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>8/8/2017</em></strong>
77 <td><div align="left">
80 <li><!-- JAL-2379 -->Revised implementation of PCA for speed and memory efficiency (~30x faster)</li>
81 <li><!-- JAL-2500 -->Trees computed on Sequence Feature Similarity may have different topology due to increased precision</li>
82 <li><!-- JAL-2360,JAL-2371, -->More robust colours and shader model for alignments and groups</li>
83 <li><!-- JAL-384 -->Custom shading schemes created via groovy scripts</li>
84 <li><!-- JAL-2491 -->linked scrolling of CDS/Protein views via Overview or sequence motif search operations</li>
85 <li><!-- JAL-2526 -->Efficiency improvements for interacting with alignment and overview windows</li>
86 <li><!-- JAL-2388 -->Hidden columns and sequences can be omitted in Overview</li>
88 <!-- JAL-2535 -->Posterior probability annotation from
89 Stockholm files imported as sequence associated annotation
92 <!-- JAL-2533 -->Sequence names don't include file
93 extension when importing structure files without embedded
94 names or PDB accessions
96 <li><!-- JAL-2547 -->Amend sequence features dialog box can be opened by double clicking gaps within sequence feature extent</li>
97 <li><!-- JAL-2631 -->Graduated feature colour style example included in the example feature file</li>
103 Experimental Features Checkbox in Desktop's Tools
104 menu to hide or show untested features in the application.
106 <li><!-- JAL-1476 -->Warning in alignment status bar when there are not enough columns to superimpose structures in Chimera</li>
107 <li><!-- JAL-1596 -->Faster Chimera/Jalview communication by file-based command exchange</li>
108 <li><!-- JAL-2316, -->URLs for viewing database cross-references provided by identifiers.org and the EMBL-EBI's MIRIAM DB</li>
109 <li><!-- JAL-2549 -->Updated JABAWS client to v2.2</li>
111 <em>Experimental features</em>
114 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
115 to transfer Chimera's structure attributes as Jalview
116 features, and vice-versa.
125 <li><!-- JAL-2474 -->Added PrivilegedAccessor to test suite</li>
126 <li><!-- JAL-2326 -->Prevent or clear modal dialogs raised during tests</li>
130 <li><!-- JAL-2344 -->FileFormatI interface for describing and identifying file formats (instead of String constants)</li>
133 </div></td><td><div align="left">
137 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
138 matrix - C->R should be '-3'<br />Old matrix restored with
139 this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
142 <!-- JAL-2397 -->Fixed Jalview's treatment of gaps in PCA
143 and substitution matrix based Tree calculations.<br />In
144 earlier versions of Jalview, gaps matching gaps were
145 penalised, and gaps matching non-gaps penalised even more.
146 In the PCA calculation, gaps were actually treated as
147 non-gaps - so different costs were applied, which meant
148 Jalview's PCAs were different to those produced by
149 SeqSpace.<br />Jalview now treats gaps in the same way as
150 SeqSpace (ie it scores them as 0). To restore pre-2.10.2
152 jalview.viewmodel.PCAModel.scoreGapAsAny=true // for
154 jalview.viewmodel.PCAModel.scoreGapAsAny=false // to
157 <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>
158 <li><!-- JAL-2430 -->Hidden regions in alignment views are not coloured in linked structure views</li>
159 <li><!-- JAL-2419 -->Current selection lost if popup menu opened on a region of alignment without groups</li>
160 <li><!-- JAL-2374 -->Popup menu not always shown for regions of an alignment with overlapping groups</li>
161 <li><!-- JAL-2310 -->Finder double counts if both a sequence's name and description match</li>
162 <li><!-- JAL-2370 -->Hiding column selection containing two hidden regions results in incorrect hidden regions</li>
163 <li><!-- JAL-2377 -->PCA calculation could hang when generating output report when working with highly redundant alignments</li>
164 <li><!-- JAL-2365 -->Cannot configure feature colours with lightGray or darkGray via features file</li>
165 <li><!-- JAL-2421 -->Overview window visible region moves erratically when hidden rows or columns are present</li>
166 <li><!-- JAL-2362 -->Per-residue colourschemes applied via the Structure Viewer's colour menu don't correspond to sequence colouring</li>
167 <li><!-- JAL-2405 -->Protein specific colours only offered in colour and group colour menu for protein alignments</li>
168 <li><!-- JAL-2386 -->'Apply to all groups' setting when changing colour does not apply Conservation slider value to all groups</li>
169 <li><!-- JAL-2385 -->Colour threshold slider doesn't update to reflect currently selected view or group's shading thresholds</li>
170 <li><!-- JAL-2373 -->Percentage identity and conservation menu items do not show a tick or allow shading to be disabled</li>
171 <li><!-- JAL-2385 -->Conservation shading or PID threshold lost when base colourscheme changed if slider not visible</li>
172 <li><!-- JAL-2547 -->Sequence features shown in tooltip for gaps before start of features</li>
173 <li><!-- JAL-2576 -->Very large alignments take a long time to load</li>
174 <li><!-- JAL-2623 -->Graduated feature colour threshold not restored to UI when feature colour is edited</li>
175 <li><!-- JAL-2624 -->Feature colour thresholds not respected when rendered on overview and structures when opacity at 100%</li>
176 <li><!-- JAL-2630 -->Structure and alignment overview update as graduate feature colour settings are modified via the dialog box</li>
177 <li><!-- JAL-147 -->Vertical scrollbar jumps one page-width at a time when scrolling vertically in wrapped mode.</li>
178 <li><!-- JAL-2034 -->Overview window doesn't always update when a group defined on the alignment is resized</li>
179 <li><!-- JAL-2605 -->Mouseovers on left/right scale region in wrapped view result in positional status updates</li>
180 <li><!-- JAL-2563 -->Status bar shows position for ambiguous amino acid and nucleotide symbols</li>
181 <li><!-- JAL-2602 -->Copy consensus sequence failed if alignment included gapped columns</li>
182 <li><!-- JAL-2589 -->User defined gap colour not shown in overview when features overlaid on alignment</li>
184 <strong>Documentation</strong>
186 <li><!-- JAL-2339 -->Release notes reformatted for readibility with the built-in Java help viewer</li>
190 <li><!-- JAL-2401 -->Easier creation of colours for all 'Lower case' residues (button in colourscheme editor debugged and new documentation and tooltips added)</li>
191 <li><!-- JAL-2399-->Text colour threshold's 'Cancel' button doesn't restore group-specific text colour thresholds</li>
192 <li><!-- JAL-2243 -->Feature settings panel does not update as new features are added to alignment</li>
193 <li><!-- JAL-2436 -->Structure viewer's View -> Colour By view selection menu changes colours of alignment views</li>
194 <li><!-- JAL-2366 -->Proxy server address and port always appear enabled in Preferences->Connections</li>
195 <li><!-- JAL-2426 -->Spurious exceptions in console raised from alignment calculation workers after alignment has been closed</li>
196 <li><!-- JAL-1608 -->Typo in selection popup menu - Create groups now 'Create Group'</li>
197 <li><!-- JAL-1608 -->CMD/CTRL and G or Shift G for Create/Undefine group doesn't always work</li>
198 <li><!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get shown again after pressing 'Cancel'</li>
199 <li><!-- JAL-2461 -->DAS registry not found exceptions removed from console output</li>
200 <li><!-- JAL-2383 -->Above PID colour threshold not recovered when alignment view imported from project</li>
201 <li><!-- JAL-2465 -->No mappings generated between structure and sequences extracted from structure files imported via URL</li>
203 <!-- JAL-2520 -->Structures loaded via URL are saved in
204 Jalview Projects rather than fetched via URL again when
205 the project is loaded and the structure viewed
207 <li><!-- JAL-1256 -->Trackpad horizontal scroll gesture adjusts start position in wrap mode</li>
208 <li><!-- JAL-2563 -->Status bar doesn't show positions for ambiguous amino acids</li>
209 <li><!-- JAL-2291 -->Hide insertions in PopUp menu excludes gaps in selection, current sequence and only within selected columns</li>
210 <li><!-- JAL-2582 -->Cannot retrieve protein products from Ensembl by Peptide ID</li>
211 <li><!-- JAL-2431 -->cDNA Consensus annotation not shown in CDS/Protein view after CDS sequences added for aligned proteins</li>
215 <li><!-- JAL-2468 -->Switching between Nucleotide and Protein score models doesn't always result in an updated PCA plot</li>
216 <li><!-- JAL-2442 -->Features not rendered as transparent on overview or linked structure view</li>
217 <li><!-- JAL-2372 -->Colour group by conservation doesn't work (since 2.8)</li>
218 <li><!-- JAL-2517 -->Hitting Cancel after applying user-defined colourscheme doesn't restore original colourscheme</li>
220 <em>New Known Issues</em>
222 <li><!-- JAL-2566 -->Protein/CDS view scrolling not always in phase after a sequence motif find operation</li>
223 <li><!-- JAL-2550 -->Importing annotation file with rows containing just upper and lower case letters are interpreted as WUSS rna secondary structure symbols</li>
224 <li><!-- JAL-2590 -->Cannot load Newick trees from eggnog ortholog database</li>
227 <ul><li><!-- JAL-2314 -->Unit test failure: jalview.ws.jabaws.RNAStructExportImport setup fails</li>
228 <li><!-- JAL- --></li>
232 <td width="60" nowrap>
234 <strong><a name="Jalview.2.10.1">2.10.1</a><br />
235 <em>29/11/2016</em></strong>
238 <td><div align="left">
242 <!-- JAL-98 -->Improved memory usage: sparse arrays used
243 for all consensus calculations
246 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released 3rd Oct 2016)
248 <li>Updated Jalview's Certum code signing certificate
254 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
255 set of database cross-references, sorted alphabetically
258 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
259 from database cross references. Users with custom links
260 will receive a <a href="webServices/urllinks.html#warning">warning
261 dialog</a> asking them to update their preferences.
