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.
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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>
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27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>8/8/2017</em></strong>
76 <td><div align="left">
80 <!-- JAL-2379 -->Revised implementation of PCA for speed
81 and memory efficiency (~30x faster)
84 <!-- JAL-2403 -->Revised implementation of sequence
85 similarity scores as used by Tree, PCA, Shading Consensus
86 and other calculations
89 <!-- JAL-2416 -->Score matrices are stored as resource
90 files within the Jalview codebase
92 <!-- JAL-2500 -->Trees computed on Sequence Feature
93 Similarity may have different topology due to
99 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
100 a calculation dialog box
103 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
104 model for alignments and groups
107 <!-- JAL-384 -->Custom shading schemes created via groovy
111 <!-- JAL-2491 -->linked scrolling of CDS/Protein views
112 via Overview or sequence motif search operations
115 <!-- JAL-2526 -->Efficiency improvements for interacting
116 with alignment and overview windows
119 <!-- JAL-2388 -->Hidden columns and sequences can be
123 <!-- JAL-2535 -->Posterior probability annotation from
124 Stockholm files imported as sequence associated annotation
127 <!-- JAL-2533 -->Sequence names don't include file
128 extension when importing structure files without embedded
129 names or PDB accessions
132 <!-- JAL-2547 -->Amend sequence features dialog box can be
133 opened by double clicking gaps within sequence feature
137 <!-- JAL-2631 -->Graduated feature colour style example
138 included in the example feature file
141 <!-- JAL-1933 -->Occupancy annotation row shows number of
142 ungapped positions in each column of the alignment.
145 <!-- JAL-2533 -->File extension pruned from Sequence ID
146 for sequences derived from structure files without
147 embedded database accession
150 <!-- JAL-1476 -->Status bar message shown when not enough
151 aligned positions were available to create a 3D structure
155 <!-- JAL-2507 -->More robust per-sequence positional
156 annotation input/output via stockholm flatfile
163 <!-- JAL-2447 --> Experimental Features Checkbox in
164 Desktop's Tools menu to hide or show untested features in
168 <!-- JAL-1476 -->Warning in alignment status bar when
169 there are not enough columns to superimpose structures in
173 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
174 file-based command exchange
177 <!-- JAL-2316, -->URLs for viewing database
178 cross-references provided by identifiers.org and the
182 <!-- JAL-2549 -->Updated JABAWS client to v2.2
185 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
186 format sequence substitution matrices
189 <!-- JAL-2375 -->Structure chooser automatically shows
190 Cached Structures rather than querying the PDBe if
191 structures are already available for sequences
194 <!-- JAL-2520 -->Structures imported via URL are cached in
195 the Jalview project rather than downloaded again when the
200 <em>Experimental features</em>
203 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
204 to transfer Chimera's structure attributes as Jalview
205 features, and vice-versa.
217 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
220 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
224 <!-- JAL-2485, -->External service integration tests for
225 Uniprot REST Free Text Search Client
228 <!-- --> <em>Scripting</em>
231 <!-- JAL-2344 -->FileFormatI interface for describing
232 and identifying file formats (instead of String
236 <!-- JAL-2228 -->FeatureCounter script refactored for
237 efficiency when counting all displayed features (not
238 backwards compatible with 2.10.1)
246 <td><div align="left">
250 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
251 matrix - C->R should be '-3'<br />Old matrix restored
252 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
255 <!-- JAL-2397 -->Fixed Jalview's treatment of gaps in PCA
256 and substitution matrix based Tree calculations.<br />In
257 earlier versions of Jalview, gaps matching gaps were
258 penalised, and gaps matching non-gaps penalised even more.
259 In the PCA calculation, gaps were actually treated as
260 non-gaps - so different costs were applied, which meant
261 Jalview's PCAs were different to those produced by
262 SeqSpace.<br />Jalview now treats gaps in the same way as
263 SeqSpace (ie it scores them as 0). To restore pre-2.10.2
265 jalview.viewmodel.PCAModel.scoreGapAsAny=true // for
267 jalview.viewmodel.PCAModel.scoreGapAsAny=false // to
271 <!-- JAL-2424 -->Fixed off-by-one bug that affected
272 scaling of branch lengths for trees computed using
273 Sequence Feature Similarity.
276 <!-- JAL-2346 -->Reopening Colour by annotation dialog
277 doesn't reselect a specific sequence's associated
278 annotation after it was used for colouring a view
281 <!-- JAL-2430 -->Hidden regions in alignment views are not
282 coloured in linked structure views
285 <!-- JAL-2419 -->Current selection lost if popup menu
286 opened on a region of alignment without groups
289 <!-- JAL-2374 -->Popup menu not always shown for regions
290 of an alignment with overlapping groups
293 <!-- JAL-2310 -->Finder double counts if both a sequence's
294 name and description match
297 <!-- JAL-2370 -->Hiding column selection containing two
298 hidden regions results in incorrect hidden regions
301 <!-- JAL-2377 -->PCA calculation could hang when
302 generating output report when working with highly
306 <!-- JAL-2365 -->Cannot configure feature colours with
307 lightGray or darkGray via features file
310 <!-- JAL-2421 -->Overview window visible region moves
311 erratically when hidden rows or columns are present
314 <!-- JAL-2362 -->Per-residue colourschemes applied via the
315 Structure Viewer's colour menu don't correspond to
319 <!-- JAL-2405 -->Protein specific colours only offered in
320 colour and group colour menu for protein alignments
323 <!-- JAL-2386 -->'Apply to all groups' setting when
324 changing colour does not apply Conservation slider value
328 <!-- JAL-2385 -->Colour threshold slider doesn't update to
329 reflect currently selected view or group's shading
333 <!-- JAL-2373 -->Percentage identity and conservation menu
334 items do not show a tick or allow shading to be disabled
337 <!-- JAL-2385 -->Conservation shading or PID threshold
338 lost when base colourscheme changed if slider not visible
341 <!-- JAL-2547 -->Sequence features shown in tooltip for
342 gaps before start of features
345 <!-- JAL-2576 -->Very large alignments take a long time to
349 <!-- JAL-2623 -->Graduated feature colour threshold not
350 restored to UI when feature colour is edited
353 <!-- JAL-2624 -->Feature colour thresholds not respected
354 when rendered on overview and structures when opacity at
358 <!-- JAL-2630 -->Structure and alignment overview update
359 as graduate feature colour settings are modified via the
363 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
364 a time when scrolling vertically in wrapped mode.
367 <!-- JAL-2034 -->Overview window doesn't always update
368 when a group defined on the alignment is resized
371 <!-- JAL-2605 -->Mouseovers on left/right scale region in
372 wrapped view result in positional status updates
375 <!-- JAL-2563 -->Status bar shows position for ambiguous
376 amino acid and nucleotide symbols
379 <!-- JAL-2602 -->Copy consensus sequence failed if
380 alignment included gapped columns
383 <!-- JAL-2589 -->User defined gap colour not shown in
384 overview when features overlaid on alignment
387 <!-- JAL-2473 -->Minimum size set for Jalview windows so
388 widgets don't permanently disappear
391 <!-- JAL-2503 -->Cannot select or filter quantitative
392 annotation that are shown only as column labels (e.g.
393 T-Coffee column reliability scores)
396 <!-- JAL-2589 -->Gap colours in user-defined colourschemes
400 <!-- JAL-2594 -->Exception thrown if trying to create a
401 sequence feature on gaps only
404 <!-- JAL-2544 --> Sort by features includes features to
405 right of selected region when gaps present on right-hand
409 <!-- JAL-2504 -->Features created with 'New feature'
410 button from a Find inherit previously defined feature type
411 rather than the Find query string
414 <!-- JAL-2423 -->incorrect title in output window when
415 exporting tree calculated in Jalview
418 <!-- JAL-2507 -->Per-sequence RNA secondary structures
419 added after a sequence was imported are not written to
423 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
424 when importing RNA secondary structure via Stockholm
427 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
428 not shown in correct direction for simple pseudoknots
431 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
432 and then revealing them reorders sequences on the
436 <!-- JAL-964 -->Group panel in sequence feature settings
437 doesn't update to reflect available set of groups after
438 interactively adding or modifying features
441 <!-- JAL-2225 -->Sequence Database chooser unusable on
454 <strong>Documentation</strong>
457 <!-- JAL-2339 -->Release notes reformatted for readibility
458 with the built-in Java help viewer
461 <!-- JAL-1644 -->Find documentation updated with 'search
462 sequence description' option
468 <!-- JAL-2225 -->Sequence Database chooser doesn't show
469 available databases panel on Linux
472 <!-- JAL-2519 -->EnsemblGenomes example failing after
473 release of Ensembl v.88
476 <!-- JAL-2361 -->User Defined Colours not added to Colour
480 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
481 case' residues (button in colourscheme editor debugged and
482 new documentation and tooltips added)
485 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
486 doesn't restore group-specific text colour thresholds
489 <!-- JAL-2243 -->Feature settings panel does not update as
490 new features are added to alignment
493 <!-- JAL-2532 -->Cancel in feature settings reverts
494 changes to feature colours via the Amend features dialog
497 <!-- JAL-2506 -->Null pointer exception when attempting to
498 edit graduated feature colour via amend features dialog
502 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
503 selection menu changes colours of alignment views
506 <!-- JAL-2366 -->Proxy server address and port always
507 appear enabled in Preferences->Connections
510 <!-- JAL-2426 -->Spurious exceptions in console raised
511 from alignment calculation workers after alignment has
515 <!-- JAL-1608 -->Typo in selection popup menu - Create
516 groups now 'Create Group'
519 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
520 Create/Undefine group doesn't always work
523 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
524 shown again after pressing 'Cancel'
527 <!-- JAL-2461 -->DAS registry not found exceptions
528 removed from console output
531 <!-- JAL-2383 -->Above PID colour threshold not recovered
532 when alignment view imported from project
535 <!-- JAL-2520,JAL-2465 -->No mappings generated between
536 structure and sequences extracted from structure files
537 imported via URL and viewed in Jmol
540 <!-- JAL-2520 -->Structures loaded via URL are saved in
541 Jalview Projects rather than fetched via URL again when
542 the project is loaded and the structure viewed
545 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
546 adjusts start position in wrap mode
549 <!-- JAL-2563 -->Status bar doesn't show positions for
550 ambiguous amino acids
553 <!-- JAL-2291 -->Hide insertions in PopUp menu excludes
554 gaps in selection, current sequence and only within
558 <!-- JAL-2582 -->Cannot retrieve protein products from
559 Ensembl by Peptide ID
562 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
563 CDS/Protein view after CDS sequences added for aligned
567 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
568 created from SIFTs, and spurious 'Couldn't open structure
569 in Chimera' errors raised after April 2017 update (problem
570 due to 'null' string rather than empty string used for
571 residues with no corresponding PDB mapping).
