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.2.9.0b2">2.10.0b1</a><br />
51 <em>18/10/2016</em></strong>
54 <td><em>Application</em>
66 <td width="60" nowrap>
68 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
74 <!-- JAL-2124 -->Updated Spanish translations.
77 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
78 for importing structure data to Jalview. Enables mmCIF and
82 <!-- JAL-192 --->Alignment ruler shows positions relative to
86 <!-- JAL-2202 -->Position/residue shown in status bar when
87 mousing over sequence associated annotation
90 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
94 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
95 '()', canonical '[]' and invalid '{}' base pair populations
99 <!-- JAL-2092 -->Feature settings popup menu options for
100 showing or hiding columns containing a feature
103 <!-- JAL-1557 -->Edit selected group by double clicking on
104 group and sequence associated annotation labels
107 <!-- JAL-2236 -->Sequence name added to annotation label in
108 select/hide columns by annotation and colour by annotation
112 </ul> <em>Application</em>
115 <!-- JAL-2050-->Automatically hide introns when opening a
119 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
123 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
124 structure mappings with the EMBL-EBI PDBe SIFTS database
127 <!-- JAL-2079 -->Updated download sites used for Rfam and
128 Pfam sources to xfam.org
131 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
134 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
135 over sequences in Jalview
138 <!-- JAL-2027-->Support for reverse-complement coding
139 regions in ENA and EMBL
142 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
143 for record retrieval via ENA rest API
146 <!-- JAL-2027 -->Support for ENA CDS records with reverse
150 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
151 groovy script execution
154 <!-- JAL-1812 -->New 'execute Groovy script' option in an
155 alignment window's Calculate menu
158 <!-- JAL-1812 -->Allow groovy scripts that call
159 Jalview.getAlignFrames() to run in headless mode
162 <!-- JAL-2068 -->Support for creating new alignment
163 calculation workers from groovy scripts
166 <!-- JAL-1369 --->Store/restore reference sequence in
170 <!-- JAL-1803 -->Chain codes for a sequence's PDB
171 associations are now saved/restored from project
174 <!-- JAL-1993 -->Database selection dialog always shown
175 before sequence fetcher is opened
178 <!-- JAL-2183 -->Double click on an entry in Jalview's
179 database chooser opens a sequence fetcher
182 <!-- JAL-1563 -->Free-text search client for UniProt using
186 <!-- JAL-2168 -->-nonews command line parameter to prevent
187 the news reader opening
190 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
191 querying stored in preferences
194 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
198 <!-- JAL-1977-->Tooltips shown on database chooser
201 <!-- JAL-391 -->Reverse complement function in calculate
202 menu for nucleotide sequences
205 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
206 and feature counts preserves alignment ordering (and
207 debugged for complex feature sets).
210 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
211 viewing structures with Jalview 2.10
214 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
215 genome, transcript CCDS and gene ids via the Ensembl and
216 Ensembl Genomes REST API
219 <!-- JAL-2049 -->Protein sequence variant annotation
220 computed for 'sequence_variant' annotation on CDS regions
224 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
228 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
229 Ref Fetcher fails to match, or otherwise updates sequence
230 data from external database records.
233 <!-- JAL-2154 -->Revised Jalview Project format for
234 efficient recovery of sequence coding and alignment
235 annotation relationships.
237 </ul> <!-- <em>Applet</em>
248 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
252 <!-- JAL-2018-->Export features in Jalview format (again)
253 includes graduated colourschemes
256 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
257 working with big alignments and lots of hidden columns
260 <!-- JAL-2053-->Hidden column markers not always rendered
261 at right of alignment window
264 <!-- JAL-2067 -->Tidied up links in help file table of
268 <!-- JAL-2072 -->Feature based tree calculation not shown
272 <!-- JAL-2075 -->Hidden columns ignored during feature
273 based tree calculation
276 <!-- JAL-2065 -->Alignment view stops updating when show
277 unconserved enabled for group on alignment
280 <!-- JAL-2086 -->Cannot insert gaps into sequence when
284 <!-- JAL-2146 -->Alignment column in status incorrectly
285 shown as "Sequence position" when mousing over
289 <!-- JAL-2099 -->Incorrect column numbers in ruler when
290 hidden columns present
293 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
294 user created annotation added to alignment
297 <!-- JAL-1841 -->RNA Structure consensus only computed for
298 '()' base pair annotation
301 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
302 in zero scores for all base pairs in RNA Structure
306 <!-- JAL-2174-->Extend selection with columns containing
310 <!-- JAL-2275 -->Pfam format writer puts extra space at
311 beginning of sequence
314 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
318 <!-- JAL-2238 -->Cannot create groups on an alignment from
319 from a tree when t-coffee scores are shown
322 <!-- JAL-1836,1967 -->Cannot import and view PDB
323 structures with chains containing negative resnums (4q4h)
326 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
330 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
331 to Clustal, PIR and PileUp output
334 <!-- JAL-2008 -->Reordering sequence features that are
335 not visible causes alignment window to repaint
338 <!-- JAL-2006 -->Threshold sliders don't work in
339 graduated colour and colour by annotation row for e-value
340 scores associated with features and annotation rows
343 <!-- JAL-1797 -->amino acid physicochemical conservation
344 calculation should be case independent
347 <!-- JAL-2173 -->Remove annotation also updates hidden
351 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
352 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
353 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
356 <!-- JAL-2065 -->Null pointer exceptions and redraw
357 problems when reference sequence defined and 'show
358 non-conserved' enabled
361 <!-- JAL-1306 -->Quality and Conservation are now shown on
362 load even when Consensus calculation is disabled
368 <!-- JAL-1552-->URLs and links can't be imported by
369 drag'n'drop on OSX when launched via webstart (note - not
370 yet fixed for El Capitan)
373 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
374 output when running on non-gb/us i18n platforms
377 <!-- JAL-1944 -->Error thrown when exporting a view with
378 hidden sequences as flat-file alignment
381 <!-- JAL-2030-->InstallAnywhere distribution fails when
385 <!-- JAL-2080-->Jalview very slow to launch via webstart
386 (also hotfix for 2.9.0b2)
389 <!-- JAL-2085 -->Cannot save project when view has a
390 reference sequence defined
393 <!-- JAL-1011 -->Columns are suddenly selected in other
394 alignments and views when revealing hidden columns
397 <!-- JAL-1989 -->Hide columns not mirrored in complement
398 view in a cDNA/Protein splitframe
401 <!-- JAL-1369 -->Cannot save/restore representative
402 sequence from project when only one sequence is
406 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
410 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
411 structure consensus didn't refresh annotation panel
414 <!-- JAL-1962 -->View mapping in structure view shows
415 mappings between sequence and all chains in a PDB file
418 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
419 dialogs format columns correctly, don't display array
420 data, sort columns according to type
423 <!-- JAL-1975 -->Export complete shown after destination
424 file chooser is cancelled during an image export
427 <!-- JAL-2025 -->Error when querying PDB Service with
428 sequence name containing special characters
431 <!-- JAL-2024 -->Manual PDB structure querying should be
435 <!-- JAL-2104 -->Large tooltips with broken HTML
436 formatting don't wrap
439 <!-- JAL-1128 -->Figures exported from wrapped view are
440 truncated so L looks like I in consensus annotation
443 <!-- JAL-2003 -->Export features should only export the
444 currently displayed features for the current selection or
448 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
449 after fetching cross-references, and restoring from project
452 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
453 followed in the structure viewer
456 <!-- JAL-2163 -->Titles for individual alignments in
457 splitframe not restored from project
460 <!-- JAL-2145 -->missing autocalculated annotation at
461 trailing end of protein alignment in transcript/product
462 splitview when pad-gaps not enabled by default
465 <!-- JAL-1797 -->amino acid physicochemical conservation
469 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
470 article has been read (reopened issue due to
471 internationalisation problems)
474 <!-- JAL-1960 -->Only offer PDB structures in structure
475 viewer based on sequence name, PDB and UniProt
480 <!-- JAL-1976 -->No progress bar shown during export of
484 <!-- JAL-2213 -->Structures not always superimposed after
485 multiple structures are shown for one or more sequences.
488 <!-- JAL-1370 -->Reference sequence characters should not
489 be replaced with '.' when 'Show unconserved' format option
493 <!-- JAL-1823 -->Cannot specify chain code when entering
494 specific PDB id for sequence
497 <!-- JAL-1944 -->File->Export->.. as doesn't work when
498 'Export hidden sequences' is enabled, but 'export hidden
499 columns' is disabled.
502 <!--JAL-2026-->Best Quality option in structure chooser
503 selects lowest rather than highest resolution structures
507 <!-- JAL-1887 -->Incorrect start and end reported for PDB
508 to sequence mapping in 'View Mappings' report
510 <!-- may exclude, this is an external service stability issue JAL-1941
511 -- > RNA 3D structure not added via DSSR service</li> -->
516 <!-- JAL-2151 -->Incorrect columns are selected when
517 hidden columns present before start of sequence
520 <!-- JAL-1986 -->Missing dependencies on applet pages
524 <!-- JAL-1947 -->Overview pixel size changes when
525 sequences are hidden in applet
528 <!-- JAL-1996 -->Updated instructions for applet
529 deployment on examples pages.
