3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
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27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.2">2.10.2</a><br />
74 <em>30/5/2017</em></strong>
77 <td><div align="left">
80 <li><!-- JAL-2360,JAL-2371, -->More robust colours and shader model for alignments and groups</li>
81 <li><!-- JAL-384 -->Custom shading schemes created via groovy scripts</li>
85 <li><!-- JAL-2447 --><em>Experimental Features</em>Checkbox in Desktop's Tools menu to hide or show untested features in the application<ul>
87 <!-- JAL-2295 -->Entry in Chimera menu to create attributes on a structure in
88 from its associated sequence's features in Jalview
91 <!-- JAL-2296 -->Entry in Chimera menu to create sequence features in Jalview
92 from structure attributes in Chimera
95 <li><!-- JAL-1476 -->Warning in alignment status bar when there are not enough columns to superimpose structures in Chimera</li>
96 <li><!-- JAL-1596 -->Faster Chimera/Jalview communication by file-based command exchange</li>
97 <li><!-- JAL-2316, -->URLs for viewing database cross-references provided by identifiers.org and the EMBL-EBI's MIRIAM DB</li>
105 <ul><li><!-- JAL-2314, -->Test suite expanded and debugged (over 940 functional unit tests, only 3 failing due to ongoing work!)</li>
106 <li><!-- JAL-2474 -->Added PrivelegedAccessor to test suite</li>
107 <li><!-- JAL-2326 -->Prevent or clear modal dialogs raised during tests</li>
110 </div></td><td><div align="left">
114 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
115 matrix - C->R should be '3'<br />Old matrix restored with
116 this one-line groovy script:<br />jalview.schemes.ResidueProperties.BLOSUM62[4][1]=3
119 <!-- JAL-2397 -->Fixed Jalview's treatment of gaps in PCA
120 and substitution matrix based Tree calculations.<br />In
121 earlier versions of Jalview, gaps matching gaps were
122 penalised, and gaps matching non-gaps penalised even more.
123 In the PCA calculation, gaps were actually treated as
124 non-gaps - so different costs were applied, which mean't
125 Jalview's PCAs were different to those produced by
126 SeqSpace.<br />Jalview now treats gaps in the same way as
127 SeqSpace (ie it scores them as 0). To restore pre-2.10.2
129 jalview.viewmodel.PCAModel.scoreGapAsAny=true // for
131 jalview.viewmodel.PCAModel.scoreGapAsAny=false // to
134 <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>
135 <li><!-- JAL-2430 -->Hidden regions in alignment views are not coloured in linked structure views</li>
136 <li><!-- JAL-2419 -->Current selection lost if popup menu opened on a region of alignment without groups</li>
137 <li><!-- JAL-2374 -->Popup menu not always shown for regions of an alignment with overlapping groups</li>
138 <li><!-- JAL-2310 -->Finder double counts if both a sequence's name and description match</li>
139 <li><!-- JAL-2370 -->Hiding column selection containing two hidden regions results in incorrect hidden regions</li>
140 <li><!-- JAL-2377 -->PCA calculation could hang when generating output report when working with highly redundant alignments</li>
141 <li><!-- JAL-2365 -->Cannot configure feature colours with lightGray or darkGray via features file</li>
142 <li><!-- JAL-2421 -->Overview window visible region moves erratically when hidden rows or columns are present</li>
143 <li><!-- JAL-2362 -->Per-residue colourschemes applied via the Structure Viewer's colour menu don't correspond to sequence colouring</li>
144 <li><!-- JAL-2405 -->Protein specific colours only offered in colour and group colour menu for protein alignments</li>
145 <li><!-- JAL-2386 -->'Apply to all groups' setting when changing colour does not apply Conservation slider value to all groups</li>
146 <li><!-- JAL-2385 -->Colour threshold slider doesn't update to reflect currently selected view or group's shading thresholds</li>
147 <li><!-- JAL-2373 -->Percentage identity and conservation menu items do not show a tick or allow shading to be disabled</li>
148 <li><!-- JAL-2385 -->Conservation shading or PID threshold lost when base colourscheme changed if slider not visible</li>
152 <li><!-- JAL-2401 -->Easier creation of colours for all 'Lower case' residues (button in colourscheme editor debugged and new documentation and tooltips added)</li>
153 <li><!-- JAL-2399-->Text colour threshold's 'Cancel' button doesn't restore group-specific text colour thresholds</li>
154 <li><!-- JAL-2243 -->Feature settings panel does not update as new features are added to alignment</li>
155 <li><!-- JAL-2436 -->Structure viewer's View -> Colour By view selection menu changes colours of alignment views</li>
156 <li><!-- JAL-2366 -->Proxy server address and port always appear enabled in Preferences->Connections</li>
157 <li><!-- JAL-2426 -->Spurious exceptions in console raised from alignment calculation workers after alignment has been closed</li>
158 <li><!-- JAL-1608 -->Typo in selection popup menu - Create groups now 'Create Group'</li>
159 <li><!-- JAL-1608 -->CMD/CTRL and G or Shift G for Create/Undefine group doesn't always work</li>
160 <li><!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get shown again after pressing 'Cancel'</li>
161 <li><!-- JAL-2461 -->DAS registry not found exceptions removed from console output</li>
162 <li><!-- JAL-2383 -->Above PID colour threshold not recovered when alignment view imported from project</li>
167 <li><!-- JAL-2442 -->Features not rendered as transparent on overview or linked structure view</li>
168 <li><!-- JAL-2372 -->Colour group by conservation doesn't work (since 2.8)</li>
170 <em>New Known Issues</em>
177 <td width="60" nowrap>
179 <strong><a name="Jalview.2.10.1">2.10.1</a><br />
180 <em>29/11/2016</em></strong>
183 <td><div align="left">
187 <!-- JAL-98 -->Improved memory usage: sparse arrays used
188 for all consensus calculations
191 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released 3rd Oct 2016)
193 <li>Updated Jalview's Certum code signing certificate
199 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
200 set of database cross-references, sorted alphabetically
203 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
204 from database cross references. Users with custom links
205 will receive a <a href="webServices/urllinks.html#warning">warning
206 dialog</a> asking them to update their preferences.
209 <!-- JAL-2287-->Cancel button and escape listener on
210 dialog warning user about disconnecting Jalview from a
214 <!-- JAL-2320-->Jalview's Chimera control window closes if
215 the Chimera it is connected to is shut down
218 <!-- JAL-1738-->New keystroke (B) and Select highlighted
219 columns menu item to mark columns containing
220 highlighted regions (e.g. from structure selections or results
224 <!-- JAL-2284-->Command line option for batch-generation
225 of HTML pages rendering alignment data with the BioJS
235 <!-- JAL-2286 -->Columns with more than one modal residue
236 are not coloured or thresholded according to percent
237 identity (first observed in Jalview 2.8.2)
240 <!-- JAL-2301 -->Threonine incorrectly reported as not
244 <!-- JAL-2318 -->Updates to documentation pages (above PID
245 threshold, amino acid properties)
248 <!-- JAL-2292 -->Lower case residues in sequences are not
249 reported as mapped to residues in a structure file in the
253 <!--JAL-2324 -->Identical features with non-numeric scores
254 could be added multiple times to a sequence
257 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
258 bond features shown as two highlighted residues rather
259 than a range in linked structure views, and treated
260 correctly when selecting and computing trees from features
263 <!-- JAL-2281-->Custom URL links for database
264 cross-references are matched to database name regardless
272 <!-- JAL-2282-->Custom URL links for specific database
273 names without regular expressions also offer links from
277 <!-- JAL-2315-->Removing a single configured link in the
278 URL links pane in Connections preferences doesn't actually
279 update Jalview configuration
282 <!-- JAL-2272-->CTRL-Click on a selected region to open
283 the alignment area popup menu doesn't work on El-Capitan
286 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
287 files with similarly named sequences if dropped onto the
291 <!-- JAL-2312 -->Additional mappings are shown for PDB
292 entries where more chains exist in the PDB accession than
293 are reported in the SIFTS file
296 <!-- JAL-2317-->Certain structures do not get mapped to
297 the structure view when displayed with Chimera
300 <!-- JAL-2317-->No chains shown in the Chimera view
301 panel's View->Show Chains submenu
304 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
305 work for wrapped alignment views
308 <!--JAL-2197 -->Rename UI components for running JPred
309 predictions from 'JNet' to 'JPred'
312 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
313 corrupted when annotation panel vertical scroll is not at
317 <!--JAL-2332 -->Attempting to view structure for Hen
318 lysozyme results in a PDB Client error dialog box
321 <!-- JAL-2319 -->Structure View's mapping report switched ranges for PDB and sequence for SIFTS</li>
322 <!-- JAL-2319 -->SIFTS 'Not_Observed' residues mapped to non-existant coordindate data</li>
324 <!-- <em>New Known Issues</em>
331 <td width="60" nowrap>
333 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
334 <em>25/10/2016</em></strong>
337 <td><em>Application</em>
339 <li>3D Structure chooser opens with 'Cached structures'
340 view if structures already loaded</li>
341 <li>Progress bar reports models as they are loaded to
348 <li>Colour by conservation always enabled and no tick
349 shown in menu when BLOSUM or PID shading applied</li>
350 <li>FER1_ARATH and FER2_ARATH labels were switched in
351 example sequences/projects/trees</li>
355 <li>Jalview projects with views of local PDB structure
356 files saved on Windows cannot be opened on OSX</li>
357 <li>Multiple structure views can be opened and
358 superposed without timeout for structures with multiple
359 models or multiple sequences in alignment</li>
360 <li>Cannot import or associated local PDB files without
361 a PDB ID HEADER line</li>
362 <li>RMSD is not output in Jmol console when
363 superposition is performed</li>
364 <li>Drag and drop of URL from Browser fails for Linux
365 and OSX versions earlier than El Capitan</li>
366 <li>ENA client ignores invalid content from ENA server</li>
367 <li>Exceptions are not raised in console when ENA
368 client attempts to fetch non-existent IDs via Fetch DB
370 <li>Exceptions are not raised in console when a new
371 view is created on the alignment</li>
372 <li>OSX right-click fixed for group selections:
373 CMD-click to insert/remove gaps in groups and CTRL-click
374 to open group pop-up menu</li>
376 <em>Build and deployment</em>
378 <li>URL link checker now copes with multi-line anchor
381 <em>New Known Issues</em>
383 <li>Drag and drop from URL links in browsers do not
390 <td width="60" nowrap>
392 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
398 <!-- JAL-2124 -->Updated Spanish translations.
