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.2.10.2b1">2.10.2b1</a><br />
74 <em>7/9/2017</em></strong>
77 <td><div align="left">
81 <!-- JAL-2588 -->Show gaps in overview window by colouring
82 in grey (sequences used to be coloured grey, and gaps were
86 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
90 <!-- JAL-2587 -->Overview updates immediately on increase
91 in size and progress bar shown as higher resolution
92 overview is recalculated
97 <td><div align="left">
101 <!-- JAL-2664 -->Overview window redraws every hidden
102 column region row by row
105 <!-- JAL-2681 -->duplicate protein sequences shown after
106 retrieving Ensembl crossrefs for sequences from Uniprot
109 <!-- JAL-2603 -->Overview window throws NPE if show boxes
110 format setting is unticked
113 <!-- JAL-2610 -->Groups are coloured wrongly in overview
114 if group has show boxes format setting unticked
117 <!-- JAL-2672,JAL-2665 -->Redraw problems when
118 autoscrolling whilst dragging current selection group to
119 include sequences and columns not currently displayed
122 <!-- JAL-2691 -->Not all chains are mapped when multimeric
123 assemblies are imported via CIF file
126 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
127 displayed when threshold or conservation colouring is also
131 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
135 <!-- JAL-2673 -->Jalview continues to scroll after
136 dragging a selected region off the visible region of the
140 <!-- JAL-2724 -->Cannot apply annotation based
141 colourscheme to all groups in a view
144 <!-- JAL-2511 -->IDs don't line up with sequences
145 initially after font size change using the Font chooser or
152 <td width="60" nowrap>
154 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
157 <td><div align="left">
158 <em>Calculations</em>
162 <!-- JAL-1933 -->Occupancy annotation row shows number of
163 ungapped positions in each column of the alignment.
166 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
167 a calculation dialog box
170 <!-- JAL-2379 -->Revised implementation of PCA for speed
171 and memory efficiency (~30x faster)
174 <!-- JAL-2403 -->Revised implementation of sequence
175 similarity scores as used by Tree, PCA, Shading Consensus
176 and other calculations
179 <!-- JAL-2416 -->Score matrices are stored as resource
180 files within the Jalview codebase
183 <!-- JAL-2500 -->Trees computed on Sequence Feature
184 Similarity may have different topology due to increased
191 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
192 model for alignments and groups
195 <!-- JAL-384 -->Custom shading schemes created via groovy
202 <!-- JAL-2526 -->Efficiency improvements for interacting
203 with alignment and overview windows
206 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
210 <!-- JAL-2388 -->Hidden columns and sequences can be
214 <!-- JAL-2611 -->Click-drag in visible area allows fine
215 adjustment of visible position
219 <em>Data import/export</em>
222 <!-- JAL-2535 -->Posterior probability annotation from
223 Stockholm files imported as sequence associated annotation
226 <!-- JAL-2507 -->More robust per-sequence positional
227 annotation input/output via stockholm flatfile
230 <!-- JAL-2533 -->Sequence names don't include file
231 extension when importing structure files without embedded
232 names or PDB accessions
235 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
236 format sequence substitution matrices
239 <em>User Interface</em>
242 <!-- JAL-2447 --> Experimental Features Checkbox in
243 Desktop's Tools menu to hide or show untested features in
247 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
248 via Overview or sequence motif search operations
251 <!-- JAL-2547 -->Amend sequence features dialog box can be
252 opened by double clicking gaps within sequence feature
256 <!-- JAL-1476 -->Status bar message shown when not enough
257 aligned positions were available to create a 3D structure
261 <em>3D Structure</em>
264 <!-- JAL-2430 -->Hidden regions in alignment views are not
265 coloured in linked structure views
268 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
269 file-based command exchange
272 <!-- JAL-2375 -->Structure chooser automatically shows
273 Cached Structures rather than querying the PDBe if
274 structures are already available for sequences
277 <!-- JAL-2520 -->Structures imported via URL are cached in
278 the Jalview project rather than downloaded again when the
282 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
283 to transfer Chimera's structure attributes as Jalview
284 features, and vice-versa (<strong>Experimental
288 <em>Web Services</em>
291 <!-- JAL-2549 -->Updated JABAWS client to v2.2
294 <!-- JAL-2335 -->Filter non-standard amino acids and
295 nucleotides when submitting to AACon and other MSA
299 <!-- JAL-2316, -->URLs for viewing database
300 cross-references provided by identifiers.org and the
308 <!-- JAL-2344 -->FileFormatI interface for describing and
309 identifying file formats (instead of String constants)
312 <!-- JAL-2228 -->FeatureCounter script refactored for
313 efficiency when counting all displayed features (not
314 backwards compatible with 2.10.1)
317 <em>Example files</em>
320 <!-- JAL-2631 -->Graduated feature colour style example
321 included in the example feature file
324 <em>Documentation</em>
327 <!-- JAL-2339 -->Release notes reformatted for readability
328 with the built-in Java help viewer
331 <!-- JAL-1644 -->Find documentation updated with 'search
332 sequence description' option
338 <!-- JAL-2485, -->External service integration tests for
339 Uniprot REST Free Text Search Client
342 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
345 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
350 <td><div align="left">
351 <em>Calculations</em>
354 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
355 matrix - C->R should be '-3'<br />Old matrix restored
356 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
358 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
359 Jalview's treatment of gaps in PCA and substitution matrix
360 based Tree calculations.<br /> <br />In earlier versions
361 of Jalview, gaps matching gaps were penalised, and gaps
362 matching non-gaps penalised even more. In the PCA
363 calculation, gaps were actually treated as non-gaps - so
364 different costs were applied, which meant Jalview's PCAs
365 were different to those produced by SeqSpace.<br />Jalview
366 now treats gaps in the same way as SeqSpace (ie it scores
367 them as 0). <br /> <br />Enter the following in the
368 Groovy console to restore pre-2.10.2 behaviour:<br />
369 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
370 // for 2.10.1 mode <br />
371 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
372 // to restore 2.10.2 mode <br /> <br /> <em>Note:
373 these settings will affect all subsequent tree and PCA
374 calculations (not recommended)</em></li>
376 <!-- JAL-2424 -->Fixed off-by-one bug that affected
377 scaling of branch lengths for trees computed using
378 Sequence Feature Similarity.
381 <!-- JAL-2377 -->PCA calculation could hang when
382 generating output report when working with highly
386 <!-- JAL-2544 --> Sort by features includes features to
387 right of selected region when gaps present on right-hand
391 <em>User Interface</em>
394 <!-- JAL-2346 -->Reopening Colour by annotation dialog
395 doesn't reselect a specific sequence's associated
396 annotation after it was used for colouring a view
399 <!-- JAL-2419 -->Current selection lost if popup menu
400 opened on a region of alignment without groups
403 <!-- JAL-2374 -->Popup menu not always shown for regions
404 of an alignment with overlapping groups
407 <!-- JAL-2310 -->Finder double counts if both a sequence's
408 name and description match
411 <!-- JAL-2370 -->Hiding column selection containing two
412 hidden regions results in incorrect hidden regions
415 <!-- JAL-2386 -->'Apply to all groups' setting when
416 changing colour does not apply Conservation slider value
420 <!-- JAL-2373 -->Percentage identity and conservation menu
421 items do not show a tick or allow shading to be disabled
424 <!-- JAL-2385 -->Conservation shading or PID threshold
425 lost when base colourscheme changed if slider not visible
428 <!-- JAL-2547 -->Sequence features shown in tooltip for
429 gaps before start of features
432 <!-- JAL-2623 -->Graduated feature colour threshold not
433 restored to UI when feature colour is edited
436 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
437 a time when scrolling vertically in wrapped mode.
440 <!-- JAL-2630 -->Structure and alignment overview update
441 as graduate feature colour settings are modified via the
445 <!-- JAL-2034 -->Overview window doesn't always update
446 when a group defined on the alignment is resized
449 <!-- JAL-2605 -->Mouseovers on left/right scale region in
450 wrapped view result in positional status updates
454 <!-- JAL-2563 -->Status bar doesn't show position for
455 ambiguous amino acid and nucleotide symbols
458 <!-- JAL-2602 -->Copy consensus sequence failed if
459 alignment included gapped columns
462 <!-- JAL-2473 -->Minimum size set for Jalview windows so
463 widgets don't permanently disappear
466 <!-- JAL-2503 -->Cannot select or filter quantitative
467 annotation that are shown only as column labels (e.g.
468 T-Coffee column reliability scores)
471 <!-- JAL-2594 -->Exception thrown if trying to create a
472 sequence feature on gaps only
475 <!-- JAL-2504 -->Features created with 'New feature'
476 button from a Find inherit previously defined feature type
477 rather than the Find query string
480 <!-- JAL-2423 -->incorrect title in output window when
481 exporting tree calculated in Jalview
484 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
485 and then revealing them reorders sequences on the
489 <!-- JAL-964 -->Group panel in sequence feature settings
490 doesn't update to reflect available set of groups after
491 interactively adding or modifying features
494 <!-- JAL-2225 -->Sequence Database chooser unusable on
498 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
499 only excluded gaps in current sequence and ignored
506 <!-- JAL-2421 -->Overview window visible region moves
507 erratically when hidden rows or columns are present
510 <!-- JAL-2362 -->Per-residue colourschemes applied via the
511 Structure Viewer's colour menu don't correspond to
515 <!-- JAL-2405 -->Protein specific colours only offered in
516 colour and group colour menu for protein alignments
519 <!-- JAL-2385 -->Colour threshold slider doesn't update to
520 reflect currently selected view or group's shading
524 <!-- JAL-2624 -->Feature colour thresholds not respected
525 when rendered on overview and structures when opacity at
529 <!-- JAL-2589 -->User defined gap colour not shown in
530 overview when features overlaid on alignment
533 <em>Data import/export</em>
536 <!-- JAL-2576 -->Very large alignments take a long time to
540 <!-- JAL-2507 -->Per-sequence RNA secondary structures
541 added after a sequence was imported are not written to
545 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
546 when importing RNA secondary structure via Stockholm
549 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
550 not shown in correct direction for simple pseudoknots
553 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
554 with lightGray or darkGray via features file (but can
558 <!-- JAL-2383 -->Above PID colour threshold not recovered
559 when alignment view imported from project
562 <!-- JAL-2520,JAL-2465 -->No mappings generated between
563 structure and sequences extracted from structure files
564 imported via URL and viewed in Jmol
567 <!-- JAL-2520 -->Structures loaded via URL are saved in
568 Jalview Projects rather than fetched via URL again when
569 the project is loaded and the structure viewed
572 <em>Web Services</em>
575 <!-- JAL-2519 -->EnsemblGenomes example failing after
576 release of Ensembl v.88
579 <!-- JAL-2366 -->Proxy server address and port always
580 appear enabled in Preferences->Connections
583 <!-- JAL-2461 -->DAS registry not found exceptions
584 removed from console output
587 <!-- JAL-2582 -->Cannot retrieve protein products from
588 Ensembl by Peptide ID
591 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
592 created from SIFTs, and spurious 'Couldn't open structure
593 in Chimera' errors raised after April 2017 update (problem
594 due to 'null' string rather than empty string used for
595 residues with no corresponding PDB mapping).
