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">
86 <li><!-- JAL-2316, -->URLs for viewing database cross-references provided by identifiers.org and the EMBL-EBI's MIRIAM DB</li>
92 </div></td><td><div align="left">
105 <em>New Known Issues</em>
112 <td width="60" nowrap>
114 <strong><a name="Jalview.2.10.1">2.10.1</a><br />
115 <em>29/11/2016</em></strong>
118 <td><div align="left">
122 <!-- JAL-98 -->Improved memory usage: sparse arrays used
123 for all consensus calculations
126 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released 3rd Oct 2016)
128 <li>Updated Jalview's Certum code signing certificate
134 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
135 set of database cross-references, sorted alphabetically
138 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
139 from database cross references. Users with custom links
140 will receive a <a href="webServices/urllinks.html#warning">warning
141 dialog</a> asking them to update their preferences.
144 <!-- JAL-2287-->Cancel button and escape listener on
145 dialog warning user about disconnecting Jalview from a
149 <!-- JAL-2320-->Jalview's Chimera control window closes if
150 the Chimera it is connected to is shut down
153 <!-- JAL-1738-->New keystroke (B) and Select highlighted
154 columns menu item to mark columns containing
155 highlighted regions (e.g. from structure selections or results
159 <!-- JAL-2284-->Command line option for batch-generation
160 of HTML pages rendering alignment data with the BioJS
170 <!-- JAL-2286 -->Columns with more than one modal residue
171 are not coloured or thresholded according to percent
172 identity (first observed in Jalview 2.8.2)
175 <!-- JAL-2301 -->Threonine incorrectly reported as not
179 <!-- JAL-2318 -->Updates to documentation pages (above PID
180 threshold, amino acid properties)
183 <!-- JAL-2292 -->Lower case residues in sequences are not
184 reported as mapped to residues in a structure file in the
188 <!--JAL-2324 -->Identical features with non-numeric scores
189 could be added multiple times to a sequence
192 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
193 bond features shown as two highlighted residues rather
194 than a range in linked structure views, and treated
195 correctly when selecting and computing trees from features
198 <!-- JAL-2281-->Custom URL links for database
199 cross-references are matched to database name regardless
207 <!-- JAL-2282-->Custom URL links for specific database
208 names without regular expressions also offer links from
212 <!-- JAL-2315-->Removing a single configured link in the
213 URL links pane in Connections preferences doesn't actually
214 update Jalview configuration
217 <!-- JAL-2272-->CTRL-Click on a selected region to open
218 the alignment area popup menu doesn't work on El-Capitan
221 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
222 files with similarly named sequences if dropped onto the
226 <!-- JAL-2312 -->Additional mappings are shown for PDB
227 entries where more chains exist in the PDB accession than
228 are reported in the SIFTS file
231 <!-- JAL-2317-->Certain structures do not get mapped to
232 the structure view when displayed with Chimera
235 <!-- JAL-2317-->No chains shown in the Chimera view
236 panel's View->Show Chains submenu
239 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
240 work for wrapped alignment views
243 <!--JAL-2197 -->Rename UI components for running JPred
244 predictions from 'JNet' to 'JPred'
247 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
248 corrupted when annotation panel vertical scroll is not at
252 <!--JAL-2332 -->Attempting to view structure for Hen
253 lysozyme results in a PDB Client error dialog box
256 <!-- <em>New Known Issues</em>
263 <td width="60" nowrap>
265 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
266 <em>25/10/2016</em></strong>
269 <td><em>Application</em>
271 <li>3D Structure chooser opens with 'Cached structures'
272 view if structures already loaded</li>
273 <li>Progress bar reports models as they are loaded to
280 <li>Colour by conservation always enabled and no tick
281 shown in menu when BLOSUM or PID shading applied</li>
282 <li>FER1_ARATH and FER2_ARATH labels were switched in
283 example sequences/projects/trees</li>
287 <li>Jalview projects with views of local PDB structure
288 files saved on Windows cannot be opened on OSX</li>
289 <li>Multiple structure views can be opened and
290 superposed without timeout for structures with multiple
291 models or multiple sequences in alignment</li>
292 <li>Cannot import or associated local PDB files without
293 a PDB ID HEADER line</li>
294 <li>RMSD is not output in Jmol console when
295 superposition is performed</li>
296 <li>Drag and drop of URL from Browser fails for Linux
297 and OSX versions earlier than El Capitan</li>
298 <li>ENA client ignores invalid content from ENA server</li>
299 <li>Exceptions are not raised in console when ENA
300 client attempts to fetch non-existent IDs via Fetch DB
302 <li>Exceptions are not raised in console when a new
303 view is created on the alignment</li>
304 <li>OSX right-click fixed for group selections:
305 CMD-click to insert/remove gaps in groups and CTRL-click
306 to open group pop-up menu</li>
308 <em>Build and deployment</em>
310 <li>URL link checker now copes with multi-line anchor
313 <em>New Known Issues</em>
315 <li>Drag and drop from URL links in browsers do not
322 <td width="60" nowrap>
324 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
330 <!-- JAL-2124 -->Updated Spanish translations.
333 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
334 for importing structure data to Jalview. Enables mmCIF and
338 <!-- JAL-192 --->Alignment ruler shows positions relative to
342 <!-- JAL-2202 -->Position/residue shown in status bar when
343 mousing over sequence associated annotation
346 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
350 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
351 '()', canonical '[]' and invalid '{}' base pair populations
355 <!-- JAL-2092 -->Feature settings popup menu options for
356 showing or hiding columns containing a feature
359 <!-- JAL-1557 -->Edit selected group by double clicking on
360 group and sequence associated annotation labels
363 <!-- JAL-2236 -->Sequence name added to annotation label in
364 select/hide columns by annotation and colour by annotation
368 </ul> <em>Application</em>
371 <!-- JAL-2050-->Automatically hide introns when opening a
375 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
379 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
380 structure mappings with the EMBL-EBI PDBe SIFTS database
383 <!-- JAL-2079 -->Updated download sites used for Rfam and
384 Pfam sources to xfam.org
387 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
390 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
391 over sequences in Jalview
394 <!-- JAL-2027-->Support for reverse-complement coding
395 regions in ENA and EMBL
398 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
399 for record retrieval via ENA rest API
402 <!-- JAL-2027 -->Support for ENA CDS records with reverse
406 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
407 groovy script execution
410 <!-- JAL-1812 -->New 'execute Groovy script' option in an
411 alignment window's Calculate menu
414 <!-- JAL-1812 -->Allow groovy scripts that call
415 Jalview.getAlignFrames() to run in headless mode
418 <!-- JAL-2068 -->Support for creating new alignment
419 calculation workers from groovy scripts
422 <!-- JAL-1369 --->Store/restore reference sequence in
426 <!-- JAL-1803 -->Chain codes for a sequence's PDB
427 associations are now saved/restored from project
430 <!-- JAL-1993 -->Database selection dialog always shown
431 before sequence fetcher is opened
434 <!-- JAL-2183 -->Double click on an entry in Jalview's
435 database chooser opens a sequence fetcher
438 <!-- JAL-1563 -->Free-text search client for UniProt using
442 <!-- JAL-2168 -->-nonews command line parameter to prevent
443 the news reader opening
446 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
447 querying stored in preferences
450 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
454 <!-- JAL-1977-->Tooltips shown on database chooser
457 <!-- JAL-391 -->Reverse complement function in calculate
458 menu for nucleotide sequences
461 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
462 and feature counts preserves alignment ordering (and
463 debugged for complex feature sets).
466 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
467 viewing structures with Jalview 2.10
470 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
471 genome, transcript CCDS and gene ids via the Ensembl and
472 Ensembl Genomes REST API
475 <!-- JAL-2049 -->Protein sequence variant annotation
476 computed for 'sequence_variant' annotation on CDS regions
480 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
484 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
485 Ref Fetcher fails to match, or otherwise updates sequence
486 data from external database records.
489 <!-- JAL-2154 -->Revised Jalview Project format for
490 efficient recovery of sequence coding and alignment
491 annotation relationships.
