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>Jalview projects with views of local PDB structure files saved on Windows cannot be opened on OSX</li>
68 <li>Multiple structure views can be opened and superposed without timeout for structures with multiple models or multiple sequences in alignment</li>
69 <li>Cannot import or associated local PDB files without a PDB ID HEADER line</li>
70 <li>RMSD is not output in Jmol console when superposition is performed</li>
71 <li>Drag and drop of URL from Browser fails for Linux and OSX versions earlier than El Capitan</li>
72 <li>ENA client ignores invalid content from ENA server</li>
73 <li>Exceptions are not raised in console when ENA client attempts to fetch non-existent IDs via Fetch DB Refs UI option</li>
74 <li>Exceptions are not raised in console when a new view is created on the alignment</li>
76 <em>New Known Issues</em>
77 <ul><li>Drag and drop from URL links in browsers do not work on Windows</li></ul>
78 <em>Build and deployment</em>
79 <ul><li>URL link checker now copes with multi-line anchor tags</li></ul>
84 <td width="60" nowrap>
86 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
92 <!-- JAL-2124 -->Updated Spanish translations.
95 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
96 for importing structure data to Jalview. Enables mmCIF and
100 <!-- JAL-192 --->Alignment ruler shows positions relative to
104 <!-- JAL-2202 -->Position/residue shown in status bar when
105 mousing over sequence associated annotation
108 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
112 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
113 '()', canonical '[]' and invalid '{}' base pair populations
117 <!-- JAL-2092 -->Feature settings popup menu options for
118 showing or hiding columns containing a feature
121 <!-- JAL-1557 -->Edit selected group by double clicking on
122 group and sequence associated annotation labels
125 <!-- JAL-2236 -->Sequence name added to annotation label in
126 select/hide columns by annotation and colour by annotation
130 </ul> <em>Application</em>
133 <!-- JAL-2050-->Automatically hide introns when opening a
137 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
141 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
142 structure mappings with the EMBL-EBI PDBe SIFTS database
145 <!-- JAL-2079 -->Updated download sites used for Rfam and
146 Pfam sources to xfam.org
149 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
152 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
153 over sequences in Jalview
156 <!-- JAL-2027-->Support for reverse-complement coding
157 regions in ENA and EMBL
160 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
161 for record retrieval via ENA rest API
164 <!-- JAL-2027 -->Support for ENA CDS records with reverse
168 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
169 groovy script execution
172 <!-- JAL-1812 -->New 'execute Groovy script' option in an
173 alignment window's Calculate menu
176 <!-- JAL-1812 -->Allow groovy scripts that call
177 Jalview.getAlignFrames() to run in headless mode
180 <!-- JAL-2068 -->Support for creating new alignment
181 calculation workers from groovy scripts
184 <!-- JAL-1369 --->Store/restore reference sequence in
188 <!-- JAL-1803 -->Chain codes for a sequence's PDB
189 associations are now saved/restored from project
192 <!-- JAL-1993 -->Database selection dialog always shown
193 before sequence fetcher is opened
196 <!-- JAL-2183 -->Double click on an entry in Jalview's
197 database chooser opens a sequence fetcher
200 <!-- JAL-1563 -->Free-text search client for UniProt using
204 <!-- JAL-2168 -->-nonews command line parameter to prevent
205 the news reader opening
208 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
209 querying stored in preferences
212 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
216 <!-- JAL-1977-->Tooltips shown on database chooser
219 <!-- JAL-391 -->Reverse complement function in calculate
220 menu for nucleotide sequences
223 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
224 and feature counts preserves alignment ordering (and
225 debugged for complex feature sets).
228 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
229 viewing structures with Jalview 2.10
232 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
233 genome, transcript CCDS and gene ids via the Ensembl and
234 Ensembl Genomes REST API
237 <!-- JAL-2049 -->Protein sequence variant annotation
238 computed for 'sequence_variant' annotation on CDS regions
242 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
246 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
247 Ref Fetcher fails to match, or otherwise updates sequence
248 data from external database records.
251 <!-- JAL-2154 -->Revised Jalview Project format for
252 efficient recovery of sequence coding and alignment
253 annotation relationships.
255 </ul> <!-- <em>Applet</em>
266 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
270 <!-- JAL-2018-->Export features in Jalview format (again)
271 includes graduated colourschemes
274 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
275 working with big alignments and lots of hidden columns
278 <!-- JAL-2053-->Hidden column markers not always rendered
279 at right of alignment window
282 <!-- JAL-2067 -->Tidied up links in help file table of
286 <!-- JAL-2072 -->Feature based tree calculation not shown
290 <!-- JAL-2075 -->Hidden columns ignored during feature
291 based tree calculation
294 <!-- JAL-2065 -->Alignment view stops updating when show
295 unconserved enabled for group on alignment
298 <!-- JAL-2086 -->Cannot insert gaps into sequence when
302 <!-- JAL-2146 -->Alignment column in status incorrectly
303 shown as "Sequence position" when mousing over
307 <!-- JAL-2099 -->Incorrect column numbers in ruler when
308 hidden columns present
311 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
312 user created annotation added to alignment
315 <!-- JAL-1841 -->RNA Structure consensus only computed for
316 '()' base pair annotation
319 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
320 in zero scores for all base pairs in RNA Structure
324 <!-- JAL-2174-->Extend selection with columns containing
328 <!-- JAL-2275 -->Pfam format writer puts extra space at
329 beginning of sequence
332 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
336 <!-- JAL-2238 -->Cannot create groups on an alignment from
337 from a tree when t-coffee scores are shown
340 <!-- JAL-1836,1967 -->Cannot import and view PDB
341 structures with chains containing negative resnums (4q4h)
344 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
348 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
349 to Clustal, PIR and PileUp output
352 <!-- JAL-2008 -->Reordering sequence features that are
353 not visible causes alignment window to repaint
356 <!-- JAL-2006 -->Threshold sliders don't work in
357 graduated colour and colour by annotation row for e-value
358 scores associated with features and annotation rows
361 <!-- JAL-1797 -->amino acid physicochemical conservation
362 calculation should be case independent
365 <!-- JAL-2173 -->Remove annotation also updates hidden
369 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
370 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
371 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
374 <!-- JAL-2065 -->Null pointer exceptions and redraw
375 problems when reference sequence defined and 'show
376 non-conserved' enabled
379 <!-- JAL-1306 -->Quality and Conservation are now shown on
380 load even when Consensus calculation is disabled
386 <!-- JAL-1552-->URLs and links can't be imported by
387 drag'n'drop on OSX when launched via webstart (note - not
388 yet fixed for El Capitan)
391 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
392 output when running on non-gb/us i18n platforms
395 <!-- JAL-1944 -->Error thrown when exporting a view with
396 hidden sequences as flat-file alignment
399 <!-- JAL-2030-->InstallAnywhere distribution fails when
403 <!-- JAL-2080-->Jalview very slow to launch via webstart
404 (also hotfix for 2.9.0b2)
407 <!-- JAL-2085 -->Cannot save project when view has a
408 reference sequence defined
411 <!-- JAL-1011 -->Columns are suddenly selected in other
412 alignments and views when revealing hidden columns
415 <!-- JAL-1989 -->Hide columns not mirrored in complement
416 view in a cDNA/Protein splitframe
419 <!-- JAL-1369 -->Cannot save/restore representative
420 sequence from project when only one sequence is
424 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
428 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
429 structure consensus didn't refresh annotation panel
432 <!-- JAL-1962 -->View mapping in structure view shows
433 mappings between sequence and all chains in a PDB file
436 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
437 dialogs format columns correctly, don't display array
438 data, sort columns according to type
441 <!-- JAL-1975 -->Export complete shown after destination
442 file chooser is cancelled during an image export
445 <!-- JAL-2025 -->Error when querying PDB Service with
446 sequence name containing special characters
449 <!-- JAL-2024 -->Manual PDB structure querying should be
453 <!-- JAL-2104 -->Large tooltips with broken HTML
454 formatting don't wrap
457 <!-- JAL-1128 -->Figures exported from wrapped view are
458 truncated so L looks like I in consensus annotation
461 <!-- JAL-2003 -->Export features should only export the
462 currently displayed features for the current selection or
466 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
467 after fetching cross-references, and restoring from project
470 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
471 followed in the structure viewer
474 <!-- JAL-2163 -->Titles for individual alignments in
475 splitframe not restored from project
478 <!-- JAL-2145 -->missing autocalculated annotation at
479 trailing end of protein alignment in transcript/product
480 splitview when pad-gaps not enabled by default
483 <!-- JAL-1797 -->amino acid physicochemical conservation
487 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
488 article has been read (reopened issue due to
489 internationalisation problems)
492 <!-- JAL-1960 -->Only offer PDB structures in structure
493 viewer based on sequence name, PDB and UniProt
498 <!-- JAL-1976 -->No progress bar shown during export of
502 <!-- JAL-2213 -->Structures not always superimposed after
503 multiple structures are shown for one or more sequences.
506 <!-- JAL-1370 -->Reference sequence characters should not
507 be replaced with '.' when 'Show unconserved' format option
511 <!-- JAL-1823 -->Cannot specify chain code when entering
512 specific PDB id for sequence
515 <!-- JAL-1944 -->File->Export->.. as doesn't work when
516 'Export hidden sequences' is enabled, but 'export hidden
517 columns' is disabled.
