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;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
74 <em>7/9/2017</em></strong>
77 <td><div align="left">
81 <!-- JAL-2588 -->Show gaps in overview window by colouring
82 in grey (sequences used to be coloured grey, and gaps were
86 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
90 <!-- JAL-2587 -->Overview updates immediately on increase
91 in size and progress bar shown as higher resolution
92 overview is recalculated
97 <td><div align="left">
101 <!-- JAL-2664 -->Overview window redraws every hidden
102 column region row by row
105 <!-- JAL-2681 -->duplicate protein sequences shown after
106 retrieving Ensembl crossrefs for sequences from Uniprot
109 <!-- JAL-2603 -->Overview window throws NPE if show boxes
110 format setting is unticked
113 <!-- JAL-2610 -->Groups are coloured wrongly in overview
114 if group has show boxes format setting unticked
117 <!-- JAL-2672,JAL-2665 -->Redraw problems when
118 autoscrolling whilst dragging current selection group to
119 include sequences and columns not currently displayed
122 <!-- JAL-2691 -->Not all chains are mapped when multimeric
123 assemblies are imported via CIF file
126 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
127 displayed when threshold or conservation colouring is also
131 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
135 <!-- JAL-2673 -->Jalview continues to scroll after
136 dragging a selected region off the visible region of the
140 <!-- JAL-2724 -->Cannot apply annotation based
141 colourscheme to all groups in a view
147 <td width="60" nowrap>
149 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
152 <td><div align="left">
153 <em>Calculations</em>
157 <!-- JAL-1933 -->Occupancy annotation row shows number of
158 ungapped positions in each column of the alignment.
161 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
162 a calculation dialog box
165 <!-- JAL-2379 -->Revised implementation of PCA for speed
166 and memory efficiency (~30x faster)
169 <!-- JAL-2403 -->Revised implementation of sequence
170 similarity scores as used by Tree, PCA, Shading Consensus
171 and other calculations
174 <!-- JAL-2416 -->Score matrices are stored as resource
175 files within the Jalview codebase
178 <!-- JAL-2500 -->Trees computed on Sequence Feature
179 Similarity may have different topology due to increased
186 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
187 model for alignments and groups
190 <!-- JAL-384 -->Custom shading schemes created via groovy
197 <!-- JAL-2526 -->Efficiency improvements for interacting
198 with alignment and overview windows
201 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
205 <!-- JAL-2388 -->Hidden columns and sequences can be
209 <!-- JAL-2611 -->Click-drag in visible area allows fine
210 adjustment of visible position
214 <em>Data import/export</em>
217 <!-- JAL-2535 -->Posterior probability annotation from
218 Stockholm files imported as sequence associated annotation
221 <!-- JAL-2507 -->More robust per-sequence positional
222 annotation input/output via stockholm flatfile
225 <!-- JAL-2533 -->Sequence names don't include file
226 extension when importing structure files without embedded
227 names or PDB accessions
230 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
231 format sequence substitution matrices
234 <em>User Interface</em>
237 <!-- JAL-2447 --> Experimental Features Checkbox in
238 Desktop's Tools menu to hide or show untested features in
242 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
243 via Overview or sequence motif search operations
246 <!-- JAL-2547 -->Amend sequence features dialog box can be
247 opened by double clicking gaps within sequence feature
251 <!-- JAL-1476 -->Status bar message shown when not enough
252 aligned positions were available to create a 3D structure
256 <em>3D Structure</em>
259 <!-- JAL-2430 -->Hidden regions in alignment views are not
260 coloured in linked structure views
263 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
264 file-based command exchange
267 <!-- JAL-2375 -->Structure chooser automatically shows
268 Cached Structures rather than querying the PDBe if
269 structures are already available for sequences
272 <!-- JAL-2520 -->Structures imported via URL are cached in
273 the Jalview project rather than downloaded again when the
277 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
278 to transfer Chimera's structure attributes as Jalview
279 features, and vice-versa (<strong>Experimental
283 <em>Web Services</em>
286 <!-- JAL-2549 -->Updated JABAWS client to v2.2
289 <!-- JAL-2335 -->Filter non-standard amino acids and
290 nucleotides when submitting to AACon and other MSA
294 <!-- JAL-2316, -->URLs for viewing database
295 cross-references provided by identifiers.org and the
303 <!-- JAL-2344 -->FileFormatI interface for describing and
304 identifying file formats (instead of String constants)
307 <!-- JAL-2228 -->FeatureCounter script refactored for
308 efficiency when counting all displayed features (not
309 backwards compatible with 2.10.1)
312 <em>Example files</em>
315 <!-- JAL-2631 -->Graduated feature colour style example
316 included in the example feature file
319 <em>Documentation</em>
322 <!-- JAL-2339 -->Release notes reformatted for readability
323 with the built-in Java help viewer
326 <!-- JAL-1644 -->Find documentation updated with 'search
327 sequence description' option
333 <!-- JAL-2485, -->External service integration tests for
334 Uniprot REST Free Text Search Client
337 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
340 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
345 <td><div align="left">
346 <em>Calculations</em>
349 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
350 matrix - C->R should be '-3'<br />Old matrix restored
351 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
353 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
354 Jalview's treatment of gaps in PCA and substitution matrix
355 based Tree calculations.<br /> <br />In earlier versions
356 of Jalview, gaps matching gaps were penalised, and gaps
357 matching non-gaps penalised even more. In the PCA
358 calculation, gaps were actually treated as non-gaps - so
359 different costs were applied, which meant Jalview's PCAs
360 were different to those produced by SeqSpace.<br />Jalview
361 now treats gaps in the same way as SeqSpace (ie it scores
362 them as 0). <br /> <br />Enter the following in the
363 Groovy console to restore pre-2.10.2 behaviour:<br />
364 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
365 // for 2.10.1 mode <br />
366 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
367 // to restore 2.10.2 mode <br /> <br /> <em>Note:
368 these settings will affect all subsequent tree and PCA
369 calculations (not recommended)</em></li>
371 <!-- JAL-2424 -->Fixed off-by-one bug that affected
372 scaling of branch lengths for trees computed using
373 Sequence Feature Similarity.
376 <!-- JAL-2377 -->PCA calculation could hang when
377 generating output report when working with highly
381 <!-- JAL-2544 --> Sort by features includes features to
382 right of selected region when gaps present on right-hand
386 <em>User Interface</em>
389 <!-- JAL-2346 -->Reopening Colour by annotation dialog
390 doesn't reselect a specific sequence's associated
391 annotation after it was used for colouring a view
394 <!-- JAL-2419 -->Current selection lost if popup menu
395 opened on a region of alignment without groups
398 <!-- JAL-2374 -->Popup menu not always shown for regions
399 of an alignment with overlapping groups
402 <!-- JAL-2310 -->Finder double counts if both a sequence's
403 name and description match
406 <!-- JAL-2370 -->Hiding column selection containing two
407 hidden regions results in incorrect hidden regions
410 <!-- JAL-2386 -->'Apply to all groups' setting when
411 changing colour does not apply Conservation slider value
415 <!-- JAL-2373 -->Percentage identity and conservation menu
416 items do not show a tick or allow shading to be disabled
419 <!-- JAL-2385 -->Conservation shading or PID threshold
420 lost when base colourscheme changed if slider not visible
423 <!-- JAL-2547 -->Sequence features shown in tooltip for
424 gaps before start of features
427 <!-- JAL-2623 -->Graduated feature colour threshold not
428 restored to UI when feature colour is edited
431 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
432 a time when scrolling vertically in wrapped mode.
435 <!-- JAL-2630 -->Structure and alignment overview update
436 as graduate feature colour settings are modified via the
440 <!-- JAL-2034 -->Overview window doesn't always update
441 when a group defined on the alignment is resized
444 <!-- JAL-2605 -->Mouseovers on left/right scale region in
445 wrapped view result in positional status updates
449 <!-- JAL-2563 -->Status bar doesn't show position for
450 ambiguous amino acid and nucleotide symbols
453 <!-- JAL-2602 -->Copy consensus sequence failed if
454 alignment included gapped columns
457 <!-- JAL-2473 -->Minimum size set for Jalview windows so
458 widgets don't permanently disappear
461 <!-- JAL-2503 -->Cannot select or filter quantitative
462 annotation that are shown only as column labels (e.g.
463 T-Coffee column reliability scores)
466 <!-- JAL-2594 -->Exception thrown if trying to create a
467 sequence feature on gaps only
470 <!-- JAL-2504 -->Features created with 'New feature'
471 button from a Find inherit previously defined feature type
472 rather than the Find query string
475 <!-- JAL-2423 -->incorrect title in output window when
476 exporting tree calculated in Jalview
479 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
480 and then revealing them reorders sequences on the
484 <!-- JAL-964 -->Group panel in sequence feature settings
485 doesn't update to reflect available set of groups after
486 interactively adding or modifying features
489 <!-- JAL-2225 -->Sequence Database chooser unusable on
493 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
494 only excluded gaps in current sequence and ignored
501 <!-- JAL-2421 -->Overview window visible region moves
502 erratically when hidden rows or columns are present
505 <!-- JAL-2362 -->Per-residue colourschemes applied via the
506 Structure Viewer's colour menu don't correspond to
510 <!-- JAL-2405 -->Protein specific colours only offered in
511 colour and group colour menu for protein alignments
514 <!-- JAL-2385 -->Colour threshold slider doesn't update to
515 reflect currently selected view or group's shading
519 <!-- JAL-2624 -->Feature colour thresholds not respected
520 when rendered on overview and structures when opacity at
524 <!-- JAL-2589 -->User defined gap colour not shown in
525 overview when features overlaid on alignment
528 <em>Data import/export</em>
531 <!-- JAL-2576 -->Very large alignments take a long time to
535 <!-- JAL-2507 -->Per-sequence RNA secondary structures
536 added after a sequence was imported are not written to
540 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
541 when importing RNA secondary structure via Stockholm
544 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
545 not shown in correct direction for simple pseudoknots
548 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
549 with lightGray or darkGray via features file (but can
553 <!-- JAL-2383 -->Above PID colour threshold not recovered
554 when alignment view imported from project
557 <!-- JAL-2520,JAL-2465 -->No mappings generated between
558 structure and sequences extracted from structure files
559 imported via URL and viewed in Jmol
562 <!-- JAL-2520 -->Structures loaded via URL are saved in
563 Jalview Projects rather than fetched via URL again when
564 the project is loaded and the structure viewed
567 <em>Web Services</em>
570 <!-- JAL-2519 -->EnsemblGenomes example failing after
571 release of Ensembl v.88
574 <!-- JAL-2366 -->Proxy server address and port always
575 appear enabled in Preferences->Connections
578 <!-- JAL-2461 -->DAS registry not found exceptions
579 removed from console output
582 <!-- JAL-2582 -->Cannot retrieve protein products from
583 Ensembl by Peptide ID
586 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
587 created from SIFTs, and spurious 'Couldn't open structure
588 in Chimera' errors raised after April 2017 update (problem
589 due to 'null' string rather than empty string used for
590 residues with no corresponding PDB mapping).
