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-2314, -->Test suite expanded and debugged (over 940 functional unit tests, only 3 failing due to ongoing work!)
87 <li><!-- JAL-1596 -->Faster Chimera/Jalview communication by file-based command exchange</li>
88 <li><!-- JAL-2316, -->URLs for viewing database cross-references provided by identifiers.org and the EMBL-EBI's MIRIAM DB</li>
95 </div></td><td><div align="left">
99 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
100 matrix - C->R should be '3'<br />Old matrix restored with
101 this one-line groovy script:<br />jalview.schemes.ResidueProperties.BLOSUM62[4][1]=3
104 <!-- JAL-2397 -->Fixed Jalview's treatment of gaps in PCA
105 and substitution matrix based Tree calculations.<br />In
106 earlier versions of Jalview, gaps matching gaps were
107 penalised, and gaps matching non-gaps penalised even more.
108 In the PCA calculation, gaps were actually treated as
109 non-gaps - so different costs were applied, which mean't
110 Jalview's PCAs were different to those produced by
111 SeqSpace.<br />Jalview now treats gaps in the same way as
112 SeqSpace (ie it scores them as 0). To restore pre-2.10.2
114 jalview.viewmodel.PCAModel.scoreGapAsAny=true // for
116 jalview.viewmodel.PCAModel.scoreGapAsAny=false // to
119 <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>
120 <li><!-- JAL-2430 -->Hidden regions in alignment views are not coloured in linked structure views</li>
121 <li><!-- JAL-2419 -->Current selection lost if popup menu opened on a region of alignment without groups</li>
122 <li><!-- JAL-2374 -->Popup menu not always shown for regions of an alignment with overlapping groups</li>
123 <li><!-- JAL-2310 -->Finder double counts if both a sequence's name and description match</li>
124 <li><!-- JAL-2370 -->Hiding column selection containing two hidden regions results in incorrect hidden regions</li>
125 <li><!-- JAL-2377 -->PCA calculation could hang when generating output report when working with highly redundant alignments</li>
126 <li><!-- JAL-2365 -->Cannot configure feature colours with lightGray or darkGray via features file</li>
127 <li><!-- JAL-2421 -->Overview window visible region moves erratically when hidden rows or columns are present</li>
128 <li><!-- JAL-2362 -->Per-residue colourschemes applied via the Structure Viewer's colour menu don't correspond to sequence colouring</li>
129 <li><!-- JAL-2405 -->Protein specific colours only offered in colour and group colour menu for protein alignments</li>
130 <li><!-- JAL-2386 -->'Apply to all groups' setting when changing colour does not apply Conservation slider value to all groups</li>
131 <li><!-- JAL-2385 -->Colour threshold slider doesn't update to reflect currently selected view or group's shading thresholds</li>
132 <li><!-- JAL-2373 -->Percentage identity and conservation menu items do not show a tick or allow shading to be disabled</li>
133 <li><!-- JAL-2385 -->Conservation shading or PID threshold lost when base colourscheme changed if slider not visible</li>
137 <li><!-- JAL-2401 -->Easier creation of colours for all 'Lower case' residues (button in colourscheme editor debugged and new documentation and tooltips added)</li>
138 <li><!-- JAL-2399-->Text colour threshold's 'Cancel' button doesn't restore group-specific text colour thresholds</li>
139 <li><!-- JAL-2243 -->Feature settings panel does not update as new features are added to alignment</li>
140 <li><!-- JAL-2436 -->Structure viewer's View -> Colour By view selection menu changes colours of alignment views</li>
141 <li><!-- JAL-2366 -->Proxy server address and port always appear enabled in Preferences->Connections</li>
142 <li><!-- JAL-2426 -->Spurious exceptions in console raised from alignment calculation workers after alignment has been closed</li>
143 <li><!-- JAL-1608 -->Typo in selection popup menu - Create groups now 'Create Group'</li>
144 <li><!-- JAL-1608 -->CMD/CTRL and G or Shift G for Create/Undefine group doesn't always work</li>
145 <li><!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get shown again after pressing 'Cancel'</li>
146 <li><!-- JAL-2461 -->DAS registry not found exceptions removed from console output</li>
147 <li><!-- JAL-2383 -->Above PID colour threshold not recovered when alignment view imported from project</li>
152 <li><!-- JAL-2442 -->Features not rendered as transparent on overview or linked structure view</li>
153 <li><!-- JAL-2372 -->Colour group by conservation doesn't work (since 2.8)</li>
155 <em>New Known Issues</em>
162 <td width="60" nowrap>
164 <strong><a name="Jalview.2.10.1">2.10.1</a><br />
165 <em>29/11/2016</em></strong>
168 <td><div align="left">
172 <!-- JAL-98 -->Improved memory usage: sparse arrays used
173 for all consensus calculations
176 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released 3rd Oct 2016)
178 <li>Updated Jalview's Certum code signing certificate
184 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
185 set of database cross-references, sorted alphabetically
188 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
189 from database cross references. Users with custom links
190 will receive a <a href="webServices/urllinks.html#warning">warning
191 dialog</a> asking them to update their preferences.
194 <!-- JAL-2287-->Cancel button and escape listener on
195 dialog warning user about disconnecting Jalview from a
199 <!-- JAL-2320-->Jalview's Chimera control window closes if
200 the Chimera it is connected to is shut down
203 <!-- JAL-1738-->New keystroke (B) and Select highlighted
204 columns menu item to mark columns containing
205 highlighted regions (e.g. from structure selections or results
209 <!-- JAL-2284-->Command line option for batch-generation
210 of HTML pages rendering alignment data with the BioJS
220 <!-- JAL-2286 -->Columns with more than one modal residue
221 are not coloured or thresholded according to percent
222 identity (first observed in Jalview 2.8.2)
225 <!-- JAL-2301 -->Threonine incorrectly reported as not
229 <!-- JAL-2318 -->Updates to documentation pages (above PID
230 threshold, amino acid properties)
233 <!-- JAL-2292 -->Lower case residues in sequences are not
234 reported as mapped to residues in a structure file in the
238 <!--JAL-2324 -->Identical features with non-numeric scores
239 could be added multiple times to a sequence
242 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
243 bond features shown as two highlighted residues rather
244 than a range in linked structure views, and treated
245 correctly when selecting and computing trees from features
248 <!-- JAL-2281-->Custom URL links for database
249 cross-references are matched to database name regardless
257 <!-- JAL-2282-->Custom URL links for specific database
258 names without regular expressions also offer links from
262 <!-- JAL-2315-->Removing a single configured link in the
263 URL links pane in Connections preferences doesn't actually
264 update Jalview configuration
267 <!-- JAL-2272-->CTRL-Click on a selected region to open
268 the alignment area popup menu doesn't work on El-Capitan
271 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
272 files with similarly named sequences if dropped onto the
276 <!-- JAL-2312 -->Additional mappings are shown for PDB
277 entries where more chains exist in the PDB accession than
278 are reported in the SIFTS file
281 <!-- JAL-2317-->Certain structures do not get mapped to
282 the structure view when displayed with Chimera
285 <!-- JAL-2317-->No chains shown in the Chimera view
286 panel's View->Show Chains submenu
289 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
290 work for wrapped alignment views
293 <!--JAL-2197 -->Rename UI components for running JPred
294 predictions from 'JNet' to 'JPred'
297 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
298 corrupted when annotation panel vertical scroll is not at
302 <!--JAL-2332 -->Attempting to view structure for Hen
303 lysozyme results in a PDB Client error dialog box
306 <!-- JAL-2319 -->Structure View's mapping report switched ranges for PDB and sequence for SIFTS</li>
307 <!-- JAL-2319 -->SIFTS 'Not_Observed' residues mapped to non-existant coordindate data</li>
309 <!-- <em>New Known Issues</em>
316 <td width="60" nowrap>
318 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
319 <em>25/10/2016</em></strong>
322 <td><em>Application</em>
324 <li>3D Structure chooser opens with 'Cached structures'
325 view if structures already loaded</li>
326 <li>Progress bar reports models as they are loaded to
333 <li>Colour by conservation always enabled and no tick
334 shown in menu when BLOSUM or PID shading applied</li>
335 <li>FER1_ARATH and FER2_ARATH labels were switched in
336 example sequences/projects/trees</li>
340 <li>Jalview projects with views of local PDB structure
341 files saved on Windows cannot be opened on OSX</li>
342 <li>Multiple structure views can be opened and
343 superposed without timeout for structures with multiple
344 models or multiple sequences in alignment</li>
345 <li>Cannot import or associated local PDB files without
346 a PDB ID HEADER line</li>
347 <li>RMSD is not output in Jmol console when
348 superposition is performed</li>
349 <li>Drag and drop of URL from Browser fails for Linux
350 and OSX versions earlier than El Capitan</li>
351 <li>ENA client ignores invalid content from ENA server</li>
352 <li>Exceptions are not raised in console when ENA
353 client attempts to fetch non-existent IDs via Fetch DB
355 <li>Exceptions are not raised in console when a new
356 view is created on the alignment</li>
357 <li>OSX right-click fixed for group selections:
358 CMD-click to insert/remove gaps in groups and CTRL-click
359 to open group pop-up menu</li>
361 <em>Build and deployment</em>
363 <li>URL link checker now copes with multi-line anchor
366 <em>New Known Issues</em>
368 <li>Drag and drop from URL links in browsers do not
375 <td width="60" nowrap>
377 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
383 <!-- JAL-2124 -->Updated Spanish translations.
