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
90 <td><div align="left">
93 <li><!-- JAL-2728 -->Protein annotation panel too high in CDS/Protein view
99 <td width="60" nowrap>
101 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
102 <em>2/10/2017</em></strong>
105 <td><div align="left">
106 <em>New features in Jalview Desktop</em>
109 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
111 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
115 <td><div align="left">
119 <td width="60" nowrap>
121 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
122 <em>7/9/2017</em></strong>
125 <td><div align="left">
129 <!-- JAL-2588 -->Show gaps in overview window by colouring
130 in grey (sequences used to be coloured grey, and gaps were
134 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
138 <!-- JAL-2587 -->Overview updates immediately on increase
139 in size and progress bar shown as higher resolution
140 overview is recalculated
145 <td><div align="left">
149 <!-- JAL-2664 -->Overview window redraws every hidden
150 column region row by row
153 <!-- JAL-2681 -->duplicate protein sequences shown after
154 retrieving Ensembl crossrefs for sequences from Uniprot
157 <!-- JAL-2603 -->Overview window throws NPE if show boxes
158 format setting is unticked
161 <!-- JAL-2610 -->Groups are coloured wrongly in overview
162 if group has show boxes format setting unticked
165 <!-- JAL-2672,JAL-2665 -->Redraw problems when
166 autoscrolling whilst dragging current selection group to
167 include sequences and columns not currently displayed
170 <!-- JAL-2691 -->Not all chains are mapped when multimeric
171 assemblies are imported via CIF file
174 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
175 displayed when threshold or conservation colouring is also
179 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
183 <!-- JAL-2673 -->Jalview continues to scroll after
184 dragging a selected region off the visible region of the
188 <!-- JAL-2724 -->Cannot apply annotation based
189 colourscheme to all groups in a view
192 <!-- JAL-2511 -->IDs don't line up with sequences
193 initially after font size change using the Font chooser or
200 <td width="60" nowrap>
202 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
205 <td><div align="left">
206 <em>Calculations</em>
210 <!-- JAL-1933 -->Occupancy annotation row shows number of
211 ungapped positions in each column of the alignment.
214 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
215 a calculation dialog box
218 <!-- JAL-2379 -->Revised implementation of PCA for speed
219 and memory efficiency (~30x faster)
222 <!-- JAL-2403 -->Revised implementation of sequence
223 similarity scores as used by Tree, PCA, Shading Consensus
224 and other calculations
227 <!-- JAL-2416 -->Score matrices are stored as resource
228 files within the Jalview codebase
231 <!-- JAL-2500 -->Trees computed on Sequence Feature
232 Similarity may have different topology due to increased
239 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
240 model for alignments and groups
243 <!-- JAL-384 -->Custom shading schemes created via groovy
250 <!-- JAL-2526 -->Efficiency improvements for interacting
251 with alignment and overview windows
254 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
258 <!-- JAL-2388 -->Hidden columns and sequences can be
262 <!-- JAL-2611 -->Click-drag in visible area allows fine
263 adjustment of visible position
267 <em>Data import/export</em>
270 <!-- JAL-2535 -->Posterior probability annotation from
271 Stockholm files imported as sequence associated annotation
274 <!-- JAL-2507 -->More robust per-sequence positional
275 annotation input/output via stockholm flatfile
278 <!-- JAL-2533 -->Sequence names don't include file
279 extension when importing structure files without embedded
280 names or PDB accessions
283 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
284 format sequence substitution matrices
287 <em>User Interface</em>
290 <!-- JAL-2447 --> Experimental Features Checkbox in
291 Desktop's Tools menu to hide or show untested features in
295 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
296 via Overview or sequence motif search operations
299 <!-- JAL-2547 -->Amend sequence features dialog box can be
300 opened by double clicking gaps within sequence feature
304 <!-- JAL-1476 -->Status bar message shown when not enough
305 aligned positions were available to create a 3D structure
309 <em>3D Structure</em>
312 <!-- JAL-2430 -->Hidden regions in alignment views are not
313 coloured in linked structure views
316 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
317 file-based command exchange
320 <!-- JAL-2375 -->Structure chooser automatically shows
321 Cached Structures rather than querying the PDBe if
322 structures are already available for sequences
325 <!-- JAL-2520 -->Structures imported via URL are cached in
326 the Jalview project rather than downloaded again when the
330 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
331 to transfer Chimera's structure attributes as Jalview
332 features, and vice-versa (<strong>Experimental
336 <em>Web Services</em>
339 <!-- JAL-2549 -->Updated JABAWS client to v2.2
342 <!-- JAL-2335 -->Filter non-standard amino acids and
343 nucleotides when submitting to AACon and other MSA
347 <!-- JAL-2316, -->URLs for viewing database
348 cross-references provided by identifiers.org and the
356 <!-- JAL-2344 -->FileFormatI interface for describing and
357 identifying file formats (instead of String constants)
360 <!-- JAL-2228 -->FeatureCounter script refactored for
361 efficiency when counting all displayed features (not
362 backwards compatible with 2.10.1)
365 <em>Example files</em>
368 <!-- JAL-2631 -->Graduated feature colour style example
369 included in the example feature file
372 <em>Documentation</em>
375 <!-- JAL-2339 -->Release notes reformatted for readability
376 with the built-in Java help viewer
379 <!-- JAL-1644 -->Find documentation updated with 'search
380 sequence description' option
386 <!-- JAL-2485, -->External service integration tests for
387 Uniprot REST Free Text Search Client
390 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
393 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
398 <td><div align="left">
399 <em>Calculations</em>
402 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
403 matrix - C->R should be '-3'<br />Old matrix restored
404 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
406 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
407 Jalview's treatment of gaps in PCA and substitution matrix
408 based Tree calculations.<br /> <br />In earlier versions
409 of Jalview, gaps matching gaps were penalised, and gaps
410 matching non-gaps penalised even more. In the PCA
411 calculation, gaps were actually treated as non-gaps - so
412 different costs were applied, which meant Jalview's PCAs
413 were different to those produced by SeqSpace.<br />Jalview
414 now treats gaps in the same way as SeqSpace (ie it scores
415 them as 0). <br /> <br />Enter the following in the
416 Groovy console to restore pre-2.10.2 behaviour:<br />
417 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
418 // for 2.10.1 mode <br />
419 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
420 // to restore 2.10.2 mode <br /> <br /> <em>Note:
421 these settings will affect all subsequent tree and PCA
422 calculations (not recommended)</em></li>
424 <!-- JAL-2424 -->Fixed off-by-one bug that affected
425 scaling of branch lengths for trees computed using
426 Sequence Feature Similarity.
429 <!-- JAL-2377 -->PCA calculation could hang when
430 generating output report when working with highly
434 <!-- JAL-2544 --> Sort by features includes features to
435 right of selected region when gaps present on right-hand
439 <em>User Interface</em>
442 <!-- JAL-2346 -->Reopening Colour by annotation dialog
443 doesn't reselect a specific sequence's associated
444 annotation after it was used for colouring a view
447 <!-- JAL-2419 -->Current selection lost if popup menu
448 opened on a region of alignment without groups
451 <!-- JAL-2374 -->Popup menu not always shown for regions
452 of an alignment with overlapping groups
455 <!-- JAL-2310 -->Finder double counts if both a sequence's
456 name and description match
459 <!-- JAL-2370 -->Hiding column selection containing two
460 hidden regions results in incorrect hidden regions
463 <!-- JAL-2386 -->'Apply to all groups' setting when
464 changing colour does not apply Conservation slider value
468 <!-- JAL-2373 -->Percentage identity and conservation menu
469 items do not show a tick or allow shading to be disabled
472 <!-- JAL-2385 -->Conservation shading or PID threshold
473 lost when base colourscheme changed if slider not visible
476 <!-- JAL-2547 -->Sequence features shown in tooltip for
477 gaps before start of features
480 <!-- JAL-2623 -->Graduated feature colour threshold not
481 restored to UI when feature colour is edited
484 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
485 a time when scrolling vertically in wrapped mode.
488 <!-- JAL-2630 -->Structure and alignment overview update
489 as graduate feature colour settings are modified via the
493 <!-- JAL-2034 -->Overview window doesn't always update
494 when a group defined on the alignment is resized
497 <!-- JAL-2605 -->Mouseovers on left/right scale region in
498 wrapped view result in positional status updates
502 <!-- JAL-2563 -->Status bar doesn't show position for
503 ambiguous amino acid and nucleotide symbols
506 <!-- JAL-2602 -->Copy consensus sequence failed if
507 alignment included gapped columns
510 <!-- JAL-2473 -->Minimum size set for Jalview windows so
511 widgets don't permanently disappear
514 <!-- JAL-2503 -->Cannot select or filter quantitative
515 annotation that are shown only as column labels (e.g.
516 T-Coffee column reliability scores)
519 <!-- JAL-2594 -->Exception thrown if trying to create a
520 sequence feature on gaps only
523 <!-- JAL-2504 -->Features created with 'New feature'
524 button from a Find inherit previously defined feature type
525 rather than the Find query string
528 <!-- JAL-2423 -->incorrect title in output window when
529 exporting tree calculated in Jalview
532 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
533 and then revealing them reorders sequences on the
537 <!-- JAL-964 -->Group panel in sequence feature settings
538 doesn't update to reflect available set of groups after
539 interactively adding or modifying features
542 <!-- JAL-2225 -->Sequence Database chooser unusable on
546 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
547 only excluded gaps in current sequence and ignored
554 <!-- JAL-2421 -->Overview window visible region moves
555 erratically when hidden rows or columns are present
558 <!-- JAL-2362 -->Per-residue colourschemes applied via the
559 Structure Viewer's colour menu don't correspond to
563 <!-- JAL-2405 -->Protein specific colours only offered in
564 colour and group colour menu for protein alignments
567 <!-- JAL-2385 -->Colour threshold slider doesn't update to
568 reflect currently selected view or group's shading
572 <!-- JAL-2624 -->Feature colour thresholds not respected
573 when rendered on overview and structures when opacity at
577 <!-- JAL-2589 -->User defined gap colour not shown in
578 overview when features overlaid on alignment
581 <em>Data import/export</em>
584 <!-- JAL-2576 -->Very large alignments take a long time to
588 <!-- JAL-2507 -->Per-sequence RNA secondary structures
589 added after a sequence was imported are not written to
593 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
594 when importing RNA secondary structure via Stockholm
597 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
598 not shown in correct direction for simple pseudoknots
601 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
602 with lightGray or darkGray via features file (but can
606 <!-- JAL-2383 -->Above PID colour threshold not recovered
607 when alignment view imported from project
610 <!-- JAL-2520,JAL-2465 -->No mappings generated between
611 structure and sequences extracted from structure files
612 imported via URL and viewed in Jmol
615 <!-- JAL-2520 -->Structures loaded via URL are saved in
616 Jalview Projects rather than fetched via URL again when
617 the project is loaded and the structure viewed
620 <em>Web Services</em>
623 <!-- JAL-2519 -->EnsemblGenomes example failing after
624 release of Ensembl v.88
627 <!-- JAL-2366 -->Proxy server address and port always
628 appear enabled in Preferences->Connections
631 <!-- JAL-2461 -->DAS registry not found exceptions
632 removed from console output
635 <!-- JAL-2582 -->Cannot retrieve protein products from
636 Ensembl by Peptide ID
639 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
640 created from SIFTs, and spurious 'Couldn't open structure
641 in Chimera' errors raised after April 2017 update (problem
642 due to 'null' string rather than empty string used for
643 residues with no corresponding PDB mapping).
