3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
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27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.2">2.10.2</a><br />
74 <em>30/5/2017</em></strong>
77 <td><div align="left">
80 <li><!-- JAL-2360,JAL-2371, -->More robust colours and shader model for alignments and groups</li>
81 <li><!-- JAL-384 -->Custom shading schemes created via groovy scripts</li>
82 <li><!-- JAL-2491 -->linked scrolling of CDS/Protein views via Overview or sequence motif search operations</li>
83 <li><!-- JAL-2526 -->Efficiency improvements for interacting with alignment and overview windows</li>
85 <!-- JAL-2535 -->Posterior probability annotation from
86 Stockholm files imported as sequence associated annotation
93 Experimental Features Checkbox in Desktop's Tools
94 menu to hide or show untested features in the application.
96 <li><!-- JAL-1476 -->Warning in alignment status bar when there are not enough columns to superimpose structures in Chimera</li>
97 <li><!-- JAL-1596 -->Faster Chimera/Jalview communication by file-based command exchange</li>
98 <li><!-- JAL-2316, -->URLs for viewing database cross-references provided by identifiers.org and the EMBL-EBI's MIRIAM DB</li>
99 <li><!-- JAL-2549 -->Updated JABAWS client to v2.2</li>
101 <em>Experimental features</em>
104 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
105 to transfer Chimera's structure attributes as Jalview
106 features, and vice-versa.
114 <li><!-- JAL-2474 -->Added PrivelegedAccessor to test suite</li>
115 <li><!-- JAL-2326 -->Prevent or clear modal dialogs raised during tests</li>
118 </div></td><td><div align="left">
122 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
123 matrix - C->R should be '3'<br />Old matrix restored with
124 this one-line groovy script:<br />jalview.schemes.ResidueProperties.BLOSUM62[4][1]=3
127 <!-- JAL-2397 -->Fixed Jalview's treatment of gaps in PCA
128 and substitution matrix based Tree calculations.<br />In
129 earlier versions of Jalview, gaps matching gaps were
130 penalised, and gaps matching non-gaps penalised even more.
131 In the PCA calculation, gaps were actually treated as
132 non-gaps - so different costs were applied, which mean't
133 Jalview's PCAs were different to those produced by
134 SeqSpace.<br />Jalview now treats gaps in the same way as
135 SeqSpace (ie it scores them as 0). To restore pre-2.10.2
137 jalview.viewmodel.PCAModel.scoreGapAsAny=true // for
139 jalview.viewmodel.PCAModel.scoreGapAsAny=false // to
142 <li><!-- JAL-2346 -->Reopening Colour by annotation dialog doesn't reselect a specific sequence's associated annotation after it was used for colouring a view</li>
143 <li><!-- JAL-2430 -->Hidden regions in alignment views are not coloured in linked structure views</li>
144 <li><!-- JAL-2419 -->Current selection lost if popup menu opened on a region of alignment without groups</li>
145 <li><!-- JAL-2374 -->Popup menu not always shown for regions of an alignment with overlapping groups</li>
146 <li><!-- JAL-2310 -->Finder double counts if both a sequence's name and description match</li>
147 <li><!-- JAL-2370 -->Hiding column selection containing two hidden regions results in incorrect hidden regions</li>
148 <li><!-- JAL-2377 -->PCA calculation could hang when generating output report when working with highly redundant alignments</li>
149 <li><!-- JAL-2365 -->Cannot configure feature colours with lightGray or darkGray via features file</li>
150 <li><!-- JAL-2421 -->Overview window visible region moves erratically when hidden rows or columns are present</li>
151 <li><!-- JAL-2362 -->Per-residue colourschemes applied via the Structure Viewer's colour menu don't correspond to sequence colouring</li>
152 <li><!-- JAL-2405 -->Protein specific colours only offered in colour and group colour menu for protein alignments</li>
153 <li><!-- JAL-2386 -->'Apply to all groups' setting when changing colour does not apply Conservation slider value to all groups</li>
154 <li><!-- JAL-2385 -->Colour threshold slider doesn't update to reflect currently selected view or group's shading thresholds</li>
155 <li><!-- JAL-2373 -->Percentage identity and conservation menu items do not show a tick or allow shading to be disabled</li>
156 <li><!-- JAL-2385 -->Conservation shading or PID threshold lost when base colourscheme changed if slider not visible</li>
157 <li><!-- JAL-2547 -->Sequence features shown in tooltip for gaps before start of features</li>
161 <li><!-- JAL-2401 -->Easier creation of colours for all 'Lower case' residues (button in colourscheme editor debugged and new documentation and tooltips added)</li>
162 <li><!-- JAL-2399-->Text colour threshold's 'Cancel' button doesn't restore group-specific text colour thresholds</li>
163 <li><!-- JAL-2243 -->Feature settings panel does not update as new features are added to alignment</li>
164 <li><!-- JAL-2436 -->Structure viewer's View -> Colour By view selection menu changes colours of alignment views</li>
165 <li><!-- JAL-2366 -->Proxy server address and port always appear enabled in Preferences->Connections</li>
166 <li><!-- JAL-2426 -->Spurious exceptions in console raised from alignment calculation workers after alignment has been closed</li>
167 <li><!-- JAL-1608 -->Typo in selection popup menu - Create groups now 'Create Group'</li>
168 <li><!-- JAL-1608 -->CMD/CTRL and G or Shift G for Create/Undefine group doesn't always work</li>
169 <li><!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get shown again after pressing 'Cancel'</li>
170 <li><!-- JAL-2461 -->DAS registry not found exceptions removed from console output</li>
171 <li><!-- JAL-2383 -->Above PID colour threshold not recovered when alignment view imported from project</li>
176 <li><!-- JAL-2442 -->Features not rendered as transparent on overview or linked structure view</li>
177 <li><!-- JAL-2372 -->Colour group by conservation doesn't work (since 2.8)</li>
179 <em>New Known Issues</em>
181 <li><!-- JAL-2566 -->Protein/CDS view scrolling not always in phase after a sequence motif find operation</li>
182 <li><!-- JAL-2563 -->Status bar doesn't show positions for ambiguous amino acids</li>
183 <li><!-- JAL-2550 -->Importing annotation file with rows containing just upper and lower case letters are interpreted as WUSS rna secondary structure symbols</li>
188 <td width="60" nowrap>
190 <strong><a name="Jalview.2.10.1">2.10.1</a><br />
191 <em>29/11/2016</em></strong>
194 <td><div align="left">
198 <!-- JAL-98 -->Improved memory usage: sparse arrays used
199 for all consensus calculations
202 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released 3rd Oct 2016)
204 <li>Updated Jalview's Certum code signing certificate
210 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
211 set of database cross-references, sorted alphabetically
214 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
215 from database cross references. Users with custom links
216 will receive a <a href="webServices/urllinks.html#warning">warning
217 dialog</a> asking them to update their preferences.
220 <!-- JAL-2287-->Cancel button and escape listener on
221 dialog warning user about disconnecting Jalview from a
225 <!-- JAL-2320-->Jalview's Chimera control window closes if
226 the Chimera it is connected to is shut down
229 <!-- JAL-1738-->New keystroke (B) and Select highlighted
230 columns menu item to mark columns containing
231 highlighted regions (e.g. from structure selections or results
235 <!-- JAL-2284-->Command line option for batch-generation
236 of HTML pages rendering alignment data with the BioJS
246 <!-- JAL-2286 -->Columns with more than one modal residue
247 are not coloured or thresholded according to percent
248 identity (first observed in Jalview 2.8.2)
251 <!-- JAL-2301 -->Threonine incorrectly reported as not
255 <!-- JAL-2318 -->Updates to documentation pages (above PID
256 threshold, amino acid properties)
259 <!-- JAL-2292 -->Lower case residues in sequences are not
260 reported as mapped to residues in a structure file in the
264 <!--JAL-2324 -->Identical features with non-numeric scores
265 could be added multiple times to a sequence
268 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
269 bond features shown as two highlighted residues rather
270 than a range in linked structure views, and treated
271 correctly when selecting and computing trees from features
274 <!-- JAL-2281-->Custom URL links for database
275 cross-references are matched to database name regardless
283 <!-- JAL-2282-->Custom URL links for specific database
284 names without regular expressions also offer links from
288 <!-- JAL-2315-->Removing a single configured link in the
289 URL links pane in Connections preferences doesn't actually
290 update Jalview configuration
293 <!-- JAL-2272-->CTRL-Click on a selected region to open
294 the alignment area popup menu doesn't work on El-Capitan
297 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
298 files with similarly named sequences if dropped onto the
302 <!-- JAL-2312 -->Additional mappings are shown for PDB
303 entries where more chains exist in the PDB accession than
304 are reported in the SIFTS file
307 <!-- JAL-2317-->Certain structures do not get mapped to
308 the structure view when displayed with Chimera
311 <!-- JAL-2317-->No chains shown in the Chimera view
312 panel's View->Show Chains submenu
315 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
316 work for wrapped alignment views
319 <!--JAL-2197 -->Rename UI components for running JPred
320 predictions from 'JNet' to 'JPred'
323 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
324 corrupted when annotation panel vertical scroll is not at
328 <!--JAL-2332 -->Attempting to view structure for Hen
329 lysozyme results in a PDB Client error dialog box
332 <!-- JAL-2319 -->Structure View's mapping report switched ranges for PDB and sequence for SIFTS</li>
333 <!-- JAL-2319 -->SIFTS 'Not_Observed' residues mapped to non-existant coordindate data</li>
335 <!-- <em>New Known Issues</em>
342 <td width="60" nowrap>
344 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
345 <em>25/10/2016</em></strong>
348 <td><em>Application</em>
350 <li>3D Structure chooser opens with 'Cached structures'
351 view if structures already loaded</li>
352 <li>Progress bar reports models as they are loaded to
359 <li>Colour by conservation always enabled and no tick
360 shown in menu when BLOSUM or PID shading applied</li>
361 <li>FER1_ARATH and FER2_ARATH labels were switched in
362 example sequences/projects/trees</li>
366 <li>Jalview projects with views of local PDB structure
367 files saved on Windows cannot be opened on OSX</li>
368 <li>Multiple structure views can be opened and
369 superposed without timeout for structures with multiple
370 models or multiple sequences in alignment</li>
371 <li>Cannot import or associated local PDB files without
372 a PDB ID HEADER line</li>
373 <li>RMSD is not output in Jmol console when
374 superposition is performed</li>
375 <li>Drag and drop of URL from Browser fails for Linux
376 and OSX versions earlier than El Capitan</li>
377 <li>ENA client ignores invalid content from ENA server</li>
378 <li>Exceptions are not raised in console when ENA
379 client attempts to fetch non-existent IDs via Fetch DB
381 <li>Exceptions are not raised in console when a new
382 view is created on the alignment</li>
383 <li>OSX right-click fixed for group selections:
384 CMD-click to insert/remove gaps in groups and CTRL-click
385 to open group pop-up menu</li>
387 <em>Build and deployment</em>
389 <li>URL link checker now copes with multi-line anchor
392 <em>New Known Issues</em>
394 <li>Drag and drop from URL links in browsers do not
401 <td width="60" nowrap>
403 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
409 <!-- JAL-2124 -->Updated Spanish translations.
