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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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>20/6/2017</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>
100 Experimental Features Checkbox in Desktop's Tools
101 menu to hide or show untested features in the application.
103 <li><!-- JAL-1476 -->Warning in alignment status bar when there are not enough columns to superimpose structures in Chimera</li>
104 <li><!-- JAL-1596 -->Faster Chimera/Jalview communication by file-based command exchange</li>
105 <li><!-- JAL-2316, -->URLs for viewing database cross-references provided by identifiers.org and the EMBL-EBI's MIRIAM DB</li>
106 <li><!-- JAL-2549 -->Updated JABAWS client to v2.2</li>
108 <em>Experimental features</em>
111 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
112 to transfer Chimera's structure attributes as Jalview
113 features, and vice-versa.
121 <li><!-- JAL-2474 -->Added PrivilegedAccessor to test suite</li>
122 <li><!-- JAL-2326 -->Prevent or clear modal dialogs raised during tests</li>
125 </div></td><td><div align="left">
129 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
130 matrix - C->R should be '-3'<br />Old matrix restored with
131 this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
134 <!-- JAL-2397 -->Fixed Jalview's treatment of gaps in PCA
135 and substitution matrix based Tree calculations.<br />In
136 earlier versions of Jalview, gaps matching gaps were
137 penalised, and gaps matching non-gaps penalised even more.
138 In the PCA calculation, gaps were actually treated as
139 non-gaps - so different costs were applied, which meant
140 Jalview's PCAs were different to those produced by
141 SeqSpace.<br />Jalview now treats gaps in the same way as
142 SeqSpace (ie it scores them as 0). To restore pre-2.10.2
144 jalview.viewmodel.PCAModel.scoreGapAsAny=true // for
146 jalview.viewmodel.PCAModel.scoreGapAsAny=false // to
149 <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>
150 <li><!-- JAL-2430 -->Hidden regions in alignment views are not coloured in linked structure views</li>
151 <li><!-- JAL-2419 -->Current selection lost if popup menu opened on a region of alignment without groups</li>
152 <li><!-- JAL-2374 -->Popup menu not always shown for regions of an alignment with overlapping groups</li>
153 <li><!-- JAL-2310 -->Finder double counts if both a sequence's name and description match</li>
154 <li><!-- JAL-2370 -->Hiding column selection containing two hidden regions results in incorrect hidden regions</li>
155 <li><!-- JAL-2377 -->PCA calculation could hang when generating output report when working with highly redundant alignments</li>
156 <li><!-- JAL-2365 -->Cannot configure feature colours with lightGray or darkGray via features file</li>
157 <li><!-- JAL-2421 -->Overview window visible region moves erratically when hidden rows or columns are present</li>
158 <li><!-- JAL-2362 -->Per-residue colourschemes applied via the Structure Viewer's colour menu don't correspond to sequence colouring</li>
159 <li><!-- JAL-2405 -->Protein specific colours only offered in colour and group colour menu for protein alignments</li>
160 <li><!-- JAL-2386 -->'Apply to all groups' setting when changing colour does not apply Conservation slider value to all groups</li>
161 <li><!-- JAL-2385 -->Colour threshold slider doesn't update to reflect currently selected view or group's shading thresholds</li>
162 <li><!-- JAL-2373 -->Percentage identity and conservation menu items do not show a tick or allow shading to be disabled</li>
163 <li><!-- JAL-2385 -->Conservation shading or PID threshold lost when base colourscheme changed if slider not visible</li>
164 <li><!-- JAL-2547 -->Sequence features shown in tooltip for gaps before start of features</li>
165 <li><!-- JAL-2576 -->Very large alignments take a long time to load</li>
166 <li><!-- JAL-2590 -->Cannot load Newick trees from eggnog ortholog database</li>
170 <li><!-- JAL-2401 -->Easier creation of colours for all 'Lower case' residues (button in colourscheme editor debugged and new documentation and tooltips added)</li>
171 <li><!-- JAL-2399-->Text colour threshold's 'Cancel' button doesn't restore group-specific text colour thresholds</li>
172 <li><!-- JAL-2243 -->Feature settings panel does not update as new features are added to alignment</li>
173 <li><!-- JAL-2436 -->Structure viewer's View -> Colour By view selection menu changes colours of alignment views</li>
174 <li><!-- JAL-2366 -->Proxy server address and port always appear enabled in Preferences->Connections</li>
175 <li><!-- JAL-2426 -->Spurious exceptions in console raised from alignment calculation workers after alignment has been closed</li>
176 <li><!-- JAL-1608 -->Typo in selection popup menu - Create groups now 'Create Group'</li>
177 <li><!-- JAL-1608 -->CMD/CTRL and G or Shift G for Create/Undefine group doesn't always work</li>
178 <li><!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get shown again after pressing 'Cancel'</li>
179 <li><!-- JAL-2461 -->DAS registry not found exceptions removed from console output</li>
180 <li><!-- JAL-2383 -->Above PID colour threshold not recovered when alignment view imported from project</li>
181 <li><!-- JAL-2465 -->No mappings generated between structure and sequences extracted from structure files imported via URL</li>
183 <!-- JAL-2520 -->Structures loaded via URL are saved in
184 Jalview Projects rather than fetched via URL again when
185 the project is loaded and the structure viewed
187 <li><!-- JAL-1256 -->Trackpad horizontal scroll gesture adjusts start position in wrap mode</li>
188 <li><!-- JAL-2563 -->Status bar doesn't show positions for ambiguous amino acids</li>
189 <li><!-- JAL-2291 -->Hide insertions in PopUp menu excludes gaps in selection, current sequence and only within selected columns</li>
193 <li><!-- JAL-2442 -->Features not rendered as transparent on overview or linked structure view</li>
194 <li><!-- JAL-2372 -->Colour group by conservation doesn't work (since 2.8)</li>
195 <li><!-- JAL-2517 -->Hitting Cancel after applying user-defined colourscheme doesn't restore original colourscheme</li>
197 <em>New Known Issues</em>
199 <li><!-- JAL-2566 -->Protein/CDS view scrolling not always in phase after a sequence motif find operation</li>
200 <li><!-- JAL-2550 -->Importing annotation file with rows containing just upper and lower case letters are interpreted as WUSS rna secondary structure symbols</li>
205 <td width="60" nowrap>
207 <strong><a name="Jalview.2.10.1">2.10.1</a><br />
208 <em>29/11/2016</em></strong>
211 <td><div align="left">
215 <!-- JAL-98 -->Improved memory usage: sparse arrays used
216 for all consensus calculations
219 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released 3rd Oct 2016)
221 <li>Updated Jalview's Certum code signing certificate
227 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
228 set of database cross-references, sorted alphabetically
231 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
232 from database cross references. Users with custom links
233 will receive a <a href="webServices/urllinks.html#warning">warning
234 dialog</a> asking them to update their preferences.
237 <!-- JAL-2287-->Cancel button and escape listener on
238 dialog warning user about disconnecting Jalview from a
242 <!-- JAL-2320-->Jalview's Chimera control window closes if
243 the Chimera it is connected to is shut down
246 <!-- JAL-1738-->New keystroke (B) and Select highlighted
247 columns menu item to mark columns containing
248 highlighted regions (e.g. from structure selections or results
252 <!-- JAL-2284-->Command line option for batch-generation
253 of HTML pages rendering alignment data with the BioJS
263 <!-- JAL-2286 -->Columns with more than one modal residue
264 are not coloured or thresholded according to percent
265 identity (first observed in Jalview 2.8.2)
268 <!-- JAL-2301 -->Threonine incorrectly reported as not
272 <!-- JAL-2318 -->Updates to documentation pages (above PID
273 threshold, amino acid properties)
276 <!-- JAL-2292 -->Lower case residues in sequences are not
277 reported as mapped to residues in a structure file in the
281 <!--JAL-2324 -->Identical features with non-numeric scores
282 could be added multiple times to a sequence
285 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
286 bond features shown as two highlighted residues rather
287 than a range in linked structure views, and treated
288 correctly when selecting and computing trees from features
291 <!-- JAL-2281-->Custom URL links for database
292 cross-references are matched to database name regardless
300 <!-- JAL-2282-->Custom URL links for specific database
301 names without regular expressions also offer links from
305 <!-- JAL-2315-->Removing a single configured link in the
306 URL links pane in Connections preferences doesn't actually
307 update Jalview configuration
310 <!-- JAL-2272-->CTRL-Click on a selected region to open
311 the alignment area popup menu doesn't work on El-Capitan
314 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
315 files with similarly named sequences if dropped onto the
319 <!-- JAL-2312 -->Additional mappings are shown for PDB
320 entries where more chains exist in the PDB accession than
321 are reported in the SIFTS file
324 <!-- JAL-2317-->Certain structures do not get mapped to
325 the structure view when displayed with Chimera
328 <!-- JAL-2317-->No chains shown in the Chimera view
329 panel's View->Show Chains submenu
332 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
333 work for wrapped alignment views
336 <!--JAL-2197 -->Rename UI components for running JPred
337 predictions from 'JNet' to 'JPred'
340 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
341 corrupted when annotation panel vertical scroll is not at
345 <!--JAL-2332 -->Attempting to view structure for Hen
346 lysozyme results in a PDB Client error dialog box
349 <!-- JAL-2319 -->Structure View's mapping report switched ranges for PDB and sequence for SIFTS</li>
350 <!-- JAL-2319 -->SIFTS 'Not_Observed' residues mapped to non-existant coordindate data</li>
352 <!-- <em>New Known Issues</em>
359 <td width="60" nowrap>
361 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
362 <em>25/10/2016</em></strong>
365 <td><em>Application</em>
367 <li>3D Structure chooser opens with 'Cached structures'
368 view if structures already loaded</li>
369 <li>Progress bar reports models as they are loaded to
376 <li>Colour by conservation always enabled and no tick
377 shown in menu when BLOSUM or PID shading applied</li>
378 <li>FER1_ARATH and FER2_ARATH labels were switched in
379 example sequences/projects/trees</li>
383 <li>Jalview projects with views of local PDB structure
384 files saved on Windows cannot be opened on OSX</li>
385 <li>Multiple structure views can be opened and
386 superposed without timeout for structures with multiple
387 models or multiple sequences in alignment</li>
388 <li>Cannot import or associated local PDB files without
389 a PDB ID HEADER line</li>
390 <li>RMSD is not output in Jmol console when
391 superposition is performed</li>
392 <li>Drag and drop of URL from Browser fails for Linux
393 and OSX versions earlier than El Capitan</li>
394 <li>ENA client ignores invalid content from ENA server</li>
395 <li>Exceptions are not raised in console when ENA
396 client attempts to fetch non-existent IDs via Fetch DB
398 <li>Exceptions are not raised in console when a new
399 view is created on the alignment</li>
400 <li>OSX right-click fixed for group selections:
401 CMD-click to insert/remove gaps in groups and CTRL-click
402 to open group pop-up menu</li>
404 <em>Build and deployment</em>
406 <li>URL link checker now copes with multi-line anchor
409 <em>New Known Issues</em>
411 <li>Drag and drop from URL links in browsers do not
418 <td width="60" nowrap>
420 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
426 <!-- JAL-2124 -->Updated Spanish translations.
