3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
27 <strong>Release History</strong>
31 <td width="60" nowrap>
33 <em><strong>Release</strong></em>
38 <em><strong>New Features</strong></em>
43 <em><strong>Issues Resolved</strong></em>
48 <td width="60" nowrap>
50 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
51 <em>25/10/2016</em></strong>
54 <td><em>Application</em>
56 <li>3D Structure chooser opens with 'Cached structures'
57 view if structures already loaded</li>
58 <li>Progress bar reports models as they are loaded to
65 <li>Colour by conservation always enabled and no tick
66 shown in menu when BLOSUM or PID shading applied</li>
67 <li>FER1_ARATH and FER2_ARATH labels were switched in
68 example sequences/projects/trees</li>
72 <li>Jalview projects with views of local PDB structure
73 files saved on Windows cannot be opened on OSX</li>
74 <li>Multiple structure views can be opened and
75 superposed without timeout for structures with multiple
76 models or multiple sequences in alignment</li>
77 <li>Cannot import or associated local PDB files without
78 a PDB ID HEADER line</li>
79 <li>RMSD is not output in Jmol console when
80 superposition is performed</li>
81 <li>Drag and drop of URL from Browser fails for Linux
82 and OSX versions earlier than El Capitan</li>
83 <li>ENA client ignores invalid content from ENA server</li>
84 <li>Exceptions are not raised in console when ENA
85 client attempts to fetch non-existent IDs via Fetch DB
87 <li>Exceptions are not raised in console when a new
88 view is created on the alignment</li>
89 <li>OSX right-click fixed for group selections:
90 CMD-click to insert/remove gaps in groups and CTRL-click
91 to open group pop-up menu</li>
93 <em>Build and deployment</em>
95 <li>URL link checker now copes with multi-line anchor
98 <em>New Known Issues</em>
100 <li>Drag and drop from URL links in browsers do not
107 <td width="60" nowrap>
109 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
115 <!-- JAL-2124 -->Updated Spanish translations.
118 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
119 for importing structure data to Jalview. Enables mmCIF and
123 <!-- JAL-192 --->Alignment ruler shows positions relative to
127 <!-- JAL-2202 -->Position/residue shown in status bar when
128 mousing over sequence associated annotation
131 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
135 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
136 '()', canonical '[]' and invalid '{}' base pair populations
140 <!-- JAL-2092 -->Feature settings popup menu options for
141 showing or hiding columns containing a feature
144 <!-- JAL-1557 -->Edit selected group by double clicking on
145 group and sequence associated annotation labels
148 <!-- JAL-2236 -->Sequence name added to annotation label in
149 select/hide columns by annotation and colour by annotation
153 </ul> <em>Application</em>
156 <!-- JAL-2050-->Automatically hide introns when opening a
160 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
164 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
165 structure mappings with the EMBL-EBI PDBe SIFTS database
168 <!-- JAL-2079 -->Updated download sites used for Rfam and
169 Pfam sources to xfam.org
172 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
175 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
176 over sequences in Jalview
179 <!-- JAL-2027-->Support for reverse-complement coding
180 regions in ENA and EMBL
183 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
184 for record retrieval via ENA rest API
187 <!-- JAL-2027 -->Support for ENA CDS records with reverse
191 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
192 groovy script execution
195 <!-- JAL-1812 -->New 'execute Groovy script' option in an
196 alignment window's Calculate menu
199 <!-- JAL-1812 -->Allow groovy scripts that call
200 Jalview.getAlignFrames() to run in headless mode
203 <!-- JAL-2068 -->Support for creating new alignment
204 calculation workers from groovy scripts
207 <!-- JAL-1369 --->Store/restore reference sequence in
211 <!-- JAL-1803 -->Chain codes for a sequence's PDB
212 associations are now saved/restored from project
215 <!-- JAL-1993 -->Database selection dialog always shown
216 before sequence fetcher is opened
219 <!-- JAL-2183 -->Double click on an entry in Jalview's
220 database chooser opens a sequence fetcher
223 <!-- JAL-1563 -->Free-text search client for UniProt using
227 <!-- JAL-2168 -->-nonews command line parameter to prevent
228 the news reader opening
231 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
232 querying stored in preferences
235 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
239 <!-- JAL-1977-->Tooltips shown on database chooser
242 <!-- JAL-391 -->Reverse complement function in calculate
243 menu for nucleotide sequences
246 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
247 and feature counts preserves alignment ordering (and
248 debugged for complex feature sets).
251 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
252 viewing structures with Jalview 2.10
255 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
256 genome, transcript CCDS and gene ids via the Ensembl and
257 Ensembl Genomes REST API
260 <!-- JAL-2049 -->Protein sequence variant annotation
261 computed for 'sequence_variant' annotation on CDS regions
265 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
269 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
270 Ref Fetcher fails to match, or otherwise updates sequence
271 data from external database records.
274 <!-- JAL-2154 -->Revised Jalview Project format for
275 efficient recovery of sequence coding and alignment
276 annotation relationships.
278 </ul> <!-- <em>Applet</em>
289 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
293 <!-- JAL-2018-->Export features in Jalview format (again)
294 includes graduated colourschemes
297 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
298 working with big alignments and lots of hidden columns
301 <!-- JAL-2053-->Hidden column markers not always rendered
302 at right of alignment window
305 <!-- JAL-2067 -->Tidied up links in help file table of
309 <!-- JAL-2072 -->Feature based tree calculation not shown
313 <!-- JAL-2075 -->Hidden columns ignored during feature
314 based tree calculation
317 <!-- JAL-2065 -->Alignment view stops updating when show
318 unconserved enabled for group on alignment
321 <!-- JAL-2086 -->Cannot insert gaps into sequence when
325 <!-- JAL-2146 -->Alignment column in status incorrectly
326 shown as "Sequence position" when mousing over
330 <!-- JAL-2099 -->Incorrect column numbers in ruler when
331 hidden columns present
334 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
335 user created annotation added to alignment
338 <!-- JAL-1841 -->RNA Structure consensus only computed for
339 '()' base pair annotation
342 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
343 in zero scores for all base pairs in RNA Structure
347 <!-- JAL-2174-->Extend selection with columns containing
351 <!-- JAL-2275 -->Pfam format writer puts extra space at
352 beginning of sequence
355 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
359 <!-- JAL-2238 -->Cannot create groups on an alignment from
360 from a tree when t-coffee scores are shown
363 <!-- JAL-1836,1967 -->Cannot import and view PDB
364 structures with chains containing negative resnums (4q4h)
367 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
371 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
372 to Clustal, PIR and PileUp output
375 <!-- JAL-2008 -->Reordering sequence features that are
376 not visible causes alignment window to repaint
379 <!-- JAL-2006 -->Threshold sliders don't work in
380 graduated colour and colour by annotation row for e-value
381 scores associated with features and annotation rows
384 <!-- JAL-1797 -->amino acid physicochemical conservation
385 calculation should be case independent
388 <!-- JAL-2173 -->Remove annotation also updates hidden
392 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
393 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
394 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
397 <!-- JAL-2065 -->Null pointer exceptions and redraw
398 problems when reference sequence defined and 'show
399 non-conserved' enabled
402 <!-- JAL-1306 -->Quality and Conservation are now shown on
403 load even when Consensus calculation is disabled
409 <!-- JAL-1552-->URLs and links can't be imported by
410 drag'n'drop on OSX when launched via webstart (note - not
411 yet fixed for El Capitan)
414 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
415 output when running on non-gb/us i18n platforms
418 <!-- JAL-1944 -->Error thrown when exporting a view with
419 hidden sequences as flat-file alignment
422 <!-- JAL-2030-->InstallAnywhere distribution fails when
426 <!-- JAL-2080-->Jalview very slow to launch via webstart
427 (also hotfix for 2.9.0b2)
430 <!-- JAL-2085 -->Cannot save project when view has a
431 reference sequence defined
434 <!-- JAL-1011 -->Columns are suddenly selected in other
435 alignments and views when revealing hidden columns
438 <!-- JAL-1989 -->Hide columns not mirrored in complement
439 view in a cDNA/Protein splitframe
442 <!-- JAL-1369 -->Cannot save/restore representative
443 sequence from project when only one sequence is
447 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
451 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
452 structure consensus didn't refresh annotation panel
455 <!-- JAL-1962 -->View mapping in structure view shows
456 mappings between sequence and all chains in a PDB file
459 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
460 dialogs format columns correctly, don't display array
461 data, sort columns according to type
464 <!-- JAL-1975 -->Export complete shown after destination
465 file chooser is cancelled during an image export
468 <!-- JAL-2025 -->Error when querying PDB Service with
469 sequence name containing special characters
472 <!-- JAL-2024 -->Manual PDB structure querying should be
476 <!-- JAL-2104 -->Large tooltips with broken HTML
477 formatting don't wrap
480 <!-- JAL-1128 -->Figures exported from wrapped view are
481 truncated so L looks like I in consensus annotation
484 <!-- JAL-2003 -->Export features should only export the
485 currently displayed features for the current selection or
489 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
490 after fetching cross-references, and restoring from project
493 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
494 followed in the structure viewer
497 <!-- JAL-2163 -->Titles for individual alignments in
498 splitframe not restored from project
501 <!-- JAL-2145 -->missing autocalculated annotation at
502 trailing end of protein alignment in transcript/product
503 splitview when pad-gaps not enabled by default
506 <!-- JAL-1797 -->amino acid physicochemical conservation
510 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
511 article has been read (reopened issue due to
512 internationalisation problems)
515 <!-- JAL-1960 -->Only offer PDB structures in structure
516 viewer based on sequence name, PDB and UniProt
521 <!-- JAL-1976 -->No progress bar shown during export of
525 <!-- JAL-2213 -->Structures not always superimposed after
526 multiple structures are shown for one or more sequences.
