3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
34 /* separate the items from eachother */
41 /* doesnt get processed in javahelp */
50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.3">2.10.3</a><br />
74 <em>10/10/2017</em></strong>
77 <td><div align="left">
81 <!-- JAL-2446 -->Faster and more efficient management and
82 rendering of sequence features
85 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
86 429 rate limit request hander
89 <!-- JAL-2773 -->Structure views don't get updated unless
90 their colours have changed
94 <td><div align="left">
97 <li><!-- JAL-2777 -->Structures with whitespace chainCode cannot be viewed in Chimera</li>
98 <li><!-- JAL-2728 -->Protein annotation panel too high in CDS/Protein view
100 <li><!-- JAL-2757 -->Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs
106 <td width="60" nowrap>
108 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
109 <em>2/10/2017</em></strong>
112 <td><div align="left">
113 <em>New features in Jalview Desktop</em>
116 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
118 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
122 <td><div align="left">
126 <td width="60" nowrap>
128 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
129 <em>7/9/2017</em></strong>
132 <td><div align="left">
136 <!-- JAL-2588 -->Show gaps in overview window by colouring
137 in grey (sequences used to be coloured grey, and gaps were
141 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
145 <!-- JAL-2587 -->Overview updates immediately on increase
146 in size and progress bar shown as higher resolution
147 overview is recalculated
152 <td><div align="left">
156 <!-- JAL-2664 -->Overview window redraws every hidden
157 column region row by row
160 <!-- JAL-2681 -->duplicate protein sequences shown after
161 retrieving Ensembl crossrefs for sequences from Uniprot
164 <!-- JAL-2603 -->Overview window throws NPE if show boxes
165 format setting is unticked
168 <!-- JAL-2610 -->Groups are coloured wrongly in overview
169 if group has show boxes format setting unticked
172 <!-- JAL-2672,JAL-2665 -->Redraw problems when
173 autoscrolling whilst dragging current selection group to
174 include sequences and columns not currently displayed
177 <!-- JAL-2691 -->Not all chains are mapped when multimeric
178 assemblies are imported via CIF file
181 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
182 displayed when threshold or conservation colouring is also
186 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
190 <!-- JAL-2673 -->Jalview continues to scroll after
191 dragging a selected region off the visible region of the
195 <!-- JAL-2724 -->Cannot apply annotation based
196 colourscheme to all groups in a view
199 <!-- JAL-2511 -->IDs don't line up with sequences
200 initially after font size change using the Font chooser or
207 <td width="60" nowrap>
209 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
212 <td><div align="left">
213 <em>Calculations</em>
217 <!-- JAL-1933 -->Occupancy annotation row shows number of
218 ungapped positions in each column of the alignment.
221 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
222 a calculation dialog box
225 <!-- JAL-2379 -->Revised implementation of PCA for speed
226 and memory efficiency (~30x faster)
229 <!-- JAL-2403 -->Revised implementation of sequence
230 similarity scores as used by Tree, PCA, Shading Consensus
231 and other calculations
234 <!-- JAL-2416 -->Score matrices are stored as resource
235 files within the Jalview codebase
238 <!-- JAL-2500 -->Trees computed on Sequence Feature
239 Similarity may have different topology due to increased
246 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
247 model for alignments and groups
250 <!-- JAL-384 -->Custom shading schemes created via groovy
257 <!-- JAL-2526 -->Efficiency improvements for interacting
258 with alignment and overview windows
261 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
265 <!-- JAL-2388 -->Hidden columns and sequences can be
269 <!-- JAL-2611 -->Click-drag in visible area allows fine
270 adjustment of visible position
274 <em>Data import/export</em>
277 <!-- JAL-2535 -->Posterior probability annotation from
278 Stockholm files imported as sequence associated annotation
281 <!-- JAL-2507 -->More robust per-sequence positional
282 annotation input/output via stockholm flatfile
285 <!-- JAL-2533 -->Sequence names don't include file
286 extension when importing structure files without embedded
287 names or PDB accessions
290 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
291 format sequence substitution matrices
294 <em>User Interface</em>
297 <!-- JAL-2447 --> Experimental Features Checkbox in
298 Desktop's Tools menu to hide or show untested features in
302 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
303 via Overview or sequence motif search operations
306 <!-- JAL-2547 -->Amend sequence features dialog box can be
307 opened by double clicking gaps within sequence feature
311 <!-- JAL-1476 -->Status bar message shown when not enough
312 aligned positions were available to create a 3D structure
316 <em>3D Structure</em>
319 <!-- JAL-2430 -->Hidden regions in alignment views are not
320 coloured in linked structure views
323 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
324 file-based command exchange
327 <!-- JAL-2375 -->Structure chooser automatically shows
328 Cached Structures rather than querying the PDBe if
329 structures are already available for sequences
332 <!-- JAL-2520 -->Structures imported via URL are cached in
333 the Jalview project rather than downloaded again when the
337 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
338 to transfer Chimera's structure attributes as Jalview
339 features, and vice-versa (<strong>Experimental
343 <em>Web Services</em>
346 <!-- JAL-2549 -->Updated JABAWS client to v2.2
349 <!-- JAL-2335 -->Filter non-standard amino acids and
350 nucleotides when submitting to AACon and other MSA
354 <!-- JAL-2316, -->URLs for viewing database
355 cross-references provided by identifiers.org and the
363 <!-- JAL-2344 -->FileFormatI interface for describing and
364 identifying file formats (instead of String constants)
367 <!-- JAL-2228 -->FeatureCounter script refactored for
368 efficiency when counting all displayed features (not
369 backwards compatible with 2.10.1)
372 <em>Example files</em>
375 <!-- JAL-2631 -->Graduated feature colour style example
376 included in the example feature file
379 <em>Documentation</em>
382 <!-- JAL-2339 -->Release notes reformatted for readability
383 with the built-in Java help viewer
386 <!-- JAL-1644 -->Find documentation updated with 'search
387 sequence description' option
393 <!-- JAL-2485, -->External service integration tests for
394 Uniprot REST Free Text Search Client
397 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
400 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
405 <td><div align="left">
406 <em>Calculations</em>
409 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
410 matrix - C->R should be '-3'<br />Old matrix restored
411 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
413 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
414 Jalview's treatment of gaps in PCA and substitution matrix
415 based Tree calculations.<br /> <br />In earlier versions
416 of Jalview, gaps matching gaps were penalised, and gaps
417 matching non-gaps penalised even more. In the PCA
418 calculation, gaps were actually treated as non-gaps - so
419 different costs were applied, which meant Jalview's PCAs
420 were different to those produced by SeqSpace.<br />Jalview
421 now treats gaps in the same way as SeqSpace (ie it scores
422 them as 0). <br /> <br />Enter the following in the
423 Groovy console to restore pre-2.10.2 behaviour:<br />
424 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
425 // for 2.10.1 mode <br />
426 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
427 // to restore 2.10.2 mode <br /> <br /> <em>Note:
428 these settings will affect all subsequent tree and PCA
429 calculations (not recommended)</em></li>
431 <!-- JAL-2424 -->Fixed off-by-one bug that affected
432 scaling of branch lengths for trees computed using
433 Sequence Feature Similarity.
436 <!-- JAL-2377 -->PCA calculation could hang when
437 generating output report when working with highly
441 <!-- JAL-2544 --> Sort by features includes features to
442 right of selected region when gaps present on right-hand
446 <em>User Interface</em>
449 <!-- JAL-2346 -->Reopening Colour by annotation dialog
450 doesn't reselect a specific sequence's associated
451 annotation after it was used for colouring a view
454 <!-- JAL-2419 -->Current selection lost if popup menu
455 opened on a region of alignment without groups
458 <!-- JAL-2374 -->Popup menu not always shown for regions
459 of an alignment with overlapping groups
462 <!-- JAL-2310 -->Finder double counts if both a sequence's
463 name and description match
466 <!-- JAL-2370 -->Hiding column selection containing two
467 hidden regions results in incorrect hidden regions
470 <!-- JAL-2386 -->'Apply to all groups' setting when
471 changing colour does not apply Conservation slider value
475 <!-- JAL-2373 -->Percentage identity and conservation menu
476 items do not show a tick or allow shading to be disabled
479 <!-- JAL-2385 -->Conservation shading or PID threshold
480 lost when base colourscheme changed if slider not visible
483 <!-- JAL-2547 -->Sequence features shown in tooltip for
484 gaps before start of features
487 <!-- JAL-2623 -->Graduated feature colour threshold not
488 restored to UI when feature colour is edited
491 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
492 a time when scrolling vertically in wrapped mode.
495 <!-- JAL-2630 -->Structure and alignment overview update
496 as graduate feature colour settings are modified via the
500 <!-- JAL-2034 -->Overview window doesn't always update
501 when a group defined on the alignment is resized
504 <!-- JAL-2605 -->Mouseovers on left/right scale region in
505 wrapped view result in positional status updates
509 <!-- JAL-2563 -->Status bar doesn't show position for
510 ambiguous amino acid and nucleotide symbols
513 <!-- JAL-2602 -->Copy consensus sequence failed if
514 alignment included gapped columns
517 <!-- JAL-2473 -->Minimum size set for Jalview windows so
518 widgets don't permanently disappear
521 <!-- JAL-2503 -->Cannot select or filter quantitative
522 annotation that are shown only as column labels (e.g.
523 T-Coffee column reliability scores)
526 <!-- JAL-2594 -->Exception thrown if trying to create a
527 sequence feature on gaps only
530 <!-- JAL-2504 -->Features created with 'New feature'
531 button from a Find inherit previously defined feature type
532 rather than the Find query string
535 <!-- JAL-2423 -->incorrect title in output window when
536 exporting tree calculated in Jalview
539 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
540 and then revealing them reorders sequences on the
544 <!-- JAL-964 -->Group panel in sequence feature settings
545 doesn't update to reflect available set of groups after
546 interactively adding or modifying features
549 <!-- JAL-2225 -->Sequence Database chooser unusable on
553 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
554 only excluded gaps in current sequence and ignored
561 <!-- JAL-2421 -->Overview window visible region moves
562 erratically when hidden rows or columns are present
565 <!-- JAL-2362 -->Per-residue colourschemes applied via the
566 Structure Viewer's colour menu don't correspond to
570 <!-- JAL-2405 -->Protein specific colours only offered in
571 colour and group colour menu for protein alignments
574 <!-- JAL-2385 -->Colour threshold slider doesn't update to
575 reflect currently selected view or group's shading
579 <!-- JAL-2624 -->Feature colour thresholds not respected
580 when rendered on overview and structures when opacity at
584 <!-- JAL-2589 -->User defined gap colour not shown in
585 overview when features overlaid on alignment
588 <em>Data import/export</em>
591 <!-- JAL-2576 -->Very large alignments take a long time to
595 <!-- JAL-2507 -->Per-sequence RNA secondary structures
596 added after a sequence was imported are not written to
600 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
601 when importing RNA secondary structure via Stockholm
604 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
605 not shown in correct direction for simple pseudoknots
608 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
609 with lightGray or darkGray via features file (but can
613 <!-- JAL-2383 -->Above PID colour threshold not recovered
614 when alignment view imported from project
617 <!-- JAL-2520,JAL-2465 -->No mappings generated between
618 structure and sequences extracted from structure files
619 imported via URL and viewed in Jmol
622 <!-- JAL-2520 -->Structures loaded via URL are saved in
623 Jalview Projects rather than fetched via URL again when
624 the project is loaded and the structure viewed
627 <em>Web Services</em>
630 <!-- JAL-2519 -->EnsemblGenomes example failing after
631 release of Ensembl v.88
634 <!-- JAL-2366 -->Proxy server address and port always
635 appear enabled in Preferences->Connections
638 <!-- JAL-2461 -->DAS registry not found exceptions
639 removed from console output
642 <!-- JAL-2582 -->Cannot retrieve protein products from
643 Ensembl by Peptide ID
646 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
647 created from SIFTs, and spurious 'Couldn't open structure
648 in Chimera' errors raised after April 2017 update (problem
649 due to 'null' string rather than empty string used for
650 residues with no corresponding PDB mapping).
