file in the
1154 <!--JAL-2324 -->Identical features with non-numeric scores
1155 could be added multiple times to a sequence
1158 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1159 bond features shown as two highlighted residues rather
1160 than a range in linked structure views, and treated
1161 correctly when selecting and computing trees from features
1164 <!-- JAL-2281-->Custom URL links for database
1165 cross-references are matched to database name regardless
1170 <em>Application</em>
1173 <!-- JAL-2282-->Custom URL links for specific database
1174 names without regular expressions also offer links from
1178 <!-- JAL-2315-->Removing a single configured link in the
1179 URL links pane in Connections preferences doesn't actually
1180 update Jalview configuration
1183 <!-- JAL-2272-->CTRL-Click on a selected region to open
1184 the alignment area popup menu doesn't work on El-Capitan
1187 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1188 files with similarly named sequences if dropped onto the
1192 <!-- JAL-2312 -->Additional mappings are shown for PDB
1193 entries where more chains exist in the PDB accession than
1194 are reported in the SIFTS file
1197 <!-- JAL-2317-->Certain structures do not get mapped to
1198 the structure view when displayed with Chimera
1201 <!-- JAL-2317-->No chains shown in the Chimera view
1202 panel's View->Show Chains submenu
1205 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1206 work for wrapped alignment views
1209 <!--JAL-2197 -->Rename UI components for running JPred
1210 predictions from 'JNet' to 'JPred'
1213 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1214 corrupted when annotation panel vertical scroll is not at
1215 first annotation row
1218 <!--JAL-2332 -->Attempting to view structure for Hen
1219 lysozyme results in a PDB Client error dialog box
1222 <!-- JAL-2319 -->Structure View's mapping report switched
1223 ranges for PDB and sequence for SIFTS
1226 SIFTS 'Not_Observed' residues mapped to non-existant
1230 <!-- <em>New Known Issues</em>
1237 <td width="60" nowrap>
1238 <div align="center">
1239 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1240 <em>25/10/2016</em></strong>
1243 <td><em>Application</em>
1245 <li>3D Structure chooser opens with 'Cached structures'
1246 view if structures already loaded</li>
1247 <li>Progress bar reports models as they are loaded to
1248 structure views</li>
1254 <li>Colour by conservation always enabled and no tick
1255 shown in menu when BLOSUM or PID shading applied</li>
1256 <li>FER1_ARATH and FER2_ARATH labels were switched in
1257 example sequences/projects/trees</li>
1259 <em>Application</em>
1261 <li>Jalview projects with views of local PDB structure
1262 files saved on Windows cannot be opened on OSX</li>
1263 <li>Multiple structure views can be opened and superposed
1264 without timeout for structures with multiple models or
1265 multiple sequences in alignment</li>
1266 <li>Cannot import or associated local PDB files without a
1267 PDB ID HEADER line</li>
1268 <li>RMSD is not output in Jmol console when superposition
1270 <li>Drag and drop of URL from Browser fails for Linux and
1271 OSX versions earlier than El Capitan</li>
1272 <li>ENA client ignores invalid content from ENA server</li>
1273 <li>Exceptions are not raised in console when ENA client
1274 attempts to fetch non-existent IDs via Fetch DB Refs UI
1276 <li>Exceptions are not raised in console when a new view
1277 is created on the alignment</li>
1278 <li>OSX right-click fixed for group selections: CMD-click
1279 to insert/remove gaps in groups and CTRL-click to open group
1282 <em>Build and deployment</em>
1284 <li>URL link checker now copes with multi-line anchor
1287 <em>New Known Issues</em>
1289 <li>Drag and drop from URL links in browsers do not work
1296 <td width="60" nowrap>
1297 <div align="center">
1298 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1301 <td><em>General</em>
1304 <!-- JAL-2124 -->Updated Spanish translations.
1307 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1308 for importing structure data to Jalview. Enables mmCIF and
1312 <!-- JAL-192 --->Alignment ruler shows positions relative to
1316 <!-- JAL-2202 -->Position/residue shown in status bar when
1317 mousing over sequence associated annotation
1320 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1324 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1325 '()', canonical '[]' and invalid '{}' base pair populations
1329 <!-- JAL-2092 -->Feature settings popup menu options for
1330 showing or hiding columns containing a feature
1333 <!-- JAL-1557 -->Edit selected group by double clicking on
1334 group and sequence associated annotation labels
1337 <!-- JAL-2236 -->Sequence name added to annotation label in
1338 select/hide columns by annotation and colour by annotation
1342 </ul> <em>Application</em>
1345 <!-- JAL-2050-->Automatically hide introns when opening a
1346 gene/transcript view
1349 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1353 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1354 structure mappings with the EMBL-EBI PDBe SIFTS database
1357 <!-- JAL-2079 -->Updated download sites used for Rfam and
1358 Pfam sources to xfam.org
1361 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1364 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1365 over sequences in Jalview
1368 <!-- JAL-2027-->Support for reverse-complement coding
1369 regions in ENA and EMBL
1372 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1373 for record retrieval via ENA rest API
1376 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1380 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1381 groovy script execution
1384 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1385 alignment window's Calculate menu
1388 <!-- JAL-1812 -->Allow groovy scripts that call
1389 Jalview.getAlignFrames() to run in headless mode
1392 <!-- JAL-2068 -->Support for creating new alignment
1393 calculation workers from groovy scripts
1396 <!-- JAL-1369 --->Store/restore reference sequence in
1400 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1401 associations are now saved/restored from project
1404 <!-- JAL-1993 -->Database selection dialog always shown
1405 before sequence fetcher is opened
1408 <!-- JAL-2183 -->Double click on an entry in Jalview's
1409 database chooser opens a sequence fetcher
1412 <!-- JAL-1563 -->Free-text search client for UniProt using
1413 the UniProt REST API
1416 <!-- JAL-2168 -->-nonews command line parameter to prevent
1417 the news reader opening
1420 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1421 querying stored in preferences
1424 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1428 <!-- JAL-1977-->Tooltips shown on database chooser
1431 <!-- JAL-391 -->Reverse complement function in calculate
1432 menu for nucleotide sequences
1435 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1436 and feature counts preserves alignment ordering (and
1437 debugged for complex feature sets).
1440 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1441 viewing structures with Jalview 2.10
1444 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1445 genome, transcript CCDS and gene ids via the Ensembl and
1446 Ensembl Genomes REST API
1449 <!-- JAL-2049 -->Protein sequence variant annotation
1450 computed for 'sequence_variant' annotation on CDS regions
1454 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1458 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1459 Ref Fetcher fails to match, or otherwise updates sequence
1460 data from external database records.
1463 <!-- JAL-2154 -->Revised Jalview Project format for
1464 efficient recovery of sequence coding and alignment
1465 annotation relationships.
1467 </ul> <!-- <em>Applet</em>
1478 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1482 <!-- JAL-2018-->Export features in Jalview format (again)
1483 includes graduated colourschemes
1486 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1487 working with big alignments and lots of hidden columns
1490 <!-- JAL-2053-->Hidden column markers not always rendered
1491 at right of alignment window
1494 <!-- JAL-2067 -->Tidied up links in help file table of
1498 <!-- JAL-2072 -->Feature based tree calculation not shown
1502 <!-- JAL-2075 -->Hidden columns ignored during feature
1503 based tree calculation
1506 <!-- JAL-2065 -->Alignment view stops updating when show
1507 unconserved enabled for group on alignment
1510 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1514 <!-- JAL-2146 -->Alignment column in status incorrectly
1515 shown as "Sequence position" when mousing over
1519 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1520 hidden columns present
1523 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1524 user created annotation added to alignment
1527 <!-- JAL-1841 -->RNA Structure consensus only computed for
1528 '()' base pair annotation
1531 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1532 in zero scores for all base pairs in RNA Structure
1536 <!-- JAL-2174-->Extend selection with columns containing
1540 <!-- JAL-2275 -->Pfam format writer puts extra space at
1541 beginning of sequence
1544 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1548 <!-- JAL-2238 -->Cannot create groups on an alignment from
1549 from a tree when t-coffee scores are shown
1552 <!-- JAL-1836,1967 -->Cannot import and view PDB
1553 structures with chains containing negative resnums (4q4h)
1556 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1560 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1561 to Clustal, PIR and PileUp output
1564 <!-- JAL-2008 -->Reordering sequence features that are
1565 not visible causes alignment window to repaint
1568 <!-- JAL-2006 -->Threshold sliders don't work in
1569 graduated colour and colour by annotation row for e-value
1570 scores associated with features and annotation rows
1573 <!-- JAL-1797 -->amino acid physicochemical conservation
1574 calculation should be case independent
1577 <!-- JAL-2173 -->Remove annotation also updates hidden
1581 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1582 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1583 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1586 <!-- JAL-2065 -->Null pointer exceptions and redraw
1587 problems when reference sequence defined and 'show
1588 non-conserved' enabled
1591 <!-- JAL-1306 -->Quality and Conservation are now shown on
1592 load even when Consensus calculation is disabled
1595 <!-- JAL-1932 -->Remove right on penultimate column of
1596 alignment does nothing
1599 <em>Application</em>
1602 <!-- JAL-1552-->URLs and links can't be imported by
1603 drag'n'drop on OSX when launched via webstart (note - not
1604 yet fixed for El Capitan)
1607 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1608 output when running on non-gb/us i18n platforms
1611 <!-- JAL-1944 -->Error thrown when exporting a view with
1612 hidden sequences as flat-file alignment
1615 <!-- JAL-2030-->InstallAnywhere distribution fails when
1619 <!-- JAL-2080-->Jalview very slow to launch via webstart
1620 (also hotfix for 2.9.0b2)
1623 <!-- JAL-2085 -->Cannot save project when view has a
1624 reference sequence defined
1627 <!-- JAL-1011 -->Columns are suddenly selected in other
1628 alignments and views when revealing hidden columns
1631 <!-- JAL-1989 -->Hide columns not mirrored in complement
1632 view in a cDNA/Protein splitframe
1635 <!-- JAL-1369 -->Cannot save/restore representative
1636 sequence from project when only one sequence is
1640 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1641 in Structure Chooser
1644 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1645 structure consensus didn't refresh annotation panel
1648 <!-- JAL-1962 -->View mapping in structure view shows
1649 mappings between sequence and all chains in a PDB file
1652 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1653 dialogs format columns correctly, don't display array
1654 data, sort columns according to type
1657 <!-- JAL-1975 -->Export complete shown after destination
1658 file chooser is cancelled during an image export
1661 <!-- JAL-2025 -->Error when querying PDB Service with
1662 sequence name containing special characters
1665 <!-- JAL-2024 -->Manual PDB structure querying should be
1669 <!-- JAL-2104 -->Large tooltips with broken HTML
1670 formatting don't wrap
1673 <!-- JAL-1128 -->Figures exported from wrapped view are
1674 truncated so L looks like I in consensus annotation
1677 <!-- JAL-2003 -->Export features should only export the
1678 currently displayed features for the current selection or
1682 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1683 after fetching cross-references, and restoring from
1687 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1688 followed in the structure viewer
1691 <!-- JAL-2163 -->Titles for individual alignments in
1692 splitframe not restored from project
1695 <!-- JAL-2145 -->missing autocalculated annotation at
1696 trailing end of protein alignment in transcript/product
1697 splitview when pad-gaps not enabled by default
1700 <!-- JAL-1797 -->amino acid physicochemical conservation
1704 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1705 article has been read (reopened issue due to
1706 internationalisation problems)
1709 <!-- JAL-1960 -->Only offer PDB structures in structure
1710 viewer based on sequence name, PDB and UniProt
1715 <!-- JAL-1976 -->No progress bar shown during export of
1719 <!-- JAL-2213 -->Structures not always superimposed after
1720 multiple structures are shown for one or more sequences.
