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>24/11/2016</em></strong>
54 <td><div align="left">
58 <!-- JAL-98 -->Improved memory usage: sparse arrays used
59 for all consensus calculations
62 <!-- JAL-2177 -->Updated Jmol shipped with applet and
73 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
74 set of database cross-references, sorted alphabetically
77 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
78 from database cross references. Users with custom links
79 will receive a <a href="webServices/urllinks.html#warning">warning
80 dialog</a> asking them to update their preferences.
83 <!-- JAL-2287-->Cancel button and escape listener on
84 dialog warning user about disconnecting Jalview from a
88 <!-- JAL-2320-->Jalview's Chimera control window closes if
89 the Chimera it is connected to is shut down
92 <!-- JAL-1738-->New keystroke (B) and Select highlighted
93 columns menu item to mark columns containing
94 highlighted regions (e.g. from structure selections or results
98 <!-- JAL-2284-->Command line option for batch-generation
99 of HTML pages rendering alignment data with the BioJS
103 <!-- --> <em>Applet</em>
106 <em>Build and deployment</em>
108 <li>Updated Jalview's Certum code signing certificate
117 <!-- JAL-2286 -->Columns with more than one modal residue
118 are not coloured or thresholded according to percent
119 identity (first observed in Jalview 2.8.2)
122 <!-- JAL-2301 -->Threonine incorrectly reported as not
126 <!-- JAL-2318 -->Updates to documentation pages (above PID
127 threshold, amino acid properties)
130 <!-- JAL-2292 -->Lower case residues in sequences are not
131 reported as mapped to residues in a structure file in the
135 <!--JAL-2324 -->Identical features with non-numeric scores
136 could be added multiple times to a sequence
139 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
140 bond features shown as two highlighted residues rather
141 than a range in linked structure views, and treated
142 correctly when selecting and computing trees from features
145 <!-- JAL-2281-->Custom URL links for database
146 cross-references are matched to database name regardless
154 <!-- JAL-2282-->Custom URL links for specific database
155 names without regular expressions also offer links from
159 <!-- JAL-2315-->Removing a single configured link in the
160 URL links pane in Connections preferences doesn't actually
161 update Jalview configuration
164 <!-- JAL-2272-->CTRL-Click on a selected region to open
165 the alignment area popup menu doesn't work on El-Capitan
168 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
169 files with similarly named sequences if dropped onto the
173 <!-- JAL-2312 -->Additional mappings are shown for PDB
174 entries where more chains exist in the PDB accession than
175 are reported in the SIFTS file
178 <!-- JAL-2317-->Certain structures do not get mapped to
179 the structure view when displayed with Chimera
182 <!-- JAL-2317-->No chains shown in the Chimera view
183 panel's View->Show Chains submenu
186 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
187 work for wrapped alignment views
190 <!--JAL-2197 -->Rename UI components for running JPred
191 predictions from 'JNet' to 'JPred'
194 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
195 corrupted when annotation panel vertical scroll is not at
199 <!--JAL-2332 -->Attempting to view structure for Hen
200 lysozyme results in a PDB Client error dialog box
207 <em>Build and deployment</em>
210 <!-- JAL-2308, -->Failing/passing unit tests
213 <em>New Known Issues</em>
220 <td width="60" nowrap>
222 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
223 <em>25/10/2016</em></strong>
226 <td><em>Application</em>
228 <li>3D Structure chooser opens with 'Cached structures'
229 view if structures already loaded</li>
230 <li>Progress bar reports models as they are loaded to
237 <li>Colour by conservation always enabled and no tick
238 shown in menu when BLOSUM or PID shading applied</li>
239 <li>FER1_ARATH and FER2_ARATH labels were switched in
240 example sequences/projects/trees</li>
244 <li>Jalview projects with views of local PDB structure
245 files saved on Windows cannot be opened on OSX</li>
246 <li>Multiple structure views can be opened and
247 superposed without timeout for structures with multiple
248 models or multiple sequences in alignment</li>
249 <li>Cannot import or associated local PDB files without
250 a PDB ID HEADER line</li>
251 <li>RMSD is not output in Jmol console when
252 superposition is performed</li>
253 <li>Drag and drop of URL from Browser fails for Linux
254 and OSX versions earlier than El Capitan</li>
255 <li>ENA client ignores invalid content from ENA server</li>
256 <li>Exceptions are not raised in console when ENA
257 client attempts to fetch non-existent IDs via Fetch DB
259 <li>Exceptions are not raised in console when a new
260 view is created on the alignment</li>
261 <li>OSX right-click fixed for group selections:
262 CMD-click to insert/remove gaps in groups and CTRL-click
263 to open group pop-up menu</li>
265 <em>Build and deployment</em>
267 <li>URL link checker now copes with multi-line anchor
270 <em>New Known Issues</em>
272 <li>Drag and drop from URL links in browsers do not
279 <td width="60" nowrap>
281 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
287 <!-- JAL-2124 -->Updated Spanish translations.
290 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
291 for importing structure data to Jalview. Enables mmCIF and
295 <!-- JAL-192 --->Alignment ruler shows positions relative to
299 <!-- JAL-2202 -->Position/residue shown in status bar when
300 mousing over sequence associated annotation
303 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
307 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
308 '()', canonical '[]' and invalid '{}' base pair populations
312 <!-- JAL-2092 -->Feature settings popup menu options for
313 showing or hiding columns containing a feature
316 <!-- JAL-1557 -->Edit selected group by double clicking on
317 group and sequence associated annotation labels
320 <!-- JAL-2236 -->Sequence name added to annotation label in
321 select/hide columns by annotation and colour by annotation
325 </ul> <em>Application</em>
328 <!-- JAL-2050-->Automatically hide introns when opening a
332 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
336 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
337 structure mappings with the EMBL-EBI PDBe SIFTS database
340 <!-- JAL-2079 -->Updated download sites used for Rfam and
341 Pfam sources to xfam.org
344 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
347 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
348 over sequences in Jalview
351 <!-- JAL-2027-->Support for reverse-complement coding
352 regions in ENA and EMBL
355 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
356 for record retrieval via ENA rest API
359 <!-- JAL-2027 -->Support for ENA CDS records with reverse
363 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
364 groovy script execution
367 <!-- JAL-1812 -->New 'execute Groovy script' option in an
368 alignment window's Calculate menu
371 <!-- JAL-1812 -->Allow groovy scripts that call
372 Jalview.getAlignFrames() to run in headless mode
375 <!-- JAL-2068 -->Support for creating new alignment
376 calculation workers from groovy scripts
379 <!-- JAL-1369 --->Store/restore reference sequence in
383 <!-- JAL-1803 -->Chain codes for a sequence's PDB
384 associations are now saved/restored from project
387 <!-- JAL-1993 -->Database selection dialog always shown
388 before sequence fetcher is opened
391 <!-- JAL-2183 -->Double click on an entry in Jalview's
392 database chooser opens a sequence fetcher
395 <!-- JAL-1563 -->Free-text search client for UniProt using
399 <!-- JAL-2168 -->-nonews command line parameter to prevent
400 the news reader opening
403 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
404 querying stored in preferences
407 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
411 <!-- JAL-1977-->Tooltips shown on database chooser
414 <!-- JAL-391 -->Reverse complement function in calculate
415 menu for nucleotide sequences
418 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
419 and feature counts preserves alignment ordering (and
420 debugged for complex feature sets).
423 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
424 viewing structures with Jalview 2.10
427 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
428 genome, transcript CCDS and gene ids via the Ensembl and
429 Ensembl Genomes REST API
432 <!-- JAL-2049 -->Protein sequence variant annotation
433 computed for 'sequence_variant' annotation on CDS regions
437 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
441 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
442 Ref Fetcher fails to match, or otherwise updates sequence
443 data from external database records.
446 <!-- JAL-2154 -->Revised Jalview Project format for
447 efficient recovery of sequence coding and alignment
448 annotation relationships.
