3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
27 <strong>Release History</strong>
31 <td width="60" nowrap>
33 <em><strong>Release</strong></em>
38 <em><strong>New Features</strong></em>
43 <em><strong>Issues Resolved</strong></em>
48 <td width="60" nowrap>
50 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
51 <em>25/10/2016</em></strong>
54 <td><em>Application</em>
56 <li>3D Structure chooser opens with 'Cached structures' view if structures already loaded</li>
57 <li>Progress bar reports models as they are loaded to structure views</li>
63 <li>Colour by conservation always enabled and no tick shown in menu when PID shading applied</li>
67 <li>Multiple structure views can be opened and superposed without timeout for structures with multiple models or multiple sequences in alignment</li>
68 <li>Cannot import or associated local PDB files without a PDB ID HEADER line</li>
69 <li>RMSD is not output in Jmol console when superposition is performed</li>
70 <li>Drag and drop of URL from Browser fails for Linux and OSX versions earlier than El Capitan</li>
71 <li>ENA client ignores invalid content from ENA server</li>
72 <li>Exceptions are not raised in console when ENA client attempts to fetch non-existent IDs via Fetch DB Refs UI option</li>
73 <li>Exceptions are not raised in console when a new view is created on the alignment</li>
75 <em>New Known Issues</em>
76 <ul><li>Drag and drop from URL links in browsers do not work on Windows</li></ul>
77 <em>Build and deployment</em>
78 <ul><li>URL link checker now copes with multi-line anchor tags</li></ul>
83 <td width="60" nowrap>
85 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
91 <!-- JAL-2124 -->Updated Spanish translations.
94 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
95 for importing structure data to Jalview. Enables mmCIF and
99 <!-- JAL-192 --->Alignment ruler shows positions relative to
103 <!-- JAL-2202 -->Position/residue shown in status bar when
104 mousing over sequence associated annotation
107 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
111 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
112 '()', canonical '[]' and invalid '{}' base pair populations
116 <!-- JAL-2092 -->Feature settings popup menu options for
117 showing or hiding columns containing a feature
120 <!-- JAL-1557 -->Edit selected group by double clicking on
121 group and sequence associated annotation labels
124 <!-- JAL-2236 -->Sequence name added to annotation label in
125 select/hide columns by annotation and colour by annotation
129 </ul> <em>Application</em>
132 <!-- JAL-2050-->Automatically hide introns when opening a
136 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
140 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
141 structure mappings with the EMBL-EBI PDBe SIFTS database
144 <!-- JAL-2079 -->Updated download sites used for Rfam and
145 Pfam sources to xfam.org
148 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
151 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
152 over sequences in Jalview
155 <!-- JAL-2027-->Support for reverse-complement coding
156 regions in ENA and EMBL
159 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
160 for record retrieval via ENA rest API
163 <!-- JAL-2027 -->Support for ENA CDS records with reverse
167 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
168 groovy script execution
171 <!-- JAL-1812 -->New 'execute Groovy script' option in an
172 alignment window's Calculate menu
175 <!-- JAL-1812 -->Allow groovy scripts that call
176 Jalview.getAlignFrames() to run in headless mode
179 <!-- JAL-2068 -->Support for creating new alignment
180 calculation workers from groovy scripts
183 <!-- JAL-1369 --->Store/restore reference sequence in
187 <!-- JAL-1803 -->Chain codes for a sequence's PDB
188 associations are now saved/restored from project
191 <!-- JAL-1993 -->Database selection dialog always shown
192 before sequence fetcher is opened
195 <!-- JAL-2183 -->Double click on an entry in Jalview's
196 database chooser opens a sequence fetcher
199 <!-- JAL-1563 -->Free-text search client for UniProt using
203 <!-- JAL-2168 -->-nonews command line parameter to prevent
204 the news reader opening
207 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
208 querying stored in preferences
211 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
215 <!-- JAL-1977-->Tooltips shown on database chooser
218 <!-- JAL-391 -->Reverse complement function in calculate
219 menu for nucleotide sequences
222 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
223 and feature counts preserves alignment ordering (and
224 debugged for complex feature sets).
227 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
228 viewing structures with Jalview 2.10
231 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
232 genome, transcript CCDS and gene ids via the Ensembl and
233 Ensembl Genomes REST API
236 <!-- JAL-2049 -->Protein sequence variant annotation
237 computed for 'sequence_variant' annotation on CDS regions
241 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
245 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
246 Ref Fetcher fails to match, or otherwise updates sequence
247 data from external database records.
250 <!-- JAL-2154 -->Revised Jalview Project format for
251 efficient recovery of sequence coding and alignment
252 annotation relationships.
254 </ul> <!-- <em>Applet</em>
265 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
269 <!-- JAL-2018-->Export features in Jalview format (again)
270 includes graduated colourschemes
273 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
274 working with big alignments and lots of hidden columns
277 <!-- JAL-2053-->Hidden column markers not always rendered
278 at right of alignment window
281 <!-- JAL-2067 -->Tidied up links in help file table of
285 <!-- JAL-2072 -->Feature based tree calculation not shown
289 <!-- JAL-2075 -->Hidden columns ignored during feature
290 based tree calculation
293 <!-- JAL-2065 -->Alignment view stops updating when show
294 unconserved enabled for group on alignment
297 <!-- JAL-2086 -->Cannot insert gaps into sequence when
301 <!-- JAL-2146 -->Alignment column in status incorrectly
302 shown as "Sequence position" when mousing over
306 <!-- JAL-2099 -->Incorrect column numbers in ruler when
307 hidden columns present
310 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
311 user created annotation added to alignment
314 <!-- JAL-1841 -->RNA Structure consensus only computed for
315 '()' base pair annotation
318 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
319 in zero scores for all base pairs in RNA Structure
323 <!-- JAL-2174-->Extend selection with columns containing
327 <!-- JAL-2275 -->Pfam format writer puts extra space at
328 beginning of sequence
331 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
335 <!-- JAL-2238 -->Cannot create groups on an alignment from
336 from a tree when t-coffee scores are shown
339 <!-- JAL-1836,1967 -->Cannot import and view PDB
340 structures with chains containing negative resnums (4q4h)
343 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
347 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
348 to Clustal, PIR and PileUp output
351 <!-- JAL-2008 -->Reordering sequence features that are
352 not visible causes alignment window to repaint
355 <!-- JAL-2006 -->Threshold sliders don't work in
356 graduated colour and colour by annotation row for e-value
357 scores associated with features and annotation rows
360 <!-- JAL-1797 -->amino acid physicochemical conservation
361 calculation should be case independent
364 <!-- JAL-2173 -->Remove annotation also updates hidden
368 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
369 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
370 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
373 <!-- JAL-2065 -->Null pointer exceptions and redraw
374 problems when reference sequence defined and 'show
375 non-conserved' enabled
378 <!-- JAL-1306 -->Quality and Conservation are now shown on
379 load even when Consensus calculation is disabled
385 <!-- JAL-1552-->URLs and links can't be imported by
386 drag'n'drop on OSX when launched via webstart (note - not
387 yet fixed for El Capitan)
390 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
391 output when running on non-gb/us i18n platforms
394 <!-- JAL-1944 -->Error thrown when exporting a view with
395 hidden sequences as flat-file alignment
398 <!-- JAL-2030-->InstallAnywhere distribution fails when
402 <!-- JAL-2080-->Jalview very slow to launch via webstart
403 (also hotfix for 2.9.0b2)
406 <!-- JAL-2085 -->Cannot save project when view has a
407 reference sequence defined
410 <!-- JAL-1011 -->Columns are suddenly selected in other
411 alignments and views when revealing hidden columns
414 <!-- JAL-1989 -->Hide columns not mirrored in complement
415 view in a cDNA/Protein splitframe
418 <!-- JAL-1369 -->Cannot save/restore representative
419 sequence from project when only one sequence is
423 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
427 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
428 structure consensus didn't refresh annotation panel
431 <!-- JAL-1962 -->View mapping in structure view shows
432 mappings between sequence and all chains in a PDB file
435 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
436 dialogs format columns correctly, don't display array
437 data, sort columns according to type
440 <!-- JAL-1975 -->Export complete shown after destination
441 file chooser is cancelled during an image export
444 <!-- JAL-2025 -->Error when querying PDB Service with
445 sequence name containing special characters
448 <!-- JAL-2024 -->Manual PDB structure querying should be
452 <!-- JAL-2104 -->Large tooltips with broken HTML
453 formatting don't wrap
456 <!-- JAL-1128 -->Figures exported from wrapped view are
457 truncated so L looks like I in consensus annotation
460 <!-- JAL-2003 -->Export features should only export the
461 currently displayed features for the current selection or
465 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
466 after fetching cross-references, and restoring from project
469 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
470 followed in the structure viewer
473 <!-- JAL-2163 -->Titles for individual alignments in
474 splitframe not restored from project
477 <!-- JAL-2145 -->missing autocalculated annotation at
478 trailing end of protein alignment in transcript/product
479 splitview when pad-gaps not enabled by default
482 <!-- JAL-1797 -->amino acid physicochemical conservation
486 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
487 article has been read (reopened issue due to
488 internationalisation problems)
491 <!-- JAL-1960 -->Only offer PDB structures in structure
492 viewer based on sequence name, PDB and UniProt
497 <!-- JAL-1976 -->No progress bar shown during export of
501 <!-- JAL-2213 -->Structures not always superimposed after
502 multiple structures are shown for one or more sequences.