646 <em>Application UI</em>
649 <!-- JAL-2361 -->User Defined Colours not added to Colour
653 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
654 case' residues (button in colourscheme editor debugged and
655 new documentation and tooltips added)
658 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
659 doesn't restore group-specific text colour thresholds
662 <!-- JAL-2243 -->Feature settings panel does not update as
663 new features are added to alignment
666 <!-- JAL-2532 -->Cancel in feature settings reverts
667 changes to feature colours via the Amend features dialog
670 <!-- JAL-2506 -->Null pointer exception when attempting to
671 edit graduated feature colour via amend features dialog
675 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
676 selection menu changes colours of alignment views
679 <!-- JAL-2426 -->Spurious exceptions in console raised
680 from alignment calculation workers after alignment has
684 <!-- JAL-1608 -->Typo in selection popup menu - Create
685 groups now 'Create Group'
688 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
689 Create/Undefine group doesn't always work
692 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
693 shown again after pressing 'Cancel'
696 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
697 adjusts start position in wrap mode
700 <!-- JAL-2563 -->Status bar doesn't show positions for
701 ambiguous amino acids
704 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
705 CDS/Protein view after CDS sequences added for aligned
709 <!-- JAL-2592 -->User defined colourschemes called 'User
710 Defined' don't appear in Colours menu
716 <!-- JAL-2468 -->Switching between Nucleotide and Protein
717 score models doesn't always result in an updated PCA plot
720 <!-- JAL-2442 -->Features not rendered as transparent on
721 overview or linked structure view
724 <!-- JAL-2372 -->Colour group by conservation doesn't
728 <!-- JAL-2517 -->Hitting Cancel after applying
729 user-defined colourscheme doesn't restore original
736 <!-- JAL-2314 -->Unit test failure:
737 jalview.ws.jabaws.RNAStructExportImport setup fails
740 <!-- JAL-2307 -->Unit test failure:
741 jalview.ws.sifts.SiftsClientTest due to compatibility
742 problems with deep array comparison equality asserts in
743 successive versions of TestNG
746 <!-- JAL-2479 -->Relocated StructureChooserTest and
747 ParameterUtilsTest Unit tests to Network suite
750 <em>New Known Issues</em>
753 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
754 phase after a sequence motif find operation
757 <!-- JAL-2550 -->Importing annotation file with rows
758 containing just upper and lower case letters are
759 interpreted as WUSS RNA secondary structure symbols
762 <!-- JAL-2590 -->Cannot load and display Newick trees
763 reliably from eggnog Ortholog database
766 <!-- JAL-2468 -->Status bar shows 'Marked x columns
767 containing features of type Highlight' when 'B' is pressed
768 to mark columns containing highlighted regions.
771 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
772 doesn't always add secondary structure annotation.
777 <td width="60" nowrap>
779 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
782 <td><div align="left">
786 <!-- JAL-98 -->Improved memory usage: sparse arrays used
787 for all consensus calculations
790 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
793 <li>Updated Jalview's Certum code signing certificate
799 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
800 set of database cross-references, sorted alphabetically
803 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
804 from database cross references. Users with custom links
805 will receive a <a href="webServices/urllinks.html#warning">warning
806 dialog</a> asking them to update their preferences.
809 <!-- JAL-2287-->Cancel button and escape listener on
810 dialog warning user about disconnecting Jalview from a
814 <!-- JAL-2320-->Jalview's Chimera control window closes if
815 the Chimera it is connected to is shut down
818 <!-- JAL-1738-->New keystroke (B) and Select highlighted
819 columns menu item to mark columns containing highlighted
820 regions (e.g. from structure selections or results of a
824 <!-- JAL-2284-->Command line option for batch-generation
825 of HTML pages rendering alignment data with the BioJS
835 <!-- JAL-2286 -->Columns with more than one modal residue
836 are not coloured or thresholded according to percent
837 identity (first observed in Jalview 2.8.2)
840 <!-- JAL-2301 -->Threonine incorrectly reported as not
844 <!-- JAL-2318 -->Updates to documentation pages (above PID
845 threshold, amino acid properties)
848 <!-- JAL-2292 -->Lower case residues in sequences are not
849 reported as mapped to residues in a structure file in the
853 <!--JAL-2324 -->Identical features with non-numeric scores
854 could be added multiple times to a sequence
857 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
858 bond features shown as two highlighted residues rather
859 than a range in linked structure views, and treated
860 correctly when selecting and computing trees from features
863 <!-- JAL-2281-->Custom URL links for database
864 cross-references are matched to database name regardless
872 <!-- JAL-2282-->Custom URL links for specific database
873 names without regular expressions also offer links from
877 <!-- JAL-2315-->Removing a single configured link in the
878 URL links pane in Connections preferences doesn't actually
879 update Jalview configuration
882 <!-- JAL-2272-->CTRL-Click on a selected region to open
883 the alignment area popup menu doesn't work on El-Capitan
886 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
887 files with similarly named sequences if dropped onto the
891 <!-- JAL-2312 -->Additional mappings are shown for PDB
892 entries where more chains exist in the PDB accession than
893 are reported in the SIFTS file
896 <!-- JAL-2317-->Certain structures do not get mapped to
897 the structure view when displayed with Chimera
900 <!-- JAL-2317-->No chains shown in the Chimera view
901 panel's View->Show Chains submenu
904 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
905 work for wrapped alignment views
908 <!--JAL-2197 -->Rename UI components for running JPred
909 predictions from 'JNet' to 'JPred'
912 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
913 corrupted when annotation panel vertical scroll is not at
917 <!--JAL-2332 -->Attempting to view structure for Hen
918 lysozyme results in a PDB Client error dialog box
921 <!-- JAL-2319 -->Structure View's mapping report switched
922 ranges for PDB and sequence for SIFTS
925 SIFTS 'Not_Observed' residues mapped to non-existant
929 <!-- <em>New Known Issues</em>
936 <td width="60" nowrap>
938 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
939 <em>25/10/2016</em></strong>
942 <td><em>Application</em>
944 <li>3D Structure chooser opens with 'Cached structures'
945 view if structures already loaded</li>
946 <li>Progress bar reports models as they are loaded to
953 <li>Colour by conservation always enabled and no tick
954 shown in menu when BLOSUM or PID shading applied</li>
955 <li>FER1_ARATH and FER2_ARATH labels were switched in
956 example sequences/projects/trees</li>
960 <li>Jalview projects with views of local PDB structure
961 files saved on Windows cannot be opened on OSX</li>
962 <li>Multiple structure views can be opened and superposed
963 without timeout for structures with multiple models or
964 multiple sequences in alignment</li>
965 <li>Cannot import or associated local PDB files without a
966 PDB ID HEADER line</li>
967 <li>RMSD is not output in Jmol console when superposition
969 <li>Drag and drop of URL from Browser fails for Linux and
970 OSX versions earlier than El Capitan</li>
971 <li>ENA client ignores invalid content from ENA server</li>
972 <li>Exceptions are not raised in console when ENA client
973 attempts to fetch non-existent IDs via Fetch DB Refs UI
975 <li>Exceptions are not raised in console when a new view
976 is created on the alignment</li>
977 <li>OSX right-click fixed for group selections: CMD-click
978 to insert/remove gaps in groups and CTRL-click to open group
981 <em>Build and deployment</em>
983 <li>URL link checker now copes with multi-line anchor
986 <em>New Known Issues</em>
988 <li>Drag and drop from URL links in browsers do not work
995 <td width="60" nowrap>
997 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1000 <td><em>General</em>
1003 <!-- JAL-2124 -->Updated Spanish translations.
1006 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1007 for importing structure data to Jalview. Enables mmCIF and
1011 <!-- JAL-192 --->Alignment ruler shows positions relative to
1015 <!-- JAL-2202 -->Position/residue shown in status bar when
1016 mousing over sequence associated annotation
1019 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1023 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1024 '()', canonical '[]' and invalid '{}' base pair populations
1028 <!-- JAL-2092 -->Feature settings popup menu options for
1029 showing or hiding columns containing a feature
1032 <!-- JAL-1557 -->Edit selected group by double clicking on
1033 group and sequence associated annotation labels
1036 <!-- JAL-2236 -->Sequence name added to annotation label in
1037 select/hide columns by annotation and colour by annotation
1041 </ul> <em>Application</em>
1044 <!-- JAL-2050-->Automatically hide introns when opening a
1045 gene/transcript view
1048 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1052 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1053 structure mappings with the EMBL-EBI PDBe SIFTS database
1056 <!-- JAL-2079 -->Updated download sites used for Rfam and
1057 Pfam sources to xfam.org
1060 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1063 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1064 over sequences in Jalview
1067 <!-- JAL-2027-->Support for reverse-complement coding
1068 regions in ENA and EMBL
1071 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1072 for record retrieval via ENA rest API
1075 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1079 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1080 groovy script execution
1083 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1084 alignment window's Calculate menu
1087 <!-- JAL-1812 -->Allow groovy scripts that call
1088 Jalview.getAlignFrames() to run in headless mode
1091 <!-- JAL-2068 -->Support for creating new alignment
1092 calculation workers from groovy scripts
1095 <!-- JAL-1369 --->Store/restore reference sequence in
1099 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1100 associations are now saved/restored from project
1103 <!-- JAL-1993 -->Database selection dialog always shown
1104 before sequence fetcher is opened
1107 <!-- JAL-2183 -->Double click on an entry in Jalview's
1108 database chooser opens a sequence fetcher
1111 <!-- JAL-1563 -->Free-text search client for UniProt using
1112 the UniProt REST API
1115 <!-- JAL-2168 -->-nonews command line parameter to prevent
1116 the news reader opening
1119 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1120 querying stored in preferences
1123 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1127 <!-- JAL-1977-->Tooltips shown on database chooser
1130 <!-- JAL-391 -->Reverse complement function in calculate
1131 menu for nucleotide sequences
1134 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1135 and feature counts preserves alignment ordering (and
1136 debugged for complex feature sets).
1139 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1140 viewing structures with Jalview 2.10
1143 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1144 genome, transcript CCDS and gene ids via the Ensembl and
1145 Ensembl Genomes REST API
1148 <!-- JAL-2049 -->Protein sequence variant annotation
1149 computed for 'sequence_variant' annotation on CDS regions
1153 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1157 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1158 Ref Fetcher fails to match, or otherwise updates sequence
1159 data from external database records.
1162 <!-- JAL-2154 -->Revised Jalview Project format for
1163 efficient recovery of sequence coding and alignment
1164 annotation relationships.