1723 <!-- JAL-1370 -->Reference sequence characters should not
1724 be replaced with '.' when 'Show unconserved' format option
1728 <!-- JAL-1823 -->Cannot specify chain code when entering
1729 specific PDB id for sequence
1732 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1733 'Export hidden sequences' is enabled, but 'export hidden
1734 columns' is disabled.
1737 <!--JAL-2026-->Best Quality option in structure chooser
1738 selects lowest rather than highest resolution structures
1742 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1743 to sequence mapping in 'View Mappings' report
1746 <!-- JAL-2284 -->Unable to read old Jalview projects that
1747 contain non-XML data added after Jalvew wrote project.
1750 <!-- JAL-2118 -->Newly created annotation row reorders
1751 after clicking on it to create new annotation for a
1755 <!-- JAL-1980 -->Null Pointer Exception raised when
1756 pressing Add on an orphaned cut'n'paste window.
1758 <!-- may exclude, this is an external service stability issue JAL-1941
1759 -- > RNA 3D structure not added via DSSR service</li> -->
1764 <!-- JAL-2151 -->Incorrect columns are selected when
1765 hidden columns present before start of sequence
1768 <!-- JAL-1986 -->Missing dependencies on applet pages
1772 <!-- JAL-1947 -->Overview pixel size changes when
1773 sequences are hidden in applet
1776 <!-- JAL-1996 -->Updated instructions for applet
1777 deployment on examples pages.
1784 <td width="60" nowrap>
1785 <div align="center">
1786 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1787 <em>16/10/2015</em></strong>
1790 <td><em>General</em>
1792 <li>Time stamps for signed Jalview application and applet
1797 <em>Application</em>
1799 <li>Duplicate group consensus and conservation rows
1800 shown when tree is partitioned</li>
1801 <li>Erratic behaviour when tree partitions made with
1802 multiple cDNA/Protein split views</li>
1808 <td width="60" nowrap>
1809 <div align="center">
1810 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1811 <em>8/10/2015</em></strong>
1814 <td><em>General</em>
1816 <li>Updated Spanish translations of localized text for
1818 </ul> <em>Application</em>
1820 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1821 <li>Signed OSX InstallAnywhere installer<br></li>
1822 <li>Support for per-sequence based annotations in BioJSON</li>
1823 </ul> <em>Applet</em>
1825 <li>Split frame example added to applet examples page</li>
1826 </ul> <em>Build and Deployment</em>
1829 <!-- JAL-1888 -->New ant target for running Jalview's test
1837 <li>Mapping of cDNA to protein in split frames
1838 incorrect when sequence start > 1</li>
1839 <li>Broken images in filter column by annotation dialog
1841 <li>Feature colours not parsed from features file</li>
1842 <li>Exceptions and incomplete link URLs recovered when
1843 loading a features file containing HTML tags in feature
1847 <em>Application</em>
1849 <li>Annotations corrupted after BioJS export and
1851 <li>Incorrect sequence limits after Fetch DB References
1852 with 'trim retrieved sequences'</li>
1853 <li>Incorrect warning about deleting all data when
1854 deleting selected columns</li>
1855 <li>Patch to build system for shipping properly signed
1856 JNLP templates for webstart launch</li>
1857 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1858 unreleased structures for download or viewing</li>
1859 <li>Tab/space/return keystroke operation of EMBL-PDBe
1860 fetcher/viewer dialogs works correctly</li>
1861 <li>Disabled 'minimise' button on Jalview windows
1862 running on OSX to workaround redraw hang bug</li>
1863 <li>Split cDNA/Protein view position and geometry not
1864 recovered from jalview project</li>
1865 <li>Initial enabled/disabled state of annotation menu
1866 sorter 'show autocalculated first/last' corresponds to
1868 <li>Restoring of Clustal, RNA Helices and T-Coffee
1869 color schemes from BioJSON</li>
1873 <li>Reorder sequences mirrored in cDNA/Protein split
1875 <li>Applet with Jmol examples not loading correctly</li>
1881 <td><div align="center">
1882 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1884 <td><em>General</em>
1886 <li>Linked visualisation and analysis of DNA and Protein
1889 <li>Translated cDNA alignments shown as split protein
1890 and DNA alignment views</li>
1891 <li>Codon consensus annotation for linked protein and
1892 cDNA alignment views</li>
1893 <li>Link cDNA or Protein product sequences by loading
1894 them onto Protein or cDNA alignments</li>
1895 <li>Reconstruct linked cDNA alignment from aligned
1896 protein sequences</li>
1899 <li>Jmol integration updated to Jmol v14.2.14</li>
1900 <li>Import and export of Jalview alignment views as <a
1901 href="features/bioJsonFormat.html">BioJSON</a></li>
1902 <li>New alignment annotation file statements for
1903 reference sequences and marking hidden columns</li>
1904 <li>Reference sequence based alignment shading to
1905 highlight variation</li>
1906 <li>Select or hide columns according to alignment
1908 <li>Find option for locating sequences by description</li>
1909 <li>Conserved physicochemical properties shown in amino
1910 acid conservation row</li>
1911 <li>Alignments can be sorted by number of RNA helices</li>
1912 </ul> <em>Application</em>
1914 <li>New cDNA/Protein analysis capabilities
1916 <li>Get Cross-References should open a Split Frame
1917 view with cDNA/Protein</li>
1918 <li>Detect when nucleotide sequences and protein
1919 sequences are placed in the same alignment</li>
1920 <li>Split cDNA/Protein views are saved in Jalview
1925 <li>Use REST API to talk to Chimera</li>
1926 <li>Selected regions in Chimera are highlighted in linked
1927 Jalview windows</li>
1929 <li>VARNA RNA viewer updated to v3.93</li>
1930 <li>VARNA views are saved in Jalview Projects</li>
1931 <li>Pseudoknots displayed as Jalview RNA annotation can
1932 be shown in VARNA</li>
1934 <li>Make groups for selection uses marked columns as well
1935 as the active selected region</li>
1937 <li>Calculate UPGMA and NJ trees using sequence feature
1939 <li>New Export options
1941 <li>New Export Settings dialog to control hidden
1942 region export in flat file generation</li>
1944 <li>Export alignment views for display with the <a
1945 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1947 <li>Export scrollable SVG in HTML page</li>
1948 <li>Optional embedding of BioJSON data when exporting
1949 alignment figures to HTML</li>
1951 <li>3D structure retrieval and display
1953 <li>Free text and structured queries with the PDBe
1955 <li>PDBe Search API based discovery and selection of
1956 PDB structures for a sequence set</li>
1960 <li>JPred4 employed for protein secondary structure
1962 <li>Hide Insertions menu option to hide unaligned columns
1963 for one or a group of sequences</li>
1964 <li>Automatically hide insertions in alignments imported
1965 from the JPred4 web server</li>
1966 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1967 system on OSX<br />LGPL libraries courtesy of <a
1968 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1970 <li>changed 'View nucleotide structure' submenu to 'View
1971 VARNA 2D Structure'</li>
1972 <li>change "View protein structure" menu option to "3D
1975 </ul> <em>Applet</em>
1977 <li>New layout for applet example pages</li>
1978 <li>New parameters to enable SplitFrame view
1979 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1980 <li>New example demonstrating linked viewing of cDNA and
1981 Protein alignments</li>
1982 </ul> <em>Development and deployment</em>
1984 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1985 <li>Include installation type and git revision in build
1986 properties and console log output</li>
1987 <li>Jalview Github organisation, and new github site for
1988 storing BioJsMSA Templates</li>
1989 <li>Jalview's unit tests now managed with TestNG</li>
1992 <!-- <em>General</em>
1994 </ul> --> <!-- issues resolved --> <em>Application</em>
1996 <li>Escape should close any open find dialogs</li>
1997 <li>Typo in select-by-features status report</li>
1998 <li>Consensus RNA secondary secondary structure
1999 predictions are not highlighted in amber</li>
2000 <li>Missing gap character in v2.7 example file means
2001 alignment appears unaligned when pad-gaps is not enabled</li>
2002 <li>First switch to RNA Helices colouring doesn't colour
2003 associated structure views</li>
2004 <li>ID width preference option is greyed out when auto
2005 width checkbox not enabled</li>
2006 <li>Stopped a warning dialog from being shown when
2007 creating user defined colours</li>
2008 <li>'View Mapping' in structure viewer shows sequence
2009 mappings for just that viewer's sequences</li>
2010 <li>Workaround for superposing PDB files containing
2011 multiple models in Chimera</li>
2012 <li>Report sequence position in status bar when hovering
2013 over Jmol structure</li>
2014 <li>Cannot output gaps as '.' symbols with Selection ->
2015 output to text box</li>
2016 <li>Flat file exports of alignments with hidden columns
2017 have incorrect sequence start/end</li>
2018 <li>'Aligning' a second chain to a Chimera structure from
2020 <li>Colour schemes applied to structure viewers don't
2021 work for nucleotide</li>
2022 <li>Loading/cut'n'pasting an empty or invalid file leads
2023 to a grey/invisible alignment window</li>
2024 <li>Exported Jpred annotation from a sequence region
2025 imports to different position</li>
2026 <li>Space at beginning of sequence feature tooltips shown
2027 on some platforms</li>
2028 <li>Chimera viewer 'View | Show Chain' menu is not
2030 <li>'New View' fails with a Null Pointer Exception in
2031 console if Chimera has been opened</li>
2032 <li>Mouseover to Chimera not working</li>
2033 <li>Miscellaneous ENA XML feature qualifiers not
2035 <li>NPE in annotation renderer after 'Extract Scores'</li>
2036 <li>If two structures in one Chimera window, mouseover of
2037 either sequence shows on first structure</li>
2038 <li>'Show annotations' options should not make
2039 non-positional annotations visible</li>
