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.2.10.0">2.10.0</a><br /> <em>04/10/2016</em></strong>
56 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
57 for importing structure data to Jalview. Enables mmCIF and
61 <!-- JAL-192 --->Alignment ruler shows positions relative to
65 <!-- JAL-2202 -->Position/residue shown in status bar when
66 mousing over sequence associated annotation
69 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
73 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
74 '()', canonical '[]' and invalid '{}' base pair populations
78 <!-- JAL-2092 -->Feature settings popup menu options for
79 showing or hiding columns containing a feature
82 <!-- JAL-1557 -->Edit selected group by double clicking on
83 group and sequence associated annotation labels
86 <!-- JAL-2236 -->Sequence name added to annotation label in
87 select/hide columns by annotation and colour by annotation
91 </ul> <em>Application</em>
94 <!-- JAL-2050-->Automatically hide introns when opening a
98 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
102 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
103 structure mappings with the EMBL-EBI PDBe SIFTS database
106 <!-- JAL-2079 -->Updated download sites used for Rfam and
107 Pfam sources to xfam.org
110 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
113 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
114 over sequences in Jalview
117 <!-- JAL-2027-->Support for reverse-complement coding
118 regions in ENA and EMBL
121 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
122 for record retrieval via ENA rest API
125 <!-- JAL-2027 -->Support for ENA CDS records with reverse
129 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
130 groovy script execution
133 <!-- JAL-1812 -->New 'execute Groovy script' option in an
134 alignment window's Calculate menu
137 <!-- JAL-1812 -->Allow groovy scripts that call
138 Jalview.getAlignFrames() to run in headless mode
141 <!-- JAL-2068 -->Support for creating new alignment
142 calculation workers from groovy scripts
145 <!-- JAL-1369 --->Store/restore reference sequence in
149 <!-- JAL-1803 -->Chain codes for a sequence's PDB
150 associations are now saved/restored from project
153 <!-- JAL-1993 -->Database selection dialog always shown
154 before sequence fetcher is opened
157 <!-- JAL-2183 -->Double click on an entry in Jalview's
158 database chooser opens a sequence fetcher
161 <!-- JAL-1563 -->Free-text search client for UniProt using
165 <!-- JAL-2168 -->-nonews command line parameter to prevent
166 the news reader opening
169 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
170 querying stored in preferences
173 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
177 <!-- JAL-1977-->Tooltips shown on database chooser
180 <!-- JAL-391 -->Reverse complement function in calculate
181 menu for nucleotide sequences
184 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
185 and feature counts preserves alignment ordering (and
186 debugged for complex feature sets).
189 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
190 viewing structures with Jalview 2.10
193 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
194 genome, transcript CCDS and gene ids via the Ensembl and
195 Ensembl Genomes REST API
198 <!-- JAL-2049 -->Protein sequence variant annotation
199 computed for 'sequence_variant' annotation on CDS regions
203 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
207 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
208 Ref Fetcher fails to match, or otherwise updates sequence
209 data from external database records.
212 </ul> <!-- <em>Applet</em>
223 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
227 <!-- JAL-2018-->Export features in Jalview format (again)
228 includes graduated colourschemes
231 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
232 working with big alignments and lots of hidden columns
235 <!-- JAL-2053-->Hidden column markers not always rendered
236 at right of alignment window
239 <!-- JAL-2067 -->Tidied up links in help file table of
243 <!-- JAL-2072 -->Feature based tree calculation not shown
247 <!-- JAL-2075 -->Hidden columns ignored during feature
248 based tree calculation
251 <!-- JAL-2065 -->Alignment view stops updating when show
252 unconserved enabled for group on alignment
255 <!-- JAL-2086 -->Cannot insert gaps into sequence when
259 <!-- JAL-2146 -->Alignment column in status incorrectly
260 shown as "Sequence position" when mousing over
264 <!-- JAL-2099 -->Incorrect column numbers in ruler when
265 hidden columns present
268 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
269 user created annotation added to alignment
272 <!-- JAL-1841 -->RNA Structure consensus only computed for
273 '()' base pair annotation
276 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
277 in zero scores for all base pairs in RNA Structure
281 <!-- JAL-2174-->Extend selection with columns containing
285 <!-- JAL-2275 -->Pfam format writer puts extra space at
286 beginning of sequence
289 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
293 <!-- JAL-2238 -->Cannot create groups on an alignment from
294 from a tree when t-coffee scores are shown
297 <!-- JAL-1836,1967 -->Cannot import and view PDB
298 structures with chains containing negative resnums (4q4h)
301 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
305 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
306 to Clustal, PIR and PileUp output
309 <!-- JAL-2008 -->Reordering sequence features that are
310 not visible causes alignment window to repaint
313 <!-- JAL-2006 -->Threshold sliders don't work in
314 graduated colour and colour by annotation row for e-value
315 scores associated with features and annotation rows
318 <!-- JAL-1797 -->amino acid physicochemical conservation
319 calculation should be case independent
322 <!-- JAL-2173 -->Remove annotation also updates hidden
326 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
327 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
328 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
331 <!-- JAL-2065 -->Null pointer exceptions and redraw
332 problems when reference sequence defined and 'show
333 non-conserved' enabled
336 <!-- JAL-1306 -->Quality and Conservation are now shown on
337 load even when Consensus calculation is disabled
343 <!-- JAL-1552-->URLs and links can't be imported by
344 drag'n'drop on OSX when launched via webstart (note - not
345 yet fixed for El Capitan)
348 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
349 output when running on non-gb/us i18n platforms
352 <!-- JAL-1944 -->Error thrown when exporting a view with
353 hidden sequences as flat-file alignment
356 <!-- JAL-2030-->InstallAnywhere distribution fails when
360 <!-- JAL-2080-->Jalview very slow to launch via webstart
361 (also hotfix for 2.9.0b2)
364 <!-- JAL-2085 -->Cannot save project when view has a
365 reference sequence defined
368 <!-- JAL-1011 -->Columns are suddenly selected in other
369 alignments and views when revealing hidden columns
372 <!-- JAL-1989 -->Hide columns not mirrored in complement
373 view in a cDNA/Protein splitframe
376 <!-- JAL-1369 -->Cannot save/restore representative
377 sequence from project when only one sequence is
381 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
385 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
386 structure consensus didn't refresh annotation panel
389 <!-- JAL-1962 -->View mapping in structure view shows
390 mappings between sequence and all chains in a PDB file
393 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
394 dialogs format columns correctly, don't display array
395 data, sort columns according to type
398 <!-- JAL-1975 -->Export complete shown after destination
399 file chooser is cancelled during an image export
402 <!-- JAL-2025 -->Error when querying PDB Service with
403 sequence name containing special characters
406 <!-- JAL-2024 -->Manual PDB structure querying should be
410 <!-- JAL-2104 -->Large tooltips with broken HTML
411 formatting don't wrap
414 <!-- JAL-1128 -->Figures exported from wrapped view are
415 truncated so L looks like I in consensus annotation
418 <!-- JAL-2003 -->Export features should only export the
419 currently displayed features for the current selection or
423 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
424 after fetching cross-references
427 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
428 followed in the structure viewer
431 <!-- JAL-2163 -->Titles for individual alignments in
432 splitframe not restored from project
435 <!-- JAL-2145 -->missing autocalculated annotation at
436 trailing end of protein alignment in transcript/product
437 splitview when pad-gaps not enabled by default
440 <!-- JAL-1797 -->amino acid physicochemical conservation
444 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
445 article has been read (reopened issue due to
446 internationalisation problems)
449 <!-- JAL-1960 -->Only offer PDB structures in structure
450 viewer based on sequence name, PDB and UniProt
455 <!-- JAL-1976 -->No progress bar shown during export of
459 <!-- JAL-2213 -->Structures not always superimposed after
460 multiple structures are shown for one or more sequences.
463 <!-- JAL-1370 -->Reference sequence characters should not
464 be replaced with '.' when 'Show unconserved' format option
468 <!-- JAL-1823 -->Cannot specify chain code when entering
469 specific PDB id for sequence
472 <!-- JAL-1944 -->File->Export->.. as doesn't work when
473 'Export hidden sequences' is enabled, but 'export hidden
474 columns' is disabled.
477 <!--JAL-2026-->Best Quality option in structure chooser
478 selects lowest rather than highest resolution structures
482 <!-- JAL-1887 -->Incorrect start and end reported for PDB
483 to sequence mapping in 'View Mappings' report
485 <!-- may exclude, this is an external service stability issue JAL-1941
486 -- > RNA 3D structure not added via DSSR service</li> -->
491 <!-- JAL-2151 -->Incorrect columns are selected when
492 hidden columns present before start of sequence
495 <!-- JAL-1986 -->Missing dependencies on applet pages
499 <!-- JAL-1947 -->Overview pixel size changes when
500 sequences are hidden in applet
503 <!-- JAL-1996 -->Updated instructions for applet
504 deployment on examples pages.