450 </ul> <!-- <em>Applet</em>
461 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
465 <!-- JAL-2018-->Export features in Jalview format (again)
466 includes graduated colourschemes
469 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
470 working with big alignments and lots of hidden columns
473 <!-- JAL-2053-->Hidden column markers not always rendered
474 at right of alignment window
477 <!-- JAL-2067 -->Tidied up links in help file table of
481 <!-- JAL-2072 -->Feature based tree calculation not shown
485 <!-- JAL-2075 -->Hidden columns ignored during feature
486 based tree calculation
489 <!-- JAL-2065 -->Alignment view stops updating when show
490 unconserved enabled for group on alignment
493 <!-- JAL-2086 -->Cannot insert gaps into sequence when
497 <!-- JAL-2146 -->Alignment column in status incorrectly
498 shown as "Sequence position" when mousing over
502 <!-- JAL-2099 -->Incorrect column numbers in ruler when
503 hidden columns present
506 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
507 user created annotation added to alignment
510 <!-- JAL-1841 -->RNA Structure consensus only computed for
511 '()' base pair annotation
514 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
515 in zero scores for all base pairs in RNA Structure
519 <!-- JAL-2174-->Extend selection with columns containing
523 <!-- JAL-2275 -->Pfam format writer puts extra space at
524 beginning of sequence
527 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
531 <!-- JAL-2238 -->Cannot create groups on an alignment from
532 from a tree when t-coffee scores are shown
535 <!-- JAL-1836,1967 -->Cannot import and view PDB
536 structures with chains containing negative resnums (4q4h)
539 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
543 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
544 to Clustal, PIR and PileUp output
547 <!-- JAL-2008 -->Reordering sequence features that are
548 not visible causes alignment window to repaint
551 <!-- JAL-2006 -->Threshold sliders don't work in
552 graduated colour and colour by annotation row for e-value
553 scores associated with features and annotation rows
556 <!-- JAL-1797 -->amino acid physicochemical conservation
557 calculation should be case independent
560 <!-- JAL-2173 -->Remove annotation also updates hidden
564 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
565 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
566 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
569 <!-- JAL-2065 -->Null pointer exceptions and redraw
570 problems when reference sequence defined and 'show
571 non-conserved' enabled
574 <!-- JAL-1306 -->Quality and Conservation are now shown on
575 load even when Consensus calculation is disabled
578 <!-- JAL-1932 -->Remove right on penultimate column of
579 alignment does nothing
585 <!-- JAL-1552-->URLs and links can't be imported by
586 drag'n'drop on OSX when launched via webstart (note - not
587 yet fixed for El Capitan)
590 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
591 output when running on non-gb/us i18n platforms
594 <!-- JAL-1944 -->Error thrown when exporting a view with
595 hidden sequences as flat-file alignment
598 <!-- JAL-2030-->InstallAnywhere distribution fails when
602 <!-- JAL-2080-->Jalview very slow to launch via webstart
603 (also hotfix for 2.9.0b2)
606 <!-- JAL-2085 -->Cannot save project when view has a
607 reference sequence defined
610 <!-- JAL-1011 -->Columns are suddenly selected in other
611 alignments and views when revealing hidden columns
614 <!-- JAL-1989 -->Hide columns not mirrored in complement
615 view in a cDNA/Protein splitframe
618 <!-- JAL-1369 -->Cannot save/restore representative
619 sequence from project when only one sequence is
623 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
627 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
628 structure consensus didn't refresh annotation panel
631 <!-- JAL-1962 -->View mapping in structure view shows
632 mappings between sequence and all chains in a PDB file
635 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
636 dialogs format columns correctly, don't display array
637 data, sort columns according to type
640 <!-- JAL-1975 -->Export complete shown after destination
641 file chooser is cancelled during an image export
644 <!-- JAL-2025 -->Error when querying PDB Service with
645 sequence name containing special characters
648 <!-- JAL-2024 -->Manual PDB structure querying should be
652 <!-- JAL-2104 -->Large tooltips with broken HTML
653 formatting don't wrap
656 <!-- JAL-1128 -->Figures exported from wrapped view are
657 truncated so L looks like I in consensus annotation
660 <!-- JAL-2003 -->Export features should only export the
661 currently displayed features for the current selection or
665 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
666 after fetching cross-references, and restoring from project
669 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
670 followed in the structure viewer
673 <!-- JAL-2163 -->Titles for individual alignments in
674 splitframe not restored from project
677 <!-- JAL-2145 -->missing autocalculated annotation at
678 trailing end of protein alignment in transcript/product
679 splitview when pad-gaps not enabled by default
682 <!-- JAL-1797 -->amino acid physicochemical conservation
686 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
687 article has been read (reopened issue due to
688 internationalisation problems)
691 <!-- JAL-1960 -->Only offer PDB structures in structure
692 viewer based on sequence name, PDB and UniProt
697 <!-- JAL-1976 -->No progress bar shown during export of
701 <!-- JAL-2213 -->Structures not always superimposed after
702 multiple structures are shown for one or more sequences.
705 <!-- JAL-1370 -->Reference sequence characters should not
706 be replaced with '.' when 'Show unconserved' format option
710 <!-- JAL-1823 -->Cannot specify chain code when entering
711 specific PDB id for sequence
714 <!-- JAL-1944 -->File->Export->.. as doesn't work when
715 'Export hidden sequences' is enabled, but 'export hidden
716 columns' is disabled.
719 <!--JAL-2026-->Best Quality option in structure chooser
720 selects lowest rather than highest resolution structures
724 <!-- JAL-1887 -->Incorrect start and end reported for PDB
725 to sequence mapping in 'View Mappings' report
728 <!-- JAL-2284 -->Unable to read old Jalview projects that
729 contain non-XML data added after Jalvew wrote project.
731 <li><!-- JAL-2118 -->Newly created annotation row reorders
732 after clicking on it to create new annotation for a
735 <!-- may exclude, this is an external service stability issue JAL-1941
736 -- > RNA 3D structure not added via DSSR service</li> -->
741 <!-- JAL-2151 -->Incorrect columns are selected when
742 hidden columns present before start of sequence
745 <!-- JAL-1986 -->Missing dependencies on applet pages
749 <!-- JAL-1947 -->Overview pixel size changes when
750 sequences are hidden in applet
753 <!-- JAL-1996 -->Updated instructions for applet
754 deployment on examples pages.
761 <td width="60" nowrap>
763 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
764 <em>16/10/2015</em></strong>
769 <li>Time stamps for signed Jalview application and applet
776 <li>Duplicate group consensus and conservation rows
777 shown when tree is partitioned</li>
778 <li>Erratic behaviour when tree partitions made with
779 multiple cDNA/Protein split views</li>
785 <td width="60" nowrap>
787 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
788 <em>8/10/2015</em></strong>
793 <li>Updated Spanish translations of localized text for
795 </ul> <em>Application</em>
797 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
798 <li>Signed OSX InstallAnywhere installer<br></li>
799 <li>Support for per-sequence based annotations in BioJSON</li>
800 </ul> <em>Applet</em>
802 <li>Split frame example added to applet examples page</li>
803 </ul><em>Build and Deployment</em>
805 <li><!-- JAL-1888 -->New ant target for running Jalview's test suite</li>
811 <li>Mapping of cDNA to protein in split frames
812 incorrect when sequence start > 1</li>
813 <li>Broken images in filter column by annotation dialog
815 <li>Feature colours not parsed from features file</li>
816 <li>Exceptions and incomplete link URLs recovered when
817 loading a features file containing HTML tags in feature
823 <li>Annotations corrupted after BioJS export and
825 <li>Incorrect sequence limits after Fetch DB References
826 with 'trim retrieved sequences'</li>
827 <li>Incorrect warning about deleting all data when
828 deleting selected columns</li>
829 <li>Patch to build system for shipping properly signed
830 JNLP templates for webstart launch</li>
831 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
832 unreleased structures for download or viewing</li>
833 <li>Tab/space/return keystroke operation of EMBL-PDBe
834 fetcher/viewer dialogs works correctly</li>
835 <li>Disabled 'minimise' button on Jalview windows
836 running on OSX to workaround redraw hang bug</li>
837 <li>Split cDNA/Protein view position and geometry not
838 recovered from jalview project</li>
839 <li>Initial enabled/disabled state of annotation menu
840 sorter 'show autocalculated first/last' corresponds to
842 <li>Restoring of Clustal, RNA Helices and T-Coffee
843 color schemes from BioJSON</li>
847 <li>Reorder sequences mirrored in cDNA/Protein split
849 <li>Applet with Jmol examples not loading correctly</li>
855 <td><div align="center">
856 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
860 <li>Linked visualisation and analysis of DNA and Protein
863 <li>Translated cDNA alignments shown as split protein
864 and DNA alignment views</li>
865 <li>Codon consensus annotation for linked protein and
866 cDNA alignment views</li>
867 <li>Link cDNA or Protein product sequences by loading
868 them onto Protein or cDNA alignments</li>
869 <li>Reconstruct linked cDNA alignment from aligned
870 protein sequences</li>
873 <li>Jmol integration updated to Jmol v14.2.14</li>
874 <li>Import and export of Jalview alignment views as <a
875 href="features/bioJsonFormat.html">BioJSON</a></li>
876 <li>New alignment annotation file statements for
877 reference sequences and marking hidden columns</li>
878 <li>Reference sequence based alignment shading to
879 highlight variation</li>
880 <li>Select or hide columns according to alignment
882 <li>Find option for locating sequences by description</li>
883 <li>Conserved physicochemical properties shown in amino
884 acid conservation row</li>
885 <li>Alignments can be sorted by number of RNA helices</li>
886 </ul> <em>Application</em>
888 <li>New cDNA/Protein analysis capabilities
890 <li>Get Cross-References should open a Split Frame
891 view with cDNA/Protein</li>
892 <li>Detect when nucleotide sequences and protein
