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.2.10.3">2.10.3</a><br />
74 <em>17/11/2017</em></strong>
77 <td><div align="left">
81 <!-- JAL-2446 -->Faster and more efficient management and
82 rendering of sequence features
85 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
86 429 rate limit request hander
89 <!-- JAL-2773 -->Structure views don't get updated unless
90 their colours have changed
92 <li><!-- JAL-2495 -->All linked sequences are highlighted for a structure mousover (Jmol) or selection (Chimera)</li>
93 <li><!-- JAL-2790 -->'Cancel' button in progress bar for JABAWS AACon, RNAAliFold and Disorder prediction jobs
96 <li><!-- JAL-2617 -->Stop codons are excluded in CDS/Protein view from Ensembl locus cross-references</li>
97 <li><!-- JAL-2685 -->Start/End limits are shown in Pairwise Alignment report</li>
98 <li><!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch' feature can be disabled</li>
99 <li><!-- JAL-2810 -->Retrieve IDs tab added for UniProt and PDB easier retrieval of sequences for lists of IDs</li>
100 <li><!-- JAL-2758 -->Short names for sequences retrieved from Uniprot</li>
104 <li>Groovy interpreter updated to 2.4.12</li>
105 <li>Example groovy script for generating a matrix of percent identity scores for current alignment.</li>
107 <em>Testing and Deployment</em>
109 <li><!-- JAL-2727 -->Test to catch memory leaks in Jalview UI</li>
113 <td><div align="left">
116 <li><!-- JAL-2643 -->Pressing tab after updating the colour threshold text field doesn't trigger an update to the alignment view</li>
117 <li><!-- JAL-2682 -->Race condition when parsing sequence ID strings in parallel</li>
118 <li><!-- JAL-2608 -->Overview windows are also closed when alignment window is closed</li>
119 <li><!-- JAL-2548 -->Export of features doesn't always respect group visibility</li>
120 <li><!-- JAL-2831 -->Jumping from column 1 to column 100,000 takes a long time in Cursor mode</li>
124 <li><!-- JAL-2777 -->Structures with whitespace chainCode cannot be viewed in Chimera</li>
125 <li><!-- JAL-2728 -->Protein annotation panel too high in CDS/Protein view
127 <li><!-- JAL-2757 -->Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs
129 <li><!-- JAL-2253 -->Slow EnsemblGenome ID lookup</li>
130 <li><!-- JAL-2529 -->Revised Ensembl REST API CDNA query</li>
131 <li><!-- JAL-2739 -->Hidden column marker in last column not rendered when switching back from Wrapped to normal view</li>
132 <li><!-- JAL-2768 -->Annotation display corrupted when scrolling right in unwapped alignment view</li>
133 <li><!-- JAL-2542 -->Existing features on subsequence incorrectly relocated when full sequence retrieved from database</li>
134 <li><!-- JAL-2733 -->Last reported memory still shown when Desktop->Show Memory is unticked (OSX only)</li>
135 <li><!-- JAL-2658 -->Amend Features dialog doesn't allow features of same type and group to be selected for amending</li>
136 <li><!-- JAL-2524 -->Jalview becomes sluggish in wide alignments when hidden columns are present</li>
137 <li><!-- JAL-2392 -->Jalview freezes when loading and displaying several structures</li>
138 <li><!-- JAL-2732 -->Black outlines left after resizing or moving a window</li>
139 <li><!-- JAL-1900,JAL-1625 -->Unable to minimise windows within the Jalview desktop on OSX</li>
140 <li><!-- JAL-2667 -->Mouse wheel doesn't scroll vertically when in wrapped alignment mode</li>
141 <li><!-- JAL-2636 -->Scale mark not shown when close to right hand end of alignment</li>
142 <li><!-- JAL-2684 -->Pairwise alignment of selected regions of each selected sequence do not have correct start/end positions</li>
143 <li><!-- JAL-2973 -->Alignment ruler height set incorrectly after canceling the Alignment Window's Font dialog</li>
144 <li><!-- JAL-2036 -->Show cross-references not enabled after restoring project until a new view is created</li>
145 <li><!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in URL links appears when only default EMBL-EBI link is configured (since 2.10.2b2)</li>
146 <li><!-- JAL-2775 -->Overview redraws whole window when box position is adjusted</li>
147 <li><!-- JAL-2225 -->Structure viewer doesn't map all chains in a multi-chain structure when viewing alignment involving more than one chain (since 2.10)</li>
148 <li><!-- JAL-2811 -->Double residue highlights in cursor mode if new selection moves alignment window</li>
149 <li><!-- JAL-2837,JAL-2840 -->Alignment vanishes when using arrow key in cursor mode to pass hidden column marker</li>
151 ><em>Applet</em><br/>
153 <li><!-- JAL-2687 -->Concurrent modification exception when closing alignment panel</li>
155 <em>BioJSON</em><br/>
158 <!-- JAL-2546 -->BioJSON export does not preserve non-positional features
161 <strong>New Known Issues</strong>
163 <li><!-- JAL-2541 -->Delete/Cut selection doesn't relocate sequence features correctly (for many previous versions of Jalview)</li>
164 <li><!-- JAL-2841 -->Cursor mode unexpectedly scrolls when using cursor in wrapped panel other than top</li>
165 <li><!-- JAL-2791 -->Select columns containing feature ignores graduated colour threshold</li>
166 <li><!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't always preserve numbering and sequence features</li>
168 <strong>Known Java 9 Issues</strong>
170 <li><!-- JAL-2902 -->Groovy Console very slow to open and is
171 not responsive when entering characters (Webstart, Java 9.01,
179 <td width="60" nowrap>
181 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
182 <em>2/10/2017</em></strong>
185 <td><div align="left">
186 <em>New features in Jalview Desktop</em>
189 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
191 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
195 <td><div align="left">
199 <td width="60" nowrap>
201 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
202 <em>7/9/2017</em></strong>
205 <td><div align="left">
209 <!-- JAL-2588 -->Show gaps in overview window by colouring
210 in grey (sequences used to be coloured grey, and gaps were
214 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
218 <!-- JAL-2587 -->Overview updates immediately on increase
219 in size and progress bar shown as higher resolution
220 overview is recalculated
225 <td><div align="left">
229 <!-- JAL-2664 -->Overview window redraws every hidden
230 column region row by row
233 <!-- JAL-2681 -->duplicate protein sequences shown after
234 retrieving Ensembl crossrefs for sequences from Uniprot
237 <!-- JAL-2603 -->Overview window throws NPE if show boxes
238 format setting is unticked
241 <!-- JAL-2610 -->Groups are coloured wrongly in overview
242 if group has show boxes format setting unticked
245 <!-- JAL-2672,JAL-2665 -->Redraw problems when
246 autoscrolling whilst dragging current selection group to
247 include sequences and columns not currently displayed
250 <!-- JAL-2691 -->Not all chains are mapped when multimeric
251 assemblies are imported via CIF file
254 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
255 displayed when threshold or conservation colouring is also
259 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
263 <!-- JAL-2673 -->Jalview continues to scroll after
264 dragging a selected region off the visible region of the
268 <!-- JAL-2724 -->Cannot apply annotation based
269 colourscheme to all groups in a view
272 <!-- JAL-2511 -->IDs don't line up with sequences
273 initially after font size change using the Font chooser or
280 <td width="60" nowrap>
282 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
285 <td><div align="left">
286 <em>Calculations</em>
290 <!-- JAL-1933 -->Occupancy annotation row shows number of
291 ungapped positions in each column of the alignment.
294 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
295 a calculation dialog box
298 <!-- JAL-2379 -->Revised implementation of PCA for speed
299 and memory efficiency (~30x faster)
302 <!-- JAL-2403 -->Revised implementation of sequence
303 similarity scores as used by Tree, PCA, Shading Consensus
304 and other calculations
307 <!-- JAL-2416 -->Score matrices are stored as resource
308 files within the Jalview codebase
311 <!-- JAL-2500 -->Trees computed on Sequence Feature
312 Similarity may have different topology due to increased
319 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
320 model for alignments and groups
323 <!-- JAL-384 -->Custom shading schemes created via groovy
330 <!-- JAL-2526 -->Efficiency improvements for interacting
331 with alignment and overview windows
334 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
338 <!-- JAL-2388 -->Hidden columns and sequences can be
342 <!-- JAL-2611 -->Click-drag in visible area allows fine
343 adjustment of visible position
347 <em>Data import/export</em>
350 <!-- JAL-2535 -->Posterior probability annotation from
351 Stockholm files imported as sequence associated annotation
354 <!-- JAL-2507 -->More robust per-sequence positional
355 annotation input/output via stockholm flatfile
358 <!-- JAL-2533 -->Sequence names don't include file
359 extension when importing structure files without embedded
360 names or PDB accessions
363 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
364 format sequence substitution matrices
367 <em>User Interface</em>
370 <!-- JAL-2447 --> Experimental Features Checkbox in
371 Desktop's Tools menu to hide or show untested features in
375 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
376 via Overview or sequence motif search operations
379 <!-- JAL-2547 -->Amend sequence features dialog box can be
380 opened by double clicking gaps within sequence feature
384 <!-- JAL-1476 -->Status bar message shown when not enough
385 aligned positions were available to create a 3D structure
389 <em>3D Structure</em>
392 <!-- JAL-2430 -->Hidden regions in alignment views are not
393 coloured in linked structure views
396 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
397 file-based command exchange
400 <!-- JAL-2375 -->Structure chooser automatically shows
401 Cached Structures rather than querying the PDBe if
402 structures are already available for sequences
405 <!-- JAL-2520 -->Structures imported via URL are cached in
406 the Jalview project rather than downloaded again when the
410 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
411 to transfer Chimera's structure attributes as Jalview
412 features, and vice-versa (<strong>Experimental
416 <em>Web Services</em>
419 <!-- JAL-2549 -->Updated JABAWS client to v2.2
422 <!-- JAL-2335 -->Filter non-standard amino acids and
423 nucleotides when submitting to AACon and other MSA
427 <!-- JAL-2316, -->URLs for viewing database
428 cross-references provided by identifiers.org and the
436 <!-- JAL-2344 -->FileFormatI interface for describing and
437 identifying file formats (instead of String constants)
440 <!-- JAL-2228 -->FeatureCounter script refactored for
441 efficiency when counting all displayed features (not
442 backwards compatible with 2.10.1)
445 <em>Example files</em>
448 <!-- JAL-2631 -->Graduated feature colour style example
449 included in the example feature file
452 <em>Documentation</em>
455 <!-- JAL-2339 -->Release notes reformatted for readability
456 with the built-in Java help viewer
459 <!-- JAL-1644 -->Find documentation updated with 'search
460 sequence description' option
466 <!-- JAL-2485, -->External service integration tests for
467 Uniprot REST Free Text Search Client
470 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
473 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
478 <td><div align="left">
479 <em>Calculations</em>
482 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
483 matrix - C->R should be '-3'<br />Old matrix restored
484 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
486 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
487 Jalview's treatment of gaps in PCA and substitution matrix
488 based Tree calculations.<br /> <br />In earlier versions
489 of Jalview, gaps matching gaps were penalised, and gaps
490 matching non-gaps penalised even more. In the PCA
491 calculation, gaps were actually treated as non-gaps - so
492 different costs were applied, which meant Jalview's PCAs
493 were different to those produced by SeqSpace.<br />Jalview
494 now treats gaps in the same way as SeqSpace (ie it scores
495 them as 0). <br /> <br />Enter the following in the
496 Groovy console to restore pre-2.10.2 behaviour:<br />
497 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
498 // for 2.10.1 mode <br />
499 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
500 // to restore 2.10.2 mode <br /> <br /> <em>Note:
501 these settings will affect all subsequent tree and PCA
502 calculations (not recommended)</em></li>
504 <!-- JAL-2424 -->Fixed off-by-one bug that affected
505 scaling of branch lengths for trees computed using
506 Sequence Feature Similarity.
509 <!-- JAL-2377 -->PCA calculation could hang when
510 generating output report when working with highly
514 <!-- JAL-2544 --> Sort by features includes features to
515 right of selected region when gaps present on right-hand
519 <em>User Interface</em>
522 <!-- JAL-2346 -->Reopening Colour by annotation dialog
523 doesn't reselect a specific sequence's associated
524 annotation after it was used for colouring a view
527 <!-- JAL-2419 -->Current selection lost if popup menu
528 opened on a region of alignment without groups
531 <!-- JAL-2374 -->Popup menu not always shown for regions
532 of an alignment with overlapping groups
535 <!-- JAL-2310 -->Finder double counts if both a sequence's
536 name and description match
539 <!-- JAL-2370 -->Hiding column selection containing two
540 hidden regions results in incorrect hidden regions
543 <!-- JAL-2386 -->'Apply to all groups' setting when
544 changing colour does not apply Conservation slider value
548 <!-- JAL-2373 -->Percentage identity and conservation menu
549 items do not show a tick or allow shading to be disabled
552 <!-- JAL-2385 -->Conservation shading or PID threshold
553 lost when base colourscheme changed if slider not visible
556 <!-- JAL-2547 -->Sequence features shown in tooltip for
557 gaps before start of features
560 <!-- JAL-2623 -->Graduated feature colour threshold not
561 restored to UI when feature colour is edited
564 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
565 a time when scrolling vertically in wrapped mode.