505 <!-- JAL-1370 -->Reference sequence characters should not
506 be replaced with '.' when 'Show unconserved' format option
510 <!-- JAL-1823 -->Cannot specify chain code when entering
511 specific PDB id for sequence
514 <!-- JAL-1944 -->File->Export->.. as doesn't work when
515 'Export hidden sequences' is enabled, but 'export hidden
516 columns' is disabled.
519 <!--JAL-2026-->Best Quality option in structure chooser
520 selects lowest rather than highest resolution structures
524 <!-- JAL-1887 -->Incorrect start and end reported for PDB
525 to sequence mapping in 'View Mappings' report
527 <!-- may exclude, this is an external service stability issue JAL-1941
528 -- > RNA 3D structure not added via DSSR service</li> -->
533 <!-- JAL-2151 -->Incorrect columns are selected when
534 hidden columns present before start of sequence
537 <!-- JAL-1986 -->Missing dependencies on applet pages
541 <!-- JAL-1947 -->Overview pixel size changes when
542 sequences are hidden in applet
545 <!-- JAL-1996 -->Updated instructions for applet
546 deployment on examples pages.
553 <td width="60" nowrap>
555 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
556 <em>16/10/2015</em></strong>
561 <li>Time stamps for signed Jalview application and applet
568 <li>Duplicate group consensus and conservation rows
569 shown when tree is partitioned</li>
570 <li>Erratic behaviour when tree partitions made with
571 multiple cDNA/Protein split views</li>
577 <td width="60" nowrap>
579 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
580 <em>8/10/2015</em></strong>
585 <li>Updated Spanish translations of localized text for
587 </ul> <em>Application</em>
589 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
590 <li>Signed OSX InstallAnywhere installer<br></li>
591 <li>Support for per-sequence based annotations in BioJSON</li>
592 </ul> <em>Applet</em>
594 <li>Split frame example added to applet examples page</li>
600 <li>Mapping of cDNA to protein in split frames
601 incorrect when sequence start > 1</li>
602 <li>Broken images in filter column by annotation dialog
604 <li>Feature colours not parsed from features file</li>
605 <li>Exceptions and incomplete link URLs recovered when
606 loading a features file containing HTML tags in feature
612 <li>Annotations corrupted after BioJS export and
614 <li>Incorrect sequence limits after Fetch DB References
615 with 'trim retrieved sequences'</li>
616 <li>Incorrect warning about deleting all data when
617 deleting selected columns</li>
618 <li>Patch to build system for shipping properly signed
619 JNLP templates for webstart launch</li>
620 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
621 unreleased structures for download or viewing</li>
622 <li>Tab/space/return keystroke operation of EMBL-PDBe
623 fetcher/viewer dialogs works correctly</li>
624 <li>Disabled 'minimise' button on Jalview windows
625 running on OSX to workaround redraw hang bug</li>
626 <li>Split cDNA/Protein view position and geometry not
627 recovered from jalview project</li>
628 <li>Initial enabled/disabled state of annotation menu
629 sorter 'show autocalculated first/last' corresponds to
631 <li>Restoring of Clustal, RNA Helices and T-Coffee
632 color schemes from BioJSON</li>
636 <li>Reorder sequences mirrored in cDNA/Protein split
638 <li>Applet with Jmol examples not loading correctly</li>
644 <td><div align="center">
645 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
649 <li>Linked visualisation and analysis of DNA and Protein
652 <li>Translated cDNA alignments shown as split protein
653 and DNA alignment views</li>
654 <li>Codon consensus annotation for linked protein and
655 cDNA alignment views</li>
656 <li>Link cDNA or Protein product sequences by loading
657 them onto Protein or cDNA alignments</li>
658 <li>Reconstruct linked cDNA alignment from aligned
659 protein sequences</li>
662 <li>Jmol integration updated to Jmol v14.2.14</li>
663 <li>Import and export of Jalview alignment views as <a
664 href="features/bioJsonFormat.html">BioJSON</a></li>
665 <li>New alignment annotation file statements for
666 reference sequences and marking hidden columns</li>
667 <li>Reference sequence based alignment shading to
668 highlight variation</li>
669 <li>Select or hide columns according to alignment
671 <li>Find option for locating sequences by description</li>
672 <li>Conserved physicochemical properties shown in amino
673 acid conservation row</li>
674 <li>Alignments can be sorted by number of RNA helices</li>
675 </ul> <em>Application</em>
677 <li>New cDNA/Protein analysis capabilities
679 <li>Get Cross-References should open a Split Frame
680 view with cDNA/Protein</li>
681 <li>Detect when nucleotide sequences and protein
682 sequences are placed in the same alignment</li>
683 <li>Split cDNA/Protein views are saved in Jalview
688 <li>Use REST API to talk to Chimera</li>
689 <li>Selected regions in Chimera are highlighted in linked
692 <li>VARNA RNA viewer updated to v3.93</li>
693 <li>VARNA views are saved in Jalview Projects</li>
694 <li>Pseudoknots displayed as Jalview RNA annotation can
695 be shown in VARNA</li>
697 <li>Make groups for selection uses marked columns as well
698 as the active selected region</li>
700 <li>Calculate UPGMA and NJ trees using sequence feature
702 <li>New Export options
704 <li>New Export Settings dialog to control hidden
705 region export in flat file generation</li>
707 <li>Export alignment views for display with the <a
708 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
710 <li>Export scrollable SVG in HTML page</li>
711 <li>Optional embedding of BioJSON data when exporting
712 alignment figures to HTML</li>
714 <li>3D structure retrieval and display
716 <li>Free text and structured queries with the PDBe
718 <li>PDBe Search API based discovery and selection of
719 PDB structures for a sequence set</li>
723 <li>JPred4 employed for protein secondary structure
725 <li>Hide Insertions menu option to hide unaligned columns
726 for one or a group of sequences</li>
727 <li>Automatically hide insertions in alignments imported
728 from the JPred4 web server</li>
729 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
730 system on OSX<br />LGPL libraries courtesy of <a
731 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
733 <li>changed 'View nucleotide structure' submenu to 'View
734 VARNA 2D Structure'</li>
735 <li>change "View protein structure" menu option to "3D
738 </ul> <em>Applet</em>
740 <li>New layout for applet example pages</li>
741 <li>New parameters to enable SplitFrame view
742 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
743 <li>New example demonstrating linked viewing of cDNA and
744 Protein alignments</li>
745 </ul> <em>Development and deployment</em>
747 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
748 <li>Include installation type and git revision in build
749 properties and console log output</li>
750 <li>Jalview Github organisation, and new github site for
751 storing BioJsMSA Templates</li>
752 <li>Jalview's unit tests now managed with TestNG</li>
755 <!-- <em>General</em>
757 </ul> --> <!-- issues resolved --> <em>Application</em>
759 <li>Escape should close any open find dialogs</li>
760 <li>Typo in select-by-features status report</li>
761 <li>Consensus RNA secondary secondary structure
762 predictions are not highlighted in amber</li>
763 <li>Missing gap character in v2.7 example file means
764 alignment appears unaligned when pad-gaps is not enabled</li>
765 <li>First switch to RNA Helices colouring doesn't colour
766 associated structure views</li>
767 <li>ID width preference option is greyed out when auto
768 width checkbox not enabled</li>
769 <li>Stopped a warning dialog from being shown when
770 creating user defined colours</li>
771 <li>'View Mapping' in structure viewer shows sequence
772 mappings for just that viewer's sequences</li>
773 <li>Workaround for superposing PDB files containing
774 multiple models in Chimera</li>
775 <li>Report sequence position in status bar when hovering
776 over Jmol structure</li>
777 <li>Cannot output gaps as '.' symbols with Selection ->
778 output to text box</li>
779 <li>Flat file exports of alignments with hidden columns
780 have incorrect sequence start/end</li>
781 <li>'Aligning' a second chain to a Chimera structure from
783 <li>Colour schemes applied to structure viewers don't
784 work for nucleotide</li>
785 <li>Loading/cut'n'pasting an empty or invalid file leads
786 to a grey/invisible alignment window</li>
787 <li>Exported Jpred annotation from a sequence region
788 imports to different position</li>
789 <li>Space at beginning of sequence feature tooltips shown
790 on some platforms</li>
791 <li>Chimera viewer 'View | Show Chain' menu is not
793 <li>'New View' fails with a Null Pointer Exception in
794 console if Chimera has been opened</li>
795 <li>Mouseover to Chimera not working</li>
796 <li>Miscellaneous ENA XML feature qualifiers not
798 <li>NPE in annotation renderer after 'Extract Scores'</li>
799 <li>If two structures in one Chimera window, mouseover of
800 either sequence shows on first structure</li>
801 <li>'Show annotations' options should not make
802 non-positional annotations visible</li>
803 <li>Subsequence secondary structure annotation not shown
804 in right place after 'view flanking regions'</li>
805 <li>File Save As type unset when current file format is
807 <li>Save as '.jar' option removed for saving Jalview
809 <li>Colour by Sequence colouring in Chimera more
811 <li>Cannot 'add reference annotation' for a sequence in
812 several views on same alignment</li>
813 <li>Cannot show linked products for EMBL / ENA records</li>
814 <li>Jalview's tooltip wraps long texts containing no
816 </ul> <em>Applet</em>
818 <li>Jmol to JalviewLite mouseover/link not working</li>
819 <li>JalviewLite can't import sequences with ID
820 descriptions containing angle brackets</li>
821 </ul> <em>General</em>
823 <li>Cannot export and reimport RNA secondary structure
824 via jalview annotation file</li>
825 <li>Random helix colour palette for colour by annotation
826 with RNA secondary structure</li>
827 <li>Mouseover to cDNA from STOP residue in protein
828 translation doesn't work.</li>
829 <li>hints when using the select by annotation dialog box</li>
830 <li>Jmol alignment incorrect if PDB file has alternate CA
832 <li>FontChooser message dialog appears to hang after
833 choosing 1pt font</li>
834 <li>Peptide secondary structure incorrectly imported from
835 annotation file when annotation display text includes 'e' or
837 <li>Cannot set colour of new feature type whilst creating
839 <li>cDNA translation alignment should not be sequence
841 <li>'Show unconserved' doesn't work for lower case
843 <li>Nucleotide ambiguity codes involving R not recognised</li>
844 </ul> <em>Deployment and Documentation</em>
846 <li>Applet example pages appear different to the rest of
848 </ul> <em>Application Known issues</em>
850 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
851 <li>Misleading message appears after trying to delete
853 <li>Jalview icon not shown in dock after InstallAnywhere
854 version launches</li>
855 <li>Fetching EMBL reference for an RNA sequence results
856 fails with a sequence mismatch</li>
857 <li>Corrupted or unreadable alignment display when
