3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
34 /* separate the items from eachother */
41 /* doesnt get processed in javahelp */
50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.3">2.10.3</a><br />
74 <em>10/10/2017</em></strong>
77 <td><div align="left">
81 <!-- JAL-2446 -->Faster and more efficient management and
82 rendering of sequence features
85 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
86 429 rate limit request hander
90 <td><div align="left">
93 <li><!-- JAL-2728 -->Protein annotation panel too high in CDS/Protein view
95 <li><!-- JAL-2757 -->Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs
101 <td width="60" nowrap>
103 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
104 <em>2/10/2017</em></strong>
107 <td><div align="left">
108 <em>New features in Jalview Desktop</em>
111 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
113 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
117 <td><div align="left">
121 <td width="60" nowrap>
123 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
124 <em>7/9/2017</em></strong>
127 <td><div align="left">
131 <!-- JAL-2588 -->Show gaps in overview window by colouring
132 in grey (sequences used to be coloured grey, and gaps were
136 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
140 <!-- JAL-2587 -->Overview updates immediately on increase
141 in size and progress bar shown as higher resolution
142 overview is recalculated
147 <td><div align="left">
151 <!-- JAL-2664 -->Overview window redraws every hidden
152 column region row by row
155 <!-- JAL-2681 -->duplicate protein sequences shown after
156 retrieving Ensembl crossrefs for sequences from Uniprot
159 <!-- JAL-2603 -->Overview window throws NPE if show boxes
160 format setting is unticked
163 <!-- JAL-2610 -->Groups are coloured wrongly in overview
164 if group has show boxes format setting unticked
167 <!-- JAL-2672,JAL-2665 -->Redraw problems when
168 autoscrolling whilst dragging current selection group to
169 include sequences and columns not currently displayed
172 <!-- JAL-2691 -->Not all chains are mapped when multimeric
173 assemblies are imported via CIF file
176 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
177 displayed when threshold or conservation colouring is also
181 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
185 <!-- JAL-2673 -->Jalview continues to scroll after
186 dragging a selected region off the visible region of the
190 <!-- JAL-2724 -->Cannot apply annotation based
191 colourscheme to all groups in a view
194 <!-- JAL-2511 -->IDs don't line up with sequences
195 initially after font size change using the Font chooser or
202 <td width="60" nowrap>
204 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
207 <td><div align="left">
208 <em>Calculations</em>
212 <!-- JAL-1933 -->Occupancy annotation row shows number of
213 ungapped positions in each column of the alignment.
216 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
217 a calculation dialog box
220 <!-- JAL-2379 -->Revised implementation of PCA for speed
221 and memory efficiency (~30x faster)
224 <!-- JAL-2403 -->Revised implementation of sequence
225 similarity scores as used by Tree, PCA, Shading Consensus
226 and other calculations
229 <!-- JAL-2416 -->Score matrices are stored as resource
230 files within the Jalview codebase
233 <!-- JAL-2500 -->Trees computed on Sequence Feature
234 Similarity may have different topology due to increased
241 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
242 model for alignments and groups
245 <!-- JAL-384 -->Custom shading schemes created via groovy
252 <!-- JAL-2526 -->Efficiency improvements for interacting
253 with alignment and overview windows
256 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
260 <!-- JAL-2388 -->Hidden columns and sequences can be
264 <!-- JAL-2611 -->Click-drag in visible area allows fine
265 adjustment of visible position
269 <em>Data import/export</em>
272 <!-- JAL-2535 -->Posterior probability annotation from
273 Stockholm files imported as sequence associated annotation
276 <!-- JAL-2507 -->More robust per-sequence positional
277 annotation input/output via stockholm flatfile
280 <!-- JAL-2533 -->Sequence names don't include file
281 extension when importing structure files without embedded
282 names or PDB accessions
285 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
286 format sequence substitution matrices
289 <em>User Interface</em>
292 <!-- JAL-2447 --> Experimental Features Checkbox in
293 Desktop's Tools menu to hide or show untested features in
297 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
298 via Overview or sequence motif search operations
301 <!-- JAL-2547 -->Amend sequence features dialog box can be
302 opened by double clicking gaps within sequence feature
306 <!-- JAL-1476 -->Status bar message shown when not enough
307 aligned positions were available to create a 3D structure
311 <em>3D Structure</em>
314 <!-- JAL-2430 -->Hidden regions in alignment views are not
315 coloured in linked structure views
318 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
319 file-based command exchange
322 <!-- JAL-2375 -->Structure chooser automatically shows
323 Cached Structures rather than querying the PDBe if
324 structures are already available for sequences
327 <!-- JAL-2520 -->Structures imported via URL are cached in
328 the Jalview project rather than downloaded again when the
332 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
333 to transfer Chimera's structure attributes as Jalview
334 features, and vice-versa (<strong>Experimental
338 <em>Web Services</em>
341 <!-- JAL-2549 -->Updated JABAWS client to v2.2
344 <!-- JAL-2335 -->Filter non-standard amino acids and
345 nucleotides when submitting to AACon and other MSA
349 <!-- JAL-2316, -->URLs for viewing database
350 cross-references provided by identifiers.org and the
358 <!-- JAL-2344 -->FileFormatI interface for describing and
359 identifying file formats (instead of String constants)
362 <!-- JAL-2228 -->FeatureCounter script refactored for
363 efficiency when counting all displayed features (not
364 backwards compatible with 2.10.1)
367 <em>Example files</em>
370 <!-- JAL-2631 -->Graduated feature colour style example
371 included in the example feature file
374 <em>Documentation</em>
377 <!-- JAL-2339 -->Release notes reformatted for readability
378 with the built-in Java help viewer
381 <!-- JAL-1644 -->Find documentation updated with 'search
382 sequence description' option
388 <!-- JAL-2485, -->External service integration tests for
389 Uniprot REST Free Text Search Client
392 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
395 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
400 <td><div align="left">
401 <em>Calculations</em>
404 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
405 matrix - C->R should be '-3'<br />Old matrix restored
406 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
408 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
409 Jalview's treatment of gaps in PCA and substitution matrix
410 based Tree calculations.<br /> <br />In earlier versions
411 of Jalview, gaps matching gaps were penalised, and gaps
412 matching non-gaps penalised even more. In the PCA
413 calculation, gaps were actually treated as non-gaps - so
414 different costs were applied, which meant Jalview's PCAs
415 were different to those produced by SeqSpace.<br />Jalview
416 now treats gaps in the same way as SeqSpace (ie it scores
417 them as 0). <br /> <br />Enter the following in the
418 Groovy console to restore pre-2.10.2 behaviour:<br />
419 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
420 // for 2.10.1 mode <br />
421 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
422 // to restore 2.10.2 mode <br /> <br /> <em>Note:
423 these settings will affect all subsequent tree and PCA
424 calculations (not recommended)</em></li>
426 <!-- JAL-2424 -->Fixed off-by-one bug that affected
427 scaling of branch lengths for trees computed using
428 Sequence Feature Similarity.
431 <!-- JAL-2377 -->PCA calculation could hang when
432 generating output report when working with highly
436 <!-- JAL-2544 --> Sort by features includes features to
437 right of selected region when gaps present on right-hand
441 <em>User Interface</em>
444 <!-- JAL-2346 -->Reopening Colour by annotation dialog
445 doesn't reselect a specific sequence's associated
446 annotation after it was used for colouring a view
449 <!-- JAL-2419 -->Current selection lost if popup menu
450 opened on a region of alignment without groups
453 <!-- JAL-2374 -->Popup menu not always shown for regions
454 of an alignment with overlapping groups
457 <!-- JAL-2310 -->Finder double counts if both a sequence's
458 name and description match
461 <!-- JAL-2370 -->Hiding column selection containing two
462 hidden regions results in incorrect hidden regions
465 <!-- JAL-2386 -->'Apply to all groups' setting when
466 changing colour does not apply Conservation slider value
470 <!-- JAL-2373 -->Percentage identity and conservation menu
471 items do not show a tick or allow shading to be disabled
474 <!-- JAL-2385 -->Conservation shading or PID threshold
475 lost when base colourscheme changed if slider not visible
478 <!-- JAL-2547 -->Sequence features shown in tooltip for
479 gaps before start of features
482 <!-- JAL-2623 -->Graduated feature colour threshold not
483 restored to UI when feature colour is edited
486 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
487 a time when scrolling vertically in wrapped mode.
490 <!-- JAL-2630 -->Structure and alignment overview update
491 as graduate feature colour settings are modified via the
495 <!-- JAL-2034 -->Overview window doesn't always update
496 when a group defined on the alignment is resized
499 <!-- JAL-2605 -->Mouseovers on left/right scale region in
500 wrapped view result in positional status updates
504 <!-- JAL-2563 -->Status bar doesn't show position for
505 ambiguous amino acid and nucleotide symbols
508 <!-- JAL-2602 -->Copy consensus sequence failed if
509 alignment included gapped columns
512 <!-- JAL-2473 -->Minimum size set for Jalview windows so
513 widgets don't permanently disappear
516 <!-- JAL-2503 -->Cannot select or filter quantitative
517 annotation that are shown only as column labels (e.g.
518 T-Coffee column reliability scores)
521 <!-- JAL-2594 -->Exception thrown if trying to create a
522 sequence feature on gaps only
525 <!-- JAL-2504 -->Features created with 'New feature'
526 button from a Find inherit previously defined feature type
527 rather than the Find query string
530 <!-- JAL-2423 -->incorrect title in output window when
531 exporting tree calculated in Jalview
534 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
535 and then revealing them reorders sequences on the
539 <!-- JAL-964 -->Group panel in sequence feature settings
540 doesn't update to reflect available set of groups after
541 interactively adding or modifying features
544 <!-- JAL-2225 -->Sequence Database chooser unusable on
548 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
549 only excluded gaps in current sequence and ignored
556 <!-- JAL-2421 -->Overview window visible region moves
557 erratically when hidden rows or columns are present
560 <!-- JAL-2362 -->Per-residue colourschemes applied via the
561 Structure Viewer's colour menu don't correspond to
565 <!-- JAL-2405 -->Protein specific colours only offered in
566 colour and group colour menu for protein alignments
569 <!-- JAL-2385 -->Colour threshold slider doesn't update to
570 reflect currently selected view or group's shading
574 <!-- JAL-2624 -->Feature colour thresholds not respected
575 when rendered on overview and structures when opacity at
579 <!-- JAL-2589 -->User defined gap colour not shown in
580 overview when features overlaid on alignment
583 <em>Data import/export</em>
586 <!-- JAL-2576 -->Very large alignments take a long time to
590 <!-- JAL-2507 -->Per-sequence RNA secondary structures
591 added after a sequence was imported are not written to
595 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
596 when importing RNA secondary structure via Stockholm
599 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
600 not shown in correct direction for simple pseudoknots
603 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
604 with lightGray or darkGray via features file (but can
608 <!-- JAL-2383 -->Above PID colour threshold not recovered
609 when alignment view imported from project
612 <!-- JAL-2520,JAL-2465 -->No mappings generated between
613 structure and sequences extracted from structure files
614 imported via URL and viewed in Jmol
617 <!-- JAL-2520 -->Structures loaded via URL are saved in
618 Jalview Projects rather than fetched via URL again when
619 the project is loaded and the structure viewed
622 <em>Web Services</em>
625 <!-- JAL-2519 -->EnsemblGenomes example failing after
626 release of Ensembl v.88
629 <!-- JAL-2366 -->Proxy server address and port always
630 appear enabled in Preferences->Connections
633 <!-- JAL-2461 -->DAS registry not found exceptions
634 removed from console output
637 <!-- JAL-2582 -->Cannot retrieve protein products from
638 Ensembl by Peptide ID
641 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
642 created from SIFTs, and spurious 'Couldn't open structure
643 in Chimera' errors raised after April 2017 update (problem
644 due to 'null' string rather than empty string used for
645 residues with no corresponding PDB mapping).
