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.2.10.0b1">2.10.0b1</a><br />
51 <em>25/10/2016</em></strong>
54 <td><em>Application</em>
56 <li>3D Structure chooser opens with 'Cached structures'
57 view if structures already loaded</li>
58 <li>Progress bar reports models as they are loaded to
65 <li>Colour by conservation always enabled and no tick
66 shown in menu when BLOSUM or PID shading applied</li>
70 <li>Jalview projects with views of local PDB structure
71 files saved on Windows cannot be opened on OSX</li>
72 <li>Multiple structure views can be opened and
73 superposed without timeout for structures with multiple
74 models or multiple sequences in alignment</li>
75 <li>Cannot import or associated local PDB files without
76 a PDB ID HEADER line</li>
77 <li>RMSD is not output in Jmol console when
78 superposition is performed</li>
79 <li>Drag and drop of URL from Browser fails for Linux
80 and OSX versions earlier than El Capitan</li>
81 <li>ENA client ignores invalid content from ENA server</li>
82 <li>Exceptions are not raised in console when ENA
83 client attempts to fetch non-existent IDs via Fetch DB
85 <li>Exceptions are not raised in console when a new
86 view is created on the alignment</li>
87 <li>OSX right-click fixed for group selections:
88 CMD-click to insert/remove gaps in groups and CTRL-click
89 to open group pop-up menu</li>
91 <em>Build and deployment</em>
93 <li>URL link checker now copes with multi-line anchor
96 <em>New Known Issues</em>
98 <li>Drag and drop from URL links in browsers do not
105 <td width="60" nowrap>
107 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
113 <!-- JAL-2124 -->Updated Spanish translations.
116 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
117 for importing structure data to Jalview. Enables mmCIF and
121 <!-- JAL-192 --->Alignment ruler shows positions relative to
125 <!-- JAL-2202 -->Position/residue shown in status bar when
126 mousing over sequence associated annotation
129 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
133 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
134 '()', canonical '[]' and invalid '{}' base pair populations
138 <!-- JAL-2092 -->Feature settings popup menu options for
139 showing or hiding columns containing a feature
142 <!-- JAL-1557 -->Edit selected group by double clicking on
143 group and sequence associated annotation labels
146 <!-- JAL-2236 -->Sequence name added to annotation label in
147 select/hide columns by annotation and colour by annotation
151 </ul> <em>Application</em>
154 <!-- JAL-2050-->Automatically hide introns when opening a
158 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
162 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
163 structure mappings with the EMBL-EBI PDBe SIFTS database
166 <!-- JAL-2079 -->Updated download sites used for Rfam and
167 Pfam sources to xfam.org
170 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
173 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
174 over sequences in Jalview
177 <!-- JAL-2027-->Support for reverse-complement coding
178 regions in ENA and EMBL
181 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
182 for record retrieval via ENA rest API
185 <!-- JAL-2027 -->Support for ENA CDS records with reverse
189 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
190 groovy script execution
193 <!-- JAL-1812 -->New 'execute Groovy script' option in an
194 alignment window's Calculate menu
197 <!-- JAL-1812 -->Allow groovy scripts that call
198 Jalview.getAlignFrames() to run in headless mode
201 <!-- JAL-2068 -->Support for creating new alignment
202 calculation workers from groovy scripts
205 <!-- JAL-1369 --->Store/restore reference sequence in
209 <!-- JAL-1803 -->Chain codes for a sequence's PDB
210 associations are now saved/restored from project
213 <!-- JAL-1993 -->Database selection dialog always shown
214 before sequence fetcher is opened
217 <!-- JAL-2183 -->Double click on an entry in Jalview's
218 database chooser opens a sequence fetcher
221 <!-- JAL-1563 -->Free-text search client for UniProt using
225 <!-- JAL-2168 -->-nonews command line parameter to prevent
226 the news reader opening
229 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
230 querying stored in preferences
233 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
237 <!-- JAL-1977-->Tooltips shown on database chooser
240 <!-- JAL-391 -->Reverse complement function in calculate
241 menu for nucleotide sequences
244 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
245 and feature counts preserves alignment ordering (and
246 debugged for complex feature sets).
249 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
250 viewing structures with Jalview 2.10
253 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
254 genome, transcript CCDS and gene ids via the Ensembl and
255 Ensembl Genomes REST API
258 <!-- JAL-2049 -->Protein sequence variant annotation
259 computed for 'sequence_variant' annotation on CDS regions
263 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
267 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
268 Ref Fetcher fails to match, or otherwise updates sequence
269 data from external database records.
272 <!-- JAL-2154 -->Revised Jalview Project format for
273 efficient recovery of sequence coding and alignment
274 annotation relationships.
276 </ul> <!-- <em>Applet</em>
287 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
291 <!-- JAL-2018-->Export features in Jalview format (again)
292 includes graduated colourschemes
295 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
296 working with big alignments and lots of hidden columns
299 <!-- JAL-2053-->Hidden column markers not always rendered
300 at right of alignment window
303 <!-- JAL-2067 -->Tidied up links in help file table of
307 <!-- JAL-2072 -->Feature based tree calculation not shown
311 <!-- JAL-2075 -->Hidden columns ignored during feature
312 based tree calculation
315 <!-- JAL-2065 -->Alignment view stops updating when show
316 unconserved enabled for group on alignment
319 <!-- JAL-2086 -->Cannot insert gaps into sequence when
323 <!-- JAL-2146 -->Alignment column in status incorrectly
324 shown as "Sequence position" when mousing over
328 <!-- JAL-2099 -->Incorrect column numbers in ruler when
329 hidden columns present
332 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
333 user created annotation added to alignment
336 <!-- JAL-1841 -->RNA Structure consensus only computed for
337 '()' base pair annotation
340 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
341 in zero scores for all base pairs in RNA Structure
345 <!-- JAL-2174-->Extend selection with columns containing
349 <!-- JAL-2275 -->Pfam format writer puts extra space at
350 beginning of sequence
353 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
357 <!-- JAL-2238 -->Cannot create groups on an alignment from
358 from a tree when t-coffee scores are shown
361 <!-- JAL-1836,1967 -->Cannot import and view PDB
362 structures with chains containing negative resnums (4q4h)
365 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
369 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
370 to Clustal, PIR and PileUp output
373 <!-- JAL-2008 -->Reordering sequence features that are
374 not visible causes alignment window to repaint
377 <!-- JAL-2006 -->Threshold sliders don't work in
378 graduated colour and colour by annotation row for e-value
379 scores associated with features and annotation rows
382 <!-- JAL-1797 -->amino acid physicochemical conservation
383 calculation should be case independent
386 <!-- JAL-2173 -->Remove annotation also updates hidden
390 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
391 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
392 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
395 <!-- JAL-2065 -->Null pointer exceptions and redraw
396 problems when reference sequence defined and 'show
397 non-conserved' enabled
400 <!-- JAL-1306 -->Quality and Conservation are now shown on
401 load even when Consensus calculation is disabled
407 <!-- JAL-1552-->URLs and links can't be imported by
408 drag'n'drop on OSX when launched via webstart (note - not
409 yet fixed for El Capitan)
412 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
413 output when running on non-gb/us i18n platforms
416 <!-- JAL-1944 -->Error thrown when exporting a view with
417 hidden sequences as flat-file alignment
420 <!-- JAL-2030-->InstallAnywhere distribution fails when
424 <!-- JAL-2080-->Jalview very slow to launch via webstart
425 (also hotfix for 2.9.0b2)
428 <!-- JAL-2085 -->Cannot save project when view has a
429 reference sequence defined
432 <!-- JAL-1011 -->Columns are suddenly selected in other
433 alignments and views when revealing hidden columns
436 <!-- JAL-1989 -->Hide columns not mirrored in complement
437 view in a cDNA/Protein splitframe
440 <!-- JAL-1369 -->Cannot save/restore representative
441 sequence from project when only one sequence is
445 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
449 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
450 structure consensus didn't refresh annotation panel
453 <!-- JAL-1962 -->View mapping in structure view shows
454 mappings between sequence and all chains in a PDB file
457 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
458 dialogs format columns correctly, don't display array
459 data, sort columns according to type
462 <!-- JAL-1975 -->Export complete shown after destination
463 file chooser is cancelled during an image export
466 <!-- JAL-2025 -->Error when querying PDB Service with
467 sequence name containing special characters
470 <!-- JAL-2024 -->Manual PDB structure querying should be
474 <!-- JAL-2104 -->Large tooltips with broken HTML
475 formatting don't wrap
478 <!-- JAL-1128 -->Figures exported from wrapped view are
479 truncated so L looks like I in consensus annotation
482 <!-- JAL-2003 -->Export features should only export the
483 currently displayed features for the current selection or
487 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
488 after fetching cross-references, and restoring from project
491 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
492 followed in the structure viewer
495 <!-- JAL-2163 -->Titles for individual alignments in
496 splitframe not restored from project
499 <!-- JAL-2145 -->missing autocalculated annotation at
500 trailing end of protein alignment in transcript/product
501 splitview when pad-gaps not enabled by default
504 <!-- JAL-1797 -->amino acid physicochemical conservation
508 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
509 article has been read (reopened issue due to
510 internationalisation problems)
513 <!-- JAL-1960 -->Only offer PDB structures in structure
514 viewer based on sequence name, PDB and UniProt
519 <!-- JAL-1976 -->No progress bar shown during export of
523 <!-- JAL-2213 -->Structures not always superimposed after
524 multiple structures are shown for one or more sequences.
