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.2.10.1">2.10.1</a><br />
51 <em>22/11/2016</em></strong>
54 <td><div align="left">
57 <li><!-- JAL-98 -->Improved memory usage: sparse arrays used for all consensus calculations</li>
58 <li><!-- JAL- --></li>
62 <li><!-- JAL-2282-->New replacement token for creating URLs <em>just</em> from database cross references. Users with custom links will receive a warning dialog asking them to update their preferences.</li>
63 <li><!-- JAL-2287-->Cancel button and escape listener on dialog warning user about disconnecting Jalview from a Chimera session</li>
64 <li><!-- JAL-2281-->Custom URL links for database cross-references are matched to database name regardless of case</li>
72 <em>Build and deployment</em>
82 <li><!-- JAL-2286 -->Columns with more than one modal residue are not coloured or thresholded according to percent identity (first observed in Jalview 2.8.2)</li>
83 <li><!-- JAL-2301 -->Threonine incorrectly reported as not hydrophobic</li>
84 <li><!-- JAL-2318 -->Updates to documentation pages (above PID threshold, amino acid properties)</li>
85 <li><!-- JAL-2292 -->Lower case residues in sequences are not reported as mapped to residues in a structure file in the View Mapping report</li>
89 <li><!-- JAL-2282-->Custom URL links for specific database names without regular expressions also offer invalid links from Sequence ID</li>
90 <li><!-- JAL-2315-->Removing a single configured link in the URL links pane in Connections preferences doesn't actually update Jalview configuration</li>
91 <li><!-- JAL-2272-->CTRL-Click on a selected region to open the alignment area popup menu doesn't work on El-Capitan</li>
92 <li><!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF files with similarly named sequences if dropped onto the alignment</li>
93 <li><!-- JAL-2312 -->Additional mappings are shown for PDB entries where more chains exist in the PDB accession than are reported in the SIFTS file</li>
101 <em>Build and deployment</em>
103 <li><!-- JAL-2308, -->Failing/passing unit tests</li>
105 <em>New Known Issues</em>
112 <td width="60" nowrap>
114 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
115 <em>25/10/2016</em></strong>
118 <td><em>Application</em>
120 <li>3D Structure chooser opens with 'Cached structures'
121 view if structures already loaded</li>
122 <li>Progress bar reports models as they are loaded to
129 <li>Colour by conservation always enabled and no tick
130 shown in menu when BLOSUM or PID shading applied</li>
131 <li>FER1_ARATH and FER2_ARATH labels were switched in
132 example sequences/projects/trees</li>
136 <li>Jalview projects with views of local PDB structure
137 files saved on Windows cannot be opened on OSX</li>
138 <li>Multiple structure views can be opened and
139 superposed without timeout for structures with multiple
140 models or multiple sequences in alignment</li>
141 <li>Cannot import or associated local PDB files without
142 a PDB ID HEADER line</li>
143 <li>RMSD is not output in Jmol console when
144 superposition is performed</li>
145 <li>Drag and drop of URL from Browser fails for Linux
146 and OSX versions earlier than El Capitan</li>
147 <li>ENA client ignores invalid content from ENA server</li>
148 <li>Exceptions are not raised in console when ENA
149 client attempts to fetch non-existent IDs via Fetch DB
151 <li>Exceptions are not raised in console when a new
152 view is created on the alignment</li>
153 <li>OSX right-click fixed for group selections:
154 CMD-click to insert/remove gaps in groups and CTRL-click
155 to open group pop-up menu</li>
157 <em>Build and deployment</em>
159 <li>URL link checker now copes with multi-line anchor
162 <em>New Known Issues</em>
164 <li>Drag and drop from URL links in browsers do not
171 <td width="60" nowrap>
173 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
179 <!-- JAL-2124 -->Updated Spanish translations.
182 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
183 for importing structure data to Jalview. Enables mmCIF and
187 <!-- JAL-192 --->Alignment ruler shows positions relative to
191 <!-- JAL-2202 -->Position/residue shown in status bar when
192 mousing over sequence associated annotation
195 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
199 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
200 '()', canonical '[]' and invalid '{}' base pair populations
204 <!-- JAL-2092 -->Feature settings popup menu options for
205 showing or hiding columns containing a feature
208 <!-- JAL-1557 -->Edit selected group by double clicking on
209 group and sequence associated annotation labels
212 <!-- JAL-2236 -->Sequence name added to annotation label in
213 select/hide columns by annotation and colour by annotation
217 </ul> <em>Application</em>
220 <!-- JAL-2050-->Automatically hide introns when opening a
224 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
228 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
229 structure mappings with the EMBL-EBI PDBe SIFTS database
232 <!-- JAL-2079 -->Updated download sites used for Rfam and
233 Pfam sources to xfam.org
236 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
239 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
240 over sequences in Jalview
243 <!-- JAL-2027-->Support for reverse-complement coding
244 regions in ENA and EMBL
247 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
248 for record retrieval via ENA rest API
251 <!-- JAL-2027 -->Support for ENA CDS records with reverse
255 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
256 groovy script execution
259 <!-- JAL-1812 -->New 'execute Groovy script' option in an
260 alignment window's Calculate menu
263 <!-- JAL-1812 -->Allow groovy scripts that call
264 Jalview.getAlignFrames() to run in headless mode
267 <!-- JAL-2068 -->Support for creating new alignment
268 calculation workers from groovy scripts
271 <!-- JAL-1369 --->Store/restore reference sequence in
275 <!-- JAL-1803 -->Chain codes for a sequence's PDB
276 associations are now saved/restored from project
279 <!-- JAL-1993 -->Database selection dialog always shown
280 before sequence fetcher is opened
283 <!-- JAL-2183 -->Double click on an entry in Jalview's
284 database chooser opens a sequence fetcher
287 <!-- JAL-1563 -->Free-text search client for UniProt using
291 <!-- JAL-2168 -->-nonews command line parameter to prevent
292 the news reader opening
295 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
296 querying stored in preferences
299 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
303 <!-- JAL-1977-->Tooltips shown on database chooser
306 <!-- JAL-391 -->Reverse complement function in calculate
307 menu for nucleotide sequences
310 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
311 and feature counts preserves alignment ordering (and
312 debugged for complex feature sets).
315 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
316 viewing structures with Jalview 2.10
319 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
320 genome, transcript CCDS and gene ids via the Ensembl and
321 Ensembl Genomes REST API
324 <!-- JAL-2049 -->Protein sequence variant annotation
325 computed for 'sequence_variant' annotation on CDS regions
329 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
333 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
334 Ref Fetcher fails to match, or otherwise updates sequence
335 data from external database records.
338 <!-- JAL-2154 -->Revised Jalview Project format for
339 efficient recovery of sequence coding and alignment
340 annotation relationships.
342 </ul> <!-- <em>Applet</em>
353 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
357 <!-- JAL-2018-->Export features in Jalview format (again)
358 includes graduated colourschemes
361 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
362 working with big alignments and lots of hidden columns
365 <!-- JAL-2053-->Hidden column markers not always rendered
366 at right of alignment window
369 <!-- JAL-2067 -->Tidied up links in help file table of
373 <!-- JAL-2072 -->Feature based tree calculation not shown
377 <!-- JAL-2075 -->Hidden columns ignored during feature
378 based tree calculation
381 <!-- JAL-2065 -->Alignment view stops updating when show
382 unconserved enabled for group on alignment
385 <!-- JAL-2086 -->Cannot insert gaps into sequence when
389 <!-- JAL-2146 -->Alignment column in status incorrectly
390 shown as "Sequence position" when mousing over
394 <!-- JAL-2099 -->Incorrect column numbers in ruler when
395 hidden columns present
398 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
399 user created annotation added to alignment
402 <!-- JAL-1841 -->RNA Structure consensus only computed for
403 '()' base pair annotation
406 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
407 in zero scores for all base pairs in RNA Structure
411 <!-- JAL-2174-->Extend selection with columns containing
415 <!-- JAL-2275 -->Pfam format writer puts extra space at
416 beginning of sequence
419 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
423 <!-- JAL-2238 -->Cannot create groups on an alignment from
424 from a tree when t-coffee scores are shown
427 <!-- JAL-1836,1967 -->Cannot import and view PDB
428 structures with chains containing negative resnums (4q4h)
431 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
435 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
436 to Clustal, PIR and PileUp output
439 <!-- JAL-2008 -->Reordering sequence features that are
440 not visible causes alignment window to repaint
443 <!-- JAL-2006 -->Threshold sliders don't work in
444 graduated colour and colour by annotation row for e-value
445 scores associated with features and annotation rows
448 <!-- JAL-1797 -->amino acid physicochemical conservation
449 calculation should be case independent
452 <!-- JAL-2173 -->Remove annotation also updates hidden
456 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
457 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
458 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
461 <!-- JAL-2065 -->Null pointer exceptions and redraw
462 problems when reference sequence defined and 'show
463 non-conserved' enabled
466 <!-- JAL-1306 -->Quality and Conservation are now shown on
467 load even when Consensus calculation is disabled
473 <!-- JAL-1552-->URLs and links can't be imported by
474 drag'n'drop on OSX when launched via webstart (note - not
475 yet fixed for El Capitan)
478 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
479 output when running on non-gb/us i18n platforms
482 <!-- JAL-1944 -->Error thrown when exporting a view with
483 hidden sequences as flat-file alignment
486 <!-- JAL-2030-->InstallAnywhere distribution fails when
490 <!-- JAL-2080-->Jalview very slow to launch via webstart
491 (also hotfix for 2.9.0b2)
494 <!-- JAL-2085 -->Cannot save project when view has a
495 reference sequence defined
498 <!-- JAL-1011 -->Columns are suddenly selected in other
499 alignments and views when revealing hidden columns
502 <!-- JAL-1989 -->Hide columns not mirrored in complement
503 view in a cDNA/Protein splitframe
506 <!-- JAL-1369 -->Cannot save/restore representative
507 sequence from project when only one sequence is
511 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
515 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
516 structure consensus didn't refresh annotation panel
519 <!-- JAL-1962 -->View mapping in structure view shows
520 mappings between sequence and all chains in a PDB file
523 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
524 dialogs format columns correctly, don't display array
525 data, sort columns according to type
528 <!-- JAL-1975 -->Export complete shown after destination
529 file chooser is cancelled during an image export
532 <!-- JAL-2025 -->Error when querying PDB Service with
533 sequence name containing special characters
536 <!-- JAL-2024 -->Manual PDB structure querying should be
540 <!-- JAL-2104 -->Large tooltips with broken HTML
541 formatting don't wrap
544 <!-- JAL-1128 -->Figures exported from wrapped view are
545 truncated so L looks like I in consensus annotation
548 <!-- JAL-2003 -->Export features should only export the
549 currently displayed features for the current selection or
553 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
554 after fetching cross-references, and restoring from project
557 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
558 followed in the structure viewer
561 <!-- JAL-2163 -->Titles for individual alignments in
562 splitframe not restored from project
565 <!-- JAL-2145 -->missing autocalculated annotation at
566 trailing end of protein alignment in transcript/product
567 splitview when pad-gaps not enabled by default
570 <!-- JAL-1797 -->amino acid physicochemical conservation
574 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
575 article has been read (reopened issue due to
576 internationalisation problems)
579 <!-- JAL-1960 -->Only offer PDB structures in structure
580 viewer based on sequence name, PDB and UniProt
585 <!-- JAL-1976 -->No progress bar shown during export of
589 <!-- JAL-2213 -->Structures not always superimposed after
590 multiple structures are shown for one or more sequences.
