3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
34 /* separate the items from eachother */
40 /* doesnt get processed in javahelp */
50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.2">2.10.2</a><br />
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 BLOSUM/Clustal type shading schemes can be created via groovy scripts</li>
83 <li><!-- JAL-2314, -->Test suite expanded and debugged (over 940 functional unit tests, only 3 failing due to ongoing work!)
88 <li><!-- JAL-1596 -->Faster Chimera/Jalview communication by file-based command exchange</li>
89 <li><!-- JAL-2316, -->URLs for viewing database cross-references provided by identifiers.org and the EMBL-EBI's MIRIAM DB</li>
96 </div></td><td><div align="left">
99 <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>
100 <li><!-- JAL-2430 -->Hidden regions in alignment views are not coloured in linked structure views</li>
101 <li><!-- JAL-2419 -->Current selection lost if popup menu opened on a region of alignment without groups</li>
102 <li><!-- JAL-2374 -->Popup menu not always shown for regions of an alignment with overlapping groups</li>
103 <li><!-- JAL-2310 -->Finder double counts if both a sequence's name and description match</li>
104 <li><!-- JAL-2370 -->Hiding column selection containing two hidden regions results in incorrect hidden regions</li>
105 <li><!-- JAL-2377 -->PCA calculation could hang when generating output report when working with highly redundant alignments</li>
106 <li><!-- JAL-2365 -->Cannot configure feature colours with lightGray or darkGray via features file</li>
107 <li><!-- JAL-2421 -->Overview window visible region moves erratically when hidden rows or columns are present</li>
108 <li><!-- JAL-2362 -->Per-residue colourschemes applied via the Structure Viewer's colour menu don't correspond to sequence colouring</li>
109 <li><!-- JAL-2405 -->Protein specific colours only offered in colour and group colour menu for protein alignments</li>
110 <li><!-- JAL-2386 -->'Apply to all groups' setting when changing colour does not apply Conservation slider value to all groups</li>
114 <li><!-- JAL-2401 -->Easier creation of colours for all 'Lower case' residues (button in colourscheme editor debugged and new documentation and tooltips added)</li>
115 <li><!-- JAL-2399-->Text colour threshold's 'Cancel' button doesn't restore group-specific text colour thresholds</li>
116 <li><!-- JAL-2243 -->Feature settings panel does not update as new features are added to alignment</li>
117 <li><!-- JAL-2436 -->Structure viewer's View -> Colour By view selection menu changes colours of alignment views</li>
118 <li><!-- JAL-2366 -->Proxy server address and port always appear enabled in Preferences->Connections</li>
119 <li><!-- JAL-2426 -->Spurious exceptions in console raised from alignment calculation workers after alignment has been closed</li>
120 <li><!-- JAL-1608 -->Typo in selection popup menu - Create groups now 'Create Group'</li>
121 <li><!-- JAL-1608 -->CMD/CTRL and G or Shift G for Create/Undefine group doesn't always work</li>
122 <li><!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get shown again after pressing 'Cancel'</li>
123 <li><!-- JAL-2461 -->DAS registry not found exceptions removed from console output</li>
128 <li><!-- JAL-2442 -->Features not rendered as transparent on overview or linked structure view</li>
129 <li><!-- JAL-2372 -->Colour group by conservation doesn't work (since 2.8)</li>
131 <em>New Known Issues</em>
138 <td width="60" nowrap>
140 <strong><a name="Jalview.2.10.1">2.10.1</a><br />
141 <em>29/11/2016</em></strong>
144 <td><div align="left">
148 <!-- JAL-98 -->Improved memory usage: sparse arrays used
149 for all consensus calculations
152 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released 3rd Oct 2016)
154 <li>Updated Jalview's Certum code signing certificate
160 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
161 set of database cross-references, sorted alphabetically
164 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
165 from database cross references. Users with custom links
166 will receive a <a href="webServices/urllinks.html#warning">warning
167 dialog</a> asking them to update their preferences.
170 <!-- JAL-2287-->Cancel button and escape listener on
171 dialog warning user about disconnecting Jalview from a
175 <!-- JAL-2320-->Jalview's Chimera control window closes if
176 the Chimera it is connected to is shut down
179 <!-- JAL-1738-->New keystroke (B) and Select highlighted
180 columns menu item to mark columns containing
181 highlighted regions (e.g. from structure selections or results
185 <!-- JAL-2284-->Command line option for batch-generation
186 of HTML pages rendering alignment data with the BioJS
196 <!-- JAL-2286 -->Columns with more than one modal residue
197 are not coloured or thresholded according to percent
198 identity (first observed in Jalview 2.8.2)
201 <!-- JAL-2301 -->Threonine incorrectly reported as not
205 <!-- JAL-2318 -->Updates to documentation pages (above PID
206 threshold, amino acid properties)
209 <!-- JAL-2292 -->Lower case residues in sequences are not
210 reported as mapped to residues in a structure file in the
214 <!--JAL-2324 -->Identical features with non-numeric scores
215 could be added multiple times to a sequence
218 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
219 bond features shown as two highlighted residues rather
220 than a range in linked structure views, and treated
221 correctly when selecting and computing trees from features
224 <!-- JAL-2281-->Custom URL links for database
225 cross-references are matched to database name regardless
233 <!-- JAL-2282-->Custom URL links for specific database
234 names without regular expressions also offer links from
238 <!-- JAL-2315-->Removing a single configured link in the
239 URL links pane in Connections preferences doesn't actually
240 update Jalview configuration
243 <!-- JAL-2272-->CTRL-Click on a selected region to open
244 the alignment area popup menu doesn't work on El-Capitan
247 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
248 files with similarly named sequences if dropped onto the
252 <!-- JAL-2312 -->Additional mappings are shown for PDB
253 entries where more chains exist in the PDB accession than
254 are reported in the SIFTS file
257 <!-- JAL-2317-->Certain structures do not get mapped to
258 the structure view when displayed with Chimera
261 <!-- JAL-2317-->No chains shown in the Chimera view
262 panel's View->Show Chains submenu
265 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
266 work for wrapped alignment views
269 <!--JAL-2197 -->Rename UI components for running JPred
270 predictions from 'JNet' to 'JPred'
273 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
274 corrupted when annotation panel vertical scroll is not at
278 <!--JAL-2332 -->Attempting to view structure for Hen
279 lysozyme results in a PDB Client error dialog box
282 <!-- JAL-2319 -->Structure View's mapping report switched ranges for PDB and sequence for SIFTS</li>
283 <!-- JAL-2319 -->SIFTS 'Not_Observed' residues mapped to non-existant coordindate data</li>
285 <!-- <em>New Known Issues</em>
292 <td width="60" nowrap>
294 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
295 <em>25/10/2016</em></strong>
298 <td><em>Application</em>
300 <li>3D Structure chooser opens with 'Cached structures'
301 view if structures already loaded</li>
302 <li>Progress bar reports models as they are loaded to
309 <li>Colour by conservation always enabled and no tick
310 shown in menu when BLOSUM or PID shading applied</li>
311 <li>FER1_ARATH and FER2_ARATH labels were switched in
312 example sequences/projects/trees</li>
316 <li>Jalview projects with views of local PDB structure
317 files saved on Windows cannot be opened on OSX</li>
318 <li>Multiple structure views can be opened and
319 superposed without timeout for structures with multiple
320 models or multiple sequences in alignment</li>
321 <li>Cannot import or associated local PDB files without
322 a PDB ID HEADER line</li>
323 <li>RMSD is not output in Jmol console when
324 superposition is performed</li>
325 <li>Drag and drop of URL from Browser fails for Linux
326 and OSX versions earlier than El Capitan</li>
327 <li>ENA client ignores invalid content from ENA server</li>
328 <li>Exceptions are not raised in console when ENA
329 client attempts to fetch non-existent IDs via Fetch DB
331 <li>Exceptions are not raised in console when a new
332 view is created on the alignment</li>
333 <li>OSX right-click fixed for group selections:
334 CMD-click to insert/remove gaps in groups and CTRL-click
335 to open group pop-up menu</li>
337 <em>Build and deployment</em>
339 <li>URL link checker now copes with multi-line anchor
342 <em>New Known Issues</em>
344 <li>Drag and drop from URL links in browsers do not
351 <td width="60" nowrap>
353 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
359 <!-- JAL-2124 -->Updated Spanish translations.
362 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
363 for importing structure data to Jalview. Enables mmCIF and
367 <!-- JAL-192 --->Alignment ruler shows positions relative to
371 <!-- JAL-2202 -->Position/residue shown in status bar when
372 mousing over sequence associated annotation
375 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
379 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
380 '()', canonical '[]' and invalid '{}' base pair populations
384 <!-- JAL-2092 -->Feature settings popup menu options for
385 showing or hiding columns containing a feature
388 <!-- JAL-1557 -->Edit selected group by double clicking on
389 group and sequence associated annotation labels
392 <!-- JAL-2236 -->Sequence name added to annotation label in
393 select/hide columns by annotation and colour by annotation
397 </ul> <em>Application</em>
400 <!-- JAL-2050-->Automatically hide introns when opening a
404 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
408 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
409 structure mappings with the EMBL-EBI PDBe SIFTS database
412 <!-- JAL-2079 -->Updated download sites used for Rfam and
413 Pfam sources to xfam.org
416 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
419 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
420 over sequences in Jalview
423 <!-- JAL-2027-->Support for reverse-complement coding
424 regions in ENA and EMBL
427 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
428 for record retrieval via ENA rest API
431 <!-- JAL-2027 -->Support for ENA CDS records with reverse
435 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
436 groovy script execution
439 <!-- JAL-1812 -->New 'execute Groovy script' option in an
440 alignment window's Calculate menu
443 <!-- JAL-1812 -->Allow groovy scripts that call
444 Jalview.getAlignFrames() to run in headless mode
447 <!-- JAL-2068 -->Support for creating new alignment
448 calculation workers from groovy scripts
451 <!-- JAL-1369 --->Store/restore reference sequence in
455 <!-- JAL-1803 -->Chain codes for a sequence's PDB
456 associations are now saved/restored from project
459 <!-- JAL-1993 -->Database selection dialog always shown
460 before sequence fetcher is opened
463 <!-- JAL-2183 -->Double click on an entry in Jalview's
464 database chooser opens a sequence fetcher
467 <!-- JAL-1563 -->Free-text search client for UniProt using
471 <!-- JAL-2168 -->-nonews command line parameter to prevent
472 the news reader opening
475 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
476 querying stored in preferences
479 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
483 <!-- JAL-1977-->Tooltips shown on database chooser
486 <!-- JAL-391 -->Reverse complement function in calculate
487 menu for nucleotide sequences
490 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
491 and feature counts preserves alignment ordering (and
492 debugged for complex feature sets).