527 <!-- JAL-1370 -->Reference sequence characters should not
528 be replaced with '.' when 'Show unconserved' format option
532 <!-- JAL-1823 -->Cannot specify chain code when entering
533 specific PDB id for sequence
536 <!-- JAL-1944 -->File->Export->.. as doesn't work when
537 'Export hidden sequences' is enabled, but 'export hidden
538 columns' is disabled.
541 <!--JAL-2026-->Best Quality option in structure chooser
542 selects lowest rather than highest resolution structures
546 <!-- JAL-1887 -->Incorrect start and end reported for PDB
547 to sequence mapping in 'View Mappings' report
549 <!-- may exclude, this is an external service stability issue JAL-1941
550 -- > RNA 3D structure not added via DSSR service</li> -->
555 <!-- JAL-2151 -->Incorrect columns are selected when
556 hidden columns present before start of sequence
559 <!-- JAL-1986 -->Missing dependencies on applet pages
563 <!-- JAL-1947 -->Overview pixel size changes when
564 sequences are hidden in applet
567 <!-- JAL-1996 -->Updated instructions for applet
568 deployment on examples pages.
575 <td width="60" nowrap>
577 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
578 <em>16/10/2015</em></strong>
583 <li>Time stamps for signed Jalview application and applet
590 <li>Duplicate group consensus and conservation rows
591 shown when tree is partitioned</li>
592 <li>Erratic behaviour when tree partitions made with
593 multiple cDNA/Protein split views</li>
599 <td width="60" nowrap>
601 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
602 <em>8/10/2015</em></strong>
607 <li>Updated Spanish translations of localized text for
609 </ul> <em>Application</em>
611 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
612 <li>Signed OSX InstallAnywhere installer<br></li>
613 <li>Support for per-sequence based annotations in BioJSON</li>
614 </ul> <em>Applet</em>
616 <li>Split frame example added to applet examples page</li>
622 <li>Mapping of cDNA to protein in split frames
623 incorrect when sequence start > 1</li>
624 <li>Broken images in filter column by annotation dialog
626 <li>Feature colours not parsed from features file</li>
627 <li>Exceptions and incomplete link URLs recovered when
628 loading a features file containing HTML tags in feature
634 <li>Annotations corrupted after BioJS export and
636 <li>Incorrect sequence limits after Fetch DB References
637 with 'trim retrieved sequences'</li>
638 <li>Incorrect warning about deleting all data when
639 deleting selected columns</li>
640 <li>Patch to build system for shipping properly signed
641 JNLP templates for webstart launch</li>
642 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
643 unreleased structures for download or viewing</li>
644 <li>Tab/space/return keystroke operation of EMBL-PDBe
645 fetcher/viewer dialogs works correctly</li>
646 <li>Disabled 'minimise' button on Jalview windows
647 running on OSX to workaround redraw hang bug</li>
648 <li>Split cDNA/Protein view position and geometry not
649 recovered from jalview project</li>
650 <li>Initial enabled/disabled state of annotation menu
651 sorter 'show autocalculated first/last' corresponds to
653 <li>Restoring of Clustal, RNA Helices and T-Coffee
654 color schemes from BioJSON</li>
658 <li>Reorder sequences mirrored in cDNA/Protein split
660 <li>Applet with Jmol examples not loading correctly</li>
666 <td><div align="center">
667 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
671 <li>Linked visualisation and analysis of DNA and Protein
674 <li>Translated cDNA alignments shown as split protein
675 and DNA alignment views</li>
676 <li>Codon consensus annotation for linked protein and
677 cDNA alignment views</li>
678 <li>Link cDNA or Protein product sequences by loading
679 them onto Protein or cDNA alignments</li>
680 <li>Reconstruct linked cDNA alignment from aligned
681 protein sequences</li>
684 <li>Jmol integration updated to Jmol v14.2.14</li>
685 <li>Import and export of Jalview alignment views as <a
686 href="features/bioJsonFormat.html">BioJSON</a></li>
687 <li>New alignment annotation file statements for
688 reference sequences and marking hidden columns</li>
689 <li>Reference sequence based alignment shading to
690 highlight variation</li>
691 <li>Select or hide columns according to alignment
693 <li>Find option for locating sequences by description</li>
694 <li>Conserved physicochemical properties shown in amino
695 acid conservation row</li>
696 <li>Alignments can be sorted by number of RNA helices</li>
697 </ul> <em>Application</em>
699 <li>New cDNA/Protein analysis capabilities
701 <li>Get Cross-References should open a Split Frame
702 view with cDNA/Protein</li>
703 <li>Detect when nucleotide sequences and protein
704 sequences are placed in the same alignment</li>
705 <li>Split cDNA/Protein views are saved in Jalview
710 <li>Use REST API to talk to Chimera</li>
711 <li>Selected regions in Chimera are highlighted in linked
714 <li>VARNA RNA viewer updated to v3.93</li>
715 <li>VARNA views are saved in Jalview Projects</li>
716 <li>Pseudoknots displayed as Jalview RNA annotation can
717 be shown in VARNA</li>
719 <li>Make groups for selection uses marked columns as well
720 as the active selected region</li>
722 <li>Calculate UPGMA and NJ trees using sequence feature
724 <li>New Export options
726 <li>New Export Settings dialog to control hidden
727 region export in flat file generation</li>
729 <li>Export alignment views for display with the <a
730 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
732 <li>Export scrollable SVG in HTML page</li>
733 <li>Optional embedding of BioJSON data when exporting
734 alignment figures to HTML</li>
736 <li>3D structure retrieval and display
738 <li>Free text and structured queries with the PDBe
740 <li>PDBe Search API based discovery and selection of
741 PDB structures for a sequence set</li>
745 <li>JPred4 employed for protein secondary structure
747 <li>Hide Insertions menu option to hide unaligned columns
748 for one or a group of sequences</li>
749 <li>Automatically hide insertions in alignments imported
750 from the JPred4 web server</li>
751 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
752 system on OSX<br />LGPL libraries courtesy of <a
753 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
755 <li>changed 'View nucleotide structure' submenu to 'View
756 VARNA 2D Structure'</li>
757 <li>change "View protein structure" menu option to "3D
760 </ul> <em>Applet</em>
762 <li>New layout for applet example pages</li>
763 <li>New parameters to enable SplitFrame view
764 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
765 <li>New example demonstrating linked viewing of cDNA and
766 Protein alignments</li>
767 </ul> <em>Development and deployment</em>
769 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
770 <li>Include installation type and git revision in build
771 properties and console log output</li>
772 <li>Jalview Github organisation, and new github site for
773 storing BioJsMSA Templates</li>
774 <li>Jalview's unit tests now managed with TestNG</li>
777 <!-- <em>General</em>
779 </ul> --> <!-- issues resolved --> <em>Application</em>
781 <li>Escape should close any open find dialogs</li>
782 <li>Typo in select-by-features status report</li>
783 <li>Consensus RNA secondary secondary structure
784 predictions are not highlighted in amber</li>
785 <li>Missing gap character in v2.7 example file means
786 alignment appears unaligned when pad-gaps is not enabled</li>
787 <li>First switch to RNA Helices colouring doesn't colour
788 associated structure views</li>
789 <li>ID width preference option is greyed out when auto
790 width checkbox not enabled</li>
791 <li>Stopped a warning dialog from being shown when
792 creating user defined colours</li>
793 <li>'View Mapping' in structure viewer shows sequence
794 mappings for just that viewer's sequences</li>
795 <li>Workaround for superposing PDB files containing
796 multiple models in Chimera</li>
797 <li>Report sequence position in status bar when hovering
798 over Jmol structure</li>
799 <li>Cannot output gaps as '.' symbols with Selection ->
800 output to text box</li>
801 <li>Flat file exports of alignments with hidden columns
802 have incorrect sequence start/end</li>
803 <li>'Aligning' a second chain to a Chimera structure from
805 <li>Colour schemes applied to structure viewers don't
806 work for nucleotide</li>
807 <li>Loading/cut'n'pasting an empty or invalid file leads
808 to a grey/invisible alignment window</li>
809 <li>Exported Jpred annotation from a sequence region
810 imports to different position</li>
811 <li>Space at beginning of sequence feature tooltips shown
812 on some platforms</li>
813 <li>Chimera viewer 'View | Show Chain' menu is not
815 <li>'New View' fails with a Null Pointer Exception in
816 console if Chimera has been opened</li>
817 <li>Mouseover to Chimera not working</li>
818 <li>Miscellaneous ENA XML feature qualifiers not
820 <li>NPE in annotation renderer after 'Extract Scores'</li>
821 <li>If two structures in one Chimera window, mouseover of
822 either sequence shows on first structure</li>
823 <li>'Show annotations' options should not make
824 non-positional annotations visible</li>
825 <li>Subsequence secondary structure annotation not shown
826 in right place after 'view flanking regions'</li>
827 <li>File Save As type unset when current file format is
829 <li>Save as '.jar' option removed for saving Jalview
831 <li>Colour by Sequence colouring in Chimera more
833 <li>Cannot 'add reference annotation' for a sequence in
834 several views on same alignment</li>
835 <li>Cannot show linked products for EMBL / ENA records</li>
836 <li>Jalview's tooltip wraps long texts containing no
838 </ul> <em>Applet</em>
840 <li>Jmol to JalviewLite mouseover/link not working</li>
841 <li>JalviewLite can't import sequences with ID
842 descriptions containing angle brackets</li>
843 </ul> <em>General</em>
845 <li>Cannot export and reimport RNA secondary structure
846 via jalview annotation file</li>
847 <li>Random helix colour palette for colour by annotation
848 with RNA secondary structure</li>
849 <li>Mouseover to cDNA from STOP residue in protein
850 translation doesn't work.</li>
851 <li>hints when using the select by annotation dialog box</li>
852 <li>Jmol alignment incorrect if PDB file has alternate CA
854 <li>FontChooser message dialog appears to hang after
855 choosing 1pt font</li>
856 <li>Peptide secondary structure incorrectly imported from
857 annotation file when annotation display text includes 'e' or
859 <li>Cannot set colour of new feature type whilst creating
861 <li>cDNA translation alignment should not be sequence
863 <li>'Show unconserved' doesn't work for lower case
865 <li>Nucleotide ambiguity codes involving R not recognised</li>
866 </ul> <em>Deployment and Documentation</em>
868 <li>Applet example pages appear different to the rest of
870 </ul> <em>Application Known issues</em>
872 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
873 <li>Misleading message appears after trying to delete
875 <li>Jalview icon not shown in dock after InstallAnywhere
876 version launches</li>
877 <li>Fetching EMBL reference for an RNA sequence results
878 fails with a sequence mismatch</li>
879 <li>Corrupted or unreadable alignment display when