529 <!-- JAL-1370 -->Reference sequence characters should not
530 be replaced with '.' when 'Show unconserved' format option
534 <!-- JAL-1823 -->Cannot specify chain code when entering
535 specific PDB id for sequence
538 <!-- JAL-1944 -->File->Export->.. as doesn't work when
539 'Export hidden sequences' is enabled, but 'export hidden
540 columns' is disabled.
543 <!--JAL-2026-->Best Quality option in structure chooser
544 selects lowest rather than highest resolution structures
548 <!-- JAL-1887 -->Incorrect start and end reported for PDB
549 to sequence mapping in 'View Mappings' report
551 <!-- may exclude, this is an external service stability issue JAL-1941
552 -- > RNA 3D structure not added via DSSR service</li> -->
557 <!-- JAL-2151 -->Incorrect columns are selected when
558 hidden columns present before start of sequence
561 <!-- JAL-1986 -->Missing dependencies on applet pages
565 <!-- JAL-1947 -->Overview pixel size changes when
566 sequences are hidden in applet
569 <!-- JAL-1996 -->Updated instructions for applet
570 deployment on examples pages.
577 <td width="60" nowrap>
579 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
580 <em>16/10/2015</em></strong>
585 <li>Time stamps for signed Jalview application and applet
592 <li>Duplicate group consensus and conservation rows
593 shown when tree is partitioned</li>
594 <li>Erratic behaviour when tree partitions made with
595 multiple cDNA/Protein split views</li>
601 <td width="60" nowrap>
603 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
604 <em>8/10/2015</em></strong>
609 <li>Updated Spanish translations of localized text for
611 </ul> <em>Application</em>
613 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
614 <li>Signed OSX InstallAnywhere installer<br></li>
615 <li>Support for per-sequence based annotations in BioJSON</li>
616 </ul> <em>Applet</em>
618 <li>Split frame example added to applet examples page</li>
624 <li>Mapping of cDNA to protein in split frames
625 incorrect when sequence start > 1</li>
626 <li>Broken images in filter column by annotation dialog
628 <li>Feature colours not parsed from features file</li>
629 <li>Exceptions and incomplete link URLs recovered when
630 loading a features file containing HTML tags in feature
636 <li>Annotations corrupted after BioJS export and
638 <li>Incorrect sequence limits after Fetch DB References
639 with 'trim retrieved sequences'</li>
640 <li>Incorrect warning about deleting all data when
641 deleting selected columns</li>
642 <li>Patch to build system for shipping properly signed
643 JNLP templates for webstart launch</li>
644 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
645 unreleased structures for download or viewing</li>
646 <li>Tab/space/return keystroke operation of EMBL-PDBe
647 fetcher/viewer dialogs works correctly</li>
648 <li>Disabled 'minimise' button on Jalview windows
649 running on OSX to workaround redraw hang bug</li>
650 <li>Split cDNA/Protein view position and geometry not
651 recovered from jalview project</li>
652 <li>Initial enabled/disabled state of annotation menu
653 sorter 'show autocalculated first/last' corresponds to
655 <li>Restoring of Clustal, RNA Helices and T-Coffee
656 color schemes from BioJSON</li>
660 <li>Reorder sequences mirrored in cDNA/Protein split
662 <li>Applet with Jmol examples not loading correctly</li>
668 <td><div align="center">
669 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
673 <li>Linked visualisation and analysis of DNA and Protein
676 <li>Translated cDNA alignments shown as split protein
677 and DNA alignment views</li>
678 <li>Codon consensus annotation for linked protein and
679 cDNA alignment views</li>
680 <li>Link cDNA or Protein product sequences by loading
681 them onto Protein or cDNA alignments</li>
682 <li>Reconstruct linked cDNA alignment from aligned
683 protein sequences</li>
686 <li>Jmol integration updated to Jmol v14.2.14</li>
687 <li>Import and export of Jalview alignment views as <a
688 href="features/bioJsonFormat.html">BioJSON</a></li>
689 <li>New alignment annotation file statements for
690 reference sequences and marking hidden columns</li>
691 <li>Reference sequence based alignment shading to
692 highlight variation</li>
693 <li>Select or hide columns according to alignment
695 <li>Find option for locating sequences by description</li>
696 <li>Conserved physicochemical properties shown in amino
697 acid conservation row</li>
698 <li>Alignments can be sorted by number of RNA helices</li>
699 </ul> <em>Application</em>
701 <li>New cDNA/Protein analysis capabilities
703 <li>Get Cross-References should open a Split Frame
704 view with cDNA/Protein</li>
705 <li>Detect when nucleotide sequences and protein
706 sequences are placed in the same alignment</li>
707 <li>Split cDNA/Protein views are saved in Jalview
712 <li>Use REST API to talk to Chimera</li>
713 <li>Selected regions in Chimera are highlighted in linked
716 <li>VARNA RNA viewer updated to v3.93</li>
717 <li>VARNA views are saved in Jalview Projects</li>
718 <li>Pseudoknots displayed as Jalview RNA annotation can
719 be shown in VARNA</li>
721 <li>Make groups for selection uses marked columns as well
722 as the active selected region</li>
724 <li>Calculate UPGMA and NJ trees using sequence feature
726 <li>New Export options
728 <li>New Export Settings dialog to control hidden
729 region export in flat file generation</li>
731 <li>Export alignment views for display with the <a
732 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
734 <li>Export scrollable SVG in HTML page</li>
735 <li>Optional embedding of BioJSON data when exporting
736 alignment figures to HTML</li>
738 <li>3D structure retrieval and display
740 <li>Free text and structured queries with the PDBe
742 <li>PDBe Search API based discovery and selection of
743 PDB structures for a sequence set</li>
747 <li>JPred4 employed for protein secondary structure
749 <li>Hide Insertions menu option to hide unaligned columns
750 for one or a group of sequences</li>
751 <li>Automatically hide insertions in alignments imported
752 from the JPred4 web server</li>
753 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
754 system on OSX<br />LGPL libraries courtesy of <a
755 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
757 <li>changed 'View nucleotide structure' submenu to 'View
758 VARNA 2D Structure'</li>
759 <li>change "View protein structure" menu option to "3D
762 </ul> <em>Applet</em>
764 <li>New layout for applet example pages</li>
765 <li>New parameters to enable SplitFrame view
766 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
767 <li>New example demonstrating linked viewing of cDNA and
768 Protein alignments</li>
769 </ul> <em>Development and deployment</em>
771 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
772 <li>Include installation type and git revision in build
773 properties and console log output</li>
774 <li>Jalview Github organisation, and new github site for
775 storing BioJsMSA Templates</li>
776 <li>Jalview's unit tests now managed with TestNG</li>
779 <!-- <em>General</em>
781 </ul> --> <!-- issues resolved --> <em>Application</em>
783 <li>Escape should close any open find dialogs</li>
784 <li>Typo in select-by-features status report</li>
785 <li>Consensus RNA secondary secondary structure
786 predictions are not highlighted in amber</li>
787 <li>Missing gap character in v2.7 example file means
788 alignment appears unaligned when pad-gaps is not enabled</li>
789 <li>First switch to RNA Helices colouring doesn't colour
790 associated structure views</li>
791 <li>ID width preference option is greyed out when auto
792 width checkbox not enabled</li>
793 <li>Stopped a warning dialog from being shown when
794 creating user defined colours</li>
795 <li>'View Mapping' in structure viewer shows sequence
796 mappings for just that viewer's sequences</li>
797 <li>Workaround for superposing PDB files containing
798 multiple models in Chimera</li>
799 <li>Report sequence position in status bar when hovering
800 over Jmol structure</li>
801 <li>Cannot output gaps as '.' symbols with Selection ->
802 output to text box</li>
803 <li>Flat file exports of alignments with hidden columns
804 have incorrect sequence start/end</li>
805 <li>'Aligning' a second chain to a Chimera structure from
807 <li>Colour schemes applied to structure viewers don't
808 work for nucleotide</li>
809 <li>Loading/cut'n'pasting an empty or invalid file leads
810 to a grey/invisible alignment window</li>
811 <li>Exported Jpred annotation from a sequence region
812 imports to different position</li>
813 <li>Space at beginning of sequence feature tooltips shown
814 on some platforms</li>
815 <li>Chimera viewer 'View | Show Chain' menu is not
817 <li>'New View' fails with a Null Pointer Exception in
818 console if Chimera has been opened</li>
819 <li>Mouseover to Chimera not working</li>
820 <li>Miscellaneous ENA XML feature qualifiers not
822 <li>NPE in annotation renderer after 'Extract Scores'</li>
823 <li>If two structures in one Chimera window, mouseover of
824 either sequence shows on first structure</li>
825 <li>'Show annotations' options should not make
826 non-positional annotations visible</li>
827 <li>Subsequence secondary structure annotation not shown
828 in right place after 'view flanking regions'</li>
829 <li>File Save As type unset when current file format is
831 <li>Save as '.jar' option removed for saving Jalview
833 <li>Colour by Sequence colouring in Chimera more
835 <li>Cannot 'add reference annotation' for a sequence in
836 several views on same alignment</li>
837 <li>Cannot show linked products for EMBL / ENA records</li>
838 <li>Jalview's tooltip wraps long texts containing no
840 </ul> <em>Applet</em>
842 <li>Jmol to JalviewLite mouseover/link not working</li>
843 <li>JalviewLite can't import sequences with ID
844 descriptions containing angle brackets</li>
845 </ul> <em>General</em>
847 <li>Cannot export and reimport RNA secondary structure
848 via jalview annotation file</li>
849 <li>Random helix colour palette for colour by annotation
850 with RNA secondary structure</li>
851 <li>Mouseover to cDNA from STOP residue in protein
852 translation doesn't work.</li>
853 <li>hints when using the select by annotation dialog box</li>
854 <li>Jmol alignment incorrect if PDB file has alternate CA
856 <li>FontChooser message dialog appears to hang after
857 choosing 1pt font</li>
858 <li>Peptide secondary structure incorrectly imported from
859 annotation file when annotation display text includes 'e' or
861 <li>Cannot set colour of new feature type whilst creating
863 <li>cDNA translation alignment should not be sequence
865 <li>'Show unconserved' doesn't work for lower case
867 <li>Nucleotide ambiguity codes involving R not recognised</li>
868 </ul> <em>Deployment and Documentation</em>
870 <li>Applet example pages appear different to the rest of
872 </ul> <em>Application Known issues</em>
874 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
875 <li>Misleading message appears after trying to delete
877 <li>Jalview icon not shown in dock after InstallAnywhere
878 version launches</li>
879 <li>Fetching EMBL reference for an RNA sequence results
880 fails with a sequence mismatch</li>
881 <li>Corrupted or unreadable alignment display when
