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-2777 -->Structure views don't get updated unless
90 their colours have changed
94 <td><div align="left">
97 <li><!-- JAL-2728 -->Protein annotation panel too high in CDS/Protein view
99 <li><!-- JAL-2757 -->Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs
105 <td width="60" nowrap>
107 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
108 <em>2/10/2017</em></strong>
111 <td><div align="left">
112 <em>New features in Jalview Desktop</em>
115 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
117 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
121 <td><div align="left">
125 <td width="60" nowrap>
127 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
128 <em>7/9/2017</em></strong>
131 <td><div align="left">
135 <!-- JAL-2588 -->Show gaps in overview window by colouring
136 in grey (sequences used to be coloured grey, and gaps were
140 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
144 <!-- JAL-2587 -->Overview updates immediately on increase
145 in size and progress bar shown as higher resolution
146 overview is recalculated
151 <td><div align="left">
155 <!-- JAL-2664 -->Overview window redraws every hidden
156 column region row by row
159 <!-- JAL-2681 -->duplicate protein sequences shown after
160 retrieving Ensembl crossrefs for sequences from Uniprot
163 <!-- JAL-2603 -->Overview window throws NPE if show boxes
164 format setting is unticked
167 <!-- JAL-2610 -->Groups are coloured wrongly in overview
168 if group has show boxes format setting unticked
171 <!-- JAL-2672,JAL-2665 -->Redraw problems when
172 autoscrolling whilst dragging current selection group to
173 include sequences and columns not currently displayed
176 <!-- JAL-2691 -->Not all chains are mapped when multimeric
177 assemblies are imported via CIF file
180 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
181 displayed when threshold or conservation colouring is also
185 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
189 <!-- JAL-2673 -->Jalview continues to scroll after
190 dragging a selected region off the visible region of the
194 <!-- JAL-2724 -->Cannot apply annotation based
195 colourscheme to all groups in a view
198 <!-- JAL-2511 -->IDs don't line up with sequences
199 initially after font size change using the Font chooser or
206 <td width="60" nowrap>
208 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
211 <td><div align="left">
212 <em>Calculations</em>
216 <!-- JAL-1933 -->Occupancy annotation row shows number of
217 ungapped positions in each column of the alignment.
220 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
221 a calculation dialog box
224 <!-- JAL-2379 -->Revised implementation of PCA for speed
225 and memory efficiency (~30x faster)
228 <!-- JAL-2403 -->Revised implementation of sequence
229 similarity scores as used by Tree, PCA, Shading Consensus
230 and other calculations
233 <!-- JAL-2416 -->Score matrices are stored as resource
234 files within the Jalview codebase
237 <!-- JAL-2500 -->Trees computed on Sequence Feature
238 Similarity may have different topology due to increased
245 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
246 model for alignments and groups
249 <!-- JAL-384 -->Custom shading schemes created via groovy
256 <!-- JAL-2526 -->Efficiency improvements for interacting
257 with alignment and overview windows
260 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
264 <!-- JAL-2388 -->Hidden columns and sequences can be
268 <!-- JAL-2611 -->Click-drag in visible area allows fine
269 adjustment of visible position
273 <em>Data import/export</em>
276 <!-- JAL-2535 -->Posterior probability annotation from
277 Stockholm files imported as sequence associated annotation
280 <!-- JAL-2507 -->More robust per-sequence positional
281 annotation input/output via stockholm flatfile
284 <!-- JAL-2533 -->Sequence names don't include file
285 extension when importing structure files without embedded
286 names or PDB accessions
289 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
290 format sequence substitution matrices
293 <em>User Interface</em>
296 <!-- JAL-2447 --> Experimental Features Checkbox in
297 Desktop's Tools menu to hide or show untested features in
301 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
302 via Overview or sequence motif search operations
305 <!-- JAL-2547 -->Amend sequence features dialog box can be
306 opened by double clicking gaps within sequence feature
310 <!-- JAL-1476 -->Status bar message shown when not enough
311 aligned positions were available to create a 3D structure
315 <em>3D Structure</em>
318 <!-- JAL-2430 -->Hidden regions in alignment views are not
319 coloured in linked structure views
322 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
323 file-based command exchange
326 <!-- JAL-2375 -->Structure chooser automatically shows
327 Cached Structures rather than querying the PDBe if
328 structures are already available for sequences
331 <!-- JAL-2520 -->Structures imported via URL are cached in
332 the Jalview project rather than downloaded again when the
336 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
337 to transfer Chimera's structure attributes as Jalview
338 features, and vice-versa (<strong>Experimental
342 <em>Web Services</em>
345 <!-- JAL-2549 -->Updated JABAWS client to v2.2
348 <!-- JAL-2335 -->Filter non-standard amino acids and
349 nucleotides when submitting to AACon and other MSA
353 <!-- JAL-2316, -->URLs for viewing database
354 cross-references provided by identifiers.org and the
362 <!-- JAL-2344 -->FileFormatI interface for describing and
363 identifying file formats (instead of String constants)
366 <!-- JAL-2228 -->FeatureCounter script refactored for
367 efficiency when counting all displayed features (not
368 backwards compatible with 2.10.1)
371 <em>Example files</em>
374 <!-- JAL-2631 -->Graduated feature colour style example
375 included in the example feature file
378 <em>Documentation</em>
381 <!-- JAL-2339 -->Release notes reformatted for readability
382 with the built-in Java help viewer
385 <!-- JAL-1644 -->Find documentation updated with 'search
386 sequence description' option
392 <!-- JAL-2485, -->External service integration tests for
393 Uniprot REST Free Text Search Client
396 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
399 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
404 <td><div align="left">
405 <em>Calculations</em>
408 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
409 matrix - C->R should be '-3'<br />Old matrix restored
410 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
412 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
413 Jalview's treatment of gaps in PCA and substitution matrix
414 based Tree calculations.<br /> <br />In earlier versions
415 of Jalview, gaps matching gaps were penalised, and gaps
416 matching non-gaps penalised even more. In the PCA
417 calculation, gaps were actually treated as non-gaps - so
418 different costs were applied, which meant Jalview's PCAs
419 were different to those produced by SeqSpace.<br />Jalview
420 now treats gaps in the same way as SeqSpace (ie it scores
421 them as 0). <br /> <br />Enter the following in the
422 Groovy console to restore pre-2.10.2 behaviour:<br />
423 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
424 // for 2.10.1 mode <br />
425 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
426 // to restore 2.10.2 mode <br /> <br /> <em>Note:
427 these settings will affect all subsequent tree and PCA
428 calculations (not recommended)</em></li>
430 <!-- JAL-2424 -->Fixed off-by-one bug that affected
431 scaling of branch lengths for trees computed using
432 Sequence Feature Similarity.
435 <!-- JAL-2377 -->PCA calculation could hang when
436 generating output report when working with highly
440 <!-- JAL-2544 --> Sort by features includes features to
441 right of selected region when gaps present on right-hand
445 <em>User Interface</em>
448 <!-- JAL-2346 -->Reopening Colour by annotation dialog
449 doesn't reselect a specific sequence's associated
450 annotation after it was used for colouring a view
453 <!-- JAL-2419 -->Current selection lost if popup menu
454 opened on a region of alignment without groups
457 <!-- JAL-2374 -->Popup menu not always shown for regions
458 of an alignment with overlapping groups
461 <!-- JAL-2310 -->Finder double counts if both a sequence's
462 name and description match
465 <!-- JAL-2370 -->Hiding column selection containing two
466 hidden regions results in incorrect hidden regions
469 <!-- JAL-2386 -->'Apply to all groups' setting when
470 changing colour does not apply Conservation slider value
474 <!-- JAL-2373 -->Percentage identity and conservation menu
475 items do not show a tick or allow shading to be disabled
478 <!-- JAL-2385 -->Conservation shading or PID threshold
479 lost when base colourscheme changed if slider not visible
482 <!-- JAL-2547 -->Sequence features shown in tooltip for
483 gaps before start of features
486 <!-- JAL-2623 -->Graduated feature colour threshold not
487 restored to UI when feature colour is edited
490 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
491 a time when scrolling vertically in wrapped mode.
494 <!-- JAL-2630 -->Structure and alignment overview update
495 as graduate feature colour settings are modified via the
499 <!-- JAL-2034 -->Overview window doesn't always update
500 when a group defined on the alignment is resized
503 <!-- JAL-2605 -->Mouseovers on left/right scale region in
504 wrapped view result in positional status updates
508 <!-- JAL-2563 -->Status bar doesn't show position for
509 ambiguous amino acid and nucleotide symbols
512 <!-- JAL-2602 -->Copy consensus sequence failed if
513 alignment included gapped columns
516 <!-- JAL-2473 -->Minimum size set for Jalview windows so
517 widgets don't permanently disappear
520 <!-- JAL-2503 -->Cannot select or filter quantitative
521 annotation that are shown only as column labels (e.g.
522 T-Coffee column reliability scores)
525 <!-- JAL-2594 -->Exception thrown if trying to create a
526 sequence feature on gaps only
529 <!-- JAL-2504 -->Features created with 'New feature'
530 button from a Find inherit previously defined feature type
531 rather than the Find query string
534 <!-- JAL-2423 -->incorrect title in output window when
535 exporting tree calculated in Jalview
538 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
539 and then revealing them reorders sequences on the
543 <!-- JAL-964 -->Group panel in sequence feature settings
544 doesn't update to reflect available set of groups after
545 interactively adding or modifying features
548 <!-- JAL-2225 -->Sequence Database chooser unusable on
552 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
553 only excluded gaps in current sequence and ignored
560 <!-- JAL-2421 -->Overview window visible region moves
561 erratically when hidden rows or columns are present
564 <!-- JAL-2362 -->Per-residue colourschemes applied via the
565 Structure Viewer's colour menu don't correspond to
569 <!-- JAL-2405 -->Protein specific colours only offered in
570 colour and group colour menu for protein alignments
573 <!-- JAL-2385 -->Colour threshold slider doesn't update to
574 reflect currently selected view or group's shading
578 <!-- JAL-2624 -->Feature colour thresholds not respected
579 when rendered on overview and structures when opacity at
583 <!-- JAL-2589 -->User defined gap colour not shown in
584 overview when features overlaid on alignment
587 <em>Data import/export</em>
590 <!-- JAL-2576 -->Very large alignments take a long time to
594 <!-- JAL-2507 -->Per-sequence RNA secondary structures
595 added after a sequence was imported are not written to
599 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
600 when importing RNA secondary structure via Stockholm
603 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
604 not shown in correct direction for simple pseudoknots
607 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
608 with lightGray or darkGray via features file (but can
612 <!-- JAL-2383 -->Above PID colour threshold not recovered
613 when alignment view imported from project
616 <!-- JAL-2520,JAL-2465 -->No mappings generated between
617 structure and sequences extracted from structure files
618 imported via URL and viewed in Jmol
621 <!-- JAL-2520 -->Structures loaded via URL are saved in
622 Jalview Projects rather than fetched via URL again when
623 the project is loaded and the structure viewed
626 <em>Web Services</em>
629 <!-- JAL-2519 -->EnsemblGenomes example failing after
630 release of Ensembl v.88
633 <!-- JAL-2366 -->Proxy server address and port always
634 appear enabled in Preferences->Connections
637 <!-- JAL-2461 -->DAS registry not found exceptions
638 removed from console output
641 <!-- JAL-2582 -->Cannot retrieve protein products from
642 Ensembl by Peptide ID
645 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
646 created from SIFTs, and spurious 'Couldn't open structure
647 in Chimera' errors raised after April 2017 update (problem
648 due to 'null' string rather than empty string used for
649 residues with no corresponding PDB mapping).