593 <!-- JAL-1370 -->Reference sequence characters should not
594 be replaced with '.' when 'Show unconserved' format option
598 <!-- JAL-1823 -->Cannot specify chain code when entering
599 specific PDB id for sequence
602 <!-- JAL-1944 -->File->Export->.. as doesn't work when
603 'Export hidden sequences' is enabled, but 'export hidden
604 columns' is disabled.
607 <!--JAL-2026-->Best Quality option in structure chooser
608 selects lowest rather than highest resolution structures
612 <!-- JAL-1887 -->Incorrect start and end reported for PDB
613 to sequence mapping in 'View Mappings' report
615 <!-- may exclude, this is an external service stability issue JAL-1941
616 -- > RNA 3D structure not added via DSSR service</li> -->
621 <!-- JAL-2151 -->Incorrect columns are selected when
622 hidden columns present before start of sequence
625 <!-- JAL-1986 -->Missing dependencies on applet pages
629 <!-- JAL-1947 -->Overview pixel size changes when
630 sequences are hidden in applet
633 <!-- JAL-1996 -->Updated instructions for applet
634 deployment on examples pages.
641 <td width="60" nowrap>
643 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
644 <em>16/10/2015</em></strong>
649 <li>Time stamps for signed Jalview application and applet
656 <li>Duplicate group consensus and conservation rows
657 shown when tree is partitioned</li>
658 <li>Erratic behaviour when tree partitions made with
659 multiple cDNA/Protein split views</li>
665 <td width="60" nowrap>
667 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
668 <em>8/10/2015</em></strong>
673 <li>Updated Spanish translations of localized text for
675 </ul> <em>Application</em>
677 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
678 <li>Signed OSX InstallAnywhere installer<br></li>
679 <li>Support for per-sequence based annotations in BioJSON</li>
680 </ul> <em>Applet</em>
682 <li>Split frame example added to applet examples page</li>
688 <li>Mapping of cDNA to protein in split frames
689 incorrect when sequence start > 1</li>
690 <li>Broken images in filter column by annotation dialog
692 <li>Feature colours not parsed from features file</li>
693 <li>Exceptions and incomplete link URLs recovered when
694 loading a features file containing HTML tags in feature
700 <li>Annotations corrupted after BioJS export and
702 <li>Incorrect sequence limits after Fetch DB References
703 with 'trim retrieved sequences'</li>
704 <li>Incorrect warning about deleting all data when
705 deleting selected columns</li>
706 <li>Patch to build system for shipping properly signed
707 JNLP templates for webstart launch</li>
708 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
709 unreleased structures for download or viewing</li>
710 <li>Tab/space/return keystroke operation of EMBL-PDBe
711 fetcher/viewer dialogs works correctly</li>
712 <li>Disabled 'minimise' button on Jalview windows
713 running on OSX to workaround redraw hang bug</li>
714 <li>Split cDNA/Protein view position and geometry not
715 recovered from jalview project</li>
716 <li>Initial enabled/disabled state of annotation menu
717 sorter 'show autocalculated first/last' corresponds to
719 <li>Restoring of Clustal, RNA Helices and T-Coffee
720 color schemes from BioJSON</li>
724 <li>Reorder sequences mirrored in cDNA/Protein split
726 <li>Applet with Jmol examples not loading correctly</li>
732 <td><div align="center">
733 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
737 <li>Linked visualisation and analysis of DNA and Protein
740 <li>Translated cDNA alignments shown as split protein
741 and DNA alignment views</li>
742 <li>Codon consensus annotation for linked protein and
743 cDNA alignment views</li>
744 <li>Link cDNA or Protein product sequences by loading
745 them onto Protein or cDNA alignments</li>
746 <li>Reconstruct linked cDNA alignment from aligned
747 protein sequences</li>
750 <li>Jmol integration updated to Jmol v14.2.14</li>
751 <li>Import and export of Jalview alignment views as <a
752 href="features/bioJsonFormat.html">BioJSON</a></li>
753 <li>New alignment annotation file statements for
754 reference sequences and marking hidden columns</li>
755 <li>Reference sequence based alignment shading to
756 highlight variation</li>
757 <li>Select or hide columns according to alignment
759 <li>Find option for locating sequences by description</li>
760 <li>Conserved physicochemical properties shown in amino
761 acid conservation row</li>
762 <li>Alignments can be sorted by number of RNA helices</li>
763 </ul> <em>Application</em>
765 <li>New cDNA/Protein analysis capabilities
767 <li>Get Cross-References should open a Split Frame
768 view with cDNA/Protein</li>
769 <li>Detect when nucleotide sequences and protein
770 sequences are placed in the same alignment</li>
771 <li>Split cDNA/Protein views are saved in Jalview
776 <li>Use REST API to talk to Chimera</li>
777 <li>Selected regions in Chimera are highlighted in linked
780 <li>VARNA RNA viewer updated to v3.93</li>
781 <li>VARNA views are saved in Jalview Projects</li>
782 <li>Pseudoknots displayed as Jalview RNA annotation can
783 be shown in VARNA</li>
785 <li>Make groups for selection uses marked columns as well
786 as the active selected region</li>
788 <li>Calculate UPGMA and NJ trees using sequence feature
790 <li>New Export options
792 <li>New Export Settings dialog to control hidden
793 region export in flat file generation</li>
795 <li>Export alignment views for display with the <a
796 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
798 <li>Export scrollable SVG in HTML page</li>
799 <li>Optional embedding of BioJSON data when exporting
800 alignment figures to HTML</li>
802 <li>3D structure retrieval and display
804 <li>Free text and structured queries with the PDBe
806 <li>PDBe Search API based discovery and selection of
807 PDB structures for a sequence set</li>
811 <li>JPred4 employed for protein secondary structure
813 <li>Hide Insertions menu option to hide unaligned columns
814 for one or a group of sequences</li>
815 <li>Automatically hide insertions in alignments imported
816 from the JPred4 web server</li>
817 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
818 system on OSX<br />LGPL libraries courtesy of <a
819 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
821 <li>changed 'View nucleotide structure' submenu to 'View
822 VARNA 2D Structure'</li>
823 <li>change "View protein structure" menu option to "3D
826 </ul> <em>Applet</em>
828 <li>New layout for applet example pages</li>
829 <li>New parameters to enable SplitFrame view
830 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
831 <li>New example demonstrating linked viewing of cDNA and
832 Protein alignments</li>
833 </ul> <em>Development and deployment</em>
835 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
836 <li>Include installation type and git revision in build
837 properties and console log output</li>
838 <li>Jalview Github organisation, and new github site for
839 storing BioJsMSA Templates</li>
840 <li>Jalview's unit tests now managed with TestNG</li>
843 <!-- <em>General</em>
845 </ul> --> <!-- issues resolved --> <em>Application</em>
847 <li>Escape should close any open find dialogs</li>
848 <li>Typo in select-by-features status report</li>
849 <li>Consensus RNA secondary secondary structure
850 predictions are not highlighted in amber</li>
851 <li>Missing gap character in v2.7 example file means
852 alignment appears unaligned when pad-gaps is not enabled</li>
853 <li>First switch to RNA Helices colouring doesn't colour
854 associated structure views</li>
855 <li>ID width preference option is greyed out when auto
856 width checkbox not enabled</li>
857 <li>Stopped a warning dialog from being shown when
858 creating user defined colours</li>
859 <li>'View Mapping' in structure viewer shows sequence
860 mappings for just that viewer's sequences</li>
861 <li>Workaround for superposing PDB files containing
862 multiple models in Chimera</li>
863 <li>Report sequence position in status bar when hovering
864 over Jmol structure</li>
865 <li>Cannot output gaps as '.' symbols with Selection ->
866 output to text box</li>
867 <li>Flat file exports of alignments with hidden columns
868 have incorrect sequence start/end</li>
869 <li>'Aligning' a second chain to a Chimera structure from
871 <li>Colour schemes applied to structure viewers don't
872 work for nucleotide</li>
873 <li>Loading/cut'n'pasting an empty or invalid file leads
874 to a grey/invisible alignment window</li>
875 <li>Exported Jpred annotation from a sequence region
876 imports to different position</li>
877 <li>Space at beginning of sequence feature tooltips shown
878 on some platforms</li>
879 <li>Chimera viewer 'View | Show Chain' menu is not
881 <li>'New View' fails with a Null Pointer Exception in
882 console if Chimera has been opened</li>
883 <li>Mouseover to Chimera not working</li>
884 <li>Miscellaneous ENA XML feature qualifiers not
886 <li>NPE in annotation renderer after 'Extract Scores'</li>
887 <li>If two structures in one Chimera window, mouseover of
888 either sequence shows on first structure</li>
889 <li>'Show annotations' options should not make
890 non-positional annotations visible</li>
891 <li>Subsequence secondary structure annotation not shown
892 in right place after 'view flanking regions'</li>
893 <li>File Save As type unset when current file format is
895 <li>Save as '.jar' option removed for saving Jalview
897 <li>Colour by Sequence colouring in Chimera more
899 <li>Cannot 'add reference annotation' for a sequence in
900 several views on same alignment</li>
901 <li>Cannot show linked products for EMBL / ENA records</li>
902 <li>Jalview's tooltip wraps long texts containing no
904 </ul> <em>Applet</em>
906 <li>Jmol to JalviewLite mouseover/link not working</li>
907 <li>JalviewLite can't import sequences with ID
908 descriptions containing angle brackets</li>
