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>
27 <strong>Release History</strong>
31 <td width="60" nowrap>
33 <em><strong>Release</strong></em>
38 <em><strong>New Features</strong></em>
43 <em><strong>Issues Resolved</strong></em>
48 <td width="60" nowrap>
50 <strong><a name="Jalview.2.10.1">2.10.1</a><br />
51 <em>22/11/2016</em></strong>
54 <td><div align="left">
57 <li><!-- JAL-98 -->Improved memory usage: sparse arrays used for all consensus calculations</li>
58 <li><!-- JAL- --></li>
62 <li><!-- JAL-1723 -->Sequence ID tool tips have been tamed (databases sorted alphabetically, abridged ID sets) </li>
63 <li><!-- JAL-2282-->New replacement token for creating URLs <em>just</em> from database cross references. Users with custom links will receive a warning dialog asking them to update their preferences.</li>
64 <li><!-- JAL-2287-->Cancel button and escape listener on dialog warning user about disconnecting Jalview from a Chimera session</li>
65 <li><!-- JAL-2281-->Custom URL links for database cross-references are matched to database name regardless of case</li>
73 <em>Build and deployment</em>
83 <li><!-- JAL-2286 -->Columns with more than one modal residue are not coloured or thresholded according to percent identity (first observed in Jalview 2.8.2)</li>
84 <li><!-- JAL-2301 -->Threonine incorrectly reported as not hydrophobic</li>
85 <li><!-- JAL-2318 -->Updates to documentation pages (above PID threshold, amino acid properties)</li>
86 <li><!-- JAL-2292 -->Lower case residues in sequences are not reported as mapped to residues in a structure file in the View Mapping report</li>
90 <li><!-- JAL-2282-->Custom URL links for specific database names without regular expressions also offer invalid links from Sequence ID</li>
91 <li><!-- JAL-2315-->Removing a single configured link in the URL links pane in Connections preferences doesn't actually update Jalview configuration</li>
92 <li><!-- JAL-2272-->CTRL-Click on a selected region to open the alignment area popup menu doesn't work on El-Capitan</li>
93 <li><!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF files with similarly named sequences if dropped onto the alignment</li>
94 <li><!-- JAL-2312 -->Additional mappings are shown for PDB entries where more chains exist in the PDB accession than are reported in the SIFTS file</li>
95 <li><!-- JAL-2317-->Certain structures do not get mapped to the structure view when displayed with Chimera</li>
96 <li><!-- JAL-2317-->No chains shown in the Chimera view panel's View->Show Chains submenu</li>
104 <em>Build and deployment</em>
106 <li><!-- JAL-2308, -->Failing/passing unit tests</li>
108 <em>New Known Issues</em>
115 <td width="60" nowrap>
117 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
118 <em>25/10/2016</em></strong>
121 <td><em>Application</em>
123 <li>3D Structure chooser opens with 'Cached structures'
124 view if structures already loaded</li>
125 <li>Progress bar reports models as they are loaded to
132 <li>Colour by conservation always enabled and no tick
133 shown in menu when BLOSUM or PID shading applied</li>
134 <li>FER1_ARATH and FER2_ARATH labels were switched in
135 example sequences/projects/trees</li>
139 <li>Jalview projects with views of local PDB structure
140 files saved on Windows cannot be opened on OSX</li>
141 <li>Multiple structure views can be opened and
142 superposed without timeout for structures with multiple
143 models or multiple sequences in alignment</li>
144 <li>Cannot import or associated local PDB files without
145 a PDB ID HEADER line</li>
146 <li>RMSD is not output in Jmol console when
147 superposition is performed</li>
148 <li>Drag and drop of URL from Browser fails for Linux
149 and OSX versions earlier than El Capitan</li>
150 <li>ENA client ignores invalid content from ENA server</li>
151 <li>Exceptions are not raised in console when ENA
152 client attempts to fetch non-existent IDs via Fetch DB
154 <li>Exceptions are not raised in console when a new
155 view is created on the alignment</li>
156 <li>OSX right-click fixed for group selections:
157 CMD-click to insert/remove gaps in groups and CTRL-click
158 to open group pop-up menu</li>
160 <em>Build and deployment</em>
162 <li>URL link checker now copes with multi-line anchor
165 <em>New Known Issues</em>
167 <li>Drag and drop from URL links in browsers do not
174 <td width="60" nowrap>
176 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
182 <!-- JAL-2124 -->Updated Spanish translations.
185 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
186 for importing structure data to Jalview. Enables mmCIF and
190 <!-- JAL-192 --->Alignment ruler shows positions relative to
194 <!-- JAL-2202 -->Position/residue shown in status bar when
195 mousing over sequence associated annotation
198 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
202 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
203 '()', canonical '[]' and invalid '{}' base pair populations
207 <!-- JAL-2092 -->Feature settings popup menu options for
208 showing or hiding columns containing a feature
211 <!-- JAL-1557 -->Edit selected group by double clicking on
212 group and sequence associated annotation labels
215 <!-- JAL-2236 -->Sequence name added to annotation label in
216 select/hide columns by annotation and colour by annotation
220 </ul> <em>Application</em>
223 <!-- JAL-2050-->Automatically hide introns when opening a
227 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
231 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
232 structure mappings with the EMBL-EBI PDBe SIFTS database
235 <!-- JAL-2079 -->Updated download sites used for Rfam and
236 Pfam sources to xfam.org
239 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
242 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
243 over sequences in Jalview
246 <!-- JAL-2027-->Support for reverse-complement coding
247 regions in ENA and EMBL
250 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
251 for record retrieval via ENA rest API
254 <!-- JAL-2027 -->Support for ENA CDS records with reverse
258 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
259 groovy script execution
262 <!-- JAL-1812 -->New 'execute Groovy script' option in an
263 alignment window's Calculate menu
266 <!-- JAL-1812 -->Allow groovy scripts that call
267 Jalview.getAlignFrames() to run in headless mode
270 <!-- JAL-2068 -->Support for creating new alignment
271 calculation workers from groovy scripts
274 <!-- JAL-1369 --->Store/restore reference sequence in
278 <!-- JAL-1803 -->Chain codes for a sequence's PDB
279 associations are now saved/restored from project
282 <!-- JAL-1993 -->Database selection dialog always shown
283 before sequence fetcher is opened
286 <!-- JAL-2183 -->Double click on an entry in Jalview's
287 database chooser opens a sequence fetcher
290 <!-- JAL-1563 -->Free-text search client for UniProt using
294 <!-- JAL-2168 -->-nonews command line parameter to prevent
295 the news reader opening
298 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
299 querying stored in preferences
302 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
306 <!-- JAL-1977-->Tooltips shown on database chooser
309 <!-- JAL-391 -->Reverse complement function in calculate
310 menu for nucleotide sequences
313 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
314 and feature counts preserves alignment ordering (and
315 debugged for complex feature sets).
318 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
319 viewing structures with Jalview 2.10
322 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
323 genome, transcript CCDS and gene ids via the Ensembl and
324 Ensembl Genomes REST API
327 <!-- JAL-2049 -->Protein sequence variant annotation
328 computed for 'sequence_variant' annotation on CDS regions
332 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
336 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
337 Ref Fetcher fails to match, or otherwise updates sequence
338 data from external database records.
341 <!-- JAL-2154 -->Revised Jalview Project format for
342 efficient recovery of sequence coding and alignment
343 annotation relationships.
345 </ul> <!-- <em>Applet</em>
356 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
360 <!-- JAL-2018-->Export features in Jalview format (again)
361 includes graduated colourschemes
364 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
365 working with big alignments and lots of hidden columns
368 <!-- JAL-2053-->Hidden column markers not always rendered
369 at right of alignment window
372 <!-- JAL-2067 -->Tidied up links in help file table of
376 <!-- JAL-2072 -->Feature based tree calculation not shown
380 <!-- JAL-2075 -->Hidden columns ignored during feature
381 based tree calculation
384 <!-- JAL-2065 -->Alignment view stops updating when show
385 unconserved enabled for group on alignment
388 <!-- JAL-2086 -->Cannot insert gaps into sequence when
392 <!-- JAL-2146 -->Alignment column in status incorrectly
393 shown as "Sequence position" when mousing over
397 <!-- JAL-2099 -->Incorrect column numbers in ruler when
398 hidden columns present
401 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
402 user created annotation added to alignment
405 <!-- JAL-1841 -->RNA Structure consensus only computed for
406 '()' base pair annotation
409 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
410 in zero scores for all base pairs in RNA Structure
414 <!-- JAL-2174-->Extend selection with columns containing
418 <!-- JAL-2275 -->Pfam format writer puts extra space at
419 beginning of sequence
422 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
426 <!-- JAL-2238 -->Cannot create groups on an alignment from
427 from a tree when t-coffee scores are shown
430 <!-- JAL-1836,1967 -->Cannot import and view PDB
431 structures with chains containing negative resnums (4q4h)
434 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
438 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
439 to Clustal, PIR and PileUp output
442 <!-- JAL-2008 -->Reordering sequence features that are
443 not visible causes alignment window to repaint
446 <!-- JAL-2006 -->Threshold sliders don't work in
447 graduated colour and colour by annotation row for e-value
448 scores associated with features and annotation rows
451 <!-- JAL-1797 -->amino acid physicochemical conservation
452 calculation should be case independent
455 <!-- JAL-2173 -->Remove annotation also updates hidden
459 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
460 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
461 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
464 <!-- JAL-2065 -->Null pointer exceptions and redraw
465 problems when reference sequence defined and 'show
466 non-conserved' enabled
469 <!-- JAL-1306 -->Quality and Conservation are now shown on
470 load even when Consensus calculation is disabled
473 <!-- JAL-1932 -->Remove right on penultimate column of
474 alignment does nothing
480 <!-- JAL-1552-->URLs and links can't be imported by
481 drag'n'drop on OSX when launched via webstart (note - not
482 yet fixed for El Capitan)
485 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
486 output when running on non-gb/us i18n platforms
489 <!-- JAL-1944 -->Error thrown when exporting a view with
490 hidden sequences as flat-file alignment
493 <!-- JAL-2030-->InstallAnywhere distribution fails when
497 <!-- JAL-2080-->Jalview very slow to launch via webstart
498 (also hotfix for 2.9.0b2)
501 <!-- JAL-2085 -->Cannot save project when view has a
502 reference sequence defined
505 <!-- JAL-1011 -->Columns are suddenly selected in other
506 alignments and views when revealing hidden columns
509 <!-- JAL-1989 -->Hide columns not mirrored in complement
510 view in a cDNA/Protein splitframe
513 <!-- JAL-1369 -->Cannot save/restore representative
514 sequence from project when only one sequence is
518 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
522 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
523 structure consensus didn't refresh annotation panel
526 <!-- JAL-1962 -->View mapping in structure view shows
527 mappings between sequence and all chains in a PDB file
530 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
531 dialogs format columns correctly, don't display array
532 data, sort columns according to type
535 <!-- JAL-1975 -->Export complete shown after destination
536 file chooser is cancelled during an image export
539 <!-- JAL-2025 -->Error when querying PDB Service with
540 sequence name containing special characters
543 <!-- JAL-2024 -->Manual PDB structure querying should be
547 <!-- JAL-2104 -->Large tooltips with broken HTML
548 formatting don't wrap
551 <!-- JAL-1128 -->Figures exported from wrapped view are
552 truncated so L looks like I in consensus annotation
555 <!-- JAL-2003 -->Export features should only export the
556 currently displayed features for the current selection or
560 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
561 after fetching cross-references, and restoring from project
564 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
565 followed in the structure viewer
568 <!-- JAL-2163 -->Titles for individual alignments in
569 splitframe not restored from project
572 <!-- JAL-2145 -->missing autocalculated annotation at
573 trailing end of protein alignment in transcript/product
574 splitview when pad-gaps not enabled by default
577 <!-- JAL-1797 -->amino acid physicochemical conservation
581 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
582 article has been read (reopened issue due to
583 internationalisation problems)
586 <!-- JAL-1960 -->Only offer PDB structures in structure
587 viewer based on sequence name, PDB and UniProt
592 <!-- JAL-1976 -->No progress bar shown during export of
596 <!-- JAL-2213 -->Structures not always superimposed after
597 multiple structures are shown for one or more sequences.