653 <em>Application UI</em>
656 <!-- JAL-2361 -->User Defined Colours not added to Colour
660 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
661 case' residues (button in colourscheme editor debugged and
662 new documentation and tooltips added)
665 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
666 doesn't restore group-specific text colour thresholds
669 <!-- JAL-2243 -->Feature settings panel does not update as
670 new features are added to alignment
673 <!-- JAL-2532 -->Cancel in feature settings reverts
674 changes to feature colours via the Amend features dialog
677 <!-- JAL-2506 -->Null pointer exception when attempting to
678 edit graduated feature colour via amend features dialog
682 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
683 selection menu changes colours of alignment views
686 <!-- JAL-2426 -->Spurious exceptions in console raised
687 from alignment calculation workers after alignment has
691 <!-- JAL-1608 -->Typo in selection popup menu - Create
692 groups now 'Create Group'
695 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
696 Create/Undefine group doesn't always work
699 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
700 shown again after pressing 'Cancel'
703 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
704 adjusts start position in wrap mode
707 <!-- JAL-2563 -->Status bar doesn't show positions for
708 ambiguous amino acids
711 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
712 CDS/Protein view after CDS sequences added for aligned
716 <!-- JAL-2592 -->User defined colourschemes called 'User
717 Defined' don't appear in Colours menu
723 <!-- JAL-2468 -->Switching between Nucleotide and Protein
724 score models doesn't always result in an updated PCA plot
727 <!-- JAL-2442 -->Features not rendered as transparent on
728 overview or linked structure view
731 <!-- JAL-2372 -->Colour group by conservation doesn't
735 <!-- JAL-2517 -->Hitting Cancel after applying
736 user-defined colourscheme doesn't restore original
743 <!-- JAL-2314 -->Unit test failure:
744 jalview.ws.jabaws.RNAStructExportImport setup fails
747 <!-- JAL-2307 -->Unit test failure:
748 jalview.ws.sifts.SiftsClientTest due to compatibility
749 problems with deep array comparison equality asserts in
750 successive versions of TestNG
753 <!-- JAL-2479 -->Relocated StructureChooserTest and
754 ParameterUtilsTest Unit tests to Network suite
757 <em>New Known Issues</em>
760 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
761 phase after a sequence motif find operation
764 <!-- JAL-2550 -->Importing annotation file with rows
765 containing just upper and lower case letters are
766 interpreted as WUSS RNA secondary structure symbols
769 <!-- JAL-2590 -->Cannot load and display Newick trees
770 reliably from eggnog Ortholog database
773 <!-- JAL-2468 -->Status bar shows 'Marked x columns
774 containing features of type Highlight' when 'B' is pressed
775 to mark columns containing highlighted regions.
778 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
779 doesn't always add secondary structure annotation.
784 <td width="60" nowrap>
786 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
789 <td><div align="left">
793 <!-- JAL-98 -->Improved memory usage: sparse arrays used
794 for all consensus calculations
797 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
800 <li>Updated Jalview's Certum code signing certificate
806 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
807 set of database cross-references, sorted alphabetically
810 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
811 from database cross references. Users with custom links
812 will receive a <a href="webServices/urllinks.html#warning">warning
813 dialog</a> asking them to update their preferences.
816 <!-- JAL-2287-->Cancel button and escape listener on
817 dialog warning user about disconnecting Jalview from a
821 <!-- JAL-2320-->Jalview's Chimera control window closes if
822 the Chimera it is connected to is shut down
825 <!-- JAL-1738-->New keystroke (B) and Select highlighted
826 columns menu item to mark columns containing highlighted
827 regions (e.g. from structure selections or results of a
831 <!-- JAL-2284-->Command line option for batch-generation
832 of HTML pages rendering alignment data with the BioJS
842 <!-- JAL-2286 -->Columns with more than one modal residue
843 are not coloured or thresholded according to percent
844 identity (first observed in Jalview 2.8.2)
847 <!-- JAL-2301 -->Threonine incorrectly reported as not
851 <!-- JAL-2318 -->Updates to documentation pages (above PID
852 threshold, amino acid properties)
855 <!-- JAL-2292 -->Lower case residues in sequences are not
856 reported as mapped to residues in a structure file in the
860 <!--JAL-2324 -->Identical features with non-numeric scores
861 could be added multiple times to a sequence
864 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
865 bond features shown as two highlighted residues rather
866 than a range in linked structure views, and treated
867 correctly when selecting and computing trees from features
870 <!-- JAL-2281-->Custom URL links for database
871 cross-references are matched to database name regardless
879 <!-- JAL-2282-->Custom URL links for specific database
880 names without regular expressions also offer links from
884 <!-- JAL-2315-->Removing a single configured link in the
885 URL links pane in Connections preferences doesn't actually
886 update Jalview configuration
889 <!-- JAL-2272-->CTRL-Click on a selected region to open
890 the alignment area popup menu doesn't work on El-Capitan
893 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
894 files with similarly named sequences if dropped onto the
898 <!-- JAL-2312 -->Additional mappings are shown for PDB
899 entries where more chains exist in the PDB accession than
900 are reported in the SIFTS file
903 <!-- JAL-2317-->Certain structures do not get mapped to
904 the structure view when displayed with Chimera
907 <!-- JAL-2317-->No chains shown in the Chimera view
908 panel's View->Show Chains submenu
911 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
912 work for wrapped alignment views
915 <!--JAL-2197 -->Rename UI components for running JPred
916 predictions from 'JNet' to 'JPred'
919 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
920 corrupted when annotation panel vertical scroll is not at
924 <!--JAL-2332 -->Attempting to view structure for Hen
925 lysozyme results in a PDB Client error dialog box
928 <!-- JAL-2319 -->Structure View's mapping report switched
929 ranges for PDB and sequence for SIFTS
932 SIFTS 'Not_Observed' residues mapped to non-existant
936 <!-- <em>New Known Issues</em>
943 <td width="60" nowrap>
945 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
946 <em>25/10/2016</em></strong>
949 <td><em>Application</em>
951 <li>3D Structure chooser opens with 'Cached structures'
952 view if structures already loaded</li>
953 <li>Progress bar reports models as they are loaded to
960 <li>Colour by conservation always enabled and no tick
961 shown in menu when BLOSUM or PID shading applied</li>
962 <li>FER1_ARATH and FER2_ARATH labels were switched in
963 example sequences/projects/trees</li>
967 <li>Jalview projects with views of local PDB structure
968 files saved on Windows cannot be opened on OSX</li>
969 <li>Multiple structure views can be opened and superposed
970 without timeout for structures with multiple models or
971 multiple sequences in alignment</li>
972 <li>Cannot import or associated local PDB files without a
973 PDB ID HEADER line</li>
974 <li>RMSD is not output in Jmol console when superposition
976 <li>Drag and drop of URL from Browser fails for Linux and
977 OSX versions earlier than El Capitan</li>
978 <li>ENA client ignores invalid content from ENA server</li>
979 <li>Exceptions are not raised in console when ENA client
980 attempts to fetch non-existent IDs via Fetch DB Refs UI
982 <li>Exceptions are not raised in console when a new view
983 is created on the alignment</li>
984 <li>OSX right-click fixed for group selections: CMD-click
985 to insert/remove gaps in groups and CTRL-click to open group
988 <em>Build and deployment</em>
990 <li>URL link checker now copes with multi-line anchor
993 <em>New Known Issues</em>
995 <li>Drag and drop from URL links in browsers do not work
1002 <td width="60" nowrap>
1003 <div align="center">
1004 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1007 <td><em>General</em>
1010 <!-- JAL-2124 -->Updated Spanish translations.
1013 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1014 for importing structure data to Jalview. Enables mmCIF and
1018 <!-- JAL-192 --->Alignment ruler shows positions relative to
1022 <!-- JAL-2202 -->Position/residue shown in status bar when
1023 mousing over sequence associated annotation
1026 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1030 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1031 '()', canonical '[]' and invalid '{}' base pair populations
1035 <!-- JAL-2092 -->Feature settings popup menu options for
1036 showing or hiding columns containing a feature
1039 <!-- JAL-1557 -->Edit selected group by double clicking on
1040 group and sequence associated annotation labels
1043 <!-- JAL-2236 -->Sequence name added to annotation label in
1044 select/hide columns by annotation and colour by annotation
1048 </ul> <em>Application</em>
1051 <!-- JAL-2050-->Automatically hide introns when opening a
1052 gene/transcript view
1055 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1059 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1060 structure mappings with the EMBL-EBI PDBe SIFTS database
1063 <!-- JAL-2079 -->Updated download sites used for Rfam and
1064 Pfam sources to xfam.org
1067 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1070 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1071 over sequences in Jalview
1074 <!-- JAL-2027-->Support for reverse-complement coding
1075 regions in ENA and EMBL
1078 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1079 for record retrieval via ENA rest API
1082 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1086 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1087 groovy script execution
1090 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1091 alignment window's Calculate menu
1094 <!-- JAL-1812 -->Allow groovy scripts that call
1095 Jalview.getAlignFrames() to run in headless mode
1098 <!-- JAL-2068 -->Support for creating new alignment
1099 calculation workers from groovy scripts
1102 <!-- JAL-1369 --->Store/restore reference sequence in
1106 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1107 associations are now saved/restored from project
1110 <!-- JAL-1993 -->Database selection dialog always shown
1111 before sequence fetcher is opened
1114 <!-- JAL-2183 -->Double click on an entry in Jalview's
1115 database chooser opens a sequence fetcher
1118 <!-- JAL-1563 -->Free-text search client for UniProt using
1119 the UniProt REST API
1122 <!-- JAL-2168 -->-nonews command line parameter to prevent
1123 the news reader opening
1126 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1127 querying stored in preferences
1130 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1134 <!-- JAL-1977-->Tooltips shown on database chooser
1137 <!-- JAL-391 -->Reverse complement function in calculate
1138 menu for nucleotide sequences
1141 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1142 and feature counts preserves alignment ordering (and
1143 debugged for complex feature sets).
1146 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1147 viewing structures with Jalview 2.10
1150 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1151 genome, transcript CCDS and gene ids via the Ensembl and
1152 Ensembl Genomes REST API
1155 <!-- JAL-2049 -->Protein sequence variant annotation
1156 computed for 'sequence_variant' annotation on CDS regions
1160 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1164 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1165 Ref Fetcher fails to match, or otherwise updates sequence
1166 data from external database records.
1169 <!-- JAL-2154 -->Revised Jalview Project format for
1170 efficient recovery of sequence coding and alignment
1171 annotation relationships.
