3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
34 /* separate the items from eachother */
41 /* doesnt get processed in javahelp */
50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.2">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 annotation input/output via stockholm flatfile
162 <!-- JAL-2447 --> Experimental Features Checkbox in
163 Desktop's Tools menu to hide or show untested features in
167 <!-- JAL-1476 -->Warning in alignment status bar when
168 there are not enough columns to superimpose structures in
172 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
173 file-based command exchange
176 <!-- JAL-2316, -->URLs for viewing database
177 cross-references provided by identifiers.org and the
181 <!-- JAL-2549 -->Updated JABAWS client to v2.2
184 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
185 format sequence substitution matrices
188 <!-- JAL-2375 -->Structure chooser automatically shows Cached Structures rather than querying the PDBe if structures are already available for sequences
191 <!-- JAL-2520 -->Structures imported via URL are cached in
192 the Jalview project rather than downloaded again when the
197 <em>Experimental features</em>
200 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
201 to transfer Chimera's structure attributes as Jalview
202 features, and vice-versa.
214 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
217 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
221 <!-- JAL-2485, -->External service integration tests for
222 Uniprot REST Free Text Search Client
225 <!-- --> <em>Scripting</em>
228 <!-- JAL-2344 -->FileFormatI interface for describing
229 and identifying file formats (instead of String
233 <!-- JAL-2228 -->FeatureCounter script refactored for efficiency when counting all displayed features (not backwards compatible with 2.10.1)
243 <td><div align="left">
247 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
248 matrix - C->R should be '-3'<br />Old matrix restored
249 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
252 <!-- JAL-2397 -->Fixed Jalview's treatment of gaps in PCA
253 and substitution matrix based Tree calculations.<br />In
254 earlier versions of Jalview, gaps matching gaps were
255 penalised, and gaps matching non-gaps penalised even more.
256 In the PCA calculation, gaps were actually treated as
257 non-gaps - so different costs were applied, which meant
258 Jalview's PCAs were different to those produced by
259 SeqSpace.<br />Jalview now treats gaps in the same way as
260 SeqSpace (ie it scores them as 0). To restore pre-2.10.2
262 jalview.viewmodel.PCAModel.scoreGapAsAny=true // for
264 jalview.viewmodel.PCAModel.scoreGapAsAny=false // to
268 <!-- JAL-2424 -->Fixed off-by-one bug that affected scaling
269 of branch lengths for trees computed using Sequence
273 <!-- JAL-2346 -->Reopening Colour by annotation dialog
274 doesn't reselect a specific sequence's associated
275 annotation after it was used for colouring a view
278 <!-- JAL-2430 -->Hidden regions in alignment views are not
279 coloured in linked structure views
282 <!-- JAL-2419 -->Current selection lost if popup menu
283 opened on a region of alignment without groups
286 <!-- JAL-2374 -->Popup menu not always shown for regions
287 of an alignment with overlapping groups
290 <!-- JAL-2310 -->Finder double counts if both a sequence's
291 name and description match
294 <!-- JAL-2370 -->Hiding column selection containing two
295 hidden regions results in incorrect hidden regions
298 <!-- JAL-2377 -->PCA calculation could hang when
299 generating output report when working with highly
303 <!-- JAL-2365 -->Cannot configure feature colours with
304 lightGray or darkGray via features file
307 <!-- JAL-2421 -->Overview window visible region moves
308 erratically when hidden rows or columns are present
311 <!-- JAL-2362 -->Per-residue colourschemes applied via the
312 Structure Viewer's colour menu don't correspond to
316 <!-- JAL-2405 -->Protein specific colours only offered in
317 colour and group colour menu for protein alignments
320 <!-- JAL-2386 -->'Apply to all groups' setting when
321 changing colour does not apply Conservation slider value
325 <!-- JAL-2385 -->Colour threshold slider doesn't update to
326 reflect currently selected view or group's shading
330 <!-- JAL-2373 -->Percentage identity and conservation menu
331 items do not show a tick or allow shading to be disabled
334 <!-- JAL-2385 -->Conservation shading or PID threshold
335 lost when base colourscheme changed if slider not visible
338 <!-- JAL-2547 -->Sequence features shown in tooltip for
339 gaps before start of features
342 <!-- JAL-2576 -->Very large alignments take a long time to
346 <!-- JAL-2623 -->Graduated feature colour threshold not
347 restored to UI when feature colour is edited
350 <!-- JAL-2624 -->Feature colour thresholds not respected
351 when rendered on overview and structures when opacity at
355 <!-- JAL-2630 -->Structure and alignment overview update
356 as graduate feature colour settings are modified via the
360 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
361 a time when scrolling vertically in wrapped mode.
364 <!-- JAL-2034 -->Overview window doesn't always update
365 when a group defined on the alignment is resized
368 <!-- JAL-2605 -->Mouseovers on left/right scale region in
369 wrapped view result in positional status updates
372 <!-- JAL-2563 -->Status bar shows position for ambiguous
373 amino acid and nucleotide symbols
376 <!-- JAL-2602 -->Copy consensus sequence failed if
377 alignment included gapped columns
380 <!-- JAL-2589 -->User defined gap colour not shown in
381 overview when features overlaid on alignment
384 <!-- JAL-2473 -->Minimum size set for Jalview windows so widgets don't permanently disappear
387 <!-- JAL-2503 -->Cannot select or filter quantitative
388 annotation that are shown only as column labels (e.g.
389 T-Coffee column reliability scores)
392 <!-- JAL-2589 -->Gap colours in user-defined colourschemes are not shown
394 <li><!-- JAL-2594 -->Exception thrown if trying to create a sequence feature on gaps only</li>
396 <!-- JAL-2544 --> Sort by features includes features to
397 right of selected region when gaps present on right-hand
401 <!-- JAL-2504 -->Features created with 'New feature'
402 button from a Find inherit previously defined feature type
403 rather than the Find query string
406 <!-- JAL-2423 -->incorrect title in output window when
407 exporting tree calculated in Jalview
410 <!-- JAL-2507 -->Per-sequence RNA secondary structures added after a sequence was imported are not written to Stockholm File
413 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost when importing RNA secondary structure via Stockholm
416 <!-- JAL-2509 -->Secondary structure arrows for [] and {} not shown in correct direction for simple pseudoknots
419 <!-- JAL-2437 -->Hiding sequences at bottom of alignment and then revealing them reorders sequences on the alignment
421 <!-- JAL-964 -->Group panel in sequence feature settings doesn't update to reflect available set of groups after interactively adding or modifying features
424 <!-- JAL-2225 -->Sequence Database chooser unusable on Linux
436 <strong>Documentation</strong>
439 <!-- JAL-2339 -->Release notes reformatted for readibility
440 with the built-in Java help viewer
442 <li><!-- JAL-1644 -->Find documentation updated with 'search sequence description' option</li>
447 <!-- JAL-2225 -->Sequence Database chooser doesn't show available databases panel on Linux
449 <li><!-- JAL-2519 -->EnsemblGenomes example failing after release of Ensembl v.88</li>
450 <li><!-- JAL-2361 -->User Defined Colours not added to Colour menu</li>
452 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
453 case' residues (button in colourscheme editor debugged and
454 new documentation and tooltips added)
457 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
458 doesn't restore group-specific text colour thresholds
461 <!-- JAL-2243 -->Feature settings panel does not update as
462 new features are added to alignment
465 <!-- JAL-2532 -->Cancel in feature settings reverts changes to feature colours via the Amend features dialog
467 <li><!-- JAL-2506 -->Null pointer exception when attempting to edit graduated feature colour via amend features dialog box</li>
469 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
470 selection menu changes colours of alignment views
473 <!-- JAL-2366 -->Proxy server address and port always
474 appear enabled in Preferences->Connections
477 <!-- JAL-2426 -->Spurious exceptions in console raised
478 from alignment calculation workers after alignment has
482 <!-- JAL-1608 -->Typo in selection popup menu - Create
483 groups now 'Create Group'
486 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
487 Create/Undefine group doesn't always work
490 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
491 shown again after pressing 'Cancel'
494 <!-- JAL-2461 -->DAS registry not found exceptions
495 removed from console output
498 <!-- JAL-2383 -->Above PID colour threshold not recovered
499 when alignment view imported from project
502 <!-- JAL-2520,JAL-2465 -->No mappings generated between structure
503 and sequences extracted from structure files imported via
504 URL and viewed in Jmol
507 <!-- JAL-2520 -->Structures loaded via URL are saved in
508 Jalview Projects rather than fetched via URL again when
509 the project is loaded and the structure viewed
512 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
513 adjusts start position in wrap mode
516 <!-- JAL-2563 -->Status bar doesn't show positions for
517 ambiguous amino acids
520 <!-- JAL-2291 -->Hide insertions in PopUp menu excludes
521 gaps in selection, current sequence and only within
525 <!-- JAL-2582 -->Cannot retrieve protein products from
526 Ensembl by Peptide ID
529 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
530 CDS/Protein view after CDS sequences added for aligned
534 <!-- JAL-2482 -->SIFTs mappings not created for some structures
545 <!-- JAL-2468 -->Switching between Nucleotide and Protein
546 score models doesn't always result in an updated PCA plot
549 <!-- JAL-2442 -->Features not rendered as transparent on
550 overview or linked structure view
553 <!-- JAL-2372 -->Colour group by conservation doesn't
557 <!-- JAL-2517 -->Hitting Cancel after applying
558 user-defined colourscheme doesn't restore original
562 <em>New Known Issues</em>
565 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
566 phase after a sequence motif find operation
569 <!-- JAL-2550 -->Importing annotation file with rows
570 containing just upper and lower case letters are
571 interpreted as WUSS rna secondary structure symbols
574 <!-- JAL-2590 -->Cannot load Newick trees from eggnog
581 <!-- JAL-2314 -->Unit test failure:
582 jalview.ws.jabaws.RNAStructExportImport setup fails
585 <!-- JAL-2307 -->Unit test failure:
586 jalview.ws.sifts.SiftsClientTest due to compatibility
587 problems with deep array comparison equality asserts in
588 successive versions of TestNG
591 <!-- JAL-2479 -->Relocated StructureChooserTest and
592 ParameterUtilsTest Unit tests to Network suite
598 <td width="60" nowrap>
600 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
603 <td><div align="left">
607 <!-- JAL-98 -->Improved memory usage: sparse arrays used
608 for all consensus calculations
611 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
614 <li>Updated Jalview's Certum code signing certificate
620 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
621 set of database cross-references, sorted alphabetically
624 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
625 from database cross references. Users with custom links
626 will receive a <a href="webServices/urllinks.html#warning">warning
627 dialog</a> asking them to update their preferences.