893 sequences are placed in the same alignment</li>
894 <li>Split cDNA/Protein views are saved in Jalview
899 <li>Use REST API to talk to Chimera</li>
900 <li>Selected regions in Chimera are highlighted in linked
903 <li>VARNA RNA viewer updated to v3.93</li>
904 <li>VARNA views are saved in Jalview Projects</li>
905 <li>Pseudoknots displayed as Jalview RNA annotation can
906 be shown in VARNA</li>
908 <li>Make groups for selection uses marked columns as well
909 as the active selected region</li>
911 <li>Calculate UPGMA and NJ trees using sequence feature
913 <li>New Export options
915 <li>New Export Settings dialog to control hidden
916 region export in flat file generation</li>
918 <li>Export alignment views for display with the <a
919 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
921 <li>Export scrollable SVG in HTML page</li>
922 <li>Optional embedding of BioJSON data when exporting
923 alignment figures to HTML</li>
925 <li>3D structure retrieval and display
927 <li>Free text and structured queries with the PDBe
929 <li>PDBe Search API based discovery and selection of
930 PDB structures for a sequence set</li>
934 <li>JPred4 employed for protein secondary structure
936 <li>Hide Insertions menu option to hide unaligned columns
937 for one or a group of sequences</li>
938 <li>Automatically hide insertions in alignments imported
939 from the JPred4 web server</li>
940 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
941 system on OSX<br />LGPL libraries courtesy of <a
942 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
944 <li>changed 'View nucleotide structure' submenu to 'View
945 VARNA 2D Structure'</li>
946 <li>change "View protein structure" menu option to "3D
949 </ul> <em>Applet</em>
951 <li>New layout for applet example pages</li>
952 <li>New parameters to enable SplitFrame view
953 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
954 <li>New example demonstrating linked viewing of cDNA and
955 Protein alignments</li>
956 </ul> <em>Development and deployment</em>
958 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
959 <li>Include installation type and git revision in build
960 properties and console log output</li>
961 <li>Jalview Github organisation, and new github site for
962 storing BioJsMSA Templates</li>
963 <li>Jalview's unit tests now managed with TestNG</li>
966 <!-- <em>General</em>
968 </ul> --> <!-- issues resolved --> <em>Application</em>
970 <li>Escape should close any open find dialogs</li>
971 <li>Typo in select-by-features status report</li>
972 <li>Consensus RNA secondary secondary structure
973 predictions are not highlighted in amber</li>
974 <li>Missing gap character in v2.7 example file means
975 alignment appears unaligned when pad-gaps is not enabled</li>
976 <li>First switch to RNA Helices colouring doesn't colour
977 associated structure views</li>
978 <li>ID width preference option is greyed out when auto
979 width checkbox not enabled</li>
980 <li>Stopped a warning dialog from being shown when
981 creating user defined colours</li>
982 <li>'View Mapping' in structure viewer shows sequence
983 mappings for just that viewer's sequences</li>
984 <li>Workaround for superposing PDB files containing
985 multiple models in Chimera</li>
986 <li>Report sequence position in status bar when hovering
987 over Jmol structure</li>
988 <li>Cannot output gaps as '.' symbols with Selection ->
989 output to text box</li>
990 <li>Flat file exports of alignments with hidden columns
991 have incorrect sequence start/end</li>
992 <li>'Aligning' a second chain to a Chimera structure from
994 <li>Colour schemes applied to structure viewers don't
995 work for nucleotide</li>
996 <li>Loading/cut'n'pasting an empty or invalid file leads
997 to a grey/invisible alignment window</li>
998 <li>Exported Jpred annotation from a sequence region
999 imports to different position</li>
1000 <li>Space at beginning of sequence feature tooltips shown
1001 on some platforms</li>
1002 <li>Chimera viewer 'View | Show Chain' menu is not
1004 <li>'New View' fails with a Null Pointer Exception in
1005 console if Chimera has been opened</li>
1006 <li>Mouseover to Chimera not working</li>
1007 <li>Miscellaneous ENA XML feature qualifiers not
1009 <li>NPE in annotation renderer after 'Extract Scores'</li>
1010 <li>If two structures in one Chimera window, mouseover of
1011 either sequence shows on first structure</li>
1012 <li>'Show annotations' options should not make
1013 non-positional annotations visible</li>
1014 <li>Subsequence secondary structure annotation not shown
1015 in right place after 'view flanking regions'</li>
1016 <li>File Save As type unset when current file format is
1018 <li>Save as '.jar' option removed for saving Jalview
1020 <li>Colour by Sequence colouring in Chimera more
1022 <li>Cannot 'add reference annotation' for a sequence in
1023 several views on same alignment</li>
1024 <li>Cannot show linked products for EMBL / ENA records</li>
1025 <li>Jalview's tooltip wraps long texts containing no
1027 </ul> <em>Applet</em>
1029 <li>Jmol to JalviewLite mouseover/link not working</li>
1030 <li>JalviewLite can't import sequences with ID
1031 descriptions containing angle brackets</li>
1032 </ul> <em>General</em>
1034 <li>Cannot export and reimport RNA secondary structure
1035 via jalview annotation file</li>
1036 <li>Random helix colour palette for colour by annotation
1037 with RNA secondary structure</li>
1038 <li>Mouseover to cDNA from STOP residue in protein
1039 translation doesn't work.</li>
1040 <li>hints when using the select by annotation dialog box</li>
1041 <li>Jmol alignment incorrect if PDB file has alternate CA
1043 <li>FontChooser message dialog appears to hang after
1044 choosing 1pt font</li>
1045 <li>Peptide secondary structure incorrectly imported from
1046 annotation file when annotation display text includes 'e' or
1048 <li>Cannot set colour of new feature type whilst creating
1050 <li>cDNA translation alignment should not be sequence
1051 order dependent</li>
1052 <li>'Show unconserved' doesn't work for lower case
1054 <li>Nucleotide ambiguity codes involving R not recognised</li>
1055 </ul> <em>Deployment and Documentation</em>
1057 <li>Applet example pages appear different to the rest of
1058 www.jalview.org</li>
1059 </ul> <em>Application Known issues</em>
1061 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1062 <li>Misleading message appears after trying to delete
1064 <li>Jalview icon not shown in dock after InstallAnywhere
1065 version launches</li>
1066 <li>Fetching EMBL reference for an RNA sequence results
1067 fails with a sequence mismatch</li>
1068 <li>Corrupted or unreadable alignment display when
1069 scrolling alignment to right</li>
1070 <li>ArrayIndexOutOfBoundsException thrown when remove
1071 empty columns called on alignment with ragged gapped ends</li>
1072 <li>auto calculated alignment annotation rows do not get
1073 placed above or below non-autocalculated rows</li>
1074 <li>Jalview dekstop becomes sluggish at full screen in
1075 ultra-high resolution</li>
1076 <li>Cannot disable consensus calculation independently of
1077 quality and conservation</li>
1078 <li>Mouseover highlighting between cDNA and protein can
1079 become sluggish with more than one splitframe shown</li>
1080 </ul> <em>Applet Known Issues</em>
1082 <li>Core PDB parsing code requires Jmol</li>
1083 <li>Sequence canvas panel goes white when alignment
1084 window is being resized</li>
1090 <td><div align="center">
1091 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1093 <td><em>General</em>
1095 <li>Updated Java code signing certificate donated by
1097 <li>Features and annotation preserved when performing
1098 pairwise alignment</li>
1099 <li>RNA pseudoknot annotation can be
1100 imported/exported/displayed</li>
1101 <li>'colour by annotation' can colour by RNA and
1102 protein secondary structure</li>
1103 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1104 post-hoc with 2.9 release</em>)
1107 </ul> <em>Application</em>
1109 <li>Extract and display secondary structure for sequences
1110 with 3D structures</li>
1111 <li>Support for parsing RNAML</li>
1112 <li>Annotations menu for layout
1114 <li>sort sequence annotation rows by alignment</li>
1115 <li>place sequence annotation above/below alignment
1118 <li>Output in Stockholm format</li>
1119 <li>Internationalisation: improved Spanish (es)
1121 <li>Structure viewer preferences tab</li>
1122 <li>Disorder and Secondary Structure annotation tracks
1123 shared between alignments</li>
1124 <li>UCSF Chimera launch and linked highlighting from
1126 <li>Show/hide all sequence associated annotation rows for
1127 all or current selection</li>
1128 <li>disorder and secondary structure predictions
1129 available as dataset annotation</li>
1130 <li>Per-sequence rna helices colouring</li>
1133 <li>Sequence database accessions imported when fetching
1134 alignments from Rfam</li>
1135 <li>update VARNA version to 3.91</li>
1137 <li>New groovy scripts for exporting aligned positions,
1138 conservation values, and calculating sum of pairs scores.</li>
1139 <li>Command line argument to set default JABAWS server</li>
1140 <li>include installation type in build properties and
1141 console log output</li>
1142 <li>Updated Jalview project format to preserve dataset
1146 <!-- issues resolved --> <em>Application</em>
1148 <li>Distinguish alignment and sequence associated RNA
1149 structure in structure->view->VARNA</li>
1150 <li>Raise dialog box if user deletes all sequences in an
1152 <li>Pressing F1 results in documentation opening twice</li>
1153 <li>Sequence feature tooltip is wrapped</li>
1154 <li>Double click on sequence associated annotation
1155 selects only first column</li>
1156 <li>Redundancy removal doesn't result in unlinked
1157 leaves shown in tree</li>
1158 <li>Undos after several redundancy removals don't undo
1160 <li>Hide sequence doesn't hide associated annotation</li>
1161 <li>User defined colours dialog box too big to fit on
1162 screen and buttons not visible</li>
1163 <li>author list isn't updated if already written to
1164 Jalview properties</li>
1165 <li>Popup menu won't open after retrieving sequence
1167 <li>File open window for associate PDB doesn't open</li>
1168 <li>Left-then-right click on a sequence id opens a
1169 browser search window</li>
1170 <li>Cannot open sequence feature shading/sort popup menu
1171 in feature settings dialog</li>
1172 <li>better tooltip placement for some areas of Jalview
1174 <li>Allow addition of JABAWS Server which doesn't
1175 pass validation</li>
1176 <li>Web services parameters dialog box is too large to
1178 <li>Muscle nucleotide alignment preset obscured by
1180 <li>JABAWS preset submenus don't contain newly
1181 defined user preset</li>
