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>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
34 /* separate the items from eachother */
40 /* doesnt get processed in javahelp */
50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.1">2.10.1</a><br />
74 <em>29/11/2016</em></strong>
77 <td><div align="left">
81 <!-- JAL-98 -->Improved memory usage: sparse arrays used
82 for all consensus calculations
85 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released 3rd Oct 2016)
87 <li>Updated Jalview's Certum code signing certificate
93 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
94 set of database cross-references, sorted alphabetically
97 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
98 from database cross references. Users with custom links
99 will receive a <a href="webServices/urllinks.html#warning">warning
100 dialog</a> asking them to update their preferences.
103 <!-- JAL-2287-->Cancel button and escape listener on
104 dialog warning user about disconnecting Jalview from a
108 <!-- JAL-2320-->Jalview's Chimera control window closes if
109 the Chimera it is connected to is shut down
112 <!-- JAL-1738-->New keystroke (B) and Select highlighted
113 columns menu item to mark columns containing
114 highlighted regions (e.g. from structure selections or results
118 <!-- JAL-2284-->Command line option for batch-generation
119 of HTML pages rendering alignment data with the BioJS
129 <!-- JAL-2286 -->Columns with more than one modal residue
130 are not coloured or thresholded according to percent
131 identity (first observed in Jalview 2.8.2)
134 <!-- JAL-2301 -->Threonine incorrectly reported as not
138 <!-- JAL-2318 -->Updates to documentation pages (above PID
139 threshold, amino acid properties)
142 <!-- JAL-2292 -->Lower case residues in sequences are not
143 reported as mapped to residues in a structure file in the
147 <!--JAL-2324 -->Identical features with non-numeric scores
148 could be added multiple times to a sequence
151 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
152 bond features shown as two highlighted residues rather
153 than a range in linked structure views, and treated
154 correctly when selecting and computing trees from features
157 <!-- JAL-2281-->Custom URL links for database
158 cross-references are matched to database name regardless
166 <!-- JAL-2282-->Custom URL links for specific database
167 names without regular expressions also offer links from
171 <!-- JAL-2315-->Removing a single configured link in the
172 URL links pane in Connections preferences doesn't actually
173 update Jalview configuration
176 <!-- JAL-2272-->CTRL-Click on a selected region to open
177 the alignment area popup menu doesn't work on El-Capitan
180 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
181 files with similarly named sequences if dropped onto the
185 <!-- JAL-2312 -->Additional mappings are shown for PDB
186 entries where more chains exist in the PDB accession than
187 are reported in the SIFTS file
190 <!-- JAL-2317-->Certain structures do not get mapped to
191 the structure view when displayed with Chimera
194 <!-- JAL-2317-->No chains shown in the Chimera view
195 panel's View->Show Chains submenu
198 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
199 work for wrapped alignment views
202 <!--JAL-2197 -->Rename UI components for running JPred
203 predictions from 'JNet' to 'JPred'
206 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
207 corrupted when annotation panel vertical scroll is not at
211 <!--JAL-2332 -->Attempting to view structure for Hen
212 lysozyme results in a PDB Client error dialog box
215 <!-- <em>New Known Issues</em>
222 <td width="60" nowrap>
224 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
225 <em>25/10/2016</em></strong>
228 <td><em>Application</em>
230 <li>3D Structure chooser opens with 'Cached structures'
231 view if structures already loaded</li>
232 <li>Progress bar reports models as they are loaded to
239 <li>Colour by conservation always enabled and no tick
240 shown in menu when BLOSUM or PID shading applied</li>
241 <li>FER1_ARATH and FER2_ARATH labels were switched in
242 example sequences/projects/trees</li>
246 <li>Jalview projects with views of local PDB structure
247 files saved on Windows cannot be opened on OSX</li>
248 <li>Multiple structure views can be opened and
249 superposed without timeout for structures with multiple
250 models or multiple sequences in alignment</li>
251 <li>Cannot import or associated local PDB files without
252 a PDB ID HEADER line</li>
253 <li>RMSD is not output in Jmol console when
254 superposition is performed</li>
255 <li>Drag and drop of URL from Browser fails for Linux
256 and OSX versions earlier than El Capitan</li>
257 <li>ENA client ignores invalid content from ENA server</li>
258 <li>Exceptions are not raised in console when ENA
259 client attempts to fetch non-existent IDs via Fetch DB
261 <li>Exceptions are not raised in console when a new
262 view is created on the alignment</li>
263 <li>OSX right-click fixed for group selections:
264 CMD-click to insert/remove gaps in groups and CTRL-click
265 to open group pop-up menu</li>
267 <em>Build and deployment</em>
269 <li>URL link checker now copes with multi-line anchor
272 <em>New Known Issues</em>
274 <li>Drag and drop from URL links in browsers do not
281 <td width="60" nowrap>
283 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
289 <!-- JAL-2124 -->Updated Spanish translations.
292 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
293 for importing structure data to Jalview. Enables mmCIF and
297 <!-- JAL-192 --->Alignment ruler shows positions relative to
301 <!-- JAL-2202 -->Position/residue shown in status bar when
302 mousing over sequence associated annotation
305 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
309 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
310 '()', canonical '[]' and invalid '{}' base pair populations
314 <!-- JAL-2092 -->Feature settings popup menu options for
315 showing or hiding columns containing a feature
318 <!-- JAL-1557 -->Edit selected group by double clicking on
319 group and sequence associated annotation labels
322 <!-- JAL-2236 -->Sequence name added to annotation label in
323 select/hide columns by annotation and colour by annotation
327 </ul> <em>Application</em>
330 <!-- JAL-2050-->Automatically hide introns when opening a
334 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
338 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
339 structure mappings with the EMBL-EBI PDBe SIFTS database
342 <!-- JAL-2079 -->Updated download sites used for Rfam and
343 Pfam sources to xfam.org
346 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
349 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
350 over sequences in Jalview
353 <!-- JAL-2027-->Support for reverse-complement coding
354 regions in ENA and EMBL
357 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
358 for record retrieval via ENA rest API
361 <!-- JAL-2027 -->Support for ENA CDS records with reverse
365 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
366 groovy script execution
369 <!-- JAL-1812 -->New 'execute Groovy script' option in an
370 alignment window's Calculate menu
373 <!-- JAL-1812 -->Allow groovy scripts that call
374 Jalview.getAlignFrames() to run in headless mode
377 <!-- JAL-2068 -->Support for creating new alignment
378 calculation workers from groovy scripts
381 <!-- JAL-1369 --->Store/restore reference sequence in
385 <!-- JAL-1803 -->Chain codes for a sequence's PDB
386 associations are now saved/restored from project
389 <!-- JAL-1993 -->Database selection dialog always shown
390 before sequence fetcher is opened
393 <!-- JAL-2183 -->Double click on an entry in Jalview's
394 database chooser opens a sequence fetcher
397 <!-- JAL-1563 -->Free-text search client for UniProt using
401 <!-- JAL-2168 -->-nonews command line parameter to prevent
402 the news reader opening
405 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
406 querying stored in preferences
409 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
413 <!-- JAL-1977-->Tooltips shown on database chooser
416 <!-- JAL-391 -->Reverse complement function in calculate
417 menu for nucleotide sequences
420 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
421 and feature counts preserves alignment ordering (and
422 debugged for complex feature sets).
425 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
426 viewing structures with Jalview 2.10
429 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
430 genome, transcript CCDS and gene ids via the Ensembl and
431 Ensembl Genomes REST API
434 <!-- JAL-2049 -->Protein sequence variant annotation
435 computed for 'sequence_variant' annotation on CDS regions
439 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
443 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
444 Ref Fetcher fails to match, or otherwise updates sequence
445 data from external database records.
448 <!-- JAL-2154 -->Revised Jalview Project format for
449 efficient recovery of sequence coding and alignment
450 annotation relationships.
