3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
34 /* separate the items from eachother */
41 /* doesnt get processed in javahelp */
50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>8/8/2017</em></strong>
76 <td><div align="left">
80 <!-- JAL-2379 -->Revised implementation of PCA for speed
81 and memory efficiency (~30x faster)
84 <!-- JAL-2403 -->Revised implementation of sequence
85 similarity scores as used by Tree, PCA, Shading Consensus
86 and other calculations
89 <!-- JAL-2416 -->Score matrices are stored as resource
90 files within the Jalview codebase
92 <!-- JAL-2500 -->Trees computed on Sequence Feature
93 Similarity may have different topology due to
99 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
100 model for alignments and groups
103 <!-- JAL-384 -->Custom shading schemes created via groovy
107 <!-- JAL-2491 -->linked scrolling of CDS/Protein views
108 via Overview or sequence motif search operations
111 <!-- JAL-2526 -->Efficiency improvements for interacting
112 with alignment and overview windows
115 <!-- JAL-2388 -->Hidden columns and sequences can be
119 <!-- JAL-2535 -->Posterior probability annotation from
120 Stockholm files imported as sequence associated annotation
123 <!-- JAL-2533 -->Sequence names don't include file
124 extension when importing structure files without embedded
125 names or PDB accessions
128 <!-- JAL-2547 -->Amend sequence features dialog box can be
129 opened by double clicking gaps within sequence feature
133 <!-- JAL-2631 -->Graduated feature colour style example
134 included in the example feature file
137 <!-- JAL-1933 -->Occupancy annotation row shows number of
138 ungapped positions in each column of the alignment.
144 <!-- JAL-2447 --> Experimental Features Checkbox in
145 Desktop's Tools menu to hide or show untested features in
149 <!-- JAL-1476 -->Warning in alignment status bar when
150 there are not enough columns to superimpose structures in
154 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
155 file-based command exchange
158 <!-- JAL-2316, -->URLs for viewing database
159 cross-references provided by identifiers.org and the
163 <!-- JAL-2549 -->Updated JABAWS client to v2.2
166 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
167 format sequence substitution matrices
170 <!-- JAL-2375 -->Structure chooser automatically shows Cached Structures rather than querying the PDBe if structures are already available for sequences
173 <em>Experimental features</em>
176 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
177 to transfer Chimera's structure attributes as Jalview
178 features, and vice-versa.
190 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
193 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
197 <!-- --> <em>Scripting</em>
200 <!-- JAL-2344 -->FileFormatI interface for describing
201 and identifying file formats (instead of String
212 <td><div align="left">
216 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
217 matrix - C->R should be '-3'<br />Old matrix restored
218 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
221 <!-- JAL-2397 -->Fixed Jalview's treatment of gaps in PCA
222 and substitution matrix based Tree calculations.<br />In
223 earlier versions of Jalview, gaps matching gaps were
224 penalised, and gaps matching non-gaps penalised even more.
225 In the PCA calculation, gaps were actually treated as
226 non-gaps - so different costs were applied, which meant
227 Jalview's PCAs were different to those produced by
228 SeqSpace.<br />Jalview now treats gaps in the same way as
229 SeqSpace (ie it scores them as 0). To restore pre-2.10.2
231 jalview.viewmodel.PCAModel.scoreGapAsAny=true // for
233 jalview.viewmodel.PCAModel.scoreGapAsAny=false // to
237 <!-- JAL-2346 -->Reopening Colour by annotation dialog
238 doesn't reselect a specific sequence's associated
239 annotation after it was used for colouring a view
242 <!-- JAL-2430 -->Hidden regions in alignment views are not
243 coloured in linked structure views
246 <!-- JAL-2419 -->Current selection lost if popup menu
247 opened on a region of alignment without groups
250 <!-- JAL-2374 -->Popup menu not always shown for regions
251 of an alignment with overlapping groups
254 <!-- JAL-2310 -->Finder double counts if both a sequence's
255 name and description match
258 <!-- JAL-2370 -->Hiding column selection containing two
259 hidden regions results in incorrect hidden regions
262 <!-- JAL-2377 -->PCA calculation could hang when
263 generating output report when working with highly
267 <!-- JAL-2365 -->Cannot configure feature colours with
268 lightGray or darkGray via features file
271 <!-- JAL-2421 -->Overview window visible region moves
272 erratically when hidden rows or columns are present
275 <!-- JAL-2362 -->Per-residue colourschemes applied via the
276 Structure Viewer's colour menu don't correspond to
280 <!-- JAL-2405 -->Protein specific colours only offered in
281 colour and group colour menu for protein alignments
284 <!-- JAL-2386 -->'Apply to all groups' setting when
285 changing colour does not apply Conservation slider value
289 <!-- JAL-2385 -->Colour threshold slider doesn't update to
290 reflect currently selected view or group's shading
294 <!-- JAL-2373 -->Percentage identity and conservation menu
295 items do not show a tick or allow shading to be disabled
298 <!-- JAL-2385 -->Conservation shading or PID threshold
299 lost when base colourscheme changed if slider not visible
302 <!-- JAL-2547 -->Sequence features shown in tooltip for
303 gaps before start of features
306 <!-- JAL-2576 -->Very large alignments take a long time to
310 <!-- JAL-2623 -->Graduated feature colour threshold not
311 restored to UI when feature colour is edited
314 <!-- JAL-2624 -->Feature colour thresholds not respected
315 when rendered on overview and structures when opacity at
319 <!-- JAL-2630 -->Structure and alignment overview update
320 as graduate feature colour settings are modified via the
324 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
325 a time when scrolling vertically in wrapped mode.
328 <!-- JAL-2034 -->Overview window doesn't always update
329 when a group defined on the alignment is resized
332 <!-- JAL-2605 -->Mouseovers on left/right scale region in
333 wrapped view result in positional status updates
336 <!-- JAL-2563 -->Status bar shows position for ambiguous
337 amino acid and nucleotide symbols
340 <!-- JAL-2602 -->Copy consensus sequence failed if
341 alignment included gapped columns
344 <!-- JAL-2589 -->User defined gap colour not shown in
345 overview when features overlaid on alignment
360 <strong>Documentation</strong>
363 <!-- JAL-2339 -->Release notes reformatted for readibility
364 with the built-in Java help viewer
370 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
371 case' residues (button in colourscheme editor debugged and
372 new documentation and tooltips added)
375 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
376 doesn't restore group-specific text colour thresholds
379 <!-- JAL-2243 -->Feature settings panel does not update as
380 new features are added to alignment
383 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
384 selection menu changes colours of alignment views
387 <!-- JAL-2366 -->Proxy server address and port always
388 appear enabled in Preferences->Connections
391 <!-- JAL-2426 -->Spurious exceptions in console raised
392 from alignment calculation workers after alignment has
396 <!-- JAL-1608 -->Typo in selection popup menu - Create
397 groups now 'Create Group'
400 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
401 Create/Undefine group doesn't always work
404 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
405 shown again after pressing 'Cancel'
408 <!-- JAL-2461 -->DAS registry not found exceptions
409 removed from console output
412 <!-- JAL-2383 -->Above PID colour threshold not recovered
413 when alignment view imported from project
416 <!-- JAL-2465 -->No mappings generated between structure
417 and sequences extracted from structure files imported via
421 <!-- JAL-2520 -->Structures loaded via URL are saved in
422 Jalview Projects rather than fetched via URL again when
423 the project is loaded and the structure viewed
426 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
427 adjusts start position in wrap mode
430 <!-- JAL-2563 -->Status bar doesn't show positions for
431 ambiguous amino acids
434 <!-- JAL-2291 -->Hide insertions in PopUp menu excludes
435 gaps in selection, current sequence and only within
439 <!-- JAL-2582 -->Cannot retrieve protein products from
440 Ensembl by Peptide ID
443 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
444 CDS/Protein view after CDS sequences added for aligned
448 <!-- JAL-2431 -->cDNA Consensus not shown
459 <!-- JAL-2468 -->Switching between Nucleotide and Protein
460 score models doesn't always result in an updated PCA plot
463 <!-- JAL-2442 -->Features not rendered as transparent on
464 overview or linked structure view
467 <!-- JAL-2372 -->Colour group by conservation doesn't
471 <!-- JAL-2517 -->Hitting Cancel after applying
472 user-defined colourscheme doesn't restore original
476 <em>New Known Issues</em>
479 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
480 phase after a sequence motif find operation
483 <!-- JAL-2550 -->Importing annotation file with rows
484 containing just upper and lower case letters are
485 interpreted as WUSS rna secondary structure symbols
488 <!-- JAL-2590 -->Cannot load Newick trees from eggnog
495 <!-- JAL-2314 -->Unit test failure:
496 jalview.ws.jabaws.RNAStructExportImport setup fails
504 <td width="60" nowrap>
506 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
509 <td><div align="left">
513 <!-- JAL-98 -->Improved memory usage: sparse arrays used
514 for all consensus calculations
517 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
520 <li>Updated Jalview's Certum code signing certificate
526 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
527 set of database cross-references, sorted alphabetically
530 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
531 from database cross references. Users with custom links
532 will receive a <a href="webServices/urllinks.html#warning">warning
533 dialog</a> asking them to update their preferences.
