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">
90 </div></td><td><div align="left">
103 <em>New Known Issues</em>
110 <td width="60" nowrap>
112 <strong><a name="Jalview.2.10.1">2.10.1</a><br />
113 <em>29/11/2016</em></strong>
116 <td><div align="left">
120 <!-- JAL-98 -->Improved memory usage: sparse arrays used
121 for all consensus calculations
124 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released 3rd Oct 2016)
126 <li>Updated Jalview's Certum code signing certificate
132 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
133 set of database cross-references, sorted alphabetically
136 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
137 from database cross references. Users with custom links
138 will receive a <a href="webServices/urllinks.html#warning">warning
139 dialog</a> asking them to update their preferences.
142 <!-- JAL-2287-->Cancel button and escape listener on
143 dialog warning user about disconnecting Jalview from a
147 <!-- JAL-2320-->Jalview's Chimera control window closes if
148 the Chimera it is connected to is shut down
151 <!-- JAL-1738-->New keystroke (B) and Select highlighted
152 columns menu item to mark columns containing
153 highlighted regions (e.g. from structure selections or results
157 <!-- JAL-2284-->Command line option for batch-generation
158 of HTML pages rendering alignment data with the BioJS
168 <!-- JAL-2286 -->Columns with more than one modal residue
169 are not coloured or thresholded according to percent
170 identity (first observed in Jalview 2.8.2)
173 <!-- JAL-2301 -->Threonine incorrectly reported as not
177 <!-- JAL-2318 -->Updates to documentation pages (above PID
178 threshold, amino acid properties)
181 <!-- JAL-2292 -->Lower case residues in sequences are not
182 reported as mapped to residues in a structure file in the
186 <!--JAL-2324 -->Identical features with non-numeric scores
187 could be added multiple times to a sequence
190 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
191 bond features shown as two highlighted residues rather
192 than a range in linked structure views, and treated
193 correctly when selecting and computing trees from features
196 <!-- JAL-2281-->Custom URL links for database
197 cross-references are matched to database name regardless
205 <!-- JAL-2282-->Custom URL links for specific database
206 names without regular expressions also offer links from
210 <!-- JAL-2315-->Removing a single configured link in the
211 URL links pane in Connections preferences doesn't actually
212 update Jalview configuration
215 <!-- JAL-2272-->CTRL-Click on a selected region to open
216 the alignment area popup menu doesn't work on El-Capitan
219 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
220 files with similarly named sequences if dropped onto the
224 <!-- JAL-2312 -->Additional mappings are shown for PDB
225 entries where more chains exist in the PDB accession than
226 are reported in the SIFTS file
229 <!-- JAL-2317-->Certain structures do not get mapped to
230 the structure view when displayed with Chimera
233 <!-- JAL-2317-->No chains shown in the Chimera view
234 panel's View->Show Chains submenu
237 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
238 work for wrapped alignment views
241 <!--JAL-2197 -->Rename UI components for running JPred
242 predictions from 'JNet' to 'JPred'
245 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
246 corrupted when annotation panel vertical scroll is not at
250 <!--JAL-2332 -->Attempting to view structure for Hen
251 lysozyme results in a PDB Client error dialog box
254 <!-- <em>New Known Issues</em>
261 <td width="60" nowrap>
263 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
264 <em>25/10/2016</em></strong>
267 <td><em>Application</em>
269 <li>3D Structure chooser opens with 'Cached structures'
270 view if structures already loaded</li>
271 <li>Progress bar reports models as they are loaded to
278 <li>Colour by conservation always enabled and no tick
279 shown in menu when BLOSUM or PID shading applied</li>
280 <li>FER1_ARATH and FER2_ARATH labels were switched in
281 example sequences/projects/trees</li>
285 <li>Jalview projects with views of local PDB structure
286 files saved on Windows cannot be opened on OSX</li>
287 <li>Multiple structure views can be opened and
288 superposed without timeout for structures with multiple
289 models or multiple sequences in alignment</li>
290 <li>Cannot import or associated local PDB files without
291 a PDB ID HEADER line</li>
292 <li>RMSD is not output in Jmol console when
293 superposition is performed</li>
294 <li>Drag and drop of URL from Browser fails for Linux
295 and OSX versions earlier than El Capitan</li>
296 <li>ENA client ignores invalid content from ENA server</li>
297 <li>Exceptions are not raised in console when ENA
298 client attempts to fetch non-existent IDs via Fetch DB
300 <li>Exceptions are not raised in console when a new
301 view is created on the alignment</li>
302 <li>OSX right-click fixed for group selections:
303 CMD-click to insert/remove gaps in groups and CTRL-click
304 to open group pop-up menu</li>
306 <em>Build and deployment</em>
308 <li>URL link checker now copes with multi-line anchor
311 <em>New Known Issues</em>
313 <li>Drag and drop from URL links in browsers do not
320 <td width="60" nowrap>
322 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
328 <!-- JAL-2124 -->Updated Spanish translations.
331 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
332 for importing structure data to Jalview. Enables mmCIF and
336 <!-- JAL-192 --->Alignment ruler shows positions relative to
340 <!-- JAL-2202 -->Position/residue shown in status bar when
341 mousing over sequence associated annotation
344 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
348 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
349 '()', canonical '[]' and invalid '{}' base pair populations
353 <!-- JAL-2092 -->Feature settings popup menu options for
354 showing or hiding columns containing a feature
357 <!-- JAL-1557 -->Edit selected group by double clicking on
358 group and sequence associated annotation labels
361 <!-- JAL-2236 -->Sequence name added to annotation label in
362 select/hide columns by annotation and colour by annotation
366 </ul> <em>Application</em>
369 <!-- JAL-2050-->Automatically hide introns when opening a
373 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
377 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
378 structure mappings with the EMBL-EBI PDBe SIFTS database
381 <!-- JAL-2079 -->Updated download sites used for Rfam and
382 Pfam sources to xfam.org
385 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
388 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
389 over sequences in Jalview
392 <!-- JAL-2027-->Support for reverse-complement coding
393 regions in ENA and EMBL
396 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
397 for record retrieval via ENA rest API
400 <!-- JAL-2027 -->Support for ENA CDS records with reverse
404 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
405 groovy script execution
408 <!-- JAL-1812 -->New 'execute Groovy script' option in an
409 alignment window's Calculate menu
412 <!-- JAL-1812 -->Allow groovy scripts that call
413 Jalview.getAlignFrames() to run in headless mode
416 <!-- JAL-2068 -->Support for creating new alignment
417 calculation workers from groovy scripts
420 <!-- JAL-1369 --->Store/restore reference sequence in
424 <!-- JAL-1803 -->Chain codes for a sequence's PDB
425 associations are now saved/restored from project
428 <!-- JAL-1993 -->Database selection dialog always shown
429 before sequence fetcher is opened
432 <!-- JAL-2183 -->Double click on an entry in Jalview's
433 database chooser opens a sequence fetcher
436 <!-- JAL-1563 -->Free-text search client for UniProt using
440 <!-- JAL-2168 -->-nonews command line parameter to prevent
441 the news reader opening
444 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
445 querying stored in preferences
448 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
452 <!-- JAL-1977-->Tooltips shown on database chooser
455 <!-- JAL-391 -->Reverse complement function in calculate
456 menu for nucleotide sequences
459 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
460 and feature counts preserves alignment ordering (and
461 debugged for complex feature sets).
464 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
465 viewing structures with Jalview 2.10
468 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
469 genome, transcript CCDS and gene ids via the Ensembl and
470 Ensembl Genomes REST API
473 <!-- JAL-2049 -->Protein sequence variant annotation
474 computed for 'sequence_variant' annotation on CDS regions
478 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
482 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
483 Ref Fetcher fails to match, or otherwise updates sequence
484 data from external database records.
487 <!-- JAL-2154 -->Revised Jalview Project format for
488 efficient recovery of sequence coding and alignment
489 annotation relationships.