630 <!-- JAL-2287-->Cancel button and escape listener on
631 dialog warning user about disconnecting Jalview from a
635 <!-- JAL-2320-->Jalview's Chimera control window closes if
636 the Chimera it is connected to is shut down
639 <!-- JAL-1738-->New keystroke (B) and Select highlighted
640 columns menu item to mark columns containing highlighted
641 regions (e.g. from structure selections or results of a
645 <!-- JAL-2284-->Command line option for batch-generation
646 of HTML pages rendering alignment data with the BioJS
656 <!-- JAL-2286 -->Columns with more than one modal residue
657 are not coloured or thresholded according to percent
658 identity (first observed in Jalview 2.8.2)
661 <!-- JAL-2301 -->Threonine incorrectly reported as not
665 <!-- JAL-2318 -->Updates to documentation pages (above PID
666 threshold, amino acid properties)
669 <!-- JAL-2292 -->Lower case residues in sequences are not
670 reported as mapped to residues in a structure file in the
674 <!--JAL-2324 -->Identical features with non-numeric scores
675 could be added multiple times to a sequence
678 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
679 bond features shown as two highlighted residues rather
680 than a range in linked structure views, and treated
681 correctly when selecting and computing trees from features
684 <!-- JAL-2281-->Custom URL links for database
685 cross-references are matched to database name regardless
693 <!-- JAL-2282-->Custom URL links for specific database
694 names without regular expressions also offer links from
698 <!-- JAL-2315-->Removing a single configured link in the
699 URL links pane in Connections preferences doesn't actually
700 update Jalview configuration
703 <!-- JAL-2272-->CTRL-Click on a selected region to open
704 the alignment area popup menu doesn't work on El-Capitan
707 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
708 files with similarly named sequences if dropped onto the
712 <!-- JAL-2312 -->Additional mappings are shown for PDB
713 entries where more chains exist in the PDB accession than
714 are reported in the SIFTS file
717 <!-- JAL-2317-->Certain structures do not get mapped to
718 the structure view when displayed with Chimera
721 <!-- JAL-2317-->No chains shown in the Chimera view
722 panel's View->Show Chains submenu
725 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
726 work for wrapped alignment views
729 <!--JAL-2197 -->Rename UI components for running JPred
730 predictions from 'JNet' to 'JPred'
733 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
734 corrupted when annotation panel vertical scroll is not at
738 <!--JAL-2332 -->Attempting to view structure for Hen
739 lysozyme results in a PDB Client error dialog box
742 <!-- JAL-2319 -->Structure View's mapping report switched
743 ranges for PDB and sequence for SIFTS
746 SIFTS 'Not_Observed' residues mapped to non-existant
750 <!-- <em>New Known Issues</em>
757 <td width="60" nowrap>
759 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
760 <em>25/10/2016</em></strong>
763 <td><em>Application</em>
765 <li>3D Structure chooser opens with 'Cached structures'
766 view if structures already loaded</li>
767 <li>Progress bar reports models as they are loaded to
774 <li>Colour by conservation always enabled and no tick
775 shown in menu when BLOSUM or PID shading applied</li>
776 <li>FER1_ARATH and FER2_ARATH labels were switched in
777 example sequences/projects/trees</li>
781 <li>Jalview projects with views of local PDB structure
782 files saved on Windows cannot be opened on OSX</li>
783 <li>Multiple structure views can be opened and superposed
784 without timeout for structures with multiple models or
785 multiple sequences in alignment</li>
786 <li>Cannot import or associated local PDB files without a
787 PDB ID HEADER line</li>
788 <li>RMSD is not output in Jmol console when superposition
790 <li>Drag and drop of URL from Browser fails for Linux and
791 OSX versions earlier than El Capitan</li>
792 <li>ENA client ignores invalid content from ENA server</li>
793 <li>Exceptions are not raised in console when ENA client
794 attempts to fetch non-existent IDs via Fetch DB Refs UI
796 <li>Exceptions are not raised in console when a new view
797 is created on the alignment</li>
798 <li>OSX right-click fixed for group selections: CMD-click
799 to insert/remove gaps in groups and CTRL-click to open group
802 <em>Build and deployment</em>
804 <li>URL link checker now copes with multi-line anchor
807 <em>New Known Issues</em>
809 <li>Drag and drop from URL links in browsers do not work
816 <td width="60" nowrap>
818 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
824 <!-- JAL-2124 -->Updated Spanish translations.
827 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
828 for importing structure data to Jalview. Enables mmCIF and
832 <!-- JAL-192 --->Alignment ruler shows positions relative to
836 <!-- JAL-2202 -->Position/residue shown in status bar when
837 mousing over sequence associated annotation
840 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
844 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
845 '()', canonical '[]' and invalid '{}' base pair populations
849 <!-- JAL-2092 -->Feature settings popup menu options for
850 showing or hiding columns containing a feature
853 <!-- JAL-1557 -->Edit selected group by double clicking on
854 group and sequence associated annotation labels
857 <!-- JAL-2236 -->Sequence name added to annotation label in
858 select/hide columns by annotation and colour by annotation
862 </ul> <em>Application</em>
865 <!-- JAL-2050-->Automatically hide introns when opening a
869 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
873 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
874 structure mappings with the EMBL-EBI PDBe SIFTS database
877 <!-- JAL-2079 -->Updated download sites used for Rfam and
878 Pfam sources to xfam.org
881 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
884 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
885 over sequences in Jalview
888 <!-- JAL-2027-->Support for reverse-complement coding
889 regions in ENA and EMBL
892 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
893 for record retrieval via ENA rest API
896 <!-- JAL-2027 -->Support for ENA CDS records with reverse
900 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
901 groovy script execution
904 <!-- JAL-1812 -->New 'execute Groovy script' option in an
905 alignment window's Calculate menu
908 <!-- JAL-1812 -->Allow groovy scripts that call
909 Jalview.getAlignFrames() to run in headless mode
912 <!-- JAL-2068 -->Support for creating new alignment
913 calculation workers from groovy scripts
916 <!-- JAL-1369 --->Store/restore reference sequence in
920 <!-- JAL-1803 -->Chain codes for a sequence's PDB
921 associations are now saved/restored from project
924 <!-- JAL-1993 -->Database selection dialog always shown
925 before sequence fetcher is opened
928 <!-- JAL-2183 -->Double click on an entry in Jalview's
929 database chooser opens a sequence fetcher
932 <!-- JAL-1563 -->Free-text search client for UniProt using
936 <!-- JAL-2168 -->-nonews command line parameter to prevent
937 the news reader opening
940 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
941 querying stored in preferences
944 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
948 <!-- JAL-1977-->Tooltips shown on database chooser
951 <!-- JAL-391 -->Reverse complement function in calculate
952 menu for nucleotide sequences
955 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
956 and feature counts preserves alignment ordering (and
957 debugged for complex feature sets).
960 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
961 viewing structures with Jalview 2.10
964 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
965 genome, transcript CCDS and gene ids via the Ensembl and
966 Ensembl Genomes REST API
969 <!-- JAL-2049 -->Protein sequence variant annotation
970 computed for 'sequence_variant' annotation on CDS regions
974 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
978 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
979 Ref Fetcher fails to match, or otherwise updates sequence
980 data from external database records.
983 <!-- JAL-2154 -->Revised Jalview Project format for
984 efficient recovery of sequence coding and alignment
985 annotation relationships.
987 </ul> <!-- <em>Applet</em>
998 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1002 <!-- JAL-2018-->Export features in Jalview format (again)
1003 includes graduated colourschemes
1006 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1007 working with big alignments and lots of hidden columns
1010 <!-- JAL-2053-->Hidden column markers not always rendered
1011 at right of alignment window
1014 <!-- JAL-2067 -->Tidied up links in help file table of
1018 <!-- JAL-2072 -->Feature based tree calculation not shown
1022 <!-- JAL-2075 -->Hidden columns ignored during feature
1023 based tree calculation
1026 <!-- JAL-2065 -->Alignment view stops updating when show
1027 unconserved enabled for group on alignment
1030 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1034 <!-- JAL-2146 -->Alignment column in status incorrectly
1035 shown as "Sequence position" when mousing over
1039 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1040 hidden columns present
1043 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1044 user created annotation added to alignment
1047 <!-- JAL-1841 -->RNA Structure consensus only computed for
1048 '()' base pair annotation
1051 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1052 in zero scores for all base pairs in RNA Structure
1056 <!-- JAL-2174-->Extend selection with columns containing
1060 <!-- JAL-2275 -->Pfam format writer puts extra space at
1061 beginning of sequence
1064 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1068 <!-- JAL-2238 -->Cannot create groups on an alignment from
1069 from a tree when t-coffee scores are shown
1072 <!-- JAL-1836,1967 -->Cannot import and view PDB
1073 structures with chains containing negative resnums (4q4h)
1076 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1080 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1081 to Clustal, PIR and PileUp output
1084 <!-- JAL-2008 -->Reordering sequence features that are
1085 not visible causes alignment window to repaint
1088 <!-- JAL-2006 -->Threshold sliders don't work in
1089 graduated colour and colour by annotation row for e-value
1090 scores associated with features and annotation rows
1093 <!-- JAL-1797 -->amino acid physicochemical conservation
1094 calculation should be case independent
1097 <!-- JAL-2173 -->Remove annotation also updates hidden
1101 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1102 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1103 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1106 <!-- JAL-2065 -->Null pointer exceptions and redraw
1107 problems when reference sequence defined and 'show
1108 non-conserved' enabled
1111 <!-- JAL-1306 -->Quality and Conservation are now shown on
1112 load even when Consensus calculation is disabled
1115 <!-- JAL-1932 -->Remove right on penultimate column of
1116 alignment does nothing
1119 <em>Application</em>
1122 <!-- JAL-1552-->URLs and links can't be imported by
1123 drag'n'drop on OSX when launched via webstart (note - not
1124 yet fixed for El Capitan)
1127 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1128 output when running on non-gb/us i18n platforms
1131 <!-- JAL-1944 -->Error thrown when exporting a view with
1132 hidden sequences as flat-file alignment
1135 <!-- JAL-2030-->InstallAnywhere distribution fails when
1139 <!-- JAL-2080-->Jalview very slow to launch via webstart
1140 (also hotfix for 2.9.0b2)
1143 <!-- JAL-2085 -->Cannot save project when view has a
1144 reference sequence defined
1147 <!-- JAL-1011 -->Columns are suddenly selected in other
1148 alignments and views when revealing hidden columns
1151 <!-- JAL-1989 -->Hide columns not mirrored in complement
1152 view in a cDNA/Protein splitframe
1155 <!-- JAL-1369 -->Cannot save/restore representative
1156 sequence from project when only one sequence is
1160 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1161 in Structure Chooser
1164 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1165 structure consensus didn't refresh annotation panel
1168 <!-- JAL-1962 -->View mapping in structure view shows
1169 mappings between sequence and all chains in a PDB file
1172 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1173 dialogs format columns correctly, don't display array
1174 data, sort columns according to type
1177 <!-- JAL-1975 -->Export complete shown after destination
1178 file chooser is cancelled during an image export
1181 <!-- JAL-2025 -->Error when querying PDB Service with
1182 sequence name containing special characters
1185 <!-- JAL-2024 -->Manual PDB structure querying should be
1189 <!-- JAL-2104 -->Large tooltips with broken HTML
1190 formatting don't wrap
1193 <!-- JAL-1128 -->Figures exported from wrapped view are
1194 truncated so L looks like I in consensus annotation
1197 <!-- JAL-2003 -->Export features should only export the
1198 currently displayed features for the current selection or
1202 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1203 after fetching cross-references, and restoring from
1207 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1208 followed in the structure viewer
1211 <!-- JAL-2163 -->Titles for individual alignments in
1212 splitframe not restored from project
1215 <!-- JAL-2145 -->missing autocalculated annotation at
1216 trailing end of protein alignment in transcript/product
1217 splitview when pad-gaps not enabled by default
1220 <!-- JAL-1797 -->amino acid physicochemical conservation
1224 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1225 article has been read (reopened issue due to
1226 internationalisation problems)
1229 <!-- JAL-1960 -->Only offer PDB structures in structure
1230 viewer based on sequence name, PDB and UniProt
1235 <!-- JAL-1976 -->No progress bar shown during export of
1239 <!-- JAL-2213 -->Structures not always superimposed after
1240 multiple structures are shown for one or more sequences.