582 <!-- JAL-2468 -->Switching between Nucleotide and Protein
583 score models doesn't always result in an updated PCA plot
586 <!-- JAL-2442 -->Features not rendered as transparent on
587 overview or linked structure view
590 <!-- JAL-2372 -->Colour group by conservation doesn't
594 <!-- JAL-2517 -->Hitting Cancel after applying
595 user-defined colourscheme doesn't restore original
599 <em>New Known Issues</em>
602 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
603 phase after a sequence motif find operation
606 <!-- JAL-2550 -->Importing annotation file with rows
607 containing just upper and lower case letters are
608 interpreted as WUSS rna secondary structure symbols
611 <!-- JAL-2590 -->Cannot load Newick trees from eggnog
618 <!-- JAL-2314 -->Unit test failure:
619 jalview.ws.jabaws.RNAStructExportImport setup fails
622 <!-- JAL-2307 -->Unit test failure:
623 jalview.ws.sifts.SiftsClientTest due to compatibility
624 problems with deep array comparison equality asserts in
625 successive versions of TestNG
628 <!-- JAL-2479 -->Relocated StructureChooserTest and
629 ParameterUtilsTest Unit tests to Network suite
636 <td width="60" nowrap>
638 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
641 <td><div align="left">
645 <!-- JAL-98 -->Improved memory usage: sparse arrays used
646 for all consensus calculations
649 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
652 <li>Updated Jalview's Certum code signing certificate
658 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
659 set of database cross-references, sorted alphabetically
662 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
663 from database cross references. Users with custom links
664 will receive a <a href="webServices/urllinks.html#warning">warning
665 dialog</a> asking them to update their preferences.
668 <!-- JAL-2287-->Cancel button and escape listener on
669 dialog warning user about disconnecting Jalview from a
673 <!-- JAL-2320-->Jalview's Chimera control window closes if
674 the Chimera it is connected to is shut down
677 <!-- JAL-1738-->New keystroke (B) and Select highlighted
678 columns menu item to mark columns containing highlighted
679 regions (e.g. from structure selections or results of a
683 <!-- JAL-2284-->Command line option for batch-generation
684 of HTML pages rendering alignment data with the BioJS
694 <!-- JAL-2286 -->Columns with more than one modal residue
695 are not coloured or thresholded according to percent
696 identity (first observed in Jalview 2.8.2)
699 <!-- JAL-2301 -->Threonine incorrectly reported as not
703 <!-- JAL-2318 -->Updates to documentation pages (above PID
704 threshold, amino acid properties)
707 <!-- JAL-2292 -->Lower case residues in sequences are not
708 reported as mapped to residues in a structure file in the
712 <!--JAL-2324 -->Identical features with non-numeric scores
713 could be added multiple times to a sequence
716 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
717 bond features shown as two highlighted residues rather
718 than a range in linked structure views, and treated
719 correctly when selecting and computing trees from features
722 <!-- JAL-2281-->Custom URL links for database
723 cross-references are matched to database name regardless
731 <!-- JAL-2282-->Custom URL links for specific database
732 names without regular expressions also offer links from
736 <!-- JAL-2315-->Removing a single configured link in the
737 URL links pane in Connections preferences doesn't actually
738 update Jalview configuration
741 <!-- JAL-2272-->CTRL-Click on a selected region to open
742 the alignment area popup menu doesn't work on El-Capitan
745 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
746 files with similarly named sequences if dropped onto the
750 <!-- JAL-2312 -->Additional mappings are shown for PDB
751 entries where more chains exist in the PDB accession than
752 are reported in the SIFTS file
755 <!-- JAL-2317-->Certain structures do not get mapped to
756 the structure view when displayed with Chimera
759 <!-- JAL-2317-->No chains shown in the Chimera view
760 panel's View->Show Chains submenu
763 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
764 work for wrapped alignment views
767 <!--JAL-2197 -->Rename UI components for running JPred
768 predictions from 'JNet' to 'JPred'
771 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
772 corrupted when annotation panel vertical scroll is not at
776 <!--JAL-2332 -->Attempting to view structure for Hen
777 lysozyme results in a PDB Client error dialog box
780 <!-- JAL-2319 -->Structure View's mapping report switched
781 ranges for PDB and sequence for SIFTS
784 SIFTS 'Not_Observed' residues mapped to non-existant
788 <!-- <em>New Known Issues</em>
795 <td width="60" nowrap>
797 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
798 <em>25/10/2016</em></strong>
801 <td><em>Application</em>
803 <li>3D Structure chooser opens with 'Cached structures'
804 view if structures already loaded</li>
805 <li>Progress bar reports models as they are loaded to
812 <li>Colour by conservation always enabled and no tick
813 shown in menu when BLOSUM or PID shading applied</li>
814 <li>FER1_ARATH and FER2_ARATH labels were switched in
815 example sequences/projects/trees</li>
819 <li>Jalview projects with views of local PDB structure
820 files saved on Windows cannot be opened on OSX</li>
821 <li>Multiple structure views can be opened and superposed
822 without timeout for structures with multiple models or
823 multiple sequences in alignment</li>
824 <li>Cannot import or associated local PDB files without a
825 PDB ID HEADER line</li>
826 <li>RMSD is not output in Jmol console when superposition
828 <li>Drag and drop of URL from Browser fails for Linux and
829 OSX versions earlier than El Capitan</li>
830 <li>ENA client ignores invalid content from ENA server</li>
831 <li>Exceptions are not raised in console when ENA client
832 attempts to fetch non-existent IDs via Fetch DB Refs UI
834 <li>Exceptions are not raised in console when a new view
835 is created on the alignment</li>
836 <li>OSX right-click fixed for group selections: CMD-click
837 to insert/remove gaps in groups and CTRL-click to open group
840 <em>Build and deployment</em>
842 <li>URL link checker now copes with multi-line anchor
845 <em>New Known Issues</em>
847 <li>Drag and drop from URL links in browsers do not work
854 <td width="60" nowrap>
856 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
862 <!-- JAL-2124 -->Updated Spanish translations.
865 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
866 for importing structure data to Jalview. Enables mmCIF and
870 <!-- JAL-192 --->Alignment ruler shows positions relative to
874 <!-- JAL-2202 -->Position/residue shown in status bar when
875 mousing over sequence associated annotation
878 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
882 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
883 '()', canonical '[]' and invalid '{}' base pair populations
887 <!-- JAL-2092 -->Feature settings popup menu options for
888 showing or hiding columns containing a feature
891 <!-- JAL-1557 -->Edit selected group by double clicking on
892 group and sequence associated annotation labels
895 <!-- JAL-2236 -->Sequence name added to annotation label in
896 select/hide columns by annotation and colour by annotation
900 </ul> <em>Application</em>
903 <!-- JAL-2050-->Automatically hide introns when opening a
907 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
911 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
912 structure mappings with the EMBL-EBI PDBe SIFTS database
915 <!-- JAL-2079 -->Updated download sites used for Rfam and
916 Pfam sources to xfam.org
919 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
922 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
923 over sequences in Jalview
926 <!-- JAL-2027-->Support for reverse-complement coding
927 regions in ENA and EMBL
930 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
931 for record retrieval via ENA rest API
934 <!-- JAL-2027 -->Support for ENA CDS records with reverse
938 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
939 groovy script execution
942 <!-- JAL-1812 -->New 'execute Groovy script' option in an
943 alignment window's Calculate menu
946 <!-- JAL-1812 -->Allow groovy scripts that call
947 Jalview.getAlignFrames() to run in headless mode
950 <!-- JAL-2068 -->Support for creating new alignment
951 calculation workers from groovy scripts
954 <!-- JAL-1369 --->Store/restore reference sequence in
958 <!-- JAL-1803 -->Chain codes for a sequence's PDB
959 associations are now saved/restored from project
962 <!-- JAL-1993 -->Database selection dialog always shown
963 before sequence fetcher is opened
966 <!-- JAL-2183 -->Double click on an entry in Jalview's
967 database chooser opens a sequence fetcher
970 <!-- JAL-1563 -->Free-text search client for UniProt using
974 <!-- JAL-2168 -->-nonews command line parameter to prevent
975 the news reader opening
978 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
979 querying stored in preferences
982 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
986 <!-- JAL-1977-->Tooltips shown on database chooser
989 <!-- JAL-391 -->Reverse complement function in calculate
990 menu for nucleotide sequences
993 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
994 and feature counts preserves alignment ordering (and
995 debugged for complex feature sets).
998 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
999 viewing structures with Jalview 2.10
1002 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1003 genome, transcript CCDS and gene ids via the Ensembl and
1004 Ensembl Genomes REST API
1007 <!-- JAL-2049 -->Protein sequence variant annotation
1008 computed for 'sequence_variant' annotation on CDS regions
1012 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1016 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1017 Ref Fetcher fails to match, or otherwise updates sequence
1018 data from external database records.
1021 <!-- JAL-2154 -->Revised Jalview Project format for
1022 efficient recovery of sequence coding and alignment
1023 annotation relationships.
1025 </ul> <!-- <em>Applet</em>
1036 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1040 <!-- JAL-2018-->Export features in Jalview format (again)
1041 includes graduated colourschemes
1044 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1045 working with big alignments and lots of hidden columns
1048 <!-- JAL-2053-->Hidden column markers not always rendered
1049 at right of alignment window
1052 <!-- JAL-2067 -->Tidied up links in help file table of
1056 <!-- JAL-2072 -->Feature based tree calculation not shown
1060 <!-- JAL-2075 -->Hidden columns ignored during feature
1061 based tree calculation
1064 <!-- JAL-2065 -->Alignment view stops updating when show
1065 unconserved enabled for group on alignment
1068 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1072 <!-- JAL-2146 -->Alignment column in status incorrectly
1073 shown as "Sequence position" when mousing over
1077 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1078 hidden columns present
1081 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1082 user created annotation added to alignment
1085 <!-- JAL-1841 -->RNA Structure consensus only computed for
1086 '()' base pair annotation
1089 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1090 in zero scores for all base pairs in RNA Structure
1094 <!-- JAL-2174-->Extend selection with columns containing
1098 <!-- JAL-2275 -->Pfam format writer puts extra space at
1099 beginning of sequence
1102 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1106 <!-- JAL-2238 -->Cannot create groups on an alignment from
1107 from a tree when t-coffee scores are shown
1110 <!-- JAL-1836,1967 -->Cannot import and view PDB
1111 structures with chains containing negative resnums (4q4h)
1114 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1118 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1119 to Clustal, PIR and PileUp output
1122 <!-- JAL-2008 -->Reordering sequence features that are
1123 not visible causes alignment window to repaint
1126 <!-- JAL-2006 -->Threshold sliders don't work in
1127 graduated colour and colour by annotation row for e-value
1128 scores associated with features and annotation rows
1131 <!-- JAL-1797 -->amino acid physicochemical conservation
1132 calculation should be case independent
1135 <!-- JAL-2173 -->Remove annotation also updates hidden
1139 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1140 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1141 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1144 <!-- JAL-2065 -->Null pointer exceptions and redraw
1145 problems when reference sequence defined and 'show
1146 non-conserved' enabled
1149 <!-- JAL-1306 -->Quality and Conservation are now shown on
1150 load even when Consensus calculation is disabled
1153 <!-- JAL-1932 -->Remove right on penultimate column of
1154 alignment does nothing
1157 <em>Application</em>
1160 <!-- JAL-1552-->URLs and links can't be imported by
1161 drag'n'drop on OSX when launched via webstart (note - not
1162 yet fixed for El Capitan)
1165 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1166 output when running on non-gb/us i18n platforms
1169 <!-- JAL-1944 -->Error thrown when exporting a view with
1170 hidden sequences as flat-file alignment
1173 <!-- JAL-2030-->InstallAnywhere distribution fails when
1177 <!-- JAL-2080-->Jalview very slow to launch via webstart
1178 (also hotfix for 2.9.0b2)
1181 <!-- JAL-2085 -->Cannot save project when view has a
1182 reference sequence defined
1185 <!-- JAL-1011 -->Columns are suddenly selected in other
1186 alignments and views when revealing hidden columns
1189 <!-- JAL-1989 -->Hide columns not mirrored in complement
1190 view in a cDNA/Protein splitframe
1193 <!-- JAL-1369 -->Cannot save/restore representative
1194 sequence from project when only one sequence is
1198 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1199 in Structure Chooser
1202 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1203 structure consensus didn't refresh annotation panel
1206 <!-- JAL-1962 -->View mapping in structure view shows
1207 mappings between sequence and all chains in a PDB file
1210 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1211 dialogs format columns correctly, don't display array
1212 data, sort columns according to type
1215 <!-- JAL-1975 -->Export complete shown after destination
1216 file chooser is cancelled during an image export
1219 <!-- JAL-2025 -->Error when querying PDB Service with
1220 sequence name containing special characters
1223 <!-- JAL-2024 -->Manual PDB structure querying should be
1227 <!-- JAL-2104 -->Large tooltips with broken HTML
1228 formatting don't wrap
1231 <!-- JAL-1128 -->Figures exported from wrapped view are
1232 truncated so L looks like I in consensus annotation
1235 <!-- JAL-2003 -->Export features should only export the
1236 currently displayed features for the current selection or
1240 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1241 after fetching cross-references, and restoring from
1245 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1246 followed in the structure viewer
1249 <!-- JAL-2163 -->Titles for individual alignments in
1250 splitframe not restored from project
1253 <!-- JAL-2145 -->missing autocalculated annotation at
1254 trailing end of protein alignment in transcript/product
1255 splitview when pad-gaps not enabled by default
1258 <!-- JAL-1797 -->amino acid physicochemical conservation
1262 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1263 article has been read (reopened issue due to
1264 internationalisation problems)
1267 <!-- JAL-1960 -->Only offer PDB structures in structure
1268 viewer based on sequence name, PDB and UniProt
1273 <!-- JAL-1976 -->No progress bar shown during export of
1277 <!-- JAL-2213 -->Structures not always superimposed after
1278 multiple structures are shown for one or more sequences.