568 <!-- JAL-2630 -->Structure and alignment overview update
569 as graduate feature colour settings are modified via the
573 <!-- JAL-2034 -->Overview window doesn't always update
574 when a group defined on the alignment is resized
577 <!-- JAL-2605 -->Mouseovers on left/right scale region in
578 wrapped view result in positional status updates
582 <!-- JAL-2563 -->Status bar doesn't show position for
583 ambiguous amino acid and nucleotide symbols
586 <!-- JAL-2602 -->Copy consensus sequence failed if
587 alignment included gapped columns
590 <!-- JAL-2473 -->Minimum size set for Jalview windows so
591 widgets don't permanently disappear
594 <!-- JAL-2503 -->Cannot select or filter quantitative
595 annotation that are shown only as column labels (e.g.
596 T-Coffee column reliability scores)
599 <!-- JAL-2594 -->Exception thrown if trying to create a
600 sequence feature on gaps only
603 <!-- JAL-2504 -->Features created with 'New feature'
604 button from a Find inherit previously defined feature type
605 rather than the Find query string
608 <!-- JAL-2423 -->incorrect title in output window when
609 exporting tree calculated in Jalview
612 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
613 and then revealing them reorders sequences on the
617 <!-- JAL-964 -->Group panel in sequence feature settings
618 doesn't update to reflect available set of groups after
619 interactively adding or modifying features
622 <!-- JAL-2225 -->Sequence Database chooser unusable on
626 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
627 only excluded gaps in current sequence and ignored
634 <!-- JAL-2421 -->Overview window visible region moves
635 erratically when hidden rows or columns are present
638 <!-- JAL-2362 -->Per-residue colourschemes applied via the
639 Structure Viewer's colour menu don't correspond to
643 <!-- JAL-2405 -->Protein specific colours only offered in
644 colour and group colour menu for protein alignments
647 <!-- JAL-2385 -->Colour threshold slider doesn't update to
648 reflect currently selected view or group's shading
652 <!-- JAL-2624 -->Feature colour thresholds not respected
653 when rendered on overview and structures when opacity at
657 <!-- JAL-2589 -->User defined gap colour not shown in
658 overview when features overlaid on alignment
661 <em>Data import/export</em>
664 <!-- JAL-2576 -->Very large alignments take a long time to
668 <!-- JAL-2507 -->Per-sequence RNA secondary structures
669 added after a sequence was imported are not written to
673 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
674 when importing RNA secondary structure via Stockholm
677 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
678 not shown in correct direction for simple pseudoknots
681 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
682 with lightGray or darkGray via features file (but can
686 <!-- JAL-2383 -->Above PID colour threshold not recovered
687 when alignment view imported from project
690 <!-- JAL-2520,JAL-2465 -->No mappings generated between
691 structure and sequences extracted from structure files
692 imported via URL and viewed in Jmol
695 <!-- JAL-2520 -->Structures loaded via URL are saved in
696 Jalview Projects rather than fetched via URL again when
697 the project is loaded and the structure viewed
700 <em>Web Services</em>
703 <!-- JAL-2519 -->EnsemblGenomes example failing after
704 release of Ensembl v.88
707 <!-- JAL-2366 -->Proxy server address and port always
708 appear enabled in Preferences->Connections
711 <!-- JAL-2461 -->DAS registry not found exceptions
712 removed from console output
715 <!-- JAL-2582 -->Cannot retrieve protein products from
716 Ensembl by Peptide ID
719 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
720 created from SIFTs, and spurious 'Couldn't open structure
721 in Chimera' errors raised after April 2017 update (problem
722 due to 'null' string rather than empty string used for
723 residues with no corresponding PDB mapping).
726 <em>Application UI</em>
729 <!-- JAL-2361 -->User Defined Colours not added to Colour
733 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
734 case' residues (button in colourscheme editor debugged and
735 new documentation and tooltips added)
738 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
739 doesn't restore group-specific text colour thresholds
742 <!-- JAL-2243 -->Feature settings panel does not update as
743 new features are added to alignment
746 <!-- JAL-2532 -->Cancel in feature settings reverts
747 changes to feature colours via the Amend features dialog
750 <!-- JAL-2506 -->Null pointer exception when attempting to
751 edit graduated feature colour via amend features dialog
755 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
756 selection menu changes colours of alignment views
759 <!-- JAL-2426 -->Spurious exceptions in console raised
760 from alignment calculation workers after alignment has
764 <!-- JAL-1608 -->Typo in selection popup menu - Create
765 groups now 'Create Group'
768 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
769 Create/Undefine group doesn't always work
772 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
773 shown again after pressing 'Cancel'
776 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
777 adjusts start position in wrap mode
780 <!-- JAL-2563 -->Status bar doesn't show positions for
781 ambiguous amino acids
784 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
785 CDS/Protein view after CDS sequences added for aligned
789 <!-- JAL-2592 -->User defined colourschemes called 'User
790 Defined' don't appear in Colours menu
796 <!-- JAL-2468 -->Switching between Nucleotide and Protein
797 score models doesn't always result in an updated PCA plot
800 <!-- JAL-2442 -->Features not rendered as transparent on
801 overview or linked structure view
804 <!-- JAL-2372 -->Colour group by conservation doesn't
808 <!-- JAL-2517 -->Hitting Cancel after applying
809 user-defined colourscheme doesn't restore original
816 <!-- JAL-2314 -->Unit test failure:
817 jalview.ws.jabaws.RNAStructExportImport setup fails
820 <!-- JAL-2307 -->Unit test failure:
821 jalview.ws.sifts.SiftsClientTest due to compatibility
822 problems with deep array comparison equality asserts in
823 successive versions of TestNG
826 <!-- JAL-2479 -->Relocated StructureChooserTest and
827 ParameterUtilsTest Unit tests to Network suite
830 <em>New Known Issues</em>
833 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
834 phase after a sequence motif find operation
837 <!-- JAL-2550 -->Importing annotation file with rows
838 containing just upper and lower case letters are
839 interpreted as WUSS RNA secondary structure symbols
842 <!-- JAL-2590 -->Cannot load and display Newick trees
843 reliably from eggnog Ortholog database
846 <!-- JAL-2468 -->Status bar shows 'Marked x columns
847 containing features of type Highlight' when 'B' is pressed
848 to mark columns containing highlighted regions.
851 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
852 doesn't always add secondary structure annotation.
857 <td width="60" nowrap>
859 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
862 <td><div align="left">
866 <!-- JAL-98 -->Improved memory usage: sparse arrays used
867 for all consensus calculations
870 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
873 <li>Updated Jalview's Certum code signing certificate
879 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
880 set of database cross-references, sorted alphabetically
883 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
884 from database cross references. Users with custom links
885 will receive a <a href="webServices/urllinks.html#warning">warning
886 dialog</a> asking them to update their preferences.
889 <!-- JAL-2287-->Cancel button and escape listener on
890 dialog warning user about disconnecting Jalview from a
894 <!-- JAL-2320-->Jalview's Chimera control window closes if
895 the Chimera it is connected to is shut down
898 <!-- JAL-1738-->New keystroke (B) and Select highlighted
899 columns menu item to mark columns containing highlighted
900 regions (e.g. from structure selections or results of a
904 <!-- JAL-2284-->Command line option for batch-generation
905 of HTML pages rendering alignment data with the BioJS
915 <!-- JAL-2286 -->Columns with more than one modal residue
916 are not coloured or thresholded according to percent
917 identity (first observed in Jalview 2.8.2)
920 <!-- JAL-2301 -->Threonine incorrectly reported as not
924 <!-- JAL-2318 -->Updates to documentation pages (above PID
925 threshold, amino acid properties)
928 <!-- JAL-2292 -->Lower case residues in sequences are not
929 reported as mapped to residues in a structure file in the
933 <!--JAL-2324 -->Identical features with non-numeric scores
934 could be added multiple times to a sequence
937 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
938 bond features shown as two highlighted residues rather
939 than a range in linked structure views, and treated
940 correctly when selecting and computing trees from features
943 <!-- JAL-2281-->Custom URL links for database
944 cross-references are matched to database name regardless
952 <!-- JAL-2282-->Custom URL links for specific database
953 names without regular expressions also offer links from
957 <!-- JAL-2315-->Removing a single configured link in the
958 URL links pane in Connections preferences doesn't actually
959 update Jalview configuration
962 <!-- JAL-2272-->CTRL-Click on a selected region to open
963 the alignment area popup menu doesn't work on El-Capitan
966 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
967 files with similarly named sequences if dropped onto the
971 <!-- JAL-2312 -->Additional mappings are shown for PDB
972 entries where more chains exist in the PDB accession than
973 are reported in the SIFTS file
976 <!-- JAL-2317-->Certain structures do not get mapped to
977 the structure view when displayed with Chimera
980 <!-- JAL-2317-->No chains shown in the Chimera view
981 panel's View->Show Chains submenu
984 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
985 work for wrapped alignment views
988 <!--JAL-2197 -->Rename UI components for running JPred
989 predictions from 'JNet' to 'JPred'
992 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
993 corrupted when annotation panel vertical scroll is not at
997 <!--JAL-2332 -->Attempting to view structure for Hen
998 lysozyme results in a PDB Client error dialog box
1001 <!-- JAL-2319 -->Structure View's mapping report switched
1002 ranges for PDB and sequence for SIFTS
1005 SIFTS 'Not_Observed' residues mapped to non-existant
1009 <!-- <em>New Known Issues</em>
1016 <td width="60" nowrap>
1017 <div align="center">
1018 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1019 <em>25/10/2016</em></strong>
1022 <td><em>Application</em>
1024 <li>3D Structure chooser opens with 'Cached structures'
1025 view if structures already loaded</li>
1026 <li>Progress bar reports models as they are loaded to
1027 structure views</li>
1033 <li>Colour by conservation always enabled and no tick
1034 shown in menu when BLOSUM or PID shading applied</li>
1035 <li>FER1_ARATH and FER2_ARATH labels were switched in
1036 example sequences/projects/trees</li>
1038 <em>Application</em>
1040 <li>Jalview projects with views of local PDB structure
1041 files saved on Windows cannot be opened on OSX</li>
1042 <li>Multiple structure views can be opened and superposed
1043 without timeout for structures with multiple models or
1044 multiple sequences in alignment</li>
1045 <li>Cannot import or associated local PDB files without a
1046 PDB ID HEADER line</li>
1047 <li>RMSD is not output in Jmol console when superposition
1049 <li>Drag and drop of URL from Browser fails for Linux and
1050 OSX versions earlier than El Capitan</li>
1051 <li>ENA client ignores invalid content from ENA server</li>
1052 <li>Exceptions are not raised in console when ENA client
1053 attempts to fetch non-existent IDs via Fetch DB Refs UI
1055 <li>Exceptions are not raised in console when a new view
1056 is created on the alignment</li>
1057 <li>OSX right-click fixed for group selections: CMD-click
1058 to insert/remove gaps in groups and CTRL-click to open group
1061 <em>Build and deployment</em>
1063 <li>URL link checker now copes with multi-line anchor
1066 <em>New Known Issues</em>
1068 <li>Drag and drop from URL links in browsers do not work
1075 <td width="60" nowrap>
1076 <div align="center">
1077 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1080 <td><em>General</em>
1083 <!-- JAL-2124 -->Updated Spanish translations.