452 </ul> <!-- <em>Applet</em>
463 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
467 <!-- JAL-2018-->Export features in Jalview format (again)
468 includes graduated colourschemes
471 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
472 working with big alignments and lots of hidden columns
475 <!-- JAL-2053-->Hidden column markers not always rendered
476 at right of alignment window
479 <!-- JAL-2067 -->Tidied up links in help file table of
483 <!-- JAL-2072 -->Feature based tree calculation not shown
487 <!-- JAL-2075 -->Hidden columns ignored during feature
488 based tree calculation
491 <!-- JAL-2065 -->Alignment view stops updating when show
492 unconserved enabled for group on alignment
495 <!-- JAL-2086 -->Cannot insert gaps into sequence when
499 <!-- JAL-2146 -->Alignment column in status incorrectly
500 shown as "Sequence position" when mousing over
504 <!-- JAL-2099 -->Incorrect column numbers in ruler when
505 hidden columns present
508 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
509 user created annotation added to alignment
512 <!-- JAL-1841 -->RNA Structure consensus only computed for
513 '()' base pair annotation
516 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
517 in zero scores for all base pairs in RNA Structure
521 <!-- JAL-2174-->Extend selection with columns containing
525 <!-- JAL-2275 -->Pfam format writer puts extra space at
526 beginning of sequence
529 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
533 <!-- JAL-2238 -->Cannot create groups on an alignment from
534 from a tree when t-coffee scores are shown
537 <!-- JAL-1836,1967 -->Cannot import and view PDB
538 structures with chains containing negative resnums (4q4h)
541 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
545 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
546 to Clustal, PIR and PileUp output
549 <!-- JAL-2008 -->Reordering sequence features that are
550 not visible causes alignment window to repaint
553 <!-- JAL-2006 -->Threshold sliders don't work in
554 graduated colour and colour by annotation row for e-value
555 scores associated with features and annotation rows
558 <!-- JAL-1797 -->amino acid physicochemical conservation
559 calculation should be case independent
562 <!-- JAL-2173 -->Remove annotation also updates hidden
566 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
567 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
568 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
571 <!-- JAL-2065 -->Null pointer exceptions and redraw
572 problems when reference sequence defined and 'show
573 non-conserved' enabled
576 <!-- JAL-1306 -->Quality and Conservation are now shown on
577 load even when Consensus calculation is disabled
580 <!-- JAL-1932 -->Remove right on penultimate column of
581 alignment does nothing
587 <!-- JAL-1552-->URLs and links can't be imported by
588 drag'n'drop on OSX when launched via webstart (note - not
589 yet fixed for El Capitan)
592 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
593 output when running on non-gb/us i18n platforms
596 <!-- JAL-1944 -->Error thrown when exporting a view with
597 hidden sequences as flat-file alignment
600 <!-- JAL-2030-->InstallAnywhere distribution fails when
604 <!-- JAL-2080-->Jalview very slow to launch via webstart
605 (also hotfix for 2.9.0b2)
608 <!-- JAL-2085 -->Cannot save project when view has a
609 reference sequence defined
612 <!-- JAL-1011 -->Columns are suddenly selected in other
613 alignments and views when revealing hidden columns
616 <!-- JAL-1989 -->Hide columns not mirrored in complement
617 view in a cDNA/Protein splitframe
620 <!-- JAL-1369 -->Cannot save/restore representative
621 sequence from project when only one sequence is
625 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
629 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
630 structure consensus didn't refresh annotation panel
633 <!-- JAL-1962 -->View mapping in structure view shows
634 mappings between sequence and all chains in a PDB file
637 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
638 dialogs format columns correctly, don't display array
639 data, sort columns according to type
642 <!-- JAL-1975 -->Export complete shown after destination
643 file chooser is cancelled during an image export
646 <!-- JAL-2025 -->Error when querying PDB Service with
647 sequence name containing special characters
650 <!-- JAL-2024 -->Manual PDB structure querying should be
654 <!-- JAL-2104 -->Large tooltips with broken HTML
655 formatting don't wrap
658 <!-- JAL-1128 -->Figures exported from wrapped view are
659 truncated so L looks like I in consensus annotation
662 <!-- JAL-2003 -->Export features should only export the
663 currently displayed features for the current selection or
667 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
668 after fetching cross-references, and restoring from project
671 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
672 followed in the structure viewer
675 <!-- JAL-2163 -->Titles for individual alignments in
676 splitframe not restored from project
679 <!-- JAL-2145 -->missing autocalculated annotation at
680 trailing end of protein alignment in transcript/product
681 splitview when pad-gaps not enabled by default
684 <!-- JAL-1797 -->amino acid physicochemical conservation
688 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
689 article has been read (reopened issue due to
690 internationalisation problems)
693 <!-- JAL-1960 -->Only offer PDB structures in structure
694 viewer based on sequence name, PDB and UniProt
699 <!-- JAL-1976 -->No progress bar shown during export of
703 <!-- JAL-2213 -->Structures not always superimposed after
704 multiple structures are shown for one or more sequences.
707 <!-- JAL-1370 -->Reference sequence characters should not
708 be replaced with '.' when 'Show unconserved' format option
712 <!-- JAL-1823 -->Cannot specify chain code when entering
713 specific PDB id for sequence
716 <!-- JAL-1944 -->File->Export->.. as doesn't work when
717 'Export hidden sequences' is enabled, but 'export hidden
718 columns' is disabled.
721 <!--JAL-2026-->Best Quality option in structure chooser
722 selects lowest rather than highest resolution structures
726 <!-- JAL-1887 -->Incorrect start and end reported for PDB
727 to sequence mapping in 'View Mappings' report
730 <!-- JAL-2284 -->Unable to read old Jalview projects that
731 contain non-XML data added after Jalvew wrote project.
733 <li><!-- JAL-2118 -->Newly created annotation row reorders
734 after clicking on it to create new annotation for a
737 <!-- may exclude, this is an external service stability issue JAL-1941
738 -- > RNA 3D structure not added via DSSR service</li> -->
743 <!-- JAL-2151 -->Incorrect columns are selected when
744 hidden columns present before start of sequence
747 <!-- JAL-1986 -->Missing dependencies on applet pages
751 <!-- JAL-1947 -->Overview pixel size changes when
752 sequences are hidden in applet
755 <!-- JAL-1996 -->Updated instructions for applet
756 deployment on examples pages.
763 <td width="60" nowrap>
765 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
766 <em>16/10/2015</em></strong>
771 <li>Time stamps for signed Jalview application and applet
778 <li>Duplicate group consensus and conservation rows
779 shown when tree is partitioned</li>
780 <li>Erratic behaviour when tree partitions made with
781 multiple cDNA/Protein split views</li>
787 <td width="60" nowrap>
789 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
790 <em>8/10/2015</em></strong>
795 <li>Updated Spanish translations of localized text for
797 </ul> <em>Application</em>
799 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
800 <li>Signed OSX InstallAnywhere installer<br></li>
801 <li>Support for per-sequence based annotations in BioJSON</li>
802 </ul> <em>Applet</em>
804 <li>Split frame example added to applet examples page</li>
805 </ul><em>Build and Deployment</em>
807 <li><!-- JAL-1888 -->New ant target for running Jalview's test suite</li>
813 <li>Mapping of cDNA to protein in split frames
814 incorrect when sequence start > 1</li>
815 <li>Broken images in filter column by annotation dialog
817 <li>Feature colours not parsed from features file</li>
818 <li>Exceptions and incomplete link URLs recovered when
819 loading a features file containing HTML tags in feature
825 <li>Annotations corrupted after BioJS export and
827 <li>Incorrect sequence limits after Fetch DB References
828 with 'trim retrieved sequences'</li>
829 <li>Incorrect warning about deleting all data when
830 deleting selected columns</li>
831 <li>Patch to build system for shipping properly signed
832 JNLP templates for webstart launch</li>
833 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
834 unreleased structures for download or viewing</li>
835 <li>Tab/space/return keystroke operation of EMBL-PDBe
836 fetcher/viewer dialogs works correctly</li>
837 <li>Disabled 'minimise' button on Jalview windows
838 running on OSX to workaround redraw hang bug</li>
839 <li>Split cDNA/Protein view position and geometry not
840 recovered from jalview project</li>
841 <li>Initial enabled/disabled state of annotation menu
842 sorter 'show autocalculated first/last' corresponds to
844 <li>Restoring of Clustal, RNA Helices and T-Coffee
845 color schemes from BioJSON</li>
849 <li>Reorder sequences mirrored in cDNA/Protein split
851 <li>Applet with Jmol examples not loading correctly</li>
857 <td><div align="center">
858 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
862 <li>Linked visualisation and analysis of DNA and Protein
865 <li>Translated cDNA alignments shown as split protein
866 and DNA alignment views</li>
867 <li>Codon consensus annotation for linked protein and
868 cDNA alignment views</li>
869 <li>Link cDNA or Protein product sequences by loading
870 them onto Protein or cDNA alignments</li>
871 <li>Reconstruct linked cDNA alignment from aligned
872 protein sequences</li>
875 <li>Jmol integration updated to Jmol v14.2.14</li>
876 <li>Import and export of Jalview alignment views as <a
877 href="features/bioJsonFormat.html">BioJSON</a></li>
878 <li>New alignment annotation file statements for
879 reference sequences and marking hidden columns</li>
880 <li>Reference sequence based alignment shading to
881 highlight variation</li>
882 <li>Select or hide columns according to alignment
884 <li>Find option for locating sequences by description</li>
885 <li>Conserved physicochemical properties shown in amino
886 acid conservation row</li>
887 <li>Alignments can be sorted by number of RNA helices</li>
888 </ul> <em>Application</em>
890 <li>New cDNA/Protein analysis capabilities
892 <li>Get Cross-References should open a Split Frame
893 view with cDNA/Protein</li>
894 <li>Detect when nucleotide sequences and protein