2040 <li>Subsequence secondary structure annotation not shown
2041 in right place after 'view flanking regions'</li>
2042 <li>File Save As type unset when current file format is
2044 <li>Save as '.jar' option removed for saving Jalview
2046 <li>Colour by Sequence colouring in Chimera more
2048 <li>Cannot 'add reference annotation' for a sequence in
2049 several views on same alignment</li>
2050 <li>Cannot show linked products for EMBL / ENA records</li>
2051 <li>Jalview's tooltip wraps long texts containing no
2053 </ul> <em>Applet</em>
2055 <li>Jmol to JalviewLite mouseover/link not working</li>
2056 <li>JalviewLite can't import sequences with ID
2057 descriptions containing angle brackets</li>
2058 </ul> <em>General</em>
2060 <li>Cannot export and reimport RNA secondary structure
2061 via jalview annotation file</li>
2062 <li>Random helix colour palette for colour by annotation
2063 with RNA secondary structure</li>
2064 <li>Mouseover to cDNA from STOP residue in protein
2065 translation doesn't work.</li>
2066 <li>hints when using the select by annotation dialog box</li>
2067 <li>Jmol alignment incorrect if PDB file has alternate CA
2069 <li>FontChooser message dialog appears to hang after
2070 choosing 1pt font</li>
2071 <li>Peptide secondary structure incorrectly imported from
2072 annotation file when annotation display text includes 'e' or
2074 <li>Cannot set colour of new feature type whilst creating
2076 <li>cDNA translation alignment should not be sequence
2077 order dependent</li>
2078 <li>'Show unconserved' doesn't work for lower case
2080 <li>Nucleotide ambiguity codes involving R not recognised</li>
2081 </ul> <em>Deployment and Documentation</em>
2083 <li>Applet example pages appear different to the rest of
2084 www.jalview.org</li>
2085 </ul> <em>Application Known issues</em>
2087 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2088 <li>Misleading message appears after trying to delete
2090 <li>Jalview icon not shown in dock after InstallAnywhere
2091 version launches</li>
2092 <li>Fetching EMBL reference for an RNA sequence results
2093 fails with a sequence mismatch</li>
2094 <li>Corrupted or unreadable alignment display when
2095 scrolling alignment to right</li>
2096 <li>ArrayIndexOutOfBoundsException thrown when remove
2097 empty columns called on alignment with ragged gapped ends</li>
2098 <li>auto calculated alignment annotation rows do not get
2099 placed above or below non-autocalculated rows</li>
2100 <li>Jalview dekstop becomes sluggish at full screen in
2101 ultra-high resolution</li>
2102 <li>Cannot disable consensus calculation independently of
2103 quality and conservation</li>
2104 <li>Mouseover highlighting between cDNA and protein can
2105 become sluggish with more than one splitframe shown</li>
2106 </ul> <em>Applet Known Issues</em>
2108 <li>Core PDB parsing code requires Jmol</li>
2109 <li>Sequence canvas panel goes white when alignment
2110 window is being resized</li>
2116 <td><div align="center">
2117 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2119 <td><em>General</em>
2121 <li>Updated Java code signing certificate donated by
2123 <li>Features and annotation preserved when performing
2124 pairwise alignment</li>
2125 <li>RNA pseudoknot annotation can be
2126 imported/exported/displayed</li>
2127 <li>'colour by annotation' can colour by RNA and
2128 protein secondary structure</li>
2129 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2130 post-hoc with 2.9 release</em>)
2133 </ul> <em>Application</em>
2135 <li>Extract and display secondary structure for sequences
2136 with 3D structures</li>
2137 <li>Support for parsing RNAML</li>
2138 <li>Annotations menu for layout
2140 <li>sort sequence annotation rows by alignment</li>
2141 <li>place sequence annotation above/below alignment
2144 <li>Output in Stockholm format</li>
2145 <li>Internationalisation: improved Spanish (es)
2147 <li>Structure viewer preferences tab</li>
2148 <li>Disorder and Secondary Structure annotation tracks
2149 shared between alignments</li>
2150 <li>UCSF Chimera launch and linked highlighting from
2152 <li>Show/hide all sequence associated annotation rows for
2153 all or current selection</li>
2154 <li>disorder and secondary structure predictions
2155 available as dataset annotation</li>
2156 <li>Per-sequence rna helices colouring</li>
2159 <li>Sequence database accessions imported when fetching
2160 alignments from Rfam</li>
2161 <li>update VARNA version to 3.91</li>
2163 <li>New groovy scripts for exporting aligned positions,
2164 conservation values, and calculating sum of pairs scores.</li>
2165 <li>Command line argument to set default JABAWS server</li>
2166 <li>include installation type in build properties and
2167 console log output</li>
2168 <li>Updated Jalview project format to preserve dataset
2172 <!-- issues resolved --> <em>Application</em>
2174 <li>Distinguish alignment and sequence associated RNA
2175 structure in structure->view->VARNA</li>
2176 <li>Raise dialog box if user deletes all sequences in an
2178 <li>Pressing F1 results in documentation opening twice</li>
2179 <li>Sequence feature tooltip is wrapped</li>
2180 <li>Double click on sequence associated annotation
2181 selects only first column</li>
2182 <li>Redundancy removal doesn't result in unlinked
2183 leaves shown in tree</li>
2184 <li>Undos after several redundancy removals don't undo
2186 <li>Hide sequence doesn't hide associated annotation</li>
2187 <li>User defined colours dialog box too big to fit on
2188 screen and buttons not visible</li>
2189 <li>author list isn't updated if already written to
2190 Jalview properties</li>
2191 <li>Popup menu won't open after retrieving sequence
2193 <li>File open window for associate PDB doesn't open</li>
2194 <li>Left-then-right click on a sequence id opens a
2195 browser search window</li>
2196 <li>Cannot open sequence feature shading/sort popup menu
2197 in feature settings dialog</li>
2198 <li>better tooltip placement for some areas of Jalview
2200 <li>Allow addition of JABAWS Server which doesn't
2201 pass validation</li>
2202 <li>Web services parameters dialog box is too large to
2204 <li>Muscle nucleotide alignment preset obscured by
2206 <li>JABAWS preset submenus don't contain newly
2207 defined user preset</li>
2208 <li>MSA web services warns user if they were launched
2209 with invalid input</li>
2210 <li>Jalview cannot contact DAS Registy when running on
2213 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2214 'Superpose with' submenu not shown when new view
2218 </ul> <!-- <em>Applet</em>
2220 </ul> <em>General</em>
2222 </ul>--> <em>Deployment and Documentation</em>
2224 <li>2G and 1G options in launchApp have no effect on
2225 memory allocation</li>
2226 <li>launchApp service doesn't automatically open
2227 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2229 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2230 InstallAnywhere reports cannot find valid JVM when Java
2231 1.7_055 is available
2233 </ul> <em>Application Known issues</em>
2236 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2237 corrupted or unreadable alignment display when scrolling
2241 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2242 retrieval fails but progress bar continues for DAS retrieval
2243 with large number of ID
2246 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2247 flatfile output of visible region has incorrect sequence
2251 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2252 rna structure consensus doesn't update when secondary
2253 structure tracks are rearranged
2256 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2257 invalid rna structure positional highlighting does not
2258 highlight position of invalid base pairs
2261 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2262 out of memory errors are not raised when saving Jalview
2263 project from alignment window file menu
2266 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2267 Switching to RNA Helices colouring doesn't propagate to
2271 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2272 colour by RNA Helices not enabled when user created
2273 annotation added to alignment
2276 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2277 Jalview icon not shown on dock in Mountain Lion/Webstart
2279 </ul> <em>Applet Known Issues</em>
2282 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2283 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2286 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2287 Jalview and Jmol example not compatible with IE9
2290 <li>Sort by annotation score doesn't reverse order
2296 <td><div align="center">
2297 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2300 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2303 <li>Internationalisation of user interface (usually
2304 called i18n support) and translation for Spanish locale</li>
2305 <li>Define/Undefine group on current selection with
2306 Ctrl-G/Shift Ctrl-G</li>
2307 <li>Improved group creation/removal options in
2308 alignment/sequence Popup menu</li>
2309 <li>Sensible precision for symbol distribution
2310 percentages shown in logo tooltip.</li>
2311 <li>Annotation panel height set according to amount of
2312 annotation when alignment first opened</li>
2313 </ul> <em>Application</em>
2315 <li>Interactive consensus RNA secondary structure
2316 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2317 <li>Select columns containing particular features from
2318 Feature Settings dialog</li>
2319 <li>View all 'representative' PDB structures for selected
2321 <li>Update Jalview project format:
2323 <li>New file extension for Jalview projects '.jvp'</li>
2324 <li>Preserve sequence and annotation dataset (to
2325 store secondary structure annotation,etc)</li>
2326 <li>Per group and alignment annotation and RNA helix
2330 <li>New similarity measures for PCA and Tree calculation
2332 <li>Experimental support for retrieval and viewing of
2333 flanking regions for an alignment</li>
2337 <!-- issues resolved --> <em>Application</em>