882 scrolling alignment to right</li>
883 <li>ArrayIndexOutOfBoundsException thrown when remove
884 empty columns called on alignment with ragged gapped ends</li>
885 <li>auto calculated alignment annotation rows do not get
886 placed above or below non-autocalculated rows</li>
887 <li>Jalview dekstop becomes sluggish at full screen in
888 ultra-high resolution</li>
889 <li>Cannot disable consensus calculation independently of
890 quality and conservation</li>
891 <li>Mouseover highlighting between cDNA and protein can
892 become sluggish with more than one splitframe shown</li>
893 </ul> <em>Applet Known Issues</em>
895 <li>Core PDB parsing code requires Jmol</li>
896 <li>Sequence canvas panel goes white when alignment
897 window is being resized</li>
903 <td><div align="center">
904 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
908 <li>Updated Java code signing certificate donated by
910 <li>Features and annotation preserved when performing
911 pairwise alignment</li>
912 <li>RNA pseudoknot annotation can be
913 imported/exported/displayed</li>
914 <li>'colour by annotation' can colour by RNA and
915 protein secondary structure</li>
916 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
917 post-hoc with 2.9 release</em>)
920 </ul> <em>Application</em>
922 <li>Extract and display secondary structure for sequences
923 with 3D structures</li>
924 <li>Support for parsing RNAML</li>
925 <li>Annotations menu for layout
927 <li>sort sequence annotation rows by alignment</li>
928 <li>place sequence annotation above/below alignment
931 <li>Output in Stockholm format</li>
932 <li>Internationalisation: improved Spanish (es)
934 <li>Structure viewer preferences tab</li>
935 <li>Disorder and Secondary Structure annotation tracks
936 shared between alignments</li>
937 <li>UCSF Chimera launch and linked highlighting from
939 <li>Show/hide all sequence associated annotation rows for
940 all or current selection</li>
941 <li>disorder and secondary structure predictions
942 available as dataset annotation</li>
943 <li>Per-sequence rna helices colouring</li>
946 <li>Sequence database accessions imported when fetching
947 alignments from Rfam</li>
948 <li>update VARNA version to 3.91</li>
950 <li>New groovy scripts for exporting aligned positions,
951 conservation values, and calculating sum of pairs scores.</li>
952 <li>Command line argument to set default JABAWS server</li>
953 <li>include installation type in build properties and
954 console log output</li>
955 <li>Updated Jalview project format to preserve dataset
959 <!-- issues resolved --> <em>Application</em>
961 <li>Distinguish alignment and sequence associated RNA
962 structure in structure->view->VARNA</li>
963 <li>Raise dialog box if user deletes all sequences in an
965 <li>Pressing F1 results in documentation opening twice</li>
966 <li>Sequence feature tooltip is wrapped</li>
967 <li>Double click on sequence associated annotation
968 selects only first column</li>
969 <li>Redundancy removal doesn't result in unlinked
970 leaves shown in tree</li>
971 <li>Undos after several redundancy removals don't undo
973 <li>Hide sequence doesn't hide associated annotation</li>
974 <li>User defined colours dialog box too big to fit on
975 screen and buttons not visible</li>
976 <li>author list isn't updated if already written to
977 Jalview properties</li>
978 <li>Popup menu won't open after retrieving sequence
980 <li>File open window for associate PDB doesn't open</li>
981 <li>Left-then-right click on a sequence id opens a
982 browser search window</li>
983 <li>Cannot open sequence feature shading/sort popup menu
984 in feature settings dialog</li>
985 <li>better tooltip placement for some areas of Jalview
987 <li>Allow addition of JABAWS Server which doesn't
989 <li>Web services parameters dialog box is too large to
991 <li>Muscle nucleotide alignment preset obscured by
993 <li>JABAWS preset submenus don't contain newly
994 defined user preset</li>
995 <li>MSA web services warns user if they were launched
996 with invalid input</li>
997 <li>Jalview cannot contact DAS Registy when running on
1000 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1001 'Superpose with' submenu not shown when new view
1005 </ul> <!-- <em>Applet</em>
1007 </ul> <em>General</em>
1009 </ul>--> <em>Deployment and Documentation</em>
1011 <li>2G and 1G options in launchApp have no effect on
1012 memory allocation</li>
1013 <li>launchApp service doesn't automatically open
1014 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1016 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1017 InstallAnywhere reports cannot find valid JVM when Java
1018 1.7_055 is available
1020 </ul> <em>Application Known issues</em>
1023 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1024 corrupted or unreadable alignment display when scrolling
1028 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1029 retrieval fails but progress bar continues for DAS retrieval
1030 with large number of ID
1033 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1034 flatfile output of visible region has incorrect sequence
1038 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1039 rna structure consensus doesn't update when secondary
1040 structure tracks are rearranged
1043 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1044 invalid rna structure positional highlighting does not
1045 highlight position of invalid base pairs
1048 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1049 out of memory errors are not raised when saving Jalview
1050 project from alignment window file menu
1053 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1054 Switching to RNA Helices colouring doesn't propagate to
1058 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1059 colour by RNA Helices not enabled when user created
1060 annotation added to alignment
1063 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1064 Jalview icon not shown on dock in Mountain Lion/Webstart
1066 </ul> <em>Applet Known Issues</em>
1069 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1070 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1073 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1074 Jalview and Jmol example not compatible with IE9
1077 <li>Sort by annotation score doesn't reverse order
1083 <td><div align="center">
1084 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1087 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1090 <li>Internationalisation of user interface (usually
1091 called i18n support) and translation for Spanish locale</li>
1092 <li>Define/Undefine group on current selection with
1093 Ctrl-G/Shift Ctrl-G</li>
1094 <li>Improved group creation/removal options in
1095 alignment/sequence Popup menu</li>
1096 <li>Sensible precision for symbol distribution
1097 percentages shown in logo tooltip.</li>
1098 <li>Annotation panel height set according to amount of
1099 annotation when alignment first opened</li>
1100 </ul> <em>Application</em>
1102 <li>Interactive consensus RNA secondary structure
1103 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1104 <li>Select columns containing particular features from
1105 Feature Settings dialog</li>
1106 <li>View all 'representative' PDB structures for selected
1108 <li>Update Jalview project format:
1110 <li>New file extension for Jalview projects '.jvp'</li>
1111 <li>Preserve sequence and annotation dataset (to
1112 store secondary structure annotation,etc)</li>
1113 <li>Per group and alignment annotation and RNA helix
1117 <li>New similarity measures for PCA and Tree calculation
1119 <li>Experimental support for retrieval and viewing of
1120 flanking regions for an alignment</li>
1124 <!-- issues resolved --> <em>Application</em>
1126 <li>logo keeps spinning and status remains at queued or
1127 running after job is cancelled</li>
1128 <li>cannot export features from alignments imported from
1129 Jalview/VAMSAS projects</li>
1130 <li>Buggy slider for web service parameters that take
1132 <li>Newly created RNA secondary structure line doesn't
1133 have 'display all symbols' flag set</li>
1134 <li>T-COFFEE alignment score shading scheme and other
1135 annotation shading not saved in Jalview project</li>
1136 <li>Local file cannot be loaded in freshly downloaded
1138 <li>Jalview icon not shown on dock in Mountain
1140 <li>Load file from desktop file browser fails</li>
1141 <li>Occasional NPE thrown when calculating large trees</li>
1142 <li>Cannot reorder or slide sequences after dragging an
1143 alignment onto desktop</li>
1144 <li>Colour by annotation dialog throws NPE after using
1145 'extract scores' function</li>
1146 <li>Loading/cut'n'pasting an empty file leads to a grey
1147 alignment window</li>
1148 <li>Disorder thresholds rendered incorrectly after
1149 performing IUPred disorder prediction</li>
1150 <li>Multiple group annotated consensus rows shown when
1151 changing 'normalise logo' display setting</li>
1152 <li>Find shows blank dialog after 'finished searching' if
1153 nothing matches query</li>
1154 <li>Null Pointer Exceptions raised when sorting by
1155 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1157 <li>Errors in Jmol console when structures in alignment
1158 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1160 <li>Not all working JABAWS services are shown in
1162 <li>JAVAWS version of Jalview fails to launch with
1163 'invalid literal/length code'</li>
1164 <li>Annotation/RNA Helix colourschemes cannot be applied
1165 to alignment with groups (actually fixed in 2.8.0b1)</li>
1166 <li>RNA Helices and T-Coffee Scores available as default
1169 </ul> <em>Applet</em>
1171 <li>Remove group option is shown even when selection is
1173 <li>Apply to all groups ticked but colourscheme changes
1174 don't affect groups</li>
1175 <li>Documented RNA Helices and T-Coffee Scores as valid
1176 colourscheme name</li>
1177 <li>Annotation labels drawn on sequence IDs when
1178 Annotation panel is not displayed</li>
1179 <li>Increased font size for dropdown menus on OSX and
1180 embedded windows</li>
1181 </ul> <em>Other</em>
1183 <li>Consensus sequence for alignments/groups with a
1184 single sequence were not calculated</li>
1185 <li>annotation files that contain only groups imported as
1186 annotation and junk sequences</li>
1187 <li>Fasta files with sequences containing '*' incorrectly
1188 recognised as PFAM or BLC</li>
1189 <li>conservation/PID slider apply all groups option
1190 doesn't affect background (2.8.0b1)
1192 <li>redundancy highlighting is erratic at 0% and 100%</li>
1193 <li>Remove gapped columns fails for sequences with ragged
1195 <li>AMSA annotation row with leading spaces is not
1196 registered correctly on import</li>
1197 <li>Jalview crashes when selecting PCA analysis for
1198 certain alignments</li>
1199 <li>Opening the colour by annotation dialog for an
1200 existing annotation based 'use original colours'
1201 colourscheme loses original colours setting</li>
1206 <td><div align="center">
1207 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
1208 <em>30/1/2014</em></strong>
1212 <li>Trusted certificates for JalviewLite applet and
1213 Jalview Desktop application<br />Certificate was donated by
1214 <a href="https://www.certum.eu">Certum</a> to the Jalview
1215 open source project).