895 sequences are placed in the same alignment</li>
896 <li>Split cDNA/Protein views are saved in Jalview
901 <li>Use REST API to talk to Chimera</li>
902 <li>Selected regions in Chimera are highlighted in linked
905 <li>VARNA RNA viewer updated to v3.93</li>
906 <li>VARNA views are saved in Jalview Projects</li>
907 <li>Pseudoknots displayed as Jalview RNA annotation can
908 be shown in VARNA</li>
910 <li>Make groups for selection uses marked columns as well
911 as the active selected region</li>
913 <li>Calculate UPGMA and NJ trees using sequence feature
915 <li>New Export options
917 <li>New Export Settings dialog to control hidden
918 region export in flat file generation</li>
920 <li>Export alignment views for display with the <a
921 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
923 <li>Export scrollable SVG in HTML page</li>
924 <li>Optional embedding of BioJSON data when exporting
925 alignment figures to HTML</li>
927 <li>3D structure retrieval and display
929 <li>Free text and structured queries with the PDBe
931 <li>PDBe Search API based discovery and selection of
932 PDB structures for a sequence set</li>
936 <li>JPred4 employed for protein secondary structure
938 <li>Hide Insertions menu option to hide unaligned columns
939 for one or a group of sequences</li>
940 <li>Automatically hide insertions in alignments imported
941 from the JPred4 web server</li>
942 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
943 system on OSX<br />LGPL libraries courtesy of <a
944 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
946 <li>changed 'View nucleotide structure' submenu to 'View
947 VARNA 2D Structure'</li>
948 <li>change "View protein structure" menu option to "3D
951 </ul> <em>Applet</em>
953 <li>New layout for applet example pages</li>
954 <li>New parameters to enable SplitFrame view
955 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
956 <li>New example demonstrating linked viewing of cDNA and
957 Protein alignments</li>
958 </ul> <em>Development and deployment</em>
960 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
961 <li>Include installation type and git revision in build
962 properties and console log output</li>
963 <li>Jalview Github organisation, and new github site for
964 storing BioJsMSA Templates</li>
965 <li>Jalview's unit tests now managed with TestNG</li>
968 <!-- <em>General</em>
970 </ul> --> <!-- issues resolved --> <em>Application</em>
972 <li>Escape should close any open find dialogs</li>
973 <li>Typo in select-by-features status report</li>
974 <li>Consensus RNA secondary secondary structure
975 predictions are not highlighted in amber</li>
976 <li>Missing gap character in v2.7 example file means
977 alignment appears unaligned when pad-gaps is not enabled</li>
978 <li>First switch to RNA Helices colouring doesn't colour
979 associated structure views</li>
980 <li>ID width preference option is greyed out when auto
981 width checkbox not enabled</li>
982 <li>Stopped a warning dialog from being shown when
983 creating user defined colours</li>
984 <li>'View Mapping' in structure viewer shows sequence
985 mappings for just that viewer's sequences</li>
986 <li>Workaround for superposing PDB files containing
987 multiple models in Chimera</li>
988 <li>Report sequence position in status bar when hovering
989 over Jmol structure</li>
990 <li>Cannot output gaps as '.' symbols with Selection ->
991 output to text box</li>
992 <li>Flat file exports of alignments with hidden columns
993 have incorrect sequence start/end</li>
994 <li>'Aligning' a second chain to a Chimera structure from
996 <li>Colour schemes applied to structure viewers don't
997 work for nucleotide</li>
998 <li>Loading/cut'n'pasting an empty or invalid file leads
999 to a grey/invisible alignment window</li>
1000 <li>Exported Jpred annotation from a sequence region
1001 imports to different position</li>
1002 <li>Space at beginning of sequence feature tooltips shown
1003 on some platforms</li>
1004 <li>Chimera viewer 'View | Show Chain' menu is not
1006 <li>'New View' fails with a Null Pointer Exception in
1007 console if Chimera has been opened</li>
1008 <li>Mouseover to Chimera not working</li>
1009 <li>Miscellaneous ENA XML feature qualifiers not
1011 <li>NPE in annotation renderer after 'Extract Scores'</li>
1012 <li>If two structures in one Chimera window, mouseover of
1013 either sequence shows on first structure</li>
1014 <li>'Show annotations' options should not make
1015 non-positional annotations visible</li>
1016 <li>Subsequence secondary structure annotation not shown
1017 in right place after 'view flanking regions'</li>
1018 <li>File Save As type unset when current file format is
1020 <li>Save as '.jar' option removed for saving Jalview
1022 <li>Colour by Sequence colouring in Chimera more
1024 <li>Cannot 'add reference annotation' for a sequence in
1025 several views on same alignment</li>
1026 <li>Cannot show linked products for EMBL / ENA records</li>
1027 <li>Jalview's tooltip wraps long texts containing no
1029 </ul> <em>Applet</em>
1031 <li>Jmol to JalviewLite mouseover/link not working</li>
1032 <li>JalviewLite can't import sequences with ID
1033 descriptions containing angle brackets</li>
1034 </ul> <em>General</em>
1036 <li>Cannot export and reimport RNA secondary structure
1037 via jalview annotation file</li>
1038 <li>Random helix colour palette for colour by annotation
1039 with RNA secondary structure</li>
1040 <li>Mouseover to cDNA from STOP residue in protein
1041 translation doesn't work.</li>
1042 <li>hints when using the select by annotation dialog box</li>
1043 <li>Jmol alignment incorrect if PDB file has alternate CA
1045 <li>FontChooser message dialog appears to hang after
1046 choosing 1pt font</li>
1047 <li>Peptide secondary structure incorrectly imported from
1048 annotation file when annotation display text includes 'e' or
1050 <li>Cannot set colour of new feature type whilst creating
1052 <li>cDNA translation alignment should not be sequence
1053 order dependent</li>
1054 <li>'Show unconserved' doesn't work for lower case
1056 <li>Nucleotide ambiguity codes involving R not recognised</li>
1057 </ul> <em>Deployment and Documentation</em>
1059 <li>Applet example pages appear different to the rest of
1060 www.jalview.org</li>
1061 </ul> <em>Application Known issues</em>
1063 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1064 <li>Misleading message appears after trying to delete
1066 <li>Jalview icon not shown in dock after InstallAnywhere
1067 version launches</li>
1068 <li>Fetching EMBL reference for an RNA sequence results
1069 fails with a sequence mismatch</li>
1070 <li>Corrupted or unreadable alignment display when
1071 scrolling alignment to right</li>
1072 <li>ArrayIndexOutOfBoundsException thrown when remove
1073 empty columns called on alignment with ragged gapped ends</li>
1074 <li>auto calculated alignment annotation rows do not get
1075 placed above or below non-autocalculated rows</li>
1076 <li>Jalview dekstop becomes sluggish at full screen in
1077 ultra-high resolution</li>
1078 <li>Cannot disable consensus calculation independently of
1079 quality and conservation</li>
1080 <li>Mouseover highlighting between cDNA and protein can
1081 become sluggish with more than one splitframe shown</li>
1082 </ul> <em>Applet Known Issues</em>
1084 <li>Core PDB parsing code requires Jmol</li>
1085 <li>Sequence canvas panel goes white when alignment
1086 window is being resized</li>
1092 <td><div align="center">
1093 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1095 <td><em>General</em>
1097 <li>Updated Java code signing certificate donated by
1099 <li>Features and annotation preserved when performing
1100 pairwise alignment</li>
1101 <li>RNA pseudoknot annotation can be
1102 imported/exported/displayed</li>
1103 <li>'colour by annotation' can colour by RNA and
1104 protein secondary structure</li>
1105 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1106 post-hoc with 2.9 release</em>)
1109 </ul> <em>Application</em>
1111 <li>Extract and display secondary structure for sequences
1112 with 3D structures</li>
1113 <li>Support for parsing RNAML</li>
1114 <li>Annotations menu for layout
1116 <li>sort sequence annotation rows by alignment</li>
1117 <li>place sequence annotation above/below alignment
1120 <li>Output in Stockholm format</li>
1121 <li>Internationalisation: improved Spanish (es)
1123 <li>Structure viewer preferences tab</li>
1124 <li>Disorder and Secondary Structure annotation tracks
1125 shared between alignments</li>
1126 <li>UCSF Chimera launch and linked highlighting from
1128 <li>Show/hide all sequence associated annotation rows for
1129 all or current selection</li>
1130 <li>disorder and secondary structure predictions
1131 available as dataset annotation</li>
1132 <li>Per-sequence rna helices colouring</li>
1135 <li>Sequence database accessions imported when fetching
1136 alignments from Rfam</li>
1137 <li>update VARNA version to 3.91</li>
1139 <li>New groovy scripts for exporting aligned positions,
1140 conservation values, and calculating sum of pairs scores.</li>
1141 <li>Command line argument to set default JABAWS server</li>
1142 <li>include installation type in build properties and
1143 console log output</li>
1144 <li>Updated Jalview project format to preserve dataset
1148 <!-- issues resolved --> <em>Application</em>
1150 <li>Distinguish alignment and sequence associated RNA
1151 structure in structure->view->VARNA</li>
1152 <li>Raise dialog box if user deletes all sequences in an
1154 <li>Pressing F1 results in documentation opening twice</li>
1155 <li>Sequence feature tooltip is wrapped</li>
1156 <li>Double click on sequence associated annotation
1157 selects only first column</li>
1158 <li>Redundancy removal doesn't result in unlinked
1159 leaves shown in tree</li>
1160 <li>Undos after several redundancy removals don't undo
1162 <li>Hide sequence doesn't hide associated annotation</li>
1163 <li>User defined colours dialog box too big to fit on
1164 screen and buttons not visible</li>
1165 <li>author list isn't updated if already written to
1166 Jalview properties</li>
1167 <li>Popup menu won't open after retrieving sequence
1169 <li>File open window for associate PDB doesn't open</li>
1170 <li>Left-then-right click on a sequence id opens a
1171 browser search window</li>
1172 <li>Cannot open sequence feature shading/sort popup menu
1173 in feature settings dialog</li>
1174 <li>better tooltip placement for some areas of Jalview
1176 <li>Allow addition of JABAWS Server which doesn't
1177 pass validation</li>
1178 <li>Web services parameters dialog box is too large to
1180 <li>Muscle nucleotide alignment preset obscured by
1182 <li>JABAWS preset submenus don't contain newly
1183 defined user preset</li>