1243 <!-- JAL-1370 -->Reference sequence characters should not
1244 be replaced with '.' when 'Show unconserved' format option
1248 <!-- JAL-1823 -->Cannot specify chain code when entering
1249 specific PDB id for sequence
1252 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1253 'Export hidden sequences' is enabled, but 'export hidden
1254 columns' is disabled.
1257 <!--JAL-2026-->Best Quality option in structure chooser
1258 selects lowest rather than highest resolution structures
1262 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1263 to sequence mapping in 'View Mappings' report
1266 <!-- JAL-2284 -->Unable to read old Jalview projects that
1267 contain non-XML data added after Jalvew wrote project.
1270 <!-- JAL-2118 -->Newly created annotation row reorders
1271 after clicking on it to create new annotation for a
1274 <!-- may exclude, this is an external service stability issue JAL-1941
1275 -- > RNA 3D structure not added via DSSR service</li> -->
1280 <!-- JAL-2151 -->Incorrect columns are selected when
1281 hidden columns present before start of sequence
1284 <!-- JAL-1986 -->Missing dependencies on applet pages
1288 <!-- JAL-1947 -->Overview pixel size changes when
1289 sequences are hidden in applet
1292 <!-- JAL-1996 -->Updated instructions for applet
1293 deployment on examples pages.
1300 <td width="60" nowrap>
1301 <div align="center">
1302 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1303 <em>16/10/2015</em></strong>
1306 <td><em>General</em>
1308 <li>Time stamps for signed Jalview application and applet
1313 <em>Application</em>
1315 <li>Duplicate group consensus and conservation rows
1316 shown when tree is partitioned</li>
1317 <li>Erratic behaviour when tree partitions made with
1318 multiple cDNA/Protein split views</li>
1324 <td width="60" nowrap>
1325 <div align="center">
1326 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1327 <em>8/10/2015</em></strong>
1330 <td><em>General</em>
1332 <li>Updated Spanish translations of localized text for
1334 </ul> <em>Application</em>
1336 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1337 <li>Signed OSX InstallAnywhere installer<br></li>
1338 <li>Support for per-sequence based annotations in BioJSON</li>
1339 </ul> <em>Applet</em>
1341 <li>Split frame example added to applet examples page</li>
1342 </ul> <em>Build and Deployment</em>
1345 <!-- JAL-1888 -->New ant target for running Jalview's test
1353 <li>Mapping of cDNA to protein in split frames
1354 incorrect when sequence start > 1</li>
1355 <li>Broken images in filter column by annotation dialog
1357 <li>Feature colours not parsed from features file</li>
1358 <li>Exceptions and incomplete link URLs recovered when
1359 loading a features file containing HTML tags in feature
1363 <em>Application</em>
1365 <li>Annotations corrupted after BioJS export and
1367 <li>Incorrect sequence limits after Fetch DB References
1368 with 'trim retrieved sequences'</li>
1369 <li>Incorrect warning about deleting all data when
1370 deleting selected columns</li>
1371 <li>Patch to build system for shipping properly signed
1372 JNLP templates for webstart launch</li>
1373 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1374 unreleased structures for download or viewing</li>
1375 <li>Tab/space/return keystroke operation of EMBL-PDBe
1376 fetcher/viewer dialogs works correctly</li>
1377 <li>Disabled 'minimise' button on Jalview windows
1378 running on OSX to workaround redraw hang bug</li>
1379 <li>Split cDNA/Protein view position and geometry not
1380 recovered from jalview project</li>
1381 <li>Initial enabled/disabled state of annotation menu
1382 sorter 'show autocalculated first/last' corresponds to
1384 <li>Restoring of Clustal, RNA Helices and T-Coffee
1385 color schemes from BioJSON</li>
1389 <li>Reorder sequences mirrored in cDNA/Protein split
1391 <li>Applet with Jmol examples not loading correctly</li>
1397 <td><div align="center">
1398 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1400 <td><em>General</em>
1402 <li>Linked visualisation and analysis of DNA and Protein
1405 <li>Translated cDNA alignments shown as split protein
1406 and DNA alignment views</li>
1407 <li>Codon consensus annotation for linked protein and
1408 cDNA alignment views</li>
1409 <li>Link cDNA or Protein product sequences by loading
1410 them onto Protein or cDNA alignments</li>
1411 <li>Reconstruct linked cDNA alignment from aligned
1412 protein sequences</li>
1415 <li>Jmol integration updated to Jmol v14.2.14</li>
1416 <li>Import and export of Jalview alignment views as <a
1417 href="features/bioJsonFormat.html">BioJSON</a></li>
1418 <li>New alignment annotation file statements for
1419 reference sequences and marking hidden columns</li>
1420 <li>Reference sequence based alignment shading to
1421 highlight variation</li>
1422 <li>Select or hide columns according to alignment
1424 <li>Find option for locating sequences by description</li>
1425 <li>Conserved physicochemical properties shown in amino
1426 acid conservation row</li>
1427 <li>Alignments can be sorted by number of RNA helices</li>
1428 </ul> <em>Application</em>
1430 <li>New cDNA/Protein analysis capabilities
1432 <li>Get Cross-References should open a Split Frame
1433 view with cDNA/Protein</li>
1434 <li>Detect when nucleotide sequences and protein
1435 sequences are placed in the same alignment</li>
1436 <li>Split cDNA/Protein views are saved in Jalview
1441 <li>Use REST API to talk to Chimera</li>
1442 <li>Selected regions in Chimera are highlighted in linked
1443 Jalview windows</li>
1445 <li>VARNA RNA viewer updated to v3.93</li>
1446 <li>VARNA views are saved in Jalview Projects</li>
1447 <li>Pseudoknots displayed as Jalview RNA annotation can
1448 be shown in VARNA</li>
1450 <li>Make groups for selection uses marked columns as well
1451 as the active selected region</li>
1453 <li>Calculate UPGMA and NJ trees using sequence feature
1455 <li>New Export options
1457 <li>New Export Settings dialog to control hidden
1458 region export in flat file generation</li>
1460 <li>Export alignment views for display with the <a
1461 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1463 <li>Export scrollable SVG in HTML page</li>
1464 <li>Optional embedding of BioJSON data when exporting
1465 alignment figures to HTML</li>
1467 <li>3D structure retrieval and display
1469 <li>Free text and structured queries with the PDBe
1471 <li>PDBe Search API based discovery and selection of
1472 PDB structures for a sequence set</li>
1476 <li>JPred4 employed for protein secondary structure
1478 <li>Hide Insertions menu option to hide unaligned columns
1479 for one or a group of sequences</li>
1480 <li>Automatically hide insertions in alignments imported
1481 from the JPred4 web server</li>
1482 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1483 system on OSX<br />LGPL libraries courtesy of <a
1484 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1486 <li>changed 'View nucleotide structure' submenu to 'View
1487 VARNA 2D Structure'</li>
1488 <li>change "View protein structure" menu option to "3D
1491 </ul> <em>Applet</em>
1493 <li>New layout for applet example pages</li>
1494 <li>New parameters to enable SplitFrame view
1495 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1496 <li>New example demonstrating linked viewing of cDNA and
1497 Protein alignments</li>
1498 </ul> <em>Development and deployment</em>
1500 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1501 <li>Include installation type and git revision in build
1502 properties and console log output</li>
1503 <li>Jalview Github organisation, and new github site for
1504 storing BioJsMSA Templates</li>
1505 <li>Jalview's unit tests now managed with TestNG</li>
1508 <!-- <em>General</em>
1510 </ul> --> <!-- issues resolved --> <em>Application</em>
1512 <li>Escape should close any open find dialogs</li>
1513 <li>Typo in select-by-features status report</li>
1514 <li>Consensus RNA secondary secondary structure
1515 predictions are not highlighted in amber</li>
1516 <li>Missing gap character in v2.7 example file means
1517 alignment appears unaligned when pad-gaps is not enabled</li>
1518 <li>First switch to RNA Helices colouring doesn't colour
1519 associated structure views</li>
1520 <li>ID width preference option is greyed out when auto
1521 width checkbox not enabled</li>
1522 <li>Stopped a warning dialog from being shown when
1523 creating user defined colours</li>
1524 <li>'View Mapping' in structure viewer shows sequence
1525 mappings for just that viewer's sequences</li>
1526 <li>Workaround for superposing PDB files containing
1527 multiple models in Chimera</li>
1528 <li>Report sequence position in status bar when hovering
1529 over Jmol structure</li>
1530 <li>Cannot output gaps as '.' symbols with Selection ->
1531 output to text box</li>
1532 <li>Flat file exports of alignments with hidden columns
1533 have incorrect sequence start/end</li>
1534 <li>'Aligning' a second chain to a Chimera structure from
1536 <li>Colour schemes applied to structure viewers don't
1537 work for nucleotide</li>
1538 <li>Loading/cut'n'pasting an empty or invalid file leads
1539 to a grey/invisible alignment window</li>
1540 <li>Exported Jpred annotation from a sequence region
1541 imports to different position</li>
1542 <li>Space at beginning of sequence feature tooltips shown
1543 on some platforms</li>
1544 <li>Chimera viewer 'View | Show Chain' menu is not
1546 <li>'New View' fails with a Null Pointer Exception in
1547 console if Chimera has been opened</li>
1548 <li>Mouseover to Chimera not working</li>
1549 <li>Miscellaneous ENA XML feature qualifiers not
1551 <li>NPE in annotation renderer after 'Extract Scores'</li>
1552 <li>If two structures in one Chimera window, mouseover of
1553 either sequence shows on first structure</li>
1554 <li>'Show annotations' options should not make
1555 non-positional annotations visible</li>
1556 <li>Subsequence secondary structure annotation not shown
1557 in right place after 'view flanking regions'</li>
1558 <li>File Save As type unset when current file format is
1560 <li>Save as '.jar' option removed for saving Jalview
1562 <li>Colour by Sequence colouring in Chimera more
1564 <li>Cannot 'add reference annotation' for a sequence in
1565 several views on same alignment</li>
1566 <li>Cannot show linked products for EMBL / ENA records</li>
1567 <li>Jalview's tooltip wraps long texts containing no
1569 </ul> <em>Applet</em>
1571 <li>Jmol to JalviewLite mouseover/link not working</li>
1572 <li>JalviewLite can't import sequences with ID
1573 descriptions containing angle brackets</li>
1574 </ul> <em>General</em>
1576 <li>Cannot export and reimport RNA secondary structure
1577 via jalview annotation file</li>
1578 <li>Random helix colour palette for colour by annotation
1579 with RNA secondary structure</li>
1580 <li>Mouseover to cDNA from STOP residue in protein
1581 translation doesn't work.</li>
1582 <li>hints when using the select by annotation dialog box</li>
1583 <li>Jmol alignment incorrect if PDB file has alternate CA
1585 <li>FontChooser message dialog appears to hang after
1586 choosing 1pt font</li>
1587 <li>Peptide secondary structure incorrectly imported from
1588 annotation file when annotation display text includes 'e' or
1590 <li>Cannot set colour of new feature type whilst creating
1592 <li>cDNA translation alignment should not be sequence
1593 order dependent</li>
1594 <li>'Show unconserved' doesn't work for lower case
1596 <li>Nucleotide ambiguity codes involving R not recognised</li>
1597 </ul> <em>Deployment and Documentation</em>
1599 <li>Applet example pages appear different to the rest of
1600 www.jalview.org</li>
1601 </ul> <em>Application Known issues</em>