652 <em>Application UI</em>
655 <!-- JAL-2361 -->User Defined Colours not added to Colour
659 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
660 case' residues (button in colourscheme editor debugged and
661 new documentation and tooltips added)
664 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
665 doesn't restore group-specific text colour thresholds
668 <!-- JAL-2243 -->Feature settings panel does not update as
669 new features are added to alignment
672 <!-- JAL-2532 -->Cancel in feature settings reverts
673 changes to feature colours via the Amend features dialog
676 <!-- JAL-2506 -->Null pointer exception when attempting to
677 edit graduated feature colour via amend features dialog
681 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
682 selection menu changes colours of alignment views
685 <!-- JAL-2426 -->Spurious exceptions in console raised
686 from alignment calculation workers after alignment has
690 <!-- JAL-1608 -->Typo in selection popup menu - Create
691 groups now 'Create Group'
694 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
695 Create/Undefine group doesn't always work
698 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
699 shown again after pressing 'Cancel'
702 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
703 adjusts start position in wrap mode
706 <!-- JAL-2563 -->Status bar doesn't show positions for
707 ambiguous amino acids
710 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
711 CDS/Protein view after CDS sequences added for aligned
715 <!-- JAL-2592 -->User defined colourschemes called 'User
716 Defined' don't appear in Colours menu
722 <!-- JAL-2468 -->Switching between Nucleotide and Protein
723 score models doesn't always result in an updated PCA plot
726 <!-- JAL-2442 -->Features not rendered as transparent on
727 overview or linked structure view
730 <!-- JAL-2372 -->Colour group by conservation doesn't
734 <!-- JAL-2517 -->Hitting Cancel after applying
735 user-defined colourscheme doesn't restore original
742 <!-- JAL-2314 -->Unit test failure:
743 jalview.ws.jabaws.RNAStructExportImport setup fails
746 <!-- JAL-2307 -->Unit test failure:
747 jalview.ws.sifts.SiftsClientTest due to compatibility
748 problems with deep array comparison equality asserts in
749 successive versions of TestNG
752 <!-- JAL-2479 -->Relocated StructureChooserTest and
753 ParameterUtilsTest Unit tests to Network suite
756 <em>New Known Issues</em>
759 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
760 phase after a sequence motif find operation
763 <!-- JAL-2550 -->Importing annotation file with rows
764 containing just upper and lower case letters are
765 interpreted as WUSS RNA secondary structure symbols
768 <!-- JAL-2590 -->Cannot load and display Newick trees
769 reliably from eggnog Ortholog database
772 <!-- JAL-2468 -->Status bar shows 'Marked x columns
773 containing features of type Highlight' when 'B' is pressed
774 to mark columns containing highlighted regions.
777 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
778 doesn't always add secondary structure annotation.
783 <td width="60" nowrap>
785 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
788 <td><div align="left">
792 <!-- JAL-98 -->Improved memory usage: sparse arrays used
793 for all consensus calculations
796 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
799 <li>Updated Jalview's Certum code signing certificate
805 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
806 set of database cross-references, sorted alphabetically
809 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
810 from database cross references. Users with custom links
811 will receive a <a href="webServices/urllinks.html#warning">warning
812 dialog</a> asking them to update their preferences.
815 <!-- JAL-2287-->Cancel button and escape listener on
816 dialog warning user about disconnecting Jalview from a
820 <!-- JAL-2320-->Jalview's Chimera control window closes if
821 the Chimera it is connected to is shut down
824 <!-- JAL-1738-->New keystroke (B) and Select highlighted
825 columns menu item to mark columns containing highlighted
826 regions (e.g. from structure selections or results of a
830 <!-- JAL-2284-->Command line option for batch-generation
831 of HTML pages rendering alignment data with the BioJS
841 <!-- JAL-2286 -->Columns with more than one modal residue
842 are not coloured or thresholded according to percent
843 identity (first observed in Jalview 2.8.2)
846 <!-- JAL-2301 -->Threonine incorrectly reported as not
850 <!-- JAL-2318 -->Updates to documentation pages (above PID
851 threshold, amino acid properties)
854 <!-- JAL-2292 -->Lower case residues in sequences are not
855 reported as mapped to residues in a structure file in the
859 <!--JAL-2324 -->Identical features with non-numeric scores
860 could be added multiple times to a sequence
863 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
864 bond features shown as two highlighted residues rather
865 than a range in linked structure views, and treated
866 correctly when selecting and computing trees from features
869 <!-- JAL-2281-->Custom URL links for database
870 cross-references are matched to database name regardless
878 <!-- JAL-2282-->Custom URL links for specific database
879 names without regular expressions also offer links from
883 <!-- JAL-2315-->Removing a single configured link in the
884 URL links pane in Connections preferences doesn't actually
885 update Jalview configuration
888 <!-- JAL-2272-->CTRL-Click on a selected region to open
889 the alignment area popup menu doesn't work on El-Capitan
892 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
893 files with similarly named sequences if dropped onto the
897 <!-- JAL-2312 -->Additional mappings are shown for PDB
898 entries where more chains exist in the PDB accession than
899 are reported in the SIFTS file
902 <!-- JAL-2317-->Certain structures do not get mapped to
903 the structure view when displayed with Chimera
906 <!-- JAL-2317-->No chains shown in the Chimera view
907 panel's View->Show Chains submenu
910 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
911 work for wrapped alignment views
914 <!--JAL-2197 -->Rename UI components for running JPred
915 predictions from 'JNet' to 'JPred'
918 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
919 corrupted when annotation panel vertical scroll is not at
923 <!--JAL-2332 -->Attempting to view structure for Hen
924 lysozyme results in a PDB Client error dialog box
927 <!-- JAL-2319 -->Structure View's mapping report switched
928 ranges for PDB and sequence for SIFTS
931 SIFTS 'Not_Observed' residues mapped to non-existant
935 <!-- <em>New Known Issues</em>
942 <td width="60" nowrap>
944 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
945 <em>25/10/2016</em></strong>
948 <td><em>Application</em>
950 <li>3D Structure chooser opens with 'Cached structures'
951 view if structures already loaded</li>
952 <li>Progress bar reports models as they are loaded to
959 <li>Colour by conservation always enabled and no tick
960 shown in menu when BLOSUM or PID shading applied</li>
961 <li>FER1_ARATH and FER2_ARATH labels were switched in
962 example sequences/projects/trees</li>
966 <li>Jalview projects with views of local PDB structure
967 files saved on Windows cannot be opened on OSX</li>
968 <li>Multiple structure views can be opened and superposed
969 without timeout for structures with multiple models or
970 multiple sequences in alignment</li>
971 <li>Cannot import or associated local PDB files without a
972 PDB ID HEADER line</li>
973 <li>RMSD is not output in Jmol console when superposition
975 <li>Drag and drop of URL from Browser fails for Linux and
976 OSX versions earlier than El Capitan</li>
977 <li>ENA client ignores invalid content from ENA server</li>
978 <li>Exceptions are not raised in console when ENA client
979 attempts to fetch non-existent IDs via Fetch DB Refs UI
981 <li>Exceptions are not raised in console when a new view
982 is created on the alignment</li>
983 <li>OSX right-click fixed for group selections: CMD-click
984 to insert/remove gaps in groups and CTRL-click to open group
987 <em>Build and deployment</em>
989 <li>URL link checker now copes with multi-line anchor
992 <em>New Known Issues</em>
994 <li>Drag and drop from URL links in browsers do not work
1001 <td width="60" nowrap>
1002 <div align="center">
1003 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1006 <td><em>General</em>
1009 <!-- JAL-2124 -->Updated Spanish translations.
1012 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1013 for importing structure data to Jalview. Enables mmCIF and
1017 <!-- JAL-192 --->Alignment ruler shows positions relative to
1021 <!-- JAL-2202 -->Position/residue shown in status bar when
1022 mousing over sequence associated annotation
1025 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1029 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1030 '()', canonical '[]' and invalid '{}' base pair populations
1034 <!-- JAL-2092 -->Feature settings popup menu options for
1035 showing or hiding columns containing a feature
1038 <!-- JAL-1557 -->Edit selected group by double clicking on
1039 group and sequence associated annotation labels
1042 <!-- JAL-2236 -->Sequence name added to annotation label in
1043 select/hide columns by annotation and colour by annotation
1047 </ul> <em>Application</em>
1050 <!-- JAL-2050-->Automatically hide introns when opening a
1051 gene/transcript view
1054 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1058 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1059 structure mappings with the EMBL-EBI PDBe SIFTS database
1062 <!-- JAL-2079 -->Updated download sites used for Rfam and
1063 Pfam sources to xfam.org
1066 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1069 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1070 over sequences in Jalview
1073 <!-- JAL-2027-->Support for reverse-complement coding
1074 regions in ENA and EMBL
1077 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1078 for record retrieval via ENA rest API
1081 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1085 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1086 groovy script execution
1089 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1090 alignment window's Calculate menu
1093 <!-- JAL-1812 -->Allow groovy scripts that call
1094 Jalview.getAlignFrames() to run in headless mode
1097 <!-- JAL-2068 -->Support for creating new alignment
1098 calculation workers from groovy scripts
1101 <!-- JAL-1369 --->Store/restore reference sequence in
1105 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1106 associations are now saved/restored from project
1109 <!-- JAL-1993 -->Database selection dialog always shown
1110 before sequence fetcher is opened
1113 <!-- JAL-2183 -->Double click on an entry in Jalview's
1114 database chooser opens a sequence fetcher
1117 <!-- JAL-1563 -->Free-text search client for UniProt using
1118 the UniProt REST API
1121 <!-- JAL-2168 -->-nonews command line parameter to prevent
1122 the news reader opening
1125 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1126 querying stored in preferences
1129 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1133 <!-- JAL-1977-->Tooltips shown on database chooser
1136 <!-- JAL-391 -->Reverse complement function in calculate
1137 menu for nucleotide sequences
1140 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1141 and feature counts preserves alignment ordering (and
1142 debugged for complex feature sets).
1145 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1146 viewing structures with Jalview 2.10
1149 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1150 genome, transcript CCDS and gene ids via the Ensembl and
1151 Ensembl Genomes REST API
1154 <!-- JAL-2049 -->Protein sequence variant annotation
1155 computed for 'sequence_variant' annotation on CDS regions
1159 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1163 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1164 Ref Fetcher fails to match, or otherwise updates sequence
1165 data from external database records.
1168 <!-- JAL-2154 -->Revised Jalview Project format for
1169 efficient recovery of sequence coding and alignment
1170 annotation relationships.