520 <!--JAL-2026-->Best Quality option in structure chooser
521 selects lowest rather than highest resolution structures
525 <!-- JAL-1887 -->Incorrect start and end reported for PDB
526 to sequence mapping in 'View Mappings' report
528 <!-- may exclude, this is an external service stability issue JAL-1941
529 -- > RNA 3D structure not added via DSSR service</li> -->
534 <!-- JAL-2151 -->Incorrect columns are selected when
535 hidden columns present before start of sequence
538 <!-- JAL-1986 -->Missing dependencies on applet pages
542 <!-- JAL-1947 -->Overview pixel size changes when
543 sequences are hidden in applet
546 <!-- JAL-1996 -->Updated instructions for applet
547 deployment on examples pages.
554 <td width="60" nowrap>
556 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
557 <em>16/10/2015</em></strong>
562 <li>Time stamps for signed Jalview application and applet
569 <li>Duplicate group consensus and conservation rows
570 shown when tree is partitioned</li>
571 <li>Erratic behaviour when tree partitions made with
572 multiple cDNA/Protein split views</li>
578 <td width="60" nowrap>
580 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
581 <em>8/10/2015</em></strong>
586 <li>Updated Spanish translations of localized text for
588 </ul> <em>Application</em>
590 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
591 <li>Signed OSX InstallAnywhere installer<br></li>
592 <li>Support for per-sequence based annotations in BioJSON</li>
593 </ul> <em>Applet</em>
595 <li>Split frame example added to applet examples page</li>
601 <li>Mapping of cDNA to protein in split frames
602 incorrect when sequence start > 1</li>
603 <li>Broken images in filter column by annotation dialog
605 <li>Feature colours not parsed from features file</li>
606 <li>Exceptions and incomplete link URLs recovered when
607 loading a features file containing HTML tags in feature
613 <li>Annotations corrupted after BioJS export and
615 <li>Incorrect sequence limits after Fetch DB References
616 with 'trim retrieved sequences'</li>
617 <li>Incorrect warning about deleting all data when
618 deleting selected columns</li>
619 <li>Patch to build system for shipping properly signed
620 JNLP templates for webstart launch</li>
621 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
622 unreleased structures for download or viewing</li>
623 <li>Tab/space/return keystroke operation of EMBL-PDBe
624 fetcher/viewer dialogs works correctly</li>
625 <li>Disabled 'minimise' button on Jalview windows
626 running on OSX to workaround redraw hang bug</li>
627 <li>Split cDNA/Protein view position and geometry not
628 recovered from jalview project</li>
629 <li>Initial enabled/disabled state of annotation menu
630 sorter 'show autocalculated first/last' corresponds to
632 <li>Restoring of Clustal, RNA Helices and T-Coffee
633 color schemes from BioJSON</li>
637 <li>Reorder sequences mirrored in cDNA/Protein split
639 <li>Applet with Jmol examples not loading correctly</li>
645 <td><div align="center">
646 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
650 <li>Linked visualisation and analysis of DNA and Protein
653 <li>Translated cDNA alignments shown as split protein
654 and DNA alignment views</li>
655 <li>Codon consensus annotation for linked protein and
656 cDNA alignment views</li>
657 <li>Link cDNA or Protein product sequences by loading
658 them onto Protein or cDNA alignments</li>
659 <li>Reconstruct linked cDNA alignment from aligned
660 protein sequences</li>
663 <li>Jmol integration updated to Jmol v14.2.14</li>
664 <li>Import and export of Jalview alignment views as <a
665 href="features/bioJsonFormat.html">BioJSON</a></li>
666 <li>New alignment annotation file statements for
667 reference sequences and marking hidden columns</li>
668 <li>Reference sequence based alignment shading to
669 highlight variation</li>
670 <li>Select or hide columns according to alignment
672 <li>Find option for locating sequences by description</li>
673 <li>Conserved physicochemical properties shown in amino
674 acid conservation row</li>
675 <li>Alignments can be sorted by number of RNA helices</li>
676 </ul> <em>Application</em>
678 <li>New cDNA/Protein analysis capabilities
680 <li>Get Cross-References should open a Split Frame
681 view with cDNA/Protein</li>
682 <li>Detect when nucleotide sequences and protein
683 sequences are placed in the same alignment</li>
684 <li>Split cDNA/Protein views are saved in Jalview
689 <li>Use REST API to talk to Chimera</li>
690 <li>Selected regions in Chimera are highlighted in linked
693 <li>VARNA RNA viewer updated to v3.93</li>
694 <li>VARNA views are saved in Jalview Projects</li>
695 <li>Pseudoknots displayed as Jalview RNA annotation can
696 be shown in VARNA</li>
698 <li>Make groups for selection uses marked columns as well
699 as the active selected region</li>
701 <li>Calculate UPGMA and NJ trees using sequence feature
703 <li>New Export options
705 <li>New Export Settings dialog to control hidden
706 region export in flat file generation</li>
708 <li>Export alignment views for display with the <a
709 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
711 <li>Export scrollable SVG in HTML page</li>
712 <li>Optional embedding of BioJSON data when exporting
713 alignment figures to HTML</li>
715 <li>3D structure retrieval and display
717 <li>Free text and structured queries with the PDBe
719 <li>PDBe Search API based discovery and selection of
720 PDB structures for a sequence set</li>
724 <li>JPred4 employed for protein secondary structure
726 <li>Hide Insertions menu option to hide unaligned columns
727 for one or a group of sequences</li>
728 <li>Automatically hide insertions in alignments imported
729 from the JPred4 web server</li>
730 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
731 system on OSX<br />LGPL libraries courtesy of <a
732 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
734 <li>changed 'View nucleotide structure' submenu to 'View
735 VARNA 2D Structure'</li>
736 <li>change "View protein structure" menu option to "3D
739 </ul> <em>Applet</em>
741 <li>New layout for applet example pages</li>
742 <li>New parameters to enable SplitFrame view
743 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
744 <li>New example demonstrating linked viewing of cDNA and
745 Protein alignments</li>
746 </ul> <em>Development and deployment</em>
748 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
749 <li>Include installation type and git revision in build
750 properties and console log output</li>
751 <li>Jalview Github organisation, and new github site for
752 storing BioJsMSA Templates</li>
753 <li>Jalview's unit tests now managed with TestNG</li>
756 <!-- <em>General</em>
758 </ul> --> <!-- issues resolved --> <em>Application</em>
760 <li>Escape should close any open find dialogs</li>
761 <li>Typo in select-by-features status report</li>
762 <li>Consensus RNA secondary secondary structure
763 predictions are not highlighted in amber</li>
764 <li>Missing gap character in v2.7 example file means
765 alignment appears unaligned when pad-gaps is not enabled</li>
766 <li>First switch to RNA Helices colouring doesn't colour
767 associated structure views</li>
768 <li>ID width preference option is greyed out when auto
769 width checkbox not enabled</li>
770 <li>Stopped a warning dialog from being shown when
771 creating user defined colours</li>
772 <li>'View Mapping' in structure viewer shows sequence
773 mappings for just that viewer's sequences</li>
774 <li>Workaround for superposing PDB files containing
775 multiple models in Chimera</li>
776 <li>Report sequence position in status bar when hovering
777 over Jmol structure</li>
778 <li>Cannot output gaps as '.' symbols with Selection ->
779 output to text box</li>
780 <li>Flat file exports of alignments with hidden columns
781 have incorrect sequence start/end</li>
782 <li>'Aligning' a second chain to a Chimera structure from
784 <li>Colour schemes applied to structure viewers don't
785 work for nucleotide</li>
786 <li>Loading/cut'n'pasting an empty or invalid file leads
787 to a grey/invisible alignment window</li>
788 <li>Exported Jpred annotation from a sequence region
789 imports to different position</li>
790 <li>Space at beginning of sequence feature tooltips shown
791 on some platforms</li>
792 <li>Chimera viewer 'View | Show Chain' menu is not
794 <li>'New View' fails with a Null Pointer Exception in
795 console if Chimera has been opened</li>
796 <li>Mouseover to Chimera not working</li>
797 <li>Miscellaneous ENA XML feature qualifiers not
799 <li>NPE in annotation renderer after 'Extract Scores'</li>
800 <li>If two structures in one Chimera window, mouseover of
801 either sequence shows on first structure</li>
802 <li>'Show annotations' options should not make
803 non-positional annotations visible</li>
804 <li>Subsequence secondary structure annotation not shown
805 in right place after 'view flanking regions'</li>
806 <li>File Save As type unset when current file format is
808 <li>Save as '.jar' option removed for saving Jalview
810 <li>Colour by Sequence colouring in Chimera more
812 <li>Cannot 'add reference annotation' for a sequence in
813 several views on same alignment</li>
814 <li>Cannot show linked products for EMBL / ENA records</li>
815 <li>Jalview's tooltip wraps long texts containing no
817 </ul> <em>Applet</em>
819 <li>Jmol to JalviewLite mouseover/link not working</li>
820 <li>JalviewLite can't import sequences with ID
821 descriptions containing angle brackets</li>
822 </ul> <em>General</em>
824 <li>Cannot export and reimport RNA secondary structure
825 via jalview annotation file</li>
826 <li>Random helix colour palette for colour by annotation
827 with RNA secondary structure</li>
828 <li>Mouseover to cDNA from STOP residue in protein
829 translation doesn't work.</li>
830 <li>hints when using the select by annotation dialog box</li>
831 <li>Jmol alignment incorrect if PDB file has alternate CA
833 <li>FontChooser message dialog appears to hang after
834 choosing 1pt font</li>
835 <li>Peptide secondary structure incorrectly imported from
836 annotation file when annotation display text includes 'e' or
838 <li>Cannot set colour of new feature type whilst creating
840 <li>cDNA translation alignment should not be sequence
842 <li>'Show unconserved' doesn't work for lower case
844 <li>Nucleotide ambiguity codes involving R not recognised</li>
845 </ul> <em>Deployment and Documentation</em>
847 <li>Applet example pages appear different to the rest of
849 </ul> <em>Application Known issues</em>
851 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
852 <li>Misleading message appears after trying to delete
854 <li>Jalview icon not shown in dock after InstallAnywhere
855 version launches</li>
856 <li>Fetching EMBL reference for an RNA sequence results
857 fails with a sequence mismatch</li>
858 <li>Corrupted or unreadable alignment display when
859 scrolling alignment to right</li>
860 <li>ArrayIndexOutOfBoundsException thrown when remove
861 empty columns called on alignment with ragged gapped ends</li>