1603 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1604 <li>Misleading message appears after trying to delete
1606 <li>Jalview icon not shown in dock after InstallAnywhere
1607 version launches</li>
1608 <li>Fetching EMBL reference for an RNA sequence results
1609 fails with a sequence mismatch</li>
1610 <li>Corrupted or unreadable alignment display when
1611 scrolling alignment to right</li>
1612 <li>ArrayIndexOutOfBoundsException thrown when remove
1613 empty columns called on alignment with ragged gapped ends</li>
1614 <li>auto calculated alignment annotation rows do not get
1615 placed above or below non-autocalculated rows</li>
1616 <li>Jalview dekstop becomes sluggish at full screen in
1617 ultra-high resolution</li>
1618 <li>Cannot disable consensus calculation independently of
1619 quality and conservation</li>
1620 <li>Mouseover highlighting between cDNA and protein can
1621 become sluggish with more than one splitframe shown</li>
1622 </ul> <em>Applet Known Issues</em>
1624 <li>Core PDB parsing code requires Jmol</li>
1625 <li>Sequence canvas panel goes white when alignment
1626 window is being resized</li>
1632 <td><div align="center">
1633 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1635 <td><em>General</em>
1637 <li>Updated Java code signing certificate donated by
1639 <li>Features and annotation preserved when performing
1640 pairwise alignment</li>
1641 <li>RNA pseudoknot annotation can be
1642 imported/exported/displayed</li>
1643 <li>'colour by annotation' can colour by RNA and
1644 protein secondary structure</li>
1645 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1646 post-hoc with 2.9 release</em>)
1649 </ul> <em>Application</em>
1651 <li>Extract and display secondary structure for sequences
1652 with 3D structures</li>
1653 <li>Support for parsing RNAML</li>
1654 <li>Annotations menu for layout
1656 <li>sort sequence annotation rows by alignment</li>
1657 <li>place sequence annotation above/below alignment
1660 <li>Output in Stockholm format</li>
1661 <li>Internationalisation: improved Spanish (es)
1663 <li>Structure viewer preferences tab</li>
1664 <li>Disorder and Secondary Structure annotation tracks
1665 shared between alignments</li>
1666 <li>UCSF Chimera launch and linked highlighting from
1668 <li>Show/hide all sequence associated annotation rows for
1669 all or current selection</li>
1670 <li>disorder and secondary structure predictions
1671 available as dataset annotation</li>
1672 <li>Per-sequence rna helices colouring</li>
1675 <li>Sequence database accessions imported when fetching
1676 alignments from Rfam</li>
1677 <li>update VARNA version to 3.91</li>
1679 <li>New groovy scripts for exporting aligned positions,
1680 conservation values, and calculating sum of pairs scores.</li>
1681 <li>Command line argument to set default JABAWS server</li>
1682 <li>include installation type in build properties and
1683 console log output</li>
1684 <li>Updated Jalview project format to preserve dataset
1688 <!-- issues resolved --> <em>Application</em>
1690 <li>Distinguish alignment and sequence associated RNA
1691 structure in structure->view->VARNA</li>
1692 <li>Raise dialog box if user deletes all sequences in an
1694 <li>Pressing F1 results in documentation opening twice</li>
1695 <li>Sequence feature tooltip is wrapped</li>
1696 <li>Double click on sequence associated annotation
1697 selects only first column</li>
1698 <li>Redundancy removal doesn't result in unlinked
1699 leaves shown in tree</li>
1700 <li>Undos after several redundancy removals don't undo
1702 <li>Hide sequence doesn't hide associated annotation</li>
1703 <li>User defined colours dialog box too big to fit on
1704 screen and buttons not visible</li>
1705 <li>author list isn't updated if already written to
1706 Jalview properties</li>
1707 <li>Popup menu won't open after retrieving sequence
1709 <li>File open window for associate PDB doesn't open</li>
1710 <li>Left-then-right click on a sequence id opens a
1711 browser search window</li>
1712 <li>Cannot open sequence feature shading/sort popup menu
1713 in feature settings dialog</li>
1714 <li>better tooltip placement for some areas of Jalview
1716 <li>Allow addition of JABAWS Server which doesn't
1717 pass validation</li>
1718 <li>Web services parameters dialog box is too large to
1720 <li>Muscle nucleotide alignment preset obscured by
1722 <li>JABAWS preset submenus don't contain newly
1723 defined user preset</li>
1724 <li>MSA web services warns user if they were launched
1725 with invalid input</li>
1726 <li>Jalview cannot contact DAS Registy when running on
1729 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1730 'Superpose with' submenu not shown when new view
1734 </ul> <!-- <em>Applet</em>
1736 </ul> <em>General</em>
1738 </ul>--> <em>Deployment and Documentation</em>
1740 <li>2G and 1G options in launchApp have no effect on
1741 memory allocation</li>
1742 <li>launchApp service doesn't automatically open
1743 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1745 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1746 InstallAnywhere reports cannot find valid JVM when Java
1747 1.7_055 is available
1749 </ul> <em>Application Known issues</em>
1752 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1753 corrupted or unreadable alignment display when scrolling
1757 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1758 retrieval fails but progress bar continues for DAS retrieval
1759 with large number of ID
1762 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1763 flatfile output of visible region has incorrect sequence
1767 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1768 rna structure consensus doesn't update when secondary
1769 structure tracks are rearranged
1772 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1773 invalid rna structure positional highlighting does not
1774 highlight position of invalid base pairs
1777 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1778 out of memory errors are not raised when saving Jalview
1779 project from alignment window file menu
1782 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1783 Switching to RNA Helices colouring doesn't propagate to
1787 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1788 colour by RNA Helices not enabled when user created
1789 annotation added to alignment
1792 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1793 Jalview icon not shown on dock in Mountain Lion/Webstart
1795 </ul> <em>Applet Known Issues</em>
1798 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1799 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1802 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1803 Jalview and Jmol example not compatible with IE9
1806 <li>Sort by annotation score doesn't reverse order
1812 <td><div align="center">
1813 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1816 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1819 <li>Internationalisation of user interface (usually
1820 called i18n support) and translation for Spanish locale</li>
1821 <li>Define/Undefine group on current selection with
1822 Ctrl-G/Shift Ctrl-G</li>
1823 <li>Improved group creation/removal options in
1824 alignment/sequence Popup menu</li>
1825 <li>Sensible precision for symbol distribution
1826 percentages shown in logo tooltip.</li>
1827 <li>Annotation panel height set according to amount of
1828 annotation when alignment first opened</li>
1829 </ul> <em>Application</em>
1831 <li>Interactive consensus RNA secondary structure
1832 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1833 <li>Select columns containing particular features from
1834 Feature Settings dialog</li>
1835 <li>View all 'representative' PDB structures for selected
1837 <li>Update Jalview project format:
1839 <li>New file extension for Jalview projects '.jvp'</li>
1840 <li>Preserve sequence and annotation dataset (to
1841 store secondary structure annotation,etc)</li>
1842 <li>Per group and alignment annotation and RNA helix
1846 <li>New similarity measures for PCA and Tree calculation
1848 <li>Experimental support for retrieval and viewing of
1849 flanking regions for an alignment</li>
1853 <!-- issues resolved --> <em>Application</em>
1855 <li>logo keeps spinning and status remains at queued or
1856 running after job is cancelled</li>
1857 <li>cannot export features from alignments imported from
1858 Jalview/VAMSAS projects</li>
1859 <li>Buggy slider for web service parameters that take
1861 <li>Newly created RNA secondary structure line doesn't
1862 have 'display all symbols' flag set</li>
1863 <li>T-COFFEE alignment score shading scheme and other
1864 annotation shading not saved in Jalview project</li>
1865 <li>Local file cannot be loaded in freshly downloaded
1867 <li>Jalview icon not shown on dock in Mountain
1869 <li>Load file from desktop file browser fails</li>
1870 <li>Occasional NPE thrown when calculating large trees</li>
1871 <li>Cannot reorder or slide sequences after dragging an
1872 alignment onto desktop</li>
1873 <li>Colour by annotation dialog throws NPE after using
1874 'extract scores' function</li>
1875 <li>Loading/cut'n'pasting an empty file leads to a grey
1876 alignment window</li>
1877 <li>Disorder thresholds rendered incorrectly after
1878 performing IUPred disorder prediction</li>
1879 <li>Multiple group annotated consensus rows shown when
1880 changing 'normalise logo' display setting</li>
1881 <li>Find shows blank dialog after 'finished searching' if
1882 nothing matches query</li>
1883 <li>Null Pointer Exceptions raised when sorting by
1884 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1886 <li>Errors in Jmol console when structures in alignment
1887 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1889 <li>Not all working JABAWS services are shown in
1891 <li>JAVAWS version of Jalview fails to launch with
1892 'invalid literal/length code'</li>
1893 <li>Annotation/RNA Helix colourschemes cannot be applied
1894 to alignment with groups (actually fixed in 2.8.0b1)</li>
1895 <li>RNA Helices and T-Coffee Scores available as default
1898 </ul> <em>Applet</em>
1900 <li>Remove group option is shown even when selection is
1902 <li>Apply to all groups ticked but colourscheme changes
1903 don't affect groups</li>
1904 <li>Documented RNA Helices and T-Coffee Scores as valid
1905 colourscheme name</li>
1906 <li>Annotation labels drawn on sequence IDs when
1907 Annotation panel is not displayed</li>
1908 <li>Increased font size for dropdown menus on OSX and
1909 embedded windows</li>
1910 </ul> <em>Other</em>
1912 <li>Consensus sequence for alignments/groups with a
1913 single sequence were not calculated</li>
1914 <li>annotation files that contain only groups imported as
1915 annotation and junk sequences</li>
1916 <li>Fasta files with sequences containing '*' incorrectly
1917 recognised as PFAM or BLC</li>
1918 <li>conservation/PID slider apply all groups option
1919 doesn't affect background (2.8.0b1)
1921 <li>redundancy highlighting is erratic at 0% and 100%</li>
1922 <li>Remove gapped columns fails for sequences with ragged
1924 <li>AMSA annotation row with leading spaces is not
1925 registered correctly on import</li>
1926 <li>Jalview crashes when selecting PCA analysis for
1927 certain alignments</li>
1928 <li>Opening the colour by annotation dialog for an
1929 existing annotation based 'use original colours'
1930 colourscheme loses original colours setting</li>
1935 <td><div align="center">
1936 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
1937 <em>30/1/2014</em></strong>
1941 <li>Trusted certificates for JalviewLite applet and
1942 Jalview Desktop application<br />Certificate was donated by
1943 <a href="https://www.certum.eu">Certum</a> to the Jalview
1944 open source project).