493 </ul> <!-- <em>Applet</em>
504 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
508 <!-- JAL-2018-->Export features in Jalview format (again)
509 includes graduated colourschemes
512 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
513 working with big alignments and lots of hidden columns
516 <!-- JAL-2053-->Hidden column markers not always rendered
517 at right of alignment window
520 <!-- JAL-2067 -->Tidied up links in help file table of
524 <!-- JAL-2072 -->Feature based tree calculation not shown
528 <!-- JAL-2075 -->Hidden columns ignored during feature
529 based tree calculation
532 <!-- JAL-2065 -->Alignment view stops updating when show
533 unconserved enabled for group on alignment
536 <!-- JAL-2086 -->Cannot insert gaps into sequence when
540 <!-- JAL-2146 -->Alignment column in status incorrectly
541 shown as "Sequence position" when mousing over
545 <!-- JAL-2099 -->Incorrect column numbers in ruler when
546 hidden columns present
549 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
550 user created annotation added to alignment
553 <!-- JAL-1841 -->RNA Structure consensus only computed for
554 '()' base pair annotation
557 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
558 in zero scores for all base pairs in RNA Structure
562 <!-- JAL-2174-->Extend selection with columns containing
566 <!-- JAL-2275 -->Pfam format writer puts extra space at
567 beginning of sequence
570 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
574 <!-- JAL-2238 -->Cannot create groups on an alignment from
575 from a tree when t-coffee scores are shown
578 <!-- JAL-1836,1967 -->Cannot import and view PDB
579 structures with chains containing negative resnums (4q4h)
582 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
586 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
587 to Clustal, PIR and PileUp output
590 <!-- JAL-2008 -->Reordering sequence features that are
591 not visible causes alignment window to repaint
594 <!-- JAL-2006 -->Threshold sliders don't work in
595 graduated colour and colour by annotation row for e-value
596 scores associated with features and annotation rows
599 <!-- JAL-1797 -->amino acid physicochemical conservation
600 calculation should be case independent
603 <!-- JAL-2173 -->Remove annotation also updates hidden
607 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
608 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
609 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
612 <!-- JAL-2065 -->Null pointer exceptions and redraw
613 problems when reference sequence defined and 'show
614 non-conserved' enabled
617 <!-- JAL-1306 -->Quality and Conservation are now shown on
618 load even when Consensus calculation is disabled
621 <!-- JAL-1932 -->Remove right on penultimate column of
622 alignment does nothing
628 <!-- JAL-1552-->URLs and links can't be imported by
629 drag'n'drop on OSX when launched via webstart (note - not
630 yet fixed for El Capitan)
633 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
634 output when running on non-gb/us i18n platforms
637 <!-- JAL-1944 -->Error thrown when exporting a view with
638 hidden sequences as flat-file alignment
641 <!-- JAL-2030-->InstallAnywhere distribution fails when
645 <!-- JAL-2080-->Jalview very slow to launch via webstart
646 (also hotfix for 2.9.0b2)
649 <!-- JAL-2085 -->Cannot save project when view has a
650 reference sequence defined
653 <!-- JAL-1011 -->Columns are suddenly selected in other
654 alignments and views when revealing hidden columns
657 <!-- JAL-1989 -->Hide columns not mirrored in complement
658 view in a cDNA/Protein splitframe
661 <!-- JAL-1369 -->Cannot save/restore representative
662 sequence from project when only one sequence is
666 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
670 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
671 structure consensus didn't refresh annotation panel
674 <!-- JAL-1962 -->View mapping in structure view shows
675 mappings between sequence and all chains in a PDB file
678 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
679 dialogs format columns correctly, don't display array
680 data, sort columns according to type
683 <!-- JAL-1975 -->Export complete shown after destination
684 file chooser is cancelled during an image export
687 <!-- JAL-2025 -->Error when querying PDB Service with
688 sequence name containing special characters
691 <!-- JAL-2024 -->Manual PDB structure querying should be
695 <!-- JAL-2104 -->Large tooltips with broken HTML
696 formatting don't wrap
699 <!-- JAL-1128 -->Figures exported from wrapped view are
700 truncated so L looks like I in consensus annotation
703 <!-- JAL-2003 -->Export features should only export the
704 currently displayed features for the current selection or
708 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
709 after fetching cross-references, and restoring from project
712 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
713 followed in the structure viewer
716 <!-- JAL-2163 -->Titles for individual alignments in
717 splitframe not restored from project
720 <!-- JAL-2145 -->missing autocalculated annotation at
721 trailing end of protein alignment in transcript/product
722 splitview when pad-gaps not enabled by default
725 <!-- JAL-1797 -->amino acid physicochemical conservation
729 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
730 article has been read (reopened issue due to
731 internationalisation problems)
734 <!-- JAL-1960 -->Only offer PDB structures in structure
735 viewer based on sequence name, PDB and UniProt
740 <!-- JAL-1976 -->No progress bar shown during export of
744 <!-- JAL-2213 -->Structures not always superimposed after
745 multiple structures are shown for one or more sequences.
748 <!-- JAL-1370 -->Reference sequence characters should not
749 be replaced with '.' when 'Show unconserved' format option
753 <!-- JAL-1823 -->Cannot specify chain code when entering
754 specific PDB id for sequence
757 <!-- JAL-1944 -->File->Export->.. as doesn't work when
758 'Export hidden sequences' is enabled, but 'export hidden
759 columns' is disabled.
762 <!--JAL-2026-->Best Quality option in structure chooser
763 selects lowest rather than highest resolution structures
767 <!-- JAL-1887 -->Incorrect start and end reported for PDB
768 to sequence mapping in 'View Mappings' report
771 <!-- JAL-2284 -->Unable to read old Jalview projects that
772 contain non-XML data added after Jalvew wrote project.
774 <li><!-- JAL-2118 -->Newly created annotation row reorders
775 after clicking on it to create new annotation for a
778 <!-- may exclude, this is an external service stability issue JAL-1941
779 -- > RNA 3D structure not added via DSSR service</li> -->
784 <!-- JAL-2151 -->Incorrect columns are selected when
785 hidden columns present before start of sequence
788 <!-- JAL-1986 -->Missing dependencies on applet pages
792 <!-- JAL-1947 -->Overview pixel size changes when
793 sequences are hidden in applet
796 <!-- JAL-1996 -->Updated instructions for applet
797 deployment on examples pages.
804 <td width="60" nowrap>
806 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
807 <em>16/10/2015</em></strong>
812 <li>Time stamps for signed Jalview application and applet
819 <li>Duplicate group consensus and conservation rows
820 shown when tree is partitioned</li>
821 <li>Erratic behaviour when tree partitions made with
822 multiple cDNA/Protein split views</li>
828 <td width="60" nowrap>
830 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
831 <em>8/10/2015</em></strong>
836 <li>Updated Spanish translations of localized text for
838 </ul> <em>Application</em>
840 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
841 <li>Signed OSX InstallAnywhere installer<br></li>
842 <li>Support for per-sequence based annotations in BioJSON</li>
843 </ul> <em>Applet</em>
845 <li>Split frame example added to applet examples page</li>
846 </ul><em>Build and Deployment</em>
848 <li><!-- JAL-1888 -->New ant target for running Jalview's test suite</li>
854 <li>Mapping of cDNA to protein in split frames
855 incorrect when sequence start > 1</li>
856 <li>Broken images in filter column by annotation dialog
858 <li>Feature colours not parsed from features file</li>
859 <li>Exceptions and incomplete link URLs recovered when
860 loading a features file containing HTML tags in feature
866 <li>Annotations corrupted after BioJS export and
868 <li>Incorrect sequence limits after Fetch DB References
869 with 'trim retrieved sequences'</li>
870 <li>Incorrect warning about deleting all data when
871 deleting selected columns</li>
872 <li>Patch to build system for shipping properly signed
873 JNLP templates for webstart launch</li>
874 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
875 unreleased structures for download or viewing</li>
876 <li>Tab/space/return keystroke operation of EMBL-PDBe
877 fetcher/viewer dialogs works correctly</li>
878 <li>Disabled 'minimise' button on Jalview windows
879 running on OSX to workaround redraw hang bug</li>
880 <li>Split cDNA/Protein view position and geometry not
881 recovered from jalview project</li>
882 <li>Initial enabled/disabled state of annotation menu
883 sorter 'show autocalculated first/last' corresponds to
885 <li>Restoring of Clustal, RNA Helices and T-Coffee
886 color schemes from BioJSON</li>
890 <li>Reorder sequences mirrored in cDNA/Protein split
892 <li>Applet with Jmol examples not loading correctly</li>
898 <td><div align="center">
899 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
903 <li>Linked visualisation and analysis of DNA and Protein
906 <li>Translated cDNA alignments shown as split protein
907 and DNA alignment views</li>
908 <li>Codon consensus annotation for linked protein and
909 cDNA alignment views</li>
910 <li>Link cDNA or Protein product sequences by loading
911 them onto Protein or cDNA alignments</li>
912 <li>Reconstruct linked cDNA alignment from aligned
913 protein sequences</li>
916 <li>Jmol integration updated to Jmol v14.2.14</li>
917 <li>Import and export of Jalview alignment views as <a
918 href="features/bioJsonFormat.html">BioJSON</a></li>
919 <li>New alignment annotation file statements for
920 reference sequences and marking hidden columns</li>
921 <li>Reference sequence based alignment shading to
922 highlight variation</li>
923 <li>Select or hide columns according to alignment
925 <li>Find option for locating sequences by description</li>
926 <li>Conserved physicochemical properties shown in amino
927 acid conservation row</li>
928 <li>Alignments can be sorted by number of RNA helices</li>
929 </ul> <em>Application</em>
931 <li>New cDNA/Protein analysis capabilities
933 <li>Get Cross-References should open a Split Frame
934 view with cDNA/Protein</li>
935 <li>Detect when nucleotide sequences and protein
