3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
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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 />
74 <em>30/5/2017</em></strong>
77 <td><div align="left">
80 <li><!-- JAL-2360,JAL-2371, -->More robust colours and shader model for alignments and groups</li>
81 <li><!-- JAL-384 -->Custom shading schemes created via groovy scripts</li>
82 <li><!-- JAL-2491 -->linked scrolling of CDS/Protein views via Overview or sequence motif search operations</li>
83 <li><!-- JAL-2526 -->Efficiency improvements for interacting with alignment and overview windows</li>
85 <!-- JAL-2535 -->Posterior probability annotation from
86 Stockholm files imported as sequence associated annotation
93 Experimental Features Checkbox in Desktop's Tools
94 menu to hide or show untested features in the application.
96 <li><!-- JAL-1476 -->Warning in alignment status bar when there are not enough columns to superimpose structures in Chimera</li>
97 <li><!-- JAL-1596 -->Faster Chimera/Jalview communication by file-based command exchange</li>
98 <li><!-- JAL-2316, -->URLs for viewing database cross-references provided by identifiers.org and the EMBL-EBI's MIRIAM DB</li>
99 <li><!-- JAL-2549 -->Updated JABAWS client to v2.2</li>
101 <em>Experimental features</em>
104 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
105 to transfer Chimera's structure attributes as Jalview
106 features, and vice-versa.
114 <li><!-- JAL-2474 -->Added PrivelegedAccessor to test suite</li>
115 <li><!-- JAL-2326 -->Prevent or clear modal dialogs raised during tests</li>
118 </div></td><td><div align="left">
122 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
123 matrix - C->R should be '3'<br />Old matrix restored with
124 this one-line groovy script:<br />jalview.schemes.ResidueProperties.BLOSUM62[4][1]=3
127 <!-- JAL-2397 -->Fixed Jalview's treatment of gaps in PCA
128 and substitution matrix based Tree calculations.<br />In
129 earlier versions of Jalview, gaps matching gaps were
130 penalised, and gaps matching non-gaps penalised even more.
131 In the PCA calculation, gaps were actually treated as
132 non-gaps - so different costs were applied, which mean't
133 Jalview's PCAs were different to those produced by
134 SeqSpace.<br />Jalview now treats gaps in the same way as
135 SeqSpace (ie it scores them as 0). To restore pre-2.10.2
137 jalview.viewmodel.PCAModel.scoreGapAsAny=true // for
139 jalview.viewmodel.PCAModel.scoreGapAsAny=false // to
142 <li><!-- JAL-2346 -->Reopening Colour by annotation dialog doesn't reselect a specific sequence's associated annotation after it was used for colouring a view</li>
143 <li><!-- JAL-2430 -->Hidden regions in alignment views are not coloured in linked structure views</li>
144 <li><!-- JAL-2419 -->Current selection lost if popup menu opened on a region of alignment without groups</li>
145 <li><!-- JAL-2374 -->Popup menu not always shown for regions of an alignment with overlapping groups</li>
146 <li><!-- JAL-2310 -->Finder double counts if both a sequence's name and description match</li>
147 <li><!-- JAL-2370 -->Hiding column selection containing two hidden regions results in incorrect hidden regions</li>
148 <li><!-- JAL-2377 -->PCA calculation could hang when generating output report when working with highly redundant alignments</li>
149 <li><!-- JAL-2365 -->Cannot configure feature colours with lightGray or darkGray via features file</li>
150 <li><!-- JAL-2421 -->Overview window visible region moves erratically when hidden rows or columns are present</li>
151 <li><!-- JAL-2362 -->Per-residue colourschemes applied via the Structure Viewer's colour menu don't correspond to sequence colouring</li>
152 <li><!-- JAL-2405 -->Protein specific colours only offered in colour and group colour menu for protein alignments</li>
153 <li><!-- JAL-2386 -->'Apply to all groups' setting when changing colour does not apply Conservation slider value to all groups</li>
154 <li><!-- JAL-2385 -->Colour threshold slider doesn't update to reflect currently selected view or group's shading thresholds</li>
155 <li><!-- JAL-2373 -->Percentage identity and conservation menu items do not show a tick or allow shading to be disabled</li>
156 <li><!-- JAL-2385 -->Conservation shading or PID threshold lost when base colourscheme changed if slider not visible</li>
157 <li><!-- JAL-2547 -->Sequence features shown in tooltip for gaps before start of features</li>
161 <li><!-- JAL-2401 -->Easier creation of colours for all 'Lower case' residues (button in colourscheme editor debugged and new documentation and tooltips added)</li>
162 <li><!-- JAL-2399-->Text colour threshold's 'Cancel' button doesn't restore group-specific text colour thresholds</li>
163 <li><!-- JAL-2243 -->Feature settings panel does not update as new features are added to alignment</li>
164 <li><!-- JAL-2436 -->Structure viewer's View -> Colour By view selection menu changes colours of alignment views</li>
165 <li><!-- JAL-2366 -->Proxy server address and port always appear enabled in Preferences->Connections</li>
166 <li><!-- JAL-2426 -->Spurious exceptions in console raised from alignment calculation workers after alignment has been closed</li>
167 <li><!-- JAL-1608 -->Typo in selection popup menu - Create groups now 'Create Group'</li>
168 <li><!-- JAL-1608 -->CMD/CTRL and G or Shift G for Create/Undefine group doesn't always work</li>
169 <li><!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get shown again after pressing 'Cancel'</li>
170 <li><!-- JAL-2461 -->DAS registry not found exceptions removed from console output</li>
171 <li><!-- JAL-2383 -->Above PID colour threshold not recovered when alignment view imported from project</li>
176 <li><!-- JAL-2442 -->Features not rendered as transparent on overview or linked structure view</li>
177 <li><!-- JAL-2372 -->Colour group by conservation doesn't work (since 2.8)</li>
178 <li><!-- JAL-2517 -->Hitting Cancel after applying user-defined colourscheme doesn't restore original colourscheme</li>
180 <em>New Known Issues</em>
182 <li><!-- JAL-2566 -->Protein/CDS view scrolling not always in phase after a sequence motif find operation</li>
183 <li><!-- JAL-2563 -->Status bar doesn't show positions for ambiguous amino acids</li>
184 <li><!-- JAL-2550 -->Importing annotation file with rows containing just upper and lower case letters are interpreted as WUSS rna secondary structure symbols</li>
189 <td width="60" nowrap>
191 <strong><a name="Jalview.2.10.1">2.10.1</a><br />
192 <em>29/11/2016</em></strong>
195 <td><div align="left">
199 <!-- JAL-98 -->Improved memory usage: sparse arrays used
200 for all consensus calculations
203 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released 3rd Oct 2016)
205 <li>Updated Jalview's Certum code signing certificate
211 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
212 set of database cross-references, sorted alphabetically
215 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
216 from database cross references. Users with custom links
217 will receive a <a href="webServices/urllinks.html#warning">warning
218 dialog</a> asking them to update their preferences.
221 <!-- JAL-2287-->Cancel button and escape listener on
222 dialog warning user about disconnecting Jalview from a
226 <!-- JAL-2320-->Jalview's Chimera control window closes if
227 the Chimera it is connected to is shut down
230 <!-- JAL-1738-->New keystroke (B) and Select highlighted
231 columns menu item to mark columns containing
232 highlighted regions (e.g. from structure selections or results
236 <!-- JAL-2284-->Command line option for batch-generation
237 of HTML pages rendering alignment data with the BioJS
247 <!-- JAL-2286 -->Columns with more than one modal residue
248 are not coloured or thresholded according to percent
249 identity (first observed in Jalview 2.8.2)
252 <!-- JAL-2301 -->Threonine incorrectly reported as not
256 <!-- JAL-2318 -->Updates to documentation pages (above PID
257 threshold, amino acid properties)
260 <!-- JAL-2292 -->Lower case residues in sequences are not
261 reported as mapped to residues in a structure file in the
265 <!--JAL-2324 -->Identical features with non-numeric scores
266 could be added multiple times to a sequence
269 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
270 bond features shown as two highlighted residues rather
271 than a range in linked structure views, and treated
272 correctly when selecting and computing trees from features
275 <!-- JAL-2281-->Custom URL links for database
276 cross-references are matched to database name regardless
284 <!-- JAL-2282-->Custom URL links for specific database
285 names without regular expressions also offer links from
289 <!-- JAL-2315-->Removing a single configured link in the
290 URL links pane in Connections preferences doesn't actually
291 update Jalview configuration
294 <!-- JAL-2272-->CTRL-Click on a selected region to open
295 the alignment area popup menu doesn't work on El-Capitan
298 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
299 files with similarly named sequences if dropped onto the
303 <!-- JAL-2312 -->Additional mappings are shown for PDB
304 entries where more chains exist in the PDB accession than
305 are reported in the SIFTS file
308 <!-- JAL-2317-->Certain structures do not get mapped to
309 the structure view when displayed with Chimera
312 <!-- JAL-2317-->No chains shown in the Chimera view
313 panel's View->Show Chains submenu
316 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
317 work for wrapped alignment views
320 <!--JAL-2197 -->Rename UI components for running JPred
321 predictions from 'JNet' to 'JPred'
324 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
325 corrupted when annotation panel vertical scroll is not at
329 <!--JAL-2332 -->Attempting to view structure for Hen
330 lysozyme results in a PDB Client error dialog box
333 <!-- JAL-2319 -->Structure View's mapping report switched ranges for PDB and sequence for SIFTS</li>
334 <!-- JAL-2319 -->SIFTS 'Not_Observed' residues mapped to non-existant coordindate data</li>
336 <!-- <em>New Known Issues</em>
343 <td width="60" nowrap>
345 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
346 <em>25/10/2016</em></strong>
349 <td><em>Application</em>
351 <li>3D Structure chooser opens with 'Cached structures'
352 view if structures already loaded</li>
353 <li>Progress bar reports models as they are loaded to
360 <li>Colour by conservation always enabled and no tick
361 shown in menu when BLOSUM or PID shading applied</li>
362 <li>FER1_ARATH and FER2_ARATH labels were switched in
363 example sequences/projects/trees</li>
367 <li>Jalview projects with views of local PDB structure
368 files saved on Windows cannot be opened on OSX</li>
369 <li>Multiple structure views can be opened and
370 superposed without timeout for structures with multiple
371 models or multiple sequences in alignment</li>
372 <li>Cannot import or associated local PDB files without
373 a PDB ID HEADER line</li>
374 <li>RMSD is not output in Jmol console when
375 superposition is performed</li>
376 <li>Drag and drop of URL from Browser fails for Linux
377 and OSX versions earlier than El Capitan</li>
378 <li>ENA client ignores invalid content from ENA server</li>
379 <li>Exceptions are not raised in console when ENA
380 client attempts to fetch non-existent IDs via Fetch DB
382 <li>Exceptions are not raised in console when a new
383 view is created on the alignment</li>
384 <li>OSX right-click fixed for group selections:
385 CMD-click to insert/remove gaps in groups and CTRL-click
386 to open group pop-up menu</li>
388 <em>Build and deployment</em>
390 <li>URL link checker now copes with multi-line anchor
393 <em>New Known Issues</em>
395 <li>Drag and drop from URL links in browsers do not
402 <td width="60" nowrap>
404 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
410 <!-- JAL-2124 -->Updated Spanish translations.