412 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
413 for importing structure data to Jalview. Enables mmCIF and
417 <!-- JAL-192 --->Alignment ruler shows positions relative to
421 <!-- JAL-2202 -->Position/residue shown in status bar when
422 mousing over sequence associated annotation
425 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
429 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
430 '()', canonical '[]' and invalid '{}' base pair populations
434 <!-- JAL-2092 -->Feature settings popup menu options for
435 showing or hiding columns containing a feature
438 <!-- JAL-1557 -->Edit selected group by double clicking on
439 group and sequence associated annotation labels
442 <!-- JAL-2236 -->Sequence name added to annotation label in
443 select/hide columns by annotation and colour by annotation
447 </ul> <em>Application</em>
450 <!-- JAL-2050-->Automatically hide introns when opening a
454 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
458 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
459 structure mappings with the EMBL-EBI PDBe SIFTS database
462 <!-- JAL-2079 -->Updated download sites used for Rfam and
463 Pfam sources to xfam.org
466 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
469 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
470 over sequences in Jalview
473 <!-- JAL-2027-->Support for reverse-complement coding
474 regions in ENA and EMBL
477 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
478 for record retrieval via ENA rest API
481 <!-- JAL-2027 -->Support for ENA CDS records with reverse
485 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
486 groovy script execution
489 <!-- JAL-1812 -->New 'execute Groovy script' option in an
490 alignment window's Calculate menu
493 <!-- JAL-1812 -->Allow groovy scripts that call
494 Jalview.getAlignFrames() to run in headless mode
497 <!-- JAL-2068 -->Support for creating new alignment
498 calculation workers from groovy scripts
501 <!-- JAL-1369 --->Store/restore reference sequence in
505 <!-- JAL-1803 -->Chain codes for a sequence's PDB
506 associations are now saved/restored from project
509 <!-- JAL-1993 -->Database selection dialog always shown
510 before sequence fetcher is opened
513 <!-- JAL-2183 -->Double click on an entry in Jalview's
514 database chooser opens a sequence fetcher
517 <!-- JAL-1563 -->Free-text search client for UniProt using
521 <!-- JAL-2168 -->-nonews command line parameter to prevent
522 the news reader opening
525 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
526 querying stored in preferences
529 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
533 <!-- JAL-1977-->Tooltips shown on database chooser
536 <!-- JAL-391 -->Reverse complement function in calculate
537 menu for nucleotide sequences
540 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
541 and feature counts preserves alignment ordering (and
542 debugged for complex feature sets).
545 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
546 viewing structures with Jalview 2.10
549 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
550 genome, transcript CCDS and gene ids via the Ensembl and
551 Ensembl Genomes REST API
554 <!-- JAL-2049 -->Protein sequence variant annotation
555 computed for 'sequence_variant' annotation on CDS regions
559 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
563 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
564 Ref Fetcher fails to match, or otherwise updates sequence
565 data from external database records.
568 <!-- JAL-2154 -->Revised Jalview Project format for
569 efficient recovery of sequence coding and alignment
570 annotation relationships.
572 </ul> <!-- <em>Applet</em>
583 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
587 <!-- JAL-2018-->Export features in Jalview format (again)
588 includes graduated colourschemes
591 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
592 working with big alignments and lots of hidden columns
595 <!-- JAL-2053-->Hidden column markers not always rendered
596 at right of alignment window
599 <!-- JAL-2067 -->Tidied up links in help file table of
603 <!-- JAL-2072 -->Feature based tree calculation not shown
607 <!-- JAL-2075 -->Hidden columns ignored during feature
608 based tree calculation
611 <!-- JAL-2065 -->Alignment view stops updating when show
612 unconserved enabled for group on alignment
615 <!-- JAL-2086 -->Cannot insert gaps into sequence when
619 <!-- JAL-2146 -->Alignment column in status incorrectly
620 shown as "Sequence position" when mousing over
624 <!-- JAL-2099 -->Incorrect column numbers in ruler when
625 hidden columns present
628 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
629 user created annotation added to alignment
632 <!-- JAL-1841 -->RNA Structure consensus only computed for
633 '()' base pair annotation
636 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
637 in zero scores for all base pairs in RNA Structure
641 <!-- JAL-2174-->Extend selection with columns containing
645 <!-- JAL-2275 -->Pfam format writer puts extra space at
646 beginning of sequence
649 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
653 <!-- JAL-2238 -->Cannot create groups on an alignment from
654 from a tree when t-coffee scores are shown
657 <!-- JAL-1836,1967 -->Cannot import and view PDB
658 structures with chains containing negative resnums (4q4h)
661 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
665 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
666 to Clustal, PIR and PileUp output
669 <!-- JAL-2008 -->Reordering sequence features that are
670 not visible causes alignment window to repaint
673 <!-- JAL-2006 -->Threshold sliders don't work in
674 graduated colour and colour by annotation row for e-value
675 scores associated with features and annotation rows
678 <!-- JAL-1797 -->amino acid physicochemical conservation
679 calculation should be case independent
682 <!-- JAL-2173 -->Remove annotation also updates hidden
686 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
687 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
688 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
691 <!-- JAL-2065 -->Null pointer exceptions and redraw
692 problems when reference sequence defined and 'show
693 non-conserved' enabled
696 <!-- JAL-1306 -->Quality and Conservation are now shown on
697 load even when Consensus calculation is disabled
700 <!-- JAL-1932 -->Remove right on penultimate column of
701 alignment does nothing
707 <!-- JAL-1552-->URLs and links can't be imported by
708 drag'n'drop on OSX when launched via webstart (note - not
709 yet fixed for El Capitan)
712 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
713 output when running on non-gb/us i18n platforms
716 <!-- JAL-1944 -->Error thrown when exporting a view with
717 hidden sequences as flat-file alignment
720 <!-- JAL-2030-->InstallAnywhere distribution fails when
724 <!-- JAL-2080-->Jalview very slow to launch via webstart
725 (also hotfix for 2.9.0b2)
728 <!-- JAL-2085 -->Cannot save project when view has a
729 reference sequence defined
732 <!-- JAL-1011 -->Columns are suddenly selected in other
733 alignments and views when revealing hidden columns
736 <!-- JAL-1989 -->Hide columns not mirrored in complement
737 view in a cDNA/Protein splitframe
740 <!-- JAL-1369 -->Cannot save/restore representative
741 sequence from project when only one sequence is
745 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
749 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
750 structure consensus didn't refresh annotation panel
753 <!-- JAL-1962 -->View mapping in structure view shows
754 mappings between sequence and all chains in a PDB file
757 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
758 dialogs format columns correctly, don't display array
759 data, sort columns according to type
762 <!-- JAL-1975 -->Export complete shown after destination
763 file chooser is cancelled during an image export
766 <!-- JAL-2025 -->Error when querying PDB Service with
767 sequence name containing special characters
770 <!-- JAL-2024 -->Manual PDB structure querying should be
774 <!-- JAL-2104 -->Large tooltips with broken HTML
775 formatting don't wrap
778 <!-- JAL-1128 -->Figures exported from wrapped view are
779 truncated so L looks like I in consensus annotation
782 <!-- JAL-2003 -->Export features should only export the
783 currently displayed features for the current selection or
787 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
788 after fetching cross-references, and restoring from project
791 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
792 followed in the structure viewer
795 <!-- JAL-2163 -->Titles for individual alignments in
796 splitframe not restored from project
799 <!-- JAL-2145 -->missing autocalculated annotation at
800 trailing end of protein alignment in transcript/product
801 splitview when pad-gaps not enabled by default
804 <!-- JAL-1797 -->amino acid physicochemical conservation
808 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
809 article has been read (reopened issue due to
810 internationalisation problems)
813 <!-- JAL-1960 -->Only offer PDB structures in structure
814 viewer based on sequence name, PDB and UniProt
819 <!-- JAL-1976 -->No progress bar shown during export of
823 <!-- JAL-2213 -->Structures not always superimposed after
824 multiple structures are shown for one or more sequences.
827 <!-- JAL-1370 -->Reference sequence characters should not
828 be replaced with '.' when 'Show unconserved' format option
832 <!-- JAL-1823 -->Cannot specify chain code when entering
833 specific PDB id for sequence
836 <!-- JAL-1944 -->File->Export->.. as doesn't work when
837 'Export hidden sequences' is enabled, but 'export hidden
838 columns' is disabled.
841 <!--JAL-2026-->Best Quality option in structure chooser
842 selects lowest rather than highest resolution structures
846 <!-- JAL-1887 -->Incorrect start and end reported for PDB
847 to sequence mapping in 'View Mappings' report
850 <!-- JAL-2284 -->Unable to read old Jalview projects that
851 contain non-XML data added after Jalvew wrote project.
853 <li><!-- JAL-2118 -->Newly created annotation row reorders
854 after clicking on it to create new annotation for a
857 <!-- may exclude, this is an external service stability issue JAL-1941
858 -- > RNA 3D structure not added via DSSR service</li> -->
863 <!-- JAL-2151 -->Incorrect columns are selected when
864 hidden columns present before start of sequence
867 <!-- JAL-1986 -->Missing dependencies on applet pages
871 <!-- JAL-1947 -->Overview pixel size changes when
872 sequences are hidden in applet
875 <!-- JAL-1996 -->Updated instructions for applet
876 deployment on examples pages.
