3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
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27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.2">2.10.2</a><br />
74 <em>8/8/2017</em></strong>
77 <td><div align="left">
80 <li><!-- JAL-2360,JAL-2371, -->More robust colours and shader model for alignments and groups</li>
81 <li><!-- JAL-384 -->Custom shading schemes created via groovy scripts</li>
82 <li><!-- JAL-2491 -->linked scrolling of CDS/Protein views via Overview or sequence motif search operations</li>
83 <li><!-- JAL-2526 -->Efficiency improvements for interacting with alignment and overview windows</li>
84 <li><!-- JAL-2388 -->Hidden columns and sequences can be omitted in Overview</li>
86 <!-- JAL-2535 -->Posterior probability annotation from
87 Stockholm files imported as sequence associated annotation
90 <!-- JAL-2533 -->Sequence names don't include file
91 extension when importing structure files without embedded
92 names or PDB accessions
94 <li><!-- JAL-2547 -->Amend sequence features dialog box can be opened by double clicking gaps within sequence feature extent</li>
95 <li><!-- JAL-2631 -->Graduated feature colour style example included in the example feature file</li>
101 Experimental Features Checkbox in Desktop's Tools
102 menu to hide or show untested features in the application.
104 <li><!-- JAL-1476 -->Warning in alignment status bar when there are not enough columns to superimpose structures in Chimera</li>
105 <li><!-- JAL-1596 -->Faster Chimera/Jalview communication by file-based command exchange</li>
106 <li><!-- JAL-2316, -->URLs for viewing database cross-references provided by identifiers.org and the EMBL-EBI's MIRIAM DB</li>
107 <li><!-- JAL-2549 -->Updated JABAWS client to v2.2</li>
109 <em>Experimental features</em>
112 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
113 to transfer Chimera's structure attributes as Jalview
114 features, and vice-versa.
122 <li><!-- JAL-2474 -->Added PrivilegedAccessor to test suite</li>
123 <li><!-- JAL-2326 -->Prevent or clear modal dialogs raised during tests</li>
126 </div></td><td><div align="left">
130 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
131 matrix - C->R should be '-3'<br />Old matrix restored with
132 this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
135 <!-- JAL-2397 -->Fixed Jalview's treatment of gaps in PCA
136 and substitution matrix based Tree calculations.<br />In
137 earlier versions of Jalview, gaps matching gaps were
138 penalised, and gaps matching non-gaps penalised even more.
139 In the PCA calculation, gaps were actually treated as
140 non-gaps - so different costs were applied, which meant
141 Jalview's PCAs were different to those produced by
142 SeqSpace.<br />Jalview now treats gaps in the same way as
143 SeqSpace (ie it scores them as 0). To restore pre-2.10.2
145 jalview.viewmodel.PCAModel.scoreGapAsAny=true // for
147 jalview.viewmodel.PCAModel.scoreGapAsAny=false // to
150 <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>
151 <li><!-- JAL-2430 -->Hidden regions in alignment views are not coloured in linked structure views</li>
152 <li><!-- JAL-2419 -->Current selection lost if popup menu opened on a region of alignment without groups</li>
153 <li><!-- JAL-2374 -->Popup menu not always shown for regions of an alignment with overlapping groups</li>
154 <li><!-- JAL-2310 -->Finder double counts if both a sequence's name and description match</li>
155 <li><!-- JAL-2370 -->Hiding column selection containing two hidden regions results in incorrect hidden regions</li>
156 <li><!-- JAL-2377 -->PCA calculation could hang when generating output report when working with highly redundant alignments</li>
157 <li><!-- JAL-2365 -->Cannot configure feature colours with lightGray or darkGray via features file</li>
158 <li><!-- JAL-2421 -->Overview window visible region moves erratically when hidden rows or columns are present</li>
159 <li><!-- JAL-2362 -->Per-residue colourschemes applied via the Structure Viewer's colour menu don't correspond to sequence colouring</li>
160 <li><!-- JAL-2405 -->Protein specific colours only offered in colour and group colour menu for protein alignments</li>
161 <li><!-- JAL-2386 -->'Apply to all groups' setting when changing colour does not apply Conservation slider value to all groups</li>
162 <li><!-- JAL-2385 -->Colour threshold slider doesn't update to reflect currently selected view or group's shading thresholds</li>
163 <li><!-- JAL-2373 -->Percentage identity and conservation menu items do not show a tick or allow shading to be disabled</li>
164 <li><!-- JAL-2385 -->Conservation shading or PID threshold lost when base colourscheme changed if slider not visible</li>
165 <li><!-- JAL-2547 -->Sequence features shown in tooltip for gaps before start of features</li>
166 <li><!-- JAL-2576 -->Very large alignments take a long time to load</li>
167 <li><!-- JAL-2623 -->Graduated feature colour threshold not restored to UI when feature colour is edited</li>
168 <li><!-- JAL-2624 -->Feature colour thresholds not respected when rendered on overview and structures when opacity at 100%</li>
169 <li><!-- JAL-2630 -->Structure and alignment overview update as graduate feature colour settings are modified via the dialog box</li>
170 <li><!-- JAL-147 -->Vertical scrollbar jumps one page-width at a time when scrolling vertically in wrapped mode.</li>
171 <li><!-- JAL-2034 -->Overview window doesn't always update when a group defined on the alignment is resized</li>
172 <li><!-- JAL-2605 -->Mouseovers on left/right scale region in wrapped view result in positional status updates</li>
173 <li><!-- JAL-2563 -->Status bar shows position for ambiguous amino acid and nucleotide symbols</li>
177 <li><!-- JAL-2401 -->Easier creation of colours for all 'Lower case' residues (button in colourscheme editor debugged and new documentation and tooltips added)</li>
178 <li><!-- JAL-2399-->Text colour threshold's 'Cancel' button doesn't restore group-specific text colour thresholds</li>
179 <li><!-- JAL-2243 -->Feature settings panel does not update as new features are added to alignment</li>
180 <li><!-- JAL-2436 -->Structure viewer's View -> Colour By view selection menu changes colours of alignment views</li>
181 <li><!-- JAL-2366 -->Proxy server address and port always appear enabled in Preferences->Connections</li>
182 <li><!-- JAL-2426 -->Spurious exceptions in console raised from alignment calculation workers after alignment has been closed</li>
183 <li><!-- JAL-1608 -->Typo in selection popup menu - Create groups now 'Create Group'</li>
184 <li><!-- JAL-1608 -->CMD/CTRL and G or Shift G for Create/Undefine group doesn't always work</li>
185 <li><!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get shown again after pressing 'Cancel'</li>
186 <li><!-- JAL-2461 -->DAS registry not found exceptions removed from console output</li>
187 <li><!-- JAL-2383 -->Above PID colour threshold not recovered when alignment view imported from project</li>
188 <li><!-- JAL-2465 -->No mappings generated between structure and sequences extracted from structure files imported via URL</li>
190 <!-- JAL-2520 -->Structures loaded via URL are saved in
191 Jalview Projects rather than fetched via URL again when
192 the project is loaded and the structure viewed
194 <li><!-- JAL-1256 -->Trackpad horizontal scroll gesture adjusts start position in wrap mode</li>
195 <li><!-- JAL-2563 -->Status bar doesn't show positions for ambiguous amino acids</li>
196 <li><!-- JAL-2291 -->Hide insertions in PopUp menu excludes gaps in selection, current sequence and only within selected columns</li>
200 <li><!-- JAL-2442 -->Features not rendered as transparent on overview or linked structure view</li>
201 <li><!-- JAL-2372 -->Colour group by conservation doesn't work (since 2.8)</li>
202 <li><!-- JAL-2517 -->Hitting Cancel after applying user-defined colourscheme doesn't restore original colourscheme</li>
204 <em>New Known Issues</em>
206 <li><!-- JAL-2566 -->Protein/CDS view scrolling not always in phase after a sequence motif find operation</li>
207 <li><!-- JAL-2550 -->Importing annotation file with rows containing just upper and lower case letters are interpreted as WUSS rna secondary structure symbols</li>
208 <li><!-- JAL-2590 -->Cannot load Newick trees from eggnog ortholog database</li>
213 <td width="60" nowrap>
215 <strong><a name="Jalview.2.10.1">2.10.1</a><br />
216 <em>29/11/2016</em></strong>
219 <td><div align="left">
223 <!-- JAL-98 -->Improved memory usage: sparse arrays used
224 for all consensus calculations
227 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released 3rd Oct 2016)
229 <li>Updated Jalview's Certum code signing certificate
235 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
236 set of database cross-references, sorted alphabetically
239 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
240 from database cross references. Users with custom links
241 will receive a <a href="webServices/urllinks.html#warning">warning
242 dialog</a> asking them to update their preferences.
245 <!-- JAL-2287-->Cancel button and escape listener on
246 dialog warning user about disconnecting Jalview from a
250 <!-- JAL-2320-->Jalview's Chimera control window closes if
251 the Chimera it is connected to is shut down
254 <!-- JAL-1738-->New keystroke (B) and Select highlighted
255 columns menu item to mark columns containing
256 highlighted regions (e.g. from structure selections or results
260 <!-- JAL-2284-->Command line option for batch-generation
261 of HTML pages rendering alignment data with the BioJS
271 <!-- JAL-2286 -->Columns with more than one modal residue
272 are not coloured or thresholded according to percent
273 identity (first observed in Jalview 2.8.2)
276 <!-- JAL-2301 -->Threonine incorrectly reported as not
280 <!-- JAL-2318 -->Updates to documentation pages (above PID
281 threshold, amino acid properties)
284 <!-- JAL-2292 -->Lower case residues in sequences are not
285 reported as mapped to residues in a structure file in the
289 <!--JAL-2324 -->Identical features with non-numeric scores
290 could be added multiple times to a sequence
293 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
294 bond features shown as two highlighted residues rather
295 than a range in linked structure views, and treated
296 correctly when selecting and computing trees from features
299 <!-- JAL-2281-->Custom URL links for database
300 cross-references are matched to database name regardless
308 <!-- JAL-2282-->Custom URL links for specific database
309 names without regular expressions also offer links from
313 <!-- JAL-2315-->Removing a single configured link in the
314 URL links pane in Connections preferences doesn't actually
315 update Jalview configuration
318 <!-- JAL-2272-->CTRL-Click on a selected region to open
319 the alignment area popup menu doesn't work on El-Capitan
322 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
323 files with similarly named sequences if dropped onto the
327 <!-- JAL-2312 -->Additional mappings are shown for PDB
328 entries where more chains exist in the PDB accession than
329 are reported in the SIFTS file
332 <!-- JAL-2317-->Certain structures do not get mapped to
333 the structure view when displayed with Chimera
336 <!-- JAL-2317-->No chains shown in the Chimera view
337 panel's View->Show Chains submenu
340 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
341 work for wrapped alignment views
344 <!--JAL-2197 -->Rename UI components for running JPred
345 predictions from 'JNet' to 'JPred'
348 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
349 corrupted when annotation panel vertical scroll is not at
353 <!--JAL-2332 -->Attempting to view structure for Hen
354 lysozyme results in a PDB Client error dialog box
357 <!-- JAL-2319 -->Structure View's mapping report switched ranges for PDB and sequence for SIFTS</li>
358 <!-- JAL-2319 -->SIFTS 'Not_Observed' residues mapped to non-existant coordindate data</li>
360 <!-- <em>New Known Issues</em>
367 <td width="60" nowrap>
369 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
370 <em>25/10/2016</em></strong>
373 <td><em>Application</em>
375 <li>3D Structure chooser opens with 'Cached structures'
376 view if structures already loaded</li>
377 <li>Progress bar reports models as they are loaded to
384 <li>Colour by conservation always enabled and no tick
385 shown in menu when BLOSUM or PID shading applied</li>
386 <li>FER1_ARATH and FER2_ARATH labels were switched in
387 example sequences/projects/trees</li>
391 <li>Jalview projects with views of local PDB structure
392 files saved on Windows cannot be opened on OSX</li>
393 <li>Multiple structure views can be opened and
394 superposed without timeout for structures with multiple
395 models or multiple sequences in alignment</li>
396 <li>Cannot import or associated local PDB files without
397 a PDB ID HEADER line</li>
398 <li>RMSD is not output in Jmol console when
399 superposition is performed</li>
400 <li>Drag and drop of URL from Browser fails for Linux
401 and OSX versions earlier than El Capitan</li>
402 <li>ENA client ignores invalid content from ENA server</li>
403 <li>Exceptions are not raised in console when ENA
404 client attempts to fetch non-existent IDs via Fetch DB
406 <li>Exceptions are not raised in console when a new
407 view is created on the alignment</li>
408 <li>OSX right-click fixed for group selections:
409 CMD-click to insert/remove gaps in groups and CTRL-click
410 to open group pop-up menu</li>
412 <em>Build and deployment</em>
414 <li>URL link checker now copes with multi-line anchor
417 <em>New Known Issues</em>
419 <li>Drag and drop from URL links in browsers do not
426 <td width="60" nowrap>
428 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
434 <!-- JAL-2124 -->Updated Spanish translations.