536 <!-- JAL-2287-->Cancel button and escape listener on
537 dialog warning user about disconnecting Jalview from a
541 <!-- JAL-2320-->Jalview's Chimera control window closes if
542 the Chimera it is connected to is shut down
545 <!-- JAL-1738-->New keystroke (B) and Select highlighted
546 columns menu item to mark columns containing highlighted
547 regions (e.g. from structure selections or results of a
551 <!-- JAL-2284-->Command line option for batch-generation
552 of HTML pages rendering alignment data with the BioJS
562 <!-- JAL-2286 -->Columns with more than one modal residue
563 are not coloured or thresholded according to percent
564 identity (first observed in Jalview 2.8.2)
567 <!-- JAL-2301 -->Threonine incorrectly reported as not
571 <!-- JAL-2318 -->Updates to documentation pages (above PID
572 threshold, amino acid properties)
575 <!-- JAL-2292 -->Lower case residues in sequences are not
576 reported as mapped to residues in a structure file in the
580 <!--JAL-2324 -->Identical features with non-numeric scores
581 could be added multiple times to a sequence
584 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
585 bond features shown as two highlighted residues rather
586 than a range in linked structure views, and treated
587 correctly when selecting and computing trees from features
590 <!-- JAL-2281-->Custom URL links for database
591 cross-references are matched to database name regardless
599 <!-- JAL-2282-->Custom URL links for specific database
600 names without regular expressions also offer links from
604 <!-- JAL-2315-->Removing a single configured link in the
605 URL links pane in Connections preferences doesn't actually
606 update Jalview configuration
609 <!-- JAL-2272-->CTRL-Click on a selected region to open
610 the alignment area popup menu doesn't work on El-Capitan
613 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
614 files with similarly named sequences if dropped onto the
618 <!-- JAL-2312 -->Additional mappings are shown for PDB
619 entries where more chains exist in the PDB accession than
620 are reported in the SIFTS file
623 <!-- JAL-2317-->Certain structures do not get mapped to
624 the structure view when displayed with Chimera
627 <!-- JAL-2317-->No chains shown in the Chimera view
628 panel's View->Show Chains submenu
631 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
632 work for wrapped alignment views
635 <!--JAL-2197 -->Rename UI components for running JPred
636 predictions from 'JNet' to 'JPred'
639 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
640 corrupted when annotation panel vertical scroll is not at
644 <!--JAL-2332 -->Attempting to view structure for Hen
645 lysozyme results in a PDB Client error dialog box
648 <!-- JAL-2319 -->Structure View's mapping report switched
649 ranges for PDB and sequence for SIFTS
652 SIFTS 'Not_Observed' residues mapped to non-existant
656 <!-- <em>New Known Issues</em>
663 <td width="60" nowrap>
665 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
666 <em>25/10/2016</em></strong>
669 <td><em>Application</em>
671 <li>3D Structure chooser opens with 'Cached structures'
672 view if structures already loaded</li>
673 <li>Progress bar reports models as they are loaded to
680 <li>Colour by conservation always enabled and no tick
681 shown in menu when BLOSUM or PID shading applied</li>
682 <li>FER1_ARATH and FER2_ARATH labels were switched in
683 example sequences/projects/trees</li>
687 <li>Jalview projects with views of local PDB structure
688 files saved on Windows cannot be opened on OSX</li>
689 <li>Multiple structure views can be opened and superposed
690 without timeout for structures with multiple models or
691 multiple sequences in alignment</li>
692 <li>Cannot import or associated local PDB files without a
693 PDB ID HEADER line</li>
694 <li>RMSD is not output in Jmol console when superposition
696 <li>Drag and drop of URL from Browser fails for Linux and
697 OSX versions earlier than El Capitan</li>
698 <li>ENA client ignores invalid content from ENA server</li>
699 <li>Exceptions are not raised in console when ENA client
700 attempts to fetch non-existent IDs via Fetch DB Refs UI
702 <li>Exceptions are not raised in console when a new view
703 is created on the alignment</li>
704 <li>OSX right-click fixed for group selections: CMD-click
705 to insert/remove gaps in groups and CTRL-click to open group
708 <em>Build and deployment</em>
710 <li>URL link checker now copes with multi-line anchor
713 <em>New Known Issues</em>
715 <li>Drag and drop from URL links in browsers do not work
722 <td width="60" nowrap>
724 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
730 <!-- JAL-2124 -->Updated Spanish translations.
733 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
734 for importing structure data to Jalview. Enables mmCIF and
738 <!-- JAL-192 --->Alignment ruler shows positions relative to
742 <!-- JAL-2202 -->Position/residue shown in status bar when
743 mousing over sequence associated annotation
746 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
750 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
751 '()', canonical '[]' and invalid '{}' base pair populations
755 <!-- JAL-2092 -->Feature settings popup menu options for
756 showing or hiding columns containing a feature
759 <!-- JAL-1557 -->Edit selected group by double clicking on
760 group and sequence associated annotation labels
763 <!-- JAL-2236 -->Sequence name added to annotation label in
764 select/hide columns by annotation and colour by annotation
768 </ul> <em>Application</em>
771 <!-- JAL-2050-->Automatically hide introns when opening a
775 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
779 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
780 structure mappings with the EMBL-EBI PDBe SIFTS database
783 <!-- JAL-2079 -->Updated download sites used for Rfam and
784 Pfam sources to xfam.org
787 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
790 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
791 over sequences in Jalview
794 <!-- JAL-2027-->Support for reverse-complement coding
795 regions in ENA and EMBL
798 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
799 for record retrieval via ENA rest API
802 <!-- JAL-2027 -->Support for ENA CDS records with reverse
806 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
807 groovy script execution
810 <!-- JAL-1812 -->New 'execute Groovy script' option in an
811 alignment window's Calculate menu
814 <!-- JAL-1812 -->Allow groovy scripts that call
815 Jalview.getAlignFrames() to run in headless mode
818 <!-- JAL-2068 -->Support for creating new alignment
819 calculation workers from groovy scripts
822 <!-- JAL-1369 --->Store/restore reference sequence in
826 <!-- JAL-1803 -->Chain codes for a sequence's PDB
827 associations are now saved/restored from project
830 <!-- JAL-1993 -->Database selection dialog always shown
831 before sequence fetcher is opened
834 <!-- JAL-2183 -->Double click on an entry in Jalview's
835 database chooser opens a sequence fetcher
838 <!-- JAL-1563 -->Free-text search client for UniProt using
842 <!-- JAL-2168 -->-nonews command line parameter to prevent
843 the news reader opening
846 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
847 querying stored in preferences
850 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
854 <!-- JAL-1977-->Tooltips shown on database chooser
857 <!-- JAL-391 -->Reverse complement function in calculate
858 menu for nucleotide sequences
861 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
862 and feature counts preserves alignment ordering (and
863 debugged for complex feature sets).
866 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
867 viewing structures with Jalview 2.10
870 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
871 genome, transcript CCDS and gene ids via the Ensembl and
872 Ensembl Genomes REST API
875 <!-- JAL-2049 -->Protein sequence variant annotation
876 computed for 'sequence_variant' annotation on CDS regions
880 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
884 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
885 Ref Fetcher fails to match, or otherwise updates sequence
886 data from external database records.
889 <!-- JAL-2154 -->Revised Jalview Project format for
890 efficient recovery of sequence coding and alignment
891 annotation relationships.
893 </ul> <!-- <em>Applet</em>
904 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
908 <!-- JAL-2018-->Export features in Jalview format (again)
909 includes graduated colourschemes
912 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
913 working with big alignments and lots of hidden columns
916 <!-- JAL-2053-->Hidden column markers not always rendered
917 at right of alignment window
920 <!-- JAL-2067 -->Tidied up links in help file table of
924 <!-- JAL-2072 -->Feature based tree calculation not shown
928 <!-- JAL-2075 -->Hidden columns ignored during feature
929 based tree calculation
932 <!-- JAL-2065 -->Alignment view stops updating when show
933 unconserved enabled for group on alignment
936 <!-- JAL-2086 -->Cannot insert gaps into sequence when
940 <!-- JAL-2146 -->Alignment column in status incorrectly
941 shown as "Sequence position" when mousing over
945 <!-- JAL-2099 -->Incorrect column numbers in ruler when
946 hidden columns present
949 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
950 user created annotation added to alignment
953 <!-- JAL-1841 -->RNA Structure consensus only computed for
954 '()' base pair annotation
957 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
958 in zero scores for all base pairs in RNA Structure
962 <!-- JAL-2174-->Extend selection with columns containing
966 <!-- JAL-2275 -->Pfam format writer puts extra space at
967 beginning of sequence
970 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
974 <!-- JAL-2238 -->Cannot create groups on an alignment from
975 from a tree when t-coffee scores are shown
978 <!-- JAL-1836,1967 -->Cannot import and view PDB
979 structures with chains containing negative resnums (4q4h)
982 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
986 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
987 to Clustal, PIR and PileUp output
990 <!-- JAL-2008 -->Reordering sequence features that are
991 not visible causes alignment window to repaint
994 <!-- JAL-2006 -->Threshold sliders don't work in
995 graduated colour and colour by annotation row for e-value
996 scores associated with features and annotation rows
999 <!-- JAL-1797 -->amino acid physicochemical conservation
1000 calculation should be case independent
1003 <!-- JAL-2173 -->Remove annotation also updates hidden
1007 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1008 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1009 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1012 <!-- JAL-2065 -->Null pointer exceptions and redraw
1013 problems when reference sequence defined and 'show
1014 non-conserved' enabled
1017 <!-- JAL-1306 -->Quality and Conservation are now shown on
1018 load even when Consensus calculation is disabled
1021 <!-- JAL-1932 -->Remove right on penultimate column of
1022 alignment does nothing
1025 <em>Application</em>
1028 <!-- JAL-1552-->URLs and links can't be imported by
1029 drag'n'drop on OSX when launched via webstart (note - not
1030 yet fixed for El Capitan)
1033 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1034 output when running on non-gb/us i18n platforms
1037 <!-- JAL-1944 -->Error thrown when exporting a view with
1038 hidden sequences as flat-file alignment
1041 <!-- JAL-2030-->InstallAnywhere distribution fails when
1045 <!-- JAL-2080-->Jalview very slow to launch via webstart
1046 (also hotfix for 2.9.0b2)
1049 <!-- JAL-2085 -->Cannot save project when view has a
1050 reference sequence defined
1053 <!-- JAL-1011 -->Columns are suddenly selected in other
1054 alignments and views when revealing hidden columns
1057 <!-- JAL-1989 -->Hide columns not mirrored in complement
1058 view in a cDNA/Protein splitframe
1061 <!-- JAL-1369 -->Cannot save/restore representative
1062 sequence from project when only one sequence is
1066 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1067 in Structure Chooser
1070 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1071 structure consensus didn't refresh annotation panel
1074 <!-- JAL-1962 -->View mapping in structure view shows
1075 mappings between sequence and all chains in a PDB file
1078 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1079 dialogs format columns correctly, don't display array
1080 data, sort columns according to type
1083 <!-- JAL-1975 -->Export complete shown after destination
1084 file chooser is cancelled during an image export
1087 <!-- JAL-2025 -->Error when querying PDB Service with
1088 sequence name containing special characters
1091 <!-- JAL-2024 -->Manual PDB structure querying should be
1095 <!-- JAL-2104 -->Large tooltips with broken HTML
1096 formatting don't wrap
1099 <!-- JAL-1128 -->Figures exported from wrapped view are
1100 truncated so L looks like I in consensus annotation
1103 <!-- JAL-2003 -->Export features should only export the
1104 currently displayed features for the current selection or
1108 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1109 after fetching cross-references, and restoring from
1113 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1114 followed in the structure viewer
1117 <!-- JAL-2163 -->Titles for individual alignments in
1118 splitframe not restored from project
1121 <!-- JAL-2145 -->missing autocalculated annotation at
1122 trailing end of protein alignment in transcript/product
1123 splitview when pad-gaps not enabled by default
1126 <!-- JAL-1797 -->amino acid physicochemical conservation
1130 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1131 article has been read (reopened issue due to
1132 internationalisation problems)
1135 <!-- JAL-1960 -->Only offer PDB structures in structure
1136 viewer based on sequence name, PDB and UniProt
1141 <!-- JAL-1976 -->No progress bar shown during export of
1145 <!-- JAL-2213 -->Structures not always superimposed after
1146 multiple structures are shown for one or more sequences.
1149 <!-- JAL-1370 -->Reference sequence characters should not
1150 be replaced with '.' when 'Show unconserved' format option
1154 <!-- JAL-1823 -->Cannot specify chain code when entering
1155 specific PDB id for sequence
1158 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1159 'Export hidden sequences' is enabled, but 'export hidden
1160 columns' is disabled.
1163 <!--JAL-2026-->Best Quality option in structure chooser
1164 selects lowest rather than highest resolution structures
1168 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1169 to sequence mapping in 'View Mappings' report
1172 <!-- JAL-2284 -->Unable to read old Jalview projects that
1173 contain non-XML data added after Jalvew wrote project.