1166 </ul> <!-- <em>Applet</em>
1177 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1181 <!-- JAL-2018-->Export features in Jalview format (again)
1182 includes graduated colourschemes
1185 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1186 working with big alignments and lots of hidden columns
1189 <!-- JAL-2053-->Hidden column markers not always rendered
1190 at right of alignment window
1193 <!-- JAL-2067 -->Tidied up links in help file table of
1197 <!-- JAL-2072 -->Feature based tree calculation not shown
1201 <!-- JAL-2075 -->Hidden columns ignored during feature
1202 based tree calculation
1205 <!-- JAL-2065 -->Alignment view stops updating when show
1206 unconserved enabled for group on alignment
1209 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1213 <!-- JAL-2146 -->Alignment column in status incorrectly
1214 shown as "Sequence position" when mousing over
1218 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1219 hidden columns present
1222 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1223 user created annotation added to alignment
1226 <!-- JAL-1841 -->RNA Structure consensus only computed for
1227 '()' base pair annotation
1230 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1231 in zero scores for all base pairs in RNA Structure
1235 <!-- JAL-2174-->Extend selection with columns containing
1239 <!-- JAL-2275 -->Pfam format writer puts extra space at
1240 beginning of sequence
1243 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1247 <!-- JAL-2238 -->Cannot create groups on an alignment from
1248 from a tree when t-coffee scores are shown
1251 <!-- JAL-1836,1967 -->Cannot import and view PDB
1252 structures with chains containing negative resnums (4q4h)
1255 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1259 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1260 to Clustal, PIR and PileUp output
1263 <!-- JAL-2008 -->Reordering sequence features that are
1264 not visible causes alignment window to repaint
1267 <!-- JAL-2006 -->Threshold sliders don't work in
1268 graduated colour and colour by annotation row for e-value
1269 scores associated with features and annotation rows
1272 <!-- JAL-1797 -->amino acid physicochemical conservation
1273 calculation should be case independent
1276 <!-- JAL-2173 -->Remove annotation also updates hidden
1280 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1281 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1282 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1285 <!-- JAL-2065 -->Null pointer exceptions and redraw
1286 problems when reference sequence defined and 'show
1287 non-conserved' enabled
1290 <!-- JAL-1306 -->Quality and Conservation are now shown on
1291 load even when Consensus calculation is disabled
1294 <!-- JAL-1932 -->Remove right on penultimate column of
1295 alignment does nothing
1298 <em>Application</em>
1301 <!-- JAL-1552-->URLs and links can't be imported by
1302 drag'n'drop on OSX when launched via webstart (note - not
1303 yet fixed for El Capitan)
1306 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1307 output when running on non-gb/us i18n platforms
1310 <!-- JAL-1944 -->Error thrown when exporting a view with
1311 hidden sequences as flat-file alignment
1314 <!-- JAL-2030-->InstallAnywhere distribution fails when
1318 <!-- JAL-2080-->Jalview very slow to launch via webstart
1319 (also hotfix for 2.9.0b2)
1322 <!-- JAL-2085 -->Cannot save project when view has a
1323 reference sequence defined
1326 <!-- JAL-1011 -->Columns are suddenly selected in other
1327 alignments and views when revealing hidden columns
1330 <!-- JAL-1989 -->Hide columns not mirrored in complement
1331 view in a cDNA/Protein splitframe
1334 <!-- JAL-1369 -->Cannot save/restore representative
1335 sequence from project when only one sequence is
1339 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1340 in Structure Chooser
1343 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1344 structure consensus didn't refresh annotation panel
1347 <!-- JAL-1962 -->View mapping in structure view shows
1348 mappings between sequence and all chains in a PDB file
1351 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1352 dialogs format columns correctly, don't display array
1353 data, sort columns according to type
1356 <!-- JAL-1975 -->Export complete shown after destination
1357 file chooser is cancelled during an image export
1360 <!-- JAL-2025 -->Error when querying PDB Service with
1361 sequence name containing special characters
1364 <!-- JAL-2024 -->Manual PDB structure querying should be
1368 <!-- JAL-2104 -->Large tooltips with broken HTML
1369 formatting don't wrap
1372 <!-- JAL-1128 -->Figures exported from wrapped view are
1373 truncated so L looks like I in consensus annotation
1376 <!-- JAL-2003 -->Export features should only export the
1377 currently displayed features for the current selection or
1381 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1382 after fetching cross-references, and restoring from
1386 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1387 followed in the structure viewer
1390 <!-- JAL-2163 -->Titles for individual alignments in
1391 splitframe not restored from project
1394 <!-- JAL-2145 -->missing autocalculated annotation at
1395 trailing end of protein alignment in transcript/product
1396 splitview when pad-gaps not enabled by default
1399 <!-- JAL-1797 -->amino acid physicochemical conservation
1403 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1404 article has been read (reopened issue due to
1405 internationalisation problems)
1408 <!-- JAL-1960 -->Only offer PDB structures in structure
1409 viewer based on sequence name, PDB and UniProt
1414 <!-- JAL-1976 -->No progress bar shown during export of
1418 <!-- JAL-2213 -->Structures not always superimposed after
1419 multiple structures are shown for one or more sequences.
1422 <!-- JAL-1370 -->Reference sequence characters should not
1423 be replaced with '.' when 'Show unconserved' format option
1427 <!-- JAL-1823 -->Cannot specify chain code when entering
1428 specific PDB id for sequence
1431 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1432 'Export hidden sequences' is enabled, but 'export hidden
1433 columns' is disabled.
1436 <!--JAL-2026-->Best Quality option in structure chooser
1437 selects lowest rather than highest resolution structures
1441 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1442 to sequence mapping in 'View Mappings' report
1445 <!-- JAL-2284 -->Unable to read old Jalview projects that
1446 contain non-XML data added after Jalvew wrote project.
1449 <!-- JAL-2118 -->Newly created annotation row reorders
1450 after clicking on it to create new annotation for a
1453 <!-- may exclude, this is an external service stability issue JAL-1941
1454 -- > RNA 3D structure not added via DSSR service</li> -->
1459 <!-- JAL-2151 -->Incorrect columns are selected when
1460 hidden columns present before start of sequence
1463 <!-- JAL-1986 -->Missing dependencies on applet pages
1467 <!-- JAL-1947 -->Overview pixel size changes when
1468 sequences are hidden in applet
1471 <!-- JAL-1996 -->Updated instructions for applet
1472 deployment on examples pages.
1479 <td width="60" nowrap>
1480 <div align="center">
1481 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1482 <em>16/10/2015</em></strong>
1485 <td><em>General</em>
1487 <li>Time stamps for signed Jalview application and applet
1492 <em>Application</em>
1494 <li>Duplicate group consensus and conservation rows
1495 shown when tree is partitioned</li>
1496 <li>Erratic behaviour when tree partitions made with
1497 multiple cDNA/Protein split views</li>
1503 <td width="60" nowrap>
1504 <div align="center">
1505 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1506 <em>8/10/2015</em></strong>
1509 <td><em>General</em>
1511 <li>Updated Spanish translations of localized text for
1513 </ul> <em>Application</em>
1515 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1516 <li>Signed OSX InstallAnywhere installer<br></li>
1517 <li>Support for per-sequence based annotations in BioJSON</li>
1518 </ul> <em>Applet</em>
1520 <li>Split frame example added to applet examples page</li>
1521 </ul> <em>Build and Deployment</em>
1524 <!-- JAL-1888 -->New ant target for running Jalview's test
1532 <li>Mapping of cDNA to protein in split frames
1533 incorrect when sequence start > 1</li>
1534 <li>Broken images in filter column by annotation dialog
1536 <li>Feature colours not parsed from features file</li>
1537 <li>Exceptions and incomplete link URLs recovered when
1538 loading a features file containing HTML tags in feature
1542 <em>Application</em>
1544 <li>Annotations corrupted after BioJS export and
1546 <li>Incorrect sequence limits after Fetch DB References
1547 with 'trim retrieved sequences'</li>
1548 <li>Incorrect warning about deleting all data when
1549 deleting selected columns</li>
1550 <li>Patch to build system for shipping properly signed
1551 JNLP templates for webstart launch</li>
1552 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1553 unreleased structures for download or viewing</li>
1554 <li>Tab/space/return keystroke operation of EMBL-PDBe
1555 fetcher/viewer dialogs works correctly</li>
1556 <li>Disabled 'minimise' button on Jalview windows
1557 running on OSX to workaround redraw hang bug</li>
1558 <li>Split cDNA/Protein view position and geometry not
1559 recovered from jalview project</li>
1560 <li>Initial enabled/disabled state of annotation menu
1561 sorter 'show autocalculated first/last' corresponds to
1563 <li>Restoring of Clustal, RNA Helices and T-Coffee
1564 color schemes from BioJSON</li>
1568 <li>Reorder sequences mirrored in cDNA/Protein split
1570 <li>Applet with Jmol examples not loading correctly</li>
1576 <td><div align="center">
1577 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1579 <td><em>General</em>
1581 <li>Linked visualisation and analysis of DNA and Protein
1584 <li>Translated cDNA alignments shown as split protein
1585 and DNA alignment views</li>
1586 <li>Codon consensus annotation for linked protein and
1587 cDNA alignment views</li>
1588 <li>Link cDNA or Protein product sequences by loading
1589 them onto Protein or cDNA alignments</li>
1590 <li>Reconstruct linked cDNA alignment from aligned
1591 protein sequences</li>
1594 <li>Jmol integration updated to Jmol v14.2.14</li>
1595 <li>Import and export of Jalview alignment views as <a
1596 href="features/bioJsonFormat.html">BioJSON</a></li>
1597 <li>New alignment annotation file statements for
1598 reference sequences and marking hidden columns</li>
1599 <li>Reference sequence based alignment shading to
1600 highlight variation</li>
1601 <li>Select or hide columns according to alignment
1603 <li>Find option for locating sequences by description</li>
1604 <li>Conserved physicochemical properties shown in amino
1605 acid conservation row</li>
1606 <li>Alignments can be sorted by number of RNA helices</li>
1607 </ul> <em>Application</em>
1609 <li>New cDNA/Protein analysis capabilities
1611 <li>Get Cross-References should open a Split Frame
1612 view with cDNA/Protein</li>
1613 <li>Detect when nucleotide sequences and protein
1614 sequences are placed in the same alignment</li>
1615 <li>Split cDNA/Protein views are saved in Jalview
1620 <li>Use REST API to talk to Chimera</li>
1621 <li>Selected regions in Chimera are highlighted in linked
1622 Jalview windows</li>
1624 <li>VARNA RNA viewer updated to v3.93</li>
1625 <li>VARNA views are saved in Jalview Projects</li>
1626 <li>Pseudoknots displayed as Jalview RNA annotation can
1627 be shown in VARNA</li>
1629 <li>Make groups for selection uses marked columns as well
1630 as the active selected region</li>
1632 <li>Calculate UPGMA and NJ trees using sequence feature
1634 <li>New Export options
1636 <li>New Export Settings dialog to control hidden
1637 region export in flat file generation</li>
1639 <li>Export alignment views for display with the <a
1640 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1642 <li>Export scrollable SVG in HTML page</li>
1643 <li>Optional embedding of BioJSON data when exporting
1644 alignment figures to HTML</li>
1646 <li>3D structure retrieval and display
1648 <li>Free text and structured queries with the PDBe
1650 <li>PDBe Search API based discovery and selection of
1651 PDB structures for a sequence set</li>
1655 <li>JPred4 employed for protein secondary structure
1657 <li>Hide Insertions menu option to hide unaligned columns
1658 for one or a group of sequences</li>
1659 <li>Automatically hide insertions in alignments imported
1660 from the JPred4 web server</li>
1661 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1662 system on OSX<br />LGPL libraries courtesy of <a
1663 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1665 <li>changed 'View nucleotide structure' submenu to 'View
1666 VARNA 2D Structure'</li>
1667 <li>change "View protein structure" menu option to "3D
1670 </ul> <em>Applet</em>
1672 <li>New layout for applet example pages</li>
1673 <li>New parameters to enable SplitFrame view
1674 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1675 <li>New example demonstrating linked viewing of cDNA and
1676 Protein alignments</li>
1677 </ul> <em>Development and deployment</em>
1679 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1680 <li>Include installation type and git revision in build
1681 properties and console log output</li>
1682 <li>Jalview Github organisation, and new github site for
1683 storing BioJsMSA Templates</li>
1684 <li>Jalview's unit tests now managed with TestNG</li>
1687 <!-- <em>General</em>
1689 </ul> --> <!-- issues resolved --> <em>Application</em>
1691 <li>Escape should close any open find dialogs</li>
1692 <li>Typo in select-by-features status report</li>
1693 <li>Consensus RNA secondary secondary structure
1694 predictions are not highlighted in amber</li>
1695 <li>Missing gap character in v2.7 example file means
1696 alignment appears unaligned when pad-gaps is not enabled</li>
1697 <li>First switch to RNA Helices colouring doesn't colour
1698 associated structure views</li>
1699 <li>ID width preference option is greyed out when auto
1700 width checkbox not enabled</li>
1701 <li>Stopped a warning dialog from being shown when
1702 creating user defined colours</li>
1703 <li>'View Mapping' in structure viewer shows sequence
1704 mappings for just that viewer's sequences</li>
1705 <li>Workaround for superposing PDB files containing
1706 multiple models in Chimera</li>
1707 <li>Report sequence position in status bar when hovering
1708 over Jmol structure</li>
1709 <li>Cannot output gaps as '.' symbols with Selection ->
