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>
84 <li><!-- JAL-2388 -->Hidden columns and sequences can be omitted in Overview</li>
86 <!-- JAL-2535 -->Posterior probability annotation from
87 Stockholm files imported as sequence associated annotation
90 <!-- JAL-2533 -->Sequence names don't include file
91 extension when importing structure files without embedded
92 names or PDB accessions
99 Experimental Features Checkbox in Desktop's Tools
100 menu to hide or show untested features in the application.
102 <li><!-- JAL-1476 -->Warning in alignment status bar when there are not enough columns to superimpose structures in Chimera</li>
103 <li><!-- JAL-1596 -->Faster Chimera/Jalview communication by file-based command exchange</li>
104 <li><!-- JAL-2316, -->URLs for viewing database cross-references provided by identifiers.org and the EMBL-EBI's MIRIAM DB</li>
105 <li><!-- JAL-2549 -->Updated JABAWS client to v2.2</li>
107 <em>Experimental features</em>
110 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
111 to transfer Chimera's structure attributes as Jalview
112 features, and vice-versa.
120 <li><!-- JAL-2474 -->Added PrivelegedAccessor to test suite</li>
121 <li><!-- JAL-2326 -->Prevent or clear modal dialogs raised during tests</li>
124 </div></td><td><div align="left">
128 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
129 matrix - C->R should be '3'<br />Old matrix restored with
130 this one-line groovy script:<br />jalview.schemes.ResidueProperties.BLOSUM62[4][1]=3
133 <!-- JAL-2397 -->Fixed Jalview's treatment of gaps in PCA
134 and substitution matrix based Tree calculations.<br />In
135 earlier versions of Jalview, gaps matching gaps were
136 penalised, and gaps matching non-gaps penalised even more.
137 In the PCA calculation, gaps were actually treated as
138 non-gaps - so different costs were applied, which mean't
139 Jalview's PCAs were different to those produced by
140 SeqSpace.<br />Jalview now treats gaps in the same way as
141 SeqSpace (ie it scores them as 0). To restore pre-2.10.2
143 jalview.viewmodel.PCAModel.scoreGapAsAny=true // for
145 jalview.viewmodel.PCAModel.scoreGapAsAny=false // to
148 <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>
149 <li><!-- JAL-2430 -->Hidden regions in alignment views are not coloured in linked structure views</li>
150 <li><!-- JAL-2419 -->Current selection lost if popup menu opened on a region of alignment without groups</li>
151 <li><!-- JAL-2374 -->Popup menu not always shown for regions of an alignment with overlapping groups</li>
152 <li><!-- JAL-2310 -->Finder double counts if both a sequence's name and description match</li>
153 <li><!-- JAL-2370 -->Hiding column selection containing two hidden regions results in incorrect hidden regions</li>
154 <li><!-- JAL-2377 -->PCA calculation could hang when generating output report when working with highly redundant alignments</li>
155 <li><!-- JAL-2365 -->Cannot configure feature colours with lightGray or darkGray via features file</li>
156 <li><!-- JAL-2421 -->Overview window visible region moves erratically when hidden rows or columns are present</li>
157 <li><!-- JAL-2362 -->Per-residue colourschemes applied via the Structure Viewer's colour menu don't correspond to sequence colouring</li>
158 <li><!-- JAL-2405 -->Protein specific colours only offered in colour and group colour menu for protein alignments</li>
159 <li><!-- JAL-2386 -->'Apply to all groups' setting when changing colour does not apply Conservation slider value to all groups</li>
160 <li><!-- JAL-2385 -->Colour threshold slider doesn't update to reflect currently selected view or group's shading thresholds</li>
161 <li><!-- JAL-2373 -->Percentage identity and conservation menu items do not show a tick or allow shading to be disabled</li>
162 <li><!-- JAL-2385 -->Conservation shading or PID threshold lost when base colourscheme changed if slider not visible</li>
163 <li><!-- JAL-2547 -->Sequence features shown in tooltip for gaps before start of features</li>
167 <li><!-- JAL-2401 -->Easier creation of colours for all 'Lower case' residues (button in colourscheme editor debugged and new documentation and tooltips added)</li>
168 <li><!-- JAL-2399-->Text colour threshold's 'Cancel' button doesn't restore group-specific text colour thresholds</li>
169 <li><!-- JAL-2243 -->Feature settings panel does not update as new features are added to alignment</li>
170 <li><!-- JAL-2436 -->Structure viewer's View -> Colour By view selection menu changes colours of alignment views</li>
171 <li><!-- JAL-2366 -->Proxy server address and port always appear enabled in Preferences->Connections</li>
172 <li><!-- JAL-2426 -->Spurious exceptions in console raised from alignment calculation workers after alignment has been closed</li>
173 <li><!-- JAL-1608 -->Typo in selection popup menu - Create groups now 'Create Group'</li>
174 <li><!-- JAL-1608 -->CMD/CTRL and G or Shift G for Create/Undefine group doesn't always work</li>
175 <li><!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get shown again after pressing 'Cancel'</li>
176 <li><!-- JAL-2461 -->DAS registry not found exceptions removed from console output</li>
177 <li><!-- JAL-2383 -->Above PID colour threshold not recovered when alignment view imported from project</li>
178 <li><!-- JAL-2465 -->No mappings generated between structure and sequences extracted from structure files imported via URL</li>
180 <!-- JAL-2520 -->Structures loaded via URL are saved in
181 Jalview Projects rather than fetched via URL again when
182 the project is loaded and the structure viewed
187 <li><!-- JAL-2442 -->Features not rendered as transparent on overview or linked structure view</li>
188 <li><!-- JAL-2372 -->Colour group by conservation doesn't work (since 2.8)</li>
189 <li><!-- JAL-2517 -->Hitting Cancel after applying user-defined colourscheme doesn't restore original colourscheme</li>
191 <em>New Known Issues</em>
193 <li><!-- JAL-2566 -->Protein/CDS view scrolling not always in phase after a sequence motif find operation</li>
194 <li><!-- JAL-2563 -->Status bar doesn't show positions for ambiguous amino acids</li>
195 <li><!-- JAL-2550 -->Importing annotation file with rows containing just upper and lower case letters are interpreted as WUSS rna secondary structure symbols</li>
200 <td width="60" nowrap>
202 <strong><a name="Jalview.2.10.1">2.10.1</a><br />
203 <em>29/11/2016</em></strong>
206 <td><div align="left">
210 <!-- JAL-98 -->Improved memory usage: sparse arrays used
211 for all consensus calculations
214 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released 3rd Oct 2016)
216 <li>Updated Jalview's Certum code signing certificate
222 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
223 set of database cross-references, sorted alphabetically
226 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
227 from database cross references. Users with custom links
228 will receive a <a href="webServices/urllinks.html#warning">warning
229 dialog</a> asking them to update their preferences.
232 <!-- JAL-2287-->Cancel button and escape listener on
233 dialog warning user about disconnecting Jalview from a
237 <!-- JAL-2320-->Jalview's Chimera control window closes if
238 the Chimera it is connected to is shut down
241 <!-- JAL-1738-->New keystroke (B) and Select highlighted
242 columns menu item to mark columns containing
243 highlighted regions (e.g. from structure selections or results
247 <!-- JAL-2284-->Command line option for batch-generation
248 of HTML pages rendering alignment data with the BioJS
258 <!-- JAL-2286 -->Columns with more than one modal residue
259 are not coloured or thresholded according to percent
260 identity (first observed in Jalview 2.8.2)
263 <!-- JAL-2301 -->Threonine incorrectly reported as not
267 <!-- JAL-2318 -->Updates to documentation pages (above PID
268 threshold, amino acid properties)
271 <!-- JAL-2292 -->Lower case residues in sequences are not
272 reported as mapped to residues in a structure file in the
276 <!--JAL-2324 -->Identical features with non-numeric scores
277 could be added multiple times to a sequence
280 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
281 bond features shown as two highlighted residues rather
282 than a range in linked structure views, and treated
283 correctly when selecting and computing trees from features
286 <!-- JAL-2281-->Custom URL links for database
287 cross-references are matched to database name regardless
295 <!-- JAL-2282-->Custom URL links for specific database
296 names without regular expressions also offer links from
300 <!-- JAL-2315-->Removing a single configured link in the
301 URL links pane in Connections preferences doesn't actually
302 update Jalview configuration
305 <!-- JAL-2272-->CTRL-Click on a selected region to open
306 the alignment area popup menu doesn't work on El-Capitan
309 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
310 files with similarly named sequences if dropped onto the
314 <!-- JAL-2312 -->Additional mappings are shown for PDB
315 entries where more chains exist in the PDB accession than
316 are reported in the SIFTS file
319 <!-- JAL-2317-->Certain structures do not get mapped to
320 the structure view when displayed with Chimera
323 <!-- JAL-2317-->No chains shown in the Chimera view
324 panel's View->Show Chains submenu
327 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
328 work for wrapped alignment views
331 <!--JAL-2197 -->Rename UI components for running JPred
332 predictions from 'JNet' to 'JPred'
335 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
336 corrupted when annotation panel vertical scroll is not at
340 <!--JAL-2332 -->Attempting to view structure for Hen
341 lysozyme results in a PDB Client error dialog box
344 <!-- JAL-2319 -->Structure View's mapping report switched ranges for PDB and sequence for SIFTS</li>
345 <!-- JAL-2319 -->SIFTS 'Not_Observed' residues mapped to non-existant coordindate data</li>
347 <!-- <em>New Known Issues</em>
354 <td width="60" nowrap>
356 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
357 <em>25/10/2016</em></strong>
360 <td><em>Application</em>
362 <li>3D Structure chooser opens with 'Cached structures'
363 view if structures already loaded</li>
364 <li>Progress bar reports models as they are loaded to
371 <li>Colour by conservation always enabled and no tick
372 shown in menu when BLOSUM or PID shading applied</li>
373 <li>FER1_ARATH and FER2_ARATH labels were switched in
374 example sequences/projects/trees</li>
378 <li>Jalview projects with views of local PDB structure
379 files saved on Windows cannot be opened on OSX</li>
380 <li>Multiple structure views can be opened and
381 superposed without timeout for structures with multiple
382 models or multiple sequences in alignment</li>
383 <li>Cannot import or associated local PDB files without
384 a PDB ID HEADER line</li>
385 <li>RMSD is not output in Jmol console when
386 superposition is performed</li>
387 <li>Drag and drop of URL from Browser fails for Linux
388 and OSX versions earlier than El Capitan</li>
389 <li>ENA client ignores invalid content from ENA server</li>
390 <li>Exceptions are not raised in console when ENA
391 client attempts to fetch non-existent IDs via Fetch DB
393 <li>Exceptions are not raised in console when a new
394 view is created on the alignment</li>
395 <li>OSX right-click fixed for group selections:
396 CMD-click to insert/remove gaps in groups and CTRL-click
397 to open group pop-up menu</li>
399 <em>Build and deployment</em>
401 <li>URL link checker now copes with multi-line anchor
404 <em>New Known Issues</em>
406 <li>Drag and drop from URL links in browsers do not
413 <td width="60" nowrap>
415 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
421 <!-- JAL-2124 -->Updated Spanish translations.