437 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
438 for importing structure data to Jalview. Enables mmCIF and
442 <!-- JAL-192 --->Alignment ruler shows positions relative to
446 <!-- JAL-2202 -->Position/residue shown in status bar when
447 mousing over sequence associated annotation
450 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
454 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
455 '()', canonical '[]' and invalid '{}' base pair populations
459 <!-- JAL-2092 -->Feature settings popup menu options for
460 showing or hiding columns containing a feature
463 <!-- JAL-1557 -->Edit selected group by double clicking on
464 group and sequence associated annotation labels
467 <!-- JAL-2236 -->Sequence name added to annotation label in
468 select/hide columns by annotation and colour by annotation
472 </ul> <em>Application</em>
475 <!-- JAL-2050-->Automatically hide introns when opening a
479 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
483 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
484 structure mappings with the EMBL-EBI PDBe SIFTS database
487 <!-- JAL-2079 -->Updated download sites used for Rfam and
488 Pfam sources to xfam.org
491 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
494 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
495 over sequences in Jalview
498 <!-- JAL-2027-->Support for reverse-complement coding
499 regions in ENA and EMBL
502 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
503 for record retrieval via ENA rest API
506 <!-- JAL-2027 -->Support for ENA CDS records with reverse
510 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
511 groovy script execution
514 <!-- JAL-1812 -->New 'execute Groovy script' option in an
515 alignment window's Calculate menu
518 <!-- JAL-1812 -->Allow groovy scripts that call
519 Jalview.getAlignFrames() to run in headless mode
522 <!-- JAL-2068 -->Support for creating new alignment
523 calculation workers from groovy scripts
526 <!-- JAL-1369 --->Store/restore reference sequence in
530 <!-- JAL-1803 -->Chain codes for a sequence's PDB
531 associations are now saved/restored from project
534 <!-- JAL-1993 -->Database selection dialog always shown
535 before sequence fetcher is opened
538 <!-- JAL-2183 -->Double click on an entry in Jalview's
539 database chooser opens a sequence fetcher
542 <!-- JAL-1563 -->Free-text search client for UniProt using
546 <!-- JAL-2168 -->-nonews command line parameter to prevent
547 the news reader opening
550 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
551 querying stored in preferences
554 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
558 <!-- JAL-1977-->Tooltips shown on database chooser
561 <!-- JAL-391 -->Reverse complement function in calculate
562 menu for nucleotide sequences
565 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
566 and feature counts preserves alignment ordering (and
567 debugged for complex feature sets).
570 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
571 viewing structures with Jalview 2.10
574 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
575 genome, transcript CCDS and gene ids via the Ensembl and
576 Ensembl Genomes REST API
579 <!-- JAL-2049 -->Protein sequence variant annotation
580 computed for 'sequence_variant' annotation on CDS regions
584 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
588 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
589 Ref Fetcher fails to match, or otherwise updates sequence
590 data from external database records.
593 <!-- JAL-2154 -->Revised Jalview Project format for
594 efficient recovery of sequence coding and alignment
595 annotation relationships.
597 </ul> <!-- <em>Applet</em>
608 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
612 <!-- JAL-2018-->Export features in Jalview format (again)
613 includes graduated colourschemes
616 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
617 working with big alignments and lots of hidden columns
620 <!-- JAL-2053-->Hidden column markers not always rendered
621 at right of alignment window
624 <!-- JAL-2067 -->Tidied up links in help file table of
628 <!-- JAL-2072 -->Feature based tree calculation not shown
632 <!-- JAL-2075 -->Hidden columns ignored during feature
633 based tree calculation
636 <!-- JAL-2065 -->Alignment view stops updating when show
637 unconserved enabled for group on alignment
640 <!-- JAL-2086 -->Cannot insert gaps into sequence when
644 <!-- JAL-2146 -->Alignment column in status incorrectly
645 shown as "Sequence position" when mousing over
649 <!-- JAL-2099 -->Incorrect column numbers in ruler when
650 hidden columns present
653 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
654 user created annotation added to alignment
657 <!-- JAL-1841 -->RNA Structure consensus only computed for
658 '()' base pair annotation
661 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
662 in zero scores for all base pairs in RNA Structure
666 <!-- JAL-2174-->Extend selection with columns containing
670 <!-- JAL-2275 -->Pfam format writer puts extra space at
671 beginning of sequence
674 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
678 <!-- JAL-2238 -->Cannot create groups on an alignment from
679 from a tree when t-coffee scores are shown
682 <!-- JAL-1836,1967 -->Cannot import and view PDB
683 structures with chains containing negative resnums (4q4h)
686 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
690 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
691 to Clustal, PIR and PileUp output
694 <!-- JAL-2008 -->Reordering sequence features that are
695 not visible causes alignment window to repaint
698 <!-- JAL-2006 -->Threshold sliders don't work in
699 graduated colour and colour by annotation row for e-value
700 scores associated with features and annotation rows
703 <!-- JAL-1797 -->amino acid physicochemical conservation
704 calculation should be case independent
707 <!-- JAL-2173 -->Remove annotation also updates hidden
711 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
712 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
713 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
716 <!-- JAL-2065 -->Null pointer exceptions and redraw
717 problems when reference sequence defined and 'show
718 non-conserved' enabled
721 <!-- JAL-1306 -->Quality and Conservation are now shown on
722 load even when Consensus calculation is disabled
725 <!-- JAL-1932 -->Remove right on penultimate column of
726 alignment does nothing
732 <!-- JAL-1552-->URLs and links can't be imported by
733 drag'n'drop on OSX when launched via webstart (note - not
734 yet fixed for El Capitan)
737 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
738 output when running on non-gb/us i18n platforms
741 <!-- JAL-1944 -->Error thrown when exporting a view with
742 hidden sequences as flat-file alignment
745 <!-- JAL-2030-->InstallAnywhere distribution fails when
749 <!-- JAL-2080-->Jalview very slow to launch via webstart
750 (also hotfix for 2.9.0b2)
753 <!-- JAL-2085 -->Cannot save project when view has a
754 reference sequence defined
757 <!-- JAL-1011 -->Columns are suddenly selected in other
758 alignments and views when revealing hidden columns
761 <!-- JAL-1989 -->Hide columns not mirrored in complement
762 view in a cDNA/Protein splitframe
765 <!-- JAL-1369 -->Cannot save/restore representative
766 sequence from project when only one sequence is
770 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
774 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
775 structure consensus didn't refresh annotation panel
778 <!-- JAL-1962 -->View mapping in structure view shows
779 mappings between sequence and all chains in a PDB file
782 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
783 dialogs format columns correctly, don't display array
784 data, sort columns according to type
787 <!-- JAL-1975 -->Export complete shown after destination
788 file chooser is cancelled during an image export
791 <!-- JAL-2025 -->Error when querying PDB Service with
792 sequence name containing special characters
795 <!-- JAL-2024 -->Manual PDB structure querying should be
799 <!-- JAL-2104 -->Large tooltips with broken HTML
800 formatting don't wrap
803 <!-- JAL-1128 -->Figures exported from wrapped view are
804 truncated so L looks like I in consensus annotation
807 <!-- JAL-2003 -->Export features should only export the
808 currently displayed features for the current selection or
812 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
813 after fetching cross-references, and restoring from project
816 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
817 followed in the structure viewer
820 <!-- JAL-2163 -->Titles for individual alignments in
821 splitframe not restored from project
824 <!-- JAL-2145 -->missing autocalculated annotation at
825 trailing end of protein alignment in transcript/product
826 splitview when pad-gaps not enabled by default
829 <!-- JAL-1797 -->amino acid physicochemical conservation
833 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
834 article has been read (reopened issue due to
835 internationalisation problems)
838 <!-- JAL-1960 -->Only offer PDB structures in structure
839 viewer based on sequence name, PDB and UniProt
844 <!-- JAL-1976 -->No progress bar shown during export of
848 <!-- JAL-2213 -->Structures not always superimposed after
849 multiple structures are shown for one or more sequences.
852 <!-- JAL-1370 -->Reference sequence characters should not
853 be replaced with '.' when 'Show unconserved' format option
857 <!-- JAL-1823 -->Cannot specify chain code when entering
858 specific PDB id for sequence
861 <!-- JAL-1944 -->File->Export->.. as doesn't work when
862 'Export hidden sequences' is enabled, but 'export hidden
863 columns' is disabled.
866 <!--JAL-2026-->Best Quality option in structure chooser
867 selects lowest rather than highest resolution structures
871 <!-- JAL-1887 -->Incorrect start and end reported for PDB
872 to sequence mapping in 'View Mappings' report
875 <!-- JAL-2284 -->Unable to read old Jalview projects that
876 contain non-XML data added after Jalvew wrote project.