909 </ul> <em>General</em>
911 <li>Cannot export and reimport RNA secondary structure
912 via jalview annotation file</li>
913 <li>Random helix colour palette for colour by annotation
914 with RNA secondary structure</li>
915 <li>Mouseover to cDNA from STOP residue in protein
916 translation doesn't work.</li>
917 <li>hints when using the select by annotation dialog box</li>
918 <li>Jmol alignment incorrect if PDB file has alternate CA
920 <li>FontChooser message dialog appears to hang after
921 choosing 1pt font</li>
922 <li>Peptide secondary structure incorrectly imported from
923 annotation file when annotation display text includes 'e' or
925 <li>Cannot set colour of new feature type whilst creating
927 <li>cDNA translation alignment should not be sequence
929 <li>'Show unconserved' doesn't work for lower case
931 <li>Nucleotide ambiguity codes involving R not recognised</li>
932 </ul> <em>Deployment and Documentation</em>
934 <li>Applet example pages appear different to the rest of
936 </ul> <em>Application Known issues</em>
938 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
939 <li>Misleading message appears after trying to delete
941 <li>Jalview icon not shown in dock after InstallAnywhere
942 version launches</li>
943 <li>Fetching EMBL reference for an RNA sequence results
944 fails with a sequence mismatch</li>
945 <li>Corrupted or unreadable alignment display when
946 scrolling alignment to right</li>
947 <li>ArrayIndexOutOfBoundsException thrown when remove
948 empty columns called on alignment with ragged gapped ends</li>
949 <li>auto calculated alignment annotation rows do not get
950 placed above or below non-autocalculated rows</li>
951 <li>Jalview dekstop becomes sluggish at full screen in
952 ultra-high resolution</li>
953 <li>Cannot disable consensus calculation independently of
954 quality and conservation</li>
955 <li>Mouseover highlighting between cDNA and protein can
956 become sluggish with more than one splitframe shown</li>
957 </ul> <em>Applet Known Issues</em>
959 <li>Core PDB parsing code requires Jmol</li>
960 <li>Sequence canvas panel goes white when alignment
961 window is being resized</li>
967 <td><div align="center">
968 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
972 <li>Updated Java code signing certificate donated by
974 <li>Features and annotation preserved when performing
975 pairwise alignment</li>
976 <li>RNA pseudoknot annotation can be
977 imported/exported/displayed</li>
978 <li>'colour by annotation' can colour by RNA and
979 protein secondary structure</li>
980 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
981 post-hoc with 2.9 release</em>)
984 </ul> <em>Application</em>
986 <li>Extract and display secondary structure for sequences
987 with 3D structures</li>
988 <li>Support for parsing RNAML</li>
989 <li>Annotations menu for layout
991 <li>sort sequence annotation rows by alignment</li>
992 <li>place sequence annotation above/below alignment
995 <li>Output in Stockholm format</li>
996 <li>Internationalisation: improved Spanish (es)
998 <li>Structure viewer preferences tab</li>
999 <li>Disorder and Secondary Structure annotation tracks
1000 shared between alignments</li>
1001 <li>UCSF Chimera launch and linked highlighting from
1003 <li>Show/hide all sequence associated annotation rows for
1004 all or current selection</li>
1005 <li>disorder and secondary structure predictions
1006 available as dataset annotation</li>
1007 <li>Per-sequence rna helices colouring</li>
1010 <li>Sequence database accessions imported when fetching
1011 alignments from Rfam</li>
1012 <li>update VARNA version to 3.91</li>
1014 <li>New groovy scripts for exporting aligned positions,
1015 conservation values, and calculating sum of pairs scores.</li>
1016 <li>Command line argument to set default JABAWS server</li>
1017 <li>include installation type in build properties and
1018 console log output</li>
1019 <li>Updated Jalview project format to preserve dataset
1023 <!-- issues resolved --> <em>Application</em>
1025 <li>Distinguish alignment and sequence associated RNA
1026 structure in structure->view->VARNA</li>
1027 <li>Raise dialog box if user deletes all sequences in an
1029 <li>Pressing F1 results in documentation opening twice</li>
1030 <li>Sequence feature tooltip is wrapped</li>
1031 <li>Double click on sequence associated annotation
1032 selects only first column</li>
1033 <li>Redundancy removal doesn't result in unlinked
1034 leaves shown in tree</li>
1035 <li>Undos after several redundancy removals don't undo
1037 <li>Hide sequence doesn't hide associated annotation</li>
1038 <li>User defined colours dialog box too big to fit on
1039 screen and buttons not visible</li>
1040 <li>author list isn't updated if already written to
1041 Jalview properties</li>
1042 <li>Popup menu won't open after retrieving sequence
1044 <li>File open window for associate PDB doesn't open</li>
1045 <li>Left-then-right click on a sequence id opens a
1046 browser search window</li>
1047 <li>Cannot open sequence feature shading/sort popup menu
1048 in feature settings dialog</li>
1049 <li>better tooltip placement for some areas of Jalview
1051 <li>Allow addition of JABAWS Server which doesn't
1052 pass validation</li>
1053 <li>Web services parameters dialog box is too large to
1055 <li>Muscle nucleotide alignment preset obscured by
1057 <li>JABAWS preset submenus don't contain newly
1058 defined user preset</li>
1059 <li>MSA web services warns user if they were launched
1060 with invalid input</li>
1061 <li>Jalview cannot contact DAS Registy when running on
1064 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1065 'Superpose with' submenu not shown when new view
1069 </ul> <!-- <em>Applet</em>
1071 </ul> <em>General</em>
1073 </ul>--> <em>Deployment and Documentation</em>
1075 <li>2G and 1G options in launchApp have no effect on
1076 memory allocation</li>
1077 <li>launchApp service doesn't automatically open
1078 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1080 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1081 InstallAnywhere reports cannot find valid JVM when Java
1082 1.7_055 is available
1084 </ul> <em>Application Known issues</em>
1087 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1088 corrupted or unreadable alignment display when scrolling
1092 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1093 retrieval fails but progress bar continues for DAS retrieval
1094 with large number of ID
1097 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1098 flatfile output of visible region has incorrect sequence
1102 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1103 rna structure consensus doesn't update when secondary
1104 structure tracks are rearranged
1107 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1108 invalid rna structure positional highlighting does not
1109 highlight position of invalid base pairs
1112 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1113 out of memory errors are not raised when saving Jalview
1114 project from alignment window file menu
1117 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1118 Switching to RNA Helices colouring doesn't propagate to
1122 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1123 colour by RNA Helices not enabled when user created
1124 annotation added to alignment
1127 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1128 Jalview icon not shown on dock in Mountain Lion/Webstart
1130 </ul> <em>Applet Known Issues</em>
1133 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1134 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1137 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1138 Jalview and Jmol example not compatible with IE9
1141 <li>Sort by annotation score doesn't reverse order
1147 <td><div align="center">
1148 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1151 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1154 <li>Internationalisation of user interface (usually
1155 called i18n support) and translation for Spanish locale</li>
1156 <li>Define/Undefine group on current selection with
1157 Ctrl-G/Shift Ctrl-G</li>
1158 <li>Improved group creation/removal options in
1159 alignment/sequence Popup menu</li>
1160 <li>Sensible precision for symbol distribution
1161 percentages shown in logo tooltip.</li>
1162 <li>Annotation panel height set according to amount of
1163 annotation when alignment first opened</li>
1164 </ul> <em>Application</em>
1166 <li>Interactive consensus RNA secondary structure
1167 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1168 <li>Select columns containing particular features from
1169 Feature Settings dialog</li>
1170 <li>View all 'representative' PDB structures for selected
1172 <li>Update Jalview project format:
1174 <li>New file extension for Jalview projects '.jvp'</li>
1175 <li>Preserve sequence and annotation dataset (to
1176 store secondary structure annotation,etc)</li>
1177 <li>Per group and alignment annotation and RNA helix
1181 <li>New similarity measures for PCA and Tree calculation
1183 <li>Experimental support for retrieval and viewing of
1184 flanking regions for an alignment</li>
1188 <!-- issues resolved --> <em>Application</em>
1190 <li>logo keeps spinning and status remains at queued or
1191 running after job is cancelled</li>
1192 <li>cannot export features from alignments imported from
1193 Jalview/VAMSAS projects</li>
1194 <li>Buggy slider for web service parameters that take
1196 <li>Newly created RNA secondary structure line doesn't
1197 have 'display all symbols' flag set</li>
1198 <li>T-COFFEE alignment score shading scheme and other
1199 annotation shading not saved in Jalview project</li>
1200 <li>Local file cannot be loaded in freshly downloaded
1202 <li>Jalview icon not shown on dock in Mountain
1204 <li>Load file from desktop file browser fails</li>
1205 <li>Occasional NPE thrown when calculating large trees</li>