1182 <li>MSA web services warns user if they were launched
1183 with invalid input</li>
1184 <li>Jalview cannot contact DAS Registy when running on
1187 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1188 'Superpose with' submenu not shown when new view
1192 </ul> <!-- <em>Applet</em>
1194 </ul> <em>General</em>
1196 </ul>--> <em>Deployment and Documentation</em>
1198 <li>2G and 1G options in launchApp have no effect on
1199 memory allocation</li>
1200 <li>launchApp service doesn't automatically open
1201 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1203 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1204 InstallAnywhere reports cannot find valid JVM when Java
1205 1.7_055 is available
1207 </ul> <em>Application Known issues</em>
1210 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1211 corrupted or unreadable alignment display when scrolling
1215 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1216 retrieval fails but progress bar continues for DAS retrieval
1217 with large number of ID
1220 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1221 flatfile output of visible region has incorrect sequence
1225 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1226 rna structure consensus doesn't update when secondary
1227 structure tracks are rearranged
1230 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1231 invalid rna structure positional highlighting does not
1232 highlight position of invalid base pairs
1235 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1236 out of memory errors are not raised when saving Jalview
1237 project from alignment window file menu
1240 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1241 Switching to RNA Helices colouring doesn't propagate to
1245 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1246 colour by RNA Helices not enabled when user created
1247 annotation added to alignment
1250 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1251 Jalview icon not shown on dock in Mountain Lion/Webstart
1253 </ul> <em>Applet Known Issues</em>
1256 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1257 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1260 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1261 Jalview and Jmol example not compatible with IE9
1264 <li>Sort by annotation score doesn't reverse order
1270 <td><div align="center">
1271 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1274 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1277 <li>Internationalisation of user interface (usually
1278 called i18n support) and translation for Spanish locale</li>
1279 <li>Define/Undefine group on current selection with
1280 Ctrl-G/Shift Ctrl-G</li>
1281 <li>Improved group creation/removal options in
1282 alignment/sequence Popup menu</li>
1283 <li>Sensible precision for symbol distribution
1284 percentages shown in logo tooltip.</li>
1285 <li>Annotation panel height set according to amount of
1286 annotation when alignment first opened</li>
1287 </ul> <em>Application</em>
1289 <li>Interactive consensus RNA secondary structure
1290 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1291 <li>Select columns containing particular features from
1292 Feature Settings dialog</li>
1293 <li>View all 'representative' PDB structures for selected
1295 <li>Update Jalview project format:
1297 <li>New file extension for Jalview projects '.jvp'</li>
1298 <li>Preserve sequence and annotation dataset (to
1299 store secondary structure annotation,etc)</li>
1300 <li>Per group and alignment annotation and RNA helix
1304 <li>New similarity measures for PCA and Tree calculation
1306 <li>Experimental support for retrieval and viewing of
1307 flanking regions for an alignment</li>
1311 <!-- issues resolved --> <em>Application</em>
1313 <li>logo keeps spinning and status remains at queued or
1314 running after job is cancelled</li>
1315 <li>cannot export features from alignments imported from
1316 Jalview/VAMSAS projects</li>
1317 <li>Buggy slider for web service parameters that take
1319 <li>Newly created RNA secondary structure line doesn't
1320 have 'display all symbols' flag set</li>
1321 <li>T-COFFEE alignment score shading scheme and other
1322 annotation shading not saved in Jalview project</li>
1323 <li>Local file cannot be loaded in freshly downloaded
1325 <li>Jalview icon not shown on dock in Mountain
1327 <li>Load file from desktop file browser fails</li>
1328 <li>Occasional NPE thrown when calculating large trees</li>
1329 <li>Cannot reorder or slide sequences after dragging an
1330 alignment onto desktop</li>
1331 <li>Colour by annotation dialog throws NPE after using
1332 'extract scores' function</li>
1333 <li>Loading/cut'n'pasting an empty file leads to a grey
1334 alignment window</li>
1335 <li>Disorder thresholds rendered incorrectly after
1336 performing IUPred disorder prediction</li>
1337 <li>Multiple group annotated consensus rows shown when
1338 changing 'normalise logo' display setting</li>
1339 <li>Find shows blank dialog after 'finished searching' if
1340 nothing matches query</li>
1341 <li>Null Pointer Exceptions raised when sorting by
1342 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1344 <li>Errors in Jmol console when structures in alignment
1345 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1347 <li>Not all working JABAWS services are shown in
1349 <li>JAVAWS version of Jalview fails to launch with
1350 'invalid literal/length code'</li>
1351 <li>Annotation/RNA Helix colourschemes cannot be applied
1352 to alignment with groups (actually fixed in 2.8.0b1)</li>
1353 <li>RNA Helices and T-Coffee Scores available as default
1356 </ul> <em>Applet</em>
1358 <li>Remove group option is shown even when selection is
1360 <li>Apply to all groups ticked but colourscheme changes
1361 don't affect groups</li>
1362 <li>Documented RNA Helices and T-Coffee Scores as valid
1363 colourscheme name</li>
1364 <li>Annotation labels drawn on sequence IDs when
1365 Annotation panel is not displayed</li>
1366 <li>Increased font size for dropdown menus on OSX and
1367 embedded windows</li>
1368 </ul> <em>Other</em>
1370 <li>Consensus sequence for alignments/groups with a
1371 single sequence were not calculated</li>
1372 <li>annotation files that contain only groups imported as
1373 annotation and junk sequences</li>
1374 <li>Fasta files with sequences containing '*' incorrectly
1375 recognised as PFAM or BLC</li>
1376 <li>conservation/PID slider apply all groups option
1377 doesn't affect background (2.8.0b1)
1379 <li>redundancy highlighting is erratic at 0% and 100%</li>
1380 <li>Remove gapped columns fails for sequences with ragged
1382 <li>AMSA annotation row with leading spaces is not
1383 registered correctly on import</li>
1384 <li>Jalview crashes when selecting PCA analysis for
1385 certain alignments</li>
1386 <li>Opening the colour by annotation dialog for an
1387 existing annotation based 'use original colours'
1388 colourscheme loses original colours setting</li>
1393 <td><div align="center">
1394 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
1395 <em>30/1/2014</em></strong>
1399 <li>Trusted certificates for JalviewLite applet and
1400 Jalview Desktop application<br />Certificate was donated by
1401 <a href="https://www.certum.eu">Certum</a> to the Jalview
1402 open source project).
1404 <li>Jalview SRS links replaced by UniProt and EBI-search
1406 <li>Output in Stockholm format</li>
1407 <li>Allow import of data from gzipped files</li>
1408 <li>Export/import group and sequence associated line
1409 graph thresholds</li>
1410 <li>Nucleotide substitution matrix that supports RNA and
1411 ambiguity codes</li>
1412 <li>Allow disorder predictions to be made on the current
1413 selection (or visible selection) in the same way that JPred
1415 <li>Groovy scripting for headless Jalview operation</li>
1416 </ul> <em>Other improvements</em>
1418 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
1419 <li>COMBINE statement uses current SEQUENCE_REF and
1420 GROUP_REF scope to group annotation rows</li>
1421 <li>Support '' style escaping of quotes in Newick
1423 <li>Group options for JABAWS service by command line name</li>
1424 <li>Empty tooltip shown for JABA service options with a
1425 link but no description</li>
1426 <li>Select primary source when selecting authority in
1427 database fetcher GUI</li>
1428 <li>Add .mfa to FASTA file extensions recognised by
1430 <li>Annotation label tooltip text wrap</li>
1435 <li>Slow scrolling when lots of annotation rows are
1437 <li>Lots of NPE (and slowness) after creating RNA
1438 secondary structure annotation line</li>
1439 <li>Sequence database accessions not imported when
1440 fetching alignments from Rfam</li>
1441 <li>Incorrect SHMR submission for sequences with
1443 <li>View all structures does not always superpose
1445 <li>Option widgets in service parameters not updated to
1446 reflect user or preset settings</li>
1447 <li>Null pointer exceptions for some services without
1448 presets or adjustable parameters</li>
1449 <li>Discover PDB IDs entry in structure menu doesn't
1450 discover PDB xRefs</li>
1451 <li>Exception encountered while trying to retrieve
1452 features with DAS</li>
1453 <li>Lowest value in annotation row isn't coloured
1454 when colour by annotation (per sequence) is coloured</li>
1455 <li>Keyboard mode P jumps to start of gapped region when
1456 residue follows a gap</li>
1457 <li>Jalview appears to hang importing an alignment with
1458 Wrap as default or after enabling Wrap</li>
1459 <li>'Right click to add annotations' message
1460 shown in wrap mode when no annotations present</li>
1461 <li>Disorder predictions fail with NPE if no automatic
1462 annotation already exists on alignment</li>
1463 <li>oninit javascript function should be called after
1464 initialisation completes</li>
1465 <li>Remove redundancy after disorder prediction corrupts
1466 alignment window display</li>
1467 <li>Example annotation file in documentation is invalid</li>
1468 <li>Grouped line graph annotation rows are not exported
1469 to annotation file</li>
1470 <li>Multi-harmony analysis cannot be run when only two
1472 <li>Cannot create multiple groups of line graphs with
1473 several 'combine' statements in annotation file</li>
1474 <li>Pressing return several times causes Number Format
1475 exceptions in keyboard mode</li>
1476 <li>Multi-harmony (SHMMR) method doesn't submit
1477 correct partitions for input data</li>
1478 <li>Translation from DNA to Amino Acids fails</li>
1479 <li>Jalview fail to load newick tree with quoted label</li>
1480 <li>--headless flag isn't understood</li>
1481 <li>ClassCastException when generating EPS in headless
1483 <li>Adjusting sequence-associated shading threshold only
1484 changes one row's threshold</li>