536 <td width="60" nowrap>
538 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
539 <em>16/10/2015</em></strong>
544 <li>Time stamps for signed Jalview application and applet
551 <li>Duplicate group consensus and conservation rows
552 shown when tree is partitioned</li>
553 <li>Erratic behaviour when tree partitions made with
554 multiple cDNA/Protein split views</li>
560 <td width="60" nowrap>
562 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
563 <em>8/10/2015</em></strong>
568 <li>Updated Spanish translations of localized text for
570 </ul> <em>Application</em>
572 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
573 <li>Signed OSX InstallAnywhere installer<br></li>
574 <li>Support for per-sequence based annotations in BioJSON</li>
575 </ul> <em>Applet</em>
577 <li>Split frame example added to applet examples page</li>
583 <li>Mapping of cDNA to protein in split frames
584 incorrect when sequence start > 1</li>
585 <li>Broken images in filter column by annotation dialog
587 <li>Feature colours not parsed from features file</li>
588 <li>Exceptions and incomplete link URLs recovered when
589 loading a features file containing HTML tags in feature
595 <li>Annotations corrupted after BioJS export and
597 <li>Incorrect sequence limits after Fetch DB References
598 with 'trim retrieved sequences'</li>
599 <li>Incorrect warning about deleting all data when
600 deleting selected columns</li>
601 <li>Patch to build system for shipping properly signed
602 JNLP templates for webstart launch</li>
603 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
604 unreleased structures for download or viewing</li>
605 <li>Tab/space/return keystroke operation of EMBL-PDBe
606 fetcher/viewer dialogs works correctly</li>
607 <li>Disabled 'minimise' button on Jalview windows
608 running on OSX to workaround redraw hang bug</li>
609 <li>Split cDNA/Protein view position and geometry not
610 recovered from jalview project</li>
611 <li>Initial enabled/disabled state of annotation menu
612 sorter 'show autocalculated first/last' corresponds to
614 <li>Restoring of Clustal, RNA Helices and T-Coffee
615 color schemes from BioJSON</li>
619 <li>Reorder sequences mirrored in cDNA/Protein split
621 <li>Applet with Jmol examples not loading correctly</li>
627 <td><div align="center">
628 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
632 <li>Linked visualisation and analysis of DNA and Protein
635 <li>Translated cDNA alignments shown as split protein
636 and DNA alignment views</li>
637 <li>Codon consensus annotation for linked protein and
638 cDNA alignment views</li>
639 <li>Link cDNA or Protein product sequences by loading
640 them onto Protein or cDNA alignments</li>
641 <li>Reconstruct linked cDNA alignment from aligned
642 protein sequences</li>
645 <li>Jmol integration updated to Jmol v14.2.14</li>
646 <li>Import and export of Jalview alignment views as <a
647 href="features/bioJsonFormat.html">BioJSON</a></li>
648 <li>New alignment annotation file statements for
649 reference sequences and marking hidden columns</li>
650 <li>Reference sequence based alignment shading to
651 highlight variation</li>
652 <li>Select or hide columns according to alignment
654 <li>Find option for locating sequences by description</li>
655 <li>Conserved physicochemical properties shown in amino
656 acid conservation row</li>
657 <li>Alignments can be sorted by number of RNA helices</li>
658 </ul> <em>Application</em>
660 <li>New cDNA/Protein analysis capabilities
662 <li>Get Cross-References should open a Split Frame
663 view with cDNA/Protein</li>
664 <li>Detect when nucleotide sequences and protein
665 sequences are placed in the same alignment</li>
666 <li>Split cDNA/Protein views are saved in Jalview
671 <li>Use REST API to talk to Chimera</li>
672 <li>Selected regions in Chimera are highlighted in linked
675 <li>VARNA RNA viewer updated to v3.93</li>
676 <li>VARNA views are saved in Jalview Projects</li>
677 <li>Pseudoknots displayed as Jalview RNA annotation can
678 be shown in VARNA</li>
680 <li>Make groups for selection uses marked columns as well
681 as the active selected region</li>
683 <li>Calculate UPGMA and NJ trees using sequence feature
685 <li>New Export options
687 <li>New Export Settings dialog to control hidden
688 region export in flat file generation</li>
690 <li>Export alignment views for display with the <a
691 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
693 <li>Export scrollable SVG in HTML page</li>
694 <li>Optional embedding of BioJSON data when exporting
695 alignment figures to HTML</li>
697 <li>3D structure retrieval and display
699 <li>Free text and structured queries with the PDBe
701 <li>PDBe Search API based discovery and selection of
702 PDB structures for a sequence set</li>
706 <li>JPred4 employed for protein secondary structure
708 <li>Hide Insertions menu option to hide unaligned columns
709 for one or a group of sequences</li>
710 <li>Automatically hide insertions in alignments imported
711 from the JPred4 web server</li>
712 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
713 system on OSX<br />LGPL libraries courtesy of <a
714 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
716 <li>changed 'View nucleotide structure' submenu to 'View
717 VARNA 2D Structure'</li>
718 <li>change "View protein structure" menu option to "3D
721 </ul> <em>Applet</em>
723 <li>New layout for applet example pages</li>
724 <li>New parameters to enable SplitFrame view
725 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
726 <li>New example demonstrating linked viewing of cDNA and
727 Protein alignments</li>
728 </ul> <em>Development and deployment</em>
730 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
731 <li>Include installation type and git revision in build
732 properties and console log output</li>
733 <li>Jalview Github organisation, and new github site for
734 storing BioJsMSA Templates</li>
735 <li>Jalview's unit tests now managed with TestNG</li>
738 <!-- <em>General</em>
740 </ul> --> <!-- issues resolved --> <em>Application</em>
742 <li>Escape should close any open find dialogs</li>
743 <li>Typo in select-by-features status report</li>
744 <li>Consensus RNA secondary secondary structure
745 predictions are not highlighted in amber</li>
746 <li>Missing gap character in v2.7 example file means
747 alignment appears unaligned when pad-gaps is not enabled</li>
748 <li>First switch to RNA Helices colouring doesn't colour
749 associated structure views</li>
750 <li>ID width preference option is greyed out when auto
751 width checkbox not enabled</li>
752 <li>Stopped a warning dialog from being shown when
753 creating user defined colours</li>
754 <li>'View Mapping' in structure viewer shows sequence
755 mappings for just that viewer's sequences</li>
756 <li>Workaround for superposing PDB files containing
757 multiple models in Chimera</li>
758 <li>Report sequence position in status bar when hovering
759 over Jmol structure</li>
760 <li>Cannot output gaps as '.' symbols with Selection ->
761 output to text box</li>
762 <li>Flat file exports of alignments with hidden columns
763 have incorrect sequence start/end</li>
764 <li>'Aligning' a second chain to a Chimera structure from
766 <li>Colour schemes applied to structure viewers don't
767 work for nucleotide</li>
768 <li>Loading/cut'n'pasting an empty or invalid file leads
769 to a grey/invisible alignment window</li>
770 <li>Exported Jpred annotation from a sequence region
771 imports to different position</li>
772 <li>Space at beginning of sequence feature tooltips shown
773 on some platforms</li>
774 <li>Chimera viewer 'View | Show Chain' menu is not
776 <li>'New View' fails with a Null Pointer Exception in
777 console if Chimera has been opened</li>
778 <li>Mouseover to Chimera not working</li>
779 <li>Miscellaneous ENA XML feature qualifiers not
781 <li>NPE in annotation renderer after 'Extract Scores'</li>
782 <li>If two structures in one Chimera window, mouseover of
783 either sequence shows on first structure</li>
784 <li>'Show annotations' options should not make
785 non-positional annotations visible</li>
786 <li>Subsequence secondary structure annotation not shown
787 in right place after 'view flanking regions'</li>
788 <li>File Save As type unset when current file format is
790 <li>Save as '.jar' option removed for saving Jalview
792 <li>Colour by Sequence colouring in Chimera more
794 <li>Cannot 'add reference annotation' for a sequence in
795 several views on same alignment</li>
796 <li>Cannot show linked products for EMBL / ENA records</li>
797 <li>Jalview's tooltip wraps long texts containing no
799 </ul> <em>Applet</em>
801 <li>Jmol to JalviewLite mouseover/link not working</li>
802 <li>JalviewLite can't import sequences with ID
803 descriptions containing angle brackets</li>
804 </ul> <em>General</em>
806 <li>Cannot export and reimport RNA secondary structure
807 via jalview annotation file</li>
808 <li>Random helix colour palette for colour by annotation
809 with RNA secondary structure</li>
810 <li>Mouseover to cDNA from STOP residue in protein
811 translation doesn't work.</li>
812 <li>hints when using the select by annotation dialog box</li>
813 <li>Jmol alignment incorrect if PDB file has alternate CA
815 <li>FontChooser message dialog appears to hang after
816 choosing 1pt font</li>
817 <li>Peptide secondary structure incorrectly imported from
818 annotation file when annotation display text includes 'e' or
820 <li>Cannot set colour of new feature type whilst creating
822 <li>cDNA translation alignment should not be sequence
824 <li>'Show unconserved' doesn't work for lower case
826 <li>Nucleotide ambiguity codes involving R not recognised</li>
827 </ul> <em>Deployment and Documentation</em>
829 <li>Applet example pages appear different to the rest of
831 </ul> <em>Application Known issues</em>
833 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
834 <li>Misleading message appears after trying to delete
836 <li>Jalview icon not shown in dock after InstallAnywhere
837 version launches</li>
838 <li>Fetching EMBL reference for an RNA sequence results
839 fails with a sequence mismatch</li>
840 <li>Corrupted or unreadable alignment display when
841 scrolling alignment to right</li>
842 <li>ArrayIndexOutOfBoundsException thrown when remove
843 empty columns called on alignment with ragged gapped ends</li>
844 <li>auto calculated alignment annotation rows do not get
845 placed above or below non-autocalculated rows</li>
846 <li>Jalview dekstop becomes sluggish at full screen in
847 ultra-high resolution</li>
848 <li>Cannot disable consensus calculation independently of
849 quality and conservation</li>
850 <li>Mouseover highlighting between cDNA and protein can