1206 <li>Cannot reorder or slide sequences after dragging an
1207 alignment onto desktop</li>
1208 <li>Colour by annotation dialog throws NPE after using
1209 'extract scores' function</li>
1210 <li>Loading/cut'n'pasting an empty file leads to a grey
1211 alignment window</li>
1212 <li>Disorder thresholds rendered incorrectly after
1213 performing IUPred disorder prediction</li>
1214 <li>Multiple group annotated consensus rows shown when
1215 changing 'normalise logo' display setting</li>
1216 <li>Find shows blank dialog after 'finished searching' if
1217 nothing matches query</li>
1218 <li>Null Pointer Exceptions raised when sorting by
1219 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1221 <li>Errors in Jmol console when structures in alignment
1222 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1224 <li>Not all working JABAWS services are shown in
1226 <li>JAVAWS version of Jalview fails to launch with
1227 'invalid literal/length code'</li>
1228 <li>Annotation/RNA Helix colourschemes cannot be applied
1229 to alignment with groups (actually fixed in 2.8.0b1)</li>
1230 <li>RNA Helices and T-Coffee Scores available as default
1233 </ul> <em>Applet</em>
1235 <li>Remove group option is shown even when selection is
1237 <li>Apply to all groups ticked but colourscheme changes
1238 don't affect groups</li>
1239 <li>Documented RNA Helices and T-Coffee Scores as valid
1240 colourscheme name</li>
1241 <li>Annotation labels drawn on sequence IDs when
1242 Annotation panel is not displayed</li>
1243 <li>Increased font size for dropdown menus on OSX and
1244 embedded windows</li>
1245 </ul> <em>Other</em>
1247 <li>Consensus sequence for alignments/groups with a
1248 single sequence were not calculated</li>
1249 <li>annotation files that contain only groups imported as
1250 annotation and junk sequences</li>
1251 <li>Fasta files with sequences containing '*' incorrectly
1252 recognised as PFAM or BLC</li>
1253 <li>conservation/PID slider apply all groups option
1254 doesn't affect background (2.8.0b1)
1256 <li>redundancy highlighting is erratic at 0% and 100%</li>
1257 <li>Remove gapped columns fails for sequences with ragged
1259 <li>AMSA annotation row with leading spaces is not
1260 registered correctly on import</li>
1261 <li>Jalview crashes when selecting PCA analysis for
1262 certain alignments</li>
1263 <li>Opening the colour by annotation dialog for an
1264 existing annotation based 'use original colours'
1265 colourscheme loses original colours setting</li>
1270 <td><div align="center">
1271 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
1272 <em>30/1/2014</em></strong>
1276 <li>Trusted certificates for JalviewLite applet and
1277 Jalview Desktop application<br />Certificate was donated by
1278 <a href="https://www.certum.eu">Certum</a> to the Jalview
1279 open source project).
1281 <li>Jalview SRS links replaced by UniProt and EBI-search
1283 <li>Output in Stockholm format</li>
1284 <li>Allow import of data from gzipped files</li>
1285 <li>Export/import group and sequence associated line
1286 graph thresholds</li>
1287 <li>Nucleotide substitution matrix that supports RNA and
1288 ambiguity codes</li>
1289 <li>Allow disorder predictions to be made on the current
1290 selection (or visible selection) in the same way that JPred
1292 <li>Groovy scripting for headless Jalview operation</li>
1293 </ul> <em>Other improvements</em>
1295 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
1296 <li>COMBINE statement uses current SEQUENCE_REF and
1297 GROUP_REF scope to group annotation rows</li>
1298 <li>Support '' style escaping of quotes in Newick
1300 <li>Group options for JABAWS service by command line name</li>
1301 <li>Empty tooltip shown for JABA service options with a
1302 link but no description</li>
1303 <li>Select primary source when selecting authority in
1304 database fetcher GUI</li>
1305 <li>Add .mfa to FASTA file extensions recognised by
1307 <li>Annotation label tooltip text wrap</li>
1312 <li>Slow scrolling when lots of annotation rows are
1314 <li>Lots of NPE (and slowness) after creating RNA
1315 secondary structure annotation line</li>
1316 <li>Sequence database accessions not imported when
1317 fetching alignments from Rfam</li>
1318 <li>Incorrect SHMR submission for sequences with
1320 <li>View all structures does not always superpose
1322 <li>Option widgets in service parameters not updated to
1323 reflect user or preset settings</li>
1324 <li>Null pointer exceptions for some services without
1325 presets or adjustable parameters</li>
1326 <li>Discover PDB IDs entry in structure menu doesn't
1327 discover PDB xRefs</li>
1328 <li>Exception encountered while trying to retrieve
1329 features with DAS</li>
1330 <li>Lowest value in annotation row isn't coloured
1331 when colour by annotation (per sequence) is coloured</li>
1332 <li>Keyboard mode P jumps to start of gapped region when
1333 residue follows a gap</li>
1334 <li>Jalview appears to hang importing an alignment with
1335 Wrap as default or after enabling Wrap</li>
1336 <li>'Right click to add annotations' message
1337 shown in wrap mode when no annotations present</li>
1338 <li>Disorder predictions fail with NPE if no automatic
1339 annotation already exists on alignment</li>
1340 <li>oninit javascript function should be called after
1341 initialisation completes</li>
1342 <li>Remove redundancy after disorder prediction corrupts
1343 alignment window display</li>
1344 <li>Example annotation file in documentation is invalid</li>
1345 <li>Grouped line graph annotation rows are not exported
1346 to annotation file</li>
1347 <li>Multi-harmony analysis cannot be run when only two
1349 <li>Cannot create multiple groups of line graphs with
1350 several 'combine' statements in annotation file</li>
1351 <li>Pressing return several times causes Number Format
1352 exceptions in keyboard mode</li>
1353 <li>Multi-harmony (SHMMR) method doesn't submit
1354 correct partitions for input data</li>
1355 <li>Translation from DNA to Amino Acids fails</li>
1356 <li>Jalview fail to load newick tree with quoted label</li>
1357 <li>--headless flag isn't understood</li>
1358 <li>ClassCastException when generating EPS in headless
1360 <li>Adjusting sequence-associated shading threshold only
1361 changes one row's threshold</li>
1362 <li>Preferences and Feature settings panel panel
1363 doesn't open</li>
1364 <li>hide consensus histogram also hides conservation and
1365 quality histograms</li>
1370 <td><div align="center">
1371 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
1373 <td><em>Application</em>
1375 <li>Support for JABAWS 2.0 Services (AACon alignment
1376 conservation, protein disorder and Clustal Omega)</li>
1377 <li>JABAWS server status indicator in Web Services
1379 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
1380 in Jalview alignment window</li>
1381 <li>Updated Jalview build and deploy framework for OSX
1382 mountain lion, windows 7, and 8</li>
1383 <li>Nucleotide substitution matrix for PCA that supports
1384 RNA and ambiguity codes</li>
1386 <li>Improved sequence database retrieval GUI</li>
1387 <li>Support fetching and database reference look up
1388 against multiple DAS sources (Fetch all from in 'fetch db
1390 <li>Jalview project improvements
1392 <li>Store and retrieve the 'belowAlignment'
1393 flag for annotation</li>
1394 <li>calcId attribute to group annotation rows on the
1396 <li>Store AACon calculation settings for a view in
1397 Jalview project</li>
1401 <li>horizontal scrolling gesture support</li>
1402 <li>Visual progress indicator when PCA calculation is
1404 <li>Simpler JABA web services menus</li>
1405 <li>visual indication that web service results are still
1406 being retrieved from server</li>
1407 <li>Serialise the dialogs that are shown when Jalview
1408 starts up for first time</li>
1409 <li>Jalview user agent string for interacting with HTTP
1411 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
1413 <li>Examples directory and Groovy library included in
1414 InstallAnywhere distribution</li>
1415 </ul> <em>Applet</em>
1417 <li>RNA alignment and secondary structure annotation
1418 visualization applet example</li>
1419 </ul> <em>General</em>
1421 <li>Normalise option for consensus sequence logo</li>
1422 <li>Reset button in PCA window to return dimensions to
1424 <li>Allow seqspace or Jalview variant of alignment PCA
1426 <li>PCA with either nucleic acid and protein substitution
1428 <li>Allow windows containing HTML reports to be exported
1430 <li>Interactive display and editing of RNA secondary
1431 structure contacts</li>
1432 <li>RNA Helix Alignment Colouring</li>
1433 <li>RNA base pair logo consensus</li>
1434 <li>Parse sequence associated secondary structure
1435 information in Stockholm files</li>
1436 <li>HTML Export database accessions and annotation
1437 information presented in tooltip for sequences</li>
1438 <li>Import secondary structure from LOCARNA clustalw
1439 style RNA alignment files</li>
1440 <li>import and visualise T-COFFEE quality scores for an
1442 <li>'colour by annotation' per sequence option to
1443 shade each sequence according to its associated alignment
1445 <li>New Jalview Logo</li>
1446 </ul> <em>Documentation and Development</em>
1448 <li>documentation for score matrices used in Jalview</li>
1449 <li>New Website!</li>
1451 <td><em>Application</em>
1453 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
1454 wsdbfetch REST service</li>
1455 <li>Stop windows being moved outside desktop on OSX</li>
1456 <li>Filetype associations not installed for webstart
1458 <li>Jalview does not always retrieve progress of a JABAWS
1459 job execution in full once it is complete</li>
1460 <li>revise SHMR RSBS definition to ensure alignment is
1461 uploaded via ali_file parameter</li>
1462 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
1463 <li>View all structures superposed fails with exception</li>