1710 output to text box</li>
1711 <li>Flat file exports of alignments with hidden columns
1712 have incorrect sequence start/end</li>
1713 <li>'Aligning' a second chain to a Chimera structure from
1715 <li>Colour schemes applied to structure viewers don't
1716 work for nucleotide</li>
1717 <li>Loading/cut'n'pasting an empty or invalid file leads
1718 to a grey/invisible alignment window</li>
1719 <li>Exported Jpred annotation from a sequence region
1720 imports to different position</li>
1721 <li>Space at beginning of sequence feature tooltips shown
1722 on some platforms</li>
1723 <li>Chimera viewer 'View | Show Chain' menu is not
1725 <li>'New View' fails with a Null Pointer Exception in
1726 console if Chimera has been opened</li>
1727 <li>Mouseover to Chimera not working</li>
1728 <li>Miscellaneous ENA XML feature qualifiers not
1730 <li>NPE in annotation renderer after 'Extract Scores'</li>
1731 <li>If two structures in one Chimera window, mouseover of
1732 either sequence shows on first structure</li>
1733 <li>'Show annotations' options should not make
1734 non-positional annotations visible</li>
1735 <li>Subsequence secondary structure annotation not shown
1736 in right place after 'view flanking regions'</li>
1737 <li>File Save As type unset when current file format is
1739 <li>Save as '.jar' option removed for saving Jalview
1741 <li>Colour by Sequence colouring in Chimera more
1743 <li>Cannot 'add reference annotation' for a sequence in
1744 several views on same alignment</li>
1745 <li>Cannot show linked products for EMBL / ENA records</li>
1746 <li>Jalview's tooltip wraps long texts containing no
1748 </ul> <em>Applet</em>
1750 <li>Jmol to JalviewLite mouseover/link not working</li>
1751 <li>JalviewLite can't import sequences with ID
1752 descriptions containing angle brackets</li>
1753 </ul> <em>General</em>
1755 <li>Cannot export and reimport RNA secondary structure
1756 via jalview annotation file</li>
1757 <li>Random helix colour palette for colour by annotation
1758 with RNA secondary structure</li>
1759 <li>Mouseover to cDNA from STOP residue in protein
1760 translation doesn't work.</li>
1761 <li>hints when using the select by annotation dialog box</li>
1762 <li>Jmol alignment incorrect if PDB file has alternate CA
1764 <li>FontChooser message dialog appears to hang after
1765 choosing 1pt font</li>
1766 <li>Peptide secondary structure incorrectly imported from
1767 annotation file when annotation display text includes 'e' or
1769 <li>Cannot set colour of new feature type whilst creating
1771 <li>cDNA translation alignment should not be sequence
1772 order dependent</li>
1773 <li>'Show unconserved' doesn't work for lower case
1775 <li>Nucleotide ambiguity codes involving R not recognised</li>
1776 </ul> <em>Deployment and Documentation</em>
1778 <li>Applet example pages appear different to the rest of
1779 www.jalview.org</li>
1780 </ul> <em>Application Known issues</em>
1782 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1783 <li>Misleading message appears after trying to delete
1785 <li>Jalview icon not shown in dock after InstallAnywhere
1786 version launches</li>
1787 <li>Fetching EMBL reference for an RNA sequence results
1788 fails with a sequence mismatch</li>
1789 <li>Corrupted or unreadable alignment display when
1790 scrolling alignment to right</li>
1791 <li>ArrayIndexOutOfBoundsException thrown when remove
1792 empty columns called on alignment with ragged gapped ends</li>
1793 <li>auto calculated alignment annotation rows do not get
1794 placed above or below non-autocalculated rows</li>
1795 <li>Jalview dekstop becomes sluggish at full screen in
1796 ultra-high resolution</li>
1797 <li>Cannot disable consensus calculation independently of
1798 quality and conservation</li>
1799 <li>Mouseover highlighting between cDNA and protein can
1800 become sluggish with more than one splitframe shown</li>
1801 </ul> <em>Applet Known Issues</em>
1803 <li>Core PDB parsing code requires Jmol</li>
1804 <li>Sequence canvas panel goes white when alignment
1805 window is being resized</li>
1811 <td><div align="center">
1812 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1814 <td><em>General</em>
1816 <li>Updated Java code signing certificate donated by
1818 <li>Features and annotation preserved when performing
1819 pairwise alignment</li>
1820 <li>RNA pseudoknot annotation can be
1821 imported/exported/displayed</li>
1822 <li>'colour by annotation' can colour by RNA and
1823 protein secondary structure</li>
1824 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1825 post-hoc with 2.9 release</em>)
1828 </ul> <em>Application</em>
1830 <li>Extract and display secondary structure for sequences
1831 with 3D structures</li>
1832 <li>Support for parsing RNAML</li>
1833 <li>Annotations menu for layout
1835 <li>sort sequence annotation rows by alignment</li>
1836 <li>place sequence annotation above/below alignment
1839 <li>Output in Stockholm format</li>
1840 <li>Internationalisation: improved Spanish (es)
1842 <li>Structure viewer preferences tab</li>
1843 <li>Disorder and Secondary Structure annotation tracks
1844 shared between alignments</li>
1845 <li>UCSF Chimera launch and linked highlighting from
1847 <li>Show/hide all sequence associated annotation rows for
1848 all or current selection</li>
1849 <li>disorder and secondary structure predictions
1850 available as dataset annotation</li>
1851 <li>Per-sequence rna helices colouring</li>
1854 <li>Sequence database accessions imported when fetching
1855 alignments from Rfam</li>
1856 <li>update VARNA version to 3.91</li>
1858 <li>New groovy scripts for exporting aligned positions,
1859 conservation values, and calculating sum of pairs scores.</li>
1860 <li>Command line argument to set default JABAWS server</li>
1861 <li>include installation type in build properties and
1862 console log output</li>
1863 <li>Updated Jalview project format to preserve dataset
1867 <!-- issues resolved --> <em>Application</em>
1869 <li>Distinguish alignment and sequence associated RNA
1870 structure in structure->view->VARNA</li>
1871 <li>Raise dialog box if user deletes all sequences in an
1873 <li>Pressing F1 results in documentation opening twice</li>
1874 <li>Sequence feature tooltip is wrapped</li>
1875 <li>Double click on sequence associated annotation
1876 selects only first column</li>
1877 <li>Redundancy removal doesn't result in unlinked
1878 leaves shown in tree</li>
1879 <li>Undos after several redundancy removals don't undo
1881 <li>Hide sequence doesn't hide associated annotation</li>
1882 <li>User defined colours dialog box too big to fit on
1883 screen and buttons not visible</li>
1884 <li>author list isn't updated if already written to
1885 Jalview properties</li>
1886 <li>Popup menu won't open after retrieving sequence
1888 <li>File open window for associate PDB doesn't open</li>
1889 <li>Left-then-right click on a sequence id opens a
1890 browser search window</li>
1891 <li>Cannot open sequence feature shading/sort popup menu
1892 in feature settings dialog</li>
1893 <li>better tooltip placement for some areas of Jalview
1895 <li>Allow addition of JABAWS Server which doesn't
1896 pass validation</li>
1897 <li>Web services parameters dialog box is too large to
1899 <li>Muscle nucleotide alignment preset obscured by
1901 <li>JABAWS preset submenus don't contain newly
1902 defined user preset</li>
1903 <li>MSA web services warns user if they were launched
1904 with invalid input</li>
1905 <li>Jalview cannot contact DAS Registy when running on
1908 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1909 'Superpose with' submenu not shown when new view
1913 </ul> <!-- <em>Applet</em>
1915 </ul> <em>General</em>
1917 </ul>--> <em>Deployment and Documentation</em>
1919 <li>2G and 1G options in launchApp have no effect on
1920 memory allocation</li>
1921 <li>launchApp service doesn't automatically open
1922 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1924 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1925 InstallAnywhere reports cannot find valid JVM when Java
1926 1.7_055 is available
1928 </ul> <em>Application Known issues</em>
1931 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1932 corrupted or unreadable alignment display when scrolling
1936 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1937 retrieval fails but progress bar continues for DAS retrieval
1938 with large number of ID
1941 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1942 flatfile output of visible region has incorrect sequence
1946 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1947 rna structure consensus doesn't update when secondary
1948 structure tracks are rearranged
1951 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1952 invalid rna structure positional highlighting does not
1953 highlight position of invalid base pairs
1956 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1957 out of memory errors are not raised when saving Jalview
1958 project from alignment window file menu
1961 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1962 Switching to RNA Helices colouring doesn't propagate to
1966 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1967 colour by RNA Helices not enabled when user created
1968 annotation added to alignment
1971 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1972 Jalview icon not shown on dock in Mountain Lion/Webstart
1974 </ul> <em>Applet Known Issues</em>
1977 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1978 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1981 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1982 Jalview and Jmol example not compatible with IE9
1985 <li>Sort by annotation score doesn't reverse order
1991 <td><div align="center">
1992 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1995 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1998 <li>Internationalisation of user interface (usually
1999 called i18n support) and translation for Spanish locale</li>
2000 <li>Define/Undefine group on current selection with
2001 Ctrl-G/Shift Ctrl-G</li>
2002 <li>Improved group creation/removal options in
2003 alignment/sequence Popup menu</li>
2004 <li>Sensible precision for symbol distribution
2005 percentages shown in logo tooltip.</li>
2006 <li>Annotation panel height set according to amount of
2007 annotation when alignment first opened</li>
2008 </ul> <em>Application</em>
2010 <li>Interactive consensus RNA secondary structure
2011 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2012 <li>Select columns containing particular features from
2013 Feature Settings dialog</li>
2014 <li>View all 'representative' PDB structures for selected
2016 <li>Update Jalview project format:
2018 <li>New file extension for Jalview projects '.jvp'</li>
2019 <li>Preserve sequence and annotation dataset (to
2020 store secondary structure annotation,etc)</li>
2021 <li>Per group and alignment annotation and RNA helix
2025 <li>New similarity measures for PCA and Tree calculation
2027 <li>Experimental support for retrieval and viewing of
2028 flanking regions for an alignment</li>
2032 <!-- issues resolved --> <em>Application</em>
2034 <li>logo keeps spinning and status remains at queued or
2035 running after job is cancelled</li>
2036 <li>cannot export features from alignments imported from
2037 Jalview/VAMSAS projects</li>
2038 <li>Buggy slider for web service parameters that take
2040 <li>Newly created RNA secondary structure line doesn't
2041 have 'display all symbols' flag set</li>
2042 <li>T-COFFEE alignment score shading scheme and other
2043 annotation shading not saved in Jalview project</li>
2044 <li>Local file cannot be loaded in freshly downloaded
2046 <li>Jalview icon not shown on dock in Mountain
2048 <li>Load file from desktop file browser fails</li>
2049 <li>Occasional NPE thrown when calculating large trees</li>
2050 <li>Cannot reorder or slide sequences after dragging an
2051 alignment onto desktop</li>
2052 <li>Colour by annotation dialog throws NPE after using
2053 'extract scores' function</li>
2054 <li>Loading/cut'n'pasting an empty file leads to a grey
2055 alignment window</li>
2056 <li>Disorder thresholds rendered incorrectly after
2057 performing IUPred disorder prediction</li>
2058 <li>Multiple group annotated consensus rows shown when
2059 changing 'normalise logo' display setting</li>
2060 <li>Find shows blank dialog after 'finished searching' if
2061 nothing matches query</li>
2062 <li>Null Pointer Exceptions raised when sorting by
2063 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2065 <li>Errors in Jmol console when structures in alignment
2066 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2068 <li>Not all working JABAWS services are shown in
2070 <li>JAVAWS version of Jalview fails to launch with
2071 'invalid literal/length code'</li>
2072 <li>Annotation/RNA Helix colourschemes cannot be applied
2073 to alignment with groups (actually fixed in 2.8.0b1)</li>
2074 <li>RNA Helices and T-Coffee Scores available as default
2077 </ul> <em>Applet</em>
2079 <li>Remove group option is shown even when selection is
2081 <li>Apply to all groups ticked but colourscheme changes
2082 don't affect groups</li>
2083 <li>Documented RNA Helices and T-Coffee Scores as valid
2084 colourscheme name</li>
2085 <li>Annotation labels drawn on sequence IDs when
2086 Annotation panel is not displayed</li>
2087 <li>Increased font size for dropdown menus on OSX and
2088 embedded windows</li>
2089 </ul> <em>Other</em>
2091 <li>Consensus sequence for alignments/groups with a
2092 single sequence were not calculated</li>
2093 <li>annotation files that contain only groups imported as
2094 annotation and junk sequences</li>
2095 <li>Fasta files with sequences containing '*' incorrectly
2096 recognised as PFAM or BLC</li>
2097 <li>conservation/PID slider apply all groups option
2098 doesn't affect background (2.8.0b1)
2100 <li>redundancy highlighting is erratic at 0% and 100%</li>
2101 <li>Remove gapped columns fails for sequences with ragged
2103 <li>AMSA annotation row with leading spaces is not
2104 registered correctly on import</li>
2105 <li>Jalview crashes when selecting PCA analysis for
2106 certain alignments</li>
2107 <li>Opening the colour by annotation dialog for an
2108 existing annotation based 'use original colours'
2109 colourscheme loses original colours setting</li>
2114 <td><div align="center">
2115 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2116 <em>30/1/2014</em></strong>
2120 <li>Trusted certificates for JalviewLite applet and
2121 Jalview Desktop application<br />Certificate was donated by
2122 <a href="https://www.certum.eu">Certum</a> to the Jalview
2123 open source project).