424 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
425 for importing structure data to Jalview. Enables mmCIF and
429 <!-- JAL-192 --->Alignment ruler shows positions relative to
433 <!-- JAL-2202 -->Position/residue shown in status bar when
434 mousing over sequence associated annotation
437 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
441 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
442 '()', canonical '[]' and invalid '{}' base pair populations
446 <!-- JAL-2092 -->Feature settings popup menu options for
447 showing or hiding columns containing a feature
450 <!-- JAL-1557 -->Edit selected group by double clicking on
451 group and sequence associated annotation labels
454 <!-- JAL-2236 -->Sequence name added to annotation label in
455 select/hide columns by annotation and colour by annotation
459 </ul> <em>Application</em>
462 <!-- JAL-2050-->Automatically hide introns when opening a
466 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
470 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
471 structure mappings with the EMBL-EBI PDBe SIFTS database
474 <!-- JAL-2079 -->Updated download sites used for Rfam and
475 Pfam sources to xfam.org
478 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
481 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
482 over sequences in Jalview
485 <!-- JAL-2027-->Support for reverse-complement coding
486 regions in ENA and EMBL
489 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
490 for record retrieval via ENA rest API
493 <!-- JAL-2027 -->Support for ENA CDS records with reverse
497 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
498 groovy script execution
501 <!-- JAL-1812 -->New 'execute Groovy script' option in an
502 alignment window's Calculate menu
505 <!-- JAL-1812 -->Allow groovy scripts that call
506 Jalview.getAlignFrames() to run in headless mode
509 <!-- JAL-2068 -->Support for creating new alignment
510 calculation workers from groovy scripts
513 <!-- JAL-1369 --->Store/restore reference sequence in
517 <!-- JAL-1803 -->Chain codes for a sequence's PDB
518 associations are now saved/restored from project
521 <!-- JAL-1993 -->Database selection dialog always shown
522 before sequence fetcher is opened
525 <!-- JAL-2183 -->Double click on an entry in Jalview's
526 database chooser opens a sequence fetcher
529 <!-- JAL-1563 -->Free-text search client for UniProt using
533 <!-- JAL-2168 -->-nonews command line parameter to prevent
534 the news reader opening
537 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
538 querying stored in preferences
541 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
545 <!-- JAL-1977-->Tooltips shown on database chooser
548 <!-- JAL-391 -->Reverse complement function in calculate
549 menu for nucleotide sequences
552 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
553 and feature counts preserves alignment ordering (and
554 debugged for complex feature sets).
557 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
558 viewing structures with Jalview 2.10
561 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
562 genome, transcript CCDS and gene ids via the Ensembl and
563 Ensembl Genomes REST API
566 <!-- JAL-2049 -->Protein sequence variant annotation
567 computed for 'sequence_variant' annotation on CDS regions
571 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
575 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
576 Ref Fetcher fails to match, or otherwise updates sequence
577 data from external database records.
580 <!-- JAL-2154 -->Revised Jalview Project format for
581 efficient recovery of sequence coding and alignment
582 annotation relationships.
584 </ul> <!-- <em>Applet</em>
595 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
599 <!-- JAL-2018-->Export features in Jalview format (again)
600 includes graduated colourschemes
603 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
604 working with big alignments and lots of hidden columns
607 <!-- JAL-2053-->Hidden column markers not always rendered
608 at right of alignment window
611 <!-- JAL-2067 -->Tidied up links in help file table of
615 <!-- JAL-2072 -->Feature based tree calculation not shown
619 <!-- JAL-2075 -->Hidden columns ignored during feature
620 based tree calculation
623 <!-- JAL-2065 -->Alignment view stops updating when show
624 unconserved enabled for group on alignment
627 <!-- JAL-2086 -->Cannot insert gaps into sequence when
631 <!-- JAL-2146 -->Alignment column in status incorrectly
632 shown as "Sequence position" when mousing over
636 <!-- JAL-2099 -->Incorrect column numbers in ruler when
637 hidden columns present
640 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
641 user created annotation added to alignment
644 <!-- JAL-1841 -->RNA Structure consensus only computed for
645 '()' base pair annotation
648 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
649 in zero scores for all base pairs in RNA Structure
653 <!-- JAL-2174-->Extend selection with columns containing
657 <!-- JAL-2275 -->Pfam format writer puts extra space at
658 beginning of sequence
661 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
665 <!-- JAL-2238 -->Cannot create groups on an alignment from
666 from a tree when t-coffee scores are shown
669 <!-- JAL-1836,1967 -->Cannot import and view PDB
670 structures with chains containing negative resnums (4q4h)
673 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
677 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
678 to Clustal, PIR and PileUp output
681 <!-- JAL-2008 -->Reordering sequence features that are
682 not visible causes alignment window to repaint
685 <!-- JAL-2006 -->Threshold sliders don't work in
686 graduated colour and colour by annotation row for e-value
687 scores associated with features and annotation rows
690 <!-- JAL-1797 -->amino acid physicochemical conservation
691 calculation should be case independent
694 <!-- JAL-2173 -->Remove annotation also updates hidden
698 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
699 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
700 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
703 <!-- JAL-2065 -->Null pointer exceptions and redraw
704 problems when reference sequence defined and 'show
705 non-conserved' enabled
708 <!-- JAL-1306 -->Quality and Conservation are now shown on
709 load even when Consensus calculation is disabled
712 <!-- JAL-1932 -->Remove right on penultimate column of
713 alignment does nothing
719 <!-- JAL-1552-->URLs and links can't be imported by
720 drag'n'drop on OSX when launched via webstart (note - not
721 yet fixed for El Capitan)
724 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
725 output when running on non-gb/us i18n platforms
728 <!-- JAL-1944 -->Error thrown when exporting a view with
729 hidden sequences as flat-file alignment
732 <!-- JAL-2030-->InstallAnywhere distribution fails when
736 <!-- JAL-2080-->Jalview very slow to launch via webstart
737 (also hotfix for 2.9.0b2)
740 <!-- JAL-2085 -->Cannot save project when view has a
741 reference sequence defined
744 <!-- JAL-1011 -->Columns are suddenly selected in other
745 alignments and views when revealing hidden columns
748 <!-- JAL-1989 -->Hide columns not mirrored in complement
749 view in a cDNA/Protein splitframe
752 <!-- JAL-1369 -->Cannot save/restore representative
753 sequence from project when only one sequence is
757 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
761 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
762 structure consensus didn't refresh annotation panel
765 <!-- JAL-1962 -->View mapping in structure view shows
766 mappings between sequence and all chains in a PDB file
769 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
770 dialogs format columns correctly, don't display array
771 data, sort columns according to type
774 <!-- JAL-1975 -->Export complete shown after destination
775 file chooser is cancelled during an image export
778 <!-- JAL-2025 -->Error when querying PDB Service with
779 sequence name containing special characters
782 <!-- JAL-2024 -->Manual PDB structure querying should be
786 <!-- JAL-2104 -->Large tooltips with broken HTML
787 formatting don't wrap
790 <!-- JAL-1128 -->Figures exported from wrapped view are
791 truncated so L looks like I in consensus annotation
794 <!-- JAL-2003 -->Export features should only export the
795 currently displayed features for the current selection or
799 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
800 after fetching cross-references, and restoring from project
803 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
804 followed in the structure viewer
807 <!-- JAL-2163 -->Titles for individual alignments in
808 splitframe not restored from project
811 <!-- JAL-2145 -->missing autocalculated annotation at
812 trailing end of protein alignment in transcript/product
813 splitview when pad-gaps not enabled by default
816 <!-- JAL-1797 -->amino acid physicochemical conservation
820 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
821 article has been read (reopened issue due to
822 internationalisation problems)
825 <!-- JAL-1960 -->Only offer PDB structures in structure
826 viewer based on sequence name, PDB and UniProt
831 <!-- JAL-1976 -->No progress bar shown during export of
835 <!-- JAL-2213 -->Structures not always superimposed after
836 multiple structures are shown for one or more sequences.
839 <!-- JAL-1370 -->Reference sequence characters should not
840 be replaced with '.' when 'Show unconserved' format option
844 <!-- JAL-1823 -->Cannot specify chain code when entering
845 specific PDB id for sequence
848 <!-- JAL-1944 -->File->Export->.. as doesn't work when
849 'Export hidden sequences' is enabled, but 'export hidden
850 columns' is disabled.
853 <!--JAL-2026-->Best Quality option in structure chooser
854 selects lowest rather than highest resolution structures
858 <!-- JAL-1887 -->Incorrect start and end reported for PDB
859 to sequence mapping in 'View Mappings' report
862 <!-- JAL-2284 -->Unable to read old Jalview projects that
863 contain non-XML data added after Jalvew wrote project.
865 <li><!-- JAL-2118 -->Newly created annotation row reorders
866 after clicking on it to create new annotation for a
869 <!-- may exclude, this is an external service stability issue JAL-1941
870 -- > RNA 3D structure not added via DSSR service</li> -->
875 <!-- JAL-2151 -->Incorrect columns are selected when
876 hidden columns present before start of sequence
879 <!-- JAL-1986 -->Missing dependencies on applet pages
883 <!-- JAL-1947 -->Overview pixel size changes when
884 sequences are hidden in applet
887 <!-- JAL-1996 -->Updated instructions for applet
888 deployment on examples pages.