851 become sluggish with more than one splitframe shown</li>
852 </ul> <em>Applet Known Issues</em>
854 <li>Core PDB parsing code requires Jmol</li>
855 <li>Sequence canvas panel goes white when alignment
856 window is being resized</li>
862 <td><div align="center">
863 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
867 <li>Updated Java code signing certificate donated by
869 <li>Features and annotation preserved when performing
870 pairwise alignment</li>
871 <li>RNA pseudoknot annotation can be
872 imported/exported/displayed</li>
873 <li>'colour by annotation' can colour by RNA and
874 protein secondary structure</li>
875 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
876 post-hoc with 2.9 release</em>)
879 </ul> <em>Application</em>
881 <li>Extract and display secondary structure for sequences
882 with 3D structures</li>
883 <li>Support for parsing RNAML</li>
884 <li>Annotations menu for layout
886 <li>sort sequence annotation rows by alignment</li>
887 <li>place sequence annotation above/below alignment
890 <li>Output in Stockholm format</li>
891 <li>Internationalisation: improved Spanish (es)
893 <li>Structure viewer preferences tab</li>
894 <li>Disorder and Secondary Structure annotation tracks
895 shared between alignments</li>
896 <li>UCSF Chimera launch and linked highlighting from
898 <li>Show/hide all sequence associated annotation rows for
899 all or current selection</li>
900 <li>disorder and secondary structure predictions
901 available as dataset annotation</li>
902 <li>Per-sequence rna helices colouring</li>
905 <li>Sequence database accessions imported when fetching
906 alignments from Rfam</li>
907 <li>update VARNA version to 3.91</li>
909 <li>New groovy scripts for exporting aligned positions,
910 conservation values, and calculating sum of pairs scores.</li>
911 <li>Command line argument to set default JABAWS server</li>
912 <li>include installation type in build properties and
913 console log output</li>
914 <li>Updated Jalview project format to preserve dataset
918 <!-- issues resolved --> <em>Application</em>
920 <li>Distinguish alignment and sequence associated RNA
921 structure in structure->view->VARNA</li>
922 <li>Raise dialog box if user deletes all sequences in an
924 <li>Pressing F1 results in documentation opening twice</li>
925 <li>Sequence feature tooltip is wrapped</li>
926 <li>Double click on sequence associated annotation
927 selects only first column</li>
928 <li>Redundancy removal doesn't result in unlinked
929 leaves shown in tree</li>
930 <li>Undos after several redundancy removals don't undo
932 <li>Hide sequence doesn't hide associated annotation</li>
933 <li>User defined colours dialog box too big to fit on
934 screen and buttons not visible</li>
935 <li>author list isn't updated if already written to
936 Jalview properties</li>
937 <li>Popup menu won't open after retrieving sequence
939 <li>File open window for associate PDB doesn't open</li>
940 <li>Left-then-right click on a sequence id opens a
941 browser search window</li>
942 <li>Cannot open sequence feature shading/sort popup menu
943 in feature settings dialog</li>
944 <li>better tooltip placement for some areas of Jalview
946 <li>Allow addition of JABAWS Server which doesn't
948 <li>Web services parameters dialog box is too large to
950 <li>Muscle nucleotide alignment preset obscured by
952 <li>JABAWS preset submenus don't contain newly
953 defined user preset</li>
954 <li>MSA web services warns user if they were launched
955 with invalid input</li>
956 <li>Jalview cannot contact DAS Registy when running on
959 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
960 'Superpose with' submenu not shown when new view
964 </ul> <!-- <em>Applet</em>
966 </ul> <em>General</em>
968 </ul>--> <em>Deployment and Documentation</em>
970 <li>2G and 1G options in launchApp have no effect on
971 memory allocation</li>
972 <li>launchApp service doesn't automatically open
973 www.jalview.org/examples/exampleFile.jar if no file is given</li>
975 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
976 InstallAnywhere reports cannot find valid JVM when Java
979 </ul> <em>Application Known issues</em>
982 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
983 corrupted or unreadable alignment display when scrolling
987 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
988 retrieval fails but progress bar continues for DAS retrieval
989 with large number of ID
992 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
993 flatfile output of visible region has incorrect sequence
997 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
998 rna structure consensus doesn't update when secondary
999 structure tracks are rearranged
1002 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1003 invalid rna structure positional highlighting does not
1004 highlight position of invalid base pairs
1007 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1008 out of memory errors are not raised when saving Jalview
1009 project from alignment window file menu
1012 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1013 Switching to RNA Helices colouring doesn't propagate to
1017 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1018 colour by RNA Helices not enabled when user created
1019 annotation added to alignment
1022 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1023 Jalview icon not shown on dock in Mountain Lion/Webstart
1025 </ul> <em>Applet Known Issues</em>
1028 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1029 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1032 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1033 Jalview and Jmol example not compatible with IE9
1036 <li>Sort by annotation score doesn't reverse order
1042 <td><div align="center">
1043 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1046 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1049 <li>Internationalisation of user interface (usually
1050 called i18n support) and translation for Spanish locale</li>
1051 <li>Define/Undefine group on current selection with
1052 Ctrl-G/Shift Ctrl-G</li>
1053 <li>Improved group creation/removal options in
1054 alignment/sequence Popup menu</li>
1055 <li>Sensible precision for symbol distribution
1056 percentages shown in logo tooltip.</li>
1057 <li>Annotation panel height set according to amount of
1058 annotation when alignment first opened</li>
1059 </ul> <em>Application</em>
1061 <li>Interactive consensus RNA secondary structure
1062 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1063 <li>Select columns containing particular features from
1064 Feature Settings dialog</li>
1065 <li>View all 'representative' PDB structures for selected
1067 <li>Update Jalview project format:
1069 <li>New file extension for Jalview projects '.jvp'</li>
1070 <li>Preserve sequence and annotation dataset (to
1071 store secondary structure annotation,etc)</li>
1072 <li>Per group and alignment annotation and RNA helix
1076 <li>New similarity measures for PCA and Tree calculation
1078 <li>Experimental support for retrieval and viewing of
1079 flanking regions for an alignment</li>
1083 <!-- issues resolved --> <em>Application</em>
1085 <li>logo keeps spinning and status remains at queued or
1086 running after job is cancelled</li>
1087 <li>cannot export features from alignments imported from
1088 Jalview/VAMSAS projects</li>
1089 <li>Buggy slider for web service parameters that take
1091 <li>Newly created RNA secondary structure line doesn't
1092 have 'display all symbols' flag set</li>
1093 <li>T-COFFEE alignment score shading scheme and other
1094 annotation shading not saved in Jalview project</li>
1095 <li>Local file cannot be loaded in freshly downloaded
1097 <li>Jalview icon not shown on dock in Mountain
1099 <li>Load file from desktop file browser fails</li>
1100 <li>Occasional NPE thrown when calculating large trees</li>
1101 <li>Cannot reorder or slide sequences after dragging an
1102 alignment onto desktop</li>
1103 <li>Colour by annotation dialog throws NPE after using
1104 'extract scores' function</li>
1105 <li>Loading/cut'n'pasting an empty file leads to a grey
1106 alignment window</li>
1107 <li>Disorder thresholds rendered incorrectly after
1108 performing IUPred disorder prediction</li>
1109 <li>Multiple group annotated consensus rows shown when
1110 changing 'normalise logo' display setting</li>
1111 <li>Find shows blank dialog after 'finished searching' if
1112 nothing matches query</li>
1113 <li>Null Pointer Exceptions raised when sorting by
1114 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1116 <li>Errors in Jmol console when structures in alignment
1117 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1119 <li>Not all working JABAWS services are shown in
1121 <li>JAVAWS version of Jalview fails to launch with
1122 'invalid literal/length code'</li>
1123 <li>Annotation/RNA Helix colourschemes cannot be applied
1124 to alignment with groups (actually fixed in 2.8.0b1)</li>
1125 <li>RNA Helices and T-Coffee Scores available as default
1128 </ul> <em>Applet</em>
1130 <li>Remove group option is shown even when selection is
1132 <li>Apply to all groups ticked but colourscheme changes
1133 don't affect groups</li>
1134 <li>Documented RNA Helices and T-Coffee Scores as valid
1135 colourscheme name</li>
1136 <li>Annotation labels drawn on sequence IDs when
1137 Annotation panel is not displayed</li>
1138 <li>Increased font size for dropdown menus on OSX and
1139 embedded windows</li>
1140 </ul> <em>Other</em>
1142 <li>Consensus sequence for alignments/groups with a
1143 single sequence were not calculated</li>
1144 <li>annotation files that contain only groups imported as
1145 annotation and junk sequences</li>
1146 <li>Fasta files with sequences containing '*' incorrectly
1147 recognised as PFAM or BLC</li>
1148 <li>conservation/PID slider apply all groups option
1149 doesn't affect background (2.8.0b1)
1151 <li>redundancy highlighting is erratic at 0% and 100%</li>
1152 <li>Remove gapped columns fails for sequences with ragged
1154 <li>AMSA annotation row with leading spaces is not
1155 registered correctly on import</li>
1156 <li>Jalview crashes when selecting PCA analysis for
1157 certain alignments</li>
1158 <li>Opening the colour by annotation dialog for an
1159 existing annotation based 'use original colours'
1160 colourscheme loses original colours setting</li>
1165 <td><div align="center">
1166 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
1167 <em>30/1/2014</em></strong>
1171 <li>Trusted certificates for JalviewLite applet and
1172 Jalview Desktop application<br />Certificate was donated by
1173 <a href="https://www.certum.eu">Certum</a> to the Jalview
1174 open source project).