1176 <!-- JAL-2118 -->Newly created annotation row reorders
1177 after clicking on it to create new annotation for a
1180 <!-- may exclude, this is an external service stability issue JAL-1941
1181 -- > RNA 3D structure not added via DSSR service</li> -->
1186 <!-- JAL-2151 -->Incorrect columns are selected when
1187 hidden columns present before start of sequence
1190 <!-- JAL-1986 -->Missing dependencies on applet pages
1194 <!-- JAL-1947 -->Overview pixel size changes when
1195 sequences are hidden in applet
1198 <!-- JAL-1996 -->Updated instructions for applet
1199 deployment on examples pages.
1206 <td width="60" nowrap>
1207 <div align="center">
1208 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1209 <em>16/10/2015</em></strong>
1212 <td><em>General</em>
1214 <li>Time stamps for signed Jalview application and applet
1219 <em>Application</em>
1221 <li>Duplicate group consensus and conservation rows
1222 shown when tree is partitioned</li>
1223 <li>Erratic behaviour when tree partitions made with
1224 multiple cDNA/Protein split views</li>
1230 <td width="60" nowrap>
1231 <div align="center">
1232 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1233 <em>8/10/2015</em></strong>
1236 <td><em>General</em>
1238 <li>Updated Spanish translations of localized text for
1240 </ul> <em>Application</em>
1242 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1243 <li>Signed OSX InstallAnywhere installer<br></li>
1244 <li>Support for per-sequence based annotations in BioJSON</li>
1245 </ul> <em>Applet</em>
1247 <li>Split frame example added to applet examples page</li>
1248 </ul> <em>Build and Deployment</em>
1251 <!-- JAL-1888 -->New ant target for running Jalview's test
1259 <li>Mapping of cDNA to protein in split frames
1260 incorrect when sequence start > 1</li>
1261 <li>Broken images in filter column by annotation dialog
1263 <li>Feature colours not parsed from features file</li>
1264 <li>Exceptions and incomplete link URLs recovered when
1265 loading a features file containing HTML tags in feature
1269 <em>Application</em>
1271 <li>Annotations corrupted after BioJS export and
1273 <li>Incorrect sequence limits after Fetch DB References
1274 with 'trim retrieved sequences'</li>
1275 <li>Incorrect warning about deleting all data when
1276 deleting selected columns</li>
1277 <li>Patch to build system for shipping properly signed
1278 JNLP templates for webstart launch</li>
1279 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1280 unreleased structures for download or viewing</li>
1281 <li>Tab/space/return keystroke operation of EMBL-PDBe
1282 fetcher/viewer dialogs works correctly</li>
1283 <li>Disabled 'minimise' button on Jalview windows
1284 running on OSX to workaround redraw hang bug</li>
1285 <li>Split cDNA/Protein view position and geometry not
1286 recovered from jalview project</li>
1287 <li>Initial enabled/disabled state of annotation menu
1288 sorter 'show autocalculated first/last' corresponds to
1290 <li>Restoring of Clustal, RNA Helices and T-Coffee
1291 color schemes from BioJSON</li>
1295 <li>Reorder sequences mirrored in cDNA/Protein split
1297 <li>Applet with Jmol examples not loading correctly</li>
1303 <td><div align="center">
1304 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1306 <td><em>General</em>
1308 <li>Linked visualisation and analysis of DNA and Protein
1311 <li>Translated cDNA alignments shown as split protein
1312 and DNA alignment views</li>
1313 <li>Codon consensus annotation for linked protein and
1314 cDNA alignment views</li>
1315 <li>Link cDNA or Protein product sequences by loading
1316 them onto Protein or cDNA alignments</li>
1317 <li>Reconstruct linked cDNA alignment from aligned
1318 protein sequences</li>
1321 <li>Jmol integration updated to Jmol v14.2.14</li>
1322 <li>Import and export of Jalview alignment views as <a
1323 href="features/bioJsonFormat.html">BioJSON</a></li>
1324 <li>New alignment annotation file statements for
1325 reference sequences and marking hidden columns</li>
1326 <li>Reference sequence based alignment shading to
1327 highlight variation</li>
1328 <li>Select or hide columns according to alignment
1330 <li>Find option for locating sequences by description</li>
1331 <li>Conserved physicochemical properties shown in amino
1332 acid conservation row</li>
1333 <li>Alignments can be sorted by number of RNA helices</li>
1334 </ul> <em>Application</em>
1336 <li>New cDNA/Protein analysis capabilities
1338 <li>Get Cross-References should open a Split Frame
1339 view with cDNA/Protein</li>
1340 <li>Detect when nucleotide sequences and protein
1341 sequences are placed in the same alignment</li>
1342 <li>Split cDNA/Protein views are saved in Jalview
1347 <li>Use REST API to talk to Chimera</li>
1348 <li>Selected regions in Chimera are highlighted in linked
1349 Jalview windows</li>
1351 <li>VARNA RNA viewer updated to v3.93</li>
1352 <li>VARNA views are saved in Jalview Projects</li>
1353 <li>Pseudoknots displayed as Jalview RNA annotation can
1354 be shown in VARNA</li>
1356 <li>Make groups for selection uses marked columns as well
1357 as the active selected region</li>
1359 <li>Calculate UPGMA and NJ trees using sequence feature
1361 <li>New Export options
1363 <li>New Export Settings dialog to control hidden
1364 region export in flat file generation</li>
1366 <li>Export alignment views for display with the <a
1367 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1369 <li>Export scrollable SVG in HTML page</li>
1370 <li>Optional embedding of BioJSON data when exporting
1371 alignment figures to HTML</li>
1373 <li>3D structure retrieval and display
1375 <li>Free text and structured queries with the PDBe
1377 <li>PDBe Search API based discovery and selection of
1378 PDB structures for a sequence set</li>
1382 <li>JPred4 employed for protein secondary structure
1384 <li>Hide Insertions menu option to hide unaligned columns
1385 for one or a group of sequences</li>
1386 <li>Automatically hide insertions in alignments imported
1387 from the JPred4 web server</li>
1388 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1389 system on OSX<br />LGPL libraries courtesy of <a
1390 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1392 <li>changed 'View nucleotide structure' submenu to 'View
1393 VARNA 2D Structure'</li>
1394 <li>change "View protein structure" menu option to "3D
1397 </ul> <em>Applet</em>
1399 <li>New layout for applet example pages</li>
1400 <li>New parameters to enable SplitFrame view
1401 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1402 <li>New example demonstrating linked viewing of cDNA and
1403 Protein alignments</li>
1404 </ul> <em>Development and deployment</em>
1406 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1407 <li>Include installation type and git revision in build
1408 properties and console log output</li>
1409 <li>Jalview Github organisation, and new github site for
1410 storing BioJsMSA Templates</li>
1411 <li>Jalview's unit tests now managed with TestNG</li>
1414 <!-- <em>General</em>
1416 </ul> --> <!-- issues resolved --> <em>Application</em>
1418 <li>Escape should close any open find dialogs</li>
1419 <li>Typo in select-by-features status report</li>
1420 <li>Consensus RNA secondary secondary structure
1421 predictions are not highlighted in amber</li>
1422 <li>Missing gap character in v2.7 example file means
1423 alignment appears unaligned when pad-gaps is not enabled</li>
1424 <li>First switch to RNA Helices colouring doesn't colour
1425 associated structure views</li>
1426 <li>ID width preference option is greyed out when auto
1427 width checkbox not enabled</li>
1428 <li>Stopped a warning dialog from being shown when
1429 creating user defined colours</li>
1430 <li>'View Mapping' in structure viewer shows sequence
1431 mappings for just that viewer's sequences</li>
1432 <li>Workaround for superposing PDB files containing
1433 multiple models in Chimera</li>
1434 <li>Report sequence position in status bar when hovering
1435 over Jmol structure</li>
1436 <li>Cannot output gaps as '.' symbols with Selection ->
1437 output to text box</li>
1438 <li>Flat file exports of alignments with hidden columns
1439 have incorrect sequence start/end</li>
1440 <li>'Aligning' a second chain to a Chimera structure from
1442 <li>Colour schemes applied to structure viewers don't
1443 work for nucleotide</li>
1444 <li>Loading/cut'n'pasting an empty or invalid file leads
1445 to a grey/invisible alignment window</li>
1446 <li>Exported Jpred annotation from a sequence region
1447 imports to different position</li>
1448 <li>Space at beginning of sequence feature tooltips shown
1449 on some platforms</li>
1450 <li>Chimera viewer 'View | Show Chain' menu is not
1452 <li>'New View' fails with a Null Pointer Exception in
1453 console if Chimera has been opened</li>
1454 <li>Mouseover to Chimera not working</li>
1455 <li>Miscellaneous ENA XML feature qualifiers not
1457 <li>NPE in annotation renderer after 'Extract Scores'</li>
1458 <li>If two structures in one Chimera window, mouseover of
1459 either sequence shows on first structure</li>
1460 <li>'Show annotations' options should not make
1461 non-positional annotations visible</li>
1462 <li>Subsequence secondary structure annotation not shown
1463 in right place after 'view flanking regions'</li>
1464 <li>File Save As type unset when current file format is
1466 <li>Save as '.jar' option removed for saving Jalview
1468 <li>Colour by Sequence colouring in Chimera more
1470 <li>Cannot 'add reference annotation' for a sequence in
1471 several views on same alignment</li>
1472 <li>Cannot show linked products for EMBL / ENA records</li>
1473 <li>Jalview's tooltip wraps long texts containing no
1475 </ul> <em>Applet</em>
1477 <li>Jmol to JalviewLite mouseover/link not working</li>
1478 <li>JalviewLite can't import sequences with ID
1479 descriptions containing angle brackets</li>
1480 </ul> <em>General</em>
1482 <li>Cannot export and reimport RNA secondary structure
1483 via jalview annotation file</li>
1484 <li>Random helix colour palette for colour by annotation
1485 with RNA secondary structure</li>
1486 <li>Mouseover to cDNA from STOP residue in protein
1487 translation doesn't work.</li>
1488 <li>hints when using the select by annotation dialog box</li>
1489 <li>Jmol alignment incorrect if PDB file has alternate CA
1491 <li>FontChooser message dialog appears to hang after
1492 choosing 1pt font</li>
1493 <li>Peptide secondary structure incorrectly imported from
1494 annotation file when annotation display text includes 'e' or
1496 <li>Cannot set colour of new feature type whilst creating
1498 <li>cDNA translation alignment should not be sequence
1499 order dependent</li>
1500 <li>'Show unconserved' doesn't work for lower case
1502 <li>Nucleotide ambiguity codes involving R not recognised</li>
1503 </ul> <em>Deployment and Documentation</em>
1505 <li>Applet example pages appear different to the rest of
1506 www.jalview.org</li>
1507 </ul> <em>Application Known issues</em>
1509 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1510 <li>Misleading message appears after trying to delete
1512 <li>Jalview icon not shown in dock after InstallAnywhere
1513 version launches</li>
1514 <li>Fetching EMBL reference for an RNA sequence results
1515 fails with a sequence mismatch</li>
1516 <li>Corrupted or unreadable alignment display when