429 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
430 for importing structure data to Jalview. Enables mmCIF and
434 <!-- JAL-192 --->Alignment ruler shows positions relative to
438 <!-- JAL-2202 -->Position/residue shown in status bar when
439 mousing over sequence associated annotation
442 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
446 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
447 '()', canonical '[]' and invalid '{}' base pair populations
451 <!-- JAL-2092 -->Feature settings popup menu options for
452 showing or hiding columns containing a feature
455 <!-- JAL-1557 -->Edit selected group by double clicking on
456 group and sequence associated annotation labels
459 <!-- JAL-2236 -->Sequence name added to annotation label in
460 select/hide columns by annotation and colour by annotation
464 </ul> <em>Application</em>
467 <!-- JAL-2050-->Automatically hide introns when opening a
471 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
475 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
476 structure mappings with the EMBL-EBI PDBe SIFTS database
479 <!-- JAL-2079 -->Updated download sites used for Rfam and
480 Pfam sources to xfam.org
483 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
486 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
487 over sequences in Jalview
490 <!-- JAL-2027-->Support for reverse-complement coding
491 regions in ENA and EMBL
494 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
495 for record retrieval via ENA rest API
498 <!-- JAL-2027 -->Support for ENA CDS records with reverse
502 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
503 groovy script execution
506 <!-- JAL-1812 -->New 'execute Groovy script' option in an
507 alignment window's Calculate menu
510 <!-- JAL-1812 -->Allow groovy scripts that call
511 Jalview.getAlignFrames() to run in headless mode
514 <!-- JAL-2068 -->Support for creating new alignment
515 calculation workers from groovy scripts
518 <!-- JAL-1369 --->Store/restore reference sequence in
522 <!-- JAL-1803 -->Chain codes for a sequence's PDB
523 associations are now saved/restored from project
526 <!-- JAL-1993 -->Database selection dialog always shown
527 before sequence fetcher is opened
530 <!-- JAL-2183 -->Double click on an entry in Jalview's
531 database chooser opens a sequence fetcher
534 <!-- JAL-1563 -->Free-text search client for UniProt using
538 <!-- JAL-2168 -->-nonews command line parameter to prevent
539 the news reader opening
542 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
543 querying stored in preferences
546 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
550 <!-- JAL-1977-->Tooltips shown on database chooser
553 <!-- JAL-391 -->Reverse complement function in calculate
554 menu for nucleotide sequences
557 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
558 and feature counts preserves alignment ordering (and
559 debugged for complex feature sets).
562 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
563 viewing structures with Jalview 2.10
566 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
567 genome, transcript CCDS and gene ids via the Ensembl and
568 Ensembl Genomes REST API
571 <!-- JAL-2049 -->Protein sequence variant annotation
572 computed for 'sequence_variant' annotation on CDS regions
576 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
580 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
581 Ref Fetcher fails to match, or otherwise updates sequence
582 data from external database records.
585 <!-- JAL-2154 -->Revised Jalview Project format for
586 efficient recovery of sequence coding and alignment
587 annotation relationships.
589 </ul> <!-- <em>Applet</em>
600 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
604 <!-- JAL-2018-->Export features in Jalview format (again)
605 includes graduated colourschemes
608 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
609 working with big alignments and lots of hidden columns
612 <!-- JAL-2053-->Hidden column markers not always rendered
613 at right of alignment window
616 <!-- JAL-2067 -->Tidied up links in help file table of
620 <!-- JAL-2072 -->Feature based tree calculation not shown
624 <!-- JAL-2075 -->Hidden columns ignored during feature
625 based tree calculation
628 <!-- JAL-2065 -->Alignment view stops updating when show
629 unconserved enabled for group on alignment
632 <!-- JAL-2086 -->Cannot insert gaps into sequence when
636 <!-- JAL-2146 -->Alignment column in status incorrectly
637 shown as "Sequence position" when mousing over
641 <!-- JAL-2099 -->Incorrect column numbers in ruler when
642 hidden columns present
645 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
646 user created annotation added to alignment
649 <!-- JAL-1841 -->RNA Structure consensus only computed for
650 '()' base pair annotation
653 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
654 in zero scores for all base pairs in RNA Structure
658 <!-- JAL-2174-->Extend selection with columns containing
662 <!-- JAL-2275 -->Pfam format writer puts extra space at
663 beginning of sequence
666 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
670 <!-- JAL-2238 -->Cannot create groups on an alignment from
671 from a tree when t-coffee scores are shown
674 <!-- JAL-1836,1967 -->Cannot import and view PDB
675 structures with chains containing negative resnums (4q4h)
678 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
682 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
683 to Clustal, PIR and PileUp output
686 <!-- JAL-2008 -->Reordering sequence features that are
687 not visible causes alignment window to repaint
690 <!-- JAL-2006 -->Threshold sliders don't work in
691 graduated colour and colour by annotation row for e-value
692 scores associated with features and annotation rows
695 <!-- JAL-1797 -->amino acid physicochemical conservation
696 calculation should be case independent
699 <!-- JAL-2173 -->Remove annotation also updates hidden
703 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
704 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
705 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
708 <!-- JAL-2065 -->Null pointer exceptions and redraw
709 problems when reference sequence defined and 'show
710 non-conserved' enabled
713 <!-- JAL-1306 -->Quality and Conservation are now shown on
714 load even when Consensus calculation is disabled
717 <!-- JAL-1932 -->Remove right on penultimate column of
718 alignment does nothing
724 <!-- JAL-1552-->URLs and links can't be imported by
725 drag'n'drop on OSX when launched via webstart (note - not
726 yet fixed for El Capitan)
729 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
730 output when running on non-gb/us i18n platforms
733 <!-- JAL-1944 -->Error thrown when exporting a view with
734 hidden sequences as flat-file alignment
737 <!-- JAL-2030-->InstallAnywhere distribution fails when
741 <!-- JAL-2080-->Jalview very slow to launch via webstart
742 (also hotfix for 2.9.0b2)
745 <!-- JAL-2085 -->Cannot save project when view has a
746 reference sequence defined
749 <!-- JAL-1011 -->Columns are suddenly selected in other
750 alignments and views when revealing hidden columns
753 <!-- JAL-1989 -->Hide columns not mirrored in complement
754 view in a cDNA/Protein splitframe
757 <!-- JAL-1369 -->Cannot save/restore representative
758 sequence from project when only one sequence is
762 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
766 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
767 structure consensus didn't refresh annotation panel
770 <!-- JAL-1962 -->View mapping in structure view shows
771 mappings between sequence and all chains in a PDB file
774 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
775 dialogs format columns correctly, don't display array
776 data, sort columns according to type
779 <!-- JAL-1975 -->Export complete shown after destination
780 file chooser is cancelled during an image export
783 <!-- JAL-2025 -->Error when querying PDB Service with
784 sequence name containing special characters
787 <!-- JAL-2024 -->Manual PDB structure querying should be
791 <!-- JAL-2104 -->Large tooltips with broken HTML
792 formatting don't wrap
795 <!-- JAL-1128 -->Figures exported from wrapped view are
796 truncated so L looks like I in consensus annotation
799 <!-- JAL-2003 -->Export features should only export the
800 currently displayed features for the current selection or
804 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
805 after fetching cross-references, and restoring from project
808 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
809 followed in the structure viewer
812 <!-- JAL-2163 -->Titles for individual alignments in
813 splitframe not restored from project
816 <!-- JAL-2145 -->missing autocalculated annotation at
817 trailing end of protein alignment in transcript/product
818 splitview when pad-gaps not enabled by default
821 <!-- JAL-1797 -->amino acid physicochemical conservation
825 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
826 article has been read (reopened issue due to
827 internationalisation problems)
830 <!-- JAL-1960 -->Only offer PDB structures in structure
831 viewer based on sequence name, PDB and UniProt
836 <!-- JAL-1976 -->No progress bar shown during export of
840 <!-- JAL-2213 -->Structures not always superimposed after
841 multiple structures are shown for one or more sequences.
844 <!-- JAL-1370 -->Reference sequence characters should not
845 be replaced with '.' when 'Show unconserved' format option
849 <!-- JAL-1823 -->Cannot specify chain code when entering
850 specific PDB id for sequence
853 <!-- JAL-1944 -->File->Export->.. as doesn't work when
854 'Export hidden sequences' is enabled, but 'export hidden
855 columns' is disabled.
858 <!--JAL-2026-->Best Quality option in structure chooser
859 selects lowest rather than highest resolution structures
863 <!-- JAL-1887 -->Incorrect start and end reported for PDB
864 to sequence mapping in 'View Mappings' report
867 <!-- JAL-2284 -->Unable to read old Jalview projects that
868 contain non-XML data added after Jalvew wrote project.
870 <li><!-- JAL-2118 -->Newly created annotation row reorders
871 after clicking on it to create new annotation for a
874 <!-- may exclude, this is an external service stability issue JAL-1941
875 -- > RNA 3D structure not added via DSSR service</li> -->
880 <!-- JAL-2151 -->Incorrect columns are selected when
881 hidden columns present before start of sequence
884 <!-- JAL-1986 -->Missing dependencies on applet pages
888 <!-- JAL-1947 -->Overview pixel size changes when
889 sequences are hidden in applet
892 <!-- JAL-1996 -->Updated instructions for applet
893 deployment on examples pages.