264 <!-- JAL-2287-->Cancel button and escape listener on
265 dialog warning user about disconnecting Jalview from a
269 <!-- JAL-2320-->Jalview's Chimera control window closes if
270 the Chimera it is connected to is shut down
273 <!-- JAL-1738-->New keystroke (B) and Select highlighted
274 columns menu item to mark columns containing
275 highlighted regions (e.g. from structure selections or results
279 <!-- JAL-2284-->Command line option for batch-generation
280 of HTML pages rendering alignment data with the BioJS
290 <!-- JAL-2286 -->Columns with more than one modal residue
291 are not coloured or thresholded according to percent
292 identity (first observed in Jalview 2.8.2)
295 <!-- JAL-2301 -->Threonine incorrectly reported as not
299 <!-- JAL-2318 -->Updates to documentation pages (above PID
300 threshold, amino acid properties)
303 <!-- JAL-2292 -->Lower case residues in sequences are not
304 reported as mapped to residues in a structure file in the
308 <!--JAL-2324 -->Identical features with non-numeric scores
309 could be added multiple times to a sequence
312 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
313 bond features shown as two highlighted residues rather
314 than a range in linked structure views, and treated
315 correctly when selecting and computing trees from features
318 <!-- JAL-2281-->Custom URL links for database
319 cross-references are matched to database name regardless
327 <!-- JAL-2282-->Custom URL links for specific database
328 names without regular expressions also offer links from
332 <!-- JAL-2315-->Removing a single configured link in the
333 URL links pane in Connections preferences doesn't actually
334 update Jalview configuration
337 <!-- JAL-2272-->CTRL-Click on a selected region to open
338 the alignment area popup menu doesn't work on El-Capitan
341 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
342 files with similarly named sequences if dropped onto the
346 <!-- JAL-2312 -->Additional mappings are shown for PDB
347 entries where more chains exist in the PDB accession than
348 are reported in the SIFTS file
351 <!-- JAL-2317-->Certain structures do not get mapped to
352 the structure view when displayed with Chimera
355 <!-- JAL-2317-->No chains shown in the Chimera view
356 panel's View->Show Chains submenu
359 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
360 work for wrapped alignment views
363 <!--JAL-2197 -->Rename UI components for running JPred
364 predictions from 'JNet' to 'JPred'
367 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
368 corrupted when annotation panel vertical scroll is not at
372 <!--JAL-2332 -->Attempting to view structure for Hen
373 lysozyme results in a PDB Client error dialog box
376 <!-- JAL-2319 -->Structure View's mapping report switched ranges for PDB and sequence for SIFTS</li>
377 <!-- JAL-2319 -->SIFTS 'Not_Observed' residues mapped to non-existant coordindate data</li>
379 <!-- <em>New Known Issues</em>
386 <td width="60" nowrap>
388 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
389 <em>25/10/2016</em></strong>
392 <td><em>Application</em>
394 <li>3D Structure chooser opens with 'Cached structures'
395 view if structures already loaded</li>
396 <li>Progress bar reports models as they are loaded to
403 <li>Colour by conservation always enabled and no tick
404 shown in menu when BLOSUM or PID shading applied</li>
405 <li>FER1_ARATH and FER2_ARATH labels were switched in
406 example sequences/projects/trees</li>
410 <li>Jalview projects with views of local PDB structure
411 files saved on Windows cannot be opened on OSX</li>
412 <li>Multiple structure views can be opened and
413 superposed without timeout for structures with multiple
414 models or multiple sequences in alignment</li>
415 <li>Cannot import or associated local PDB files without
416 a PDB ID HEADER line</li>
417 <li>RMSD is not output in Jmol console when
418 superposition is performed</li>
419 <li>Drag and drop of URL from Browser fails for Linux
420 and OSX versions earlier than El Capitan</li>
421 <li>ENA client ignores invalid content from ENA server</li>
422 <li>Exceptions are not raised in console when ENA
423 client attempts to fetch non-existent IDs via Fetch DB
425 <li>Exceptions are not raised in console when a new
426 view is created on the alignment</li>
427 <li>OSX right-click fixed for group selections:
428 CMD-click to insert/remove gaps in groups and CTRL-click
429 to open group pop-up menu</li>
431 <em>Build and deployment</em>
433 <li>URL link checker now copes with multi-line anchor
436 <em>New Known Issues</em>
438 <li>Drag and drop from URL links in browsers do not
445 <td width="60" nowrap>
447 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
453 <!-- JAL-2124 -->Updated Spanish translations.
456 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
457 for importing structure data to Jalview. Enables mmCIF and
461 <!-- JAL-192 --->Alignment ruler shows positions relative to
465 <!-- JAL-2202 -->Position/residue shown in status bar when
466 mousing over sequence associated annotation
469 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
473 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
474 '()', canonical '[]' and invalid '{}' base pair populations
478 <!-- JAL-2092 -->Feature settings popup menu options for
479 showing or hiding columns containing a feature
482 <!-- JAL-1557 -->Edit selected group by double clicking on
483 group and sequence associated annotation labels
486 <!-- JAL-2236 -->Sequence name added to annotation label in
487 select/hide columns by annotation and colour by annotation
491 </ul> <em>Application</em>
494 <!-- JAL-2050-->Automatically hide introns when opening a
498 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
502 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
503 structure mappings with the EMBL-EBI PDBe SIFTS database
506 <!-- JAL-2079 -->Updated download sites used for Rfam and
507 Pfam sources to xfam.org
510 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
513 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
514 over sequences in Jalview
517 <!-- JAL-2027-->Support for reverse-complement coding
518 regions in ENA and EMBL
521 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
522 for record retrieval via ENA rest API
525 <!-- JAL-2027 -->Support for ENA CDS records with reverse
529 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
530 groovy script execution
533 <!-- JAL-1812 -->New 'execute Groovy script' option in an
534 alignment window's Calculate menu
537 <!-- JAL-1812 -->Allow groovy scripts that call
538 Jalview.getAlignFrames() to run in headless mode
541 <!-- JAL-2068 -->Support for creating new alignment
542 calculation workers from groovy scripts
545 <!-- JAL-1369 --->Store/restore reference sequence in
549 <!-- JAL-1803 -->Chain codes for a sequence's PDB
550 associations are now saved/restored from project
553 <!-- JAL-1993 -->Database selection dialog always shown
554 before sequence fetcher is opened
557 <!-- JAL-2183 -->Double click on an entry in Jalview's
558 database chooser opens a sequence fetcher
561 <!-- JAL-1563 -->Free-text search client for UniProt using
565 <!-- JAL-2168 -->-nonews command line parameter to prevent
566 the news reader opening
569 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
570 querying stored in preferences
573 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
577 <!-- JAL-1977-->Tooltips shown on database chooser
580 <!-- JAL-391 -->Reverse complement function in calculate
581 menu for nucleotide sequences
584 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
585 and feature counts preserves alignment ordering (and
586 debugged for complex feature sets).
589 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
590 viewing structures with Jalview 2.10
593 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
594 genome, transcript CCDS and gene ids via the Ensembl and
595 Ensembl Genomes REST API
598 <!-- JAL-2049 -->Protein sequence variant annotation
599 computed for 'sequence_variant' annotation on CDS regions
603 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
607 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
608 Ref Fetcher fails to match, or otherwise updates sequence
609 data from external database records.
612 <!-- JAL-2154 -->Revised Jalview Project format for
613 efficient recovery of sequence coding and alignment
614 annotation relationships.
616 </ul> <!-- <em>Applet</em>
627 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
631 <!-- JAL-2018-->Export features in Jalview format (again)
632 includes graduated colourschemes
635 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
636 working with big alignments and lots of hidden columns
639 <!-- JAL-2053-->Hidden column markers not always rendered
640 at right of alignment window
643 <!-- JAL-2067 -->Tidied up links in help file table of
647 <!-- JAL-2072 -->Feature based tree calculation not shown
651 <!-- JAL-2075 -->Hidden columns ignored during feature
652 based tree calculation
655 <!-- JAL-2065 -->Alignment view stops updating when show
656 unconserved enabled for group on alignment
659 <!-- JAL-2086 -->Cannot insert gaps into sequence when
663 <!-- JAL-2146 -->Alignment column in status incorrectly
664 shown as "Sequence position" when mousing over
668 <!-- JAL-2099 -->Incorrect column numbers in ruler when
669 hidden columns present
672 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
673 user created annotation added to alignment
676 <!-- JAL-1841 -->RNA Structure consensus only computed for
677 '()' base pair annotation
680 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
681 in zero scores for all base pairs in RNA Structure
685 <!-- JAL-2174-->Extend selection with columns containing
689 <!-- JAL-2275 -->Pfam format writer puts extra space at
690 beginning of sequence
693 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
697 <!-- JAL-2238 -->Cannot create groups on an alignment from
698 from a tree when t-coffee scores are shown
701 <!-- JAL-1836,1967 -->Cannot import and view PDB
702 structures with chains containing negative resnums (4q4h)
705 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
709 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
710 to Clustal, PIR and PileUp output
713 <!-- JAL-2008 -->Reordering sequence features that are
714 not visible causes alignment window to repaint
717 <!-- JAL-2006 -->Threshold sliders don't work in
718 graduated colour and colour by annotation row for e-value
719 scores associated with features and annotation rows
722 <!-- JAL-1797 -->amino acid physicochemical conservation
723 calculation should be case independent
726 <!-- JAL-2173 -->Remove annotation also updates hidden
730 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
731 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
732 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
735 <!-- JAL-2065 -->Null pointer exceptions and redraw
736 problems when reference sequence defined and 'show
737 non-conserved' enabled
740 <!-- JAL-1306 -->Quality and Conservation are now shown on
741 load even when Consensus calculation is disabled
744 <!-- JAL-1932 -->Remove right on penultimate column of
745 alignment does nothing
751 <!-- JAL-1552-->URLs and links can't be imported by
752 drag'n'drop on OSX when launched via webstart (note - not
753 yet fixed for El Capitan)
756 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
757 output when running on non-gb/us i18n platforms
760 <!-- JAL-1944 -->Error thrown when exporting a view with
761 hidden sequences as flat-file alignment
764 <!-- JAL-2030-->InstallAnywhere distribution fails when
768 <!-- JAL-2080-->Jalview very slow to launch via webstart
769 (also hotfix for 2.9.0b2)
772 <!-- JAL-2085 -->Cannot save project when view has a
773 reference sequence defined
776 <!-- JAL-1011 -->Columns are suddenly selected in other
777 alignments and views when revealing hidden columns
780 <!-- JAL-1989 -->Hide columns not mirrored in complement
781 view in a cDNA/Protein splitframe
784 <!-- JAL-1369 -->Cannot save/restore representative
785 sequence from project when only one sequence is
789 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
793 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
794 structure consensus didn't refresh annotation panel
797 <!-- JAL-1962 -->View mapping in structure view shows
798 mappings between sequence and all chains in a PDB file
801 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
802 dialogs format columns correctly, don't display array
803 data, sort columns according to type
806 <!-- JAL-1975 -->Export complete shown after destination
807 file chooser is cancelled during an image export
810 <!-- JAL-2025 -->Error when querying PDB Service with
811 sequence name containing special characters
814 <!-- JAL-2024 -->Manual PDB structure querying should be
818 <!-- JAL-2104 -->Large tooltips with broken HTML
819 formatting don't wrap
822 <!-- JAL-1128 -->Figures exported from wrapped view are
823 truncated so L looks like I in consensus annotation
826 <!-- JAL-2003 -->Export features should only export the
827 currently displayed features for the current selection or
831 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
832 after fetching cross-references, and restoring from project
835 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
836 followed in the structure viewer
839 <!-- JAL-2163 -->Titles for individual alignments in
840 splitframe not restored from project
843 <!-- JAL-2145 -->missing autocalculated annotation at
844 trailing end of protein alignment in transcript/product
845 splitview when pad-gaps not enabled by default
848 <!-- JAL-1797 -->amino acid physicochemical conservation
852 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
853 article has been read (reopened issue due to
854 internationalisation problems)
857 <!-- JAL-1960 -->Only offer PDB structures in structure
858 viewer based on sequence name, PDB and UniProt
863 <!-- JAL-1976 -->No progress bar shown during export of
867 <!-- JAL-2213 -->Structures not always superimposed after
868 multiple structures are shown for one or more sequences.