878 <li><!-- JAL-2118 -->Newly created annotation row reorders
879 after clicking on it to create new annotation for a
882 <!-- may exclude, this is an external service stability issue JAL-1941
883 -- > RNA 3D structure not added via DSSR service</li> -->
888 <!-- JAL-2151 -->Incorrect columns are selected when
889 hidden columns present before start of sequence
892 <!-- JAL-1986 -->Missing dependencies on applet pages
896 <!-- JAL-1947 -->Overview pixel size changes when
897 sequences are hidden in applet
900 <!-- JAL-1996 -->Updated instructions for applet
901 deployment on examples pages.
908 <td width="60" nowrap>
910 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
911 <em>16/10/2015</em></strong>
916 <li>Time stamps for signed Jalview application and applet
923 <li>Duplicate group consensus and conservation rows
924 shown when tree is partitioned</li>
925 <li>Erratic behaviour when tree partitions made with
926 multiple cDNA/Protein split views</li>
932 <td width="60" nowrap>
934 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
935 <em>8/10/2015</em></strong>
940 <li>Updated Spanish translations of localized text for
942 </ul> <em>Application</em>
944 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
945 <li>Signed OSX InstallAnywhere installer<br></li>
946 <li>Support for per-sequence based annotations in BioJSON</li>
947 </ul> <em>Applet</em>
949 <li>Split frame example added to applet examples page</li>
950 </ul><em>Build and Deployment</em>
952 <li><!-- JAL-1888 -->New ant target for running Jalview's test suite</li>
958 <li>Mapping of cDNA to protein in split frames
959 incorrect when sequence start > 1</li>
960 <li>Broken images in filter column by annotation dialog
962 <li>Feature colours not parsed from features file</li>
963 <li>Exceptions and incomplete link URLs recovered when
964 loading a features file containing HTML tags in feature
970 <li>Annotations corrupted after BioJS export and
972 <li>Incorrect sequence limits after Fetch DB References
973 with 'trim retrieved sequences'</li>
974 <li>Incorrect warning about deleting all data when
975 deleting selected columns</li>
976 <li>Patch to build system for shipping properly signed
977 JNLP templates for webstart launch</li>
978 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
979 unreleased structures for download or viewing</li>
980 <li>Tab/space/return keystroke operation of EMBL-PDBe
981 fetcher/viewer dialogs works correctly</li>
982 <li>Disabled 'minimise' button on Jalview windows
983 running on OSX to workaround redraw hang bug</li>
984 <li>Split cDNA/Protein view position and geometry not
985 recovered from jalview project</li>
986 <li>Initial enabled/disabled state of annotation menu
987 sorter 'show autocalculated first/last' corresponds to
989 <li>Restoring of Clustal, RNA Helices and T-Coffee
990 color schemes from BioJSON</li>
994 <li>Reorder sequences mirrored in cDNA/Protein split
996 <li>Applet with Jmol examples not loading correctly</li>
1002 <td><div align="center">
1003 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1005 <td><em>General</em>
1007 <li>Linked visualisation and analysis of DNA and Protein
1010 <li>Translated cDNA alignments shown as split protein
1011 and DNA alignment views</li>
1012 <li>Codon consensus annotation for linked protein and
1013 cDNA alignment views</li>
1014 <li>Link cDNA or Protein product sequences by loading
1015 them onto Protein or cDNA alignments</li>
1016 <li>Reconstruct linked cDNA alignment from aligned
1017 protein sequences</li>
1020 <li>Jmol integration updated to Jmol v14.2.14</li>
1021 <li>Import and export of Jalview alignment views as <a
1022 href="features/bioJsonFormat.html">BioJSON</a></li>
1023 <li>New alignment annotation file statements for
1024 reference sequences and marking hidden columns</li>
1025 <li>Reference sequence based alignment shading to
1026 highlight variation</li>
1027 <li>Select or hide columns according to alignment
1029 <li>Find option for locating sequences by description</li>
1030 <li>Conserved physicochemical properties shown in amino
1031 acid conservation row</li>
1032 <li>Alignments can be sorted by number of RNA helices</li>
1033 </ul> <em>Application</em>
1035 <li>New cDNA/Protein analysis capabilities
1037 <li>Get Cross-References should open a Split Frame
1038 view with cDNA/Protein</li>
1039 <li>Detect when nucleotide sequences and protein
1040 sequences are placed in the same alignment</li>
1041 <li>Split cDNA/Protein views are saved in Jalview
1046 <li>Use REST API to talk to Chimera</li>
1047 <li>Selected regions in Chimera are highlighted in linked
1048 Jalview windows</li>
1050 <li>VARNA RNA viewer updated to v3.93</li>
1051 <li>VARNA views are saved in Jalview Projects</li>
1052 <li>Pseudoknots displayed as Jalview RNA annotation can
1053 be shown in VARNA</li>
1055 <li>Make groups for selection uses marked columns as well
1056 as the active selected region</li>
1058 <li>Calculate UPGMA and NJ trees using sequence feature
1060 <li>New Export options
1062 <li>New Export Settings dialog to control hidden
1063 region export in flat file generation</li>
1065 <li>Export alignment views for display with the <a
1066 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1068 <li>Export scrollable SVG in HTML page</li>
1069 <li>Optional embedding of BioJSON data when exporting
1070 alignment figures to HTML</li>
1072 <li>3D structure retrieval and display
1074 <li>Free text and structured queries with the PDBe
1076 <li>PDBe Search API based discovery and selection of
1077 PDB structures for a sequence set</li>
1081 <li>JPred4 employed for protein secondary structure
1083 <li>Hide Insertions menu option to hide unaligned columns
1084 for one or a group of sequences</li>
1085 <li>Automatically hide insertions in alignments imported
1086 from the JPred4 web server</li>
1087 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1088 system on OSX<br />LGPL libraries courtesy of <a
1089 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1091 <li>changed 'View nucleotide structure' submenu to 'View
1092 VARNA 2D Structure'</li>
1093 <li>change "View protein structure" menu option to "3D
1096 </ul> <em>Applet</em>
1098 <li>New layout for applet example pages</li>
1099 <li>New parameters to enable SplitFrame view
1100 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1101 <li>New example demonstrating linked viewing of cDNA and
1102 Protein alignments</li>
1103 </ul> <em>Development and deployment</em>
1105 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1106 <li>Include installation type and git revision in build
1107 properties and console log output</li>
1108 <li>Jalview Github organisation, and new github site for
1109 storing BioJsMSA Templates</li>
1110 <li>Jalview's unit tests now managed with TestNG</li>
1113 <!-- <em>General</em>
1115 </ul> --> <!-- issues resolved --> <em>Application</em>
1117 <li>Escape should close any open find dialogs</li>
1118 <li>Typo in select-by-features status report</li>
1119 <li>Consensus RNA secondary secondary structure
1120 predictions are not highlighted in amber</li>
1121 <li>Missing gap character in v2.7 example file means
1122 alignment appears unaligned when pad-gaps is not enabled</li>
1123 <li>First switch to RNA Helices colouring doesn't colour
1124 associated structure views</li>
1125 <li>ID width preference option is greyed out when auto
1126 width checkbox not enabled</li>
1127 <li>Stopped a warning dialog from being shown when
1128 creating user defined colours</li>
1129 <li>'View Mapping' in structure viewer shows sequence
1130 mappings for just that viewer's sequences</li>
1131 <li>Workaround for superposing PDB files containing
1132 multiple models in Chimera</li>
1133 <li>Report sequence position in status bar when hovering
1134 over Jmol structure</li>
1135 <li>Cannot output gaps as '.' symbols with Selection ->
1136 output to text box</li>
1137 <li>Flat file exports of alignments with hidden columns
1138 have incorrect sequence start/end</li>
1139 <li>'Aligning' a second chain to a Chimera structure from
1141 <li>Colour schemes applied to structure viewers don't
1142 work for nucleotide</li>
1143 <li>Loading/cut'n'pasting an empty or invalid file leads
1144 to a grey/invisible alignment window</li>
1145 <li>Exported Jpred annotation from a sequence region
1146 imports to different position</li>
1147 <li>Space at beginning of sequence feature tooltips shown
1148 on some platforms</li>
1149 <li>Chimera viewer 'View | Show Chain' menu is not
1151 <li>'New View' fails with a Null Pointer Exception in
1152 console if Chimera has been opened</li>
1153 <li>Mouseover to Chimera not working</li>
1154 <li>Miscellaneous ENA XML feature qualifiers not
1156 <li>NPE in annotation renderer after 'Extract Scores'</li>
1157 <li>If two structures in one Chimera window, mouseover of
1158 either sequence shows on first structure</li>
1159 <li>'Show annotations' options should not make
1160 non-positional annotations visible</li>
1161 <li>Subsequence secondary structure annotation not shown
1162 in right place after 'view flanking regions'</li>
1163 <li>File Save As type unset when current file format is
1165 <li>Save as '.jar' option removed for saving Jalview
1167 <li>Colour by Sequence colouring in Chimera more
1169 <li>Cannot 'add reference annotation' for a sequence in
1170 several views on same alignment</li>
1171 <li>Cannot show linked products for EMBL / ENA records</li>
1172 <li>Jalview's tooltip wraps long texts containing no
1174 </ul> <em>Applet</em>
1176 <li>Jmol to JalviewLite mouseover/link not working</li>
1177 <li>JalviewLite can't import sequences with ID
1178 descriptions containing angle brackets</li>
1179 </ul> <em>General</em>
1181 <li>Cannot export and reimport RNA secondary structure
1182 via jalview annotation file</li>
1183 <li>Random helix colour palette for colour by annotation
1184 with RNA secondary structure</li>
1185 <li>Mouseover to cDNA from STOP residue in protein
1186 translation doesn't work.</li>
1187 <li>hints when using the select by annotation dialog box</li>
1188 <li>Jmol alignment incorrect if PDB file has alternate CA
1190 <li>FontChooser message dialog appears to hang after
1191 choosing 1pt font</li>
1192 <li>Peptide secondary structure incorrectly imported from
1193 annotation file when annotation display text includes 'e' or
1195 <li>Cannot set colour of new feature type whilst creating
1197 <li>cDNA translation alignment should not be sequence
1198 order dependent</li>
1199 <li>'Show unconserved' doesn't work for lower case
1201 <li>Nucleotide ambiguity codes involving R not recognised</li>
1202 </ul> <em>Deployment and Documentation</em>
1204 <li>Applet example pages appear different to the rest of
1205 www.jalview.org</li>
1206 </ul> <em>Application Known issues</em>
1208 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1209 <li>Misleading message appears after trying to delete
1211 <li>Jalview icon not shown in dock after InstallAnywhere
1212 version launches</li>
1213 <li>Fetching EMBL reference for an RNA sequence results
1214 fails with a sequence mismatch</li>
1215 <li>Corrupted or unreadable alignment display when
1216 scrolling alignment to right</li>
1217 <li>ArrayIndexOutOfBoundsException thrown when remove