495 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
496 viewing structures with Jalview 2.10
499 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
500 genome, transcript CCDS and gene ids via the Ensembl and
501 Ensembl Genomes REST API
504 <!-- JAL-2049 -->Protein sequence variant annotation
505 computed for 'sequence_variant' annotation on CDS regions
509 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
513 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
514 Ref Fetcher fails to match, or otherwise updates sequence
515 data from external database records.
518 <!-- JAL-2154 -->Revised Jalview Project format for
519 efficient recovery of sequence coding and alignment
520 annotation relationships.
522 </ul> <!-- <em>Applet</em>
533 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
537 <!-- JAL-2018-->Export features in Jalview format (again)
538 includes graduated colourschemes
541 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
542 working with big alignments and lots of hidden columns
545 <!-- JAL-2053-->Hidden column markers not always rendered
546 at right of alignment window
549 <!-- JAL-2067 -->Tidied up links in help file table of
553 <!-- JAL-2072 -->Feature based tree calculation not shown
557 <!-- JAL-2075 -->Hidden columns ignored during feature
558 based tree calculation
561 <!-- JAL-2065 -->Alignment view stops updating when show
562 unconserved enabled for group on alignment
565 <!-- JAL-2086 -->Cannot insert gaps into sequence when
569 <!-- JAL-2146 -->Alignment column in status incorrectly
570 shown as "Sequence position" when mousing over
574 <!-- JAL-2099 -->Incorrect column numbers in ruler when
575 hidden columns present
578 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
579 user created annotation added to alignment
582 <!-- JAL-1841 -->RNA Structure consensus only computed for
583 '()' base pair annotation
586 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
587 in zero scores for all base pairs in RNA Structure
591 <!-- JAL-2174-->Extend selection with columns containing
595 <!-- JAL-2275 -->Pfam format writer puts extra space at
596 beginning of sequence
599 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
603 <!-- JAL-2238 -->Cannot create groups on an alignment from
604 from a tree when t-coffee scores are shown
607 <!-- JAL-1836,1967 -->Cannot import and view PDB
608 structures with chains containing negative resnums (4q4h)
611 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
615 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
616 to Clustal, PIR and PileUp output
619 <!-- JAL-2008 -->Reordering sequence features that are
620 not visible causes alignment window to repaint
623 <!-- JAL-2006 -->Threshold sliders don't work in
624 graduated colour and colour by annotation row for e-value
625 scores associated with features and annotation rows
628 <!-- JAL-1797 -->amino acid physicochemical conservation
629 calculation should be case independent
632 <!-- JAL-2173 -->Remove annotation also updates hidden
636 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
637 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
638 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
641 <!-- JAL-2065 -->Null pointer exceptions and redraw
642 problems when reference sequence defined and 'show
643 non-conserved' enabled
646 <!-- JAL-1306 -->Quality and Conservation are now shown on
647 load even when Consensus calculation is disabled
650 <!-- JAL-1932 -->Remove right on penultimate column of
651 alignment does nothing
657 <!-- JAL-1552-->URLs and links can't be imported by
658 drag'n'drop on OSX when launched via webstart (note - not
659 yet fixed for El Capitan)
662 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
663 output when running on non-gb/us i18n platforms
666 <!-- JAL-1944 -->Error thrown when exporting a view with
667 hidden sequences as flat-file alignment
670 <!-- JAL-2030-->InstallAnywhere distribution fails when
674 <!-- JAL-2080-->Jalview very slow to launch via webstart
675 (also hotfix for 2.9.0b2)
678 <!-- JAL-2085 -->Cannot save project when view has a
679 reference sequence defined
682 <!-- JAL-1011 -->Columns are suddenly selected in other
683 alignments and views when revealing hidden columns
686 <!-- JAL-1989 -->Hide columns not mirrored in complement
687 view in a cDNA/Protein splitframe
690 <!-- JAL-1369 -->Cannot save/restore representative
691 sequence from project when only one sequence is
695 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
699 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
700 structure consensus didn't refresh annotation panel
703 <!-- JAL-1962 -->View mapping in structure view shows
704 mappings between sequence and all chains in a PDB file
707 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
708 dialogs format columns correctly, don't display array
709 data, sort columns according to type
712 <!-- JAL-1975 -->Export complete shown after destination
713 file chooser is cancelled during an image export
716 <!-- JAL-2025 -->Error when querying PDB Service with
717 sequence name containing special characters
720 <!-- JAL-2024 -->Manual PDB structure querying should be
724 <!-- JAL-2104 -->Large tooltips with broken HTML
725 formatting don't wrap
728 <!-- JAL-1128 -->Figures exported from wrapped view are
729 truncated so L looks like I in consensus annotation
732 <!-- JAL-2003 -->Export features should only export the
733 currently displayed features for the current selection or
737 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
738 after fetching cross-references, and restoring from project
741 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
742 followed in the structure viewer
745 <!-- JAL-2163 -->Titles for individual alignments in
746 splitframe not restored from project
749 <!-- JAL-2145 -->missing autocalculated annotation at
750 trailing end of protein alignment in transcript/product
751 splitview when pad-gaps not enabled by default
754 <!-- JAL-1797 -->amino acid physicochemical conservation
758 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
759 article has been read (reopened issue due to
760 internationalisation problems)
763 <!-- JAL-1960 -->Only offer PDB structures in structure
764 viewer based on sequence name, PDB and UniProt
769 <!-- JAL-1976 -->No progress bar shown during export of
773 <!-- JAL-2213 -->Structures not always superimposed after
774 multiple structures are shown for one or more sequences.
777 <!-- JAL-1370 -->Reference sequence characters should not
778 be replaced with '.' when 'Show unconserved' format option
782 <!-- JAL-1823 -->Cannot specify chain code when entering
783 specific PDB id for sequence
786 <!-- JAL-1944 -->File->Export->.. as doesn't work when
787 'Export hidden sequences' is enabled, but 'export hidden
788 columns' is disabled.
791 <!--JAL-2026-->Best Quality option in structure chooser
792 selects lowest rather than highest resolution structures
796 <!-- JAL-1887 -->Incorrect start and end reported for PDB
797 to sequence mapping in 'View Mappings' report
800 <!-- JAL-2284 -->Unable to read old Jalview projects that
801 contain non-XML data added after Jalvew wrote project.
803 <li><!-- JAL-2118 -->Newly created annotation row reorders
804 after clicking on it to create new annotation for a
807 <!-- may exclude, this is an external service stability issue JAL-1941
808 -- > RNA 3D structure not added via DSSR service</li> -->
813 <!-- JAL-2151 -->Incorrect columns are selected when
814 hidden columns present before start of sequence
817 <!-- JAL-1986 -->Missing dependencies on applet pages
821 <!-- JAL-1947 -->Overview pixel size changes when
822 sequences are hidden in applet
825 <!-- JAL-1996 -->Updated instructions for applet
826 deployment on examples pages.
833 <td width="60" nowrap>
835 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
836 <em>16/10/2015</em></strong>
841 <li>Time stamps for signed Jalview application and applet
848 <li>Duplicate group consensus and conservation rows
849 shown when tree is partitioned</li>
850 <li>Erratic behaviour when tree partitions made with
851 multiple cDNA/Protein split views</li>
857 <td width="60" nowrap>
859 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
860 <em>8/10/2015</em></strong>
865 <li>Updated Spanish translations of localized text for
867 </ul> <em>Application</em>
869 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
870 <li>Signed OSX InstallAnywhere installer<br></li>
871 <li>Support for per-sequence based annotations in BioJSON</li>
872 </ul> <em>Applet</em>
874 <li>Split frame example added to applet examples page</li>
875 </ul><em>Build and Deployment</em>
877 <li><!-- JAL-1888 -->New ant target for running Jalview's test suite</li>
883 <li>Mapping of cDNA to protein in split frames
884 incorrect when sequence start > 1</li>
885 <li>Broken images in filter column by annotation dialog
887 <li>Feature colours not parsed from features file</li>
888 <li>Exceptions and incomplete link URLs recovered when
889 loading a features file containing HTML tags in feature
895 <li>Annotations corrupted after BioJS export and
897 <li>Incorrect sequence limits after Fetch DB References
898 with 'trim retrieved sequences'</li>
899 <li>Incorrect warning about deleting all data when
900 deleting selected columns</li>
901 <li>Patch to build system for shipping properly signed
902 JNLP templates for webstart launch</li>
903 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
904 unreleased structures for download or viewing</li>
905 <li>Tab/space/return keystroke operation of EMBL-PDBe
906 fetcher/viewer dialogs works correctly</li>
907 <li>Disabled 'minimise' button on Jalview windows
908 running on OSX to workaround redraw hang bug</li>
909 <li>Split cDNA/Protein view position and geometry not
910 recovered from jalview project</li>
911 <li>Initial enabled/disabled state of annotation menu
912 sorter 'show autocalculated first/last' corresponds to
914 <li>Restoring of Clustal, RNA Helices and T-Coffee
915 color schemes from BioJSON</li>
919 <li>Reorder sequences mirrored in cDNA/Protein split
921 <li>Applet with Jmol examples not loading correctly</li>
927 <td><div align="center">
928 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
932 <li>Linked visualisation and analysis of DNA and Protein
935 <li>Translated cDNA alignments shown as split protein
936 and DNA alignment views</li>
937 <li>Codon consensus annotation for linked protein and
938 cDNA alignment views</li>
939 <li>Link cDNA or Protein product sequences by loading
940 them onto Protein or cDNA alignments</li>
941 <li>Reconstruct linked cDNA alignment from aligned
942 protein sequences</li>
945 <li>Jmol integration updated to Jmol v14.2.14</li>
946 <li>Import and export of Jalview alignment views as <a
947 href="features/bioJsonFormat.html">BioJSON</a></li>
948 <li>New alignment annotation file statements for