600 <!-- JAL-1370 -->Reference sequence characters should not
601 be replaced with '.' when 'Show unconserved' format option
605 <!-- JAL-1823 -->Cannot specify chain code when entering
606 specific PDB id for sequence
609 <!-- JAL-1944 -->File->Export->.. as doesn't work when
610 'Export hidden sequences' is enabled, but 'export hidden
611 columns' is disabled.
614 <!--JAL-2026-->Best Quality option in structure chooser
615 selects lowest rather than highest resolution structures
619 <!-- JAL-1887 -->Incorrect start and end reported for PDB
620 to sequence mapping in 'View Mappings' report
623 <!-- JAL-2284 -->Unable to read old Jalview projects that
624 contain non-XML data added after Jalvew wrote project.
626 <!-- may exclude, this is an external service stability issue JAL-1941
627 -- > RNA 3D structure not added via DSSR service</li> -->
632 <!-- JAL-2151 -->Incorrect columns are selected when
633 hidden columns present before start of sequence
636 <!-- JAL-1986 -->Missing dependencies on applet pages
640 <!-- JAL-1947 -->Overview pixel size changes when
641 sequences are hidden in applet
644 <!-- JAL-1996 -->Updated instructions for applet
645 deployment on examples pages.
652 <td width="60" nowrap>
654 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
655 <em>16/10/2015</em></strong>
660 <li>Time stamps for signed Jalview application and applet
667 <li>Duplicate group consensus and conservation rows
668 shown when tree is partitioned</li>
669 <li>Erratic behaviour when tree partitions made with
670 multiple cDNA/Protein split views</li>
676 <td width="60" nowrap>
678 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
679 <em>8/10/2015</em></strong>
684 <li>Updated Spanish translations of localized text for
686 </ul> <em>Application</em>
688 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
689 <li>Signed OSX InstallAnywhere installer<br></li>
690 <li>Support for per-sequence based annotations in BioJSON</li>
691 </ul> <em>Applet</em>
693 <li>Split frame example added to applet examples page</li>
694 </ul><em>Build and Deployment</em>
696 <li><!-- JAL-1888 -->New ant target for running Jalview's test suite</li>
702 <li>Mapping of cDNA to protein in split frames
703 incorrect when sequence start > 1</li>
704 <li>Broken images in filter column by annotation dialog
706 <li>Feature colours not parsed from features file</li>
707 <li>Exceptions and incomplete link URLs recovered when
708 loading a features file containing HTML tags in feature
714 <li>Annotations corrupted after BioJS export and
716 <li>Incorrect sequence limits after Fetch DB References
717 with 'trim retrieved sequences'</li>
718 <li>Incorrect warning about deleting all data when
719 deleting selected columns</li>
720 <li>Patch to build system for shipping properly signed
721 JNLP templates for webstart launch</li>
722 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
723 unreleased structures for download or viewing</li>
724 <li>Tab/space/return keystroke operation of EMBL-PDBe
725 fetcher/viewer dialogs works correctly</li>
726 <li>Disabled 'minimise' button on Jalview windows
727 running on OSX to workaround redraw hang bug</li>
728 <li>Split cDNA/Protein view position and geometry not
729 recovered from jalview project</li>
730 <li>Initial enabled/disabled state of annotation menu
731 sorter 'show autocalculated first/last' corresponds to
733 <li>Restoring of Clustal, RNA Helices and T-Coffee
734 color schemes from BioJSON</li>
738 <li>Reorder sequences mirrored in cDNA/Protein split
740 <li>Applet with Jmol examples not loading correctly</li>
746 <td><div align="center">
747 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
751 <li>Linked visualisation and analysis of DNA and Protein
754 <li>Translated cDNA alignments shown as split protein
755 and DNA alignment views</li>
756 <li>Codon consensus annotation for linked protein and
757 cDNA alignment views</li>
758 <li>Link cDNA or Protein product sequences by loading
759 them onto Protein or cDNA alignments</li>
760 <li>Reconstruct linked cDNA alignment from aligned
761 protein sequences</li>
764 <li>Jmol integration updated to Jmol v14.2.14</li>
765 <li>Import and export of Jalview alignment views as <a
766 href="features/bioJsonFormat.html">BioJSON</a></li>
767 <li>New alignment annotation file statements for
768 reference sequences and marking hidden columns</li>
769 <li>Reference sequence based alignment shading to
770 highlight variation</li>
771 <li>Select or hide columns according to alignment
773 <li>Find option for locating sequences by description</li>
774 <li>Conserved physicochemical properties shown in amino
775 acid conservation row</li>
776 <li>Alignments can be sorted by number of RNA helices</li>
777 </ul> <em>Application</em>
779 <li>New cDNA/Protein analysis capabilities
781 <li>Get Cross-References should open a Split Frame
782 view with cDNA/Protein</li>
783 <li>Detect when nucleotide sequences and protein
784 sequences are placed in the same alignment</li>
785 <li>Split cDNA/Protein views are saved in Jalview
790 <li>Use REST API to talk to Chimera</li>
791 <li>Selected regions in Chimera are highlighted in linked
794 <li>VARNA RNA viewer updated to v3.93</li>
795 <li>VARNA views are saved in Jalview Projects</li>
796 <li>Pseudoknots displayed as Jalview RNA annotation can
797 be shown in VARNA</li>
799 <li>Make groups for selection uses marked columns as well
800 as the active selected region</li>
802 <li>Calculate UPGMA and NJ trees using sequence feature
804 <li>New Export options
806 <li>New Export Settings dialog to control hidden
807 region export in flat file generation</li>
809 <li>Export alignment views for display with the <a
810 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
812 <li>Export scrollable SVG in HTML page</li>
813 <li>Optional embedding of BioJSON data when exporting
814 alignment figures to HTML</li>
816 <li>3D structure retrieval and display
818 <li>Free text and structured queries with the PDBe
820 <li>PDBe Search API based discovery and selection of
821 PDB structures for a sequence set</li>
825 <li>JPred4 employed for protein secondary structure
827 <li>Hide Insertions menu option to hide unaligned columns
828 for one or a group of sequences</li>
829 <li>Automatically hide insertions in alignments imported
830 from the JPred4 web server</li>
831 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
832 system on OSX<br />LGPL libraries courtesy of <a
833 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
835 <li>changed 'View nucleotide structure' submenu to 'View
836 VARNA 2D Structure'</li>
837 <li>change "View protein structure" menu option to "3D
840 </ul> <em>Applet</em>
842 <li>New layout for applet example pages</li>
843 <li>New parameters to enable SplitFrame view
844 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
845 <li>New example demonstrating linked viewing of cDNA and
846 Protein alignments</li>
847 </ul> <em>Development and deployment</em>
849 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
850 <li>Include installation type and git revision in build
851 properties and console log output</li>
852 <li>Jalview Github organisation, and new github site for
853 storing BioJsMSA Templates</li>
854 <li>Jalview's unit tests now managed with TestNG</li>
857 <!-- <em>General</em>
859 </ul> --> <!-- issues resolved --> <em>Application</em>
861 <li>Escape should close any open find dialogs</li>
862 <li>Typo in select-by-features status report</li>
863 <li>Consensus RNA secondary secondary structure
864 predictions are not highlighted in amber</li>
865 <li>Missing gap character in v2.7 example file means
866 alignment appears unaligned when pad-gaps is not enabled</li>
867 <li>First switch to RNA Helices colouring doesn't colour
868 associated structure views</li>
869 <li>ID width preference option is greyed out when auto
870 width checkbox not enabled</li>
871 <li>Stopped a warning dialog from being shown when
872 creating user defined colours</li>
873 <li>'View Mapping' in structure viewer shows sequence
874 mappings for just that viewer's sequences</li>
875 <li>Workaround for superposing PDB files containing
876 multiple models in Chimera</li>
877 <li>Report sequence position in status bar when hovering
878 over Jmol structure</li>
879 <li>Cannot output gaps as '.' symbols with Selection ->
880 output to text box</li>
881 <li>Flat file exports of alignments with hidden columns
882 have incorrect sequence start/end</li>
883 <li>'Aligning' a second chain to a Chimera structure from
885 <li>Colour schemes applied to structure viewers don't
886 work for nucleotide</li>
887 <li>Loading/cut'n'pasting an empty or invalid file leads
888 to a grey/invisible alignment window</li>
889 <li>Exported Jpred annotation from a sequence region
890 imports to different position</li>
891 <li>Space at beginning of sequence feature tooltips shown
892 on some platforms</li>
893 <li>Chimera viewer 'View | Show Chain' menu is not
895 <li>'New View' fails with a Null Pointer Exception in
896 console if Chimera has been opened</li>
897 <li>Mouseover to Chimera not working</li>
898 <li>Miscellaneous ENA XML feature qualifiers not
900 <li>NPE in annotation renderer after 'Extract Scores'</li>
901 <li>If two structures in one Chimera window, mouseover of
902 either sequence shows on first structure</li>
903 <li>'Show annotations' options should not make
904 non-positional annotations visible</li>
905 <li>Subsequence secondary structure annotation not shown
906 in right place after 'view flanking regions'</li>
907 <li>File Save As type unset when current file format is
909 <li>Save as '.jar' option removed for saving Jalview
911 <li>Colour by Sequence colouring in Chimera more
913 <li>Cannot 'add reference annotation' for a sequence in
914 several views on same alignment</li>
915 <li>Cannot show linked products for EMBL / ENA records</li>
916 <li>Jalview's tooltip wraps long texts containing no
