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>
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27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>8/8/2017</em></strong>
76 <td><div align="left">
80 <!-- JAL-2379 -->Revised implementation of PCA for speed
81 and memory efficiency (~30x faster)
84 <!-- JAL-2403 -->Revised implementation of sequence
85 similarity scores as used by Tree, PCA, Shading Consensus
86 and other calculations
89 <!-- JAL-2416 -->Score matrices are stored as resource
90 files within the Jalview codebase
92 <!-- JAL-2500 -->Trees computed on Sequence Feature
93 Similarity may have different topology due to
99 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
100 a calculation dialog box
103 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
104 model for alignments and groups
107 <!-- JAL-384 -->Custom shading schemes created via groovy
110 <li>Improved overview window
113 <!-- JAL-2526 -->Efficiency improvements for
114 interacting with alignment and overview windows
117 <!-- JAL-2491 -->Linked scrolling of CDS/Protein
118 views via Overview or sequence motif search operations
121 <!-- JAL-2514 -->Scrolling of wrapped alignment views
125 <!-- JAL-2388 -->Hidden columns and sequences can be
129 <!-- JAL-2611 -->Click-drag in visible area allows
130 fine adjustment of visible position
135 <!-- JAL-2535 -->Posterior probability annotation from
136 Stockholm files imported as sequence associated annotation
139 <!-- JAL-2533 -->Sequence names don't include file
140 extension when importing structure files without embedded
141 names or PDB accessions
144 <!-- JAL-2547 -->Amend sequence features dialog box can be
145 opened by double clicking gaps within sequence feature
149 <!-- JAL-2631 -->Graduated feature colour style example
150 included in the example feature file
153 <!-- JAL-1933 -->Occupancy annotation row shows number of
154 ungapped positions in each column of the alignment.
157 <!-- JAL-2533 -->File extension pruned from Sequence ID
158 for sequences derived from structure files without
159 embedded database accession
162 <!-- JAL-1476 -->Status bar message shown when not enough
163 aligned positions were available to create a 3D structure
167 <!-- JAL-2507 -->More robust per-sequence positional
168 annotation input/output via stockholm flatfile
175 <!-- JAL-2447 --> Experimental Features Checkbox in
176 Desktop's Tools menu to hide or show untested features in
180 <!-- JAL-1476 -->Warning in alignment status bar when
181 there are not enough columns to superimpose structures in
185 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
186 file-based command exchange
189 <!-- JAL-2316, -->URLs for viewing database
190 cross-references provided by identifiers.org and the
194 <!-- JAL-2549 -->Updated JABAWS client to v2.2
197 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
198 format sequence substitution matrices
201 <!-- JAL-2375 -->Structure chooser automatically shows
202 Cached Structures rather than querying the PDBe if
203 structures are already available for sequences
206 <!-- JAL-2520 -->Structures imported via URL are cached in
207 the Jalview project rather than downloaded again when the
212 <em>Experimental features</em>
215 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
216 to transfer Chimera's structure attributes as Jalview
217 features, and vice-versa.
229 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
232 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
236 <!-- JAL-2485, -->External service integration tests for
237 Uniprot REST Free Text Search Client
240 <!-- --> <em>Scripting</em>
243 <!-- JAL-2344 -->FileFormatI interface for describing
244 and identifying file formats (instead of String
248 <!-- JAL-2228 -->FeatureCounter script refactored for
249 efficiency when counting all displayed features (not
250 backwards compatible with 2.10.1)
258 <td><div align="left">
262 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
263 matrix - C->R should be '-3'<br />Old matrix restored
264 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
267 <!-- JAL-2397 -->Fixed Jalview's treatment of gaps in PCA
268 and substitution matrix based Tree calculations.<br />In
269 earlier versions of Jalview, gaps matching gaps were
270 penalised, and gaps matching non-gaps penalised even more.
271 In the PCA calculation, gaps were actually treated as
272 non-gaps - so different costs were applied, which meant
273 Jalview's PCAs were different to those produced by
274 SeqSpace.<br />Jalview now treats gaps in the same way as
275 SeqSpace (ie it scores them as 0). To restore pre-2.10.2
277 jalview.viewmodel.PCAModel.scoreGapAsAny=true // for
279 jalview.viewmodel.PCAModel.scoreGapAsAny=false // to
283 <!-- JAL-2424 -->Fixed off-by-one bug that affected
284 scaling of branch lengths for trees computed using
285 Sequence Feature Similarity.
288 <!-- JAL-2346 -->Reopening Colour by annotation dialog
289 doesn't reselect a specific sequence's associated
290 annotation after it was used for colouring a view
293 <!-- JAL-2430 -->Hidden regions in alignment views are not
294 coloured in linked structure views
297 <!-- JAL-2419 -->Current selection lost if popup menu
298 opened on a region of alignment without groups
301 <!-- JAL-2374 -->Popup menu not always shown for regions
302 of an alignment with overlapping groups
305 <!-- JAL-2310 -->Finder double counts if both a sequence's
306 name and description match
309 <!-- JAL-2370 -->Hiding column selection containing two
310 hidden regions results in incorrect hidden regions
313 <!-- JAL-2377 -->PCA calculation could hang when
314 generating output report when working with highly
318 <!-- JAL-2365 -->Cannot configure feature colours with
319 lightGray or darkGray via features file
322 <!-- JAL-2421 -->Overview window visible region moves
323 erratically when hidden rows or columns are present
326 <!-- JAL-2362 -->Per-residue colourschemes applied via the
327 Structure Viewer's colour menu don't correspond to
331 <!-- JAL-2405 -->Protein specific colours only offered in
332 colour and group colour menu for protein alignments
335 <!-- JAL-2386 -->'Apply to all groups' setting when
336 changing colour does not apply Conservation slider value
340 <!-- JAL-2385 -->Colour threshold slider doesn't update to
341 reflect currently selected view or group's shading
345 <!-- JAL-2373 -->Percentage identity and conservation menu
346 items do not show a tick or allow shading to be disabled
349 <!-- JAL-2385 -->Conservation shading or PID threshold
350 lost when base colourscheme changed if slider not visible
353 <!-- JAL-2547 -->Sequence features shown in tooltip for
354 gaps before start of features
357 <!-- JAL-2576 -->Very large alignments take a long time to
361 <!-- JAL-2623 -->Graduated feature colour threshold not
362 restored to UI when feature colour is edited
365 <!-- JAL-2624 -->Feature colour thresholds not respected
366 when rendered on overview and structures when opacity at
370 <!-- JAL-2630 -->Structure and alignment overview update
371 as graduate feature colour settings are modified via the
375 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
376 a time when scrolling vertically in wrapped mode.
379 <!-- JAL-2034 -->Overview window doesn't always update
380 when a group defined on the alignment is resized
383 <!-- JAL-2605 -->Mouseovers on left/right scale region in
384 wrapped view result in positional status updates
387 <!-- JAL-2563 -->Status bar shows position for ambiguous
388 amino acid and nucleotide symbols
391 <!-- JAL-2602 -->Copy consensus sequence failed if
392 alignment included gapped columns
395 <!-- JAL-2589 -->User defined gap colour not shown in
396 overview when features overlaid on alignment
399 <!-- JAL-2473 -->Minimum size set for Jalview windows so
400 widgets don't permanently disappear
403 <!-- JAL-2503 -->Cannot select or filter quantitative
404 annotation that are shown only as column labels (e.g.
405 T-Coffee column reliability scores)
408 <!-- JAL-2589 -->Gap colours in user-defined colourschemes
412 <!-- JAL-2594 -->Exception thrown if trying to create a
413 sequence feature on gaps only
416 <!-- JAL-2544 --> Sort by features includes features to
417 right of selected region when gaps present on right-hand
421 <!-- JAL-2504 -->Features created with 'New feature'
422 button from a Find inherit previously defined feature type
423 rather than the Find query string
426 <!-- JAL-2423 -->incorrect title in output window when
427 exporting tree calculated in Jalview
430 <!-- JAL-2507 -->Per-sequence RNA secondary structures
431 added after a sequence was imported are not written to
435 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
436 when importing RNA secondary structure via Stockholm
439 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
440 not shown in correct direction for simple pseudoknots
443 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
444 and then revealing them reorders sequences on the
448 <!-- JAL-964 -->Group panel in sequence feature settings
449 doesn't update to reflect available set of groups after
450 interactively adding or modifying features
453 <!-- JAL-2225 -->Sequence Database chooser unusable on
466 <strong>Documentation</strong>
469 <!-- JAL-2339 -->Release notes reformatted for readibility
470 with the built-in Java help viewer
473 <!-- JAL-1644 -->Find documentation updated with 'search
474 sequence description' option
480 <!-- JAL-2225 -->Sequence Database chooser doesn't show
481 available databases panel on Linux
484 <!-- JAL-2519 -->EnsemblGenomes example failing after
485 release of Ensembl v.88
488 <!-- JAL-2361 -->User Defined Colours not added to Colour
492 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
493 case' residues (button in colourscheme editor debugged and
494 new documentation and tooltips added)
497 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
498 doesn't restore group-specific text colour thresholds
501 <!-- JAL-2243 -->Feature settings panel does not update as
502 new features are added to alignment
505 <!-- JAL-2532 -->Cancel in feature settings reverts
506 changes to feature colours via the Amend features dialog
509 <!-- JAL-2506 -->Null pointer exception when attempting to
510 edit graduated feature colour via amend features dialog
514 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
515 selection menu changes colours of alignment views
518 <!-- JAL-2366 -->Proxy server address and port always
519 appear enabled in Preferences->Connections
522 <!-- JAL-2426 -->Spurious exceptions in console raised
523 from alignment calculation workers after alignment has
527 <!-- JAL-1608 -->Typo in selection popup menu - Create
528 groups now 'Create Group'
531 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
532 Create/Undefine group doesn't always work
535 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
536 shown again after pressing 'Cancel'
539 <!-- JAL-2461 -->DAS registry not found exceptions
540 removed from console output
543 <!-- JAL-2383 -->Above PID colour threshold not recovered
544 when alignment view imported from project
547 <!-- JAL-2520,JAL-2465 -->No mappings generated between
548 structure and sequences extracted from structure files
549 imported via URL and viewed in Jmol
552 <!-- JAL-2520 -->Structures loaded via URL are saved in
553 Jalview Projects rather than fetched via URL again when
554 the project is loaded and the structure viewed
557 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
558 adjusts start position in wrap mode
561 <!-- JAL-2563 -->Status bar doesn't show positions for
562 ambiguous amino acids
565 <!-- JAL-2291 -->Hide insertions in PopUp menu excludes
566 gaps in selection, current sequence and only within
570 <!-- JAL-2582 -->Cannot retrieve protein products from
571 Ensembl by Peptide ID
574 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
575 CDS/Protein view after CDS sequences added for aligned
579 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
580 created from SIFTs, and spurious 'Couldn't open structure
581 in Chimera' errors raised after April 2017 update (problem
582 due to 'null' string rather than empty string used for
583 residues with no corresponding PDB mapping).
585 <li><!-- JAL-2592 -->User defined colourschemes called 'User Defined' don't appear in Colours menu</li>
596 <!-- JAL-2468 -->Switching between Nucleotide and Protein
597 score models doesn't always result in an updated PCA plot
600 <!-- JAL-2442 -->Features not rendered as transparent on
601 overview or linked structure view
604 <!-- JAL-2372 -->Colour group by conservation doesn't
608 <!-- JAL-2517 -->Hitting Cancel after applying
609 user-defined colourscheme doesn't restore original
613 <em>New Known Issues</em>
616 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
617 phase after a sequence motif find operation
620 <!-- JAL-2550 -->Importing annotation file with rows
621 containing just upper and lower case letters are
622 interpreted as WUSS rna secondary structure symbols
625 <!-- JAL-2590 -->Cannot load Newick trees from eggnog
629 <!-- JAL-2468 -->Status bar shows 'Marked x columns
630 containing features of type Highlight' when 'B" is pressed
631 to mark columns containing highlighted regions.