401 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
402 for importing structure data to Jalview. Enables mmCIF and
406 <!-- JAL-192 --->Alignment ruler shows positions relative to
410 <!-- JAL-2202 -->Position/residue shown in status bar when
411 mousing over sequence associated annotation
414 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
418 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
419 '()', canonical '[]' and invalid '{}' base pair populations
423 <!-- JAL-2092 -->Feature settings popup menu options for
424 showing or hiding columns containing a feature
427 <!-- JAL-1557 -->Edit selected group by double clicking on
428 group and sequence associated annotation labels
431 <!-- JAL-2236 -->Sequence name added to annotation label in
432 select/hide columns by annotation and colour by annotation
436 </ul> <em>Application</em>
439 <!-- JAL-2050-->Automatically hide introns when opening a
443 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
447 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
448 structure mappings with the EMBL-EBI PDBe SIFTS database
451 <!-- JAL-2079 -->Updated download sites used for Rfam and
452 Pfam sources to xfam.org
455 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
458 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
459 over sequences in Jalview
462 <!-- JAL-2027-->Support for reverse-complement coding
463 regions in ENA and EMBL
466 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
467 for record retrieval via ENA rest API
470 <!-- JAL-2027 -->Support for ENA CDS records with reverse
474 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
475 groovy script execution
478 <!-- JAL-1812 -->New 'execute Groovy script' option in an
479 alignment window's Calculate menu
482 <!-- JAL-1812 -->Allow groovy scripts that call
483 Jalview.getAlignFrames() to run in headless mode
486 <!-- JAL-2068 -->Support for creating new alignment
487 calculation workers from groovy scripts
490 <!-- JAL-1369 --->Store/restore reference sequence in
494 <!-- JAL-1803 -->Chain codes for a sequence's PDB
495 associations are now saved/restored from project
498 <!-- JAL-1993 -->Database selection dialog always shown
499 before sequence fetcher is opened
502 <!-- JAL-2183 -->Double click on an entry in Jalview's
503 database chooser opens a sequence fetcher
506 <!-- JAL-1563 -->Free-text search client for UniProt using
510 <!-- JAL-2168 -->-nonews command line parameter to prevent
511 the news reader opening
514 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
515 querying stored in preferences
518 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
522 <!-- JAL-1977-->Tooltips shown on database chooser
525 <!-- JAL-391 -->Reverse complement function in calculate
526 menu for nucleotide sequences
529 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
530 and feature counts preserves alignment ordering (and
531 debugged for complex feature sets).
534 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
535 viewing structures with Jalview 2.10
538 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
539 genome, transcript CCDS and gene ids via the Ensembl and
540 Ensembl Genomes REST API
543 <!-- JAL-2049 -->Protein sequence variant annotation
544 computed for 'sequence_variant' annotation on CDS regions
548 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
552 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
553 Ref Fetcher fails to match, or otherwise updates sequence
554 data from external database records.
557 <!-- JAL-2154 -->Revised Jalview Project format for
558 efficient recovery of sequence coding and alignment
559 annotation relationships.
561 </ul> <!-- <em>Applet</em>
572 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
576 <!-- JAL-2018-->Export features in Jalview format (again)
577 includes graduated colourschemes
580 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
581 working with big alignments and lots of hidden columns
584 <!-- JAL-2053-->Hidden column markers not always rendered
585 at right of alignment window
588 <!-- JAL-2067 -->Tidied up links in help file table of
592 <!-- JAL-2072 -->Feature based tree calculation not shown
596 <!-- JAL-2075 -->Hidden columns ignored during feature
597 based tree calculation
600 <!-- JAL-2065 -->Alignment view stops updating when show
601 unconserved enabled for group on alignment
604 <!-- JAL-2086 -->Cannot insert gaps into sequence when
608 <!-- JAL-2146 -->Alignment column in status incorrectly
609 shown as "Sequence position" when mousing over
613 <!-- JAL-2099 -->Incorrect column numbers in ruler when
614 hidden columns present
617 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
618 user created annotation added to alignment
621 <!-- JAL-1841 -->RNA Structure consensus only computed for
622 '()' base pair annotation
625 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
626 in zero scores for all base pairs in RNA Structure
630 <!-- JAL-2174-->Extend selection with columns containing
634 <!-- JAL-2275 -->Pfam format writer puts extra space at
635 beginning of sequence
638 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
642 <!-- JAL-2238 -->Cannot create groups on an alignment from
643 from a tree when t-coffee scores are shown
646 <!-- JAL-1836,1967 -->Cannot import and view PDB
647 structures with chains containing negative resnums (4q4h)
650 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
654 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
655 to Clustal, PIR and PileUp output
658 <!-- JAL-2008 -->Reordering sequence features that are
659 not visible causes alignment window to repaint
662 <!-- JAL-2006 -->Threshold sliders don't work in
663 graduated colour and colour by annotation row for e-value
664 scores associated with features and annotation rows
667 <!-- JAL-1797 -->amino acid physicochemical conservation
668 calculation should be case independent
671 <!-- JAL-2173 -->Remove annotation also updates hidden
675 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
676 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
677 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
680 <!-- JAL-2065 -->Null pointer exceptions and redraw
681 problems when reference sequence defined and 'show
682 non-conserved' enabled
685 <!-- JAL-1306 -->Quality and Conservation are now shown on
686 load even when Consensus calculation is disabled
689 <!-- JAL-1932 -->Remove right on penultimate column of
690 alignment does nothing
696 <!-- JAL-1552-->URLs and links can't be imported by
697 drag'n'drop on OSX when launched via webstart (note - not
698 yet fixed for El Capitan)
701 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
702 output when running on non-gb/us i18n platforms
705 <!-- JAL-1944 -->Error thrown when exporting a view with
706 hidden sequences as flat-file alignment
709 <!-- JAL-2030-->InstallAnywhere distribution fails when
713 <!-- JAL-2080-->Jalview very slow to launch via webstart
714 (also hotfix for 2.9.0b2)
717 <!-- JAL-2085 -->Cannot save project when view has a
718 reference sequence defined
721 <!-- JAL-1011 -->Columns are suddenly selected in other
722 alignments and views when revealing hidden columns
725 <!-- JAL-1989 -->Hide columns not mirrored in complement
726 view in a cDNA/Protein splitframe
729 <!-- JAL-1369 -->Cannot save/restore representative
730 sequence from project when only one sequence is
734 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
738 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
739 structure consensus didn't refresh annotation panel
742 <!-- JAL-1962 -->View mapping in structure view shows
743 mappings between sequence and all chains in a PDB file
746 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
747 dialogs format columns correctly, don't display array
748 data, sort columns according to type
751 <!-- JAL-1975 -->Export complete shown after destination
752 file chooser is cancelled during an image export
755 <!-- JAL-2025 -->Error when querying PDB Service with
756 sequence name containing special characters
759 <!-- JAL-2024 -->Manual PDB structure querying should be
763 <!-- JAL-2104 -->Large tooltips with broken HTML
764 formatting don't wrap
767 <!-- JAL-1128 -->Figures exported from wrapped view are
768 truncated so L looks like I in consensus annotation
771 <!-- JAL-2003 -->Export features should only export the
772 currently displayed features for the current selection or
776 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
777 after fetching cross-references, and restoring from project
780 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
781 followed in the structure viewer
784 <!-- JAL-2163 -->Titles for individual alignments in
785 splitframe not restored from project
788 <!-- JAL-2145 -->missing autocalculated annotation at
789 trailing end of protein alignment in transcript/product
790 splitview when pad-gaps not enabled by default
793 <!-- JAL-1797 -->amino acid physicochemical conservation
797 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
798 article has been read (reopened issue due to
799 internationalisation problems)
802 <!-- JAL-1960 -->Only offer PDB structures in structure
803 viewer based on sequence name, PDB and UniProt
808 <!-- JAL-1976 -->No progress bar shown during export of
812 <!-- JAL-2213 -->Structures not always superimposed after
813 multiple structures are shown for one or more sequences.
816 <!-- JAL-1370 -->Reference sequence characters should not
817 be replaced with '.' when 'Show unconserved' format option
821 <!-- JAL-1823 -->Cannot specify chain code when entering
822 specific PDB id for sequence
825 <!-- JAL-1944 -->File->Export->.. as doesn't work when
826 'Export hidden sequences' is enabled, but 'export hidden
827 columns' is disabled.
830 <!--JAL-2026-->Best Quality option in structure chooser
831 selects lowest rather than highest resolution structures
835 <!-- JAL-1887 -->Incorrect start and end reported for PDB
836 to sequence mapping in 'View Mappings' report
839 <!-- JAL-2284 -->Unable to read old Jalview projects that
840 contain non-XML data added after Jalvew wrote project.
842 <li><!-- JAL-2118 -->Newly created annotation row reorders
843 after clicking on it to create new annotation for a
846 <!-- may exclude, this is an external service stability issue JAL-1941
847 -- > RNA 3D structure not added via DSSR service</li> -->
852 <!-- JAL-2151 -->Incorrect columns are selected when
853 hidden columns present before start of sequence
856 <!-- JAL-1986 -->Missing dependencies on applet pages
860 <!-- JAL-1947 -->Overview pixel size changes when
861 sequences are hidden in applet
864 <!-- JAL-1996 -->Updated instructions for applet
865 deployment on examples pages.