1217 <li>Jalview SRS links replaced by UniProt and EBI-search
1219 <li>Output in Stockholm format</li>
1220 <li>Allow import of data from gzipped files</li>
1221 <li>Export/import group and sequence associated line
1222 graph thresholds</li>
1223 <li>Nucleotide substitution matrix that supports RNA and
1224 ambiguity codes</li>
1225 <li>Allow disorder predictions to be made on the current
1226 selection (or visible selection) in the same way that JPred
1228 <li>Groovy scripting for headless Jalview operation</li>
1229 </ul> <em>Other improvements</em>
1231 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
1232 <li>COMBINE statement uses current SEQUENCE_REF and
1233 GROUP_REF scope to group annotation rows</li>
1234 <li>Support '' style escaping of quotes in Newick
1236 <li>Group options for JABAWS service by command line name</li>
1237 <li>Empty tooltip shown for JABA service options with a
1238 link but no description</li>
1239 <li>Select primary source when selecting authority in
1240 database fetcher GUI</li>
1241 <li>Add .mfa to FASTA file extensions recognised by
1243 <li>Annotation label tooltip text wrap</li>
1248 <li>Slow scrolling when lots of annotation rows are
1250 <li>Lots of NPE (and slowness) after creating RNA
1251 secondary structure annotation line</li>
1252 <li>Sequence database accessions not imported when
1253 fetching alignments from Rfam</li>
1254 <li>Incorrect SHMR submission for sequences with
1256 <li>View all structures does not always superpose
1258 <li>Option widgets in service parameters not updated to
1259 reflect user or preset settings</li>
1260 <li>Null pointer exceptions for some services without
1261 presets or adjustable parameters</li>
1262 <li>Discover PDB IDs entry in structure menu doesn't
1263 discover PDB xRefs</li>
1264 <li>Exception encountered while trying to retrieve
1265 features with DAS</li>
1266 <li>Lowest value in annotation row isn't coloured
1267 when colour by annotation (per sequence) is coloured</li>
1268 <li>Keyboard mode P jumps to start of gapped region when
1269 residue follows a gap</li>
1270 <li>Jalview appears to hang importing an alignment with
1271 Wrap as default or after enabling Wrap</li>
1272 <li>'Right click to add annotations' message
1273 shown in wrap mode when no annotations present</li>
1274 <li>Disorder predictions fail with NPE if no automatic
1275 annotation already exists on alignment</li>
1276 <li>oninit javascript function should be called after
1277 initialisation completes</li>
1278 <li>Remove redundancy after disorder prediction corrupts
1279 alignment window display</li>
1280 <li>Example annotation file in documentation is invalid</li>
1281 <li>Grouped line graph annotation rows are not exported
1282 to annotation file</li>
1283 <li>Multi-harmony analysis cannot be run when only two
1285 <li>Cannot create multiple groups of line graphs with
1286 several 'combine' statements in annotation file</li>
1287 <li>Pressing return several times causes Number Format
1288 exceptions in keyboard mode</li>
1289 <li>Multi-harmony (SHMMR) method doesn't submit
1290 correct partitions for input data</li>
1291 <li>Translation from DNA to Amino Acids fails</li>
1292 <li>Jalview fail to load newick tree with quoted label</li>
1293 <li>--headless flag isn't understood</li>
1294 <li>ClassCastException when generating EPS in headless
1296 <li>Adjusting sequence-associated shading threshold only
1297 changes one row's threshold</li>
1298 <li>Preferences and Feature settings panel panel
1299 doesn't open</li>
1300 <li>hide consensus histogram also hides conservation and
1301 quality histograms</li>
1306 <td><div align="center">
1307 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
1309 <td><em>Application</em>
1311 <li>Support for JABAWS 2.0 Services (AACon alignment
1312 conservation, protein disorder and Clustal Omega)</li>
1313 <li>JABAWS server status indicator in Web Services
1315 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
1316 in Jalview alignment window</li>
1317 <li>Updated Jalview build and deploy framework for OSX
1318 mountain lion, windows 7, and 8</li>
1319 <li>Nucleotide substitution matrix for PCA that supports
1320 RNA and ambiguity codes</li>
1322 <li>Improved sequence database retrieval GUI</li>
1323 <li>Support fetching and database reference look up
1324 against multiple DAS sources (Fetch all from in 'fetch db
1326 <li>Jalview project improvements
1328 <li>Store and retrieve the 'belowAlignment'
1329 flag for annotation</li>
1330 <li>calcId attribute to group annotation rows on the
1332 <li>Store AACon calculation settings for a view in
1333 Jalview project</li>
1337 <li>horizontal scrolling gesture support</li>
1338 <li>Visual progress indicator when PCA calculation is
1340 <li>Simpler JABA web services menus</li>
1341 <li>visual indication that web service results are still
1342 being retrieved from server</li>
1343 <li>Serialise the dialogs that are shown when Jalview
1344 starts up for first time</li>
1345 <li>Jalview user agent string for interacting with HTTP
1347 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
1349 <li>Examples directory and Groovy library included in
1350 InstallAnywhere distribution</li>
1351 </ul> <em>Applet</em>
1353 <li>RNA alignment and secondary structure annotation
1354 visualization applet example</li>
1355 </ul> <em>General</em>
1357 <li>Normalise option for consensus sequence logo</li>
1358 <li>Reset button in PCA window to return dimensions to
1360 <li>Allow seqspace or Jalview variant of alignment PCA
1362 <li>PCA with either nucleic acid and protein substitution
1364 <li>Allow windows containing HTML reports to be exported
1366 <li>Interactive display and editing of RNA secondary
1367 structure contacts</li>
1368 <li>RNA Helix Alignment Colouring</li>
1369 <li>RNA base pair logo consensus</li>
1370 <li>Parse sequence associated secondary structure
1371 information in Stockholm files</li>
1372 <li>HTML Export database accessions and annotation
1373 information presented in tooltip for sequences</li>
1374 <li>Import secondary structure from LOCARNA clustalw
1375 style RNA alignment files</li>
1376 <li>import and visualise T-COFFEE quality scores for an
1378 <li>'colour by annotation' per sequence option to
1379 shade each sequence according to its associated alignment
1381 <li>New Jalview Logo</li>
1382 </ul> <em>Documentation and Development</em>
1384 <li>documentation for score matrices used in Jalview</li>
1385 <li>New Website!</li>
1387 <td><em>Application</em>
1389 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
1390 wsdbfetch REST service</li>
1391 <li>Stop windows being moved outside desktop on OSX</li>
1392 <li>Filetype associations not installed for webstart
1394 <li>Jalview does not always retrieve progress of a JABAWS
1395 job execution in full once it is complete</li>
1396 <li>revise SHMR RSBS definition to ensure alignment is
1397 uploaded via ali_file parameter</li>
1398 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
1399 <li>View all structures superposed fails with exception</li>
1400 <li>Jnet job queues forever if a very short sequence is
1401 submitted for prediction</li>
1402 <li>Cut and paste menu not opened when mouse clicked on
1404 <li>Putting fractional value into integer text box in
1405 alignment parameter dialog causes Jalview to hang</li>
1406 <li>Structure view highlighting doesn't work on
1408 <li>View all structures fails with exception shown in
1410 <li>Characters in filename associated with PDBEntry not
1411 escaped in a platform independent way</li>
1412 <li>Jalview desktop fails to launch with exception when
1414 <li>Tree calculation reports 'you must have 2 or more
1415 sequences selected' when selection is empty</li>
1416 <li>Jalview desktop fails to launch with jar signature
1417 failure when java web start temporary file caching is
1419 <li>DAS Sequence retrieval with range qualification
1420 results in sequence xref which includes range qualification</li>
1421 <li>Errors during processing of command line arguments
1422 cause progress bar (JAL-898) to be removed</li>
1423 <li>Replace comma for semi-colon option not disabled for
1424 DAS sources in sequence fetcher</li>
1425 <li>Cannot close news reader when JABAWS server warning
1426 dialog is shown</li>
1427 <li>Option widgets not updated to reflect user settings</li>
1428 <li>Edited sequence not submitted to web service</li>
1429 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
1430 <li>InstallAnywhere installer doesn't unpack and run
1431 on OSX Mountain Lion</li>
1432 <li>Annotation panel not given a scroll bar when
1433 sequences with alignment annotation are pasted into the
1435 <li>Sequence associated annotation rows not associated
1436 when loaded from Jalview project</li>
1437 <li>Browser launch fails with NPE on java 1.7</li>
1438 <li>JABAWS alignment marked as finished when job was
1439 cancelled or job failed due to invalid input</li>
1440 <li>NPE with v2.7 example when clicking on Tree
1441 associated with all views</li>
1442 <li>Exceptions when copy/paste sequences with grouped
1443 annotation rows to new window</li>
1444 </ul> <em>Applet</em>
1446 <li>Sequence features are momentarily displayed before
1447 they are hidden using hidefeaturegroups applet parameter</li>
1448 <li>loading features via javascript API automatically
