3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
34 /* separate the items from eachother */
41 /* doesnt get processed in javahelp */
50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>8/8/2017</em></strong>
76 <td><div align="left">
80 <!-- JAL-2379 -->Revised implementation of PCA for speed
81 and memory efficiency (~30x faster)
84 <!-- JAL-2403 -->Revised implementation of sequence
85 similarity scores as used by Tree, PCA, Shading Consensus
86 and other calculations
89 <!-- JAL-2416 -->Score matrices are stored as resource
90 files within the Jalview codebase
92 <!-- JAL-2500 -->Trees computed on Sequence Feature
93 Similarity may have different topology due to
99 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
100 a calculation dialog box
103 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
104 model for alignments and groups
107 <!-- JAL-384 -->Custom shading schemes created via groovy
111 <!-- JAL-2491 -->linked scrolling of CDS/Protein views
112 via Overview or sequence motif search operations
115 <!-- JAL-2526 -->Efficiency improvements for interacting
116 with alignment and overview windows
119 <!-- JAL-2388 -->Hidden columns and sequences can be
123 <!-- JAL-2535 -->Posterior probability annotation from
124 Stockholm files imported as sequence associated annotation
127 <!-- JAL-2533 -->Sequence names don't include file
128 extension when importing structure files without embedded
129 names or PDB accessions
132 <!-- JAL-2547 -->Amend sequence features dialog box can be
133 opened by double clicking gaps within sequence feature
137 <!-- JAL-2631 -->Graduated feature colour style example
138 included in the example feature file
141 <!-- JAL-1933 -->Occupancy annotation row shows number of
142 ungapped positions in each column of the alignment.
148 <!-- JAL-2447 --> Experimental Features Checkbox in
149 Desktop's Tools menu to hide or show untested features in
153 <!-- JAL-1476 -->Warning in alignment status bar when
154 there are not enough columns to superimpose structures in
158 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
159 file-based command exchange
162 <!-- JAL-2316, -->URLs for viewing database
163 cross-references provided by identifiers.org and the
167 <!-- JAL-2549 -->Updated JABAWS client to v2.2
170 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
171 format sequence substitution matrices
174 <!-- JAL-2375 -->Structure chooser automatically shows Cached Structures rather than querying the PDBe if structures are already available for sequences
177 <em>Experimental features</em>
180 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
181 to transfer Chimera's structure attributes as Jalview
182 features, and vice-versa.
194 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
197 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
201 <!-- --> <em>Scripting</em>
204 <!-- JAL-2344 -->FileFormatI interface for describing
205 and identifying file formats (instead of String
216 <td><div align="left">
220 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
221 matrix - C->R should be '-3'<br />Old matrix restored
222 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
225 <!-- JAL-2397 -->Fixed Jalview's treatment of gaps in PCA
226 and substitution matrix based Tree calculations.<br />In
227 earlier versions of Jalview, gaps matching gaps were
228 penalised, and gaps matching non-gaps penalised even more.
229 In the PCA calculation, gaps were actually treated as
230 non-gaps - so different costs were applied, which meant
231 Jalview's PCAs were different to those produced by
232 SeqSpace.<br />Jalview now treats gaps in the same way as
233 SeqSpace (ie it scores them as 0). To restore pre-2.10.2
235 jalview.viewmodel.PCAModel.scoreGapAsAny=true // for
237 jalview.viewmodel.PCAModel.scoreGapAsAny=false // to
241 <!-- JAL-2346 -->Reopening Colour by annotation dialog
242 doesn't reselect a specific sequence's associated
243 annotation after it was used for colouring a view
246 <!-- JAL-2430 -->Hidden regions in alignment views are not
247 coloured in linked structure views
250 <!-- JAL-2419 -->Current selection lost if popup menu
251 opened on a region of alignment without groups
254 <!-- JAL-2374 -->Popup menu not always shown for regions
255 of an alignment with overlapping groups
258 <!-- JAL-2310 -->Finder double counts if both a sequence's
259 name and description match
262 <!-- JAL-2370 -->Hiding column selection containing two
263 hidden regions results in incorrect hidden regions
266 <!-- JAL-2377 -->PCA calculation could hang when
267 generating output report when working with highly
271 <!-- JAL-2365 -->Cannot configure feature colours with
272 lightGray or darkGray via features file
275 <!-- JAL-2421 -->Overview window visible region moves
276 erratically when hidden rows or columns are present
279 <!-- JAL-2362 -->Per-residue colourschemes applied via the
280 Structure Viewer's colour menu don't correspond to
284 <!-- JAL-2405 -->Protein specific colours only offered in
285 colour and group colour menu for protein alignments
288 <!-- JAL-2386 -->'Apply to all groups' setting when
289 changing colour does not apply Conservation slider value
293 <!-- JAL-2385 -->Colour threshold slider doesn't update to
294 reflect currently selected view or group's shading
298 <!-- JAL-2373 -->Percentage identity and conservation menu
299 items do not show a tick or allow shading to be disabled
302 <!-- JAL-2385 -->Conservation shading or PID threshold
303 lost when base colourscheme changed if slider not visible
306 <!-- JAL-2547 -->Sequence features shown in tooltip for
307 gaps before start of features
310 <!-- JAL-2576 -->Very large alignments take a long time to
314 <!-- JAL-2623 -->Graduated feature colour threshold not
315 restored to UI when feature colour is edited
318 <!-- JAL-2624 -->Feature colour thresholds not respected
319 when rendered on overview and structures when opacity at
323 <!-- JAL-2630 -->Structure and alignment overview update
324 as graduate feature colour settings are modified via the
328 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
329 a time when scrolling vertically in wrapped mode.
332 <!-- JAL-2034 -->Overview window doesn't always update
333 when a group defined on the alignment is resized
336 <!-- JAL-2605 -->Mouseovers on left/right scale region in
337 wrapped view result in positional status updates
340 <!-- JAL-2563 -->Status bar shows position for ambiguous
341 amino acid and nucleotide symbols
344 <!-- JAL-2602 -->Copy consensus sequence failed if
345 alignment included gapped columns
348 <!-- JAL-2589 -->User defined gap colour not shown in
349 overview when features overlaid on alignment
364 <strong>Documentation</strong>
367 <!-- JAL-2339 -->Release notes reformatted for readibility
368 with the built-in Java help viewer
374 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
375 case' residues (button in colourscheme editor debugged and
376 new documentation and tooltips added)
379 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
380 doesn't restore group-specific text colour thresholds
383 <!-- JAL-2243 -->Feature settings panel does not update as
384 new features are added to alignment
387 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
388 selection menu changes colours of alignment views
391 <!-- JAL-2366 -->Proxy server address and port always
392 appear enabled in Preferences->Connections
395 <!-- JAL-2426 -->Spurious exceptions in console raised
396 from alignment calculation workers after alignment has
400 <!-- JAL-1608 -->Typo in selection popup menu - Create
401 groups now 'Create Group'
404 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
405 Create/Undefine group doesn't always work
408 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
409 shown again after pressing 'Cancel'
412 <!-- JAL-2461 -->DAS registry not found exceptions
413 removed from console output
416 <!-- JAL-2383 -->Above PID colour threshold not recovered
417 when alignment view imported from project
420 <!-- JAL-2465 -->No mappings generated between structure
421 and sequences extracted from structure files imported via
425 <!-- JAL-2520 -->Structures loaded via URL are saved in
426 Jalview Projects rather than fetched via URL again when
427 the project is loaded and the structure viewed
430 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
431 adjusts start position in wrap mode
434 <!-- JAL-2563 -->Status bar doesn't show positions for
435 ambiguous amino acids
438 <!-- JAL-2291 -->Hide insertions in PopUp menu excludes
439 gaps in selection, current sequence and only within
443 <!-- JAL-2582 -->Cannot retrieve protein products from
444 Ensembl by Peptide ID
447 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
448 CDS/Protein view after CDS sequences added for aligned
452 <!-- JAL-2431 -->cDNA Consensus not shown
463 <!-- JAL-2468 -->Switching between Nucleotide and Protein
464 score models doesn't always result in an updated PCA plot
467 <!-- JAL-2442 -->Features not rendered as transparent on
468 overview or linked structure view
471 <!-- JAL-2372 -->Colour group by conservation doesn't
475 <!-- JAL-2517 -->Hitting Cancel after applying
476 user-defined colourscheme doesn't restore original
480 <em>New Known Issues</em>
483 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
484 phase after a sequence motif find operation
487 <!-- JAL-2550 -->Importing annotation file with rows
488 containing just upper and lower case letters are
489 interpreted as WUSS rna secondary structure symbols
492 <!-- JAL-2590 -->Cannot load Newick trees from eggnog
499 <!-- JAL-2314 -->Unit test failure:
500 jalview.ws.jabaws.RNAStructExportImport setup fails
508 <td width="60" nowrap>
510 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
513 <td><div align="left">
517 <!-- JAL-98 -->Improved memory usage: sparse arrays used
518 for all consensus calculations
521 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
524 <li>Updated Jalview's Certum code signing certificate
530 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
531 set of database cross-references, sorted alphabetically
534 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
535 from database cross references. Users with custom links
536 will receive a <a href="webServices/urllinks.html#warning">warning
537 dialog</a> asking them to update their preferences.