949 reference sequences and marking hidden columns</li>
950 <li>Reference sequence based alignment shading to
951 highlight variation</li>
952 <li>Select or hide columns according to alignment
954 <li>Find option for locating sequences by description</li>
955 <li>Conserved physicochemical properties shown in amino
956 acid conservation row</li>
957 <li>Alignments can be sorted by number of RNA helices</li>
958 </ul> <em>Application</em>
960 <li>New cDNA/Protein analysis capabilities
962 <li>Get Cross-References should open a Split Frame
963 view with cDNA/Protein</li>
964 <li>Detect when nucleotide sequences and protein
965 sequences are placed in the same alignment</li>
966 <li>Split cDNA/Protein views are saved in Jalview
971 <li>Use REST API to talk to Chimera</li>
972 <li>Selected regions in Chimera are highlighted in linked
975 <li>VARNA RNA viewer updated to v3.93</li>
976 <li>VARNA views are saved in Jalview Projects</li>
977 <li>Pseudoknots displayed as Jalview RNA annotation can
978 be shown in VARNA</li>
980 <li>Make groups for selection uses marked columns as well
981 as the active selected region</li>
983 <li>Calculate UPGMA and NJ trees using sequence feature
985 <li>New Export options
987 <li>New Export Settings dialog to control hidden
988 region export in flat file generation</li>
990 <li>Export alignment views for display with the <a
991 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
993 <li>Export scrollable SVG in HTML page</li>
994 <li>Optional embedding of BioJSON data when exporting
995 alignment figures to HTML</li>
997 <li>3D structure retrieval and display
999 <li>Free text and structured queries with the PDBe
1001 <li>PDBe Search API based discovery and selection of
1002 PDB structures for a sequence set</li>
1006 <li>JPred4 employed for protein secondary structure
1008 <li>Hide Insertions menu option to hide unaligned columns
1009 for one or a group of sequences</li>
1010 <li>Automatically hide insertions in alignments imported
1011 from the JPred4 web server</li>
1012 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1013 system on OSX<br />LGPL libraries courtesy of <a
1014 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1016 <li>changed 'View nucleotide structure' submenu to 'View
1017 VARNA 2D Structure'</li>
1018 <li>change "View protein structure" menu option to "3D
1021 </ul> <em>Applet</em>
1023 <li>New layout for applet example pages</li>
1024 <li>New parameters to enable SplitFrame view
1025 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1026 <li>New example demonstrating linked viewing of cDNA and
1027 Protein alignments</li>
1028 </ul> <em>Development and deployment</em>
1030 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1031 <li>Include installation type and git revision in build
1032 properties and console log output</li>
1033 <li>Jalview Github organisation, and new github site for
1034 storing BioJsMSA Templates</li>
1035 <li>Jalview's unit tests now managed with TestNG</li>
1038 <!-- <em>General</em>
1040 </ul> --> <!-- issues resolved --> <em>Application</em>
1042 <li>Escape should close any open find dialogs</li>
1043 <li>Typo in select-by-features status report</li>
1044 <li>Consensus RNA secondary secondary structure
1045 predictions are not highlighted in amber</li>
1046 <li>Missing gap character in v2.7 example file means
1047 alignment appears unaligned when pad-gaps is not enabled</li>
1048 <li>First switch to RNA Helices colouring doesn't colour
1049 associated structure views</li>
1050 <li>ID width preference option is greyed out when auto
1051 width checkbox not enabled</li>
1052 <li>Stopped a warning dialog from being shown when
1053 creating user defined colours</li>
1054 <li>'View Mapping' in structure viewer shows sequence
1055 mappings for just that viewer's sequences</li>
1056 <li>Workaround for superposing PDB files containing
1057 multiple models in Chimera</li>
1058 <li>Report sequence position in status bar when hovering
1059 over Jmol structure</li>
1060 <li>Cannot output gaps as '.' symbols with Selection ->
1061 output to text box</li>
1062 <li>Flat file exports of alignments with hidden columns
1063 have incorrect sequence start/end</li>
1064 <li>'Aligning' a second chain to a Chimera structure from
1066 <li>Colour schemes applied to structure viewers don't
1067 work for nucleotide</li>
1068 <li>Loading/cut'n'pasting an empty or invalid file leads
1069 to a grey/invisible alignment window</li>
1070 <li>Exported Jpred annotation from a sequence region
1071 imports to different position</li>
1072 <li>Space at beginning of sequence feature tooltips shown
1073 on some platforms</li>
1074 <li>Chimera viewer 'View | Show Chain' menu is not
1076 <li>'New View' fails with a Null Pointer Exception in
1077 console if Chimera has been opened</li>
1078 <li>Mouseover to Chimera not working</li>
1079 <li>Miscellaneous ENA XML feature qualifiers not
1081 <li>NPE in annotation renderer after 'Extract Scores'</li>
1082 <li>If two structures in one Chimera window, mouseover of
1083 either sequence shows on first structure</li>
1084 <li>'Show annotations' options should not make
1085 non-positional annotations visible</li>
1086 <li>Subsequence secondary structure annotation not shown
1087 in right place after 'view flanking regions'</li>
1088 <li>File Save As type unset when current file format is
1090 <li>Save as '.jar' option removed for saving Jalview
1092 <li>Colour by Sequence colouring in Chimera more
1094 <li>Cannot 'add reference annotation' for a sequence in
1095 several views on same alignment</li>
1096 <li>Cannot show linked products for EMBL / ENA records</li>
1097 <li>Jalview's tooltip wraps long texts containing no
1099 </ul> <em>Applet</em>
1101 <li>Jmol to JalviewLite mouseover/link not working</li>
1102 <li>JalviewLite can't import sequences with ID
1103 descriptions containing angle brackets</li>
1104 </ul> <em>General</em>
1106 <li>Cannot export and reimport RNA secondary structure
1107 via jalview annotation file</li>
1108 <li>Random helix colour palette for colour by annotation
1109 with RNA secondary structure</li>
1110 <li>Mouseover to cDNA from STOP residue in protein
1111 translation doesn't work.</li>
1112 <li>hints when using the select by annotation dialog box</li>
1113 <li>Jmol alignment incorrect if PDB file has alternate CA
1115 <li>FontChooser message dialog appears to hang after
1116 choosing 1pt font</li>
1117 <li>Peptide secondary structure incorrectly imported from
1118 annotation file when annotation display text includes 'e' or
1120 <li>Cannot set colour of new feature type whilst creating
1122 <li>cDNA translation alignment should not be sequence
1123 order dependent</li>
1124 <li>'Show unconserved' doesn't work for lower case
1126 <li>Nucleotide ambiguity codes involving R not recognised</li>
1127 </ul> <em>Deployment and Documentation</em>
1129 <li>Applet example pages appear different to the rest of
1130 www.jalview.org</li>
1131 </ul> <em>Application Known issues</em>
1133 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1134 <li>Misleading message appears after trying to delete
1136 <li>Jalview icon not shown in dock after InstallAnywhere
1137 version launches</li>
1138 <li>Fetching EMBL reference for an RNA sequence results
1139 fails with a sequence mismatch</li>
1140 <li>Corrupted or unreadable alignment display when
1141 scrolling alignment to right</li>
1142 <li>ArrayIndexOutOfBoundsException thrown when remove
1143 empty columns called on alignment with ragged gapped ends</li>
1144 <li>auto calculated alignment annotation rows do not get
1145 placed above or below non-autocalculated rows</li>
1146 <li>Jalview dekstop becomes sluggish at full screen in
1147 ultra-high resolution</li>
1148 <li>Cannot disable consensus calculation independently of
1149 quality and conservation</li>
1150 <li>Mouseover highlighting between cDNA and protein can
1151 become sluggish with more than one splitframe shown</li>
1152 </ul> <em>Applet Known Issues</em>
1154 <li>Core PDB parsing code requires Jmol</li>
1155 <li>Sequence canvas panel goes white when alignment
1156 window is being resized</li>
1162 <td><div align="center">
1163 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1165 <td><em>General</em>
1167 <li>Updated Java code signing certificate donated by
1169 <li>Features and annotation preserved when performing
1170 pairwise alignment</li>
1171 <li>RNA pseudoknot annotation can be
1172 imported/exported/displayed</li>
1173 <li>'colour by annotation' can colour by RNA and
1174 protein secondary structure</li>
1175 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1176 post-hoc with 2.9 release</em>)
1179 </ul> <em>Application</em>
1181 <li>Extract and display secondary structure for sequences
1182 with 3D structures</li>
1183 <li>Support for parsing RNAML</li>
1184 <li>Annotations menu for layout
1186 <li>sort sequence annotation rows by alignment</li>
1187 <li>place sequence annotation above/below alignment
1190 <li>Output in Stockholm format</li>
1191 <li>Internationalisation: improved Spanish (es)
1193 <li>Structure viewer preferences tab</li>
1194 <li>Disorder and Secondary Structure annotation tracks
1195 shared between alignments</li>
1196 <li>UCSF Chimera launch and linked highlighting from
1198 <li>Show/hide all sequence associated annotation rows for
1199 all or current selection</li>
1200 <li>disorder and secondary structure predictions
1201 available as dataset annotation</li>
1202 <li>Per-sequence rna helices colouring</li>
1205 <li>Sequence database accessions imported when fetching
1206 alignments from Rfam</li>
1207 <li>update VARNA version to 3.91</li>
1209 <li>New groovy scripts for exporting aligned positions,
1210 conservation values, and calculating sum of pairs scores.</li>
1211 <li>Command line argument to set default JABAWS server</li>
1212 <li>include installation type in build properties and
1213 console log output</li>
1214 <li>Updated Jalview project format to preserve dataset
1218 <!-- issues resolved --> <em>Application</em>
1220 <li>Distinguish alignment and sequence associated RNA
1221 structure in structure->view->VARNA</li>
1222 <li>Raise dialog box if user deletes all sequences in an
1224 <li>Pressing F1 results in documentation opening twice</li>
1225 <li>Sequence feature tooltip is wrapped</li>
1226 <li>Double click on sequence associated annotation
1227 selects only first column</li>
1228 <li>Redundancy removal doesn't result in unlinked
1229 leaves shown in tree</li>
1230 <li>Undos after several redundancy removals don't undo
1232 <li>Hide sequence doesn't hide associated annotation</li>
1233 <li>User defined colours dialog box too big to fit on
1234 screen and buttons not visible</li>
1235 <li>author list isn't updated if already written to
1236 Jalview properties</li>
1237 <li>Popup menu won't open after retrieving sequence
1239 <li>File open window for associate PDB doesn't open</li>