1172 </ul> <!-- <em>Applet</em>
1183 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1187 <!-- JAL-2018-->Export features in Jalview format (again)
1188 includes graduated colourschemes
1191 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1192 working with big alignments and lots of hidden columns
1195 <!-- JAL-2053-->Hidden column markers not always rendered
1196 at right of alignment window
1199 <!-- JAL-2067 -->Tidied up links in help file table of
1203 <!-- JAL-2072 -->Feature based tree calculation not shown
1207 <!-- JAL-2075 -->Hidden columns ignored during feature
1208 based tree calculation
1211 <!-- JAL-2065 -->Alignment view stops updating when show
1212 unconserved enabled for group on alignment
1215 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1219 <!-- JAL-2146 -->Alignment column in status incorrectly
1220 shown as "Sequence position" when mousing over
1224 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1225 hidden columns present
1228 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1229 user created annotation added to alignment
1232 <!-- JAL-1841 -->RNA Structure consensus only computed for
1233 '()' base pair annotation
1236 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1237 in zero scores for all base pairs in RNA Structure
1241 <!-- JAL-2174-->Extend selection with columns containing
1245 <!-- JAL-2275 -->Pfam format writer puts extra space at
1246 beginning of sequence
1249 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1253 <!-- JAL-2238 -->Cannot create groups on an alignment from
1254 from a tree when t-coffee scores are shown
1257 <!-- JAL-1836,1967 -->Cannot import and view PDB
1258 structures with chains containing negative resnums (4q4h)
1261 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1265 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1266 to Clustal, PIR and PileUp output
1269 <!-- JAL-2008 -->Reordering sequence features that are
1270 not visible causes alignment window to repaint
1273 <!-- JAL-2006 -->Threshold sliders don't work in
1274 graduated colour and colour by annotation row for e-value
1275 scores associated with features and annotation rows
1278 <!-- JAL-1797 -->amino acid physicochemical conservation
1279 calculation should be case independent
1282 <!-- JAL-2173 -->Remove annotation also updates hidden
1286 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1287 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1288 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1291 <!-- JAL-2065 -->Null pointer exceptions and redraw
1292 problems when reference sequence defined and 'show
1293 non-conserved' enabled
1296 <!-- JAL-1306 -->Quality and Conservation are now shown on
1297 load even when Consensus calculation is disabled
1300 <!-- JAL-1932 -->Remove right on penultimate column of
1301 alignment does nothing
1304 <em>Application</em>
1307 <!-- JAL-1552-->URLs and links can't be imported by
1308 drag'n'drop on OSX when launched via webstart (note - not
1309 yet fixed for El Capitan)
1312 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1313 output when running on non-gb/us i18n platforms
1316 <!-- JAL-1944 -->Error thrown when exporting a view with
1317 hidden sequences as flat-file alignment
1320 <!-- JAL-2030-->InstallAnywhere distribution fails when
1324 <!-- JAL-2080-->Jalview very slow to launch via webstart
1325 (also hotfix for 2.9.0b2)
1328 <!-- JAL-2085 -->Cannot save project when view has a
1329 reference sequence defined
1332 <!-- JAL-1011 -->Columns are suddenly selected in other
1333 alignments and views when revealing hidden columns
1336 <!-- JAL-1989 -->Hide columns not mirrored in complement
1337 view in a cDNA/Protein splitframe
1340 <!-- JAL-1369 -->Cannot save/restore representative
1341 sequence from project when only one sequence is
1345 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1346 in Structure Chooser
1349 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1350 structure consensus didn't refresh annotation panel
1353 <!-- JAL-1962 -->View mapping in structure view shows
1354 mappings between sequence and all chains in a PDB file
1357 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1358 dialogs format columns correctly, don't display array
1359 data, sort columns according to type
1362 <!-- JAL-1975 -->Export complete shown after destination
1363 file chooser is cancelled during an image export
1366 <!-- JAL-2025 -->Error when querying PDB Service with
1367 sequence name containing special characters
1370 <!-- JAL-2024 -->Manual PDB structure querying should be
1374 <!-- JAL-2104 -->Large tooltips with broken HTML
1375 formatting don't wrap
1378 <!-- JAL-1128 -->Figures exported from wrapped view are
1379 truncated so L looks like I in consensus annotation
1382 <!-- JAL-2003 -->Export features should only export the
1383 currently displayed features for the current selection or
1387 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1388 after fetching cross-references, and restoring from
1392 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1393 followed in the structure viewer
1396 <!-- JAL-2163 -->Titles for individual alignments in
1397 splitframe not restored from project
1400 <!-- JAL-2145 -->missing autocalculated annotation at
1401 trailing end of protein alignment in transcript/product
1402 splitview when pad-gaps not enabled by default
1405 <!-- JAL-1797 -->amino acid physicochemical conservation
1409 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1410 article has been read (reopened issue due to
1411 internationalisation problems)
1414 <!-- JAL-1960 -->Only offer PDB structures in structure
1415 viewer based on sequence name, PDB and UniProt
1420 <!-- JAL-1976 -->No progress bar shown during export of
1424 <!-- JAL-2213 -->Structures not always superimposed after
1425 multiple structures are shown for one or more sequences.
1428 <!-- JAL-1370 -->Reference sequence characters should not
1429 be replaced with '.' when 'Show unconserved' format option
1433 <!-- JAL-1823 -->Cannot specify chain code when entering
1434 specific PDB id for sequence
1437 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1438 'Export hidden sequences' is enabled, but 'export hidden
1439 columns' is disabled.
1442 <!--JAL-2026-->Best Quality option in structure chooser
1443 selects lowest rather than highest resolution structures
1447 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1448 to sequence mapping in 'View Mappings' report
1451 <!-- JAL-2284 -->Unable to read old Jalview projects that
1452 contain non-XML data added after Jalvew wrote project.
1455 <!-- JAL-2118 -->Newly created annotation row reorders
1456 after clicking on it to create new annotation for a
1459 <!-- may exclude, this is an external service stability issue JAL-1941
1460 -- > RNA 3D structure not added via DSSR service</li> -->
1465 <!-- JAL-2151 -->Incorrect columns are selected when
1466 hidden columns present before start of sequence
1469 <!-- JAL-1986 -->Missing dependencies on applet pages
1473 <!-- JAL-1947 -->Overview pixel size changes when
1474 sequences are hidden in applet
1477 <!-- JAL-1996 -->Updated instructions for applet
1478 deployment on examples pages.
1485 <td width="60" nowrap>
1486 <div align="center">
1487 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1488 <em>16/10/2015</em></strong>
1491 <td><em>General</em>
1493 <li>Time stamps for signed Jalview application and applet
1498 <em>Application</em>
1500 <li>Duplicate group consensus and conservation rows
1501 shown when tree is partitioned</li>
1502 <li>Erratic behaviour when tree partitions made with
1503 multiple cDNA/Protein split views</li>
1509 <td width="60" nowrap>
1510 <div align="center">
1511 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1512 <em>8/10/2015</em></strong>
1515 <td><em>General</em>
1517 <li>Updated Spanish translations of localized text for
1519 </ul> <em>Application</em>
1521 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1522 <li>Signed OSX InstallAnywhere installer<br></li>
1523 <li>Support for per-sequence based annotations in BioJSON</li>
1524 </ul> <em>Applet</em>
1526 <li>Split frame example added to applet examples page</li>
1527 </ul> <em>Build and Deployment</em>
1530 <!-- JAL-1888 -->New ant target for running Jalview's test
1538 <li>Mapping of cDNA to protein in split frames
1539 incorrect when sequence start > 1</li>
1540 <li>Broken images in filter column by annotation dialog
1542 <li>Feature colours not parsed from features file</li>
1543 <li>Exceptions and incomplete link URLs recovered when
1544 loading a features file containing HTML tags in feature
1548 <em>Application</em>
1550 <li>Annotations corrupted after BioJS export and
1552 <li>Incorrect sequence limits after Fetch DB References
1553 with 'trim retrieved sequences'</li>
1554 <li>Incorrect warning about deleting all data when
1555 deleting selected columns</li>
1556 <li>Patch to build system for shipping properly signed
1557 JNLP templates for webstart launch</li>
1558 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1559 unreleased structures for download or viewing</li>
1560 <li>Tab/space/return keystroke operation of EMBL-PDBe
1561 fetcher/viewer dialogs works correctly</li>
1562 <li>Disabled 'minimise' button on Jalview windows
1563 running on OSX to workaround redraw hang bug</li>
1564 <li>Split cDNA/Protein view position and geometry not
1565 recovered from jalview project</li>
1566 <li>Initial enabled/disabled state of annotation menu
1567 sorter 'show autocalculated first/last' corresponds to
1569 <li>Restoring of Clustal, RNA Helices and T-Coffee
1570 color schemes from BioJSON</li>
1574 <li>Reorder sequences mirrored in cDNA/Protein split
1576 <li>Applet with Jmol examples not loading correctly</li>
1582 <td><div align="center">
1583 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1585 <td><em>General</em>
1587 <li>Linked visualisation and analysis of DNA and Protein
1590 <li>Translated cDNA alignments shown as split protein
1591 and DNA alignment views</li>
1592 <li>Codon consensus annotation for linked protein and
1593 cDNA alignment views</li>
1594 <li>Link cDNA or Protein product sequences by loading
1595 them onto Protein or cDNA alignments</li>
1596 <li>Reconstruct linked cDNA alignment from aligned
1597 protein sequences</li>
1600 <li>Jmol integration updated to Jmol v14.2.14</li>
1601 <li>Import and export of Jalview alignment views as <a
1602 href="features/bioJsonFormat.html">BioJSON</a></li>
1603 <li>New alignment annotation file statements for
1604 reference sequences and marking hidden columns</li>
1605 <li>Reference sequence based alignment shading to
1606 highlight variation</li>
1607 <li>Select or hide columns according to alignment
1609 <li>Find option for locating sequences by description</li>
1610 <li>Conserved physicochemical properties shown in amino
1611 acid conservation row</li>
1612 <li>Alignments can be sorted by number of RNA helices</li>
1613 </ul> <em>Application</em>
1615 <li>New cDNA/Protein analysis capabilities
1617 <li>Get Cross-References should open a Split Frame
1618 view with cDNA/Protein</li>
1619 <li>Detect when nucleotide sequences and protein
1620 sequences are placed in the same alignment</li>
1621 <li>Split cDNA/Protein views are saved in Jalview
1626 <li>Use REST API to talk to Chimera</li>
1627 <li>Selected regions in Chimera are highlighted in linked
1628 Jalview windows</li>
1630 <li>VARNA RNA viewer updated to v3.93</li>
1631 <li>VARNA views are saved in Jalview Projects</li>
1632 <li>Pseudoknots displayed as Jalview RNA annotation can
1633 be shown in VARNA</li>
1635 <li>Make groups for selection uses marked columns as well
1636 as the active selected region</li>
1638 <li>Calculate UPGMA and NJ trees using sequence feature
1640 <li>New Export options
1642 <li>New Export Settings dialog to control hidden
1643 region export in flat file generation</li>
1645 <li>Export alignment views for display with the <a
1646 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1648 <li>Export scrollable SVG in HTML page</li>
1649 <li>Optional embedding of BioJSON data when exporting
1650 alignment figures to HTML</li>
1652 <li>3D structure retrieval and display
1654 <li>Free text and structured queries with the PDBe
1656 <li>PDBe Search API based discovery and selection of
1657 PDB structures for a sequence set</li>
1661 <li>JPred4 employed for protein secondary structure
1663 <li>Hide Insertions menu option to hide unaligned columns
1664 for one or a group of sequences</li>
1665 <li>Automatically hide insertions in alignments imported
1666 from the JPred4 web server</li>
1667 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1668 system on OSX<br />LGPL libraries courtesy of <a
1669 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1671 <li>changed 'View nucleotide structure' submenu to 'View
1672 VARNA 2D Structure'</li>
1673 <li>change "View protein structure" menu option to "3D
1676 </ul> <em>Applet</em>
1678 <li>New layout for applet example pages</li>
1679 <li>New parameters to enable SplitFrame view
1680 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1681 <li>New example demonstrating linked viewing of cDNA and
1682 Protein alignments</li>
1683 </ul> <em>Development and deployment</em>
1685 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1686 <li>Include installation type and git revision in build
1687 properties and console log output</li>
1688 <li>Jalview Github organisation, and new github site for
1689 storing BioJsMSA Templates</li>
1690 <li>Jalview's unit tests now managed with TestNG</li>
1693 <!-- <em>General</em>
1695 </ul> --> <!-- issues resolved --> <em>Application</em>
1697 <li>Escape should close any open find dialogs</li>
1698 <li>Typo in select-by-features status report</li>
1699 <li>Consensus RNA secondary secondary structure
1700 predictions are not highlighted in amber</li>
1701 <li>Missing gap character in v2.7 example file means
1702 alignment appears unaligned when pad-gaps is not enabled</li>
1703 <li>First switch to RNA Helices colouring doesn't colour
1704 associated structure views</li>
1705 <li>ID width preference option is greyed out when auto
1706 width checkbox not enabled</li>
1707 <li>Stopped a warning dialog from being shown when
1708 creating user defined colours</li>
1709 <li>'View Mapping' in structure viewer shows sequence
1710 mappings for just that viewer's sequences</li>
1711 <li>Workaround for superposing PDB files containing
1712 multiple models in Chimera</li>
1713 <li>Report sequence position in status bar when hovering
1714 over Jmol structure</li>
1715 <li>Cannot output gaps as '.' symbols with Selection ->