1218 empty columns called on alignment with ragged gapped ends</li>
1219 <li>auto calculated alignment annotation rows do not get
1220 placed above or below non-autocalculated rows</li>
1221 <li>Jalview dekstop becomes sluggish at full screen in
1222 ultra-high resolution</li>
1223 <li>Cannot disable consensus calculation independently of
1224 quality and conservation</li>
1225 <li>Mouseover highlighting between cDNA and protein can
1226 become sluggish with more than one splitframe shown</li>
1227 </ul> <em>Applet Known Issues</em>
1229 <li>Core PDB parsing code requires Jmol</li>
1230 <li>Sequence canvas panel goes white when alignment
1231 window is being resized</li>
1237 <td><div align="center">
1238 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1240 <td><em>General</em>
1242 <li>Updated Java code signing certificate donated by
1244 <li>Features and annotation preserved when performing
1245 pairwise alignment</li>
1246 <li>RNA pseudoknot annotation can be
1247 imported/exported/displayed</li>
1248 <li>'colour by annotation' can colour by RNA and
1249 protein secondary structure</li>
1250 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1251 post-hoc with 2.9 release</em>)
1254 </ul> <em>Application</em>
1256 <li>Extract and display secondary structure for sequences
1257 with 3D structures</li>
1258 <li>Support for parsing RNAML</li>
1259 <li>Annotations menu for layout
1261 <li>sort sequence annotation rows by alignment</li>
1262 <li>place sequence annotation above/below alignment
1265 <li>Output in Stockholm format</li>
1266 <li>Internationalisation: improved Spanish (es)
1268 <li>Structure viewer preferences tab</li>
1269 <li>Disorder and Secondary Structure annotation tracks
1270 shared between alignments</li>
1271 <li>UCSF Chimera launch and linked highlighting from
1273 <li>Show/hide all sequence associated annotation rows for
1274 all or current selection</li>
1275 <li>disorder and secondary structure predictions
1276 available as dataset annotation</li>
1277 <li>Per-sequence rna helices colouring</li>
1280 <li>Sequence database accessions imported when fetching
1281 alignments from Rfam</li>
1282 <li>update VARNA version to 3.91</li>
1284 <li>New groovy scripts for exporting aligned positions,
1285 conservation values, and calculating sum of pairs scores.</li>
1286 <li>Command line argument to set default JABAWS server</li>
1287 <li>include installation type in build properties and
1288 console log output</li>
1289 <li>Updated Jalview project format to preserve dataset
1293 <!-- issues resolved --> <em>Application</em>
1295 <li>Distinguish alignment and sequence associated RNA
1296 structure in structure->view->VARNA</li>
1297 <li>Raise dialog box if user deletes all sequences in an
1299 <li>Pressing F1 results in documentation opening twice</li>
1300 <li>Sequence feature tooltip is wrapped</li>
1301 <li>Double click on sequence associated annotation
1302 selects only first column</li>
1303 <li>Redundancy removal doesn't result in unlinked
1304 leaves shown in tree</li>
1305 <li>Undos after several redundancy removals don't undo
1307 <li>Hide sequence doesn't hide associated annotation</li>
1308 <li>User defined colours dialog box too big to fit on
1309 screen and buttons not visible</li>
1310 <li>author list isn't updated if already written to
1311 Jalview properties</li>
1312 <li>Popup menu won't open after retrieving sequence
1314 <li>File open window for associate PDB doesn't open</li>
1315 <li>Left-then-right click on a sequence id opens a
1316 browser search window</li>
1317 <li>Cannot open sequence feature shading/sort popup menu
1318 in feature settings dialog</li>
1319 <li>better tooltip placement for some areas of Jalview
1321 <li>Allow addition of JABAWS Server which doesn't
1322 pass validation</li>
1323 <li>Web services parameters dialog box is too large to
1325 <li>Muscle nucleotide alignment preset obscured by
1327 <li>JABAWS preset submenus don't contain newly
1328 defined user preset</li>
1329 <li>MSA web services warns user if they were launched
1330 with invalid input</li>
1331 <li>Jalview cannot contact DAS Registy when running on
1334 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1335 'Superpose with' submenu not shown when new view
1339 </ul> <!-- <em>Applet</em>
1341 </ul> <em>General</em>
1343 </ul>--> <em>Deployment and Documentation</em>
1345 <li>2G and 1G options in launchApp have no effect on
1346 memory allocation</li>
1347 <li>launchApp service doesn't automatically open
1348 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1350 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1351 InstallAnywhere reports cannot find valid JVM when Java
1352 1.7_055 is available
1354 </ul> <em>Application Known issues</em>
1357 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1358 corrupted or unreadable alignment display when scrolling
1362 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1363 retrieval fails but progress bar continues for DAS retrieval
1364 with large number of ID
1367 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1368 flatfile output of visible region has incorrect sequence
1372 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1373 rna structure consensus doesn't update when secondary
1374 structure tracks are rearranged
1377 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1378 invalid rna structure positional highlighting does not
1379 highlight position of invalid base pairs
1382 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1383 out of memory errors are not raised when saving Jalview
1384 project from alignment window file menu
1387 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1388 Switching to RNA Helices colouring doesn't propagate to
1392 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1393 colour by RNA Helices not enabled when user created
1394 annotation added to alignment
1397 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1398 Jalview icon not shown on dock in Mountain Lion/Webstart
1400 </ul> <em>Applet Known Issues</em>
1403 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1404 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1407 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1408 Jalview and Jmol example not compatible with IE9
1411 <li>Sort by annotation score doesn't reverse order
1417 <td><div align="center">
1418 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1421 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1424 <li>Internationalisation of user interface (usually
1425 called i18n support) and translation for Spanish locale</li>
1426 <li>Define/Undefine group on current selection with
1427 Ctrl-G/Shift Ctrl-G</li>
1428 <li>Improved group creation/removal options in
1429 alignment/sequence Popup menu</li>
1430 <li>Sensible precision for symbol distribution
1431 percentages shown in logo tooltip.</li>
1432 <li>Annotation panel height set according to amount of
1433 annotation when alignment first opened</li>
1434 </ul> <em>Application</em>
1436 <li>Interactive consensus RNA secondary structure
1437 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1438 <li>Select columns containing particular features from
1439 Feature Settings dialog</li>
1440 <li>View all 'representative' PDB structures for selected
1442 <li>Update Jalview project format:
1444 <li>New file extension for Jalview projects '.jvp'</li>
1445 <li>Preserve sequence and annotation dataset (to
1446 store secondary structure annotation,etc)</li>
1447 <li>Per group and alignment annotation and RNA helix
1451 <li>New similarity measures for PCA and Tree calculation
1453 <li>Experimental support for retrieval and viewing of
1454 flanking regions for an alignment</li>
1458 <!-- issues resolved --> <em>Application</em>
1460 <li>logo keeps spinning and status remains at queued or
1461 running after job is cancelled</li>
1462 <li>cannot export features from alignments imported from
1463 Jalview/VAMSAS projects</li>
1464 <li>Buggy slider for web service parameters that take
1466 <li>Newly created RNA secondary structure line doesn't
1467 have 'display all symbols' flag set</li>
1468 <li>T-COFFEE alignment score shading scheme and other
1469 annotation shading not saved in Jalview project</li>
1470 <li>Local file cannot be loaded in freshly downloaded
1472 <li>Jalview icon not shown on dock in Mountain
1474 <li>Load file from desktop file browser fails</li>
1475 <li>Occasional NPE thrown when calculating large trees</li>
1476 <li>Cannot reorder or slide sequences after dragging an
1477 alignment onto desktop</li>
1478 <li>Colour by annotation dialog throws NPE after using
1479 'extract scores' function</li>
1480 <li>Loading/cut'n'pasting an empty file leads to a grey
1481 alignment window</li>
1482 <li>Disorder thresholds rendered incorrectly after
1483 performing IUPred disorder prediction</li>
1484 <li>Multiple group annotated consensus rows shown when
1485 changing 'normalise logo' display setting</li>
1486 <li>Find shows blank dialog after 'finished searching' if
1487 nothing matches query</li>
1488 <li>Null Pointer Exceptions raised when sorting by
1489 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1491 <li>Errors in Jmol console when structures in alignment
1492 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1494 <li>Not all working JABAWS services are shown in
1496 <li>JAVAWS version of Jalview fails to launch with
1497 'invalid literal/length code'</li>
1498 <li>Annotation/RNA Helix colourschemes cannot be applied
1499 to alignment with groups (actually fixed in 2.8.0b1)</li>
1500 <li>RNA Helices and T-Coffee Scores available as default
1503 </ul> <em>Applet</em>
1505 <li>Remove group option is shown even when selection is
1507 <li>Apply to all groups ticked but colourscheme changes
1508 don't affect groups</li>
1509 <li>Documented RNA Helices and T-Coffee Scores as valid
1510 colourscheme name</li>
1511 <li>Annotation labels drawn on sequence IDs when
1512 Annotation panel is not displayed</li>
1513 <li>Increased font size for dropdown menus on OSX and
1514 embedded windows</li>
1515 </ul> <em>Other</em>
1517 <li>Consensus sequence for alignments/groups with a
1518 single sequence were not calculated</li>
1519 <li>annotation files that contain only groups imported as
1520 annotation and junk sequences</li>
1521 <li>Fasta files with sequences containing '*' incorrectly
1522 recognised as PFAM or BLC</li>
1523 <li>conservation/PID slider apply all groups option
1524 doesn't affect background (2.8.0b1)
1526 <li>redundancy highlighting is erratic at 0% and 100%</li>
1527 <li>Remove gapped columns fails for sequences with ragged
1529 <li>AMSA annotation row with leading spaces is not
1530 registered correctly on import</li>
1531 <li>Jalview crashes when selecting PCA analysis for
1532 certain alignments</li>
1533 <li>Opening the colour by annotation dialog for an
1534 existing annotation based 'use original colours'
1535 colourscheme loses original colours setting</li>
1540 <td><div align="center">
1541 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
1542 <em>30/1/2014</em></strong>
1546 <li>Trusted certificates for JalviewLite applet and
1547 Jalview Desktop application<br />Certificate was donated by
1548 <a href="https://www.certum.eu">Certum</a> to the Jalview
1549 open source project).