386 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
387 for importing structure data to Jalview. Enables mmCIF and
391 <!-- JAL-192 --->Alignment ruler shows positions relative to
395 <!-- JAL-2202 -->Position/residue shown in status bar when
396 mousing over sequence associated annotation
399 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
403 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
404 '()', canonical '[]' and invalid '{}' base pair populations
408 <!-- JAL-2092 -->Feature settings popup menu options for
409 showing or hiding columns containing a feature
412 <!-- JAL-1557 -->Edit selected group by double clicking on
413 group and sequence associated annotation labels
416 <!-- JAL-2236 -->Sequence name added to annotation label in
417 select/hide columns by annotation and colour by annotation
421 </ul> <em>Application</em>
424 <!-- JAL-2050-->Automatically hide introns when opening a
428 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
432 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
433 structure mappings with the EMBL-EBI PDBe SIFTS database
436 <!-- JAL-2079 -->Updated download sites used for Rfam and
437 Pfam sources to xfam.org
440 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
443 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
444 over sequences in Jalview
447 <!-- JAL-2027-->Support for reverse-complement coding
448 regions in ENA and EMBL
451 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
452 for record retrieval via ENA rest API
455 <!-- JAL-2027 -->Support for ENA CDS records with reverse
459 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
460 groovy script execution
463 <!-- JAL-1812 -->New 'execute Groovy script' option in an
464 alignment window's Calculate menu
467 <!-- JAL-1812 -->Allow groovy scripts that call
468 Jalview.getAlignFrames() to run in headless mode
471 <!-- JAL-2068 -->Support for creating new alignment
472 calculation workers from groovy scripts
475 <!-- JAL-1369 --->Store/restore reference sequence in
479 <!-- JAL-1803 -->Chain codes for a sequence's PDB
480 associations are now saved/restored from project
483 <!-- JAL-1993 -->Database selection dialog always shown
484 before sequence fetcher is opened
487 <!-- JAL-2183 -->Double click on an entry in Jalview's
488 database chooser opens a sequence fetcher
491 <!-- JAL-1563 -->Free-text search client for UniProt using
495 <!-- JAL-2168 -->-nonews command line parameter to prevent
496 the news reader opening
499 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
500 querying stored in preferences
503 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
507 <!-- JAL-1977-->Tooltips shown on database chooser
510 <!-- JAL-391 -->Reverse complement function in calculate
511 menu for nucleotide sequences
514 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
515 and feature counts preserves alignment ordering (and
516 debugged for complex feature sets).
519 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
520 viewing structures with Jalview 2.10
523 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
524 genome, transcript CCDS and gene ids via the Ensembl and
525 Ensembl Genomes REST API
528 <!-- JAL-2049 -->Protein sequence variant annotation
529 computed for 'sequence_variant' annotation on CDS regions
533 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
537 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
538 Ref Fetcher fails to match, or otherwise updates sequence
539 data from external database records.
542 <!-- JAL-2154 -->Revised Jalview Project format for
543 efficient recovery of sequence coding and alignment
544 annotation relationships.
546 </ul> <!-- <em>Applet</em>
557 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
561 <!-- JAL-2018-->Export features in Jalview format (again)
562 includes graduated colourschemes
565 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
566 working with big alignments and lots of hidden columns
569 <!-- JAL-2053-->Hidden column markers not always rendered
570 at right of alignment window
573 <!-- JAL-2067 -->Tidied up links in help file table of
577 <!-- JAL-2072 -->Feature based tree calculation not shown
581 <!-- JAL-2075 -->Hidden columns ignored during feature
582 based tree calculation
585 <!-- JAL-2065 -->Alignment view stops updating when show
586 unconserved enabled for group on alignment
589 <!-- JAL-2086 -->Cannot insert gaps into sequence when
593 <!-- JAL-2146 -->Alignment column in status incorrectly
594 shown as "Sequence position" when mousing over
598 <!-- JAL-2099 -->Incorrect column numbers in ruler when
599 hidden columns present
602 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
603 user created annotation added to alignment
606 <!-- JAL-1841 -->RNA Structure consensus only computed for
607 '()' base pair annotation
610 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
611 in zero scores for all base pairs in RNA Structure
615 <!-- JAL-2174-->Extend selection with columns containing
619 <!-- JAL-2275 -->Pfam format writer puts extra space at
620 beginning of sequence
623 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
627 <!-- JAL-2238 -->Cannot create groups on an alignment from
628 from a tree when t-coffee scores are shown
631 <!-- JAL-1836,1967 -->Cannot import and view PDB
632 structures with chains containing negative resnums (4q4h)
635 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
639 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
640 to Clustal, PIR and PileUp output
643 <!-- JAL-2008 -->Reordering sequence features that are
644 not visible causes alignment window to repaint
647 <!-- JAL-2006 -->Threshold sliders don't work in
648 graduated colour and colour by annotation row for e-value
649 scores associated with features and annotation rows
652 <!-- JAL-1797 -->amino acid physicochemical conservation
653 calculation should be case independent
656 <!-- JAL-2173 -->Remove annotation also updates hidden
660 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
661 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
662 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
665 <!-- JAL-2065 -->Null pointer exceptions and redraw
666 problems when reference sequence defined and 'show
667 non-conserved' enabled
670 <!-- JAL-1306 -->Quality and Conservation are now shown on
671 load even when Consensus calculation is disabled
674 <!-- JAL-1932 -->Remove right on penultimate column of
675 alignment does nothing
681 <!-- JAL-1552-->URLs and links can't be imported by
682 drag'n'drop on OSX when launched via webstart (note - not
683 yet fixed for El Capitan)
686 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
687 output when running on non-gb/us i18n platforms
690 <!-- JAL-1944 -->Error thrown when exporting a view with
691 hidden sequences as flat-file alignment
694 <!-- JAL-2030-->InstallAnywhere distribution fails when
698 <!-- JAL-2080-->Jalview very slow to launch via webstart
699 (also hotfix for 2.9.0b2)
702 <!-- JAL-2085 -->Cannot save project when view has a
703 reference sequence defined
706 <!-- JAL-1011 -->Columns are suddenly selected in other
707 alignments and views when revealing hidden columns
710 <!-- JAL-1989 -->Hide columns not mirrored in complement
711 view in a cDNA/Protein splitframe
714 <!-- JAL-1369 -->Cannot save/restore representative
715 sequence from project when only one sequence is
719 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
723 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
724 structure consensus didn't refresh annotation panel
727 <!-- JAL-1962 -->View mapping in structure view shows
728 mappings between sequence and all chains in a PDB file
731 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
732 dialogs format columns correctly, don't display array
733 data, sort columns according to type
736 <!-- JAL-1975 -->Export complete shown after destination
737 file chooser is cancelled during an image export
740 <!-- JAL-2025 -->Error when querying PDB Service with
741 sequence name containing special characters
744 <!-- JAL-2024 -->Manual PDB structure querying should be
748 <!-- JAL-2104 -->Large tooltips with broken HTML
749 formatting don't wrap
752 <!-- JAL-1128 -->Figures exported from wrapped view are
753 truncated so L looks like I in consensus annotation
756 <!-- JAL-2003 -->Export features should only export the
757 currently displayed features for the current selection or
761 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
762 after fetching cross-references, and restoring from project
765 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
766 followed in the structure viewer
769 <!-- JAL-2163 -->Titles for individual alignments in
770 splitframe not restored from project
773 <!-- JAL-2145 -->missing autocalculated annotation at
774 trailing end of protein alignment in transcript/product
775 splitview when pad-gaps not enabled by default
778 <!-- JAL-1797 -->amino acid physicochemical conservation
782 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
783 article has been read (reopened issue due to
784 internationalisation problems)
787 <!-- JAL-1960 -->Only offer PDB structures in structure
788 viewer based on sequence name, PDB and UniProt
793 <!-- JAL-1976 -->No progress bar shown during export of
797 <!-- JAL-2213 -->Structures not always superimposed after
798 multiple structures are shown for one or more sequences.
801 <!-- JAL-1370 -->Reference sequence characters should not
802 be replaced with '.' when 'Show unconserved' format option
806 <!-- JAL-1823 -->Cannot specify chain code when entering
807 specific PDB id for sequence
810 <!-- JAL-1944 -->File->Export->.. as doesn't work when
811 'Export hidden sequences' is enabled, but 'export hidden
812 columns' is disabled.
815 <!--JAL-2026-->Best Quality option in structure chooser
816 selects lowest rather than highest resolution structures
820 <!-- JAL-1887 -->Incorrect start and end reported for PDB
821 to sequence mapping in 'View Mappings' report
824 <!-- JAL-2284 -->Unable to read old Jalview projects that
825 contain non-XML data added after Jalvew wrote project.
827 <li><!-- JAL-2118 -->Newly created annotation row reorders
828 after clicking on it to create new annotation for a
831 <!-- may exclude, this is an external service stability issue JAL-1941
832 -- > RNA 3D structure not added via DSSR service</li> -->
837 <!-- JAL-2151 -->Incorrect columns are selected when
838 hidden columns present before start of sequence
841 <!-- JAL-1986 -->Missing dependencies on applet pages
845 <!-- JAL-1947 -->Overview pixel size changes when
846 sequences are hidden in applet
849 <!-- JAL-1996 -->Updated instructions for applet
850 deployment on examples pages.