1716 output to text box</li>
1717 <li>Flat file exports of alignments with hidden columns
1718 have incorrect sequence start/end</li>
1719 <li>'Aligning' a second chain to a Chimera structure from
1721 <li>Colour schemes applied to structure viewers don't
1722 work for nucleotide</li>
1723 <li>Loading/cut'n'pasting an empty or invalid file leads
1724 to a grey/invisible alignment window</li>
1725 <li>Exported Jpred annotation from a sequence region
1726 imports to different position</li>
1727 <li>Space at beginning of sequence feature tooltips shown
1728 on some platforms</li>
1729 <li>Chimera viewer 'View | Show Chain' menu is not
1731 <li>'New View' fails with a Null Pointer Exception in
1732 console if Chimera has been opened</li>
1733 <li>Mouseover to Chimera not working</li>
1734 <li>Miscellaneous ENA XML feature qualifiers not
1736 <li>NPE in annotation renderer after 'Extract Scores'</li>
1737 <li>If two structures in one Chimera window, mouseover of
1738 either sequence shows on first structure</li>
1739 <li>'Show annotations' options should not make
1740 non-positional annotations visible</li>
1741 <li>Subsequence secondary structure annotation not shown
1742 in right place after 'view flanking regions'</li>
1743 <li>File Save As type unset when current file format is
1745 <li>Save as '.jar' option removed for saving Jalview
1747 <li>Colour by Sequence colouring in Chimera more
1749 <li>Cannot 'add reference annotation' for a sequence in
1750 several views on same alignment</li>
1751 <li>Cannot show linked products for EMBL / ENA records</li>
1752 <li>Jalview's tooltip wraps long texts containing no
1754 </ul> <em>Applet</em>
1756 <li>Jmol to JalviewLite mouseover/link not working</li>
1757 <li>JalviewLite can't import sequences with ID
1758 descriptions containing angle brackets</li>
1759 </ul> <em>General</em>
1761 <li>Cannot export and reimport RNA secondary structure
1762 via jalview annotation file</li>
1763 <li>Random helix colour palette for colour by annotation
1764 with RNA secondary structure</li>
1765 <li>Mouseover to cDNA from STOP residue in protein
1766 translation doesn't work.</li>
1767 <li>hints when using the select by annotation dialog box</li>
1768 <li>Jmol alignment incorrect if PDB file has alternate CA
1770 <li>FontChooser message dialog appears to hang after
1771 choosing 1pt font</li>
1772 <li>Peptide secondary structure incorrectly imported from
1773 annotation file when annotation display text includes 'e' or
1775 <li>Cannot set colour of new feature type whilst creating
1777 <li>cDNA translation alignment should not be sequence
1778 order dependent</li>
1779 <li>'Show unconserved' doesn't work for lower case
1781 <li>Nucleotide ambiguity codes involving R not recognised</li>
1782 </ul> <em>Deployment and Documentation</em>
1784 <li>Applet example pages appear different to the rest of
1785 www.jalview.org</li>
1786 </ul> <em>Application Known issues</em>
1788 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1789 <li>Misleading message appears after trying to delete
1791 <li>Jalview icon not shown in dock after InstallAnywhere
1792 version launches</li>
1793 <li>Fetching EMBL reference for an RNA sequence results
1794 fails with a sequence mismatch</li>
1795 <li>Corrupted or unreadable alignment display when
1796 scrolling alignment to right</li>
1797 <li>ArrayIndexOutOfBoundsException thrown when remove
1798 empty columns called on alignment with ragged gapped ends</li>
1799 <li>auto calculated alignment annotation rows do not get
1800 placed above or below non-autocalculated rows</li>
1801 <li>Jalview dekstop becomes sluggish at full screen in
1802 ultra-high resolution</li>
1803 <li>Cannot disable consensus calculation independently of
1804 quality and conservation</li>
1805 <li>Mouseover highlighting between cDNA and protein can
1806 become sluggish with more than one splitframe shown</li>
1807 </ul> <em>Applet Known Issues</em>
1809 <li>Core PDB parsing code requires Jmol</li>
1810 <li>Sequence canvas panel goes white when alignment
1811 window is being resized</li>
1817 <td><div align="center">
1818 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1820 <td><em>General</em>
1822 <li>Updated Java code signing certificate donated by
1824 <li>Features and annotation preserved when performing
1825 pairwise alignment</li>
1826 <li>RNA pseudoknot annotation can be
1827 imported/exported/displayed</li>
1828 <li>'colour by annotation' can colour by RNA and
1829 protein secondary structure</li>
1830 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1831 post-hoc with 2.9 release</em>)
1834 </ul> <em>Application</em>
1836 <li>Extract and display secondary structure for sequences
1837 with 3D structures</li>
1838 <li>Support for parsing RNAML</li>
1839 <li>Annotations menu for layout
1841 <li>sort sequence annotation rows by alignment</li>
1842 <li>place sequence annotation above/below alignment
1845 <li>Output in Stockholm format</li>
1846 <li>Internationalisation: improved Spanish (es)
1848 <li>Structure viewer preferences tab</li>
1849 <li>Disorder and Secondary Structure annotation tracks
1850 shared between alignments</li>
1851 <li>UCSF Chimera launch and linked highlighting from
1853 <li>Show/hide all sequence associated annotation rows for
1854 all or current selection</li>
1855 <li>disorder and secondary structure predictions
1856 available as dataset annotation</li>
1857 <li>Per-sequence rna helices colouring</li>
1860 <li>Sequence database accessions imported when fetching
1861 alignments from Rfam</li>
1862 <li>update VARNA version to 3.91</li>
1864 <li>New groovy scripts for exporting aligned positions,
1865 conservation values, and calculating sum of pairs scores.</li>
1866 <li>Command line argument to set default JABAWS server</li>
1867 <li>include installation type in build properties and
1868 console log output</li>
1869 <li>Updated Jalview project format to preserve dataset
1873 <!-- issues resolved --> <em>Application</em>
1875 <li>Distinguish alignment and sequence associated RNA
1876 structure in structure->view->VARNA</li>
1877 <li>Raise dialog box if user deletes all sequences in an
1879 <li>Pressing F1 results in documentation opening twice</li>
1880 <li>Sequence feature tooltip is wrapped</li>
1881 <li>Double click on sequence associated annotation
1882 selects only first column</li>
1883 <li>Redundancy removal doesn't result in unlinked
1884 leaves shown in tree</li>
1885 <li>Undos after several redundancy removals don't undo
1887 <li>Hide sequence doesn't hide associated annotation</li>
1888 <li>User defined colours dialog box too big to fit on
1889 screen and buttons not visible</li>
1890 <li>author list isn't updated if already written to
1891 Jalview properties</li>
1892 <li>Popup menu won't open after retrieving sequence
1894 <li>File open window for associate PDB doesn't open</li>
1895 <li>Left-then-right click on a sequence id opens a
1896 browser search window</li>
1897 <li>Cannot open sequence feature shading/sort popup menu
1898 in feature settings dialog</li>
1899 <li>better tooltip placement for some areas of Jalview
1901 <li>Allow addition of JABAWS Server which doesn't
1902 pass validation</li>
1903 <li>Web services parameters dialog box is too large to
1905 <li>Muscle nucleotide alignment preset obscured by
1907 <li>JABAWS preset submenus don't contain newly
1908 defined user preset</li>
1909 <li>MSA web services warns user if they were launched
1910 with invalid input</li>
1911 <li>Jalview cannot contact DAS Registy when running on
1914 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1915 'Superpose with' submenu not shown when new view
1919 </ul> <!-- <em>Applet</em>
1921 </ul> <em>General</em>
1923 </ul>--> <em>Deployment and Documentation</em>
1925 <li>2G and 1G options in launchApp have no effect on
1926 memory allocation</li>
1927 <li>launchApp service doesn't automatically open
1928 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1930 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1931 InstallAnywhere reports cannot find valid JVM when Java
1932 1.7_055 is available
1934 </ul> <em>Application Known issues</em>
1937 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1938 corrupted or unreadable alignment display when scrolling
1942 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1943 retrieval fails but progress bar continues for DAS retrieval
1944 with large number of ID
1947 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1948 flatfile output of visible region has incorrect sequence
1952 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1953 rna structure consensus doesn't update when secondary
1954 structure tracks are rearranged
1957 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1958 invalid rna structure positional highlighting does not
1959 highlight position of invalid base pairs
1962 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1963 out of memory errors are not raised when saving Jalview
1964 project from alignment window file menu
1967 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1968 Switching to RNA Helices colouring doesn't propagate to
1972 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1973 colour by RNA Helices not enabled when user created
1974 annotation added to alignment
1977 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1978 Jalview icon not shown on dock in Mountain Lion/Webstart
1980 </ul> <em>Applet Known Issues</em>
1983 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1984 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1987 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1988 Jalview and Jmol example not compatible with IE9
1991 <li>Sort by annotation score doesn't reverse order
1997 <td><div align="center">
1998 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2001 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2004 <li>Internationalisation of user interface (usually
2005 called i18n support) and translation for Spanish locale</li>
2006 <li>Define/Undefine group on current selection with
2007 Ctrl-G/Shift Ctrl-G</li>
2008 <li>Improved group creation/removal options in
2009 alignment/sequence Popup menu</li>
2010 <li>Sensible precision for symbol distribution
2011 percentages shown in logo tooltip.</li>
2012 <li>Annotation panel height set according to amount of
2013 annotation when alignment first opened</li>
2014 </ul> <em>Application</em>
2016 <li>Interactive consensus RNA secondary structure
2017 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2018 <li>Select columns containing particular features from
2019 Feature Settings dialog</li>
2020 <li>View all 'representative' PDB structures for selected
2022 <li>Update Jalview project format:
2024 <li>New file extension for Jalview projects '.jvp'</li>
2025 <li>Preserve sequence and annotation dataset (to
2026 store secondary structure annotation,etc)</li>
2027 <li>Per group and alignment annotation and RNA helix
2031 <li>New similarity measures for PCA and Tree calculation
2033 <li>Experimental support for retrieval and viewing of
2034 flanking regions for an alignment</li>
2038 <!-- issues resolved --> <em>Application</em>
2040 <li>logo keeps spinning and status remains at queued or
2041 running after job is cancelled</li>
2042 <li>cannot export features from alignments imported from
2043 Jalview/VAMSAS projects</li>
2044 <li>Buggy slider for web service parameters that take
2046 <li>Newly created RNA secondary structure line doesn't
2047 have 'display all symbols' flag set</li>
2048 <li>T-COFFEE alignment score shading scheme and other
2049 annotation shading not saved in Jalview project</li>
2050 <li>Local file cannot be loaded in freshly downloaded
2052 <li>Jalview icon not shown on dock in Mountain
2054 <li>Load file from desktop file browser fails</li>
2055 <li>Occasional NPE thrown when calculating large trees</li>
2056 <li>Cannot reorder or slide sequences after dragging an
2057 alignment onto desktop</li>
2058 <li>Colour by annotation dialog throws NPE after using
2059 'extract scores' function</li>
2060 <li>Loading/cut'n'pasting an empty file leads to a grey
2061 alignment window</li>
2062 <li>Disorder thresholds rendered incorrectly after
2063 performing IUPred disorder prediction</li>
2064 <li>Multiple group annotated consensus rows shown when
2065 changing 'normalise logo' display setting</li>
2066 <li>Find shows blank dialog after 'finished searching' if
2067 nothing matches query</li>
2068 <li>Null Pointer Exceptions raised when sorting by
2069 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2071 <li>Errors in Jmol console when structures in alignment
2072 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2074 <li>Not all working JABAWS services are shown in
2076 <li>JAVAWS version of Jalview fails to launch with
2077 'invalid literal/length code'</li>
2078 <li>Annotation/RNA Helix colourschemes cannot be applied
2079 to alignment with groups (actually fixed in 2.8.0b1)</li>
2080 <li>RNA Helices and T-Coffee Scores available as default
2083 </ul> <em>Applet</em>
2085 <li>Remove group option is shown even when selection is
2087 <li>Apply to all groups ticked but colourscheme changes
2088 don't affect groups</li>
2089 <li>Documented RNA Helices and T-Coffee Scores as valid
2090 colourscheme name</li>
2091 <li>Annotation labels drawn on sequence IDs when
2092 Annotation panel is not displayed</li>
2093 <li>Increased font size for dropdown menus on OSX and
2094 embedded windows</li>
2095 </ul> <em>Other</em>
2097 <li>Consensus sequence for alignments/groups with a
2098 single sequence were not calculated</li>
2099 <li>annotation files that contain only groups imported as
2100 annotation and junk sequences</li>
2101 <li>Fasta files with sequences containing '*' incorrectly
2102 recognised as PFAM or BLC</li>
2103 <li>conservation/PID slider apply all groups option
2104 doesn't affect background (2.8.0b1)
2106 <li>redundancy highlighting is erratic at 0% and 100%</li>
2107 <li>Remove gapped columns fails for sequences with ragged
2109 <li>AMSA annotation row with leading spaces is not
2110 registered correctly on import</li>
2111 <li>Jalview crashes when selecting PCA analysis for
2112 certain alignments</li>
2113 <li>Opening the colour by annotation dialog for an
2114 existing annotation based 'use original colours'
2115 colourscheme loses original colours setting</li>
2120 <td><div align="center">
2121 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2122 <em>30/1/2014</em></strong>
2126 <li>Trusted certificates for JalviewLite applet and
2127 Jalview Desktop application<br />Certificate was donated by
2128 <a href="https://www.certum.eu">Certum</a> to the Jalview
2129 open source project).