1281 <!-- JAL-1370 -->Reference sequence characters should not
1282 be replaced with '.' when 'Show unconserved' format option
1286 <!-- JAL-1823 -->Cannot specify chain code when entering
1287 specific PDB id for sequence
1290 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1291 'Export hidden sequences' is enabled, but 'export hidden
1292 columns' is disabled.
1295 <!--JAL-2026-->Best Quality option in structure chooser
1296 selects lowest rather than highest resolution structures
1300 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1301 to sequence mapping in 'View Mappings' report
1304 <!-- JAL-2284 -->Unable to read old Jalview projects that
1305 contain non-XML data added after Jalvew wrote project.
1308 <!-- JAL-2118 -->Newly created annotation row reorders
1309 after clicking on it to create new annotation for a
1312 <!-- may exclude, this is an external service stability issue JAL-1941
1313 -- > RNA 3D structure not added via DSSR service</li> -->
1318 <!-- JAL-2151 -->Incorrect columns are selected when
1319 hidden columns present before start of sequence
1322 <!-- JAL-1986 -->Missing dependencies on applet pages
1326 <!-- JAL-1947 -->Overview pixel size changes when
1327 sequences are hidden in applet
1330 <!-- JAL-1996 -->Updated instructions for applet
1331 deployment on examples pages.
1338 <td width="60" nowrap>
1339 <div align="center">
1340 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1341 <em>16/10/2015</em></strong>
1344 <td><em>General</em>
1346 <li>Time stamps for signed Jalview application and applet
1351 <em>Application</em>
1353 <li>Duplicate group consensus and conservation rows
1354 shown when tree is partitioned</li>
1355 <li>Erratic behaviour when tree partitions made with
1356 multiple cDNA/Protein split views</li>
1362 <td width="60" nowrap>
1363 <div align="center">
1364 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1365 <em>8/10/2015</em></strong>
1368 <td><em>General</em>
1370 <li>Updated Spanish translations of localized text for
1372 </ul> <em>Application</em>
1374 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1375 <li>Signed OSX InstallAnywhere installer<br></li>
1376 <li>Support for per-sequence based annotations in BioJSON</li>
1377 </ul> <em>Applet</em>
1379 <li>Split frame example added to applet examples page</li>
1380 </ul> <em>Build and Deployment</em>
1383 <!-- JAL-1888 -->New ant target for running Jalview's test
1391 <li>Mapping of cDNA to protein in split frames
1392 incorrect when sequence start > 1</li>
1393 <li>Broken images in filter column by annotation dialog
1395 <li>Feature colours not parsed from features file</li>
1396 <li>Exceptions and incomplete link URLs recovered when
1397 loading a features file containing HTML tags in feature
1401 <em>Application</em>
1403 <li>Annotations corrupted after BioJS export and
1405 <li>Incorrect sequence limits after Fetch DB References
1406 with 'trim retrieved sequences'</li>
1407 <li>Incorrect warning about deleting all data when
1408 deleting selected columns</li>
1409 <li>Patch to build system for shipping properly signed
1410 JNLP templates for webstart launch</li>
1411 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1412 unreleased structures for download or viewing</li>
1413 <li>Tab/space/return keystroke operation of EMBL-PDBe
1414 fetcher/viewer dialogs works correctly</li>
1415 <li>Disabled 'minimise' button on Jalview windows
1416 running on OSX to workaround redraw hang bug</li>
1417 <li>Split cDNA/Protein view position and geometry not
1418 recovered from jalview project</li>
1419 <li>Initial enabled/disabled state of annotation menu
1420 sorter 'show autocalculated first/last' corresponds to
1422 <li>Restoring of Clustal, RNA Helices and T-Coffee
1423 color schemes from BioJSON</li>
1427 <li>Reorder sequences mirrored in cDNA/Protein split
1429 <li>Applet with Jmol examples not loading correctly</li>
1435 <td><div align="center">
1436 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1438 <td><em>General</em>
1440 <li>Linked visualisation and analysis of DNA and Protein
1443 <li>Translated cDNA alignments shown as split protein
1444 and DNA alignment views</li>
1445 <li>Codon consensus annotation for linked protein and
1446 cDNA alignment views</li>
1447 <li>Link cDNA or Protein product sequences by loading
1448 them onto Protein or cDNA alignments</li>
1449 <li>Reconstruct linked cDNA alignment from aligned
1450 protein sequences</li>
1453 <li>Jmol integration updated to Jmol v14.2.14</li>
1454 <li>Import and export of Jalview alignment views as <a
1455 href="features/bioJsonFormat.html">BioJSON</a></li>
1456 <li>New alignment annotation file statements for
1457 reference sequences and marking hidden columns</li>
1458 <li>Reference sequence based alignment shading to
1459 highlight variation</li>
1460 <li>Select or hide columns according to alignment
1462 <li>Find option for locating sequences by description</li>
1463 <li>Conserved physicochemical properties shown in amino
1464 acid conservation row</li>
1465 <li>Alignments can be sorted by number of RNA helices</li>
1466 </ul> <em>Application</em>
1468 <li>New cDNA/Protein analysis capabilities
1470 <li>Get Cross-References should open a Split Frame
1471 view with cDNA/Protein</li>
1472 <li>Detect when nucleotide sequences and protein
1473 sequences are placed in the same alignment</li>
1474 <li>Split cDNA/Protein views are saved in Jalview
1479 <li>Use REST API to talk to Chimera</li>
1480 <li>Selected regions in Chimera are highlighted in linked
1481 Jalview windows</li>
1483 <li>VARNA RNA viewer updated to v3.93</li>
1484 <li>VARNA views are saved in Jalview Projects</li>
1485 <li>Pseudoknots displayed as Jalview RNA annotation can
1486 be shown in VARNA</li>
1488 <li>Make groups for selection uses marked columns as well
1489 as the active selected region</li>
1491 <li>Calculate UPGMA and NJ trees using sequence feature
1493 <li>New Export options
1495 <li>New Export Settings dialog to control hidden
1496 region export in flat file generation</li>
1498 <li>Export alignment views for display with the <a
1499 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1501 <li>Export scrollable SVG in HTML page</li>
1502 <li>Optional embedding of BioJSON data when exporting
1503 alignment figures to HTML</li>
1505 <li>3D structure retrieval and display
1507 <li>Free text and structured queries with the PDBe
1509 <li>PDBe Search API based discovery and selection of
1510 PDB structures for a sequence set</li>
1514 <li>JPred4 employed for protein secondary structure
1516 <li>Hide Insertions menu option to hide unaligned columns
1517 for one or a group of sequences</li>
1518 <li>Automatically hide insertions in alignments imported
1519 from the JPred4 web server</li>
1520 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1521 system on OSX<br />LGPL libraries courtesy of <a
1522 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1524 <li>changed 'View nucleotide structure' submenu to 'View
1525 VARNA 2D Structure'</li>
1526 <li>change "View protein structure" menu option to "3D
1529 </ul> <em>Applet</em>
1531 <li>New layout for applet example pages</li>
1532 <li>New parameters to enable SplitFrame view
1533 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1534 <li>New example demonstrating linked viewing of cDNA and
1535 Protein alignments</li>
1536 </ul> <em>Development and deployment</em>
1538 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1539 <li>Include installation type and git revision in build
1540 properties and console log output</li>
1541 <li>Jalview Github organisation, and new github site for
1542 storing BioJsMSA Templates</li>
1543 <li>Jalview's unit tests now managed with TestNG</li>
1546 <!-- <em>General</em>
1548 </ul> --> <!-- issues resolved --> <em>Application</em>
1550 <li>Escape should close any open find dialogs</li>
1551 <li>Typo in select-by-features status report</li>
1552 <li>Consensus RNA secondary secondary structure
1553 predictions are not highlighted in amber</li>
1554 <li>Missing gap character in v2.7 example file means
1555 alignment appears unaligned when pad-gaps is not enabled</li>
1556 <li>First switch to RNA Helices colouring doesn't colour
1557 associated structure views</li>
1558 <li>ID width preference option is greyed out when auto
1559 width checkbox not enabled</li>
1560 <li>Stopped a warning dialog from being shown when
1561 creating user defined colours</li>
1562 <li>'View Mapping' in structure viewer shows sequence
1563 mappings for just that viewer's sequences</li>
1564 <li>Workaround for superposing PDB files containing
1565 multiple models in Chimera</li>
1566 <li>Report sequence position in status bar when hovering
1567 over Jmol structure</li>
1568 <li>Cannot output gaps as '.' symbols with Selection ->
1569 output to text box</li>
1570 <li>Flat file exports of alignments with hidden columns
1571 have incorrect sequence start/end</li>
1572 <li>'Aligning' a second chain to a Chimera structure from
1574 <li>Colour schemes applied to structure viewers don't
1575 work for nucleotide</li>
1576 <li>Loading/cut'n'pasting an empty or invalid file leads
1577 to a grey/invisible alignment window</li>
1578 <li>Exported Jpred annotation from a sequence region
1579 imports to different position</li>
1580 <li>Space at beginning of sequence feature tooltips shown
1581 on some platforms</li>
1582 <li>Chimera viewer 'View | Show Chain' menu is not
1584 <li>'New View' fails with a Null Pointer Exception in
1585 console if Chimera has been opened</li>
1586 <li>Mouseover to Chimera not working</li>
1587 <li>Miscellaneous ENA XML feature qualifiers not
1589 <li>NPE in annotation renderer after 'Extract Scores'</li>
1590 <li>If two structures in one Chimera window, mouseover of
1591 either sequence shows on first structure</li>
1592 <li>'Show annotations' options should not make
1593 non-positional annotations visible</li>
1594 <li>Subsequence secondary structure annotation not shown
1595 in right place after 'view flanking regions'</li>
1596 <li>File Save As type unset when current file format is
1598 <li>Save as '.jar' option removed for saving Jalview
1600 <li>Colour by Sequence colouring in Chimera more
1602 <li>Cannot 'add reference annotation' for a sequence in
1603 several views on same alignment</li>
1604 <li>Cannot show linked products for EMBL / ENA records</li>
1605 <li>Jalview's tooltip wraps long texts containing no
1607 </ul> <em>Applet</em>
1609 <li>Jmol to JalviewLite mouseover/link not working</li>
1610 <li>JalviewLite can't import sequences with ID
1611 descriptions containing angle brackets</li>
1612 </ul> <em>General</em>
1614 <li>Cannot export and reimport RNA secondary structure
1615 via jalview annotation file</li>
1616 <li>Random helix colour palette for colour by annotation
1617 with RNA secondary structure</li>
1618 <li>Mouseover to cDNA from STOP residue in protein
1619 translation doesn't work.</li>
1620 <li>hints when using the select by annotation dialog box</li>
1621 <li>Jmol alignment incorrect if PDB file has alternate CA
1623 <li>FontChooser message dialog appears to hang after
1624 choosing 1pt font</li>
1625 <li>Peptide secondary structure incorrectly imported from
1626 annotation file when annotation display text includes 'e' or
1628 <li>Cannot set colour of new feature type whilst creating
1630 <li>cDNA translation alignment should not be sequence
1631 order dependent</li>
1632 <li>'Show unconserved' doesn't work for lower case
1634 <li>Nucleotide ambiguity codes involving R not recognised</li>
1635 </ul> <em>Deployment and Documentation</em>
1637 <li>Applet example pages appear different to the rest of
1638 www.jalview.org</li>
1639 </ul> <em>Application Known issues</em>
