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>
25 this tip works for the browser and the Java help browser:
26 http://stackoverflow.com/questions/13626531/swing-html-rendering-shows-very-large-bullet-point
27 this tip works for the browser but not in the Java help browser:
28 http://stackoverflow.com/questions/17158253/indenting-the-2nd-line-of-a-paragraph-with-css
32 list-style-type: none;
43 <strong>Release History</strong>
47 <td width="60" nowrap>
49 <em><strong>Release</strong></em>
54 <em><strong>New Features</strong></em>
59 <em><strong>Issues Resolved</strong></em>
64 <td width="60" nowrap>
66 <strong><a name="Jalview.2.10.1">2.10.1</a><br />
67 <em>29/11/2016</em></strong>
70 <td><div align="left">
74 <!-- JAL-98 -->Improved memory usage: sparse arrays used
75 for all consensus calculations
78 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released 3rd Oct 2016)
80 <li>• Updated Jalview's Certum code signing certificate
86 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
87 set of database cross-references, sorted alphabetically
90 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
91 from database cross references. Users with custom links
92 will receive a <a href="webServices/urllinks.html#warning">warning
93 dialog</a> asking them to update their preferences.
96 <!-- JAL-2287-->Cancel button and escape listener on
97 dialog warning user about disconnecting Jalview from a
101 <!-- JAL-2320-->Jalview's Chimera control window closes if
102 the Chimera it is connected to is shut down
105 <!-- JAL-1738-->New keystroke (B) and Select highlighted
106 columns menu item to mark columns containing
107 highlighted regions (e.g. from structure selections or results
111 <!-- JAL-2284-->Command line option for batch-generation
112 of HTML pages rendering alignment data with the BioJS
122 <!-- JAL-2286 -->Columns with more than one modal residue
123 are not coloured or thresholded according to percent
124 identity (first observed in Jalview 2.8.2)
127 <!-- JAL-2301 -->Threonine incorrectly reported as not
131 <!-- JAL-2318 -->Updates to documentation pages (above PID
132 threshold, amino acid properties)
135 <!-- JAL-2292 -->Lower case residues in sequences are not
136 reported as mapped to residues in a structure file in the
140 <!--JAL-2324 -->Identical features with non-numeric scores
141 could be added multiple times to a sequence
144 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
145 bond features shown as two highlighted residues rather
146 than a range in linked structure views, and treated
147 correctly when selecting and computing trees from features
150 <!-- JAL-2281-->Custom URL links for database
151 cross-references are matched to database name regardless
159 <!-- JAL-2282-->Custom URL links for specific database
160 names without regular expressions also offer links from
164 <!-- JAL-2315-->Removing a single configured link in the
165 URL links pane in Connections preferences doesn't actually
166 update Jalview configuration
169 <!-- JAL-2272-->CTRL-Click on a selected region to open
170 the alignment area popup menu doesn't work on El-Capitan
173 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
174 files with similarly named sequences if dropped onto the
178 <!-- JAL-2312 -->Additional mappings are shown for PDB
179 entries where more chains exist in the PDB accession than
180 are reported in the SIFTS file
183 <!-- JAL-2317-->Certain structures do not get mapped to
184 the structure view when displayed with Chimera
187 <!-- JAL-2317-->No chains shown in the Chimera view
188 panel's View->Show Chains submenu
191 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
192 work for wrapped alignment views
195 <!--JAL-2197 -->Rename UI components for running JPred
196 predictions from 'JNet' to 'JPred'
199 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
200 corrupted when annotation panel vertical scroll is not at
204 <!--JAL-2332 -->Attempting to view structure for Hen
205 lysozyme results in a PDB Client error dialog box
208 <!-- <em>New Known Issues</em>
210 <li>• </li>
215 <td width="60" nowrap>
217 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
218 <em>25/10/2016</em></strong>
221 <td><em>Application</em>
223 <li>• 3D Structure chooser opens with 'Cached structures'
224 view if structures already loaded</li>
225 <li>• Progress bar reports models as they are loaded to
232 <li>• Colour by conservation always enabled and no tick
233 shown in menu when BLOSUM or PID shading applied</li>
234 <li>• FER1_ARATH and FER2_ARATH labels were switched in
235 example sequences/projects/trees</li>
239 <li>• Jalview projects with views of local PDB structure
240 files saved on Windows cannot be opened on OSX</li>
241 <li>• Multiple structure views can be opened and
242 superposed without timeout for structures with multiple
243 models or multiple sequences in alignment</li>
244 <li>• Cannot import or associated local PDB files without
245 a PDB ID HEADER line</li>
246 <li>• RMSD is not output in Jmol console when
247 superposition is performed</li>
248 <li>• Drag and drop of URL from Browser fails for Linux
249 and OSX versions earlier than El Capitan</li>
250 <li>• ENA client ignores invalid content from ENA server</li>
251 <li>• Exceptions are not raised in console when ENA
252 client attempts to fetch non-existent IDs via Fetch DB
254 <li>• Exceptions are not raised in console when a new
255 view is created on the alignment</li>
256 <li>• OSX right-click fixed for group selections:
257 CMD-click to insert/remove gaps in groups and CTRL-click
258 to open group pop-up menu</li>
260 <em>Build and deployment</em>
262 <li>• URL link checker now copes with multi-line anchor
265 <em>New Known Issues</em>
267 <li>• Drag and drop from URL links in browsers do not
274 <td width="60" nowrap>
276 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
282 <!-- JAL-2124 -->Updated Spanish translations.