637 <!-- JAL-2314 -->Unit test failure:
638 jalview.ws.jabaws.RNAStructExportImport setup fails
641 <!-- JAL-2307 -->Unit test failure:
642 jalview.ws.sifts.SiftsClientTest due to compatibility
643 problems with deep array comparison equality asserts in
644 successive versions of TestNG
647 <!-- JAL-2479 -->Relocated StructureChooserTest and
648 ParameterUtilsTest Unit tests to Network suite
655 <td width="60" nowrap>
657 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
660 <td><div align="left">
664 <!-- JAL-98 -->Improved memory usage: sparse arrays used
665 for all consensus calculations
668 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
671 <li>Updated Jalview's Certum code signing certificate
677 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
678 set of database cross-references, sorted alphabetically
681 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
682 from database cross references. Users with custom links
683 will receive a <a href="webServices/urllinks.html#warning">warning
684 dialog</a> asking them to update their preferences.
687 <!-- JAL-2287-->Cancel button and escape listener on
688 dialog warning user about disconnecting Jalview from a
692 <!-- JAL-2320-->Jalview's Chimera control window closes if
693 the Chimera it is connected to is shut down
696 <!-- JAL-1738-->New keystroke (B) and Select highlighted
697 columns menu item to mark columns containing highlighted
698 regions (e.g. from structure selections or results of a
702 <!-- JAL-2284-->Command line option for batch-generation
703 of HTML pages rendering alignment data with the BioJS
713 <!-- JAL-2286 -->Columns with more than one modal residue
714 are not coloured or thresholded according to percent
715 identity (first observed in Jalview 2.8.2)
718 <!-- JAL-2301 -->Threonine incorrectly reported as not
722 <!-- JAL-2318 -->Updates to documentation pages (above PID
723 threshold, amino acid properties)
726 <!-- JAL-2292 -->Lower case residues in sequences are not
727 reported as mapped to residues in a structure file in the
731 <!--JAL-2324 -->Identical features with non-numeric scores
732 could be added multiple times to a sequence
735 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
736 bond features shown as two highlighted residues rather
737 than a range in linked structure views, and treated
738 correctly when selecting and computing trees from features
741 <!-- JAL-2281-->Custom URL links for database
742 cross-references are matched to database name regardless
750 <!-- JAL-2282-->Custom URL links for specific database
751 names without regular expressions also offer links from
755 <!-- JAL-2315-->Removing a single configured link in the
756 URL links pane in Connections preferences doesn't actually
757 update Jalview configuration
760 <!-- JAL-2272-->CTRL-Click on a selected region to open
761 the alignment area popup menu doesn't work on El-Capitan
764 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
765 files with similarly named sequences if dropped onto the
769 <!-- JAL-2312 -->Additional mappings are shown for PDB
770 entries where more chains exist in the PDB accession than
771 are reported in the SIFTS file
774 <!-- JAL-2317-->Certain structures do not get mapped to
775 the structure view when displayed with Chimera
778 <!-- JAL-2317-->No chains shown in the Chimera view
779 panel's View->Show Chains submenu
782 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
783 work for wrapped alignment views
786 <!--JAL-2197 -->Rename UI components for running JPred
787 predictions from 'JNet' to 'JPred'
790 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
791 corrupted when annotation panel vertical scroll is not at
795 <!--JAL-2332 -->Attempting to view structure for Hen
796 lysozyme results in a PDB Client error dialog box
799 <!-- JAL-2319 -->Structure View's mapping report switched
800 ranges for PDB and sequence for SIFTS
803 SIFTS 'Not_Observed' residues mapped to non-existant
807 <!-- <em>New Known Issues</em>
814 <td width="60" nowrap>
816 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
817 <em>25/10/2016</em></strong>
820 <td><em>Application</em>
822 <li>3D Structure chooser opens with 'Cached structures'
823 view if structures already loaded</li>
824 <li>Progress bar reports models as they are loaded to
831 <li>Colour by conservation always enabled and no tick
832 shown in menu when BLOSUM or PID shading applied</li>
833 <li>FER1_ARATH and FER2_ARATH labels were switched in
834 example sequences/projects/trees</li>
838 <li>Jalview projects with views of local PDB structure
839 files saved on Windows cannot be opened on OSX</li>
840 <li>Multiple structure views can be opened and superposed
841 without timeout for structures with multiple models or
842 multiple sequences in alignment</li>
843 <li>Cannot import or associated local PDB files without a
844 PDB ID HEADER line</li>
845 <li>RMSD is not output in Jmol console when superposition
847 <li>Drag and drop of URL from Browser fails for Linux and
848 OSX versions earlier than El Capitan</li>
849 <li>ENA client ignores invalid content from ENA server</li>
850 <li>Exceptions are not raised in console when ENA client
851 attempts to fetch non-existent IDs via Fetch DB Refs UI
853 <li>Exceptions are not raised in console when a new view
854 is created on the alignment</li>
855 <li>OSX right-click fixed for group selections: CMD-click
856 to insert/remove gaps in groups and CTRL-click to open group
859 <em>Build and deployment</em>
861 <li>URL link checker now copes with multi-line anchor
864 <em>New Known Issues</em>
866 <li>Drag and drop from URL links in browsers do not work
873 <td width="60" nowrap>
875 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
881 <!-- JAL-2124 -->Updated Spanish translations.
884 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
885 for importing structure data to Jalview. Enables mmCIF and
889 <!-- JAL-192 --->Alignment ruler shows positions relative to
893 <!-- JAL-2202 -->Position/residue shown in status bar when
894 mousing over sequence associated annotation
897 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
901 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
902 '()', canonical '[]' and invalid '{}' base pair populations
906 <!-- JAL-2092 -->Feature settings popup menu options for
907 showing or hiding columns containing a feature
910 <!-- JAL-1557 -->Edit selected group by double clicking on
911 group and sequence associated annotation labels
914 <!-- JAL-2236 -->Sequence name added to annotation label in
915 select/hide columns by annotation and colour by annotation
919 </ul> <em>Application</em>
922 <!-- JAL-2050-->Automatically hide introns when opening a
926 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
930 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
931 structure mappings with the EMBL-EBI PDBe SIFTS database
934 <!-- JAL-2079 -->Updated download sites used for Rfam and
935 Pfam sources to xfam.org
938 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
941 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
942 over sequences in Jalview
945 <!-- JAL-2027-->Support for reverse-complement coding
946 regions in ENA and EMBL
949 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
950 for record retrieval via ENA rest API
953 <!-- JAL-2027 -->Support for ENA CDS records with reverse
957 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
958 groovy script execution
961 <!-- JAL-1812 -->New 'execute Groovy script' option in an
962 alignment window's Calculate menu
965 <!-- JAL-1812 -->Allow groovy scripts that call
966 Jalview.getAlignFrames() to run in headless mode
969 <!-- JAL-2068 -->Support for creating new alignment
970 calculation workers from groovy scripts
973 <!-- JAL-1369 --->Store/restore reference sequence in
977 <!-- JAL-1803 -->Chain codes for a sequence's PDB
978 associations are now saved/restored from project
981 <!-- JAL-1993 -->Database selection dialog always shown
982 before sequence fetcher is opened
985 <!-- JAL-2183 -->Double click on an entry in Jalview's
986 database chooser opens a sequence fetcher
989 <!-- JAL-1563 -->Free-text search client for UniProt using
993 <!-- JAL-2168 -->-nonews command line parameter to prevent
994 the news reader opening
997 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
998 querying stored in preferences
1001 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1005 <!-- JAL-1977-->Tooltips shown on database chooser
1008 <!-- JAL-391 -->Reverse complement function in calculate
1009 menu for nucleotide sequences
1012 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1013 and feature counts preserves alignment ordering (and
1014 debugged for complex feature sets).
1017 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1018 viewing structures with Jalview 2.10
1021 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1022 genome, transcript CCDS and gene ids via the Ensembl and
1023 Ensembl Genomes REST API
1026 <!-- JAL-2049 -->Protein sequence variant annotation
1027 computed for 'sequence_variant' annotation on CDS regions
1031 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1035 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1036 Ref Fetcher fails to match, or otherwise updates sequence
1037 data from external database records.
1040 <!-- JAL-2154 -->Revised Jalview Project format for
1041 efficient recovery of sequence coding and alignment
1042 annotation relationships.
1044 </ul> <!-- <em>Applet</em>
1055 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1059 <!-- JAL-2018-->Export features in Jalview format (again)
1060 includes graduated colourschemes
1063 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1064 working with big alignments and lots of hidden columns
1067 <!-- JAL-2053-->Hidden column markers not always rendered
1068 at right of alignment window
1071 <!-- JAL-2067 -->Tidied up links in help file table of
1075 <!-- JAL-2072 -->Feature based tree calculation not shown
1079 <!-- JAL-2075 -->Hidden columns ignored during feature
1080 based tree calculation
1083 <!-- JAL-2065 -->Alignment view stops updating when show
1084 unconserved enabled for group on alignment
1087 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1091 <!-- JAL-2146 -->Alignment column in status incorrectly
1092 shown as "Sequence position" when mousing over
1096 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1097 hidden columns present
1100 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1101 user created annotation added to alignment
1104 <!-- JAL-1841 -->RNA Structure consensus only computed for
1105 '()' base pair annotation
1108 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1109 in zero scores for all base pairs in RNA Structure
1113 <!-- JAL-2174-->Extend selection with columns containing
1117 <!-- JAL-2275 -->Pfam format writer puts extra space at
1118 beginning of sequence
1121 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1125 <!-- JAL-2238 -->Cannot create groups on an alignment from
1126 from a tree when t-coffee scores are shown
1129 <!-- JAL-1836,1967 -->Cannot import and view PDB
1130 structures with chains containing negative resnums (4q4h)
1133 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1137 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1138 to Clustal, PIR and PileUp output
1141 <!-- JAL-2008 -->Reordering sequence features that are
1142 not visible causes alignment window to repaint
1145 <!-- JAL-2006 -->Threshold sliders don't work in
1146 graduated colour and colour by annotation row for e-value
1147 scores associated with features and annotation rows
1150 <!-- JAL-1797 -->amino acid physicochemical conservation
1151 calculation should be case independent
1154 <!-- JAL-2173 -->Remove annotation also updates hidden
1158 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1159 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1160 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1163 <!-- JAL-2065 -->Null pointer exceptions and redraw
1164 problems when reference sequence defined and 'show
1165 non-conserved' enabled
1168 <!-- JAL-1306 -->Quality and Conservation are now shown on
1169 load even when Consensus calculation is disabled
1172 <!-- JAL-1932 -->Remove right on penultimate column of
1173 alignment does nothing
1176 <em>Application</em>
1179 <!-- JAL-1552-->URLs and links can't be imported by
1180 drag'n'drop on OSX when launched via webstart (note - not
1181 yet fixed for El Capitan)
1184 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1185 output when running on non-gb/us i18n platforms
1188 <!-- JAL-1944 -->Error thrown when exporting a view with
1189 hidden sequences as flat-file alignment
1192 <!-- JAL-2030-->InstallAnywhere distribution fails when
1196 <!-- JAL-2080-->Jalview very slow to launch via webstart
1197 (also hotfix for 2.9.0b2)
1200 <!-- JAL-2085 -->Cannot save project when view has a
1201 reference sequence defined
1204 <!-- JAL-1011 -->Columns are suddenly selected in other
1205 alignments and views when revealing hidden columns
1208 <!-- JAL-1989 -->Hide columns not mirrored in complement
1209 view in a cDNA/Protein splitframe
1212 <!-- JAL-1369 -->Cannot save/restore representative
1213 sequence from project when only one sequence is
1217 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1218 in Structure Chooser
1221 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1222 structure consensus didn't refresh annotation panel
1225 <!-- JAL-1962 -->View mapping in structure view shows
1226 mappings between sequence and all chains in a PDB file
1229 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1230 dialogs format columns correctly, don't display array
1231 data, sort columns according to type
1234 <!-- JAL-1975 -->Export complete shown after destination
1235 file chooser is cancelled during an image export
1238 <!-- JAL-2025 -->Error when querying PDB Service with
1239 sequence name containing special characters
1242 <!-- JAL-2024 -->Manual PDB structure querying should be
1246 <!-- JAL-2104 -->Large tooltips with broken HTML
1247 formatting don't wrap
1250 <!-- JAL-1128 -->Figures exported from wrapped view are
1251 truncated so L looks like I in consensus annotation
1254 <!-- JAL-2003 -->Export features should only export the
1255 currently displayed features for the current selection or
1259 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1260 after fetching cross-references, and restoring from
1264 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1265 followed in the structure viewer
1268 <!-- JAL-2163 -->Titles for individual alignments in
1269 splitframe not restored from project
1272 <!-- JAL-2145 -->missing autocalculated annotation at
1273 trailing end of protein alignment in transcript/product
1274 splitview when pad-gaps not enabled by default
1277 <!-- JAL-1797 -->amino acid physicochemical conservation
1281 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1282 article has been read (reopened issue due to
1283 internationalisation problems)
1286 <!-- JAL-1960 -->Only offer PDB structures in structure
1287 viewer based on sequence name, PDB and UniProt
1292 <!-- JAL-1976 -->No progress bar shown during export of
1296 <!-- JAL-2213 -->Structures not always superimposed after
1297 multiple structures are shown for one or more sequences.