491 </ul> <!-- <em>Applet</em>
502 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
506 <!-- JAL-2018-->Export features in Jalview format (again)
507 includes graduated colourschemes
510 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
511 working with big alignments and lots of hidden columns
514 <!-- JAL-2053-->Hidden column markers not always rendered
515 at right of alignment window
518 <!-- JAL-2067 -->Tidied up links in help file table of
522 <!-- JAL-2072 -->Feature based tree calculation not shown
526 <!-- JAL-2075 -->Hidden columns ignored during feature
527 based tree calculation
530 <!-- JAL-2065 -->Alignment view stops updating when show
531 unconserved enabled for group on alignment
534 <!-- JAL-2086 -->Cannot insert gaps into sequence when
538 <!-- JAL-2146 -->Alignment column in status incorrectly
539 shown as "Sequence position" when mousing over
543 <!-- JAL-2099 -->Incorrect column numbers in ruler when
544 hidden columns present
547 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
548 user created annotation added to alignment
551 <!-- JAL-1841 -->RNA Structure consensus only computed for
552 '()' base pair annotation
555 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
556 in zero scores for all base pairs in RNA Structure
560 <!-- JAL-2174-->Extend selection with columns containing
564 <!-- JAL-2275 -->Pfam format writer puts extra space at
565 beginning of sequence
568 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
572 <!-- JAL-2238 -->Cannot create groups on an alignment from
573 from a tree when t-coffee scores are shown
576 <!-- JAL-1836,1967 -->Cannot import and view PDB
577 structures with chains containing negative resnums (4q4h)
580 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
584 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
585 to Clustal, PIR and PileUp output
588 <!-- JAL-2008 -->Reordering sequence features that are
589 not visible causes alignment window to repaint
592 <!-- JAL-2006 -->Threshold sliders don't work in
593 graduated colour and colour by annotation row for e-value
594 scores associated with features and annotation rows
597 <!-- JAL-1797 -->amino acid physicochemical conservation
598 calculation should be case independent
601 <!-- JAL-2173 -->Remove annotation also updates hidden
605 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
606 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
607 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
610 <!-- JAL-2065 -->Null pointer exceptions and redraw
611 problems when reference sequence defined and 'show
612 non-conserved' enabled
615 <!-- JAL-1306 -->Quality and Conservation are now shown on
616 load even when Consensus calculation is disabled
619 <!-- JAL-1932 -->Remove right on penultimate column of
620 alignment does nothing
626 <!-- JAL-1552-->URLs and links can't be imported by
627 drag'n'drop on OSX when launched via webstart (note - not
628 yet fixed for El Capitan)
631 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
632 output when running on non-gb/us i18n platforms
635 <!-- JAL-1944 -->Error thrown when exporting a view with
636 hidden sequences as flat-file alignment
639 <!-- JAL-2030-->InstallAnywhere distribution fails when
643 <!-- JAL-2080-->Jalview very slow to launch via webstart
644 (also hotfix for 2.9.0b2)
647 <!-- JAL-2085 -->Cannot save project when view has a
648 reference sequence defined
651 <!-- JAL-1011 -->Columns are suddenly selected in other
652 alignments and views when revealing hidden columns
655 <!-- JAL-1989 -->Hide columns not mirrored in complement
656 view in a cDNA/Protein splitframe
659 <!-- JAL-1369 -->Cannot save/restore representative
660 sequence from project when only one sequence is
664 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
668 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
669 structure consensus didn't refresh annotation panel
672 <!-- JAL-1962 -->View mapping in structure view shows
673 mappings between sequence and all chains in a PDB file
676 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
677 dialogs format columns correctly, don't display array
678 data, sort columns according to type
681 <!-- JAL-1975 -->Export complete shown after destination
682 file chooser is cancelled during an image export
685 <!-- JAL-2025 -->Error when querying PDB Service with
686 sequence name containing special characters
689 <!-- JAL-2024 -->Manual PDB structure querying should be
693 <!-- JAL-2104 -->Large tooltips with broken HTML
694 formatting don't wrap
697 <!-- JAL-1128 -->Figures exported from wrapped view are
698 truncated so L looks like I in consensus annotation
701 <!-- JAL-2003 -->Export features should only export the
702 currently displayed features for the current selection or
706 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
707 after fetching cross-references, and restoring from project
710 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
711 followed in the structure viewer
714 <!-- JAL-2163 -->Titles for individual alignments in
715 splitframe not restored from project
718 <!-- JAL-2145 -->missing autocalculated annotation at
719 trailing end of protein alignment in transcript/product
720 splitview when pad-gaps not enabled by default
723 <!-- JAL-1797 -->amino acid physicochemical conservation
727 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
728 article has been read (reopened issue due to
729 internationalisation problems)
732 <!-- JAL-1960 -->Only offer PDB structures in structure
733 viewer based on sequence name, PDB and UniProt
738 <!-- JAL-1976 -->No progress bar shown during export of
742 <!-- JAL-2213 -->Structures not always superimposed after
743 multiple structures are shown for one or more sequences.
746 <!-- JAL-1370 -->Reference sequence characters should not
747 be replaced with '.' when 'Show unconserved' format option
751 <!-- JAL-1823 -->Cannot specify chain code when entering
752 specific PDB id for sequence
755 <!-- JAL-1944 -->File->Export->.. as doesn't work when
756 'Export hidden sequences' is enabled, but 'export hidden
757 columns' is disabled.
760 <!--JAL-2026-->Best Quality option in structure chooser
761 selects lowest rather than highest resolution structures
765 <!-- JAL-1887 -->Incorrect start and end reported for PDB
766 to sequence mapping in 'View Mappings' report
769 <!-- JAL-2284 -->Unable to read old Jalview projects that
770 contain non-XML data added after Jalvew wrote project.
772 <li><!-- JAL-2118 -->Newly created annotation row reorders
773 after clicking on it to create new annotation for a
776 <!-- may exclude, this is an external service stability issue JAL-1941
777 -- > RNA 3D structure not added via DSSR service</li> -->
782 <!-- JAL-2151 -->Incorrect columns are selected when
783 hidden columns present before start of sequence
786 <!-- JAL-1986 -->Missing dependencies on applet pages
790 <!-- JAL-1947 -->Overview pixel size changes when
791 sequences are hidden in applet
794 <!-- JAL-1996 -->Updated instructions for applet
795 deployment on examples pages.
802 <td width="60" nowrap>
804 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
805 <em>16/10/2015</em></strong>
810 <li>Time stamps for signed Jalview application and applet
817 <li>Duplicate group consensus and conservation rows
818 shown when tree is partitioned</li>
819 <li>Erratic behaviour when tree partitions made with
820 multiple cDNA/Protein split views</li>
826 <td width="60" nowrap>
828 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
829 <em>8/10/2015</em></strong>
834 <li>Updated Spanish translations of localized text for
836 </ul> <em>Application</em>
838 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
839 <li>Signed OSX InstallAnywhere installer<br></li>
840 <li>Support for per-sequence based annotations in BioJSON</li>
841 </ul> <em>Applet</em>
843 <li>Split frame example added to applet examples page</li>
844 </ul><em>Build and Deployment</em>
846 <li><!-- JAL-1888 -->New ant target for running Jalview's test suite</li>
852 <li>Mapping of cDNA to protein in split frames
853 incorrect when sequence start > 1</li>
854 <li>Broken images in filter column by annotation dialog
856 <li>Feature colours not parsed from features file</li>
857 <li>Exceptions and incomplete link URLs recovered when
858 loading a features file containing HTML tags in feature
864 <li>Annotations corrupted after BioJS export and
866 <li>Incorrect sequence limits after Fetch DB References
867 with 'trim retrieved sequences'</li>
868 <li>Incorrect warning about deleting all data when
869 deleting selected columns</li>
870 <li>Patch to build system for shipping properly signed
871 JNLP templates for webstart launch</li>
872 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
873 unreleased structures for download or viewing</li>
874 <li>Tab/space/return keystroke operation of EMBL-PDBe
875 fetcher/viewer dialogs works correctly</li>
876 <li>Disabled 'minimise' button on Jalview windows
877 running on OSX to workaround redraw hang bug</li>
878 <li>Split cDNA/Protein view position and geometry not
879 recovered from jalview project</li>
880 <li>Initial enabled/disabled state of annotation menu
881 sorter 'show autocalculated first/last' corresponds to
883 <li>Restoring of Clustal, RNA Helices and T-Coffee
884 color schemes from BioJSON</li>
888 <li>Reorder sequences mirrored in cDNA/Protein split
890 <li>Applet with Jmol examples not loading correctly</li>
896 <td><div align="center">
897 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
901 <li>Linked visualisation and analysis of DNA and Protein
904 <li>Translated cDNA alignments shown as split protein
905 and DNA alignment views</li>
906 <li>Codon consensus annotation for linked protein and
907 cDNA alignment views</li>
908 <li>Link cDNA or Protein product sequences by loading
909 them onto Protein or cDNA alignments</li>
910 <li>Reconstruct linked cDNA alignment from aligned
911 protein sequences</li>
914 <li>Jmol integration updated to Jmol v14.2.14</li>
915 <li>Import and export of Jalview alignment views as <a
916 href="features/bioJsonFormat.html">BioJSON</a></li>
917 <li>New alignment annotation file statements for
918 reference sequences and marking hidden columns</li>
919 <li>Reference sequence based alignment shading to
920 highlight variation</li>
921 <li>Select or hide columns according to alignment
923 <li>Find option for locating sequences by description</li>
924 <li>Conserved physicochemical properties shown in amino
925 acid conservation row</li>
926 <li>Alignments can be sorted by number of RNA helices</li>
927 </ul> <em>Application</em>
929 <li>New cDNA/Protein analysis capabilities
931 <li>Get Cross-References should open a Split Frame
932 view with cDNA/Protein</li>
933 <li>Detect when nucleotide sequences and protein