880 scrolling alignment to right</li>
881 <li>ArrayIndexOutOfBoundsException thrown when remove
882 empty columns called on alignment with ragged gapped ends</li>
883 <li>auto calculated alignment annotation rows do not get
884 placed above or below non-autocalculated rows</li>
885 <li>Jalview dekstop becomes sluggish at full screen in
886 ultra-high resolution</li>
887 <li>Cannot disable consensus calculation independently of
888 quality and conservation</li>
889 <li>Mouseover highlighting between cDNA and protein can
890 become sluggish with more than one splitframe shown</li>
891 </ul> <em>Applet Known Issues</em>
893 <li>Core PDB parsing code requires Jmol</li>
894 <li>Sequence canvas panel goes white when alignment
895 window is being resized</li>
901 <td><div align="center">
902 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
906 <li>Updated Java code signing certificate donated by
908 <li>Features and annotation preserved when performing
909 pairwise alignment</li>
910 <li>RNA pseudoknot annotation can be
911 imported/exported/displayed</li>
912 <li>'colour by annotation' can colour by RNA and
913 protein secondary structure</li>
914 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
915 post-hoc with 2.9 release</em>)
918 </ul> <em>Application</em>
920 <li>Extract and display secondary structure for sequences
921 with 3D structures</li>
922 <li>Support for parsing RNAML</li>
923 <li>Annotations menu for layout
925 <li>sort sequence annotation rows by alignment</li>
926 <li>place sequence annotation above/below alignment
929 <li>Output in Stockholm format</li>
930 <li>Internationalisation: improved Spanish (es)
932 <li>Structure viewer preferences tab</li>
933 <li>Disorder and Secondary Structure annotation tracks
934 shared between alignments</li>
935 <li>UCSF Chimera launch and linked highlighting from
937 <li>Show/hide all sequence associated annotation rows for
938 all or current selection</li>
939 <li>disorder and secondary structure predictions
940 available as dataset annotation</li>
941 <li>Per-sequence rna helices colouring</li>
944 <li>Sequence database accessions imported when fetching
945 alignments from Rfam</li>
946 <li>update VARNA version to 3.91</li>
948 <li>New groovy scripts for exporting aligned positions,
949 conservation values, and calculating sum of pairs scores.</li>
950 <li>Command line argument to set default JABAWS server</li>
951 <li>include installation type in build properties and
952 console log output</li>
953 <li>Updated Jalview project format to preserve dataset
957 <!-- issues resolved --> <em>Application</em>
959 <li>Distinguish alignment and sequence associated RNA
960 structure in structure->view->VARNA</li>
961 <li>Raise dialog box if user deletes all sequences in an
963 <li>Pressing F1 results in documentation opening twice</li>
964 <li>Sequence feature tooltip is wrapped</li>
965 <li>Double click on sequence associated annotation
966 selects only first column</li>
967 <li>Redundancy removal doesn't result in unlinked
968 leaves shown in tree</li>
969 <li>Undos after several redundancy removals don't undo
971 <li>Hide sequence doesn't hide associated annotation</li>
972 <li>User defined colours dialog box too big to fit on
973 screen and buttons not visible</li>
974 <li>author list isn't updated if already written to
975 Jalview properties</li>
976 <li>Popup menu won't open after retrieving sequence
978 <li>File open window for associate PDB doesn't open</li>
979 <li>Left-then-right click on a sequence id opens a
980 browser search window</li>
981 <li>Cannot open sequence feature shading/sort popup menu
982 in feature settings dialog</li>
983 <li>better tooltip placement for some areas of Jalview
985 <li>Allow addition of JABAWS Server which doesn't
987 <li>Web services parameters dialog box is too large to
989 <li>Muscle nucleotide alignment preset obscured by
991 <li>JABAWS preset submenus don't contain newly
992 defined user preset</li>
993 <li>MSA web services warns user if they were launched
994 with invalid input</li>
995 <li>Jalview cannot contact DAS Registy when running on
998 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
999 'Superpose with' submenu not shown when new view
1003 </ul> <!-- <em>Applet</em>
1005 </ul> <em>General</em>
1007 </ul>--> <em>Deployment and Documentation</em>
1009 <li>2G and 1G options in launchApp have no effect on
1010 memory allocation</li>
1011 <li>launchApp service doesn't automatically open
1012 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1014 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1015 InstallAnywhere reports cannot find valid JVM when Java
1016 1.7_055 is available
1018 </ul> <em>Application Known issues</em>
1021 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1022 corrupted or unreadable alignment display when scrolling
1026 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1027 retrieval fails but progress bar continues for DAS retrieval
1028 with large number of ID
1031 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1032 flatfile output of visible region has incorrect sequence
1036 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1037 rna structure consensus doesn't update when secondary
1038 structure tracks are rearranged
1041 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1042 invalid rna structure positional highlighting does not
1043 highlight position of invalid base pairs
1046 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1047 out of memory errors are not raised when saving Jalview
1048 project from alignment window file menu
1051 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1052 Switching to RNA Helices colouring doesn't propagate to
1056 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1057 colour by RNA Helices not enabled when user created
1058 annotation added to alignment
1061 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1062 Jalview icon not shown on dock in Mountain Lion/Webstart
1064 </ul> <em>Applet Known Issues</em>
1067 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1068 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1071 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1072 Jalview and Jmol example not compatible with IE9
1075 <li>Sort by annotation score doesn't reverse order
1081 <td><div align="center">
1082 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1085 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1088 <li>Internationalisation of user interface (usually
1089 called i18n support) and translation for Spanish locale</li>
1090 <li>Define/Undefine group on current selection with
1091 Ctrl-G/Shift Ctrl-G</li>
1092 <li>Improved group creation/removal options in
1093 alignment/sequence Popup menu</li>
1094 <li>Sensible precision for symbol distribution
1095 percentages shown in logo tooltip.</li>
1096 <li>Annotation panel height set according to amount of
1097 annotation when alignment first opened</li>
1098 </ul> <em>Application</em>
1100 <li>Interactive consensus RNA secondary structure
1101 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1102 <li>Select columns containing particular features from
1103 Feature Settings dialog</li>
1104 <li>View all 'representative' PDB structures for selected
1106 <li>Update Jalview project format:
1108 <li>New file extension for Jalview projects '.jvp'</li>
1109 <li>Preserve sequence and annotation dataset (to
1110 store secondary structure annotation,etc)</li>
1111 <li>Per group and alignment annotation and RNA helix
1115 <li>New similarity measures for PCA and Tree calculation
1117 <li>Experimental support for retrieval and viewing of
1118 flanking regions for an alignment</li>
1122 <!-- issues resolved --> <em>Application</em>
1124 <li>logo keeps spinning and status remains at queued or
1125 running after job is cancelled</li>
1126 <li>cannot export features from alignments imported from
1127 Jalview/VAMSAS projects</li>
1128 <li>Buggy slider for web service parameters that take
1130 <li>Newly created RNA secondary structure line doesn't
1131 have 'display all symbols' flag set</li>
1132 <li>T-COFFEE alignment score shading scheme and other
1133 annotation shading not saved in Jalview project</li>
1134 <li>Local file cannot be loaded in freshly downloaded
1136 <li>Jalview icon not shown on dock in Mountain
1138 <li>Load file from desktop file browser fails</li>
1139 <li>Occasional NPE thrown when calculating large trees</li>
1140 <li>Cannot reorder or slide sequences after dragging an
1141 alignment onto desktop</li>
1142 <li>Colour by annotation dialog throws NPE after using
1143 'extract scores' function</li>
1144 <li>Loading/cut'n'pasting an empty file leads to a grey
1145 alignment window</li>
1146 <li>Disorder thresholds rendered incorrectly after
1147 performing IUPred disorder prediction</li>
1148 <li>Multiple group annotated consensus rows shown when
1149 changing 'normalise logo' display setting</li>
1150 <li>Find shows blank dialog after 'finished searching' if
1151 nothing matches query</li>
1152 <li>Null Pointer Exceptions raised when sorting by
1153 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1155 <li>Errors in Jmol console when structures in alignment
1156 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1158 <li>Not all working JABAWS services are shown in
1160 <li>JAVAWS version of Jalview fails to launch with
1161 'invalid literal/length code'</li>
1162 <li>Annotation/RNA Helix colourschemes cannot be applied
1163 to alignment with groups (actually fixed in 2.8.0b1)</li>
1164 <li>RNA Helices and T-Coffee Scores available as default
1167 </ul> <em>Applet</em>
1169 <li>Remove group option is shown even when selection is
1171 <li>Apply to all groups ticked but colourscheme changes
1172 don't affect groups</li>
1173 <li>Documented RNA Helices and T-Coffee Scores as valid
1174 colourscheme name</li>
1175 <li>Annotation labels drawn on sequence IDs when
1176 Annotation panel is not displayed</li>
1177 <li>Increased font size for dropdown menus on OSX and
1178 embedded windows</li>
1179 </ul> <em>Other</em>
1181 <li>Consensus sequence for alignments/groups with a
1182 single sequence were not calculated</li>
1183 <li>annotation files that contain only groups imported as
1184 annotation and junk sequences</li>
1185 <li>Fasta files with sequences containing '*' incorrectly
1186 recognised as PFAM or BLC</li>
1187 <li>conservation/PID slider apply all groups option
1188 doesn't affect background (2.8.0b1)
1190 <li>redundancy highlighting is erratic at 0% and 100%</li>
1191 <li>Remove gapped columns fails for sequences with ragged
1193 <li>AMSA annotation row with leading spaces is not
1194 registered correctly on import</li>
1195 <li>Jalview crashes when selecting PCA analysis for
1196 certain alignments</li>
1197 <li>Opening the colour by annotation dialog for an
1198 existing annotation based 'use original colours'
1199 colourscheme loses original colours setting</li>
1204 <td><div align="center">
1205 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
1206 <em>30/1/2014</em></strong>
1210 <li>Trusted certificates for JalviewLite applet and
1211 Jalview Desktop application<br />Certificate was donated by
1212 <a href="https://www.certum.eu">Certum</a> to the Jalview
1213 open source project).