1641 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1642 <li>Misleading message appears after trying to delete
1644 <li>Jalview icon not shown in dock after InstallAnywhere
1645 version launches</li>
1646 <li>Fetching EMBL reference for an RNA sequence results
1647 fails with a sequence mismatch</li>
1648 <li>Corrupted or unreadable alignment display when
1649 scrolling alignment to right</li>
1650 <li>ArrayIndexOutOfBoundsException thrown when remove
1651 empty columns called on alignment with ragged gapped ends</li>
1652 <li>auto calculated alignment annotation rows do not get
1653 placed above or below non-autocalculated rows</li>
1654 <li>Jalview dekstop becomes sluggish at full screen in
1655 ultra-high resolution</li>
1656 <li>Cannot disable consensus calculation independently of
1657 quality and conservation</li>
1658 <li>Mouseover highlighting between cDNA and protein can
1659 become sluggish with more than one splitframe shown</li>
1660 </ul> <em>Applet Known Issues</em>
1662 <li>Core PDB parsing code requires Jmol</li>
1663 <li>Sequence canvas panel goes white when alignment
1664 window is being resized</li>
1670 <td><div align="center">
1671 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1673 <td><em>General</em>
1675 <li>Updated Java code signing certificate donated by
1677 <li>Features and annotation preserved when performing
1678 pairwise alignment</li>
1679 <li>RNA pseudoknot annotation can be
1680 imported/exported/displayed</li>
1681 <li>'colour by annotation' can colour by RNA and
1682 protein secondary structure</li>
1683 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1684 post-hoc with 2.9 release</em>)
1687 </ul> <em>Application</em>
1689 <li>Extract and display secondary structure for sequences
1690 with 3D structures</li>
1691 <li>Support for parsing RNAML</li>
1692 <li>Annotations menu for layout
1694 <li>sort sequence annotation rows by alignment</li>
1695 <li>place sequence annotation above/below alignment
1698 <li>Output in Stockholm format</li>
1699 <li>Internationalisation: improved Spanish (es)
1701 <li>Structure viewer preferences tab</li>
1702 <li>Disorder and Secondary Structure annotation tracks
1703 shared between alignments</li>
1704 <li>UCSF Chimera launch and linked highlighting from
1706 <li>Show/hide all sequence associated annotation rows for
1707 all or current selection</li>
1708 <li>disorder and secondary structure predictions
1709 available as dataset annotation</li>
1710 <li>Per-sequence rna helices colouring</li>
1713 <li>Sequence database accessions imported when fetching
1714 alignments from Rfam</li>
1715 <li>update VARNA version to 3.91</li>
1717 <li>New groovy scripts for exporting aligned positions,
1718 conservation values, and calculating sum of pairs scores.</li>
1719 <li>Command line argument to set default JABAWS server</li>
1720 <li>include installation type in build properties and
1721 console log output</li>
1722 <li>Updated Jalview project format to preserve dataset
1726 <!-- issues resolved --> <em>Application</em>
1728 <li>Distinguish alignment and sequence associated RNA
1729 structure in structure->view->VARNA</li>
1730 <li>Raise dialog box if user deletes all sequences in an
1732 <li>Pressing F1 results in documentation opening twice</li>
1733 <li>Sequence feature tooltip is wrapped</li>
1734 <li>Double click on sequence associated annotation
1735 selects only first column</li>
1736 <li>Redundancy removal doesn't result in unlinked
1737 leaves shown in tree</li>
1738 <li>Undos after several redundancy removals don't undo
1740 <li>Hide sequence doesn't hide associated annotation</li>
1741 <li>User defined colours dialog box too big to fit on
1742 screen and buttons not visible</li>
1743 <li>author list isn't updated if already written to
1744 Jalview properties</li>
1745 <li>Popup menu won't open after retrieving sequence
1747 <li>File open window for associate PDB doesn't open</li>
1748 <li>Left-then-right click on a sequence id opens a
1749 browser search window</li>
1750 <li>Cannot open sequence feature shading/sort popup menu
1751 in feature settings dialog</li>
1752 <li>better tooltip placement for some areas of Jalview
1754 <li>Allow addition of JABAWS Server which doesn't
1755 pass validation</li>
1756 <li>Web services parameters dialog box is too large to
1758 <li>Muscle nucleotide alignment preset obscured by
1760 <li>JABAWS preset submenus don't contain newly
1761 defined user preset</li>
1762 <li>MSA web services warns user if they were launched
1763 with invalid input</li>
1764 <li>Jalview cannot contact DAS Registy when running on
1767 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1768 'Superpose with' submenu not shown when new view
1772 </ul> <!-- <em>Applet</em>
1774 </ul> <em>General</em>
1776 </ul>--> <em>Deployment and Documentation</em>
1778 <li>2G and 1G options in launchApp have no effect on
1779 memory allocation</li>
1780 <li>launchApp service doesn't automatically open
1781 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1783 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1784 InstallAnywhere reports cannot find valid JVM when Java
1785 1.7_055 is available
1787 </ul> <em>Application Known issues</em>
1790 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1791 corrupted or unreadable alignment display when scrolling
1795 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1796 retrieval fails but progress bar continues for DAS retrieval
1797 with large number of ID
1800 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1801 flatfile output of visible region has incorrect sequence
1805 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1806 rna structure consensus doesn't update when secondary
1807 structure tracks are rearranged
1810 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1811 invalid rna structure positional highlighting does not
1812 highlight position of invalid base pairs
1815 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1816 out of memory errors are not raised when saving Jalview
1817 project from alignment window file menu
1820 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1821 Switching to RNA Helices colouring doesn't propagate to
1825 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1826 colour by RNA Helices not enabled when user created
1827 annotation added to alignment
1830 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1831 Jalview icon not shown on dock in Mountain Lion/Webstart
1833 </ul> <em>Applet Known Issues</em>
1836 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1837 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1840 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1841 Jalview and Jmol example not compatible with IE9
1844 <li>Sort by annotation score doesn't reverse order
1850 <td><div align="center">
1851 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1854 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1857 <li>Internationalisation of user interface (usually
1858 called i18n support) and translation for Spanish locale</li>
1859 <li>Define/Undefine group on current selection with
1860 Ctrl-G/Shift Ctrl-G</li>
1861 <li>Improved group creation/removal options in
1862 alignment/sequence Popup menu</li>
1863 <li>Sensible precision for symbol distribution
1864 percentages shown in logo tooltip.</li>
1865 <li>Annotation panel height set according to amount of
1866 annotation when alignment first opened</li>
1867 </ul> <em>Application</em>
1869 <li>Interactive consensus RNA secondary structure
1870 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1871 <li>Select columns containing particular features from
1872 Feature Settings dialog</li>
1873 <li>View all 'representative' PDB structures for selected
1875 <li>Update Jalview project format:
1877 <li>New file extension for Jalview projects '.jvp'</li>
1878 <li>Preserve sequence and annotation dataset (to
1879 store secondary structure annotation,etc)</li>
1880 <li>Per group and alignment annotation and RNA helix
1884 <li>New similarity measures for PCA and Tree calculation
1886 <li>Experimental support for retrieval and viewing of
1887 flanking regions for an alignment</li>
1891 <!-- issues resolved --> <em>Application</em>
1893 <li>logo keeps spinning and status remains at queued or
1894 running after job is cancelled</li>
1895 <li>cannot export features from alignments imported from
1896 Jalview/VAMSAS projects</li>
1897 <li>Buggy slider for web service parameters that take
1899 <li>Newly created RNA secondary structure line doesn't
1900 have 'display all symbols' flag set</li>
1901 <li>T-COFFEE alignment score shading scheme and other
1902 annotation shading not saved in Jalview project</li>
1903 <li>Local file cannot be loaded in freshly downloaded
1905 <li>Jalview icon not shown on dock in Mountain
1907 <li>Load file from desktop file browser fails</li>
1908 <li>Occasional NPE thrown when calculating large trees</li>
1909 <li>Cannot reorder or slide sequences after dragging an
1910 alignment onto desktop</li>
1911 <li>Colour by annotation dialog throws NPE after using
1912 'extract scores' function</li>
1913 <li>Loading/cut'n'pasting an empty file leads to a grey
1914 alignment window</li>
1915 <li>Disorder thresholds rendered incorrectly after
1916 performing IUPred disorder prediction</li>
1917 <li>Multiple group annotated consensus rows shown when
1918 changing 'normalise logo' display setting</li>
1919 <li>Find shows blank dialog after 'finished searching' if
1920 nothing matches query</li>
1921 <li>Null Pointer Exceptions raised when sorting by
1922 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1924 <li>Errors in Jmol console when structures in alignment
1925 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1927 <li>Not all working JABAWS services are shown in
1929 <li>JAVAWS version of Jalview fails to launch with
1930 'invalid literal/length code'</li>
1931 <li>Annotation/RNA Helix colourschemes cannot be applied
1932 to alignment with groups (actually fixed in 2.8.0b1)</li>
1933 <li>RNA Helices and T-Coffee Scores available as default
1936 </ul> <em>Applet</em>
1938 <li>Remove group option is shown even when selection is
1940 <li>Apply to all groups ticked but colourscheme changes
1941 don't affect groups</li>
1942 <li>Documented RNA Helices and T-Coffee Scores as valid
1943 colourscheme name</li>
1944 <li>Annotation labels drawn on sequence IDs when
1945 Annotation panel is not displayed</li>
1946 <li>Increased font size for dropdown menus on OSX and
1947 embedded windows</li>
1948 </ul> <em>Other</em>
1950 <li>Consensus sequence for alignments/groups with a
1951 single sequence were not calculated</li>
1952 <li>annotation files that contain only groups imported as
1953 annotation and junk sequences</li>
1954 <li>Fasta files with sequences containing '*' incorrectly
1955 recognised as PFAM or BLC</li>
1956 <li>conservation/PID slider apply all groups option
1957 doesn't affect background (2.8.0b1)
1959 <li>redundancy highlighting is erratic at 0% and 100%</li>
1960 <li>Remove gapped columns fails for sequences with ragged
1962 <li>AMSA annotation row with leading spaces is not
1963 registered correctly on import</li>
1964 <li>Jalview crashes when selecting PCA analysis for
1965 certain alignments</li>
1966 <li>Opening the colour by annotation dialog for an
1967 existing annotation based 'use original colours'
1968 colourscheme loses original colours setting</li>
1973 <td><div align="center">
1974 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
1975 <em>30/1/2014</em></strong>
1979 <li>Trusted certificates for JalviewLite applet and
1980 Jalview Desktop application<br />Certificate was donated by
1981 <a href="https://www.certum.eu">Certum</a> to the Jalview
1982 open source project).