871 <!-- JAL-1370 -->Reference sequence characters should not
872 be replaced with '.' when 'Show unconserved' format option
876 <!-- JAL-1823 -->Cannot specify chain code when entering
877 specific PDB id for sequence
880 <!-- JAL-1944 -->File->Export->.. as doesn't work when
881 'Export hidden sequences' is enabled, but 'export hidden
882 columns' is disabled.
885 <!--JAL-2026-->Best Quality option in structure chooser
886 selects lowest rather than highest resolution structures
890 <!-- JAL-1887 -->Incorrect start and end reported for PDB
891 to sequence mapping in 'View Mappings' report
894 <!-- JAL-2284 -->Unable to read old Jalview projects that
895 contain non-XML data added after Jalvew wrote project.
897 <li><!-- JAL-2118 -->Newly created annotation row reorders
898 after clicking on it to create new annotation for a
901 <!-- may exclude, this is an external service stability issue JAL-1941
902 -- > RNA 3D structure not added via DSSR service</li> -->
907 <!-- JAL-2151 -->Incorrect columns are selected when
908 hidden columns present before start of sequence
911 <!-- JAL-1986 -->Missing dependencies on applet pages
915 <!-- JAL-1947 -->Overview pixel size changes when
916 sequences are hidden in applet
919 <!-- JAL-1996 -->Updated instructions for applet
920 deployment on examples pages.
927 <td width="60" nowrap>
929 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
930 <em>16/10/2015</em></strong>
935 <li>Time stamps for signed Jalview application and applet
942 <li>Duplicate group consensus and conservation rows
943 shown when tree is partitioned</li>
944 <li>Erratic behaviour when tree partitions made with
945 multiple cDNA/Protein split views</li>
951 <td width="60" nowrap>
953 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
954 <em>8/10/2015</em></strong>
959 <li>Updated Spanish translations of localized text for
961 </ul> <em>Application</em>
963 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
964 <li>Signed OSX InstallAnywhere installer<br></li>
965 <li>Support for per-sequence based annotations in BioJSON</li>
966 </ul> <em>Applet</em>
968 <li>Split frame example added to applet examples page</li>
969 </ul><em>Build and Deployment</em>
971 <li><!-- JAL-1888 -->New ant target for running Jalview's test suite</li>
977 <li>Mapping of cDNA to protein in split frames
978 incorrect when sequence start > 1</li>
979 <li>Broken images in filter column by annotation dialog
981 <li>Feature colours not parsed from features file</li>
982 <li>Exceptions and incomplete link URLs recovered when
983 loading a features file containing HTML tags in feature
989 <li>Annotations corrupted after BioJS export and
991 <li>Incorrect sequence limits after Fetch DB References
992 with 'trim retrieved sequences'</li>
993 <li>Incorrect warning about deleting all data when
994 deleting selected columns</li>
995 <li>Patch to build system for shipping properly signed
996 JNLP templates for webstart launch</li>
997 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
998 unreleased structures for download or viewing</li>
999 <li>Tab/space/return keystroke operation of EMBL-PDBe
1000 fetcher/viewer dialogs works correctly</li>
1001 <li>Disabled 'minimise' button on Jalview windows
1002 running on OSX to workaround redraw hang bug</li>
1003 <li>Split cDNA/Protein view position and geometry not
1004 recovered from jalview project</li>
1005 <li>Initial enabled/disabled state of annotation menu
1006 sorter 'show autocalculated first/last' corresponds to
1008 <li>Restoring of Clustal, RNA Helices and T-Coffee
1009 color schemes from BioJSON</li>
1013 <li>Reorder sequences mirrored in cDNA/Protein split
1015 <li>Applet with Jmol examples not loading correctly</li>
1021 <td><div align="center">
1022 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1024 <td><em>General</em>
1026 <li>Linked visualisation and analysis of DNA and Protein
1029 <li>Translated cDNA alignments shown as split protein
1030 and DNA alignment views</li>
1031 <li>Codon consensus annotation for linked protein and
1032 cDNA alignment views</li>
1033 <li>Link cDNA or Protein product sequences by loading
1034 them onto Protein or cDNA alignments</li>
1035 <li>Reconstruct linked cDNA alignment from aligned
1036 protein sequences</li>
1039 <li>Jmol integration updated to Jmol v14.2.14</li>
1040 <li>Import and export of Jalview alignment views as <a
1041 href="features/bioJsonFormat.html">BioJSON</a></li>
1042 <li>New alignment annotation file statements for
1043 reference sequences and marking hidden columns</li>
1044 <li>Reference sequence based alignment shading to
1045 highlight variation</li>
1046 <li>Select or hide columns according to alignment
1048 <li>Find option for locating sequences by description</li>
1049 <li>Conserved physicochemical properties shown in amino
1050 acid conservation row</li>
1051 <li>Alignments can be sorted by number of RNA helices</li>
1052 </ul> <em>Application</em>
1054 <li>New cDNA/Protein analysis capabilities
1056 <li>Get Cross-References should open a Split Frame
1057 view with cDNA/Protein</li>
1058 <li>Detect when nucleotide sequences and protein
1059 sequences are placed in the same alignment</li>
1060 <li>Split cDNA/Protein views are saved in Jalview
1065 <li>Use REST API to talk to Chimera</li>
1066 <li>Selected regions in Chimera are highlighted in linked
1067 Jalview windows</li>
1069 <li>VARNA RNA viewer updated to v3.93</li>
1070 <li>VARNA views are saved in Jalview Projects</li>
1071 <li>Pseudoknots displayed as Jalview RNA annotation can
1072 be shown in VARNA</li>
1074 <li>Make groups for selection uses marked columns as well
1075 as the active selected region</li>
1077 <li>Calculate UPGMA and NJ trees using sequence feature
1079 <li>New Export options
1081 <li>New Export Settings dialog to control hidden
1082 region export in flat file generation</li>
1084 <li>Export alignment views for display with the <a
1085 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1087 <li>Export scrollable SVG in HTML page</li>
1088 <li>Optional embedding of BioJSON data when exporting
1089 alignment figures to HTML</li>
1091 <li>3D structure retrieval and display
1093 <li>Free text and structured queries with the PDBe
1095 <li>PDBe Search API based discovery and selection of
1096 PDB structures for a sequence set</li>
1100 <li>JPred4 employed for protein secondary structure
1102 <li>Hide Insertions menu option to hide unaligned columns
1103 for one or a group of sequences</li>
1104 <li>Automatically hide insertions in alignments imported
1105 from the JPred4 web server</li>
1106 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1107 system on OSX<br />LGPL libraries courtesy of <a
1108 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1110 <li>changed 'View nucleotide structure' submenu to 'View
1111 VARNA 2D Structure'</li>
1112 <li>change "View protein structure" menu option to "3D
1115 </ul> <em>Applet</em>
1117 <li>New layout for applet example pages</li>
1118 <li>New parameters to enable SplitFrame view
1119 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1120 <li>New example demonstrating linked viewing of cDNA and
1121 Protein alignments</li>
1122 </ul> <em>Development and deployment</em>
1124 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1125 <li>Include installation type and git revision in build
1126 properties and console log output</li>
1127 <li>Jalview Github organisation, and new github site for
1128 storing BioJsMSA Templates</li>
1129 <li>Jalview's unit tests now managed with TestNG</li>
1132 <!-- <em>General</em>
1134 </ul> --> <!-- issues resolved --> <em>Application</em>
1136 <li>Escape should close any open find dialogs</li>
1137 <li>Typo in select-by-features status report</li>
1138 <li>Consensus RNA secondary secondary structure
1139 predictions are not highlighted in amber</li>
1140 <li>Missing gap character in v2.7 example file means
1141 alignment appears unaligned when pad-gaps is not enabled</li>
1142 <li>First switch to RNA Helices colouring doesn't colour
1143 associated structure views</li>
1144 <li>ID width preference option is greyed out when auto
1145 width checkbox not enabled</li>
1146 <li>Stopped a warning dialog from being shown when
1147 creating user defined colours</li>
1148 <li>'View Mapping' in structure viewer shows sequence
1149 mappings for just that viewer's sequences</li>
1150 <li>Workaround for superposing PDB files containing
1151 multiple models in Chimera</li>
1152 <li>Report sequence position in status bar when hovering
1153 over Jmol structure</li>
1154 <li>Cannot output gaps as '.' symbols with Selection ->
1155 output to text box</li>
1156 <li>Flat file exports of alignments with hidden columns
1157 have incorrect sequence start/end</li>
1158 <li>'Aligning' a second chain to a Chimera structure from
1160 <li>Colour schemes applied to structure viewers don't
1161 work for nucleotide</li>
1162 <li>Loading/cut'n'pasting an empty or invalid file leads
1163 to a grey/invisible alignment window</li>
1164 <li>Exported Jpred annotation from a sequence region
1165 imports to different position</li>
1166 <li>Space at beginning of sequence feature tooltips shown
1167 on some platforms</li>
1168 <li>Chimera viewer 'View | Show Chain' menu is not
1170 <li>'New View' fails with a Null Pointer Exception in
1171 console if Chimera has been opened</li>
1172 <li>Mouseover to Chimera not working</li>
1173 <li>Miscellaneous ENA XML feature qualifiers not
1175 <li>NPE in annotation renderer after 'Extract Scores'</li>
1176 <li>If two structures in one Chimera window, mouseover of
1177 either sequence shows on first structure</li>
1178 <li>'Show annotations' options should not make
1179 non-positional annotations visible</li>
1180 <li>Subsequence secondary structure annotation not shown
1181 in right place after 'view flanking regions'</li>
1182 <li>File Save As type unset when current file format is
1184 <li>Save as '.jar' option removed for saving Jalview
1186 <li>Colour by Sequence colouring in Chimera more
1188 <li>Cannot 'add reference annotation' for a sequence in
1189 several views on same alignment</li>
1190 <li>Cannot show linked products for EMBL / ENA records</li>
1191 <li>Jalview's tooltip wraps long texts containing no
1193 </ul> <em>Applet</em>
1195 <li>Jmol to JalviewLite mouseover/link not working</li>
1196 <li>JalviewLite can't import sequences with ID
1197 descriptions containing angle brackets</li>
1198 </ul> <em>General</em>
1200 <li>Cannot export and reimport RNA secondary structure
1201 via jalview annotation file</li>
1202 <li>Random helix colour palette for colour by annotation
1203 with RNA secondary structure</li>
1204 <li>Mouseover to cDNA from STOP residue in protein
1205 translation doesn't work.</li>
1206 <li>hints when using the select by annotation dialog box</li>
1207 <li>Jmol alignment incorrect if PDB file has alternate CA
1209 <li>FontChooser message dialog appears to hang after
1210 choosing 1pt font</li>
1211 <li>Peptide secondary structure incorrectly imported from
1212 annotation file when annotation display text includes 'e' or
1214 <li>Cannot set colour of new feature type whilst creating
1216 <li>cDNA translation alignment should not be sequence
1217 order dependent</li>
1218 <li>'Show unconserved' doesn't work for lower case
1220 <li>Nucleotide ambiguity codes involving R not recognised</li>
1221 </ul> <em>Deployment and Documentation</em>
1223 <li>Applet example pages appear different to the rest of
1224 www.jalview.org</li>
1225 </ul> <em>Application Known issues</em>
1227 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1228 <li>Misleading message appears after trying to delete