862 <li>auto calculated alignment annotation rows do not get
863 placed above or below non-autocalculated rows</li>
864 <li>Jalview dekstop becomes sluggish at full screen in
865 ultra-high resolution</li>
866 <li>Cannot disable consensus calculation independently of
867 quality and conservation</li>
868 <li>Mouseover highlighting between cDNA and protein can
869 become sluggish with more than one splitframe shown</li>
870 </ul> <em>Applet Known Issues</em>
872 <li>Core PDB parsing code requires Jmol</li>
873 <li>Sequence canvas panel goes white when alignment
874 window is being resized</li>
880 <td><div align="center">
881 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
885 <li>Updated Java code signing certificate donated by
887 <li>Features and annotation preserved when performing
888 pairwise alignment</li>
889 <li>RNA pseudoknot annotation can be
890 imported/exported/displayed</li>
891 <li>'colour by annotation' can colour by RNA and
892 protein secondary structure</li>
893 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
894 post-hoc with 2.9 release</em>)
897 </ul> <em>Application</em>
899 <li>Extract and display secondary structure for sequences
900 with 3D structures</li>
901 <li>Support for parsing RNAML</li>
902 <li>Annotations menu for layout
904 <li>sort sequence annotation rows by alignment</li>
905 <li>place sequence annotation above/below alignment
908 <li>Output in Stockholm format</li>
909 <li>Internationalisation: improved Spanish (es)
911 <li>Structure viewer preferences tab</li>
912 <li>Disorder and Secondary Structure annotation tracks
913 shared between alignments</li>
914 <li>UCSF Chimera launch and linked highlighting from
916 <li>Show/hide all sequence associated annotation rows for
917 all or current selection</li>
918 <li>disorder and secondary structure predictions
919 available as dataset annotation</li>
920 <li>Per-sequence rna helices colouring</li>
923 <li>Sequence database accessions imported when fetching
924 alignments from Rfam</li>
925 <li>update VARNA version to 3.91</li>
927 <li>New groovy scripts for exporting aligned positions,
928 conservation values, and calculating sum of pairs scores.</li>
929 <li>Command line argument to set default JABAWS server</li>
930 <li>include installation type in build properties and
931 console log output</li>
932 <li>Updated Jalview project format to preserve dataset
936 <!-- issues resolved --> <em>Application</em>
938 <li>Distinguish alignment and sequence associated RNA
939 structure in structure->view->VARNA</li>
940 <li>Raise dialog box if user deletes all sequences in an
942 <li>Pressing F1 results in documentation opening twice</li>
943 <li>Sequence feature tooltip is wrapped</li>
944 <li>Double click on sequence associated annotation
945 selects only first column</li>
946 <li>Redundancy removal doesn't result in unlinked
947 leaves shown in tree</li>
948 <li>Undos after several redundancy removals don't undo
950 <li>Hide sequence doesn't hide associated annotation</li>
951 <li>User defined colours dialog box too big to fit on
952 screen and buttons not visible</li>
953 <li>author list isn't updated if already written to
954 Jalview properties</li>
955 <li>Popup menu won't open after retrieving sequence
957 <li>File open window for associate PDB doesn't open</li>
958 <li>Left-then-right click on a sequence id opens a
959 browser search window</li>
960 <li>Cannot open sequence feature shading/sort popup menu
961 in feature settings dialog</li>
962 <li>better tooltip placement for some areas of Jalview
964 <li>Allow addition of JABAWS Server which doesn't
966 <li>Web services parameters dialog box is too large to
968 <li>Muscle nucleotide alignment preset obscured by
970 <li>JABAWS preset submenus don't contain newly
971 defined user preset</li>
972 <li>MSA web services warns user if they were launched
973 with invalid input</li>
974 <li>Jalview cannot contact DAS Registy when running on
977 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
978 'Superpose with' submenu not shown when new view
982 </ul> <!-- <em>Applet</em>
984 </ul> <em>General</em>
986 </ul>--> <em>Deployment and Documentation</em>
988 <li>2G and 1G options in launchApp have no effect on
989 memory allocation</li>
990 <li>launchApp service doesn't automatically open
991 www.jalview.org/examples/exampleFile.jar if no file is given</li>
993 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
994 InstallAnywhere reports cannot find valid JVM when Java
997 </ul> <em>Application Known issues</em>
1000 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1001 corrupted or unreadable alignment display when scrolling
1005 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1006 retrieval fails but progress bar continues for DAS retrieval
1007 with large number of ID
1010 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1011 flatfile output of visible region has incorrect sequence
1015 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1016 rna structure consensus doesn't update when secondary
1017 structure tracks are rearranged
1020 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1021 invalid rna structure positional highlighting does not
1022 highlight position of invalid base pairs
1025 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1026 out of memory errors are not raised when saving Jalview
1027 project from alignment window file menu
1030 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1031 Switching to RNA Helices colouring doesn't propagate to
1035 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1036 colour by RNA Helices not enabled when user created
1037 annotation added to alignment
1040 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1041 Jalview icon not shown on dock in Mountain Lion/Webstart
1043 </ul> <em>Applet Known Issues</em>
1046 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1047 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1050 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1051 Jalview and Jmol example not compatible with IE9
1054 <li>Sort by annotation score doesn't reverse order
1060 <td><div align="center">
1061 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1064 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1067 <li>Internationalisation of user interface (usually
1068 called i18n support) and translation for Spanish locale</li>
1069 <li>Define/Undefine group on current selection with
1070 Ctrl-G/Shift Ctrl-G</li>
1071 <li>Improved group creation/removal options in
1072 alignment/sequence Popup menu</li>
1073 <li>Sensible precision for symbol distribution
1074 percentages shown in logo tooltip.</li>
1075 <li>Annotation panel height set according to amount of
1076 annotation when alignment first opened</li>
1077 </ul> <em>Application</em>
1079 <li>Interactive consensus RNA secondary structure
1080 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1081 <li>Select columns containing particular features from
1082 Feature Settings dialog</li>
1083 <li>View all 'representative' PDB structures for selected
1085 <li>Update Jalview project format:
1087 <li>New file extension for Jalview projects '.jvp'</li>
1088 <li>Preserve sequence and annotation dataset (to
1089 store secondary structure annotation,etc)</li>
1090 <li>Per group and alignment annotation and RNA helix
1094 <li>New similarity measures for PCA and Tree calculation
1096 <li>Experimental support for retrieval and viewing of
1097 flanking regions for an alignment</li>
1101 <!-- issues resolved --> <em>Application</em>
1103 <li>logo keeps spinning and status remains at queued or
1104 running after job is cancelled</li>
1105 <li>cannot export features from alignments imported from
1106 Jalview/VAMSAS projects</li>
1107 <li>Buggy slider for web service parameters that take
1109 <li>Newly created RNA secondary structure line doesn't
1110 have 'display all symbols' flag set</li>
1111 <li>T-COFFEE alignment score shading scheme and other
1112 annotation shading not saved in Jalview project</li>
1113 <li>Local file cannot be loaded in freshly downloaded
1115 <li>Jalview icon not shown on dock in Mountain
1117 <li>Load file from desktop file browser fails</li>
1118 <li>Occasional NPE thrown when calculating large trees</li>
1119 <li>Cannot reorder or slide sequences after dragging an
1120 alignment onto desktop</li>
1121 <li>Colour by annotation dialog throws NPE after using
1122 'extract scores' function</li>
1123 <li>Loading/cut'n'pasting an empty file leads to a grey
1124 alignment window</li>
1125 <li>Disorder thresholds rendered incorrectly after
1126 performing IUPred disorder prediction</li>
1127 <li>Multiple group annotated consensus rows shown when
1128 changing 'normalise logo' display setting</li>
1129 <li>Find shows blank dialog after 'finished searching' if
1130 nothing matches query</li>
1131 <li>Null Pointer Exceptions raised when sorting by
1132 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1134 <li>Errors in Jmol console when structures in alignment
1135 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1137 <li>Not all working JABAWS services are shown in
1139 <li>JAVAWS version of Jalview fails to launch with
1140 'invalid literal/length code'</li>
1141 <li>Annotation/RNA Helix colourschemes cannot be applied
1142 to alignment with groups (actually fixed in 2.8.0b1)</li>
1143 <li>RNA Helices and T-Coffee Scores available as default
1146 </ul> <em>Applet</em>
1148 <li>Remove group option is shown even when selection is
1150 <li>Apply to all groups ticked but colourscheme changes
1151 don't affect groups</li>
1152 <li>Documented RNA Helices and T-Coffee Scores as valid
1153 colourscheme name</li>
1154 <li>Annotation labels drawn on sequence IDs when
1155 Annotation panel is not displayed</li>
1156 <li>Increased font size for dropdown menus on OSX and
1157 embedded windows</li>
1158 </ul> <em>Other</em>
1160 <li>Consensus sequence for alignments/groups with a
1161 single sequence were not calculated</li>
1162 <li>annotation files that contain only groups imported as
1163 annotation and junk sequences</li>
1164 <li>Fasta files with sequences containing '*' incorrectly
1165 recognised as PFAM or BLC</li>
1166 <li>conservation/PID slider apply all groups option
1167 doesn't affect background (2.8.0b1)
1169 <li>redundancy highlighting is erratic at 0% and 100%</li>
1170 <li>Remove gapped columns fails for sequences with ragged
1172 <li>AMSA annotation row with leading spaces is not
1173 registered correctly on import</li>
1174 <li>Jalview crashes when selecting PCA analysis for
1175 certain alignments</li>
1176 <li>Opening the colour by annotation dialog for an
1177 existing annotation based 'use original colours'
1178 colourscheme loses original colours setting</li>
1183 <td><div align="center">
1184 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
1185 <em>30/1/2014</em></strong>
1189 <li>Trusted certificates for JalviewLite applet and
1190 Jalview Desktop application<br />Certificate was donated by
1191 <a href="https://www.certum.eu">Certum</a> to the Jalview
1192 open source project).