1517 scrolling alignment to right</li>
1518 <li>ArrayIndexOutOfBoundsException thrown when remove
1519 empty columns called on alignment with ragged gapped ends</li>
1520 <li>auto calculated alignment annotation rows do not get
1521 placed above or below non-autocalculated rows</li>
1522 <li>Jalview dekstop becomes sluggish at full screen in
1523 ultra-high resolution</li>
1524 <li>Cannot disable consensus calculation independently of
1525 quality and conservation</li>
1526 <li>Mouseover highlighting between cDNA and protein can
1527 become sluggish with more than one splitframe shown</li>
1528 </ul> <em>Applet Known Issues</em>
1530 <li>Core PDB parsing code requires Jmol</li>
1531 <li>Sequence canvas panel goes white when alignment
1532 window is being resized</li>
1538 <td><div align="center">
1539 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1541 <td><em>General</em>
1543 <li>Updated Java code signing certificate donated by
1545 <li>Features and annotation preserved when performing
1546 pairwise alignment</li>
1547 <li>RNA pseudoknot annotation can be
1548 imported/exported/displayed</li>
1549 <li>'colour by annotation' can colour by RNA and
1550 protein secondary structure</li>
1551 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1552 post-hoc with 2.9 release</em>)
1555 </ul> <em>Application</em>
1557 <li>Extract and display secondary structure for sequences
1558 with 3D structures</li>
1559 <li>Support for parsing RNAML</li>
1560 <li>Annotations menu for layout
1562 <li>sort sequence annotation rows by alignment</li>
1563 <li>place sequence annotation above/below alignment
1566 <li>Output in Stockholm format</li>
1567 <li>Internationalisation: improved Spanish (es)
1569 <li>Structure viewer preferences tab</li>
1570 <li>Disorder and Secondary Structure annotation tracks
1571 shared between alignments</li>
1572 <li>UCSF Chimera launch and linked highlighting from
1574 <li>Show/hide all sequence associated annotation rows for
1575 all or current selection</li>
1576 <li>disorder and secondary structure predictions
1577 available as dataset annotation</li>
1578 <li>Per-sequence rna helices colouring</li>
1581 <li>Sequence database accessions imported when fetching
1582 alignments from Rfam</li>
1583 <li>update VARNA version to 3.91</li>
1585 <li>New groovy scripts for exporting aligned positions,
1586 conservation values, and calculating sum of pairs scores.</li>
1587 <li>Command line argument to set default JABAWS server</li>
1588 <li>include installation type in build properties and
1589 console log output</li>
1590 <li>Updated Jalview project format to preserve dataset
1594 <!-- issues resolved --> <em>Application</em>
1596 <li>Distinguish alignment and sequence associated RNA
1597 structure in structure->view->VARNA</li>
1598 <li>Raise dialog box if user deletes all sequences in an
1600 <li>Pressing F1 results in documentation opening twice</li>
1601 <li>Sequence feature tooltip is wrapped</li>
1602 <li>Double click on sequence associated annotation
1603 selects only first column</li>
1604 <li>Redundancy removal doesn't result in unlinked
1605 leaves shown in tree</li>
1606 <li>Undos after several redundancy removals don't undo
1608 <li>Hide sequence doesn't hide associated annotation</li>
1609 <li>User defined colours dialog box too big to fit on
1610 screen and buttons not visible</li>
1611 <li>author list isn't updated if already written to
1612 Jalview properties</li>
1613 <li>Popup menu won't open after retrieving sequence
1615 <li>File open window for associate PDB doesn't open</li>
1616 <li>Left-then-right click on a sequence id opens a
1617 browser search window</li>
1618 <li>Cannot open sequence feature shading/sort popup menu
1619 in feature settings dialog</li>
1620 <li>better tooltip placement for some areas of Jalview
1622 <li>Allow addition of JABAWS Server which doesn't
1623 pass validation</li>
1624 <li>Web services parameters dialog box is too large to
1626 <li>Muscle nucleotide alignment preset obscured by
1628 <li>JABAWS preset submenus don't contain newly
1629 defined user preset</li>
1630 <li>MSA web services warns user if they were launched
1631 with invalid input</li>
1632 <li>Jalview cannot contact DAS Registy when running on
1635 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1636 'Superpose with' submenu not shown when new view
1640 </ul> <!-- <em>Applet</em>
1642 </ul> <em>General</em>
1644 </ul>--> <em>Deployment and Documentation</em>
1646 <li>2G and 1G options in launchApp have no effect on
1647 memory allocation</li>
1648 <li>launchApp service doesn't automatically open
1649 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1651 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1652 InstallAnywhere reports cannot find valid JVM when Java
1653 1.7_055 is available
1655 </ul> <em>Application Known issues</em>
1658 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1659 corrupted or unreadable alignment display when scrolling
1663 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1664 retrieval fails but progress bar continues for DAS retrieval
1665 with large number of ID
1668 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1669 flatfile output of visible region has incorrect sequence
1673 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1674 rna structure consensus doesn't update when secondary
1675 structure tracks are rearranged
1678 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1679 invalid rna structure positional highlighting does not
1680 highlight position of invalid base pairs
1683 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1684 out of memory errors are not raised when saving Jalview
1685 project from alignment window file menu
1688 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1689 Switching to RNA Helices colouring doesn't propagate to
1693 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1694 colour by RNA Helices not enabled when user created
1695 annotation added to alignment
1698 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1699 Jalview icon not shown on dock in Mountain Lion/Webstart
1701 </ul> <em>Applet Known Issues</em>
1704 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1705 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1708 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1709 Jalview and Jmol example not compatible with IE9
1712 <li>Sort by annotation score doesn't reverse order
1718 <td><div align="center">
1719 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1722 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1725 <li>Internationalisation of user interface (usually
1726 called i18n support) and translation for Spanish locale</li>
1727 <li>Define/Undefine group on current selection with
1728 Ctrl-G/Shift Ctrl-G</li>
1729 <li>Improved group creation/removal options in
1730 alignment/sequence Popup menu</li>
1731 <li>Sensible precision for symbol distribution
1732 percentages shown in logo tooltip.</li>
1733 <li>Annotation panel height set according to amount of
1734 annotation when alignment first opened</li>
1735 </ul> <em>Application</em>
1737 <li>Interactive consensus RNA secondary structure
1738 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1739 <li>Select columns containing particular features from
1740 Feature Settings dialog</li>
1741 <li>View all 'representative' PDB structures for selected
1743 <li>Update Jalview project format:
1745 <li>New file extension for Jalview projects '.jvp'</li>
1746 <li>Preserve sequence and annotation dataset (to
1747 store secondary structure annotation,etc)</li>
1748 <li>Per group and alignment annotation and RNA helix
1752 <li>New similarity measures for PCA and Tree calculation
1754 <li>Experimental support for retrieval and viewing of
1755 flanking regions for an alignment</li>
1759 <!-- issues resolved --> <em>Application</em>
1761 <li>logo keeps spinning and status remains at queued or
1762 running after job is cancelled</li>
1763 <li>cannot export features from alignments imported from
1764 Jalview/VAMSAS projects</li>
1765 <li>Buggy slider for web service parameters that take
1767 <li>Newly created RNA secondary structure line doesn't
1768 have 'display all symbols' flag set</li>
1769 <li>T-COFFEE alignment score shading scheme and other
1770 annotation shading not saved in Jalview project</li>
1771 <li>Local file cannot be loaded in freshly downloaded
1773 <li>Jalview icon not shown on dock in Mountain
1775 <li>Load file from desktop file browser fails</li>
1776 <li>Occasional NPE thrown when calculating large trees</li>
1777 <li>Cannot reorder or slide sequences after dragging an
1778 alignment onto desktop</li>
1779 <li>Colour by annotation dialog throws NPE after using
1780 'extract scores' function</li>
1781 <li>Loading/cut'n'pasting an empty file leads to a grey
1782 alignment window</li>
1783 <li>Disorder thresholds rendered incorrectly after
1784 performing IUPred disorder prediction</li>
1785 <li>Multiple group annotated consensus rows shown when
1786 changing 'normalise logo' display setting</li>
1787 <li>Find shows blank dialog after 'finished searching' if
1788 nothing matches query</li>
1789 <li>Null Pointer Exceptions raised when sorting by
1790 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1792 <li>Errors in Jmol console when structures in alignment
1793 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1795 <li>Not all working JABAWS services are shown in
1797 <li>JAVAWS version of Jalview fails to launch with
1798 'invalid literal/length code'</li>
1799 <li>Annotation/RNA Helix colourschemes cannot be applied
1800 to alignment with groups (actually fixed in 2.8.0b1)</li>
1801 <li>RNA Helices and T-Coffee Scores available as default
1804 </ul> <em>Applet</em>
1806 <li>Remove group option is shown even when selection is
1808 <li>Apply to all groups ticked but colourscheme changes
1809 don't affect groups</li>
1810 <li>Documented RNA Helices and T-Coffee Scores as valid
1811 colourscheme name</li>
1812 <li>Annotation labels drawn on sequence IDs when
1813 Annotation panel is not displayed</li>
1814 <li>Increased font size for dropdown menus on OSX and
1815 embedded windows</li>
1816 </ul> <em>Other</em>
1818 <li>Consensus sequence for alignments/groups with a
1819 single sequence were not calculated</li>
1820 <li>annotation files that contain only groups imported as
1821 annotation and junk sequences</li>
1822 <li>Fasta files with sequences containing '*' incorrectly
1823 recognised as PFAM or BLC</li>
1824 <li>conservation/PID slider apply all groups option
1825 doesn't affect background (2.8.0b1)
1827 <li>redundancy highlighting is erratic at 0% and 100%</li>
1828 <li>Remove gapped columns fails for sequences with ragged
1830 <li>AMSA annotation row with leading spaces is not
1831 registered correctly on import</li>
1832 <li>Jalview crashes when selecting PCA analysis for
1833 certain alignments</li>
1834 <li>Opening the colour by annotation dialog for an
1835 existing annotation based 'use original colours'
1836 colourscheme loses original colours setting</li>
1841 <td><div align="center">
1842 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
1843 <em>30/1/2014</em></strong>
1847 <li>Trusted certificates for JalviewLite applet and
1848 Jalview Desktop application<br />Certificate was donated by
1849 <a href="https://www.certum.eu">Certum</a> to the Jalview
1850 open source project).