1230 <li>Jalview icon not shown in dock after InstallAnywhere
1231 version launches</li>
1232 <li>Fetching EMBL reference for an RNA sequence results
1233 fails with a sequence mismatch</li>
1234 <li>Corrupted or unreadable alignment display when
1235 scrolling alignment to right</li>
1236 <li>ArrayIndexOutOfBoundsException thrown when remove
1237 empty columns called on alignment with ragged gapped ends</li>
1238 <li>auto calculated alignment annotation rows do not get
1239 placed above or below non-autocalculated rows</li>
1240 <li>Jalview dekstop becomes sluggish at full screen in
1241 ultra-high resolution</li>
1242 <li>Cannot disable consensus calculation independently of
1243 quality and conservation</li>
1244 <li>Mouseover highlighting between cDNA and protein can
1245 become sluggish with more than one splitframe shown</li>
1246 </ul> <em>Applet Known Issues</em>
1248 <li>Core PDB parsing code requires Jmol</li>
1249 <li>Sequence canvas panel goes white when alignment
1250 window is being resized</li>
1256 <td><div align="center">
1257 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1259 <td><em>General</em>
1261 <li>Updated Java code signing certificate donated by
1263 <li>Features and annotation preserved when performing
1264 pairwise alignment</li>
1265 <li>RNA pseudoknot annotation can be
1266 imported/exported/displayed</li>
1267 <li>'colour by annotation' can colour by RNA and
1268 protein secondary structure</li>
1269 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1270 post-hoc with 2.9 release</em>)
1273 </ul> <em>Application</em>
1275 <li>Extract and display secondary structure for sequences
1276 with 3D structures</li>
1277 <li>Support for parsing RNAML</li>
1278 <li>Annotations menu for layout
1280 <li>sort sequence annotation rows by alignment</li>
1281 <li>place sequence annotation above/below alignment
1284 <li>Output in Stockholm format</li>
1285 <li>Internationalisation: improved Spanish (es)
1287 <li>Structure viewer preferences tab</li>
1288 <li>Disorder and Secondary Structure annotation tracks
1289 shared between alignments</li>
1290 <li>UCSF Chimera launch and linked highlighting from
1292 <li>Show/hide all sequence associated annotation rows for
1293 all or current selection</li>
1294 <li>disorder and secondary structure predictions
1295 available as dataset annotation</li>
1296 <li>Per-sequence rna helices colouring</li>
1299 <li>Sequence database accessions imported when fetching
1300 alignments from Rfam</li>
1301 <li>update VARNA version to 3.91</li>
1303 <li>New groovy scripts for exporting aligned positions,
1304 conservation values, and calculating sum of pairs scores.</li>
1305 <li>Command line argument to set default JABAWS server</li>
1306 <li>include installation type in build properties and
1307 console log output</li>
1308 <li>Updated Jalview project format to preserve dataset
1312 <!-- issues resolved --> <em>Application</em>
1314 <li>Distinguish alignment and sequence associated RNA
1315 structure in structure->view->VARNA</li>
1316 <li>Raise dialog box if user deletes all sequences in an
1318 <li>Pressing F1 results in documentation opening twice</li>
1319 <li>Sequence feature tooltip is wrapped</li>
1320 <li>Double click on sequence associated annotation
1321 selects only first column</li>
1322 <li>Redundancy removal doesn't result in unlinked
1323 leaves shown in tree</li>
1324 <li>Undos after several redundancy removals don't undo
1326 <li>Hide sequence doesn't hide associated annotation</li>
1327 <li>User defined colours dialog box too big to fit on
1328 screen and buttons not visible</li>
1329 <li>author list isn't updated if already written to
1330 Jalview properties</li>
1331 <li>Popup menu won't open after retrieving sequence
1333 <li>File open window for associate PDB doesn't open</li>
1334 <li>Left-then-right click on a sequence id opens a
1335 browser search window</li>
1336 <li>Cannot open sequence feature shading/sort popup menu
1337 in feature settings dialog</li>
1338 <li>better tooltip placement for some areas of Jalview
1340 <li>Allow addition of JABAWS Server which doesn't
1341 pass validation</li>
1342 <li>Web services parameters dialog box is too large to
1344 <li>Muscle nucleotide alignment preset obscured by
1346 <li>JABAWS preset submenus don't contain newly
1347 defined user preset</li>
1348 <li>MSA web services warns user if they were launched
1349 with invalid input</li>
1350 <li>Jalview cannot contact DAS Registy when running on
1353 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1354 'Superpose with' submenu not shown when new view
1358 </ul> <!-- <em>Applet</em>
1360 </ul> <em>General</em>
1362 </ul>--> <em>Deployment and Documentation</em>
1364 <li>2G and 1G options in launchApp have no effect on
1365 memory allocation</li>
1366 <li>launchApp service doesn't automatically open
1367 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1369 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1370 InstallAnywhere reports cannot find valid JVM when Java
1371 1.7_055 is available
1373 </ul> <em>Application Known issues</em>
1376 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1377 corrupted or unreadable alignment display when scrolling
1381 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1382 retrieval fails but progress bar continues for DAS retrieval
1383 with large number of ID
1386 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1387 flatfile output of visible region has incorrect sequence
1391 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1392 rna structure consensus doesn't update when secondary
1393 structure tracks are rearranged
1396 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1397 invalid rna structure positional highlighting does not
1398 highlight position of invalid base pairs
1401 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1402 out of memory errors are not raised when saving Jalview
1403 project from alignment window file menu
1406 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1407 Switching to RNA Helices colouring doesn't propagate to
1411 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1412 colour by RNA Helices not enabled when user created
1413 annotation added to alignment
1416 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1417 Jalview icon not shown on dock in Mountain Lion/Webstart
1419 </ul> <em>Applet Known Issues</em>
1422 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1423 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1426 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1427 Jalview and Jmol example not compatible with IE9
1430 <li>Sort by annotation score doesn't reverse order
1436 <td><div align="center">
1437 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1440 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1443 <li>Internationalisation of user interface (usually
1444 called i18n support) and translation for Spanish locale</li>
1445 <li>Define/Undefine group on current selection with
1446 Ctrl-G/Shift Ctrl-G</li>
1447 <li>Improved group creation/removal options in
1448 alignment/sequence Popup menu</li>
1449 <li>Sensible precision for symbol distribution
1450 percentages shown in logo tooltip.</li>
1451 <li>Annotation panel height set according to amount of
1452 annotation when alignment first opened</li>
1453 </ul> <em>Application</em>
1455 <li>Interactive consensus RNA secondary structure
1456 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1457 <li>Select columns containing particular features from
1458 Feature Settings dialog</li>
1459 <li>View all 'representative' PDB structures for selected
1461 <li>Update Jalview project format:
1463 <li>New file extension for Jalview projects '.jvp'</li>
1464 <li>Preserve sequence and annotation dataset (to
1465 store secondary structure annotation,etc)</li>
1466 <li>Per group and alignment annotation and RNA helix
1470 <li>New similarity measures for PCA and Tree calculation
1472 <li>Experimental support for retrieval and viewing of
1473 flanking regions for an alignment</li>
1477 <!-- issues resolved --> <em>Application</em>
1479 <li>logo keeps spinning and status remains at queued or
1480 running after job is cancelled</li>
1481 <li>cannot export features from alignments imported from
1482 Jalview/VAMSAS projects</li>
1483 <li>Buggy slider for web service parameters that take
1485 <li>Newly created RNA secondary structure line doesn't
1486 have 'display all symbols' flag set</li>
1487 <li>T-COFFEE alignment score shading scheme and other
1488 annotation shading not saved in Jalview project</li>
1489 <li>Local file cannot be loaded in freshly downloaded
1491 <li>Jalview icon not shown on dock in Mountain
1493 <li>Load file from desktop file browser fails</li>
1494 <li>Occasional NPE thrown when calculating large trees</li>
1495 <li>Cannot reorder or slide sequences after dragging an
1496 alignment onto desktop</li>
1497 <li>Colour by annotation dialog throws NPE after using
1498 'extract scores' function</li>
1499 <li>Loading/cut'n'pasting an empty file leads to a grey
1500 alignment window</li>
1501 <li>Disorder thresholds rendered incorrectly after
1502 performing IUPred disorder prediction</li>
1503 <li>Multiple group annotated consensus rows shown when
1504 changing 'normalise logo' display setting</li>
1505 <li>Find shows blank dialog after 'finished searching' if
1506 nothing matches query</li>
1507 <li>Null Pointer Exceptions raised when sorting by
1508 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1510 <li>Errors in Jmol console when structures in alignment
1511 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1513 <li>Not all working JABAWS services are shown in
1515 <li>JAVAWS version of Jalview fails to launch with
1516 'invalid literal/length code'</li>
1517 <li>Annotation/RNA Helix colourschemes cannot be applied
1518 to alignment with groups (actually fixed in 2.8.0b1)</li>
1519 <li>RNA Helices and T-Coffee Scores available as default
1522 </ul> <em>Applet</em>
1524 <li>Remove group option is shown even when selection is
1526 <li>Apply to all groups ticked but colourscheme changes
1527 don't affect groups</li>
1528 <li>Documented RNA Helices and T-Coffee Scores as valid
1529 colourscheme name</li>
1530 <li>Annotation labels drawn on sequence IDs when
1531 Annotation panel is not displayed</li>
1532 <li>Increased font size for dropdown menus on OSX and
1533 embedded windows</li>
1534 </ul> <em>Other</em>
1536 <li>Consensus sequence for alignments/groups with a
1537 single sequence were not calculated</li>
1538 <li>annotation files that contain only groups imported as
1539 annotation and junk sequences</li>
1540 <li>Fasta files with sequences containing '*' incorrectly
1541 recognised as PFAM or BLC</li>
1542 <li>conservation/PID slider apply all groups option
1543 doesn't affect background (2.8.0b1)
1545 <li>redundancy highlighting is erratic at 0% and 100%</li>
1546 <li>Remove gapped columns fails for sequences with ragged
1548 <li>AMSA annotation row with leading spaces is not
1549 registered correctly on import</li>
1550 <li>Jalview crashes when selecting PCA analysis for
1551 certain alignments</li>
1552 <li>Opening the colour by annotation dialog for an
1553 existing annotation based 'use original colours'
1554 colourscheme loses original colours setting</li>
1559 <td><div align="center">
1560 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
1561 <em>30/1/2014</em></strong>
1565 <li>Trusted certificates for JalviewLite applet and
1566 Jalview Desktop application<br />Certificate was donated by
1567 <a href="https://www.certum.eu">Certum</a> to the Jalview
1568 open source project).