895 <td width="60" nowrap>
897 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
898 <em>16/10/2015</em></strong>
903 <li>Time stamps for signed Jalview application and applet
910 <li>Duplicate group consensus and conservation rows
911 shown when tree is partitioned</li>
912 <li>Erratic behaviour when tree partitions made with
913 multiple cDNA/Protein split views</li>
919 <td width="60" nowrap>
921 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
922 <em>8/10/2015</em></strong>
927 <li>Updated Spanish translations of localized text for
929 </ul> <em>Application</em>
931 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
932 <li>Signed OSX InstallAnywhere installer<br></li>
933 <li>Support for per-sequence based annotations in BioJSON</li>
934 </ul> <em>Applet</em>
936 <li>Split frame example added to applet examples page</li>
937 </ul><em>Build and Deployment</em>
939 <li><!-- JAL-1888 -->New ant target for running Jalview's test suite</li>
945 <li>Mapping of cDNA to protein in split frames
946 incorrect when sequence start > 1</li>
947 <li>Broken images in filter column by annotation dialog
949 <li>Feature colours not parsed from features file</li>
950 <li>Exceptions and incomplete link URLs recovered when
951 loading a features file containing HTML tags in feature
957 <li>Annotations corrupted after BioJS export and
959 <li>Incorrect sequence limits after Fetch DB References
960 with 'trim retrieved sequences'</li>
961 <li>Incorrect warning about deleting all data when
962 deleting selected columns</li>
963 <li>Patch to build system for shipping properly signed
964 JNLP templates for webstart launch</li>
965 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
966 unreleased structures for download or viewing</li>
967 <li>Tab/space/return keystroke operation of EMBL-PDBe
968 fetcher/viewer dialogs works correctly</li>
969 <li>Disabled 'minimise' button on Jalview windows
970 running on OSX to workaround redraw hang bug</li>
971 <li>Split cDNA/Protein view position and geometry not
972 recovered from jalview project</li>
973 <li>Initial enabled/disabled state of annotation menu
974 sorter 'show autocalculated first/last' corresponds to
976 <li>Restoring of Clustal, RNA Helices and T-Coffee
977 color schemes from BioJSON</li>
981 <li>Reorder sequences mirrored in cDNA/Protein split
983 <li>Applet with Jmol examples not loading correctly</li>
989 <td><div align="center">
990 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
994 <li>Linked visualisation and analysis of DNA and Protein
997 <li>Translated cDNA alignments shown as split protein
998 and DNA alignment views</li>
999 <li>Codon consensus annotation for linked protein and
1000 cDNA alignment views</li>
1001 <li>Link cDNA or Protein product sequences by loading
1002 them onto Protein or cDNA alignments</li>
1003 <li>Reconstruct linked cDNA alignment from aligned
1004 protein sequences</li>
1007 <li>Jmol integration updated to Jmol v14.2.14</li>
1008 <li>Import and export of Jalview alignment views as <a
1009 href="features/bioJsonFormat.html">BioJSON</a></li>
1010 <li>New alignment annotation file statements for
1011 reference sequences and marking hidden columns</li>
1012 <li>Reference sequence based alignment shading to
1013 highlight variation</li>
1014 <li>Select or hide columns according to alignment
1016 <li>Find option for locating sequences by description</li>
1017 <li>Conserved physicochemical properties shown in amino
1018 acid conservation row</li>
1019 <li>Alignments can be sorted by number of RNA helices</li>
1020 </ul> <em>Application</em>
1022 <li>New cDNA/Protein analysis capabilities
1024 <li>Get Cross-References should open a Split Frame
1025 view with cDNA/Protein</li>
1026 <li>Detect when nucleotide sequences and protein
1027 sequences are placed in the same alignment</li>
1028 <li>Split cDNA/Protein views are saved in Jalview
1033 <li>Use REST API to talk to Chimera</li>
1034 <li>Selected regions in Chimera are highlighted in linked
1035 Jalview windows</li>
1037 <li>VARNA RNA viewer updated to v3.93</li>
1038 <li>VARNA views are saved in Jalview Projects</li>
1039 <li>Pseudoknots displayed as Jalview RNA annotation can
1040 be shown in VARNA</li>
1042 <li>Make groups for selection uses marked columns as well
1043 as the active selected region</li>
1045 <li>Calculate UPGMA and NJ trees using sequence feature
1047 <li>New Export options
1049 <li>New Export Settings dialog to control hidden
1050 region export in flat file generation</li>
1052 <li>Export alignment views for display with the <a
1053 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1055 <li>Export scrollable SVG in HTML page</li>
1056 <li>Optional embedding of BioJSON data when exporting
1057 alignment figures to HTML</li>
1059 <li>3D structure retrieval and display
1061 <li>Free text and structured queries with the PDBe
1063 <li>PDBe Search API based discovery and selection of
1064 PDB structures for a sequence set</li>
1068 <li>JPred4 employed for protein secondary structure
1070 <li>Hide Insertions menu option to hide unaligned columns
1071 for one or a group of sequences</li>
1072 <li>Automatically hide insertions in alignments imported
1073 from the JPred4 web server</li>
1074 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1075 system on OSX<br />LGPL libraries courtesy of <a
1076 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1078 <li>changed 'View nucleotide structure' submenu to 'View
1079 VARNA 2D Structure'</li>
1080 <li>change "View protein structure" menu option to "3D
1083 </ul> <em>Applet</em>
1085 <li>New layout for applet example pages</li>
1086 <li>New parameters to enable SplitFrame view
1087 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1088 <li>New example demonstrating linked viewing of cDNA and
1089 Protein alignments</li>
1090 </ul> <em>Development and deployment</em>
1092 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1093 <li>Include installation type and git revision in build
1094 properties and console log output</li>
1095 <li>Jalview Github organisation, and new github site for
1096 storing BioJsMSA Templates</li>
1097 <li>Jalview's unit tests now managed with TestNG</li>
1100 <!-- <em>General</em>
1102 </ul> --> <!-- issues resolved --> <em>Application</em>
1104 <li>Escape should close any open find dialogs</li>
1105 <li>Typo in select-by-features status report</li>
1106 <li>Consensus RNA secondary secondary structure
1107 predictions are not highlighted in amber</li>
1108 <li>Missing gap character in v2.7 example file means
1109 alignment appears unaligned when pad-gaps is not enabled</li>
1110 <li>First switch to RNA Helices colouring doesn't colour
1111 associated structure views</li>
1112 <li>ID width preference option is greyed out when auto
1113 width checkbox not enabled</li>
1114 <li>Stopped a warning dialog from being shown when
1115 creating user defined colours</li>
1116 <li>'View Mapping' in structure viewer shows sequence
1117 mappings for just that viewer's sequences</li>
1118 <li>Workaround for superposing PDB files containing
1119 multiple models in Chimera</li>
1120 <li>Report sequence position in status bar when hovering
1121 over Jmol structure</li>
1122 <li>Cannot output gaps as '.' symbols with Selection ->
1123 output to text box</li>
1124 <li>Flat file exports of alignments with hidden columns
1125 have incorrect sequence start/end</li>
1126 <li>'Aligning' a second chain to a Chimera structure from
1128 <li>Colour schemes applied to structure viewers don't
1129 work for nucleotide</li>
1130 <li>Loading/cut'n'pasting an empty or invalid file leads
1131 to a grey/invisible alignment window</li>
1132 <li>Exported Jpred annotation from a sequence region
1133 imports to different position</li>
1134 <li>Space at beginning of sequence feature tooltips shown
1135 on some platforms</li>
1136 <li>Chimera viewer 'View | Show Chain' menu is not
1138 <li>'New View' fails with a Null Pointer Exception in
1139 console if Chimera has been opened</li>
1140 <li>Mouseover to Chimera not working</li>
1141 <li>Miscellaneous ENA XML feature qualifiers not
1143 <li>NPE in annotation renderer after 'Extract Scores'</li>
1144 <li>If two structures in one Chimera window, mouseover of
1145 either sequence shows on first structure</li>
1146 <li>'Show annotations' options should not make
1147 non-positional annotations visible</li>
1148 <li>Subsequence secondary structure annotation not shown
1149 in right place after 'view flanking regions'</li>
1150 <li>File Save As type unset when current file format is
1152 <li>Save as '.jar' option removed for saving Jalview
1154 <li>Colour by Sequence colouring in Chimera more
1156 <li>Cannot 'add reference annotation' for a sequence in
1157 several views on same alignment</li>
1158 <li>Cannot show linked products for EMBL / ENA records</li>
1159 <li>Jalview's tooltip wraps long texts containing no
1161 </ul> <em>Applet</em>
1163 <li>Jmol to JalviewLite mouseover/link not working</li>
1164 <li>JalviewLite can't import sequences with ID
1165 descriptions containing angle brackets</li>
1166 </ul> <em>General</em>
1168 <li>Cannot export and reimport RNA secondary structure
1169 via jalview annotation file</li>
1170 <li>Random helix colour palette for colour by annotation
1171 with RNA secondary structure</li>
1172 <li>Mouseover to cDNA from STOP residue in protein
1173 translation doesn't work.</li>
1174 <li>hints when using the select by annotation dialog box</li>
1175 <li>Jmol alignment incorrect if PDB file has alternate CA
1177 <li>FontChooser message dialog appears to hang after
1178 choosing 1pt font</li>
1179 <li>Peptide secondary structure incorrectly imported from
1180 annotation file when annotation display text includes 'e' or
1182 <li>Cannot set colour of new feature type whilst creating
1184 <li>cDNA translation alignment should not be sequence
1185 order dependent</li>
1186 <li>'Show unconserved' doesn't work for lower case
1188 <li>Nucleotide ambiguity codes involving R not recognised</li>
1189 </ul> <em>Deployment and Documentation</em>
1191 <li>Applet example pages appear different to the rest of
1192 www.jalview.org</li>
1193 </ul> <em>Application Known issues</em>
1195 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1196 <li>Misleading message appears after trying to delete
1198 <li>Jalview icon not shown in dock after InstallAnywhere
1199 version launches</li>
1200 <li>Fetching EMBL reference for an RNA sequence results
1201 fails with a sequence mismatch</li>
1202 <li>Corrupted or unreadable alignment display when
1203 scrolling alignment to right</li>
1204 <li>ArrayIndexOutOfBoundsException thrown when remove
1205 empty columns called on alignment with ragged gapped ends</li>
1206 <li>auto calculated alignment annotation rows do not get
1207 placed above or below non-autocalculated rows</li>
1208 <li>Jalview dekstop becomes sluggish at full screen in
1209 ultra-high resolution</li>
1210 <li>Cannot disable consensus calculation independently of