1215 <li>Jalview SRS links replaced by UniProt and EBI-search
1217 <li>Output in Stockholm format</li>
1218 <li>Allow import of data from gzipped files</li>
1219 <li>Export/import group and sequence associated line
1220 graph thresholds</li>
1221 <li>Nucleotide substitution matrix that supports RNA and
1222 ambiguity codes</li>
1223 <li>Allow disorder predictions to be made on the current
1224 selection (or visible selection) in the same way that JPred
1226 <li>Groovy scripting for headless Jalview operation</li>
1227 </ul> <em>Other improvements</em>
1229 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
1230 <li>COMBINE statement uses current SEQUENCE_REF and
1231 GROUP_REF scope to group annotation rows</li>
1232 <li>Support '' style escaping of quotes in Newick
1234 <li>Group options for JABAWS service by command line name</li>
1235 <li>Empty tooltip shown for JABA service options with a
1236 link but no description</li>
1237 <li>Select primary source when selecting authority in
1238 database fetcher GUI</li>
1239 <li>Add .mfa to FASTA file extensions recognised by
1241 <li>Annotation label tooltip text wrap</li>
1246 <li>Slow scrolling when lots of annotation rows are
1248 <li>Lots of NPE (and slowness) after creating RNA
1249 secondary structure annotation line</li>
1250 <li>Sequence database accessions not imported when
1251 fetching alignments from Rfam</li>
1252 <li>Incorrect SHMR submission for sequences with
1254 <li>View all structures does not always superpose
1256 <li>Option widgets in service parameters not updated to
1257 reflect user or preset settings</li>
1258 <li>Null pointer exceptions for some services without
1259 presets or adjustable parameters</li>
1260 <li>Discover PDB IDs entry in structure menu doesn't
1261 discover PDB xRefs</li>
1262 <li>Exception encountered while trying to retrieve
1263 features with DAS</li>
1264 <li>Lowest value in annotation row isn't coloured
1265 when colour by annotation (per sequence) is coloured</li>
1266 <li>Keyboard mode P jumps to start of gapped region when
1267 residue follows a gap</li>
1268 <li>Jalview appears to hang importing an alignment with
1269 Wrap as default or after enabling Wrap</li>
1270 <li>'Right click to add annotations' message
1271 shown in wrap mode when no annotations present</li>
1272 <li>Disorder predictions fail with NPE if no automatic
1273 annotation already exists on alignment</li>
1274 <li>oninit javascript function should be called after
1275 initialisation completes</li>
1276 <li>Remove redundancy after disorder prediction corrupts
1277 alignment window display</li>
1278 <li>Example annotation file in documentation is invalid</li>
1279 <li>Grouped line graph annotation rows are not exported
1280 to annotation file</li>
1281 <li>Multi-harmony analysis cannot be run when only two
1283 <li>Cannot create multiple groups of line graphs with
1284 several 'combine' statements in annotation file</li>
1285 <li>Pressing return several times causes Number Format
1286 exceptions in keyboard mode</li>
1287 <li>Multi-harmony (SHMMR) method doesn't submit
1288 correct partitions for input data</li>
1289 <li>Translation from DNA to Amino Acids fails</li>
1290 <li>Jalview fail to load newick tree with quoted label</li>
1291 <li>--headless flag isn't understood</li>
1292 <li>ClassCastException when generating EPS in headless
1294 <li>Adjusting sequence-associated shading threshold only
1295 changes one row's threshold</li>
1296 <li>Preferences and Feature settings panel panel
1297 doesn't open</li>
1298 <li>hide consensus histogram also hides conservation and
1299 quality histograms</li>
1304 <td><div align="center">
1305 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
1307 <td><em>Application</em>
1309 <li>Support for JABAWS 2.0 Services (AACon alignment
1310 conservation, protein disorder and Clustal Omega)</li>
1311 <li>JABAWS server status indicator in Web Services
1313 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
1314 in Jalview alignment window</li>
1315 <li>Updated Jalview build and deploy framework for OSX
1316 mountain lion, windows 7, and 8</li>
1317 <li>Nucleotide substitution matrix for PCA that supports
1318 RNA and ambiguity codes</li>
1320 <li>Improved sequence database retrieval GUI</li>
1321 <li>Support fetching and database reference look up
1322 against multiple DAS sources (Fetch all from in 'fetch db
1324 <li>Jalview project improvements
1326 <li>Store and retrieve the 'belowAlignment'
1327 flag for annotation</li>
1328 <li>calcId attribute to group annotation rows on the
1330 <li>Store AACon calculation settings for a view in
1331 Jalview project</li>
1335 <li>horizontal scrolling gesture support</li>
1336 <li>Visual progress indicator when PCA calculation is
1338 <li>Simpler JABA web services menus</li>
1339 <li>visual indication that web service results are still
1340 being retrieved from server</li>
1341 <li>Serialise the dialogs that are shown when Jalview
1342 starts up for first time</li>
1343 <li>Jalview user agent string for interacting with HTTP
1345 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
1347 <li>Examples directory and Groovy library included in
1348 InstallAnywhere distribution</li>
1349 </ul> <em>Applet</em>
1351 <li>RNA alignment and secondary structure annotation
1352 visualization applet example</li>
1353 </ul> <em>General</em>
1355 <li>Normalise option for consensus sequence logo</li>
1356 <li>Reset button in PCA window to return dimensions to
1358 <li>Allow seqspace or Jalview variant of alignment PCA
1360 <li>PCA with either nucleic acid and protein substitution
1362 <li>Allow windows containing HTML reports to be exported
1364 <li>Interactive display and editing of RNA secondary
1365 structure contacts</li>
1366 <li>RNA Helix Alignment Colouring</li>
1367 <li>RNA base pair logo consensus</li>
1368 <li>Parse sequence associated secondary structure
1369 information in Stockholm files</li>
1370 <li>HTML Export database accessions and annotation
1371 information presented in tooltip for sequences</li>
1372 <li>Import secondary structure from LOCARNA clustalw
1373 style RNA alignment files</li>
1374 <li>import and visualise T-COFFEE quality scores for an
1376 <li>'colour by annotation' per sequence option to
1377 shade each sequence according to its associated alignment
1379 <li>New Jalview Logo</li>
1380 </ul> <em>Documentation and Development</em>
1382 <li>documentation for score matrices used in Jalview</li>
1383 <li>New Website!</li>
1385 <td><em>Application</em>
1387 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
1388 wsdbfetch REST service</li>
1389 <li>Stop windows being moved outside desktop on OSX</li>
1390 <li>Filetype associations not installed for webstart
1392 <li>Jalview does not always retrieve progress of a JABAWS
1393 job execution in full once it is complete</li>
1394 <li>revise SHMR RSBS definition to ensure alignment is
1395 uploaded via ali_file parameter</li>
1396 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
1397 <li>View all structures superposed fails with exception</li>
1398 <li>Jnet job queues forever if a very short sequence is
1399 submitted for prediction</li>
1400 <li>Cut and paste menu not opened when mouse clicked on
1402 <li>Putting fractional value into integer text box in
1403 alignment parameter dialog causes Jalview to hang</li>
1404 <li>Structure view highlighting doesn't work on
1406 <li>View all structures fails with exception shown in
1408 <li>Characters in filename associated with PDBEntry not
1409 escaped in a platform independent way</li>
1410 <li>Jalview desktop fails to launch with exception when
1412 <li>Tree calculation reports 'you must have 2 or more
1413 sequences selected' when selection is empty</li>
1414 <li>Jalview desktop fails to launch with jar signature
1415 failure when java web start temporary file caching is
1417 <li>DAS Sequence retrieval with range qualification
1418 results in sequence xref which includes range qualification</li>
1419 <li>Errors during processing of command line arguments
1420 cause progress bar (JAL-898) to be removed</li>
1421 <li>Replace comma for semi-colon option not disabled for
1422 DAS sources in sequence fetcher</li>
1423 <li>Cannot close news reader when JABAWS server warning
1424 dialog is shown</li>
1425 <li>Option widgets not updated to reflect user settings</li>
1426 <li>Edited sequence not submitted to web service</li>
1427 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
1428 <li>InstallAnywhere installer doesn't unpack and run
1429 on OSX Mountain Lion</li>
1430 <li>Annotation panel not given a scroll bar when
1431 sequences with alignment annotation are pasted into the
1433 <li>Sequence associated annotation rows not associated
1434 when loaded from Jalview project</li>
1435 <li>Browser launch fails with NPE on java 1.7</li>
1436 <li>JABAWS alignment marked as finished when job was
1437 cancelled or job failed due to invalid input</li>
1438 <li>NPE with v2.7 example when clicking on Tree
1439 associated with all views</li>
1440 <li>Exceptions when copy/paste sequences with grouped
1441 annotation rows to new window</li>
1442 </ul> <em>Applet</em>
1444 <li>Sequence features are momentarily displayed before
1445 they are hidden using hidefeaturegroups applet parameter</li>
1446 <li>loading features via javascript API automatically