857 <td width="60" nowrap>
859 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
860 <em>16/10/2015</em></strong>
865 <li>Time stamps for signed Jalview application and applet
872 <li>Duplicate group consensus and conservation rows
873 shown when tree is partitioned</li>
874 <li>Erratic behaviour when tree partitions made with
875 multiple cDNA/Protein split views</li>
881 <td width="60" nowrap>
883 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
884 <em>8/10/2015</em></strong>
889 <li>Updated Spanish translations of localized text for
891 </ul> <em>Application</em>
893 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
894 <li>Signed OSX InstallAnywhere installer<br></li>
895 <li>Support for per-sequence based annotations in BioJSON</li>
896 </ul> <em>Applet</em>
898 <li>Split frame example added to applet examples page</li>
899 </ul><em>Build and Deployment</em>
901 <li><!-- JAL-1888 -->New ant target for running Jalview's test suite</li>
907 <li>Mapping of cDNA to protein in split frames
908 incorrect when sequence start > 1</li>
909 <li>Broken images in filter column by annotation dialog
911 <li>Feature colours not parsed from features file</li>
912 <li>Exceptions and incomplete link URLs recovered when
913 loading a features file containing HTML tags in feature
919 <li>Annotations corrupted after BioJS export and
921 <li>Incorrect sequence limits after Fetch DB References
922 with 'trim retrieved sequences'</li>
923 <li>Incorrect warning about deleting all data when
924 deleting selected columns</li>
925 <li>Patch to build system for shipping properly signed
926 JNLP templates for webstart launch</li>
927 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
928 unreleased structures for download or viewing</li>
929 <li>Tab/space/return keystroke operation of EMBL-PDBe
930 fetcher/viewer dialogs works correctly</li>
931 <li>Disabled 'minimise' button on Jalview windows
932 running on OSX to workaround redraw hang bug</li>
933 <li>Split cDNA/Protein view position and geometry not
934 recovered from jalview project</li>
935 <li>Initial enabled/disabled state of annotation menu
936 sorter 'show autocalculated first/last' corresponds to
938 <li>Restoring of Clustal, RNA Helices and T-Coffee
939 color schemes from BioJSON</li>
943 <li>Reorder sequences mirrored in cDNA/Protein split
945 <li>Applet with Jmol examples not loading correctly</li>
951 <td><div align="center">
952 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
956 <li>Linked visualisation and analysis of DNA and Protein
959 <li>Translated cDNA alignments shown as split protein
960 and DNA alignment views</li>
961 <li>Codon consensus annotation for linked protein and
962 cDNA alignment views</li>
963 <li>Link cDNA or Protein product sequences by loading
964 them onto Protein or cDNA alignments</li>
965 <li>Reconstruct linked cDNA alignment from aligned
966 protein sequences</li>
969 <li>Jmol integration updated to Jmol v14.2.14</li>
970 <li>Import and export of Jalview alignment views as <a
971 href="features/bioJsonFormat.html">BioJSON</a></li>
972 <li>New alignment annotation file statements for
973 reference sequences and marking hidden columns</li>
974 <li>Reference sequence based alignment shading to
975 highlight variation</li>
976 <li>Select or hide columns according to alignment
978 <li>Find option for locating sequences by description</li>
979 <li>Conserved physicochemical properties shown in amino
980 acid conservation row</li>
981 <li>Alignments can be sorted by number of RNA helices</li>
982 </ul> <em>Application</em>
984 <li>New cDNA/Protein analysis capabilities
986 <li>Get Cross-References should open a Split Frame
987 view with cDNA/Protein</li>
988 <li>Detect when nucleotide sequences and protein
989 sequences are placed in the same alignment</li>
990 <li>Split cDNA/Protein views are saved in Jalview
995 <li>Use REST API to talk to Chimera</li>
996 <li>Selected regions in Chimera are highlighted in linked
999 <li>VARNA RNA viewer updated to v3.93</li>
1000 <li>VARNA views are saved in Jalview Projects</li>
1001 <li>Pseudoknots displayed as Jalview RNA annotation can
1002 be shown in VARNA</li>
1004 <li>Make groups for selection uses marked columns as well
1005 as the active selected region</li>
1007 <li>Calculate UPGMA and NJ trees using sequence feature
1009 <li>New Export options
1011 <li>New Export Settings dialog to control hidden
1012 region export in flat file generation</li>
1014 <li>Export alignment views for display with the <a
1015 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1017 <li>Export scrollable SVG in HTML page</li>
1018 <li>Optional embedding of BioJSON data when exporting
1019 alignment figures to HTML</li>
1021 <li>3D structure retrieval and display
1023 <li>Free text and structured queries with the PDBe
1025 <li>PDBe Search API based discovery and selection of
1026 PDB structures for a sequence set</li>
1030 <li>JPred4 employed for protein secondary structure
1032 <li>Hide Insertions menu option to hide unaligned columns
1033 for one or a group of sequences</li>
1034 <li>Automatically hide insertions in alignments imported
1035 from the JPred4 web server</li>
1036 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1037 system on OSX<br />LGPL libraries courtesy of <a
1038 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1040 <li>changed 'View nucleotide structure' submenu to 'View
1041 VARNA 2D Structure'</li>
1042 <li>change "View protein structure" menu option to "3D
1045 </ul> <em>Applet</em>
1047 <li>New layout for applet example pages</li>
1048 <li>New parameters to enable SplitFrame view
1049 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1050 <li>New example demonstrating linked viewing of cDNA and
1051 Protein alignments</li>
1052 </ul> <em>Development and deployment</em>
1054 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1055 <li>Include installation type and git revision in build
1056 properties and console log output</li>
1057 <li>Jalview Github organisation, and new github site for
1058 storing BioJsMSA Templates</li>
1059 <li>Jalview's unit tests now managed with TestNG</li>
1062 <!-- <em>General</em>
1064 </ul> --> <!-- issues resolved --> <em>Application</em>
1066 <li>Escape should close any open find dialogs</li>
1067 <li>Typo in select-by-features status report</li>
1068 <li>Consensus RNA secondary secondary structure
1069 predictions are not highlighted in amber</li>
1070 <li>Missing gap character in v2.7 example file means
1071 alignment appears unaligned when pad-gaps is not enabled</li>
1072 <li>First switch to RNA Helices colouring doesn't colour
1073 associated structure views</li>
1074 <li>ID width preference option is greyed out when auto
1075 width checkbox not enabled</li>
1076 <li>Stopped a warning dialog from being shown when
1077 creating user defined colours</li>
1078 <li>'View Mapping' in structure viewer shows sequence
1079 mappings for just that viewer's sequences</li>
1080 <li>Workaround for superposing PDB files containing
1081 multiple models in Chimera</li>
1082 <li>Report sequence position in status bar when hovering
1083 over Jmol structure</li>
1084 <li>Cannot output gaps as '.' symbols with Selection ->
1085 output to text box</li>
1086 <li>Flat file exports of alignments with hidden columns
1087 have incorrect sequence start/end</li>
1088 <li>'Aligning' a second chain to a Chimera structure from
1090 <li>Colour schemes applied to structure viewers don't
1091 work for nucleotide</li>
1092 <li>Loading/cut'n'pasting an empty or invalid file leads
1093 to a grey/invisible alignment window</li>
1094 <li>Exported Jpred annotation from a sequence region
1095 imports to different position</li>
1096 <li>Space at beginning of sequence feature tooltips shown
1097 on some platforms</li>
1098 <li>Chimera viewer 'View | Show Chain' menu is not
1100 <li>'New View' fails with a Null Pointer Exception in
1101 console if Chimera has been opened</li>
1102 <li>Mouseover to Chimera not working</li>
1103 <li>Miscellaneous ENA XML feature qualifiers not
1105 <li>NPE in annotation renderer after 'Extract Scores'</li>
1106 <li>If two structures in one Chimera window, mouseover of
1107 either sequence shows on first structure</li>
1108 <li>'Show annotations' options should not make
1109 non-positional annotations visible</li>
1110 <li>Subsequence secondary structure annotation not shown
1111 in right place after 'view flanking regions'</li>
1112 <li>File Save As type unset when current file format is
1114 <li>Save as '.jar' option removed for saving Jalview
1116 <li>Colour by Sequence colouring in Chimera more
1118 <li>Cannot 'add reference annotation' for a sequence in
1119 several views on same alignment</li>
1120 <li>Cannot show linked products for EMBL / ENA records</li>
1121 <li>Jalview's tooltip wraps long texts containing no
1123 </ul> <em>Applet</em>
1125 <li>Jmol to JalviewLite mouseover/link not working</li>
1126 <li>JalviewLite can't import sequences with ID
1127 descriptions containing angle brackets</li>
1128 </ul> <em>General</em>
1130 <li>Cannot export and reimport RNA secondary structure
1131 via jalview annotation file</li>
1132 <li>Random helix colour palette for colour by annotation
1133 with RNA secondary structure</li>
1134 <li>Mouseover to cDNA from STOP residue in protein
1135 translation doesn't work.</li>
1136 <li>hints when using the select by annotation dialog box</li>
1137 <li>Jmol alignment incorrect if PDB file has alternate CA
1139 <li>FontChooser message dialog appears to hang after
1140 choosing 1pt font</li>
1141 <li>Peptide secondary structure incorrectly imported from
1142 annotation file when annotation display text includes 'e' or
1144 <li>Cannot set colour of new feature type whilst creating
1146 <li>cDNA translation alignment should not be sequence
1147 order dependent</li>
1148 <li>'Show unconserved' doesn't work for lower case
1150 <li>Nucleotide ambiguity codes involving R not recognised</li>
1151 </ul> <em>Deployment and Documentation</em>
1153 <li>Applet example pages appear different to the rest of
1154 www.jalview.org</li>
1155 </ul> <em>Application Known issues</em>
1157 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1158 <li>Misleading message appears after trying to delete
1160 <li>Jalview icon not shown in dock after InstallAnywhere
1161 version launches</li>
1162 <li>Fetching EMBL reference for an RNA sequence results
1163 fails with a sequence mismatch</li>
1164 <li>Corrupted or unreadable alignment display when
1165 scrolling alignment to right</li>
1166 <li>ArrayIndexOutOfBoundsException thrown when remove
1167 empty columns called on alignment with ragged gapped ends</li>
1168 <li>auto calculated alignment annotation rows do not get
1169 placed above or below non-autocalculated rows</li>
1170 <li>Jalview dekstop becomes sluggish at full screen in
1171 ultra-high resolution</li>
1172 <li>Cannot disable consensus calculation independently of
