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>
26 /* remove bullets, narrower indent */
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 -->Incorrect PDB-Uniprot mappings created
568 from SIFTs for April 2017 update due to 'null' strings in
580 <!-- JAL-2468 -->Switching between Nucleotide and Protein
581 score models doesn't always result in an updated PCA plot
584 <!-- JAL-2442 -->Features not rendered as transparent on
585 overview or linked structure view
588 <!-- JAL-2372 -->Colour group by conservation doesn't
592 <!-- JAL-2517 -->Hitting Cancel after applying
593 user-defined colourscheme doesn't restore original
597 <em>New Known Issues</em>
600 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
601 phase after a sequence motif find operation
604 <!-- JAL-2550 -->Importing annotation file with rows
605 containing just upper and lower case letters are
606 interpreted as WUSS rna secondary structure symbols
609 <!-- JAL-2590 -->Cannot load Newick trees from eggnog
616 <!-- JAL-2314 -->Unit test failure:
617 jalview.ws.jabaws.RNAStructExportImport setup fails
620 <!-- JAL-2307 -->Unit test failure:
621 jalview.ws.sifts.SiftsClientTest due to compatibility
622 problems with deep array comparison equality asserts in
623 successive versions of TestNG
626 <!-- JAL-2479 -->Relocated StructureChooserTest and
627 ParameterUtilsTest Unit tests to Network suite
634 <td width="60" nowrap>
636 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
639 <td><div align="left">
643 <!-- JAL-98 -->Improved memory usage: sparse arrays used
644 for all consensus calculations
647 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
650 <li>Updated Jalview's Certum code signing certificate
656 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
657 set of database cross-references, sorted alphabetically
660 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
661 from database cross references. Users with custom links
662 will receive a <a href="webServices/urllinks.html#warning">warning
663 dialog</a> asking them to update their preferences.
666 <!-- JAL-2287-->Cancel button and escape listener on
667 dialog warning user about disconnecting Jalview from a
671 <!-- JAL-2320-->Jalview's Chimera control window closes if
672 the Chimera it is connected to is shut down
675 <!-- JAL-1738-->New keystroke (B) and Select highlighted
676 columns menu item to mark columns containing highlighted
677 regions (e.g. from structure selections or results of a
681 <!-- JAL-2284-->Command line option for batch-generation
682 of HTML pages rendering alignment data with the BioJS
692 <!-- JAL-2286 -->Columns with more than one modal residue
693 are not coloured or thresholded according to percent
694 identity (first observed in Jalview 2.8.2)
697 <!-- JAL-2301 -->Threonine incorrectly reported as not
701 <!-- JAL-2318 -->Updates to documentation pages (above PID
702 threshold, amino acid properties)
705 <!-- JAL-2292 -->Lower case residues in sequences are not
706 reported as mapped to residues in a structure file in the
710 <!--JAL-2324 -->Identical features with non-numeric scores
711 could be added multiple times to a sequence
714 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
715 bond features shown as two highlighted residues rather
716 than a range in linked structure views, and treated
717 correctly when selecting and computing trees from features
720 <!-- JAL-2281-->Custom URL links for database
721 cross-references are matched to database name regardless
729 <!-- JAL-2282-->Custom URL links for specific database
730 names without regular expressions also offer links from
734 <!-- JAL-2315-->Removing a single configured link in the
735 URL links pane in Connections preferences doesn't actually
736 update Jalview configuration
739 <!-- JAL-2272-->CTRL-Click on a selected region to open
740 the alignment area popup menu doesn't work on El-Capitan
743 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
744 files with similarly named sequences if dropped onto the
748 <!-- JAL-2312 -->Additional mappings are shown for PDB
749 entries where more chains exist in the PDB accession than
750 are reported in the SIFTS file
753 <!-- JAL-2317-->Certain structures do not get mapped to
754 the structure view when displayed with Chimera
757 <!-- JAL-2317-->No chains shown in the Chimera view
758 panel's View->Show Chains submenu
761 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
762 work for wrapped alignment views
765 <!--JAL-2197 -->Rename UI components for running JPred
766 predictions from 'JNet' to 'JPred'
769 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
770 corrupted when annotation panel vertical scroll is not at
774 <!--JAL-2332 -->Attempting to view structure for Hen
775 lysozyme results in a PDB Client error dialog box
778 <!-- JAL-2319 -->Structure View's mapping report switched
779 ranges for PDB and sequence for SIFTS
782 SIFTS 'Not_Observed' residues mapped to non-existant
786 <!-- <em>New Known Issues</em>
793 <td width="60" nowrap>
795 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
796 <em>25/10/2016</em></strong>
799 <td><em>Application</em>
801 <li>3D Structure chooser opens with 'Cached structures'
802 view if structures already loaded</li>
803 <li>Progress bar reports models as they are loaded to
810 <li>Colour by conservation always enabled and no tick
811 shown in menu when BLOSUM or PID shading applied</li>
812 <li>FER1_ARATH and FER2_ARATH labels were switched in
813 example sequences/projects/trees</li>
817 <li>Jalview projects with views of local PDB structure
818 files saved on Windows cannot be opened on OSX</li>
819 <li>Multiple structure views can be opened and superposed
820 without timeout for structures with multiple models or
821 multiple sequences in alignment</li>
822 <li>Cannot import or associated local PDB files without a
823 PDB ID HEADER line</li>
824 <li>RMSD is not output in Jmol console when superposition
826 <li>Drag and drop of URL from Browser fails for Linux and
827 OSX versions earlier than El Capitan</li>
828 <li>ENA client ignores invalid content from ENA server</li>
829 <li>Exceptions are not raised in console when ENA client
830 attempts to fetch non-existent IDs via Fetch DB Refs UI
832 <li>Exceptions are not raised in console when a new view
833 is created on the alignment</li>
834 <li>OSX right-click fixed for group selections: CMD-click
835 to insert/remove gaps in groups and CTRL-click to open group
838 <em>Build and deployment</em>
840 <li>URL link checker now copes with multi-line anchor
843 <em>New Known Issues</em>
845 <li>Drag and drop from URL links in browsers do not work
852 <td width="60" nowrap>
854 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
860 <!-- JAL-2124 -->Updated Spanish translations.
863 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
864 for importing structure data to Jalview. Enables mmCIF and
868 <!-- JAL-192 --->Alignment ruler shows positions relative to
872 <!-- JAL-2202 -->Position/residue shown in status bar when
873 mousing over sequence associated annotation
876 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
880 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
881 '()', canonical '[]' and invalid '{}' base pair populations
885 <!-- JAL-2092 -->Feature settings popup menu options for
886 showing or hiding columns containing a feature
889 <!-- JAL-1557 -->Edit selected group by double clicking on
890 group and sequence associated annotation labels
893 <!-- JAL-2236 -->Sequence name added to annotation label in
894 select/hide columns by annotation and colour by annotation
898 </ul> <em>Application</em>
901 <!-- JAL-2050-->Automatically hide introns when opening a
905 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
909 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
910 structure mappings with the EMBL-EBI PDBe SIFTS database
913 <!-- JAL-2079 -->Updated download sites used for Rfam and
914 Pfam sources to xfam.org
917 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
920 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
921 over sequences in Jalview
924 <!-- JAL-2027-->Support for reverse-complement coding
925 regions in ENA and EMBL
928 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
929 for record retrieval via ENA rest API
932 <!-- JAL-2027 -->Support for ENA CDS records with reverse
936 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
937 groovy script execution
940 <!-- JAL-1812 -->New 'execute Groovy script' option in an
941 alignment window's Calculate menu
944 <!-- JAL-1812 -->Allow groovy scripts that call
945 Jalview.getAlignFrames() to run in headless mode
948 <!-- JAL-2068 -->Support for creating new alignment
949 calculation workers from groovy scripts
952 <!-- JAL-1369 --->Store/restore reference sequence in
956 <!-- JAL-1803 -->Chain codes for a sequence's PDB
957 associations are now saved/restored from project
960 <!-- JAL-1993 -->Database selection dialog always shown
961 before sequence fetcher is opened
964 <!-- JAL-2183 -->Double click on an entry in Jalview's
965 database chooser opens a sequence fetcher
968 <!-- JAL-1563 -->Free-text search client for UniProt using
972 <!-- JAL-2168 -->-nonews command line parameter to prevent
973 the news reader opening
976 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
977 querying stored in preferences
980 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
984 <!-- JAL-1977-->Tooltips shown on database chooser
987 <!-- JAL-391 -->Reverse complement function in calculate
988 menu for nucleotide sequences
991 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
992 and feature counts preserves alignment ordering (and
993 debugged for complex feature sets).
996 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
997 viewing structures with Jalview 2.10
1000 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1001 genome, transcript CCDS and gene ids via the Ensembl and
1002 Ensembl Genomes REST API
1005 <!-- JAL-2049 -->Protein sequence variant annotation
1006 computed for 'sequence_variant' annotation on CDS regions
1010 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1014 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1015 Ref Fetcher fails to match, or otherwise updates sequence
1016 data from external database records.
1019 <!-- JAL-2154 -->Revised Jalview Project format for
1020 efficient recovery of sequence coding and alignment
1021 annotation relationships.