1173 </ul> <!-- <em>Applet</em>
1184 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1188 <!-- JAL-2018-->Export features in Jalview format (again)
1189 includes graduated colourschemes
1192 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1193 working with big alignments and lots of hidden columns
1196 <!-- JAL-2053-->Hidden column markers not always rendered
1197 at right of alignment window
1200 <!-- JAL-2067 -->Tidied up links in help file table of
1204 <!-- JAL-2072 -->Feature based tree calculation not shown
1208 <!-- JAL-2075 -->Hidden columns ignored during feature
1209 based tree calculation
1212 <!-- JAL-2065 -->Alignment view stops updating when show
1213 unconserved enabled for group on alignment
1216 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1220 <!-- JAL-2146 -->Alignment column in status incorrectly
1221 shown as "Sequence position" when mousing over
1225 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1226 hidden columns present
1229 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1230 user created annotation added to alignment
1233 <!-- JAL-1841 -->RNA Structure consensus only computed for
1234 '()' base pair annotation
1237 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1238 in zero scores for all base pairs in RNA Structure
1242 <!-- JAL-2174-->Extend selection with columns containing
1246 <!-- JAL-2275 -->Pfam format writer puts extra space at
1247 beginning of sequence
1250 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1254 <!-- JAL-2238 -->Cannot create groups on an alignment from
1255 from a tree when t-coffee scores are shown
1258 <!-- JAL-1836,1967 -->Cannot import and view PDB
1259 structures with chains containing negative resnums (4q4h)
1262 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1266 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1267 to Clustal, PIR and PileUp output
1270 <!-- JAL-2008 -->Reordering sequence features that are
1271 not visible causes alignment window to repaint
1274 <!-- JAL-2006 -->Threshold sliders don't work in
1275 graduated colour and colour by annotation row for e-value
1276 scores associated with features and annotation rows
1279 <!-- JAL-1797 -->amino acid physicochemical conservation
1280 calculation should be case independent
1283 <!-- JAL-2173 -->Remove annotation also updates hidden
1287 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1288 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1289 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1292 <!-- JAL-2065 -->Null pointer exceptions and redraw
1293 problems when reference sequence defined and 'show
1294 non-conserved' enabled
1297 <!-- JAL-1306 -->Quality and Conservation are now shown on
1298 load even when Consensus calculation is disabled
1301 <!-- JAL-1932 -->Remove right on penultimate column of
1302 alignment does nothing
1305 <em>Application</em>
1308 <!-- JAL-1552-->URLs and links can't be imported by
1309 drag'n'drop on OSX when launched via webstart (note - not
1310 yet fixed for El Capitan)
1313 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1314 output when running on non-gb/us i18n platforms
1317 <!-- JAL-1944 -->Error thrown when exporting a view with
1318 hidden sequences as flat-file alignment
1321 <!-- JAL-2030-->InstallAnywhere distribution fails when
1325 <!-- JAL-2080-->Jalview very slow to launch via webstart
1326 (also hotfix for 2.9.0b2)
1329 <!-- JAL-2085 -->Cannot save project when view has a
1330 reference sequence defined
1333 <!-- JAL-1011 -->Columns are suddenly selected in other
1334 alignments and views when revealing hidden columns
1337 <!-- JAL-1989 -->Hide columns not mirrored in complement
1338 view in a cDNA/Protein splitframe
1341 <!-- JAL-1369 -->Cannot save/restore representative
1342 sequence from project when only one sequence is
1346 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1347 in Structure Chooser
1350 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1351 structure consensus didn't refresh annotation panel
1354 <!-- JAL-1962 -->View mapping in structure view shows
1355 mappings between sequence and all chains in a PDB file
1358 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1359 dialogs format columns correctly, don't display array
1360 data, sort columns according to type
1363 <!-- JAL-1975 -->Export complete shown after destination
1364 file chooser is cancelled during an image export
1367 <!-- JAL-2025 -->Error when querying PDB Service with
1368 sequence name containing special characters
1371 <!-- JAL-2024 -->Manual PDB structure querying should be
1375 <!-- JAL-2104 -->Large tooltips with broken HTML
1376 formatting don't wrap
1379 <!-- JAL-1128 -->Figures exported from wrapped view are
1380 truncated so L looks like I in consensus annotation
1383 <!-- JAL-2003 -->Export features should only export the
1384 currently displayed features for the current selection or
1388 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1389 after fetching cross-references, and restoring from
1393 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1394 followed in the structure viewer
1397 <!-- JAL-2163 -->Titles for individual alignments in
1398 splitframe not restored from project
1401 <!-- JAL-2145 -->missing autocalculated annotation at
1402 trailing end of protein alignment in transcript/product
1403 splitview when pad-gaps not enabled by default
1406 <!-- JAL-1797 -->amino acid physicochemical conservation
1410 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1411 article has been read (reopened issue due to
1412 internationalisation problems)
1415 <!-- JAL-1960 -->Only offer PDB structures in structure
1416 viewer based on sequence name, PDB and UniProt
1421 <!-- JAL-1976 -->No progress bar shown during export of
1425 <!-- JAL-2213 -->Structures not always superimposed after
1426 multiple structures are shown for one or more sequences.
1429 <!-- JAL-1370 -->Reference sequence characters should not
1430 be replaced with '.' when 'Show unconserved' format option
1434 <!-- JAL-1823 -->Cannot specify chain code when entering
1435 specific PDB id for sequence
1438 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1439 'Export hidden sequences' is enabled, but 'export hidden
1440 columns' is disabled.
1443 <!--JAL-2026-->Best Quality option in structure chooser
1444 selects lowest rather than highest resolution structures
1448 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1449 to sequence mapping in 'View Mappings' report
1452 <!-- JAL-2284 -->Unable to read old Jalview projects that
1453 contain non-XML data added after Jalvew wrote project.
1456 <!-- JAL-2118 -->Newly created annotation row reorders
1457 after clicking on it to create new annotation for a
1460 <!-- may exclude, this is an external service stability issue JAL-1941
1461 -- > RNA 3D structure not added via DSSR service</li> -->
1466 <!-- JAL-2151 -->Incorrect columns are selected when
1467 hidden columns present before start of sequence
1470 <!-- JAL-1986 -->Missing dependencies on applet pages
1474 <!-- JAL-1947 -->Overview pixel size changes when
1475 sequences are hidden in applet
1478 <!-- JAL-1996 -->Updated instructions for applet
1479 deployment on examples pages.
1486 <td width="60" nowrap>
1487 <div align="center">
1488 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1489 <em>16/10/2015</em></strong>
1492 <td><em>General</em>
1494 <li>Time stamps for signed Jalview application and applet
1499 <em>Application</em>
1501 <li>Duplicate group consensus and conservation rows
1502 shown when tree is partitioned</li>
1503 <li>Erratic behaviour when tree partitions made with
1504 multiple cDNA/Protein split views</li>
1510 <td width="60" nowrap>
1511 <div align="center">
1512 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1513 <em>8/10/2015</em></strong>
1516 <td><em>General</em>
1518 <li>Updated Spanish translations of localized text for
1520 </ul> <em>Application</em>
1522 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1523 <li>Signed OSX InstallAnywhere installer<br></li>
1524 <li>Support for per-sequence based annotations in BioJSON</li>
1525 </ul> <em>Applet</em>
1527 <li>Split frame example added to applet examples page</li>
1528 </ul> <em>Build and Deployment</em>
1531 <!-- JAL-1888 -->New ant target for running Jalview's test
1539 <li>Mapping of cDNA to protein in split frames
1540 incorrect when sequence start > 1</li>
1541 <li>Broken images in filter column by annotation dialog
1543 <li>Feature colours not parsed from features file</li>
1544 <li>Exceptions and incomplete link URLs recovered when
1545 loading a features file containing HTML tags in feature
1549 <em>Application</em>
1551 <li>Annotations corrupted after BioJS export and
1553 <li>Incorrect sequence limits after Fetch DB References
1554 with 'trim retrieved sequences'</li>
1555 <li>Incorrect warning about deleting all data when
1556 deleting selected columns</li>
1557 <li>Patch to build system for shipping properly signed
1558 JNLP templates for webstart launch</li>
1559 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1560 unreleased structures for download or viewing</li>
1561 <li>Tab/space/return keystroke operation of EMBL-PDBe
1562 fetcher/viewer dialogs works correctly</li>
1563 <li>Disabled 'minimise' button on Jalview windows
1564 running on OSX to workaround redraw hang bug</li>
1565 <li>Split cDNA/Protein view position and geometry not
1566 recovered from jalview project</li>
1567 <li>Initial enabled/disabled state of annotation menu
1568 sorter 'show autocalculated first/last' corresponds to
1570 <li>Restoring of Clustal, RNA Helices and T-Coffee
1571 color schemes from BioJSON</li>
1575 <li>Reorder sequences mirrored in cDNA/Protein split
1577 <li>Applet with Jmol examples not loading correctly</li>
1583 <td><div align="center">
1584 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1586 <td><em>General</em>
1588 <li>Linked visualisation and analysis of DNA and Protein
1591 <li>Translated cDNA alignments shown as split protein
1592 and DNA alignment views</li>
1593 <li>Codon consensus annotation for linked protein and
1594 cDNA alignment views</li>
1595 <li>Link cDNA or Protein product sequences by loading
1596 them onto Protein or cDNA alignments</li>
1597 <li>Reconstruct linked cDNA alignment from aligned
1598 protein sequences</li>
1601 <li>Jmol integration updated to Jmol v14.2.14</li>
1602 <li>Import and export of Jalview alignment views as <a
1603 href="features/bioJsonFormat.html">BioJSON</a></li>
1604 <li>New alignment annotation file statements for
1605 reference sequences and marking hidden columns</li>
1606 <li>Reference sequence based alignment shading to
1607 highlight variation</li>
1608 <li>Select or hide columns according to alignment
1610 <li>Find option for locating sequences by description</li>
1611 <li>Conserved physicochemical properties shown in amino
1612 acid conservation row</li>
1613 <li>Alignments can be sorted by number of RNA helices</li>
1614 </ul> <em>Application</em>
1616 <li>New cDNA/Protein analysis capabilities
1618 <li>Get Cross-References should open a Split Frame
1619 view with cDNA/Protein</li>
1620 <li>Detect when nucleotide sequences and protein
1621 sequences are placed in the same alignment</li>
1622 <li>Split cDNA/Protein views are saved in Jalview
1627 <li>Use REST API to talk to Chimera</li>
1628 <li>Selected regions in Chimera are highlighted in linked
1629 Jalview windows</li>
1631 <li>VARNA RNA viewer updated to v3.93</li>
1632 <li>VARNA views are saved in Jalview Projects</li>
1633 <li>Pseudoknots displayed as Jalview RNA annotation can
1634 be shown in VARNA</li>
1636 <li>Make groups for selection uses marked columns as well
1637 as the active selected region</li>
1639 <li>Calculate UPGMA and NJ trees using sequence feature
1641 <li>New Export options
1643 <li>New Export Settings dialog to control hidden
1644 region export in flat file generation</li>
1646 <li>Export alignment views for display with the <a
1647 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1649 <li>Export scrollable SVG in HTML page</li>
1650 <li>Optional embedding of BioJSON data when exporting
1651 alignment figures to HTML</li>
1653 <li>3D structure retrieval and display
1655 <li>Free text and structured queries with the PDBe
1657 <li>PDBe Search API based discovery and selection of
1658 PDB structures for a sequence set</li>
1662 <li>JPred4 employed for protein secondary structure
1664 <li>Hide Insertions menu option to hide unaligned columns
1665 for one or a group of sequences</li>
1666 <li>Automatically hide insertions in alignments imported
1667 from the JPred4 web server</li>
1668 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1669 system on OSX<br />LGPL libraries courtesy of <a
1670 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1672 <li>changed 'View nucleotide structure' submenu to 'View
1673 VARNA 2D Structure'</li>
1674 <li>change "View protein structure" menu option to "3D
1677 </ul> <em>Applet</em>
1679 <li>New layout for applet example pages</li>
1680 <li>New parameters to enable SplitFrame view
1681 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1682 <li>New example demonstrating linked viewing of cDNA and
1683 Protein alignments</li>
1684 </ul> <em>Development and deployment</em>
1686 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1687 <li>Include installation type and git revision in build
1688 properties and console log output</li>
1689 <li>Jalview Github organisation, and new github site for
1690 storing BioJsMSA Templates</li>
1691 <li>Jalview's unit tests now managed with TestNG</li>
1694 <!-- <em>General</em>
1696 </ul> --> <!-- issues resolved --> <em>Application</em>
1698 <li>Escape should close any open find dialogs</li>
1699 <li>Typo in select-by-features status report</li>
1700 <li>Consensus RNA secondary secondary structure
1701 predictions are not highlighted in amber</li>
1702 <li>Missing gap character in v2.7 example file means
1703 alignment appears unaligned when pad-gaps is not enabled</li>
1704 <li>First switch to RNA Helices colouring doesn't colour
1705 associated structure views</li>
1706 <li>ID width preference option is greyed out when auto
1707 width checkbox not enabled</li>
1708 <li>Stopped a warning dialog from being shown when
1709 creating user defined colours</li>
1710 <li>'View Mapping' in structure viewer shows sequence
1711 mappings for just that viewer's sequences</li>
1712 <li>Workaround for superposing PDB files containing
1713 multiple models in Chimera</li>
1714 <li>Report sequence position in status bar when hovering
1715 over Jmol structure</li>
1716 <li>Cannot output gaps as '.' symbols with Selection ->