1184 <li>MSA web services warns user if they were launched
1185 with invalid input</li>
1186 <li>Jalview cannot contact DAS Registy when running on
1189 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1190 'Superpose with' submenu not shown when new view
1194 </ul> <!-- <em>Applet</em>
1196 </ul> <em>General</em>
1198 </ul>--> <em>Deployment and Documentation</em>
1200 <li>2G and 1G options in launchApp have no effect on
1201 memory allocation</li>
1202 <li>launchApp service doesn't automatically open
1203 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1205 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1206 InstallAnywhere reports cannot find valid JVM when Java
1207 1.7_055 is available
1209 </ul> <em>Application Known issues</em>
1212 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1213 corrupted or unreadable alignment display when scrolling
1217 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1218 retrieval fails but progress bar continues for DAS retrieval
1219 with large number of ID
1222 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1223 flatfile output of visible region has incorrect sequence
1227 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1228 rna structure consensus doesn't update when secondary
1229 structure tracks are rearranged
1232 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1233 invalid rna structure positional highlighting does not
1234 highlight position of invalid base pairs
1237 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1238 out of memory errors are not raised when saving Jalview
1239 project from alignment window file menu
1242 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1243 Switching to RNA Helices colouring doesn't propagate to
1247 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1248 colour by RNA Helices not enabled when user created
1249 annotation added to alignment
1252 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1253 Jalview icon not shown on dock in Mountain Lion/Webstart
1255 </ul> <em>Applet Known Issues</em>
1258 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1259 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1262 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1263 Jalview and Jmol example not compatible with IE9
1266 <li>Sort by annotation score doesn't reverse order
1272 <td><div align="center">
1273 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1276 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1279 <li>Internationalisation of user interface (usually
1280 called i18n support) and translation for Spanish locale</li>
1281 <li>Define/Undefine group on current selection with
1282 Ctrl-G/Shift Ctrl-G</li>
1283 <li>Improved group creation/removal options in
1284 alignment/sequence Popup menu</li>
1285 <li>Sensible precision for symbol distribution
1286 percentages shown in logo tooltip.</li>
1287 <li>Annotation panel height set according to amount of
1288 annotation when alignment first opened</li>
1289 </ul> <em>Application</em>
1291 <li>Interactive consensus RNA secondary structure
1292 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1293 <li>Select columns containing particular features from
1294 Feature Settings dialog</li>
1295 <li>View all 'representative' PDB structures for selected
1297 <li>Update Jalview project format:
1299 <li>New file extension for Jalview projects '.jvp'</li>
1300 <li>Preserve sequence and annotation dataset (to
1301 store secondary structure annotation,etc)</li>
1302 <li>Per group and alignment annotation and RNA helix
1306 <li>New similarity measures for PCA and Tree calculation
1308 <li>Experimental support for retrieval and viewing of
1309 flanking regions for an alignment</li>
1313 <!-- issues resolved --> <em>Application</em>
1315 <li>logo keeps spinning and status remains at queued or
1316 running after job is cancelled</li>
1317 <li>cannot export features from alignments imported from
1318 Jalview/VAMSAS projects</li>
1319 <li>Buggy slider for web service parameters that take
1321 <li>Newly created RNA secondary structure line doesn't
1322 have 'display all symbols' flag set</li>
1323 <li>T-COFFEE alignment score shading scheme and other
1324 annotation shading not saved in Jalview project</li>
1325 <li>Local file cannot be loaded in freshly downloaded
1327 <li>Jalview icon not shown on dock in Mountain
1329 <li>Load file from desktop file browser fails</li>
1330 <li>Occasional NPE thrown when calculating large trees</li>
1331 <li>Cannot reorder or slide sequences after dragging an
1332 alignment onto desktop</li>
1333 <li>Colour by annotation dialog throws NPE after using
1334 'extract scores' function</li>
1335 <li>Loading/cut'n'pasting an empty file leads to a grey
1336 alignment window</li>
1337 <li>Disorder thresholds rendered incorrectly after
1338 performing IUPred disorder prediction</li>
1339 <li>Multiple group annotated consensus rows shown when
1340 changing 'normalise logo' display setting</li>
1341 <li>Find shows blank dialog after 'finished searching' if
1342 nothing matches query</li>
1343 <li>Null Pointer Exceptions raised when sorting by
1344 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1346 <li>Errors in Jmol console when structures in alignment
1347 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1349 <li>Not all working JABAWS services are shown in
1351 <li>JAVAWS version of Jalview fails to launch with
1352 'invalid literal/length code'</li>
1353 <li>Annotation/RNA Helix colourschemes cannot be applied
1354 to alignment with groups (actually fixed in 2.8.0b1)</li>
1355 <li>RNA Helices and T-Coffee Scores available as default
1358 </ul> <em>Applet</em>
1360 <li>Remove group option is shown even when selection is
1362 <li>Apply to all groups ticked but colourscheme changes
1363 don't affect groups</li>
1364 <li>Documented RNA Helices and T-Coffee Scores as valid
1365 colourscheme name</li>
1366 <li>Annotation labels drawn on sequence IDs when
1367 Annotation panel is not displayed</li>
1368 <li>Increased font size for dropdown menus on OSX and
1369 embedded windows</li>
1370 </ul> <em>Other</em>
1372 <li>Consensus sequence for alignments/groups with a
1373 single sequence were not calculated</li>
1374 <li>annotation files that contain only groups imported as
1375 annotation and junk sequences</li>
1376 <li>Fasta files with sequences containing '*' incorrectly
1377 recognised as PFAM or BLC</li>
1378 <li>conservation/PID slider apply all groups option
1379 doesn't affect background (2.8.0b1)
1381 <li>redundancy highlighting is erratic at 0% and 100%</li>
1382 <li>Remove gapped columns fails for sequences with ragged
1384 <li>AMSA annotation row with leading spaces is not
1385 registered correctly on import</li>
1386 <li>Jalview crashes when selecting PCA analysis for
1387 certain alignments</li>
1388 <li>Opening the colour by annotation dialog for an
1389 existing annotation based 'use original colours'
1390 colourscheme loses original colours setting</li>
1395 <td><div align="center">
1396 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
1397 <em>30/1/2014</em></strong>
1401 <li>Trusted certificates for JalviewLite applet and
1402 Jalview Desktop application<br />Certificate was donated by
1403 <a href="https://www.certum.eu">Certum</a> to the Jalview
1404 open source project).
1406 <li>Jalview SRS links replaced by UniProt and EBI-search
1408 <li>Output in Stockholm format</li>
1409 <li>Allow import of data from gzipped files</li>
1410 <li>Export/import group and sequence associated line
1411 graph thresholds</li>
1412 <li>Nucleotide substitution matrix that supports RNA and
1413 ambiguity codes</li>
1414 <li>Allow disorder predictions to be made on the current
1415 selection (or visible selection) in the same way that JPred
1417 <li>Groovy scripting for headless Jalview operation</li>
1418 </ul> <em>Other improvements</em>
1420 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
1421 <li>COMBINE statement uses current SEQUENCE_REF and
1422 GROUP_REF scope to group annotation rows</li>
1423 <li>Support '' style escaping of quotes in Newick
1425 <li>Group options for JABAWS service by command line name</li>
1426 <li>Empty tooltip shown for JABA service options with a
1427 link but no description</li>
1428 <li>Select primary source when selecting authority in
1429 database fetcher GUI</li>
1430 <li>Add .mfa to FASTA file extensions recognised by
1432 <li>Annotation label tooltip text wrap</li>
1437 <li>Slow scrolling when lots of annotation rows are
1439 <li>Lots of NPE (and slowness) after creating RNA
1440 secondary structure annotation line</li>
1441 <li>Sequence database accessions not imported when
1442 fetching alignments from Rfam</li>
1443 <li>Incorrect SHMR submission for sequences with
1445 <li>View all structures does not always superpose
1447 <li>Option widgets in service parameters not updated to
1448 reflect user or preset settings</li>
1449 <li>Null pointer exceptions for some services without
1450 presets or adjustable parameters</li>
1451 <li>Discover PDB IDs entry in structure menu doesn't
1452 discover PDB xRefs</li>
1453 <li>Exception encountered while trying to retrieve
1454 features with DAS</li>
1455 <li>Lowest value in annotation row isn't coloured
1456 when colour by annotation (per sequence) is coloured</li>
1457 <li>Keyboard mode P jumps to start of gapped region when
1458 residue follows a gap</li>
1459 <li>Jalview appears to hang importing an alignment with
1460 Wrap as default or after enabling Wrap</li>
1461 <li>'Right click to add annotations' message
1462 shown in wrap mode when no annotations present</li>
1463 <li>Disorder predictions fail with NPE if no automatic
1464 annotation already exists on alignment</li>
1465 <li>oninit javascript function should be called after
1466 initialisation completes</li>
1467 <li>Remove redundancy after disorder prediction corrupts
1468 alignment window display</li>
1469 <li>Example annotation file in documentation is invalid</li>
1470 <li>Grouped line graph annotation rows are not exported
1471 to annotation file</li>
1472 <li>Multi-harmony analysis cannot be run when only two
1474 <li>Cannot create multiple groups of line graphs with
1475 several 'combine' statements in annotation file</li>
1476 <li>Pressing return several times causes Number Format
1477 exceptions in keyboard mode</li>
1478 <li>Multi-harmony (SHMMR) method doesn't submit
1479 correct partitions for input data</li>
1480 <li>Translation from DNA to Amino Acids fails</li>
1481 <li>Jalview fail to load newick tree with quoted label</li>
1482 <li>--headless flag isn't understood</li>
1483 <li>ClassCastException when generating EPS in headless
1485 <li>Adjusting sequence-associated shading threshold only
1486 changes one row's threshold</li>