1447 enables feature display</li>
1448 <li>scrollToColumnIn javascript API method doesn't
1450 </ul> <em>General</em>
1452 <li>Redundancy removal fails for rna alignment</li>
1453 <li>PCA calculation fails when sequence has been selected
1454 and then deselected</li>
1455 <li>PCA window shows grey box when first opened on OSX</li>
1456 <li>Letters coloured pink in sequence logo when alignment
1457 coloured with clustalx</li>
1458 <li>Choosing fonts without letter symbols defined causes
1459 exceptions and redraw errors</li>
1460 <li>Initial PCA plot view is not same as manually
1461 reconfigured view</li>
1462 <li>Grouped annotation graph label has incorrect line
1464 <li>Grouped annotation graph label display is corrupted
1465 for lots of labels</li>
1470 <div align="center">
1471 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
1474 <td><em>Application</em>
1476 <li>Jalview Desktop News Reader</li>
1477 <li>Tweaked default layout of web services menu</li>
1478 <li>View/alignment association menu to enable user to
1479 easily specify which alignment a multi-structure view takes
1480 its colours/correspondences from</li>
1481 <li>Allow properties file location to be specified as URL</li>
1482 <li>Extend Jalview project to preserve associations
1483 between many alignment views and a single Jmol display</li>
1484 <li>Store annotation row height in Jalview project file</li>
1485 <li>Annotation row column label formatting attributes
1486 stored in project file</li>
1487 <li>Annotation row order for auto-calculated annotation
1488 rows preserved in Jalview project file</li>
1489 <li>Visual progress indication when Jalview state is
1490 saved using Desktop window menu</li>
1491 <li>Visual indication that command line arguments are
1492 still being processed</li>
1493 <li>Groovy script execution from URL</li>
1494 <li>Colour by annotation default min and max colours in
1496 <li>Automatically associate PDB files dragged onto an
1497 alignment with sequences that have high similarity and
1499 <li>Update JGoogleAnalytics to latest release (0.3)</li>
1500 <li>'view structures' option to open many
1501 structures in same window</li>
1502 <li>Sort associated views menu option for tree panel</li>
1503 <li>Group all JABA and non-JABA services for a particular
1504 analysis function in its own submenu</li>
1505 </ul> <em>Applet</em>
1507 <li>Userdefined and autogenerated annotation rows for
1509 <li>Adjustment of alignment annotation pane height</li>
1510 <li>Annotation scrollbar for annotation panel</li>
1511 <li>Drag to reorder annotation rows in annotation panel</li>
1512 <li>'automaticScrolling' parameter</li>
1513 <li>Allow sequences with partial ID string matches to be
1514 annotated from GFF/Jalview features files</li>
1515 <li>Sequence logo annotation row in applet</li>
1516 <li>Absolute paths relative to host server in applet
1517 parameters are treated as such</li>
1518 <li>New in the JalviewLite javascript API:
1520 <li>JalviewLite.js javascript library</li>
1521 <li>Javascript callbacks for
1523 <li>Applet initialisation</li>
1524 <li>Sequence/alignment mouse-overs and selections</li>
1527 <li>scrollTo row and column alignment scrolling
1529 <li>Select sequence/alignment regions from javascript</li>
1530 <li>javascript structure viewer harness to pass
1531 messages between Jmol and Jalview when running as
1532 distinct applets</li>
1533 <li>sortBy method</li>
1534 <li>Set of applet and application examples shipped
1535 with documentation</li>
1536 <li>New example to demonstrate JalviewLite and Jmol
1537 javascript message exchange</li>
1539 </ul> <em>General</em>
1541 <li>Enable Jmol displays to be associated with multiple
1542 multiple alignments</li>
1543 <li>Option to automatically sort alignment with new tree</li>
1544 <li>User configurable link to enable redirects to a
1545 www.Jalview.org mirror</li>
1546 <li>Jmol colours option for Jmol displays</li>
1547 <li>Configurable newline string when writing alignment
1548 and other flat files</li>
1549 <li>Allow alignment annotation description lines to
1550 contain html tags</li>
1551 </ul> <em>Documentation and Development</em>
1553 <li>Add groovy test harness for bulk load testing to
1555 <li>Groovy script to load and align a set of sequences
1556 using a web service before displaying the result in the
1557 Jalview desktop</li>
1558 <li>Restructured javascript and applet api documentation</li>
1559 <li>Ant target to publish example html files with applet
1561 <li>Netbeans project for building Jalview from source</li>
1562 <li>ant task to create online javadoc for Jalview source</li>
1564 <td><em>Application</em>
1566 <li>User defined colourscheme throws exception when
1567 current built in colourscheme is saved as new scheme</li>
1568 <li>AlignFrame->Save in application pops up save
1569 dialog for valid filename/format</li>
1570 <li>Cannot view associated structure for UniProt sequence</li>
1571 <li>PDB file association breaks for UniProt sequence
1573 <li>Associate PDB from file dialog does not tell you
1574 which sequence is to be associated with the file</li>
1575 <li>Find All raises null pointer exception when query
1576 only matches sequence IDs</li>
1577 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
1578 <li>Jalview project with Jmol views created with Jalview
1579 2.4 cannot be loaded</li>
1580 <li>Filetype associations not installed for webstart
1582 <li>Two or more chains in a single PDB file associated
1583 with sequences in different alignments do not get coloured
1584 by their associated sequence</li>
1585 <li>Visibility status of autocalculated annotation row
1586 not preserved when project is loaded</li>
1587 <li>Annotation row height and visibility attributes not
1588 stored in Jalview project</li>
1589 <li>Tree bootstraps are not preserved when saved as a
1590 Jalview project</li>
1591 <li>Envision2 workflow tooltips are corrupted</li>
1592 <li>Enabling show group conservation also enables colour
1593 by conservation</li>
1594 <li>Duplicate group associated conservation or consensus
1595 created on new view</li>
1596 <li>Annotation scrollbar not displayed after 'show
1597 all hidden annotation rows' option selected</li>
1598 <li>Alignment quality not updated after alignment
1599 annotation row is hidden then shown</li>
1600 <li>Preserve colouring of structures coloured by
1601 sequences in pre Jalview 2.7 projects</li>
1602 <li>Web service job parameter dialog is not laid out
1604 <li>Web services menu not refreshed after 'reset
1605 services' button is pressed in preferences</li>
1606 <li>Annotation off by one in Jalview v2_3 example project</li>
1607 <li>Structures imported from file and saved in project
1608 get name like jalview_pdb1234.txt when reloaded</li>
1609 <li>Jalview does not always retrieve progress of a JABAWS
1610 job execution in full once it is complete</li>
1611 </ul> <em>Applet</em>
1613 <li>Alignment height set incorrectly when lots of
1614 annotation rows are displayed</li>
1615 <li>Relative URLs in feature HTML text not resolved to
1617 <li>View follows highlighting does not work for positions
1619 <li><= shown as = in tooltip</li>
1620 <li>Export features raises exception when no features
1622 <li>Separator string used for serialising lists of IDs
1623 for javascript api is modified when separator string
1624 provided as parameter</li>
1625 <li>Null pointer exception when selecting tree leaves for
1626 alignment with no existing selection</li>
1627 <li>Relative URLs for datasources assumed to be relative
1628 to applet's codebase</li>
1629 <li>Status bar not updated after finished searching and
1630 search wraps around to first result</li>
1631 <li>StructureSelectionManager instance shared between
1632 several Jalview applets causes race conditions and memory
1634 <li>Hover tooltip and mouseover of position on structure
1635 not sent from Jmol in applet</li>
1636 <li>Certain sequences of javascript method calls to
1637 applet API fatally hang browser</li>
1638 </ul> <em>General</em>
1640 <li>View follows structure mouseover scrolls beyond
1641 position with wrapped view and hidden regions</li>
1642 <li>Find sequence position moves to wrong residue
1643 with/without hidden columns</li>
1644 <li>Sequence length given in alignment properties window
1646 <li>InvalidNumberFormat exceptions thrown when trying to
1647 import PDB like structure files</li>
1648 <li>Positional search results are only highlighted
1649 between user-supplied sequence start/end bounds</li>
1650 <li>End attribute of sequence is not validated</li>
1651 <li>Find dialog only finds first sequence containing a
1652 given sequence position</li>
1653 <li>Sequence numbering not preserved in MSF alignment
1655 <li>Jalview PDB file reader does not extract sequence
1656 from nucleotide chains correctly</li>
1657 <li>Structure colours not updated when tree partition
1658 changed in alignment</li>
1659 <li>Sequence associated secondary structure not correctly
1660 parsed in interleaved stockholm</li>
1661 <li>Colour by annotation dialog does not restore current
1663 <li>Hiding (nearly) all sequences doesn't work
1665 <li>Sequences containing lowercase letters are not
1666 properly associated with their pdb files</li>
1667 </ul> <em>Documentation and Development</em>
1669 <li>schemas/JalviewWsParamSet.xsd corrupted by
