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>10/10/2017</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
93 <ul><li>Example groovy script for generating a matrix of percent identity scores for current alignment.</li></ul>
95 <td><div align="left">
98 <li><!-- JAL-2777 -->Structures with whitespace chainCode cannot be viewed in Chimera</li>
99 <li><!-- JAL-2728 -->Protein annotation panel too high in CDS/Protein view
101 <li><!-- JAL-2757 -->Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs
103 <li><!-- JAL-2253 -->Slow EnsemblGenome ID lookup</li>
108 <td width="60" nowrap>
110 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
111 <em>2/10/2017</em></strong>
114 <td><div align="left">
115 <em>New features in Jalview Desktop</em>
118 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
120 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
124 <td><div align="left">
128 <td width="60" nowrap>
130 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
131 <em>7/9/2017</em></strong>
134 <td><div align="left">
138 <!-- JAL-2588 -->Show gaps in overview window by colouring
139 in grey (sequences used to be coloured grey, and gaps were
143 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
147 <!-- JAL-2587 -->Overview updates immediately on increase
148 in size and progress bar shown as higher resolution
149 overview is recalculated
154 <td><div align="left">
158 <!-- JAL-2664 -->Overview window redraws every hidden
159 column region row by row
162 <!-- JAL-2681 -->duplicate protein sequences shown after
163 retrieving Ensembl crossrefs for sequences from Uniprot
166 <!-- JAL-2603 -->Overview window throws NPE if show boxes
167 format setting is unticked
170 <!-- JAL-2610 -->Groups are coloured wrongly in overview
171 if group has show boxes format setting unticked
174 <!-- JAL-2672,JAL-2665 -->Redraw problems when
175 autoscrolling whilst dragging current selection group to
176 include sequences and columns not currently displayed
179 <!-- JAL-2691 -->Not all chains are mapped when multimeric
180 assemblies are imported via CIF file
183 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
184 displayed when threshold or conservation colouring is also
188 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
192 <!-- JAL-2673 -->Jalview continues to scroll after
193 dragging a selected region off the visible region of the
197 <!-- JAL-2724 -->Cannot apply annotation based
198 colourscheme to all groups in a view
201 <!-- JAL-2511 -->IDs don't line up with sequences
202 initially after font size change using the Font chooser or
209 <td width="60" nowrap>
211 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
214 <td><div align="left">
215 <em>Calculations</em>
219 <!-- JAL-1933 -->Occupancy annotation row shows number of
220 ungapped positions in each column of the alignment.
223 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
224 a calculation dialog box
227 <!-- JAL-2379 -->Revised implementation of PCA for speed
228 and memory efficiency (~30x faster)
231 <!-- JAL-2403 -->Revised implementation of sequence
232 similarity scores as used by Tree, PCA, Shading Consensus
233 and other calculations
236 <!-- JAL-2416 -->Score matrices are stored as resource
237 files within the Jalview codebase
240 <!-- JAL-2500 -->Trees computed on Sequence Feature
241 Similarity may have different topology due to increased
248 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
249 model for alignments and groups
252 <!-- JAL-384 -->Custom shading schemes created via groovy
259 <!-- JAL-2526 -->Efficiency improvements for interacting
260 with alignment and overview windows
263 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
267 <!-- JAL-2388 -->Hidden columns and sequences can be
271 <!-- JAL-2611 -->Click-drag in visible area allows fine
272 adjustment of visible position
276 <em>Data import/export</em>
279 <!-- JAL-2535 -->Posterior probability annotation from
280 Stockholm files imported as sequence associated annotation
283 <!-- JAL-2507 -->More robust per-sequence positional
284 annotation input/output via stockholm flatfile
287 <!-- JAL-2533 -->Sequence names don't include file
288 extension when importing structure files without embedded
289 names or PDB accessions
292 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
293 format sequence substitution matrices
296 <em>User Interface</em>
299 <!-- JAL-2447 --> Experimental Features Checkbox in
300 Desktop's Tools menu to hide or show untested features in
304 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
305 via Overview or sequence motif search operations
308 <!-- JAL-2547 -->Amend sequence features dialog box can be
309 opened by double clicking gaps within sequence feature
313 <!-- JAL-1476 -->Status bar message shown when not enough
314 aligned positions were available to create a 3D structure
318 <em>3D Structure</em>
321 <!-- JAL-2430 -->Hidden regions in alignment views are not
322 coloured in linked structure views
325 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
326 file-based command exchange
329 <!-- JAL-2375 -->Structure chooser automatically shows
330 Cached Structures rather than querying the PDBe if
331 structures are already available for sequences
334 <!-- JAL-2520 -->Structures imported via URL are cached in
335 the Jalview project rather than downloaded again when the
339 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
340 to transfer Chimera's structure attributes as Jalview
341 features, and vice-versa (<strong>Experimental
345 <em>Web Services</em>
348 <!-- JAL-2549 -->Updated JABAWS client to v2.2
351 <!-- JAL-2335 -->Filter non-standard amino acids and
352 nucleotides when submitting to AACon and other MSA
356 <!-- JAL-2316, -->URLs for viewing database
357 cross-references provided by identifiers.org and the
365 <!-- JAL-2344 -->FileFormatI interface for describing and
366 identifying file formats (instead of String constants)
369 <!-- JAL-2228 -->FeatureCounter script refactored for
370 efficiency when counting all displayed features (not
371 backwards compatible with 2.10.1)
374 <em>Example files</em>
377 <!-- JAL-2631 -->Graduated feature colour style example
378 included in the example feature file
381 <em>Documentation</em>
384 <!-- JAL-2339 -->Release notes reformatted for readability
385 with the built-in Java help viewer
388 <!-- JAL-1644 -->Find documentation updated with 'search
389 sequence description' option
395 <!-- JAL-2485, -->External service integration tests for
396 Uniprot REST Free Text Search Client
399 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
402 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
407 <td><div align="left">
408 <em>Calculations</em>
411 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
412 matrix - C->R should be '-3'<br />Old matrix restored
413 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
415 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
416 Jalview's treatment of gaps in PCA and substitution matrix
417 based Tree calculations.<br /> <br />In earlier versions
418 of Jalview, gaps matching gaps were penalised, and gaps
419 matching non-gaps penalised even more. In the PCA
420 calculation, gaps were actually treated as non-gaps - so
421 different costs were applied, which meant Jalview's PCAs
422 were different to those produced by SeqSpace.<br />Jalview
423 now treats gaps in the same way as SeqSpace (ie it scores
424 them as 0). <br /> <br />Enter the following in the
425 Groovy console to restore pre-2.10.2 behaviour:<br />
426 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
427 // for 2.10.1 mode <br />
428 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
429 // to restore 2.10.2 mode <br /> <br /> <em>Note:
430 these settings will affect all subsequent tree and PCA
431 calculations (not recommended)</em></li>
433 <!-- JAL-2424 -->Fixed off-by-one bug that affected
434 scaling of branch lengths for trees computed using
435 Sequence Feature Similarity.
438 <!-- JAL-2377 -->PCA calculation could hang when
439 generating output report when working with highly
443 <!-- JAL-2544 --> Sort by features includes features to
444 right of selected region when gaps present on right-hand
448 <em>User Interface</em>
451 <!-- JAL-2346 -->Reopening Colour by annotation dialog
452 doesn't reselect a specific sequence's associated
453 annotation after it was used for colouring a view
456 <!-- JAL-2419 -->Current selection lost if popup menu
457 opened on a region of alignment without groups
460 <!-- JAL-2374 -->Popup menu not always shown for regions
461 of an alignment with overlapping groups
464 <!-- JAL-2310 -->Finder double counts if both a sequence's
465 name and description match
468 <!-- JAL-2370 -->Hiding column selection containing two
469 hidden regions results in incorrect hidden regions
472 <!-- JAL-2386 -->'Apply to all groups' setting when
473 changing colour does not apply Conservation slider value
477 <!-- JAL-2373 -->Percentage identity and conservation menu
478 items do not show a tick or allow shading to be disabled
481 <!-- JAL-2385 -->Conservation shading or PID threshold
482 lost when base colourscheme changed if slider not visible
485 <!-- JAL-2547 -->Sequence features shown in tooltip for
486 gaps before start of features
489 <!-- JAL-2623 -->Graduated feature colour threshold not
490 restored to UI when feature colour is edited
493 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
494 a time when scrolling vertically in wrapped mode.
497 <!-- JAL-2630 -->Structure and alignment overview update
498 as graduate feature colour settings are modified via the
502 <!-- JAL-2034 -->Overview window doesn't always update
503 when a group defined on the alignment is resized
506 <!-- JAL-2605 -->Mouseovers on left/right scale region in
507 wrapped view result in positional status updates
511 <!-- JAL-2563 -->Status bar doesn't show position for
512 ambiguous amino acid and nucleotide symbols
515 <!-- JAL-2602 -->Copy consensus sequence failed if
516 alignment included gapped columns
519 <!-- JAL-2473 -->Minimum size set for Jalview windows so
520 widgets don't permanently disappear
523 <!-- JAL-2503 -->Cannot select or filter quantitative
524 annotation that are shown only as column labels (e.g.
525 T-Coffee column reliability scores)
528 <!-- JAL-2594 -->Exception thrown if trying to create a
529 sequence feature on gaps only
532 <!-- JAL-2504 -->Features created with 'New feature'
533 button from a Find inherit previously defined feature type
534 rather than the Find query string
537 <!-- JAL-2423 -->incorrect title in output window when
538 exporting tree calculated in Jalview
541 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
542 and then revealing them reorders sequences on the
546 <!-- JAL-964 -->Group panel in sequence feature settings
547 doesn't update to reflect available set of groups after
548 interactively adding or modifying features
551 <!-- JAL-2225 -->Sequence Database chooser unusable on
555 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
556 only excluded gaps in current sequence and ignored
563 <!-- JAL-2421 -->Overview window visible region moves
564 erratically when hidden rows or columns are present
567 <!-- JAL-2362 -->Per-residue colourschemes applied via the
568 Structure Viewer's colour menu don't correspond to
572 <!-- JAL-2405 -->Protein specific colours only offered in
573 colour and group colour menu for protein alignments
576 <!-- JAL-2385 -->Colour threshold slider doesn't update to
577 reflect currently selected view or group's shading
581 <!-- JAL-2624 -->Feature colour thresholds not respected
582 when rendered on overview and structures when opacity at
586 <!-- JAL-2589 -->User defined gap colour not shown in
587 overview when features overlaid on alignment
590 <em>Data import/export</em>
593 <!-- JAL-2576 -->Very large alignments take a long time to
597 <!-- JAL-2507 -->Per-sequence RNA secondary structures
598 added after a sequence was imported are not written to
602 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
603 when importing RNA secondary structure via Stockholm
606 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
607 not shown in correct direction for simple pseudoknots
610 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
611 with lightGray or darkGray via features file (but can
615 <!-- JAL-2383 -->Above PID colour threshold not recovered
616 when alignment view imported from project
619 <!-- JAL-2520,JAL-2465 -->No mappings generated between
620 structure and sequences extracted from structure files
621 imported via URL and viewed in Jmol
624 <!-- JAL-2520 -->Structures loaded via URL are saved in
625 Jalview Projects rather than fetched via URL again when
626 the project is loaded and the structure viewed
629 <em>Web Services</em>
632 <!-- JAL-2519 -->EnsemblGenomes example failing after
633 release of Ensembl v.88
636 <!-- JAL-2366 -->Proxy server address and port always
637 appear enabled in Preferences->Connections
640 <!-- JAL-2461 -->DAS registry not found exceptions
641 removed from console output
644 <!-- JAL-2582 -->Cannot retrieve protein products from
645 Ensembl by Peptide ID
648 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
649 created from SIFTs, and spurious 'Couldn't open structure
650 in Chimera' errors raised after April 2017 update (problem
651 due to 'null' string rather than empty string used for
652 residues with no corresponding PDB mapping).