936 sequences are placed in the same alignment</li>
937 <li>Split cDNA/Protein views are saved in Jalview
942 <li>Use REST API to talk to Chimera</li>
943 <li>Selected regions in Chimera are highlighted in linked
946 <li>VARNA RNA viewer updated to v3.93</li>
947 <li>VARNA views are saved in Jalview Projects</li>
948 <li>Pseudoknots displayed as Jalview RNA annotation can
949 be shown in VARNA</li>
951 <li>Make groups for selection uses marked columns as well
952 as the active selected region</li>
954 <li>Calculate UPGMA and NJ trees using sequence feature
956 <li>New Export options
958 <li>New Export Settings dialog to control hidden
959 region export in flat file generation</li>
961 <li>Export alignment views for display with the <a
962 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
964 <li>Export scrollable SVG in HTML page</li>
965 <li>Optional embedding of BioJSON data when exporting
966 alignment figures to HTML</li>
968 <li>3D structure retrieval and display
970 <li>Free text and structured queries with the PDBe
972 <li>PDBe Search API based discovery and selection of
973 PDB structures for a sequence set</li>
977 <li>JPred4 employed for protein secondary structure
979 <li>Hide Insertions menu option to hide unaligned columns
980 for one or a group of sequences</li>
981 <li>Automatically hide insertions in alignments imported
982 from the JPred4 web server</li>
983 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
984 system on OSX<br />LGPL libraries courtesy of <a
985 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
987 <li>changed 'View nucleotide structure' submenu to 'View
988 VARNA 2D Structure'</li>
989 <li>change "View protein structure" menu option to "3D
992 </ul> <em>Applet</em>
994 <li>New layout for applet example pages</li>
995 <li>New parameters to enable SplitFrame view
996 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
997 <li>New example demonstrating linked viewing of cDNA and
998 Protein alignments</li>
999 </ul> <em>Development and deployment</em>
1001 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1002 <li>Include installation type and git revision in build
1003 properties and console log output</li>
1004 <li>Jalview Github organisation, and new github site for
1005 storing BioJsMSA Templates</li>
1006 <li>Jalview's unit tests now managed with TestNG</li>
1009 <!-- <em>General</em>
1011 </ul> --> <!-- issues resolved --> <em>Application</em>
1013 <li>Escape should close any open find dialogs</li>
1014 <li>Typo in select-by-features status report</li>
1015 <li>Consensus RNA secondary secondary structure
1016 predictions are not highlighted in amber</li>
1017 <li>Missing gap character in v2.7 example file means
1018 alignment appears unaligned when pad-gaps is not enabled</li>
1019 <li>First switch to RNA Helices colouring doesn't colour
1020 associated structure views</li>
1021 <li>ID width preference option is greyed out when auto
1022 width checkbox not enabled</li>
1023 <li>Stopped a warning dialog from being shown when
1024 creating user defined colours</li>
1025 <li>'View Mapping' in structure viewer shows sequence
1026 mappings for just that viewer's sequences</li>
1027 <li>Workaround for superposing PDB files containing
1028 multiple models in Chimera</li>
1029 <li>Report sequence position in status bar when hovering
1030 over Jmol structure</li>
1031 <li>Cannot output gaps as '.' symbols with Selection ->
1032 output to text box</li>
1033 <li>Flat file exports of alignments with hidden columns
1034 have incorrect sequence start/end</li>
1035 <li>'Aligning' a second chain to a Chimera structure from
1037 <li>Colour schemes applied to structure viewers don't
1038 work for nucleotide</li>
1039 <li>Loading/cut'n'pasting an empty or invalid file leads
1040 to a grey/invisible alignment window</li>
1041 <li>Exported Jpred annotation from a sequence region
1042 imports to different position</li>
1043 <li>Space at beginning of sequence feature tooltips shown
1044 on some platforms</li>
1045 <li>Chimera viewer 'View | Show Chain' menu is not
1047 <li>'New View' fails with a Null Pointer Exception in
1048 console if Chimera has been opened</li>
1049 <li>Mouseover to Chimera not working</li>
1050 <li>Miscellaneous ENA XML feature qualifiers not
1052 <li>NPE in annotation renderer after 'Extract Scores'</li>
1053 <li>If two structures in one Chimera window, mouseover of
1054 either sequence shows on first structure</li>
1055 <li>'Show annotations' options should not make
1056 non-positional annotations visible</li>
1057 <li>Subsequence secondary structure annotation not shown
1058 in right place after 'view flanking regions'</li>
1059 <li>File Save As type unset when current file format is
1061 <li>Save as '.jar' option removed for saving Jalview
1063 <li>Colour by Sequence colouring in Chimera more
1065 <li>Cannot 'add reference annotation' for a sequence in
1066 several views on same alignment</li>
1067 <li>Cannot show linked products for EMBL / ENA records</li>
1068 <li>Jalview's tooltip wraps long texts containing no
1070 </ul> <em>Applet</em>
1072 <li>Jmol to JalviewLite mouseover/link not working</li>
1073 <li>JalviewLite can't import sequences with ID
1074 descriptions containing angle brackets</li>
1075 </ul> <em>General</em>
1077 <li>Cannot export and reimport RNA secondary structure
1078 via jalview annotation file</li>
1079 <li>Random helix colour palette for colour by annotation
1080 with RNA secondary structure</li>
1081 <li>Mouseover to cDNA from STOP residue in protein
1082 translation doesn't work.</li>
1083 <li>hints when using the select by annotation dialog box</li>
1084 <li>Jmol alignment incorrect if PDB file has alternate CA
1086 <li>FontChooser message dialog appears to hang after
1087 choosing 1pt font</li>
1088 <li>Peptide secondary structure incorrectly imported from
1089 annotation file when annotation display text includes 'e' or
1091 <li>Cannot set colour of new feature type whilst creating
1093 <li>cDNA translation alignment should not be sequence
1094 order dependent</li>
1095 <li>'Show unconserved' doesn't work for lower case
1097 <li>Nucleotide ambiguity codes involving R not recognised</li>
1098 </ul> <em>Deployment and Documentation</em>
1100 <li>Applet example pages appear different to the rest of
1101 www.jalview.org</li>
1102 </ul> <em>Application Known issues</em>
1104 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1105 <li>Misleading message appears after trying to delete
1107 <li>Jalview icon not shown in dock after InstallAnywhere
1108 version launches</li>
1109 <li>Fetching EMBL reference for an RNA sequence results
1110 fails with a sequence mismatch</li>
1111 <li>Corrupted or unreadable alignment display when
1112 scrolling alignment to right</li>
1113 <li>ArrayIndexOutOfBoundsException thrown when remove
1114 empty columns called on alignment with ragged gapped ends</li>
1115 <li>auto calculated alignment annotation rows do not get
1116 placed above or below non-autocalculated rows</li>
1117 <li>Jalview dekstop becomes sluggish at full screen in
1118 ultra-high resolution</li>
1119 <li>Cannot disable consensus calculation independently of
1120 quality and conservation</li>
1121 <li>Mouseover highlighting between cDNA and protein can
1122 become sluggish with more than one splitframe shown</li>
1123 </ul> <em>Applet Known Issues</em>
1125 <li>Core PDB parsing code requires Jmol</li>
1126 <li>Sequence canvas panel goes white when alignment
1127 window is being resized</li>
1133 <td><div align="center">
1134 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1136 <td><em>General</em>
1138 <li>Updated Java code signing certificate donated by
1140 <li>Features and annotation preserved when performing
1141 pairwise alignment</li>
1142 <li>RNA pseudoknot annotation can be
1143 imported/exported/displayed</li>
1144 <li>'colour by annotation' can colour by RNA and
1145 protein secondary structure</li>
1146 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1147 post-hoc with 2.9 release</em>)
1150 </ul> <em>Application</em>
1152 <li>Extract and display secondary structure for sequences
1153 with 3D structures</li>
1154 <li>Support for parsing RNAML</li>
1155 <li>Annotations menu for layout
1157 <li>sort sequence annotation rows by alignment</li>
1158 <li>place sequence annotation above/below alignment
1161 <li>Output in Stockholm format</li>
1162 <li>Internationalisation: improved Spanish (es)
1164 <li>Structure viewer preferences tab</li>
1165 <li>Disorder and Secondary Structure annotation tracks
1166 shared between alignments</li>
1167 <li>UCSF Chimera launch and linked highlighting from
1169 <li>Show/hide all sequence associated annotation rows for
1170 all or current selection</li>
1171 <li>disorder and secondary structure predictions
1172 available as dataset annotation</li>
1173 <li>Per-sequence rna helices colouring</li>
1176 <li>Sequence database accessions imported when fetching
1177 alignments from Rfam</li>
1178 <li>update VARNA version to 3.91</li>
1180 <li>New groovy scripts for exporting aligned positions,
1181 conservation values, and calculating sum of pairs scores.</li>
1182 <li>Command line argument to set default JABAWS server</li>
1183 <li>include installation type in build properties and
1184 console log output</li>
1185 <li>Updated Jalview project format to preserve dataset
1189 <!-- issues resolved --> <em>Application</em>
1191 <li>Distinguish alignment and sequence associated RNA
1192 structure in structure->view->VARNA</li>
1193 <li>Raise dialog box if user deletes all sequences in an
1195 <li>Pressing F1 results in documentation opening twice</li>
1196 <li>Sequence feature tooltip is wrapped</li>
1197 <li>Double click on sequence associated annotation
1198 selects only first column</li>
1199 <li>Redundancy removal doesn't result in unlinked
1200 leaves shown in tree</li>
1201 <li>Undos after several redundancy removals don't undo
1203 <li>Hide sequence doesn't hide associated annotation</li>
1204 <li>User defined colours dialog box too big to fit on
1205 screen and buttons not visible</li>
1206 <li>author list isn't updated if already written to
1207 Jalview properties</li>
1208 <li>Popup menu won't open after retrieving sequence
1210 <li>File open window for associate PDB doesn't open</li>
1211 <li>Left-then-right click on a sequence id opens a
1212 browser search window</li>
1213 <li>Cannot open sequence feature shading/sort popup menu
1214 in feature settings dialog</li>
1215 <li>better tooltip placement for some areas of Jalview
1217 <li>Allow addition of JABAWS Server which doesn't
1218 pass validation</li>
1219 <li>Web services parameters dialog box is too large to
1221 <li>Muscle nucleotide alignment preset obscured by
1223 <li>JABAWS preset submenus don't contain newly