2125 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2126 <li>Output in Stockholm format</li>
2127 <li>Allow import of data from gzipped files</li>
2128 <li>Export/import group and sequence associated line
2129 graph thresholds</li>
2130 <li>Nucleotide substitution matrix that supports RNA and
2131 ambiguity codes</li>
2132 <li>Allow disorder predictions to be made on the current
2133 selection (or visible selection) in the same way that JPred
2135 <li>Groovy scripting for headless Jalview operation</li>
2136 </ul> <em>Other improvements</em>
2138 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2139 <li>COMBINE statement uses current SEQUENCE_REF and
2140 GROUP_REF scope to group annotation rows</li>
2141 <li>Support '' style escaping of quotes in Newick
2143 <li>Group options for JABAWS service by command line name</li>
2144 <li>Empty tooltip shown for JABA service options with a
2145 link but no description</li>
2146 <li>Select primary source when selecting authority in
2147 database fetcher GUI</li>
2148 <li>Add .mfa to FASTA file extensions recognised by
2150 <li>Annotation label tooltip text wrap</li>
2155 <li>Slow scrolling when lots of annotation rows are
2157 <li>Lots of NPE (and slowness) after creating RNA
2158 secondary structure annotation line</li>
2159 <li>Sequence database accessions not imported when
2160 fetching alignments from Rfam</li>
2161 <li>Incorrect SHMR submission for sequences with
2163 <li>View all structures does not always superpose
2165 <li>Option widgets in service parameters not updated to
2166 reflect user or preset settings</li>
2167 <li>Null pointer exceptions for some services without
2168 presets or adjustable parameters</li>
2169 <li>Discover PDB IDs entry in structure menu doesn't
2170 discover PDB xRefs</li>
2171 <li>Exception encountered while trying to retrieve
2172 features with DAS</li>
2173 <li>Lowest value in annotation row isn't coloured
2174 when colour by annotation (per sequence) is coloured</li>
2175 <li>Keyboard mode P jumps to start of gapped region when
2176 residue follows a gap</li>
2177 <li>Jalview appears to hang importing an alignment with
2178 Wrap as default or after enabling Wrap</li>
2179 <li>'Right click to add annotations' message
2180 shown in wrap mode when no annotations present</li>
2181 <li>Disorder predictions fail with NPE if no automatic
2182 annotation already exists on alignment</li>
2183 <li>oninit javascript function should be called after
2184 initialisation completes</li>
2185 <li>Remove redundancy after disorder prediction corrupts
2186 alignment window display</li>
2187 <li>Example annotation file in documentation is invalid</li>
2188 <li>Grouped line graph annotation rows are not exported
2189 to annotation file</li>
2190 <li>Multi-harmony analysis cannot be run when only two
2192 <li>Cannot create multiple groups of line graphs with
2193 several 'combine' statements in annotation file</li>
2194 <li>Pressing return several times causes Number Format
2195 exceptions in keyboard mode</li>
2196 <li>Multi-harmony (SHMMR) method doesn't submit
2197 correct partitions for input data</li>
2198 <li>Translation from DNA to Amino Acids fails</li>
2199 <li>Jalview fail to load newick tree with quoted label</li>
2200 <li>--headless flag isn't understood</li>
2201 <li>ClassCastException when generating EPS in headless
2203 <li>Adjusting sequence-associated shading threshold only
2204 changes one row's threshold</li>
2205 <li>Preferences and Feature settings panel panel
2206 doesn't open</li>
2207 <li>hide consensus histogram also hides conservation and
2208 quality histograms</li>
2213 <td><div align="center">
2214 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2216 <td><em>Application</em>
2218 <li>Support for JABAWS 2.0 Services (AACon alignment
2219 conservation, protein disorder and Clustal Omega)</li>
2220 <li>JABAWS server status indicator in Web Services
2222 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2223 in Jalview alignment window</li>
2224 <li>Updated Jalview build and deploy framework for OSX
2225 mountain lion, windows 7, and 8</li>
2226 <li>Nucleotide substitution matrix for PCA that supports
2227 RNA and ambiguity codes</li>
2229 <li>Improved sequence database retrieval GUI</li>
2230 <li>Support fetching and database reference look up
2231 against multiple DAS sources (Fetch all from in 'fetch db
2233 <li>Jalview project improvements
2235 <li>Store and retrieve the 'belowAlignment'
2236 flag for annotation</li>
2237 <li>calcId attribute to group annotation rows on the
2239 <li>Store AACon calculation settings for a view in
2240 Jalview project</li>
2244 <li>horizontal scrolling gesture support</li>
2245 <li>Visual progress indicator when PCA calculation is
2247 <li>Simpler JABA web services menus</li>
2248 <li>visual indication that web service results are still
2249 being retrieved from server</li>
2250 <li>Serialise the dialogs that are shown when Jalview
2251 starts up for first time</li>
2252 <li>Jalview user agent string for interacting with HTTP
2254 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2256 <li>Examples directory and Groovy library included in
2257 InstallAnywhere distribution</li>
2258 </ul> <em>Applet</em>
2260 <li>RNA alignment and secondary structure annotation
2261 visualization applet example</li>
2262 </ul> <em>General</em>
2264 <li>Normalise option for consensus sequence logo</li>
2265 <li>Reset button in PCA window to return dimensions to
2267 <li>Allow seqspace or Jalview variant of alignment PCA
2269 <li>PCA with either nucleic acid and protein substitution
2271 <li>Allow windows containing HTML reports to be exported
2273 <li>Interactive display and editing of RNA secondary
2274 structure contacts</li>
2275 <li>RNA Helix Alignment Colouring</li>
2276 <li>RNA base pair logo consensus</li>
2277 <li>Parse sequence associated secondary structure
2278 information in Stockholm files</li>
2279 <li>HTML Export database accessions and annotation
2280 information presented in tooltip for sequences</li>
2281 <li>Import secondary structure from LOCARNA clustalw
2282 style RNA alignment files</li>
2283 <li>import and visualise T-COFFEE quality scores for an
2285 <li>'colour by annotation' per sequence option to
2286 shade each sequence according to its associated alignment
2288 <li>New Jalview Logo</li>
2289 </ul> <em>Documentation and Development</em>
2291 <li>documentation for score matrices used in Jalview</li>
2292 <li>New Website!</li>
2294 <td><em>Application</em>
2296 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2297 wsdbfetch REST service</li>
2298 <li>Stop windows being moved outside desktop on OSX</li>
2299 <li>Filetype associations not installed for webstart
2301 <li>Jalview does not always retrieve progress of a JABAWS
2302 job execution in full once it is complete</li>
2303 <li>revise SHMR RSBS definition to ensure alignment is
2304 uploaded via ali_file parameter</li>
2305 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2306 <li>View all structures superposed fails with exception</li>
2307 <li>Jnet job queues forever if a very short sequence is
2308 submitted for prediction</li>
2309 <li>Cut and paste menu not opened when mouse clicked on
2311 <li>Putting fractional value into integer text box in
2312 alignment parameter dialog causes Jalview to hang</li>
2313 <li>Structure view highlighting doesn't work on
2315 <li>View all structures fails with exception shown in
2317 <li>Characters in filename associated with PDBEntry not
2318 escaped in a platform independent way</li>
2319 <li>Jalview desktop fails to launch with exception when
2321 <li>Tree calculation reports 'you must have 2 or more
2322 sequences selected' when selection is empty</li>
2323 <li>Jalview desktop fails to launch with jar signature
2324 failure when java web start temporary file caching is
2326 <li>DAS Sequence retrieval with range qualification
2327 results in sequence xref which includes range qualification</li>
2328 <li>Errors during processing of command line arguments
2329 cause progress bar (JAL-898) to be removed</li>
2330 <li>Replace comma for semi-colon option not disabled for
2331 DAS sources in sequence fetcher</li>
2332 <li>Cannot close news reader when JABAWS server warning
2333 dialog is shown</li>
2334 <li>Option widgets not updated to reflect user settings</li>
2335 <li>Edited sequence not submitted to web service</li>
2336 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2337 <li>InstallAnywhere installer doesn't unpack and run
2338 on OSX Mountain Lion</li>
2339 <li>Annotation panel not given a scroll bar when
2340 sequences with alignment annotation are pasted into the
2342 <li>Sequence associated annotation rows not associated
2343 when loaded from Jalview project</li>
2344 <li>Browser launch fails with NPE on java 1.7</li>
2345 <li>JABAWS alignment marked as finished when job was
2346 cancelled or job failed due to invalid input</li>
2347 <li>NPE with v2.7 example when clicking on Tree
2348 associated with all views</li>
2349 <li>Exceptions when copy/paste sequences with grouped
2350 annotation rows to new window</li>
2351 </ul> <em>Applet</em>
2353 <li>Sequence features are momentarily displayed before
2354 they are hidden using hidefeaturegroups applet parameter</li>
2355 <li>loading features via javascript API automatically
2356 enables feature display</li>
2357 <li>scrollToColumnIn javascript API method doesn't
2359 </ul> <em>General</em>
2361 <li>Redundancy removal fails for rna alignment</li>
2362 <li>PCA calculation fails when sequence has been selected
2363 and then deselected</li>
2364 <li>PCA window shows grey box when first opened on OSX</li>
2365 <li>Letters coloured pink in sequence logo when alignment
2366 coloured with clustalx</li>
2367 <li>Choosing fonts without letter symbols defined causes
2368 exceptions and redraw errors</li>
2369 <li>Initial PCA plot view is not same as manually
2370 reconfigured view</li>
2371 <li>Grouped annotation graph label has incorrect line
2373 <li>Grouped annotation graph label display is corrupted
2374 for lots of labels</li>
2379 <div align="center">
2380 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2383 <td><em>Application</em>
2385 <li>Jalview Desktop News Reader</li>
2386 <li>Tweaked default layout of web services menu</li>
2387 <li>View/alignment association menu to enable user to
2388 easily specify which alignment a multi-structure view takes
2389 its colours/correspondences from</li>
2390 <li>Allow properties file location to be specified as URL</li>
2391 <li>Extend Jalview project to preserve associations
2392 between many alignment views and a single Jmol display</li>
2393 <li>Store annotation row height in Jalview project file</li>
2394 <li>Annotation row column label formatting attributes
2395 stored in project file</li>
2396 <li>Annotation row order for auto-calculated annotation
2397 rows preserved in Jalview project file</li>
2398 <li>Visual progress indication when Jalview state is
2399 saved using Desktop window menu</li>
2400 <li>Visual indication that command line arguments are
2401 still being processed</li>
2402 <li>Groovy script execution from URL</li>
2403 <li>Colour by annotation default min and max colours in
2405 <li>Automatically associate PDB files dragged onto an
2406 alignment with sequences that have high similarity and
2408 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2409 <li>'view structures' option to open many
2410 structures in same window</li>
2411 <li>Sort associated views menu option for tree panel</li>
2412 <li>Group all JABA and non-JABA services for a particular
2413 analysis function in its own submenu</li>