1240 <li>Left-then-right click on a sequence id opens a
1241 browser search window</li>
1242 <li>Cannot open sequence feature shading/sort popup menu
1243 in feature settings dialog</li>
1244 <li>better tooltip placement for some areas of Jalview
1246 <li>Allow addition of JABAWS Server which doesn't
1247 pass validation</li>
1248 <li>Web services parameters dialog box is too large to
1250 <li>Muscle nucleotide alignment preset obscured by
1252 <li>JABAWS preset submenus don't contain newly
1253 defined user preset</li>
1254 <li>MSA web services warns user if they were launched
1255 with invalid input</li>
1256 <li>Jalview cannot contact DAS Registy when running on
1259 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1260 'Superpose with' submenu not shown when new view
1264 </ul> <!-- <em>Applet</em>
1266 </ul> <em>General</em>
1268 </ul>--> <em>Deployment and Documentation</em>
1270 <li>2G and 1G options in launchApp have no effect on
1271 memory allocation</li>
1272 <li>launchApp service doesn't automatically open
1273 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1275 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1276 InstallAnywhere reports cannot find valid JVM when Java
1277 1.7_055 is available
1279 </ul> <em>Application Known issues</em>
1282 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1283 corrupted or unreadable alignment display when scrolling
1287 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1288 retrieval fails but progress bar continues for DAS retrieval
1289 with large number of ID
1292 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1293 flatfile output of visible region has incorrect sequence
1297 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1298 rna structure consensus doesn't update when secondary
1299 structure tracks are rearranged
1302 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1303 invalid rna structure positional highlighting does not
1304 highlight position of invalid base pairs
1307 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1308 out of memory errors are not raised when saving Jalview
1309 project from alignment window file menu
1312 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1313 Switching to RNA Helices colouring doesn't propagate to
1317 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1318 colour by RNA Helices not enabled when user created
1319 annotation added to alignment
1322 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1323 Jalview icon not shown on dock in Mountain Lion/Webstart
1325 </ul> <em>Applet Known Issues</em>
1328 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1329 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1332 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1333 Jalview and Jmol example not compatible with IE9
1336 <li>Sort by annotation score doesn't reverse order
1342 <td><div align="center">
1343 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1346 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1349 <li>Internationalisation of user interface (usually
1350 called i18n support) and translation for Spanish locale</li>
1351 <li>Define/Undefine group on current selection with
1352 Ctrl-G/Shift Ctrl-G</li>
1353 <li>Improved group creation/removal options in
1354 alignment/sequence Popup menu</li>
1355 <li>Sensible precision for symbol distribution
1356 percentages shown in logo tooltip.</li>
1357 <li>Annotation panel height set according to amount of
1358 annotation when alignment first opened</li>
1359 </ul> <em>Application</em>
1361 <li>Interactive consensus RNA secondary structure
1362 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1363 <li>Select columns containing particular features from
1364 Feature Settings dialog</li>
1365 <li>View all 'representative' PDB structures for selected
1367 <li>Update Jalview project format:
1369 <li>New file extension for Jalview projects '.jvp'</li>
1370 <li>Preserve sequence and annotation dataset (to
1371 store secondary structure annotation,etc)</li>
1372 <li>Per group and alignment annotation and RNA helix
1376 <li>New similarity measures for PCA and Tree calculation
1378 <li>Experimental support for retrieval and viewing of
1379 flanking regions for an alignment</li>
1383 <!-- issues resolved --> <em>Application</em>
1385 <li>logo keeps spinning and status remains at queued or
1386 running after job is cancelled</li>
1387 <li>cannot export features from alignments imported from
1388 Jalview/VAMSAS projects</li>
1389 <li>Buggy slider for web service parameters that take
1391 <li>Newly created RNA secondary structure line doesn't
1392 have 'display all symbols' flag set</li>
1393 <li>T-COFFEE alignment score shading scheme and other
1394 annotation shading not saved in Jalview project</li>
1395 <li>Local file cannot be loaded in freshly downloaded
1397 <li>Jalview icon not shown on dock in Mountain
1399 <li>Load file from desktop file browser fails</li>
1400 <li>Occasional NPE thrown when calculating large trees</li>
1401 <li>Cannot reorder or slide sequences after dragging an
1402 alignment onto desktop</li>
1403 <li>Colour by annotation dialog throws NPE after using
1404 'extract scores' function</li>
1405 <li>Loading/cut'n'pasting an empty file leads to a grey
1406 alignment window</li>
1407 <li>Disorder thresholds rendered incorrectly after
1408 performing IUPred disorder prediction</li>
1409 <li>Multiple group annotated consensus rows shown when
1410 changing 'normalise logo' display setting</li>
1411 <li>Find shows blank dialog after 'finished searching' if
1412 nothing matches query</li>
1413 <li>Null Pointer Exceptions raised when sorting by
1414 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1416 <li>Errors in Jmol console when structures in alignment
1417 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1419 <li>Not all working JABAWS services are shown in
1421 <li>JAVAWS version of Jalview fails to launch with
1422 'invalid literal/length code'</li>
1423 <li>Annotation/RNA Helix colourschemes cannot be applied
1424 to alignment with groups (actually fixed in 2.8.0b1)</li>
1425 <li>RNA Helices and T-Coffee Scores available as default
1428 </ul> <em>Applet</em>
1430 <li>Remove group option is shown even when selection is
1432 <li>Apply to all groups ticked but colourscheme changes
1433 don't affect groups</li>
1434 <li>Documented RNA Helices and T-Coffee Scores as valid
1435 colourscheme name</li>
1436 <li>Annotation labels drawn on sequence IDs when
1437 Annotation panel is not displayed</li>
1438 <li>Increased font size for dropdown menus on OSX and
1439 embedded windows</li>
1440 </ul> <em>Other</em>
1442 <li>Consensus sequence for alignments/groups with a
1443 single sequence were not calculated</li>
1444 <li>annotation files that contain only groups imported as
1445 annotation and junk sequences</li>
1446 <li>Fasta files with sequences containing '*' incorrectly
1447 recognised as PFAM or BLC</li>
1448 <li>conservation/PID slider apply all groups option
1449 doesn't affect background (2.8.0b1)
1451 <li>redundancy highlighting is erratic at 0% and 100%</li>
1452 <li>Remove gapped columns fails for sequences with ragged
1454 <li>AMSA annotation row with leading spaces is not
1455 registered correctly on import</li>
1456 <li>Jalview crashes when selecting PCA analysis for
1457 certain alignments</li>
1458 <li>Opening the colour by annotation dialog for an
1459 existing annotation based 'use original colours'
1460 colourscheme loses original colours setting</li>
1465 <td><div align="center">
1466 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
1467 <em>30/1/2014</em></strong>
1471 <li>Trusted certificates for JalviewLite applet and
1472 Jalview Desktop application<br />Certificate was donated by
1473 <a href="https://www.certum.eu">Certum</a> to the Jalview
1474 open source project).
1476 <li>Jalview SRS links replaced by UniProt and EBI-search
1478 <li>Output in Stockholm format</li>
1479 <li>Allow import of data from gzipped files</li>
1480 <li>Export/import group and sequence associated line
1481 graph thresholds</li>
1482 <li>Nucleotide substitution matrix that supports RNA and
1483 ambiguity codes</li>
1484 <li>Allow disorder predictions to be made on the current
1485 selection (or visible selection) in the same way that JPred
1487 <li>Groovy scripting for headless Jalview operation</li>
1488 </ul> <em>Other improvements</em>
1490 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
1491 <li>COMBINE statement uses current SEQUENCE_REF and
1492 GROUP_REF scope to group annotation rows</li>
1493 <li>Support '' style escaping of quotes in Newick
1495 <li>Group options for JABAWS service by command line name</li>
1496 <li>Empty tooltip shown for JABA service options with a
1497 link but no description</li>
1498 <li>Select primary source when selecting authority in
1499 database fetcher GUI</li>
1500 <li>Add .mfa to FASTA file extensions recognised by
1502 <li>Annotation label tooltip text wrap</li>
1507 <li>Slow scrolling when lots of annotation rows are
1509 <li>Lots of NPE (and slowness) after creating RNA
1510 secondary structure annotation line</li>
1511 <li>Sequence database accessions not imported when
1512 fetching alignments from Rfam</li>
1513 <li>Incorrect SHMR submission for sequences with
1515 <li>View all structures does not always superpose
1517 <li>Option widgets in service parameters not updated to
1518 reflect user or preset settings</li>
1519 <li>Null pointer exceptions for some services without
1520 presets or adjustable parameters</li>
1521 <li>Discover PDB IDs entry in structure menu doesn't
1522 discover PDB xRefs</li>
1523 <li>Exception encountered while trying to retrieve
1524 features with DAS</li>
1525 <li>Lowest value in annotation row isn't coloured
1526 when colour by annotation (per sequence) is coloured</li>
1527 <li>Keyboard mode P jumps to start of gapped region when
1528 residue follows a gap</li>
1529 <li>Jalview appears to hang importing an alignment with
1530 Wrap as default or after enabling Wrap</li>
1531 <li>'Right click to add annotations' message
1532 shown in wrap mode when no annotations present</li>
1533 <li>Disorder predictions fail with NPE if no automatic
1534 annotation already exists on alignment</li>
1535 <li>oninit javascript function should be called after
1536 initialisation completes</li>
1537 <li>Remove redundancy after disorder prediction corrupts
1538 alignment window display</li>
1539 <li>Example annotation file in documentation is invalid</li>
1540 <li>Grouped line graph annotation rows are not exported
1541 to annotation file</li>
1542 <li>Multi-harmony analysis cannot be run when only two
1544 <li>Cannot create multiple groups of line graphs with
1545 several 'combine' statements in annotation file</li>
1546 <li>Pressing return several times causes Number Format
1547 exceptions in keyboard mode</li>