1984 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
1985 <li>Output in Stockholm format</li>
1986 <li>Allow import of data from gzipped files</li>
1987 <li>Export/import group and sequence associated line
1988 graph thresholds</li>
1989 <li>Nucleotide substitution matrix that supports RNA and
1990 ambiguity codes</li>
1991 <li>Allow disorder predictions to be made on the current
1992 selection (or visible selection) in the same way that JPred
1994 <li>Groovy scripting for headless Jalview operation</li>
1995 </ul> <em>Other improvements</em>
1997 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
1998 <li>COMBINE statement uses current SEQUENCE_REF and
1999 GROUP_REF scope to group annotation rows</li>
2000 <li>Support '' style escaping of quotes in Newick
2002 <li>Group options for JABAWS service by command line name</li>
2003 <li>Empty tooltip shown for JABA service options with a
2004 link but no description</li>
2005 <li>Select primary source when selecting authority in
2006 database fetcher GUI</li>
2007 <li>Add .mfa to FASTA file extensions recognised by
2009 <li>Annotation label tooltip text wrap</li>
2014 <li>Slow scrolling when lots of annotation rows are
2016 <li>Lots of NPE (and slowness) after creating RNA
2017 secondary structure annotation line</li>
2018 <li>Sequence database accessions not imported when
2019 fetching alignments from Rfam</li>
2020 <li>Incorrect SHMR submission for sequences with
2022 <li>View all structures does not always superpose
2024 <li>Option widgets in service parameters not updated to
2025 reflect user or preset settings</li>
2026 <li>Null pointer exceptions for some services without
2027 presets or adjustable parameters</li>
2028 <li>Discover PDB IDs entry in structure menu doesn't
2029 discover PDB xRefs</li>
2030 <li>Exception encountered while trying to retrieve
2031 features with DAS</li>
2032 <li>Lowest value in annotation row isn't coloured
2033 when colour by annotation (per sequence) is coloured</li>
2034 <li>Keyboard mode P jumps to start of gapped region when
2035 residue follows a gap</li>
2036 <li>Jalview appears to hang importing an alignment with
2037 Wrap as default or after enabling Wrap</li>
2038 <li>'Right click to add annotations' message
2039 shown in wrap mode when no annotations present</li>
2040 <li>Disorder predictions fail with NPE if no automatic
2041 annotation already exists on alignment</li>
2042 <li>oninit javascript function should be called after
2043 initialisation completes</li>
2044 <li>Remove redundancy after disorder prediction corrupts
2045 alignment window display</li>
2046 <li>Example annotation file in documentation is invalid</li>
2047 <li>Grouped line graph annotation rows are not exported
2048 to annotation file</li>
2049 <li>Multi-harmony analysis cannot be run when only two
2051 <li>Cannot create multiple groups of line graphs with
2052 several 'combine' statements in annotation file</li>
2053 <li>Pressing return several times causes Number Format
2054 exceptions in keyboard mode</li>
2055 <li>Multi-harmony (SHMMR) method doesn't submit
2056 correct partitions for input data</li>
2057 <li>Translation from DNA to Amino Acids fails</li>
2058 <li>Jalview fail to load newick tree with quoted label</li>
2059 <li>--headless flag isn't understood</li>
2060 <li>ClassCastException when generating EPS in headless
2062 <li>Adjusting sequence-associated shading threshold only
2063 changes one row's threshold</li>
2064 <li>Preferences and Feature settings panel panel
2065 doesn't open</li>
2066 <li>hide consensus histogram also hides conservation and
2067 quality histograms</li>
2072 <td><div align="center">
2073 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2075 <td><em>Application</em>
2077 <li>Support for JABAWS 2.0 Services (AACon alignment
2078 conservation, protein disorder and Clustal Omega)</li>
2079 <li>JABAWS server status indicator in Web Services
2081 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2082 in Jalview alignment window</li>
2083 <li>Updated Jalview build and deploy framework for OSX
2084 mountain lion, windows 7, and 8</li>
2085 <li>Nucleotide substitution matrix for PCA that supports
2086 RNA and ambiguity codes</li>
2088 <li>Improved sequence database retrieval GUI</li>
2089 <li>Support fetching and database reference look up
2090 against multiple DAS sources (Fetch all from in 'fetch db
2092 <li>Jalview project improvements
2094 <li>Store and retrieve the 'belowAlignment'
2095 flag for annotation</li>
2096 <li>calcId attribute to group annotation rows on the
2098 <li>Store AACon calculation settings for a view in
2099 Jalview project</li>
2103 <li>horizontal scrolling gesture support</li>
2104 <li>Visual progress indicator when PCA calculation is
2106 <li>Simpler JABA web services menus</li>
2107 <li>visual indication that web service results are still
2108 being retrieved from server</li>
2109 <li>Serialise the dialogs that are shown when Jalview
2110 starts up for first time</li>
2111 <li>Jalview user agent string for interacting with HTTP
2113 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2115 <li>Examples directory and Groovy library included in
2116 InstallAnywhere distribution</li>
2117 </ul> <em>Applet</em>
2119 <li>RNA alignment and secondary structure annotation
2120 visualization applet example</li>
2121 </ul> <em>General</em>
2123 <li>Normalise option for consensus sequence logo</li>
2124 <li>Reset button in PCA window to return dimensions to
2126 <li>Allow seqspace or Jalview variant of alignment PCA
2128 <li>PCA with either nucleic acid and protein substitution
2130 <li>Allow windows containing HTML reports to be exported
2132 <li>Interactive display and editing of RNA secondary
2133 structure contacts</li>
2134 <li>RNA Helix Alignment Colouring</li>
2135 <li>RNA base pair logo consensus</li>
2136 <li>Parse sequence associated secondary structure
2137 information in Stockholm files</li>
2138 <li>HTML Export database accessions and annotation
2139 information presented in tooltip for sequences</li>
2140 <li>Import secondary structure from LOCARNA clustalw
2141 style RNA alignment files</li>
2142 <li>import and visualise T-COFFEE quality scores for an
2144 <li>'colour by annotation' per sequence option to
2145 shade each sequence according to its associated alignment
2147 <li>New Jalview Logo</li>
2148 </ul> <em>Documentation and Development</em>
2150 <li>documentation for score matrices used in Jalview</li>
2151 <li>New Website!</li>
2153 <td><em>Application</em>
2155 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2156 wsdbfetch REST service</li>
2157 <li>Stop windows being moved outside desktop on OSX</li>
2158 <li>Filetype associations not installed for webstart
2160 <li>Jalview does not always retrieve progress of a JABAWS
2161 job execution in full once it is complete</li>
2162 <li>revise SHMR RSBS definition to ensure alignment is
2163 uploaded via ali_file parameter</li>
2164 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2165 <li>View all structures superposed fails with exception</li>
2166 <li>Jnet job queues forever if a very short sequence is
2167 submitted for prediction</li>
2168 <li>Cut and paste menu not opened when mouse clicked on
2170 <li>Putting fractional value into integer text box in
2171 alignment parameter dialog causes Jalview to hang</li>
2172 <li>Structure view highlighting doesn't work on
2174 <li>View all structures fails with exception shown in
2176 <li>Characters in filename associated with PDBEntry not
2177 escaped in a platform independent way</li>
2178 <li>Jalview desktop fails to launch with exception when
2180 <li>Tree calculation reports 'you must have 2 or more
2181 sequences selected' when selection is empty</li>
2182 <li>Jalview desktop fails to launch with jar signature
2183 failure when java web start temporary file caching is
2185 <li>DAS Sequence retrieval with range qualification
2186 results in sequence xref which includes range qualification</li>
2187 <li>Errors during processing of command line arguments
2188 cause progress bar (JAL-898) to be removed</li>
2189 <li>Replace comma for semi-colon option not disabled for
2190 DAS sources in sequence fetcher</li>
2191 <li>Cannot close news reader when JABAWS server warning
2192 dialog is shown</li>
2193 <li>Option widgets not updated to reflect user settings</li>
2194 <li>Edited sequence not submitted to web service</li>
2195 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2196 <li>InstallAnywhere installer doesn't unpack and run
2197 on OSX Mountain Lion</li>
2198 <li>Annotation panel not given a scroll bar when
2199 sequences with alignment annotation are pasted into the
2201 <li>Sequence associated annotation rows not associated
2202 when loaded from Jalview project</li>
2203 <li>Browser launch fails with NPE on java 1.7</li>
2204 <li>JABAWS alignment marked as finished when job was
2205 cancelled or job failed due to invalid input</li>
2206 <li>NPE with v2.7 example when clicking on Tree
2207 associated with all views</li>
2208 <li>Exceptions when copy/paste sequences with grouped
2209 annotation rows to new window</li>
2210 </ul> <em>Applet</em>
2212 <li>Sequence features are momentarily displayed before
2213 they are hidden using hidefeaturegroups applet parameter</li>
2214 <li>loading features via javascript API automatically
2215 enables feature display</li>
2216 <li>scrollToColumnIn javascript API method doesn't
2218 </ul> <em>General</em>
2220 <li>Redundancy removal fails for rna alignment</li>
2221 <li>PCA calculation fails when sequence has been selected
2222 and then deselected</li>
2223 <li>PCA window shows grey box when first opened on OSX</li>
2224 <li>Letters coloured pink in sequence logo when alignment
2225 coloured with clustalx</li>
2226 <li>Choosing fonts without letter symbols defined causes
2227 exceptions and redraw errors</li>
2228 <li>Initial PCA plot view is not same as manually
2229 reconfigured view</li>
2230 <li>Grouped annotation graph label has incorrect line
2232 <li>Grouped annotation graph label display is corrupted
2233 for lots of labels</li>
2238 <div align="center">
2239 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2242 <td><em>Application</em>
2244 <li>Jalview Desktop News Reader</li>
2245 <li>Tweaked default layout of web services menu</li>
2246 <li>View/alignment association menu to enable user to
2247 easily specify which alignment a multi-structure view takes
2248 its colours/correspondences from</li>
2249 <li>Allow properties file location to be specified as URL</li>
2250 <li>Extend Jalview project to preserve associations
2251 between many alignment views and a single Jmol display</li>
2252 <li>Store annotation row height in Jalview project file</li>
2253 <li>Annotation row column label formatting attributes
2254 stored in project file</li>
2255 <li>Annotation row order for auto-calculated annotation
2256 rows preserved in Jalview project file</li>
2257 <li>Visual progress indication when Jalview state is
2258 saved using Desktop window menu</li>
2259 <li>Visual indication that command line arguments are
2260 still being processed</li>
2261 <li>Groovy script execution from URL</li>
2262 <li>Colour by annotation default min and max colours in
2264 <li>Automatically associate PDB files dragged onto an
2265 alignment with sequences that have high similarity and
2267 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2268 <li>'view structures' option to open many
2269 structures in same window</li>
2270 <li>Sort associated views menu option for tree panel</li>
2271 <li>Group all JABA and non-JABA services for a particular
2272 analysis function in its own submenu</li>