900 <td width="60" nowrap>
902 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
903 <em>16/10/2015</em></strong>
908 <li>Time stamps for signed Jalview application and applet
915 <li>Duplicate group consensus and conservation rows
916 shown when tree is partitioned</li>
917 <li>Erratic behaviour when tree partitions made with
918 multiple cDNA/Protein split views</li>
924 <td width="60" nowrap>
926 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
927 <em>8/10/2015</em></strong>
932 <li>Updated Spanish translations of localized text for
934 </ul> <em>Application</em>
936 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
937 <li>Signed OSX InstallAnywhere installer<br></li>
938 <li>Support for per-sequence based annotations in BioJSON</li>
939 </ul> <em>Applet</em>
941 <li>Split frame example added to applet examples page</li>
942 </ul><em>Build and Deployment</em>
944 <li><!-- JAL-1888 -->New ant target for running Jalview's test suite</li>
950 <li>Mapping of cDNA to protein in split frames
951 incorrect when sequence start > 1</li>
952 <li>Broken images in filter column by annotation dialog
954 <li>Feature colours not parsed from features file</li>
955 <li>Exceptions and incomplete link URLs recovered when
956 loading a features file containing HTML tags in feature
962 <li>Annotations corrupted after BioJS export and
964 <li>Incorrect sequence limits after Fetch DB References
965 with 'trim retrieved sequences'</li>
966 <li>Incorrect warning about deleting all data when
967 deleting selected columns</li>
968 <li>Patch to build system for shipping properly signed
969 JNLP templates for webstart launch</li>
970 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
971 unreleased structures for download or viewing</li>
972 <li>Tab/space/return keystroke operation of EMBL-PDBe
973 fetcher/viewer dialogs works correctly</li>
974 <li>Disabled 'minimise' button on Jalview windows
975 running on OSX to workaround redraw hang bug</li>
976 <li>Split cDNA/Protein view position and geometry not
977 recovered from jalview project</li>
978 <li>Initial enabled/disabled state of annotation menu
979 sorter 'show autocalculated first/last' corresponds to
981 <li>Restoring of Clustal, RNA Helices and T-Coffee
982 color schemes from BioJSON</li>
986 <li>Reorder sequences mirrored in cDNA/Protein split
988 <li>Applet with Jmol examples not loading correctly</li>
994 <td><div align="center">
995 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
999 <li>Linked visualisation and analysis of DNA and Protein
1002 <li>Translated cDNA alignments shown as split protein
1003 and DNA alignment views</li>
1004 <li>Codon consensus annotation for linked protein and
1005 cDNA alignment views</li>
1006 <li>Link cDNA or Protein product sequences by loading
1007 them onto Protein or cDNA alignments</li>
1008 <li>Reconstruct linked cDNA alignment from aligned
1009 protein sequences</li>
1012 <li>Jmol integration updated to Jmol v14.2.14</li>
1013 <li>Import and export of Jalview alignment views as <a
1014 href="features/bioJsonFormat.html">BioJSON</a></li>
1015 <li>New alignment annotation file statements for
1016 reference sequences and marking hidden columns</li>
1017 <li>Reference sequence based alignment shading to
1018 highlight variation</li>
1019 <li>Select or hide columns according to alignment
1021 <li>Find option for locating sequences by description</li>
1022 <li>Conserved physicochemical properties shown in amino
1023 acid conservation row</li>
1024 <li>Alignments can be sorted by number of RNA helices</li>
1025 </ul> <em>Application</em>
1027 <li>New cDNA/Protein analysis capabilities
1029 <li>Get Cross-References should open a Split Frame
1030 view with cDNA/Protein</li>
1031 <li>Detect when nucleotide sequences and protein
1032 sequences are placed in the same alignment</li>
1033 <li>Split cDNA/Protein views are saved in Jalview
1038 <li>Use REST API to talk to Chimera</li>
1039 <li>Selected regions in Chimera are highlighted in linked
1040 Jalview windows</li>
1042 <li>VARNA RNA viewer updated to v3.93</li>
1043 <li>VARNA views are saved in Jalview Projects</li>
1044 <li>Pseudoknots displayed as Jalview RNA annotation can
1045 be shown in VARNA</li>
1047 <li>Make groups for selection uses marked columns as well
1048 as the active selected region</li>
1050 <li>Calculate UPGMA and NJ trees using sequence feature
1052 <li>New Export options
1054 <li>New Export Settings dialog to control hidden
1055 region export in flat file generation</li>
1057 <li>Export alignment views for display with the <a
1058 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1060 <li>Export scrollable SVG in HTML page</li>
1061 <li>Optional embedding of BioJSON data when exporting
1062 alignment figures to HTML</li>
1064 <li>3D structure retrieval and display
1066 <li>Free text and structured queries with the PDBe
1068 <li>PDBe Search API based discovery and selection of
1069 PDB structures for a sequence set</li>
1073 <li>JPred4 employed for protein secondary structure
1075 <li>Hide Insertions menu option to hide unaligned columns
1076 for one or a group of sequences</li>
1077 <li>Automatically hide insertions in alignments imported
1078 from the JPred4 web server</li>
1079 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1080 system on OSX<br />LGPL libraries courtesy of <a
1081 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1083 <li>changed 'View nucleotide structure' submenu to 'View
1084 VARNA 2D Structure'</li>
1085 <li>change "View protein structure" menu option to "3D
1088 </ul> <em>Applet</em>
1090 <li>New layout for applet example pages</li>
1091 <li>New parameters to enable SplitFrame view
1092 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1093 <li>New example demonstrating linked viewing of cDNA and
1094 Protein alignments</li>
1095 </ul> <em>Development and deployment</em>
1097 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1098 <li>Include installation type and git revision in build
1099 properties and console log output</li>
1100 <li>Jalview Github organisation, and new github site for
1101 storing BioJsMSA Templates</li>
1102 <li>Jalview's unit tests now managed with TestNG</li>
1105 <!-- <em>General</em>
1107 </ul> --> <!-- issues resolved --> <em>Application</em>
1109 <li>Escape should close any open find dialogs</li>
1110 <li>Typo in select-by-features status report</li>
1111 <li>Consensus RNA secondary secondary structure
1112 predictions are not highlighted in amber</li>
1113 <li>Missing gap character in v2.7 example file means
1114 alignment appears unaligned when pad-gaps is not enabled</li>
1115 <li>First switch to RNA Helices colouring doesn't colour
1116 associated structure views</li>
1117 <li>ID width preference option is greyed out when auto
1118 width checkbox not enabled</li>
1119 <li>Stopped a warning dialog from being shown when
1120 creating user defined colours</li>
1121 <li>'View Mapping' in structure viewer shows sequence
1122 mappings for just that viewer's sequences</li>
1123 <li>Workaround for superposing PDB files containing
1124 multiple models in Chimera</li>
1125 <li>Report sequence position in status bar when hovering
1126 over Jmol structure</li>
1127 <li>Cannot output gaps as '.' symbols with Selection ->
1128 output to text box</li>
1129 <li>Flat file exports of alignments with hidden columns
1130 have incorrect sequence start/end</li>
1131 <li>'Aligning' a second chain to a Chimera structure from
1133 <li>Colour schemes applied to structure viewers don't
1134 work for nucleotide</li>
1135 <li>Loading/cut'n'pasting an empty or invalid file leads
1136 to a grey/invisible alignment window</li>
1137 <li>Exported Jpred annotation from a sequence region
1138 imports to different position</li>
1139 <li>Space at beginning of sequence feature tooltips shown
1140 on some platforms</li>
1141 <li>Chimera viewer 'View | Show Chain' menu is not
1143 <li>'New View' fails with a Null Pointer Exception in
1144 console if Chimera has been opened</li>
1145 <li>Mouseover to Chimera not working</li>
1146 <li>Miscellaneous ENA XML feature qualifiers not
1148 <li>NPE in annotation renderer after 'Extract Scores'</li>
1149 <li>If two structures in one Chimera window, mouseover of
1150 either sequence shows on first structure</li>
1151 <li>'Show annotations' options should not make
1152 non-positional annotations visible</li>
1153 <li>Subsequence secondary structure annotation not shown
1154 in right place after 'view flanking regions'</li>
1155 <li>File Save As type unset when current file format is
1157 <li>Save as '.jar' option removed for saving Jalview
1159 <li>Colour by Sequence colouring in Chimera more
1161 <li>Cannot 'add reference annotation' for a sequence in
1162 several views on same alignment</li>
1163 <li>Cannot show linked products for EMBL / ENA records</li>
1164 <li>Jalview's tooltip wraps long texts containing no
1166 </ul> <em>Applet</em>
1168 <li>Jmol to JalviewLite mouseover/link not working</li>
1169 <li>JalviewLite can't import sequences with ID
1170 descriptions containing angle brackets</li>
1171 </ul> <em>General</em>
1173 <li>Cannot export and reimport RNA secondary structure
1174 via jalview annotation file</li>
1175 <li>Random helix colour palette for colour by annotation
1176 with RNA secondary structure</li>
1177 <li>Mouseover to cDNA from STOP residue in protein
1178 translation doesn't work.</li>
1179 <li>hints when using the select by annotation dialog box</li>
1180 <li>Jmol alignment incorrect if PDB file has alternate CA
1182 <li>FontChooser message dialog appears to hang after
1183 choosing 1pt font</li>
1184 <li>Peptide secondary structure incorrectly imported from
1185 annotation file when annotation display text includes 'e' or
1187 <li>Cannot set colour of new feature type whilst creating
1189 <li>cDNA translation alignment should not be sequence
1190 order dependent</li>
1191 <li>'Show unconserved' doesn't work for lower case
1193 <li>Nucleotide ambiguity codes involving R not recognised</li>
1194 </ul> <em>Deployment and Documentation</em>
1196 <li>Applet example pages appear different to the rest of
1197 www.jalview.org</li>
1198 </ul> <em>Application Known issues</em>
1200 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1201 <li>Misleading message appears after trying to delete
1203 <li>Jalview icon not shown in dock after InstallAnywhere
1204 version launches</li>
1205 <li>Fetching EMBL reference for an RNA sequence results
1206 fails with a sequence mismatch</li>
1207 <li>Corrupted or unreadable alignment display when
1208 scrolling alignment to right</li>
1209 <li>ArrayIndexOutOfBoundsException thrown when remove
1210 empty columns called on alignment with ragged gapped ends</li>
1211 <li>auto calculated alignment annotation rows do not get
1212 placed above or below non-autocalculated rows</li>
1213 <li>Jalview dekstop becomes sluggish at full screen in
1214 ultra-high resolution</li>
1215 <li>Cannot disable consensus calculation independently of