1946 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
1947 <li>Output in Stockholm format</li>
1948 <li>Allow import of data from gzipped files</li>
1949 <li>Export/import group and sequence associated line
1950 graph thresholds</li>
1951 <li>Nucleotide substitution matrix that supports RNA and
1952 ambiguity codes</li>
1953 <li>Allow disorder predictions to be made on the current
1954 selection (or visible selection) in the same way that JPred
1956 <li>Groovy scripting for headless Jalview operation</li>
1957 </ul> <em>Other improvements</em>
1959 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
1960 <li>COMBINE statement uses current SEQUENCE_REF and
1961 GROUP_REF scope to group annotation rows</li>
1962 <li>Support '' style escaping of quotes in Newick
1964 <li>Group options for JABAWS service by command line name</li>
1965 <li>Empty tooltip shown for JABA service options with a
1966 link but no description</li>
1967 <li>Select primary source when selecting authority in
1968 database fetcher GUI</li>
1969 <li>Add .mfa to FASTA file extensions recognised by
1971 <li>Annotation label tooltip text wrap</li>
1976 <li>Slow scrolling when lots of annotation rows are
1978 <li>Lots of NPE (and slowness) after creating RNA
1979 secondary structure annotation line</li>
1980 <li>Sequence database accessions not imported when
1981 fetching alignments from Rfam</li>
1982 <li>Incorrect SHMR submission for sequences with
1984 <li>View all structures does not always superpose
1986 <li>Option widgets in service parameters not updated to
1987 reflect user or preset settings</li>
1988 <li>Null pointer exceptions for some services without
1989 presets or adjustable parameters</li>
1990 <li>Discover PDB IDs entry in structure menu doesn't
1991 discover PDB xRefs</li>
1992 <li>Exception encountered while trying to retrieve
1993 features with DAS</li>
1994 <li>Lowest value in annotation row isn't coloured
1995 when colour by annotation (per sequence) is coloured</li>
1996 <li>Keyboard mode P jumps to start of gapped region when
1997 residue follows a gap</li>
1998 <li>Jalview appears to hang importing an alignment with
1999 Wrap as default or after enabling Wrap</li>
2000 <li>'Right click to add annotations' message
2001 shown in wrap mode when no annotations present</li>
2002 <li>Disorder predictions fail with NPE if no automatic
2003 annotation already exists on alignment</li>
2004 <li>oninit javascript function should be called after
2005 initialisation completes</li>
2006 <li>Remove redundancy after disorder prediction corrupts
2007 alignment window display</li>
2008 <li>Example annotation file in documentation is invalid</li>
2009 <li>Grouped line graph annotation rows are not exported
2010 to annotation file</li>
2011 <li>Multi-harmony analysis cannot be run when only two
2013 <li>Cannot create multiple groups of line graphs with
2014 several 'combine' statements in annotation file</li>
2015 <li>Pressing return several times causes Number Format
2016 exceptions in keyboard mode</li>
2017 <li>Multi-harmony (SHMMR) method doesn't submit
2018 correct partitions for input data</li>
2019 <li>Translation from DNA to Amino Acids fails</li>
2020 <li>Jalview fail to load newick tree with quoted label</li>
2021 <li>--headless flag isn't understood</li>
2022 <li>ClassCastException when generating EPS in headless
2024 <li>Adjusting sequence-associated shading threshold only
2025 changes one row's threshold</li>
2026 <li>Preferences and Feature settings panel panel
2027 doesn't open</li>
2028 <li>hide consensus histogram also hides conservation and
2029 quality histograms</li>
2034 <td><div align="center">
2035 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2037 <td><em>Application</em>
2039 <li>Support for JABAWS 2.0 Services (AACon alignment
2040 conservation, protein disorder and Clustal Omega)</li>
2041 <li>JABAWS server status indicator in Web Services
2043 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2044 in Jalview alignment window</li>
2045 <li>Updated Jalview build and deploy framework for OSX
2046 mountain lion, windows 7, and 8</li>
2047 <li>Nucleotide substitution matrix for PCA that supports
2048 RNA and ambiguity codes</li>
2050 <li>Improved sequence database retrieval GUI</li>
2051 <li>Support fetching and database reference look up
2052 against multiple DAS sources (Fetch all from in 'fetch db
2054 <li>Jalview project improvements
2056 <li>Store and retrieve the 'belowAlignment'
2057 flag for annotation</li>
2058 <li>calcId attribute to group annotation rows on the
2060 <li>Store AACon calculation settings for a view in
2061 Jalview project</li>
2065 <li>horizontal scrolling gesture support</li>
2066 <li>Visual progress indicator when PCA calculation is
2068 <li>Simpler JABA web services menus</li>
2069 <li>visual indication that web service results are still
2070 being retrieved from server</li>
2071 <li>Serialise the dialogs that are shown when Jalview
2072 starts up for first time</li>
2073 <li>Jalview user agent string for interacting with HTTP
2075 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2077 <li>Examples directory and Groovy library included in
2078 InstallAnywhere distribution</li>
2079 </ul> <em>Applet</em>
2081 <li>RNA alignment and secondary structure annotation
2082 visualization applet example</li>
2083 </ul> <em>General</em>
2085 <li>Normalise option for consensus sequence logo</li>
2086 <li>Reset button in PCA window to return dimensions to
2088 <li>Allow seqspace or Jalview variant of alignment PCA
2090 <li>PCA with either nucleic acid and protein substitution
2092 <li>Allow windows containing HTML reports to be exported
2094 <li>Interactive display and editing of RNA secondary
2095 structure contacts</li>
2096 <li>RNA Helix Alignment Colouring</li>
2097 <li>RNA base pair logo consensus</li>
2098 <li>Parse sequence associated secondary structure
2099 information in Stockholm files</li>
2100 <li>HTML Export database accessions and annotation
2101 information presented in tooltip for sequences</li>
2102 <li>Import secondary structure from LOCARNA clustalw
2103 style RNA alignment files</li>
2104 <li>import and visualise T-COFFEE quality scores for an
2106 <li>'colour by annotation' per sequence option to
2107 shade each sequence according to its associated alignment
2109 <li>New Jalview Logo</li>
2110 </ul> <em>Documentation and Development</em>
2112 <li>documentation for score matrices used in Jalview</li>
2113 <li>New Website!</li>
2115 <td><em>Application</em>
2117 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2118 wsdbfetch REST service</li>
2119 <li>Stop windows being moved outside desktop on OSX</li>
2120 <li>Filetype associations not installed for webstart
2122 <li>Jalview does not always retrieve progress of a JABAWS
2123 job execution in full once it is complete</li>
2124 <li>revise SHMR RSBS definition to ensure alignment is
2125 uploaded via ali_file parameter</li>
2126 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2127 <li>View all structures superposed fails with exception</li>
2128 <li>Jnet job queues forever if a very short sequence is
2129 submitted for prediction</li>
2130 <li>Cut and paste menu not opened when mouse clicked on
2132 <li>Putting fractional value into integer text box in
2133 alignment parameter dialog causes Jalview to hang</li>
2134 <li>Structure view highlighting doesn't work on
2136 <li>View all structures fails with exception shown in
2138 <li>Characters in filename associated with PDBEntry not
2139 escaped in a platform independent way</li>
2140 <li>Jalview desktop fails to launch with exception when
2142 <li>Tree calculation reports 'you must have 2 or more
2143 sequences selected' when selection is empty</li>
2144 <li>Jalview desktop fails to launch with jar signature
2145 failure when java web start temporary file caching is
2147 <li>DAS Sequence retrieval with range qualification
2148 results in sequence xref which includes range qualification</li>
2149 <li>Errors during processing of command line arguments
2150 cause progress bar (JAL-898) to be removed</li>
2151 <li>Replace comma for semi-colon option not disabled for
2152 DAS sources in sequence fetcher</li>
2153 <li>Cannot close news reader when JABAWS server warning
2154 dialog is shown</li>
2155 <li>Option widgets not updated to reflect user settings</li>
2156 <li>Edited sequence not submitted to web service</li>
2157 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2158 <li>InstallAnywhere installer doesn't unpack and run
2159 on OSX Mountain Lion</li>
2160 <li>Annotation panel not given a scroll bar when
2161 sequences with alignment annotation are pasted into the
2163 <li>Sequence associated annotation rows not associated
2164 when loaded from Jalview project</li>
2165 <li>Browser launch fails with NPE on java 1.7</li>
2166 <li>JABAWS alignment marked as finished when job was
2167 cancelled or job failed due to invalid input</li>
2168 <li>NPE with v2.7 example when clicking on Tree
2169 associated with all views</li>
2170 <li>Exceptions when copy/paste sequences with grouped
2171 annotation rows to new window</li>
2172 </ul> <em>Applet</em>
2174 <li>Sequence features are momentarily displayed before
2175 they are hidden using hidefeaturegroups applet parameter</li>
2176 <li>loading features via javascript API automatically
2177 enables feature display</li>
2178 <li>scrollToColumnIn javascript API method doesn't
2180 </ul> <em>General</em>
2182 <li>Redundancy removal fails for rna alignment</li>
2183 <li>PCA calculation fails when sequence has been selected
2184 and then deselected</li>
2185 <li>PCA window shows grey box when first opened on OSX</li>
2186 <li>Letters coloured pink in sequence logo when alignment
2187 coloured with clustalx</li>
2188 <li>Choosing fonts without letter symbols defined causes
2189 exceptions and redraw errors</li>
2190 <li>Initial PCA plot view is not same as manually
2191 reconfigured view</li>
2192 <li>Grouped annotation graph label has incorrect line
2194 <li>Grouped annotation graph label display is corrupted
2195 for lots of labels</li>
2200 <div align="center">
2201 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2204 <td><em>Application</em>
2206 <li>Jalview Desktop News Reader</li>
2207 <li>Tweaked default layout of web services menu</li>
2208 <li>View/alignment association menu to enable user to
2209 easily specify which alignment a multi-structure view takes
2210 its colours/correspondences from</li>
2211 <li>Allow properties file location to be specified as URL</li>
2212 <li>Extend Jalview project to preserve associations
2213 between many alignment views and a single Jmol display</li>
2214 <li>Store annotation row height in Jalview project file</li>
2215 <li>Annotation row column label formatting attributes
2216 stored in project file</li>
2217 <li>Annotation row order for auto-calculated annotation
2218 rows preserved in Jalview project file</li>
2219 <li>Visual progress indication when Jalview state is
2220 saved using Desktop window menu</li>
2221 <li>Visual indication that command line arguments are
2222 still being processed</li>
2223 <li>Groovy script execution from URL</li>
2224 <li>Colour by annotation default min and max colours in
2226 <li>Automatically associate PDB files dragged onto an
2227 alignment with sequences that have high similarity and
2229 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2230 <li>'view structures' option to open many
2231 structures in same window</li>
2232 <li>Sort associated views menu option for tree panel</li>
2233 <li>Group all JABA and non-JABA services for a particular
2234 analysis function in its own submenu</li>