858 scrolling alignment to right</li>
859 <li>ArrayIndexOutOfBoundsException thrown when remove
860 empty columns called on alignment with ragged gapped ends</li>
861 <li>auto calculated alignment annotation rows do not get
862 placed above or below non-autocalculated rows</li>
863 <li>Jalview dekstop becomes sluggish at full screen in
864 ultra-high resolution</li>
865 <li>Cannot disable consensus calculation independently of
866 quality and conservation</li>
867 <li>Mouseover highlighting between cDNA and protein can
868 become sluggish with more than one splitframe shown</li>
869 </ul> <em>Applet Known Issues</em>
871 <li>Core PDB parsing code requires Jmol</li>
872 <li>Sequence canvas panel goes white when alignment
873 window is being resized</li>
879 <td><div align="center">
880 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
884 <li>Updated Java code signing certificate donated by
886 <li>Features and annotation preserved when performing
887 pairwise alignment</li>
888 <li>RNA pseudoknot annotation can be
889 imported/exported/displayed</li>
890 <li>'colour by annotation' can colour by RNA and
891 protein secondary structure</li>
892 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
893 post-hoc with 2.9 release</em>)
896 </ul> <em>Application</em>
898 <li>Extract and display secondary structure for sequences
899 with 3D structures</li>
900 <li>Support for parsing RNAML</li>
901 <li>Annotations menu for layout
903 <li>sort sequence annotation rows by alignment</li>
904 <li>place sequence annotation above/below alignment
907 <li>Output in Stockholm format</li>
908 <li>Internationalisation: improved Spanish (es)
910 <li>Structure viewer preferences tab</li>
911 <li>Disorder and Secondary Structure annotation tracks
912 shared between alignments</li>
913 <li>UCSF Chimera launch and linked highlighting from
915 <li>Show/hide all sequence associated annotation rows for
916 all or current selection</li>
917 <li>disorder and secondary structure predictions
918 available as dataset annotation</li>
919 <li>Per-sequence rna helices colouring</li>
922 <li>Sequence database accessions imported when fetching
923 alignments from Rfam</li>
924 <li>update VARNA version to 3.91</li>
926 <li>New groovy scripts for exporting aligned positions,
927 conservation values, and calculating sum of pairs scores.</li>
928 <li>Command line argument to set default JABAWS server</li>
929 <li>include installation type in build properties and
930 console log output</li>
931 <li>Updated Jalview project format to preserve dataset
935 <!-- issues resolved --> <em>Application</em>
937 <li>Distinguish alignment and sequence associated RNA
938 structure in structure->view->VARNA</li>
939 <li>Raise dialog box if user deletes all sequences in an
941 <li>Pressing F1 results in documentation opening twice</li>
942 <li>Sequence feature tooltip is wrapped</li>
943 <li>Double click on sequence associated annotation
944 selects only first column</li>
945 <li>Redundancy removal doesn't result in unlinked
946 leaves shown in tree</li>
947 <li>Undos after several redundancy removals don't undo
949 <li>Hide sequence doesn't hide associated annotation</li>
950 <li>User defined colours dialog box too big to fit on
951 screen and buttons not visible</li>
952 <li>author list isn't updated if already written to
953 Jalview properties</li>
954 <li>Popup menu won't open after retrieving sequence
956 <li>File open window for associate PDB doesn't open</li>
957 <li>Left-then-right click on a sequence id opens a
958 browser search window</li>
959 <li>Cannot open sequence feature shading/sort popup menu
960 in feature settings dialog</li>
961 <li>better tooltip placement for some areas of Jalview
963 <li>Allow addition of JABAWS Server which doesn't
965 <li>Web services parameters dialog box is too large to
967 <li>Muscle nucleotide alignment preset obscured by
969 <li>JABAWS preset submenus don't contain newly
970 defined user preset</li>
971 <li>MSA web services warns user if they were launched
972 with invalid input</li>
973 <li>Jalview cannot contact DAS Registy when running on
976 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
977 'Superpose with' submenu not shown when new view
981 </ul> <!-- <em>Applet</em>
983 </ul> <em>General</em>
985 </ul>--> <em>Deployment and Documentation</em>
987 <li>2G and 1G options in launchApp have no effect on
988 memory allocation</li>
989 <li>launchApp service doesn't automatically open
990 www.jalview.org/examples/exampleFile.jar if no file is given</li>
992 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
993 InstallAnywhere reports cannot find valid JVM when Java
996 </ul> <em>Application Known issues</em>
999 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1000 corrupted or unreadable alignment display when scrolling
1004 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1005 retrieval fails but progress bar continues for DAS retrieval
1006 with large number of ID
1009 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1010 flatfile output of visible region has incorrect sequence
1014 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1015 rna structure consensus doesn't update when secondary
1016 structure tracks are rearranged
1019 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1020 invalid rna structure positional highlighting does not
1021 highlight position of invalid base pairs
1024 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1025 out of memory errors are not raised when saving Jalview
1026 project from alignment window file menu
1029 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1030 Switching to RNA Helices colouring doesn't propagate to
1034 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1035 colour by RNA Helices not enabled when user created
1036 annotation added to alignment
1039 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1040 Jalview icon not shown on dock in Mountain Lion/Webstart
1042 </ul> <em>Applet Known Issues</em>
1045 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1046 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1049 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1050 Jalview and Jmol example not compatible with IE9
1053 <li>Sort by annotation score doesn't reverse order
1059 <td><div align="center">
1060 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1063 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1066 <li>Internationalisation of user interface (usually
1067 called i18n support) and translation for Spanish locale</li>
1068 <li>Define/Undefine group on current selection with
1069 Ctrl-G/Shift Ctrl-G</li>
1070 <li>Improved group creation/removal options in
1071 alignment/sequence Popup menu</li>
1072 <li>Sensible precision for symbol distribution
1073 percentages shown in logo tooltip.</li>
1074 <li>Annotation panel height set according to amount of
1075 annotation when alignment first opened</li>
1076 </ul> <em>Application</em>
1078 <li>Interactive consensus RNA secondary structure
1079 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1080 <li>Select columns containing particular features from
1081 Feature Settings dialog</li>
1082 <li>View all 'representative' PDB structures for selected
1084 <li>Update Jalview project format:
1086 <li>New file extension for Jalview projects '.jvp'</li>
1087 <li>Preserve sequence and annotation dataset (to
1088 store secondary structure annotation,etc)</li>
1089 <li>Per group and alignment annotation and RNA helix
1093 <li>New similarity measures for PCA and Tree calculation
1095 <li>Experimental support for retrieval and viewing of
1096 flanking regions for an alignment</li>
1100 <!-- issues resolved --> <em>Application</em>
1102 <li>logo keeps spinning and status remains at queued or
1103 running after job is cancelled</li>
1104 <li>cannot export features from alignments imported from
1105 Jalview/VAMSAS projects</li>
1106 <li>Buggy slider for web service parameters that take
1108 <li>Newly created RNA secondary structure line doesn't
1109 have 'display all symbols' flag set</li>
1110 <li>T-COFFEE alignment score shading scheme and other
1111 annotation shading not saved in Jalview project</li>
1112 <li>Local file cannot be loaded in freshly downloaded
1114 <li>Jalview icon not shown on dock in Mountain
1116 <li>Load file from desktop file browser fails</li>
1117 <li>Occasional NPE thrown when calculating large trees</li>
1118 <li>Cannot reorder or slide sequences after dragging an
1119 alignment onto desktop</li>
1120 <li>Colour by annotation dialog throws NPE after using
1121 'extract scores' function</li>
1122 <li>Loading/cut'n'pasting an empty file leads to a grey
1123 alignment window</li>
1124 <li>Disorder thresholds rendered incorrectly after
1125 performing IUPred disorder prediction</li>
1126 <li>Multiple group annotated consensus rows shown when
1127 changing 'normalise logo' display setting</li>
1128 <li>Find shows blank dialog after 'finished searching' if
1129 nothing matches query</li>
1130 <li>Null Pointer Exceptions raised when sorting by
1131 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1133 <li>Errors in Jmol console when structures in alignment
1134 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1136 <li>Not all working JABAWS services are shown in
1138 <li>JAVAWS version of Jalview fails to launch with
1139 'invalid literal/length code'</li>
1140 <li>Annotation/RNA Helix colourschemes cannot be applied
1141 to alignment with groups (actually fixed in 2.8.0b1)</li>
1142 <li>RNA Helices and T-Coffee Scores available as default
1145 </ul> <em>Applet</em>
1147 <li>Remove group option is shown even when selection is
1149 <li>Apply to all groups ticked but colourscheme changes
1150 don't affect groups</li>
1151 <li>Documented RNA Helices and T-Coffee Scores as valid
1152 colourscheme name</li>
1153 <li>Annotation labels drawn on sequence IDs when
1154 Annotation panel is not displayed</li>
1155 <li>Increased font size for dropdown menus on OSX and
1156 embedded windows</li>
1157 </ul> <em>Other</em>
1159 <li>Consensus sequence for alignments/groups with a
1160 single sequence were not calculated</li>
1161 <li>annotation files that contain only groups imported as
1162 annotation and junk sequences</li>
1163 <li>Fasta files with sequences containing '*' incorrectly
1164 recognised as PFAM or BLC</li>
1165 <li>conservation/PID slider apply all groups option
1166 doesn't affect background (2.8.0b1)
1168 <li>redundancy highlighting is erratic at 0% and 100%</li>
1169 <li>Remove gapped columns fails for sequences with ragged
1171 <li>AMSA annotation row with leading spaces is not
1172 registered correctly on import</li>
1173 <li>Jalview crashes when selecting PCA analysis for
1174 certain alignments</li>
1175 <li>Opening the colour by annotation dialog for an
1176 existing annotation based 'use original colours'
1177 colourscheme loses original colours setting</li>
1182 <td><div align="center">
1183 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
1184 <em>30/1/2014</em></strong>
1188 <li>Trusted certificates for JalviewLite applet and
1189 Jalview Desktop application<br />Certificate was donated by
1190 <a href="https://www.certum.eu">Certum</a> to the Jalview
1191 open source project).