2339 <li>logo keeps spinning and status remains at queued or
2340 running after job is cancelled</li>
2341 <li>cannot export features from alignments imported from
2342 Jalview/VAMSAS projects</li>
2343 <li>Buggy slider for web service parameters that take
2345 <li>Newly created RNA secondary structure line doesn't
2346 have 'display all symbols' flag set</li>
2347 <li>T-COFFEE alignment score shading scheme and other
2348 annotation shading not saved in Jalview project</li>
2349 <li>Local file cannot be loaded in freshly downloaded
2351 <li>Jalview icon not shown on dock in Mountain
2353 <li>Load file from desktop file browser fails</li>
2354 <li>Occasional NPE thrown when calculating large trees</li>
2355 <li>Cannot reorder or slide sequences after dragging an
2356 alignment onto desktop</li>
2357 <li>Colour by annotation dialog throws NPE after using
2358 'extract scores' function</li>
2359 <li>Loading/cut'n'pasting an empty file leads to a grey
2360 alignment window</li>
2361 <li>Disorder thresholds rendered incorrectly after
2362 performing IUPred disorder prediction</li>
2363 <li>Multiple group annotated consensus rows shown when
2364 changing 'normalise logo' display setting</li>
2365 <li>Find shows blank dialog after 'finished searching' if
2366 nothing matches query</li>
2367 <li>Null Pointer Exceptions raised when sorting by
2368 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2370 <li>Errors in Jmol console when structures in alignment
2371 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2373 <li>Not all working JABAWS services are shown in
2375 <li>JAVAWS version of Jalview fails to launch with
2376 'invalid literal/length code'</li>
2377 <li>Annotation/RNA Helix colourschemes cannot be applied
2378 to alignment with groups (actually fixed in 2.8.0b1)</li>
2379 <li>RNA Helices and T-Coffee Scores available as default
2382 </ul> <em>Applet</em>
2384 <li>Remove group option is shown even when selection is
2386 <li>Apply to all groups ticked but colourscheme changes
2387 don't affect groups</li>
2388 <li>Documented RNA Helices and T-Coffee Scores as valid
2389 colourscheme name</li>
2390 <li>Annotation labels drawn on sequence IDs when
2391 Annotation panel is not displayed</li>
2392 <li>Increased font size for dropdown menus on OSX and
2393 embedded windows</li>
2394 </ul> <em>Other</em>
2396 <li>Consensus sequence for alignments/groups with a
2397 single sequence were not calculated</li>
2398 <li>annotation files that contain only groups imported as
2399 annotation and junk sequences</li>
2400 <li>Fasta files with sequences containing '*' incorrectly
2401 recognised as PFAM or BLC</li>
2402 <li>conservation/PID slider apply all groups option
2403 doesn't affect background (2.8.0b1)
2405 <li>redundancy highlighting is erratic at 0% and 100%</li>
2406 <li>Remove gapped columns fails for sequences with ragged
2408 <li>AMSA annotation row with leading spaces is not
2409 registered correctly on import</li>
2410 <li>Jalview crashes when selecting PCA analysis for
2411 certain alignments</li>
2412 <li>Opening the colour by annotation dialog for an
2413 existing annotation based 'use original colours'
2414 colourscheme loses original colours setting</li>
2419 <td><div align="center">
2420 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2421 <em>30/1/2014</em></strong>
2425 <li>Trusted certificates for JalviewLite applet and
2426 Jalview Desktop application<br />Certificate was donated by
2427 <a href="https://www.certum.eu">Certum</a> to the Jalview
2428 open source project).
2430 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2431 <li>Output in Stockholm format</li>
2432 <li>Allow import of data from gzipped files</li>
2433 <li>Export/import group and sequence associated line
2434 graph thresholds</li>
2435 <li>Nucleotide substitution matrix that supports RNA and
2436 ambiguity codes</li>
2437 <li>Allow disorder predictions to be made on the current
2438 selection (or visible selection) in the same way that JPred
2440 <li>Groovy scripting for headless Jalview operation</li>
2441 </ul> <em>Other improvements</em>
2443 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2444 <li>COMBINE statement uses current SEQUENCE_REF and
2445 GROUP_REF scope to group annotation rows</li>
2446 <li>Support '' style escaping of quotes in Newick
2448 <li>Group options for JABAWS service by command line name</li>
2449 <li>Empty tooltip shown for JABA service options with a
2450 link but no description</li>
2451 <li>Select primary source when selecting authority in
2452 database fetcher GUI</li>
2453 <li>Add .mfa to FASTA file extensions recognised by
2455 <li>Annotation label tooltip text wrap</li>
2460 <li>Slow scrolling when lots of annotation rows are
2462 <li>Lots of NPE (and slowness) after creating RNA
2463 secondary structure annotation line</li>
2464 <li>Sequence database accessions not imported when
2465 fetching alignments from Rfam</li>
2466 <li>Incorrect SHMR submission for sequences with
2468 <li>View all structures does not always superpose
2470 <li>Option widgets in service parameters not updated to
2471 reflect user or preset settings</li>
2472 <li>Null pointer exceptions for some services without
2473 presets or adjustable parameters</li>
2474 <li>Discover PDB IDs entry in structure menu doesn't
2475 discover PDB xRefs</li>
2476 <li>Exception encountered while trying to retrieve
2477 features with DAS</li>
2478 <li>Lowest value in annotation row isn't coloured
2479 when colour by annotation (per sequence) is coloured</li>
2480 <li>Keyboard mode P jumps to start of gapped region when
2481 residue follows a gap</li>
2482 <li>Jalview appears to hang importing an alignment with
2483 Wrap as default or after enabling Wrap</li>
2484 <li>'Right click to add annotations' message
2485 shown in wrap mode when no annotations present</li>
2486 <li>Disorder predictions fail with NPE if no automatic
2487 annotation already exists on alignment</li>
2488 <li>oninit javascript function should be called after
2489 initialisation completes</li>
2490 <li>Remove redundancy after disorder prediction corrupts
2491 alignment window display</li>
2492 <li>Example annotation file in documentation is invalid</li>
2493 <li>Grouped line graph annotation rows are not exported
2494 to annotation file</li>
2495 <li>Multi-harmony analysis cannot be run when only two
2497 <li>Cannot create multiple groups of line graphs with
2498 several 'combine' statements in annotation file</li>
2499 <li>Pressing return several times causes Number Format
2500 exceptions in keyboard mode</li>
2501 <li>Multi-harmony (SHMMR) method doesn't submit
2502 correct partitions for input data</li>
2503 <li>Translation from DNA to Amino Acids fails</li>
2504 <li>Jalview fail to load newick tree with quoted label</li>
2505 <li>--headless flag isn't understood</li>
2506 <li>ClassCastException when generating EPS in headless
2508 <li>Adjusting sequence-associated shading threshold only
2509 changes one row's threshold</li>
2510 <li>Preferences and Feature settings panel panel
2511 doesn't open</li>
2512 <li>hide consensus histogram also hides conservation and
2513 quality histograms</li>
2518 <td><div align="center">
2519 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2521 <td><em>Application</em>
2523 <li>Support for JABAWS 2.0 Services (AACon alignment
2524 conservation, protein disorder and Clustal Omega)</li>
2525 <li>JABAWS server status indicator in Web Services
2527 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2528 in Jalview alignment window</li>
2529 <li>Updated Jalview build and deploy framework for OSX
2530 mountain lion, windows 7, and 8</li>
2531 <li>Nucleotide substitution matrix for PCA that supports
2532 RNA and ambiguity codes</li>
2534 <li>Improved sequence database retrieval GUI</li>
2535 <li>Support fetching and database reference look up
2536 against multiple DAS sources (Fetch all from in 'fetch db
2538 <li>Jalview project improvements
2540 <li>Store and retrieve the 'belowAlignment'
2541 flag for annotation</li>
2542 <li>calcId attribute to group annotation rows on the
2544 <li>Store AACon calculation settings for a view in
2545 Jalview project</li>
2549 <li>horizontal scrolling gesture support</li>
2550 <li>Visual progress indicator when PCA calculation is
2552 <li>Simpler JABA web services menus</li>
2553 <li>visual indication that web service results are still
2554 being retrieved from server</li>
2555 <li>Serialise the dialogs that are shown when Jalview
2556 starts up for first time</li>
2557 <li>Jalview user agent string for interacting with HTTP
2559 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2561 <li>Examples directory and Groovy library included in
2562 InstallAnywhere distribution</li>
2563 </ul> <em>Applet</em>
2565 <li>RNA alignment and secondary structure annotation
2566 visualization applet example</li>
2567 </ul> <em>General</em>
2569 <li>Normalise option for consensus sequence logo</li>
2570 <li>Reset button in PCA window to return dimensions to
2572 <li>Allow seqspace or Jalview variant of alignment PCA
2574 <li>PCA with either nucleic acid and protein substitution
2576 <li>Allow windows containing HTML reports to be exported
2578 <li>Interactive display and editing of RNA secondary
2579 structure contacts</li>
2580 <li>RNA Helix Alignment Colouring</li>
2581 <li>RNA base pair logo consensus</li>
2582 <li>Parse sequence associated secondary structure
2583 information in Stockholm files</li>
2584 <li>HTML Export database accessions and annotation
2585 information presented in tooltip for sequences</li>
2586 <li>Import secondary structure from LOCARNA clustalw
2587 style RNA alignment files</li>
2588 <li>import and visualise T-COFFEE quality scores for an
2590 <li>'colour by annotation' per sequence option to
2591 shade each sequence according to its associated alignment
2593 <li>New Jalview Logo</li>
2594 </ul> <em>Documentation and Development</em>
2596 <li>documentation for score matrices used in Jalview</li>
2597 <li>New Website!</li>
2599 <td><em>Application</em>