648 <em>Application UI</em>
651 <!-- JAL-2361 -->User Defined Colours not added to Colour
655 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
656 case' residues (button in colourscheme editor debugged and
657 new documentation and tooltips added)
660 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
661 doesn't restore group-specific text colour thresholds
664 <!-- JAL-2243 -->Feature settings panel does not update as
665 new features are added to alignment
668 <!-- JAL-2532 -->Cancel in feature settings reverts
669 changes to feature colours via the Amend features dialog
672 <!-- JAL-2506 -->Null pointer exception when attempting to
673 edit graduated feature colour via amend features dialog
677 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
678 selection menu changes colours of alignment views
681 <!-- JAL-2426 -->Spurious exceptions in console raised
682 from alignment calculation workers after alignment has
686 <!-- JAL-1608 -->Typo in selection popup menu - Create
687 groups now 'Create Group'
690 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
691 Create/Undefine group doesn't always work
694 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
695 shown again after pressing 'Cancel'
698 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
699 adjusts start position in wrap mode
702 <!-- JAL-2563 -->Status bar doesn't show positions for
703 ambiguous amino acids
706 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
707 CDS/Protein view after CDS sequences added for aligned
711 <!-- JAL-2592 -->User defined colourschemes called 'User
712 Defined' don't appear in Colours menu
718 <!-- JAL-2468 -->Switching between Nucleotide and Protein
719 score models doesn't always result in an updated PCA plot
722 <!-- JAL-2442 -->Features not rendered as transparent on
723 overview or linked structure view
726 <!-- JAL-2372 -->Colour group by conservation doesn't
730 <!-- JAL-2517 -->Hitting Cancel after applying
731 user-defined colourscheme doesn't restore original
738 <!-- JAL-2314 -->Unit test failure:
739 jalview.ws.jabaws.RNAStructExportImport setup fails
742 <!-- JAL-2307 -->Unit test failure:
743 jalview.ws.sifts.SiftsClientTest due to compatibility
744 problems with deep array comparison equality asserts in
745 successive versions of TestNG
748 <!-- JAL-2479 -->Relocated StructureChooserTest and
749 ParameterUtilsTest Unit tests to Network suite
752 <em>New Known Issues</em>
755 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
756 phase after a sequence motif find operation
759 <!-- JAL-2550 -->Importing annotation file with rows
760 containing just upper and lower case letters are
761 interpreted as WUSS RNA secondary structure symbols
764 <!-- JAL-2590 -->Cannot load and display Newick trees
765 reliably from eggnog Ortholog database
768 <!-- JAL-2468 -->Status bar shows 'Marked x columns
769 containing features of type Highlight' when 'B' is pressed
770 to mark columns containing highlighted regions.
773 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
774 doesn't always add secondary structure annotation.
779 <td width="60" nowrap>
781 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
784 <td><div align="left">
788 <!-- JAL-98 -->Improved memory usage: sparse arrays used
789 for all consensus calculations
792 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
795 <li>Updated Jalview's Certum code signing certificate
801 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
802 set of database cross-references, sorted alphabetically
805 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
806 from database cross references. Users with custom links
807 will receive a <a href="webServices/urllinks.html#warning">warning
808 dialog</a> asking them to update their preferences.
811 <!-- JAL-2287-->Cancel button and escape listener on
812 dialog warning user about disconnecting Jalview from a
816 <!-- JAL-2320-->Jalview's Chimera control window closes if
817 the Chimera it is connected to is shut down
820 <!-- JAL-1738-->New keystroke (B) and Select highlighted
821 columns menu item to mark columns containing highlighted
822 regions (e.g. from structure selections or results of a
826 <!-- JAL-2284-->Command line option for batch-generation
827 of HTML pages rendering alignment data with the BioJS
837 <!-- JAL-2286 -->Columns with more than one modal residue
838 are not coloured or thresholded according to percent
839 identity (first observed in Jalview 2.8.2)
842 <!-- JAL-2301 -->Threonine incorrectly reported as not
846 <!-- JAL-2318 -->Updates to documentation pages (above PID
847 threshold, amino acid properties)
850 <!-- JAL-2292 -->Lower case residues in sequences are not
851 reported as mapped to residues in a structure file in the
855 <!--JAL-2324 -->Identical features with non-numeric scores
856 could be added multiple times to a sequence
859 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
860 bond features shown as two highlighted residues rather
861 than a range in linked structure views, and treated
862 correctly when selecting and computing trees from features
865 <!-- JAL-2281-->Custom URL links for database
866 cross-references are matched to database name regardless
874 <!-- JAL-2282-->Custom URL links for specific database
875 names without regular expressions also offer links from
879 <!-- JAL-2315-->Removing a single configured link in the
880 URL links pane in Connections preferences doesn't actually
881 update Jalview configuration
884 <!-- JAL-2272-->CTRL-Click on a selected region to open
885 the alignment area popup menu doesn't work on El-Capitan
888 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
889 files with similarly named sequences if dropped onto the
893 <!-- JAL-2312 -->Additional mappings are shown for PDB
894 entries where more chains exist in the PDB accession than
895 are reported in the SIFTS file
898 <!-- JAL-2317-->Certain structures do not get mapped to
899 the structure view when displayed with Chimera
902 <!-- JAL-2317-->No chains shown in the Chimera view
903 panel's View->Show Chains submenu
906 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
907 work for wrapped alignment views
910 <!--JAL-2197 -->Rename UI components for running JPred
911 predictions from 'JNet' to 'JPred'
914 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
915 corrupted when annotation panel vertical scroll is not at
919 <!--JAL-2332 -->Attempting to view structure for Hen
920 lysozyme results in a PDB Client error dialog box
923 <!-- JAL-2319 -->Structure View's mapping report switched
924 ranges for PDB and sequence for SIFTS
927 SIFTS 'Not_Observed' residues mapped to non-existant
931 <!-- <em>New Known Issues</em>
938 <td width="60" nowrap>
940 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
941 <em>25/10/2016</em></strong>
944 <td><em>Application</em>
946 <li>3D Structure chooser opens with 'Cached structures'
947 view if structures already loaded</li>
948 <li>Progress bar reports models as they are loaded to
955 <li>Colour by conservation always enabled and no tick
956 shown in menu when BLOSUM or PID shading applied</li>
957 <li>FER1_ARATH and FER2_ARATH labels were switched in
958 example sequences/projects/trees</li>
962 <li>Jalview projects with views of local PDB structure
963 files saved on Windows cannot be opened on OSX</li>
964 <li>Multiple structure views can be opened and superposed
965 without timeout for structures with multiple models or
966 multiple sequences in alignment</li>
967 <li>Cannot import or associated local PDB files without a
968 PDB ID HEADER line</li>
969 <li>RMSD is not output in Jmol console when superposition
971 <li>Drag and drop of URL from Browser fails for Linux and
972 OSX versions earlier than El Capitan</li>
973 <li>ENA client ignores invalid content from ENA server</li>
974 <li>Exceptions are not raised in console when ENA client
975 attempts to fetch non-existent IDs via Fetch DB Refs UI
977 <li>Exceptions are not raised in console when a new view
978 is created on the alignment</li>
979 <li>OSX right-click fixed for group selections: CMD-click
980 to insert/remove gaps in groups and CTRL-click to open group
983 <em>Build and deployment</em>
985 <li>URL link checker now copes with multi-line anchor
988 <em>New Known Issues</em>
990 <li>Drag and drop from URL links in browsers do not work
997 <td width="60" nowrap>
999 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1002 <td><em>General</em>
1005 <!-- JAL-2124 -->Updated Spanish translations.
1008 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1009 for importing structure data to Jalview. Enables mmCIF and
1013 <!-- JAL-192 --->Alignment ruler shows positions relative to
1017 <!-- JAL-2202 -->Position/residue shown in status bar when
1018 mousing over sequence associated annotation
1021 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1025 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1026 '()', canonical '[]' and invalid '{}' base pair populations
1030 <!-- JAL-2092 -->Feature settings popup menu options for
1031 showing or hiding columns containing a feature
1034 <!-- JAL-1557 -->Edit selected group by double clicking on
1035 group and sequence associated annotation labels
1038 <!-- JAL-2236 -->Sequence name added to annotation label in
1039 select/hide columns by annotation and colour by annotation
1043 </ul> <em>Application</em>
1046 <!-- JAL-2050-->Automatically hide introns when opening a
1047 gene/transcript view
1050 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1054 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1055 structure mappings with the EMBL-EBI PDBe SIFTS database
1058 <!-- JAL-2079 -->Updated download sites used for Rfam and
1059 Pfam sources to xfam.org
1062 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1065 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1066 over sequences in Jalview
1069 <!-- JAL-2027-->Support for reverse-complement coding
1070 regions in ENA and EMBL
1073 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1074 for record retrieval via ENA rest API
1077 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1081 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1082 groovy script execution
1085 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1086 alignment window's Calculate menu
1089 <!-- JAL-1812 -->Allow groovy scripts that call
1090 Jalview.getAlignFrames() to run in headless mode
1093 <!-- JAL-2068 -->Support for creating new alignment
1094 calculation workers from groovy scripts
1097 <!-- JAL-1369 --->Store/restore reference sequence in
1101 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1102 associations are now saved/restored from project
1105 <!-- JAL-1993 -->Database selection dialog always shown
1106 before sequence fetcher is opened
1109 <!-- JAL-2183 -->Double click on an entry in Jalview's
1110 database chooser opens a sequence fetcher
1113 <!-- JAL-1563 -->Free-text search client for UniProt using
1114 the UniProt REST API
1117 <!-- JAL-2168 -->-nonews command line parameter to prevent
1118 the news reader opening
1121 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1122 querying stored in preferences
1125 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1129 <!-- JAL-1977-->Tooltips shown on database chooser
1132 <!-- JAL-391 -->Reverse complement function in calculate
1133 menu for nucleotide sequences
1136 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1137 and feature counts preserves alignment ordering (and
1138 debugged for complex feature sets).
1141 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1142 viewing structures with Jalview 2.10
1145 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1146 genome, transcript CCDS and gene ids via the Ensembl and
1147 Ensembl Genomes REST API
1150 <!-- JAL-2049 -->Protein sequence variant annotation
1151 computed for 'sequence_variant' annotation on CDS regions
1155 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1159 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1160 Ref Fetcher fails to match, or otherwise updates sequence
1161 data from external database records.
1164 <!-- JAL-2154 -->Revised Jalview Project format for
1165 efficient recovery of sequence coding and alignment
1166 annotation relationships.