1548 <li>Multi-harmony (SHMMR) method doesn't submit
1549 correct partitions for input data</li>
1550 <li>Translation from DNA to Amino Acids fails</li>
1551 <li>Jalview fail to load newick tree with quoted label</li>
1552 <li>--headless flag isn't understood</li>
1553 <li>ClassCastException when generating EPS in headless
1555 <li>Adjusting sequence-associated shading threshold only
1556 changes one row's threshold</li>
1557 <li>Preferences and Feature settings panel panel
1558 doesn't open</li>
1559 <li>hide consensus histogram also hides conservation and
1560 quality histograms</li>
1565 <td><div align="center">
1566 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
1568 <td><em>Application</em>
1570 <li>Support for JABAWS 2.0 Services (AACon alignment
1571 conservation, protein disorder and Clustal Omega)</li>
1572 <li>JABAWS server status indicator in Web Services
1574 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
1575 in Jalview alignment window</li>
1576 <li>Updated Jalview build and deploy framework for OSX
1577 mountain lion, windows 7, and 8</li>
1578 <li>Nucleotide substitution matrix for PCA that supports
1579 RNA and ambiguity codes</li>
1581 <li>Improved sequence database retrieval GUI</li>
1582 <li>Support fetching and database reference look up
1583 against multiple DAS sources (Fetch all from in 'fetch db
1585 <li>Jalview project improvements
1587 <li>Store and retrieve the 'belowAlignment'
1588 flag for annotation</li>
1589 <li>calcId attribute to group annotation rows on the
1591 <li>Store AACon calculation settings for a view in
1592 Jalview project</li>
1596 <li>horizontal scrolling gesture support</li>
1597 <li>Visual progress indicator when PCA calculation is
1599 <li>Simpler JABA web services menus</li>
1600 <li>visual indication that web service results are still
1601 being retrieved from server</li>
1602 <li>Serialise the dialogs that are shown when Jalview
1603 starts up for first time</li>
1604 <li>Jalview user agent string for interacting with HTTP
1606 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
1608 <li>Examples directory and Groovy library included in
1609 InstallAnywhere distribution</li>
1610 </ul> <em>Applet</em>
1612 <li>RNA alignment and secondary structure annotation
1613 visualization applet example</li>
1614 </ul> <em>General</em>
1616 <li>Normalise option for consensus sequence logo</li>
1617 <li>Reset button in PCA window to return dimensions to
1619 <li>Allow seqspace or Jalview variant of alignment PCA
1621 <li>PCA with either nucleic acid and protein substitution
1623 <li>Allow windows containing HTML reports to be exported
1625 <li>Interactive display and editing of RNA secondary
1626 structure contacts</li>
1627 <li>RNA Helix Alignment Colouring</li>
1628 <li>RNA base pair logo consensus</li>
1629 <li>Parse sequence associated secondary structure
1630 information in Stockholm files</li>
1631 <li>HTML Export database accessions and annotation
1632 information presented in tooltip for sequences</li>
1633 <li>Import secondary structure from LOCARNA clustalw
1634 style RNA alignment files</li>
1635 <li>import and visualise T-COFFEE quality scores for an
1637 <li>'colour by annotation' per sequence option to
1638 shade each sequence according to its associated alignment
1640 <li>New Jalview Logo</li>
1641 </ul> <em>Documentation and Development</em>
1643 <li>documentation for score matrices used in Jalview</li>
1644 <li>New Website!</li>
1646 <td><em>Application</em>
1648 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
1649 wsdbfetch REST service</li>
1650 <li>Stop windows being moved outside desktop on OSX</li>
1651 <li>Filetype associations not installed for webstart
1653 <li>Jalview does not always retrieve progress of a JABAWS
1654 job execution in full once it is complete</li>
1655 <li>revise SHMR RSBS definition to ensure alignment is
1656 uploaded via ali_file parameter</li>
1657 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
1658 <li>View all structures superposed fails with exception</li>
1659 <li>Jnet job queues forever if a very short sequence is
1660 submitted for prediction</li>
1661 <li>Cut and paste menu not opened when mouse clicked on
1663 <li>Putting fractional value into integer text box in
1664 alignment parameter dialog causes Jalview to hang</li>
1665 <li>Structure view highlighting doesn't work on
1667 <li>View all structures fails with exception shown in
1669 <li>Characters in filename associated with PDBEntry not
1670 escaped in a platform independent way</li>
1671 <li>Jalview desktop fails to launch with exception when
1673 <li>Tree calculation reports 'you must have 2 or more
1674 sequences selected' when selection is empty</li>
1675 <li>Jalview desktop fails to launch with jar signature
1676 failure when java web start temporary file caching is
1678 <li>DAS Sequence retrieval with range qualification
1679 results in sequence xref which includes range qualification</li>
1680 <li>Errors during processing of command line arguments
1681 cause progress bar (JAL-898) to be removed</li>
1682 <li>Replace comma for semi-colon option not disabled for
1683 DAS sources in sequence fetcher</li>
1684 <li>Cannot close news reader when JABAWS server warning
1685 dialog is shown</li>
1686 <li>Option widgets not updated to reflect user settings</li>
1687 <li>Edited sequence not submitted to web service</li>
1688 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
1689 <li>InstallAnywhere installer doesn't unpack and run
1690 on OSX Mountain Lion</li>
1691 <li>Annotation panel not given a scroll bar when
1692 sequences with alignment annotation are pasted into the
1694 <li>Sequence associated annotation rows not associated
1695 when loaded from Jalview project</li>
1696 <li>Browser launch fails with NPE on java 1.7</li>
1697 <li>JABAWS alignment marked as finished when job was
1698 cancelled or job failed due to invalid input</li>
1699 <li>NPE with v2.7 example when clicking on Tree
1700 associated with all views</li>
1701 <li>Exceptions when copy/paste sequences with grouped
1702 annotation rows to new window</li>
1703 </ul> <em>Applet</em>
1705 <li>Sequence features are momentarily displayed before
1706 they are hidden using hidefeaturegroups applet parameter</li>
1707 <li>loading features via javascript API automatically
1708 enables feature display</li>
1709 <li>scrollToColumnIn javascript API method doesn't
1711 </ul> <em>General</em>
1713 <li>Redundancy removal fails for rna alignment</li>
1714 <li>PCA calculation fails when sequence has been selected
1715 and then deselected</li>
1716 <li>PCA window shows grey box when first opened on OSX</li>
1717 <li>Letters coloured pink in sequence logo when alignment
1718 coloured with clustalx</li>
1719 <li>Choosing fonts without letter symbols defined causes
1720 exceptions and redraw errors</li>
1721 <li>Initial PCA plot view is not same as manually
1722 reconfigured view</li>
1723 <li>Grouped annotation graph label has incorrect line
1725 <li>Grouped annotation graph label display is corrupted
1726 for lots of labels</li>
1731 <div align="center">
1732 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
1735 <td><em>Application</em>
1737 <li>Jalview Desktop News Reader</li>
1738 <li>Tweaked default layout of web services menu</li>
1739 <li>View/alignment association menu to enable user to
1740 easily specify which alignment a multi-structure view takes
1741 its colours/correspondences from</li>
1742 <li>Allow properties file location to be specified as URL</li>
1743 <li>Extend Jalview project to preserve associations
1744 between many alignment views and a single Jmol display</li>
1745 <li>Store annotation row height in Jalview project file</li>
1746 <li>Annotation row column label formatting attributes
1747 stored in project file</li>
1748 <li>Annotation row order for auto-calculated annotation
1749 rows preserved in Jalview project file</li>
1750 <li>Visual progress indication when Jalview state is
1751 saved using Desktop window menu</li>
1752 <li>Visual indication that command line arguments are
1753 still being processed</li>
1754 <li>Groovy script execution from URL</li>
1755 <li>Colour by annotation default min and max colours in
1757 <li>Automatically associate PDB files dragged onto an
1758 alignment with sequences that have high similarity and
1760 <li>Update JGoogleAnalytics to latest release (0.3)</li>
1761 <li>'view structures' option to open many
1762 structures in same window</li>
1763 <li>Sort associated views menu option for tree panel</li>
1764 <li>Group all JABA and non-JABA services for a particular
1765 analysis function in its own submenu</li>
1766 </ul> <em>Applet</em>
1768 <li>Userdefined and autogenerated annotation rows for
1770 <li>Adjustment of alignment annotation pane height</li>
1771 <li>Annotation scrollbar for annotation panel</li>
1772 <li>Drag to reorder annotation rows in annotation panel</li>
1773 <li>'automaticScrolling' parameter</li>
1774 <li>Allow sequences with partial ID string matches to be
1775 annotated from GFF/Jalview features files</li>
1776 <li>Sequence logo annotation row in applet</li>
1777 <li>Absolute paths relative to host server in applet
1778 parameters are treated as such</li>
1779 <li>New in the JalviewLite javascript API:
1781 <li>JalviewLite.js javascript library</li>
1782 <li>Javascript callbacks for
1784 <li>Applet initialisation</li>
1785 <li>Sequence/alignment mouse-overs and selections</li>
1788 <li>scrollTo row and column alignment scrolling
1790 <li>Select sequence/alignment regions from javascript</li>
1791 <li>javascript structure viewer harness to pass
1792 messages between Jmol and Jalview when running as
1793 distinct applets</li>
1794 <li>sortBy method</li>
1795 <li>Set of applet and application examples shipped
1796 with documentation</li>
1797 <li>New example to demonstrate JalviewLite and Jmol
1798 javascript message exchange</li>
1800 </ul> <em>General</em>
1802 <li>Enable Jmol displays to be associated with multiple
1803 multiple alignments</li>
1804 <li>Option to automatically sort alignment with new tree</li>
1805 <li>User configurable link to enable redirects to a
1806 www.Jalview.org mirror</li>
1807 <li>Jmol colours option for Jmol displays</li>
1808 <li>Configurable newline string when writing alignment
1809 and other flat files</li>
1810 <li>Allow alignment annotation description lines to
1811 contain html tags</li>
1812 </ul> <em>Documentation and Development</em>
1814 <li>Add groovy test harness for bulk load testing to
1816 <li>Groovy script to load and align a set of sequences
1817 using a web service before displaying the result in the
1818 Jalview desktop</li>
1819 <li>Restructured javascript and applet api documentation</li>
1820 <li>Ant target to publish example html files with applet
1822 <li>Netbeans project for building Jalview from source</li>
1823 <li>ant task to create online javadoc for Jalview source</li>