872 <td width="60" nowrap>
874 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
875 <em>16/10/2015</em></strong>
880 <li>Time stamps for signed Jalview application and applet
887 <li>Duplicate group consensus and conservation rows
888 shown when tree is partitioned</li>
889 <li>Erratic behaviour when tree partitions made with
890 multiple cDNA/Protein split views</li>
896 <td width="60" nowrap>
898 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
899 <em>8/10/2015</em></strong>
904 <li>Updated Spanish translations of localized text for
906 </ul> <em>Application</em>
908 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
909 <li>Signed OSX InstallAnywhere installer<br></li>
910 <li>Support for per-sequence based annotations in BioJSON</li>
911 </ul> <em>Applet</em>
913 <li>Split frame example added to applet examples page</li>
914 </ul><em>Build and Deployment</em>
916 <li><!-- JAL-1888 -->New ant target for running Jalview's test suite</li>
922 <li>Mapping of cDNA to protein in split frames
923 incorrect when sequence start > 1</li>
924 <li>Broken images in filter column by annotation dialog
926 <li>Feature colours not parsed from features file</li>
927 <li>Exceptions and incomplete link URLs recovered when
928 loading a features file containing HTML tags in feature
934 <li>Annotations corrupted after BioJS export and
936 <li>Incorrect sequence limits after Fetch DB References
937 with 'trim retrieved sequences'</li>
938 <li>Incorrect warning about deleting all data when
939 deleting selected columns</li>
940 <li>Patch to build system for shipping properly signed
941 JNLP templates for webstart launch</li>
942 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
943 unreleased structures for download or viewing</li>
944 <li>Tab/space/return keystroke operation of EMBL-PDBe
945 fetcher/viewer dialogs works correctly</li>
946 <li>Disabled 'minimise' button on Jalview windows
947 running on OSX to workaround redraw hang bug</li>
948 <li>Split cDNA/Protein view position and geometry not
949 recovered from jalview project</li>
950 <li>Initial enabled/disabled state of annotation menu
951 sorter 'show autocalculated first/last' corresponds to
953 <li>Restoring of Clustal, RNA Helices and T-Coffee
954 color schemes from BioJSON</li>
958 <li>Reorder sequences mirrored in cDNA/Protein split
960 <li>Applet with Jmol examples not loading correctly</li>
966 <td><div align="center">
967 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
971 <li>Linked visualisation and analysis of DNA and Protein
974 <li>Translated cDNA alignments shown as split protein
975 and DNA alignment views</li>
976 <li>Codon consensus annotation for linked protein and
977 cDNA alignment views</li>
978 <li>Link cDNA or Protein product sequences by loading
979 them onto Protein or cDNA alignments</li>
980 <li>Reconstruct linked cDNA alignment from aligned
981 protein sequences</li>
984 <li>Jmol integration updated to Jmol v14.2.14</li>
985 <li>Import and export of Jalview alignment views as <a
986 href="features/bioJsonFormat.html">BioJSON</a></li>
987 <li>New alignment annotation file statements for
988 reference sequences and marking hidden columns</li>
989 <li>Reference sequence based alignment shading to
990 highlight variation</li>
991 <li>Select or hide columns according to alignment
993 <li>Find option for locating sequences by description</li>
994 <li>Conserved physicochemical properties shown in amino
995 acid conservation row</li>
996 <li>Alignments can be sorted by number of RNA helices</li>
997 </ul> <em>Application</em>
999 <li>New cDNA/Protein analysis capabilities
1001 <li>Get Cross-References should open a Split Frame
1002 view with cDNA/Protein</li>
1003 <li>Detect when nucleotide sequences and protein
1004 sequences are placed in the same alignment</li>
1005 <li>Split cDNA/Protein views are saved in Jalview
1010 <li>Use REST API to talk to Chimera</li>
1011 <li>Selected regions in Chimera are highlighted in linked
1012 Jalview windows</li>
1014 <li>VARNA RNA viewer updated to v3.93</li>
1015 <li>VARNA views are saved in Jalview Projects</li>
1016 <li>Pseudoknots displayed as Jalview RNA annotation can
1017 be shown in VARNA</li>
1019 <li>Make groups for selection uses marked columns as well
1020 as the active selected region</li>
1022 <li>Calculate UPGMA and NJ trees using sequence feature
1024 <li>New Export options
1026 <li>New Export Settings dialog to control hidden
1027 region export in flat file generation</li>
1029 <li>Export alignment views for display with the <a
1030 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1032 <li>Export scrollable SVG in HTML page</li>
1033 <li>Optional embedding of BioJSON data when exporting
1034 alignment figures to HTML</li>
1036 <li>3D structure retrieval and display
1038 <li>Free text and structured queries with the PDBe
1040 <li>PDBe Search API based discovery and selection of
1041 PDB structures for a sequence set</li>
1045 <li>JPred4 employed for protein secondary structure
1047 <li>Hide Insertions menu option to hide unaligned columns
1048 for one or a group of sequences</li>
1049 <li>Automatically hide insertions in alignments imported
1050 from the JPred4 web server</li>
1051 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1052 system on OSX<br />LGPL libraries courtesy of <a
1053 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1055 <li>changed 'View nucleotide structure' submenu to 'View
1056 VARNA 2D Structure'</li>
1057 <li>change "View protein structure" menu option to "3D
1060 </ul> <em>Applet</em>
1062 <li>New layout for applet example pages</li>
1063 <li>New parameters to enable SplitFrame view
1064 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1065 <li>New example demonstrating linked viewing of cDNA and
1066 Protein alignments</li>
1067 </ul> <em>Development and deployment</em>
1069 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1070 <li>Include installation type and git revision in build
1071 properties and console log output</li>
1072 <li>Jalview Github organisation, and new github site for
1073 storing BioJsMSA Templates</li>
1074 <li>Jalview's unit tests now managed with TestNG</li>
1077 <!-- <em>General</em>
1079 </ul> --> <!-- issues resolved --> <em>Application</em>
1081 <li>Escape should close any open find dialogs</li>
1082 <li>Typo in select-by-features status report</li>
1083 <li>Consensus RNA secondary secondary structure
1084 predictions are not highlighted in amber</li>
1085 <li>Missing gap character in v2.7 example file means
1086 alignment appears unaligned when pad-gaps is not enabled</li>
1087 <li>First switch to RNA Helices colouring doesn't colour
1088 associated structure views</li>
1089 <li>ID width preference option is greyed out when auto
1090 width checkbox not enabled</li>
1091 <li>Stopped a warning dialog from being shown when
1092 creating user defined colours</li>
1093 <li>'View Mapping' in structure viewer shows sequence
1094 mappings for just that viewer's sequences</li>
1095 <li>Workaround for superposing PDB files containing
1096 multiple models in Chimera</li>
1097 <li>Report sequence position in status bar when hovering
1098 over Jmol structure</li>
1099 <li>Cannot output gaps as '.' symbols with Selection ->
1100 output to text box</li>
1101 <li>Flat file exports of alignments with hidden columns
1102 have incorrect sequence start/end</li>
1103 <li>'Aligning' a second chain to a Chimera structure from
1105 <li>Colour schemes applied to structure viewers don't
1106 work for nucleotide</li>
1107 <li>Loading/cut'n'pasting an empty or invalid file leads
1108 to a grey/invisible alignment window</li>
1109 <li>Exported Jpred annotation from a sequence region
1110 imports to different position</li>
1111 <li>Space at beginning of sequence feature tooltips shown
1112 on some platforms</li>
1113 <li>Chimera viewer 'View | Show Chain' menu is not
1115 <li>'New View' fails with a Null Pointer Exception in
1116 console if Chimera has been opened</li>
1117 <li>Mouseover to Chimera not working</li>
1118 <li>Miscellaneous ENA XML feature qualifiers not
1120 <li>NPE in annotation renderer after 'Extract Scores'</li>
1121 <li>If two structures in one Chimera window, mouseover of
1122 either sequence shows on first structure</li>
1123 <li>'Show annotations' options should not make
1124 non-positional annotations visible</li>
1125 <li>Subsequence secondary structure annotation not shown
1126 in right place after 'view flanking regions'</li>
1127 <li>File Save As type unset when current file format is
1129 <li>Save as '.jar' option removed for saving Jalview
1131 <li>Colour by Sequence colouring in Chimera more
1133 <li>Cannot 'add reference annotation' for a sequence in
1134 several views on same alignment</li>
1135 <li>Cannot show linked products for EMBL / ENA records</li>
1136 <li>Jalview's tooltip wraps long texts containing no
1138 </ul> <em>Applet</em>
1140 <li>Jmol to JalviewLite mouseover/link not working</li>
1141 <li>JalviewLite can't import sequences with ID
1142 descriptions containing angle brackets</li>
1143 </ul> <em>General</em>
1145 <li>Cannot export and reimport RNA secondary structure
1146 via jalview annotation file</li>
1147 <li>Random helix colour palette for colour by annotation
1148 with RNA secondary structure</li>
1149 <li>Mouseover to cDNA from STOP residue in protein
1150 translation doesn't work.</li>
1151 <li>hints when using the select by annotation dialog box</li>
1152 <li>Jmol alignment incorrect if PDB file has alternate CA
1154 <li>FontChooser message dialog appears to hang after
1155 choosing 1pt font</li>
1156 <li>Peptide secondary structure incorrectly imported from
1157 annotation file when annotation display text includes 'e' or
1159 <li>Cannot set colour of new feature type whilst creating
1161 <li>cDNA translation alignment should not be sequence
1162 order dependent</li>
1163 <li>'Show unconserved' doesn't work for lower case
1165 <li>Nucleotide ambiguity codes involving R not recognised</li>
1166 </ul> <em>Deployment and Documentation</em>
1168 <li>Applet example pages appear different to the rest of
1169 www.jalview.org</li>
1170 </ul> <em>Application Known issues</em>
1172 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1173 <li>Misleading message appears after trying to delete
1175 <li>Jalview icon not shown in dock after InstallAnywhere
1176 version launches</li>
1177 <li>Fetching EMBL reference for an RNA sequence results
1178 fails with a sequence mismatch</li>
1179 <li>Corrupted or unreadable alignment display when
1180 scrolling alignment to right</li>
1181 <li>ArrayIndexOutOfBoundsException thrown when remove
1182 empty columns called on alignment with ragged gapped ends</li>
1183 <li>auto calculated alignment annotation rows do not get
1184 placed above or below non-autocalculated rows</li>
1185 <li>Jalview dekstop becomes sluggish at full screen in
1186 ultra-high resolution</li>
1187 <li>Cannot disable consensus calculation independently of