540 <!-- JAL-2287-->Cancel button and escape listener on
541 dialog warning user about disconnecting Jalview from a
545 <!-- JAL-2320-->Jalview's Chimera control window closes if
546 the Chimera it is connected to is shut down
549 <!-- JAL-1738-->New keystroke (B) and Select highlighted
550 columns menu item to mark columns containing highlighted
551 regions (e.g. from structure selections or results of a
555 <!-- JAL-2284-->Command line option for batch-generation
556 of HTML pages rendering alignment data with the BioJS
566 <!-- JAL-2286 -->Columns with more than one modal residue
567 are not coloured or thresholded according to percent
568 identity (first observed in Jalview 2.8.2)
571 <!-- JAL-2301 -->Threonine incorrectly reported as not
575 <!-- JAL-2318 -->Updates to documentation pages (above PID
576 threshold, amino acid properties)
579 <!-- JAL-2292 -->Lower case residues in sequences are not
580 reported as mapped to residues in a structure file in the
584 <!--JAL-2324 -->Identical features with non-numeric scores
585 could be added multiple times to a sequence
588 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
589 bond features shown as two highlighted residues rather
590 than a range in linked structure views, and treated
591 correctly when selecting and computing trees from features
594 <!-- JAL-2281-->Custom URL links for database
595 cross-references are matched to database name regardless
603 <!-- JAL-2282-->Custom URL links for specific database
604 names without regular expressions also offer links from
608 <!-- JAL-2315-->Removing a single configured link in the
609 URL links pane in Connections preferences doesn't actually
610 update Jalview configuration
613 <!-- JAL-2272-->CTRL-Click on a selected region to open
614 the alignment area popup menu doesn't work on El-Capitan
617 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
618 files with similarly named sequences if dropped onto the
622 <!-- JAL-2312 -->Additional mappings are shown for PDB
623 entries where more chains exist in the PDB accession than
624 are reported in the SIFTS file
627 <!-- JAL-2317-->Certain structures do not get mapped to
628 the structure view when displayed with Chimera
631 <!-- JAL-2317-->No chains shown in the Chimera view
632 panel's View->Show Chains submenu
635 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
636 work for wrapped alignment views
639 <!--JAL-2197 -->Rename UI components for running JPred
640 predictions from 'JNet' to 'JPred'
643 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
644 corrupted when annotation panel vertical scroll is not at
648 <!--JAL-2332 -->Attempting to view structure for Hen
649 lysozyme results in a PDB Client error dialog box
652 <!-- JAL-2319 -->Structure View's mapping report switched
653 ranges for PDB and sequence for SIFTS
656 SIFTS 'Not_Observed' residues mapped to non-existant
660 <!-- <em>New Known Issues</em>
667 <td width="60" nowrap>
669 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
670 <em>25/10/2016</em></strong>
673 <td><em>Application</em>
675 <li>3D Structure chooser opens with 'Cached structures'
676 view if structures already loaded</li>
677 <li>Progress bar reports models as they are loaded to
684 <li>Colour by conservation always enabled and no tick
685 shown in menu when BLOSUM or PID shading applied</li>
686 <li>FER1_ARATH and FER2_ARATH labels were switched in
687 example sequences/projects/trees</li>
691 <li>Jalview projects with views of local PDB structure
692 files saved on Windows cannot be opened on OSX</li>
693 <li>Multiple structure views can be opened and superposed
694 without timeout for structures with multiple models or
695 multiple sequences in alignment</li>
696 <li>Cannot import or associated local PDB files without a
697 PDB ID HEADER line</li>
698 <li>RMSD is not output in Jmol console when superposition
700 <li>Drag and drop of URL from Browser fails for Linux and
701 OSX versions earlier than El Capitan</li>
702 <li>ENA client ignores invalid content from ENA server</li>
703 <li>Exceptions are not raised in console when ENA client
704 attempts to fetch non-existent IDs via Fetch DB Refs UI
706 <li>Exceptions are not raised in console when a new view
707 is created on the alignment</li>
708 <li>OSX right-click fixed for group selections: CMD-click
709 to insert/remove gaps in groups and CTRL-click to open group
712 <em>Build and deployment</em>
714 <li>URL link checker now copes with multi-line anchor
717 <em>New Known Issues</em>
719 <li>Drag and drop from URL links in browsers do not work
726 <td width="60" nowrap>
728 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
734 <!-- JAL-2124 -->Updated Spanish translations.
737 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
738 for importing structure data to Jalview. Enables mmCIF and
742 <!-- JAL-192 --->Alignment ruler shows positions relative to
746 <!-- JAL-2202 -->Position/residue shown in status bar when
747 mousing over sequence associated annotation
750 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
754 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
755 '()', canonical '[]' and invalid '{}' base pair populations
759 <!-- JAL-2092 -->Feature settings popup menu options for
760 showing or hiding columns containing a feature
763 <!-- JAL-1557 -->Edit selected group by double clicking on
764 group and sequence associated annotation labels
767 <!-- JAL-2236 -->Sequence name added to annotation label in
768 select/hide columns by annotation and colour by annotation
772 </ul> <em>Application</em>
775 <!-- JAL-2050-->Automatically hide introns when opening a
779 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
783 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
784 structure mappings with the EMBL-EBI PDBe SIFTS database
787 <!-- JAL-2079 -->Updated download sites used for Rfam and
788 Pfam sources to xfam.org
791 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
794 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
795 over sequences in Jalview
798 <!-- JAL-2027-->Support for reverse-complement coding
799 regions in ENA and EMBL
802 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
803 for record retrieval via ENA rest API
806 <!-- JAL-2027 -->Support for ENA CDS records with reverse
810 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
811 groovy script execution
814 <!-- JAL-1812 -->New 'execute Groovy script' option in an
815 alignment window's Calculate menu
818 <!-- JAL-1812 -->Allow groovy scripts that call
819 Jalview.getAlignFrames() to run in headless mode
822 <!-- JAL-2068 -->Support for creating new alignment
823 calculation workers from groovy scripts
826 <!-- JAL-1369 --->Store/restore reference sequence in
830 <!-- JAL-1803 -->Chain codes for a sequence's PDB
831 associations are now saved/restored from project
834 <!-- JAL-1993 -->Database selection dialog always shown
835 before sequence fetcher is opened
838 <!-- JAL-2183 -->Double click on an entry in Jalview's
839 database chooser opens a sequence fetcher
842 <!-- JAL-1563 -->Free-text search client for UniProt using
846 <!-- JAL-2168 -->-nonews command line parameter to prevent
847 the news reader opening
850 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
851 querying stored in preferences
854 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
858 <!-- JAL-1977-->Tooltips shown on database chooser
861 <!-- JAL-391 -->Reverse complement function in calculate
862 menu for nucleotide sequences
865 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
866 and feature counts preserves alignment ordering (and
867 debugged for complex feature sets).
870 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
871 viewing structures with Jalview 2.10
874 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
875 genome, transcript CCDS and gene ids via the Ensembl and
876 Ensembl Genomes REST API
879 <!-- JAL-2049 -->Protein sequence variant annotation
880 computed for 'sequence_variant' annotation on CDS regions
884 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
888 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
889 Ref Fetcher fails to match, or otherwise updates sequence
890 data from external database records.
893 <!-- JAL-2154 -->Revised Jalview Project format for
894 efficient recovery of sequence coding and alignment
895 annotation relationships.
897 </ul> <!-- <em>Applet</em>
908 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
912 <!-- JAL-2018-->Export features in Jalview format (again)
913 includes graduated colourschemes
916 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
917 working with big alignments and lots of hidden columns
920 <!-- JAL-2053-->Hidden column markers not always rendered
921 at right of alignment window
924 <!-- JAL-2067 -->Tidied up links in help file table of
928 <!-- JAL-2072 -->Feature based tree calculation not shown
932 <!-- JAL-2075 -->Hidden columns ignored during feature
933 based tree calculation
936 <!-- JAL-2065 -->Alignment view stops updating when show
937 unconserved enabled for group on alignment
940 <!-- JAL-2086 -->Cannot insert gaps into sequence when
944 <!-- JAL-2146 -->Alignment column in status incorrectly
945 shown as "Sequence position" when mousing over
949 <!-- JAL-2099 -->Incorrect column numbers in ruler when
950 hidden columns present
953 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
954 user created annotation added to alignment
957 <!-- JAL-1841 -->RNA Structure consensus only computed for
958 '()' base pair annotation
961 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
962 in zero scores for all base pairs in RNA Structure
966 <!-- JAL-2174-->Extend selection with columns containing
970 <!-- JAL-2275 -->Pfam format writer puts extra space at
971 beginning of sequence
974 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
978 <!-- JAL-2238 -->Cannot create groups on an alignment from
979 from a tree when t-coffee scores are shown
982 <!-- JAL-1836,1967 -->Cannot import and view PDB
983 structures with chains containing negative resnums (4q4h)
986 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
990 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
991 to Clustal, PIR and PileUp output
994 <!-- JAL-2008 -->Reordering sequence features that are
995 not visible causes alignment window to repaint
998 <!-- JAL-2006 -->Threshold sliders don't work in
999 graduated colour and colour by annotation row for e-value
1000 scores associated with features and annotation rows
1003 <!-- JAL-1797 -->amino acid physicochemical conservation
1004 calculation should be case independent
1007 <!-- JAL-2173 -->Remove annotation also updates hidden
1011 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1012 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1013 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1016 <!-- JAL-2065 -->Null pointer exceptions and redraw
1017 problems when reference sequence defined and 'show
1018 non-conserved' enabled
1021 <!-- JAL-1306 -->Quality and Conservation are now shown on
1022 load even when Consensus calculation is disabled
1025 <!-- JAL-1932 -->Remove right on penultimate column of
1026 alignment does nothing
1029 <em>Application</em>
1032 <!-- JAL-1552-->URLs and links can't be imported by
1033 drag'n'drop on OSX when launched via webstart (note - not
1034 yet fixed for El Capitan)
1037 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1038 output when running on non-gb/us i18n platforms
1041 <!-- JAL-1944 -->Error thrown when exporting a view with
1042 hidden sequences as flat-file alignment
1045 <!-- JAL-2030-->InstallAnywhere distribution fails when
1049 <!-- JAL-2080-->Jalview very slow to launch via webstart
1050 (also hotfix for 2.9.0b2)
1053 <!-- JAL-2085 -->Cannot save project when view has a
1054 reference sequence defined
1057 <!-- JAL-1011 -->Columns are suddenly selected in other
1058 alignments and views when revealing hidden columns
1061 <!-- JAL-1989 -->Hide columns not mirrored in complement
1062 view in a cDNA/Protein splitframe
1065 <!-- JAL-1369 -->Cannot save/restore representative
1066 sequence from project when only one sequence is
1070 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1071 in Structure Chooser
1074 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1075 structure consensus didn't refresh annotation panel
1078 <!-- JAL-1962 -->View mapping in structure view shows
1079 mappings between sequence and all chains in a PDB file
1082 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1083 dialogs format columns correctly, don't display array
1084 data, sort columns according to type
1087 <!-- JAL-1975 -->Export complete shown after destination
1088 file chooser is cancelled during an image export
1091 <!-- JAL-2025 -->Error when querying PDB Service with
1092 sequence name containing special characters
1095 <!-- JAL-2024 -->Manual PDB structure querying should be
1099 <!-- JAL-2104 -->Large tooltips with broken HTML
1100 formatting don't wrap
1103 <!-- JAL-1128 -->Figures exported from wrapped view are
1104 truncated so L looks like I in consensus annotation
1107 <!-- JAL-2003 -->Export features should only export the
1108 currently displayed features for the current selection or
1112 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1113 after fetching cross-references, and restoring from
1117 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1118 followed in the structure viewer
1121 <!-- JAL-2163 -->Titles for individual alignments in
1122 splitframe not restored from project
1125 <!-- JAL-2145 -->missing autocalculated annotation at
1126 trailing end of protein alignment in transcript/product
1127 splitview when pad-gaps not enabled by default
1130 <!-- JAL-1797 -->amino acid physicochemical conservation
1134 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1135 article has been read (reopened issue due to
1136 internationalisation problems)
1139 <!-- JAL-1960 -->Only offer PDB structures in structure
1140 viewer based on sequence name, PDB and UniProt
1145 <!-- JAL-1976 -->No progress bar shown during export of
1149 <!-- JAL-2213 -->Structures not always superimposed after
1150 multiple structures are shown for one or more sequences.
1153 <!-- JAL-1370 -->Reference sequence characters should not
1154 be replaced with '.' when 'Show unconserved' format option
1158 <!-- JAL-1823 -->Cannot specify chain code when entering
1159 specific PDB id for sequence
1162 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1163 'Export hidden sequences' is enabled, but 'export hidden
1164 columns' is disabled.
1167 <!--JAL-2026-->Best Quality option in structure chooser
1168 selects lowest rather than highest resolution structures
1172 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1173 to sequence mapping in 'View Mappings' report
1176 <!-- JAL-2284 -->Unable to read old Jalview projects that
1177 contain non-XML data added after Jalvew wrote project.