2601 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2602 wsdbfetch REST service</li>
2603 <li>Stop windows being moved outside desktop on OSX</li>
2604 <li>Filetype associations not installed for webstart
2606 <li>Jalview does not always retrieve progress of a JABAWS
2607 job execution in full once it is complete</li>
2608 <li>revise SHMR RSBS definition to ensure alignment is
2609 uploaded via ali_file parameter</li>
2610 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2611 <li>View all structures superposed fails with exception</li>
2612 <li>Jnet job queues forever if a very short sequence is
2613 submitted for prediction</li>
2614 <li>Cut and paste menu not opened when mouse clicked on
2616 <li>Putting fractional value into integer text box in
2617 alignment parameter dialog causes Jalview to hang</li>
2618 <li>Structure view highlighting doesn't work on
2620 <li>View all structures fails with exception shown in
2622 <li>Characters in filename associated with PDBEntry not
2623 escaped in a platform independent way</li>
2624 <li>Jalview desktop fails to launch with exception when
2626 <li>Tree calculation reports 'you must have 2 or more
2627 sequences selected' when selection is empty</li>
2628 <li>Jalview desktop fails to launch with jar signature
2629 failure when java web start temporary file caching is
2631 <li>DAS Sequence retrieval with range qualification
2632 results in sequence xref which includes range qualification</li>
2633 <li>Errors during processing of command line arguments
2634 cause progress bar (JAL-898) to be removed</li>
2635 <li>Replace comma for semi-colon option not disabled for
2636 DAS sources in sequence fetcher</li>
2637 <li>Cannot close news reader when JABAWS server warning
2638 dialog is shown</li>
2639 <li>Option widgets not updated to reflect user settings</li>
2640 <li>Edited sequence not submitted to web service</li>
2641 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2642 <li>InstallAnywhere installer doesn't unpack and run
2643 on OSX Mountain Lion</li>
2644 <li>Annotation panel not given a scroll bar when
2645 sequences with alignment annotation are pasted into the
2647 <li>Sequence associated annotation rows not associated
2648 when loaded from Jalview project</li>
2649 <li>Browser launch fails with NPE on java 1.7</li>
2650 <li>JABAWS alignment marked as finished when job was
2651 cancelled or job failed due to invalid input</li>
2652 <li>NPE with v2.7 example when clicking on Tree
2653 associated with all views</li>
2654 <li>Exceptions when copy/paste sequences with grouped
2655 annotation rows to new window</li>
2656 </ul> <em>Applet</em>
2658 <li>Sequence features are momentarily displayed before
2659 they are hidden using hidefeaturegroups applet parameter</li>
2660 <li>loading features via javascript API automatically
2661 enables feature display</li>
2662 <li>scrollToColumnIn javascript API method doesn't
2664 </ul> <em>General</em>
2666 <li>Redundancy removal fails for rna alignment</li>
2667 <li>PCA calculation fails when sequence has been selected
2668 and then deselected</li>
2669 <li>PCA window shows grey box when first opened on OSX</li>
2670 <li>Letters coloured pink in sequence logo when alignment
2671 coloured with clustalx</li>
2672 <li>Choosing fonts without letter symbols defined causes
2673 exceptions and redraw errors</li>
2674 <li>Initial PCA plot view is not same as manually
2675 reconfigured view</li>
2676 <li>Grouped annotation graph label has incorrect line
2678 <li>Grouped annotation graph label display is corrupted
2679 for lots of labels</li>
2684 <div align="center">
2685 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2688 <td><em>Application</em>
2690 <li>Jalview Desktop News Reader</li>
2691 <li>Tweaked default layout of web services menu</li>
2692 <li>View/alignment association menu to enable user to
2693 easily specify which alignment a multi-structure view takes
2694 its colours/correspondences from</li>
2695 <li>Allow properties file location to be specified as URL</li>
2696 <li>Extend Jalview project to preserve associations
2697 between many alignment views and a single Jmol display</li>
2698 <li>Store annotation row height in Jalview project file</li>
2699 <li>Annotation row column label formatting attributes
2700 stored in project file</li>
2701 <li>Annotation row order for auto-calculated annotation
2702 rows preserved in Jalview project file</li>
2703 <li>Visual progress indication when Jalview state is
2704 saved using Desktop window menu</li>
2705 <li>Visual indication that command line arguments are
2706 still being processed</li>
2707 <li>Groovy script execution from URL</li>
2708 <li>Colour by annotation default min and max colours in
2710 <li>Automatically associate PDB files dragged onto an
2711 alignment with sequences that have high similarity and
2713 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2714 <li>'view structures' option to open many
2715 structures in same window</li>
2716 <li>Sort associated views menu option for tree panel</li>
2717 <li>Group all JABA and non-JABA services for a particular
2718 analysis function in its own submenu</li>
2719 </ul> <em>Applet</em>
2721 <li>Userdefined and autogenerated annotation rows for
2723 <li>Adjustment of alignment annotation pane height</li>
2724 <li>Annotation scrollbar for annotation panel</li>
2725 <li>Drag to reorder annotation rows in annotation panel</li>
2726 <li>'automaticScrolling' parameter</li>
2727 <li>Allow sequences with partial ID string matches to be
2728 annotated from GFF/Jalview features files</li>
2729 <li>Sequence logo annotation row in applet</li>
2730 <li>Absolute paths relative to host server in applet
2731 parameters are treated as such</li>
2732 <li>New in the JalviewLite javascript API:
2734 <li>JalviewLite.js javascript library</li>
2735 <li>Javascript callbacks for
2737 <li>Applet initialisation</li>
2738 <li>Sequence/alignment mouse-overs and selections</li>
2741 <li>scrollTo row and column alignment scrolling
2743 <li>Select sequence/alignment regions from javascript</li>
2744 <li>javascript structure viewer harness to pass
2745 messages between Jmol and Jalview when running as
2746 distinct applets</li>
2747 <li>sortBy method</li>
2748 <li>Set of applet and application examples shipped
2749 with documentation</li>
2750 <li>New example to demonstrate JalviewLite and Jmol
2751 javascript message exchange</li>
2753 </ul> <em>General</em>
2755 <li>Enable Jmol displays to be associated with multiple
2756 multiple alignments</li>
2757 <li>Option to automatically sort alignment with new tree</li>
2758 <li>User configurable link to enable redirects to a
2759 www.Jalview.org mirror</li>
2760 <li>Jmol colours option for Jmol displays</li>
2761 <li>Configurable newline string when writing alignment
2762 and other flat files</li>
2763 <li>Allow alignment annotation description lines to
2764 contain html tags</li>
2765 </ul> <em>Documentation and Development</em>
2767 <li>Add groovy test harness for bulk load testing to
2769 <li>Groovy script to load and align a set of sequences
2770 using a web service before displaying the result in the
2771 Jalview desktop</li>
2772 <li>Restructured javascript and applet api documentation</li>
2773 <li>Ant target to publish example html files with applet
2775 <li>Netbeans project for building Jalview from source</li>
2776 <li>ant task to create online javadoc for Jalview source</li>
2778 <td><em>Application</em>
2780 <li>User defined colourscheme throws exception when
2781 current built in colourscheme is saved as new scheme</li>
2782 <li>AlignFrame->Save in application pops up save
2783 dialog for valid filename/format</li>
2784 <li>Cannot view associated structure for UniProt sequence</li>
2785 <li>PDB file association breaks for UniProt sequence
2787 <li>Associate PDB from file dialog does not tell you
2788 which sequence is to be associated with the file</li>
2789 <li>Find All raises null pointer exception when query
2790 only matches sequence IDs</li>
2791 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2792 <li>Jalview project with Jmol views created with Jalview
2793 2.4 cannot be loaded</li>
2794 <li>Filetype associations not installed for webstart
2796 <li>Two or more chains in a single PDB file associated
2797 with sequences in different alignments do not get coloured
2798 by their associated sequence</li>
2799 <li>Visibility status of autocalculated annotation row
2800 not preserved when project is loaded</li>
2801 <li>Annotation row height and visibility attributes not
2802 stored in Jalview project</li>
2803 <li>Tree bootstraps are not preserved when saved as a
2804 Jalview project</li>
2805 <li>Envision2 workflow tooltips are corrupted</li>
2806 <li>Enabling show group conservation also enables colour
2807 by conservation</li>
2808 <li>Duplicate group associated conservation or consensus
2809 created on new view</li>
2810 <li>Annotation scrollbar not displayed after 'show
2811 all hidden annotation rows' option selected</li>
2812 <li>Alignment quality not updated after alignment
2813 annotation row is hidden then shown</li>
2814 <li>Preserve colouring of structures coloured by
2815 sequences in pre Jalview 2.7 projects</li>
2816 <li>Web service job parameter dialog is not laid out
2818 <li>Web services menu not refreshed after 'reset
2819 services' button is pressed in preferences</li>
2820 <li>Annotation off by one in Jalview v2_3 example project</li>
2821 <li>Structures imported from file and saved in project
2822 get name like jalview_pdb1234.txt when reloaded</li>
2823 <li>Jalview does not always retrieve progress of a JABAWS
2824 job execution in full once it is complete</li>
2825 </ul> <em>Applet</em>
2827 <li>Alignment height set incorrectly when lots of
2828 annotation rows are displayed</li>
2829 <li>Relative URLs in feature HTML text not resolved to
2831 <li>View follows highlighting does not work for positions
2833 <li><= shown as = in tooltip</li>
2834 <li>Export features raises exception when no features