883 <td width="60" nowrap>
885 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
886 <em>16/10/2015</em></strong>
891 <li>Time stamps for signed Jalview application and applet
898 <li>Duplicate group consensus and conservation rows
899 shown when tree is partitioned</li>
900 <li>Erratic behaviour when tree partitions made with
901 multiple cDNA/Protein split views</li>
907 <td width="60" nowrap>
909 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
910 <em>8/10/2015</em></strong>
915 <li>Updated Spanish translations of localized text for
917 </ul> <em>Application</em>
919 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
920 <li>Signed OSX InstallAnywhere installer<br></li>
921 <li>Support for per-sequence based annotations in BioJSON</li>
922 </ul> <em>Applet</em>
924 <li>Split frame example added to applet examples page</li>
925 </ul><em>Build and Deployment</em>
927 <li><!-- JAL-1888 -->New ant target for running Jalview's test suite</li>
933 <li>Mapping of cDNA to protein in split frames
934 incorrect when sequence start > 1</li>
935 <li>Broken images in filter column by annotation dialog
937 <li>Feature colours not parsed from features file</li>
938 <li>Exceptions and incomplete link URLs recovered when
939 loading a features file containing HTML tags in feature
945 <li>Annotations corrupted after BioJS export and
947 <li>Incorrect sequence limits after Fetch DB References
948 with 'trim retrieved sequences'</li>
949 <li>Incorrect warning about deleting all data when
950 deleting selected columns</li>
951 <li>Patch to build system for shipping properly signed
952 JNLP templates for webstart launch</li>
953 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
954 unreleased structures for download or viewing</li>
955 <li>Tab/space/return keystroke operation of EMBL-PDBe
956 fetcher/viewer dialogs works correctly</li>
957 <li>Disabled 'minimise' button on Jalview windows
958 running on OSX to workaround redraw hang bug</li>
959 <li>Split cDNA/Protein view position and geometry not
960 recovered from jalview project</li>
961 <li>Initial enabled/disabled state of annotation menu
962 sorter 'show autocalculated first/last' corresponds to
964 <li>Restoring of Clustal, RNA Helices and T-Coffee
965 color schemes from BioJSON</li>
969 <li>Reorder sequences mirrored in cDNA/Protein split
971 <li>Applet with Jmol examples not loading correctly</li>
977 <td><div align="center">
978 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
982 <li>Linked visualisation and analysis of DNA and Protein
985 <li>Translated cDNA alignments shown as split protein
986 and DNA alignment views</li>
987 <li>Codon consensus annotation for linked protein and
988 cDNA alignment views</li>
989 <li>Link cDNA or Protein product sequences by loading
990 them onto Protein or cDNA alignments</li>
991 <li>Reconstruct linked cDNA alignment from aligned
992 protein sequences</li>
995 <li>Jmol integration updated to Jmol v14.2.14</li>
996 <li>Import and export of Jalview alignment views as <a
997 href="features/bioJsonFormat.html">BioJSON</a></li>
998 <li>New alignment annotation file statements for
999 reference sequences and marking hidden columns</li>
1000 <li>Reference sequence based alignment shading to
1001 highlight variation</li>
1002 <li>Select or hide columns according to alignment
1004 <li>Find option for locating sequences by description</li>
1005 <li>Conserved physicochemical properties shown in amino
1006 acid conservation row</li>
1007 <li>Alignments can be sorted by number of RNA helices</li>
1008 </ul> <em>Application</em>
1010 <li>New cDNA/Protein analysis capabilities
1012 <li>Get Cross-References should open a Split Frame
1013 view with cDNA/Protein</li>
1014 <li>Detect when nucleotide sequences and protein
1015 sequences are placed in the same alignment</li>
1016 <li>Split cDNA/Protein views are saved in Jalview
1021 <li>Use REST API to talk to Chimera</li>
1022 <li>Selected regions in Chimera are highlighted in linked
1023 Jalview windows</li>
1025 <li>VARNA RNA viewer updated to v3.93</li>
1026 <li>VARNA views are saved in Jalview Projects</li>
1027 <li>Pseudoknots displayed as Jalview RNA annotation can
1028 be shown in VARNA</li>
1030 <li>Make groups for selection uses marked columns as well
1031 as the active selected region</li>
1033 <li>Calculate UPGMA and NJ trees using sequence feature
1035 <li>New Export options
1037 <li>New Export Settings dialog to control hidden
1038 region export in flat file generation</li>
1040 <li>Export alignment views for display with the <a
1041 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1043 <li>Export scrollable SVG in HTML page</li>
1044 <li>Optional embedding of BioJSON data when exporting
1045 alignment figures to HTML</li>
1047 <li>3D structure retrieval and display
1049 <li>Free text and structured queries with the PDBe
1051 <li>PDBe Search API based discovery and selection of
1052 PDB structures for a sequence set</li>
1056 <li>JPred4 employed for protein secondary structure
1058 <li>Hide Insertions menu option to hide unaligned columns
1059 for one or a group of sequences</li>
1060 <li>Automatically hide insertions in alignments imported
1061 from the JPred4 web server</li>
1062 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1063 system on OSX<br />LGPL libraries courtesy of <a
1064 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1066 <li>changed 'View nucleotide structure' submenu to 'View
1067 VARNA 2D Structure'</li>
1068 <li>change "View protein structure" menu option to "3D
1071 </ul> <em>Applet</em>
1073 <li>New layout for applet example pages</li>
1074 <li>New parameters to enable SplitFrame view
1075 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1076 <li>New example demonstrating linked viewing of cDNA and
1077 Protein alignments</li>
1078 </ul> <em>Development and deployment</em>
1080 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1081 <li>Include installation type and git revision in build
1082 properties and console log output</li>
1083 <li>Jalview Github organisation, and new github site for
1084 storing BioJsMSA Templates</li>
1085 <li>Jalview's unit tests now managed with TestNG</li>
1088 <!-- <em>General</em>
1090 </ul> --> <!-- issues resolved --> <em>Application</em>
1092 <li>Escape should close any open find dialogs</li>
1093 <li>Typo in select-by-features status report</li>
1094 <li>Consensus RNA secondary secondary structure
1095 predictions are not highlighted in amber</li>
1096 <li>Missing gap character in v2.7 example file means
1097 alignment appears unaligned when pad-gaps is not enabled</li>
1098 <li>First switch to RNA Helices colouring doesn't colour
1099 associated structure views</li>
1100 <li>ID width preference option is greyed out when auto
1101 width checkbox not enabled</li>
1102 <li>Stopped a warning dialog from being shown when
1103 creating user defined colours</li>
1104 <li>'View Mapping' in structure viewer shows sequence
1105 mappings for just that viewer's sequences</li>
1106 <li>Workaround for superposing PDB files containing
1107 multiple models in Chimera</li>
1108 <li>Report sequence position in status bar when hovering
1109 over Jmol structure</li>
1110 <li>Cannot output gaps as '.' symbols with Selection ->
1111 output to text box</li>
1112 <li>Flat file exports of alignments with hidden columns
1113 have incorrect sequence start/end</li>
1114 <li>'Aligning' a second chain to a Chimera structure from
1116 <li>Colour schemes applied to structure viewers don't
1117 work for nucleotide</li>
1118 <li>Loading/cut'n'pasting an empty or invalid file leads
1119 to a grey/invisible alignment window</li>
1120 <li>Exported Jpred annotation from a sequence region
1121 imports to different position</li>
1122 <li>Space at beginning of sequence feature tooltips shown
1123 on some platforms</li>
1124 <li>Chimera viewer 'View | Show Chain' menu is not
1126 <li>'New View' fails with a Null Pointer Exception in
1127 console if Chimera has been opened</li>
1128 <li>Mouseover to Chimera not working</li>
1129 <li>Miscellaneous ENA XML feature qualifiers not
1131 <li>NPE in annotation renderer after 'Extract Scores'</li>
1132 <li>If two structures in one Chimera window, mouseover of
1133 either sequence shows on first structure</li>
1134 <li>'Show annotations' options should not make
1135 non-positional annotations visible</li>
1136 <li>Subsequence secondary structure annotation not shown
1137 in right place after 'view flanking regions'</li>
1138 <li>File Save As type unset when current file format is
1140 <li>Save as '.jar' option removed for saving Jalview
1142 <li>Colour by Sequence colouring in Chimera more
1144 <li>Cannot 'add reference annotation' for a sequence in
1145 several views on same alignment</li>
1146 <li>Cannot show linked products for EMBL / ENA records</li>
1147 <li>Jalview's tooltip wraps long texts containing no
1149 </ul> <em>Applet</em>
1151 <li>Jmol to JalviewLite mouseover/link not working</li>
1152 <li>JalviewLite can't import sequences with ID
1153 descriptions containing angle brackets</li>
1154 </ul> <em>General</em>
1156 <li>Cannot export and reimport RNA secondary structure
1157 via jalview annotation file</li>
1158 <li>Random helix colour palette for colour by annotation
1159 with RNA secondary structure</li>
1160 <li>Mouseover to cDNA from STOP residue in protein
1161 translation doesn't work.</li>
1162 <li>hints when using the select by annotation dialog box</li>
1163 <li>Jmol alignment incorrect if PDB file has alternate CA
1165 <li>FontChooser message dialog appears to hang after
1166 choosing 1pt font</li>
1167 <li>Peptide secondary structure incorrectly imported from
1168 annotation file when annotation display text includes 'e' or
1170 <li>Cannot set colour of new feature type whilst creating
1172 <li>cDNA translation alignment should not be sequence
1173 order dependent</li>
1174 <li>'Show unconserved' doesn't work for lower case
1176 <li>Nucleotide ambiguity codes involving R not recognised</li>
1177 </ul> <em>Deployment and Documentation</em>
1179 <li>Applet example pages appear different to the rest of
1180 www.jalview.org</li>
1181 </ul> <em>Application Known issues</em>
1183 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1184 <li>Misleading message appears after trying to delete
1186 <li>Jalview icon not shown in dock after InstallAnywhere
1187 version launches</li>
1188 <li>Fetching EMBL reference for an RNA sequence results
1189 fails with a sequence mismatch</li>
1190 <li>Corrupted or unreadable alignment display when
1191 scrolling alignment to right</li>
1192 <li>ArrayIndexOutOfBoundsException thrown when remove
1193 empty columns called on alignment with ragged gapped ends</li>
1194 <li>auto calculated alignment annotation rows do not get
1195 placed above or below non-autocalculated rows</li>
1196 <li>Jalview dekstop becomes sluggish at full screen in
1197 ultra-high resolution</li>
1198 <li>Cannot disable consensus calculation independently of