1180 <!-- JAL-2118 -->Newly created annotation row reorders
1181 after clicking on it to create new annotation for a
1184 <!-- may exclude, this is an external service stability issue JAL-1941
1185 -- > RNA 3D structure not added via DSSR service</li> -->
1190 <!-- JAL-2151 -->Incorrect columns are selected when
1191 hidden columns present before start of sequence
1194 <!-- JAL-1986 -->Missing dependencies on applet pages
1198 <!-- JAL-1947 -->Overview pixel size changes when
1199 sequences are hidden in applet
1202 <!-- JAL-1996 -->Updated instructions for applet
1203 deployment on examples pages.
1210 <td width="60" nowrap>
1211 <div align="center">
1212 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1213 <em>16/10/2015</em></strong>
1216 <td><em>General</em>
1218 <li>Time stamps for signed Jalview application and applet
1223 <em>Application</em>
1225 <li>Duplicate group consensus and conservation rows
1226 shown when tree is partitioned</li>
1227 <li>Erratic behaviour when tree partitions made with
1228 multiple cDNA/Protein split views</li>
1234 <td width="60" nowrap>
1235 <div align="center">
1236 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1237 <em>8/10/2015</em></strong>
1240 <td><em>General</em>
1242 <li>Updated Spanish translations of localized text for
1244 </ul> <em>Application</em>
1246 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1247 <li>Signed OSX InstallAnywhere installer<br></li>
1248 <li>Support for per-sequence based annotations in BioJSON</li>
1249 </ul> <em>Applet</em>
1251 <li>Split frame example added to applet examples page</li>
1252 </ul> <em>Build and Deployment</em>
1255 <!-- JAL-1888 -->New ant target for running Jalview's test
1263 <li>Mapping of cDNA to protein in split frames
1264 incorrect when sequence start > 1</li>
1265 <li>Broken images in filter column by annotation dialog
1267 <li>Feature colours not parsed from features file</li>
1268 <li>Exceptions and incomplete link URLs recovered when
1269 loading a features file containing HTML tags in feature
1273 <em>Application</em>
1275 <li>Annotations corrupted after BioJS export and
1277 <li>Incorrect sequence limits after Fetch DB References
1278 with 'trim retrieved sequences'</li>
1279 <li>Incorrect warning about deleting all data when
1280 deleting selected columns</li>
1281 <li>Patch to build system for shipping properly signed
1282 JNLP templates for webstart launch</li>
1283 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1284 unreleased structures for download or viewing</li>
1285 <li>Tab/space/return keystroke operation of EMBL-PDBe
1286 fetcher/viewer dialogs works correctly</li>
1287 <li>Disabled 'minimise' button on Jalview windows
1288 running on OSX to workaround redraw hang bug</li>
1289 <li>Split cDNA/Protein view position and geometry not
1290 recovered from jalview project</li>
1291 <li>Initial enabled/disabled state of annotation menu
1292 sorter 'show autocalculated first/last' corresponds to
1294 <li>Restoring of Clustal, RNA Helices and T-Coffee
1295 color schemes from BioJSON</li>
1299 <li>Reorder sequences mirrored in cDNA/Protein split
1301 <li>Applet with Jmol examples not loading correctly</li>
1307 <td><div align="center">
1308 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1310 <td><em>General</em>
1312 <li>Linked visualisation and analysis of DNA and Protein
1315 <li>Translated cDNA alignments shown as split protein
1316 and DNA alignment views</li>
1317 <li>Codon consensus annotation for linked protein and
1318 cDNA alignment views</li>
1319 <li>Link cDNA or Protein product sequences by loading
1320 them onto Protein or cDNA alignments</li>
1321 <li>Reconstruct linked cDNA alignment from aligned
1322 protein sequences</li>
1325 <li>Jmol integration updated to Jmol v14.2.14</li>
1326 <li>Import and export of Jalview alignment views as <a
1327 href="features/bioJsonFormat.html">BioJSON</a></li>
1328 <li>New alignment annotation file statements for
1329 reference sequences and marking hidden columns</li>
1330 <li>Reference sequence based alignment shading to
1331 highlight variation</li>
1332 <li>Select or hide columns according to alignment
1334 <li>Find option for locating sequences by description</li>
1335 <li>Conserved physicochemical properties shown in amino
1336 acid conservation row</li>
1337 <li>Alignments can be sorted by number of RNA helices</li>
1338 </ul> <em>Application</em>
1340 <li>New cDNA/Protein analysis capabilities
1342 <li>Get Cross-References should open a Split Frame
1343 view with cDNA/Protein</li>
1344 <li>Detect when nucleotide sequences and protein
1345 sequences are placed in the same alignment</li>
1346 <li>Split cDNA/Protein views are saved in Jalview
1351 <li>Use REST API to talk to Chimera</li>
1352 <li>Selected regions in Chimera are highlighted in linked
1353 Jalview windows</li>
1355 <li>VARNA RNA viewer updated to v3.93</li>
1356 <li>VARNA views are saved in Jalview Projects</li>
1357 <li>Pseudoknots displayed as Jalview RNA annotation can
1358 be shown in VARNA</li>
1360 <li>Make groups for selection uses marked columns as well
1361 as the active selected region</li>
1363 <li>Calculate UPGMA and NJ trees using sequence feature
1365 <li>New Export options
1367 <li>New Export Settings dialog to control hidden
1368 region export in flat file generation</li>
1370 <li>Export alignment views for display with the <a
1371 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1373 <li>Export scrollable SVG in HTML page</li>
1374 <li>Optional embedding of BioJSON data when exporting
1375 alignment figures to HTML</li>
1377 <li>3D structure retrieval and display
1379 <li>Free text and structured queries with the PDBe
1381 <li>PDBe Search API based discovery and selection of
1382 PDB structures for a sequence set</li>
1386 <li>JPred4 employed for protein secondary structure
1388 <li>Hide Insertions menu option to hide unaligned columns
1389 for one or a group of sequences</li>
1390 <li>Automatically hide insertions in alignments imported
1391 from the JPred4 web server</li>
1392 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1393 system on OSX<br />LGPL libraries courtesy of <a
1394 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1396 <li>changed 'View nucleotide structure' submenu to 'View
1397 VARNA 2D Structure'</li>
1398 <li>change "View protein structure" menu option to "3D
1401 </ul> <em>Applet</em>
1403 <li>New layout for applet example pages</li>
1404 <li>New parameters to enable SplitFrame view
1405 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1406 <li>New example demonstrating linked viewing of cDNA and
1407 Protein alignments</li>
1408 </ul> <em>Development and deployment</em>
1410 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1411 <li>Include installation type and git revision in build
1412 properties and console log output</li>
1413 <li>Jalview Github organisation, and new github site for
1414 storing BioJsMSA Templates</li>
1415 <li>Jalview's unit tests now managed with TestNG</li>
1418 <!-- <em>General</em>
1420 </ul> --> <!-- issues resolved --> <em>Application</em>
1422 <li>Escape should close any open find dialogs</li>
1423 <li>Typo in select-by-features status report</li>
1424 <li>Consensus RNA secondary secondary structure
1425 predictions are not highlighted in amber</li>
1426 <li>Missing gap character in v2.7 example file means
1427 alignment appears unaligned when pad-gaps is not enabled</li>
1428 <li>First switch to RNA Helices colouring doesn't colour
1429 associated structure views</li>
1430 <li>ID width preference option is greyed out when auto
1431 width checkbox not enabled</li>
1432 <li>Stopped a warning dialog from being shown when
1433 creating user defined colours</li>
1434 <li>'View Mapping' in structure viewer shows sequence
1435 mappings for just that viewer's sequences</li>
1436 <li>Workaround for superposing PDB files containing
1437 multiple models in Chimera</li>
1438 <li>Report sequence position in status bar when hovering
1439 over Jmol structure</li>
1440 <li>Cannot output gaps as '.' symbols with Selection ->
1441 output to text box</li>
1442 <li>Flat file exports of alignments with hidden columns
1443 have incorrect sequence start/end</li>
1444 <li>'Aligning' a second chain to a Chimera structure from
1446 <li>Colour schemes applied to structure viewers don't
1447 work for nucleotide</li>
1448 <li>Loading/cut'n'pasting an empty or invalid file leads
1449 to a grey/invisible alignment window</li>
1450 <li>Exported Jpred annotation from a sequence region
1451 imports to different position</li>
1452 <li>Space at beginning of sequence feature tooltips shown
1453 on some platforms</li>
1454 <li>Chimera viewer 'View | Show Chain' menu is not
1456 <li>'New View' fails with a Null Pointer Exception in
1457 console if Chimera has been opened</li>
1458 <li>Mouseover to Chimera not working</li>
1459 <li>Miscellaneous ENA XML feature qualifiers not
1461 <li>NPE in annotation renderer after 'Extract Scores'</li>
1462 <li>If two structures in one Chimera window, mouseover of
1463 either sequence shows on first structure</li>
1464 <li>'Show annotations' options should not make
1465 non-positional annotations visible</li>
1466 <li>Subsequence secondary structure annotation not shown
1467 in right place after 'view flanking regions'</li>
1468 <li>File Save As type unset when current file format is
1470 <li>Save as '.jar' option removed for saving Jalview
1472 <li>Colour by Sequence colouring in Chimera more
1474 <li>Cannot 'add reference annotation' for a sequence in
1475 several views on same alignment</li>
1476 <li>Cannot show linked products for EMBL / ENA records</li>
1477 <li>Jalview's tooltip wraps long texts containing no
1479 </ul> <em>Applet</em>
1481 <li>Jmol to JalviewLite mouseover/link not working</li>
1482 <li>JalviewLite can't import sequences with ID
1483 descriptions containing angle brackets</li>
1484 </ul> <em>General</em>
1486 <li>Cannot export and reimport RNA secondary structure
1487 via jalview annotation file</li>
1488 <li>Random helix colour palette for colour by annotation
1489 with RNA secondary structure</li>
1490 <li>Mouseover to cDNA from STOP residue in protein
1491 translation doesn't work.</li>
1492 <li>hints when using the select by annotation dialog box</li>
1493 <li>Jmol alignment incorrect if PDB file has alternate CA
1495 <li>FontChooser message dialog appears to hang after
1496 choosing 1pt font</li>
1497 <li>Peptide secondary structure incorrectly imported from
1498 annotation file when annotation display text includes 'e' or
1500 <li>Cannot set colour of new feature type whilst creating
1502 <li>cDNA translation alignment should not be sequence
1503 order dependent</li>
1504 <li>'Show unconserved' doesn't work for lower case
1506 <li>Nucleotide ambiguity codes involving R not recognised</li>
1507 </ul> <em>Deployment and Documentation</em>
1509 <li>Applet example pages appear different to the rest of
1510 www.jalview.org</li>
1511 </ul> <em>Application Known issues</em>
1513 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1514 <li>Misleading message appears after trying to delete
1516 <li>Jalview icon not shown in dock after InstallAnywhere
1517 version launches</li>
1518 <li>Fetching EMBL reference for an RNA sequence results
1519 fails with a sequence mismatch</li>
1520 <li>Corrupted or unreadable alignment display when