1194 <li>Jalview SRS links replaced by UniProt and EBI-search
1196 <li>Output in Stockholm format</li>
1197 <li>Allow import of data from gzipped files</li>
1198 <li>Export/import group and sequence associated line
1199 graph thresholds</li>
1200 <li>Nucleotide substitution matrix that supports RNA and
1201 ambiguity codes</li>
1202 <li>Allow disorder predictions to be made on the current
1203 selection (or visible selection) in the same way that JPred
1205 <li>Groovy scripting for headless Jalview operation</li>
1206 </ul> <em>Other improvements</em>
1208 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
1209 <li>COMBINE statement uses current SEQUENCE_REF and
1210 GROUP_REF scope to group annotation rows</li>
1211 <li>Support '' style escaping of quotes in Newick
1213 <li>Group options for JABAWS service by command line name</li>
1214 <li>Empty tooltip shown for JABA service options with a
1215 link but no description</li>
1216 <li>Select primary source when selecting authority in
1217 database fetcher GUI</li>
1218 <li>Add .mfa to FASTA file extensions recognised by
1220 <li>Annotation label tooltip text wrap</li>
1225 <li>Slow scrolling when lots of annotation rows are
1227 <li>Lots of NPE (and slowness) after creating RNA
1228 secondary structure annotation line</li>
1229 <li>Sequence database accessions not imported when
1230 fetching alignments from Rfam</li>
1231 <li>Incorrect SHMR submission for sequences with
1233 <li>View all structures does not always superpose
1235 <li>Option widgets in service parameters not updated to
1236 reflect user or preset settings</li>
1237 <li>Null pointer exceptions for some services without
1238 presets or adjustable parameters</li>
1239 <li>Discover PDB IDs entry in structure menu doesn't
1240 discover PDB xRefs</li>
1241 <li>Exception encountered while trying to retrieve
1242 features with DAS</li>
1243 <li>Lowest value in annotation row isn't coloured
1244 when colour by annotation (per sequence) is coloured</li>
1245 <li>Keyboard mode P jumps to start of gapped region when
1246 residue follows a gap</li>
1247 <li>Jalview appears to hang importing an alignment with
1248 Wrap as default or after enabling Wrap</li>
1249 <li>'Right click to add annotations' message
1250 shown in wrap mode when no annotations present</li>
1251 <li>Disorder predictions fail with NPE if no automatic
1252 annotation already exists on alignment</li>
1253 <li>oninit javascript function should be called after
1254 initialisation completes</li>
1255 <li>Remove redundancy after disorder prediction corrupts
1256 alignment window display</li>
1257 <li>Example annotation file in documentation is invalid</li>
1258 <li>Grouped line graph annotation rows are not exported
1259 to annotation file</li>
1260 <li>Multi-harmony analysis cannot be run when only two
1262 <li>Cannot create multiple groups of line graphs with
1263 several 'combine' statements in annotation file</li>
1264 <li>Pressing return several times causes Number Format
1265 exceptions in keyboard mode</li>
1266 <li>Multi-harmony (SHMMR) method doesn't submit
1267 correct partitions for input data</li>
1268 <li>Translation from DNA to Amino Acids fails</li>
1269 <li>Jalview fail to load newick tree with quoted label</li>
1270 <li>--headless flag isn't understood</li>
1271 <li>ClassCastException when generating EPS in headless
1273 <li>Adjusting sequence-associated shading threshold only
1274 changes one row's threshold</li>
1275 <li>Preferences and Feature settings panel panel
1276 doesn't open</li>
1277 <li>hide consensus histogram also hides conservation and
1278 quality histograms</li>
1283 <td><div align="center">
1284 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
1286 <td><em>Application</em>
1288 <li>Support for JABAWS 2.0 Services (AACon alignment
1289 conservation, protein disorder and Clustal Omega)</li>
1290 <li>JABAWS server status indicator in Web Services
1292 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
1293 in Jalview alignment window</li>
1294 <li>Updated Jalview build and deploy framework for OSX
1295 mountain lion, windows 7, and 8</li>
1296 <li>Nucleotide substitution matrix for PCA that supports
1297 RNA and ambiguity codes</li>
1299 <li>Improved sequence database retrieval GUI</li>
1300 <li>Support fetching and database reference look up
1301 against multiple DAS sources (Fetch all from in 'fetch db
1303 <li>Jalview project improvements
1305 <li>Store and retrieve the 'belowAlignment'
1306 flag for annotation</li>
1307 <li>calcId attribute to group annotation rows on the
1309 <li>Store AACon calculation settings for a view in
1310 Jalview project</li>
1314 <li>horizontal scrolling gesture support</li>
1315 <li>Visual progress indicator when PCA calculation is
1317 <li>Simpler JABA web services menus</li>
1318 <li>visual indication that web service results are still
1319 being retrieved from server</li>
1320 <li>Serialise the dialogs that are shown when Jalview
1321 starts up for first time</li>
1322 <li>Jalview user agent string for interacting with HTTP
1324 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
1326 <li>Examples directory and Groovy library included in
1327 InstallAnywhere distribution</li>
1328 </ul> <em>Applet</em>
1330 <li>RNA alignment and secondary structure annotation
1331 visualization applet example</li>
1332 </ul> <em>General</em>
1334 <li>Normalise option for consensus sequence logo</li>
1335 <li>Reset button in PCA window to return dimensions to
1337 <li>Allow seqspace or Jalview variant of alignment PCA
1339 <li>PCA with either nucleic acid and protein substitution
1341 <li>Allow windows containing HTML reports to be exported
1343 <li>Interactive display and editing of RNA secondary
1344 structure contacts</li>
1345 <li>RNA Helix Alignment Colouring</li>
1346 <li>RNA base pair logo consensus</li>
1347 <li>Parse sequence associated secondary structure
1348 information in Stockholm files</li>
1349 <li>HTML Export database accessions and annotation
1350 information presented in tooltip for sequences</li>
1351 <li>Import secondary structure from LOCARNA clustalw
1352 style RNA alignment files</li>
1353 <li>import and visualise T-COFFEE quality scores for an
1355 <li>'colour by annotation' per sequence option to
1356 shade each sequence according to its associated alignment
1358 <li>New Jalview Logo</li>
1359 </ul> <em>Documentation and Development</em>
1361 <li>documentation for score matrices used in Jalview</li>
1362 <li>New Website!</li>
1364 <td><em>Application</em>
1366 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
1367 wsdbfetch REST service</li>
1368 <li>Stop windows being moved outside desktop on OSX</li>
1369 <li>Filetype associations not installed for webstart
1371 <li>Jalview does not always retrieve progress of a JABAWS
1372 job execution in full once it is complete</li>
1373 <li>revise SHMR RSBS definition to ensure alignment is
1374 uploaded via ali_file parameter</li>
1375 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
1376 <li>View all structures superposed fails with exception</li>
1377 <li>Jnet job queues forever if a very short sequence is
1378 submitted for prediction</li>
1379 <li>Cut and paste menu not opened when mouse clicked on
1381 <li>Putting fractional value into integer text box in
1382 alignment parameter dialog causes Jalview to hang</li>
1383 <li>Structure view highlighting doesn't work on
1385 <li>View all structures fails with exception shown in
1387 <li>Characters in filename associated with PDBEntry not
1388 escaped in a platform independent way</li>
1389 <li>Jalview desktop fails to launch with exception when
1391 <li>Tree calculation reports 'you must have 2 or more
1392 sequences selected' when selection is empty</li>
1393 <li>Jalview desktop fails to launch with jar signature
1394 failure when java web start temporary file caching is
1396 <li>DAS Sequence retrieval with range qualification
1397 results in sequence xref which includes range qualification</li>
1398 <li>Errors during processing of command line arguments
1399 cause progress bar (JAL-898) to be removed</li>
1400 <li>Replace comma for semi-colon option not disabled for
1401 DAS sources in sequence fetcher</li>
1402 <li>Cannot close news reader when JABAWS server warning
1403 dialog is shown</li>
1404 <li>Option widgets not updated to reflect user settings</li>
1405 <li>Edited sequence not submitted to web service</li>
1406 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
1407 <li>InstallAnywhere installer doesn't unpack and run
1408 on OSX Mountain Lion</li>
1409 <li>Annotation panel not given a scroll bar when
1410 sequences with alignment annotation are pasted into the
1412 <li>Sequence associated annotation rows not associated
1413 when loaded from Jalview project</li>
1414 <li>Browser launch fails with NPE on java 1.7</li>
1415 <li>JABAWS alignment marked as finished when job was
1416 cancelled or job failed due to invalid input</li>
1417 <li>NPE with v2.7 example when clicking on Tree
1418 associated with all views</li>
1419 <li>Exceptions when copy/paste sequences with grouped
1420 annotation rows to new window</li>
1421 </ul> <em>Applet</em>
1423 <li>Sequence features are momentarily displayed before
1424 they are hidden using hidefeaturegroups applet parameter</li>
1425 <li>loading features via javascript API automatically