934 sequences are placed in the same alignment</li>
935 <li>Split cDNA/Protein views are saved in Jalview
940 <li>Use REST API to talk to Chimera</li>
941 <li>Selected regions in Chimera are highlighted in linked
944 <li>VARNA RNA viewer updated to v3.93</li>
945 <li>VARNA views are saved in Jalview Projects</li>
946 <li>Pseudoknots displayed as Jalview RNA annotation can
947 be shown in VARNA</li>
949 <li>Make groups for selection uses marked columns as well
950 as the active selected region</li>
952 <li>Calculate UPGMA and NJ trees using sequence feature
954 <li>New Export options
956 <li>New Export Settings dialog to control hidden
957 region export in flat file generation</li>
959 <li>Export alignment views for display with the <a
960 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
962 <li>Export scrollable SVG in HTML page</li>
963 <li>Optional embedding of BioJSON data when exporting
964 alignment figures to HTML</li>
966 <li>3D structure retrieval and display
968 <li>Free text and structured queries with the PDBe
970 <li>PDBe Search API based discovery and selection of
971 PDB structures for a sequence set</li>
975 <li>JPred4 employed for protein secondary structure
977 <li>Hide Insertions menu option to hide unaligned columns
978 for one or a group of sequences</li>
979 <li>Automatically hide insertions in alignments imported
980 from the JPred4 web server</li>
981 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
982 system on OSX<br />LGPL libraries courtesy of <a
983 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
985 <li>changed 'View nucleotide structure' submenu to 'View
986 VARNA 2D Structure'</li>
987 <li>change "View protein structure" menu option to "3D
990 </ul> <em>Applet</em>
992 <li>New layout for applet example pages</li>
993 <li>New parameters to enable SplitFrame view
994 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
995 <li>New example demonstrating linked viewing of cDNA and
996 Protein alignments</li>
997 </ul> <em>Development and deployment</em>
999 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1000 <li>Include installation type and git revision in build
1001 properties and console log output</li>
1002 <li>Jalview Github organisation, and new github site for
1003 storing BioJsMSA Templates</li>
1004 <li>Jalview's unit tests now managed with TestNG</li>
1007 <!-- <em>General</em>
1009 </ul> --> <!-- issues resolved --> <em>Application</em>
1011 <li>Escape should close any open find dialogs</li>
1012 <li>Typo in select-by-features status report</li>
1013 <li>Consensus RNA secondary secondary structure
1014 predictions are not highlighted in amber</li>
1015 <li>Missing gap character in v2.7 example file means
1016 alignment appears unaligned when pad-gaps is not enabled</li>
1017 <li>First switch to RNA Helices colouring doesn't colour
1018 associated structure views</li>
1019 <li>ID width preference option is greyed out when auto
1020 width checkbox not enabled</li>
1021 <li>Stopped a warning dialog from being shown when
1022 creating user defined colours</li>
1023 <li>'View Mapping' in structure viewer shows sequence
1024 mappings for just that viewer's sequences</li>
1025 <li>Workaround for superposing PDB files containing
1026 multiple models in Chimera</li>
1027 <li>Report sequence position in status bar when hovering
1028 over Jmol structure</li>
1029 <li>Cannot output gaps as '.' symbols with Selection ->
1030 output to text box</li>
1031 <li>Flat file exports of alignments with hidden columns
1032 have incorrect sequence start/end</li>
1033 <li>'Aligning' a second chain to a Chimera structure from
1035 <li>Colour schemes applied to structure viewers don't
1036 work for nucleotide</li>
1037 <li>Loading/cut'n'pasting an empty or invalid file leads
1038 to a grey/invisible alignment window</li>
1039 <li>Exported Jpred annotation from a sequence region
1040 imports to different position</li>
1041 <li>Space at beginning of sequence feature tooltips shown
1042 on some platforms</li>
1043 <li>Chimera viewer 'View | Show Chain' menu is not
1045 <li>'New View' fails with a Null Pointer Exception in
1046 console if Chimera has been opened</li>
1047 <li>Mouseover to Chimera not working</li>
1048 <li>Miscellaneous ENA XML feature qualifiers not
1050 <li>NPE in annotation renderer after 'Extract Scores'</li>
1051 <li>If two structures in one Chimera window, mouseover of
1052 either sequence shows on first structure</li>
1053 <li>'Show annotations' options should not make
1054 non-positional annotations visible</li>
1055 <li>Subsequence secondary structure annotation not shown
1056 in right place after 'view flanking regions'</li>
1057 <li>File Save As type unset when current file format is
1059 <li>Save as '.jar' option removed for saving Jalview
1061 <li>Colour by Sequence colouring in Chimera more
1063 <li>Cannot 'add reference annotation' for a sequence in
1064 several views on same alignment</li>
1065 <li>Cannot show linked products for EMBL / ENA records</li>
1066 <li>Jalview's tooltip wraps long texts containing no
1068 </ul> <em>Applet</em>
1070 <li>Jmol to JalviewLite mouseover/link not working</li>
1071 <li>JalviewLite can't import sequences with ID
1072 descriptions containing angle brackets</li>
1073 </ul> <em>General</em>
1075 <li>Cannot export and reimport RNA secondary structure
1076 via jalview annotation file</li>
1077 <li>Random helix colour palette for colour by annotation
1078 with RNA secondary structure</li>
1079 <li>Mouseover to cDNA from STOP residue in protein
1080 translation doesn't work.</li>
1081 <li>hints when using the select by annotation dialog box</li>
1082 <li>Jmol alignment incorrect if PDB file has alternate CA
1084 <li>FontChooser message dialog appears to hang after
1085 choosing 1pt font</li>
1086 <li>Peptide secondary structure incorrectly imported from
1087 annotation file when annotation display text includes 'e' or
1089 <li>Cannot set colour of new feature type whilst creating
1091 <li>cDNA translation alignment should not be sequence
1092 order dependent</li>
1093 <li>'Show unconserved' doesn't work for lower case
1095 <li>Nucleotide ambiguity codes involving R not recognised</li>
1096 </ul> <em>Deployment and Documentation</em>
1098 <li>Applet example pages appear different to the rest of
1099 www.jalview.org</li>
1100 </ul> <em>Application Known issues</em>
1102 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1103 <li>Misleading message appears after trying to delete
1105 <li>Jalview icon not shown in dock after InstallAnywhere
1106 version launches</li>
1107 <li>Fetching EMBL reference for an RNA sequence results
1108 fails with a sequence mismatch</li>
1109 <li>Corrupted or unreadable alignment display when
1110 scrolling alignment to right</li>
1111 <li>ArrayIndexOutOfBoundsException thrown when remove
1112 empty columns called on alignment with ragged gapped ends</li>
1113 <li>auto calculated alignment annotation rows do not get
1114 placed above or below non-autocalculated rows</li>
1115 <li>Jalview dekstop becomes sluggish at full screen in
1116 ultra-high resolution</li>
1117 <li>Cannot disable consensus calculation independently of
1118 quality and conservation</li>
1119 <li>Mouseover highlighting between cDNA and protein can
1120 become sluggish with more than one splitframe shown</li>
1121 </ul> <em>Applet Known Issues</em>
1123 <li>Core PDB parsing code requires Jmol</li>
1124 <li>Sequence canvas panel goes white when alignment
1125 window is being resized</li>
1131 <td><div align="center">
1132 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1134 <td><em>General</em>
1136 <li>Updated Java code signing certificate donated by
1138 <li>Features and annotation preserved when performing
1139 pairwise alignment</li>
1140 <li>RNA pseudoknot annotation can be
1141 imported/exported/displayed</li>
1142 <li>'colour by annotation' can colour by RNA and
1143 protein secondary structure</li>
1144 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1145 post-hoc with 2.9 release</em>)
1148 </ul> <em>Application</em>
1150 <li>Extract and display secondary structure for sequences
1151 with 3D structures</li>
1152 <li>Support for parsing RNAML</li>
1153 <li>Annotations menu for layout
1155 <li>sort sequence annotation rows by alignment</li>
1156 <li>place sequence annotation above/below alignment
1159 <li>Output in Stockholm format</li>
1160 <li>Internationalisation: improved Spanish (es)
1162 <li>Structure viewer preferences tab</li>
1163 <li>Disorder and Secondary Structure annotation tracks
1164 shared between alignments</li>
1165 <li>UCSF Chimera launch and linked highlighting from
1167 <li>Show/hide all sequence associated annotation rows for
1168 all or current selection</li>
1169 <li>disorder and secondary structure predictions
1170 available as dataset annotation</li>
1171 <li>Per-sequence rna helices colouring</li>
1174 <li>Sequence database accessions imported when fetching
1175 alignments from Rfam</li>
1176 <li>update VARNA version to 3.91</li>
1178 <li>New groovy scripts for exporting aligned positions,
1179 conservation values, and calculating sum of pairs scores.</li>
1180 <li>Command line argument to set default JABAWS server</li>
1181 <li>include installation type in build properties and
1182 console log output</li>
1183 <li>Updated Jalview project format to preserve dataset
1187 <!-- issues resolved --> <em>Application</em>
1189 <li>Distinguish alignment and sequence associated RNA
1190 structure in structure->view->VARNA</li>
1191 <li>Raise dialog box if user deletes all sequences in an
1193 <li>Pressing F1 results in documentation opening twice</li>
1194 <li>Sequence feature tooltip is wrapped</li>
1195 <li>Double click on sequence associated annotation
1196 selects only first column</li>
1197 <li>Redundancy removal doesn't result in unlinked
1198 leaves shown in tree</li>
1199 <li>Undos after several redundancy removals don't undo
1201 <li>Hide sequence doesn't hide associated annotation</li>
1202 <li>User defined colours dialog box too big to fit on
1203 screen and buttons not visible</li>
1204 <li>author list isn't updated if already written to
1205 Jalview properties</li>
1206 <li>Popup menu won't open after retrieving sequence
1208 <li>File open window for associate PDB doesn't open</li>
1209 <li>Left-then-right click on a sequence id opens a
1210 browser search window</li>
1211 <li>Cannot open sequence feature shading/sort popup menu
1212 in feature settings dialog</li>
1213 <li>better tooltip placement for some areas of Jalview
1215 <li>Allow addition of JABAWS Server which doesn't
1216 pass validation</li>
1217 <li>Web services parameters dialog box is too large to
1219 <li>Muscle nucleotide alignment preset obscured by
1221 <li>JABAWS preset submenus don't contain newly