1464 <li>Jnet job queues forever if a very short sequence is
1465 submitted for prediction</li>
1466 <li>Cut and paste menu not opened when mouse clicked on
1468 <li>Putting fractional value into integer text box in
1469 alignment parameter dialog causes Jalview to hang</li>
1470 <li>Structure view highlighting doesn't work on
1472 <li>View all structures fails with exception shown in
1474 <li>Characters in filename associated with PDBEntry not
1475 escaped in a platform independent way</li>
1476 <li>Jalview desktop fails to launch with exception when
1478 <li>Tree calculation reports 'you must have 2 or more
1479 sequences selected' when selection is empty</li>
1480 <li>Jalview desktop fails to launch with jar signature
1481 failure when java web start temporary file caching is
1483 <li>DAS Sequence retrieval with range qualification
1484 results in sequence xref which includes range qualification</li>
1485 <li>Errors during processing of command line arguments
1486 cause progress bar (JAL-898) to be removed</li>
1487 <li>Replace comma for semi-colon option not disabled for
1488 DAS sources in sequence fetcher</li>
1489 <li>Cannot close news reader when JABAWS server warning
1490 dialog is shown</li>
1491 <li>Option widgets not updated to reflect user settings</li>
1492 <li>Edited sequence not submitted to web service</li>
1493 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
1494 <li>InstallAnywhere installer doesn't unpack and run
1495 on OSX Mountain Lion</li>
1496 <li>Annotation panel not given a scroll bar when
1497 sequences with alignment annotation are pasted into the
1499 <li>Sequence associated annotation rows not associated
1500 when loaded from Jalview project</li>
1501 <li>Browser launch fails with NPE on java 1.7</li>
1502 <li>JABAWS alignment marked as finished when job was
1503 cancelled or job failed due to invalid input</li>
1504 <li>NPE with v2.7 example when clicking on Tree
1505 associated with all views</li>
1506 <li>Exceptions when copy/paste sequences with grouped
1507 annotation rows to new window</li>
1508 </ul> <em>Applet</em>
1510 <li>Sequence features are momentarily displayed before
1511 they are hidden using hidefeaturegroups applet parameter</li>
1512 <li>loading features via javascript API automatically
1513 enables feature display</li>
1514 <li>scrollToColumnIn javascript API method doesn't
1516 </ul> <em>General</em>
1518 <li>Redundancy removal fails for rna alignment</li>
1519 <li>PCA calculation fails when sequence has been selected
1520 and then deselected</li>
1521 <li>PCA window shows grey box when first opened on OSX</li>
1522 <li>Letters coloured pink in sequence logo when alignment
1523 coloured with clustalx</li>
1524 <li>Choosing fonts without letter symbols defined causes
1525 exceptions and redraw errors</li>
1526 <li>Initial PCA plot view is not same as manually
1527 reconfigured view</li>
1528 <li>Grouped annotation graph label has incorrect line
1530 <li>Grouped annotation graph label display is corrupted
1531 for lots of labels</li>
1536 <div align="center">
1537 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
1540 <td><em>Application</em>
1542 <li>Jalview Desktop News Reader</li>
1543 <li>Tweaked default layout of web services menu</li>
1544 <li>View/alignment association menu to enable user to
1545 easily specify which alignment a multi-structure view takes
1546 its colours/correspondences from</li>
1547 <li>Allow properties file location to be specified as URL</li>
1548 <li>Extend Jalview project to preserve associations
1549 between many alignment views and a single Jmol display</li>
1550 <li>Store annotation row height in Jalview project file</li>
1551 <li>Annotation row column label formatting attributes
1552 stored in project file</li>
1553 <li>Annotation row order for auto-calculated annotation
1554 rows preserved in Jalview project file</li>
1555 <li>Visual progress indication when Jalview state is
1556 saved using Desktop window menu</li>
1557 <li>Visual indication that command line arguments are
1558 still being processed</li>
1559 <li>Groovy script execution from URL</li>
1560 <li>Colour by annotation default min and max colours in
1562 <li>Automatically associate PDB files dragged onto an
1563 alignment with sequences that have high similarity and
1565 <li>Update JGoogleAnalytics to latest release (0.3)</li>
1566 <li>'view structures' option to open many
1567 structures in same window</li>
1568 <li>Sort associated views menu option for tree panel</li>
1569 <li>Group all JABA and non-JABA services for a particular
1570 analysis function in its own submenu</li>
1571 </ul> <em>Applet</em>
1573 <li>Userdefined and autogenerated annotation rows for
1575 <li>Adjustment of alignment annotation pane height</li>
1576 <li>Annotation scrollbar for annotation panel</li>
1577 <li>Drag to reorder annotation rows in annotation panel</li>
1578 <li>'automaticScrolling' parameter</li>
1579 <li>Allow sequences with partial ID string matches to be
1580 annotated from GFF/Jalview features files</li>
1581 <li>Sequence logo annotation row in applet</li>
1582 <li>Absolute paths relative to host server in applet
1583 parameters are treated as such</li>
1584 <li>New in the JalviewLite javascript API:
1586 <li>JalviewLite.js javascript library</li>
1587 <li>Javascript callbacks for
1589 <li>Applet initialisation</li>
1590 <li>Sequence/alignment mouse-overs and selections</li>
1593 <li>scrollTo row and column alignment scrolling
1595 <li>Select sequence/alignment regions from javascript</li>
1596 <li>javascript structure viewer harness to pass
1597 messages between Jmol and Jalview when running as
1598 distinct applets</li>
1599 <li>sortBy method</li>
1600 <li>Set of applet and application examples shipped
1601 with documentation</li>
1602 <li>New example to demonstrate JalviewLite and Jmol
1603 javascript message exchange</li>
1605 </ul> <em>General</em>
1607 <li>Enable Jmol displays to be associated with multiple
1608 multiple alignments</li>
1609 <li>Option to automatically sort alignment with new tree</li>
1610 <li>User configurable link to enable redirects to a
1611 www.Jalview.org mirror</li>
1612 <li>Jmol colours option for Jmol displays</li>
1613 <li>Configurable newline string when writing alignment
1614 and other flat files</li>
1615 <li>Allow alignment annotation description lines to
1616 contain html tags</li>
1617 </ul> <em>Documentation and Development</em>
1619 <li>Add groovy test harness for bulk load testing to
1621 <li>Groovy script to load and align a set of sequences
1622 using a web service before displaying the result in the
1623 Jalview desktop</li>
1624 <li>Restructured javascript and applet api documentation</li>
1625 <li>Ant target to publish example html files with applet
1627 <li>Netbeans project for building Jalview from source</li>
1628 <li>ant task to create online javadoc for Jalview source</li>
1630 <td><em>Application</em>
1632 <li>User defined colourscheme throws exception when
1633 current built in colourscheme is saved as new scheme</li>
1634 <li>AlignFrame->Save in application pops up save
1635 dialog for valid filename/format</li>
1636 <li>Cannot view associated structure for UniProt sequence</li>
1637 <li>PDB file association breaks for UniProt sequence
1639 <li>Associate PDB from file dialog does not tell you
1640 which sequence is to be associated with the file</li>
1641 <li>Find All raises null pointer exception when query
1642 only matches sequence IDs</li>
1643 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
1644 <li>Jalview project with Jmol views created with Jalview
1645 2.4 cannot be loaded</li>
1646 <li>Filetype associations not installed for webstart
1648 <li>Two or more chains in a single PDB file associated
1649 with sequences in different alignments do not get coloured
1650 by their associated sequence</li>
1651 <li>Visibility status of autocalculated annotation row
1652 not preserved when project is loaded</li>
1653 <li>Annotation row height and visibility attributes not
1654 stored in Jalview project</li>
1655 <li>Tree bootstraps are not preserved when saved as a
1656 Jalview project</li>
1657 <li>Envision2 workflow tooltips are corrupted</li>
1658 <li>Enabling show group conservation also enables colour
1659 by conservation</li>
1660 <li>Duplicate group associated conservation or consensus
1661 created on new view</li>
1662 <li>Annotation scrollbar not displayed after 'show
1663 all hidden annotation rows' option selected</li>
1664 <li>Alignment quality not updated after alignment
1665 annotation row is hidden then shown</li>
1666 <li>Preserve colouring of structures coloured by
1667 sequences in pre Jalview 2.7 projects</li>
1668 <li>Web service job parameter dialog is not laid out
1670 <li>Web services menu not refreshed after 'reset
1671 services' button is pressed in preferences</li>
1672 <li>Annotation off by one in Jalview v2_3 example project</li>
1673 <li>Structures imported from file and saved in project
1674 get name like jalview_pdb1234.txt when reloaded</li>
1675 <li>Jalview does not always retrieve progress of a JABAWS
1676 job execution in full once it is complete</li>
1677 </ul> <em>Applet</em>
1679 <li>Alignment height set incorrectly when lots of
1680 annotation rows are displayed</li>
1681 <li>Relative URLs in feature HTML text not resolved to
1683 <li>View follows highlighting does not work for positions
1685 <li><= shown as = in tooltip</li>
1686 <li>Export features raises exception when no features
1688 <li>Separator string used for serialising lists of IDs
1689 for javascript api is modified when separator string
1690 provided as parameter</li>
1691 <li>Null pointer exception when selecting tree leaves for
1692 alignment with no existing selection</li>
1693 <li>Relative URLs for datasources assumed to be relative
1694 to applet's codebase</li>
1695 <li>Status bar not updated after finished searching and