1188 quality and conservation</li>
1189 <li>Mouseover highlighting between cDNA and protein can
1190 become sluggish with more than one splitframe shown</li>
1191 </ul> <em>Applet Known Issues</em>
1193 <li>Core PDB parsing code requires Jmol</li>
1194 <li>Sequence canvas panel goes white when alignment
1195 window is being resized</li>
1201 <td><div align="center">
1202 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1204 <td><em>General</em>
1206 <li>Updated Java code signing certificate donated by
1208 <li>Features and annotation preserved when performing
1209 pairwise alignment</li>
1210 <li>RNA pseudoknot annotation can be
1211 imported/exported/displayed</li>
1212 <li>'colour by annotation' can colour by RNA and
1213 protein secondary structure</li>
1214 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1215 post-hoc with 2.9 release</em>)
1218 </ul> <em>Application</em>
1220 <li>Extract and display secondary structure for sequences
1221 with 3D structures</li>
1222 <li>Support for parsing RNAML</li>
1223 <li>Annotations menu for layout
1225 <li>sort sequence annotation rows by alignment</li>
1226 <li>place sequence annotation above/below alignment
1229 <li>Output in Stockholm format</li>
1230 <li>Internationalisation: improved Spanish (es)
1232 <li>Structure viewer preferences tab</li>
1233 <li>Disorder and Secondary Structure annotation tracks
1234 shared between alignments</li>
1235 <li>UCSF Chimera launch and linked highlighting from
1237 <li>Show/hide all sequence associated annotation rows for
1238 all or current selection</li>
1239 <li>disorder and secondary structure predictions
1240 available as dataset annotation</li>
1241 <li>Per-sequence rna helices colouring</li>
1244 <li>Sequence database accessions imported when fetching
1245 alignments from Rfam</li>
1246 <li>update VARNA version to 3.91</li>
1248 <li>New groovy scripts for exporting aligned positions,
1249 conservation values, and calculating sum of pairs scores.</li>
1250 <li>Command line argument to set default JABAWS server</li>
1251 <li>include installation type in build properties and
1252 console log output</li>
1253 <li>Updated Jalview project format to preserve dataset
1257 <!-- issues resolved --> <em>Application</em>
1259 <li>Distinguish alignment and sequence associated RNA
1260 structure in structure->view->VARNA</li>
1261 <li>Raise dialog box if user deletes all sequences in an
1263 <li>Pressing F1 results in documentation opening twice</li>
1264 <li>Sequence feature tooltip is wrapped</li>
1265 <li>Double click on sequence associated annotation
1266 selects only first column</li>
1267 <li>Redundancy removal doesn't result in unlinked
1268 leaves shown in tree</li>
1269 <li>Undos after several redundancy removals don't undo
1271 <li>Hide sequence doesn't hide associated annotation</li>
1272 <li>User defined colours dialog box too big to fit on
1273 screen and buttons not visible</li>
1274 <li>author list isn't updated if already written to
1275 Jalview properties</li>
1276 <li>Popup menu won't open after retrieving sequence
1278 <li>File open window for associate PDB doesn't open</li>
1279 <li>Left-then-right click on a sequence id opens a
1280 browser search window</li>
1281 <li>Cannot open sequence feature shading/sort popup menu
1282 in feature settings dialog</li>
1283 <li>better tooltip placement for some areas of Jalview
1285 <li>Allow addition of JABAWS Server which doesn't
1286 pass validation</li>
1287 <li>Web services parameters dialog box is too large to
1289 <li>Muscle nucleotide alignment preset obscured by
1291 <li>JABAWS preset submenus don't contain newly
1292 defined user preset</li>
1293 <li>MSA web services warns user if they were launched
1294 with invalid input</li>
1295 <li>Jalview cannot contact DAS Registy when running on
1298 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1299 'Superpose with' submenu not shown when new view
1303 </ul> <!-- <em>Applet</em>
1305 </ul> <em>General</em>
1307 </ul>--> <em>Deployment and Documentation</em>
1309 <li>2G and 1G options in launchApp have no effect on
1310 memory allocation</li>
1311 <li>launchApp service doesn't automatically open
1312 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1314 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1315 InstallAnywhere reports cannot find valid JVM when Java
1316 1.7_055 is available
1318 </ul> <em>Application Known issues</em>
1321 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1322 corrupted or unreadable alignment display when scrolling
1326 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1327 retrieval fails but progress bar continues for DAS retrieval
1328 with large number of ID
1331 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1332 flatfile output of visible region has incorrect sequence
1336 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1337 rna structure consensus doesn't update when secondary
1338 structure tracks are rearranged
1341 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1342 invalid rna structure positional highlighting does not
1343 highlight position of invalid base pairs
1346 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1347 out of memory errors are not raised when saving Jalview
1348 project from alignment window file menu
1351 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1352 Switching to RNA Helices colouring doesn't propagate to
1356 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1357 colour by RNA Helices not enabled when user created
1358 annotation added to alignment
1361 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1362 Jalview icon not shown on dock in Mountain Lion/Webstart
1364 </ul> <em>Applet Known Issues</em>
1367 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1368 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1371 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1372 Jalview and Jmol example not compatible with IE9
1375 <li>Sort by annotation score doesn't reverse order
1381 <td><div align="center">
1382 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1385 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1388 <li>Internationalisation of user interface (usually
1389 called i18n support) and translation for Spanish locale</li>
1390 <li>Define/Undefine group on current selection with
1391 Ctrl-G/Shift Ctrl-G</li>
1392 <li>Improved group creation/removal options in
1393 alignment/sequence Popup menu</li>
1394 <li>Sensible precision for symbol distribution
1395 percentages shown in logo tooltip.</li>
1396 <li>Annotation panel height set according to amount of
1397 annotation when alignment first opened</li>
1398 </ul> <em>Application</em>
1400 <li>Interactive consensus RNA secondary structure
1401 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1402 <li>Select columns containing particular features from
1403 Feature Settings dialog</li>
1404 <li>View all 'representative' PDB structures for selected
1406 <li>Update Jalview project format:
1408 <li>New file extension for Jalview projects '.jvp'</li>
1409 <li>Preserve sequence and annotation dataset (to
1410 store secondary structure annotation,etc)</li>
1411 <li>Per group and alignment annotation and RNA helix
1415 <li>New similarity measures for PCA and Tree calculation
1417 <li>Experimental support for retrieval and viewing of
1418 flanking regions for an alignment</li>
1422 <!-- issues resolved --> <em>Application</em>
1424 <li>logo keeps spinning and status remains at queued or
1425 running after job is cancelled</li>
1426 <li>cannot export features from alignments imported from
1427 Jalview/VAMSAS projects</li>
1428 <li>Buggy slider for web service parameters that take
1430 <li>Newly created RNA secondary structure line doesn't
1431 have 'display all symbols' flag set</li>
1432 <li>T-COFFEE alignment score shading scheme and other
1433 annotation shading not saved in Jalview project</li>
1434 <li>Local file cannot be loaded in freshly downloaded
1436 <li>Jalview icon not shown on dock in Mountain
1438 <li>Load file from desktop file browser fails</li>
1439 <li>Occasional NPE thrown when calculating large trees</li>
1440 <li>Cannot reorder or slide sequences after dragging an
1441 alignment onto desktop</li>
1442 <li>Colour by annotation dialog throws NPE after using
1443 'extract scores' function</li>
1444 <li>Loading/cut'n'pasting an empty file leads to a grey
1445 alignment window</li>
1446 <li>Disorder thresholds rendered incorrectly after
1447 performing IUPred disorder prediction</li>
1448 <li>Multiple group annotated consensus rows shown when
1449 changing 'normalise logo' display setting</li>
1450 <li>Find shows blank dialog after 'finished searching' if
1451 nothing matches query</li>
1452 <li>Null Pointer Exceptions raised when sorting by
1453 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1455 <li>Errors in Jmol console when structures in alignment
1456 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1458 <li>Not all working JABAWS services are shown in
1460 <li>JAVAWS version of Jalview fails to launch with
1461 'invalid literal/length code'</li>
1462 <li>Annotation/RNA Helix colourschemes cannot be applied
1463 to alignment with groups (actually fixed in 2.8.0b1)</li>
1464 <li>RNA Helices and T-Coffee Scores available as default
1467 </ul> <em>Applet</em>
1469 <li>Remove group option is shown even when selection is
1471 <li>Apply to all groups ticked but colourscheme changes
1472 don't affect groups</li>
1473 <li>Documented RNA Helices and T-Coffee Scores as valid
1474 colourscheme name</li>
1475 <li>Annotation labels drawn on sequence IDs when
1476 Annotation panel is not displayed</li>
1477 <li>Increased font size for dropdown menus on OSX and
1478 embedded windows</li>
1479 </ul> <em>Other</em>
1481 <li>Consensus sequence for alignments/groups with a
1482 single sequence were not calculated</li>
1483 <li>annotation files that contain only groups imported as
1484 annotation and junk sequences</li>
1485 <li>Fasta files with sequences containing '*' incorrectly
1486 recognised as PFAM or BLC</li>
1487 <li>conservation/PID slider apply all groups option
1488 doesn't affect background (2.8.0b1)
1490 <li>redundancy highlighting is erratic at 0% and 100%</li>
1491 <li>Remove gapped columns fails for sequences with ragged
1493 <li>AMSA annotation row with leading spaces is not
1494 registered correctly on import</li>
1495 <li>Jalview crashes when selecting PCA analysis for
1496 certain alignments</li>
1497 <li>Opening the colour by annotation dialog for an
1498 existing annotation based 'use original colours'
1499 colourscheme loses original colours setting</li>
1504 <td><div align="center">
1505 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
1506 <em>30/1/2014</em></strong>
1510 <li>Trusted certificates for JalviewLite applet and
1511 Jalview Desktop application<br />Certificate was donated by
1512 <a href="https://www.certum.eu">Certum</a> to the Jalview
1513 open source project).