2273 </ul> <em>Applet</em>
2275 <li>Userdefined and autogenerated annotation rows for
2277 <li>Adjustment of alignment annotation pane height</li>
2278 <li>Annotation scrollbar for annotation panel</li>
2279 <li>Drag to reorder annotation rows in annotation panel</li>
2280 <li>'automaticScrolling' parameter</li>
2281 <li>Allow sequences with partial ID string matches to be
2282 annotated from GFF/Jalview features files</li>
2283 <li>Sequence logo annotation row in applet</li>
2284 <li>Absolute paths relative to host server in applet
2285 parameters are treated as such</li>
2286 <li>New in the JalviewLite javascript API:
2288 <li>JalviewLite.js javascript library</li>
2289 <li>Javascript callbacks for
2291 <li>Applet initialisation</li>
2292 <li>Sequence/alignment mouse-overs and selections</li>
2295 <li>scrollTo row and column alignment scrolling
2297 <li>Select sequence/alignment regions from javascript</li>
2298 <li>javascript structure viewer harness to pass
2299 messages between Jmol and Jalview when running as
2300 distinct applets</li>
2301 <li>sortBy method</li>
2302 <li>Set of applet and application examples shipped
2303 with documentation</li>
2304 <li>New example to demonstrate JalviewLite and Jmol
2305 javascript message exchange</li>
2307 </ul> <em>General</em>
2309 <li>Enable Jmol displays to be associated with multiple
2310 multiple alignments</li>
2311 <li>Option to automatically sort alignment with new tree</li>
2312 <li>User configurable link to enable redirects to a
2313 www.Jalview.org mirror</li>
2314 <li>Jmol colours option for Jmol displays</li>
2315 <li>Configurable newline string when writing alignment
2316 and other flat files</li>
2317 <li>Allow alignment annotation description lines to
2318 contain html tags</li>
2319 </ul> <em>Documentation and Development</em>
2321 <li>Add groovy test harness for bulk load testing to
2323 <li>Groovy script to load and align a set of sequences
2324 using a web service before displaying the result in the
2325 Jalview desktop</li>
2326 <li>Restructured javascript and applet api documentation</li>
2327 <li>Ant target to publish example html files with applet
2329 <li>Netbeans project for building Jalview from source</li>
2330 <li>ant task to create online javadoc for Jalview source</li>
2332 <td><em>Application</em>
2334 <li>User defined colourscheme throws exception when
2335 current built in colourscheme is saved as new scheme</li>
2336 <li>AlignFrame->Save in application pops up save
2337 dialog for valid filename/format</li>
2338 <li>Cannot view associated structure for UniProt sequence</li>
2339 <li>PDB file association breaks for UniProt sequence
2341 <li>Associate PDB from file dialog does not tell you
2342 which sequence is to be associated with the file</li>
2343 <li>Find All raises null pointer exception when query
2344 only matches sequence IDs</li>
2345 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2346 <li>Jalview project with Jmol views created with Jalview
2347 2.4 cannot be loaded</li>
2348 <li>Filetype associations not installed for webstart
2350 <li>Two or more chains in a single PDB file associated
2351 with sequences in different alignments do not get coloured
2352 by their associated sequence</li>
2353 <li>Visibility status of autocalculated annotation row
2354 not preserved when project is loaded</li>
2355 <li>Annotation row height and visibility attributes not
2356 stored in Jalview project</li>
2357 <li>Tree bootstraps are not preserved when saved as a
2358 Jalview project</li>
2359 <li>Envision2 workflow tooltips are corrupted</li>
2360 <li>Enabling show group conservation also enables colour
2361 by conservation</li>
2362 <li>Duplicate group associated conservation or consensus
2363 created on new view</li>
2364 <li>Annotation scrollbar not displayed after 'show
2365 all hidden annotation rows' option selected</li>
2366 <li>Alignment quality not updated after alignment
2367 annotation row is hidden then shown</li>
2368 <li>Preserve colouring of structures coloured by
2369 sequences in pre Jalview 2.7 projects</li>
2370 <li>Web service job parameter dialog is not laid out
2372 <li>Web services menu not refreshed after 'reset
2373 services' button is pressed in preferences</li>
2374 <li>Annotation off by one in Jalview v2_3 example project</li>
2375 <li>Structures imported from file and saved in project
2376 get name like jalview_pdb1234.txt when reloaded</li>
2377 <li>Jalview does not always retrieve progress of a JABAWS
2378 job execution in full once it is complete</li>
2379 </ul> <em>Applet</em>
2381 <li>Alignment height set incorrectly when lots of
2382 annotation rows are displayed</li>
2383 <li>Relative URLs in feature HTML text not resolved to
2385 <li>View follows highlighting does not work for positions
2387 <li><= shown as = in tooltip</li>
2388 <li>Export features raises exception when no features
2390 <li>Separator string used for serialising lists of IDs
2391 for javascript api is modified when separator string
2392 provided as parameter</li>
2393 <li>Null pointer exception when selecting tree leaves for
2394 alignment with no existing selection</li>
2395 <li>Relative URLs for datasources assumed to be relative
2396 to applet's codebase</li>
2397 <li>Status bar not updated after finished searching and
2398 search wraps around to first result</li>
2399 <li>StructureSelectionManager instance shared between
2400 several Jalview applets causes race conditions and memory
2402 <li>Hover tooltip and mouseover of position on structure
2403 not sent from Jmol in applet</li>
2404 <li>Certain sequences of javascript method calls to
2405 applet API fatally hang browser</li>
2406 </ul> <em>General</em>
2408 <li>View follows structure mouseover scrolls beyond
2409 position with wrapped view and hidden regions</li>
2410 <li>Find sequence position moves to wrong residue
2411 with/without hidden columns</li>
2412 <li>Sequence length given in alignment properties window
2414 <li>InvalidNumberFormat exceptions thrown when trying to
2415 import PDB like structure files</li>
2416 <li>Positional search results are only highlighted
2417 between user-supplied sequence start/end bounds</li>
2418 <li>End attribute of sequence is not validated</li>
2419 <li>Find dialog only finds first sequence containing a
2420 given sequence position</li>
2421 <li>Sequence numbering not preserved in MSF alignment
2423 <li>Jalview PDB file reader does not extract sequence
2424 from nucleotide chains correctly</li>
2425 <li>Structure colours not updated when tree partition
2426 changed in alignment</li>
2427 <li>Sequence associated secondary structure not correctly
2428 parsed in interleaved stockholm</li>
2429 <li>Colour by annotation dialog does not restore current
2431 <li>Hiding (nearly) all sequences doesn't work
2433 <li>Sequences containing lowercase letters are not
2434 properly associated with their pdb files</li>
2435 </ul> <em>Documentation and Development</em>
2437 <li>schemas/JalviewWsParamSet.xsd corrupted by
2438 ApplyCopyright tool</li>
2443 <div align="center">
2444 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2447 <td><em>Application</em>
2449 <li>New warning dialog when the Jalview Desktop cannot
2450 contact web services</li>
2451 <li>JABA service parameters for a preset are shown in
2452 service job window</li>
2453 <li>JABA Service menu entries reworded</li>
2457 <li>Modeller PIR IO broken - cannot correctly import a
2458 pir file emitted by Jalview</li>
2459 <li>Existing feature settings transferred to new
2460 alignment view created from cut'n'paste</li>
2461 <li>Improved test for mixed amino/nucleotide chains when
2462 parsing PDB files</li>
2463 <li>Consensus and conservation annotation rows
2464 occasionally become blank for all new windows</li>
2465 <li>Exception raised when right clicking above sequences
2466 in wrapped view mode</li>
2467 </ul> <em>Application</em>
2469 <li>multiple multiply aligned structure views cause cpu
2470 usage to hit 100% and computer to hang</li>
2471 <li>Web Service parameter layout breaks for long user
2472 parameter names</li>
2473 <li>Jaba service discovery hangs desktop if Jaba server
2480 <div align="center">
2481 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2484 <td><em>Application</em>
2486 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2487 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2490 <li>Web Services preference tab</li>
2491 <li>Analysis parameters dialog box and user defined
2493 <li>Improved speed and layout of Envision2 service menu</li>
2494 <li>Superpose structures using associated sequence
2496 <li>Export coordinates and projection as CSV from PCA
2498 </ul> <em>Applet</em>
2500 <li>enable javascript: execution by the applet via the
2501 link out mechanism</li>
2502 </ul> <em>Other</em>
2504 <li>Updated the Jmol Jalview interface to work with Jmol
2506 <li>The Jalview Desktop and JalviewLite applet now
2507 require Java 1.5</li>
2508 <li>Allow Jalview feature colour specification for GFF
2509 sequence annotation files</li>
2510 <li>New 'colour by label' keword in Jalview feature file
2511 type colour specification</li>
2512 <li>New Jalview Desktop Groovy API method that allows a
2513 script to check if it being run in an interactive session or
2514 in a batch operation from the Jalview command line</li>
2518 <li>clustalx colourscheme colours Ds preferentially when
2519 both D+E are present in over 50% of the column</li>
2520 </ul> <em>Application</em>
2522 <li>typo in AlignmentFrame->View->Hide->all but
2523 selected Regions menu item</li>
2524 <li>sequence fetcher replaces ',' for ';' when the ',' is
2525 part of a valid accession ID</li>
2526 <li>fatal OOM if object retrieved by sequence fetcher
2527 runs out of memory</li>
2528 <li>unhandled Out of Memory Error when viewing pca
2529 analysis results</li>
2530 <li>InstallAnywhere builds fail to launch on OS X java
2531 10.5 update 4 (due to apple Java 1.6 update)</li>
2532 <li>Installanywhere Jalview silently fails to launch</li>
2533 </ul> <em>Applet</em>
2535 <li>Jalview.getFeatureGroups() raises an
2536 ArrayIndexOutOfBoundsException if no feature groups are
2543 <div align="center">
2544 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2550 <li>Alignment prettyprinter doesn't cope with long
2552 <li>clustalx colourscheme colours Ds preferentially when
2553 both D+E are present in over 50% of the column</li>
2554 <li>nucleic acid structures retrieved from PDB do not
2555 import correctly</li>
2556 <li>More columns get selected than were clicked on when a
2557 number of columns are hidden</li>
2558 <li>annotation label popup menu not providing correct
2559 add/hide/show options when rows are hidden or none are
2561 <li>Stockholm format shown in list of readable formats,
2562 and parser copes better with alignments from RFAM.</li>
2563 <li>CSV output of consensus only includes the percentage
2564 of all symbols if sequence logo display is enabled</li>
2566 </ul> <em>Applet</em>
2568 <li>annotation panel disappears when annotation is
2570 </ul> <em>Application</em>
2572 <li>Alignment view not redrawn properly when new
2573 alignment opened where annotation panel is visible but no
2574 annotations are present on alignment</li>
2575 <li>pasted region containing hidden columns is
2576 incorrectly displayed in new alignment window</li>
2577 <li>Jalview slow to complete operations when stdout is
2578 flooded (fix is to close the Jalview console)</li>
2579 <li>typo in AlignmentFrame->View->Hide->all but
2580 selected Rregions menu item.</li>
2581 <li>inconsistent group submenu and Format submenu entry
2582 'Un' or 'Non'conserved</li>
2583 <li>Sequence feature settings are being shared by