598 <em>Application UI</em>
601 <!-- JAL-2361 -->User Defined Colours not added to Colour
605 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
606 case' residues (button in colourscheme editor debugged and
607 new documentation and tooltips added)
610 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
611 doesn't restore group-specific text colour thresholds
614 <!-- JAL-2243 -->Feature settings panel does not update as
615 new features are added to alignment
618 <!-- JAL-2532 -->Cancel in feature settings reverts
619 changes to feature colours via the Amend features dialog
622 <!-- JAL-2506 -->Null pointer exception when attempting to
623 edit graduated feature colour via amend features dialog
627 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
628 selection menu changes colours of alignment views
631 <!-- JAL-2426 -->Spurious exceptions in console raised
632 from alignment calculation workers after alignment has
636 <!-- JAL-1608 -->Typo in selection popup menu - Create
637 groups now 'Create Group'
640 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
641 Create/Undefine group doesn't always work
644 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
645 shown again after pressing 'Cancel'
648 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
649 adjusts start position in wrap mode
652 <!-- JAL-2563 -->Status bar doesn't show positions for
653 ambiguous amino acids
656 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
657 CDS/Protein view after CDS sequences added for aligned
661 <!-- JAL-2592 -->User defined colourschemes called 'User
662 Defined' don't appear in Colours menu
668 <!-- JAL-2468 -->Switching between Nucleotide and Protein
669 score models doesn't always result in an updated PCA plot
672 <!-- JAL-2442 -->Features not rendered as transparent on
673 overview or linked structure view
676 <!-- JAL-2372 -->Colour group by conservation doesn't
680 <!-- JAL-2517 -->Hitting Cancel after applying
681 user-defined colourscheme doesn't restore original
688 <!-- JAL-2314 -->Unit test failure:
689 jalview.ws.jabaws.RNAStructExportImport setup fails
692 <!-- JAL-2307 -->Unit test failure:
693 jalview.ws.sifts.SiftsClientTest due to compatibility
694 problems with deep array comparison equality asserts in
695 successive versions of TestNG
698 <!-- JAL-2479 -->Relocated StructureChooserTest and
699 ParameterUtilsTest Unit tests to Network suite
702 <em>New Known Issues</em>
705 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
706 phase after a sequence motif find operation
709 <!-- JAL-2550 -->Importing annotation file with rows
710 containing just upper and lower case letters are
711 interpreted as WUSS RNA secondary structure symbols
714 <!-- JAL-2590 -->Cannot load and display Newick trees
715 reliably from eggnog Ortholog database
718 <!-- JAL-2468 -->Status bar shows 'Marked x columns
719 containing features of type Highlight' when 'B' is pressed
720 to mark columns containing highlighted regions.
723 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
724 doesn't always add secondary structure annotation.
729 <td width="60" nowrap>
731 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
734 <td><div align="left">
738 <!-- JAL-98 -->Improved memory usage: sparse arrays used
739 for all consensus calculations
742 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
745 <li>Updated Jalview's Certum code signing certificate
751 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
752 set of database cross-references, sorted alphabetically
755 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
756 from database cross references. Users with custom links
757 will receive a <a href="webServices/urllinks.html#warning">warning
758 dialog</a> asking them to update their preferences.
761 <!-- JAL-2287-->Cancel button and escape listener on
762 dialog warning user about disconnecting Jalview from a
766 <!-- JAL-2320-->Jalview's Chimera control window closes if
767 the Chimera it is connected to is shut down
770 <!-- JAL-1738-->New keystroke (B) and Select highlighted
771 columns menu item to mark columns containing highlighted
772 regions (e.g. from structure selections or results of a
776 <!-- JAL-2284-->Command line option for batch-generation
777 of HTML pages rendering alignment data with the BioJS
787 <!-- JAL-2286 -->Columns with more than one modal residue
788 are not coloured or thresholded according to percent
789 identity (first observed in Jalview 2.8.2)
792 <!-- JAL-2301 -->Threonine incorrectly reported as not
796 <!-- JAL-2318 -->Updates to documentation pages (above PID
797 threshold, amino acid properties)
800 <!-- JAL-2292 -->Lower case residues in sequences are not
801 reported as mapped to residues in a structure file in the
805 <!--JAL-2324 -->Identical features with non-numeric scores
806 could be added multiple times to a sequence
809 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
810 bond features shown as two highlighted residues rather
811 than a range in linked structure views, and treated
812 correctly when selecting and computing trees from features
815 <!-- JAL-2281-->Custom URL links for database
816 cross-references are matched to database name regardless
824 <!-- JAL-2282-->Custom URL links for specific database
825 names without regular expressions also offer links from
829 <!-- JAL-2315-->Removing a single configured link in the
830 URL links pane in Connections preferences doesn't actually
831 update Jalview configuration
834 <!-- JAL-2272-->CTRL-Click on a selected region to open
835 the alignment area popup menu doesn't work on El-Capitan
838 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
839 files with similarly named sequences if dropped onto the
843 <!-- JAL-2312 -->Additional mappings are shown for PDB
844 entries where more chains exist in the PDB accession than
845 are reported in the SIFTS file
848 <!-- JAL-2317-->Certain structures do not get mapped to
849 the structure view when displayed with Chimera
852 <!-- JAL-2317-->No chains shown in the Chimera view
853 panel's View->Show Chains submenu
856 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
857 work for wrapped alignment views
860 <!--JAL-2197 -->Rename UI components for running JPred
861 predictions from 'JNet' to 'JPred'
864 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
865 corrupted when annotation panel vertical scroll is not at
869 <!--JAL-2332 -->Attempting to view structure for Hen
870 lysozyme results in a PDB Client error dialog box
873 <!-- JAL-2319 -->Structure View's mapping report switched
874 ranges for PDB and sequence for SIFTS
877 SIFTS 'Not_Observed' residues mapped to non-existant
881 <!-- <em>New Known Issues</em>
888 <td width="60" nowrap>
890 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
891 <em>25/10/2016</em></strong>
894 <td><em>Application</em>
896 <li>3D Structure chooser opens with 'Cached structures'
897 view if structures already loaded</li>
898 <li>Progress bar reports models as they are loaded to
905 <li>Colour by conservation always enabled and no tick
906 shown in menu when BLOSUM or PID shading applied</li>
907 <li>FER1_ARATH and FER2_ARATH labels were switched in
908 example sequences/projects/trees</li>
912 <li>Jalview projects with views of local PDB structure
913 files saved on Windows cannot be opened on OSX</li>
914 <li>Multiple structure views can be opened and superposed
915 without timeout for structures with multiple models or
916 multiple sequences in alignment</li>
917 <li>Cannot import or associated local PDB files without a
918 PDB ID HEADER line</li>
919 <li>RMSD is not output in Jmol console when superposition
921 <li>Drag and drop of URL from Browser fails for Linux and
922 OSX versions earlier than El Capitan</li>
923 <li>ENA client ignores invalid content from ENA server</li>
924 <li>Exceptions are not raised in console when ENA client
925 attempts to fetch non-existent IDs via Fetch DB Refs UI
927 <li>Exceptions are not raised in console when a new view
928 is created on the alignment</li>
929 <li>OSX right-click fixed for group selections: CMD-click
930 to insert/remove gaps in groups and CTRL-click to open group
933 <em>Build and deployment</em>
935 <li>URL link checker now copes with multi-line anchor
938 <em>New Known Issues</em>
940 <li>Drag and drop from URL links in browsers do not work
947 <td width="60" nowrap>
949 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
955 <!-- JAL-2124 -->Updated Spanish translations.
958 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
959 for importing structure data to Jalview. Enables mmCIF and
963 <!-- JAL-192 --->Alignment ruler shows positions relative to
967 <!-- JAL-2202 -->Position/residue shown in status bar when
968 mousing over sequence associated annotation
971 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
975 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
976 '()', canonical '[]' and invalid '{}' base pair populations
980 <!-- JAL-2092 -->Feature settings popup menu options for
981 showing or hiding columns containing a feature
984 <!-- JAL-1557 -->Edit selected group by double clicking on
985 group and sequence associated annotation labels
988 <!-- JAL-2236 -->Sequence name added to annotation label in
989 select/hide columns by annotation and colour by annotation
993 </ul> <em>Application</em>
996 <!-- JAL-2050-->Automatically hide introns when opening a
1000 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1004 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1005 structure mappings with the EMBL-EBI PDBe SIFTS database
1008 <!-- JAL-2079 -->Updated download sites used for Rfam and
1009 Pfam sources to xfam.org
1012 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1015 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1016 over sequences in Jalview
1019 <!-- JAL-2027-->Support for reverse-complement coding
1020 regions in ENA and EMBL
1023 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1024 for record retrieval via ENA rest API
1027 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1031 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1032 groovy script execution
1035 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1036 alignment window's Calculate menu
1039 <!-- JAL-1812 -->Allow groovy scripts that call
1040 Jalview.getAlignFrames() to run in headless mode
1043 <!-- JAL-2068 -->Support for creating new alignment
1044 calculation workers from groovy scripts
1047 <!-- JAL-1369 --->Store/restore reference sequence in
1051 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1052 associations are now saved/restored from project
1055 <!-- JAL-1993 -->Database selection dialog always shown
1056 before sequence fetcher is opened
1059 <!-- JAL-2183 -->Double click on an entry in Jalview's
1060 database chooser opens a sequence fetcher
1063 <!-- JAL-1563 -->Free-text search client for UniProt using
1064 the UniProt REST API
1067 <!-- JAL-2168 -->-nonews command line parameter to prevent
1068 the news reader opening
1071 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1072 querying stored in preferences
1075 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1079 <!-- JAL-1977-->Tooltips shown on database chooser
1082 <!-- JAL-391 -->Reverse complement function in calculate
1083 menu for nucleotide sequences
1086 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1087 and feature counts preserves alignment ordering (and
1088 debugged for complex feature sets).
1091 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1092 viewing structures with Jalview 2.10
1095 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1096 genome, transcript CCDS and gene ids via the Ensembl and
1097 Ensembl Genomes REST API
1100 <!-- JAL-2049 -->Protein sequence variant annotation
1101 computed for 'sequence_variant' annotation on CDS regions
1105 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1109 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1110 Ref Fetcher fails to match, or otherwise updates sequence
1111 data from external database records.
1114 <!-- JAL-2154 -->Revised Jalview Project format for
1115 efficient recovery of sequence coding and alignment
1116 annotation relationships.