1485 <li>Preferences and Feature settings panel panel
1486 doesn't open</li>
1487 <li>hide consensus histogram also hides conservation and
1488 quality histograms</li>
1493 <td><div align="center">
1494 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
1496 <td><em>Application</em>
1498 <li>Support for JABAWS 2.0 Services (AACon alignment
1499 conservation, protein disorder and Clustal Omega)</li>
1500 <li>JABAWS server status indicator in Web Services
1502 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
1503 in Jalview alignment window</li>
1504 <li>Updated Jalview build and deploy framework for OSX
1505 mountain lion, windows 7, and 8</li>
1506 <li>Nucleotide substitution matrix for PCA that supports
1507 RNA and ambiguity codes</li>
1509 <li>Improved sequence database retrieval GUI</li>
1510 <li>Support fetching and database reference look up
1511 against multiple DAS sources (Fetch all from in 'fetch db
1513 <li>Jalview project improvements
1515 <li>Store and retrieve the 'belowAlignment'
1516 flag for annotation</li>
1517 <li>calcId attribute to group annotation rows on the
1519 <li>Store AACon calculation settings for a view in
1520 Jalview project</li>
1524 <li>horizontal scrolling gesture support</li>
1525 <li>Visual progress indicator when PCA calculation is
1527 <li>Simpler JABA web services menus</li>
1528 <li>visual indication that web service results are still
1529 being retrieved from server</li>
1530 <li>Serialise the dialogs that are shown when Jalview
1531 starts up for first time</li>
1532 <li>Jalview user agent string for interacting with HTTP
1534 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
1536 <li>Examples directory and Groovy library included in
1537 InstallAnywhere distribution</li>
1538 </ul> <em>Applet</em>
1540 <li>RNA alignment and secondary structure annotation
1541 visualization applet example</li>
1542 </ul> <em>General</em>
1544 <li>Normalise option for consensus sequence logo</li>
1545 <li>Reset button in PCA window to return dimensions to
1547 <li>Allow seqspace or Jalview variant of alignment PCA
1549 <li>PCA with either nucleic acid and protein substitution
1551 <li>Allow windows containing HTML reports to be exported
1553 <li>Interactive display and editing of RNA secondary
1554 structure contacts</li>
1555 <li>RNA Helix Alignment Colouring</li>
1556 <li>RNA base pair logo consensus</li>
1557 <li>Parse sequence associated secondary structure
1558 information in Stockholm files</li>
1559 <li>HTML Export database accessions and annotation
1560 information presented in tooltip for sequences</li>
1561 <li>Import secondary structure from LOCARNA clustalw
1562 style RNA alignment files</li>
1563 <li>import and visualise T-COFFEE quality scores for an
1565 <li>'colour by annotation' per sequence option to
1566 shade each sequence according to its associated alignment
1568 <li>New Jalview Logo</li>
1569 </ul> <em>Documentation and Development</em>
1571 <li>documentation for score matrices used in Jalview</li>
1572 <li>New Website!</li>
1574 <td><em>Application</em>
1576 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
1577 wsdbfetch REST service</li>
1578 <li>Stop windows being moved outside desktop on OSX</li>
1579 <li>Filetype associations not installed for webstart
1581 <li>Jalview does not always retrieve progress of a JABAWS
1582 job execution in full once it is complete</li>
1583 <li>revise SHMR RSBS definition to ensure alignment is
1584 uploaded via ali_file parameter</li>
1585 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
1586 <li>View all structures superposed fails with exception</li>
1587 <li>Jnet job queues forever if a very short sequence is
1588 submitted for prediction</li>
1589 <li>Cut and paste menu not opened when mouse clicked on
1591 <li>Putting fractional value into integer text box in
1592 alignment parameter dialog causes Jalview to hang</li>
1593 <li>Structure view highlighting doesn't work on
1595 <li>View all structures fails with exception shown in
1597 <li>Characters in filename associated with PDBEntry not
1598 escaped in a platform independent way</li>
1599 <li>Jalview desktop fails to launch with exception when
1601 <li>Tree calculation reports 'you must have 2 or more
1602 sequences selected' when selection is empty</li>
1603 <li>Jalview desktop fails to launch with jar signature
1604 failure when java web start temporary file caching is
1606 <li>DAS Sequence retrieval with range qualification
1607 results in sequence xref which includes range qualification</li>
1608 <li>Errors during processing of command line arguments
1609 cause progress bar (JAL-898) to be removed</li>
1610 <li>Replace comma for semi-colon option not disabled for
1611 DAS sources in sequence fetcher</li>
1612 <li>Cannot close news reader when JABAWS server warning
1613 dialog is shown</li>
1614 <li>Option widgets not updated to reflect user settings</li>
1615 <li>Edited sequence not submitted to web service</li>
1616 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
1617 <li>InstallAnywhere installer doesn't unpack and run
1618 on OSX Mountain Lion</li>
1619 <li>Annotation panel not given a scroll bar when
1620 sequences with alignment annotation are pasted into the
1622 <li>Sequence associated annotation rows not associated
1623 when loaded from Jalview project</li>
1624 <li>Browser launch fails with NPE on java 1.7</li>
1625 <li>JABAWS alignment marked as finished when job was
1626 cancelled or job failed due to invalid input</li>
1627 <li>NPE with v2.7 example when clicking on Tree
1628 associated with all views</li>
1629 <li>Exceptions when copy/paste sequences with grouped
1630 annotation rows to new window</li>
1631 </ul> <em>Applet</em>
1633 <li>Sequence features are momentarily displayed before
1634 they are hidden using hidefeaturegroups applet parameter</li>
1635 <li>loading features via javascript API automatically
1636 enables feature display</li>
1637 <li>scrollToColumnIn javascript API method doesn't
1639 </ul> <em>General</em>
1641 <li>Redundancy removal fails for rna alignment</li>
1642 <li>PCA calculation fails when sequence has been selected
1643 and then deselected</li>
1644 <li>PCA window shows grey box when first opened on OSX</li>
1645 <li>Letters coloured pink in sequence logo when alignment
1646 coloured with clustalx</li>
1647 <li>Choosing fonts without letter symbols defined causes
1648 exceptions and redraw errors</li>
1649 <li>Initial PCA plot view is not same as manually
1650 reconfigured view</li>
1651 <li>Grouped annotation graph label has incorrect line
1653 <li>Grouped annotation graph label display is corrupted
1654 for lots of labels</li>
1659 <div align="center">
1660 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
1663 <td><em>Application</em>
1665 <li>Jalview Desktop News Reader</li>
1666 <li>Tweaked default layout of web services menu</li>
1667 <li>View/alignment association menu to enable user to
1668 easily specify which alignment a multi-structure view takes
1669 its colours/correspondences from</li>
1670 <li>Allow properties file location to be specified as URL</li>
1671 <li>Extend Jalview project to preserve associations
1672 between many alignment views and a single Jmol display</li>
1673 <li>Store annotation row height in Jalview project file</li>
1674 <li>Annotation row column label formatting attributes
1675 stored in project file</li>
1676 <li>Annotation row order for auto-calculated annotation
1677 rows preserved in Jalview project file</li>
1678 <li>Visual progress indication when Jalview state is
1679 saved using Desktop window menu</li>
1680 <li>Visual indication that command line arguments are
1681 still being processed</li>
1682 <li>Groovy script execution from URL</li>
1683 <li>Colour by annotation default min and max colours in
1685 <li>Automatically associate PDB files dragged onto an
1686 alignment with sequences that have high similarity and
1688 <li>Update JGoogleAnalytics to latest release (0.3)</li>
1689 <li>'view structures' option to open many
1690 structures in same window</li>
1691 <li>Sort associated views menu option for tree panel</li>
1692 <li>Group all JABA and non-JABA services for a particular
1693 analysis function in its own submenu</li>
1694 </ul> <em>Applet</em>
1696 <li>Userdefined and autogenerated annotation rows for
1698 <li>Adjustment of alignment annotation pane height</li>
1699 <li>Annotation scrollbar for annotation panel</li>
1700 <li>Drag to reorder annotation rows in annotation panel</li>
1701 <li>'automaticScrolling' parameter</li>
1702 <li>Allow sequences with partial ID string matches to be
1703 annotated from GFF/Jalview features files</li>
1704 <li>Sequence logo annotation row in applet</li>
1705 <li>Absolute paths relative to host server in applet
1706 parameters are treated as such</li>
1707 <li>New in the JalviewLite javascript API:
1709 <li>JalviewLite.js javascript library</li>
1710 <li>Javascript callbacks for
1712 <li>Applet initialisation</li>
1713 <li>Sequence/alignment mouse-overs and selections</li>
1716 <li>scrollTo row and column alignment scrolling
1718 <li>Select sequence/alignment regions from javascript</li>
1719 <li>javascript structure viewer harness to pass
1720 messages between Jmol and Jalview when running as
1721 distinct applets</li>
1722 <li>sortBy method</li>
1723 <li>Set of applet and application examples shipped
1724 with documentation</li>
1725 <li>New example to demonstrate JalviewLite and Jmol
1726 javascript message exchange</li>
1728 </ul> <em>General</em>
1730 <li>Enable Jmol displays to be associated with multiple
1731 multiple alignments</li>
1732 <li>Option to automatically sort alignment with new tree</li>
1733 <li>User configurable link to enable redirects to a
1734 www.Jalview.org mirror</li>
1735 <li>Jmol colours option for Jmol displays</li>
1736 <li>Configurable newline string when writing alignment
1737 and other flat files</li>
1738 <li>Allow alignment annotation description lines to
1739 contain html tags</li>
1740 </ul> <em>Documentation and Development</em>
1742 <li>Add groovy test harness for bulk load testing to
1744 <li>Groovy script to load and align a set of sequences
1745 using a web service before displaying the result in the
1746 Jalview desktop</li>
1747 <li>Restructured javascript and applet api documentation</li>
1748 <li>Ant target to publish example html files with applet
1750 <li>Netbeans project for building Jalview from source</li>
1751 <li>ant task to create online javadoc for Jalview source</li>
1753 <td><em>Application</em>
1755 <li>User defined colourscheme throws exception when
1756 current built in colourscheme is saved as new scheme</li>
1757 <li>AlignFrame->Save in application pops up save
1758 dialog for valid filename/format</li>
1759 <li>Cannot view associated structure for UniProt sequence</li>