1487 <li>Preferences and Feature settings panel panel
1488 doesn't open</li>
1489 <li>hide consensus histogram also hides conservation and
1490 quality histograms</li>
1495 <td><div align="center">
1496 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
1498 <td><em>Application</em>
1500 <li>Support for JABAWS 2.0 Services (AACon alignment
1501 conservation, protein disorder and Clustal Omega)</li>
1502 <li>JABAWS server status indicator in Web Services
1504 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
1505 in Jalview alignment window</li>
1506 <li>Updated Jalview build and deploy framework for OSX
1507 mountain lion, windows 7, and 8</li>
1508 <li>Nucleotide substitution matrix for PCA that supports
1509 RNA and ambiguity codes</li>
1511 <li>Improved sequence database retrieval GUI</li>
1512 <li>Support fetching and database reference look up
1513 against multiple DAS sources (Fetch all from in 'fetch db
1515 <li>Jalview project improvements
1517 <li>Store and retrieve the 'belowAlignment'
1518 flag for annotation</li>
1519 <li>calcId attribute to group annotation rows on the
1521 <li>Store AACon calculation settings for a view in
1522 Jalview project</li>
1526 <li>horizontal scrolling gesture support</li>
1527 <li>Visual progress indicator when PCA calculation is
1529 <li>Simpler JABA web services menus</li>
1530 <li>visual indication that web service results are still
1531 being retrieved from server</li>
1532 <li>Serialise the dialogs that are shown when Jalview
1533 starts up for first time</li>
1534 <li>Jalview user agent string for interacting with HTTP
1536 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
1538 <li>Examples directory and Groovy library included in
1539 InstallAnywhere distribution</li>
1540 </ul> <em>Applet</em>
1542 <li>RNA alignment and secondary structure annotation
1543 visualization applet example</li>
1544 </ul> <em>General</em>
1546 <li>Normalise option for consensus sequence logo</li>
1547 <li>Reset button in PCA window to return dimensions to
1549 <li>Allow seqspace or Jalview variant of alignment PCA
1551 <li>PCA with either nucleic acid and protein substitution
1553 <li>Allow windows containing HTML reports to be exported
1555 <li>Interactive display and editing of RNA secondary
1556 structure contacts</li>
1557 <li>RNA Helix Alignment Colouring</li>
1558 <li>RNA base pair logo consensus</li>
1559 <li>Parse sequence associated secondary structure
1560 information in Stockholm files</li>
1561 <li>HTML Export database accessions and annotation
1562 information presented in tooltip for sequences</li>
1563 <li>Import secondary structure from LOCARNA clustalw
1564 style RNA alignment files</li>
1565 <li>import and visualise T-COFFEE quality scores for an
1567 <li>'colour by annotation' per sequence option to
1568 shade each sequence according to its associated alignment
1570 <li>New Jalview Logo</li>
1571 </ul> <em>Documentation and Development</em>
1573 <li>documentation for score matrices used in Jalview</li>
1574 <li>New Website!</li>
1576 <td><em>Application</em>
1578 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
1579 wsdbfetch REST service</li>
1580 <li>Stop windows being moved outside desktop on OSX</li>
1581 <li>Filetype associations not installed for webstart
1583 <li>Jalview does not always retrieve progress of a JABAWS
1584 job execution in full once it is complete</li>
1585 <li>revise SHMR RSBS definition to ensure alignment is
1586 uploaded via ali_file parameter</li>
1587 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
1588 <li>View all structures superposed fails with exception</li>
1589 <li>Jnet job queues forever if a very short sequence is
1590 submitted for prediction</li>
1591 <li>Cut and paste menu not opened when mouse clicked on
1593 <li>Putting fractional value into integer text box in
1594 alignment parameter dialog causes Jalview to hang</li>
1595 <li>Structure view highlighting doesn't work on
1597 <li>View all structures fails with exception shown in
1599 <li>Characters in filename associated with PDBEntry not
1600 escaped in a platform independent way</li>
1601 <li>Jalview desktop fails to launch with exception when
1603 <li>Tree calculation reports 'you must have 2 or more
1604 sequences selected' when selection is empty</li>
1605 <li>Jalview desktop fails to launch with jar signature
1606 failure when java web start temporary file caching is
1608 <li>DAS Sequence retrieval with range qualification
1609 results in sequence xref which includes range qualification</li>
1610 <li>Errors during processing of command line arguments
1611 cause progress bar (JAL-898) to be removed</li>
1612 <li>Replace comma for semi-colon option not disabled for
1613 DAS sources in sequence fetcher</li>
1614 <li>Cannot close news reader when JABAWS server warning
1615 dialog is shown</li>
1616 <li>Option widgets not updated to reflect user settings</li>
1617 <li>Edited sequence not submitted to web service</li>
1618 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
1619 <li>InstallAnywhere installer doesn't unpack and run
1620 on OSX Mountain Lion</li>
1621 <li>Annotation panel not given a scroll bar when
1622 sequences with alignment annotation are pasted into the
1624 <li>Sequence associated annotation rows not associated
1625 when loaded from Jalview project</li>
1626 <li>Browser launch fails with NPE on java 1.7</li>
1627 <li>JABAWS alignment marked as finished when job was
1628 cancelled or job failed due to invalid input</li>
1629 <li>NPE with v2.7 example when clicking on Tree
1630 associated with all views</li>
1631 <li>Exceptions when copy/paste sequences with grouped
1632 annotation rows to new window</li>
1633 </ul> <em>Applet</em>
1635 <li>Sequence features are momentarily displayed before
1636 they are hidden using hidefeaturegroups applet parameter</li>
1637 <li>loading features via javascript API automatically
1638 enables feature display</li>
1639 <li>scrollToColumnIn javascript API method doesn't
1641 </ul> <em>General</em>
1643 <li>Redundancy removal fails for rna alignment</li>
1644 <li>PCA calculation fails when sequence has been selected
1645 and then deselected</li>
1646 <li>PCA window shows grey box when first opened on OSX</li>
1647 <li>Letters coloured pink in sequence logo when alignment
1648 coloured with clustalx</li>
1649 <li>Choosing fonts without letter symbols defined causes
1650 exceptions and redraw errors</li>
1651 <li>Initial PCA plot view is not same as manually
1652 reconfigured view</li>
1653 <li>Grouped annotation graph label has incorrect line
1655 <li>Grouped annotation graph label display is corrupted
1656 for lots of labels</li>
1661 <div align="center">
1662 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
1665 <td><em>Application</em>
1667 <li>Jalview Desktop News Reader</li>
1668 <li>Tweaked default layout of web services menu</li>
1669 <li>View/alignment association menu to enable user to
1670 easily specify which alignment a multi-structure view takes
1671 its colours/correspondences from</li>
1672 <li>Allow properties file location to be specified as URL</li>
1673 <li>Extend Jalview project to preserve associations
1674 between many alignment views and a single Jmol display</li>
1675 <li>Store annotation row height in Jalview project file</li>
1676 <li>Annotation row column label formatting attributes
1677 stored in project file</li>
1678 <li>Annotation row order for auto-calculated annotation
1679 rows preserved in Jalview project file</li>
1680 <li>Visual progress indication when Jalview state is
1681 saved using Desktop window menu</li>
1682 <li>Visual indication that command line arguments are
1683 still being processed</li>
1684 <li>Groovy script execution from URL</li>
1685 <li>Colour by annotation default min and max colours in
1687 <li>Automatically associate PDB files dragged onto an
1688 alignment with sequences that have high similarity and
1690 <li>Update JGoogleAnalytics to latest release (0.3)</li>
1691 <li>'view structures' option to open many
1692 structures in same window</li>
1693 <li>Sort associated views menu option for tree panel</li>
1694 <li>Group all JABA and non-JABA services for a particular
1695 analysis function in its own submenu</li>
1696 </ul> <em>Applet</em>
1698 <li>Userdefined and autogenerated annotation rows for
1700 <li>Adjustment of alignment annotation pane height</li>
1701 <li>Annotation scrollbar for annotation panel</li>
1702 <li>Drag to reorder annotation rows in annotation panel</li>
1703 <li>'automaticScrolling' parameter</li>
1704 <li>Allow sequences with partial ID string matches to be
1705 annotated from GFF/Jalview features files</li>
1706 <li>Sequence logo annotation row in applet</li>
1707 <li>Absolute paths relative to host server in applet
1708 parameters are treated as such</li>
1709 <li>New in the JalviewLite javascript API:
1711 <li>JalviewLite.js javascript library</li>
1712 <li>Javascript callbacks for
1714 <li>Applet initialisation</li>
1715 <li>Sequence/alignment mouse-overs and selections</li>
1718 <li>scrollTo row and column alignment scrolling
1720 <li>Select sequence/alignment regions from javascript</li>
1721 <li>javascript structure viewer harness to pass
1722 messages between Jmol and Jalview when running as
1723 distinct applets</li>
1724 <li>sortBy method</li>
1725 <li>Set of applet and application examples shipped
1726 with documentation</li>
1727 <li>New example to demonstrate JalviewLite and Jmol
1728 javascript message exchange</li>
1730 </ul> <em>General</em>
1732 <li>Enable Jmol displays to be associated with multiple
1733 multiple alignments</li>
1734 <li>Option to automatically sort alignment with new tree</li>
1735 <li>User configurable link to enable redirects to a
1736 www.Jalview.org mirror</li>
1737 <li>Jmol colours option for Jmol displays</li>
1738 <li>Configurable newline string when writing alignment
1739 and other flat files</li>
1740 <li>Allow alignment annotation description lines to
1741 contain html tags</li>
1742 </ul> <em>Documentation and Development</em>
1744 <li>Add groovy test harness for bulk load testing to
1746 <li>Groovy script to load and align a set of sequences
1747 using a web service before displaying the result in the
1748 Jalview desktop</li>
1749 <li>Restructured javascript and applet api documentation</li>
1750 <li>Ant target to publish example html files with applet
1752 <li>Netbeans project for building Jalview from source</li>
1753 <li>ant task to create online javadoc for Jalview source</li>
1755 <td><em>Application</em>
1757 <li>User defined colourscheme throws exception when
1758 current built in colourscheme is saved as new scheme</li>
1759 <li>AlignFrame->Save in application pops up save
1760 dialog for valid filename/format</li>
1761 <li>Cannot view associated structure for UniProt sequence</li>