2414 </ul> <em>Applet</em>
2416 <li>Userdefined and autogenerated annotation rows for
2418 <li>Adjustment of alignment annotation pane height</li>
2419 <li>Annotation scrollbar for annotation panel</li>
2420 <li>Drag to reorder annotation rows in annotation panel</li>
2421 <li>'automaticScrolling' parameter</li>
2422 <li>Allow sequences with partial ID string matches to be
2423 annotated from GFF/Jalview features files</li>
2424 <li>Sequence logo annotation row in applet</li>
2425 <li>Absolute paths relative to host server in applet
2426 parameters are treated as such</li>
2427 <li>New in the JalviewLite javascript API:
2429 <li>JalviewLite.js javascript library</li>
2430 <li>Javascript callbacks for
2432 <li>Applet initialisation</li>
2433 <li>Sequence/alignment mouse-overs and selections</li>
2436 <li>scrollTo row and column alignment scrolling
2438 <li>Select sequence/alignment regions from javascript</li>
2439 <li>javascript structure viewer harness to pass
2440 messages between Jmol and Jalview when running as
2441 distinct applets</li>
2442 <li>sortBy method</li>
2443 <li>Set of applet and application examples shipped
2444 with documentation</li>
2445 <li>New example to demonstrate JalviewLite and Jmol
2446 javascript message exchange</li>
2448 </ul> <em>General</em>
2450 <li>Enable Jmol displays to be associated with multiple
2451 multiple alignments</li>
2452 <li>Option to automatically sort alignment with new tree</li>
2453 <li>User configurable link to enable redirects to a
2454 www.Jalview.org mirror</li>
2455 <li>Jmol colours option for Jmol displays</li>
2456 <li>Configurable newline string when writing alignment
2457 and other flat files</li>
2458 <li>Allow alignment annotation description lines to
2459 contain html tags</li>
2460 </ul> <em>Documentation and Development</em>
2462 <li>Add groovy test harness for bulk load testing to
2464 <li>Groovy script to load and align a set of sequences
2465 using a web service before displaying the result in the
2466 Jalview desktop</li>
2467 <li>Restructured javascript and applet api documentation</li>
2468 <li>Ant target to publish example html files with applet
2470 <li>Netbeans project for building Jalview from source</li>
2471 <li>ant task to create online javadoc for Jalview source</li>
2473 <td><em>Application</em>
2475 <li>User defined colourscheme throws exception when
2476 current built in colourscheme is saved as new scheme</li>
2477 <li>AlignFrame->Save in application pops up save
2478 dialog for valid filename/format</li>
2479 <li>Cannot view associated structure for UniProt sequence</li>
2480 <li>PDB file association breaks for UniProt sequence
2482 <li>Associate PDB from file dialog does not tell you
2483 which sequence is to be associated with the file</li>
2484 <li>Find All raises null pointer exception when query
2485 only matches sequence IDs</li>
2486 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2487 <li>Jalview project with Jmol views created with Jalview
2488 2.4 cannot be loaded</li>
2489 <li>Filetype associations not installed for webstart
2491 <li>Two or more chains in a single PDB file associated
2492 with sequences in different alignments do not get coloured
2493 by their associated sequence</li>
2494 <li>Visibility status of autocalculated annotation row
2495 not preserved when project is loaded</li>
2496 <li>Annotation row height and visibility attributes not
2497 stored in Jalview project</li>
2498 <li>Tree bootstraps are not preserved when saved as a
2499 Jalview project</li>
2500 <li>Envision2 workflow tooltips are corrupted</li>
2501 <li>Enabling show group conservation also enables colour
2502 by conservation</li>
2503 <li>Duplicate group associated conservation or consensus
2504 created on new view</li>
2505 <li>Annotation scrollbar not displayed after 'show
2506 all hidden annotation rows' option selected</li>
2507 <li>Alignment quality not updated after alignment
2508 annotation row is hidden then shown</li>
2509 <li>Preserve colouring of structures coloured by
2510 sequences in pre Jalview 2.7 projects</li>
2511 <li>Web service job parameter dialog is not laid out
2513 <li>Web services menu not refreshed after 'reset
2514 services' button is pressed in preferences</li>
2515 <li>Annotation off by one in Jalview v2_3 example project</li>
2516 <li>Structures imported from file and saved in project
2517 get name like jalview_pdb1234.txt when reloaded</li>
2518 <li>Jalview does not always retrieve progress of a JABAWS
2519 job execution in full once it is complete</li>
2520 </ul> <em>Applet</em>
2522 <li>Alignment height set incorrectly when lots of
2523 annotation rows are displayed</li>
2524 <li>Relative URLs in feature HTML text not resolved to
2526 <li>View follows highlighting does not work for positions
2528 <li><= shown as = in tooltip</li>
2529 <li>Export features raises exception when no features
2531 <li>Separator string used for serialising lists of IDs
2532 for javascript api is modified when separator string
2533 provided as parameter</li>
2534 <li>Null pointer exception when selecting tree leaves for
2535 alignment with no existing selection</li>
2536 <li>Relative URLs for datasources assumed to be relative
2537 to applet's codebase</li>
2538 <li>Status bar not updated after finished searching and
2539 search wraps around to first result</li>
2540 <li>StructureSelectionManager instance shared between
2541 several Jalview applets causes race conditions and memory
2543 <li>Hover tooltip and mouseover of position on structure
2544 not sent from Jmol in applet</li>
2545 <li>Certain sequences of javascript method calls to
2546 applet API fatally hang browser</li>
2547 </ul> <em>General</em>
2549 <li>View follows structure mouseover scrolls beyond
2550 position with wrapped view and hidden regions</li>
2551 <li>Find sequence position moves to wrong residue
2552 with/without hidden columns</li>
2553 <li>Sequence length given in alignment properties window
2555 <li>InvalidNumberFormat exceptions thrown when trying to
2556 import PDB like structure files</li>
2557 <li>Positional search results are only highlighted
2558 between user-supplied sequence start/end bounds</li>
2559 <li>End attribute of sequence is not validated</li>
2560 <li>Find dialog only finds first sequence containing a
2561 given sequence position</li>
2562 <li>Sequence numbering not preserved in MSF alignment
2564 <li>Jalview PDB file reader does not extract sequence
2565 from nucleotide chains correctly</li>
2566 <li>Structure colours not updated when tree partition
2567 changed in alignment</li>
2568 <li>Sequence associated secondary structure not correctly
2569 parsed in interleaved stockholm</li>
2570 <li>Colour by annotation dialog does not restore current
2572 <li>Hiding (nearly) all sequences doesn't work
2574 <li>Sequences containing lowercase letters are not
2575 properly associated with their pdb files</li>
2576 </ul> <em>Documentation and Development</em>
2578 <li>schemas/JalviewWsParamSet.xsd corrupted by
2579 ApplyCopyright tool</li>
2584 <div align="center">
2585 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2588 <td><em>Application</em>
2590 <li>New warning dialog when the Jalview Desktop cannot
2591 contact web services</li>
2592 <li>JABA service parameters for a preset are shown in
2593 service job window</li>
2594 <li>JABA Service menu entries reworded</li>
2598 <li>Modeller PIR IO broken - cannot correctly import a
2599 pir file emitted by Jalview</li>
2600 <li>Existing feature settings transferred to new
2601 alignment view created from cut'n'paste</li>
2602 <li>Improved test for mixed amino/nucleotide chains when
2603 parsing PDB files</li>
2604 <li>Consensus and conservation annotation rows
2605 occasionally become blank for all new windows</li>
2606 <li>Exception raised when right clicking above sequences
2607 in wrapped view mode</li>
2608 </ul> <em>Application</em>
2610 <li>multiple multiply aligned structure views cause cpu
2611 usage to hit 100% and computer to hang</li>
2612 <li>Web Service parameter layout breaks for long user
2613 parameter names</li>
2614 <li>Jaba service discovery hangs desktop if Jaba server
2621 <div align="center">
2622 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2625 <td><em>Application</em>
2627 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2628 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2631 <li>Web Services preference tab</li>
2632 <li>Analysis parameters dialog box and user defined
2634 <li>Improved speed and layout of Envision2 service menu</li>
2635 <li>Superpose structures using associated sequence
2637 <li>Export coordinates and projection as CSV from PCA
2639 </ul> <em>Applet</em>
2641 <li>enable javascript: execution by the applet via the
2642 link out mechanism</li>
2643 </ul> <em>Other</em>
2645 <li>Updated the Jmol Jalview interface to work with Jmol
2647 <li>The Jalview Desktop and JalviewLite applet now
2648 require Java 1.5</li>
2649 <li>Allow Jalview feature colour specification for GFF
2650 sequence annotation files</li>
2651 <li>New 'colour by label' keword in Jalview feature file
2652 type colour specification</li>
2653 <li>New Jalview Desktop Groovy API method that allows a
2654 script to check if it being run in an interactive session or
2655 in a batch operation from the Jalview command line</li>
2659 <li>clustalx colourscheme colours Ds preferentially when
2660 both D+E are present in over 50% of the column</li>
2661 </ul> <em>Application</em>
2663 <li>typo in AlignmentFrame->View->Hide->all but
2664 selected Regions menu item</li>
2665 <li>sequence fetcher replaces ',' for ';' when the ',' is
2666 part of a valid accession ID</li>
2667 <li>fatal OOM if object retrieved by sequence fetcher
2668 runs out of memory</li>
2669 <li>unhandled Out of Memory Error when viewing pca
2670 analysis results</li>
2671 <li>InstallAnywhere builds fail to launch on OS X java
2672 10.5 update 4 (due to apple Java 1.6 update)</li>
2673 <li>Installanywhere Jalview silently fails to launch</li>
2674 </ul> <em>Applet</em>
2676 <li>Jalview.getFeatureGroups() raises an
2677 ArrayIndexOutOfBoundsException if no feature groups are
2684 <div align="center">
2685 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2691 <li>Alignment prettyprinter doesn't cope with long
2693 <li>clustalx colourscheme colours Ds preferentially when
2694 both D+E are present in over 50% of the column</li>
2695 <li>nucleic acid structures retrieved from PDB do not
2696 import correctly</li>
2697 <li>More columns get selected than were clicked on when a
2698 number of columns are hidden</li>
2699 <li>annotation label popup menu not providing correct
2700 add/hide/show options when rows are hidden or none are
2702 <li>Stockholm format shown in list of readable formats,
2703 and parser copes better with alignments from RFAM.</li>
2704 <li>CSV output of consensus only includes the percentage
2705 of all symbols if sequence logo display is enabled</li>
2707 </ul> <em>Applet</em>
2709 <li>annotation panel disappears when annotation is
2711 </ul> <em>Application</em>
2713 <li>Alignment view not redrawn properly when new
2714 alignment opened where annotation panel is visible but no
2715 annotations are present on alignment</li>
2716 <li>pasted region containing hidden columns is
2717 incorrectly displayed in new alignment window</li>
2718 <li>Jalview slow to complete operations when stdout is
2719 flooded (fix is to close the Jalview console)</li>
2720 <li>typo in AlignmentFrame->View->Hide->all but
2721 selected Rregions menu item.</li>
2722 <li>inconsistent group submenu and Format submenu entry
2723 'Un' or 'Non'conserved</li>
2724 <li>Sequence feature settings are being shared by