1173 quality and conservation</li>
1174 <li>Mouseover highlighting between cDNA and protein can
1175 become sluggish with more than one splitframe shown</li>
1176 </ul> <em>Applet Known Issues</em>
1178 <li>Core PDB parsing code requires Jmol</li>
1179 <li>Sequence canvas panel goes white when alignment
1180 window is being resized</li>
1186 <td><div align="center">
1187 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1189 <td><em>General</em>
1191 <li>Updated Java code signing certificate donated by
1193 <li>Features and annotation preserved when performing
1194 pairwise alignment</li>
1195 <li>RNA pseudoknot annotation can be
1196 imported/exported/displayed</li>
1197 <li>'colour by annotation' can colour by RNA and
1198 protein secondary structure</li>
1199 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1200 post-hoc with 2.9 release</em>)
1203 </ul> <em>Application</em>
1205 <li>Extract and display secondary structure for sequences
1206 with 3D structures</li>
1207 <li>Support for parsing RNAML</li>
1208 <li>Annotations menu for layout
1210 <li>sort sequence annotation rows by alignment</li>
1211 <li>place sequence annotation above/below alignment
1214 <li>Output in Stockholm format</li>
1215 <li>Internationalisation: improved Spanish (es)
1217 <li>Structure viewer preferences tab</li>
1218 <li>Disorder and Secondary Structure annotation tracks
1219 shared between alignments</li>
1220 <li>UCSF Chimera launch and linked highlighting from
1222 <li>Show/hide all sequence associated annotation rows for
1223 all or current selection</li>
1224 <li>disorder and secondary structure predictions
1225 available as dataset annotation</li>
1226 <li>Per-sequence rna helices colouring</li>
1229 <li>Sequence database accessions imported when fetching
1230 alignments from Rfam</li>
1231 <li>update VARNA version to 3.91</li>
1233 <li>New groovy scripts for exporting aligned positions,
1234 conservation values, and calculating sum of pairs scores.</li>
1235 <li>Command line argument to set default JABAWS server</li>
1236 <li>include installation type in build properties and
1237 console log output</li>
1238 <li>Updated Jalview project format to preserve dataset
1242 <!-- issues resolved --> <em>Application</em>
1244 <li>Distinguish alignment and sequence associated RNA
1245 structure in structure->view->VARNA</li>
1246 <li>Raise dialog box if user deletes all sequences in an
1248 <li>Pressing F1 results in documentation opening twice</li>
1249 <li>Sequence feature tooltip is wrapped</li>
1250 <li>Double click on sequence associated annotation
1251 selects only first column</li>
1252 <li>Redundancy removal doesn't result in unlinked
1253 leaves shown in tree</li>
1254 <li>Undos after several redundancy removals don't undo
1256 <li>Hide sequence doesn't hide associated annotation</li>
1257 <li>User defined colours dialog box too big to fit on
1258 screen and buttons not visible</li>
1259 <li>author list isn't updated if already written to
1260 Jalview properties</li>
1261 <li>Popup menu won't open after retrieving sequence
1263 <li>File open window for associate PDB doesn't open</li>
1264 <li>Left-then-right click on a sequence id opens a
1265 browser search window</li>
1266 <li>Cannot open sequence feature shading/sort popup menu
1267 in feature settings dialog</li>
1268 <li>better tooltip placement for some areas of Jalview
1270 <li>Allow addition of JABAWS Server which doesn't
1271 pass validation</li>
1272 <li>Web services parameters dialog box is too large to
1274 <li>Muscle nucleotide alignment preset obscured by
1276 <li>JABAWS preset submenus don't contain newly
1277 defined user preset</li>
1278 <li>MSA web services warns user if they were launched
1279 with invalid input</li>
1280 <li>Jalview cannot contact DAS Registy when running on
1283 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1284 'Superpose with' submenu not shown when new view
1288 </ul> <!-- <em>Applet</em>
1290 </ul> <em>General</em>
1292 </ul>--> <em>Deployment and Documentation</em>
1294 <li>2G and 1G options in launchApp have no effect on
1295 memory allocation</li>
1296 <li>launchApp service doesn't automatically open
1297 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1299 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1300 InstallAnywhere reports cannot find valid JVM when Java
1301 1.7_055 is available
1303 </ul> <em>Application Known issues</em>
1306 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1307 corrupted or unreadable alignment display when scrolling
1311 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1312 retrieval fails but progress bar continues for DAS retrieval
1313 with large number of ID
1316 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1317 flatfile output of visible region has incorrect sequence
1321 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1322 rna structure consensus doesn't update when secondary
1323 structure tracks are rearranged
1326 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1327 invalid rna structure positional highlighting does not
1328 highlight position of invalid base pairs
1331 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1332 out of memory errors are not raised when saving Jalview
1333 project from alignment window file menu
1336 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1337 Switching to RNA Helices colouring doesn't propagate to
1341 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1342 colour by RNA Helices not enabled when user created
1343 annotation added to alignment
1346 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1347 Jalview icon not shown on dock in Mountain Lion/Webstart
1349 </ul> <em>Applet Known Issues</em>
1352 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1353 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1356 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1357 Jalview and Jmol example not compatible with IE9
1360 <li>Sort by annotation score doesn't reverse order
1366 <td><div align="center">
1367 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1370 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1373 <li>Internationalisation of user interface (usually
1374 called i18n support) and translation for Spanish locale</li>
1375 <li>Define/Undefine group on current selection with
1376 Ctrl-G/Shift Ctrl-G</li>
1377 <li>Improved group creation/removal options in
1378 alignment/sequence Popup menu</li>
1379 <li>Sensible precision for symbol distribution
1380 percentages shown in logo tooltip.</li>
1381 <li>Annotation panel height set according to amount of
1382 annotation when alignment first opened</li>
1383 </ul> <em>Application</em>
1385 <li>Interactive consensus RNA secondary structure
1386 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1387 <li>Select columns containing particular features from
1388 Feature Settings dialog</li>
1389 <li>View all 'representative' PDB structures for selected
1391 <li>Update Jalview project format:
1393 <li>New file extension for Jalview projects '.jvp'</li>
1394 <li>Preserve sequence and annotation dataset (to
1395 store secondary structure annotation,etc)</li>
1396 <li>Per group and alignment annotation and RNA helix
1400 <li>New similarity measures for PCA and Tree calculation
1402 <li>Experimental support for retrieval and viewing of
1403 flanking regions for an alignment</li>
1407 <!-- issues resolved --> <em>Application</em>
1409 <li>logo keeps spinning and status remains at queued or
1410 running after job is cancelled</li>
1411 <li>cannot export features from alignments imported from
1412 Jalview/VAMSAS projects</li>
1413 <li>Buggy slider for web service parameters that take
1415 <li>Newly created RNA secondary structure line doesn't
1416 have 'display all symbols' flag set</li>
1417 <li>T-COFFEE alignment score shading scheme and other
1418 annotation shading not saved in Jalview project</li>
1419 <li>Local file cannot be loaded in freshly downloaded
1421 <li>Jalview icon not shown on dock in Mountain
1423 <li>Load file from desktop file browser fails</li>
1424 <li>Occasional NPE thrown when calculating large trees</li>
1425 <li>Cannot reorder or slide sequences after dragging an
1426 alignment onto desktop</li>
1427 <li>Colour by annotation dialog throws NPE after using
1428 'extract scores' function</li>
1429 <li>Loading/cut'n'pasting an empty file leads to a grey
1430 alignment window</li>
1431 <li>Disorder thresholds rendered incorrectly after
1432 performing IUPred disorder prediction</li>
1433 <li>Multiple group annotated consensus rows shown when
1434 changing 'normalise logo' display setting</li>
1435 <li>Find shows blank dialog after 'finished searching' if
1436 nothing matches query</li>
1437 <li>Null Pointer Exceptions raised when sorting by
1438 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1440 <li>Errors in Jmol console when structures in alignment
1441 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1443 <li>Not all working JABAWS services are shown in
1445 <li>JAVAWS version of Jalview fails to launch with
1446 'invalid literal/length code'</li>
1447 <li>Annotation/RNA Helix colourschemes cannot be applied
1448 to alignment with groups (actually fixed in 2.8.0b1)</li>
1449 <li>RNA Helices and T-Coffee Scores available as default
1452 </ul> <em>Applet</em>
1454 <li>Remove group option is shown even when selection is
1456 <li>Apply to all groups ticked but colourscheme changes
1457 don't affect groups</li>
1458 <li>Documented RNA Helices and T-Coffee Scores as valid
1459 colourscheme name</li>
1460 <li>Annotation labels drawn on sequence IDs when
1461 Annotation panel is not displayed</li>
1462 <li>Increased font size for dropdown menus on OSX and
1463 embedded windows</li>
1464 </ul> <em>Other</em>
1466 <li>Consensus sequence for alignments/groups with a
1467 single sequence were not calculated</li>
1468 <li>annotation files that contain only groups imported as
1469 annotation and junk sequences</li>
1470 <li>Fasta files with sequences containing '*' incorrectly
1471 recognised as PFAM or BLC</li>
1472 <li>conservation/PID slider apply all groups option
1473 doesn't affect background (2.8.0b1)
1475 <li>redundancy highlighting is erratic at 0% and 100%</li>
1476 <li>Remove gapped columns fails for sequences with ragged
1478 <li>AMSA annotation row with leading spaces is not
1479 registered correctly on import</li>
1480 <li>Jalview crashes when selecting PCA analysis for
1481 certain alignments</li>
1482 <li>Opening the colour by annotation dialog for an
1483 existing annotation based 'use original colours'
1484 colourscheme loses original colours setting</li>
1489 <td><div align="center">
1490 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
1491 <em>30/1/2014</em></strong>
1495 <li>Trusted certificates for JalviewLite applet and
1496 Jalview Desktop application<br />Certificate was donated by
1497 <a href="https://www.certum.eu">Certum</a> to the Jalview
1498 open source project).