593 <em>Application UI</em>
596 <!-- JAL-2361 -->User Defined Colours not added to Colour
600 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
601 case' residues (button in colourscheme editor debugged and
602 new documentation and tooltips added)
605 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
606 doesn't restore group-specific text colour thresholds
609 <!-- JAL-2243 -->Feature settings panel does not update as
610 new features are added to alignment
613 <!-- JAL-2532 -->Cancel in feature settings reverts
614 changes to feature colours via the Amend features dialog
617 <!-- JAL-2506 -->Null pointer exception when attempting to
618 edit graduated feature colour via amend features dialog
622 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
623 selection menu changes colours of alignment views
626 <!-- JAL-2426 -->Spurious exceptions in console raised
627 from alignment calculation workers after alignment has
631 <!-- JAL-1608 -->Typo in selection popup menu - Create
632 groups now 'Create Group'
635 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
636 Create/Undefine group doesn't always work
639 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
640 shown again after pressing 'Cancel'
643 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
644 adjusts start position in wrap mode
647 <!-- JAL-2563 -->Status bar doesn't show positions for
648 ambiguous amino acids
651 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
652 CDS/Protein view after CDS sequences added for aligned
656 <!-- JAL-2592 -->User defined colourschemes called 'User
657 Defined' don't appear in Colours menu
663 <!-- JAL-2468 -->Switching between Nucleotide and Protein
664 score models doesn't always result in an updated PCA plot
667 <!-- JAL-2442 -->Features not rendered as transparent on
668 overview or linked structure view
671 <!-- JAL-2372 -->Colour group by conservation doesn't
675 <!-- JAL-2517 -->Hitting Cancel after applying
676 user-defined colourscheme doesn't restore original
683 <!-- JAL-2314 -->Unit test failure:
684 jalview.ws.jabaws.RNAStructExportImport setup fails
687 <!-- JAL-2307 -->Unit test failure:
688 jalview.ws.sifts.SiftsClientTest due to compatibility
689 problems with deep array comparison equality asserts in
690 successive versions of TestNG
693 <!-- JAL-2479 -->Relocated StructureChooserTest and
694 ParameterUtilsTest Unit tests to Network suite
697 <em>New Known Issues</em>
700 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
701 phase after a sequence motif find operation
704 <!-- JAL-2550 -->Importing annotation file with rows
705 containing just upper and lower case letters are
706 interpreted as WUSS RNA secondary structure symbols
709 <!-- JAL-2590 -->Cannot load and display Newick trees
710 reliably from eggnog Ortholog database
713 <!-- JAL-2468 -->Status bar shows 'Marked x columns
714 containing features of type Highlight' when 'B' is pressed
715 to mark columns containing highlighted regions.
718 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
719 doesn't always add secondary structure annotation.
724 <td width="60" nowrap>
726 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
729 <td><div align="left">
733 <!-- JAL-98 -->Improved memory usage: sparse arrays used
734 for all consensus calculations
737 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
740 <li>Updated Jalview's Certum code signing certificate
746 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
747 set of database cross-references, sorted alphabetically
750 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
751 from database cross references. Users with custom links
752 will receive a <a href="webServices/urllinks.html#warning">warning
753 dialog</a> asking them to update their preferences.
756 <!-- JAL-2287-->Cancel button and escape listener on
757 dialog warning user about disconnecting Jalview from a
761 <!-- JAL-2320-->Jalview's Chimera control window closes if
762 the Chimera it is connected to is shut down
765 <!-- JAL-1738-->New keystroke (B) and Select highlighted
766 columns menu item to mark columns containing highlighted
767 regions (e.g. from structure selections or results of a
771 <!-- JAL-2284-->Command line option for batch-generation
772 of HTML pages rendering alignment data with the BioJS
782 <!-- JAL-2286 -->Columns with more than one modal residue
783 are not coloured or thresholded according to percent
784 identity (first observed in Jalview 2.8.2)
787 <!-- JAL-2301 -->Threonine incorrectly reported as not
791 <!-- JAL-2318 -->Updates to documentation pages (above PID
792 threshold, amino acid properties)
795 <!-- JAL-2292 -->Lower case residues in sequences are not
796 reported as mapped to residues in a structure file in the
800 <!--JAL-2324 -->Identical features with non-numeric scores
801 could be added multiple times to a sequence
804 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
805 bond features shown as two highlighted residues rather
806 than a range in linked structure views, and treated
807 correctly when selecting and computing trees from features
810 <!-- JAL-2281-->Custom URL links for database
811 cross-references are matched to database name regardless
819 <!-- JAL-2282-->Custom URL links for specific database
820 names without regular expressions also offer links from
824 <!-- JAL-2315-->Removing a single configured link in the
825 URL links pane in Connections preferences doesn't actually
826 update Jalview configuration
829 <!-- JAL-2272-->CTRL-Click on a selected region to open
830 the alignment area popup menu doesn't work on El-Capitan
833 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
834 files with similarly named sequences if dropped onto the
838 <!-- JAL-2312 -->Additional mappings are shown for PDB
839 entries where more chains exist in the PDB accession than
840 are reported in the SIFTS file
843 <!-- JAL-2317-->Certain structures do not get mapped to
844 the structure view when displayed with Chimera
847 <!-- JAL-2317-->No chains shown in the Chimera view
848 panel's View->Show Chains submenu
851 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
852 work for wrapped alignment views
855 <!--JAL-2197 -->Rename UI components for running JPred
856 predictions from 'JNet' to 'JPred'
859 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
860 corrupted when annotation panel vertical scroll is not at
864 <!--JAL-2332 -->Attempting to view structure for Hen
865 lysozyme results in a PDB Client error dialog box
868 <!-- JAL-2319 -->Structure View's mapping report switched
869 ranges for PDB and sequence for SIFTS
872 SIFTS 'Not_Observed' residues mapped to non-existant
876 <!-- <em>New Known Issues</em>
883 <td width="60" nowrap>
885 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
886 <em>25/10/2016</em></strong>
889 <td><em>Application</em>
891 <li>3D Structure chooser opens with 'Cached structures'
892 view if structures already loaded</li>
893 <li>Progress bar reports models as they are loaded to
900 <li>Colour by conservation always enabled and no tick
901 shown in menu when BLOSUM or PID shading applied</li>
902 <li>FER1_ARATH and FER2_ARATH labels were switched in
903 example sequences/projects/trees</li>
907 <li>Jalview projects with views of local PDB structure
908 files saved on Windows cannot be opened on OSX</li>
909 <li>Multiple structure views can be opened and superposed
910 without timeout for structures with multiple models or
911 multiple sequences in alignment</li>
912 <li>Cannot import or associated local PDB files without a
913 PDB ID HEADER line</li>
914 <li>RMSD is not output in Jmol console when superposition
916 <li>Drag and drop of URL from Browser fails for Linux and
917 OSX versions earlier than El Capitan</li>
918 <li>ENA client ignores invalid content from ENA server</li>
919 <li>Exceptions are not raised in console when ENA client
920 attempts to fetch non-existent IDs via Fetch DB Refs UI
922 <li>Exceptions are not raised in console when a new view
923 is created on the alignment</li>
924 <li>OSX right-click fixed for group selections: CMD-click
925 to insert/remove gaps in groups and CTRL-click to open group
928 <em>Build and deployment</em>
930 <li>URL link checker now copes with multi-line anchor
933 <em>New Known Issues</em>
935 <li>Drag and drop from URL links in browsers do not work
942 <td width="60" nowrap>
944 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
950 <!-- JAL-2124 -->Updated Spanish translations.
953 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
954 for importing structure data to Jalview. Enables mmCIF and
958 <!-- JAL-192 --->Alignment ruler shows positions relative to
962 <!-- JAL-2202 -->Position/residue shown in status bar when
963 mousing over sequence associated annotation
966 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
970 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
971 '()', canonical '[]' and invalid '{}' base pair populations
975 <!-- JAL-2092 -->Feature settings popup menu options for
976 showing or hiding columns containing a feature
979 <!-- JAL-1557 -->Edit selected group by double clicking on
980 group and sequence associated annotation labels
983 <!-- JAL-2236 -->Sequence name added to annotation label in
984 select/hide columns by annotation and colour by annotation
988 </ul> <em>Application</em>
991 <!-- JAL-2050-->Automatically hide introns when opening a
995 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
999 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1000 structure mappings with the EMBL-EBI PDBe SIFTS database
1003 <!-- JAL-2079 -->Updated download sites used for Rfam and
1004 Pfam sources to xfam.org
1007 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1010 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1011 over sequences in Jalview
1014 <!-- JAL-2027-->Support for reverse-complement coding
1015 regions in ENA and EMBL
1018 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1019 for record retrieval via ENA rest API
1022 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1026 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1027 groovy script execution
1030 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1031 alignment window's Calculate menu
1034 <!-- JAL-1812 -->Allow groovy scripts that call
1035 Jalview.getAlignFrames() to run in headless mode
1038 <!-- JAL-2068 -->Support for creating new alignment
1039 calculation workers from groovy scripts
1042 <!-- JAL-1369 --->Store/restore reference sequence in
1046 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1047 associations are now saved/restored from project
1050 <!-- JAL-1993 -->Database selection dialog always shown
1051 before sequence fetcher is opened
1054 <!-- JAL-2183 -->Double click on an entry in Jalview's
1055 database chooser opens a sequence fetcher
1058 <!-- JAL-1563 -->Free-text search client for UniProt using
1059 the UniProt REST API
1062 <!-- JAL-2168 -->-nonews command line parameter to prevent
1063 the news reader opening
1066 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1067 querying stored in preferences
1070 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1074 <!-- JAL-1977-->Tooltips shown on database chooser
1077 <!-- JAL-391 -->Reverse complement function in calculate
1078 menu for nucleotide sequences
1081 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1082 and feature counts preserves alignment ordering (and
1083 debugged for complex feature sets).
1086 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1087 viewing structures with Jalview 2.10
1090 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1091 genome, transcript CCDS and gene ids via the Ensembl and
1092 Ensembl Genomes REST API
1095 <!-- JAL-2049 -->Protein sequence variant annotation
1096 computed for 'sequence_variant' annotation on CDS regions
1100 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1104 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1105 Ref Fetcher fails to match, or otherwise updates sequence
1106 data from external database records.
1109 <!-- JAL-2154 -->Revised Jalview Project format for
1110 efficient recovery of sequence coding and alignment
1111 annotation relationships.