2725 multiple distinct alignments</li>
2726 <li>group annotation not recreated when tree partition is
2728 <li>double click on group annotation to select sequences
2729 does not propagate to associated trees</li>
2730 <li>Mac OSX specific issues:
2732 <li>exception raised when mouse clicked on desktop
2733 window background</li>
2734 <li>Desktop menu placed on menu bar and application
2735 name set correctly</li>
2736 <li>sequence feature settings not wide enough for the
2737 save feature colourscheme button</li>
2746 <div align="center">
2747 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2750 <td><em>New Capabilities</em>
2752 <li>URL links generated from description line for
2753 regular-expression based URL links (applet and application)
2755 <li>Non-positional feature URL links are shown in link
2757 <li>Linked viewing of nucleic acid sequences and
2759 <li>Automatic Scrolling option in View menu to display
2760 the currently highlighted region of an alignment.</li>
2761 <li>Order an alignment by sequence length, or using the
2762 average score or total feature count for each sequence.</li>
2763 <li>Shading features by score or associated description</li>
2764 <li>Subdivide alignment and groups based on identity of
2765 selected subsequence (Make Groups from Selection).</li>
2766 <li>New hide/show options including Shift+Control+H to
2767 hide everything but the currently selected region.</li>
2768 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2769 </ul> <em>Application</em>
2771 <li>Fetch DB References capabilities and UI expanded to
2772 support retrieval from DAS sequence sources</li>
2773 <li>Local DAS Sequence sources can be added via the
2774 command line or via the Add local source dialog box.</li>
2775 <li>DAS Dbref and DbxRef feature types are parsed as
2776 database references and protein_name is parsed as
2777 description line (BioSapiens terms).</li>
2778 <li>Enable or disable non-positional feature and database
2779 references in sequence ID tooltip from View menu in
2781 <!-- <li>New hidden columns and rows and representatives capabilities
2782 in annotations file (in progress - not yet fully implemented)</li> -->
2783 <li>Group-associated consensus, sequence logos and
2784 conservation plots</li>
2785 <li>Symbol distributions for each column can be exported
2786 and visualized as sequence logos</li>
2787 <li>Optionally scale multi-character column labels to fit
2788 within each column of annotation row<!-- todo for applet -->
2790 <li>Optional automatic sort of associated alignment view
2791 when a new tree is opened.</li>
2792 <li>Jalview Java Console</li>
2793 <li>Better placement of desktop window when moving
2794 between different screens.</li>
2795 <li>New preference items for sequence ID tooltip and
2796 consensus annotation</li>
2797 <li>Client to submit sequences and IDs to Envision2
2799 <li><em>Vamsas Capabilities</em>
2801 <li>Improved VAMSAS synchronization (Jalview archive
2802 used to preserve views, structures, and tree display
2804 <li>Import of vamsas documents from disk or URL via
2806 <li>Sharing of selected regions between views and
2807 with other VAMSAS applications (Experimental feature!)</li>
2808 <li>Updated API to VAMSAS version 0.2</li>
2810 </ul> <em>Applet</em>
2812 <li>Middle button resizes annotation row height</li>
2815 <li>sortByTree (true/false) - automatically sort the
2816 associated alignment view by the tree when a new tree is
2818 <li>showTreeBootstraps (true/false) - show or hide
2819 branch bootstraps (default is to show them if available)</li>
2820 <li>showTreeDistances (true/false) - show or hide
2821 branch lengths (default is to show them if available)</li>
2822 <li>showUnlinkedTreeNodes (true/false) - indicate if
2823 unassociated nodes should be highlighted in the tree
2825 <li>heightScale and widthScale (1.0 or more) -
2826 increase the height or width of a cell in the alignment
2827 grid relative to the current font size.</li>
2830 <li>Non-positional features displayed in sequence ID
2832 </ul> <em>Other</em>
2834 <li>Features format: graduated colour definitions and
2835 specification of feature scores</li>
2836 <li>Alignment Annotations format: new keywords for group
2837 associated annotation (GROUP_REF) and annotation row display
2838 properties (ROW_PROPERTIES)</li>
2839 <li>XML formats extended to support graduated feature
2840 colourschemes, group associated annotation, and profile
2841 visualization settings.</li></td>
2844 <li>Source field in GFF files parsed as feature source
2845 rather than description</li>
2846 <li>Non-positional features are now included in sequence
2847 feature and gff files (controlled via non-positional feature
2848 visibility in tooltip).</li>
2849 <li>URL links generated for all feature links (bugfix)</li>
2850 <li>Added URL embedding instructions to features file
2852 <li>Codons containing ambiguous nucleotides translated as
2853 'X' in peptide product</li>
2854 <li>Match case switch in find dialog box works for both
2855 sequence ID and sequence string and query strings do not
2856 have to be in upper case to match case-insensitively.</li>
2857 <li>AMSA files only contain first column of
2858 multi-character column annotation labels</li>
2859 <li>Jalview Annotation File generation/parsing consistent
2860 with documentation (e.g. Stockholm annotation can be
2861 exported and re-imported)</li>
2862 <li>PDB files without embedded PDB IDs given a friendly
2864 <li>Find incrementally searches ID string matches as well
2865 as subsequence matches, and correctly reports total number
2869 <li>Better handling of exceptions during sequence
2871 <li>Dasobert generated non-positional feature URL
2872 link text excludes the start_end suffix</li>
2873 <li>DAS feature and source retrieval buttons disabled
2874 when fetch or registry operations in progress.</li>
2875 <li>PDB files retrieved from URLs are cached properly</li>
2876 <li>Sequence description lines properly shared via
2878 <li>Sequence fetcher fetches multiple records for all
2880 <li>Ensured that command line das feature retrieval
2881 completes before alignment figures are generated.</li>
2882 <li>Reduced time taken when opening file browser for
2884 <li>isAligned check prior to calculating tree, PCA or
2885 submitting an MSA to JNet now excludes hidden sequences.</li>
2886 <li>User defined group colours properly recovered
2887 from Jalview projects.</li>
2896 <div align="center">
2897 <strong>2.4.0.b2</strong><br> 28/10/2009
2902 <li>Experimental support for google analytics usage
2904 <li>Jalview privacy settings (user preferences and docs).</li>
2909 <li>Race condition in applet preventing startup in
2911 <li>Exception when feature created from selection beyond
2912 length of sequence.</li>
2913 <li>Allow synthetic PDB files to be imported gracefully</li>
2914 <li>Sequence associated annotation rows associate with
2915 all sequences with a given id</li>
2916 <li>Find function matches case-insensitively for sequence
2917 ID string searches</li>
2918 <li>Non-standard characters do not cause pairwise
2919 alignment to fail with exception</li>
2920 </ul> <em>Application Issues</em>
2922 <li>Sequences are now validated against EMBL database</li>
2923 <li>Sequence fetcher fetches multiple records for all
2925 </ul> <em>InstallAnywhere Issues</em>
2927 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2928 issue with installAnywhere mechanism)</li>
2929 <li>Command line launching of JARs from InstallAnywhere
2930 version (java class versioning error fixed)</li>
2937 <div align="center">
2938 <strong>2.4</strong><br> 27/8/2008
2941 <td><em>User Interface</em>
2943 <li>Linked highlighting of codon and amino acid from
2944 translation and protein products</li>
2945 <li>Linked highlighting of structure associated with
2946 residue mapping to codon position</li>
2947 <li>Sequence Fetcher provides example accession numbers
2948 and 'clear' button</li>
2949 <li>MemoryMonitor added as an option under Desktop's
2951 <li>Extract score function to parse whitespace separated
2952 numeric data in description line</li>
2953 <li>Column labels in alignment annotation can be centred.</li>
2954 <li>Tooltip for sequence associated annotation give name
2956 </ul> <em>Web Services and URL fetching</em>
2958 <li>JPred3 web service</li>
2959 <li>Prototype sequence search client (no public services
2961 <li>Fetch either seed alignment or full alignment from
2963 <li>URL Links created for matching database cross
2964 references as well as sequence ID</li>
2965 <li>URL Links can be created using regular-expressions</li>
2966 </ul> <em>Sequence Database Connectivity</em>
2968 <li>Retrieval of cross-referenced sequences from other
2970 <li>Generalised database reference retrieval and
2971 validation to all fetchable databases</li>
2972 <li>Fetch sequences from DAS sources supporting the
2973 sequence command</li>
2974 </ul> <em>Import and Export</em>
2975 <li>export annotation rows as CSV for spreadsheet import</li>
2976 <li>Jalview projects record alignment dataset associations,
2977 EMBL products, and cDNA sequence mappings</li>
2978 <li>Sequence Group colour can be specified in Annotation
2980 <li>Ad-hoc colouring of group in Annotation File using RGB
2981 triplet as name of colourscheme</li>
2982 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2984 <li>treenode binding for VAMSAS tree exchange</li>
2985 <li>local editing and update of sequences in VAMSAS
2986 alignments (experimental)</li>
2987 <li>Create new or select existing session to join</li>
2988 <li>load and save of vamsas documents</li>
2989 </ul> <em>Application command line</em>
2991 <li>-tree parameter to open trees (introduced for passing
2993 <li>-fetchfrom command line argument to specify nicknames
2994 of DAS servers to query for alignment features</li>
2995 <li>-dasserver command line argument to add new servers
2996 that are also automatically queried for features</li>
2997 <li>-groovy command line argument executes a given groovy
2998 script after all input data has been loaded and parsed</li>
2999 </ul> <em>Applet-Application data exchange</em>
3001 <li>Trees passed as applet parameters can be passed to
3002 application (when using "View in full
3003 application")</li>
3004 </ul> <em>Applet Parameters</em>
3006 <li>feature group display control parameter</li>
3007 <li>debug parameter</li>
3008 <li>showbutton parameter</li>
3009 </ul> <em>Applet API methods</em>
3011 <li>newView public method</li>
3012 <li>Window (current view) specific get/set public methods</li>
3013 <li>Feature display control methods</li>
3014 <li>get list of currently selected sequences</li>
3015 </ul> <em>New Jalview distribution features</em>
3017 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3018 <li>RELEASE file gives build properties for the latest
3019 Jalview release.</li>
3020 <li>Java 1.1 Applet build made easier and donotobfuscate
3021 property controls execution of obfuscator</li>
3022 <li>Build target for generating source distribution</li>
3023 <li>Debug flag for javacc</li>
3024 <li>.jalview_properties file is documented (slightly) in
3025 jalview.bin.Cache</li>
3026 <li>Continuous Build Integration for stable and
3027 development version of Application, Applet and source
3032 <li>selected region output includes visible annotations
3033 (for certain formats)</li>
3034 <li>edit label/displaychar contains existing label/char
3036 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3037 <li>shorter peptide product names from EMBL records</li>
3038 <li>Newick string generator makes compact representations</li>