1199 quality and conservation</li>
1200 <li>Mouseover highlighting between cDNA and protein can
1201 become sluggish with more than one splitframe shown</li>
1202 </ul> <em>Applet Known Issues</em>
1204 <li>Core PDB parsing code requires Jmol</li>
1205 <li>Sequence canvas panel goes white when alignment
1206 window is being resized</li>
1212 <td><div align="center">
1213 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1215 <td><em>General</em>
1217 <li>Updated Java code signing certificate donated by
1219 <li>Features and annotation preserved when performing
1220 pairwise alignment</li>
1221 <li>RNA pseudoknot annotation can be
1222 imported/exported/displayed</li>
1223 <li>'colour by annotation' can colour by RNA and
1224 protein secondary structure</li>
1225 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1226 post-hoc with 2.9 release</em>)
1229 </ul> <em>Application</em>
1231 <li>Extract and display secondary structure for sequences
1232 with 3D structures</li>
1233 <li>Support for parsing RNAML</li>
1234 <li>Annotations menu for layout
1236 <li>sort sequence annotation rows by alignment</li>
1237 <li>place sequence annotation above/below alignment
1240 <li>Output in Stockholm format</li>
1241 <li>Internationalisation: improved Spanish (es)
1243 <li>Structure viewer preferences tab</li>
1244 <li>Disorder and Secondary Structure annotation tracks
1245 shared between alignments</li>
1246 <li>UCSF Chimera launch and linked highlighting from
1248 <li>Show/hide all sequence associated annotation rows for
1249 all or current selection</li>
1250 <li>disorder and secondary structure predictions
1251 available as dataset annotation</li>
1252 <li>Per-sequence rna helices colouring</li>
1255 <li>Sequence database accessions imported when fetching
1256 alignments from Rfam</li>
1257 <li>update VARNA version to 3.91</li>
1259 <li>New groovy scripts for exporting aligned positions,
1260 conservation values, and calculating sum of pairs scores.</li>
1261 <li>Command line argument to set default JABAWS server</li>
1262 <li>include installation type in build properties and
1263 console log output</li>
1264 <li>Updated Jalview project format to preserve dataset
1268 <!-- issues resolved --> <em>Application</em>
1270 <li>Distinguish alignment and sequence associated RNA
1271 structure in structure->view->VARNA</li>
1272 <li>Raise dialog box if user deletes all sequences in an
1274 <li>Pressing F1 results in documentation opening twice</li>
1275 <li>Sequence feature tooltip is wrapped</li>
1276 <li>Double click on sequence associated annotation
1277 selects only first column</li>
1278 <li>Redundancy removal doesn't result in unlinked
1279 leaves shown in tree</li>
1280 <li>Undos after several redundancy removals don't undo
1282 <li>Hide sequence doesn't hide associated annotation</li>
1283 <li>User defined colours dialog box too big to fit on
1284 screen and buttons not visible</li>
1285 <li>author list isn't updated if already written to
1286 Jalview properties</li>
1287 <li>Popup menu won't open after retrieving sequence
1289 <li>File open window for associate PDB doesn't open</li>
1290 <li>Left-then-right click on a sequence id opens a
1291 browser search window</li>
1292 <li>Cannot open sequence feature shading/sort popup menu
1293 in feature settings dialog</li>
1294 <li>better tooltip placement for some areas of Jalview
1296 <li>Allow addition of JABAWS Server which doesn't
1297 pass validation</li>
1298 <li>Web services parameters dialog box is too large to
1300 <li>Muscle nucleotide alignment preset obscured by
1302 <li>JABAWS preset submenus don't contain newly
1303 defined user preset</li>
1304 <li>MSA web services warns user if they were launched
1305 with invalid input</li>
1306 <li>Jalview cannot contact DAS Registy when running on
1309 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1310 'Superpose with' submenu not shown when new view
1314 </ul> <!-- <em>Applet</em>
1316 </ul> <em>General</em>
1318 </ul>--> <em>Deployment and Documentation</em>
1320 <li>2G and 1G options in launchApp have no effect on
1321 memory allocation</li>
1322 <li>launchApp service doesn't automatically open
1323 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1325 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1326 InstallAnywhere reports cannot find valid JVM when Java
1327 1.7_055 is available
1329 </ul> <em>Application Known issues</em>
1332 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1333 corrupted or unreadable alignment display when scrolling
1337 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1338 retrieval fails but progress bar continues for DAS retrieval
1339 with large number of ID
1342 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1343 flatfile output of visible region has incorrect sequence
1347 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1348 rna structure consensus doesn't update when secondary
1349 structure tracks are rearranged
1352 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1353 invalid rna structure positional highlighting does not
1354 highlight position of invalid base pairs
1357 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1358 out of memory errors are not raised when saving Jalview
1359 project from alignment window file menu
1362 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1363 Switching to RNA Helices colouring doesn't propagate to
1367 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1368 colour by RNA Helices not enabled when user created
1369 annotation added to alignment
1372 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1373 Jalview icon not shown on dock in Mountain Lion/Webstart
1375 </ul> <em>Applet Known Issues</em>
1378 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1379 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1382 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1383 Jalview and Jmol example not compatible with IE9
1386 <li>Sort by annotation score doesn't reverse order
1392 <td><div align="center">
1393 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1396 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1399 <li>Internationalisation of user interface (usually
1400 called i18n support) and translation for Spanish locale</li>
1401 <li>Define/Undefine group on current selection with
1402 Ctrl-G/Shift Ctrl-G</li>
1403 <li>Improved group creation/removal options in
1404 alignment/sequence Popup menu</li>
1405 <li>Sensible precision for symbol distribution
1406 percentages shown in logo tooltip.</li>
1407 <li>Annotation panel height set according to amount of
1408 annotation when alignment first opened</li>
1409 </ul> <em>Application</em>
1411 <li>Interactive consensus RNA secondary structure
1412 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1413 <li>Select columns containing particular features from
1414 Feature Settings dialog</li>
1415 <li>View all 'representative' PDB structures for selected
1417 <li>Update Jalview project format:
1419 <li>New file extension for Jalview projects '.jvp'</li>
1420 <li>Preserve sequence and annotation dataset (to
1421 store secondary structure annotation,etc)</li>
1422 <li>Per group and alignment annotation and RNA helix
1426 <li>New similarity measures for PCA and Tree calculation
1428 <li>Experimental support for retrieval and viewing of
1429 flanking regions for an alignment</li>
1433 <!-- issues resolved --> <em>Application</em>
1435 <li>logo keeps spinning and status remains at queued or
1436 running after job is cancelled</li>
1437 <li>cannot export features from alignments imported from
1438 Jalview/VAMSAS projects</li>
1439 <li>Buggy slider for web service parameters that take
1441 <li>Newly created RNA secondary structure line doesn't
1442 have 'display all symbols' flag set</li>
1443 <li>T-COFFEE alignment score shading scheme and other
1444 annotation shading not saved in Jalview project</li>
1445 <li>Local file cannot be loaded in freshly downloaded
1447 <li>Jalview icon not shown on dock in Mountain
1449 <li>Load file from desktop file browser fails</li>
1450 <li>Occasional NPE thrown when calculating large trees</li>
1451 <li>Cannot reorder or slide sequences after dragging an
1452 alignment onto desktop</li>
1453 <li>Colour by annotation dialog throws NPE after using
1454 'extract scores' function</li>
1455 <li>Loading/cut'n'pasting an empty file leads to a grey
1456 alignment window</li>
1457 <li>Disorder thresholds rendered incorrectly after
1458 performing IUPred disorder prediction</li>
1459 <li>Multiple group annotated consensus rows shown when
1460 changing 'normalise logo' display setting</li>
1461 <li>Find shows blank dialog after 'finished searching' if
1462 nothing matches query</li>
1463 <li>Null Pointer Exceptions raised when sorting by
1464 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1466 <li>Errors in Jmol console when structures in alignment
1467 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1469 <li>Not all working JABAWS services are shown in
1471 <li>JAVAWS version of Jalview fails to launch with
1472 'invalid literal/length code'</li>
1473 <li>Annotation/RNA Helix colourschemes cannot be applied
1474 to alignment with groups (actually fixed in 2.8.0b1)</li>
1475 <li>RNA Helices and T-Coffee Scores available as default
1478 </ul> <em>Applet</em>
1480 <li>Remove group option is shown even when selection is
1482 <li>Apply to all groups ticked but colourscheme changes
1483 don't affect groups</li>
1484 <li>Documented RNA Helices and T-Coffee Scores as valid
1485 colourscheme name</li>
1486 <li>Annotation labels drawn on sequence IDs when
1487 Annotation panel is not displayed</li>
1488 <li>Increased font size for dropdown menus on OSX and
1489 embedded windows</li>
1490 </ul> <em>Other</em>
1492 <li>Consensus sequence for alignments/groups with a
1493 single sequence were not calculated</li>
1494 <li>annotation files that contain only groups imported as
1495 annotation and junk sequences</li>
1496 <li>Fasta files with sequences containing '*' incorrectly
1497 recognised as PFAM or BLC</li>
1498 <li>conservation/PID slider apply all groups option
1499 doesn't affect background (2.8.0b1)
1501 <li>redundancy highlighting is erratic at 0% and 100%</li>
1502 <li>Remove gapped columns fails for sequences with ragged
1504 <li>AMSA annotation row with leading spaces is not
1505 registered correctly on import</li>
1506 <li>Jalview crashes when selecting PCA analysis for
1507 certain alignments</li>
1508 <li>Opening the colour by annotation dialog for an
1509 existing annotation based 'use original colours'
1510 colourscheme loses original colours setting</li>
1515 <td><div align="center">
1516 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
1517 <em>30/1/2014</em></strong>
1521 <li>Trusted certificates for JalviewLite applet and
1522 Jalview Desktop application<br />Certificate was donated by
1523 <a href="https://www.certum.eu">Certum</a> to the Jalview
1524 open source project).