511 <td width="60" nowrap>
513 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
514 <em>16/10/2015</em></strong>
519 <li>Time stamps for signed Jalview application and applet
526 <li>Duplicate group consensus and conservation rows
527 shown when tree is partitioned</li>
528 <li>Erratic behaviour when tree partitions made with
529 multiple cDNA/Protein split views</li>
535 <td width="60" nowrap>
537 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
538 <em>8/10/2015</em></strong>
543 <li>Updated Spanish translations of localized text for
545 </ul> <em>Application</em>
547 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
548 <li>Signed OSX InstallAnywhere installer<br></li>
549 <li>Support for per-sequence based annotations in BioJSON</li>
550 </ul> <em>Applet</em>
552 <li>Split frame example added to applet examples page</li>
558 <li>Mapping of cDNA to protein in split frames
559 incorrect when sequence start > 1</li>
560 <li>Broken images in filter column by annotation dialog
562 <li>Feature colours not parsed from features file</li>
563 <li>Exceptions and incomplete link URLs recovered when
564 loading a features file containing HTML tags in feature
570 <li>Annotations corrupted after BioJS export and
572 <li>Incorrect sequence limits after Fetch DB References
573 with 'trim retrieved sequences'</li>
574 <li>Incorrect warning about deleting all data when
575 deleting selected columns</li>
576 <li>Patch to build system for shipping properly signed
577 JNLP templates for webstart launch</li>
578 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
579 unreleased structures for download or viewing</li>
580 <li>Tab/space/return keystroke operation of EMBL-PDBe
581 fetcher/viewer dialogs works correctly</li>
582 <li>Disabled 'minimise' button on Jalview windows
583 running on OSX to workaround redraw hang bug</li>
584 <li>Split cDNA/Protein view position and geometry not
585 recovered from jalview project</li>
586 <li>Initial enabled/disabled state of annotation menu
587 sorter 'show autocalculated first/last' corresponds to
589 <li>Restoring of Clustal, RNA Helices and T-Coffee
590 color schemes from BioJSON</li>
594 <li>Reorder sequences mirrored in cDNA/Protein split
596 <li>Applet with Jmol examples not loading correctly</li>
602 <td><div align="center">
603 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
607 <li>Linked visualisation and analysis of DNA and Protein
610 <li>Translated cDNA alignments shown as split protein
611 and DNA alignment views</li>
612 <li>Codon consensus annotation for linked protein and
613 cDNA alignment views</li>
614 <li>Link cDNA or Protein product sequences by loading
615 them onto Protein or cDNA alignments</li>
616 <li>Reconstruct linked cDNA alignment from aligned
617 protein sequences</li>
620 <li>Jmol integration updated to Jmol v14.2.14</li>
621 <li>Import and export of Jalview alignment views as <a
622 href="features/bioJsonFormat.html">BioJSON</a></li>
623 <li>New alignment annotation file statements for
624 reference sequences and marking hidden columns</li>
625 <li>Reference sequence based alignment shading to
626 highlight variation</li>
627 <li>Select or hide columns according to alignment
629 <li>Find option for locating sequences by description</li>
630 <li>Conserved physicochemical properties shown in amino
631 acid conservation row</li>
632 <li>Alignments can be sorted by number of RNA helices</li>
633 </ul> <em>Application</em>
635 <li>New cDNA/Protein analysis capabilities
637 <li>Get Cross-References should open a Split Frame
638 view with cDNA/Protein</li>
639 <li>Detect when nucleotide sequences and protein
640 sequences are placed in the same alignment</li>
641 <li>Split cDNA/Protein views are saved in Jalview
646 <li>Use REST API to talk to Chimera</li>
647 <li>Selected regions in Chimera are highlighted in linked
650 <li>VARNA RNA viewer updated to v3.93</li>
651 <li>VARNA views are saved in Jalview Projects</li>
652 <li>Pseudoknots displayed as Jalview RNA annotation can
653 be shown in VARNA</li>
655 <li>Make groups for selection uses marked columns as well
656 as the active selected region</li>
658 <li>Calculate UPGMA and NJ trees using sequence feature
660 <li>New Export options
662 <li>New Export Settings dialog to control hidden
663 region export in flat file generation</li>
665 <li>Export alignment views for display with the <a
666 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
668 <li>Export scrollable SVG in HTML page</li>
669 <li>Optional embedding of BioJSON data when exporting
670 alignment figures to HTML</li>
672 <li>3D structure retrieval and display
674 <li>Free text and structured queries with the PDBe
676 <li>PDBe Search API based discovery and selection of
677 PDB structures for a sequence set</li>
681 <li>JPred4 employed for protein secondary structure
683 <li>Hide Insertions menu option to hide unaligned columns
684 for one or a group of sequences</li>
685 <li>Automatically hide insertions in alignments imported
686 from the JPred4 web server</li>
687 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
688 system on OSX<br />LGPL libraries courtesy of <a
689 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
691 <li>changed 'View nucleotide structure' submenu to 'View
692 VARNA 2D Structure'</li>
693 <li>change "View protein structure" menu option to "3D
696 </ul> <em>Applet</em>
698 <li>New layout for applet example pages</li>
699 <li>New parameters to enable SplitFrame view
700 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
701 <li>New example demonstrating linked viewing of cDNA and
702 Protein alignments</li>
703 </ul> <em>Development and deployment</em>
705 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
706 <li>Include installation type and git revision in build
707 properties and console log output</li>
708 <li>Jalview Github organisation, and new github site for
709 storing BioJsMSA Templates</li>
710 <li>Jalview's unit tests now managed with TestNG</li>
713 <!-- <em>General</em>
715 </ul> --> <!-- issues resolved --> <em>Application</em>
717 <li>Escape should close any open find dialogs</li>
718 <li>Typo in select-by-features status report</li>
719 <li>Consensus RNA secondary secondary structure
720 predictions are not highlighted in amber</li>
721 <li>Missing gap character in v2.7 example file means
722 alignment appears unaligned when pad-gaps is not enabled</li>
723 <li>First switch to RNA Helices colouring doesn't colour
724 associated structure views</li>
725 <li>ID width preference option is greyed out when auto
726 width checkbox not enabled</li>
727 <li>Stopped a warning dialog from being shown when
728 creating user defined colours</li>
729 <li>'View Mapping' in structure viewer shows sequence
730 mappings for just that viewer's sequences</li>
731 <li>Workaround for superposing PDB files containing
732 multiple models in Chimera</li>
733 <li>Report sequence position in status bar when hovering
734 over Jmol structure</li>
735 <li>Cannot output gaps as '.' symbols with Selection ->
736 output to text box</li>
737 <li>Flat file exports of alignments with hidden columns
738 have incorrect sequence start/end</li>
739 <li>'Aligning' a second chain to a Chimera structure from
741 <li>Colour schemes applied to structure viewers don't
742 work for nucleotide</li>
743 <li>Loading/cut'n'pasting an empty or invalid file leads
744 to a grey/invisible alignment window</li>
745 <li>Exported Jpred annotation from a sequence region
746 imports to different position</li>
747 <li>Space at beginning of sequence feature tooltips shown
748 on some platforms</li>
749 <li>Chimera viewer 'View | Show Chain' menu is not
751 <li>'New View' fails with a Null Pointer Exception in
752 console if Chimera has been opened</li>
753 <li>Mouseover to Chimera not working</li>
754 <li>Miscellaneous ENA XML feature qualifiers not
756 <li>NPE in annotation renderer after 'Extract Scores'</li>
757 <li>If two structures in one Chimera window, mouseover of
758 either sequence shows on first structure</li>
759 <li>'Show annotations' options should not make
760 non-positional annotations visible</li>
761 <li>Subsequence secondary structure annotation not shown
762 in right place after 'view flanking regions'</li>
763 <li>File Save As type unset when current file format is
765 <li>Save as '.jar' option removed for saving Jalview
767 <li>Colour by Sequence colouring in Chimera more
769 <li>Cannot 'add reference annotation' for a sequence in
770 several views on same alignment</li>
771 <li>Cannot show linked products for EMBL / ENA records</li>
772 <li>Jalview's tooltip wraps long texts containing no
774 </ul> <em>Applet</em>
776 <li>Jmol to JalviewLite mouseover/link not working</li>
777 <li>JalviewLite can't import sequences with ID
778 descriptions containing angle brackets</li>
779 </ul> <em>General</em>
781 <li>Cannot export and reimport RNA secondary structure
782 via jalview annotation file</li>
783 <li>Random helix colour palette for colour by annotation
784 with RNA secondary structure</li>
785 <li>Mouseover to cDNA from STOP residue in protein
786 translation doesn't work.</li>
787 <li>hints when using the select by annotation dialog box</li>
788 <li>Jmol alignment incorrect if PDB file has alternate CA
790 <li>FontChooser message dialog appears to hang after
791 choosing 1pt font</li>
792 <li>Peptide secondary structure incorrectly imported from
793 annotation file when annotation display text includes 'e' or
795 <li>Cannot set colour of new feature type whilst creating
797 <li>cDNA translation alignment should not be sequence
799 <li>'Show unconserved' doesn't work for lower case
801 <li>Nucleotide ambiguity codes involving R not recognised</li>
802 </ul> <em>Deployment and Documentation</em>
804 <li>Applet example pages appear different to the rest of
806 </ul> <em>Application Known issues</em>
808 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
809 <li>Misleading message appears after trying to delete
811 <li>Jalview icon not shown in dock after InstallAnywhere
812 version launches</li>
813 <li>Fetching EMBL reference for an RNA sequence results
814 fails with a sequence mismatch</li>
815 <li>Corrupted or unreadable alignment display when
816 scrolling alignment to right</li>
817 <li>ArrayIndexOutOfBoundsException thrown when remove
818 empty columns called on alignment with ragged gapped ends</li>
819 <li>auto calculated alignment annotation rows do not get
820 placed above or below non-autocalculated rows</li>
821 <li>Jalview dekstop becomes sluggish at full screen in
822 ultra-high resolution</li>
823 <li>Cannot disable consensus calculation independently of
824 quality and conservation</li>
825 <li>Mouseover highlighting between cDNA and protein can