655 <em>Application UI</em>
658 <!-- JAL-2361 -->User Defined Colours not added to Colour
662 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
663 case' residues (button in colourscheme editor debugged and
664 new documentation and tooltips added)
667 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
668 doesn't restore group-specific text colour thresholds
671 <!-- JAL-2243 -->Feature settings panel does not update as
672 new features are added to alignment
675 <!-- JAL-2532 -->Cancel in feature settings reverts
676 changes to feature colours via the Amend features dialog
679 <!-- JAL-2506 -->Null pointer exception when attempting to
680 edit graduated feature colour via amend features dialog
684 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
685 selection menu changes colours of alignment views
688 <!-- JAL-2426 -->Spurious exceptions in console raised
689 from alignment calculation workers after alignment has
693 <!-- JAL-1608 -->Typo in selection popup menu - Create
694 groups now 'Create Group'
697 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
698 Create/Undefine group doesn't always work
701 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
702 shown again after pressing 'Cancel'
705 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
706 adjusts start position in wrap mode
709 <!-- JAL-2563 -->Status bar doesn't show positions for
710 ambiguous amino acids
713 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
714 CDS/Protein view after CDS sequences added for aligned
718 <!-- JAL-2592 -->User defined colourschemes called 'User
719 Defined' don't appear in Colours menu
725 <!-- JAL-2468 -->Switching between Nucleotide and Protein
726 score models doesn't always result in an updated PCA plot
729 <!-- JAL-2442 -->Features not rendered as transparent on
730 overview or linked structure view
733 <!-- JAL-2372 -->Colour group by conservation doesn't
737 <!-- JAL-2517 -->Hitting Cancel after applying
738 user-defined colourscheme doesn't restore original
745 <!-- JAL-2314 -->Unit test failure:
746 jalview.ws.jabaws.RNAStructExportImport setup fails
749 <!-- JAL-2307 -->Unit test failure:
750 jalview.ws.sifts.SiftsClientTest due to compatibility
751 problems with deep array comparison equality asserts in
752 successive versions of TestNG
755 <!-- JAL-2479 -->Relocated StructureChooserTest and
756 ParameterUtilsTest Unit tests to Network suite
759 <em>New Known Issues</em>
762 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
763 phase after a sequence motif find operation
766 <!-- JAL-2550 -->Importing annotation file with rows
767 containing just upper and lower case letters are
768 interpreted as WUSS RNA secondary structure symbols
771 <!-- JAL-2590 -->Cannot load and display Newick trees
772 reliably from eggnog Ortholog database
775 <!-- JAL-2468 -->Status bar shows 'Marked x columns
776 containing features of type Highlight' when 'B' is pressed
777 to mark columns containing highlighted regions.
780 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
781 doesn't always add secondary structure annotation.
786 <td width="60" nowrap>
788 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
791 <td><div align="left">
795 <!-- JAL-98 -->Improved memory usage: sparse arrays used
796 for all consensus calculations
799 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
802 <li>Updated Jalview's Certum code signing certificate
808 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
809 set of database cross-references, sorted alphabetically
812 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
813 from database cross references. Users with custom links
814 will receive a <a href="webServices/urllinks.html#warning">warning
815 dialog</a> asking them to update their preferences.
818 <!-- JAL-2287-->Cancel button and escape listener on
819 dialog warning user about disconnecting Jalview from a
823 <!-- JAL-2320-->Jalview's Chimera control window closes if
824 the Chimera it is connected to is shut down
827 <!-- JAL-1738-->New keystroke (B) and Select highlighted
828 columns menu item to mark columns containing highlighted
829 regions (e.g. from structure selections or results of a
833 <!-- JAL-2284-->Command line option for batch-generation
834 of HTML pages rendering alignment data with the BioJS
844 <!-- JAL-2286 -->Columns with more than one modal residue
845 are not coloured or thresholded according to percent
846 identity (first observed in Jalview 2.8.2)
849 <!-- JAL-2301 -->Threonine incorrectly reported as not
853 <!-- JAL-2318 -->Updates to documentation pages (above PID
854 threshold, amino acid properties)
857 <!-- JAL-2292 -->Lower case residues in sequences are not
858 reported as mapped to residues in a structure file in the
862 <!--JAL-2324 -->Identical features with non-numeric scores
863 could be added multiple times to a sequence
866 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
867 bond features shown as two highlighted residues rather
868 than a range in linked structure views, and treated
869 correctly when selecting and computing trees from features
872 <!-- JAL-2281-->Custom URL links for database
873 cross-references are matched to database name regardless
881 <!-- JAL-2282-->Custom URL links for specific database
882 names without regular expressions also offer links from
886 <!-- JAL-2315-->Removing a single configured link in the
887 URL links pane in Connections preferences doesn't actually
888 update Jalview configuration
891 <!-- JAL-2272-->CTRL-Click on a selected region to open
892 the alignment area popup menu doesn't work on El-Capitan
895 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
896 files with similarly named sequences if dropped onto the
900 <!-- JAL-2312 -->Additional mappings are shown for PDB
901 entries where more chains exist in the PDB accession than
902 are reported in the SIFTS file
905 <!-- JAL-2317-->Certain structures do not get mapped to
906 the structure view when displayed with Chimera
909 <!-- JAL-2317-->No chains shown in the Chimera view
910 panel's View->Show Chains submenu
913 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
914 work for wrapped alignment views
917 <!--JAL-2197 -->Rename UI components for running JPred
918 predictions from 'JNet' to 'JPred'
921 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
922 corrupted when annotation panel vertical scroll is not at
926 <!--JAL-2332 -->Attempting to view structure for Hen
927 lysozyme results in a PDB Client error dialog box
930 <!-- JAL-2319 -->Structure View's mapping report switched
931 ranges for PDB and sequence for SIFTS
934 SIFTS 'Not_Observed' residues mapped to non-existant
938 <!-- <em>New Known Issues</em>
945 <td width="60" nowrap>
947 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
948 <em>25/10/2016</em></strong>
951 <td><em>Application</em>
953 <li>3D Structure chooser opens with 'Cached structures'
954 view if structures already loaded</li>
955 <li>Progress bar reports models as they are loaded to
962 <li>Colour by conservation always enabled and no tick
963 shown in menu when BLOSUM or PID shading applied</li>
964 <li>FER1_ARATH and FER2_ARATH labels were switched in
965 example sequences/projects/trees</li>
969 <li>Jalview projects with views of local PDB structure
970 files saved on Windows cannot be opened on OSX</li>
971 <li>Multiple structure views can be opened and superposed
972 without timeout for structures with multiple models or
973 multiple sequences in alignment</li>
974 <li>Cannot import or associated local PDB files without a
975 PDB ID HEADER line</li>
976 <li>RMSD is not output in Jmol console when superposition
978 <li>Drag and drop of URL from Browser fails for Linux and
979 OSX versions earlier than El Capitan</li>
980 <li>ENA client ignores invalid content from ENA server</li>
981 <li>Exceptions are not raised in console when ENA client
982 attempts to fetch non-existent IDs via Fetch DB Refs UI
984 <li>Exceptions are not raised in console when a new view
985 is created on the alignment</li>
986 <li>OSX right-click fixed for group selections: CMD-click
987 to insert/remove gaps in groups and CTRL-click to open group
990 <em>Build and deployment</em>
992 <li>URL link checker now copes with multi-line anchor
995 <em>New Known Issues</em>
997 <li>Drag and drop from URL links in browsers do not work
1004 <td width="60" nowrap>
1005 <div align="center">
1006 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1009 <td><em>General</em>
1012 <!-- JAL-2124 -->Updated Spanish translations.
1015 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1016 for importing structure data to Jalview. Enables mmCIF and
1020 <!-- JAL-192 --->Alignment ruler shows positions relative to
1024 <!-- JAL-2202 -->Position/residue shown in status bar when
1025 mousing over sequence associated annotation
1028 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1032 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1033 '()', canonical '[]' and invalid '{}' base pair populations
1037 <!-- JAL-2092 -->Feature settings popup menu options for
1038 showing or hiding columns containing a feature
1041 <!-- JAL-1557 -->Edit selected group by double clicking on
1042 group and sequence associated annotation labels
1045 <!-- JAL-2236 -->Sequence name added to annotation label in
1046 select/hide columns by annotation and colour by annotation
1050 </ul> <em>Application</em>
1053 <!-- JAL-2050-->Automatically hide introns when opening a
1054 gene/transcript view
1057 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1061 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1062 structure mappings with the EMBL-EBI PDBe SIFTS database
1065 <!-- JAL-2079 -->Updated download sites used for Rfam and
1066 Pfam sources to xfam.org
1069 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1072 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1073 over sequences in Jalview
1076 <!-- JAL-2027-->Support for reverse-complement coding
1077 regions in ENA and EMBL
1080 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1081 for record retrieval via ENA rest API
1084 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1088 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1089 groovy script execution
1092 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1093 alignment window's Calculate menu
1096 <!-- JAL-1812 -->Allow groovy scripts that call
1097 Jalview.getAlignFrames() to run in headless mode
1100 <!-- JAL-2068 -->Support for creating new alignment
1101 calculation workers from groovy scripts
1104 <!-- JAL-1369 --->Store/restore reference sequence in
1108 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1109 associations are now saved/restored from project
1112 <!-- JAL-1993 -->Database selection dialog always shown
1113 before sequence fetcher is opened
1116 <!-- JAL-2183 -->Double click on an entry in Jalview's
1117 database chooser opens a sequence fetcher
1120 <!-- JAL-1563 -->Free-text search client for UniProt using
1121 the UniProt REST API
1124 <!-- JAL-2168 -->-nonews command line parameter to prevent
1125 the news reader opening
1128 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1129 querying stored in preferences
1132 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1136 <!-- JAL-1977-->Tooltips shown on database chooser
1139 <!-- JAL-391 -->Reverse complement function in calculate
1140 menu for nucleotide sequences
1143 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1144 and feature counts preserves alignment ordering (and
1145 debugged for complex feature sets).
1148 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1149 viewing structures with Jalview 2.10
1152 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1153 genome, transcript CCDS and gene ids via the Ensembl and
1154 Ensembl Genomes REST API
1157 <!-- JAL-2049 -->Protein sequence variant annotation
1158 computed for 'sequence_variant' annotation on CDS regions
1162 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1166 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1167 Ref Fetcher fails to match, or otherwise updates sequence
1168 data from external database records.
1171 <!-- JAL-2154 -->Revised Jalview Project format for
1172 efficient recovery of sequence coding and alignment
1173 annotation relationships.