1521 scrolling alignment to right</li>
1522 <li>ArrayIndexOutOfBoundsException thrown when remove
1523 empty columns called on alignment with ragged gapped ends</li>
1524 <li>auto calculated alignment annotation rows do not get
1525 placed above or below non-autocalculated rows</li>
1526 <li>Jalview dekstop becomes sluggish at full screen in
1527 ultra-high resolution</li>
1528 <li>Cannot disable consensus calculation independently of
1529 quality and conservation</li>
1530 <li>Mouseover highlighting between cDNA and protein can
1531 become sluggish with more than one splitframe shown</li>
1532 </ul> <em>Applet Known Issues</em>
1534 <li>Core PDB parsing code requires Jmol</li>
1535 <li>Sequence canvas panel goes white when alignment
1536 window is being resized</li>
1542 <td><div align="center">
1543 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1545 <td><em>General</em>
1547 <li>Updated Java code signing certificate donated by
1549 <li>Features and annotation preserved when performing
1550 pairwise alignment</li>
1551 <li>RNA pseudoknot annotation can be
1552 imported/exported/displayed</li>
1553 <li>'colour by annotation' can colour by RNA and
1554 protein secondary structure</li>
1555 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1556 post-hoc with 2.9 release</em>)
1559 </ul> <em>Application</em>
1561 <li>Extract and display secondary structure for sequences
1562 with 3D structures</li>
1563 <li>Support for parsing RNAML</li>
1564 <li>Annotations menu for layout
1566 <li>sort sequence annotation rows by alignment</li>
1567 <li>place sequence annotation above/below alignment
1570 <li>Output in Stockholm format</li>
1571 <li>Internationalisation: improved Spanish (es)
1573 <li>Structure viewer preferences tab</li>
1574 <li>Disorder and Secondary Structure annotation tracks
1575 shared between alignments</li>
1576 <li>UCSF Chimera launch and linked highlighting from
1578 <li>Show/hide all sequence associated annotation rows for
1579 all or current selection</li>
1580 <li>disorder and secondary structure predictions
1581 available as dataset annotation</li>
1582 <li>Per-sequence rna helices colouring</li>
1585 <li>Sequence database accessions imported when fetching
1586 alignments from Rfam</li>
1587 <li>update VARNA version to 3.91</li>
1589 <li>New groovy scripts for exporting aligned positions,
1590 conservation values, and calculating sum of pairs scores.</li>
1591 <li>Command line argument to set default JABAWS server</li>
1592 <li>include installation type in build properties and
1593 console log output</li>
1594 <li>Updated Jalview project format to preserve dataset
1598 <!-- issues resolved --> <em>Application</em>
1600 <li>Distinguish alignment and sequence associated RNA
1601 structure in structure->view->VARNA</li>
1602 <li>Raise dialog box if user deletes all sequences in an
1604 <li>Pressing F1 results in documentation opening twice</li>
1605 <li>Sequence feature tooltip is wrapped</li>
1606 <li>Double click on sequence associated annotation
1607 selects only first column</li>
1608 <li>Redundancy removal doesn't result in unlinked
1609 leaves shown in tree</li>
1610 <li>Undos after several redundancy removals don't undo
1612 <li>Hide sequence doesn't hide associated annotation</li>
1613 <li>User defined colours dialog box too big to fit on
1614 screen and buttons not visible</li>
1615 <li>author list isn't updated if already written to
1616 Jalview properties</li>
1617 <li>Popup menu won't open after retrieving sequence
1619 <li>File open window for associate PDB doesn't open</li>
1620 <li>Left-then-right click on a sequence id opens a
1621 browser search window</li>
1622 <li>Cannot open sequence feature shading/sort popup menu
1623 in feature settings dialog</li>
1624 <li>better tooltip placement for some areas of Jalview
1626 <li>Allow addition of JABAWS Server which doesn't
1627 pass validation</li>
1628 <li>Web services parameters dialog box is too large to
1630 <li>Muscle nucleotide alignment preset obscured by
1632 <li>JABAWS preset submenus don't contain newly
1633 defined user preset</li>
1634 <li>MSA web services warns user if they were launched
1635 with invalid input</li>
1636 <li>Jalview cannot contact DAS Registy when running on
1639 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1640 'Superpose with' submenu not shown when new view
1644 </ul> <!-- <em>Applet</em>
1646 </ul> <em>General</em>
1648 </ul>--> <em>Deployment and Documentation</em>
1650 <li>2G and 1G options in launchApp have no effect on
1651 memory allocation</li>
1652 <li>launchApp service doesn't automatically open
1653 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1655 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1656 InstallAnywhere reports cannot find valid JVM when Java
1657 1.7_055 is available
1659 </ul> <em>Application Known issues</em>
1662 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1663 corrupted or unreadable alignment display when scrolling
1667 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1668 retrieval fails but progress bar continues for DAS retrieval
1669 with large number of ID
1672 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1673 flatfile output of visible region has incorrect sequence
1677 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1678 rna structure consensus doesn't update when secondary
1679 structure tracks are rearranged
1682 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1683 invalid rna structure positional highlighting does not
1684 highlight position of invalid base pairs
1687 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1688 out of memory errors are not raised when saving Jalview
1689 project from alignment window file menu
1692 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1693 Switching to RNA Helices colouring doesn't propagate to
1697 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1698 colour by RNA Helices not enabled when user created
1699 annotation added to alignment
1702 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1703 Jalview icon not shown on dock in Mountain Lion/Webstart
1705 </ul> <em>Applet Known Issues</em>
1708 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1709 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1712 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1713 Jalview and Jmol example not compatible with IE9
1716 <li>Sort by annotation score doesn't reverse order
1722 <td><div align="center">
1723 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1726 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1729 <li>Internationalisation of user interface (usually
1730 called i18n support) and translation for Spanish locale</li>
1731 <li>Define/Undefine group on current selection with
1732 Ctrl-G/Shift Ctrl-G</li>
1733 <li>Improved group creation/removal options in
1734 alignment/sequence Popup menu</li>
1735 <li>Sensible precision for symbol distribution
1736 percentages shown in logo tooltip.</li>
1737 <li>Annotation panel height set according to amount of
1738 annotation when alignment first opened</li>
1739 </ul> <em>Application</em>
1741 <li>Interactive consensus RNA secondary structure
1742 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1743 <li>Select columns containing particular features from
1744 Feature Settings dialog</li>
1745 <li>View all 'representative' PDB structures for selected
1747 <li>Update Jalview project format:
1749 <li>New file extension for Jalview projects '.jvp'</li>
1750 <li>Preserve sequence and annotation dataset (to
1751 store secondary structure annotation,etc)</li>
1752 <li>Per group and alignment annotation and RNA helix
1756 <li>New similarity measures for PCA and Tree calculation
1758 <li>Experimental support for retrieval and viewing of
1759 flanking regions for an alignment</li>
1763 <!-- issues resolved --> <em>Application</em>
1765 <li>logo keeps spinning and status remains at queued or
1766 running after job is cancelled</li>
1767 <li>cannot export features from alignments imported from
1768 Jalview/VAMSAS projects</li>
1769 <li>Buggy slider for web service parameters that take
1771 <li>Newly created RNA secondary structure line doesn't
1772 have 'display all symbols' flag set</li>
1773 <li>T-COFFEE alignment score shading scheme and other
1774 annotation shading not saved in Jalview project</li>
1775 <li>Local file cannot be loaded in freshly downloaded
1777 <li>Jalview icon not shown on dock in Mountain
1779 <li>Load file from desktop file browser fails</li>
1780 <li>Occasional NPE thrown when calculating large trees</li>
1781 <li>Cannot reorder or slide sequences after dragging an
1782 alignment onto desktop</li>
1783 <li>Colour by annotation dialog throws NPE after using
1784 'extract scores' function</li>
1785 <li>Loading/cut'n'pasting an empty file leads to a grey
1786 alignment window</li>
1787 <li>Disorder thresholds rendered incorrectly after
1788 performing IUPred disorder prediction</li>
1789 <li>Multiple group annotated consensus rows shown when
1790 changing 'normalise logo' display setting</li>
1791 <li>Find shows blank dialog after 'finished searching' if
1792 nothing matches query</li>
1793 <li>Null Pointer Exceptions raised when sorting by
1794 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1796 <li>Errors in Jmol console when structures in alignment
1797 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1799 <li>Not all working JABAWS services are shown in
1801 <li>JAVAWS version of Jalview fails to launch with
1802 'invalid literal/length code'</li>
1803 <li>Annotation/RNA Helix colourschemes cannot be applied
1804 to alignment with groups (actually fixed in 2.8.0b1)</li>
1805 <li>RNA Helices and T-Coffee Scores available as default
1808 </ul> <em>Applet</em>
1810 <li>Remove group option is shown even when selection is
1812 <li>Apply to all groups ticked but colourscheme changes
1813 don't affect groups</li>
1814 <li>Documented RNA Helices and T-Coffee Scores as valid
1815 colourscheme name</li>
1816 <li>Annotation labels drawn on sequence IDs when
1817 Annotation panel is not displayed</li>
1818 <li>Increased font size for dropdown menus on OSX and
1819 embedded windows</li>
1820 </ul> <em>Other</em>
1822 <li>Consensus sequence for alignments/groups with a
1823 single sequence were not calculated</li>
1824 <li>annotation files that contain only groups imported as
1825 annotation and junk sequences</li>
1826 <li>Fasta files with sequences containing '*' incorrectly
1827 recognised as PFAM or BLC</li>
1828 <li>conservation/PID slider apply all groups option
1829 doesn't affect background (2.8.0b1)
1831 <li>redundancy highlighting is erratic at 0% and 100%</li>
1832 <li>Remove gapped columns fails for sequences with ragged
1834 <li>AMSA annotation row with leading spaces is not
1835 registered correctly on import</li>
1836 <li>Jalview crashes when selecting PCA analysis for
1837 certain alignments</li>
1838 <li>Opening the colour by annotation dialog for an
1839 existing annotation based 'use original colours'
1840 colourscheme loses original colours setting</li>
1845 <td><div align="center">
1846 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
1847 <em>30/1/2014</em></strong>
1851 <li>Trusted certificates for JalviewLite applet and
1852 Jalview Desktop application<br />Certificate was donated by
1853 <a href="https://www.certum.eu">Certum</a> to the Jalview
1854 open source project).