1216 quality and conservation</li>
1217 <li>Mouseover highlighting between cDNA and protein can
1218 become sluggish with more than one splitframe shown</li>
1219 </ul> <em>Applet Known Issues</em>
1221 <li>Core PDB parsing code requires Jmol</li>
1222 <li>Sequence canvas panel goes white when alignment
1223 window is being resized</li>
1229 <td><div align="center">
1230 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1232 <td><em>General</em>
1234 <li>Updated Java code signing certificate donated by
1236 <li>Features and annotation preserved when performing
1237 pairwise alignment</li>
1238 <li>RNA pseudoknot annotation can be
1239 imported/exported/displayed</li>
1240 <li>'colour by annotation' can colour by RNA and
1241 protein secondary structure</li>
1242 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1243 post-hoc with 2.9 release</em>)
1246 </ul> <em>Application</em>
1248 <li>Extract and display secondary structure for sequences
1249 with 3D structures</li>
1250 <li>Support for parsing RNAML</li>
1251 <li>Annotations menu for layout
1253 <li>sort sequence annotation rows by alignment</li>
1254 <li>place sequence annotation above/below alignment
1257 <li>Output in Stockholm format</li>
1258 <li>Internationalisation: improved Spanish (es)
1260 <li>Structure viewer preferences tab</li>
1261 <li>Disorder and Secondary Structure annotation tracks
1262 shared between alignments</li>
1263 <li>UCSF Chimera launch and linked highlighting from
1265 <li>Show/hide all sequence associated annotation rows for
1266 all or current selection</li>
1267 <li>disorder and secondary structure predictions
1268 available as dataset annotation</li>
1269 <li>Per-sequence rna helices colouring</li>
1272 <li>Sequence database accessions imported when fetching
1273 alignments from Rfam</li>
1274 <li>update VARNA version to 3.91</li>
1276 <li>New groovy scripts for exporting aligned positions,
1277 conservation values, and calculating sum of pairs scores.</li>
1278 <li>Command line argument to set default JABAWS server</li>
1279 <li>include installation type in build properties and
1280 console log output</li>
1281 <li>Updated Jalview project format to preserve dataset
1285 <!-- issues resolved --> <em>Application</em>
1287 <li>Distinguish alignment and sequence associated RNA
1288 structure in structure->view->VARNA</li>
1289 <li>Raise dialog box if user deletes all sequences in an
1291 <li>Pressing F1 results in documentation opening twice</li>
1292 <li>Sequence feature tooltip is wrapped</li>
1293 <li>Double click on sequence associated annotation
1294 selects only first column</li>
1295 <li>Redundancy removal doesn't result in unlinked
1296 leaves shown in tree</li>
1297 <li>Undos after several redundancy removals don't undo
1299 <li>Hide sequence doesn't hide associated annotation</li>
1300 <li>User defined colours dialog box too big to fit on
1301 screen and buttons not visible</li>
1302 <li>author list isn't updated if already written to
1303 Jalview properties</li>
1304 <li>Popup menu won't open after retrieving sequence
1306 <li>File open window for associate PDB doesn't open</li>
1307 <li>Left-then-right click on a sequence id opens a
1308 browser search window</li>
1309 <li>Cannot open sequence feature shading/sort popup menu
1310 in feature settings dialog</li>
1311 <li>better tooltip placement for some areas of Jalview
1313 <li>Allow addition of JABAWS Server which doesn't
1314 pass validation</li>
1315 <li>Web services parameters dialog box is too large to
1317 <li>Muscle nucleotide alignment preset obscured by
1319 <li>JABAWS preset submenus don't contain newly
1320 defined user preset</li>
1321 <li>MSA web services warns user if they were launched
1322 with invalid input</li>
1323 <li>Jalview cannot contact DAS Registy when running on
1326 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1327 'Superpose with' submenu not shown when new view
1331 </ul> <!-- <em>Applet</em>
1333 </ul> <em>General</em>
1335 </ul>--> <em>Deployment and Documentation</em>
1337 <li>2G and 1G options in launchApp have no effect on
1338 memory allocation</li>
1339 <li>launchApp service doesn't automatically open
1340 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1342 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1343 InstallAnywhere reports cannot find valid JVM when Java
1344 1.7_055 is available
1346 </ul> <em>Application Known issues</em>
1349 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1350 corrupted or unreadable alignment display when scrolling
1354 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1355 retrieval fails but progress bar continues for DAS retrieval
1356 with large number of ID
1359 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1360 flatfile output of visible region has incorrect sequence
1364 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1365 rna structure consensus doesn't update when secondary
1366 structure tracks are rearranged
1369 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1370 invalid rna structure positional highlighting does not
1371 highlight position of invalid base pairs
1374 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1375 out of memory errors are not raised when saving Jalview
1376 project from alignment window file menu
1379 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1380 Switching to RNA Helices colouring doesn't propagate to
1384 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1385 colour by RNA Helices not enabled when user created
1386 annotation added to alignment
1389 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1390 Jalview icon not shown on dock in Mountain Lion/Webstart
1392 </ul> <em>Applet Known Issues</em>
1395 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1396 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1399 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1400 Jalview and Jmol example not compatible with IE9
1403 <li>Sort by annotation score doesn't reverse order
1409 <td><div align="center">
1410 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1413 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1416 <li>Internationalisation of user interface (usually
1417 called i18n support) and translation for Spanish locale</li>
1418 <li>Define/Undefine group on current selection with
1419 Ctrl-G/Shift Ctrl-G</li>
1420 <li>Improved group creation/removal options in
1421 alignment/sequence Popup menu</li>
1422 <li>Sensible precision for symbol distribution
1423 percentages shown in logo tooltip.</li>
1424 <li>Annotation panel height set according to amount of
1425 annotation when alignment first opened</li>
1426 </ul> <em>Application</em>
1428 <li>Interactive consensus RNA secondary structure
1429 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1430 <li>Select columns containing particular features from
1431 Feature Settings dialog</li>
1432 <li>View all 'representative' PDB structures for selected
1434 <li>Update Jalview project format:
1436 <li>New file extension for Jalview projects '.jvp'</li>
1437 <li>Preserve sequence and annotation dataset (to
1438 store secondary structure annotation,etc)</li>
1439 <li>Per group and alignment annotation and RNA helix
1443 <li>New similarity measures for PCA and Tree calculation
1445 <li>Experimental support for retrieval and viewing of
1446 flanking regions for an alignment</li>
1450 <!-- issues resolved --> <em>Application</em>
1452 <li>logo keeps spinning and status remains at queued or
1453 running after job is cancelled</li>
1454 <li>cannot export features from alignments imported from
1455 Jalview/VAMSAS projects</li>
1456 <li>Buggy slider for web service parameters that take
1458 <li>Newly created RNA secondary structure line doesn't
1459 have 'display all symbols' flag set</li>
1460 <li>T-COFFEE alignment score shading scheme and other
1461 annotation shading not saved in Jalview project</li>
1462 <li>Local file cannot be loaded in freshly downloaded
1464 <li>Jalview icon not shown on dock in Mountain
1466 <li>Load file from desktop file browser fails</li>
1467 <li>Occasional NPE thrown when calculating large trees</li>
1468 <li>Cannot reorder or slide sequences after dragging an
1469 alignment onto desktop</li>
1470 <li>Colour by annotation dialog throws NPE after using
1471 'extract scores' function</li>
1472 <li>Loading/cut'n'pasting an empty file leads to a grey
1473 alignment window</li>
1474 <li>Disorder thresholds rendered incorrectly after
1475 performing IUPred disorder prediction</li>
1476 <li>Multiple group annotated consensus rows shown when
1477 changing 'normalise logo' display setting</li>
1478 <li>Find shows blank dialog after 'finished searching' if
1479 nothing matches query</li>
1480 <li>Null Pointer Exceptions raised when sorting by
1481 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1483 <li>Errors in Jmol console when structures in alignment
1484 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1486 <li>Not all working JABAWS services are shown in
1488 <li>JAVAWS version of Jalview fails to launch with
1489 'invalid literal/length code'</li>
1490 <li>Annotation/RNA Helix colourschemes cannot be applied
1491 to alignment with groups (actually fixed in 2.8.0b1)</li>
1492 <li>RNA Helices and T-Coffee Scores available as default
1495 </ul> <em>Applet</em>
1497 <li>Remove group option is shown even when selection is
1499 <li>Apply to all groups ticked but colourscheme changes
1500 don't affect groups</li>
1501 <li>Documented RNA Helices and T-Coffee Scores as valid
1502 colourscheme name</li>
1503 <li>Annotation labels drawn on sequence IDs when
1504 Annotation panel is not displayed</li>
1505 <li>Increased font size for dropdown menus on OSX and
1506 embedded windows</li>
1507 </ul> <em>Other</em>
1509 <li>Consensus sequence for alignments/groups with a
1510 single sequence were not calculated</li>
1511 <li>annotation files that contain only groups imported as
1512 annotation and junk sequences</li>
1513 <li>Fasta files with sequences containing '*' incorrectly
1514 recognised as PFAM or BLC</li>
1515 <li>conservation/PID slider apply all groups option
1516 doesn't affect background (2.8.0b1)
1518 <li>redundancy highlighting is erratic at 0% and 100%</li>
1519 <li>Remove gapped columns fails for sequences with ragged
1521 <li>AMSA annotation row with leading spaces is not
1522 registered correctly on import</li>
1523 <li>Jalview crashes when selecting PCA analysis for
1524 certain alignments</li>
1525 <li>Opening the colour by annotation dialog for an
1526 existing annotation based 'use original colours'
1527 colourscheme loses original colours setting</li>
1532 <td><div align="center">
1533 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
1534 <em>30/1/2014</em></strong>
1538 <li>Trusted certificates for JalviewLite applet and
1539 Jalview Desktop application<br />Certificate was donated by
1540 <a href="https://www.certum.eu">Certum</a> to the Jalview
1541 open source project).