1211 quality and conservation</li>
1212 <li>Mouseover highlighting between cDNA and protein can
1213 become sluggish with more than one splitframe shown</li>
1214 </ul> <em>Applet Known Issues</em>
1216 <li>Core PDB parsing code requires Jmol</li>
1217 <li>Sequence canvas panel goes white when alignment
1218 window is being resized</li>
1224 <td><div align="center">
1225 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1227 <td><em>General</em>
1229 <li>Updated Java code signing certificate donated by
1231 <li>Features and annotation preserved when performing
1232 pairwise alignment</li>
1233 <li>RNA pseudoknot annotation can be
1234 imported/exported/displayed</li>
1235 <li>'colour by annotation' can colour by RNA and
1236 protein secondary structure</li>
1237 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1238 post-hoc with 2.9 release</em>)
1241 </ul> <em>Application</em>
1243 <li>Extract and display secondary structure for sequences
1244 with 3D structures</li>
1245 <li>Support for parsing RNAML</li>
1246 <li>Annotations menu for layout
1248 <li>sort sequence annotation rows by alignment</li>
1249 <li>place sequence annotation above/below alignment
1252 <li>Output in Stockholm format</li>
1253 <li>Internationalisation: improved Spanish (es)
1255 <li>Structure viewer preferences tab</li>
1256 <li>Disorder and Secondary Structure annotation tracks
1257 shared between alignments</li>
1258 <li>UCSF Chimera launch and linked highlighting from
1260 <li>Show/hide all sequence associated annotation rows for
1261 all or current selection</li>
1262 <li>disorder and secondary structure predictions
1263 available as dataset annotation</li>
1264 <li>Per-sequence rna helices colouring</li>
1267 <li>Sequence database accessions imported when fetching
1268 alignments from Rfam</li>
1269 <li>update VARNA version to 3.91</li>
1271 <li>New groovy scripts for exporting aligned positions,
1272 conservation values, and calculating sum of pairs scores.</li>
1273 <li>Command line argument to set default JABAWS server</li>
1274 <li>include installation type in build properties and
1275 console log output</li>
1276 <li>Updated Jalview project format to preserve dataset
1280 <!-- issues resolved --> <em>Application</em>
1282 <li>Distinguish alignment and sequence associated RNA
1283 structure in structure->view->VARNA</li>
1284 <li>Raise dialog box if user deletes all sequences in an
1286 <li>Pressing F1 results in documentation opening twice</li>
1287 <li>Sequence feature tooltip is wrapped</li>
1288 <li>Double click on sequence associated annotation
1289 selects only first column</li>
1290 <li>Redundancy removal doesn't result in unlinked
1291 leaves shown in tree</li>
1292 <li>Undos after several redundancy removals don't undo
1294 <li>Hide sequence doesn't hide associated annotation</li>
1295 <li>User defined colours dialog box too big to fit on
1296 screen and buttons not visible</li>
1297 <li>author list isn't updated if already written to
1298 Jalview properties</li>
1299 <li>Popup menu won't open after retrieving sequence
1301 <li>File open window for associate PDB doesn't open</li>
1302 <li>Left-then-right click on a sequence id opens a
1303 browser search window</li>
1304 <li>Cannot open sequence feature shading/sort popup menu
1305 in feature settings dialog</li>
1306 <li>better tooltip placement for some areas of Jalview
1308 <li>Allow addition of JABAWS Server which doesn't
1309 pass validation</li>
1310 <li>Web services parameters dialog box is too large to
1312 <li>Muscle nucleotide alignment preset obscured by
1314 <li>JABAWS preset submenus don't contain newly
1315 defined user preset</li>
1316 <li>MSA web services warns user if they were launched
1317 with invalid input</li>
1318 <li>Jalview cannot contact DAS Registy when running on
1321 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1322 'Superpose with' submenu not shown when new view
1326 </ul> <!-- <em>Applet</em>
1328 </ul> <em>General</em>
1330 </ul>--> <em>Deployment and Documentation</em>
1332 <li>2G and 1G options in launchApp have no effect on
1333 memory allocation</li>
1334 <li>launchApp service doesn't automatically open
1335 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1337 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1338 InstallAnywhere reports cannot find valid JVM when Java
1339 1.7_055 is available
1341 </ul> <em>Application Known issues</em>
1344 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1345 corrupted or unreadable alignment display when scrolling
1349 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1350 retrieval fails but progress bar continues for DAS retrieval
1351 with large number of ID
1354 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1355 flatfile output of visible region has incorrect sequence
1359 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1360 rna structure consensus doesn't update when secondary
1361 structure tracks are rearranged
1364 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1365 invalid rna structure positional highlighting does not
1366 highlight position of invalid base pairs
1369 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1370 out of memory errors are not raised when saving Jalview
1371 project from alignment window file menu
1374 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1375 Switching to RNA Helices colouring doesn't propagate to
1379 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1380 colour by RNA Helices not enabled when user created
1381 annotation added to alignment
1384 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1385 Jalview icon not shown on dock in Mountain Lion/Webstart
1387 </ul> <em>Applet Known Issues</em>
1390 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1391 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1394 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1395 Jalview and Jmol example not compatible with IE9
1398 <li>Sort by annotation score doesn't reverse order
1404 <td><div align="center">
1405 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1408 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1411 <li>Internationalisation of user interface (usually
1412 called i18n support) and translation for Spanish locale</li>
1413 <li>Define/Undefine group on current selection with
1414 Ctrl-G/Shift Ctrl-G</li>
1415 <li>Improved group creation/removal options in
1416 alignment/sequence Popup menu</li>
1417 <li>Sensible precision for symbol distribution
1418 percentages shown in logo tooltip.</li>
1419 <li>Annotation panel height set according to amount of
1420 annotation when alignment first opened</li>
1421 </ul> <em>Application</em>
1423 <li>Interactive consensus RNA secondary structure
1424 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1425 <li>Select columns containing particular features from
1426 Feature Settings dialog</li>
1427 <li>View all 'representative' PDB structures for selected
1429 <li>Update Jalview project format:
1431 <li>New file extension for Jalview projects '.jvp'</li>
1432 <li>Preserve sequence and annotation dataset (to
1433 store secondary structure annotation,etc)</li>
1434 <li>Per group and alignment annotation and RNA helix
1438 <li>New similarity measures for PCA and Tree calculation
1440 <li>Experimental support for retrieval and viewing of
1441 flanking regions for an alignment</li>
1445 <!-- issues resolved --> <em>Application</em>
1447 <li>logo keeps spinning and status remains at queued or
1448 running after job is cancelled</li>
1449 <li>cannot export features from alignments imported from
1450 Jalview/VAMSAS projects</li>
1451 <li>Buggy slider for web service parameters that take
1453 <li>Newly created RNA secondary structure line doesn't
1454 have 'display all symbols' flag set</li>
1455 <li>T-COFFEE alignment score shading scheme and other
1456 annotation shading not saved in Jalview project</li>
1457 <li>Local file cannot be loaded in freshly downloaded
1459 <li>Jalview icon not shown on dock in Mountain
1461 <li>Load file from desktop file browser fails</li>
1462 <li>Occasional NPE thrown when calculating large trees</li>
1463 <li>Cannot reorder or slide sequences after dragging an
1464 alignment onto desktop</li>
1465 <li>Colour by annotation dialog throws NPE after using
1466 'extract scores' function</li>
1467 <li>Loading/cut'n'pasting an empty file leads to a grey
1468 alignment window</li>
1469 <li>Disorder thresholds rendered incorrectly after
1470 performing IUPred disorder prediction</li>
1471 <li>Multiple group annotated consensus rows shown when
1472 changing 'normalise logo' display setting</li>
1473 <li>Find shows blank dialog after 'finished searching' if
1474 nothing matches query</li>
1475 <li>Null Pointer Exceptions raised when sorting by
1476 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1478 <li>Errors in Jmol console when structures in alignment
1479 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1481 <li>Not all working JABAWS services are shown in
1483 <li>JAVAWS version of Jalview fails to launch with
1484 'invalid literal/length code'</li>
1485 <li>Annotation/RNA Helix colourschemes cannot be applied
1486 to alignment with groups (actually fixed in 2.8.0b1)</li>
1487 <li>RNA Helices and T-Coffee Scores available as default
1490 </ul> <em>Applet</em>
1492 <li>Remove group option is shown even when selection is
1494 <li>Apply to all groups ticked but colourscheme changes
1495 don't affect groups</li>
1496 <li>Documented RNA Helices and T-Coffee Scores as valid
1497 colourscheme name</li>
1498 <li>Annotation labels drawn on sequence IDs when
1499 Annotation panel is not displayed</li>
1500 <li>Increased font size for dropdown menus on OSX and
1501 embedded windows</li>
1502 </ul> <em>Other</em>
1504 <li>Consensus sequence for alignments/groups with a
1505 single sequence were not calculated</li>
1506 <li>annotation files that contain only groups imported as
1507 annotation and junk sequences</li>
1508 <li>Fasta files with sequences containing '*' incorrectly
1509 recognised as PFAM or BLC</li>
1510 <li>conservation/PID slider apply all groups option
1511 doesn't affect background (2.8.0b1)
1513 <li>redundancy highlighting is erratic at 0% and 100%</li>
1514 <li>Remove gapped columns fails for sequences with ragged
1516 <li>AMSA annotation row with leading spaces is not
1517 registered correctly on import</li>
1518 <li>Jalview crashes when selecting PCA analysis for
1519 certain alignments</li>
1520 <li>Opening the colour by annotation dialog for an
1521 existing annotation based 'use original colours'
1522 colourscheme loses original colours setting</li>
1527 <td><div align="center">
1528 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
1529 <em>30/1/2014</em></strong>
1533 <li>Trusted certificates for JalviewLite applet and
1534 Jalview Desktop application<br />Certificate was donated by
1535 <a href="https://www.certum.eu">Certum</a> to the Jalview
1536 open source project).