1300 <!-- JAL-1370 -->Reference sequence characters should not
1301 be replaced with '.' when 'Show unconserved' format option
1305 <!-- JAL-1823 -->Cannot specify chain code when entering
1306 specific PDB id for sequence
1309 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1310 'Export hidden sequences' is enabled, but 'export hidden
1311 columns' is disabled.
1314 <!--JAL-2026-->Best Quality option in structure chooser
1315 selects lowest rather than highest resolution structures
1319 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1320 to sequence mapping in 'View Mappings' report
1323 <!-- JAL-2284 -->Unable to read old Jalview projects that
1324 contain non-XML data added after Jalvew wrote project.
1327 <!-- JAL-2118 -->Newly created annotation row reorders
1328 after clicking on it to create new annotation for a
1331 <!-- may exclude, this is an external service stability issue JAL-1941
1332 -- > RNA 3D structure not added via DSSR service</li> -->
1337 <!-- JAL-2151 -->Incorrect columns are selected when
1338 hidden columns present before start of sequence
1341 <!-- JAL-1986 -->Missing dependencies on applet pages
1345 <!-- JAL-1947 -->Overview pixel size changes when
1346 sequences are hidden in applet
1349 <!-- JAL-1996 -->Updated instructions for applet
1350 deployment on examples pages.
1357 <td width="60" nowrap>
1358 <div align="center">
1359 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1360 <em>16/10/2015</em></strong>
1363 <td><em>General</em>
1365 <li>Time stamps for signed Jalview application and applet
1370 <em>Application</em>
1372 <li>Duplicate group consensus and conservation rows
1373 shown when tree is partitioned</li>
1374 <li>Erratic behaviour when tree partitions made with
1375 multiple cDNA/Protein split views</li>
1381 <td width="60" nowrap>
1382 <div align="center">
1383 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1384 <em>8/10/2015</em></strong>
1387 <td><em>General</em>
1389 <li>Updated Spanish translations of localized text for
1391 </ul> <em>Application</em>
1393 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1394 <li>Signed OSX InstallAnywhere installer<br></li>
1395 <li>Support for per-sequence based annotations in BioJSON</li>
1396 </ul> <em>Applet</em>
1398 <li>Split frame example added to applet examples page</li>
1399 </ul> <em>Build and Deployment</em>
1402 <!-- JAL-1888 -->New ant target for running Jalview's test
1410 <li>Mapping of cDNA to protein in split frames
1411 incorrect when sequence start > 1</li>
1412 <li>Broken images in filter column by annotation dialog
1414 <li>Feature colours not parsed from features file</li>
1415 <li>Exceptions and incomplete link URLs recovered when
1416 loading a features file containing HTML tags in feature
1420 <em>Application</em>
1422 <li>Annotations corrupted after BioJS export and
1424 <li>Incorrect sequence limits after Fetch DB References
1425 with 'trim retrieved sequences'</li>
1426 <li>Incorrect warning about deleting all data when
1427 deleting selected columns</li>
1428 <li>Patch to build system for shipping properly signed
1429 JNLP templates for webstart launch</li>
1430 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1431 unreleased structures for download or viewing</li>
1432 <li>Tab/space/return keystroke operation of EMBL-PDBe
1433 fetcher/viewer dialogs works correctly</li>
1434 <li>Disabled 'minimise' button on Jalview windows
1435 running on OSX to workaround redraw hang bug</li>
1436 <li>Split cDNA/Protein view position and geometry not
1437 recovered from jalview project</li>
1438 <li>Initial enabled/disabled state of annotation menu
1439 sorter 'show autocalculated first/last' corresponds to
1441 <li>Restoring of Clustal, RNA Helices and T-Coffee
1442 color schemes from BioJSON</li>
1446 <li>Reorder sequences mirrored in cDNA/Protein split
1448 <li>Applet with Jmol examples not loading correctly</li>
1454 <td><div align="center">
1455 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1457 <td><em>General</em>
1459 <li>Linked visualisation and analysis of DNA and Protein
1462 <li>Translated cDNA alignments shown as split protein
1463 and DNA alignment views</li>
1464 <li>Codon consensus annotation for linked protein and
1465 cDNA alignment views</li>
1466 <li>Link cDNA or Protein product sequences by loading
1467 them onto Protein or cDNA alignments</li>
1468 <li>Reconstruct linked cDNA alignment from aligned
1469 protein sequences</li>
1472 <li>Jmol integration updated to Jmol v14.2.14</li>
1473 <li>Import and export of Jalview alignment views as <a
1474 href="features/bioJsonFormat.html">BioJSON</a></li>
1475 <li>New alignment annotation file statements for
1476 reference sequences and marking hidden columns</li>
1477 <li>Reference sequence based alignment shading to
1478 highlight variation</li>
1479 <li>Select or hide columns according to alignment
1481 <li>Find option for locating sequences by description</li>
1482 <li>Conserved physicochemical properties shown in amino
1483 acid conservation row</li>
1484 <li>Alignments can be sorted by number of RNA helices</li>
1485 </ul> <em>Application</em>
1487 <li>New cDNA/Protein analysis capabilities
1489 <li>Get Cross-References should open a Split Frame
1490 view with cDNA/Protein</li>
1491 <li>Detect when nucleotide sequences and protein
1492 sequences are placed in the same alignment</li>
1493 <li>Split cDNA/Protein views are saved in Jalview
1498 <li>Use REST API to talk to Chimera</li>
1499 <li>Selected regions in Chimera are highlighted in linked
1500 Jalview windows</li>
1502 <li>VARNA RNA viewer updated to v3.93</li>
1503 <li>VARNA views are saved in Jalview Projects</li>
1504 <li>Pseudoknots displayed as Jalview RNA annotation can
1505 be shown in VARNA</li>
1507 <li>Make groups for selection uses marked columns as well
1508 as the active selected region</li>
1510 <li>Calculate UPGMA and NJ trees using sequence feature
1512 <li>New Export options
1514 <li>New Export Settings dialog to control hidden
1515 region export in flat file generation</li>
1517 <li>Export alignment views for display with the <a
1518 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1520 <li>Export scrollable SVG in HTML page</li>
1521 <li>Optional embedding of BioJSON data when exporting
1522 alignment figures to HTML</li>
1524 <li>3D structure retrieval and display
1526 <li>Free text and structured queries with the PDBe
1528 <li>PDBe Search API based discovery and selection of
1529 PDB structures for a sequence set</li>
1533 <li>JPred4 employed for protein secondary structure
1535 <li>Hide Insertions menu option to hide unaligned columns
1536 for one or a group of sequences</li>
1537 <li>Automatically hide insertions in alignments imported
1538 from the JPred4 web server</li>
1539 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1540 system on OSX<br />LGPL libraries courtesy of <a
1541 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1543 <li>changed 'View nucleotide structure' submenu to 'View
1544 VARNA 2D Structure'</li>
1545 <li>change "View protein structure" menu option to "3D
1548 </ul> <em>Applet</em>
1550 <li>New layout for applet example pages</li>
1551 <li>New parameters to enable SplitFrame view
1552 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1553 <li>New example demonstrating linked viewing of cDNA and
1554 Protein alignments</li>
1555 </ul> <em>Development and deployment</em>
1557 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1558 <li>Include installation type and git revision in build
1559 properties and console log output</li>
1560 <li>Jalview Github organisation, and new github site for
1561 storing BioJsMSA Templates</li>
1562 <li>Jalview's unit tests now managed with TestNG</li>
1565 <!-- <em>General</em>
1567 </ul> --> <!-- issues resolved --> <em>Application</em>
1569 <li>Escape should close any open find dialogs</li>
1570 <li>Typo in select-by-features status report</li>
1571 <li>Consensus RNA secondary secondary structure
1572 predictions are not highlighted in amber</li>
1573 <li>Missing gap character in v2.7 example file means
1574 alignment appears unaligned when pad-gaps is not enabled</li>
1575 <li>First switch to RNA Helices colouring doesn't colour
1576 associated structure views</li>
1577 <li>ID width preference option is greyed out when auto
1578 width checkbox not enabled</li>
1579 <li>Stopped a warning dialog from being shown when
1580 creating user defined colours</li>
1581 <li>'View Mapping' in structure viewer shows sequence
1582 mappings for just that viewer's sequences</li>
1583 <li>Workaround for superposing PDB files containing
1584 multiple models in Chimera</li>
1585 <li>Report sequence position in status bar when hovering
1586 over Jmol structure</li>
1587 <li>Cannot output gaps as '.' symbols with Selection ->
1588 output to text box</li>
1589 <li>Flat file exports of alignments with hidden columns
1590 have incorrect sequence start/end</li>
1591 <li>'Aligning' a second chain to a Chimera structure from
1593 <li>Colour schemes applied to structure viewers don't
1594 work for nucleotide</li>
1595 <li>Loading/cut'n'pasting an empty or invalid file leads
1596 to a grey/invisible alignment window</li>
1597 <li>Exported Jpred annotation from a sequence region
1598 imports to different position</li>
1599 <li>Space at beginning of sequence feature tooltips shown
1600 on some platforms</li>
1601 <li>Chimera viewer 'View | Show Chain' menu is not
1603 <li>'New View' fails with a Null Pointer Exception in
1604 console if Chimera has been opened</li>
1605 <li>Mouseover to Chimera not working</li>
1606 <li>Miscellaneous ENA XML feature qualifiers not
1608 <li>NPE in annotation renderer after 'Extract Scores'</li>
1609 <li>If two structures in one Chimera window, mouseover of
1610 either sequence shows on first structure</li>
1611 <li>'Show annotations' options should not make
1612 non-positional annotations visible</li>
1613 <li>Subsequence secondary structure annotation not shown
1614 in right place after 'view flanking regions'</li>
1615 <li>File Save As type unset when current file format is
1617 <li>Save as '.jar' option removed for saving Jalview
1619 <li>Colour by Sequence colouring in Chimera more
1621 <li>Cannot 'add reference annotation' for a sequence in
1622 several views on same alignment</li>
1623 <li>Cannot show linked products for EMBL / ENA records</li>
1624 <li>Jalview's tooltip wraps long texts containing no
1626 </ul> <em>Applet</em>
1628 <li>Jmol to JalviewLite mouseover/link not working</li>
1629 <li>JalviewLite can't import sequences with ID
1630 descriptions containing angle brackets</li>
1631 </ul> <em>General</em>
1633 <li>Cannot export and reimport RNA secondary structure
1634 via jalview annotation file</li>
1635 <li>Random helix colour palette for colour by annotation
1636 with RNA secondary structure</li>
1637 <li>Mouseover to cDNA from STOP residue in protein
1638 translation doesn't work.</li>
1639 <li>hints when using the select by annotation dialog box</li>
1640 <li>Jmol alignment incorrect if PDB file has alternate CA
1642 <li>FontChooser message dialog appears to hang after
1643 choosing 1pt font</li>
1644 <li>Peptide secondary structure incorrectly imported from
1645 annotation file when annotation display text includes 'e' or
1647 <li>Cannot set colour of new feature type whilst creating
1649 <li>cDNA translation alignment should not be sequence
1650 order dependent</li>
1651 <li>'Show unconserved' doesn't work for lower case
1653 <li>Nucleotide ambiguity codes involving R not recognised</li>
1654 </ul> <em>Deployment and Documentation</em>
1656 <li>Applet example pages appear different to the rest of
1657 www.jalview.org</li>
1658 </ul> <em>Application Known issues</em>