413 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
414 for importing structure data to Jalview. Enables mmCIF and
418 <!-- JAL-192 --->Alignment ruler shows positions relative to
422 <!-- JAL-2202 -->Position/residue shown in status bar when
423 mousing over sequence associated annotation
426 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
430 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
431 '()', canonical '[]' and invalid '{}' base pair populations
435 <!-- JAL-2092 -->Feature settings popup menu options for
436 showing or hiding columns containing a feature
439 <!-- JAL-1557 -->Edit selected group by double clicking on
440 group and sequence associated annotation labels
443 <!-- JAL-2236 -->Sequence name added to annotation label in
444 select/hide columns by annotation and colour by annotation
448 </ul> <em>Application</em>
451 <!-- JAL-2050-->Automatically hide introns when opening a
455 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
459 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
460 structure mappings with the EMBL-EBI PDBe SIFTS database
463 <!-- JAL-2079 -->Updated download sites used for Rfam and
464 Pfam sources to xfam.org
467 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
470 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
471 over sequences in Jalview
474 <!-- JAL-2027-->Support for reverse-complement coding
475 regions in ENA and EMBL
478 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
479 for record retrieval via ENA rest API
482 <!-- JAL-2027 -->Support for ENA CDS records with reverse
486 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
487 groovy script execution
490 <!-- JAL-1812 -->New 'execute Groovy script' option in an
491 alignment window's Calculate menu
494 <!-- JAL-1812 -->Allow groovy scripts that call
495 Jalview.getAlignFrames() to run in headless mode
498 <!-- JAL-2068 -->Support for creating new alignment
499 calculation workers from groovy scripts
502 <!-- JAL-1369 --->Store/restore reference sequence in
506 <!-- JAL-1803 -->Chain codes for a sequence's PDB
507 associations are now saved/restored from project
510 <!-- JAL-1993 -->Database selection dialog always shown
511 before sequence fetcher is opened
514 <!-- JAL-2183 -->Double click on an entry in Jalview's
515 database chooser opens a sequence fetcher
518 <!-- JAL-1563 -->Free-text search client for UniProt using
522 <!-- JAL-2168 -->-nonews command line parameter to prevent
523 the news reader opening
526 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
527 querying stored in preferences
530 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
534 <!-- JAL-1977-->Tooltips shown on database chooser
537 <!-- JAL-391 -->Reverse complement function in calculate
538 menu for nucleotide sequences
541 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
542 and feature counts preserves alignment ordering (and
543 debugged for complex feature sets).
546 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
547 viewing structures with Jalview 2.10
550 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
551 genome, transcript CCDS and gene ids via the Ensembl and
552 Ensembl Genomes REST API
555 <!-- JAL-2049 -->Protein sequence variant annotation
556 computed for 'sequence_variant' annotation on CDS regions
560 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
564 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
565 Ref Fetcher fails to match, or otherwise updates sequence
566 data from external database records.
569 <!-- JAL-2154 -->Revised Jalview Project format for
570 efficient recovery of sequence coding and alignment
571 annotation relationships.
573 </ul> <!-- <em>Applet</em>
584 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
588 <!-- JAL-2018-->Export features in Jalview format (again)
589 includes graduated colourschemes
592 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
593 working with big alignments and lots of hidden columns
596 <!-- JAL-2053-->Hidden column markers not always rendered
597 at right of alignment window
600 <!-- JAL-2067 -->Tidied up links in help file table of
604 <!-- JAL-2072 -->Feature based tree calculation not shown
608 <!-- JAL-2075 -->Hidden columns ignored during feature
609 based tree calculation
612 <!-- JAL-2065 -->Alignment view stops updating when show
613 unconserved enabled for group on alignment
616 <!-- JAL-2086 -->Cannot insert gaps into sequence when
620 <!-- JAL-2146 -->Alignment column in status incorrectly
621 shown as "Sequence position" when mousing over
625 <!-- JAL-2099 -->Incorrect column numbers in ruler when
626 hidden columns present
629 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
630 user created annotation added to alignment
633 <!-- JAL-1841 -->RNA Structure consensus only computed for
634 '()' base pair annotation
637 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
638 in zero scores for all base pairs in RNA Structure
642 <!-- JAL-2174-->Extend selection with columns containing
646 <!-- JAL-2275 -->Pfam format writer puts extra space at
647 beginning of sequence
650 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
654 <!-- JAL-2238 -->Cannot create groups on an alignment from
655 from a tree when t-coffee scores are shown
658 <!-- JAL-1836,1967 -->Cannot import and view PDB
659 structures with chains containing negative resnums (4q4h)
662 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
666 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
667 to Clustal, PIR and PileUp output
670 <!-- JAL-2008 -->Reordering sequence features that are
671 not visible causes alignment window to repaint
674 <!-- JAL-2006 -->Threshold sliders don't work in
675 graduated colour and colour by annotation row for e-value
676 scores associated with features and annotation rows
679 <!-- JAL-1797 -->amino acid physicochemical conservation
680 calculation should be case independent
683 <!-- JAL-2173 -->Remove annotation also updates hidden
687 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
688 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
689 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
692 <!-- JAL-2065 -->Null pointer exceptions and redraw
693 problems when reference sequence defined and 'show
694 non-conserved' enabled
697 <!-- JAL-1306 -->Quality and Conservation are now shown on
698 load even when Consensus calculation is disabled
701 <!-- JAL-1932 -->Remove right on penultimate column of
702 alignment does nothing
708 <!-- JAL-1552-->URLs and links can't be imported by
709 drag'n'drop on OSX when launched via webstart (note - not
710 yet fixed for El Capitan)
713 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
714 output when running on non-gb/us i18n platforms
717 <!-- JAL-1944 -->Error thrown when exporting a view with
718 hidden sequences as flat-file alignment
721 <!-- JAL-2030-->InstallAnywhere distribution fails when
725 <!-- JAL-2080-->Jalview very slow to launch via webstart
726 (also hotfix for 2.9.0b2)
729 <!-- JAL-2085 -->Cannot save project when view has a
730 reference sequence defined
733 <!-- JAL-1011 -->Columns are suddenly selected in other
734 alignments and views when revealing hidden columns
737 <!-- JAL-1989 -->Hide columns not mirrored in complement
738 view in a cDNA/Protein splitframe
741 <!-- JAL-1369 -->Cannot save/restore representative
742 sequence from project when only one sequence is
746 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
750 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
751 structure consensus didn't refresh annotation panel
754 <!-- JAL-1962 -->View mapping in structure view shows
755 mappings between sequence and all chains in a PDB file
758 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
759 dialogs format columns correctly, don't display array
760 data, sort columns according to type
763 <!-- JAL-1975 -->Export complete shown after destination
764 file chooser is cancelled during an image export
767 <!-- JAL-2025 -->Error when querying PDB Service with
768 sequence name containing special characters
771 <!-- JAL-2024 -->Manual PDB structure querying should be
775 <!-- JAL-2104 -->Large tooltips with broken HTML
776 formatting don't wrap
779 <!-- JAL-1128 -->Figures exported from wrapped view are
780 truncated so L looks like I in consensus annotation
783 <!-- JAL-2003 -->Export features should only export the
784 currently displayed features for the current selection or
788 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
789 after fetching cross-references, and restoring from project
792 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
793 followed in the structure viewer
796 <!-- JAL-2163 -->Titles for individual alignments in
797 splitframe not restored from project
800 <!-- JAL-2145 -->missing autocalculated annotation at
801 trailing end of protein alignment in transcript/product
802 splitview when pad-gaps not enabled by default
805 <!-- JAL-1797 -->amino acid physicochemical conservation
809 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
810 article has been read (reopened issue due to
811 internationalisation problems)
814 <!-- JAL-1960 -->Only offer PDB structures in structure
815 viewer based on sequence name, PDB and UniProt
820 <!-- JAL-1976 -->No progress bar shown during export of
824 <!-- JAL-2213 -->Structures not always superimposed after
825 multiple structures are shown for one or more sequences.
828 <!-- JAL-1370 -->Reference sequence characters should not
829 be replaced with '.' when 'Show unconserved' format option
833 <!-- JAL-1823 -->Cannot specify chain code when entering
834 specific PDB id for sequence
837 <!-- JAL-1944 -->File->Export->.. as doesn't work when
838 'Export hidden sequences' is enabled, but 'export hidden
839 columns' is disabled.
842 <!--JAL-2026-->Best Quality option in structure chooser
843 selects lowest rather than highest resolution structures
847 <!-- JAL-1887 -->Incorrect start and end reported for PDB
848 to sequence mapping in 'View Mappings' report
851 <!-- JAL-2284 -->Unable to read old Jalview projects that
852 contain non-XML data added after Jalvew wrote project.
854 <li><!-- JAL-2118 -->Newly created annotation row reorders
855 after clicking on it to create new annotation for a
858 <!-- may exclude, this is an external service stability issue JAL-1941
859 -- > RNA 3D structure not added via DSSR service</li> -->
864 <!-- JAL-2151 -->Incorrect columns are selected when
865 hidden columns present before start of sequence
868 <!-- JAL-1986 -->Missing dependencies on applet pages
872 <!-- JAL-1947 -->Overview pixel size changes when
873 sequences are hidden in applet
876 <!-- JAL-1996 -->Updated instructions for applet
877 deployment on examples pages.