1856 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
1857 <li>Output in Stockholm format</li>
1858 <li>Allow import of data from gzipped files</li>
1859 <li>Export/import group and sequence associated line
1860 graph thresholds</li>
1861 <li>Nucleotide substitution matrix that supports RNA and
1862 ambiguity codes</li>
1863 <li>Allow disorder predictions to be made on the current
1864 selection (or visible selection) in the same way that JPred
1866 <li>Groovy scripting for headless Jalview operation</li>
1867 </ul> <em>Other improvements</em>
1869 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
1870 <li>COMBINE statement uses current SEQUENCE_REF and
1871 GROUP_REF scope to group annotation rows</li>
1872 <li>Support '' style escaping of quotes in Newick
1874 <li>Group options for JABAWS service by command line name</li>
1875 <li>Empty tooltip shown for JABA service options with a
1876 link but no description</li>
1877 <li>Select primary source when selecting authority in
1878 database fetcher GUI</li>
1879 <li>Add .mfa to FASTA file extensions recognised by
1881 <li>Annotation label tooltip text wrap</li>
1886 <li>Slow scrolling when lots of annotation rows are
1888 <li>Lots of NPE (and slowness) after creating RNA
1889 secondary structure annotation line</li>
1890 <li>Sequence database accessions not imported when
1891 fetching alignments from Rfam</li>
1892 <li>Incorrect SHMR submission for sequences with
1894 <li>View all structures does not always superpose
1896 <li>Option widgets in service parameters not updated to
1897 reflect user or preset settings</li>
1898 <li>Null pointer exceptions for some services without
1899 presets or adjustable parameters</li>
1900 <li>Discover PDB IDs entry in structure menu doesn't
1901 discover PDB xRefs</li>
1902 <li>Exception encountered while trying to retrieve
1903 features with DAS</li>
1904 <li>Lowest value in annotation row isn't coloured
1905 when colour by annotation (per sequence) is coloured</li>
1906 <li>Keyboard mode P jumps to start of gapped region when
1907 residue follows a gap</li>
1908 <li>Jalview appears to hang importing an alignment with
1909 Wrap as default or after enabling Wrap</li>
1910 <li>'Right click to add annotations' message
1911 shown in wrap mode when no annotations present</li>
1912 <li>Disorder predictions fail with NPE if no automatic
1913 annotation already exists on alignment</li>
1914 <li>oninit javascript function should be called after
1915 initialisation completes</li>
1916 <li>Remove redundancy after disorder prediction corrupts
1917 alignment window display</li>
1918 <li>Example annotation file in documentation is invalid</li>
1919 <li>Grouped line graph annotation rows are not exported
1920 to annotation file</li>
1921 <li>Multi-harmony analysis cannot be run when only two
1923 <li>Cannot create multiple groups of line graphs with
1924 several 'combine' statements in annotation file</li>
1925 <li>Pressing return several times causes Number Format
1926 exceptions in keyboard mode</li>
1927 <li>Multi-harmony (SHMMR) method doesn't submit
1928 correct partitions for input data</li>
1929 <li>Translation from DNA to Amino Acids fails</li>
1930 <li>Jalview fail to load newick tree with quoted label</li>
1931 <li>--headless flag isn't understood</li>
1932 <li>ClassCastException when generating EPS in headless
1934 <li>Adjusting sequence-associated shading threshold only
1935 changes one row's threshold</li>
1936 <li>Preferences and Feature settings panel panel
1937 doesn't open</li>
1938 <li>hide consensus histogram also hides conservation and
1939 quality histograms</li>
1944 <td><div align="center">
1945 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
1947 <td><em>Application</em>
1949 <li>Support for JABAWS 2.0 Services (AACon alignment
1950 conservation, protein disorder and Clustal Omega)</li>
1951 <li>JABAWS server status indicator in Web Services
1953 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
1954 in Jalview alignment window</li>
1955 <li>Updated Jalview build and deploy framework for OSX
1956 mountain lion, windows 7, and 8</li>
1957 <li>Nucleotide substitution matrix for PCA that supports
1958 RNA and ambiguity codes</li>
1960 <li>Improved sequence database retrieval GUI</li>
1961 <li>Support fetching and database reference look up
1962 against multiple DAS sources (Fetch all from in 'fetch db
1964 <li>Jalview project improvements
1966 <li>Store and retrieve the 'belowAlignment'
1967 flag for annotation</li>
1968 <li>calcId attribute to group annotation rows on the
1970 <li>Store AACon calculation settings for a view in
1971 Jalview project</li>
1975 <li>horizontal scrolling gesture support</li>
1976 <li>Visual progress indicator when PCA calculation is
1978 <li>Simpler JABA web services menus</li>
1979 <li>visual indication that web service results are still
1980 being retrieved from server</li>
1981 <li>Serialise the dialogs that are shown when Jalview
1982 starts up for first time</li>
1983 <li>Jalview user agent string for interacting with HTTP
1985 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
1987 <li>Examples directory and Groovy library included in
1988 InstallAnywhere distribution</li>
1989 </ul> <em>Applet</em>
1991 <li>RNA alignment and secondary structure annotation
1992 visualization applet example</li>
1993 </ul> <em>General</em>
1995 <li>Normalise option for consensus sequence logo</li>
1996 <li>Reset button in PCA window to return dimensions to
1998 <li>Allow seqspace or Jalview variant of alignment PCA
2000 <li>PCA with either nucleic acid and protein substitution
2002 <li>Allow windows containing HTML reports to be exported
2004 <li>Interactive display and editing of RNA secondary
2005 structure contacts</li>
2006 <li>RNA Helix Alignment Colouring</li>
2007 <li>RNA base pair logo consensus</li>
2008 <li>Parse sequence associated secondary structure
2009 information in Stockholm files</li>
2010 <li>HTML Export database accessions and annotation
2011 information presented in tooltip for sequences</li>
2012 <li>Import secondary structure from LOCARNA clustalw
2013 style RNA alignment files</li>
2014 <li>import and visualise T-COFFEE quality scores for an
2016 <li>'colour by annotation' per sequence option to
2017 shade each sequence according to its associated alignment
2019 <li>New Jalview Logo</li>
2020 </ul> <em>Documentation and Development</em>
2022 <li>documentation for score matrices used in Jalview</li>
2023 <li>New Website!</li>
2025 <td><em>Application</em>
2027 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2028 wsdbfetch REST service</li>
2029 <li>Stop windows being moved outside desktop on OSX</li>
2030 <li>Filetype associations not installed for webstart
2032 <li>Jalview does not always retrieve progress of a JABAWS
2033 job execution in full once it is complete</li>
2034 <li>revise SHMR RSBS definition to ensure alignment is
2035 uploaded via ali_file parameter</li>
2036 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2037 <li>View all structures superposed fails with exception</li>
2038 <li>Jnet job queues forever if a very short sequence is
2039 submitted for prediction</li>
2040 <li>Cut and paste menu not opened when mouse clicked on
2042 <li>Putting fractional value into integer text box in
2043 alignment parameter dialog causes Jalview to hang</li>
2044 <li>Structure view highlighting doesn't work on
2046 <li>View all structures fails with exception shown in
2048 <li>Characters in filename associated with PDBEntry not
2049 escaped in a platform independent way</li>
2050 <li>Jalview desktop fails to launch with exception when
2052 <li>Tree calculation reports 'you must have 2 or more
2053 sequences selected' when selection is empty</li>
2054 <li>Jalview desktop fails to launch with jar signature
2055 failure when java web start temporary file caching is
2057 <li>DAS Sequence retrieval with range qualification
2058 results in sequence xref which includes range qualification</li>
2059 <li>Errors during processing of command line arguments
2060 cause progress bar (JAL-898) to be removed</li>
2061 <li>Replace comma for semi-colon option not disabled for
2062 DAS sources in sequence fetcher</li>
2063 <li>Cannot close news reader when JABAWS server warning
2064 dialog is shown</li>
2065 <li>Option widgets not updated to reflect user settings</li>
2066 <li>Edited sequence not submitted to web service</li>
2067 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2068 <li>InstallAnywhere installer doesn't unpack and run
2069 on OSX Mountain Lion</li>
2070 <li>Annotation panel not given a scroll bar when
2071 sequences with alignment annotation are pasted into the
2073 <li>Sequence associated annotation rows not associated
2074 when loaded from Jalview project</li>
2075 <li>Browser launch fails with NPE on java 1.7</li>
2076 <li>JABAWS alignment marked as finished when job was
2077 cancelled or job failed due to invalid input</li>
2078 <li>NPE with v2.7 example when clicking on Tree
2079 associated with all views</li>
2080 <li>Exceptions when copy/paste sequences with grouped
2081 annotation rows to new window</li>
2082 </ul> <em>Applet</em>
2084 <li>Sequence features are momentarily displayed before
2085 they are hidden using hidefeaturegroups applet parameter</li>
2086 <li>loading features via javascript API automatically
2087 enables feature display</li>
2088 <li>scrollToColumnIn javascript API method doesn't
2090 </ul> <em>General</em>
2092 <li>Redundancy removal fails for rna alignment</li>
2093 <li>PCA calculation fails when sequence has been selected
2094 and then deselected</li>
2095 <li>PCA window shows grey box when first opened on OSX</li>
2096 <li>Letters coloured pink in sequence logo when alignment
2097 coloured with clustalx</li>
2098 <li>Choosing fonts without letter symbols defined causes
2099 exceptions and redraw errors</li>
2100 <li>Initial PCA plot view is not same as manually
2101 reconfigured view</li>
2102 <li>Grouped annotation graph label has incorrect line
2104 <li>Grouped annotation graph label display is corrupted
2105 for lots of labels</li>
2110 <div align="center">
2111 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2114 <td><em>Application</em>
2116 <li>Jalview Desktop News Reader</li>
2117 <li>Tweaked default layout of web services menu</li>
2118 <li>View/alignment association menu to enable user to
2119 easily specify which alignment a multi-structure view takes
2120 its colours/correspondences from</li>
2121 <li>Allow properties file location to be specified as URL</li>
2122 <li>Extend Jalview project to preserve associations
2123 between many alignment views and a single Jmol display</li>
2124 <li>Store annotation row height in Jalview project file</li>
2125 <li>Annotation row column label formatting attributes
2126 stored in project file</li>
2127 <li>Annotation row order for auto-calculated annotation
2128 rows preserved in Jalview project file</li>
2129 <li>Visual progress indication when Jalview state is
2130 saved using Desktop window menu</li>
2131 <li>Visual indication that command line arguments are
2132 still being processed</li>
2133 <li>Groovy script execution from URL</li>
2134 <li>Colour by annotation default min and max colours in
2136 <li>Automatically associate PDB files dragged onto an
2137 alignment with sequences that have high similarity and
2139 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2140 <li>'view structures' option to open many
2141 structures in same window</li>
2142 <li>Sort associated views menu option for tree panel</li>
2143 <li>Group all JABA and non-JABA services for a particular
2144 analysis function in its own submenu</li>