1543 <li>Jalview SRS links replaced by UniProt and EBI-search
1545 <li>Output in Stockholm format</li>
1546 <li>Allow import of data from gzipped files</li>
1547 <li>Export/import group and sequence associated line
1548 graph thresholds</li>
1549 <li>Nucleotide substitution matrix that supports RNA and
1550 ambiguity codes</li>
1551 <li>Allow disorder predictions to be made on the current
1552 selection (or visible selection) in the same way that JPred
1554 <li>Groovy scripting for headless Jalview operation</li>
1555 </ul> <em>Other improvements</em>
1557 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
1558 <li>COMBINE statement uses current SEQUENCE_REF and
1559 GROUP_REF scope to group annotation rows</li>
1560 <li>Support '' style escaping of quotes in Newick
1562 <li>Group options for JABAWS service by command line name</li>
1563 <li>Empty tooltip shown for JABA service options with a
1564 link but no description</li>
1565 <li>Select primary source when selecting authority in
1566 database fetcher GUI</li>
1567 <li>Add .mfa to FASTA file extensions recognised by
1569 <li>Annotation label tooltip text wrap</li>
1574 <li>Slow scrolling when lots of annotation rows are
1576 <li>Lots of NPE (and slowness) after creating RNA
1577 secondary structure annotation line</li>
1578 <li>Sequence database accessions not imported when
1579 fetching alignments from Rfam</li>
1580 <li>Incorrect SHMR submission for sequences with
1582 <li>View all structures does not always superpose
1584 <li>Option widgets in service parameters not updated to
1585 reflect user or preset settings</li>
1586 <li>Null pointer exceptions for some services without
1587 presets or adjustable parameters</li>
1588 <li>Discover PDB IDs entry in structure menu doesn't
1589 discover PDB xRefs</li>
1590 <li>Exception encountered while trying to retrieve
1591 features with DAS</li>
1592 <li>Lowest value in annotation row isn't coloured
1593 when colour by annotation (per sequence) is coloured</li>
1594 <li>Keyboard mode P jumps to start of gapped region when
1595 residue follows a gap</li>
1596 <li>Jalview appears to hang importing an alignment with
1597 Wrap as default or after enabling Wrap</li>
1598 <li>'Right click to add annotations' message
1599 shown in wrap mode when no annotations present</li>
1600 <li>Disorder predictions fail with NPE if no automatic
1601 annotation already exists on alignment</li>
1602 <li>oninit javascript function should be called after
1603 initialisation completes</li>
1604 <li>Remove redundancy after disorder prediction corrupts
1605 alignment window display</li>
1606 <li>Example annotation file in documentation is invalid</li>
1607 <li>Grouped line graph annotation rows are not exported
1608 to annotation file</li>
1609 <li>Multi-harmony analysis cannot be run when only two
1611 <li>Cannot create multiple groups of line graphs with
1612 several 'combine' statements in annotation file</li>
1613 <li>Pressing return several times causes Number Format
1614 exceptions in keyboard mode</li>
1615 <li>Multi-harmony (SHMMR) method doesn't submit
1616 correct partitions for input data</li>
1617 <li>Translation from DNA to Amino Acids fails</li>
1618 <li>Jalview fail to load newick tree with quoted label</li>
1619 <li>--headless flag isn't understood</li>
1620 <li>ClassCastException when generating EPS in headless
1622 <li>Adjusting sequence-associated shading threshold only
1623 changes one row's threshold</li>
1624 <li>Preferences and Feature settings panel panel
1625 doesn't open</li>
1626 <li>hide consensus histogram also hides conservation and
1627 quality histograms</li>
1632 <td><div align="center">
1633 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
1635 <td><em>Application</em>
1637 <li>Support for JABAWS 2.0 Services (AACon alignment
1638 conservation, protein disorder and Clustal Omega)</li>
1639 <li>JABAWS server status indicator in Web Services
1641 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
1642 in Jalview alignment window</li>
1643 <li>Updated Jalview build and deploy framework for OSX
1644 mountain lion, windows 7, and 8</li>
1645 <li>Nucleotide substitution matrix for PCA that supports
1646 RNA and ambiguity codes</li>
1648 <li>Improved sequence database retrieval GUI</li>
1649 <li>Support fetching and database reference look up
1650 against multiple DAS sources (Fetch all from in 'fetch db
1652 <li>Jalview project improvements
1654 <li>Store and retrieve the 'belowAlignment'
1655 flag for annotation</li>
1656 <li>calcId attribute to group annotation rows on the
1658 <li>Store AACon calculation settings for a view in
1659 Jalview project</li>
1663 <li>horizontal scrolling gesture support</li>
1664 <li>Visual progress indicator when PCA calculation is
1666 <li>Simpler JABA web services menus</li>
1667 <li>visual indication that web service results are still
1668 being retrieved from server</li>
1669 <li>Serialise the dialogs that are shown when Jalview
1670 starts up for first time</li>
1671 <li>Jalview user agent string for interacting with HTTP
1673 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
1675 <li>Examples directory and Groovy library included in
1676 InstallAnywhere distribution</li>
1677 </ul> <em>Applet</em>
1679 <li>RNA alignment and secondary structure annotation
1680 visualization applet example</li>
1681 </ul> <em>General</em>
1683 <li>Normalise option for consensus sequence logo</li>
1684 <li>Reset button in PCA window to return dimensions to
1686 <li>Allow seqspace or Jalview variant of alignment PCA
1688 <li>PCA with either nucleic acid and protein substitution
1690 <li>Allow windows containing HTML reports to be exported
1692 <li>Interactive display and editing of RNA secondary
1693 structure contacts</li>
1694 <li>RNA Helix Alignment Colouring</li>
1695 <li>RNA base pair logo consensus</li>
1696 <li>Parse sequence associated secondary structure
1697 information in Stockholm files</li>
1698 <li>HTML Export database accessions and annotation
1699 information presented in tooltip for sequences</li>
1700 <li>Import secondary structure from LOCARNA clustalw
1701 style RNA alignment files</li>
1702 <li>import and visualise T-COFFEE quality scores for an
1704 <li>'colour by annotation' per sequence option to
1705 shade each sequence according to its associated alignment
1707 <li>New Jalview Logo</li>
1708 </ul> <em>Documentation and Development</em>
1710 <li>documentation for score matrices used in Jalview</li>
1711 <li>New Website!</li>
1713 <td><em>Application</em>
1715 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
1716 wsdbfetch REST service</li>
1717 <li>Stop windows being moved outside desktop on OSX</li>
1718 <li>Filetype associations not installed for webstart
1720 <li>Jalview does not always retrieve progress of a JABAWS
1721 job execution in full once it is complete</li>
1722 <li>revise SHMR RSBS definition to ensure alignment is
1723 uploaded via ali_file parameter</li>
1724 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
1725 <li>View all structures superposed fails with exception</li>
1726 <li>Jnet job queues forever if a very short sequence is
1727 submitted for prediction</li>
1728 <li>Cut and paste menu not opened when mouse clicked on
1730 <li>Putting fractional value into integer text box in
1731 alignment parameter dialog causes Jalview to hang</li>
1732 <li>Structure view highlighting doesn't work on
1734 <li>View all structures fails with exception shown in
1736 <li>Characters in filename associated with PDBEntry not
1737 escaped in a platform independent way</li>
1738 <li>Jalview desktop fails to launch with exception when
1740 <li>Tree calculation reports 'you must have 2 or more
1741 sequences selected' when selection is empty</li>
1742 <li>Jalview desktop fails to launch with jar signature
1743 failure when java web start temporary file caching is
1745 <li>DAS Sequence retrieval with range qualification
1746 results in sequence xref which includes range qualification</li>
1747 <li>Errors during processing of command line arguments
1748 cause progress bar (JAL-898) to be removed</li>
1749 <li>Replace comma for semi-colon option not disabled for
1750 DAS sources in sequence fetcher</li>
1751 <li>Cannot close news reader when JABAWS server warning
1752 dialog is shown</li>
1753 <li>Option widgets not updated to reflect user settings</li>
1754 <li>Edited sequence not submitted to web service</li>
1755 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
1756 <li>InstallAnywhere installer doesn't unpack and run
1757 on OSX Mountain Lion</li>
1758 <li>Annotation panel not given a scroll bar when
1759 sequences with alignment annotation are pasted into the
1761 <li>Sequence associated annotation rows not associated
1762 when loaded from Jalview project</li>
1763 <li>Browser launch fails with NPE on java 1.7</li>
1764 <li>JABAWS alignment marked as finished when job was
1765 cancelled or job failed due to invalid input</li>
1766 <li>NPE with v2.7 example when clicking on Tree
1767 associated with all views</li>
1768 <li>Exceptions when copy/paste sequences with grouped
1769 annotation rows to new window</li>
1770 </ul> <em>Applet</em>
1772 <li>Sequence features are momentarily displayed before
1773 they are hidden using hidefeaturegroups applet parameter</li>
1774 <li>loading features via javascript API automatically
1775 enables feature display</li>
1776 <li>scrollToColumnIn javascript API method doesn't
1778 </ul> <em>General</em>
1780 <li>Redundancy removal fails for rna alignment</li>
1781 <li>PCA calculation fails when sequence has been selected
1782 and then deselected</li>
1783 <li>PCA window shows grey box when first opened on OSX</li>
1784 <li>Letters coloured pink in sequence logo when alignment
1785 coloured with clustalx</li>
1786 <li>Choosing fonts without letter symbols defined causes
1787 exceptions and redraw errors</li>
1788 <li>Initial PCA plot view is not same as manually
1789 reconfigured view</li>
1790 <li>Grouped annotation graph label has incorrect line
1792 <li>Grouped annotation graph label display is corrupted
1793 for lots of labels</li>
1798 <div align="center">
1799 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
1802 <td><em>Application</em>
1804 <li>Jalview Desktop News Reader</li>
1805 <li>Tweaked default layout of web services menu</li>
1806 <li>View/alignment association menu to enable user to
1807 easily specify which alignment a multi-structure view takes
1808 its colours/correspondences from</li>
1809 <li>Allow properties file location to be specified as URL</li>
1810 <li>Extend Jalview project to preserve associations
1811 between many alignment views and a single Jmol display</li>
1812 <li>Store annotation row height in Jalview project file</li>
1813 <li>Annotation row column label formatting attributes
1814 stored in project file</li>
1815 <li>Annotation row order for auto-calculated annotation
1816 rows preserved in Jalview project file</li>
1817 <li>Visual progress indication when Jalview state is
1818 saved using Desktop window menu</li>
1819 <li>Visual indication that command line arguments are
1820 still being processed</li>
1821 <li>Groovy script execution from URL</li>
1822 <li>Colour by annotation default min and max colours in
1824 <li>Automatically associate PDB files dragged onto an
1825 alignment with sequences that have high similarity and
1827 <li>Update JGoogleAnalytics to latest release (0.3)</li>
1828 <li>'view structures' option to open many
1829 structures in same window</li>
1830 <li>Sort associated views menu option for tree panel</li>
1831 <li>Group all JABA and non-JABA services for a particular
1832 analysis function in its own submenu</li>