1852 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
1853 <li>Output in Stockholm format</li>
1854 <li>Allow import of data from gzipped files</li>
1855 <li>Export/import group and sequence associated line
1856 graph thresholds</li>
1857 <li>Nucleotide substitution matrix that supports RNA and
1858 ambiguity codes</li>
1859 <li>Allow disorder predictions to be made on the current
1860 selection (or visible selection) in the same way that JPred
1862 <li>Groovy scripting for headless Jalview operation</li>
1863 </ul> <em>Other improvements</em>
1865 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
1866 <li>COMBINE statement uses current SEQUENCE_REF and
1867 GROUP_REF scope to group annotation rows</li>
1868 <li>Support '' style escaping of quotes in Newick
1870 <li>Group options for JABAWS service by command line name</li>
1871 <li>Empty tooltip shown for JABA service options with a
1872 link but no description</li>
1873 <li>Select primary source when selecting authority in
1874 database fetcher GUI</li>
1875 <li>Add .mfa to FASTA file extensions recognised by
1877 <li>Annotation label tooltip text wrap</li>
1882 <li>Slow scrolling when lots of annotation rows are
1884 <li>Lots of NPE (and slowness) after creating RNA
1885 secondary structure annotation line</li>
1886 <li>Sequence database accessions not imported when
1887 fetching alignments from Rfam</li>
1888 <li>Incorrect SHMR submission for sequences with
1890 <li>View all structures does not always superpose
1892 <li>Option widgets in service parameters not updated to
1893 reflect user or preset settings</li>
1894 <li>Null pointer exceptions for some services without
1895 presets or adjustable parameters</li>
1896 <li>Discover PDB IDs entry in structure menu doesn't
1897 discover PDB xRefs</li>
1898 <li>Exception encountered while trying to retrieve
1899 features with DAS</li>
1900 <li>Lowest value in annotation row isn't coloured
1901 when colour by annotation (per sequence) is coloured</li>
1902 <li>Keyboard mode P jumps to start of gapped region when
1903 residue follows a gap</li>
1904 <li>Jalview appears to hang importing an alignment with
1905 Wrap as default or after enabling Wrap</li>
1906 <li>'Right click to add annotations' message
1907 shown in wrap mode when no annotations present</li>
1908 <li>Disorder predictions fail with NPE if no automatic
1909 annotation already exists on alignment</li>
1910 <li>oninit javascript function should be called after
1911 initialisation completes</li>
1912 <li>Remove redundancy after disorder prediction corrupts
1913 alignment window display</li>
1914 <li>Example annotation file in documentation is invalid</li>
1915 <li>Grouped line graph annotation rows are not exported
1916 to annotation file</li>
1917 <li>Multi-harmony analysis cannot be run when only two
1919 <li>Cannot create multiple groups of line graphs with
1920 several 'combine' statements in annotation file</li>
1921 <li>Pressing return several times causes Number Format
1922 exceptions in keyboard mode</li>
1923 <li>Multi-harmony (SHMMR) method doesn't submit
1924 correct partitions for input data</li>
1925 <li>Translation from DNA to Amino Acids fails</li>
1926 <li>Jalview fail to load newick tree with quoted label</li>
1927 <li>--headless flag isn't understood</li>
1928 <li>ClassCastException when generating EPS in headless
1930 <li>Adjusting sequence-associated shading threshold only
1931 changes one row's threshold</li>
1932 <li>Preferences and Feature settings panel panel
1933 doesn't open</li>
1934 <li>hide consensus histogram also hides conservation and
1935 quality histograms</li>
1940 <td><div align="center">
1941 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
1943 <td><em>Application</em>
1945 <li>Support for JABAWS 2.0 Services (AACon alignment
1946 conservation, protein disorder and Clustal Omega)</li>
1947 <li>JABAWS server status indicator in Web Services
1949 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
1950 in Jalview alignment window</li>
1951 <li>Updated Jalview build and deploy framework for OSX
1952 mountain lion, windows 7, and 8</li>
1953 <li>Nucleotide substitution matrix for PCA that supports
1954 RNA and ambiguity codes</li>
1956 <li>Improved sequence database retrieval GUI</li>
1957 <li>Support fetching and database reference look up
1958 against multiple DAS sources (Fetch all from in 'fetch db
1960 <li>Jalview project improvements
1962 <li>Store and retrieve the 'belowAlignment'
1963 flag for annotation</li>
1964 <li>calcId attribute to group annotation rows on the
1966 <li>Store AACon calculation settings for a view in
1967 Jalview project</li>
1971 <li>horizontal scrolling gesture support</li>
1972 <li>Visual progress indicator when PCA calculation is
1974 <li>Simpler JABA web services menus</li>
1975 <li>visual indication that web service results are still
1976 being retrieved from server</li>
1977 <li>Serialise the dialogs that are shown when Jalview
1978 starts up for first time</li>
1979 <li>Jalview user agent string for interacting with HTTP
1981 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
1983 <li>Examples directory and Groovy library included in
1984 InstallAnywhere distribution</li>
1985 </ul> <em>Applet</em>
1987 <li>RNA alignment and secondary structure annotation
1988 visualization applet example</li>
1989 </ul> <em>General</em>
1991 <li>Normalise option for consensus sequence logo</li>
1992 <li>Reset button in PCA window to return dimensions to
1994 <li>Allow seqspace or Jalview variant of alignment PCA
1996 <li>PCA with either nucleic acid and protein substitution
1998 <li>Allow windows containing HTML reports to be exported
2000 <li>Interactive display and editing of RNA secondary
2001 structure contacts</li>
2002 <li>RNA Helix Alignment Colouring</li>
2003 <li>RNA base pair logo consensus</li>
2004 <li>Parse sequence associated secondary structure
2005 information in Stockholm files</li>
2006 <li>HTML Export database accessions and annotation
2007 information presented in tooltip for sequences</li>
2008 <li>Import secondary structure from LOCARNA clustalw
2009 style RNA alignment files</li>
2010 <li>import and visualise T-COFFEE quality scores for an
2012 <li>'colour by annotation' per sequence option to
2013 shade each sequence according to its associated alignment
2015 <li>New Jalview Logo</li>
2016 </ul> <em>Documentation and Development</em>
2018 <li>documentation for score matrices used in Jalview</li>
2019 <li>New Website!</li>
2021 <td><em>Application</em>
2023 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2024 wsdbfetch REST service</li>
2025 <li>Stop windows being moved outside desktop on OSX</li>
2026 <li>Filetype associations not installed for webstart
2028 <li>Jalview does not always retrieve progress of a JABAWS
2029 job execution in full once it is complete</li>
2030 <li>revise SHMR RSBS definition to ensure alignment is
2031 uploaded via ali_file parameter</li>
2032 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2033 <li>View all structures superposed fails with exception</li>
2034 <li>Jnet job queues forever if a very short sequence is
2035 submitted for prediction</li>
2036 <li>Cut and paste menu not opened when mouse clicked on
2038 <li>Putting fractional value into integer text box in
2039 alignment parameter dialog causes Jalview to hang</li>
2040 <li>Structure view highlighting doesn't work on
2042 <li>View all structures fails with exception shown in
2044 <li>Characters in filename associated with PDBEntry not
2045 escaped in a platform independent way</li>
2046 <li>Jalview desktop fails to launch with exception when
2048 <li>Tree calculation reports 'you must have 2 or more
2049 sequences selected' when selection is empty</li>
2050 <li>Jalview desktop fails to launch with jar signature
2051 failure when java web start temporary file caching is
2053 <li>DAS Sequence retrieval with range qualification
2054 results in sequence xref which includes range qualification</li>
2055 <li>Errors during processing of command line arguments
2056 cause progress bar (JAL-898) to be removed</li>
2057 <li>Replace comma for semi-colon option not disabled for
2058 DAS sources in sequence fetcher</li>
2059 <li>Cannot close news reader when JABAWS server warning
2060 dialog is shown</li>
2061 <li>Option widgets not updated to reflect user settings</li>
2062 <li>Edited sequence not submitted to web service</li>
2063 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2064 <li>InstallAnywhere installer doesn't unpack and run
2065 on OSX Mountain Lion</li>
2066 <li>Annotation panel not given a scroll bar when
2067 sequences with alignment annotation are pasted into the
2069 <li>Sequence associated annotation rows not associated
2070 when loaded from Jalview project</li>
2071 <li>Browser launch fails with NPE on java 1.7</li>
2072 <li>JABAWS alignment marked as finished when job was
2073 cancelled or job failed due to invalid input</li>
2074 <li>NPE with v2.7 example when clicking on Tree
2075 associated with all views</li>
2076 <li>Exceptions when copy/paste sequences with grouped
2077 annotation rows to new window</li>
2078 </ul> <em>Applet</em>
2080 <li>Sequence features are momentarily displayed before
2081 they are hidden using hidefeaturegroups applet parameter</li>
2082 <li>loading features via javascript API automatically
2083 enables feature display</li>
2084 <li>scrollToColumnIn javascript API method doesn't
2086 </ul> <em>General</em>
2088 <li>Redundancy removal fails for rna alignment</li>
2089 <li>PCA calculation fails when sequence has been selected
2090 and then deselected</li>
2091 <li>PCA window shows grey box when first opened on OSX</li>
2092 <li>Letters coloured pink in sequence logo when alignment
2093 coloured with clustalx</li>
2094 <li>Choosing fonts without letter symbols defined causes
2095 exceptions and redraw errors</li>
2096 <li>Initial PCA plot view is not same as manually
2097 reconfigured view</li>
2098 <li>Grouped annotation graph label has incorrect line
2100 <li>Grouped annotation graph label display is corrupted
2101 for lots of labels</li>
2106 <div align="center">
2107 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2110 <td><em>Application</em>
2112 <li>Jalview Desktop News Reader</li>
2113 <li>Tweaked default layout of web services menu</li>
2114 <li>View/alignment association menu to enable user to
2115 easily specify which alignment a multi-structure view takes
2116 its colours/correspondences from</li>
2117 <li>Allow properties file location to be specified as URL</li>
2118 <li>Extend Jalview project to preserve associations
2119 between many alignment views and a single Jmol display</li>
2120 <li>Store annotation row height in Jalview project file</li>
2121 <li>Annotation row column label formatting attributes
2122 stored in project file</li>
2123 <li>Annotation row order for auto-calculated annotation
2124 rows preserved in Jalview project file</li>
2125 <li>Visual progress indication when Jalview state is
2126 saved using Desktop window menu</li>
2127 <li>Visual indication that command line arguments are
2128 still being processed</li>
2129 <li>Groovy script execution from URL</li>
2130 <li>Colour by annotation default min and max colours in
2132 <li>Automatically associate PDB files dragged onto an
2133 alignment with sequences that have high similarity and
2135 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2136 <li>'view structures' option to open many
2137 structures in same window</li>
2138 <li>Sort associated views menu option for tree panel</li>
2139 <li>Group all JABA and non-JABA services for a particular
2140 analysis function in its own submenu</li>