1023 </ul> <!-- <em>Applet</em>
1034 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1038 <!-- JAL-2018-->Export features in Jalview format (again)
1039 includes graduated colourschemes
1042 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1043 working with big alignments and lots of hidden columns
1046 <!-- JAL-2053-->Hidden column markers not always rendered
1047 at right of alignment window
1050 <!-- JAL-2067 -->Tidied up links in help file table of
1054 <!-- JAL-2072 -->Feature based tree calculation not shown
1058 <!-- JAL-2075 -->Hidden columns ignored during feature
1059 based tree calculation
1062 <!-- JAL-2065 -->Alignment view stops updating when show
1063 unconserved enabled for group on alignment
1066 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1070 <!-- JAL-2146 -->Alignment column in status incorrectly
1071 shown as "Sequence position" when mousing over
1075 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1076 hidden columns present
1079 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1080 user created annotation added to alignment
1083 <!-- JAL-1841 -->RNA Structure consensus only computed for
1084 '()' base pair annotation
1087 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1088 in zero scores for all base pairs in RNA Structure
1092 <!-- JAL-2174-->Extend selection with columns containing
1096 <!-- JAL-2275 -->Pfam format writer puts extra space at
1097 beginning of sequence
1100 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1104 <!-- JAL-2238 -->Cannot create groups on an alignment from
1105 from a tree when t-coffee scores are shown
1108 <!-- JAL-1836,1967 -->Cannot import and view PDB
1109 structures with chains containing negative resnums (4q4h)
1112 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1116 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1117 to Clustal, PIR and PileUp output
1120 <!-- JAL-2008 -->Reordering sequence features that are
1121 not visible causes alignment window to repaint
1124 <!-- JAL-2006 -->Threshold sliders don't work in
1125 graduated colour and colour by annotation row for e-value
1126 scores associated with features and annotation rows
1129 <!-- JAL-1797 -->amino acid physicochemical conservation
1130 calculation should be case independent
1133 <!-- JAL-2173 -->Remove annotation also updates hidden
1137 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1138 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1139 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1142 <!-- JAL-2065 -->Null pointer exceptions and redraw
1143 problems when reference sequence defined and 'show
1144 non-conserved' enabled
1147 <!-- JAL-1306 -->Quality and Conservation are now shown on
1148 load even when Consensus calculation is disabled
1151 <!-- JAL-1932 -->Remove right on penultimate column of
1152 alignment does nothing
1155 <em>Application</em>
1158 <!-- JAL-1552-->URLs and links can't be imported by
1159 drag'n'drop on OSX when launched via webstart (note - not
1160 yet fixed for El Capitan)
1163 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1164 output when running on non-gb/us i18n platforms
1167 <!-- JAL-1944 -->Error thrown when exporting a view with
1168 hidden sequences as flat-file alignment
1171 <!-- JAL-2030-->InstallAnywhere distribution fails when
1175 <!-- JAL-2080-->Jalview very slow to launch via webstart
1176 (also hotfix for 2.9.0b2)
1179 <!-- JAL-2085 -->Cannot save project when view has a
1180 reference sequence defined
1183 <!-- JAL-1011 -->Columns are suddenly selected in other
1184 alignments and views when revealing hidden columns
1187 <!-- JAL-1989 -->Hide columns not mirrored in complement
1188 view in a cDNA/Protein splitframe
1191 <!-- JAL-1369 -->Cannot save/restore representative
1192 sequence from project when only one sequence is
1196 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1197 in Structure Chooser
1200 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1201 structure consensus didn't refresh annotation panel
1204 <!-- JAL-1962 -->View mapping in structure view shows
1205 mappings between sequence and all chains in a PDB file
1208 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1209 dialogs format columns correctly, don't display array
1210 data, sort columns according to type
1213 <!-- JAL-1975 -->Export complete shown after destination
1214 file chooser is cancelled during an image export
1217 <!-- JAL-2025 -->Error when querying PDB Service with
1218 sequence name containing special characters
1221 <!-- JAL-2024 -->Manual PDB structure querying should be
1225 <!-- JAL-2104 -->Large tooltips with broken HTML
1226 formatting don't wrap
1229 <!-- JAL-1128 -->Figures exported from wrapped view are
1230 truncated so L looks like I in consensus annotation
1233 <!-- JAL-2003 -->Export features should only export the
1234 currently displayed features for the current selection or
1238 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1239 after fetching cross-references, and restoring from
1243 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1244 followed in the structure viewer
1247 <!-- JAL-2163 -->Titles for individual alignments in
1248 splitframe not restored from project
1251 <!-- JAL-2145 -->missing autocalculated annotation at
1252 trailing end of protein alignment in transcript/product
1253 splitview when pad-gaps not enabled by default
1256 <!-- JAL-1797 -->amino acid physicochemical conservation
1260 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1261 article has been read (reopened issue due to
1262 internationalisation problems)
1265 <!-- JAL-1960 -->Only offer PDB structures in structure
1266 viewer based on sequence name, PDB and UniProt
1271 <!-- JAL-1976 -->No progress bar shown during export of
1275 <!-- JAL-2213 -->Structures not always superimposed after
1276 multiple structures are shown for one or more sequences.
1279 <!-- JAL-1370 -->Reference sequence characters should not
1280 be replaced with '.' when 'Show unconserved' format option
1284 <!-- JAL-1823 -->Cannot specify chain code when entering
1285 specific PDB id for sequence
1288 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1289 'Export hidden sequences' is enabled, but 'export hidden
1290 columns' is disabled.
1293 <!--JAL-2026-->Best Quality option in structure chooser
1294 selects lowest rather than highest resolution structures
1298 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1299 to sequence mapping in 'View Mappings' report
1302 <!-- JAL-2284 -->Unable to read old Jalview projects that
1303 contain non-XML data added after Jalvew wrote project.
1306 <!-- JAL-2118 -->Newly created annotation row reorders
1307 after clicking on it to create new annotation for a
1310 <!-- may exclude, this is an external service stability issue JAL-1941
1311 -- > RNA 3D structure not added via DSSR service</li> -->
1316 <!-- JAL-2151 -->Incorrect columns are selected when
1317 hidden columns present before start of sequence
1320 <!-- JAL-1986 -->Missing dependencies on applet pages
1324 <!-- JAL-1947 -->Overview pixel size changes when
1325 sequences are hidden in applet
1328 <!-- JAL-1996 -->Updated instructions for applet
1329 deployment on examples pages.
1336 <td width="60" nowrap>
1337 <div align="center">
1338 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1339 <em>16/10/2015</em></strong>
1342 <td><em>General</em>
1344 <li>Time stamps for signed Jalview application and applet
1349 <em>Application</em>
1351 <li>Duplicate group consensus and conservation rows
1352 shown when tree is partitioned</li>
1353 <li>Erratic behaviour when tree partitions made with
1354 multiple cDNA/Protein split views</li>
1360 <td width="60" nowrap>
1361 <div align="center">
1362 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1363 <em>8/10/2015</em></strong>
1366 <td><em>General</em>
1368 <li>Updated Spanish translations of localized text for
1370 </ul> <em>Application</em>
1372 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1373 <li>Signed OSX InstallAnywhere installer<br></li>
1374 <li>Support for per-sequence based annotations in BioJSON</li>
1375 </ul> <em>Applet</em>
1377 <li>Split frame example added to applet examples page</li>
1378 </ul> <em>Build and Deployment</em>
1381 <!-- JAL-1888 -->New ant target for running Jalview's test
1389 <li>Mapping of cDNA to protein in split frames
1390 incorrect when sequence start > 1</li>
1391 <li>Broken images in filter column by annotation dialog
1393 <li>Feature colours not parsed from features file</li>
1394 <li>Exceptions and incomplete link URLs recovered when
1395 loading a features file containing HTML tags in feature
1399 <em>Application</em>
1401 <li>Annotations corrupted after BioJS export and
1403 <li>Incorrect sequence limits after Fetch DB References
1404 with 'trim retrieved sequences'</li>
1405 <li>Incorrect warning about deleting all data when
1406 deleting selected columns</li>
1407 <li>Patch to build system for shipping properly signed
1408 JNLP templates for webstart launch</li>
1409 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1410 unreleased structures for download or viewing</li>
1411 <li>Tab/space/return keystroke operation of EMBL-PDBe
1412 fetcher/viewer dialogs works correctly</li>
1413 <li>Disabled 'minimise' button on Jalview windows
1414 running on OSX to workaround redraw hang bug</li>
1415 <li>Split cDNA/Protein view position and geometry not
1416 recovered from jalview project</li>
1417 <li>Initial enabled/disabled state of annotation menu
1418 sorter 'show autocalculated first/last' corresponds to
1420 <li>Restoring of Clustal, RNA Helices and T-Coffee
1421 color schemes from BioJSON</li>
1425 <li>Reorder sequences mirrored in cDNA/Protein split
1427 <li>Applet with Jmol examples not loading correctly</li>
1433 <td><div align="center">
1434 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1436 <td><em>General</em>
1438 <li>Linked visualisation and analysis of DNA and Protein
1441 <li>Translated cDNA alignments shown as split protein
1442 and DNA alignment views</li>
1443 <li>Codon consensus annotation for linked protein and
1444 cDNA alignment views</li>
1445 <li>Link cDNA or Protein product sequences by loading
1446 them onto Protein or cDNA alignments</li>
1447 <li>Reconstruct linked cDNA alignment from aligned
1448 protein sequences</li>
1451 <li>Jmol integration updated to Jmol v14.2.14</li>
1452 <li>Import and export of Jalview alignment views as <a
1453 href="features/bioJsonFormat.html">BioJSON</a></li>
1454 <li>New alignment annotation file statements for
1455 reference sequences and marking hidden columns</li>
1456 <li>Reference sequence based alignment shading to
1457 highlight variation</li>
1458 <li>Select or hide columns according to alignment
1460 <li>Find option for locating sequences by description</li>
1461 <li>Conserved physicochemical properties shown in amino