2584 multiple distinct alignments</li>
2585 <li>group annotation not recreated when tree partition is
2587 <li>double click on group annotation to select sequences
2588 does not propagate to associated trees</li>
2589 <li>Mac OSX specific issues:
2591 <li>exception raised when mouse clicked on desktop
2592 window background</li>
2593 <li>Desktop menu placed on menu bar and application
2594 name set correctly</li>
2595 <li>sequence feature settings not wide enough for the
2596 save feature colourscheme button</li>
2605 <div align="center">
2606 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2609 <td><em>New Capabilities</em>
2611 <li>URL links generated from description line for
2612 regular-expression based URL links (applet and application)
2614 <li>Non-positional feature URL links are shown in link
2616 <li>Linked viewing of nucleic acid sequences and
2618 <li>Automatic Scrolling option in View menu to display
2619 the currently highlighted region of an alignment.</li>
2620 <li>Order an alignment by sequence length, or using the
2621 average score or total feature count for each sequence.</li>
2622 <li>Shading features by score or associated description</li>
2623 <li>Subdivide alignment and groups based on identity of
2624 selected subsequence (Make Groups from Selection).</li>
2625 <li>New hide/show options including Shift+Control+H to
2626 hide everything but the currently selected region.</li>
2627 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2628 </ul> <em>Application</em>
2630 <li>Fetch DB References capabilities and UI expanded to
2631 support retrieval from DAS sequence sources</li>
2632 <li>Local DAS Sequence sources can be added via the
2633 command line or via the Add local source dialog box.</li>
2634 <li>DAS Dbref and DbxRef feature types are parsed as
2635 database references and protein_name is parsed as
2636 description line (BioSapiens terms).</li>
2637 <li>Enable or disable non-positional feature and database
2638 references in sequence ID tooltip from View menu in
2640 <!-- <li>New hidden columns and rows and representatives capabilities
2641 in annotations file (in progress - not yet fully implemented)</li> -->
2642 <li>Group-associated consensus, sequence logos and
2643 conservation plots</li>
2644 <li>Symbol distributions for each column can be exported
2645 and visualized as sequence logos</li>
2646 <li>Optionally scale multi-character column labels to fit
2647 within each column of annotation row<!-- todo for applet -->
2649 <li>Optional automatic sort of associated alignment view
2650 when a new tree is opened.</li>
2651 <li>Jalview Java Console</li>
2652 <li>Better placement of desktop window when moving
2653 between different screens.</li>
2654 <li>New preference items for sequence ID tooltip and
2655 consensus annotation</li>
2656 <li>Client to submit sequences and IDs to Envision2
2658 <li><em>Vamsas Capabilities</em>
2660 <li>Improved VAMSAS synchronization (Jalview archive
2661 used to preserve views, structures, and tree display
2663 <li>Import of vamsas documents from disk or URL via
2665 <li>Sharing of selected regions between views and
2666 with other VAMSAS applications (Experimental feature!)</li>
2667 <li>Updated API to VAMSAS version 0.2</li>
2669 </ul> <em>Applet</em>
2671 <li>Middle button resizes annotation row height</li>
2674 <li>sortByTree (true/false) - automatically sort the
2675 associated alignment view by the tree when a new tree is
2677 <li>showTreeBootstraps (true/false) - show or hide
2678 branch bootstraps (default is to show them if available)</li>
2679 <li>showTreeDistances (true/false) - show or hide
2680 branch lengths (default is to show them if available)</li>
2681 <li>showUnlinkedTreeNodes (true/false) - indicate if
2682 unassociated nodes should be highlighted in the tree
2684 <li>heightScale and widthScale (1.0 or more) -
2685 increase the height or width of a cell in the alignment
2686 grid relative to the current font size.</li>
2689 <li>Non-positional features displayed in sequence ID
2691 </ul> <em>Other</em>
2693 <li>Features format: graduated colour definitions and
2694 specification of feature scores</li>
2695 <li>Alignment Annotations format: new keywords for group
2696 associated annotation (GROUP_REF) and annotation row display
2697 properties (ROW_PROPERTIES)</li>
2698 <li>XML formats extended to support graduated feature
2699 colourschemes, group associated annotation, and profile
2700 visualization settings.</li></td>
2703 <li>Source field in GFF files parsed as feature source
2704 rather than description</li>
2705 <li>Non-positional features are now included in sequence
2706 feature and gff files (controlled via non-positional feature
2707 visibility in tooltip).</li>
2708 <li>URL links generated for all feature links (bugfix)</li>
2709 <li>Added URL embedding instructions to features file
2711 <li>Codons containing ambiguous nucleotides translated as
2712 'X' in peptide product</li>
2713 <li>Match case switch in find dialog box works for both
2714 sequence ID and sequence string and query strings do not
2715 have to be in upper case to match case-insensitively.</li>
2716 <li>AMSA files only contain first column of
2717 multi-character column annotation labels</li>
2718 <li>Jalview Annotation File generation/parsing consistent
2719 with documentation (e.g. Stockholm annotation can be
2720 exported and re-imported)</li>
2721 <li>PDB files without embedded PDB IDs given a friendly
2723 <li>Find incrementally searches ID string matches as well
2724 as subsequence matches, and correctly reports total number
2728 <li>Better handling of exceptions during sequence
2730 <li>Dasobert generated non-positional feature URL
2731 link text excludes the start_end suffix</li>
2732 <li>DAS feature and source retrieval buttons disabled
2733 when fetch or registry operations in progress.</li>
2734 <li>PDB files retrieved from URLs are cached properly</li>
2735 <li>Sequence description lines properly shared via
2737 <li>Sequence fetcher fetches multiple records for all
2739 <li>Ensured that command line das feature retrieval
2740 completes before alignment figures are generated.</li>
2741 <li>Reduced time taken when opening file browser for
2743 <li>isAligned check prior to calculating tree, PCA or
2744 submitting an MSA to JNet now excludes hidden sequences.</li>
2745 <li>User defined group colours properly recovered
2746 from Jalview projects.</li>
2755 <div align="center">
2756 <strong>2.4.0.b2</strong><br> 28/10/2009
2761 <li>Experimental support for google analytics usage
2763 <li>Jalview privacy settings (user preferences and docs).</li>
2768 <li>Race condition in applet preventing startup in
2770 <li>Exception when feature created from selection beyond
2771 length of sequence.</li>
2772 <li>Allow synthetic PDB files to be imported gracefully</li>
2773 <li>Sequence associated annotation rows associate with
2774 all sequences with a given id</li>
2775 <li>Find function matches case-insensitively for sequence
2776 ID string searches</li>
2777 <li>Non-standard characters do not cause pairwise
2778 alignment to fail with exception</li>
2779 </ul> <em>Application Issues</em>
2781 <li>Sequences are now validated against EMBL database</li>
2782 <li>Sequence fetcher fetches multiple records for all
2784 </ul> <em>InstallAnywhere Issues</em>
2786 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2787 issue with installAnywhere mechanism)</li>
2788 <li>Command line launching of JARs from InstallAnywhere
2789 version (java class versioning error fixed)</li>
2796 <div align="center">
2797 <strong>2.4</strong><br> 27/8/2008
2800 <td><em>User Interface</em>
2802 <li>Linked highlighting of codon and amino acid from
2803 translation and protein products</li>
2804 <li>Linked highlighting of structure associated with
2805 residue mapping to codon position</li>
2806 <li>Sequence Fetcher provides example accession numbers
2807 and 'clear' button</li>
2808 <li>MemoryMonitor added as an option under Desktop's
2810 <li>Extract score function to parse whitespace separated
2811 numeric data in description line</li>
2812 <li>Column labels in alignment annotation can be centred.</li>
2813 <li>Tooltip for sequence associated annotation give name
2815 </ul> <em>Web Services and URL fetching</em>
2817 <li>JPred3 web service</li>
2818 <li>Prototype sequence search client (no public services
2820 <li>Fetch either seed alignment or full alignment from
2822 <li>URL Links created for matching database cross
2823 references as well as sequence ID</li>
2824 <li>URL Links can be created using regular-expressions</li>
2825 </ul> <em>Sequence Database Connectivity</em>
2827 <li>Retrieval of cross-referenced sequences from other
2829 <li>Generalised database reference retrieval and
2830 validation to all fetchable databases</li>
2831 <li>Fetch sequences from DAS sources supporting the
2832 sequence command</li>
2833 </ul> <em>Import and Export</em>
2834 <li>export annotation rows as CSV for spreadsheet import</li>
2835 <li>Jalview projects record alignment dataset associations,
2836 EMBL products, and cDNA sequence mappings</li>
2837 <li>Sequence Group colour can be specified in Annotation
2839 <li>Ad-hoc colouring of group in Annotation File using RGB
2840 triplet as name of colourscheme</li>
2841 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2843 <li>treenode binding for VAMSAS tree exchange</li>
2844 <li>local editing and update of sequences in VAMSAS
2845 alignments (experimental)</li>
2846 <li>Create new or select existing session to join</li>
2847 <li>load and save of vamsas documents</li>
2848 </ul> <em>Application command line</em>
2850 <li>-tree parameter to open trees (introduced for passing
2852 <li>-fetchfrom command line argument to specify nicknames
2853 of DAS servers to query for alignment features</li>
2854 <li>-dasserver command line argument to add new servers
2855 that are also automatically queried for features</li>
2856 <li>-groovy command line argument executes a given groovy
2857 script after all input data has been loaded and parsed</li>
2858 </ul> <em>Applet-Application data exchange</em>
2860 <li>Trees passed as applet parameters can be passed to
2861 application (when using "View in full
2862 application")</li>
2863 </ul> <em>Applet Parameters</em>
2865 <li>feature group display control parameter</li>
2866 <li>debug parameter</li>
2867 <li>showbutton parameter</li>
2868 </ul> <em>Applet API methods</em>
2870 <li>newView public method</li>
2871 <li>Window (current view) specific get/set public methods</li>
2872 <li>Feature display control methods</li>
2873 <li>get list of currently selected sequences</li>
2874 </ul> <em>New Jalview distribution features</em>
2876 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2877 <li>RELEASE file gives build properties for the latest
2878 Jalview release.</li>
2879 <li>Java 1.1 Applet build made easier and donotobfuscate
2880 property controls execution of obfuscator</li>
2881 <li>Build target for generating source distribution</li>
2882 <li>Debug flag for javacc</li>
2883 <li>.jalview_properties file is documented (slightly) in
2884 jalview.bin.Cache</li>
2885 <li>Continuous Build Integration for stable and
2886 development version of Application, Applet and source
2891 <li>selected region output includes visible annotations
2892 (for certain formats)</li>
2893 <li>edit label/displaychar contains existing label/char
2895 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2896 <li>shorter peptide product names from EMBL records</li>
2897 <li>Newick string generator makes compact representations</li>