1086 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1087 for importing structure data to Jalview. Enables mmCIF and
1091 <!-- JAL-192 --->Alignment ruler shows positions relative to
1095 <!-- JAL-2202 -->Position/residue shown in status bar when
1096 mousing over sequence associated annotation
1099 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1103 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1104 '()', canonical '[]' and invalid '{}' base pair populations
1108 <!-- JAL-2092 -->Feature settings popup menu options for
1109 showing or hiding columns containing a feature
1112 <!-- JAL-1557 -->Edit selected group by double clicking on
1113 group and sequence associated annotation labels
1116 <!-- JAL-2236 -->Sequence name added to annotation label in
1117 select/hide columns by annotation and colour by annotation
1121 </ul> <em>Application</em>
1124 <!-- JAL-2050-->Automatically hide introns when opening a
1125 gene/transcript view
1128 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1132 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1133 structure mappings with the EMBL-EBI PDBe SIFTS database
1136 <!-- JAL-2079 -->Updated download sites used for Rfam and
1137 Pfam sources to xfam.org
1140 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1143 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1144 over sequences in Jalview
1147 <!-- JAL-2027-->Support for reverse-complement coding
1148 regions in ENA and EMBL
1151 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1152 for record retrieval via ENA rest API
1155 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1159 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1160 groovy script execution
1163 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1164 alignment window's Calculate menu
1167 <!-- JAL-1812 -->Allow groovy scripts that call
1168 Jalview.getAlignFrames() to run in headless mode
1171 <!-- JAL-2068 -->Support for creating new alignment
1172 calculation workers from groovy scripts
1175 <!-- JAL-1369 --->Store/restore reference sequence in
1179 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1180 associations are now saved/restored from project
1183 <!-- JAL-1993 -->Database selection dialog always shown
1184 before sequence fetcher is opened
1187 <!-- JAL-2183 -->Double click on an entry in Jalview's
1188 database chooser opens a sequence fetcher
1191 <!-- JAL-1563 -->Free-text search client for UniProt using
1192 the UniProt REST API
1195 <!-- JAL-2168 -->-nonews command line parameter to prevent
1196 the news reader opening
1199 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1200 querying stored in preferences
1203 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1207 <!-- JAL-1977-->Tooltips shown on database chooser
1210 <!-- JAL-391 -->Reverse complement function in calculate
1211 menu for nucleotide sequences
1214 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1215 and feature counts preserves alignment ordering (and
1216 debugged for complex feature sets).
1219 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1220 viewing structures with Jalview 2.10
1223 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1224 genome, transcript CCDS and gene ids via the Ensembl and
1225 Ensembl Genomes REST API
1228 <!-- JAL-2049 -->Protein sequence variant annotation
1229 computed for 'sequence_variant' annotation on CDS regions
1233 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1237 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1238 Ref Fetcher fails to match, or otherwise updates sequence
1239 data from external database records.
1242 <!-- JAL-2154 -->Revised Jalview Project format for
1243 efficient recovery of sequence coding and alignment
1244 annotation relationships.
1246 </ul> <!-- <em>Applet</em>
1257 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1261 <!-- JAL-2018-->Export features in Jalview format (again)
1262 includes graduated colourschemes
1265 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1266 working with big alignments and lots of hidden columns
1269 <!-- JAL-2053-->Hidden column markers not always rendered
1270 at right of alignment window
1273 <!-- JAL-2067 -->Tidied up links in help file table of
1277 <!-- JAL-2072 -->Feature based tree calculation not shown
1281 <!-- JAL-2075 -->Hidden columns ignored during feature
1282 based tree calculation
1285 <!-- JAL-2065 -->Alignment view stops updating when show
1286 unconserved enabled for group on alignment
1289 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1293 <!-- JAL-2146 -->Alignment column in status incorrectly
1294 shown as "Sequence position" when mousing over
1298 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1299 hidden columns present
1302 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1303 user created annotation added to alignment
1306 <!-- JAL-1841 -->RNA Structure consensus only computed for
1307 '()' base pair annotation
1310 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1311 in zero scores for all base pairs in RNA Structure
1315 <!-- JAL-2174-->Extend selection with columns containing
1319 <!-- JAL-2275 -->Pfam format writer puts extra space at
1320 beginning of sequence
1323 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1327 <!-- JAL-2238 -->Cannot create groups on an alignment from
1328 from a tree when t-coffee scores are shown
1331 <!-- JAL-1836,1967 -->Cannot import and view PDB
1332 structures with chains containing negative resnums (4q4h)
1335 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1339 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1340 to Clustal, PIR and PileUp output
1343 <!-- JAL-2008 -->Reordering sequence features that are
1344 not visible causes alignment window to repaint
1347 <!-- JAL-2006 -->Threshold sliders don't work in
1348 graduated colour and colour by annotation row for e-value
1349 scores associated with features and annotation rows
1352 <!-- JAL-1797 -->amino acid physicochemical conservation
1353 calculation should be case independent
1356 <!-- JAL-2173 -->Remove annotation also updates hidden
1360 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1361 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1362 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1365 <!-- JAL-2065 -->Null pointer exceptions and redraw
1366 problems when reference sequence defined and 'show
1367 non-conserved' enabled
1370 <!-- JAL-1306 -->Quality and Conservation are now shown on
1371 load even when Consensus calculation is disabled
1374 <!-- JAL-1932 -->Remove right on penultimate column of
1375 alignment does nothing
1378 <em>Application</em>
1381 <!-- JAL-1552-->URLs and links can't be imported by
1382 drag'n'drop on OSX when launched via webstart (note - not
1383 yet fixed for El Capitan)
1386 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1387 output when running on non-gb/us i18n platforms
1390 <!-- JAL-1944 -->Error thrown when exporting a view with
1391 hidden sequences as flat-file alignment
1394 <!-- JAL-2030-->InstallAnywhere distribution fails when
1398 <!-- JAL-2080-->Jalview very slow to launch via webstart
1399 (also hotfix for 2.9.0b2)
1402 <!-- JAL-2085 -->Cannot save project when view has a
1403 reference sequence defined
1406 <!-- JAL-1011 -->Columns are suddenly selected in other
1407 alignments and views when revealing hidden columns
1410 <!-- JAL-1989 -->Hide columns not mirrored in complement
1411 view in a cDNA/Protein splitframe
1414 <!-- JAL-1369 -->Cannot save/restore representative
1415 sequence from project when only one sequence is
1419 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1420 in Structure Chooser
1423 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1424 structure consensus didn't refresh annotation panel
1427 <!-- JAL-1962 -->View mapping in structure view shows
1428 mappings between sequence and all chains in a PDB file
1431 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1432 dialogs format columns correctly, don't display array
1433 data, sort columns according to type
1436 <!-- JAL-1975 -->Export complete shown after destination
1437 file chooser is cancelled during an image export
1440 <!-- JAL-2025 -->Error when querying PDB Service with
1441 sequence name containing special characters
1444 <!-- JAL-2024 -->Manual PDB structure querying should be
1448 <!-- JAL-2104 -->Large tooltips with broken HTML
1449 formatting don't wrap
1452 <!-- JAL-1128 -->Figures exported from wrapped view are
1453 truncated so L looks like I in consensus annotation
1456 <!-- JAL-2003 -->Export features should only export the
1457 currently displayed features for the current selection or
1461 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1462 after fetching cross-references, and restoring from
1466 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1467 followed in the structure viewer
1470 <!-- JAL-2163 -->Titles for individual alignments in
1471 splitframe not restored from project
1474 <!-- JAL-2145 -->missing autocalculated annotation at
1475 trailing end of protein alignment in transcript/product
1476 splitview when pad-gaps not enabled by default
1479 <!-- JAL-1797 -->amino acid physicochemical conservation
1483 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1484 article has been read (reopened issue due to
1485 internationalisation problems)
1488 <!-- JAL-1960 -->Only offer PDB structures in structure
1489 viewer based on sequence name, PDB and UniProt
1494 <!-- JAL-1976 -->No progress bar shown during export of
1498 <!-- JAL-2213 -->Structures not always superimposed after
1499 multiple structures are shown for one or more sequences.
1502 <!-- JAL-1370 -->Reference sequence characters should not
1503 be replaced with '.' when 'Show unconserved' format option
1507 <!-- JAL-1823 -->Cannot specify chain code when entering
1508 specific PDB id for sequence
1511 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1512 'Export hidden sequences' is enabled, but 'export hidden
1513 columns' is disabled.
1516 <!--JAL-2026-->Best Quality option in structure chooser
1517 selects lowest rather than highest resolution structures
1521 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1522 to sequence mapping in 'View Mappings' report
1525 <!-- JAL-2284 -->Unable to read old Jalview projects that
1526 contain non-XML data added after Jalvew wrote project.
1529 <!-- JAL-2118 -->Newly created annotation row reorders
1530 after clicking on it to create new annotation for a
1534 <!-- JAL-1980 -->Null Pointer Exception raised when
1535 pressing Add on an orphaned cut'n'paste window.
1537 <!-- may exclude, this is an external service stability issue JAL-1941
1538 -- > RNA 3D structure not added via DSSR service</li> -->
1543 <!-- JAL-2151 -->Incorrect columns are selected when
1544 hidden columns present before start of sequence
1547 <!-- JAL-1986 -->Missing dependencies on applet pages
1551 <!-- JAL-1947 -->Overview pixel size changes when
1552 sequences are hidden in applet
1555 <!-- JAL-1996 -->Updated instructions for applet
1556 deployment on examples pages.