1833 </ul> <em>Applet</em>
1835 <li>Userdefined and autogenerated annotation rows for
1837 <li>Adjustment of alignment annotation pane height</li>
1838 <li>Annotation scrollbar for annotation panel</li>
1839 <li>Drag to reorder annotation rows in annotation panel</li>
1840 <li>'automaticScrolling' parameter</li>
1841 <li>Allow sequences with partial ID string matches to be
1842 annotated from GFF/Jalview features files</li>
1843 <li>Sequence logo annotation row in applet</li>
1844 <li>Absolute paths relative to host server in applet
1845 parameters are treated as such</li>
1846 <li>New in the JalviewLite javascript API:
1848 <li>JalviewLite.js javascript library</li>
1849 <li>Javascript callbacks for
1851 <li>Applet initialisation</li>
1852 <li>Sequence/alignment mouse-overs and selections</li>
1855 <li>scrollTo row and column alignment scrolling
1857 <li>Select sequence/alignment regions from javascript</li>
1858 <li>javascript structure viewer harness to pass
1859 messages between Jmol and Jalview when running as
1860 distinct applets</li>
1861 <li>sortBy method</li>
1862 <li>Set of applet and application examples shipped
1863 with documentation</li>
1864 <li>New example to demonstrate JalviewLite and Jmol
1865 javascript message exchange</li>
1867 </ul> <em>General</em>
1869 <li>Enable Jmol displays to be associated with multiple
1870 multiple alignments</li>
1871 <li>Option to automatically sort alignment with new tree</li>
1872 <li>User configurable link to enable redirects to a
1873 www.Jalview.org mirror</li>
1874 <li>Jmol colours option for Jmol displays</li>
1875 <li>Configurable newline string when writing alignment
1876 and other flat files</li>
1877 <li>Allow alignment annotation description lines to
1878 contain html tags</li>
1879 </ul> <em>Documentation and Development</em>
1881 <li>Add groovy test harness for bulk load testing to
1883 <li>Groovy script to load and align a set of sequences
1884 using a web service before displaying the result in the
1885 Jalview desktop</li>
1886 <li>Restructured javascript and applet api documentation</li>
1887 <li>Ant target to publish example html files with applet
1889 <li>Netbeans project for building Jalview from source</li>
1890 <li>ant task to create online javadoc for Jalview source</li>
1892 <td><em>Application</em>
1894 <li>User defined colourscheme throws exception when
1895 current built in colourscheme is saved as new scheme</li>
1896 <li>AlignFrame->Save in application pops up save
1897 dialog for valid filename/format</li>
1898 <li>Cannot view associated structure for UniProt sequence</li>
1899 <li>PDB file association breaks for UniProt sequence
1901 <li>Associate PDB from file dialog does not tell you
1902 which sequence is to be associated with the file</li>
1903 <li>Find All raises null pointer exception when query
1904 only matches sequence IDs</li>
1905 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
1906 <li>Jalview project with Jmol views created with Jalview
1907 2.4 cannot be loaded</li>
1908 <li>Filetype associations not installed for webstart
1910 <li>Two or more chains in a single PDB file associated
1911 with sequences in different alignments do not get coloured
1912 by their associated sequence</li>
1913 <li>Visibility status of autocalculated annotation row
1914 not preserved when project is loaded</li>
1915 <li>Annotation row height and visibility attributes not
1916 stored in Jalview project</li>
1917 <li>Tree bootstraps are not preserved when saved as a
1918 Jalview project</li>
1919 <li>Envision2 workflow tooltips are corrupted</li>
1920 <li>Enabling show group conservation also enables colour
1921 by conservation</li>
1922 <li>Duplicate group associated conservation or consensus
1923 created on new view</li>
1924 <li>Annotation scrollbar not displayed after 'show
1925 all hidden annotation rows' option selected</li>
1926 <li>Alignment quality not updated after alignment
1927 annotation row is hidden then shown</li>
1928 <li>Preserve colouring of structures coloured by
1929 sequences in pre Jalview 2.7 projects</li>
1930 <li>Web service job parameter dialog is not laid out
1932 <li>Web services menu not refreshed after 'reset
1933 services' button is pressed in preferences</li>
1934 <li>Annotation off by one in Jalview v2_3 example project</li>
1935 <li>Structures imported from file and saved in project
1936 get name like jalview_pdb1234.txt when reloaded</li>
1937 <li>Jalview does not always retrieve progress of a JABAWS
1938 job execution in full once it is complete</li>
1939 </ul> <em>Applet</em>
1941 <li>Alignment height set incorrectly when lots of
1942 annotation rows are displayed</li>
1943 <li>Relative URLs in feature HTML text not resolved to
1945 <li>View follows highlighting does not work for positions
1947 <li><= shown as = in tooltip</li>
1948 <li>Export features raises exception when no features
1950 <li>Separator string used for serialising lists of IDs
1951 for javascript api is modified when separator string
1952 provided as parameter</li>
1953 <li>Null pointer exception when selecting tree leaves for
1954 alignment with no existing selection</li>
1955 <li>Relative URLs for datasources assumed to be relative
1956 to applet's codebase</li>
1957 <li>Status bar not updated after finished searching and
1958 search wraps around to first result</li>
1959 <li>StructureSelectionManager instance shared between
1960 several Jalview applets causes race conditions and memory
1962 <li>Hover tooltip and mouseover of position on structure
1963 not sent from Jmol in applet</li>
1964 <li>Certain sequences of javascript method calls to
1965 applet API fatally hang browser</li>
1966 </ul> <em>General</em>
1968 <li>View follows structure mouseover scrolls beyond
1969 position with wrapped view and hidden regions</li>
1970 <li>Find sequence position moves to wrong residue
1971 with/without hidden columns</li>
1972 <li>Sequence length given in alignment properties window
1974 <li>InvalidNumberFormat exceptions thrown when trying to
1975 import PDB like structure files</li>
1976 <li>Positional search results are only highlighted
1977 between user-supplied sequence start/end bounds</li>
1978 <li>End attribute of sequence is not validated</li>
1979 <li>Find dialog only finds first sequence containing a
1980 given sequence position</li>
1981 <li>Sequence numbering not preserved in MSF alignment
1983 <li>Jalview PDB file reader does not extract sequence
1984 from nucleotide chains correctly</li>
1985 <li>Structure colours not updated when tree partition
1986 changed in alignment</li>
1987 <li>Sequence associated secondary structure not correctly
1988 parsed in interleaved stockholm</li>
1989 <li>Colour by annotation dialog does not restore current
1991 <li>Hiding (nearly) all sequences doesn't work
1993 <li>Sequences containing lowercase letters are not
1994 properly associated with their pdb files</li>
1995 </ul> <em>Documentation and Development</em>
1997 <li>schemas/JalviewWsParamSet.xsd corrupted by
1998 ApplyCopyright tool</li>
2003 <div align="center">
2004 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2007 <td><em>Application</em>
2009 <li>New warning dialog when the Jalview Desktop cannot
2010 contact web services</li>
2011 <li>JABA service parameters for a preset are shown in
2012 service job window</li>
2013 <li>JABA Service menu entries reworded</li>
2017 <li>Modeller PIR IO broken - cannot correctly import a
2018 pir file emitted by Jalview</li>
2019 <li>Existing feature settings transferred to new
2020 alignment view created from cut'n'paste</li>
2021 <li>Improved test for mixed amino/nucleotide chains when
2022 parsing PDB files</li>
2023 <li>Consensus and conservation annotation rows
2024 occasionally become blank for all new windows</li>
2025 <li>Exception raised when right clicking above sequences
2026 in wrapped view mode</li>
2027 </ul> <em>Application</em>
2029 <li>multiple multiply aligned structure views cause cpu
2030 usage to hit 100% and computer to hang</li>
2031 <li>Web Service parameter layout breaks for long user
2032 parameter names</li>
2033 <li>Jaba service discovery hangs desktop if Jaba server
2040 <div align="center">
2041 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2044 <td><em>Application</em>
2046 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2047 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2050 <li>Web Services preference tab</li>
2051 <li>Analysis parameters dialog box and user defined
2053 <li>Improved speed and layout of Envision2 service menu</li>
2054 <li>Superpose structures using associated sequence
2056 <li>Export coordinates and projection as CSV from PCA
2058 </ul> <em>Applet</em>
2060 <li>enable javascript: execution by the applet via the
2061 link out mechanism</li>
2062 </ul> <em>Other</em>
2064 <li>Updated the Jmol Jalview interface to work with Jmol
2066 <li>The Jalview Desktop and JalviewLite applet now
2067 require Java 1.5</li>
2068 <li>Allow Jalview feature colour specification for GFF
2069 sequence annotation files</li>
2070 <li>New 'colour by label' keword in Jalview feature file
2071 type colour specification</li>
2072 <li>New Jalview Desktop Groovy API method that allows a
2073 script to check if it being run in an interactive session or
2074 in a batch operation from the Jalview command line</li>
2078 <li>clustalx colourscheme colours Ds preferentially when
2079 both D+E are present in over 50% of the column</li>
2080 </ul> <em>Application</em>
2082 <li>typo in AlignmentFrame->View->Hide->all but
2083 selected Regions menu item</li>
2084 <li>sequence fetcher replaces ',' for ';' when the ',' is
2085 part of a valid accession ID</li>
2086 <li>fatal OOM if object retrieved by sequence fetcher
2087 runs out of memory</li>
2088 <li>unhandled Out of Memory Error when viewing pca
2089 analysis results</li>
2090 <li>InstallAnywhere builds fail to launch on OS X java
2091 10.5 update 4 (due to apple Java 1.6 update)</li>
2092 <li>Installanywhere Jalview silently fails to launch</li>
2093 </ul> <em>Applet</em>
2095 <li>Jalview.getFeatureGroups() raises an
2096 ArrayIndexOutOfBoundsException if no feature groups are
2103 <div align="center">
2104 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2110 <li>Alignment prettyprinter doesn't cope with long
2112 <li>clustalx colourscheme colours Ds preferentially when
2113 both D+E are present in over 50% of the column</li>
2114 <li>nucleic acid structures retrieved from PDB do not
2115 import correctly</li>
2116 <li>More columns get selected than were clicked on when a
2117 number of columns are hidden</li>
2118 <li>annotation label popup menu not providing correct
2119 add/hide/show options when rows are hidden or none are
2121 <li>Stockholm format shown in list of readable formats,
2122 and parser copes better with alignments from RFAM.</li>
2123 <li>CSV output of consensus only includes the percentage
2124 of all symbols if sequence logo display is enabled</li>
2126 </ul> <em>Applet</em>
2128 <li>annotation panel disappears when annotation is
2130 </ul> <em>Application</em>
2132 <li>Alignment view not redrawn properly when new
2133 alignment opened where annotation panel is visible but no
2134 annotations are present on alignment</li>
2135 <li>pasted region containing hidden columns is
2136 incorrectly displayed in new alignment window</li>
2137 <li>Jalview slow to complete operations when stdout is
2138 flooded (fix is to close the Jalview console)</li>
2139 <li>typo in AlignmentFrame->View->Hide->all but
2140 selected Rregions menu item.</li>
2141 <li>inconsistent group submenu and Format submenu entry
2142 'Un' or 'Non'conserved</li>