2141 </ul> <em>Applet</em>
2143 <li>Userdefined and autogenerated annotation rows for
2145 <li>Adjustment of alignment annotation pane height</li>
2146 <li>Annotation scrollbar for annotation panel</li>
2147 <li>Drag to reorder annotation rows in annotation panel</li>
2148 <li>'automaticScrolling' parameter</li>
2149 <li>Allow sequences with partial ID string matches to be
2150 annotated from GFF/Jalview features files</li>
2151 <li>Sequence logo annotation row in applet</li>
2152 <li>Absolute paths relative to host server in applet
2153 parameters are treated as such</li>
2154 <li>New in the JalviewLite javascript API:
2156 <li>JalviewLite.js javascript library</li>
2157 <li>Javascript callbacks for
2159 <li>Applet initialisation</li>
2160 <li>Sequence/alignment mouse-overs and selections</li>
2163 <li>scrollTo row and column alignment scrolling
2165 <li>Select sequence/alignment regions from javascript</li>
2166 <li>javascript structure viewer harness to pass
2167 messages between Jmol and Jalview when running as
2168 distinct applets</li>
2169 <li>sortBy method</li>
2170 <li>Set of applet and application examples shipped
2171 with documentation</li>
2172 <li>New example to demonstrate JalviewLite and Jmol
2173 javascript message exchange</li>
2175 </ul> <em>General</em>
2177 <li>Enable Jmol displays to be associated with multiple
2178 multiple alignments</li>
2179 <li>Option to automatically sort alignment with new tree</li>
2180 <li>User configurable link to enable redirects to a
2181 www.Jalview.org mirror</li>
2182 <li>Jmol colours option for Jmol displays</li>
2183 <li>Configurable newline string when writing alignment
2184 and other flat files</li>
2185 <li>Allow alignment annotation description lines to
2186 contain html tags</li>
2187 </ul> <em>Documentation and Development</em>
2189 <li>Add groovy test harness for bulk load testing to
2191 <li>Groovy script to load and align a set of sequences
2192 using a web service before displaying the result in the
2193 Jalview desktop</li>
2194 <li>Restructured javascript and applet api documentation</li>
2195 <li>Ant target to publish example html files with applet
2197 <li>Netbeans project for building Jalview from source</li>
2198 <li>ant task to create online javadoc for Jalview source</li>
2200 <td><em>Application</em>
2202 <li>User defined colourscheme throws exception when
2203 current built in colourscheme is saved as new scheme</li>
2204 <li>AlignFrame->Save in application pops up save
2205 dialog for valid filename/format</li>
2206 <li>Cannot view associated structure for UniProt sequence</li>
2207 <li>PDB file association breaks for UniProt sequence
2209 <li>Associate PDB from file dialog does not tell you
2210 which sequence is to be associated with the file</li>
2211 <li>Find All raises null pointer exception when query
2212 only matches sequence IDs</li>
2213 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2214 <li>Jalview project with Jmol views created with Jalview
2215 2.4 cannot be loaded</li>
2216 <li>Filetype associations not installed for webstart
2218 <li>Two or more chains in a single PDB file associated
2219 with sequences in different alignments do not get coloured
2220 by their associated sequence</li>
2221 <li>Visibility status of autocalculated annotation row
2222 not preserved when project is loaded</li>
2223 <li>Annotation row height and visibility attributes not
2224 stored in Jalview project</li>
2225 <li>Tree bootstraps are not preserved when saved as a
2226 Jalview project</li>
2227 <li>Envision2 workflow tooltips are corrupted</li>
2228 <li>Enabling show group conservation also enables colour
2229 by conservation</li>
2230 <li>Duplicate group associated conservation or consensus
2231 created on new view</li>
2232 <li>Annotation scrollbar not displayed after 'show
2233 all hidden annotation rows' option selected</li>
2234 <li>Alignment quality not updated after alignment
2235 annotation row is hidden then shown</li>
2236 <li>Preserve colouring of structures coloured by
2237 sequences in pre Jalview 2.7 projects</li>
2238 <li>Web service job parameter dialog is not laid out
2240 <li>Web services menu not refreshed after 'reset
2241 services' button is pressed in preferences</li>
2242 <li>Annotation off by one in Jalview v2_3 example project</li>
2243 <li>Structures imported from file and saved in project
2244 get name like jalview_pdb1234.txt when reloaded</li>
2245 <li>Jalview does not always retrieve progress of a JABAWS
2246 job execution in full once it is complete</li>
2247 </ul> <em>Applet</em>
2249 <li>Alignment height set incorrectly when lots of
2250 annotation rows are displayed</li>
2251 <li>Relative URLs in feature HTML text not resolved to
2253 <li>View follows highlighting does not work for positions
2255 <li><= shown as = in tooltip</li>
2256 <li>Export features raises exception when no features
2258 <li>Separator string used for serialising lists of IDs
2259 for javascript api is modified when separator string
2260 provided as parameter</li>
2261 <li>Null pointer exception when selecting tree leaves for
2262 alignment with no existing selection</li>
2263 <li>Relative URLs for datasources assumed to be relative
2264 to applet's codebase</li>
2265 <li>Status bar not updated after finished searching and
2266 search wraps around to first result</li>
2267 <li>StructureSelectionManager instance shared between
2268 several Jalview applets causes race conditions and memory
2270 <li>Hover tooltip and mouseover of position on structure
2271 not sent from Jmol in applet</li>
2272 <li>Certain sequences of javascript method calls to
2273 applet API fatally hang browser</li>
2274 </ul> <em>General</em>
2276 <li>View follows structure mouseover scrolls beyond
2277 position with wrapped view and hidden regions</li>
2278 <li>Find sequence position moves to wrong residue
2279 with/without hidden columns</li>
2280 <li>Sequence length given in alignment properties window
2282 <li>InvalidNumberFormat exceptions thrown when trying to
2283 import PDB like structure files</li>
2284 <li>Positional search results are only highlighted
2285 between user-supplied sequence start/end bounds</li>
2286 <li>End attribute of sequence is not validated</li>
2287 <li>Find dialog only finds first sequence containing a
2288 given sequence position</li>
2289 <li>Sequence numbering not preserved in MSF alignment
2291 <li>Jalview PDB file reader does not extract sequence
2292 from nucleotide chains correctly</li>
2293 <li>Structure colours not updated when tree partition
2294 changed in alignment</li>
2295 <li>Sequence associated secondary structure not correctly
2296 parsed in interleaved stockholm</li>
2297 <li>Colour by annotation dialog does not restore current
2299 <li>Hiding (nearly) all sequences doesn't work
2301 <li>Sequences containing lowercase letters are not
2302 properly associated with their pdb files</li>
2303 </ul> <em>Documentation and Development</em>
2305 <li>schemas/JalviewWsParamSet.xsd corrupted by
2306 ApplyCopyright tool</li>
2311 <div align="center">
2312 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2315 <td><em>Application</em>
2317 <li>New warning dialog when the Jalview Desktop cannot
2318 contact web services</li>
2319 <li>JABA service parameters for a preset are shown in
2320 service job window</li>
2321 <li>JABA Service menu entries reworded</li>
2325 <li>Modeller PIR IO broken - cannot correctly import a
2326 pir file emitted by Jalview</li>
2327 <li>Existing feature settings transferred to new
2328 alignment view created from cut'n'paste</li>
2329 <li>Improved test for mixed amino/nucleotide chains when
2330 parsing PDB files</li>
2331 <li>Consensus and conservation annotation rows
2332 occasionally become blank for all new windows</li>
2333 <li>Exception raised when right clicking above sequences
2334 in wrapped view mode</li>
2335 </ul> <em>Application</em>
2337 <li>multiple multiply aligned structure views cause cpu
2338 usage to hit 100% and computer to hang</li>
2339 <li>Web Service parameter layout breaks for long user
2340 parameter names</li>
2341 <li>Jaba service discovery hangs desktop if Jaba server
2348 <div align="center">
2349 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2352 <td><em>Application</em>
2354 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2355 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2358 <li>Web Services preference tab</li>
2359 <li>Analysis parameters dialog box and user defined
2361 <li>Improved speed and layout of Envision2 service menu</li>
2362 <li>Superpose structures using associated sequence
2364 <li>Export coordinates and projection as CSV from PCA
2366 </ul> <em>Applet</em>
2368 <li>enable javascript: execution by the applet via the
2369 link out mechanism</li>
2370 </ul> <em>Other</em>
2372 <li>Updated the Jmol Jalview interface to work with Jmol
2374 <li>The Jalview Desktop and JalviewLite applet now
2375 require Java 1.5</li>
2376 <li>Allow Jalview feature colour specification for GFF
2377 sequence annotation files</li>
2378 <li>New 'colour by label' keword in Jalview feature file
2379 type colour specification</li>
2380 <li>New Jalview Desktop Groovy API method that allows a
2381 script to check if it being run in an interactive session or
2382 in a batch operation from the Jalview command line</li>
2386 <li>clustalx colourscheme colours Ds preferentially when
2387 both D+E are present in over 50% of the column</li>
2388 </ul> <em>Application</em>
2390 <li>typo in AlignmentFrame->View->Hide->all but
2391 selected Regions menu item</li>
2392 <li>sequence fetcher replaces ',' for ';' when the ',' is
2393 part of a valid accession ID</li>
2394 <li>fatal OOM if object retrieved by sequence fetcher
2395 runs out of memory</li>
2396 <li>unhandled Out of Memory Error when viewing pca
2397 analysis results</li>
2398 <li>InstallAnywhere builds fail to launch on OS X java
2399 10.5 update 4 (due to apple Java 1.6 update)</li>
2400 <li>Installanywhere Jalview silently fails to launch</li>
2401 </ul> <em>Applet</em>
2403 <li>Jalview.getFeatureGroups() raises an
2404 ArrayIndexOutOfBoundsException if no feature groups are
2411 <div align="center">
2412 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2418 <li>Alignment prettyprinter doesn't cope with long
2420 <li>clustalx colourscheme colours Ds preferentially when
2421 both D+E are present in over 50% of the column</li>
2422 <li>nucleic acid structures retrieved from PDB do not
2423 import correctly</li>
2424 <li>More columns get selected than were clicked on when a
2425 number of columns are hidden</li>
2426 <li>annotation label popup menu not providing correct
2427 add/hide/show options when rows are hidden or none are
2429 <li>Stockholm format shown in list of readable formats,
2430 and parser copes better with alignments from RFAM.</li>
2431 <li>CSV output of consensus only includes the percentage
2432 of all symbols if sequence logo display is enabled</li>
2434 </ul> <em>Applet</em>
2436 <li>annotation panel disappears when annotation is
2438 </ul> <em>Application</em>
2440 <li>Alignment view not redrawn properly when new
2441 alignment opened where annotation panel is visible but no
2442 annotations are present on alignment</li>
2443 <li>pasted region containing hidden columns is
2444 incorrectly displayed in new alignment window</li>
2445 <li>Jalview slow to complete operations when stdout is
2446 flooded (fix is to close the Jalview console)</li>
2447 <li>typo in AlignmentFrame->View->Hide->all but
2448 selected Rregions menu item.</li>
2449 <li>inconsistent group submenu and Format submenu entry
2450 'Un' or 'Non'conserved</li>