2131 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2132 <li>Output in Stockholm format</li>
2133 <li>Allow import of data from gzipped files</li>
2134 <li>Export/import group and sequence associated line
2135 graph thresholds</li>
2136 <li>Nucleotide substitution matrix that supports RNA and
2137 ambiguity codes</li>
2138 <li>Allow disorder predictions to be made on the current
2139 selection (or visible selection) in the same way that JPred
2141 <li>Groovy scripting for headless Jalview operation</li>
2142 </ul> <em>Other improvements</em>
2144 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2145 <li>COMBINE statement uses current SEQUENCE_REF and
2146 GROUP_REF scope to group annotation rows</li>
2147 <li>Support '' style escaping of quotes in Newick
2149 <li>Group options for JABAWS service by command line name</li>
2150 <li>Empty tooltip shown for JABA service options with a
2151 link but no description</li>
2152 <li>Select primary source when selecting authority in
2153 database fetcher GUI</li>
2154 <li>Add .mfa to FASTA file extensions recognised by
2156 <li>Annotation label tooltip text wrap</li>
2161 <li>Slow scrolling when lots of annotation rows are
2163 <li>Lots of NPE (and slowness) after creating RNA
2164 secondary structure annotation line</li>
2165 <li>Sequence database accessions not imported when
2166 fetching alignments from Rfam</li>
2167 <li>Incorrect SHMR submission for sequences with
2169 <li>View all structures does not always superpose
2171 <li>Option widgets in service parameters not updated to
2172 reflect user or preset settings</li>
2173 <li>Null pointer exceptions for some services without
2174 presets or adjustable parameters</li>
2175 <li>Discover PDB IDs entry in structure menu doesn't
2176 discover PDB xRefs</li>
2177 <li>Exception encountered while trying to retrieve
2178 features with DAS</li>
2179 <li>Lowest value in annotation row isn't coloured
2180 when colour by annotation (per sequence) is coloured</li>
2181 <li>Keyboard mode P jumps to start of gapped region when
2182 residue follows a gap</li>
2183 <li>Jalview appears to hang importing an alignment with
2184 Wrap as default or after enabling Wrap</li>
2185 <li>'Right click to add annotations' message
2186 shown in wrap mode when no annotations present</li>
2187 <li>Disorder predictions fail with NPE if no automatic
2188 annotation already exists on alignment</li>
2189 <li>oninit javascript function should be called after
2190 initialisation completes</li>
2191 <li>Remove redundancy after disorder prediction corrupts
2192 alignment window display</li>
2193 <li>Example annotation file in documentation is invalid</li>
2194 <li>Grouped line graph annotation rows are not exported
2195 to annotation file</li>
2196 <li>Multi-harmony analysis cannot be run when only two
2198 <li>Cannot create multiple groups of line graphs with
2199 several 'combine' statements in annotation file</li>
2200 <li>Pressing return several times causes Number Format
2201 exceptions in keyboard mode</li>
2202 <li>Multi-harmony (SHMMR) method doesn't submit
2203 correct partitions for input data</li>
2204 <li>Translation from DNA to Amino Acids fails</li>
2205 <li>Jalview fail to load newick tree with quoted label</li>
2206 <li>--headless flag isn't understood</li>
2207 <li>ClassCastException when generating EPS in headless
2209 <li>Adjusting sequence-associated shading threshold only
2210 changes one row's threshold</li>
2211 <li>Preferences and Feature settings panel panel
2212 doesn't open</li>
2213 <li>hide consensus histogram also hides conservation and
2214 quality histograms</li>
2219 <td><div align="center">
2220 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2222 <td><em>Application</em>
2224 <li>Support for JABAWS 2.0 Services (AACon alignment
2225 conservation, protein disorder and Clustal Omega)</li>
2226 <li>JABAWS server status indicator in Web Services
2228 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2229 in Jalview alignment window</li>
2230 <li>Updated Jalview build and deploy framework for OSX
2231 mountain lion, windows 7, and 8</li>
2232 <li>Nucleotide substitution matrix for PCA that supports
2233 RNA and ambiguity codes</li>
2235 <li>Improved sequence database retrieval GUI</li>
2236 <li>Support fetching and database reference look up
2237 against multiple DAS sources (Fetch all from in 'fetch db
2239 <li>Jalview project improvements
2241 <li>Store and retrieve the 'belowAlignment'
2242 flag for annotation</li>
2243 <li>calcId attribute to group annotation rows on the
2245 <li>Store AACon calculation settings for a view in
2246 Jalview project</li>
2250 <li>horizontal scrolling gesture support</li>
2251 <li>Visual progress indicator when PCA calculation is
2253 <li>Simpler JABA web services menus</li>
2254 <li>visual indication that web service results are still
2255 being retrieved from server</li>
2256 <li>Serialise the dialogs that are shown when Jalview
2257 starts up for first time</li>
2258 <li>Jalview user agent string for interacting with HTTP
2260 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2262 <li>Examples directory and Groovy library included in
2263 InstallAnywhere distribution</li>
2264 </ul> <em>Applet</em>
2266 <li>RNA alignment and secondary structure annotation
2267 visualization applet example</li>
2268 </ul> <em>General</em>
2270 <li>Normalise option for consensus sequence logo</li>
2271 <li>Reset button in PCA window to return dimensions to
2273 <li>Allow seqspace or Jalview variant of alignment PCA
2275 <li>PCA with either nucleic acid and protein substitution
2277 <li>Allow windows containing HTML reports to be exported
2279 <li>Interactive display and editing of RNA secondary
2280 structure contacts</li>
2281 <li>RNA Helix Alignment Colouring</li>
2282 <li>RNA base pair logo consensus</li>
2283 <li>Parse sequence associated secondary structure
2284 information in Stockholm files</li>
2285 <li>HTML Export database accessions and annotation
2286 information presented in tooltip for sequences</li>
2287 <li>Import secondary structure from LOCARNA clustalw
2288 style RNA alignment files</li>
2289 <li>import and visualise T-COFFEE quality scores for an
2291 <li>'colour by annotation' per sequence option to
2292 shade each sequence according to its associated alignment
2294 <li>New Jalview Logo</li>
2295 </ul> <em>Documentation and Development</em>
2297 <li>documentation for score matrices used in Jalview</li>
2298 <li>New Website!</li>
2300 <td><em>Application</em>
2302 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2303 wsdbfetch REST service</li>
2304 <li>Stop windows being moved outside desktop on OSX</li>
2305 <li>Filetype associations not installed for webstart
2307 <li>Jalview does not always retrieve progress of a JABAWS
2308 job execution in full once it is complete</li>
2309 <li>revise SHMR RSBS definition to ensure alignment is
2310 uploaded via ali_file parameter</li>
2311 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2312 <li>View all structures superposed fails with exception</li>
2313 <li>Jnet job queues forever if a very short sequence is
2314 submitted for prediction</li>
2315 <li>Cut and paste menu not opened when mouse clicked on
2317 <li>Putting fractional value into integer text box in
2318 alignment parameter dialog causes Jalview to hang</li>
2319 <li>Structure view highlighting doesn't work on
2321 <li>View all structures fails with exception shown in
2323 <li>Characters in filename associated with PDBEntry not
2324 escaped in a platform independent way</li>
2325 <li>Jalview desktop fails to launch with exception when
2327 <li>Tree calculation reports 'you must have 2 or more
2328 sequences selected' when selection is empty</li>
2329 <li>Jalview desktop fails to launch with jar signature
2330 failure when java web start temporary file caching is
2332 <li>DAS Sequence retrieval with range qualification
2333 results in sequence xref which includes range qualification</li>
2334 <li>Errors during processing of command line arguments
2335 cause progress bar (JAL-898) to be removed</li>
2336 <li>Replace comma for semi-colon option not disabled for
2337 DAS sources in sequence fetcher</li>
2338 <li>Cannot close news reader when JABAWS server warning
2339 dialog is shown</li>
2340 <li>Option widgets not updated to reflect user settings</li>
2341 <li>Edited sequence not submitted to web service</li>
2342 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2343 <li>InstallAnywhere installer doesn't unpack and run
2344 on OSX Mountain Lion</li>
2345 <li>Annotation panel not given a scroll bar when
2346 sequences with alignment annotation are pasted into the
2348 <li>Sequence associated annotation rows not associated
2349 when loaded from Jalview project</li>
2350 <li>Browser launch fails with NPE on java 1.7</li>
2351 <li>JABAWS alignment marked as finished when job was
2352 cancelled or job failed due to invalid input</li>
2353 <li>NPE with v2.7 example when clicking on Tree
2354 associated with all views</li>
2355 <li>Exceptions when copy/paste sequences with grouped
2356 annotation rows to new window</li>
2357 </ul> <em>Applet</em>
2359 <li>Sequence features are momentarily displayed before
2360 they are hidden using hidefeaturegroups applet parameter</li>
2361 <li>loading features via javascript API automatically
2362 enables feature display</li>
2363 <li>scrollToColumnIn javascript API method doesn't
2365 </ul> <em>General</em>
2367 <li>Redundancy removal fails for rna alignment</li>
2368 <li>PCA calculation fails when sequence has been selected
2369 and then deselected</li>
2370 <li>PCA window shows grey box when first opened on OSX</li>
2371 <li>Letters coloured pink in sequence logo when alignment
2372 coloured with clustalx</li>
2373 <li>Choosing fonts without letter symbols defined causes
2374 exceptions and redraw errors</li>
2375 <li>Initial PCA plot view is not same as manually
2376 reconfigured view</li>
2377 <li>Grouped annotation graph label has incorrect line
2379 <li>Grouped annotation graph label display is corrupted
2380 for lots of labels</li>
2385 <div align="center">
2386 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2389 <td><em>Application</em>
2391 <li>Jalview Desktop News Reader</li>
2392 <li>Tweaked default layout of web services menu</li>
2393 <li>View/alignment association menu to enable user to
2394 easily specify which alignment a multi-structure view takes
2395 its colours/correspondences from</li>
2396 <li>Allow properties file location to be specified as URL</li>
2397 <li>Extend Jalview project to preserve associations
2398 between many alignment views and a single Jmol display</li>
2399 <li>Store annotation row height in Jalview project file</li>
2400 <li>Annotation row column label formatting attributes
2401 stored in project file</li>
2402 <li>Annotation row order for auto-calculated annotation
2403 rows preserved in Jalview project file</li>
2404 <li>Visual progress indication when Jalview state is
2405 saved using Desktop window menu</li>
2406 <li>Visual indication that command line arguments are
2407 still being processed</li>
2408 <li>Groovy script execution from URL</li>
2409 <li>Colour by annotation default min and max colours in
2411 <li>Automatically associate PDB files dragged onto an
2412 alignment with sequences that have high similarity and
2414 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2415 <li>'view structures' option to open many
2416 structures in same window</li>
2417 <li>Sort associated views menu option for tree panel</li>
2418 <li>Group all JABA and non-JABA services for a particular
2419 analysis function in its own submenu</li>