1224 defined user preset</li>
1225 <li>MSA web services warns user if they were launched
1226 with invalid input</li>
1227 <li>Jalview cannot contact DAS Registy when running on
1230 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1231 'Superpose with' submenu not shown when new view
1235 </ul> <!-- <em>Applet</em>
1237 </ul> <em>General</em>
1239 </ul>--> <em>Deployment and Documentation</em>
1241 <li>2G and 1G options in launchApp have no effect on
1242 memory allocation</li>
1243 <li>launchApp service doesn't automatically open
1244 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1246 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1247 InstallAnywhere reports cannot find valid JVM when Java
1248 1.7_055 is available
1250 </ul> <em>Application Known issues</em>
1253 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1254 corrupted or unreadable alignment display when scrolling
1258 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1259 retrieval fails but progress bar continues for DAS retrieval
1260 with large number of ID
1263 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1264 flatfile output of visible region has incorrect sequence
1268 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1269 rna structure consensus doesn't update when secondary
1270 structure tracks are rearranged
1273 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1274 invalid rna structure positional highlighting does not
1275 highlight position of invalid base pairs
1278 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1279 out of memory errors are not raised when saving Jalview
1280 project from alignment window file menu
1283 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1284 Switching to RNA Helices colouring doesn't propagate to
1288 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1289 colour by RNA Helices not enabled when user created
1290 annotation added to alignment
1293 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1294 Jalview icon not shown on dock in Mountain Lion/Webstart
1296 </ul> <em>Applet Known Issues</em>
1299 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1300 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1303 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1304 Jalview and Jmol example not compatible with IE9
1307 <li>Sort by annotation score doesn't reverse order
1313 <td><div align="center">
1314 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1317 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1320 <li>Internationalisation of user interface (usually
1321 called i18n support) and translation for Spanish locale</li>
1322 <li>Define/Undefine group on current selection with
1323 Ctrl-G/Shift Ctrl-G</li>
1324 <li>Improved group creation/removal options in
1325 alignment/sequence Popup menu</li>
1326 <li>Sensible precision for symbol distribution
1327 percentages shown in logo tooltip.</li>
1328 <li>Annotation panel height set according to amount of
1329 annotation when alignment first opened</li>
1330 </ul> <em>Application</em>
1332 <li>Interactive consensus RNA secondary structure
1333 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1334 <li>Select columns containing particular features from
1335 Feature Settings dialog</li>
1336 <li>View all 'representative' PDB structures for selected
1338 <li>Update Jalview project format:
1340 <li>New file extension for Jalview projects '.jvp'</li>
1341 <li>Preserve sequence and annotation dataset (to
1342 store secondary structure annotation,etc)</li>
1343 <li>Per group and alignment annotation and RNA helix
1347 <li>New similarity measures for PCA and Tree calculation
1349 <li>Experimental support for retrieval and viewing of
1350 flanking regions for an alignment</li>
1354 <!-- issues resolved --> <em>Application</em>
1356 <li>logo keeps spinning and status remains at queued or
1357 running after job is cancelled</li>
1358 <li>cannot export features from alignments imported from
1359 Jalview/VAMSAS projects</li>
1360 <li>Buggy slider for web service parameters that take
1362 <li>Newly created RNA secondary structure line doesn't
1363 have 'display all symbols' flag set</li>
1364 <li>T-COFFEE alignment score shading scheme and other
1365 annotation shading not saved in Jalview project</li>
1366 <li>Local file cannot be loaded in freshly downloaded
1368 <li>Jalview icon not shown on dock in Mountain
1370 <li>Load file from desktop file browser fails</li>
1371 <li>Occasional NPE thrown when calculating large trees</li>
1372 <li>Cannot reorder or slide sequences after dragging an
1373 alignment onto desktop</li>
1374 <li>Colour by annotation dialog throws NPE after using
1375 'extract scores' function</li>
1376 <li>Loading/cut'n'pasting an empty file leads to a grey
1377 alignment window</li>
1378 <li>Disorder thresholds rendered incorrectly after
1379 performing IUPred disorder prediction</li>
1380 <li>Multiple group annotated consensus rows shown when
1381 changing 'normalise logo' display setting</li>
1382 <li>Find shows blank dialog after 'finished searching' if
1383 nothing matches query</li>
1384 <li>Null Pointer Exceptions raised when sorting by
1385 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1387 <li>Errors in Jmol console when structures in alignment
1388 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1390 <li>Not all working JABAWS services are shown in
1392 <li>JAVAWS version of Jalview fails to launch with
1393 'invalid literal/length code'</li>
1394 <li>Annotation/RNA Helix colourschemes cannot be applied
1395 to alignment with groups (actually fixed in 2.8.0b1)</li>
1396 <li>RNA Helices and T-Coffee Scores available as default
1399 </ul> <em>Applet</em>
1401 <li>Remove group option is shown even when selection is
1403 <li>Apply to all groups ticked but colourscheme changes
1404 don't affect groups</li>
1405 <li>Documented RNA Helices and T-Coffee Scores as valid
1406 colourscheme name</li>
1407 <li>Annotation labels drawn on sequence IDs when
1408 Annotation panel is not displayed</li>
1409 <li>Increased font size for dropdown menus on OSX and
1410 embedded windows</li>
1411 </ul> <em>Other</em>
1413 <li>Consensus sequence for alignments/groups with a
1414 single sequence were not calculated</li>
1415 <li>annotation files that contain only groups imported as
1416 annotation and junk sequences</li>
1417 <li>Fasta files with sequences containing '*' incorrectly
1418 recognised as PFAM or BLC</li>
1419 <li>conservation/PID slider apply all groups option
1420 doesn't affect background (2.8.0b1)
1422 <li>redundancy highlighting is erratic at 0% and 100%</li>
1423 <li>Remove gapped columns fails for sequences with ragged
1425 <li>AMSA annotation row with leading spaces is not
1426 registered correctly on import</li>
1427 <li>Jalview crashes when selecting PCA analysis for
1428 certain alignments</li>
1429 <li>Opening the colour by annotation dialog for an
1430 existing annotation based 'use original colours'
1431 colourscheme loses original colours setting</li>
1436 <td><div align="center">
1437 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
1438 <em>30/1/2014</em></strong>
1442 <li>Trusted certificates for JalviewLite applet and
1443 Jalview Desktop application<br />Certificate was donated by
1444 <a href="https://www.certum.eu">Certum</a> to the Jalview
1445 open source project).
1447 <li>Jalview SRS links replaced by UniProt and EBI-search
1449 <li>Output in Stockholm format</li>
1450 <li>Allow import of data from gzipped files</li>
1451 <li>Export/import group and sequence associated line
1452 graph thresholds</li>
1453 <li>Nucleotide substitution matrix that supports RNA and
1454 ambiguity codes</li>
1455 <li>Allow disorder predictions to be made on the current
1456 selection (or visible selection) in the same way that JPred
1458 <li>Groovy scripting for headless Jalview operation</li>
1459 </ul> <em>Other improvements</em>
1461 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
1462 <li>COMBINE statement uses current SEQUENCE_REF and
1463 GROUP_REF scope to group annotation rows</li>
1464 <li>Support '' style escaping of quotes in Newick
1466 <li>Group options for JABAWS service by command line name</li>
1467 <li>Empty tooltip shown for JABA service options with a
1468 link but no description</li>
1469 <li>Select primary source when selecting authority in
1470 database fetcher GUI</li>
1471 <li>Add .mfa to FASTA file extensions recognised by
1473 <li>Annotation label tooltip text wrap</li>
1478 <li>Slow scrolling when lots of annotation rows are
1480 <li>Lots of NPE (and slowness) after creating RNA
1481 secondary structure annotation line</li>
1482 <li>Sequence database accessions not imported when
1483 fetching alignments from Rfam</li>
1484 <li>Incorrect SHMR submission for sequences with
1486 <li>View all structures does not always superpose
1488 <li>Option widgets in service parameters not updated to
1489 reflect user or preset settings</li>
1490 <li>Null pointer exceptions for some services without
1491 presets or adjustable parameters</li>
1492 <li>Discover PDB IDs entry in structure menu doesn't
1493 discover PDB xRefs</li>
1494 <li>Exception encountered while trying to retrieve
1495 features with DAS</li>
1496 <li>Lowest value in annotation row isn't coloured
1497 when colour by annotation (per sequence) is coloured</li>
1498 <li>Keyboard mode P jumps to start of gapped region when
1499 residue follows a gap</li>
1500 <li>Jalview appears to hang importing an alignment with
1501 Wrap as default or after enabling Wrap</li>
1502 <li>'Right click to add annotations' message
1503 shown in wrap mode when no annotations present</li>
1504 <li>Disorder predictions fail with NPE if no automatic
1505 annotation already exists on alignment</li>
1506 <li>oninit javascript function should be called after
1507 initialisation completes</li>
1508 <li>Remove redundancy after disorder prediction corrupts
1509 alignment window display</li>
1510 <li>Example annotation file in documentation is invalid</li>
1511 <li>Grouped line graph annotation rows are not exported
1512 to annotation file</li>
1513 <li>Multi-harmony analysis cannot be run when only two
1515 <li>Cannot create multiple groups of line graphs with
1516 several 'combine' statements in annotation file</li>
1517 <li>Pressing return several times causes Number Format
1518 exceptions in keyboard mode</li>
1519 <li>Multi-harmony (SHMMR) method doesn't submit
1520 correct partitions for input data</li>
1521 <li>Translation from DNA to Amino Acids fails</li>
1522 <li>Jalview fail to load newick tree with quoted label</li>
1523 <li>--headless flag isn't understood</li>
1524 <li>ClassCastException when generating EPS in headless
1526 <li>Adjusting sequence-associated shading threshold only
1527 changes one row's threshold</li>