1176 <li>Jalview SRS links replaced by UniProt and EBI-search
1178 <li>Output in Stockholm format</li>
1179 <li>Allow import of data from gzipped files</li>
1180 <li>Export/import group and sequence associated line
1181 graph thresholds</li>
1182 <li>Nucleotide substitution matrix that supports RNA and
1183 ambiguity codes</li>
1184 <li>Allow disorder predictions to be made on the current
1185 selection (or visible selection) in the same way that JPred
1187 <li>Groovy scripting for headless Jalview operation</li>
1188 </ul> <em>Other improvements</em>
1190 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
1191 <li>COMBINE statement uses current SEQUENCE_REF and
1192 GROUP_REF scope to group annotation rows</li>
1193 <li>Support '' style escaping of quotes in Newick
1195 <li>Group options for JABAWS service by command line name</li>
1196 <li>Empty tooltip shown for JABA service options with a
1197 link but no description</li>
1198 <li>Select primary source when selecting authority in
1199 database fetcher GUI</li>
1200 <li>Add .mfa to FASTA file extensions recognised by
1202 <li>Annotation label tooltip text wrap</li>
1207 <li>Slow scrolling when lots of annotation rows are
1209 <li>Lots of NPE (and slowness) after creating RNA
1210 secondary structure annotation line</li>
1211 <li>Sequence database accessions not imported when
1212 fetching alignments from Rfam</li>
1213 <li>Incorrect SHMR submission for sequences with
1215 <li>View all structures does not always superpose
1217 <li>Option widgets in service parameters not updated to
1218 reflect user or preset settings</li>
1219 <li>Null pointer exceptions for some services without
1220 presets or adjustable parameters</li>
1221 <li>Discover PDB IDs entry in structure menu doesn't
1222 discover PDB xRefs</li>
1223 <li>Exception encountered while trying to retrieve
1224 features with DAS</li>
1225 <li>Lowest value in annotation row isn't coloured
1226 when colour by annotation (per sequence) is coloured</li>
1227 <li>Keyboard mode P jumps to start of gapped region when
1228 residue follows a gap</li>
1229 <li>Jalview appears to hang importing an alignment with
1230 Wrap as default or after enabling Wrap</li>
1231 <li>'Right click to add annotations' message
1232 shown in wrap mode when no annotations present</li>
1233 <li>Disorder predictions fail with NPE if no automatic
1234 annotation already exists on alignment</li>
1235 <li>oninit javascript function should be called after
1236 initialisation completes</li>
1237 <li>Remove redundancy after disorder prediction corrupts
1238 alignment window display</li>
1239 <li>Example annotation file in documentation is invalid</li>
1240 <li>Grouped line graph annotation rows are not exported
1241 to annotation file</li>
1242 <li>Multi-harmony analysis cannot be run when only two
1244 <li>Cannot create multiple groups of line graphs with
1245 several 'combine' statements in annotation file</li>
1246 <li>Pressing return several times causes Number Format
1247 exceptions in keyboard mode</li>
1248 <li>Multi-harmony (SHMMR) method doesn't submit
1249 correct partitions for input data</li>
1250 <li>Translation from DNA to Amino Acids fails</li>
1251 <li>Jalview fail to load newick tree with quoted label</li>
1252 <li>--headless flag isn't understood</li>
1253 <li>ClassCastException when generating EPS in headless
1255 <li>Adjusting sequence-associated shading threshold only
1256 changes one row's threshold</li>
1257 <li>Preferences and Feature settings panel panel
1258 doesn't open</li>
1259 <li>hide consensus histogram also hides conservation and
1260 quality histograms</li>
1265 <td><div align="center">
1266 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
1268 <td><em>Application</em>
1270 <li>Support for JABAWS 2.0 Services (AACon alignment
1271 conservation, protein disorder and Clustal Omega)</li>
1272 <li>JABAWS server status indicator in Web Services
1274 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
1275 in Jalview alignment window</li>
1276 <li>Updated Jalview build and deploy framework for OSX
1277 mountain lion, windows 7, and 8</li>
1278 <li>Nucleotide substitution matrix for PCA that supports
1279 RNA and ambiguity codes</li>
1281 <li>Improved sequence database retrieval GUI</li>
1282 <li>Support fetching and database reference look up
1283 against multiple DAS sources (Fetch all from in 'fetch db
1285 <li>Jalview project improvements
1287 <li>Store and retrieve the 'belowAlignment'
1288 flag for annotation</li>
1289 <li>calcId attribute to group annotation rows on the
1291 <li>Store AACon calculation settings for a view in
1292 Jalview project</li>
1296 <li>horizontal scrolling gesture support</li>
1297 <li>Visual progress indicator when PCA calculation is
1299 <li>Simpler JABA web services menus</li>
1300 <li>visual indication that web service results are still
1301 being retrieved from server</li>
1302 <li>Serialise the dialogs that are shown when Jalview
1303 starts up for first time</li>
1304 <li>Jalview user agent string for interacting with HTTP
1306 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
1308 <li>Examples directory and Groovy library included in
1309 InstallAnywhere distribution</li>
1310 </ul> <em>Applet</em>
1312 <li>RNA alignment and secondary structure annotation
1313 visualization applet example</li>
1314 </ul> <em>General</em>
1316 <li>Normalise option for consensus sequence logo</li>
1317 <li>Reset button in PCA window to return dimensions to
1319 <li>Allow seqspace or Jalview variant of alignment PCA
1321 <li>PCA with either nucleic acid and protein substitution
1323 <li>Allow windows containing HTML reports to be exported
1325 <li>Interactive display and editing of RNA secondary
1326 structure contacts</li>
1327 <li>RNA Helix Alignment Colouring</li>
1328 <li>RNA base pair logo consensus</li>
1329 <li>Parse sequence associated secondary structure
1330 information in Stockholm files</li>
1331 <li>HTML Export database accessions and annotation
1332 information presented in tooltip for sequences</li>
1333 <li>Import secondary structure from LOCARNA clustalw
1334 style RNA alignment files</li>
1335 <li>import and visualise T-COFFEE quality scores for an
1337 <li>'colour by annotation' per sequence option to
1338 shade each sequence according to its associated alignment
1340 <li>New Jalview Logo</li>
1341 </ul> <em>Documentation and Development</em>
1343 <li>documentation for score matrices used in Jalview</li>
1344 <li>New Website!</li>
1346 <td><em>Application</em>
1348 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
1349 wsdbfetch REST service</li>
1350 <li>Stop windows being moved outside desktop on OSX</li>
1351 <li>Filetype associations not installed for webstart
1353 <li>Jalview does not always retrieve progress of a JABAWS
1354 job execution in full once it is complete</li>
1355 <li>revise SHMR RSBS definition to ensure alignment is
1356 uploaded via ali_file parameter</li>
1357 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
1358 <li>View all structures superposed fails with exception</li>
1359 <li>Jnet job queues forever if a very short sequence is
1360 submitted for prediction</li>
1361 <li>Cut and paste menu not opened when mouse clicked on
1363 <li>Putting fractional value into integer text box in
1364 alignment parameter dialog causes Jalview to hang</li>
1365 <li>Structure view highlighting doesn't work on
1367 <li>View all structures fails with exception shown in
1369 <li>Characters in filename associated with PDBEntry not
1370 escaped in a platform independent way</li>
1371 <li>Jalview desktop fails to launch with exception when
1373 <li>Tree calculation reports 'you must have 2 or more
1374 sequences selected' when selection is empty</li>
1375 <li>Jalview desktop fails to launch with jar signature
1376 failure when java web start temporary file caching is
1378 <li>DAS Sequence retrieval with range qualification
1379 results in sequence xref which includes range qualification</li>
1380 <li>Errors during processing of command line arguments
1381 cause progress bar (JAL-898) to be removed</li>
1382 <li>Replace comma for semi-colon option not disabled for
1383 DAS sources in sequence fetcher</li>
1384 <li>Cannot close news reader when JABAWS server warning
1385 dialog is shown</li>
1386 <li>Option widgets not updated to reflect user settings</li>
1387 <li>Edited sequence not submitted to web service</li>
1388 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
1389 <li>InstallAnywhere installer doesn't unpack and run
1390 on OSX Mountain Lion</li>
1391 <li>Annotation panel not given a scroll bar when
1392 sequences with alignment annotation are pasted into the
1394 <li>Sequence associated annotation rows not associated
1395 when loaded from Jalview project</li>
1396 <li>Browser launch fails with NPE on java 1.7</li>
1397 <li>JABAWS alignment marked as finished when job was
1398 cancelled or job failed due to invalid input</li>
1399 <li>NPE with v2.7 example when clicking on Tree
1400 associated with all views</li>
1401 <li>Exceptions when copy/paste sequences with grouped
1402 annotation rows to new window</li>
1403 </ul> <em>Applet</em>
1405 <li>Sequence features are momentarily displayed before
1406 they are hidden using hidefeaturegroups applet parameter</li>
1407 <li>loading features via javascript API automatically