826 become sluggish with more than one splitframe shown</li>
827 </ul> <em>Applet Known Issues</em>
829 <li>Core PDB parsing code requires Jmol</li>
830 <li>Sequence canvas panel goes white when alignment
831 window is being resized</li>
837 <td><div align="center">
838 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
842 <li>Updated Java code signing certificate donated by
844 <li>Features and annotation preserved when performing
845 pairwise alignment</li>
846 <li>RNA pseudoknot annotation can be
847 imported/exported/displayed</li>
848 <li>'colour by annotation' can colour by RNA and
849 protein secondary structure</li>
850 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
851 post-hoc with 2.9 release</em>)
854 </ul> <em>Application</em>
856 <li>Extract and display secondary structure for sequences
857 with 3D structures</li>
858 <li>Support for parsing RNAML</li>
859 <li>Annotations menu for layout
861 <li>sort sequence annotation rows by alignment</li>
862 <li>place sequence annotation above/below alignment
865 <li>Output in Stockholm format</li>
866 <li>Internationalisation: improved Spanish (es)
868 <li>Structure viewer preferences tab</li>
869 <li>Disorder and Secondary Structure annotation tracks
870 shared between alignments</li>
871 <li>UCSF Chimera launch and linked highlighting from
873 <li>Show/hide all sequence associated annotation rows for
874 all or current selection</li>
875 <li>disorder and secondary structure predictions
876 available as dataset annotation</li>
877 <li>Per-sequence rna helices colouring</li>
880 <li>Sequence database accessions imported when fetching
881 alignments from Rfam</li>
882 <li>update VARNA version to 3.91</li>
884 <li>New groovy scripts for exporting aligned positions,
885 conservation values, and calculating sum of pairs scores.</li>
886 <li>Command line argument to set default JABAWS server</li>
887 <li>include installation type in build properties and
888 console log output</li>
889 <li>Updated Jalview project format to preserve dataset
893 <!-- issues resolved --> <em>Application</em>
895 <li>Distinguish alignment and sequence associated RNA
896 structure in structure->view->VARNA</li>
897 <li>Raise dialog box if user deletes all sequences in an
899 <li>Pressing F1 results in documentation opening twice</li>
900 <li>Sequence feature tooltip is wrapped</li>
901 <li>Double click on sequence associated annotation
902 selects only first column</li>
903 <li>Redundancy removal doesn't result in unlinked
904 leaves shown in tree</li>
905 <li>Undos after several redundancy removals don't undo
907 <li>Hide sequence doesn't hide associated annotation</li>
908 <li>User defined colours dialog box too big to fit on
909 screen and buttons not visible</li>
910 <li>author list isn't updated if already written to
911 Jalview properties</li>
912 <li>Popup menu won't open after retrieving sequence
914 <li>File open window for associate PDB doesn't open</li>
915 <li>Left-then-right click on a sequence id opens a
916 browser search window</li>
917 <li>Cannot open sequence feature shading/sort popup menu
918 in feature settings dialog</li>
919 <li>better tooltip placement for some areas of Jalview
921 <li>Allow addition of JABAWS Server which doesn't
923 <li>Web services parameters dialog box is too large to
925 <li>Muscle nucleotide alignment preset obscured by
927 <li>JABAWS preset submenus don't contain newly
928 defined user preset</li>
929 <li>MSA web services warns user if they were launched
930 with invalid input</li>
931 <li>Jalview cannot contact DAS Registy when running on
934 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
935 'Superpose with' submenu not shown when new view
939 </ul> <!-- <em>Applet</em>
941 </ul> <em>General</em>
943 </ul>--> <em>Deployment and Documentation</em>
945 <li>2G and 1G options in launchApp have no effect on
946 memory allocation</li>
947 <li>launchApp service doesn't automatically open
948 www.jalview.org/examples/exampleFile.jar if no file is given</li>
950 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
951 InstallAnywhere reports cannot find valid JVM when Java
954 </ul> <em>Application Known issues</em>
957 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
958 corrupted or unreadable alignment display when scrolling
962 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
963 retrieval fails but progress bar continues for DAS retrieval
964 with large number of ID
967 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
968 flatfile output of visible region has incorrect sequence
972 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
973 rna structure consensus doesn't update when secondary
974 structure tracks are rearranged
977 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
978 invalid rna structure positional highlighting does not
979 highlight position of invalid base pairs
982 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
983 out of memory errors are not raised when saving Jalview
984 project from alignment window file menu
987 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
988 Switching to RNA Helices colouring doesn't propagate to
992 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
993 colour by RNA Helices not enabled when user created
994 annotation added to alignment
997 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
998 Jalview icon not shown on dock in Mountain Lion/Webstart
1000 </ul> <em>Applet Known Issues</em>
1003 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1004 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1007 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1008 Jalview and Jmol example not compatible with IE9
1011 <li>Sort by annotation score doesn't reverse order
1017 <td><div align="center">
1018 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1021 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1024 <li>Internationalisation of user interface (usually
1025 called i18n support) and translation for Spanish locale</li>
1026 <li>Define/Undefine group on current selection with
1027 Ctrl-G/Shift Ctrl-G</li>
1028 <li>Improved group creation/removal options in
1029 alignment/sequence Popup menu</li>
1030 <li>Sensible precision for symbol distribution
1031 percentages shown in logo tooltip.</li>
1032 <li>Annotation panel height set according to amount of
1033 annotation when alignment first opened</li>
1034 </ul> <em>Application</em>
1036 <li>Interactive consensus RNA secondary structure
1037 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1038 <li>Select columns containing particular features from
1039 Feature Settings dialog</li>
1040 <li>View all 'representative' PDB structures for selected
1042 <li>Update Jalview project format:
1044 <li>New file extension for Jalview projects '.jvp'</li>
1045 <li>Preserve sequence and annotation dataset (to
1046 store secondary structure annotation,etc)</li>
1047 <li>Per group and alignment annotation and RNA helix
1051 <li>New similarity measures for PCA and Tree calculation
1053 <li>Experimental support for retrieval and viewing of
1054 flanking regions for an alignment</li>
1058 <!-- issues resolved --> <em>Application</em>
1060 <li>logo keeps spinning and status remains at queued or
1061 running after job is cancelled</li>
1062 <li>cannot export features from alignments imported from
1063 Jalview/VAMSAS projects</li>
1064 <li>Buggy slider for web service parameters that take
1066 <li>Newly created RNA secondary structure line doesn't
1067 have 'display all symbols' flag set</li>
1068 <li>T-COFFEE alignment score shading scheme and other
1069 annotation shading not saved in Jalview project</li>
1070 <li>Local file cannot be loaded in freshly downloaded
1072 <li>Jalview icon not shown on dock in Mountain
1074 <li>Load file from desktop file browser fails</li>
1075 <li>Occasional NPE thrown when calculating large trees</li>
1076 <li>Cannot reorder or slide sequences after dragging an
1077 alignment onto desktop</li>
1078 <li>Colour by annotation dialog throws NPE after using
1079 'extract scores' function</li>
1080 <li>Loading/cut'n'pasting an empty file leads to a grey
1081 alignment window</li>
1082 <li>Disorder thresholds rendered incorrectly after
1083 performing IUPred disorder prediction</li>
1084 <li>Multiple group annotated consensus rows shown when
1085 changing 'normalise logo' display setting</li>
1086 <li>Find shows blank dialog after 'finished searching' if
1087 nothing matches query</li>
1088 <li>Null Pointer Exceptions raised when sorting by
1089 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1091 <li>Errors in Jmol console when structures in alignment
1092 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1094 <li>Not all working JABAWS services are shown in
1096 <li>JAVAWS version of Jalview fails to launch with
1097 'invalid literal/length code'</li>
1098 <li>Annotation/RNA Helix colourschemes cannot be applied
1099 to alignment with groups (actually fixed in 2.8.0b1)</li>
1100 <li>RNA Helices and T-Coffee Scores available as default
1103 </ul> <em>Applet</em>
1105 <li>Remove group option is shown even when selection is
1107 <li>Apply to all groups ticked but colourscheme changes
1108 don't affect groups</li>
1109 <li>Documented RNA Helices and T-Coffee Scores as valid
1110 colourscheme name</li>
1111 <li>Annotation labels drawn on sequence IDs when
1112 Annotation panel is not displayed</li>
1113 <li>Increased font size for dropdown menus on OSX and
1114 embedded windows</li>
1115 </ul> <em>Other</em>
1117 <li>Consensus sequence for alignments/groups with a
1118 single sequence were not calculated</li>
1119 <li>annotation files that contain only groups imported as
1120 annotation and junk sequences</li>
1121 <li>Fasta files with sequences containing '*' incorrectly
1122 recognised as PFAM or BLC</li>
1123 <li>conservation/PID slider apply all groups option
1124 doesn't affect background (2.8.0b1)
1126 <li>redundancy highlighting is erratic at 0% and 100%</li>
1127 <li>Remove gapped columns fails for sequences with ragged
1129 <li>AMSA annotation row with leading spaces is not
1130 registered correctly on import</li>
1131 <li>Jalview crashes when selecting PCA analysis for
1132 certain alignments</li>
1133 <li>Opening the colour by annotation dialog for an
1134 existing annotation based 'use original colours'
1135 colourscheme loses original colours setting</li>
1140 <td><div align="center">
1141 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
1142 <em>30/1/2014</em></strong>
1146 <li>Trusted certificates for JalviewLite applet and
1147 Jalview Desktop application<br />Certificate was donated by
1148 <a href="https://www.certum.eu">Certum</a> to the Jalview
1149 open source project).