1426 enables feature display</li>
1427 <li>scrollToColumnIn javascript API method doesn't
1429 </ul> <em>General</em>
1431 <li>Redundancy removal fails for rna alignment</li>
1432 <li>PCA calculation fails when sequence has been selected
1433 and then deselected</li>
1434 <li>PCA window shows grey box when first opened on OSX</li>
1435 <li>Letters coloured pink in sequence logo when alignment
1436 coloured with clustalx</li>
1437 <li>Choosing fonts without letter symbols defined causes
1438 exceptions and redraw errors</li>
1439 <li>Initial PCA plot view is not same as manually
1440 reconfigured view</li>
1441 <li>Grouped annotation graph label has incorrect line
1443 <li>Grouped annotation graph label display is corrupted
1444 for lots of labels</li>
1449 <div align="center">
1450 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
1453 <td><em>Application</em>
1455 <li>Jalview Desktop News Reader</li>
1456 <li>Tweaked default layout of web services menu</li>
1457 <li>View/alignment association menu to enable user to
1458 easily specify which alignment a multi-structure view takes
1459 its colours/correspondences from</li>
1460 <li>Allow properties file location to be specified as URL</li>
1461 <li>Extend Jalview project to preserve associations
1462 between many alignment views and a single Jmol display</li>
1463 <li>Store annotation row height in Jalview project file</li>
1464 <li>Annotation row column label formatting attributes
1465 stored in project file</li>
1466 <li>Annotation row order for auto-calculated annotation
1467 rows preserved in Jalview project file</li>
1468 <li>Visual progress indication when Jalview state is
1469 saved using Desktop window menu</li>
1470 <li>Visual indication that command line arguments are
1471 still being processed</li>
1472 <li>Groovy script execution from URL</li>
1473 <li>Colour by annotation default min and max colours in
1475 <li>Automatically associate PDB files dragged onto an
1476 alignment with sequences that have high similarity and
1478 <li>Update JGoogleAnalytics to latest release (0.3)</li>
1479 <li>'view structures' option to open many
1480 structures in same window</li>
1481 <li>Sort associated views menu option for tree panel</li>
1482 <li>Group all JABA and non-JABA services for a particular
1483 analysis function in its own submenu</li>
1484 </ul> <em>Applet</em>
1486 <li>Userdefined and autogenerated annotation rows for
1488 <li>Adjustment of alignment annotation pane height</li>
1489 <li>Annotation scrollbar for annotation panel</li>
1490 <li>Drag to reorder annotation rows in annotation panel</li>
1491 <li>'automaticScrolling' parameter</li>
1492 <li>Allow sequences with partial ID string matches to be
1493 annotated from GFF/Jalview features files</li>
1494 <li>Sequence logo annotation row in applet</li>
1495 <li>Absolute paths relative to host server in applet
1496 parameters are treated as such</li>
1497 <li>New in the JalviewLite javascript API:
1499 <li>JalviewLite.js javascript library</li>
1500 <li>Javascript callbacks for
1502 <li>Applet initialisation</li>
1503 <li>Sequence/alignment mouse-overs and selections</li>
1506 <li>scrollTo row and column alignment scrolling
1508 <li>Select sequence/alignment regions from javascript</li>
1509 <li>javascript structure viewer harness to pass
1510 messages between Jmol and Jalview when running as
1511 distinct applets</li>
1512 <li>sortBy method</li>
1513 <li>Set of applet and application examples shipped
1514 with documentation</li>
1515 <li>New example to demonstrate JalviewLite and Jmol
1516 javascript message exchange</li>
1518 </ul> <em>General</em>
1520 <li>Enable Jmol displays to be associated with multiple
1521 multiple alignments</li>
1522 <li>Option to automatically sort alignment with new tree</li>
1523 <li>User configurable link to enable redirects to a
1524 www.Jalview.org mirror</li>
1525 <li>Jmol colours option for Jmol displays</li>
1526 <li>Configurable newline string when writing alignment
1527 and other flat files</li>
1528 <li>Allow alignment annotation description lines to
1529 contain html tags</li>
1530 </ul> <em>Documentation and Development</em>
1532 <li>Add groovy test harness for bulk load testing to
1534 <li>Groovy script to load and align a set of sequences
1535 using a web service before displaying the result in the
1536 Jalview desktop</li>
1537 <li>Restructured javascript and applet api documentation</li>
1538 <li>Ant target to publish example html files with applet
1540 <li>Netbeans project for building Jalview from source</li>
1541 <li>ant task to create online javadoc for Jalview source</li>
1543 <td><em>Application</em>
1545 <li>User defined colourscheme throws exception when
1546 current built in colourscheme is saved as new scheme</li>
1547 <li>AlignFrame->Save in application pops up save
1548 dialog for valid filename/format</li>
1549 <li>Cannot view associated structure for UniProt sequence</li>
1550 <li>PDB file association breaks for UniProt sequence
1552 <li>Associate PDB from file dialog does not tell you
1553 which sequence is to be associated with the file</li>
1554 <li>Find All raises null pointer exception when query
1555 only matches sequence IDs</li>
1556 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
1557 <li>Jalview project with Jmol views created with Jalview
1558 2.4 cannot be loaded</li>
1559 <li>Filetype associations not installed for webstart
1561 <li>Two or more chains in a single PDB file associated
1562 with sequences in different alignments do not get coloured
1563 by their associated sequence</li>
1564 <li>Visibility status of autocalculated annotation row
1565 not preserved when project is loaded</li>
1566 <li>Annotation row height and visibility attributes not
1567 stored in Jalview project</li>
1568 <li>Tree bootstraps are not preserved when saved as a
1569 Jalview project</li>
1570 <li>Envision2 workflow tooltips are corrupted</li>
1571 <li>Enabling show group conservation also enables colour
1572 by conservation</li>
1573 <li>Duplicate group associated conservation or consensus
1574 created on new view</li>
1575 <li>Annotation scrollbar not displayed after 'show
1576 all hidden annotation rows' option selected</li>
1577 <li>Alignment quality not updated after alignment
1578 annotation row is hidden then shown</li>
1579 <li>Preserve colouring of structures coloured by
1580 sequences in pre Jalview 2.7 projects</li>
1581 <li>Web service job parameter dialog is not laid out
1583 <li>Web services menu not refreshed after 'reset
1584 services' button is pressed in preferences</li>
1585 <li>Annotation off by one in Jalview v2_3 example project</li>
1586 <li>Structures imported from file and saved in project
1587 get name like jalview_pdb1234.txt when reloaded</li>
1588 <li>Jalview does not always retrieve progress of a JABAWS
1589 job execution in full once it is complete</li>
1590 </ul> <em>Applet</em>
1592 <li>Alignment height set incorrectly when lots of
1593 annotation rows are displayed</li>
1594 <li>Relative URLs in feature HTML text not resolved to
1596 <li>View follows highlighting does not work for positions
1598 <li><= shown as = in tooltip</li>
1599 <li>Export features raises exception when no features
1601 <li>Separator string used for serialising lists of IDs
1602 for javascript api is modified when separator string
1603 provided as parameter</li>
1604 <li>Null pointer exception when selecting tree leaves for
1605 alignment with no existing selection</li>
1606 <li>Relative URLs for datasources assumed to be relative
1607 to applet's codebase</li>
1608 <li>Status bar not updated after finished searching and
1609 search wraps around to first result</li>
1610 <li>StructureSelectionManager instance shared between
1611 several Jalview applets causes race conditions and memory
1613 <li>Hover tooltip and mouseover of position on structure
1614 not sent from Jmol in applet</li>
1615 <li>Certain sequences of javascript method calls to
1616 applet API fatally hang browser</li>
1617 </ul> <em>General</em>
1619 <li>View follows structure mouseover scrolls beyond
1620 position with wrapped view and hidden regions</li>
1621 <li>Find sequence position moves to wrong residue
1622 with/without hidden columns</li>
1623 <li>Sequence length given in alignment properties window
1625 <li>InvalidNumberFormat exceptions thrown when trying to
1626 import PDB like structure files</li>
1627 <li>Positional search results are only highlighted
1628 between user-supplied sequence start/end bounds</li>
1629 <li>End attribute of sequence is not validated</li>
1630 <li>Find dialog only finds first sequence containing a
1631 given sequence position</li>
1632 <li>Sequence numbering not preserved in MSF alignment
1634 <li>Jalview PDB file reader does not extract sequence
1635 from nucleotide chains correctly</li>
1636 <li>Structure colours not updated when tree partition
1637 changed in alignment</li>
1638 <li>Sequence associated secondary structure not correctly
1639 parsed in interleaved stockholm</li>
1640 <li>Colour by annotation dialog does not restore current
1642 <li>Hiding (nearly) all sequences doesn't work
1644 <li>Sequences containing lowercase letters are not
1645 properly associated with their pdb files</li>
1646 </ul> <em>Documentation and Development</em>
1648 <li>schemas/JalviewWsParamSet.xsd corrupted by