1500 <li>Jalview SRS links replaced by UniProt and EBI-search
1502 <li>Output in Stockholm format</li>
1503 <li>Allow import of data from gzipped files</li>
1504 <li>Export/import group and sequence associated line
1505 graph thresholds</li>
1506 <li>Nucleotide substitution matrix that supports RNA and
1507 ambiguity codes</li>
1508 <li>Allow disorder predictions to be made on the current
1509 selection (or visible selection) in the same way that JPred
1511 <li>Groovy scripting for headless Jalview operation</li>
1512 </ul> <em>Other improvements</em>
1514 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
1515 <li>COMBINE statement uses current SEQUENCE_REF and
1516 GROUP_REF scope to group annotation rows</li>
1517 <li>Support '' style escaping of quotes in Newick
1519 <li>Group options for JABAWS service by command line name</li>
1520 <li>Empty tooltip shown for JABA service options with a
1521 link but no description</li>
1522 <li>Select primary source when selecting authority in
1523 database fetcher GUI</li>
1524 <li>Add .mfa to FASTA file extensions recognised by
1526 <li>Annotation label tooltip text wrap</li>
1531 <li>Slow scrolling when lots of annotation rows are
1533 <li>Lots of NPE (and slowness) after creating RNA
1534 secondary structure annotation line</li>
1535 <li>Sequence database accessions not imported when
1536 fetching alignments from Rfam</li>
1537 <li>Incorrect SHMR submission for sequences with
1539 <li>View all structures does not always superpose
1541 <li>Option widgets in service parameters not updated to
1542 reflect user or preset settings</li>
1543 <li>Null pointer exceptions for some services without
1544 presets or adjustable parameters</li>
1545 <li>Discover PDB IDs entry in structure menu doesn't
1546 discover PDB xRefs</li>
1547 <li>Exception encountered while trying to retrieve
1548 features with DAS</li>
1549 <li>Lowest value in annotation row isn't coloured
1550 when colour by annotation (per sequence) is coloured</li>
1551 <li>Keyboard mode P jumps to start of gapped region when
1552 residue follows a gap</li>
1553 <li>Jalview appears to hang importing an alignment with
1554 Wrap as default or after enabling Wrap</li>
1555 <li>'Right click to add annotations' message
1556 shown in wrap mode when no annotations present</li>
1557 <li>Disorder predictions fail with NPE if no automatic
1558 annotation already exists on alignment</li>
1559 <li>oninit javascript function should be called after
1560 initialisation completes</li>
1561 <li>Remove redundancy after disorder prediction corrupts
1562 alignment window display</li>
1563 <li>Example annotation file in documentation is invalid</li>
1564 <li>Grouped line graph annotation rows are not exported
1565 to annotation file</li>
1566 <li>Multi-harmony analysis cannot be run when only two
1568 <li>Cannot create multiple groups of line graphs with
1569 several 'combine' statements in annotation file</li>
1570 <li>Pressing return several times causes Number Format
1571 exceptions in keyboard mode</li>
1572 <li>Multi-harmony (SHMMR) method doesn't submit
1573 correct partitions for input data</li>
1574 <li>Translation from DNA to Amino Acids fails</li>
1575 <li>Jalview fail to load newick tree with quoted label</li>
1576 <li>--headless flag isn't understood</li>
1577 <li>ClassCastException when generating EPS in headless
1579 <li>Adjusting sequence-associated shading threshold only
1580 changes one row's threshold</li>
1581 <li>Preferences and Feature settings panel panel
1582 doesn't open</li>
1583 <li>hide consensus histogram also hides conservation and
1584 quality histograms</li>
1589 <td><div align="center">
1590 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
1592 <td><em>Application</em>
1594 <li>Support for JABAWS 2.0 Services (AACon alignment
1595 conservation, protein disorder and Clustal Omega)</li>
1596 <li>JABAWS server status indicator in Web Services
1598 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
1599 in Jalview alignment window</li>
1600 <li>Updated Jalview build and deploy framework for OSX
1601 mountain lion, windows 7, and 8</li>
1602 <li>Nucleotide substitution matrix for PCA that supports
1603 RNA and ambiguity codes</li>
1605 <li>Improved sequence database retrieval GUI</li>
1606 <li>Support fetching and database reference look up
1607 against multiple DAS sources (Fetch all from in 'fetch db
1609 <li>Jalview project improvements
1611 <li>Store and retrieve the 'belowAlignment'
1612 flag for annotation</li>
1613 <li>calcId attribute to group annotation rows on the
1615 <li>Store AACon calculation settings for a view in
1616 Jalview project</li>
1620 <li>horizontal scrolling gesture support</li>
1621 <li>Visual progress indicator when PCA calculation is
1623 <li>Simpler JABA web services menus</li>
1624 <li>visual indication that web service results are still
1625 being retrieved from server</li>
1626 <li>Serialise the dialogs that are shown when Jalview
1627 starts up for first time</li>
1628 <li>Jalview user agent string for interacting with HTTP
1630 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
1632 <li>Examples directory and Groovy library included in
1633 InstallAnywhere distribution</li>
1634 </ul> <em>Applet</em>
1636 <li>RNA alignment and secondary structure annotation
1637 visualization applet example</li>
1638 </ul> <em>General</em>
1640 <li>Normalise option for consensus sequence logo</li>
1641 <li>Reset button in PCA window to return dimensions to
1643 <li>Allow seqspace or Jalview variant of alignment PCA
1645 <li>PCA with either nucleic acid and protein substitution
1647 <li>Allow windows containing HTML reports to be exported
1649 <li>Interactive display and editing of RNA secondary
1650 structure contacts</li>
1651 <li>RNA Helix Alignment Colouring</li>
1652 <li>RNA base pair logo consensus</li>
1653 <li>Parse sequence associated secondary structure
1654 information in Stockholm files</li>
1655 <li>HTML Export database accessions and annotation
1656 information presented in tooltip for sequences</li>
1657 <li>Import secondary structure from LOCARNA clustalw
1658 style RNA alignment files</li>
1659 <li>import and visualise T-COFFEE quality scores for an
1661 <li>'colour by annotation' per sequence option to
1662 shade each sequence according to its associated alignment
1664 <li>New Jalview Logo</li>
1665 </ul> <em>Documentation and Development</em>
1667 <li>documentation for score matrices used in Jalview</li>
1668 <li>New Website!</li>
1670 <td><em>Application</em>
1672 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
1673 wsdbfetch REST service</li>
1674 <li>Stop windows being moved outside desktop on OSX</li>
1675 <li>Filetype associations not installed for webstart
1677 <li>Jalview does not always retrieve progress of a JABAWS
1678 job execution in full once it is complete</li>
1679 <li>revise SHMR RSBS definition to ensure alignment is
1680 uploaded via ali_file parameter</li>
1681 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
1682 <li>View all structures superposed fails with exception</li>
1683 <li>Jnet job queues forever if a very short sequence is
1684 submitted for prediction</li>
1685 <li>Cut and paste menu not opened when mouse clicked on
1687 <li>Putting fractional value into integer text box in
1688 alignment parameter dialog causes Jalview to hang</li>
1689 <li>Structure view highlighting doesn't work on
1691 <li>View all structures fails with exception shown in
1693 <li>Characters in filename associated with PDBEntry not
1694 escaped in a platform independent way</li>
1695 <li>Jalview desktop fails to launch with exception when
1697 <li>Tree calculation reports 'you must have 2 or more
1698 sequences selected' when selection is empty</li>
1699 <li>Jalview desktop fails to launch with jar signature
1700 failure when java web start temporary file caching is
1702 <li>DAS Sequence retrieval with range qualification
1703 results in sequence xref which includes range qualification</li>
1704 <li>Errors during processing of command line arguments
1705 cause progress bar (JAL-898) to be removed</li>
1706 <li>Replace comma for semi-colon option not disabled for
1707 DAS sources in sequence fetcher</li>
1708 <li>Cannot close news reader when JABAWS server warning
1709 dialog is shown</li>
1710 <li>Option widgets not updated to reflect user settings</li>
1711 <li>Edited sequence not submitted to web service</li>
1712 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
1713 <li>InstallAnywhere installer doesn't unpack and run
1714 on OSX Mountain Lion</li>
1715 <li>Annotation panel not given a scroll bar when
1716 sequences with alignment annotation are pasted into the
1718 <li>Sequence associated annotation rows not associated
1719 when loaded from Jalview project</li>
1720 <li>Browser launch fails with NPE on java 1.7</li>
1721 <li>JABAWS alignment marked as finished when job was
1722 cancelled or job failed due to invalid input</li>
1723 <li>NPE with v2.7 example when clicking on Tree
1724 associated with all views</li>
1725 <li>Exceptions when copy/paste sequences with grouped
1726 annotation rows to new window</li>
1727 </ul> <em>Applet</em>
1729 <li>Sequence features are momentarily displayed before
1730 they are hidden using hidefeaturegroups applet parameter</li>
1731 <li>loading features via javascript API automatically
1732 enables feature display</li>
1733 <li>scrollToColumnIn javascript API method doesn't
1735 </ul> <em>General</em>
1737 <li>Redundancy removal fails for rna alignment</li>
1738 <li>PCA calculation fails when sequence has been selected
1739 and then deselected</li>
1740 <li>PCA window shows grey box when first opened on OSX</li>
1741 <li>Letters coloured pink in sequence logo when alignment
1742 coloured with clustalx</li>
1743 <li>Choosing fonts without letter symbols defined causes
1744 exceptions and redraw errors</li>
1745 <li>Initial PCA plot view is not same as manually
1746 reconfigured view</li>
1747 <li>Grouped annotation graph label has incorrect line
1749 <li>Grouped annotation graph label display is corrupted
1750 for lots of labels</li>
1755 <div align="center">
1756 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
1759 <td><em>Application</em>
1761 <li>Jalview Desktop News Reader</li>
1762 <li>Tweaked default layout of web services menu</li>
1763 <li>View/alignment association menu to enable user to
1764 easily specify which alignment a multi-structure view takes
1765 its colours/correspondences from</li>
1766 <li>Allow properties file location to be specified as URL</li>
1767 <li>Extend Jalview project to preserve associations
1768 between many alignment views and a single Jmol display</li>
1769 <li>Store annotation row height in Jalview project file</li>
1770 <li>Annotation row column label formatting attributes
1771 stored in project file</li>
1772 <li>Annotation row order for auto-calculated annotation
1773 rows preserved in Jalview project file</li>
1774 <li>Visual progress indication when Jalview state is
1775 saved using Desktop window menu</li>
1776 <li>Visual indication that command line arguments are
1777 still being processed</li>
1778 <li>Groovy script execution from URL</li>
1779 <li>Colour by annotation default min and max colours in
1781 <li>Automatically associate PDB files dragged onto an
1782 alignment with sequences that have high similarity and
1784 <li>Update JGoogleAnalytics to latest release (0.3)</li>
1785 <li>'view structures' option to open many
1786 structures in same window</li>
1787 <li>Sort associated views menu option for tree panel</li>
1788 <li>Group all JABA and non-JABA services for a particular
1789 analysis function in its own submenu</li>