1660 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1661 <li>Misleading message appears after trying to delete
1663 <li>Jalview icon not shown in dock after InstallAnywhere
1664 version launches</li>
1665 <li>Fetching EMBL reference for an RNA sequence results
1666 fails with a sequence mismatch</li>
1667 <li>Corrupted or unreadable alignment display when
1668 scrolling alignment to right</li>
1669 <li>ArrayIndexOutOfBoundsException thrown when remove
1670 empty columns called on alignment with ragged gapped ends</li>
1671 <li>auto calculated alignment annotation rows do not get
1672 placed above or below non-autocalculated rows</li>
1673 <li>Jalview dekstop becomes sluggish at full screen in
1674 ultra-high resolution</li>
1675 <li>Cannot disable consensus calculation independently of
1676 quality and conservation</li>
1677 <li>Mouseover highlighting between cDNA and protein can
1678 become sluggish with more than one splitframe shown</li>
1679 </ul> <em>Applet Known Issues</em>
1681 <li>Core PDB parsing code requires Jmol</li>
1682 <li>Sequence canvas panel goes white when alignment
1683 window is being resized</li>
1689 <td><div align="center">
1690 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1692 <td><em>General</em>
1694 <li>Updated Java code signing certificate donated by
1696 <li>Features and annotation preserved when performing
1697 pairwise alignment</li>
1698 <li>RNA pseudoknot annotation can be
1699 imported/exported/displayed</li>
1700 <li>'colour by annotation' can colour by RNA and
1701 protein secondary structure</li>
1702 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1703 post-hoc with 2.9 release</em>)
1706 </ul> <em>Application</em>
1708 <li>Extract and display secondary structure for sequences
1709 with 3D structures</li>
1710 <li>Support for parsing RNAML</li>
1711 <li>Annotations menu for layout
1713 <li>sort sequence annotation rows by alignment</li>
1714 <li>place sequence annotation above/below alignment
1717 <li>Output in Stockholm format</li>
1718 <li>Internationalisation: improved Spanish (es)
1720 <li>Structure viewer preferences tab</li>
1721 <li>Disorder and Secondary Structure annotation tracks
1722 shared between alignments</li>
1723 <li>UCSF Chimera launch and linked highlighting from
1725 <li>Show/hide all sequence associated annotation rows for
1726 all or current selection</li>
1727 <li>disorder and secondary structure predictions
1728 available as dataset annotation</li>
1729 <li>Per-sequence rna helices colouring</li>
1732 <li>Sequence database accessions imported when fetching
1733 alignments from Rfam</li>
1734 <li>update VARNA version to 3.91</li>
1736 <li>New groovy scripts for exporting aligned positions,
1737 conservation values, and calculating sum of pairs scores.</li>
1738 <li>Command line argument to set default JABAWS server</li>
1739 <li>include installation type in build properties and
1740 console log output</li>
1741 <li>Updated Jalview project format to preserve dataset
1745 <!-- issues resolved --> <em>Application</em>
1747 <li>Distinguish alignment and sequence associated RNA
1748 structure in structure->view->VARNA</li>
1749 <li>Raise dialog box if user deletes all sequences in an
1751 <li>Pressing F1 results in documentation opening twice</li>
1752 <li>Sequence feature tooltip is wrapped</li>
1753 <li>Double click on sequence associated annotation
1754 selects only first column</li>
1755 <li>Redundancy removal doesn't result in unlinked
1756 leaves shown in tree</li>
1757 <li>Undos after several redundancy removals don't undo
1759 <li>Hide sequence doesn't hide associated annotation</li>
1760 <li>User defined colours dialog box too big to fit on
1761 screen and buttons not visible</li>
1762 <li>author list isn't updated if already written to
1763 Jalview properties</li>
1764 <li>Popup menu won't open after retrieving sequence
1766 <li>File open window for associate PDB doesn't open</li>
1767 <li>Left-then-right click on a sequence id opens a
1768 browser search window</li>
1769 <li>Cannot open sequence feature shading/sort popup menu
1770 in feature settings dialog</li>
1771 <li>better tooltip placement for some areas of Jalview
1773 <li>Allow addition of JABAWS Server which doesn't
1774 pass validation</li>
1775 <li>Web services parameters dialog box is too large to
1777 <li>Muscle nucleotide alignment preset obscured by
1779 <li>JABAWS preset submenus don't contain newly
1780 defined user preset</li>
1781 <li>MSA web services warns user if they were launched
1782 with invalid input</li>
1783 <li>Jalview cannot contact DAS Registy when running on
1786 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1787 'Superpose with' submenu not shown when new view
1791 </ul> <!-- <em>Applet</em>
1793 </ul> <em>General</em>
1795 </ul>--> <em>Deployment and Documentation</em>
1797 <li>2G and 1G options in launchApp have no effect on
1798 memory allocation</li>
1799 <li>launchApp service doesn't automatically open
1800 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1802 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1803 InstallAnywhere reports cannot find valid JVM when Java
1804 1.7_055 is available
1806 </ul> <em>Application Known issues</em>
1809 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1810 corrupted or unreadable alignment display when scrolling
1814 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1815 retrieval fails but progress bar continues for DAS retrieval
1816 with large number of ID
1819 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1820 flatfile output of visible region has incorrect sequence
1824 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1825 rna structure consensus doesn't update when secondary
1826 structure tracks are rearranged
1829 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1830 invalid rna structure positional highlighting does not
1831 highlight position of invalid base pairs
1834 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1835 out of memory errors are not raised when saving Jalview
1836 project from alignment window file menu
1839 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1840 Switching to RNA Helices colouring doesn't propagate to
1844 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1845 colour by RNA Helices not enabled when user created
1846 annotation added to alignment
1849 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1850 Jalview icon not shown on dock in Mountain Lion/Webstart
1852 </ul> <em>Applet Known Issues</em>
1855 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1856 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1859 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1860 Jalview and Jmol example not compatible with IE9
1863 <li>Sort by annotation score doesn't reverse order
1869 <td><div align="center">
1870 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1873 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1876 <li>Internationalisation of user interface (usually
1877 called i18n support) and translation for Spanish locale</li>
1878 <li>Define/Undefine group on current selection with
1879 Ctrl-G/Shift Ctrl-G</li>
1880 <li>Improved group creation/removal options in
1881 alignment/sequence Popup menu</li>
1882 <li>Sensible precision for symbol distribution
1883 percentages shown in logo tooltip.</li>
1884 <li>Annotation panel height set according to amount of
1885 annotation when alignment first opened</li>
1886 </ul> <em>Application</em>
1888 <li>Interactive consensus RNA secondary structure
1889 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1890 <li>Select columns containing particular features from
1891 Feature Settings dialog</li>
1892 <li>View all 'representative' PDB structures for selected
1894 <li>Update Jalview project format:
1896 <li>New file extension for Jalview projects '.jvp'</li>
1897 <li>Preserve sequence and annotation dataset (to
1898 store secondary structure annotation,etc)</li>
1899 <li>Per group and alignment annotation and RNA helix
1903 <li>New similarity measures for PCA and Tree calculation
1905 <li>Experimental support for retrieval and viewing of
1906 flanking regions for an alignment</li>
1910 <!-- issues resolved --> <em>Application</em>
1912 <li>logo keeps spinning and status remains at queued or
1913 running after job is cancelled</li>
1914 <li>cannot export features from alignments imported from
1915 Jalview/VAMSAS projects</li>
1916 <li>Buggy slider for web service parameters that take
1918 <li>Newly created RNA secondary structure line doesn't
1919 have 'display all symbols' flag set</li>
1920 <li>T-COFFEE alignment score shading scheme and other
1921 annotation shading not saved in Jalview project</li>
1922 <li>Local file cannot be loaded in freshly downloaded
1924 <li>Jalview icon not shown on dock in Mountain
1926 <li>Load file from desktop file browser fails</li>
1927 <li>Occasional NPE thrown when calculating large trees</li>
1928 <li>Cannot reorder or slide sequences after dragging an
1929 alignment onto desktop</li>
1930 <li>Colour by annotation dialog throws NPE after using
1931 'extract scores' function</li>
1932 <li>Loading/cut'n'pasting an empty file leads to a grey
1933 alignment window</li>
1934 <li>Disorder thresholds rendered incorrectly after
1935 performing IUPred disorder prediction</li>
1936 <li>Multiple group annotated consensus rows shown when
1937 changing 'normalise logo' display setting</li>
1938 <li>Find shows blank dialog after 'finished searching' if
1939 nothing matches query</li>
1940 <li>Null Pointer Exceptions raised when sorting by
1941 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1943 <li>Errors in Jmol console when structures in alignment
1944 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1946 <li>Not all working JABAWS services are shown in
1948 <li>JAVAWS version of Jalview fails to launch with
1949 'invalid literal/length code'</li>
1950 <li>Annotation/RNA Helix colourschemes cannot be applied
1951 to alignment with groups (actually fixed in 2.8.0b1)</li>
1952 <li>RNA Helices and T-Coffee Scores available as default
1955 </ul> <em>Applet</em>
1957 <li>Remove group option is shown even when selection is
1959 <li>Apply to all groups ticked but colourscheme changes
1960 don't affect groups</li>
1961 <li>Documented RNA Helices and T-Coffee Scores as valid
1962 colourscheme name</li>
1963 <li>Annotation labels drawn on sequence IDs when
1964 Annotation panel is not displayed</li>
1965 <li>Increased font size for dropdown menus on OSX and
1966 embedded windows</li>
1967 </ul> <em>Other</em>
1969 <li>Consensus sequence for alignments/groups with a
1970 single sequence were not calculated</li>
1971 <li>annotation files that contain only groups imported as
1972 annotation and junk sequences</li>
1973 <li>Fasta files with sequences containing '*' incorrectly
1974 recognised as PFAM or BLC</li>
1975 <li>conservation/PID slider apply all groups option
1976 doesn't affect background (2.8.0b1)
1978 <li>redundancy highlighting is erratic at 0% and 100%</li>
1979 <li>Remove gapped columns fails for sequences with ragged
1981 <li>AMSA annotation row with leading spaces is not
1982 registered correctly on import</li>
1983 <li>Jalview crashes when selecting PCA analysis for
1984 certain alignments</li>
1985 <li>Opening the colour by annotation dialog for an
1986 existing annotation based 'use original colours'
1987 colourscheme loses original colours setting</li>
1992 <td><div align="center">
1993 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
1994 <em>30/1/2014</em></strong>
1998 <li>Trusted certificates for JalviewLite applet and
1999 Jalview Desktop application<br />Certificate was donated by
2000 <a href="https://www.certum.eu">Certum</a> to the Jalview
2001 open source project).