1408 enables feature display</li>
1409 <li>scrollToColumnIn javascript API method doesn't
1411 </ul> <em>General</em>
1413 <li>Redundancy removal fails for rna alignment</li>
1414 <li>PCA calculation fails when sequence has been selected
1415 and then deselected</li>
1416 <li>PCA window shows grey box when first opened on OSX</li>
1417 <li>Letters coloured pink in sequence logo when alignment
1418 coloured with clustalx</li>
1419 <li>Choosing fonts without letter symbols defined causes
1420 exceptions and redraw errors</li>
1421 <li>Initial PCA plot view is not same as manually
1422 reconfigured view</li>
1423 <li>Grouped annotation graph label has incorrect line
1425 <li>Grouped annotation graph label display is corrupted
1426 for lots of labels</li>
1431 <div align="center">
1432 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
1435 <td><em>Application</em>
1437 <li>Jalview Desktop News Reader</li>
1438 <li>Tweaked default layout of web services menu</li>
1439 <li>View/alignment association menu to enable user to
1440 easily specify which alignment a multi-structure view takes
1441 its colours/correspondences from</li>
1442 <li>Allow properties file location to be specified as URL</li>
1443 <li>Extend Jalview project to preserve associations
1444 between many alignment views and a single Jmol display</li>
1445 <li>Store annotation row height in Jalview project file</li>
1446 <li>Annotation row column label formatting attributes
1447 stored in project file</li>
1448 <li>Annotation row order for auto-calculated annotation
1449 rows preserved in Jalview project file</li>
1450 <li>Visual progress indication when Jalview state is
1451 saved using Desktop window menu</li>
1452 <li>Visual indication that command line arguments are
1453 still being processed</li>
1454 <li>Groovy script execution from URL</li>
1455 <li>Colour by annotation default min and max colours in
1457 <li>Automatically associate PDB files dragged onto an
1458 alignment with sequences that have high similarity and
1460 <li>Update JGoogleAnalytics to latest release (0.3)</li>
1461 <li>'view structures' option to open many
1462 structures in same window</li>
1463 <li>Sort associated views menu option for tree panel</li>
1464 <li>Group all JABA and non-JABA services for a particular
1465 analysis function in its own submenu</li>
1466 </ul> <em>Applet</em>
1468 <li>Userdefined and autogenerated annotation rows for
1470 <li>Adjustment of alignment annotation pane height</li>
1471 <li>Annotation scrollbar for annotation panel</li>
1472 <li>Drag to reorder annotation rows in annotation panel</li>
1473 <li>'automaticScrolling' parameter</li>
1474 <li>Allow sequences with partial ID string matches to be
1475 annotated from GFF/Jalview features files</li>
1476 <li>Sequence logo annotation row in applet</li>
1477 <li>Absolute paths relative to host server in applet
1478 parameters are treated as such</li>
1479 <li>New in the JalviewLite javascript API:
1481 <li>JalviewLite.js javascript library</li>
1482 <li>Javascript callbacks for
1484 <li>Applet initialisation</li>
1485 <li>Sequence/alignment mouse-overs and selections</li>
1488 <li>scrollTo row and column alignment scrolling
1490 <li>Select sequence/alignment regions from javascript</li>
1491 <li>javascript structure viewer harness to pass
1492 messages between Jmol and Jalview when running as
1493 distinct applets</li>
1494 <li>sortBy method</li>
1495 <li>Set of applet and application examples shipped
1496 with documentation</li>
1497 <li>New example to demonstrate JalviewLite and Jmol
1498 javascript message exchange</li>
1500 </ul> <em>General</em>
1502 <li>Enable Jmol displays to be associated with multiple
1503 multiple alignments</li>
1504 <li>Option to automatically sort alignment with new tree</li>
1505 <li>User configurable link to enable redirects to a
1506 www.Jalview.org mirror</li>
1507 <li>Jmol colours option for Jmol displays</li>
1508 <li>Configurable newline string when writing alignment
1509 and other flat files</li>
1510 <li>Allow alignment annotation description lines to
1511 contain html tags</li>
1512 </ul> <em>Documentation and Development</em>
1514 <li>Add groovy test harness for bulk load testing to
1516 <li>Groovy script to load and align a set of sequences
1517 using a web service before displaying the result in the
1518 Jalview desktop</li>
1519 <li>Restructured javascript and applet api documentation</li>
1520 <li>Ant target to publish example html files with applet
1522 <li>Netbeans project for building Jalview from source</li>
1523 <li>ant task to create online javadoc for Jalview source</li>
1525 <td><em>Application</em>
1527 <li>User defined colourscheme throws exception when
1528 current built in colourscheme is saved as new scheme</li>
1529 <li>AlignFrame->Save in application pops up save
1530 dialog for valid filename/format</li>
1531 <li>Cannot view associated structure for UniProt sequence</li>
1532 <li>PDB file association breaks for UniProt sequence
1534 <li>Associate PDB from file dialog does not tell you
1535 which sequence is to be associated with the file</li>
1536 <li>Find All raises null pointer exception when query
1537 only matches sequence IDs</li>
1538 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
1539 <li>Jalview project with Jmol views created with Jalview
1540 2.4 cannot be loaded</li>
1541 <li>Filetype associations not installed for webstart
1543 <li>Two or more chains in a single PDB file associated
1544 with sequences in different alignments do not get coloured
1545 by their associated sequence</li>
1546 <li>Visibility status of autocalculated annotation row
1547 not preserved when project is loaded</li>
1548 <li>Annotation row height and visibility attributes not
1549 stored in Jalview project</li>
1550 <li>Tree bootstraps are not preserved when saved as a
1551 Jalview project</li>
1552 <li>Envision2 workflow tooltips are corrupted</li>
1553 <li>Enabling show group conservation also enables colour
1554 by conservation</li>
1555 <li>Duplicate group associated conservation or consensus
1556 created on new view</li>
1557 <li>Annotation scrollbar not displayed after 'show
1558 all hidden annotation rows' option selected</li>
1559 <li>Alignment quality not updated after alignment
1560 annotation row is hidden then shown</li>
1561 <li>Preserve colouring of structures coloured by
1562 sequences in pre Jalview 2.7 projects</li>
1563 <li>Web service job parameter dialog is not laid out
1565 <li>Web services menu not refreshed after 'reset
1566 services' button is pressed in preferences</li>
1567 <li>Annotation off by one in Jalview v2_3 example project</li>
1568 <li>Structures imported from file and saved in project
1569 get name like jalview_pdb1234.txt when reloaded</li>
1570 <li>Jalview does not always retrieve progress of a JABAWS
1571 job execution in full once it is complete</li>
1572 </ul> <em>Applet</em>
1574 <li>Alignment height set incorrectly when lots of
1575 annotation rows are displayed</li>
1576 <li>Relative URLs in feature HTML text not resolved to
1578 <li>View follows highlighting does not work for positions
1580 <li><= shown as = in tooltip</li>
1581 <li>Export features raises exception when no features
1583 <li>Separator string used for serialising lists of IDs
1584 for javascript api is modified when separator string
1585 provided as parameter</li>
1586 <li>Null pointer exception when selecting tree leaves for
1587 alignment with no existing selection</li>
1588 <li>Relative URLs for datasources assumed to be relative
1589 to applet's codebase</li>
1590 <li>Status bar not updated after finished searching and
1591 search wraps around to first result</li>
1592 <li>StructureSelectionManager instance shared between
1593 several Jalview applets causes race conditions and memory
1595 <li>Hover tooltip and mouseover of position on structure
1596 not sent from Jmol in applet</li>
1597 <li>Certain sequences of javascript method calls to
1598 applet API fatally hang browser</li>
1599 </ul> <em>General</em>
1601 <li>View follows structure mouseover scrolls beyond
1602 position with wrapped view and hidden regions</li>
1603 <li>Find sequence position moves to wrong residue
1604 with/without hidden columns</li>
1605 <li>Sequence length given in alignment properties window
1607 <li>InvalidNumberFormat exceptions thrown when trying to
1608 import PDB like structure files</li>
1609 <li>Positional search results are only highlighted
1610 between user-supplied sequence start/end bounds</li>
1611 <li>End attribute of sequence is not validated</li>
1612 <li>Find dialog only finds first sequence containing a
1613 given sequence position</li>
1614 <li>Sequence numbering not preserved in MSF alignment
1616 <li>Jalview PDB file reader does not extract sequence
1617 from nucleotide chains correctly</li>
1618 <li>Structure colours not updated when tree partition
1619 changed in alignment</li>
1620 <li>Sequence associated secondary structure not correctly
1621 parsed in interleaved stockholm</li>
1622 <li>Colour by annotation dialog does not restore current
1624 <li>Hiding (nearly) all sequences doesn't work
1626 <li>Sequences containing lowercase letters are not
1627 properly associated with their pdb files</li>
1628 </ul> <em>Documentation and Development</em>
1630 <li>schemas/JalviewWsParamSet.xsd corrupted by