2836 <li>Separator string used for serialising lists of IDs
2837 for javascript api is modified when separator string
2838 provided as parameter</li>
2839 <li>Null pointer exception when selecting tree leaves for
2840 alignment with no existing selection</li>
2841 <li>Relative URLs for datasources assumed to be relative
2842 to applet's codebase</li>
2843 <li>Status bar not updated after finished searching and
2844 search wraps around to first result</li>
2845 <li>StructureSelectionManager instance shared between
2846 several Jalview applets causes race conditions and memory
2848 <li>Hover tooltip and mouseover of position on structure
2849 not sent from Jmol in applet</li>
2850 <li>Certain sequences of javascript method calls to
2851 applet API fatally hang browser</li>
2852 </ul> <em>General</em>
2854 <li>View follows structure mouseover scrolls beyond
2855 position with wrapped view and hidden regions</li>
2856 <li>Find sequence position moves to wrong residue
2857 with/without hidden columns</li>
2858 <li>Sequence length given in alignment properties window
2860 <li>InvalidNumberFormat exceptions thrown when trying to
2861 import PDB like structure files</li>
2862 <li>Positional search results are only highlighted
2863 between user-supplied sequence start/end bounds</li>
2864 <li>End attribute of sequence is not validated</li>
2865 <li>Find dialog only finds first sequence containing a
2866 given sequence position</li>
2867 <li>Sequence numbering not preserved in MSF alignment
2869 <li>Jalview PDB file reader does not extract sequence
2870 from nucleotide chains correctly</li>
2871 <li>Structure colours not updated when tree partition
2872 changed in alignment</li>
2873 <li>Sequence associated secondary structure not correctly
2874 parsed in interleaved stockholm</li>
2875 <li>Colour by annotation dialog does not restore current
2877 <li>Hiding (nearly) all sequences doesn't work
2879 <li>Sequences containing lowercase letters are not
2880 properly associated with their pdb files</li>
2881 </ul> <em>Documentation and Development</em>
2883 <li>schemas/JalviewWsParamSet.xsd corrupted by
2884 ApplyCopyright tool</li>
2889 <div align="center">
2890 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2893 <td><em>Application</em>
2895 <li>New warning dialog when the Jalview Desktop cannot
2896 contact web services</li>
2897 <li>JABA service parameters for a preset are shown in
2898 service job window</li>
2899 <li>JABA Service menu entries reworded</li>
2903 <li>Modeller PIR IO broken - cannot correctly import a
2904 pir file emitted by Jalview</li>
2905 <li>Existing feature settings transferred to new
2906 alignment view created from cut'n'paste</li>
2907 <li>Improved test for mixed amino/nucleotide chains when
2908 parsing PDB files</li>
2909 <li>Consensus and conservation annotation rows
2910 occasionally become blank for all new windows</li>
2911 <li>Exception raised when right clicking above sequences
2912 in wrapped view mode</li>
2913 </ul> <em>Application</em>
2915 <li>multiple multiply aligned structure views cause cpu
2916 usage to hit 100% and computer to hang</li>
2917 <li>Web Service parameter layout breaks for long user
2918 parameter names</li>
2919 <li>Jaba service discovery hangs desktop if Jaba server
2926 <div align="center">
2927 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2930 <td><em>Application</em>
2932 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2933 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2936 <li>Web Services preference tab</li>
2937 <li>Analysis parameters dialog box and user defined
2939 <li>Improved speed and layout of Envision2 service menu</li>
2940 <li>Superpose structures using associated sequence
2942 <li>Export coordinates and projection as CSV from PCA
2944 </ul> <em>Applet</em>
2946 <li>enable javascript: execution by the applet via the
2947 link out mechanism</li>
2948 </ul> <em>Other</em>
2950 <li>Updated the Jmol Jalview interface to work with Jmol
2952 <li>The Jalview Desktop and JalviewLite applet now
2953 require Java 1.5</li>
2954 <li>Allow Jalview feature colour specification for GFF
2955 sequence annotation files</li>
2956 <li>New 'colour by label' keword in Jalview feature file
2957 type colour specification</li>
2958 <li>New Jalview Desktop Groovy API method that allows a
2959 script to check if it being run in an interactive session or
2960 in a batch operation from the Jalview command line</li>
2964 <li>clustalx colourscheme colours Ds preferentially when
2965 both D+E are present in over 50% of the column</li>
2966 </ul> <em>Application</em>
2968 <li>typo in AlignmentFrame->View->Hide->all but
2969 selected Regions menu item</li>
2970 <li>sequence fetcher replaces ',' for ';' when the ',' is
2971 part of a valid accession ID</li>
2972 <li>fatal OOM if object retrieved by sequence fetcher
2973 runs out of memory</li>
2974 <li>unhandled Out of Memory Error when viewing pca
2975 analysis results</li>
2976 <li>InstallAnywhere builds fail to launch on OS X java
2977 10.5 update 4 (due to apple Java 1.6 update)</li>
2978 <li>Installanywhere Jalview silently fails to launch</li>
2979 </ul> <em>Applet</em>
2981 <li>Jalview.getFeatureGroups() raises an
2982 ArrayIndexOutOfBoundsException if no feature groups are
2989 <div align="center">
2990 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2996 <li>Alignment prettyprinter doesn't cope with long
2998 <li>clustalx colourscheme colours Ds preferentially when
2999 both D+E are present in over 50% of the column</li>
3000 <li>nucleic acid structures retrieved from PDB do not
3001 import correctly</li>
3002 <li>More columns get selected than were clicked on when a
3003 number of columns are hidden</li>
3004 <li>annotation label popup menu not providing correct
3005 add/hide/show options when rows are hidden or none are
3007 <li>Stockholm format shown in list of readable formats,
3008 and parser copes better with alignments from RFAM.</li>
3009 <li>CSV output of consensus only includes the percentage
3010 of all symbols if sequence logo display is enabled</li>
3012 </ul> <em>Applet</em>
3014 <li>annotation panel disappears when annotation is
3016 </ul> <em>Application</em>
3018 <li>Alignment view not redrawn properly when new
3019 alignment opened where annotation panel is visible but no
3020 annotations are present on alignment</li>
3021 <li>pasted region containing hidden columns is
3022 incorrectly displayed in new alignment window</li>
3023 <li>Jalview slow to complete operations when stdout is
3024 flooded (fix is to close the Jalview console)</li>
3025 <li>typo in AlignmentFrame->View->Hide->all but
3026 selected Rregions menu item.</li>
3027 <li>inconsistent group submenu and Format submenu entry
3028 'Un' or 'Non'conserved</li>
3029 <li>Sequence feature settings are being shared by
3030 multiple distinct alignments</li>
3031 <li>group annotation not recreated when tree partition is
3033 <li>double click on group annotation to select sequences
3034 does not propagate to associated trees</li>
3035 <li>Mac OSX specific issues:
3037 <li>exception raised when mouse clicked on desktop
3038 window background</li>
3039 <li>Desktop menu placed on menu bar and application
3040 name set correctly</li>
3041 <li>sequence feature settings not wide enough for the
3042 save feature colourscheme button</li>
3051 <div align="center">
3052 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3055 <td><em>New Capabilities</em>
3057 <li>URL links generated from description line for
3058 regular-expression based URL links (applet and application)
3060 <li>Non-positional feature URL links are shown in link
3062 <li>Linked viewing of nucleic acid sequences and
3064 <li>Automatic Scrolling option in View menu to display
3065 the currently highlighted region of an alignment.</li>
3066 <li>Order an alignment by sequence length, or using the
3067 average score or total feature count for each sequence.</li>
3068 <li>Shading features by score or associated description</li>
3069 <li>Subdivide alignment and groups based on identity of
3070 selected subsequence (Make Groups from Selection).</li>
3071 <li>New hide/show options including Shift+Control+H to
3072 hide everything but the currently selected region.</li>
3073 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3074 </ul> <em>Application</em>
3076 <li>Fetch DB References capabilities and UI expanded to
3077 support retrieval from DAS sequence sources</li>
3078 <li>Local DAS Sequence sources can be added via the
3079 command line or via the Add local source dialog box.</li>
3080 <li>DAS Dbref and DbxRef feature types are parsed as
3081 database references and protein_name is parsed as
3082 description line (BioSapiens terms).</li>
3083 <li>Enable or disable non-positional feature and database
3084 references in sequence ID tooltip from View menu in
3086 <!-- <li>New hidden columns and rows and representatives capabilities
3087 in annotations file (in progress - not yet fully implemented)</li> -->
3088 <li>Group-associated consensus, sequence logos and
3089 conservation plots</li>
3090 <li>Symbol distributions for each column can be exported
3091 and visualized as sequence logos</li>
3092 <li>Optionally scale multi-character column labels to fit
3093 within each column of annotation row<!-- todo for applet -->
3095 <li>Optional automatic sort of associated alignment view
3096 when a new tree is opened.</li>
3097 <li>Jalview Java Console</li>
3098 <li>Better placement of desktop window when moving
3099 between different screens.</li>
3100 <li>New preference items for sequence ID tooltip and
3101 consensus annotation</li>
3102 <li>Client to submit sequences and IDs to Envision2
3104 <li><em>Vamsas Capabilities</em>
3106 <li>Improved VAMSAS synchronization (Jalview archive
3107 used to preserve views, structures, and tree display
3109 <li>Import of vamsas documents from disk or URL via
3111 <li>Sharing of selected regions between views and
3112 with other VAMSAS applications (Experimental feature!)</li>