1825 <td><em>Application</em>
1827 <li>User defined colourscheme throws exception when
1828 current built in colourscheme is saved as new scheme</li>
1829 <li>AlignFrame->Save in application pops up save
1830 dialog for valid filename/format</li>
1831 <li>Cannot view associated structure for UniProt sequence</li>
1832 <li>PDB file association breaks for UniProt sequence
1834 <li>Associate PDB from file dialog does not tell you
1835 which sequence is to be associated with the file</li>
1836 <li>Find All raises null pointer exception when query
1837 only matches sequence IDs</li>
1838 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
1839 <li>Jalview project with Jmol views created with Jalview
1840 2.4 cannot be loaded</li>
1841 <li>Filetype associations not installed for webstart
1843 <li>Two or more chains in a single PDB file associated
1844 with sequences in different alignments do not get coloured
1845 by their associated sequence</li>
1846 <li>Visibility status of autocalculated annotation row
1847 not preserved when project is loaded</li>
1848 <li>Annotation row height and visibility attributes not
1849 stored in Jalview project</li>
1850 <li>Tree bootstraps are not preserved when saved as a
1851 Jalview project</li>
1852 <li>Envision2 workflow tooltips are corrupted</li>
1853 <li>Enabling show group conservation also enables colour
1854 by conservation</li>
1855 <li>Duplicate group associated conservation or consensus
1856 created on new view</li>
1857 <li>Annotation scrollbar not displayed after 'show
1858 all hidden annotation rows' option selected</li>
1859 <li>Alignment quality not updated after alignment
1860 annotation row is hidden then shown</li>
1861 <li>Preserve colouring of structures coloured by
1862 sequences in pre Jalview 2.7 projects</li>
1863 <li>Web service job parameter dialog is not laid out
1865 <li>Web services menu not refreshed after 'reset
1866 services' button is pressed in preferences</li>
1867 <li>Annotation off by one in Jalview v2_3 example project</li>
1868 <li>Structures imported from file and saved in project
1869 get name like jalview_pdb1234.txt when reloaded</li>
1870 <li>Jalview does not always retrieve progress of a JABAWS
1871 job execution in full once it is complete</li>
1872 </ul> <em>Applet</em>
1874 <li>Alignment height set incorrectly when lots of
1875 annotation rows are displayed</li>
1876 <li>Relative URLs in feature HTML text not resolved to
1878 <li>View follows highlighting does not work for positions
1880 <li><= shown as = in tooltip</li>
1881 <li>Export features raises exception when no features
1883 <li>Separator string used for serialising lists of IDs
1884 for javascript api is modified when separator string
1885 provided as parameter</li>
1886 <li>Null pointer exception when selecting tree leaves for
1887 alignment with no existing selection</li>
1888 <li>Relative URLs for datasources assumed to be relative
1889 to applet's codebase</li>
1890 <li>Status bar not updated after finished searching and
1891 search wraps around to first result</li>
1892 <li>StructureSelectionManager instance shared between
1893 several Jalview applets causes race conditions and memory
1895 <li>Hover tooltip and mouseover of position on structure
1896 not sent from Jmol in applet</li>
1897 <li>Certain sequences of javascript method calls to
1898 applet API fatally hang browser</li>
1899 </ul> <em>General</em>
1901 <li>View follows structure mouseover scrolls beyond
1902 position with wrapped view and hidden regions</li>
1903 <li>Find sequence position moves to wrong residue
1904 with/without hidden columns</li>
1905 <li>Sequence length given in alignment properties window
1907 <li>InvalidNumberFormat exceptions thrown when trying to
1908 import PDB like structure files</li>
1909 <li>Positional search results are only highlighted
1910 between user-supplied sequence start/end bounds</li>
1911 <li>End attribute of sequence is not validated</li>
1912 <li>Find dialog only finds first sequence containing a
1913 given sequence position</li>
1914 <li>Sequence numbering not preserved in MSF alignment
1916 <li>Jalview PDB file reader does not extract sequence
1917 from nucleotide chains correctly</li>
1918 <li>Structure colours not updated when tree partition
1919 changed in alignment</li>
1920 <li>Sequence associated secondary structure not correctly
1921 parsed in interleaved stockholm</li>
1922 <li>Colour by annotation dialog does not restore current
1924 <li>Hiding (nearly) all sequences doesn't work
1926 <li>Sequences containing lowercase letters are not
1927 properly associated with their pdb files</li>
1928 </ul> <em>Documentation and Development</em>
1930 <li>schemas/JalviewWsParamSet.xsd corrupted by
1931 ApplyCopyright tool</li>
1936 <div align="center">
1937 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
1940 <td><em>Application</em>
1942 <li>New warning dialog when the Jalview Desktop cannot
1943 contact web services</li>
1944 <li>JABA service parameters for a preset are shown in
1945 service job window</li>
1946 <li>JABA Service menu entries reworded</li>
1950 <li>Modeller PIR IO broken - cannot correctly import a
1951 pir file emitted by Jalview</li>
1952 <li>Existing feature settings transferred to new
1953 alignment view created from cut'n'paste</li>
1954 <li>Improved test for mixed amino/nucleotide chains when
1955 parsing PDB files</li>
1956 <li>Consensus and conservation annotation rows
1957 occasionally become blank for all new windows</li>
1958 <li>Exception raised when right clicking above sequences
1959 in wrapped view mode</li>
1960 </ul> <em>Application</em>
1962 <li>multiple multiply aligned structure views cause cpu
1963 usage to hit 100% and computer to hang</li>
1964 <li>Web Service parameter layout breaks for long user
1965 parameter names</li>
1966 <li>Jaba service discovery hangs desktop if Jaba server
1973 <div align="center">
1974 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
1977 <td><em>Application</em>
1979 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
1980 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
1983 <li>Web Services preference tab</li>
1984 <li>Analysis parameters dialog box and user defined
1986 <li>Improved speed and layout of Envision2 service menu</li>
1987 <li>Superpose structures using associated sequence
1989 <li>Export coordinates and projection as CSV from PCA
1991 </ul> <em>Applet</em>
1993 <li>enable javascript: execution by the applet via the
1994 link out mechanism</li>
1995 </ul> <em>Other</em>
1997 <li>Updated the Jmol Jalview interface to work with Jmol
1999 <li>The Jalview Desktop and JalviewLite applet now
2000 require Java 1.5</li>
2001 <li>Allow Jalview feature colour specification for GFF
2002 sequence annotation files</li>
2003 <li>New 'colour by label' keword in Jalview feature file
2004 type colour specification</li>
2005 <li>New Jalview Desktop Groovy API method that allows a
2006 script to check if it being run in an interactive session or
2007 in a batch operation from the Jalview command line</li>
2011 <li>clustalx colourscheme colours Ds preferentially when
2012 both D+E are present in over 50% of the column</li>
2013 </ul> <em>Application</em>
2015 <li>typo in AlignmentFrame->View->Hide->all but
2016 selected Regions menu item</li>
2017 <li>sequence fetcher replaces ',' for ';' when the ',' is
2018 part of a valid accession ID</li>
2019 <li>fatal OOM if object retrieved by sequence fetcher
2020 runs out of memory</li>
2021 <li>unhandled Out of Memory Error when viewing pca
2022 analysis results</li>
2023 <li>InstallAnywhere builds fail to launch on OS X java
2024 10.5 update 4 (due to apple Java 1.6 update)</li>
2025 <li>Installanywhere Jalview silently fails to launch</li>
2026 </ul> <em>Applet</em>
2028 <li>Jalview.getFeatureGroups() raises an
2029 ArrayIndexOutOfBoundsException if no feature groups are
2036 <div align="center">
2037 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2043 <li>Alignment prettyprinter doesn't cope with long
2045 <li>clustalx colourscheme colours Ds preferentially when
2046 both D+E are present in over 50% of the column</li>
2047 <li>nucleic acid structures retrieved from PDB do not
2048 import correctly</li>
2049 <li>More columns get selected than were clicked on when a
2050 number of columns are hidden</li>
2051 <li>annotation label popup menu not providing correct
2052 add/hide/show options when rows are hidden or none are
2054 <li>Stockholm format shown in list of readable formats,
2055 and parser copes better with alignments from RFAM.</li>
2056 <li>CSV output of consensus only includes the percentage
2057 of all symbols if sequence logo display is enabled</li>
2059 </ul> <em>Applet</em>
2061 <li>annotation panel disappears when annotation is
2063 </ul> <em>Application</em>
2065 <li>Alignment view not redrawn properly when new
2066 alignment opened where annotation panel is visible but no
2067 annotations are present on alignment</li>
2068 <li>pasted region containing hidden columns is
2069 incorrectly displayed in new alignment window</li>
2070 <li>Jalview slow to complete operations when stdout is
2071 flooded (fix is to close the Jalview console)</li>
2072 <li>typo in AlignmentFrame->View->Hide->all but
2073 selected Rregions menu item.</li>
2074 <li>inconsistent group submenu and Format submenu entry
2075 'Un' or 'Non'conserved</li>
2076 <li>Sequence feature settings are being shared by
2077 multiple distinct alignments</li>
2078 <li>group annotation not recreated when tree partition is
2080 <li>double click on group annotation to select sequences
2081 does not propagate to associated trees</li>
2082 <li>Mac OSX specific issues:
2084 <li>exception raised when mouse clicked on desktop
2085 window background</li>
2086 <li>Desktop menu placed on menu bar and application
2087 name set correctly</li>
2088 <li>sequence feature settings not wide enough for the
2089 save feature colourscheme button</li>
2098 <div align="center">
2099 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2102 <td><em>New Capabilities</em>
2104 <li>URL links generated from description line for
2105 regular-expression based URL links (applet and application)
2112 <li>Non-positional feature URL links are shown in link
2114 <li>Linked viewing of nucleic acid sequences and
2116 <li>Automatic Scrolling option in View menu to display
2117 the currently highlighted region of an alignment.</li>
2118 <li>Order an alignment by sequence length, or using the
2119 average score or total feature count for each sequence.</li>
2120 <li>Shading features by score or associated description</li>
2121 <li>Subdivide alignment and groups based on identity of
2122 selected subsequence (Make Groups from Selection).</li>
2123 <li>New hide/show options including Shift+Control+H to
2124 hide everything but the currently selected region.</li>
2125 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2126 </ul> <em>Application</em>