1168 </ul> <!-- <em>Applet</em>
1179 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1183 <!-- JAL-2018-->Export features in Jalview format (again)
1184 includes graduated colourschemes
1187 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1188 working with big alignments and lots of hidden columns
1191 <!-- JAL-2053-->Hidden column markers not always rendered
1192 at right of alignment window
1195 <!-- JAL-2067 -->Tidied up links in help file table of
1199 <!-- JAL-2072 -->Feature based tree calculation not shown
1203 <!-- JAL-2075 -->Hidden columns ignored during feature
1204 based tree calculation
1207 <!-- JAL-2065 -->Alignment view stops updating when show
1208 unconserved enabled for group on alignment
1211 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1215 <!-- JAL-2146 -->Alignment column in status incorrectly
1216 shown as "Sequence position" when mousing over
1220 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1221 hidden columns present
1224 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1225 user created annotation added to alignment
1228 <!-- JAL-1841 -->RNA Structure consensus only computed for
1229 '()' base pair annotation
1232 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1233 in zero scores for all base pairs in RNA Structure
1237 <!-- JAL-2174-->Extend selection with columns containing
1241 <!-- JAL-2275 -->Pfam format writer puts extra space at
1242 beginning of sequence
1245 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1249 <!-- JAL-2238 -->Cannot create groups on an alignment from
1250 from a tree when t-coffee scores are shown
1253 <!-- JAL-1836,1967 -->Cannot import and view PDB
1254 structures with chains containing negative resnums (4q4h)
1257 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1261 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1262 to Clustal, PIR and PileUp output
1265 <!-- JAL-2008 -->Reordering sequence features that are
1266 not visible causes alignment window to repaint
1269 <!-- JAL-2006 -->Threshold sliders don't work in
1270 graduated colour and colour by annotation row for e-value
1271 scores associated with features and annotation rows
1274 <!-- JAL-1797 -->amino acid physicochemical conservation
1275 calculation should be case independent
1278 <!-- JAL-2173 -->Remove annotation also updates hidden
1282 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1283 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1284 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1287 <!-- JAL-2065 -->Null pointer exceptions and redraw
1288 problems when reference sequence defined and 'show
1289 non-conserved' enabled
1292 <!-- JAL-1306 -->Quality and Conservation are now shown on
1293 load even when Consensus calculation is disabled
1296 <!-- JAL-1932 -->Remove right on penultimate column of
1297 alignment does nothing
1300 <em>Application</em>
1303 <!-- JAL-1552-->URLs and links can't be imported by
1304 drag'n'drop on OSX when launched via webstart (note - not
1305 yet fixed for El Capitan)
1308 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1309 output when running on non-gb/us i18n platforms
1312 <!-- JAL-1944 -->Error thrown when exporting a view with
1313 hidden sequences as flat-file alignment
1316 <!-- JAL-2030-->InstallAnywhere distribution fails when
1320 <!-- JAL-2080-->Jalview very slow to launch via webstart
1321 (also hotfix for 2.9.0b2)
1324 <!-- JAL-2085 -->Cannot save project when view has a
1325 reference sequence defined
1328 <!-- JAL-1011 -->Columns are suddenly selected in other
1329 alignments and views when revealing hidden columns
1332 <!-- JAL-1989 -->Hide columns not mirrored in complement
1333 view in a cDNA/Protein splitframe
1336 <!-- JAL-1369 -->Cannot save/restore representative
1337 sequence from project when only one sequence is
1341 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1342 in Structure Chooser
1345 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1346 structure consensus didn't refresh annotation panel
1349 <!-- JAL-1962 -->View mapping in structure view shows
1350 mappings between sequence and all chains in a PDB file
1353 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1354 dialogs format columns correctly, don't display array
1355 data, sort columns according to type
1358 <!-- JAL-1975 -->Export complete shown after destination
1359 file chooser is cancelled during an image export
1362 <!-- JAL-2025 -->Error when querying PDB Service with
1363 sequence name containing special characters
1366 <!-- JAL-2024 -->Manual PDB structure querying should be
1370 <!-- JAL-2104 -->Large tooltips with broken HTML
1371 formatting don't wrap
1374 <!-- JAL-1128 -->Figures exported from wrapped view are
1375 truncated so L looks like I in consensus annotation
1378 <!-- JAL-2003 -->Export features should only export the
1379 currently displayed features for the current selection or
1383 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1384 after fetching cross-references, and restoring from
1388 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1389 followed in the structure viewer
1392 <!-- JAL-2163 -->Titles for individual alignments in
1393 splitframe not restored from project
1396 <!-- JAL-2145 -->missing autocalculated annotation at
1397 trailing end of protein alignment in transcript/product
1398 splitview when pad-gaps not enabled by default
1401 <!-- JAL-1797 -->amino acid physicochemical conservation
1405 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1406 article has been read (reopened issue due to
1407 internationalisation problems)
1410 <!-- JAL-1960 -->Only offer PDB structures in structure
1411 viewer based on sequence name, PDB and UniProt
1416 <!-- JAL-1976 -->No progress bar shown during export of
1420 <!-- JAL-2213 -->Structures not always superimposed after
1421 multiple structures are shown for one or more sequences.
1424 <!-- JAL-1370 -->Reference sequence characters should not
1425 be replaced with '.' when 'Show unconserved' format option
1429 <!-- JAL-1823 -->Cannot specify chain code when entering
1430 specific PDB id for sequence
1433 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1434 'Export hidden sequences' is enabled, but 'export hidden
1435 columns' is disabled.
1438 <!--JAL-2026-->Best Quality option in structure chooser
1439 selects lowest rather than highest resolution structures
1443 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1444 to sequence mapping in 'View Mappings' report
1447 <!-- JAL-2284 -->Unable to read old Jalview projects that
1448 contain non-XML data added after Jalvew wrote project.
1451 <!-- JAL-2118 -->Newly created annotation row reorders
1452 after clicking on it to create new annotation for a
1455 <!-- may exclude, this is an external service stability issue JAL-1941
1456 -- > RNA 3D structure not added via DSSR service</li> -->
1461 <!-- JAL-2151 -->Incorrect columns are selected when
1462 hidden columns present before start of sequence
1465 <!-- JAL-1986 -->Missing dependencies on applet pages
1469 <!-- JAL-1947 -->Overview pixel size changes when
1470 sequences are hidden in applet
1473 <!-- JAL-1996 -->Updated instructions for applet
1474 deployment on examples pages.
1481 <td width="60" nowrap>
1482 <div align="center">
1483 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1484 <em>16/10/2015</em></strong>
1487 <td><em>General</em>
1489 <li>Time stamps for signed Jalview application and applet
1494 <em>Application</em>
1496 <li>Duplicate group consensus and conservation rows
1497 shown when tree is partitioned</li>
1498 <li>Erratic behaviour when tree partitions made with
1499 multiple cDNA/Protein split views</li>
1505 <td width="60" nowrap>
1506 <div align="center">
1507 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1508 <em>8/10/2015</em></strong>
1511 <td><em>General</em>
1513 <li>Updated Spanish translations of localized text for
1515 </ul> <em>Application</em>
1517 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1518 <li>Signed OSX InstallAnywhere installer<br></li>
1519 <li>Support for per-sequence based annotations in BioJSON</li>
1520 </ul> <em>Applet</em>
1522 <li>Split frame example added to applet examples page</li>
1523 </ul> <em>Build and Deployment</em>
1526 <!-- JAL-1888 -->New ant target for running Jalview's test
1534 <li>Mapping of cDNA to protein in split frames
1535 incorrect when sequence start > 1</li>
1536 <li>Broken images in filter column by annotation dialog
1538 <li>Feature colours not parsed from features file</li>
1539 <li>Exceptions and incomplete link URLs recovered when
1540 loading a features file containing HTML tags in feature
1544 <em>Application</em>
1546 <li>Annotations corrupted after BioJS export and
1548 <li>Incorrect sequence limits after Fetch DB References
1549 with 'trim retrieved sequences'</li>
1550 <li>Incorrect warning about deleting all data when
1551 deleting selected columns</li>
1552 <li>Patch to build system for shipping properly signed
1553 JNLP templates for webstart launch</li>
1554 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1555 unreleased structures for download or viewing</li>
1556 <li>Tab/space/return keystroke operation of EMBL-PDBe
1557 fetcher/viewer dialogs works correctly</li>
1558 <li>Disabled 'minimise' button on Jalview windows
1559 running on OSX to workaround redraw hang bug</li>
1560 <li>Split cDNA/Protein view position and geometry not
1561 recovered from jalview project</li>
1562 <li>Initial enabled/disabled state of annotation menu
1563 sorter 'show autocalculated first/last' corresponds to
1565 <li>Restoring of Clustal, RNA Helices and T-Coffee
1566 color schemes from BioJSON</li>
1570 <li>Reorder sequences mirrored in cDNA/Protein split
1572 <li>Applet with Jmol examples not loading correctly</li>
1578 <td><div align="center">
1579 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1581 <td><em>General</em>
1583 <li>Linked visualisation and analysis of DNA and Protein
1586 <li>Translated cDNA alignments shown as split protein
1587 and DNA alignment views</li>
1588 <li>Codon consensus annotation for linked protein and
1589 cDNA alignment views</li>
1590 <li>Link cDNA or Protein product sequences by loading
1591 them onto Protein or cDNA alignments</li>
1592 <li>Reconstruct linked cDNA alignment from aligned
1593 protein sequences</li>
1596 <li>Jmol integration updated to Jmol v14.2.14</li>
1597 <li>Import and export of Jalview alignment views as <a
1598 href="features/bioJsonFormat.html">BioJSON</a></li>
1599 <li>New alignment annotation file statements for
1600 reference sequences and marking hidden columns</li>
1601 <li>Reference sequence based alignment shading to
1602 highlight variation</li>
1603 <li>Select or hide columns according to alignment
1605 <li>Find option for locating sequences by description</li>
1606 <li>Conserved physicochemical properties shown in amino
1607 acid conservation row</li>
1608 <li>Alignments can be sorted by number of RNA helices</li>
1609 </ul> <em>Application</em>
1611 <li>New cDNA/Protein analysis capabilities
1613 <li>Get Cross-References should open a Split Frame
1614 view with cDNA/Protein</li>
1615 <li>Detect when nucleotide sequences and protein
1616 sequences are placed in the same alignment</li>
1617 <li>Split cDNA/Protein views are saved in Jalview
1622 <li>Use REST API to talk to Chimera</li>
1623 <li>Selected regions in Chimera are highlighted in linked
1624 Jalview windows</li>
1626 <li>VARNA RNA viewer updated to v3.93</li>
1627 <li>VARNA views are saved in Jalview Projects</li>
1628 <li>Pseudoknots displayed as Jalview RNA annotation can
1629 be shown in VARNA</li>
1631 <li>Make groups for selection uses marked columns as well
1632 as the active selected region</li>
1634 <li>Calculate UPGMA and NJ trees using sequence feature
1636 <li>New Export options
1638 <li>New Export Settings dialog to control hidden
1639 region export in flat file generation</li>
1641 <li>Export alignment views for display with the <a
1642 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1644 <li>Export scrollable SVG in HTML page</li>
1645 <li>Optional embedding of BioJSON data when exporting
1646 alignment figures to HTML</li>
1648 <li>3D structure retrieval and display
1650 <li>Free text and structured queries with the PDBe
1652 <li>PDBe Search API based discovery and selection of
1653 PDB structures for a sequence set</li>
1657 <li>JPred4 employed for protein secondary structure
1659 <li>Hide Insertions menu option to hide unaligned columns
1660 for one or a group of sequences</li>
1661 <li>Automatically hide insertions in alignments imported
1662 from the JPred4 web server</li>
1663 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1664 system on OSX<br />LGPL libraries courtesy of <a
1665 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1667 <li>changed 'View nucleotide structure' submenu to 'View
1668 VARNA 2D Structure'</li>
1669 <li>change "View protein structure" menu option to "3D
1672 </ul> <em>Applet</em>
1674 <li>New layout for applet example pages</li>
1675 <li>New parameters to enable SplitFrame view
1676 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1677 <li>New example demonstrating linked viewing of cDNA and
1678 Protein alignments</li>
1679 </ul> <em>Development and deployment</em>
1681 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1682 <li>Include installation type and git revision in build
1683 properties and console log output</li>
1684 <li>Jalview Github organisation, and new github site for
1685 storing BioJsMSA Templates</li>
1686 <li>Jalview's unit tests now managed with TestNG</li>
1689 <!-- <em>General</em>
1691 </ul> --> <!-- issues resolved --> <em>Application</em>
1693 <li>Escape should close any open find dialogs</li>
1694 <li>Typo in select-by-features status report</li>
1695 <li>Consensus RNA secondary secondary structure
1696 predictions are not highlighted in amber</li>
1697 <li>Missing gap character in v2.7 example file means
1698 alignment appears unaligned when pad-gaps is not enabled</li>
1699 <li>First switch to RNA Helices colouring doesn't colour
1700 associated structure views</li>
1701 <li>ID width preference option is greyed out when auto
1702 width checkbox not enabled</li>
1703 <li>Stopped a warning dialog from being shown when
1704 creating user defined colours</li>
1705 <li>'View Mapping' in structure viewer shows sequence
1706 mappings for just that viewer's sequences</li>
1707 <li>Workaround for superposing PDB files containing
1708 multiple models in Chimera</li>
1709 <li>Report sequence position in status bar when hovering
1710 over Jmol structure</li>
1711 <li>Cannot output gaps as '.' symbols with Selection ->