285 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
286 for importing structure data to Jalview. Enables mmCIF and
290 <!-- JAL-192 --->Alignment ruler shows positions relative to
294 <!-- JAL-2202 -->Position/residue shown in status bar when
295 mousing over sequence associated annotation
298 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
302 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
303 '()', canonical '[]' and invalid '{}' base pair populations
307 <!-- JAL-2092 -->Feature settings popup menu options for
308 showing or hiding columns containing a feature
311 <!-- JAL-1557 -->Edit selected group by double clicking on
312 group and sequence associated annotation labels
315 <!-- JAL-2236 -->Sequence name added to annotation label in
316 select/hide columns by annotation and colour by annotation
320 </ul> <em>Application</em>
323 <!-- JAL-2050-->Automatically hide introns when opening a
327 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
331 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
332 structure mappings with the EMBL-EBI PDBe SIFTS database
335 <!-- JAL-2079 -->Updated download sites used for Rfam and
336 Pfam sources to xfam.org
339 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
342 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
343 over sequences in Jalview
346 <!-- JAL-2027-->Support for reverse-complement coding
347 regions in ENA and EMBL
350 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
351 for record retrieval via ENA rest API
354 <!-- JAL-2027 -->Support for ENA CDS records with reverse
358 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
359 groovy script execution
362 <!-- JAL-1812 -->New 'execute Groovy script' option in an
363 alignment window's Calculate menu
366 <!-- JAL-1812 -->Allow groovy scripts that call
367 Jalview.getAlignFrames() to run in headless mode
370 <!-- JAL-2068 -->Support for creating new alignment
371 calculation workers from groovy scripts
374 <!-- JAL-1369 --->Store/restore reference sequence in
378 <!-- JAL-1803 -->Chain codes for a sequence's PDB
379 associations are now saved/restored from project
382 <!-- JAL-1993 -->Database selection dialog always shown
383 before sequence fetcher is opened
386 <!-- JAL-2183 -->Double click on an entry in Jalview's
387 database chooser opens a sequence fetcher
390 <!-- JAL-1563 -->Free-text search client for UniProt using
394 <!-- JAL-2168 -->-nonews command line parameter to prevent
395 the news reader opening
398 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
399 querying stored in preferences
402 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
406 <!-- JAL-1977-->Tooltips shown on database chooser
409 <!-- JAL-391 -->Reverse complement function in calculate
410 menu for nucleotide sequences
413 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
414 and feature counts preserves alignment ordering (and
415 debugged for complex feature sets).
418 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
419 viewing structures with Jalview 2.10
422 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
423 genome, transcript CCDS and gene ids via the Ensembl and
424 Ensembl Genomes REST API
427 <!-- JAL-2049 -->Protein sequence variant annotation
428 computed for 'sequence_variant' annotation on CDS regions
432 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
436 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
437 Ref Fetcher fails to match, or otherwise updates sequence
438 data from external database records.
441 <!-- JAL-2154 -->Revised Jalview Project format for
442 efficient recovery of sequence coding and alignment
443 annotation relationships.