1790 </ul> <em>Applet</em>
1792 <li>Userdefined and autogenerated annotation rows for
1794 <li>Adjustment of alignment annotation pane height</li>
1795 <li>Annotation scrollbar for annotation panel</li>
1796 <li>Drag to reorder annotation rows in annotation panel</li>
1797 <li>'automaticScrolling' parameter</li>
1798 <li>Allow sequences with partial ID string matches to be
1799 annotated from GFF/Jalview features files</li>
1800 <li>Sequence logo annotation row in applet</li>
1801 <li>Absolute paths relative to host server in applet
1802 parameters are treated as such</li>
1803 <li>New in the JalviewLite javascript API:
1805 <li>JalviewLite.js javascript library</li>
1806 <li>Javascript callbacks for
1808 <li>Applet initialisation</li>
1809 <li>Sequence/alignment mouse-overs and selections</li>
1812 <li>scrollTo row and column alignment scrolling
1814 <li>Select sequence/alignment regions from javascript</li>
1815 <li>javascript structure viewer harness to pass
1816 messages between Jmol and Jalview when running as
1817 distinct applets</li>
1818 <li>sortBy method</li>
1819 <li>Set of applet and application examples shipped
1820 with documentation</li>
1821 <li>New example to demonstrate JalviewLite and Jmol
1822 javascript message exchange</li>
1824 </ul> <em>General</em>
1826 <li>Enable Jmol displays to be associated with multiple
1827 multiple alignments</li>
1828 <li>Option to automatically sort alignment with new tree</li>
1829 <li>User configurable link to enable redirects to a
1830 www.Jalview.org mirror</li>
1831 <li>Jmol colours option for Jmol displays</li>
1832 <li>Configurable newline string when writing alignment
1833 and other flat files</li>
1834 <li>Allow alignment annotation description lines to
1835 contain html tags</li>
1836 </ul> <em>Documentation and Development</em>
1838 <li>Add groovy test harness for bulk load testing to
1840 <li>Groovy script to load and align a set of sequences
1841 using a web service before displaying the result in the
1842 Jalview desktop</li>
1843 <li>Restructured javascript and applet api documentation</li>
1844 <li>Ant target to publish example html files with applet
1846 <li>Netbeans project for building Jalview from source</li>
1847 <li>ant task to create online javadoc for Jalview source</li>
1849 <td><em>Application</em>
1851 <li>User defined colourscheme throws exception when
1852 current built in colourscheme is saved as new scheme</li>
1853 <li>AlignFrame->Save in application pops up save
1854 dialog for valid filename/format</li>
1855 <li>Cannot view associated structure for UniProt sequence</li>
1856 <li>PDB file association breaks for UniProt sequence
1858 <li>Associate PDB from file dialog does not tell you
1859 which sequence is to be associated with the file</li>
1860 <li>Find All raises null pointer exception when query
1861 only matches sequence IDs</li>
1862 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
1863 <li>Jalview project with Jmol views created with Jalview
1864 2.4 cannot be loaded</li>
1865 <li>Filetype associations not installed for webstart
1867 <li>Two or more chains in a single PDB file associated
1868 with sequences in different alignments do not get coloured
1869 by their associated sequence</li>
1870 <li>Visibility status of autocalculated annotation row
1871 not preserved when project is loaded</li>
1872 <li>Annotation row height and visibility attributes not
1873 stored in Jalview project</li>
1874 <li>Tree bootstraps are not preserved when saved as a
1875 Jalview project</li>
1876 <li>Envision2 workflow tooltips are corrupted</li>
1877 <li>Enabling show group conservation also enables colour
1878 by conservation</li>
1879 <li>Duplicate group associated conservation or consensus
1880 created on new view</li>
1881 <li>Annotation scrollbar not displayed after 'show
1882 all hidden annotation rows' option selected</li>
1883 <li>Alignment quality not updated after alignment
1884 annotation row is hidden then shown</li>
1885 <li>Preserve colouring of structures coloured by
1886 sequences in pre Jalview 2.7 projects</li>
1887 <li>Web service job parameter dialog is not laid out
1889 <li>Web services menu not refreshed after 'reset
1890 services' button is pressed in preferences</li>
1891 <li>Annotation off by one in Jalview v2_3 example project</li>
1892 <li>Structures imported from file and saved in project
1893 get name like jalview_pdb1234.txt when reloaded</li>
1894 <li>Jalview does not always retrieve progress of a JABAWS
1895 job execution in full once it is complete</li>
1896 </ul> <em>Applet</em>
1898 <li>Alignment height set incorrectly when lots of
1899 annotation rows are displayed</li>
1900 <li>Relative URLs in feature HTML text not resolved to
1902 <li>View follows highlighting does not work for positions
1904 <li><= shown as = in tooltip</li>
1905 <li>Export features raises exception when no features
1907 <li>Separator string used for serialising lists of IDs
1908 for javascript api is modified when separator string
1909 provided as parameter</li>
1910 <li>Null pointer exception when selecting tree leaves for
1911 alignment with no existing selection</li>
1912 <li>Relative URLs for datasources assumed to be relative
1913 to applet's codebase</li>
1914 <li>Status bar not updated after finished searching and
1915 search wraps around to first result</li>
1916 <li>StructureSelectionManager instance shared between
1917 several Jalview applets causes race conditions and memory
1919 <li>Hover tooltip and mouseover of position on structure
1920 not sent from Jmol in applet</li>
1921 <li>Certain sequences of javascript method calls to
1922 applet API fatally hang browser</li>
1923 </ul> <em>General</em>
1925 <li>View follows structure mouseover scrolls beyond
1926 position with wrapped view and hidden regions</li>
1927 <li>Find sequence position moves to wrong residue
1928 with/without hidden columns</li>
1929 <li>Sequence length given in alignment properties window
1931 <li>InvalidNumberFormat exceptions thrown when trying to
1932 import PDB like structure files</li>
1933 <li>Positional search results are only highlighted
1934 between user-supplied sequence start/end bounds</li>
1935 <li>End attribute of sequence is not validated</li>
1936 <li>Find dialog only finds first sequence containing a
1937 given sequence position</li>
1938 <li>Sequence numbering not preserved in MSF alignment
1940 <li>Jalview PDB file reader does not extract sequence
1941 from nucleotide chains correctly</li>
1942 <li>Structure colours not updated when tree partition
1943 changed in alignment</li>
1944 <li>Sequence associated secondary structure not correctly
1945 parsed in interleaved stockholm</li>
1946 <li>Colour by annotation dialog does not restore current
1948 <li>Hiding (nearly) all sequences doesn't work
1950 <li>Sequences containing lowercase letters are not
1951 properly associated with their pdb files</li>
1952 </ul> <em>Documentation and Development</em>
1954 <li>schemas/JalviewWsParamSet.xsd corrupted by
1955 ApplyCopyright tool</li>
1960 <div align="center">
1961 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
1964 <td><em>Application</em>
1966 <li>New warning dialog when the Jalview Desktop cannot
1967 contact web services</li>
1968 <li>JABA service parameters for a preset are shown in
1969 service job window</li>
1970 <li>JABA Service menu entries reworded</li>
1974 <li>Modeller PIR IO broken - cannot correctly import a
1975 pir file emitted by Jalview</li>
1976 <li>Existing feature settings transferred to new
1977 alignment view created from cut'n'paste</li>
1978 <li>Improved test for mixed amino/nucleotide chains when
1979 parsing PDB files</li>
1980 <li>Consensus and conservation annotation rows
1981 occasionally become blank for all new windows</li>
1982 <li>Exception raised when right clicking above sequences
1983 in wrapped view mode</li>
1984 </ul> <em>Application</em>
1986 <li>multiple multiply aligned structure views cause cpu
1987 usage to hit 100% and computer to hang</li>
1988 <li>Web Service parameter layout breaks for long user
1989 parameter names</li>
1990 <li>Jaba service discovery hangs desktop if Jaba server
1997 <div align="center">
1998 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2001 <td><em>Application</em>
2003 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2004 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2007 <li>Web Services preference tab</li>
2008 <li>Analysis parameters dialog box and user defined
2010 <li>Improved speed and layout of Envision2 service menu</li>
2011 <li>Superpose structures using associated sequence
2013 <li>Export coordinates and projection as CSV from PCA
2015 </ul> <em>Applet</em>
2017 <li>enable javascript: execution by the applet via the
2018 link out mechanism</li>
2019 </ul> <em>Other</em>
2021 <li>Updated the Jmol Jalview interface to work with Jmol
2023 <li>The Jalview Desktop and JalviewLite applet now
2024 require Java 1.5</li>
2025 <li>Allow Jalview feature colour specification for GFF
2026 sequence annotation files</li>
2027 <li>New 'colour by label' keword in Jalview feature file
2028 type colour specification</li>
2029 <li>New Jalview Desktop Groovy API method that allows a
2030 script to check if it being run in an interactive session or
2031 in a batch operation from the Jalview command line</li>
2035 <li>clustalx colourscheme colours Ds preferentially when
2036 both D+E are present in over 50% of the column</li>
2037 </ul> <em>Application</em>
2039 <li>typo in AlignmentFrame->View->Hide->all but
2040 selected Regions menu item</li>
2041 <li>sequence fetcher replaces ',' for ';' when the ',' is
2042 part of a valid accession ID</li>
2043 <li>fatal OOM if object retrieved by sequence fetcher
2044 runs out of memory</li>
2045 <li>unhandled Out of Memory Error when viewing pca
2046 analysis results</li>
2047 <li>InstallAnywhere builds fail to launch on OS X java
2048 10.5 update 4 (due to apple Java 1.6 update)</li>
2049 <li>Installanywhere Jalview silently fails to launch</li>
2050 </ul> <em>Applet</em>
2052 <li>Jalview.getFeatureGroups() raises an
2053 ArrayIndexOutOfBoundsException if no feature groups are
2060 <div align="center">
2061 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2067 <li>Alignment prettyprinter doesn't cope with long
2069 <li>clustalx colourscheme colours Ds preferentially when
2070 both D+E are present in over 50% of the column</li>
2071 <li>nucleic acid structures retrieved from PDB do not
2072 import correctly</li>
2073 <li>More columns get selected than were clicked on when a
2074 number of columns are hidden</li>
2075 <li>annotation label popup menu not providing correct
2076 add/hide/show options when rows are hidden or none are
2078 <li>Stockholm format shown in list of readable formats,
2079 and parser copes better with alignments from RFAM.</li>
2080 <li>CSV output of consensus only includes the percentage
2081 of all symbols if sequence logo display is enabled</li>
2083 </ul> <em>Applet</em>
2085 <li>annotation panel disappears when annotation is
2087 </ul> <em>Application</em>
2089 <li>Alignment view not redrawn properly when new
2090 alignment opened where annotation panel is visible but no
2091 annotations are present on alignment</li>
2092 <li>pasted region containing hidden columns is
2093 incorrectly displayed in new alignment window</li>
2094 <li>Jalview slow to complete operations when stdout is
2095 flooded (fix is to close the Jalview console)</li>
2096 <li>typo in AlignmentFrame->View->Hide->all but
2097 selected Rregions menu item.</li>
2098 <li>inconsistent group submenu and Format submenu entry
2099 'Un' or 'Non'conserved</li>