1151 <li>Jalview SRS links replaced by UniProt and EBI-search
1153 <li>Output in Stockholm format</li>
1154 <li>Allow import of data from gzipped files</li>
1155 <li>Export/import group and sequence associated line
1156 graph thresholds</li>
1157 <li>Nucleotide substitution matrix that supports RNA and
1158 ambiguity codes</li>
1159 <li>Allow disorder predictions to be made on the current
1160 selection (or visible selection) in the same way that JPred
1162 <li>Groovy scripting for headless Jalview operation</li>
1163 </ul> <em>Other improvements</em>
1165 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
1166 <li>COMBINE statement uses current SEQUENCE_REF and
1167 GROUP_REF scope to group annotation rows</li>
1168 <li>Support '' style escaping of quotes in Newick
1170 <li>Group options for JABAWS service by command line name</li>
1171 <li>Empty tooltip shown for JABA service options with a
1172 link but no description</li>
1173 <li>Select primary source when selecting authority in
1174 database fetcher GUI</li>
1175 <li>Add .mfa to FASTA file extensions recognised by
1177 <li>Annotation label tooltip text wrap</li>
1182 <li>Slow scrolling when lots of annotation rows are
1184 <li>Lots of NPE (and slowness) after creating RNA
1185 secondary structure annotation line</li>
1186 <li>Sequence database accessions not imported when
1187 fetching alignments from Rfam</li>
1188 <li>Incorrect SHMR submission for sequences with
1190 <li>View all structures does not always superpose
1192 <li>Option widgets in service parameters not updated to
1193 reflect user or preset settings</li>
1194 <li>Null pointer exceptions for some services without
1195 presets or adjustable parameters</li>
1196 <li>Discover PDB IDs entry in structure menu doesn't
1197 discover PDB xRefs</li>
1198 <li>Exception encountered while trying to retrieve
1199 features with DAS</li>
1200 <li>Lowest value in annotation row isn't coloured
1201 when colour by annotation (per sequence) is coloured</li>
1202 <li>Keyboard mode P jumps to start of gapped region when
1203 residue follows a gap</li>
1204 <li>Jalview appears to hang importing an alignment with
1205 Wrap as default or after enabling Wrap</li>
1206 <li>'Right click to add annotations' message
1207 shown in wrap mode when no annotations present</li>
1208 <li>Disorder predictions fail with NPE if no automatic
1209 annotation already exists on alignment</li>
1210 <li>oninit javascript function should be called after
1211 initialisation completes</li>
1212 <li>Remove redundancy after disorder prediction corrupts
1213 alignment window display</li>
1214 <li>Example annotation file in documentation is invalid</li>
1215 <li>Grouped line graph annotation rows are not exported
1216 to annotation file</li>
1217 <li>Multi-harmony analysis cannot be run when only two
1219 <li>Cannot create multiple groups of line graphs with
1220 several 'combine' statements in annotation file</li>
1221 <li>Pressing return several times causes Number Format
1222 exceptions in keyboard mode</li>
1223 <li>Multi-harmony (SHMMR) method doesn't submit
1224 correct partitions for input data</li>
1225 <li>Translation from DNA to Amino Acids fails</li>
1226 <li>Jalview fail to load newick tree with quoted label</li>
1227 <li>--headless flag isn't understood</li>
1228 <li>ClassCastException when generating EPS in headless
1230 <li>Adjusting sequence-associated shading threshold only
1231 changes one row's threshold</li>
1232 <li>Preferences and Feature settings panel panel
1233 doesn't open</li>
1234 <li>hide consensus histogram also hides conservation and
1235 quality histograms</li>
1240 <td><div align="center">
1241 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
1243 <td><em>Application</em>
1245 <li>Support for JABAWS 2.0 Services (AACon alignment
1246 conservation, protein disorder and Clustal Omega)</li>
1247 <li>JABAWS server status indicator in Web Services
1249 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
1250 in Jalview alignment window</li>
1251 <li>Updated Jalview build and deploy framework for OSX
1252 mountain lion, windows 7, and 8</li>
1253 <li>Nucleotide substitution matrix for PCA that supports
1254 RNA and ambiguity codes</li>
1256 <li>Improved sequence database retrieval GUI</li>
1257 <li>Support fetching and database reference look up
1258 against multiple DAS sources (Fetch all from in 'fetch db
1260 <li>Jalview project improvements
1262 <li>Store and retrieve the 'belowAlignment'
1263 flag for annotation</li>
1264 <li>calcId attribute to group annotation rows on the
1266 <li>Store AACon calculation settings for a view in
1267 Jalview project</li>
1271 <li>horizontal scrolling gesture support</li>
1272 <li>Visual progress indicator when PCA calculation is
1274 <li>Simpler JABA web services menus</li>
1275 <li>visual indication that web service results are still
1276 being retrieved from server</li>
1277 <li>Serialise the dialogs that are shown when Jalview
1278 starts up for first time</li>
1279 <li>Jalview user agent string for interacting with HTTP
1281 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
1283 <li>Examples directory and Groovy library included in
1284 InstallAnywhere distribution</li>
1285 </ul> <em>Applet</em>
1287 <li>RNA alignment and secondary structure annotation
1288 visualization applet example</li>
1289 </ul> <em>General</em>
1291 <li>Normalise option for consensus sequence logo</li>
1292 <li>Reset button in PCA window to return dimensions to
1294 <li>Allow seqspace or Jalview variant of alignment PCA
1296 <li>PCA with either nucleic acid and protein substitution
1298 <li>Allow windows containing HTML reports to be exported
1300 <li>Interactive display and editing of RNA secondary
1301 structure contacts</li>
1302 <li>RNA Helix Alignment Colouring</li>
1303 <li>RNA base pair logo consensus</li>
1304 <li>Parse sequence associated secondary structure
1305 information in Stockholm files</li>
1306 <li>HTML Export database accessions and annotation
1307 information presented in tooltip for sequences</li>
1308 <li>Import secondary structure from LOCARNA clustalw
1309 style RNA alignment files</li>
1310 <li>import and visualise T-COFFEE quality scores for an
1312 <li>'colour by annotation' per sequence option to
1313 shade each sequence according to its associated alignment
1315 <li>New Jalview Logo</li>
1316 </ul> <em>Documentation and Development</em>
1318 <li>documentation for score matrices used in Jalview</li>
1319 <li>New Website!</li>
1321 <td><em>Application</em>
1323 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
1324 wsdbfetch REST service</li>
1325 <li>Stop windows being moved outside desktop on OSX</li>
1326 <li>Filetype associations not installed for webstart
1328 <li>Jalview does not always retrieve progress of a JABAWS
1329 job execution in full once it is complete</li>
1330 <li>revise SHMR RSBS definition to ensure alignment is
1331 uploaded via ali_file parameter</li>
1332 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
1333 <li>View all structures superposed fails with exception</li>
1334 <li>Jnet job queues forever if a very short sequence is
1335 submitted for prediction</li>
1336 <li>Cut and paste menu not opened when mouse clicked on
1338 <li>Putting fractional value into integer text box in
1339 alignment parameter dialog causes Jalview to hang</li>
1340 <li>Structure view highlighting doesn't work on
1342 <li>View all structures fails with exception shown in
1344 <li>Characters in filename associated with PDBEntry not
1345 escaped in a platform independent way</li>
1346 <li>Jalview desktop fails to launch with exception when
1348 <li>Tree calculation reports 'you must have 2 or more
1349 sequences selected' when selection is empty</li>
1350 <li>Jalview desktop fails to launch with jar signature
1351 failure when java web start temporary file caching is
1353 <li>DAS Sequence retrieval with range qualification
1354 results in sequence xref which includes range qualification</li>
1355 <li>Errors during processing of command line arguments
1356 cause progress bar (JAL-898) to be removed</li>
1357 <li>Replace comma for semi-colon option not disabled for
1358 DAS sources in sequence fetcher</li>
1359 <li>Cannot close news reader when JABAWS server warning
1360 dialog is shown</li>
1361 <li>Option widgets not updated to reflect user settings</li>
1362 <li>Edited sequence not submitted to web service</li>
1363 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
1364 <li>InstallAnywhere installer doesn't unpack and run
1365 on OSX Mountain Lion</li>
1366 <li>Annotation panel not given a scroll bar when
1367 sequences with alignment annotation are pasted into the
1369 <li>Sequence associated annotation rows not associated
1370 when loaded from Jalview project</li>
1371 <li>Browser launch fails with NPE on java 1.7</li>
1372 <li>JABAWS alignment marked as finished when job was
1373 cancelled or job failed due to invalid input</li>
1374 <li>NPE with v2.7 example when clicking on Tree
1375 associated with all views</li>
1376 <li>Exceptions when copy/paste sequences with grouped
1377 annotation rows to new window</li>
1378 </ul> <em>Applet</em>
1380 <li>Sequence features are momentarily displayed before
1381 they are hidden using hidefeaturegroups applet parameter</li>
1382 <li>loading features via javascript API automatically