884 <td width="60" nowrap>
886 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
887 <em>16/10/2015</em></strong>
892 <li>Time stamps for signed Jalview application and applet
899 <li>Duplicate group consensus and conservation rows
900 shown when tree is partitioned</li>
901 <li>Erratic behaviour when tree partitions made with
902 multiple cDNA/Protein split views</li>
908 <td width="60" nowrap>
910 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
911 <em>8/10/2015</em></strong>
916 <li>Updated Spanish translations of localized text for
918 </ul> <em>Application</em>
920 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
921 <li>Signed OSX InstallAnywhere installer<br></li>
922 <li>Support for per-sequence based annotations in BioJSON</li>
923 </ul> <em>Applet</em>
925 <li>Split frame example added to applet examples page</li>
926 </ul><em>Build and Deployment</em>
928 <li><!-- JAL-1888 -->New ant target for running Jalview's test suite</li>
934 <li>Mapping of cDNA to protein in split frames
935 incorrect when sequence start > 1</li>
936 <li>Broken images in filter column by annotation dialog
938 <li>Feature colours not parsed from features file</li>
939 <li>Exceptions and incomplete link URLs recovered when
940 loading a features file containing HTML tags in feature
946 <li>Annotations corrupted after BioJS export and
948 <li>Incorrect sequence limits after Fetch DB References
949 with 'trim retrieved sequences'</li>
950 <li>Incorrect warning about deleting all data when
951 deleting selected columns</li>
952 <li>Patch to build system for shipping properly signed
953 JNLP templates for webstart launch</li>
954 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
955 unreleased structures for download or viewing</li>
956 <li>Tab/space/return keystroke operation of EMBL-PDBe
957 fetcher/viewer dialogs works correctly</li>
958 <li>Disabled 'minimise' button on Jalview windows
959 running on OSX to workaround redraw hang bug</li>
960 <li>Split cDNA/Protein view position and geometry not
961 recovered from jalview project</li>
962 <li>Initial enabled/disabled state of annotation menu
963 sorter 'show autocalculated first/last' corresponds to
965 <li>Restoring of Clustal, RNA Helices and T-Coffee
966 color schemes from BioJSON</li>
970 <li>Reorder sequences mirrored in cDNA/Protein split
972 <li>Applet with Jmol examples not loading correctly</li>
978 <td><div align="center">
979 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
983 <li>Linked visualisation and analysis of DNA and Protein
986 <li>Translated cDNA alignments shown as split protein
987 and DNA alignment views</li>
988 <li>Codon consensus annotation for linked protein and
989 cDNA alignment views</li>
990 <li>Link cDNA or Protein product sequences by loading
991 them onto Protein or cDNA alignments</li>
992 <li>Reconstruct linked cDNA alignment from aligned
993 protein sequences</li>
996 <li>Jmol integration updated to Jmol v14.2.14</li>
997 <li>Import and export of Jalview alignment views as <a
998 href="features/bioJsonFormat.html">BioJSON</a></li>
999 <li>New alignment annotation file statements for
1000 reference sequences and marking hidden columns</li>
1001 <li>Reference sequence based alignment shading to
1002 highlight variation</li>
1003 <li>Select or hide columns according to alignment
1005 <li>Find option for locating sequences by description</li>
1006 <li>Conserved physicochemical properties shown in amino
1007 acid conservation row</li>
1008 <li>Alignments can be sorted by number of RNA helices</li>
1009 </ul> <em>Application</em>
1011 <li>New cDNA/Protein analysis capabilities
1013 <li>Get Cross-References should open a Split Frame
1014 view with cDNA/Protein</li>
1015 <li>Detect when nucleotide sequences and protein
1016 sequences are placed in the same alignment</li>
1017 <li>Split cDNA/Protein views are saved in Jalview
1022 <li>Use REST API to talk to Chimera</li>
1023 <li>Selected regions in Chimera are highlighted in linked
1024 Jalview windows</li>
1026 <li>VARNA RNA viewer updated to v3.93</li>
1027 <li>VARNA views are saved in Jalview Projects</li>
1028 <li>Pseudoknots displayed as Jalview RNA annotation can
1029 be shown in VARNA</li>
1031 <li>Make groups for selection uses marked columns as well
1032 as the active selected region</li>
1034 <li>Calculate UPGMA and NJ trees using sequence feature
1036 <li>New Export options
1038 <li>New Export Settings dialog to control hidden
1039 region export in flat file generation</li>
1041 <li>Export alignment views for display with the <a
1042 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1044 <li>Export scrollable SVG in HTML page</li>
1045 <li>Optional embedding of BioJSON data when exporting
1046 alignment figures to HTML</li>
1048 <li>3D structure retrieval and display
1050 <li>Free text and structured queries with the PDBe
1052 <li>PDBe Search API based discovery and selection of
1053 PDB structures for a sequence set</li>
1057 <li>JPred4 employed for protein secondary structure
1059 <li>Hide Insertions menu option to hide unaligned columns
1060 for one or a group of sequences</li>
1061 <li>Automatically hide insertions in alignments imported
1062 from the JPred4 web server</li>
1063 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1064 system on OSX<br />LGPL libraries courtesy of <a
1065 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1067 <li>changed 'View nucleotide structure' submenu to 'View
1068 VARNA 2D Structure'</li>
1069 <li>change "View protein structure" menu option to "3D
1072 </ul> <em>Applet</em>
1074 <li>New layout for applet example pages</li>
1075 <li>New parameters to enable SplitFrame view
1076 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1077 <li>New example demonstrating linked viewing of cDNA and
1078 Protein alignments</li>
1079 </ul> <em>Development and deployment</em>
1081 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1082 <li>Include installation type and git revision in build
1083 properties and console log output</li>
1084 <li>Jalview Github organisation, and new github site for
1085 storing BioJsMSA Templates</li>
1086 <li>Jalview's unit tests now managed with TestNG</li>
1089 <!-- <em>General</em>
1091 </ul> --> <!-- issues resolved --> <em>Application</em>
1093 <li>Escape should close any open find dialogs</li>
1094 <li>Typo in select-by-features status report</li>
1095 <li>Consensus RNA secondary secondary structure
1096 predictions are not highlighted in amber</li>
1097 <li>Missing gap character in v2.7 example file means
1098 alignment appears unaligned when pad-gaps is not enabled</li>
1099 <li>First switch to RNA Helices colouring doesn't colour
1100 associated structure views</li>
1101 <li>ID width preference option is greyed out when auto
1102 width checkbox not enabled</li>
1103 <li>Stopped a warning dialog from being shown when
1104 creating user defined colours</li>
1105 <li>'View Mapping' in structure viewer shows sequence
1106 mappings for just that viewer's sequences</li>
1107 <li>Workaround for superposing PDB files containing
1108 multiple models in Chimera</li>
1109 <li>Report sequence position in status bar when hovering
1110 over Jmol structure</li>
1111 <li>Cannot output gaps as '.' symbols with Selection ->
1112 output to text box</li>
1113 <li>Flat file exports of alignments with hidden columns
1114 have incorrect sequence start/end</li>
1115 <li>'Aligning' a second chain to a Chimera structure from
1117 <li>Colour schemes applied to structure viewers don't
1118 work for nucleotide</li>
1119 <li>Loading/cut'n'pasting an empty or invalid file leads
1120 to a grey/invisible alignment window</li>
1121 <li>Exported Jpred annotation from a sequence region
1122 imports to different position</li>
1123 <li>Space at beginning of sequence feature tooltips shown
1124 on some platforms</li>
1125 <li>Chimera viewer 'View | Show Chain' menu is not
1127 <li>'New View' fails with a Null Pointer Exception in
1128 console if Chimera has been opened</li>
1129 <li>Mouseover to Chimera not working</li>
1130 <li>Miscellaneous ENA XML feature qualifiers not
1132 <li>NPE in annotation renderer after 'Extract Scores'</li>
1133 <li>If two structures in one Chimera window, mouseover of
1134 either sequence shows on first structure</li>
1135 <li>'Show annotations' options should not make
1136 non-positional annotations visible</li>
1137 <li>Subsequence secondary structure annotation not shown
1138 in right place after 'view flanking regions'</li>
1139 <li>File Save As type unset when current file format is
1141 <li>Save as '.jar' option removed for saving Jalview
1143 <li>Colour by Sequence colouring in Chimera more
1145 <li>Cannot 'add reference annotation' for a sequence in
1146 several views on same alignment</li>
1147 <li>Cannot show linked products for EMBL / ENA records</li>
1148 <li>Jalview's tooltip wraps long texts containing no
1150 </ul> <em>Applet</em>
1152 <li>Jmol to JalviewLite mouseover/link not working</li>
1153 <li>JalviewLite can't import sequences with ID
1154 descriptions containing angle brackets</li>
1155 </ul> <em>General</em>
1157 <li>Cannot export and reimport RNA secondary structure
1158 via jalview annotation file</li>
1159 <li>Random helix colour palette for colour by annotation
1160 with RNA secondary structure</li>
1161 <li>Mouseover to cDNA from STOP residue in protein
1162 translation doesn't work.</li>
1163 <li>hints when using the select by annotation dialog box</li>
1164 <li>Jmol alignment incorrect if PDB file has alternate CA
1166 <li>FontChooser message dialog appears to hang after
1167 choosing 1pt font</li>
1168 <li>Peptide secondary structure incorrectly imported from
1169 annotation file when annotation display text includes 'e' or
1171 <li>Cannot set colour of new feature type whilst creating
1173 <li>cDNA translation alignment should not be sequence
1174 order dependent</li>
1175 <li>'Show unconserved' doesn't work for lower case
1177 <li>Nucleotide ambiguity codes involving R not recognised</li>
1178 </ul> <em>Deployment and Documentation</em>
1180 <li>Applet example pages appear different to the rest of
1181 www.jalview.org</li>
1182 </ul> <em>Application Known issues</em>
1184 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1185 <li>Misleading message appears after trying to delete
1187 <li>Jalview icon not shown in dock after InstallAnywhere
1188 version launches</li>
1189 <li>Fetching EMBL reference for an RNA sequence results
1190 fails with a sequence mismatch</li>
1191 <li>Corrupted or unreadable alignment display when
1192 scrolling alignment to right</li>
1193 <li>ArrayIndexOutOfBoundsException thrown when remove
1194 empty columns called on alignment with ragged gapped ends</li>
1195 <li>auto calculated alignment annotation rows do not get
1196 placed above or below non-autocalculated rows</li>
1197 <li>Jalview dekstop becomes sluggish at full screen in
1198 ultra-high resolution</li>
1199 <li>Cannot disable consensus calculation independently of