1649 ApplyCopyright tool</li>
1654 <div align="center">
1655 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
1658 <td><em>Application</em>
1660 <li>New warning dialog when the Jalview Desktop cannot
1661 contact web services</li>
1662 <li>JABA service parameters for a preset are shown in
1663 service job window</li>
1664 <li>JABA Service menu entries reworded</li>
1668 <li>Modeller PIR IO broken - cannot correctly import a
1669 pir file emitted by Jalview</li>
1670 <li>Existing feature settings transferred to new
1671 alignment view created from cut'n'paste</li>
1672 <li>Improved test for mixed amino/nucleotide chains when
1673 parsing PDB files</li>
1674 <li>Consensus and conservation annotation rows
1675 occasionally become blank for all new windows</li>
1676 <li>Exception raised when right clicking above sequences
1677 in wrapped view mode</li>
1678 </ul> <em>Application</em>
1680 <li>multiple multiply aligned structure views cause cpu
1681 usage to hit 100% and computer to hang</li>
1682 <li>Web Service parameter layout breaks for long user
1683 parameter names</li>
1684 <li>Jaba service discovery hangs desktop if Jaba server
1691 <div align="center">
1692 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
1695 <td><em>Application</em>
1697 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
1698 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
1701 <li>Web Services preference tab</li>
1702 <li>Analysis parameters dialog box and user defined
1704 <li>Improved speed and layout of Envision2 service menu</li>
1705 <li>Superpose structures using associated sequence
1707 <li>Export coordinates and projection as CSV from PCA
1709 </ul> <em>Applet</em>
1711 <li>enable javascript: execution by the applet via the
1712 link out mechanism</li>
1713 </ul> <em>Other</em>
1715 <li>Updated the Jmol Jalview interface to work with Jmol
1717 <li>The Jalview Desktop and JalviewLite applet now
1718 require Java 1.5</li>
1719 <li>Allow Jalview feature colour specification for GFF
1720 sequence annotation files</li>
1721 <li>New 'colour by label' keword in Jalview feature file
1722 type colour specification</li>
1723 <li>New Jalview Desktop Groovy API method that allows a
1724 script to check if it being run in an interactive session or
1725 in a batch operation from the Jalview command line</li>
1729 <li>clustalx colourscheme colours Ds preferentially when
1730 both D+E are present in over 50% of the column</li>
1731 </ul> <em>Application</em>
1733 <li>typo in AlignmentFrame->View->Hide->all but
1734 selected Regions menu item</li>
1735 <li>sequence fetcher replaces ',' for ';' when the ',' is
1736 part of a valid accession ID</li>
1737 <li>fatal OOM if object retrieved by sequence fetcher
1738 runs out of memory</li>
1739 <li>unhandled Out of Memory Error when viewing pca
1740 analysis results</li>
1741 <li>InstallAnywhere builds fail to launch on OS X java
1742 10.5 update 4 (due to apple Java 1.6 update)</li>
1743 <li>Installanywhere Jalview silently fails to launch</li>
1744 </ul> <em>Applet</em>
1746 <li>Jalview.getFeatureGroups() raises an
1747 ArrayIndexOutOfBoundsException if no feature groups are
1754 <div align="center">
1755 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
1761 <li>Alignment prettyprinter doesn't cope with long
1763 <li>clustalx colourscheme colours Ds preferentially when
1764 both D+E are present in over 50% of the column</li>
1765 <li>nucleic acid structures retrieved from PDB do not
1766 import correctly</li>
1767 <li>More columns get selected than were clicked on when a
1768 number of columns are hidden</li>
1769 <li>annotation label popup menu not providing correct
1770 add/hide/show options when rows are hidden or none are
1772 <li>Stockholm format shown in list of readable formats,
1773 and parser copes better with alignments from RFAM.</li>
1774 <li>CSV output of consensus only includes the percentage
1775 of all symbols if sequence logo display is enabled</li>
1777 </ul> <em>Applet</em>
1779 <li>annotation panel disappears when annotation is
1781 </ul> <em>Application</em>
1783 <li>Alignment view not redrawn properly when new
1784 alignment opened where annotation panel is visible but no
1785 annotations are present on alignment</li>
1786 <li>pasted region containing hidden columns is
1787 incorrectly displayed in new alignment window</li>
1788 <li>Jalview slow to complete operations when stdout is
1789 flooded (fix is to close the Jalview console)</li>
1790 <li>typo in AlignmentFrame->View->Hide->all but
1791 selected Rregions menu item.</li>
1792 <li>inconsistent group submenu and Format submenu entry
1793 'Un' or 'Non'conserved</li>
1794 <li>Sequence feature settings are being shared by
1795 multiple distinct alignments</li>
1796 <li>group annotation not recreated when tree partition is
1798 <li>double click on group annotation to select sequences
1799 does not propagate to associated trees</li>
1800 <li>Mac OSX specific issues:
1802 <li>exception raised when mouse clicked on desktop
1803 window background</li>
1804 <li>Desktop menu placed on menu bar and application
1805 name set correctly</li>
1806 <li>sequence feature settings not wide enough for the
1807 save feature colourscheme button</li>
1816 <div align="center">
1817 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
1820 <td><em>New Capabilities</em>
1822 <li>URL links generated from description line for
1823 regular-expression based URL links (applet and application)
1830 <li>Non-positional feature URL links are shown in link
1832 <li>Linked viewing of nucleic acid sequences and
1834 <li>Automatic Scrolling option in View menu to display
1835 the currently highlighted region of an alignment.</li>
1836 <li>Order an alignment by sequence length, or using the
1837 average score or total feature count for each sequence.</li>
1838 <li>Shading features by score or associated description</li>
1839 <li>Subdivide alignment and groups based on identity of
1840 selected subsequence (Make Groups from Selection).</li>
1841 <li>New hide/show options including Shift+Control+H to
1842 hide everything but the currently selected region.</li>
1843 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
1844 </ul> <em>Application</em>
1846 <li>Fetch DB References capabilities and UI expanded to
1847 support retrieval from DAS sequence sources</li>
1848 <li>Local DAS Sequence sources can be added via the
1849 command line or via the Add local source dialog box.</li>
1850 <li>DAS Dbref and DbxRef feature types are parsed as
1851 database references and protein_name is parsed as
1852 description line (BioSapiens terms).</li>
1853 <li>Enable or disable non-positional feature and database
1854 references in sequence ID tooltip from View menu in
1856 <!-- <li>New hidden columns and rows and representatives capabilities
1857 in annotations file (in progress - not yet fully implemented)</li> -->
1858 <li>Group-associated consensus, sequence logos and
1859 conservation plots</li>
1860 <li>Symbol distributions for each column can be exported
1861 and visualized as sequence logos</li>
1862 <li>Optionally scale multi-character column labels to fit
1863 within each column of annotation row<!-- todo for applet -->
1865 <li>Optional automatic sort of associated alignment view
1866 when a new tree is opened.</li>
1867 <li>Jalview Java Console</li>
1868 <li>Better placement of desktop window when moving
1869 between different screens.</li>
1870 <li>New preference items for sequence ID tooltip and
1871 consensus annotation</li>
1872 <li>Client to submit sequences and IDs to Envision2
1874 <li><em>Vamsas Capabilities</em>
1876 <li>Improved VAMSAS synchronization (Jalview archive
1877 used to preserve views, structures, and tree display
1879 <li>Import of vamsas documents from disk or URL via
1881 <li>Sharing of selected regions between views and
1882 with other VAMSAS applications (Experimental feature!)</li>
1883 <li>Updated API to VAMSAS version 0.2</li>
1885 </ul> <em>Applet</em>
1887 <li>Middle button resizes annotation row height</li>
1890 <li>sortByTree (true/false) - automatically sort the
1891 associated alignment view by the tree when a new tree is
1893 <li>showTreeBootstraps (true/false) - show or hide
1894 branch bootstraps (default is to show them if available)</li>
1895 <li>showTreeDistances (true/false) - show or hide
1896 branch lengths (default is to show them if available)</li>
1897 <li>showUnlinkedTreeNodes (true/false) - indicate if
1898 unassociated nodes should be highlighted in the tree
1900 <li>heightScale and widthScale (1.0 or more) -
1901 increase the height or width of a cell in the alignment
1902 grid relative to the current font size.</li>
1905 <li>Non-positional features displayed in sequence ID
1907 </ul> <em>Other</em>
1909 <li>Features format: graduated colour definitions and
1910 specification of feature scores</li>
1911 <li>Alignment Annotations format: new keywords for group
1912 associated annotation (GROUP_REF) and annotation row display
1913 properties (ROW_PROPERTIES)</li>
1914 <li>XML formats extended to support graduated feature
1915 colourschemes, group associated annotation, and profile
1916 visualization settings.</li></td>
1919 <li>Source field in GFF files parsed as feature source
1920 rather than description</li>
1921 <li>Non-positional features are now included in sequence