1528 <li>Preferences and Feature settings panel panel
1529 doesn't open</li>
1530 <li>hide consensus histogram also hides conservation and
1531 quality histograms</li>
1536 <td><div align="center">
1537 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
1539 <td><em>Application</em>
1541 <li>Support for JABAWS 2.0 Services (AACon alignment
1542 conservation, protein disorder and Clustal Omega)</li>
1543 <li>JABAWS server status indicator in Web Services
1545 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
1546 in Jalview alignment window</li>
1547 <li>Updated Jalview build and deploy framework for OSX
1548 mountain lion, windows 7, and 8</li>
1549 <li>Nucleotide substitution matrix for PCA that supports
1550 RNA and ambiguity codes</li>
1552 <li>Improved sequence database retrieval GUI</li>
1553 <li>Support fetching and database reference look up
1554 against multiple DAS sources (Fetch all from in 'fetch db
1556 <li>Jalview project improvements
1558 <li>Store and retrieve the 'belowAlignment'
1559 flag for annotation</li>
1560 <li>calcId attribute to group annotation rows on the
1562 <li>Store AACon calculation settings for a view in
1563 Jalview project</li>
1567 <li>horizontal scrolling gesture support</li>
1568 <li>Visual progress indicator when PCA calculation is
1570 <li>Simpler JABA web services menus</li>
1571 <li>visual indication that web service results are still
1572 being retrieved from server</li>
1573 <li>Serialise the dialogs that are shown when Jalview
1574 starts up for first time</li>
1575 <li>Jalview user agent string for interacting with HTTP
1577 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
1579 <li>Examples directory and Groovy library included in
1580 InstallAnywhere distribution</li>
1581 </ul> <em>Applet</em>
1583 <li>RNA alignment and secondary structure annotation
1584 visualization applet example</li>
1585 </ul> <em>General</em>
1587 <li>Normalise option for consensus sequence logo</li>
1588 <li>Reset button in PCA window to return dimensions to
1590 <li>Allow seqspace or Jalview variant of alignment PCA
1592 <li>PCA with either nucleic acid and protein substitution
1594 <li>Allow windows containing HTML reports to be exported
1596 <li>Interactive display and editing of RNA secondary
1597 structure contacts</li>
1598 <li>RNA Helix Alignment Colouring</li>
1599 <li>RNA base pair logo consensus</li>
1600 <li>Parse sequence associated secondary structure
1601 information in Stockholm files</li>
1602 <li>HTML Export database accessions and annotation
1603 information presented in tooltip for sequences</li>
1604 <li>Import secondary structure from LOCARNA clustalw
1605 style RNA alignment files</li>
1606 <li>import and visualise T-COFFEE quality scores for an
1608 <li>'colour by annotation' per sequence option to
1609 shade each sequence according to its associated alignment
1611 <li>New Jalview Logo</li>
1612 </ul> <em>Documentation and Development</em>
1614 <li>documentation for score matrices used in Jalview</li>
1615 <li>New Website!</li>
1617 <td><em>Application</em>
1619 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
1620 wsdbfetch REST service</li>
1621 <li>Stop windows being moved outside desktop on OSX</li>
1622 <li>Filetype associations not installed for webstart
1624 <li>Jalview does not always retrieve progress of a JABAWS
1625 job execution in full once it is complete</li>
1626 <li>revise SHMR RSBS definition to ensure alignment is
1627 uploaded via ali_file parameter</li>
1628 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
1629 <li>View all structures superposed fails with exception</li>
1630 <li>Jnet job queues forever if a very short sequence is
1631 submitted for prediction</li>
1632 <li>Cut and paste menu not opened when mouse clicked on
1634 <li>Putting fractional value into integer text box in
1635 alignment parameter dialog causes Jalview to hang</li>
1636 <li>Structure view highlighting doesn't work on
1638 <li>View all structures fails with exception shown in
1640 <li>Characters in filename associated with PDBEntry not
1641 escaped in a platform independent way</li>
1642 <li>Jalview desktop fails to launch with exception when
1644 <li>Tree calculation reports 'you must have 2 or more
1645 sequences selected' when selection is empty</li>
1646 <li>Jalview desktop fails to launch with jar signature
1647 failure when java web start temporary file caching is
1649 <li>DAS Sequence retrieval with range qualification
1650 results in sequence xref which includes range qualification</li>
1651 <li>Errors during processing of command line arguments
1652 cause progress bar (JAL-898) to be removed</li>
1653 <li>Replace comma for semi-colon option not disabled for
1654 DAS sources in sequence fetcher</li>
1655 <li>Cannot close news reader when JABAWS server warning
1656 dialog is shown</li>
1657 <li>Option widgets not updated to reflect user settings</li>
1658 <li>Edited sequence not submitted to web service</li>
1659 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
1660 <li>InstallAnywhere installer doesn't unpack and run
1661 on OSX Mountain Lion</li>
1662 <li>Annotation panel not given a scroll bar when
1663 sequences with alignment annotation are pasted into the
1665 <li>Sequence associated annotation rows not associated
1666 when loaded from Jalview project</li>
1667 <li>Browser launch fails with NPE on java 1.7</li>
1668 <li>JABAWS alignment marked as finished when job was
1669 cancelled or job failed due to invalid input</li>
1670 <li>NPE with v2.7 example when clicking on Tree
1671 associated with all views</li>
1672 <li>Exceptions when copy/paste sequences with grouped
1673 annotation rows to new window</li>
1674 </ul> <em>Applet</em>
1676 <li>Sequence features are momentarily displayed before
1677 they are hidden using hidefeaturegroups applet parameter</li>
1678 <li>loading features via javascript API automatically
1679 enables feature display</li>
1680 <li>scrollToColumnIn javascript API method doesn't
1682 </ul> <em>General</em>
1684 <li>Redundancy removal fails for rna alignment</li>
1685 <li>PCA calculation fails when sequence has been selected
1686 and then deselected</li>
1687 <li>PCA window shows grey box when first opened on OSX</li>
1688 <li>Letters coloured pink in sequence logo when alignment
1689 coloured with clustalx</li>
1690 <li>Choosing fonts without letter symbols defined causes
1691 exceptions and redraw errors</li>
1692 <li>Initial PCA plot view is not same as manually
1693 reconfigured view</li>
1694 <li>Grouped annotation graph label has incorrect line
1696 <li>Grouped annotation graph label display is corrupted
1697 for lots of labels</li>
1702 <div align="center">
1703 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
1706 <td><em>Application</em>
1708 <li>Jalview Desktop News Reader</li>
1709 <li>Tweaked default layout of web services menu</li>
1710 <li>View/alignment association menu to enable user to
1711 easily specify which alignment a multi-structure view takes
1712 its colours/correspondences from</li>
1713 <li>Allow properties file location to be specified as URL</li>
1714 <li>Extend Jalview project to preserve associations
1715 between many alignment views and a single Jmol display</li>
1716 <li>Store annotation row height in Jalview project file</li>
1717 <li>Annotation row column label formatting attributes
1718 stored in project file</li>
1719 <li>Annotation row order for auto-calculated annotation
1720 rows preserved in Jalview project file</li>
1721 <li>Visual progress indication when Jalview state is
1722 saved using Desktop window menu</li>
1723 <li>Visual indication that command line arguments are
1724 still being processed</li>
1725 <li>Groovy script execution from URL</li>
1726 <li>Colour by annotation default min and max colours in
1728 <li>Automatically associate PDB files dragged onto an
1729 alignment with sequences that have high similarity and
1731 <li>Update JGoogleAnalytics to latest release (0.3)</li>
1732 <li>'view structures' option to open many
1733 structures in same window</li>
1734 <li>Sort associated views menu option for tree panel</li>
1735 <li>Group all JABA and non-JABA services for a particular
1736 analysis function in its own submenu</li>
1737 </ul> <em>Applet</em>
1739 <li>Userdefined and autogenerated annotation rows for
1741 <li>Adjustment of alignment annotation pane height</li>
1742 <li>Annotation scrollbar for annotation panel</li>
1743 <li>Drag to reorder annotation rows in annotation panel</li>
1744 <li>'automaticScrolling' parameter</li>
1745 <li>Allow sequences with partial ID string matches to be
1746 annotated from GFF/Jalview features files</li>
1747 <li>Sequence logo annotation row in applet</li>
1748 <li>Absolute paths relative to host server in applet
1749 parameters are treated as such</li>
1750 <li>New in the JalviewLite javascript API:
1752 <li>JalviewLite.js javascript library</li>
1753 <li>Javascript callbacks for
1755 <li>Applet initialisation</li>
1756 <li>Sequence/alignment mouse-overs and selections</li>
1759 <li>scrollTo row and column alignment scrolling
1761 <li>Select sequence/alignment regions from javascript</li>
1762 <li>javascript structure viewer harness to pass
1763 messages between Jmol and Jalview when running as
1764 distinct applets</li>
1765 <li>sortBy method</li>
1766 <li>Set of applet and application examples shipped
1767 with documentation</li>
1768 <li>New example to demonstrate JalviewLite and Jmol
1769 javascript message exchange</li>
1771 </ul> <em>General</em>
1773 <li>Enable Jmol displays to be associated with multiple
1774 multiple alignments</li>
1775 <li>Option to automatically sort alignment with new tree</li>
1776 <li>User configurable link to enable redirects to a
1777 www.Jalview.org mirror</li>
1778 <li>Jmol colours option for Jmol displays</li>
1779 <li>Configurable newline string when writing alignment
1780 and other flat files</li>
1781 <li>Allow alignment annotation description lines to
1782 contain html tags</li>
1783 </ul> <em>Documentation and Development</em>
1785 <li>Add groovy test harness for bulk load testing to
1787 <li>Groovy script to load and align a set of sequences
1788 using a web service before displaying the result in the
1789 Jalview desktop</li>
1790 <li>Restructured javascript and applet api documentation</li>
1791 <li>Ant target to publish example html files with applet
1793 <li>Netbeans project for building Jalview from source</li>
1794 <li>ant task to create online javadoc for Jalview source</li>
1796 <td><em>Application</em>
1798 <li>User defined colourscheme throws exception when
1799 current built in colourscheme is saved as new scheme</li>
1800 <li>AlignFrame->Save in application pops up save
1801 dialog for valid filename/format</li>
1802 <li>Cannot view associated structure for UniProt sequence</li>