1200 quality and conservation</li>
1201 <li>Mouseover highlighting between cDNA and protein can
1202 become sluggish with more than one splitframe shown</li>
1203 </ul> <em>Applet Known Issues</em>
1205 <li>Core PDB parsing code requires Jmol</li>
1206 <li>Sequence canvas panel goes white when alignment
1207 window is being resized</li>
1213 <td><div align="center">
1214 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1216 <td><em>General</em>
1218 <li>Updated Java code signing certificate donated by
1220 <li>Features and annotation preserved when performing
1221 pairwise alignment</li>
1222 <li>RNA pseudoknot annotation can be
1223 imported/exported/displayed</li>
1224 <li>'colour by annotation' can colour by RNA and
1225 protein secondary structure</li>
1226 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1227 post-hoc with 2.9 release</em>)
1230 </ul> <em>Application</em>
1232 <li>Extract and display secondary structure for sequences
1233 with 3D structures</li>
1234 <li>Support for parsing RNAML</li>
1235 <li>Annotations menu for layout
1237 <li>sort sequence annotation rows by alignment</li>
1238 <li>place sequence annotation above/below alignment
1241 <li>Output in Stockholm format</li>
1242 <li>Internationalisation: improved Spanish (es)
1244 <li>Structure viewer preferences tab</li>
1245 <li>Disorder and Secondary Structure annotation tracks
1246 shared between alignments</li>
1247 <li>UCSF Chimera launch and linked highlighting from
1249 <li>Show/hide all sequence associated annotation rows for
1250 all or current selection</li>
1251 <li>disorder and secondary structure predictions
1252 available as dataset annotation</li>
1253 <li>Per-sequence rna helices colouring</li>
1256 <li>Sequence database accessions imported when fetching
1257 alignments from Rfam</li>
1258 <li>update VARNA version to 3.91</li>
1260 <li>New groovy scripts for exporting aligned positions,
1261 conservation values, and calculating sum of pairs scores.</li>
1262 <li>Command line argument to set default JABAWS server</li>
1263 <li>include installation type in build properties and
1264 console log output</li>
1265 <li>Updated Jalview project format to preserve dataset
1269 <!-- issues resolved --> <em>Application</em>
1271 <li>Distinguish alignment and sequence associated RNA
1272 structure in structure->view->VARNA</li>
1273 <li>Raise dialog box if user deletes all sequences in an
1275 <li>Pressing F1 results in documentation opening twice</li>
1276 <li>Sequence feature tooltip is wrapped</li>
1277 <li>Double click on sequence associated annotation
1278 selects only first column</li>
1279 <li>Redundancy removal doesn't result in unlinked
1280 leaves shown in tree</li>
1281 <li>Undos after several redundancy removals don't undo
1283 <li>Hide sequence doesn't hide associated annotation</li>
1284 <li>User defined colours dialog box too big to fit on
1285 screen and buttons not visible</li>
1286 <li>author list isn't updated if already written to
1287 Jalview properties</li>
1288 <li>Popup menu won't open after retrieving sequence
1290 <li>File open window for associate PDB doesn't open</li>
1291 <li>Left-then-right click on a sequence id opens a
1292 browser search window</li>
1293 <li>Cannot open sequence feature shading/sort popup menu
1294 in feature settings dialog</li>
1295 <li>better tooltip placement for some areas of Jalview
1297 <li>Allow addition of JABAWS Server which doesn't
1298 pass validation</li>
1299 <li>Web services parameters dialog box is too large to
1301 <li>Muscle nucleotide alignment preset obscured by
1303 <li>JABAWS preset submenus don't contain newly
1304 defined user preset</li>
1305 <li>MSA web services warns user if they were launched
1306 with invalid input</li>
1307 <li>Jalview cannot contact DAS Registy when running on
1310 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1311 'Superpose with' submenu not shown when new view
1315 </ul> <!-- <em>Applet</em>
1317 </ul> <em>General</em>
1319 </ul>--> <em>Deployment and Documentation</em>
1321 <li>2G and 1G options in launchApp have no effect on
1322 memory allocation</li>
1323 <li>launchApp service doesn't automatically open
1324 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1326 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1327 InstallAnywhere reports cannot find valid JVM when Java
1328 1.7_055 is available
1330 </ul> <em>Application Known issues</em>
1333 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1334 corrupted or unreadable alignment display when scrolling
1338 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1339 retrieval fails but progress bar continues for DAS retrieval
1340 with large number of ID
1343 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1344 flatfile output of visible region has incorrect sequence
1348 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1349 rna structure consensus doesn't update when secondary
1350 structure tracks are rearranged
1353 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1354 invalid rna structure positional highlighting does not
1355 highlight position of invalid base pairs
1358 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1359 out of memory errors are not raised when saving Jalview
1360 project from alignment window file menu
1363 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1364 Switching to RNA Helices colouring doesn't propagate to
1368 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1369 colour by RNA Helices not enabled when user created
1370 annotation added to alignment
1373 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1374 Jalview icon not shown on dock in Mountain Lion/Webstart
1376 </ul> <em>Applet Known Issues</em>
1379 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1380 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1383 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1384 Jalview and Jmol example not compatible with IE9
1387 <li>Sort by annotation score doesn't reverse order
1393 <td><div align="center">
1394 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1397 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1400 <li>Internationalisation of user interface (usually
1401 called i18n support) and translation for Spanish locale</li>
1402 <li>Define/Undefine group on current selection with
1403 Ctrl-G/Shift Ctrl-G</li>
1404 <li>Improved group creation/removal options in
1405 alignment/sequence Popup menu</li>
1406 <li>Sensible precision for symbol distribution
1407 percentages shown in logo tooltip.</li>
1408 <li>Annotation panel height set according to amount of
1409 annotation when alignment first opened</li>
1410 </ul> <em>Application</em>
1412 <li>Interactive consensus RNA secondary structure
1413 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1414 <li>Select columns containing particular features from
1415 Feature Settings dialog</li>
1416 <li>View all 'representative' PDB structures for selected
1418 <li>Update Jalview project format:
1420 <li>New file extension for Jalview projects '.jvp'</li>
1421 <li>Preserve sequence and annotation dataset (to
1422 store secondary structure annotation,etc)</li>
1423 <li>Per group and alignment annotation and RNA helix
1427 <li>New similarity measures for PCA and Tree calculation
1429 <li>Experimental support for retrieval and viewing of
1430 flanking regions for an alignment</li>
1434 <!-- issues resolved --> <em>Application</em>
1436 <li>logo keeps spinning and status remains at queued or
1437 running after job is cancelled</li>
1438 <li>cannot export features from alignments imported from
1439 Jalview/VAMSAS projects</li>
1440 <li>Buggy slider for web service parameters that take
1442 <li>Newly created RNA secondary structure line doesn't
1443 have 'display all symbols' flag set</li>
1444 <li>T-COFFEE alignment score shading scheme and other
1445 annotation shading not saved in Jalview project</li>
1446 <li>Local file cannot be loaded in freshly downloaded
1448 <li>Jalview icon not shown on dock in Mountain
1450 <li>Load file from desktop file browser fails</li>
1451 <li>Occasional NPE thrown when calculating large trees</li>
1452 <li>Cannot reorder or slide sequences after dragging an
1453 alignment onto desktop</li>
1454 <li>Colour by annotation dialog throws NPE after using
1455 'extract scores' function</li>
1456 <li>Loading/cut'n'pasting an empty file leads to a grey
1457 alignment window</li>
1458 <li>Disorder thresholds rendered incorrectly after
1459 performing IUPred disorder prediction</li>
1460 <li>Multiple group annotated consensus rows shown when
1461 changing 'normalise logo' display setting</li>
1462 <li>Find shows blank dialog after 'finished searching' if
1463 nothing matches query</li>
1464 <li>Null Pointer Exceptions raised when sorting by
1465 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1467 <li>Errors in Jmol console when structures in alignment
1468 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1470 <li>Not all working JABAWS services are shown in
1472 <li>JAVAWS version of Jalview fails to launch with
1473 'invalid literal/length code'</li>
1474 <li>Annotation/RNA Helix colourschemes cannot be applied
1475 to alignment with groups (actually fixed in 2.8.0b1)</li>
1476 <li>RNA Helices and T-Coffee Scores available as default
1479 </ul> <em>Applet</em>
1481 <li>Remove group option is shown even when selection is
1483 <li>Apply to all groups ticked but colourscheme changes
1484 don't affect groups</li>
1485 <li>Documented RNA Helices and T-Coffee Scores as valid
1486 colourscheme name</li>
1487 <li>Annotation labels drawn on sequence IDs when
1488 Annotation panel is not displayed</li>
1489 <li>Increased font size for dropdown menus on OSX and
1490 embedded windows</li>
1491 </ul> <em>Other</em>
1493 <li>Consensus sequence for alignments/groups with a
1494 single sequence were not calculated</li>
1495 <li>annotation files that contain only groups imported as
1496 annotation and junk sequences</li>
1497 <li>Fasta files with sequences containing '*' incorrectly
1498 recognised as PFAM or BLC</li>
1499 <li>conservation/PID slider apply all groups option
1500 doesn't affect background (2.8.0b1)
1502 <li>redundancy highlighting is erratic at 0% and 100%</li>
1503 <li>Remove gapped columns fails for sequences with ragged
1505 <li>AMSA annotation row with leading spaces is not
1506 registered correctly on import</li>
1507 <li>Jalview crashes when selecting PCA analysis for
1508 certain alignments</li>
1509 <li>Opening the colour by annotation dialog for an
1510 existing annotation based 'use original colours'
1511 colourscheme loses original colours setting</li>
1516 <td><div align="center">
1517 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
1518 <em>30/1/2014</em></strong>
1522 <li>Trusted certificates for JalviewLite applet and
1523 Jalview Desktop application<br />Certificate was donated by
1524 <a href="https://www.certum.eu">Certum</a> to the Jalview
1525 open source project).