1526 <li>Jalview SRS links replaced by UniProt and EBI-search
1528 <li>Output in Stockholm format</li>
1529 <li>Allow import of data from gzipped files</li>
1530 <li>Export/import group and sequence associated line
1531 graph thresholds</li>
1532 <li>Nucleotide substitution matrix that supports RNA and
1533 ambiguity codes</li>
1534 <li>Allow disorder predictions to be made on the current
1535 selection (or visible selection) in the same way that JPred
1537 <li>Groovy scripting for headless Jalview operation</li>
1538 </ul> <em>Other improvements</em>
1540 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
1541 <li>COMBINE statement uses current SEQUENCE_REF and
1542 GROUP_REF scope to group annotation rows</li>
1543 <li>Support '' style escaping of quotes in Newick
1545 <li>Group options for JABAWS service by command line name</li>
1546 <li>Empty tooltip shown for JABA service options with a
1547 link but no description</li>
1548 <li>Select primary source when selecting authority in
1549 database fetcher GUI</li>
1550 <li>Add .mfa to FASTA file extensions recognised by
1552 <li>Annotation label tooltip text wrap</li>
1557 <li>Slow scrolling when lots of annotation rows are
1559 <li>Lots of NPE (and slowness) after creating RNA
1560 secondary structure annotation line</li>
1561 <li>Sequence database accessions not imported when
1562 fetching alignments from Rfam</li>
1563 <li>Incorrect SHMR submission for sequences with
1565 <li>View all structures does not always superpose
1567 <li>Option widgets in service parameters not updated to
1568 reflect user or preset settings</li>
1569 <li>Null pointer exceptions for some services without
1570 presets or adjustable parameters</li>
1571 <li>Discover PDB IDs entry in structure menu doesn't
1572 discover PDB xRefs</li>
1573 <li>Exception encountered while trying to retrieve
1574 features with DAS</li>
1575 <li>Lowest value in annotation row isn't coloured
1576 when colour by annotation (per sequence) is coloured</li>
1577 <li>Keyboard mode P jumps to start of gapped region when
1578 residue follows a gap</li>
1579 <li>Jalview appears to hang importing an alignment with
1580 Wrap as default or after enabling Wrap</li>
1581 <li>'Right click to add annotations' message
1582 shown in wrap mode when no annotations present</li>
1583 <li>Disorder predictions fail with NPE if no automatic
1584 annotation already exists on alignment</li>
1585 <li>oninit javascript function should be called after
1586 initialisation completes</li>
1587 <li>Remove redundancy after disorder prediction corrupts
1588 alignment window display</li>
1589 <li>Example annotation file in documentation is invalid</li>
1590 <li>Grouped line graph annotation rows are not exported
1591 to annotation file</li>
1592 <li>Multi-harmony analysis cannot be run when only two
1594 <li>Cannot create multiple groups of line graphs with
1595 several 'combine' statements in annotation file</li>
1596 <li>Pressing return several times causes Number Format
1597 exceptions in keyboard mode</li>
1598 <li>Multi-harmony (SHMMR) method doesn't submit
1599 correct partitions for input data</li>
1600 <li>Translation from DNA to Amino Acids fails</li>
1601 <li>Jalview fail to load newick tree with quoted label</li>
1602 <li>--headless flag isn't understood</li>
1603 <li>ClassCastException when generating EPS in headless
1605 <li>Adjusting sequence-associated shading threshold only
1606 changes one row's threshold</li>
1607 <li>Preferences and Feature settings panel panel
1608 doesn't open</li>
1609 <li>hide consensus histogram also hides conservation and
1610 quality histograms</li>
1615 <td><div align="center">
1616 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
1618 <td><em>Application</em>
1620 <li>Support for JABAWS 2.0 Services (AACon alignment
1621 conservation, protein disorder and Clustal Omega)</li>
1622 <li>JABAWS server status indicator in Web Services
1624 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
1625 in Jalview alignment window</li>
1626 <li>Updated Jalview build and deploy framework for OSX
1627 mountain lion, windows 7, and 8</li>
1628 <li>Nucleotide substitution matrix for PCA that supports
1629 RNA and ambiguity codes</li>
1631 <li>Improved sequence database retrieval GUI</li>
1632 <li>Support fetching and database reference look up
1633 against multiple DAS sources (Fetch all from in 'fetch db
1635 <li>Jalview project improvements
1637 <li>Store and retrieve the 'belowAlignment'
1638 flag for annotation</li>
1639 <li>calcId attribute to group annotation rows on the
1641 <li>Store AACon calculation settings for a view in
1642 Jalview project</li>
1646 <li>horizontal scrolling gesture support</li>
1647 <li>Visual progress indicator when PCA calculation is
1649 <li>Simpler JABA web services menus</li>
1650 <li>visual indication that web service results are still
1651 being retrieved from server</li>
1652 <li>Serialise the dialogs that are shown when Jalview
1653 starts up for first time</li>
1654 <li>Jalview user agent string for interacting with HTTP
1656 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
1658 <li>Examples directory and Groovy library included in
1659 InstallAnywhere distribution</li>
1660 </ul> <em>Applet</em>
1662 <li>RNA alignment and secondary structure annotation
1663 visualization applet example</li>
1664 </ul> <em>General</em>
1666 <li>Normalise option for consensus sequence logo</li>
1667 <li>Reset button in PCA window to return dimensions to
1669 <li>Allow seqspace or Jalview variant of alignment PCA
1671 <li>PCA with either nucleic acid and protein substitution
1673 <li>Allow windows containing HTML reports to be exported
1675 <li>Interactive display and editing of RNA secondary
1676 structure contacts</li>
1677 <li>RNA Helix Alignment Colouring</li>
1678 <li>RNA base pair logo consensus</li>
1679 <li>Parse sequence associated secondary structure
1680 information in Stockholm files</li>
1681 <li>HTML Export database accessions and annotation
1682 information presented in tooltip for sequences</li>
1683 <li>Import secondary structure from LOCARNA clustalw
1684 style RNA alignment files</li>
1685 <li>import and visualise T-COFFEE quality scores for an
1687 <li>'colour by annotation' per sequence option to
1688 shade each sequence according to its associated alignment
1690 <li>New Jalview Logo</li>
1691 </ul> <em>Documentation and Development</em>
1693 <li>documentation for score matrices used in Jalview</li>
1694 <li>New Website!</li>
1696 <td><em>Application</em>
1698 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
1699 wsdbfetch REST service</li>
1700 <li>Stop windows being moved outside desktop on OSX</li>
1701 <li>Filetype associations not installed for webstart
1703 <li>Jalview does not always retrieve progress of a JABAWS
1704 job execution in full once it is complete</li>
1705 <li>revise SHMR RSBS definition to ensure alignment is
1706 uploaded via ali_file parameter</li>
1707 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
1708 <li>View all structures superposed fails with exception</li>
1709 <li>Jnet job queues forever if a very short sequence is
1710 submitted for prediction</li>
1711 <li>Cut and paste menu not opened when mouse clicked on
1713 <li>Putting fractional value into integer text box in
1714 alignment parameter dialog causes Jalview to hang</li>
1715 <li>Structure view highlighting doesn't work on
1717 <li>View all structures fails with exception shown in
1719 <li>Characters in filename associated with PDBEntry not
1720 escaped in a platform independent way</li>
1721 <li>Jalview desktop fails to launch with exception when
1723 <li>Tree calculation reports 'you must have 2 or more
1724 sequences selected' when selection is empty</li>
1725 <li>Jalview desktop fails to launch with jar signature
1726 failure when java web start temporary file caching is
1728 <li>DAS Sequence retrieval with range qualification
1729 results in sequence xref which includes range qualification</li>
1730 <li>Errors during processing of command line arguments
1731 cause progress bar (JAL-898) to be removed</li>
1732 <li>Replace comma for semi-colon option not disabled for
1733 DAS sources in sequence fetcher</li>
1734 <li>Cannot close news reader when JABAWS server warning
1735 dialog is shown</li>
1736 <li>Option widgets not updated to reflect user settings</li>
1737 <li>Edited sequence not submitted to web service</li>
1738 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
1739 <li>InstallAnywhere installer doesn't unpack and run
1740 on OSX Mountain Lion</li>
1741 <li>Annotation panel not given a scroll bar when
1742 sequences with alignment annotation are pasted into the
1744 <li>Sequence associated annotation rows not associated
1745 when loaded from Jalview project</li>
1746 <li>Browser launch fails with NPE on java 1.7</li>
1747 <li>JABAWS alignment marked as finished when job was
1748 cancelled or job failed due to invalid input</li>
1749 <li>NPE with v2.7 example when clicking on Tree
1750 associated with all views</li>
1751 <li>Exceptions when copy/paste sequences with grouped
1752 annotation rows to new window</li>
1753 </ul> <em>Applet</em>
1755 <li>Sequence features are momentarily displayed before
1756 they are hidden using hidefeaturegroups applet parameter</li>
1757 <li>loading features via javascript API automatically
1758 enables feature display</li>
1759 <li>scrollToColumnIn javascript API method doesn't
1761 </ul> <em>General</em>
1763 <li>Redundancy removal fails for rna alignment</li>
1764 <li>PCA calculation fails when sequence has been selected
1765 and then deselected</li>
1766 <li>PCA window shows grey box when first opened on OSX</li>
1767 <li>Letters coloured pink in sequence logo when alignment
1768 coloured with clustalx</li>
1769 <li>Choosing fonts without letter symbols defined causes
1770 exceptions and redraw errors</li>
1771 <li>Initial PCA plot view is not same as manually
1772 reconfigured view</li>
1773 <li>Grouped annotation graph label has incorrect line
1775 <li>Grouped annotation graph label display is corrupted
1776 for lots of labels</li>
1781 <div align="center">
1782 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
1785 <td><em>Application</em>
1787 <li>Jalview Desktop News Reader</li>
1788 <li>Tweaked default layout of web services menu</li>
1789 <li>View/alignment association menu to enable user to
1790 easily specify which alignment a multi-structure view takes
1791 its colours/correspondences from</li>
1792 <li>Allow properties file location to be specified as URL</li>
1793 <li>Extend Jalview project to preserve associations
1794 between many alignment views and a single Jmol display</li>
1795 <li>Store annotation row height in Jalview project file</li>
1796 <li>Annotation row column label formatting attributes
1797 stored in project file</li>
1798 <li>Annotation row order for auto-calculated annotation
1799 rows preserved in Jalview project file</li>
1800 <li>Visual progress indication when Jalview state is
1801 saved using Desktop window menu</li>
1802 <li>Visual indication that command line arguments are
1803 still being processed</li>
1804 <li>Groovy script execution from URL</li>
1805 <li>Colour by annotation default min and max colours in
1807 <li>Automatically associate PDB files dragged onto an
1808 alignment with sequences that have high similarity and
1810 <li>Update JGoogleAnalytics to latest release (0.3)</li>
1811 <li>'view structures' option to open many
1812 structures in same window</li>
1813 <li>Sort associated views menu option for tree panel</li>
1814 <li>Group all JABA and non-JABA services for a particular
1815 analysis function in its own submenu</li>