1462 acid conservation row</li>
1463 <li>Alignments can be sorted by number of RNA helices</li>
1464 </ul> <em>Application</em>
1466 <li>New cDNA/Protein analysis capabilities
1468 <li>Get Cross-References should open a Split Frame
1469 view with cDNA/Protein</li>
1470 <li>Detect when nucleotide sequences and protein
1471 sequences are placed in the same alignment</li>
1472 <li>Split cDNA/Protein views are saved in Jalview
1477 <li>Use REST API to talk to Chimera</li>
1478 <li>Selected regions in Chimera are highlighted in linked
1479 Jalview windows</li>
1481 <li>VARNA RNA viewer updated to v3.93</li>
1482 <li>VARNA views are saved in Jalview Projects</li>
1483 <li>Pseudoknots displayed as Jalview RNA annotation can
1484 be shown in VARNA</li>
1486 <li>Make groups for selection uses marked columns as well
1487 as the active selected region</li>
1489 <li>Calculate UPGMA and NJ trees using sequence feature
1491 <li>New Export options
1493 <li>New Export Settings dialog to control hidden
1494 region export in flat file generation</li>
1496 <li>Export alignment views for display with the <a
1497 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1499 <li>Export scrollable SVG in HTML page</li>
1500 <li>Optional embedding of BioJSON data when exporting
1501 alignment figures to HTML</li>
1503 <li>3D structure retrieval and display
1505 <li>Free text and structured queries with the PDBe
1507 <li>PDBe Search API based discovery and selection of
1508 PDB structures for a sequence set</li>
1512 <li>JPred4 employed for protein secondary structure
1514 <li>Hide Insertions menu option to hide unaligned columns
1515 for one or a group of sequences</li>
1516 <li>Automatically hide insertions in alignments imported
1517 from the JPred4 web server</li>
1518 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1519 system on OSX<br />LGPL libraries courtesy of <a
1520 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1522 <li>changed 'View nucleotide structure' submenu to 'View
1523 VARNA 2D Structure'</li>
1524 <li>change "View protein structure" menu option to "3D
1527 </ul> <em>Applet</em>
1529 <li>New layout for applet example pages</li>
1530 <li>New parameters to enable SplitFrame view
1531 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1532 <li>New example demonstrating linked viewing of cDNA and
1533 Protein alignments</li>
1534 </ul> <em>Development and deployment</em>
1536 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1537 <li>Include installation type and git revision in build
1538 properties and console log output</li>
1539 <li>Jalview Github organisation, and new github site for
1540 storing BioJsMSA Templates</li>
1541 <li>Jalview's unit tests now managed with TestNG</li>
1544 <!-- <em>General</em>
1546 </ul> --> <!-- issues resolved --> <em>Application</em>
1548 <li>Escape should close any open find dialogs</li>
1549 <li>Typo in select-by-features status report</li>
1550 <li>Consensus RNA secondary secondary structure
1551 predictions are not highlighted in amber</li>
1552 <li>Missing gap character in v2.7 example file means
1553 alignment appears unaligned when pad-gaps is not enabled</li>
1554 <li>First switch to RNA Helices colouring doesn't colour
1555 associated structure views</li>
1556 <li>ID width preference option is greyed out when auto
1557 width checkbox not enabled</li>
1558 <li>Stopped a warning dialog from being shown when
1559 creating user defined colours</li>
1560 <li>'View Mapping' in structure viewer shows sequence
1561 mappings for just that viewer's sequences</li>
1562 <li>Workaround for superposing PDB files containing
1563 multiple models in Chimera</li>
1564 <li>Report sequence position in status bar when hovering
1565 over Jmol structure</li>
1566 <li>Cannot output gaps as '.' symbols with Selection ->
1567 output to text box</li>
1568 <li>Flat file exports of alignments with hidden columns
1569 have incorrect sequence start/end</li>
1570 <li>'Aligning' a second chain to a Chimera structure from
1572 <li>Colour schemes applied to structure viewers don't
1573 work for nucleotide</li>
1574 <li>Loading/cut'n'pasting an empty or invalid file leads
1575 to a grey/invisible alignment window</li>
1576 <li>Exported Jpred annotation from a sequence region
1577 imports to different position</li>
1578 <li>Space at beginning of sequence feature tooltips shown
1579 on some platforms</li>
1580 <li>Chimera viewer 'View | Show Chain' menu is not
1582 <li>'New View' fails with a Null Pointer Exception in
1583 console if Chimera has been opened</li>
1584 <li>Mouseover to Chimera not working</li>
1585 <li>Miscellaneous ENA XML feature qualifiers not
1587 <li>NPE in annotation renderer after 'Extract Scores'</li>
1588 <li>If two structures in one Chimera window, mouseover of
1589 either sequence shows on first structure</li>
1590 <li>'Show annotations' options should not make
1591 non-positional annotations visible</li>
1592 <li>Subsequence secondary structure annotation not shown
1593 in right place after 'view flanking regions'</li>
1594 <li>File Save As type unset when current file format is
1596 <li>Save as '.jar' option removed for saving Jalview
1598 <li>Colour by Sequence colouring in Chimera more
1600 <li>Cannot 'add reference annotation' for a sequence in
1601 several views on same alignment</li>
1602 <li>Cannot show linked products for EMBL / ENA records</li>
1603 <li>Jalview's tooltip wraps long texts containing no
1605 </ul> <em>Applet</em>
1607 <li>Jmol to JalviewLite mouseover/link not working</li>
1608 <li>JalviewLite can't import sequences with ID
1609 descriptions containing angle brackets</li>
1610 </ul> <em>General</em>
1612 <li>Cannot export and reimport RNA secondary structure
1613 via jalview annotation file</li>
1614 <li>Random helix colour palette for colour by annotation
1615 with RNA secondary structure</li>
1616 <li>Mouseover to cDNA from STOP residue in protein
1617 translation doesn't work.</li>
1618 <li>hints when using the select by annotation dialog box</li>
1619 <li>Jmol alignment incorrect if PDB file has alternate CA
1621 <li>FontChooser message dialog appears to hang after
1622 choosing 1pt font</li>
1623 <li>Peptide secondary structure incorrectly imported from
1624 annotation file when annotation display text includes 'e' or
1626 <li>Cannot set colour of new feature type whilst creating
1628 <li>cDNA translation alignment should not be sequence
1629 order dependent</li>
1630 <li>'Show unconserved' doesn't work for lower case
1632 <li>Nucleotide ambiguity codes involving R not recognised</li>
1633 </ul> <em>Deployment and Documentation</em>
1635 <li>Applet example pages appear different to the rest of
1636 www.jalview.org</li>
1637 </ul> <em>Application Known issues</em>
1639 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1640 <li>Misleading message appears after trying to delete
1642 <li>Jalview icon not shown in dock after InstallAnywhere
1643 version launches</li>
1644 <li>Fetching EMBL reference for an RNA sequence results
1645 fails with a sequence mismatch</li>
1646 <li>Corrupted or unreadable alignment display when
1647 scrolling alignment to right</li>
1648 <li>ArrayIndexOutOfBoundsException thrown when remove
1649 empty columns called on alignment with ragged gapped ends</li>
1650 <li>auto calculated alignment annotation rows do not get
1651 placed above or below non-autocalculated rows</li>
1652 <li>Jalview dekstop becomes sluggish at full screen in
1653 ultra-high resolution</li>
1654 <li>Cannot disable consensus calculation independently of
1655 quality and conservation</li>
1656 <li>Mouseover highlighting between cDNA and protein can
1657 become sluggish with more than one splitframe shown</li>
1658 </ul> <em>Applet Known Issues</em>
1660 <li>Core PDB parsing code requires Jmol</li>
1661 <li>Sequence canvas panel goes white when alignment
1662 window is being resized</li>
1668 <td><div align="center">
1669 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1671 <td><em>General</em>
1673 <li>Updated Java code signing certificate donated by
1675 <li>Features and annotation preserved when performing
1676 pairwise alignment</li>
1677 <li>RNA pseudoknot annotation can be
1678 imported/exported/displayed</li>
1679 <li>'colour by annotation' can colour by RNA and
1680 protein secondary structure</li>
1681 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1682 post-hoc with 2.9 release</em>)
1685 </ul> <em>Application</em>
1687 <li>Extract and display secondary structure for sequences
1688 with 3D structures</li>
1689 <li>Support for parsing RNAML</li>
1690 <li>Annotations menu for layout
1692 <li>sort sequence annotation rows by alignment</li>
1693 <li>place sequence annotation above/below alignment
1696 <li>Output in Stockholm format</li>
1697 <li>Internationalisation: improved Spanish (es)
1699 <li>Structure viewer preferences tab</li>
1700 <li>Disorder and Secondary Structure annotation tracks
1701 shared between alignments</li>
1702 <li>UCSF Chimera launch and linked highlighting from
1704 <li>Show/hide all sequence associated annotation rows for
1705 all or current selection</li>
1706 <li>disorder and secondary structure predictions
1707 available as dataset annotation</li>
1708 <li>Per-sequence rna helices colouring</li>
1711 <li>Sequence database accessions imported when fetching
1712 alignments from Rfam</li>
1713 <li>update VARNA version to 3.91</li>
1715 <li>New groovy scripts for exporting aligned positions,
1716 conservation values, and calculating sum of pairs scores.</li>
1717 <li>Command line argument to set default JABAWS server</li>
1718 <li>include installation type in build properties and
1719 console log output</li>
1720 <li>Updated Jalview project format to preserve dataset
1724 <!-- issues resolved --> <em>Application</em>
1726 <li>Distinguish alignment and sequence associated RNA
1727 structure in structure->view->VARNA</li>
1728 <li>Raise dialog box if user deletes all sequences in an
1730 <li>Pressing F1 results in documentation opening twice</li>
1731 <li>Sequence feature tooltip is wrapped</li>
1732 <li>Double click on sequence associated annotation
1733 selects only first column</li>
1734 <li>Redundancy removal doesn't result in unlinked
1735 leaves shown in tree</li>
1736 <li>Undos after several redundancy removals don't undo
1738 <li>Hide sequence doesn't hide associated annotation</li>
1739 <li>User defined colours dialog box too big to fit on
1740 screen and buttons not visible</li>
1741 <li>author list isn't updated if already written to
1742 Jalview properties</li>
1743 <li>Popup menu won't open after retrieving sequence
1745 <li>File open window for associate PDB doesn't open</li>
1746 <li>Left-then-right click on a sequence id opens a
1747 browser search window</li>
1748 <li>Cannot open sequence feature shading/sort popup menu
1749 in feature settings dialog</li>