1760 <li>PDB file association breaks for UniProt sequence
1762 <li>Associate PDB from file dialog does not tell you
1763 which sequence is to be associated with the file</li>
1764 <li>Find All raises null pointer exception when query
1765 only matches sequence IDs</li>
1766 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
1767 <li>Jalview project with Jmol views created with Jalview
1768 2.4 cannot be loaded</li>
1769 <li>Filetype associations not installed for webstart
1771 <li>Two or more chains in a single PDB file associated
1772 with sequences in different alignments do not get coloured
1773 by their associated sequence</li>
1774 <li>Visibility status of autocalculated annotation row
1775 not preserved when project is loaded</li>
1776 <li>Annotation row height and visibility attributes not
1777 stored in Jalview project</li>
1778 <li>Tree bootstraps are not preserved when saved as a
1779 Jalview project</li>
1780 <li>Envision2 workflow tooltips are corrupted</li>
1781 <li>Enabling show group conservation also enables colour
1782 by conservation</li>
1783 <li>Duplicate group associated conservation or consensus
1784 created on new view</li>
1785 <li>Annotation scrollbar not displayed after 'show
1786 all hidden annotation rows' option selected</li>
1787 <li>Alignment quality not updated after alignment
1788 annotation row is hidden then shown</li>
1789 <li>Preserve colouring of structures coloured by
1790 sequences in pre Jalview 2.7 projects</li>
1791 <li>Web service job parameter dialog is not laid out
1793 <li>Web services menu not refreshed after 'reset
1794 services' button is pressed in preferences</li>
1795 <li>Annotation off by one in Jalview v2_3 example project</li>
1796 <li>Structures imported from file and saved in project
1797 get name like jalview_pdb1234.txt when reloaded</li>
1798 <li>Jalview does not always retrieve progress of a JABAWS
1799 job execution in full once it is complete</li>
1800 </ul> <em>Applet</em>
1802 <li>Alignment height set incorrectly when lots of
1803 annotation rows are displayed</li>
1804 <li>Relative URLs in feature HTML text not resolved to
1806 <li>View follows highlighting does not work for positions
1808 <li><= shown as = in tooltip</li>
1809 <li>Export features raises exception when no features
1811 <li>Separator string used for serialising lists of IDs
1812 for javascript api is modified when separator string
1813 provided as parameter</li>
1814 <li>Null pointer exception when selecting tree leaves for
1815 alignment with no existing selection</li>
1816 <li>Relative URLs for datasources assumed to be relative
1817 to applet's codebase</li>
1818 <li>Status bar not updated after finished searching and
1819 search wraps around to first result</li>
1820 <li>StructureSelectionManager instance shared between
1821 several Jalview applets causes race conditions and memory
1823 <li>Hover tooltip and mouseover of position on structure
1824 not sent from Jmol in applet</li>
1825 <li>Certain sequences of javascript method calls to
1826 applet API fatally hang browser</li>
1827 </ul> <em>General</em>
1829 <li>View follows structure mouseover scrolls beyond
1830 position with wrapped view and hidden regions</li>
1831 <li>Find sequence position moves to wrong residue
1832 with/without hidden columns</li>
1833 <li>Sequence length given in alignment properties window
1835 <li>InvalidNumberFormat exceptions thrown when trying to
1836 import PDB like structure files</li>
1837 <li>Positional search results are only highlighted
1838 between user-supplied sequence start/end bounds</li>
1839 <li>End attribute of sequence is not validated</li>
1840 <li>Find dialog only finds first sequence containing a
1841 given sequence position</li>
1842 <li>Sequence numbering not preserved in MSF alignment
1844 <li>Jalview PDB file reader does not extract sequence
1845 from nucleotide chains correctly</li>
1846 <li>Structure colours not updated when tree partition
1847 changed in alignment</li>
1848 <li>Sequence associated secondary structure not correctly
1849 parsed in interleaved stockholm</li>
1850 <li>Colour by annotation dialog does not restore current
1852 <li>Hiding (nearly) all sequences doesn't work
1854 <li>Sequences containing lowercase letters are not
1855 properly associated with their pdb files</li>
1856 </ul> <em>Documentation and Development</em>
1858 <li>schemas/JalviewWsParamSet.xsd corrupted by
1859 ApplyCopyright tool</li>
1864 <div align="center">
1865 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
1868 <td><em>Application</em>
1870 <li>New warning dialog when the Jalview Desktop cannot
1871 contact web services</li>
1872 <li>JABA service parameters for a preset are shown in
1873 service job window</li>
1874 <li>JABA Service menu entries reworded</li>
1878 <li>Modeller PIR IO broken - cannot correctly import a
1879 pir file emitted by Jalview</li>
1880 <li>Existing feature settings transferred to new
1881 alignment view created from cut'n'paste</li>
1882 <li>Improved test for mixed amino/nucleotide chains when
1883 parsing PDB files</li>
1884 <li>Consensus and conservation annotation rows
1885 occasionally become blank for all new windows</li>
1886 <li>Exception raised when right clicking above sequences
1887 in wrapped view mode</li>
1888 </ul> <em>Application</em>
1890 <li>multiple multiply aligned structure views cause cpu
1891 usage to hit 100% and computer to hang</li>
1892 <li>Web Service parameter layout breaks for long user
1893 parameter names</li>
1894 <li>Jaba service discovery hangs desktop if Jaba server
1901 <div align="center">
1902 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
1905 <td><em>Application</em>
1907 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
1908 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
1911 <li>Web Services preference tab</li>
1912 <li>Analysis parameters dialog box and user defined
1914 <li>Improved speed and layout of Envision2 service menu</li>
1915 <li>Superpose structures using associated sequence
1917 <li>Export coordinates and projection as CSV from PCA
1919 </ul> <em>Applet</em>
1921 <li>enable javascript: execution by the applet via the
1922 link out mechanism</li>
1923 </ul> <em>Other</em>
1925 <li>Updated the Jmol Jalview interface to work with Jmol
1927 <li>The Jalview Desktop and JalviewLite applet now
1928 require Java 1.5</li>
1929 <li>Allow Jalview feature colour specification for GFF
1930 sequence annotation files</li>
1931 <li>New 'colour by label' keword in Jalview feature file
1932 type colour specification</li>
1933 <li>New Jalview Desktop Groovy API method that allows a
1934 script to check if it being run in an interactive session or
1935 in a batch operation from the Jalview command line</li>
1939 <li>clustalx colourscheme colours Ds preferentially when
1940 both D+E are present in over 50% of the column</li>
1941 </ul> <em>Application</em>
1943 <li>typo in AlignmentFrame->View->Hide->all but
1944 selected Regions menu item</li>
1945 <li>sequence fetcher replaces ',' for ';' when the ',' is
1946 part of a valid accession ID</li>
1947 <li>fatal OOM if object retrieved by sequence fetcher
1948 runs out of memory</li>
1949 <li>unhandled Out of Memory Error when viewing pca
1950 analysis results</li>
1951 <li>InstallAnywhere builds fail to launch on OS X java
1952 10.5 update 4 (due to apple Java 1.6 update)</li>
1953 <li>Installanywhere Jalview silently fails to launch</li>
1954 </ul> <em>Applet</em>
1956 <li>Jalview.getFeatureGroups() raises an
1957 ArrayIndexOutOfBoundsException if no feature groups are
1964 <div align="center">
1965 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
1971 <li>Alignment prettyprinter doesn't cope with long
1973 <li>clustalx colourscheme colours Ds preferentially when
1974 both D+E are present in over 50% of the column</li>
1975 <li>nucleic acid structures retrieved from PDB do not
1976 import correctly</li>
1977 <li>More columns get selected than were clicked on when a
1978 number of columns are hidden</li>
1979 <li>annotation label popup menu not providing correct
1980 add/hide/show options when rows are hidden or none are
1982 <li>Stockholm format shown in list of readable formats,
1983 and parser copes better with alignments from RFAM.</li>
1984 <li>CSV output of consensus only includes the percentage
1985 of all symbols if sequence logo display is enabled</li>
1987 </ul> <em>Applet</em>
1989 <li>annotation panel disappears when annotation is
1991 </ul> <em>Application</em>
1993 <li>Alignment view not redrawn properly when new
1994 alignment opened where annotation panel is visible but no
1995 annotations are present on alignment</li>
1996 <li>pasted region containing hidden columns is
1997 incorrectly displayed in new alignment window</li>
1998 <li>Jalview slow to complete operations when stdout is
1999 flooded (fix is to close the Jalview console)</li>
2000 <li>typo in AlignmentFrame->View->Hide->all but
2001 selected Rregions menu item.</li>
2002 <li>inconsistent group submenu and Format submenu entry
2003 'Un' or 'Non'conserved</li>
2004 <li>Sequence feature settings are being shared by
2005 multiple distinct alignments</li>
2006 <li>group annotation not recreated when tree partition is
2008 <li>double click on group annotation to select sequences
2009 does not propagate to associated trees</li>
2010 <li>Mac OSX specific issues:
2012 <li>exception raised when mouse clicked on desktop
2013 window background</li>
2014 <li>Desktop menu placed on menu bar and application
2015 name set correctly</li>
2016 <li>sequence feature settings not wide enough for the
2017 save feature colourscheme button</li>
2026 <div align="center">
2027 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2030 <td><em>New Capabilities</em>
2032 <li>URL links generated from description line for
2033 regular-expression based URL links (applet and application)
2040 <li>Non-positional feature URL links are shown in link
2042 <li>Linked viewing of nucleic acid sequences and
2044 <li>Automatic Scrolling option in View menu to display
2045 the currently highlighted region of an alignment.</li>
2046 <li>Order an alignment by sequence length, or using the
2047 average score or total feature count for each sequence.</li>
2048 <li>Shading features by score or associated description</li>
2049 <li>Subdivide alignment and groups based on identity of
2050 selected subsequence (Make Groups from Selection).</li>
2051 <li>New hide/show options including Shift+Control+H to
2052 hide everything but the currently selected region.</li>
2053 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2054 </ul> <em>Application</em>
2056 <li>Fetch DB References capabilities and UI expanded to
2057 support retrieval from DAS sequence sources</li>
2058 <li>Local DAS Sequence sources can be added via the