1717 output to text box</li>
1718 <li>Flat file exports of alignments with hidden columns
1719 have incorrect sequence start/end</li>
1720 <li>'Aligning' a second chain to a Chimera structure from
1722 <li>Colour schemes applied to structure viewers don't
1723 work for nucleotide</li>
1724 <li>Loading/cut'n'pasting an empty or invalid file leads
1725 to a grey/invisible alignment window</li>
1726 <li>Exported Jpred annotation from a sequence region
1727 imports to different position</li>
1728 <li>Space at beginning of sequence feature tooltips shown
1729 on some platforms</li>
1730 <li>Chimera viewer 'View | Show Chain' menu is not
1732 <li>'New View' fails with a Null Pointer Exception in
1733 console if Chimera has been opened</li>
1734 <li>Mouseover to Chimera not working</li>
1735 <li>Miscellaneous ENA XML feature qualifiers not
1737 <li>NPE in annotation renderer after 'Extract Scores'</li>
1738 <li>If two structures in one Chimera window, mouseover of
1739 either sequence shows on first structure</li>
1740 <li>'Show annotations' options should not make
1741 non-positional annotations visible</li>
1742 <li>Subsequence secondary structure annotation not shown
1743 in right place after 'view flanking regions'</li>
1744 <li>File Save As type unset when current file format is
1746 <li>Save as '.jar' option removed for saving Jalview
1748 <li>Colour by Sequence colouring in Chimera more
1750 <li>Cannot 'add reference annotation' for a sequence in
1751 several views on same alignment</li>
1752 <li>Cannot show linked products for EMBL / ENA records</li>
1753 <li>Jalview's tooltip wraps long texts containing no
1755 </ul> <em>Applet</em>
1757 <li>Jmol to JalviewLite mouseover/link not working</li>
1758 <li>JalviewLite can't import sequences with ID
1759 descriptions containing angle brackets</li>
1760 </ul> <em>General</em>
1762 <li>Cannot export and reimport RNA secondary structure
1763 via jalview annotation file</li>
1764 <li>Random helix colour palette for colour by annotation
1765 with RNA secondary structure</li>
1766 <li>Mouseover to cDNA from STOP residue in protein
1767 translation doesn't work.</li>
1768 <li>hints when using the select by annotation dialog box</li>
1769 <li>Jmol alignment incorrect if PDB file has alternate CA
1771 <li>FontChooser message dialog appears to hang after
1772 choosing 1pt font</li>
1773 <li>Peptide secondary structure incorrectly imported from
1774 annotation file when annotation display text includes 'e' or
1776 <li>Cannot set colour of new feature type whilst creating
1778 <li>cDNA translation alignment should not be sequence
1779 order dependent</li>
1780 <li>'Show unconserved' doesn't work for lower case
1782 <li>Nucleotide ambiguity codes involving R not recognised</li>
1783 </ul> <em>Deployment and Documentation</em>
1785 <li>Applet example pages appear different to the rest of
1786 www.jalview.org</li>
1787 </ul> <em>Application Known issues</em>
1789 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1790 <li>Misleading message appears after trying to delete
1792 <li>Jalview icon not shown in dock after InstallAnywhere
1793 version launches</li>
1794 <li>Fetching EMBL reference for an RNA sequence results
1795 fails with a sequence mismatch</li>
1796 <li>Corrupted or unreadable alignment display when
1797 scrolling alignment to right</li>
1798 <li>ArrayIndexOutOfBoundsException thrown when remove
1799 empty columns called on alignment with ragged gapped ends</li>
1800 <li>auto calculated alignment annotation rows do not get
1801 placed above or below non-autocalculated rows</li>
1802 <li>Jalview dekstop becomes sluggish at full screen in
1803 ultra-high resolution</li>
1804 <li>Cannot disable consensus calculation independently of
1805 quality and conservation</li>
1806 <li>Mouseover highlighting between cDNA and protein can
1807 become sluggish with more than one splitframe shown</li>
1808 </ul> <em>Applet Known Issues</em>
1810 <li>Core PDB parsing code requires Jmol</li>
1811 <li>Sequence canvas panel goes white when alignment
1812 window is being resized</li>
1818 <td><div align="center">
1819 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1821 <td><em>General</em>
1823 <li>Updated Java code signing certificate donated by
1825 <li>Features and annotation preserved when performing
1826 pairwise alignment</li>
1827 <li>RNA pseudoknot annotation can be
1828 imported/exported/displayed</li>
1829 <li>'colour by annotation' can colour by RNA and
1830 protein secondary structure</li>
1831 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1832 post-hoc with 2.9 release</em>)
1835 </ul> <em>Application</em>
1837 <li>Extract and display secondary structure for sequences
1838 with 3D structures</li>
1839 <li>Support for parsing RNAML</li>
1840 <li>Annotations menu for layout
1842 <li>sort sequence annotation rows by alignment</li>
1843 <li>place sequence annotation above/below alignment
1846 <li>Output in Stockholm format</li>
1847 <li>Internationalisation: improved Spanish (es)
1849 <li>Structure viewer preferences tab</li>
1850 <li>Disorder and Secondary Structure annotation tracks
1851 shared between alignments</li>
1852 <li>UCSF Chimera launch and linked highlighting from
1854 <li>Show/hide all sequence associated annotation rows for
1855 all or current selection</li>
1856 <li>disorder and secondary structure predictions
1857 available as dataset annotation</li>
1858 <li>Per-sequence rna helices colouring</li>
1861 <li>Sequence database accessions imported when fetching
1862 alignments from Rfam</li>
1863 <li>update VARNA version to 3.91</li>
1865 <li>New groovy scripts for exporting aligned positions,
1866 conservation values, and calculating sum of pairs scores.</li>
1867 <li>Command line argument to set default JABAWS server</li>
1868 <li>include installation type in build properties and
1869 console log output</li>
1870 <li>Updated Jalview project format to preserve dataset
1874 <!-- issues resolved --> <em>Application</em>
1876 <li>Distinguish alignment and sequence associated RNA
1877 structure in structure->view->VARNA</li>
1878 <li>Raise dialog box if user deletes all sequences in an
1880 <li>Pressing F1 results in documentation opening twice</li>
1881 <li>Sequence feature tooltip is wrapped</li>
1882 <li>Double click on sequence associated annotation
1883 selects only first column</li>
1884 <li>Redundancy removal doesn't result in unlinked
1885 leaves shown in tree</li>
1886 <li>Undos after several redundancy removals don't undo
1888 <li>Hide sequence doesn't hide associated annotation</li>
1889 <li>User defined colours dialog box too big to fit on
1890 screen and buttons not visible</li>
1891 <li>author list isn't updated if already written to
1892 Jalview properties</li>
1893 <li>Popup menu won't open after retrieving sequence
1895 <li>File open window for associate PDB doesn't open</li>
1896 <li>Left-then-right click on a sequence id opens a
1897 browser search window</li>
1898 <li>Cannot open sequence feature shading/sort popup menu
1899 in feature settings dialog</li>
1900 <li>better tooltip placement for some areas of Jalview
1902 <li>Allow addition of JABAWS Server which doesn't
1903 pass validation</li>
1904 <li>Web services parameters dialog box is too large to
1906 <li>Muscle nucleotide alignment preset obscured by
1908 <li>JABAWS preset submenus don't contain newly
1909 defined user preset</li>
1910 <li>MSA web services warns user if they were launched
1911 with invalid input</li>
1912 <li>Jalview cannot contact DAS Registy when running on
1915 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1916 'Superpose with' submenu not shown when new view
1920 </ul> <!-- <em>Applet</em>
1922 </ul> <em>General</em>
1924 </ul>--> <em>Deployment and Documentation</em>
1926 <li>2G and 1G options in launchApp have no effect on
1927 memory allocation</li>
1928 <li>launchApp service doesn't automatically open
1929 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1931 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1932 InstallAnywhere reports cannot find valid JVM when Java
1933 1.7_055 is available
1935 </ul> <em>Application Known issues</em>
1938 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1939 corrupted or unreadable alignment display when scrolling
1943 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1944 retrieval fails but progress bar continues for DAS retrieval
1945 with large number of ID
1948 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1949 flatfile output of visible region has incorrect sequence
1953 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1954 rna structure consensus doesn't update when secondary
1955 structure tracks are rearranged
1958 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1959 invalid rna structure positional highlighting does not
1960 highlight position of invalid base pairs
1963 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1964 out of memory errors are not raised when saving Jalview
1965 project from alignment window file menu
1968 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1969 Switching to RNA Helices colouring doesn't propagate to
1973 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1974 colour by RNA Helices not enabled when user created
1975 annotation added to alignment
1978 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1979 Jalview icon not shown on dock in Mountain Lion/Webstart
1981 </ul> <em>Applet Known Issues</em>
1984 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1985 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1988 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1989 Jalview and Jmol example not compatible with IE9
1992 <li>Sort by annotation score doesn't reverse order
1998 <td><div align="center">
1999 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2002 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2005 <li>Internationalisation of user interface (usually
2006 called i18n support) and translation for Spanish locale</li>
2007 <li>Define/Undefine group on current selection with
2008 Ctrl-G/Shift Ctrl-G</li>
2009 <li>Improved group creation/removal options in
2010 alignment/sequence Popup menu</li>
2011 <li>Sensible precision for symbol distribution
2012 percentages shown in logo tooltip.</li>
2013 <li>Annotation panel height set according to amount of
2014 annotation when alignment first opened</li>
2015 </ul> <em>Application</em>
2017 <li>Interactive consensus RNA secondary structure
2018 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2019 <li>Select columns containing particular features from
2020 Feature Settings dialog</li>
2021 <li>View all 'representative' PDB structures for selected
2023 <li>Update Jalview project format:
2025 <li>New file extension for Jalview projects '.jvp'</li>
2026 <li>Preserve sequence and annotation dataset (to
2027 store secondary structure annotation,etc)</li>
2028 <li>Per group and alignment annotation and RNA helix
2032 <li>New similarity measures for PCA and Tree calculation
2034 <li>Experimental support for retrieval and viewing of
2035 flanking regions for an alignment</li>
2039 <!-- issues resolved --> <em>Application</em>
2041 <li>logo keeps spinning and status remains at queued or
2042 running after job is cancelled</li>
2043 <li>cannot export features from alignments imported from
2044 Jalview/VAMSAS projects</li>
2045 <li>Buggy slider for web service parameters that take
2047 <li>Newly created RNA secondary structure line doesn't
2048 have 'display all symbols' flag set</li>
2049 <li>T-COFFEE alignment score shading scheme and other
2050 annotation shading not saved in Jalview project</li>
2051 <li>Local file cannot be loaded in freshly downloaded
2053 <li>Jalview icon not shown on dock in Mountain
2055 <li>Load file from desktop file browser fails</li>
2056 <li>Occasional NPE thrown when calculating large trees</li>
2057 <li>Cannot reorder or slide sequences after dragging an
2058 alignment onto desktop</li>
2059 <li>Colour by annotation dialog throws NPE after using
2060 'extract scores' function</li>
2061 <li>Loading/cut'n'pasting an empty file leads to a grey
2062 alignment window</li>
2063 <li>Disorder thresholds rendered incorrectly after
2064 performing IUPred disorder prediction</li>
2065 <li>Multiple group annotated consensus rows shown when
2066 changing 'normalise logo' display setting</li>
2067 <li>Find shows blank dialog after 'finished searching' if
2068 nothing matches query</li>
2069 <li>Null Pointer Exceptions raised when sorting by
2070 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2072 <li>Errors in Jmol console when structures in alignment
2073 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2075 <li>Not all working JABAWS services are shown in
2077 <li>JAVAWS version of Jalview fails to launch with
2078 'invalid literal/length code'</li>
2079 <li>Annotation/RNA Helix colourschemes cannot be applied
2080 to alignment with groups (actually fixed in 2.8.0b1)</li>
2081 <li>RNA Helices and T-Coffee Scores available as default
2084 </ul> <em>Applet</em>
2086 <li>Remove group option is shown even when selection is
2088 <li>Apply to all groups ticked but colourscheme changes
2089 don't affect groups</li>
2090 <li>Documented RNA Helices and T-Coffee Scores as valid
2091 colourscheme name</li>
2092 <li>Annotation labels drawn on sequence IDs when
2093 Annotation panel is not displayed</li>
2094 <li>Increased font size for dropdown menus on OSX and
2095 embedded windows</li>
2096 </ul> <em>Other</em>
2098 <li>Consensus sequence for alignments/groups with a
2099 single sequence were not calculated</li>
2100 <li>annotation files that contain only groups imported as
2101 annotation and junk sequences</li>
2102 <li>Fasta files with sequences containing '*' incorrectly
2103 recognised as PFAM or BLC</li>
2104 <li>conservation/PID slider apply all groups option
2105 doesn't affect background (2.8.0b1)
2107 <li>redundancy highlighting is erratic at 0% and 100%</li>
2108 <li>Remove gapped columns fails for sequences with ragged
2110 <li>AMSA annotation row with leading spaces is not
2111 registered correctly on import</li>
2112 <li>Jalview crashes when selecting PCA analysis for
2113 certain alignments</li>
2114 <li>Opening the colour by annotation dialog for an
2115 existing annotation based 'use original colours'
2116 colourscheme loses original colours setting</li>
2121 <td><div align="center">
2122 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2123 <em>30/1/2014</em></strong>
2127 <li>Trusted certificates for JalviewLite applet and
2128 Jalview Desktop application<br />Certificate was donated by
2129 <a href="https://www.certum.eu">Certum</a> to the Jalview
2130 open source project).