1803 <li>PDB file association breaks for UniProt sequence
1805 <li>Associate PDB from file dialog does not tell you
1806 which sequence is to be associated with the file</li>
1807 <li>Find All raises null pointer exception when query
1808 only matches sequence IDs</li>
1809 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
1810 <li>Jalview project with Jmol views created with Jalview
1811 2.4 cannot be loaded</li>
1812 <li>Filetype associations not installed for webstart
1814 <li>Two or more chains in a single PDB file associated
1815 with sequences in different alignments do not get coloured
1816 by their associated sequence</li>
1817 <li>Visibility status of autocalculated annotation row
1818 not preserved when project is loaded</li>
1819 <li>Annotation row height and visibility attributes not
1820 stored in Jalview project</li>
1821 <li>Tree bootstraps are not preserved when saved as a
1822 Jalview project</li>
1823 <li>Envision2 workflow tooltips are corrupted</li>
1824 <li>Enabling show group conservation also enables colour
1825 by conservation</li>
1826 <li>Duplicate group associated conservation or consensus
1827 created on new view</li>
1828 <li>Annotation scrollbar not displayed after 'show
1829 all hidden annotation rows' option selected</li>
1830 <li>Alignment quality not updated after alignment
1831 annotation row is hidden then shown</li>
1832 <li>Preserve colouring of structures coloured by
1833 sequences in pre Jalview 2.7 projects</li>
1834 <li>Web service job parameter dialog is not laid out
1836 <li>Web services menu not refreshed after 'reset
1837 services' button is pressed in preferences</li>
1838 <li>Annotation off by one in Jalview v2_3 example project</li>
1839 <li>Structures imported from file and saved in project
1840 get name like jalview_pdb1234.txt when reloaded</li>
1841 <li>Jalview does not always retrieve progress of a JABAWS
1842 job execution in full once it is complete</li>
1843 </ul> <em>Applet</em>
1845 <li>Alignment height set incorrectly when lots of
1846 annotation rows are displayed</li>
1847 <li>Relative URLs in feature HTML text not resolved to
1849 <li>View follows highlighting does not work for positions
1851 <li><= shown as = in tooltip</li>
1852 <li>Export features raises exception when no features
1854 <li>Separator string used for serialising lists of IDs
1855 for javascript api is modified when separator string
1856 provided as parameter</li>
1857 <li>Null pointer exception when selecting tree leaves for
1858 alignment with no existing selection</li>
1859 <li>Relative URLs for datasources assumed to be relative
1860 to applet's codebase</li>
1861 <li>Status bar not updated after finished searching and
1862 search wraps around to first result</li>
1863 <li>StructureSelectionManager instance shared between
1864 several Jalview applets causes race conditions and memory
1866 <li>Hover tooltip and mouseover of position on structure
1867 not sent from Jmol in applet</li>
1868 <li>Certain sequences of javascript method calls to
1869 applet API fatally hang browser</li>
1870 </ul> <em>General</em>
1872 <li>View follows structure mouseover scrolls beyond
1873 position with wrapped view and hidden regions</li>
1874 <li>Find sequence position moves to wrong residue
1875 with/without hidden columns</li>
1876 <li>Sequence length given in alignment properties window
1878 <li>InvalidNumberFormat exceptions thrown when trying to
1879 import PDB like structure files</li>
1880 <li>Positional search results are only highlighted
1881 between user-supplied sequence start/end bounds</li>
1882 <li>End attribute of sequence is not validated</li>
1883 <li>Find dialog only finds first sequence containing a
1884 given sequence position</li>
1885 <li>Sequence numbering not preserved in MSF alignment
1887 <li>Jalview PDB file reader does not extract sequence
1888 from nucleotide chains correctly</li>
1889 <li>Structure colours not updated when tree partition
1890 changed in alignment</li>
1891 <li>Sequence associated secondary structure not correctly
1892 parsed in interleaved stockholm</li>
1893 <li>Colour by annotation dialog does not restore current
1895 <li>Hiding (nearly) all sequences doesn't work
1897 <li>Sequences containing lowercase letters are not
1898 properly associated with their pdb files</li>
1899 </ul> <em>Documentation and Development</em>
1901 <li>schemas/JalviewWsParamSet.xsd corrupted by
1902 ApplyCopyright tool</li>
1907 <div align="center">
1908 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
1911 <td><em>Application</em>
1913 <li>New warning dialog when the Jalview Desktop cannot
1914 contact web services</li>
1915 <li>JABA service parameters for a preset are shown in
1916 service job window</li>
1917 <li>JABA Service menu entries reworded</li>
1921 <li>Modeller PIR IO broken - cannot correctly import a
1922 pir file emitted by Jalview</li>
1923 <li>Existing feature settings transferred to new
1924 alignment view created from cut'n'paste</li>
1925 <li>Improved test for mixed amino/nucleotide chains when
1926 parsing PDB files</li>
1927 <li>Consensus and conservation annotation rows
1928 occasionally become blank for all new windows</li>
1929 <li>Exception raised when right clicking above sequences
1930 in wrapped view mode</li>
1931 </ul> <em>Application</em>
1933 <li>multiple multiply aligned structure views cause cpu
1934 usage to hit 100% and computer to hang</li>
1935 <li>Web Service parameter layout breaks for long user
1936 parameter names</li>
1937 <li>Jaba service discovery hangs desktop if Jaba server
1944 <div align="center">
1945 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
1948 <td><em>Application</em>
1950 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
1951 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
1954 <li>Web Services preference tab</li>
1955 <li>Analysis parameters dialog box and user defined
1957 <li>Improved speed and layout of Envision2 service menu</li>
1958 <li>Superpose structures using associated sequence
1960 <li>Export coordinates and projection as CSV from PCA
1962 </ul> <em>Applet</em>
1964 <li>enable javascript: execution by the applet via the
1965 link out mechanism</li>
1966 </ul> <em>Other</em>
1968 <li>Updated the Jmol Jalview interface to work with Jmol
1970 <li>The Jalview Desktop and JalviewLite applet now
1971 require Java 1.5</li>
1972 <li>Allow Jalview feature colour specification for GFF
1973 sequence annotation files</li>
1974 <li>New 'colour by label' keword in Jalview feature file
1975 type colour specification</li>
1976 <li>New Jalview Desktop Groovy API method that allows a
1977 script to check if it being run in an interactive session or
1978 in a batch operation from the Jalview command line</li>
1982 <li>clustalx colourscheme colours Ds preferentially when
1983 both D+E are present in over 50% of the column</li>
1984 </ul> <em>Application</em>
1986 <li>typo in AlignmentFrame->View->Hide->all but
1987 selected Regions menu item</li>
1988 <li>sequence fetcher replaces ',' for ';' when the ',' is
1989 part of a valid accession ID</li>
1990 <li>fatal OOM if object retrieved by sequence fetcher
1991 runs out of memory</li>
1992 <li>unhandled Out of Memory Error when viewing pca
1993 analysis results</li>
1994 <li>InstallAnywhere builds fail to launch on OS X java
1995 10.5 update 4 (due to apple Java 1.6 update)</li>
1996 <li>Installanywhere Jalview silently fails to launch</li>
1997 </ul> <em>Applet</em>
1999 <li>Jalview.getFeatureGroups() raises an
2000 ArrayIndexOutOfBoundsException if no feature groups are
2007 <div align="center">
2008 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2014 <li>Alignment prettyprinter doesn't cope with long
2016 <li>clustalx colourscheme colours Ds preferentially when
2017 both D+E are present in over 50% of the column</li>
2018 <li>nucleic acid structures retrieved from PDB do not
2019 import correctly</li>
2020 <li>More columns get selected than were clicked on when a
2021 number of columns are hidden</li>
2022 <li>annotation label popup menu not providing correct
2023 add/hide/show options when rows are hidden or none are
2025 <li>Stockholm format shown in list of readable formats,
2026 and parser copes better with alignments from RFAM.</li>
2027 <li>CSV output of consensus only includes the percentage
2028 of all symbols if sequence logo display is enabled</li>
2030 </ul> <em>Applet</em>
2032 <li>annotation panel disappears when annotation is
2034 </ul> <em>Application</em>
2036 <li>Alignment view not redrawn properly when new
2037 alignment opened where annotation panel is visible but no
2038 annotations are present on alignment</li>
2039 <li>pasted region containing hidden columns is
2040 incorrectly displayed in new alignment window</li>
2041 <li>Jalview slow to complete operations when stdout is
2042 flooded (fix is to close the Jalview console)</li>
2043 <li>typo in AlignmentFrame->View->Hide->all but
2044 selected Rregions menu item.</li>
2045 <li>inconsistent group submenu and Format submenu entry
2046 'Un' or 'Non'conserved</li>
2047 <li>Sequence feature settings are being shared by
2048 multiple distinct alignments</li>
2049 <li>group annotation not recreated when tree partition is
2051 <li>double click on group annotation to select sequences
2052 does not propagate to associated trees</li>
2053 <li>Mac OSX specific issues:
2055 <li>exception raised when mouse clicked on desktop
2056 window background</li>
2057 <li>Desktop menu placed on menu bar and application
2058 name set correctly</li>
2059 <li>sequence feature settings not wide enough for the
2060 save feature colourscheme button</li>
2069 <div align="center">
2070 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2073 <td><em>New Capabilities</em>
2075 <li>URL links generated from description line for
2076 regular-expression based URL links (applet and application)
2083 <li>Non-positional feature URL links are shown in link
2085 <li>Linked viewing of nucleic acid sequences and
2087 <li>Automatic Scrolling option in View menu to display
2088 the currently highlighted region of an alignment.</li>
2089 <li>Order an alignment by sequence length, or using the
2090 average score or total feature count for each sequence.</li>
2091 <li>Shading features by score or associated description</li>
2092 <li>Subdivide alignment and groups based on identity of
2093 selected subsequence (Make Groups from Selection).</li>
2094 <li>New hide/show options including Shift+Control+H to
2095 hide everything but the currently selected region.</li>
2096 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2097 </ul> <em>Application</em>
2099 <li>Fetch DB References capabilities and UI expanded to
2100 support retrieval from DAS sequence sources</li>
2101 <li>Local DAS Sequence sources can be added via the