1118 </ul> <!-- <em>Applet</em>
1129 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1133 <!-- JAL-2018-->Export features in Jalview format (again)
1134 includes graduated colourschemes
1137 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1138 working with big alignments and lots of hidden columns
1141 <!-- JAL-2053-->Hidden column markers not always rendered
1142 at right of alignment window
1145 <!-- JAL-2067 -->Tidied up links in help file table of
1149 <!-- JAL-2072 -->Feature based tree calculation not shown
1153 <!-- JAL-2075 -->Hidden columns ignored during feature
1154 based tree calculation
1157 <!-- JAL-2065 -->Alignment view stops updating when show
1158 unconserved enabled for group on alignment
1161 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1165 <!-- JAL-2146 -->Alignment column in status incorrectly
1166 shown as "Sequence position" when mousing over
1170 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1171 hidden columns present
1174 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1175 user created annotation added to alignment
1178 <!-- JAL-1841 -->RNA Structure consensus only computed for
1179 '()' base pair annotation
1182 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1183 in zero scores for all base pairs in RNA Structure
1187 <!-- JAL-2174-->Extend selection with columns containing
1191 <!-- JAL-2275 -->Pfam format writer puts extra space at
1192 beginning of sequence
1195 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1199 <!-- JAL-2238 -->Cannot create groups on an alignment from
1200 from a tree when t-coffee scores are shown
1203 <!-- JAL-1836,1967 -->Cannot import and view PDB
1204 structures with chains containing negative resnums (4q4h)
1207 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1211 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1212 to Clustal, PIR and PileUp output
1215 <!-- JAL-2008 -->Reordering sequence features that are
1216 not visible causes alignment window to repaint
1219 <!-- JAL-2006 -->Threshold sliders don't work in
1220 graduated colour and colour by annotation row for e-value
1221 scores associated with features and annotation rows
1224 <!-- JAL-1797 -->amino acid physicochemical conservation
1225 calculation should be case independent
1228 <!-- JAL-2173 -->Remove annotation also updates hidden
1232 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1233 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1234 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1237 <!-- JAL-2065 -->Null pointer exceptions and redraw
1238 problems when reference sequence defined and 'show
1239 non-conserved' enabled
1242 <!-- JAL-1306 -->Quality and Conservation are now shown on
1243 load even when Consensus calculation is disabled
1246 <!-- JAL-1932 -->Remove right on penultimate column of
1247 alignment does nothing
1250 <em>Application</em>
1253 <!-- JAL-1552-->URLs and links can't be imported by
1254 drag'n'drop on OSX when launched via webstart (note - not
1255 yet fixed for El Capitan)
1258 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1259 output when running on non-gb/us i18n platforms
1262 <!-- JAL-1944 -->Error thrown when exporting a view with
1263 hidden sequences as flat-file alignment
1266 <!-- JAL-2030-->InstallAnywhere distribution fails when
1270 <!-- JAL-2080-->Jalview very slow to launch via webstart
1271 (also hotfix for 2.9.0b2)
1274 <!-- JAL-2085 -->Cannot save project when view has a
1275 reference sequence defined
1278 <!-- JAL-1011 -->Columns are suddenly selected in other
1279 alignments and views when revealing hidden columns
1282 <!-- JAL-1989 -->Hide columns not mirrored in complement
1283 view in a cDNA/Protein splitframe
1286 <!-- JAL-1369 -->Cannot save/restore representative
1287 sequence from project when only one sequence is
1291 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1292 in Structure Chooser
1295 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1296 structure consensus didn't refresh annotation panel
1299 <!-- JAL-1962 -->View mapping in structure view shows
1300 mappings between sequence and all chains in a PDB file
1303 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1304 dialogs format columns correctly, don't display array
1305 data, sort columns according to type
1308 <!-- JAL-1975 -->Export complete shown after destination
1309 file chooser is cancelled during an image export
1312 <!-- JAL-2025 -->Error when querying PDB Service with
1313 sequence name containing special characters
1316 <!-- JAL-2024 -->Manual PDB structure querying should be
1320 <!-- JAL-2104 -->Large tooltips with broken HTML
1321 formatting don't wrap
1324 <!-- JAL-1128 -->Figures exported from wrapped view are
1325 truncated so L looks like I in consensus annotation
1328 <!-- JAL-2003 -->Export features should only export the
1329 currently displayed features for the current selection or
1333 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1334 after fetching cross-references, and restoring from
1338 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1339 followed in the structure viewer
1342 <!-- JAL-2163 -->Titles for individual alignments in
1343 splitframe not restored from project
1346 <!-- JAL-2145 -->missing autocalculated annotation at
1347 trailing end of protein alignment in transcript/product
1348 splitview when pad-gaps not enabled by default
1351 <!-- JAL-1797 -->amino acid physicochemical conservation
1355 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1356 article has been read (reopened issue due to
1357 internationalisation problems)
1360 <!-- JAL-1960 -->Only offer PDB structures in structure
1361 viewer based on sequence name, PDB and UniProt
1366 <!-- JAL-1976 -->No progress bar shown during export of
1370 <!-- JAL-2213 -->Structures not always superimposed after
1371 multiple structures are shown for one or more sequences.
1374 <!-- JAL-1370 -->Reference sequence characters should not
1375 be replaced with '.' when 'Show unconserved' format option
1379 <!-- JAL-1823 -->Cannot specify chain code when entering
1380 specific PDB id for sequence
1383 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1384 'Export hidden sequences' is enabled, but 'export hidden
1385 columns' is disabled.
1388 <!--JAL-2026-->Best Quality option in structure chooser
1389 selects lowest rather than highest resolution structures
1393 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1394 to sequence mapping in 'View Mappings' report
1397 <!-- JAL-2284 -->Unable to read old Jalview projects that
1398 contain non-XML data added after Jalvew wrote project.
1401 <!-- JAL-2118 -->Newly created annotation row reorders
1402 after clicking on it to create new annotation for a
1405 <!-- may exclude, this is an external service stability issue JAL-1941
1406 -- > RNA 3D structure not added via DSSR service</li> -->
1411 <!-- JAL-2151 -->Incorrect columns are selected when
1412 hidden columns present before start of sequence
1415 <!-- JAL-1986 -->Missing dependencies on applet pages
1419 <!-- JAL-1947 -->Overview pixel size changes when
1420 sequences are hidden in applet
1423 <!-- JAL-1996 -->Updated instructions for applet
1424 deployment on examples pages.
1431 <td width="60" nowrap>
1432 <div align="center">
1433 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1434 <em>16/10/2015</em></strong>
1437 <td><em>General</em>
1439 <li>Time stamps for signed Jalview application and applet
1444 <em>Application</em>
1446 <li>Duplicate group consensus and conservation rows
1447 shown when tree is partitioned</li>
1448 <li>Erratic behaviour when tree partitions made with
1449 multiple cDNA/Protein split views</li>
1455 <td width="60" nowrap>
1456 <div align="center">
1457 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1458 <em>8/10/2015</em></strong>
1461 <td><em>General</em>
1463 <li>Updated Spanish translations of localized text for
1465 </ul> <em>Application</em>
1467 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1468 <li>Signed OSX InstallAnywhere installer<br></li>
1469 <li>Support for per-sequence based annotations in BioJSON</li>
1470 </ul> <em>Applet</em>
1472 <li>Split frame example added to applet examples page</li>
1473 </ul> <em>Build and Deployment</em>
1476 <!-- JAL-1888 -->New ant target for running Jalview's test
1484 <li>Mapping of cDNA to protein in split frames
1485 incorrect when sequence start > 1</li>
1486 <li>Broken images in filter column by annotation dialog
1488 <li>Feature colours not parsed from features file</li>
1489 <li>Exceptions and incomplete link URLs recovered when
1490 loading a features file containing HTML tags in feature
1494 <em>Application</em>
1496 <li>Annotations corrupted after BioJS export and
1498 <li>Incorrect sequence limits after Fetch DB References
1499 with 'trim retrieved sequences'</li>
1500 <li>Incorrect warning about deleting all data when
1501 deleting selected columns</li>
1502 <li>Patch to build system for shipping properly signed
1503 JNLP templates for webstart launch</li>
1504 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1505 unreleased structures for download or viewing</li>
1506 <li>Tab/space/return keystroke operation of EMBL-PDBe
1507 fetcher/viewer dialogs works correctly</li>
1508 <li>Disabled 'minimise' button on Jalview windows
1509 running on OSX to workaround redraw hang bug</li>
1510 <li>Split cDNA/Protein view position and geometry not
1511 recovered from jalview project</li>
1512 <li>Initial enabled/disabled state of annotation menu
1513 sorter 'show autocalculated first/last' corresponds to
1515 <li>Restoring of Clustal, RNA Helices and T-Coffee
1516 color schemes from BioJSON</li>
1520 <li>Reorder sequences mirrored in cDNA/Protein split
1522 <li>Applet with Jmol examples not loading correctly</li>
1528 <td><div align="center">
1529 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1531 <td><em>General</em>
1533 <li>Linked visualisation and analysis of DNA and Protein
1536 <li>Translated cDNA alignments shown as split protein
1537 and DNA alignment views</li>
1538 <li>Codon consensus annotation for linked protein and
1539 cDNA alignment views</li>
1540 <li>Link cDNA or Protein product sequences by loading
1541 them onto Protein or cDNA alignments</li>
1542 <li>Reconstruct linked cDNA alignment from aligned
1543 protein sequences</li>
1546 <li>Jmol integration updated to Jmol v14.2.14</li>
1547 <li>Import and export of Jalview alignment views as <a
1548 href="features/bioJsonFormat.html">BioJSON</a></li>
1549 <li>New alignment annotation file statements for
1550 reference sequences and marking hidden columns</li>
1551 <li>Reference sequence based alignment shading to
1552 highlight variation</li>
1553 <li>Select or hide columns according to alignment
1555 <li>Find option for locating sequences by description</li>
1556 <li>Conserved physicochemical properties shown in amino
1557 acid conservation row</li>
1558 <li>Alignments can be sorted by number of RNA helices</li>
1559 </ul> <em>Application</em>
1561 <li>New cDNA/Protein analysis capabilities
1563 <li>Get Cross-References should open a Split Frame
1564 view with cDNA/Protein</li>
1565 <li>Detect when nucleotide sequences and protein
1566 sequences are placed in the same alignment</li>
1567 <li>Split cDNA/Protein views are saved in Jalview
1572 <li>Use REST API to talk to Chimera</li>
1573 <li>Selected regions in Chimera are highlighted in linked
1574 Jalview windows</li>
1576 <li>VARNA RNA viewer updated to v3.93</li>
1577 <li>VARNA views are saved in Jalview Projects</li>
1578 <li>Pseudoknots displayed as Jalview RNA annotation can
1579 be shown in VARNA</li>
1581 <li>Make groups for selection uses marked columns as well
1582 as the active selected region</li>
1584 <li>Calculate UPGMA and NJ trees using sequence feature
1586 <li>New Export options
1588 <li>New Export Settings dialog to control hidden
1589 region export in flat file generation</li>
1591 <li>Export alignment views for display with the <a
1592 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1594 <li>Export scrollable SVG in HTML page</li>
1595 <li>Optional embedding of BioJSON data when exporting
1596 alignment figures to HTML</li>
1598 <li>3D structure retrieval and display
1600 <li>Free text and structured queries with the PDBe
1602 <li>PDBe Search API based discovery and selection of
1603 PDB structures for a sequence set</li>
1607 <li>JPred4 employed for protein secondary structure
1609 <li>Hide Insertions menu option to hide unaligned columns
1610 for one or a group of sequences</li>
1611 <li>Automatically hide insertions in alignments imported
1612 from the JPred4 web server</li>
1613 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1614 system on OSX<br />LGPL libraries courtesy of <a
1615 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1617 <li>changed 'View nucleotide structure' submenu to 'View
1618 VARNA 2D Structure'</li>
1619 <li>change "View protein structure" menu option to "3D
1622 </ul> <em>Applet</em>
1624 <li>New layout for applet example pages</li>
1625 <li>New parameters to enable SplitFrame view
1626 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1627 <li>New example demonstrating linked viewing of cDNA and
1628 Protein alignments</li>
1629 </ul> <em>Development and deployment</em>
1631 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1632 <li>Include installation type and git revision in build
1633 properties and console log output</li>
1634 <li>Jalview Github organisation, and new github site for
1635 storing BioJsMSA Templates</li>
1636 <li>Jalview's unit tests now managed with TestNG</li>
1639 <!-- <em>General</em>
1641 </ul> --> <!-- issues resolved --> <em>Application</em>
1643 <li>Escape should close any open find dialogs</li>
1644 <li>Typo in select-by-features status report</li>
1645 <li>Consensus RNA secondary secondary structure
1646 predictions are not highlighted in amber</li>
1647 <li>Missing gap character in v2.7 example file means
1648 alignment appears unaligned when pad-gaps is not enabled</li>
1649 <li>First switch to RNA Helices colouring doesn't colour
1650 associated structure views</li>
1651 <li>ID width preference option is greyed out when auto
1652 width checkbox not enabled</li>
1653 <li>Stopped a warning dialog from being shown when
1654 creating user defined colours</li>
1655 <li>'View Mapping' in structure viewer shows sequence
1656 mappings for just that viewer's sequences</li>
1657 <li>Workaround for superposing PDB files containing
1658 multiple models in Chimera</li>
1659 <li>Report sequence position in status bar when hovering
1660 over Jmol structure</li>
1661 <li>Cannot output gaps as '.' symbols with Selection ->