445 </ul> <!-- <em>Applet</em>
456 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
460 <!-- JAL-2018-->Export features in Jalview format (again)
461 includes graduated colourschemes
464 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
465 working with big alignments and lots of hidden columns
468 <!-- JAL-2053-->Hidden column markers not always rendered
469 at right of alignment window
472 <!-- JAL-2067 -->Tidied up links in help file table of
476 <!-- JAL-2072 -->Feature based tree calculation not shown
480 <!-- JAL-2075 -->Hidden columns ignored during feature
481 based tree calculation
484 <!-- JAL-2065 -->Alignment view stops updating when show
485 unconserved enabled for group on alignment
488 <!-- JAL-2086 -->Cannot insert gaps into sequence when
492 <!-- JAL-2146 -->Alignment column in status incorrectly
493 shown as "Sequence position" when mousing over
497 <!-- JAL-2099 -->Incorrect column numbers in ruler when
498 hidden columns present
501 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
502 user created annotation added to alignment
505 <!-- JAL-1841 -->RNA Structure consensus only computed for
506 '()' base pair annotation
509 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
510 in zero scores for all base pairs in RNA Structure
514 <!-- JAL-2174-->Extend selection with columns containing
518 <!-- JAL-2275 -->Pfam format writer puts extra space at
519 beginning of sequence
522 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
526 <!-- JAL-2238 -->Cannot create groups on an alignment from
527 from a tree when t-coffee scores are shown
530 <!-- JAL-1836,1967 -->Cannot import and view PDB
531 structures with chains containing negative resnums (4q4h)
534 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
538 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
539 to Clustal, PIR and PileUp output
542 <!-- JAL-2008 -->Reordering sequence features that are
543 not visible causes alignment window to repaint
546 <!-- JAL-2006 -->Threshold sliders don't work in
547 graduated colour and colour by annotation row for e-value
548 scores associated with features and annotation rows
551 <!-- JAL-1797 -->amino acid physicochemical conservation
552 calculation should be case independent
555 <!-- JAL-2173 -->Remove annotation also updates hidden
559 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
560 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
561 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
564 <!-- JAL-2065 -->Null pointer exceptions and redraw
565 problems when reference sequence defined and 'show
566 non-conserved' enabled
569 <!-- JAL-1306 -->Quality and Conservation are now shown on
570 load even when Consensus calculation is disabled
573 <!-- JAL-1932 -->Remove right on penultimate column of
574 alignment does nothing
580 <!-- JAL-1552-->URLs and links can't be imported by
581 drag'n'drop on OSX when launched via webstart (note - not
582 yet fixed for El Capitan)
585 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
586 output when running on non-gb/us i18n platforms
589 <!-- JAL-1944 -->Error thrown when exporting a view with
590 hidden sequences as flat-file alignment
593 <!-- JAL-2030-->InstallAnywhere distribution fails when
597 <!-- JAL-2080-->Jalview very slow to launch via webstart
598 (also hotfix for 2.9.0b2)
601 <!-- JAL-2085 -->Cannot save project when view has a
602 reference sequence defined
605 <!-- JAL-1011 -->Columns are suddenly selected in other
606 alignments and views when revealing hidden columns
609 <!-- JAL-1989 -->Hide columns not mirrored in complement
610 view in a cDNA/Protein splitframe
613 <!-- JAL-1369 -->Cannot save/restore representative
614 sequence from project when only one sequence is
618 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
622 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
623 structure consensus didn't refresh annotation panel
626 <!-- JAL-1962 -->View mapping in structure view shows
627 mappings between sequence and all chains in a PDB file
630 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
631 dialogs format columns correctly, don't display array
632 data, sort columns according to type
635 <!-- JAL-1975 -->Export complete shown after destination
636 file chooser is cancelled during an image export
639 <!-- JAL-2025 -->Error when querying PDB Service with
640 sequence name containing special characters
643 <!-- JAL-2024 -->Manual PDB structure querying should be
647 <!-- JAL-2104 -->Large tooltips with broken HTML
648 formatting don't wrap
651 <!-- JAL-1128 -->Figures exported from wrapped view are
652 truncated so L looks like I in consensus annotation
655 <!-- JAL-2003 -->Export features should only export the
656 currently displayed features for the current selection or
660 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
661 after fetching cross-references, and restoring from project
664 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
665 followed in the structure viewer
668 <!-- JAL-2163 -->Titles for individual alignments in
669 splitframe not restored from project
672 <!-- JAL-2145 -->missing autocalculated annotation at
673 trailing end of protein alignment in transcript/product
674 splitview when pad-gaps not enabled by default
677 <!-- JAL-1797 -->amino acid physicochemical conservation
681 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
682 article has been read (reopened issue due to
683 internationalisation problems)
686 <!-- JAL-1960 -->Only offer PDB structures in structure
687 viewer based on sequence name, PDB and UniProt
692 <!-- JAL-1976 -->No progress bar shown during export of
696 <!-- JAL-2213 -->Structures not always superimposed after
697 multiple structures are shown for one or more sequences.