1193 <li>Jalview SRS links replaced by UniProt and EBI-search
1195 <li>Output in Stockholm format</li>
1196 <li>Allow import of data from gzipped files</li>
1197 <li>Export/import group and sequence associated line
1198 graph thresholds</li>
1199 <li>Nucleotide substitution matrix that supports RNA and
1200 ambiguity codes</li>
1201 <li>Allow disorder predictions to be made on the current
1202 selection (or visible selection) in the same way that JPred
1204 <li>Groovy scripting for headless Jalview operation</li>
1205 </ul> <em>Other improvements</em>
1207 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
1208 <li>COMBINE statement uses current SEQUENCE_REF and
1209 GROUP_REF scope to group annotation rows</li>
1210 <li>Support '' style escaping of quotes in Newick
1212 <li>Group options for JABAWS service by command line name</li>
1213 <li>Empty tooltip shown for JABA service options with a
1214 link but no description</li>
1215 <li>Select primary source when selecting authority in
1216 database fetcher GUI</li>
1217 <li>Add .mfa to FASTA file extensions recognised by
1219 <li>Annotation label tooltip text wrap</li>
1224 <li>Slow scrolling when lots of annotation rows are
1226 <li>Lots of NPE (and slowness) after creating RNA
1227 secondary structure annotation line</li>
1228 <li>Sequence database accessions not imported when
1229 fetching alignments from Rfam</li>
1230 <li>Incorrect SHMR submission for sequences with
1232 <li>View all structures does not always superpose
1234 <li>Option widgets in service parameters not updated to
1235 reflect user or preset settings</li>
1236 <li>Null pointer exceptions for some services without
1237 presets or adjustable parameters</li>
1238 <li>Discover PDB IDs entry in structure menu doesn't
1239 discover PDB xRefs</li>
1240 <li>Exception encountered while trying to retrieve
1241 features with DAS</li>
1242 <li>Lowest value in annotation row isn't coloured
1243 when colour by annotation (per sequence) is coloured</li>
1244 <li>Keyboard mode P jumps to start of gapped region when
1245 residue follows a gap</li>
1246 <li>Jalview appears to hang importing an alignment with
1247 Wrap as default or after enabling Wrap</li>
1248 <li>'Right click to add annotations' message
1249 shown in wrap mode when no annotations present</li>
1250 <li>Disorder predictions fail with NPE if no automatic
1251 annotation already exists on alignment</li>
1252 <li>oninit javascript function should be called after
1253 initialisation completes</li>
1254 <li>Remove redundancy after disorder prediction corrupts
1255 alignment window display</li>
1256 <li>Example annotation file in documentation is invalid</li>
1257 <li>Grouped line graph annotation rows are not exported
1258 to annotation file</li>
1259 <li>Multi-harmony analysis cannot be run when only two
1261 <li>Cannot create multiple groups of line graphs with
1262 several 'combine' statements in annotation file</li>
1263 <li>Pressing return several times causes Number Format
1264 exceptions in keyboard mode</li>
1265 <li>Multi-harmony (SHMMR) method doesn't submit
1266 correct partitions for input data</li>
1267 <li>Translation from DNA to Amino Acids fails</li>
1268 <li>Jalview fail to load newick tree with quoted label</li>
1269 <li>--headless flag isn't understood</li>
1270 <li>ClassCastException when generating EPS in headless
1272 <li>Adjusting sequence-associated shading threshold only
1273 changes one row's threshold</li>
1274 <li>Preferences and Feature settings panel panel
1275 doesn't open</li>
1276 <li>hide consensus histogram also hides conservation and
1277 quality histograms</li>
1282 <td><div align="center">
1283 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
1285 <td><em>Application</em>
1287 <li>Support for JABAWS 2.0 Services (AACon alignment
1288 conservation, protein disorder and Clustal Omega)</li>
1289 <li>JABAWS server status indicator in Web Services
1291 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
1292 in Jalview alignment window</li>
1293 <li>Updated Jalview build and deploy framework for OSX
1294 mountain lion, windows 7, and 8</li>
1295 <li>Nucleotide substitution matrix for PCA that supports
1296 RNA and ambiguity codes</li>
1298 <li>Improved sequence database retrieval GUI</li>
1299 <li>Support fetching and database reference look up
1300 against multiple DAS sources (Fetch all from in 'fetch db
1302 <li>Jalview project improvements
1304 <li>Store and retrieve the 'belowAlignment'
1305 flag for annotation</li>
1306 <li>calcId attribute to group annotation rows on the
1308 <li>Store AACon calculation settings for a view in
1309 Jalview project</li>
1313 <li>horizontal scrolling gesture support</li>
1314 <li>Visual progress indicator when PCA calculation is
1316 <li>Simpler JABA web services menus</li>
1317 <li>visual indication that web service results are still
1318 being retrieved from server</li>
1319 <li>Serialise the dialogs that are shown when Jalview
1320 starts up for first time</li>
1321 <li>Jalview user agent string for interacting with HTTP
1323 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
1325 <li>Examples directory and Groovy library included in
1326 InstallAnywhere distribution</li>
1327 </ul> <em>Applet</em>
1329 <li>RNA alignment and secondary structure annotation
1330 visualization applet example</li>
1331 </ul> <em>General</em>
1333 <li>Normalise option for consensus sequence logo</li>
1334 <li>Reset button in PCA window to return dimensions to
1336 <li>Allow seqspace or Jalview variant of alignment PCA
1338 <li>PCA with either nucleic acid and protein substitution
1340 <li>Allow windows containing HTML reports to be exported
1342 <li>Interactive display and editing of RNA secondary
1343 structure contacts</li>
1344 <li>RNA Helix Alignment Colouring</li>
1345 <li>RNA base pair logo consensus</li>
1346 <li>Parse sequence associated secondary structure
1347 information in Stockholm files</li>
1348 <li>HTML Export database accessions and annotation
1349 information presented in tooltip for sequences</li>
1350 <li>Import secondary structure from LOCARNA clustalw
1351 style RNA alignment files</li>
1352 <li>import and visualise T-COFFEE quality scores for an
1354 <li>'colour by annotation' per sequence option to
1355 shade each sequence according to its associated alignment
1357 <li>New Jalview Logo</li>
1358 </ul> <em>Documentation and Development</em>
1360 <li>documentation for score matrices used in Jalview</li>
1361 <li>New Website!</li>
1363 <td><em>Application</em>
1365 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
1366 wsdbfetch REST service</li>
1367 <li>Stop windows being moved outside desktop on OSX</li>
1368 <li>Filetype associations not installed for webstart
1370 <li>Jalview does not always retrieve progress of a JABAWS
1371 job execution in full once it is complete</li>
1372 <li>revise SHMR RSBS definition to ensure alignment is
1373 uploaded via ali_file parameter</li>
1374 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
1375 <li>View all structures superposed fails with exception</li>
1376 <li>Jnet job queues forever if a very short sequence is
1377 submitted for prediction</li>
1378 <li>Cut and paste menu not opened when mouse clicked on
1380 <li>Putting fractional value into integer text box in
1381 alignment parameter dialog causes Jalview to hang</li>
1382 <li>Structure view highlighting doesn't work on
1384 <li>View all structures fails with exception shown in
1386 <li>Characters in filename associated with PDBEntry not
1387 escaped in a platform independent way</li>
1388 <li>Jalview desktop fails to launch with exception when
1390 <li>Tree calculation reports 'you must have 2 or more
1391 sequences selected' when selection is empty</li>
1392 <li>Jalview desktop fails to launch with jar signature
1393 failure when java web start temporary file caching is
1395 <li>DAS Sequence retrieval with range qualification
1396 results in sequence xref which includes range qualification</li>
1397 <li>Errors during processing of command line arguments
1398 cause progress bar (JAL-898) to be removed</li>
1399 <li>Replace comma for semi-colon option not disabled for
1400 DAS sources in sequence fetcher</li>
1401 <li>Cannot close news reader when JABAWS server warning
1402 dialog is shown</li>
1403 <li>Option widgets not updated to reflect user settings</li>
1404 <li>Edited sequence not submitted to web service</li>
1405 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
1406 <li>InstallAnywhere installer doesn't unpack and run
1407 on OSX Mountain Lion</li>
1408 <li>Annotation panel not given a scroll bar when
1409 sequences with alignment annotation are pasted into the
1411 <li>Sequence associated annotation rows not associated
1412 when loaded from Jalview project</li>
1413 <li>Browser launch fails with NPE on java 1.7</li>
1414 <li>JABAWS alignment marked as finished when job was
1415 cancelled or job failed due to invalid input</li>
1416 <li>NPE with v2.7 example when clicking on Tree
1417 associated with all views</li>
1418 <li>Exceptions when copy/paste sequences with grouped
1419 annotation rows to new window</li>
1420 </ul> <em>Applet</em>
1422 <li>Sequence features are momentarily displayed before
1423 they are hidden using hidefeaturegroups applet parameter</li>
1424 <li>loading features via javascript API automatically