2145 </ul> <em>Applet</em>
2147 <li>Userdefined and autogenerated annotation rows for
2149 <li>Adjustment of alignment annotation pane height</li>
2150 <li>Annotation scrollbar for annotation panel</li>
2151 <li>Drag to reorder annotation rows in annotation panel</li>
2152 <li>'automaticScrolling' parameter</li>
2153 <li>Allow sequences with partial ID string matches to be
2154 annotated from GFF/Jalview features files</li>
2155 <li>Sequence logo annotation row in applet</li>
2156 <li>Absolute paths relative to host server in applet
2157 parameters are treated as such</li>
2158 <li>New in the JalviewLite javascript API:
2160 <li>JalviewLite.js javascript library</li>
2161 <li>Javascript callbacks for
2163 <li>Applet initialisation</li>
2164 <li>Sequence/alignment mouse-overs and selections</li>
2167 <li>scrollTo row and column alignment scrolling
2169 <li>Select sequence/alignment regions from javascript</li>
2170 <li>javascript structure viewer harness to pass
2171 messages between Jmol and Jalview when running as
2172 distinct applets</li>
2173 <li>sortBy method</li>
2174 <li>Set of applet and application examples shipped
2175 with documentation</li>
2176 <li>New example to demonstrate JalviewLite and Jmol
2177 javascript message exchange</li>
2179 </ul> <em>General</em>
2181 <li>Enable Jmol displays to be associated with multiple
2182 multiple alignments</li>
2183 <li>Option to automatically sort alignment with new tree</li>
2184 <li>User configurable link to enable redirects to a
2185 www.Jalview.org mirror</li>
2186 <li>Jmol colours option for Jmol displays</li>
2187 <li>Configurable newline string when writing alignment
2188 and other flat files</li>
2189 <li>Allow alignment annotation description lines to
2190 contain html tags</li>
2191 </ul> <em>Documentation and Development</em>
2193 <li>Add groovy test harness for bulk load testing to
2195 <li>Groovy script to load and align a set of sequences
2196 using a web service before displaying the result in the
2197 Jalview desktop</li>
2198 <li>Restructured javascript and applet api documentation</li>
2199 <li>Ant target to publish example html files with applet
2201 <li>Netbeans project for building Jalview from source</li>
2202 <li>ant task to create online javadoc for Jalview source</li>
2204 <td><em>Application</em>
2206 <li>User defined colourscheme throws exception when
2207 current built in colourscheme is saved as new scheme</li>
2208 <li>AlignFrame->Save in application pops up save
2209 dialog for valid filename/format</li>
2210 <li>Cannot view associated structure for UniProt sequence</li>
2211 <li>PDB file association breaks for UniProt sequence
2213 <li>Associate PDB from file dialog does not tell you
2214 which sequence is to be associated with the file</li>
2215 <li>Find All raises null pointer exception when query
2216 only matches sequence IDs</li>
2217 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2218 <li>Jalview project with Jmol views created with Jalview
2219 2.4 cannot be loaded</li>
2220 <li>Filetype associations not installed for webstart
2222 <li>Two or more chains in a single PDB file associated
2223 with sequences in different alignments do not get coloured
2224 by their associated sequence</li>
2225 <li>Visibility status of autocalculated annotation row
2226 not preserved when project is loaded</li>
2227 <li>Annotation row height and visibility attributes not
2228 stored in Jalview project</li>
2229 <li>Tree bootstraps are not preserved when saved as a
2230 Jalview project</li>
2231 <li>Envision2 workflow tooltips are corrupted</li>
2232 <li>Enabling show group conservation also enables colour
2233 by conservation</li>
2234 <li>Duplicate group associated conservation or consensus
2235 created on new view</li>
2236 <li>Annotation scrollbar not displayed after 'show
2237 all hidden annotation rows' option selected</li>
2238 <li>Alignment quality not updated after alignment
2239 annotation row is hidden then shown</li>
2240 <li>Preserve colouring of structures coloured by
2241 sequences in pre Jalview 2.7 projects</li>
2242 <li>Web service job parameter dialog is not laid out
2244 <li>Web services menu not refreshed after 'reset
2245 services' button is pressed in preferences</li>
2246 <li>Annotation off by one in Jalview v2_3 example project</li>
2247 <li>Structures imported from file and saved in project
2248 get name like jalview_pdb1234.txt when reloaded</li>
2249 <li>Jalview does not always retrieve progress of a JABAWS
2250 job execution in full once it is complete</li>
2251 </ul> <em>Applet</em>
2253 <li>Alignment height set incorrectly when lots of
2254 annotation rows are displayed</li>
2255 <li>Relative URLs in feature HTML text not resolved to
2257 <li>View follows highlighting does not work for positions
2259 <li><= shown as = in tooltip</li>
2260 <li>Export features raises exception when no features
2262 <li>Separator string used for serialising lists of IDs
2263 for javascript api is modified when separator string
2264 provided as parameter</li>
2265 <li>Null pointer exception when selecting tree leaves for
2266 alignment with no existing selection</li>
2267 <li>Relative URLs for datasources assumed to be relative
2268 to applet's codebase</li>
2269 <li>Status bar not updated after finished searching and
2270 search wraps around to first result</li>
2271 <li>StructureSelectionManager instance shared between
2272 several Jalview applets causes race conditions and memory
2274 <li>Hover tooltip and mouseover of position on structure
2275 not sent from Jmol in applet</li>
2276 <li>Certain sequences of javascript method calls to
2277 applet API fatally hang browser</li>
2278 </ul> <em>General</em>
2280 <li>View follows structure mouseover scrolls beyond
2281 position with wrapped view and hidden regions</li>
2282 <li>Find sequence position moves to wrong residue
2283 with/without hidden columns</li>
2284 <li>Sequence length given in alignment properties window
2286 <li>InvalidNumberFormat exceptions thrown when trying to
2287 import PDB like structure files</li>
2288 <li>Positional search results are only highlighted
2289 between user-supplied sequence start/end bounds</li>
2290 <li>End attribute of sequence is not validated</li>
2291 <li>Find dialog only finds first sequence containing a
2292 given sequence position</li>
2293 <li>Sequence numbering not preserved in MSF alignment
2295 <li>Jalview PDB file reader does not extract sequence
2296 from nucleotide chains correctly</li>
2297 <li>Structure colours not updated when tree partition
2298 changed in alignment</li>
2299 <li>Sequence associated secondary structure not correctly
2300 parsed in interleaved stockholm</li>
2301 <li>Colour by annotation dialog does not restore current
2303 <li>Hiding (nearly) all sequences doesn't work
2305 <li>Sequences containing lowercase letters are not
2306 properly associated with their pdb files</li>
2307 </ul> <em>Documentation and Development</em>
2309 <li>schemas/JalviewWsParamSet.xsd corrupted by
2310 ApplyCopyright tool</li>
2315 <div align="center">
2316 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2319 <td><em>Application</em>
2321 <li>New warning dialog when the Jalview Desktop cannot
2322 contact web services</li>
2323 <li>JABA service parameters for a preset are shown in
2324 service job window</li>
2325 <li>JABA Service menu entries reworded</li>
2329 <li>Modeller PIR IO broken - cannot correctly import a
2330 pir file emitted by Jalview</li>
2331 <li>Existing feature settings transferred to new
2332 alignment view created from cut'n'paste</li>
2333 <li>Improved test for mixed amino/nucleotide chains when
2334 parsing PDB files</li>
2335 <li>Consensus and conservation annotation rows
2336 occasionally become blank for all new windows</li>
2337 <li>Exception raised when right clicking above sequences
2338 in wrapped view mode</li>
2339 </ul> <em>Application</em>
2341 <li>multiple multiply aligned structure views cause cpu
2342 usage to hit 100% and computer to hang</li>
2343 <li>Web Service parameter layout breaks for long user
2344 parameter names</li>
2345 <li>Jaba service discovery hangs desktop if Jaba server
2352 <div align="center">
2353 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2356 <td><em>Application</em>
2358 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2359 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2362 <li>Web Services preference tab</li>
2363 <li>Analysis parameters dialog box and user defined
2365 <li>Improved speed and layout of Envision2 service menu</li>
2366 <li>Superpose structures using associated sequence
2368 <li>Export coordinates and projection as CSV from PCA
2370 </ul> <em>Applet</em>
2372 <li>enable javascript: execution by the applet via the
2373 link out mechanism</li>
2374 </ul> <em>Other</em>
2376 <li>Updated the Jmol Jalview interface to work with Jmol
2378 <li>The Jalview Desktop and JalviewLite applet now
2379 require Java 1.5</li>
2380 <li>Allow Jalview feature colour specification for GFF
2381 sequence annotation files</li>
2382 <li>New 'colour by label' keword in Jalview feature file
2383 type colour specification</li>
2384 <li>New Jalview Desktop Groovy API method that allows a
2385 script to check if it being run in an interactive session or
2386 in a batch operation from the Jalview command line</li>
2390 <li>clustalx colourscheme colours Ds preferentially when
2391 both D+E are present in over 50% of the column</li>
2392 </ul> <em>Application</em>
2394 <li>typo in AlignmentFrame->View->Hide->all but
2395 selected Regions menu item</li>
2396 <li>sequence fetcher replaces ',' for ';' when the ',' is
2397 part of a valid accession ID</li>
2398 <li>fatal OOM if object retrieved by sequence fetcher
2399 runs out of memory</li>
2400 <li>unhandled Out of Memory Error when viewing pca
2401 analysis results</li>
2402 <li>InstallAnywhere builds fail to launch on OS X java
2403 10.5 update 4 (due to apple Java 1.6 update)</li>
2404 <li>Installanywhere Jalview silently fails to launch</li>
2405 </ul> <em>Applet</em>
2407 <li>Jalview.getFeatureGroups() raises an
2408 ArrayIndexOutOfBoundsException if no feature groups are
2415 <div align="center">
2416 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2422 <li>Alignment prettyprinter doesn't cope with long
2424 <li>clustalx colourscheme colours Ds preferentially when
2425 both D+E are present in over 50% of the column</li>
2426 <li>nucleic acid structures retrieved from PDB do not
2427 import correctly</li>
2428 <li>More columns get selected than were clicked on when a
2429 number of columns are hidden</li>
2430 <li>annotation label popup menu not providing correct
2431 add/hide/show options when rows are hidden or none are
2433 <li>Stockholm format shown in list of readable formats,
2434 and parser copes better with alignments from RFAM.</li>
2435 <li>CSV output of consensus only includes the percentage
2436 of all symbols if sequence logo display is enabled</li>
2438 </ul> <em>Applet</em>
2440 <li>annotation panel disappears when annotation is
2442 </ul> <em>Application</em>
2444 <li>Alignment view not redrawn properly when new
2445 alignment opened where annotation panel is visible but no
2446 annotations are present on alignment</li>
2447 <li>pasted region containing hidden columns is
2448 incorrectly displayed in new alignment window</li>
2449 <li>Jalview slow to complete operations when stdout is
2450 flooded (fix is to close the Jalview console)</li>
2451 <li>typo in AlignmentFrame->View->Hide->all but
2452 selected Rregions menu item.</li>
2453 <li>inconsistent group submenu and Format submenu entry
2454 'Un' or 'Non'conserved</li>