2100 <li>Sequence feature settings are being shared by
2101 multiple distinct alignments</li>
2102 <li>group annotation not recreated when tree partition is
2104 <li>double click on group annotation to select sequences
2105 does not propagate to associated trees</li>
2106 <li>Mac OSX specific issues:
2108 <li>exception raised when mouse clicked on desktop
2109 window background</li>
2110 <li>Desktop menu placed on menu bar and application
2111 name set correctly</li>
2112 <li>sequence feature settings not wide enough for the
2113 save feature colourscheme button</li>
2122 <div align="center">
2123 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2126 <td><em>New Capabilities</em>
2128 <li>URL links generated from description line for
2129 regular-expression based URL links (applet and application)
2136 <li>Non-positional feature URL links are shown in link
2138 <li>Linked viewing of nucleic acid sequences and
2140 <li>Automatic Scrolling option in View menu to display
2141 the currently highlighted region of an alignment.</li>
2142 <li>Order an alignment by sequence length, or using the
2143 average score or total feature count for each sequence.</li>
2144 <li>Shading features by score or associated description</li>
2145 <li>Subdivide alignment and groups based on identity of
2146 selected subsequence (Make Groups from Selection).</li>
2147 <li>New hide/show options including Shift+Control+H to
2148 hide everything but the currently selected region.</li>
2149 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2150 </ul> <em>Application</em>
2152 <li>Fetch DB References capabilities and UI expanded to
2153 support retrieval from DAS sequence sources</li>
2154 <li>Local DAS Sequence sources can be added via the
2155 command line or via the Add local source dialog box.</li>
2156 <li>DAS Dbref and DbxRef feature types are parsed as
2157 database references and protein_name is parsed as
2158 description line (BioSapiens terms).</li>
2159 <li>Enable or disable non-positional feature and database
2160 references in sequence ID tooltip from View menu in
2162 <!-- <li>New hidden columns and rows and representatives capabilities
2163 in annotations file (in progress - not yet fully implemented)</li> -->
2164 <li>Group-associated consensus, sequence logos and
2165 conservation plots</li>
2166 <li>Symbol distributions for each column can be exported
2167 and visualized as sequence logos</li>
2168 <li>Optionally scale multi-character column labels to fit
2169 within each column of annotation row<!-- todo for applet -->
2171 <li>Optional automatic sort of associated alignment view
2172 when a new tree is opened.</li>
2173 <li>Jalview Java Console</li>
2174 <li>Better placement of desktop window when moving
2175 between different screens.</li>
2176 <li>New preference items for sequence ID tooltip and
2177 consensus annotation</li>
2178 <li>Client to submit sequences and IDs to Envision2
2180 <li><em>Vamsas Capabilities</em>
2182 <li>Improved VAMSAS synchronization (Jalview archive
2183 used to preserve views, structures, and tree display
2185 <li>Import of vamsas documents from disk or URL via
2187 <li>Sharing of selected regions between views and
2188 with other VAMSAS applications (Experimental feature!)</li>
2189 <li>Updated API to VAMSAS version 0.2</li>
2191 </ul> <em>Applet</em>
2193 <li>Middle button resizes annotation row height</li>
2196 <li>sortByTree (true/false) - automatically sort the
2197 associated alignment view by the tree when a new tree is
2199 <li>showTreeBootstraps (true/false) - show or hide
2200 branch bootstraps (default is to show them if available)</li>
2201 <li>showTreeDistances (true/false) - show or hide
2202 branch lengths (default is to show them if available)</li>
2203 <li>showUnlinkedTreeNodes (true/false) - indicate if
2204 unassociated nodes should be highlighted in the tree
2206 <li>heightScale and widthScale (1.0 or more) -
2207 increase the height or width of a cell in the alignment
2208 grid relative to the current font size.</li>
2211 <li>Non-positional features displayed in sequence ID
2213 </ul> <em>Other</em>
2215 <li>Features format: graduated colour definitions and
2216 specification of feature scores</li>
2217 <li>Alignment Annotations format: new keywords for group
2218 associated annotation (GROUP_REF) and annotation row display
2219 properties (ROW_PROPERTIES)</li>
2220 <li>XML formats extended to support graduated feature
2221 colourschemes, group associated annotation, and profile
2222 visualization settings.</li></td>
2225 <li>Source field in GFF files parsed as feature source
2226 rather than description</li>
2227 <li>Non-positional features are now included in sequence
2228 feature and gff files (controlled via non-positional feature
2229 visibility in tooltip).</li>
2230 <li>URL links generated for all feature links (bugfix)</li>
2231 <li>Added URL embedding instructions to features file
2233 <li>Codons containing ambiguous nucleotides translated as
2234 'X' in peptide product</li>
2235 <li>Match case switch in find dialog box works for both
2236 sequence ID and sequence string and query strings do not
2237 have to be in upper case to match case-insensitively.</li>
2238 <li>AMSA files only contain first column of
2239 multi-character column annotation labels</li>
2240 <li>Jalview Annotation File generation/parsing consistent
2241 with documentation (e.g. Stockholm annotation can be
2242 exported and re-imported)</li>
2243 <li>PDB files without embedded PDB IDs given a friendly
2245 <li>Find incrementally searches ID string matches as well
2246 as subsequence matches, and correctly reports total number
2250 <li>Better handling of exceptions during sequence
2252 <li>Dasobert generated non-positional feature URL
2253 link text excludes the start_end suffix</li>
2254 <li>DAS feature and source retrieval buttons disabled
2255 when fetch or registry operations in progress.</li>
2256 <li>PDB files retrieved from URLs are cached properly</li>
2257 <li>Sequence description lines properly shared via
2259 <li>Sequence fetcher fetches multiple records for all
2261 <li>Ensured that command line das feature retrieval
2262 completes before alignment figures are generated.</li>
2263 <li>Reduced time taken when opening file browser for
2265 <li>isAligned check prior to calculating tree, PCA or
2266 submitting an MSA to JNet now excludes hidden sequences.</li>
2267 <li>User defined group colours properly recovered
2268 from Jalview projects.</li>
2277 <div align="center">
2278 <strong>2.4.0.b2</strong><br> 28/10/2009
2283 <li>Experimental support for google analytics usage
2285 <li>Jalview privacy settings (user preferences and docs).</li>
2290 <li>Race condition in applet preventing startup in
2292 <li>Exception when feature created from selection beyond
2293 length of sequence.</li>
2294 <li>Allow synthetic PDB files to be imported gracefully</li>
2295 <li>Sequence associated annotation rows associate with
2296 all sequences with a given id</li>
2297 <li>Find function matches case-insensitively for sequence
2298 ID string searches</li>
2299 <li>Non-standard characters do not cause pairwise
2300 alignment to fail with exception</li>
2301 </ul> <em>Application Issues</em>
2303 <li>Sequences are now validated against EMBL database</li>
2304 <li>Sequence fetcher fetches multiple records for all
2306 </ul> <em>InstallAnywhere Issues</em>
2308 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2309 issue with installAnywhere mechanism)</li>
2310 <li>Command line launching of JARs from InstallAnywhere
2311 version (java class versioning error fixed)</li>
2318 <div align="center">
2319 <strong>2.4</strong><br> 27/8/2008
2322 <td><em>User Interface</em>
2324 <li>Linked highlighting of codon and amino acid from
2325 translation and protein products</li>
2326 <li>Linked highlighting of structure associated with
2327 residue mapping to codon position</li>
2328 <li>Sequence Fetcher provides example accession numbers
2329 and 'clear' button</li>
2330 <li>MemoryMonitor added as an option under Desktop's
2332 <li>Extract score function to parse whitespace separated
2333 numeric data in description line</li>
2334 <li>Column labels in alignment annotation can be centred.</li>
2335 <li>Tooltip for sequence associated annotation give name
2337 </ul> <em>Web Services and URL fetching</em>
2339 <li>JPred3 web service</li>
2340 <li>Prototype sequence search client (no public services
2342 <li>Fetch either seed alignment or full alignment from
2344 <li>URL Links created for matching database cross
2345 references as well as sequence ID</li>
2346 <li>URL Links can be created using regular-expressions</li>
2347 </ul> <em>Sequence Database Connectivity</em>
2349 <li>Retrieval of cross-referenced sequences from other
2351 <li>Generalised database reference retrieval and
2352 validation to all fetchable databases</li>
2353 <li>Fetch sequences from DAS sources supporting the
2354 sequence command</li>
2355 </ul> <em>Import and Export</em>
2356 <li>export annotation rows as CSV for spreadsheet import</li>
2357 <li>Jalview projects record alignment dataset associations,
2358 EMBL products, and cDNA sequence mappings</li>
2359 <li>Sequence Group colour can be specified in Annotation
2361 <li>Ad-hoc colouring of group in Annotation File using RGB
2362 triplet as name of colourscheme</li>
2363 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2365 <li>treenode binding for VAMSAS tree exchange</li>
2366 <li>local editing and update of sequences in VAMSAS
2367 alignments (experimental)</li>
2368 <li>Create new or select existing session to join</li>
2369 <li>load and save of vamsas documents</li>
2370 </ul> <em>Application command line</em>
2372 <li>-tree parameter to open trees (introduced for passing
2374 <li>-fetchfrom command line argument to specify nicknames
2375 of DAS servers to query for alignment features</li>
2376 <li>-dasserver command line argument to add new servers
2377 that are also automatically queried for features</li>
2378 <li>-groovy command line argument executes a given groovy
2379 script after all input data has been loaded and parsed</li>
2380 </ul> <em>Applet-Application data exchange</em>
2382 <li>Trees passed as applet parameters can be passed to
2383 application (when using "View in full
2384 application")</li>
2385 </ul> <em>Applet Parameters</em>
2387 <li>feature group display control parameter</li>
2388 <li>debug parameter</li>
2389 <li>showbutton parameter</li>
2390 </ul> <em>Applet API methods</em>
2392 <li>newView public method</li>
2393 <li>Window (current view) specific get/set public methods</li>
2394 <li>Feature display control methods</li>
2395 <li>get list of currently selected sequences</li>
2396 </ul> <em>New Jalview distribution features</em>
2398 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2399 <li>RELEASE file gives build properties for the latest
2400 Jalview release.</li>
2401 <li>Java 1.1 Applet build made easier and donotobfuscate
2402 property controls execution of obfuscator</li>
2403 <li>Build target for generating source distribution</li>
2404 <li>Debug flag for javacc</li>
2405 <li>.jalview_properties file is documented (slightly) in
2406 jalview.bin.Cache</li>
2407 <li>Continuous Build Integration for stable and
2408 development version of Application, Applet and source
2413 <li>selected region output includes visible annotations
2414 (for certain formats)</li>
2415 <li>edit label/displaychar contains existing label/char
2417 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2418 <li>shorter peptide product names from EMBL records</li>
2419 <li>Newick string generator makes compact representations</li>