1222 defined user preset</li>
1223 <li>MSA web services warns user if they were launched
1224 with invalid input</li>
1225 <li>Jalview cannot contact DAS Registy when running on
1228 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1229 'Superpose with' submenu not shown when new view
1233 </ul> <!-- <em>Applet</em>
1235 </ul> <em>General</em>
1237 </ul>--> <em>Deployment and Documentation</em>
1239 <li>2G and 1G options in launchApp have no effect on
1240 memory allocation</li>
1241 <li>launchApp service doesn't automatically open
1242 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1244 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1245 InstallAnywhere reports cannot find valid JVM when Java
1246 1.7_055 is available
1248 </ul> <em>Application Known issues</em>
1251 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1252 corrupted or unreadable alignment display when scrolling
1256 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1257 retrieval fails but progress bar continues for DAS retrieval
1258 with large number of ID
1261 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1262 flatfile output of visible region has incorrect sequence
1266 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1267 rna structure consensus doesn't update when secondary
1268 structure tracks are rearranged
1271 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1272 invalid rna structure positional highlighting does not
1273 highlight position of invalid base pairs
1276 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1277 out of memory errors are not raised when saving Jalview
1278 project from alignment window file menu
1281 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1282 Switching to RNA Helices colouring doesn't propagate to
1286 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1287 colour by RNA Helices not enabled when user created
1288 annotation added to alignment
1291 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1292 Jalview icon not shown on dock in Mountain Lion/Webstart
1294 </ul> <em>Applet Known Issues</em>
1297 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1298 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1301 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1302 Jalview and Jmol example not compatible with IE9
1305 <li>Sort by annotation score doesn't reverse order
1311 <td><div align="center">
1312 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1315 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1318 <li>Internationalisation of user interface (usually
1319 called i18n support) and translation for Spanish locale</li>
1320 <li>Define/Undefine group on current selection with
1321 Ctrl-G/Shift Ctrl-G</li>
1322 <li>Improved group creation/removal options in
1323 alignment/sequence Popup menu</li>
1324 <li>Sensible precision for symbol distribution
1325 percentages shown in logo tooltip.</li>
1326 <li>Annotation panel height set according to amount of
1327 annotation when alignment first opened</li>
1328 </ul> <em>Application</em>
1330 <li>Interactive consensus RNA secondary structure
1331 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1332 <li>Select columns containing particular features from
1333 Feature Settings dialog</li>
1334 <li>View all 'representative' PDB structures for selected
1336 <li>Update Jalview project format:
1338 <li>New file extension for Jalview projects '.jvp'</li>
1339 <li>Preserve sequence and annotation dataset (to
1340 store secondary structure annotation,etc)</li>
1341 <li>Per group and alignment annotation and RNA helix
1345 <li>New similarity measures for PCA and Tree calculation
1347 <li>Experimental support for retrieval and viewing of
1348 flanking regions for an alignment</li>
1352 <!-- issues resolved --> <em>Application</em>
1354 <li>logo keeps spinning and status remains at queued or
1355 running after job is cancelled</li>
1356 <li>cannot export features from alignments imported from
1357 Jalview/VAMSAS projects</li>
1358 <li>Buggy slider for web service parameters that take
1360 <li>Newly created RNA secondary structure line doesn't
1361 have 'display all symbols' flag set</li>
1362 <li>T-COFFEE alignment score shading scheme and other
1363 annotation shading not saved in Jalview project</li>
1364 <li>Local file cannot be loaded in freshly downloaded
1366 <li>Jalview icon not shown on dock in Mountain
1368 <li>Load file from desktop file browser fails</li>
1369 <li>Occasional NPE thrown when calculating large trees</li>
1370 <li>Cannot reorder or slide sequences after dragging an
1371 alignment onto desktop</li>
1372 <li>Colour by annotation dialog throws NPE after using
1373 'extract scores' function</li>
1374 <li>Loading/cut'n'pasting an empty file leads to a grey
1375 alignment window</li>
1376 <li>Disorder thresholds rendered incorrectly after
1377 performing IUPred disorder prediction</li>
1378 <li>Multiple group annotated consensus rows shown when
1379 changing 'normalise logo' display setting</li>
1380 <li>Find shows blank dialog after 'finished searching' if
1381 nothing matches query</li>
1382 <li>Null Pointer Exceptions raised when sorting by
1383 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1385 <li>Errors in Jmol console when structures in alignment
1386 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1388 <li>Not all working JABAWS services are shown in
1390 <li>JAVAWS version of Jalview fails to launch with
1391 'invalid literal/length code'</li>
1392 <li>Annotation/RNA Helix colourschemes cannot be applied
1393 to alignment with groups (actually fixed in 2.8.0b1)</li>
1394 <li>RNA Helices and T-Coffee Scores available as default
1397 </ul> <em>Applet</em>
1399 <li>Remove group option is shown even when selection is
1401 <li>Apply to all groups ticked but colourscheme changes
1402 don't affect groups</li>
1403 <li>Documented RNA Helices and T-Coffee Scores as valid
1404 colourscheme name</li>
1405 <li>Annotation labels drawn on sequence IDs when
1406 Annotation panel is not displayed</li>
1407 <li>Increased font size for dropdown menus on OSX and
1408 embedded windows</li>
1409 </ul> <em>Other</em>
1411 <li>Consensus sequence for alignments/groups with a
1412 single sequence were not calculated</li>
1413 <li>annotation files that contain only groups imported as
1414 annotation and junk sequences</li>
1415 <li>Fasta files with sequences containing '*' incorrectly
1416 recognised as PFAM or BLC</li>
1417 <li>conservation/PID slider apply all groups option
1418 doesn't affect background (2.8.0b1)
1420 <li>redundancy highlighting is erratic at 0% and 100%</li>
1421 <li>Remove gapped columns fails for sequences with ragged
1423 <li>AMSA annotation row with leading spaces is not
1424 registered correctly on import</li>
1425 <li>Jalview crashes when selecting PCA analysis for
1426 certain alignments</li>
1427 <li>Opening the colour by annotation dialog for an
1428 existing annotation based 'use original colours'
1429 colourscheme loses original colours setting</li>
1434 <td><div align="center">
1435 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
1436 <em>30/1/2014</em></strong>
1440 <li>Trusted certificates for JalviewLite applet and
1441 Jalview Desktop application<br />Certificate was donated by
1442 <a href="https://www.certum.eu">Certum</a> to the Jalview
1443 open source project).
1445 <li>Jalview SRS links replaced by UniProt and EBI-search
1447 <li>Output in Stockholm format</li>
1448 <li>Allow import of data from gzipped files</li>
1449 <li>Export/import group and sequence associated line
1450 graph thresholds</li>
1451 <li>Nucleotide substitution matrix that supports RNA and
1452 ambiguity codes</li>
1453 <li>Allow disorder predictions to be made on the current
1454 selection (or visible selection) in the same way that JPred
1456 <li>Groovy scripting for headless Jalview operation</li>
1457 </ul> <em>Other improvements</em>
1459 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
1460 <li>COMBINE statement uses current SEQUENCE_REF and
1461 GROUP_REF scope to group annotation rows</li>
1462 <li>Support '' style escaping of quotes in Newick
1464 <li>Group options for JABAWS service by command line name</li>
1465 <li>Empty tooltip shown for JABA service options with a
1466 link but no description</li>
1467 <li>Select primary source when selecting authority in
1468 database fetcher GUI</li>
1469 <li>Add .mfa to FASTA file extensions recognised by
1471 <li>Annotation label tooltip text wrap</li>
1476 <li>Slow scrolling when lots of annotation rows are
1478 <li>Lots of NPE (and slowness) after creating RNA
1479 secondary structure annotation line</li>
1480 <li>Sequence database accessions not imported when
1481 fetching alignments from Rfam</li>
1482 <li>Incorrect SHMR submission for sequences with
1484 <li>View all structures does not always superpose
1486 <li>Option widgets in service parameters not updated to
1487 reflect user or preset settings</li>
1488 <li>Null pointer exceptions for some services without
1489 presets or adjustable parameters</li>
1490 <li>Discover PDB IDs entry in structure menu doesn't
1491 discover PDB xRefs</li>
1492 <li>Exception encountered while trying to retrieve
1493 features with DAS</li>
1494 <li>Lowest value in annotation row isn't coloured
1495 when colour by annotation (per sequence) is coloured</li>
1496 <li>Keyboard mode P jumps to start of gapped region when
1497 residue follows a gap</li>
1498 <li>Jalview appears to hang importing an alignment with
1499 Wrap as default or after enabling Wrap</li>
1500 <li>'Right click to add annotations' message
1501 shown in wrap mode when no annotations present</li>
1502 <li>Disorder predictions fail with NPE if no automatic
1503 annotation already exists on alignment</li>
1504 <li>oninit javascript function should be called after
1505 initialisation completes</li>
1506 <li>Remove redundancy after disorder prediction corrupts
1507 alignment window display</li>
1508 <li>Example annotation file in documentation is invalid</li>
1509 <li>Grouped line graph annotation rows are not exported
1510 to annotation file</li>
1511 <li>Multi-harmony analysis cannot be run when only two
1513 <li>Cannot create multiple groups of line graphs with
1514 several 'combine' statements in annotation file</li>
1515 <li>Pressing return several times causes Number Format
1516 exceptions in keyboard mode</li>
1517 <li>Multi-harmony (SHMMR) method doesn't submit
1518 correct partitions for input data</li>
1519 <li>Translation from DNA to Amino Acids fails</li>
1520 <li>Jalview fail to load newick tree with quoted label</li>
1521 <li>--headless flag isn't understood</li>
1522 <li>ClassCastException when generating EPS in headless
1524 <li>Adjusting sequence-associated shading threshold only
1525 changes one row's threshold</li>