1922 feature and gff files (controlled via non-positional feature
1923 visibility in tooltip).</li>
1924 <li>URL links generated for all feature links (bugfix)</li>
1925 <li>Added URL embedding instructions to features file
1927 <li>Codons containing ambiguous nucleotides translated as
1928 'X' in peptide product</li>
1929 <li>Match case switch in find dialog box works for both
1930 sequence ID and sequence string and query strings do not
1931 have to be in upper case to match case-insensitively.</li>
1932 <li>AMSA files only contain first column of
1933 multi-character column annotation labels</li>
1934 <li>Jalview Annotation File generation/parsing consistent
1935 with documentation (e.g. Stockholm annotation can be
1936 exported and re-imported)</li>
1937 <li>PDB files without embedded PDB IDs given a friendly
1939 <li>Find incrementally searches ID string matches as well
1940 as subsequence matches, and correctly reports total number
1944 <li>Better handling of exceptions during sequence
1946 <li>Dasobert generated non-positional feature URL
1947 link text excludes the start_end suffix</li>
1948 <li>DAS feature and source retrieval buttons disabled
1949 when fetch or registry operations in progress.</li>
1950 <li>PDB files retrieved from URLs are cached properly</li>
1951 <li>Sequence description lines properly shared via
1953 <li>Sequence fetcher fetches multiple records for all
1955 <li>Ensured that command line das feature retrieval
1956 completes before alignment figures are generated.</li>
1957 <li>Reduced time taken when opening file browser for
1959 <li>isAligned check prior to calculating tree, PCA or
1960 submitting an MSA to JNet now excludes hidden sequences.</li>
1961 <li>User defined group colours properly recovered
1962 from Jalview projects.</li>
1971 <div align="center">
1972 <strong>2.4.0.b2</strong><br> 28/10/2009
1977 <li>Experimental support for google analytics usage
1979 <li>Jalview privacy settings (user preferences and docs).</li>
1984 <li>Race condition in applet preventing startup in
1986 <li>Exception when feature created from selection beyond
1987 length of sequence.</li>
1988 <li>Allow synthetic PDB files to be imported gracefully</li>
1989 <li>Sequence associated annotation rows associate with
1990 all sequences with a given id</li>
1991 <li>Find function matches case-insensitively for sequence
1992 ID string searches</li>
1993 <li>Non-standard characters do not cause pairwise
1994 alignment to fail with exception</li>
1995 </ul> <em>Application Issues</em>
1997 <li>Sequences are now validated against EMBL database</li>
1998 <li>Sequence fetcher fetches multiple records for all
2000 </ul> <em>InstallAnywhere Issues</em>
2002 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2003 issue with installAnywhere mechanism)</li>
2004 <li>Command line launching of JARs from InstallAnywhere
2005 version (java class versioning error fixed)</li>
2012 <div align="center">
2013 <strong>2.4</strong><br> 27/8/2008
2016 <td><em>User Interface</em>
2018 <li>Linked highlighting of codon and amino acid from
2019 translation and protein products</li>
2020 <li>Linked highlighting of structure associated with
2021 residue mapping to codon position</li>
2022 <li>Sequence Fetcher provides example accession numbers
2023 and 'clear' button</li>
2024 <li>MemoryMonitor added as an option under Desktop's
2026 <li>Extract score function to parse whitespace separated
2027 numeric data in description line</li>
2028 <li>Column labels in alignment annotation can be centred.</li>
2029 <li>Tooltip for sequence associated annotation give name
2031 </ul> <em>Web Services and URL fetching</em>
2033 <li>JPred3 web service</li>
2034 <li>Prototype sequence search client (no public services
2036 <li>Fetch either seed alignment or full alignment from
2038 <li>URL Links created for matching database cross
2039 references as well as sequence ID</li>
2040 <li>URL Links can be created using regular-expressions</li>
2041 </ul> <em>Sequence Database Connectivity</em>
2043 <li>Retrieval of cross-referenced sequences from other
2045 <li>Generalised database reference retrieval and
2046 validation to all fetchable databases</li>
2047 <li>Fetch sequences from DAS sources supporting the
2048 sequence command</li>
2049 </ul> <em>Import and Export</em>
2050 <li>export annotation rows as CSV for spreadsheet import</li>
2051 <li>Jalview projects record alignment dataset associations,
2052 EMBL products, and cDNA sequence mappings</li>
2053 <li>Sequence Group colour can be specified in Annotation
2055 <li>Ad-hoc colouring of group in Annotation File using RGB
2056 triplet as name of colourscheme</li>
2057 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2059 <li>treenode binding for VAMSAS tree exchange</li>
2060 <li>local editing and update of sequences in VAMSAS
2061 alignments (experimental)</li>
2062 <li>Create new or select existing session to join</li>
2063 <li>load and save of vamsas documents</li>
2064 </ul> <em>Application command line</em>
2066 <li>-tree parameter to open trees (introduced for passing
2068 <li>-fetchfrom command line argument to specify nicknames
2069 of DAS servers to query for alignment features</li>
2070 <li>-dasserver command line argument to add new servers
2071 that are also automatically queried for features</li>
2072 <li>-groovy command line argument executes a given groovy
2073 script after all input data has been loaded and parsed</li>
2074 </ul> <em>Applet-Application data exchange</em>
2076 <li>Trees passed as applet parameters can be passed to
2077 application (when using "View in full
2078 application")</li>
2079 </ul> <em>Applet Parameters</em>
2081 <li>feature group display control parameter</li>
2082 <li>debug parameter</li>
2083 <li>showbutton parameter</li>
2084 </ul> <em>Applet API methods</em>
2086 <li>newView public method</li>
2087 <li>Window (current view) specific get/set public methods</li>
2088 <li>Feature display control methods</li>
2089 <li>get list of currently selected sequences</li>
2090 </ul> <em>New Jalview distribution features</em>
2092 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2093 <li>RELEASE file gives build properties for the latest
2094 Jalview release.</li>
2095 <li>Java 1.1 Applet build made easier and donotobfuscate
2096 property controls execution of obfuscator</li>
2097 <li>Build target for generating source distribution</li>
2098 <li>Debug flag for javacc</li>
2099 <li>.jalview_properties file is documented (slightly) in
2100 jalview.bin.Cache</li>
2101 <li>Continuous Build Integration for stable and
2102 development version of Application, Applet and source
2107 <li>selected region output includes visible annotations
2108 (for certain formats)</li>
2109 <li>edit label/displaychar contains existing label/char
2111 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2112 <li>shorter peptide product names from EMBL records</li>
2113 <li>Newick string generator makes compact representations</li>
2114 <li>bootstrap values parsed correctly for tree files with
2116 <li>pathological filechooser bug avoided by not allowing
2117 filenames containing a ':'</li>
2118 <li>Fixed exception when parsing GFF files containing
2119 global sequence features</li>
2120 <li>Alignment datasets are finalized only when number of
2121 references from alignment sequences goes to zero</li>
2122 <li>Close of tree branch colour box without colour
2123 selection causes cascading exceptions</li>
2124 <li>occasional negative imgwidth exceptions</li>
2125 <li>better reporting of non-fatal warnings to user when
2126 file parsing fails.</li>
2127 <li>Save works when Jalview project is default format</li>
2128 <li>Save as dialog opened if current alignment format is
2129 not a valid output format</li>
2130 <li>UniProt canonical names introduced for both das and
2132 <li>Histidine should be midblue (not pink!) in Zappo</li>
2133 <li>error messages passed up and output when data read
2135 <li>edit undo recovers previous dataset sequence when
2136 sequence is edited</li>
2137 <li>allow PDB files without pdb ID HEADER lines (like
2138 those generated by MODELLER) to be read in properly</li>
2139 <li>allow reading of JPred concise files as a normal
2141 <li>Stockholm annotation parsing and alignment properties
2142 import fixed for PFAM records</li>
2143 <li>Structure view windows have correct name in Desktop
2145 <li>annotation consisting of sequence associated scores
2146 can be read and written correctly to annotation file</li>
2147 <li>Aligned cDNA translation to aligned peptide works
2149 <li>Fixed display of hidden sequence markers and
2150 non-italic font for representatives in Applet</li>
2151 <li>Applet Menus are always embedded in applet window on
2153 <li>Newly shown features appear at top of stack (in
2155 <li>Annotations added via parameter not drawn properly
2156 due to null pointer exceptions</li>
2157 <li>Secondary structure lines are drawn starting from
2158 first column of alignment</li>
2159 <li>UniProt XML import updated for new schema release in
2161 <li>Sequence feature to sequence ID match for Features
2162 file is case-insensitive</li>
2163 <li>Sequence features read from Features file appended to
2164 all sequences with matching IDs</li>
2165 <li>PDB structure coloured correctly for associated views
2166 containing a sub-sequence</li>