918 </ul> <em>Applet</em>
920 <li>Jmol to JalviewLite mouseover/link not working</li>
921 <li>JalviewLite can't import sequences with ID
922 descriptions containing angle brackets</li>
923 </ul> <em>General</em>
925 <li>Cannot export and reimport RNA secondary structure
926 via jalview annotation file</li>
927 <li>Random helix colour palette for colour by annotation
928 with RNA secondary structure</li>
929 <li>Mouseover to cDNA from STOP residue in protein
930 translation doesn't work.</li>
931 <li>hints when using the select by annotation dialog box</li>
932 <li>Jmol alignment incorrect if PDB file has alternate CA
934 <li>FontChooser message dialog appears to hang after
935 choosing 1pt font</li>
936 <li>Peptide secondary structure incorrectly imported from
937 annotation file when annotation display text includes 'e' or
939 <li>Cannot set colour of new feature type whilst creating
941 <li>cDNA translation alignment should not be sequence
943 <li>'Show unconserved' doesn't work for lower case
945 <li>Nucleotide ambiguity codes involving R not recognised</li>
946 </ul> <em>Deployment and Documentation</em>
948 <li>Applet example pages appear different to the rest of
950 </ul> <em>Application Known issues</em>
952 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
953 <li>Misleading message appears after trying to delete
955 <li>Jalview icon not shown in dock after InstallAnywhere
956 version launches</li>
957 <li>Fetching EMBL reference for an RNA sequence results
958 fails with a sequence mismatch</li>
959 <li>Corrupted or unreadable alignment display when
960 scrolling alignment to right</li>
961 <li>ArrayIndexOutOfBoundsException thrown when remove
962 empty columns called on alignment with ragged gapped ends</li>
963 <li>auto calculated alignment annotation rows do not get
964 placed above or below non-autocalculated rows</li>
965 <li>Jalview dekstop becomes sluggish at full screen in
966 ultra-high resolution</li>
967 <li>Cannot disable consensus calculation independently of
968 quality and conservation</li>
969 <li>Mouseover highlighting between cDNA and protein can
970 become sluggish with more than one splitframe shown</li>
971 </ul> <em>Applet Known Issues</em>
973 <li>Core PDB parsing code requires Jmol</li>
974 <li>Sequence canvas panel goes white when alignment
975 window is being resized</li>
981 <td><div align="center">
982 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
986 <li>Updated Java code signing certificate donated by
988 <li>Features and annotation preserved when performing
989 pairwise alignment</li>
990 <li>RNA pseudoknot annotation can be
991 imported/exported/displayed</li>
992 <li>'colour by annotation' can colour by RNA and
993 protein secondary structure</li>
994 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
995 post-hoc with 2.9 release</em>)
998 </ul> <em>Application</em>
1000 <li>Extract and display secondary structure for sequences
1001 with 3D structures</li>
1002 <li>Support for parsing RNAML</li>
1003 <li>Annotations menu for layout
1005 <li>sort sequence annotation rows by alignment</li>
1006 <li>place sequence annotation above/below alignment
1009 <li>Output in Stockholm format</li>
1010 <li>Internationalisation: improved Spanish (es)
1012 <li>Structure viewer preferences tab</li>
1013 <li>Disorder and Secondary Structure annotation tracks
1014 shared between alignments</li>
1015 <li>UCSF Chimera launch and linked highlighting from
1017 <li>Show/hide all sequence associated annotation rows for
1018 all or current selection</li>
1019 <li>disorder and secondary structure predictions
1020 available as dataset annotation</li>
1021 <li>Per-sequence rna helices colouring</li>
1024 <li>Sequence database accessions imported when fetching
1025 alignments from Rfam</li>
1026 <li>update VARNA version to 3.91</li>
1028 <li>New groovy scripts for exporting aligned positions,
1029 conservation values, and calculating sum of pairs scores.</li>
1030 <li>Command line argument to set default JABAWS server</li>
1031 <li>include installation type in build properties and
1032 console log output</li>
1033 <li>Updated Jalview project format to preserve dataset
1037 <!-- issues resolved --> <em>Application</em>
1039 <li>Distinguish alignment and sequence associated RNA
1040 structure in structure->view->VARNA</li>
1041 <li>Raise dialog box if user deletes all sequences in an
1043 <li>Pressing F1 results in documentation opening twice</li>
1044 <li>Sequence feature tooltip is wrapped</li>
1045 <li>Double click on sequence associated annotation
1046 selects only first column</li>
1047 <li>Redundancy removal doesn't result in unlinked
1048 leaves shown in tree</li>
1049 <li>Undos after several redundancy removals don't undo
1051 <li>Hide sequence doesn't hide associated annotation</li>
1052 <li>User defined colours dialog box too big to fit on
1053 screen and buttons not visible</li>
1054 <li>author list isn't updated if already written to
1055 Jalview properties</li>
1056 <li>Popup menu won't open after retrieving sequence
1058 <li>File open window for associate PDB doesn't open</li>
1059 <li>Left-then-right click on a sequence id opens a
1060 browser search window</li>
1061 <li>Cannot open sequence feature shading/sort popup menu
1062 in feature settings dialog</li>
1063 <li>better tooltip placement for some areas of Jalview
1065 <li>Allow addition of JABAWS Server which doesn't
1066 pass validation</li>
1067 <li>Web services parameters dialog box is too large to
1069 <li>Muscle nucleotide alignment preset obscured by
1071 <li>JABAWS preset submenus don't contain newly
1072 defined user preset</li>
1073 <li>MSA web services warns user if they were launched
1074 with invalid input</li>
1075 <li>Jalview cannot contact DAS Registy when running on
1078 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1079 'Superpose with' submenu not shown when new view
1083 </ul> <!-- <em>Applet</em>
1085 </ul> <em>General</em>
1087 </ul>--> <em>Deployment and Documentation</em>
1089 <li>2G and 1G options in launchApp have no effect on
1090 memory allocation</li>
1091 <li>launchApp service doesn't automatically open
1092 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1094 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1095 InstallAnywhere reports cannot find valid JVM when Java
1096 1.7_055 is available
1098 </ul> <em>Application Known issues</em>
1101 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1102 corrupted or unreadable alignment display when scrolling
1106 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1107 retrieval fails but progress bar continues for DAS retrieval
1108 with large number of ID
1111 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1112 flatfile output of visible region has incorrect sequence
1116 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1117 rna structure consensus doesn't update when secondary
1118 structure tracks are rearranged
1121 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1122 invalid rna structure positional highlighting does not
1123 highlight position of invalid base pairs
1126 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1127 out of memory errors are not raised when saving Jalview
1128 project from alignment window file menu
1131 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1132 Switching to RNA Helices colouring doesn't propagate to
1136 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1137 colour by RNA Helices not enabled when user created
1138 annotation added to alignment
1141 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1142 Jalview icon not shown on dock in Mountain Lion/Webstart
1144 </ul> <em>Applet Known Issues</em>
1147 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1148 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1151 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1152 Jalview and Jmol example not compatible with IE9
1155 <li>Sort by annotation score doesn't reverse order
1161 <td><div align="center">
1162 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1165 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1168 <li>Internationalisation of user interface (usually
1169 called i18n support) and translation for Spanish locale</li>
1170 <li>Define/Undefine group on current selection with
1171 Ctrl-G/Shift Ctrl-G</li>
1172 <li>Improved group creation/removal options in
1173 alignment/sequence Popup menu</li>
1174 <li>Sensible precision for symbol distribution
1175 percentages shown in logo tooltip.</li>
1176 <li>Annotation panel height set according to amount of
1177 annotation when alignment first opened</li>
1178 </ul> <em>Application</em>
1180 <li>Interactive consensus RNA secondary structure
1181 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1182 <li>Select columns containing particular features from
1183 Feature Settings dialog</li>
1184 <li>View all 'representative' PDB structures for selected
1186 <li>Update Jalview project format:
1188 <li>New file extension for Jalview projects '.jvp'</li>
1189 <li>Preserve sequence and annotation dataset (to
1190 store secondary structure annotation,etc)</li>
1191 <li>Per group and alignment annotation and RNA helix
1195 <li>New similarity measures for PCA and Tree calculation
1197 <li>Experimental support for retrieval and viewing of
1198 flanking regions for an alignment</li>
1202 <!-- issues resolved --> <em>Application</em>
1204 <li>logo keeps spinning and status remains at queued or
1205 running after job is cancelled</li>
1206 <li>cannot export features from alignments imported from
1207 Jalview/VAMSAS projects</li>
1208 <li>Buggy slider for web service parameters that take
1210 <li>Newly created RNA secondary structure line doesn't
1211 have 'display all symbols' flag set</li>
1212 <li>T-COFFEE alignment score shading scheme and other
1213 annotation shading not saved in Jalview project</li>
1214 <li>Local file cannot be loaded in freshly downloaded