1383 enables feature display</li>
1384 <li>scrollToColumnIn javascript API method doesn't
1386 </ul> <em>General</em>
1388 <li>Redundancy removal fails for rna alignment</li>
1389 <li>PCA calculation fails when sequence has been selected
1390 and then deselected</li>
1391 <li>PCA window shows grey box when first opened on OSX</li>
1392 <li>Letters coloured pink in sequence logo when alignment
1393 coloured with clustalx</li>
1394 <li>Choosing fonts without letter symbols defined causes
1395 exceptions and redraw errors</li>
1396 <li>Initial PCA plot view is not same as manually
1397 reconfigured view</li>
1398 <li>Grouped annotation graph label has incorrect line
1400 <li>Grouped annotation graph label display is corrupted
1401 for lots of labels</li>
1406 <div align="center">
1407 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
1410 <td><em>Application</em>
1412 <li>Jalview Desktop News Reader</li>
1413 <li>Tweaked default layout of web services menu</li>
1414 <li>View/alignment association menu to enable user to
1415 easily specify which alignment a multi-structure view takes
1416 its colours/correspondences from</li>
1417 <li>Allow properties file location to be specified as URL</li>
1418 <li>Extend Jalview project to preserve associations
1419 between many alignment views and a single Jmol display</li>
1420 <li>Store annotation row height in Jalview project file</li>
1421 <li>Annotation row column label formatting attributes
1422 stored in project file</li>
1423 <li>Annotation row order for auto-calculated annotation
1424 rows preserved in Jalview project file</li>
1425 <li>Visual progress indication when Jalview state is
1426 saved using Desktop window menu</li>
1427 <li>Visual indication that command line arguments are
1428 still being processed</li>
1429 <li>Groovy script execution from URL</li>
1430 <li>Colour by annotation default min and max colours in
1432 <li>Automatically associate PDB files dragged onto an
1433 alignment with sequences that have high similarity and
1435 <li>Update JGoogleAnalytics to latest release (0.3)</li>
1436 <li>'view structures' option to open many
1437 structures in same window</li>
1438 <li>Sort associated views menu option for tree panel</li>
1439 <li>Group all JABA and non-JABA services for a particular
1440 analysis function in its own submenu</li>
1441 </ul> <em>Applet</em>
1443 <li>Userdefined and autogenerated annotation rows for
1445 <li>Adjustment of alignment annotation pane height</li>
1446 <li>Annotation scrollbar for annotation panel</li>
1447 <li>Drag to reorder annotation rows in annotation panel</li>
1448 <li>'automaticScrolling' parameter</li>
1449 <li>Allow sequences with partial ID string matches to be
1450 annotated from GFF/Jalview features files</li>
1451 <li>Sequence logo annotation row in applet</li>
1452 <li>Absolute paths relative to host server in applet
1453 parameters are treated as such</li>
1454 <li>New in the JalviewLite javascript API:
1456 <li>JalviewLite.js javascript library</li>
1457 <li>Javascript callbacks for
1459 <li>Applet initialisation</li>
1460 <li>Sequence/alignment mouse-overs and selections</li>
1463 <li>scrollTo row and column alignment scrolling
1465 <li>Select sequence/alignment regions from javascript</li>
1466 <li>javascript structure viewer harness to pass
1467 messages between Jmol and Jalview when running as
1468 distinct applets</li>
1469 <li>sortBy method</li>
1470 <li>Set of applet and application examples shipped
1471 with documentation</li>
1472 <li>New example to demonstrate JalviewLite and Jmol
1473 javascript message exchange</li>
1475 </ul> <em>General</em>
1477 <li>Enable Jmol displays to be associated with multiple
1478 multiple alignments</li>
1479 <li>Option to automatically sort alignment with new tree</li>
1480 <li>User configurable link to enable redirects to a
1481 www.Jalview.org mirror</li>
1482 <li>Jmol colours option for Jmol displays</li>
1483 <li>Configurable newline string when writing alignment
1484 and other flat files</li>
1485 <li>Allow alignment annotation description lines to
1486 contain html tags</li>
1487 </ul> <em>Documentation and Development</em>
1489 <li>Add groovy test harness for bulk load testing to
1491 <li>Groovy script to load and align a set of sequences
1492 using a web service before displaying the result in the
1493 Jalview desktop</li>
1494 <li>Restructured javascript and applet api documentation</li>
1495 <li>Ant target to publish example html files with applet
1497 <li>Netbeans project for building Jalview from source</li>
1498 <li>ant task to create online javadoc for Jalview source</li>
1500 <td><em>Application</em>
1502 <li>User defined colourscheme throws exception when
1503 current built in colourscheme is saved as new scheme</li>
1504 <li>AlignFrame->Save in application pops up save
1505 dialog for valid filename/format</li>
1506 <li>Cannot view associated structure for UniProt sequence</li>
1507 <li>PDB file association breaks for UniProt sequence
1509 <li>Associate PDB from file dialog does not tell you
1510 which sequence is to be associated with the file</li>
1511 <li>Find All raises null pointer exception when query
1512 only matches sequence IDs</li>
1513 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
1514 <li>Jalview project with Jmol views created with Jalview
1515 2.4 cannot be loaded</li>
1516 <li>Filetype associations not installed for webstart
1518 <li>Two or more chains in a single PDB file associated
1519 with sequences in different alignments do not get coloured
1520 by their associated sequence</li>
1521 <li>Visibility status of autocalculated annotation row
1522 not preserved when project is loaded</li>
1523 <li>Annotation row height and visibility attributes not
1524 stored in Jalview project</li>
1525 <li>Tree bootstraps are not preserved when saved as a
1526 Jalview project</li>
1527 <li>Envision2 workflow tooltips are corrupted</li>
1528 <li>Enabling show group conservation also enables colour
1529 by conservation</li>
1530 <li>Duplicate group associated conservation or consensus
1531 created on new view</li>
1532 <li>Annotation scrollbar not displayed after 'show
1533 all hidden annotation rows' option selected</li>
1534 <li>Alignment quality not updated after alignment
1535 annotation row is hidden then shown</li>
1536 <li>Preserve colouring of structures coloured by
1537 sequences in pre Jalview 2.7 projects</li>
1538 <li>Web service job parameter dialog is not laid out
1540 <li>Web services menu not refreshed after 'reset
1541 services' button is pressed in preferences</li>
1542 <li>Annotation off by one in Jalview v2_3 example project</li>
1543 <li>Structures imported from file and saved in project
1544 get name like jalview_pdb1234.txt when reloaded</li>
1545 <li>Jalview does not always retrieve progress of a JABAWS
1546 job execution in full once it is complete</li>
1547 </ul> <em>Applet</em>
1549 <li>Alignment height set incorrectly when lots of
1550 annotation rows are displayed</li>
1551 <li>Relative URLs in feature HTML text not resolved to
1553 <li>View follows highlighting does not work for positions
1555 <li><= shown as = in tooltip</li>
1556 <li>Export features raises exception when no features
1558 <li>Separator string used for serialising lists of IDs
1559 for javascript api is modified when separator string
1560 provided as parameter</li>
1561 <li>Null pointer exception when selecting tree leaves for
1562 alignment with no existing selection</li>
1563 <li>Relative URLs for datasources assumed to be relative
1564 to applet's codebase</li>
1565 <li>Status bar not updated after finished searching and
1566 search wraps around to first result</li>
1567 <li>StructureSelectionManager instance shared between
1568 several Jalview applets causes race conditions and memory
1570 <li>Hover tooltip and mouseover of position on structure
1571 not sent from Jmol in applet</li>
1572 <li>Certain sequences of javascript method calls to
1573 applet API fatally hang browser</li>
1574 </ul> <em>General</em>
1576 <li>View follows structure mouseover scrolls beyond
1577 position with wrapped view and hidden regions</li>
1578 <li>Find sequence position moves to wrong residue
1579 with/without hidden columns</li>
1580 <li>Sequence length given in alignment properties window
1582 <li>InvalidNumberFormat exceptions thrown when trying to
1583 import PDB like structure files</li>
1584 <li>Positional search results are only highlighted
1585 between user-supplied sequence start/end bounds</li>
1586 <li>End attribute of sequence is not validated</li>
1587 <li>Find dialog only finds first sequence containing a
1588 given sequence position</li>
1589 <li>Sequence numbering not preserved in MSF alignment
1591 <li>Jalview PDB file reader does not extract sequence
1592 from nucleotide chains correctly</li>
1593 <li>Structure colours not updated when tree partition
1594 changed in alignment</li>
1595 <li>Sequence associated secondary structure not correctly
1596 parsed in interleaved stockholm</li>
1597 <li>Colour by annotation dialog does not restore current
1599 <li>Hiding (nearly) all sequences doesn't work
1601 <li>Sequences containing lowercase letters are not
1602 properly associated with their pdb files</li>
1603 </ul> <em>Documentation and Development</em>
1605 <li>schemas/JalviewWsParamSet.xsd corrupted by