1526 <li>Preferences and Feature settings panel panel
1527 doesn't open</li>
1528 <li>hide consensus histogram also hides conservation and
1529 quality histograms</li>
1534 <td><div align="center">
1535 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
1537 <td><em>Application</em>
1539 <li>Support for JABAWS 2.0 Services (AACon alignment
1540 conservation, protein disorder and Clustal Omega)</li>
1541 <li>JABAWS server status indicator in Web Services
1543 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
1544 in Jalview alignment window</li>
1545 <li>Updated Jalview build and deploy framework for OSX
1546 mountain lion, windows 7, and 8</li>
1547 <li>Nucleotide substitution matrix for PCA that supports
1548 RNA and ambiguity codes</li>
1550 <li>Improved sequence database retrieval GUI</li>
1551 <li>Support fetching and database reference look up
1552 against multiple DAS sources (Fetch all from in 'fetch db
1554 <li>Jalview project improvements
1556 <li>Store and retrieve the 'belowAlignment'
1557 flag for annotation</li>
1558 <li>calcId attribute to group annotation rows on the
1560 <li>Store AACon calculation settings for a view in
1561 Jalview project</li>
1565 <li>horizontal scrolling gesture support</li>
1566 <li>Visual progress indicator when PCA calculation is
1568 <li>Simpler JABA web services menus</li>
1569 <li>visual indication that web service results are still
1570 being retrieved from server</li>
1571 <li>Serialise the dialogs that are shown when Jalview
1572 starts up for first time</li>
1573 <li>Jalview user agent string for interacting with HTTP
1575 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
1577 <li>Examples directory and Groovy library included in
1578 InstallAnywhere distribution</li>
1579 </ul> <em>Applet</em>
1581 <li>RNA alignment and secondary structure annotation
1582 visualization applet example</li>
1583 </ul> <em>General</em>
1585 <li>Normalise option for consensus sequence logo</li>
1586 <li>Reset button in PCA window to return dimensions to
1588 <li>Allow seqspace or Jalview variant of alignment PCA
1590 <li>PCA with either nucleic acid and protein substitution
1592 <li>Allow windows containing HTML reports to be exported
1594 <li>Interactive display and editing of RNA secondary
1595 structure contacts</li>
1596 <li>RNA Helix Alignment Colouring</li>
1597 <li>RNA base pair logo consensus</li>
1598 <li>Parse sequence associated secondary structure
1599 information in Stockholm files</li>
1600 <li>HTML Export database accessions and annotation
1601 information presented in tooltip for sequences</li>
1602 <li>Import secondary structure from LOCARNA clustalw
1603 style RNA alignment files</li>
1604 <li>import and visualise T-COFFEE quality scores for an
1606 <li>'colour by annotation' per sequence option to
1607 shade each sequence according to its associated alignment
1609 <li>New Jalview Logo</li>
1610 </ul> <em>Documentation and Development</em>
1612 <li>documentation for score matrices used in Jalview</li>
1613 <li>New Website!</li>
1615 <td><em>Application</em>
1617 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
1618 wsdbfetch REST service</li>
1619 <li>Stop windows being moved outside desktop on OSX</li>
1620 <li>Filetype associations not installed for webstart
1622 <li>Jalview does not always retrieve progress of a JABAWS
1623 job execution in full once it is complete</li>
1624 <li>revise SHMR RSBS definition to ensure alignment is
1625 uploaded via ali_file parameter</li>
1626 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
1627 <li>View all structures superposed fails with exception</li>
1628 <li>Jnet job queues forever if a very short sequence is
1629 submitted for prediction</li>
1630 <li>Cut and paste menu not opened when mouse clicked on
1632 <li>Putting fractional value into integer text box in
1633 alignment parameter dialog causes Jalview to hang</li>
1634 <li>Structure view highlighting doesn't work on
1636 <li>View all structures fails with exception shown in
1638 <li>Characters in filename associated with PDBEntry not
1639 escaped in a platform independent way</li>
1640 <li>Jalview desktop fails to launch with exception when
1642 <li>Tree calculation reports 'you must have 2 or more
1643 sequences selected' when selection is empty</li>
1644 <li>Jalview desktop fails to launch with jar signature
1645 failure when java web start temporary file caching is
1647 <li>DAS Sequence retrieval with range qualification
1648 results in sequence xref which includes range qualification</li>
1649 <li>Errors during processing of command line arguments
1650 cause progress bar (JAL-898) to be removed</li>
1651 <li>Replace comma for semi-colon option not disabled for
1652 DAS sources in sequence fetcher</li>
1653 <li>Cannot close news reader when JABAWS server warning
1654 dialog is shown</li>
1655 <li>Option widgets not updated to reflect user settings</li>
1656 <li>Edited sequence not submitted to web service</li>
1657 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
1658 <li>InstallAnywhere installer doesn't unpack and run
1659 on OSX Mountain Lion</li>
1660 <li>Annotation panel not given a scroll bar when
1661 sequences with alignment annotation are pasted into the
1663 <li>Sequence associated annotation rows not associated
1664 when loaded from Jalview project</li>
1665 <li>Browser launch fails with NPE on java 1.7</li>
1666 <li>JABAWS alignment marked as finished when job was
1667 cancelled or job failed due to invalid input</li>
1668 <li>NPE with v2.7 example when clicking on Tree
1669 associated with all views</li>
1670 <li>Exceptions when copy/paste sequences with grouped
1671 annotation rows to new window</li>
1672 </ul> <em>Applet</em>
1674 <li>Sequence features are momentarily displayed before
1675 they are hidden using hidefeaturegroups applet parameter</li>
1676 <li>loading features via javascript API automatically
1677 enables feature display</li>
1678 <li>scrollToColumnIn javascript API method doesn't
1680 </ul> <em>General</em>
1682 <li>Redundancy removal fails for rna alignment</li>
1683 <li>PCA calculation fails when sequence has been selected
1684 and then deselected</li>
1685 <li>PCA window shows grey box when first opened on OSX</li>
1686 <li>Letters coloured pink in sequence logo when alignment
1687 coloured with clustalx</li>
1688 <li>Choosing fonts without letter symbols defined causes
1689 exceptions and redraw errors</li>
1690 <li>Initial PCA plot view is not same as manually
1691 reconfigured view</li>
1692 <li>Grouped annotation graph label has incorrect line
1694 <li>Grouped annotation graph label display is corrupted
1695 for lots of labels</li>
1700 <div align="center">
1701 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
1704 <td><em>Application</em>
1706 <li>Jalview Desktop News Reader</li>
1707 <li>Tweaked default layout of web services menu</li>
1708 <li>View/alignment association menu to enable user to
1709 easily specify which alignment a multi-structure view takes
1710 its colours/correspondences from</li>
1711 <li>Allow properties file location to be specified as URL</li>
1712 <li>Extend Jalview project to preserve associations
1713 between many alignment views and a single Jmol display</li>
1714 <li>Store annotation row height in Jalview project file</li>
1715 <li>Annotation row column label formatting attributes
1716 stored in project file</li>
1717 <li>Annotation row order for auto-calculated annotation
1718 rows preserved in Jalview project file</li>
1719 <li>Visual progress indication when Jalview state is
1720 saved using Desktop window menu</li>
1721 <li>Visual indication that command line arguments are
1722 still being processed</li>
1723 <li>Groovy script execution from URL</li>
1724 <li>Colour by annotation default min and max colours in
1726 <li>Automatically associate PDB files dragged onto an
1727 alignment with sequences that have high similarity and
1729 <li>Update JGoogleAnalytics to latest release (0.3)</li>
1730 <li>'view structures' option to open many
1731 structures in same window</li>
1732 <li>Sort associated views menu option for tree panel</li>
1733 <li>Group all JABA and non-JABA services for a particular
1734 analysis function in its own submenu</li>
1735 </ul> <em>Applet</em>
1737 <li>Userdefined and autogenerated annotation rows for
1739 <li>Adjustment of alignment annotation pane height</li>
1740 <li>Annotation scrollbar for annotation panel</li>
1741 <li>Drag to reorder annotation rows in annotation panel</li>
1742 <li>'automaticScrolling' parameter</li>
1743 <li>Allow sequences with partial ID string matches to be
1744 annotated from GFF/Jalview features files</li>
1745 <li>Sequence logo annotation row in applet</li>
1746 <li>Absolute paths relative to host server in applet
1747 parameters are treated as such</li>
1748 <li>New in the JalviewLite javascript API:
1750 <li>JalviewLite.js javascript library</li>
1751 <li>Javascript callbacks for
1753 <li>Applet initialisation</li>
1754 <li>Sequence/alignment mouse-overs and selections</li>
1757 <li>scrollTo row and column alignment scrolling
1759 <li>Select sequence/alignment regions from javascript</li>
1760 <li>javascript structure viewer harness to pass
1761 messages between Jmol and Jalview when running as
1762 distinct applets</li>
1763 <li>sortBy method</li>
1764 <li>Set of applet and application examples shipped
1765 with documentation</li>
1766 <li>New example to demonstrate JalviewLite and Jmol
1767 javascript message exchange</li>
1769 </ul> <em>General</em>
1771 <li>Enable Jmol displays to be associated with multiple
1772 multiple alignments</li>
1773 <li>Option to automatically sort alignment with new tree</li>
1774 <li>User configurable link to enable redirects to a
1775 www.Jalview.org mirror</li>
1776 <li>Jmol colours option for Jmol displays</li>
1777 <li>Configurable newline string when writing alignment
1778 and other flat files</li>
1779 <li>Allow alignment annotation description lines to
1780 contain html tags</li>
1781 </ul> <em>Documentation and Development</em>
1783 <li>Add groovy test harness for bulk load testing to
1785 <li>Groovy script to load and align a set of sequences
1786 using a web service before displaying the result in the
1787 Jalview desktop</li>
1788 <li>Restructured javascript and applet api documentation</li>
1789 <li>Ant target to publish example html files with applet
1791 <li>Netbeans project for building Jalview from source</li>
1792 <li>ant task to create online javadoc for Jalview source</li>
1794 <td><em>Application</em>
1796 <li>User defined colourscheme throws exception when
1797 current built in colourscheme is saved as new scheme</li>
1798 <li>AlignFrame->Save in application pops up save
1799 dialog for valid filename/format</li>
1800 <li>Cannot view associated structure for UniProt sequence</li>