1175 </ul> <!-- <em>Applet</em>
1186 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1190 <!-- JAL-2018-->Export features in Jalview format (again)
1191 includes graduated colourschemes
1194 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1195 working with big alignments and lots of hidden columns
1198 <!-- JAL-2053-->Hidden column markers not always rendered
1199 at right of alignment window
1202 <!-- JAL-2067 -->Tidied up links in help file table of
1206 <!-- JAL-2072 -->Feature based tree calculation not shown
1210 <!-- JAL-2075 -->Hidden columns ignored during feature
1211 based tree calculation
1214 <!-- JAL-2065 -->Alignment view stops updating when show
1215 unconserved enabled for group on alignment
1218 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1222 <!-- JAL-2146 -->Alignment column in status incorrectly
1223 shown as "Sequence position" when mousing over
1227 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1228 hidden columns present
1231 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1232 user created annotation added to alignment
1235 <!-- JAL-1841 -->RNA Structure consensus only computed for
1236 '()' base pair annotation
1239 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1240 in zero scores for all base pairs in RNA Structure
1244 <!-- JAL-2174-->Extend selection with columns containing
1248 <!-- JAL-2275 -->Pfam format writer puts extra space at
1249 beginning of sequence
1252 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1256 <!-- JAL-2238 -->Cannot create groups on an alignment from
1257 from a tree when t-coffee scores are shown
1260 <!-- JAL-1836,1967 -->Cannot import and view PDB
1261 structures with chains containing negative resnums (4q4h)
1264 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1268 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1269 to Clustal, PIR and PileUp output
1272 <!-- JAL-2008 -->Reordering sequence features that are
1273 not visible causes alignment window to repaint
1276 <!-- JAL-2006 -->Threshold sliders don't work in
1277 graduated colour and colour by annotation row for e-value
1278 scores associated with features and annotation rows
1281 <!-- JAL-1797 -->amino acid physicochemical conservation
1282 calculation should be case independent
1285 <!-- JAL-2173 -->Remove annotation also updates hidden
1289 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1290 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1291 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1294 <!-- JAL-2065 -->Null pointer exceptions and redraw
1295 problems when reference sequence defined and 'show
1296 non-conserved' enabled
1299 <!-- JAL-1306 -->Quality and Conservation are now shown on
1300 load even when Consensus calculation is disabled
1303 <!-- JAL-1932 -->Remove right on penultimate column of
1304 alignment does nothing
1307 <em>Application</em>
1310 <!-- JAL-1552-->URLs and links can't be imported by
1311 drag'n'drop on OSX when launched via webstart (note - not
1312 yet fixed for El Capitan)
1315 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1316 output when running on non-gb/us i18n platforms
1319 <!-- JAL-1944 -->Error thrown when exporting a view with
1320 hidden sequences as flat-file alignment
1323 <!-- JAL-2030-->InstallAnywhere distribution fails when
1327 <!-- JAL-2080-->Jalview very slow to launch via webstart
1328 (also hotfix for 2.9.0b2)
1331 <!-- JAL-2085 -->Cannot save project when view has a
1332 reference sequence defined
1335 <!-- JAL-1011 -->Columns are suddenly selected in other
1336 alignments and views when revealing hidden columns
1339 <!-- JAL-1989 -->Hide columns not mirrored in complement
1340 view in a cDNA/Protein splitframe
1343 <!-- JAL-1369 -->Cannot save/restore representative
1344 sequence from project when only one sequence is
1348 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1349 in Structure Chooser
1352 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1353 structure consensus didn't refresh annotation panel
1356 <!-- JAL-1962 -->View mapping in structure view shows
1357 mappings between sequence and all chains in a PDB file
1360 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1361 dialogs format columns correctly, don't display array
1362 data, sort columns according to type
1365 <!-- JAL-1975 -->Export complete shown after destination
1366 file chooser is cancelled during an image export
1369 <!-- JAL-2025 -->Error when querying PDB Service with
1370 sequence name containing special characters
1373 <!-- JAL-2024 -->Manual PDB structure querying should be
1377 <!-- JAL-2104 -->Large tooltips with broken HTML
1378 formatting don't wrap
1381 <!-- JAL-1128 -->Figures exported from wrapped view are
1382 truncated so L looks like I in consensus annotation
1385 <!-- JAL-2003 -->Export features should only export the
1386 currently displayed features for the current selection or
1390 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1391 after fetching cross-references, and restoring from
1395 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1396 followed in the structure viewer
1399 <!-- JAL-2163 -->Titles for individual alignments in
1400 splitframe not restored from project
1403 <!-- JAL-2145 -->missing autocalculated annotation at
1404 trailing end of protein alignment in transcript/product
1405 splitview when pad-gaps not enabled by default
1408 <!-- JAL-1797 -->amino acid physicochemical conservation
1412 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1413 article has been read (reopened issue due to
1414 internationalisation problems)
1417 <!-- JAL-1960 -->Only offer PDB structures in structure
1418 viewer based on sequence name, PDB and UniProt
1423 <!-- JAL-1976 -->No progress bar shown during export of
1427 <!-- JAL-2213 -->Structures not always superimposed after
1428 multiple structures are shown for one or more sequences.
1431 <!-- JAL-1370 -->Reference sequence characters should not
1432 be replaced with '.' when 'Show unconserved' format option
1436 <!-- JAL-1823 -->Cannot specify chain code when entering
1437 specific PDB id for sequence
1440 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1441 'Export hidden sequences' is enabled, but 'export hidden
1442 columns' is disabled.
1445 <!--JAL-2026-->Best Quality option in structure chooser
1446 selects lowest rather than highest resolution structures
1450 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1451 to sequence mapping in 'View Mappings' report
1454 <!-- JAL-2284 -->Unable to read old Jalview projects that
1455 contain non-XML data added after Jalvew wrote project.
1458 <!-- JAL-2118 -->Newly created annotation row reorders
1459 after clicking on it to create new annotation for a
1462 <!-- may exclude, this is an external service stability issue JAL-1941
1463 -- > RNA 3D structure not added via DSSR service</li> -->
1468 <!-- JAL-2151 -->Incorrect columns are selected when
1469 hidden columns present before start of sequence
1472 <!-- JAL-1986 -->Missing dependencies on applet pages
1476 <!-- JAL-1947 -->Overview pixel size changes when
1477 sequences are hidden in applet
1480 <!-- JAL-1996 -->Updated instructions for applet
1481 deployment on examples pages.
1488 <td width="60" nowrap>
1489 <div align="center">
1490 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1491 <em>16/10/2015</em></strong>
1494 <td><em>General</em>
1496 <li>Time stamps for signed Jalview application and applet
1501 <em>Application</em>
1503 <li>Duplicate group consensus and conservation rows
1504 shown when tree is partitioned</li>
1505 <li>Erratic behaviour when tree partitions made with
1506 multiple cDNA/Protein split views</li>
1512 <td width="60" nowrap>
1513 <div align="center">
1514 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1515 <em>8/10/2015</em></strong>
1518 <td><em>General</em>
1520 <li>Updated Spanish translations of localized text for
1522 </ul> <em>Application</em>
1524 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1525 <li>Signed OSX InstallAnywhere installer<br></li>
1526 <li>Support for per-sequence based annotations in BioJSON</li>
1527 </ul> <em>Applet</em>
1529 <li>Split frame example added to applet examples page</li>
1530 </ul> <em>Build and Deployment</em>
1533 <!-- JAL-1888 -->New ant target for running Jalview's test
1541 <li>Mapping of cDNA to protein in split frames
1542 incorrect when sequence start > 1</li>
1543 <li>Broken images in filter column by annotation dialog
1545 <li>Feature colours not parsed from features file</li>
1546 <li>Exceptions and incomplete link URLs recovered when
1547 loading a features file containing HTML tags in feature
1551 <em>Application</em>
1553 <li>Annotations corrupted after BioJS export and
1555 <li>Incorrect sequence limits after Fetch DB References
1556 with 'trim retrieved sequences'</li>
1557 <li>Incorrect warning about deleting all data when
1558 deleting selected columns</li>
1559 <li>Patch to build system for shipping properly signed
1560 JNLP templates for webstart launch</li>
1561 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1562 unreleased structures for download or viewing</li>
1563 <li>Tab/space/return keystroke operation of EMBL-PDBe
1564 fetcher/viewer dialogs works correctly</li>
1565 <li>Disabled 'minimise' button on Jalview windows
1566 running on OSX to workaround redraw hang bug</li>
1567 <li>Split cDNA/Protein view position and geometry not
1568 recovered from jalview project</li>
1569 <li>Initial enabled/disabled state of annotation menu
1570 sorter 'show autocalculated first/last' corresponds to
1572 <li>Restoring of Clustal, RNA Helices and T-Coffee
1573 color schemes from BioJSON</li>
1577 <li>Reorder sequences mirrored in cDNA/Protein split
1579 <li>Applet with Jmol examples not loading correctly</li>
1585 <td><div align="center">
1586 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1588 <td><em>General</em>
1590 <li>Linked visualisation and analysis of DNA and Protein
1593 <li>Translated cDNA alignments shown as split protein
1594 and DNA alignment views</li>
1595 <li>Codon consensus annotation for linked protein and
1596 cDNA alignment views</li>
1597 <li>Link cDNA or Protein product sequences by loading
1598 them onto Protein or cDNA alignments</li>
1599 <li>Reconstruct linked cDNA alignment from aligned
1600 protein sequences</li>
1603 <li>Jmol integration updated to Jmol v14.2.14</li>
1604 <li>Import and export of Jalview alignment views as <a
1605 href="features/bioJsonFormat.html">BioJSON</a></li>
1606 <li>New alignment annotation file statements for
1607 reference sequences and marking hidden columns</li>
1608 <li>Reference sequence based alignment shading to
1609 highlight variation</li>
1610 <li>Select or hide columns according to alignment
1612 <li>Find option for locating sequences by description</li>
1613 <li>Conserved physicochemical properties shown in amino
1614 acid conservation row</li>
1615 <li>Alignments can be sorted by number of RNA helices</li>
1616 </ul> <em>Application</em>
1618 <li>New cDNA/Protein analysis capabilities
1620 <li>Get Cross-References should open a Split Frame
1621 view with cDNA/Protein</li>
1622 <li>Detect when nucleotide sequences and protein
1623 sequences are placed in the same alignment</li>
1624 <li>Split cDNA/Protein views are saved in Jalview
1629 <li>Use REST API to talk to Chimera</li>
1630 <li>Selected regions in Chimera are highlighted in linked
1631 Jalview windows</li>
1633 <li>VARNA RNA viewer updated to v3.93</li>
1634 <li>VARNA views are saved in Jalview Projects</li>
1635 <li>Pseudoknots displayed as Jalview RNA annotation can
1636 be shown in VARNA</li>
1638 <li>Make groups for selection uses marked columns as well
1639 as the active selected region</li>
1641 <li>Calculate UPGMA and NJ trees using sequence feature
1643 <li>New Export options
1645 <li>New Export Settings dialog to control hidden
1646 region export in flat file generation</li>
1648 <li>Export alignment views for display with the <a
1649 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1651 <li>Export scrollable SVG in HTML page</li>
1652 <li>Optional embedding of BioJSON data when exporting
1653 alignment figures to HTML</li>
1655 <li>3D structure retrieval and display
1657 <li>Free text and structured queries with the PDBe
1659 <li>PDBe Search API based discovery and selection of
1660 PDB structures for a sequence set</li>
1664 <li>JPred4 employed for protein secondary structure
1666 <li>Hide Insertions menu option to hide unaligned columns
1667 for one or a group of sequences</li>
1668 <li>Automatically hide insertions in alignments imported
1669 from the JPred4 web server</li>
1670 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1671 system on OSX<br />LGPL libraries courtesy of <a
1672 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1674 <li>changed 'View nucleotide structure' submenu to 'View
1675 VARNA 2D Structure'</li>
1676 <li>change "View protein structure" menu option to "3D
1679 </ul> <em>Applet</em>
1681 <li>New layout for applet example pages</li>
1682 <li>New parameters to enable SplitFrame view
1683 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1684 <li>New example demonstrating linked viewing of cDNA and
1685 Protein alignments</li>
1686 </ul> <em>Development and deployment</em>
1688 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1689 <li>Include installation type and git revision in build
1690 properties and console log output</li>
1691 <li>Jalview Github organisation, and new github site for
1692 storing BioJsMSA Templates</li>
1693 <li>Jalview's unit tests now managed with TestNG</li>
1696 <!-- <em>General</em>
1698 </ul> --> <!-- issues resolved --> <em>Application</em>
1700 <li>Escape should close any open find dialogs</li>
1701 <li>Typo in select-by-features status report</li>
1702 <li>Consensus RNA secondary secondary structure
1703 predictions are not highlighted in amber</li>
1704 <li>Missing gap character in v2.7 example file means
1705 alignment appears unaligned when pad-gaps is not enabled</li>
1706 <li>First switch to RNA Helices colouring doesn't colour
1707 associated structure views</li>
1708 <li>ID width preference option is greyed out when auto
1709 width checkbox not enabled</li>
1710 <li>Stopped a warning dialog from being shown when
1711 creating user defined colours</li>
1712 <li>'View Mapping' in structure viewer shows sequence
1713 mappings for just that viewer's sequences</li>
1714 <li>Workaround for superposing PDB files containing
1715 multiple models in Chimera</li>
1716 <li>Report sequence position in status bar when hovering
1717 over Jmol structure</li>
1718 <li>Cannot output gaps as '.' symbols with Selection ->