1606 ApplyCopyright tool</li>
1611 <div align="center">
1612 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
1615 <td><em>Application</em>
1617 <li>New warning dialog when the Jalview Desktop cannot
1618 contact web services</li>
1619 <li>JABA service parameters for a preset are shown in
1620 service job window</li>
1621 <li>JABA Service menu entries reworded</li>
1625 <li>Modeller PIR IO broken - cannot correctly import a
1626 pir file emitted by Jalview</li>
1627 <li>Existing feature settings transferred to new
1628 alignment view created from cut'n'paste</li>
1629 <li>Improved test for mixed amino/nucleotide chains when
1630 parsing PDB files</li>
1631 <li>Consensus and conservation annotation rows
1632 occasionally become blank for all new windows</li>
1633 <li>Exception raised when right clicking above sequences
1634 in wrapped view mode</li>
1635 </ul> <em>Application</em>
1637 <li>multiple multiply aligned structure views cause cpu
1638 usage to hit 100% and computer to hang</li>
1639 <li>Web Service parameter layout breaks for long user
1640 parameter names</li>
1641 <li>Jaba service discovery hangs desktop if Jaba server
1648 <div align="center">
1649 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
1652 <td><em>Application</em>
1654 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
1655 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
1658 <li>Web Services preference tab</li>
1659 <li>Analysis parameters dialog box and user defined
1661 <li>Improved speed and layout of Envision2 service menu</li>
1662 <li>Superpose structures using associated sequence
1664 <li>Export coordinates and projection as CSV from PCA
1666 </ul> <em>Applet</em>
1668 <li>enable javascript: execution by the applet via the
1669 link out mechanism</li>
1670 </ul> <em>Other</em>
1672 <li>Updated the Jmol Jalview interface to work with Jmol
1674 <li>The Jalview Desktop and JalviewLite applet now
1675 require Java 1.5</li>
1676 <li>Allow Jalview feature colour specification for GFF
1677 sequence annotation files</li>
1678 <li>New 'colour by label' keword in Jalview feature file
1679 type colour specification</li>
1680 <li>New Jalview Desktop Groovy API method that allows a
1681 script to check if it being run in an interactive session or
1682 in a batch operation from the Jalview command line</li>
1686 <li>clustalx colourscheme colours Ds preferentially when
1687 both D+E are present in over 50% of the column</li>
1688 </ul> <em>Application</em>
1690 <li>typo in AlignmentFrame->View->Hide->all but
1691 selected Regions menu item</li>
1692 <li>sequence fetcher replaces ',' for ';' when the ',' is
1693 part of a valid accession ID</li>
1694 <li>fatal OOM if object retrieved by sequence fetcher
1695 runs out of memory</li>
1696 <li>unhandled Out of Memory Error when viewing pca
1697 analysis results</li>
1698 <li>InstallAnywhere builds fail to launch on OS X java
1699 10.5 update 4 (due to apple Java 1.6 update)</li>
1700 <li>Installanywhere Jalview silently fails to launch</li>
1701 </ul> <em>Applet</em>
1703 <li>Jalview.getFeatureGroups() raises an
1704 ArrayIndexOutOfBoundsException if no feature groups are
1711 <div align="center">
1712 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
1718 <li>Alignment prettyprinter doesn't cope with long
1720 <li>clustalx colourscheme colours Ds preferentially when
1721 both D+E are present in over 50% of the column</li>
1722 <li>nucleic acid structures retrieved from PDB do not
1723 import correctly</li>
1724 <li>More columns get selected than were clicked on when a
1725 number of columns are hidden</li>
1726 <li>annotation label popup menu not providing correct
1727 add/hide/show options when rows are hidden or none are
1729 <li>Stockholm format shown in list of readable formats,
1730 and parser copes better with alignments from RFAM.</li>
1731 <li>CSV output of consensus only includes the percentage
1732 of all symbols if sequence logo display is enabled</li>
1734 </ul> <em>Applet</em>
1736 <li>annotation panel disappears when annotation is
1738 </ul> <em>Application</em>
1740 <li>Alignment view not redrawn properly when new
1741 alignment opened where annotation panel is visible but no
1742 annotations are present on alignment</li>
1743 <li>pasted region containing hidden columns is
1744 incorrectly displayed in new alignment window</li>
1745 <li>Jalview slow to complete operations when stdout is
1746 flooded (fix is to close the Jalview console)</li>
1747 <li>typo in AlignmentFrame->View->Hide->all but
1748 selected Rregions menu item.</li>
1749 <li>inconsistent group submenu and Format submenu entry
1750 'Un' or 'Non'conserved</li>
1751 <li>Sequence feature settings are being shared by
1752 multiple distinct alignments</li>
1753 <li>group annotation not recreated when tree partition is
1755 <li>double click on group annotation to select sequences
1756 does not propagate to associated trees</li>
1757 <li>Mac OSX specific issues:
1759 <li>exception raised when mouse clicked on desktop
1760 window background</li>
1761 <li>Desktop menu placed on menu bar and application
1762 name set correctly</li>
1763 <li>sequence feature settings not wide enough for the
1764 save feature colourscheme button</li>
1773 <div align="center">
1774 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
1777 <td><em>New Capabilities</em>
1779 <li>URL links generated from description line for
1780 regular-expression based URL links (applet and application)
1787 <li>Non-positional feature URL links are shown in link
1789 <li>Linked viewing of nucleic acid sequences and
1791 <li>Automatic Scrolling option in View menu to display
1792 the currently highlighted region of an alignment.</li>
1793 <li>Order an alignment by sequence length, or using the
1794 average score or total feature count for each sequence.</li>
1795 <li>Shading features by score or associated description</li>
1796 <li>Subdivide alignment and groups based on identity of
1797 selected subsequence (Make Groups from Selection).</li>
1798 <li>New hide/show options including Shift+Control+H to
1799 hide everything but the currently selected region.</li>
1800 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
1801 </ul> <em>Application</em>
1803 <li>Fetch DB References capabilities and UI expanded to
1804 support retrieval from DAS sequence sources</li>
1805 <li>Local DAS Sequence sources can be added via the
1806 command line or via the Add local source dialog box.</li>
1807 <li>DAS Dbref and DbxRef feature types are parsed as
1808 database references and protein_name is parsed as
1809 description line (BioSapiens terms).</li>
1810 <li>Enable or disable non-positional feature and database
1811 references in sequence ID tooltip from View menu in
1813 <!-- <li>New hidden columns and rows and representatives capabilities
1814 in annotations file (in progress - not yet fully implemented)</li> -->
1815 <li>Group-associated consensus, sequence logos and
1816 conservation plots</li>
1817 <li>Symbol distributions for each column can be exported
1818 and visualized as sequence logos</li>
1819 <li>Optionally scale multi-character column labels to fit
1820 within each column of annotation row<!-- todo for applet -->
1822 <li>Optional automatic sort of associated alignment view
1823 when a new tree is opened.</li>
1824 <li>Jalview Java Console</li>
1825 <li>Better placement of desktop window when moving
1826 between different screens.</li>
1827 <li>New preference items for sequence ID tooltip and
1828 consensus annotation</li>
1829 <li>Client to submit sequences and IDs to Envision2
1831 <li><em>Vamsas Capabilities</em>
1833 <li>Improved VAMSAS synchronization (Jalview archive
1834 used to preserve views, structures, and tree display
1836 <li>Import of vamsas documents from disk or URL via
1838 <li>Sharing of selected regions between views and
1839 with other VAMSAS applications (Experimental feature!)</li>
1840 <li>Updated API to VAMSAS version 0.2</li>
1842 </ul> <em>Applet</em>
1844 <li>Middle button resizes annotation row height</li>
1847 <li>sortByTree (true/false) - automatically sort the
1848 associated alignment view by the tree when a new tree is
1850 <li>showTreeBootstraps (true/false) - show or hide
1851 branch bootstraps (default is to show them if available)</li>
1852 <li>showTreeDistances (true/false) - show or hide
1853 branch lengths (default is to show them if available)</li>
1854 <li>showUnlinkedTreeNodes (true/false) - indicate if
1855 unassociated nodes should be highlighted in the tree
1857 <li>heightScale and widthScale (1.0 or more) -
1858 increase the height or width of a cell in the alignment
1859 grid relative to the current font size.</li>
1862 <li>Non-positional features displayed in sequence ID
1864 </ul> <em>Other</em>
1866 <li>Features format: graduated colour definitions and
1867 specification of feature scores</li>
1868 <li>Alignment Annotations format: new keywords for group
1869 associated annotation (GROUP_REF) and annotation row display
1870 properties (ROW_PROPERTIES)</li>
1871 <li>XML formats extended to support graduated feature
1872 colourschemes, group associated annotation, and profile
1873 visualization settings.</li></td>
1876 <li>Source field in GFF files parsed as feature source
1877 rather than description</li>
1878 <li>Non-positional features are now included in sequence