1670 ApplyCopyright tool</li>
1675 <div align="center">
1676 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
1679 <td><em>Application</em>
1681 <li>New warning dialog when the Jalview Desktop cannot
1682 contact web services</li>
1683 <li>JABA service parameters for a preset are shown in
1684 service job window</li>
1685 <li>JABA Service menu entries reworded</li>
1689 <li>Modeller PIR IO broken - cannot correctly import a
1690 pir file emitted by Jalview</li>
1691 <li>Existing feature settings transferred to new
1692 alignment view created from cut'n'paste</li>
1693 <li>Improved test for mixed amino/nucleotide chains when
1694 parsing PDB files</li>
1695 <li>Consensus and conservation annotation rows
1696 occasionally become blank for all new windows</li>
1697 <li>Exception raised when right clicking above sequences
1698 in wrapped view mode</li>
1699 </ul> <em>Application</em>
1701 <li>multiple multiply aligned structure views cause cpu
1702 usage to hit 100% and computer to hang</li>
1703 <li>Web Service parameter layout breaks for long user
1704 parameter names</li>
1705 <li>Jaba service discovery hangs desktop if Jaba server
1712 <div align="center">
1713 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
1716 <td><em>Application</em>
1718 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
1719 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
1722 <li>Web Services preference tab</li>
1723 <li>Analysis parameters dialog box and user defined
1725 <li>Improved speed and layout of Envision2 service menu</li>
1726 <li>Superpose structures using associated sequence
1728 <li>Export coordinates and projection as CSV from PCA
1730 </ul> <em>Applet</em>
1732 <li>enable javascript: execution by the applet via the
1733 link out mechanism</li>
1734 </ul> <em>Other</em>
1736 <li>Updated the Jmol Jalview interface to work with Jmol
1738 <li>The Jalview Desktop and JalviewLite applet now
1739 require Java 1.5</li>
1740 <li>Allow Jalview feature colour specification for GFF
1741 sequence annotation files</li>
1742 <li>New 'colour by label' keword in Jalview feature file
1743 type colour specification</li>
1744 <li>New Jalview Desktop Groovy API method that allows a
1745 script to check if it being run in an interactive session or
1746 in a batch operation from the Jalview command line</li>
1750 <li>clustalx colourscheme colours Ds preferentially when
1751 both D+E are present in over 50% of the column</li>
1752 </ul> <em>Application</em>
1754 <li>typo in AlignmentFrame->View->Hide->all but
1755 selected Regions menu item</li>
1756 <li>sequence fetcher replaces ',' for ';' when the ',' is
1757 part of a valid accession ID</li>
1758 <li>fatal OOM if object retrieved by sequence fetcher
1759 runs out of memory</li>
1760 <li>unhandled Out of Memory Error when viewing pca
1761 analysis results</li>
1762 <li>InstallAnywhere builds fail to launch on OS X java
1763 10.5 update 4 (due to apple Java 1.6 update)</li>
1764 <li>Installanywhere Jalview silently fails to launch</li>
1765 </ul> <em>Applet</em>
1767 <li>Jalview.getFeatureGroups() raises an
1768 ArrayIndexOutOfBoundsException if no feature groups are
1775 <div align="center">
1776 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
1782 <li>Alignment prettyprinter doesn't cope with long
1784 <li>clustalx colourscheme colours Ds preferentially when
1785 both D+E are present in over 50% of the column</li>
1786 <li>nucleic acid structures retrieved from PDB do not
1787 import correctly</li>
1788 <li>More columns get selected than were clicked on when a
1789 number of columns are hidden</li>
1790 <li>annotation label popup menu not providing correct
1791 add/hide/show options when rows are hidden or none are
1793 <li>Stockholm format shown in list of readable formats,
1794 and parser copes better with alignments from RFAM.</li>
1795 <li>CSV output of consensus only includes the percentage
1796 of all symbols if sequence logo display is enabled</li>
1798 </ul> <em>Applet</em>
1800 <li>annotation panel disappears when annotation is
1802 </ul> <em>Application</em>
1804 <li>Alignment view not redrawn properly when new
1805 alignment opened where annotation panel is visible but no
1806 annotations are present on alignment</li>
1807 <li>pasted region containing hidden columns is
1808 incorrectly displayed in new alignment window</li>
1809 <li>Jalview slow to complete operations when stdout is
1810 flooded (fix is to close the Jalview console)</li>
1811 <li>typo in AlignmentFrame->View->Hide->all but
1812 selected Rregions menu item.</li>
1813 <li>inconsistent group submenu and Format submenu entry
1814 'Un' or 'Non'conserved</li>
1815 <li>Sequence feature settings are being shared by
1816 multiple distinct alignments</li>
1817 <li>group annotation not recreated when tree partition is
1819 <li>double click on group annotation to select sequences
1820 does not propagate to associated trees</li>
1821 <li>Mac OSX specific issues:
1823 <li>exception raised when mouse clicked on desktop
1824 window background</li>
1825 <li>Desktop menu placed on menu bar and application
1826 name set correctly</li>
1827 <li>sequence feature settings not wide enough for the
1828 save feature colourscheme button</li>
1837 <div align="center">
1838 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
1841 <td><em>New Capabilities</em>
1843 <li>URL links generated from description line for
1844 regular-expression based URL links (applet and application)
1851 <li>Non-positional feature URL links are shown in link
1853 <li>Linked viewing of nucleic acid sequences and
1855 <li>Automatic Scrolling option in View menu to display
1856 the currently highlighted region of an alignment.</li>
1857 <li>Order an alignment by sequence length, or using the
1858 average score or total feature count for each sequence.</li>
1859 <li>Shading features by score or associated description</li>
1860 <li>Subdivide alignment and groups based on identity of
1861 selected subsequence (Make Groups from Selection).</li>
1862 <li>New hide/show options including Shift+Control+H to
1863 hide everything but the currently selected region.</li>
1864 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
1865 </ul> <em>Application</em>
1867 <li>Fetch DB References capabilities and UI expanded to
1868 support retrieval from DAS sequence sources</li>
1869 <li>Local DAS Sequence sources can be added via the
1870 command line or via the Add local source dialog box.</li>
1871 <li>DAS Dbref and DbxRef feature types are parsed as
1872 database references and protein_name is parsed as
1873 description line (BioSapiens terms).</li>
1874 <li>Enable or disable non-positional feature and database
1875 references in sequence ID tooltip from View menu in
1877 <!-- <li>New hidden columns and rows and representatives capabilities
1878 in annotations file (in progress - not yet fully implemented)</li> -->
1879 <li>Group-associated consensus, sequence logos and
1880 conservation plots</li>
1881 <li>Symbol distributions for each column can be exported
1882 and visualized as sequence logos</li>
1883 <li>Optionally scale multi-character column labels to fit
1884 within each column of annotation row<!-- todo for applet -->
1886 <li>Optional automatic sort of associated alignment view
1887 when a new tree is opened.</li>
1888 <li>Jalview Java Console</li>
1889 <li>Better placement of desktop window when moving
1890 between different screens.</li>
1891 <li>New preference items for sequence ID tooltip and
1892 consensus annotation</li>
1893 <li>Client to submit sequences and IDs to Envision2
1895 <li><em>Vamsas Capabilities</em>
1897 <li>Improved VAMSAS synchronization (Jalview archive
1898 used to preserve views, structures, and tree display
1900 <li>Import of vamsas documents from disk or URL via
1902 <li>Sharing of selected regions between views and
1903 with other VAMSAS applications (Experimental feature!)</li>
1904 <li>Updated API to VAMSAS version 0.2</li>
1906 </ul> <em>Applet</em>
1908 <li>Middle button resizes annotation row height</li>
1911 <li>sortByTree (true/false) - automatically sort the
1912 associated alignment view by the tree when a new tree is
1914 <li>showTreeBootstraps (true/false) - show or hide
1915 branch bootstraps (default is to show them if available)</li>
1916 <li>showTreeDistances (true/false) - show or hide
1917 branch lengths (default is to show them if available)</li>
1918 <li>showUnlinkedTreeNodes (true/false) - indicate if
1919 unassociated nodes should be highlighted in the tree
1921 <li>heightScale and widthScale (1.0 or more) -
1922 increase the height or width of a cell in the alignment
1923 grid relative to the current font size.</li>
1926 <li>Non-positional features displayed in sequence ID
1928 </ul> <em>Other</em>
1930 <li>Features format: graduated colour definitions and
1931 specification of feature scores</li>
1932 <li>Alignment Annotations format: new keywords for group
1933 associated annotation (GROUP_REF) and annotation row display
1934 properties (ROW_PROPERTIES)</li>
1935 <li>XML formats extended to support graduated feature
1936 colourschemes, group associated annotation, and profile
1937 visualization settings.</li></td>
1940 <li>Source field in GFF files parsed as feature source
1941 rather than description</li>
1942 <li>Non-positional features are now included in sequence