1113 </ul> <!-- <em>Applet</em>
1124 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1128 <!-- JAL-2018-->Export features in Jalview format (again)
1129 includes graduated colourschemes
1132 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1133 working with big alignments and lots of hidden columns
1136 <!-- JAL-2053-->Hidden column markers not always rendered
1137 at right of alignment window
1140 <!-- JAL-2067 -->Tidied up links in help file table of
1144 <!-- JAL-2072 -->Feature based tree calculation not shown
1148 <!-- JAL-2075 -->Hidden columns ignored during feature
1149 based tree calculation
1152 <!-- JAL-2065 -->Alignment view stops updating when show
1153 unconserved enabled for group on alignment
1156 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1160 <!-- JAL-2146 -->Alignment column in status incorrectly
1161 shown as "Sequence position" when mousing over
1165 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1166 hidden columns present
1169 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1170 user created annotation added to alignment
1173 <!-- JAL-1841 -->RNA Structure consensus only computed for
1174 '()' base pair annotation
1177 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1178 in zero scores for all base pairs in RNA Structure
1182 <!-- JAL-2174-->Extend selection with columns containing
1186 <!-- JAL-2275 -->Pfam format writer puts extra space at
1187 beginning of sequence
1190 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1194 <!-- JAL-2238 -->Cannot create groups on an alignment from
1195 from a tree when t-coffee scores are shown
1198 <!-- JAL-1836,1967 -->Cannot import and view PDB
1199 structures with chains containing negative resnums (4q4h)
1202 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1206 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1207 to Clustal, PIR and PileUp output
1210 <!-- JAL-2008 -->Reordering sequence features that are
1211 not visible causes alignment window to repaint
1214 <!-- JAL-2006 -->Threshold sliders don't work in
1215 graduated colour and colour by annotation row for e-value
1216 scores associated with features and annotation rows
1219 <!-- JAL-1797 -->amino acid physicochemical conservation
1220 calculation should be case independent
1223 <!-- JAL-2173 -->Remove annotation also updates hidden
1227 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1228 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1229 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1232 <!-- JAL-2065 -->Null pointer exceptions and redraw
1233 problems when reference sequence defined and 'show
1234 non-conserved' enabled
1237 <!-- JAL-1306 -->Quality and Conservation are now shown on
1238 load even when Consensus calculation is disabled
1241 <!-- JAL-1932 -->Remove right on penultimate column of
1242 alignment does nothing
1245 <em>Application</em>
1248 <!-- JAL-1552-->URLs and links can't be imported by
1249 drag'n'drop on OSX when launched via webstart (note - not
1250 yet fixed for El Capitan)
1253 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1254 output when running on non-gb/us i18n platforms
1257 <!-- JAL-1944 -->Error thrown when exporting a view with
1258 hidden sequences as flat-file alignment
1261 <!-- JAL-2030-->InstallAnywhere distribution fails when
1265 <!-- JAL-2080-->Jalview very slow to launch via webstart
1266 (also hotfix for 2.9.0b2)
1269 <!-- JAL-2085 -->Cannot save project when view has a
1270 reference sequence defined
1273 <!-- JAL-1011 -->Columns are suddenly selected in other
1274 alignments and views when revealing hidden columns
1277 <!-- JAL-1989 -->Hide columns not mirrored in complement
1278 view in a cDNA/Protein splitframe
1281 <!-- JAL-1369 -->Cannot save/restore representative
1282 sequence from project when only one sequence is
1286 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1287 in Structure Chooser
1290 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1291 structure consensus didn't refresh annotation panel
1294 <!-- JAL-1962 -->View mapping in structure view shows
1295 mappings between sequence and all chains in a PDB file
1298 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1299 dialogs format columns correctly, don't display array
1300 data, sort columns according to type
1303 <!-- JAL-1975 -->Export complete shown after destination
1304 file chooser is cancelled during an image export
1307 <!-- JAL-2025 -->Error when querying PDB Service with
1308 sequence name containing special characters
1311 <!-- JAL-2024 -->Manual PDB structure querying should be
1315 <!-- JAL-2104 -->Large tooltips with broken HTML
1316 formatting don't wrap
1319 <!-- JAL-1128 -->Figures exported from wrapped view are
1320 truncated so L looks like I in consensus annotation
1323 <!-- JAL-2003 -->Export features should only export the
1324 currently displayed features for the current selection or
1328 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1329 after fetching cross-references, and restoring from
1333 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1334 followed in the structure viewer
1337 <!-- JAL-2163 -->Titles for individual alignments in
1338 splitframe not restored from project
1341 <!-- JAL-2145 -->missing autocalculated annotation at
1342 trailing end of protein alignment in transcript/product
1343 splitview when pad-gaps not enabled by default
1346 <!-- JAL-1797 -->amino acid physicochemical conservation
1350 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1351 article has been read (reopened issue due to
1352 internationalisation problems)
1355 <!-- JAL-1960 -->Only offer PDB structures in structure
1356 viewer based on sequence name, PDB and UniProt
1361 <!-- JAL-1976 -->No progress bar shown during export of
1365 <!-- JAL-2213 -->Structures not always superimposed after
1366 multiple structures are shown for one or more sequences.
1369 <!-- JAL-1370 -->Reference sequence characters should not
1370 be replaced with '.' when 'Show unconserved' format option
1374 <!-- JAL-1823 -->Cannot specify chain code when entering
1375 specific PDB id for sequence
1378 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1379 'Export hidden sequences' is enabled, but 'export hidden
1380 columns' is disabled.
1383 <!--JAL-2026-->Best Quality option in structure chooser
1384 selects lowest rather than highest resolution structures
1388 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1389 to sequence mapping in 'View Mappings' report
1392 <!-- JAL-2284 -->Unable to read old Jalview projects that
1393 contain non-XML data added after Jalvew wrote project.
1396 <!-- JAL-2118 -->Newly created annotation row reorders
1397 after clicking on it to create new annotation for a
1400 <!-- may exclude, this is an external service stability issue JAL-1941
1401 -- > RNA 3D structure not added via DSSR service</li> -->
1406 <!-- JAL-2151 -->Incorrect columns are selected when
1407 hidden columns present before start of sequence
1410 <!-- JAL-1986 -->Missing dependencies on applet pages
1414 <!-- JAL-1947 -->Overview pixel size changes when
1415 sequences are hidden in applet
1418 <!-- JAL-1996 -->Updated instructions for applet
1419 deployment on examples pages.
1426 <td width="60" nowrap>
1427 <div align="center">
1428 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1429 <em>16/10/2015</em></strong>
1432 <td><em>General</em>
1434 <li>Time stamps for signed Jalview application and applet
1439 <em>Application</em>
1441 <li>Duplicate group consensus and conservation rows
1442 shown when tree is partitioned</li>
1443 <li>Erratic behaviour when tree partitions made with
1444 multiple cDNA/Protein split views</li>
1450 <td width="60" nowrap>
1451 <div align="center">
1452 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1453 <em>8/10/2015</em></strong>
1456 <td><em>General</em>
1458 <li>Updated Spanish translations of localized text for
1460 </ul> <em>Application</em>
1462 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1463 <li>Signed OSX InstallAnywhere installer<br></li>
1464 <li>Support for per-sequence based annotations in BioJSON</li>
1465 </ul> <em>Applet</em>
1467 <li>Split frame example added to applet examples page</li>
1468 </ul> <em>Build and Deployment</em>
1471 <!-- JAL-1888 -->New ant target for running Jalview's test
1479 <li>Mapping of cDNA to protein in split frames
1480 incorrect when sequence start > 1</li>
1481 <li>Broken images in filter column by annotation dialog
1483 <li>Feature colours not parsed from features file</li>
1484 <li>Exceptions and incomplete link URLs recovered when
1485 loading a features file containing HTML tags in feature
1489 <em>Application</em>
1491 <li>Annotations corrupted after BioJS export and
1493 <li>Incorrect sequence limits after Fetch DB References
1494 with 'trim retrieved sequences'</li>
1495 <li>Incorrect warning about deleting all data when
1496 deleting selected columns</li>
1497 <li>Patch to build system for shipping properly signed
1498 JNLP templates for webstart launch</li>
1499 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1500 unreleased structures for download or viewing</li>
1501 <li>Tab/space/return keystroke operation of EMBL-PDBe
1502 fetcher/viewer dialogs works correctly</li>
1503 <li>Disabled 'minimise' button on Jalview windows
1504 running on OSX to workaround redraw hang bug</li>
1505 <li>Split cDNA/Protein view position and geometry not
1506 recovered from jalview project</li>
1507 <li>Initial enabled/disabled state of annotation menu
1508 sorter 'show autocalculated first/last' corresponds to
1510 <li>Restoring of Clustal, RNA Helices and T-Coffee
1511 color schemes from BioJSON</li>
1515 <li>Reorder sequences mirrored in cDNA/Protein split
1517 <li>Applet with Jmol examples not loading correctly</li>
1523 <td><div align="center">
1524 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1526 <td><em>General</em>
1528 <li>Linked visualisation and analysis of DNA and Protein
1531 <li>Translated cDNA alignments shown as split protein
1532 and DNA alignment views</li>
1533 <li>Codon consensus annotation for linked protein and
1534 cDNA alignment views</li>
1535 <li>Link cDNA or Protein product sequences by loading
1536 them onto Protein or cDNA alignments</li>
1537 <li>Reconstruct linked cDNA alignment from aligned
1538 protein sequences</li>
1541 <li>Jmol integration updated to Jmol v14.2.14</li>
1542 <li>Import and export of Jalview alignment views as <a
1543 href="features/bioJsonFormat.html">BioJSON</a></li>
1544 <li>New alignment annotation file statements for
1545 reference sequences and marking hidden columns</li>
1546 <li>Reference sequence based alignment shading to
1547 highlight variation</li>
1548 <li>Select or hide columns according to alignment
1550 <li>Find option for locating sequences by description</li>
1551 <li>Conserved physicochemical properties shown in amino
1552 acid conservation row</li>
1553 <li>Alignments can be sorted by number of RNA helices</li>
1554 </ul> <em>Application</em>
1556 <li>New cDNA/Protein analysis capabilities
1558 <li>Get Cross-References should open a Split Frame
1559 view with cDNA/Protein</li>
1560 <li>Detect when nucleotide sequences and protein
1561 sequences are placed in the same alignment</li>
1562 <li>Split cDNA/Protein views are saved in Jalview
1567 <li>Use REST API to talk to Chimera</li>
1568 <li>Selected regions in Chimera are highlighted in linked
1569 Jalview windows</li>
1571 <li>VARNA RNA viewer updated to v3.93</li>
1572 <li>VARNA views are saved in Jalview Projects</li>
1573 <li>Pseudoknots displayed as Jalview RNA annotation can
1574 be shown in VARNA</li>
1576 <li>Make groups for selection uses marked columns as well
1577 as the active selected region</li>
1579 <li>Calculate UPGMA and NJ trees using sequence feature
1581 <li>New Export options
1583 <li>New Export Settings dialog to control hidden
1584 region export in flat file generation</li>
1586 <li>Export alignment views for display with the <a
1587 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1589 <li>Export scrollable SVG in HTML page</li>
1590 <li>Optional embedding of BioJSON data when exporting
1591 alignment figures to HTML</li>
1593 <li>3D structure retrieval and display
1595 <li>Free text and structured queries with the PDBe
1597 <li>PDBe Search API based discovery and selection of
1598 PDB structures for a sequence set</li>
1602 <li>JPred4 employed for protein secondary structure
1604 <li>Hide Insertions menu option to hide unaligned columns
1605 for one or a group of sequences</li>
1606 <li>Automatically hide insertions in alignments imported
1607 from the JPred4 web server</li>
1608 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1609 system on OSX<br />LGPL libraries courtesy of <a
1610 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1612 <li>changed 'View nucleotide structure' submenu to 'View
1613 VARNA 2D Structure'</li>
1614 <li>change "View protein structure" menu option to "3D
1617 </ul> <em>Applet</em>
1619 <li>New layout for applet example pages</li>
1620 <li>New parameters to enable SplitFrame view
1621 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1622 <li>New example demonstrating linked viewing of cDNA and
1623 Protein alignments</li>
1624 </ul> <em>Development and deployment</em>
1626 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1627 <li>Include installation type and git revision in build
1628 properties and console log output</li>
1629 <li>Jalview Github organisation, and new github site for
1630 storing BioJsMSA Templates</li>
1631 <li>Jalview's unit tests now managed with TestNG</li>
1634 <!-- <em>General</em>
1636 </ul> --> <!-- issues resolved --> <em>Application</em>
1638 <li>Escape should close any open find dialogs</li>
1639 <li>Typo in select-by-features status report</li>
1640 <li>Consensus RNA secondary secondary structure
1641 predictions are not highlighted in amber</li>
1642 <li>Missing gap character in v2.7 example file means
1643 alignment appears unaligned when pad-gaps is not enabled</li>
1644 <li>First switch to RNA Helices colouring doesn't colour
1645 associated structure views</li>
1646 <li>ID width preference option is greyed out when auto
1647 width checkbox not enabled</li>
1648 <li>Stopped a warning dialog from being shown when
1649 creating user defined colours</li>
1650 <li>'View Mapping' in structure viewer shows sequence
1651 mappings for just that viewer's sequences</li>
1652 <li>Workaround for superposing PDB files containing
1653 multiple models in Chimera</li>
1654 <li>Report sequence position in status bar when hovering
1655 over Jmol structure</li>
1656 <li>Cannot output gaps as '.' symbols with Selection ->