1762 <li>PDB file association breaks for UniProt sequence
1764 <li>Associate PDB from file dialog does not tell you
1765 which sequence is to be associated with the file</li>
1766 <li>Find All raises null pointer exception when query
1767 only matches sequence IDs</li>
1768 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
1769 <li>Jalview project with Jmol views created with Jalview
1770 2.4 cannot be loaded</li>
1771 <li>Filetype associations not installed for webstart
1773 <li>Two or more chains in a single PDB file associated
1774 with sequences in different alignments do not get coloured
1775 by their associated sequence</li>
1776 <li>Visibility status of autocalculated annotation row
1777 not preserved when project is loaded</li>
1778 <li>Annotation row height and visibility attributes not
1779 stored in Jalview project</li>
1780 <li>Tree bootstraps are not preserved when saved as a
1781 Jalview project</li>
1782 <li>Envision2 workflow tooltips are corrupted</li>
1783 <li>Enabling show group conservation also enables colour
1784 by conservation</li>
1785 <li>Duplicate group associated conservation or consensus
1786 created on new view</li>
1787 <li>Annotation scrollbar not displayed after 'show
1788 all hidden annotation rows' option selected</li>
1789 <li>Alignment quality not updated after alignment
1790 annotation row is hidden then shown</li>
1791 <li>Preserve colouring of structures coloured by
1792 sequences in pre Jalview 2.7 projects</li>
1793 <li>Web service job parameter dialog is not laid out
1795 <li>Web services menu not refreshed after 'reset
1796 services' button is pressed in preferences</li>
1797 <li>Annotation off by one in Jalview v2_3 example project</li>
1798 <li>Structures imported from file and saved in project
1799 get name like jalview_pdb1234.txt when reloaded</li>
1800 <li>Jalview does not always retrieve progress of a JABAWS
1801 job execution in full once it is complete</li>
1802 </ul> <em>Applet</em>
1804 <li>Alignment height set incorrectly when lots of
1805 annotation rows are displayed</li>
1806 <li>Relative URLs in feature HTML text not resolved to
1808 <li>View follows highlighting does not work for positions
1810 <li><= shown as = in tooltip</li>
1811 <li>Export features raises exception when no features
1813 <li>Separator string used for serialising lists of IDs
1814 for javascript api is modified when separator string
1815 provided as parameter</li>
1816 <li>Null pointer exception when selecting tree leaves for
1817 alignment with no existing selection</li>
1818 <li>Relative URLs for datasources assumed to be relative
1819 to applet's codebase</li>
1820 <li>Status bar not updated after finished searching and
1821 search wraps around to first result</li>
1822 <li>StructureSelectionManager instance shared between
1823 several Jalview applets causes race conditions and memory
1825 <li>Hover tooltip and mouseover of position on structure
1826 not sent from Jmol in applet</li>
1827 <li>Certain sequences of javascript method calls to
1828 applet API fatally hang browser</li>
1829 </ul> <em>General</em>
1831 <li>View follows structure mouseover scrolls beyond
1832 position with wrapped view and hidden regions</li>
1833 <li>Find sequence position moves to wrong residue
1834 with/without hidden columns</li>
1835 <li>Sequence length given in alignment properties window
1837 <li>InvalidNumberFormat exceptions thrown when trying to
1838 import PDB like structure files</li>
1839 <li>Positional search results are only highlighted
1840 between user-supplied sequence start/end bounds</li>
1841 <li>End attribute of sequence is not validated</li>
1842 <li>Find dialog only finds first sequence containing a
1843 given sequence position</li>
1844 <li>Sequence numbering not preserved in MSF alignment
1846 <li>Jalview PDB file reader does not extract sequence
1847 from nucleotide chains correctly</li>
1848 <li>Structure colours not updated when tree partition
1849 changed in alignment</li>
1850 <li>Sequence associated secondary structure not correctly
1851 parsed in interleaved stockholm</li>
1852 <li>Colour by annotation dialog does not restore current
1854 <li>Hiding (nearly) all sequences doesn't work
1856 <li>Sequences containing lowercase letters are not
1857 properly associated with their pdb files</li>
1858 </ul> <em>Documentation and Development</em>
1860 <li>schemas/JalviewWsParamSet.xsd corrupted by
1861 ApplyCopyright tool</li>
1866 <div align="center">
1867 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
1870 <td><em>Application</em>
1872 <li>New warning dialog when the Jalview Desktop cannot
1873 contact web services</li>
1874 <li>JABA service parameters for a preset are shown in
1875 service job window</li>
1876 <li>JABA Service menu entries reworded</li>
1880 <li>Modeller PIR IO broken - cannot correctly import a
1881 pir file emitted by Jalview</li>
1882 <li>Existing feature settings transferred to new
1883 alignment view created from cut'n'paste</li>
1884 <li>Improved test for mixed amino/nucleotide chains when
1885 parsing PDB files</li>
1886 <li>Consensus and conservation annotation rows
1887 occasionally become blank for all new windows</li>
1888 <li>Exception raised when right clicking above sequences
1889 in wrapped view mode</li>
1890 </ul> <em>Application</em>
1892 <li>multiple multiply aligned structure views cause cpu
1893 usage to hit 100% and computer to hang</li>
1894 <li>Web Service parameter layout breaks for long user
1895 parameter names</li>
1896 <li>Jaba service discovery hangs desktop if Jaba server
1903 <div align="center">
1904 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
1907 <td><em>Application</em>
1909 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
1910 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
1913 <li>Web Services preference tab</li>
1914 <li>Analysis parameters dialog box and user defined
1916 <li>Improved speed and layout of Envision2 service menu</li>
1917 <li>Superpose structures using associated sequence
1919 <li>Export coordinates and projection as CSV from PCA
1921 </ul> <em>Applet</em>
1923 <li>enable javascript: execution by the applet via the
1924 link out mechanism</li>
1925 </ul> <em>Other</em>
1927 <li>Updated the Jmol Jalview interface to work with Jmol
1929 <li>The Jalview Desktop and JalviewLite applet now
1930 require Java 1.5</li>
1931 <li>Allow Jalview feature colour specification for GFF
1932 sequence annotation files</li>
1933 <li>New 'colour by label' keword in Jalview feature file
1934 type colour specification</li>
1935 <li>New Jalview Desktop Groovy API method that allows a
1936 script to check if it being run in an interactive session or
1937 in a batch operation from the Jalview command line</li>
1941 <li>clustalx colourscheme colours Ds preferentially when
1942 both D+E are present in over 50% of the column</li>
1943 </ul> <em>Application</em>
1945 <li>typo in AlignmentFrame->View->Hide->all but
1946 selected Regions menu item</li>
1947 <li>sequence fetcher replaces ',' for ';' when the ',' is
1948 part of a valid accession ID</li>
1949 <li>fatal OOM if object retrieved by sequence fetcher
1950 runs out of memory</li>
1951 <li>unhandled Out of Memory Error when viewing pca
1952 analysis results</li>
1953 <li>InstallAnywhere builds fail to launch on OS X java
1954 10.5 update 4 (due to apple Java 1.6 update)</li>
1955 <li>Installanywhere Jalview silently fails to launch</li>
1956 </ul> <em>Applet</em>
1958 <li>Jalview.getFeatureGroups() raises an
1959 ArrayIndexOutOfBoundsException if no feature groups are
1966 <div align="center">
1967 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
1973 <li>Alignment prettyprinter doesn't cope with long
1975 <li>clustalx colourscheme colours Ds preferentially when
1976 both D+E are present in over 50% of the column</li>
1977 <li>nucleic acid structures retrieved from PDB do not
1978 import correctly</li>
1979 <li>More columns get selected than were clicked on when a
1980 number of columns are hidden</li>
1981 <li>annotation label popup menu not providing correct
1982 add/hide/show options when rows are hidden or none are
1984 <li>Stockholm format shown in list of readable formats,
1985 and parser copes better with alignments from RFAM.</li>
1986 <li>CSV output of consensus only includes the percentage
1987 of all symbols if sequence logo display is enabled</li>
1989 </ul> <em>Applet</em>
1991 <li>annotation panel disappears when annotation is
1993 </ul> <em>Application</em>
1995 <li>Alignment view not redrawn properly when new
1996 alignment opened where annotation panel is visible but no
1997 annotations are present on alignment</li>
1998 <li>pasted region containing hidden columns is
1999 incorrectly displayed in new alignment window</li>
2000 <li>Jalview slow to complete operations when stdout is
2001 flooded (fix is to close the Jalview console)</li>
2002 <li>typo in AlignmentFrame->View->Hide->all but
2003 selected Rregions menu item.</li>
2004 <li>inconsistent group submenu and Format submenu entry
2005 'Un' or 'Non'conserved</li>
2006 <li>Sequence feature settings are being shared by
2007 multiple distinct alignments</li>
2008 <li>group annotation not recreated when tree partition is
2010 <li>double click on group annotation to select sequences
2011 does not propagate to associated trees</li>
2012 <li>Mac OSX specific issues:
2014 <li>exception raised when mouse clicked on desktop
2015 window background</li>
2016 <li>Desktop menu placed on menu bar and application
2017 name set correctly</li>
2018 <li>sequence feature settings not wide enough for the
2019 save feature colourscheme button</li>
2028 <div align="center">
2029 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2032 <td><em>New Capabilities</em>
2034 <li>URL links generated from description line for
2035 regular-expression based URL links (applet and application)
2042 <li>Non-positional feature URL links are shown in link
2044 <li>Linked viewing of nucleic acid sequences and
2046 <li>Automatic Scrolling option in View menu to display
2047 the currently highlighted region of an alignment.</li>
2048 <li>Order an alignment by sequence length, or using the
2049 average score or total feature count for each sequence.</li>
2050 <li>Shading features by score or associated description</li>
2051 <li>Subdivide alignment and groups based on identity of
2052 selected subsequence (Make Groups from Selection).</li>
2053 <li>New hide/show options including Shift+Control+H to
2054 hide everything but the currently selected region.</li>
2055 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2056 </ul> <em>Application</em>
2058 <li>Fetch DB References capabilities and UI expanded to
2059 support retrieval from DAS sequence sources</li>
2060 <li>Local DAS Sequence sources can be added via the