700 <!-- JAL-1370 -->Reference sequence characters should not
701 be replaced with '.' when 'Show unconserved' format option
705 <!-- JAL-1823 -->Cannot specify chain code when entering
706 specific PDB id for sequence
709 <!-- JAL-1944 -->File->Export->.. as doesn't work when
710 'Export hidden sequences' is enabled, but 'export hidden
711 columns' is disabled.
714 <!--JAL-2026-->Best Quality option in structure chooser
715 selects lowest rather than highest resolution structures
719 <!-- JAL-1887 -->Incorrect start and end reported for PDB
720 to sequence mapping in 'View Mappings' report
723 <!-- JAL-2284 -->Unable to read old Jalview projects that
724 contain non-XML data added after Jalvew wrote project.
726 <li>• <!-- JAL-2118 -->Newly created annotation row reorders
727 after clicking on it to create new annotation for a
730 <!-- may exclude, this is an external service stability issue JAL-1941
731 -- > RNA 3D structure not added via DSSR service</li> -->
736 <!-- JAL-2151 -->Incorrect columns are selected when
737 hidden columns present before start of sequence
740 <!-- JAL-1986 -->Missing dependencies on applet pages
744 <!-- JAL-1947 -->Overview pixel size changes when
745 sequences are hidden in applet
748 <!-- JAL-1996 -->Updated instructions for applet
749 deployment on examples pages.
756 <td width="60" nowrap>
758 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
759 <em>16/10/2015</em></strong>
764 <li>• Time stamps for signed Jalview application and applet
771 <li>• Duplicate group consensus and conservation rows
772 shown when tree is partitioned</li>
773 <li>• Erratic behaviour when tree partitions made with
774 multiple cDNA/Protein split views</li>
780 <td width="60" nowrap>
782 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
783 <em>8/10/2015</em></strong>
788 <li>• Updated Spanish translations of localized text for
790 </ul> <em>Application</em>
792 <!-- <li>• cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
793 <li>• Signed OSX InstallAnywhere installer<br></li>
794 <li>• Support for per-sequence based annotations in BioJSON</li>
795 </ul> <em>Applet</em>
797 <li>• Split frame example added to applet examples page</li>
798 </ul><em>Build and Deployment</em>
800 <li>• <!-- JAL-1888 -->New ant target for running Jalview's test suite</li>
806 <li>• Mapping of cDNA to protein in split frames
807 incorrect when sequence start > 1</li>
808 <li>• Broken images in filter column by annotation dialog
810 <li>• Feature colours not parsed from features file</li>
811 <li>• Exceptions and incomplete link URLs recovered when
812 loading a features file containing HTML tags in feature
818 <li>• Annotations corrupted after BioJS export and
820 <li>• Incorrect sequence limits after Fetch DB References
821 with 'trim retrieved sequences'</li>
822 <li>• Incorrect warning about deleting all data when
823 deleting selected columns</li>
824 <li>• Patch to build system for shipping properly signed
825 JNLP templates for webstart launch</li>
826 <li>• EMBL-PDBe fetcher/viewer dialogs do not offer
827 unreleased structures for download or viewing</li>
828 <li>• Tab/space/return keystroke operation of EMBL-PDBe
829 fetcher/viewer dialogs works correctly</li>
830 <li>• Disabled 'minimise' button on Jalview windows
831 running on OSX to workaround redraw hang bug</li>
832 <li>• Split cDNA/Protein view position and geometry not
833 recovered from jalview project</li>
834 <li>• Initial enabled/disabled state of annotation menu
835 sorter 'show autocalculated first/last' corresponds to
837 <li>• Restoring of Clustal, RNA Helices and T-Coffee
838 color schemes from BioJSON</li>
842 <li>• Reorder sequences mirrored in cDNA/Protein split
844 <li>• Applet with Jmol examples not loading correctly</li>
850 <td><div align="center">
851 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
855 <li>• Linked visualisation and analysis of DNA and Protein
858 <li>• Translated cDNA alignments shown as split protein
859 and DNA alignment views</li>
860 <li>• Codon consensus annotation for linked protein and
861 cDNA alignment views</li>
862 <li>• Link cDNA or Protein product sequences by loading
863 them onto Protein or cDNA alignments</li>
864 <li>• Reconstruct linked cDNA alignment from aligned