1657 output to text box</li>
1658 <li>Flat file exports of alignments with hidden columns
1659 have incorrect sequence start/end</li>
1660 <li>'Aligning' a second chain to a Chimera structure from
1662 <li>Colour schemes applied to structure viewers don't
1663 work for nucleotide</li>
1664 <li>Loading/cut'n'pasting an empty or invalid file leads
1665 to a grey/invisible alignment window</li>
1666 <li>Exported Jpred annotation from a sequence region
1667 imports to different position</li>
1668 <li>Space at beginning of sequence feature tooltips shown
1669 on some platforms</li>
1670 <li>Chimera viewer 'View | Show Chain' menu is not
1672 <li>'New View' fails with a Null Pointer Exception in
1673 console if Chimera has been opened</li>
1674 <li>Mouseover to Chimera not working</li>
1675 <li>Miscellaneous ENA XML feature qualifiers not
1677 <li>NPE in annotation renderer after 'Extract Scores'</li>
1678 <li>If two structures in one Chimera window, mouseover of
1679 either sequence shows on first structure</li>
1680 <li>'Show annotations' options should not make
1681 non-positional annotations visible</li>
1682 <li>Subsequence secondary structure annotation not shown
1683 in right place after 'view flanking regions'</li>
1684 <li>File Save As type unset when current file format is
1686 <li>Save as '.jar' option removed for saving Jalview
1688 <li>Colour by Sequence colouring in Chimera more
1690 <li>Cannot 'add reference annotation' for a sequence in
1691 several views on same alignment</li>
1692 <li>Cannot show linked products for EMBL / ENA records</li>
1693 <li>Jalview's tooltip wraps long texts containing no
1695 </ul> <em>Applet</em>
1697 <li>Jmol to JalviewLite mouseover/link not working</li>
1698 <li>JalviewLite can't import sequences with ID
1699 descriptions containing angle brackets</li>
1700 </ul> <em>General</em>
1702 <li>Cannot export and reimport RNA secondary structure
1703 via jalview annotation file</li>
1704 <li>Random helix colour palette for colour by annotation
1705 with RNA secondary structure</li>
1706 <li>Mouseover to cDNA from STOP residue in protein
1707 translation doesn't work.</li>
1708 <li>hints when using the select by annotation dialog box</li>
1709 <li>Jmol alignment incorrect if PDB file has alternate CA
1711 <li>FontChooser message dialog appears to hang after
1712 choosing 1pt font</li>
1713 <li>Peptide secondary structure incorrectly imported from
1714 annotation file when annotation display text includes 'e' or
1716 <li>Cannot set colour of new feature type whilst creating
1718 <li>cDNA translation alignment should not be sequence
1719 order dependent</li>
1720 <li>'Show unconserved' doesn't work for lower case
1722 <li>Nucleotide ambiguity codes involving R not recognised</li>
1723 </ul> <em>Deployment and Documentation</em>
1725 <li>Applet example pages appear different to the rest of
1726 www.jalview.org</li>
1727 </ul> <em>Application Known issues</em>
1729 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1730 <li>Misleading message appears after trying to delete
1732 <li>Jalview icon not shown in dock after InstallAnywhere
1733 version launches</li>
1734 <li>Fetching EMBL reference for an RNA sequence results
1735 fails with a sequence mismatch</li>
1736 <li>Corrupted or unreadable alignment display when
1737 scrolling alignment to right</li>
1738 <li>ArrayIndexOutOfBoundsException thrown when remove
1739 empty columns called on alignment with ragged gapped ends</li>
1740 <li>auto calculated alignment annotation rows do not get
1741 placed above or below non-autocalculated rows</li>
1742 <li>Jalview dekstop becomes sluggish at full screen in
1743 ultra-high resolution</li>
1744 <li>Cannot disable consensus calculation independently of
1745 quality and conservation</li>
1746 <li>Mouseover highlighting between cDNA and protein can
1747 become sluggish with more than one splitframe shown</li>
1748 </ul> <em>Applet Known Issues</em>
1750 <li>Core PDB parsing code requires Jmol</li>
1751 <li>Sequence canvas panel goes white when alignment
1752 window is being resized</li>
1758 <td><div align="center">
1759 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1761 <td><em>General</em>
1763 <li>Updated Java code signing certificate donated by
1765 <li>Features and annotation preserved when performing
1766 pairwise alignment</li>
1767 <li>RNA pseudoknot annotation can be
1768 imported/exported/displayed</li>
1769 <li>'colour by annotation' can colour by RNA and
1770 protein secondary structure</li>
1771 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1772 post-hoc with 2.9 release</em>)
1775 </ul> <em>Application</em>
1777 <li>Extract and display secondary structure for sequences
1778 with 3D structures</li>
1779 <li>Support for parsing RNAML</li>
1780 <li>Annotations menu for layout
1782 <li>sort sequence annotation rows by alignment</li>
1783 <li>place sequence annotation above/below alignment
1786 <li>Output in Stockholm format</li>
1787 <li>Internationalisation: improved Spanish (es)
1789 <li>Structure viewer preferences tab</li>
1790 <li>Disorder and Secondary Structure annotation tracks
1791 shared between alignments</li>
1792 <li>UCSF Chimera launch and linked highlighting from
1794 <li>Show/hide all sequence associated annotation rows for
1795 all or current selection</li>
1796 <li>disorder and secondary structure predictions
1797 available as dataset annotation</li>
1798 <li>Per-sequence rna helices colouring</li>
1801 <li>Sequence database accessions imported when fetching
1802 alignments from Rfam</li>
1803 <li>update VARNA version to 3.91</li>
1805 <li>New groovy scripts for exporting aligned positions,
1806 conservation values, and calculating sum of pairs scores.</li>
1807 <li>Command line argument to set default JABAWS server</li>
1808 <li>include installation type in build properties and
1809 console log output</li>
1810 <li>Updated Jalview project format to preserve dataset
1814 <!-- issues resolved --> <em>Application</em>
1816 <li>Distinguish alignment and sequence associated RNA
1817 structure in structure->view->VARNA</li>
1818 <li>Raise dialog box if user deletes all sequences in an
1820 <li>Pressing F1 results in documentation opening twice</li>
1821 <li>Sequence feature tooltip is wrapped</li>
1822 <li>Double click on sequence associated annotation
1823 selects only first column</li>
1824 <li>Redundancy removal doesn't result in unlinked
1825 leaves shown in tree</li>
1826 <li>Undos after several redundancy removals don't undo
1828 <li>Hide sequence doesn't hide associated annotation</li>
1829 <li>User defined colours dialog box too big to fit on
1830 screen and buttons not visible</li>
1831 <li>author list isn't updated if already written to
1832 Jalview properties</li>
1833 <li>Popup menu won't open after retrieving sequence
1835 <li>File open window for associate PDB doesn't open</li>
1836 <li>Left-then-right click on a sequence id opens a
1837 browser search window</li>
1838 <li>Cannot open sequence feature shading/sort popup menu
1839 in feature settings dialog</li>
1840 <li>better tooltip placement for some areas of Jalview
1842 <li>Allow addition of JABAWS Server which doesn't
1843 pass validation</li>
1844 <li>Web services parameters dialog box is too large to
1846 <li>Muscle nucleotide alignment preset obscured by
1848 <li>JABAWS preset submenus don't contain newly
1849 defined user preset</li>
1850 <li>MSA web services warns user if they were launched
1851 with invalid input</li>
1852 <li>Jalview cannot contact DAS Registy when running on
1855 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1856 'Superpose with' submenu not shown when new view
1860 </ul> <!-- <em>Applet</em>
1862 </ul> <em>General</em>
1864 </ul>--> <em>Deployment and Documentation</em>
1866 <li>2G and 1G options in launchApp have no effect on
1867 memory allocation</li>
1868 <li>launchApp service doesn't automatically open
1869 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1871 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1872 InstallAnywhere reports cannot find valid JVM when Java
1873 1.7_055 is available
1875 </ul> <em>Application Known issues</em>
1878 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1879 corrupted or unreadable alignment display when scrolling
1883 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1884 retrieval fails but progress bar continues for DAS retrieval
1885 with large number of ID
1888 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1889 flatfile output of visible region has incorrect sequence
1893 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1894 rna structure consensus doesn't update when secondary
1895 structure tracks are rearranged
1898 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1899 invalid rna structure positional highlighting does not
1900 highlight position of invalid base pairs
1903 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1904 out of memory errors are not raised when saving Jalview
1905 project from alignment window file menu
1908 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1909 Switching to RNA Helices colouring doesn't propagate to
1913 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1914 colour by RNA Helices not enabled when user created
1915 annotation added to alignment
1918 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1919 Jalview icon not shown on dock in Mountain Lion/Webstart
1921 </ul> <em>Applet Known Issues</em>
1924 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1925 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1928 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1929 Jalview and Jmol example not compatible with IE9
1932 <li>Sort by annotation score doesn't reverse order
1938 <td><div align="center">
1939 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1942 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1945 <li>Internationalisation of user interface (usually
1946 called i18n support) and translation for Spanish locale</li>
1947 <li>Define/Undefine group on current selection with
1948 Ctrl-G/Shift Ctrl-G</li>
1949 <li>Improved group creation/removal options in
1950 alignment/sequence Popup menu</li>
1951 <li>Sensible precision for symbol distribution
1952 percentages shown in logo tooltip.</li>
1953 <li>Annotation panel height set according to amount of
1954 annotation when alignment first opened</li>
1955 </ul> <em>Application</em>
1957 <li>Interactive consensus RNA secondary structure
1958 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1959 <li>Select columns containing particular features from
1960 Feature Settings dialog</li>
1961 <li>View all 'representative' PDB structures for selected
1963 <li>Update Jalview project format:
1965 <li>New file extension for Jalview projects '.jvp'</li>
1966 <li>Preserve sequence and annotation dataset (to
1967 store secondary structure annotation,etc)</li>
1968 <li>Per group and alignment annotation and RNA helix
1972 <li>New similarity measures for PCA and Tree calculation
1974 <li>Experimental support for retrieval and viewing of
1975 flanking regions for an alignment</li>
1979 <!-- issues resolved --> <em>Application</em>
1981 <li>logo keeps spinning and status remains at queued or
1982 running after job is cancelled</li>
1983 <li>cannot export features from alignments imported from
1984 Jalview/VAMSAS projects</li>
1985 <li>Buggy slider for web service parameters that take
1987 <li>Newly created RNA secondary structure line doesn't
1988 have 'display all symbols' flag set</li>
1989 <li>T-COFFEE alignment score shading scheme and other
1990 annotation shading not saved in Jalview project</li>
1991 <li>Local file cannot be loaded in freshly downloaded
1993 <li>Jalview icon not shown on dock in Mountain
1995 <li>Load file from desktop file browser fails</li>
1996 <li>Occasional NPE thrown when calculating large trees</li>
1997 <li>Cannot reorder or slide sequences after dragging an
1998 alignment onto desktop</li>
1999 <li>Colour by annotation dialog throws NPE after using
2000 'extract scores' function</li>
2001 <li>Loading/cut'n'pasting an empty file leads to a grey
2002 alignment window</li>
2003 <li>Disorder thresholds rendered incorrectly after
2004 performing IUPred disorder prediction</li>
2005 <li>Multiple group annotated consensus rows shown when
2006 changing 'normalise logo' display setting</li>
2007 <li>Find shows blank dialog after 'finished searching' if
2008 nothing matches query</li>
2009 <li>Null Pointer Exceptions raised when sorting by
2010 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2012 <li>Errors in Jmol console when structures in alignment
2013 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2015 <li>Not all working JABAWS services are shown in
2017 <li>JAVAWS version of Jalview fails to launch with
2018 'invalid literal/length code'</li>
2019 <li>Annotation/RNA Helix colourschemes cannot be applied
2020 to alignment with groups (actually fixed in 2.8.0b1)</li>
2021 <li>RNA Helices and T-Coffee Scores available as default
2024 </ul> <em>Applet</em>
2026 <li>Remove group option is shown even when selection is
2028 <li>Apply to all groups ticked but colourscheme changes
2029 don't affect groups</li>
2030 <li>Documented RNA Helices and T-Coffee Scores as valid
2031 colourscheme name</li>
2032 <li>Annotation labels drawn on sequence IDs when
2033 Annotation panel is not displayed</li>
2034 <li>Increased font size for dropdown menus on OSX and
2035 embedded windows</li>
2036 </ul> <em>Other</em>
2038 <li>Consensus sequence for alignments/groups with a
2039 single sequence were not calculated</li>
2040 <li>annotation files that contain only groups imported as
2041 annotation and junk sequences</li>
2042 <li>Fasta files with sequences containing '*' incorrectly
2043 recognised as PFAM or BLC</li>
2044 <li>conservation/PID slider apply all groups option
2045 doesn't affect background (2.8.0b1)
2047 <li>redundancy highlighting is erratic at 0% and 100%</li>
2048 <li>Remove gapped columns fails for sequences with ragged
2050 <li>AMSA annotation row with leading spaces is not
2051 registered correctly on import</li>
2052 <li>Jalview crashes when selecting PCA analysis for
2053 certain alignments</li>
2054 <li>Opening the colour by annotation dialog for an
2055 existing annotation based 'use original colours'
2056 colourscheme loses original colours setting</li>
2061 <td><div align="center">
2062 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2063 <em>30/1/2014</em></strong>
2067 <li>Trusted certificates for JalviewLite applet and
2068 Jalview Desktop application<br />Certificate was donated by
2069 <a href="https://www.certum.eu">Certum</a> to the Jalview
2070 open source project).