1662 output to text box</li>
1663 <li>Flat file exports of alignments with hidden columns
1664 have incorrect sequence start/end</li>
1665 <li>'Aligning' a second chain to a Chimera structure from
1667 <li>Colour schemes applied to structure viewers don't
1668 work for nucleotide</li>
1669 <li>Loading/cut'n'pasting an empty or invalid file leads
1670 to a grey/invisible alignment window</li>
1671 <li>Exported Jpred annotation from a sequence region
1672 imports to different position</li>
1673 <li>Space at beginning of sequence feature tooltips shown
1674 on some platforms</li>
1675 <li>Chimera viewer 'View | Show Chain' menu is not
1677 <li>'New View' fails with a Null Pointer Exception in
1678 console if Chimera has been opened</li>
1679 <li>Mouseover to Chimera not working</li>
1680 <li>Miscellaneous ENA XML feature qualifiers not
1682 <li>NPE in annotation renderer after 'Extract Scores'</li>
1683 <li>If two structures in one Chimera window, mouseover of
1684 either sequence shows on first structure</li>
1685 <li>'Show annotations' options should not make
1686 non-positional annotations visible</li>
1687 <li>Subsequence secondary structure annotation not shown
1688 in right place after 'view flanking regions'</li>
1689 <li>File Save As type unset when current file format is
1691 <li>Save as '.jar' option removed for saving Jalview
1693 <li>Colour by Sequence colouring in Chimera more
1695 <li>Cannot 'add reference annotation' for a sequence in
1696 several views on same alignment</li>
1697 <li>Cannot show linked products for EMBL / ENA records</li>
1698 <li>Jalview's tooltip wraps long texts containing no
1700 </ul> <em>Applet</em>
1702 <li>Jmol to JalviewLite mouseover/link not working</li>
1703 <li>JalviewLite can't import sequences with ID
1704 descriptions containing angle brackets</li>
1705 </ul> <em>General</em>
1707 <li>Cannot export and reimport RNA secondary structure
1708 via jalview annotation file</li>
1709 <li>Random helix colour palette for colour by annotation
1710 with RNA secondary structure</li>
1711 <li>Mouseover to cDNA from STOP residue in protein
1712 translation doesn't work.</li>
1713 <li>hints when using the select by annotation dialog box</li>
1714 <li>Jmol alignment incorrect if PDB file has alternate CA
1716 <li>FontChooser message dialog appears to hang after
1717 choosing 1pt font</li>
1718 <li>Peptide secondary structure incorrectly imported from
1719 annotation file when annotation display text includes 'e' or
1721 <li>Cannot set colour of new feature type whilst creating
1723 <li>cDNA translation alignment should not be sequence
1724 order dependent</li>
1725 <li>'Show unconserved' doesn't work for lower case
1727 <li>Nucleotide ambiguity codes involving R not recognised</li>
1728 </ul> <em>Deployment and Documentation</em>
1730 <li>Applet example pages appear different to the rest of
1731 www.jalview.org</li>
1732 </ul> <em>Application Known issues</em>
1734 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1735 <li>Misleading message appears after trying to delete
1737 <li>Jalview icon not shown in dock after InstallAnywhere
1738 version launches</li>
1739 <li>Fetching EMBL reference for an RNA sequence results
1740 fails with a sequence mismatch</li>
1741 <li>Corrupted or unreadable alignment display when
1742 scrolling alignment to right</li>
1743 <li>ArrayIndexOutOfBoundsException thrown when remove
1744 empty columns called on alignment with ragged gapped ends</li>
1745 <li>auto calculated alignment annotation rows do not get
1746 placed above or below non-autocalculated rows</li>
1747 <li>Jalview dekstop becomes sluggish at full screen in
1748 ultra-high resolution</li>
1749 <li>Cannot disable consensus calculation independently of
1750 quality and conservation</li>
1751 <li>Mouseover highlighting between cDNA and protein can
1752 become sluggish with more than one splitframe shown</li>
1753 </ul> <em>Applet Known Issues</em>
1755 <li>Core PDB parsing code requires Jmol</li>
1756 <li>Sequence canvas panel goes white when alignment
1757 window is being resized</li>
1763 <td><div align="center">
1764 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1766 <td><em>General</em>
1768 <li>Updated Java code signing certificate donated by
1770 <li>Features and annotation preserved when performing
1771 pairwise alignment</li>
1772 <li>RNA pseudoknot annotation can be
1773 imported/exported/displayed</li>
1774 <li>'colour by annotation' can colour by RNA and
1775 protein secondary structure</li>
1776 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1777 post-hoc with 2.9 release</em>)
1780 </ul> <em>Application</em>
1782 <li>Extract and display secondary structure for sequences
1783 with 3D structures</li>
1784 <li>Support for parsing RNAML</li>
1785 <li>Annotations menu for layout
1787 <li>sort sequence annotation rows by alignment</li>
1788 <li>place sequence annotation above/below alignment
1791 <li>Output in Stockholm format</li>
1792 <li>Internationalisation: improved Spanish (es)
1794 <li>Structure viewer preferences tab</li>
1795 <li>Disorder and Secondary Structure annotation tracks
1796 shared between alignments</li>
1797 <li>UCSF Chimera launch and linked highlighting from
1799 <li>Show/hide all sequence associated annotation rows for
1800 all or current selection</li>
1801 <li>disorder and secondary structure predictions
1802 available as dataset annotation</li>
1803 <li>Per-sequence rna helices colouring</li>
1806 <li>Sequence database accessions imported when fetching
1807 alignments from Rfam</li>
1808 <li>update VARNA version to 3.91</li>
1810 <li>New groovy scripts for exporting aligned positions,
1811 conservation values, and calculating sum of pairs scores.</li>
1812 <li>Command line argument to set default JABAWS server</li>
1813 <li>include installation type in build properties and
1814 console log output</li>
1815 <li>Updated Jalview project format to preserve dataset
1819 <!-- issues resolved --> <em>Application</em>
1821 <li>Distinguish alignment and sequence associated RNA
1822 structure in structure->view->VARNA</li>
1823 <li>Raise dialog box if user deletes all sequences in an
1825 <li>Pressing F1 results in documentation opening twice</li>
1826 <li>Sequence feature tooltip is wrapped</li>
1827 <li>Double click on sequence associated annotation
1828 selects only first column</li>
1829 <li>Redundancy removal doesn't result in unlinked
1830 leaves shown in tree</li>
1831 <li>Undos after several redundancy removals don't undo
1833 <li>Hide sequence doesn't hide associated annotation</li>
1834 <li>User defined colours dialog box too big to fit on
1835 screen and buttons not visible</li>
1836 <li>author list isn't updated if already written to
1837 Jalview properties</li>
1838 <li>Popup menu won't open after retrieving sequence
1840 <li>File open window for associate PDB doesn't open</li>
1841 <li>Left-then-right click on a sequence id opens a
1842 browser search window</li>
1843 <li>Cannot open sequence feature shading/sort popup menu
1844 in feature settings dialog</li>
1845 <li>better tooltip placement for some areas of Jalview
1847 <li>Allow addition of JABAWS Server which doesn't
1848 pass validation</li>
1849 <li>Web services parameters dialog box is too large to
1851 <li>Muscle nucleotide alignment preset obscured by
1853 <li>JABAWS preset submenus don't contain newly
1854 defined user preset</li>
1855 <li>MSA web services warns user if they were launched
1856 with invalid input</li>
1857 <li>Jalview cannot contact DAS Registy when running on
1860 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1861 'Superpose with' submenu not shown when new view
1865 </ul> <!-- <em>Applet</em>
1867 </ul> <em>General</em>
1869 </ul>--> <em>Deployment and Documentation</em>
1871 <li>2G and 1G options in launchApp have no effect on
1872 memory allocation</li>
1873 <li>launchApp service doesn't automatically open
1874 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1876 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1877 InstallAnywhere reports cannot find valid JVM when Java
1878 1.7_055 is available
1880 </ul> <em>Application Known issues</em>
1883 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1884 corrupted or unreadable alignment display when scrolling
1888 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1889 retrieval fails but progress bar continues for DAS retrieval
1890 with large number of ID
1893 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1894 flatfile output of visible region has incorrect sequence
1898 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1899 rna structure consensus doesn't update when secondary
1900 structure tracks are rearranged
1903 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1904 invalid rna structure positional highlighting does not
1905 highlight position of invalid base pairs
1908 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1909 out of memory errors are not raised when saving Jalview
1910 project from alignment window file menu
1913 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1914 Switching to RNA Helices colouring doesn't propagate to
1918 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1919 colour by RNA Helices not enabled when user created
1920 annotation added to alignment
1923 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1924 Jalview icon not shown on dock in Mountain Lion/Webstart
1926 </ul> <em>Applet Known Issues</em>
1929 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1930 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1933 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1934 Jalview and Jmol example not compatible with IE9
1937 <li>Sort by annotation score doesn't reverse order
1943 <td><div align="center">
1944 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1947 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1950 <li>Internationalisation of user interface (usually
1951 called i18n support) and translation for Spanish locale</li>
1952 <li>Define/Undefine group on current selection with
1953 Ctrl-G/Shift Ctrl-G</li>
1954 <li>Improved group creation/removal options in
1955 alignment/sequence Popup menu</li>
1956 <li>Sensible precision for symbol distribution
1957 percentages shown in logo tooltip.</li>
1958 <li>Annotation panel height set according to amount of
1959 annotation when alignment first opened</li>
1960 </ul> <em>Application</em>
1962 <li>Interactive consensus RNA secondary structure
1963 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1964 <li>Select columns containing particular features from
1965 Feature Settings dialog</li>
1966 <li>View all 'representative' PDB structures for selected
1968 <li>Update Jalview project format:
1970 <li>New file extension for Jalview projects '.jvp'</li>
1971 <li>Preserve sequence and annotation dataset (to
1972 store secondary structure annotation,etc)</li>
1973 <li>Per group and alignment annotation and RNA helix
1977 <li>New similarity measures for PCA and Tree calculation
1979 <li>Experimental support for retrieval and viewing of
1980 flanking regions for an alignment</li>
1984 <!-- issues resolved --> <em>Application</em>
1986 <li>logo keeps spinning and status remains at queued or
1987 running after job is cancelled</li>
1988 <li>cannot export features from alignments imported from
1989 Jalview/VAMSAS projects</li>
1990 <li>Buggy slider for web service parameters that take
1992 <li>Newly created RNA secondary structure line doesn't
1993 have 'display all symbols' flag set</li>
1994 <li>T-COFFEE alignment score shading scheme and other
1995 annotation shading not saved in Jalview project</li>
1996 <li>Local file cannot be loaded in freshly downloaded
1998 <li>Jalview icon not shown on dock in Mountain
2000 <li>Load file from desktop file browser fails</li>
2001 <li>Occasional NPE thrown when calculating large trees</li>
2002 <li>Cannot reorder or slide sequences after dragging an
2003 alignment onto desktop</li>
2004 <li>Colour by annotation dialog throws NPE after using
2005 'extract scores' function</li>
2006 <li>Loading/cut'n'pasting an empty file leads to a grey
2007 alignment window</li>
2008 <li>Disorder thresholds rendered incorrectly after
2009 performing IUPred disorder prediction</li>
2010 <li>Multiple group annotated consensus rows shown when
2011 changing 'normalise logo' display setting</li>
2012 <li>Find shows blank dialog after 'finished searching' if
2013 nothing matches query</li>
2014 <li>Null Pointer Exceptions raised when sorting by
2015 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2017 <li>Errors in Jmol console when structures in alignment
2018 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2020 <li>Not all working JABAWS services are shown in
2022 <li>JAVAWS version of Jalview fails to launch with
2023 'invalid literal/length code'</li>
2024 <li>Annotation/RNA Helix colourschemes cannot be applied
2025 to alignment with groups (actually fixed in 2.8.0b1)</li>
2026 <li>RNA Helices and T-Coffee Scores available as default
2029 </ul> <em>Applet</em>
2031 <li>Remove group option is shown even when selection is
2033 <li>Apply to all groups ticked but colourscheme changes
2034 don't affect groups</li>
2035 <li>Documented RNA Helices and T-Coffee Scores as valid
2036 colourscheme name</li>
2037 <li>Annotation labels drawn on sequence IDs when
2038 Annotation panel is not displayed</li>
2039 <li>Increased font size for dropdown menus on OSX and
2040 embedded windows</li>
2041 </ul> <em>Other</em>
2043 <li>Consensus sequence for alignments/groups with a
2044 single sequence were not calculated</li>
2045 <li>annotation files that contain only groups imported as
2046 annotation and junk sequences</li>
2047 <li>Fasta files with sequences containing '*' incorrectly
2048 recognised as PFAM or BLC</li>
2049 <li>conservation/PID slider apply all groups option
2050 doesn't affect background (2.8.0b1)
2052 <li>redundancy highlighting is erratic at 0% and 100%</li>
2053 <li>Remove gapped columns fails for sequences with ragged
2055 <li>AMSA annotation row with leading spaces is not
2056 registered correctly on import</li>
2057 <li>Jalview crashes when selecting PCA analysis for
2058 certain alignments</li>
2059 <li>Opening the colour by annotation dialog for an
2060 existing annotation based 'use original colours'
2061 colourscheme loses original colours setting</li>
2066 <td><div align="center">
2067 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2068 <em>30/1/2014</em></strong>
2072 <li>Trusted certificates for JalviewLite applet and
2073 Jalview Desktop application<br />Certificate was donated by
2074 <a href="https://www.certum.eu">Certum</a> to the Jalview
2075 open source project).