1712 output to text box</li>
1713 <li>Flat file exports of alignments with hidden columns
1714 have incorrect sequence start/end</li>
1715 <li>'Aligning' a second chain to a Chimera structure from
1717 <li>Colour schemes applied to structure viewers don't
1718 work for nucleotide</li>
1719 <li>Loading/cut'n'pasting an empty or invalid file leads
1720 to a grey/invisible alignment window</li>
1721 <li>Exported Jpred annotation from a sequence region
1722 imports to different position</li>
1723 <li>Space at beginning of sequence feature tooltips shown
1724 on some platforms</li>
1725 <li>Chimera viewer 'View | Show Chain' menu is not
1727 <li>'New View' fails with a Null Pointer Exception in
1728 console if Chimera has been opened</li>
1729 <li>Mouseover to Chimera not working</li>
1730 <li>Miscellaneous ENA XML feature qualifiers not
1732 <li>NPE in annotation renderer after 'Extract Scores'</li>
1733 <li>If two structures in one Chimera window, mouseover of
1734 either sequence shows on first structure</li>
1735 <li>'Show annotations' options should not make
1736 non-positional annotations visible</li>
1737 <li>Subsequence secondary structure annotation not shown
1738 in right place after 'view flanking regions'</li>
1739 <li>File Save As type unset when current file format is
1741 <li>Save as '.jar' option removed for saving Jalview
1743 <li>Colour by Sequence colouring in Chimera more
1745 <li>Cannot 'add reference annotation' for a sequence in
1746 several views on same alignment</li>
1747 <li>Cannot show linked products for EMBL / ENA records</li>
1748 <li>Jalview's tooltip wraps long texts containing no
1750 </ul> <em>Applet</em>
1752 <li>Jmol to JalviewLite mouseover/link not working</li>
1753 <li>JalviewLite can't import sequences with ID
1754 descriptions containing angle brackets</li>
1755 </ul> <em>General</em>
1757 <li>Cannot export and reimport RNA secondary structure
1758 via jalview annotation file</li>
1759 <li>Random helix colour palette for colour by annotation
1760 with RNA secondary structure</li>
1761 <li>Mouseover to cDNA from STOP residue in protein
1762 translation doesn't work.</li>
1763 <li>hints when using the select by annotation dialog box</li>
1764 <li>Jmol alignment incorrect if PDB file has alternate CA
1766 <li>FontChooser message dialog appears to hang after
1767 choosing 1pt font</li>
1768 <li>Peptide secondary structure incorrectly imported from
1769 annotation file when annotation display text includes 'e' or
1771 <li>Cannot set colour of new feature type whilst creating
1773 <li>cDNA translation alignment should not be sequence
1774 order dependent</li>
1775 <li>'Show unconserved' doesn't work for lower case
1777 <li>Nucleotide ambiguity codes involving R not recognised</li>
1778 </ul> <em>Deployment and Documentation</em>
1780 <li>Applet example pages appear different to the rest of
1781 www.jalview.org</li>
1782 </ul> <em>Application Known issues</em>
1784 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1785 <li>Misleading message appears after trying to delete
1787 <li>Jalview icon not shown in dock after InstallAnywhere
1788 version launches</li>
1789 <li>Fetching EMBL reference for an RNA sequence results
1790 fails with a sequence mismatch</li>
1791 <li>Corrupted or unreadable alignment display when
1792 scrolling alignment to right</li>
1793 <li>ArrayIndexOutOfBoundsException thrown when remove
1794 empty columns called on alignment with ragged gapped ends</li>
1795 <li>auto calculated alignment annotation rows do not get
1796 placed above or below non-autocalculated rows</li>
1797 <li>Jalview dekstop becomes sluggish at full screen in
1798 ultra-high resolution</li>
1799 <li>Cannot disable consensus calculation independently of
1800 quality and conservation</li>
1801 <li>Mouseover highlighting between cDNA and protein can
1802 become sluggish with more than one splitframe shown</li>
1803 </ul> <em>Applet Known Issues</em>
1805 <li>Core PDB parsing code requires Jmol</li>
1806 <li>Sequence canvas panel goes white when alignment
1807 window is being resized</li>
1813 <td><div align="center">
1814 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1816 <td><em>General</em>
1818 <li>Updated Java code signing certificate donated by
1820 <li>Features and annotation preserved when performing
1821 pairwise alignment</li>
1822 <li>RNA pseudoknot annotation can be
1823 imported/exported/displayed</li>
1824 <li>'colour by annotation' can colour by RNA and
1825 protein secondary structure</li>
1826 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1827 post-hoc with 2.9 release</em>)
1830 </ul> <em>Application</em>
1832 <li>Extract and display secondary structure for sequences
1833 with 3D structures</li>
1834 <li>Support for parsing RNAML</li>
1835 <li>Annotations menu for layout
1837 <li>sort sequence annotation rows by alignment</li>
1838 <li>place sequence annotation above/below alignment
1841 <li>Output in Stockholm format</li>
1842 <li>Internationalisation: improved Spanish (es)
1844 <li>Structure viewer preferences tab</li>
1845 <li>Disorder and Secondary Structure annotation tracks
1846 shared between alignments</li>
1847 <li>UCSF Chimera launch and linked highlighting from
1849 <li>Show/hide all sequence associated annotation rows for
1850 all or current selection</li>
1851 <li>disorder and secondary structure predictions
1852 available as dataset annotation</li>
1853 <li>Per-sequence rna helices colouring</li>
1856 <li>Sequence database accessions imported when fetching
1857 alignments from Rfam</li>
1858 <li>update VARNA version to 3.91</li>
1860 <li>New groovy scripts for exporting aligned positions,
1861 conservation values, and calculating sum of pairs scores.</li>
1862 <li>Command line argument to set default JABAWS server</li>
1863 <li>include installation type in build properties and
1864 console log output</li>
1865 <li>Updated Jalview project format to preserve dataset
1869 <!-- issues resolved --> <em>Application</em>
1871 <li>Distinguish alignment and sequence associated RNA
1872 structure in structure->view->VARNA</li>
1873 <li>Raise dialog box if user deletes all sequences in an
1875 <li>Pressing F1 results in documentation opening twice</li>
1876 <li>Sequence feature tooltip is wrapped</li>
1877 <li>Double click on sequence associated annotation
1878 selects only first column</li>
1879 <li>Redundancy removal doesn't result in unlinked
1880 leaves shown in tree</li>
1881 <li>Undos after several redundancy removals don't undo
1883 <li>Hide sequence doesn't hide associated annotation</li>
1884 <li>User defined colours dialog box too big to fit on
1885 screen and buttons not visible</li>
1886 <li>author list isn't updated if already written to
1887 Jalview properties</li>
1888 <li>Popup menu won't open after retrieving sequence
1890 <li>File open window for associate PDB doesn't open</li>
1891 <li>Left-then-right click on a sequence id opens a
1892 browser search window</li>
1893 <li>Cannot open sequence feature shading/sort popup menu
1894 in feature settings dialog</li>
1895 <li>better tooltip placement for some areas of Jalview
1897 <li>Allow addition of JABAWS Server which doesn't
1898 pass validation</li>
1899 <li>Web services parameters dialog box is too large to
1901 <li>Muscle nucleotide alignment preset obscured by
1903 <li>JABAWS preset submenus don't contain newly
1904 defined user preset</li>
1905 <li>MSA web services warns user if they were launched
1906 with invalid input</li>
1907 <li>Jalview cannot contact DAS Registy when running on
1910 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1911 'Superpose with' submenu not shown when new view
1915 </ul> <!-- <em>Applet</em>
1917 </ul> <em>General</em>
1919 </ul>--> <em>Deployment and Documentation</em>
1921 <li>2G and 1G options in launchApp have no effect on
1922 memory allocation</li>
1923 <li>launchApp service doesn't automatically open
1924 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1926 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1927 InstallAnywhere reports cannot find valid JVM when Java
1928 1.7_055 is available
1930 </ul> <em>Application Known issues</em>
1933 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1934 corrupted or unreadable alignment display when scrolling
1938 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1939 retrieval fails but progress bar continues for DAS retrieval
1940 with large number of ID
1943 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1944 flatfile output of visible region has incorrect sequence
1948 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1949 rna structure consensus doesn't update when secondary
1950 structure tracks are rearranged
1953 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1954 invalid rna structure positional highlighting does not
1955 highlight position of invalid base pairs
1958 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1959 out of memory errors are not raised when saving Jalview
1960 project from alignment window file menu
1963 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1964 Switching to RNA Helices colouring doesn't propagate to
1968 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1969 colour by RNA Helices not enabled when user created
1970 annotation added to alignment
1973 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1974 Jalview icon not shown on dock in Mountain Lion/Webstart
1976 </ul> <em>Applet Known Issues</em>
1979 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1980 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1983 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1984 Jalview and Jmol example not compatible with IE9
1987 <li>Sort by annotation score doesn't reverse order
1993 <td><div align="center">
1994 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1997 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2000 <li>Internationalisation of user interface (usually
2001 called i18n support) and translation for Spanish locale</li>
2002 <li>Define/Undefine group on current selection with
2003 Ctrl-G/Shift Ctrl-G</li>
2004 <li>Improved group creation/removal options in
2005 alignment/sequence Popup menu</li>
2006 <li>Sensible precision for symbol distribution
2007 percentages shown in logo tooltip.</li>
2008 <li>Annotation panel height set according to amount of
2009 annotation when alignment first opened</li>
2010 </ul> <em>Application</em>
2012 <li>Interactive consensus RNA secondary structure
2013 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2014 <li>Select columns containing particular features from
2015 Feature Settings dialog</li>
2016 <li>View all 'representative' PDB structures for selected
2018 <li>Update Jalview project format:
2020 <li>New file extension for Jalview projects '.jvp'</li>
2021 <li>Preserve sequence and annotation dataset (to
2022 store secondary structure annotation,etc)</li>
2023 <li>Per group and alignment annotation and RNA helix
2027 <li>New similarity measures for PCA and Tree calculation
2029 <li>Experimental support for retrieval and viewing of
2030 flanking regions for an alignment</li>
2034 <!-- issues resolved --> <em>Application</em>
2036 <li>logo keeps spinning and status remains at queued or
2037 running after job is cancelled</li>
2038 <li>cannot export features from alignments imported from
2039 Jalview/VAMSAS projects</li>
2040 <li>Buggy slider for web service parameters that take
2042 <li>Newly created RNA secondary structure line doesn't
2043 have 'display all symbols' flag set</li>
2044 <li>T-COFFEE alignment score shading scheme and other
2045 annotation shading not saved in Jalview project</li>
2046 <li>Local file cannot be loaded in freshly downloaded
2048 <li>Jalview icon not shown on dock in Mountain
2050 <li>Load file from desktop file browser fails</li>
2051 <li>Occasional NPE thrown when calculating large trees</li>
2052 <li>Cannot reorder or slide sequences after dragging an
2053 alignment onto desktop</li>
2054 <li>Colour by annotation dialog throws NPE after using
2055 'extract scores' function</li>
2056 <li>Loading/cut'n'pasting an empty file leads to a grey
2057 alignment window</li>
2058 <li>Disorder thresholds rendered incorrectly after
2059 performing IUPred disorder prediction</li>
2060 <li>Multiple group annotated consensus rows shown when
2061 changing 'normalise logo' display setting</li>
2062 <li>Find shows blank dialog after 'finished searching' if
2063 nothing matches query</li>
2064 <li>Null Pointer Exceptions raised when sorting by
2065 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2067 <li>Errors in Jmol console when structures in alignment
2068 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2070 <li>Not all working JABAWS services are shown in
2072 <li>JAVAWS version of Jalview fails to launch with
2073 'invalid literal/length code'</li>
2074 <li>Annotation/RNA Helix colourschemes cannot be applied
2075 to alignment with groups (actually fixed in 2.8.0b1)</li>
2076 <li>RNA Helices and T-Coffee Scores available as default
2079 </ul> <em>Applet</em>
2081 <li>Remove group option is shown even when selection is
2083 <li>Apply to all groups ticked but colourscheme changes
2084 don't affect groups</li>
2085 <li>Documented RNA Helices and T-Coffee Scores as valid
2086 colourscheme name</li>
2087 <li>Annotation labels drawn on sequence IDs when
2088 Annotation panel is not displayed</li>
2089 <li>Increased font size for dropdown menus on OSX and
2090 embedded windows</li>
2091 </ul> <em>Other</em>
2093 <li>Consensus sequence for alignments/groups with a
2094 single sequence were not calculated</li>
2095 <li>annotation files that contain only groups imported as
2096 annotation and junk sequences</li>
2097 <li>Fasta files with sequences containing '*' incorrectly
2098 recognised as PFAM or BLC</li>
2099 <li>conservation/PID slider apply all groups option
2100 doesn't affect background (2.8.0b1)
2102 <li>redundancy highlighting is erratic at 0% and 100%</li>
2103 <li>Remove gapped columns fails for sequences with ragged
2105 <li>AMSA annotation row with leading spaces is not
2106 registered correctly on import</li>
2107 <li>Jalview crashes when selecting PCA analysis for
2108 certain alignments</li>
2109 <li>Opening the colour by annotation dialog for an
2110 existing annotation based 'use original colours'
2111 colourscheme loses original colours setting</li>
2116 <td><div align="center">
2117 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2118 <em>30/1/2014</em></strong>
2122 <li>Trusted certificates for JalviewLite applet and
2123 Jalview Desktop application<br />Certificate was donated by
2124 <a href="https://www.certum.eu">Certum</a> to the Jalview
2125 open source project).