2061 command line or via the Add local source dialog box.</li>
2062 <li>DAS Dbref and DbxRef feature types are parsed as
2063 database references and protein_name is parsed as
2064 description line (BioSapiens terms).</li>
2065 <li>Enable or disable non-positional feature and database
2066 references in sequence ID tooltip from View menu in
2068 <!-- <li>New hidden columns and rows and representatives capabilities
2069 in annotations file (in progress - not yet fully implemented)</li> -->
2070 <li>Group-associated consensus, sequence logos and
2071 conservation plots</li>
2072 <li>Symbol distributions for each column can be exported
2073 and visualized as sequence logos</li>
2074 <li>Optionally scale multi-character column labels to fit
2075 within each column of annotation row<!-- todo for applet -->
2077 <li>Optional automatic sort of associated alignment view
2078 when a new tree is opened.</li>
2079 <li>Jalview Java Console</li>
2080 <li>Better placement of desktop window when moving
2081 between different screens.</li>
2082 <li>New preference items for sequence ID tooltip and
2083 consensus annotation</li>
2084 <li>Client to submit sequences and IDs to Envision2
2086 <li><em>Vamsas Capabilities</em>
2088 <li>Improved VAMSAS synchronization (Jalview archive
2089 used to preserve views, structures, and tree display
2091 <li>Import of vamsas documents from disk or URL via
2093 <li>Sharing of selected regions between views and
2094 with other VAMSAS applications (Experimental feature!)</li>
2095 <li>Updated API to VAMSAS version 0.2</li>
2097 </ul> <em>Applet</em>
2099 <li>Middle button resizes annotation row height</li>
2102 <li>sortByTree (true/false) - automatically sort the
2103 associated alignment view by the tree when a new tree is
2105 <li>showTreeBootstraps (true/false) - show or hide
2106 branch bootstraps (default is to show them if available)</li>
2107 <li>showTreeDistances (true/false) - show or hide
2108 branch lengths (default is to show them if available)</li>
2109 <li>showUnlinkedTreeNodes (true/false) - indicate if
2110 unassociated nodes should be highlighted in the tree
2112 <li>heightScale and widthScale (1.0 or more) -
2113 increase the height or width of a cell in the alignment
2114 grid relative to the current font size.</li>
2117 <li>Non-positional features displayed in sequence ID
2119 </ul> <em>Other</em>
2121 <li>Features format: graduated colour definitions and
2122 specification of feature scores</li>
2123 <li>Alignment Annotations format: new keywords for group
2124 associated annotation (GROUP_REF) and annotation row display
2125 properties (ROW_PROPERTIES)</li>
2126 <li>XML formats extended to support graduated feature
2127 colourschemes, group associated annotation, and profile
2128 visualization settings.</li></td>
2131 <li>Source field in GFF files parsed as feature source
2132 rather than description</li>
2133 <li>Non-positional features are now included in sequence
2134 feature and gff files (controlled via non-positional feature
2135 visibility in tooltip).</li>
2136 <li>URL links generated for all feature links (bugfix)</li>
2137 <li>Added URL embedding instructions to features file
2139 <li>Codons containing ambiguous nucleotides translated as
2140 'X' in peptide product</li>
2141 <li>Match case switch in find dialog box works for both
2142 sequence ID and sequence string and query strings do not
2143 have to be in upper case to match case-insensitively.</li>
2144 <li>AMSA files only contain first column of
2145 multi-character column annotation labels</li>
2146 <li>Jalview Annotation File generation/parsing consistent
2147 with documentation (e.g. Stockholm annotation can be
2148 exported and re-imported)</li>
2149 <li>PDB files without embedded PDB IDs given a friendly
2151 <li>Find incrementally searches ID string matches as well
2152 as subsequence matches, and correctly reports total number
2156 <li>Better handling of exceptions during sequence
2158 <li>Dasobert generated non-positional feature URL
2159 link text excludes the start_end suffix</li>
2160 <li>DAS feature and source retrieval buttons disabled
2161 when fetch or registry operations in progress.</li>
2162 <li>PDB files retrieved from URLs are cached properly</li>
2163 <li>Sequence description lines properly shared via
2165 <li>Sequence fetcher fetches multiple records for all
2167 <li>Ensured that command line das feature retrieval
2168 completes before alignment figures are generated.</li>
2169 <li>Reduced time taken when opening file browser for
2171 <li>isAligned check prior to calculating tree, PCA or
2172 submitting an MSA to JNet now excludes hidden sequences.</li>
2173 <li>User defined group colours properly recovered
2174 from Jalview projects.</li>
2183 <div align="center">
2184 <strong>2.4.0.b2</strong><br> 28/10/2009
2189 <li>Experimental support for google analytics usage
2191 <li>Jalview privacy settings (user preferences and docs).</li>
2196 <li>Race condition in applet preventing startup in
2198 <li>Exception when feature created from selection beyond
2199 length of sequence.</li>
2200 <li>Allow synthetic PDB files to be imported gracefully</li>
2201 <li>Sequence associated annotation rows associate with
2202 all sequences with a given id</li>
2203 <li>Find function matches case-insensitively for sequence
2204 ID string searches</li>
2205 <li>Non-standard characters do not cause pairwise
2206 alignment to fail with exception</li>
2207 </ul> <em>Application Issues</em>
2209 <li>Sequences are now validated against EMBL database</li>
2210 <li>Sequence fetcher fetches multiple records for all
2212 </ul> <em>InstallAnywhere Issues</em>
2214 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2215 issue with installAnywhere mechanism)</li>
2216 <li>Command line launching of JARs from InstallAnywhere
2217 version (java class versioning error fixed)</li>
2224 <div align="center">
2225 <strong>2.4</strong><br> 27/8/2008
2228 <td><em>User Interface</em>
2230 <li>Linked highlighting of codon and amino acid from
2231 translation and protein products</li>
2232 <li>Linked highlighting of structure associated with
2233 residue mapping to codon position</li>
2234 <li>Sequence Fetcher provides example accession numbers
2235 and 'clear' button</li>
2236 <li>MemoryMonitor added as an option under Desktop's
2238 <li>Extract score function to parse whitespace separated
2239 numeric data in description line</li>
2240 <li>Column labels in alignment annotation can be centred.</li>
2241 <li>Tooltip for sequence associated annotation give name
2243 </ul> <em>Web Services and URL fetching</em>
2245 <li>JPred3 web service</li>
2246 <li>Prototype sequence search client (no public services
2248 <li>Fetch either seed alignment or full alignment from
2250 <li>URL Links created for matching database cross
2251 references as well as sequence ID</li>
2252 <li>URL Links can be created using regular-expressions</li>
2253 </ul> <em>Sequence Database Connectivity</em>
2255 <li>Retrieval of cross-referenced sequences from other
2257 <li>Generalised database reference retrieval and
2258 validation to all fetchable databases</li>
2259 <li>Fetch sequences from DAS sources supporting the
2260 sequence command</li>
2261 </ul> <em>Import and Export</em>
2262 <li>export annotation rows as CSV for spreadsheet import</li>
2263 <li>Jalview projects record alignment dataset associations,
2264 EMBL products, and cDNA sequence mappings</li>
2265 <li>Sequence Group colour can be specified in Annotation
2267 <li>Ad-hoc colouring of group in Annotation File using RGB
2268 triplet as name of colourscheme</li>
2269 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2271 <li>treenode binding for VAMSAS tree exchange</li>
2272 <li>local editing and update of sequences in VAMSAS
2273 alignments (experimental)</li>
2274 <li>Create new or select existing session to join</li>
2275 <li>load and save of vamsas documents</li>
2276 </ul> <em>Application command line</em>
2278 <li>-tree parameter to open trees (introduced for passing
2280 <li>-fetchfrom command line argument to specify nicknames
2281 of DAS servers to query for alignment features</li>
2282 <li>-dasserver command line argument to add new servers
2283 that are also automatically queried for features</li>
2284 <li>-groovy command line argument executes a given groovy
2285 script after all input data has been loaded and parsed</li>
2286 </ul> <em>Applet-Application data exchange</em>
2288 <li>Trees passed as applet parameters can be passed to
2289 application (when using "View in full
2290 application")</li>
2291 </ul> <em>Applet Parameters</em>
2293 <li>feature group display control parameter</li>
2294 <li>debug parameter</li>
2295 <li>showbutton parameter</li>
2296 </ul> <em>Applet API methods</em>
2298 <li>newView public method</li>
2299 <li>Window (current view) specific get/set public methods</li>
2300 <li>Feature display control methods</li>
2301 <li>get list of currently selected sequences</li>
2302 </ul> <em>New Jalview distribution features</em>
2304 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2305 <li>RELEASE file gives build properties for the latest
2306 Jalview release.</li>
2307 <li>Java 1.1 Applet build made easier and donotobfuscate
2308 property controls execution of obfuscator</li>
2309 <li>Build target for generating source distribution</li>
2310 <li>Debug flag for javacc</li>
2311 <li>.jalview_properties file is documented (slightly) in
2312 jalview.bin.Cache</li>
2313 <li>Continuous Build Integration for stable and
2314 development version of Application, Applet and source
2319 <li>selected region output includes visible annotations
2320 (for certain formats)</li>
2321 <li>edit label/displaychar contains existing label/char
2323 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2324 <li>shorter peptide product names from EMBL records</li>
2325 <li>Newick string generator makes compact representations</li>
2326 <li>bootstrap values parsed correctly for tree files with
2328 <li>pathological filechooser bug avoided by not allowing
2329 filenames containing a ':'</li>
2330 <li>Fixed exception when parsing GFF files containing
2331 global sequence features</li>
2332 <li>Alignment datasets are finalized only when number of
2333 references from alignment sequences goes to zero</li>
2334 <li>Close of tree branch colour box without colour
2335 selection causes cascading exceptions</li>
2336 <li>occasional negative imgwidth exceptions</li>
2337 <li>better reporting of non-fatal warnings to user when
2338 file parsing fails.</li>
2339 <li>Save works when Jalview project is default format</li>
2340 <li>Save as dialog opened if current alignment format is
2341 not a valid output format</li>
2342 <li>UniProt canonical names introduced for both das and
2344 <li>Histidine should be midblue (not pink!) in Zappo</li>