2003 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2004 <li>Output in Stockholm format</li>
2005 <li>Allow import of data from gzipped files</li>
2006 <li>Export/import group and sequence associated line
2007 graph thresholds</li>
2008 <li>Nucleotide substitution matrix that supports RNA and
2009 ambiguity codes</li>
2010 <li>Allow disorder predictions to be made on the current
2011 selection (or visible selection) in the same way that JPred
2013 <li>Groovy scripting for headless Jalview operation</li>
2014 </ul> <em>Other improvements</em>
2016 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2017 <li>COMBINE statement uses current SEQUENCE_REF and
2018 GROUP_REF scope to group annotation rows</li>
2019 <li>Support '' style escaping of quotes in Newick
2021 <li>Group options for JABAWS service by command line name</li>
2022 <li>Empty tooltip shown for JABA service options with a
2023 link but no description</li>
2024 <li>Select primary source when selecting authority in
2025 database fetcher GUI</li>
2026 <li>Add .mfa to FASTA file extensions recognised by
2028 <li>Annotation label tooltip text wrap</li>
2033 <li>Slow scrolling when lots of annotation rows are
2035 <li>Lots of NPE (and slowness) after creating RNA
2036 secondary structure annotation line</li>
2037 <li>Sequence database accessions not imported when
2038 fetching alignments from Rfam</li>
2039 <li>Incorrect SHMR submission for sequences with
2041 <li>View all structures does not always superpose
2043 <li>Option widgets in service parameters not updated to
2044 reflect user or preset settings</li>
2045 <li>Null pointer exceptions for some services without
2046 presets or adjustable parameters</li>
2047 <li>Discover PDB IDs entry in structure menu doesn't
2048 discover PDB xRefs</li>
2049 <li>Exception encountered while trying to retrieve
2050 features with DAS</li>
2051 <li>Lowest value in annotation row isn't coloured
2052 when colour by annotation (per sequence) is coloured</li>
2053 <li>Keyboard mode P jumps to start of gapped region when
2054 residue follows a gap</li>
2055 <li>Jalview appears to hang importing an alignment with
2056 Wrap as default or after enabling Wrap</li>
2057 <li>'Right click to add annotations' message
2058 shown in wrap mode when no annotations present</li>
2059 <li>Disorder predictions fail with NPE if no automatic
2060 annotation already exists on alignment</li>
2061 <li>oninit javascript function should be called after
2062 initialisation completes</li>
2063 <li>Remove redundancy after disorder prediction corrupts
2064 alignment window display</li>
2065 <li>Example annotation file in documentation is invalid</li>
2066 <li>Grouped line graph annotation rows are not exported
2067 to annotation file</li>
2068 <li>Multi-harmony analysis cannot be run when only two
2070 <li>Cannot create multiple groups of line graphs with
2071 several 'combine' statements in annotation file</li>
2072 <li>Pressing return several times causes Number Format
2073 exceptions in keyboard mode</li>
2074 <li>Multi-harmony (SHMMR) method doesn't submit
2075 correct partitions for input data</li>
2076 <li>Translation from DNA to Amino Acids fails</li>
2077 <li>Jalview fail to load newick tree with quoted label</li>
2078 <li>--headless flag isn't understood</li>
2079 <li>ClassCastException when generating EPS in headless
2081 <li>Adjusting sequence-associated shading threshold only
2082 changes one row's threshold</li>
2083 <li>Preferences and Feature settings panel panel
2084 doesn't open</li>
2085 <li>hide consensus histogram also hides conservation and
2086 quality histograms</li>
2091 <td><div align="center">
2092 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2094 <td><em>Application</em>
2096 <li>Support for JABAWS 2.0 Services (AACon alignment
2097 conservation, protein disorder and Clustal Omega)</li>
2098 <li>JABAWS server status indicator in Web Services
2100 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2101 in Jalview alignment window</li>
2102 <li>Updated Jalview build and deploy framework for OSX
2103 mountain lion, windows 7, and 8</li>
2104 <li>Nucleotide substitution matrix for PCA that supports
2105 RNA and ambiguity codes</li>
2107 <li>Improved sequence database retrieval GUI</li>
2108 <li>Support fetching and database reference look up
2109 against multiple DAS sources (Fetch all from in 'fetch db
2111 <li>Jalview project improvements
2113 <li>Store and retrieve the 'belowAlignment'
2114 flag for annotation</li>
2115 <li>calcId attribute to group annotation rows on the
2117 <li>Store AACon calculation settings for a view in
2118 Jalview project</li>
2122 <li>horizontal scrolling gesture support</li>
2123 <li>Visual progress indicator when PCA calculation is
2125 <li>Simpler JABA web services menus</li>
2126 <li>visual indication that web service results are still
2127 being retrieved from server</li>
2128 <li>Serialise the dialogs that are shown when Jalview
2129 starts up for first time</li>
2130 <li>Jalview user agent string for interacting with HTTP
2132 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2134 <li>Examples directory and Groovy library included in
2135 InstallAnywhere distribution</li>
2136 </ul> <em>Applet</em>
2138 <li>RNA alignment and secondary structure annotation
2139 visualization applet example</li>
2140 </ul> <em>General</em>
2142 <li>Normalise option for consensus sequence logo</li>
2143 <li>Reset button in PCA window to return dimensions to
2145 <li>Allow seqspace or Jalview variant of alignment PCA
2147 <li>PCA with either nucleic acid and protein substitution
2149 <li>Allow windows containing HTML reports to be exported
2151 <li>Interactive display and editing of RNA secondary
2152 structure contacts</li>
2153 <li>RNA Helix Alignment Colouring</li>
2154 <li>RNA base pair logo consensus</li>
2155 <li>Parse sequence associated secondary structure
2156 information in Stockholm files</li>
2157 <li>HTML Export database accessions and annotation
2158 information presented in tooltip for sequences</li>
2159 <li>Import secondary structure from LOCARNA clustalw
2160 style RNA alignment files</li>
2161 <li>import and visualise T-COFFEE quality scores for an
2163 <li>'colour by annotation' per sequence option to
2164 shade each sequence according to its associated alignment
2166 <li>New Jalview Logo</li>
2167 </ul> <em>Documentation and Development</em>
2169 <li>documentation for score matrices used in Jalview</li>
2170 <li>New Website!</li>
2172 <td><em>Application</em>
2174 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2175 wsdbfetch REST service</li>
2176 <li>Stop windows being moved outside desktop on OSX</li>
2177 <li>Filetype associations not installed for webstart
2179 <li>Jalview does not always retrieve progress of a JABAWS
2180 job execution in full once it is complete</li>
2181 <li>revise SHMR RSBS definition to ensure alignment is
2182 uploaded via ali_file parameter</li>
2183 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2184 <li>View all structures superposed fails with exception</li>
2185 <li>Jnet job queues forever if a very short sequence is
2186 submitted for prediction</li>
2187 <li>Cut and paste menu not opened when mouse clicked on
2189 <li>Putting fractional value into integer text box in
2190 alignment parameter dialog causes Jalview to hang</li>
2191 <li>Structure view highlighting doesn't work on
2193 <li>View all structures fails with exception shown in
2195 <li>Characters in filename associated with PDBEntry not
2196 escaped in a platform independent way</li>
2197 <li>Jalview desktop fails to launch with exception when
2199 <li>Tree calculation reports 'you must have 2 or more
2200 sequences selected' when selection is empty</li>
2201 <li>Jalview desktop fails to launch with jar signature
2202 failure when java web start temporary file caching is
2204 <li>DAS Sequence retrieval with range qualification
2205 results in sequence xref which includes range qualification</li>
2206 <li>Errors during processing of command line arguments
2207 cause progress bar (JAL-898) to be removed</li>
2208 <li>Replace comma for semi-colon option not disabled for
2209 DAS sources in sequence fetcher</li>
2210 <li>Cannot close news reader when JABAWS server warning
2211 dialog is shown</li>
2212 <li>Option widgets not updated to reflect user settings</li>
2213 <li>Edited sequence not submitted to web service</li>
2214 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2215 <li>InstallAnywhere installer doesn't unpack and run
2216 on OSX Mountain Lion</li>
2217 <li>Annotation panel not given a scroll bar when
2218 sequences with alignment annotation are pasted into the
2220 <li>Sequence associated annotation rows not associated
2221 when loaded from Jalview project</li>
2222 <li>Browser launch fails with NPE on java 1.7</li>
2223 <li>JABAWS alignment marked as finished when job was
2224 cancelled or job failed due to invalid input</li>
2225 <li>NPE with v2.7 example when clicking on Tree
2226 associated with all views</li>
2227 <li>Exceptions when copy/paste sequences with grouped
2228 annotation rows to new window</li>
2229 </ul> <em>Applet</em>
2231 <li>Sequence features are momentarily displayed before
2232 they are hidden using hidefeaturegroups applet parameter</li>
2233 <li>loading features via javascript API automatically
2234 enables feature display</li>
2235 <li>scrollToColumnIn javascript API method doesn't
2237 </ul> <em>General</em>
2239 <li>Redundancy removal fails for rna alignment</li>
2240 <li>PCA calculation fails when sequence has been selected
2241 and then deselected</li>
2242 <li>PCA window shows grey box when first opened on OSX</li>
2243 <li>Letters coloured pink in sequence logo when alignment
2244 coloured with clustalx</li>
2245 <li>Choosing fonts without letter symbols defined causes
2246 exceptions and redraw errors</li>
2247 <li>Initial PCA plot view is not same as manually
2248 reconfigured view</li>
2249 <li>Grouped annotation graph label has incorrect line
2251 <li>Grouped annotation graph label display is corrupted
2252 for lots of labels</li>
2257 <div align="center">
2258 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2261 <td><em>Application</em>
2263 <li>Jalview Desktop News Reader</li>
2264 <li>Tweaked default layout of web services menu</li>
2265 <li>View/alignment association menu to enable user to
2266 easily specify which alignment a multi-structure view takes
2267 its colours/correspondences from</li>
2268 <li>Allow properties file location to be specified as URL</li>
2269 <li>Extend Jalview project to preserve associations
2270 between many alignment views and a single Jmol display</li>
2271 <li>Store annotation row height in Jalview project file</li>
2272 <li>Annotation row column label formatting attributes
2273 stored in project file</li>
2274 <li>Annotation row order for auto-calculated annotation
2275 rows preserved in Jalview project file</li>
2276 <li>Visual progress indication when Jalview state is
2277 saved using Desktop window menu</li>
2278 <li>Visual indication that command line arguments are
2279 still being processed</li>
2280 <li>Groovy script execution from URL</li>
2281 <li>Colour by annotation default min and max colours in
2283 <li>Automatically associate PDB files dragged onto an
2284 alignment with sequences that have high similarity and
2286 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2287 <li>'view structures' option to open many
2288 structures in same window</li>
2289 <li>Sort associated views menu option for tree panel</li>
2290 <li>Group all JABA and non-JABA services for a particular
2291 analysis function in its own submenu</li>