1515 <li>Jalview SRS links replaced by UniProt and EBI-search
1517 <li>Output in Stockholm format</li>
1518 <li>Allow import of data from gzipped files</li>
1519 <li>Export/import group and sequence associated line
1520 graph thresholds</li>
1521 <li>Nucleotide substitution matrix that supports RNA and
1522 ambiguity codes</li>
1523 <li>Allow disorder predictions to be made on the current
1524 selection (or visible selection) in the same way that JPred
1526 <li>Groovy scripting for headless Jalview operation</li>
1527 </ul> <em>Other improvements</em>
1529 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
1530 <li>COMBINE statement uses current SEQUENCE_REF and
1531 GROUP_REF scope to group annotation rows</li>
1532 <li>Support '' style escaping of quotes in Newick
1534 <li>Group options for JABAWS service by command line name</li>
1535 <li>Empty tooltip shown for JABA service options with a
1536 link but no description</li>
1537 <li>Select primary source when selecting authority in
1538 database fetcher GUI</li>
1539 <li>Add .mfa to FASTA file extensions recognised by
1541 <li>Annotation label tooltip text wrap</li>
1546 <li>Slow scrolling when lots of annotation rows are
1548 <li>Lots of NPE (and slowness) after creating RNA
1549 secondary structure annotation line</li>
1550 <li>Sequence database accessions not imported when
1551 fetching alignments from Rfam</li>
1552 <li>Incorrect SHMR submission for sequences with
1554 <li>View all structures does not always superpose
1556 <li>Option widgets in service parameters not updated to
1557 reflect user or preset settings</li>
1558 <li>Null pointer exceptions for some services without
1559 presets or adjustable parameters</li>
1560 <li>Discover PDB IDs entry in structure menu doesn't
1561 discover PDB xRefs</li>
1562 <li>Exception encountered while trying to retrieve
1563 features with DAS</li>
1564 <li>Lowest value in annotation row isn't coloured
1565 when colour by annotation (per sequence) is coloured</li>
1566 <li>Keyboard mode P jumps to start of gapped region when
1567 residue follows a gap</li>
1568 <li>Jalview appears to hang importing an alignment with
1569 Wrap as default or after enabling Wrap</li>
1570 <li>'Right click to add annotations' message
1571 shown in wrap mode when no annotations present</li>
1572 <li>Disorder predictions fail with NPE if no automatic
1573 annotation already exists on alignment</li>
1574 <li>oninit javascript function should be called after
1575 initialisation completes</li>
1576 <li>Remove redundancy after disorder prediction corrupts
1577 alignment window display</li>
1578 <li>Example annotation file in documentation is invalid</li>
1579 <li>Grouped line graph annotation rows are not exported
1580 to annotation file</li>
1581 <li>Multi-harmony analysis cannot be run when only two
1583 <li>Cannot create multiple groups of line graphs with
1584 several 'combine' statements in annotation file</li>
1585 <li>Pressing return several times causes Number Format
1586 exceptions in keyboard mode</li>
1587 <li>Multi-harmony (SHMMR) method doesn't submit
1588 correct partitions for input data</li>
1589 <li>Translation from DNA to Amino Acids fails</li>
1590 <li>Jalview fail to load newick tree with quoted label</li>
1591 <li>--headless flag isn't understood</li>
1592 <li>ClassCastException when generating EPS in headless
1594 <li>Adjusting sequence-associated shading threshold only
1595 changes one row's threshold</li>
1596 <li>Preferences and Feature settings panel panel
1597 doesn't open</li>
1598 <li>hide consensus histogram also hides conservation and
1599 quality histograms</li>
1604 <td><div align="center">
1605 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
1607 <td><em>Application</em>
1609 <li>Support for JABAWS 2.0 Services (AACon alignment
1610 conservation, protein disorder and Clustal Omega)</li>
1611 <li>JABAWS server status indicator in Web Services
1613 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
1614 in Jalview alignment window</li>
1615 <li>Updated Jalview build and deploy framework for OSX
1616 mountain lion, windows 7, and 8</li>
1617 <li>Nucleotide substitution matrix for PCA that supports
1618 RNA and ambiguity codes</li>
1620 <li>Improved sequence database retrieval GUI</li>
1621 <li>Support fetching and database reference look up
1622 against multiple DAS sources (Fetch all from in 'fetch db
1624 <li>Jalview project improvements
1626 <li>Store and retrieve the 'belowAlignment'
1627 flag for annotation</li>
1628 <li>calcId attribute to group annotation rows on the
1630 <li>Store AACon calculation settings for a view in
1631 Jalview project</li>
1635 <li>horizontal scrolling gesture support</li>
1636 <li>Visual progress indicator when PCA calculation is
1638 <li>Simpler JABA web services menus</li>
1639 <li>visual indication that web service results are still
1640 being retrieved from server</li>
1641 <li>Serialise the dialogs that are shown when Jalview
1642 starts up for first time</li>
1643 <li>Jalview user agent string for interacting with HTTP
1645 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
1647 <li>Examples directory and Groovy library included in
1648 InstallAnywhere distribution</li>
1649 </ul> <em>Applet</em>
1651 <li>RNA alignment and secondary structure annotation
1652 visualization applet example</li>
1653 </ul> <em>General</em>
1655 <li>Normalise option for consensus sequence logo</li>
1656 <li>Reset button in PCA window to return dimensions to
1658 <li>Allow seqspace or Jalview variant of alignment PCA
1660 <li>PCA with either nucleic acid and protein substitution
1662 <li>Allow windows containing HTML reports to be exported
1664 <li>Interactive display and editing of RNA secondary
1665 structure contacts</li>
1666 <li>RNA Helix Alignment Colouring</li>
1667 <li>RNA base pair logo consensus</li>
1668 <li>Parse sequence associated secondary structure
1669 information in Stockholm files</li>
1670 <li>HTML Export database accessions and annotation
1671 information presented in tooltip for sequences</li>
1672 <li>Import secondary structure from LOCARNA clustalw
1673 style RNA alignment files</li>
1674 <li>import and visualise T-COFFEE quality scores for an
1676 <li>'colour by annotation' per sequence option to
1677 shade each sequence according to its associated alignment
1679 <li>New Jalview Logo</li>
1680 </ul> <em>Documentation and Development</em>
1682 <li>documentation for score matrices used in Jalview</li>
1683 <li>New Website!</li>
1685 <td><em>Application</em>
1687 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
1688 wsdbfetch REST service</li>
1689 <li>Stop windows being moved outside desktop on OSX</li>
1690 <li>Filetype associations not installed for webstart
1692 <li>Jalview does not always retrieve progress of a JABAWS
1693 job execution in full once it is complete</li>
1694 <li>revise SHMR RSBS definition to ensure alignment is
1695 uploaded via ali_file parameter</li>
1696 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
1697 <li>View all structures superposed fails with exception</li>
1698 <li>Jnet job queues forever if a very short sequence is
1699 submitted for prediction</li>
1700 <li>Cut and paste menu not opened when mouse clicked on
1702 <li>Putting fractional value into integer text box in
1703 alignment parameter dialog causes Jalview to hang</li>
1704 <li>Structure view highlighting doesn't work on
1706 <li>View all structures fails with exception shown in
1708 <li>Characters in filename associated with PDBEntry not
1709 escaped in a platform independent way</li>
1710 <li>Jalview desktop fails to launch with exception when
1712 <li>Tree calculation reports 'you must have 2 or more
1713 sequences selected' when selection is empty</li>
1714 <li>Jalview desktop fails to launch with jar signature
1715 failure when java web start temporary file caching is
1717 <li>DAS Sequence retrieval with range qualification
1718 results in sequence xref which includes range qualification</li>
1719 <li>Errors during processing of command line arguments
1720 cause progress bar (JAL-898) to be removed</li>
1721 <li>Replace comma for semi-colon option not disabled for
1722 DAS sources in sequence fetcher</li>
1723 <li>Cannot close news reader when JABAWS server warning
1724 dialog is shown</li>
1725 <li>Option widgets not updated to reflect user settings</li>
1726 <li>Edited sequence not submitted to web service</li>
1727 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
1728 <li>InstallAnywhere installer doesn't unpack and run
1729 on OSX Mountain Lion</li>
1730 <li>Annotation panel not given a scroll bar when
1731 sequences with alignment annotation are pasted into the
1733 <li>Sequence associated annotation rows not associated
1734 when loaded from Jalview project</li>
1735 <li>Browser launch fails with NPE on java 1.7</li>
1736 <li>JABAWS alignment marked as finished when job was
1737 cancelled or job failed due to invalid input</li>
1738 <li>NPE with v2.7 example when clicking on Tree
1739 associated with all views</li>
1740 <li>Exceptions when copy/paste sequences with grouped
1741 annotation rows to new window</li>
1742 </ul> <em>Applet</em>
1744 <li>Sequence features are momentarily displayed before
1745 they are hidden using hidefeaturegroups applet parameter</li>
1746 <li>loading features via javascript API automatically
1747 enables feature display</li>
1748 <li>scrollToColumnIn javascript API method doesn't
1750 </ul> <em>General</em>
1752 <li>Redundancy removal fails for rna alignment</li>
1753 <li>PCA calculation fails when sequence has been selected
1754 and then deselected</li>
1755 <li>PCA window shows grey box when first opened on OSX</li>
1756 <li>Letters coloured pink in sequence logo when alignment
1757 coloured with clustalx</li>
1758 <li>Choosing fonts without letter symbols defined causes
1759 exceptions and redraw errors</li>
1760 <li>Initial PCA plot view is not same as manually
1761 reconfigured view</li>
1762 <li>Grouped annotation graph label has incorrect line
1764 <li>Grouped annotation graph label display is corrupted
1765 for lots of labels</li>
1770 <div align="center">
1771 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
1774 <td><em>Application</em>
1776 <li>Jalview Desktop News Reader</li>
1777 <li>Tweaked default layout of web services menu</li>
1778 <li>View/alignment association menu to enable user to
1779 easily specify which alignment a multi-structure view takes
1780 its colours/correspondences from</li>
1781 <li>Allow properties file location to be specified as URL</li>
1782 <li>Extend Jalview project to preserve associations
1783 between many alignment views and a single Jmol display</li>
1784 <li>Store annotation row height in Jalview project file</li>
1785 <li>Annotation row column label formatting attributes
1786 stored in project file</li>
1787 <li>Annotation row order for auto-calculated annotation
1788 rows preserved in Jalview project file</li>
1789 <li>Visual progress indication when Jalview state is
1790 saved using Desktop window menu</li>
1791 <li>Visual indication that command line arguments are
1792 still being processed</li>
1793 <li>Groovy script execution from URL</li>
1794 <li>Colour by annotation default min and max colours in
1796 <li>Automatically associate PDB files dragged onto an
1797 alignment with sequences that have high similarity and
1799 <li>Update JGoogleAnalytics to latest release (0.3)</li>
1800 <li>'view structures' option to open many
1801 structures in same window</li>
1802 <li>Sort associated views menu option for tree panel</li>
1803 <li>Group all JABA and non-JABA services for a particular
1804 analysis function in its own submenu</li>