2345 <li>error messages passed up and output when data read
2347 <li>edit undo recovers previous dataset sequence when
2348 sequence is edited</li>
2349 <li>allow PDB files without pdb ID HEADER lines (like
2350 those generated by MODELLER) to be read in properly</li>
2351 <li>allow reading of JPred concise files as a normal
2353 <li>Stockholm annotation parsing and alignment properties
2354 import fixed for PFAM records</li>
2355 <li>Structure view windows have correct name in Desktop
2357 <li>annotation consisting of sequence associated scores
2358 can be read and written correctly to annotation file</li>
2359 <li>Aligned cDNA translation to aligned peptide works
2361 <li>Fixed display of hidden sequence markers and
2362 non-italic font for representatives in Applet</li>
2363 <li>Applet Menus are always embedded in applet window on
2365 <li>Newly shown features appear at top of stack (in
2367 <li>Annotations added via parameter not drawn properly
2368 due to null pointer exceptions</li>
2369 <li>Secondary structure lines are drawn starting from
2370 first column of alignment</li>
2371 <li>UniProt XML import updated for new schema release in
2373 <li>Sequence feature to sequence ID match for Features
2374 file is case-insensitive</li>
2375 <li>Sequence features read from Features file appended to
2376 all sequences with matching IDs</li>
2377 <li>PDB structure coloured correctly for associated views
2378 containing a sub-sequence</li>
2379 <li>PDB files can be retrieved by applet from Jar files</li>
2380 <li>feature and annotation file applet parameters
2381 referring to different directories are retrieved correctly</li>
2382 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
2383 <li>Fixed application hang whilst waiting for
2384 splash-screen version check to complete</li>
2385 <li>Applet properly URLencodes input parameter values
2386 when passing them to the launchApp service</li>
2387 <li>display name and local features preserved in results
2388 retrieved from web service</li>
2389 <li>Visual delay indication for sequence retrieval and
2390 sequence fetcher initialisation</li>
2391 <li>updated Application to use DAS 1.53e version of
2392 dasobert DAS client</li>
2393 <li>Re-instated Full AMSA support and .amsa file
2395 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
2403 <div align="center">
2404 <strong>2.3</strong><br> 9/5/07
2409 <li>Jmol 11.0.2 integration</li>
2410 <li>PDB views stored in Jalview XML files</li>
2411 <li>Slide sequences</li>
2412 <li>Edit sequence in place</li>
2413 <li>EMBL CDS features</li>
2414 <li>DAS Feature mapping</li>
2415 <li>Feature ordering</li>
2416 <li>Alignment Properties</li>
2417 <li>Annotation Scores</li>
2418 <li>Sort by scores</li>
2419 <li>Feature/annotation editing in applet</li>
2424 <li>Headless state operation in 2.2.1</li>
2425 <li>Incorrect and unstable DNA pairwise alignment</li>
2426 <li>Cut and paste of sequences with annotation</li>
2427 <li>Feature group display state in XML</li>
2428 <li>Feature ordering in XML</li>
2429 <li>blc file iteration selection using filename # suffix</li>
2430 <li>Stockholm alignment properties</li>
2431 <li>Stockhom alignment secondary structure annotation</li>
2432 <li>2.2.1 applet had no feature transparency</li>
2433 <li>Number pad keys can be used in cursor mode</li>
2434 <li>Structure Viewer mirror image resolved</li>
2441 <div align="center">
2442 <strong>2.2.1</strong><br> 12/2/07
2447 <li>Non standard characters can be read and displayed
2448 <li>Annotations/Features can be imported/exported to the
2450 <li>Applet allows editing of sequence/annotation/group
2451 name & description
2452 <li>Preference setting to display sequence name in
2454 <li>Annotation file format extended to allow
2455 Sequence_groups to be defined
2456 <li>Default opening of alignment overview panel can be
2457 specified in preferences
2458 <li>PDB residue numbering annotation added to associated
2464 <li>Applet crash under certain Linux OS with Java 1.6
2466 <li>Annotation file export / import bugs fixed
2467 <li>PNG / EPS image output bugs fixed
2473 <div align="center">
2474 <strong>2.2</strong><br> 27/11/06
2479 <li>Multiple views on alignment
2480 <li>Sequence feature editing
2481 <li>"Reload" alignment
2482 <li>"Save" to current filename
2483 <li>Background dependent text colour
2484 <li>Right align sequence ids
2485 <li>User-defined lower case residue colours
2488 <li>Menu item accelerator keys
2489 <li>Control-V pastes to current alignment
2490 <li>Cancel button for DAS Feature Fetching
2491 <li>PCA and PDB Viewers zoom via mouse roller
2492 <li>User-defined sub-tree colours and sub-tree selection
2499 <li>'New Window' button on the 'Output to Text box'
2504 <li>New memory efficient Undo/Redo System
2505 <li>Optimised symbol lookups and conservation/consensus
2507 <li>Region Conservation/Consensus recalculated after
2509 <li>Fixed Remove Empty Columns Bug (empty columns at end
2511 <li>Slowed DAS Feature Fetching for increased robustness.
2518 <li>Made angle brackets in ASCII feature descriptions
2520 <li>Re-instated Zoom function for PCA
2521 <li>Sequence descriptions conserved in web service
2523 <li>UniProt ID discoverer uses any word separated by
2525 <li>WsDbFetch query/result association resolved
2526 <li>Tree leaf to sequence mapping improved
2527 <li>Smooth fonts switch moved to FontChooser dialog box.
2539 <div align="center">
2540 <strong>2.1.1</strong><br> 12/9/06
2545 <li>Copy consensus sequence to clipboard</li>
2550 <li>Image output - rightmost residues are rendered if
2551 sequence id panel has been resized</li>
2552 <li>Image output - all offscreen group boundaries are
2554 <li>Annotation files with sequence references - all
2555 elements in file are relative to sequence position</li>
2556 <li>Mac Applet users can use Alt key for group editing</li>
2562 <div align="center">
2563 <strong>2.1</strong><br> 22/8/06
2568 <li>MAFFT Multiple Alignment in default Web Service list</li>
2569 <li>DAS Feature fetching</li>
2570 <li>Hide sequences and columns</li>
2571 <li>Export Annotations and Features</li>
2572 <li>GFF file reading / writing</li>
2573 <li>Associate structures with sequences from local PDB
2575 <li>Add sequences to exisiting alignment</li>
2576 <li>Recently opened files / URL lists</li>
2577 <li>Applet can launch the full application</li>
2578 <li>Applet has transparency for features (Java 1.2
2580 <li>Applet has user defined colours parameter</li>
2581 <li>Applet can load sequences from parameter
2582 "sequence<em>x</em>"
2588 <li>Redundancy Panel reinstalled in the Applet</li>
2589 <li>Monospaced font - EPS / rescaling bug fixed</li>
2590 <li>Annotation files with sequence references bug fixed</li>
2596 <div align="center">
2597 <strong>2.08.1</strong><br> 2/5/06
2602 <li>Change case of selected region from Popup menu</li>
2603 <li>Choose to match case when searching</li>
2604 <li>Middle mouse button and mouse movement can compress /
2605 expand the visible width and height of the alignment</li>
2610 <li>Annotation Panel displays complete JNet results</li>
2616 <div align="center">
2617 <strong>2.08b</strong><br> 18/4/06
2623 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
2624 <li>Righthand label on wrapped alignments shows correct
2631 <div align="center">
2632 <strong>2.08</strong><br> 10/4/06
2637 <li>Editing can be locked to the selection area</li>
2638 <li>Keyboard editing</li>
2639 <li>Create sequence features from searches</li>
2640 <li>Precalculated annotations can be loaded onto
2642 <li>Features file allows grouping of features</li>
2643 <li>Annotation Colouring scheme added</li>
2644 <li>Smooth fonts off by default - Faster rendering</li>
2645 <li>Choose to toggle Autocalculate Consensus On/Off</li>
2650 <li>Drag & Drop fixed on Linux</li>
2651 <li>Jalview Archive file faster to load/save, sequence
2652 descriptions saved.</li>
2658 <div align="center">
2659 <strong>2.07</strong><br> 12/12/05
2664 <li>PDB Structure Viewer enhanced</li>
2665 <li>Sequence Feature retrieval and display enhanced</li>
2666 <li>Choose to output sequence start-end after sequence
2667 name for file output</li>
2668 <li>Sequence Fetcher WSDBFetch@EBI</li>
2669 <li>Applet can read feature files, PDB files and can be
2670 used for HTML form input</li>
2675 <li>HTML output writes groups and features</li>
2676 <li>Group editing is Control and mouse click</li>
2677 <li>File IO bugs</li>
2683 <div align="center">
2684 <strong>2.06</strong><br> 28/9/05
2689 <li>View annotations in wrapped mode</li>
2690 <li>More options for PCA viewer</li>
2695 <li>GUI bugs resolved</li>
2696 <li>Runs with -nodisplay from command line</li>
2702 <div align="center">
2703 <strong>2.05b</strong><br> 15/9/05
2708 <li>Choose EPS export as lineart or text</li>
2709 <li>Jar files are executable</li>
2710 <li>Can read in Uracil - maps to unknown residue</li>
2715 <li>Known OutOfMemory errors give warning message</li>
2716 <li>Overview window calculated more efficiently</li>
2717 <li>Several GUI bugs resolved</li>
2723 <div align="center">
2724 <strong>2.05</strong><br> 30/8/05
2729 <li>Edit and annotate in "Wrapped" view</li>
2734 <li>Several GUI bugs resolved</li>
2740 <div align="center">
2741 <strong>2.04</strong><br> 24/8/05
2746 <li>Hold down mouse wheel & scroll to change font
2752 <li>Improved JPred client reliability</li>
2753 <li>Improved loading of Jalview files</li>
2759 <div align="center">
2760 <strong>2.03</strong><br> 18/8/05
2765 <li>Set Proxy server name and port in preferences</li>
2766 <li>Multiple URL links from sequence ids</li>
2767 <li>User Defined Colours can have a scheme name and added
2769 <li>Choose to ignore gaps in consensus calculation</li>
2770 <li>Unix users can set default web browser</li>
2771 <li>Runs without GUI for batch processing</li>
2772 <li>Dynamically generated Web Service Menus</li>
2777 <li>InstallAnywhere download for Sparc Solaris</li>
2783 <div align="center">
2784 <strong>2.02</strong><br> 18/7/05
2790 <li>Copy & Paste order of sequences maintains
2791 alignment order.</li>
2797 <div align="center">
2798 <strong>2.01</strong><br> 12/7/05
2803 <li>Use delete key for deleting selection.</li>
2804 <li>Use Mouse wheel to scroll sequences.</li>
2805 <li>Help file updated to describe how to add alignment
2807 <li>Version and build date written to build properties
2809 <li>InstallAnywhere installation will check for updates
2810 at launch of Jalview.</li>
2815 <li>Delete gaps bug fixed.</li>
2816 <li>FileChooser sorts columns.</li>
2817 <li>Can remove groups one by one.</li>
2818 <li>Filechooser icons installed.</li>
2819 <li>Finder ignores return character when searching.
2820 Return key will initiate a search.<br>
2827 <div align="center">
2828 <strong>2.0</strong><br> 20/6/05
2833 <li>New codebase</li>