2451 <li>Sequence feature settings are being shared by
2452 multiple distinct alignments</li>
2453 <li>group annotation not recreated when tree partition is
2455 <li>double click on group annotation to select sequences
2456 does not propagate to associated trees</li>
2457 <li>Mac OSX specific issues:
2459 <li>exception raised when mouse clicked on desktop
2460 window background</li>
2461 <li>Desktop menu placed on menu bar and application
2462 name set correctly</li>
2463 <li>sequence feature settings not wide enough for the
2464 save feature colourscheme button</li>
2473 <div align="center">
2474 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2477 <td><em>New Capabilities</em>
2479 <li>URL links generated from description line for
2480 regular-expression based URL links (applet and application)
2482 <li>Non-positional feature URL links are shown in link
2484 <li>Linked viewing of nucleic acid sequences and
2486 <li>Automatic Scrolling option in View menu to display
2487 the currently highlighted region of an alignment.</li>
2488 <li>Order an alignment by sequence length, or using the
2489 average score or total feature count for each sequence.</li>
2490 <li>Shading features by score or associated description</li>
2491 <li>Subdivide alignment and groups based on identity of
2492 selected subsequence (Make Groups from Selection).</li>
2493 <li>New hide/show options including Shift+Control+H to
2494 hide everything but the currently selected region.</li>
2495 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2496 </ul> <em>Application</em>
2498 <li>Fetch DB References capabilities and UI expanded to
2499 support retrieval from DAS sequence sources</li>
2500 <li>Local DAS Sequence sources can be added via the
2501 command line or via the Add local source dialog box.</li>
2502 <li>DAS Dbref and DbxRef feature types are parsed as
2503 database references and protein_name is parsed as
2504 description line (BioSapiens terms).</li>
2505 <li>Enable or disable non-positional feature and database
2506 references in sequence ID tooltip from View menu in
2508 <!-- <li>New hidden columns and rows and representatives capabilities
2509 in annotations file (in progress - not yet fully implemented)</li> -->
2510 <li>Group-associated consensus, sequence logos and
2511 conservation plots</li>
2512 <li>Symbol distributions for each column can be exported
2513 and visualized as sequence logos</li>
2514 <li>Optionally scale multi-character column labels to fit
2515 within each column of annotation row<!-- todo for applet -->
2517 <li>Optional automatic sort of associated alignment view
2518 when a new tree is opened.</li>
2519 <li>Jalview Java Console</li>
2520 <li>Better placement of desktop window when moving
2521 between different screens.</li>
2522 <li>New preference items for sequence ID tooltip and
2523 consensus annotation</li>
2524 <li>Client to submit sequences and IDs to Envision2
2526 <li><em>Vamsas Capabilities</em>
2528 <li>Improved VAMSAS synchronization (Jalview archive
2529 used to preserve views, structures, and tree display
2531 <li>Import of vamsas documents from disk or URL via
2533 <li>Sharing of selected regions between views and
2534 with other VAMSAS applications (Experimental feature!)</li>
2535 <li>Updated API to VAMSAS version 0.2</li>
2537 </ul> <em>Applet</em>
2539 <li>Middle button resizes annotation row height</li>
2542 <li>sortByTree (true/false) - automatically sort the
2543 associated alignment view by the tree when a new tree is
2545 <li>showTreeBootstraps (true/false) - show or hide
2546 branch bootstraps (default is to show them if available)</li>
2547 <li>showTreeDistances (true/false) - show or hide
2548 branch lengths (default is to show them if available)</li>
2549 <li>showUnlinkedTreeNodes (true/false) - indicate if
2550 unassociated nodes should be highlighted in the tree
2552 <li>heightScale and widthScale (1.0 or more) -
2553 increase the height or width of a cell in the alignment
2554 grid relative to the current font size.</li>
2557 <li>Non-positional features displayed in sequence ID
2559 </ul> <em>Other</em>
2561 <li>Features format: graduated colour definitions and
2562 specification of feature scores</li>
2563 <li>Alignment Annotations format: new keywords for group
2564 associated annotation (GROUP_REF) and annotation row display
2565 properties (ROW_PROPERTIES)</li>
2566 <li>XML formats extended to support graduated feature
2567 colourschemes, group associated annotation, and profile
2568 visualization settings.</li></td>
2571 <li>Source field in GFF files parsed as feature source
2572 rather than description</li>
2573 <li>Non-positional features are now included in sequence
2574 feature and gff files (controlled via non-positional feature
2575 visibility in tooltip).</li>
2576 <li>URL links generated for all feature links (bugfix)</li>
2577 <li>Added URL embedding instructions to features file
2579 <li>Codons containing ambiguous nucleotides translated as
2580 'X' in peptide product</li>
2581 <li>Match case switch in find dialog box works for both
2582 sequence ID and sequence string and query strings do not
2583 have to be in upper case to match case-insensitively.</li>
2584 <li>AMSA files only contain first column of
2585 multi-character column annotation labels</li>
2586 <li>Jalview Annotation File generation/parsing consistent
2587 with documentation (e.g. Stockholm annotation can be
2588 exported and re-imported)</li>
2589 <li>PDB files without embedded PDB IDs given a friendly
2591 <li>Find incrementally searches ID string matches as well
2592 as subsequence matches, and correctly reports total number
2596 <li>Better handling of exceptions during sequence
2598 <li>Dasobert generated non-positional feature URL
2599 link text excludes the start_end suffix</li>
2600 <li>DAS feature and source retrieval buttons disabled
2601 when fetch or registry operations in progress.</li>
2602 <li>PDB files retrieved from URLs are cached properly</li>
2603 <li>Sequence description lines properly shared via
2605 <li>Sequence fetcher fetches multiple records for all
2607 <li>Ensured that command line das feature retrieval
2608 completes before alignment figures are generated.</li>
2609 <li>Reduced time taken when opening file browser for
2611 <li>isAligned check prior to calculating tree, PCA or
2612 submitting an MSA to JNet now excludes hidden sequences.</li>
2613 <li>User defined group colours properly recovered
2614 from Jalview projects.</li>
2623 <div align="center">
2624 <strong>2.4.0.b2</strong><br> 28/10/2009
2629 <li>Experimental support for google analytics usage
2631 <li>Jalview privacy settings (user preferences and docs).</li>
2636 <li>Race condition in applet preventing startup in
2638 <li>Exception when feature created from selection beyond
2639 length of sequence.</li>
2640 <li>Allow synthetic PDB files to be imported gracefully</li>
2641 <li>Sequence associated annotation rows associate with
2642 all sequences with a given id</li>
2643 <li>Find function matches case-insensitively for sequence
2644 ID string searches</li>
2645 <li>Non-standard characters do not cause pairwise
2646 alignment to fail with exception</li>
2647 </ul> <em>Application Issues</em>
2649 <li>Sequences are now validated against EMBL database</li>
2650 <li>Sequence fetcher fetches multiple records for all
2652 </ul> <em>InstallAnywhere Issues</em>
2654 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2655 issue with installAnywhere mechanism)</li>
2656 <li>Command line launching of JARs from InstallAnywhere
2657 version (java class versioning error fixed)</li>
2664 <div align="center">
2665 <strong>2.4</strong><br> 27/8/2008
2668 <td><em>User Interface</em>
2670 <li>Linked highlighting of codon and amino acid from
2671 translation and protein products</li>
2672 <li>Linked highlighting of structure associated with
2673 residue mapping to codon position</li>
2674 <li>Sequence Fetcher provides example accession numbers
2675 and 'clear' button</li>
2676 <li>MemoryMonitor added as an option under Desktop's
2678 <li>Extract score function to parse whitespace separated
2679 numeric data in description line</li>
2680 <li>Column labels in alignment annotation can be centred.</li>
2681 <li>Tooltip for sequence associated annotation give name
2683 </ul> <em>Web Services and URL fetching</em>
2685 <li>JPred3 web service</li>
2686 <li>Prototype sequence search client (no public services
2688 <li>Fetch either seed alignment or full alignment from
2690 <li>URL Links created for matching database cross
2691 references as well as sequence ID</li>
2692 <li>URL Links can be created using regular-expressions</li>
2693 </ul> <em>Sequence Database Connectivity</em>
2695 <li>Retrieval of cross-referenced sequences from other
2697 <li>Generalised database reference retrieval and
2698 validation to all fetchable databases</li>
2699 <li>Fetch sequences from DAS sources supporting the
2700 sequence command</li>
2701 </ul> <em>Import and Export</em>
2702 <li>export annotation rows as CSV for spreadsheet import</li>
2703 <li>Jalview projects record alignment dataset associations,
2704 EMBL products, and cDNA sequence mappings</li>
2705 <li>Sequence Group colour can be specified in Annotation
2707 <li>Ad-hoc colouring of group in Annotation File using RGB
2708 triplet as name of colourscheme</li>
2709 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2711 <li>treenode binding for VAMSAS tree exchange</li>
2712 <li>local editing and update of sequences in VAMSAS
2713 alignments (experimental)</li>
2714 <li>Create new or select existing session to join</li>
2715 <li>load and save of vamsas documents</li>
2716 </ul> <em>Application command line</em>
2718 <li>-tree parameter to open trees (introduced for passing
2720 <li>-fetchfrom command line argument to specify nicknames
2721 of DAS servers to query for alignment features</li>
2722 <li>-dasserver command line argument to add new servers
2723 that are also automatically queried for features</li>
2724 <li>-groovy command line argument executes a given groovy
2725 script after all input data has been loaded and parsed</li>
2726 </ul> <em>Applet-Application data exchange</em>
2728 <li>Trees passed as applet parameters can be passed to
2729 application (when using "View in full
2730 application")</li>
2731 </ul> <em>Applet Parameters</em>
2733 <li>feature group display control parameter</li>
2734 <li>debug parameter</li>
2735 <li>showbutton parameter</li>
2736 </ul> <em>Applet API methods</em>
2738 <li>newView public method</li>
2739 <li>Window (current view) specific get/set public methods</li>
2740 <li>Feature display control methods</li>
2741 <li>get list of currently selected sequences</li>
2742 </ul> <em>New Jalview distribution features</em>
2744 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2745 <li>RELEASE file gives build properties for the latest
2746 Jalview release.</li>
2747 <li>Java 1.1 Applet build made easier and donotobfuscate
2748 property controls execution of obfuscator</li>
2749 <li>Build target for generating source distribution</li>
2750 <li>Debug flag for javacc</li>
2751 <li>.jalview_properties file is documented (slightly) in
2752 jalview.bin.Cache</li>
2753 <li>Continuous Build Integration for stable and
2754 development version of Application, Applet and source
2759 <li>selected region output includes visible annotations
2760 (for certain formats)</li>
2761 <li>edit label/displaychar contains existing label/char
2763 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2764 <li>shorter peptide product names from EMBL records</li>
2765 <li>Newick string generator makes compact representations</li>