1943 feature and gff files (controlled via non-positional feature
1944 visibility in tooltip).</li>
1945 <li>URL links generated for all feature links (bugfix)</li>
1946 <li>Added URL embedding instructions to features file
1948 <li>Codons containing ambiguous nucleotides translated as
1949 'X' in peptide product</li>
1950 <li>Match case switch in find dialog box works for both
1951 sequence ID and sequence string and query strings do not
1952 have to be in upper case to match case-insensitively.</li>
1953 <li>AMSA files only contain first column of
1954 multi-character column annotation labels</li>
1955 <li>Jalview Annotation File generation/parsing consistent
1956 with documentation (e.g. Stockholm annotation can be
1957 exported and re-imported)</li>
1958 <li>PDB files without embedded PDB IDs given a friendly
1960 <li>Find incrementally searches ID string matches as well
1961 as subsequence matches, and correctly reports total number
1965 <li>Better handling of exceptions during sequence
1967 <li>Dasobert generated non-positional feature URL
1968 link text excludes the start_end suffix</li>
1969 <li>DAS feature and source retrieval buttons disabled
1970 when fetch or registry operations in progress.</li>
1971 <li>PDB files retrieved from URLs are cached properly</li>
1972 <li>Sequence description lines properly shared via
1974 <li>Sequence fetcher fetches multiple records for all
1976 <li>Ensured that command line das feature retrieval
1977 completes before alignment figures are generated.</li>
1978 <li>Reduced time taken when opening file browser for
1980 <li>isAligned check prior to calculating tree, PCA or
1981 submitting an MSA to JNet now excludes hidden sequences.</li>
1982 <li>User defined group colours properly recovered
1983 from Jalview projects.</li>
1992 <div align="center">
1993 <strong>2.4.0.b2</strong><br> 28/10/2009
1998 <li>Experimental support for google analytics usage
2000 <li>Jalview privacy settings (user preferences and docs).</li>
2005 <li>Race condition in applet preventing startup in
2007 <li>Exception when feature created from selection beyond
2008 length of sequence.</li>
2009 <li>Allow synthetic PDB files to be imported gracefully</li>
2010 <li>Sequence associated annotation rows associate with
2011 all sequences with a given id</li>
2012 <li>Find function matches case-insensitively for sequence
2013 ID string searches</li>
2014 <li>Non-standard characters do not cause pairwise
2015 alignment to fail with exception</li>
2016 </ul> <em>Application Issues</em>
2018 <li>Sequences are now validated against EMBL database</li>
2019 <li>Sequence fetcher fetches multiple records for all
2021 </ul> <em>InstallAnywhere Issues</em>
2023 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2024 issue with installAnywhere mechanism)</li>
2025 <li>Command line launching of JARs from InstallAnywhere
2026 version (java class versioning error fixed)</li>
2033 <div align="center">
2034 <strong>2.4</strong><br> 27/8/2008
2037 <td><em>User Interface</em>
2039 <li>Linked highlighting of codon and amino acid from
2040 translation and protein products</li>
2041 <li>Linked highlighting of structure associated with
2042 residue mapping to codon position</li>
2043 <li>Sequence Fetcher provides example accession numbers
2044 and 'clear' button</li>
2045 <li>MemoryMonitor added as an option under Desktop's
2047 <li>Extract score function to parse whitespace separated
2048 numeric data in description line</li>
2049 <li>Column labels in alignment annotation can be centred.</li>
2050 <li>Tooltip for sequence associated annotation give name
2052 </ul> <em>Web Services and URL fetching</em>
2054 <li>JPred3 web service</li>
2055 <li>Prototype sequence search client (no public services
2057 <li>Fetch either seed alignment or full alignment from
2059 <li>URL Links created for matching database cross
2060 references as well as sequence ID</li>
2061 <li>URL Links can be created using regular-expressions</li>
2062 </ul> <em>Sequence Database Connectivity</em>
2064 <li>Retrieval of cross-referenced sequences from other
2066 <li>Generalised database reference retrieval and
2067 validation to all fetchable databases</li>
2068 <li>Fetch sequences from DAS sources supporting the
2069 sequence command</li>
2070 </ul> <em>Import and Export</em>
2071 <li>export annotation rows as CSV for spreadsheet import</li>
2072 <li>Jalview projects record alignment dataset associations,
2073 EMBL products, and cDNA sequence mappings</li>
2074 <li>Sequence Group colour can be specified in Annotation
2076 <li>Ad-hoc colouring of group in Annotation File using RGB
2077 triplet as name of colourscheme</li>
2078 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2080 <li>treenode binding for VAMSAS tree exchange</li>
2081 <li>local editing and update of sequences in VAMSAS
2082 alignments (experimental)</li>
2083 <li>Create new or select existing session to join</li>
2084 <li>load and save of vamsas documents</li>
2085 </ul> <em>Application command line</em>
2087 <li>-tree parameter to open trees (introduced for passing
2089 <li>-fetchfrom command line argument to specify nicknames
2090 of DAS servers to query for alignment features</li>
2091 <li>-dasserver command line argument to add new servers
2092 that are also automatically queried for features</li>
2093 <li>-groovy command line argument executes a given groovy
2094 script after all input data has been loaded and parsed</li>
2095 </ul> <em>Applet-Application data exchange</em>
2097 <li>Trees passed as applet parameters can be passed to
2098 application (when using "View in full
2099 application")</li>
2100 </ul> <em>Applet Parameters</em>
2102 <li>feature group display control parameter</li>
2103 <li>debug parameter</li>
2104 <li>showbutton parameter</li>
2105 </ul> <em>Applet API methods</em>
2107 <li>newView public method</li>
2108 <li>Window (current view) specific get/set public methods</li>
2109 <li>Feature display control methods</li>
2110 <li>get list of currently selected sequences</li>
2111 </ul> <em>New Jalview distribution features</em>
2113 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2114 <li>RELEASE file gives build properties for the latest
2115 Jalview release.</li>
2116 <li>Java 1.1 Applet build made easier and donotobfuscate
2117 property controls execution of obfuscator</li>
2118 <li>Build target for generating source distribution</li>
2119 <li>Debug flag for javacc</li>
2120 <li>.jalview_properties file is documented (slightly) in
2121 jalview.bin.Cache</li>
2122 <li>Continuous Build Integration for stable and
2123 development version of Application, Applet and source
2128 <li>selected region output includes visible annotations
2129 (for certain formats)</li>
2130 <li>edit label/displaychar contains existing label/char
2132 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2133 <li>shorter peptide product names from EMBL records</li>
2134 <li>Newick string generator makes compact representations</li>
2135 <li>bootstrap values parsed correctly for tree files with
2137 <li>pathological filechooser bug avoided by not allowing
2138 filenames containing a ':'</li>
2139 <li>Fixed exception when parsing GFF files containing
2140 global sequence features</li>
2141 <li>Alignment datasets are finalized only when number of
2142 references from alignment sequences goes to zero</li>
2143 <li>Close of tree branch colour box without colour
2144 selection causes cascading exceptions</li>
2145 <li>occasional negative imgwidth exceptions</li>
2146 <li>better reporting of non-fatal warnings to user when
2147 file parsing fails.</li>
2148 <li>Save works when Jalview project is default format</li>
2149 <li>Save as dialog opened if current alignment format is
2150 not a valid output format</li>
2151 <li>UniProt canonical names introduced for both das and
2153 <li>Histidine should be midblue (not pink!) in Zappo</li>
2154 <li>error messages passed up and output when data read
2156 <li>edit undo recovers previous dataset sequence when
2157 sequence is edited</li>
2158 <li>allow PDB files without pdb ID HEADER lines (like
2159 those generated by MODELLER) to be read in properly</li>
2160 <li>allow reading of JPred concise files as a normal
2162 <li>Stockholm annotation parsing and alignment properties
2163 import fixed for PFAM records</li>
2164 <li>Structure view windows have correct name in Desktop
2166 <li>annotation consisting of sequence associated scores
2167 can be read and written correctly to annotation file</li>
2168 <li>Aligned cDNA translation to aligned peptide works
2170 <li>Fixed display of hidden sequence markers and
2171 non-italic font for representatives in Applet</li>
2172 <li>Applet Menus are always embedded in applet window on
2174 <li>Newly shown features appear at top of stack (in
2176 <li>Annotations added via parameter not drawn properly
2177 due to null pointer exceptions</li>
2178 <li>Secondary structure lines are drawn starting from
2179 first column of alignment</li>
2180 <li>UniProt XML import updated for new schema release in
2182 <li>Sequence feature to sequence ID match for Features
2183 file is case-insensitive</li>
2184 <li>Sequence features read from Features file appended to
2185 all sequences with matching IDs</li>
2186 <li>PDB structure coloured correctly for associated views
2187 containing a sub-sequence</li>