1563 <td width="60" nowrap>
1564 <div align="center">
1565 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1566 <em>16/10/2015</em></strong>
1569 <td><em>General</em>
1571 <li>Time stamps for signed Jalview application and applet
1576 <em>Application</em>
1578 <li>Duplicate group consensus and conservation rows
1579 shown when tree is partitioned</li>
1580 <li>Erratic behaviour when tree partitions made with
1581 multiple cDNA/Protein split views</li>
1587 <td width="60" nowrap>
1588 <div align="center">
1589 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1590 <em>8/10/2015</em></strong>
1593 <td><em>General</em>
1595 <li>Updated Spanish translations of localized text for
1597 </ul> <em>Application</em>
1599 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1600 <li>Signed OSX InstallAnywhere installer<br></li>
1601 <li>Support for per-sequence based annotations in BioJSON</li>
1602 </ul> <em>Applet</em>
1604 <li>Split frame example added to applet examples page</li>
1605 </ul> <em>Build and Deployment</em>
1608 <!-- JAL-1888 -->New ant target for running Jalview's test
1616 <li>Mapping of cDNA to protein in split frames
1617 incorrect when sequence start > 1</li>
1618 <li>Broken images in filter column by annotation dialog
1620 <li>Feature colours not parsed from features file</li>
1621 <li>Exceptions and incomplete link URLs recovered when
1622 loading a features file containing HTML tags in feature
1626 <em>Application</em>
1628 <li>Annotations corrupted after BioJS export and
1630 <li>Incorrect sequence limits after Fetch DB References
1631 with 'trim retrieved sequences'</li>
1632 <li>Incorrect warning about deleting all data when
1633 deleting selected columns</li>
1634 <li>Patch to build system for shipping properly signed
1635 JNLP templates for webstart launch</li>
1636 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1637 unreleased structures for download or viewing</li>
1638 <li>Tab/space/return keystroke operation of EMBL-PDBe
1639 fetcher/viewer dialogs works correctly</li>
1640 <li>Disabled 'minimise' button on Jalview windows
1641 running on OSX to workaround redraw hang bug</li>
1642 <li>Split cDNA/Protein view position and geometry not
1643 recovered from jalview project</li>
1644 <li>Initial enabled/disabled state of annotation menu
1645 sorter 'show autocalculated first/last' corresponds to
1647 <li>Restoring of Clustal, RNA Helices and T-Coffee
1648 color schemes from BioJSON</li>
1652 <li>Reorder sequences mirrored in cDNA/Protein split
1654 <li>Applet with Jmol examples not loading correctly</li>
1660 <td><div align="center">
1661 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1663 <td><em>General</em>
1665 <li>Linked visualisation and analysis of DNA and Protein
1668 <li>Translated cDNA alignments shown as split protein
1669 and DNA alignment views</li>
1670 <li>Codon consensus annotation for linked protein and
1671 cDNA alignment views</li>
1672 <li>Link cDNA or Protein product sequences by loading
1673 them onto Protein or cDNA alignments</li>
1674 <li>Reconstruct linked cDNA alignment from aligned
1675 protein sequences</li>
1678 <li>Jmol integration updated to Jmol v14.2.14</li>
1679 <li>Import and export of Jalview alignment views as <a
1680 href="features/bioJsonFormat.html">BioJSON</a></li>
1681 <li>New alignment annotation file statements for
1682 reference sequences and marking hidden columns</li>
1683 <li>Reference sequence based alignment shading to
1684 highlight variation</li>
1685 <li>Select or hide columns according to alignment
1687 <li>Find option for locating sequences by description</li>
1688 <li>Conserved physicochemical properties shown in amino
1689 acid conservation row</li>
1690 <li>Alignments can be sorted by number of RNA helices</li>
1691 </ul> <em>Application</em>
1693 <li>New cDNA/Protein analysis capabilities
1695 <li>Get Cross-References should open a Split Frame
1696 view with cDNA/Protein</li>
1697 <li>Detect when nucleotide sequences and protein
1698 sequences are placed in the same alignment</li>
1699 <li>Split cDNA/Protein views are saved in Jalview
1704 <li>Use REST API to talk to Chimera</li>
1705 <li>Selected regions in Chimera are highlighted in linked
1706 Jalview windows</li>
1708 <li>VARNA RNA viewer updated to v3.93</li>
1709 <li>VARNA views are saved in Jalview Projects</li>
1710 <li>Pseudoknots displayed as Jalview RNA annotation can
1711 be shown in VARNA</li>
1713 <li>Make groups for selection uses marked columns as well
1714 as the active selected region</li>
1716 <li>Calculate UPGMA and NJ trees using sequence feature
1718 <li>New Export options
1720 <li>New Export Settings dialog to control hidden
1721 region export in flat file generation</li>
1723 <li>Export alignment views for display with the <a
1724 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1726 <li>Export scrollable SVG in HTML page</li>
1727 <li>Optional embedding of BioJSON data when exporting
1728 alignment figures to HTML</li>
1730 <li>3D structure retrieval and display
1732 <li>Free text and structured queries with the PDBe
1734 <li>PDBe Search API based discovery and selection of
1735 PDB structures for a sequence set</li>
1739 <li>JPred4 employed for protein secondary structure
1741 <li>Hide Insertions menu option to hide unaligned columns
1742 for one or a group of sequences</li>
1743 <li>Automatically hide insertions in alignments imported
1744 from the JPred4 web server</li>
1745 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1746 system on OSX<br />LGPL libraries courtesy of <a
1747 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1749 <li>changed 'View nucleotide structure' submenu to 'View
1750 VARNA 2D Structure'</li>
1751 <li>change "View protein structure" menu option to "3D
1754 </ul> <em>Applet</em>
1756 <li>New layout for applet example pages</li>
1757 <li>New parameters to enable SplitFrame view
1758 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1759 <li>New example demonstrating linked viewing of cDNA and
1760 Protein alignments</li>
1761 </ul> <em>Development and deployment</em>
1763 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1764 <li>Include installation type and git revision in build
1765 properties and console log output</li>
1766 <li>Jalview Github organisation, and new github site for
1767 storing BioJsMSA Templates</li>
1768 <li>Jalview's unit tests now managed with TestNG</li>
1771 <!-- <em>General</em>
1773 </ul> --> <!-- issues resolved --> <em>Application</em>
1775 <li>Escape should close any open find dialogs</li>
1776 <li>Typo in select-by-features status report</li>
1777 <li>Consensus RNA secondary secondary structure
1778 predictions are not highlighted in amber</li>
1779 <li>Missing gap character in v2.7 example file means
1780 alignment appears unaligned when pad-gaps is not enabled</li>
1781 <li>First switch to RNA Helices colouring doesn't colour
1782 associated structure views</li>
1783 <li>ID width preference option is greyed out when auto
1784 width checkbox not enabled</li>
1785 <li>Stopped a warning dialog from being shown when
1786 creating user defined colours</li>
1787 <li>'View Mapping' in structure viewer shows sequence
1788 mappings for just that viewer's sequences</li>
1789 <li>Workaround for superposing PDB files containing
1790 multiple models in Chimera</li>
1791 <li>Report sequence position in status bar when hovering
1792 over Jmol structure</li>
1793 <li>Cannot output gaps as '.' symbols with Selection ->
1794 output to text box</li>
1795 <li>Flat file exports of alignments with hidden columns
1796 have incorrect sequence start/end</li>
1797 <li>'Aligning' a second chain to a Chimera structure from
1799 <li>Colour schemes applied to structure viewers don't
1800 work for nucleotide</li>
1801 <li>Loading/cut'n'pasting an empty or invalid file leads
1802 to a grey/invisible alignment window</li>
1803 <li>Exported Jpred annotation from a sequence region
1804 imports to different position</li>
1805 <li>Space at beginning of sequence feature tooltips shown
1806 on some platforms</li>
1807 <li>Chimera viewer 'View | Show Chain' menu is not
1809 <li>'New View' fails with a Null Pointer Exception in
1810 console if Chimera has been opened</li>
1811 <li>Mouseover to Chimera not working</li>
1812 <li>Miscellaneous ENA XML feature qualifiers not
1814 <li>NPE in annotation renderer after 'Extract Scores'</li>
1815 <li>If two structures in one Chimera window, mouseover of
1816 either sequence shows on first structure</li>
1817 <li>'Show annotations' options should not make
1818 non-positional annotations visible</li>
1819 <li>Subsequence secondary structure annotation not shown
1820 in right place after 'view flanking regions'</li>
1821 <li>File Save As type unset when current file format is
1823 <li>Save as '.jar' option removed for saving Jalview
1825 <li>Colour by Sequence colouring in Chimera more
1827 <li>Cannot 'add reference annotation' for a sequence in
1828 several views on same alignment</li>
1829 <li>Cannot show linked products for EMBL / ENA records</li>
1830 <li>Jalview's tooltip wraps long texts containing no
1832 </ul> <em>Applet</em>
1834 <li>Jmol to JalviewLite mouseover/link not working</li>
1835 <li>JalviewLite can't import sequences with ID
1836 descriptions containing angle brackets</li>
1837 </ul> <em>General</em>
1839 <li>Cannot export and reimport RNA secondary structure
1840 via jalview annotation file</li>
1841 <li>Random helix colour palette for colour by annotation
1842 with RNA secondary structure</li>
1843 <li>Mouseover to cDNA from STOP residue in protein
1844 translation doesn't work.</li>
1845 <li>hints when using the select by annotation dialog box</li>
1846 <li>Jmol alignment incorrect if PDB file has alternate CA
1848 <li>FontChooser message dialog appears to hang after
1849 choosing 1pt font</li>
1850 <li>Peptide secondary structure incorrectly imported from
1851 annotation file when annotation display text includes 'e' or
1853 <li>Cannot set colour of new feature type whilst creating
1855 <li>cDNA translation alignment should not be sequence
1856 order dependent</li>
1857 <li>'Show unconserved' doesn't work for lower case
1859 <li>Nucleotide ambiguity codes involving R not recognised</li>
1860 </ul> <em>Deployment and Documentation</em>
1862 <li>Applet example pages appear different to the rest of
1863 www.jalview.org</li>
1864 </ul> <em>Application Known issues</em>
1866 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1867 <li>Misleading message appears after trying to delete
1869 <li>Jalview icon not shown in dock after InstallAnywhere
1870 version launches</li>
1871 <li>Fetching EMBL reference for an RNA sequence results
1872 fails with a sequence mismatch</li>
1873 <li>Corrupted or unreadable alignment display when
1874 scrolling alignment to right</li>
1875 <li>ArrayIndexOutOfBoundsException thrown when remove
1876 empty columns called on alignment with ragged gapped ends</li>
1877 <li>auto calculated alignment annotation rows do not get
1878 placed above or below non-autocalculated rows</li>
1879 <li>Jalview dekstop becomes sluggish at full screen in
1880 ultra-high resolution</li>
1881 <li>Cannot disable consensus calculation independently of
1882 quality and conservation</li>
1883 <li>Mouseover highlighting between cDNA and protein can
1884 become sluggish with more than one splitframe shown</li>
1885 </ul> <em>Applet Known Issues</em>
1887 <li>Core PDB parsing code requires Jmol</li>
1888 <li>Sequence canvas panel goes white when alignment
1889 window is being resized</li>
1895 <td><div align="center">
1896 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1898 <td><em>General</em>
1900 <li>Updated Java code signing certificate donated by
1902 <li>Features and annotation preserved when performing
1903 pairwise alignment</li>
1904 <li>RNA pseudoknot annotation can be
1905 imported/exported/displayed</li>
1906 <li>'colour by annotation' can colour by RNA and
1907 protein secondary structure</li>
1908 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1909 post-hoc with 2.9 release</em>)
1912 </ul> <em>Application</em>
1914 <li>Extract and display secondary structure for sequences
1915 with 3D structures</li>
1916 <li>Support for parsing RNAML</li>
1917 <li>Annotations menu for layout
1919 <li>sort sequence annotation rows by alignment</li>
1920 <li>place sequence annotation above/below alignment
1923 <li>Output in Stockholm format</li>
1924 <li>Internationalisation: improved Spanish (es)
1926 <li>Structure viewer preferences tab</li>
1927 <li>Disorder and Secondary Structure annotation tracks
1928 shared between alignments</li>
1929 <li>UCSF Chimera launch and linked highlighting from
1931 <li>Show/hide all sequence associated annotation rows for
1932 all or current selection</li>
1933 <li>disorder and secondary structure predictions
1934 available as dataset annotation</li>
1935 <li>Per-sequence rna helices colouring</li>
1938 <li>Sequence database accessions imported when fetching
1939 alignments from Rfam</li>
1940 <li>update VARNA version to 3.91</li>
1942 <li>New groovy scripts for exporting aligned positions,
1943 conservation values, and calculating sum of pairs scores.</li>
1944 <li>Command line argument to set default JABAWS server</li>
1945 <li>include installation type in build properties and
1946 console log output</li>
1947 <li>Updated Jalview project format to preserve dataset
1951 <!-- issues resolved --> <em>Application</em>
1953 <li>Distinguish alignment and sequence associated RNA
1954 structure in structure->view->VARNA</li>
1955 <li>Raise dialog box if user deletes all sequences in an
1957 <li>Pressing F1 results in documentation opening twice</li>
1958 <li>Sequence feature tooltip is wrapped</li>
1959 <li>Double click on sequence associated annotation