1551 <li>Jalview SRS links replaced by UniProt and EBI-search
1553 <li>Output in Stockholm format</li>
1554 <li>Allow import of data from gzipped files</li>
1555 <li>Export/import group and sequence associated line
1556 graph thresholds</li>
1557 <li>Nucleotide substitution matrix that supports RNA and
1558 ambiguity codes</li>
1559 <li>Allow disorder predictions to be made on the current
1560 selection (or visible selection) in the same way that JPred
1562 <li>Groovy scripting for headless Jalview operation</li>
1563 </ul> <em>Other improvements</em>
1565 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
1566 <li>COMBINE statement uses current SEQUENCE_REF and
1567 GROUP_REF scope to group annotation rows</li>
1568 <li>Support '' style escaping of quotes in Newick
1570 <li>Group options for JABAWS service by command line name</li>
1571 <li>Empty tooltip shown for JABA service options with a
1572 link but no description</li>
1573 <li>Select primary source when selecting authority in
1574 database fetcher GUI</li>
1575 <li>Add .mfa to FASTA file extensions recognised by
1577 <li>Annotation label tooltip text wrap</li>
1582 <li>Slow scrolling when lots of annotation rows are
1584 <li>Lots of NPE (and slowness) after creating RNA
1585 secondary structure annotation line</li>
1586 <li>Sequence database accessions not imported when
1587 fetching alignments from Rfam</li>
1588 <li>Incorrect SHMR submission for sequences with
1590 <li>View all structures does not always superpose
1592 <li>Option widgets in service parameters not updated to
1593 reflect user or preset settings</li>
1594 <li>Null pointer exceptions for some services without
1595 presets or adjustable parameters</li>
1596 <li>Discover PDB IDs entry in structure menu doesn't
1597 discover PDB xRefs</li>
1598 <li>Exception encountered while trying to retrieve
1599 features with DAS</li>
1600 <li>Lowest value in annotation row isn't coloured
1601 when colour by annotation (per sequence) is coloured</li>
1602 <li>Keyboard mode P jumps to start of gapped region when
1603 residue follows a gap</li>
1604 <li>Jalview appears to hang importing an alignment with
1605 Wrap as default or after enabling Wrap</li>
1606 <li>'Right click to add annotations' message
1607 shown in wrap mode when no annotations present</li>
1608 <li>Disorder predictions fail with NPE if no automatic
1609 annotation already exists on alignment</li>
1610 <li>oninit javascript function should be called after
1611 initialisation completes</li>
1612 <li>Remove redundancy after disorder prediction corrupts
1613 alignment window display</li>
1614 <li>Example annotation file in documentation is invalid</li>
1615 <li>Grouped line graph annotation rows are not exported
1616 to annotation file</li>
1617 <li>Multi-harmony analysis cannot be run when only two
1619 <li>Cannot create multiple groups of line graphs with
1620 several 'combine' statements in annotation file</li>
1621 <li>Pressing return several times causes Number Format
1622 exceptions in keyboard mode</li>
1623 <li>Multi-harmony (SHMMR) method doesn't submit
1624 correct partitions for input data</li>
1625 <li>Translation from DNA to Amino Acids fails</li>
1626 <li>Jalview fail to load newick tree with quoted label</li>
1627 <li>--headless flag isn't understood</li>
1628 <li>ClassCastException when generating EPS in headless
1630 <li>Adjusting sequence-associated shading threshold only
1631 changes one row's threshold</li>
1632 <li>Preferences and Feature settings panel panel
1633 doesn't open</li>
1634 <li>hide consensus histogram also hides conservation and
1635 quality histograms</li>
1640 <td><div align="center">
1641 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
1643 <td><em>Application</em>
1645 <li>Support for JABAWS 2.0 Services (AACon alignment
1646 conservation, protein disorder and Clustal Omega)</li>
1647 <li>JABAWS server status indicator in Web Services
1649 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
1650 in Jalview alignment window</li>
1651 <li>Updated Jalview build and deploy framework for OSX
1652 mountain lion, windows 7, and 8</li>
1653 <li>Nucleotide substitution matrix for PCA that supports
1654 RNA and ambiguity codes</li>
1656 <li>Improved sequence database retrieval GUI</li>
1657 <li>Support fetching and database reference look up
1658 against multiple DAS sources (Fetch all from in 'fetch db
1660 <li>Jalview project improvements
1662 <li>Store and retrieve the 'belowAlignment'
1663 flag for annotation</li>
1664 <li>calcId attribute to group annotation rows on the
1666 <li>Store AACon calculation settings for a view in
1667 Jalview project</li>
1671 <li>horizontal scrolling gesture support</li>
1672 <li>Visual progress indicator when PCA calculation is
1674 <li>Simpler JABA web services menus</li>
1675 <li>visual indication that web service results are still
1676 being retrieved from server</li>
1677 <li>Serialise the dialogs that are shown when Jalview
1678 starts up for first time</li>
1679 <li>Jalview user agent string for interacting with HTTP
1681 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
1683 <li>Examples directory and Groovy library included in
1684 InstallAnywhere distribution</li>
1685 </ul> <em>Applet</em>
1687 <li>RNA alignment and secondary structure annotation
1688 visualization applet example</li>
1689 </ul> <em>General</em>
1691 <li>Normalise option for consensus sequence logo</li>
1692 <li>Reset button in PCA window to return dimensions to
1694 <li>Allow seqspace or Jalview variant of alignment PCA
1696 <li>PCA with either nucleic acid and protein substitution
1698 <li>Allow windows containing HTML reports to be exported
1700 <li>Interactive display and editing of RNA secondary
1701 structure contacts</li>
1702 <li>RNA Helix Alignment Colouring</li>
1703 <li>RNA base pair logo consensus</li>
1704 <li>Parse sequence associated secondary structure
1705 information in Stockholm files</li>
1706 <li>HTML Export database accessions and annotation
1707 information presented in tooltip for sequences</li>
1708 <li>Import secondary structure from LOCARNA clustalw
1709 style RNA alignment files</li>
1710 <li>import and visualise T-COFFEE quality scores for an
1712 <li>'colour by annotation' per sequence option to
1713 shade each sequence according to its associated alignment
1715 <li>New Jalview Logo</li>
1716 </ul> <em>Documentation and Development</em>
1718 <li>documentation for score matrices used in Jalview</li>
1719 <li>New Website!</li>
1721 <td><em>Application</em>
1723 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
1724 wsdbfetch REST service</li>
1725 <li>Stop windows being moved outside desktop on OSX</li>
1726 <li>Filetype associations not installed for webstart
1728 <li>Jalview does not always retrieve progress of a JABAWS
1729 job execution in full once it is complete</li>
1730 <li>revise SHMR RSBS definition to ensure alignment is
1731 uploaded via ali_file parameter</li>
1732 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
1733 <li>View all structures superposed fails with exception</li>
1734 <li>Jnet job queues forever if a very short sequence is
1735 submitted for prediction</li>
1736 <li>Cut and paste menu not opened when mouse clicked on
1738 <li>Putting fractional value into integer text box in
1739 alignment parameter dialog causes Jalview to hang</li>
1740 <li>Structure view highlighting doesn't work on
1742 <li>View all structures fails with exception shown in
1744 <li>Characters in filename associated with PDBEntry not
1745 escaped in a platform independent way</li>
1746 <li>Jalview desktop fails to launch with exception when
1748 <li>Tree calculation reports 'you must have 2 or more
1749 sequences selected' when selection is empty</li>
1750 <li>Jalview desktop fails to launch with jar signature
1751 failure when java web start temporary file caching is
1753 <li>DAS Sequence retrieval with range qualification
1754 results in sequence xref which includes range qualification</li>
1755 <li>Errors during processing of command line arguments
1756 cause progress bar (JAL-898) to be removed</li>
1757 <li>Replace comma for semi-colon option not disabled for
1758 DAS sources in sequence fetcher</li>
1759 <li>Cannot close news reader when JABAWS server warning
1760 dialog is shown</li>
1761 <li>Option widgets not updated to reflect user settings</li>
1762 <li>Edited sequence not submitted to web service</li>
1763 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
1764 <li>InstallAnywhere installer doesn't unpack and run
1765 on OSX Mountain Lion</li>
1766 <li>Annotation panel not given a scroll bar when
1767 sequences with alignment annotation are pasted into the
1769 <li>Sequence associated annotation rows not associated
1770 when loaded from Jalview project</li>
1771 <li>Browser launch fails with NPE on java 1.7</li>
1772 <li>JABAWS alignment marked as finished when job was
1773 cancelled or job failed due to invalid input</li>
1774 <li>NPE with v2.7 example when clicking on Tree
1775 associated with all views</li>
1776 <li>Exceptions when copy/paste sequences with grouped
1777 annotation rows to new window</li>
1778 </ul> <em>Applet</em>
1780 <li>Sequence features are momentarily displayed before
1781 they are hidden using hidefeaturegroups applet parameter</li>
1782 <li>loading features via javascript API automatically
1783 enables feature display</li>
1784 <li>scrollToColumnIn javascript API method doesn't
1786 </ul> <em>General</em>
1788 <li>Redundancy removal fails for rna alignment</li>
1789 <li>PCA calculation fails when sequence has been selected
1790 and then deselected</li>
1791 <li>PCA window shows grey box when first opened on OSX</li>
1792 <li>Letters coloured pink in sequence logo when alignment
1793 coloured with clustalx</li>
1794 <li>Choosing fonts without letter symbols defined causes
1795 exceptions and redraw errors</li>
1796 <li>Initial PCA plot view is not same as manually
1797 reconfigured view</li>
1798 <li>Grouped annotation graph label has incorrect line
1800 <li>Grouped annotation graph label display is corrupted
1801 for lots of labels</li>
1806 <div align="center">
1807 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
1810 <td><em>Application</em>
1812 <li>Jalview Desktop News Reader</li>
1813 <li>Tweaked default layout of web services menu</li>
1814 <li>View/alignment association menu to enable user to
1815 easily specify which alignment a multi-structure view takes
1816 its colours/correspondences from</li>
1817 <li>Allow properties file location to be specified as URL</li>
1818 <li>Extend Jalview project to preserve associations
1819 between many alignment views and a single Jmol display</li>
1820 <li>Store annotation row height in Jalview project file</li>
1821 <li>Annotation row column label formatting attributes
1822 stored in project file</li>
1823 <li>Annotation row order for auto-calculated annotation
1824 rows preserved in Jalview project file</li>
1825 <li>Visual progress indication when Jalview state is
1826 saved using Desktop window menu</li>
1827 <li>Visual indication that command line arguments are
1828 still being processed</li>
1829 <li>Groovy script execution from URL</li>
1830 <li>Colour by annotation default min and max colours in
1832 <li>Automatically associate PDB files dragged onto an
1833 alignment with sequences that have high similarity and
1835 <li>Update JGoogleAnalytics to latest release (0.3)</li>
1836 <li>'view structures' option to open many
1837 structures in same window</li>
1838 <li>Sort associated views menu option for tree panel</li>
1839 <li>Group all JABA and non-JABA services for a particular
1840 analysis function in its own submenu</li>