2127 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2128 <li>Output in Stockholm format</li>
2129 <li>Allow import of data from gzipped files</li>
2130 <li>Export/import group and sequence associated line
2131 graph thresholds</li>
2132 <li>Nucleotide substitution matrix that supports RNA and
2133 ambiguity codes</li>
2134 <li>Allow disorder predictions to be made on the current
2135 selection (or visible selection) in the same way that JPred
2137 <li>Groovy scripting for headless Jalview operation</li>
2138 </ul> <em>Other improvements</em>
2140 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2141 <li>COMBINE statement uses current SEQUENCE_REF and
2142 GROUP_REF scope to group annotation rows</li>
2143 <li>Support '' style escaping of quotes in Newick
2145 <li>Group options for JABAWS service by command line name</li>
2146 <li>Empty tooltip shown for JABA service options with a
2147 link but no description</li>
2148 <li>Select primary source when selecting authority in
2149 database fetcher GUI</li>
2150 <li>Add .mfa to FASTA file extensions recognised by
2152 <li>Annotation label tooltip text wrap</li>
2157 <li>Slow scrolling when lots of annotation rows are
2159 <li>Lots of NPE (and slowness) after creating RNA
2160 secondary structure annotation line</li>
2161 <li>Sequence database accessions not imported when
2162 fetching alignments from Rfam</li>
2163 <li>Incorrect SHMR submission for sequences with
2165 <li>View all structures does not always superpose
2167 <li>Option widgets in service parameters not updated to
2168 reflect user or preset settings</li>
2169 <li>Null pointer exceptions for some services without
2170 presets or adjustable parameters</li>
2171 <li>Discover PDB IDs entry in structure menu doesn't
2172 discover PDB xRefs</li>
2173 <li>Exception encountered while trying to retrieve
2174 features with DAS</li>
2175 <li>Lowest value in annotation row isn't coloured
2176 when colour by annotation (per sequence) is coloured</li>
2177 <li>Keyboard mode P jumps to start of gapped region when
2178 residue follows a gap</li>
2179 <li>Jalview appears to hang importing an alignment with
2180 Wrap as default or after enabling Wrap</li>
2181 <li>'Right click to add annotations' message
2182 shown in wrap mode when no annotations present</li>
2183 <li>Disorder predictions fail with NPE if no automatic
2184 annotation already exists on alignment</li>
2185 <li>oninit javascript function should be called after
2186 initialisation completes</li>
2187 <li>Remove redundancy after disorder prediction corrupts
2188 alignment window display</li>
2189 <li>Example annotation file in documentation is invalid</li>
2190 <li>Grouped line graph annotation rows are not exported
2191 to annotation file</li>
2192 <li>Multi-harmony analysis cannot be run when only two
2194 <li>Cannot create multiple groups of line graphs with
2195 several 'combine' statements in annotation file</li>
2196 <li>Pressing return several times causes Number Format
2197 exceptions in keyboard mode</li>
2198 <li>Multi-harmony (SHMMR) method doesn't submit
2199 correct partitions for input data</li>
2200 <li>Translation from DNA to Amino Acids fails</li>
2201 <li>Jalview fail to load newick tree with quoted label</li>
2202 <li>--headless flag isn't understood</li>
2203 <li>ClassCastException when generating EPS in headless
2205 <li>Adjusting sequence-associated shading threshold only
2206 changes one row's threshold</li>
2207 <li>Preferences and Feature settings panel panel
2208 doesn't open</li>
2209 <li>hide consensus histogram also hides conservation and
2210 quality histograms</li>
2215 <td><div align="center">
2216 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2218 <td><em>Application</em>
2220 <li>Support for JABAWS 2.0 Services (AACon alignment
2221 conservation, protein disorder and Clustal Omega)</li>
2222 <li>JABAWS server status indicator in Web Services
2224 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2225 in Jalview alignment window</li>
2226 <li>Updated Jalview build and deploy framework for OSX
2227 mountain lion, windows 7, and 8</li>
2228 <li>Nucleotide substitution matrix for PCA that supports
2229 RNA and ambiguity codes</li>
2231 <li>Improved sequence database retrieval GUI</li>
2232 <li>Support fetching and database reference look up
2233 against multiple DAS sources (Fetch all from in 'fetch db
2235 <li>Jalview project improvements
2237 <li>Store and retrieve the 'belowAlignment'
2238 flag for annotation</li>
2239 <li>calcId attribute to group annotation rows on the
2241 <li>Store AACon calculation settings for a view in
2242 Jalview project</li>
2246 <li>horizontal scrolling gesture support</li>
2247 <li>Visual progress indicator when PCA calculation is
2249 <li>Simpler JABA web services menus</li>
2250 <li>visual indication that web service results are still
2251 being retrieved from server</li>
2252 <li>Serialise the dialogs that are shown when Jalview
2253 starts up for first time</li>
2254 <li>Jalview user agent string for interacting with HTTP
2256 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2258 <li>Examples directory and Groovy library included in
2259 InstallAnywhere distribution</li>
2260 </ul> <em>Applet</em>
2262 <li>RNA alignment and secondary structure annotation
2263 visualization applet example</li>
2264 </ul> <em>General</em>
2266 <li>Normalise option for consensus sequence logo</li>
2267 <li>Reset button in PCA window to return dimensions to
2269 <li>Allow seqspace or Jalview variant of alignment PCA
2271 <li>PCA with either nucleic acid and protein substitution
2273 <li>Allow windows containing HTML reports to be exported
2275 <li>Interactive display and editing of RNA secondary
2276 structure contacts</li>
2277 <li>RNA Helix Alignment Colouring</li>
2278 <li>RNA base pair logo consensus</li>
2279 <li>Parse sequence associated secondary structure
2280 information in Stockholm files</li>
2281 <li>HTML Export database accessions and annotation
2282 information presented in tooltip for sequences</li>
2283 <li>Import secondary structure from LOCARNA clustalw
2284 style RNA alignment files</li>
2285 <li>import and visualise T-COFFEE quality scores for an
2287 <li>'colour by annotation' per sequence option to
2288 shade each sequence according to its associated alignment
2290 <li>New Jalview Logo</li>
2291 </ul> <em>Documentation and Development</em>
2293 <li>documentation for score matrices used in Jalview</li>
2294 <li>New Website!</li>
2296 <td><em>Application</em>
2298 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2299 wsdbfetch REST service</li>
2300 <li>Stop windows being moved outside desktop on OSX</li>
2301 <li>Filetype associations not installed for webstart
2303 <li>Jalview does not always retrieve progress of a JABAWS
2304 job execution in full once it is complete</li>
2305 <li>revise SHMR RSBS definition to ensure alignment is
2306 uploaded via ali_file parameter</li>
2307 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2308 <li>View all structures superposed fails with exception</li>
2309 <li>Jnet job queues forever if a very short sequence is
2310 submitted for prediction</li>
2311 <li>Cut and paste menu not opened when mouse clicked on
2313 <li>Putting fractional value into integer text box in
2314 alignment parameter dialog causes Jalview to hang</li>
2315 <li>Structure view highlighting doesn't work on
2317 <li>View all structures fails with exception shown in
2319 <li>Characters in filename associated with PDBEntry not
2320 escaped in a platform independent way</li>
2321 <li>Jalview desktop fails to launch with exception when
2323 <li>Tree calculation reports 'you must have 2 or more
2324 sequences selected' when selection is empty</li>
2325 <li>Jalview desktop fails to launch with jar signature
2326 failure when java web start temporary file caching is
2328 <li>DAS Sequence retrieval with range qualification
2329 results in sequence xref which includes range qualification</li>
2330 <li>Errors during processing of command line arguments
2331 cause progress bar (JAL-898) to be removed</li>
2332 <li>Replace comma for semi-colon option not disabled for
2333 DAS sources in sequence fetcher</li>
2334 <li>Cannot close news reader when JABAWS server warning
2335 dialog is shown</li>
2336 <li>Option widgets not updated to reflect user settings</li>
2337 <li>Edited sequence not submitted to web service</li>
2338 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2339 <li>InstallAnywhere installer doesn't unpack and run
2340 on OSX Mountain Lion</li>
2341 <li>Annotation panel not given a scroll bar when
2342 sequences with alignment annotation are pasted into the
2344 <li>Sequence associated annotation rows not associated
2345 when loaded from Jalview project</li>
2346 <li>Browser launch fails with NPE on java 1.7</li>
2347 <li>JABAWS alignment marked as finished when job was
2348 cancelled or job failed due to invalid input</li>
2349 <li>NPE with v2.7 example when clicking on Tree
2350 associated with all views</li>
2351 <li>Exceptions when copy/paste sequences with grouped
2352 annotation rows to new window</li>
2353 </ul> <em>Applet</em>
2355 <li>Sequence features are momentarily displayed before
2356 they are hidden using hidefeaturegroups applet parameter</li>
2357 <li>loading features via javascript API automatically
2358 enables feature display</li>
2359 <li>scrollToColumnIn javascript API method doesn't
2361 </ul> <em>General</em>
2363 <li>Redundancy removal fails for rna alignment</li>
2364 <li>PCA calculation fails when sequence has been selected
2365 and then deselected</li>
2366 <li>PCA window shows grey box when first opened on OSX</li>
2367 <li>Letters coloured pink in sequence logo when alignment
2368 coloured with clustalx</li>
2369 <li>Choosing fonts without letter symbols defined causes
2370 exceptions and redraw errors</li>
2371 <li>Initial PCA plot view is not same as manually
2372 reconfigured view</li>
2373 <li>Grouped annotation graph label has incorrect line
2375 <li>Grouped annotation graph label display is corrupted
2376 for lots of labels</li>
2381 <div align="center">
2382 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2385 <td><em>Application</em>
2387 <li>Jalview Desktop News Reader</li>
2388 <li>Tweaked default layout of web services menu</li>
2389 <li>View/alignment association menu to enable user to
2390 easily specify which alignment a multi-structure view takes
2391 its colours/correspondences from</li>
2392 <li>Allow properties file location to be specified as URL</li>
2393 <li>Extend Jalview project to preserve associations
2394 between many alignment views and a single Jmol display</li>
2395 <li>Store annotation row height in Jalview project file</li>
2396 <li>Annotation row column label formatting attributes
2397 stored in project file</li>
2398 <li>Annotation row order for auto-calculated annotation
2399 rows preserved in Jalview project file</li>
2400 <li>Visual progress indication when Jalview state is
2401 saved using Desktop window menu</li>
2402 <li>Visual indication that command line arguments are
2403 still being processed</li>
2404 <li>Groovy script execution from URL</li>
2405 <li>Colour by annotation default min and max colours in
2407 <li>Automatically associate PDB files dragged onto an
2408 alignment with sequences that have high similarity and
2410 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2411 <li>'view structures' option to open many
2412 structures in same window</li>
2413 <li>Sort associated views menu option for tree panel</li>
2414 <li>Group all JABA and non-JABA services for a particular
2415 analysis function in its own submenu</li>