2455 <li>Sequence feature settings are being shared by
2456 multiple distinct alignments</li>
2457 <li>group annotation not recreated when tree partition is
2459 <li>double click on group annotation to select sequences
2460 does not propagate to associated trees</li>
2461 <li>Mac OSX specific issues:
2463 <li>exception raised when mouse clicked on desktop
2464 window background</li>
2465 <li>Desktop menu placed on menu bar and application
2466 name set correctly</li>
2467 <li>sequence feature settings not wide enough for the
2468 save feature colourscheme button</li>
2477 <div align="center">
2478 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2481 <td><em>New Capabilities</em>
2483 <li>URL links generated from description line for
2484 regular-expression based URL links (applet and application)
2486 <li>Non-positional feature URL links are shown in link
2488 <li>Linked viewing of nucleic acid sequences and
2490 <li>Automatic Scrolling option in View menu to display
2491 the currently highlighted region of an alignment.</li>
2492 <li>Order an alignment by sequence length, or using the
2493 average score or total feature count for each sequence.</li>
2494 <li>Shading features by score or associated description</li>
2495 <li>Subdivide alignment and groups based on identity of
2496 selected subsequence (Make Groups from Selection).</li>
2497 <li>New hide/show options including Shift+Control+H to
2498 hide everything but the currently selected region.</li>
2499 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2500 </ul> <em>Application</em>
2502 <li>Fetch DB References capabilities and UI expanded to
2503 support retrieval from DAS sequence sources</li>
2504 <li>Local DAS Sequence sources can be added via the
2505 command line or via the Add local source dialog box.</li>
2506 <li>DAS Dbref and DbxRef feature types are parsed as
2507 database references and protein_name is parsed as
2508 description line (BioSapiens terms).</li>
2509 <li>Enable or disable non-positional feature and database
2510 references in sequence ID tooltip from View menu in
2512 <!-- <li>New hidden columns and rows and representatives capabilities
2513 in annotations file (in progress - not yet fully implemented)</li> -->
2514 <li>Group-associated consensus, sequence logos and
2515 conservation plots</li>
2516 <li>Symbol distributions for each column can be exported
2517 and visualized as sequence logos</li>
2518 <li>Optionally scale multi-character column labels to fit
2519 within each column of annotation row<!-- todo for applet -->
2521 <li>Optional automatic sort of associated alignment view
2522 when a new tree is opened.</li>
2523 <li>Jalview Java Console</li>
2524 <li>Better placement of desktop window when moving
2525 between different screens.</li>
2526 <li>New preference items for sequence ID tooltip and
2527 consensus annotation</li>
2528 <li>Client to submit sequences and IDs to Envision2
2530 <li><em>Vamsas Capabilities</em>
2532 <li>Improved VAMSAS synchronization (Jalview archive
2533 used to preserve views, structures, and tree display
2535 <li>Import of vamsas documents from disk or URL via
2537 <li>Sharing of selected regions between views and
2538 with other VAMSAS applications (Experimental feature!)</li>
2539 <li>Updated API to VAMSAS version 0.2</li>
2541 </ul> <em>Applet</em>
2543 <li>Middle button resizes annotation row height</li>
2546 <li>sortByTree (true/false) - automatically sort the
2547 associated alignment view by the tree when a new tree is
2549 <li>showTreeBootstraps (true/false) - show or hide
2550 branch bootstraps (default is to show them if available)</li>
2551 <li>showTreeDistances (true/false) - show or hide
2552 branch lengths (default is to show them if available)</li>
2553 <li>showUnlinkedTreeNodes (true/false) - indicate if
2554 unassociated nodes should be highlighted in the tree
2556 <li>heightScale and widthScale (1.0 or more) -
2557 increase the height or width of a cell in the alignment
2558 grid relative to the current font size.</li>
2561 <li>Non-positional features displayed in sequence ID
2563 </ul> <em>Other</em>
2565 <li>Features format: graduated colour definitions and
2566 specification of feature scores</li>
2567 <li>Alignment Annotations format: new keywords for group
2568 associated annotation (GROUP_REF) and annotation row display
2569 properties (ROW_PROPERTIES)</li>
2570 <li>XML formats extended to support graduated feature
2571 colourschemes, group associated annotation, and profile
2572 visualization settings.</li></td>
2575 <li>Source field in GFF files parsed as feature source
2576 rather than description</li>
2577 <li>Non-positional features are now included in sequence
2578 feature and gff files (controlled via non-positional feature
2579 visibility in tooltip).</li>
2580 <li>URL links generated for all feature links (bugfix)</li>
2581 <li>Added URL embedding instructions to features file
2583 <li>Codons containing ambiguous nucleotides translated as
2584 'X' in peptide product</li>
2585 <li>Match case switch in find dialog box works for both
2586 sequence ID and sequence string and query strings do not
2587 have to be in upper case to match case-insensitively.</li>
2588 <li>AMSA files only contain first column of
2589 multi-character column annotation labels</li>
2590 <li>Jalview Annotation File generation/parsing consistent
2591 with documentation (e.g. Stockholm annotation can be
2592 exported and re-imported)</li>
2593 <li>PDB files without embedded PDB IDs given a friendly
2595 <li>Find incrementally searches ID string matches as well
2596 as subsequence matches, and correctly reports total number
2600 <li>Better handling of exceptions during sequence
2602 <li>Dasobert generated non-positional feature URL
2603 link text excludes the start_end suffix</li>
2604 <li>DAS feature and source retrieval buttons disabled
2605 when fetch or registry operations in progress.</li>
2606 <li>PDB files retrieved from URLs are cached properly</li>
2607 <li>Sequence description lines properly shared via
2609 <li>Sequence fetcher fetches multiple records for all
2611 <li>Ensured that command line das feature retrieval
2612 completes before alignment figures are generated.</li>
2613 <li>Reduced time taken when opening file browser for
2615 <li>isAligned check prior to calculating tree, PCA or
2616 submitting an MSA to JNet now excludes hidden sequences.</li>
2617 <li>User defined group colours properly recovered
2618 from Jalview projects.</li>
2627 <div align="center">
2628 <strong>2.4.0.b2</strong><br> 28/10/2009
2633 <li>Experimental support for google analytics usage
2635 <li>Jalview privacy settings (user preferences and docs).</li>
2640 <li>Race condition in applet preventing startup in
2642 <li>Exception when feature created from selection beyond
2643 length of sequence.</li>
2644 <li>Allow synthetic PDB files to be imported gracefully</li>
2645 <li>Sequence associated annotation rows associate with
2646 all sequences with a given id</li>
2647 <li>Find function matches case-insensitively for sequence
2648 ID string searches</li>
2649 <li>Non-standard characters do not cause pairwise
2650 alignment to fail with exception</li>
2651 </ul> <em>Application Issues</em>
2653 <li>Sequences are now validated against EMBL database</li>
2654 <li>Sequence fetcher fetches multiple records for all
2656 </ul> <em>InstallAnywhere Issues</em>
2658 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2659 issue with installAnywhere mechanism)</li>
2660 <li>Command line launching of JARs from InstallAnywhere
2661 version (java class versioning error fixed)</li>
2668 <div align="center">
2669 <strong>2.4</strong><br> 27/8/2008
2672 <td><em>User Interface</em>
2674 <li>Linked highlighting of codon and amino acid from
2675 translation and protein products</li>
2676 <li>Linked highlighting of structure associated with
2677 residue mapping to codon position</li>
2678 <li>Sequence Fetcher provides example accession numbers
2679 and 'clear' button</li>
2680 <li>MemoryMonitor added as an option under Desktop's
2682 <li>Extract score function to parse whitespace separated
2683 numeric data in description line</li>
2684 <li>Column labels in alignment annotation can be centred.</li>
2685 <li>Tooltip for sequence associated annotation give name
2687 </ul> <em>Web Services and URL fetching</em>
2689 <li>JPred3 web service</li>
2690 <li>Prototype sequence search client (no public services
2692 <li>Fetch either seed alignment or full alignment from
2694 <li>URL Links created for matching database cross
2695 references as well as sequence ID</li>
2696 <li>URL Links can be created using regular-expressions</li>
2697 </ul> <em>Sequence Database Connectivity</em>
2699 <li>Retrieval of cross-referenced sequences from other
2701 <li>Generalised database reference retrieval and
2702 validation to all fetchable databases</li>
2703 <li>Fetch sequences from DAS sources supporting the
2704 sequence command</li>
2705 </ul> <em>Import and Export</em>
2706 <li>export annotation rows as CSV for spreadsheet import</li>
2707 <li>Jalview projects record alignment dataset associations,
2708 EMBL products, and cDNA sequence mappings</li>
2709 <li>Sequence Group colour can be specified in Annotation
2711 <li>Ad-hoc colouring of group in Annotation File using RGB
2712 triplet as name of colourscheme</li>
2713 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2715 <li>treenode binding for VAMSAS tree exchange</li>
2716 <li>local editing and update of sequences in VAMSAS
2717 alignments (experimental)</li>
2718 <li>Create new or select existing session to join</li>
2719 <li>load and save of vamsas documents</li>
2720 </ul> <em>Application command line</em>
2722 <li>-tree parameter to open trees (introduced for passing
2724 <li>-fetchfrom command line argument to specify nicknames
2725 of DAS servers to query for alignment features</li>
2726 <li>-dasserver command line argument to add new servers
2727 that are also automatically queried for features</li>
2728 <li>-groovy command line argument executes a given groovy
2729 script after all input data has been loaded and parsed</li>
2730 </ul> <em>Applet-Application data exchange</em>
2732 <li>Trees passed as applet parameters can be passed to
2733 application (when using "View in full
2734 application")</li>
2735 </ul> <em>Applet Parameters</em>
2737 <li>feature group display control parameter</li>
2738 <li>debug parameter</li>
2739 <li>showbutton parameter</li>
2740 </ul> <em>Applet API methods</em>
2742 <li>newView public method</li>
2743 <li>Window (current view) specific get/set public methods</li>
2744 <li>Feature display control methods</li>
2745 <li>get list of currently selected sequences</li>
2746 </ul> <em>New Jalview distribution features</em>
2748 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2749 <li>RELEASE file gives build properties for the latest
2750 Jalview release.</li>
2751 <li>Java 1.1 Applet build made easier and donotobfuscate
2752 property controls execution of obfuscator</li>
2753 <li>Build target for generating source distribution</li>
2754 <li>Debug flag for javacc</li>
2755 <li>.jalview_properties file is documented (slightly) in
2756 jalview.bin.Cache</li>
2757 <li>Continuous Build Integration for stable and
2758 development version of Application, Applet and source
2763 <li>selected region output includes visible annotations
2764 (for certain formats)</li>
2765 <li>edit label/displaychar contains existing label/char
2767 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2768 <li>shorter peptide product names from EMBL records</li>
2769 <li>Newick string generator makes compact representations</li>