1216 <li>Jalview icon not shown on dock in Mountain
1218 <li>Load file from desktop file browser fails</li>
1219 <li>Occasional NPE thrown when calculating large trees</li>
1220 <li>Cannot reorder or slide sequences after dragging an
1221 alignment onto desktop</li>
1222 <li>Colour by annotation dialog throws NPE after using
1223 'extract scores' function</li>
1224 <li>Loading/cut'n'pasting an empty file leads to a grey
1225 alignment window</li>
1226 <li>Disorder thresholds rendered incorrectly after
1227 performing IUPred disorder prediction</li>
1228 <li>Multiple group annotated consensus rows shown when
1229 changing 'normalise logo' display setting</li>
1230 <li>Find shows blank dialog after 'finished searching' if
1231 nothing matches query</li>
1232 <li>Null Pointer Exceptions raised when sorting by
1233 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1235 <li>Errors in Jmol console when structures in alignment
1236 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1238 <li>Not all working JABAWS services are shown in
1240 <li>JAVAWS version of Jalview fails to launch with
1241 'invalid literal/length code'</li>
1242 <li>Annotation/RNA Helix colourschemes cannot be applied
1243 to alignment with groups (actually fixed in 2.8.0b1)</li>
1244 <li>RNA Helices and T-Coffee Scores available as default
1247 </ul> <em>Applet</em>
1249 <li>Remove group option is shown even when selection is
1251 <li>Apply to all groups ticked but colourscheme changes
1252 don't affect groups</li>
1253 <li>Documented RNA Helices and T-Coffee Scores as valid
1254 colourscheme name</li>
1255 <li>Annotation labels drawn on sequence IDs when
1256 Annotation panel is not displayed</li>
1257 <li>Increased font size for dropdown menus on OSX and
1258 embedded windows</li>
1259 </ul> <em>Other</em>
1261 <li>Consensus sequence for alignments/groups with a
1262 single sequence were not calculated</li>
1263 <li>annotation files that contain only groups imported as
1264 annotation and junk sequences</li>
1265 <li>Fasta files with sequences containing '*' incorrectly
1266 recognised as PFAM or BLC</li>
1267 <li>conservation/PID slider apply all groups option
1268 doesn't affect background (2.8.0b1)
1270 <li>redundancy highlighting is erratic at 0% and 100%</li>
1271 <li>Remove gapped columns fails for sequences with ragged
1273 <li>AMSA annotation row with leading spaces is not
1274 registered correctly on import</li>
1275 <li>Jalview crashes when selecting PCA analysis for
1276 certain alignments</li>
1277 <li>Opening the colour by annotation dialog for an
1278 existing annotation based 'use original colours'
1279 colourscheme loses original colours setting</li>
1284 <td><div align="center">
1285 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
1286 <em>30/1/2014</em></strong>
1290 <li>Trusted certificates for JalviewLite applet and
1291 Jalview Desktop application<br />Certificate was donated by
1292 <a href="https://www.certum.eu">Certum</a> to the Jalview
1293 open source project).
1295 <li>Jalview SRS links replaced by UniProt and EBI-search
1297 <li>Output in Stockholm format</li>
1298 <li>Allow import of data from gzipped files</li>
1299 <li>Export/import group and sequence associated line
1300 graph thresholds</li>
1301 <li>Nucleotide substitution matrix that supports RNA and
1302 ambiguity codes</li>
1303 <li>Allow disorder predictions to be made on the current
1304 selection (or visible selection) in the same way that JPred
1306 <li>Groovy scripting for headless Jalview operation</li>
1307 </ul> <em>Other improvements</em>
1309 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
1310 <li>COMBINE statement uses current SEQUENCE_REF and
1311 GROUP_REF scope to group annotation rows</li>
1312 <li>Support '' style escaping of quotes in Newick
1314 <li>Group options for JABAWS service by command line name</li>
1315 <li>Empty tooltip shown for JABA service options with a
1316 link but no description</li>
1317 <li>Select primary source when selecting authority in
1318 database fetcher GUI</li>
1319 <li>Add .mfa to FASTA file extensions recognised by
1321 <li>Annotation label tooltip text wrap</li>
1326 <li>Slow scrolling when lots of annotation rows are
1328 <li>Lots of NPE (and slowness) after creating RNA
1329 secondary structure annotation line</li>
1330 <li>Sequence database accessions not imported when
1331 fetching alignments from Rfam</li>
1332 <li>Incorrect SHMR submission for sequences with
1334 <li>View all structures does not always superpose
1336 <li>Option widgets in service parameters not updated to
1337 reflect user or preset settings</li>
1338 <li>Null pointer exceptions for some services without
1339 presets or adjustable parameters</li>
1340 <li>Discover PDB IDs entry in structure menu doesn't
1341 discover PDB xRefs</li>
1342 <li>Exception encountered while trying to retrieve
1343 features with DAS</li>
1344 <li>Lowest value in annotation row isn't coloured
1345 when colour by annotation (per sequence) is coloured</li>
1346 <li>Keyboard mode P jumps to start of gapped region when
1347 residue follows a gap</li>
1348 <li>Jalview appears to hang importing an alignment with
1349 Wrap as default or after enabling Wrap</li>
1350 <li>'Right click to add annotations' message
1351 shown in wrap mode when no annotations present</li>
1352 <li>Disorder predictions fail with NPE if no automatic
1353 annotation already exists on alignment</li>
1354 <li>oninit javascript function should be called after
1355 initialisation completes</li>
1356 <li>Remove redundancy after disorder prediction corrupts
1357 alignment window display</li>
1358 <li>Example annotation file in documentation is invalid</li>
1359 <li>Grouped line graph annotation rows are not exported
1360 to annotation file</li>
1361 <li>Multi-harmony analysis cannot be run when only two
1363 <li>Cannot create multiple groups of line graphs with
1364 several 'combine' statements in annotation file</li>
1365 <li>Pressing return several times causes Number Format
1366 exceptions in keyboard mode</li>
1367 <li>Multi-harmony (SHMMR) method doesn't submit
1368 correct partitions for input data</li>
1369 <li>Translation from DNA to Amino Acids fails</li>
1370 <li>Jalview fail to load newick tree with quoted label</li>
1371 <li>--headless flag isn't understood</li>
1372 <li>ClassCastException when generating EPS in headless
1374 <li>Adjusting sequence-associated shading threshold only
1375 changes one row's threshold</li>
1376 <li>Preferences and Feature settings panel panel
1377 doesn't open</li>
1378 <li>hide consensus histogram also hides conservation and
1379 quality histograms</li>
1384 <td><div align="center">
1385 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
1387 <td><em>Application</em>
1389 <li>Support for JABAWS 2.0 Services (AACon alignment
1390 conservation, protein disorder and Clustal Omega)</li>
1391 <li>JABAWS server status indicator in Web Services
1393 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
1394 in Jalview alignment window</li>
1395 <li>Updated Jalview build and deploy framework for OSX
1396 mountain lion, windows 7, and 8</li>
1397 <li>Nucleotide substitution matrix for PCA that supports
1398 RNA and ambiguity codes</li>
1400 <li>Improved sequence database retrieval GUI</li>
1401 <li>Support fetching and database reference look up
1402 against multiple DAS sources (Fetch all from in 'fetch db
1404 <li>Jalview project improvements
1406 <li>Store and retrieve the 'belowAlignment'
1407 flag for annotation</li>
1408 <li>calcId attribute to group annotation rows on the
1410 <li>Store AACon calculation settings for a view in
1411 Jalview project</li>
1415 <li>horizontal scrolling gesture support</li>
1416 <li>Visual progress indicator when PCA calculation is
1418 <li>Simpler JABA web services menus</li>
1419 <li>visual indication that web service results are still
1420 being retrieved from server</li>
1421 <li>Serialise the dialogs that are shown when Jalview
1422 starts up for first time</li>
1423 <li>Jalview user agent string for interacting with HTTP
1425 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
1427 <li>Examples directory and Groovy library included in
1428 InstallAnywhere distribution</li>
1429 </ul> <em>Applet</em>
1431 <li>RNA alignment and secondary structure annotation
1432 visualization applet example</li>
1433 </ul> <em>General</em>
1435 <li>Normalise option for consensus sequence logo</li>
1436 <li>Reset button in PCA window to return dimensions to
1438 <li>Allow seqspace or Jalview variant of alignment PCA
1440 <li>PCA with either nucleic acid and protein substitution
1442 <li>Allow windows containing HTML reports to be exported
1444 <li>Interactive display and editing of RNA secondary
1445 structure contacts</li>
1446 <li>RNA Helix Alignment Colouring</li>
1447 <li>RNA base pair logo consensus</li>
1448 <li>Parse sequence associated secondary structure
1449 information in Stockholm files</li>
1450 <li>HTML Export database accessions and annotation
1451 information presented in tooltip for sequences</li>
1452 <li>Import secondary structure from LOCARNA clustalw
1453 style RNA alignment files</li>
1454 <li>import and visualise T-COFFEE quality scores for an
1456 <li>'colour by annotation' per sequence option to
1457 shade each sequence according to its associated alignment
1459 <li>New Jalview Logo</li>
1460 </ul> <em>Documentation and Development</em>
1462 <li>documentation for score matrices used in Jalview</li>
1463 <li>New Website!</li>
1465 <td><em>Application</em>
1467 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
1468 wsdbfetch REST service</li>
1469 <li>Stop windows being moved outside desktop on OSX</li>
1470 <li>Filetype associations not installed for webstart
1472 <li>Jalview does not always retrieve progress of a JABAWS
1473 job execution in full once it is complete</li>
1474 <li>revise SHMR RSBS definition to ensure alignment is
1475 uploaded via ali_file parameter</li>