865 protein sequences</li>
868 <li>• Jmol integration updated to Jmol v14.2.14</li>
869 <li>• Import and export of Jalview alignment views as <a
870 href="features/bioJsonFormat.html">BioJSON</a></li>
871 <li>• New alignment annotation file statements for
872 reference sequences and marking hidden columns</li>
873 <li>• Reference sequence based alignment shading to
874 highlight variation</li>
875 <li>• Select or hide columns according to alignment
877 <li>• Find option for locating sequences by description</li>
878 <li>• Conserved physicochemical properties shown in amino
879 acid conservation row</li>
880 <li>• Alignments can be sorted by number of RNA helices</li>
881 </ul> <em>Application</em>
883 <li>• New cDNA/Protein analysis capabilities
885 <li>• Get Cross-References should open a Split Frame
886 view with cDNA/Protein</li>
887 <li>• Detect when nucleotide sequences and protein
888 sequences are placed in the same alignment</li>
889 <li>• Split cDNA/Protein views are saved in Jalview
894 <li>• Use REST API to talk to Chimera</li>
895 <li>• Selected regions in Chimera are highlighted in linked
898 <li>• VARNA RNA viewer updated to v3.93</li>
899 <li>• VARNA views are saved in Jalview Projects</li>
900 <li>• Pseudoknots displayed as Jalview RNA annotation can
901 be shown in VARNA</li>
903 <li>• Make groups for selection uses marked columns as well
904 as the active selected region</li>
906 <li>• Calculate UPGMA and NJ trees using sequence feature
908 <li>• New Export options
910 <li>• New Export Settings dialog to control hidden
911 region export in flat file generation</li>
913 <li>• Export alignment views for display with the <a
914 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
916 <li>• Export scrollable SVG in HTML page</li>
917 <li>• Optional embedding of BioJSON data when exporting
918 alignment figures to HTML</li>
920 <li>• 3D structure retrieval and display
922 <li>• Free text and structured queries with the PDBe
924 <li>• PDBe Search API based discovery and selection of
925 PDB structures for a sequence set</li>
929 <li>• JPred4 employed for protein secondary structure
931 <li>• Hide Insertions menu option to hide unaligned columns
932 for one or a group of sequences</li>
933 <li>• Automatically hide insertions in alignments imported
934 from the JPred4 web server</li>
935 <li>• (Nearly) Native 'Quaqua' dialogs for browsing file
936 system on OSX<br />LGPL libraries courtesy of <a
937 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
939 <li>• changed 'View nucleotide structure' submenu to 'View
940 VARNA 2D Structure'</li>
941 <li>• change "View protein structure" menu option to "3D
944 </ul> <em>Applet</em>
946 <li>• New layout for applet example pages</li>
947 <li>• New parameters to enable SplitFrame view
948 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
949 <li>• New example demonstrating linked viewing of cDNA and
950 Protein alignments</li>
951 </ul> <em>Development and deployment</em>
953 <li>• Java 1.7 minimum requirement for Jalview 2.9</li>
954 <li>• Include installation type and git revision in build
955 properties and console log output</li>
956 <li>• Jalview Github organisation, and new github site for
957 storing BioJsMSA Templates</li>
958 <li>• Jalview's unit tests now managed with TestNG</li>
961 <!-- <em>General</em>
963 </ul> --> <!-- issues resolved --> <em>Application</em>
965 <li>• Escape should close any open find dialogs</li>
966 <li>• Typo in select-by-features status report</li>
967 <li>• Consensus RNA secondary secondary structure
968 predictions are not highlighted in amber</li>
969 <li>• Missing gap character in v2.7 example file means
970 alignment appears unaligned when pad-gaps is not enabled</li>
971 <li>• First switch to RNA Helices colouring doesn't colour
972 associated structure views</li>
973 <li>• ID width preference option is greyed out when auto
974 width checkbox not enabled</li>
975 <li>• Stopped a warning dialog from being shown when
976 creating user defined colours</li>
977 <li>• 'View Mapping' in structure viewer shows sequence
978 mappings for just that viewer's sequences</li>
979 <li>• Workaround for superposing PDB files containing
980 multiple models in Chimera</li>