1719 output to text box</li>
1720 <li>Flat file exports of alignments with hidden columns
1721 have incorrect sequence start/end</li>
1722 <li>'Aligning' a second chain to a Chimera structure from
1724 <li>Colour schemes applied to structure viewers don't
1725 work for nucleotide</li>
1726 <li>Loading/cut'n'pasting an empty or invalid file leads
1727 to a grey/invisible alignment window</li>
1728 <li>Exported Jpred annotation from a sequence region
1729 imports to different position</li>
1730 <li>Space at beginning of sequence feature tooltips shown
1731 on some platforms</li>
1732 <li>Chimera viewer 'View | Show Chain' menu is not
1734 <li>'New View' fails with a Null Pointer Exception in
1735 console if Chimera has been opened</li>
1736 <li>Mouseover to Chimera not working</li>
1737 <li>Miscellaneous ENA XML feature qualifiers not
1739 <li>NPE in annotation renderer after 'Extract Scores'</li>
1740 <li>If two structures in one Chimera window, mouseover of
1741 either sequence shows on first structure</li>
1742 <li>'Show annotations' options should not make
1743 non-positional annotations visible</li>
1744 <li>Subsequence secondary structure annotation not shown
1745 in right place after 'view flanking regions'</li>
1746 <li>File Save As type unset when current file format is
1748 <li>Save as '.jar' option removed for saving Jalview
1750 <li>Colour by Sequence colouring in Chimera more
1752 <li>Cannot 'add reference annotation' for a sequence in
1753 several views on same alignment</li>
1754 <li>Cannot show linked products for EMBL / ENA records</li>
1755 <li>Jalview's tooltip wraps long texts containing no
1757 </ul> <em>Applet</em>
1759 <li>Jmol to JalviewLite mouseover/link not working</li>
1760 <li>JalviewLite can't import sequences with ID
1761 descriptions containing angle brackets</li>
1762 </ul> <em>General</em>
1764 <li>Cannot export and reimport RNA secondary structure
1765 via jalview annotation file</li>
1766 <li>Random helix colour palette for colour by annotation
1767 with RNA secondary structure</li>
1768 <li>Mouseover to cDNA from STOP residue in protein
1769 translation doesn't work.</li>
1770 <li>hints when using the select by annotation dialog box</li>
1771 <li>Jmol alignment incorrect if PDB file has alternate CA
1773 <li>FontChooser message dialog appears to hang after
1774 choosing 1pt font</li>
1775 <li>Peptide secondary structure incorrectly imported from
1776 annotation file when annotation display text includes 'e' or
1778 <li>Cannot set colour of new feature type whilst creating
1780 <li>cDNA translation alignment should not be sequence
1781 order dependent</li>
1782 <li>'Show unconserved' doesn't work for lower case
1784 <li>Nucleotide ambiguity codes involving R not recognised</li>
1785 </ul> <em>Deployment and Documentation</em>
1787 <li>Applet example pages appear different to the rest of
1788 www.jalview.org</li>
1789 </ul> <em>Application Known issues</em>
1791 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1792 <li>Misleading message appears after trying to delete
1794 <li>Jalview icon not shown in dock after InstallAnywhere
1795 version launches</li>
1796 <li>Fetching EMBL reference for an RNA sequence results
1797 fails with a sequence mismatch</li>
1798 <li>Corrupted or unreadable alignment display when
1799 scrolling alignment to right</li>
1800 <li>ArrayIndexOutOfBoundsException thrown when remove
1801 empty columns called on alignment with ragged gapped ends</li>
1802 <li>auto calculated alignment annotation rows do not get
1803 placed above or below non-autocalculated rows</li>
1804 <li>Jalview dekstop becomes sluggish at full screen in
1805 ultra-high resolution</li>
1806 <li>Cannot disable consensus calculation independently of
1807 quality and conservation</li>
1808 <li>Mouseover highlighting between cDNA and protein can
1809 become sluggish with more than one splitframe shown</li>
1810 </ul> <em>Applet Known Issues</em>
1812 <li>Core PDB parsing code requires Jmol</li>
1813 <li>Sequence canvas panel goes white when alignment
1814 window is being resized</li>
1820 <td><div align="center">
1821 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1823 <td><em>General</em>
1825 <li>Updated Java code signing certificate donated by
1827 <li>Features and annotation preserved when performing
1828 pairwise alignment</li>
1829 <li>RNA pseudoknot annotation can be
1830 imported/exported/displayed</li>
1831 <li>'colour by annotation' can colour by RNA and
1832 protein secondary structure</li>
1833 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1834 post-hoc with 2.9 release</em>)
1837 </ul> <em>Application</em>
1839 <li>Extract and display secondary structure for sequences
1840 with 3D structures</li>
1841 <li>Support for parsing RNAML</li>
1842 <li>Annotations menu for layout
1844 <li>sort sequence annotation rows by alignment</li>
1845 <li>place sequence annotation above/below alignment
1848 <li>Output in Stockholm format</li>
1849 <li>Internationalisation: improved Spanish (es)
1851 <li>Structure viewer preferences tab</li>
1852 <li>Disorder and Secondary Structure annotation tracks
1853 shared between alignments</li>
1854 <li>UCSF Chimera launch and linked highlighting from
1856 <li>Show/hide all sequence associated annotation rows for
1857 all or current selection</li>
1858 <li>disorder and secondary structure predictions
1859 available as dataset annotation</li>
1860 <li>Per-sequence rna helices colouring</li>
1863 <li>Sequence database accessions imported when fetching
1864 alignments from Rfam</li>
1865 <li>update VARNA version to 3.91</li>
1867 <li>New groovy scripts for exporting aligned positions,
1868 conservation values, and calculating sum of pairs scores.</li>
1869 <li>Command line argument to set default JABAWS server</li>
1870 <li>include installation type in build properties and
1871 console log output</li>
1872 <li>Updated Jalview project format to preserve dataset
1876 <!-- issues resolved --> <em>Application</em>
1878 <li>Distinguish alignment and sequence associated RNA
1879 structure in structure->view->VARNA</li>
1880 <li>Raise dialog box if user deletes all sequences in an
1882 <li>Pressing F1 results in documentation opening twice</li>
1883 <li>Sequence feature tooltip is wrapped</li>
1884 <li>Double click on sequence associated annotation
1885 selects only first column</li>
1886 <li>Redundancy removal doesn't result in unlinked
1887 leaves shown in tree</li>
1888 <li>Undos after several redundancy removals don't undo
1890 <li>Hide sequence doesn't hide associated annotation</li>
1891 <li>User defined colours dialog box too big to fit on
1892 screen and buttons not visible</li>
1893 <li>author list isn't updated if already written to
1894 Jalview properties</li>
1895 <li>Popup menu won't open after retrieving sequence
1897 <li>File open window for associate PDB doesn't open</li>
1898 <li>Left-then-right click on a sequence id opens a
1899 browser search window</li>
1900 <li>Cannot open sequence feature shading/sort popup menu
1901 in feature settings dialog</li>
1902 <li>better tooltip placement for some areas of Jalview
1904 <li>Allow addition of JABAWS Server which doesn't
1905 pass validation</li>
1906 <li>Web services parameters dialog box is too large to
1908 <li>Muscle nucleotide alignment preset obscured by
1910 <li>JABAWS preset submenus don't contain newly
1911 defined user preset</li>
1912 <li>MSA web services warns user if they were launched
1913 with invalid input</li>
1914 <li>Jalview cannot contact DAS Registy when running on
1917 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1918 'Superpose with' submenu not shown when new view
1922 </ul> <!-- <em>Applet</em>
1924 </ul> <em>General</em>
1926 </ul>--> <em>Deployment and Documentation</em>
1928 <li>2G and 1G options in launchApp have no effect on
1929 memory allocation</li>
1930 <li>launchApp service doesn't automatically open
1931 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1933 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1934 InstallAnywhere reports cannot find valid JVM when Java
1935 1.7_055 is available
1937 </ul> <em>Application Known issues</em>
1940 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1941 corrupted or unreadable alignment display when scrolling
1945 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1946 retrieval fails but progress bar continues for DAS retrieval
1947 with large number of ID
1950 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1951 flatfile output of visible region has incorrect sequence
1955 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1956 rna structure consensus doesn't update when secondary
1957 structure tracks are rearranged
1960 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1961 invalid rna structure positional highlighting does not
1962 highlight position of invalid base pairs
1965 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1966 out of memory errors are not raised when saving Jalview
1967 project from alignment window file menu
1970 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1971 Switching to RNA Helices colouring doesn't propagate to
1975 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1976 colour by RNA Helices not enabled when user created
1977 annotation added to alignment
1980 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1981 Jalview icon not shown on dock in Mountain Lion/Webstart
1983 </ul> <em>Applet Known Issues</em>
1986 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1987 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1990 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1991 Jalview and Jmol example not compatible with IE9
1994 <li>Sort by annotation score doesn't reverse order
2000 <td><div align="center">
2001 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2004 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2007 <li>Internationalisation of user interface (usually
2008 called i18n support) and translation for Spanish locale</li>
2009 <li>Define/Undefine group on current selection with
2010 Ctrl-G/Shift Ctrl-G</li>
2011 <li>Improved group creation/removal options in
2012 alignment/sequence Popup menu</li>
2013 <li>Sensible precision for symbol distribution
2014 percentages shown in logo tooltip.</li>
2015 <li>Annotation panel height set according to amount of
2016 annotation when alignment first opened</li>
2017 </ul> <em>Application</em>
2019 <li>Interactive consensus RNA secondary structure
2020 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2021 <li>Select columns containing particular features from
2022 Feature Settings dialog</li>
2023 <li>View all 'representative' PDB structures for selected
2025 <li>Update Jalview project format:
2027 <li>New file extension for Jalview projects '.jvp'</li>
2028 <li>Preserve sequence and annotation dataset (to
2029 store secondary structure annotation,etc)</li>
2030 <li>Per group and alignment annotation and RNA helix
2034 <li>New similarity measures for PCA and Tree calculation
2036 <li>Experimental support for retrieval and viewing of
2037 flanking regions for an alignment</li>
2041 <!-- issues resolved --> <em>Application</em>
2043 <li>logo keeps spinning and status remains at queued or
2044 running after job is cancelled</li>
2045 <li>cannot export features from alignments imported from
2046 Jalview/VAMSAS projects</li>
2047 <li>Buggy slider for web service parameters that take
2049 <li>Newly created RNA secondary structure line doesn't
2050 have 'display all symbols' flag set</li>
2051 <li>T-COFFEE alignment score shading scheme and other
2052 annotation shading not saved in Jalview project</li>
2053 <li>Local file cannot be loaded in freshly downloaded
2055 <li>Jalview icon not shown on dock in Mountain
2057 <li>Load file from desktop file browser fails</li>
2058 <li>Occasional NPE thrown when calculating large trees</li>
2059 <li>Cannot reorder or slide sequences after dragging an
2060 alignment onto desktop</li>
2061 <li>Colour by annotation dialog throws NPE after using
2062 'extract scores' function</li>
2063 <li>Loading/cut'n'pasting an empty file leads to a grey
2064 alignment window</li>
2065 <li>Disorder thresholds rendered incorrectly after
2066 performing IUPred disorder prediction</li>
2067 <li>Multiple group annotated consensus rows shown when
2068 changing 'normalise logo' display setting</li>
2069 <li>Find shows blank dialog after 'finished searching' if
2070 nothing matches query</li>
2071 <li>Null Pointer Exceptions raised when sorting by
2072 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2074 <li>Errors in Jmol console when structures in alignment
2075 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2077 <li>Not all working JABAWS services are shown in
2079 <li>JAVAWS version of Jalview fails to launch with
2080 'invalid literal/length code'</li>
2081 <li>Annotation/RNA Helix colourschemes cannot be applied
2082 to alignment with groups (actually fixed in 2.8.0b1)</li>
2083 <li>RNA Helices and T-Coffee Scores available as default
2086 </ul> <em>Applet</em>
2088 <li>Remove group option is shown even when selection is
2090 <li>Apply to all groups ticked but colourscheme changes
2091 don't affect groups</li>
2092 <li>Documented RNA Helices and T-Coffee Scores as valid
2093 colourscheme name</li>
2094 <li>Annotation labels drawn on sequence IDs when
2095 Annotation panel is not displayed</li>
2096 <li>Increased font size for dropdown menus on OSX and
2097 embedded windows</li>
2098 </ul> <em>Other</em>
2100 <li>Consensus sequence for alignments/groups with a
2101 single sequence were not calculated</li>
2102 <li>annotation files that contain only groups imported as
2103 annotation and junk sequences</li>
2104 <li>Fasta files with sequences containing '*' incorrectly
2105 recognised as PFAM or BLC</li>
2106 <li>conservation/PID slider apply all groups option
2107 doesn't affect background (2.8.0b1)
2109 <li>redundancy highlighting is erratic at 0% and 100%</li>
2110 <li>Remove gapped columns fails for sequences with ragged
2112 <li>AMSA annotation row with leading spaces is not
2113 registered correctly on import</li>
2114 <li>Jalview crashes when selecting PCA analysis for
2115 certain alignments</li>
2116 <li>Opening the colour by annotation dialog for an
2117 existing annotation based 'use original colours'
2118 colourscheme loses original colours setting</li>
2123 <td><div align="center">
2124 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2125 <em>30/1/2014</em></strong>
2129 <li>Trusted certificates for JalviewLite applet and
2130 Jalview Desktop application<br />Certificate was donated by
2131 <a href="https://www.certum.eu">Certum</a> to the Jalview
2132 open source project).