3113 <li>Updated API to VAMSAS version 0.2</li>
3115 </ul> <em>Applet</em>
3117 <li>Middle button resizes annotation row height</li>
3120 <li>sortByTree (true/false) - automatically sort the
3121 associated alignment view by the tree when a new tree is
3123 <li>showTreeBootstraps (true/false) - show or hide
3124 branch bootstraps (default is to show them if available)</li>
3125 <li>showTreeDistances (true/false) - show or hide
3126 branch lengths (default is to show them if available)</li>
3127 <li>showUnlinkedTreeNodes (true/false) - indicate if
3128 unassociated nodes should be highlighted in the tree
3130 <li>heightScale and widthScale (1.0 or more) -
3131 increase the height or width of a cell in the alignment
3132 grid relative to the current font size.</li>
3135 <li>Non-positional features displayed in sequence ID
3137 </ul> <em>Other</em>
3139 <li>Features format: graduated colour definitions and
3140 specification of feature scores</li>
3141 <li>Alignment Annotations format: new keywords for group
3142 associated annotation (GROUP_REF) and annotation row display
3143 properties (ROW_PROPERTIES)</li>
3144 <li>XML formats extended to support graduated feature
3145 colourschemes, group associated annotation, and profile
3146 visualization settings.</li></td>
3149 <li>Source field in GFF files parsed as feature source
3150 rather than description</li>
3151 <li>Non-positional features are now included in sequence
3152 feature and gff files (controlled via non-positional feature
3153 visibility in tooltip).</li>
3154 <li>URL links generated for all feature links (bugfix)</li>
3155 <li>Added URL embedding instructions to features file
3157 <li>Codons containing ambiguous nucleotides translated as
3158 'X' in peptide product</li>
3159 <li>Match case switch in find dialog box works for both
3160 sequence ID and sequence string and query strings do not
3161 have to be in upper case to match case-insensitively.</li>
3162 <li>AMSA files only contain first column of
3163 multi-character column annotation labels</li>
3164 <li>Jalview Annotation File generation/parsing consistent
3165 with documentation (e.g. Stockholm annotation can be
3166 exported and re-imported)</li>
3167 <li>PDB files without embedded PDB IDs given a friendly
3169 <li>Find incrementally searches ID string matches as well
3170 as subsequence matches, and correctly reports total number
3174 <li>Better handling of exceptions during sequence
3176 <li>Dasobert generated non-positional feature URL
3177 link text excludes the start_end suffix</li>
3178 <li>DAS feature and source retrieval buttons disabled
3179 when fetch or registry operations in progress.</li>
3180 <li>PDB files retrieved from URLs are cached properly</li>
3181 <li>Sequence description lines properly shared via
3183 <li>Sequence fetcher fetches multiple records for all
3185 <li>Ensured that command line das feature retrieval
3186 completes before alignment figures are generated.</li>
3187 <li>Reduced time taken when opening file browser for
3189 <li>isAligned check prior to calculating tree, PCA or
3190 submitting an MSA to JNet now excludes hidden sequences.</li>
3191 <li>User defined group colours properly recovered
3192 from Jalview projects.</li>
3201 <div align="center">
3202 <strong>2.4.0.b2</strong><br> 28/10/2009
3207 <li>Experimental support for google analytics usage
3209 <li>Jalview privacy settings (user preferences and docs).</li>
3214 <li>Race condition in applet preventing startup in
3216 <li>Exception when feature created from selection beyond
3217 length of sequence.</li>
3218 <li>Allow synthetic PDB files to be imported gracefully</li>
3219 <li>Sequence associated annotation rows associate with
3220 all sequences with a given id</li>
3221 <li>Find function matches case-insensitively for sequence
3222 ID string searches</li>
3223 <li>Non-standard characters do not cause pairwise
3224 alignment to fail with exception</li>
3225 </ul> <em>Application Issues</em>
3227 <li>Sequences are now validated against EMBL database</li>
3228 <li>Sequence fetcher fetches multiple records for all
3230 </ul> <em>InstallAnywhere Issues</em>
3232 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3233 issue with installAnywhere mechanism)</li>
3234 <li>Command line launching of JARs from InstallAnywhere
3235 version (java class versioning error fixed)</li>
3242 <div align="center">
3243 <strong>2.4</strong><br> 27/8/2008
3246 <td><em>User Interface</em>
3248 <li>Linked highlighting of codon and amino acid from
3249 translation and protein products</li>
3250 <li>Linked highlighting of structure associated with
3251 residue mapping to codon position</li>
3252 <li>Sequence Fetcher provides example accession numbers
3253 and 'clear' button</li>
3254 <li>MemoryMonitor added as an option under Desktop's
3256 <li>Extract score function to parse whitespace separated
3257 numeric data in description line</li>
3258 <li>Column labels in alignment annotation can be centred.</li>
3259 <li>Tooltip for sequence associated annotation give name
3261 </ul> <em>Web Services and URL fetching</em>
3263 <li>JPred3 web service</li>
3264 <li>Prototype sequence search client (no public services
3266 <li>Fetch either seed alignment or full alignment from
3268 <li>URL Links created for matching database cross
3269 references as well as sequence ID</li>
3270 <li>URL Links can be created using regular-expressions</li>
3271 </ul> <em>Sequence Database Connectivity</em>
3273 <li>Retrieval of cross-referenced sequences from other
3275 <li>Generalised database reference retrieval and
3276 validation to all fetchable databases</li>
3277 <li>Fetch sequences from DAS sources supporting the
3278 sequence command</li>
3279 </ul> <em>Import and Export</em>
3280 <li>export annotation rows as CSV for spreadsheet import</li>
3281 <li>Jalview projects record alignment dataset associations,
3282 EMBL products, and cDNA sequence mappings</li>
3283 <li>Sequence Group colour can be specified in Annotation
3285 <li>Ad-hoc colouring of group in Annotation File using RGB
3286 triplet as name of colourscheme</li>
3287 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3289 <li>treenode binding for VAMSAS tree exchange</li>
3290 <li>local editing and update of sequences in VAMSAS
3291 alignments (experimental)</li>
3292 <li>Create new or select existing session to join</li>
3293 <li>load and save of vamsas documents</li>
3294 </ul> <em>Application command line</em>
3296 <li>-tree parameter to open trees (introduced for passing
3298 <li>-fetchfrom command line argument to specify nicknames
3299 of DAS servers to query for alignment features</li>
3300 <li>-dasserver command line argument to add new servers
3301 that are also automatically queried for features</li>
3302 <li>-groovy command line argument executes a given groovy
3303 script after all input data has been loaded and parsed</li>
3304 </ul> <em>Applet-Application data exchange</em>
3306 <li>Trees passed as applet parameters can be passed to
3307 application (when using "View in full
3308 application")</li>
3309 </ul> <em>Applet Parameters</em>
3311 <li>feature group display control parameter</li>
3312 <li>debug parameter</li>
3313 <li>showbutton parameter</li>
3314 </ul> <em>Applet API methods</em>
3316 <li>newView public method</li>
3317 <li>Window (current view) specific get/set public methods</li>
3318 <li>Feature display control methods</li>
3319 <li>get list of currently selected sequences</li>
3320 </ul> <em>New Jalview distribution features</em>
3322 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3323 <li>RELEASE file gives build properties for the latest
3324 Jalview release.</li>
3325 <li>Java 1.1 Applet build made easier and donotobfuscate
3326 property controls execution of obfuscator</li>
3327 <li>Build target for generating source distribution</li>
3328 <li>Debug flag for javacc</li>
3329 <li>.jalview_properties file is documented (slightly) in
3330 jalview.bin.Cache</li>
3331 <li>Continuous Build Integration for stable and
3332 development version of Application, Applet and source
3337 <li>selected region output includes visible annotations
3338 (for certain formats)</li>
3339 <li>edit label/displaychar contains existing label/char
3341 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3342 <li>shorter peptide product names from EMBL records</li>
3343 <li>Newick string generator makes compact representations</li>
3344 <li>bootstrap values parsed correctly for tree files with
3346 <li>pathological filechooser bug avoided by not allowing
3347 filenames containing a ':'</li>
3348 <li>Fixed exception when parsing GFF files containing
3349 global sequence features</li>
3350 <li>Alignment datasets are finalized only when number of
3351 references from alignment sequences goes to zero</li>
3352 <li>Close of tree branch colour box without colour
3353 selection causes cascading exceptions</li>
3354 <li>occasional negative imgwidth exceptions</li>
3355 <li>better reporting of non-fatal warnings to user when
3356 file parsing fails.</li>
3357 <li>Save works when Jalview project is default format</li>
3358 <li>Save as dialog opened if current alignment format is
3359 not a valid output format</li>
3360 <li>UniProt canonical names introduced for both das and
3362 <li>Histidine should be midblue (not pink!) in Zappo</li>
3363 <li>error messages passed up and output when data read
3365 <li>edit undo recovers previous dataset sequence when
3366 sequence is edited</li>
3367 <li>allow PDB files without pdb ID HEADER lines (like
3368 those generated by MODELLER) to be read in properly</li>
3369 <li>allow reading of JPred concise files as a normal
3371 <li>Stockholm annotation parsing and alignment properties
3372 import fixed for PFAM records</li>
3373 <li>Structure view windows have correct name in Desktop
3375 <li>annotation consisting of sequence associated scores
3376 can be read and written correctly to annotation file</li>
3377 <li>Aligned cDNA translation to aligned peptide works
3379 <li>Fixed display of hidden sequence markers and