1960 selects only first column</li>
1961 <li>Redundancy removal doesn't result in unlinked
1962 leaves shown in tree</li>
1963 <li>Undos after several redundancy removals don't undo
1965 <li>Hide sequence doesn't hide associated annotation</li>
1966 <li>User defined colours dialog box too big to fit on
1967 screen and buttons not visible</li>
1968 <li>author list isn't updated if already written to
1969 Jalview properties</li>
1970 <li>Popup menu won't open after retrieving sequence
1972 <li>File open window for associate PDB doesn't open</li>
1973 <li>Left-then-right click on a sequence id opens a
1974 browser search window</li>
1975 <li>Cannot open sequence feature shading/sort popup menu
1976 in feature settings dialog</li>
1977 <li>better tooltip placement for some areas of Jalview
1979 <li>Allow addition of JABAWS Server which doesn't
1980 pass validation</li>
1981 <li>Web services parameters dialog box is too large to
1983 <li>Muscle nucleotide alignment preset obscured by
1985 <li>JABAWS preset submenus don't contain newly
1986 defined user preset</li>
1987 <li>MSA web services warns user if they were launched
1988 with invalid input</li>
1989 <li>Jalview cannot contact DAS Registy when running on
1992 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1993 'Superpose with' submenu not shown when new view
1997 </ul> <!-- <em>Applet</em>
1999 </ul> <em>General</em>
2001 </ul>--> <em>Deployment and Documentation</em>
2003 <li>2G and 1G options in launchApp have no effect on
2004 memory allocation</li>
2005 <li>launchApp service doesn't automatically open
2006 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2008 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2009 InstallAnywhere reports cannot find valid JVM when Java
2010 1.7_055 is available
2012 </ul> <em>Application Known issues</em>
2015 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2016 corrupted or unreadable alignment display when scrolling
2020 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2021 retrieval fails but progress bar continues for DAS retrieval
2022 with large number of ID
2025 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2026 flatfile output of visible region has incorrect sequence
2030 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2031 rna structure consensus doesn't update when secondary
2032 structure tracks are rearranged
2035 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2036 invalid rna structure positional highlighting does not
2037 highlight position of invalid base pairs
2040 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2041 out of memory errors are not raised when saving Jalview
2042 project from alignment window file menu
2045 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2046 Switching to RNA Helices colouring doesn't propagate to
2050 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2051 colour by RNA Helices not enabled when user created
2052 annotation added to alignment
2055 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2056 Jalview icon not shown on dock in Mountain Lion/Webstart
2058 </ul> <em>Applet Known Issues</em>
2061 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2062 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2065 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2066 Jalview and Jmol example not compatible with IE9
2069 <li>Sort by annotation score doesn't reverse order
2075 <td><div align="center">
2076 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2079 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2082 <li>Internationalisation of user interface (usually
2083 called i18n support) and translation for Spanish locale</li>
2084 <li>Define/Undefine group on current selection with
2085 Ctrl-G/Shift Ctrl-G</li>
2086 <li>Improved group creation/removal options in
2087 alignment/sequence Popup menu</li>
2088 <li>Sensible precision for symbol distribution
2089 percentages shown in logo tooltip.</li>
2090 <li>Annotation panel height set according to amount of
2091 annotation when alignment first opened</li>
2092 </ul> <em>Application</em>
2094 <li>Interactive consensus RNA secondary structure
2095 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2096 <li>Select columns containing particular features from
2097 Feature Settings dialog</li>
2098 <li>View all 'representative' PDB structures for selected
2100 <li>Update Jalview project format:
2102 <li>New file extension for Jalview projects '.jvp'</li>
2103 <li>Preserve sequence and annotation dataset (to
2104 store secondary structure annotation,etc)</li>
2105 <li>Per group and alignment annotation and RNA helix
2109 <li>New similarity measures for PCA and Tree calculation
2111 <li>Experimental support for retrieval and viewing of
2112 flanking regions for an alignment</li>
2116 <!-- issues resolved --> <em>Application</em>
2118 <li>logo keeps spinning and status remains at queued or
2119 running after job is cancelled</li>
2120 <li>cannot export features from alignments imported from
2121 Jalview/VAMSAS projects</li>
2122 <li>Buggy slider for web service parameters that take
2124 <li>Newly created RNA secondary structure line doesn't
2125 have 'display all symbols' flag set</li>
2126 <li>T-COFFEE alignment score shading scheme and other
2127 annotation shading not saved in Jalview project</li>
2128 <li>Local file cannot be loaded in freshly downloaded
2130 <li>Jalview icon not shown on dock in Mountain
2132 <li>Load file from desktop file browser fails</li>
2133 <li>Occasional NPE thrown when calculating large trees</li>
2134 <li>Cannot reorder or slide sequences after dragging an
2135 alignment onto desktop</li>
2136 <li>Colour by annotation dialog throws NPE after using
2137 'extract scores' function</li>
2138 <li>Loading/cut'n'pasting an empty file leads to a grey
2139 alignment window</li>
2140 <li>Disorder thresholds rendered incorrectly after
2141 performing IUPred disorder prediction</li>
2142 <li>Multiple group annotated consensus rows shown when
2143 changing 'normalise logo' display setting</li>
2144 <li>Find shows blank dialog after 'finished searching' if
2145 nothing matches query</li>
2146 <li>Null Pointer Exceptions raised when sorting by
2147 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2149 <li>Errors in Jmol console when structures in alignment
2150 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2152 <li>Not all working JABAWS services are shown in
2154 <li>JAVAWS version of Jalview fails to launch with
2155 'invalid literal/length code'</li>
2156 <li>Annotation/RNA Helix colourschemes cannot be applied
2157 to alignment with groups (actually fixed in 2.8.0b1)</li>
2158 <li>RNA Helices and T-Coffee Scores available as default
2161 </ul> <em>Applet</em>
2163 <li>Remove group option is shown even when selection is
2165 <li>Apply to all groups ticked but colourscheme changes
2166 don't affect groups</li>
2167 <li>Documented RNA Helices and T-Coffee Scores as valid
2168 colourscheme name</li>
2169 <li>Annotation labels drawn on sequence IDs when
2170 Annotation panel is not displayed</li>
2171 <li>Increased font size for dropdown menus on OSX and
2172 embedded windows</li>
2173 </ul> <em>Other</em>
2175 <li>Consensus sequence for alignments/groups with a
2176 single sequence were not calculated</li>
2177 <li>annotation files that contain only groups imported as
2178 annotation and junk sequences</li>
2179 <li>Fasta files with sequences containing '*' incorrectly
2180 recognised as PFAM or BLC</li>
2181 <li>conservation/PID slider apply all groups option
2182 doesn't affect background (2.8.0b1)
2184 <li>redundancy highlighting is erratic at 0% and 100%</li>
2185 <li>Remove gapped columns fails for sequences with ragged
2187 <li>AMSA annotation row with leading spaces is not
2188 registered correctly on import</li>
2189 <li>Jalview crashes when selecting PCA analysis for
2190 certain alignments</li>
2191 <li>Opening the colour by annotation dialog for an
2192 existing annotation based 'use original colours'
2193 colourscheme loses original colours setting</li>
2198 <td><div align="center">
2199 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2200 <em>30/1/2014</em></strong>
2204 <li>Trusted certificates for JalviewLite applet and
2205 Jalview Desktop application<br />Certificate was donated by
2206 <a href="https://www.certum.eu">Certum</a> to the Jalview
2207 open source project).
2209 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2210 <li>Output in Stockholm format</li>
2211 <li>Allow import of data from gzipped files</li>
2212 <li>Export/import group and sequence associated line
2213 graph thresholds</li>
2214 <li>Nucleotide substitution matrix that supports RNA and
2215 ambiguity codes</li>
2216 <li>Allow disorder predictions to be made on the current
2217 selection (or visible selection) in the same way that JPred
2219 <li>Groovy scripting for headless Jalview operation</li>
2220 </ul> <em>Other improvements</em>
2222 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2223 <li>COMBINE statement uses current SEQUENCE_REF and
2224 GROUP_REF scope to group annotation rows</li>
2225 <li>Support '' style escaping of quotes in Newick
2227 <li>Group options for JABAWS service by command line name</li>
2228 <li>Empty tooltip shown for JABA service options with a
2229 link but no description</li>
2230 <li>Select primary source when selecting authority in
2231 database fetcher GUI</li>
2232 <li>Add .mfa to FASTA file extensions recognised by
2234 <li>Annotation label tooltip text wrap</li>
2239 <li>Slow scrolling when lots of annotation rows are
2241 <li>Lots of NPE (and slowness) after creating RNA
2242 secondary structure annotation line</li>
2243 <li>Sequence database accessions not imported when
2244 fetching alignments from Rfam</li>
2245 <li>Incorrect SHMR submission for sequences with
2247 <li>View all structures does not always superpose
2249 <li>Option widgets in service parameters not updated to
2250 reflect user or preset settings</li>
2251 <li>Null pointer exceptions for some services without
2252 presets or adjustable parameters</li>
2253 <li>Discover PDB IDs entry in structure menu doesn't
2254 discover PDB xRefs</li>
2255 <li>Exception encountered while trying to retrieve
2256 features with DAS</li>
2257 <li>Lowest value in annotation row isn't coloured
2258 when colour by annotation (per sequence) is coloured</li>
2259 <li>Keyboard mode P jumps to start of gapped region when
2260 residue follows a gap</li>
2261 <li>Jalview appears to hang importing an alignment with
2262 Wrap as default or after enabling Wrap</li>
2263 <li>'Right click to add annotations' message
2264 shown in wrap mode when no annotations present</li>
2265 <li>Disorder predictions fail with NPE if no automatic
2266 annotation already exists on alignment</li>
2267 <li>oninit javascript function should be called after
2268 initialisation completes</li>
2269 <li>Remove redundancy after disorder prediction corrupts
2270 alignment window display</li>
2271 <li>Example annotation file in documentation is invalid</li>
2272 <li>Grouped line graph annotation rows are not exported
2273 to annotation file</li>
2274 <li>Multi-harmony analysis cannot be run when only two
2276 <li>Cannot create multiple groups of line graphs with
2277 several 'combine' statements in annotation file</li>
2278 <li>Pressing return several times causes Number Format
2279 exceptions in keyboard mode</li>
2280 <li>Multi-harmony (SHMMR) method doesn't submit
2281 correct partitions for input data</li>
2282 <li>Translation from DNA to Amino Acids fails</li>
2283 <li>Jalview fail to load newick tree with quoted label</li>
2284 <li>--headless flag isn't understood</li>
2285 <li>ClassCastException when generating EPS in headless
2287 <li>Adjusting sequence-associated shading threshold only
2288 changes one row's threshold</li>
2289 <li>Preferences and Feature settings panel panel
2290 doesn't open</li>
2291 <li>hide consensus histogram also hides conservation and
2292 quality histograms</li>
2297 <td><div align="center">
2298 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2300 <td><em>Application</em>
2302 <li>Support for JABAWS 2.0 Services (AACon alignment
2303 conservation, protein disorder and Clustal Omega)</li>
2304 <li>JABAWS server status indicator in Web Services
2306 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2307 in Jalview alignment window</li>
2308 <li>Updated Jalview build and deploy framework for OSX
2309 mountain lion, windows 7, and 8</li>
2310 <li>Nucleotide substitution matrix for PCA that supports
2311 RNA and ambiguity codes</li>
2313 <li>Improved sequence database retrieval GUI</li>
2314 <li>Support fetching and database reference look up
2315 against multiple DAS sources (Fetch all from in 'fetch db
2317 <li>Jalview project improvements
2319 <li>Store and retrieve the 'belowAlignment'
2320 flag for annotation</li>
2321 <li>calcId attribute to group annotation rows on the
2323 <li>Store AACon calculation settings for a view in
2324 Jalview project</li>
2328 <li>horizontal scrolling gesture support</li>
2329 <li>Visual progress indicator when PCA calculation is
2331 <li>Simpler JABA web services menus</li>
2332 <li>visual indication that web service results are still
2333 being retrieved from server</li>
2334 <li>Serialise the dialogs that are shown when Jalview
2335 starts up for first time</li>
2336 <li>Jalview user agent string for interacting with HTTP
2338 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2340 <li>Examples directory and Groovy library included in
2341 InstallAnywhere distribution</li>
2342 </ul> <em>Applet</em>
2344 <li>RNA alignment and secondary structure annotation
2345 visualization applet example</li>
2346 </ul> <em>General</em>