1538 <li>Jalview SRS links replaced by UniProt and EBI-search
1540 <li>Output in Stockholm format</li>
1541 <li>Allow import of data from gzipped files</li>
1542 <li>Export/import group and sequence associated line
1543 graph thresholds</li>
1544 <li>Nucleotide substitution matrix that supports RNA and
1545 ambiguity codes</li>
1546 <li>Allow disorder predictions to be made on the current
1547 selection (or visible selection) in the same way that JPred
1549 <li>Groovy scripting for headless Jalview operation</li>
1550 </ul> <em>Other improvements</em>
1552 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
1553 <li>COMBINE statement uses current SEQUENCE_REF and
1554 GROUP_REF scope to group annotation rows</li>
1555 <li>Support '' style escaping of quotes in Newick
1557 <li>Group options for JABAWS service by command line name</li>
1558 <li>Empty tooltip shown for JABA service options with a
1559 link but no description</li>
1560 <li>Select primary source when selecting authority in
1561 database fetcher GUI</li>
1562 <li>Add .mfa to FASTA file extensions recognised by
1564 <li>Annotation label tooltip text wrap</li>
1569 <li>Slow scrolling when lots of annotation rows are
1571 <li>Lots of NPE (and slowness) after creating RNA
1572 secondary structure annotation line</li>
1573 <li>Sequence database accessions not imported when
1574 fetching alignments from Rfam</li>
1575 <li>Incorrect SHMR submission for sequences with
1577 <li>View all structures does not always superpose
1579 <li>Option widgets in service parameters not updated to
1580 reflect user or preset settings</li>
1581 <li>Null pointer exceptions for some services without
1582 presets or adjustable parameters</li>
1583 <li>Discover PDB IDs entry in structure menu doesn't
1584 discover PDB xRefs</li>
1585 <li>Exception encountered while trying to retrieve
1586 features with DAS</li>
1587 <li>Lowest value in annotation row isn't coloured
1588 when colour by annotation (per sequence) is coloured</li>
1589 <li>Keyboard mode P jumps to start of gapped region when
1590 residue follows a gap</li>
1591 <li>Jalview appears to hang importing an alignment with
1592 Wrap as default or after enabling Wrap</li>
1593 <li>'Right click to add annotations' message
1594 shown in wrap mode when no annotations present</li>
1595 <li>Disorder predictions fail with NPE if no automatic
1596 annotation already exists on alignment</li>
1597 <li>oninit javascript function should be called after
1598 initialisation completes</li>
1599 <li>Remove redundancy after disorder prediction corrupts
1600 alignment window display</li>
1601 <li>Example annotation file in documentation is invalid</li>
1602 <li>Grouped line graph annotation rows are not exported
1603 to annotation file</li>
1604 <li>Multi-harmony analysis cannot be run when only two
1606 <li>Cannot create multiple groups of line graphs with
1607 several 'combine' statements in annotation file</li>
1608 <li>Pressing return several times causes Number Format
1609 exceptions in keyboard mode</li>
1610 <li>Multi-harmony (SHMMR) method doesn't submit
1611 correct partitions for input data</li>
1612 <li>Translation from DNA to Amino Acids fails</li>
1613 <li>Jalview fail to load newick tree with quoted label</li>
1614 <li>--headless flag isn't understood</li>
1615 <li>ClassCastException when generating EPS in headless
1617 <li>Adjusting sequence-associated shading threshold only
1618 changes one row's threshold</li>
1619 <li>Preferences and Feature settings panel panel
1620 doesn't open</li>
1621 <li>hide consensus histogram also hides conservation and
1622 quality histograms</li>
1627 <td><div align="center">
1628 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
1630 <td><em>Application</em>
1632 <li>Support for JABAWS 2.0 Services (AACon alignment
1633 conservation, protein disorder and Clustal Omega)</li>
1634 <li>JABAWS server status indicator in Web Services
1636 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
1637 in Jalview alignment window</li>
1638 <li>Updated Jalview build and deploy framework for OSX
1639 mountain lion, windows 7, and 8</li>
1640 <li>Nucleotide substitution matrix for PCA that supports
1641 RNA and ambiguity codes</li>
1643 <li>Improved sequence database retrieval GUI</li>
1644 <li>Support fetching and database reference look up
1645 against multiple DAS sources (Fetch all from in 'fetch db
1647 <li>Jalview project improvements
1649 <li>Store and retrieve the 'belowAlignment'
1650 flag for annotation</li>
1651 <li>calcId attribute to group annotation rows on the
1653 <li>Store AACon calculation settings for a view in
1654 Jalview project</li>
1658 <li>horizontal scrolling gesture support</li>
1659 <li>Visual progress indicator when PCA calculation is
1661 <li>Simpler JABA web services menus</li>
1662 <li>visual indication that web service results are still
1663 being retrieved from server</li>
1664 <li>Serialise the dialogs that are shown when Jalview
1665 starts up for first time</li>
1666 <li>Jalview user agent string for interacting with HTTP
1668 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
1670 <li>Examples directory and Groovy library included in
1671 InstallAnywhere distribution</li>
1672 </ul> <em>Applet</em>
1674 <li>RNA alignment and secondary structure annotation
1675 visualization applet example</li>
1676 </ul> <em>General</em>
1678 <li>Normalise option for consensus sequence logo</li>
1679 <li>Reset button in PCA window to return dimensions to
1681 <li>Allow seqspace or Jalview variant of alignment PCA
1683 <li>PCA with either nucleic acid and protein substitution
1685 <li>Allow windows containing HTML reports to be exported
1687 <li>Interactive display and editing of RNA secondary
1688 structure contacts</li>
1689 <li>RNA Helix Alignment Colouring</li>
1690 <li>RNA base pair logo consensus</li>
1691 <li>Parse sequence associated secondary structure
1692 information in Stockholm files</li>
1693 <li>HTML Export database accessions and annotation
1694 information presented in tooltip for sequences</li>
1695 <li>Import secondary structure from LOCARNA clustalw
1696 style RNA alignment files</li>
1697 <li>import and visualise T-COFFEE quality scores for an
1699 <li>'colour by annotation' per sequence option to
1700 shade each sequence according to its associated alignment
1702 <li>New Jalview Logo</li>
1703 </ul> <em>Documentation and Development</em>
1705 <li>documentation for score matrices used in Jalview</li>
1706 <li>New Website!</li>
1708 <td><em>Application</em>
1710 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
1711 wsdbfetch REST service</li>
1712 <li>Stop windows being moved outside desktop on OSX</li>
1713 <li>Filetype associations not installed for webstart
1715 <li>Jalview does not always retrieve progress of a JABAWS
1716 job execution in full once it is complete</li>
1717 <li>revise SHMR RSBS definition to ensure alignment is
1718 uploaded via ali_file parameter</li>
1719 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
1720 <li>View all structures superposed fails with exception</li>
1721 <li>Jnet job queues forever if a very short sequence is
1722 submitted for prediction</li>
1723 <li>Cut and paste menu not opened when mouse clicked on
1725 <li>Putting fractional value into integer text box in
1726 alignment parameter dialog causes Jalview to hang</li>
1727 <li>Structure view highlighting doesn't work on
1729 <li>View all structures fails with exception shown in
1731 <li>Characters in filename associated with PDBEntry not
1732 escaped in a platform independent way</li>
1733 <li>Jalview desktop fails to launch with exception when
1735 <li>Tree calculation reports 'you must have 2 or more
1736 sequences selected' when selection is empty</li>
1737 <li>Jalview desktop fails to launch with jar signature
1738 failure when java web start temporary file caching is
1740 <li>DAS Sequence retrieval with range qualification
1741 results in sequence xref which includes range qualification</li>
1742 <li>Errors during processing of command line arguments
1743 cause progress bar (JAL-898) to be removed</li>
1744 <li>Replace comma for semi-colon option not disabled for
1745 DAS sources in sequence fetcher</li>
1746 <li>Cannot close news reader when JABAWS server warning
1747 dialog is shown</li>
1748 <li>Option widgets not updated to reflect user settings</li>
1749 <li>Edited sequence not submitted to web service</li>
1750 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
1751 <li>InstallAnywhere installer doesn't unpack and run
1752 on OSX Mountain Lion</li>
1753 <li>Annotation panel not given a scroll bar when
1754 sequences with alignment annotation are pasted into the
1756 <li>Sequence associated annotation rows not associated
1757 when loaded from Jalview project</li>
1758 <li>Browser launch fails with NPE on java 1.7</li>
1759 <li>JABAWS alignment marked as finished when job was
1760 cancelled or job failed due to invalid input</li>
1761 <li>NPE with v2.7 example when clicking on Tree
1762 associated with all views</li>
1763 <li>Exceptions when copy/paste sequences with grouped
1764 annotation rows to new window</li>
1765 </ul> <em>Applet</em>
1767 <li>Sequence features are momentarily displayed before
1768 they are hidden using hidefeaturegroups applet parameter</li>
1769 <li>loading features via javascript API automatically
1770 enables feature display</li>
1771 <li>scrollToColumnIn javascript API method doesn't
1773 </ul> <em>General</em>
1775 <li>Redundancy removal fails for rna alignment</li>
1776 <li>PCA calculation fails when sequence has been selected
1777 and then deselected</li>
1778 <li>PCA window shows grey box when first opened on OSX</li>
1779 <li>Letters coloured pink in sequence logo when alignment
1780 coloured with clustalx</li>
1781 <li>Choosing fonts without letter symbols defined causes
1782 exceptions and redraw errors</li>
1783 <li>Initial PCA plot view is not same as manually
1784 reconfigured view</li>
1785 <li>Grouped annotation graph label has incorrect line
1787 <li>Grouped annotation graph label display is corrupted
1788 for lots of labels</li>
1793 <div align="center">
1794 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
1797 <td><em>Application</em>
1799 <li>Jalview Desktop News Reader</li>
1800 <li>Tweaked default layout of web services menu</li>
1801 <li>View/alignment association menu to enable user to
1802 easily specify which alignment a multi-structure view takes
1803 its colours/correspondences from</li>
1804 <li>Allow properties file location to be specified as URL</li>
1805 <li>Extend Jalview project to preserve associations
1806 between many alignment views and a single Jmol display</li>
1807 <li>Store annotation row height in Jalview project file</li>
1808 <li>Annotation row column label formatting attributes
1809 stored in project file</li>
1810 <li>Annotation row order for auto-calculated annotation
1811 rows preserved in Jalview project file</li>
1812 <li>Visual progress indication when Jalview state is
1813 saved using Desktop window menu</li>
1814 <li>Visual indication that command line arguments are
1815 still being processed</li>
1816 <li>Groovy script execution from URL</li>
1817 <li>Colour by annotation default min and max colours in
1819 <li>Automatically associate PDB files dragged onto an
1820 alignment with sequences that have high similarity and
1822 <li>Update JGoogleAnalytics to latest release (0.3)</li>
1823 <li>'view structures' option to open many
1824 structures in same window</li>
1825 <li>Sort associated views menu option for tree panel</li>
1826 <li>Group all JABA and non-JABA services for a particular
1827 analysis function in its own submenu</li>