1696 search wraps around to first result</li>
1697 <li>StructureSelectionManager instance shared between
1698 several Jalview applets causes race conditions and memory
1700 <li>Hover tooltip and mouseover of position on structure
1701 not sent from Jmol in applet</li>
1702 <li>Certain sequences of javascript method calls to
1703 applet API fatally hang browser</li>
1704 </ul> <em>General</em>
1706 <li>View follows structure mouseover scrolls beyond
1707 position with wrapped view and hidden regions</li>
1708 <li>Find sequence position moves to wrong residue
1709 with/without hidden columns</li>
1710 <li>Sequence length given in alignment properties window
1712 <li>InvalidNumberFormat exceptions thrown when trying to
1713 import PDB like structure files</li>
1714 <li>Positional search results are only highlighted
1715 between user-supplied sequence start/end bounds</li>
1716 <li>End attribute of sequence is not validated</li>
1717 <li>Find dialog only finds first sequence containing a
1718 given sequence position</li>
1719 <li>Sequence numbering not preserved in MSF alignment
1721 <li>Jalview PDB file reader does not extract sequence
1722 from nucleotide chains correctly</li>
1723 <li>Structure colours not updated when tree partition
1724 changed in alignment</li>
1725 <li>Sequence associated secondary structure not correctly
1726 parsed in interleaved stockholm</li>
1727 <li>Colour by annotation dialog does not restore current
1729 <li>Hiding (nearly) all sequences doesn't work
1731 <li>Sequences containing lowercase letters are not
1732 properly associated with their pdb files</li>
1733 </ul> <em>Documentation and Development</em>
1735 <li>schemas/JalviewWsParamSet.xsd corrupted by
1736 ApplyCopyright tool</li>
1741 <div align="center">
1742 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
1745 <td><em>Application</em>
1747 <li>New warning dialog when the Jalview Desktop cannot
1748 contact web services</li>
1749 <li>JABA service parameters for a preset are shown in
1750 service job window</li>
1751 <li>JABA Service menu entries reworded</li>
1755 <li>Modeller PIR IO broken - cannot correctly import a
1756 pir file emitted by Jalview</li>
1757 <li>Existing feature settings transferred to new
1758 alignment view created from cut'n'paste</li>
1759 <li>Improved test for mixed amino/nucleotide chains when
1760 parsing PDB files</li>
1761 <li>Consensus and conservation annotation rows
1762 occasionally become blank for all new windows</li>
1763 <li>Exception raised when right clicking above sequences
1764 in wrapped view mode</li>
1765 </ul> <em>Application</em>
1767 <li>multiple multiply aligned structure views cause cpu
1768 usage to hit 100% and computer to hang</li>
1769 <li>Web Service parameter layout breaks for long user
1770 parameter names</li>
1771 <li>Jaba service discovery hangs desktop if Jaba server
1778 <div align="center">
1779 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
1782 <td><em>Application</em>
1784 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
1785 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
1788 <li>Web Services preference tab</li>
1789 <li>Analysis parameters dialog box and user defined
1791 <li>Improved speed and layout of Envision2 service menu</li>
1792 <li>Superpose structures using associated sequence
1794 <li>Export coordinates and projection as CSV from PCA
1796 </ul> <em>Applet</em>
1798 <li>enable javascript: execution by the applet via the
1799 link out mechanism</li>
1800 </ul> <em>Other</em>
1802 <li>Updated the Jmol Jalview interface to work with Jmol
1804 <li>The Jalview Desktop and JalviewLite applet now
1805 require Java 1.5</li>
1806 <li>Allow Jalview feature colour specification for GFF
1807 sequence annotation files</li>
1808 <li>New 'colour by label' keword in Jalview feature file
1809 type colour specification</li>
1810 <li>New Jalview Desktop Groovy API method that allows a
1811 script to check if it being run in an interactive session or
1812 in a batch operation from the Jalview command line</li>
1816 <li>clustalx colourscheme colours Ds preferentially when
1817 both D+E are present in over 50% of the column</li>
1818 </ul> <em>Application</em>
1820 <li>typo in AlignmentFrame->View->Hide->all but
1821 selected Regions menu item</li>
1822 <li>sequence fetcher replaces ',' for ';' when the ',' is
1823 part of a valid accession ID</li>
1824 <li>fatal OOM if object retrieved by sequence fetcher
1825 runs out of memory</li>
1826 <li>unhandled Out of Memory Error when viewing pca
1827 analysis results</li>
1828 <li>InstallAnywhere builds fail to launch on OS X java
1829 10.5 update 4 (due to apple Java 1.6 update)</li>
1830 <li>Installanywhere Jalview silently fails to launch</li>
1831 </ul> <em>Applet</em>
1833 <li>Jalview.getFeatureGroups() raises an
1834 ArrayIndexOutOfBoundsException if no feature groups are
1841 <div align="center">
1842 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
1848 <li>Alignment prettyprinter doesn't cope with long
1850 <li>clustalx colourscheme colours Ds preferentially when
1851 both D+E are present in over 50% of the column</li>
1852 <li>nucleic acid structures retrieved from PDB do not
1853 import correctly</li>
1854 <li>More columns get selected than were clicked on when a
1855 number of columns are hidden</li>
1856 <li>annotation label popup menu not providing correct
1857 add/hide/show options when rows are hidden or none are
1859 <li>Stockholm format shown in list of readable formats,
1860 and parser copes better with alignments from RFAM.</li>
1861 <li>CSV output of consensus only includes the percentage
1862 of all symbols if sequence logo display is enabled</li>
1864 </ul> <em>Applet</em>
1866 <li>annotation panel disappears when annotation is
1868 </ul> <em>Application</em>
1870 <li>Alignment view not redrawn properly when new
1871 alignment opened where annotation panel is visible but no
1872 annotations are present on alignment</li>
1873 <li>pasted region containing hidden columns is
1874 incorrectly displayed in new alignment window</li>
1875 <li>Jalview slow to complete operations when stdout is
1876 flooded (fix is to close the Jalview console)</li>
1877 <li>typo in AlignmentFrame->View->Hide->all but
1878 selected Rregions menu item.</li>
1879 <li>inconsistent group submenu and Format submenu entry
1880 'Un' or 'Non'conserved</li>
1881 <li>Sequence feature settings are being shared by
1882 multiple distinct alignments</li>
1883 <li>group annotation not recreated when tree partition is
1885 <li>double click on group annotation to select sequences
1886 does not propagate to associated trees</li>
1887 <li>Mac OSX specific issues:
1889 <li>exception raised when mouse clicked on desktop
1890 window background</li>
1891 <li>Desktop menu placed on menu bar and application
1892 name set correctly</li>
1893 <li>sequence feature settings not wide enough for the
1894 save feature colourscheme button</li>
1903 <div align="center">
1904 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
1907 <td><em>New Capabilities</em>
1909 <li>URL links generated from description line for
1910 regular-expression based URL links (applet and application)
1917 <li>Non-positional feature URL links are shown in link
1919 <li>Linked viewing of nucleic acid sequences and
1921 <li>Automatic Scrolling option in View menu to display
1922 the currently highlighted region of an alignment.</li>
1923 <li>Order an alignment by sequence length, or using the
1924 average score or total feature count for each sequence.</li>
1925 <li>Shading features by score or associated description</li>
1926 <li>Subdivide alignment and groups based on identity of
1927 selected subsequence (Make Groups from Selection).</li>
1928 <li>New hide/show options including Shift+Control+H to
1929 hide everything but the currently selected region.</li>
1930 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
1931 </ul> <em>Application</em>
1933 <li>Fetch DB References capabilities and UI expanded to
1934 support retrieval from DAS sequence sources</li>
1935 <li>Local DAS Sequence sources can be added via the
1936 command line or via the Add local source dialog box.</li>
1937 <li>DAS Dbref and DbxRef feature types are parsed as
1938 database references and protein_name is parsed as
1939 description line (BioSapiens terms).</li>
1940 <li>Enable or disable non-positional feature and database
1941 references in sequence ID tooltip from View menu in
1943 <!-- <li>New hidden columns and rows and representatives capabilities
1944 in annotations file (in progress - not yet fully implemented)</li> -->
1945 <li>Group-associated consensus, sequence logos and
1946 conservation plots</li>
1947 <li>Symbol distributions for each column can be exported
1948 and visualized as sequence logos</li>
1949 <li>Optionally scale multi-character column labels to fit
1950 within each column of annotation row<!-- todo for applet -->
1952 <li>Optional automatic sort of associated alignment view
1953 when a new tree is opened.</li>
1954 <li>Jalview Java Console</li>
1955 <li>Better placement of desktop window when moving
1956 between different screens.</li>
1957 <li>New preference items for sequence ID tooltip and
1958 consensus annotation</li>
1959 <li>Client to submit sequences and IDs to Envision2
1961 <li><em>Vamsas Capabilities</em>
1963 <li>Improved VAMSAS synchronization (Jalview archive
1964 used to preserve views, structures, and tree display
1966 <li>Import of vamsas documents from disk or URL via
1968 <li>Sharing of selected regions between views and
1969 with other VAMSAS applications (Experimental feature!)</li>
1970 <li>Updated API to VAMSAS version 0.2</li>
1972 </ul> <em>Applet</em>
1974 <li>Middle button resizes annotation row height</li>
1977 <li>sortByTree (true/false) - automatically sort the
1978 associated alignment view by the tree when a new tree is
1980 <li>showTreeBootstraps (true/false) - show or hide