1841 </ul> <em>Applet</em>
1843 <li>Userdefined and autogenerated annotation rows for
1845 <li>Adjustment of alignment annotation pane height</li>
1846 <li>Annotation scrollbar for annotation panel</li>
1847 <li>Drag to reorder annotation rows in annotation panel</li>
1848 <li>'automaticScrolling' parameter</li>
1849 <li>Allow sequences with partial ID string matches to be
1850 annotated from GFF/Jalview features files</li>
1851 <li>Sequence logo annotation row in applet</li>
1852 <li>Absolute paths relative to host server in applet
1853 parameters are treated as such</li>
1854 <li>New in the JalviewLite javascript API:
1856 <li>JalviewLite.js javascript library</li>
1857 <li>Javascript callbacks for
1859 <li>Applet initialisation</li>
1860 <li>Sequence/alignment mouse-overs and selections</li>
1863 <li>scrollTo row and column alignment scrolling
1865 <li>Select sequence/alignment regions from javascript</li>
1866 <li>javascript structure viewer harness to pass
1867 messages between Jmol and Jalview when running as
1868 distinct applets</li>
1869 <li>sortBy method</li>
1870 <li>Set of applet and application examples shipped
1871 with documentation</li>
1872 <li>New example to demonstrate JalviewLite and Jmol
1873 javascript message exchange</li>
1875 </ul> <em>General</em>
1877 <li>Enable Jmol displays to be associated with multiple
1878 multiple alignments</li>
1879 <li>Option to automatically sort alignment with new tree</li>
1880 <li>User configurable link to enable redirects to a
1881 www.Jalview.org mirror</li>
1882 <li>Jmol colours option for Jmol displays</li>
1883 <li>Configurable newline string when writing alignment
1884 and other flat files</li>
1885 <li>Allow alignment annotation description lines to
1886 contain html tags</li>
1887 </ul> <em>Documentation and Development</em>
1889 <li>Add groovy test harness for bulk load testing to
1891 <li>Groovy script to load and align a set of sequences
1892 using a web service before displaying the result in the
1893 Jalview desktop</li>
1894 <li>Restructured javascript and applet api documentation</li>
1895 <li>Ant target to publish example html files with applet
1897 <li>Netbeans project for building Jalview from source</li>
1898 <li>ant task to create online javadoc for Jalview source</li>
1900 <td><em>Application</em>
1902 <li>User defined colourscheme throws exception when
1903 current built in colourscheme is saved as new scheme</li>
1904 <li>AlignFrame->Save in application pops up save
1905 dialog for valid filename/format</li>
1906 <li>Cannot view associated structure for UniProt sequence</li>
1907 <li>PDB file association breaks for UniProt sequence
1909 <li>Associate PDB from file dialog does not tell you
1910 which sequence is to be associated with the file</li>
1911 <li>Find All raises null pointer exception when query
1912 only matches sequence IDs</li>
1913 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
1914 <li>Jalview project with Jmol views created with Jalview
1915 2.4 cannot be loaded</li>
1916 <li>Filetype associations not installed for webstart
1918 <li>Two or more chains in a single PDB file associated
1919 with sequences in different alignments do not get coloured
1920 by their associated sequence</li>
1921 <li>Visibility status of autocalculated annotation row
1922 not preserved when project is loaded</li>
1923 <li>Annotation row height and visibility attributes not
1924 stored in Jalview project</li>
1925 <li>Tree bootstraps are not preserved when saved as a
1926 Jalview project</li>
1927 <li>Envision2 workflow tooltips are corrupted</li>
1928 <li>Enabling show group conservation also enables colour
1929 by conservation</li>
1930 <li>Duplicate group associated conservation or consensus
1931 created on new view</li>
1932 <li>Annotation scrollbar not displayed after 'show
1933 all hidden annotation rows' option selected</li>
1934 <li>Alignment quality not updated after alignment
1935 annotation row is hidden then shown</li>
1936 <li>Preserve colouring of structures coloured by
1937 sequences in pre Jalview 2.7 projects</li>
1938 <li>Web service job parameter dialog is not laid out
1940 <li>Web services menu not refreshed after 'reset
1941 services' button is pressed in preferences</li>
1942 <li>Annotation off by one in Jalview v2_3 example project</li>
1943 <li>Structures imported from file and saved in project
1944 get name like jalview_pdb1234.txt when reloaded</li>
1945 <li>Jalview does not always retrieve progress of a JABAWS
1946 job execution in full once it is complete</li>
1947 </ul> <em>Applet</em>
1949 <li>Alignment height set incorrectly when lots of
1950 annotation rows are displayed</li>
1951 <li>Relative URLs in feature HTML text not resolved to
1953 <li>View follows highlighting does not work for positions
1955 <li><= shown as = in tooltip</li>
1956 <li>Export features raises exception when no features
1958 <li>Separator string used for serialising lists of IDs
1959 for javascript api is modified when separator string
1960 provided as parameter</li>
1961 <li>Null pointer exception when selecting tree leaves for
1962 alignment with no existing selection</li>
1963 <li>Relative URLs for datasources assumed to be relative
1964 to applet's codebase</li>
1965 <li>Status bar not updated after finished searching and
1966 search wraps around to first result</li>
1967 <li>StructureSelectionManager instance shared between
1968 several Jalview applets causes race conditions and memory
1970 <li>Hover tooltip and mouseover of position on structure
1971 not sent from Jmol in applet</li>
1972 <li>Certain sequences of javascript method calls to
1973 applet API fatally hang browser</li>
1974 </ul> <em>General</em>
1976 <li>View follows structure mouseover scrolls beyond
1977 position with wrapped view and hidden regions</li>
1978 <li>Find sequence position moves to wrong residue
1979 with/without hidden columns</li>
1980 <li>Sequence length given in alignment properties window
1982 <li>InvalidNumberFormat exceptions thrown when trying to
1983 import PDB like structure files</li>
1984 <li>Positional search results are only highlighted
1985 between user-supplied sequence start/end bounds</li>
1986 <li>End attribute of sequence is not validated</li>
1987 <li>Find dialog only finds first sequence containing a
1988 given sequence position</li>
1989 <li>Sequence numbering not preserved in MSF alignment
1991 <li>Jalview PDB file reader does not extract sequence
1992 from nucleotide chains correctly</li>
1993 <li>Structure colours not updated when tree partition
1994 changed in alignment</li>
1995 <li>Sequence associated secondary structure not correctly
1996 parsed in interleaved stockholm</li>
1997 <li>Colour by annotation dialog does not restore current
1999 <li>Hiding (nearly) all sequences doesn't work
2001 <li>Sequences containing lowercase letters are not
2002 properly associated with their pdb files</li>
2003 </ul> <em>Documentation and Development</em>
2005 <li>schemas/JalviewWsParamSet.xsd corrupted by
2006 ApplyCopyright tool</li>
2011 <div align="center">
2012 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2015 <td><em>Application</em>
2017 <li>New warning dialog when the Jalview Desktop cannot
2018 contact web services</li>
2019 <li>JABA service parameters for a preset are shown in
2020 service job window</li>
2021 <li>JABA Service menu entries reworded</li>
2025 <li>Modeller PIR IO broken - cannot correctly import a
2026 pir file emitted by Jalview</li>
2027 <li>Existing feature settings transferred to new
2028 alignment view created from cut'n'paste</li>
2029 <li>Improved test for mixed amino/nucleotide chains when
2030 parsing PDB files</li>
2031 <li>Consensus and conservation annotation rows
2032 occasionally become blank for all new windows</li>
2033 <li>Exception raised when right clicking above sequences
2034 in wrapped view mode</li>
2035 </ul> <em>Application</em>
2037 <li>multiple multiply aligned structure views cause cpu
2038 usage to hit 100% and computer to hang</li>
2039 <li>Web Service parameter layout breaks for long user
2040 parameter names</li>
2041 <li>Jaba service discovery hangs desktop if Jaba server
2048 <div align="center">
2049 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2052 <td><em>Application</em>
2054 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2055 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2058 <li>Web Services preference tab</li>
2059 <li>Analysis parameters dialog box and user defined
2061 <li>Improved speed and layout of Envision2 service menu</li>
2062 <li>Superpose structures using associated sequence
2064 <li>Export coordinates and projection as CSV from PCA
2066 </ul> <em>Applet</em>
2068 <li>enable javascript: execution by the applet via the
2069 link out mechanism</li>
2070 </ul> <em>Other</em>
2072 <li>Updated the Jmol Jalview interface to work with Jmol
2074 <li>The Jalview Desktop and JalviewLite applet now
2075 require Java 1.5</li>
2076 <li>Allow Jalview feature colour specification for GFF
2077 sequence annotation files</li>
2078 <li>New 'colour by label' keword in Jalview feature file
2079 type colour specification</li>
2080 <li>New Jalview Desktop Groovy API method that allows a
2081 script to check if it being run in an interactive session or
2082 in a batch operation from the Jalview command line</li>
2086 <li>clustalx colourscheme colours Ds preferentially when
2087 both D+E are present in over 50% of the column</li>
2088 </ul> <em>Application</em>
2090 <li>typo in AlignmentFrame->View->Hide->all but
2091 selected Regions menu item</li>
2092 <li>sequence fetcher replaces ',' for ';' when the ',' is
2093 part of a valid accession ID</li>
2094 <li>fatal OOM if object retrieved by sequence fetcher
2095 runs out of memory</li>
2096 <li>unhandled Out of Memory Error when viewing pca
2097 analysis results</li>
2098 <li>InstallAnywhere builds fail to launch on OS X java
2099 10.5 update 4 (due to apple Java 1.6 update)</li>
2100 <li>Installanywhere Jalview silently fails to launch</li>
2101 </ul> <em>Applet</em>
2103 <li>Jalview.getFeatureGroups() raises an
2104 ArrayIndexOutOfBoundsException if no feature groups are
2111 <div align="center">
2112 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2118 <li>Alignment prettyprinter doesn't cope with long
2120 <li>clustalx colourscheme colours Ds preferentially when
2121 both D+E are present in over 50% of the column</li>
2122 <li>nucleic acid structures retrieved from PDB do not
2123 import correctly</li>
2124 <li>More columns get selected than were clicked on when a
2125 number of columns are hidden</li>
2126 <li>annotation label popup menu not providing correct
2127 add/hide/show options when rows are hidden or none are
2129 <li>Stockholm format shown in list of readable formats,
2130 and parser copes better with alignments from RFAM.</li>
2131 <li>CSV output of consensus only includes the percentage
2132 of all symbols if sequence logo display is enabled</li>
2134 </ul> <em>Applet</em>
2136 <li>annotation panel disappears when annotation is
2138 </ul> <em>Application</em>
2140 <li>Alignment view not redrawn properly when new
2141 alignment opened where annotation panel is visible but no
2142 annotations are present on alignment</li>
2143 <li>pasted region containing hidden columns is
2144 incorrectly displayed in new alignment window</li>
2145 <li>Jalview slow to complete operations when stdout is
2146 flooded (fix is to close the Jalview console)</li>
2147 <li>typo in AlignmentFrame->View->Hide->all but
2148 selected Rregions menu item.</li>
2149 <li>inconsistent group submenu and Format submenu entry
2150 'Un' or 'Non'conserved</li>