2416 </ul> <em>Applet</em>
2418 <li>Userdefined and autogenerated annotation rows for
2420 <li>Adjustment of alignment annotation pane height</li>
2421 <li>Annotation scrollbar for annotation panel</li>
2422 <li>Drag to reorder annotation rows in annotation panel</li>
2423 <li>'automaticScrolling' parameter</li>
2424 <li>Allow sequences with partial ID string matches to be
2425 annotated from GFF/Jalview features files</li>
2426 <li>Sequence logo annotation row in applet</li>
2427 <li>Absolute paths relative to host server in applet
2428 parameters are treated as such</li>
2429 <li>New in the JalviewLite javascript API:
2431 <li>JalviewLite.js javascript library</li>
2432 <li>Javascript callbacks for
2434 <li>Applet initialisation</li>
2435 <li>Sequence/alignment mouse-overs and selections</li>
2438 <li>scrollTo row and column alignment scrolling
2440 <li>Select sequence/alignment regions from javascript</li>
2441 <li>javascript structure viewer harness to pass
2442 messages between Jmol and Jalview when running as
2443 distinct applets</li>
2444 <li>sortBy method</li>
2445 <li>Set of applet and application examples shipped
2446 with documentation</li>
2447 <li>New example to demonstrate JalviewLite and Jmol
2448 javascript message exchange</li>
2450 </ul> <em>General</em>
2452 <li>Enable Jmol displays to be associated with multiple
2453 multiple alignments</li>
2454 <li>Option to automatically sort alignment with new tree</li>
2455 <li>User configurable link to enable redirects to a
2456 www.Jalview.org mirror</li>
2457 <li>Jmol colours option for Jmol displays</li>
2458 <li>Configurable newline string when writing alignment
2459 and other flat files</li>
2460 <li>Allow alignment annotation description lines to
2461 contain html tags</li>
2462 </ul> <em>Documentation and Development</em>
2464 <li>Add groovy test harness for bulk load testing to
2466 <li>Groovy script to load and align a set of sequences
2467 using a web service before displaying the result in the
2468 Jalview desktop</li>
2469 <li>Restructured javascript and applet api documentation</li>
2470 <li>Ant target to publish example html files with applet
2472 <li>Netbeans project for building Jalview from source</li>
2473 <li>ant task to create online javadoc for Jalview source</li>
2475 <td><em>Application</em>
2477 <li>User defined colourscheme throws exception when
2478 current built in colourscheme is saved as new scheme</li>
2479 <li>AlignFrame->Save in application pops up save
2480 dialog for valid filename/format</li>
2481 <li>Cannot view associated structure for UniProt sequence</li>
2482 <li>PDB file association breaks for UniProt sequence
2484 <li>Associate PDB from file dialog does not tell you
2485 which sequence is to be associated with the file</li>
2486 <li>Find All raises null pointer exception when query
2487 only matches sequence IDs</li>
2488 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2489 <li>Jalview project with Jmol views created with Jalview
2490 2.4 cannot be loaded</li>
2491 <li>Filetype associations not installed for webstart
2493 <li>Two or more chains in a single PDB file associated
2494 with sequences in different alignments do not get coloured
2495 by their associated sequence</li>
2496 <li>Visibility status of autocalculated annotation row
2497 not preserved when project is loaded</li>
2498 <li>Annotation row height and visibility attributes not
2499 stored in Jalview project</li>
2500 <li>Tree bootstraps are not preserved when saved as a
2501 Jalview project</li>
2502 <li>Envision2 workflow tooltips are corrupted</li>
2503 <li>Enabling show group conservation also enables colour
2504 by conservation</li>
2505 <li>Duplicate group associated conservation or consensus
2506 created on new view</li>
2507 <li>Annotation scrollbar not displayed after 'show
2508 all hidden annotation rows' option selected</li>
2509 <li>Alignment quality not updated after alignment
2510 annotation row is hidden then shown</li>
2511 <li>Preserve colouring of structures coloured by
2512 sequences in pre Jalview 2.7 projects</li>
2513 <li>Web service job parameter dialog is not laid out
2515 <li>Web services menu not refreshed after 'reset
2516 services' button is pressed in preferences</li>
2517 <li>Annotation off by one in Jalview v2_3 example project</li>
2518 <li>Structures imported from file and saved in project
2519 get name like jalview_pdb1234.txt when reloaded</li>
2520 <li>Jalview does not always retrieve progress of a JABAWS
2521 job execution in full once it is complete</li>
2522 </ul> <em>Applet</em>
2524 <li>Alignment height set incorrectly when lots of
2525 annotation rows are displayed</li>
2526 <li>Relative URLs in feature HTML text not resolved to
2528 <li>View follows highlighting does not work for positions
2530 <li><= shown as = in tooltip</li>
2531 <li>Export features raises exception when no features
2533 <li>Separator string used for serialising lists of IDs
2534 for javascript api is modified when separator string
2535 provided as parameter</li>
2536 <li>Null pointer exception when selecting tree leaves for
2537 alignment with no existing selection</li>
2538 <li>Relative URLs for datasources assumed to be relative
2539 to applet's codebase</li>
2540 <li>Status bar not updated after finished searching and
2541 search wraps around to first result</li>
2542 <li>StructureSelectionManager instance shared between
2543 several Jalview applets causes race conditions and memory
2545 <li>Hover tooltip and mouseover of position on structure
2546 not sent from Jmol in applet</li>
2547 <li>Certain sequences of javascript method calls to
2548 applet API fatally hang browser</li>
2549 </ul> <em>General</em>
2551 <li>View follows structure mouseover scrolls beyond
2552 position with wrapped view and hidden regions</li>
2553 <li>Find sequence position moves to wrong residue
2554 with/without hidden columns</li>
2555 <li>Sequence length given in alignment properties window
2557 <li>InvalidNumberFormat exceptions thrown when trying to
2558 import PDB like structure files</li>
2559 <li>Positional search results are only highlighted
2560 between user-supplied sequence start/end bounds</li>
2561 <li>End attribute of sequence is not validated</li>
2562 <li>Find dialog only finds first sequence containing a
2563 given sequence position</li>
2564 <li>Sequence numbering not preserved in MSF alignment
2566 <li>Jalview PDB file reader does not extract sequence
2567 from nucleotide chains correctly</li>
2568 <li>Structure colours not updated when tree partition
2569 changed in alignment</li>
2570 <li>Sequence associated secondary structure not correctly
2571 parsed in interleaved stockholm</li>
2572 <li>Colour by annotation dialog does not restore current
2574 <li>Hiding (nearly) all sequences doesn't work
2576 <li>Sequences containing lowercase letters are not
2577 properly associated with their pdb files</li>
2578 </ul> <em>Documentation and Development</em>
2580 <li>schemas/JalviewWsParamSet.xsd corrupted by
2581 ApplyCopyright tool</li>
2586 <div align="center">
2587 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2590 <td><em>Application</em>
2592 <li>New warning dialog when the Jalview Desktop cannot
2593 contact web services</li>
2594 <li>JABA service parameters for a preset are shown in
2595 service job window</li>
2596 <li>JABA Service menu entries reworded</li>
2600 <li>Modeller PIR IO broken - cannot correctly import a
2601 pir file emitted by Jalview</li>
2602 <li>Existing feature settings transferred to new
2603 alignment view created from cut'n'paste</li>
2604 <li>Improved test for mixed amino/nucleotide chains when
2605 parsing PDB files</li>
2606 <li>Consensus and conservation annotation rows
2607 occasionally become blank for all new windows</li>
2608 <li>Exception raised when right clicking above sequences
2609 in wrapped view mode</li>
2610 </ul> <em>Application</em>
2612 <li>multiple multiply aligned structure views cause cpu
2613 usage to hit 100% and computer to hang</li>
2614 <li>Web Service parameter layout breaks for long user
2615 parameter names</li>
2616 <li>Jaba service discovery hangs desktop if Jaba server
2623 <div align="center">
2624 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2627 <td><em>Application</em>
2629 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2630 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2633 <li>Web Services preference tab</li>
2634 <li>Analysis parameters dialog box and user defined
2636 <li>Improved speed and layout of Envision2 service menu</li>
2637 <li>Superpose structures using associated sequence
2639 <li>Export coordinates and projection as CSV from PCA
2641 </ul> <em>Applet</em>
2643 <li>enable javascript: execution by the applet via the
2644 link out mechanism</li>
2645 </ul> <em>Other</em>
2647 <li>Updated the Jmol Jalview interface to work with Jmol
2649 <li>The Jalview Desktop and JalviewLite applet now
2650 require Java 1.5</li>
2651 <li>Allow Jalview feature colour specification for GFF
2652 sequence annotation files</li>
2653 <li>New 'colour by label' keword in Jalview feature file
2654 type colour specification</li>
2655 <li>New Jalview Desktop Groovy API method that allows a
2656 script to check if it being run in an interactive session or
2657 in a batch operation from the Jalview command line</li>
2661 <li>clustalx colourscheme colours Ds preferentially when
2662 both D+E are present in over 50% of the column</li>
2663 </ul> <em>Application</em>
2665 <li>typo in AlignmentFrame->View->Hide->all but
2666 selected Regions menu item</li>
2667 <li>sequence fetcher replaces ',' for ';' when the ',' is
2668 part of a valid accession ID</li>
2669 <li>fatal OOM if object retrieved by sequence fetcher
2670 runs out of memory</li>
2671 <li>unhandled Out of Memory Error when viewing pca
2672 analysis results</li>
2673 <li>InstallAnywhere builds fail to launch on OS X java
2674 10.5 update 4 (due to apple Java 1.6 update)</li>
2675 <li>Installanywhere Jalview silently fails to launch</li>
2676 </ul> <em>Applet</em>
2678 <li>Jalview.getFeatureGroups() raises an
2679 ArrayIndexOutOfBoundsException if no feature groups are
2686 <div align="center">
2687 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2693 <li>Alignment prettyprinter doesn't cope with long
2695 <li>clustalx colourscheme colours Ds preferentially when
2696 both D+E are present in over 50% of the column</li>
2697 <li>nucleic acid structures retrieved from PDB do not
2698 import correctly</li>
2699 <li>More columns get selected than were clicked on when a
2700 number of columns are hidden</li>
2701 <li>annotation label popup menu not providing correct
2702 add/hide/show options when rows are hidden or none are
2704 <li>Stockholm format shown in list of readable formats,
2705 and parser copes better with alignments from RFAM.</li>
2706 <li>CSV output of consensus only includes the percentage
2707 of all symbols if sequence logo display is enabled</li>
2709 </ul> <em>Applet</em>
2711 <li>annotation panel disappears when annotation is
2713 </ul> <em>Application</em>
2715 <li>Alignment view not redrawn properly when new
2716 alignment opened where annotation panel is visible but no
2717 annotations are present on alignment</li>
2718 <li>pasted region containing hidden columns is
2719 incorrectly displayed in new alignment window</li>
2720 <li>Jalview slow to complete operations when stdout is
2721 flooded (fix is to close the Jalview console)</li>
2722 <li>typo in AlignmentFrame->View->Hide->all but
2723 selected Rregions menu item.</li>
2724 <li>inconsistent group submenu and Format submenu entry
2725 'Un' or 'Non'conserved</li>
2726 <li>Sequence feature settings are being shared by