2766 <li>bootstrap values parsed correctly for tree files with
2768 <li>pathological filechooser bug avoided by not allowing
2769 filenames containing a ':'</li>
2770 <li>Fixed exception when parsing GFF files containing
2771 global sequence features</li>
2772 <li>Alignment datasets are finalized only when number of
2773 references from alignment sequences goes to zero</li>
2774 <li>Close of tree branch colour box without colour
2775 selection causes cascading exceptions</li>
2776 <li>occasional negative imgwidth exceptions</li>
2777 <li>better reporting of non-fatal warnings to user when
2778 file parsing fails.</li>
2779 <li>Save works when Jalview project is default format</li>
2780 <li>Save as dialog opened if current alignment format is
2781 not a valid output format</li>
2782 <li>UniProt canonical names introduced for both das and
2784 <li>Histidine should be midblue (not pink!) in Zappo</li>
2785 <li>error messages passed up and output when data read
2787 <li>edit undo recovers previous dataset sequence when
2788 sequence is edited</li>
2789 <li>allow PDB files without pdb ID HEADER lines (like
2790 those generated by MODELLER) to be read in properly</li>
2791 <li>allow reading of JPred concise files as a normal
2793 <li>Stockholm annotation parsing and alignment properties
2794 import fixed for PFAM records</li>
2795 <li>Structure view windows have correct name in Desktop
2797 <li>annotation consisting of sequence associated scores
2798 can be read and written correctly to annotation file</li>
2799 <li>Aligned cDNA translation to aligned peptide works
2801 <li>Fixed display of hidden sequence markers and
2802 non-italic font for representatives in Applet</li>
2803 <li>Applet Menus are always embedded in applet window on
2805 <li>Newly shown features appear at top of stack (in
2807 <li>Annotations added via parameter not drawn properly
2808 due to null pointer exceptions</li>
2809 <li>Secondary structure lines are drawn starting from
2810 first column of alignment</li>
2811 <li>UniProt XML import updated for new schema release in
2813 <li>Sequence feature to sequence ID match for Features
2814 file is case-insensitive</li>
2815 <li>Sequence features read from Features file appended to
2816 all sequences with matching IDs</li>
2817 <li>PDB structure coloured correctly for associated views
2818 containing a sub-sequence</li>
2819 <li>PDB files can be retrieved by applet from Jar files</li>
2820 <li>feature and annotation file applet parameters
2821 referring to different directories are retrieved correctly</li>
2822 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
2823 <li>Fixed application hang whilst waiting for
2824 splash-screen version check to complete</li>
2825 <li>Applet properly URLencodes input parameter values
2826 when passing them to the launchApp service</li>
2827 <li>display name and local features preserved in results
2828 retrieved from web service</li>
2829 <li>Visual delay indication for sequence retrieval and
2830 sequence fetcher initialisation</li>
2831 <li>updated Application to use DAS 1.53e version of
2832 dasobert DAS client</li>
2833 <li>Re-instated Full AMSA support and .amsa file
2835 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
2843 <div align="center">
2844 <strong>2.3</strong><br> 9/5/07
2849 <li>Jmol 11.0.2 integration</li>
2850 <li>PDB views stored in Jalview XML files</li>
2851 <li>Slide sequences</li>
2852 <li>Edit sequence in place</li>
2853 <li>EMBL CDS features</li>
2854 <li>DAS Feature mapping</li>
2855 <li>Feature ordering</li>
2856 <li>Alignment Properties</li>
2857 <li>Annotation Scores</li>
2858 <li>Sort by scores</li>
2859 <li>Feature/annotation editing in applet</li>
2864 <li>Headless state operation in 2.2.1</li>
2865 <li>Incorrect and unstable DNA pairwise alignment</li>
2866 <li>Cut and paste of sequences with annotation</li>
2867 <li>Feature group display state in XML</li>
2868 <li>Feature ordering in XML</li>
2869 <li>blc file iteration selection using filename # suffix</li>
2870 <li>Stockholm alignment properties</li>
2871 <li>Stockhom alignment secondary structure annotation</li>
2872 <li>2.2.1 applet had no feature transparency</li>
2873 <li>Number pad keys can be used in cursor mode</li>
2874 <li>Structure Viewer mirror image resolved</li>
2881 <div align="center">
2882 <strong>2.2.1</strong><br> 12/2/07
2887 <li>Non standard characters can be read and displayed
2888 <li>Annotations/Features can be imported/exported to the
2890 <li>Applet allows editing of sequence/annotation/group
2891 name & description
2892 <li>Preference setting to display sequence name in
2894 <li>Annotation file format extended to allow
2895 Sequence_groups to be defined
2896 <li>Default opening of alignment overview panel can be
2897 specified in preferences
2898 <li>PDB residue numbering annotation added to associated
2904 <li>Applet crash under certain Linux OS with Java 1.6
2906 <li>Annotation file export / import bugs fixed
2907 <li>PNG / EPS image output bugs fixed
2913 <div align="center">
2914 <strong>2.2</strong><br> 27/11/06
2919 <li>Multiple views on alignment
2920 <li>Sequence feature editing
2921 <li>"Reload" alignment
2922 <li>"Save" to current filename
2923 <li>Background dependent text colour
2924 <li>Right align sequence ids
2925 <li>User-defined lower case residue colours
2928 <li>Menu item accelerator keys
2929 <li>Control-V pastes to current alignment
2930 <li>Cancel button for DAS Feature Fetching
2931 <li>PCA and PDB Viewers zoom via mouse roller
2932 <li>User-defined sub-tree colours and sub-tree selection
2934 <li>'New Window' button on the 'Output to Text box'
2939 <li>New memory efficient Undo/Redo System
2940 <li>Optimised symbol lookups and conservation/consensus
2942 <li>Region Conservation/Consensus recalculated after
2944 <li>Fixed Remove Empty Columns Bug (empty columns at end
2946 <li>Slowed DAS Feature Fetching for increased robustness.
2948 <li>Made angle brackets in ASCII feature descriptions
2950 <li>Re-instated Zoom function for PCA
2951 <li>Sequence descriptions conserved in web service
2953 <li>UniProt ID discoverer uses any word separated by
2955 <li>WsDbFetch query/result association resolved
2956 <li>Tree leaf to sequence mapping improved
2957 <li>Smooth fonts switch moved to FontChooser dialog box.
2964 <div align="center">
2965 <strong>2.1.1</strong><br> 12/9/06
2970 <li>Copy consensus sequence to clipboard</li>
2975 <li>Image output - rightmost residues are rendered if
2976 sequence id panel has been resized</li>
2977 <li>Image output - all offscreen group boundaries are
2979 <li>Annotation files with sequence references - all
2980 elements in file are relative to sequence position</li>
2981 <li>Mac Applet users can use Alt key for group editing</li>
2987 <div align="center">
2988 <strong>2.1</strong><br> 22/8/06
2993 <li>MAFFT Multiple Alignment in default Web Service list</li>
2994 <li>DAS Feature fetching</li>
2995 <li>Hide sequences and columns</li>
2996 <li>Export Annotations and Features</li>
2997 <li>GFF file reading / writing</li>
2998 <li>Associate structures with sequences from local PDB
3000 <li>Add sequences to exisiting alignment</li>
3001 <li>Recently opened files / URL lists</li>
3002 <li>Applet can launch the full application</li>
3003 <li>Applet has transparency for features (Java 1.2
3005 <li>Applet has user defined colours parameter</li>
3006 <li>Applet can load sequences from parameter
3007 "sequence<em>x</em>"
3013 <li>Redundancy Panel reinstalled in the Applet</li>
3014 <li>Monospaced font - EPS / rescaling bug fixed</li>
3015 <li>Annotation files with sequence references bug fixed</li>
3021 <div align="center">
3022 <strong>2.08.1</strong><br> 2/5/06
3027 <li>Change case of selected region from Popup menu</li>
3028 <li>Choose to match case when searching</li>
3029 <li>Middle mouse button and mouse movement can compress /
3030 expand the visible width and height of the alignment</li>
3035 <li>Annotation Panel displays complete JNet results</li>
3041 <div align="center">
3042 <strong>2.08b</strong><br> 18/4/06
3048 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3049 <li>Righthand label on wrapped alignments shows correct
3056 <div align="center">
3057 <strong>2.08</strong><br> 10/4/06
3062 <li>Editing can be locked to the selection area</li>
3063 <li>Keyboard editing</li>
3064 <li>Create sequence features from searches</li>
3065 <li>Precalculated annotations can be loaded onto
3067 <li>Features file allows grouping of features</li>
3068 <li>Annotation Colouring scheme added</li>
3069 <li>Smooth fonts off by default - Faster rendering</li>
3070 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3075 <li>Drag & Drop fixed on Linux</li>
3076 <li>Jalview Archive file faster to load/save, sequence
3077 descriptions saved.</li>
3083 <div align="center">
3084 <strong>2.07</strong><br> 12/12/05
3089 <li>PDB Structure Viewer enhanced</li>
3090 <li>Sequence Feature retrieval and display enhanced</li>
3091 <li>Choose to output sequence start-end after sequence
3092 name for file output</li>
3093 <li>Sequence Fetcher WSDBFetch@EBI</li>
3094 <li>Applet can read feature files, PDB files and can be
3095 used for HTML form input</li>
3100 <li>HTML output writes groups and features</li>
3101 <li>Group editing is Control and mouse click</li>
3102 <li>File IO bugs</li>
3108 <div align="center">
3109 <strong>2.06</strong><br> 28/9/05
3114 <li>View annotations in wrapped mode</li>
3115 <li>More options for PCA viewer</li>
3120 <li>GUI bugs resolved</li>
3121 <li>Runs with -nodisplay from command line</li>
3127 <div align="center">
3128 <strong>2.05b</strong><br> 15/9/05
3133 <li>Choose EPS export as lineart or text</li>
3134 <li>Jar files are executable</li>
3135 <li>Can read in Uracil - maps to unknown residue</li>
3140 <li>Known OutOfMemory errors give warning message</li>
3141 <li>Overview window calculated more efficiently</li>
3142 <li>Several GUI bugs resolved</li>
3148 <div align="center">
3149 <strong>2.05</strong><br> 30/8/05
3154 <li>Edit and annotate in "Wrapped" view</li>
3159 <li>Several GUI bugs resolved</li>
3165 <div align="center">
3166 <strong>2.04</strong><br> 24/8/05
3171 <li>Hold down mouse wheel & scroll to change font
3177 <li>Improved JPred client reliability</li>
3178 <li>Improved loading of Jalview files</li>
3184 <div align="center">
3185 <strong>2.03</strong><br> 18/8/05
3190 <li>Set Proxy server name and port in preferences</li>
3191 <li>Multiple URL links from sequence ids</li>
3192 <li>User Defined Colours can have a scheme name and added
3194 <li>Choose to ignore gaps in consensus calculation</li>
3195 <li>Unix users can set default web browser</li>
3196 <li>Runs without GUI for batch processing</li>
3197 <li>Dynamically generated Web Service Menus</li>
3202 <li>InstallAnywhere download for Sparc Solaris</li>
3208 <div align="center">
3209 <strong>2.02</strong><br> 18/7/05
3215 <li>Copy & Paste order of sequences maintains
3216 alignment order.</li>
3222 <div align="center">
3223 <strong>2.01</strong><br> 12/7/05
3228 <li>Use delete key for deleting selection.</li>
3229 <li>Use Mouse wheel to scroll sequences.</li>
3230 <li>Help file updated to describe how to add alignment
3232 <li>Version and build date written to build properties
3234 <li>InstallAnywhere installation will check for updates
3235 at launch of Jalview.</li>
3240 <li>Delete gaps bug fixed.</li>
3241 <li>FileChooser sorts columns.</li>
3242 <li>Can remove groups one by one.</li>
3243 <li>Filechooser icons installed.</li>
3244 <li>Finder ignores return character when searching.
3245 Return key will initiate a search.<br>
3252 <div align="center">
3253 <strong>2.0</strong><br> 20/6/05
3258 <li>New codebase</li>