2072 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2073 <li>Output in Stockholm format</li>
2074 <li>Allow import of data from gzipped files</li>
2075 <li>Export/import group and sequence associated line
2076 graph thresholds</li>
2077 <li>Nucleotide substitution matrix that supports RNA and
2078 ambiguity codes</li>
2079 <li>Allow disorder predictions to be made on the current
2080 selection (or visible selection) in the same way that JPred
2082 <li>Groovy scripting for headless Jalview operation</li>
2083 </ul> <em>Other improvements</em>
2085 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2086 <li>COMBINE statement uses current SEQUENCE_REF and
2087 GROUP_REF scope to group annotation rows</li>
2088 <li>Support '' style escaping of quotes in Newick
2090 <li>Group options for JABAWS service by command line name</li>
2091 <li>Empty tooltip shown for JABA service options with a
2092 link but no description</li>
2093 <li>Select primary source when selecting authority in
2094 database fetcher GUI</li>
2095 <li>Add .mfa to FASTA file extensions recognised by
2097 <li>Annotation label tooltip text wrap</li>
2102 <li>Slow scrolling when lots of annotation rows are
2104 <li>Lots of NPE (and slowness) after creating RNA
2105 secondary structure annotation line</li>
2106 <li>Sequence database accessions not imported when
2107 fetching alignments from Rfam</li>
2108 <li>Incorrect SHMR submission for sequences with
2110 <li>View all structures does not always superpose
2112 <li>Option widgets in service parameters not updated to
2113 reflect user or preset settings</li>
2114 <li>Null pointer exceptions for some services without
2115 presets or adjustable parameters</li>
2116 <li>Discover PDB IDs entry in structure menu doesn't
2117 discover PDB xRefs</li>
2118 <li>Exception encountered while trying to retrieve
2119 features with DAS</li>
2120 <li>Lowest value in annotation row isn't coloured
2121 when colour by annotation (per sequence) is coloured</li>
2122 <li>Keyboard mode P jumps to start of gapped region when
2123 residue follows a gap</li>
2124 <li>Jalview appears to hang importing an alignment with
2125 Wrap as default or after enabling Wrap</li>
2126 <li>'Right click to add annotations' message
2127 shown in wrap mode when no annotations present</li>
2128 <li>Disorder predictions fail with NPE if no automatic
2129 annotation already exists on alignment</li>
2130 <li>oninit javascript function should be called after
2131 initialisation completes</li>
2132 <li>Remove redundancy after disorder prediction corrupts
2133 alignment window display</li>
2134 <li>Example annotation file in documentation is invalid</li>
2135 <li>Grouped line graph annotation rows are not exported
2136 to annotation file</li>
2137 <li>Multi-harmony analysis cannot be run when only two
2139 <li>Cannot create multiple groups of line graphs with
2140 several 'combine' statements in annotation file</li>
2141 <li>Pressing return several times causes Number Format
2142 exceptions in keyboard mode</li>
2143 <li>Multi-harmony (SHMMR) method doesn't submit
2144 correct partitions for input data</li>
2145 <li>Translation from DNA to Amino Acids fails</li>
2146 <li>Jalview fail to load newick tree with quoted label</li>
2147 <li>--headless flag isn't understood</li>
2148 <li>ClassCastException when generating EPS in headless
2150 <li>Adjusting sequence-associated shading threshold only
2151 changes one row's threshold</li>
2152 <li>Preferences and Feature settings panel panel
2153 doesn't open</li>
2154 <li>hide consensus histogram also hides conservation and
2155 quality histograms</li>
2160 <td><div align="center">
2161 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2163 <td><em>Application</em>
2165 <li>Support for JABAWS 2.0 Services (AACon alignment
2166 conservation, protein disorder and Clustal Omega)</li>
2167 <li>JABAWS server status indicator in Web Services
2169 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2170 in Jalview alignment window</li>
2171 <li>Updated Jalview build and deploy framework for OSX
2172 mountain lion, windows 7, and 8</li>
2173 <li>Nucleotide substitution matrix for PCA that supports
2174 RNA and ambiguity codes</li>
2176 <li>Improved sequence database retrieval GUI</li>
2177 <li>Support fetching and database reference look up
2178 against multiple DAS sources (Fetch all from in 'fetch db
2180 <li>Jalview project improvements
2182 <li>Store and retrieve the 'belowAlignment'
2183 flag for annotation</li>
2184 <li>calcId attribute to group annotation rows on the
2186 <li>Store AACon calculation settings for a view in
2187 Jalview project</li>
2191 <li>horizontal scrolling gesture support</li>
2192 <li>Visual progress indicator when PCA calculation is
2194 <li>Simpler JABA web services menus</li>
2195 <li>visual indication that web service results are still
2196 being retrieved from server</li>
2197 <li>Serialise the dialogs that are shown when Jalview
2198 starts up for first time</li>
2199 <li>Jalview user agent string for interacting with HTTP
2201 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2203 <li>Examples directory and Groovy library included in
2204 InstallAnywhere distribution</li>
2205 </ul> <em>Applet</em>
2207 <li>RNA alignment and secondary structure annotation
2208 visualization applet example</li>
2209 </ul> <em>General</em>
2211 <li>Normalise option for consensus sequence logo</li>
2212 <li>Reset button in PCA window to return dimensions to
2214 <li>Allow seqspace or Jalview variant of alignment PCA
2216 <li>PCA with either nucleic acid and protein substitution
2218 <li>Allow windows containing HTML reports to be exported
2220 <li>Interactive display and editing of RNA secondary
2221 structure contacts</li>
2222 <li>RNA Helix Alignment Colouring</li>
2223 <li>RNA base pair logo consensus</li>
2224 <li>Parse sequence associated secondary structure
2225 information in Stockholm files</li>
2226 <li>HTML Export database accessions and annotation
2227 information presented in tooltip for sequences</li>
2228 <li>Import secondary structure from LOCARNA clustalw
2229 style RNA alignment files</li>
2230 <li>import and visualise T-COFFEE quality scores for an
2232 <li>'colour by annotation' per sequence option to
2233 shade each sequence according to its associated alignment
2235 <li>New Jalview Logo</li>
2236 </ul> <em>Documentation and Development</em>
2238 <li>documentation for score matrices used in Jalview</li>
2239 <li>New Website!</li>
2241 <td><em>Application</em>
2243 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2244 wsdbfetch REST service</li>
2245 <li>Stop windows being moved outside desktop on OSX</li>
2246 <li>Filetype associations not installed for webstart
2248 <li>Jalview does not always retrieve progress of a JABAWS
2249 job execution in full once it is complete</li>
2250 <li>revise SHMR RSBS definition to ensure alignment is
2251 uploaded via ali_file parameter</li>
2252 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2253 <li>View all structures superposed fails with exception</li>
2254 <li>Jnet job queues forever if a very short sequence is
2255 submitted for prediction</li>
2256 <li>Cut and paste menu not opened when mouse clicked on
2258 <li>Putting fractional value into integer text box in
2259 alignment parameter dialog causes Jalview to hang</li>
2260 <li>Structure view highlighting doesn't work on
2262 <li>View all structures fails with exception shown in
2264 <li>Characters in filename associated with PDBEntry not
2265 escaped in a platform independent way</li>
2266 <li>Jalview desktop fails to launch with exception when
2268 <li>Tree calculation reports 'you must have 2 or more
2269 sequences selected' when selection is empty</li>
2270 <li>Jalview desktop fails to launch with jar signature
2271 failure when java web start temporary file caching is
2273 <li>DAS Sequence retrieval with range qualification
2274 results in sequence xref which includes range qualification</li>
2275 <li>Errors during processing of command line arguments
2276 cause progress bar (JAL-898) to be removed</li>
2277 <li>Replace comma for semi-colon option not disabled for
2278 DAS sources in sequence fetcher</li>
2279 <li>Cannot close news reader when JABAWS server warning
2280 dialog is shown</li>
2281 <li>Option widgets not updated to reflect user settings</li>
2282 <li>Edited sequence not submitted to web service</li>
2283 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2284 <li>InstallAnywhere installer doesn't unpack and run
2285 on OSX Mountain Lion</li>
2286 <li>Annotation panel not given a scroll bar when
2287 sequences with alignment annotation are pasted into the
2289 <li>Sequence associated annotation rows not associated
2290 when loaded from Jalview project</li>
2291 <li>Browser launch fails with NPE on java 1.7</li>
2292 <li>JABAWS alignment marked as finished when job was
2293 cancelled or job failed due to invalid input</li>
2294 <li>NPE with v2.7 example when clicking on Tree
2295 associated with all views</li>
2296 <li>Exceptions when copy/paste sequences with grouped
2297 annotation rows to new window</li>
2298 </ul> <em>Applet</em>
2300 <li>Sequence features are momentarily displayed before
2301 they are hidden using hidefeaturegroups applet parameter</li>
2302 <li>loading features via javascript API automatically
2303 enables feature display</li>
2304 <li>scrollToColumnIn javascript API method doesn't
2306 </ul> <em>General</em>
2308 <li>Redundancy removal fails for rna alignment</li>
2309 <li>PCA calculation fails when sequence has been selected
2310 and then deselected</li>
2311 <li>PCA window shows grey box when first opened on OSX</li>
2312 <li>Letters coloured pink in sequence logo when alignment
2313 coloured with clustalx</li>
2314 <li>Choosing fonts without letter symbols defined causes
2315 exceptions and redraw errors</li>
2316 <li>Initial PCA plot view is not same as manually
2317 reconfigured view</li>
2318 <li>Grouped annotation graph label has incorrect line
2320 <li>Grouped annotation graph label display is corrupted
2321 for lots of labels</li>
2326 <div align="center">
2327 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2330 <td><em>Application</em>
2332 <li>Jalview Desktop News Reader</li>
2333 <li>Tweaked default layout of web services menu</li>
2334 <li>View/alignment association menu to enable user to
2335 easily specify which alignment a multi-structure view takes
2336 its colours/correspondences from</li>
2337 <li>Allow properties file location to be specified as URL</li>
2338 <li>Extend Jalview project to preserve associations
2339 between many alignment views and a single Jmol display</li>
2340 <li>Store annotation row height in Jalview project file</li>
2341 <li>Annotation row column label formatting attributes
2342 stored in project file</li>
2343 <li>Annotation row order for auto-calculated annotation
2344 rows preserved in Jalview project file</li>
2345 <li>Visual progress indication when Jalview state is
2346 saved using Desktop window menu</li>
2347 <li>Visual indication that command line arguments are
2348 still being processed</li>
2349 <li>Groovy script execution from URL</li>
2350 <li>Colour by annotation default min and max colours in
2352 <li>Automatically associate PDB files dragged onto an
2353 alignment with sequences that have high similarity and
2355 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2356 <li>'view structures' option to open many
2357 structures in same window</li>
2358 <li>Sort associated views menu option for tree panel</li>
2359 <li>Group all JABA and non-JABA services for a particular
2360 analysis function in its own submenu</li>