2077 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2078 <li>Output in Stockholm format</li>
2079 <li>Allow import of data from gzipped files</li>
2080 <li>Export/import group and sequence associated line
2081 graph thresholds</li>
2082 <li>Nucleotide substitution matrix that supports RNA and
2083 ambiguity codes</li>
2084 <li>Allow disorder predictions to be made on the current
2085 selection (or visible selection) in the same way that JPred
2087 <li>Groovy scripting for headless Jalview operation</li>
2088 </ul> <em>Other improvements</em>
2090 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2091 <li>COMBINE statement uses current SEQUENCE_REF and
2092 GROUP_REF scope to group annotation rows</li>
2093 <li>Support '' style escaping of quotes in Newick
2095 <li>Group options for JABAWS service by command line name</li>
2096 <li>Empty tooltip shown for JABA service options with a
2097 link but no description</li>
2098 <li>Select primary source when selecting authority in
2099 database fetcher GUI</li>
2100 <li>Add .mfa to FASTA file extensions recognised by
2102 <li>Annotation label tooltip text wrap</li>
2107 <li>Slow scrolling when lots of annotation rows are
2109 <li>Lots of NPE (and slowness) after creating RNA
2110 secondary structure annotation line</li>
2111 <li>Sequence database accessions not imported when
2112 fetching alignments from Rfam</li>
2113 <li>Incorrect SHMR submission for sequences with
2115 <li>View all structures does not always superpose
2117 <li>Option widgets in service parameters not updated to
2118 reflect user or preset settings</li>
2119 <li>Null pointer exceptions for some services without
2120 presets or adjustable parameters</li>
2121 <li>Discover PDB IDs entry in structure menu doesn't
2122 discover PDB xRefs</li>
2123 <li>Exception encountered while trying to retrieve
2124 features with DAS</li>
2125 <li>Lowest value in annotation row isn't coloured
2126 when colour by annotation (per sequence) is coloured</li>
2127 <li>Keyboard mode P jumps to start of gapped region when
2128 residue follows a gap</li>
2129 <li>Jalview appears to hang importing an alignment with
2130 Wrap as default or after enabling Wrap</li>
2131 <li>'Right click to add annotations' message
2132 shown in wrap mode when no annotations present</li>
2133 <li>Disorder predictions fail with NPE if no automatic
2134 annotation already exists on alignment</li>
2135 <li>oninit javascript function should be called after
2136 initialisation completes</li>
2137 <li>Remove redundancy after disorder prediction corrupts
2138 alignment window display</li>
2139 <li>Example annotation file in documentation is invalid</li>
2140 <li>Grouped line graph annotation rows are not exported
2141 to annotation file</li>
2142 <li>Multi-harmony analysis cannot be run when only two
2144 <li>Cannot create multiple groups of line graphs with
2145 several 'combine' statements in annotation file</li>
2146 <li>Pressing return several times causes Number Format
2147 exceptions in keyboard mode</li>
2148 <li>Multi-harmony (SHMMR) method doesn't submit
2149 correct partitions for input data</li>
2150 <li>Translation from DNA to Amino Acids fails</li>
2151 <li>Jalview fail to load newick tree with quoted label</li>
2152 <li>--headless flag isn't understood</li>
2153 <li>ClassCastException when generating EPS in headless
2155 <li>Adjusting sequence-associated shading threshold only
2156 changes one row's threshold</li>
2157 <li>Preferences and Feature settings panel panel
2158 doesn't open</li>
2159 <li>hide consensus histogram also hides conservation and
2160 quality histograms</li>
2165 <td><div align="center">
2166 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2168 <td><em>Application</em>
2170 <li>Support for JABAWS 2.0 Services (AACon alignment
2171 conservation, protein disorder and Clustal Omega)</li>
2172 <li>JABAWS server status indicator in Web Services
2174 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2175 in Jalview alignment window</li>
2176 <li>Updated Jalview build and deploy framework for OSX
2177 mountain lion, windows 7, and 8</li>
2178 <li>Nucleotide substitution matrix for PCA that supports
2179 RNA and ambiguity codes</li>
2181 <li>Improved sequence database retrieval GUI</li>
2182 <li>Support fetching and database reference look up
2183 against multiple DAS sources (Fetch all from in 'fetch db
2185 <li>Jalview project improvements
2187 <li>Store and retrieve the 'belowAlignment'
2188 flag for annotation</li>
2189 <li>calcId attribute to group annotation rows on the
2191 <li>Store AACon calculation settings for a view in
2192 Jalview project</li>
2196 <li>horizontal scrolling gesture support</li>
2197 <li>Visual progress indicator when PCA calculation is
2199 <li>Simpler JABA web services menus</li>
2200 <li>visual indication that web service results are still
2201 being retrieved from server</li>
2202 <li>Serialise the dialogs that are shown when Jalview
2203 starts up for first time</li>
2204 <li>Jalview user agent string for interacting with HTTP
2206 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2208 <li>Examples directory and Groovy library included in
2209 InstallAnywhere distribution</li>
2210 </ul> <em>Applet</em>
2212 <li>RNA alignment and secondary structure annotation
2213 visualization applet example</li>
2214 </ul> <em>General</em>
2216 <li>Normalise option for consensus sequence logo</li>
2217 <li>Reset button in PCA window to return dimensions to
2219 <li>Allow seqspace or Jalview variant of alignment PCA
2221 <li>PCA with either nucleic acid and protein substitution
2223 <li>Allow windows containing HTML reports to be exported
2225 <li>Interactive display and editing of RNA secondary
2226 structure contacts</li>
2227 <li>RNA Helix Alignment Colouring</li>
2228 <li>RNA base pair logo consensus</li>
2229 <li>Parse sequence associated secondary structure
2230 information in Stockholm files</li>
2231 <li>HTML Export database accessions and annotation
2232 information presented in tooltip for sequences</li>
2233 <li>Import secondary structure from LOCARNA clustalw
2234 style RNA alignment files</li>
2235 <li>import and visualise T-COFFEE quality scores for an
2237 <li>'colour by annotation' per sequence option to
2238 shade each sequence according to its associated alignment
2240 <li>New Jalview Logo</li>
2241 </ul> <em>Documentation and Development</em>
2243 <li>documentation for score matrices used in Jalview</li>
2244 <li>New Website!</li>
2246 <td><em>Application</em>
2248 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2249 wsdbfetch REST service</li>
2250 <li>Stop windows being moved outside desktop on OSX</li>
2251 <li>Filetype associations not installed for webstart
2253 <li>Jalview does not always retrieve progress of a JABAWS
2254 job execution in full once it is complete</li>
2255 <li>revise SHMR RSBS definition to ensure alignment is
2256 uploaded via ali_file parameter</li>
2257 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2258 <li>View all structures superposed fails with exception</li>
2259 <li>Jnet job queues forever if a very short sequence is
2260 submitted for prediction</li>
2261 <li>Cut and paste menu not opened when mouse clicked on
2263 <li>Putting fractional value into integer text box in
2264 alignment parameter dialog causes Jalview to hang</li>
2265 <li>Structure view highlighting doesn't work on
2267 <li>View all structures fails with exception shown in
2269 <li>Characters in filename associated with PDBEntry not
2270 escaped in a platform independent way</li>
2271 <li>Jalview desktop fails to launch with exception when
2273 <li>Tree calculation reports 'you must have 2 or more
2274 sequences selected' when selection is empty</li>
2275 <li>Jalview desktop fails to launch with jar signature
2276 failure when java web start temporary file caching is
2278 <li>DAS Sequence retrieval with range qualification
2279 results in sequence xref which includes range qualification</li>
2280 <li>Errors during processing of command line arguments
2281 cause progress bar (JAL-898) to be removed</li>
2282 <li>Replace comma for semi-colon option not disabled for
2283 DAS sources in sequence fetcher</li>
2284 <li>Cannot close news reader when JABAWS server warning
2285 dialog is shown</li>
2286 <li>Option widgets not updated to reflect user settings</li>
2287 <li>Edited sequence not submitted to web service</li>
2288 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2289 <li>InstallAnywhere installer doesn't unpack and run
2290 on OSX Mountain Lion</li>
2291 <li>Annotation panel not given a scroll bar when
2292 sequences with alignment annotation are pasted into the
2294 <li>Sequence associated annotation rows not associated
2295 when loaded from Jalview project</li>
2296 <li>Browser launch fails with NPE on java 1.7</li>
2297 <li>JABAWS alignment marked as finished when job was
2298 cancelled or job failed due to invalid input</li>
2299 <li>NPE with v2.7 example when clicking on Tree
2300 associated with all views</li>
2301 <li>Exceptions when copy/paste sequences with grouped
2302 annotation rows to new window</li>
2303 </ul> <em>Applet</em>
2305 <li>Sequence features are momentarily displayed before
2306 they are hidden using hidefeaturegroups applet parameter</li>
2307 <li>loading features via javascript API automatically
2308 enables feature display</li>
2309 <li>scrollToColumnIn javascript API method doesn't
2311 </ul> <em>General</em>
2313 <li>Redundancy removal fails for rna alignment</li>
2314 <li>PCA calculation fails when sequence has been selected
2315 and then deselected</li>
2316 <li>PCA window shows grey box when first opened on OSX</li>
2317 <li>Letters coloured pink in sequence logo when alignment
2318 coloured with clustalx</li>
2319 <li>Choosing fonts without letter symbols defined causes
2320 exceptions and redraw errors</li>
2321 <li>Initial PCA plot view is not same as manually
2322 reconfigured view</li>
2323 <li>Grouped annotation graph label has incorrect line
2325 <li>Grouped annotation graph label display is corrupted
2326 for lots of labels</li>
2331 <div align="center">
2332 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2335 <td><em>Application</em>
2337 <li>Jalview Desktop News Reader</li>
2338 <li>Tweaked default layout of web services menu</li>
2339 <li>View/alignment association menu to enable user to
2340 easily specify which alignment a multi-structure view takes
2341 its colours/correspondences from</li>
2342 <li>Allow properties file location to be specified as URL</li>
2343 <li>Extend Jalview project to preserve associations
2344 between many alignment views and a single Jmol display</li>
2345 <li>Store annotation row height in Jalview project file</li>
2346 <li>Annotation row column label formatting attributes
2347 stored in project file</li>
2348 <li>Annotation row order for auto-calculated annotation
2349 rows preserved in Jalview project file</li>
2350 <li>Visual progress indication when Jalview state is
2351 saved using Desktop window menu</li>
2352 <li>Visual indication that command line arguments are
2353 still being processed</li>
2354 <li>Groovy script execution from URL</li>
2355 <li>Colour by annotation default min and max colours in
2357 <li>Automatically associate PDB files dragged onto an
2358 alignment with sequences that have high similarity and
2360 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2361 <li>'view structures' option to open many
2362 structures in same window</li>
2363 <li>Sort associated views menu option for tree panel</li>
2364 <li>Group all JABA and non-JABA services for a particular
2365 analysis function in its own submenu</li>