1476 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
1477 <li>View all structures superposed fails with exception</li>
1478 <li>Jnet job queues forever if a very short sequence is
1479 submitted for prediction</li>
1480 <li>Cut and paste menu not opened when mouse clicked on
1482 <li>Putting fractional value into integer text box in
1483 alignment parameter dialog causes Jalview to hang</li>
1484 <li>Structure view highlighting doesn't work on
1486 <li>View all structures fails with exception shown in
1488 <li>Characters in filename associated with PDBEntry not
1489 escaped in a platform independent way</li>
1490 <li>Jalview desktop fails to launch with exception when
1492 <li>Tree calculation reports 'you must have 2 or more
1493 sequences selected' when selection is empty</li>
1494 <li>Jalview desktop fails to launch with jar signature
1495 failure when java web start temporary file caching is
1497 <li>DAS Sequence retrieval with range qualification
1498 results in sequence xref which includes range qualification</li>
1499 <li>Errors during processing of command line arguments
1500 cause progress bar (JAL-898) to be removed</li>
1501 <li>Replace comma for semi-colon option not disabled for
1502 DAS sources in sequence fetcher</li>
1503 <li>Cannot close news reader when JABAWS server warning
1504 dialog is shown</li>
1505 <li>Option widgets not updated to reflect user settings</li>
1506 <li>Edited sequence not submitted to web service</li>
1507 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
1508 <li>InstallAnywhere installer doesn't unpack and run
1509 on OSX Mountain Lion</li>
1510 <li>Annotation panel not given a scroll bar when
1511 sequences with alignment annotation are pasted into the
1513 <li>Sequence associated annotation rows not associated
1514 when loaded from Jalview project</li>
1515 <li>Browser launch fails with NPE on java 1.7</li>
1516 <li>JABAWS alignment marked as finished when job was
1517 cancelled or job failed due to invalid input</li>
1518 <li>NPE with v2.7 example when clicking on Tree
1519 associated with all views</li>
1520 <li>Exceptions when copy/paste sequences with grouped
1521 annotation rows to new window</li>
1522 </ul> <em>Applet</em>
1524 <li>Sequence features are momentarily displayed before
1525 they are hidden using hidefeaturegroups applet parameter</li>
1526 <li>loading features via javascript API automatically
1527 enables feature display</li>
1528 <li>scrollToColumnIn javascript API method doesn't
1530 </ul> <em>General</em>
1532 <li>Redundancy removal fails for rna alignment</li>
1533 <li>PCA calculation fails when sequence has been selected
1534 and then deselected</li>
1535 <li>PCA window shows grey box when first opened on OSX</li>
1536 <li>Letters coloured pink in sequence logo when alignment
1537 coloured with clustalx</li>
1538 <li>Choosing fonts without letter symbols defined causes
1539 exceptions and redraw errors</li>
1540 <li>Initial PCA plot view is not same as manually
1541 reconfigured view</li>
1542 <li>Grouped annotation graph label has incorrect line
1544 <li>Grouped annotation graph label display is corrupted
1545 for lots of labels</li>
1550 <div align="center">
1551 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
1554 <td><em>Application</em>
1556 <li>Jalview Desktop News Reader</li>
1557 <li>Tweaked default layout of web services menu</li>
1558 <li>View/alignment association menu to enable user to
1559 easily specify which alignment a multi-structure view takes
1560 its colours/correspondences from</li>
1561 <li>Allow properties file location to be specified as URL</li>
1562 <li>Extend Jalview project to preserve associations
1563 between many alignment views and a single Jmol display</li>
1564 <li>Store annotation row height in Jalview project file</li>
1565 <li>Annotation row column label formatting attributes
1566 stored in project file</li>
1567 <li>Annotation row order for auto-calculated annotation
1568 rows preserved in Jalview project file</li>
1569 <li>Visual progress indication when Jalview state is
1570 saved using Desktop window menu</li>
1571 <li>Visual indication that command line arguments are
1572 still being processed</li>
1573 <li>Groovy script execution from URL</li>
1574 <li>Colour by annotation default min and max colours in
1576 <li>Automatically associate PDB files dragged onto an
1577 alignment with sequences that have high similarity and
1579 <li>Update JGoogleAnalytics to latest release (0.3)</li>
1580 <li>'view structures' option to open many
1581 structures in same window</li>
1582 <li>Sort associated views menu option for tree panel</li>
1583 <li>Group all JABA and non-JABA services for a particular
1584 analysis function in its own submenu</li>
1585 </ul> <em>Applet</em>
1587 <li>Userdefined and autogenerated annotation rows for
1589 <li>Adjustment of alignment annotation pane height</li>
1590 <li>Annotation scrollbar for annotation panel</li>
1591 <li>Drag to reorder annotation rows in annotation panel</li>
1592 <li>'automaticScrolling' parameter</li>
1593 <li>Allow sequences with partial ID string matches to be
1594 annotated from GFF/Jalview features files</li>
1595 <li>Sequence logo annotation row in applet</li>
1596 <li>Absolute paths relative to host server in applet
1597 parameters are treated as such</li>
1598 <li>New in the JalviewLite javascript API:
1600 <li>JalviewLite.js javascript library</li>
1601 <li>Javascript callbacks for
1603 <li>Applet initialisation</li>
1604 <li>Sequence/alignment mouse-overs and selections</li>
1607 <li>scrollTo row and column alignment scrolling
1609 <li>Select sequence/alignment regions from javascript</li>
1610 <li>javascript structure viewer harness to pass
1611 messages between Jmol and Jalview when running as
1612 distinct applets</li>
1613 <li>sortBy method</li>
1614 <li>Set of applet and application examples shipped
1615 with documentation</li>
1616 <li>New example to demonstrate JalviewLite and Jmol
1617 javascript message exchange</li>
1619 </ul> <em>General</em>
1621 <li>Enable Jmol displays to be associated with multiple
1622 multiple alignments</li>
1623 <li>Option to automatically sort alignment with new tree</li>
1624 <li>User configurable link to enable redirects to a
1625 www.Jalview.org mirror</li>
1626 <li>Jmol colours option for Jmol displays</li>
1627 <li>Configurable newline string when writing alignment
1628 and other flat files</li>
1629 <li>Allow alignment annotation description lines to
1630 contain html tags</li>
1631 </ul> <em>Documentation and Development</em>
1633 <li>Add groovy test harness for bulk load testing to
1635 <li>Groovy script to load and align a set of sequences
1636 using a web service before displaying the result in the
1637 Jalview desktop</li>
1638 <li>Restructured javascript and applet api documentation</li>
1639 <li>Ant target to publish example html files with applet
1641 <li>Netbeans project for building Jalview from source</li>
1642 <li>ant task to create online javadoc for Jalview source</li>
1644 <td><em>Application</em>
1646 <li>User defined colourscheme throws exception when
1647 current built in colourscheme is saved as new scheme</li>
1648 <li>AlignFrame->Save in application pops up save
1649 dialog for valid filename/format</li>
1650 <li>Cannot view associated structure for UniProt sequence</li>
1651 <li>PDB file association breaks for UniProt sequence
1653 <li>Associate PDB from file dialog does not tell you
1654 which sequence is to be associated with the file</li>
1655 <li>Find All raises null pointer exception when query
1656 only matches sequence IDs</li>
1657 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
1658 <li>Jalview project with Jmol views created with Jalview
1659 2.4 cannot be loaded</li>
1660 <li>Filetype associations not installed for webstart
1662 <li>Two or more chains in a single PDB file associated
1663 with sequences in different alignments do not get coloured
1664 by their associated sequence</li>
1665 <li>Visibility status of autocalculated annotation row
1666 not preserved when project is loaded</li>
1667 <li>Annotation row height and visibility attributes not
1668 stored in Jalview project</li>
1669 <li>Tree bootstraps are not preserved when saved as a
1670 Jalview project</li>
1671 <li>Envision2 workflow tooltips are corrupted</li>
1672 <li>Enabling show group conservation also enables colour
1673 by conservation</li>
1674 <li>Duplicate group associated conservation or consensus
1675 created on new view</li>
1676 <li>Annotation scrollbar not displayed after 'show
1677 all hidden annotation rows' option selected</li>
1678 <li>Alignment quality not updated after alignment
1679 annotation row is hidden then shown</li>
1680 <li>Preserve colouring of structures coloured by
1681 sequences in pre Jalview 2.7 projects</li>
1682 <li>Web service job parameter dialog is not laid out
1684 <li>Web services menu not refreshed after 'reset
1685 services' button is pressed in preferences</li>
1686 <li>Annotation off by one in Jalview v2_3 example project</li>
1687 <li>Structures imported from file and saved in project
1688 get name like jalview_pdb1234.txt when reloaded</li>
1689 <li>Jalview does not always retrieve progress of a JABAWS
1690 job execution in full once it is complete</li>
1691 </ul> <em>Applet</em>
1693 <li>Alignment height set incorrectly when lots of
1694 annotation rows are displayed</li>
1695 <li>Relative URLs in feature HTML text not resolved to
1697 <li>View follows highlighting does not work for positions
1699 <li><= shown as = in tooltip</li>
1700 <li>Export features raises exception when no features
1702 <li>Separator string used for serialising lists of IDs
1703 for javascript api is modified when separator string
1704 provided as parameter</li>
1705 <li>Null pointer exception when selecting tree leaves for
1706 alignment with no existing selection</li>
1707 <li>Relative URLs for datasources assumed to be relative