2361 </ul> <em>Applet</em>
2363 <li>Userdefined and autogenerated annotation rows for
2365 <li>Adjustment of alignment annotation pane height</li>
2366 <li>Annotation scrollbar for annotation panel</li>
2367 <li>Drag to reorder annotation rows in annotation panel</li>
2368 <li>'automaticScrolling' parameter</li>
2369 <li>Allow sequences with partial ID string matches to be
2370 annotated from GFF/Jalview features files</li>
2371 <li>Sequence logo annotation row in applet</li>
2372 <li>Absolute paths relative to host server in applet
2373 parameters are treated as such</li>
2374 <li>New in the JalviewLite javascript API:
2376 <li>JalviewLite.js javascript library</li>
2377 <li>Javascript callbacks for
2379 <li>Applet initialisation</li>
2380 <li>Sequence/alignment mouse-overs and selections</li>
2383 <li>scrollTo row and column alignment scrolling
2385 <li>Select sequence/alignment regions from javascript</li>
2386 <li>javascript structure viewer harness to pass
2387 messages between Jmol and Jalview when running as
2388 distinct applets</li>
2389 <li>sortBy method</li>
2390 <li>Set of applet and application examples shipped
2391 with documentation</li>
2392 <li>New example to demonstrate JalviewLite and Jmol
2393 javascript message exchange</li>
2395 </ul> <em>General</em>
2397 <li>Enable Jmol displays to be associated with multiple
2398 multiple alignments</li>
2399 <li>Option to automatically sort alignment with new tree</li>
2400 <li>User configurable link to enable redirects to a
2401 www.Jalview.org mirror</li>
2402 <li>Jmol colours option for Jmol displays</li>
2403 <li>Configurable newline string when writing alignment
2404 and other flat files</li>
2405 <li>Allow alignment annotation description lines to
2406 contain html tags</li>
2407 </ul> <em>Documentation and Development</em>
2409 <li>Add groovy test harness for bulk load testing to
2411 <li>Groovy script to load and align a set of sequences
2412 using a web service before displaying the result in the
2413 Jalview desktop</li>
2414 <li>Restructured javascript and applet api documentation</li>
2415 <li>Ant target to publish example html files with applet
2417 <li>Netbeans project for building Jalview from source</li>
2418 <li>ant task to create online javadoc for Jalview source</li>
2420 <td><em>Application</em>
2422 <li>User defined colourscheme throws exception when
2423 current built in colourscheme is saved as new scheme</li>
2424 <li>AlignFrame->Save in application pops up save
2425 dialog for valid filename/format</li>
2426 <li>Cannot view associated structure for UniProt sequence</li>
2427 <li>PDB file association breaks for UniProt sequence
2429 <li>Associate PDB from file dialog does not tell you
2430 which sequence is to be associated with the file</li>
2431 <li>Find All raises null pointer exception when query
2432 only matches sequence IDs</li>
2433 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2434 <li>Jalview project with Jmol views created with Jalview
2435 2.4 cannot be loaded</li>
2436 <li>Filetype associations not installed for webstart
2438 <li>Two or more chains in a single PDB file associated
2439 with sequences in different alignments do not get coloured
2440 by their associated sequence</li>
2441 <li>Visibility status of autocalculated annotation row
2442 not preserved when project is loaded</li>
2443 <li>Annotation row height and visibility attributes not
2444 stored in Jalview project</li>
2445 <li>Tree bootstraps are not preserved when saved as a
2446 Jalview project</li>
2447 <li>Envision2 workflow tooltips are corrupted</li>
2448 <li>Enabling show group conservation also enables colour
2449 by conservation</li>
2450 <li>Duplicate group associated conservation or consensus
2451 created on new view</li>
2452 <li>Annotation scrollbar not displayed after 'show
2453 all hidden annotation rows' option selected</li>
2454 <li>Alignment quality not updated after alignment
2455 annotation row is hidden then shown</li>
2456 <li>Preserve colouring of structures coloured by
2457 sequences in pre Jalview 2.7 projects</li>
2458 <li>Web service job parameter dialog is not laid out
2460 <li>Web services menu not refreshed after 'reset
2461 services' button is pressed in preferences</li>
2462 <li>Annotation off by one in Jalview v2_3 example project</li>
2463 <li>Structures imported from file and saved in project
2464 get name like jalview_pdb1234.txt when reloaded</li>
2465 <li>Jalview does not always retrieve progress of a JABAWS
2466 job execution in full once it is complete</li>
2467 </ul> <em>Applet</em>
2469 <li>Alignment height set incorrectly when lots of
2470 annotation rows are displayed</li>
2471 <li>Relative URLs in feature HTML text not resolved to
2473 <li>View follows highlighting does not work for positions
2475 <li><= shown as = in tooltip</li>
2476 <li>Export features raises exception when no features
2478 <li>Separator string used for serialising lists of IDs
2479 for javascript api is modified when separator string
2480 provided as parameter</li>
2481 <li>Null pointer exception when selecting tree leaves for
2482 alignment with no existing selection</li>
2483 <li>Relative URLs for datasources assumed to be relative
2484 to applet's codebase</li>
2485 <li>Status bar not updated after finished searching and
2486 search wraps around to first result</li>
2487 <li>StructureSelectionManager instance shared between
2488 several Jalview applets causes race conditions and memory
2490 <li>Hover tooltip and mouseover of position on structure
2491 not sent from Jmol in applet</li>
2492 <li>Certain sequences of javascript method calls to
2493 applet API fatally hang browser</li>
2494 </ul> <em>General</em>
2496 <li>View follows structure mouseover scrolls beyond
2497 position with wrapped view and hidden regions</li>
2498 <li>Find sequence position moves to wrong residue
2499 with/without hidden columns</li>
2500 <li>Sequence length given in alignment properties window
2502 <li>InvalidNumberFormat exceptions thrown when trying to
2503 import PDB like structure files</li>
2504 <li>Positional search results are only highlighted
2505 between user-supplied sequence start/end bounds</li>
2506 <li>End attribute of sequence is not validated</li>
2507 <li>Find dialog only finds first sequence containing a
2508 given sequence position</li>
2509 <li>Sequence numbering not preserved in MSF alignment
2511 <li>Jalview PDB file reader does not extract sequence
2512 from nucleotide chains correctly</li>
2513 <li>Structure colours not updated when tree partition
2514 changed in alignment</li>
2515 <li>Sequence associated secondary structure not correctly
2516 parsed in interleaved stockholm</li>
2517 <li>Colour by annotation dialog does not restore current
2519 <li>Hiding (nearly) all sequences doesn't work
2521 <li>Sequences containing lowercase letters are not
2522 properly associated with their pdb files</li>
2523 </ul> <em>Documentation and Development</em>
2525 <li>schemas/JalviewWsParamSet.xsd corrupted by
2526 ApplyCopyright tool</li>
2531 <div align="center">
2532 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2535 <td><em>Application</em>
2537 <li>New warning dialog when the Jalview Desktop cannot
2538 contact web services</li>
2539 <li>JABA service parameters for a preset are shown in
2540 service job window</li>
2541 <li>JABA Service menu entries reworded</li>
2545 <li>Modeller PIR IO broken - cannot correctly import a
2546 pir file emitted by Jalview</li>
2547 <li>Existing feature settings transferred to new
2548 alignment view created from cut'n'paste</li>
2549 <li>Improved test for mixed amino/nucleotide chains when
2550 parsing PDB files</li>
2551 <li>Consensus and conservation annotation rows
2552 occasionally become blank for all new windows</li>
2553 <li>Exception raised when right clicking above sequences
2554 in wrapped view mode</li>
2555 </ul> <em>Application</em>
2557 <li>multiple multiply aligned structure views cause cpu
2558 usage to hit 100% and computer to hang</li>
2559 <li>Web Service parameter layout breaks for long user
2560 parameter names</li>
2561 <li>Jaba service discovery hangs desktop if Jaba server
2568 <div align="center">
2569 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2572 <td><em>Application</em>
2574 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2575 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2578 <li>Web Services preference tab</li>
2579 <li>Analysis parameters dialog box and user defined
2581 <li>Improved speed and layout of Envision2 service menu</li>
2582 <li>Superpose structures using associated sequence
2584 <li>Export coordinates and projection as CSV from PCA
2586 </ul> <em>Applet</em>
2588 <li>enable javascript: execution by the applet via the
2589 link out mechanism</li>
2590 </ul> <em>Other</em>
2592 <li>Updated the Jmol Jalview interface to work with Jmol
2594 <li>The Jalview Desktop and JalviewLite applet now
2595 require Java 1.5</li>
2596 <li>Allow Jalview feature colour specification for GFF
2597 sequence annotation files</li>
2598 <li>New 'colour by label' keword in Jalview feature file
2599 type colour specification</li>
2600 <li>New Jalview Desktop Groovy API method that allows a
2601 script to check if it being run in an interactive session or
2602 in a batch operation from the Jalview command line</li>
2606 <li>clustalx colourscheme colours Ds preferentially when
2607 both D+E are present in over 50% of the column</li>
2608 </ul> <em>Application</em>
2610 <li>typo in AlignmentFrame->View->Hide->all but
2611 selected Regions menu item</li>
2612 <li>sequence fetcher replaces ',' for ';' when the ',' is
2613 part of a valid accession ID</li>
2614 <li>fatal OOM if object retrieved by sequence fetcher
2615 runs out of memory</li>
2616 <li>unhandled Out of Memory Error when viewing pca
2617 analysis results</li>
2618 <li>InstallAnywhere builds fail to launch on OS X java
2619 10.5 update 4 (due to apple Java 1.6 update)</li>
2620 <li>Installanywhere Jalview silently fails to launch</li>
2621 </ul> <em>Applet</em>
2623 <li>Jalview.getFeatureGroups() raises an
2624 ArrayIndexOutOfBoundsException if no feature groups are
2631 <div align="center">
2632 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2638 <li>Alignment prettyprinter doesn't cope with long
2640 <li>clustalx colourscheme colours Ds preferentially when
2641 both D+E are present in over 50% of the column</li>
2642 <li>nucleic acid structures retrieved from PDB do not
2643 import correctly</li>
2644 <li>More columns get selected than were clicked on when a
2645 number of columns are hidden</li>
2646 <li>annotation label popup menu not providing correct
2647 add/hide/show options when rows are hidden or none are
2649 <li>Stockholm format shown in list of readable formats,
2650 and parser copes better with alignments from RFAM.</li>
2651 <li>CSV output of consensus only includes the percentage
2652 of all symbols if sequence logo display is enabled</li>
2654 </ul> <em>Applet</em>
2656 <li>annotation panel disappears when annotation is
2658 </ul> <em>Application</em>
2660 <li>Alignment view not redrawn properly when new
2661 alignment opened where annotation panel is visible but no
2662 annotations are present on alignment</li>
2663 <li>pasted region containing hidden columns is
2664 incorrectly displayed in new alignment window</li>
2665 <li>Jalview slow to complete operations when stdout is
2666 flooded (fix is to close the Jalview console)</li>
2667 <li>typo in AlignmentFrame->View->Hide->all but
2668 selected Rregions menu item.</li>
2669 <li>inconsistent group submenu and Format submenu entry
2670 'Un' or 'Non'conserved</li>
2671 <li>Sequence feature settings are being shared by