2132 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2133 <li>Output in Stockholm format</li>
2134 <li>Allow import of data from gzipped files</li>
2135 <li>Export/import group and sequence associated line
2136 graph thresholds</li>
2137 <li>Nucleotide substitution matrix that supports RNA and
2138 ambiguity codes</li>
2139 <li>Allow disorder predictions to be made on the current
2140 selection (or visible selection) in the same way that JPred
2142 <li>Groovy scripting for headless Jalview operation</li>
2143 </ul> <em>Other improvements</em>
2145 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2146 <li>COMBINE statement uses current SEQUENCE_REF and
2147 GROUP_REF scope to group annotation rows</li>
2148 <li>Support '' style escaping of quotes in Newick
2150 <li>Group options for JABAWS service by command line name</li>
2151 <li>Empty tooltip shown for JABA service options with a
2152 link but no description</li>
2153 <li>Select primary source when selecting authority in
2154 database fetcher GUI</li>
2155 <li>Add .mfa to FASTA file extensions recognised by
2157 <li>Annotation label tooltip text wrap</li>
2162 <li>Slow scrolling when lots of annotation rows are
2164 <li>Lots of NPE (and slowness) after creating RNA
2165 secondary structure annotation line</li>
2166 <li>Sequence database accessions not imported when
2167 fetching alignments from Rfam</li>
2168 <li>Incorrect SHMR submission for sequences with
2170 <li>View all structures does not always superpose
2172 <li>Option widgets in service parameters not updated to
2173 reflect user or preset settings</li>
2174 <li>Null pointer exceptions for some services without
2175 presets or adjustable parameters</li>
2176 <li>Discover PDB IDs entry in structure menu doesn't
2177 discover PDB xRefs</li>
2178 <li>Exception encountered while trying to retrieve
2179 features with DAS</li>
2180 <li>Lowest value in annotation row isn't coloured
2181 when colour by annotation (per sequence) is coloured</li>
2182 <li>Keyboard mode P jumps to start of gapped region when
2183 residue follows a gap</li>
2184 <li>Jalview appears to hang importing an alignment with
2185 Wrap as default or after enabling Wrap</li>
2186 <li>'Right click to add annotations' message
2187 shown in wrap mode when no annotations present</li>
2188 <li>Disorder predictions fail with NPE if no automatic
2189 annotation already exists on alignment</li>
2190 <li>oninit javascript function should be called after
2191 initialisation completes</li>
2192 <li>Remove redundancy after disorder prediction corrupts
2193 alignment window display</li>
2194 <li>Example annotation file in documentation is invalid</li>
2195 <li>Grouped line graph annotation rows are not exported
2196 to annotation file</li>
2197 <li>Multi-harmony analysis cannot be run when only two
2199 <li>Cannot create multiple groups of line graphs with
2200 several 'combine' statements in annotation file</li>
2201 <li>Pressing return several times causes Number Format
2202 exceptions in keyboard mode</li>
2203 <li>Multi-harmony (SHMMR) method doesn't submit
2204 correct partitions for input data</li>
2205 <li>Translation from DNA to Amino Acids fails</li>
2206 <li>Jalview fail to load newick tree with quoted label</li>
2207 <li>--headless flag isn't understood</li>
2208 <li>ClassCastException when generating EPS in headless
2210 <li>Adjusting sequence-associated shading threshold only
2211 changes one row's threshold</li>
2212 <li>Preferences and Feature settings panel panel
2213 doesn't open</li>
2214 <li>hide consensus histogram also hides conservation and
2215 quality histograms</li>
2220 <td><div align="center">
2221 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2223 <td><em>Application</em>
2225 <li>Support for JABAWS 2.0 Services (AACon alignment
2226 conservation, protein disorder and Clustal Omega)</li>
2227 <li>JABAWS server status indicator in Web Services
2229 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2230 in Jalview alignment window</li>
2231 <li>Updated Jalview build and deploy framework for OSX
2232 mountain lion, windows 7, and 8</li>
2233 <li>Nucleotide substitution matrix for PCA that supports
2234 RNA and ambiguity codes</li>
2236 <li>Improved sequence database retrieval GUI</li>
2237 <li>Support fetching and database reference look up
2238 against multiple DAS sources (Fetch all from in 'fetch db
2240 <li>Jalview project improvements
2242 <li>Store and retrieve the 'belowAlignment'
2243 flag for annotation</li>
2244 <li>calcId attribute to group annotation rows on the
2246 <li>Store AACon calculation settings for a view in
2247 Jalview project</li>
2251 <li>horizontal scrolling gesture support</li>
2252 <li>Visual progress indicator when PCA calculation is
2254 <li>Simpler JABA web services menus</li>
2255 <li>visual indication that web service results are still
2256 being retrieved from server</li>
2257 <li>Serialise the dialogs that are shown when Jalview
2258 starts up for first time</li>
2259 <li>Jalview user agent string for interacting with HTTP
2261 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2263 <li>Examples directory and Groovy library included in
2264 InstallAnywhere distribution</li>
2265 </ul> <em>Applet</em>
2267 <li>RNA alignment and secondary structure annotation
2268 visualization applet example</li>
2269 </ul> <em>General</em>
2271 <li>Normalise option for consensus sequence logo</li>
2272 <li>Reset button in PCA window to return dimensions to
2274 <li>Allow seqspace or Jalview variant of alignment PCA
2276 <li>PCA with either nucleic acid and protein substitution
2278 <li>Allow windows containing HTML reports to be exported
2280 <li>Interactive display and editing of RNA secondary
2281 structure contacts</li>
2282 <li>RNA Helix Alignment Colouring</li>
2283 <li>RNA base pair logo consensus</li>
2284 <li>Parse sequence associated secondary structure
2285 information in Stockholm files</li>
2286 <li>HTML Export database accessions and annotation
2287 information presented in tooltip for sequences</li>
2288 <li>Import secondary structure from LOCARNA clustalw
2289 style RNA alignment files</li>
2290 <li>import and visualise T-COFFEE quality scores for an
2292 <li>'colour by annotation' per sequence option to
2293 shade each sequence according to its associated alignment
2295 <li>New Jalview Logo</li>
2296 </ul> <em>Documentation and Development</em>
2298 <li>documentation for score matrices used in Jalview</li>
2299 <li>New Website!</li>
2301 <td><em>Application</em>
2303 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2304 wsdbfetch REST service</li>
2305 <li>Stop windows being moved outside desktop on OSX</li>
2306 <li>Filetype associations not installed for webstart
2308 <li>Jalview does not always retrieve progress of a JABAWS
2309 job execution in full once it is complete</li>
2310 <li>revise SHMR RSBS definition to ensure alignment is
2311 uploaded via ali_file parameter</li>
2312 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2313 <li>View all structures superposed fails with exception</li>
2314 <li>Jnet job queues forever if a very short sequence is
2315 submitted for prediction</li>
2316 <li>Cut and paste menu not opened when mouse clicked on
2318 <li>Putting fractional value into integer text box in
2319 alignment parameter dialog causes Jalview to hang</li>
2320 <li>Structure view highlighting doesn't work on
2322 <li>View all structures fails with exception shown in
2324 <li>Characters in filename associated with PDBEntry not
2325 escaped in a platform independent way</li>
2326 <li>Jalview desktop fails to launch with exception when
2328 <li>Tree calculation reports 'you must have 2 or more
2329 sequences selected' when selection is empty</li>
2330 <li>Jalview desktop fails to launch with jar signature
2331 failure when java web start temporary file caching is
2333 <li>DAS Sequence retrieval with range qualification
2334 results in sequence xref which includes range qualification</li>
2335 <li>Errors during processing of command line arguments
2336 cause progress bar (JAL-898) to be removed</li>
2337 <li>Replace comma for semi-colon option not disabled for
2338 DAS sources in sequence fetcher</li>
2339 <li>Cannot close news reader when JABAWS server warning
2340 dialog is shown</li>
2341 <li>Option widgets not updated to reflect user settings</li>
2342 <li>Edited sequence not submitted to web service</li>
2343 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2344 <li>InstallAnywhere installer doesn't unpack and run
2345 on OSX Mountain Lion</li>
2346 <li>Annotation panel not given a scroll bar when
2347 sequences with alignment annotation are pasted into the
2349 <li>Sequence associated annotation rows not associated
2350 when loaded from Jalview project</li>
2351 <li>Browser launch fails with NPE on java 1.7</li>
2352 <li>JABAWS alignment marked as finished when job was
2353 cancelled or job failed due to invalid input</li>
2354 <li>NPE with v2.7 example when clicking on Tree
2355 associated with all views</li>
2356 <li>Exceptions when copy/paste sequences with grouped
2357 annotation rows to new window</li>
2358 </ul> <em>Applet</em>
2360 <li>Sequence features are momentarily displayed before
2361 they are hidden using hidefeaturegroups applet parameter</li>
2362 <li>loading features via javascript API automatically
2363 enables feature display</li>
2364 <li>scrollToColumnIn javascript API method doesn't
2366 </ul> <em>General</em>
2368 <li>Redundancy removal fails for rna alignment</li>
2369 <li>PCA calculation fails when sequence has been selected
2370 and then deselected</li>
2371 <li>PCA window shows grey box when first opened on OSX</li>
2372 <li>Letters coloured pink in sequence logo when alignment
2373 coloured with clustalx</li>
2374 <li>Choosing fonts without letter symbols defined causes
2375 exceptions and redraw errors</li>
2376 <li>Initial PCA plot view is not same as manually
2377 reconfigured view</li>
2378 <li>Grouped annotation graph label has incorrect line
2380 <li>Grouped annotation graph label display is corrupted
2381 for lots of labels</li>
2386 <div align="center">
2387 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2390 <td><em>Application</em>
2392 <li>Jalview Desktop News Reader</li>
2393 <li>Tweaked default layout of web services menu</li>
2394 <li>View/alignment association menu to enable user to
2395 easily specify which alignment a multi-structure view takes
2396 its colours/correspondences from</li>
2397 <li>Allow properties file location to be specified as URL</li>
2398 <li>Extend Jalview project to preserve associations
2399 between many alignment views and a single Jmol display</li>
2400 <li>Store annotation row height in Jalview project file</li>
2401 <li>Annotation row column label formatting attributes
2402 stored in project file</li>
2403 <li>Annotation row order for auto-calculated annotation
2404 rows preserved in Jalview project file</li>
2405 <li>Visual progress indication when Jalview state is
2406 saved using Desktop window menu</li>
2407 <li>Visual indication that command line arguments are
2408 still being processed</li>
2409 <li>Groovy script execution from URL</li>
2410 <li>Colour by annotation default min and max colours in
2412 <li>Automatically associate PDB files dragged onto an
2413 alignment with sequences that have high similarity and
2415 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2416 <li>'view structures' option to open many
2417 structures in same window</li>
2418 <li>Sort associated views menu option for tree panel</li>
2419 <li>Group all JABA and non-JABA services for a particular
2420 analysis function in its own submenu</li>