1449 enables feature display</li>
1450 <li>scrollToColumnIn javascript API method doesn't
1452 </ul> <em>General</em>
1454 <li>Redundancy removal fails for rna alignment</li>
1455 <li>PCA calculation fails when sequence has been selected
1456 and then deselected</li>
1457 <li>PCA window shows grey box when first opened on OSX</li>
1458 <li>Letters coloured pink in sequence logo when alignment
1459 coloured with clustalx</li>
1460 <li>Choosing fonts without letter symbols defined causes
1461 exceptions and redraw errors</li>
1462 <li>Initial PCA plot view is not same as manually
1463 reconfigured view</li>
1464 <li>Grouped annotation graph label has incorrect line
1466 <li>Grouped annotation graph label display is corrupted
1467 for lots of labels</li>
1472 <div align="center">
1473 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
1476 <td><em>Application</em>
1478 <li>Jalview Desktop News Reader</li>
1479 <li>Tweaked default layout of web services menu</li>
1480 <li>View/alignment association menu to enable user to
1481 easily specify which alignment a multi-structure view takes
1482 its colours/correspondences from</li>
1483 <li>Allow properties file location to be specified as URL</li>
1484 <li>Extend Jalview project to preserve associations
1485 between many alignment views and a single Jmol display</li>
1486 <li>Store annotation row height in Jalview project file</li>
1487 <li>Annotation row column label formatting attributes
1488 stored in project file</li>
1489 <li>Annotation row order for auto-calculated annotation
1490 rows preserved in Jalview project file</li>
1491 <li>Visual progress indication when Jalview state is
1492 saved using Desktop window menu</li>
1493 <li>Visual indication that command line arguments are
1494 still being processed</li>
1495 <li>Groovy script execution from URL</li>
1496 <li>Colour by annotation default min and max colours in
1498 <li>Automatically associate PDB files dragged onto an
1499 alignment with sequences that have high similarity and
1501 <li>Update JGoogleAnalytics to latest release (0.3)</li>
1502 <li>'view structures' option to open many
1503 structures in same window</li>
1504 <li>Sort associated views menu option for tree panel</li>
1505 <li>Group all JABA and non-JABA services for a particular
1506 analysis function in its own submenu</li>
1507 </ul> <em>Applet</em>
1509 <li>Userdefined and autogenerated annotation rows for
1511 <li>Adjustment of alignment annotation pane height</li>
1512 <li>Annotation scrollbar for annotation panel</li>
1513 <li>Drag to reorder annotation rows in annotation panel</li>
1514 <li>'automaticScrolling' parameter</li>
1515 <li>Allow sequences with partial ID string matches to be
1516 annotated from GFF/Jalview features files</li>
1517 <li>Sequence logo annotation row in applet</li>
1518 <li>Absolute paths relative to host server in applet
1519 parameters are treated as such</li>
1520 <li>New in the JalviewLite javascript API:
1522 <li>JalviewLite.js javascript library</li>
1523 <li>Javascript callbacks for
1525 <li>Applet initialisation</li>
1526 <li>Sequence/alignment mouse-overs and selections</li>
1529 <li>scrollTo row and column alignment scrolling
1531 <li>Select sequence/alignment regions from javascript</li>
1532 <li>javascript structure viewer harness to pass
1533 messages between Jmol and Jalview when running as
1534 distinct applets</li>
1535 <li>sortBy method</li>
1536 <li>Set of applet and application examples shipped
1537 with documentation</li>
1538 <li>New example to demonstrate JalviewLite and Jmol
1539 javascript message exchange</li>
1541 </ul> <em>General</em>
1543 <li>Enable Jmol displays to be associated with multiple
1544 multiple alignments</li>
1545 <li>Option to automatically sort alignment with new tree</li>
1546 <li>User configurable link to enable redirects to a
1547 www.Jalview.org mirror</li>
1548 <li>Jmol colours option for Jmol displays</li>
1549 <li>Configurable newline string when writing alignment
1550 and other flat files</li>
1551 <li>Allow alignment annotation description lines to
1552 contain html tags</li>
1553 </ul> <em>Documentation and Development</em>
1555 <li>Add groovy test harness for bulk load testing to
1557 <li>Groovy script to load and align a set of sequences
1558 using a web service before displaying the result in the
1559 Jalview desktop</li>
1560 <li>Restructured javascript and applet api documentation</li>
1561 <li>Ant target to publish example html files with applet
1563 <li>Netbeans project for building Jalview from source</li>
1564 <li>ant task to create online javadoc for Jalview source</li>
1566 <td><em>Application</em>
1568 <li>User defined colourscheme throws exception when
1569 current built in colourscheme is saved as new scheme</li>
1570 <li>AlignFrame->Save in application pops up save
1571 dialog for valid filename/format</li>
1572 <li>Cannot view associated structure for UniProt sequence</li>
1573 <li>PDB file association breaks for UniProt sequence
1575 <li>Associate PDB from file dialog does not tell you
1576 which sequence is to be associated with the file</li>
1577 <li>Find All raises null pointer exception when query
1578 only matches sequence IDs</li>
1579 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
1580 <li>Jalview project with Jmol views created with Jalview
1581 2.4 cannot be loaded</li>
1582 <li>Filetype associations not installed for webstart
1584 <li>Two or more chains in a single PDB file associated
1585 with sequences in different alignments do not get coloured
1586 by their associated sequence</li>
1587 <li>Visibility status of autocalculated annotation row
1588 not preserved when project is loaded</li>
1589 <li>Annotation row height and visibility attributes not
1590 stored in Jalview project</li>
1591 <li>Tree bootstraps are not preserved when saved as a
1592 Jalview project</li>
1593 <li>Envision2 workflow tooltips are corrupted</li>
1594 <li>Enabling show group conservation also enables colour
1595 by conservation</li>
1596 <li>Duplicate group associated conservation or consensus
1597 created on new view</li>
1598 <li>Annotation scrollbar not displayed after 'show
1599 all hidden annotation rows' option selected</li>
1600 <li>Alignment quality not updated after alignment
1601 annotation row is hidden then shown</li>
1602 <li>Preserve colouring of structures coloured by
1603 sequences in pre Jalview 2.7 projects</li>
1604 <li>Web service job parameter dialog is not laid out
1606 <li>Web services menu not refreshed after 'reset
1607 services' button is pressed in preferences</li>
1608 <li>Annotation off by one in Jalview v2_3 example project</li>
1609 <li>Structures imported from file and saved in project
1610 get name like jalview_pdb1234.txt when reloaded</li>
1611 <li>Jalview does not always retrieve progress of a JABAWS
1612 job execution in full once it is complete</li>
1613 </ul> <em>Applet</em>
1615 <li>Alignment height set incorrectly when lots of
1616 annotation rows are displayed</li>
1617 <li>Relative URLs in feature HTML text not resolved to
1619 <li>View follows highlighting does not work for positions
1621 <li><= shown as = in tooltip</li>
1622 <li>Export features raises exception when no features
1624 <li>Separator string used for serialising lists of IDs
1625 for javascript api is modified when separator string
1626 provided as parameter</li>
1627 <li>Null pointer exception when selecting tree leaves for
1628 alignment with no existing selection</li>
1629 <li>Relative URLs for datasources assumed to be relative
1630 to applet's codebase</li>
1631 <li>Status bar not updated after finished searching and
1632 search wraps around to first result</li>
1633 <li>StructureSelectionManager instance shared between
1634 several Jalview applets causes race conditions and memory
1636 <li>Hover tooltip and mouseover of position on structure
1637 not sent from Jmol in applet</li>
1638 <li>Certain sequences of javascript method calls to
1639 applet API fatally hang browser</li>
1640 </ul> <em>General</em>
1642 <li>View follows structure mouseover scrolls beyond
1643 position with wrapped view and hidden regions</li>
1644 <li>Find sequence position moves to wrong residue
1645 with/without hidden columns</li>
1646 <li>Sequence length given in alignment properties window
1648 <li>InvalidNumberFormat exceptions thrown when trying to
1649 import PDB like structure files</li>
1650 <li>Positional search results are only highlighted
1651 between user-supplied sequence start/end bounds</li>
1652 <li>End attribute of sequence is not validated</li>
1653 <li>Find dialog only finds first sequence containing a
1654 given sequence position</li>
1655 <li>Sequence numbering not preserved in MSF alignment
1657 <li>Jalview PDB file reader does not extract sequence
1658 from nucleotide chains correctly</li>
1659 <li>Structure colours not updated when tree partition
1660 changed in alignment</li>
1661 <li>Sequence associated secondary structure not correctly
1662 parsed in interleaved stockholm</li>
1663 <li>Colour by annotation dialog does not restore current
1665 <li>Hiding (nearly) all sequences doesn't work
1667 <li>Sequences containing lowercase letters are not
1668 properly associated with their pdb files</li>
1669 </ul> <em>Documentation and Development</em>
1671 <li>schemas/JalviewWsParamSet.xsd corrupted by