3039 <li>bootstrap values parsed correctly for tree files with
3041 <li>pathological filechooser bug avoided by not allowing
3042 filenames containing a ':'</li>
3043 <li>Fixed exception when parsing GFF files containing
3044 global sequence features</li>
3045 <li>Alignment datasets are finalized only when number of
3046 references from alignment sequences goes to zero</li>
3047 <li>Close of tree branch colour box without colour
3048 selection causes cascading exceptions</li>
3049 <li>occasional negative imgwidth exceptions</li>
3050 <li>better reporting of non-fatal warnings to user when
3051 file parsing fails.</li>
3052 <li>Save works when Jalview project is default format</li>
3053 <li>Save as dialog opened if current alignment format is
3054 not a valid output format</li>
3055 <li>UniProt canonical names introduced for both das and
3057 <li>Histidine should be midblue (not pink!) in Zappo</li>
3058 <li>error messages passed up and output when data read
3060 <li>edit undo recovers previous dataset sequence when
3061 sequence is edited</li>
3062 <li>allow PDB files without pdb ID HEADER lines (like
3063 those generated by MODELLER) to be read in properly</li>
3064 <li>allow reading of JPred concise files as a normal
3066 <li>Stockholm annotation parsing and alignment properties
3067 import fixed for PFAM records</li>
3068 <li>Structure view windows have correct name in Desktop
3070 <li>annotation consisting of sequence associated scores
3071 can be read and written correctly to annotation file</li>
3072 <li>Aligned cDNA translation to aligned peptide works
3074 <li>Fixed display of hidden sequence markers and
3075 non-italic font for representatives in Applet</li>
3076 <li>Applet Menus are always embedded in applet window on
3078 <li>Newly shown features appear at top of stack (in
3080 <li>Annotations added via parameter not drawn properly
3081 due to null pointer exceptions</li>
3082 <li>Secondary structure lines are drawn starting from
3083 first column of alignment</li>
3084 <li>UniProt XML import updated for new schema release in
3086 <li>Sequence feature to sequence ID match for Features
3087 file is case-insensitive</li>
3088 <li>Sequence features read from Features file appended to
3089 all sequences with matching IDs</li>
3090 <li>PDB structure coloured correctly for associated views
3091 containing a sub-sequence</li>
3092 <li>PDB files can be retrieved by applet from Jar files</li>
3093 <li>feature and annotation file applet parameters
3094 referring to different directories are retrieved correctly</li>
3095 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3096 <li>Fixed application hang whilst waiting for
3097 splash-screen version check to complete</li>
3098 <li>Applet properly URLencodes input parameter values
3099 when passing them to the launchApp service</li>
3100 <li>display name and local features preserved in results
3101 retrieved from web service</li>
3102 <li>Visual delay indication for sequence retrieval and
3103 sequence fetcher initialisation</li>
3104 <li>updated Application to use DAS 1.53e version of
3105 dasobert DAS client</li>
3106 <li>Re-instated Full AMSA support and .amsa file
3108 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3116 <div align="center">
3117 <strong>2.3</strong><br> 9/5/07
3122 <li>Jmol 11.0.2 integration</li>
3123 <li>PDB views stored in Jalview XML files</li>
3124 <li>Slide sequences</li>
3125 <li>Edit sequence in place</li>
3126 <li>EMBL CDS features</li>
3127 <li>DAS Feature mapping</li>
3128 <li>Feature ordering</li>
3129 <li>Alignment Properties</li>
3130 <li>Annotation Scores</li>
3131 <li>Sort by scores</li>
3132 <li>Feature/annotation editing in applet</li>
3137 <li>Headless state operation in 2.2.1</li>
3138 <li>Incorrect and unstable DNA pairwise alignment</li>
3139 <li>Cut and paste of sequences with annotation</li>
3140 <li>Feature group display state in XML</li>
3141 <li>Feature ordering in XML</li>
3142 <li>blc file iteration selection using filename # suffix</li>
3143 <li>Stockholm alignment properties</li>
3144 <li>Stockhom alignment secondary structure annotation</li>
3145 <li>2.2.1 applet had no feature transparency</li>
3146 <li>Number pad keys can be used in cursor mode</li>
3147 <li>Structure Viewer mirror image resolved</li>
3154 <div align="center">
3155 <strong>2.2.1</strong><br> 12/2/07
3160 <li>Non standard characters can be read and displayed
3161 <li>Annotations/Features can be imported/exported to the
3163 <li>Applet allows editing of sequence/annotation/group
3164 name & description
3165 <li>Preference setting to display sequence name in
3167 <li>Annotation file format extended to allow
3168 Sequence_groups to be defined
3169 <li>Default opening of alignment overview panel can be
3170 specified in preferences
3171 <li>PDB residue numbering annotation added to associated
3177 <li>Applet crash under certain Linux OS with Java 1.6
3179 <li>Annotation file export / import bugs fixed
3180 <li>PNG / EPS image output bugs fixed
3186 <div align="center">
3187 <strong>2.2</strong><br> 27/11/06
3192 <li>Multiple views on alignment
3193 <li>Sequence feature editing
3194 <li>"Reload" alignment
3195 <li>"Save" to current filename
3196 <li>Background dependent text colour
3197 <li>Right align sequence ids
3198 <li>User-defined lower case residue colours
3201 <li>Menu item accelerator keys
3202 <li>Control-V pastes to current alignment
3203 <li>Cancel button for DAS Feature Fetching
3204 <li>PCA and PDB Viewers zoom via mouse roller
3205 <li>User-defined sub-tree colours and sub-tree selection
3207 <li>'New Window' button on the 'Output to Text box'
3212 <li>New memory efficient Undo/Redo System
3213 <li>Optimised symbol lookups and conservation/consensus
3215 <li>Region Conservation/Consensus recalculated after
3217 <li>Fixed Remove Empty Columns Bug (empty columns at end
3219 <li>Slowed DAS Feature Fetching for increased robustness.
3221 <li>Made angle brackets in ASCII feature descriptions
3223 <li>Re-instated Zoom function for PCA
3224 <li>Sequence descriptions conserved in web service
3226 <li>UniProt ID discoverer uses any word separated by
3228 <li>WsDbFetch query/result association resolved
3229 <li>Tree leaf to sequence mapping improved
3230 <li>Smooth fonts switch moved to FontChooser dialog box.
3237 <div align="center">
3238 <strong>2.1.1</strong><br> 12/9/06
3243 <li>Copy consensus sequence to clipboard</li>
3248 <li>Image output - rightmost residues are rendered if
3249 sequence id panel has been resized</li>
3250 <li>Image output - all offscreen group boundaries are
3252 <li>Annotation files with sequence references - all
3253 elements in file are relative to sequence position</li>
3254 <li>Mac Applet users can use Alt key for group editing</li>
3260 <div align="center">
3261 <strong>2.1</strong><br> 22/8/06
3266 <li>MAFFT Multiple Alignment in default Web Service list</li>
3267 <li>DAS Feature fetching</li>
3268 <li>Hide sequences and columns</li>
3269 <li>Export Annotations and Features</li>
3270 <li>GFF file reading / writing</li>
3271 <li>Associate structures with sequences from local PDB
3273 <li>Add sequences to exisiting alignment</li>
3274 <li>Recently opened files / URL lists</li>
3275 <li>Applet can launch the full application</li>
3276 <li>Applet has transparency for features (Java 1.2
3278 <li>Applet has user defined colours parameter</li>
3279 <li>Applet can load sequences from parameter
3280 "sequence<em>x</em>"
3286 <li>Redundancy Panel reinstalled in the Applet</li>
3287 <li>Monospaced font - EPS / rescaling bug fixed</li>
3288 <li>Annotation files with sequence references bug fixed</li>
3294 <div align="center">
3295 <strong>2.08.1</strong><br> 2/5/06
3300 <li>Change case of selected region from Popup menu</li>
3301 <li>Choose to match case when searching</li>
3302 <li>Middle mouse button and mouse movement can compress /
3303 expand the visible width and height of the alignment</li>
3308 <li>Annotation Panel displays complete JNet results</li>
3314 <div align="center">
3315 <strong>2.08b</strong><br> 18/4/06
3321 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3322 <li>Righthand label on wrapped alignments shows correct
3329 <div align="center">
3330 <strong>2.08</strong><br> 10/4/06
3335 <li>Editing can be locked to the selection area</li>
3336 <li>Keyboard editing</li>
3337 <li>Create sequence features from searches</li>
3338 <li>Precalculated annotations can be loaded onto
3340 <li>Features file allows grouping of features</li>
3341 <li>Annotation Colouring scheme added</li>
3342 <li>Smooth fonts off by default - Faster rendering</li>
3343 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3348 <li>Drag & Drop fixed on Linux</li>
3349 <li>Jalview Archive file faster to load/save, sequence
3350 descriptions saved.</li>
3356 <div align="center">
3357 <strong>2.07</strong><br> 12/12/05
3362 <li>PDB Structure Viewer enhanced</li>
3363 <li>Sequence Feature retrieval and display enhanced</li>
3364 <li>Choose to output sequence start-end after sequence
3365 name for file output</li>
3366 <li>Sequence Fetcher WSDBFetch@EBI</li>
3367 <li>Applet can read feature files, PDB files and can be
3368 used for HTML form input</li>
3373 <li>HTML output writes groups and features</li>
3374 <li>Group editing is Control and mouse click</li>
3375 <li>File IO bugs</li>
3381 <div align="center">
3382 <strong>2.06</strong><br> 28/9/05
3387 <li>View annotations in wrapped mode</li>
3388 <li>More options for PCA viewer</li>
3393 <li>GUI bugs resolved</li>
3394 <li>Runs with -nodisplay from command line</li>
3400 <div align="center">
3401 <strong>2.05b</strong><br> 15/9/05
3406 <li>Choose EPS export as lineart or text</li>
3407 <li>Jar files are executable</li>
3408 <li>Can read in Uracil - maps to unknown residue</li>
3413 <li>Known OutOfMemory errors give warning message</li>
3414 <li>Overview window calculated more efficiently</li>
3415 <li>Several GUI bugs resolved</li>
3421 <div align="center">
3422 <strong>2.05</strong><br> 30/8/05
3427 <li>Edit and annotate in "Wrapped" view</li>
3432 <li>Several GUI bugs resolved</li>
3438 <div align="center">
3439 <strong>2.04</strong><br> 24/8/05
3444 <li>Hold down mouse wheel & scroll to change font
3450 <li>Improved JPred client reliability</li>
3451 <li>Improved loading of Jalview files</li>
3457 <div align="center">
3458 <strong>2.03</strong><br> 18/8/05
3463 <li>Set Proxy server name and port in preferences</li>
3464 <li>Multiple URL links from sequence ids</li>
3465 <li>User Defined Colours can have a scheme name and added
3467 <li>Choose to ignore gaps in consensus calculation</li>
3468 <li>Unix users can set default web browser</li>
3469 <li>Runs without GUI for batch processing</li>
3470 <li>Dynamically generated Web Service Menus</li>
3475 <li>InstallAnywhere download for Sparc Solaris</li>
3481 <div align="center">
3482 <strong>2.02</strong><br> 18/7/05
3488 <li>Copy & Paste order of sequences maintains
3489 alignment order.</li>
3495 <div align="center">
3496 <strong>2.01</strong><br> 12/7/05
3501 <li>Use delete key for deleting selection.</li>
3502 <li>Use Mouse wheel to scroll sequences.</li>
3503 <li>Help file updated to describe how to add alignment
3505 <li>Version and build date written to build properties
3507 <li>InstallAnywhere installation will check for updates
3508 at launch of Jalview.</li>
3513 <li>Delete gaps bug fixed.</li>
3514 <li>FileChooser sorts columns.</li>
3515 <li>Can remove groups one by one.</li>
3516 <li>Filechooser icons installed.</li>
3517 <li>Finder ignores return character when searching.
3518 Return key will initiate a search.<br>
3525 <div align="center">
3526 <strong>2.0</strong><br> 20/6/05
3531 <li>New codebase</li>