2134 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2135 <li>Output in Stockholm format</li>
2136 <li>Allow import of data from gzipped files</li>
2137 <li>Export/import group and sequence associated line
2138 graph thresholds</li>
2139 <li>Nucleotide substitution matrix that supports RNA and
2140 ambiguity codes</li>
2141 <li>Allow disorder predictions to be made on the current
2142 selection (or visible selection) in the same way that JPred
2144 <li>Groovy scripting for headless Jalview operation</li>
2145 </ul> <em>Other improvements</em>
2147 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2148 <li>COMBINE statement uses current SEQUENCE_REF and
2149 GROUP_REF scope to group annotation rows</li>
2150 <li>Support '' style escaping of quotes in Newick
2152 <li>Group options for JABAWS service by command line name</li>
2153 <li>Empty tooltip shown for JABA service options with a
2154 link but no description</li>
2155 <li>Select primary source when selecting authority in
2156 database fetcher GUI</li>
2157 <li>Add .mfa to FASTA file extensions recognised by
2159 <li>Annotation label tooltip text wrap</li>
2164 <li>Slow scrolling when lots of annotation rows are
2166 <li>Lots of NPE (and slowness) after creating RNA
2167 secondary structure annotation line</li>
2168 <li>Sequence database accessions not imported when
2169 fetching alignments from Rfam</li>
2170 <li>Incorrect SHMR submission for sequences with
2172 <li>View all structures does not always superpose
2174 <li>Option widgets in service parameters not updated to
2175 reflect user or preset settings</li>
2176 <li>Null pointer exceptions for some services without
2177 presets or adjustable parameters</li>
2178 <li>Discover PDB IDs entry in structure menu doesn't
2179 discover PDB xRefs</li>
2180 <li>Exception encountered while trying to retrieve
2181 features with DAS</li>
2182 <li>Lowest value in annotation row isn't coloured
2183 when colour by annotation (per sequence) is coloured</li>
2184 <li>Keyboard mode P jumps to start of gapped region when
2185 residue follows a gap</li>
2186 <li>Jalview appears to hang importing an alignment with
2187 Wrap as default or after enabling Wrap</li>
2188 <li>'Right click to add annotations' message
2189 shown in wrap mode when no annotations present</li>
2190 <li>Disorder predictions fail with NPE if no automatic
2191 annotation already exists on alignment</li>
2192 <li>oninit javascript function should be called after
2193 initialisation completes</li>
2194 <li>Remove redundancy after disorder prediction corrupts
2195 alignment window display</li>
2196 <li>Example annotation file in documentation is invalid</li>
2197 <li>Grouped line graph annotation rows are not exported
2198 to annotation file</li>
2199 <li>Multi-harmony analysis cannot be run when only two
2201 <li>Cannot create multiple groups of line graphs with
2202 several 'combine' statements in annotation file</li>
2203 <li>Pressing return several times causes Number Format
2204 exceptions in keyboard mode</li>
2205 <li>Multi-harmony (SHMMR) method doesn't submit
2206 correct partitions for input data</li>
2207 <li>Translation from DNA to Amino Acids fails</li>
2208 <li>Jalview fail to load newick tree with quoted label</li>
2209 <li>--headless flag isn't understood</li>
2210 <li>ClassCastException when generating EPS in headless
2212 <li>Adjusting sequence-associated shading threshold only
2213 changes one row's threshold</li>
2214 <li>Preferences and Feature settings panel panel
2215 doesn't open</li>
2216 <li>hide consensus histogram also hides conservation and
2217 quality histograms</li>
2222 <td><div align="center">
2223 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2225 <td><em>Application</em>
2227 <li>Support for JABAWS 2.0 Services (AACon alignment
2228 conservation, protein disorder and Clustal Omega)</li>
2229 <li>JABAWS server status indicator in Web Services
2231 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2232 in Jalview alignment window</li>
2233 <li>Updated Jalview build and deploy framework for OSX
2234 mountain lion, windows 7, and 8</li>
2235 <li>Nucleotide substitution matrix for PCA that supports
2236 RNA and ambiguity codes</li>
2238 <li>Improved sequence database retrieval GUI</li>
2239 <li>Support fetching and database reference look up
2240 against multiple DAS sources (Fetch all from in 'fetch db
2242 <li>Jalview project improvements
2244 <li>Store and retrieve the 'belowAlignment'
2245 flag for annotation</li>
2246 <li>calcId attribute to group annotation rows on the
2248 <li>Store AACon calculation settings for a view in
2249 Jalview project</li>
2253 <li>horizontal scrolling gesture support</li>
2254 <li>Visual progress indicator when PCA calculation is
2256 <li>Simpler JABA web services menus</li>
2257 <li>visual indication that web service results are still
2258 being retrieved from server</li>
2259 <li>Serialise the dialogs that are shown when Jalview
2260 starts up for first time</li>
2261 <li>Jalview user agent string for interacting with HTTP
2263 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2265 <li>Examples directory and Groovy library included in
2266 InstallAnywhere distribution</li>
2267 </ul> <em>Applet</em>
2269 <li>RNA alignment and secondary structure annotation
2270 visualization applet example</li>
2271 </ul> <em>General</em>
2273 <li>Normalise option for consensus sequence logo</li>
2274 <li>Reset button in PCA window to return dimensions to
2276 <li>Allow seqspace or Jalview variant of alignment PCA
2278 <li>PCA with either nucleic acid and protein substitution
2280 <li>Allow windows containing HTML reports to be exported
2282 <li>Interactive display and editing of RNA secondary
2283 structure contacts</li>
2284 <li>RNA Helix Alignment Colouring</li>
2285 <li>RNA base pair logo consensus</li>
2286 <li>Parse sequence associated secondary structure
2287 information in Stockholm files</li>
2288 <li>HTML Export database accessions and annotation
2289 information presented in tooltip for sequences</li>
2290 <li>Import secondary structure from LOCARNA clustalw
2291 style RNA alignment files</li>
2292 <li>import and visualise T-COFFEE quality scores for an
2294 <li>'colour by annotation' per sequence option to
2295 shade each sequence according to its associated alignment
2297 <li>New Jalview Logo</li>
2298 </ul> <em>Documentation and Development</em>
2300 <li>documentation for score matrices used in Jalview</li>
2301 <li>New Website!</li>
2303 <td><em>Application</em>
2305 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2306 wsdbfetch REST service</li>
2307 <li>Stop windows being moved outside desktop on OSX</li>
2308 <li>Filetype associations not installed for webstart
2310 <li>Jalview does not always retrieve progress of a JABAWS
2311 job execution in full once it is complete</li>
2312 <li>revise SHMR RSBS definition to ensure alignment is
2313 uploaded via ali_file parameter</li>
2314 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2315 <li>View all structures superposed fails with exception</li>
2316 <li>Jnet job queues forever if a very short sequence is
2317 submitted for prediction</li>
2318 <li>Cut and paste menu not opened when mouse clicked on
2320 <li>Putting fractional value into integer text box in
2321 alignment parameter dialog causes Jalview to hang</li>
2322 <li>Structure view highlighting doesn't work on
2324 <li>View all structures fails with exception shown in
2326 <li>Characters in filename associated with PDBEntry not
2327 escaped in a platform independent way</li>
2328 <li>Jalview desktop fails to launch with exception when
2330 <li>Tree calculation reports 'you must have 2 or more
2331 sequences selected' when selection is empty</li>
2332 <li>Jalview desktop fails to launch with jar signature
2333 failure when java web start temporary file caching is
2335 <li>DAS Sequence retrieval with range qualification
2336 results in sequence xref which includes range qualification</li>
2337 <li>Errors during processing of command line arguments
2338 cause progress bar (JAL-898) to be removed</li>
2339 <li>Replace comma for semi-colon option not disabled for
2340 DAS sources in sequence fetcher</li>
2341 <li>Cannot close news reader when JABAWS server warning
2342 dialog is shown</li>
2343 <li>Option widgets not updated to reflect user settings</li>
2344 <li>Edited sequence not submitted to web service</li>
2345 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2346 <li>InstallAnywhere installer doesn't unpack and run
2347 on OSX Mountain Lion</li>
2348 <li>Annotation panel not given a scroll bar when
2349 sequences with alignment annotation are pasted into the
2351 <li>Sequence associated annotation rows not associated
2352 when loaded from Jalview project</li>
2353 <li>Browser launch fails with NPE on java 1.7</li>
2354 <li>JABAWS alignment marked as finished when job was
2355 cancelled or job failed due to invalid input</li>
2356 <li>NPE with v2.7 example when clicking on Tree
2357 associated with all views</li>
2358 <li>Exceptions when copy/paste sequences with grouped
2359 annotation rows to new window</li>
2360 </ul> <em>Applet</em>
2362 <li>Sequence features are momentarily displayed before
2363 they are hidden using hidefeaturegroups applet parameter</li>
2364 <li>loading features via javascript API automatically
2365 enables feature display</li>
2366 <li>scrollToColumnIn javascript API method doesn't
2368 </ul> <em>General</em>
2370 <li>Redundancy removal fails for rna alignment</li>
2371 <li>PCA calculation fails when sequence has been selected
2372 and then deselected</li>
2373 <li>PCA window shows grey box when first opened on OSX</li>
2374 <li>Letters coloured pink in sequence logo when alignment
2375 coloured with clustalx</li>
2376 <li>Choosing fonts without letter symbols defined causes
2377 exceptions and redraw errors</li>
2378 <li>Initial PCA plot view is not same as manually
2379 reconfigured view</li>
2380 <li>Grouped annotation graph label has incorrect line
2382 <li>Grouped annotation graph label display is corrupted
2383 for lots of labels</li>
2388 <div align="center">
2389 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2392 <td><em>Application</em>
2394 <li>Jalview Desktop News Reader</li>
2395 <li>Tweaked default layout of web services menu</li>
2396 <li>View/alignment association menu to enable user to
2397 easily specify which alignment a multi-structure view takes
2398 its colours/correspondences from</li>
2399 <li>Allow properties file location to be specified as URL</li>
2400 <li>Extend Jalview project to preserve associations
2401 between many alignment views and a single Jmol display</li>
2402 <li>Store annotation row height in Jalview project file</li>
2403 <li>Annotation row column label formatting attributes
2404 stored in project file</li>
2405 <li>Annotation row order for auto-calculated annotation
2406 rows preserved in Jalview project file</li>
2407 <li>Visual progress indication when Jalview state is
2408 saved using Desktop window menu</li>
2409 <li>Visual indication that command line arguments are
2410 still being processed</li>
2411 <li>Groovy script execution from URL</li>
2412 <li>Colour by annotation default min and max colours in
2414 <li>Automatically associate PDB files dragged onto an
2415 alignment with sequences that have high similarity and
2417 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2418 <li>'view structures' option to open many
2419 structures in same window</li>
2420 <li>Sort associated views menu option for tree panel</li>
2421 <li>Group all JABA and non-JABA services for a particular
2422 analysis function in its own submenu</li>