2128 <li>Fetch DB References capabilities and UI expanded to
2129 support retrieval from DAS sequence sources</li>
2130 <li>Local DAS Sequence sources can be added via the
2131 command line or via the Add local source dialog box.</li>
2132 <li>DAS Dbref and DbxRef feature types are parsed as
2133 database references and protein_name is parsed as
2134 description line (BioSapiens terms).</li>
2135 <li>Enable or disable non-positional feature and database
2136 references in sequence ID tooltip from View menu in
2138 <!-- <li>New hidden columns and rows and representatives capabilities
2139 in annotations file (in progress - not yet fully implemented)</li> -->
2140 <li>Group-associated consensus, sequence logos and
2141 conservation plots</li>
2142 <li>Symbol distributions for each column can be exported
2143 and visualized as sequence logos</li>
2144 <li>Optionally scale multi-character column labels to fit
2145 within each column of annotation row<!-- todo for applet -->
2147 <li>Optional automatic sort of associated alignment view
2148 when a new tree is opened.</li>
2149 <li>Jalview Java Console</li>
2150 <li>Better placement of desktop window when moving
2151 between different screens.</li>
2152 <li>New preference items for sequence ID tooltip and
2153 consensus annotation</li>
2154 <li>Client to submit sequences and IDs to Envision2
2156 <li><em>Vamsas Capabilities</em>
2158 <li>Improved VAMSAS synchronization (Jalview archive
2159 used to preserve views, structures, and tree display
2161 <li>Import of vamsas documents from disk or URL via
2163 <li>Sharing of selected regions between views and
2164 with other VAMSAS applications (Experimental feature!)</li>
2165 <li>Updated API to VAMSAS version 0.2</li>
2167 </ul> <em>Applet</em>
2169 <li>Middle button resizes annotation row height</li>
2172 <li>sortByTree (true/false) - automatically sort the
2173 associated alignment view by the tree when a new tree is
2175 <li>showTreeBootstraps (true/false) - show or hide
2176 branch bootstraps (default is to show them if available)</li>
2177 <li>showTreeDistances (true/false) - show or hide
2178 branch lengths (default is to show them if available)</li>
2179 <li>showUnlinkedTreeNodes (true/false) - indicate if
2180 unassociated nodes should be highlighted in the tree
2182 <li>heightScale and widthScale (1.0 or more) -
2183 increase the height or width of a cell in the alignment
2184 grid relative to the current font size.</li>
2187 <li>Non-positional features displayed in sequence ID
2189 </ul> <em>Other</em>
2191 <li>Features format: graduated colour definitions and
2192 specification of feature scores</li>
2193 <li>Alignment Annotations format: new keywords for group
2194 associated annotation (GROUP_REF) and annotation row display
2195 properties (ROW_PROPERTIES)</li>
2196 <li>XML formats extended to support graduated feature
2197 colourschemes, group associated annotation, and profile
2198 visualization settings.</li></td>
2201 <li>Source field in GFF files parsed as feature source
2202 rather than description</li>
2203 <li>Non-positional features are now included in sequence
2204 feature and gff files (controlled via non-positional feature
2205 visibility in tooltip).</li>
2206 <li>URL links generated for all feature links (bugfix)</li>
2207 <li>Added URL embedding instructions to features file
2209 <li>Codons containing ambiguous nucleotides translated as
2210 'X' in peptide product</li>
2211 <li>Match case switch in find dialog box works for both
2212 sequence ID and sequence string and query strings do not
2213 have to be in upper case to match case-insensitively.</li>
2214 <li>AMSA files only contain first column of
2215 multi-character column annotation labels</li>
2216 <li>Jalview Annotation File generation/parsing consistent
2217 with documentation (e.g. Stockholm annotation can be
2218 exported and re-imported)</li>
2219 <li>PDB files without embedded PDB IDs given a friendly
2221 <li>Find incrementally searches ID string matches as well
2222 as subsequence matches, and correctly reports total number
2226 <li>Better handling of exceptions during sequence
2228 <li>Dasobert generated non-positional feature URL
2229 link text excludes the start_end suffix</li>
2230 <li>DAS feature and source retrieval buttons disabled
2231 when fetch or registry operations in progress.</li>
2232 <li>PDB files retrieved from URLs are cached properly</li>
2233 <li>Sequence description lines properly shared via
2235 <li>Sequence fetcher fetches multiple records for all
2237 <li>Ensured that command line das feature retrieval
2238 completes before alignment figures are generated.</li>
2239 <li>Reduced time taken when opening file browser for
2241 <li>isAligned check prior to calculating tree, PCA or
2242 submitting an MSA to JNet now excludes hidden sequences.</li>
2243 <li>User defined group colours properly recovered
2244 from Jalview projects.</li>
2253 <div align="center">
2254 <strong>2.4.0.b2</strong><br> 28/10/2009
2259 <li>Experimental support for google analytics usage
2261 <li>Jalview privacy settings (user preferences and docs).</li>
2266 <li>Race condition in applet preventing startup in
2268 <li>Exception when feature created from selection beyond
2269 length of sequence.</li>
2270 <li>Allow synthetic PDB files to be imported gracefully</li>
2271 <li>Sequence associated annotation rows associate with
2272 all sequences with a given id</li>
2273 <li>Find function matches case-insensitively for sequence
2274 ID string searches</li>
2275 <li>Non-standard characters do not cause pairwise
2276 alignment to fail with exception</li>
2277 </ul> <em>Application Issues</em>
2279 <li>Sequences are now validated against EMBL database</li>
2280 <li>Sequence fetcher fetches multiple records for all
2282 </ul> <em>InstallAnywhere Issues</em>
2284 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2285 issue with installAnywhere mechanism)</li>
2286 <li>Command line launching of JARs from InstallAnywhere
2287 version (java class versioning error fixed)</li>
2294 <div align="center">
2295 <strong>2.4</strong><br> 27/8/2008
2298 <td><em>User Interface</em>
2300 <li>Linked highlighting of codon and amino acid from
2301 translation and protein products</li>
2302 <li>Linked highlighting of structure associated with
2303 residue mapping to codon position</li>
2304 <li>Sequence Fetcher provides example accession numbers
2305 and 'clear' button</li>
2306 <li>MemoryMonitor added as an option under Desktop's
2308 <li>Extract score function to parse whitespace separated
2309 numeric data in description line</li>
2310 <li>Column labels in alignment annotation can be centred.</li>
2311 <li>Tooltip for sequence associated annotation give name
2313 </ul> <em>Web Services and URL fetching</em>
2315 <li>JPred3 web service</li>
2316 <li>Prototype sequence search client (no public services
2318 <li>Fetch either seed alignment or full alignment from
2320 <li>URL Links created for matching database cross
2321 references as well as sequence ID</li>
2322 <li>URL Links can be created using regular-expressions</li>
2323 </ul> <em>Sequence Database Connectivity</em>
2325 <li>Retrieval of cross-referenced sequences from other
2327 <li>Generalised database reference retrieval and
2328 validation to all fetchable databases</li>
2329 <li>Fetch sequences from DAS sources supporting the
2330 sequence command</li>
2331 </ul> <em>Import and Export</em>
2332 <li>export annotation rows as CSV for spreadsheet import</li>
2333 <li>Jalview projects record alignment dataset associations,
2334 EMBL products, and cDNA sequence mappings</li>
2335 <li>Sequence Group colour can be specified in Annotation
2337 <li>Ad-hoc colouring of group in Annotation File using RGB
2338 triplet as name of colourscheme</li>
2339 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2341 <li>treenode binding for VAMSAS tree exchange</li>
2342 <li>local editing and update of sequences in VAMSAS
2343 alignments (experimental)</li>
2344 <li>Create new or select existing session to join</li>
2345 <li>load and save of vamsas documents</li>
2346 </ul> <em>Application command line</em>
2348 <li>-tree parameter to open trees (introduced for passing
2350 <li>-fetchfrom command line argument to specify nicknames
2351 of DAS servers to query for alignment features</li>
2352 <li>-dasserver command line argument to add new servers
2353 that are also automatically queried for features</li>
2354 <li>-groovy command line argument executes a given groovy
2355 script after all input data has been loaded and parsed</li>
2356 </ul> <em>Applet-Application data exchange</em>
2358 <li>Trees passed as applet parameters can be passed to
2359 application (when using "View in full
2360 application")</li>
2361 </ul> <em>Applet Parameters</em>
2363 <li>feature group display control parameter</li>
2364 <li>debug parameter</li>
2365 <li>showbutton parameter</li>
2366 </ul> <em>Applet API methods</em>
2368 <li>newView public method</li>
2369 <li>Window (current view) specific get/set public methods</li>
2370 <li>Feature display control methods</li>
2371 <li>get list of currently selected sequences</li>
2372 </ul> <em>New Jalview distribution features</em>
2374 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2375 <li>RELEASE file gives build properties for the latest
2376 Jalview release.</li>
2377 <li>Java 1.1 Applet build made easier and donotobfuscate
2378 property controls execution of obfuscator</li>
2379 <li>Build target for generating source distribution</li>
2380 <li>Debug flag for javacc</li>
2381 <li>.jalview_properties file is documented (slightly) in
2382 jalview.bin.Cache</li>
2383 <li>Continuous Build Integration for stable and
2384 development version of Application, Applet and source
2389 <li>selected region output includes visible annotations
2390 (for certain formats)</li>
2391 <li>edit label/displaychar contains existing label/char
2393 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2394 <li>shorter peptide product names from EMBL records</li>
2395 <li>Newick string generator makes compact representations</li>
2396 <li>bootstrap values parsed correctly for tree files with
2398 <li>pathological filechooser bug avoided by not allowing
2399 filenames containing a ':'</li>
2400 <li>Fixed exception when parsing GFF files containing
2401 global sequence features</li>
2402 <li>Alignment datasets are finalized only when number of
2403 references from alignment sequences goes to zero</li>
2404 <li>Close of tree branch colour box without colour
2405 selection causes cascading exceptions</li>
2406 <li>occasional negative imgwidth exceptions</li>
2407 <li>better reporting of non-fatal warnings to user when
2408 file parsing fails.</li>
2409 <li>Save works when Jalview project is default format</li>
2410 <li>Save as dialog opened if current alignment format is
2411 not a valid output format</li>