2420 <li>bootstrap values parsed correctly for tree files with
2422 <li>pathological filechooser bug avoided by not allowing
2423 filenames containing a ':'</li>
2424 <li>Fixed exception when parsing GFF files containing
2425 global sequence features</li>
2426 <li>Alignment datasets are finalized only when number of
2427 references from alignment sequences goes to zero</li>
2428 <li>Close of tree branch colour box without colour
2429 selection causes cascading exceptions</li>
2430 <li>occasional negative imgwidth exceptions</li>
2431 <li>better reporting of non-fatal warnings to user when
2432 file parsing fails.</li>
2433 <li>Save works when Jalview project is default format</li>
2434 <li>Save as dialog opened if current alignment format is
2435 not a valid output format</li>
2436 <li>UniProt canonical names introduced for both das and
2438 <li>Histidine should be midblue (not pink!) in Zappo</li>
2439 <li>error messages passed up and output when data read
2441 <li>edit undo recovers previous dataset sequence when
2442 sequence is edited</li>
2443 <li>allow PDB files without pdb ID HEADER lines (like
2444 those generated by MODELLER) to be read in properly</li>
2445 <li>allow reading of JPred concise files as a normal
2447 <li>Stockholm annotation parsing and alignment properties
2448 import fixed for PFAM records</li>
2449 <li>Structure view windows have correct name in Desktop
2451 <li>annotation consisting of sequence associated scores
2452 can be read and written correctly to annotation file</li>
2453 <li>Aligned cDNA translation to aligned peptide works
2455 <li>Fixed display of hidden sequence markers and
2456 non-italic font for representatives in Applet</li>
2457 <li>Applet Menus are always embedded in applet window on
2459 <li>Newly shown features appear at top of stack (in
2461 <li>Annotations added via parameter not drawn properly
2462 due to null pointer exceptions</li>
2463 <li>Secondary structure lines are drawn starting from
2464 first column of alignment</li>
2465 <li>UniProt XML import updated for new schema release in
2467 <li>Sequence feature to sequence ID match for Features
2468 file is case-insensitive</li>
2469 <li>Sequence features read from Features file appended to
2470 all sequences with matching IDs</li>
2471 <li>PDB structure coloured correctly for associated views
2472 containing a sub-sequence</li>
2473 <li>PDB files can be retrieved by applet from Jar files</li>
2474 <li>feature and annotation file applet parameters
2475 referring to different directories are retrieved correctly</li>
2476 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
2477 <li>Fixed application hang whilst waiting for
2478 splash-screen version check to complete</li>
2479 <li>Applet properly URLencodes input parameter values
2480 when passing them to the launchApp service</li>
2481 <li>display name and local features preserved in results
2482 retrieved from web service</li>
2483 <li>Visual delay indication for sequence retrieval and
2484 sequence fetcher initialisation</li>
2485 <li>updated Application to use DAS 1.53e version of
2486 dasobert DAS client</li>
2487 <li>Re-instated Full AMSA support and .amsa file
2489 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
2497 <div align="center">
2498 <strong>2.3</strong><br> 9/5/07
2503 <li>Jmol 11.0.2 integration</li>
2504 <li>PDB views stored in Jalview XML files</li>
2505 <li>Slide sequences</li>
2506 <li>Edit sequence in place</li>
2507 <li>EMBL CDS features</li>
2508 <li>DAS Feature mapping</li>
2509 <li>Feature ordering</li>
2510 <li>Alignment Properties</li>
2511 <li>Annotation Scores</li>
2512 <li>Sort by scores</li>
2513 <li>Feature/annotation editing in applet</li>
2518 <li>Headless state operation in 2.2.1</li>
2519 <li>Incorrect and unstable DNA pairwise alignment</li>
2520 <li>Cut and paste of sequences with annotation</li>
2521 <li>Feature group display state in XML</li>
2522 <li>Feature ordering in XML</li>
2523 <li>blc file iteration selection using filename # suffix</li>
2524 <li>Stockholm alignment properties</li>
2525 <li>Stockhom alignment secondary structure annotation</li>
2526 <li>2.2.1 applet had no feature transparency</li>
2527 <li>Number pad keys can be used in cursor mode</li>
2528 <li>Structure Viewer mirror image resolved</li>
2535 <div align="center">
2536 <strong>2.2.1</strong><br> 12/2/07
2541 <li>Non standard characters can be read and displayed
2542 <li>Annotations/Features can be imported/exported to the
2544 <li>Applet allows editing of sequence/annotation/group
2545 name & description
2546 <li>Preference setting to display sequence name in
2548 <li>Annotation file format extended to allow
2549 Sequence_groups to be defined
2550 <li>Default opening of alignment overview panel can be
2551 specified in preferences
2552 <li>PDB residue numbering annotation added to associated
2558 <li>Applet crash under certain Linux OS with Java 1.6
2560 <li>Annotation file export / import bugs fixed
2561 <li>PNG / EPS image output bugs fixed
2567 <div align="center">
2568 <strong>2.2</strong><br> 27/11/06
2573 <li>Multiple views on alignment
2574 <li>Sequence feature editing
2575 <li>"Reload" alignment
2576 <li>"Save" to current filename
2577 <li>Background dependent text colour
2578 <li>Right align sequence ids
2579 <li>User-defined lower case residue colours
2582 <li>Menu item accelerator keys
2583 <li>Control-V pastes to current alignment
2584 <li>Cancel button for DAS Feature Fetching
2585 <li>PCA and PDB Viewers zoom via mouse roller
2586 <li>User-defined sub-tree colours and sub-tree selection
2593 <li>'New Window' button on the 'Output to Text box'
2598 <li>New memory efficient Undo/Redo System
2599 <li>Optimised symbol lookups and conservation/consensus
2601 <li>Region Conservation/Consensus recalculated after
2603 <li>Fixed Remove Empty Columns Bug (empty columns at end
2605 <li>Slowed DAS Feature Fetching for increased robustness.
2612 <li>Made angle brackets in ASCII feature descriptions
2614 <li>Re-instated Zoom function for PCA
2615 <li>Sequence descriptions conserved in web service
2617 <li>UniProt ID discoverer uses any word separated by
2619 <li>WsDbFetch query/result association resolved
2620 <li>Tree leaf to sequence mapping improved
2621 <li>Smooth fonts switch moved to FontChooser dialog box.
2633 <div align="center">
2634 <strong>2.1.1</strong><br> 12/9/06
2639 <li>Copy consensus sequence to clipboard</li>
2644 <li>Image output - rightmost residues are rendered if
2645 sequence id panel has been resized</li>
2646 <li>Image output - all offscreen group boundaries are
2648 <li>Annotation files with sequence references - all
2649 elements in file are relative to sequence position</li>
2650 <li>Mac Applet users can use Alt key for group editing</li>
2656 <div align="center">
2657 <strong>2.1</strong><br> 22/8/06
2662 <li>MAFFT Multiple Alignment in default Web Service list</li>
2663 <li>DAS Feature fetching</li>
2664 <li>Hide sequences and columns</li>
2665 <li>Export Annotations and Features</li>
2666 <li>GFF file reading / writing</li>
2667 <li>Associate structures with sequences from local PDB
2669 <li>Add sequences to exisiting alignment</li>
2670 <li>Recently opened files / URL lists</li>
2671 <li>Applet can launch the full application</li>
2672 <li>Applet has transparency for features (Java 1.2
2674 <li>Applet has user defined colours parameter</li>
2675 <li>Applet can load sequences from parameter
2676 "sequence<em>x</em>"
2682 <li>Redundancy Panel reinstalled in the Applet</li>
2683 <li>Monospaced font - EPS / rescaling bug fixed</li>
2684 <li>Annotation files with sequence references bug fixed</li>
2690 <div align="center">
2691 <strong>2.08.1</strong><br> 2/5/06
2696 <li>Change case of selected region from Popup menu</li>
2697 <li>Choose to match case when searching</li>
2698 <li>Middle mouse button and mouse movement can compress /
2699 expand the visible width and height of the alignment</li>
2704 <li>Annotation Panel displays complete JNet results</li>
2710 <div align="center">
2711 <strong>2.08b</strong><br> 18/4/06
2717 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
2718 <li>Righthand label on wrapped alignments shows correct
2725 <div align="center">
2726 <strong>2.08</strong><br> 10/4/06
2731 <li>Editing can be locked to the selection area</li>
2732 <li>Keyboard editing</li>
2733 <li>Create sequence features from searches</li>
2734 <li>Precalculated annotations can be loaded onto
2736 <li>Features file allows grouping of features</li>
2737 <li>Annotation Colouring scheme added</li>
2738 <li>Smooth fonts off by default - Faster rendering</li>
2739 <li>Choose to toggle Autocalculate Consensus On/Off</li>
2744 <li>Drag & Drop fixed on Linux</li>
2745 <li>Jalview Archive file faster to load/save, sequence
2746 descriptions saved.</li>
2752 <div align="center">
2753 <strong>2.07</strong><br> 12/12/05
2758 <li>PDB Structure Viewer enhanced</li>
2759 <li>Sequence Feature retrieval and display enhanced</li>
2760 <li>Choose to output sequence start-end after sequence
2761 name for file output</li>
2762 <li>Sequence Fetcher WSDBFetch@EBI</li>
2763 <li>Applet can read feature files, PDB files and can be
2764 used for HTML form input</li>
2769 <li>HTML output writes groups and features</li>
2770 <li>Group editing is Control and mouse click</li>
2771 <li>File IO bugs</li>
2777 <div align="center">
2778 <strong>2.06</strong><br> 28/9/05
2783 <li>View annotations in wrapped mode</li>
2784 <li>More options for PCA viewer</li>
2789 <li>GUI bugs resolved</li>
2790 <li>Runs with -nodisplay from command line</li>
2796 <div align="center">
2797 <strong>2.05b</strong><br> 15/9/05
2802 <li>Choose EPS export as lineart or text</li>
2803 <li>Jar files are executable</li>
2804 <li>Can read in Uracil - maps to unknown residue</li>
2809 <li>Known OutOfMemory errors give warning message</li>
2810 <li>Overview window calculated more efficiently</li>
2811 <li>Several GUI bugs resolved</li>
2817 <div align="center">
2818 <strong>2.05</strong><br> 30/8/05
2823 <li>Edit and annotate in "Wrapped" view</li>
2828 <li>Several GUI bugs resolved</li>
2834 <div align="center">
2835 <strong>2.04</strong><br> 24/8/05
2840 <li>Hold down mouse wheel & scroll to change font
2846 <li>Improved JPred client reliability</li>
2847 <li>Improved loading of Jalview files</li>
2853 <div align="center">
2854 <strong>2.03</strong><br> 18/8/05
2859 <li>Set Proxy server name and port in preferences</li>
2860 <li>Multiple URL links from sequence ids</li>
2861 <li>User Defined Colours can have a scheme name and added
2863 <li>Choose to ignore gaps in consensus calculation</li>
2864 <li>Unix users can set default web browser</li>
2865 <li>Runs without GUI for batch processing</li>
2866 <li>Dynamically generated Web Service Menus</li>
2871 <li>InstallAnywhere download for Sparc Solaris</li>
2877 <div align="center">
2878 <strong>2.02</strong><br> 18/7/05
2884 <li>Copy & Paste order of sequences maintains
2885 alignment order.</li>
2891 <div align="center">
2892 <strong>2.01</strong><br> 12/7/05
2897 <li>Use delete key for deleting selection.</li>
2898 <li>Use Mouse wheel to scroll sequences.</li>
2899 <li>Help file updated to describe how to add alignment
2901 <li>Version and build date written to build properties
2903 <li>InstallAnywhere installation will check for updates
2904 at launch of Jalview.</li>
2909 <li>Delete gaps bug fixed.</li>
2910 <li>FileChooser sorts columns.</li>
2911 <li>Can remove groups one by one.</li>
2912 <li>Filechooser icons installed.</li>
2913 <li>Finder ignores return character when searching.
2914 Return key will initiate a search.<br>
2921 <div align="center">
2922 <strong>2.0</strong><br> 20/6/05
2927 <li>New codebase</li>