1805 </ul> <em>Applet</em>
1807 <li>Userdefined and autogenerated annotation rows for
1809 <li>Adjustment of alignment annotation pane height</li>
1810 <li>Annotation scrollbar for annotation panel</li>
1811 <li>Drag to reorder annotation rows in annotation panel</li>
1812 <li>'automaticScrolling' parameter</li>
1813 <li>Allow sequences with partial ID string matches to be
1814 annotated from GFF/Jalview features files</li>
1815 <li>Sequence logo annotation row in applet</li>
1816 <li>Absolute paths relative to host server in applet
1817 parameters are treated as such</li>
1818 <li>New in the JalviewLite javascript API:
1820 <li>JalviewLite.js javascript library</li>
1821 <li>Javascript callbacks for
1823 <li>Applet initialisation</li>
1824 <li>Sequence/alignment mouse-overs and selections</li>
1827 <li>scrollTo row and column alignment scrolling
1829 <li>Select sequence/alignment regions from javascript</li>
1830 <li>javascript structure viewer harness to pass
1831 messages between Jmol and Jalview when running as
1832 distinct applets</li>
1833 <li>sortBy method</li>
1834 <li>Set of applet and application examples shipped
1835 with documentation</li>
1836 <li>New example to demonstrate JalviewLite and Jmol
1837 javascript message exchange</li>
1839 </ul> <em>General</em>
1841 <li>Enable Jmol displays to be associated with multiple
1842 multiple alignments</li>
1843 <li>Option to automatically sort alignment with new tree</li>
1844 <li>User configurable link to enable redirects to a
1845 www.Jalview.org mirror</li>
1846 <li>Jmol colours option for Jmol displays</li>
1847 <li>Configurable newline string when writing alignment
1848 and other flat files</li>
1849 <li>Allow alignment annotation description lines to
1850 contain html tags</li>
1851 </ul> <em>Documentation and Development</em>
1853 <li>Add groovy test harness for bulk load testing to
1855 <li>Groovy script to load and align a set of sequences
1856 using a web service before displaying the result in the
1857 Jalview desktop</li>
1858 <li>Restructured javascript and applet api documentation</li>
1859 <li>Ant target to publish example html files with applet
1861 <li>Netbeans project for building Jalview from source</li>
1862 <li>ant task to create online javadoc for Jalview source</li>
1864 <td><em>Application</em>
1866 <li>User defined colourscheme throws exception when
1867 current built in colourscheme is saved as new scheme</li>
1868 <li>AlignFrame->Save in application pops up save
1869 dialog for valid filename/format</li>
1870 <li>Cannot view associated structure for UniProt sequence</li>
1871 <li>PDB file association breaks for UniProt sequence
1873 <li>Associate PDB from file dialog does not tell you
1874 which sequence is to be associated with the file</li>
1875 <li>Find All raises null pointer exception when query
1876 only matches sequence IDs</li>
1877 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
1878 <li>Jalview project with Jmol views created with Jalview
1879 2.4 cannot be loaded</li>
1880 <li>Filetype associations not installed for webstart
1882 <li>Two or more chains in a single PDB file associated
1883 with sequences in different alignments do not get coloured
1884 by their associated sequence</li>
1885 <li>Visibility status of autocalculated annotation row
1886 not preserved when project is loaded</li>
1887 <li>Annotation row height and visibility attributes not
1888 stored in Jalview project</li>
1889 <li>Tree bootstraps are not preserved when saved as a
1890 Jalview project</li>
1891 <li>Envision2 workflow tooltips are corrupted</li>
1892 <li>Enabling show group conservation also enables colour
1893 by conservation</li>
1894 <li>Duplicate group associated conservation or consensus
1895 created on new view</li>
1896 <li>Annotation scrollbar not displayed after 'show
1897 all hidden annotation rows' option selected</li>
1898 <li>Alignment quality not updated after alignment
1899 annotation row is hidden then shown</li>
1900 <li>Preserve colouring of structures coloured by
1901 sequences in pre Jalview 2.7 projects</li>
1902 <li>Web service job parameter dialog is not laid out
1904 <li>Web services menu not refreshed after 'reset
1905 services' button is pressed in preferences</li>
1906 <li>Annotation off by one in Jalview v2_3 example project</li>
1907 <li>Structures imported from file and saved in project
1908 get name like jalview_pdb1234.txt when reloaded</li>
1909 <li>Jalview does not always retrieve progress of a JABAWS
1910 job execution in full once it is complete</li>
1911 </ul> <em>Applet</em>
1913 <li>Alignment height set incorrectly when lots of
1914 annotation rows are displayed</li>
1915 <li>Relative URLs in feature HTML text not resolved to
1917 <li>View follows highlighting does not work for positions
1919 <li><= shown as = in tooltip</li>
1920 <li>Export features raises exception when no features
1922 <li>Separator string used for serialising lists of IDs
1923 for javascript api is modified when separator string
1924 provided as parameter</li>
1925 <li>Null pointer exception when selecting tree leaves for
1926 alignment with no existing selection</li>
1927 <li>Relative URLs for datasources assumed to be relative
1928 to applet's codebase</li>
1929 <li>Status bar not updated after finished searching and
1930 search wraps around to first result</li>
1931 <li>StructureSelectionManager instance shared between
1932 several Jalview applets causes race conditions and memory
1934 <li>Hover tooltip and mouseover of position on structure
1935 not sent from Jmol in applet</li>
1936 <li>Certain sequences of javascript method calls to
1937 applet API fatally hang browser</li>
1938 </ul> <em>General</em>
1940 <li>View follows structure mouseover scrolls beyond
1941 position with wrapped view and hidden regions</li>
1942 <li>Find sequence position moves to wrong residue
1943 with/without hidden columns</li>
1944 <li>Sequence length given in alignment properties window
1946 <li>InvalidNumberFormat exceptions thrown when trying to
1947 import PDB like structure files</li>
1948 <li>Positional search results are only highlighted
1949 between user-supplied sequence start/end bounds</li>
1950 <li>End attribute of sequence is not validated</li>
1951 <li>Find dialog only finds first sequence containing a
1952 given sequence position</li>
1953 <li>Sequence numbering not preserved in MSF alignment
1955 <li>Jalview PDB file reader does not extract sequence
1956 from nucleotide chains correctly</li>
1957 <li>Structure colours not updated when tree partition
1958 changed in alignment</li>
1959 <li>Sequence associated secondary structure not correctly
1960 parsed in interleaved stockholm</li>
1961 <li>Colour by annotation dialog does not restore current
1963 <li>Hiding (nearly) all sequences doesn't work
1965 <li>Sequences containing lowercase letters are not
1966 properly associated with their pdb files</li>
1967 </ul> <em>Documentation and Development</em>
1969 <li>schemas/JalviewWsParamSet.xsd corrupted by
1970 ApplyCopyright tool</li>
1975 <div align="center">
1976 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
1979 <td><em>Application</em>
1981 <li>New warning dialog when the Jalview Desktop cannot
1982 contact web services</li>
1983 <li>JABA service parameters for a preset are shown in
1984 service job window</li>
1985 <li>JABA Service menu entries reworded</li>
1989 <li>Modeller PIR IO broken - cannot correctly import a
1990 pir file emitted by Jalview</li>
1991 <li>Existing feature settings transferred to new
1992 alignment view created from cut'n'paste</li>
1993 <li>Improved test for mixed amino/nucleotide chains when
1994 parsing PDB files</li>
1995 <li>Consensus and conservation annotation rows
1996 occasionally become blank for all new windows</li>
1997 <li>Exception raised when right clicking above sequences
1998 in wrapped view mode</li>
1999 </ul> <em>Application</em>
2001 <li>multiple multiply aligned structure views cause cpu
2002 usage to hit 100% and computer to hang</li>
2003 <li>Web Service parameter layout breaks for long user
2004 parameter names</li>
2005 <li>Jaba service discovery hangs desktop if Jaba server
2012 <div align="center">
2013 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2016 <td><em>Application</em>
2018 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2019 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2022 <li>Web Services preference tab</li>
2023 <li>Analysis parameters dialog box and user defined
2025 <li>Improved speed and layout of Envision2 service menu</li>
2026 <li>Superpose structures using associated sequence
2028 <li>Export coordinates and projection as CSV from PCA
2030 </ul> <em>Applet</em>
2032 <li>enable javascript: execution by the applet via the
2033 link out mechanism</li>
2034 </ul> <em>Other</em>
2036 <li>Updated the Jmol Jalview interface to work with Jmol
2038 <li>The Jalview Desktop and JalviewLite applet now
2039 require Java 1.5</li>
2040 <li>Allow Jalview feature colour specification for GFF
2041 sequence annotation files</li>
2042 <li>New 'colour by label' keword in Jalview feature file
2043 type colour specification</li>
2044 <li>New Jalview Desktop Groovy API method that allows a
2045 script to check if it being run in an interactive session or
2046 in a batch operation from the Jalview command line</li>
2050 <li>clustalx colourscheme colours Ds preferentially when
2051 both D+E are present in over 50% of the column</li>
2052 </ul> <em>Application</em>
2054 <li>typo in AlignmentFrame->View->Hide->all but
2055 selected Regions menu item</li>
2056 <li>sequence fetcher replaces ',' for ';' when the ',' is
2057 part of a valid accession ID</li>
2058 <li>fatal OOM if object retrieved by sequence fetcher
2059 runs out of memory</li>
2060 <li>unhandled Out of Memory Error when viewing pca
2061 analysis results</li>
2062 <li>InstallAnywhere builds fail to launch on OS X java
2063 10.5 update 4 (due to apple Java 1.6 update)</li>
2064 <li>Installanywhere Jalview silently fails to launch</li>
2065 </ul> <em>Applet</em>
2067 <li>Jalview.getFeatureGroups() raises an
2068 ArrayIndexOutOfBoundsException if no feature groups are
2075 <div align="center">
2076 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2082 <li>Alignment prettyprinter doesn't cope with long
2084 <li>clustalx colourscheme colours Ds preferentially when
2085 both D+E are present in over 50% of the column</li>
2086 <li>nucleic acid structures retrieved from PDB do not
2087 import correctly</li>
2088 <li>More columns get selected than were clicked on when a
2089 number of columns are hidden</li>
2090 <li>annotation label popup menu not providing correct
2091 add/hide/show options when rows are hidden or none are
2093 <li>Stockholm format shown in list of readable formats,
2094 and parser copes better with alignments from RFAM.</li>
2095 <li>CSV output of consensus only includes the percentage
2096 of all symbols if sequence logo display is enabled</li>
2098 </ul> <em>Applet</em>
2100 <li>annotation panel disappears when annotation is
2102 </ul> <em>Application</em>
2104 <li>Alignment view not redrawn properly when new
2105 alignment opened where annotation panel is visible but no
2106 annotations are present on alignment</li>
2107 <li>pasted region containing hidden columns is
2108 incorrectly displayed in new alignment window</li>
2109 <li>Jalview slow to complete operations when stdout is
2110 flooded (fix is to close the Jalview console)</li>
2111 <li>typo in AlignmentFrame->View->Hide->all but
2112 selected Rregions menu item.</li>
2113 <li>inconsistent group submenu and Format submenu entry
2114 'Un' or 'Non'conserved</li>