2423 </ul> <em>Applet</em>
2425 <li>Userdefined and autogenerated annotation rows for
2427 <li>Adjustment of alignment annotation pane height</li>
2428 <li>Annotation scrollbar for annotation panel</li>
2429 <li>Drag to reorder annotation rows in annotation panel</li>
2430 <li>'automaticScrolling' parameter</li>
2431 <li>Allow sequences with partial ID string matches to be
2432 annotated from GFF/Jalview features files</li>
2433 <li>Sequence logo annotation row in applet</li>
2434 <li>Absolute paths relative to host server in applet
2435 parameters are treated as such</li>
2436 <li>New in the JalviewLite javascript API:
2438 <li>JalviewLite.js javascript library</li>
2439 <li>Javascript callbacks for
2441 <li>Applet initialisation</li>
2442 <li>Sequence/alignment mouse-overs and selections</li>
2445 <li>scrollTo row and column alignment scrolling
2447 <li>Select sequence/alignment regions from javascript</li>
2448 <li>javascript structure viewer harness to pass
2449 messages between Jmol and Jalview when running as
2450 distinct applets</li>
2451 <li>sortBy method</li>
2452 <li>Set of applet and application examples shipped
2453 with documentation</li>
2454 <li>New example to demonstrate JalviewLite and Jmol
2455 javascript message exchange</li>
2457 </ul> <em>General</em>
2459 <li>Enable Jmol displays to be associated with multiple
2460 multiple alignments</li>
2461 <li>Option to automatically sort alignment with new tree</li>
2462 <li>User configurable link to enable redirects to a
2463 www.Jalview.org mirror</li>
2464 <li>Jmol colours option for Jmol displays</li>
2465 <li>Configurable newline string when writing alignment
2466 and other flat files</li>
2467 <li>Allow alignment annotation description lines to
2468 contain html tags</li>
2469 </ul> <em>Documentation and Development</em>
2471 <li>Add groovy test harness for bulk load testing to
2473 <li>Groovy script to load and align a set of sequences
2474 using a web service before displaying the result in the
2475 Jalview desktop</li>
2476 <li>Restructured javascript and applet api documentation</li>
2477 <li>Ant target to publish example html files with applet
2479 <li>Netbeans project for building Jalview from source</li>
2480 <li>ant task to create online javadoc for Jalview source</li>
2482 <td><em>Application</em>
2484 <li>User defined colourscheme throws exception when
2485 current built in colourscheme is saved as new scheme</li>
2486 <li>AlignFrame->Save in application pops up save
2487 dialog for valid filename/format</li>
2488 <li>Cannot view associated structure for UniProt sequence</li>
2489 <li>PDB file association breaks for UniProt sequence
2491 <li>Associate PDB from file dialog does not tell you
2492 which sequence is to be associated with the file</li>
2493 <li>Find All raises null pointer exception when query
2494 only matches sequence IDs</li>
2495 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2496 <li>Jalview project with Jmol views created with Jalview
2497 2.4 cannot be loaded</li>
2498 <li>Filetype associations not installed for webstart
2500 <li>Two or more chains in a single PDB file associated
2501 with sequences in different alignments do not get coloured
2502 by their associated sequence</li>
2503 <li>Visibility status of autocalculated annotation row
2504 not preserved when project is loaded</li>
2505 <li>Annotation row height and visibility attributes not
2506 stored in Jalview project</li>
2507 <li>Tree bootstraps are not preserved when saved as a
2508 Jalview project</li>
2509 <li>Envision2 workflow tooltips are corrupted</li>
2510 <li>Enabling show group conservation also enables colour
2511 by conservation</li>
2512 <li>Duplicate group associated conservation or consensus
2513 created on new view</li>
2514 <li>Annotation scrollbar not displayed after 'show
2515 all hidden annotation rows' option selected</li>
2516 <li>Alignment quality not updated after alignment
2517 annotation row is hidden then shown</li>
2518 <li>Preserve colouring of structures coloured by
2519 sequences in pre Jalview 2.7 projects</li>
2520 <li>Web service job parameter dialog is not laid out
2522 <li>Web services menu not refreshed after 'reset
2523 services' button is pressed in preferences</li>
2524 <li>Annotation off by one in Jalview v2_3 example project</li>
2525 <li>Structures imported from file and saved in project
2526 get name like jalview_pdb1234.txt when reloaded</li>
2527 <li>Jalview does not always retrieve progress of a JABAWS
2528 job execution in full once it is complete</li>
2529 </ul> <em>Applet</em>
2531 <li>Alignment height set incorrectly when lots of
2532 annotation rows are displayed</li>
2533 <li>Relative URLs in feature HTML text not resolved to
2535 <li>View follows highlighting does not work for positions
2537 <li><= shown as = in tooltip</li>
2538 <li>Export features raises exception when no features
2540 <li>Separator string used for serialising lists of IDs
2541 for javascript api is modified when separator string
2542 provided as parameter</li>
2543 <li>Null pointer exception when selecting tree leaves for
2544 alignment with no existing selection</li>
2545 <li>Relative URLs for datasources assumed to be relative
2546 to applet's codebase</li>
2547 <li>Status bar not updated after finished searching and
2548 search wraps around to first result</li>
2549 <li>StructureSelectionManager instance shared between
2550 several Jalview applets causes race conditions and memory
2552 <li>Hover tooltip and mouseover of position on structure
2553 not sent from Jmol in applet</li>
2554 <li>Certain sequences of javascript method calls to
2555 applet API fatally hang browser</li>
2556 </ul> <em>General</em>
2558 <li>View follows structure mouseover scrolls beyond
2559 position with wrapped view and hidden regions</li>
2560 <li>Find sequence position moves to wrong residue
2561 with/without hidden columns</li>
2562 <li>Sequence length given in alignment properties window
2564 <li>InvalidNumberFormat exceptions thrown when trying to
2565 import PDB like structure files</li>
2566 <li>Positional search results are only highlighted
2567 between user-supplied sequence start/end bounds</li>
2568 <li>End attribute of sequence is not validated</li>
2569 <li>Find dialog only finds first sequence containing a
2570 given sequence position</li>
2571 <li>Sequence numbering not preserved in MSF alignment
2573 <li>Jalview PDB file reader does not extract sequence
2574 from nucleotide chains correctly</li>
2575 <li>Structure colours not updated when tree partition
2576 changed in alignment</li>
2577 <li>Sequence associated secondary structure not correctly
2578 parsed in interleaved stockholm</li>
2579 <li>Colour by annotation dialog does not restore current
2581 <li>Hiding (nearly) all sequences doesn't work
2583 <li>Sequences containing lowercase letters are not
2584 properly associated with their pdb files</li>
2585 </ul> <em>Documentation and Development</em>
2587 <li>schemas/JalviewWsParamSet.xsd corrupted by
2588 ApplyCopyright tool</li>
2593 <div align="center">
2594 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2597 <td><em>Application</em>
2599 <li>New warning dialog when the Jalview Desktop cannot
2600 contact web services</li>
2601 <li>JABA service parameters for a preset are shown in
2602 service job window</li>
2603 <li>JABA Service menu entries reworded</li>
2607 <li>Modeller PIR IO broken - cannot correctly import a
2608 pir file emitted by Jalview</li>
2609 <li>Existing feature settings transferred to new
2610 alignment view created from cut'n'paste</li>
2611 <li>Improved test for mixed amino/nucleotide chains when
2612 parsing PDB files</li>
2613 <li>Consensus and conservation annotation rows
2614 occasionally become blank for all new windows</li>
2615 <li>Exception raised when right clicking above sequences
2616 in wrapped view mode</li>
2617 </ul> <em>Application</em>
2619 <li>multiple multiply aligned structure views cause cpu
2620 usage to hit 100% and computer to hang</li>
2621 <li>Web Service parameter layout breaks for long user
2622 parameter names</li>
2623 <li>Jaba service discovery hangs desktop if Jaba server
2630 <div align="center">
2631 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2634 <td><em>Application</em>
2636 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2637 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2640 <li>Web Services preference tab</li>
2641 <li>Analysis parameters dialog box and user defined
2643 <li>Improved speed and layout of Envision2 service menu</li>
2644 <li>Superpose structures using associated sequence
2646 <li>Export coordinates and projection as CSV from PCA
2648 </ul> <em>Applet</em>
2650 <li>enable javascript: execution by the applet via the
2651 link out mechanism</li>
2652 </ul> <em>Other</em>
2654 <li>Updated the Jmol Jalview interface to work with Jmol
2656 <li>The Jalview Desktop and JalviewLite applet now
2657 require Java 1.5</li>
2658 <li>Allow Jalview feature colour specification for GFF
2659 sequence annotation files</li>
2660 <li>New 'colour by label' keword in Jalview feature file
2661 type colour specification</li>
2662 <li>New Jalview Desktop Groovy API method that allows a
2663 script to check if it being run in an interactive session or
2664 in a batch operation from the Jalview command line</li>
2668 <li>clustalx colourscheme colours Ds preferentially when
2669 both D+E are present in over 50% of the column</li>
2670 </ul> <em>Application</em>
2672 <li>typo in AlignmentFrame->View->Hide->all but
2673 selected Regions menu item</li>
2674 <li>sequence fetcher replaces ',' for ';' when the ',' is
2675 part of a valid accession ID</li>
2676 <li>fatal OOM if object retrieved by sequence fetcher
2677 runs out of memory</li>
2678 <li>unhandled Out of Memory Error when viewing pca
2679 analysis results</li>
2680 <li>InstallAnywhere builds fail to launch on OS X java
2681 10.5 update 4 (due to apple Java 1.6 update)</li>
2682 <li>Installanywhere Jalview silently fails to launch</li>
2683 </ul> <em>Applet</em>
2685 <li>Jalview.getFeatureGroups() raises an
2686 ArrayIndexOutOfBoundsException if no feature groups are
2693 <div align="center">
2694 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2700 <li>Alignment prettyprinter doesn't cope with long
2702 <li>clustalx colourscheme colours Ds preferentially when
2703 both D+E are present in over 50% of the column</li>
2704 <li>nucleic acid structures retrieved from PDB do not
2705 import correctly</li>
2706 <li>More columns get selected than were clicked on when a
2707 number of columns are hidden</li>
2708 <li>annotation label popup menu not providing correct
2709 add/hide/show options when rows are hidden or none are
2711 <li>Stockholm format shown in list of readable formats,
2712 and parser copes better with alignments from RFAM.</li>
2713 <li>CSV output of consensus only includes the percentage
2714 of all symbols if sequence logo display is enabled</li>
2716 </ul> <em>Applet</em>
2718 <li>annotation panel disappears when annotation is
2720 </ul> <em>Application</em>
2722 <li>Alignment view not redrawn properly when new
2723 alignment opened where annotation panel is visible but no
2724 annotations are present on alignment</li>
2725 <li>pasted region containing hidden columns is
2726 incorrectly displayed in new alignment window</li>
2727 <li>Jalview slow to complete operations when stdout is
2728 flooded (fix is to close the Jalview console)</li>
2729 <li>typo in AlignmentFrame->View->Hide->all but
2730 selected Rregions menu item.</li>
2731 <li>inconsistent group submenu and Format submenu entry
2732 'Un' or 'Non'conserved</li>
2733 <li>Sequence feature settings are being shared by