1816 </ul> <em>Applet</em>
1818 <li>Userdefined and autogenerated annotation rows for
1820 <li>Adjustment of alignment annotation pane height</li>
1821 <li>Annotation scrollbar for annotation panel</li>
1822 <li>Drag to reorder annotation rows in annotation panel</li>
1823 <li>'automaticScrolling' parameter</li>
1824 <li>Allow sequences with partial ID string matches to be
1825 annotated from GFF/Jalview features files</li>
1826 <li>Sequence logo annotation row in applet</li>
1827 <li>Absolute paths relative to host server in applet
1828 parameters are treated as such</li>
1829 <li>New in the JalviewLite javascript API:
1831 <li>JalviewLite.js javascript library</li>
1832 <li>Javascript callbacks for
1834 <li>Applet initialisation</li>
1835 <li>Sequence/alignment mouse-overs and selections</li>
1838 <li>scrollTo row and column alignment scrolling
1840 <li>Select sequence/alignment regions from javascript</li>
1841 <li>javascript structure viewer harness to pass
1842 messages between Jmol and Jalview when running as
1843 distinct applets</li>
1844 <li>sortBy method</li>
1845 <li>Set of applet and application examples shipped
1846 with documentation</li>
1847 <li>New example to demonstrate JalviewLite and Jmol
1848 javascript message exchange</li>
1850 </ul> <em>General</em>
1852 <li>Enable Jmol displays to be associated with multiple
1853 multiple alignments</li>
1854 <li>Option to automatically sort alignment with new tree</li>
1855 <li>User configurable link to enable redirects to a
1856 www.Jalview.org mirror</li>
1857 <li>Jmol colours option for Jmol displays</li>
1858 <li>Configurable newline string when writing alignment
1859 and other flat files</li>
1860 <li>Allow alignment annotation description lines to
1861 contain html tags</li>
1862 </ul> <em>Documentation and Development</em>
1864 <li>Add groovy test harness for bulk load testing to
1866 <li>Groovy script to load and align a set of sequences
1867 using a web service before displaying the result in the
1868 Jalview desktop</li>
1869 <li>Restructured javascript and applet api documentation</li>
1870 <li>Ant target to publish example html files with applet
1872 <li>Netbeans project for building Jalview from source</li>
1873 <li>ant task to create online javadoc for Jalview source</li>
1875 <td><em>Application</em>
1877 <li>User defined colourscheme throws exception when
1878 current built in colourscheme is saved as new scheme</li>
1879 <li>AlignFrame->Save in application pops up save
1880 dialog for valid filename/format</li>
1881 <li>Cannot view associated structure for UniProt sequence</li>
1882 <li>PDB file association breaks for UniProt sequence
1884 <li>Associate PDB from file dialog does not tell you
1885 which sequence is to be associated with the file</li>
1886 <li>Find All raises null pointer exception when query
1887 only matches sequence IDs</li>
1888 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
1889 <li>Jalview project with Jmol views created with Jalview
1890 2.4 cannot be loaded</li>
1891 <li>Filetype associations not installed for webstart
1893 <li>Two or more chains in a single PDB file associated
1894 with sequences in different alignments do not get coloured
1895 by their associated sequence</li>
1896 <li>Visibility status of autocalculated annotation row
1897 not preserved when project is loaded</li>
1898 <li>Annotation row height and visibility attributes not
1899 stored in Jalview project</li>
1900 <li>Tree bootstraps are not preserved when saved as a
1901 Jalview project</li>
1902 <li>Envision2 workflow tooltips are corrupted</li>
1903 <li>Enabling show group conservation also enables colour
1904 by conservation</li>
1905 <li>Duplicate group associated conservation or consensus
1906 created on new view</li>
1907 <li>Annotation scrollbar not displayed after 'show
1908 all hidden annotation rows' option selected</li>
1909 <li>Alignment quality not updated after alignment
1910 annotation row is hidden then shown</li>
1911 <li>Preserve colouring of structures coloured by
1912 sequences in pre Jalview 2.7 projects</li>
1913 <li>Web service job parameter dialog is not laid out
1915 <li>Web services menu not refreshed after 'reset
1916 services' button is pressed in preferences</li>
1917 <li>Annotation off by one in Jalview v2_3 example project</li>
1918 <li>Structures imported from file and saved in project
1919 get name like jalview_pdb1234.txt when reloaded</li>
1920 <li>Jalview does not always retrieve progress of a JABAWS
1921 job execution in full once it is complete</li>
1922 </ul> <em>Applet</em>
1924 <li>Alignment height set incorrectly when lots of
1925 annotation rows are displayed</li>
1926 <li>Relative URLs in feature HTML text not resolved to
1928 <li>View follows highlighting does not work for positions
1930 <li><= shown as = in tooltip</li>
1931 <li>Export features raises exception when no features
1933 <li>Separator string used for serialising lists of IDs
1934 for javascript api is modified when separator string
1935 provided as parameter</li>
1936 <li>Null pointer exception when selecting tree leaves for
1937 alignment with no existing selection</li>
1938 <li>Relative URLs for datasources assumed to be relative
1939 to applet's codebase</li>
1940 <li>Status bar not updated after finished searching and
1941 search wraps around to first result</li>
1942 <li>StructureSelectionManager instance shared between
1943 several Jalview applets causes race conditions and memory
1945 <li>Hover tooltip and mouseover of position on structure
1946 not sent from Jmol in applet</li>
1947 <li>Certain sequences of javascript method calls to
1948 applet API fatally hang browser</li>
1949 </ul> <em>General</em>
1951 <li>View follows structure mouseover scrolls beyond
1952 position with wrapped view and hidden regions</li>
1953 <li>Find sequence position moves to wrong residue
1954 with/without hidden columns</li>
1955 <li>Sequence length given in alignment properties window
1957 <li>InvalidNumberFormat exceptions thrown when trying to
1958 import PDB like structure files</li>
1959 <li>Positional search results are only highlighted
1960 between user-supplied sequence start/end bounds</li>
1961 <li>End attribute of sequence is not validated</li>
1962 <li>Find dialog only finds first sequence containing a
1963 given sequence position</li>
1964 <li>Sequence numbering not preserved in MSF alignment
1966 <li>Jalview PDB file reader does not extract sequence
1967 from nucleotide chains correctly</li>
1968 <li>Structure colours not updated when tree partition
1969 changed in alignment</li>
1970 <li>Sequence associated secondary structure not correctly
1971 parsed in interleaved stockholm</li>
1972 <li>Colour by annotation dialog does not restore current
1974 <li>Hiding (nearly) all sequences doesn't work
1976 <li>Sequences containing lowercase letters are not
1977 properly associated with their pdb files</li>
1978 </ul> <em>Documentation and Development</em>
1980 <li>schemas/JalviewWsParamSet.xsd corrupted by
1981 ApplyCopyright tool</li>
1986 <div align="center">
1987 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
1990 <td><em>Application</em>
1992 <li>New warning dialog when the Jalview Desktop cannot
1993 contact web services</li>
1994 <li>JABA service parameters for a preset are shown in
1995 service job window</li>
1996 <li>JABA Service menu entries reworded</li>
2000 <li>Modeller PIR IO broken - cannot correctly import a
2001 pir file emitted by Jalview</li>
2002 <li>Existing feature settings transferred to new
2003 alignment view created from cut'n'paste</li>
2004 <li>Improved test for mixed amino/nucleotide chains when
2005 parsing PDB files</li>
2006 <li>Consensus and conservation annotation rows
2007 occasionally become blank for all new windows</li>
2008 <li>Exception raised when right clicking above sequences
2009 in wrapped view mode</li>
2010 </ul> <em>Application</em>
2012 <li>multiple multiply aligned structure views cause cpu
2013 usage to hit 100% and computer to hang</li>
2014 <li>Web Service parameter layout breaks for long user
2015 parameter names</li>
2016 <li>Jaba service discovery hangs desktop if Jaba server
2023 <div align="center">
2024 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2027 <td><em>Application</em>
2029 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2030 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2033 <li>Web Services preference tab</li>
2034 <li>Analysis parameters dialog box and user defined
2036 <li>Improved speed and layout of Envision2 service menu</li>
2037 <li>Superpose structures using associated sequence
2039 <li>Export coordinates and projection as CSV from PCA
2041 </ul> <em>Applet</em>
2043 <li>enable javascript: execution by the applet via the
2044 link out mechanism</li>
2045 </ul> <em>Other</em>
2047 <li>Updated the Jmol Jalview interface to work with Jmol
2049 <li>The Jalview Desktop and JalviewLite applet now
2050 require Java 1.5</li>
2051 <li>Allow Jalview feature colour specification for GFF
2052 sequence annotation files</li>
2053 <li>New 'colour by label' keword in Jalview feature file
2054 type colour specification</li>
2055 <li>New Jalview Desktop Groovy API method that allows a
2056 script to check if it being run in an interactive session or
2057 in a batch operation from the Jalview command line</li>
2061 <li>clustalx colourscheme colours Ds preferentially when
2062 both D+E are present in over 50% of the column</li>
2063 </ul> <em>Application</em>
2065 <li>typo in AlignmentFrame->View->Hide->all but
2066 selected Regions menu item</li>
2067 <li>sequence fetcher replaces ',' for ';' when the ',' is
2068 part of a valid accession ID</li>
2069 <li>fatal OOM if object retrieved by sequence fetcher
2070 runs out of memory</li>
2071 <li>unhandled Out of Memory Error when viewing pca
2072 analysis results</li>
2073 <li>InstallAnywhere builds fail to launch on OS X java
2074 10.5 update 4 (due to apple Java 1.6 update)</li>
2075 <li>Installanywhere Jalview silently fails to launch</li>
2076 </ul> <em>Applet</em>
2078 <li>Jalview.getFeatureGroups() raises an
2079 ArrayIndexOutOfBoundsException if no feature groups are
2086 <div align="center">
2087 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2093 <li>Alignment prettyprinter doesn't cope with long
2095 <li>clustalx colourscheme colours Ds preferentially when
2096 both D+E are present in over 50% of the column</li>
2097 <li>nucleic acid structures retrieved from PDB do not
2098 import correctly</li>
2099 <li>More columns get selected than were clicked on when a
2100 number of columns are hidden</li>
2101 <li>annotation label popup menu not providing correct
2102 add/hide/show options when rows are hidden or none are
2104 <li>Stockholm format shown in list of readable formats,
2105 and parser copes better with alignments from RFAM.</li>
2106 <li>CSV output of consensus only includes the percentage
2107 of all symbols if sequence logo display is enabled</li>
2109 </ul> <em>Applet</em>
2111 <li>annotation panel disappears when annotation is
2113 </ul> <em>Application</em>
2115 <li>Alignment view not redrawn properly when new
2116 alignment opened where annotation panel is visible but no
2117 annotations are present on alignment</li>
2118 <li>pasted region containing hidden columns is
2119 incorrectly displayed in new alignment window</li>
2120 <li>Jalview slow to complete operations when stdout is
2121 flooded (fix is to close the Jalview console)</li>
2122 <li>typo in AlignmentFrame->View->Hide->all but
2123 selected Rregions menu item.</li>
2124 <li>inconsistent group submenu and Format submenu entry
2125 'Un' or 'Non'conserved</li>