2115 <li>Sequence feature settings are being shared by
2116 multiple distinct alignments</li>
2117 <li>group annotation not recreated when tree partition is
2119 <li>double click on group annotation to select sequences
2120 does not propagate to associated trees</li>
2121 <li>Mac OSX specific issues:
2123 <li>exception raised when mouse clicked on desktop
2124 window background</li>
2125 <li>Desktop menu placed on menu bar and application
2126 name set correctly</li>
2127 <li>sequence feature settings not wide enough for the
2128 save feature colourscheme button</li>
2137 <div align="center">
2138 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2141 <td><em>New Capabilities</em>
2143 <li>URL links generated from description line for
2144 regular-expression based URL links (applet and application)
2151 <li>Non-positional feature URL links are shown in link
2153 <li>Linked viewing of nucleic acid sequences and
2155 <li>Automatic Scrolling option in View menu to display
2156 the currently highlighted region of an alignment.</li>
2157 <li>Order an alignment by sequence length, or using the
2158 average score or total feature count for each sequence.</li>
2159 <li>Shading features by score or associated description</li>
2160 <li>Subdivide alignment and groups based on identity of
2161 selected subsequence (Make Groups from Selection).</li>
2162 <li>New hide/show options including Shift+Control+H to
2163 hide everything but the currently selected region.</li>
2164 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2165 </ul> <em>Application</em>
2167 <li>Fetch DB References capabilities and UI expanded to
2168 support retrieval from DAS sequence sources</li>
2169 <li>Local DAS Sequence sources can be added via the
2170 command line or via the Add local source dialog box.</li>
2171 <li>DAS Dbref and DbxRef feature types are parsed as
2172 database references and protein_name is parsed as
2173 description line (BioSapiens terms).</li>
2174 <li>Enable or disable non-positional feature and database
2175 references in sequence ID tooltip from View menu in
2177 <!-- <li>New hidden columns and rows and representatives capabilities
2178 in annotations file (in progress - not yet fully implemented)</li> -->
2179 <li>Group-associated consensus, sequence logos and
2180 conservation plots</li>
2181 <li>Symbol distributions for each column can be exported
2182 and visualized as sequence logos</li>
2183 <li>Optionally scale multi-character column labels to fit
2184 within each column of annotation row<!-- todo for applet -->
2186 <li>Optional automatic sort of associated alignment view
2187 when a new tree is opened.</li>
2188 <li>Jalview Java Console</li>
2189 <li>Better placement of desktop window when moving
2190 between different screens.</li>
2191 <li>New preference items for sequence ID tooltip and
2192 consensus annotation</li>
2193 <li>Client to submit sequences and IDs to Envision2
2195 <li><em>Vamsas Capabilities</em>
2197 <li>Improved VAMSAS synchronization (Jalview archive
2198 used to preserve views, structures, and tree display
2200 <li>Import of vamsas documents from disk or URL via
2202 <li>Sharing of selected regions between views and
2203 with other VAMSAS applications (Experimental feature!)</li>
2204 <li>Updated API to VAMSAS version 0.2</li>
2206 </ul> <em>Applet</em>
2208 <li>Middle button resizes annotation row height</li>
2211 <li>sortByTree (true/false) - automatically sort the
2212 associated alignment view by the tree when a new tree is
2214 <li>showTreeBootstraps (true/false) - show or hide
2215 branch bootstraps (default is to show them if available)</li>
2216 <li>showTreeDistances (true/false) - show or hide
2217 branch lengths (default is to show them if available)</li>
2218 <li>showUnlinkedTreeNodes (true/false) - indicate if
2219 unassociated nodes should be highlighted in the tree
2221 <li>heightScale and widthScale (1.0 or more) -
2222 increase the height or width of a cell in the alignment
2223 grid relative to the current font size.</li>
2226 <li>Non-positional features displayed in sequence ID
2228 </ul> <em>Other</em>
2230 <li>Features format: graduated colour definitions and
2231 specification of feature scores</li>
2232 <li>Alignment Annotations format: new keywords for group
2233 associated annotation (GROUP_REF) and annotation row display
2234 properties (ROW_PROPERTIES)</li>
2235 <li>XML formats extended to support graduated feature
2236 colourschemes, group associated annotation, and profile
2237 visualization settings.</li></td>
2240 <li>Source field in GFF files parsed as feature source
2241 rather than description</li>
2242 <li>Non-positional features are now included in sequence
2243 feature and gff files (controlled via non-positional feature
2244 visibility in tooltip).</li>
2245 <li>URL links generated for all feature links (bugfix)</li>
2246 <li>Added URL embedding instructions to features file
2248 <li>Codons containing ambiguous nucleotides translated as
2249 'X' in peptide product</li>
2250 <li>Match case switch in find dialog box works for both
2251 sequence ID and sequence string and query strings do not
2252 have to be in upper case to match case-insensitively.</li>
2253 <li>AMSA files only contain first column of
2254 multi-character column annotation labels</li>
2255 <li>Jalview Annotation File generation/parsing consistent
2256 with documentation (e.g. Stockholm annotation can be
2257 exported and re-imported)</li>
2258 <li>PDB files without embedded PDB IDs given a friendly
2260 <li>Find incrementally searches ID string matches as well
2261 as subsequence matches, and correctly reports total number
2265 <li>Better handling of exceptions during sequence
2267 <li>Dasobert generated non-positional feature URL
2268 link text excludes the start_end suffix</li>
2269 <li>DAS feature and source retrieval buttons disabled
2270 when fetch or registry operations in progress.</li>
2271 <li>PDB files retrieved from URLs are cached properly</li>
2272 <li>Sequence description lines properly shared via
2274 <li>Sequence fetcher fetches multiple records for all
2276 <li>Ensured that command line das feature retrieval
2277 completes before alignment figures are generated.</li>
2278 <li>Reduced time taken when opening file browser for
2280 <li>isAligned check prior to calculating tree, PCA or
2281 submitting an MSA to JNet now excludes hidden sequences.</li>
2282 <li>User defined group colours properly recovered
2283 from Jalview projects.</li>
2292 <div align="center">
2293 <strong>2.4.0.b2</strong><br> 28/10/2009
2298 <li>Experimental support for google analytics usage
2300 <li>Jalview privacy settings (user preferences and docs).</li>
2305 <li>Race condition in applet preventing startup in
2307 <li>Exception when feature created from selection beyond
2308 length of sequence.</li>
2309 <li>Allow synthetic PDB files to be imported gracefully</li>
2310 <li>Sequence associated annotation rows associate with
2311 all sequences with a given id</li>
2312 <li>Find function matches case-insensitively for sequence
2313 ID string searches</li>
2314 <li>Non-standard characters do not cause pairwise
2315 alignment to fail with exception</li>
2316 </ul> <em>Application Issues</em>
2318 <li>Sequences are now validated against EMBL database</li>
2319 <li>Sequence fetcher fetches multiple records for all
2321 </ul> <em>InstallAnywhere Issues</em>
2323 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2324 issue with installAnywhere mechanism)</li>
2325 <li>Command line launching of JARs from InstallAnywhere
2326 version (java class versioning error fixed)</li>
2333 <div align="center">
2334 <strong>2.4</strong><br> 27/8/2008
2337 <td><em>User Interface</em>
2339 <li>Linked highlighting of codon and amino acid from
2340 translation and protein products</li>
2341 <li>Linked highlighting of structure associated with
2342 residue mapping to codon position</li>
2343 <li>Sequence Fetcher provides example accession numbers
2344 and 'clear' button</li>
2345 <li>MemoryMonitor added as an option under Desktop's
2347 <li>Extract score function to parse whitespace separated
2348 numeric data in description line</li>
2349 <li>Column labels in alignment annotation can be centred.</li>
2350 <li>Tooltip for sequence associated annotation give name
2352 </ul> <em>Web Services and URL fetching</em>
2354 <li>JPred3 web service</li>
2355 <li>Prototype sequence search client (no public services
2357 <li>Fetch either seed alignment or full alignment from
2359 <li>URL Links created for matching database cross
2360 references as well as sequence ID</li>
2361 <li>URL Links can be created using regular-expressions</li>
2362 </ul> <em>Sequence Database Connectivity</em>
2364 <li>Retrieval of cross-referenced sequences from other
2366 <li>Generalised database reference retrieval and
2367 validation to all fetchable databases</li>
2368 <li>Fetch sequences from DAS sources supporting the
2369 sequence command</li>
2370 </ul> <em>Import and Export</em>
2371 <li>export annotation rows as CSV for spreadsheet import</li>
2372 <li>Jalview projects record alignment dataset associations,
2373 EMBL products, and cDNA sequence mappings</li>
2374 <li>Sequence Group colour can be specified in Annotation
2376 <li>Ad-hoc colouring of group in Annotation File using RGB
2377 triplet as name of colourscheme</li>
2378 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2380 <li>treenode binding for VAMSAS tree exchange</li>
2381 <li>local editing and update of sequences in VAMSAS
2382 alignments (experimental)</li>
2383 <li>Create new or select existing session to join</li>
2384 <li>load and save of vamsas documents</li>
2385 </ul> <em>Application command line</em>
2387 <li>-tree parameter to open trees (introduced for passing
2389 <li>-fetchfrom command line argument to specify nicknames
2390 of DAS servers to query for alignment features</li>
2391 <li>-dasserver command line argument to add new servers
2392 that are also automatically queried for features</li>
2393 <li>-groovy command line argument executes a given groovy
2394 script after all input data has been loaded and parsed</li>
2395 </ul> <em>Applet-Application data exchange</em>
2397 <li>Trees passed as applet parameters can be passed to
2398 application (when using "View in full
2399 application")</li>
2400 </ul> <em>Applet Parameters</em>
2402 <li>feature group display control parameter</li>
2403 <li>debug parameter</li>
2404 <li>showbutton parameter</li>
2405 </ul> <em>Applet API methods</em>
2407 <li>newView public method</li>
2408 <li>Window (current view) specific get/set public methods</li>
2409 <li>Feature display control methods</li>
2410 <li>get list of currently selected sequences</li>
2411 </ul> <em>New Jalview distribution features</em>
2413 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2414 <li>RELEASE file gives build properties for the latest
2415 Jalview release.</li>
2416 <li>Java 1.1 Applet build made easier and donotobfuscate
2417 property controls execution of obfuscator</li>
2418 <li>Build target for generating source distribution</li>
2419 <li>Debug flag for javacc</li>
2420 <li>.jalview_properties file is documented (slightly) in
2421 jalview.bin.Cache</li>
2422 <li>Continuous Build Integration for stable and
2423 development version of Application, Applet and source
2428 <li>selected region output includes visible annotations
2429 (for certain formats)</li>
2430 <li>edit label/displaychar contains existing label/char
2432 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2433 <li>shorter peptide product names from EMBL records</li>
2434 <li>Newick string generator makes compact representations</li>