2421 </ul> <em>Applet</em>
2423 <li>Userdefined and autogenerated annotation rows for
2425 <li>Adjustment of alignment annotation pane height</li>
2426 <li>Annotation scrollbar for annotation panel</li>
2427 <li>Drag to reorder annotation rows in annotation panel</li>
2428 <li>'automaticScrolling' parameter</li>
2429 <li>Allow sequences with partial ID string matches to be
2430 annotated from GFF/Jalview features files</li>
2431 <li>Sequence logo annotation row in applet</li>
2432 <li>Absolute paths relative to host server in applet
2433 parameters are treated as such</li>
2434 <li>New in the JalviewLite javascript API:
2436 <li>JalviewLite.js javascript library</li>
2437 <li>Javascript callbacks for
2439 <li>Applet initialisation</li>
2440 <li>Sequence/alignment mouse-overs and selections</li>
2443 <li>scrollTo row and column alignment scrolling
2445 <li>Select sequence/alignment regions from javascript</li>
2446 <li>javascript structure viewer harness to pass
2447 messages between Jmol and Jalview when running as
2448 distinct applets</li>
2449 <li>sortBy method</li>
2450 <li>Set of applet and application examples shipped
2451 with documentation</li>
2452 <li>New example to demonstrate JalviewLite and Jmol
2453 javascript message exchange</li>
2455 </ul> <em>General</em>
2457 <li>Enable Jmol displays to be associated with multiple
2458 multiple alignments</li>
2459 <li>Option to automatically sort alignment with new tree</li>
2460 <li>User configurable link to enable redirects to a
2461 www.Jalview.org mirror</li>
2462 <li>Jmol colours option for Jmol displays</li>
2463 <li>Configurable newline string when writing alignment
2464 and other flat files</li>
2465 <li>Allow alignment annotation description lines to
2466 contain html tags</li>
2467 </ul> <em>Documentation and Development</em>
2469 <li>Add groovy test harness for bulk load testing to
2471 <li>Groovy script to load and align a set of sequences
2472 using a web service before displaying the result in the
2473 Jalview desktop</li>
2474 <li>Restructured javascript and applet api documentation</li>
2475 <li>Ant target to publish example html files with applet
2477 <li>Netbeans project for building Jalview from source</li>
2478 <li>ant task to create online javadoc for Jalview source</li>
2480 <td><em>Application</em>
2482 <li>User defined colourscheme throws exception when
2483 current built in colourscheme is saved as new scheme</li>
2484 <li>AlignFrame->Save in application pops up save
2485 dialog for valid filename/format</li>
2486 <li>Cannot view associated structure for UniProt sequence</li>
2487 <li>PDB file association breaks for UniProt sequence
2489 <li>Associate PDB from file dialog does not tell you
2490 which sequence is to be associated with the file</li>
2491 <li>Find All raises null pointer exception when query
2492 only matches sequence IDs</li>
2493 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2494 <li>Jalview project with Jmol views created with Jalview
2495 2.4 cannot be loaded</li>
2496 <li>Filetype associations not installed for webstart
2498 <li>Two or more chains in a single PDB file associated
2499 with sequences in different alignments do not get coloured
2500 by their associated sequence</li>
2501 <li>Visibility status of autocalculated annotation row
2502 not preserved when project is loaded</li>
2503 <li>Annotation row height and visibility attributes not
2504 stored in Jalview project</li>
2505 <li>Tree bootstraps are not preserved when saved as a
2506 Jalview project</li>
2507 <li>Envision2 workflow tooltips are corrupted</li>
2508 <li>Enabling show group conservation also enables colour
2509 by conservation</li>
2510 <li>Duplicate group associated conservation or consensus
2511 created on new view</li>
2512 <li>Annotation scrollbar not displayed after 'show
2513 all hidden annotation rows' option selected</li>
2514 <li>Alignment quality not updated after alignment
2515 annotation row is hidden then shown</li>
2516 <li>Preserve colouring of structures coloured by
2517 sequences in pre Jalview 2.7 projects</li>
2518 <li>Web service job parameter dialog is not laid out
2520 <li>Web services menu not refreshed after 'reset
2521 services' button is pressed in preferences</li>
2522 <li>Annotation off by one in Jalview v2_3 example project</li>
2523 <li>Structures imported from file and saved in project
2524 get name like jalview_pdb1234.txt when reloaded</li>
2525 <li>Jalview does not always retrieve progress of a JABAWS
2526 job execution in full once it is complete</li>
2527 </ul> <em>Applet</em>
2529 <li>Alignment height set incorrectly when lots of
2530 annotation rows are displayed</li>
2531 <li>Relative URLs in feature HTML text not resolved to
2533 <li>View follows highlighting does not work for positions
2535 <li><= shown as = in tooltip</li>
2536 <li>Export features raises exception when no features
2538 <li>Separator string used for serialising lists of IDs
2539 for javascript api is modified when separator string
2540 provided as parameter</li>
2541 <li>Null pointer exception when selecting tree leaves for
2542 alignment with no existing selection</li>
2543 <li>Relative URLs for datasources assumed to be relative
2544 to applet's codebase</li>
2545 <li>Status bar not updated after finished searching and
2546 search wraps around to first result</li>
2547 <li>StructureSelectionManager instance shared between
2548 several Jalview applets causes race conditions and memory
2550 <li>Hover tooltip and mouseover of position on structure
2551 not sent from Jmol in applet</li>
2552 <li>Certain sequences of javascript method calls to
2553 applet API fatally hang browser</li>
2554 </ul> <em>General</em>
2556 <li>View follows structure mouseover scrolls beyond
2557 position with wrapped view and hidden regions</li>
2558 <li>Find sequence position moves to wrong residue
2559 with/without hidden columns</li>
2560 <li>Sequence length given in alignment properties window
2562 <li>InvalidNumberFormat exceptions thrown when trying to
2563 import PDB like structure files</li>
2564 <li>Positional search results are only highlighted
2565 between user-supplied sequence start/end bounds</li>
2566 <li>End attribute of sequence is not validated</li>
2567 <li>Find dialog only finds first sequence containing a
2568 given sequence position</li>
2569 <li>Sequence numbering not preserved in MSF alignment
2571 <li>Jalview PDB file reader does not extract sequence
2572 from nucleotide chains correctly</li>
2573 <li>Structure colours not updated when tree partition
2574 changed in alignment</li>
2575 <li>Sequence associated secondary structure not correctly
2576 parsed in interleaved stockholm</li>
2577 <li>Colour by annotation dialog does not restore current
2579 <li>Hiding (nearly) all sequences doesn't work
2581 <li>Sequences containing lowercase letters are not
2582 properly associated with their pdb files</li>
2583 </ul> <em>Documentation and Development</em>
2585 <li>schemas/JalviewWsParamSet.xsd corrupted by
2586 ApplyCopyright tool</li>
2591 <div align="center">
2592 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2595 <td><em>Application</em>
2597 <li>New warning dialog when the Jalview Desktop cannot
2598 contact web services</li>
2599 <li>JABA service parameters for a preset are shown in
2600 service job window</li>
2601 <li>JABA Service menu entries reworded</li>
2605 <li>Modeller PIR IO broken - cannot correctly import a
2606 pir file emitted by Jalview</li>
2607 <li>Existing feature settings transferred to new
2608 alignment view created from cut'n'paste</li>
2609 <li>Improved test for mixed amino/nucleotide chains when
2610 parsing PDB files</li>
2611 <li>Consensus and conservation annotation rows
2612 occasionally become blank for all new windows</li>
2613 <li>Exception raised when right clicking above sequences
2614 in wrapped view mode</li>
2615 </ul> <em>Application</em>
2617 <li>multiple multiply aligned structure views cause cpu
2618 usage to hit 100% and computer to hang</li>
2619 <li>Web Service parameter layout breaks for long user
2620 parameter names</li>
2621 <li>Jaba service discovery hangs desktop if Jaba server
2628 <div align="center">
2629 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2632 <td><em>Application</em>
2634 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2635 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2638 <li>Web Services preference tab</li>
2639 <li>Analysis parameters dialog box and user defined
2641 <li>Improved speed and layout of Envision2 service menu</li>
2642 <li>Superpose structures using associated sequence
2644 <li>Export coordinates and projection as CSV from PCA
2646 </ul> <em>Applet</em>
2648 <li>enable javascript: execution by the applet via the
2649 link out mechanism</li>
2650 </ul> <em>Other</em>
2652 <li>Updated the Jmol Jalview interface to work with Jmol
2654 <li>The Jalview Desktop and JalviewLite applet now
2655 require Java 1.5</li>
2656 <li>Allow Jalview feature colour specification for GFF
2657 sequence annotation files</li>
2658 <li>New 'colour by label' keword in Jalview feature file
2659 type colour specification</li>
2660 <li>New Jalview Desktop Groovy API method that allows a
2661 script to check if it being run in an interactive session or
2662 in a batch operation from the Jalview command line</li>
2666 <li>clustalx colourscheme colours Ds preferentially when
2667 both D+E are present in over 50% of the column</li>
2668 </ul> <em>Application</em>
2670 <li>typo in AlignmentFrame->View->Hide->all but
2671 selected Regions menu item</li>
2672 <li>sequence fetcher replaces ',' for ';' when the ',' is
2673 part of a valid accession ID</li>
2674 <li>fatal OOM if object retrieved by sequence fetcher
2675 runs out of memory</li>
2676 <li>unhandled Out of Memory Error when viewing pca
2677 analysis results</li>
2678 <li>InstallAnywhere builds fail to launch on OS X java
2679 10.5 update 4 (due to apple Java 1.6 update)</li>
2680 <li>Installanywhere Jalview silently fails to launch</li>
2681 </ul> <em>Applet</em>
2683 <li>Jalview.getFeatureGroups() raises an
2684 ArrayIndexOutOfBoundsException if no feature groups are
2691 <div align="center">
2692 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2698 <li>Alignment prettyprinter doesn't cope with long
2700 <li>clustalx colourscheme colours Ds preferentially when
2701 both D+E are present in over 50% of the column</li>
2702 <li>nucleic acid structures retrieved from PDB do not
2703 import correctly</li>
2704 <li>More columns get selected than were clicked on when a
2705 number of columns are hidden</li>
2706 <li>annotation label popup menu not providing correct
2707 add/hide/show options when rows are hidden or none are
2709 <li>Stockholm format shown in list of readable formats,
2710 and parser copes better with alignments from RFAM.</li>
2711 <li>CSV output of consensus only includes the percentage
2712 of all symbols if sequence logo display is enabled</li>
2714 </ul> <em>Applet</em>
2716 <li>annotation panel disappears when annotation is
2718 </ul> <em>Application</em>
2720 <li>Alignment view not redrawn properly when new
2721 alignment opened where annotation panel is visible but no
2722 annotations are present on alignment</li>
2723 <li>pasted region containing hidden columns is
2724 incorrectly displayed in new alignment window</li>
2725 <li>Jalview slow to complete operations when stdout is
2726 flooded (fix is to close the Jalview console)</li>
2727 <li>typo in AlignmentFrame->View->Hide->all but
2728 selected Rregions menu item.</li>
2729 <li>inconsistent group submenu and Format submenu entry
2730 'Un' or 'Non'conserved</li>
2731 <li>Sequence feature settings are being shared by