1425 enables feature display</li>
1426 <li>scrollToColumnIn javascript API method doesn't
1428 </ul> <em>General</em>
1430 <li>Redundancy removal fails for rna alignment</li>
1431 <li>PCA calculation fails when sequence has been selected
1432 and then deselected</li>
1433 <li>PCA window shows grey box when first opened on OSX</li>
1434 <li>Letters coloured pink in sequence logo when alignment
1435 coloured with clustalx</li>
1436 <li>Choosing fonts without letter symbols defined causes
1437 exceptions and redraw errors</li>
1438 <li>Initial PCA plot view is not same as manually
1439 reconfigured view</li>
1440 <li>Grouped annotation graph label has incorrect line
1442 <li>Grouped annotation graph label display is corrupted
1443 for lots of labels</li>
1448 <div align="center">
1449 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
1452 <td><em>Application</em>
1454 <li>Jalview Desktop News Reader</li>
1455 <li>Tweaked default layout of web services menu</li>
1456 <li>View/alignment association menu to enable user to
1457 easily specify which alignment a multi-structure view takes
1458 its colours/correspondences from</li>
1459 <li>Allow properties file location to be specified as URL</li>
1460 <li>Extend Jalview project to preserve associations
1461 between many alignment views and a single Jmol display</li>
1462 <li>Store annotation row height in Jalview project file</li>
1463 <li>Annotation row column label formatting attributes
1464 stored in project file</li>
1465 <li>Annotation row order for auto-calculated annotation
1466 rows preserved in Jalview project file</li>
1467 <li>Visual progress indication when Jalview state is
1468 saved using Desktop window menu</li>
1469 <li>Visual indication that command line arguments are
1470 still being processed</li>
1471 <li>Groovy script execution from URL</li>
1472 <li>Colour by annotation default min and max colours in
1474 <li>Automatically associate PDB files dragged onto an
1475 alignment with sequences that have high similarity and
1477 <li>Update JGoogleAnalytics to latest release (0.3)</li>
1478 <li>'view structures' option to open many
1479 structures in same window</li>
1480 <li>Sort associated views menu option for tree panel</li>
1481 <li>Group all JABA and non-JABA services for a particular
1482 analysis function in its own submenu</li>
1483 </ul> <em>Applet</em>
1485 <li>Userdefined and autogenerated annotation rows for
1487 <li>Adjustment of alignment annotation pane height</li>
1488 <li>Annotation scrollbar for annotation panel</li>
1489 <li>Drag to reorder annotation rows in annotation panel</li>
1490 <li>'automaticScrolling' parameter</li>
1491 <li>Allow sequences with partial ID string matches to be
1492 annotated from GFF/Jalview features files</li>
1493 <li>Sequence logo annotation row in applet</li>
1494 <li>Absolute paths relative to host server in applet
1495 parameters are treated as such</li>
1496 <li>New in the JalviewLite javascript API:
1498 <li>JalviewLite.js javascript library</li>
1499 <li>Javascript callbacks for
1501 <li>Applet initialisation</li>
1502 <li>Sequence/alignment mouse-overs and selections</li>
1505 <li>scrollTo row and column alignment scrolling
1507 <li>Select sequence/alignment regions from javascript</li>
1508 <li>javascript structure viewer harness to pass
1509 messages between Jmol and Jalview when running as
1510 distinct applets</li>
1511 <li>sortBy method</li>
1512 <li>Set of applet and application examples shipped
1513 with documentation</li>
1514 <li>New example to demonstrate JalviewLite and Jmol
1515 javascript message exchange</li>
1517 </ul> <em>General</em>
1519 <li>Enable Jmol displays to be associated with multiple
1520 multiple alignments</li>
1521 <li>Option to automatically sort alignment with new tree</li>
1522 <li>User configurable link to enable redirects to a
1523 www.Jalview.org mirror</li>
1524 <li>Jmol colours option for Jmol displays</li>
1525 <li>Configurable newline string when writing alignment
1526 and other flat files</li>
1527 <li>Allow alignment annotation description lines to
1528 contain html tags</li>
1529 </ul> <em>Documentation and Development</em>
1531 <li>Add groovy test harness for bulk load testing to
1533 <li>Groovy script to load and align a set of sequences
1534 using a web service before displaying the result in the
1535 Jalview desktop</li>
1536 <li>Restructured javascript and applet api documentation</li>
1537 <li>Ant target to publish example html files with applet
1539 <li>Netbeans project for building Jalview from source</li>
1540 <li>ant task to create online javadoc for Jalview source</li>
1542 <td><em>Application</em>
1544 <li>User defined colourscheme throws exception when
1545 current built in colourscheme is saved as new scheme</li>
1546 <li>AlignFrame->Save in application pops up save
1547 dialog for valid filename/format</li>
1548 <li>Cannot view associated structure for UniProt sequence</li>
1549 <li>PDB file association breaks for UniProt sequence
1551 <li>Associate PDB from file dialog does not tell you
1552 which sequence is to be associated with the file</li>
1553 <li>Find All raises null pointer exception when query
1554 only matches sequence IDs</li>
1555 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
1556 <li>Jalview project with Jmol views created with Jalview
1557 2.4 cannot be loaded</li>
1558 <li>Filetype associations not installed for webstart
1560 <li>Two or more chains in a single PDB file associated
1561 with sequences in different alignments do not get coloured
1562 by their associated sequence</li>
1563 <li>Visibility status of autocalculated annotation row
1564 not preserved when project is loaded</li>
1565 <li>Annotation row height and visibility attributes not
1566 stored in Jalview project</li>
1567 <li>Tree bootstraps are not preserved when saved as a
1568 Jalview project</li>
1569 <li>Envision2 workflow tooltips are corrupted</li>
1570 <li>Enabling show group conservation also enables colour
1571 by conservation</li>
1572 <li>Duplicate group associated conservation or consensus
1573 created on new view</li>
1574 <li>Annotation scrollbar not displayed after 'show
1575 all hidden annotation rows' option selected</li>
1576 <li>Alignment quality not updated after alignment
1577 annotation row is hidden then shown</li>
1578 <li>Preserve colouring of structures coloured by
1579 sequences in pre Jalview 2.7 projects</li>
1580 <li>Web service job parameter dialog is not laid out
1582 <li>Web services menu not refreshed after 'reset
1583 services' button is pressed in preferences</li>
1584 <li>Annotation off by one in Jalview v2_3 example project</li>
1585 <li>Structures imported from file and saved in project
1586 get name like jalview_pdb1234.txt when reloaded</li>
1587 <li>Jalview does not always retrieve progress of a JABAWS
1588 job execution in full once it is complete</li>
1589 </ul> <em>Applet</em>
1591 <li>Alignment height set incorrectly when lots of
1592 annotation rows are displayed</li>
1593 <li>Relative URLs in feature HTML text not resolved to
1595 <li>View follows highlighting does not work for positions
1597 <li><= shown as = in tooltip</li>
1598 <li>Export features raises exception when no features
1600 <li>Separator string used for serialising lists of IDs
1601 for javascript api is modified when separator string
1602 provided as parameter</li>
1603 <li>Null pointer exception when selecting tree leaves for
1604 alignment with no existing selection</li>
1605 <li>Relative URLs for datasources assumed to be relative
1606 to applet's codebase</li>
1607 <li>Status bar not updated after finished searching and
1608 search wraps around to first result</li>
1609 <li>StructureSelectionManager instance shared between
1610 several Jalview applets causes race conditions and memory
1612 <li>Hover tooltip and mouseover of position on structure
1613 not sent from Jmol in applet</li>
1614 <li>Certain sequences of javascript method calls to
1615 applet API fatally hang browser</li>
1616 </ul> <em>General</em>
1618 <li>View follows structure mouseover scrolls beyond
1619 position with wrapped view and hidden regions</li>
1620 <li>Find sequence position moves to wrong residue
1621 with/without hidden columns</li>
1622 <li>Sequence length given in alignment properties window
1624 <li>InvalidNumberFormat exceptions thrown when trying to
1625 import PDB like structure files</li>
1626 <li>Positional search results are only highlighted
1627 between user-supplied sequence start/end bounds</li>
1628 <li>End attribute of sequence is not validated</li>
1629 <li>Find dialog only finds first sequence containing a
1630 given sequence position</li>
1631 <li>Sequence numbering not preserved in MSF alignment
1633 <li>Jalview PDB file reader does not extract sequence
1634 from nucleotide chains correctly</li>
1635 <li>Structure colours not updated when tree partition
1636 changed in alignment</li>
1637 <li>Sequence associated secondary structure not correctly
1638 parsed in interleaved stockholm</li>
1639 <li>Colour by annotation dialog does not restore current
1641 <li>Hiding (nearly) all sequences doesn't work
1643 <li>Sequences containing lowercase letters are not
1644 properly associated with their pdb files</li>
1645 </ul> <em>Documentation and Development</em>
1647 <li>schemas/JalviewWsParamSet.xsd corrupted by