3380 non-italic font for representatives in Applet</li>
3381 <li>Applet Menus are always embedded in applet window on
3383 <li>Newly shown features appear at top of stack (in
3385 <li>Annotations added via parameter not drawn properly
3386 due to null pointer exceptions</li>
3387 <li>Secondary structure lines are drawn starting from
3388 first column of alignment</li>
3389 <li>UniProt XML import updated for new schema release in
3391 <li>Sequence feature to sequence ID match for Features
3392 file is case-insensitive</li>
3393 <li>Sequence features read from Features file appended to
3394 all sequences with matching IDs</li>
3395 <li>PDB structure coloured correctly for associated views
3396 containing a sub-sequence</li>
3397 <li>PDB files can be retrieved by applet from Jar files</li>
3398 <li>feature and annotation file applet parameters
3399 referring to different directories are retrieved correctly</li>
3400 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3401 <li>Fixed application hang whilst waiting for
3402 splash-screen version check to complete</li>
3403 <li>Applet properly URLencodes input parameter values
3404 when passing them to the launchApp service</li>
3405 <li>display name and local features preserved in results
3406 retrieved from web service</li>
3407 <li>Visual delay indication for sequence retrieval and
3408 sequence fetcher initialisation</li>
3409 <li>updated Application to use DAS 1.53e version of
3410 dasobert DAS client</li>
3411 <li>Re-instated Full AMSA support and .amsa file
3413 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3421 <div align="center">
3422 <strong>2.3</strong><br> 9/5/07
3427 <li>Jmol 11.0.2 integration</li>
3428 <li>PDB views stored in Jalview XML files</li>
3429 <li>Slide sequences</li>
3430 <li>Edit sequence in place</li>
3431 <li>EMBL CDS features</li>
3432 <li>DAS Feature mapping</li>
3433 <li>Feature ordering</li>
3434 <li>Alignment Properties</li>
3435 <li>Annotation Scores</li>
3436 <li>Sort by scores</li>
3437 <li>Feature/annotation editing in applet</li>
3442 <li>Headless state operation in 2.2.1</li>
3443 <li>Incorrect and unstable DNA pairwise alignment</li>
3444 <li>Cut and paste of sequences with annotation</li>
3445 <li>Feature group display state in XML</li>
3446 <li>Feature ordering in XML</li>
3447 <li>blc file iteration selection using filename # suffix</li>
3448 <li>Stockholm alignment properties</li>
3449 <li>Stockhom alignment secondary structure annotation</li>
3450 <li>2.2.1 applet had no feature transparency</li>
3451 <li>Number pad keys can be used in cursor mode</li>
3452 <li>Structure Viewer mirror image resolved</li>
3459 <div align="center">
3460 <strong>2.2.1</strong><br> 12/2/07
3465 <li>Non standard characters can be read and displayed
3466 <li>Annotations/Features can be imported/exported to the
3468 <li>Applet allows editing of sequence/annotation/group
3469 name & description
3470 <li>Preference setting to display sequence name in
3472 <li>Annotation file format extended to allow
3473 Sequence_groups to be defined
3474 <li>Default opening of alignment overview panel can be
3475 specified in preferences
3476 <li>PDB residue numbering annotation added to associated
3482 <li>Applet crash under certain Linux OS with Java 1.6
3484 <li>Annotation file export / import bugs fixed
3485 <li>PNG / EPS image output bugs fixed
3491 <div align="center">
3492 <strong>2.2</strong><br> 27/11/06
3497 <li>Multiple views on alignment
3498 <li>Sequence feature editing
3499 <li>"Reload" alignment
3500 <li>"Save" to current filename
3501 <li>Background dependent text colour
3502 <li>Right align sequence ids
3503 <li>User-defined lower case residue colours
3506 <li>Menu item accelerator keys
3507 <li>Control-V pastes to current alignment
3508 <li>Cancel button for DAS Feature Fetching
3509 <li>PCA and PDB Viewers zoom via mouse roller
3510 <li>User-defined sub-tree colours and sub-tree selection
3512 <li>'New Window' button on the 'Output to Text box'
3517 <li>New memory efficient Undo/Redo System
3518 <li>Optimised symbol lookups and conservation/consensus
3520 <li>Region Conservation/Consensus recalculated after
3522 <li>Fixed Remove Empty Columns Bug (empty columns at end
3524 <li>Slowed DAS Feature Fetching for increased robustness.
3526 <li>Made angle brackets in ASCII feature descriptions
3528 <li>Re-instated Zoom function for PCA
3529 <li>Sequence descriptions conserved in web service
3531 <li>UniProt ID discoverer uses any word separated by
3533 <li>WsDbFetch query/result association resolved
3534 <li>Tree leaf to sequence mapping improved
3535 <li>Smooth fonts switch moved to FontChooser dialog box.
3542 <div align="center">
3543 <strong>2.1.1</strong><br> 12/9/06
3548 <li>Copy consensus sequence to clipboard</li>
3553 <li>Image output - rightmost residues are rendered if
3554 sequence id panel has been resized</li>
3555 <li>Image output - all offscreen group boundaries are
3557 <li>Annotation files with sequence references - all
3558 elements in file are relative to sequence position</li>
3559 <li>Mac Applet users can use Alt key for group editing</li>
3565 <div align="center">
3566 <strong>2.1</strong><br> 22/8/06
3571 <li>MAFFT Multiple Alignment in default Web Service list</li>
3572 <li>DAS Feature fetching</li>
3573 <li>Hide sequences and columns</li>
3574 <li>Export Annotations and Features</li>
3575 <li>GFF file reading / writing</li>
3576 <li>Associate structures with sequences from local PDB
3578 <li>Add sequences to exisiting alignment</li>
3579 <li>Recently opened files / URL lists</li>
3580 <li>Applet can launch the full application</li>
3581 <li>Applet has transparency for features (Java 1.2
3583 <li>Applet has user defined colours parameter</li>
3584 <li>Applet can load sequences from parameter
3585 "sequence<em>x</em>"
3591 <li>Redundancy Panel reinstalled in the Applet</li>
3592 <li>Monospaced font - EPS / rescaling bug fixed</li>
3593 <li>Annotation files with sequence references bug fixed</li>
3599 <div align="center">
3600 <strong>2.08.1</strong><br> 2/5/06
3605 <li>Change case of selected region from Popup menu</li>
3606 <li>Choose to match case when searching</li>
3607 <li>Middle mouse button and mouse movement can compress /
3608 expand the visible width and height of the alignment</li>
3613 <li>Annotation Panel displays complete JNet results</li>
3619 <div align="center">
3620 <strong>2.08b</strong><br> 18/4/06
3626 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3627 <li>Righthand label on wrapped alignments shows correct
3634 <div align="center">
3635 <strong>2.08</strong><br> 10/4/06
3640 <li>Editing can be locked to the selection area</li>
3641 <li>Keyboard editing</li>
3642 <li>Create sequence features from searches</li>
3643 <li>Precalculated annotations can be loaded onto
3645 <li>Features file allows grouping of features</li>
3646 <li>Annotation Colouring scheme added</li>
3647 <li>Smooth fonts off by default - Faster rendering</li>
3648 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3653 <li>Drag & Drop fixed on Linux</li>
3654 <li>Jalview Archive file faster to load/save, sequence
3655 descriptions saved.</li>
3661 <div align="center">
3662 <strong>2.07</strong><br> 12/12/05
3667 <li>PDB Structure Viewer enhanced</li>
3668 <li>Sequence Feature retrieval and display enhanced</li>
3669 <li>Choose to output sequence start-end after sequence
3670 name for file output</li>
3671 <li>Sequence Fetcher WSDBFetch@EBI</li>
3672 <li>Applet can read feature files, PDB files and can be
3673 used for HTML form input</li>
3678 <li>HTML output writes groups and features</li>
3679 <li>Group editing is Control and mouse click</li>
3680 <li>File IO bugs</li>
3686 <div align="center">
3687 <strong>2.06</strong><br> 28/9/05
3692 <li>View annotations in wrapped mode</li>
3693 <li>More options for PCA viewer</li>
3698 <li>GUI bugs resolved</li>
3699 <li>Runs with -nodisplay from command line</li>
3705 <div align="center">
3706 <strong>2.05b</strong><br> 15/9/05
3711 <li>Choose EPS export as lineart or text</li>
3712 <li>Jar files are executable</li>
3713 <li>Can read in Uracil - maps to unknown residue</li>
3718 <li>Known OutOfMemory errors give warning message</li>
3719 <li>Overview window calculated more efficiently</li>
3720 <li>Several GUI bugs resolved</li>
3726 <div align="center">
3727 <strong>2.05</strong><br> 30/8/05
3732 <li>Edit and annotate in "Wrapped" view</li>
3737 <li>Several GUI bugs resolved</li>
3743 <div align="center">
3744 <strong>2.04</strong><br> 24/8/05
3749 <li>Hold down mouse wheel & scroll to change font
3755 <li>Improved JPred client reliability</li>
3756 <li>Improved loading of Jalview files</li>
3762 <div align="center">
3763 <strong>2.03</strong><br> 18/8/05
3768 <li>Set Proxy server name and port in preferences</li>
3769 <li>Multiple URL links from sequence ids</li>
3770 <li>User Defined Colours can have a scheme name and added
3772 <li>Choose to ignore gaps in consensus calculation</li>
3773 <li>Unix users can set default web browser</li>
3774 <li>Runs without GUI for batch processing</li>
3775 <li>Dynamically generated Web Service Menus</li>
3780 <li>InstallAnywhere download for Sparc Solaris</li>
3786 <div align="center">
3787 <strong>2.02</strong><br> 18/7/05
3793 <li>Copy & Paste order of sequences maintains
3794 alignment order.</li>
3800 <div align="center">
3801 <strong>2.01</strong><br> 12/7/05
3806 <li>Use delete key for deleting selection.</li>
3807 <li>Use Mouse wheel to scroll sequences.</li>
3808 <li>Help file updated to describe how to add alignment
3810 <li>Version and build date written to build properties
3812 <li>InstallAnywhere installation will check for updates
3813 at launch of Jalview.</li>
3818 <li>Delete gaps bug fixed.</li>
3819 <li>FileChooser sorts columns.</li>
3820 <li>Can remove groups one by one.</li>
3821 <li>Filechooser icons installed.</li>
3822 <li>Finder ignores return character when searching.
3823 Return key will initiate a search.<br>
3830 <div align="center">
3831 <strong>2.0</strong><br> 20/6/05
3836 <li>New codebase</li>