2420 </ul> <em>Applet</em>
2422 <li>Userdefined and autogenerated annotation rows for
2424 <li>Adjustment of alignment annotation pane height</li>
2425 <li>Annotation scrollbar for annotation panel</li>
2426 <li>Drag to reorder annotation rows in annotation panel</li>
2427 <li>'automaticScrolling' parameter</li>
2428 <li>Allow sequences with partial ID string matches to be
2429 annotated from GFF/Jalview features files</li>
2430 <li>Sequence logo annotation row in applet</li>
2431 <li>Absolute paths relative to host server in applet
2432 parameters are treated as such</li>
2433 <li>New in the JalviewLite javascript API:
2435 <li>JalviewLite.js javascript library</li>
2436 <li>Javascript callbacks for
2438 <li>Applet initialisation</li>
2439 <li>Sequence/alignment mouse-overs and selections</li>
2442 <li>scrollTo row and column alignment scrolling
2444 <li>Select sequence/alignment regions from javascript</li>
2445 <li>javascript structure viewer harness to pass
2446 messages between Jmol and Jalview when running as
2447 distinct applets</li>
2448 <li>sortBy method</li>
2449 <li>Set of applet and application examples shipped
2450 with documentation</li>
2451 <li>New example to demonstrate JalviewLite and Jmol
2452 javascript message exchange</li>
2454 </ul> <em>General</em>
2456 <li>Enable Jmol displays to be associated with multiple
2457 multiple alignments</li>
2458 <li>Option to automatically sort alignment with new tree</li>
2459 <li>User configurable link to enable redirects to a
2460 www.Jalview.org mirror</li>
2461 <li>Jmol colours option for Jmol displays</li>
2462 <li>Configurable newline string when writing alignment
2463 and other flat files</li>
2464 <li>Allow alignment annotation description lines to
2465 contain html tags</li>
2466 </ul> <em>Documentation and Development</em>
2468 <li>Add groovy test harness for bulk load testing to
2470 <li>Groovy script to load and align a set of sequences
2471 using a web service before displaying the result in the
2472 Jalview desktop</li>
2473 <li>Restructured javascript and applet api documentation</li>
2474 <li>Ant target to publish example html files with applet
2476 <li>Netbeans project for building Jalview from source</li>
2477 <li>ant task to create online javadoc for Jalview source</li>
2479 <td><em>Application</em>
2481 <li>User defined colourscheme throws exception when
2482 current built in colourscheme is saved as new scheme</li>
2483 <li>AlignFrame->Save in application pops up save
2484 dialog for valid filename/format</li>
2485 <li>Cannot view associated structure for UniProt sequence</li>
2486 <li>PDB file association breaks for UniProt sequence
2488 <li>Associate PDB from file dialog does not tell you
2489 which sequence is to be associated with the file</li>
2490 <li>Find All raises null pointer exception when query
2491 only matches sequence IDs</li>
2492 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2493 <li>Jalview project with Jmol views created with Jalview
2494 2.4 cannot be loaded</li>
2495 <li>Filetype associations not installed for webstart
2497 <li>Two or more chains in a single PDB file associated
2498 with sequences in different alignments do not get coloured
2499 by their associated sequence</li>
2500 <li>Visibility status of autocalculated annotation row
2501 not preserved when project is loaded</li>
2502 <li>Annotation row height and visibility attributes not
2503 stored in Jalview project</li>
2504 <li>Tree bootstraps are not preserved when saved as a
2505 Jalview project</li>
2506 <li>Envision2 workflow tooltips are corrupted</li>
2507 <li>Enabling show group conservation also enables colour
2508 by conservation</li>
2509 <li>Duplicate group associated conservation or consensus
2510 created on new view</li>
2511 <li>Annotation scrollbar not displayed after 'show
2512 all hidden annotation rows' option selected</li>
2513 <li>Alignment quality not updated after alignment
2514 annotation row is hidden then shown</li>
2515 <li>Preserve colouring of structures coloured by
2516 sequences in pre Jalview 2.7 projects</li>
2517 <li>Web service job parameter dialog is not laid out
2519 <li>Web services menu not refreshed after 'reset
2520 services' button is pressed in preferences</li>
2521 <li>Annotation off by one in Jalview v2_3 example project</li>
2522 <li>Structures imported from file and saved in project
2523 get name like jalview_pdb1234.txt when reloaded</li>
2524 <li>Jalview does not always retrieve progress of a JABAWS
2525 job execution in full once it is complete</li>
2526 </ul> <em>Applet</em>
2528 <li>Alignment height set incorrectly when lots of
2529 annotation rows are displayed</li>
2530 <li>Relative URLs in feature HTML text not resolved to
2532 <li>View follows highlighting does not work for positions
2534 <li><= shown as = in tooltip</li>
2535 <li>Export features raises exception when no features
2537 <li>Separator string used for serialising lists of IDs
2538 for javascript api is modified when separator string
2539 provided as parameter</li>
2540 <li>Null pointer exception when selecting tree leaves for
2541 alignment with no existing selection</li>
2542 <li>Relative URLs for datasources assumed to be relative
2543 to applet's codebase</li>
2544 <li>Status bar not updated after finished searching and
2545 search wraps around to first result</li>
2546 <li>StructureSelectionManager instance shared between
2547 several Jalview applets causes race conditions and memory
2549 <li>Hover tooltip and mouseover of position on structure
2550 not sent from Jmol in applet</li>
2551 <li>Certain sequences of javascript method calls to
2552 applet API fatally hang browser</li>
2553 </ul> <em>General</em>
2555 <li>View follows structure mouseover scrolls beyond
2556 position with wrapped view and hidden regions</li>
2557 <li>Find sequence position moves to wrong residue
2558 with/without hidden columns</li>
2559 <li>Sequence length given in alignment properties window
2561 <li>InvalidNumberFormat exceptions thrown when trying to
2562 import PDB like structure files</li>
2563 <li>Positional search results are only highlighted
2564 between user-supplied sequence start/end bounds</li>
2565 <li>End attribute of sequence is not validated</li>
2566 <li>Find dialog only finds first sequence containing a
2567 given sequence position</li>
2568 <li>Sequence numbering not preserved in MSF alignment
2570 <li>Jalview PDB file reader does not extract sequence
2571 from nucleotide chains correctly</li>
2572 <li>Structure colours not updated when tree partition
2573 changed in alignment</li>
2574 <li>Sequence associated secondary structure not correctly
2575 parsed in interleaved stockholm</li>
2576 <li>Colour by annotation dialog does not restore current
2578 <li>Hiding (nearly) all sequences doesn't work
2580 <li>Sequences containing lowercase letters are not
2581 properly associated with their pdb files</li>
2582 </ul> <em>Documentation and Development</em>
2584 <li>schemas/JalviewWsParamSet.xsd corrupted by
2585 ApplyCopyright tool</li>
2590 <div align="center">
2591 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2594 <td><em>Application</em>
2596 <li>New warning dialog when the Jalview Desktop cannot
2597 contact web services</li>
2598 <li>JABA service parameters for a preset are shown in
2599 service job window</li>
2600 <li>JABA Service menu entries reworded</li>
2604 <li>Modeller PIR IO broken - cannot correctly import a
2605 pir file emitted by Jalview</li>
2606 <li>Existing feature settings transferred to new
2607 alignment view created from cut'n'paste</li>
2608 <li>Improved test for mixed amino/nucleotide chains when
2609 parsing PDB files</li>
2610 <li>Consensus and conservation annotation rows
2611 occasionally become blank for all new windows</li>
2612 <li>Exception raised when right clicking above sequences
2613 in wrapped view mode</li>
2614 </ul> <em>Application</em>
2616 <li>multiple multiply aligned structure views cause cpu
2617 usage to hit 100% and computer to hang</li>
2618 <li>Web Service parameter layout breaks for long user
2619 parameter names</li>
2620 <li>Jaba service discovery hangs desktop if Jaba server
2627 <div align="center">
2628 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2631 <td><em>Application</em>
2633 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2634 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2637 <li>Web Services preference tab</li>
2638 <li>Analysis parameters dialog box and user defined
2640 <li>Improved speed and layout of Envision2 service menu</li>
2641 <li>Superpose structures using associated sequence
2643 <li>Export coordinates and projection as CSV from PCA
2645 </ul> <em>Applet</em>
2647 <li>enable javascript: execution by the applet via the
2648 link out mechanism</li>
2649 </ul> <em>Other</em>
2651 <li>Updated the Jmol Jalview interface to work with Jmol
2653 <li>The Jalview Desktop and JalviewLite applet now
2654 require Java 1.5</li>
2655 <li>Allow Jalview feature colour specification for GFF
2656 sequence annotation files</li>
2657 <li>New 'colour by label' keword in Jalview feature file
2658 type colour specification</li>
2659 <li>New Jalview Desktop Groovy API method that allows a
2660 script to check if it being run in an interactive session or
2661 in a batch operation from the Jalview command line</li>
2665 <li>clustalx colourscheme colours Ds preferentially when
2666 both D+E are present in over 50% of the column</li>
2667 </ul> <em>Application</em>
2669 <li>typo in AlignmentFrame->View->Hide->all but
2670 selected Regions menu item</li>
2671 <li>sequence fetcher replaces ',' for ';' when the ',' is
2672 part of a valid accession ID</li>
2673 <li>fatal OOM if object retrieved by sequence fetcher
2674 runs out of memory</li>
2675 <li>unhandled Out of Memory Error when viewing pca
2676 analysis results</li>
2677 <li>InstallAnywhere builds fail to launch on OS X java
2678 10.5 update 4 (due to apple Java 1.6 update)</li>
2679 <li>Installanywhere Jalview silently fails to launch</li>
2680 </ul> <em>Applet</em>
2682 <li>Jalview.getFeatureGroups() raises an
2683 ArrayIndexOutOfBoundsException if no feature groups are
2690 <div align="center">
2691 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2697 <li>Alignment prettyprinter doesn't cope with long
2699 <li>clustalx colourscheme colours Ds preferentially when
2700 both D+E are present in over 50% of the column</li>
2701 <li>nucleic acid structures retrieved from PDB do not
2702 import correctly</li>
2703 <li>More columns get selected than were clicked on when a
2704 number of columns are hidden</li>
2705 <li>annotation label popup menu not providing correct
2706 add/hide/show options when rows are hidden or none are
2708 <li>Stockholm format shown in list of readable formats,
2709 and parser copes better with alignments from RFAM.</li>
2710 <li>CSV output of consensus only includes the percentage
2711 of all symbols if sequence logo display is enabled</li>
2713 </ul> <em>Applet</em>
2715 <li>annotation panel disappears when annotation is
2717 </ul> <em>Application</em>
2719 <li>Alignment view not redrawn properly when new
2720 alignment opened where annotation panel is visible but no
2721 annotations are present on alignment</li>
2722 <li>pasted region containing hidden columns is
2723 incorrectly displayed in new alignment window</li>
2724 <li>Jalview slow to complete operations when stdout is
2725 flooded (fix is to close the Jalview console)</li>
2726 <li>typo in AlignmentFrame->View->Hide->all but
2727 selected Rregions menu item.</li>
2728 <li>inconsistent group submenu and Format submenu entry
2729 'Un' or 'Non'conserved</li>
2730 <li>Sequence feature settings are being shared by