1672 ApplyCopyright tool</li>
1677 <div align="center">
1678 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
1681 <td><em>Application</em>
1683 <li>New warning dialog when the Jalview Desktop cannot
1684 contact web services</li>
1685 <li>JABA service parameters for a preset are shown in
1686 service job window</li>
1687 <li>JABA Service menu entries reworded</li>
1691 <li>Modeller PIR IO broken - cannot correctly import a
1692 pir file emitted by Jalview</li>
1693 <li>Existing feature settings transferred to new
1694 alignment view created from cut'n'paste</li>
1695 <li>Improved test for mixed amino/nucleotide chains when
1696 parsing PDB files</li>
1697 <li>Consensus and conservation annotation rows
1698 occasionally become blank for all new windows</li>
1699 <li>Exception raised when right clicking above sequences
1700 in wrapped view mode</li>
1701 </ul> <em>Application</em>
1703 <li>multiple multiply aligned structure views cause cpu
1704 usage to hit 100% and computer to hang</li>
1705 <li>Web Service parameter layout breaks for long user
1706 parameter names</li>
1707 <li>Jaba service discovery hangs desktop if Jaba server
1714 <div align="center">
1715 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
1718 <td><em>Application</em>
1720 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
1721 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
1724 <li>Web Services preference tab</li>
1725 <li>Analysis parameters dialog box and user defined
1727 <li>Improved speed and layout of Envision2 service menu</li>
1728 <li>Superpose structures using associated sequence
1730 <li>Export coordinates and projection as CSV from PCA
1732 </ul> <em>Applet</em>
1734 <li>enable javascript: execution by the applet via the
1735 link out mechanism</li>
1736 </ul> <em>Other</em>
1738 <li>Updated the Jmol Jalview interface to work with Jmol
1740 <li>The Jalview Desktop and JalviewLite applet now
1741 require Java 1.5</li>
1742 <li>Allow Jalview feature colour specification for GFF
1743 sequence annotation files</li>
1744 <li>New 'colour by label' keword in Jalview feature file
1745 type colour specification</li>
1746 <li>New Jalview Desktop Groovy API method that allows a
1747 script to check if it being run in an interactive session or
1748 in a batch operation from the Jalview command line</li>
1752 <li>clustalx colourscheme colours Ds preferentially when
1753 both D+E are present in over 50% of the column</li>
1754 </ul> <em>Application</em>
1756 <li>typo in AlignmentFrame->View->Hide->all but
1757 selected Regions menu item</li>
1758 <li>sequence fetcher replaces ',' for ';' when the ',' is
1759 part of a valid accession ID</li>
1760 <li>fatal OOM if object retrieved by sequence fetcher
1761 runs out of memory</li>
1762 <li>unhandled Out of Memory Error when viewing pca
1763 analysis results</li>
1764 <li>InstallAnywhere builds fail to launch on OS X java
1765 10.5 update 4 (due to apple Java 1.6 update)</li>
1766 <li>Installanywhere Jalview silently fails to launch</li>
1767 </ul> <em>Applet</em>
1769 <li>Jalview.getFeatureGroups() raises an
1770 ArrayIndexOutOfBoundsException if no feature groups are
1777 <div align="center">
1778 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
1784 <li>Alignment prettyprinter doesn't cope with long
1786 <li>clustalx colourscheme colours Ds preferentially when
1787 both D+E are present in over 50% of the column</li>
1788 <li>nucleic acid structures retrieved from PDB do not
1789 import correctly</li>
1790 <li>More columns get selected than were clicked on when a
1791 number of columns are hidden</li>
1792 <li>annotation label popup menu not providing correct
1793 add/hide/show options when rows are hidden or none are
1795 <li>Stockholm format shown in list of readable formats,
1796 and parser copes better with alignments from RFAM.</li>
1797 <li>CSV output of consensus only includes the percentage
1798 of all symbols if sequence logo display is enabled</li>
1800 </ul> <em>Applet</em>
1802 <li>annotation panel disappears when annotation is
1804 </ul> <em>Application</em>
1806 <li>Alignment view not redrawn properly when new
1807 alignment opened where annotation panel is visible but no
1808 annotations are present on alignment</li>
1809 <li>pasted region containing hidden columns is
1810 incorrectly displayed in new alignment window</li>
1811 <li>Jalview slow to complete operations when stdout is
1812 flooded (fix is to close the Jalview console)</li>
1813 <li>typo in AlignmentFrame->View->Hide->all but
1814 selected Rregions menu item.</li>
1815 <li>inconsistent group submenu and Format submenu entry
1816 'Un' or 'Non'conserved</li>
1817 <li>Sequence feature settings are being shared by
1818 multiple distinct alignments</li>
1819 <li>group annotation not recreated when tree partition is
1821 <li>double click on group annotation to select sequences
1822 does not propagate to associated trees</li>
1823 <li>Mac OSX specific issues:
1825 <li>exception raised when mouse clicked on desktop
1826 window background</li>
1827 <li>Desktop menu placed on menu bar and application
1828 name set correctly</li>
1829 <li>sequence feature settings not wide enough for the
1830 save feature colourscheme button</li>
1839 <div align="center">
1840 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
1843 <td><em>New Capabilities</em>
1845 <li>URL links generated from description line for
1846 regular-expression based URL links (applet and application)
1853 <li>Non-positional feature URL links are shown in link
1855 <li>Linked viewing of nucleic acid sequences and
1857 <li>Automatic Scrolling option in View menu to display
1858 the currently highlighted region of an alignment.</li>
1859 <li>Order an alignment by sequence length, or using the
1860 average score or total feature count for each sequence.</li>
1861 <li>Shading features by score or associated description</li>
1862 <li>Subdivide alignment and groups based on identity of
1863 selected subsequence (Make Groups from Selection).</li>
1864 <li>New hide/show options including Shift+Control+H to
1865 hide everything but the currently selected region.</li>
1866 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
1867 </ul> <em>Application</em>
1869 <li>Fetch DB References capabilities and UI expanded to
1870 support retrieval from DAS sequence sources</li>
1871 <li>Local DAS Sequence sources can be added via the
1872 command line or via the Add local source dialog box.</li>
1873 <li>DAS Dbref and DbxRef feature types are parsed as
1874 database references and protein_name is parsed as
1875 description line (BioSapiens terms).</li>
1876 <li>Enable or disable non-positional feature and database
1877 references in sequence ID tooltip from View menu in
1879 <!-- <li>New hidden columns and rows and representatives capabilities
1880 in annotations file (in progress - not yet fully implemented)</li> -->
1881 <li>Group-associated consensus, sequence logos and
1882 conservation plots</li>
1883 <li>Symbol distributions for each column can be exported
1884 and visualized as sequence logos</li>
1885 <li>Optionally scale multi-character column labels to fit
1886 within each column of annotation row<!-- todo for applet -->
1888 <li>Optional automatic sort of associated alignment view
1889 when a new tree is opened.</li>
1890 <li>Jalview Java Console</li>
1891 <li>Better placement of desktop window when moving
1892 between different screens.</li>
1893 <li>New preference items for sequence ID tooltip and
1894 consensus annotation</li>
1895 <li>Client to submit sequences and IDs to Envision2
1897 <li><em>Vamsas Capabilities</em>
1899 <li>Improved VAMSAS synchronization (Jalview archive
1900 used to preserve views, structures, and tree display
1902 <li>Import of vamsas documents from disk or URL via
1904 <li>Sharing of selected regions between views and
1905 with other VAMSAS applications (Experimental feature!)</li>
1906 <li>Updated API to VAMSAS version 0.2</li>
1908 </ul> <em>Applet</em>
1910 <li>Middle button resizes annotation row height</li>
1913 <li>sortByTree (true/false) - automatically sort the
1914 associated alignment view by the tree when a new tree is
1916 <li>showTreeBootstraps (true/false) - show or hide
1917 branch bootstraps (default is to show them if available)</li>
1918 <li>showTreeDistances (true/false) - show or hide
1919 branch lengths (default is to show them if available)</li>
1920 <li>showUnlinkedTreeNodes (true/false) - indicate if
1921 unassociated nodes should be highlighted in the tree
1923 <li>heightScale and widthScale (1.0 or more) -
1924 increase the height or width of a cell in the alignment
1925 grid relative to the current font size.</li>
1928 <li>Non-positional features displayed in sequence ID
1930 </ul> <em>Other</em>
1932 <li>Features format: graduated colour definitions and
1933 specification of feature scores</li>
1934 <li>Alignment Annotations format: new keywords for group
1935 associated annotation (GROUP_REF) and annotation row display
1936 properties (ROW_PROPERTIES)</li>
1937 <li>XML formats extended to support graduated feature
1938 colourschemes, group associated annotation, and profile
1939 visualization settings.</li></td>
1942 <li>Source field in GFF files parsed as feature source
1943 rather than description</li>
1944 <li>Non-positional features are now included in sequence