1828 </ul> <em>Applet</em>
1830 <li>Userdefined and autogenerated annotation rows for
1832 <li>Adjustment of alignment annotation pane height</li>
1833 <li>Annotation scrollbar for annotation panel</li>
1834 <li>Drag to reorder annotation rows in annotation panel</li>
1835 <li>'automaticScrolling' parameter</li>
1836 <li>Allow sequences with partial ID string matches to be
1837 annotated from GFF/Jalview features files</li>
1838 <li>Sequence logo annotation row in applet</li>
1839 <li>Absolute paths relative to host server in applet
1840 parameters are treated as such</li>
1841 <li>New in the JalviewLite javascript API:
1843 <li>JalviewLite.js javascript library</li>
1844 <li>Javascript callbacks for
1846 <li>Applet initialisation</li>
1847 <li>Sequence/alignment mouse-overs and selections</li>
1850 <li>scrollTo row and column alignment scrolling
1852 <li>Select sequence/alignment regions from javascript</li>
1853 <li>javascript structure viewer harness to pass
1854 messages between Jmol and Jalview when running as
1855 distinct applets</li>
1856 <li>sortBy method</li>
1857 <li>Set of applet and application examples shipped
1858 with documentation</li>
1859 <li>New example to demonstrate JalviewLite and Jmol
1860 javascript message exchange</li>
1862 </ul> <em>General</em>
1864 <li>Enable Jmol displays to be associated with multiple
1865 multiple alignments</li>
1866 <li>Option to automatically sort alignment with new tree</li>
1867 <li>User configurable link to enable redirects to a
1868 www.Jalview.org mirror</li>
1869 <li>Jmol colours option for Jmol displays</li>
1870 <li>Configurable newline string when writing alignment
1871 and other flat files</li>
1872 <li>Allow alignment annotation description lines to
1873 contain html tags</li>
1874 </ul> <em>Documentation and Development</em>
1876 <li>Add groovy test harness for bulk load testing to
1878 <li>Groovy script to load and align a set of sequences
1879 using a web service before displaying the result in the
1880 Jalview desktop</li>
1881 <li>Restructured javascript and applet api documentation</li>
1882 <li>Ant target to publish example html files with applet
1884 <li>Netbeans project for building Jalview from source</li>
1885 <li>ant task to create online javadoc for Jalview source</li>
1887 <td><em>Application</em>
1889 <li>User defined colourscheme throws exception when
1890 current built in colourscheme is saved as new scheme</li>
1891 <li>AlignFrame->Save in application pops up save
1892 dialog for valid filename/format</li>
1893 <li>Cannot view associated structure for UniProt sequence</li>
1894 <li>PDB file association breaks for UniProt sequence
1896 <li>Associate PDB from file dialog does not tell you
1897 which sequence is to be associated with the file</li>
1898 <li>Find All raises null pointer exception when query
1899 only matches sequence IDs</li>
1900 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
1901 <li>Jalview project with Jmol views created with Jalview
1902 2.4 cannot be loaded</li>
1903 <li>Filetype associations not installed for webstart
1905 <li>Two or more chains in a single PDB file associated
1906 with sequences in different alignments do not get coloured
1907 by their associated sequence</li>
1908 <li>Visibility status of autocalculated annotation row
1909 not preserved when project is loaded</li>
1910 <li>Annotation row height and visibility attributes not
1911 stored in Jalview project</li>
1912 <li>Tree bootstraps are not preserved when saved as a
1913 Jalview project</li>
1914 <li>Envision2 workflow tooltips are corrupted</li>
1915 <li>Enabling show group conservation also enables colour
1916 by conservation</li>
1917 <li>Duplicate group associated conservation or consensus
1918 created on new view</li>
1919 <li>Annotation scrollbar not displayed after 'show
1920 all hidden annotation rows' option selected</li>
1921 <li>Alignment quality not updated after alignment
1922 annotation row is hidden then shown</li>
1923 <li>Preserve colouring of structures coloured by
1924 sequences in pre Jalview 2.7 projects</li>
1925 <li>Web service job parameter dialog is not laid out
1927 <li>Web services menu not refreshed after 'reset
1928 services' button is pressed in preferences</li>
1929 <li>Annotation off by one in Jalview v2_3 example project</li>
1930 <li>Structures imported from file and saved in project
1931 get name like jalview_pdb1234.txt when reloaded</li>
1932 <li>Jalview does not always retrieve progress of a JABAWS
1933 job execution in full once it is complete</li>
1934 </ul> <em>Applet</em>
1936 <li>Alignment height set incorrectly when lots of
1937 annotation rows are displayed</li>
1938 <li>Relative URLs in feature HTML text not resolved to
1940 <li>View follows highlighting does not work for positions
1942 <li><= shown as = in tooltip</li>
1943 <li>Export features raises exception when no features
1945 <li>Separator string used for serialising lists of IDs
1946 for javascript api is modified when separator string
1947 provided as parameter</li>
1948 <li>Null pointer exception when selecting tree leaves for
1949 alignment with no existing selection</li>
1950 <li>Relative URLs for datasources assumed to be relative
1951 to applet's codebase</li>
1952 <li>Status bar not updated after finished searching and
1953 search wraps around to first result</li>
1954 <li>StructureSelectionManager instance shared between
1955 several Jalview applets causes race conditions and memory
1957 <li>Hover tooltip and mouseover of position on structure
1958 not sent from Jmol in applet</li>
1959 <li>Certain sequences of javascript method calls to
1960 applet API fatally hang browser</li>
1961 </ul> <em>General</em>
1963 <li>View follows structure mouseover scrolls beyond
1964 position with wrapped view and hidden regions</li>
1965 <li>Find sequence position moves to wrong residue
1966 with/without hidden columns</li>
1967 <li>Sequence length given in alignment properties window
1969 <li>InvalidNumberFormat exceptions thrown when trying to
1970 import PDB like structure files</li>
1971 <li>Positional search results are only highlighted
1972 between user-supplied sequence start/end bounds</li>
1973 <li>End attribute of sequence is not validated</li>
1974 <li>Find dialog only finds first sequence containing a
1975 given sequence position</li>
1976 <li>Sequence numbering not preserved in MSF alignment
1978 <li>Jalview PDB file reader does not extract sequence
1979 from nucleotide chains correctly</li>
1980 <li>Structure colours not updated when tree partition
1981 changed in alignment</li>
1982 <li>Sequence associated secondary structure not correctly
1983 parsed in interleaved stockholm</li>
1984 <li>Colour by annotation dialog does not restore current
1986 <li>Hiding (nearly) all sequences doesn't work
1988 <li>Sequences containing lowercase letters are not
1989 properly associated with their pdb files</li>
1990 </ul> <em>Documentation and Development</em>
1992 <li>schemas/JalviewWsParamSet.xsd corrupted by
1993 ApplyCopyright tool</li>
1998 <div align="center">
1999 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2002 <td><em>Application</em>
2004 <li>New warning dialog when the Jalview Desktop cannot
2005 contact web services</li>
2006 <li>JABA service parameters for a preset are shown in
2007 service job window</li>
2008 <li>JABA Service menu entries reworded</li>
2012 <li>Modeller PIR IO broken - cannot correctly import a
2013 pir file emitted by Jalview</li>
2014 <li>Existing feature settings transferred to new
2015 alignment view created from cut'n'paste</li>
2016 <li>Improved test for mixed amino/nucleotide chains when
2017 parsing PDB files</li>
2018 <li>Consensus and conservation annotation rows
2019 occasionally become blank for all new windows</li>
2020 <li>Exception raised when right clicking above sequences
2021 in wrapped view mode</li>
2022 </ul> <em>Application</em>
2024 <li>multiple multiply aligned structure views cause cpu
2025 usage to hit 100% and computer to hang</li>
2026 <li>Web Service parameter layout breaks for long user
2027 parameter names</li>
2028 <li>Jaba service discovery hangs desktop if Jaba server
2035 <div align="center">
2036 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2039 <td><em>Application</em>
2041 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2042 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2045 <li>Web Services preference tab</li>
2046 <li>Analysis parameters dialog box and user defined
2048 <li>Improved speed and layout of Envision2 service menu</li>
2049 <li>Superpose structures using associated sequence
2051 <li>Export coordinates and projection as CSV from PCA
2053 </ul> <em>Applet</em>
2055 <li>enable javascript: execution by the applet via the
2056 link out mechanism</li>
2057 </ul> <em>Other</em>
2059 <li>Updated the Jmol Jalview interface to work with Jmol
2061 <li>The Jalview Desktop and JalviewLite applet now
2062 require Java 1.5</li>
2063 <li>Allow Jalview feature colour specification for GFF
2064 sequence annotation files</li>
2065 <li>New 'colour by label' keword in Jalview feature file
2066 type colour specification</li>
2067 <li>New Jalview Desktop Groovy API method that allows a
2068 script to check if it being run in an interactive session or
2069 in a batch operation from the Jalview command line</li>
2073 <li>clustalx colourscheme colours Ds preferentially when
2074 both D+E are present in over 50% of the column</li>
2075 </ul> <em>Application</em>
2077 <li>typo in AlignmentFrame->View->Hide->all but
2078 selected Regions menu item</li>
2079 <li>sequence fetcher replaces ',' for ';' when the ',' is
2080 part of a valid accession ID</li>
2081 <li>fatal OOM if object retrieved by sequence fetcher
2082 runs out of memory</li>
2083 <li>unhandled Out of Memory Error when viewing pca
2084 analysis results</li>
2085 <li>InstallAnywhere builds fail to launch on OS X java
2086 10.5 update 4 (due to apple Java 1.6 update)</li>
2087 <li>Installanywhere Jalview silently fails to launch</li>
2088 </ul> <em>Applet</em>
2090 <li>Jalview.getFeatureGroups() raises an
2091 ArrayIndexOutOfBoundsException if no feature groups are
2098 <div align="center">
2099 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2105 <li>Alignment prettyprinter doesn't cope with long
2107 <li>clustalx colourscheme colours Ds preferentially when
2108 both D+E are present in over 50% of the column</li>
2109 <li>nucleic acid structures retrieved from PDB do not
2110 import correctly</li>
2111 <li>More columns get selected than were clicked on when a
2112 number of columns are hidden</li>
2113 <li>annotation label popup menu not providing correct
2114 add/hide/show options when rows are hidden or none are
2116 <li>Stockholm format shown in list of readable formats,
2117 and parser copes better with alignments from RFAM.</li>
2118 <li>CSV output of consensus only includes the percentage
2119 of all symbols if sequence logo display is enabled</li>
2121 </ul> <em>Applet</em>
2123 <li>annotation panel disappears when annotation is
2125 </ul> <em>Application</em>
2127 <li>Alignment view not redrawn properly when new
2128 alignment opened where annotation panel is visible but no
2129 annotations are present on alignment</li>
2130 <li>pasted region containing hidden columns is
2131 incorrectly displayed in new alignment window</li>
2132 <li>Jalview slow to complete operations when stdout is
2133 flooded (fix is to close the Jalview console)</li>
2134 <li>typo in AlignmentFrame->View->Hide->all but
2135 selected Rregions menu item.</li>
2136 <li>inconsistent group submenu and Format submenu entry
2137 'Un' or 'Non'conserved</li>