1981 branch bootstraps (default is to show them if available)</li>
1982 <li>showTreeDistances (true/false) - show or hide
1983 branch lengths (default is to show them if available)</li>
1984 <li>showUnlinkedTreeNodes (true/false) - indicate if
1985 unassociated nodes should be highlighted in the tree
1987 <li>heightScale and widthScale (1.0 or more) -
1988 increase the height or width of a cell in the alignment
1989 grid relative to the current font size.</li>
1992 <li>Non-positional features displayed in sequence ID
1994 </ul> <em>Other</em>
1996 <li>Features format: graduated colour definitions and
1997 specification of feature scores</li>
1998 <li>Alignment Annotations format: new keywords for group
1999 associated annotation (GROUP_REF) and annotation row display
2000 properties (ROW_PROPERTIES)</li>
2001 <li>XML formats extended to support graduated feature
2002 colourschemes, group associated annotation, and profile
2003 visualization settings.</li></td>
2006 <li>Source field in GFF files parsed as feature source
2007 rather than description</li>
2008 <li>Non-positional features are now included in sequence
2009 feature and gff files (controlled via non-positional feature
2010 visibility in tooltip).</li>
2011 <li>URL links generated for all feature links (bugfix)</li>
2012 <li>Added URL embedding instructions to features file
2014 <li>Codons containing ambiguous nucleotides translated as
2015 'X' in peptide product</li>
2016 <li>Match case switch in find dialog box works for both
2017 sequence ID and sequence string and query strings do not
2018 have to be in upper case to match case-insensitively.</li>
2019 <li>AMSA files only contain first column of
2020 multi-character column annotation labels</li>
2021 <li>Jalview Annotation File generation/parsing consistent
2022 with documentation (e.g. Stockholm annotation can be
2023 exported and re-imported)</li>
2024 <li>PDB files without embedded PDB IDs given a friendly
2026 <li>Find incrementally searches ID string matches as well
2027 as subsequence matches, and correctly reports total number
2031 <li>Better handling of exceptions during sequence
2033 <li>Dasobert generated non-positional feature URL
2034 link text excludes the start_end suffix</li>
2035 <li>DAS feature and source retrieval buttons disabled
2036 when fetch or registry operations in progress.</li>
2037 <li>PDB files retrieved from URLs are cached properly</li>
2038 <li>Sequence description lines properly shared via
2040 <li>Sequence fetcher fetches multiple records for all
2042 <li>Ensured that command line das feature retrieval
2043 completes before alignment figures are generated.</li>
2044 <li>Reduced time taken when opening file browser for
2046 <li>isAligned check prior to calculating tree, PCA or
2047 submitting an MSA to JNet now excludes hidden sequences.</li>
2048 <li>User defined group colours properly recovered
2049 from Jalview projects.</li>
2058 <div align="center">
2059 <strong>2.4.0.b2</strong><br> 28/10/2009
2064 <li>Experimental support for google analytics usage
2066 <li>Jalview privacy settings (user preferences and docs).</li>
2071 <li>Race condition in applet preventing startup in
2073 <li>Exception when feature created from selection beyond
2074 length of sequence.</li>
2075 <li>Allow synthetic PDB files to be imported gracefully</li>
2076 <li>Sequence associated annotation rows associate with
2077 all sequences with a given id</li>
2078 <li>Find function matches case-insensitively for sequence
2079 ID string searches</li>
2080 <li>Non-standard characters do not cause pairwise
2081 alignment to fail with exception</li>
2082 </ul> <em>Application Issues</em>
2084 <li>Sequences are now validated against EMBL database</li>
2085 <li>Sequence fetcher fetches multiple records for all
2087 </ul> <em>InstallAnywhere Issues</em>
2089 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2090 issue with installAnywhere mechanism)</li>
2091 <li>Command line launching of JARs from InstallAnywhere
2092 version (java class versioning error fixed)</li>
2099 <div align="center">
2100 <strong>2.4</strong><br> 27/8/2008
2103 <td><em>User Interface</em>
2105 <li>Linked highlighting of codon and amino acid from
2106 translation and protein products</li>
2107 <li>Linked highlighting of structure associated with
2108 residue mapping to codon position</li>
2109 <li>Sequence Fetcher provides example accession numbers
2110 and 'clear' button</li>
2111 <li>MemoryMonitor added as an option under Desktop's
2113 <li>Extract score function to parse whitespace separated
2114 numeric data in description line</li>
2115 <li>Column labels in alignment annotation can be centred.</li>
2116 <li>Tooltip for sequence associated annotation give name
2118 </ul> <em>Web Services and URL fetching</em>
2120 <li>JPred3 web service</li>
2121 <li>Prototype sequence search client (no public services
2123 <li>Fetch either seed alignment or full alignment from
2125 <li>URL Links created for matching database cross
2126 references as well as sequence ID</li>
2127 <li>URL Links can be created using regular-expressions</li>
2128 </ul> <em>Sequence Database Connectivity</em>
2130 <li>Retrieval of cross-referenced sequences from other
2132 <li>Generalised database reference retrieval and
2133 validation to all fetchable databases</li>
2134 <li>Fetch sequences from DAS sources supporting the
2135 sequence command</li>
2136 </ul> <em>Import and Export</em>
2137 <li>export annotation rows as CSV for spreadsheet import</li>
2138 <li>Jalview projects record alignment dataset associations,
2139 EMBL products, and cDNA sequence mappings</li>
2140 <li>Sequence Group colour can be specified in Annotation
2142 <li>Ad-hoc colouring of group in Annotation File using RGB
2143 triplet as name of colourscheme</li>
2144 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2146 <li>treenode binding for VAMSAS tree exchange</li>
2147 <li>local editing and update of sequences in VAMSAS
2148 alignments (experimental)</li>
2149 <li>Create new or select existing session to join</li>
2150 <li>load and save of vamsas documents</li>
2151 </ul> <em>Application command line</em>
2153 <li>-tree parameter to open trees (introduced for passing
2155 <li>-fetchfrom command line argument to specify nicknames
2156 of DAS servers to query for alignment features</li>
2157 <li>-dasserver command line argument to add new servers
2158 that are also automatically queried for features</li>
2159 <li>-groovy command line argument executes a given groovy
2160 script after all input data has been loaded and parsed</li>
2161 </ul> <em>Applet-Application data exchange</em>
2163 <li>Trees passed as applet parameters can be passed to
2164 application (when using "View in full
2165 application")</li>
2166 </ul> <em>Applet Parameters</em>
2168 <li>feature group display control parameter</li>
2169 <li>debug parameter</li>
2170 <li>showbutton parameter</li>
2171 </ul> <em>Applet API methods</em>
2173 <li>newView public method</li>
2174 <li>Window (current view) specific get/set public methods</li>
2175 <li>Feature display control methods</li>
2176 <li>get list of currently selected sequences</li>
2177 </ul> <em>New Jalview distribution features</em>
2179 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2180 <li>RELEASE file gives build properties for the latest
2181 Jalview release.</li>
2182 <li>Java 1.1 Applet build made easier and donotobfuscate
2183 property controls execution of obfuscator</li>
2184 <li>Build target for generating source distribution</li>
2185 <li>Debug flag for javacc</li>
2186 <li>.jalview_properties file is documented (slightly) in
2187 jalview.bin.Cache</li>
2188 <li>Continuous Build Integration for stable and
2189 development version of Application, Applet and source
2194 <li>selected region output includes visible annotations
2195 (for certain formats)</li>
2196 <li>edit label/displaychar contains existing label/char
2198 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2199 <li>shorter peptide product names from EMBL records</li>
2200 <li>Newick string generator makes compact representations</li>
2201 <li>bootstrap values parsed correctly for tree files with
2203 <li>pathological filechooser bug avoided by not allowing
2204 filenames containing a ':'</li>
2205 <li>Fixed exception when parsing GFF files containing
2206 global sequence features</li>
2207 <li>Alignment datasets are finalized only when number of
2208 references from alignment sequences goes to zero</li>
2209 <li>Close of tree branch colour box without colour
2210 selection causes cascading exceptions</li>
2211 <li>occasional negative imgwidth exceptions</li>
2212 <li>better reporting of non-fatal warnings to user when
2213 file parsing fails.</li>
2214 <li>Save works when Jalview project is default format</li>
2215 <li>Save as dialog opened if current alignment format is
2216 not a valid output format</li>
2217 <li>UniProt canonical names introduced for both das and
2219 <li>Histidine should be midblue (not pink!) in Zappo</li>
2220 <li>error messages passed up and output when data read
2222 <li>edit undo recovers previous dataset sequence when
2223 sequence is edited</li>
2224 <li>allow PDB files without pdb ID HEADER lines (like
2225 those generated by MODELLER) to be read in properly</li>
2226 <li>allow reading of JPred concise files as a normal
2228 <li>Stockholm annotation parsing and alignment properties
2229 import fixed for PFAM records</li>
2230 <li>Structure view windows have correct name in Desktop
2232 <li>annotation consisting of sequence associated scores
2233 can be read and written correctly to annotation file</li>
2234 <li>Aligned cDNA translation to aligned peptide works
2236 <li>Fixed display of hidden sequence markers and
2237 non-italic font for representatives in Applet</li>
2238 <li>Applet Menus are always embedded in applet window on
2240 <li>Newly shown features appear at top of stack (in