1801 <li>PDB file association breaks for UniProt sequence
1803 <li>Associate PDB from file dialog does not tell you
1804 which sequence is to be associated with the file</li>
1805 <li>Find All raises null pointer exception when query
1806 only matches sequence IDs</li>
1807 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
1808 <li>Jalview project with Jmol views created with Jalview
1809 2.4 cannot be loaded</li>
1810 <li>Filetype associations not installed for webstart
1812 <li>Two or more chains in a single PDB file associated
1813 with sequences in different alignments do not get coloured
1814 by their associated sequence</li>
1815 <li>Visibility status of autocalculated annotation row
1816 not preserved when project is loaded</li>
1817 <li>Annotation row height and visibility attributes not
1818 stored in Jalview project</li>
1819 <li>Tree bootstraps are not preserved when saved as a
1820 Jalview project</li>
1821 <li>Envision2 workflow tooltips are corrupted</li>
1822 <li>Enabling show group conservation also enables colour
1823 by conservation</li>
1824 <li>Duplicate group associated conservation or consensus
1825 created on new view</li>
1826 <li>Annotation scrollbar not displayed after 'show
1827 all hidden annotation rows' option selected</li>
1828 <li>Alignment quality not updated after alignment
1829 annotation row is hidden then shown</li>
1830 <li>Preserve colouring of structures coloured by
1831 sequences in pre Jalview 2.7 projects</li>
1832 <li>Web service job parameter dialog is not laid out
1834 <li>Web services menu not refreshed after 'reset
1835 services' button is pressed in preferences</li>
1836 <li>Annotation off by one in Jalview v2_3 example project</li>
1837 <li>Structures imported from file and saved in project
1838 get name like jalview_pdb1234.txt when reloaded</li>
1839 <li>Jalview does not always retrieve progress of a JABAWS
1840 job execution in full once it is complete</li>
1841 </ul> <em>Applet</em>
1843 <li>Alignment height set incorrectly when lots of
1844 annotation rows are displayed</li>
1845 <li>Relative URLs in feature HTML text not resolved to
1847 <li>View follows highlighting does not work for positions
1849 <li><= shown as = in tooltip</li>
1850 <li>Export features raises exception when no features
1852 <li>Separator string used for serialising lists of IDs
1853 for javascript api is modified when separator string
1854 provided as parameter</li>
1855 <li>Null pointer exception when selecting tree leaves for
1856 alignment with no existing selection</li>
1857 <li>Relative URLs for datasources assumed to be relative
1858 to applet's codebase</li>
1859 <li>Status bar not updated after finished searching and
1860 search wraps around to first result</li>
1861 <li>StructureSelectionManager instance shared between
1862 several Jalview applets causes race conditions and memory
1864 <li>Hover tooltip and mouseover of position on structure
1865 not sent from Jmol in applet</li>
1866 <li>Certain sequences of javascript method calls to
1867 applet API fatally hang browser</li>
1868 </ul> <em>General</em>
1870 <li>View follows structure mouseover scrolls beyond
1871 position with wrapped view and hidden regions</li>
1872 <li>Find sequence position moves to wrong residue
1873 with/without hidden columns</li>
1874 <li>Sequence length given in alignment properties window
1876 <li>InvalidNumberFormat exceptions thrown when trying to
1877 import PDB like structure files</li>
1878 <li>Positional search results are only highlighted
1879 between user-supplied sequence start/end bounds</li>
1880 <li>End attribute of sequence is not validated</li>
1881 <li>Find dialog only finds first sequence containing a
1882 given sequence position</li>
1883 <li>Sequence numbering not preserved in MSF alignment
1885 <li>Jalview PDB file reader does not extract sequence
1886 from nucleotide chains correctly</li>
1887 <li>Structure colours not updated when tree partition
1888 changed in alignment</li>
1889 <li>Sequence associated secondary structure not correctly
1890 parsed in interleaved stockholm</li>
1891 <li>Colour by annotation dialog does not restore current
1893 <li>Hiding (nearly) all sequences doesn't work
1895 <li>Sequences containing lowercase letters are not
1896 properly associated with their pdb files</li>
1897 </ul> <em>Documentation and Development</em>
1899 <li>schemas/JalviewWsParamSet.xsd corrupted by
1900 ApplyCopyright tool</li>
1905 <div align="center">
1906 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
1909 <td><em>Application</em>
1911 <li>New warning dialog when the Jalview Desktop cannot
1912 contact web services</li>
1913 <li>JABA service parameters for a preset are shown in
1914 service job window</li>
1915 <li>JABA Service menu entries reworded</li>
1919 <li>Modeller PIR IO broken - cannot correctly import a
1920 pir file emitted by Jalview</li>
1921 <li>Existing feature settings transferred to new
1922 alignment view created from cut'n'paste</li>
1923 <li>Improved test for mixed amino/nucleotide chains when
1924 parsing PDB files</li>
1925 <li>Consensus and conservation annotation rows
1926 occasionally become blank for all new windows</li>
1927 <li>Exception raised when right clicking above sequences
1928 in wrapped view mode</li>
1929 </ul> <em>Application</em>
1931 <li>multiple multiply aligned structure views cause cpu
1932 usage to hit 100% and computer to hang</li>
1933 <li>Web Service parameter layout breaks for long user
1934 parameter names</li>
1935 <li>Jaba service discovery hangs desktop if Jaba server
1942 <div align="center">
1943 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
1946 <td><em>Application</em>
1948 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
1949 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
1952 <li>Web Services preference tab</li>
1953 <li>Analysis parameters dialog box and user defined
1955 <li>Improved speed and layout of Envision2 service menu</li>
1956 <li>Superpose structures using associated sequence
1958 <li>Export coordinates and projection as CSV from PCA
1960 </ul> <em>Applet</em>
1962 <li>enable javascript: execution by the applet via the
1963 link out mechanism</li>
1964 </ul> <em>Other</em>
1966 <li>Updated the Jmol Jalview interface to work with Jmol
1968 <li>The Jalview Desktop and JalviewLite applet now
1969 require Java 1.5</li>
1970 <li>Allow Jalview feature colour specification for GFF
1971 sequence annotation files</li>
1972 <li>New 'colour by label' keword in Jalview feature file
1973 type colour specification</li>
1974 <li>New Jalview Desktop Groovy API method that allows a
1975 script to check if it being run in an interactive session or
1976 in a batch operation from the Jalview command line</li>
1980 <li>clustalx colourscheme colours Ds preferentially when
1981 both D+E are present in over 50% of the column</li>
1982 </ul> <em>Application</em>
1984 <li>typo in AlignmentFrame->View->Hide->all but
1985 selected Regions menu item</li>
1986 <li>sequence fetcher replaces ',' for ';' when the ',' is
1987 part of a valid accession ID</li>
1988 <li>fatal OOM if object retrieved by sequence fetcher
1989 runs out of memory</li>
1990 <li>unhandled Out of Memory Error when viewing pca
1991 analysis results</li>
1992 <li>InstallAnywhere builds fail to launch on OS X java
1993 10.5 update 4 (due to apple Java 1.6 update)</li>
1994 <li>Installanywhere Jalview silently fails to launch</li>
1995 </ul> <em>Applet</em>
1997 <li>Jalview.getFeatureGroups() raises an
1998 ArrayIndexOutOfBoundsException if no feature groups are
2005 <div align="center">
2006 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2012 <li>Alignment prettyprinter doesn't cope with long
2014 <li>clustalx colourscheme colours Ds preferentially when
2015 both D+E are present in over 50% of the column</li>
2016 <li>nucleic acid structures retrieved from PDB do not
2017 import correctly</li>
2018 <li>More columns get selected than were clicked on when a
2019 number of columns are hidden</li>
2020 <li>annotation label popup menu not providing correct
2021 add/hide/show options when rows are hidden or none are
2023 <li>Stockholm format shown in list of readable formats,
2024 and parser copes better with alignments from RFAM.</li>
2025 <li>CSV output of consensus only includes the percentage
2026 of all symbols if sequence logo display is enabled</li>
2028 </ul> <em>Applet</em>
2030 <li>annotation panel disappears when annotation is
2032 </ul> <em>Application</em>
2034 <li>Alignment view not redrawn properly when new
2035 alignment opened where annotation panel is visible but no
2036 annotations are present on alignment</li>
2037 <li>pasted region containing hidden columns is
2038 incorrectly displayed in new alignment window</li>
2039 <li>Jalview slow to complete operations when stdout is
2040 flooded (fix is to close the Jalview console)</li>
2041 <li>typo in AlignmentFrame->View->Hide->all but
2042 selected Rregions menu item.</li>
2043 <li>inconsistent group submenu and Format submenu entry
2044 'Un' or 'Non'conserved</li>
2045 <li>Sequence feature settings are being shared by
2046 multiple distinct alignments</li>
2047 <li>group annotation not recreated when tree partition is
2049 <li>double click on group annotation to select sequences
2050 does not propagate to associated trees</li>
2051 <li>Mac OSX specific issues:
2053 <li>exception raised when mouse clicked on desktop
2054 window background</li>
2055 <li>Desktop menu placed on menu bar and application
2056 name set correctly</li>
2057 <li>sequence feature settings not wide enough for the
2058 save feature colourscheme button</li>
2067 <div align="center">
2068 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2071 <td><em>New Capabilities</em>
2073 <li>URL links generated from description line for
2074 regular-expression based URL links (applet and application)
2081 <li>Non-positional feature URL links are shown in link
2083 <li>Linked viewing of nucleic acid sequences and
2085 <li>Automatic Scrolling option in View menu to display
2086 the currently highlighted region of an alignment.</li>
2087 <li>Order an alignment by sequence length, or using the
2088 average score or total feature count for each sequence.</li>
2089 <li>Shading features by score or associated description</li>
2090 <li>Subdivide alignment and groups based on identity of
2091 selected subsequence (Make Groups from Selection).</li>
2092 <li>New hide/show options including Shift+Control+H to
2093 hide everything but the currently selected region.</li>
2094 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2095 </ul> <em>Application</em>
2097 <li>Fetch DB References capabilities and UI expanded to
2098 support retrieval from DAS sequence sources</li>
2099 <li>Local DAS Sequence sources can be added via the