2732 multiple distinct alignments</li>
2733 <li>group annotation not recreated when tree partition is
2735 <li>double click on group annotation to select sequences
2736 does not propagate to associated trees</li>
2737 <li>Mac OSX specific issues:
2739 <li>exception raised when mouse clicked on desktop
2740 window background</li>
2741 <li>Desktop menu placed on menu bar and application
2742 name set correctly</li>
2743 <li>sequence feature settings not wide enough for the
2744 save feature colourscheme button</li>
2753 <div align="center">
2754 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2757 <td><em>New Capabilities</em>
2759 <li>URL links generated from description line for
2760 regular-expression based URL links (applet and application)
2762 <li>Non-positional feature URL links are shown in link
2764 <li>Linked viewing of nucleic acid sequences and
2766 <li>Automatic Scrolling option in View menu to display
2767 the currently highlighted region of an alignment.</li>
2768 <li>Order an alignment by sequence length, or using the
2769 average score or total feature count for each sequence.</li>
2770 <li>Shading features by score or associated description</li>
2771 <li>Subdivide alignment and groups based on identity of
2772 selected subsequence (Make Groups from Selection).</li>
2773 <li>New hide/show options including Shift+Control+H to
2774 hide everything but the currently selected region.</li>
2775 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2776 </ul> <em>Application</em>
2778 <li>Fetch DB References capabilities and UI expanded to
2779 support retrieval from DAS sequence sources</li>
2780 <li>Local DAS Sequence sources can be added via the
2781 command line or via the Add local source dialog box.</li>
2782 <li>DAS Dbref and DbxRef feature types are parsed as
2783 database references and protein_name is parsed as
2784 description line (BioSapiens terms).</li>
2785 <li>Enable or disable non-positional feature and database
2786 references in sequence ID tooltip from View menu in
2788 <!-- <li>New hidden columns and rows and representatives capabilities
2789 in annotations file (in progress - not yet fully implemented)</li> -->
2790 <li>Group-associated consensus, sequence logos and
2791 conservation plots</li>
2792 <li>Symbol distributions for each column can be exported
2793 and visualized as sequence logos</li>
2794 <li>Optionally scale multi-character column labels to fit
2795 within each column of annotation row<!-- todo for applet -->
2797 <li>Optional automatic sort of associated alignment view
2798 when a new tree is opened.</li>
2799 <li>Jalview Java Console</li>
2800 <li>Better placement of desktop window when moving
2801 between different screens.</li>
2802 <li>New preference items for sequence ID tooltip and
2803 consensus annotation</li>
2804 <li>Client to submit sequences and IDs to Envision2
2806 <li><em>Vamsas Capabilities</em>
2808 <li>Improved VAMSAS synchronization (Jalview archive
2809 used to preserve views, structures, and tree display
2811 <li>Import of vamsas documents from disk or URL via
2813 <li>Sharing of selected regions between views and
2814 with other VAMSAS applications (Experimental feature!)</li>
2815 <li>Updated API to VAMSAS version 0.2</li>
2817 </ul> <em>Applet</em>
2819 <li>Middle button resizes annotation row height</li>
2822 <li>sortByTree (true/false) - automatically sort the
2823 associated alignment view by the tree when a new tree is
2825 <li>showTreeBootstraps (true/false) - show or hide
2826 branch bootstraps (default is to show them if available)</li>
2827 <li>showTreeDistances (true/false) - show or hide
2828 branch lengths (default is to show them if available)</li>
2829 <li>showUnlinkedTreeNodes (true/false) - indicate if
2830 unassociated nodes should be highlighted in the tree
2832 <li>heightScale and widthScale (1.0 or more) -
2833 increase the height or width of a cell in the alignment
2834 grid relative to the current font size.</li>
2837 <li>Non-positional features displayed in sequence ID
2839 </ul> <em>Other</em>
2841 <li>Features format: graduated colour definitions and
2842 specification of feature scores</li>
2843 <li>Alignment Annotations format: new keywords for group
2844 associated annotation (GROUP_REF) and annotation row display
2845 properties (ROW_PROPERTIES)</li>
2846 <li>XML formats extended to support graduated feature
2847 colourschemes, group associated annotation, and profile
2848 visualization settings.</li></td>
2851 <li>Source field in GFF files parsed as feature source
2852 rather than description</li>
2853 <li>Non-positional features are now included in sequence
2854 feature and gff files (controlled via non-positional feature
2855 visibility in tooltip).</li>
2856 <li>URL links generated for all feature links (bugfix)</li>
2857 <li>Added URL embedding instructions to features file
2859 <li>Codons containing ambiguous nucleotides translated as
2860 'X' in peptide product</li>
2861 <li>Match case switch in find dialog box works for both
2862 sequence ID and sequence string and query strings do not
2863 have to be in upper case to match case-insensitively.</li>
2864 <li>AMSA files only contain first column of
2865 multi-character column annotation labels</li>
2866 <li>Jalview Annotation File generation/parsing consistent
2867 with documentation (e.g. Stockholm annotation can be
2868 exported and re-imported)</li>
2869 <li>PDB files without embedded PDB IDs given a friendly
2871 <li>Find incrementally searches ID string matches as well
2872 as subsequence matches, and correctly reports total number
2876 <li>Better handling of exceptions during sequence
2878 <li>Dasobert generated non-positional feature URL
2879 link text excludes the start_end suffix</li>
2880 <li>DAS feature and source retrieval buttons disabled
2881 when fetch or registry operations in progress.</li>
2882 <li>PDB files retrieved from URLs are cached properly</li>
2883 <li>Sequence description lines properly shared via
2885 <li>Sequence fetcher fetches multiple records for all
2887 <li>Ensured that command line das feature retrieval
2888 completes before alignment figures are generated.</li>
2889 <li>Reduced time taken when opening file browser for
2891 <li>isAligned check prior to calculating tree, PCA or
2892 submitting an MSA to JNet now excludes hidden sequences.</li>
2893 <li>User defined group colours properly recovered
2894 from Jalview projects.</li>
2903 <div align="center">
2904 <strong>2.4.0.b2</strong><br> 28/10/2009
2909 <li>Experimental support for google analytics usage
2911 <li>Jalview privacy settings (user preferences and docs).</li>
2916 <li>Race condition in applet preventing startup in
2918 <li>Exception when feature created from selection beyond
2919 length of sequence.</li>
2920 <li>Allow synthetic PDB files to be imported gracefully</li>
2921 <li>Sequence associated annotation rows associate with
2922 all sequences with a given id</li>
2923 <li>Find function matches case-insensitively for sequence
2924 ID string searches</li>
2925 <li>Non-standard characters do not cause pairwise
2926 alignment to fail with exception</li>
2927 </ul> <em>Application Issues</em>
2929 <li>Sequences are now validated against EMBL database</li>
2930 <li>Sequence fetcher fetches multiple records for all
2932 </ul> <em>InstallAnywhere Issues</em>
2934 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2935 issue with installAnywhere mechanism)</li>
2936 <li>Command line launching of JARs from InstallAnywhere
2937 version (java class versioning error fixed)</li>
2944 <div align="center">
2945 <strong>2.4</strong><br> 27/8/2008
2948 <td><em>User Interface</em>
2950 <li>Linked highlighting of codon and amino acid from
2951 translation and protein products</li>
2952 <li>Linked highlighting of structure associated with
2953 residue mapping to codon position</li>
2954 <li>Sequence Fetcher provides example accession numbers
2955 and 'clear' button</li>
2956 <li>MemoryMonitor added as an option under Desktop's
2958 <li>Extract score function to parse whitespace separated
2959 numeric data in description line</li>
2960 <li>Column labels in alignment annotation can be centred.</li>
2961 <li>Tooltip for sequence associated annotation give name
2963 </ul> <em>Web Services and URL fetching</em>
2965 <li>JPred3 web service</li>
2966 <li>Prototype sequence search client (no public services
2968 <li>Fetch either seed alignment or full alignment from
2970 <li>URL Links created for matching database cross
2971 references as well as sequence ID</li>
2972 <li>URL Links can be created using regular-expressions</li>
2973 </ul> <em>Sequence Database Connectivity</em>
2975 <li>Retrieval of cross-referenced sequences from other
2977 <li>Generalised database reference retrieval and
2978 validation to all fetchable databases</li>
2979 <li>Fetch sequences from DAS sources supporting the
2980 sequence command</li>
2981 </ul> <em>Import and Export</em>
2982 <li>export annotation rows as CSV for spreadsheet import</li>
2983 <li>Jalview projects record alignment dataset associations,
2984 EMBL products, and cDNA sequence mappings</li>
2985 <li>Sequence Group colour can be specified in Annotation
2987 <li>Ad-hoc colouring of group in Annotation File using RGB
2988 triplet as name of colourscheme</li>
2989 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2991 <li>treenode binding for VAMSAS tree exchange</li>
2992 <li>local editing and update of sequences in VAMSAS
2993 alignments (experimental)</li>
2994 <li>Create new or select existing session to join</li>
2995 <li>load and save of vamsas documents</li>
2996 </ul> <em>Application command line</em>
2998 <li>-tree parameter to open trees (introduced for passing
3000 <li>-fetchfrom command line argument to specify nicknames
3001 of DAS servers to query for alignment features</li>
3002 <li>-dasserver command line argument to add new servers
3003 that are also automatically queried for features</li>
3004 <li>-groovy command line argument executes a given groovy
3005 script after all input data has been loaded and parsed</li>
3006 </ul> <em>Applet-Application data exchange</em>
3008 <li>Trees passed as applet parameters can be passed to
3009 application (when using "View in full
3010 application")</li>
3011 </ul> <em>Applet Parameters</em>
3013 <li>feature group display control parameter</li>
3014 <li>debug parameter</li>
3015 <li>showbutton parameter</li>
3016 </ul> <em>Applet API methods</em>
3018 <li>newView public method</li>
3019 <li>Window (current view) specific get/set public methods</li>
3020 <li>Feature display control methods</li>
3021 <li>get list of currently selected sequences</li>
3022 </ul> <em>New Jalview distribution features</em>
3024 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3025 <li>RELEASE file gives build properties for the latest
3026 Jalview release.</li>
3027 <li>Java 1.1 Applet build made easier and donotobfuscate
3028 property controls execution of obfuscator</li>
3029 <li>Build target for generating source distribution</li>
3030 <li>Debug flag for javacc</li>
3031 <li>.jalview_properties file is documented (slightly) in
3032 jalview.bin.Cache</li>
3033 <li>Continuous Build Integration for stable and
3034 development version of Application, Applet and source
3039 <li>selected region output includes visible annotations
3040 (for certain formats)</li>
3041 <li>edit label/displaychar contains existing label/char
3043 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3044 <li>shorter peptide product names from EMBL records</li>
3045 <li>Newick string generator makes compact representations</li>