2366 </ul> <em>Applet</em>
2368 <li>Userdefined and autogenerated annotation rows for
2370 <li>Adjustment of alignment annotation pane height</li>
2371 <li>Annotation scrollbar for annotation panel</li>
2372 <li>Drag to reorder annotation rows in annotation panel</li>
2373 <li>'automaticScrolling' parameter</li>
2374 <li>Allow sequences with partial ID string matches to be
2375 annotated from GFF/Jalview features files</li>
2376 <li>Sequence logo annotation row in applet</li>
2377 <li>Absolute paths relative to host server in applet
2378 parameters are treated as such</li>
2379 <li>New in the JalviewLite javascript API:
2381 <li>JalviewLite.js javascript library</li>
2382 <li>Javascript callbacks for
2384 <li>Applet initialisation</li>
2385 <li>Sequence/alignment mouse-overs and selections</li>
2388 <li>scrollTo row and column alignment scrolling
2390 <li>Select sequence/alignment regions from javascript</li>
2391 <li>javascript structure viewer harness to pass
2392 messages between Jmol and Jalview when running as
2393 distinct applets</li>
2394 <li>sortBy method</li>
2395 <li>Set of applet and application examples shipped
2396 with documentation</li>
2397 <li>New example to demonstrate JalviewLite and Jmol
2398 javascript message exchange</li>
2400 </ul> <em>General</em>
2402 <li>Enable Jmol displays to be associated with multiple
2403 multiple alignments</li>
2404 <li>Option to automatically sort alignment with new tree</li>
2405 <li>User configurable link to enable redirects to a
2406 www.Jalview.org mirror</li>
2407 <li>Jmol colours option for Jmol displays</li>
2408 <li>Configurable newline string when writing alignment
2409 and other flat files</li>
2410 <li>Allow alignment annotation description lines to
2411 contain html tags</li>
2412 </ul> <em>Documentation and Development</em>
2414 <li>Add groovy test harness for bulk load testing to
2416 <li>Groovy script to load and align a set of sequences
2417 using a web service before displaying the result in the
2418 Jalview desktop</li>
2419 <li>Restructured javascript and applet api documentation</li>
2420 <li>Ant target to publish example html files with applet
2422 <li>Netbeans project for building Jalview from source</li>
2423 <li>ant task to create online javadoc for Jalview source</li>
2425 <td><em>Application</em>
2427 <li>User defined colourscheme throws exception when
2428 current built in colourscheme is saved as new scheme</li>
2429 <li>AlignFrame->Save in application pops up save
2430 dialog for valid filename/format</li>
2431 <li>Cannot view associated structure for UniProt sequence</li>
2432 <li>PDB file association breaks for UniProt sequence
2434 <li>Associate PDB from file dialog does not tell you
2435 which sequence is to be associated with the file</li>
2436 <li>Find All raises null pointer exception when query
2437 only matches sequence IDs</li>
2438 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2439 <li>Jalview project with Jmol views created with Jalview
2440 2.4 cannot be loaded</li>
2441 <li>Filetype associations not installed for webstart
2443 <li>Two or more chains in a single PDB file associated
2444 with sequences in different alignments do not get coloured
2445 by their associated sequence</li>
2446 <li>Visibility status of autocalculated annotation row
2447 not preserved when project is loaded</li>
2448 <li>Annotation row height and visibility attributes not
2449 stored in Jalview project</li>
2450 <li>Tree bootstraps are not preserved when saved as a
2451 Jalview project</li>
2452 <li>Envision2 workflow tooltips are corrupted</li>
2453 <li>Enabling show group conservation also enables colour
2454 by conservation</li>
2455 <li>Duplicate group associated conservation or consensus
2456 created on new view</li>
2457 <li>Annotation scrollbar not displayed after 'show
2458 all hidden annotation rows' option selected</li>
2459 <li>Alignment quality not updated after alignment
2460 annotation row is hidden then shown</li>
2461 <li>Preserve colouring of structures coloured by
2462 sequences in pre Jalview 2.7 projects</li>
2463 <li>Web service job parameter dialog is not laid out
2465 <li>Web services menu not refreshed after 'reset
2466 services' button is pressed in preferences</li>
2467 <li>Annotation off by one in Jalview v2_3 example project</li>
2468 <li>Structures imported from file and saved in project
2469 get name like jalview_pdb1234.txt when reloaded</li>
2470 <li>Jalview does not always retrieve progress of a JABAWS
2471 job execution in full once it is complete</li>
2472 </ul> <em>Applet</em>
2474 <li>Alignment height set incorrectly when lots of
2475 annotation rows are displayed</li>
2476 <li>Relative URLs in feature HTML text not resolved to
2478 <li>View follows highlighting does not work for positions
2480 <li><= shown as = in tooltip</li>
2481 <li>Export features raises exception when no features
2483 <li>Separator string used for serialising lists of IDs
2484 for javascript api is modified when separator string
2485 provided as parameter</li>
2486 <li>Null pointer exception when selecting tree leaves for
2487 alignment with no existing selection</li>
2488 <li>Relative URLs for datasources assumed to be relative
2489 to applet's codebase</li>
2490 <li>Status bar not updated after finished searching and
2491 search wraps around to first result</li>
2492 <li>StructureSelectionManager instance shared between
2493 several Jalview applets causes race conditions and memory
2495 <li>Hover tooltip and mouseover of position on structure
2496 not sent from Jmol in applet</li>
2497 <li>Certain sequences of javascript method calls to
2498 applet API fatally hang browser</li>
2499 </ul> <em>General</em>
2501 <li>View follows structure mouseover scrolls beyond
2502 position with wrapped view and hidden regions</li>
2503 <li>Find sequence position moves to wrong residue
2504 with/without hidden columns</li>
2505 <li>Sequence length given in alignment properties window
2507 <li>InvalidNumberFormat exceptions thrown when trying to
2508 import PDB like structure files</li>
2509 <li>Positional search results are only highlighted
2510 between user-supplied sequence start/end bounds</li>
2511 <li>End attribute of sequence is not validated</li>
2512 <li>Find dialog only finds first sequence containing a
2513 given sequence position</li>
2514 <li>Sequence numbering not preserved in MSF alignment
2516 <li>Jalview PDB file reader does not extract sequence
2517 from nucleotide chains correctly</li>
2518 <li>Structure colours not updated when tree partition
2519 changed in alignment</li>
2520 <li>Sequence associated secondary structure not correctly
2521 parsed in interleaved stockholm</li>
2522 <li>Colour by annotation dialog does not restore current
2524 <li>Hiding (nearly) all sequences doesn't work
2526 <li>Sequences containing lowercase letters are not
2527 properly associated with their pdb files</li>
2528 </ul> <em>Documentation and Development</em>
2530 <li>schemas/JalviewWsParamSet.xsd corrupted by
2531 ApplyCopyright tool</li>
2536 <div align="center">
2537 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2540 <td><em>Application</em>
2542 <li>New warning dialog when the Jalview Desktop cannot
2543 contact web services</li>
2544 <li>JABA service parameters for a preset are shown in
2545 service job window</li>
2546 <li>JABA Service menu entries reworded</li>
2550 <li>Modeller PIR IO broken - cannot correctly import a
2551 pir file emitted by Jalview</li>
2552 <li>Existing feature settings transferred to new
2553 alignment view created from cut'n'paste</li>
2554 <li>Improved test for mixed amino/nucleotide chains when
2555 parsing PDB files</li>
2556 <li>Consensus and conservation annotation rows
2557 occasionally become blank for all new windows</li>
2558 <li>Exception raised when right clicking above sequences
2559 in wrapped view mode</li>
2560 </ul> <em>Application</em>
2562 <li>multiple multiply aligned structure views cause cpu
2563 usage to hit 100% and computer to hang</li>
2564 <li>Web Service parameter layout breaks for long user
2565 parameter names</li>
2566 <li>Jaba service discovery hangs desktop if Jaba server
2573 <div align="center">
2574 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2577 <td><em>Application</em>
2579 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2580 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2583 <li>Web Services preference tab</li>
2584 <li>Analysis parameters dialog box and user defined
2586 <li>Improved speed and layout of Envision2 service menu</li>
2587 <li>Superpose structures using associated sequence
2589 <li>Export coordinates and projection as CSV from PCA
2591 </ul> <em>Applet</em>
2593 <li>enable javascript: execution by the applet via the
2594 link out mechanism</li>
2595 </ul> <em>Other</em>
2597 <li>Updated the Jmol Jalview interface to work with Jmol
2599 <li>The Jalview Desktop and JalviewLite applet now
2600 require Java 1.5</li>
2601 <li>Allow Jalview feature colour specification for GFF
2602 sequence annotation files</li>
2603 <li>New 'colour by label' keword in Jalview feature file
2604 type colour specification</li>
2605 <li>New Jalview Desktop Groovy API method that allows a
2606 script to check if it being run in an interactive session or
2607 in a batch operation from the Jalview command line</li>
2611 <li>clustalx colourscheme colours Ds preferentially when
2612 both D+E are present in over 50% of the column</li>
2613 </ul> <em>Application</em>
2615 <li>typo in AlignmentFrame->View->Hide->all but
2616 selected Regions menu item</li>
2617 <li>sequence fetcher replaces ',' for ';' when the ',' is
2618 part of a valid accession ID</li>
2619 <li>fatal OOM if object retrieved by sequence fetcher
2620 runs out of memory</li>
2621 <li>unhandled Out of Memory Error when viewing pca
2622 analysis results</li>
2623 <li>InstallAnywhere builds fail to launch on OS X java
2624 10.5 update 4 (due to apple Java 1.6 update)</li>
2625 <li>Installanywhere Jalview silently fails to launch</li>
2626 </ul> <em>Applet</em>
2628 <li>Jalview.getFeatureGroups() raises an
2629 ArrayIndexOutOfBoundsException if no feature groups are
2636 <div align="center">
2637 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2643 <li>Alignment prettyprinter doesn't cope with long
2645 <li>clustalx colourscheme colours Ds preferentially when
2646 both D+E are present in over 50% of the column</li>
2647 <li>nucleic acid structures retrieved from PDB do not
2648 import correctly</li>
2649 <li>More columns get selected than were clicked on when a
2650 number of columns are hidden</li>
2651 <li>annotation label popup menu not providing correct
2652 add/hide/show options when rows are hidden or none are
2654 <li>Stockholm format shown in list of readable formats,
2655 and parser copes better with alignments from RFAM.</li>
2656 <li>CSV output of consensus only includes the percentage
2657 of all symbols if sequence logo display is enabled</li>
2659 </ul> <em>Applet</em>
2661 <li>annotation panel disappears when annotation is
2663 </ul> <em>Application</em>
2665 <li>Alignment view not redrawn properly when new
2666 alignment opened where annotation panel is visible but no
2667 annotations are present on alignment</li>
2668 <li>pasted region containing hidden columns is
2669 incorrectly displayed in new alignment window</li>
2670 <li>Jalview slow to complete operations when stdout is
2671 flooded (fix is to close the Jalview console)</li>
2672 <li>typo in AlignmentFrame->View->Hide->all but
2673 selected Rregions menu item.</li>
2674 <li>inconsistent group submenu and Format submenu entry
2675 'Un' or 'Non'conserved</li>
2676 <li>Sequence feature settings are being shared by