1708 to applet's codebase</li>
1709 <li>Status bar not updated after finished searching and
1710 search wraps around to first result</li>
1711 <li>StructureSelectionManager instance shared between
1712 several Jalview applets causes race conditions and memory
1714 <li>Hover tooltip and mouseover of position on structure
1715 not sent from Jmol in applet</li>
1716 <li>Certain sequences of javascript method calls to
1717 applet API fatally hang browser</li>
1718 </ul> <em>General</em>
1720 <li>View follows structure mouseover scrolls beyond
1721 position with wrapped view and hidden regions</li>
1722 <li>Find sequence position moves to wrong residue
1723 with/without hidden columns</li>
1724 <li>Sequence length given in alignment properties window
1726 <li>InvalidNumberFormat exceptions thrown when trying to
1727 import PDB like structure files</li>
1728 <li>Positional search results are only highlighted
1729 between user-supplied sequence start/end bounds</li>
1730 <li>End attribute of sequence is not validated</li>
1731 <li>Find dialog only finds first sequence containing a
1732 given sequence position</li>
1733 <li>Sequence numbering not preserved in MSF alignment
1735 <li>Jalview PDB file reader does not extract sequence
1736 from nucleotide chains correctly</li>
1737 <li>Structure colours not updated when tree partition
1738 changed in alignment</li>
1739 <li>Sequence associated secondary structure not correctly
1740 parsed in interleaved stockholm</li>
1741 <li>Colour by annotation dialog does not restore current
1743 <li>Hiding (nearly) all sequences doesn't work
1745 <li>Sequences containing lowercase letters are not
1746 properly associated with their pdb files</li>
1747 </ul> <em>Documentation and Development</em>
1749 <li>schemas/JalviewWsParamSet.xsd corrupted by
1750 ApplyCopyright tool</li>
1755 <div align="center">
1756 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
1759 <td><em>Application</em>
1761 <li>New warning dialog when the Jalview Desktop cannot
1762 contact web services</li>
1763 <li>JABA service parameters for a preset are shown in
1764 service job window</li>
1765 <li>JABA Service menu entries reworded</li>
1769 <li>Modeller PIR IO broken - cannot correctly import a
1770 pir file emitted by Jalview</li>
1771 <li>Existing feature settings transferred to new
1772 alignment view created from cut'n'paste</li>
1773 <li>Improved test for mixed amino/nucleotide chains when
1774 parsing PDB files</li>
1775 <li>Consensus and conservation annotation rows
1776 occasionally become blank for all new windows</li>
1777 <li>Exception raised when right clicking above sequences
1778 in wrapped view mode</li>
1779 </ul> <em>Application</em>
1781 <li>multiple multiply aligned structure views cause cpu
1782 usage to hit 100% and computer to hang</li>
1783 <li>Web Service parameter layout breaks for long user
1784 parameter names</li>
1785 <li>Jaba service discovery hangs desktop if Jaba server
1792 <div align="center">
1793 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
1796 <td><em>Application</em>
1798 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
1799 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
1802 <li>Web Services preference tab</li>
1803 <li>Analysis parameters dialog box and user defined
1805 <li>Improved speed and layout of Envision2 service menu</li>
1806 <li>Superpose structures using associated sequence
1808 <li>Export coordinates and projection as CSV from PCA
1810 </ul> <em>Applet</em>
1812 <li>enable javascript: execution by the applet via the
1813 link out mechanism</li>
1814 </ul> <em>Other</em>
1816 <li>Updated the Jmol Jalview interface to work with Jmol
1818 <li>The Jalview Desktop and JalviewLite applet now
1819 require Java 1.5</li>
1820 <li>Allow Jalview feature colour specification for GFF
1821 sequence annotation files</li>
1822 <li>New 'colour by label' keword in Jalview feature file
1823 type colour specification</li>
1824 <li>New Jalview Desktop Groovy API method that allows a
1825 script to check if it being run in an interactive session or
1826 in a batch operation from the Jalview command line</li>
1830 <li>clustalx colourscheme colours Ds preferentially when
1831 both D+E are present in over 50% of the column</li>
1832 </ul> <em>Application</em>
1834 <li>typo in AlignmentFrame->View->Hide->all but
1835 selected Regions menu item</li>
1836 <li>sequence fetcher replaces ',' for ';' when the ',' is
1837 part of a valid accession ID</li>
1838 <li>fatal OOM if object retrieved by sequence fetcher
1839 runs out of memory</li>
1840 <li>unhandled Out of Memory Error when viewing pca
1841 analysis results</li>
1842 <li>InstallAnywhere builds fail to launch on OS X java
1843 10.5 update 4 (due to apple Java 1.6 update)</li>
1844 <li>Installanywhere Jalview silently fails to launch</li>
1845 </ul> <em>Applet</em>
1847 <li>Jalview.getFeatureGroups() raises an
1848 ArrayIndexOutOfBoundsException if no feature groups are
1855 <div align="center">
1856 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
1862 <li>Alignment prettyprinter doesn't cope with long
1864 <li>clustalx colourscheme colours Ds preferentially when
1865 both D+E are present in over 50% of the column</li>
1866 <li>nucleic acid structures retrieved from PDB do not
1867 import correctly</li>
1868 <li>More columns get selected than were clicked on when a
1869 number of columns are hidden</li>
1870 <li>annotation label popup menu not providing correct
1871 add/hide/show options when rows are hidden or none are
1873 <li>Stockholm format shown in list of readable formats,
1874 and parser copes better with alignments from RFAM.</li>
1875 <li>CSV output of consensus only includes the percentage
1876 of all symbols if sequence logo display is enabled</li>
1878 </ul> <em>Applet</em>
1880 <li>annotation panel disappears when annotation is
1882 </ul> <em>Application</em>
1884 <li>Alignment view not redrawn properly when new
1885 alignment opened where annotation panel is visible but no
1886 annotations are present on alignment</li>
1887 <li>pasted region containing hidden columns is
1888 incorrectly displayed in new alignment window</li>
1889 <li>Jalview slow to complete operations when stdout is
1890 flooded (fix is to close the Jalview console)</li>
1891 <li>typo in AlignmentFrame->View->Hide->all but
1892 selected Rregions menu item.</li>
1893 <li>inconsistent group submenu and Format submenu entry
1894 'Un' or 'Non'conserved</li>
1895 <li>Sequence feature settings are being shared by
1896 multiple distinct alignments</li>
1897 <li>group annotation not recreated when tree partition is
1899 <li>double click on group annotation to select sequences
1900 does not propagate to associated trees</li>
1901 <li>Mac OSX specific issues:
1903 <li>exception raised when mouse clicked on desktop
1904 window background</li>
1905 <li>Desktop menu placed on menu bar and application
1906 name set correctly</li>
1907 <li>sequence feature settings not wide enough for the
1908 save feature colourscheme button</li>
1917 <div align="center">
1918 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
1921 <td><em>New Capabilities</em>
1923 <li>URL links generated from description line for
1924 regular-expression based URL links (applet and application)
1931 <li>Non-positional feature URL links are shown in link
1933 <li>Linked viewing of nucleic acid sequences and
1935 <li>Automatic Scrolling option in View menu to display
1936 the currently highlighted region of an alignment.</li>
1937 <li>Order an alignment by sequence length, or using the
1938 average score or total feature count for each sequence.</li>
1939 <li>Shading features by score or associated description</li>
1940 <li>Subdivide alignment and groups based on identity of
1941 selected subsequence (Make Groups from Selection).</li>
1942 <li>New hide/show options including Shift+Control+H to
1943 hide everything but the currently selected region.</li>
1944 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
1945 </ul> <em>Application</em>
1947 <li>Fetch DB References capabilities and UI expanded to
1948 support retrieval from DAS sequence sources</li>
1949 <li>Local DAS Sequence sources can be added via the
1950 command line or via the Add local source dialog box.</li>
1951 <li>DAS Dbref and DbxRef feature types are parsed as
1952 database references and protein_name is parsed as
1953 description line (BioSapiens terms).</li>
1954 <li>Enable or disable non-positional feature and database
1955 references in sequence ID tooltip from View menu in
1957 <!-- <li>New hidden columns and rows and representatives capabilities
1958 in annotations file (in progress - not yet fully implemented)</li> -->
1959 <li>Group-associated consensus, sequence logos and
1960 conservation plots</li>
1961 <li>Symbol distributions for each column can be exported
1962 and visualized as sequence logos</li>
1963 <li>Optionally scale multi-character column labels to fit
1964 within each column of annotation row<!-- todo for applet -->
1966 <li>Optional automatic sort of associated alignment view
1967 when a new tree is opened.</li>
1968 <li>Jalview Java Console</li>
1969 <li>Better placement of desktop window when moving
1970 between different screens.</li>
1971 <li>New preference items for sequence ID tooltip and
1972 consensus annotation</li>
1973 <li>Client to submit sequences and IDs to Envision2
1975 <li><em>Vamsas Capabilities</em>
1977 <li>Improved VAMSAS synchronization (Jalview archive
1978 used to preserve views, structures, and tree display
1980 <li>Import of vamsas documents from disk or URL via
1982 <li>Sharing of selected regions between views and
1983 with other VAMSAS applications (Experimental feature!)</li>
1984 <li>Updated API to VAMSAS version 0.2</li>
1986 </ul> <em>Applet</em>
1988 <li>Middle button resizes annotation row height</li>
1991 <li>sortByTree (true/false) - automatically sort the
1992 associated alignment view by the tree when a new tree is