2235 </ul> <em>Applet</em>
2237 <li>Userdefined and autogenerated annotation rows for
2239 <li>Adjustment of alignment annotation pane height</li>
2240 <li>Annotation scrollbar for annotation panel</li>
2241 <li>Drag to reorder annotation rows in annotation panel</li>
2242 <li>'automaticScrolling' parameter</li>
2243 <li>Allow sequences with partial ID string matches to be
2244 annotated from GFF/Jalview features files</li>
2245 <li>Sequence logo annotation row in applet</li>
2246 <li>Absolute paths relative to host server in applet
2247 parameters are treated as such</li>
2248 <li>New in the JalviewLite javascript API:
2250 <li>JalviewLite.js javascript library</li>
2251 <li>Javascript callbacks for
2253 <li>Applet initialisation</li>
2254 <li>Sequence/alignment mouse-overs and selections</li>
2257 <li>scrollTo row and column alignment scrolling
2259 <li>Select sequence/alignment regions from javascript</li>
2260 <li>javascript structure viewer harness to pass
2261 messages between Jmol and Jalview when running as
2262 distinct applets</li>
2263 <li>sortBy method</li>
2264 <li>Set of applet and application examples shipped
2265 with documentation</li>
2266 <li>New example to demonstrate JalviewLite and Jmol
2267 javascript message exchange</li>
2269 </ul> <em>General</em>
2271 <li>Enable Jmol displays to be associated with multiple
2272 multiple alignments</li>
2273 <li>Option to automatically sort alignment with new tree</li>
2274 <li>User configurable link to enable redirects to a
2275 www.Jalview.org mirror</li>
2276 <li>Jmol colours option for Jmol displays</li>
2277 <li>Configurable newline string when writing alignment
2278 and other flat files</li>
2279 <li>Allow alignment annotation description lines to
2280 contain html tags</li>
2281 </ul> <em>Documentation and Development</em>
2283 <li>Add groovy test harness for bulk load testing to
2285 <li>Groovy script to load and align a set of sequences
2286 using a web service before displaying the result in the
2287 Jalview desktop</li>
2288 <li>Restructured javascript and applet api documentation</li>
2289 <li>Ant target to publish example html files with applet
2291 <li>Netbeans project for building Jalview from source</li>
2292 <li>ant task to create online javadoc for Jalview source</li>
2294 <td><em>Application</em>
2296 <li>User defined colourscheme throws exception when
2297 current built in colourscheme is saved as new scheme</li>
2298 <li>AlignFrame->Save in application pops up save
2299 dialog for valid filename/format</li>
2300 <li>Cannot view associated structure for UniProt sequence</li>
2301 <li>PDB file association breaks for UniProt sequence
2303 <li>Associate PDB from file dialog does not tell you
2304 which sequence is to be associated with the file</li>
2305 <li>Find All raises null pointer exception when query
2306 only matches sequence IDs</li>
2307 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2308 <li>Jalview project with Jmol views created with Jalview
2309 2.4 cannot be loaded</li>
2310 <li>Filetype associations not installed for webstart
2312 <li>Two or more chains in a single PDB file associated
2313 with sequences in different alignments do not get coloured
2314 by their associated sequence</li>
2315 <li>Visibility status of autocalculated annotation row
2316 not preserved when project is loaded</li>
2317 <li>Annotation row height and visibility attributes not
2318 stored in Jalview project</li>
2319 <li>Tree bootstraps are not preserved when saved as a
2320 Jalview project</li>
2321 <li>Envision2 workflow tooltips are corrupted</li>
2322 <li>Enabling show group conservation also enables colour
2323 by conservation</li>
2324 <li>Duplicate group associated conservation or consensus
2325 created on new view</li>
2326 <li>Annotation scrollbar not displayed after 'show
2327 all hidden annotation rows' option selected</li>
2328 <li>Alignment quality not updated after alignment
2329 annotation row is hidden then shown</li>
2330 <li>Preserve colouring of structures coloured by
2331 sequences in pre Jalview 2.7 projects</li>
2332 <li>Web service job parameter dialog is not laid out
2334 <li>Web services menu not refreshed after 'reset
2335 services' button is pressed in preferences</li>
2336 <li>Annotation off by one in Jalview v2_3 example project</li>
2337 <li>Structures imported from file and saved in project
2338 get name like jalview_pdb1234.txt when reloaded</li>
2339 <li>Jalview does not always retrieve progress of a JABAWS
2340 job execution in full once it is complete</li>
2341 </ul> <em>Applet</em>
2343 <li>Alignment height set incorrectly when lots of
2344 annotation rows are displayed</li>
2345 <li>Relative URLs in feature HTML text not resolved to
2347 <li>View follows highlighting does not work for positions
2349 <li><= shown as = in tooltip</li>
2350 <li>Export features raises exception when no features
2352 <li>Separator string used for serialising lists of IDs
2353 for javascript api is modified when separator string
2354 provided as parameter</li>
2355 <li>Null pointer exception when selecting tree leaves for
2356 alignment with no existing selection</li>
2357 <li>Relative URLs for datasources assumed to be relative
2358 to applet's codebase</li>
2359 <li>Status bar not updated after finished searching and
2360 search wraps around to first result</li>
2361 <li>StructureSelectionManager instance shared between
2362 several Jalview applets causes race conditions and memory
2364 <li>Hover tooltip and mouseover of position on structure
2365 not sent from Jmol in applet</li>
2366 <li>Certain sequences of javascript method calls to
2367 applet API fatally hang browser</li>
2368 </ul> <em>General</em>
2370 <li>View follows structure mouseover scrolls beyond
2371 position with wrapped view and hidden regions</li>
2372 <li>Find sequence position moves to wrong residue
2373 with/without hidden columns</li>
2374 <li>Sequence length given in alignment properties window
2376 <li>InvalidNumberFormat exceptions thrown when trying to
2377 import PDB like structure files</li>
2378 <li>Positional search results are only highlighted
2379 between user-supplied sequence start/end bounds</li>
2380 <li>End attribute of sequence is not validated</li>
2381 <li>Find dialog only finds first sequence containing a
2382 given sequence position</li>
2383 <li>Sequence numbering not preserved in MSF alignment
2385 <li>Jalview PDB file reader does not extract sequence
2386 from nucleotide chains correctly</li>
2387 <li>Structure colours not updated when tree partition
2388 changed in alignment</li>
2389 <li>Sequence associated secondary structure not correctly
2390 parsed in interleaved stockholm</li>
2391 <li>Colour by annotation dialog does not restore current
2393 <li>Hiding (nearly) all sequences doesn't work
2395 <li>Sequences containing lowercase letters are not
2396 properly associated with their pdb files</li>
2397 </ul> <em>Documentation and Development</em>
2399 <li>schemas/JalviewWsParamSet.xsd corrupted by
2400 ApplyCopyright tool</li>
2405 <div align="center">
2406 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2409 <td><em>Application</em>
2411 <li>New warning dialog when the Jalview Desktop cannot
2412 contact web services</li>
2413 <li>JABA service parameters for a preset are shown in
2414 service job window</li>
2415 <li>JABA Service menu entries reworded</li>
2419 <li>Modeller PIR IO broken - cannot correctly import a
2420 pir file emitted by Jalview</li>
2421 <li>Existing feature settings transferred to new
2422 alignment view created from cut'n'paste</li>
2423 <li>Improved test for mixed amino/nucleotide chains when
2424 parsing PDB files</li>
2425 <li>Consensus and conservation annotation rows
2426 occasionally become blank for all new windows</li>
2427 <li>Exception raised when right clicking above sequences
2428 in wrapped view mode</li>
2429 </ul> <em>Application</em>
2431 <li>multiple multiply aligned structure views cause cpu
2432 usage to hit 100% and computer to hang</li>
2433 <li>Web Service parameter layout breaks for long user
2434 parameter names</li>
2435 <li>Jaba service discovery hangs desktop if Jaba server
2442 <div align="center">
2443 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2446 <td><em>Application</em>
2448 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2449 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2452 <li>Web Services preference tab</li>
2453 <li>Analysis parameters dialog box and user defined
2455 <li>Improved speed and layout of Envision2 service menu</li>
2456 <li>Superpose structures using associated sequence
2458 <li>Export coordinates and projection as CSV from PCA
2460 </ul> <em>Applet</em>
2462 <li>enable javascript: execution by the applet via the
2463 link out mechanism</li>
2464 </ul> <em>Other</em>
2466 <li>Updated the Jmol Jalview interface to work with Jmol
2468 <li>The Jalview Desktop and JalviewLite applet now
2469 require Java 1.5</li>
2470 <li>Allow Jalview feature colour specification for GFF
2471 sequence annotation files</li>
2472 <li>New 'colour by label' keword in Jalview feature file
2473 type colour specification</li>
2474 <li>New Jalview Desktop Groovy API method that allows a
2475 script to check if it being run in an interactive session or
2476 in a batch operation from the Jalview command line</li>
2480 <li>clustalx colourscheme colours Ds preferentially when
2481 both D+E are present in over 50% of the column</li>
2482 </ul> <em>Application</em>
2484 <li>typo in AlignmentFrame->View->Hide->all but
2485 selected Regions menu item</li>
2486 <li>sequence fetcher replaces ',' for ';' when the ',' is
2487 part of a valid accession ID</li>
2488 <li>fatal OOM if object retrieved by sequence fetcher
2489 runs out of memory</li>
2490 <li>unhandled Out of Memory Error when viewing pca
2491 analysis results</li>
2492 <li>InstallAnywhere builds fail to launch on OS X java
2493 10.5 update 4 (due to apple Java 1.6 update)</li>
2494 <li>Installanywhere Jalview silently fails to launch</li>
2495 </ul> <em>Applet</em>
2497 <li>Jalview.getFeatureGroups() raises an
2498 ArrayIndexOutOfBoundsException if no feature groups are
2505 <div align="center">
2506 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2512 <li>Alignment prettyprinter doesn't cope with long
2514 <li>clustalx colourscheme colours Ds preferentially when
2515 both D+E are present in over 50% of the column</li>
2516 <li>nucleic acid structures retrieved from PDB do not
2517 import correctly</li>
2518 <li>More columns get selected than were clicked on when a
2519 number of columns are hidden</li>
2520 <li>annotation label popup menu not providing correct
2521 add/hide/show options when rows are hidden or none are
2523 <li>Stockholm format shown in list of readable formats,
2524 and parser copes better with alignments from RFAM.</li>
2525 <li>CSV output of consensus only includes the percentage
2526 of all symbols if sequence logo display is enabled</li>
2528 </ul> <em>Applet</em>
2530 <li>annotation panel disappears when annotation is
2532 </ul> <em>Application</em>
2534 <li>Alignment view not redrawn properly when new
2535 alignment opened where annotation panel is visible but no
2536 annotations are present on alignment</li>
2537 <li>pasted region containing hidden columns is
2538 incorrectly displayed in new alignment window</li>
2539 <li>Jalview slow to complete operations when stdout is
2540 flooded (fix is to close the Jalview console)</li>
2541 <li>typo in AlignmentFrame->View->Hide->all but
2542 selected Rregions menu item.</li>
2543 <li>inconsistent group submenu and Format submenu entry
2544 'Un' or 'Non'conserved</li>
2545 <li>Sequence feature settings are being shared by