1527 <li>Jalview SRS links replaced by UniProt and EBI-search
1529 <li>Output in Stockholm format</li>
1530 <li>Allow import of data from gzipped files</li>
1531 <li>Export/import group and sequence associated line
1532 graph thresholds</li>
1533 <li>Nucleotide substitution matrix that supports RNA and
1534 ambiguity codes</li>
1535 <li>Allow disorder predictions to be made on the current
1536 selection (or visible selection) in the same way that JPred
1538 <li>Groovy scripting for headless Jalview operation</li>
1539 </ul> <em>Other improvements</em>
1541 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
1542 <li>COMBINE statement uses current SEQUENCE_REF and
1543 GROUP_REF scope to group annotation rows</li>
1544 <li>Support '' style escaping of quotes in Newick
1546 <li>Group options for JABAWS service by command line name</li>
1547 <li>Empty tooltip shown for JABA service options with a
1548 link but no description</li>
1549 <li>Select primary source when selecting authority in
1550 database fetcher GUI</li>
1551 <li>Add .mfa to FASTA file extensions recognised by
1553 <li>Annotation label tooltip text wrap</li>
1558 <li>Slow scrolling when lots of annotation rows are
1560 <li>Lots of NPE (and slowness) after creating RNA
1561 secondary structure annotation line</li>
1562 <li>Sequence database accessions not imported when
1563 fetching alignments from Rfam</li>
1564 <li>Incorrect SHMR submission for sequences with
1566 <li>View all structures does not always superpose
1568 <li>Option widgets in service parameters not updated to
1569 reflect user or preset settings</li>
1570 <li>Null pointer exceptions for some services without
1571 presets or adjustable parameters</li>
1572 <li>Discover PDB IDs entry in structure menu doesn't
1573 discover PDB xRefs</li>
1574 <li>Exception encountered while trying to retrieve
1575 features with DAS</li>
1576 <li>Lowest value in annotation row isn't coloured
1577 when colour by annotation (per sequence) is coloured</li>
1578 <li>Keyboard mode P jumps to start of gapped region when
1579 residue follows a gap</li>
1580 <li>Jalview appears to hang importing an alignment with
1581 Wrap as default or after enabling Wrap</li>
1582 <li>'Right click to add annotations' message
1583 shown in wrap mode when no annotations present</li>
1584 <li>Disorder predictions fail with NPE if no automatic
1585 annotation already exists on alignment</li>
1586 <li>oninit javascript function should be called after
1587 initialisation completes</li>
1588 <li>Remove redundancy after disorder prediction corrupts
1589 alignment window display</li>
1590 <li>Example annotation file in documentation is invalid</li>
1591 <li>Grouped line graph annotation rows are not exported
1592 to annotation file</li>
1593 <li>Multi-harmony analysis cannot be run when only two
1595 <li>Cannot create multiple groups of line graphs with
1596 several 'combine' statements in annotation file</li>
1597 <li>Pressing return several times causes Number Format
1598 exceptions in keyboard mode</li>
1599 <li>Multi-harmony (SHMMR) method doesn't submit
1600 correct partitions for input data</li>
1601 <li>Translation from DNA to Amino Acids fails</li>
1602 <li>Jalview fail to load newick tree with quoted label</li>
1603 <li>--headless flag isn't understood</li>
1604 <li>ClassCastException when generating EPS in headless
1606 <li>Adjusting sequence-associated shading threshold only
1607 changes one row's threshold</li>
1608 <li>Preferences and Feature settings panel panel
1609 doesn't open</li>
1610 <li>hide consensus histogram also hides conservation and
1611 quality histograms</li>
1616 <td><div align="center">
1617 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
1619 <td><em>Application</em>
1621 <li>Support for JABAWS 2.0 Services (AACon alignment
1622 conservation, protein disorder and Clustal Omega)</li>
1623 <li>JABAWS server status indicator in Web Services
1625 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
1626 in Jalview alignment window</li>
1627 <li>Updated Jalview build and deploy framework for OSX
1628 mountain lion, windows 7, and 8</li>
1629 <li>Nucleotide substitution matrix for PCA that supports
1630 RNA and ambiguity codes</li>
1632 <li>Improved sequence database retrieval GUI</li>
1633 <li>Support fetching and database reference look up
1634 against multiple DAS sources (Fetch all from in 'fetch db
1636 <li>Jalview project improvements
1638 <li>Store and retrieve the 'belowAlignment'
1639 flag for annotation</li>
1640 <li>calcId attribute to group annotation rows on the
1642 <li>Store AACon calculation settings for a view in
1643 Jalview project</li>
1647 <li>horizontal scrolling gesture support</li>
1648 <li>Visual progress indicator when PCA calculation is
1650 <li>Simpler JABA web services menus</li>
1651 <li>visual indication that web service results are still
1652 being retrieved from server</li>
1653 <li>Serialise the dialogs that are shown when Jalview
1654 starts up for first time</li>
1655 <li>Jalview user agent string for interacting with HTTP
1657 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
1659 <li>Examples directory and Groovy library included in
1660 InstallAnywhere distribution</li>
1661 </ul> <em>Applet</em>
1663 <li>RNA alignment and secondary structure annotation
1664 visualization applet example</li>
1665 </ul> <em>General</em>
1667 <li>Normalise option for consensus sequence logo</li>
1668 <li>Reset button in PCA window to return dimensions to
1670 <li>Allow seqspace or Jalview variant of alignment PCA
1672 <li>PCA with either nucleic acid and protein substitution
1674 <li>Allow windows containing HTML reports to be exported
1676 <li>Interactive display and editing of RNA secondary
1677 structure contacts</li>
1678 <li>RNA Helix Alignment Colouring</li>
1679 <li>RNA base pair logo consensus</li>
1680 <li>Parse sequence associated secondary structure
1681 information in Stockholm files</li>
1682 <li>HTML Export database accessions and annotation
1683 information presented in tooltip for sequences</li>
1684 <li>Import secondary structure from LOCARNA clustalw
1685 style RNA alignment files</li>
1686 <li>import and visualise T-COFFEE quality scores for an
1688 <li>'colour by annotation' per sequence option to
1689 shade each sequence according to its associated alignment
1691 <li>New Jalview Logo</li>
1692 </ul> <em>Documentation and Development</em>
1694 <li>documentation for score matrices used in Jalview</li>
1695 <li>New Website!</li>
1697 <td><em>Application</em>
1699 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
1700 wsdbfetch REST service</li>
1701 <li>Stop windows being moved outside desktop on OSX</li>
1702 <li>Filetype associations not installed for webstart
1704 <li>Jalview does not always retrieve progress of a JABAWS
1705 job execution in full once it is complete</li>
1706 <li>revise SHMR RSBS definition to ensure alignment is
1707 uploaded via ali_file parameter</li>
1708 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
1709 <li>View all structures superposed fails with exception</li>
1710 <li>Jnet job queues forever if a very short sequence is
1711 submitted for prediction</li>
1712 <li>Cut and paste menu not opened when mouse clicked on
1714 <li>Putting fractional value into integer text box in
1715 alignment parameter dialog causes Jalview to hang</li>
1716 <li>Structure view highlighting doesn't work on
1718 <li>View all structures fails with exception shown in
1720 <li>Characters in filename associated with PDBEntry not
1721 escaped in a platform independent way</li>
1722 <li>Jalview desktop fails to launch with exception when
1724 <li>Tree calculation reports 'you must have 2 or more
1725 sequences selected' when selection is empty</li>
1726 <li>Jalview desktop fails to launch with jar signature
1727 failure when java web start temporary file caching is
1729 <li>DAS Sequence retrieval with range qualification
1730 results in sequence xref which includes range qualification</li>
1731 <li>Errors during processing of command line arguments
1732 cause progress bar (JAL-898) to be removed</li>
1733 <li>Replace comma for semi-colon option not disabled for
1734 DAS sources in sequence fetcher</li>
1735 <li>Cannot close news reader when JABAWS server warning
1736 dialog is shown</li>
1737 <li>Option widgets not updated to reflect user settings</li>
1738 <li>Edited sequence not submitted to web service</li>
1739 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
1740 <li>InstallAnywhere installer doesn't unpack and run
1741 on OSX Mountain Lion</li>
1742 <li>Annotation panel not given a scroll bar when
1743 sequences with alignment annotation are pasted into the
1745 <li>Sequence associated annotation rows not associated
1746 when loaded from Jalview project</li>
1747 <li>Browser launch fails with NPE on java 1.7</li>
1748 <li>JABAWS alignment marked as finished when job was
1749 cancelled or job failed due to invalid input</li>
1750 <li>NPE with v2.7 example when clicking on Tree
1751 associated with all views</li>
1752 <li>Exceptions when copy/paste sequences with grouped
1753 annotation rows to new window</li>
1754 </ul> <em>Applet</em>
1756 <li>Sequence features are momentarily displayed before
1757 they are hidden using hidefeaturegroups applet parameter</li>
1758 <li>loading features via javascript API automatically
1759 enables feature display</li>
1760 <li>scrollToColumnIn javascript API method doesn't
1762 </ul> <em>General</em>
1764 <li>Redundancy removal fails for rna alignment</li>
1765 <li>PCA calculation fails when sequence has been selected
1766 and then deselected</li>
1767 <li>PCA window shows grey box when first opened on OSX</li>
1768 <li>Letters coloured pink in sequence logo when alignment
1769 coloured with clustalx</li>
1770 <li>Choosing fonts without letter symbols defined causes
1771 exceptions and redraw errors</li>
1772 <li>Initial PCA plot view is not same as manually
1773 reconfigured view</li>
1774 <li>Grouped annotation graph label has incorrect line
1776 <li>Grouped annotation graph label display is corrupted
1777 for lots of labels</li>
1782 <div align="center">
1783 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
1786 <td><em>Application</em>
1788 <li>Jalview Desktop News Reader</li>
1789 <li>Tweaked default layout of web services menu</li>
1790 <li>View/alignment association menu to enable user to
1791 easily specify which alignment a multi-structure view takes
1792 its colours/correspondences from</li>
1793 <li>Allow properties file location to be specified as URL</li>
1794 <li>Extend Jalview project to preserve associations
1795 between many alignment views and a single Jmol display</li>
1796 <li>Store annotation row height in Jalview project file</li>
1797 <li>Annotation row column label formatting attributes
1798 stored in project file</li>
1799 <li>Annotation row order for auto-calculated annotation
1800 rows preserved in Jalview project file</li>
1801 <li>Visual progress indication when Jalview state is
1802 saved using Desktop window menu</li>
1803 <li>Visual indication that command line arguments are
1804 still being processed</li>
1805 <li>Groovy script execution from URL</li>
1806 <li>Colour by annotation default min and max colours in
1808 <li>Automatically associate PDB files dragged onto an
1809 alignment with sequences that have high similarity and
1811 <li>Update JGoogleAnalytics to latest release (0.3)</li>
1812 <li>'view structures' option to open many
1813 structures in same window</li>
1814 <li>Sort associated views menu option for tree panel</li>
1815 <li>Group all JABA and non-JABA services for a particular
1816 analysis function in its own submenu</li>