1750 <li>better tooltip placement for some areas of Jalview
1752 <li>Allow addition of JABAWS Server which doesn't
1753 pass validation</li>
1754 <li>Web services parameters dialog box is too large to
1756 <li>Muscle nucleotide alignment preset obscured by
1758 <li>JABAWS preset submenus don't contain newly
1759 defined user preset</li>
1760 <li>MSA web services warns user if they were launched
1761 with invalid input</li>
1762 <li>Jalview cannot contact DAS Registy when running on
1765 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1766 'Superpose with' submenu not shown when new view
1770 </ul> <!-- <em>Applet</em>
1772 </ul> <em>General</em>
1774 </ul>--> <em>Deployment and Documentation</em>
1776 <li>2G and 1G options in launchApp have no effect on
1777 memory allocation</li>
1778 <li>launchApp service doesn't automatically open
1779 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1781 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1782 InstallAnywhere reports cannot find valid JVM when Java
1783 1.7_055 is available
1785 </ul> <em>Application Known issues</em>
1788 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1789 corrupted or unreadable alignment display when scrolling
1793 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1794 retrieval fails but progress bar continues for DAS retrieval
1795 with large number of ID
1798 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1799 flatfile output of visible region has incorrect sequence
1803 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1804 rna structure consensus doesn't update when secondary
1805 structure tracks are rearranged
1808 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1809 invalid rna structure positional highlighting does not
1810 highlight position of invalid base pairs
1813 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1814 out of memory errors are not raised when saving Jalview
1815 project from alignment window file menu
1818 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1819 Switching to RNA Helices colouring doesn't propagate to
1823 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1824 colour by RNA Helices not enabled when user created
1825 annotation added to alignment
1828 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1829 Jalview icon not shown on dock in Mountain Lion/Webstart
1831 </ul> <em>Applet Known Issues</em>
1834 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1835 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1838 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1839 Jalview and Jmol example not compatible with IE9
1842 <li>Sort by annotation score doesn't reverse order
1848 <td><div align="center">
1849 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1852 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1855 <li>Internationalisation of user interface (usually
1856 called i18n support) and translation for Spanish locale</li>
1857 <li>Define/Undefine group on current selection with
1858 Ctrl-G/Shift Ctrl-G</li>
1859 <li>Improved group creation/removal options in
1860 alignment/sequence Popup menu</li>
1861 <li>Sensible precision for symbol distribution
1862 percentages shown in logo tooltip.</li>
1863 <li>Annotation panel height set according to amount of
1864 annotation when alignment first opened</li>
1865 </ul> <em>Application</em>
1867 <li>Interactive consensus RNA secondary structure
1868 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1869 <li>Select columns containing particular features from
1870 Feature Settings dialog</li>
1871 <li>View all 'representative' PDB structures for selected
1873 <li>Update Jalview project format:
1875 <li>New file extension for Jalview projects '.jvp'</li>
1876 <li>Preserve sequence and annotation dataset (to
1877 store secondary structure annotation,etc)</li>
1878 <li>Per group and alignment annotation and RNA helix
1882 <li>New similarity measures for PCA and Tree calculation
1884 <li>Experimental support for retrieval and viewing of
1885 flanking regions for an alignment</li>
1889 <!-- issues resolved --> <em>Application</em>
1891 <li>logo keeps spinning and status remains at queued or
1892 running after job is cancelled</li>
1893 <li>cannot export features from alignments imported from
1894 Jalview/VAMSAS projects</li>
1895 <li>Buggy slider for web service parameters that take
1897 <li>Newly created RNA secondary structure line doesn't
1898 have 'display all symbols' flag set</li>
1899 <li>T-COFFEE alignment score shading scheme and other
1900 annotation shading not saved in Jalview project</li>
1901 <li>Local file cannot be loaded in freshly downloaded
1903 <li>Jalview icon not shown on dock in Mountain
1905 <li>Load file from desktop file browser fails</li>
1906 <li>Occasional NPE thrown when calculating large trees</li>
1907 <li>Cannot reorder or slide sequences after dragging an
1908 alignment onto desktop</li>
1909 <li>Colour by annotation dialog throws NPE after using
1910 'extract scores' function</li>
1911 <li>Loading/cut'n'pasting an empty file leads to a grey
1912 alignment window</li>
1913 <li>Disorder thresholds rendered incorrectly after
1914 performing IUPred disorder prediction</li>
1915 <li>Multiple group annotated consensus rows shown when
1916 changing 'normalise logo' display setting</li>
1917 <li>Find shows blank dialog after 'finished searching' if
1918 nothing matches query</li>
1919 <li>Null Pointer Exceptions raised when sorting by
1920 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1922 <li>Errors in Jmol console when structures in alignment
1923 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1925 <li>Not all working JABAWS services are shown in
1927 <li>JAVAWS version of Jalview fails to launch with
1928 'invalid literal/length code'</li>
1929 <li>Annotation/RNA Helix colourschemes cannot be applied
1930 to alignment with groups (actually fixed in 2.8.0b1)</li>
1931 <li>RNA Helices and T-Coffee Scores available as default
1934 </ul> <em>Applet</em>
1936 <li>Remove group option is shown even when selection is
1938 <li>Apply to all groups ticked but colourscheme changes
1939 don't affect groups</li>
1940 <li>Documented RNA Helices and T-Coffee Scores as valid
1941 colourscheme name</li>
1942 <li>Annotation labels drawn on sequence IDs when
1943 Annotation panel is not displayed</li>
1944 <li>Increased font size for dropdown menus on OSX and
1945 embedded windows</li>
1946 </ul> <em>Other</em>
1948 <li>Consensus sequence for alignments/groups with a
1949 single sequence were not calculated</li>
1950 <li>annotation files that contain only groups imported as
1951 annotation and junk sequences</li>
1952 <li>Fasta files with sequences containing '*' incorrectly
1953 recognised as PFAM or BLC</li>
1954 <li>conservation/PID slider apply all groups option
1955 doesn't affect background (2.8.0b1)
1957 <li>redundancy highlighting is erratic at 0% and 100%</li>
1958 <li>Remove gapped columns fails for sequences with ragged
1960 <li>AMSA annotation row with leading spaces is not
1961 registered correctly on import</li>
1962 <li>Jalview crashes when selecting PCA analysis for
1963 certain alignments</li>
1964 <li>Opening the colour by annotation dialog for an
1965 existing annotation based 'use original colours'
1966 colourscheme loses original colours setting</li>
1971 <td><div align="center">
1972 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
1973 <em>30/1/2014</em></strong>
1977 <li>Trusted certificates for JalviewLite applet and
1978 Jalview Desktop application<br />Certificate was donated by
1979 <a href="https://www.certum.eu">Certum</a> to the Jalview
1980 open source project).
1982 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
1983 <li>Output in Stockholm format</li>
1984 <li>Allow import of data from gzipped files</li>
1985 <li>Export/import group and sequence associated line
1986 graph thresholds</li>
1987 <li>Nucleotide substitution matrix that supports RNA and
1988 ambiguity codes</li>
1989 <li>Allow disorder predictions to be made on the current
1990 selection (or visible selection) in the same way that JPred
1992 <li>Groovy scripting for headless Jalview operation</li>
1993 </ul> <em>Other improvements</em>
1995 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
1996 <li>COMBINE statement uses current SEQUENCE_REF and
1997 GROUP_REF scope to group annotation rows</li>
1998 <li>Support '' style escaping of quotes in Newick
2000 <li>Group options for JABAWS service by command line name</li>
2001 <li>Empty tooltip shown for JABA service options with a
2002 link but no description</li>
2003 <li>Select primary source when selecting authority in
2004 database fetcher GUI</li>
2005 <li>Add .mfa to FASTA file extensions recognised by
2007 <li>Annotation label tooltip text wrap</li>
2012 <li>Slow scrolling when lots of annotation rows are
2014 <li>Lots of NPE (and slowness) after creating RNA
2015 secondary structure annotation line</li>
2016 <li>Sequence database accessions not imported when
2017 fetching alignments from Rfam</li>
2018 <li>Incorrect SHMR submission for sequences with
2020 <li>View all structures does not always superpose
2022 <li>Option widgets in service parameters not updated to
2023 reflect user or preset settings</li>
2024 <li>Null pointer exceptions for some services without
2025 presets or adjustable parameters</li>
2026 <li>Discover PDB IDs entry in structure menu doesn't
2027 discover PDB xRefs</li>
2028 <li>Exception encountered while trying to retrieve
2029 features with DAS</li>
2030 <li>Lowest value in annotation row isn't coloured
2031 when colour by annotation (per sequence) is coloured</li>
2032 <li>Keyboard mode P jumps to start of gapped region when
2033 residue follows a gap</li>
2034 <li>Jalview appears to hang importing an alignment with
2035 Wrap as default or after enabling Wrap</li>
2036 <li>'Right click to add annotations' message
2037 shown in wrap mode when no annotations present</li>
2038 <li>Disorder predictions fail with NPE if no automatic
2039 annotation already exists on alignment</li>
2040 <li>oninit javascript function should be called after
2041 initialisation completes</li>
2042 <li>Remove redundancy after disorder prediction corrupts
2043 alignment window display</li>
2044 <li>Example annotation file in documentation is invalid</li>
2045 <li>Grouped line graph annotation rows are not exported
2046 to annotation file</li>
2047 <li>Multi-harmony analysis cannot be run when only two
2049 <li>Cannot create multiple groups of line graphs with
2050 several 'combine' statements in annotation file</li>
2051 <li>Pressing return several times causes Number Format
2052 exceptions in keyboard mode</li>
2053 <li>Multi-harmony (SHMMR) method doesn't submit
2054 correct partitions for input data</li>
2055 <li>Translation from DNA to Amino Acids fails</li>