2435 <li>bootstrap values parsed correctly for tree files with
2437 <li>pathological filechooser bug avoided by not allowing
2438 filenames containing a ':'</li>
2439 <li>Fixed exception when parsing GFF files containing
2440 global sequence features</li>
2441 <li>Alignment datasets are finalized only when number of
2442 references from alignment sequences goes to zero</li>
2443 <li>Close of tree branch colour box without colour
2444 selection causes cascading exceptions</li>
2445 <li>occasional negative imgwidth exceptions</li>
2446 <li>better reporting of non-fatal warnings to user when
2447 file parsing fails.</li>
2448 <li>Save works when Jalview project is default format</li>
2449 <li>Save as dialog opened if current alignment format is
2450 not a valid output format</li>
2451 <li>UniProt canonical names introduced for both das and
2453 <li>Histidine should be midblue (not pink!) in Zappo</li>
2454 <li>error messages passed up and output when data read
2456 <li>edit undo recovers previous dataset sequence when
2457 sequence is edited</li>
2458 <li>allow PDB files without pdb ID HEADER lines (like
2459 those generated by MODELLER) to be read in properly</li>
2460 <li>allow reading of JPred concise files as a normal
2462 <li>Stockholm annotation parsing and alignment properties
2463 import fixed for PFAM records</li>
2464 <li>Structure view windows have correct name in Desktop
2466 <li>annotation consisting of sequence associated scores
2467 can be read and written correctly to annotation file</li>
2468 <li>Aligned cDNA translation to aligned peptide works
2470 <li>Fixed display of hidden sequence markers and
2471 non-italic font for representatives in Applet</li>
2472 <li>Applet Menus are always embedded in applet window on
2474 <li>Newly shown features appear at top of stack (in
2476 <li>Annotations added via parameter not drawn properly
2477 due to null pointer exceptions</li>
2478 <li>Secondary structure lines are drawn starting from
2479 first column of alignment</li>
2480 <li>UniProt XML import updated for new schema release in
2482 <li>Sequence feature to sequence ID match for Features
2483 file is case-insensitive</li>
2484 <li>Sequence features read from Features file appended to
2485 all sequences with matching IDs</li>
2486 <li>PDB structure coloured correctly for associated views
2487 containing a sub-sequence</li>
2488 <li>PDB files can be retrieved by applet from Jar files</li>
2489 <li>feature and annotation file applet parameters
2490 referring to different directories are retrieved correctly</li>
2491 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
2492 <li>Fixed application hang whilst waiting for
2493 splash-screen version check to complete</li>
2494 <li>Applet properly URLencodes input parameter values
2495 when passing them to the launchApp service</li>
2496 <li>display name and local features preserved in results
2497 retrieved from web service</li>
2498 <li>Visual delay indication for sequence retrieval and
2499 sequence fetcher initialisation</li>
2500 <li>updated Application to use DAS 1.53e version of
2501 dasobert DAS client</li>
2502 <li>Re-instated Full AMSA support and .amsa file
2504 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
2512 <div align="center">
2513 <strong>2.3</strong><br> 9/5/07
2518 <li>Jmol 11.0.2 integration</li>
2519 <li>PDB views stored in Jalview XML files</li>
2520 <li>Slide sequences</li>
2521 <li>Edit sequence in place</li>
2522 <li>EMBL CDS features</li>
2523 <li>DAS Feature mapping</li>
2524 <li>Feature ordering</li>
2525 <li>Alignment Properties</li>
2526 <li>Annotation Scores</li>
2527 <li>Sort by scores</li>
2528 <li>Feature/annotation editing in applet</li>
2533 <li>Headless state operation in 2.2.1</li>
2534 <li>Incorrect and unstable DNA pairwise alignment</li>
2535 <li>Cut and paste of sequences with annotation</li>
2536 <li>Feature group display state in XML</li>
2537 <li>Feature ordering in XML</li>
2538 <li>blc file iteration selection using filename # suffix</li>
2539 <li>Stockholm alignment properties</li>
2540 <li>Stockhom alignment secondary structure annotation</li>
2541 <li>2.2.1 applet had no feature transparency</li>
2542 <li>Number pad keys can be used in cursor mode</li>
2543 <li>Structure Viewer mirror image resolved</li>
2550 <div align="center">
2551 <strong>2.2.1</strong><br> 12/2/07
2556 <li>Non standard characters can be read and displayed
2557 <li>Annotations/Features can be imported/exported to the
2559 <li>Applet allows editing of sequence/annotation/group
2560 name & description
2561 <li>Preference setting to display sequence name in
2563 <li>Annotation file format extended to allow
2564 Sequence_groups to be defined
2565 <li>Default opening of alignment overview panel can be
2566 specified in preferences
2567 <li>PDB residue numbering annotation added to associated
2573 <li>Applet crash under certain Linux OS with Java 1.6
2575 <li>Annotation file export / import bugs fixed
2576 <li>PNG / EPS image output bugs fixed
2582 <div align="center">
2583 <strong>2.2</strong><br> 27/11/06
2588 <li>Multiple views on alignment
2589 <li>Sequence feature editing
2590 <li>"Reload" alignment
2591 <li>"Save" to current filename
2592 <li>Background dependent text colour
2593 <li>Right align sequence ids
2594 <li>User-defined lower case residue colours
2597 <li>Menu item accelerator keys
2598 <li>Control-V pastes to current alignment
2599 <li>Cancel button for DAS Feature Fetching
2600 <li>PCA and PDB Viewers zoom via mouse roller
2601 <li>User-defined sub-tree colours and sub-tree selection
2608 <li>'New Window' button on the 'Output to Text box'
2613 <li>New memory efficient Undo/Redo System
2614 <li>Optimised symbol lookups and conservation/consensus
2616 <li>Region Conservation/Consensus recalculated after
2618 <li>Fixed Remove Empty Columns Bug (empty columns at end
2620 <li>Slowed DAS Feature Fetching for increased robustness.
2627 <li>Made angle brackets in ASCII feature descriptions
2629 <li>Re-instated Zoom function for PCA
2630 <li>Sequence descriptions conserved in web service
2632 <li>UniProt ID discoverer uses any word separated by
2634 <li>WsDbFetch query/result association resolved
2635 <li>Tree leaf to sequence mapping improved
2636 <li>Smooth fonts switch moved to FontChooser dialog box.
2648 <div align="center">
2649 <strong>2.1.1</strong><br> 12/9/06
2654 <li>Copy consensus sequence to clipboard</li>
2659 <li>Image output - rightmost residues are rendered if
2660 sequence id panel has been resized</li>
2661 <li>Image output - all offscreen group boundaries are
2663 <li>Annotation files with sequence references - all
2664 elements in file are relative to sequence position</li>
2665 <li>Mac Applet users can use Alt key for group editing</li>
2671 <div align="center">
2672 <strong>2.1</strong><br> 22/8/06
2677 <li>MAFFT Multiple Alignment in default Web Service list</li>
2678 <li>DAS Feature fetching</li>
2679 <li>Hide sequences and columns</li>
2680 <li>Export Annotations and Features</li>
2681 <li>GFF file reading / writing</li>
2682 <li>Associate structures with sequences from local PDB
2684 <li>Add sequences to exisiting alignment</li>
2685 <li>Recently opened files / URL lists</li>
2686 <li>Applet can launch the full application</li>
2687 <li>Applet has transparency for features (Java 1.2
2689 <li>Applet has user defined colours parameter</li>
2690 <li>Applet can load sequences from parameter
2691 "sequence<em>x</em>"
2697 <li>Redundancy Panel reinstalled in the Applet</li>
2698 <li>Monospaced font - EPS / rescaling bug fixed</li>
2699 <li>Annotation files with sequence references bug fixed</li>
2705 <div align="center">
2706 <strong>2.08.1</strong><br> 2/5/06
2711 <li>Change case of selected region from Popup menu</li>
2712 <li>Choose to match case when searching</li>
2713 <li>Middle mouse button and mouse movement can compress /
2714 expand the visible width and height of the alignment</li>
2719 <li>Annotation Panel displays complete JNet results</li>
2725 <div align="center">
2726 <strong>2.08b</strong><br> 18/4/06
2732 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
2733 <li>Righthand label on wrapped alignments shows correct
2740 <div align="center">
2741 <strong>2.08</strong><br> 10/4/06
2746 <li>Editing can be locked to the selection area</li>
2747 <li>Keyboard editing</li>
2748 <li>Create sequence features from searches</li>
2749 <li>Precalculated annotations can be loaded onto
2751 <li>Features file allows grouping of features</li>
2752 <li>Annotation Colouring scheme added</li>
2753 <li>Smooth fonts off by default - Faster rendering</li>
2754 <li>Choose to toggle Autocalculate Consensus On/Off</li>
2759 <li>Drag & Drop fixed on Linux</li>
2760 <li>Jalview Archive file faster to load/save, sequence
2761 descriptions saved.</li>
2767 <div align="center">
2768 <strong>2.07</strong><br> 12/12/05
2773 <li>PDB Structure Viewer enhanced</li>
2774 <li>Sequence Feature retrieval and display enhanced</li>
2775 <li>Choose to output sequence start-end after sequence
2776 name for file output</li>
2777 <li>Sequence Fetcher WSDBFetch@EBI</li>
2778 <li>Applet can read feature files, PDB files and can be
2779 used for HTML form input</li>
2784 <li>HTML output writes groups and features</li>
2785 <li>Group editing is Control and mouse click</li>
2786 <li>File IO bugs</li>
2792 <div align="center">
2793 <strong>2.06</strong><br> 28/9/05
2798 <li>View annotations in wrapped mode</li>
2799 <li>More options for PCA viewer</li>
2804 <li>GUI bugs resolved</li>
2805 <li>Runs with -nodisplay from command line</li>
2811 <div align="center">
2812 <strong>2.05b</strong><br> 15/9/05
2817 <li>Choose EPS export as lineart or text</li>
2818 <li>Jar files are executable</li>
2819 <li>Can read in Uracil - maps to unknown residue</li>
2824 <li>Known OutOfMemory errors give warning message</li>
2825 <li>Overview window calculated more efficiently</li>
2826 <li>Several GUI bugs resolved</li>
2832 <div align="center">
2833 <strong>2.05</strong><br> 30/8/05
2838 <li>Edit and annotate in "Wrapped" view</li>
2843 <li>Several GUI bugs resolved</li>
2849 <div align="center">
2850 <strong>2.04</strong><br> 24/8/05
2855 <li>Hold down mouse wheel & scroll to change font
2861 <li>Improved JPred client reliability</li>
2862 <li>Improved loading of Jalview files</li>
2868 <div align="center">
2869 <strong>2.03</strong><br> 18/8/05
2874 <li>Set Proxy server name and port in preferences</li>
2875 <li>Multiple URL links from sequence ids</li>
2876 <li>User Defined Colours can have a scheme name and added
2878 <li>Choose to ignore gaps in consensus calculation</li>
2879 <li>Unix users can set default web browser</li>
2880 <li>Runs without GUI for batch processing</li>
2881 <li>Dynamically generated Web Service Menus</li>
2886 <li>InstallAnywhere download for Sparc Solaris</li>
2892 <div align="center">
2893 <strong>2.02</strong><br> 18/7/05
2899 <li>Copy & Paste order of sequences maintains
2900 alignment order.</li>
2906 <div align="center">
2907 <strong>2.01</strong><br> 12/7/05
2912 <li>Use delete key for deleting selection.</li>
2913 <li>Use Mouse wheel to scroll sequences.</li>
2914 <li>Help file updated to describe how to add alignment
2916 <li>Version and build date written to build properties
2918 <li>InstallAnywhere installation will check for updates
2919 at launch of Jalview.</li>
2924 <li>Delete gaps bug fixed.</li>
2925 <li>FileChooser sorts columns.</li>
2926 <li>Can remove groups one by one.</li>
2927 <li>Filechooser icons installed.</li>
2928 <li>Finder ignores return character when searching.
2929 Return key will initiate a search.<br>
2936 <div align="center">
2937 <strong>2.0</strong><br> 20/6/05
2942 <li>New codebase</li>