2143 <li>Sequence feature settings are being shared by
2144 multiple distinct alignments</li>
2145 <li>group annotation not recreated when tree partition is
2147 <li>double click on group annotation to select sequences
2148 does not propagate to associated trees</li>
2149 <li>Mac OSX specific issues:
2151 <li>exception raised when mouse clicked on desktop
2152 window background</li>
2153 <li>Desktop menu placed on menu bar and application
2154 name set correctly</li>
2155 <li>sequence feature settings not wide enough for the
2156 save feature colourscheme button</li>
2165 <div align="center">
2166 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2169 <td><em>New Capabilities</em>
2171 <li>URL links generated from description line for
2172 regular-expression based URL links (applet and application)
2179 <li>Non-positional feature URL links are shown in link
2181 <li>Linked viewing of nucleic acid sequences and
2183 <li>Automatic Scrolling option in View menu to display
2184 the currently highlighted region of an alignment.</li>
2185 <li>Order an alignment by sequence length, or using the
2186 average score or total feature count for each sequence.</li>
2187 <li>Shading features by score or associated description</li>
2188 <li>Subdivide alignment and groups based on identity of
2189 selected subsequence (Make Groups from Selection).</li>
2190 <li>New hide/show options including Shift+Control+H to
2191 hide everything but the currently selected region.</li>
2192 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2193 </ul> <em>Application</em>
2195 <li>Fetch DB References capabilities and UI expanded to
2196 support retrieval from DAS sequence sources</li>
2197 <li>Local DAS Sequence sources can be added via the
2198 command line or via the Add local source dialog box.</li>
2199 <li>DAS Dbref and DbxRef feature types are parsed as
2200 database references and protein_name is parsed as
2201 description line (BioSapiens terms).</li>
2202 <li>Enable or disable non-positional feature and database
2203 references in sequence ID tooltip from View menu in
2205 <!-- <li>New hidden columns and rows and representatives capabilities
2206 in annotations file (in progress - not yet fully implemented)</li> -->
2207 <li>Group-associated consensus, sequence logos and
2208 conservation plots</li>
2209 <li>Symbol distributions for each column can be exported
2210 and visualized as sequence logos</li>
2211 <li>Optionally scale multi-character column labels to fit
2212 within each column of annotation row<!-- todo for applet -->
2214 <li>Optional automatic sort of associated alignment view
2215 when a new tree is opened.</li>
2216 <li>Jalview Java Console</li>
2217 <li>Better placement of desktop window when moving
2218 between different screens.</li>
2219 <li>New preference items for sequence ID tooltip and
2220 consensus annotation</li>
2221 <li>Client to submit sequences and IDs to Envision2
2223 <li><em>Vamsas Capabilities</em>
2225 <li>Improved VAMSAS synchronization (Jalview archive
2226 used to preserve views, structures, and tree display
2228 <li>Import of vamsas documents from disk or URL via
2230 <li>Sharing of selected regions between views and
2231 with other VAMSAS applications (Experimental feature!)</li>
2232 <li>Updated API to VAMSAS version 0.2</li>
2234 </ul> <em>Applet</em>
2236 <li>Middle button resizes annotation row height</li>
2239 <li>sortByTree (true/false) - automatically sort the
2240 associated alignment view by the tree when a new tree is
2242 <li>showTreeBootstraps (true/false) - show or hide
2243 branch bootstraps (default is to show them if available)</li>
2244 <li>showTreeDistances (true/false) - show or hide
2245 branch lengths (default is to show them if available)</li>
2246 <li>showUnlinkedTreeNodes (true/false) - indicate if
2247 unassociated nodes should be highlighted in the tree
2249 <li>heightScale and widthScale (1.0 or more) -
2250 increase the height or width of a cell in the alignment
2251 grid relative to the current font size.</li>
2254 <li>Non-positional features displayed in sequence ID
2256 </ul> <em>Other</em>
2258 <li>Features format: graduated colour definitions and
2259 specification of feature scores</li>
2260 <li>Alignment Annotations format: new keywords for group
2261 associated annotation (GROUP_REF) and annotation row display
2262 properties (ROW_PROPERTIES)</li>
2263 <li>XML formats extended to support graduated feature
2264 colourschemes, group associated annotation, and profile
2265 visualization settings.</li></td>
2268 <li>Source field in GFF files parsed as feature source
2269 rather than description</li>
2270 <li>Non-positional features are now included in sequence
2271 feature and gff files (controlled via non-positional feature
2272 visibility in tooltip).</li>
2273 <li>URL links generated for all feature links (bugfix)</li>
2274 <li>Added URL embedding instructions to features file
2276 <li>Codons containing ambiguous nucleotides translated as
2277 'X' in peptide product</li>
2278 <li>Match case switch in find dialog box works for both
2279 sequence ID and sequence string and query strings do not
2280 have to be in upper case to match case-insensitively.</li>
2281 <li>AMSA files only contain first column of
2282 multi-character column annotation labels</li>
2283 <li>Jalview Annotation File generation/parsing consistent
2284 with documentation (e.g. Stockholm annotation can be
2285 exported and re-imported)</li>
2286 <li>PDB files without embedded PDB IDs given a friendly
2288 <li>Find incrementally searches ID string matches as well
2289 as subsequence matches, and correctly reports total number
2293 <li>Better handling of exceptions during sequence
2295 <li>Dasobert generated non-positional feature URL
2296 link text excludes the start_end suffix</li>
2297 <li>DAS feature and source retrieval buttons disabled
2298 when fetch or registry operations in progress.</li>
2299 <li>PDB files retrieved from URLs are cached properly</li>
2300 <li>Sequence description lines properly shared via
2302 <li>Sequence fetcher fetches multiple records for all
2304 <li>Ensured that command line das feature retrieval
2305 completes before alignment figures are generated.</li>
2306 <li>Reduced time taken when opening file browser for
2308 <li>isAligned check prior to calculating tree, PCA or
2309 submitting an MSA to JNet now excludes hidden sequences.</li>
2310 <li>User defined group colours properly recovered
2311 from Jalview projects.</li>
2320 <div align="center">
2321 <strong>2.4.0.b2</strong><br> 28/10/2009
2326 <li>Experimental support for google analytics usage
2328 <li>Jalview privacy settings (user preferences and docs).</li>
2333 <li>Race condition in applet preventing startup in
2335 <li>Exception when feature created from selection beyond
2336 length of sequence.</li>
2337 <li>Allow synthetic PDB files to be imported gracefully</li>
2338 <li>Sequence associated annotation rows associate with
2339 all sequences with a given id</li>
2340 <li>Find function matches case-insensitively for sequence
2341 ID string searches</li>
2342 <li>Non-standard characters do not cause pairwise
2343 alignment to fail with exception</li>
2344 </ul> <em>Application Issues</em>
2346 <li>Sequences are now validated against EMBL database</li>
2347 <li>Sequence fetcher fetches multiple records for all
2349 </ul> <em>InstallAnywhere Issues</em>
2351 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2352 issue with installAnywhere mechanism)</li>
2353 <li>Command line launching of JARs from InstallAnywhere
2354 version (java class versioning error fixed)</li>
2361 <div align="center">
2362 <strong>2.4</strong><br> 27/8/2008
2365 <td><em>User Interface</em>
2367 <li>Linked highlighting of codon and amino acid from
2368 translation and protein products</li>
2369 <li>Linked highlighting of structure associated with
2370 residue mapping to codon position</li>
2371 <li>Sequence Fetcher provides example accession numbers
2372 and 'clear' button</li>
2373 <li>MemoryMonitor added as an option under Desktop's
2375 <li>Extract score function to parse whitespace separated
2376 numeric data in description line</li>
2377 <li>Column labels in alignment annotation can be centred.</li>
2378 <li>Tooltip for sequence associated annotation give name
2380 </ul> <em>Web Services and URL fetching</em>
2382 <li>JPred3 web service</li>
2383 <li>Prototype sequence search client (no public services
2385 <li>Fetch either seed alignment or full alignment from
2387 <li>URL Links created for matching database cross
2388 references as well as sequence ID</li>
2389 <li>URL Links can be created using regular-expressions</li>
2390 </ul> <em>Sequence Database Connectivity</em>
2392 <li>Retrieval of cross-referenced sequences from other
2394 <li>Generalised database reference retrieval and
2395 validation to all fetchable databases</li>
2396 <li>Fetch sequences from DAS sources supporting the
2397 sequence command</li>
2398 </ul> <em>Import and Export</em>
2399 <li>export annotation rows as CSV for spreadsheet import</li>
2400 <li>Jalview projects record alignment dataset associations,
2401 EMBL products, and cDNA sequence mappings</li>
2402 <li>Sequence Group colour can be specified in Annotation
2404 <li>Ad-hoc colouring of group in Annotation File using RGB
2405 triplet as name of colourscheme</li>
2406 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2408 <li>treenode binding for VAMSAS tree exchange</li>
2409 <li>local editing and update of sequences in VAMSAS
2410 alignments (experimental)</li>
2411 <li>Create new or select existing session to join</li>
2412 <li>load and save of vamsas documents</li>
2413 </ul> <em>Application command line</em>
2415 <li>-tree parameter to open trees (introduced for passing
2417 <li>-fetchfrom command line argument to specify nicknames
2418 of DAS servers to query for alignment features</li>
2419 <li>-dasserver command line argument to add new servers
2420 that are also automatically queried for features</li>
2421 <li>-groovy command line argument executes a given groovy
2422 script after all input data has been loaded and parsed</li>
2423 </ul> <em>Applet-Application data exchange</em>
2425 <li>Trees passed as applet parameters can be passed to
2426 application (when using "View in full
2427 application")</li>
2428 </ul> <em>Applet Parameters</em>
2430 <li>feature group display control parameter</li>
2431 <li>debug parameter</li>
2432 <li>showbutton parameter</li>
2433 </ul> <em>Applet API methods</em>
2435 <li>newView public method</li>
2436 <li>Window (current view) specific get/set public methods</li>
2437 <li>Feature display control methods</li>
2438 <li>get list of currently selected sequences</li>
2439 </ul> <em>New Jalview distribution features</em>
2441 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2442 <li>RELEASE file gives build properties for the latest
2443 Jalview release.</li>
2444 <li>Java 1.1 Applet build made easier and donotobfuscate
2445 property controls execution of obfuscator</li>
2446 <li>Build target for generating source distribution</li>
2447 <li>Debug flag for javacc</li>
2448 <li>.jalview_properties file is documented (slightly) in
2449 jalview.bin.Cache</li>
2450 <li>Continuous Build Integration for stable and
2451 development version of Application, Applet and source
2456 <li>selected region output includes visible annotations
2457 (for certain formats)</li>
2458 <li>edit label/displaychar contains existing label/char
2460 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2461 <li>shorter peptide product names from EMBL records</li>
2462 <li>Newick string generator makes compact representations</li>