2672 multiple distinct alignments</li>
2673 <li>group annotation not recreated when tree partition is
2675 <li>double click on group annotation to select sequences
2676 does not propagate to associated trees</li>
2677 <li>Mac OSX specific issues:
2679 <li>exception raised when mouse clicked on desktop
2680 window background</li>
2681 <li>Desktop menu placed on menu bar and application
2682 name set correctly</li>
2683 <li>sequence feature settings not wide enough for the
2684 save feature colourscheme button</li>
2693 <div align="center">
2694 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2697 <td><em>New Capabilities</em>
2699 <li>URL links generated from description line for
2700 regular-expression based URL links (applet and application)
2702 <li>Non-positional feature URL links are shown in link
2704 <li>Linked viewing of nucleic acid sequences and
2706 <li>Automatic Scrolling option in View menu to display
2707 the currently highlighted region of an alignment.</li>
2708 <li>Order an alignment by sequence length, or using the
2709 average score or total feature count for each sequence.</li>
2710 <li>Shading features by score or associated description</li>
2711 <li>Subdivide alignment and groups based on identity of
2712 selected subsequence (Make Groups from Selection).</li>
2713 <li>New hide/show options including Shift+Control+H to
2714 hide everything but the currently selected region.</li>
2715 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2716 </ul> <em>Application</em>
2718 <li>Fetch DB References capabilities and UI expanded to
2719 support retrieval from DAS sequence sources</li>
2720 <li>Local DAS Sequence sources can be added via the
2721 command line or via the Add local source dialog box.</li>
2722 <li>DAS Dbref and DbxRef feature types are parsed as
2723 database references and protein_name is parsed as
2724 description line (BioSapiens terms).</li>
2725 <li>Enable or disable non-positional feature and database
2726 references in sequence ID tooltip from View menu in
2728 <!-- <li>New hidden columns and rows and representatives capabilities
2729 in annotations file (in progress - not yet fully implemented)</li> -->
2730 <li>Group-associated consensus, sequence logos and
2731 conservation plots</li>
2732 <li>Symbol distributions for each column can be exported
2733 and visualized as sequence logos</li>
2734 <li>Optionally scale multi-character column labels to fit
2735 within each column of annotation row<!-- todo for applet -->
2737 <li>Optional automatic sort of associated alignment view
2738 when a new tree is opened.</li>
2739 <li>Jalview Java Console</li>
2740 <li>Better placement of desktop window when moving
2741 between different screens.</li>
2742 <li>New preference items for sequence ID tooltip and
2743 consensus annotation</li>
2744 <li>Client to submit sequences and IDs to Envision2
2746 <li><em>Vamsas Capabilities</em>
2748 <li>Improved VAMSAS synchronization (Jalview archive
2749 used to preserve views, structures, and tree display
2751 <li>Import of vamsas documents from disk or URL via
2753 <li>Sharing of selected regions between views and
2754 with other VAMSAS applications (Experimental feature!)</li>
2755 <li>Updated API to VAMSAS version 0.2</li>
2757 </ul> <em>Applet</em>
2759 <li>Middle button resizes annotation row height</li>
2762 <li>sortByTree (true/false) - automatically sort the
2763 associated alignment view by the tree when a new tree is
2765 <li>showTreeBootstraps (true/false) - show or hide
2766 branch bootstraps (default is to show them if available)</li>
2767 <li>showTreeDistances (true/false) - show or hide
2768 branch lengths (default is to show them if available)</li>
2769 <li>showUnlinkedTreeNodes (true/false) - indicate if
2770 unassociated nodes should be highlighted in the tree
2772 <li>heightScale and widthScale (1.0 or more) -
2773 increase the height or width of a cell in the alignment
2774 grid relative to the current font size.</li>
2777 <li>Non-positional features displayed in sequence ID
2779 </ul> <em>Other</em>
2781 <li>Features format: graduated colour definitions and
2782 specification of feature scores</li>
2783 <li>Alignment Annotations format: new keywords for group
2784 associated annotation (GROUP_REF) and annotation row display
2785 properties (ROW_PROPERTIES)</li>
2786 <li>XML formats extended to support graduated feature
2787 colourschemes, group associated annotation, and profile
2788 visualization settings.</li></td>
2791 <li>Source field in GFF files parsed as feature source
2792 rather than description</li>
2793 <li>Non-positional features are now included in sequence
2794 feature and gff files (controlled via non-positional feature
2795 visibility in tooltip).</li>
2796 <li>URL links generated for all feature links (bugfix)</li>
2797 <li>Added URL embedding instructions to features file
2799 <li>Codons containing ambiguous nucleotides translated as
2800 'X' in peptide product</li>
2801 <li>Match case switch in find dialog box works for both
2802 sequence ID and sequence string and query strings do not
2803 have to be in upper case to match case-insensitively.</li>
2804 <li>AMSA files only contain first column of
2805 multi-character column annotation labels</li>
2806 <li>Jalview Annotation File generation/parsing consistent
2807 with documentation (e.g. Stockholm annotation can be
2808 exported and re-imported)</li>
2809 <li>PDB files without embedded PDB IDs given a friendly
2811 <li>Find incrementally searches ID string matches as well
2812 as subsequence matches, and correctly reports total number
2816 <li>Better handling of exceptions during sequence
2818 <li>Dasobert generated non-positional feature URL
2819 link text excludes the start_end suffix</li>
2820 <li>DAS feature and source retrieval buttons disabled
2821 when fetch or registry operations in progress.</li>
2822 <li>PDB files retrieved from URLs are cached properly</li>
2823 <li>Sequence description lines properly shared via
2825 <li>Sequence fetcher fetches multiple records for all
2827 <li>Ensured that command line das feature retrieval
2828 completes before alignment figures are generated.</li>
2829 <li>Reduced time taken when opening file browser for
2831 <li>isAligned check prior to calculating tree, PCA or
2832 submitting an MSA to JNet now excludes hidden sequences.</li>
2833 <li>User defined group colours properly recovered
2834 from Jalview projects.</li>
2843 <div align="center">
2844 <strong>2.4.0.b2</strong><br> 28/10/2009
2849 <li>Experimental support for google analytics usage
2851 <li>Jalview privacy settings (user preferences and docs).</li>
2856 <li>Race condition in applet preventing startup in
2858 <li>Exception when feature created from selection beyond
2859 length of sequence.</li>
2860 <li>Allow synthetic PDB files to be imported gracefully</li>
2861 <li>Sequence associated annotation rows associate with
2862 all sequences with a given id</li>
2863 <li>Find function matches case-insensitively for sequence
2864 ID string searches</li>
2865 <li>Non-standard characters do not cause pairwise
2866 alignment to fail with exception</li>
2867 </ul> <em>Application Issues</em>
2869 <li>Sequences are now validated against EMBL database</li>
2870 <li>Sequence fetcher fetches multiple records for all
2872 </ul> <em>InstallAnywhere Issues</em>
2874 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2875 issue with installAnywhere mechanism)</li>
2876 <li>Command line launching of JARs from InstallAnywhere
2877 version (java class versioning error fixed)</li>
2884 <div align="center">
2885 <strong>2.4</strong><br> 27/8/2008
2888 <td><em>User Interface</em>
2890 <li>Linked highlighting of codon and amino acid from
2891 translation and protein products</li>
2892 <li>Linked highlighting of structure associated with
2893 residue mapping to codon position</li>
2894 <li>Sequence Fetcher provides example accession numbers
2895 and 'clear' button</li>
2896 <li>MemoryMonitor added as an option under Desktop's
2898 <li>Extract score function to parse whitespace separated
2899 numeric data in description line</li>
2900 <li>Column labels in alignment annotation can be centred.</li>
2901 <li>Tooltip for sequence associated annotation give name
2903 </ul> <em>Web Services and URL fetching</em>
2905 <li>JPred3 web service</li>
2906 <li>Prototype sequence search client (no public services
2908 <li>Fetch either seed alignment or full alignment from
2910 <li>URL Links created for matching database cross
2911 references as well as sequence ID</li>
2912 <li>URL Links can be created using regular-expressions</li>
2913 </ul> <em>Sequence Database Connectivity</em>
2915 <li>Retrieval of cross-referenced sequences from other
2917 <li>Generalised database reference retrieval and
2918 validation to all fetchable databases</li>
2919 <li>Fetch sequences from DAS sources supporting the
2920 sequence command</li>
2921 </ul> <em>Import and Export</em>
2922 <li>export annotation rows as CSV for spreadsheet import</li>
2923 <li>Jalview projects record alignment dataset associations,
2924 EMBL products, and cDNA sequence mappings</li>
2925 <li>Sequence Group colour can be specified in Annotation
2927 <li>Ad-hoc colouring of group in Annotation File using RGB
2928 triplet as name of colourscheme</li>
2929 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2931 <li>treenode binding for VAMSAS tree exchange</li>
2932 <li>local editing and update of sequences in VAMSAS
2933 alignments (experimental)</li>
2934 <li>Create new or select existing session to join</li>
2935 <li>load and save of vamsas documents</li>
2936 </ul> <em>Application command line</em>
2938 <li>-tree parameter to open trees (introduced for passing
2940 <li>-fetchfrom command line argument to specify nicknames
2941 of DAS servers to query for alignment features</li>
2942 <li>-dasserver command line argument to add new servers
2943 that are also automatically queried for features</li>
2944 <li>-groovy command line argument executes a given groovy
2945 script after all input data has been loaded and parsed</li>
2946 </ul> <em>Applet-Application data exchange</em>
2948 <li>Trees passed as applet parameters can be passed to
2949 application (when using "View in full
2950 application")</li>
2951 </ul> <em>Applet Parameters</em>
2953 <li>feature group display control parameter</li>
2954 <li>debug parameter</li>
2955 <li>showbutton parameter</li>
2956 </ul> <em>Applet API methods</em>
2958 <li>newView public method</li>
2959 <li>Window (current view) specific get/set public methods</li>
2960 <li>Feature display control methods</li>
2961 <li>get list of currently selected sequences</li>
2962 </ul> <em>New Jalview distribution features</em>
2964 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2965 <li>RELEASE file gives build properties for the latest
2966 Jalview release.</li>
2967 <li>Java 1.1 Applet build made easier and donotobfuscate
2968 property controls execution of obfuscator</li>
2969 <li>Build target for generating source distribution</li>
2970 <li>Debug flag for javacc</li>
2971 <li>.jalview_properties file is documented (slightly) in
2972 jalview.bin.Cache</li>
2973 <li>Continuous Build Integration for stable and
2974 development version of Application, Applet and source
2979 <li>selected region output includes visible annotations
2980 (for certain formats)</li>
2981 <li>edit label/displaychar contains existing label/char
2983 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2984 <li>shorter peptide product names from EMBL records</li>
2985 <li>Newick string generator makes compact representations</li>