2100 command line or via the Add local source dialog box.</li>
2101 <li>DAS Dbref and DbxRef feature types are parsed as
2102 database references and protein_name is parsed as
2103 description line (BioSapiens terms).</li>
2104 <li>Enable or disable non-positional feature and database
2105 references in sequence ID tooltip from View menu in
2107 <!-- <li>New hidden columns and rows and representatives capabilities
2108 in annotations file (in progress - not yet fully implemented)</li> -->
2109 <li>Group-associated consensus, sequence logos and
2110 conservation plots</li>
2111 <li>Symbol distributions for each column can be exported
2112 and visualized as sequence logos</li>
2113 <li>Optionally scale multi-character column labels to fit
2114 within each column of annotation row<!-- todo for applet -->
2116 <li>Optional automatic sort of associated alignment view
2117 when a new tree is opened.</li>
2118 <li>Jalview Java Console</li>
2119 <li>Better placement of desktop window when moving
2120 between different screens.</li>
2121 <li>New preference items for sequence ID tooltip and
2122 consensus annotation</li>
2123 <li>Client to submit sequences and IDs to Envision2
2125 <li><em>Vamsas Capabilities</em>
2127 <li>Improved VAMSAS synchronization (Jalview archive
2128 used to preserve views, structures, and tree display
2130 <li>Import of vamsas documents from disk or URL via
2132 <li>Sharing of selected regions between views and
2133 with other VAMSAS applications (Experimental feature!)</li>
2134 <li>Updated API to VAMSAS version 0.2</li>
2136 </ul> <em>Applet</em>
2138 <li>Middle button resizes annotation row height</li>
2141 <li>sortByTree (true/false) - automatically sort the
2142 associated alignment view by the tree when a new tree is
2144 <li>showTreeBootstraps (true/false) - show or hide
2145 branch bootstraps (default is to show them if available)</li>
2146 <li>showTreeDistances (true/false) - show or hide
2147 branch lengths (default is to show them if available)</li>
2148 <li>showUnlinkedTreeNodes (true/false) - indicate if
2149 unassociated nodes should be highlighted in the tree
2151 <li>heightScale and widthScale (1.0 or more) -
2152 increase the height or width of a cell in the alignment
2153 grid relative to the current font size.</li>
2156 <li>Non-positional features displayed in sequence ID
2158 </ul> <em>Other</em>
2160 <li>Features format: graduated colour definitions and
2161 specification of feature scores</li>
2162 <li>Alignment Annotations format: new keywords for group
2163 associated annotation (GROUP_REF) and annotation row display
2164 properties (ROW_PROPERTIES)</li>
2165 <li>XML formats extended to support graduated feature
2166 colourschemes, group associated annotation, and profile
2167 visualization settings.</li></td>
2170 <li>Source field in GFF files parsed as feature source
2171 rather than description</li>
2172 <li>Non-positional features are now included in sequence
2173 feature and gff files (controlled via non-positional feature
2174 visibility in tooltip).</li>
2175 <li>URL links generated for all feature links (bugfix)</li>
2176 <li>Added URL embedding instructions to features file
2178 <li>Codons containing ambiguous nucleotides translated as
2179 'X' in peptide product</li>
2180 <li>Match case switch in find dialog box works for both
2181 sequence ID and sequence string and query strings do not
2182 have to be in upper case to match case-insensitively.</li>
2183 <li>AMSA files only contain first column of
2184 multi-character column annotation labels</li>
2185 <li>Jalview Annotation File generation/parsing consistent
2186 with documentation (e.g. Stockholm annotation can be
2187 exported and re-imported)</li>
2188 <li>PDB files without embedded PDB IDs given a friendly
2190 <li>Find incrementally searches ID string matches as well
2191 as subsequence matches, and correctly reports total number
2195 <li>Better handling of exceptions during sequence
2197 <li>Dasobert generated non-positional feature URL
2198 link text excludes the start_end suffix</li>
2199 <li>DAS feature and source retrieval buttons disabled
2200 when fetch or registry operations in progress.</li>
2201 <li>PDB files retrieved from URLs are cached properly</li>
2202 <li>Sequence description lines properly shared via
2204 <li>Sequence fetcher fetches multiple records for all
2206 <li>Ensured that command line das feature retrieval
2207 completes before alignment figures are generated.</li>
2208 <li>Reduced time taken when opening file browser for
2210 <li>isAligned check prior to calculating tree, PCA or
2211 submitting an MSA to JNet now excludes hidden sequences.</li>
2212 <li>User defined group colours properly recovered
2213 from Jalview projects.</li>
2222 <div align="center">
2223 <strong>2.4.0.b2</strong><br> 28/10/2009
2228 <li>Experimental support for google analytics usage
2230 <li>Jalview privacy settings (user preferences and docs).</li>
2235 <li>Race condition in applet preventing startup in
2237 <li>Exception when feature created from selection beyond
2238 length of sequence.</li>
2239 <li>Allow synthetic PDB files to be imported gracefully</li>
2240 <li>Sequence associated annotation rows associate with
2241 all sequences with a given id</li>
2242 <li>Find function matches case-insensitively for sequence
2243 ID string searches</li>
2244 <li>Non-standard characters do not cause pairwise
2245 alignment to fail with exception</li>
2246 </ul> <em>Application Issues</em>
2248 <li>Sequences are now validated against EMBL database</li>
2249 <li>Sequence fetcher fetches multiple records for all
2251 </ul> <em>InstallAnywhere Issues</em>
2253 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2254 issue with installAnywhere mechanism)</li>
2255 <li>Command line launching of JARs from InstallAnywhere
2256 version (java class versioning error fixed)</li>
2263 <div align="center">
2264 <strong>2.4</strong><br> 27/8/2008
2267 <td><em>User Interface</em>
2269 <li>Linked highlighting of codon and amino acid from
2270 translation and protein products</li>
2271 <li>Linked highlighting of structure associated with
2272 residue mapping to codon position</li>
2273 <li>Sequence Fetcher provides example accession numbers
2274 and 'clear' button</li>
2275 <li>MemoryMonitor added as an option under Desktop's
2277 <li>Extract score function to parse whitespace separated
2278 numeric data in description line</li>
2279 <li>Column labels in alignment annotation can be centred.</li>
2280 <li>Tooltip for sequence associated annotation give name
2282 </ul> <em>Web Services and URL fetching</em>
2284 <li>JPred3 web service</li>
2285 <li>Prototype sequence search client (no public services
2287 <li>Fetch either seed alignment or full alignment from
2289 <li>URL Links created for matching database cross
2290 references as well as sequence ID</li>
2291 <li>URL Links can be created using regular-expressions</li>
2292 </ul> <em>Sequence Database Connectivity</em>
2294 <li>Retrieval of cross-referenced sequences from other
2296 <li>Generalised database reference retrieval and
2297 validation to all fetchable databases</li>
2298 <li>Fetch sequences from DAS sources supporting the
2299 sequence command</li>
2300 </ul> <em>Import and Export</em>
2301 <li>export annotation rows as CSV for spreadsheet import</li>
2302 <li>Jalview projects record alignment dataset associations,
2303 EMBL products, and cDNA sequence mappings</li>
2304 <li>Sequence Group colour can be specified in Annotation
2306 <li>Ad-hoc colouring of group in Annotation File using RGB
2307 triplet as name of colourscheme</li>
2308 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2310 <li>treenode binding for VAMSAS tree exchange</li>
2311 <li>local editing and update of sequences in VAMSAS
2312 alignments (experimental)</li>
2313 <li>Create new or select existing session to join</li>
2314 <li>load and save of vamsas documents</li>
2315 </ul> <em>Application command line</em>
2317 <li>-tree parameter to open trees (introduced for passing
2319 <li>-fetchfrom command line argument to specify nicknames
2320 of DAS servers to query for alignment features</li>
2321 <li>-dasserver command line argument to add new servers
2322 that are also automatically queried for features</li>
2323 <li>-groovy command line argument executes a given groovy
2324 script after all input data has been loaded and parsed</li>
2325 </ul> <em>Applet-Application data exchange</em>
2327 <li>Trees passed as applet parameters can be passed to
2328 application (when using "View in full
2329 application")</li>
2330 </ul> <em>Applet Parameters</em>
2332 <li>feature group display control parameter</li>
2333 <li>debug parameter</li>
2334 <li>showbutton parameter</li>
2335 </ul> <em>Applet API methods</em>
2337 <li>newView public method</li>
2338 <li>Window (current view) specific get/set public methods</li>
2339 <li>Feature display control methods</li>
2340 <li>get list of currently selected sequences</li>
2341 </ul> <em>New Jalview distribution features</em>
2343 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2344 <li>RELEASE file gives build properties for the latest
2345 Jalview release.</li>
2346 <li>Java 1.1 Applet build made easier and donotobfuscate
2347 property controls execution of obfuscator</li>
2348 <li>Build target for generating source distribution</li>
2349 <li>Debug flag for javacc</li>
2350 <li>.jalview_properties file is documented (slightly) in
2351 jalview.bin.Cache</li>
2352 <li>Continuous Build Integration for stable and
2353 development version of Application, Applet and source
2358 <li>selected region output includes visible annotations
2359 (for certain formats)</li>
2360 <li>edit label/displaychar contains existing label/char
2362 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2363 <li>shorter peptide product names from EMBL records</li>
2364 <li>Newick string generator makes compact representations</li>
2365 <li>bootstrap values parsed correctly for tree files with
2367 <li>pathological filechooser bug avoided by not allowing
2368 filenames containing a ':'</li>
2369 <li>Fixed exception when parsing GFF files containing
2370 global sequence features</li>
2371 <li>Alignment datasets are finalized only when number of
2372 references from alignment sequences goes to zero</li>
2373 <li>Close of tree branch colour box without colour
2374 selection causes cascading exceptions</li>
2375 <li>occasional negative imgwidth exceptions</li>
2376 <li>better reporting of non-fatal warnings to user when
2377 file parsing fails.</li>
2378 <li>Save works when Jalview project is default format</li>
2379 <li>Save as dialog opened if current alignment format is
2380 not a valid output format</li>
2381 <li>UniProt canonical names introduced for both das and
2383 <li>Histidine should be midblue (not pink!) in Zappo</li>