2677 multiple distinct alignments</li>
2678 <li>group annotation not recreated when tree partition is
2680 <li>double click on group annotation to select sequences
2681 does not propagate to associated trees</li>
2682 <li>Mac OSX specific issues:
2684 <li>exception raised when mouse clicked on desktop
2685 window background</li>
2686 <li>Desktop menu placed on menu bar and application
2687 name set correctly</li>
2688 <li>sequence feature settings not wide enough for the
2689 save feature colourscheme button</li>
2698 <div align="center">
2699 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2702 <td><em>New Capabilities</em>
2704 <li>URL links generated from description line for
2705 regular-expression based URL links (applet and application)
2707 <li>Non-positional feature URL links are shown in link
2709 <li>Linked viewing of nucleic acid sequences and
2711 <li>Automatic Scrolling option in View menu to display
2712 the currently highlighted region of an alignment.</li>
2713 <li>Order an alignment by sequence length, or using the
2714 average score or total feature count for each sequence.</li>
2715 <li>Shading features by score or associated description</li>
2716 <li>Subdivide alignment and groups based on identity of
2717 selected subsequence (Make Groups from Selection).</li>
2718 <li>New hide/show options including Shift+Control+H to
2719 hide everything but the currently selected region.</li>
2720 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2721 </ul> <em>Application</em>
2723 <li>Fetch DB References capabilities and UI expanded to
2724 support retrieval from DAS sequence sources</li>
2725 <li>Local DAS Sequence sources can be added via the
2726 command line or via the Add local source dialog box.</li>
2727 <li>DAS Dbref and DbxRef feature types are parsed as
2728 database references and protein_name is parsed as
2729 description line (BioSapiens terms).</li>
2730 <li>Enable or disable non-positional feature and database
2731 references in sequence ID tooltip from View menu in
2733 <!-- <li>New hidden columns and rows and representatives capabilities
2734 in annotations file (in progress - not yet fully implemented)</li> -->
2735 <li>Group-associated consensus, sequence logos and
2736 conservation plots</li>
2737 <li>Symbol distributions for each column can be exported
2738 and visualized as sequence logos</li>
2739 <li>Optionally scale multi-character column labels to fit
2740 within each column of annotation row<!-- todo for applet -->
2742 <li>Optional automatic sort of associated alignment view
2743 when a new tree is opened.</li>
2744 <li>Jalview Java Console</li>
2745 <li>Better placement of desktop window when moving
2746 between different screens.</li>
2747 <li>New preference items for sequence ID tooltip and
2748 consensus annotation</li>
2749 <li>Client to submit sequences and IDs to Envision2
2751 <li><em>Vamsas Capabilities</em>
2753 <li>Improved VAMSAS synchronization (Jalview archive
2754 used to preserve views, structures, and tree display
2756 <li>Import of vamsas documents from disk or URL via
2758 <li>Sharing of selected regions between views and
2759 with other VAMSAS applications (Experimental feature!)</li>
2760 <li>Updated API to VAMSAS version 0.2</li>
2762 </ul> <em>Applet</em>
2764 <li>Middle button resizes annotation row height</li>
2767 <li>sortByTree (true/false) - automatically sort the
2768 associated alignment view by the tree when a new tree is
2770 <li>showTreeBootstraps (true/false) - show or hide
2771 branch bootstraps (default is to show them if available)</li>
2772 <li>showTreeDistances (true/false) - show or hide
2773 branch lengths (default is to show them if available)</li>
2774 <li>showUnlinkedTreeNodes (true/false) - indicate if
2775 unassociated nodes should be highlighted in the tree
2777 <li>heightScale and widthScale (1.0 or more) -
2778 increase the height or width of a cell in the alignment
2779 grid relative to the current font size.</li>
2782 <li>Non-positional features displayed in sequence ID
2784 </ul> <em>Other</em>
2786 <li>Features format: graduated colour definitions and
2787 specification of feature scores</li>
2788 <li>Alignment Annotations format: new keywords for group
2789 associated annotation (GROUP_REF) and annotation row display
2790 properties (ROW_PROPERTIES)</li>
2791 <li>XML formats extended to support graduated feature
2792 colourschemes, group associated annotation, and profile
2793 visualization settings.</li></td>
2796 <li>Source field in GFF files parsed as feature source
2797 rather than description</li>
2798 <li>Non-positional features are now included in sequence
2799 feature and gff files (controlled via non-positional feature
2800 visibility in tooltip).</li>
2801 <li>URL links generated for all feature links (bugfix)</li>
2802 <li>Added URL embedding instructions to features file
2804 <li>Codons containing ambiguous nucleotides translated as
2805 'X' in peptide product</li>
2806 <li>Match case switch in find dialog box works for both
2807 sequence ID and sequence string and query strings do not
2808 have to be in upper case to match case-insensitively.</li>
2809 <li>AMSA files only contain first column of
2810 multi-character column annotation labels</li>
2811 <li>Jalview Annotation File generation/parsing consistent
2812 with documentation (e.g. Stockholm annotation can be
2813 exported and re-imported)</li>
2814 <li>PDB files without embedded PDB IDs given a friendly
2816 <li>Find incrementally searches ID string matches as well
2817 as subsequence matches, and correctly reports total number
2821 <li>Better handling of exceptions during sequence
2823 <li>Dasobert generated non-positional feature URL
2824 link text excludes the start_end suffix</li>
2825 <li>DAS feature and source retrieval buttons disabled
2826 when fetch or registry operations in progress.</li>
2827 <li>PDB files retrieved from URLs are cached properly</li>
2828 <li>Sequence description lines properly shared via
2830 <li>Sequence fetcher fetches multiple records for all
2832 <li>Ensured that command line das feature retrieval
2833 completes before alignment figures are generated.</li>
2834 <li>Reduced time taken when opening file browser for
2836 <li>isAligned check prior to calculating tree, PCA or
2837 submitting an MSA to JNet now excludes hidden sequences.</li>
2838 <li>User defined group colours properly recovered
2839 from Jalview projects.</li>
2848 <div align="center">
2849 <strong>2.4.0.b2</strong><br> 28/10/2009
2854 <li>Experimental support for google analytics usage
2856 <li>Jalview privacy settings (user preferences and docs).</li>
2861 <li>Race condition in applet preventing startup in
2863 <li>Exception when feature created from selection beyond
2864 length of sequence.</li>
2865 <li>Allow synthetic PDB files to be imported gracefully</li>
2866 <li>Sequence associated annotation rows associate with
2867 all sequences with a given id</li>
2868 <li>Find function matches case-insensitively for sequence
2869 ID string searches</li>
2870 <li>Non-standard characters do not cause pairwise
2871 alignment to fail with exception</li>
2872 </ul> <em>Application Issues</em>
2874 <li>Sequences are now validated against EMBL database</li>
2875 <li>Sequence fetcher fetches multiple records for all
2877 </ul> <em>InstallAnywhere Issues</em>
2879 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2880 issue with installAnywhere mechanism)</li>
2881 <li>Command line launching of JARs from InstallAnywhere
2882 version (java class versioning error fixed)</li>
2889 <div align="center">
2890 <strong>2.4</strong><br> 27/8/2008
2893 <td><em>User Interface</em>
2895 <li>Linked highlighting of codon and amino acid from
2896 translation and protein products</li>
2897 <li>Linked highlighting of structure associated with
2898 residue mapping to codon position</li>
2899 <li>Sequence Fetcher provides example accession numbers
2900 and 'clear' button</li>
2901 <li>MemoryMonitor added as an option under Desktop's
2903 <li>Extract score function to parse whitespace separated
2904 numeric data in description line</li>
2905 <li>Column labels in alignment annotation can be centred.</li>
2906 <li>Tooltip for sequence associated annotation give name
2908 </ul> <em>Web Services and URL fetching</em>
2910 <li>JPred3 web service</li>
2911 <li>Prototype sequence search client (no public services
2913 <li>Fetch either seed alignment or full alignment from
2915 <li>URL Links created for matching database cross
2916 references as well as sequence ID</li>
2917 <li>URL Links can be created using regular-expressions</li>
2918 </ul> <em>Sequence Database Connectivity</em>
2920 <li>Retrieval of cross-referenced sequences from other
2922 <li>Generalised database reference retrieval and
2923 validation to all fetchable databases</li>
2924 <li>Fetch sequences from DAS sources supporting the
2925 sequence command</li>
2926 </ul> <em>Import and Export</em>
2927 <li>export annotation rows as CSV for spreadsheet import</li>
2928 <li>Jalview projects record alignment dataset associations,
2929 EMBL products, and cDNA sequence mappings</li>
2930 <li>Sequence Group colour can be specified in Annotation
2932 <li>Ad-hoc colouring of group in Annotation File using RGB
2933 triplet as name of colourscheme</li>
2934 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2936 <li>treenode binding for VAMSAS tree exchange</li>
2937 <li>local editing and update of sequences in VAMSAS
2938 alignments (experimental)</li>
2939 <li>Create new or select existing session to join</li>
2940 <li>load and save of vamsas documents</li>
2941 </ul> <em>Application command line</em>
2943 <li>-tree parameter to open trees (introduced for passing
2945 <li>-fetchfrom command line argument to specify nicknames
2946 of DAS servers to query for alignment features</li>
2947 <li>-dasserver command line argument to add new servers
2948 that are also automatically queried for features</li>
2949 <li>-groovy command line argument executes a given groovy
2950 script after all input data has been loaded and parsed</li>
2951 </ul> <em>Applet-Application data exchange</em>
2953 <li>Trees passed as applet parameters can be passed to
2954 application (when using "View in full
2955 application")</li>
2956 </ul> <em>Applet Parameters</em>
2958 <li>feature group display control parameter</li>
2959 <li>debug parameter</li>
2960 <li>showbutton parameter</li>
2961 </ul> <em>Applet API methods</em>
2963 <li>newView public method</li>
2964 <li>Window (current view) specific get/set public methods</li>
2965 <li>Feature display control methods</li>
2966 <li>get list of currently selected sequences</li>
2967 </ul> <em>New Jalview distribution features</em>
2969 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2970 <li>RELEASE file gives build properties for the latest
2971 Jalview release.</li>
2972 <li>Java 1.1 Applet build made easier and donotobfuscate
2973 property controls execution of obfuscator</li>
2974 <li>Build target for generating source distribution</li>
2975 <li>Debug flag for javacc</li>
2976 <li>.jalview_properties file is documented (slightly) in
2977 jalview.bin.Cache</li>
2978 <li>Continuous Build Integration for stable and
2979 development version of Application, Applet and source
2984 <li>selected region output includes visible annotations
2985 (for certain formats)</li>
2986 <li>edit label/displaychar contains existing label/char
2988 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2989 <li>shorter peptide product names from EMBL records</li>
2990 <li>Newick string generator makes compact representations</li>