2731 multiple distinct alignments</li>
2732 <li>group annotation not recreated when tree partition is
2734 <li>double click on group annotation to select sequences
2735 does not propagate to associated trees</li>
2736 <li>Mac OSX specific issues:
2738 <li>exception raised when mouse clicked on desktop
2739 window background</li>
2740 <li>Desktop menu placed on menu bar and application
2741 name set correctly</li>
2742 <li>sequence feature settings not wide enough for the
2743 save feature colourscheme button</li>
2752 <div align="center">
2753 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2756 <td><em>New Capabilities</em>
2758 <li>URL links generated from description line for
2759 regular-expression based URL links (applet and application)
2761 <li>Non-positional feature URL links are shown in link
2763 <li>Linked viewing of nucleic acid sequences and
2765 <li>Automatic Scrolling option in View menu to display
2766 the currently highlighted region of an alignment.</li>
2767 <li>Order an alignment by sequence length, or using the
2768 average score or total feature count for each sequence.</li>
2769 <li>Shading features by score or associated description</li>
2770 <li>Subdivide alignment and groups based on identity of
2771 selected subsequence (Make Groups from Selection).</li>
2772 <li>New hide/show options including Shift+Control+H to
2773 hide everything but the currently selected region.</li>
2774 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2775 </ul> <em>Application</em>
2777 <li>Fetch DB References capabilities and UI expanded to
2778 support retrieval from DAS sequence sources</li>
2779 <li>Local DAS Sequence sources can be added via the
2780 command line or via the Add local source dialog box.</li>
2781 <li>DAS Dbref and DbxRef feature types are parsed as
2782 database references and protein_name is parsed as
2783 description line (BioSapiens terms).</li>
2784 <li>Enable or disable non-positional feature and database
2785 references in sequence ID tooltip from View menu in
2787 <!-- <li>New hidden columns and rows and representatives capabilities
2788 in annotations file (in progress - not yet fully implemented)</li> -->
2789 <li>Group-associated consensus, sequence logos and
2790 conservation plots</li>
2791 <li>Symbol distributions for each column can be exported
2792 and visualized as sequence logos</li>
2793 <li>Optionally scale multi-character column labels to fit
2794 within each column of annotation row<!-- todo for applet -->
2796 <li>Optional automatic sort of associated alignment view
2797 when a new tree is opened.</li>
2798 <li>Jalview Java Console</li>
2799 <li>Better placement of desktop window when moving
2800 between different screens.</li>
2801 <li>New preference items for sequence ID tooltip and
2802 consensus annotation</li>
2803 <li>Client to submit sequences and IDs to Envision2
2805 <li><em>Vamsas Capabilities</em>
2807 <li>Improved VAMSAS synchronization (Jalview archive
2808 used to preserve views, structures, and tree display
2810 <li>Import of vamsas documents from disk or URL via
2812 <li>Sharing of selected regions between views and
2813 with other VAMSAS applications (Experimental feature!)</li>
2814 <li>Updated API to VAMSAS version 0.2</li>
2816 </ul> <em>Applet</em>
2818 <li>Middle button resizes annotation row height</li>
2821 <li>sortByTree (true/false) - automatically sort the
2822 associated alignment view by the tree when a new tree is
2824 <li>showTreeBootstraps (true/false) - show or hide
2825 branch bootstraps (default is to show them if available)</li>
2826 <li>showTreeDistances (true/false) - show or hide
2827 branch lengths (default is to show them if available)</li>
2828 <li>showUnlinkedTreeNodes (true/false) - indicate if
2829 unassociated nodes should be highlighted in the tree
2831 <li>heightScale and widthScale (1.0 or more) -
2832 increase the height or width of a cell in the alignment
2833 grid relative to the current font size.</li>
2836 <li>Non-positional features displayed in sequence ID
2838 </ul> <em>Other</em>
2840 <li>Features format: graduated colour definitions and
2841 specification of feature scores</li>
2842 <li>Alignment Annotations format: new keywords for group
2843 associated annotation (GROUP_REF) and annotation row display
2844 properties (ROW_PROPERTIES)</li>
2845 <li>XML formats extended to support graduated feature
2846 colourschemes, group associated annotation, and profile
2847 visualization settings.</li></td>
2850 <li>Source field in GFF files parsed as feature source
2851 rather than description</li>
2852 <li>Non-positional features are now included in sequence
2853 feature and gff files (controlled via non-positional feature
2854 visibility in tooltip).</li>
2855 <li>URL links generated for all feature links (bugfix)</li>
2856 <li>Added URL embedding instructions to features file
2858 <li>Codons containing ambiguous nucleotides translated as
2859 'X' in peptide product</li>
2860 <li>Match case switch in find dialog box works for both
2861 sequence ID and sequence string and query strings do not
2862 have to be in upper case to match case-insensitively.</li>
2863 <li>AMSA files only contain first column of
2864 multi-character column annotation labels</li>
2865 <li>Jalview Annotation File generation/parsing consistent
2866 with documentation (e.g. Stockholm annotation can be
2867 exported and re-imported)</li>
2868 <li>PDB files without embedded PDB IDs given a friendly
2870 <li>Find incrementally searches ID string matches as well
2871 as subsequence matches, and correctly reports total number
2875 <li>Better handling of exceptions during sequence
2877 <li>Dasobert generated non-positional feature URL
2878 link text excludes the start_end suffix</li>
2879 <li>DAS feature and source retrieval buttons disabled
2880 when fetch or registry operations in progress.</li>
2881 <li>PDB files retrieved from URLs are cached properly</li>
2882 <li>Sequence description lines properly shared via
2884 <li>Sequence fetcher fetches multiple records for all
2886 <li>Ensured that command line das feature retrieval
2887 completes before alignment figures are generated.</li>
2888 <li>Reduced time taken when opening file browser for
2890 <li>isAligned check prior to calculating tree, PCA or
2891 submitting an MSA to JNet now excludes hidden sequences.</li>
2892 <li>User defined group colours properly recovered
2893 from Jalview projects.</li>
2902 <div align="center">
2903 <strong>2.4.0.b2</strong><br> 28/10/2009
2908 <li>Experimental support for google analytics usage
2910 <li>Jalview privacy settings (user preferences and docs).</li>
2915 <li>Race condition in applet preventing startup in
2917 <li>Exception when feature created from selection beyond
2918 length of sequence.</li>
2919 <li>Allow synthetic PDB files to be imported gracefully</li>
2920 <li>Sequence associated annotation rows associate with
2921 all sequences with a given id</li>
2922 <li>Find function matches case-insensitively for sequence
2923 ID string searches</li>
2924 <li>Non-standard characters do not cause pairwise
2925 alignment to fail with exception</li>
2926 </ul> <em>Application Issues</em>
2928 <li>Sequences are now validated against EMBL database</li>
2929 <li>Sequence fetcher fetches multiple records for all
2931 </ul> <em>InstallAnywhere Issues</em>
2933 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2934 issue with installAnywhere mechanism)</li>
2935 <li>Command line launching of JARs from InstallAnywhere
2936 version (java class versioning error fixed)</li>
2943 <div align="center">
2944 <strong>2.4</strong><br> 27/8/2008
2947 <td><em>User Interface</em>
2949 <li>Linked highlighting of codon and amino acid from
2950 translation and protein products</li>
2951 <li>Linked highlighting of structure associated with
2952 residue mapping to codon position</li>
2953 <li>Sequence Fetcher provides example accession numbers
2954 and 'clear' button</li>
2955 <li>MemoryMonitor added as an option under Desktop's
2957 <li>Extract score function to parse whitespace separated
2958 numeric data in description line</li>
2959 <li>Column labels in alignment annotation can be centred.</li>
2960 <li>Tooltip for sequence associated annotation give name
2962 </ul> <em>Web Services and URL fetching</em>
2964 <li>JPred3 web service</li>
2965 <li>Prototype sequence search client (no public services
2967 <li>Fetch either seed alignment or full alignment from
2969 <li>URL Links created for matching database cross
2970 references as well as sequence ID</li>
2971 <li>URL Links can be created using regular-expressions</li>
2972 </ul> <em>Sequence Database Connectivity</em>
2974 <li>Retrieval of cross-referenced sequences from other
2976 <li>Generalised database reference retrieval and
2977 validation to all fetchable databases</li>
2978 <li>Fetch sequences from DAS sources supporting the
2979 sequence command</li>
2980 </ul> <em>Import and Export</em>
2981 <li>export annotation rows as CSV for spreadsheet import</li>
2982 <li>Jalview projects record alignment dataset associations,
2983 EMBL products, and cDNA sequence mappings</li>
2984 <li>Sequence Group colour can be specified in Annotation
2986 <li>Ad-hoc colouring of group in Annotation File using RGB
2987 triplet as name of colourscheme</li>
2988 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2990 <li>treenode binding for VAMSAS tree exchange</li>
2991 <li>local editing and update of sequences in VAMSAS
2992 alignments (experimental)</li>
2993 <li>Create new or select existing session to join</li>
2994 <li>load and save of vamsas documents</li>
2995 </ul> <em>Application command line</em>
2997 <li>-tree parameter to open trees (introduced for passing
2999 <li>-fetchfrom command line argument to specify nicknames
3000 of DAS servers to query for alignment features</li>
3001 <li>-dasserver command line argument to add new servers
3002 that are also automatically queried for features</li>
3003 <li>-groovy command line argument executes a given groovy
3004 script after all input data has been loaded and parsed</li>
3005 </ul> <em>Applet-Application data exchange</em>
3007 <li>Trees passed as applet parameters can be passed to
3008 application (when using "View in full
3009 application")</li>
3010 </ul> <em>Applet Parameters</em>
3012 <li>feature group display control parameter</li>
3013 <li>debug parameter</li>
3014 <li>showbutton parameter</li>
3015 </ul> <em>Applet API methods</em>
3017 <li>newView public method</li>
3018 <li>Window (current view) specific get/set public methods</li>
3019 <li>Feature display control methods</li>
3020 <li>get list of currently selected sequences</li>
3021 </ul> <em>New Jalview distribution features</em>
3023 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3024 <li>RELEASE file gives build properties for the latest
3025 Jalview release.</li>
3026 <li>Java 1.1 Applet build made easier and donotobfuscate
3027 property controls execution of obfuscator</li>
3028 <li>Build target for generating source distribution</li>
3029 <li>Debug flag for javacc</li>
3030 <li>.jalview_properties file is documented (slightly) in
3031 jalview.bin.Cache</li>
3032 <li>Continuous Build Integration for stable and
3033 development version of Application, Applet and source
3038 <li>selected region output includes visible annotations
3039 (for certain formats)</li>
3040 <li>edit label/displaychar contains existing label/char
3042 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3043 <li>shorter peptide product names from EMBL records</li>
3044 <li>Newick string generator makes compact representations</li>