1817 </ul> <em>Applet</em>
1819 <li>Userdefined and autogenerated annotation rows for
1821 <li>Adjustment of alignment annotation pane height</li>
1822 <li>Annotation scrollbar for annotation panel</li>
1823 <li>Drag to reorder annotation rows in annotation panel</li>
1824 <li>'automaticScrolling' parameter</li>
1825 <li>Allow sequences with partial ID string matches to be
1826 annotated from GFF/Jalview features files</li>
1827 <li>Sequence logo annotation row in applet</li>
1828 <li>Absolute paths relative to host server in applet
1829 parameters are treated as such</li>
1830 <li>New in the JalviewLite javascript API:
1832 <li>JalviewLite.js javascript library</li>
1833 <li>Javascript callbacks for
1835 <li>Applet initialisation</li>
1836 <li>Sequence/alignment mouse-overs and selections</li>
1839 <li>scrollTo row and column alignment scrolling
1841 <li>Select sequence/alignment regions from javascript</li>
1842 <li>javascript structure viewer harness to pass
1843 messages between Jmol and Jalview when running as
1844 distinct applets</li>
1845 <li>sortBy method</li>
1846 <li>Set of applet and application examples shipped
1847 with documentation</li>
1848 <li>New example to demonstrate JalviewLite and Jmol
1849 javascript message exchange</li>
1851 </ul> <em>General</em>
1853 <li>Enable Jmol displays to be associated with multiple
1854 multiple alignments</li>
1855 <li>Option to automatically sort alignment with new tree</li>
1856 <li>User configurable link to enable redirects to a
1857 www.Jalview.org mirror</li>
1858 <li>Jmol colours option for Jmol displays</li>
1859 <li>Configurable newline string when writing alignment
1860 and other flat files</li>
1861 <li>Allow alignment annotation description lines to
1862 contain html tags</li>
1863 </ul> <em>Documentation and Development</em>
1865 <li>Add groovy test harness for bulk load testing to
1867 <li>Groovy script to load and align a set of sequences
1868 using a web service before displaying the result in the
1869 Jalview desktop</li>
1870 <li>Restructured javascript and applet api documentation</li>
1871 <li>Ant target to publish example html files with applet
1873 <li>Netbeans project for building Jalview from source</li>
1874 <li>ant task to create online javadoc for Jalview source</li>
1876 <td><em>Application</em>
1878 <li>User defined colourscheme throws exception when
1879 current built in colourscheme is saved as new scheme</li>
1880 <li>AlignFrame->Save in application pops up save
1881 dialog for valid filename/format</li>
1882 <li>Cannot view associated structure for UniProt sequence</li>
1883 <li>PDB file association breaks for UniProt sequence
1885 <li>Associate PDB from file dialog does not tell you
1886 which sequence is to be associated with the file</li>
1887 <li>Find All raises null pointer exception when query
1888 only matches sequence IDs</li>
1889 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
1890 <li>Jalview project with Jmol views created with Jalview
1891 2.4 cannot be loaded</li>
1892 <li>Filetype associations not installed for webstart
1894 <li>Two or more chains in a single PDB file associated
1895 with sequences in different alignments do not get coloured
1896 by their associated sequence</li>
1897 <li>Visibility status of autocalculated annotation row
1898 not preserved when project is loaded</li>
1899 <li>Annotation row height and visibility attributes not
1900 stored in Jalview project</li>
1901 <li>Tree bootstraps are not preserved when saved as a
1902 Jalview project</li>
1903 <li>Envision2 workflow tooltips are corrupted</li>
1904 <li>Enabling show group conservation also enables colour
1905 by conservation</li>
1906 <li>Duplicate group associated conservation or consensus
1907 created on new view</li>
1908 <li>Annotation scrollbar not displayed after 'show
1909 all hidden annotation rows' option selected</li>
1910 <li>Alignment quality not updated after alignment
1911 annotation row is hidden then shown</li>
1912 <li>Preserve colouring of structures coloured by
1913 sequences in pre Jalview 2.7 projects</li>
1914 <li>Web service job parameter dialog is not laid out
1916 <li>Web services menu not refreshed after 'reset
1917 services' button is pressed in preferences</li>
1918 <li>Annotation off by one in Jalview v2_3 example project</li>
1919 <li>Structures imported from file and saved in project
1920 get name like jalview_pdb1234.txt when reloaded</li>
1921 <li>Jalview does not always retrieve progress of a JABAWS
1922 job execution in full once it is complete</li>
1923 </ul> <em>Applet</em>
1925 <li>Alignment height set incorrectly when lots of
1926 annotation rows are displayed</li>
1927 <li>Relative URLs in feature HTML text not resolved to
1929 <li>View follows highlighting does not work for positions
1931 <li><= shown as = in tooltip</li>
1932 <li>Export features raises exception when no features
1934 <li>Separator string used for serialising lists of IDs
1935 for javascript api is modified when separator string
1936 provided as parameter</li>
1937 <li>Null pointer exception when selecting tree leaves for
1938 alignment with no existing selection</li>
1939 <li>Relative URLs for datasources assumed to be relative
1940 to applet's codebase</li>
1941 <li>Status bar not updated after finished searching and
1942 search wraps around to first result</li>
1943 <li>StructureSelectionManager instance shared between
1944 several Jalview applets causes race conditions and memory
1946 <li>Hover tooltip and mouseover of position on structure
1947 not sent from Jmol in applet</li>
1948 <li>Certain sequences of javascript method calls to
1949 applet API fatally hang browser</li>
1950 </ul> <em>General</em>
1952 <li>View follows structure mouseover scrolls beyond
1953 position with wrapped view and hidden regions</li>
1954 <li>Find sequence position moves to wrong residue
1955 with/without hidden columns</li>
1956 <li>Sequence length given in alignment properties window
1958 <li>InvalidNumberFormat exceptions thrown when trying to
1959 import PDB like structure files</li>
1960 <li>Positional search results are only highlighted
1961 between user-supplied sequence start/end bounds</li>
1962 <li>End attribute of sequence is not validated</li>
1963 <li>Find dialog only finds first sequence containing a
1964 given sequence position</li>
1965 <li>Sequence numbering not preserved in MSF alignment
1967 <li>Jalview PDB file reader does not extract sequence
1968 from nucleotide chains correctly</li>
1969 <li>Structure colours not updated when tree partition
1970 changed in alignment</li>
1971 <li>Sequence associated secondary structure not correctly
1972 parsed in interleaved stockholm</li>
1973 <li>Colour by annotation dialog does not restore current
1975 <li>Hiding (nearly) all sequences doesn't work
1977 <li>Sequences containing lowercase letters are not
1978 properly associated with their pdb files</li>
1979 </ul> <em>Documentation and Development</em>
1981 <li>schemas/JalviewWsParamSet.xsd corrupted by
1982 ApplyCopyright tool</li>
1987 <div align="center">
1988 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
1991 <td><em>Application</em>
1993 <li>New warning dialog when the Jalview Desktop cannot
1994 contact web services</li>
1995 <li>JABA service parameters for a preset are shown in
1996 service job window</li>
1997 <li>JABA Service menu entries reworded</li>
2001 <li>Modeller PIR IO broken - cannot correctly import a
2002 pir file emitted by Jalview</li>
2003 <li>Existing feature settings transferred to new
2004 alignment view created from cut'n'paste</li>
2005 <li>Improved test for mixed amino/nucleotide chains when
2006 parsing PDB files</li>
2007 <li>Consensus and conservation annotation rows
2008 occasionally become blank for all new windows</li>
2009 <li>Exception raised when right clicking above sequences
2010 in wrapped view mode</li>
2011 </ul> <em>Application</em>
2013 <li>multiple multiply aligned structure views cause cpu
2014 usage to hit 100% and computer to hang</li>
2015 <li>Web Service parameter layout breaks for long user
2016 parameter names</li>
2017 <li>Jaba service discovery hangs desktop if Jaba server
2024 <div align="center">
2025 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2028 <td><em>Application</em>
2030 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2031 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2034 <li>Web Services preference tab</li>
2035 <li>Analysis parameters dialog box and user defined
2037 <li>Improved speed and layout of Envision2 service menu</li>
2038 <li>Superpose structures using associated sequence
2040 <li>Export coordinates and projection as CSV from PCA
2042 </ul> <em>Applet</em>
2044 <li>enable javascript: execution by the applet via the
2045 link out mechanism</li>
2046 </ul> <em>Other</em>
2048 <li>Updated the Jmol Jalview interface to work with Jmol
2050 <li>The Jalview Desktop and JalviewLite applet now
2051 require Java 1.5</li>
2052 <li>Allow Jalview feature colour specification for GFF
2053 sequence annotation files</li>
2054 <li>New 'colour by label' keword in Jalview feature file
2055 type colour specification</li>
2056 <li>New Jalview Desktop Groovy API method that allows a
2057 script to check if it being run in an interactive session or
2058 in a batch operation from the Jalview command line</li>
2062 <li>clustalx colourscheme colours Ds preferentially when
2063 both D+E are present in over 50% of the column</li>
2064 </ul> <em>Application</em>
2066 <li>typo in AlignmentFrame->View->Hide->all but
2067 selected Regions menu item</li>
2068 <li>sequence fetcher replaces ',' for ';' when the ',' is
2069 part of a valid accession ID</li>
2070 <li>fatal OOM if object retrieved by sequence fetcher
2071 runs out of memory</li>
2072 <li>unhandled Out of Memory Error when viewing pca
2073 analysis results</li>
2074 <li>InstallAnywhere builds fail to launch on OS X java
2075 10.5 update 4 (due to apple Java 1.6 update)</li>
2076 <li>Installanywhere Jalview silently fails to launch</li>
2077 </ul> <em>Applet</em>
2079 <li>Jalview.getFeatureGroups() raises an
2080 ArrayIndexOutOfBoundsException if no feature groups are
2087 <div align="center">
2088 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2094 <li>Alignment prettyprinter doesn't cope with long
2096 <li>clustalx colourscheme colours Ds preferentially when
2097 both D+E are present in over 50% of the column</li>
2098 <li>nucleic acid structures retrieved from PDB do not
2099 import correctly</li>
2100 <li>More columns get selected than were clicked on when a
2101 number of columns are hidden</li>
2102 <li>annotation label popup menu not providing correct
2103 add/hide/show options when rows are hidden or none are
2105 <li>Stockholm format shown in list of readable formats,
2106 and parser copes better with alignments from RFAM.</li>
2107 <li>CSV output of consensus only includes the percentage
2108 of all symbols if sequence logo display is enabled</li>
2110 </ul> <em>Applet</em>
2112 <li>annotation panel disappears when annotation is
2114 </ul> <em>Application</em>
2116 <li>Alignment view not redrawn properly when new
2117 alignment opened where annotation panel is visible but no
2118 annotations are present on alignment</li>
2119 <li>pasted region containing hidden columns is
2120 incorrectly displayed in new alignment window</li>
2121 <li>Jalview slow to complete operations when stdout is
2122 flooded (fix is to close the Jalview console)</li>
2123 <li>typo in AlignmentFrame->View->Hide->all but
2124 selected Rregions menu item.</li>
2125 <li>inconsistent group submenu and Format submenu entry
2126 'Un' or 'Non'conserved</li>