2734 multiple distinct alignments</li>
2735 <li>group annotation not recreated when tree partition is
2737 <li>double click on group annotation to select sequences
2738 does not propagate to associated trees</li>
2739 <li>Mac OSX specific issues:
2741 <li>exception raised when mouse clicked on desktop
2742 window background</li>
2743 <li>Desktop menu placed on menu bar and application
2744 name set correctly</li>
2745 <li>sequence feature settings not wide enough for the
2746 save feature colourscheme button</li>
2755 <div align="center">
2756 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2759 <td><em>New Capabilities</em>
2761 <li>URL links generated from description line for
2762 regular-expression based URL links (applet and application)
2764 <li>Non-positional feature URL links are shown in link
2766 <li>Linked viewing of nucleic acid sequences and
2768 <li>Automatic Scrolling option in View menu to display
2769 the currently highlighted region of an alignment.</li>
2770 <li>Order an alignment by sequence length, or using the
2771 average score or total feature count for each sequence.</li>
2772 <li>Shading features by score or associated description</li>
2773 <li>Subdivide alignment and groups based on identity of
2774 selected subsequence (Make Groups from Selection).</li>
2775 <li>New hide/show options including Shift+Control+H to
2776 hide everything but the currently selected region.</li>
2777 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2778 </ul> <em>Application</em>
2780 <li>Fetch DB References capabilities and UI expanded to
2781 support retrieval from DAS sequence sources</li>
2782 <li>Local DAS Sequence sources can be added via the
2783 command line or via the Add local source dialog box.</li>
2784 <li>DAS Dbref and DbxRef feature types are parsed as
2785 database references and protein_name is parsed as
2786 description line (BioSapiens terms).</li>
2787 <li>Enable or disable non-positional feature and database
2788 references in sequence ID tooltip from View menu in
2790 <!-- <li>New hidden columns and rows and representatives capabilities
2791 in annotations file (in progress - not yet fully implemented)</li> -->
2792 <li>Group-associated consensus, sequence logos and
2793 conservation plots</li>
2794 <li>Symbol distributions for each column can be exported
2795 and visualized as sequence logos</li>
2796 <li>Optionally scale multi-character column labels to fit
2797 within each column of annotation row<!-- todo for applet -->
2799 <li>Optional automatic sort of associated alignment view
2800 when a new tree is opened.</li>
2801 <li>Jalview Java Console</li>
2802 <li>Better placement of desktop window when moving
2803 between different screens.</li>
2804 <li>New preference items for sequence ID tooltip and
2805 consensus annotation</li>
2806 <li>Client to submit sequences and IDs to Envision2
2808 <li><em>Vamsas Capabilities</em>
2810 <li>Improved VAMSAS synchronization (Jalview archive
2811 used to preserve views, structures, and tree display
2813 <li>Import of vamsas documents from disk or URL via
2815 <li>Sharing of selected regions between views and
2816 with other VAMSAS applications (Experimental feature!)</li>
2817 <li>Updated API to VAMSAS version 0.2</li>
2819 </ul> <em>Applet</em>
2821 <li>Middle button resizes annotation row height</li>
2824 <li>sortByTree (true/false) - automatically sort the
2825 associated alignment view by the tree when a new tree is
2827 <li>showTreeBootstraps (true/false) - show or hide
2828 branch bootstraps (default is to show them if available)</li>
2829 <li>showTreeDistances (true/false) - show or hide
2830 branch lengths (default is to show them if available)</li>
2831 <li>showUnlinkedTreeNodes (true/false) - indicate if
2832 unassociated nodes should be highlighted in the tree
2834 <li>heightScale and widthScale (1.0 or more) -
2835 increase the height or width of a cell in the alignment
2836 grid relative to the current font size.</li>
2839 <li>Non-positional features displayed in sequence ID
2841 </ul> <em>Other</em>
2843 <li>Features format: graduated colour definitions and
2844 specification of feature scores</li>
2845 <li>Alignment Annotations format: new keywords for group
2846 associated annotation (GROUP_REF) and annotation row display
2847 properties (ROW_PROPERTIES)</li>
2848 <li>XML formats extended to support graduated feature
2849 colourschemes, group associated annotation, and profile
2850 visualization settings.</li></td>
2853 <li>Source field in GFF files parsed as feature source
2854 rather than description</li>
2855 <li>Non-positional features are now included in sequence
2856 feature and gff files (controlled via non-positional feature
2857 visibility in tooltip).</li>
2858 <li>URL links generated for all feature links (bugfix)</li>
2859 <li>Added URL embedding instructions to features file
2861 <li>Codons containing ambiguous nucleotides translated as
2862 'X' in peptide product</li>
2863 <li>Match case switch in find dialog box works for both
2864 sequence ID and sequence string and query strings do not
2865 have to be in upper case to match case-insensitively.</li>
2866 <li>AMSA files only contain first column of
2867 multi-character column annotation labels</li>
2868 <li>Jalview Annotation File generation/parsing consistent
2869 with documentation (e.g. Stockholm annotation can be
2870 exported and re-imported)</li>
2871 <li>PDB files without embedded PDB IDs given a friendly
2873 <li>Find incrementally searches ID string matches as well
2874 as subsequence matches, and correctly reports total number
2878 <li>Better handling of exceptions during sequence
2880 <li>Dasobert generated non-positional feature URL
2881 link text excludes the start_end suffix</li>
2882 <li>DAS feature and source retrieval buttons disabled
2883 when fetch or registry operations in progress.</li>
2884 <li>PDB files retrieved from URLs are cached properly</li>
2885 <li>Sequence description lines properly shared via
2887 <li>Sequence fetcher fetches multiple records for all
2889 <li>Ensured that command line das feature retrieval
2890 completes before alignment figures are generated.</li>
2891 <li>Reduced time taken when opening file browser for
2893 <li>isAligned check prior to calculating tree, PCA or
2894 submitting an MSA to JNet now excludes hidden sequences.</li>
2895 <li>User defined group colours properly recovered
2896 from Jalview projects.</li>
2905 <div align="center">
2906 <strong>2.4.0.b2</strong><br> 28/10/2009
2911 <li>Experimental support for google analytics usage
2913 <li>Jalview privacy settings (user preferences and docs).</li>
2918 <li>Race condition in applet preventing startup in
2920 <li>Exception when feature created from selection beyond
2921 length of sequence.</li>
2922 <li>Allow synthetic PDB files to be imported gracefully</li>
2923 <li>Sequence associated annotation rows associate with
2924 all sequences with a given id</li>
2925 <li>Find function matches case-insensitively for sequence
2926 ID string searches</li>
2927 <li>Non-standard characters do not cause pairwise
2928 alignment to fail with exception</li>
2929 </ul> <em>Application Issues</em>
2931 <li>Sequences are now validated against EMBL database</li>
2932 <li>Sequence fetcher fetches multiple records for all
2934 </ul> <em>InstallAnywhere Issues</em>
2936 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2937 issue with installAnywhere mechanism)</li>
2938 <li>Command line launching of JARs from InstallAnywhere
2939 version (java class versioning error fixed)</li>
2946 <div align="center">
2947 <strong>2.4</strong><br> 27/8/2008
2950 <td><em>User Interface</em>
2952 <li>Linked highlighting of codon and amino acid from
2953 translation and protein products</li>
2954 <li>Linked highlighting of structure associated with
2955 residue mapping to codon position</li>
2956 <li>Sequence Fetcher provides example accession numbers
2957 and 'clear' button</li>
2958 <li>MemoryMonitor added as an option under Desktop's
2960 <li>Extract score function to parse whitespace separated
2961 numeric data in description line</li>
2962 <li>Column labels in alignment annotation can be centred.</li>
2963 <li>Tooltip for sequence associated annotation give name
2965 </ul> <em>Web Services and URL fetching</em>
2967 <li>JPred3 web service</li>
2968 <li>Prototype sequence search client (no public services
2970 <li>Fetch either seed alignment or full alignment from
2972 <li>URL Links created for matching database cross
2973 references as well as sequence ID</li>
2974 <li>URL Links can be created using regular-expressions</li>
2975 </ul> <em>Sequence Database Connectivity</em>
2977 <li>Retrieval of cross-referenced sequences from other
2979 <li>Generalised database reference retrieval and
2980 validation to all fetchable databases</li>
2981 <li>Fetch sequences from DAS sources supporting the
2982 sequence command</li>
2983 </ul> <em>Import and Export</em>
2984 <li>export annotation rows as CSV for spreadsheet import</li>
2985 <li>Jalview projects record alignment dataset associations,
2986 EMBL products, and cDNA sequence mappings</li>
2987 <li>Sequence Group colour can be specified in Annotation
2989 <li>Ad-hoc colouring of group in Annotation File using RGB
2990 triplet as name of colourscheme</li>
2991 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2993 <li>treenode binding for VAMSAS tree exchange</li>
2994 <li>local editing and update of sequences in VAMSAS
2995 alignments (experimental)</li>
2996 <li>Create new or select existing session to join</li>
2997 <li>load and save of vamsas documents</li>
2998 </ul> <em>Application command line</em>
3000 <li>-tree parameter to open trees (introduced for passing
3002 <li>-fetchfrom command line argument to specify nicknames
3003 of DAS servers to query for alignment features</li>
3004 <li>-dasserver command line argument to add new servers
3005 that are also automatically queried for features</li>
3006 <li>-groovy command line argument executes a given groovy
3007 script after all input data has been loaded and parsed</li>
3008 </ul> <em>Applet-Application data exchange</em>
3010 <li>Trees passed as applet parameters can be passed to
3011 application (when using "View in full
3012 application")</li>
3013 </ul> <em>Applet Parameters</em>
3015 <li>feature group display control parameter</li>
3016 <li>debug parameter</li>
3017 <li>showbutton parameter</li>
3018 </ul> <em>Applet API methods</em>
3020 <li>newView public method</li>
3021 <li>Window (current view) specific get/set public methods</li>
3022 <li>Feature display control methods</li>
3023 <li>get list of currently selected sequences</li>
3024 </ul> <em>New Jalview distribution features</em>
3026 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3027 <li>RELEASE file gives build properties for the latest
3028 Jalview release.</li>
3029 <li>Java 1.1 Applet build made easier and donotobfuscate
3030 property controls execution of obfuscator</li>
3031 <li>Build target for generating source distribution</li>
3032 <li>Debug flag for javacc</li>
3033 <li>.jalview_properties file is documented (slightly) in
3034 jalview.bin.Cache</li>
3035 <li>Continuous Build Integration for stable and
3036 development version of Application, Applet and source
3041 <li>selected region output includes visible annotations
3042 (for certain formats)</li>
3043 <li>edit label/displaychar contains existing label/char
3045 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3046 <li>shorter peptide product names from EMBL records</li>
3047 <li>Newick string generator makes compact representations</li>