2348 <li>Normalise option for consensus sequence logo</li>
2349 <li>Reset button in PCA window to return dimensions to
2351 <li>Allow seqspace or Jalview variant of alignment PCA
2353 <li>PCA with either nucleic acid and protein substitution
2355 <li>Allow windows containing HTML reports to be exported
2357 <li>Interactive display and editing of RNA secondary
2358 structure contacts</li>
2359 <li>RNA Helix Alignment Colouring</li>
2360 <li>RNA base pair logo consensus</li>
2361 <li>Parse sequence associated secondary structure
2362 information in Stockholm files</li>
2363 <li>HTML Export database accessions and annotation
2364 information presented in tooltip for sequences</li>
2365 <li>Import secondary structure from LOCARNA clustalw
2366 style RNA alignment files</li>
2367 <li>import and visualise T-COFFEE quality scores for an
2369 <li>'colour by annotation' per sequence option to
2370 shade each sequence according to its associated alignment
2372 <li>New Jalview Logo</li>
2373 </ul> <em>Documentation and Development</em>
2375 <li>documentation for score matrices used in Jalview</li>
2376 <li>New Website!</li>
2378 <td><em>Application</em>
2380 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2381 wsdbfetch REST service</li>
2382 <li>Stop windows being moved outside desktop on OSX</li>
2383 <li>Filetype associations not installed for webstart
2385 <li>Jalview does not always retrieve progress of a JABAWS
2386 job execution in full once it is complete</li>
2387 <li>revise SHMR RSBS definition to ensure alignment is
2388 uploaded via ali_file parameter</li>
2389 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2390 <li>View all structures superposed fails with exception</li>
2391 <li>Jnet job queues forever if a very short sequence is
2392 submitted for prediction</li>
2393 <li>Cut and paste menu not opened when mouse clicked on
2395 <li>Putting fractional value into integer text box in
2396 alignment parameter dialog causes Jalview to hang</li>
2397 <li>Structure view highlighting doesn't work on
2399 <li>View all structures fails with exception shown in
2401 <li>Characters in filename associated with PDBEntry not
2402 escaped in a platform independent way</li>
2403 <li>Jalview desktop fails to launch with exception when
2405 <li>Tree calculation reports 'you must have 2 or more
2406 sequences selected' when selection is empty</li>
2407 <li>Jalview desktop fails to launch with jar signature
2408 failure when java web start temporary file caching is
2410 <li>DAS Sequence retrieval with range qualification
2411 results in sequence xref which includes range qualification</li>
2412 <li>Errors during processing of command line arguments
2413 cause progress bar (JAL-898) to be removed</li>
2414 <li>Replace comma for semi-colon option not disabled for
2415 DAS sources in sequence fetcher</li>
2416 <li>Cannot close news reader when JABAWS server warning
2417 dialog is shown</li>
2418 <li>Option widgets not updated to reflect user settings</li>
2419 <li>Edited sequence not submitted to web service</li>
2420 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2421 <li>InstallAnywhere installer doesn't unpack and run
2422 on OSX Mountain Lion</li>
2423 <li>Annotation panel not given a scroll bar when
2424 sequences with alignment annotation are pasted into the
2426 <li>Sequence associated annotation rows not associated
2427 when loaded from Jalview project</li>
2428 <li>Browser launch fails with NPE on java 1.7</li>
2429 <li>JABAWS alignment marked as finished when job was
2430 cancelled or job failed due to invalid input</li>
2431 <li>NPE with v2.7 example when clicking on Tree
2432 associated with all views</li>
2433 <li>Exceptions when copy/paste sequences with grouped
2434 annotation rows to new window</li>
2435 </ul> <em>Applet</em>
2437 <li>Sequence features are momentarily displayed before
2438 they are hidden using hidefeaturegroups applet parameter</li>
2439 <li>loading features via javascript API automatically
2440 enables feature display</li>
2441 <li>scrollToColumnIn javascript API method doesn't
2443 </ul> <em>General</em>
2445 <li>Redundancy removal fails for rna alignment</li>
2446 <li>PCA calculation fails when sequence has been selected
2447 and then deselected</li>
2448 <li>PCA window shows grey box when first opened on OSX</li>
2449 <li>Letters coloured pink in sequence logo when alignment
2450 coloured with clustalx</li>
2451 <li>Choosing fonts without letter symbols defined causes
2452 exceptions and redraw errors</li>
2453 <li>Initial PCA plot view is not same as manually
2454 reconfigured view</li>
2455 <li>Grouped annotation graph label has incorrect line
2457 <li>Grouped annotation graph label display is corrupted
2458 for lots of labels</li>
2463 <div align="center">
2464 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2467 <td><em>Application</em>
2469 <li>Jalview Desktop News Reader</li>
2470 <li>Tweaked default layout of web services menu</li>
2471 <li>View/alignment association menu to enable user to
2472 easily specify which alignment a multi-structure view takes
2473 its colours/correspondences from</li>
2474 <li>Allow properties file location to be specified as URL</li>
2475 <li>Extend Jalview project to preserve associations
2476 between many alignment views and a single Jmol display</li>
2477 <li>Store annotation row height in Jalview project file</li>
2478 <li>Annotation row column label formatting attributes
2479 stored in project file</li>
2480 <li>Annotation row order for auto-calculated annotation
2481 rows preserved in Jalview project file</li>
2482 <li>Visual progress indication when Jalview state is
2483 saved using Desktop window menu</li>
2484 <li>Visual indication that command line arguments are
2485 still being processed</li>
2486 <li>Groovy script execution from URL</li>
2487 <li>Colour by annotation default min and max colours in
2489 <li>Automatically associate PDB files dragged onto an
2490 alignment with sequences that have high similarity and
2492 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2493 <li>'view structures' option to open many
2494 structures in same window</li>
2495 <li>Sort associated views menu option for tree panel</li>
2496 <li>Group all JABA and non-JABA services for a particular
2497 analysis function in its own submenu</li>
2498 </ul> <em>Applet</em>
2500 <li>Userdefined and autogenerated annotation rows for
2502 <li>Adjustment of alignment annotation pane height</li>
2503 <li>Annotation scrollbar for annotation panel</li>
2504 <li>Drag to reorder annotation rows in annotation panel</li>
2505 <li>'automaticScrolling' parameter</li>
2506 <li>Allow sequences with partial ID string matches to be
2507 annotated from GFF/Jalview features files</li>
2508 <li>Sequence logo annotation row in applet</li>
2509 <li>Absolute paths relative to host server in applet
2510 parameters are treated as such</li>
2511 <li>New in the JalviewLite javascript API:
2513 <li>JalviewLite.js javascript library</li>
2514 <li>Javascript callbacks for
2516 <li>Applet initialisation</li>
2517 <li>Sequence/alignment mouse-overs and selections</li>
2520 <li>scrollTo row and column alignment scrolling
2522 <li>Select sequence/alignment regions from javascript</li>
2523 <li>javascript structure viewer harness to pass
2524 messages between Jmol and Jalview when running as
2525 distinct applets</li>
2526 <li>sortBy method</li>
2527 <li>Set of applet and application examples shipped
2528 with documentation</li>
2529 <li>New example to demonstrate JalviewLite and Jmol
2530 javascript message exchange</li>
2532 </ul> <em>General</em>
2534 <li>Enable Jmol displays to be associated with multiple
2535 multiple alignments</li>
2536 <li>Option to automatically sort alignment with new tree</li>
2537 <li>User configurable link to enable redirects to a
2538 www.Jalview.org mirror</li>
2539 <li>Jmol colours option for Jmol displays</li>
2540 <li>Configurable newline string when writing alignment
2541 and other flat files</li>
2542 <li>Allow alignment annotation description lines to
2543 contain html tags</li>
2544 </ul> <em>Documentation and Development</em>
2546 <li>Add groovy test harness for bulk load testing to
2548 <li>Groovy script to load and align a set of sequences
2549 using a web service before displaying the result in the
2550 Jalview desktop</li>
2551 <li>Restructured javascript and applet api documentation</li>
2552 <li>Ant target to publish example html files with applet
2554 <li>Netbeans project for building Jalview from source</li>
2555 <li>ant task to create online javadoc for Jalview source</li>
2557 <td><em>Application</em>
2559 <li>User defined colourscheme throws exception when
2560 current built in colourscheme is saved as new scheme</li>
2561 <li>AlignFrame->Save in application pops up save
2562 dialog for valid filename/format</li>
2563 <li>Cannot view associated structure for UniProt sequence</li>
2564 <li>PDB file association breaks for UniProt sequence
2566 <li>Associate PDB from file dialog does not tell you
2567 which sequence is to be associated with the file</li>
2568 <li>Find All raises null pointer exception when query
2569 only matches sequence IDs</li>
2570 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2571 <li>Jalview project with Jmol views created with Jalview
2572 2.4 cannot be loaded</li>
2573 <li>Filetype associations not installed for webstart
2575 <li>Two or more chains in a single PDB file associated
2576 with sequences in different alignments do not get coloured
2577 by their associated sequence</li>
2578 <li>Visibility status of autocalculated annotation row
2579 not preserved when project is loaded</li>
2580 <li>Annotation row height and visibility attributes not
2581 stored in Jalview project</li>
2582 <li>Tree bootstraps are not preserved when saved as a
2583 Jalview project</li>
2584 <li>Envision2 workflow tooltips are corrupted</li>
2585 <li>Enabling show group conservation also enables colour
2586 by conservation</li>
2587 <li>Duplicate group associated conservation or consensus
2588 created on new view</li>
2589 <li>Annotation scrollbar not displayed after 'show
2590 all hidden annotation rows' option selected</li>
2591 <li>Alignment quality not updated after alignment
2592 annotation row is hidden then shown</li>
2593 <li>Preserve colouring of structures coloured by
2594 sequences in pre Jalview 2.7 projects</li>
2595 <li>Web service job parameter dialog is not laid out
2597 <li>Web services menu not refreshed after 'reset
2598 services' button is pressed in preferences</li>
2599 <li>Annotation off by one in Jalview v2_3 example project</li>
2600 <li>Structures imported from file and saved in project
2601 get name like jalview_pdb1234.txt when reloaded</li>
2602 <li>Jalview does not always retrieve progress of a JABAWS
2603 job execution in full once it is complete</li>
2604 </ul> <em>Applet</em>
2606 <li>Alignment height set incorrectly when lots of
2607 annotation rows are displayed</li>
2608 <li>Relative URLs in feature HTML text not resolved to
2610 <li>View follows highlighting does not work for positions
2612 <li><= shown as = in tooltip</li>
2613 <li>Export features raises exception when no features
2615 <li>Separator string used for serialising lists of IDs
2616 for javascript api is modified when separator string
2617 provided as parameter</li>
2618 <li>Null pointer exception when selecting tree leaves for
2619 alignment with no existing selection</li>
2620 <li>Relative URLs for datasources assumed to be relative
2621 to applet's codebase</li>
2622 <li>Status bar not updated after finished searching and
2623 search wraps around to first result</li>
2624 <li>StructureSelectionManager instance shared between
2625 several Jalview applets causes race conditions and memory
2627 <li>Hover tooltip and mouseover of position on structure
2628 not sent from Jmol in applet</li>
2629 <li>Certain sequences of javascript method calls to
2630 applet API fatally hang browser</li>
2631 </ul> <em>General</em>
2633 <li>View follows structure mouseover scrolls beyond
2634 position with wrapped view and hidden regions</li>
2635 <li>Find sequence position moves to wrong residue
2636 with/without hidden columns</li>
2637 <li>Sequence length given in alignment properties window
2639 <li>InvalidNumberFormat exceptions thrown when trying to
2640 import PDB like structure files</li>
2641 <li>Positional search results are only highlighted
2642 between user-supplied sequence start/end bounds</li>
2643 <li>End attribute of sequence is not validated</li>
2644 <li>Find dialog only finds first sequence containing a
2645 given sequence position</li>
2646 <li>Sequence numbering not preserved in MSF alignment
2648 <li>Jalview PDB file reader does not extract sequence
2649 from nucleotide chains correctly</li>
2650 <li>Structure colours not updated when tree partition
2651 changed in alignment</li>
2652 <li>Sequence associated secondary structure not correctly
2653 parsed in interleaved stockholm</li>
2654 <li>Colour by annotation dialog does not restore current
2656 <li>Hiding (nearly) all sequences doesn't work
2658 <li>Sequences containing lowercase letters are not
2659 properly associated with their pdb files</li>
2660 </ul> <em>Documentation and Development</em>
2662 <li>schemas/JalviewWsParamSet.xsd corrupted by
2663 ApplyCopyright tool</li>
2668 <div align="center">
2669 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2672 <td><em>Application</em>
2674 <li>New warning dialog when the Jalview Desktop cannot
2675 contact web services</li>
2676 <li>JABA service parameters for a preset are shown in
2677 service job window</li>
2678 <li>JABA Service menu entries reworded</li>
2682 <li>Modeller PIR IO broken - cannot correctly import a
2683 pir file emitted by Jalview</li>