1648 ApplyCopyright tool</li>
1653 <div align="center">
1654 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
1657 <td><em>Application</em>
1659 <li>New warning dialog when the Jalview Desktop cannot
1660 contact web services</li>
1661 <li>JABA service parameters for a preset are shown in
1662 service job window</li>
1663 <li>JABA Service menu entries reworded</li>
1667 <li>Modeller PIR IO broken - cannot correctly import a
1668 pir file emitted by Jalview</li>
1669 <li>Existing feature settings transferred to new
1670 alignment view created from cut'n'paste</li>
1671 <li>Improved test for mixed amino/nucleotide chains when
1672 parsing PDB files</li>
1673 <li>Consensus and conservation annotation rows
1674 occasionally become blank for all new windows</li>
1675 <li>Exception raised when right clicking above sequences
1676 in wrapped view mode</li>
1677 </ul> <em>Application</em>
1679 <li>multiple multiply aligned structure views cause cpu
1680 usage to hit 100% and computer to hang</li>
1681 <li>Web Service parameter layout breaks for long user
1682 parameter names</li>
1683 <li>Jaba service discovery hangs desktop if Jaba server
1690 <div align="center">
1691 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
1694 <td><em>Application</em>
1696 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
1697 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
1700 <li>Web Services preference tab</li>
1701 <li>Analysis parameters dialog box and user defined
1703 <li>Improved speed and layout of Envision2 service menu</li>
1704 <li>Superpose structures using associated sequence
1706 <li>Export coordinates and projection as CSV from PCA
1708 </ul> <em>Applet</em>
1710 <li>enable javascript: execution by the applet via the
1711 link out mechanism</li>
1712 </ul> <em>Other</em>
1714 <li>Updated the Jmol Jalview interface to work with Jmol
1716 <li>The Jalview Desktop and JalviewLite applet now
1717 require Java 1.5</li>
1718 <li>Allow Jalview feature colour specification for GFF
1719 sequence annotation files</li>
1720 <li>New 'colour by label' keword in Jalview feature file
1721 type colour specification</li>
1722 <li>New Jalview Desktop Groovy API method that allows a
1723 script to check if it being run in an interactive session or
1724 in a batch operation from the Jalview command line</li>
1728 <li>clustalx colourscheme colours Ds preferentially when
1729 both D+E are present in over 50% of the column</li>
1730 </ul> <em>Application</em>
1732 <li>typo in AlignmentFrame->View->Hide->all but
1733 selected Regions menu item</li>
1734 <li>sequence fetcher replaces ',' for ';' when the ',' is
1735 part of a valid accession ID</li>
1736 <li>fatal OOM if object retrieved by sequence fetcher
1737 runs out of memory</li>
1738 <li>unhandled Out of Memory Error when viewing pca
1739 analysis results</li>
1740 <li>InstallAnywhere builds fail to launch on OS X java
1741 10.5 update 4 (due to apple Java 1.6 update)</li>
1742 <li>Installanywhere Jalview silently fails to launch</li>
1743 </ul> <em>Applet</em>
1745 <li>Jalview.getFeatureGroups() raises an
1746 ArrayIndexOutOfBoundsException if no feature groups are
1753 <div align="center">
1754 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
1760 <li>Alignment prettyprinter doesn't cope with long
1762 <li>clustalx colourscheme colours Ds preferentially when
1763 both D+E are present in over 50% of the column</li>
1764 <li>nucleic acid structures retrieved from PDB do not
1765 import correctly</li>
1766 <li>More columns get selected than were clicked on when a
1767 number of columns are hidden</li>
1768 <li>annotation label popup menu not providing correct
1769 add/hide/show options when rows are hidden or none are
1771 <li>Stockholm format shown in list of readable formats,
1772 and parser copes better with alignments from RFAM.</li>
1773 <li>CSV output of consensus only includes the percentage
1774 of all symbols if sequence logo display is enabled</li>
1776 </ul> <em>Applet</em>
1778 <li>annotation panel disappears when annotation is
1780 </ul> <em>Application</em>
1782 <li>Alignment view not redrawn properly when new
1783 alignment opened where annotation panel is visible but no
1784 annotations are present on alignment</li>
1785 <li>pasted region containing hidden columns is
1786 incorrectly displayed in new alignment window</li>
1787 <li>Jalview slow to complete operations when stdout is
1788 flooded (fix is to close the Jalview console)</li>
1789 <li>typo in AlignmentFrame->View->Hide->all but
1790 selected Rregions menu item.</li>
1791 <li>inconsistent group submenu and Format submenu entry
1792 'Un' or 'Non'conserved</li>
1793 <li>Sequence feature settings are being shared by
1794 multiple distinct alignments</li>
1795 <li>group annotation not recreated when tree partition is
1797 <li>double click on group annotation to select sequences
1798 does not propagate to associated trees</li>
1799 <li>Mac OSX specific issues:
1801 <li>exception raised when mouse clicked on desktop
1802 window background</li>
1803 <li>Desktop menu placed on menu bar and application
1804 name set correctly</li>
1805 <li>sequence feature settings not wide enough for the
1806 save feature colourscheme button</li>
1815 <div align="center">
1816 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
1819 <td><em>New Capabilities</em>
1821 <li>URL links generated from description line for
1822 regular-expression based URL links (applet and application)
1829 <li>Non-positional feature URL links are shown in link
1831 <li>Linked viewing of nucleic acid sequences and
1833 <li>Automatic Scrolling option in View menu to display
1834 the currently highlighted region of an alignment.</li>
1835 <li>Order an alignment by sequence length, or using the
1836 average score or total feature count for each sequence.</li>
1837 <li>Shading features by score or associated description</li>
1838 <li>Subdivide alignment and groups based on identity of
1839 selected subsequence (Make Groups from Selection).</li>
1840 <li>New hide/show options including Shift+Control+H to
1841 hide everything but the currently selected region.</li>
1842 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
1843 </ul> <em>Application</em>
1845 <li>Fetch DB References capabilities and UI expanded to
1846 support retrieval from DAS sequence sources</li>
1847 <li>Local DAS Sequence sources can be added via the
1848 command line or via the Add local source dialog box.</li>
1849 <li>DAS Dbref and DbxRef feature types are parsed as
1850 database references and protein_name is parsed as
1851 description line (BioSapiens terms).</li>
1852 <li>Enable or disable non-positional feature and database
1853 references in sequence ID tooltip from View menu in
1855 <!-- <li>New hidden columns and rows and representatives capabilities
1856 in annotations file (in progress - not yet fully implemented)</li> -->
1857 <li>Group-associated consensus, sequence logos and
1858 conservation plots</li>
1859 <li>Symbol distributions for each column can be exported
1860 and visualized as sequence logos</li>
1861 <li>Optionally scale multi-character column labels to fit
1862 within each column of annotation row<!-- todo for applet -->
1864 <li>Optional automatic sort of associated alignment view
1865 when a new tree is opened.</li>
1866 <li>Jalview Java Console</li>
1867 <li>Better placement of desktop window when moving
1868 between different screens.</li>
1869 <li>New preference items for sequence ID tooltip and
1870 consensus annotation</li>
1871 <li>Client to submit sequences and IDs to Envision2
1873 <li><em>Vamsas Capabilities</em>
1875 <li>Improved VAMSAS synchronization (Jalview archive
1876 used to preserve views, structures, and tree display
1878 <li>Import of vamsas documents from disk or URL via
1880 <li>Sharing of selected regions between views and
1881 with other VAMSAS applications (Experimental feature!)</li>
1882 <li>Updated API to VAMSAS version 0.2</li>
1884 </ul> <em>Applet</em>
1886 <li>Middle button resizes annotation row height</li>
1889 <li>sortByTree (true/false) - automatically sort the
1890 associated alignment view by the tree when a new tree is
1892 <li>showTreeBootstraps (true/false) - show or hide
1893 branch bootstraps (default is to show them if available)</li>
1894 <li>showTreeDistances (true/false) - show or hide
1895 branch lengths (default is to show them if available)</li>
1896 <li>showUnlinkedTreeNodes (true/false) - indicate if
1897 unassociated nodes should be highlighted in the tree
1899 <li>heightScale and widthScale (1.0 or more) -
1900 increase the height or width of a cell in the alignment
1901 grid relative to the current font size.</li>
1904 <li>Non-positional features displayed in sequence ID
1906 </ul> <em>Other</em>
1908 <li>Features format: graduated colour definitions and
1909 specification of feature scores</li>
1910 <li>Alignment Annotations format: new keywords for group
1911 associated annotation (GROUP_REF) and annotation row display
1912 properties (ROW_PROPERTIES)</li>
1913 <li>XML formats extended to support graduated feature
1914 colourschemes, group associated annotation, and profile
1915 visualization settings.</li></td>
1918 <li>Source field in GFF files parsed as feature source
1919 rather than description</li>
1920 <li>Non-positional features are now included in sequence