2138 <li>Sequence feature settings are being shared by
2139 multiple distinct alignments</li>
2140 <li>group annotation not recreated when tree partition is
2142 <li>double click on group annotation to select sequences
2143 does not propagate to associated trees</li>
2144 <li>Mac OSX specific issues:
2146 <li>exception raised when mouse clicked on desktop
2147 window background</li>
2148 <li>Desktop menu placed on menu bar and application
2149 name set correctly</li>
2150 <li>sequence feature settings not wide enough for the
2151 save feature colourscheme button</li>
2160 <div align="center">
2161 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2164 <td><em>New Capabilities</em>
2166 <li>URL links generated from description line for
2167 regular-expression based URL links (applet and application)
2174 <li>Non-positional feature URL links are shown in link
2176 <li>Linked viewing of nucleic acid sequences and
2178 <li>Automatic Scrolling option in View menu to display
2179 the currently highlighted region of an alignment.</li>
2180 <li>Order an alignment by sequence length, or using the
2181 average score or total feature count for each sequence.</li>
2182 <li>Shading features by score or associated description</li>
2183 <li>Subdivide alignment and groups based on identity of
2184 selected subsequence (Make Groups from Selection).</li>
2185 <li>New hide/show options including Shift+Control+H to
2186 hide everything but the currently selected region.</li>
2187 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2188 </ul> <em>Application</em>
2190 <li>Fetch DB References capabilities and UI expanded to
2191 support retrieval from DAS sequence sources</li>
2192 <li>Local DAS Sequence sources can be added via the
2193 command line or via the Add local source dialog box.</li>
2194 <li>DAS Dbref and DbxRef feature types are parsed as
2195 database references and protein_name is parsed as
2196 description line (BioSapiens terms).</li>
2197 <li>Enable or disable non-positional feature and database
2198 references in sequence ID tooltip from View menu in
2200 <!-- <li>New hidden columns and rows and representatives capabilities
2201 in annotations file (in progress - not yet fully implemented)</li> -->
2202 <li>Group-associated consensus, sequence logos and
2203 conservation plots</li>
2204 <li>Symbol distributions for each column can be exported
2205 and visualized as sequence logos</li>
2206 <li>Optionally scale multi-character column labels to fit
2207 within each column of annotation row<!-- todo for applet -->
2209 <li>Optional automatic sort of associated alignment view
2210 when a new tree is opened.</li>
2211 <li>Jalview Java Console</li>
2212 <li>Better placement of desktop window when moving
2213 between different screens.</li>
2214 <li>New preference items for sequence ID tooltip and
2215 consensus annotation</li>
2216 <li>Client to submit sequences and IDs to Envision2
2218 <li><em>Vamsas Capabilities</em>
2220 <li>Improved VAMSAS synchronization (Jalview archive
2221 used to preserve views, structures, and tree display
2223 <li>Import of vamsas documents from disk or URL via
2225 <li>Sharing of selected regions between views and
2226 with other VAMSAS applications (Experimental feature!)</li>
2227 <li>Updated API to VAMSAS version 0.2</li>
2229 </ul> <em>Applet</em>
2231 <li>Middle button resizes annotation row height</li>
2234 <li>sortByTree (true/false) - automatically sort the
2235 associated alignment view by the tree when a new tree is
2237 <li>showTreeBootstraps (true/false) - show or hide
2238 branch bootstraps (default is to show them if available)</li>
2239 <li>showTreeDistances (true/false) - show or hide
2240 branch lengths (default is to show them if available)</li>
2241 <li>showUnlinkedTreeNodes (true/false) - indicate if
2242 unassociated nodes should be highlighted in the tree
2244 <li>heightScale and widthScale (1.0 or more) -
2245 increase the height or width of a cell in the alignment
2246 grid relative to the current font size.</li>
2249 <li>Non-positional features displayed in sequence ID
2251 </ul> <em>Other</em>
2253 <li>Features format: graduated colour definitions and
2254 specification of feature scores</li>
2255 <li>Alignment Annotations format: new keywords for group
2256 associated annotation (GROUP_REF) and annotation row display
2257 properties (ROW_PROPERTIES)</li>
2258 <li>XML formats extended to support graduated feature
2259 colourschemes, group associated annotation, and profile
2260 visualization settings.</li></td>
2263 <li>Source field in GFF files parsed as feature source
2264 rather than description</li>
2265 <li>Non-positional features are now included in sequence
2266 feature and gff files (controlled via non-positional feature
2267 visibility in tooltip).</li>
2268 <li>URL links generated for all feature links (bugfix)</li>
2269 <li>Added URL embedding instructions to features file
2271 <li>Codons containing ambiguous nucleotides translated as
2272 'X' in peptide product</li>
2273 <li>Match case switch in find dialog box works for both
2274 sequence ID and sequence string and query strings do not
2275 have to be in upper case to match case-insensitively.</li>
2276 <li>AMSA files only contain first column of
2277 multi-character column annotation labels</li>
2278 <li>Jalview Annotation File generation/parsing consistent
2279 with documentation (e.g. Stockholm annotation can be
2280 exported and re-imported)</li>
2281 <li>PDB files without embedded PDB IDs given a friendly
2283 <li>Find incrementally searches ID string matches as well
2284 as subsequence matches, and correctly reports total number
2288 <li>Better handling of exceptions during sequence
2290 <li>Dasobert generated non-positional feature URL
2291 link text excludes the start_end suffix</li>
2292 <li>DAS feature and source retrieval buttons disabled
2293 when fetch or registry operations in progress.</li>
2294 <li>PDB files retrieved from URLs are cached properly</li>
2295 <li>Sequence description lines properly shared via
2297 <li>Sequence fetcher fetches multiple records for all
2299 <li>Ensured that command line das feature retrieval
2300 completes before alignment figures are generated.</li>
2301 <li>Reduced time taken when opening file browser for
2303 <li>isAligned check prior to calculating tree, PCA or
2304 submitting an MSA to JNet now excludes hidden sequences.</li>
2305 <li>User defined group colours properly recovered
2306 from Jalview projects.</li>
2315 <div align="center">
2316 <strong>2.4.0.b2</strong><br> 28/10/2009
2321 <li>Experimental support for google analytics usage
2323 <li>Jalview privacy settings (user preferences and docs).</li>
2328 <li>Race condition in applet preventing startup in
2330 <li>Exception when feature created from selection beyond
2331 length of sequence.</li>
2332 <li>Allow synthetic PDB files to be imported gracefully</li>
2333 <li>Sequence associated annotation rows associate with
2334 all sequences with a given id</li>
2335 <li>Find function matches case-insensitively for sequence
2336 ID string searches</li>
2337 <li>Non-standard characters do not cause pairwise
2338 alignment to fail with exception</li>
2339 </ul> <em>Application Issues</em>
2341 <li>Sequences are now validated against EMBL database</li>
2342 <li>Sequence fetcher fetches multiple records for all
2344 </ul> <em>InstallAnywhere Issues</em>
2346 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2347 issue with installAnywhere mechanism)</li>
2348 <li>Command line launching of JARs from InstallAnywhere
2349 version (java class versioning error fixed)</li>
2356 <div align="center">
2357 <strong>2.4</strong><br> 27/8/2008
2360 <td><em>User Interface</em>
2362 <li>Linked highlighting of codon and amino acid from
2363 translation and protein products</li>
2364 <li>Linked highlighting of structure associated with
2365 residue mapping to codon position</li>
2366 <li>Sequence Fetcher provides example accession numbers
2367 and 'clear' button</li>
2368 <li>MemoryMonitor added as an option under Desktop's
2370 <li>Extract score function to parse whitespace separated
2371 numeric data in description line</li>
2372 <li>Column labels in alignment annotation can be centred.</li>
2373 <li>Tooltip for sequence associated annotation give name
2375 </ul> <em>Web Services and URL fetching</em>
2377 <li>JPred3 web service</li>
2378 <li>Prototype sequence search client (no public services
2380 <li>Fetch either seed alignment or full alignment from
2382 <li>URL Links created for matching database cross
2383 references as well as sequence ID</li>
2384 <li>URL Links can be created using regular-expressions</li>
2385 </ul> <em>Sequence Database Connectivity</em>
2387 <li>Retrieval of cross-referenced sequences from other
2389 <li>Generalised database reference retrieval and
2390 validation to all fetchable databases</li>
2391 <li>Fetch sequences from DAS sources supporting the
2392 sequence command</li>
2393 </ul> <em>Import and Export</em>
2394 <li>export annotation rows as CSV for spreadsheet import</li>
2395 <li>Jalview projects record alignment dataset associations,
2396 EMBL products, and cDNA sequence mappings</li>
2397 <li>Sequence Group colour can be specified in Annotation
2399 <li>Ad-hoc colouring of group in Annotation File using RGB
2400 triplet as name of colourscheme</li>
2401 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2403 <li>treenode binding for VAMSAS tree exchange</li>
2404 <li>local editing and update of sequences in VAMSAS
2405 alignments (experimental)</li>
2406 <li>Create new or select existing session to join</li>
2407 <li>load and save of vamsas documents</li>
2408 </ul> <em>Application command line</em>
2410 <li>-tree parameter to open trees (introduced for passing
2412 <li>-fetchfrom command line argument to specify nicknames
2413 of DAS servers to query for alignment features</li>
2414 <li>-dasserver command line argument to add new servers
2415 that are also automatically queried for features</li>
2416 <li>-groovy command line argument executes a given groovy
2417 script after all input data has been loaded and parsed</li>
2418 </ul> <em>Applet-Application data exchange</em>
2420 <li>Trees passed as applet parameters can be passed to
2421 application (when using "View in full
2422 application")</li>
2423 </ul> <em>Applet Parameters</em>
2425 <li>feature group display control parameter</li>
2426 <li>debug parameter</li>
2427 <li>showbutton parameter</li>
2428 </ul> <em>Applet API methods</em>
2430 <li>newView public method</li>
2431 <li>Window (current view) specific get/set public methods</li>
2432 <li>Feature display control methods</li>
2433 <li>get list of currently selected sequences</li>
2434 </ul> <em>New Jalview distribution features</em>
2436 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2437 <li>RELEASE file gives build properties for the latest
2438 Jalview release.</li>
2439 <li>Java 1.1 Applet build made easier and donotobfuscate
2440 property controls execution of obfuscator</li>
2441 <li>Build target for generating source distribution</li>
2442 <li>Debug flag for javacc</li>
2443 <li>.jalview_properties file is documented (slightly) in
2444 jalview.bin.Cache</li>
2445 <li>Continuous Build Integration for stable and
2446 development version of Application, Applet and source
2451 <li>selected region output includes visible annotations
2452 (for certain formats)</li>
2453 <li>edit label/displaychar contains existing label/char
2455 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2456 <li>shorter peptide product names from EMBL records</li>
2457 <li>Newick string generator makes compact representations</li>