2684 <li>Existing feature settings transferred to new
2685 alignment view created from cut'n'paste</li>
2686 <li>Improved test for mixed amino/nucleotide chains when
2687 parsing PDB files</li>
2688 <li>Consensus and conservation annotation rows
2689 occasionally become blank for all new windows</li>
2690 <li>Exception raised when right clicking above sequences
2691 in wrapped view mode</li>
2692 </ul> <em>Application</em>
2694 <li>multiple multiply aligned structure views cause cpu
2695 usage to hit 100% and computer to hang</li>
2696 <li>Web Service parameter layout breaks for long user
2697 parameter names</li>
2698 <li>Jaba service discovery hangs desktop if Jaba server
2705 <div align="center">
2706 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2709 <td><em>Application</em>
2711 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2712 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2715 <li>Web Services preference tab</li>
2716 <li>Analysis parameters dialog box and user defined
2718 <li>Improved speed and layout of Envision2 service menu</li>
2719 <li>Superpose structures using associated sequence
2721 <li>Export coordinates and projection as CSV from PCA
2723 </ul> <em>Applet</em>
2725 <li>enable javascript: execution by the applet via the
2726 link out mechanism</li>
2727 </ul> <em>Other</em>
2729 <li>Updated the Jmol Jalview interface to work with Jmol
2731 <li>The Jalview Desktop and JalviewLite applet now
2732 require Java 1.5</li>
2733 <li>Allow Jalview feature colour specification for GFF
2734 sequence annotation files</li>
2735 <li>New 'colour by label' keword in Jalview feature file
2736 type colour specification</li>
2737 <li>New Jalview Desktop Groovy API method that allows a
2738 script to check if it being run in an interactive session or
2739 in a batch operation from the Jalview command line</li>
2743 <li>clustalx colourscheme colours Ds preferentially when
2744 both D+E are present in over 50% of the column</li>
2745 </ul> <em>Application</em>
2747 <li>typo in AlignmentFrame->View->Hide->all but
2748 selected Regions menu item</li>
2749 <li>sequence fetcher replaces ',' for ';' when the ',' is
2750 part of a valid accession ID</li>
2751 <li>fatal OOM if object retrieved by sequence fetcher
2752 runs out of memory</li>
2753 <li>unhandled Out of Memory Error when viewing pca
2754 analysis results</li>
2755 <li>InstallAnywhere builds fail to launch on OS X java
2756 10.5 update 4 (due to apple Java 1.6 update)</li>
2757 <li>Installanywhere Jalview silently fails to launch</li>
2758 </ul> <em>Applet</em>
2760 <li>Jalview.getFeatureGroups() raises an
2761 ArrayIndexOutOfBoundsException if no feature groups are
2768 <div align="center">
2769 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2775 <li>Alignment prettyprinter doesn't cope with long
2777 <li>clustalx colourscheme colours Ds preferentially when
2778 both D+E are present in over 50% of the column</li>
2779 <li>nucleic acid structures retrieved from PDB do not
2780 import correctly</li>
2781 <li>More columns get selected than were clicked on when a
2782 number of columns are hidden</li>
2783 <li>annotation label popup menu not providing correct
2784 add/hide/show options when rows are hidden or none are
2786 <li>Stockholm format shown in list of readable formats,
2787 and parser copes better with alignments from RFAM.</li>
2788 <li>CSV output of consensus only includes the percentage
2789 of all symbols if sequence logo display is enabled</li>
2791 </ul> <em>Applet</em>
2793 <li>annotation panel disappears when annotation is
2795 </ul> <em>Application</em>
2797 <li>Alignment view not redrawn properly when new
2798 alignment opened where annotation panel is visible but no
2799 annotations are present on alignment</li>
2800 <li>pasted region containing hidden columns is
2801 incorrectly displayed in new alignment window</li>
2802 <li>Jalview slow to complete operations when stdout is
2803 flooded (fix is to close the Jalview console)</li>
2804 <li>typo in AlignmentFrame->View->Hide->all but
2805 selected Rregions menu item.</li>
2806 <li>inconsistent group submenu and Format submenu entry
2807 'Un' or 'Non'conserved</li>
2808 <li>Sequence feature settings are being shared by
2809 multiple distinct alignments</li>
2810 <li>group annotation not recreated when tree partition is
2812 <li>double click on group annotation to select sequences
2813 does not propagate to associated trees</li>
2814 <li>Mac OSX specific issues:
2816 <li>exception raised when mouse clicked on desktop
2817 window background</li>
2818 <li>Desktop menu placed on menu bar and application
2819 name set correctly</li>
2820 <li>sequence feature settings not wide enough for the
2821 save feature colourscheme button</li>
2830 <div align="center">
2831 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2834 <td><em>New Capabilities</em>
2836 <li>URL links generated from description line for
2837 regular-expression based URL links (applet and application)
2839 <li>Non-positional feature URL links are shown in link
2841 <li>Linked viewing of nucleic acid sequences and
2843 <li>Automatic Scrolling option in View menu to display
2844 the currently highlighted region of an alignment.</li>
2845 <li>Order an alignment by sequence length, or using the
2846 average score or total feature count for each sequence.</li>
2847 <li>Shading features by score or associated description</li>
2848 <li>Subdivide alignment and groups based on identity of
2849 selected subsequence (Make Groups from Selection).</li>
2850 <li>New hide/show options including Shift+Control+H to
2851 hide everything but the currently selected region.</li>
2852 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2853 </ul> <em>Application</em>
2855 <li>Fetch DB References capabilities and UI expanded to
2856 support retrieval from DAS sequence sources</li>
2857 <li>Local DAS Sequence sources can be added via the
2858 command line or via the Add local source dialog box.</li>
2859 <li>DAS Dbref and DbxRef feature types are parsed as
2860 database references and protein_name is parsed as
2861 description line (BioSapiens terms).</li>
2862 <li>Enable or disable non-positional feature and database
2863 references in sequence ID tooltip from View menu in
2865 <!-- <li>New hidden columns and rows and representatives capabilities
2866 in annotations file (in progress - not yet fully implemented)</li> -->
2867 <li>Group-associated consensus, sequence logos and
2868 conservation plots</li>
2869 <li>Symbol distributions for each column can be exported
2870 and visualized as sequence logos</li>
2871 <li>Optionally scale multi-character column labels to fit
2872 within each column of annotation row<!-- todo for applet -->
2874 <li>Optional automatic sort of associated alignment view
2875 when a new tree is opened.</li>
2876 <li>Jalview Java Console</li>
2877 <li>Better placement of desktop window when moving
2878 between different screens.</li>
2879 <li>New preference items for sequence ID tooltip and
2880 consensus annotation</li>
2881 <li>Client to submit sequences and IDs to Envision2
2883 <li><em>Vamsas Capabilities</em>
2885 <li>Improved VAMSAS synchronization (Jalview archive
2886 used to preserve views, structures, and tree display
2888 <li>Import of vamsas documents from disk or URL via
2890 <li>Sharing of selected regions between views and
2891 with other VAMSAS applications (Experimental feature!)</li>
2892 <li>Updated API to VAMSAS version 0.2</li>
2894 </ul> <em>Applet</em>
2896 <li>Middle button resizes annotation row height</li>
2899 <li>sortByTree (true/false) - automatically sort the
2900 associated alignment view by the tree when a new tree is
2902 <li>showTreeBootstraps (true/false) - show or hide
2903 branch bootstraps (default is to show them if available)</li>
2904 <li>showTreeDistances (true/false) - show or hide
2905 branch lengths (default is to show them if available)</li>
2906 <li>showUnlinkedTreeNodes (true/false) - indicate if
2907 unassociated nodes should be highlighted in the tree
2909 <li>heightScale and widthScale (1.0 or more) -
2910 increase the height or width of a cell in the alignment
2911 grid relative to the current font size.</li>
2914 <li>Non-positional features displayed in sequence ID
2916 </ul> <em>Other</em>
2918 <li>Features format: graduated colour definitions and
2919 specification of feature scores</li>
2920 <li>Alignment Annotations format: new keywords for group
2921 associated annotation (GROUP_REF) and annotation row display
2922 properties (ROW_PROPERTIES)</li>
2923 <li>XML formats extended to support graduated feature
2924 colourschemes, group associated annotation, and profile
2925 visualization settings.</li></td>
2928 <li>Source field in GFF files parsed as feature source
2929 rather than description</li>
2930 <li>Non-positional features are now included in sequence
2931 feature and gff files (controlled via non-positional feature
2932 visibility in tooltip).</li>
2933 <li>URL links generated for all feature links (bugfix)</li>
2934 <li>Added URL embedding instructions to features file
2936 <li>Codons containing ambiguous nucleotides translated as
2937 'X' in peptide product</li>
2938 <li>Match case switch in find dialog box works for both
2939 sequence ID and sequence string and query strings do not
2940 have to be in upper case to match case-insensitively.</li>
2941 <li>AMSA files only contain first column of
2942 multi-character column annotation labels</li>
2943 <li>Jalview Annotation File generation/parsing consistent
2944 with documentation (e.g. Stockholm annotation can be
2945 exported and re-imported)</li>
2946 <li>PDB files without embedded PDB IDs given a friendly
2948 <li>Find incrementally searches ID string matches as well
2949 as subsequence matches, and correctly reports total number
2953 <li>Better handling of exceptions during sequence
2955 <li>Dasobert generated non-positional feature URL
2956 link text excludes the start_end suffix</li>
2957 <li>DAS feature and source retrieval buttons disabled
2958 when fetch or registry operations in progress.</li>
2959 <li>PDB files retrieved from URLs are cached properly</li>
2960 <li>Sequence description lines properly shared via
2962 <li>Sequence fetcher fetches multiple records for all
2964 <li>Ensured that command line das feature retrieval
2965 completes before alignment figures are generated.</li>
2966 <li>Reduced time taken when opening file browser for
2968 <li>isAligned check prior to calculating tree, PCA or
2969 submitting an MSA to JNet now excludes hidden sequences.</li>
2970 <li>User defined group colours properly recovered
2971 from Jalview projects.</li>
2980 <div align="center">
2981 <strong>2.4.0.b2</strong><br> 28/10/2009
2986 <li>Experimental support for google analytics usage
2988 <li>Jalview privacy settings (user preferences and docs).</li>
2993 <li>Race condition in applet preventing startup in
2995 <li>Exception when feature created from selection beyond
2996 length of sequence.</li>
2997 <li>Allow synthetic PDB files to be imported gracefully</li>
2998 <li>Sequence associated annotation rows associate with
2999 all sequences with a given id</li>
3000 <li>Find function matches case-insensitively for sequence
3001 ID string searches</li>
3002 <li>Non-standard characters do not cause pairwise
3003 alignment to fail with exception</li>
3004 </ul> <em>Application Issues</em>
3006 <li>Sequences are now validated against EMBL database</li>
3007 <li>Sequence fetcher fetches multiple records for all
3009 </ul> <em>InstallAnywhere Issues</em>
3011 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3012 issue with installAnywhere mechanism)</li>
3013 <li>Command line launching of JARs from InstallAnywhere
3014 version (java class versioning error fixed)</li>
3021 <div align="center">
3022 <strong>2.4</strong><br> 27/8/2008
3025 <td><em>User Interface</em>
3027 <li>Linked highlighting of codon and amino acid from
3028 translation and protein products</li>
3029 <li>Linked highlighting of structure associated with
3030 residue mapping to codon position</li>
3031 <li>Sequence Fetcher provides example accession numbers
3032 and 'clear' button</li>
3033 <li>MemoryMonitor added as an option under Desktop's
3035 <li>Extract score function to parse whitespace separated
3036 numeric data in description line</li>
3037 <li>Column labels in alignment annotation can be centred.</li>
3038 <li>Tooltip for sequence associated annotation give name
3040 </ul> <em>Web Services and URL fetching</em>
3042 <li>JPred3 web service</li>
3043 <li>Prototype sequence search client (no public services
3045 <li>Fetch either seed alignment or full alignment from
3047 <li>URL Links created for matching database cross
3048 references as well as sequence ID</li>
3049 <li>URL Links can be created using regular-expressions</li>
3050 </ul> <em>Sequence Database Connectivity</em>
3052 <li>Retrieval of cross-referenced sequences from other
3054 <li>Generalised database reference retrieval and
3055 validation to all fetchable databases</li>
3056 <li>Fetch sequences from DAS sources supporting the
3057 sequence command</li>
3058 </ul> <em>Import and Export</em>
3059 <li>export annotation rows as CSV for spreadsheet import</li>
3060 <li>Jalview projects record alignment dataset associations,
3061 EMBL products, and cDNA sequence mappings</li>
3062 <li>Sequence Group colour can be specified in Annotation
3064 <li>Ad-hoc colouring of group in Annotation File using RGB
3065 triplet as name of colourscheme</li>
3066 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3068 <li>treenode binding for VAMSAS tree exchange</li>
3069 <li>local editing and update of sequences in VAMSAS
3070 alignments (experimental)</li>
3071 <li>Create new or select existing session to join</li>