1921 feature and gff files (controlled via non-positional feature
1922 visibility in tooltip).</li>
1923 <li>URL links generated for all feature links (bugfix)</li>
1924 <li>Added URL embedding instructions to features file
1926 <li>Codons containing ambiguous nucleotides translated as
1927 'X' in peptide product</li>
1928 <li>Match case switch in find dialog box works for both
1929 sequence ID and sequence string and query strings do not
1930 have to be in upper case to match case-insensitively.</li>
1931 <li>AMSA files only contain first column of
1932 multi-character column annotation labels</li>
1933 <li>Jalview Annotation File generation/parsing consistent
1934 with documentation (e.g. Stockholm annotation can be
1935 exported and re-imported)</li>
1936 <li>PDB files without embedded PDB IDs given a friendly
1938 <li>Find incrementally searches ID string matches as well
1939 as subsequence matches, and correctly reports total number
1943 <li>Better handling of exceptions during sequence
1945 <li>Dasobert generated non-positional feature URL
1946 link text excludes the start_end suffix</li>
1947 <li>DAS feature and source retrieval buttons disabled
1948 when fetch or registry operations in progress.</li>
1949 <li>PDB files retrieved from URLs are cached properly</li>
1950 <li>Sequence description lines properly shared via
1952 <li>Sequence fetcher fetches multiple records for all
1954 <li>Ensured that command line das feature retrieval
1955 completes before alignment figures are generated.</li>
1956 <li>Reduced time taken when opening file browser for
1958 <li>isAligned check prior to calculating tree, PCA or
1959 submitting an MSA to JNet now excludes hidden sequences.</li>
1960 <li>User defined group colours properly recovered
1961 from Jalview projects.</li>
1970 <div align="center">
1971 <strong>2.4.0.b2</strong><br> 28/10/2009
1976 <li>Experimental support for google analytics usage
1978 <li>Jalview privacy settings (user preferences and docs).</li>
1983 <li>Race condition in applet preventing startup in
1985 <li>Exception when feature created from selection beyond
1986 length of sequence.</li>
1987 <li>Allow synthetic PDB files to be imported gracefully</li>
1988 <li>Sequence associated annotation rows associate with
1989 all sequences with a given id</li>
1990 <li>Find function matches case-insensitively for sequence
1991 ID string searches</li>
1992 <li>Non-standard characters do not cause pairwise
1993 alignment to fail with exception</li>
1994 </ul> <em>Application Issues</em>
1996 <li>Sequences are now validated against EMBL database</li>
1997 <li>Sequence fetcher fetches multiple records for all
1999 </ul> <em>InstallAnywhere Issues</em>
2001 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2002 issue with installAnywhere mechanism)</li>
2003 <li>Command line launching of JARs from InstallAnywhere
2004 version (java class versioning error fixed)</li>
2011 <div align="center">
2012 <strong>2.4</strong><br> 27/8/2008
2015 <td><em>User Interface</em>
2017 <li>Linked highlighting of codon and amino acid from
2018 translation and protein products</li>
2019 <li>Linked highlighting of structure associated with
2020 residue mapping to codon position</li>
2021 <li>Sequence Fetcher provides example accession numbers
2022 and 'clear' button</li>
2023 <li>MemoryMonitor added as an option under Desktop's
2025 <li>Extract score function to parse whitespace separated
2026 numeric data in description line</li>
2027 <li>Column labels in alignment annotation can be centred.</li>
2028 <li>Tooltip for sequence associated annotation give name
2030 </ul> <em>Web Services and URL fetching</em>
2032 <li>JPred3 web service</li>
2033 <li>Prototype sequence search client (no public services
2035 <li>Fetch either seed alignment or full alignment from
2037 <li>URL Links created for matching database cross
2038 references as well as sequence ID</li>
2039 <li>URL Links can be created using regular-expressions</li>
2040 </ul> <em>Sequence Database Connectivity</em>
2042 <li>Retrieval of cross-referenced sequences from other
2044 <li>Generalised database reference retrieval and
2045 validation to all fetchable databases</li>
2046 <li>Fetch sequences from DAS sources supporting the
2047 sequence command</li>
2048 </ul> <em>Import and Export</em>
2049 <li>export annotation rows as CSV for spreadsheet import</li>
2050 <li>Jalview projects record alignment dataset associations,
2051 EMBL products, and cDNA sequence mappings</li>
2052 <li>Sequence Group colour can be specified in Annotation
2054 <li>Ad-hoc colouring of group in Annotation File using RGB
2055 triplet as name of colourscheme</li>
2056 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2058 <li>treenode binding for VAMSAS tree exchange</li>
2059 <li>local editing and update of sequences in VAMSAS
2060 alignments (experimental)</li>
2061 <li>Create new or select existing session to join</li>
2062 <li>load and save of vamsas documents</li>
2063 </ul> <em>Application command line</em>
2065 <li>-tree parameter to open trees (introduced for passing
2067 <li>-fetchfrom command line argument to specify nicknames
2068 of DAS servers to query for alignment features</li>
2069 <li>-dasserver command line argument to add new servers
2070 that are also automatically queried for features</li>
2071 <li>-groovy command line argument executes a given groovy
2072 script after all input data has been loaded and parsed</li>
2073 </ul> <em>Applet-Application data exchange</em>
2075 <li>Trees passed as applet parameters can be passed to
2076 application (when using "View in full
2077 application")</li>
2078 </ul> <em>Applet Parameters</em>
2080 <li>feature group display control parameter</li>
2081 <li>debug parameter</li>
2082 <li>showbutton parameter</li>
2083 </ul> <em>Applet API methods</em>
2085 <li>newView public method</li>
2086 <li>Window (current view) specific get/set public methods</li>
2087 <li>Feature display control methods</li>
2088 <li>get list of currently selected sequences</li>
2089 </ul> <em>New Jalview distribution features</em>
2091 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2092 <li>RELEASE file gives build properties for the latest
2093 Jalview release.</li>
2094 <li>Java 1.1 Applet build made easier and donotobfuscate
2095 property controls execution of obfuscator</li>
2096 <li>Build target for generating source distribution</li>
2097 <li>Debug flag for javacc</li>
2098 <li>.jalview_properties file is documented (slightly) in
2099 jalview.bin.Cache</li>
2100 <li>Continuous Build Integration for stable and
2101 development version of Application, Applet and source
2106 <li>selected region output includes visible annotations
2107 (for certain formats)</li>
2108 <li>edit label/displaychar contains existing label/char
2110 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2111 <li>shorter peptide product names from EMBL records</li>
2112 <li>Newick string generator makes compact representations</li>
2113 <li>bootstrap values parsed correctly for tree files with
2115 <li>pathological filechooser bug avoided by not allowing
2116 filenames containing a ':'</li>
2117 <li>Fixed exception when parsing GFF files containing
2118 global sequence features</li>
2119 <li>Alignment datasets are finalized only when number of
2120 references from alignment sequences goes to zero</li>
2121 <li>Close of tree branch colour box without colour
2122 selection causes cascading exceptions</li>
2123 <li>occasional negative imgwidth exceptions</li>
2124 <li>better reporting of non-fatal warnings to user when
2125 file parsing fails.</li>
2126 <li>Save works when Jalview project is default format</li>
2127 <li>Save as dialog opened if current alignment format is
2128 not a valid output format</li>
2129 <li>UniProt canonical names introduced for both das and
2131 <li>Histidine should be midblue (not pink!) in Zappo</li>
2132 <li>error messages passed up and output when data read
2134 <li>edit undo recovers previous dataset sequence when
2135 sequence is edited</li>
2136 <li>allow PDB files without pdb ID HEADER lines (like
2137 those generated by MODELLER) to be read in properly</li>
2138 <li>allow reading of JPred concise files as a normal
2140 <li>Stockholm annotation parsing and alignment properties
2141 import fixed for PFAM records</li>
2142 <li>Structure view windows have correct name in Desktop
2144 <li>annotation consisting of sequence associated scores
2145 can be read and written correctly to annotation file</li>
2146 <li>Aligned cDNA translation to aligned peptide works
2148 <li>Fixed display of hidden sequence markers and
2149 non-italic font for representatives in Applet</li>
2150 <li>Applet Menus are always embedded in applet window on
2152 <li>Newly shown features appear at top of stack (in
2154 <li>Annotations added via parameter not drawn properly
2155 due to null pointer exceptions</li>
2156 <li>Secondary structure lines are drawn starting from
2157 first column of alignment</li>
2158 <li>UniProt XML import updated for new schema release in
2160 <li>Sequence feature to sequence ID match for Features
2161 file is case-insensitive</li>
2162 <li>Sequence features read from Features file appended to
2163 all sequences with matching IDs</li>
2164 <li>PDB structure coloured correctly for associated views
2165 containing a sub-sequence</li>