3048 <li>bootstrap values parsed correctly for tree files with
3050 <li>pathological filechooser bug avoided by not allowing
3051 filenames containing a ':'</li>
3052 <li>Fixed exception when parsing GFF files containing
3053 global sequence features</li>
3054 <li>Alignment datasets are finalized only when number of
3055 references from alignment sequences goes to zero</li>
3056 <li>Close of tree branch colour box without colour
3057 selection causes cascading exceptions</li>
3058 <li>occasional negative imgwidth exceptions</li>
3059 <li>better reporting of non-fatal warnings to user when
3060 file parsing fails.</li>
3061 <li>Save works when Jalview project is default format</li>
3062 <li>Save as dialog opened if current alignment format is
3063 not a valid output format</li>
3064 <li>UniProt canonical names introduced for both das and
3066 <li>Histidine should be midblue (not pink!) in Zappo</li>
3067 <li>error messages passed up and output when data read
3069 <li>edit undo recovers previous dataset sequence when
3070 sequence is edited</li>
3071 <li>allow PDB files without pdb ID HEADER lines (like
3072 those generated by MODELLER) to be read in properly</li>
3073 <li>allow reading of JPred concise files as a normal
3075 <li>Stockholm annotation parsing and alignment properties
3076 import fixed for PFAM records</li>
3077 <li>Structure view windows have correct name in Desktop
3079 <li>annotation consisting of sequence associated scores
3080 can be read and written correctly to annotation file</li>
3081 <li>Aligned cDNA translation to aligned peptide works
3083 <li>Fixed display of hidden sequence markers and
3084 non-italic font for representatives in Applet</li>
3085 <li>Applet Menus are always embedded in applet window on
3087 <li>Newly shown features appear at top of stack (in
3089 <li>Annotations added via parameter not drawn properly
3090 due to null pointer exceptions</li>
3091 <li>Secondary structure lines are drawn starting from
3092 first column of alignment</li>
3093 <li>UniProt XML import updated for new schema release in
3095 <li>Sequence feature to sequence ID match for Features
3096 file is case-insensitive</li>
3097 <li>Sequence features read from Features file appended to
3098 all sequences with matching IDs</li>
3099 <li>PDB structure coloured correctly for associated views
3100 containing a sub-sequence</li>
3101 <li>PDB files can be retrieved by applet from Jar files</li>
3102 <li>feature and annotation file applet parameters
3103 referring to different directories are retrieved correctly</li>
3104 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3105 <li>Fixed application hang whilst waiting for
3106 splash-screen version check to complete</li>
3107 <li>Applet properly URLencodes input parameter values
3108 when passing them to the launchApp service</li>
3109 <li>display name and local features preserved in results
3110 retrieved from web service</li>
3111 <li>Visual delay indication for sequence retrieval and
3112 sequence fetcher initialisation</li>
3113 <li>updated Application to use DAS 1.53e version of
3114 dasobert DAS client</li>
3115 <li>Re-instated Full AMSA support and .amsa file
3117 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3125 <div align="center">
3126 <strong>2.3</strong><br> 9/5/07
3131 <li>Jmol 11.0.2 integration</li>
3132 <li>PDB views stored in Jalview XML files</li>
3133 <li>Slide sequences</li>
3134 <li>Edit sequence in place</li>
3135 <li>EMBL CDS features</li>
3136 <li>DAS Feature mapping</li>
3137 <li>Feature ordering</li>
3138 <li>Alignment Properties</li>
3139 <li>Annotation Scores</li>
3140 <li>Sort by scores</li>
3141 <li>Feature/annotation editing in applet</li>
3146 <li>Headless state operation in 2.2.1</li>
3147 <li>Incorrect and unstable DNA pairwise alignment</li>
3148 <li>Cut and paste of sequences with annotation</li>
3149 <li>Feature group display state in XML</li>
3150 <li>Feature ordering in XML</li>
3151 <li>blc file iteration selection using filename # suffix</li>
3152 <li>Stockholm alignment properties</li>
3153 <li>Stockhom alignment secondary structure annotation</li>
3154 <li>2.2.1 applet had no feature transparency</li>
3155 <li>Number pad keys can be used in cursor mode</li>
3156 <li>Structure Viewer mirror image resolved</li>
3163 <div align="center">
3164 <strong>2.2.1</strong><br> 12/2/07
3169 <li>Non standard characters can be read and displayed
3170 <li>Annotations/Features can be imported/exported to the
3172 <li>Applet allows editing of sequence/annotation/group
3173 name & description
3174 <li>Preference setting to display sequence name in
3176 <li>Annotation file format extended to allow
3177 Sequence_groups to be defined
3178 <li>Default opening of alignment overview panel can be
3179 specified in preferences
3180 <li>PDB residue numbering annotation added to associated
3186 <li>Applet crash under certain Linux OS with Java 1.6
3188 <li>Annotation file export / import bugs fixed
3189 <li>PNG / EPS image output bugs fixed
3195 <div align="center">
3196 <strong>2.2</strong><br> 27/11/06
3201 <li>Multiple views on alignment
3202 <li>Sequence feature editing
3203 <li>"Reload" alignment
3204 <li>"Save" to current filename
3205 <li>Background dependent text colour
3206 <li>Right align sequence ids
3207 <li>User-defined lower case residue colours
3210 <li>Menu item accelerator keys
3211 <li>Control-V pastes to current alignment
3212 <li>Cancel button for DAS Feature Fetching
3213 <li>PCA and PDB Viewers zoom via mouse roller
3214 <li>User-defined sub-tree colours and sub-tree selection
3216 <li>'New Window' button on the 'Output to Text box'
3221 <li>New memory efficient Undo/Redo System
3222 <li>Optimised symbol lookups and conservation/consensus
3224 <li>Region Conservation/Consensus recalculated after
3226 <li>Fixed Remove Empty Columns Bug (empty columns at end
3228 <li>Slowed DAS Feature Fetching for increased robustness.
3230 <li>Made angle brackets in ASCII feature descriptions
3232 <li>Re-instated Zoom function for PCA
3233 <li>Sequence descriptions conserved in web service
3235 <li>UniProt ID discoverer uses any word separated by
3237 <li>WsDbFetch query/result association resolved
3238 <li>Tree leaf to sequence mapping improved
3239 <li>Smooth fonts switch moved to FontChooser dialog box.
3246 <div align="center">
3247 <strong>2.1.1</strong><br> 12/9/06
3252 <li>Copy consensus sequence to clipboard</li>
3257 <li>Image output - rightmost residues are rendered if
3258 sequence id panel has been resized</li>
3259 <li>Image output - all offscreen group boundaries are
3261 <li>Annotation files with sequence references - all
3262 elements in file are relative to sequence position</li>
3263 <li>Mac Applet users can use Alt key for group editing</li>
3269 <div align="center">
3270 <strong>2.1</strong><br> 22/8/06
3275 <li>MAFFT Multiple Alignment in default Web Service list</li>
3276 <li>DAS Feature fetching</li>
3277 <li>Hide sequences and columns</li>
3278 <li>Export Annotations and Features</li>
3279 <li>GFF file reading / writing</li>
3280 <li>Associate structures with sequences from local PDB
3282 <li>Add sequences to exisiting alignment</li>
3283 <li>Recently opened files / URL lists</li>
3284 <li>Applet can launch the full application</li>
3285 <li>Applet has transparency for features (Java 1.2
3287 <li>Applet has user defined colours parameter</li>
3288 <li>Applet can load sequences from parameter
3289 "sequence<em>x</em>"
3295 <li>Redundancy Panel reinstalled in the Applet</li>
3296 <li>Monospaced font - EPS / rescaling bug fixed</li>
3297 <li>Annotation files with sequence references bug fixed</li>
3303 <div align="center">
3304 <strong>2.08.1</strong><br> 2/5/06
3309 <li>Change case of selected region from Popup menu</li>
3310 <li>Choose to match case when searching</li>
3311 <li>Middle mouse button and mouse movement can compress /
3312 expand the visible width and height of the alignment</li>
3317 <li>Annotation Panel displays complete JNet results</li>
3323 <div align="center">
3324 <strong>2.08b</strong><br> 18/4/06
3330 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3331 <li>Righthand label on wrapped alignments shows correct
3338 <div align="center">
3339 <strong>2.08</strong><br> 10/4/06
3344 <li>Editing can be locked to the selection area</li>
3345 <li>Keyboard editing</li>
3346 <li>Create sequence features from searches</li>
3347 <li>Precalculated annotations can be loaded onto
3349 <li>Features file allows grouping of features</li>
3350 <li>Annotation Colouring scheme added</li>
3351 <li>Smooth fonts off by default - Faster rendering</li>
3352 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3357 <li>Drag & Drop fixed on Linux</li>
3358 <li>Jalview Archive file faster to load/save, sequence
3359 descriptions saved.</li>
3365 <div align="center">
3366 <strong>2.07</strong><br> 12/12/05
3371 <li>PDB Structure Viewer enhanced</li>
3372 <li>Sequence Feature retrieval and display enhanced</li>
3373 <li>Choose to output sequence start-end after sequence
3374 name for file output</li>
3375 <li>Sequence Fetcher WSDBFetch@EBI</li>
3376 <li>Applet can read feature files, PDB files and can be
3377 used for HTML form input</li>
3382 <li>HTML output writes groups and features</li>
3383 <li>Group editing is Control and mouse click</li>
3384 <li>File IO bugs</li>
3390 <div align="center">
3391 <strong>2.06</strong><br> 28/9/05
3396 <li>View annotations in wrapped mode</li>
3397 <li>More options for PCA viewer</li>
3402 <li>GUI bugs resolved</li>
3403 <li>Runs with -nodisplay from command line</li>
3409 <div align="center">
3410 <strong>2.05b</strong><br> 15/9/05
3415 <li>Choose EPS export as lineart or text</li>
3416 <li>Jar files are executable</li>
3417 <li>Can read in Uracil - maps to unknown residue</li>
3422 <li>Known OutOfMemory errors give warning message</li>
3423 <li>Overview window calculated more efficiently</li>
3424 <li>Several GUI bugs resolved</li>
3430 <div align="center">
3431 <strong>2.05</strong><br> 30/8/05
3436 <li>Edit and annotate in "Wrapped" view</li>
3441 <li>Several GUI bugs resolved</li>
3447 <div align="center">
3448 <strong>2.04</strong><br> 24/8/05
3453 <li>Hold down mouse wheel & scroll to change font
3459 <li>Improved JPred client reliability</li>
3460 <li>Improved loading of Jalview files</li>
3466 <div align="center">
3467 <strong>2.03</strong><br> 18/8/05
3472 <li>Set Proxy server name and port in preferences</li>
3473 <li>Multiple URL links from sequence ids</li>
3474 <li>User Defined Colours can have a scheme name and added
3476 <li>Choose to ignore gaps in consensus calculation</li>
3477 <li>Unix users can set default web browser</li>
3478 <li>Runs without GUI for batch processing</li>
3479 <li>Dynamically generated Web Service Menus</li>
3484 <li>InstallAnywhere download for Sparc Solaris</li>
3490 <div align="center">
3491 <strong>2.02</strong><br> 18/7/05
3497 <li>Copy & Paste order of sequences maintains
3498 alignment order.</li>
3504 <div align="center">
3505 <strong>2.01</strong><br> 12/7/05
3510 <li>Use delete key for deleting selection.</li>
3511 <li>Use Mouse wheel to scroll sequences.</li>
3512 <li>Help file updated to describe how to add alignment
3514 <li>Version and build date written to build properties
3516 <li>InstallAnywhere installation will check for updates
3517 at launch of Jalview.</li>
3522 <li>Delete gaps bug fixed.</li>
3523 <li>FileChooser sorts columns.</li>
3524 <li>Can remove groups one by one.</li>
3525 <li>Filechooser icons installed.</li>
3526 <li>Finder ignores return character when searching.
3527 Return key will initiate a search.<br>
3534 <div align="center">
3535 <strong>2.0</strong><br> 20/6/05
3540 <li>New codebase</li>