2292 </ul> <em>Applet</em>
2294 <li>Userdefined and autogenerated annotation rows for
2296 <li>Adjustment of alignment annotation pane height</li>
2297 <li>Annotation scrollbar for annotation panel</li>
2298 <li>Drag to reorder annotation rows in annotation panel</li>
2299 <li>'automaticScrolling' parameter</li>
2300 <li>Allow sequences with partial ID string matches to be
2301 annotated from GFF/Jalview features files</li>
2302 <li>Sequence logo annotation row in applet</li>
2303 <li>Absolute paths relative to host server in applet
2304 parameters are treated as such</li>
2305 <li>New in the JalviewLite javascript API:
2307 <li>JalviewLite.js javascript library</li>
2308 <li>Javascript callbacks for
2310 <li>Applet initialisation</li>
2311 <li>Sequence/alignment mouse-overs and selections</li>
2314 <li>scrollTo row and column alignment scrolling
2316 <li>Select sequence/alignment regions from javascript</li>
2317 <li>javascript structure viewer harness to pass
2318 messages between Jmol and Jalview when running as
2319 distinct applets</li>
2320 <li>sortBy method</li>
2321 <li>Set of applet and application examples shipped
2322 with documentation</li>
2323 <li>New example to demonstrate JalviewLite and Jmol
2324 javascript message exchange</li>
2326 </ul> <em>General</em>
2328 <li>Enable Jmol displays to be associated with multiple
2329 multiple alignments</li>
2330 <li>Option to automatically sort alignment with new tree</li>
2331 <li>User configurable link to enable redirects to a
2332 www.Jalview.org mirror</li>
2333 <li>Jmol colours option for Jmol displays</li>
2334 <li>Configurable newline string when writing alignment
2335 and other flat files</li>
2336 <li>Allow alignment annotation description lines to
2337 contain html tags</li>
2338 </ul> <em>Documentation and Development</em>
2340 <li>Add groovy test harness for bulk load testing to
2342 <li>Groovy script to load and align a set of sequences
2343 using a web service before displaying the result in the
2344 Jalview desktop</li>
2345 <li>Restructured javascript and applet api documentation</li>
2346 <li>Ant target to publish example html files with applet
2348 <li>Netbeans project for building Jalview from source</li>
2349 <li>ant task to create online javadoc for Jalview source</li>
2351 <td><em>Application</em>
2353 <li>User defined colourscheme throws exception when
2354 current built in colourscheme is saved as new scheme</li>
2355 <li>AlignFrame->Save in application pops up save
2356 dialog for valid filename/format</li>
2357 <li>Cannot view associated structure for UniProt sequence</li>
2358 <li>PDB file association breaks for UniProt sequence
2360 <li>Associate PDB from file dialog does not tell you
2361 which sequence is to be associated with the file</li>
2362 <li>Find All raises null pointer exception when query
2363 only matches sequence IDs</li>
2364 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2365 <li>Jalview project with Jmol views created with Jalview
2366 2.4 cannot be loaded</li>
2367 <li>Filetype associations not installed for webstart
2369 <li>Two or more chains in a single PDB file associated
2370 with sequences in different alignments do not get coloured
2371 by their associated sequence</li>
2372 <li>Visibility status of autocalculated annotation row
2373 not preserved when project is loaded</li>
2374 <li>Annotation row height and visibility attributes not
2375 stored in Jalview project</li>
2376 <li>Tree bootstraps are not preserved when saved as a
2377 Jalview project</li>
2378 <li>Envision2 workflow tooltips are corrupted</li>
2379 <li>Enabling show group conservation also enables colour
2380 by conservation</li>
2381 <li>Duplicate group associated conservation or consensus
2382 created on new view</li>
2383 <li>Annotation scrollbar not displayed after 'show
2384 all hidden annotation rows' option selected</li>
2385 <li>Alignment quality not updated after alignment
2386 annotation row is hidden then shown</li>
2387 <li>Preserve colouring of structures coloured by
2388 sequences in pre Jalview 2.7 projects</li>
2389 <li>Web service job parameter dialog is not laid out
2391 <li>Web services menu not refreshed after 'reset
2392 services' button is pressed in preferences</li>
2393 <li>Annotation off by one in Jalview v2_3 example project</li>
2394 <li>Structures imported from file and saved in project
2395 get name like jalview_pdb1234.txt when reloaded</li>
2396 <li>Jalview does not always retrieve progress of a JABAWS
2397 job execution in full once it is complete</li>
2398 </ul> <em>Applet</em>
2400 <li>Alignment height set incorrectly when lots of
2401 annotation rows are displayed</li>
2402 <li>Relative URLs in feature HTML text not resolved to
2404 <li>View follows highlighting does not work for positions
2406 <li><= shown as = in tooltip</li>
2407 <li>Export features raises exception when no features
2409 <li>Separator string used for serialising lists of IDs
2410 for javascript api is modified when separator string
2411 provided as parameter</li>
2412 <li>Null pointer exception when selecting tree leaves for
2413 alignment with no existing selection</li>
2414 <li>Relative URLs for datasources assumed to be relative
2415 to applet's codebase</li>
2416 <li>Status bar not updated after finished searching and
2417 search wraps around to first result</li>
2418 <li>StructureSelectionManager instance shared between
2419 several Jalview applets causes race conditions and memory
2421 <li>Hover tooltip and mouseover of position on structure
2422 not sent from Jmol in applet</li>
2423 <li>Certain sequences of javascript method calls to
2424 applet API fatally hang browser</li>
2425 </ul> <em>General</em>
2427 <li>View follows structure mouseover scrolls beyond
2428 position with wrapped view and hidden regions</li>
2429 <li>Find sequence position moves to wrong residue
2430 with/without hidden columns</li>
2431 <li>Sequence length given in alignment properties window
2433 <li>InvalidNumberFormat exceptions thrown when trying to
2434 import PDB like structure files</li>
2435 <li>Positional search results are only highlighted
2436 between user-supplied sequence start/end bounds</li>
2437 <li>End attribute of sequence is not validated</li>
2438 <li>Find dialog only finds first sequence containing a
2439 given sequence position</li>
2440 <li>Sequence numbering not preserved in MSF alignment
2442 <li>Jalview PDB file reader does not extract sequence
2443 from nucleotide chains correctly</li>
2444 <li>Structure colours not updated when tree partition
2445 changed in alignment</li>
2446 <li>Sequence associated secondary structure not correctly
2447 parsed in interleaved stockholm</li>
2448 <li>Colour by annotation dialog does not restore current
2450 <li>Hiding (nearly) all sequences doesn't work
2452 <li>Sequences containing lowercase letters are not
2453 properly associated with their pdb files</li>
2454 </ul> <em>Documentation and Development</em>
2456 <li>schemas/JalviewWsParamSet.xsd corrupted by
2457 ApplyCopyright tool</li>
2462 <div align="center">
2463 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2466 <td><em>Application</em>
2468 <li>New warning dialog when the Jalview Desktop cannot
2469 contact web services</li>
2470 <li>JABA service parameters for a preset are shown in
2471 service job window</li>
2472 <li>JABA Service menu entries reworded</li>
2476 <li>Modeller PIR IO broken - cannot correctly import a
2477 pir file emitted by Jalview</li>
2478 <li>Existing feature settings transferred to new
2479 alignment view created from cut'n'paste</li>
2480 <li>Improved test for mixed amino/nucleotide chains when
2481 parsing PDB files</li>
2482 <li>Consensus and conservation annotation rows
2483 occasionally become blank for all new windows</li>
2484 <li>Exception raised when right clicking above sequences
2485 in wrapped view mode</li>
2486 </ul> <em>Application</em>
2488 <li>multiple multiply aligned structure views cause cpu
2489 usage to hit 100% and computer to hang</li>
2490 <li>Web Service parameter layout breaks for long user
2491 parameter names</li>
2492 <li>Jaba service discovery hangs desktop if Jaba server
2499 <div align="center">
2500 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2503 <td><em>Application</em>
2505 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2506 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2509 <li>Web Services preference tab</li>
2510 <li>Analysis parameters dialog box and user defined
2512 <li>Improved speed and layout of Envision2 service menu</li>
2513 <li>Superpose structures using associated sequence
2515 <li>Export coordinates and projection as CSV from PCA
2517 </ul> <em>Applet</em>
2519 <li>enable javascript: execution by the applet via the
2520 link out mechanism</li>
2521 </ul> <em>Other</em>
2523 <li>Updated the Jmol Jalview interface to work with Jmol
2525 <li>The Jalview Desktop and JalviewLite applet now
2526 require Java 1.5</li>
2527 <li>Allow Jalview feature colour specification for GFF
2528 sequence annotation files</li>
2529 <li>New 'colour by label' keword in Jalview feature file
2530 type colour specification</li>
2531 <li>New Jalview Desktop Groovy API method that allows a
2532 script to check if it being run in an interactive session or
2533 in a batch operation from the Jalview command line</li>
2537 <li>clustalx colourscheme colours Ds preferentially when
2538 both D+E are present in over 50% of the column</li>
2539 </ul> <em>Application</em>
2541 <li>typo in AlignmentFrame->View->Hide->all but
2542 selected Regions menu item</li>
2543 <li>sequence fetcher replaces ',' for ';' when the ',' is
2544 part of a valid accession ID</li>
2545 <li>fatal OOM if object retrieved by sequence fetcher
2546 runs out of memory</li>
2547 <li>unhandled Out of Memory Error when viewing pca
2548 analysis results</li>
2549 <li>InstallAnywhere builds fail to launch on OS X java
2550 10.5 update 4 (due to apple Java 1.6 update)</li>
2551 <li>Installanywhere Jalview silently fails to launch</li>
2552 </ul> <em>Applet</em>
2554 <li>Jalview.getFeatureGroups() raises an
2555 ArrayIndexOutOfBoundsException if no feature groups are
2562 <div align="center">
2563 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2569 <li>Alignment prettyprinter doesn't cope with long
2571 <li>clustalx colourscheme colours Ds preferentially when
2572 both D+E are present in over 50% of the column</li>
2573 <li>nucleic acid structures retrieved from PDB do not
2574 import correctly</li>
2575 <li>More columns get selected than were clicked on when a
2576 number of columns are hidden</li>
2577 <li>annotation label popup menu not providing correct
2578 add/hide/show options when rows are hidden or none are
2580 <li>Stockholm format shown in list of readable formats,
2581 and parser copes better with alignments from RFAM.</li>
2582 <li>CSV output of consensus only includes the percentage
2583 of all symbols if sequence logo display is enabled</li>
2585 </ul> <em>Applet</em>
2587 <li>annotation panel disappears when annotation is
2589 </ul> <em>Application</em>
2591 <li>Alignment view not redrawn properly when new
2592 alignment opened where annotation panel is visible but no
2593 annotations are present on alignment</li>
2594 <li>pasted region containing hidden columns is
2595 incorrectly displayed in new alignment window</li>
2596 <li>Jalview slow to complete operations when stdout is
2597 flooded (fix is to close the Jalview console)</li>
2598 <li>typo in AlignmentFrame->View->Hide->all but
2599 selected Rregions menu item.</li>
2600 <li>inconsistent group submenu and Format submenu entry
2601 'Un' or 'Non'conserved</li>
2602 <li>Sequence feature settings are being shared by