3046 <li>bootstrap values parsed correctly for tree files with
3048 <li>pathological filechooser bug avoided by not allowing
3049 filenames containing a ':'</li>
3050 <li>Fixed exception when parsing GFF files containing
3051 global sequence features</li>
3052 <li>Alignment datasets are finalized only when number of
3053 references from alignment sequences goes to zero</li>
3054 <li>Close of tree branch colour box without colour
3055 selection causes cascading exceptions</li>
3056 <li>occasional negative imgwidth exceptions</li>
3057 <li>better reporting of non-fatal warnings to user when
3058 file parsing fails.</li>
3059 <li>Save works when Jalview project is default format</li>
3060 <li>Save as dialog opened if current alignment format is
3061 not a valid output format</li>
3062 <li>UniProt canonical names introduced for both das and
3064 <li>Histidine should be midblue (not pink!) in Zappo</li>
3065 <li>error messages passed up and output when data read
3067 <li>edit undo recovers previous dataset sequence when
3068 sequence is edited</li>
3069 <li>allow PDB files without pdb ID HEADER lines (like
3070 those generated by MODELLER) to be read in properly</li>
3071 <li>allow reading of JPred concise files as a normal
3073 <li>Stockholm annotation parsing and alignment properties
3074 import fixed for PFAM records</li>
3075 <li>Structure view windows have correct name in Desktop
3077 <li>annotation consisting of sequence associated scores
3078 can be read and written correctly to annotation file</li>
3079 <li>Aligned cDNA translation to aligned peptide works
3081 <li>Fixed display of hidden sequence markers and
3082 non-italic font for representatives in Applet</li>
3083 <li>Applet Menus are always embedded in applet window on
3085 <li>Newly shown features appear at top of stack (in
3087 <li>Annotations added via parameter not drawn properly
3088 due to null pointer exceptions</li>
3089 <li>Secondary structure lines are drawn starting from
3090 first column of alignment</li>
3091 <li>UniProt XML import updated for new schema release in
3093 <li>Sequence feature to sequence ID match for Features
3094 file is case-insensitive</li>
3095 <li>Sequence features read from Features file appended to
3096 all sequences with matching IDs</li>
3097 <li>PDB structure coloured correctly for associated views
3098 containing a sub-sequence</li>
3099 <li>PDB files can be retrieved by applet from Jar files</li>
3100 <li>feature and annotation file applet parameters
3101 referring to different directories are retrieved correctly</li>
3102 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3103 <li>Fixed application hang whilst waiting for
3104 splash-screen version check to complete</li>
3105 <li>Applet properly URLencodes input parameter values
3106 when passing them to the launchApp service</li>
3107 <li>display name and local features preserved in results
3108 retrieved from web service</li>
3109 <li>Visual delay indication for sequence retrieval and
3110 sequence fetcher initialisation</li>
3111 <li>updated Application to use DAS 1.53e version of
3112 dasobert DAS client</li>
3113 <li>Re-instated Full AMSA support and .amsa file
3115 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3123 <div align="center">
3124 <strong>2.3</strong><br> 9/5/07
3129 <li>Jmol 11.0.2 integration</li>
3130 <li>PDB views stored in Jalview XML files</li>
3131 <li>Slide sequences</li>
3132 <li>Edit sequence in place</li>
3133 <li>EMBL CDS features</li>
3134 <li>DAS Feature mapping</li>
3135 <li>Feature ordering</li>
3136 <li>Alignment Properties</li>
3137 <li>Annotation Scores</li>
3138 <li>Sort by scores</li>
3139 <li>Feature/annotation editing in applet</li>
3144 <li>Headless state operation in 2.2.1</li>
3145 <li>Incorrect and unstable DNA pairwise alignment</li>
3146 <li>Cut and paste of sequences with annotation</li>
3147 <li>Feature group display state in XML</li>
3148 <li>Feature ordering in XML</li>
3149 <li>blc file iteration selection using filename # suffix</li>
3150 <li>Stockholm alignment properties</li>
3151 <li>Stockhom alignment secondary structure annotation</li>
3152 <li>2.2.1 applet had no feature transparency</li>
3153 <li>Number pad keys can be used in cursor mode</li>
3154 <li>Structure Viewer mirror image resolved</li>
3161 <div align="center">
3162 <strong>2.2.1</strong><br> 12/2/07
3167 <li>Non standard characters can be read and displayed
3168 <li>Annotations/Features can be imported/exported to the
3170 <li>Applet allows editing of sequence/annotation/group
3171 name & description
3172 <li>Preference setting to display sequence name in
3174 <li>Annotation file format extended to allow
3175 Sequence_groups to be defined
3176 <li>Default opening of alignment overview panel can be
3177 specified in preferences
3178 <li>PDB residue numbering annotation added to associated
3184 <li>Applet crash under certain Linux OS with Java 1.6
3186 <li>Annotation file export / import bugs fixed
3187 <li>PNG / EPS image output bugs fixed
3193 <div align="center">
3194 <strong>2.2</strong><br> 27/11/06
3199 <li>Multiple views on alignment
3200 <li>Sequence feature editing
3201 <li>"Reload" alignment
3202 <li>"Save" to current filename
3203 <li>Background dependent text colour
3204 <li>Right align sequence ids
3205 <li>User-defined lower case residue colours
3208 <li>Menu item accelerator keys
3209 <li>Control-V pastes to current alignment
3210 <li>Cancel button for DAS Feature Fetching
3211 <li>PCA and PDB Viewers zoom via mouse roller
3212 <li>User-defined sub-tree colours and sub-tree selection
3214 <li>'New Window' button on the 'Output to Text box'
3219 <li>New memory efficient Undo/Redo System
3220 <li>Optimised symbol lookups and conservation/consensus
3222 <li>Region Conservation/Consensus recalculated after
3224 <li>Fixed Remove Empty Columns Bug (empty columns at end
3226 <li>Slowed DAS Feature Fetching for increased robustness.
3228 <li>Made angle brackets in ASCII feature descriptions
3230 <li>Re-instated Zoom function for PCA
3231 <li>Sequence descriptions conserved in web service
3233 <li>UniProt ID discoverer uses any word separated by
3235 <li>WsDbFetch query/result association resolved
3236 <li>Tree leaf to sequence mapping improved
3237 <li>Smooth fonts switch moved to FontChooser dialog box.
3244 <div align="center">
3245 <strong>2.1.1</strong><br> 12/9/06
3250 <li>Copy consensus sequence to clipboard</li>
3255 <li>Image output - rightmost residues are rendered if
3256 sequence id panel has been resized</li>
3257 <li>Image output - all offscreen group boundaries are
3259 <li>Annotation files with sequence references - all
3260 elements in file are relative to sequence position</li>
3261 <li>Mac Applet users can use Alt key for group editing</li>
3267 <div align="center">
3268 <strong>2.1</strong><br> 22/8/06
3273 <li>MAFFT Multiple Alignment in default Web Service list</li>
3274 <li>DAS Feature fetching</li>
3275 <li>Hide sequences and columns</li>
3276 <li>Export Annotations and Features</li>
3277 <li>GFF file reading / writing</li>
3278 <li>Associate structures with sequences from local PDB
3280 <li>Add sequences to exisiting alignment</li>
3281 <li>Recently opened files / URL lists</li>
3282 <li>Applet can launch the full application</li>
3283 <li>Applet has transparency for features (Java 1.2
3285 <li>Applet has user defined colours parameter</li>
3286 <li>Applet can load sequences from parameter
3287 "sequence<em>x</em>"
3293 <li>Redundancy Panel reinstalled in the Applet</li>
3294 <li>Monospaced font - EPS / rescaling bug fixed</li>
3295 <li>Annotation files with sequence references bug fixed</li>
3301 <div align="center">
3302 <strong>2.08.1</strong><br> 2/5/06
3307 <li>Change case of selected region from Popup menu</li>
3308 <li>Choose to match case when searching</li>
3309 <li>Middle mouse button and mouse movement can compress /
3310 expand the visible width and height of the alignment</li>
3315 <li>Annotation Panel displays complete JNet results</li>
3321 <div align="center">
3322 <strong>2.08b</strong><br> 18/4/06
3328 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3329 <li>Righthand label on wrapped alignments shows correct
3336 <div align="center">
3337 <strong>2.08</strong><br> 10/4/06
3342 <li>Editing can be locked to the selection area</li>
3343 <li>Keyboard editing</li>
3344 <li>Create sequence features from searches</li>
3345 <li>Precalculated annotations can be loaded onto
3347 <li>Features file allows grouping of features</li>
3348 <li>Annotation Colouring scheme added</li>
3349 <li>Smooth fonts off by default - Faster rendering</li>
3350 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3355 <li>Drag & Drop fixed on Linux</li>
3356 <li>Jalview Archive file faster to load/save, sequence
3357 descriptions saved.</li>
3363 <div align="center">
3364 <strong>2.07</strong><br> 12/12/05
3369 <li>PDB Structure Viewer enhanced</li>
3370 <li>Sequence Feature retrieval and display enhanced</li>
3371 <li>Choose to output sequence start-end after sequence
3372 name for file output</li>
3373 <li>Sequence Fetcher WSDBFetch@EBI</li>
3374 <li>Applet can read feature files, PDB files and can be
3375 used for HTML form input</li>
3380 <li>HTML output writes groups and features</li>
3381 <li>Group editing is Control and mouse click</li>
3382 <li>File IO bugs</li>
3388 <div align="center">
3389 <strong>2.06</strong><br> 28/9/05
3394 <li>View annotations in wrapped mode</li>
3395 <li>More options for PCA viewer</li>
3400 <li>GUI bugs resolved</li>
3401 <li>Runs with -nodisplay from command line</li>
3407 <div align="center">
3408 <strong>2.05b</strong><br> 15/9/05
3413 <li>Choose EPS export as lineart or text</li>
3414 <li>Jar files are executable</li>
3415 <li>Can read in Uracil - maps to unknown residue</li>
3420 <li>Known OutOfMemory errors give warning message</li>
3421 <li>Overview window calculated more efficiently</li>
3422 <li>Several GUI bugs resolved</li>
3428 <div align="center">
3429 <strong>2.05</strong><br> 30/8/05
3434 <li>Edit and annotate in "Wrapped" view</li>
3439 <li>Several GUI bugs resolved</li>
3445 <div align="center">
3446 <strong>2.04</strong><br> 24/8/05
3451 <li>Hold down mouse wheel & scroll to change font
3457 <li>Improved JPred client reliability</li>
3458 <li>Improved loading of Jalview files</li>
3464 <div align="center">
3465 <strong>2.03</strong><br> 18/8/05
3470 <li>Set Proxy server name and port in preferences</li>
3471 <li>Multiple URL links from sequence ids</li>
3472 <li>User Defined Colours can have a scheme name and added
3474 <li>Choose to ignore gaps in consensus calculation</li>
3475 <li>Unix users can set default web browser</li>
3476 <li>Runs without GUI for batch processing</li>
3477 <li>Dynamically generated Web Service Menus</li>
3482 <li>InstallAnywhere download for Sparc Solaris</li>
3488 <div align="center">
3489 <strong>2.02</strong><br> 18/7/05
3495 <li>Copy & Paste order of sequences maintains
3496 alignment order.</li>
3502 <div align="center">
3503 <strong>2.01</strong><br> 12/7/05
3508 <li>Use delete key for deleting selection.</li>
3509 <li>Use Mouse wheel to scroll sequences.</li>
3510 <li>Help file updated to describe how to add alignment
3512 <li>Version and build date written to build properties
3514 <li>InstallAnywhere installation will check for updates
3515 at launch of Jalview.</li>
3520 <li>Delete gaps bug fixed.</li>
3521 <li>FileChooser sorts columns.</li>
3522 <li>Can remove groups one by one.</li>
3523 <li>Filechooser icons installed.</li>
3524 <li>Finder ignores return character when searching.
3525 Return key will initiate a search.<br>
3532 <div align="center">
3533 <strong>2.0</strong><br> 20/6/05
3538 <li>New codebase</li>