2056 <li>Jalview fail to load newick tree with quoted label</li>
2057 <li>--headless flag isn't understood</li>
2058 <li>ClassCastException when generating EPS in headless
2060 <li>Adjusting sequence-associated shading threshold only
2061 changes one row's threshold</li>
2062 <li>Preferences and Feature settings panel panel
2063 doesn't open</li>
2064 <li>hide consensus histogram also hides conservation and
2065 quality histograms</li>
2070 <td><div align="center">
2071 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2073 <td><em>Application</em>
2075 <li>Support for JABAWS 2.0 Services (AACon alignment
2076 conservation, protein disorder and Clustal Omega)</li>
2077 <li>JABAWS server status indicator in Web Services
2079 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2080 in Jalview alignment window</li>
2081 <li>Updated Jalview build and deploy framework for OSX
2082 mountain lion, windows 7, and 8</li>
2083 <li>Nucleotide substitution matrix for PCA that supports
2084 RNA and ambiguity codes</li>
2086 <li>Improved sequence database retrieval GUI</li>
2087 <li>Support fetching and database reference look up
2088 against multiple DAS sources (Fetch all from in 'fetch db
2090 <li>Jalview project improvements
2092 <li>Store and retrieve the 'belowAlignment'
2093 flag for annotation</li>
2094 <li>calcId attribute to group annotation rows on the
2096 <li>Store AACon calculation settings for a view in
2097 Jalview project</li>
2101 <li>horizontal scrolling gesture support</li>
2102 <li>Visual progress indicator when PCA calculation is
2104 <li>Simpler JABA web services menus</li>
2105 <li>visual indication that web service results are still
2106 being retrieved from server</li>
2107 <li>Serialise the dialogs that are shown when Jalview
2108 starts up for first time</li>
2109 <li>Jalview user agent string for interacting with HTTP
2111 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2113 <li>Examples directory and Groovy library included in
2114 InstallAnywhere distribution</li>
2115 </ul> <em>Applet</em>
2117 <li>RNA alignment and secondary structure annotation
2118 visualization applet example</li>
2119 </ul> <em>General</em>
2121 <li>Normalise option for consensus sequence logo</li>
2122 <li>Reset button in PCA window to return dimensions to
2124 <li>Allow seqspace or Jalview variant of alignment PCA
2126 <li>PCA with either nucleic acid and protein substitution
2128 <li>Allow windows containing HTML reports to be exported
2130 <li>Interactive display and editing of RNA secondary
2131 structure contacts</li>
2132 <li>RNA Helix Alignment Colouring</li>
2133 <li>RNA base pair logo consensus</li>
2134 <li>Parse sequence associated secondary structure
2135 information in Stockholm files</li>
2136 <li>HTML Export database accessions and annotation
2137 information presented in tooltip for sequences</li>
2138 <li>Import secondary structure from LOCARNA clustalw
2139 style RNA alignment files</li>
2140 <li>import and visualise T-COFFEE quality scores for an
2142 <li>'colour by annotation' per sequence option to
2143 shade each sequence according to its associated alignment
2145 <li>New Jalview Logo</li>
2146 </ul> <em>Documentation and Development</em>
2148 <li>documentation for score matrices used in Jalview</li>
2149 <li>New Website!</li>
2151 <td><em>Application</em>
2153 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2154 wsdbfetch REST service</li>
2155 <li>Stop windows being moved outside desktop on OSX</li>
2156 <li>Filetype associations not installed for webstart
2158 <li>Jalview does not always retrieve progress of a JABAWS
2159 job execution in full once it is complete</li>
2160 <li>revise SHMR RSBS definition to ensure alignment is
2161 uploaded via ali_file parameter</li>
2162 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2163 <li>View all structures superposed fails with exception</li>
2164 <li>Jnet job queues forever if a very short sequence is
2165 submitted for prediction</li>
2166 <li>Cut and paste menu not opened when mouse clicked on
2168 <li>Putting fractional value into integer text box in
2169 alignment parameter dialog causes Jalview to hang</li>
2170 <li>Structure view highlighting doesn't work on
2172 <li>View all structures fails with exception shown in
2174 <li>Characters in filename associated with PDBEntry not
2175 escaped in a platform independent way</li>
2176 <li>Jalview desktop fails to launch with exception when
2178 <li>Tree calculation reports 'you must have 2 or more
2179 sequences selected' when selection is empty</li>
2180 <li>Jalview desktop fails to launch with jar signature
2181 failure when java web start temporary file caching is
2183 <li>DAS Sequence retrieval with range qualification
2184 results in sequence xref which includes range qualification</li>
2185 <li>Errors during processing of command line arguments
2186 cause progress bar (JAL-898) to be removed</li>
2187 <li>Replace comma for semi-colon option not disabled for
2188 DAS sources in sequence fetcher</li>
2189 <li>Cannot close news reader when JABAWS server warning
2190 dialog is shown</li>
2191 <li>Option widgets not updated to reflect user settings</li>
2192 <li>Edited sequence not submitted to web service</li>
2193 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2194 <li>InstallAnywhere installer doesn't unpack and run
2195 on OSX Mountain Lion</li>
2196 <li>Annotation panel not given a scroll bar when
2197 sequences with alignment annotation are pasted into the
2199 <li>Sequence associated annotation rows not associated
2200 when loaded from Jalview project</li>
2201 <li>Browser launch fails with NPE on java 1.7</li>
2202 <li>JABAWS alignment marked as finished when job was
2203 cancelled or job failed due to invalid input</li>
2204 <li>NPE with v2.7 example when clicking on Tree
2205 associated with all views</li>
2206 <li>Exceptions when copy/paste sequences with grouped
2207 annotation rows to new window</li>
2208 </ul> <em>Applet</em>
2210 <li>Sequence features are momentarily displayed before
2211 they are hidden using hidefeaturegroups applet parameter</li>
2212 <li>loading features via javascript API automatically
2213 enables feature display</li>
2214 <li>scrollToColumnIn javascript API method doesn't
2216 </ul> <em>General</em>
2218 <li>Redundancy removal fails for rna alignment</li>
2219 <li>PCA calculation fails when sequence has been selected
2220 and then deselected</li>
2221 <li>PCA window shows grey box when first opened on OSX</li>
2222 <li>Letters coloured pink in sequence logo when alignment
2223 coloured with clustalx</li>
2224 <li>Choosing fonts without letter symbols defined causes
2225 exceptions and redraw errors</li>
2226 <li>Initial PCA plot view is not same as manually
2227 reconfigured view</li>
2228 <li>Grouped annotation graph label has incorrect line
2230 <li>Grouped annotation graph label display is corrupted
2231 for lots of labels</li>
2236 <div align="center">
2237 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2240 <td><em>Application</em>
2242 <li>Jalview Desktop News Reader</li>
2243 <li>Tweaked default layout of web services menu</li>
2244 <li>View/alignment association menu to enable user to
2245 easily specify which alignment a multi-structure view takes
2246 its colours/correspondences from</li>
2247 <li>Allow properties file location to be specified as URL</li>
2248 <li>Extend Jalview project to preserve associations
2249 between many alignment views and a single Jmol display</li>
2250 <li>Store annotation row height in Jalview project file</li>
2251 <li>Annotation row column label formatting attributes
2252 stored in project file</li>
2253 <li>Annotation row order for auto-calculated annotation
2254 rows preserved in Jalview project file</li>
2255 <li>Visual progress indication when Jalview state is
2256 saved using Desktop window menu</li>
2257 <li>Visual indication that command line arguments are
2258 still being processed</li>
2259 <li>Groovy script execution from URL</li>
2260 <li>Colour by annotation default min and max colours in
2262 <li>Automatically associate PDB files dragged onto an
2263 alignment with sequences that have high similarity and
2265 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2266 <li>'view structures' option to open many
2267 structures in same window</li>
2268 <li>Sort associated views menu option for tree panel</li>
2269 <li>Group all JABA and non-JABA services for a particular
2270 analysis function in its own submenu</li>
2271 </ul> <em>Applet</em>
2273 <li>Userdefined and autogenerated annotation rows for
2275 <li>Adjustment of alignment annotation pane height</li>
2276 <li>Annotation scrollbar for annotation panel</li>
2277 <li>Drag to reorder annotation rows in annotation panel</li>
2278 <li>'automaticScrolling' parameter</li>
2279 <li>Allow sequences with partial ID string matches to be
2280 annotated from GFF/Jalview features files</li>
2281 <li>Sequence logo annotation row in applet</li>
2282 <li>Absolute paths relative to host server in applet
2283 parameters are treated as such</li>
2284 <li>New in the JalviewLite javascript API:
2286 <li>JalviewLite.js javascript library</li>
2287 <li>Javascript callbacks for
2289 <li>Applet initialisation</li>
2290 <li>Sequence/alignment mouse-overs and selections</li>
2293 <li>scrollTo row and column alignment scrolling
2295 <li>Select sequence/alignment regions from javascript</li>
2296 <li>javascript structure viewer harness to pass
2297 messages between Jmol and Jalview when running as
2298 distinct applets</li>
2299 <li>sortBy method</li>
2300 <li>Set of applet and application examples shipped
2301 with documentation</li>
2302 <li>New example to demonstrate JalviewLite and Jmol
2303 javascript message exchange</li>
2305 </ul> <em>General</em>
2307 <li>Enable Jmol displays to be associated with multiple
2308 multiple alignments</li>
2309 <li>Option to automatically sort alignment with new tree</li>
2310 <li>User configurable link to enable redirects to a
2311 www.Jalview.org mirror</li>
2312 <li>Jmol colours option for Jmol displays</li>
2313 <li>Configurable newline string when writing alignment
2314 and other flat files</li>
2315 <li>Allow alignment annotation description lines to
2316 contain html tags</li>
2317 </ul> <em>Documentation and Development</em>
2319 <li>Add groovy test harness for bulk load testing to
2321 <li>Groovy script to load and align a set of sequences
2322 using a web service before displaying the result in the
2323 Jalview desktop</li>
2324 <li>Restructured javascript and applet api documentation</li>
2325 <li>Ant target to publish example html files with applet
2327 <li>Netbeans project for building Jalview from source</li>
2328 <li>ant task to create online javadoc for Jalview source</li>
2330 <td><em>Application</em>
2332 <li>User defined colourscheme throws exception when
2333 current built in colourscheme is saved as new scheme</li>