2384 <li>error messages passed up and output when data read
2386 <li>edit undo recovers previous dataset sequence when
2387 sequence is edited</li>
2388 <li>allow PDB files without pdb ID HEADER lines (like
2389 those generated by MODELLER) to be read in properly</li>
2390 <li>allow reading of JPred concise files as a normal
2392 <li>Stockholm annotation parsing and alignment properties
2393 import fixed for PFAM records</li>
2394 <li>Structure view windows have correct name in Desktop
2396 <li>annotation consisting of sequence associated scores
2397 can be read and written correctly to annotation file</li>
2398 <li>Aligned cDNA translation to aligned peptide works
2400 <li>Fixed display of hidden sequence markers and
2401 non-italic font for representatives in Applet</li>
2402 <li>Applet Menus are always embedded in applet window on
2404 <li>Newly shown features appear at top of stack (in
2406 <li>Annotations added via parameter not drawn properly
2407 due to null pointer exceptions</li>
2408 <li>Secondary structure lines are drawn starting from
2409 first column of alignment</li>
2410 <li>UniProt XML import updated for new schema release in
2412 <li>Sequence feature to sequence ID match for Features
2413 file is case-insensitive</li>
2414 <li>Sequence features read from Features file appended to
2415 all sequences with matching IDs</li>
2416 <li>PDB structure coloured correctly for associated views
2417 containing a sub-sequence</li>
2418 <li>PDB files can be retrieved by applet from Jar files</li>
2419 <li>feature and annotation file applet parameters
2420 referring to different directories are retrieved correctly</li>
2421 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
2422 <li>Fixed application hang whilst waiting for
2423 splash-screen version check to complete</li>
2424 <li>Applet properly URLencodes input parameter values
2425 when passing them to the launchApp service</li>
2426 <li>display name and local features preserved in results
2427 retrieved from web service</li>
2428 <li>Visual delay indication for sequence retrieval and
2429 sequence fetcher initialisation</li>
2430 <li>updated Application to use DAS 1.53e version of
2431 dasobert DAS client</li>
2432 <li>Re-instated Full AMSA support and .amsa file
2434 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
2442 <div align="center">
2443 <strong>2.3</strong><br> 9/5/07
2448 <li>Jmol 11.0.2 integration</li>
2449 <li>PDB views stored in Jalview XML files</li>
2450 <li>Slide sequences</li>
2451 <li>Edit sequence in place</li>
2452 <li>EMBL CDS features</li>
2453 <li>DAS Feature mapping</li>
2454 <li>Feature ordering</li>
2455 <li>Alignment Properties</li>
2456 <li>Annotation Scores</li>
2457 <li>Sort by scores</li>
2458 <li>Feature/annotation editing in applet</li>
2463 <li>Headless state operation in 2.2.1</li>
2464 <li>Incorrect and unstable DNA pairwise alignment</li>
2465 <li>Cut and paste of sequences with annotation</li>
2466 <li>Feature group display state in XML</li>
2467 <li>Feature ordering in XML</li>
2468 <li>blc file iteration selection using filename # suffix</li>
2469 <li>Stockholm alignment properties</li>
2470 <li>Stockhom alignment secondary structure annotation</li>
2471 <li>2.2.1 applet had no feature transparency</li>
2472 <li>Number pad keys can be used in cursor mode</li>
2473 <li>Structure Viewer mirror image resolved</li>
2480 <div align="center">
2481 <strong>2.2.1</strong><br> 12/2/07
2486 <li>Non standard characters can be read and displayed
2487 <li>Annotations/Features can be imported/exported to the
2489 <li>Applet allows editing of sequence/annotation/group
2490 name & description
2491 <li>Preference setting to display sequence name in
2493 <li>Annotation file format extended to allow
2494 Sequence_groups to be defined
2495 <li>Default opening of alignment overview panel can be
2496 specified in preferences
2497 <li>PDB residue numbering annotation added to associated
2503 <li>Applet crash under certain Linux OS with Java 1.6
2505 <li>Annotation file export / import bugs fixed
2506 <li>PNG / EPS image output bugs fixed
2512 <div align="center">
2513 <strong>2.2</strong><br> 27/11/06
2518 <li>Multiple views on alignment
2519 <li>Sequence feature editing
2520 <li>"Reload" alignment
2521 <li>"Save" to current filename
2522 <li>Background dependent text colour
2523 <li>Right align sequence ids
2524 <li>User-defined lower case residue colours
2527 <li>Menu item accelerator keys
2528 <li>Control-V pastes to current alignment
2529 <li>Cancel button for DAS Feature Fetching
2530 <li>PCA and PDB Viewers zoom via mouse roller
2531 <li>User-defined sub-tree colours and sub-tree selection
2538 <li>'New Window' button on the 'Output to Text box'
2543 <li>New memory efficient Undo/Redo System
2544 <li>Optimised symbol lookups and conservation/consensus
2546 <li>Region Conservation/Consensus recalculated after
2548 <li>Fixed Remove Empty Columns Bug (empty columns at end
2550 <li>Slowed DAS Feature Fetching for increased robustness.
2557 <li>Made angle brackets in ASCII feature descriptions
2559 <li>Re-instated Zoom function for PCA
2560 <li>Sequence descriptions conserved in web service
2562 <li>UniProt ID discoverer uses any word separated by
2564 <li>WsDbFetch query/result association resolved
2565 <li>Tree leaf to sequence mapping improved
2566 <li>Smooth fonts switch moved to FontChooser dialog box.
2578 <div align="center">
2579 <strong>2.1.1</strong><br> 12/9/06
2584 <li>Copy consensus sequence to clipboard</li>
2589 <li>Image output - rightmost residues are rendered if
2590 sequence id panel has been resized</li>
2591 <li>Image output - all offscreen group boundaries are
2593 <li>Annotation files with sequence references - all
2594 elements in file are relative to sequence position</li>
2595 <li>Mac Applet users can use Alt key for group editing</li>
2601 <div align="center">
2602 <strong>2.1</strong><br> 22/8/06
2607 <li>MAFFT Multiple Alignment in default Web Service list</li>
2608 <li>DAS Feature fetching</li>
2609 <li>Hide sequences and columns</li>
2610 <li>Export Annotations and Features</li>
2611 <li>GFF file reading / writing</li>
2612 <li>Associate structures with sequences from local PDB
2614 <li>Add sequences to exisiting alignment</li>
2615 <li>Recently opened files / URL lists</li>
2616 <li>Applet can launch the full application</li>
2617 <li>Applet has transparency for features (Java 1.2
2619 <li>Applet has user defined colours parameter</li>
2620 <li>Applet can load sequences from parameter
2621 "sequence<em>x</em>"
2627 <li>Redundancy Panel reinstalled in the Applet</li>
2628 <li>Monospaced font - EPS / rescaling bug fixed</li>
2629 <li>Annotation files with sequence references bug fixed</li>
2635 <div align="center">
2636 <strong>2.08.1</strong><br> 2/5/06
2641 <li>Change case of selected region from Popup menu</li>
2642 <li>Choose to match case when searching</li>
2643 <li>Middle mouse button and mouse movement can compress /
2644 expand the visible width and height of the alignment</li>
2649 <li>Annotation Panel displays complete JNet results</li>
2655 <div align="center">
2656 <strong>2.08b</strong><br> 18/4/06
2662 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
2663 <li>Righthand label on wrapped alignments shows correct
2670 <div align="center">
2671 <strong>2.08</strong><br> 10/4/06
2676 <li>Editing can be locked to the selection area</li>
2677 <li>Keyboard editing</li>
2678 <li>Create sequence features from searches</li>
2679 <li>Precalculated annotations can be loaded onto
2681 <li>Features file allows grouping of features</li>
2682 <li>Annotation Colouring scheme added</li>
2683 <li>Smooth fonts off by default - Faster rendering</li>
2684 <li>Choose to toggle Autocalculate Consensus On/Off</li>
2689 <li>Drag & Drop fixed on Linux</li>
2690 <li>Jalview Archive file faster to load/save, sequence
2691 descriptions saved.</li>
2697 <div align="center">
2698 <strong>2.07</strong><br> 12/12/05
2703 <li>PDB Structure Viewer enhanced</li>
2704 <li>Sequence Feature retrieval and display enhanced</li>
2705 <li>Choose to output sequence start-end after sequence
2706 name for file output</li>
2707 <li>Sequence Fetcher WSDBFetch@EBI</li>
2708 <li>Applet can read feature files, PDB files and can be
2709 used for HTML form input</li>
2714 <li>HTML output writes groups and features</li>
2715 <li>Group editing is Control and mouse click</li>
2716 <li>File IO bugs</li>
2722 <div align="center">
2723 <strong>2.06</strong><br> 28/9/05
2728 <li>View annotations in wrapped mode</li>
2729 <li>More options for PCA viewer</li>
2734 <li>GUI bugs resolved</li>
2735 <li>Runs with -nodisplay from command line</li>
2741 <div align="center">
2742 <strong>2.05b</strong><br> 15/9/05
2747 <li>Choose EPS export as lineart or text</li>
2748 <li>Jar files are executable</li>
2749 <li>Can read in Uracil - maps to unknown residue</li>
2754 <li>Known OutOfMemory errors give warning message</li>
2755 <li>Overview window calculated more efficiently</li>
2756 <li>Several GUI bugs resolved</li>
2762 <div align="center">
2763 <strong>2.05</strong><br> 30/8/05
2768 <li>Edit and annotate in "Wrapped" view</li>
2773 <li>Several GUI bugs resolved</li>
2779 <div align="center">
2780 <strong>2.04</strong><br> 24/8/05
2785 <li>Hold down mouse wheel & scroll to change font
2791 <li>Improved JPred client reliability</li>
2792 <li>Improved loading of Jalview files</li>
2798 <div align="center">
2799 <strong>2.03</strong><br> 18/8/05
2804 <li>Set Proxy server name and port in preferences</li>
2805 <li>Multiple URL links from sequence ids</li>
2806 <li>User Defined Colours can have a scheme name and added
2808 <li>Choose to ignore gaps in consensus calculation</li>
2809 <li>Unix users can set default web browser</li>
2810 <li>Runs without GUI for batch processing</li>
2811 <li>Dynamically generated Web Service Menus</li>
2816 <li>InstallAnywhere download for Sparc Solaris</li>
2822 <div align="center">
2823 <strong>2.02</strong><br> 18/7/05
2829 <li>Copy & Paste order of sequences maintains
2830 alignment order.</li>
2836 <div align="center">
2837 <strong>2.01</strong><br> 12/7/05
2842 <li>Use delete key for deleting selection.</li>
2843 <li>Use Mouse wheel to scroll sequences.</li>
2844 <li>Help file updated to describe how to add alignment
2846 <li>Version and build date written to build properties
2848 <li>InstallAnywhere installation will check for updates
2849 at launch of Jalview.</li>
2854 <li>Delete gaps bug fixed.</li>
2855 <li>FileChooser sorts columns.</li>
2856 <li>Can remove groups one by one.</li>
2857 <li>Filechooser icons installed.</li>
2858 <li>Finder ignores return character when searching.
2859 Return key will initiate a search.<br>
2866 <div align="center">
2867 <strong>2.0</strong><br> 20/6/05
2872 <li>New codebase</li>