2127 <li>Sequence feature settings are being shared by
2128 multiple distinct alignments</li>
2129 <li>group annotation not recreated when tree partition is
2131 <li>double click on group annotation to select sequences
2132 does not propagate to associated trees</li>
2133 <li>Mac OSX specific issues:
2135 <li>exception raised when mouse clicked on desktop
2136 window background</li>
2137 <li>Desktop menu placed on menu bar and application
2138 name set correctly</li>
2139 <li>sequence feature settings not wide enough for the
2140 save feature colourscheme button</li>
2149 <div align="center">
2150 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2153 <td><em>New Capabilities</em>
2155 <li>URL links generated from description line for
2156 regular-expression based URL links (applet and application)
2163 <li>Non-positional feature URL links are shown in link
2165 <li>Linked viewing of nucleic acid sequences and
2167 <li>Automatic Scrolling option in View menu to display
2168 the currently highlighted region of an alignment.</li>
2169 <li>Order an alignment by sequence length, or using the
2170 average score or total feature count for each sequence.</li>
2171 <li>Shading features by score or associated description</li>
2172 <li>Subdivide alignment and groups based on identity of
2173 selected subsequence (Make Groups from Selection).</li>
2174 <li>New hide/show options including Shift+Control+H to
2175 hide everything but the currently selected region.</li>
2176 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2177 </ul> <em>Application</em>
2179 <li>Fetch DB References capabilities and UI expanded to
2180 support retrieval from DAS sequence sources</li>
2181 <li>Local DAS Sequence sources can be added via the
2182 command line or via the Add local source dialog box.</li>
2183 <li>DAS Dbref and DbxRef feature types are parsed as
2184 database references and protein_name is parsed as
2185 description line (BioSapiens terms).</li>
2186 <li>Enable or disable non-positional feature and database
2187 references in sequence ID tooltip from View menu in
2189 <!-- <li>New hidden columns and rows and representatives capabilities
2190 in annotations file (in progress - not yet fully implemented)</li> -->
2191 <li>Group-associated consensus, sequence logos and
2192 conservation plots</li>
2193 <li>Symbol distributions for each column can be exported
2194 and visualized as sequence logos</li>
2195 <li>Optionally scale multi-character column labels to fit
2196 within each column of annotation row<!-- todo for applet -->
2198 <li>Optional automatic sort of associated alignment view
2199 when a new tree is opened.</li>
2200 <li>Jalview Java Console</li>
2201 <li>Better placement of desktop window when moving
2202 between different screens.</li>
2203 <li>New preference items for sequence ID tooltip and
2204 consensus annotation</li>
2205 <li>Client to submit sequences and IDs to Envision2
2207 <li><em>Vamsas Capabilities</em>
2209 <li>Improved VAMSAS synchronization (Jalview archive
2210 used to preserve views, structures, and tree display
2212 <li>Import of vamsas documents from disk or URL via
2214 <li>Sharing of selected regions between views and
2215 with other VAMSAS applications (Experimental feature!)</li>
2216 <li>Updated API to VAMSAS version 0.2</li>
2218 </ul> <em>Applet</em>
2220 <li>Middle button resizes annotation row height</li>
2223 <li>sortByTree (true/false) - automatically sort the
2224 associated alignment view by the tree when a new tree is
2226 <li>showTreeBootstraps (true/false) - show or hide
2227 branch bootstraps (default is to show them if available)</li>
2228 <li>showTreeDistances (true/false) - show or hide
2229 branch lengths (default is to show them if available)</li>
2230 <li>showUnlinkedTreeNodes (true/false) - indicate if
2231 unassociated nodes should be highlighted in the tree
2233 <li>heightScale and widthScale (1.0 or more) -
2234 increase the height or width of a cell in the alignment
2235 grid relative to the current font size.</li>
2238 <li>Non-positional features displayed in sequence ID
2240 </ul> <em>Other</em>
2242 <li>Features format: graduated colour definitions and
2243 specification of feature scores</li>
2244 <li>Alignment Annotations format: new keywords for group
2245 associated annotation (GROUP_REF) and annotation row display
2246 properties (ROW_PROPERTIES)</li>
2247 <li>XML formats extended to support graduated feature
2248 colourschemes, group associated annotation, and profile
2249 visualization settings.</li></td>
2252 <li>Source field in GFF files parsed as feature source
2253 rather than description</li>
2254 <li>Non-positional features are now included in sequence
2255 feature and gff files (controlled via non-positional feature
2256 visibility in tooltip).</li>
2257 <li>URL links generated for all feature links (bugfix)</li>
2258 <li>Added URL embedding instructions to features file
2260 <li>Codons containing ambiguous nucleotides translated as
2261 'X' in peptide product</li>
2262 <li>Match case switch in find dialog box works for both
2263 sequence ID and sequence string and query strings do not
2264 have to be in upper case to match case-insensitively.</li>
2265 <li>AMSA files only contain first column of
2266 multi-character column annotation labels</li>
2267 <li>Jalview Annotation File generation/parsing consistent
2268 with documentation (e.g. Stockholm annotation can be
2269 exported and re-imported)</li>
2270 <li>PDB files without embedded PDB IDs given a friendly
2272 <li>Find incrementally searches ID string matches as well
2273 as subsequence matches, and correctly reports total number
2277 <li>Better handling of exceptions during sequence
2279 <li>Dasobert generated non-positional feature URL
2280 link text excludes the start_end suffix</li>
2281 <li>DAS feature and source retrieval buttons disabled
2282 when fetch or registry operations in progress.</li>
2283 <li>PDB files retrieved from URLs are cached properly</li>
2284 <li>Sequence description lines properly shared via
2286 <li>Sequence fetcher fetches multiple records for all
2288 <li>Ensured that command line das feature retrieval
2289 completes before alignment figures are generated.</li>
2290 <li>Reduced time taken when opening file browser for
2292 <li>isAligned check prior to calculating tree, PCA or
2293 submitting an MSA to JNet now excludes hidden sequences.</li>
2294 <li>User defined group colours properly recovered
2295 from Jalview projects.</li>
2304 <div align="center">
2305 <strong>2.4.0.b2</strong><br> 28/10/2009
2310 <li>Experimental support for google analytics usage
2312 <li>Jalview privacy settings (user preferences and docs).</li>
2317 <li>Race condition in applet preventing startup in
2319 <li>Exception when feature created from selection beyond
2320 length of sequence.</li>
2321 <li>Allow synthetic PDB files to be imported gracefully</li>
2322 <li>Sequence associated annotation rows associate with
2323 all sequences with a given id</li>
2324 <li>Find function matches case-insensitively for sequence
2325 ID string searches</li>
2326 <li>Non-standard characters do not cause pairwise
2327 alignment to fail with exception</li>
2328 </ul> <em>Application Issues</em>
2330 <li>Sequences are now validated against EMBL database</li>
2331 <li>Sequence fetcher fetches multiple records for all
2333 </ul> <em>InstallAnywhere Issues</em>
2335 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2336 issue with installAnywhere mechanism)</li>
2337 <li>Command line launching of JARs from InstallAnywhere
2338 version (java class versioning error fixed)</li>
2345 <div align="center">
2346 <strong>2.4</strong><br> 27/8/2008
2349 <td><em>User Interface</em>
2351 <li>Linked highlighting of codon and amino acid from
2352 translation and protein products</li>
2353 <li>Linked highlighting of structure associated with
2354 residue mapping to codon position</li>
2355 <li>Sequence Fetcher provides example accession numbers
2356 and 'clear' button</li>
2357 <li>MemoryMonitor added as an option under Desktop's
2359 <li>Extract score function to parse whitespace separated
2360 numeric data in description line</li>
2361 <li>Column labels in alignment annotation can be centred.</li>
2362 <li>Tooltip for sequence associated annotation give name
2364 </ul> <em>Web Services and URL fetching</em>
2366 <li>JPred3 web service</li>
2367 <li>Prototype sequence search client (no public services
2369 <li>Fetch either seed alignment or full alignment from
2371 <li>URL Links created for matching database cross
2372 references as well as sequence ID</li>
2373 <li>URL Links can be created using regular-expressions</li>
2374 </ul> <em>Sequence Database Connectivity</em>
2376 <li>Retrieval of cross-referenced sequences from other
2378 <li>Generalised database reference retrieval and
2379 validation to all fetchable databases</li>
2380 <li>Fetch sequences from DAS sources supporting the
2381 sequence command</li>
2382 </ul> <em>Import and Export</em>
2383 <li>export annotation rows as CSV for spreadsheet import</li>
2384 <li>Jalview projects record alignment dataset associations,
2385 EMBL products, and cDNA sequence mappings</li>
2386 <li>Sequence Group colour can be specified in Annotation
2388 <li>Ad-hoc colouring of group in Annotation File using RGB
2389 triplet as name of colourscheme</li>
2390 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2392 <li>treenode binding for VAMSAS tree exchange</li>
2393 <li>local editing and update of sequences in VAMSAS
2394 alignments (experimental)</li>
2395 <li>Create new or select existing session to join</li>
2396 <li>load and save of vamsas documents</li>
2397 </ul> <em>Application command line</em>
2399 <li>-tree parameter to open trees (introduced for passing
2401 <li>-fetchfrom command line argument to specify nicknames
2402 of DAS servers to query for alignment features</li>
2403 <li>-dasserver command line argument to add new servers
2404 that are also automatically queried for features</li>
2405 <li>-groovy command line argument executes a given groovy
2406 script after all input data has been loaded and parsed</li>
2407 </ul> <em>Applet-Application data exchange</em>
2409 <li>Trees passed as applet parameters can be passed to
2410 application (when using "View in full
2411 application")</li>
2412 </ul> <em>Applet Parameters</em>
2414 <li>feature group display control parameter</li>
2415 <li>debug parameter</li>
2416 <li>showbutton parameter</li>
2417 </ul> <em>Applet API methods</em>
2419 <li>newView public method</li>
2420 <li>Window (current view) specific get/set public methods</li>
2421 <li>Feature display control methods</li>
2422 <li>get list of currently selected sequences</li>
2423 </ul> <em>New Jalview distribution features</em>
2425 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2426 <li>RELEASE file gives build properties for the latest
2427 Jalview release.</li>
2428 <li>Java 1.1 Applet build made easier and donotobfuscate
2429 property controls execution of obfuscator</li>
2430 <li>Build target for generating source distribution</li>
2431 <li>Debug flag for javacc</li>
2432 <li>.jalview_properties file is documented (slightly) in
2433 jalview.bin.Cache</li>
2434 <li>Continuous Build Integration for stable and
2435 development version of Application, Applet and source
2440 <li>selected region output includes visible annotations
2441 (for certain formats)</li>
2442 <li>edit label/displaychar contains existing label/char
2444 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2445 <li>shorter peptide product names from EMBL records</li>
2446 <li>Newick string generator makes compact representations</li>