2603 multiple distinct alignments</li>
2604 <li>group annotation not recreated when tree partition is
2606 <li>double click on group annotation to select sequences
2607 does not propagate to associated trees</li>
2608 <li>Mac OSX specific issues:
2610 <li>exception raised when mouse clicked on desktop
2611 window background</li>
2612 <li>Desktop menu placed on menu bar and application
2613 name set correctly</li>
2614 <li>sequence feature settings not wide enough for the
2615 save feature colourscheme button</li>
2624 <div align="center">
2625 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2628 <td><em>New Capabilities</em>
2630 <li>URL links generated from description line for
2631 regular-expression based URL links (applet and application)
2633 <li>Non-positional feature URL links are shown in link
2635 <li>Linked viewing of nucleic acid sequences and
2637 <li>Automatic Scrolling option in View menu to display
2638 the currently highlighted region of an alignment.</li>
2639 <li>Order an alignment by sequence length, or using the
2640 average score or total feature count for each sequence.</li>
2641 <li>Shading features by score or associated description</li>
2642 <li>Subdivide alignment and groups based on identity of
2643 selected subsequence (Make Groups from Selection).</li>
2644 <li>New hide/show options including Shift+Control+H to
2645 hide everything but the currently selected region.</li>
2646 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2647 </ul> <em>Application</em>
2649 <li>Fetch DB References capabilities and UI expanded to
2650 support retrieval from DAS sequence sources</li>
2651 <li>Local DAS Sequence sources can be added via the
2652 command line or via the Add local source dialog box.</li>
2653 <li>DAS Dbref and DbxRef feature types are parsed as
2654 database references and protein_name is parsed as
2655 description line (BioSapiens terms).</li>
2656 <li>Enable or disable non-positional feature and database
2657 references in sequence ID tooltip from View menu in
2659 <!-- <li>New hidden columns and rows and representatives capabilities
2660 in annotations file (in progress - not yet fully implemented)</li> -->
2661 <li>Group-associated consensus, sequence logos and
2662 conservation plots</li>
2663 <li>Symbol distributions for each column can be exported
2664 and visualized as sequence logos</li>
2665 <li>Optionally scale multi-character column labels to fit
2666 within each column of annotation row<!-- todo for applet -->
2668 <li>Optional automatic sort of associated alignment view
2669 when a new tree is opened.</li>
2670 <li>Jalview Java Console</li>
2671 <li>Better placement of desktop window when moving
2672 between different screens.</li>
2673 <li>New preference items for sequence ID tooltip and
2674 consensus annotation</li>
2675 <li>Client to submit sequences and IDs to Envision2
2677 <li><em>Vamsas Capabilities</em>
2679 <li>Improved VAMSAS synchronization (Jalview archive
2680 used to preserve views, structures, and tree display
2682 <li>Import of vamsas documents from disk or URL via
2684 <li>Sharing of selected regions between views and
2685 with other VAMSAS applications (Experimental feature!)</li>
2686 <li>Updated API to VAMSAS version 0.2</li>
2688 </ul> <em>Applet</em>
2690 <li>Middle button resizes annotation row height</li>
2693 <li>sortByTree (true/false) - automatically sort the
2694 associated alignment view by the tree when a new tree is
2696 <li>showTreeBootstraps (true/false) - show or hide
2697 branch bootstraps (default is to show them if available)</li>
2698 <li>showTreeDistances (true/false) - show or hide
2699 branch lengths (default is to show them if available)</li>
2700 <li>showUnlinkedTreeNodes (true/false) - indicate if
2701 unassociated nodes should be highlighted in the tree
2703 <li>heightScale and widthScale (1.0 or more) -
2704 increase the height or width of a cell in the alignment
2705 grid relative to the current font size.</li>
2708 <li>Non-positional features displayed in sequence ID
2710 </ul> <em>Other</em>
2712 <li>Features format: graduated colour definitions and
2713 specification of feature scores</li>
2714 <li>Alignment Annotations format: new keywords for group
2715 associated annotation (GROUP_REF) and annotation row display
2716 properties (ROW_PROPERTIES)</li>
2717 <li>XML formats extended to support graduated feature
2718 colourschemes, group associated annotation, and profile
2719 visualization settings.</li></td>
2722 <li>Source field in GFF files parsed as feature source
2723 rather than description</li>
2724 <li>Non-positional features are now included in sequence
2725 feature and gff files (controlled via non-positional feature
2726 visibility in tooltip).</li>
2727 <li>URL links generated for all feature links (bugfix)</li>
2728 <li>Added URL embedding instructions to features file
2730 <li>Codons containing ambiguous nucleotides translated as
2731 'X' in peptide product</li>
2732 <li>Match case switch in find dialog box works for both
2733 sequence ID and sequence string and query strings do not
2734 have to be in upper case to match case-insensitively.</li>
2735 <li>AMSA files only contain first column of
2736 multi-character column annotation labels</li>
2737 <li>Jalview Annotation File generation/parsing consistent
2738 with documentation (e.g. Stockholm annotation can be
2739 exported and re-imported)</li>
2740 <li>PDB files without embedded PDB IDs given a friendly
2742 <li>Find incrementally searches ID string matches as well
2743 as subsequence matches, and correctly reports total number
2747 <li>Better handling of exceptions during sequence
2749 <li>Dasobert generated non-positional feature URL
2750 link text excludes the start_end suffix</li>
2751 <li>DAS feature and source retrieval buttons disabled
2752 when fetch or registry operations in progress.</li>
2753 <li>PDB files retrieved from URLs are cached properly</li>
2754 <li>Sequence description lines properly shared via
2756 <li>Sequence fetcher fetches multiple records for all
2758 <li>Ensured that command line das feature retrieval
2759 completes before alignment figures are generated.</li>
2760 <li>Reduced time taken when opening file browser for
2762 <li>isAligned check prior to calculating tree, PCA or
2763 submitting an MSA to JNet now excludes hidden sequences.</li>
2764 <li>User defined group colours properly recovered
2765 from Jalview projects.</li>
2774 <div align="center">
2775 <strong>2.4.0.b2</strong><br> 28/10/2009
2780 <li>Experimental support for google analytics usage
2782 <li>Jalview privacy settings (user preferences and docs).</li>
2787 <li>Race condition in applet preventing startup in
2789 <li>Exception when feature created from selection beyond
2790 length of sequence.</li>
2791 <li>Allow synthetic PDB files to be imported gracefully</li>
2792 <li>Sequence associated annotation rows associate with
2793 all sequences with a given id</li>
2794 <li>Find function matches case-insensitively for sequence
2795 ID string searches</li>
2796 <li>Non-standard characters do not cause pairwise
2797 alignment to fail with exception</li>
2798 </ul> <em>Application Issues</em>
2800 <li>Sequences are now validated against EMBL database</li>
2801 <li>Sequence fetcher fetches multiple records for all
2803 </ul> <em>InstallAnywhere Issues</em>
2805 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2806 issue with installAnywhere mechanism)</li>
2807 <li>Command line launching of JARs from InstallAnywhere
2808 version (java class versioning error fixed)</li>
2815 <div align="center">
2816 <strong>2.4</strong><br> 27/8/2008
2819 <td><em>User Interface</em>
2821 <li>Linked highlighting of codon and amino acid from
2822 translation and protein products</li>
2823 <li>Linked highlighting of structure associated with
2824 residue mapping to codon position</li>
2825 <li>Sequence Fetcher provides example accession numbers
2826 and 'clear' button</li>
2827 <li>MemoryMonitor added as an option under Desktop's
2829 <li>Extract score function to parse whitespace separated
2830 numeric data in description line</li>
2831 <li>Column labels in alignment annotation can be centred.</li>
2832 <li>Tooltip for sequence associated annotation give name
2834 </ul> <em>Web Services and URL fetching</em>
2836 <li>JPred3 web service</li>
2837 <li>Prototype sequence search client (no public services
2839 <li>Fetch either seed alignment or full alignment from
2841 <li>URL Links created for matching database cross
2842 references as well as sequence ID</li>
2843 <li>URL Links can be created using regular-expressions</li>
2844 </ul> <em>Sequence Database Connectivity</em>
2846 <li>Retrieval of cross-referenced sequences from other
2848 <li>Generalised database reference retrieval and
2849 validation to all fetchable databases</li>
2850 <li>Fetch sequences from DAS sources supporting the
2851 sequence command</li>
2852 </ul> <em>Import and Export</em>
2853 <li>export annotation rows as CSV for spreadsheet import</li>
2854 <li>Jalview projects record alignment dataset associations,
2855 EMBL products, and cDNA sequence mappings</li>
2856 <li>Sequence Group colour can be specified in Annotation
2858 <li>Ad-hoc colouring of group in Annotation File using RGB
2859 triplet as name of colourscheme</li>
2860 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2862 <li>treenode binding for VAMSAS tree exchange</li>
2863 <li>local editing and update of sequences in VAMSAS
2864 alignments (experimental)</li>
2865 <li>Create new or select existing session to join</li>
2866 <li>load and save of vamsas documents</li>
2867 </ul> <em>Application command line</em>
2869 <li>-tree parameter to open trees (introduced for passing
2871 <li>-fetchfrom command line argument to specify nicknames
2872 of DAS servers to query for alignment features</li>
2873 <li>-dasserver command line argument to add new servers
2874 that are also automatically queried for features</li>
2875 <li>-groovy command line argument executes a given groovy
2876 script after all input data has been loaded and parsed</li>
2877 </ul> <em>Applet-Application data exchange</em>
2879 <li>Trees passed as applet parameters can be passed to
2880 application (when using "View in full
2881 application")</li>
2882 </ul> <em>Applet Parameters</em>
2884 <li>feature group display control parameter</li>
2885 <li>debug parameter</li>
2886 <li>showbutton parameter</li>
2887 </ul> <em>Applet API methods</em>
2889 <li>newView public method</li>
2890 <li>Window (current view) specific get/set public methods</li>
2891 <li>Feature display control methods</li>
2892 <li>get list of currently selected sequences</li>
2893 </ul> <em>New Jalview distribution features</em>
2895 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2896 <li>RELEASE file gives build properties for the latest
2897 Jalview release.</li>
2898 <li>Java 1.1 Applet build made easier and donotobfuscate
2899 property controls execution of obfuscator</li>
2900 <li>Build target for generating source distribution</li>
2901 <li>Debug flag for javacc</li>
2902 <li>.jalview_properties file is documented (slightly) in
2903 jalview.bin.Cache</li>
2904 <li>Continuous Build Integration for stable and
2905 development version of Application, Applet and source
2910 <li>selected region output includes visible annotations
2911 (for certain formats)</li>
2912 <li>edit label/displaychar contains existing label/char
2914 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2915 <li>shorter peptide product names from EMBL records</li>
2916 <li>Newick string generator makes compact representations</li>
2917 <li>bootstrap values parsed correctly for tree files with