1570 <li>Jalview SRS links replaced by UniProt and EBI-search
1572 <li>Output in Stockholm format</li>
1573 <li>Allow import of data from gzipped files</li>
1574 <li>Export/import group and sequence associated line
1575 graph thresholds</li>
1576 <li>Nucleotide substitution matrix that supports RNA and
1577 ambiguity codes</li>
1578 <li>Allow disorder predictions to be made on the current
1579 selection (or visible selection) in the same way that JPred
1581 <li>Groovy scripting for headless Jalview operation</li>
1582 </ul> <em>Other improvements</em>
1584 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
1585 <li>COMBINE statement uses current SEQUENCE_REF and
1586 GROUP_REF scope to group annotation rows</li>
1587 <li>Support '' style escaping of quotes in Newick
1589 <li>Group options for JABAWS service by command line name</li>
1590 <li>Empty tooltip shown for JABA service options with a
1591 link but no description</li>
1592 <li>Select primary source when selecting authority in
1593 database fetcher GUI</li>
1594 <li>Add .mfa to FASTA file extensions recognised by
1596 <li>Annotation label tooltip text wrap</li>
1601 <li>Slow scrolling when lots of annotation rows are
1603 <li>Lots of NPE (and slowness) after creating RNA
1604 secondary structure annotation line</li>
1605 <li>Sequence database accessions not imported when
1606 fetching alignments from Rfam</li>
1607 <li>Incorrect SHMR submission for sequences with
1609 <li>View all structures does not always superpose
1611 <li>Option widgets in service parameters not updated to
1612 reflect user or preset settings</li>
1613 <li>Null pointer exceptions for some services without
1614 presets or adjustable parameters</li>
1615 <li>Discover PDB IDs entry in structure menu doesn't
1616 discover PDB xRefs</li>
1617 <li>Exception encountered while trying to retrieve
1618 features with DAS</li>
1619 <li>Lowest value in annotation row isn't coloured
1620 when colour by annotation (per sequence) is coloured</li>
1621 <li>Keyboard mode P jumps to start of gapped region when
1622 residue follows a gap</li>
1623 <li>Jalview appears to hang importing an alignment with
1624 Wrap as default or after enabling Wrap</li>
1625 <li>'Right click to add annotations' message
1626 shown in wrap mode when no annotations present</li>
1627 <li>Disorder predictions fail with NPE if no automatic
1628 annotation already exists on alignment</li>
1629 <li>oninit javascript function should be called after
1630 initialisation completes</li>
1631 <li>Remove redundancy after disorder prediction corrupts
1632 alignment window display</li>
1633 <li>Example annotation file in documentation is invalid</li>
1634 <li>Grouped line graph annotation rows are not exported
1635 to annotation file</li>
1636 <li>Multi-harmony analysis cannot be run when only two
1638 <li>Cannot create multiple groups of line graphs with
1639 several 'combine' statements in annotation file</li>
1640 <li>Pressing return several times causes Number Format
1641 exceptions in keyboard mode</li>
1642 <li>Multi-harmony (SHMMR) method doesn't submit
1643 correct partitions for input data</li>
1644 <li>Translation from DNA to Amino Acids fails</li>
1645 <li>Jalview fail to load newick tree with quoted label</li>
1646 <li>--headless flag isn't understood</li>
1647 <li>ClassCastException when generating EPS in headless
1649 <li>Adjusting sequence-associated shading threshold only
1650 changes one row's threshold</li>
1651 <li>Preferences and Feature settings panel panel
1652 doesn't open</li>
1653 <li>hide consensus histogram also hides conservation and
1654 quality histograms</li>
1659 <td><div align="center">
1660 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
1662 <td><em>Application</em>
1664 <li>Support for JABAWS 2.0 Services (AACon alignment
1665 conservation, protein disorder and Clustal Omega)</li>
1666 <li>JABAWS server status indicator in Web Services
1668 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
1669 in Jalview alignment window</li>
1670 <li>Updated Jalview build and deploy framework for OSX
1671 mountain lion, windows 7, and 8</li>
1672 <li>Nucleotide substitution matrix for PCA that supports
1673 RNA and ambiguity codes</li>
1675 <li>Improved sequence database retrieval GUI</li>
1676 <li>Support fetching and database reference look up
1677 against multiple DAS sources (Fetch all from in 'fetch db
1679 <li>Jalview project improvements
1681 <li>Store and retrieve the 'belowAlignment'
1682 flag for annotation</li>
1683 <li>calcId attribute to group annotation rows on the
1685 <li>Store AACon calculation settings for a view in
1686 Jalview project</li>
1690 <li>horizontal scrolling gesture support</li>
1691 <li>Visual progress indicator when PCA calculation is
1693 <li>Simpler JABA web services menus</li>
1694 <li>visual indication that web service results are still
1695 being retrieved from server</li>
1696 <li>Serialise the dialogs that are shown when Jalview
1697 starts up for first time</li>
1698 <li>Jalview user agent string for interacting with HTTP
1700 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
1702 <li>Examples directory and Groovy library included in
1703 InstallAnywhere distribution</li>
1704 </ul> <em>Applet</em>
1706 <li>RNA alignment and secondary structure annotation
1707 visualization applet example</li>
1708 </ul> <em>General</em>
1710 <li>Normalise option for consensus sequence logo</li>
1711 <li>Reset button in PCA window to return dimensions to
1713 <li>Allow seqspace or Jalview variant of alignment PCA
1715 <li>PCA with either nucleic acid and protein substitution
1717 <li>Allow windows containing HTML reports to be exported
1719 <li>Interactive display and editing of RNA secondary
1720 structure contacts</li>
1721 <li>RNA Helix Alignment Colouring</li>
1722 <li>RNA base pair logo consensus</li>
1723 <li>Parse sequence associated secondary structure
1724 information in Stockholm files</li>
1725 <li>HTML Export database accessions and annotation
1726 information presented in tooltip for sequences</li>
1727 <li>Import secondary structure from LOCARNA clustalw
1728 style RNA alignment files</li>
1729 <li>import and visualise T-COFFEE quality scores for an
1731 <li>'colour by annotation' per sequence option to
1732 shade each sequence according to its associated alignment
1734 <li>New Jalview Logo</li>
1735 </ul> <em>Documentation and Development</em>
1737 <li>documentation for score matrices used in Jalview</li>
1738 <li>New Website!</li>
1740 <td><em>Application</em>
1742 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
1743 wsdbfetch REST service</li>
1744 <li>Stop windows being moved outside desktop on OSX</li>
1745 <li>Filetype associations not installed for webstart
1747 <li>Jalview does not always retrieve progress of a JABAWS
1748 job execution in full once it is complete</li>
1749 <li>revise SHMR RSBS definition to ensure alignment is
1750 uploaded via ali_file parameter</li>
1751 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
1752 <li>View all structures superposed fails with exception</li>
1753 <li>Jnet job queues forever if a very short sequence is
1754 submitted for prediction</li>
1755 <li>Cut and paste menu not opened when mouse clicked on
1757 <li>Putting fractional value into integer text box in
1758 alignment parameter dialog causes Jalview to hang</li>
1759 <li>Structure view highlighting doesn't work on
1761 <li>View all structures fails with exception shown in
1763 <li>Characters in filename associated with PDBEntry not
1764 escaped in a platform independent way</li>
1765 <li>Jalview desktop fails to launch with exception when
1767 <li>Tree calculation reports 'you must have 2 or more
1768 sequences selected' when selection is empty</li>
1769 <li>Jalview desktop fails to launch with jar signature
1770 failure when java web start temporary file caching is
1772 <li>DAS Sequence retrieval with range qualification
1773 results in sequence xref which includes range qualification</li>
1774 <li>Errors during processing of command line arguments
1775 cause progress bar (JAL-898) to be removed</li>
1776 <li>Replace comma for semi-colon option not disabled for
1777 DAS sources in sequence fetcher</li>
1778 <li>Cannot close news reader when JABAWS server warning
1779 dialog is shown</li>
1780 <li>Option widgets not updated to reflect user settings</li>
1781 <li>Edited sequence not submitted to web service</li>
1782 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
1783 <li>InstallAnywhere installer doesn't unpack and run
1784 on OSX Mountain Lion</li>
1785 <li>Annotation panel not given a scroll bar when
1786 sequences with alignment annotation are pasted into the
1788 <li>Sequence associated annotation rows not associated
1789 when loaded from Jalview project</li>
1790 <li>Browser launch fails with NPE on java 1.7</li>
1791 <li>JABAWS alignment marked as finished when job was
1792 cancelled or job failed due to invalid input</li>
1793 <li>NPE with v2.7 example when clicking on Tree
1794 associated with all views</li>
1795 <li>Exceptions when copy/paste sequences with grouped
1796 annotation rows to new window</li>
1797 </ul> <em>Applet</em>
1799 <li>Sequence features are momentarily displayed before
1800 they are hidden using hidefeaturegroups applet parameter</li>
1801 <li>loading features via javascript API automatically
1802 enables feature display</li>
1803 <li>scrollToColumnIn javascript API method doesn't
1805 </ul> <em>General</em>
1807 <li>Redundancy removal fails for rna alignment</li>
1808 <li>PCA calculation fails when sequence has been selected
1809 and then deselected</li>
1810 <li>PCA window shows grey box when first opened on OSX</li>
1811 <li>Letters coloured pink in sequence logo when alignment
1812 coloured with clustalx</li>
1813 <li>Choosing fonts without letter symbols defined causes
1814 exceptions and redraw errors</li>
1815 <li>Initial PCA plot view is not same as manually
1816 reconfigured view</li>
1817 <li>Grouped annotation graph label has incorrect line
1819 <li>Grouped annotation graph label display is corrupted
1820 for lots of labels</li>
1825 <div align="center">
1826 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
1829 <td><em>Application</em>
1831 <li>Jalview Desktop News Reader</li>
1832 <li>Tweaked default layout of web services menu</li>
1833 <li>View/alignment association menu to enable user to
1834 easily specify which alignment a multi-structure view takes
1835 its colours/correspondences from</li>
1836 <li>Allow properties file location to be specified as URL</li>
1837 <li>Extend Jalview project to preserve associations
1838 between many alignment views and a single Jmol display</li>
1839 <li>Store annotation row height in Jalview project file</li>
1840 <li>Annotation row column label formatting attributes
1841 stored in project file</li>
1842 <li>Annotation row order for auto-calculated annotation
1843 rows preserved in Jalview project file</li>
1844 <li>Visual progress indication when Jalview state is
1845 saved using Desktop window menu</li>
1846 <li>Visual indication that command line arguments are
1847 still being processed</li>
1848 <li>Groovy script execution from URL</li>
1849 <li>Colour by annotation default min and max colours in
1851 <li>Automatically associate PDB files dragged onto an
1852 alignment with sequences that have high similarity and
1854 <li>Update JGoogleAnalytics to latest release (0.3)</li>
1855 <li>'view structures' option to open many
1856 structures in same window</li>
1857 <li>Sort associated views menu option for tree panel</li>
1858 <li>Group all JABA and non-JABA services for a particular
1859 analysis function in its own submenu</li>