2151 <li>Sequence feature settings are being shared by
2152 multiple distinct alignments</li>
2153 <li>group annotation not recreated when tree partition is
2155 <li>double click on group annotation to select sequences
2156 does not propagate to associated trees</li>
2157 <li>Mac OSX specific issues:
2159 <li>exception raised when mouse clicked on desktop
2160 window background</li>
2161 <li>Desktop menu placed on menu bar and application
2162 name set correctly</li>
2163 <li>sequence feature settings not wide enough for the
2164 save feature colourscheme button</li>
2173 <div align="center">
2174 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2177 <td><em>New Capabilities</em>
2179 <li>URL links generated from description line for
2180 regular-expression based URL links (applet and application)
2187 <li>Non-positional feature URL links are shown in link
2189 <li>Linked viewing of nucleic acid sequences and
2191 <li>Automatic Scrolling option in View menu to display
2192 the currently highlighted region of an alignment.</li>
2193 <li>Order an alignment by sequence length, or using the
2194 average score or total feature count for each sequence.</li>
2195 <li>Shading features by score or associated description</li>
2196 <li>Subdivide alignment and groups based on identity of
2197 selected subsequence (Make Groups from Selection).</li>
2198 <li>New hide/show options including Shift+Control+H to
2199 hide everything but the currently selected region.</li>
2200 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2201 </ul> <em>Application</em>
2203 <li>Fetch DB References capabilities and UI expanded to
2204 support retrieval from DAS sequence sources</li>
2205 <li>Local DAS Sequence sources can be added via the
2206 command line or via the Add local source dialog box.</li>
2207 <li>DAS Dbref and DbxRef feature types are parsed as
2208 database references and protein_name is parsed as
2209 description line (BioSapiens terms).</li>
2210 <li>Enable or disable non-positional feature and database
2211 references in sequence ID tooltip from View menu in
2213 <!-- <li>New hidden columns and rows and representatives capabilities
2214 in annotations file (in progress - not yet fully implemented)</li> -->
2215 <li>Group-associated consensus, sequence logos and
2216 conservation plots</li>
2217 <li>Symbol distributions for each column can be exported
2218 and visualized as sequence logos</li>
2219 <li>Optionally scale multi-character column labels to fit
2220 within each column of annotation row<!-- todo for applet -->
2222 <li>Optional automatic sort of associated alignment view
2223 when a new tree is opened.</li>
2224 <li>Jalview Java Console</li>
2225 <li>Better placement of desktop window when moving
2226 between different screens.</li>
2227 <li>New preference items for sequence ID tooltip and
2228 consensus annotation</li>
2229 <li>Client to submit sequences and IDs to Envision2
2231 <li><em>Vamsas Capabilities</em>
2233 <li>Improved VAMSAS synchronization (Jalview archive
2234 used to preserve views, structures, and tree display
2236 <li>Import of vamsas documents from disk or URL via
2238 <li>Sharing of selected regions between views and
2239 with other VAMSAS applications (Experimental feature!)</li>
2240 <li>Updated API to VAMSAS version 0.2</li>
2242 </ul> <em>Applet</em>
2244 <li>Middle button resizes annotation row height</li>
2247 <li>sortByTree (true/false) - automatically sort the
2248 associated alignment view by the tree when a new tree is
2250 <li>showTreeBootstraps (true/false) - show or hide
2251 branch bootstraps (default is to show them if available)</li>
2252 <li>showTreeDistances (true/false) - show or hide
2253 branch lengths (default is to show them if available)</li>
2254 <li>showUnlinkedTreeNodes (true/false) - indicate if
2255 unassociated nodes should be highlighted in the tree
2257 <li>heightScale and widthScale (1.0 or more) -
2258 increase the height or width of a cell in the alignment
2259 grid relative to the current font size.</li>
2262 <li>Non-positional features displayed in sequence ID
2264 </ul> <em>Other</em>
2266 <li>Features format: graduated colour definitions and
2267 specification of feature scores</li>
2268 <li>Alignment Annotations format: new keywords for group
2269 associated annotation (GROUP_REF) and annotation row display
2270 properties (ROW_PROPERTIES)</li>
2271 <li>XML formats extended to support graduated feature
2272 colourschemes, group associated annotation, and profile
2273 visualization settings.</li></td>
2276 <li>Source field in GFF files parsed as feature source
2277 rather than description</li>
2278 <li>Non-positional features are now included in sequence
2279 feature and gff files (controlled via non-positional feature
2280 visibility in tooltip).</li>
2281 <li>URL links generated for all feature links (bugfix)</li>
2282 <li>Added URL embedding instructions to features file
2284 <li>Codons containing ambiguous nucleotides translated as
2285 'X' in peptide product</li>
2286 <li>Match case switch in find dialog box works for both
2287 sequence ID and sequence string and query strings do not
2288 have to be in upper case to match case-insensitively.</li>
2289 <li>AMSA files only contain first column of
2290 multi-character column annotation labels</li>
2291 <li>Jalview Annotation File generation/parsing consistent
2292 with documentation (e.g. Stockholm annotation can be
2293 exported and re-imported)</li>
2294 <li>PDB files without embedded PDB IDs given a friendly
2296 <li>Find incrementally searches ID string matches as well
2297 as subsequence matches, and correctly reports total number
2301 <li>Better handling of exceptions during sequence
2303 <li>Dasobert generated non-positional feature URL
2304 link text excludes the start_end suffix</li>
2305 <li>DAS feature and source retrieval buttons disabled
2306 when fetch or registry operations in progress.</li>
2307 <li>PDB files retrieved from URLs are cached properly</li>
2308 <li>Sequence description lines properly shared via
2310 <li>Sequence fetcher fetches multiple records for all
2312 <li>Ensured that command line das feature retrieval
2313 completes before alignment figures are generated.</li>
2314 <li>Reduced time taken when opening file browser for
2316 <li>isAligned check prior to calculating tree, PCA or
2317 submitting an MSA to JNet now excludes hidden sequences.</li>
2318 <li>User defined group colours properly recovered
2319 from Jalview projects.</li>
2328 <div align="center">
2329 <strong>2.4.0.b2</strong><br> 28/10/2009
2334 <li>Experimental support for google analytics usage
2336 <li>Jalview privacy settings (user preferences and docs).</li>
2341 <li>Race condition in applet preventing startup in
2343 <li>Exception when feature created from selection beyond
2344 length of sequence.</li>
2345 <li>Allow synthetic PDB files to be imported gracefully</li>
2346 <li>Sequence associated annotation rows associate with
2347 all sequences with a given id</li>
2348 <li>Find function matches case-insensitively for sequence
2349 ID string searches</li>
2350 <li>Non-standard characters do not cause pairwise
2351 alignment to fail with exception</li>
2352 </ul> <em>Application Issues</em>
2354 <li>Sequences are now validated against EMBL database</li>
2355 <li>Sequence fetcher fetches multiple records for all
2357 </ul> <em>InstallAnywhere Issues</em>
2359 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2360 issue with installAnywhere mechanism)</li>
2361 <li>Command line launching of JARs from InstallAnywhere
2362 version (java class versioning error fixed)</li>
2369 <div align="center">
2370 <strong>2.4</strong><br> 27/8/2008
2373 <td><em>User Interface</em>
2375 <li>Linked highlighting of codon and amino acid from
2376 translation and protein products</li>
2377 <li>Linked highlighting of structure associated with
2378 residue mapping to codon position</li>
2379 <li>Sequence Fetcher provides example accession numbers
2380 and 'clear' button</li>
2381 <li>MemoryMonitor added as an option under Desktop's
2383 <li>Extract score function to parse whitespace separated
2384 numeric data in description line</li>
2385 <li>Column labels in alignment annotation can be centred.</li>
2386 <li>Tooltip for sequence associated annotation give name
2388 </ul> <em>Web Services and URL fetching</em>
2390 <li>JPred3 web service</li>
2391 <li>Prototype sequence search client (no public services
2393 <li>Fetch either seed alignment or full alignment from
2395 <li>URL Links created for matching database cross
2396 references as well as sequence ID</li>
2397 <li>URL Links can be created using regular-expressions</li>
2398 </ul> <em>Sequence Database Connectivity</em>
2400 <li>Retrieval of cross-referenced sequences from other
2402 <li>Generalised database reference retrieval and
2403 validation to all fetchable databases</li>
2404 <li>Fetch sequences from DAS sources supporting the
2405 sequence command</li>
2406 </ul> <em>Import and Export</em>
2407 <li>export annotation rows as CSV for spreadsheet import</li>
2408 <li>Jalview projects record alignment dataset associations,
2409 EMBL products, and cDNA sequence mappings</li>
2410 <li>Sequence Group colour can be specified in Annotation
2412 <li>Ad-hoc colouring of group in Annotation File using RGB
2413 triplet as name of colourscheme</li>
2414 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2416 <li>treenode binding for VAMSAS tree exchange</li>
2417 <li>local editing and update of sequences in VAMSAS
2418 alignments (experimental)</li>
2419 <li>Create new or select existing session to join</li>
2420 <li>load and save of vamsas documents</li>
2421 </ul> <em>Application command line</em>
2423 <li>-tree parameter to open trees (introduced for passing
2425 <li>-fetchfrom command line argument to specify nicknames
2426 of DAS servers to query for alignment features</li>
2427 <li>-dasserver command line argument to add new servers
2428 that are also automatically queried for features</li>
2429 <li>-groovy command line argument executes a given groovy
2430 script after all input data has been loaded and parsed</li>
2431 </ul> <em>Applet-Application data exchange</em>
2433 <li>Trees passed as applet parameters can be passed to
2434 application (when using "View in full
2435 application")</li>
2436 </ul> <em>Applet Parameters</em>
2438 <li>feature group display control parameter</li>
2439 <li>debug parameter</li>
2440 <li>showbutton parameter</li>
2441 </ul> <em>Applet API methods</em>
2443 <li>newView public method</li>
2444 <li>Window (current view) specific get/set public methods</li>
2445 <li>Feature display control methods</li>
2446 <li>get list of currently selected sequences</li>
2447 </ul> <em>New Jalview distribution features</em>
2449 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2450 <li>RELEASE file gives build properties for the latest
2451 Jalview release.</li>
2452 <li>Java 1.1 Applet build made easier and donotobfuscate
2453 property controls execution of obfuscator</li>
2454 <li>Build target for generating source distribution</li>
2455 <li>Debug flag for javacc</li>
2456 <li>.jalview_properties file is documented (slightly) in
2457 jalview.bin.Cache</li>
2458 <li>Continuous Build Integration for stable and
2459 development version of Application, Applet and source
2464 <li>selected region output includes visible annotations
2465 (for certain formats)</li>
2466 <li>edit label/displaychar contains existing label/char
2468 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2469 <li>shorter peptide product names from EMBL records</li>
2470 <li>Newick string generator makes compact representations</li>