2919 <li>pathological filechooser bug avoided by not allowing
2920 filenames containing a ':'</li>
2921 <li>Fixed exception when parsing GFF files containing
2922 global sequence features</li>
2923 <li>Alignment datasets are finalized only when number of
2924 references from alignment sequences goes to zero</li>
2925 <li>Close of tree branch colour box without colour
2926 selection causes cascading exceptions</li>
2927 <li>occasional negative imgwidth exceptions</li>
2928 <li>better reporting of non-fatal warnings to user when
2929 file parsing fails.</li>
2930 <li>Save works when Jalview project is default format</li>
2931 <li>Save as dialog opened if current alignment format is
2932 not a valid output format</li>
2933 <li>UniProt canonical names introduced for both das and
2935 <li>Histidine should be midblue (not pink!) in Zappo</li>
2936 <li>error messages passed up and output when data read
2938 <li>edit undo recovers previous dataset sequence when
2939 sequence is edited</li>
2940 <li>allow PDB files without pdb ID HEADER lines (like
2941 those generated by MODELLER) to be read in properly</li>
2942 <li>allow reading of JPred concise files as a normal
2944 <li>Stockholm annotation parsing and alignment properties
2945 import fixed for PFAM records</li>
2946 <li>Structure view windows have correct name in Desktop
2948 <li>annotation consisting of sequence associated scores
2949 can be read and written correctly to annotation file</li>
2950 <li>Aligned cDNA translation to aligned peptide works
2952 <li>Fixed display of hidden sequence markers and
2953 non-italic font for representatives in Applet</li>
2954 <li>Applet Menus are always embedded in applet window on
2956 <li>Newly shown features appear at top of stack (in
2958 <li>Annotations added via parameter not drawn properly
2959 due to null pointer exceptions</li>
2960 <li>Secondary structure lines are drawn starting from
2961 first column of alignment</li>
2962 <li>UniProt XML import updated for new schema release in
2964 <li>Sequence feature to sequence ID match for Features
2965 file is case-insensitive</li>
2966 <li>Sequence features read from Features file appended to
2967 all sequences with matching IDs</li>
2968 <li>PDB structure coloured correctly for associated views
2969 containing a sub-sequence</li>
2970 <li>PDB files can be retrieved by applet from Jar files</li>
2971 <li>feature and annotation file applet parameters
2972 referring to different directories are retrieved correctly</li>
2973 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
2974 <li>Fixed application hang whilst waiting for
2975 splash-screen version check to complete</li>
2976 <li>Applet properly URLencodes input parameter values
2977 when passing them to the launchApp service</li>
2978 <li>display name and local features preserved in results
2979 retrieved from web service</li>
2980 <li>Visual delay indication for sequence retrieval and
2981 sequence fetcher initialisation</li>
2982 <li>updated Application to use DAS 1.53e version of
2983 dasobert DAS client</li>
2984 <li>Re-instated Full AMSA support and .amsa file
2986 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
2994 <div align="center">
2995 <strong>2.3</strong><br> 9/5/07
3000 <li>Jmol 11.0.2 integration</li>
3001 <li>PDB views stored in Jalview XML files</li>
3002 <li>Slide sequences</li>
3003 <li>Edit sequence in place</li>
3004 <li>EMBL CDS features</li>
3005 <li>DAS Feature mapping</li>
3006 <li>Feature ordering</li>
3007 <li>Alignment Properties</li>
3008 <li>Annotation Scores</li>
3009 <li>Sort by scores</li>
3010 <li>Feature/annotation editing in applet</li>
3015 <li>Headless state operation in 2.2.1</li>
3016 <li>Incorrect and unstable DNA pairwise alignment</li>
3017 <li>Cut and paste of sequences with annotation</li>
3018 <li>Feature group display state in XML</li>
3019 <li>Feature ordering in XML</li>
3020 <li>blc file iteration selection using filename # suffix</li>
3021 <li>Stockholm alignment properties</li>
3022 <li>Stockhom alignment secondary structure annotation</li>
3023 <li>2.2.1 applet had no feature transparency</li>
3024 <li>Number pad keys can be used in cursor mode</li>
3025 <li>Structure Viewer mirror image resolved</li>
3032 <div align="center">
3033 <strong>2.2.1</strong><br> 12/2/07
3038 <li>Non standard characters can be read and displayed
3039 <li>Annotations/Features can be imported/exported to the
3041 <li>Applet allows editing of sequence/annotation/group
3042 name & description
3043 <li>Preference setting to display sequence name in
3045 <li>Annotation file format extended to allow
3046 Sequence_groups to be defined
3047 <li>Default opening of alignment overview panel can be
3048 specified in preferences
3049 <li>PDB residue numbering annotation added to associated
3055 <li>Applet crash under certain Linux OS with Java 1.6
3057 <li>Annotation file export / import bugs fixed
3058 <li>PNG / EPS image output bugs fixed
3064 <div align="center">
3065 <strong>2.2</strong><br> 27/11/06
3070 <li>Multiple views on alignment
3071 <li>Sequence feature editing
3072 <li>"Reload" alignment
3073 <li>"Save" to current filename
3074 <li>Background dependent text colour
3075 <li>Right align sequence ids
3076 <li>User-defined lower case residue colours
3079 <li>Menu item accelerator keys
3080 <li>Control-V pastes to current alignment
3081 <li>Cancel button for DAS Feature Fetching
3082 <li>PCA and PDB Viewers zoom via mouse roller
3083 <li>User-defined sub-tree colours and sub-tree selection
3085 <li>'New Window' button on the 'Output to Text box'
3090 <li>New memory efficient Undo/Redo System
3091 <li>Optimised symbol lookups and conservation/consensus
3093 <li>Region Conservation/Consensus recalculated after
3095 <li>Fixed Remove Empty Columns Bug (empty columns at end
3097 <li>Slowed DAS Feature Fetching for increased robustness.
3099 <li>Made angle brackets in ASCII feature descriptions
3101 <li>Re-instated Zoom function for PCA
3102 <li>Sequence descriptions conserved in web service
3104 <li>UniProt ID discoverer uses any word separated by
3106 <li>WsDbFetch query/result association resolved
3107 <li>Tree leaf to sequence mapping improved
3108 <li>Smooth fonts switch moved to FontChooser dialog box.
3115 <div align="center">
3116 <strong>2.1.1</strong><br> 12/9/06
3121 <li>Copy consensus sequence to clipboard</li>
3126 <li>Image output - rightmost residues are rendered if
3127 sequence id panel has been resized</li>
3128 <li>Image output - all offscreen group boundaries are
3130 <li>Annotation files with sequence references - all
3131 elements in file are relative to sequence position</li>
3132 <li>Mac Applet users can use Alt key for group editing</li>
3138 <div align="center">
3139 <strong>2.1</strong><br> 22/8/06
3144 <li>MAFFT Multiple Alignment in default Web Service list</li>
3145 <li>DAS Feature fetching</li>
3146 <li>Hide sequences and columns</li>
3147 <li>Export Annotations and Features</li>
3148 <li>GFF file reading / writing</li>
3149 <li>Associate structures with sequences from local PDB
3151 <li>Add sequences to exisiting alignment</li>
3152 <li>Recently opened files / URL lists</li>
3153 <li>Applet can launch the full application</li>
3154 <li>Applet has transparency for features (Java 1.2
3156 <li>Applet has user defined colours parameter</li>
3157 <li>Applet can load sequences from parameter
3158 "sequence<em>x</em>"
3164 <li>Redundancy Panel reinstalled in the Applet</li>
3165 <li>Monospaced font - EPS / rescaling bug fixed</li>
3166 <li>Annotation files with sequence references bug fixed</li>
3172 <div align="center">
3173 <strong>2.08.1</strong><br> 2/5/06
3178 <li>Change case of selected region from Popup menu</li>
3179 <li>Choose to match case when searching</li>
3180 <li>Middle mouse button and mouse movement can compress /
3181 expand the visible width and height of the alignment</li>
3186 <li>Annotation Panel displays complete JNet results</li>
3192 <div align="center">
3193 <strong>2.08b</strong><br> 18/4/06
3199 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3200 <li>Righthand label on wrapped alignments shows correct
3207 <div align="center">
3208 <strong>2.08</strong><br> 10/4/06
3213 <li>Editing can be locked to the selection area</li>
3214 <li>Keyboard editing</li>
3215 <li>Create sequence features from searches</li>
3216 <li>Precalculated annotations can be loaded onto
3218 <li>Features file allows grouping of features</li>
3219 <li>Annotation Colouring scheme added</li>
3220 <li>Smooth fonts off by default - Faster rendering</li>
3221 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3226 <li>Drag & Drop fixed on Linux</li>
3227 <li>Jalview Archive file faster to load/save, sequence
3228 descriptions saved.</li>
3234 <div align="center">
3235 <strong>2.07</strong><br> 12/12/05
3240 <li>PDB Structure Viewer enhanced</li>
3241 <li>Sequence Feature retrieval and display enhanced</li>
3242 <li>Choose to output sequence start-end after sequence
3243 name for file output</li>
3244 <li>Sequence Fetcher WSDBFetch@EBI</li>
3245 <li>Applet can read feature files, PDB files and can be
3246 used for HTML form input</li>
3251 <li>HTML output writes groups and features</li>
3252 <li>Group editing is Control and mouse click</li>
3253 <li>File IO bugs</li>
3259 <div align="center">
3260 <strong>2.06</strong><br> 28/9/05
3265 <li>View annotations in wrapped mode</li>
3266 <li>More options for PCA viewer</li>
3271 <li>GUI bugs resolved</li>
3272 <li>Runs with -nodisplay from command line</li>
3278 <div align="center">
3279 <strong>2.05b</strong><br> 15/9/05
3284 <li>Choose EPS export as lineart or text</li>
3285 <li>Jar files are executable</li>
3286 <li>Can read in Uracil - maps to unknown residue</li>
3291 <li>Known OutOfMemory errors give warning message</li>
3292 <li>Overview window calculated more efficiently</li>
3293 <li>Several GUI bugs resolved</li>
3299 <div align="center">
3300 <strong>2.05</strong><br> 30/8/05
3305 <li>Edit and annotate in "Wrapped" view</li>
3310 <li>Several GUI bugs resolved</li>
3316 <div align="center">
3317 <strong>2.04</strong><br> 24/8/05
3322 <li>Hold down mouse wheel & scroll to change font
3328 <li>Improved JPred client reliability</li>
3329 <li>Improved loading of Jalview files</li>
3335 <div align="center">
3336 <strong>2.03</strong><br> 18/8/05
3341 <li>Set Proxy server name and port in preferences</li>
3342 <li>Multiple URL links from sequence ids</li>
3343 <li>User Defined Colours can have a scheme name and added
3345 <li>Choose to ignore gaps in consensus calculation</li>
3346 <li>Unix users can set default web browser</li>
3347 <li>Runs without GUI for batch processing</li>
3348 <li>Dynamically generated Web Service Menus</li>
3353 <li>InstallAnywhere download for Sparc Solaris</li>
3359 <div align="center">
3360 <strong>2.02</strong><br> 18/7/05
3366 <li>Copy & Paste order of sequences maintains
3367 alignment order.</li>
3373 <div align="center">
3374 <strong>2.01</strong><br> 12/7/05
3379 <li>Use delete key for deleting selection.</li>
3380 <li>Use Mouse wheel to scroll sequences.</li>
3381 <li>Help file updated to describe how to add alignment
3383 <li>Version and build date written to build properties
3385 <li>InstallAnywhere installation will check for updates
3386 at launch of Jalview.</li>
3391 <li>Delete gaps bug fixed.</li>
3392 <li>FileChooser sorts columns.</li>
3393 <li>Can remove groups one by one.</li>
3394 <li>Filechooser icons installed.</li>
3395 <li>Finder ignores return character when searching.
3396 Return key will initiate a search.<br>
3403 <div align="center">
3404 <strong>2.0</strong><br> 20/6/05
3409 <li>New codebase</li>