1945 feature and gff files (controlled via non-positional feature
1946 visibility in tooltip).</li>
1947 <li>URL links generated for all feature links (bugfix)</li>
1948 <li>Added URL embedding instructions to features file
1950 <li>Codons containing ambiguous nucleotides translated as
1951 'X' in peptide product</li>
1952 <li>Match case switch in find dialog box works for both
1953 sequence ID and sequence string and query strings do not
1954 have to be in upper case to match case-insensitively.</li>
1955 <li>AMSA files only contain first column of
1956 multi-character column annotation labels</li>
1957 <li>Jalview Annotation File generation/parsing consistent
1958 with documentation (e.g. Stockholm annotation can be
1959 exported and re-imported)</li>
1960 <li>PDB files without embedded PDB IDs given a friendly
1962 <li>Find incrementally searches ID string matches as well
1963 as subsequence matches, and correctly reports total number
1967 <li>Better handling of exceptions during sequence
1969 <li>Dasobert generated non-positional feature URL
1970 link text excludes the start_end suffix</li>
1971 <li>DAS feature and source retrieval buttons disabled
1972 when fetch or registry operations in progress.</li>
1973 <li>PDB files retrieved from URLs are cached properly</li>
1974 <li>Sequence description lines properly shared via
1976 <li>Sequence fetcher fetches multiple records for all
1978 <li>Ensured that command line das feature retrieval
1979 completes before alignment figures are generated.</li>
1980 <li>Reduced time taken when opening file browser for
1982 <li>isAligned check prior to calculating tree, PCA or
1983 submitting an MSA to JNet now excludes hidden sequences.</li>
1984 <li>User defined group colours properly recovered
1985 from Jalview projects.</li>
1994 <div align="center">
1995 <strong>2.4.0.b2</strong><br> 28/10/2009
2000 <li>Experimental support for google analytics usage
2002 <li>Jalview privacy settings (user preferences and docs).</li>
2007 <li>Race condition in applet preventing startup in
2009 <li>Exception when feature created from selection beyond
2010 length of sequence.</li>
2011 <li>Allow synthetic PDB files to be imported gracefully</li>
2012 <li>Sequence associated annotation rows associate with
2013 all sequences with a given id</li>
2014 <li>Find function matches case-insensitively for sequence
2015 ID string searches</li>
2016 <li>Non-standard characters do not cause pairwise
2017 alignment to fail with exception</li>
2018 </ul> <em>Application Issues</em>
2020 <li>Sequences are now validated against EMBL database</li>
2021 <li>Sequence fetcher fetches multiple records for all
2023 </ul> <em>InstallAnywhere Issues</em>
2025 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2026 issue with installAnywhere mechanism)</li>
2027 <li>Command line launching of JARs from InstallAnywhere
2028 version (java class versioning error fixed)</li>
2035 <div align="center">
2036 <strong>2.4</strong><br> 27/8/2008
2039 <td><em>User Interface</em>
2041 <li>Linked highlighting of codon and amino acid from
2042 translation and protein products</li>
2043 <li>Linked highlighting of structure associated with
2044 residue mapping to codon position</li>
2045 <li>Sequence Fetcher provides example accession numbers
2046 and 'clear' button</li>
2047 <li>MemoryMonitor added as an option under Desktop's
2049 <li>Extract score function to parse whitespace separated
2050 numeric data in description line</li>
2051 <li>Column labels in alignment annotation can be centred.</li>
2052 <li>Tooltip for sequence associated annotation give name
2054 </ul> <em>Web Services and URL fetching</em>
2056 <li>JPred3 web service</li>
2057 <li>Prototype sequence search client (no public services
2059 <li>Fetch either seed alignment or full alignment from
2061 <li>URL Links created for matching database cross
2062 references as well as sequence ID</li>
2063 <li>URL Links can be created using regular-expressions</li>
2064 </ul> <em>Sequence Database Connectivity</em>
2066 <li>Retrieval of cross-referenced sequences from other
2068 <li>Generalised database reference retrieval and
2069 validation to all fetchable databases</li>
2070 <li>Fetch sequences from DAS sources supporting the
2071 sequence command</li>
2072 </ul> <em>Import and Export</em>
2073 <li>export annotation rows as CSV for spreadsheet import</li>
2074 <li>Jalview projects record alignment dataset associations,
2075 EMBL products, and cDNA sequence mappings</li>
2076 <li>Sequence Group colour can be specified in Annotation
2078 <li>Ad-hoc colouring of group in Annotation File using RGB
2079 triplet as name of colourscheme</li>
2080 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2082 <li>treenode binding for VAMSAS tree exchange</li>
2083 <li>local editing and update of sequences in VAMSAS
2084 alignments (experimental)</li>
2085 <li>Create new or select existing session to join</li>
2086 <li>load and save of vamsas documents</li>
2087 </ul> <em>Application command line</em>
2089 <li>-tree parameter to open trees (introduced for passing
2091 <li>-fetchfrom command line argument to specify nicknames
2092 of DAS servers to query for alignment features</li>
2093 <li>-dasserver command line argument to add new servers
2094 that are also automatically queried for features</li>
2095 <li>-groovy command line argument executes a given groovy
2096 script after all input data has been loaded and parsed</li>
2097 </ul> <em>Applet-Application data exchange</em>
2099 <li>Trees passed as applet parameters can be passed to
2100 application (when using "View in full
2101 application")</li>
2102 </ul> <em>Applet Parameters</em>
2104 <li>feature group display control parameter</li>
2105 <li>debug parameter</li>
2106 <li>showbutton parameter</li>
2107 </ul> <em>Applet API methods</em>
2109 <li>newView public method</li>
2110 <li>Window (current view) specific get/set public methods</li>
2111 <li>Feature display control methods</li>
2112 <li>get list of currently selected sequences</li>
2113 </ul> <em>New Jalview distribution features</em>
2115 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2116 <li>RELEASE file gives build properties for the latest
2117 Jalview release.</li>
2118 <li>Java 1.1 Applet build made easier and donotobfuscate
2119 property controls execution of obfuscator</li>
2120 <li>Build target for generating source distribution</li>
2121 <li>Debug flag for javacc</li>
2122 <li>.jalview_properties file is documented (slightly) in
2123 jalview.bin.Cache</li>
2124 <li>Continuous Build Integration for stable and
2125 development version of Application, Applet and source
2130 <li>selected region output includes visible annotations
2131 (for certain formats)</li>
2132 <li>edit label/displaychar contains existing label/char
2134 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2135 <li>shorter peptide product names from EMBL records</li>
2136 <li>Newick string generator makes compact representations</li>
2137 <li>bootstrap values parsed correctly for tree files with
2139 <li>pathological filechooser bug avoided by not allowing
2140 filenames containing a ':'</li>
2141 <li>Fixed exception when parsing GFF files containing
2142 global sequence features</li>
2143 <li>Alignment datasets are finalized only when number of
2144 references from alignment sequences goes to zero</li>
2145 <li>Close of tree branch colour box without colour
2146 selection causes cascading exceptions</li>
2147 <li>occasional negative imgwidth exceptions</li>
2148 <li>better reporting of non-fatal warnings to user when
2149 file parsing fails.</li>
2150 <li>Save works when Jalview project is default format</li>
2151 <li>Save as dialog opened if current alignment format is
2152 not a valid output format</li>
2153 <li>UniProt canonical names introduced for both das and
2155 <li>Histidine should be midblue (not pink!) in Zappo</li>
2156 <li>error messages passed up and output when data read
2158 <li>edit undo recovers previous dataset sequence when
2159 sequence is edited</li>
2160 <li>allow PDB files without pdb ID HEADER lines (like
2161 those generated by MODELLER) to be read in properly</li>
2162 <li>allow reading of JPred concise files as a normal
2164 <li>Stockholm annotation parsing and alignment properties
2165 import fixed for PFAM records</li>
2166 <li>Structure view windows have correct name in Desktop
2168 <li>annotation consisting of sequence associated scores
2169 can be read and written correctly to annotation file</li>
2170 <li>Aligned cDNA translation to aligned peptide works
2172 <li>Fixed display of hidden sequence markers and
2173 non-italic font for representatives in Applet</li>
2174 <li>Applet Menus are always embedded in applet window on
2176 <li>Newly shown features appear at top of stack (in
2178 <li>Annotations added via parameter not drawn properly
2179 due to null pointer exceptions</li>
2180 <li>Secondary structure lines are drawn starting from
2181 first column of alignment</li>
2182 <li>UniProt XML import updated for new schema release in
2184 <li>Sequence feature to sequence ID match for Features
2185 file is case-insensitive</li>
2186 <li>Sequence features read from Features file appended to
2187 all sequences with matching IDs</li>
2188 <li>PDB structure coloured correctly for associated views
2189 containing a sub-sequence</li>