2242 <li>Annotations added via parameter not drawn properly
2243 due to null pointer exceptions</li>
2244 <li>Secondary structure lines are drawn starting from
2245 first column of alignment</li>
2246 <li>UniProt XML import updated for new schema release in
2248 <li>Sequence feature to sequence ID match for Features
2249 file is case-insensitive</li>
2250 <li>Sequence features read from Features file appended to
2251 all sequences with matching IDs</li>
2252 <li>PDB structure coloured correctly for associated views
2253 containing a sub-sequence</li>
2254 <li>PDB files can be retrieved by applet from Jar files</li>
2255 <li>feature and annotation file applet parameters
2256 referring to different directories are retrieved correctly</li>
2257 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
2258 <li>Fixed application hang whilst waiting for
2259 splash-screen version check to complete</li>
2260 <li>Applet properly URLencodes input parameter values
2261 when passing them to the launchApp service</li>
2262 <li>display name and local features preserved in results
2263 retrieved from web service</li>
2264 <li>Visual delay indication for sequence retrieval and
2265 sequence fetcher initialisation</li>
2266 <li>updated Application to use DAS 1.53e version of
2267 dasobert DAS client</li>
2268 <li>Re-instated Full AMSA support and .amsa file
2270 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
2278 <div align="center">
2279 <strong>2.3</strong><br> 9/5/07
2284 <li>Jmol 11.0.2 integration</li>
2285 <li>PDB views stored in Jalview XML files</li>
2286 <li>Slide sequences</li>
2287 <li>Edit sequence in place</li>
2288 <li>EMBL CDS features</li>
2289 <li>DAS Feature mapping</li>
2290 <li>Feature ordering</li>
2291 <li>Alignment Properties</li>
2292 <li>Annotation Scores</li>
2293 <li>Sort by scores</li>
2294 <li>Feature/annotation editing in applet</li>
2299 <li>Headless state operation in 2.2.1</li>
2300 <li>Incorrect and unstable DNA pairwise alignment</li>
2301 <li>Cut and paste of sequences with annotation</li>
2302 <li>Feature group display state in XML</li>
2303 <li>Feature ordering in XML</li>
2304 <li>blc file iteration selection using filename # suffix</li>
2305 <li>Stockholm alignment properties</li>
2306 <li>Stockhom alignment secondary structure annotation</li>
2307 <li>2.2.1 applet had no feature transparency</li>
2308 <li>Number pad keys can be used in cursor mode</li>
2309 <li>Structure Viewer mirror image resolved</li>
2316 <div align="center">
2317 <strong>2.2.1</strong><br> 12/2/07
2322 <li>Non standard characters can be read and displayed
2323 <li>Annotations/Features can be imported/exported to the
2325 <li>Applet allows editing of sequence/annotation/group
2326 name & description
2327 <li>Preference setting to display sequence name in
2329 <li>Annotation file format extended to allow
2330 Sequence_groups to be defined
2331 <li>Default opening of alignment overview panel can be
2332 specified in preferences
2333 <li>PDB residue numbering annotation added to associated
2339 <li>Applet crash under certain Linux OS with Java 1.6
2341 <li>Annotation file export / import bugs fixed
2342 <li>PNG / EPS image output bugs fixed
2348 <div align="center">
2349 <strong>2.2</strong><br> 27/11/06
2354 <li>Multiple views on alignment
2355 <li>Sequence feature editing
2356 <li>"Reload" alignment
2357 <li>"Save" to current filename
2358 <li>Background dependent text colour
2359 <li>Right align sequence ids
2360 <li>User-defined lower case residue colours
2363 <li>Menu item accelerator keys
2364 <li>Control-V pastes to current alignment
2365 <li>Cancel button for DAS Feature Fetching
2366 <li>PCA and PDB Viewers zoom via mouse roller
2367 <li>User-defined sub-tree colours and sub-tree selection
2374 <li>'New Window' button on the 'Output to Text box'
2379 <li>New memory efficient Undo/Redo System
2380 <li>Optimised symbol lookups and conservation/consensus
2382 <li>Region Conservation/Consensus recalculated after
2384 <li>Fixed Remove Empty Columns Bug (empty columns at end
2386 <li>Slowed DAS Feature Fetching for increased robustness.
2393 <li>Made angle brackets in ASCII feature descriptions
2395 <li>Re-instated Zoom function for PCA
2396 <li>Sequence descriptions conserved in web service
2398 <li>UniProt ID discoverer uses any word separated by
2400 <li>WsDbFetch query/result association resolved
2401 <li>Tree leaf to sequence mapping improved
2402 <li>Smooth fonts switch moved to FontChooser dialog box.
2414 <div align="center">
2415 <strong>2.1.1</strong><br> 12/9/06
2420 <li>Copy consensus sequence to clipboard</li>
2425 <li>Image output - rightmost residues are rendered if
2426 sequence id panel has been resized</li>
2427 <li>Image output - all offscreen group boundaries are
2429 <li>Annotation files with sequence references - all
2430 elements in file are relative to sequence position</li>
2431 <li>Mac Applet users can use Alt key for group editing</li>
2437 <div align="center">
2438 <strong>2.1</strong><br> 22/8/06
2443 <li>MAFFT Multiple Alignment in default Web Service list</li>
2444 <li>DAS Feature fetching</li>
2445 <li>Hide sequences and columns</li>
2446 <li>Export Annotations and Features</li>
2447 <li>GFF file reading / writing</li>
2448 <li>Associate structures with sequences from local PDB
2450 <li>Add sequences to exisiting alignment</li>
2451 <li>Recently opened files / URL lists</li>
2452 <li>Applet can launch the full application</li>
2453 <li>Applet has transparency for features (Java 1.2
2455 <li>Applet has user defined colours parameter</li>
2456 <li>Applet can load sequences from parameter
2457 "sequence<em>x</em>"
2463 <li>Redundancy Panel reinstalled in the Applet</li>
2464 <li>Monospaced font - EPS / rescaling bug fixed</li>
2465 <li>Annotation files with sequence references bug fixed</li>
2471 <div align="center">
2472 <strong>2.08.1</strong><br> 2/5/06
2477 <li>Change case of selected region from Popup menu</li>
2478 <li>Choose to match case when searching</li>
2479 <li>Middle mouse button and mouse movement can compress /
2480 expand the visible width and height of the alignment</li>
2485 <li>Annotation Panel displays complete JNet results</li>
2491 <div align="center">
2492 <strong>2.08b</strong><br> 18/4/06
2498 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
2499 <li>Righthand label on wrapped alignments shows correct
2506 <div align="center">
2507 <strong>2.08</strong><br> 10/4/06
2512 <li>Editing can be locked to the selection area</li>
2513 <li>Keyboard editing</li>
2514 <li>Create sequence features from searches</li>
2515 <li>Precalculated annotations can be loaded onto
2517 <li>Features file allows grouping of features</li>
2518 <li>Annotation Colouring scheme added</li>
2519 <li>Smooth fonts off by default - Faster rendering</li>
2520 <li>Choose to toggle Autocalculate Consensus On/Off</li>
2525 <li>Drag & Drop fixed on Linux</li>
2526 <li>Jalview Archive file faster to load/save, sequence
2527 descriptions saved.</li>
2533 <div align="center">
2534 <strong>2.07</strong><br> 12/12/05
2539 <li>PDB Structure Viewer enhanced</li>
2540 <li>Sequence Feature retrieval and display enhanced</li>
2541 <li>Choose to output sequence start-end after sequence
2542 name for file output</li>
2543 <li>Sequence Fetcher WSDBFetch@EBI</li>
2544 <li>Applet can read feature files, PDB files and can be
2545 used for HTML form input</li>
2550 <li>HTML output writes groups and features</li>
2551 <li>Group editing is Control and mouse click</li>
2552 <li>File IO bugs</li>
2558 <div align="center">
2559 <strong>2.06</strong><br> 28/9/05
2564 <li>View annotations in wrapped mode</li>
2565 <li>More options for PCA viewer</li>
2570 <li>GUI bugs resolved</li>
2571 <li>Runs with -nodisplay from command line</li>
2577 <div align="center">
2578 <strong>2.05b</strong><br> 15/9/05
2583 <li>Choose EPS export as lineart or text</li>
2584 <li>Jar files are executable</li>
2585 <li>Can read in Uracil - maps to unknown residue</li>
2590 <li>Known OutOfMemory errors give warning message</li>
2591 <li>Overview window calculated more efficiently</li>
2592 <li>Several GUI bugs resolved</li>
2598 <div align="center">
2599 <strong>2.05</strong><br> 30/8/05
2604 <li>Edit and annotate in "Wrapped" view</li>
2609 <li>Several GUI bugs resolved</li>
2615 <div align="center">
2616 <strong>2.04</strong><br> 24/8/05
2621 <li>Hold down mouse wheel & scroll to change font
2627 <li>Improved JPred client reliability</li>
2628 <li>Improved loading of Jalview files</li>
2634 <div align="center">
2635 <strong>2.03</strong><br> 18/8/05
2640 <li>Set Proxy server name and port in preferences</li>
2641 <li>Multiple URL links from sequence ids</li>
2642 <li>User Defined Colours can have a scheme name and added
2644 <li>Choose to ignore gaps in consensus calculation</li>
2645 <li>Unix users can set default web browser</li>
2646 <li>Runs without GUI for batch processing</li>
2647 <li>Dynamically generated Web Service Menus</li>
2652 <li>InstallAnywhere download for Sparc Solaris</li>
2658 <div align="center">
2659 <strong>2.02</strong><br> 18/7/05
2665 <li>Copy & Paste order of sequences maintains
2666 alignment order.</li>
2672 <div align="center">
2673 <strong>2.01</strong><br> 12/7/05
2678 <li>Use delete key for deleting selection.</li>
2679 <li>Use Mouse wheel to scroll sequences.</li>
2680 <li>Help file updated to describe how to add alignment
2682 <li>Version and build date written to build properties
2684 <li>InstallAnywhere installation will check for updates
2685 at launch of Jalview.</li>
2690 <li>Delete gaps bug fixed.</li>
2691 <li>FileChooser sorts columns.</li>
2692 <li>Can remove groups one by one.</li>
2693 <li>Filechooser icons installed.</li>
2694 <li>Finder ignores return character when searching.
2695 Return key will initiate a search.<br>
2702 <div align="center">
2703 <strong>2.0</strong><br> 20/6/05
2708 <li>New codebase</li>