2166 <li>PDB files can be retrieved by applet from Jar files</li>
2167 <li>feature and annotation file applet parameters
2168 referring to different directories are retrieved correctly</li>
2169 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
2170 <li>Fixed application hang whilst waiting for
2171 splash-screen version check to complete</li>
2172 <li>Applet properly URLencodes input parameter values
2173 when passing them to the launchApp service</li>
2174 <li>display name and local features preserved in results
2175 retrieved from web service</li>
2176 <li>Visual delay indication for sequence retrieval and
2177 sequence fetcher initialisation</li>
2178 <li>updated Application to use DAS 1.53e version of
2179 dasobert DAS client</li>
2180 <li>Re-instated Full AMSA support and .amsa file
2182 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
2190 <div align="center">
2191 <strong>2.3</strong><br> 9/5/07
2196 <li>Jmol 11.0.2 integration</li>
2197 <li>PDB views stored in Jalview XML files</li>
2198 <li>Slide sequences</li>
2199 <li>Edit sequence in place</li>
2200 <li>EMBL CDS features</li>
2201 <li>DAS Feature mapping</li>
2202 <li>Feature ordering</li>
2203 <li>Alignment Properties</li>
2204 <li>Annotation Scores</li>
2205 <li>Sort by scores</li>
2206 <li>Feature/annotation editing in applet</li>
2211 <li>Headless state operation in 2.2.1</li>
2212 <li>Incorrect and unstable DNA pairwise alignment</li>
2213 <li>Cut and paste of sequences with annotation</li>
2214 <li>Feature group display state in XML</li>
2215 <li>Feature ordering in XML</li>
2216 <li>blc file iteration selection using filename # suffix</li>
2217 <li>Stockholm alignment properties</li>
2218 <li>Stockhom alignment secondary structure annotation</li>
2219 <li>2.2.1 applet had no feature transparency</li>
2220 <li>Number pad keys can be used in cursor mode</li>
2221 <li>Structure Viewer mirror image resolved</li>
2228 <div align="center">
2229 <strong>2.2.1</strong><br> 12/2/07
2234 <li>Non standard characters can be read and displayed
2235 <li>Annotations/Features can be imported/exported to the
2237 <li>Applet allows editing of sequence/annotation/group
2238 name & description
2239 <li>Preference setting to display sequence name in
2241 <li>Annotation file format extended to allow
2242 Sequence_groups to be defined
2243 <li>Default opening of alignment overview panel can be
2244 specified in preferences
2245 <li>PDB residue numbering annotation added to associated
2251 <li>Applet crash under certain Linux OS with Java 1.6
2253 <li>Annotation file export / import bugs fixed
2254 <li>PNG / EPS image output bugs fixed
2260 <div align="center">
2261 <strong>2.2</strong><br> 27/11/06
2266 <li>Multiple views on alignment
2267 <li>Sequence feature editing
2268 <li>"Reload" alignment
2269 <li>"Save" to current filename
2270 <li>Background dependent text colour
2271 <li>Right align sequence ids
2272 <li>User-defined lower case residue colours
2275 <li>Menu item accelerator keys
2276 <li>Control-V pastes to current alignment
2277 <li>Cancel button for DAS Feature Fetching
2278 <li>PCA and PDB Viewers zoom via mouse roller
2279 <li>User-defined sub-tree colours and sub-tree selection
2286 <li>'New Window' button on the 'Output to Text box'
2291 <li>New memory efficient Undo/Redo System
2292 <li>Optimised symbol lookups and conservation/consensus
2294 <li>Region Conservation/Consensus recalculated after
2296 <li>Fixed Remove Empty Columns Bug (empty columns at end
2298 <li>Slowed DAS Feature Fetching for increased robustness.
2305 <li>Made angle brackets in ASCII feature descriptions
2307 <li>Re-instated Zoom function for PCA
2308 <li>Sequence descriptions conserved in web service
2310 <li>UniProt ID discoverer uses any word separated by
2312 <li>WsDbFetch query/result association resolved
2313 <li>Tree leaf to sequence mapping improved
2314 <li>Smooth fonts switch moved to FontChooser dialog box.
2326 <div align="center">
2327 <strong>2.1.1</strong><br> 12/9/06
2332 <li>Copy consensus sequence to clipboard</li>
2337 <li>Image output - rightmost residues are rendered if
2338 sequence id panel has been resized</li>
2339 <li>Image output - all offscreen group boundaries are
2341 <li>Annotation files with sequence references - all
2342 elements in file are relative to sequence position</li>
2343 <li>Mac Applet users can use Alt key for group editing</li>
2349 <div align="center">
2350 <strong>2.1</strong><br> 22/8/06
2355 <li>MAFFT Multiple Alignment in default Web Service list</li>
2356 <li>DAS Feature fetching</li>
2357 <li>Hide sequences and columns</li>
2358 <li>Export Annotations and Features</li>
2359 <li>GFF file reading / writing</li>
2360 <li>Associate structures with sequences from local PDB
2362 <li>Add sequences to exisiting alignment</li>
2363 <li>Recently opened files / URL lists</li>
2364 <li>Applet can launch the full application</li>
2365 <li>Applet has transparency for features (Java 1.2
2367 <li>Applet has user defined colours parameter</li>
2368 <li>Applet can load sequences from parameter
2369 "sequence<em>x</em>"
2375 <li>Redundancy Panel reinstalled in the Applet</li>
2376 <li>Monospaced font - EPS / rescaling bug fixed</li>
2377 <li>Annotation files with sequence references bug fixed</li>
2383 <div align="center">
2384 <strong>2.08.1</strong><br> 2/5/06
2389 <li>Change case of selected region from Popup menu</li>
2390 <li>Choose to match case when searching</li>
2391 <li>Middle mouse button and mouse movement can compress /
2392 expand the visible width and height of the alignment</li>
2397 <li>Annotation Panel displays complete JNet results</li>
2403 <div align="center">
2404 <strong>2.08b</strong><br> 18/4/06
2410 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
2411 <li>Righthand label on wrapped alignments shows correct
2418 <div align="center">
2419 <strong>2.08</strong><br> 10/4/06
2424 <li>Editing can be locked to the selection area</li>
2425 <li>Keyboard editing</li>
2426 <li>Create sequence features from searches</li>
2427 <li>Precalculated annotations can be loaded onto
2429 <li>Features file allows grouping of features</li>
2430 <li>Annotation Colouring scheme added</li>
2431 <li>Smooth fonts off by default - Faster rendering</li>
2432 <li>Choose to toggle Autocalculate Consensus On/Off</li>
2437 <li>Drag & Drop fixed on Linux</li>
2438 <li>Jalview Archive file faster to load/save, sequence
2439 descriptions saved.</li>
2445 <div align="center">
2446 <strong>2.07</strong><br> 12/12/05
2451 <li>PDB Structure Viewer enhanced</li>
2452 <li>Sequence Feature retrieval and display enhanced</li>
2453 <li>Choose to output sequence start-end after sequence
2454 name for file output</li>
2455 <li>Sequence Fetcher WSDBFetch@EBI</li>
2456 <li>Applet can read feature files, PDB files and can be
2457 used for HTML form input</li>
2462 <li>HTML output writes groups and features</li>
2463 <li>Group editing is Control and mouse click</li>
2464 <li>File IO bugs</li>
2470 <div align="center">
2471 <strong>2.06</strong><br> 28/9/05
2476 <li>View annotations in wrapped mode</li>
2477 <li>More options for PCA viewer</li>
2482 <li>GUI bugs resolved</li>
2483 <li>Runs with -nodisplay from command line</li>
2489 <div align="center">
2490 <strong>2.05b</strong><br> 15/9/05
2495 <li>Choose EPS export as lineart or text</li>
2496 <li>Jar files are executable</li>
2497 <li>Can read in Uracil - maps to unknown residue</li>
2502 <li>Known OutOfMemory errors give warning message</li>
2503 <li>Overview window calculated more efficiently</li>
2504 <li>Several GUI bugs resolved</li>
2510 <div align="center">
2511 <strong>2.05</strong><br> 30/8/05
2516 <li>Edit and annotate in "Wrapped" view</li>
2521 <li>Several GUI bugs resolved</li>
2527 <div align="center">
2528 <strong>2.04</strong><br> 24/8/05
2533 <li>Hold down mouse wheel & scroll to change font
2539 <li>Improved JPred client reliability</li>
2540 <li>Improved loading of Jalview files</li>
2546 <div align="center">
2547 <strong>2.03</strong><br> 18/8/05
2552 <li>Set Proxy server name and port in preferences</li>
2553 <li>Multiple URL links from sequence ids</li>
2554 <li>User Defined Colours can have a scheme name and added
2556 <li>Choose to ignore gaps in consensus calculation</li>
2557 <li>Unix users can set default web browser</li>
2558 <li>Runs without GUI for batch processing</li>
2559 <li>Dynamically generated Web Service Menus</li>
2564 <li>InstallAnywhere download for Sparc Solaris</li>
2570 <div align="center">
2571 <strong>2.02</strong><br> 18/7/05
2577 <li>Copy & Paste order of sequences maintains
2578 alignment order.</li>
2584 <div align="center">
2585 <strong>2.01</strong><br> 12/7/05
2590 <li>Use delete key for deleting selection.</li>
2591 <li>Use Mouse wheel to scroll sequences.</li>
2592 <li>Help file updated to describe how to add alignment
2594 <li>Version and build date written to build properties
2596 <li>InstallAnywhere installation will check for updates
2597 at launch of Jalview.</li>
2602 <li>Delete gaps bug fixed.</li>
2603 <li>FileChooser sorts columns.</li>
2604 <li>Can remove groups one by one.</li>
2605 <li>Filechooser icons installed.</li>
2606 <li>Finder ignores return character when searching.
2607 Return key will initiate a search.<br>
2614 <div align="center">
2615 <strong>2.0</strong><br> 20/6/05
2620 <li>New codebase</li>