2167 <li>PDB files can be retrieved by applet from Jar files</li>
2168 <li>feature and annotation file applet parameters
2169 referring to different directories are retrieved correctly</li>
2170 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
2171 <li>Fixed application hang whilst waiting for
2172 splash-screen version check to complete</li>
2173 <li>Applet properly URLencodes input parameter values
2174 when passing them to the launchApp service</li>
2175 <li>display name and local features preserved in results
2176 retrieved from web service</li>
2177 <li>Visual delay indication for sequence retrieval and
2178 sequence fetcher initialisation</li>
2179 <li>updated Application to use DAS 1.53e version of
2180 dasobert DAS client</li>
2181 <li>Re-instated Full AMSA support and .amsa file
2183 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
2191 <div align="center">
2192 <strong>2.3</strong><br> 9/5/07
2197 <li>Jmol 11.0.2 integration</li>
2198 <li>PDB views stored in Jalview XML files</li>
2199 <li>Slide sequences</li>
2200 <li>Edit sequence in place</li>
2201 <li>EMBL CDS features</li>
2202 <li>DAS Feature mapping</li>
2203 <li>Feature ordering</li>
2204 <li>Alignment Properties</li>
2205 <li>Annotation Scores</li>
2206 <li>Sort by scores</li>
2207 <li>Feature/annotation editing in applet</li>
2212 <li>Headless state operation in 2.2.1</li>
2213 <li>Incorrect and unstable DNA pairwise alignment</li>
2214 <li>Cut and paste of sequences with annotation</li>
2215 <li>Feature group display state in XML</li>
2216 <li>Feature ordering in XML</li>
2217 <li>blc file iteration selection using filename # suffix</li>
2218 <li>Stockholm alignment properties</li>
2219 <li>Stockhom alignment secondary structure annotation</li>
2220 <li>2.2.1 applet had no feature transparency</li>
2221 <li>Number pad keys can be used in cursor mode</li>
2222 <li>Structure Viewer mirror image resolved</li>
2229 <div align="center">
2230 <strong>2.2.1</strong><br> 12/2/07
2235 <li>Non standard characters can be read and displayed
2236 <li>Annotations/Features can be imported/exported to the
2238 <li>Applet allows editing of sequence/annotation/group
2239 name & description
2240 <li>Preference setting to display sequence name in
2242 <li>Annotation file format extended to allow
2243 Sequence_groups to be defined
2244 <li>Default opening of alignment overview panel can be
2245 specified in preferences
2246 <li>PDB residue numbering annotation added to associated
2252 <li>Applet crash under certain Linux OS with Java 1.6
2254 <li>Annotation file export / import bugs fixed
2255 <li>PNG / EPS image output bugs fixed
2261 <div align="center">
2262 <strong>2.2</strong><br> 27/11/06
2267 <li>Multiple views on alignment
2268 <li>Sequence feature editing
2269 <li>"Reload" alignment
2270 <li>"Save" to current filename
2271 <li>Background dependent text colour
2272 <li>Right align sequence ids
2273 <li>User-defined lower case residue colours
2276 <li>Menu item accelerator keys
2277 <li>Control-V pastes to current alignment
2278 <li>Cancel button for DAS Feature Fetching
2279 <li>PCA and PDB Viewers zoom via mouse roller
2280 <li>User-defined sub-tree colours and sub-tree selection
2287 <li>'New Window' button on the 'Output to Text box'
2292 <li>New memory efficient Undo/Redo System
2293 <li>Optimised symbol lookups and conservation/consensus
2295 <li>Region Conservation/Consensus recalculated after
2297 <li>Fixed Remove Empty Columns Bug (empty columns at end
2299 <li>Slowed DAS Feature Fetching for increased robustness.
2306 <li>Made angle brackets in ASCII feature descriptions
2308 <li>Re-instated Zoom function for PCA
2309 <li>Sequence descriptions conserved in web service
2311 <li>UniProt ID discoverer uses any word separated by
2313 <li>WsDbFetch query/result association resolved
2314 <li>Tree leaf to sequence mapping improved
2315 <li>Smooth fonts switch moved to FontChooser dialog box.
2327 <div align="center">
2328 <strong>2.1.1</strong><br> 12/9/06
2333 <li>Copy consensus sequence to clipboard</li>
2338 <li>Image output - rightmost residues are rendered if
2339 sequence id panel has been resized</li>
2340 <li>Image output - all offscreen group boundaries are
2342 <li>Annotation files with sequence references - all
2343 elements in file are relative to sequence position</li>
2344 <li>Mac Applet users can use Alt key for group editing</li>
2350 <div align="center">
2351 <strong>2.1</strong><br> 22/8/06
2356 <li>MAFFT Multiple Alignment in default Web Service list</li>
2357 <li>DAS Feature fetching</li>
2358 <li>Hide sequences and columns</li>
2359 <li>Export Annotations and Features</li>
2360 <li>GFF file reading / writing</li>
2361 <li>Associate structures with sequences from local PDB
2363 <li>Add sequences to exisiting alignment</li>
2364 <li>Recently opened files / URL lists</li>
2365 <li>Applet can launch the full application</li>
2366 <li>Applet has transparency for features (Java 1.2
2368 <li>Applet has user defined colours parameter</li>
2369 <li>Applet can load sequences from parameter
2370 "sequence<em>x</em>"
2376 <li>Redundancy Panel reinstalled in the Applet</li>
2377 <li>Monospaced font - EPS / rescaling bug fixed</li>
2378 <li>Annotation files with sequence references bug fixed</li>
2384 <div align="center">
2385 <strong>2.08.1</strong><br> 2/5/06
2390 <li>Change case of selected region from Popup menu</li>
2391 <li>Choose to match case when searching</li>
2392 <li>Middle mouse button and mouse movement can compress /
2393 expand the visible width and height of the alignment</li>
2398 <li>Annotation Panel displays complete JNet results</li>
2404 <div align="center">
2405 <strong>2.08b</strong><br> 18/4/06
2411 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
2412 <li>Righthand label on wrapped alignments shows correct
2419 <div align="center">
2420 <strong>2.08</strong><br> 10/4/06
2425 <li>Editing can be locked to the selection area</li>
2426 <li>Keyboard editing</li>
2427 <li>Create sequence features from searches</li>
2428 <li>Precalculated annotations can be loaded onto
2430 <li>Features file allows grouping of features</li>
2431 <li>Annotation Colouring scheme added</li>
2432 <li>Smooth fonts off by default - Faster rendering</li>
2433 <li>Choose to toggle Autocalculate Consensus On/Off</li>
2438 <li>Drag & Drop fixed on Linux</li>
2439 <li>Jalview Archive file faster to load/save, sequence
2440 descriptions saved.</li>
2446 <div align="center">
2447 <strong>2.07</strong><br> 12/12/05
2452 <li>PDB Structure Viewer enhanced</li>
2453 <li>Sequence Feature retrieval and display enhanced</li>
2454 <li>Choose to output sequence start-end after sequence
2455 name for file output</li>
2456 <li>Sequence Fetcher WSDBFetch@EBI</li>
2457 <li>Applet can read feature files, PDB files and can be
2458 used for HTML form input</li>
2463 <li>HTML output writes groups and features</li>
2464 <li>Group editing is Control and mouse click</li>
2465 <li>File IO bugs</li>
2471 <div align="center">
2472 <strong>2.06</strong><br> 28/9/05
2477 <li>View annotations in wrapped mode</li>
2478 <li>More options for PCA viewer</li>
2483 <li>GUI bugs resolved</li>
2484 <li>Runs with -nodisplay from command line</li>
2490 <div align="center">
2491 <strong>2.05b</strong><br> 15/9/05
2496 <li>Choose EPS export as lineart or text</li>
2497 <li>Jar files are executable</li>
2498 <li>Can read in Uracil - maps to unknown residue</li>
2503 <li>Known OutOfMemory errors give warning message</li>
2504 <li>Overview window calculated more efficiently</li>
2505 <li>Several GUI bugs resolved</li>
2511 <div align="center">
2512 <strong>2.05</strong><br> 30/8/05
2517 <li>Edit and annotate in "Wrapped" view</li>
2522 <li>Several GUI bugs resolved</li>
2528 <div align="center">
2529 <strong>2.04</strong><br> 24/8/05
2534 <li>Hold down mouse wheel & scroll to change font
2540 <li>Improved JPred client reliability</li>
2541 <li>Improved loading of Jalview files</li>
2547 <div align="center">
2548 <strong>2.03</strong><br> 18/8/05
2553 <li>Set Proxy server name and port in preferences</li>
2554 <li>Multiple URL links from sequence ids</li>
2555 <li>User Defined Colours can have a scheme name and added
2557 <li>Choose to ignore gaps in consensus calculation</li>
2558 <li>Unix users can set default web browser</li>
2559 <li>Runs without GUI for batch processing</li>
2560 <li>Dynamically generated Web Service Menus</li>
2565 <li>InstallAnywhere download for Sparc Solaris</li>
2571 <div align="center">
2572 <strong>2.02</strong><br> 18/7/05
2578 <li>Copy & Paste order of sequences maintains
2579 alignment order.</li>
2585 <div align="center">
2586 <strong>2.01</strong><br> 12/7/05
2591 <li>Use delete key for deleting selection.</li>
2592 <li>Use Mouse wheel to scroll sequences.</li>
2593 <li>Help file updated to describe how to add alignment
2595 <li>Version and build date written to build properties
2597 <li>InstallAnywhere installation will check for updates
2598 at launch of Jalview.</li>
2603 <li>Delete gaps bug fixed.</li>
2604 <li>FileChooser sorts columns.</li>
2605 <li>Can remove groups one by one.</li>
2606 <li>Filechooser icons installed.</li>
2607 <li>Finder ignores return character when searching.
2608 Return key will initiate a search.<br>
2615 <div align="center">
2616 <strong>2.0</strong><br> 20/6/05
2621 <li>New codebase</li>