2102 command line or via the Add local source dialog box.</li>
2103 <li>DAS Dbref and DbxRef feature types are parsed as
2104 database references and protein_name is parsed as
2105 description line (BioSapiens terms).</li>
2106 <li>Enable or disable non-positional feature and database
2107 references in sequence ID tooltip from View menu in
2109 <!-- <li>New hidden columns and rows and representatives capabilities
2110 in annotations file (in progress - not yet fully implemented)</li> -->
2111 <li>Group-associated consensus, sequence logos and
2112 conservation plots</li>
2113 <li>Symbol distributions for each column can be exported
2114 and visualized as sequence logos</li>
2115 <li>Optionally scale multi-character column labels to fit
2116 within each column of annotation row<!-- todo for applet -->
2118 <li>Optional automatic sort of associated alignment view
2119 when a new tree is opened.</li>
2120 <li>Jalview Java Console</li>
2121 <li>Better placement of desktop window when moving
2122 between different screens.</li>
2123 <li>New preference items for sequence ID tooltip and
2124 consensus annotation</li>
2125 <li>Client to submit sequences and IDs to Envision2
2127 <li><em>Vamsas Capabilities</em>
2129 <li>Improved VAMSAS synchronization (Jalview archive
2130 used to preserve views, structures, and tree display
2132 <li>Import of vamsas documents from disk or URL via
2134 <li>Sharing of selected regions between views and
2135 with other VAMSAS applications (Experimental feature!)</li>
2136 <li>Updated API to VAMSAS version 0.2</li>
2138 </ul> <em>Applet</em>
2140 <li>Middle button resizes annotation row height</li>
2143 <li>sortByTree (true/false) - automatically sort the
2144 associated alignment view by the tree when a new tree is
2146 <li>showTreeBootstraps (true/false) - show or hide
2147 branch bootstraps (default is to show them if available)</li>
2148 <li>showTreeDistances (true/false) - show or hide
2149 branch lengths (default is to show them if available)</li>
2150 <li>showUnlinkedTreeNodes (true/false) - indicate if
2151 unassociated nodes should be highlighted in the tree
2153 <li>heightScale and widthScale (1.0 or more) -
2154 increase the height or width of a cell in the alignment
2155 grid relative to the current font size.</li>
2158 <li>Non-positional features displayed in sequence ID
2160 </ul> <em>Other</em>
2162 <li>Features format: graduated colour definitions and
2163 specification of feature scores</li>
2164 <li>Alignment Annotations format: new keywords for group
2165 associated annotation (GROUP_REF) and annotation row display
2166 properties (ROW_PROPERTIES)</li>
2167 <li>XML formats extended to support graduated feature
2168 colourschemes, group associated annotation, and profile
2169 visualization settings.</li></td>
2172 <li>Source field in GFF files parsed as feature source
2173 rather than description</li>
2174 <li>Non-positional features are now included in sequence
2175 feature and gff files (controlled via non-positional feature
2176 visibility in tooltip).</li>
2177 <li>URL links generated for all feature links (bugfix)</li>
2178 <li>Added URL embedding instructions to features file
2180 <li>Codons containing ambiguous nucleotides translated as
2181 'X' in peptide product</li>
2182 <li>Match case switch in find dialog box works for both
2183 sequence ID and sequence string and query strings do not
2184 have to be in upper case to match case-insensitively.</li>
2185 <li>AMSA files only contain first column of
2186 multi-character column annotation labels</li>
2187 <li>Jalview Annotation File generation/parsing consistent
2188 with documentation (e.g. Stockholm annotation can be
2189 exported and re-imported)</li>
2190 <li>PDB files without embedded PDB IDs given a friendly
2192 <li>Find incrementally searches ID string matches as well
2193 as subsequence matches, and correctly reports total number
2197 <li>Better handling of exceptions during sequence
2199 <li>Dasobert generated non-positional feature URL
2200 link text excludes the start_end suffix</li>
2201 <li>DAS feature and source retrieval buttons disabled
2202 when fetch or registry operations in progress.</li>
2203 <li>PDB files retrieved from URLs are cached properly</li>
2204 <li>Sequence description lines properly shared via
2206 <li>Sequence fetcher fetches multiple records for all
2208 <li>Ensured that command line das feature retrieval
2209 completes before alignment figures are generated.</li>
2210 <li>Reduced time taken when opening file browser for
2212 <li>isAligned check prior to calculating tree, PCA or
2213 submitting an MSA to JNet now excludes hidden sequences.</li>
2214 <li>User defined group colours properly recovered
2215 from Jalview projects.</li>
2224 <div align="center">
2225 <strong>2.4.0.b2</strong><br> 28/10/2009
2230 <li>Experimental support for google analytics usage
2232 <li>Jalview privacy settings (user preferences and docs).</li>
2237 <li>Race condition in applet preventing startup in
2239 <li>Exception when feature created from selection beyond
2240 length of sequence.</li>
2241 <li>Allow synthetic PDB files to be imported gracefully</li>
2242 <li>Sequence associated annotation rows associate with
2243 all sequences with a given id</li>
2244 <li>Find function matches case-insensitively for sequence
2245 ID string searches</li>
2246 <li>Non-standard characters do not cause pairwise
2247 alignment to fail with exception</li>
2248 </ul> <em>Application Issues</em>
2250 <li>Sequences are now validated against EMBL database</li>
2251 <li>Sequence fetcher fetches multiple records for all
2253 </ul> <em>InstallAnywhere Issues</em>
2255 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2256 issue with installAnywhere mechanism)</li>
2257 <li>Command line launching of JARs from InstallAnywhere
2258 version (java class versioning error fixed)</li>
2265 <div align="center">
2266 <strong>2.4</strong><br> 27/8/2008
2269 <td><em>User Interface</em>
2271 <li>Linked highlighting of codon and amino acid from
2272 translation and protein products</li>
2273 <li>Linked highlighting of structure associated with
2274 residue mapping to codon position</li>
2275 <li>Sequence Fetcher provides example accession numbers
2276 and 'clear' button</li>
2277 <li>MemoryMonitor added as an option under Desktop's
2279 <li>Extract score function to parse whitespace separated
2280 numeric data in description line</li>
2281 <li>Column labels in alignment annotation can be centred.</li>
2282 <li>Tooltip for sequence associated annotation give name
2284 </ul> <em>Web Services and URL fetching</em>
2286 <li>JPred3 web service</li>
2287 <li>Prototype sequence search client (no public services
2289 <li>Fetch either seed alignment or full alignment from
2291 <li>URL Links created for matching database cross
2292 references as well as sequence ID</li>
2293 <li>URL Links can be created using regular-expressions</li>
2294 </ul> <em>Sequence Database Connectivity</em>
2296 <li>Retrieval of cross-referenced sequences from other
2298 <li>Generalised database reference retrieval and
2299 validation to all fetchable databases</li>
2300 <li>Fetch sequences from DAS sources supporting the
2301 sequence command</li>
2302 </ul> <em>Import and Export</em>
2303 <li>export annotation rows as CSV for spreadsheet import</li>
2304 <li>Jalview projects record alignment dataset associations,
2305 EMBL products, and cDNA sequence mappings</li>
2306 <li>Sequence Group colour can be specified in Annotation
2308 <li>Ad-hoc colouring of group in Annotation File using RGB
2309 triplet as name of colourscheme</li>
2310 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2312 <li>treenode binding for VAMSAS tree exchange</li>
2313 <li>local editing and update of sequences in VAMSAS
2314 alignments (experimental)</li>
2315 <li>Create new or select existing session to join</li>
2316 <li>load and save of vamsas documents</li>
2317 </ul> <em>Application command line</em>
2319 <li>-tree parameter to open trees (introduced for passing
2321 <li>-fetchfrom command line argument to specify nicknames
2322 of DAS servers to query for alignment features</li>
2323 <li>-dasserver command line argument to add new servers
2324 that are also automatically queried for features</li>
2325 <li>-groovy command line argument executes a given groovy
2326 script after all input data has been loaded and parsed</li>
2327 </ul> <em>Applet-Application data exchange</em>
2329 <li>Trees passed as applet parameters can be passed to
2330 application (when using "View in full
2331 application")</li>
2332 </ul> <em>Applet Parameters</em>
2334 <li>feature group display control parameter</li>
2335 <li>debug parameter</li>
2336 <li>showbutton parameter</li>
2337 </ul> <em>Applet API methods</em>
2339 <li>newView public method</li>
2340 <li>Window (current view) specific get/set public methods</li>
2341 <li>Feature display control methods</li>
2342 <li>get list of currently selected sequences</li>
2343 </ul> <em>New Jalview distribution features</em>
2345 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2346 <li>RELEASE file gives build properties for the latest
2347 Jalview release.</li>
2348 <li>Java 1.1 Applet build made easier and donotobfuscate
2349 property controls execution of obfuscator</li>
2350 <li>Build target for generating source distribution</li>
2351 <li>Debug flag for javacc</li>
2352 <li>.jalview_properties file is documented (slightly) in
2353 jalview.bin.Cache</li>
2354 <li>Continuous Build Integration for stable and
2355 development version of Application, Applet and source
2360 <li>selected region output includes visible annotations
2361 (for certain formats)</li>
2362 <li>edit label/displaychar contains existing label/char
2364 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2365 <li>shorter peptide product names from EMBL records</li>
2366 <li>Newick string generator makes compact representations</li>
2367 <li>bootstrap values parsed correctly for tree files with
2369 <li>pathological filechooser bug avoided by not allowing
2370 filenames containing a ':'</li>
2371 <li>Fixed exception when parsing GFF files containing
2372 global sequence features</li>
2373 <li>Alignment datasets are finalized only when number of
2374 references from alignment sequences goes to zero</li>
2375 <li>Close of tree branch colour box without colour
2376 selection causes cascading exceptions</li>
2377 <li>occasional negative imgwidth exceptions</li>
2378 <li>better reporting of non-fatal warnings to user when
2379 file parsing fails.</li>
2380 <li>Save works when Jalview project is default format</li>
2381 <li>Save as dialog opened if current alignment format is
2382 not a valid output format</li>
2383 <li>UniProt canonical names introduced for both das and
2385 <li>Histidine should be midblue (not pink!) in Zappo</li>