2546 multiple distinct alignments</li>
2547 <li>group annotation not recreated when tree partition is
2549 <li>double click on group annotation to select sequences
2550 does not propagate to associated trees</li>
2551 <li>Mac OSX specific issues:
2553 <li>exception raised when mouse clicked on desktop
2554 window background</li>
2555 <li>Desktop menu placed on menu bar and application
2556 name set correctly</li>
2557 <li>sequence feature settings not wide enough for the
2558 save feature colourscheme button</li>
2567 <div align="center">
2568 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2571 <td><em>New Capabilities</em>
2573 <li>URL links generated from description line for
2574 regular-expression based URL links (applet and application)
2576 <li>Non-positional feature URL links are shown in link
2578 <li>Linked viewing of nucleic acid sequences and
2580 <li>Automatic Scrolling option in View menu to display
2581 the currently highlighted region of an alignment.</li>
2582 <li>Order an alignment by sequence length, or using the
2583 average score or total feature count for each sequence.</li>
2584 <li>Shading features by score or associated description</li>
2585 <li>Subdivide alignment and groups based on identity of
2586 selected subsequence (Make Groups from Selection).</li>
2587 <li>New hide/show options including Shift+Control+H to
2588 hide everything but the currently selected region.</li>
2589 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2590 </ul> <em>Application</em>
2592 <li>Fetch DB References capabilities and UI expanded to
2593 support retrieval from DAS sequence sources</li>
2594 <li>Local DAS Sequence sources can be added via the
2595 command line or via the Add local source dialog box.</li>
2596 <li>DAS Dbref and DbxRef feature types are parsed as
2597 database references and protein_name is parsed as
2598 description line (BioSapiens terms).</li>
2599 <li>Enable or disable non-positional feature and database
2600 references in sequence ID tooltip from View menu in
2602 <!-- <li>New hidden columns and rows and representatives capabilities
2603 in annotations file (in progress - not yet fully implemented)</li> -->
2604 <li>Group-associated consensus, sequence logos and
2605 conservation plots</li>
2606 <li>Symbol distributions for each column can be exported
2607 and visualized as sequence logos</li>
2608 <li>Optionally scale multi-character column labels to fit
2609 within each column of annotation row<!-- todo for applet -->
2611 <li>Optional automatic sort of associated alignment view
2612 when a new tree is opened.</li>
2613 <li>Jalview Java Console</li>
2614 <li>Better placement of desktop window when moving
2615 between different screens.</li>
2616 <li>New preference items for sequence ID tooltip and
2617 consensus annotation</li>
2618 <li>Client to submit sequences and IDs to Envision2
2620 <li><em>Vamsas Capabilities</em>
2622 <li>Improved VAMSAS synchronization (Jalview archive
2623 used to preserve views, structures, and tree display
2625 <li>Import of vamsas documents from disk or URL via
2627 <li>Sharing of selected regions between views and
2628 with other VAMSAS applications (Experimental feature!)</li>
2629 <li>Updated API to VAMSAS version 0.2</li>
2631 </ul> <em>Applet</em>
2633 <li>Middle button resizes annotation row height</li>
2636 <li>sortByTree (true/false) - automatically sort the
2637 associated alignment view by the tree when a new tree is
2639 <li>showTreeBootstraps (true/false) - show or hide
2640 branch bootstraps (default is to show them if available)</li>
2641 <li>showTreeDistances (true/false) - show or hide
2642 branch lengths (default is to show them if available)</li>
2643 <li>showUnlinkedTreeNodes (true/false) - indicate if
2644 unassociated nodes should be highlighted in the tree
2646 <li>heightScale and widthScale (1.0 or more) -
2647 increase the height or width of a cell in the alignment
2648 grid relative to the current font size.</li>
2651 <li>Non-positional features displayed in sequence ID
2653 </ul> <em>Other</em>
2655 <li>Features format: graduated colour definitions and
2656 specification of feature scores</li>
2657 <li>Alignment Annotations format: new keywords for group
2658 associated annotation (GROUP_REF) and annotation row display
2659 properties (ROW_PROPERTIES)</li>
2660 <li>XML formats extended to support graduated feature
2661 colourschemes, group associated annotation, and profile
2662 visualization settings.</li></td>
2665 <li>Source field in GFF files parsed as feature source
2666 rather than description</li>
2667 <li>Non-positional features are now included in sequence
2668 feature and gff files (controlled via non-positional feature
2669 visibility in tooltip).</li>
2670 <li>URL links generated for all feature links (bugfix)</li>
2671 <li>Added URL embedding instructions to features file
2673 <li>Codons containing ambiguous nucleotides translated as
2674 'X' in peptide product</li>
2675 <li>Match case switch in find dialog box works for both
2676 sequence ID and sequence string and query strings do not
2677 have to be in upper case to match case-insensitively.</li>
2678 <li>AMSA files only contain first column of
2679 multi-character column annotation labels</li>
2680 <li>Jalview Annotation File generation/parsing consistent
2681 with documentation (e.g. Stockholm annotation can be
2682 exported and re-imported)</li>
2683 <li>PDB files without embedded PDB IDs given a friendly
2685 <li>Find incrementally searches ID string matches as well
2686 as subsequence matches, and correctly reports total number
2690 <li>Better handling of exceptions during sequence
2692 <li>Dasobert generated non-positional feature URL
2693 link text excludes the start_end suffix</li>
2694 <li>DAS feature and source retrieval buttons disabled
2695 when fetch or registry operations in progress.</li>
2696 <li>PDB files retrieved from URLs are cached properly</li>
2697 <li>Sequence description lines properly shared via
2699 <li>Sequence fetcher fetches multiple records for all
2701 <li>Ensured that command line das feature retrieval
2702 completes before alignment figures are generated.</li>
2703 <li>Reduced time taken when opening file browser for
2705 <li>isAligned check prior to calculating tree, PCA or
2706 submitting an MSA to JNet now excludes hidden sequences.</li>
2707 <li>User defined group colours properly recovered
2708 from Jalview projects.</li>
2717 <div align="center">
2718 <strong>2.4.0.b2</strong><br> 28/10/2009
2723 <li>Experimental support for google analytics usage
2725 <li>Jalview privacy settings (user preferences and docs).</li>
2730 <li>Race condition in applet preventing startup in
2732 <li>Exception when feature created from selection beyond
2733 length of sequence.</li>
2734 <li>Allow synthetic PDB files to be imported gracefully</li>
2735 <li>Sequence associated annotation rows associate with
2736 all sequences with a given id</li>
2737 <li>Find function matches case-insensitively for sequence
2738 ID string searches</li>
2739 <li>Non-standard characters do not cause pairwise
2740 alignment to fail with exception</li>
2741 </ul> <em>Application Issues</em>
2743 <li>Sequences are now validated against EMBL database</li>
2744 <li>Sequence fetcher fetches multiple records for all
2746 </ul> <em>InstallAnywhere Issues</em>
2748 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2749 issue with installAnywhere mechanism)</li>
2750 <li>Command line launching of JARs from InstallAnywhere
2751 version (java class versioning error fixed)</li>
2758 <div align="center">
2759 <strong>2.4</strong><br> 27/8/2008
2762 <td><em>User Interface</em>
2764 <li>Linked highlighting of codon and amino acid from
2765 translation and protein products</li>
2766 <li>Linked highlighting of structure associated with
2767 residue mapping to codon position</li>
2768 <li>Sequence Fetcher provides example accession numbers
2769 and 'clear' button</li>
2770 <li>MemoryMonitor added as an option under Desktop's
2772 <li>Extract score function to parse whitespace separated
2773 numeric data in description line</li>
2774 <li>Column labels in alignment annotation can be centred.</li>
2775 <li>Tooltip for sequence associated annotation give name
2777 </ul> <em>Web Services and URL fetching</em>
2779 <li>JPred3 web service</li>
2780 <li>Prototype sequence search client (no public services
2782 <li>Fetch either seed alignment or full alignment from
2784 <li>URL Links created for matching database cross
2785 references as well as sequence ID</li>
2786 <li>URL Links can be created using regular-expressions</li>
2787 </ul> <em>Sequence Database Connectivity</em>
2789 <li>Retrieval of cross-referenced sequences from other
2791 <li>Generalised database reference retrieval and
2792 validation to all fetchable databases</li>
2793 <li>Fetch sequences from DAS sources supporting the
2794 sequence command</li>
2795 </ul> <em>Import and Export</em>
2796 <li>export annotation rows as CSV for spreadsheet import</li>
2797 <li>Jalview projects record alignment dataset associations,
2798 EMBL products, and cDNA sequence mappings</li>
2799 <li>Sequence Group colour can be specified in Annotation
2801 <li>Ad-hoc colouring of group in Annotation File using RGB
2802 triplet as name of colourscheme</li>
2803 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2805 <li>treenode binding for VAMSAS tree exchange</li>
2806 <li>local editing and update of sequences in VAMSAS
2807 alignments (experimental)</li>
2808 <li>Create new or select existing session to join</li>
2809 <li>load and save of vamsas documents</li>
2810 </ul> <em>Application command line</em>
2812 <li>-tree parameter to open trees (introduced for passing
2814 <li>-fetchfrom command line argument to specify nicknames
2815 of DAS servers to query for alignment features</li>
2816 <li>-dasserver command line argument to add new servers
2817 that are also automatically queried for features</li>
2818 <li>-groovy command line argument executes a given groovy
2819 script after all input data has been loaded and parsed</li>
2820 </ul> <em>Applet-Application data exchange</em>
2822 <li>Trees passed as applet parameters can be passed to
2823 application (when using "View in full
2824 application")</li>
2825 </ul> <em>Applet Parameters</em>
2827 <li>feature group display control parameter</li>
2828 <li>debug parameter</li>
2829 <li>showbutton parameter</li>
2830 </ul> <em>Applet API methods</em>
2832 <li>newView public method</li>
2833 <li>Window (current view) specific get/set public methods</li>
2834 <li>Feature display control methods</li>
2835 <li>get list of currently selected sequences</li>
2836 </ul> <em>New Jalview distribution features</em>
2838 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2839 <li>RELEASE file gives build properties for the latest
2840 Jalview release.</li>
2841 <li>Java 1.1 Applet build made easier and donotobfuscate
2842 property controls execution of obfuscator</li>
2843 <li>Build target for generating source distribution</li>
2844 <li>Debug flag for javacc</li>
2845 <li>.jalview_properties file is documented (slightly) in
2846 jalview.bin.Cache</li>
2847 <li>Continuous Build Integration for stable and
2848 development version of Application, Applet and source
2853 <li>selected region output includes visible annotations
2854 (for certain formats)</li>
2855 <li>edit label/displaychar contains existing label/char
2857 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2858 <li>shorter peptide product names from EMBL records</li>
2859 <li>Newick string generator makes compact representations</li>