2059 command line or via the Add local source dialog box.</li>
2060 <li>DAS Dbref and DbxRef feature types are parsed as
2061 database references and protein_name is parsed as
2062 description line (BioSapiens terms).</li>
2063 <li>Enable or disable non-positional feature and database
2064 references in sequence ID tooltip from View menu in
2066 <!-- <li>New hidden columns and rows and representatives capabilities
2067 in annotations file (in progress - not yet fully implemented)</li> -->
2068 <li>Group-associated consensus, sequence logos and
2069 conservation plots</li>
2070 <li>Symbol distributions for each column can be exported
2071 and visualized as sequence logos</li>
2072 <li>Optionally scale multi-character column labels to fit
2073 within each column of annotation row<!-- todo for applet -->
2075 <li>Optional automatic sort of associated alignment view
2076 when a new tree is opened.</li>
2077 <li>Jalview Java Console</li>
2078 <li>Better placement of desktop window when moving
2079 between different screens.</li>
2080 <li>New preference items for sequence ID tooltip and
2081 consensus annotation</li>
2082 <li>Client to submit sequences and IDs to Envision2
2084 <li><em>Vamsas Capabilities</em>
2086 <li>Improved VAMSAS synchronization (Jalview archive
2087 used to preserve views, structures, and tree display
2089 <li>Import of vamsas documents from disk or URL via
2091 <li>Sharing of selected regions between views and
2092 with other VAMSAS applications (Experimental feature!)</li>
2093 <li>Updated API to VAMSAS version 0.2</li>
2095 </ul> <em>Applet</em>
2097 <li>Middle button resizes annotation row height</li>
2100 <li>sortByTree (true/false) - automatically sort the
2101 associated alignment view by the tree when a new tree is
2103 <li>showTreeBootstraps (true/false) - show or hide
2104 branch bootstraps (default is to show them if available)</li>
2105 <li>showTreeDistances (true/false) - show or hide
2106 branch lengths (default is to show them if available)</li>
2107 <li>showUnlinkedTreeNodes (true/false) - indicate if
2108 unassociated nodes should be highlighted in the tree
2110 <li>heightScale and widthScale (1.0 or more) -
2111 increase the height or width of a cell in the alignment
2112 grid relative to the current font size.</li>
2115 <li>Non-positional features displayed in sequence ID
2117 </ul> <em>Other</em>
2119 <li>Features format: graduated colour definitions and
2120 specification of feature scores</li>
2121 <li>Alignment Annotations format: new keywords for group
2122 associated annotation (GROUP_REF) and annotation row display
2123 properties (ROW_PROPERTIES)</li>
2124 <li>XML formats extended to support graduated feature
2125 colourschemes, group associated annotation, and profile
2126 visualization settings.</li></td>
2129 <li>Source field in GFF files parsed as feature source
2130 rather than description</li>
2131 <li>Non-positional features are now included in sequence
2132 feature and gff files (controlled via non-positional feature
2133 visibility in tooltip).</li>
2134 <li>URL links generated for all feature links (bugfix)</li>
2135 <li>Added URL embedding instructions to features file
2137 <li>Codons containing ambiguous nucleotides translated as
2138 'X' in peptide product</li>
2139 <li>Match case switch in find dialog box works for both
2140 sequence ID and sequence string and query strings do not
2141 have to be in upper case to match case-insensitively.</li>
2142 <li>AMSA files only contain first column of
2143 multi-character column annotation labels</li>
2144 <li>Jalview Annotation File generation/parsing consistent
2145 with documentation (e.g. Stockholm annotation can be
2146 exported and re-imported)</li>
2147 <li>PDB files without embedded PDB IDs given a friendly
2149 <li>Find incrementally searches ID string matches as well
2150 as subsequence matches, and correctly reports total number
2154 <li>Better handling of exceptions during sequence
2156 <li>Dasobert generated non-positional feature URL
2157 link text excludes the start_end suffix</li>
2158 <li>DAS feature and source retrieval buttons disabled
2159 when fetch or registry operations in progress.</li>
2160 <li>PDB files retrieved from URLs are cached properly</li>
2161 <li>Sequence description lines properly shared via
2163 <li>Sequence fetcher fetches multiple records for all
2165 <li>Ensured that command line das feature retrieval
2166 completes before alignment figures are generated.</li>
2167 <li>Reduced time taken when opening file browser for
2169 <li>isAligned check prior to calculating tree, PCA or
2170 submitting an MSA to JNet now excludes hidden sequences.</li>
2171 <li>User defined group colours properly recovered
2172 from Jalview projects.</li>
2181 <div align="center">
2182 <strong>2.4.0.b2</strong><br> 28/10/2009
2187 <li>Experimental support for google analytics usage
2189 <li>Jalview privacy settings (user preferences and docs).</li>
2194 <li>Race condition in applet preventing startup in
2196 <li>Exception when feature created from selection beyond
2197 length of sequence.</li>
2198 <li>Allow synthetic PDB files to be imported gracefully</li>
2199 <li>Sequence associated annotation rows associate with
2200 all sequences with a given id</li>
2201 <li>Find function matches case-insensitively for sequence
2202 ID string searches</li>
2203 <li>Non-standard characters do not cause pairwise
2204 alignment to fail with exception</li>
2205 </ul> <em>Application Issues</em>
2207 <li>Sequences are now validated against EMBL database</li>
2208 <li>Sequence fetcher fetches multiple records for all
2210 </ul> <em>InstallAnywhere Issues</em>
2212 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2213 issue with installAnywhere mechanism)</li>
2214 <li>Command line launching of JARs from InstallAnywhere
2215 version (java class versioning error fixed)</li>
2222 <div align="center">
2223 <strong>2.4</strong><br> 27/8/2008
2226 <td><em>User Interface</em>
2228 <li>Linked highlighting of codon and amino acid from
2229 translation and protein products</li>
2230 <li>Linked highlighting of structure associated with
2231 residue mapping to codon position</li>
2232 <li>Sequence Fetcher provides example accession numbers
2233 and 'clear' button</li>
2234 <li>MemoryMonitor added as an option under Desktop's
2236 <li>Extract score function to parse whitespace separated
2237 numeric data in description line</li>
2238 <li>Column labels in alignment annotation can be centred.</li>
2239 <li>Tooltip for sequence associated annotation give name
2241 </ul> <em>Web Services and URL fetching</em>
2243 <li>JPred3 web service</li>
2244 <li>Prototype sequence search client (no public services
2246 <li>Fetch either seed alignment or full alignment from
2248 <li>URL Links created for matching database cross
2249 references as well as sequence ID</li>
2250 <li>URL Links can be created using regular-expressions</li>
2251 </ul> <em>Sequence Database Connectivity</em>
2253 <li>Retrieval of cross-referenced sequences from other
2255 <li>Generalised database reference retrieval and
2256 validation to all fetchable databases</li>
2257 <li>Fetch sequences from DAS sources supporting the
2258 sequence command</li>
2259 </ul> <em>Import and Export</em>
2260 <li>export annotation rows as CSV for spreadsheet import</li>
2261 <li>Jalview projects record alignment dataset associations,
2262 EMBL products, and cDNA sequence mappings</li>
2263 <li>Sequence Group colour can be specified in Annotation
2265 <li>Ad-hoc colouring of group in Annotation File using RGB
2266 triplet as name of colourscheme</li>
2267 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2269 <li>treenode binding for VAMSAS tree exchange</li>
2270 <li>local editing and update of sequences in VAMSAS
2271 alignments (experimental)</li>
2272 <li>Create new or select existing session to join</li>
2273 <li>load and save of vamsas documents</li>
2274 </ul> <em>Application command line</em>
2276 <li>-tree parameter to open trees (introduced for passing
2278 <li>-fetchfrom command line argument to specify nicknames
2279 of DAS servers to query for alignment features</li>
2280 <li>-dasserver command line argument to add new servers
2281 that are also automatically queried for features</li>
2282 <li>-groovy command line argument executes a given groovy
2283 script after all input data has been loaded and parsed</li>
2284 </ul> <em>Applet-Application data exchange</em>
2286 <li>Trees passed as applet parameters can be passed to
2287 application (when using "View in full
2288 application")</li>
2289 </ul> <em>Applet Parameters</em>
2291 <li>feature group display control parameter</li>
2292 <li>debug parameter</li>
2293 <li>showbutton parameter</li>
2294 </ul> <em>Applet API methods</em>
2296 <li>newView public method</li>
2297 <li>Window (current view) specific get/set public methods</li>
2298 <li>Feature display control methods</li>
2299 <li>get list of currently selected sequences</li>
2300 </ul> <em>New Jalview distribution features</em>
2302 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2303 <li>RELEASE file gives build properties for the latest
2304 Jalview release.</li>
2305 <li>Java 1.1 Applet build made easier and donotobfuscate
2306 property controls execution of obfuscator</li>
2307 <li>Build target for generating source distribution</li>
2308 <li>Debug flag for javacc</li>
2309 <li>.jalview_properties file is documented (slightly) in
2310 jalview.bin.Cache</li>
2311 <li>Continuous Build Integration for stable and
2312 development version of Application, Applet and source
2317 <li>selected region output includes visible annotations
2318 (for certain formats)</li>
2319 <li>edit label/displaychar contains existing label/char
2321 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2322 <li>shorter peptide product names from EMBL records</li>
2323 <li>Newick string generator makes compact representations</li>
2324 <li>bootstrap values parsed correctly for tree files with
2326 <li>pathological filechooser bug avoided by not allowing
2327 filenames containing a ':'</li>
2328 <li>Fixed exception when parsing GFF files containing
2329 global sequence features</li>
2330 <li>Alignment datasets are finalized only when number of
2331 references from alignment sequences goes to zero</li>
2332 <li>Close of tree branch colour box without colour
2333 selection causes cascading exceptions</li>
2334 <li>occasional negative imgwidth exceptions</li>
2335 <li>better reporting of non-fatal warnings to user when
2336 file parsing fails.</li>
2337 <li>Save works when Jalview project is default format</li>
2338 <li>Save as dialog opened if current alignment format is
2339 not a valid output format</li>
2340 <li>UniProt canonical names introduced for both das and
2342 <li>Histidine should be midblue (not pink!) in Zappo</li>