981 <li>• Report sequence position in status bar when hovering
982 over Jmol structure</li>
983 <li>• Cannot output gaps as '.' symbols with Selection ->
984 output to text box</li>
985 <li>• Flat file exports of alignments with hidden columns
986 have incorrect sequence start/end</li>
987 <li>• 'Aligning' a second chain to a Chimera structure from
989 <li>• Colour schemes applied to structure viewers don't
990 work for nucleotide</li>
991 <li>• Loading/cut'n'pasting an empty or invalid file leads
992 to a grey/invisible alignment window</li>
993 <li>• Exported Jpred annotation from a sequence region
994 imports to different position</li>
995 <li>• Space at beginning of sequence feature tooltips shown
996 on some platforms</li>
997 <li>• Chimera viewer 'View | Show Chain' menu is not
999 <li>• 'New View' fails with a Null Pointer Exception in
1000 console if Chimera has been opened</li>
1001 <li>• Mouseover to Chimera not working</li>
1002 <li>• Miscellaneous ENA XML feature qualifiers not
1004 <li>• NPE in annotation renderer after 'Extract Scores'</li>
1005 <li>• If two structures in one Chimera window, mouseover of
1006 either sequence shows on first structure</li>
1007 <li>• 'Show annotations' options should not make
1008 non-positional annotations visible</li>
1009 <li>• Subsequence secondary structure annotation not shown
1010 in right place after 'view flanking regions'</li>
1011 <li>• File Save As type unset when current file format is
1013 <li>• Save as '.jar' option removed for saving Jalview
1015 <li>• Colour by Sequence colouring in Chimera more
1017 <li>• Cannot 'add reference annotation' for a sequence in
1018 several views on same alignment</li>
1019 <li>• Cannot show linked products for EMBL / ENA records</li>
1020 <li>• Jalview's tooltip wraps long texts containing no
1022 </ul> <em>Applet</em>
1024 <li>• Jmol to JalviewLite mouseover/link not working</li>
1025 <li>• JalviewLite can't import sequences with ID
1026 descriptions containing angle brackets</li>
1027 </ul> <em>General</em>
1029 <li>• Cannot export and reimport RNA secondary structure
1030 via jalview annotation file</li>
1031 <li>• Random helix colour palette for colour by annotation
1032 with RNA secondary structure</li>
1033 <li>• Mouseover to cDNA from STOP residue in protein
1034 translation doesn't work.</li>
1035 <li>• hints when using the select by annotation dialog box</li>
1036 <li>• Jmol alignment incorrect if PDB file has alternate CA
1038 <li>• FontChooser message dialog appears to hang after
1039 choosing 1pt font</li>
1040 <li>• Peptide secondary structure incorrectly imported from
1041 annotation file when annotation display text includes 'e' or
1043 <li>• Cannot set colour of new feature type whilst creating
1045 <li>• cDNA translation alignment should not be sequence
1046 order dependent</li>
1047 <li>• 'Show unconserved' doesn't work for lower case
1049 <li>• Nucleotide ambiguity codes involving R not recognised</li>
1050 </ul> <em>Deployment and Documentation</em>
1052 <li>• Applet example pages appear different to the rest of
1053 www.jalview.org</li>
1054 </ul> <em>Application Known issues</em>
1056 <li>• Incomplete sequence extracted from PDB entry 3a6s</li>
1057 <li>• Misleading message appears after trying to delete
1059 <li>• Jalview icon not shown in dock after InstallAnywhere
1060 version launches</li>
1061 <li>• Fetching EMBL reference for an RNA sequence results
1062 fails with a sequence mismatch</li>
1063 <li>• Corrupted or unreadable alignment display when
1064 scrolling alignment to right</li>
1065 <li>• ArrayIndexOutOfBoundsException thrown when remove
1066 empty columns called on alignment with ragged gapped ends</li>
1067 <li>• auto calculated alignment annotation rows do not get
1068 placed above or below non-autocalculated rows</li>
1069 <li>• Jalview dekstop becomes sluggish at full screen in
1070 ultra-high resolution</li>
1071 <li>• Cannot disable consensus calculation independently of
1072 quality and conservation</li>
1073 <li>• Mouseover highlighting between cDNA and protein can
1074 become sluggish with more than one splitframe shown</li>
1075 </ul> <em>Applet Known Issues</em>
1077 <li>• Core PDB parsing code requires Jmol</li>