2463 <li>bootstrap values parsed correctly for tree files with
2465 <li>pathological filechooser bug avoided by not allowing
2466 filenames containing a ':'</li>
2467 <li>Fixed exception when parsing GFF files containing
2468 global sequence features</li>
2469 <li>Alignment datasets are finalized only when number of
2470 references from alignment sequences goes to zero</li>
2471 <li>Close of tree branch colour box without colour
2472 selection causes cascading exceptions</li>
2473 <li>occasional negative imgwidth exceptions</li>
2474 <li>better reporting of non-fatal warnings to user when
2475 file parsing fails.</li>
2476 <li>Save works when Jalview project is default format</li>
2477 <li>Save as dialog opened if current alignment format is
2478 not a valid output format</li>
2479 <li>UniProt canonical names introduced for both das and
2481 <li>Histidine should be midblue (not pink!) in Zappo</li>
2482 <li>error messages passed up and output when data read
2484 <li>edit undo recovers previous dataset sequence when
2485 sequence is edited</li>
2486 <li>allow PDB files without pdb ID HEADER lines (like
2487 those generated by MODELLER) to be read in properly</li>
2488 <li>allow reading of JPred concise files as a normal
2490 <li>Stockholm annotation parsing and alignment properties
2491 import fixed for PFAM records</li>
2492 <li>Structure view windows have correct name in Desktop
2494 <li>annotation consisting of sequence associated scores
2495 can be read and written correctly to annotation file</li>
2496 <li>Aligned cDNA translation to aligned peptide works
2498 <li>Fixed display of hidden sequence markers and
2499 non-italic font for representatives in Applet</li>
2500 <li>Applet Menus are always embedded in applet window on
2502 <li>Newly shown features appear at top of stack (in
2504 <li>Annotations added via parameter not drawn properly
2505 due to null pointer exceptions</li>
2506 <li>Secondary structure lines are drawn starting from
2507 first column of alignment</li>
2508 <li>UniProt XML import updated for new schema release in
2510 <li>Sequence feature to sequence ID match for Features
2511 file is case-insensitive</li>
2512 <li>Sequence features read from Features file appended to
2513 all sequences with matching IDs</li>
2514 <li>PDB structure coloured correctly for associated views
2515 containing a sub-sequence</li>
2516 <li>PDB files can be retrieved by applet from Jar files</li>
2517 <li>feature and annotation file applet parameters
2518 referring to different directories are retrieved correctly</li>
2519 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
2520 <li>Fixed application hang whilst waiting for
2521 splash-screen version check to complete</li>
2522 <li>Applet properly URLencodes input parameter values
2523 when passing them to the launchApp service</li>
2524 <li>display name and local features preserved in results
2525 retrieved from web service</li>
2526 <li>Visual delay indication for sequence retrieval and
2527 sequence fetcher initialisation</li>
2528 <li>updated Application to use DAS 1.53e version of
2529 dasobert DAS client</li>
2530 <li>Re-instated Full AMSA support and .amsa file
2532 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
2540 <div align="center">
2541 <strong>2.3</strong><br> 9/5/07
2546 <li>Jmol 11.0.2 integration</li>
2547 <li>PDB views stored in Jalview XML files</li>
2548 <li>Slide sequences</li>
2549 <li>Edit sequence in place</li>
2550 <li>EMBL CDS features</li>
2551 <li>DAS Feature mapping</li>
2552 <li>Feature ordering</li>
2553 <li>Alignment Properties</li>
2554 <li>Annotation Scores</li>
2555 <li>Sort by scores</li>
2556 <li>Feature/annotation editing in applet</li>
2561 <li>Headless state operation in 2.2.1</li>
2562 <li>Incorrect and unstable DNA pairwise alignment</li>
2563 <li>Cut and paste of sequences with annotation</li>
2564 <li>Feature group display state in XML</li>
2565 <li>Feature ordering in XML</li>
2566 <li>blc file iteration selection using filename # suffix</li>
2567 <li>Stockholm alignment properties</li>
2568 <li>Stockhom alignment secondary structure annotation</li>
2569 <li>2.2.1 applet had no feature transparency</li>
2570 <li>Number pad keys can be used in cursor mode</li>
2571 <li>Structure Viewer mirror image resolved</li>
2578 <div align="center">
2579 <strong>2.2.1</strong><br> 12/2/07
2584 <li>Non standard characters can be read and displayed
2585 <li>Annotations/Features can be imported/exported to the
2587 <li>Applet allows editing of sequence/annotation/group
2588 name & description
2589 <li>Preference setting to display sequence name in
2591 <li>Annotation file format extended to allow
2592 Sequence_groups to be defined
2593 <li>Default opening of alignment overview panel can be
2594 specified in preferences
2595 <li>PDB residue numbering annotation added to associated
2601 <li>Applet crash under certain Linux OS with Java 1.6
2603 <li>Annotation file export / import bugs fixed
2604 <li>PNG / EPS image output bugs fixed
2610 <div align="center">
2611 <strong>2.2</strong><br> 27/11/06
2616 <li>Multiple views on alignment
2617 <li>Sequence feature editing
2618 <li>"Reload" alignment
2619 <li>"Save" to current filename
2620 <li>Background dependent text colour
2621 <li>Right align sequence ids
2622 <li>User-defined lower case residue colours
2625 <li>Menu item accelerator keys
2626 <li>Control-V pastes to current alignment
2627 <li>Cancel button for DAS Feature Fetching
2628 <li>PCA and PDB Viewers zoom via mouse roller
2629 <li>User-defined sub-tree colours and sub-tree selection
2636 <li>'New Window' button on the 'Output to Text box'
2641 <li>New memory efficient Undo/Redo System
2642 <li>Optimised symbol lookups and conservation/consensus
2644 <li>Region Conservation/Consensus recalculated after
2646 <li>Fixed Remove Empty Columns Bug (empty columns at end
2648 <li>Slowed DAS Feature Fetching for increased robustness.
2655 <li>Made angle brackets in ASCII feature descriptions
2657 <li>Re-instated Zoom function for PCA
2658 <li>Sequence descriptions conserved in web service
2660 <li>UniProt ID discoverer uses any word separated by
2662 <li>WsDbFetch query/result association resolved
2663 <li>Tree leaf to sequence mapping improved
2664 <li>Smooth fonts switch moved to FontChooser dialog box.
2676 <div align="center">
2677 <strong>2.1.1</strong><br> 12/9/06
2682 <li>Copy consensus sequence to clipboard</li>
2687 <li>Image output - rightmost residues are rendered if
2688 sequence id panel has been resized</li>
2689 <li>Image output - all offscreen group boundaries are
2691 <li>Annotation files with sequence references - all
2692 elements in file are relative to sequence position</li>
2693 <li>Mac Applet users can use Alt key for group editing</li>
2699 <div align="center">
2700 <strong>2.1</strong><br> 22/8/06
2705 <li>MAFFT Multiple Alignment in default Web Service list</li>
2706 <li>DAS Feature fetching</li>
2707 <li>Hide sequences and columns</li>
2708 <li>Export Annotations and Features</li>
2709 <li>GFF file reading / writing</li>
2710 <li>Associate structures with sequences from local PDB
2712 <li>Add sequences to exisiting alignment</li>
2713 <li>Recently opened files / URL lists</li>
2714 <li>Applet can launch the full application</li>
2715 <li>Applet has transparency for features (Java 1.2
2717 <li>Applet has user defined colours parameter</li>
2718 <li>Applet can load sequences from parameter
2719 "sequence<em>x</em>"
2725 <li>Redundancy Panel reinstalled in the Applet</li>
2726 <li>Monospaced font - EPS / rescaling bug fixed</li>
2727 <li>Annotation files with sequence references bug fixed</li>
2733 <div align="center">
2734 <strong>2.08.1</strong><br> 2/5/06
2739 <li>Change case of selected region from Popup menu</li>
2740 <li>Choose to match case when searching</li>
2741 <li>Middle mouse button and mouse movement can compress /
2742 expand the visible width and height of the alignment</li>
2747 <li>Annotation Panel displays complete JNet results</li>
2753 <div align="center">
2754 <strong>2.08b</strong><br> 18/4/06
2760 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
2761 <li>Righthand label on wrapped alignments shows correct
2768 <div align="center">
2769 <strong>2.08</strong><br> 10/4/06
2774 <li>Editing can be locked to the selection area</li>
2775 <li>Keyboard editing</li>
2776 <li>Create sequence features from searches</li>
2777 <li>Precalculated annotations can be loaded onto
2779 <li>Features file allows grouping of features</li>
2780 <li>Annotation Colouring scheme added</li>
2781 <li>Smooth fonts off by default - Faster rendering</li>
2782 <li>Choose to toggle Autocalculate Consensus On/Off</li>
2787 <li>Drag & Drop fixed on Linux</li>
2788 <li>Jalview Archive file faster to load/save, sequence
2789 descriptions saved.</li>
2795 <div align="center">
2796 <strong>2.07</strong><br> 12/12/05
2801 <li>PDB Structure Viewer enhanced</li>
2802 <li>Sequence Feature retrieval and display enhanced</li>
2803 <li>Choose to output sequence start-end after sequence
2804 name for file output</li>
2805 <li>Sequence Fetcher WSDBFetch@EBI</li>
2806 <li>Applet can read feature files, PDB files and can be
2807 used for HTML form input</li>
2812 <li>HTML output writes groups and features</li>
2813 <li>Group editing is Control and mouse click</li>
2814 <li>File IO bugs</li>
2820 <div align="center">
2821 <strong>2.06</strong><br> 28/9/05
2826 <li>View annotations in wrapped mode</li>
2827 <li>More options for PCA viewer</li>
2832 <li>GUI bugs resolved</li>
2833 <li>Runs with -nodisplay from command line</li>
2839 <div align="center">
2840 <strong>2.05b</strong><br> 15/9/05
2845 <li>Choose EPS export as lineart or text</li>
2846 <li>Jar files are executable</li>
2847 <li>Can read in Uracil - maps to unknown residue</li>
2852 <li>Known OutOfMemory errors give warning message</li>
2853 <li>Overview window calculated more efficiently</li>
2854 <li>Several GUI bugs resolved</li>
2860 <div align="center">
2861 <strong>2.05</strong><br> 30/8/05
2866 <li>Edit and annotate in "Wrapped" view</li>
2871 <li>Several GUI bugs resolved</li>
2877 <div align="center">
2878 <strong>2.04</strong><br> 24/8/05
2883 <li>Hold down mouse wheel & scroll to change font
2889 <li>Improved JPred client reliability</li>
2890 <li>Improved loading of Jalview files</li>
2896 <div align="center">
2897 <strong>2.03</strong><br> 18/8/05
2902 <li>Set Proxy server name and port in preferences</li>
2903 <li>Multiple URL links from sequence ids</li>
2904 <li>User Defined Colours can have a scheme name and added
2906 <li>Choose to ignore gaps in consensus calculation</li>
2907 <li>Unix users can set default web browser</li>
2908 <li>Runs without GUI for batch processing</li>
2909 <li>Dynamically generated Web Service Menus</li>
2914 <li>InstallAnywhere download for Sparc Solaris</li>
2920 <div align="center">
2921 <strong>2.02</strong><br> 18/7/05
2927 <li>Copy & Paste order of sequences maintains
2928 alignment order.</li>
2934 <div align="center">
2935 <strong>2.01</strong><br> 12/7/05
2940 <li>Use delete key for deleting selection.</li>
2941 <li>Use Mouse wheel to scroll sequences.</li>
2942 <li>Help file updated to describe how to add alignment
2944 <li>Version and build date written to build properties
2946 <li>InstallAnywhere installation will check for updates
2947 at launch of Jalview.</li>
2952 <li>Delete gaps bug fixed.</li>
2953 <li>FileChooser sorts columns.</li>
2954 <li>Can remove groups one by one.</li>
2955 <li>Filechooser icons installed.</li>
2956 <li>Finder ignores return character when searching.
2957 Return key will initiate a search.<br>
2964 <div align="center">
2965 <strong>2.0</strong><br> 20/6/05
2970 <li>New codebase</li>