2727 multiple distinct alignments</li>
2728 <li>group annotation not recreated when tree partition is
2730 <li>double click on group annotation to select sequences
2731 does not propagate to associated trees</li>
2732 <li>Mac OSX specific issues:
2734 <li>exception raised when mouse clicked on desktop
2735 window background</li>
2736 <li>Desktop menu placed on menu bar and application
2737 name set correctly</li>
2738 <li>sequence feature settings not wide enough for the
2739 save feature colourscheme button</li>
2748 <div align="center">
2749 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2752 <td><em>New Capabilities</em>
2754 <li>URL links generated from description line for
2755 regular-expression based URL links (applet and application)
2757 <li>Non-positional feature URL links are shown in link
2759 <li>Linked viewing of nucleic acid sequences and
2761 <li>Automatic Scrolling option in View menu to display
2762 the currently highlighted region of an alignment.</li>
2763 <li>Order an alignment by sequence length, or using the
2764 average score or total feature count for each sequence.</li>
2765 <li>Shading features by score or associated description</li>
2766 <li>Subdivide alignment and groups based on identity of
2767 selected subsequence (Make Groups from Selection).</li>
2768 <li>New hide/show options including Shift+Control+H to
2769 hide everything but the currently selected region.</li>
2770 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2771 </ul> <em>Application</em>
2773 <li>Fetch DB References capabilities and UI expanded to
2774 support retrieval from DAS sequence sources</li>
2775 <li>Local DAS Sequence sources can be added via the
2776 command line or via the Add local source dialog box.</li>
2777 <li>DAS Dbref and DbxRef feature types are parsed as
2778 database references and protein_name is parsed as
2779 description line (BioSapiens terms).</li>
2780 <li>Enable or disable non-positional feature and database
2781 references in sequence ID tooltip from View menu in
2783 <!-- <li>New hidden columns and rows and representatives capabilities
2784 in annotations file (in progress - not yet fully implemented)</li> -->
2785 <li>Group-associated consensus, sequence logos and
2786 conservation plots</li>
2787 <li>Symbol distributions for each column can be exported
2788 and visualized as sequence logos</li>
2789 <li>Optionally scale multi-character column labels to fit
2790 within each column of annotation row<!-- todo for applet -->
2792 <li>Optional automatic sort of associated alignment view
2793 when a new tree is opened.</li>
2794 <li>Jalview Java Console</li>
2795 <li>Better placement of desktop window when moving
2796 between different screens.</li>
2797 <li>New preference items for sequence ID tooltip and
2798 consensus annotation</li>
2799 <li>Client to submit sequences and IDs to Envision2
2801 <li><em>Vamsas Capabilities</em>
2803 <li>Improved VAMSAS synchronization (Jalview archive
2804 used to preserve views, structures, and tree display
2806 <li>Import of vamsas documents from disk or URL via
2808 <li>Sharing of selected regions between views and
2809 with other VAMSAS applications (Experimental feature!)</li>
2810 <li>Updated API to VAMSAS version 0.2</li>
2812 </ul> <em>Applet</em>
2814 <li>Middle button resizes annotation row height</li>
2817 <li>sortByTree (true/false) - automatically sort the
2818 associated alignment view by the tree when a new tree is
2820 <li>showTreeBootstraps (true/false) - show or hide
2821 branch bootstraps (default is to show them if available)</li>
2822 <li>showTreeDistances (true/false) - show or hide
2823 branch lengths (default is to show them if available)</li>
2824 <li>showUnlinkedTreeNodes (true/false) - indicate if
2825 unassociated nodes should be highlighted in the tree
2827 <li>heightScale and widthScale (1.0 or more) -
2828 increase the height or width of a cell in the alignment
2829 grid relative to the current font size.</li>
2832 <li>Non-positional features displayed in sequence ID
2834 </ul> <em>Other</em>
2836 <li>Features format: graduated colour definitions and
2837 specification of feature scores</li>
2838 <li>Alignment Annotations format: new keywords for group
2839 associated annotation (GROUP_REF) and annotation row display
2840 properties (ROW_PROPERTIES)</li>
2841 <li>XML formats extended to support graduated feature
2842 colourschemes, group associated annotation, and profile
2843 visualization settings.</li></td>
2846 <li>Source field in GFF files parsed as feature source
2847 rather than description</li>
2848 <li>Non-positional features are now included in sequence
2849 feature and gff files (controlled via non-positional feature
2850 visibility in tooltip).</li>
2851 <li>URL links generated for all feature links (bugfix)</li>
2852 <li>Added URL embedding instructions to features file
2854 <li>Codons containing ambiguous nucleotides translated as
2855 'X' in peptide product</li>
2856 <li>Match case switch in find dialog box works for both
2857 sequence ID and sequence string and query strings do not
2858 have to be in upper case to match case-insensitively.</li>
2859 <li>AMSA files only contain first column of
2860 multi-character column annotation labels</li>
2861 <li>Jalview Annotation File generation/parsing consistent
2862 with documentation (e.g. Stockholm annotation can be
2863 exported and re-imported)</li>
2864 <li>PDB files without embedded PDB IDs given a friendly
2866 <li>Find incrementally searches ID string matches as well
2867 as subsequence matches, and correctly reports total number
2871 <li>Better handling of exceptions during sequence
2873 <li>Dasobert generated non-positional feature URL
2874 link text excludes the start_end suffix</li>
2875 <li>DAS feature and source retrieval buttons disabled
2876 when fetch or registry operations in progress.</li>
2877 <li>PDB files retrieved from URLs are cached properly</li>
2878 <li>Sequence description lines properly shared via
2880 <li>Sequence fetcher fetches multiple records for all
2882 <li>Ensured that command line das feature retrieval
2883 completes before alignment figures are generated.</li>
2884 <li>Reduced time taken when opening file browser for
2886 <li>isAligned check prior to calculating tree, PCA or
2887 submitting an MSA to JNet now excludes hidden sequences.</li>
2888 <li>User defined group colours properly recovered
2889 from Jalview projects.</li>
2898 <div align="center">
2899 <strong>2.4.0.b2</strong><br> 28/10/2009
2904 <li>Experimental support for google analytics usage
2906 <li>Jalview privacy settings (user preferences and docs).</li>
2911 <li>Race condition in applet preventing startup in
2913 <li>Exception when feature created from selection beyond
2914 length of sequence.</li>
2915 <li>Allow synthetic PDB files to be imported gracefully</li>
2916 <li>Sequence associated annotation rows associate with
2917 all sequences with a given id</li>
2918 <li>Find function matches case-insensitively for sequence
2919 ID string searches</li>
2920 <li>Non-standard characters do not cause pairwise
2921 alignment to fail with exception</li>
2922 </ul> <em>Application Issues</em>
2924 <li>Sequences are now validated against EMBL database</li>
2925 <li>Sequence fetcher fetches multiple records for all
2927 </ul> <em>InstallAnywhere Issues</em>
2929 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2930 issue with installAnywhere mechanism)</li>
2931 <li>Command line launching of JARs from InstallAnywhere
2932 version (java class versioning error fixed)</li>
2939 <div align="center">
2940 <strong>2.4</strong><br> 27/8/2008
2943 <td><em>User Interface</em>
2945 <li>Linked highlighting of codon and amino acid from
2946 translation and protein products</li>
2947 <li>Linked highlighting of structure associated with
2948 residue mapping to codon position</li>
2949 <li>Sequence Fetcher provides example accession numbers
2950 and 'clear' button</li>
2951 <li>MemoryMonitor added as an option under Desktop's
2953 <li>Extract score function to parse whitespace separated
2954 numeric data in description line</li>
2955 <li>Column labels in alignment annotation can be centred.</li>
2956 <li>Tooltip for sequence associated annotation give name
2958 </ul> <em>Web Services and URL fetching</em>
2960 <li>JPred3 web service</li>
2961 <li>Prototype sequence search client (no public services
2963 <li>Fetch either seed alignment or full alignment from
2965 <li>URL Links created for matching database cross
2966 references as well as sequence ID</li>
2967 <li>URL Links can be created using regular-expressions</li>
2968 </ul> <em>Sequence Database Connectivity</em>
2970 <li>Retrieval of cross-referenced sequences from other
2972 <li>Generalised database reference retrieval and
2973 validation to all fetchable databases</li>
2974 <li>Fetch sequences from DAS sources supporting the
2975 sequence command</li>
2976 </ul> <em>Import and Export</em>
2977 <li>export annotation rows as CSV for spreadsheet import</li>
2978 <li>Jalview projects record alignment dataset associations,
2979 EMBL products, and cDNA sequence mappings</li>
2980 <li>Sequence Group colour can be specified in Annotation
2982 <li>Ad-hoc colouring of group in Annotation File using RGB
2983 triplet as name of colourscheme</li>
2984 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2986 <li>treenode binding for VAMSAS tree exchange</li>
2987 <li>local editing and update of sequences in VAMSAS
2988 alignments (experimental)</li>
2989 <li>Create new or select existing session to join</li>
2990 <li>load and save of vamsas documents</li>
2991 </ul> <em>Application command line</em>
2993 <li>-tree parameter to open trees (introduced for passing
2995 <li>-fetchfrom command line argument to specify nicknames
2996 of DAS servers to query for alignment features</li>
2997 <li>-dasserver command line argument to add new servers
2998 that are also automatically queried for features</li>
2999 <li>-groovy command line argument executes a given groovy
3000 script after all input data has been loaded and parsed</li>
3001 </ul> <em>Applet-Application data exchange</em>
3003 <li>Trees passed as applet parameters can be passed to
3004 application (when using "View in full
3005 application")</li>
3006 </ul> <em>Applet Parameters</em>
3008 <li>feature group display control parameter</li>
3009 <li>debug parameter</li>
3010 <li>showbutton parameter</li>
3011 </ul> <em>Applet API methods</em>
3013 <li>newView public method</li>
3014 <li>Window (current view) specific get/set public methods</li>
3015 <li>Feature display control methods</li>
3016 <li>get list of currently selected sequences</li>
3017 </ul> <em>New Jalview distribution features</em>
3019 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3020 <li>RELEASE file gives build properties for the latest
3021 Jalview release.</li>
3022 <li>Java 1.1 Applet build made easier and donotobfuscate
3023 property controls execution of obfuscator</li>
3024 <li>Build target for generating source distribution</li>
3025 <li>Debug flag for javacc</li>
3026 <li>.jalview_properties file is documented (slightly) in
3027 jalview.bin.Cache</li>
3028 <li>Continuous Build Integration for stable and
3029 development version of Application, Applet and source
3034 <li>selected region output includes visible annotations
3035 (for certain formats)</li>
3036 <li>edit label/displaychar contains existing label/char
3038 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3039 <li>shorter peptide product names from EMBL records</li>
3040 <li>Newick string generator makes compact representations</li>