1879 feature and gff files (controlled via non-positional feature
1880 visibility in tooltip).</li>
1881 <li>URL links generated for all feature links (bugfix)</li>
1882 <li>Added URL embedding instructions to features file
1884 <li>Codons containing ambiguous nucleotides translated as
1885 'X' in peptide product</li>
1886 <li>Match case switch in find dialog box works for both
1887 sequence ID and sequence string and query strings do not
1888 have to be in upper case to match case-insensitively.</li>
1889 <li>AMSA files only contain first column of
1890 multi-character column annotation labels</li>
1891 <li>Jalview Annotation File generation/parsing consistent
1892 with documentation (e.g. Stockholm annotation can be
1893 exported and re-imported)</li>
1894 <li>PDB files without embedded PDB IDs given a friendly
1896 <li>Find incrementally searches ID string matches as well
1897 as subsequence matches, and correctly reports total number
1901 <li>Better handling of exceptions during sequence
1903 <li>Dasobert generated non-positional feature URL
1904 link text excludes the start_end suffix</li>
1905 <li>DAS feature and source retrieval buttons disabled
1906 when fetch or registry operations in progress.</li>
1907 <li>PDB files retrieved from URLs are cached properly</li>
1908 <li>Sequence description lines properly shared via
1910 <li>Sequence fetcher fetches multiple records for all
1912 <li>Ensured that command line das feature retrieval
1913 completes before alignment figures are generated.</li>
1914 <li>Reduced time taken when opening file browser for
1916 <li>isAligned check prior to calculating tree, PCA or
1917 submitting an MSA to JNet now excludes hidden sequences.</li>
1918 <li>User defined group colours properly recovered
1919 from Jalview projects.</li>
1928 <div align="center">
1929 <strong>2.4.0.b2</strong><br> 28/10/2009
1934 <li>Experimental support for google analytics usage
1936 <li>Jalview privacy settings (user preferences and docs).</li>
1941 <li>Race condition in applet preventing startup in
1943 <li>Exception when feature created from selection beyond
1944 length of sequence.</li>
1945 <li>Allow synthetic PDB files to be imported gracefully</li>
1946 <li>Sequence associated annotation rows associate with
1947 all sequences with a given id</li>
1948 <li>Find function matches case-insensitively for sequence
1949 ID string searches</li>
1950 <li>Non-standard characters do not cause pairwise
1951 alignment to fail with exception</li>
1952 </ul> <em>Application Issues</em>
1954 <li>Sequences are now validated against EMBL database</li>
1955 <li>Sequence fetcher fetches multiple records for all
1957 </ul> <em>InstallAnywhere Issues</em>
1959 <li>Dock icon works for Mac OS X java (Mac 1.6 update
1960 issue with installAnywhere mechanism)</li>
1961 <li>Command line launching of JARs from InstallAnywhere
1962 version (java class versioning error fixed)</li>
1969 <div align="center">
1970 <strong>2.4</strong><br> 27/8/2008
1973 <td><em>User Interface</em>
1975 <li>Linked highlighting of codon and amino acid from
1976 translation and protein products</li>
1977 <li>Linked highlighting of structure associated with
1978 residue mapping to codon position</li>
1979 <li>Sequence Fetcher provides example accession numbers
1980 and 'clear' button</li>
1981 <li>MemoryMonitor added as an option under Desktop's
1983 <li>Extract score function to parse whitespace separated
1984 numeric data in description line</li>
1985 <li>Column labels in alignment annotation can be centred.</li>
1986 <li>Tooltip for sequence associated annotation give name
1988 </ul> <em>Web Services and URL fetching</em>
1990 <li>JPred3 web service</li>
1991 <li>Prototype sequence search client (no public services
1993 <li>Fetch either seed alignment or full alignment from
1995 <li>URL Links created for matching database cross
1996 references as well as sequence ID</li>
1997 <li>URL Links can be created using regular-expressions</li>
1998 </ul> <em>Sequence Database Connectivity</em>
2000 <li>Retrieval of cross-referenced sequences from other
2002 <li>Generalised database reference retrieval and
2003 validation to all fetchable databases</li>
2004 <li>Fetch sequences from DAS sources supporting the
2005 sequence command</li>
2006 </ul> <em>Import and Export</em>
2007 <li>export annotation rows as CSV for spreadsheet import</li>
2008 <li>Jalview projects record alignment dataset associations,
2009 EMBL products, and cDNA sequence mappings</li>
2010 <li>Sequence Group colour can be specified in Annotation
2012 <li>Ad-hoc colouring of group in Annotation File using RGB
2013 triplet as name of colourscheme</li>
2014 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2016 <li>treenode binding for VAMSAS tree exchange</li>
2017 <li>local editing and update of sequences in VAMSAS
2018 alignments (experimental)</li>
2019 <li>Create new or select existing session to join</li>
2020 <li>load and save of vamsas documents</li>
2021 </ul> <em>Application command line</em>
2023 <li>-tree parameter to open trees (introduced for passing
2025 <li>-fetchfrom command line argument to specify nicknames
2026 of DAS servers to query for alignment features</li>
2027 <li>-dasserver command line argument to add new servers
2028 that are also automatically queried for features</li>
2029 <li>-groovy command line argument executes a given groovy
2030 script after all input data has been loaded and parsed</li>
2031 </ul> <em>Applet-Application data exchange</em>
2033 <li>Trees passed as applet parameters can be passed to
2034 application (when using "View in full
2035 application")</li>
2036 </ul> <em>Applet Parameters</em>
2038 <li>feature group display control parameter</li>
2039 <li>debug parameter</li>
2040 <li>showbutton parameter</li>
2041 </ul> <em>Applet API methods</em>
2043 <li>newView public method</li>
2044 <li>Window (current view) specific get/set public methods</li>
2045 <li>Feature display control methods</li>
2046 <li>get list of currently selected sequences</li>
2047 </ul> <em>New Jalview distribution features</em>
2049 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2050 <li>RELEASE file gives build properties for the latest
2051 Jalview release.</li>
2052 <li>Java 1.1 Applet build made easier and donotobfuscate
2053 property controls execution of obfuscator</li>
2054 <li>Build target for generating source distribution</li>
2055 <li>Debug flag for javacc</li>
2056 <li>.jalview_properties file is documented (slightly) in
2057 jalview.bin.Cache</li>
2058 <li>Continuous Build Integration for stable and
2059 development version of Application, Applet and source
2064 <li>selected region output includes visible annotations
2065 (for certain formats)</li>
2066 <li>edit label/displaychar contains existing label/char
2068 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2069 <li>shorter peptide product names from EMBL records</li>
2070 <li>Newick string generator makes compact representations</li>
2071 <li>bootstrap values parsed correctly for tree files with
2073 <li>pathological filechooser bug avoided by not allowing
2074 filenames containing a ':'</li>
2075 <li>Fixed exception when parsing GFF files containing
2076 global sequence features</li>
2077 <li>Alignment datasets are finalized only when number of
2078 references from alignment sequences goes to zero</li>
2079 <li>Close of tree branch colour box without colour
2080 selection causes cascading exceptions</li>
2081 <li>occasional negative imgwidth exceptions</li>
2082 <li>better reporting of non-fatal warnings to user when
2083 file parsing fails.</li>
2084 <li>Save works when Jalview project is default format</li>
2085 <li>Save as dialog opened if current alignment format is
2086 not a valid output format</li>
2087 <li>UniProt canonical names introduced for both das and
2089 <li>Histidine should be midblue (not pink!) in Zappo</li>
2090 <li>error messages passed up and output when data read
2092 <li>edit undo recovers previous dataset sequence when
2093 sequence is edited</li>
2094 <li>allow PDB files without pdb ID HEADER lines (like
2095 those generated by MODELLER) to be read in properly</li>
2096 <li>allow reading of JPred concise files as a normal
2098 <li>Stockholm annotation parsing and alignment properties
2099 import fixed for PFAM records</li>
2100 <li>Structure view windows have correct name in Desktop
2102 <li>annotation consisting of sequence associated scores
2103 can be read and written correctly to annotation file</li>
2104 <li>Aligned cDNA translation to aligned peptide works
2106 <li>Fixed display of hidden sequence markers and
2107 non-italic font for representatives in Applet</li>
2108 <li>Applet Menus are always embedded in applet window on
2110 <li>Newly shown features appear at top of stack (in
2112 <li>Annotations added via parameter not drawn properly
2113 due to null pointer exceptions</li>
2114 <li>Secondary structure lines are drawn starting from
2115 first column of alignment</li>
2116 <li>UniProt XML import updated for new schema release in
2118 <li>Sequence feature to sequence ID match for Features
2119 file is case-insensitive</li>
2120 <li>Sequence features read from Features file appended to
2121 all sequences with matching IDs</li>
2122 <li>PDB structure coloured correctly for associated views
2123 containing a sub-sequence</li>