2386 <li>error messages passed up and output when data read
2388 <li>edit undo recovers previous dataset sequence when
2389 sequence is edited</li>
2390 <li>allow PDB files without pdb ID HEADER lines (like
2391 those generated by MODELLER) to be read in properly</li>
2392 <li>allow reading of JPred concise files as a normal
2394 <li>Stockholm annotation parsing and alignment properties
2395 import fixed for PFAM records</li>
2396 <li>Structure view windows have correct name in Desktop
2398 <li>annotation consisting of sequence associated scores
2399 can be read and written correctly to annotation file</li>
2400 <li>Aligned cDNA translation to aligned peptide works
2402 <li>Fixed display of hidden sequence markers and
2403 non-italic font for representatives in Applet</li>
2404 <li>Applet Menus are always embedded in applet window on
2406 <li>Newly shown features appear at top of stack (in
2408 <li>Annotations added via parameter not drawn properly
2409 due to null pointer exceptions</li>
2410 <li>Secondary structure lines are drawn starting from
2411 first column of alignment</li>
2412 <li>UniProt XML import updated for new schema release in
2414 <li>Sequence feature to sequence ID match for Features
2415 file is case-insensitive</li>
2416 <li>Sequence features read from Features file appended to
2417 all sequences with matching IDs</li>
2418 <li>PDB structure coloured correctly for associated views
2419 containing a sub-sequence</li>
2420 <li>PDB files can be retrieved by applet from Jar files</li>
2421 <li>feature and annotation file applet parameters
2422 referring to different directories are retrieved correctly</li>
2423 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
2424 <li>Fixed application hang whilst waiting for
2425 splash-screen version check to complete</li>
2426 <li>Applet properly URLencodes input parameter values
2427 when passing them to the launchApp service</li>
2428 <li>display name and local features preserved in results
2429 retrieved from web service</li>
2430 <li>Visual delay indication for sequence retrieval and
2431 sequence fetcher initialisation</li>
2432 <li>updated Application to use DAS 1.53e version of
2433 dasobert DAS client</li>
2434 <li>Re-instated Full AMSA support and .amsa file
2436 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
2444 <div align="center">
2445 <strong>2.3</strong><br> 9/5/07
2450 <li>Jmol 11.0.2 integration</li>
2451 <li>PDB views stored in Jalview XML files</li>
2452 <li>Slide sequences</li>
2453 <li>Edit sequence in place</li>
2454 <li>EMBL CDS features</li>
2455 <li>DAS Feature mapping</li>
2456 <li>Feature ordering</li>
2457 <li>Alignment Properties</li>
2458 <li>Annotation Scores</li>
2459 <li>Sort by scores</li>
2460 <li>Feature/annotation editing in applet</li>
2465 <li>Headless state operation in 2.2.1</li>
2466 <li>Incorrect and unstable DNA pairwise alignment</li>
2467 <li>Cut and paste of sequences with annotation</li>
2468 <li>Feature group display state in XML</li>
2469 <li>Feature ordering in XML</li>
2470 <li>blc file iteration selection using filename # suffix</li>
2471 <li>Stockholm alignment properties</li>
2472 <li>Stockhom alignment secondary structure annotation</li>
2473 <li>2.2.1 applet had no feature transparency</li>
2474 <li>Number pad keys can be used in cursor mode</li>
2475 <li>Structure Viewer mirror image resolved</li>
2482 <div align="center">
2483 <strong>2.2.1</strong><br> 12/2/07
2488 <li>Non standard characters can be read and displayed
2489 <li>Annotations/Features can be imported/exported to the
2491 <li>Applet allows editing of sequence/annotation/group
2492 name & description
2493 <li>Preference setting to display sequence name in
2495 <li>Annotation file format extended to allow
2496 Sequence_groups to be defined
2497 <li>Default opening of alignment overview panel can be
2498 specified in preferences
2499 <li>PDB residue numbering annotation added to associated
2505 <li>Applet crash under certain Linux OS with Java 1.6
2507 <li>Annotation file export / import bugs fixed
2508 <li>PNG / EPS image output bugs fixed
2514 <div align="center">
2515 <strong>2.2</strong><br> 27/11/06
2520 <li>Multiple views on alignment
2521 <li>Sequence feature editing
2522 <li>"Reload" alignment
2523 <li>"Save" to current filename
2524 <li>Background dependent text colour
2525 <li>Right align sequence ids
2526 <li>User-defined lower case residue colours
2529 <li>Menu item accelerator keys
2530 <li>Control-V pastes to current alignment
2531 <li>Cancel button for DAS Feature Fetching
2532 <li>PCA and PDB Viewers zoom via mouse roller
2533 <li>User-defined sub-tree colours and sub-tree selection
2540 <li>'New Window' button on the 'Output to Text box'
2545 <li>New memory efficient Undo/Redo System
2546 <li>Optimised symbol lookups and conservation/consensus
2548 <li>Region Conservation/Consensus recalculated after
2550 <li>Fixed Remove Empty Columns Bug (empty columns at end
2552 <li>Slowed DAS Feature Fetching for increased robustness.
2559 <li>Made angle brackets in ASCII feature descriptions
2561 <li>Re-instated Zoom function for PCA
2562 <li>Sequence descriptions conserved in web service
2564 <li>UniProt ID discoverer uses any word separated by
2566 <li>WsDbFetch query/result association resolved
2567 <li>Tree leaf to sequence mapping improved
2568 <li>Smooth fonts switch moved to FontChooser dialog box.
2580 <div align="center">
2581 <strong>2.1.1</strong><br> 12/9/06
2586 <li>Copy consensus sequence to clipboard</li>
2591 <li>Image output - rightmost residues are rendered if
2592 sequence id panel has been resized</li>
2593 <li>Image output - all offscreen group boundaries are
2595 <li>Annotation files with sequence references - all
2596 elements in file are relative to sequence position</li>
2597 <li>Mac Applet users can use Alt key for group editing</li>
2603 <div align="center">
2604 <strong>2.1</strong><br> 22/8/06
2609 <li>MAFFT Multiple Alignment in default Web Service list</li>
2610 <li>DAS Feature fetching</li>
2611 <li>Hide sequences and columns</li>
2612 <li>Export Annotations and Features</li>
2613 <li>GFF file reading / writing</li>
2614 <li>Associate structures with sequences from local PDB
2616 <li>Add sequences to exisiting alignment</li>
2617 <li>Recently opened files / URL lists</li>
2618 <li>Applet can launch the full application</li>
2619 <li>Applet has transparency for features (Java 1.2
2621 <li>Applet has user defined colours parameter</li>
2622 <li>Applet can load sequences from parameter
2623 "sequence<em>x</em>"
2629 <li>Redundancy Panel reinstalled in the Applet</li>
2630 <li>Monospaced font - EPS / rescaling bug fixed</li>
2631 <li>Annotation files with sequence references bug fixed</li>
2637 <div align="center">
2638 <strong>2.08.1</strong><br> 2/5/06
2643 <li>Change case of selected region from Popup menu</li>
2644 <li>Choose to match case when searching</li>
2645 <li>Middle mouse button and mouse movement can compress /
2646 expand the visible width and height of the alignment</li>
2651 <li>Annotation Panel displays complete JNet results</li>
2657 <div align="center">
2658 <strong>2.08b</strong><br> 18/4/06
2664 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
2665 <li>Righthand label on wrapped alignments shows correct
2672 <div align="center">
2673 <strong>2.08</strong><br> 10/4/06
2678 <li>Editing can be locked to the selection area</li>
2679 <li>Keyboard editing</li>
2680 <li>Create sequence features from searches</li>
2681 <li>Precalculated annotations can be loaded onto
2683 <li>Features file allows grouping of features</li>
2684 <li>Annotation Colouring scheme added</li>
2685 <li>Smooth fonts off by default - Faster rendering</li>
2686 <li>Choose to toggle Autocalculate Consensus On/Off</li>
2691 <li>Drag & Drop fixed on Linux</li>
2692 <li>Jalview Archive file faster to load/save, sequence
2693 descriptions saved.</li>
2699 <div align="center">
2700 <strong>2.07</strong><br> 12/12/05
2705 <li>PDB Structure Viewer enhanced</li>
2706 <li>Sequence Feature retrieval and display enhanced</li>
2707 <li>Choose to output sequence start-end after sequence
2708 name for file output</li>
2709 <li>Sequence Fetcher WSDBFetch@EBI</li>
2710 <li>Applet can read feature files, PDB files and can be
2711 used for HTML form input</li>
2716 <li>HTML output writes groups and features</li>
2717 <li>Group editing is Control and mouse click</li>
2718 <li>File IO bugs</li>
2724 <div align="center">
2725 <strong>2.06</strong><br> 28/9/05
2730 <li>View annotations in wrapped mode</li>
2731 <li>More options for PCA viewer</li>
2736 <li>GUI bugs resolved</li>
2737 <li>Runs with -nodisplay from command line</li>
2743 <div align="center">
2744 <strong>2.05b</strong><br> 15/9/05
2749 <li>Choose EPS export as lineart or text</li>
2750 <li>Jar files are executable</li>
2751 <li>Can read in Uracil - maps to unknown residue</li>
2756 <li>Known OutOfMemory errors give warning message</li>
2757 <li>Overview window calculated more efficiently</li>
2758 <li>Several GUI bugs resolved</li>
2764 <div align="center">
2765 <strong>2.05</strong><br> 30/8/05
2770 <li>Edit and annotate in "Wrapped" view</li>
2775 <li>Several GUI bugs resolved</li>
2781 <div align="center">
2782 <strong>2.04</strong><br> 24/8/05
2787 <li>Hold down mouse wheel & scroll to change font
2793 <li>Improved JPred client reliability</li>
2794 <li>Improved loading of Jalview files</li>
2800 <div align="center">
2801 <strong>2.03</strong><br> 18/8/05
2806 <li>Set Proxy server name and port in preferences</li>
2807 <li>Multiple URL links from sequence ids</li>
2808 <li>User Defined Colours can have a scheme name and added
2810 <li>Choose to ignore gaps in consensus calculation</li>
2811 <li>Unix users can set default web browser</li>
2812 <li>Runs without GUI for batch processing</li>
2813 <li>Dynamically generated Web Service Menus</li>
2818 <li>InstallAnywhere download for Sparc Solaris</li>
2824 <div align="center">
2825 <strong>2.02</strong><br> 18/7/05
2831 <li>Copy & Paste order of sequences maintains
2832 alignment order.</li>
2838 <div align="center">
2839 <strong>2.01</strong><br> 12/7/05
2844 <li>Use delete key for deleting selection.</li>
2845 <li>Use Mouse wheel to scroll sequences.</li>
2846 <li>Help file updated to describe how to add alignment
2848 <li>Version and build date written to build properties
2850 <li>InstallAnywhere installation will check for updates
2851 at launch of Jalview.</li>
2856 <li>Delete gaps bug fixed.</li>
2857 <li>FileChooser sorts columns.</li>
2858 <li>Can remove groups one by one.</li>
2859 <li>Filechooser icons installed.</li>
2860 <li>Finder ignores return character when searching.
2861 Return key will initiate a search.<br>
2868 <div align="center">
2869 <strong>2.0</strong><br> 20/6/05
2874 <li>New codebase</li>