2412 <li>UniProt canonical names introduced for both das and
2414 <li>Histidine should be midblue (not pink!) in Zappo</li>
2415 <li>error messages passed up and output when data read
2417 <li>edit undo recovers previous dataset sequence when
2418 sequence is edited</li>
2419 <li>allow PDB files without pdb ID HEADER lines (like
2420 those generated by MODELLER) to be read in properly</li>
2421 <li>allow reading of JPred concise files as a normal
2423 <li>Stockholm annotation parsing and alignment properties
2424 import fixed for PFAM records</li>
2425 <li>Structure view windows have correct name in Desktop
2427 <li>annotation consisting of sequence associated scores
2428 can be read and written correctly to annotation file</li>
2429 <li>Aligned cDNA translation to aligned peptide works
2431 <li>Fixed display of hidden sequence markers and
2432 non-italic font for representatives in Applet</li>
2433 <li>Applet Menus are always embedded in applet window on
2435 <li>Newly shown features appear at top of stack (in
2437 <li>Annotations added via parameter not drawn properly
2438 due to null pointer exceptions</li>
2439 <li>Secondary structure lines are drawn starting from
2440 first column of alignment</li>
2441 <li>UniProt XML import updated for new schema release in
2443 <li>Sequence feature to sequence ID match for Features
2444 file is case-insensitive</li>
2445 <li>Sequence features read from Features file appended to
2446 all sequences with matching IDs</li>
2447 <li>PDB structure coloured correctly for associated views
2448 containing a sub-sequence</li>
2449 <li>PDB files can be retrieved by applet from Jar files</li>
2450 <li>feature and annotation file applet parameters
2451 referring to different directories are retrieved correctly</li>
2452 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
2453 <li>Fixed application hang whilst waiting for
2454 splash-screen version check to complete</li>
2455 <li>Applet properly URLencodes input parameter values
2456 when passing them to the launchApp service</li>
2457 <li>display name and local features preserved in results
2458 retrieved from web service</li>
2459 <li>Visual delay indication for sequence retrieval and
2460 sequence fetcher initialisation</li>
2461 <li>updated Application to use DAS 1.53e version of
2462 dasobert DAS client</li>
2463 <li>Re-instated Full AMSA support and .amsa file
2465 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
2473 <div align="center">
2474 <strong>2.3</strong><br> 9/5/07
2479 <li>Jmol 11.0.2 integration</li>
2480 <li>PDB views stored in Jalview XML files</li>
2481 <li>Slide sequences</li>
2482 <li>Edit sequence in place</li>
2483 <li>EMBL CDS features</li>
2484 <li>DAS Feature mapping</li>
2485 <li>Feature ordering</li>
2486 <li>Alignment Properties</li>
2487 <li>Annotation Scores</li>
2488 <li>Sort by scores</li>
2489 <li>Feature/annotation editing in applet</li>
2494 <li>Headless state operation in 2.2.1</li>
2495 <li>Incorrect and unstable DNA pairwise alignment</li>
2496 <li>Cut and paste of sequences with annotation</li>
2497 <li>Feature group display state in XML</li>
2498 <li>Feature ordering in XML</li>
2499 <li>blc file iteration selection using filename # suffix</li>
2500 <li>Stockholm alignment properties</li>
2501 <li>Stockhom alignment secondary structure annotation</li>
2502 <li>2.2.1 applet had no feature transparency</li>
2503 <li>Number pad keys can be used in cursor mode</li>
2504 <li>Structure Viewer mirror image resolved</li>
2511 <div align="center">
2512 <strong>2.2.1</strong><br> 12/2/07
2517 <li>Non standard characters can be read and displayed
2518 <li>Annotations/Features can be imported/exported to the
2520 <li>Applet allows editing of sequence/annotation/group
2521 name & description
2522 <li>Preference setting to display sequence name in
2524 <li>Annotation file format extended to allow
2525 Sequence_groups to be defined
2526 <li>Default opening of alignment overview panel can be
2527 specified in preferences
2528 <li>PDB residue numbering annotation added to associated
2534 <li>Applet crash under certain Linux OS with Java 1.6
2536 <li>Annotation file export / import bugs fixed
2537 <li>PNG / EPS image output bugs fixed
2543 <div align="center">
2544 <strong>2.2</strong><br> 27/11/06
2549 <li>Multiple views on alignment
2550 <li>Sequence feature editing
2551 <li>"Reload" alignment
2552 <li>"Save" to current filename
2553 <li>Background dependent text colour
2554 <li>Right align sequence ids
2555 <li>User-defined lower case residue colours
2558 <li>Menu item accelerator keys
2559 <li>Control-V pastes to current alignment
2560 <li>Cancel button for DAS Feature Fetching
2561 <li>PCA and PDB Viewers zoom via mouse roller
2562 <li>User-defined sub-tree colours and sub-tree selection
2569 <li>'New Window' button on the 'Output to Text box'
2574 <li>New memory efficient Undo/Redo System
2575 <li>Optimised symbol lookups and conservation/consensus
2577 <li>Region Conservation/Consensus recalculated after
2579 <li>Fixed Remove Empty Columns Bug (empty columns at end
2581 <li>Slowed DAS Feature Fetching for increased robustness.
2588 <li>Made angle brackets in ASCII feature descriptions
2590 <li>Re-instated Zoom function for PCA
2591 <li>Sequence descriptions conserved in web service
2593 <li>UniProt ID discoverer uses any word separated by
2595 <li>WsDbFetch query/result association resolved
2596 <li>Tree leaf to sequence mapping improved
2597 <li>Smooth fonts switch moved to FontChooser dialog box.
2609 <div align="center">
2610 <strong>2.1.1</strong><br> 12/9/06
2615 <li>Copy consensus sequence to clipboard</li>
2620 <li>Image output - rightmost residues are rendered if
2621 sequence id panel has been resized</li>
2622 <li>Image output - all offscreen group boundaries are
2624 <li>Annotation files with sequence references - all
2625 elements in file are relative to sequence position</li>
2626 <li>Mac Applet users can use Alt key for group editing</li>
2632 <div align="center">
2633 <strong>2.1</strong><br> 22/8/06
2638 <li>MAFFT Multiple Alignment in default Web Service list</li>
2639 <li>DAS Feature fetching</li>
2640 <li>Hide sequences and columns</li>
2641 <li>Export Annotations and Features</li>
2642 <li>GFF file reading / writing</li>
2643 <li>Associate structures with sequences from local PDB
2645 <li>Add sequences to exisiting alignment</li>
2646 <li>Recently opened files / URL lists</li>
2647 <li>Applet can launch the full application</li>
2648 <li>Applet has transparency for features (Java 1.2
2650 <li>Applet has user defined colours parameter</li>
2651 <li>Applet can load sequences from parameter
2652 "sequence<em>x</em>"
2658 <li>Redundancy Panel reinstalled in the Applet</li>
2659 <li>Monospaced font - EPS / rescaling bug fixed</li>
2660 <li>Annotation files with sequence references bug fixed</li>
2666 <div align="center">
2667 <strong>2.08.1</strong><br> 2/5/06
2672 <li>Change case of selected region from Popup menu</li>
2673 <li>Choose to match case when searching</li>
2674 <li>Middle mouse button and mouse movement can compress /
2675 expand the visible width and height of the alignment</li>
2680 <li>Annotation Panel displays complete JNet results</li>
2686 <div align="center">
2687 <strong>2.08b</strong><br> 18/4/06
2693 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
2694 <li>Righthand label on wrapped alignments shows correct
2701 <div align="center">
2702 <strong>2.08</strong><br> 10/4/06
2707 <li>Editing can be locked to the selection area</li>
2708 <li>Keyboard editing</li>
2709 <li>Create sequence features from searches</li>
2710 <li>Precalculated annotations can be loaded onto
2712 <li>Features file allows grouping of features</li>
2713 <li>Annotation Colouring scheme added</li>
2714 <li>Smooth fonts off by default - Faster rendering</li>
2715 <li>Choose to toggle Autocalculate Consensus On/Off</li>
2720 <li>Drag & Drop fixed on Linux</li>
2721 <li>Jalview Archive file faster to load/save, sequence
2722 descriptions saved.</li>
2728 <div align="center">
2729 <strong>2.07</strong><br> 12/12/05
2734 <li>PDB Structure Viewer enhanced</li>
2735 <li>Sequence Feature retrieval and display enhanced</li>
2736 <li>Choose to output sequence start-end after sequence
2737 name for file output</li>
2738 <li>Sequence Fetcher WSDBFetch@EBI</li>
2739 <li>Applet can read feature files, PDB files and can be
2740 used for HTML form input</li>
2745 <li>HTML output writes groups and features</li>
2746 <li>Group editing is Control and mouse click</li>
2747 <li>File IO bugs</li>
2753 <div align="center">
2754 <strong>2.06</strong><br> 28/9/05
2759 <li>View annotations in wrapped mode</li>
2760 <li>More options for PCA viewer</li>
2765 <li>GUI bugs resolved</li>
2766 <li>Runs with -nodisplay from command line</li>
2772 <div align="center">
2773 <strong>2.05b</strong><br> 15/9/05
2778 <li>Choose EPS export as lineart or text</li>
2779 <li>Jar files are executable</li>
2780 <li>Can read in Uracil - maps to unknown residue</li>
2785 <li>Known OutOfMemory errors give warning message</li>
2786 <li>Overview window calculated more efficiently</li>
2787 <li>Several GUI bugs resolved</li>
2793 <div align="center">
2794 <strong>2.05</strong><br> 30/8/05
2799 <li>Edit and annotate in "Wrapped" view</li>
2804 <li>Several GUI bugs resolved</li>
2810 <div align="center">
2811 <strong>2.04</strong><br> 24/8/05
2816 <li>Hold down mouse wheel & scroll to change font
2822 <li>Improved JPred client reliability</li>
2823 <li>Improved loading of Jalview files</li>
2829 <div align="center">
2830 <strong>2.03</strong><br> 18/8/05
2835 <li>Set Proxy server name and port in preferences</li>
2836 <li>Multiple URL links from sequence ids</li>
2837 <li>User Defined Colours can have a scheme name and added
2839 <li>Choose to ignore gaps in consensus calculation</li>
2840 <li>Unix users can set default web browser</li>
2841 <li>Runs without GUI for batch processing</li>
2842 <li>Dynamically generated Web Service Menus</li>
2847 <li>InstallAnywhere download for Sparc Solaris</li>
2853 <div align="center">
2854 <strong>2.02</strong><br> 18/7/05
2860 <li>Copy & Paste order of sequences maintains
2861 alignment order.</li>
2867 <div align="center">
2868 <strong>2.01</strong><br> 12/7/05
2873 <li>Use delete key for deleting selection.</li>
2874 <li>Use Mouse wheel to scroll sequences.</li>
2875 <li>Help file updated to describe how to add alignment
2877 <li>Version and build date written to build properties
2879 <li>InstallAnywhere installation will check for updates
2880 at launch of Jalview.</li>
2885 <li>Delete gaps bug fixed.</li>
2886 <li>FileChooser sorts columns.</li>
2887 <li>Can remove groups one by one.</li>
2888 <li>Filechooser icons installed.</li>
2889 <li>Finder ignores return character when searching.
2890 Return key will initiate a search.<br>
2897 <div align="center">
2898 <strong>2.0</strong><br> 20/6/05
2903 <li>New codebase</li>