1994 <li>showTreeBootstraps (true/false) - show or hide
1995 branch bootstraps (default is to show them if available)</li>
1996 <li>showTreeDistances (true/false) - show or hide
1997 branch lengths (default is to show them if available)</li>
1998 <li>showUnlinkedTreeNodes (true/false) - indicate if
1999 unassociated nodes should be highlighted in the tree
2001 <li>heightScale and widthScale (1.0 or more) -
2002 increase the height or width of a cell in the alignment
2003 grid relative to the current font size.</li>
2006 <li>Non-positional features displayed in sequence ID
2008 </ul> <em>Other</em>
2010 <li>Features format: graduated colour definitions and
2011 specification of feature scores</li>
2012 <li>Alignment Annotations format: new keywords for group
2013 associated annotation (GROUP_REF) and annotation row display
2014 properties (ROW_PROPERTIES)</li>
2015 <li>XML formats extended to support graduated feature
2016 colourschemes, group associated annotation, and profile
2017 visualization settings.</li></td>
2020 <li>Source field in GFF files parsed as feature source
2021 rather than description</li>
2022 <li>Non-positional features are now included in sequence
2023 feature and gff files (controlled via non-positional feature
2024 visibility in tooltip).</li>
2025 <li>URL links generated for all feature links (bugfix)</li>
2026 <li>Added URL embedding instructions to features file
2028 <li>Codons containing ambiguous nucleotides translated as
2029 'X' in peptide product</li>
2030 <li>Match case switch in find dialog box works for both
2031 sequence ID and sequence string and query strings do not
2032 have to be in upper case to match case-insensitively.</li>
2033 <li>AMSA files only contain first column of
2034 multi-character column annotation labels</li>
2035 <li>Jalview Annotation File generation/parsing consistent
2036 with documentation (e.g. Stockholm annotation can be
2037 exported and re-imported)</li>
2038 <li>PDB files without embedded PDB IDs given a friendly
2040 <li>Find incrementally searches ID string matches as well
2041 as subsequence matches, and correctly reports total number
2045 <li>Better handling of exceptions during sequence
2047 <li>Dasobert generated non-positional feature URL
2048 link text excludes the start_end suffix</li>
2049 <li>DAS feature and source retrieval buttons disabled
2050 when fetch or registry operations in progress.</li>
2051 <li>PDB files retrieved from URLs are cached properly</li>
2052 <li>Sequence description lines properly shared via
2054 <li>Sequence fetcher fetches multiple records for all
2056 <li>Ensured that command line das feature retrieval
2057 completes before alignment figures are generated.</li>
2058 <li>Reduced time taken when opening file browser for
2060 <li>isAligned check prior to calculating tree, PCA or
2061 submitting an MSA to JNet now excludes hidden sequences.</li>
2062 <li>User defined group colours properly recovered
2063 from Jalview projects.</li>
2072 <div align="center">
2073 <strong>2.4.0.b2</strong><br> 28/10/2009
2078 <li>Experimental support for google analytics usage
2080 <li>Jalview privacy settings (user preferences and docs).</li>
2085 <li>Race condition in applet preventing startup in
2087 <li>Exception when feature created from selection beyond
2088 length of sequence.</li>
2089 <li>Allow synthetic PDB files to be imported gracefully</li>
2090 <li>Sequence associated annotation rows associate with
2091 all sequences with a given id</li>
2092 <li>Find function matches case-insensitively for sequence
2093 ID string searches</li>
2094 <li>Non-standard characters do not cause pairwise
2095 alignment to fail with exception</li>
2096 </ul> <em>Application Issues</em>
2098 <li>Sequences are now validated against EMBL database</li>
2099 <li>Sequence fetcher fetches multiple records for all
2101 </ul> <em>InstallAnywhere Issues</em>
2103 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2104 issue with installAnywhere mechanism)</li>
2105 <li>Command line launching of JARs from InstallAnywhere
2106 version (java class versioning error fixed)</li>
2113 <div align="center">
2114 <strong>2.4</strong><br> 27/8/2008
2117 <td><em>User Interface</em>
2119 <li>Linked highlighting of codon and amino acid from
2120 translation and protein products</li>
2121 <li>Linked highlighting of structure associated with
2122 residue mapping to codon position</li>
2123 <li>Sequence Fetcher provides example accession numbers
2124 and 'clear' button</li>
2125 <li>MemoryMonitor added as an option under Desktop's
2127 <li>Extract score function to parse whitespace separated
2128 numeric data in description line</li>
2129 <li>Column labels in alignment annotation can be centred.</li>
2130 <li>Tooltip for sequence associated annotation give name
2132 </ul> <em>Web Services and URL fetching</em>
2134 <li>JPred3 web service</li>
2135 <li>Prototype sequence search client (no public services
2137 <li>Fetch either seed alignment or full alignment from
2139 <li>URL Links created for matching database cross
2140 references as well as sequence ID</li>
2141 <li>URL Links can be created using regular-expressions</li>
2142 </ul> <em>Sequence Database Connectivity</em>
2144 <li>Retrieval of cross-referenced sequences from other
2146 <li>Generalised database reference retrieval and
2147 validation to all fetchable databases</li>
2148 <li>Fetch sequences from DAS sources supporting the
2149 sequence command</li>
2150 </ul> <em>Import and Export</em>
2151 <li>export annotation rows as CSV for spreadsheet import</li>
2152 <li>Jalview projects record alignment dataset associations,
2153 EMBL products, and cDNA sequence mappings</li>
2154 <li>Sequence Group colour can be specified in Annotation
2156 <li>Ad-hoc colouring of group in Annotation File using RGB
2157 triplet as name of colourscheme</li>
2158 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2160 <li>treenode binding for VAMSAS tree exchange</li>
2161 <li>local editing and update of sequences in VAMSAS
2162 alignments (experimental)</li>
2163 <li>Create new or select existing session to join</li>
2164 <li>load and save of vamsas documents</li>
2165 </ul> <em>Application command line</em>
2167 <li>-tree parameter to open trees (introduced for passing
2169 <li>-fetchfrom command line argument to specify nicknames
2170 of DAS servers to query for alignment features</li>
2171 <li>-dasserver command line argument to add new servers
2172 that are also automatically queried for features</li>
2173 <li>-groovy command line argument executes a given groovy
2174 script after all input data has been loaded and parsed</li>
2175 </ul> <em>Applet-Application data exchange</em>
2177 <li>Trees passed as applet parameters can be passed to
2178 application (when using "View in full
2179 application")</li>
2180 </ul> <em>Applet Parameters</em>
2182 <li>feature group display control parameter</li>
2183 <li>debug parameter</li>
2184 <li>showbutton parameter</li>
2185 </ul> <em>Applet API methods</em>
2187 <li>newView public method</li>
2188 <li>Window (current view) specific get/set public methods</li>
2189 <li>Feature display control methods</li>
2190 <li>get list of currently selected sequences</li>
2191 </ul> <em>New Jalview distribution features</em>
2193 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2194 <li>RELEASE file gives build properties for the latest
2195 Jalview release.</li>
2196 <li>Java 1.1 Applet build made easier and donotobfuscate
2197 property controls execution of obfuscator</li>
2198 <li>Build target for generating source distribution</li>
2199 <li>Debug flag for javacc</li>
2200 <li>.jalview_properties file is documented (slightly) in
2201 jalview.bin.Cache</li>
2202 <li>Continuous Build Integration for stable and
2203 development version of Application, Applet and source
2208 <li>selected region output includes visible annotations
2209 (for certain formats)</li>
2210 <li>edit label/displaychar contains existing label/char
2212 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2213 <li>shorter peptide product names from EMBL records</li>
2214 <li>Newick string generator makes compact representations</li>
2215 <li>bootstrap values parsed correctly for tree files with
2217 <li>pathological filechooser bug avoided by not allowing
2218 filenames containing a ':'</li>
2219 <li>Fixed exception when parsing GFF files containing
2220 global sequence features</li>
2221 <li>Alignment datasets are finalized only when number of
2222 references from alignment sequences goes to zero</li>
2223 <li>Close of tree branch colour box without colour
2224 selection causes cascading exceptions</li>
2225 <li>occasional negative imgwidth exceptions</li>
2226 <li>better reporting of non-fatal warnings to user when
2227 file parsing fails.</li>
2228 <li>Save works when Jalview project is default format</li>
2229 <li>Save as dialog opened if current alignment format is
2230 not a valid output format</li>
2231 <li>UniProt canonical names introduced for both das and
2233 <li>Histidine should be midblue (not pink!) in Zappo</li>
2234 <li>error messages passed up and output when data read
2236 <li>edit undo recovers previous dataset sequence when
2237 sequence is edited</li>
2238 <li>allow PDB files without pdb ID HEADER lines (like
2239 those generated by MODELLER) to be read in properly</li>
2240 <li>allow reading of JPred concise files as a normal
2242 <li>Stockholm annotation parsing and alignment properties
2243 import fixed for PFAM records</li>
2244 <li>Structure view windows have correct name in Desktop
2246 <li>annotation consisting of sequence associated scores
2247 can be read and written correctly to annotation file</li>
2248 <li>Aligned cDNA translation to aligned peptide works
2250 <li>Fixed display of hidden sequence markers and
2251 non-italic font for representatives in Applet</li>
2252 <li>Applet Menus are always embedded in applet window on