2126 <li>Sequence feature settings are being shared by
2127 multiple distinct alignments</li>
2128 <li>group annotation not recreated when tree partition is
2130 <li>double click on group annotation to select sequences
2131 does not propagate to associated trees</li>
2132 <li>Mac OSX specific issues:
2134 <li>exception raised when mouse clicked on desktop
2135 window background</li>
2136 <li>Desktop menu placed on menu bar and application
2137 name set correctly</li>
2138 <li>sequence feature settings not wide enough for the
2139 save feature colourscheme button</li>
2148 <div align="center">
2149 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2152 <td><em>New Capabilities</em>
2154 <li>URL links generated from description line for
2155 regular-expression based URL links (applet and application)
2162 <li>Non-positional feature URL links are shown in link
2164 <li>Linked viewing of nucleic acid sequences and
2166 <li>Automatic Scrolling option in View menu to display
2167 the currently highlighted region of an alignment.</li>
2168 <li>Order an alignment by sequence length, or using the
2169 average score or total feature count for each sequence.</li>
2170 <li>Shading features by score or associated description</li>
2171 <li>Subdivide alignment and groups based on identity of
2172 selected subsequence (Make Groups from Selection).</li>
2173 <li>New hide/show options including Shift+Control+H to
2174 hide everything but the currently selected region.</li>
2175 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2176 </ul> <em>Application</em>
2178 <li>Fetch DB References capabilities and UI expanded to
2179 support retrieval from DAS sequence sources</li>
2180 <li>Local DAS Sequence sources can be added via the
2181 command line or via the Add local source dialog box.</li>
2182 <li>DAS Dbref and DbxRef feature types are parsed as
2183 database references and protein_name is parsed as
2184 description line (BioSapiens terms).</li>
2185 <li>Enable or disable non-positional feature and database
2186 references in sequence ID tooltip from View menu in
2188 <!-- <li>New hidden columns and rows and representatives capabilities
2189 in annotations file (in progress - not yet fully implemented)</li> -->
2190 <li>Group-associated consensus, sequence logos and
2191 conservation plots</li>
2192 <li>Symbol distributions for each column can be exported
2193 and visualized as sequence logos</li>
2194 <li>Optionally scale multi-character column labels to fit
2195 within each column of annotation row<!-- todo for applet -->
2197 <li>Optional automatic sort of associated alignment view
2198 when a new tree is opened.</li>
2199 <li>Jalview Java Console</li>
2200 <li>Better placement of desktop window when moving
2201 between different screens.</li>
2202 <li>New preference items for sequence ID tooltip and
2203 consensus annotation</li>
2204 <li>Client to submit sequences and IDs to Envision2
2206 <li><em>Vamsas Capabilities</em>
2208 <li>Improved VAMSAS synchronization (Jalview archive
2209 used to preserve views, structures, and tree display
2211 <li>Import of vamsas documents from disk or URL via
2213 <li>Sharing of selected regions between views and
2214 with other VAMSAS applications (Experimental feature!)</li>
2215 <li>Updated API to VAMSAS version 0.2</li>
2217 </ul> <em>Applet</em>
2219 <li>Middle button resizes annotation row height</li>
2222 <li>sortByTree (true/false) - automatically sort the
2223 associated alignment view by the tree when a new tree is
2225 <li>showTreeBootstraps (true/false) - show or hide
2226 branch bootstraps (default is to show them if available)</li>
2227 <li>showTreeDistances (true/false) - show or hide
2228 branch lengths (default is to show them if available)</li>
2229 <li>showUnlinkedTreeNodes (true/false) - indicate if
2230 unassociated nodes should be highlighted in the tree
2232 <li>heightScale and widthScale (1.0 or more) -
2233 increase the height or width of a cell in the alignment
2234 grid relative to the current font size.</li>
2237 <li>Non-positional features displayed in sequence ID
2239 </ul> <em>Other</em>
2241 <li>Features format: graduated colour definitions and
2242 specification of feature scores</li>
2243 <li>Alignment Annotations format: new keywords for group
2244 associated annotation (GROUP_REF) and annotation row display
2245 properties (ROW_PROPERTIES)</li>
2246 <li>XML formats extended to support graduated feature
2247 colourschemes, group associated annotation, and profile
2248 visualization settings.</li></td>
2251 <li>Source field in GFF files parsed as feature source
2252 rather than description</li>
2253 <li>Non-positional features are now included in sequence
2254 feature and gff files (controlled via non-positional feature
2255 visibility in tooltip).</li>
2256 <li>URL links generated for all feature links (bugfix)</li>
2257 <li>Added URL embedding instructions to features file
2259 <li>Codons containing ambiguous nucleotides translated as
2260 'X' in peptide product</li>
2261 <li>Match case switch in find dialog box works for both
2262 sequence ID and sequence string and query strings do not
2263 have to be in upper case to match case-insensitively.</li>
2264 <li>AMSA files only contain first column of
2265 multi-character column annotation labels</li>
2266 <li>Jalview Annotation File generation/parsing consistent
2267 with documentation (e.g. Stockholm annotation can be
2268 exported and re-imported)</li>
2269 <li>PDB files without embedded PDB IDs given a friendly
2271 <li>Find incrementally searches ID string matches as well
2272 as subsequence matches, and correctly reports total number
2276 <li>Better handling of exceptions during sequence
2278 <li>Dasobert generated non-positional feature URL
2279 link text excludes the start_end suffix</li>
2280 <li>DAS feature and source retrieval buttons disabled
2281 when fetch or registry operations in progress.</li>
2282 <li>PDB files retrieved from URLs are cached properly</li>
2283 <li>Sequence description lines properly shared via
2285 <li>Sequence fetcher fetches multiple records for all
2287 <li>Ensured that command line das feature retrieval
2288 completes before alignment figures are generated.</li>
2289 <li>Reduced time taken when opening file browser for
2291 <li>isAligned check prior to calculating tree, PCA or
2292 submitting an MSA to JNet now excludes hidden sequences.</li>
2293 <li>User defined group colours properly recovered
2294 from Jalview projects.</li>
2303 <div align="center">
2304 <strong>2.4.0.b2</strong><br> 28/10/2009
2309 <li>Experimental support for google analytics usage
2311 <li>Jalview privacy settings (user preferences and docs).</li>
2316 <li>Race condition in applet preventing startup in
2318 <li>Exception when feature created from selection beyond
2319 length of sequence.</li>
2320 <li>Allow synthetic PDB files to be imported gracefully</li>
2321 <li>Sequence associated annotation rows associate with
2322 all sequences with a given id</li>
2323 <li>Find function matches case-insensitively for sequence
2324 ID string searches</li>
2325 <li>Non-standard characters do not cause pairwise
2326 alignment to fail with exception</li>
2327 </ul> <em>Application Issues</em>
2329 <li>Sequences are now validated against EMBL database</li>
2330 <li>Sequence fetcher fetches multiple records for all
2332 </ul> <em>InstallAnywhere Issues</em>
2334 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2335 issue with installAnywhere mechanism)</li>
2336 <li>Command line launching of JARs from InstallAnywhere
2337 version (java class versioning error fixed)</li>
2344 <div align="center">
2345 <strong>2.4</strong><br> 27/8/2008
2348 <td><em>User Interface</em>
2350 <li>Linked highlighting of codon and amino acid from
2351 translation and protein products</li>
2352 <li>Linked highlighting of structure associated with
2353 residue mapping to codon position</li>
2354 <li>Sequence Fetcher provides example accession numbers
2355 and 'clear' button</li>
2356 <li>MemoryMonitor added as an option under Desktop's
2358 <li>Extract score function to parse whitespace separated
2359 numeric data in description line</li>
2360 <li>Column labels in alignment annotation can be centred.</li>
2361 <li>Tooltip for sequence associated annotation give name
2363 </ul> <em>Web Services and URL fetching</em>
2365 <li>JPred3 web service</li>
2366 <li>Prototype sequence search client (no public services
2368 <li>Fetch either seed alignment or full alignment from
2370 <li>URL Links created for matching database cross
2371 references as well as sequence ID</li>
2372 <li>URL Links can be created using regular-expressions</li>
2373 </ul> <em>Sequence Database Connectivity</em>
2375 <li>Retrieval of cross-referenced sequences from other
2377 <li>Generalised database reference retrieval and
2378 validation to all fetchable databases</li>
2379 <li>Fetch sequences from DAS sources supporting the
2380 sequence command</li>
2381 </ul> <em>Import and Export</em>
2382 <li>export annotation rows as CSV for spreadsheet import</li>
2383 <li>Jalview projects record alignment dataset associations,
2384 EMBL products, and cDNA sequence mappings</li>
2385 <li>Sequence Group colour can be specified in Annotation
2387 <li>Ad-hoc colouring of group in Annotation File using RGB
2388 triplet as name of colourscheme</li>
2389 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2391 <li>treenode binding for VAMSAS tree exchange</li>
2392 <li>local editing and update of sequences in VAMSAS
2393 alignments (experimental)</li>
2394 <li>Create new or select existing session to join</li>
2395 <li>load and save of vamsas documents</li>
2396 </ul> <em>Application command line</em>
2398 <li>-tree parameter to open trees (introduced for passing
2400 <li>-fetchfrom command line argument to specify nicknames
2401 of DAS servers to query for alignment features</li>
2402 <li>-dasserver command line argument to add new servers
2403 that are also automatically queried for features</li>
2404 <li>-groovy command line argument executes a given groovy
2405 script after all input data has been loaded and parsed</li>
2406 </ul> <em>Applet-Application data exchange</em>
2408 <li>Trees passed as applet parameters can be passed to
2409 application (when using "View in full
2410 application")</li>
2411 </ul> <em>Applet Parameters</em>
2413 <li>feature group display control parameter</li>
2414 <li>debug parameter</li>
2415 <li>showbutton parameter</li>
2416 </ul> <em>Applet API methods</em>
2418 <li>newView public method</li>
2419 <li>Window (current view) specific get/set public methods</li>
2420 <li>Feature display control methods</li>
2421 <li>get list of currently selected sequences</li>
2422 </ul> <em>New Jalview distribution features</em>
2424 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2425 <li>RELEASE file gives build properties for the latest
2426 Jalview release.</li>
2427 <li>Java 1.1 Applet build made easier and donotobfuscate
2428 property controls execution of obfuscator</li>
2429 <li>Build target for generating source distribution</li>
2430 <li>Debug flag for javacc</li>
2431 <li>.jalview_properties file is documented (slightly) in
2432 jalview.bin.Cache</li>
2433 <li>Continuous Build Integration for stable and
2434 development version of Application, Applet and source
2439 <li>selected region output includes visible annotations
2440 (for certain formats)</li>
2441 <li>edit label/displaychar contains existing label/char
2443 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2444 <li>shorter peptide product names from EMBL records</li>
2445 <li>Newick string generator makes compact representations</li>