2124 <li>PDB files can be retrieved by applet from Jar files</li>
2125 <li>feature and annotation file applet parameters
2126 referring to different directories are retrieved correctly</li>
2127 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
2128 <li>Fixed application hang whilst waiting for
2129 splash-screen version check to complete</li>
2130 <li>Applet properly URLencodes input parameter values
2131 when passing them to the launchApp service</li>
2132 <li>display name and local features preserved in results
2133 retrieved from web service</li>
2134 <li>Visual delay indication for sequence retrieval and
2135 sequence fetcher initialisation</li>
2136 <li>updated Application to use DAS 1.53e version of
2137 dasobert DAS client</li>
2138 <li>Re-instated Full AMSA support and .amsa file
2140 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
2148 <div align="center">
2149 <strong>2.3</strong><br> 9/5/07
2154 <li>Jmol 11.0.2 integration</li>
2155 <li>PDB views stored in Jalview XML files</li>
2156 <li>Slide sequences</li>
2157 <li>Edit sequence in place</li>
2158 <li>EMBL CDS features</li>
2159 <li>DAS Feature mapping</li>
2160 <li>Feature ordering</li>
2161 <li>Alignment Properties</li>
2162 <li>Annotation Scores</li>
2163 <li>Sort by scores</li>
2164 <li>Feature/annotation editing in applet</li>
2169 <li>Headless state operation in 2.2.1</li>
2170 <li>Incorrect and unstable DNA pairwise alignment</li>
2171 <li>Cut and paste of sequences with annotation</li>
2172 <li>Feature group display state in XML</li>
2173 <li>Feature ordering in XML</li>
2174 <li>blc file iteration selection using filename # suffix</li>
2175 <li>Stockholm alignment properties</li>
2176 <li>Stockhom alignment secondary structure annotation</li>
2177 <li>2.2.1 applet had no feature transparency</li>
2178 <li>Number pad keys can be used in cursor mode</li>
2179 <li>Structure Viewer mirror image resolved</li>
2186 <div align="center">
2187 <strong>2.2.1</strong><br> 12/2/07
2192 <li>Non standard characters can be read and displayed
2193 <li>Annotations/Features can be imported/exported to the
2195 <li>Applet allows editing of sequence/annotation/group
2196 name & description
2197 <li>Preference setting to display sequence name in
2199 <li>Annotation file format extended to allow
2200 Sequence_groups to be defined
2201 <li>Default opening of alignment overview panel can be
2202 specified in preferences
2203 <li>PDB residue numbering annotation added to associated
2209 <li>Applet crash under certain Linux OS with Java 1.6
2211 <li>Annotation file export / import bugs fixed
2212 <li>PNG / EPS image output bugs fixed
2218 <div align="center">
2219 <strong>2.2</strong><br> 27/11/06
2224 <li>Multiple views on alignment
2225 <li>Sequence feature editing
2226 <li>"Reload" alignment
2227 <li>"Save" to current filename
2228 <li>Background dependent text colour
2229 <li>Right align sequence ids
2230 <li>User-defined lower case residue colours
2233 <li>Menu item accelerator keys
2234 <li>Control-V pastes to current alignment
2235 <li>Cancel button for DAS Feature Fetching
2236 <li>PCA and PDB Viewers zoom via mouse roller
2237 <li>User-defined sub-tree colours and sub-tree selection
2244 <li>'New Window' button on the 'Output to Text box'
2249 <li>New memory efficient Undo/Redo System
2250 <li>Optimised symbol lookups and conservation/consensus
2252 <li>Region Conservation/Consensus recalculated after
2254 <li>Fixed Remove Empty Columns Bug (empty columns at end
2256 <li>Slowed DAS Feature Fetching for increased robustness.
2263 <li>Made angle brackets in ASCII feature descriptions
2265 <li>Re-instated Zoom function for PCA
2266 <li>Sequence descriptions conserved in web service
2268 <li>UniProt ID discoverer uses any word separated by
2270 <li>WsDbFetch query/result association resolved
2271 <li>Tree leaf to sequence mapping improved
2272 <li>Smooth fonts switch moved to FontChooser dialog box.
2284 <div align="center">
2285 <strong>2.1.1</strong><br> 12/9/06
2290 <li>Copy consensus sequence to clipboard</li>
2295 <li>Image output - rightmost residues are rendered if
2296 sequence id panel has been resized</li>
2297 <li>Image output - all offscreen group boundaries are
2299 <li>Annotation files with sequence references - all
2300 elements in file are relative to sequence position</li>
2301 <li>Mac Applet users can use Alt key for group editing</li>
2307 <div align="center">
2308 <strong>2.1</strong><br> 22/8/06
2313 <li>MAFFT Multiple Alignment in default Web Service list</li>
2314 <li>DAS Feature fetching</li>
2315 <li>Hide sequences and columns</li>
2316 <li>Export Annotations and Features</li>
2317 <li>GFF file reading / writing</li>
2318 <li>Associate structures with sequences from local PDB
2320 <li>Add sequences to exisiting alignment</li>
2321 <li>Recently opened files / URL lists</li>
2322 <li>Applet can launch the full application</li>
2323 <li>Applet has transparency for features (Java 1.2
2325 <li>Applet has user defined colours parameter</li>
2326 <li>Applet can load sequences from parameter
2327 "sequence<em>x</em>"
2333 <li>Redundancy Panel reinstalled in the Applet</li>
2334 <li>Monospaced font - EPS / rescaling bug fixed</li>
2335 <li>Annotation files with sequence references bug fixed</li>
2341 <div align="center">
2342 <strong>2.08.1</strong><br> 2/5/06
2347 <li>Change case of selected region from Popup menu</li>
2348 <li>Choose to match case when searching</li>
2349 <li>Middle mouse button and mouse movement can compress /
2350 expand the visible width and height of the alignment</li>
2355 <li>Annotation Panel displays complete JNet results</li>
2361 <div align="center">
2362 <strong>2.08b</strong><br> 18/4/06
2368 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
2369 <li>Righthand label on wrapped alignments shows correct
2376 <div align="center">
2377 <strong>2.08</strong><br> 10/4/06
2382 <li>Editing can be locked to the selection area</li>
2383 <li>Keyboard editing</li>
2384 <li>Create sequence features from searches</li>
2385 <li>Precalculated annotations can be loaded onto
2387 <li>Features file allows grouping of features</li>
2388 <li>Annotation Colouring scheme added</li>
2389 <li>Smooth fonts off by default - Faster rendering</li>
2390 <li>Choose to toggle Autocalculate Consensus On/Off</li>
2395 <li>Drag & Drop fixed on Linux</li>
2396 <li>Jalview Archive file faster to load/save, sequence
2397 descriptions saved.</li>
2403 <div align="center">
2404 <strong>2.07</strong><br> 12/12/05
2409 <li>PDB Structure Viewer enhanced</li>
2410 <li>Sequence Feature retrieval and display enhanced</li>
2411 <li>Choose to output sequence start-end after sequence
2412 name for file output</li>
2413 <li>Sequence Fetcher WSDBFetch@EBI</li>
2414 <li>Applet can read feature files, PDB files and can be
2415 used for HTML form input</li>
2420 <li>HTML output writes groups and features</li>
2421 <li>Group editing is Control and mouse click</li>
2422 <li>File IO bugs</li>
2428 <div align="center">
2429 <strong>2.06</strong><br> 28/9/05
2434 <li>View annotations in wrapped mode</li>
2435 <li>More options for PCA viewer</li>
2440 <li>GUI bugs resolved</li>
2441 <li>Runs with -nodisplay from command line</li>
2447 <div align="center">
2448 <strong>2.05b</strong><br> 15/9/05
2453 <li>Choose EPS export as lineart or text</li>
2454 <li>Jar files are executable</li>
2455 <li>Can read in Uracil - maps to unknown residue</li>
2460 <li>Known OutOfMemory errors give warning message</li>
2461 <li>Overview window calculated more efficiently</li>
2462 <li>Several GUI bugs resolved</li>
2468 <div align="center">
2469 <strong>2.05</strong><br> 30/8/05
2474 <li>Edit and annotate in "Wrapped" view</li>
2479 <li>Several GUI bugs resolved</li>
2485 <div align="center">
2486 <strong>2.04</strong><br> 24/8/05
2491 <li>Hold down mouse wheel & scroll to change font
2497 <li>Improved JPred client reliability</li>
2498 <li>Improved loading of Jalview files</li>
2504 <div align="center">
2505 <strong>2.03</strong><br> 18/8/05
2510 <li>Set Proxy server name and port in preferences</li>
2511 <li>Multiple URL links from sequence ids</li>
2512 <li>User Defined Colours can have a scheme name and added
2514 <li>Choose to ignore gaps in consensus calculation</li>
2515 <li>Unix users can set default web browser</li>
2516 <li>Runs without GUI for batch processing</li>
2517 <li>Dynamically generated Web Service Menus</li>
2522 <li>InstallAnywhere download for Sparc Solaris</li>
2528 <div align="center">
2529 <strong>2.02</strong><br> 18/7/05
2535 <li>Copy & Paste order of sequences maintains
2536 alignment order.</li>
2542 <div align="center">
2543 <strong>2.01</strong><br> 12/7/05
2548 <li>Use delete key for deleting selection.</li>
2549 <li>Use Mouse wheel to scroll sequences.</li>
2550 <li>Help file updated to describe how to add alignment
2552 <li>Version and build date written to build properties
2554 <li>InstallAnywhere installation will check for updates
2555 at launch of Jalview.</li>
2560 <li>Delete gaps bug fixed.</li>
2561 <li>FileChooser sorts columns.</li>
2562 <li>Can remove groups one by one.</li>
2563 <li>Filechooser icons installed.</li>
2564 <li>Finder ignores return character when searching.
2565 Return key will initiate a search.<br>
2572 <div align="center">
2573 <strong>2.0</strong><br> 20/6/05
2578 <li>New codebase</li>