1631 ApplyCopyright tool</li>
1636 <div align="center">
1637 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
1640 <td><em>Application</em>
1642 <li>New warning dialog when the Jalview Desktop cannot
1643 contact web services</li>
1644 <li>JABA service parameters for a preset are shown in
1645 service job window</li>
1646 <li>JABA Service menu entries reworded</li>
1650 <li>Modeller PIR IO broken - cannot correctly import a
1651 pir file emitted by Jalview</li>
1652 <li>Existing feature settings transferred to new
1653 alignment view created from cut'n'paste</li>
1654 <li>Improved test for mixed amino/nucleotide chains when
1655 parsing PDB files</li>
1656 <li>Consensus and conservation annotation rows
1657 occasionally become blank for all new windows</li>
1658 <li>Exception raised when right clicking above sequences
1659 in wrapped view mode</li>
1660 </ul> <em>Application</em>
1662 <li>multiple multiply aligned structure views cause cpu
1663 usage to hit 100% and computer to hang</li>
1664 <li>Web Service parameter layout breaks for long user
1665 parameter names</li>
1666 <li>Jaba service discovery hangs desktop if Jaba server
1673 <div align="center">
1674 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
1677 <td><em>Application</em>
1679 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
1680 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
1683 <li>Web Services preference tab</li>
1684 <li>Analysis parameters dialog box and user defined
1686 <li>Improved speed and layout of Envision2 service menu</li>
1687 <li>Superpose structures using associated sequence
1689 <li>Export coordinates and projection as CSV from PCA
1691 </ul> <em>Applet</em>
1693 <li>enable javascript: execution by the applet via the
1694 link out mechanism</li>
1695 </ul> <em>Other</em>
1697 <li>Updated the Jmol Jalview interface to work with Jmol
1699 <li>The Jalview Desktop and JalviewLite applet now
1700 require Java 1.5</li>
1701 <li>Allow Jalview feature colour specification for GFF
1702 sequence annotation files</li>
1703 <li>New 'colour by label' keword in Jalview feature file
1704 type colour specification</li>
1705 <li>New Jalview Desktop Groovy API method that allows a
1706 script to check if it being run in an interactive session or
1707 in a batch operation from the Jalview command line</li>
1711 <li>clustalx colourscheme colours Ds preferentially when
1712 both D+E are present in over 50% of the column</li>
1713 </ul> <em>Application</em>
1715 <li>typo in AlignmentFrame->View->Hide->all but
1716 selected Regions menu item</li>
1717 <li>sequence fetcher replaces ',' for ';' when the ',' is
1718 part of a valid accession ID</li>
1719 <li>fatal OOM if object retrieved by sequence fetcher
1720 runs out of memory</li>
1721 <li>unhandled Out of Memory Error when viewing pca
1722 analysis results</li>
1723 <li>InstallAnywhere builds fail to launch on OS X java
1724 10.5 update 4 (due to apple Java 1.6 update)</li>
1725 <li>Installanywhere Jalview silently fails to launch</li>
1726 </ul> <em>Applet</em>
1728 <li>Jalview.getFeatureGroups() raises an
1729 ArrayIndexOutOfBoundsException if no feature groups are
1736 <div align="center">
1737 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
1743 <li>Alignment prettyprinter doesn't cope with long
1745 <li>clustalx colourscheme colours Ds preferentially when
1746 both D+E are present in over 50% of the column</li>
1747 <li>nucleic acid structures retrieved from PDB do not
1748 import correctly</li>
1749 <li>More columns get selected than were clicked on when a
1750 number of columns are hidden</li>
1751 <li>annotation label popup menu not providing correct
1752 add/hide/show options when rows are hidden or none are
1754 <li>Stockholm format shown in list of readable formats,
1755 and parser copes better with alignments from RFAM.</li>
1756 <li>CSV output of consensus only includes the percentage
1757 of all symbols if sequence logo display is enabled</li>
1759 </ul> <em>Applet</em>
1761 <li>annotation panel disappears when annotation is
1763 </ul> <em>Application</em>
1765 <li>Alignment view not redrawn properly when new
1766 alignment opened where annotation panel is visible but no
1767 annotations are present on alignment</li>
1768 <li>pasted region containing hidden columns is
1769 incorrectly displayed in new alignment window</li>
1770 <li>Jalview slow to complete operations when stdout is
1771 flooded (fix is to close the Jalview console)</li>
1772 <li>typo in AlignmentFrame->View->Hide->all but
1773 selected Rregions menu item.</li>
1774 <li>inconsistent group submenu and Format submenu entry
1775 'Un' or 'Non'conserved</li>
1776 <li>Sequence feature settings are being shared by
1777 multiple distinct alignments</li>
1778 <li>group annotation not recreated when tree partition is
1780 <li>double click on group annotation to select sequences
1781 does not propagate to associated trees</li>
1782 <li>Mac OSX specific issues:
1784 <li>exception raised when mouse clicked on desktop
1785 window background</li>
1786 <li>Desktop menu placed on menu bar and application
1787 name set correctly</li>
1788 <li>sequence feature settings not wide enough for the
1789 save feature colourscheme button</li>
1798 <div align="center">
1799 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
1802 <td><em>New Capabilities</em>
1804 <li>URL links generated from description line for
1805 regular-expression based URL links (applet and application)
1812 <li>Non-positional feature URL links are shown in link
1814 <li>Linked viewing of nucleic acid sequences and
1816 <li>Automatic Scrolling option in View menu to display
1817 the currently highlighted region of an alignment.</li>
1818 <li>Order an alignment by sequence length, or using the
1819 average score or total feature count for each sequence.</li>
1820 <li>Shading features by score or associated description</li>
1821 <li>Subdivide alignment and groups based on identity of
1822 selected subsequence (Make Groups from Selection).</li>
1823 <li>New hide/show options including Shift+Control+H to
1824 hide everything but the currently selected region.</li>
1825 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
1826 </ul> <em>Application</em>
1828 <li>Fetch DB References capabilities and UI expanded to
1829 support retrieval from DAS sequence sources</li>
1830 <li>Local DAS Sequence sources can be added via the
1831 command line or via the Add local source dialog box.</li>
1832 <li>DAS Dbref and DbxRef feature types are parsed as
1833 database references and protein_name is parsed as
1834 description line (BioSapiens terms).</li>
1835 <li>Enable or disable non-positional feature and database
1836 references in sequence ID tooltip from View menu in
1838 <!-- <li>New hidden columns and rows and representatives capabilities
1839 in annotations file (in progress - not yet fully implemented)</li> -->
1840 <li>Group-associated consensus, sequence logos and
1841 conservation plots</li>
1842 <li>Symbol distributions for each column can be exported
1843 and visualized as sequence logos</li>
1844 <li>Optionally scale multi-character column labels to fit
1845 within each column of annotation row<!-- todo for applet -->
1847 <li>Optional automatic sort of associated alignment view
1848 when a new tree is opened.</li>
1849 <li>Jalview Java Console</li>
1850 <li>Better placement of desktop window when moving
1851 between different screens.</li>
1852 <li>New preference items for sequence ID tooltip and
1853 consensus annotation</li>
1854 <li>Client to submit sequences and IDs to Envision2
1856 <li><em>Vamsas Capabilities</em>
1858 <li>Improved VAMSAS synchronization (Jalview archive
1859 used to preserve views, structures, and tree display
1861 <li>Import of vamsas documents from disk or URL via
1863 <li>Sharing of selected regions between views and
1864 with other VAMSAS applications (Experimental feature!)</li>
1865 <li>Updated API to VAMSAS version 0.2</li>
1867 </ul> <em>Applet</em>
1869 <li>Middle button resizes annotation row height</li>
1872 <li>sortByTree (true/false) - automatically sort the
1873 associated alignment view by the tree when a new tree is
1875 <li>showTreeBootstraps (true/false) - show or hide
1876 branch bootstraps (default is to show them if available)</li>
1877 <li>showTreeDistances (true/false) - show or hide
1878 branch lengths (default is to show them if available)</li>
1879 <li>showUnlinkedTreeNodes (true/false) - indicate if
1880 unassociated nodes should be highlighted in the tree
1882 <li>heightScale and widthScale (1.0 or more) -
1883 increase the height or width of a cell in the alignment
1884 grid relative to the current font size.</li>
1887 <li>Non-positional features displayed in sequence ID
1889 </ul> <em>Other</em>
1891 <li>Features format: graduated colour definitions and
1892 specification of feature scores</li>
1893 <li>Alignment Annotations format: new keywords for group
1894 associated annotation (GROUP_REF) and annotation row display
1895 properties (ROW_PROPERTIES)</li>
1896 <li>XML formats extended to support graduated feature
1897 colourschemes, group associated annotation, and profile
1898 visualization settings.</li></td>
1901 <li>Source field in GFF files parsed as feature source
1902 rather than description</li>
1903 <li>Non-positional features are now included in sequence