2770 <li>bootstrap values parsed correctly for tree files with
2772 <li>pathological filechooser bug avoided by not allowing
2773 filenames containing a ':'</li>
2774 <li>Fixed exception when parsing GFF files containing
2775 global sequence features</li>
2776 <li>Alignment datasets are finalized only when number of
2777 references from alignment sequences goes to zero</li>
2778 <li>Close of tree branch colour box without colour
2779 selection causes cascading exceptions</li>
2780 <li>occasional negative imgwidth exceptions</li>
2781 <li>better reporting of non-fatal warnings to user when
2782 file parsing fails.</li>
2783 <li>Save works when Jalview project is default format</li>
2784 <li>Save as dialog opened if current alignment format is
2785 not a valid output format</li>
2786 <li>UniProt canonical names introduced for both das and
2788 <li>Histidine should be midblue (not pink!) in Zappo</li>
2789 <li>error messages passed up and output when data read
2791 <li>edit undo recovers previous dataset sequence when
2792 sequence is edited</li>
2793 <li>allow PDB files without pdb ID HEADER lines (like
2794 those generated by MODELLER) to be read in properly</li>
2795 <li>allow reading of JPred concise files as a normal
2797 <li>Stockholm annotation parsing and alignment properties
2798 import fixed for PFAM records</li>
2799 <li>Structure view windows have correct name in Desktop
2801 <li>annotation consisting of sequence associated scores
2802 can be read and written correctly to annotation file</li>
2803 <li>Aligned cDNA translation to aligned peptide works
2805 <li>Fixed display of hidden sequence markers and
2806 non-italic font for representatives in Applet</li>
2807 <li>Applet Menus are always embedded in applet window on
2809 <li>Newly shown features appear at top of stack (in
2811 <li>Annotations added via parameter not drawn properly
2812 due to null pointer exceptions</li>
2813 <li>Secondary structure lines are drawn starting from
2814 first column of alignment</li>
2815 <li>UniProt XML import updated for new schema release in
2817 <li>Sequence feature to sequence ID match for Features
2818 file is case-insensitive</li>
2819 <li>Sequence features read from Features file appended to
2820 all sequences with matching IDs</li>
2821 <li>PDB structure coloured correctly for associated views
2822 containing a sub-sequence</li>
2823 <li>PDB files can be retrieved by applet from Jar files</li>
2824 <li>feature and annotation file applet parameters
2825 referring to different directories are retrieved correctly</li>
2826 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
2827 <li>Fixed application hang whilst waiting for
2828 splash-screen version check to complete</li>
2829 <li>Applet properly URLencodes input parameter values
2830 when passing them to the launchApp service</li>
2831 <li>display name and local features preserved in results
2832 retrieved from web service</li>
2833 <li>Visual delay indication for sequence retrieval and
2834 sequence fetcher initialisation</li>
2835 <li>updated Application to use DAS 1.53e version of
2836 dasobert DAS client</li>
2837 <li>Re-instated Full AMSA support and .amsa file
2839 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
2847 <div align="center">
2848 <strong>2.3</strong><br> 9/5/07
2853 <li>Jmol 11.0.2 integration</li>
2854 <li>PDB views stored in Jalview XML files</li>
2855 <li>Slide sequences</li>
2856 <li>Edit sequence in place</li>
2857 <li>EMBL CDS features</li>
2858 <li>DAS Feature mapping</li>
2859 <li>Feature ordering</li>
2860 <li>Alignment Properties</li>
2861 <li>Annotation Scores</li>
2862 <li>Sort by scores</li>
2863 <li>Feature/annotation editing in applet</li>
2868 <li>Headless state operation in 2.2.1</li>
2869 <li>Incorrect and unstable DNA pairwise alignment</li>
2870 <li>Cut and paste of sequences with annotation</li>
2871 <li>Feature group display state in XML</li>
2872 <li>Feature ordering in XML</li>
2873 <li>blc file iteration selection using filename # suffix</li>
2874 <li>Stockholm alignment properties</li>
2875 <li>Stockhom alignment secondary structure annotation</li>
2876 <li>2.2.1 applet had no feature transparency</li>
2877 <li>Number pad keys can be used in cursor mode</li>
2878 <li>Structure Viewer mirror image resolved</li>
2885 <div align="center">
2886 <strong>2.2.1</strong><br> 12/2/07
2891 <li>Non standard characters can be read and displayed
2892 <li>Annotations/Features can be imported/exported to the
2894 <li>Applet allows editing of sequence/annotation/group
2895 name & description
2896 <li>Preference setting to display sequence name in
2898 <li>Annotation file format extended to allow
2899 Sequence_groups to be defined
2900 <li>Default opening of alignment overview panel can be
2901 specified in preferences
2902 <li>PDB residue numbering annotation added to associated
2908 <li>Applet crash under certain Linux OS with Java 1.6
2910 <li>Annotation file export / import bugs fixed
2911 <li>PNG / EPS image output bugs fixed
2917 <div align="center">
2918 <strong>2.2</strong><br> 27/11/06
2923 <li>Multiple views on alignment
2924 <li>Sequence feature editing
2925 <li>"Reload" alignment
2926 <li>"Save" to current filename
2927 <li>Background dependent text colour
2928 <li>Right align sequence ids
2929 <li>User-defined lower case residue colours
2932 <li>Menu item accelerator keys
2933 <li>Control-V pastes to current alignment
2934 <li>Cancel button for DAS Feature Fetching
2935 <li>PCA and PDB Viewers zoom via mouse roller
2936 <li>User-defined sub-tree colours and sub-tree selection
2938 <li>'New Window' button on the 'Output to Text box'
2943 <li>New memory efficient Undo/Redo System
2944 <li>Optimised symbol lookups and conservation/consensus
2946 <li>Region Conservation/Consensus recalculated after
2948 <li>Fixed Remove Empty Columns Bug (empty columns at end
2950 <li>Slowed DAS Feature Fetching for increased robustness.
2952 <li>Made angle brackets in ASCII feature descriptions
2954 <li>Re-instated Zoom function for PCA
2955 <li>Sequence descriptions conserved in web service
2957 <li>UniProt ID discoverer uses any word separated by
2959 <li>WsDbFetch query/result association resolved
2960 <li>Tree leaf to sequence mapping improved
2961 <li>Smooth fonts switch moved to FontChooser dialog box.
2968 <div align="center">
2969 <strong>2.1.1</strong><br> 12/9/06
2974 <li>Copy consensus sequence to clipboard</li>
2979 <li>Image output - rightmost residues are rendered if
2980 sequence id panel has been resized</li>
2981 <li>Image output - all offscreen group boundaries are
2983 <li>Annotation files with sequence references - all
2984 elements in file are relative to sequence position</li>
2985 <li>Mac Applet users can use Alt key for group editing</li>
2991 <div align="center">
2992 <strong>2.1</strong><br> 22/8/06
2997 <li>MAFFT Multiple Alignment in default Web Service list</li>
2998 <li>DAS Feature fetching</li>
2999 <li>Hide sequences and columns</li>
3000 <li>Export Annotations and Features</li>
3001 <li>GFF file reading / writing</li>
3002 <li>Associate structures with sequences from local PDB
3004 <li>Add sequences to exisiting alignment</li>
3005 <li>Recently opened files / URL lists</li>
3006 <li>Applet can launch the full application</li>
3007 <li>Applet has transparency for features (Java 1.2
3009 <li>Applet has user defined colours parameter</li>
3010 <li>Applet can load sequences from parameter
3011 "sequence<em>x</em>"
3017 <li>Redundancy Panel reinstalled in the Applet</li>
3018 <li>Monospaced font - EPS / rescaling bug fixed</li>
3019 <li>Annotation files with sequence references bug fixed</li>
3025 <div align="center">
3026 <strong>2.08.1</strong><br> 2/5/06
3031 <li>Change case of selected region from Popup menu</li>
3032 <li>Choose to match case when searching</li>
3033 <li>Middle mouse button and mouse movement can compress /
3034 expand the visible width and height of the alignment</li>
3039 <li>Annotation Panel displays complete JNet results</li>
3045 <div align="center">
3046 <strong>2.08b</strong><br> 18/4/06
3052 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3053 <li>Righthand label on wrapped alignments shows correct
3060 <div align="center">
3061 <strong>2.08</strong><br> 10/4/06
3066 <li>Editing can be locked to the selection area</li>
3067 <li>Keyboard editing</li>
3068 <li>Create sequence features from searches</li>
3069 <li>Precalculated annotations can be loaded onto
3071 <li>Features file allows grouping of features</li>
3072 <li>Annotation Colouring scheme added</li>
3073 <li>Smooth fonts off by default - Faster rendering</li>
3074 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3079 <li>Drag & Drop fixed on Linux</li>
3080 <li>Jalview Archive file faster to load/save, sequence
3081 descriptions saved.</li>
3087 <div align="center">
3088 <strong>2.07</strong><br> 12/12/05
3093 <li>PDB Structure Viewer enhanced</li>
3094 <li>Sequence Feature retrieval and display enhanced</li>
3095 <li>Choose to output sequence start-end after sequence
3096 name for file output</li>
3097 <li>Sequence Fetcher WSDBFetch@EBI</li>
3098 <li>Applet can read feature files, PDB files and can be
3099 used for HTML form input</li>
3104 <li>HTML output writes groups and features</li>
3105 <li>Group editing is Control and mouse click</li>
3106 <li>File IO bugs</li>
3112 <div align="center">
3113 <strong>2.06</strong><br> 28/9/05
3118 <li>View annotations in wrapped mode</li>
3119 <li>More options for PCA viewer</li>
3124 <li>GUI bugs resolved</li>
3125 <li>Runs with -nodisplay from command line</li>
3131 <div align="center">
3132 <strong>2.05b</strong><br> 15/9/05
3137 <li>Choose EPS export as lineart or text</li>
3138 <li>Jar files are executable</li>
3139 <li>Can read in Uracil - maps to unknown residue</li>
3144 <li>Known OutOfMemory errors give warning message</li>
3145 <li>Overview window calculated more efficiently</li>
3146 <li>Several GUI bugs resolved</li>
3152 <div align="center">
3153 <strong>2.05</strong><br> 30/8/05
3158 <li>Edit and annotate in "Wrapped" view</li>
3163 <li>Several GUI bugs resolved</li>
3169 <div align="center">
3170 <strong>2.04</strong><br> 24/8/05
3175 <li>Hold down mouse wheel & scroll to change font
3181 <li>Improved JPred client reliability</li>
3182 <li>Improved loading of Jalview files</li>
3188 <div align="center">
3189 <strong>2.03</strong><br> 18/8/05
3194 <li>Set Proxy server name and port in preferences</li>
3195 <li>Multiple URL links from sequence ids</li>
3196 <li>User Defined Colours can have a scheme name and added
3198 <li>Choose to ignore gaps in consensus calculation</li>
3199 <li>Unix users can set default web browser</li>
3200 <li>Runs without GUI for batch processing</li>
3201 <li>Dynamically generated Web Service Menus</li>
3206 <li>InstallAnywhere download for Sparc Solaris</li>
3212 <div align="center">
3213 <strong>2.02</strong><br> 18/7/05
3219 <li>Copy & Paste order of sequences maintains
3220 alignment order.</li>
3226 <div align="center">
3227 <strong>2.01</strong><br> 12/7/05
3232 <li>Use delete key for deleting selection.</li>
3233 <li>Use Mouse wheel to scroll sequences.</li>
3234 <li>Help file updated to describe how to add alignment
3236 <li>Version and build date written to build properties
3238 <li>InstallAnywhere installation will check for updates
3239 at launch of Jalview.</li>
3244 <li>Delete gaps bug fixed.</li>
3245 <li>FileChooser sorts columns.</li>
3246 <li>Can remove groups one by one.</li>
3247 <li>Filechooser icons installed.</li>
3248 <li>Finder ignores return character when searching.
3249 Return key will initiate a search.<br>
3256 <div align="center">
3257 <strong>2.0</strong><br> 20/6/05
3262 <li>New codebase</li>