2334 <li>AlignFrame->Save in application pops up save
2335 dialog for valid filename/format</li>
2336 <li>Cannot view associated structure for UniProt sequence</li>
2337 <li>PDB file association breaks for UniProt sequence
2339 <li>Associate PDB from file dialog does not tell you
2340 which sequence is to be associated with the file</li>
2341 <li>Find All raises null pointer exception when query
2342 only matches sequence IDs</li>
2343 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2344 <li>Jalview project with Jmol views created with Jalview
2345 2.4 cannot be loaded</li>
2346 <li>Filetype associations not installed for webstart
2348 <li>Two or more chains in a single PDB file associated
2349 with sequences in different alignments do not get coloured
2350 by their associated sequence</li>
2351 <li>Visibility status of autocalculated annotation row
2352 not preserved when project is loaded</li>
2353 <li>Annotation row height and visibility attributes not
2354 stored in Jalview project</li>
2355 <li>Tree bootstraps are not preserved when saved as a
2356 Jalview project</li>
2357 <li>Envision2 workflow tooltips are corrupted</li>
2358 <li>Enabling show group conservation also enables colour
2359 by conservation</li>
2360 <li>Duplicate group associated conservation or consensus
2361 created on new view</li>
2362 <li>Annotation scrollbar not displayed after 'show
2363 all hidden annotation rows' option selected</li>
2364 <li>Alignment quality not updated after alignment
2365 annotation row is hidden then shown</li>
2366 <li>Preserve colouring of structures coloured by
2367 sequences in pre Jalview 2.7 projects</li>
2368 <li>Web service job parameter dialog is not laid out
2370 <li>Web services menu not refreshed after 'reset
2371 services' button is pressed in preferences</li>
2372 <li>Annotation off by one in Jalview v2_3 example project</li>
2373 <li>Structures imported from file and saved in project
2374 get name like jalview_pdb1234.txt when reloaded</li>
2375 <li>Jalview does not always retrieve progress of a JABAWS
2376 job execution in full once it is complete</li>
2377 </ul> <em>Applet</em>
2379 <li>Alignment height set incorrectly when lots of
2380 annotation rows are displayed</li>
2381 <li>Relative URLs in feature HTML text not resolved to
2383 <li>View follows highlighting does not work for positions
2385 <li><= shown as = in tooltip</li>
2386 <li>Export features raises exception when no features
2388 <li>Separator string used for serialising lists of IDs
2389 for javascript api is modified when separator string
2390 provided as parameter</li>
2391 <li>Null pointer exception when selecting tree leaves for
2392 alignment with no existing selection</li>
2393 <li>Relative URLs for datasources assumed to be relative
2394 to applet's codebase</li>
2395 <li>Status bar not updated after finished searching and
2396 search wraps around to first result</li>
2397 <li>StructureSelectionManager instance shared between
2398 several Jalview applets causes race conditions and memory
2400 <li>Hover tooltip and mouseover of position on structure
2401 not sent from Jmol in applet</li>
2402 <li>Certain sequences of javascript method calls to
2403 applet API fatally hang browser</li>
2404 </ul> <em>General</em>
2406 <li>View follows structure mouseover scrolls beyond
2407 position with wrapped view and hidden regions</li>
2408 <li>Find sequence position moves to wrong residue
2409 with/without hidden columns</li>
2410 <li>Sequence length given in alignment properties window
2412 <li>InvalidNumberFormat exceptions thrown when trying to
2413 import PDB like structure files</li>
2414 <li>Positional search results are only highlighted
2415 between user-supplied sequence start/end bounds</li>
2416 <li>End attribute of sequence is not validated</li>
2417 <li>Find dialog only finds first sequence containing a
2418 given sequence position</li>
2419 <li>Sequence numbering not preserved in MSF alignment
2421 <li>Jalview PDB file reader does not extract sequence
2422 from nucleotide chains correctly</li>
2423 <li>Structure colours not updated when tree partition
2424 changed in alignment</li>
2425 <li>Sequence associated secondary structure not correctly
2426 parsed in interleaved stockholm</li>
2427 <li>Colour by annotation dialog does not restore current
2429 <li>Hiding (nearly) all sequences doesn't work
2431 <li>Sequences containing lowercase letters are not
2432 properly associated with their pdb files</li>
2433 </ul> <em>Documentation and Development</em>
2435 <li>schemas/JalviewWsParamSet.xsd corrupted by
2436 ApplyCopyright tool</li>
2441 <div align="center">
2442 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2445 <td><em>Application</em>
2447 <li>New warning dialog when the Jalview Desktop cannot
2448 contact web services</li>
2449 <li>JABA service parameters for a preset are shown in
2450 service job window</li>
2451 <li>JABA Service menu entries reworded</li>
2455 <li>Modeller PIR IO broken - cannot correctly import a
2456 pir file emitted by Jalview</li>
2457 <li>Existing feature settings transferred to new
2458 alignment view created from cut'n'paste</li>
2459 <li>Improved test for mixed amino/nucleotide chains when
2460 parsing PDB files</li>
2461 <li>Consensus and conservation annotation rows
2462 occasionally become blank for all new windows</li>
2463 <li>Exception raised when right clicking above sequences
2464 in wrapped view mode</li>
2465 </ul> <em>Application</em>
2467 <li>multiple multiply aligned structure views cause cpu
2468 usage to hit 100% and computer to hang</li>
2469 <li>Web Service parameter layout breaks for long user
2470 parameter names</li>
2471 <li>Jaba service discovery hangs desktop if Jaba server
2478 <div align="center">
2479 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2482 <td><em>Application</em>
2484 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2485 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2488 <li>Web Services preference tab</li>
2489 <li>Analysis parameters dialog box and user defined
2491 <li>Improved speed and layout of Envision2 service menu</li>
2492 <li>Superpose structures using associated sequence
2494 <li>Export coordinates and projection as CSV from PCA
2496 </ul> <em>Applet</em>
2498 <li>enable javascript: execution by the applet via the
2499 link out mechanism</li>
2500 </ul> <em>Other</em>
2502 <li>Updated the Jmol Jalview interface to work with Jmol
2504 <li>The Jalview Desktop and JalviewLite applet now
2505 require Java 1.5</li>
2506 <li>Allow Jalview feature colour specification for GFF
2507 sequence annotation files</li>
2508 <li>New 'colour by label' keword in Jalview feature file
2509 type colour specification</li>
2510 <li>New Jalview Desktop Groovy API method that allows a
2511 script to check if it being run in an interactive session or
2512 in a batch operation from the Jalview command line</li>
2516 <li>clustalx colourscheme colours Ds preferentially when
2517 both D+E are present in over 50% of the column</li>
2518 </ul> <em>Application</em>
2520 <li>typo in AlignmentFrame->View->Hide->all but
2521 selected Regions menu item</li>
2522 <li>sequence fetcher replaces ',' for ';' when the ',' is
2523 part of a valid accession ID</li>
2524 <li>fatal OOM if object retrieved by sequence fetcher
2525 runs out of memory</li>
2526 <li>unhandled Out of Memory Error when viewing pca
2527 analysis results</li>
2528 <li>InstallAnywhere builds fail to launch on OS X java
2529 10.5 update 4 (due to apple Java 1.6 update)</li>
2530 <li>Installanywhere Jalview silently fails to launch</li>
2531 </ul> <em>Applet</em>
2533 <li>Jalview.getFeatureGroups() raises an
2534 ArrayIndexOutOfBoundsException if no feature groups are
2541 <div align="center">
2542 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2548 <li>Alignment prettyprinter doesn't cope with long
2550 <li>clustalx colourscheme colours Ds preferentially when
2551 both D+E are present in over 50% of the column</li>
2552 <li>nucleic acid structures retrieved from PDB do not
2553 import correctly</li>
2554 <li>More columns get selected than were clicked on when a
2555 number of columns are hidden</li>
2556 <li>annotation label popup menu not providing correct
2557 add/hide/show options when rows are hidden or none are
2559 <li>Stockholm format shown in list of readable formats,
2560 and parser copes better with alignments from RFAM.</li>
2561 <li>CSV output of consensus only includes the percentage
2562 of all symbols if sequence logo display is enabled</li>
2564 </ul> <em>Applet</em>
2566 <li>annotation panel disappears when annotation is
2568 </ul> <em>Application</em>
2570 <li>Alignment view not redrawn properly when new
2571 alignment opened where annotation panel is visible but no
2572 annotations are present on alignment</li>
2573 <li>pasted region containing hidden columns is
2574 incorrectly displayed in new alignment window</li>
2575 <li>Jalview slow to complete operations when stdout is
2576 flooded (fix is to close the Jalview console)</li>
2577 <li>typo in AlignmentFrame->View->Hide->all but
2578 selected Rregions menu item.</li>
2579 <li>inconsistent group submenu and Format submenu entry
2580 'Un' or 'Non'conserved</li>
2581 <li>Sequence feature settings are being shared by
2582 multiple distinct alignments</li>
2583 <li>group annotation not recreated when tree partition is
2585 <li>double click on group annotation to select sequences
2586 does not propagate to associated trees</li>
2587 <li>Mac OSX specific issues:
2589 <li>exception raised when mouse clicked on desktop
2590 window background</li>
2591 <li>Desktop menu placed on menu bar and application
2592 name set correctly</li>
2593 <li>sequence feature settings not wide enough for the
2594 save feature colourscheme button</li>
2603 <div align="center">
2604 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2607 <td><em>New Capabilities</em>
2609 <li>URL links generated from description line for
2610 regular-expression based URL links (applet and application)
2612 <li>Non-positional feature URL links are shown in link
2614 <li>Linked viewing of nucleic acid sequences and
2616 <li>Automatic Scrolling option in View menu to display
2617 the currently highlighted region of an alignment.</li>
2618 <li>Order an alignment by sequence length, or using the
2619 average score or total feature count for each sequence.</li>
2620 <li>Shading features by score or associated description</li>
2621 <li>Subdivide alignment and groups based on identity of
2622 selected subsequence (Make Groups from Selection).</li>
2623 <li>New hide/show options including Shift+Control+H to
2624 hide everything but the currently selected region.</li>
2625 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2626 </ul> <em>Application</em>
2628 <li>Fetch DB References capabilities and UI expanded to