1860 </ul> <em>Applet</em>
1862 <li>Userdefined and autogenerated annotation rows for
1864 <li>Adjustment of alignment annotation pane height</li>
1865 <li>Annotation scrollbar for annotation panel</li>
1866 <li>Drag to reorder annotation rows in annotation panel</li>
1867 <li>'automaticScrolling' parameter</li>
1868 <li>Allow sequences with partial ID string matches to be
1869 annotated from GFF/Jalview features files</li>
1870 <li>Sequence logo annotation row in applet</li>
1871 <li>Absolute paths relative to host server in applet
1872 parameters are treated as such</li>
1873 <li>New in the JalviewLite javascript API:
1875 <li>JalviewLite.js javascript library</li>
1876 <li>Javascript callbacks for
1878 <li>Applet initialisation</li>
1879 <li>Sequence/alignment mouse-overs and selections</li>
1882 <li>scrollTo row and column alignment scrolling
1884 <li>Select sequence/alignment regions from javascript</li>
1885 <li>javascript structure viewer harness to pass
1886 messages between Jmol and Jalview when running as
1887 distinct applets</li>
1888 <li>sortBy method</li>
1889 <li>Set of applet and application examples shipped
1890 with documentation</li>
1891 <li>New example to demonstrate JalviewLite and Jmol
1892 javascript message exchange</li>
1894 </ul> <em>General</em>
1896 <li>Enable Jmol displays to be associated with multiple
1897 multiple alignments</li>
1898 <li>Option to automatically sort alignment with new tree</li>
1899 <li>User configurable link to enable redirects to a
1900 www.Jalview.org mirror</li>
1901 <li>Jmol colours option for Jmol displays</li>
1902 <li>Configurable newline string when writing alignment
1903 and other flat files</li>
1904 <li>Allow alignment annotation description lines to
1905 contain html tags</li>
1906 </ul> <em>Documentation and Development</em>
1908 <li>Add groovy test harness for bulk load testing to
1910 <li>Groovy script to load and align a set of sequences
1911 using a web service before displaying the result in the
1912 Jalview desktop</li>
1913 <li>Restructured javascript and applet api documentation</li>
1914 <li>Ant target to publish example html files with applet
1916 <li>Netbeans project for building Jalview from source</li>
1917 <li>ant task to create online javadoc for Jalview source</li>
1919 <td><em>Application</em>
1921 <li>User defined colourscheme throws exception when
1922 current built in colourscheme is saved as new scheme</li>
1923 <li>AlignFrame->Save in application pops up save
1924 dialog for valid filename/format</li>
1925 <li>Cannot view associated structure for UniProt sequence</li>
1926 <li>PDB file association breaks for UniProt sequence
1928 <li>Associate PDB from file dialog does not tell you
1929 which sequence is to be associated with the file</li>
1930 <li>Find All raises null pointer exception when query
1931 only matches sequence IDs</li>
1932 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
1933 <li>Jalview project with Jmol views created with Jalview
1934 2.4 cannot be loaded</li>
1935 <li>Filetype associations not installed for webstart
1937 <li>Two or more chains in a single PDB file associated
1938 with sequences in different alignments do not get coloured
1939 by their associated sequence</li>
1940 <li>Visibility status of autocalculated annotation row
1941 not preserved when project is loaded</li>
1942 <li>Annotation row height and visibility attributes not
1943 stored in Jalview project</li>
1944 <li>Tree bootstraps are not preserved when saved as a
1945 Jalview project</li>
1946 <li>Envision2 workflow tooltips are corrupted</li>
1947 <li>Enabling show group conservation also enables colour
1948 by conservation</li>
1949 <li>Duplicate group associated conservation or consensus
1950 created on new view</li>
1951 <li>Annotation scrollbar not displayed after 'show
1952 all hidden annotation rows' option selected</li>
1953 <li>Alignment quality not updated after alignment
1954 annotation row is hidden then shown</li>
1955 <li>Preserve colouring of structures coloured by
1956 sequences in pre Jalview 2.7 projects</li>
1957 <li>Web service job parameter dialog is not laid out
1959 <li>Web services menu not refreshed after 'reset
1960 services' button is pressed in preferences</li>
1961 <li>Annotation off by one in Jalview v2_3 example project</li>
1962 <li>Structures imported from file and saved in project
1963 get name like jalview_pdb1234.txt when reloaded</li>
1964 <li>Jalview does not always retrieve progress of a JABAWS
1965 job execution in full once it is complete</li>
1966 </ul> <em>Applet</em>
1968 <li>Alignment height set incorrectly when lots of
1969 annotation rows are displayed</li>
1970 <li>Relative URLs in feature HTML text not resolved to
1972 <li>View follows highlighting does not work for positions
1974 <li><= shown as = in tooltip</li>
1975 <li>Export features raises exception when no features
1977 <li>Separator string used for serialising lists of IDs
1978 for javascript api is modified when separator string
1979 provided as parameter</li>
1980 <li>Null pointer exception when selecting tree leaves for
1981 alignment with no existing selection</li>
1982 <li>Relative URLs for datasources assumed to be relative
1983 to applet's codebase</li>
1984 <li>Status bar not updated after finished searching and
1985 search wraps around to first result</li>
1986 <li>StructureSelectionManager instance shared between
1987 several Jalview applets causes race conditions and memory
1989 <li>Hover tooltip and mouseover of position on structure
1990 not sent from Jmol in applet</li>
1991 <li>Certain sequences of javascript method calls to
1992 applet API fatally hang browser</li>
1993 </ul> <em>General</em>
1995 <li>View follows structure mouseover scrolls beyond
1996 position with wrapped view and hidden regions</li>
1997 <li>Find sequence position moves to wrong residue
1998 with/without hidden columns</li>
1999 <li>Sequence length given in alignment properties window
2001 <li>InvalidNumberFormat exceptions thrown when trying to
2002 import PDB like structure files</li>
2003 <li>Positional search results are only highlighted
2004 between user-supplied sequence start/end bounds</li>
2005 <li>End attribute of sequence is not validated</li>
2006 <li>Find dialog only finds first sequence containing a
2007 given sequence position</li>
2008 <li>Sequence numbering not preserved in MSF alignment
2010 <li>Jalview PDB file reader does not extract sequence
2011 from nucleotide chains correctly</li>
2012 <li>Structure colours not updated when tree partition
2013 changed in alignment</li>
2014 <li>Sequence associated secondary structure not correctly
2015 parsed in interleaved stockholm</li>
2016 <li>Colour by annotation dialog does not restore current
2018 <li>Hiding (nearly) all sequences doesn't work
2020 <li>Sequences containing lowercase letters are not
2021 properly associated with their pdb files</li>
2022 </ul> <em>Documentation and Development</em>
2024 <li>schemas/JalviewWsParamSet.xsd corrupted by
2025 ApplyCopyright tool</li>
2030 <div align="center">
2031 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2034 <td><em>Application</em>
2036 <li>New warning dialog when the Jalview Desktop cannot
2037 contact web services</li>
2038 <li>JABA service parameters for a preset are shown in
2039 service job window</li>
2040 <li>JABA Service menu entries reworded</li>
2044 <li>Modeller PIR IO broken - cannot correctly import a
2045 pir file emitted by Jalview</li>
2046 <li>Existing feature settings transferred to new
2047 alignment view created from cut'n'paste</li>
2048 <li>Improved test for mixed amino/nucleotide chains when
2049 parsing PDB files</li>
2050 <li>Consensus and conservation annotation rows
2051 occasionally become blank for all new windows</li>
2052 <li>Exception raised when right clicking above sequences
2053 in wrapped view mode</li>
2054 </ul> <em>Application</em>
2056 <li>multiple multiply aligned structure views cause cpu
2057 usage to hit 100% and computer to hang</li>
2058 <li>Web Service parameter layout breaks for long user
2059 parameter names</li>
2060 <li>Jaba service discovery hangs desktop if Jaba server
2067 <div align="center">
2068 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2071 <td><em>Application</em>
2073 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2074 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2077 <li>Web Services preference tab</li>
2078 <li>Analysis parameters dialog box and user defined
2080 <li>Improved speed and layout of Envision2 service menu</li>
2081 <li>Superpose structures using associated sequence
2083 <li>Export coordinates and projection as CSV from PCA
2085 </ul> <em>Applet</em>
2087 <li>enable javascript: execution by the applet via the
2088 link out mechanism</li>
2089 </ul> <em>Other</em>
2091 <li>Updated the Jmol Jalview interface to work with Jmol
2093 <li>The Jalview Desktop and JalviewLite applet now
2094 require Java 1.5</li>
2095 <li>Allow Jalview feature colour specification for GFF
2096 sequence annotation files</li>
2097 <li>New 'colour by label' keword in Jalview feature file
2098 type colour specification</li>
2099 <li>New Jalview Desktop Groovy API method that allows a
2100 script to check if it being run in an interactive session or
2101 in a batch operation from the Jalview command line</li>
2105 <li>clustalx colourscheme colours Ds preferentially when
2106 both D+E are present in over 50% of the column</li>
2107 </ul> <em>Application</em>
2109 <li>typo in AlignmentFrame->View->Hide->all but
2110 selected Regions menu item</li>
2111 <li>sequence fetcher replaces ',' for ';' when the ',' is
2112 part of a valid accession ID</li>
2113 <li>fatal OOM if object retrieved by sequence fetcher
2114 runs out of memory</li>
2115 <li>unhandled Out of Memory Error when viewing pca
2116 analysis results</li>
2117 <li>InstallAnywhere builds fail to launch on OS X java
2118 10.5 update 4 (due to apple Java 1.6 update)</li>
2119 <li>Installanywhere Jalview silently fails to launch</li>
2120 </ul> <em>Applet</em>
2122 <li>Jalview.getFeatureGroups() raises an
2123 ArrayIndexOutOfBoundsException if no feature groups are
2130 <div align="center">
2131 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2137 <li>Alignment prettyprinter doesn't cope with long
2139 <li>clustalx colourscheme colours Ds preferentially when
2140 both D+E are present in over 50% of the column</li>
2141 <li>nucleic acid structures retrieved from PDB do not
2142 import correctly</li>
2143 <li>More columns get selected than were clicked on when a
2144 number of columns are hidden</li>
2145 <li>annotation label popup menu not providing correct
2146 add/hide/show options when rows are hidden or none are
2148 <li>Stockholm format shown in list of readable formats,
2149 and parser copes better with alignments from RFAM.</li>
2150 <li>CSV output of consensus only includes the percentage
2151 of all symbols if sequence logo display is enabled</li>
2153 </ul> <em>Applet</em>
2155 <li>annotation panel disappears when annotation is
2157 </ul> <em>Application</em>
2159 <li>Alignment view not redrawn properly when new
2160 alignment opened where annotation panel is visible but no
2161 annotations are present on alignment</li>
2162 <li>pasted region containing hidden columns is
2163 incorrectly displayed in new alignment window</li>
2164 <li>Jalview slow to complete operations when stdout is
2165 flooded (fix is to close the Jalview console)</li>
2166 <li>typo in AlignmentFrame->View->Hide->all but
2167 selected Rregions menu item.</li>
2168 <li>inconsistent group submenu and Format submenu entry
2169 'Un' or 'Non'conserved</li>