1904 feature and gff files (controlled via non-positional feature
1905 visibility in tooltip).</li>
1906 <li>URL links generated for all feature links (bugfix)</li>
1907 <li>Added URL embedding instructions to features file
1909 <li>Codons containing ambiguous nucleotides translated as
1910 'X' in peptide product</li>
1911 <li>Match case switch in find dialog box works for both
1912 sequence ID and sequence string and query strings do not
1913 have to be in upper case to match case-insensitively.</li>
1914 <li>AMSA files only contain first column of
1915 multi-character column annotation labels</li>
1916 <li>Jalview Annotation File generation/parsing consistent
1917 with documentation (e.g. Stockholm annotation can be
1918 exported and re-imported)</li>
1919 <li>PDB files without embedded PDB IDs given a friendly
1921 <li>Find incrementally searches ID string matches as well
1922 as subsequence matches, and correctly reports total number
1926 <li>Better handling of exceptions during sequence
1928 <li>Dasobert generated non-positional feature URL
1929 link text excludes the start_end suffix</li>
1930 <li>DAS feature and source retrieval buttons disabled
1931 when fetch or registry operations in progress.</li>
1932 <li>PDB files retrieved from URLs are cached properly</li>
1933 <li>Sequence description lines properly shared via
1935 <li>Sequence fetcher fetches multiple records for all
1937 <li>Ensured that command line das feature retrieval
1938 completes before alignment figures are generated.</li>
1939 <li>Reduced time taken when opening file browser for
1941 <li>isAligned check prior to calculating tree, PCA or
1942 submitting an MSA to JNet now excludes hidden sequences.</li>
1943 <li>User defined group colours properly recovered
1944 from Jalview projects.</li>
1953 <div align="center">
1954 <strong>2.4.0.b2</strong><br> 28/10/2009
1959 <li>Experimental support for google analytics usage
1961 <li>Jalview privacy settings (user preferences and docs).</li>
1966 <li>Race condition in applet preventing startup in
1968 <li>Exception when feature created from selection beyond
1969 length of sequence.</li>
1970 <li>Allow synthetic PDB files to be imported gracefully</li>
1971 <li>Sequence associated annotation rows associate with
1972 all sequences with a given id</li>
1973 <li>Find function matches case-insensitively for sequence
1974 ID string searches</li>
1975 <li>Non-standard characters do not cause pairwise
1976 alignment to fail with exception</li>
1977 </ul> <em>Application Issues</em>
1979 <li>Sequences are now validated against EMBL database</li>
1980 <li>Sequence fetcher fetches multiple records for all
1982 </ul> <em>InstallAnywhere Issues</em>
1984 <li>Dock icon works for Mac OS X java (Mac 1.6 update
1985 issue with installAnywhere mechanism)</li>
1986 <li>Command line launching of JARs from InstallAnywhere
1987 version (java class versioning error fixed)</li>
1994 <div align="center">
1995 <strong>2.4</strong><br> 27/8/2008
1998 <td><em>User Interface</em>
2000 <li>Linked highlighting of codon and amino acid from
2001 translation and protein products</li>
2002 <li>Linked highlighting of structure associated with
2003 residue mapping to codon position</li>
2004 <li>Sequence Fetcher provides example accession numbers
2005 and 'clear' button</li>
2006 <li>MemoryMonitor added as an option under Desktop's
2008 <li>Extract score function to parse whitespace separated
2009 numeric data in description line</li>
2010 <li>Column labels in alignment annotation can be centred.</li>
2011 <li>Tooltip for sequence associated annotation give name
2013 </ul> <em>Web Services and URL fetching</em>
2015 <li>JPred3 web service</li>
2016 <li>Prototype sequence search client (no public services
2018 <li>Fetch either seed alignment or full alignment from
2020 <li>URL Links created for matching database cross
2021 references as well as sequence ID</li>
2022 <li>URL Links can be created using regular-expressions</li>
2023 </ul> <em>Sequence Database Connectivity</em>
2025 <li>Retrieval of cross-referenced sequences from other
2027 <li>Generalised database reference retrieval and
2028 validation to all fetchable databases</li>
2029 <li>Fetch sequences from DAS sources supporting the
2030 sequence command</li>
2031 </ul> <em>Import and Export</em>
2032 <li>export annotation rows as CSV for spreadsheet import</li>
2033 <li>Jalview projects record alignment dataset associations,
2034 EMBL products, and cDNA sequence mappings</li>
2035 <li>Sequence Group colour can be specified in Annotation
2037 <li>Ad-hoc colouring of group in Annotation File using RGB
2038 triplet as name of colourscheme</li>
2039 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2041 <li>treenode binding for VAMSAS tree exchange</li>
2042 <li>local editing and update of sequences in VAMSAS
2043 alignments (experimental)</li>
2044 <li>Create new or select existing session to join</li>
2045 <li>load and save of vamsas documents</li>
2046 </ul> <em>Application command line</em>
2048 <li>-tree parameter to open trees (introduced for passing
2050 <li>-fetchfrom command line argument to specify nicknames
2051 of DAS servers to query for alignment features</li>
2052 <li>-dasserver command line argument to add new servers
2053 that are also automatically queried for features</li>
2054 <li>-groovy command line argument executes a given groovy
2055 script after all input data has been loaded and parsed</li>
2056 </ul> <em>Applet-Application data exchange</em>
2058 <li>Trees passed as applet parameters can be passed to
2059 application (when using "View in full
2060 application")</li>
2061 </ul> <em>Applet Parameters</em>
2063 <li>feature group display control parameter</li>
2064 <li>debug parameter</li>
2065 <li>showbutton parameter</li>
2066 </ul> <em>Applet API methods</em>
2068 <li>newView public method</li>
2069 <li>Window (current view) specific get/set public methods</li>
2070 <li>Feature display control methods</li>
2071 <li>get list of currently selected sequences</li>
2072 </ul> <em>New Jalview distribution features</em>
2074 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2075 <li>RELEASE file gives build properties for the latest
2076 Jalview release.</li>
2077 <li>Java 1.1 Applet build made easier and donotobfuscate
2078 property controls execution of obfuscator</li>
2079 <li>Build target for generating source distribution</li>
2080 <li>Debug flag for javacc</li>
2081 <li>.jalview_properties file is documented (slightly) in
2082 jalview.bin.Cache</li>
2083 <li>Continuous Build Integration for stable and
2084 development version of Application, Applet and source
2089 <li>selected region output includes visible annotations
2090 (for certain formats)</li>
2091 <li>edit label/displaychar contains existing label/char
2093 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2094 <li>shorter peptide product names from EMBL records</li>
2095 <li>Newick string generator makes compact representations</li>
2096 <li>bootstrap values parsed correctly for tree files with
2098 <li>pathological filechooser bug avoided by not allowing
2099 filenames containing a ':'</li>
2100 <li>Fixed exception when parsing GFF files containing
2101 global sequence features</li>
2102 <li>Alignment datasets are finalized only when number of
2103 references from alignment sequences goes to zero</li>
2104 <li>Close of tree branch colour box without colour
2105 selection causes cascading exceptions</li>
2106 <li>occasional negative imgwidth exceptions</li>
2107 <li>better reporting of non-fatal warnings to user when
2108 file parsing fails.</li>
2109 <li>Save works when Jalview project is default format</li>
2110 <li>Save as dialog opened if current alignment format is
2111 not a valid output format</li>
2112 <li>UniProt canonical names introduced for both das and
2114 <li>Histidine should be midblue (not pink!) in Zappo</li>
2115 <li>error messages passed up and output when data read
2117 <li>edit undo recovers previous dataset sequence when
2118 sequence is edited</li>
2119 <li>allow PDB files without pdb ID HEADER lines (like
2120 those generated by MODELLER) to be read in properly</li>
2121 <li>allow reading of JPred concise files as a normal
2123 <li>Stockholm annotation parsing and alignment properties
2124 import fixed for PFAM records</li>
2125 <li>Structure view windows have correct name in Desktop
2127 <li>annotation consisting of sequence associated scores
2128 can be read and written correctly to annotation file</li>
2129 <li>Aligned cDNA translation to aligned peptide works
2131 <li>Fixed display of hidden sequence markers and
2132 non-italic font for representatives in Applet</li>
2133 <li>Applet Menus are always embedded in applet window on
2135 <li>Newly shown features appear at top of stack (in
2137 <li>Annotations added via parameter not drawn properly
2138 due to null pointer exceptions</li>
2139 <li>Secondary structure lines are drawn starting from
2140 first column of alignment</li>
2141 <li>UniProt XML import updated for new schema release in
2143 <li>Sequence feature to sequence ID match for Features
2144 file is case-insensitive</li>
2145 <li>Sequence features read from Features file appended to
2146 all sequences with matching IDs</li>
2147 <li>PDB structure coloured correctly for associated views
2148 containing a sub-sequence</li>