2991 <li>bootstrap values parsed correctly for tree files with
2993 <li>pathological filechooser bug avoided by not allowing
2994 filenames containing a ':'</li>
2995 <li>Fixed exception when parsing GFF files containing
2996 global sequence features</li>
2997 <li>Alignment datasets are finalized only when number of
2998 references from alignment sequences goes to zero</li>
2999 <li>Close of tree branch colour box without colour
3000 selection causes cascading exceptions</li>
3001 <li>occasional negative imgwidth exceptions</li>
3002 <li>better reporting of non-fatal warnings to user when
3003 file parsing fails.</li>
3004 <li>Save works when Jalview project is default format</li>
3005 <li>Save as dialog opened if current alignment format is
3006 not a valid output format</li>
3007 <li>UniProt canonical names introduced for both das and
3009 <li>Histidine should be midblue (not pink!) in Zappo</li>
3010 <li>error messages passed up and output when data read
3012 <li>edit undo recovers previous dataset sequence when
3013 sequence is edited</li>
3014 <li>allow PDB files without pdb ID HEADER lines (like
3015 those generated by MODELLER) to be read in properly</li>
3016 <li>allow reading of JPred concise files as a normal
3018 <li>Stockholm annotation parsing and alignment properties
3019 import fixed for PFAM records</li>
3020 <li>Structure view windows have correct name in Desktop
3022 <li>annotation consisting of sequence associated scores
3023 can be read and written correctly to annotation file</li>
3024 <li>Aligned cDNA translation to aligned peptide works
3026 <li>Fixed display of hidden sequence markers and
3027 non-italic font for representatives in Applet</li>
3028 <li>Applet Menus are always embedded in applet window on
3030 <li>Newly shown features appear at top of stack (in
3032 <li>Annotations added via parameter not drawn properly
3033 due to null pointer exceptions</li>
3034 <li>Secondary structure lines are drawn starting from
3035 first column of alignment</li>
3036 <li>UniProt XML import updated for new schema release in
3038 <li>Sequence feature to sequence ID match for Features
3039 file is case-insensitive</li>
3040 <li>Sequence features read from Features file appended to
3041 all sequences with matching IDs</li>
3042 <li>PDB structure coloured correctly for associated views
3043 containing a sub-sequence</li>
3044 <li>PDB files can be retrieved by applet from Jar files</li>
3045 <li>feature and annotation file applet parameters
3046 referring to different directories are retrieved correctly</li>
3047 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3048 <li>Fixed application hang whilst waiting for
3049 splash-screen version check to complete</li>
3050 <li>Applet properly URLencodes input parameter values
3051 when passing them to the launchApp service</li>
3052 <li>display name and local features preserved in results
3053 retrieved from web service</li>
3054 <li>Visual delay indication for sequence retrieval and
3055 sequence fetcher initialisation</li>
3056 <li>updated Application to use DAS 1.53e version of
3057 dasobert DAS client</li>
3058 <li>Re-instated Full AMSA support and .amsa file
3060 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3068 <div align="center">
3069 <strong>2.3</strong><br> 9/5/07
3074 <li>Jmol 11.0.2 integration</li>
3075 <li>PDB views stored in Jalview XML files</li>
3076 <li>Slide sequences</li>
3077 <li>Edit sequence in place</li>
3078 <li>EMBL CDS features</li>
3079 <li>DAS Feature mapping</li>
3080 <li>Feature ordering</li>
3081 <li>Alignment Properties</li>
3082 <li>Annotation Scores</li>
3083 <li>Sort by scores</li>
3084 <li>Feature/annotation editing in applet</li>
3089 <li>Headless state operation in 2.2.1</li>
3090 <li>Incorrect and unstable DNA pairwise alignment</li>
3091 <li>Cut and paste of sequences with annotation</li>
3092 <li>Feature group display state in XML</li>
3093 <li>Feature ordering in XML</li>
3094 <li>blc file iteration selection using filename # suffix</li>
3095 <li>Stockholm alignment properties</li>
3096 <li>Stockhom alignment secondary structure annotation</li>
3097 <li>2.2.1 applet had no feature transparency</li>
3098 <li>Number pad keys can be used in cursor mode</li>
3099 <li>Structure Viewer mirror image resolved</li>
3106 <div align="center">
3107 <strong>2.2.1</strong><br> 12/2/07
3112 <li>Non standard characters can be read and displayed
3113 <li>Annotations/Features can be imported/exported to the
3115 <li>Applet allows editing of sequence/annotation/group
3116 name & description
3117 <li>Preference setting to display sequence name in
3119 <li>Annotation file format extended to allow
3120 Sequence_groups to be defined
3121 <li>Default opening of alignment overview panel can be
3122 specified in preferences
3123 <li>PDB residue numbering annotation added to associated
3129 <li>Applet crash under certain Linux OS with Java 1.6
3131 <li>Annotation file export / import bugs fixed
3132 <li>PNG / EPS image output bugs fixed
3138 <div align="center">
3139 <strong>2.2</strong><br> 27/11/06
3144 <li>Multiple views on alignment
3145 <li>Sequence feature editing
3146 <li>"Reload" alignment
3147 <li>"Save" to current filename
3148 <li>Background dependent text colour
3149 <li>Right align sequence ids
3150 <li>User-defined lower case residue colours
3153 <li>Menu item accelerator keys
3154 <li>Control-V pastes to current alignment
3155 <li>Cancel button for DAS Feature Fetching
3156 <li>PCA and PDB Viewers zoom via mouse roller
3157 <li>User-defined sub-tree colours and sub-tree selection
3159 <li>'New Window' button on the 'Output to Text box'
3164 <li>New memory efficient Undo/Redo System
3165 <li>Optimised symbol lookups and conservation/consensus
3167 <li>Region Conservation/Consensus recalculated after
3169 <li>Fixed Remove Empty Columns Bug (empty columns at end
3171 <li>Slowed DAS Feature Fetching for increased robustness.
3173 <li>Made angle brackets in ASCII feature descriptions
3175 <li>Re-instated Zoom function for PCA
3176 <li>Sequence descriptions conserved in web service
3178 <li>UniProt ID discoverer uses any word separated by
3180 <li>WsDbFetch query/result association resolved
3181 <li>Tree leaf to sequence mapping improved
3182 <li>Smooth fonts switch moved to FontChooser dialog box.
3189 <div align="center">
3190 <strong>2.1.1</strong><br> 12/9/06
3195 <li>Copy consensus sequence to clipboard</li>
3200 <li>Image output - rightmost residues are rendered if
3201 sequence id panel has been resized</li>
3202 <li>Image output - all offscreen group boundaries are
3204 <li>Annotation files with sequence references - all
3205 elements in file are relative to sequence position</li>
3206 <li>Mac Applet users can use Alt key for group editing</li>
3212 <div align="center">
3213 <strong>2.1</strong><br> 22/8/06
3218 <li>MAFFT Multiple Alignment in default Web Service list</li>
3219 <li>DAS Feature fetching</li>
3220 <li>Hide sequences and columns</li>
3221 <li>Export Annotations and Features</li>
3222 <li>GFF file reading / writing</li>
3223 <li>Associate structures with sequences from local PDB
3225 <li>Add sequences to exisiting alignment</li>
3226 <li>Recently opened files / URL lists</li>
3227 <li>Applet can launch the full application</li>
3228 <li>Applet has transparency for features (Java 1.2
3230 <li>Applet has user defined colours parameter</li>
3231 <li>Applet can load sequences from parameter
3232 "sequence<em>x</em>"
3238 <li>Redundancy Panel reinstalled in the Applet</li>
3239 <li>Monospaced font - EPS / rescaling bug fixed</li>
3240 <li>Annotation files with sequence references bug fixed</li>
3246 <div align="center">
3247 <strong>2.08.1</strong><br> 2/5/06
3252 <li>Change case of selected region from Popup menu</li>
3253 <li>Choose to match case when searching</li>
3254 <li>Middle mouse button and mouse movement can compress /
3255 expand the visible width and height of the alignment</li>
3260 <li>Annotation Panel displays complete JNet results</li>
3266 <div align="center">
3267 <strong>2.08b</strong><br> 18/4/06
3273 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3274 <li>Righthand label on wrapped alignments shows correct
3281 <div align="center">
3282 <strong>2.08</strong><br> 10/4/06
3287 <li>Editing can be locked to the selection area</li>
3288 <li>Keyboard editing</li>
3289 <li>Create sequence features from searches</li>
3290 <li>Precalculated annotations can be loaded onto
3292 <li>Features file allows grouping of features</li>
3293 <li>Annotation Colouring scheme added</li>
3294 <li>Smooth fonts off by default - Faster rendering</li>
3295 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3300 <li>Drag & Drop fixed on Linux</li>
3301 <li>Jalview Archive file faster to load/save, sequence
3302 descriptions saved.</li>
3308 <div align="center">
3309 <strong>2.07</strong><br> 12/12/05
3314 <li>PDB Structure Viewer enhanced</li>
3315 <li>Sequence Feature retrieval and display enhanced</li>
3316 <li>Choose to output sequence start-end after sequence
3317 name for file output</li>
3318 <li>Sequence Fetcher WSDBFetch@EBI</li>
3319 <li>Applet can read feature files, PDB files and can be
3320 used for HTML form input</li>
3325 <li>HTML output writes groups and features</li>
3326 <li>Group editing is Control and mouse click</li>
3327 <li>File IO bugs</li>
3333 <div align="center">
3334 <strong>2.06</strong><br> 28/9/05
3339 <li>View annotations in wrapped mode</li>
3340 <li>More options for PCA viewer</li>
3345 <li>GUI bugs resolved</li>
3346 <li>Runs with -nodisplay from command line</li>
3352 <div align="center">
3353 <strong>2.05b</strong><br> 15/9/05
3358 <li>Choose EPS export as lineart or text</li>
3359 <li>Jar files are executable</li>
3360 <li>Can read in Uracil - maps to unknown residue</li>
3365 <li>Known OutOfMemory errors give warning message</li>
3366 <li>Overview window calculated more efficiently</li>
3367 <li>Several GUI bugs resolved</li>
3373 <div align="center">
3374 <strong>2.05</strong><br> 30/8/05
3379 <li>Edit and annotate in "Wrapped" view</li>
3384 <li>Several GUI bugs resolved</li>
3390 <div align="center">
3391 <strong>2.04</strong><br> 24/8/05
3396 <li>Hold down mouse wheel & scroll to change font
3402 <li>Improved JPred client reliability</li>
3403 <li>Improved loading of Jalview files</li>
3409 <div align="center">
3410 <strong>2.03</strong><br> 18/8/05
3415 <li>Set Proxy server name and port in preferences</li>
3416 <li>Multiple URL links from sequence ids</li>
3417 <li>User Defined Colours can have a scheme name and added
3419 <li>Choose to ignore gaps in consensus calculation</li>
3420 <li>Unix users can set default web browser</li>
3421 <li>Runs without GUI for batch processing</li>
3422 <li>Dynamically generated Web Service Menus</li>
3427 <li>InstallAnywhere download for Sparc Solaris</li>
3433 <div align="center">
3434 <strong>2.02</strong><br> 18/7/05
3440 <li>Copy & Paste order of sequences maintains
3441 alignment order.</li>
3447 <div align="center">
3448 <strong>2.01</strong><br> 12/7/05
3453 <li>Use delete key for deleting selection.</li>
3454 <li>Use Mouse wheel to scroll sequences.</li>
3455 <li>Help file updated to describe how to add alignment
3457 <li>Version and build date written to build properties
3459 <li>InstallAnywhere installation will check for updates
3460 at launch of Jalview.</li>
3465 <li>Delete gaps bug fixed.</li>
3466 <li>FileChooser sorts columns.</li>
3467 <li>Can remove groups one by one.</li>
3468 <li>Filechooser icons installed.</li>
3469 <li>Finder ignores return character when searching.
3470 Return key will initiate a search.<br>
3477 <div align="center">
3478 <strong>2.0</strong><br> 20/6/05
3483 <li>New codebase</li>