3045 <li>bootstrap values parsed correctly for tree files with
3047 <li>pathological filechooser bug avoided by not allowing
3048 filenames containing a ':'</li>
3049 <li>Fixed exception when parsing GFF files containing
3050 global sequence features</li>
3051 <li>Alignment datasets are finalized only when number of
3052 references from alignment sequences goes to zero</li>
3053 <li>Close of tree branch colour box without colour
3054 selection causes cascading exceptions</li>
3055 <li>occasional negative imgwidth exceptions</li>
3056 <li>better reporting of non-fatal warnings to user when
3057 file parsing fails.</li>
3058 <li>Save works when Jalview project is default format</li>
3059 <li>Save as dialog opened if current alignment format is
3060 not a valid output format</li>
3061 <li>UniProt canonical names introduced for both das and
3063 <li>Histidine should be midblue (not pink!) in Zappo</li>
3064 <li>error messages passed up and output when data read
3066 <li>edit undo recovers previous dataset sequence when
3067 sequence is edited</li>
3068 <li>allow PDB files without pdb ID HEADER lines (like
3069 those generated by MODELLER) to be read in properly</li>
3070 <li>allow reading of JPred concise files as a normal
3072 <li>Stockholm annotation parsing and alignment properties
3073 import fixed for PFAM records</li>
3074 <li>Structure view windows have correct name in Desktop
3076 <li>annotation consisting of sequence associated scores
3077 can be read and written correctly to annotation file</li>
3078 <li>Aligned cDNA translation to aligned peptide works
3080 <li>Fixed display of hidden sequence markers and
3081 non-italic font for representatives in Applet</li>
3082 <li>Applet Menus are always embedded in applet window on
3084 <li>Newly shown features appear at top of stack (in
3086 <li>Annotations added via parameter not drawn properly
3087 due to null pointer exceptions</li>
3088 <li>Secondary structure lines are drawn starting from
3089 first column of alignment</li>
3090 <li>UniProt XML import updated for new schema release in
3092 <li>Sequence feature to sequence ID match for Features
3093 file is case-insensitive</li>
3094 <li>Sequence features read from Features file appended to
3095 all sequences with matching IDs</li>
3096 <li>PDB structure coloured correctly for associated views
3097 containing a sub-sequence</li>
3098 <li>PDB files can be retrieved by applet from Jar files</li>
3099 <li>feature and annotation file applet parameters
3100 referring to different directories are retrieved correctly</li>
3101 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3102 <li>Fixed application hang whilst waiting for
3103 splash-screen version check to complete</li>
3104 <li>Applet properly URLencodes input parameter values
3105 when passing them to the launchApp service</li>
3106 <li>display name and local features preserved in results
3107 retrieved from web service</li>
3108 <li>Visual delay indication for sequence retrieval and
3109 sequence fetcher initialisation</li>
3110 <li>updated Application to use DAS 1.53e version of
3111 dasobert DAS client</li>
3112 <li>Re-instated Full AMSA support and .amsa file
3114 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3122 <div align="center">
3123 <strong>2.3</strong><br> 9/5/07
3128 <li>Jmol 11.0.2 integration</li>
3129 <li>PDB views stored in Jalview XML files</li>
3130 <li>Slide sequences</li>
3131 <li>Edit sequence in place</li>
3132 <li>EMBL CDS features</li>
3133 <li>DAS Feature mapping</li>
3134 <li>Feature ordering</li>
3135 <li>Alignment Properties</li>
3136 <li>Annotation Scores</li>
3137 <li>Sort by scores</li>
3138 <li>Feature/annotation editing in applet</li>
3143 <li>Headless state operation in 2.2.1</li>
3144 <li>Incorrect and unstable DNA pairwise alignment</li>
3145 <li>Cut and paste of sequences with annotation</li>
3146 <li>Feature group display state in XML</li>
3147 <li>Feature ordering in XML</li>
3148 <li>blc file iteration selection using filename # suffix</li>
3149 <li>Stockholm alignment properties</li>
3150 <li>Stockhom alignment secondary structure annotation</li>
3151 <li>2.2.1 applet had no feature transparency</li>
3152 <li>Number pad keys can be used in cursor mode</li>
3153 <li>Structure Viewer mirror image resolved</li>
3160 <div align="center">
3161 <strong>2.2.1</strong><br> 12/2/07
3166 <li>Non standard characters can be read and displayed
3167 <li>Annotations/Features can be imported/exported to the
3169 <li>Applet allows editing of sequence/annotation/group
3170 name & description
3171 <li>Preference setting to display sequence name in
3173 <li>Annotation file format extended to allow
3174 Sequence_groups to be defined
3175 <li>Default opening of alignment overview panel can be
3176 specified in preferences
3177 <li>PDB residue numbering annotation added to associated
3183 <li>Applet crash under certain Linux OS with Java 1.6
3185 <li>Annotation file export / import bugs fixed
3186 <li>PNG / EPS image output bugs fixed
3192 <div align="center">
3193 <strong>2.2</strong><br> 27/11/06
3198 <li>Multiple views on alignment
3199 <li>Sequence feature editing
3200 <li>"Reload" alignment
3201 <li>"Save" to current filename
3202 <li>Background dependent text colour
3203 <li>Right align sequence ids
3204 <li>User-defined lower case residue colours
3207 <li>Menu item accelerator keys
3208 <li>Control-V pastes to current alignment
3209 <li>Cancel button for DAS Feature Fetching
3210 <li>PCA and PDB Viewers zoom via mouse roller
3211 <li>User-defined sub-tree colours and sub-tree selection
3213 <li>'New Window' button on the 'Output to Text box'
3218 <li>New memory efficient Undo/Redo System
3219 <li>Optimised symbol lookups and conservation/consensus
3221 <li>Region Conservation/Consensus recalculated after
3223 <li>Fixed Remove Empty Columns Bug (empty columns at end
3225 <li>Slowed DAS Feature Fetching for increased robustness.
3227 <li>Made angle brackets in ASCII feature descriptions
3229 <li>Re-instated Zoom function for PCA
3230 <li>Sequence descriptions conserved in web service
3232 <li>UniProt ID discoverer uses any word separated by
3234 <li>WsDbFetch query/result association resolved
3235 <li>Tree leaf to sequence mapping improved
3236 <li>Smooth fonts switch moved to FontChooser dialog box.
3243 <div align="center">
3244 <strong>2.1.1</strong><br> 12/9/06
3249 <li>Copy consensus sequence to clipboard</li>
3254 <li>Image output - rightmost residues are rendered if
3255 sequence id panel has been resized</li>
3256 <li>Image output - all offscreen group boundaries are
3258 <li>Annotation files with sequence references - all
3259 elements in file are relative to sequence position</li>
3260 <li>Mac Applet users can use Alt key for group editing</li>
3266 <div align="center">
3267 <strong>2.1</strong><br> 22/8/06
3272 <li>MAFFT Multiple Alignment in default Web Service list</li>
3273 <li>DAS Feature fetching</li>
3274 <li>Hide sequences and columns</li>
3275 <li>Export Annotations and Features</li>
3276 <li>GFF file reading / writing</li>
3277 <li>Associate structures with sequences from local PDB
3279 <li>Add sequences to exisiting alignment</li>
3280 <li>Recently opened files / URL lists</li>
3281 <li>Applet can launch the full application</li>
3282 <li>Applet has transparency for features (Java 1.2
3284 <li>Applet has user defined colours parameter</li>
3285 <li>Applet can load sequences from parameter
3286 "sequence<em>x</em>"
3292 <li>Redundancy Panel reinstalled in the Applet</li>
3293 <li>Monospaced font - EPS / rescaling bug fixed</li>
3294 <li>Annotation files with sequence references bug fixed</li>
3300 <div align="center">
3301 <strong>2.08.1</strong><br> 2/5/06
3306 <li>Change case of selected region from Popup menu</li>
3307 <li>Choose to match case when searching</li>
3308 <li>Middle mouse button and mouse movement can compress /
3309 expand the visible width and height of the alignment</li>
3314 <li>Annotation Panel displays complete JNet results</li>
3320 <div align="center">
3321 <strong>2.08b</strong><br> 18/4/06
3327 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3328 <li>Righthand label on wrapped alignments shows correct
3335 <div align="center">
3336 <strong>2.08</strong><br> 10/4/06
3341 <li>Editing can be locked to the selection area</li>
3342 <li>Keyboard editing</li>
3343 <li>Create sequence features from searches</li>
3344 <li>Precalculated annotations can be loaded onto
3346 <li>Features file allows grouping of features</li>
3347 <li>Annotation Colouring scheme added</li>
3348 <li>Smooth fonts off by default - Faster rendering</li>
3349 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3354 <li>Drag & Drop fixed on Linux</li>
3355 <li>Jalview Archive file faster to load/save, sequence
3356 descriptions saved.</li>
3362 <div align="center">
3363 <strong>2.07</strong><br> 12/12/05
3368 <li>PDB Structure Viewer enhanced</li>
3369 <li>Sequence Feature retrieval and display enhanced</li>
3370 <li>Choose to output sequence start-end after sequence
3371 name for file output</li>
3372 <li>Sequence Fetcher WSDBFetch@EBI</li>
3373 <li>Applet can read feature files, PDB files and can be
3374 used for HTML form input</li>
3379 <li>HTML output writes groups and features</li>
3380 <li>Group editing is Control and mouse click</li>
3381 <li>File IO bugs</li>
3387 <div align="center">
3388 <strong>2.06</strong><br> 28/9/05
3393 <li>View annotations in wrapped mode</li>
3394 <li>More options for PCA viewer</li>
3399 <li>GUI bugs resolved</li>
3400 <li>Runs with -nodisplay from command line</li>
3406 <div align="center">
3407 <strong>2.05b</strong><br> 15/9/05
3412 <li>Choose EPS export as lineart or text</li>
3413 <li>Jar files are executable</li>
3414 <li>Can read in Uracil - maps to unknown residue</li>
3419 <li>Known OutOfMemory errors give warning message</li>
3420 <li>Overview window calculated more efficiently</li>
3421 <li>Several GUI bugs resolved</li>
3427 <div align="center">
3428 <strong>2.05</strong><br> 30/8/05
3433 <li>Edit and annotate in "Wrapped" view</li>
3438 <li>Several GUI bugs resolved</li>
3444 <div align="center">
3445 <strong>2.04</strong><br> 24/8/05
3450 <li>Hold down mouse wheel & scroll to change font
3456 <li>Improved JPred client reliability</li>
3457 <li>Improved loading of Jalview files</li>
3463 <div align="center">
3464 <strong>2.03</strong><br> 18/8/05
3469 <li>Set Proxy server name and port in preferences</li>
3470 <li>Multiple URL links from sequence ids</li>
3471 <li>User Defined Colours can have a scheme name and added
3473 <li>Choose to ignore gaps in consensus calculation</li>
3474 <li>Unix users can set default web browser</li>
3475 <li>Runs without GUI for batch processing</li>
3476 <li>Dynamically generated Web Service Menus</li>
3481 <li>InstallAnywhere download for Sparc Solaris</li>
3487 <div align="center">
3488 <strong>2.02</strong><br> 18/7/05
3494 <li>Copy & Paste order of sequences maintains
3495 alignment order.</li>
3501 <div align="center">
3502 <strong>2.01</strong><br> 12/7/05
3507 <li>Use delete key for deleting selection.</li>
3508 <li>Use Mouse wheel to scroll sequences.</li>
3509 <li>Help file updated to describe how to add alignment
3511 <li>Version and build date written to build properties
3513 <li>InstallAnywhere installation will check for updates
3514 at launch of Jalview.</li>
3519 <li>Delete gaps bug fixed.</li>
3520 <li>FileChooser sorts columns.</li>
3521 <li>Can remove groups one by one.</li>
3522 <li>Filechooser icons installed.</li>
3523 <li>Finder ignores return character when searching.
3524 Return key will initiate a search.<br>
3531 <div align="center">
3532 <strong>2.0</strong><br> 20/6/05
3537 <li>New codebase</li>