2343 <li>error messages passed up and output when data read
2345 <li>edit undo recovers previous dataset sequence when
2346 sequence is edited</li>
2347 <li>allow PDB files without pdb ID HEADER lines (like
2348 those generated by MODELLER) to be read in properly</li>
2349 <li>allow reading of JPred concise files as a normal
2351 <li>Stockholm annotation parsing and alignment properties
2352 import fixed for PFAM records</li>
2353 <li>Structure view windows have correct name in Desktop
2355 <li>annotation consisting of sequence associated scores
2356 can be read and written correctly to annotation file</li>
2357 <li>Aligned cDNA translation to aligned peptide works
2359 <li>Fixed display of hidden sequence markers and
2360 non-italic font for representatives in Applet</li>
2361 <li>Applet Menus are always embedded in applet window on
2363 <li>Newly shown features appear at top of stack (in
2365 <li>Annotations added via parameter not drawn properly
2366 due to null pointer exceptions</li>
2367 <li>Secondary structure lines are drawn starting from
2368 first column of alignment</li>
2369 <li>UniProt XML import updated for new schema release in
2371 <li>Sequence feature to sequence ID match for Features
2372 file is case-insensitive</li>
2373 <li>Sequence features read from Features file appended to
2374 all sequences with matching IDs</li>
2375 <li>PDB structure coloured correctly for associated views
2376 containing a sub-sequence</li>
2377 <li>PDB files can be retrieved by applet from Jar files</li>
2378 <li>feature and annotation file applet parameters
2379 referring to different directories are retrieved correctly</li>
2380 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
2381 <li>Fixed application hang whilst waiting for
2382 splash-screen version check to complete</li>
2383 <li>Applet properly URLencodes input parameter values
2384 when passing them to the launchApp service</li>
2385 <li>display name and local features preserved in results
2386 retrieved from web service</li>
2387 <li>Visual delay indication for sequence retrieval and
2388 sequence fetcher initialisation</li>
2389 <li>updated Application to use DAS 1.53e version of
2390 dasobert DAS client</li>
2391 <li>Re-instated Full AMSA support and .amsa file
2393 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
2401 <div align="center">
2402 <strong>2.3</strong><br> 9/5/07
2407 <li>Jmol 11.0.2 integration</li>
2408 <li>PDB views stored in Jalview XML files</li>
2409 <li>Slide sequences</li>
2410 <li>Edit sequence in place</li>
2411 <li>EMBL CDS features</li>
2412 <li>DAS Feature mapping</li>
2413 <li>Feature ordering</li>
2414 <li>Alignment Properties</li>
2415 <li>Annotation Scores</li>
2416 <li>Sort by scores</li>
2417 <li>Feature/annotation editing in applet</li>
2422 <li>Headless state operation in 2.2.1</li>
2423 <li>Incorrect and unstable DNA pairwise alignment</li>
2424 <li>Cut and paste of sequences with annotation</li>
2425 <li>Feature group display state in XML</li>
2426 <li>Feature ordering in XML</li>
2427 <li>blc file iteration selection using filename # suffix</li>
2428 <li>Stockholm alignment properties</li>
2429 <li>Stockhom alignment secondary structure annotation</li>
2430 <li>2.2.1 applet had no feature transparency</li>
2431 <li>Number pad keys can be used in cursor mode</li>
2432 <li>Structure Viewer mirror image resolved</li>
2439 <div align="center">
2440 <strong>2.2.1</strong><br> 12/2/07
2445 <li>Non standard characters can be read and displayed
2446 <li>Annotations/Features can be imported/exported to the
2448 <li>Applet allows editing of sequence/annotation/group
2449 name & description
2450 <li>Preference setting to display sequence name in
2452 <li>Annotation file format extended to allow
2453 Sequence_groups to be defined
2454 <li>Default opening of alignment overview panel can be
2455 specified in preferences
2456 <li>PDB residue numbering annotation added to associated
2462 <li>Applet crash under certain Linux OS with Java 1.6
2464 <li>Annotation file export / import bugs fixed
2465 <li>PNG / EPS image output bugs fixed
2471 <div align="center">
2472 <strong>2.2</strong><br> 27/11/06
2477 <li>Multiple views on alignment
2478 <li>Sequence feature editing
2479 <li>"Reload" alignment
2480 <li>"Save" to current filename
2481 <li>Background dependent text colour
2482 <li>Right align sequence ids
2483 <li>User-defined lower case residue colours
2486 <li>Menu item accelerator keys
2487 <li>Control-V pastes to current alignment
2488 <li>Cancel button for DAS Feature Fetching
2489 <li>PCA and PDB Viewers zoom via mouse roller
2490 <li>User-defined sub-tree colours and sub-tree selection
2497 <li>'New Window' button on the 'Output to Text box'
2502 <li>New memory efficient Undo/Redo System
2503 <li>Optimised symbol lookups and conservation/consensus
2505 <li>Region Conservation/Consensus recalculated after
2507 <li>Fixed Remove Empty Columns Bug (empty columns at end
2509 <li>Slowed DAS Feature Fetching for increased robustness.
2516 <li>Made angle brackets in ASCII feature descriptions
2518 <li>Re-instated Zoom function for PCA
2519 <li>Sequence descriptions conserved in web service
2521 <li>UniProt ID discoverer uses any word separated by
2523 <li>WsDbFetch query/result association resolved
2524 <li>Tree leaf to sequence mapping improved
2525 <li>Smooth fonts switch moved to FontChooser dialog box.
2537 <div align="center">
2538 <strong>2.1.1</strong><br> 12/9/06
2543 <li>Copy consensus sequence to clipboard</li>
2548 <li>Image output - rightmost residues are rendered if
2549 sequence id panel has been resized</li>
2550 <li>Image output - all offscreen group boundaries are
2552 <li>Annotation files with sequence references - all
2553 elements in file are relative to sequence position</li>
2554 <li>Mac Applet users can use Alt key for group editing</li>
2560 <div align="center">
2561 <strong>2.1</strong><br> 22/8/06
2566 <li>MAFFT Multiple Alignment in default Web Service list</li>
2567 <li>DAS Feature fetching</li>
2568 <li>Hide sequences and columns</li>
2569 <li>Export Annotations and Features</li>
2570 <li>GFF file reading / writing</li>
2571 <li>Associate structures with sequences from local PDB
2573 <li>Add sequences to exisiting alignment</li>
2574 <li>Recently opened files / URL lists</li>
2575 <li>Applet can launch the full application</li>
2576 <li>Applet has transparency for features (Java 1.2
2578 <li>Applet has user defined colours parameter</li>
2579 <li>Applet can load sequences from parameter
2580 "sequence<em>x</em>"
2586 <li>Redundancy Panel reinstalled in the Applet</li>
2587 <li>Monospaced font - EPS / rescaling bug fixed</li>
2588 <li>Annotation files with sequence references bug fixed</li>
2594 <div align="center">
2595 <strong>2.08.1</strong><br> 2/5/06
2600 <li>Change case of selected region from Popup menu</li>
2601 <li>Choose to match case when searching</li>
2602 <li>Middle mouse button and mouse movement can compress /
2603 expand the visible width and height of the alignment</li>
2608 <li>Annotation Panel displays complete JNet results</li>
2614 <div align="center">
2615 <strong>2.08b</strong><br> 18/4/06
2621 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
2622 <li>Righthand label on wrapped alignments shows correct
2629 <div align="center">
2630 <strong>2.08</strong><br> 10/4/06
2635 <li>Editing can be locked to the selection area</li>
2636 <li>Keyboard editing</li>
2637 <li>Create sequence features from searches</li>
2638 <li>Precalculated annotations can be loaded onto
2640 <li>Features file allows grouping of features</li>
2641 <li>Annotation Colouring scheme added</li>
2642 <li>Smooth fonts off by default - Faster rendering</li>
2643 <li>Choose to toggle Autocalculate Consensus On/Off</li>
2648 <li>Drag & Drop fixed on Linux</li>
2649 <li>Jalview Archive file faster to load/save, sequence
2650 descriptions saved.</li>
2656 <div align="center">
2657 <strong>2.07</strong><br> 12/12/05
2662 <li>PDB Structure Viewer enhanced</li>
2663 <li>Sequence Feature retrieval and display enhanced</li>
2664 <li>Choose to output sequence start-end after sequence
2665 name for file output</li>
2666 <li>Sequence Fetcher WSDBFetch@EBI</li>
2667 <li>Applet can read feature files, PDB files and can be
2668 used for HTML form input</li>
2673 <li>HTML output writes groups and features</li>
2674 <li>Group editing is Control and mouse click</li>
2675 <li>File IO bugs</li>
2681 <div align="center">
2682 <strong>2.06</strong><br> 28/9/05
2687 <li>View annotations in wrapped mode</li>
2688 <li>More options for PCA viewer</li>
2693 <li>GUI bugs resolved</li>
2694 <li>Runs with -nodisplay from command line</li>
2700 <div align="center">
2701 <strong>2.05b</strong><br> 15/9/05
2706 <li>Choose EPS export as lineart or text</li>
2707 <li>Jar files are executable</li>
2708 <li>Can read in Uracil - maps to unknown residue</li>
2713 <li>Known OutOfMemory errors give warning message</li>
2714 <li>Overview window calculated more efficiently</li>
2715 <li>Several GUI bugs resolved</li>
2721 <div align="center">
2722 <strong>2.05</strong><br> 30/8/05
2727 <li>Edit and annotate in "Wrapped" view</li>
2732 <li>Several GUI bugs resolved</li>
2738 <div align="center">
2739 <strong>2.04</strong><br> 24/8/05
2744 <li>Hold down mouse wheel & scroll to change font
2750 <li>Improved JPred client reliability</li>
2751 <li>Improved loading of Jalview files</li>
2757 <div align="center">
2758 <strong>2.03</strong><br> 18/8/05
2763 <li>Set Proxy server name and port in preferences</li>
2764 <li>Multiple URL links from sequence ids</li>
2765 <li>User Defined Colours can have a scheme name and added
2767 <li>Choose to ignore gaps in consensus calculation</li>
2768 <li>Unix users can set default web browser</li>
2769 <li>Runs without GUI for batch processing</li>
2770 <li>Dynamically generated Web Service Menus</li>
2775 <li>InstallAnywhere download for Sparc Solaris</li>
2781 <div align="center">
2782 <strong>2.02</strong><br> 18/7/05
2788 <li>Copy & Paste order of sequences maintains
2789 alignment order.</li>
2795 <div align="center">
2796 <strong>2.01</strong><br> 12/7/05
2801 <li>Use delete key for deleting selection.</li>
2802 <li>Use Mouse wheel to scroll sequences.</li>
2803 <li>Help file updated to describe how to add alignment
2805 <li>Version and build date written to build properties
2807 <li>InstallAnywhere installation will check for updates
2808 at launch of Jalview.</li>
2813 <li>Delete gaps bug fixed.</li>
2814 <li>FileChooser sorts columns.</li>
2815 <li>Can remove groups one by one.</li>
2816 <li>Filechooser icons installed.</li>
2817 <li>Finder ignores return character when searching.
2818 Return key will initiate a search.<br>
2825 <div align="center">
2826 <strong>2.0</strong><br> 20/6/05
2831 <li>New codebase</li>