2860 <li>bootstrap values parsed correctly for tree files with
2862 <li>pathological filechooser bug avoided by not allowing
2863 filenames containing a ':'</li>
2864 <li>Fixed exception when parsing GFF files containing
2865 global sequence features</li>
2866 <li>Alignment datasets are finalized only when number of
2867 references from alignment sequences goes to zero</li>
2868 <li>Close of tree branch colour box without colour
2869 selection causes cascading exceptions</li>
2870 <li>occasional negative imgwidth exceptions</li>
2871 <li>better reporting of non-fatal warnings to user when
2872 file parsing fails.</li>
2873 <li>Save works when Jalview project is default format</li>
2874 <li>Save as dialog opened if current alignment format is
2875 not a valid output format</li>
2876 <li>UniProt canonical names introduced for both das and
2878 <li>Histidine should be midblue (not pink!) in Zappo</li>
2879 <li>error messages passed up and output when data read
2881 <li>edit undo recovers previous dataset sequence when
2882 sequence is edited</li>
2883 <li>allow PDB files without pdb ID HEADER lines (like
2884 those generated by MODELLER) to be read in properly</li>
2885 <li>allow reading of JPred concise files as a normal
2887 <li>Stockholm annotation parsing and alignment properties
2888 import fixed for PFAM records</li>
2889 <li>Structure view windows have correct name in Desktop
2891 <li>annotation consisting of sequence associated scores
2892 can be read and written correctly to annotation file</li>
2893 <li>Aligned cDNA translation to aligned peptide works
2895 <li>Fixed display of hidden sequence markers and
2896 non-italic font for representatives in Applet</li>
2897 <li>Applet Menus are always embedded in applet window on
2899 <li>Newly shown features appear at top of stack (in
2901 <li>Annotations added via parameter not drawn properly
2902 due to null pointer exceptions</li>
2903 <li>Secondary structure lines are drawn starting from
2904 first column of alignment</li>
2905 <li>UniProt XML import updated for new schema release in
2907 <li>Sequence feature to sequence ID match for Features
2908 file is case-insensitive</li>
2909 <li>Sequence features read from Features file appended to
2910 all sequences with matching IDs</li>
2911 <li>PDB structure coloured correctly for associated views
2912 containing a sub-sequence</li>
2913 <li>PDB files can be retrieved by applet from Jar files</li>
2914 <li>feature and annotation file applet parameters
2915 referring to different directories are retrieved correctly</li>
2916 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
2917 <li>Fixed application hang whilst waiting for
2918 splash-screen version check to complete</li>
2919 <li>Applet properly URLencodes input parameter values
2920 when passing them to the launchApp service</li>
2921 <li>display name and local features preserved in results
2922 retrieved from web service</li>
2923 <li>Visual delay indication for sequence retrieval and
2924 sequence fetcher initialisation</li>
2925 <li>updated Application to use DAS 1.53e version of
2926 dasobert DAS client</li>
2927 <li>Re-instated Full AMSA support and .amsa file
2929 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
2937 <div align="center">
2938 <strong>2.3</strong><br> 9/5/07
2943 <li>Jmol 11.0.2 integration</li>
2944 <li>PDB views stored in Jalview XML files</li>
2945 <li>Slide sequences</li>
2946 <li>Edit sequence in place</li>
2947 <li>EMBL CDS features</li>
2948 <li>DAS Feature mapping</li>
2949 <li>Feature ordering</li>
2950 <li>Alignment Properties</li>
2951 <li>Annotation Scores</li>
2952 <li>Sort by scores</li>
2953 <li>Feature/annotation editing in applet</li>
2958 <li>Headless state operation in 2.2.1</li>
2959 <li>Incorrect and unstable DNA pairwise alignment</li>
2960 <li>Cut and paste of sequences with annotation</li>
2961 <li>Feature group display state in XML</li>
2962 <li>Feature ordering in XML</li>
2963 <li>blc file iteration selection using filename # suffix</li>
2964 <li>Stockholm alignment properties</li>
2965 <li>Stockhom alignment secondary structure annotation</li>
2966 <li>2.2.1 applet had no feature transparency</li>
2967 <li>Number pad keys can be used in cursor mode</li>
2968 <li>Structure Viewer mirror image resolved</li>
2975 <div align="center">
2976 <strong>2.2.1</strong><br> 12/2/07
2981 <li>Non standard characters can be read and displayed
2982 <li>Annotations/Features can be imported/exported to the
2984 <li>Applet allows editing of sequence/annotation/group
2985 name & description
2986 <li>Preference setting to display sequence name in
2988 <li>Annotation file format extended to allow
2989 Sequence_groups to be defined
2990 <li>Default opening of alignment overview panel can be
2991 specified in preferences
2992 <li>PDB residue numbering annotation added to associated
2998 <li>Applet crash under certain Linux OS with Java 1.6
3000 <li>Annotation file export / import bugs fixed
3001 <li>PNG / EPS image output bugs fixed
3007 <div align="center">
3008 <strong>2.2</strong><br> 27/11/06
3013 <li>Multiple views on alignment
3014 <li>Sequence feature editing
3015 <li>"Reload" alignment
3016 <li>"Save" to current filename
3017 <li>Background dependent text colour
3018 <li>Right align sequence ids
3019 <li>User-defined lower case residue colours
3022 <li>Menu item accelerator keys
3023 <li>Control-V pastes to current alignment
3024 <li>Cancel button for DAS Feature Fetching
3025 <li>PCA and PDB Viewers zoom via mouse roller
3026 <li>User-defined sub-tree colours and sub-tree selection
3028 <li>'New Window' button on the 'Output to Text box'
3033 <li>New memory efficient Undo/Redo System
3034 <li>Optimised symbol lookups and conservation/consensus
3036 <li>Region Conservation/Consensus recalculated after
3038 <li>Fixed Remove Empty Columns Bug (empty columns at end
3040 <li>Slowed DAS Feature Fetching for increased robustness.
3042 <li>Made angle brackets in ASCII feature descriptions
3044 <li>Re-instated Zoom function for PCA
3045 <li>Sequence descriptions conserved in web service
3047 <li>UniProt ID discoverer uses any word separated by
3049 <li>WsDbFetch query/result association resolved
3050 <li>Tree leaf to sequence mapping improved
3051 <li>Smooth fonts switch moved to FontChooser dialog box.
3058 <div align="center">
3059 <strong>2.1.1</strong><br> 12/9/06
3064 <li>Copy consensus sequence to clipboard</li>
3069 <li>Image output - rightmost residues are rendered if
3070 sequence id panel has been resized</li>
3071 <li>Image output - all offscreen group boundaries are
3073 <li>Annotation files with sequence references - all
3074 elements in file are relative to sequence position</li>
3075 <li>Mac Applet users can use Alt key for group editing</li>
3081 <div align="center">
3082 <strong>2.1</strong><br> 22/8/06
3087 <li>MAFFT Multiple Alignment in default Web Service list</li>
3088 <li>DAS Feature fetching</li>
3089 <li>Hide sequences and columns</li>
3090 <li>Export Annotations and Features</li>
3091 <li>GFF file reading / writing</li>
3092 <li>Associate structures with sequences from local PDB
3094 <li>Add sequences to exisiting alignment</li>
3095 <li>Recently opened files / URL lists</li>
3096 <li>Applet can launch the full application</li>
3097 <li>Applet has transparency for features (Java 1.2
3099 <li>Applet has user defined colours parameter</li>
3100 <li>Applet can load sequences from parameter
3101 "sequence<em>x</em>"
3107 <li>Redundancy Panel reinstalled in the Applet</li>
3108 <li>Monospaced font - EPS / rescaling bug fixed</li>
3109 <li>Annotation files with sequence references bug fixed</li>
3115 <div align="center">
3116 <strong>2.08.1</strong><br> 2/5/06
3121 <li>Change case of selected region from Popup menu</li>
3122 <li>Choose to match case when searching</li>
3123 <li>Middle mouse button and mouse movement can compress /
3124 expand the visible width and height of the alignment</li>
3129 <li>Annotation Panel displays complete JNet results</li>
3135 <div align="center">
3136 <strong>2.08b</strong><br> 18/4/06
3142 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3143 <li>Righthand label on wrapped alignments shows correct
3150 <div align="center">
3151 <strong>2.08</strong><br> 10/4/06
3156 <li>Editing can be locked to the selection area</li>
3157 <li>Keyboard editing</li>
3158 <li>Create sequence features from searches</li>
3159 <li>Precalculated annotations can be loaded onto
3161 <li>Features file allows grouping of features</li>
3162 <li>Annotation Colouring scheme added</li>
3163 <li>Smooth fonts off by default - Faster rendering</li>
3164 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3169 <li>Drag & Drop fixed on Linux</li>
3170 <li>Jalview Archive file faster to load/save, sequence
3171 descriptions saved.</li>
3177 <div align="center">
3178 <strong>2.07</strong><br> 12/12/05
3183 <li>PDB Structure Viewer enhanced</li>
3184 <li>Sequence Feature retrieval and display enhanced</li>
3185 <li>Choose to output sequence start-end after sequence
3186 name for file output</li>
3187 <li>Sequence Fetcher WSDBFetch@EBI</li>
3188 <li>Applet can read feature files, PDB files and can be
3189 used for HTML form input</li>
3194 <li>HTML output writes groups and features</li>
3195 <li>Group editing is Control and mouse click</li>
3196 <li>File IO bugs</li>
3202 <div align="center">
3203 <strong>2.06</strong><br> 28/9/05
3208 <li>View annotations in wrapped mode</li>
3209 <li>More options for PCA viewer</li>
3214 <li>GUI bugs resolved</li>
3215 <li>Runs with -nodisplay from command line</li>
3221 <div align="center">
3222 <strong>2.05b</strong><br> 15/9/05
3227 <li>Choose EPS export as lineart or text</li>
3228 <li>Jar files are executable</li>
3229 <li>Can read in Uracil - maps to unknown residue</li>
3234 <li>Known OutOfMemory errors give warning message</li>
3235 <li>Overview window calculated more efficiently</li>
3236 <li>Several GUI bugs resolved</li>
3242 <div align="center">
3243 <strong>2.05</strong><br> 30/8/05
3248 <li>Edit and annotate in "Wrapped" view</li>
3253 <li>Several GUI bugs resolved</li>
3259 <div align="center">
3260 <strong>2.04</strong><br> 24/8/05
3265 <li>Hold down mouse wheel & scroll to change font
3271 <li>Improved JPred client reliability</li>
3272 <li>Improved loading of Jalview files</li>
3278 <div align="center">
3279 <strong>2.03</strong><br> 18/8/05
3284 <li>Set Proxy server name and port in preferences</li>
3285 <li>Multiple URL links from sequence ids</li>
3286 <li>User Defined Colours can have a scheme name and added
3288 <li>Choose to ignore gaps in consensus calculation</li>
3289 <li>Unix users can set default web browser</li>
3290 <li>Runs without GUI for batch processing</li>
3291 <li>Dynamically generated Web Service Menus</li>
3296 <li>InstallAnywhere download for Sparc Solaris</li>
3302 <div align="center">
3303 <strong>2.02</strong><br> 18/7/05
3309 <li>Copy & Paste order of sequences maintains
3310 alignment order.</li>
3316 <div align="center">
3317 <strong>2.01</strong><br> 12/7/05
3322 <li>Use delete key for deleting selection.</li>
3323 <li>Use Mouse wheel to scroll sequences.</li>
3324 <li>Help file updated to describe how to add alignment
3326 <li>Version and build date written to build properties
3328 <li>InstallAnywhere installation will check for updates
3329 at launch of Jalview.</li>
3334 <li>Delete gaps bug fixed.</li>
3335 <li>FileChooser sorts columns.</li>
3336 <li>Can remove groups one by one.</li>
3337 <li>Filechooser icons installed.</li>
3338 <li>Finder ignores return character when searching.
3339 Return key will initiate a search.<br>
3346 <div align="center">
3347 <strong>2.0</strong><br> 20/6/05
3352 <li>New codebase</li>