3072 <li>load and save of vamsas documents</li>
3073 </ul> <em>Application command line</em>
3075 <li>-tree parameter to open trees (introduced for passing
3077 <li>-fetchfrom command line argument to specify nicknames
3078 of DAS servers to query for alignment features</li>
3079 <li>-dasserver command line argument to add new servers
3080 that are also automatically queried for features</li>
3081 <li>-groovy command line argument executes a given groovy
3082 script after all input data has been loaded and parsed</li>
3083 </ul> <em>Applet-Application data exchange</em>
3085 <li>Trees passed as applet parameters can be passed to
3086 application (when using "View in full
3087 application")</li>
3088 </ul> <em>Applet Parameters</em>
3090 <li>feature group display control parameter</li>
3091 <li>debug parameter</li>
3092 <li>showbutton parameter</li>
3093 </ul> <em>Applet API methods</em>
3095 <li>newView public method</li>
3096 <li>Window (current view) specific get/set public methods</li>
3097 <li>Feature display control methods</li>
3098 <li>get list of currently selected sequences</li>
3099 </ul> <em>New Jalview distribution features</em>
3101 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3102 <li>RELEASE file gives build properties for the latest
3103 Jalview release.</li>
3104 <li>Java 1.1 Applet build made easier and donotobfuscate
3105 property controls execution of obfuscator</li>
3106 <li>Build target for generating source distribution</li>
3107 <li>Debug flag for javacc</li>
3108 <li>.jalview_properties file is documented (slightly) in
3109 jalview.bin.Cache</li>
3110 <li>Continuous Build Integration for stable and
3111 development version of Application, Applet and source
3116 <li>selected region output includes visible annotations
3117 (for certain formats)</li>
3118 <li>edit label/displaychar contains existing label/char
3120 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3121 <li>shorter peptide product names from EMBL records</li>
3122 <li>Newick string generator makes compact representations</li>
3123 <li>bootstrap values parsed correctly for tree files with
3125 <li>pathological filechooser bug avoided by not allowing
3126 filenames containing a ':'</li>
3127 <li>Fixed exception when parsing GFF files containing
3128 global sequence features</li>
3129 <li>Alignment datasets are finalized only when number of
3130 references from alignment sequences goes to zero</li>
3131 <li>Close of tree branch colour box without colour
3132 selection causes cascading exceptions</li>
3133 <li>occasional negative imgwidth exceptions</li>
3134 <li>better reporting of non-fatal warnings to user when
3135 file parsing fails.</li>
3136 <li>Save works when Jalview project is default format</li>
3137 <li>Save as dialog opened if current alignment format is
3138 not a valid output format</li>
3139 <li>UniProt canonical names introduced for both das and
3141 <li>Histidine should be midblue (not pink!) in Zappo</li>
3142 <li>error messages passed up and output when data read
3144 <li>edit undo recovers previous dataset sequence when
3145 sequence is edited</li>
3146 <li>allow PDB files without pdb ID HEADER lines (like
3147 those generated by MODELLER) to be read in properly</li>
3148 <li>allow reading of JPred concise files as a normal
3150 <li>Stockholm annotation parsing and alignment properties
3151 import fixed for PFAM records</li>
3152 <li>Structure view windows have correct name in Desktop
3154 <li>annotation consisting of sequence associated scores
3155 can be read and written correctly to annotation file</li>
3156 <li>Aligned cDNA translation to aligned peptide works
3158 <li>Fixed display of hidden sequence markers and
3159 non-italic font for representatives in Applet</li>
3160 <li>Applet Menus are always embedded in applet window on
3162 <li>Newly shown features appear at top of stack (in
3164 <li>Annotations added via parameter not drawn properly
3165 due to null pointer exceptions</li>
3166 <li>Secondary structure lines are drawn starting from
3167 first column of alignment</li>
3168 <li>UniProt XML import updated for new schema release in
3170 <li>Sequence feature to sequence ID match for Features
3171 file is case-insensitive</li>
3172 <li>Sequence features read from Features file appended to
3173 all sequences with matching IDs</li>
3174 <li>PDB structure coloured correctly for associated views
3175 containing a sub-sequence</li>
3176 <li>PDB files can be retrieved by applet from Jar files</li>
3177 <li>feature and annotation file applet parameters
3178 referring to different directories are retrieved correctly</li>
3179 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3180 <li>Fixed application hang whilst waiting for
3181 splash-screen version check to complete</li>
3182 <li>Applet properly URLencodes input parameter values
3183 when passing them to the launchApp service</li>
3184 <li>display name and local features preserved in results
3185 retrieved from web service</li>
3186 <li>Visual delay indication for sequence retrieval and
3187 sequence fetcher initialisation</li>
3188 <li>updated Application to use DAS 1.53e version of
3189 dasobert DAS client</li>
3190 <li>Re-instated Full AMSA support and .amsa file
3192 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3200 <div align="center">
3201 <strong>2.3</strong><br> 9/5/07
3206 <li>Jmol 11.0.2 integration</li>
3207 <li>PDB views stored in Jalview XML files</li>
3208 <li>Slide sequences</li>
3209 <li>Edit sequence in place</li>
3210 <li>EMBL CDS features</li>
3211 <li>DAS Feature mapping</li>
3212 <li>Feature ordering</li>
3213 <li>Alignment Properties</li>
3214 <li>Annotation Scores</li>
3215 <li>Sort by scores</li>
3216 <li>Feature/annotation editing in applet</li>
3221 <li>Headless state operation in 2.2.1</li>
3222 <li>Incorrect and unstable DNA pairwise alignment</li>
3223 <li>Cut and paste of sequences with annotation</li>
3224 <li>Feature group display state in XML</li>
3225 <li>Feature ordering in XML</li>
3226 <li>blc file iteration selection using filename # suffix</li>
3227 <li>Stockholm alignment properties</li>
3228 <li>Stockhom alignment secondary structure annotation</li>
3229 <li>2.2.1 applet had no feature transparency</li>
3230 <li>Number pad keys can be used in cursor mode</li>
3231 <li>Structure Viewer mirror image resolved</li>
3238 <div align="center">
3239 <strong>2.2.1</strong><br> 12/2/07
3244 <li>Non standard characters can be read and displayed
3245 <li>Annotations/Features can be imported/exported to the
3247 <li>Applet allows editing of sequence/annotation/group
3248 name & description
3249 <li>Preference setting to display sequence name in
3251 <li>Annotation file format extended to allow
3252 Sequence_groups to be defined
3253 <li>Default opening of alignment overview panel can be
3254 specified in preferences
3255 <li>PDB residue numbering annotation added to associated
3261 <li>Applet crash under certain Linux OS with Java 1.6
3263 <li>Annotation file export / import bugs fixed
3264 <li>PNG / EPS image output bugs fixed
3270 <div align="center">
3271 <strong>2.2</strong><br> 27/11/06
3276 <li>Multiple views on alignment
3277 <li>Sequence feature editing
3278 <li>"Reload" alignment
3279 <li>"Save" to current filename
3280 <li>Background dependent text colour
3281 <li>Right align sequence ids
3282 <li>User-defined lower case residue colours
3285 <li>Menu item accelerator keys
3286 <li>Control-V pastes to current alignment
3287 <li>Cancel button for DAS Feature Fetching
3288 <li>PCA and PDB Viewers zoom via mouse roller
3289 <li>User-defined sub-tree colours and sub-tree selection
3291 <li>'New Window' button on the 'Output to Text box'
3296 <li>New memory efficient Undo/Redo System
3297 <li>Optimised symbol lookups and conservation/consensus
3299 <li>Region Conservation/Consensus recalculated after
3301 <li>Fixed Remove Empty Columns Bug (empty columns at end
3303 <li>Slowed DAS Feature Fetching for increased robustness.
3305 <li>Made angle brackets in ASCII feature descriptions
3307 <li>Re-instated Zoom function for PCA
3308 <li>Sequence descriptions conserved in web service
3310 <li>UniProt ID discoverer uses any word separated by
3312 <li>WsDbFetch query/result association resolved
3313 <li>Tree leaf to sequence mapping improved
3314 <li>Smooth fonts switch moved to FontChooser dialog box.
3321 <div align="center">
3322 <strong>2.1.1</strong><br> 12/9/06
3327 <li>Copy consensus sequence to clipboard</li>
3332 <li>Image output - rightmost residues are rendered if
3333 sequence id panel has been resized</li>
3334 <li>Image output - all offscreen group boundaries are
3336 <li>Annotation files with sequence references - all
3337 elements in file are relative to sequence position</li>
3338 <li>Mac Applet users can use Alt key for group editing</li>
3344 <div align="center">
3345 <strong>2.1</strong><br> 22/8/06
3350 <li>MAFFT Multiple Alignment in default Web Service list</li>
3351 <li>DAS Feature fetching</li>
3352 <li>Hide sequences and columns</li>
3353 <li>Export Annotations and Features</li>
3354 <li>GFF file reading / writing</li>
3355 <li>Associate structures with sequences from local PDB
3357 <li>Add sequences to exisiting alignment</li>
3358 <li>Recently opened files / URL lists</li>
3359 <li>Applet can launch the full application</li>
3360 <li>Applet has transparency for features (Java 1.2
3362 <li>Applet has user defined colours parameter</li>
3363 <li>Applet can load sequences from parameter
3364 "sequence<em>x</em>"
3370 <li>Redundancy Panel reinstalled in the Applet</li>
3371 <li>Monospaced font - EPS / rescaling bug fixed</li>
3372 <li>Annotation files with sequence references bug fixed</li>
3378 <div align="center">
3379 <strong>2.08.1</strong><br> 2/5/06
3384 <li>Change case of selected region from Popup menu</li>
3385 <li>Choose to match case when searching</li>
3386 <li>Middle mouse button and mouse movement can compress /
3387 expand the visible width and height of the alignment</li>
3392 <li>Annotation Panel displays complete JNet results</li>
3398 <div align="center">
3399 <strong>2.08b</strong><br> 18/4/06
3405 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3406 <li>Righthand label on wrapped alignments shows correct
3413 <div align="center">
3414 <strong>2.08</strong><br> 10/4/06
3419 <li>Editing can be locked to the selection area</li>
3420 <li>Keyboard editing</li>
3421 <li>Create sequence features from searches</li>
3422 <li>Precalculated annotations can be loaded onto
3424 <li>Features file allows grouping of features</li>
3425 <li>Annotation Colouring scheme added</li>
3426 <li>Smooth fonts off by default - Faster rendering</li>
3427 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3432 <li>Drag & Drop fixed on Linux</li>
3433 <li>Jalview Archive file faster to load/save, sequence
3434 descriptions saved.</li>
3440 <div align="center">
3441 <strong>2.07</strong><br> 12/12/05
3446 <li>PDB Structure Viewer enhanced</li>
3447 <li>Sequence Feature retrieval and display enhanced</li>
3448 <li>Choose to output sequence start-end after sequence
3449 name for file output</li>
3450 <li>Sequence Fetcher WSDBFetch@EBI</li>
3451 <li>Applet can read feature files, PDB files and can be
3452 used for HTML form input</li>
3457 <li>HTML output writes groups and features</li>
3458 <li>Group editing is Control and mouse click</li>
3459 <li>File IO bugs</li>
3465 <div align="center">
3466 <strong>2.06</strong><br> 28/9/05
3471 <li>View annotations in wrapped mode</li>
3472 <li>More options for PCA viewer</li>
3477 <li>GUI bugs resolved</li>
3478 <li>Runs with -nodisplay from command line</li>
3484 <div align="center">
3485 <strong>2.05b</strong><br> 15/9/05
3490 <li>Choose EPS export as lineart or text</li>
3491 <li>Jar files are executable</li>
3492 <li>Can read in Uracil - maps to unknown residue</li>
3497 <li>Known OutOfMemory errors give warning message</li>
3498 <li>Overview window calculated more efficiently</li>
3499 <li>Several GUI bugs resolved</li>
3505 <div align="center">
3506 <strong>2.05</strong><br> 30/8/05
3511 <li>Edit and annotate in "Wrapped" view</li>
3516 <li>Several GUI bugs resolved</li>
3522 <div align="center">
3523 <strong>2.04</strong><br> 24/8/05
3528 <li>Hold down mouse wheel & scroll to change font
3534 <li>Improved JPred client reliability</li>
3535 <li>Improved loading of Jalview files</li>
3541 <div align="center">
3542 <strong>2.03</strong><br> 18/8/05
3547 <li>Set Proxy server name and port in preferences</li>
3548 <li>Multiple URL links from sequence ids</li>
3549 <li>User Defined Colours can have a scheme name and added
3551 <li>Choose to ignore gaps in consensus calculation</li>
3552 <li>Unix users can set default web browser</li>
3553 <li>Runs without GUI for batch processing</li>
3554 <li>Dynamically generated Web Service Menus</li>
3559 <li>InstallAnywhere download for Sparc Solaris</li>
3565 <div align="center">
3566 <strong>2.02</strong><br> 18/7/05
3572 <li>Copy & Paste order of sequences maintains
3573 alignment order.</li>
3579 <div align="center">
3580 <strong>2.01</strong><br> 12/7/05
3585 <li>Use delete key for deleting selection.</li>
3586 <li>Use Mouse wheel to scroll sequences.</li>
3587 <li>Help file updated to describe how to add alignment
3589 <li>Version and build date written to build properties
3591 <li>InstallAnywhere installation will check for updates
3592 at launch of Jalview.</li>
3597 <li>Delete gaps bug fixed.</li>
3598 <li>FileChooser sorts columns.</li>
3599 <li>Can remove groups one by one.</li>
3600 <li>Filechooser icons installed.</li>
3601 <li>Finder ignores return character when searching.
3602 Return key will initiate a search.<br>
3609 <div align="center">
3610 <strong>2.0</strong><br> 20/6/05
3615 <li>New codebase</li>