2629 support retrieval from DAS sequence sources</li>
2630 <li>Local DAS Sequence sources can be added via the
2631 command line or via the Add local source dialog box.</li>
2632 <li>DAS Dbref and DbxRef feature types are parsed as
2633 database references and protein_name is parsed as
2634 description line (BioSapiens terms).</li>
2635 <li>Enable or disable non-positional feature and database
2636 references in sequence ID tooltip from View menu in
2638 <!-- <li>New hidden columns and rows and representatives capabilities
2639 in annotations file (in progress - not yet fully implemented)</li> -->
2640 <li>Group-associated consensus, sequence logos and
2641 conservation plots</li>
2642 <li>Symbol distributions for each column can be exported
2643 and visualized as sequence logos</li>
2644 <li>Optionally scale multi-character column labels to fit
2645 within each column of annotation row<!-- todo for applet -->
2647 <li>Optional automatic sort of associated alignment view
2648 when a new tree is opened.</li>
2649 <li>Jalview Java Console</li>
2650 <li>Better placement of desktop window when moving
2651 between different screens.</li>
2652 <li>New preference items for sequence ID tooltip and
2653 consensus annotation</li>
2654 <li>Client to submit sequences and IDs to Envision2
2656 <li><em>Vamsas Capabilities</em>
2658 <li>Improved VAMSAS synchronization (Jalview archive
2659 used to preserve views, structures, and tree display
2661 <li>Import of vamsas documents from disk or URL via
2663 <li>Sharing of selected regions between views and
2664 with other VAMSAS applications (Experimental feature!)</li>
2665 <li>Updated API to VAMSAS version 0.2</li>
2667 </ul> <em>Applet</em>
2669 <li>Middle button resizes annotation row height</li>
2672 <li>sortByTree (true/false) - automatically sort the
2673 associated alignment view by the tree when a new tree is
2675 <li>showTreeBootstraps (true/false) - show or hide
2676 branch bootstraps (default is to show them if available)</li>
2677 <li>showTreeDistances (true/false) - show or hide
2678 branch lengths (default is to show them if available)</li>
2679 <li>showUnlinkedTreeNodes (true/false) - indicate if
2680 unassociated nodes should be highlighted in the tree
2682 <li>heightScale and widthScale (1.0 or more) -
2683 increase the height or width of a cell in the alignment
2684 grid relative to the current font size.</li>
2687 <li>Non-positional features displayed in sequence ID
2689 </ul> <em>Other</em>
2691 <li>Features format: graduated colour definitions and
2692 specification of feature scores</li>
2693 <li>Alignment Annotations format: new keywords for group
2694 associated annotation (GROUP_REF) and annotation row display
2695 properties (ROW_PROPERTIES)</li>
2696 <li>XML formats extended to support graduated feature
2697 colourschemes, group associated annotation, and profile
2698 visualization settings.</li></td>
2701 <li>Source field in GFF files parsed as feature source
2702 rather than description</li>
2703 <li>Non-positional features are now included in sequence
2704 feature and gff files (controlled via non-positional feature
2705 visibility in tooltip).</li>
2706 <li>URL links generated for all feature links (bugfix)</li>
2707 <li>Added URL embedding instructions to features file
2709 <li>Codons containing ambiguous nucleotides translated as
2710 'X' in peptide product</li>
2711 <li>Match case switch in find dialog box works for both
2712 sequence ID and sequence string and query strings do not
2713 have to be in upper case to match case-insensitively.</li>
2714 <li>AMSA files only contain first column of
2715 multi-character column annotation labels</li>
2716 <li>Jalview Annotation File generation/parsing consistent
2717 with documentation (e.g. Stockholm annotation can be
2718 exported and re-imported)</li>
2719 <li>PDB files without embedded PDB IDs given a friendly
2721 <li>Find incrementally searches ID string matches as well
2722 as subsequence matches, and correctly reports total number
2726 <li>Better handling of exceptions during sequence
2728 <li>Dasobert generated non-positional feature URL
2729 link text excludes the start_end suffix</li>
2730 <li>DAS feature and source retrieval buttons disabled
2731 when fetch or registry operations in progress.</li>
2732 <li>PDB files retrieved from URLs are cached properly</li>
2733 <li>Sequence description lines properly shared via
2735 <li>Sequence fetcher fetches multiple records for all
2737 <li>Ensured that command line das feature retrieval
2738 completes before alignment figures are generated.</li>
2739 <li>Reduced time taken when opening file browser for
2741 <li>isAligned check prior to calculating tree, PCA or
2742 submitting an MSA to JNet now excludes hidden sequences.</li>
2743 <li>User defined group colours properly recovered
2744 from Jalview projects.</li>
2753 <div align="center">
2754 <strong>2.4.0.b2</strong><br> 28/10/2009
2759 <li>Experimental support for google analytics usage
2761 <li>Jalview privacy settings (user preferences and docs).</li>
2766 <li>Race condition in applet preventing startup in
2768 <li>Exception when feature created from selection beyond
2769 length of sequence.</li>
2770 <li>Allow synthetic PDB files to be imported gracefully</li>
2771 <li>Sequence associated annotation rows associate with
2772 all sequences with a given id</li>
2773 <li>Find function matches case-insensitively for sequence
2774 ID string searches</li>
2775 <li>Non-standard characters do not cause pairwise
2776 alignment to fail with exception</li>
2777 </ul> <em>Application Issues</em>
2779 <li>Sequences are now validated against EMBL database</li>
2780 <li>Sequence fetcher fetches multiple records for all
2782 </ul> <em>InstallAnywhere Issues</em>
2784 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2785 issue with installAnywhere mechanism)</li>
2786 <li>Command line launching of JARs from InstallAnywhere
2787 version (java class versioning error fixed)</li>
2794 <div align="center">
2795 <strong>2.4</strong><br> 27/8/2008
2798 <td><em>User Interface</em>
2800 <li>Linked highlighting of codon and amino acid from
2801 translation and protein products</li>
2802 <li>Linked highlighting of structure associated with
2803 residue mapping to codon position</li>
2804 <li>Sequence Fetcher provides example accession numbers
2805 and 'clear' button</li>
2806 <li>MemoryMonitor added as an option under Desktop's
2808 <li>Extract score function to parse whitespace separated
2809 numeric data in description line</li>
2810 <li>Column labels in alignment annotation can be centred.</li>
2811 <li>Tooltip for sequence associated annotation give name
2813 </ul> <em>Web Services and URL fetching</em>
2815 <li>JPred3 web service</li>
2816 <li>Prototype sequence search client (no public services
2818 <li>Fetch either seed alignment or full alignment from
2820 <li>URL Links created for matching database cross
2821 references as well as sequence ID</li>
2822 <li>URL Links can be created using regular-expressions</li>
2823 </ul> <em>Sequence Database Connectivity</em>
2825 <li>Retrieval of cross-referenced sequences from other
2827 <li>Generalised database reference retrieval and
2828 validation to all fetchable databases</li>
2829 <li>Fetch sequences from DAS sources supporting the
2830 sequence command</li>
2831 </ul> <em>Import and Export</em>
2832 <li>export annotation rows as CSV for spreadsheet import</li>
2833 <li>Jalview projects record alignment dataset associations,
2834 EMBL products, and cDNA sequence mappings</li>
2835 <li>Sequence Group colour can be specified in Annotation
2837 <li>Ad-hoc colouring of group in Annotation File using RGB
2838 triplet as name of colourscheme</li>
2839 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2841 <li>treenode binding for VAMSAS tree exchange</li>
2842 <li>local editing and update of sequences in VAMSAS
2843 alignments (experimental)</li>
2844 <li>Create new or select existing session to join</li>
2845 <li>load and save of vamsas documents</li>
2846 </ul> <em>Application command line</em>
2848 <li>-tree parameter to open trees (introduced for passing
2850 <li>-fetchfrom command line argument to specify nicknames
2851 of DAS servers to query for alignment features</li>
2852 <li>-dasserver command line argument to add new servers
2853 that are also automatically queried for features</li>
2854 <li>-groovy command line argument executes a given groovy
2855 script after all input data has been loaded and parsed</li>
2856 </ul> <em>Applet-Application data exchange</em>
2858 <li>Trees passed as applet parameters can be passed to
2859 application (when using "View in full
2860 application")</li>
2861 </ul> <em>Applet Parameters</em>
2863 <li>feature group display control parameter</li>
2864 <li>debug parameter</li>
2865 <li>showbutton parameter</li>
2866 </ul> <em>Applet API methods</em>
2868 <li>newView public method</li>
2869 <li>Window (current view) specific get/set public methods</li>
2870 <li>Feature display control methods</li>
2871 <li>get list of currently selected sequences</li>
2872 </ul> <em>New Jalview distribution features</em>
2874 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2875 <li>RELEASE file gives build properties for the latest
2876 Jalview release.</li>
2877 <li>Java 1.1 Applet build made easier and donotobfuscate
2878 property controls execution of obfuscator</li>
2879 <li>Build target for generating source distribution</li>
2880 <li>Debug flag for javacc</li>
2881 <li>.jalview_properties file is documented (slightly) in
2882 jalview.bin.Cache</li>
2883 <li>Continuous Build Integration for stable and
2884 development version of Application, Applet and source
2889 <li>selected region output includes visible annotations
2890 (for certain formats)</li>
2891 <li>edit label/displaychar contains existing label/char
2893 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2894 <li>shorter peptide product names from EMBL records</li>
2895 <li>Newick string generator makes compact representations</li>
2896 <li>bootstrap values parsed correctly for tree files with
2898 <li>pathological filechooser bug avoided by not allowing
2899 filenames containing a ':'</li>
2900 <li>Fixed exception when parsing GFF files containing
2901 global sequence features</li>
2902 <li>Alignment datasets are finalized only when number of
2903 references from alignment sequences goes to zero</li>
2904 <li>Close of tree branch colour box without colour
2905 selection causes cascading exceptions</li>
2906 <li>occasional negative imgwidth exceptions</li>
2907 <li>better reporting of non-fatal warnings to user when
2908 file parsing fails.</li>
2909 <li>Save works when Jalview project is default format</li>
2910 <li>Save as dialog opened if current alignment format is
2911 not a valid output format</li>
2912 <li>UniProt canonical names introduced for both das and