2190 <li>PDB files can be retrieved by applet from Jar files</li>
2191 <li>feature and annotation file applet parameters
2192 referring to different directories are retrieved correctly</li>
2193 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
2194 <li>Fixed application hang whilst waiting for
2195 splash-screen version check to complete</li>
2196 <li>Applet properly URLencodes input parameter values
2197 when passing them to the launchApp service</li>
2198 <li>display name and local features preserved in results
2199 retrieved from web service</li>
2200 <li>Visual delay indication for sequence retrieval and
2201 sequence fetcher initialisation</li>
2202 <li>updated Application to use DAS 1.53e version of
2203 dasobert DAS client</li>
2204 <li>Re-instated Full AMSA support and .amsa file
2206 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
2214 <div align="center">
2215 <strong>2.3</strong><br> 9/5/07
2220 <li>Jmol 11.0.2 integration</li>
2221 <li>PDB views stored in Jalview XML files</li>
2222 <li>Slide sequences</li>
2223 <li>Edit sequence in place</li>
2224 <li>EMBL CDS features</li>
2225 <li>DAS Feature mapping</li>
2226 <li>Feature ordering</li>
2227 <li>Alignment Properties</li>
2228 <li>Annotation Scores</li>
2229 <li>Sort by scores</li>
2230 <li>Feature/annotation editing in applet</li>
2235 <li>Headless state operation in 2.2.1</li>
2236 <li>Incorrect and unstable DNA pairwise alignment</li>
2237 <li>Cut and paste of sequences with annotation</li>
2238 <li>Feature group display state in XML</li>
2239 <li>Feature ordering in XML</li>
2240 <li>blc file iteration selection using filename # suffix</li>
2241 <li>Stockholm alignment properties</li>
2242 <li>Stockhom alignment secondary structure annotation</li>
2243 <li>2.2.1 applet had no feature transparency</li>
2244 <li>Number pad keys can be used in cursor mode</li>
2245 <li>Structure Viewer mirror image resolved</li>
2252 <div align="center">
2253 <strong>2.2.1</strong><br> 12/2/07
2258 <li>Non standard characters can be read and displayed
2259 <li>Annotations/Features can be imported/exported to the
2261 <li>Applet allows editing of sequence/annotation/group
2262 name & description
2263 <li>Preference setting to display sequence name in
2265 <li>Annotation file format extended to allow
2266 Sequence_groups to be defined
2267 <li>Default opening of alignment overview panel can be
2268 specified in preferences
2269 <li>PDB residue numbering annotation added to associated
2275 <li>Applet crash under certain Linux OS with Java 1.6
2277 <li>Annotation file export / import bugs fixed
2278 <li>PNG / EPS image output bugs fixed
2284 <div align="center">
2285 <strong>2.2</strong><br> 27/11/06
2290 <li>Multiple views on alignment
2291 <li>Sequence feature editing
2292 <li>"Reload" alignment
2293 <li>"Save" to current filename
2294 <li>Background dependent text colour
2295 <li>Right align sequence ids
2296 <li>User-defined lower case residue colours
2299 <li>Menu item accelerator keys
2300 <li>Control-V pastes to current alignment
2301 <li>Cancel button for DAS Feature Fetching
2302 <li>PCA and PDB Viewers zoom via mouse roller
2303 <li>User-defined sub-tree colours and sub-tree selection
2310 <li>'New Window' button on the 'Output to Text box'
2315 <li>New memory efficient Undo/Redo System
2316 <li>Optimised symbol lookups and conservation/consensus
2318 <li>Region Conservation/Consensus recalculated after
2320 <li>Fixed Remove Empty Columns Bug (empty columns at end
2322 <li>Slowed DAS Feature Fetching for increased robustness.
2329 <li>Made angle brackets in ASCII feature descriptions
2331 <li>Re-instated Zoom function for PCA
2332 <li>Sequence descriptions conserved in web service
2334 <li>UniProt ID discoverer uses any word separated by
2336 <li>WsDbFetch query/result association resolved
2337 <li>Tree leaf to sequence mapping improved
2338 <li>Smooth fonts switch moved to FontChooser dialog box.
2350 <div align="center">
2351 <strong>2.1.1</strong><br> 12/9/06
2356 <li>Copy consensus sequence to clipboard</li>
2361 <li>Image output - rightmost residues are rendered if
2362 sequence id panel has been resized</li>
2363 <li>Image output - all offscreen group boundaries are
2365 <li>Annotation files with sequence references - all
2366 elements in file are relative to sequence position</li>
2367 <li>Mac Applet users can use Alt key for group editing</li>
2373 <div align="center">
2374 <strong>2.1</strong><br> 22/8/06
2379 <li>MAFFT Multiple Alignment in default Web Service list</li>
2380 <li>DAS Feature fetching</li>
2381 <li>Hide sequences and columns</li>
2382 <li>Export Annotations and Features</li>
2383 <li>GFF file reading / writing</li>
2384 <li>Associate structures with sequences from local PDB
2386 <li>Add sequences to exisiting alignment</li>
2387 <li>Recently opened files / URL lists</li>
2388 <li>Applet can launch the full application</li>
2389 <li>Applet has transparency for features (Java 1.2
2391 <li>Applet has user defined colours parameter</li>
2392 <li>Applet can load sequences from parameter
2393 "sequence<em>x</em>"
2399 <li>Redundancy Panel reinstalled in the Applet</li>
2400 <li>Monospaced font - EPS / rescaling bug fixed</li>
2401 <li>Annotation files with sequence references bug fixed</li>
2407 <div align="center">
2408 <strong>2.08.1</strong><br> 2/5/06
2413 <li>Change case of selected region from Popup menu</li>
2414 <li>Choose to match case when searching</li>
2415 <li>Middle mouse button and mouse movement can compress /
2416 expand the visible width and height of the alignment</li>
2421 <li>Annotation Panel displays complete JNet results</li>
2427 <div align="center">
2428 <strong>2.08b</strong><br> 18/4/06
2434 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
2435 <li>Righthand label on wrapped alignments shows correct
2442 <div align="center">
2443 <strong>2.08</strong><br> 10/4/06
2448 <li>Editing can be locked to the selection area</li>
2449 <li>Keyboard editing</li>
2450 <li>Create sequence features from searches</li>
2451 <li>Precalculated annotations can be loaded onto
2453 <li>Features file allows grouping of features</li>
2454 <li>Annotation Colouring scheme added</li>
2455 <li>Smooth fonts off by default - Faster rendering</li>
2456 <li>Choose to toggle Autocalculate Consensus On/Off</li>
2461 <li>Drag & Drop fixed on Linux</li>
2462 <li>Jalview Archive file faster to load/save, sequence
2463 descriptions saved.</li>
2469 <div align="center">
2470 <strong>2.07</strong><br> 12/12/05
2475 <li>PDB Structure Viewer enhanced</li>
2476 <li>Sequence Feature retrieval and display enhanced</li>
2477 <li>Choose to output sequence start-end after sequence
2478 name for file output</li>
2479 <li>Sequence Fetcher WSDBFetch@EBI</li>
2480 <li>Applet can read feature files, PDB files and can be
2481 used for HTML form input</li>
2486 <li>HTML output writes groups and features</li>
2487 <li>Group editing is Control and mouse click</li>
2488 <li>File IO bugs</li>
2494 <div align="center">
2495 <strong>2.06</strong><br> 28/9/05
2500 <li>View annotations in wrapped mode</li>
2501 <li>More options for PCA viewer</li>
2506 <li>GUI bugs resolved</li>
2507 <li>Runs with -nodisplay from command line</li>
2513 <div align="center">
2514 <strong>2.05b</strong><br> 15/9/05
2519 <li>Choose EPS export as lineart or text</li>
2520 <li>Jar files are executable</li>
2521 <li>Can read in Uracil - maps to unknown residue</li>
2526 <li>Known OutOfMemory errors give warning message</li>
2527 <li>Overview window calculated more efficiently</li>
2528 <li>Several GUI bugs resolved</li>
2534 <div align="center">
2535 <strong>2.05</strong><br> 30/8/05
2540 <li>Edit and annotate in "Wrapped" view</li>
2545 <li>Several GUI bugs resolved</li>
2551 <div align="center">
2552 <strong>2.04</strong><br> 24/8/05
2557 <li>Hold down mouse wheel & scroll to change font
2563 <li>Improved JPred client reliability</li>
2564 <li>Improved loading of Jalview files</li>
2570 <div align="center">
2571 <strong>2.03</strong><br> 18/8/05
2576 <li>Set Proxy server name and port in preferences</li>
2577 <li>Multiple URL links from sequence ids</li>
2578 <li>User Defined Colours can have a scheme name and added
2580 <li>Choose to ignore gaps in consensus calculation</li>
2581 <li>Unix users can set default web browser</li>
2582 <li>Runs without GUI for batch processing</li>
2583 <li>Dynamically generated Web Service Menus</li>
2588 <li>InstallAnywhere download for Sparc Solaris</li>
2594 <div align="center">
2595 <strong>2.02</strong><br> 18/7/05
2601 <li>Copy & Paste order of sequences maintains
2602 alignment order.</li>
2608 <div align="center">
2609 <strong>2.01</strong><br> 12/7/05
2614 <li>Use delete key for deleting selection.</li>
2615 <li>Use Mouse wheel to scroll sequences.</li>
2616 <li>Help file updated to describe how to add alignment
2618 <li>Version and build date written to build properties
2620 <li>InstallAnywhere installation will check for updates
2621 at launch of Jalview.</li>
2626 <li>Delete gaps bug fixed.</li>
2627 <li>FileChooser sorts columns.</li>
2628 <li>Can remove groups one by one.</li>
2629 <li>Filechooser icons installed.</li>
2630 <li>Finder ignores return character when searching.
2631 Return key will initiate a search.<br>
2638 <div align="center">
2639 <strong>2.0</strong><br> 20/6/05
2644 <li>New codebase</li>