2149 <li>PDB files can be retrieved by applet from Jar files</li>
2150 <li>feature and annotation file applet parameters
2151 referring to different directories are retrieved correctly</li>
2152 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
2153 <li>Fixed application hang whilst waiting for
2154 splash-screen version check to complete</li>
2155 <li>Applet properly URLencodes input parameter values
2156 when passing them to the launchApp service</li>
2157 <li>display name and local features preserved in results
2158 retrieved from web service</li>
2159 <li>Visual delay indication for sequence retrieval and
2160 sequence fetcher initialisation</li>
2161 <li>updated Application to use DAS 1.53e version of
2162 dasobert DAS client</li>
2163 <li>Re-instated Full AMSA support and .amsa file
2165 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
2173 <div align="center">
2174 <strong>2.3</strong><br> 9/5/07
2179 <li>Jmol 11.0.2 integration</li>
2180 <li>PDB views stored in Jalview XML files</li>
2181 <li>Slide sequences</li>
2182 <li>Edit sequence in place</li>
2183 <li>EMBL CDS features</li>
2184 <li>DAS Feature mapping</li>
2185 <li>Feature ordering</li>
2186 <li>Alignment Properties</li>
2187 <li>Annotation Scores</li>
2188 <li>Sort by scores</li>
2189 <li>Feature/annotation editing in applet</li>
2194 <li>Headless state operation in 2.2.1</li>
2195 <li>Incorrect and unstable DNA pairwise alignment</li>
2196 <li>Cut and paste of sequences with annotation</li>
2197 <li>Feature group display state in XML</li>
2198 <li>Feature ordering in XML</li>
2199 <li>blc file iteration selection using filename # suffix</li>
2200 <li>Stockholm alignment properties</li>
2201 <li>Stockhom alignment secondary structure annotation</li>
2202 <li>2.2.1 applet had no feature transparency</li>
2203 <li>Number pad keys can be used in cursor mode</li>
2204 <li>Structure Viewer mirror image resolved</li>
2211 <div align="center">
2212 <strong>2.2.1</strong><br> 12/2/07
2217 <li>Non standard characters can be read and displayed
2218 <li>Annotations/Features can be imported/exported to the
2220 <li>Applet allows editing of sequence/annotation/group
2221 name & description
2222 <li>Preference setting to display sequence name in
2224 <li>Annotation file format extended to allow
2225 Sequence_groups to be defined
2226 <li>Default opening of alignment overview panel can be
2227 specified in preferences
2228 <li>PDB residue numbering annotation added to associated
2234 <li>Applet crash under certain Linux OS with Java 1.6
2236 <li>Annotation file export / import bugs fixed
2237 <li>PNG / EPS image output bugs fixed
2243 <div align="center">
2244 <strong>2.2</strong><br> 27/11/06
2249 <li>Multiple views on alignment
2250 <li>Sequence feature editing
2251 <li>"Reload" alignment
2252 <li>"Save" to current filename
2253 <li>Background dependent text colour
2254 <li>Right align sequence ids
2255 <li>User-defined lower case residue colours
2258 <li>Menu item accelerator keys
2259 <li>Control-V pastes to current alignment
2260 <li>Cancel button for DAS Feature Fetching
2261 <li>PCA and PDB Viewers zoom via mouse roller
2262 <li>User-defined sub-tree colours and sub-tree selection
2269 <li>'New Window' button on the 'Output to Text box'
2274 <li>New memory efficient Undo/Redo System
2275 <li>Optimised symbol lookups and conservation/consensus
2277 <li>Region Conservation/Consensus recalculated after
2279 <li>Fixed Remove Empty Columns Bug (empty columns at end
2281 <li>Slowed DAS Feature Fetching for increased robustness.
2288 <li>Made angle brackets in ASCII feature descriptions
2290 <li>Re-instated Zoom function for PCA
2291 <li>Sequence descriptions conserved in web service
2293 <li>UniProt ID discoverer uses any word separated by
2295 <li>WsDbFetch query/result association resolved
2296 <li>Tree leaf to sequence mapping improved
2297 <li>Smooth fonts switch moved to FontChooser dialog box.
2309 <div align="center">
2310 <strong>2.1.1</strong><br> 12/9/06
2315 <li>Copy consensus sequence to clipboard</li>
2320 <li>Image output - rightmost residues are rendered if
2321 sequence id panel has been resized</li>
2322 <li>Image output - all offscreen group boundaries are
2324 <li>Annotation files with sequence references - all
2325 elements in file are relative to sequence position</li>
2326 <li>Mac Applet users can use Alt key for group editing</li>
2332 <div align="center">
2333 <strong>2.1</strong><br> 22/8/06
2338 <li>MAFFT Multiple Alignment in default Web Service list</li>
2339 <li>DAS Feature fetching</li>
2340 <li>Hide sequences and columns</li>
2341 <li>Export Annotations and Features</li>
2342 <li>GFF file reading / writing</li>
2343 <li>Associate structures with sequences from local PDB
2345 <li>Add sequences to exisiting alignment</li>
2346 <li>Recently opened files / URL lists</li>
2347 <li>Applet can launch the full application</li>
2348 <li>Applet has transparency for features (Java 1.2
2350 <li>Applet has user defined colours parameter</li>
2351 <li>Applet can load sequences from parameter
2352 "sequence<em>x</em>"
2358 <li>Redundancy Panel reinstalled in the Applet</li>
2359 <li>Monospaced font - EPS / rescaling bug fixed</li>
2360 <li>Annotation files with sequence references bug fixed</li>
2366 <div align="center">
2367 <strong>2.08.1</strong><br> 2/5/06
2372 <li>Change case of selected region from Popup menu</li>
2373 <li>Choose to match case when searching</li>
2374 <li>Middle mouse button and mouse movement can compress /
2375 expand the visible width and height of the alignment</li>
2380 <li>Annotation Panel displays complete JNet results</li>
2386 <div align="center">
2387 <strong>2.08b</strong><br> 18/4/06
2393 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
2394 <li>Righthand label on wrapped alignments shows correct
2401 <div align="center">
2402 <strong>2.08</strong><br> 10/4/06
2407 <li>Editing can be locked to the selection area</li>
2408 <li>Keyboard editing</li>
2409 <li>Create sequence features from searches</li>
2410 <li>Precalculated annotations can be loaded onto
2412 <li>Features file allows grouping of features</li>
2413 <li>Annotation Colouring scheme added</li>
2414 <li>Smooth fonts off by default - Faster rendering</li>
2415 <li>Choose to toggle Autocalculate Consensus On/Off</li>
2420 <li>Drag & Drop fixed on Linux</li>
2421 <li>Jalview Archive file faster to load/save, sequence
2422 descriptions saved.</li>
2428 <div align="center">
2429 <strong>2.07</strong><br> 12/12/05
2434 <li>PDB Structure Viewer enhanced</li>
2435 <li>Sequence Feature retrieval and display enhanced</li>
2436 <li>Choose to output sequence start-end after sequence
2437 name for file output</li>
2438 <li>Sequence Fetcher WSDBFetch@EBI</li>
2439 <li>Applet can read feature files, PDB files and can be
2440 used for HTML form input</li>
2445 <li>HTML output writes groups and features</li>
2446 <li>Group editing is Control and mouse click</li>
2447 <li>File IO bugs</li>
2453 <div align="center">
2454 <strong>2.06</strong><br> 28/9/05
2459 <li>View annotations in wrapped mode</li>
2460 <li>More options for PCA viewer</li>
2465 <li>GUI bugs resolved</li>
2466 <li>Runs with -nodisplay from command line</li>
2472 <div align="center">
2473 <strong>2.05b</strong><br> 15/9/05
2478 <li>Choose EPS export as lineart or text</li>
2479 <li>Jar files are executable</li>
2480 <li>Can read in Uracil - maps to unknown residue</li>
2485 <li>Known OutOfMemory errors give warning message</li>
2486 <li>Overview window calculated more efficiently</li>
2487 <li>Several GUI bugs resolved</li>
2493 <div align="center">
2494 <strong>2.05</strong><br> 30/8/05
2499 <li>Edit and annotate in "Wrapped" view</li>
2504 <li>Several GUI bugs resolved</li>
2510 <div align="center">
2511 <strong>2.04</strong><br> 24/8/05
2516 <li>Hold down mouse wheel & scroll to change font
2522 <li>Improved JPred client reliability</li>
2523 <li>Improved loading of Jalview files</li>
2529 <div align="center">
2530 <strong>2.03</strong><br> 18/8/05
2535 <li>Set Proxy server name and port in preferences</li>
2536 <li>Multiple URL links from sequence ids</li>
2537 <li>User Defined Colours can have a scheme name and added
2539 <li>Choose to ignore gaps in consensus calculation</li>
2540 <li>Unix users can set default web browser</li>
2541 <li>Runs without GUI for batch processing</li>
2542 <li>Dynamically generated Web Service Menus</li>
2547 <li>InstallAnywhere download for Sparc Solaris</li>
2553 <div align="center">
2554 <strong>2.02</strong><br> 18/7/05
2560 <li>Copy & Paste order of sequences maintains
2561 alignment order.</li>
2567 <div align="center">
2568 <strong>2.01</strong><br> 12/7/05
2573 <li>Use delete key for deleting selection.</li>
2574 <li>Use Mouse wheel to scroll sequences.</li>
2575 <li>Help file updated to describe how to add alignment
2577 <li>Version and build date written to build properties
2579 <li>InstallAnywhere installation will check for updates
2580 at launch of Jalview.</li>
2585 <li>Delete gaps bug fixed.</li>
2586 <li>FileChooser sorts columns.</li>
2587 <li>Can remove groups one by one.</li>
2588 <li>Filechooser icons installed.</li>
2589 <li>Finder ignores return character when searching.
2590 Return key will initiate a search.<br>
2597 <div align="center">
2598 <strong>2.0</strong><br> 20/6/05
2603 <li>New codebase</li>