2170 <li>Sequence feature settings are being shared by
2171 multiple distinct alignments</li>
2172 <li>group annotation not recreated when tree partition is
2174 <li>double click on group annotation to select sequences
2175 does not propagate to associated trees</li>
2176 <li>Mac OSX specific issues:
2178 <li>exception raised when mouse clicked on desktop
2179 window background</li>
2180 <li>Desktop menu placed on menu bar and application
2181 name set correctly</li>
2182 <li>sequence feature settings not wide enough for the
2183 save feature colourscheme button</li>
2192 <div align="center">
2193 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2196 <td><em>New Capabilities</em>
2198 <li>URL links generated from description line for
2199 regular-expression based URL links (applet and application)
2206 <li>Non-positional feature URL links are shown in link
2208 <li>Linked viewing of nucleic acid sequences and
2210 <li>Automatic Scrolling option in View menu to display
2211 the currently highlighted region of an alignment.</li>
2212 <li>Order an alignment by sequence length, or using the
2213 average score or total feature count for each sequence.</li>
2214 <li>Shading features by score or associated description</li>
2215 <li>Subdivide alignment and groups based on identity of
2216 selected subsequence (Make Groups from Selection).</li>
2217 <li>New hide/show options including Shift+Control+H to
2218 hide everything but the currently selected region.</li>
2219 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2220 </ul> <em>Application</em>
2222 <li>Fetch DB References capabilities and UI expanded to
2223 support retrieval from DAS sequence sources</li>
2224 <li>Local DAS Sequence sources can be added via the
2225 command line or via the Add local source dialog box.</li>
2226 <li>DAS Dbref and DbxRef feature types are parsed as
2227 database references and protein_name is parsed as
2228 description line (BioSapiens terms).</li>
2229 <li>Enable or disable non-positional feature and database
2230 references in sequence ID tooltip from View menu in
2232 <!-- <li>New hidden columns and rows and representatives capabilities
2233 in annotations file (in progress - not yet fully implemented)</li> -->
2234 <li>Group-associated consensus, sequence logos and
2235 conservation plots</li>
2236 <li>Symbol distributions for each column can be exported
2237 and visualized as sequence logos</li>
2238 <li>Optionally scale multi-character column labels to fit
2239 within each column of annotation row<!-- todo for applet -->
2241 <li>Optional automatic sort of associated alignment view
2242 when a new tree is opened.</li>
2243 <li>Jalview Java Console</li>
2244 <li>Better placement of desktop window when moving
2245 between different screens.</li>
2246 <li>New preference items for sequence ID tooltip and
2247 consensus annotation</li>
2248 <li>Client to submit sequences and IDs to Envision2
2250 <li><em>Vamsas Capabilities</em>
2252 <li>Improved VAMSAS synchronization (Jalview archive
2253 used to preserve views, structures, and tree display
2255 <li>Import of vamsas documents from disk or URL via
2257 <li>Sharing of selected regions between views and
2258 with other VAMSAS applications (Experimental feature!)</li>
2259 <li>Updated API to VAMSAS version 0.2</li>
2261 </ul> <em>Applet</em>
2263 <li>Middle button resizes annotation row height</li>
2266 <li>sortByTree (true/false) - automatically sort the
2267 associated alignment view by the tree when a new tree is
2269 <li>showTreeBootstraps (true/false) - show or hide
2270 branch bootstraps (default is to show them if available)</li>
2271 <li>showTreeDistances (true/false) - show or hide
2272 branch lengths (default is to show them if available)</li>
2273 <li>showUnlinkedTreeNodes (true/false) - indicate if
2274 unassociated nodes should be highlighted in the tree
2276 <li>heightScale and widthScale (1.0 or more) -
2277 increase the height or width of a cell in the alignment
2278 grid relative to the current font size.</li>
2281 <li>Non-positional features displayed in sequence ID
2283 </ul> <em>Other</em>
2285 <li>Features format: graduated colour definitions and
2286 specification of feature scores</li>
2287 <li>Alignment Annotations format: new keywords for group
2288 associated annotation (GROUP_REF) and annotation row display
2289 properties (ROW_PROPERTIES)</li>
2290 <li>XML formats extended to support graduated feature
2291 colourschemes, group associated annotation, and profile
2292 visualization settings.</li></td>
2295 <li>Source field in GFF files parsed as feature source
2296 rather than description</li>
2297 <li>Non-positional features are now included in sequence
2298 feature and gff files (controlled via non-positional feature
2299 visibility in tooltip).</li>
2300 <li>URL links generated for all feature links (bugfix)</li>
2301 <li>Added URL embedding instructions to features file
2303 <li>Codons containing ambiguous nucleotides translated as
2304 'X' in peptide product</li>
2305 <li>Match case switch in find dialog box works for both
2306 sequence ID and sequence string and query strings do not
2307 have to be in upper case to match case-insensitively.</li>
2308 <li>AMSA files only contain first column of
2309 multi-character column annotation labels</li>
2310 <li>Jalview Annotation File generation/parsing consistent
2311 with documentation (e.g. Stockholm annotation can be
2312 exported and re-imported)</li>
2313 <li>PDB files without embedded PDB IDs given a friendly
2315 <li>Find incrementally searches ID string matches as well
2316 as subsequence matches, and correctly reports total number
2320 <li>Better handling of exceptions during sequence
2322 <li>Dasobert generated non-positional feature URL
2323 link text excludes the start_end suffix</li>
2324 <li>DAS feature and source retrieval buttons disabled
2325 when fetch or registry operations in progress.</li>
2326 <li>PDB files retrieved from URLs are cached properly</li>
2327 <li>Sequence description lines properly shared via
2329 <li>Sequence fetcher fetches multiple records for all
2331 <li>Ensured that command line das feature retrieval
2332 completes before alignment figures are generated.</li>
2333 <li>Reduced time taken when opening file browser for
2335 <li>isAligned check prior to calculating tree, PCA or
2336 submitting an MSA to JNet now excludes hidden sequences.</li>
2337 <li>User defined group colours properly recovered
2338 from Jalview projects.</li>
2347 <div align="center">
2348 <strong>2.4.0.b2</strong><br> 28/10/2009
2353 <li>Experimental support for google analytics usage
2355 <li>Jalview privacy settings (user preferences and docs).</li>
2360 <li>Race condition in applet preventing startup in
2362 <li>Exception when feature created from selection beyond
2363 length of sequence.</li>
2364 <li>Allow synthetic PDB files to be imported gracefully</li>
2365 <li>Sequence associated annotation rows associate with
2366 all sequences with a given id</li>
2367 <li>Find function matches case-insensitively for sequence
2368 ID string searches</li>
2369 <li>Non-standard characters do not cause pairwise
2370 alignment to fail with exception</li>
2371 </ul> <em>Application Issues</em>
2373 <li>Sequences are now validated against EMBL database</li>
2374 <li>Sequence fetcher fetches multiple records for all
2376 </ul> <em>InstallAnywhere Issues</em>
2378 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2379 issue with installAnywhere mechanism)</li>
2380 <li>Command line launching of JARs from InstallAnywhere
2381 version (java class versioning error fixed)</li>
2388 <div align="center">
2389 <strong>2.4</strong><br> 27/8/2008
2392 <td><em>User Interface</em>
2394 <li>Linked highlighting of codon and amino acid from
2395 translation and protein products</li>
2396 <li>Linked highlighting of structure associated with
2397 residue mapping to codon position</li>
2398 <li>Sequence Fetcher provides example accession numbers
2399 and 'clear' button</li>
2400 <li>MemoryMonitor added as an option under Desktop's
2402 <li>Extract score function to parse whitespace separated
2403 numeric data in description line</li>
2404 <li>Column labels in alignment annotation can be centred.</li>
2405 <li>Tooltip for sequence associated annotation give name
2407 </ul> <em>Web Services and URL fetching</em>
2409 <li>JPred3 web service</li>
2410 <li>Prototype sequence search client (no public services
2412 <li>Fetch either seed alignment or full alignment from
2414 <li>URL Links created for matching database cross
2415 references as well as sequence ID</li>
2416 <li>URL Links can be created using regular-expressions</li>
2417 </ul> <em>Sequence Database Connectivity</em>
2419 <li>Retrieval of cross-referenced sequences from other
2421 <li>Generalised database reference retrieval and
2422 validation to all fetchable databases</li>
2423 <li>Fetch sequences from DAS sources supporting the
2424 sequence command</li>
2425 </ul> <em>Import and Export</em>
2426 <li>export annotation rows as CSV for spreadsheet import</li>
2427 <li>Jalview projects record alignment dataset associations,
2428 EMBL products, and cDNA sequence mappings</li>
2429 <li>Sequence Group colour can be specified in Annotation
2431 <li>Ad-hoc colouring of group in Annotation File using RGB
2432 triplet as name of colourscheme</li>
2433 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2435 <li>treenode binding for VAMSAS tree exchange</li>
2436 <li>local editing and update of sequences in VAMSAS
2437 alignments (experimental)</li>
2438 <li>Create new or select existing session to join</li>
2439 <li>load and save of vamsas documents</li>
2440 </ul> <em>Application command line</em>
2442 <li>-tree parameter to open trees (introduced for passing
2444 <li>-fetchfrom command line argument to specify nicknames
2445 of DAS servers to query for alignment features</li>
2446 <li>-dasserver command line argument to add new servers
2447 that are also automatically queried for features</li>
2448 <li>-groovy command line argument executes a given groovy
2449 script after all input data has been loaded and parsed</li>
2450 </ul> <em>Applet-Application data exchange</em>
2452 <li>Trees passed as applet parameters can be passed to
2453 application (when using "View in full
2454 application")</li>
2455 </ul> <em>Applet Parameters</em>
2457 <li>feature group display control parameter</li>
2458 <li>debug parameter</li>
2459 <li>showbutton parameter</li>
2460 </ul> <em>Applet API methods</em>
2462 <li>newView public method</li>
2463 <li>Window (current view) specific get/set public methods</li>
2464 <li>Feature display control methods</li>
2465 <li>get list of currently selected sequences</li>
2466 </ul> <em>New Jalview distribution features</em>
2468 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2469 <li>RELEASE file gives build properties for the latest
2470 Jalview release.</li>
2471 <li>Java 1.1 Applet build made easier and donotobfuscate
2472 property controls execution of obfuscator</li>
2473 <li>Build target for generating source distribution</li>
2474 <li>Debug flag for javacc</li>
2475 <li>.jalview_properties file is documented (slightly) in
2476 jalview.bin.Cache</li>
2477 <li>Continuous Build Integration for stable and
2478 development version of Application, Applet and source
2483 <li>selected region output includes visible annotations
2484 (for certain formats)</li>
2485 <li>edit label/displaychar contains existing label/char
2487 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2488 <li>shorter peptide product names from EMBL records</li>
2489 <li>Newick string generator makes compact representations</li>