2458 <li>bootstrap values parsed correctly for tree files with
2460 <li>pathological filechooser bug avoided by not allowing
2461 filenames containing a ':'</li>
2462 <li>Fixed exception when parsing GFF files containing
2463 global sequence features</li>
2464 <li>Alignment datasets are finalized only when number of
2465 references from alignment sequences goes to zero</li>
2466 <li>Close of tree branch colour box without colour
2467 selection causes cascading exceptions</li>
2468 <li>occasional negative imgwidth exceptions</li>
2469 <li>better reporting of non-fatal warnings to user when
2470 file parsing fails.</li>
2471 <li>Save works when Jalview project is default format</li>
2472 <li>Save as dialog opened if current alignment format is
2473 not a valid output format</li>
2474 <li>UniProt canonical names introduced for both das and
2476 <li>Histidine should be midblue (not pink!) in Zappo</li>
2477 <li>error messages passed up and output when data read
2479 <li>edit undo recovers previous dataset sequence when
2480 sequence is edited</li>
2481 <li>allow PDB files without pdb ID HEADER lines (like
2482 those generated by MODELLER) to be read in properly</li>
2483 <li>allow reading of JPred concise files as a normal
2485 <li>Stockholm annotation parsing and alignment properties
2486 import fixed for PFAM records</li>
2487 <li>Structure view windows have correct name in Desktop
2489 <li>annotation consisting of sequence associated scores
2490 can be read and written correctly to annotation file</li>
2491 <li>Aligned cDNA translation to aligned peptide works
2493 <li>Fixed display of hidden sequence markers and
2494 non-italic font for representatives in Applet</li>
2495 <li>Applet Menus are always embedded in applet window on
2497 <li>Newly shown features appear at top of stack (in
2499 <li>Annotations added via parameter not drawn properly
2500 due to null pointer exceptions</li>
2501 <li>Secondary structure lines are drawn starting from
2502 first column of alignment</li>
2503 <li>UniProt XML import updated for new schema release in
2505 <li>Sequence feature to sequence ID match for Features
2506 file is case-insensitive</li>
2507 <li>Sequence features read from Features file appended to
2508 all sequences with matching IDs</li>
2509 <li>PDB structure coloured correctly for associated views
2510 containing a sub-sequence</li>
2511 <li>PDB files can be retrieved by applet from Jar files</li>
2512 <li>feature and annotation file applet parameters
2513 referring to different directories are retrieved correctly</li>
2514 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
2515 <li>Fixed application hang whilst waiting for
2516 splash-screen version check to complete</li>
2517 <li>Applet properly URLencodes input parameter values
2518 when passing them to the launchApp service</li>
2519 <li>display name and local features preserved in results
2520 retrieved from web service</li>
2521 <li>Visual delay indication for sequence retrieval and
2522 sequence fetcher initialisation</li>
2523 <li>updated Application to use DAS 1.53e version of
2524 dasobert DAS client</li>
2525 <li>Re-instated Full AMSA support and .amsa file
2527 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
2535 <div align="center">
2536 <strong>2.3</strong><br> 9/5/07
2541 <li>Jmol 11.0.2 integration</li>
2542 <li>PDB views stored in Jalview XML files</li>
2543 <li>Slide sequences</li>
2544 <li>Edit sequence in place</li>
2545 <li>EMBL CDS features</li>
2546 <li>DAS Feature mapping</li>
2547 <li>Feature ordering</li>
2548 <li>Alignment Properties</li>
2549 <li>Annotation Scores</li>
2550 <li>Sort by scores</li>
2551 <li>Feature/annotation editing in applet</li>
2556 <li>Headless state operation in 2.2.1</li>
2557 <li>Incorrect and unstable DNA pairwise alignment</li>
2558 <li>Cut and paste of sequences with annotation</li>
2559 <li>Feature group display state in XML</li>
2560 <li>Feature ordering in XML</li>
2561 <li>blc file iteration selection using filename # suffix</li>
2562 <li>Stockholm alignment properties</li>
2563 <li>Stockhom alignment secondary structure annotation</li>
2564 <li>2.2.1 applet had no feature transparency</li>
2565 <li>Number pad keys can be used in cursor mode</li>
2566 <li>Structure Viewer mirror image resolved</li>
2573 <div align="center">
2574 <strong>2.2.1</strong><br> 12/2/07
2579 <li>Non standard characters can be read and displayed
2580 <li>Annotations/Features can be imported/exported to the
2582 <li>Applet allows editing of sequence/annotation/group
2583 name & description
2584 <li>Preference setting to display sequence name in
2586 <li>Annotation file format extended to allow
2587 Sequence_groups to be defined
2588 <li>Default opening of alignment overview panel can be
2589 specified in preferences
2590 <li>PDB residue numbering annotation added to associated
2596 <li>Applet crash under certain Linux OS with Java 1.6
2598 <li>Annotation file export / import bugs fixed
2599 <li>PNG / EPS image output bugs fixed
2605 <div align="center">
2606 <strong>2.2</strong><br> 27/11/06
2611 <li>Multiple views on alignment
2612 <li>Sequence feature editing
2613 <li>"Reload" alignment
2614 <li>"Save" to current filename
2615 <li>Background dependent text colour
2616 <li>Right align sequence ids
2617 <li>User-defined lower case residue colours
2620 <li>Menu item accelerator keys
2621 <li>Control-V pastes to current alignment
2622 <li>Cancel button for DAS Feature Fetching
2623 <li>PCA and PDB Viewers zoom via mouse roller
2624 <li>User-defined sub-tree colours and sub-tree selection
2631 <li>'New Window' button on the 'Output to Text box'
2636 <li>New memory efficient Undo/Redo System
2637 <li>Optimised symbol lookups and conservation/consensus
2639 <li>Region Conservation/Consensus recalculated after
2641 <li>Fixed Remove Empty Columns Bug (empty columns at end
2643 <li>Slowed DAS Feature Fetching for increased robustness.
2650 <li>Made angle brackets in ASCII feature descriptions
2652 <li>Re-instated Zoom function for PCA
2653 <li>Sequence descriptions conserved in web service
2655 <li>UniProt ID discoverer uses any word separated by
2657 <li>WsDbFetch query/result association resolved
2658 <li>Tree leaf to sequence mapping improved
2659 <li>Smooth fonts switch moved to FontChooser dialog box.
2671 <div align="center">
2672 <strong>2.1.1</strong><br> 12/9/06
2677 <li>Copy consensus sequence to clipboard</li>
2682 <li>Image output - rightmost residues are rendered if
2683 sequence id panel has been resized</li>
2684 <li>Image output - all offscreen group boundaries are
2686 <li>Annotation files with sequence references - all
2687 elements in file are relative to sequence position</li>
2688 <li>Mac Applet users can use Alt key for group editing</li>
2694 <div align="center">
2695 <strong>2.1</strong><br> 22/8/06
2700 <li>MAFFT Multiple Alignment in default Web Service list</li>
2701 <li>DAS Feature fetching</li>
2702 <li>Hide sequences and columns</li>
2703 <li>Export Annotations and Features</li>
2704 <li>GFF file reading / writing</li>
2705 <li>Associate structures with sequences from local PDB
2707 <li>Add sequences to exisiting alignment</li>
2708 <li>Recently opened files / URL lists</li>
2709 <li>Applet can launch the full application</li>
2710 <li>Applet has transparency for features (Java 1.2
2712 <li>Applet has user defined colours parameter</li>
2713 <li>Applet can load sequences from parameter
2714 "sequence<em>x</em>"
2720 <li>Redundancy Panel reinstalled in the Applet</li>
2721 <li>Monospaced font - EPS / rescaling bug fixed</li>
2722 <li>Annotation files with sequence references bug fixed</li>
2728 <div align="center">
2729 <strong>2.08.1</strong><br> 2/5/06
2734 <li>Change case of selected region from Popup menu</li>
2735 <li>Choose to match case when searching</li>
2736 <li>Middle mouse button and mouse movement can compress /
2737 expand the visible width and height of the alignment</li>
2742 <li>Annotation Panel displays complete JNet results</li>
2748 <div align="center">
2749 <strong>2.08b</strong><br> 18/4/06
2755 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
2756 <li>Righthand label on wrapped alignments shows correct
2763 <div align="center">
2764 <strong>2.08</strong><br> 10/4/06
2769 <li>Editing can be locked to the selection area</li>
2770 <li>Keyboard editing</li>
2771 <li>Create sequence features from searches</li>
2772 <li>Precalculated annotations can be loaded onto
2774 <li>Features file allows grouping of features</li>
2775 <li>Annotation Colouring scheme added</li>
2776 <li>Smooth fonts off by default - Faster rendering</li>
2777 <li>Choose to toggle Autocalculate Consensus On/Off</li>
2782 <li>Drag & Drop fixed on Linux</li>
2783 <li>Jalview Archive file faster to load/save, sequence
2784 descriptions saved.</li>
2790 <div align="center">
2791 <strong>2.07</strong><br> 12/12/05
2796 <li>PDB Structure Viewer enhanced</li>
2797 <li>Sequence Feature retrieval and display enhanced</li>
2798 <li>Choose to output sequence start-end after sequence
2799 name for file output</li>
2800 <li>Sequence Fetcher WSDBFetch@EBI</li>
2801 <li>Applet can read feature files, PDB files and can be
2802 used for HTML form input</li>
2807 <li>HTML output writes groups and features</li>
2808 <li>Group editing is Control and mouse click</li>
2809 <li>File IO bugs</li>
2815 <div align="center">
2816 <strong>2.06</strong><br> 28/9/05
2821 <li>View annotations in wrapped mode</li>
2822 <li>More options for PCA viewer</li>
2827 <li>GUI bugs resolved</li>
2828 <li>Runs with -nodisplay from command line</li>
2834 <div align="center">
2835 <strong>2.05b</strong><br> 15/9/05
2840 <li>Choose EPS export as lineart or text</li>
2841 <li>Jar files are executable</li>
2842 <li>Can read in Uracil - maps to unknown residue</li>
2847 <li>Known OutOfMemory errors give warning message</li>
2848 <li>Overview window calculated more efficiently</li>
2849 <li>Several GUI bugs resolved</li>
2855 <div align="center">
2856 <strong>2.05</strong><br> 30/8/05
2861 <li>Edit and annotate in "Wrapped" view</li>
2866 <li>Several GUI bugs resolved</li>
2872 <div align="center">
2873 <strong>2.04</strong><br> 24/8/05
2878 <li>Hold down mouse wheel & scroll to change font
2884 <li>Improved JPred client reliability</li>
2885 <li>Improved loading of Jalview files</li>
2891 <div align="center">
2892 <strong>2.03</strong><br> 18/8/05
2897 <li>Set Proxy server name and port in preferences</li>
2898 <li>Multiple URL links from sequence ids</li>
2899 <li>User Defined Colours can have a scheme name and added
2901 <li>Choose to ignore gaps in consensus calculation</li>
2902 <li>Unix users can set default web browser</li>
2903 <li>Runs without GUI for batch processing</li>
2904 <li>Dynamically generated Web Service Menus</li>
2909 <li>InstallAnywhere download for Sparc Solaris</li>
2915 <div align="center">
2916 <strong>2.02</strong><br> 18/7/05
2922 <li>Copy & Paste order of sequences maintains
2923 alignment order.</li>
2929 <div align="center">
2930 <strong>2.01</strong><br> 12/7/05
2935 <li>Use delete key for deleting selection.</li>
2936 <li>Use Mouse wheel to scroll sequences.</li>
2937 <li>Help file updated to describe how to add alignment
2939 <li>Version and build date written to build properties
2941 <li>InstallAnywhere installation will check for updates
2942 at launch of Jalview.</li>
2947 <li>Delete gaps bug fixed.</li>
2948 <li>FileChooser sorts columns.</li>
2949 <li>Can remove groups one by one.</li>
2950 <li>Filechooser icons installed.</li>
2951 <li>Finder ignores return character when searching.
2952 Return key will initiate a search.<br>
2959 <div align="center">
2960 <strong>2.0</strong><br> 20/6/05
2965 <li>New codebase</li>