2446 <li>bootstrap values parsed correctly for tree files with
2448 <li>pathological filechooser bug avoided by not allowing
2449 filenames containing a ':'</li>
2450 <li>Fixed exception when parsing GFF files containing
2451 global sequence features</li>
2452 <li>Alignment datasets are finalized only when number of
2453 references from alignment sequences goes to zero</li>
2454 <li>Close of tree branch colour box without colour
2455 selection causes cascading exceptions</li>
2456 <li>occasional negative imgwidth exceptions</li>
2457 <li>better reporting of non-fatal warnings to user when
2458 file parsing fails.</li>
2459 <li>Save works when Jalview project is default format</li>
2460 <li>Save as dialog opened if current alignment format is
2461 not a valid output format</li>
2462 <li>UniProt canonical names introduced for both das and
2464 <li>Histidine should be midblue (not pink!) in Zappo</li>
2465 <li>error messages passed up and output when data read
2467 <li>edit undo recovers previous dataset sequence when
2468 sequence is edited</li>
2469 <li>allow PDB files without pdb ID HEADER lines (like
2470 those generated by MODELLER) to be read in properly</li>
2471 <li>allow reading of JPred concise files as a normal
2473 <li>Stockholm annotation parsing and alignment properties
2474 import fixed for PFAM records</li>
2475 <li>Structure view windows have correct name in Desktop
2477 <li>annotation consisting of sequence associated scores
2478 can be read and written correctly to annotation file</li>
2479 <li>Aligned cDNA translation to aligned peptide works
2481 <li>Fixed display of hidden sequence markers and
2482 non-italic font for representatives in Applet</li>
2483 <li>Applet Menus are always embedded in applet window on
2485 <li>Newly shown features appear at top of stack (in
2487 <li>Annotations added via parameter not drawn properly
2488 due to null pointer exceptions</li>
2489 <li>Secondary structure lines are drawn starting from
2490 first column of alignment</li>
2491 <li>UniProt XML import updated for new schema release in
2493 <li>Sequence feature to sequence ID match for Features
2494 file is case-insensitive</li>
2495 <li>Sequence features read from Features file appended to
2496 all sequences with matching IDs</li>
2497 <li>PDB structure coloured correctly for associated views
2498 containing a sub-sequence</li>
2499 <li>PDB files can be retrieved by applet from Jar files</li>
2500 <li>feature and annotation file applet parameters
2501 referring to different directories are retrieved correctly</li>
2502 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
2503 <li>Fixed application hang whilst waiting for
2504 splash-screen version check to complete</li>
2505 <li>Applet properly URLencodes input parameter values
2506 when passing them to the launchApp service</li>
2507 <li>display name and local features preserved in results
2508 retrieved from web service</li>
2509 <li>Visual delay indication for sequence retrieval and
2510 sequence fetcher initialisation</li>
2511 <li>updated Application to use DAS 1.53e version of
2512 dasobert DAS client</li>
2513 <li>Re-instated Full AMSA support and .amsa file
2515 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
2523 <div align="center">
2524 <strong>2.3</strong><br> 9/5/07
2529 <li>Jmol 11.0.2 integration</li>
2530 <li>PDB views stored in Jalview XML files</li>
2531 <li>Slide sequences</li>
2532 <li>Edit sequence in place</li>
2533 <li>EMBL CDS features</li>
2534 <li>DAS Feature mapping</li>
2535 <li>Feature ordering</li>
2536 <li>Alignment Properties</li>
2537 <li>Annotation Scores</li>
2538 <li>Sort by scores</li>
2539 <li>Feature/annotation editing in applet</li>
2544 <li>Headless state operation in 2.2.1</li>
2545 <li>Incorrect and unstable DNA pairwise alignment</li>
2546 <li>Cut and paste of sequences with annotation</li>
2547 <li>Feature group display state in XML</li>
2548 <li>Feature ordering in XML</li>
2549 <li>blc file iteration selection using filename # suffix</li>
2550 <li>Stockholm alignment properties</li>
2551 <li>Stockhom alignment secondary structure annotation</li>
2552 <li>2.2.1 applet had no feature transparency</li>
2553 <li>Number pad keys can be used in cursor mode</li>
2554 <li>Structure Viewer mirror image resolved</li>
2561 <div align="center">
2562 <strong>2.2.1</strong><br> 12/2/07
2567 <li>Non standard characters can be read and displayed
2568 <li>Annotations/Features can be imported/exported to the
2570 <li>Applet allows editing of sequence/annotation/group
2571 name & description
2572 <li>Preference setting to display sequence name in
2574 <li>Annotation file format extended to allow
2575 Sequence_groups to be defined
2576 <li>Default opening of alignment overview panel can be
2577 specified in preferences
2578 <li>PDB residue numbering annotation added to associated
2584 <li>Applet crash under certain Linux OS with Java 1.6
2586 <li>Annotation file export / import bugs fixed
2587 <li>PNG / EPS image output bugs fixed
2593 <div align="center">
2594 <strong>2.2</strong><br> 27/11/06
2599 <li>Multiple views on alignment
2600 <li>Sequence feature editing
2601 <li>"Reload" alignment
2602 <li>"Save" to current filename
2603 <li>Background dependent text colour
2604 <li>Right align sequence ids
2605 <li>User-defined lower case residue colours
2608 <li>Menu item accelerator keys
2609 <li>Control-V pastes to current alignment
2610 <li>Cancel button for DAS Feature Fetching
2611 <li>PCA and PDB Viewers zoom via mouse roller
2612 <li>User-defined sub-tree colours and sub-tree selection
2619 <li>'New Window' button on the 'Output to Text box'
2624 <li>New memory efficient Undo/Redo System
2625 <li>Optimised symbol lookups and conservation/consensus
2627 <li>Region Conservation/Consensus recalculated after
2629 <li>Fixed Remove Empty Columns Bug (empty columns at end
2631 <li>Slowed DAS Feature Fetching for increased robustness.
2638 <li>Made angle brackets in ASCII feature descriptions
2640 <li>Re-instated Zoom function for PCA
2641 <li>Sequence descriptions conserved in web service
2643 <li>UniProt ID discoverer uses any word separated by
2645 <li>WsDbFetch query/result association resolved
2646 <li>Tree leaf to sequence mapping improved
2647 <li>Smooth fonts switch moved to FontChooser dialog box.
2659 <div align="center">
2660 <strong>2.1.1</strong><br> 12/9/06
2665 <li>Copy consensus sequence to clipboard</li>
2670 <li>Image output - rightmost residues are rendered if
2671 sequence id panel has been resized</li>
2672 <li>Image output - all offscreen group boundaries are
2674 <li>Annotation files with sequence references - all
2675 elements in file are relative to sequence position</li>
2676 <li>Mac Applet users can use Alt key for group editing</li>
2682 <div align="center">
2683 <strong>2.1</strong><br> 22/8/06
2688 <li>MAFFT Multiple Alignment in default Web Service list</li>
2689 <li>DAS Feature fetching</li>
2690 <li>Hide sequences and columns</li>
2691 <li>Export Annotations and Features</li>
2692 <li>GFF file reading / writing</li>
2693 <li>Associate structures with sequences from local PDB
2695 <li>Add sequences to exisiting alignment</li>
2696 <li>Recently opened files / URL lists</li>
2697 <li>Applet can launch the full application</li>
2698 <li>Applet has transparency for features (Java 1.2
2700 <li>Applet has user defined colours parameter</li>
2701 <li>Applet can load sequences from parameter
2702 "sequence<em>x</em>"
2708 <li>Redundancy Panel reinstalled in the Applet</li>
2709 <li>Monospaced font - EPS / rescaling bug fixed</li>
2710 <li>Annotation files with sequence references bug fixed</li>
2716 <div align="center">
2717 <strong>2.08.1</strong><br> 2/5/06
2722 <li>Change case of selected region from Popup menu</li>
2723 <li>Choose to match case when searching</li>
2724 <li>Middle mouse button and mouse movement can compress /
2725 expand the visible width and height of the alignment</li>
2730 <li>Annotation Panel displays complete JNet results</li>
2736 <div align="center">
2737 <strong>2.08b</strong><br> 18/4/06
2743 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
2744 <li>Righthand label on wrapped alignments shows correct
2751 <div align="center">
2752 <strong>2.08</strong><br> 10/4/06
2757 <li>Editing can be locked to the selection area</li>
2758 <li>Keyboard editing</li>
2759 <li>Create sequence features from searches</li>
2760 <li>Precalculated annotations can be loaded onto
2762 <li>Features file allows grouping of features</li>
2763 <li>Annotation Colouring scheme added</li>
2764 <li>Smooth fonts off by default - Faster rendering</li>
2765 <li>Choose to toggle Autocalculate Consensus On/Off</li>
2770 <li>Drag & Drop fixed on Linux</li>
2771 <li>Jalview Archive file faster to load/save, sequence
2772 descriptions saved.</li>
2778 <div align="center">
2779 <strong>2.07</strong><br> 12/12/05
2784 <li>PDB Structure Viewer enhanced</li>
2785 <li>Sequence Feature retrieval and display enhanced</li>
2786 <li>Choose to output sequence start-end after sequence
2787 name for file output</li>
2788 <li>Sequence Fetcher WSDBFetch@EBI</li>
2789 <li>Applet can read feature files, PDB files and can be
2790 used for HTML form input</li>
2795 <li>HTML output writes groups and features</li>
2796 <li>Group editing is Control and mouse click</li>
2797 <li>File IO bugs</li>
2803 <div align="center">
2804 <strong>2.06</strong><br> 28/9/05
2809 <li>View annotations in wrapped mode</li>
2810 <li>More options for PCA viewer</li>
2815 <li>GUI bugs resolved</li>
2816 <li>Runs with -nodisplay from command line</li>
2822 <div align="center">
2823 <strong>2.05b</strong><br> 15/9/05
2828 <li>Choose EPS export as lineart or text</li>
2829 <li>Jar files are executable</li>
2830 <li>Can read in Uracil - maps to unknown residue</li>
2835 <li>Known OutOfMemory errors give warning message</li>
2836 <li>Overview window calculated more efficiently</li>
2837 <li>Several GUI bugs resolved</li>
2843 <div align="center">
2844 <strong>2.05</strong><br> 30/8/05
2849 <li>Edit and annotate in "Wrapped" view</li>
2854 <li>Several GUI bugs resolved</li>
2860 <div align="center">
2861 <strong>2.04</strong><br> 24/8/05
2866 <li>Hold down mouse wheel & scroll to change font
2872 <li>Improved JPred client reliability</li>
2873 <li>Improved loading of Jalview files</li>
2879 <div align="center">
2880 <strong>2.03</strong><br> 18/8/05
2885 <li>Set Proxy server name and port in preferences</li>
2886 <li>Multiple URL links from sequence ids</li>
2887 <li>User Defined Colours can have a scheme name and added
2889 <li>Choose to ignore gaps in consensus calculation</li>
2890 <li>Unix users can set default web browser</li>
2891 <li>Runs without GUI for batch processing</li>
2892 <li>Dynamically generated Web Service Menus</li>
2897 <li>InstallAnywhere download for Sparc Solaris</li>
2903 <div align="center">
2904 <strong>2.02</strong><br> 18/7/05
2910 <li>Copy & Paste order of sequences maintains
2911 alignment order.</li>
2917 <div align="center">
2918 <strong>2.01</strong><br> 12/7/05
2923 <li>Use delete key for deleting selection.</li>
2924 <li>Use Mouse wheel to scroll sequences.</li>
2925 <li>Help file updated to describe how to add alignment
2927 <li>Version and build date written to build properties
2929 <li>InstallAnywhere installation will check for updates
2930 at launch of Jalview.</li>
2935 <li>Delete gaps bug fixed.</li>
2936 <li>FileChooser sorts columns.</li>
2937 <li>Can remove groups one by one.</li>
2938 <li>Filechooser icons installed.</li>
2939 <li>Finder ignores return character when searching.
2940 Return key will initiate a search.<br>
2947 <div align="center">
2948 <strong>2.0</strong><br> 20/6/05
2953 <li>New codebase</li>