2254 <li>Newly shown features appear at top of stack (in
2256 <li>Annotations added via parameter not drawn properly
2257 due to null pointer exceptions</li>
2258 <li>Secondary structure lines are drawn starting from
2259 first column of alignment</li>
2260 <li>UniProt XML import updated for new schema release in
2262 <li>Sequence feature to sequence ID match for Features
2263 file is case-insensitive</li>
2264 <li>Sequence features read from Features file appended to
2265 all sequences with matching IDs</li>
2266 <li>PDB structure coloured correctly for associated views
2267 containing a sub-sequence</li>
2268 <li>PDB files can be retrieved by applet from Jar files</li>
2269 <li>feature and annotation file applet parameters
2270 referring to different directories are retrieved correctly</li>
2271 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
2272 <li>Fixed application hang whilst waiting for
2273 splash-screen version check to complete</li>
2274 <li>Applet properly URLencodes input parameter values
2275 when passing them to the launchApp service</li>
2276 <li>display name and local features preserved in results
2277 retrieved from web service</li>
2278 <li>Visual delay indication for sequence retrieval and
2279 sequence fetcher initialisation</li>
2280 <li>updated Application to use DAS 1.53e version of
2281 dasobert DAS client</li>
2282 <li>Re-instated Full AMSA support and .amsa file
2284 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
2292 <div align="center">
2293 <strong>2.3</strong><br> 9/5/07
2298 <li>Jmol 11.0.2 integration</li>
2299 <li>PDB views stored in Jalview XML files</li>
2300 <li>Slide sequences</li>
2301 <li>Edit sequence in place</li>
2302 <li>EMBL CDS features</li>
2303 <li>DAS Feature mapping</li>
2304 <li>Feature ordering</li>
2305 <li>Alignment Properties</li>
2306 <li>Annotation Scores</li>
2307 <li>Sort by scores</li>
2308 <li>Feature/annotation editing in applet</li>
2313 <li>Headless state operation in 2.2.1</li>
2314 <li>Incorrect and unstable DNA pairwise alignment</li>
2315 <li>Cut and paste of sequences with annotation</li>
2316 <li>Feature group display state in XML</li>
2317 <li>Feature ordering in XML</li>
2318 <li>blc file iteration selection using filename # suffix</li>
2319 <li>Stockholm alignment properties</li>
2320 <li>Stockhom alignment secondary structure annotation</li>
2321 <li>2.2.1 applet had no feature transparency</li>
2322 <li>Number pad keys can be used in cursor mode</li>
2323 <li>Structure Viewer mirror image resolved</li>
2330 <div align="center">
2331 <strong>2.2.1</strong><br> 12/2/07
2336 <li>Non standard characters can be read and displayed
2337 <li>Annotations/Features can be imported/exported to the
2339 <li>Applet allows editing of sequence/annotation/group
2340 name & description
2341 <li>Preference setting to display sequence name in
2343 <li>Annotation file format extended to allow
2344 Sequence_groups to be defined
2345 <li>Default opening of alignment overview panel can be
2346 specified in preferences
2347 <li>PDB residue numbering annotation added to associated
2353 <li>Applet crash under certain Linux OS with Java 1.6
2355 <li>Annotation file export / import bugs fixed
2356 <li>PNG / EPS image output bugs fixed
2362 <div align="center">
2363 <strong>2.2</strong><br> 27/11/06
2368 <li>Multiple views on alignment
2369 <li>Sequence feature editing
2370 <li>"Reload" alignment
2371 <li>"Save" to current filename
2372 <li>Background dependent text colour
2373 <li>Right align sequence ids
2374 <li>User-defined lower case residue colours
2377 <li>Menu item accelerator keys
2378 <li>Control-V pastes to current alignment
2379 <li>Cancel button for DAS Feature Fetching
2380 <li>PCA and PDB Viewers zoom via mouse roller
2381 <li>User-defined sub-tree colours and sub-tree selection
2388 <li>'New Window' button on the 'Output to Text box'
2393 <li>New memory efficient Undo/Redo System
2394 <li>Optimised symbol lookups and conservation/consensus
2396 <li>Region Conservation/Consensus recalculated after
2398 <li>Fixed Remove Empty Columns Bug (empty columns at end
2400 <li>Slowed DAS Feature Fetching for increased robustness.
2407 <li>Made angle brackets in ASCII feature descriptions
2409 <li>Re-instated Zoom function for PCA
2410 <li>Sequence descriptions conserved in web service
2412 <li>UniProt ID discoverer uses any word separated by
2414 <li>WsDbFetch query/result association resolved
2415 <li>Tree leaf to sequence mapping improved
2416 <li>Smooth fonts switch moved to FontChooser dialog box.
2428 <div align="center">
2429 <strong>2.1.1</strong><br> 12/9/06
2434 <li>Copy consensus sequence to clipboard</li>
2439 <li>Image output - rightmost residues are rendered if
2440 sequence id panel has been resized</li>
2441 <li>Image output - all offscreen group boundaries are
2443 <li>Annotation files with sequence references - all
2444 elements in file are relative to sequence position</li>
2445 <li>Mac Applet users can use Alt key for group editing</li>
2451 <div align="center">
2452 <strong>2.1</strong><br> 22/8/06
2457 <li>MAFFT Multiple Alignment in default Web Service list</li>
2458 <li>DAS Feature fetching</li>
2459 <li>Hide sequences and columns</li>
2460 <li>Export Annotations and Features</li>
2461 <li>GFF file reading / writing</li>
2462 <li>Associate structures with sequences from local PDB
2464 <li>Add sequences to exisiting alignment</li>
2465 <li>Recently opened files / URL lists</li>
2466 <li>Applet can launch the full application</li>
2467 <li>Applet has transparency for features (Java 1.2
2469 <li>Applet has user defined colours parameter</li>
2470 <li>Applet can load sequences from parameter
2471 "sequence<em>x</em>"
2477 <li>Redundancy Panel reinstalled in the Applet</li>
2478 <li>Monospaced font - EPS / rescaling bug fixed</li>
2479 <li>Annotation files with sequence references bug fixed</li>
2485 <div align="center">
2486 <strong>2.08.1</strong><br> 2/5/06
2491 <li>Change case of selected region from Popup menu</li>
2492 <li>Choose to match case when searching</li>
2493 <li>Middle mouse button and mouse movement can compress /
2494 expand the visible width and height of the alignment</li>
2499 <li>Annotation Panel displays complete JNet results</li>
2505 <div align="center">
2506 <strong>2.08b</strong><br> 18/4/06
2512 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
2513 <li>Righthand label on wrapped alignments shows correct
2520 <div align="center">
2521 <strong>2.08</strong><br> 10/4/06
2526 <li>Editing can be locked to the selection area</li>
2527 <li>Keyboard editing</li>
2528 <li>Create sequence features from searches</li>
2529 <li>Precalculated annotations can be loaded onto
2531 <li>Features file allows grouping of features</li>
2532 <li>Annotation Colouring scheme added</li>
2533 <li>Smooth fonts off by default - Faster rendering</li>
2534 <li>Choose to toggle Autocalculate Consensus On/Off</li>
2539 <li>Drag & Drop fixed on Linux</li>
2540 <li>Jalview Archive file faster to load/save, sequence
2541 descriptions saved.</li>
2547 <div align="center">
2548 <strong>2.07</strong><br> 12/12/05
2553 <li>PDB Structure Viewer enhanced</li>
2554 <li>Sequence Feature retrieval and display enhanced</li>
2555 <li>Choose to output sequence start-end after sequence
2556 name for file output</li>
2557 <li>Sequence Fetcher WSDBFetch@EBI</li>
2558 <li>Applet can read feature files, PDB files and can be
2559 used for HTML form input</li>
2564 <li>HTML output writes groups and features</li>
2565 <li>Group editing is Control and mouse click</li>
2566 <li>File IO bugs</li>
2572 <div align="center">
2573 <strong>2.06</strong><br> 28/9/05
2578 <li>View annotations in wrapped mode</li>
2579 <li>More options for PCA viewer</li>
2584 <li>GUI bugs resolved</li>
2585 <li>Runs with -nodisplay from command line</li>
2591 <div align="center">
2592 <strong>2.05b</strong><br> 15/9/05
2597 <li>Choose EPS export as lineart or text</li>
2598 <li>Jar files are executable</li>
2599 <li>Can read in Uracil - maps to unknown residue</li>
2604 <li>Known OutOfMemory errors give warning message</li>
2605 <li>Overview window calculated more efficiently</li>
2606 <li>Several GUI bugs resolved</li>
2612 <div align="center">
2613 <strong>2.05</strong><br> 30/8/05
2618 <li>Edit and annotate in "Wrapped" view</li>
2623 <li>Several GUI bugs resolved</li>
2629 <div align="center">
2630 <strong>2.04</strong><br> 24/8/05
2635 <li>Hold down mouse wheel & scroll to change font
2641 <li>Improved JPred client reliability</li>
2642 <li>Improved loading of Jalview files</li>
2648 <div align="center">
2649 <strong>2.03</strong><br> 18/8/05
2654 <li>Set Proxy server name and port in preferences</li>
2655 <li>Multiple URL links from sequence ids</li>
2656 <li>User Defined Colours can have a scheme name and added
2658 <li>Choose to ignore gaps in consensus calculation</li>
2659 <li>Unix users can set default web browser</li>
2660 <li>Runs without GUI for batch processing</li>
2661 <li>Dynamically generated Web Service Menus</li>
2666 <li>InstallAnywhere download for Sparc Solaris</li>
2672 <div align="center">
2673 <strong>2.02</strong><br> 18/7/05
2679 <li>Copy & Paste order of sequences maintains
2680 alignment order.</li>
2686 <div align="center">
2687 <strong>2.01</strong><br> 12/7/05
2692 <li>Use delete key for deleting selection.</li>
2693 <li>Use Mouse wheel to scroll sequences.</li>
2694 <li>Help file updated to describe how to add alignment
2696 <li>Version and build date written to build properties
2698 <li>InstallAnywhere installation will check for updates
2699 at launch of Jalview.</li>
2704 <li>Delete gaps bug fixed.</li>
2705 <li>FileChooser sorts columns.</li>
2706 <li>Can remove groups one by one.</li>
2707 <li>Filechooser icons installed.</li>
2708 <li>Finder ignores return character when searching.
2709 Return key will initiate a search.<br>
2716 <div align="center">
2717 <strong>2.0</strong><br> 20/6/05
2722 <li>New codebase</li>