2188 <li>PDB files can be retrieved by applet from Jar files</li>
2189 <li>feature and annotation file applet parameters
2190 referring to different directories are retrieved correctly</li>
2191 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
2192 <li>Fixed application hang whilst waiting for
2193 splash-screen version check to complete</li>
2194 <li>Applet properly URLencodes input parameter values
2195 when passing them to the launchApp service</li>
2196 <li>display name and local features preserved in results
2197 retrieved from web service</li>
2198 <li>Visual delay indication for sequence retrieval and
2199 sequence fetcher initialisation</li>
2200 <li>updated Application to use DAS 1.53e version of
2201 dasobert DAS client</li>
2202 <li>Re-instated Full AMSA support and .amsa file
2204 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
2212 <div align="center">
2213 <strong>2.3</strong><br> 9/5/07
2218 <li>Jmol 11.0.2 integration</li>
2219 <li>PDB views stored in Jalview XML files</li>
2220 <li>Slide sequences</li>
2221 <li>Edit sequence in place</li>
2222 <li>EMBL CDS features</li>
2223 <li>DAS Feature mapping</li>
2224 <li>Feature ordering</li>
2225 <li>Alignment Properties</li>
2226 <li>Annotation Scores</li>
2227 <li>Sort by scores</li>
2228 <li>Feature/annotation editing in applet</li>
2233 <li>Headless state operation in 2.2.1</li>
2234 <li>Incorrect and unstable DNA pairwise alignment</li>
2235 <li>Cut and paste of sequences with annotation</li>
2236 <li>Feature group display state in XML</li>
2237 <li>Feature ordering in XML</li>
2238 <li>blc file iteration selection using filename # suffix</li>
2239 <li>Stockholm alignment properties</li>
2240 <li>Stockhom alignment secondary structure annotation</li>
2241 <li>2.2.1 applet had no feature transparency</li>
2242 <li>Number pad keys can be used in cursor mode</li>
2243 <li>Structure Viewer mirror image resolved</li>
2250 <div align="center">
2251 <strong>2.2.1</strong><br> 12/2/07
2256 <li>Non standard characters can be read and displayed
2257 <li>Annotations/Features can be imported/exported to the
2259 <li>Applet allows editing of sequence/annotation/group
2260 name & description
2261 <li>Preference setting to display sequence name in
2263 <li>Annotation file format extended to allow
2264 Sequence_groups to be defined
2265 <li>Default opening of alignment overview panel can be
2266 specified in preferences
2267 <li>PDB residue numbering annotation added to associated
2273 <li>Applet crash under certain Linux OS with Java 1.6
2275 <li>Annotation file export / import bugs fixed
2276 <li>PNG / EPS image output bugs fixed
2282 <div align="center">
2283 <strong>2.2</strong><br> 27/11/06
2288 <li>Multiple views on alignment
2289 <li>Sequence feature editing
2290 <li>"Reload" alignment
2291 <li>"Save" to current filename
2292 <li>Background dependent text colour
2293 <li>Right align sequence ids
2294 <li>User-defined lower case residue colours
2297 <li>Menu item accelerator keys
2298 <li>Control-V pastes to current alignment
2299 <li>Cancel button for DAS Feature Fetching
2300 <li>PCA and PDB Viewers zoom via mouse roller
2301 <li>User-defined sub-tree colours and sub-tree selection
2308 <li>'New Window' button on the 'Output to Text box'
2313 <li>New memory efficient Undo/Redo System
2314 <li>Optimised symbol lookups and conservation/consensus
2316 <li>Region Conservation/Consensus recalculated after
2318 <li>Fixed Remove Empty Columns Bug (empty columns at end
2320 <li>Slowed DAS Feature Fetching for increased robustness.
2327 <li>Made angle brackets in ASCII feature descriptions
2329 <li>Re-instated Zoom function for PCA
2330 <li>Sequence descriptions conserved in web service
2332 <li>UniProt ID discoverer uses any word separated by
2334 <li>WsDbFetch query/result association resolved
2335 <li>Tree leaf to sequence mapping improved
2336 <li>Smooth fonts switch moved to FontChooser dialog box.
2348 <div align="center">
2349 <strong>2.1.1</strong><br> 12/9/06
2354 <li>Copy consensus sequence to clipboard</li>
2359 <li>Image output - rightmost residues are rendered if
2360 sequence id panel has been resized</li>
2361 <li>Image output - all offscreen group boundaries are
2363 <li>Annotation files with sequence references - all
2364 elements in file are relative to sequence position</li>
2365 <li>Mac Applet users can use Alt key for group editing</li>
2371 <div align="center">
2372 <strong>2.1</strong><br> 22/8/06
2377 <li>MAFFT Multiple Alignment in default Web Service list</li>
2378 <li>DAS Feature fetching</li>
2379 <li>Hide sequences and columns</li>
2380 <li>Export Annotations and Features</li>
2381 <li>GFF file reading / writing</li>
2382 <li>Associate structures with sequences from local PDB
2384 <li>Add sequences to exisiting alignment</li>
2385 <li>Recently opened files / URL lists</li>
2386 <li>Applet can launch the full application</li>
2387 <li>Applet has transparency for features (Java 1.2
2389 <li>Applet has user defined colours parameter</li>
2390 <li>Applet can load sequences from parameter
2391 "sequence<em>x</em>"
2397 <li>Redundancy Panel reinstalled in the Applet</li>
2398 <li>Monospaced font - EPS / rescaling bug fixed</li>
2399 <li>Annotation files with sequence references bug fixed</li>
2405 <div align="center">
2406 <strong>2.08.1</strong><br> 2/5/06
2411 <li>Change case of selected region from Popup menu</li>
2412 <li>Choose to match case when searching</li>
2413 <li>Middle mouse button and mouse movement can compress /
2414 expand the visible width and height of the alignment</li>
2419 <li>Annotation Panel displays complete JNet results</li>
2425 <div align="center">
2426 <strong>2.08b</strong><br> 18/4/06
2432 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
2433 <li>Righthand label on wrapped alignments shows correct
2440 <div align="center">
2441 <strong>2.08</strong><br> 10/4/06
2446 <li>Editing can be locked to the selection area</li>
2447 <li>Keyboard editing</li>
2448 <li>Create sequence features from searches</li>
2449 <li>Precalculated annotations can be loaded onto
2451 <li>Features file allows grouping of features</li>
2452 <li>Annotation Colouring scheme added</li>
2453 <li>Smooth fonts off by default - Faster rendering</li>
2454 <li>Choose to toggle Autocalculate Consensus On/Off</li>
2459 <li>Drag & Drop fixed on Linux</li>
2460 <li>Jalview Archive file faster to load/save, sequence
2461 descriptions saved.</li>
2467 <div align="center">
2468 <strong>2.07</strong><br> 12/12/05
2473 <li>PDB Structure Viewer enhanced</li>
2474 <li>Sequence Feature retrieval and display enhanced</li>
2475 <li>Choose to output sequence start-end after sequence
2476 name for file output</li>
2477 <li>Sequence Fetcher WSDBFetch@EBI</li>
2478 <li>Applet can read feature files, PDB files and can be
2479 used for HTML form input</li>
2484 <li>HTML output writes groups and features</li>
2485 <li>Group editing is Control and mouse click</li>
2486 <li>File IO bugs</li>
2492 <div align="center">
2493 <strong>2.06</strong><br> 28/9/05
2498 <li>View annotations in wrapped mode</li>
2499 <li>More options for PCA viewer</li>
2504 <li>GUI bugs resolved</li>
2505 <li>Runs with -nodisplay from command line</li>
2511 <div align="center">
2512 <strong>2.05b</strong><br> 15/9/05
2517 <li>Choose EPS export as lineart or text</li>
2518 <li>Jar files are executable</li>
2519 <li>Can read in Uracil - maps to unknown residue</li>
2524 <li>Known OutOfMemory errors give warning message</li>
2525 <li>Overview window calculated more efficiently</li>
2526 <li>Several GUI bugs resolved</li>
2532 <div align="center">
2533 <strong>2.05</strong><br> 30/8/05
2538 <li>Edit and annotate in "Wrapped" view</li>
2543 <li>Several GUI bugs resolved</li>
2549 <div align="center">
2550 <strong>2.04</strong><br> 24/8/05
2555 <li>Hold down mouse wheel & scroll to change font
2561 <li>Improved JPred client reliability</li>
2562 <li>Improved loading of Jalview files</li>
2568 <div align="center">
2569 <strong>2.03</strong><br> 18/8/05
2574 <li>Set Proxy server name and port in preferences</li>
2575 <li>Multiple URL links from sequence ids</li>
2576 <li>User Defined Colours can have a scheme name and added
2578 <li>Choose to ignore gaps in consensus calculation</li>
2579 <li>Unix users can set default web browser</li>
2580 <li>Runs without GUI for batch processing</li>
2581 <li>Dynamically generated Web Service Menus</li>
2586 <li>InstallAnywhere download for Sparc Solaris</li>
2592 <div align="center">
2593 <strong>2.02</strong><br> 18/7/05
2599 <li>Copy & Paste order of sequences maintains
2600 alignment order.</li>
2606 <div align="center">
2607 <strong>2.01</strong><br> 12/7/05
2612 <li>Use delete key for deleting selection.</li>
2613 <li>Use Mouse wheel to scroll sequences.</li>
2614 <li>Help file updated to describe how to add alignment
2616 <li>Version and build date written to build properties
2618 <li>InstallAnywhere installation will check for updates
2619 at launch of Jalview.</li>
2624 <li>Delete gaps bug fixed.</li>
2625 <li>FileChooser sorts columns.</li>
2626 <li>Can remove groups one by one.</li>
2627 <li>Filechooser icons installed.</li>
2628 <li>Finder ignores return character when searching.
2629 Return key will initiate a search.<br>
2636 <div align="center">
2637 <strong>2.0</strong><br> 20/6/05
2642 <li>New codebase</li>