2471 <li>bootstrap values parsed correctly for tree files with
2473 <li>pathological filechooser bug avoided by not allowing
2474 filenames containing a ':'</li>
2475 <li>Fixed exception when parsing GFF files containing
2476 global sequence features</li>
2477 <li>Alignment datasets are finalized only when number of
2478 references from alignment sequences goes to zero</li>
2479 <li>Close of tree branch colour box without colour
2480 selection causes cascading exceptions</li>
2481 <li>occasional negative imgwidth exceptions</li>
2482 <li>better reporting of non-fatal warnings to user when
2483 file parsing fails.</li>
2484 <li>Save works when Jalview project is default format</li>
2485 <li>Save as dialog opened if current alignment format is
2486 not a valid output format</li>
2487 <li>UniProt canonical names introduced for both das and
2489 <li>Histidine should be midblue (not pink!) in Zappo</li>
2490 <li>error messages passed up and output when data read
2492 <li>edit undo recovers previous dataset sequence when
2493 sequence is edited</li>
2494 <li>allow PDB files without pdb ID HEADER lines (like
2495 those generated by MODELLER) to be read in properly</li>
2496 <li>allow reading of JPred concise files as a normal
2498 <li>Stockholm annotation parsing and alignment properties
2499 import fixed for PFAM records</li>
2500 <li>Structure view windows have correct name in Desktop
2502 <li>annotation consisting of sequence associated scores
2503 can be read and written correctly to annotation file</li>
2504 <li>Aligned cDNA translation to aligned peptide works
2506 <li>Fixed display of hidden sequence markers and
2507 non-italic font for representatives in Applet</li>
2508 <li>Applet Menus are always embedded in applet window on
2510 <li>Newly shown features appear at top of stack (in
2512 <li>Annotations added via parameter not drawn properly
2513 due to null pointer exceptions</li>
2514 <li>Secondary structure lines are drawn starting from
2515 first column of alignment</li>
2516 <li>UniProt XML import updated for new schema release in
2518 <li>Sequence feature to sequence ID match for Features
2519 file is case-insensitive</li>
2520 <li>Sequence features read from Features file appended to
2521 all sequences with matching IDs</li>
2522 <li>PDB structure coloured correctly for associated views
2523 containing a sub-sequence</li>
2524 <li>PDB files can be retrieved by applet from Jar files</li>
2525 <li>feature and annotation file applet parameters
2526 referring to different directories are retrieved correctly</li>
2527 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
2528 <li>Fixed application hang whilst waiting for
2529 splash-screen version check to complete</li>
2530 <li>Applet properly URLencodes input parameter values
2531 when passing them to the launchApp service</li>
2532 <li>display name and local features preserved in results
2533 retrieved from web service</li>
2534 <li>Visual delay indication for sequence retrieval and
2535 sequence fetcher initialisation</li>
2536 <li>updated Application to use DAS 1.53e version of
2537 dasobert DAS client</li>
2538 <li>Re-instated Full AMSA support and .amsa file
2540 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
2548 <div align="center">
2549 <strong>2.3</strong><br> 9/5/07
2554 <li>Jmol 11.0.2 integration</li>
2555 <li>PDB views stored in Jalview XML files</li>
2556 <li>Slide sequences</li>
2557 <li>Edit sequence in place</li>
2558 <li>EMBL CDS features</li>
2559 <li>DAS Feature mapping</li>
2560 <li>Feature ordering</li>
2561 <li>Alignment Properties</li>
2562 <li>Annotation Scores</li>
2563 <li>Sort by scores</li>
2564 <li>Feature/annotation editing in applet</li>
2569 <li>Headless state operation in 2.2.1</li>
2570 <li>Incorrect and unstable DNA pairwise alignment</li>
2571 <li>Cut and paste of sequences with annotation</li>
2572 <li>Feature group display state in XML</li>
2573 <li>Feature ordering in XML</li>
2574 <li>blc file iteration selection using filename # suffix</li>
2575 <li>Stockholm alignment properties</li>
2576 <li>Stockhom alignment secondary structure annotation</li>
2577 <li>2.2.1 applet had no feature transparency</li>
2578 <li>Number pad keys can be used in cursor mode</li>
2579 <li>Structure Viewer mirror image resolved</li>
2586 <div align="center">
2587 <strong>2.2.1</strong><br> 12/2/07
2592 <li>Non standard characters can be read and displayed
2593 <li>Annotations/Features can be imported/exported to the
2595 <li>Applet allows editing of sequence/annotation/group
2596 name & description
2597 <li>Preference setting to display sequence name in
2599 <li>Annotation file format extended to allow
2600 Sequence_groups to be defined
2601 <li>Default opening of alignment overview panel can be
2602 specified in preferences
2603 <li>PDB residue numbering annotation added to associated
2609 <li>Applet crash under certain Linux OS with Java 1.6
2611 <li>Annotation file export / import bugs fixed
2612 <li>PNG / EPS image output bugs fixed
2618 <div align="center">
2619 <strong>2.2</strong><br> 27/11/06
2624 <li>Multiple views on alignment
2625 <li>Sequence feature editing
2626 <li>"Reload" alignment
2627 <li>"Save" to current filename
2628 <li>Background dependent text colour
2629 <li>Right align sequence ids
2630 <li>User-defined lower case residue colours
2633 <li>Menu item accelerator keys
2634 <li>Control-V pastes to current alignment
2635 <li>Cancel button for DAS Feature Fetching
2636 <li>PCA and PDB Viewers zoom via mouse roller
2637 <li>User-defined sub-tree colours and sub-tree selection
2644 <li>'New Window' button on the 'Output to Text box'
2649 <li>New memory efficient Undo/Redo System
2650 <li>Optimised symbol lookups and conservation/consensus
2652 <li>Region Conservation/Consensus recalculated after
2654 <li>Fixed Remove Empty Columns Bug (empty columns at end
2656 <li>Slowed DAS Feature Fetching for increased robustness.
2663 <li>Made angle brackets in ASCII feature descriptions
2665 <li>Re-instated Zoom function for PCA
2666 <li>Sequence descriptions conserved in web service
2668 <li>UniProt ID discoverer uses any word separated by
2670 <li>WsDbFetch query/result association resolved
2671 <li>Tree leaf to sequence mapping improved
2672 <li>Smooth fonts switch moved to FontChooser dialog box.
2684 <div align="center">
2685 <strong>2.1.1</strong><br> 12/9/06
2690 <li>Copy consensus sequence to clipboard</li>
2695 <li>Image output - rightmost residues are rendered if
2696 sequence id panel has been resized</li>
2697 <li>Image output - all offscreen group boundaries are
2699 <li>Annotation files with sequence references - all
2700 elements in file are relative to sequence position</li>
2701 <li>Mac Applet users can use Alt key for group editing</li>
2707 <div align="center">
2708 <strong>2.1</strong><br> 22/8/06
2713 <li>MAFFT Multiple Alignment in default Web Service list</li>
2714 <li>DAS Feature fetching</li>
2715 <li>Hide sequences and columns</li>
2716 <li>Export Annotations and Features</li>
2717 <li>GFF file reading / writing</li>
2718 <li>Associate structures with sequences from local PDB
2720 <li>Add sequences to exisiting alignment</li>
2721 <li>Recently opened files / URL lists</li>
2722 <li>Applet can launch the full application</li>
2723 <li>Applet has transparency for features (Java 1.2
2725 <li>Applet has user defined colours parameter</li>
2726 <li>Applet can load sequences from parameter
2727 "sequence<em>x</em>"
2733 <li>Redundancy Panel reinstalled in the Applet</li>
2734 <li>Monospaced font - EPS / rescaling bug fixed</li>
2735 <li>Annotation files with sequence references bug fixed</li>
2741 <div align="center">
2742 <strong>2.08.1</strong><br> 2/5/06
2747 <li>Change case of selected region from Popup menu</li>
2748 <li>Choose to match case when searching</li>
2749 <li>Middle mouse button and mouse movement can compress /
2750 expand the visible width and height of the alignment</li>
2755 <li>Annotation Panel displays complete JNet results</li>
2761 <div align="center">
2762 <strong>2.08b</strong><br> 18/4/06
2768 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
2769 <li>Righthand label on wrapped alignments shows correct
2776 <div align="center">
2777 <strong>2.08</strong><br> 10/4/06
2782 <li>Editing can be locked to the selection area</li>
2783 <li>Keyboard editing</li>
2784 <li>Create sequence features from searches</li>
2785 <li>Precalculated annotations can be loaded onto
2787 <li>Features file allows grouping of features</li>
2788 <li>Annotation Colouring scheme added</li>
2789 <li>Smooth fonts off by default - Faster rendering</li>
2790 <li>Choose to toggle Autocalculate Consensus On/Off</li>
2795 <li>Drag & Drop fixed on Linux</li>
2796 <li>Jalview Archive file faster to load/save, sequence
2797 descriptions saved.</li>
2803 <div align="center">
2804 <strong>2.07</strong><br> 12/12/05
2809 <li>PDB Structure Viewer enhanced</li>
2810 <li>Sequence Feature retrieval and display enhanced</li>
2811 <li>Choose to output sequence start-end after sequence
2812 name for file output</li>
2813 <li>Sequence Fetcher WSDBFetch@EBI</li>
2814 <li>Applet can read feature files, PDB files and can be
2815 used for HTML form input</li>
2820 <li>HTML output writes groups and features</li>
2821 <li>Group editing is Control and mouse click</li>
2822 <li>File IO bugs</li>
2828 <div align="center">
2829 <strong>2.06</strong><br> 28/9/05
2834 <li>View annotations in wrapped mode</li>
2835 <li>More options for PCA viewer</li>
2840 <li>GUI bugs resolved</li>
2841 <li>Runs with -nodisplay from command line</li>
2847 <div align="center">
2848 <strong>2.05b</strong><br> 15/9/05
2853 <li>Choose EPS export as lineart or text</li>
2854 <li>Jar files are executable</li>
2855 <li>Can read in Uracil - maps to unknown residue</li>
2860 <li>Known OutOfMemory errors give warning message</li>
2861 <li>Overview window calculated more efficiently</li>
2862 <li>Several GUI bugs resolved</li>
2868 <div align="center">
2869 <strong>2.05</strong><br> 30/8/05
2874 <li>Edit and annotate in "Wrapped" view</li>
2879 <li>Several GUI bugs resolved</li>
2885 <div align="center">
2886 <strong>2.04</strong><br> 24/8/05
2891 <li>Hold down mouse wheel & scroll to change font
2897 <li>Improved JPred client reliability</li>
2898 <li>Improved loading of Jalview files</li>
2904 <div align="center">
2905 <strong>2.03</strong><br> 18/8/05
2910 <li>Set Proxy server name and port in preferences</li>
2911 <li>Multiple URL links from sequence ids</li>
2912 <li>User Defined Colours can have a scheme name and added
2914 <li>Choose to ignore gaps in consensus calculation</li>
2915 <li>Unix users can set default web browser</li>
2916 <li>Runs without GUI for batch processing</li>
2917 <li>Dynamically generated Web Service Menus</li>
2922 <li>InstallAnywhere download for Sparc Solaris</li>
2928 <div align="center">
2929 <strong>2.02</strong><br> 18/7/05
2935 <li>Copy & Paste order of sequences maintains
2936 alignment order.</li>
2942 <div align="center">
2943 <strong>2.01</strong><br> 12/7/05
2948 <li>Use delete key for deleting selection.</li>
2949 <li>Use Mouse wheel to scroll sequences.</li>
2950 <li>Help file updated to describe how to add alignment
2952 <li>Version and build date written to build properties
2954 <li>InstallAnywhere installation will check for updates
2955 at launch of Jalview.</li>
2960 <li>Delete gaps bug fixed.</li>
2961 <li>FileChooser sorts columns.</li>
2962 <li>Can remove groups one by one.</li>
2963 <li>Filechooser icons installed.</li>
2964 <li>Finder ignores return character when searching.
2965 Return key will initiate a search.<br>
2972 <div align="center">
2973 <strong>2.0</strong><br> 20/6/05
2978 <li>New codebase</li>