3041 <li>bootstrap values parsed correctly for tree files with
3043 <li>pathological filechooser bug avoided by not allowing
3044 filenames containing a ':'</li>
3045 <li>Fixed exception when parsing GFF files containing
3046 global sequence features</li>
3047 <li>Alignment datasets are finalized only when number of
3048 references from alignment sequences goes to zero</li>
3049 <li>Close of tree branch colour box without colour
3050 selection causes cascading exceptions</li>
3051 <li>occasional negative imgwidth exceptions</li>
3052 <li>better reporting of non-fatal warnings to user when
3053 file parsing fails.</li>
3054 <li>Save works when Jalview project is default format</li>
3055 <li>Save as dialog opened if current alignment format is
3056 not a valid output format</li>
3057 <li>UniProt canonical names introduced for both das and
3059 <li>Histidine should be midblue (not pink!) in Zappo</li>
3060 <li>error messages passed up and output when data read
3062 <li>edit undo recovers previous dataset sequence when
3063 sequence is edited</li>
3064 <li>allow PDB files without pdb ID HEADER lines (like
3065 those generated by MODELLER) to be read in properly</li>
3066 <li>allow reading of JPred concise files as a normal
3068 <li>Stockholm annotation parsing and alignment properties
3069 import fixed for PFAM records</li>
3070 <li>Structure view windows have correct name in Desktop
3072 <li>annotation consisting of sequence associated scores
3073 can be read and written correctly to annotation file</li>
3074 <li>Aligned cDNA translation to aligned peptide works
3076 <li>Fixed display of hidden sequence markers and
3077 non-italic font for representatives in Applet</li>
3078 <li>Applet Menus are always embedded in applet window on
3080 <li>Newly shown features appear at top of stack (in
3082 <li>Annotations added via parameter not drawn properly
3083 due to null pointer exceptions</li>
3084 <li>Secondary structure lines are drawn starting from
3085 first column of alignment</li>
3086 <li>UniProt XML import updated for new schema release in
3088 <li>Sequence feature to sequence ID match for Features
3089 file is case-insensitive</li>
3090 <li>Sequence features read from Features file appended to
3091 all sequences with matching IDs</li>
3092 <li>PDB structure coloured correctly for associated views
3093 containing a sub-sequence</li>
3094 <li>PDB files can be retrieved by applet from Jar files</li>
3095 <li>feature and annotation file applet parameters
3096 referring to different directories are retrieved correctly</li>
3097 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3098 <li>Fixed application hang whilst waiting for
3099 splash-screen version check to complete</li>
3100 <li>Applet properly URLencodes input parameter values
3101 when passing them to the launchApp service</li>
3102 <li>display name and local features preserved in results
3103 retrieved from web service</li>
3104 <li>Visual delay indication for sequence retrieval and
3105 sequence fetcher initialisation</li>
3106 <li>updated Application to use DAS 1.53e version of
3107 dasobert DAS client</li>
3108 <li>Re-instated Full AMSA support and .amsa file
3110 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3118 <div align="center">
3119 <strong>2.3</strong><br> 9/5/07
3124 <li>Jmol 11.0.2 integration</li>
3125 <li>PDB views stored in Jalview XML files</li>
3126 <li>Slide sequences</li>
3127 <li>Edit sequence in place</li>
3128 <li>EMBL CDS features</li>
3129 <li>DAS Feature mapping</li>
3130 <li>Feature ordering</li>
3131 <li>Alignment Properties</li>
3132 <li>Annotation Scores</li>
3133 <li>Sort by scores</li>
3134 <li>Feature/annotation editing in applet</li>
3139 <li>Headless state operation in 2.2.1</li>
3140 <li>Incorrect and unstable DNA pairwise alignment</li>
3141 <li>Cut and paste of sequences with annotation</li>
3142 <li>Feature group display state in XML</li>
3143 <li>Feature ordering in XML</li>
3144 <li>blc file iteration selection using filename # suffix</li>
3145 <li>Stockholm alignment properties</li>
3146 <li>Stockhom alignment secondary structure annotation</li>
3147 <li>2.2.1 applet had no feature transparency</li>
3148 <li>Number pad keys can be used in cursor mode</li>
3149 <li>Structure Viewer mirror image resolved</li>
3156 <div align="center">
3157 <strong>2.2.1</strong><br> 12/2/07
3162 <li>Non standard characters can be read and displayed
3163 <li>Annotations/Features can be imported/exported to the
3165 <li>Applet allows editing of sequence/annotation/group
3166 name & description
3167 <li>Preference setting to display sequence name in
3169 <li>Annotation file format extended to allow
3170 Sequence_groups to be defined
3171 <li>Default opening of alignment overview panel can be
3172 specified in preferences
3173 <li>PDB residue numbering annotation added to associated
3179 <li>Applet crash under certain Linux OS with Java 1.6
3181 <li>Annotation file export / import bugs fixed
3182 <li>PNG / EPS image output bugs fixed
3188 <div align="center">
3189 <strong>2.2</strong><br> 27/11/06
3194 <li>Multiple views on alignment
3195 <li>Sequence feature editing
3196 <li>"Reload" alignment
3197 <li>"Save" to current filename
3198 <li>Background dependent text colour
3199 <li>Right align sequence ids
3200 <li>User-defined lower case residue colours
3203 <li>Menu item accelerator keys
3204 <li>Control-V pastes to current alignment
3205 <li>Cancel button for DAS Feature Fetching
3206 <li>PCA and PDB Viewers zoom via mouse roller
3207 <li>User-defined sub-tree colours and sub-tree selection
3209 <li>'New Window' button on the 'Output to Text box'
3214 <li>New memory efficient Undo/Redo System
3215 <li>Optimised symbol lookups and conservation/consensus
3217 <li>Region Conservation/Consensus recalculated after
3219 <li>Fixed Remove Empty Columns Bug (empty columns at end
3221 <li>Slowed DAS Feature Fetching for increased robustness.
3223 <li>Made angle brackets in ASCII feature descriptions
3225 <li>Re-instated Zoom function for PCA
3226 <li>Sequence descriptions conserved in web service
3228 <li>UniProt ID discoverer uses any word separated by
3230 <li>WsDbFetch query/result association resolved
3231 <li>Tree leaf to sequence mapping improved
3232 <li>Smooth fonts switch moved to FontChooser dialog box.
3239 <div align="center">
3240 <strong>2.1.1</strong><br> 12/9/06
3245 <li>Copy consensus sequence to clipboard</li>
3250 <li>Image output - rightmost residues are rendered if
3251 sequence id panel has been resized</li>
3252 <li>Image output - all offscreen group boundaries are
3254 <li>Annotation files with sequence references - all
3255 elements in file are relative to sequence position</li>
3256 <li>Mac Applet users can use Alt key for group editing</li>
3262 <div align="center">
3263 <strong>2.1</strong><br> 22/8/06
3268 <li>MAFFT Multiple Alignment in default Web Service list</li>
3269 <li>DAS Feature fetching</li>
3270 <li>Hide sequences and columns</li>
3271 <li>Export Annotations and Features</li>
3272 <li>GFF file reading / writing</li>
3273 <li>Associate structures with sequences from local PDB
3275 <li>Add sequences to exisiting alignment</li>
3276 <li>Recently opened files / URL lists</li>
3277 <li>Applet can launch the full application</li>
3278 <li>Applet has transparency for features (Java 1.2
3280 <li>Applet has user defined colours parameter</li>
3281 <li>Applet can load sequences from parameter
3282 "sequence<em>x</em>"
3288 <li>Redundancy Panel reinstalled in the Applet</li>
3289 <li>Monospaced font - EPS / rescaling bug fixed</li>
3290 <li>Annotation files with sequence references bug fixed</li>
3296 <div align="center">
3297 <strong>2.08.1</strong><br> 2/5/06
3302 <li>Change case of selected region from Popup menu</li>
3303 <li>Choose to match case when searching</li>
3304 <li>Middle mouse button and mouse movement can compress /
3305 expand the visible width and height of the alignment</li>
3310 <li>Annotation Panel displays complete JNet results</li>
3316 <div align="center">
3317 <strong>2.08b</strong><br> 18/4/06
3323 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3324 <li>Righthand label on wrapped alignments shows correct
3331 <div align="center">
3332 <strong>2.08</strong><br> 10/4/06
3337 <li>Editing can be locked to the selection area</li>
3338 <li>Keyboard editing</li>
3339 <li>Create sequence features from searches</li>
3340 <li>Precalculated annotations can be loaded onto
3342 <li>Features file allows grouping of features</li>
3343 <li>Annotation Colouring scheme added</li>
3344 <li>Smooth fonts off by default - Faster rendering</li>
3345 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3350 <li>Drag & Drop fixed on Linux</li>
3351 <li>Jalview Archive file faster to load/save, sequence
3352 descriptions saved.</li>
3358 <div align="center">
3359 <strong>2.07</strong><br> 12/12/05
3364 <li>PDB Structure Viewer enhanced</li>
3365 <li>Sequence Feature retrieval and display enhanced</li>
3366 <li>Choose to output sequence start-end after sequence
3367 name for file output</li>
3368 <li>Sequence Fetcher WSDBFetch@EBI</li>
3369 <li>Applet can read feature files, PDB files and can be
3370 used for HTML form input</li>
3375 <li>HTML output writes groups and features</li>
3376 <li>Group editing is Control and mouse click</li>
3377 <li>File IO bugs</li>
3383 <div align="center">
3384 <strong>2.06</strong><br> 28/9/05
3389 <li>View annotations in wrapped mode</li>
3390 <li>More options for PCA viewer</li>
3395 <li>GUI bugs resolved</li>
3396 <li>Runs with -nodisplay from command line</li>
3402 <div align="center">
3403 <strong>2.05b</strong><br> 15/9/05
3408 <li>Choose EPS export as lineart or text</li>
3409 <li>Jar files are executable</li>
3410 <li>Can read in Uracil - maps to unknown residue</li>
3415 <li>Known OutOfMemory errors give warning message</li>
3416 <li>Overview window calculated more efficiently</li>
3417 <li>Several GUI bugs resolved</li>
3423 <div align="center">
3424 <strong>2.05</strong><br> 30/8/05
3429 <li>Edit and annotate in "Wrapped" view</li>
3434 <li>Several GUI bugs resolved</li>
3440 <div align="center">
3441 <strong>2.04</strong><br> 24/8/05
3446 <li>Hold down mouse wheel & scroll to change font
3452 <li>Improved JPred client reliability</li>
3453 <li>Improved loading of Jalview files</li>
3459 <div align="center">
3460 <strong>2.03</strong><br> 18/8/05
3465 <li>Set Proxy server name and port in preferences</li>
3466 <li>Multiple URL links from sequence ids</li>
3467 <li>User Defined Colours can have a scheme name and added
3469 <li>Choose to ignore gaps in consensus calculation</li>
3470 <li>Unix users can set default web browser</li>
3471 <li>Runs without GUI for batch processing</li>
3472 <li>Dynamically generated Web Service Menus</li>
3477 <li>InstallAnywhere download for Sparc Solaris</li>
3483 <div align="center">
3484 <strong>2.02</strong><br> 18/7/05
3490 <li>Copy & Paste order of sequences maintains
3491 alignment order.</li>
3497 <div align="center">
3498 <strong>2.01</strong><br> 12/7/05
3503 <li>Use delete key for deleting selection.</li>
3504 <li>Use Mouse wheel to scroll sequences.</li>
3505 <li>Help file updated to describe how to add alignment
3507 <li>Version and build date written to build properties
3509 <li>InstallAnywhere installation will check for updates
3510 at launch of Jalview.</li>
3515 <li>Delete gaps bug fixed.</li>
3516 <li>FileChooser sorts columns.</li>
3517 <li>Can remove groups one by one.</li>
3518 <li>Filechooser icons installed.</li>
3519 <li>Finder ignores return character when searching.
3520 Return key will initiate a search.<br>
3527 <div align="center">
3528 <strong>2.0</strong><br> 20/6/05
3533 <li>New codebase</li>