2490 <li>bootstrap values parsed correctly for tree files with
2492 <li>pathological filechooser bug avoided by not allowing
2493 filenames containing a ':'</li>
2494 <li>Fixed exception when parsing GFF files containing
2495 global sequence features</li>
2496 <li>Alignment datasets are finalized only when number of
2497 references from alignment sequences goes to zero</li>
2498 <li>Close of tree branch colour box without colour
2499 selection causes cascading exceptions</li>
2500 <li>occasional negative imgwidth exceptions</li>
2501 <li>better reporting of non-fatal warnings to user when
2502 file parsing fails.</li>
2503 <li>Save works when Jalview project is default format</li>
2504 <li>Save as dialog opened if current alignment format is
2505 not a valid output format</li>
2506 <li>UniProt canonical names introduced for both das and
2508 <li>Histidine should be midblue (not pink!) in Zappo</li>
2509 <li>error messages passed up and output when data read
2511 <li>edit undo recovers previous dataset sequence when
2512 sequence is edited</li>
2513 <li>allow PDB files without pdb ID HEADER lines (like
2514 those generated by MODELLER) to be read in properly</li>
2515 <li>allow reading of JPred concise files as a normal
2517 <li>Stockholm annotation parsing and alignment properties
2518 import fixed for PFAM records</li>
2519 <li>Structure view windows have correct name in Desktop
2521 <li>annotation consisting of sequence associated scores
2522 can be read and written correctly to annotation file</li>
2523 <li>Aligned cDNA translation to aligned peptide works
2525 <li>Fixed display of hidden sequence markers and
2526 non-italic font for representatives in Applet</li>
2527 <li>Applet Menus are always embedded in applet window on
2529 <li>Newly shown features appear at top of stack (in
2531 <li>Annotations added via parameter not drawn properly
2532 due to null pointer exceptions</li>
2533 <li>Secondary structure lines are drawn starting from
2534 first column of alignment</li>
2535 <li>UniProt XML import updated for new schema release in
2537 <li>Sequence feature to sequence ID match for Features
2538 file is case-insensitive</li>
2539 <li>Sequence features read from Features file appended to
2540 all sequences with matching IDs</li>
2541 <li>PDB structure coloured correctly for associated views
2542 containing a sub-sequence</li>
2543 <li>PDB files can be retrieved by applet from Jar files</li>
2544 <li>feature and annotation file applet parameters
2545 referring to different directories are retrieved correctly</li>
2546 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
2547 <li>Fixed application hang whilst waiting for
2548 splash-screen version check to complete</li>
2549 <li>Applet properly URLencodes input parameter values
2550 when passing them to the launchApp service</li>
2551 <li>display name and local features preserved in results
2552 retrieved from web service</li>
2553 <li>Visual delay indication for sequence retrieval and
2554 sequence fetcher initialisation</li>
2555 <li>updated Application to use DAS 1.53e version of
2556 dasobert DAS client</li>
2557 <li>Re-instated Full AMSA support and .amsa file
2559 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
2567 <div align="center">
2568 <strong>2.3</strong><br> 9/5/07
2573 <li>Jmol 11.0.2 integration</li>
2574 <li>PDB views stored in Jalview XML files</li>
2575 <li>Slide sequences</li>
2576 <li>Edit sequence in place</li>
2577 <li>EMBL CDS features</li>
2578 <li>DAS Feature mapping</li>
2579 <li>Feature ordering</li>
2580 <li>Alignment Properties</li>
2581 <li>Annotation Scores</li>
2582 <li>Sort by scores</li>
2583 <li>Feature/annotation editing in applet</li>
2588 <li>Headless state operation in 2.2.1</li>
2589 <li>Incorrect and unstable DNA pairwise alignment</li>
2590 <li>Cut and paste of sequences with annotation</li>
2591 <li>Feature group display state in XML</li>
2592 <li>Feature ordering in XML</li>
2593 <li>blc file iteration selection using filename # suffix</li>
2594 <li>Stockholm alignment properties</li>
2595 <li>Stockhom alignment secondary structure annotation</li>
2596 <li>2.2.1 applet had no feature transparency</li>
2597 <li>Number pad keys can be used in cursor mode</li>
2598 <li>Structure Viewer mirror image resolved</li>
2605 <div align="center">
2606 <strong>2.2.1</strong><br> 12/2/07
2611 <li>Non standard characters can be read and displayed
2612 <li>Annotations/Features can be imported/exported to the
2614 <li>Applet allows editing of sequence/annotation/group
2615 name & description
2616 <li>Preference setting to display sequence name in
2618 <li>Annotation file format extended to allow
2619 Sequence_groups to be defined
2620 <li>Default opening of alignment overview panel can be
2621 specified in preferences
2622 <li>PDB residue numbering annotation added to associated
2628 <li>Applet crash under certain Linux OS with Java 1.6
2630 <li>Annotation file export / import bugs fixed
2631 <li>PNG / EPS image output bugs fixed
2637 <div align="center">
2638 <strong>2.2</strong><br> 27/11/06
2643 <li>Multiple views on alignment
2644 <li>Sequence feature editing
2645 <li>"Reload" alignment
2646 <li>"Save" to current filename
2647 <li>Background dependent text colour
2648 <li>Right align sequence ids
2649 <li>User-defined lower case residue colours
2652 <li>Menu item accelerator keys
2653 <li>Control-V pastes to current alignment
2654 <li>Cancel button for DAS Feature Fetching
2655 <li>PCA and PDB Viewers zoom via mouse roller
2656 <li>User-defined sub-tree colours and sub-tree selection
2663 <li>'New Window' button on the 'Output to Text box'
2668 <li>New memory efficient Undo/Redo System
2669 <li>Optimised symbol lookups and conservation/consensus
2671 <li>Region Conservation/Consensus recalculated after
2673 <li>Fixed Remove Empty Columns Bug (empty columns at end
2675 <li>Slowed DAS Feature Fetching for increased robustness.
2682 <li>Made angle brackets in ASCII feature descriptions
2684 <li>Re-instated Zoom function for PCA
2685 <li>Sequence descriptions conserved in web service
2687 <li>UniProt ID discoverer uses any word separated by
2689 <li>WsDbFetch query/result association resolved
2690 <li>Tree leaf to sequence mapping improved
2691 <li>Smooth fonts switch moved to FontChooser dialog box.
2703 <div align="center">
2704 <strong>2.1.1</strong><br> 12/9/06
2709 <li>Copy consensus sequence to clipboard</li>
2714 <li>Image output - rightmost residues are rendered if
2715 sequence id panel has been resized</li>
2716 <li>Image output - all offscreen group boundaries are
2718 <li>Annotation files with sequence references - all
2719 elements in file are relative to sequence position</li>
2720 <li>Mac Applet users can use Alt key for group editing</li>
2726 <div align="center">
2727 <strong>2.1</strong><br> 22/8/06
2732 <li>MAFFT Multiple Alignment in default Web Service list</li>
2733 <li>DAS Feature fetching</li>
2734 <li>Hide sequences and columns</li>
2735 <li>Export Annotations and Features</li>
2736 <li>GFF file reading / writing</li>
2737 <li>Associate structures with sequences from local PDB
2739 <li>Add sequences to exisiting alignment</li>
2740 <li>Recently opened files / URL lists</li>
2741 <li>Applet can launch the full application</li>
2742 <li>Applet has transparency for features (Java 1.2
2744 <li>Applet has user defined colours parameter</li>
2745 <li>Applet can load sequences from parameter
2746 "sequence<em>x</em>"
2752 <li>Redundancy Panel reinstalled in the Applet</li>
2753 <li>Monospaced font - EPS / rescaling bug fixed</li>
2754 <li>Annotation files with sequence references bug fixed</li>
2760 <div align="center">
2761 <strong>2.08.1</strong><br> 2/5/06
2766 <li>Change case of selected region from Popup menu</li>
2767 <li>Choose to match case when searching</li>
2768 <li>Middle mouse button and mouse movement can compress /
2769 expand the visible width and height of the alignment</li>
2774 <li>Annotation Panel displays complete JNet results</li>
2780 <div align="center">
2781 <strong>2.08b</strong><br> 18/4/06
2787 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
2788 <li>Righthand label on wrapped alignments shows correct
2795 <div align="center">
2796 <strong>2.08</strong><br> 10/4/06
2801 <li>Editing can be locked to the selection area</li>
2802 <li>Keyboard editing</li>
2803 <li>Create sequence features from searches</li>
2804 <li>Precalculated annotations can be loaded onto
2806 <li>Features file allows grouping of features</li>
2807 <li>Annotation Colouring scheme added</li>
2808 <li>Smooth fonts off by default - Faster rendering</li>
2809 <li>Choose to toggle Autocalculate Consensus On/Off</li>
2814 <li>Drag & Drop fixed on Linux</li>
2815 <li>Jalview Archive file faster to load/save, sequence
2816 descriptions saved.</li>
2822 <div align="center">
2823 <strong>2.07</strong><br> 12/12/05
2828 <li>PDB Structure Viewer enhanced</li>
2829 <li>Sequence Feature retrieval and display enhanced</li>
2830 <li>Choose to output sequence start-end after sequence
2831 name for file output</li>
2832 <li>Sequence Fetcher WSDBFetch@EBI</li>
2833 <li>Applet can read feature files, PDB files and can be
2834 used for HTML form input</li>
2839 <li>HTML output writes groups and features</li>
2840 <li>Group editing is Control and mouse click</li>
2841 <li>File IO bugs</li>
2847 <div align="center">
2848 <strong>2.06</strong><br> 28/9/05
2853 <li>View annotations in wrapped mode</li>
2854 <li>More options for PCA viewer</li>
2859 <li>GUI bugs resolved</li>
2860 <li>Runs with -nodisplay from command line</li>
2866 <div align="center">
2867 <strong>2.05b</strong><br> 15/9/05
2872 <li>Choose EPS export as lineart or text</li>
2873 <li>Jar files are executable</li>
2874 <li>Can read in Uracil - maps to unknown residue</li>
2879 <li>Known OutOfMemory errors give warning message</li>
2880 <li>Overview window calculated more efficiently</li>
2881 <li>Several GUI bugs resolved</li>
2887 <div align="center">
2888 <strong>2.05</strong><br> 30/8/05
2893 <li>Edit and annotate in "Wrapped" view</li>
2898 <li>Several GUI bugs resolved</li>
2904 <div align="center">
2905 <strong>2.04</strong><br> 24/8/05
2910 <li>Hold down mouse wheel & scroll to change font
2916 <li>Improved JPred client reliability</li>
2917 <li>Improved loading of Jalview files</li>
2923 <div align="center">
2924 <strong>2.03</strong><br> 18/8/05
2929 <li>Set Proxy server name and port in preferences</li>
2930 <li>Multiple URL links from sequence ids</li>
2931 <li>User Defined Colours can have a scheme name and added
2933 <li>Choose to ignore gaps in consensus calculation</li>
2934 <li>Unix users can set default web browser</li>
2935 <li>Runs without GUI for batch processing</li>
2936 <li>Dynamically generated Web Service Menus</li>
2941 <li>InstallAnywhere download for Sparc Solaris</li>
2947 <div align="center">
2948 <strong>2.02</strong><br> 18/7/05
2954 <li>Copy & Paste order of sequences maintains
2955 alignment order.</li>
2961 <div align="center">
2962 <strong>2.01</strong><br> 12/7/05
2967 <li>Use delete key for deleting selection.</li>
2968 <li>Use Mouse wheel to scroll sequences.</li>
2969 <li>Help file updated to describe how to add alignment
2971 <li>Version and build date written to build properties
2973 <li>InstallAnywhere installation will check for updates
2974 at launch of Jalview.</li>
2979 <li>Delete gaps bug fixed.</li>
2980 <li>FileChooser sorts columns.</li>
2981 <li>Can remove groups one by one.</li>
2982 <li>Filechooser icons installed.</li>
2983 <li>Finder ignores return character when searching.
2984 Return key will initiate a search.<br>
2991 <div align="center">
2992 <strong>2.0</strong><br> 20/6/05
2997 <li>New codebase</li>