2986 <li>bootstrap values parsed correctly for tree files with
2988 <li>pathological filechooser bug avoided by not allowing
2989 filenames containing a ':'</li>
2990 <li>Fixed exception when parsing GFF files containing
2991 global sequence features</li>
2992 <li>Alignment datasets are finalized only when number of
2993 references from alignment sequences goes to zero</li>
2994 <li>Close of tree branch colour box without colour
2995 selection causes cascading exceptions</li>
2996 <li>occasional negative imgwidth exceptions</li>
2997 <li>better reporting of non-fatal warnings to user when
2998 file parsing fails.</li>
2999 <li>Save works when Jalview project is default format</li>
3000 <li>Save as dialog opened if current alignment format is
3001 not a valid output format</li>
3002 <li>UniProt canonical names introduced for both das and
3004 <li>Histidine should be midblue (not pink!) in Zappo</li>
3005 <li>error messages passed up and output when data read
3007 <li>edit undo recovers previous dataset sequence when
3008 sequence is edited</li>
3009 <li>allow PDB files without pdb ID HEADER lines (like
3010 those generated by MODELLER) to be read in properly</li>
3011 <li>allow reading of JPred concise files as a normal
3013 <li>Stockholm annotation parsing and alignment properties
3014 import fixed for PFAM records</li>
3015 <li>Structure view windows have correct name in Desktop
3017 <li>annotation consisting of sequence associated scores
3018 can be read and written correctly to annotation file</li>
3019 <li>Aligned cDNA translation to aligned peptide works
3021 <li>Fixed display of hidden sequence markers and
3022 non-italic font for representatives in Applet</li>
3023 <li>Applet Menus are always embedded in applet window on
3025 <li>Newly shown features appear at top of stack (in
3027 <li>Annotations added via parameter not drawn properly
3028 due to null pointer exceptions</li>
3029 <li>Secondary structure lines are drawn starting from
3030 first column of alignment</li>
3031 <li>UniProt XML import updated for new schema release in
3033 <li>Sequence feature to sequence ID match for Features
3034 file is case-insensitive</li>
3035 <li>Sequence features read from Features file appended to
3036 all sequences with matching IDs</li>
3037 <li>PDB structure coloured correctly for associated views
3038 containing a sub-sequence</li>
3039 <li>PDB files can be retrieved by applet from Jar files</li>
3040 <li>feature and annotation file applet parameters
3041 referring to different directories are retrieved correctly</li>
3042 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3043 <li>Fixed application hang whilst waiting for
3044 splash-screen version check to complete</li>
3045 <li>Applet properly URLencodes input parameter values
3046 when passing them to the launchApp service</li>
3047 <li>display name and local features preserved in results
3048 retrieved from web service</li>
3049 <li>Visual delay indication for sequence retrieval and
3050 sequence fetcher initialisation</li>
3051 <li>updated Application to use DAS 1.53e version of
3052 dasobert DAS client</li>
3053 <li>Re-instated Full AMSA support and .amsa file
3055 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3063 <div align="center">
3064 <strong>2.3</strong><br> 9/5/07
3069 <li>Jmol 11.0.2 integration</li>
3070 <li>PDB views stored in Jalview XML files</li>
3071 <li>Slide sequences</li>
3072 <li>Edit sequence in place</li>
3073 <li>EMBL CDS features</li>
3074 <li>DAS Feature mapping</li>
3075 <li>Feature ordering</li>
3076 <li>Alignment Properties</li>
3077 <li>Annotation Scores</li>
3078 <li>Sort by scores</li>
3079 <li>Feature/annotation editing in applet</li>
3084 <li>Headless state operation in 2.2.1</li>
3085 <li>Incorrect and unstable DNA pairwise alignment</li>
3086 <li>Cut and paste of sequences with annotation</li>
3087 <li>Feature group display state in XML</li>
3088 <li>Feature ordering in XML</li>
3089 <li>blc file iteration selection using filename # suffix</li>
3090 <li>Stockholm alignment properties</li>
3091 <li>Stockhom alignment secondary structure annotation</li>
3092 <li>2.2.1 applet had no feature transparency</li>
3093 <li>Number pad keys can be used in cursor mode</li>
3094 <li>Structure Viewer mirror image resolved</li>
3101 <div align="center">
3102 <strong>2.2.1</strong><br> 12/2/07
3107 <li>Non standard characters can be read and displayed
3108 <li>Annotations/Features can be imported/exported to the
3110 <li>Applet allows editing of sequence/annotation/group
3111 name & description
3112 <li>Preference setting to display sequence name in
3114 <li>Annotation file format extended to allow
3115 Sequence_groups to be defined
3116 <li>Default opening of alignment overview panel can be
3117 specified in preferences
3118 <li>PDB residue numbering annotation added to associated
3124 <li>Applet crash under certain Linux OS with Java 1.6
3126 <li>Annotation file export / import bugs fixed
3127 <li>PNG / EPS image output bugs fixed
3133 <div align="center">
3134 <strong>2.2</strong><br> 27/11/06
3139 <li>Multiple views on alignment
3140 <li>Sequence feature editing
3141 <li>"Reload" alignment
3142 <li>"Save" to current filename
3143 <li>Background dependent text colour
3144 <li>Right align sequence ids
3145 <li>User-defined lower case residue colours
3148 <li>Menu item accelerator keys
3149 <li>Control-V pastes to current alignment
3150 <li>Cancel button for DAS Feature Fetching
3151 <li>PCA and PDB Viewers zoom via mouse roller
3152 <li>User-defined sub-tree colours and sub-tree selection
3154 <li>'New Window' button on the 'Output to Text box'
3159 <li>New memory efficient Undo/Redo System
3160 <li>Optimised symbol lookups and conservation/consensus
3162 <li>Region Conservation/Consensus recalculated after
3164 <li>Fixed Remove Empty Columns Bug (empty columns at end
3166 <li>Slowed DAS Feature Fetching for increased robustness.
3168 <li>Made angle brackets in ASCII feature descriptions
3170 <li>Re-instated Zoom function for PCA
3171 <li>Sequence descriptions conserved in web service
3173 <li>UniProt ID discoverer uses any word separated by
3175 <li>WsDbFetch query/result association resolved
3176 <li>Tree leaf to sequence mapping improved
3177 <li>Smooth fonts switch moved to FontChooser dialog box.
3184 <div align="center">
3185 <strong>2.1.1</strong><br> 12/9/06
3190 <li>Copy consensus sequence to clipboard</li>
3195 <li>Image output - rightmost residues are rendered if
3196 sequence id panel has been resized</li>
3197 <li>Image output - all offscreen group boundaries are
3199 <li>Annotation files with sequence references - all
3200 elements in file are relative to sequence position</li>
3201 <li>Mac Applet users can use Alt key for group editing</li>
3207 <div align="center">
3208 <strong>2.1</strong><br> 22/8/06
3213 <li>MAFFT Multiple Alignment in default Web Service list</li>
3214 <li>DAS Feature fetching</li>
3215 <li>Hide sequences and columns</li>
3216 <li>Export Annotations and Features</li>
3217 <li>GFF file reading / writing</li>
3218 <li>Associate structures with sequences from local PDB
3220 <li>Add sequences to exisiting alignment</li>
3221 <li>Recently opened files / URL lists</li>
3222 <li>Applet can launch the full application</li>
3223 <li>Applet has transparency for features (Java 1.2
3225 <li>Applet has user defined colours parameter</li>
3226 <li>Applet can load sequences from parameter
3227 "sequence<em>x</em>"
3233 <li>Redundancy Panel reinstalled in the Applet</li>
3234 <li>Monospaced font - EPS / rescaling bug fixed</li>
3235 <li>Annotation files with sequence references bug fixed</li>
3241 <div align="center">
3242 <strong>2.08.1</strong><br> 2/5/06
3247 <li>Change case of selected region from Popup menu</li>
3248 <li>Choose to match case when searching</li>
3249 <li>Middle mouse button and mouse movement can compress /
3250 expand the visible width and height of the alignment</li>
3255 <li>Annotation Panel displays complete JNet results</li>
3261 <div align="center">
3262 <strong>2.08b</strong><br> 18/4/06
3268 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3269 <li>Righthand label on wrapped alignments shows correct
3276 <div align="center">
3277 <strong>2.08</strong><br> 10/4/06
3282 <li>Editing can be locked to the selection area</li>
3283 <li>Keyboard editing</li>
3284 <li>Create sequence features from searches</li>
3285 <li>Precalculated annotations can be loaded onto
3287 <li>Features file allows grouping of features</li>
3288 <li>Annotation Colouring scheme added</li>
3289 <li>Smooth fonts off by default - Faster rendering</li>
3290 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3295 <li>Drag & Drop fixed on Linux</li>
3296 <li>Jalview Archive file faster to load/save, sequence
3297 descriptions saved.</li>
3303 <div align="center">
3304 <strong>2.07</strong><br> 12/12/05
3309 <li>PDB Structure Viewer enhanced</li>
3310 <li>Sequence Feature retrieval and display enhanced</li>
3311 <li>Choose to output sequence start-end after sequence
3312 name for file output</li>
3313 <li>Sequence Fetcher WSDBFetch@EBI</li>
3314 <li>Applet can read feature files, PDB files and can be
3315 used for HTML form input</li>
3320 <li>HTML output writes groups and features</li>
3321 <li>Group editing is Control and mouse click</li>
3322 <li>File IO bugs</li>
3328 <div align="center">
3329 <strong>2.06</strong><br> 28/9/05
3334 <li>View annotations in wrapped mode</li>
3335 <li>More options for PCA viewer</li>
3340 <li>GUI bugs resolved</li>
3341 <li>Runs with -nodisplay from command line</li>
3347 <div align="center">
3348 <strong>2.05b</strong><br> 15/9/05
3353 <li>Choose EPS export as lineart or text</li>
3354 <li>Jar files are executable</li>
3355 <li>Can read in Uracil - maps to unknown residue</li>
3360 <li>Known OutOfMemory errors give warning message</li>
3361 <li>Overview window calculated more efficiently</li>
3362 <li>Several GUI bugs resolved</li>
3368 <div align="center">
3369 <strong>2.05</strong><br> 30/8/05
3374 <li>Edit and annotate in "Wrapped" view</li>
3379 <li>Several GUI bugs resolved</li>
3385 <div align="center">
3386 <strong>2.04</strong><br> 24/8/05
3391 <li>Hold down mouse wheel & scroll to change font
3397 <li>Improved JPred client reliability</li>
3398 <li>Improved loading of Jalview files</li>
3404 <div align="center">
3405 <strong>2.03</strong><br> 18/8/05
3410 <li>Set Proxy server name and port in preferences</li>
3411 <li>Multiple URL links from sequence ids</li>
3412 <li>User Defined Colours can have a scheme name and added
3414 <li>Choose to ignore gaps in consensus calculation</li>
3415 <li>Unix users can set default web browser</li>
3416 <li>Runs without GUI for batch processing</li>
3417 <li>Dynamically generated Web Service Menus</li>
3422 <li>InstallAnywhere download for Sparc Solaris</li>
3428 <div align="center">
3429 <strong>2.02</strong><br> 18/7/05
3435 <li>Copy & Paste order of sequences maintains
3436 alignment order.</li>
3442 <div align="center">
3443 <strong>2.01</strong><br> 12/7/05
3448 <li>Use delete key for deleting selection.</li>
3449 <li>Use Mouse wheel to scroll sequences.</li>
3450 <li>Help file updated to describe how to add alignment
3452 <li>Version and build date written to build properties
3454 <li>InstallAnywhere installation will check for updates
3455 at launch of Jalview.</li>
3460 <li>Delete gaps bug fixed.</li>
3461 <li>FileChooser sorts columns.</li>
3462 <li>Can remove groups one by one.</li>
3463 <li>Filechooser icons installed.</li>
3464 <li>Finder ignores return character when searching.
3465 Return key will initiate a search.<br>
3472 <div align="center">
3473 <strong>2.0</strong><br> 20/6/05
3478 <li>New codebase</li>