2898 <li>bootstrap values parsed correctly for tree files with
2900 <li>pathological filechooser bug avoided by not allowing
2901 filenames containing a ':'</li>
2902 <li>Fixed exception when parsing GFF files containing
2903 global sequence features</li>
2904 <li>Alignment datasets are finalized only when number of
2905 references from alignment sequences goes to zero</li>
2906 <li>Close of tree branch colour box without colour
2907 selection causes cascading exceptions</li>
2908 <li>occasional negative imgwidth exceptions</li>
2909 <li>better reporting of non-fatal warnings to user when
2910 file parsing fails.</li>
2911 <li>Save works when Jalview project is default format</li>
2912 <li>Save as dialog opened if current alignment format is
2913 not a valid output format</li>
2914 <li>UniProt canonical names introduced for both das and
2916 <li>Histidine should be midblue (not pink!) in Zappo</li>
2917 <li>error messages passed up and output when data read
2919 <li>edit undo recovers previous dataset sequence when
2920 sequence is edited</li>
2921 <li>allow PDB files without pdb ID HEADER lines (like
2922 those generated by MODELLER) to be read in properly</li>
2923 <li>allow reading of JPred concise files as a normal
2925 <li>Stockholm annotation parsing and alignment properties
2926 import fixed for PFAM records</li>
2927 <li>Structure view windows have correct name in Desktop
2929 <li>annotation consisting of sequence associated scores
2930 can be read and written correctly to annotation file</li>
2931 <li>Aligned cDNA translation to aligned peptide works
2933 <li>Fixed display of hidden sequence markers and
2934 non-italic font for representatives in Applet</li>
2935 <li>Applet Menus are always embedded in applet window on
2937 <li>Newly shown features appear at top of stack (in
2939 <li>Annotations added via parameter not drawn properly
2940 due to null pointer exceptions</li>
2941 <li>Secondary structure lines are drawn starting from
2942 first column of alignment</li>
2943 <li>UniProt XML import updated for new schema release in
2945 <li>Sequence feature to sequence ID match for Features
2946 file is case-insensitive</li>
2947 <li>Sequence features read from Features file appended to
2948 all sequences with matching IDs</li>
2949 <li>PDB structure coloured correctly for associated views
2950 containing a sub-sequence</li>
2951 <li>PDB files can be retrieved by applet from Jar files</li>
2952 <li>feature and annotation file applet parameters
2953 referring to different directories are retrieved correctly</li>
2954 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
2955 <li>Fixed application hang whilst waiting for
2956 splash-screen version check to complete</li>
2957 <li>Applet properly URLencodes input parameter values
2958 when passing them to the launchApp service</li>
2959 <li>display name and local features preserved in results
2960 retrieved from web service</li>
2961 <li>Visual delay indication for sequence retrieval and
2962 sequence fetcher initialisation</li>
2963 <li>updated Application to use DAS 1.53e version of
2964 dasobert DAS client</li>
2965 <li>Re-instated Full AMSA support and .amsa file
2967 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
2975 <div align="center">
2976 <strong>2.3</strong><br> 9/5/07
2981 <li>Jmol 11.0.2 integration</li>
2982 <li>PDB views stored in Jalview XML files</li>
2983 <li>Slide sequences</li>
2984 <li>Edit sequence in place</li>
2985 <li>EMBL CDS features</li>
2986 <li>DAS Feature mapping</li>
2987 <li>Feature ordering</li>
2988 <li>Alignment Properties</li>
2989 <li>Annotation Scores</li>
2990 <li>Sort by scores</li>
2991 <li>Feature/annotation editing in applet</li>
2996 <li>Headless state operation in 2.2.1</li>
2997 <li>Incorrect and unstable DNA pairwise alignment</li>
2998 <li>Cut and paste of sequences with annotation</li>
2999 <li>Feature group display state in XML</li>
3000 <li>Feature ordering in XML</li>
3001 <li>blc file iteration selection using filename # suffix</li>
3002 <li>Stockholm alignment properties</li>
3003 <li>Stockhom alignment secondary structure annotation</li>
3004 <li>2.2.1 applet had no feature transparency</li>
3005 <li>Number pad keys can be used in cursor mode</li>
3006 <li>Structure Viewer mirror image resolved</li>
3013 <div align="center">
3014 <strong>2.2.1</strong><br> 12/2/07
3019 <li>Non standard characters can be read and displayed
3020 <li>Annotations/Features can be imported/exported to the
3022 <li>Applet allows editing of sequence/annotation/group
3023 name & description
3024 <li>Preference setting to display sequence name in
3026 <li>Annotation file format extended to allow
3027 Sequence_groups to be defined
3028 <li>Default opening of alignment overview panel can be
3029 specified in preferences
3030 <li>PDB residue numbering annotation added to associated
3036 <li>Applet crash under certain Linux OS with Java 1.6
3038 <li>Annotation file export / import bugs fixed
3039 <li>PNG / EPS image output bugs fixed
3045 <div align="center">
3046 <strong>2.2</strong><br> 27/11/06
3051 <li>Multiple views on alignment
3052 <li>Sequence feature editing
3053 <li>"Reload" alignment
3054 <li>"Save" to current filename
3055 <li>Background dependent text colour
3056 <li>Right align sequence ids
3057 <li>User-defined lower case residue colours
3060 <li>Menu item accelerator keys
3061 <li>Control-V pastes to current alignment
3062 <li>Cancel button for DAS Feature Fetching
3063 <li>PCA and PDB Viewers zoom via mouse roller
3064 <li>User-defined sub-tree colours and sub-tree selection
3066 <li>'New Window' button on the 'Output to Text box'
3071 <li>New memory efficient Undo/Redo System
3072 <li>Optimised symbol lookups and conservation/consensus
3074 <li>Region Conservation/Consensus recalculated after
3076 <li>Fixed Remove Empty Columns Bug (empty columns at end
3078 <li>Slowed DAS Feature Fetching for increased robustness.
3080 <li>Made angle brackets in ASCII feature descriptions
3082 <li>Re-instated Zoom function for PCA
3083 <li>Sequence descriptions conserved in web service
3085 <li>UniProt ID discoverer uses any word separated by
3087 <li>WsDbFetch query/result association resolved
3088 <li>Tree leaf to sequence mapping improved
3089 <li>Smooth fonts switch moved to FontChooser dialog box.
3096 <div align="center">
3097 <strong>2.1.1</strong><br> 12/9/06
3102 <li>Copy consensus sequence to clipboard</li>
3107 <li>Image output - rightmost residues are rendered if
3108 sequence id panel has been resized</li>
3109 <li>Image output - all offscreen group boundaries are
3111 <li>Annotation files with sequence references - all
3112 elements in file are relative to sequence position</li>
3113 <li>Mac Applet users can use Alt key for group editing</li>
3119 <div align="center">
3120 <strong>2.1</strong><br> 22/8/06
3125 <li>MAFFT Multiple Alignment in default Web Service list</li>
3126 <li>DAS Feature fetching</li>
3127 <li>Hide sequences and columns</li>
3128 <li>Export Annotations and Features</li>
3129 <li>GFF file reading / writing</li>
3130 <li>Associate structures with sequences from local PDB
3132 <li>Add sequences to exisiting alignment</li>
3133 <li>Recently opened files / URL lists</li>
3134 <li>Applet can launch the full application</li>
3135 <li>Applet has transparency for features (Java 1.2
3137 <li>Applet has user defined colours parameter</li>
3138 <li>Applet can load sequences from parameter
3139 "sequence<em>x</em>"
3145 <li>Redundancy Panel reinstalled in the Applet</li>
3146 <li>Monospaced font - EPS / rescaling bug fixed</li>
3147 <li>Annotation files with sequence references bug fixed</li>
3153 <div align="center">
3154 <strong>2.08.1</strong><br> 2/5/06
3159 <li>Change case of selected region from Popup menu</li>
3160 <li>Choose to match case when searching</li>
3161 <li>Middle mouse button and mouse movement can compress /
3162 expand the visible width and height of the alignment</li>
3167 <li>Annotation Panel displays complete JNet results</li>
3173 <div align="center">
3174 <strong>2.08b</strong><br> 18/4/06
3180 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3181 <li>Righthand label on wrapped alignments shows correct
3188 <div align="center">
3189 <strong>2.08</strong><br> 10/4/06
3194 <li>Editing can be locked to the selection area</li>
3195 <li>Keyboard editing</li>
3196 <li>Create sequence features from searches</li>
3197 <li>Precalculated annotations can be loaded onto
3199 <li>Features file allows grouping of features</li>
3200 <li>Annotation Colouring scheme added</li>
3201 <li>Smooth fonts off by default - Faster rendering</li>
3202 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3207 <li>Drag & Drop fixed on Linux</li>
3208 <li>Jalview Archive file faster to load/save, sequence
3209 descriptions saved.</li>
3215 <div align="center">
3216 <strong>2.07</strong><br> 12/12/05
3221 <li>PDB Structure Viewer enhanced</li>
3222 <li>Sequence Feature retrieval and display enhanced</li>
3223 <li>Choose to output sequence start-end after sequence
3224 name for file output</li>
3225 <li>Sequence Fetcher WSDBFetch@EBI</li>
3226 <li>Applet can read feature files, PDB files and can be
3227 used for HTML form input</li>
3232 <li>HTML output writes groups and features</li>
3233 <li>Group editing is Control and mouse click</li>
3234 <li>File IO bugs</li>
3240 <div align="center">
3241 <strong>2.06</strong><br> 28/9/05
3246 <li>View annotations in wrapped mode</li>
3247 <li>More options for PCA viewer</li>
3252 <li>GUI bugs resolved</li>
3253 <li>Runs with -nodisplay from command line</li>
3259 <div align="center">
3260 <strong>2.05b</strong><br> 15/9/05
3265 <li>Choose EPS export as lineart or text</li>
3266 <li>Jar files are executable</li>
3267 <li>Can read in Uracil - maps to unknown residue</li>
3272 <li>Known OutOfMemory errors give warning message</li>
3273 <li>Overview window calculated more efficiently</li>
3274 <li>Several GUI bugs resolved</li>
3280 <div align="center">
3281 <strong>2.05</strong><br> 30/8/05
3286 <li>Edit and annotate in "Wrapped" view</li>
3291 <li>Several GUI bugs resolved</li>
3297 <div align="center">
3298 <strong>2.04</strong><br> 24/8/05
3303 <li>Hold down mouse wheel & scroll to change font
3309 <li>Improved JPred client reliability</li>
3310 <li>Improved loading of Jalview files</li>
3316 <div align="center">
3317 <strong>2.03</strong><br> 18/8/05
3322 <li>Set Proxy server name and port in preferences</li>
3323 <li>Multiple URL links from sequence ids</li>
3324 <li>User Defined Colours can have a scheme name and added
3326 <li>Choose to ignore gaps in consensus calculation</li>
3327 <li>Unix users can set default web browser</li>
3328 <li>Runs without GUI for batch processing</li>
3329 <li>Dynamically generated Web Service Menus</li>
3334 <li>InstallAnywhere download for Sparc Solaris</li>
3340 <div align="center">
3341 <strong>2.02</strong><br> 18/7/05
3347 <li>Copy & Paste order of sequences maintains
3348 alignment order.</li>
3354 <div align="center">
3355 <strong>2.01</strong><br> 12/7/05
3360 <li>Use delete key for deleting selection.</li>
3361 <li>Use Mouse wheel to scroll sequences.</li>
3362 <li>Help file updated to describe how to add alignment
3364 <li>Version and build date written to build properties
3366 <li>InstallAnywhere installation will check for updates
3367 at launch of Jalview.</li>
3372 <li>Delete gaps bug fixed.</li>
3373 <li>FileChooser sorts columns.</li>
3374 <li>Can remove groups one by one.</li>
3375 <li>Filechooser icons installed.</li>
3376 <li>Finder ignores return character when searching.
3377 Return key will initiate a search.<br>
3384 <div align="center">
3385 <strong>2.0</strong><br> 20/6/05
3390 <li>New codebase</li>