2447 <li>bootstrap values parsed correctly for tree files with
2449 <li>pathological filechooser bug avoided by not allowing
2450 filenames containing a ':'</li>
2451 <li>Fixed exception when parsing GFF files containing
2452 global sequence features</li>
2453 <li>Alignment datasets are finalized only when number of
2454 references from alignment sequences goes to zero</li>
2455 <li>Close of tree branch colour box without colour
2456 selection causes cascading exceptions</li>
2457 <li>occasional negative imgwidth exceptions</li>
2458 <li>better reporting of non-fatal warnings to user when
2459 file parsing fails.</li>
2460 <li>Save works when Jalview project is default format</li>
2461 <li>Save as dialog opened if current alignment format is
2462 not a valid output format</li>
2463 <li>UniProt canonical names introduced for both das and
2465 <li>Histidine should be midblue (not pink!) in Zappo</li>
2466 <li>error messages passed up and output when data read
2468 <li>edit undo recovers previous dataset sequence when
2469 sequence is edited</li>
2470 <li>allow PDB files without pdb ID HEADER lines (like
2471 those generated by MODELLER) to be read in properly</li>
2472 <li>allow reading of JPred concise files as a normal
2474 <li>Stockholm annotation parsing and alignment properties
2475 import fixed for PFAM records</li>
2476 <li>Structure view windows have correct name in Desktop
2478 <li>annotation consisting of sequence associated scores
2479 can be read and written correctly to annotation file</li>
2480 <li>Aligned cDNA translation to aligned peptide works
2482 <li>Fixed display of hidden sequence markers and
2483 non-italic font for representatives in Applet</li>
2484 <li>Applet Menus are always embedded in applet window on
2486 <li>Newly shown features appear at top of stack (in
2488 <li>Annotations added via parameter not drawn properly
2489 due to null pointer exceptions</li>
2490 <li>Secondary structure lines are drawn starting from
2491 first column of alignment</li>
2492 <li>UniProt XML import updated for new schema release in
2494 <li>Sequence feature to sequence ID match for Features
2495 file is case-insensitive</li>
2496 <li>Sequence features read from Features file appended to
2497 all sequences with matching IDs</li>
2498 <li>PDB structure coloured correctly for associated views
2499 containing a sub-sequence</li>
2500 <li>PDB files can be retrieved by applet from Jar files</li>
2501 <li>feature and annotation file applet parameters
2502 referring to different directories are retrieved correctly</li>
2503 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
2504 <li>Fixed application hang whilst waiting for
2505 splash-screen version check to complete</li>
2506 <li>Applet properly URLencodes input parameter values
2507 when passing them to the launchApp service</li>
2508 <li>display name and local features preserved in results
2509 retrieved from web service</li>
2510 <li>Visual delay indication for sequence retrieval and
2511 sequence fetcher initialisation</li>
2512 <li>updated Application to use DAS 1.53e version of
2513 dasobert DAS client</li>
2514 <li>Re-instated Full AMSA support and .amsa file
2516 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
2524 <div align="center">
2525 <strong>2.3</strong><br> 9/5/07
2530 <li>Jmol 11.0.2 integration</li>
2531 <li>PDB views stored in Jalview XML files</li>
2532 <li>Slide sequences</li>
2533 <li>Edit sequence in place</li>
2534 <li>EMBL CDS features</li>
2535 <li>DAS Feature mapping</li>
2536 <li>Feature ordering</li>
2537 <li>Alignment Properties</li>
2538 <li>Annotation Scores</li>
2539 <li>Sort by scores</li>
2540 <li>Feature/annotation editing in applet</li>
2545 <li>Headless state operation in 2.2.1</li>
2546 <li>Incorrect and unstable DNA pairwise alignment</li>
2547 <li>Cut and paste of sequences with annotation</li>
2548 <li>Feature group display state in XML</li>
2549 <li>Feature ordering in XML</li>
2550 <li>blc file iteration selection using filename # suffix</li>
2551 <li>Stockholm alignment properties</li>
2552 <li>Stockhom alignment secondary structure annotation</li>
2553 <li>2.2.1 applet had no feature transparency</li>
2554 <li>Number pad keys can be used in cursor mode</li>
2555 <li>Structure Viewer mirror image resolved</li>
2562 <div align="center">
2563 <strong>2.2.1</strong><br> 12/2/07
2568 <li>Non standard characters can be read and displayed
2569 <li>Annotations/Features can be imported/exported to the
2571 <li>Applet allows editing of sequence/annotation/group
2572 name & description
2573 <li>Preference setting to display sequence name in
2575 <li>Annotation file format extended to allow
2576 Sequence_groups to be defined
2577 <li>Default opening of alignment overview panel can be
2578 specified in preferences
2579 <li>PDB residue numbering annotation added to associated
2585 <li>Applet crash under certain Linux OS with Java 1.6
2587 <li>Annotation file export / import bugs fixed
2588 <li>PNG / EPS image output bugs fixed
2594 <div align="center">
2595 <strong>2.2</strong><br> 27/11/06
2600 <li>Multiple views on alignment
2601 <li>Sequence feature editing
2602 <li>"Reload" alignment
2603 <li>"Save" to current filename
2604 <li>Background dependent text colour
2605 <li>Right align sequence ids
2606 <li>User-defined lower case residue colours
2609 <li>Menu item accelerator keys
2610 <li>Control-V pastes to current alignment
2611 <li>Cancel button for DAS Feature Fetching
2612 <li>PCA and PDB Viewers zoom via mouse roller
2613 <li>User-defined sub-tree colours and sub-tree selection
2620 <li>'New Window' button on the 'Output to Text box'
2625 <li>New memory efficient Undo/Redo System
2626 <li>Optimised symbol lookups and conservation/consensus
2628 <li>Region Conservation/Consensus recalculated after
2630 <li>Fixed Remove Empty Columns Bug (empty columns at end
2632 <li>Slowed DAS Feature Fetching for increased robustness.
2639 <li>Made angle brackets in ASCII feature descriptions
2641 <li>Re-instated Zoom function for PCA
2642 <li>Sequence descriptions conserved in web service
2644 <li>UniProt ID discoverer uses any word separated by
2646 <li>WsDbFetch query/result association resolved
2647 <li>Tree leaf to sequence mapping improved
2648 <li>Smooth fonts switch moved to FontChooser dialog box.
2660 <div align="center">
2661 <strong>2.1.1</strong><br> 12/9/06
2666 <li>Copy consensus sequence to clipboard</li>
2671 <li>Image output - rightmost residues are rendered if
2672 sequence id panel has been resized</li>
2673 <li>Image output - all offscreen group boundaries are
2675 <li>Annotation files with sequence references - all
2676 elements in file are relative to sequence position</li>
2677 <li>Mac Applet users can use Alt key for group editing</li>
2683 <div align="center">
2684 <strong>2.1</strong><br> 22/8/06
2689 <li>MAFFT Multiple Alignment in default Web Service list</li>
2690 <li>DAS Feature fetching</li>
2691 <li>Hide sequences and columns</li>
2692 <li>Export Annotations and Features</li>
2693 <li>GFF file reading / writing</li>
2694 <li>Associate structures with sequences from local PDB
2696 <li>Add sequences to exisiting alignment</li>
2697 <li>Recently opened files / URL lists</li>
2698 <li>Applet can launch the full application</li>
2699 <li>Applet has transparency for features (Java 1.2
2701 <li>Applet has user defined colours parameter</li>
2702 <li>Applet can load sequences from parameter
2703 "sequence<em>x</em>"
2709 <li>Redundancy Panel reinstalled in the Applet</li>
2710 <li>Monospaced font - EPS / rescaling bug fixed</li>
2711 <li>Annotation files with sequence references bug fixed</li>
2717 <div align="center">
2718 <strong>2.08.1</strong><br> 2/5/06
2723 <li>Change case of selected region from Popup menu</li>
2724 <li>Choose to match case when searching</li>
2725 <li>Middle mouse button and mouse movement can compress /
2726 expand the visible width and height of the alignment</li>
2731 <li>Annotation Panel displays complete JNet results</li>
2737 <div align="center">
2738 <strong>2.08b</strong><br> 18/4/06
2744 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
2745 <li>Righthand label on wrapped alignments shows correct
2752 <div align="center">
2753 <strong>2.08</strong><br> 10/4/06
2758 <li>Editing can be locked to the selection area</li>
2759 <li>Keyboard editing</li>
2760 <li>Create sequence features from searches</li>
2761 <li>Precalculated annotations can be loaded onto
2763 <li>Features file allows grouping of features</li>
2764 <li>Annotation Colouring scheme added</li>
2765 <li>Smooth fonts off by default - Faster rendering</li>
2766 <li>Choose to toggle Autocalculate Consensus On/Off</li>
2771 <li>Drag & Drop fixed on Linux</li>
2772 <li>Jalview Archive file faster to load/save, sequence
2773 descriptions saved.</li>
2779 <div align="center">
2780 <strong>2.07</strong><br> 12/12/05
2785 <li>PDB Structure Viewer enhanced</li>
2786 <li>Sequence Feature retrieval and display enhanced</li>
2787 <li>Choose to output sequence start-end after sequence
2788 name for file output</li>
2789 <li>Sequence Fetcher WSDBFetch@EBI</li>
2790 <li>Applet can read feature files, PDB files and can be
2791 used for HTML form input</li>
2796 <li>HTML output writes groups and features</li>
2797 <li>Group editing is Control and mouse click</li>
2798 <li>File IO bugs</li>
2804 <div align="center">
2805 <strong>2.06</strong><br> 28/9/05
2810 <li>View annotations in wrapped mode</li>
2811 <li>More options for PCA viewer</li>
2816 <li>GUI bugs resolved</li>
2817 <li>Runs with -nodisplay from command line</li>
2823 <div align="center">
2824 <strong>2.05b</strong><br> 15/9/05
2829 <li>Choose EPS export as lineart or text</li>
2830 <li>Jar files are executable</li>
2831 <li>Can read in Uracil - maps to unknown residue</li>
2836 <li>Known OutOfMemory errors give warning message</li>
2837 <li>Overview window calculated more efficiently</li>
2838 <li>Several GUI bugs resolved</li>
2844 <div align="center">
2845 <strong>2.05</strong><br> 30/8/05
2850 <li>Edit and annotate in "Wrapped" view</li>
2855 <li>Several GUI bugs resolved</li>
2861 <div align="center">
2862 <strong>2.04</strong><br> 24/8/05
2867 <li>Hold down mouse wheel & scroll to change font
2873 <li>Improved JPred client reliability</li>
2874 <li>Improved loading of Jalview files</li>
2880 <div align="center">
2881 <strong>2.03</strong><br> 18/8/05
2886 <li>Set Proxy server name and port in preferences</li>
2887 <li>Multiple URL links from sequence ids</li>
2888 <li>User Defined Colours can have a scheme name and added
2890 <li>Choose to ignore gaps in consensus calculation</li>
2891 <li>Unix users can set default web browser</li>
2892 <li>Runs without GUI for batch processing</li>
2893 <li>Dynamically generated Web Service Menus</li>
2898 <li>InstallAnywhere download for Sparc Solaris</li>
2904 <div align="center">
2905 <strong>2.02</strong><br> 18/7/05
2911 <li>Copy & Paste order of sequences maintains
2912 alignment order.</li>
2918 <div align="center">
2919 <strong>2.01</strong><br> 12/7/05
2924 <li>Use delete key for deleting selection.</li>
2925 <li>Use Mouse wheel to scroll sequences.</li>
2926 <li>Help file updated to describe how to add alignment
2928 <li>Version and build date written to build properties
2930 <li>InstallAnywhere installation will check for updates
2931 at launch of Jalview.</li>
2936 <li>Delete gaps bug fixed.</li>
2937 <li>FileChooser sorts columns.</li>
2938 <li>Can remove groups one by one.</li>
2939 <li>Filechooser icons installed.</li>
2940 <li>Finder ignores return character when searching.
2941 Return key will initiate a search.<br>
2948 <div align="center">
2949 <strong>2.0</strong><br> 20/6/05
2954 <li>New codebase</li>