2914 <li>Histidine should be midblue (not pink!) in Zappo</li>
2915 <li>error messages passed up and output when data read
2917 <li>edit undo recovers previous dataset sequence when
2918 sequence is edited</li>
2919 <li>allow PDB files without pdb ID HEADER lines (like
2920 those generated by MODELLER) to be read in properly</li>
2921 <li>allow reading of JPred concise files as a normal
2923 <li>Stockholm annotation parsing and alignment properties
2924 import fixed for PFAM records</li>
2925 <li>Structure view windows have correct name in Desktop
2927 <li>annotation consisting of sequence associated scores
2928 can be read and written correctly to annotation file</li>
2929 <li>Aligned cDNA translation to aligned peptide works
2931 <li>Fixed display of hidden sequence markers and
2932 non-italic font for representatives in Applet</li>
2933 <li>Applet Menus are always embedded in applet window on
2935 <li>Newly shown features appear at top of stack (in
2937 <li>Annotations added via parameter not drawn properly
2938 due to null pointer exceptions</li>
2939 <li>Secondary structure lines are drawn starting from
2940 first column of alignment</li>
2941 <li>UniProt XML import updated for new schema release in
2943 <li>Sequence feature to sequence ID match for Features
2944 file is case-insensitive</li>
2945 <li>Sequence features read from Features file appended to
2946 all sequences with matching IDs</li>
2947 <li>PDB structure coloured correctly for associated views
2948 containing a sub-sequence</li>
2949 <li>PDB files can be retrieved by applet from Jar files</li>
2950 <li>feature and annotation file applet parameters
2951 referring to different directories are retrieved correctly</li>
2952 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
2953 <li>Fixed application hang whilst waiting for
2954 splash-screen version check to complete</li>
2955 <li>Applet properly URLencodes input parameter values
2956 when passing them to the launchApp service</li>
2957 <li>display name and local features preserved in results
2958 retrieved from web service</li>
2959 <li>Visual delay indication for sequence retrieval and
2960 sequence fetcher initialisation</li>
2961 <li>updated Application to use DAS 1.53e version of
2962 dasobert DAS client</li>
2963 <li>Re-instated Full AMSA support and .amsa file
2965 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
2973 <div align="center">
2974 <strong>2.3</strong><br> 9/5/07
2979 <li>Jmol 11.0.2 integration</li>
2980 <li>PDB views stored in Jalview XML files</li>
2981 <li>Slide sequences</li>
2982 <li>Edit sequence in place</li>
2983 <li>EMBL CDS features</li>
2984 <li>DAS Feature mapping</li>
2985 <li>Feature ordering</li>
2986 <li>Alignment Properties</li>
2987 <li>Annotation Scores</li>
2988 <li>Sort by scores</li>
2989 <li>Feature/annotation editing in applet</li>
2994 <li>Headless state operation in 2.2.1</li>
2995 <li>Incorrect and unstable DNA pairwise alignment</li>
2996 <li>Cut and paste of sequences with annotation</li>
2997 <li>Feature group display state in XML</li>
2998 <li>Feature ordering in XML</li>
2999 <li>blc file iteration selection using filename # suffix</li>
3000 <li>Stockholm alignment properties</li>
3001 <li>Stockhom alignment secondary structure annotation</li>
3002 <li>2.2.1 applet had no feature transparency</li>
3003 <li>Number pad keys can be used in cursor mode</li>
3004 <li>Structure Viewer mirror image resolved</li>
3011 <div align="center">
3012 <strong>2.2.1</strong><br> 12/2/07
3017 <li>Non standard characters can be read and displayed
3018 <li>Annotations/Features can be imported/exported to the
3020 <li>Applet allows editing of sequence/annotation/group
3021 name & description
3022 <li>Preference setting to display sequence name in
3024 <li>Annotation file format extended to allow
3025 Sequence_groups to be defined
3026 <li>Default opening of alignment overview panel can be
3027 specified in preferences
3028 <li>PDB residue numbering annotation added to associated
3034 <li>Applet crash under certain Linux OS with Java 1.6
3036 <li>Annotation file export / import bugs fixed
3037 <li>PNG / EPS image output bugs fixed
3043 <div align="center">
3044 <strong>2.2</strong><br> 27/11/06
3049 <li>Multiple views on alignment
3050 <li>Sequence feature editing
3051 <li>"Reload" alignment
3052 <li>"Save" to current filename
3053 <li>Background dependent text colour
3054 <li>Right align sequence ids
3055 <li>User-defined lower case residue colours
3058 <li>Menu item accelerator keys
3059 <li>Control-V pastes to current alignment
3060 <li>Cancel button for DAS Feature Fetching
3061 <li>PCA and PDB Viewers zoom via mouse roller
3062 <li>User-defined sub-tree colours and sub-tree selection
3064 <li>'New Window' button on the 'Output to Text box'
3069 <li>New memory efficient Undo/Redo System
3070 <li>Optimised symbol lookups and conservation/consensus
3072 <li>Region Conservation/Consensus recalculated after
3074 <li>Fixed Remove Empty Columns Bug (empty columns at end
3076 <li>Slowed DAS Feature Fetching for increased robustness.
3078 <li>Made angle brackets in ASCII feature descriptions
3080 <li>Re-instated Zoom function for PCA
3081 <li>Sequence descriptions conserved in web service
3083 <li>UniProt ID discoverer uses any word separated by
3085 <li>WsDbFetch query/result association resolved
3086 <li>Tree leaf to sequence mapping improved
3087 <li>Smooth fonts switch moved to FontChooser dialog box.
3094 <div align="center">
3095 <strong>2.1.1</strong><br> 12/9/06
3100 <li>Copy consensus sequence to clipboard</li>
3105 <li>Image output - rightmost residues are rendered if
3106 sequence id panel has been resized</li>
3107 <li>Image output - all offscreen group boundaries are
3109 <li>Annotation files with sequence references - all
3110 elements in file are relative to sequence position</li>
3111 <li>Mac Applet users can use Alt key for group editing</li>
3117 <div align="center">
3118 <strong>2.1</strong><br> 22/8/06
3123 <li>MAFFT Multiple Alignment in default Web Service list</li>
3124 <li>DAS Feature fetching</li>
3125 <li>Hide sequences and columns</li>
3126 <li>Export Annotations and Features</li>
3127 <li>GFF file reading / writing</li>
3128 <li>Associate structures with sequences from local PDB
3130 <li>Add sequences to exisiting alignment</li>
3131 <li>Recently opened files / URL lists</li>
3132 <li>Applet can launch the full application</li>
3133 <li>Applet has transparency for features (Java 1.2
3135 <li>Applet has user defined colours parameter</li>
3136 <li>Applet can load sequences from parameter
3137 "sequence<em>x</em>"
3143 <li>Redundancy Panel reinstalled in the Applet</li>
3144 <li>Monospaced font - EPS / rescaling bug fixed</li>
3145 <li>Annotation files with sequence references bug fixed</li>
3151 <div align="center">
3152 <strong>2.08.1</strong><br> 2/5/06
3157 <li>Change case of selected region from Popup menu</li>
3158 <li>Choose to match case when searching</li>
3159 <li>Middle mouse button and mouse movement can compress /
3160 expand the visible width and height of the alignment</li>
3165 <li>Annotation Panel displays complete JNet results</li>
3171 <div align="center">
3172 <strong>2.08b</strong><br> 18/4/06
3178 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3179 <li>Righthand label on wrapped alignments shows correct
3186 <div align="center">
3187 <strong>2.08</strong><br> 10/4/06
3192 <li>Editing can be locked to the selection area</li>
3193 <li>Keyboard editing</li>
3194 <li>Create sequence features from searches</li>
3195 <li>Precalculated annotations can be loaded onto
3197 <li>Features file allows grouping of features</li>
3198 <li>Annotation Colouring scheme added</li>
3199 <li>Smooth fonts off by default - Faster rendering</li>
3200 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3205 <li>Drag & Drop fixed on Linux</li>
3206 <li>Jalview Archive file faster to load/save, sequence
3207 descriptions saved.</li>
3213 <div align="center">
3214 <strong>2.07</strong><br> 12/12/05
3219 <li>PDB Structure Viewer enhanced</li>
3220 <li>Sequence Feature retrieval and display enhanced</li>
3221 <li>Choose to output sequence start-end after sequence
3222 name for file output</li>
3223 <li>Sequence Fetcher WSDBFetch@EBI</li>
3224 <li>Applet can read feature files, PDB files and can be
3225 used for HTML form input</li>
3230 <li>HTML output writes groups and features</li>
3231 <li>Group editing is Control and mouse click</li>
3232 <li>File IO bugs</li>
3238 <div align="center">
3239 <strong>2.06</strong><br> 28/9/05
3244 <li>View annotations in wrapped mode</li>
3245 <li>More options for PCA viewer</li>
3250 <li>GUI bugs resolved</li>
3251 <li>Runs with -nodisplay from command line</li>
3257 <div align="center">
3258 <strong>2.05b</strong><br> 15/9/05
3263 <li>Choose EPS export as lineart or text</li>
3264 <li>Jar files are executable</li>
3265 <li>Can read in Uracil - maps to unknown residue</li>
3270 <li>Known OutOfMemory errors give warning message</li>
3271 <li>Overview window calculated more efficiently</li>
3272 <li>Several GUI bugs resolved</li>
3278 <div align="center">
3279 <strong>2.05</strong><br> 30/8/05
3284 <li>Edit and annotate in "Wrapped" view</li>
3289 <li>Several GUI bugs resolved</li>
3295 <div align="center">
3296 <strong>2.04</strong><br> 24/8/05
3301 <li>Hold down mouse wheel & scroll to change font
3307 <li>Improved JPred client reliability</li>
3308 <li>Improved loading of Jalview files</li>
3314 <div align="center">
3315 <strong>2.03</strong><br> 18/8/05
3320 <li>Set Proxy server name and port in preferences</li>
3321 <li>Multiple URL links from sequence ids</li>
3322 <li>User Defined Colours can have a scheme name and added
3324 <li>Choose to ignore gaps in consensus calculation</li>
3325 <li>Unix users can set default web browser</li>
3326 <li>Runs without GUI for batch processing</li>
3327 <li>Dynamically generated Web Service Menus</li>
3332 <li>InstallAnywhere download for Sparc Solaris</li>
3338 <div align="center">
3339 <strong>2.02</strong><br> 18/7/05
3345 <li>Copy & Paste order of sequences maintains
3346 alignment order.</li>
3352 <div align="center">
3353 <strong>2.01</strong><br> 12/7/05
3358 <li>Use delete key for deleting selection.</li>
3359 <li>Use Mouse wheel to scroll sequences.</li>
3360 <li>Help file updated to describe how to add alignment
3362 <li>Version and build date written to build properties
3364 <li>InstallAnywhere installation will check for updates
3365 at launch of Jalview.</li>
3370 <li>Delete gaps bug fixed.</li>
3371 <li>FileChooser sorts columns.</li>
3372 <li>Can remove groups one by one.</li>
3373 <li>Filechooser icons installed.</li>
3374 <li>Finder ignores return character when searching.
3375 Return key will initiate a search.<br>
3382 <div align="center">
3383 <strong>2.0</strong><br> 20/6/05
3388 <li>New codebase</li>