1078 <li>• Sequence canvas panel goes white when alignment
1079 window is being resized</li>
1085 <td><div align="center">
1086 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1088 <td><em>General</em>
1090 <li>• Updated Java code signing certificate donated by
1092 <li>• Features and annotation preserved when performing
1093 pairwise alignment</li>
1094 <li>• RNA pseudoknot annotation can be
1095 imported/exported/displayed</li>
1096 <li>• 'colour by annotation' can colour by RNA and
1097 protein secondary structure</li>
1098 <li>• Warn user if 'Find' regular expression is invalid (<em>mentioned
1099 post-hoc with 2.9 release</em>)
1102 </ul> <em>Application</em>
1104 <li>• Extract and display secondary structure for sequences
1105 with 3D structures</li>
1106 <li>• Support for parsing RNAML</li>
1107 <li>• Annotations menu for layout
1109 <li>• sort sequence annotation rows by alignment</li>
1110 <li>• place sequence annotation above/below alignment
1113 <li>• Output in Stockholm format</li>
1114 <li>• Internationalisation: improved Spanish (es)
1116 <li>• Structure viewer preferences tab</li>
1117 <li>• Disorder and Secondary Structure annotation tracks
1118 shared between alignments</li>
1119 <li>• UCSF Chimera launch and linked highlighting from
1121 <li>• Show/hide all sequence associated annotation rows for
1122 all or current selection</li>
1123 <li>• disorder and secondary structure predictions
1124 available as dataset annotation</li>
1125 <li>• Per-sequence rna helices colouring</li>
1128 <li>• Sequence database accessions imported when fetching
1129 alignments from Rfam</li>
1130 <li>• update VARNA version to 3.91</li>
1132 <li>• New groovy scripts for exporting aligned positions,
1133 conservation values, and calculating sum of pairs scores.</li>
1134 <li>• Command line argument to set default JABAWS server</li>
1135 <li>• include installation type in build properties and
1136 console log output</li>
1137 <li>• Updated Jalview project format to preserve dataset
1141 <!-- issues resolved --> <em>Application</em>
1143 <li>• Distinguish alignment and sequence associated RNA
1144 structure in structure->view->VARNA</li>
1145 <li>• Raise dialog box if user deletes all sequences in an
1147 <li>• Pressing F1 results in documentation opening twice</li>
1148 <li>• Sequence feature tooltip is wrapped</li>
1149 <li>• Double click on sequence associated annotation
1150 selects only first column</li>
1151 <li>• Redundancy removal doesn't result in unlinked
1152 leaves shown in tree</li>
1153 <li>• Undos after several redundancy removals don't undo
1155 <li>• Hide sequence doesn't hide associated annotation</li>
1156 <li>• User defined colours dialog box too big to fit on
1157 screen and buttons not visible</li>
1158 <li>• author list isn't updated if already written to
1159 Jalview properties</li>
1160 <li>• Popup menu won't open after retrieving sequence
1162 <li>• File open window for associate PDB doesn't open</li>
1163 <li>• Left-then-right click on a sequence id opens a
1164 browser search window</li>
1165 <li>• Cannot open sequence feature shading/sort popup menu
1166 in feature settings dialog</li>
1167 <li>• better tooltip placement for some areas of Jalview
1169 <li>• Allow addition of JABAWS Server which doesn't
1170 pass validation</li>
1171 <li>• Web services parameters dialog box is too large to
1173 <li>• Muscle nucleotide alignment preset obscured by
1175 <li>• JABAWS preset submenus don't contain newly
1176 defined user preset</li>
1177 <li>• MSA web services warns user if they were launched
1178 with invalid input</li>
1179 <li>• Jalview cannot contact DAS Registy when running on
1182 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1183 'Superpose with' submenu not shown when new view
1187 </ul> <!-- <em>Applet</em>
1189 </ul> <em>General</em>
1191 </ul>--> <em>Deployment and Documentation</em>
1193 <li>• 2G and 1G options in launchApp have no effect on
1194 memory allocation</li>
1195 <li>• launchApp service doesn't automatically open
1196 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1198 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1199 InstallAnywhere reports cannot find valid JVM when Java
1200 1.7_055 is available
1202 </ul> <em>Application Known issues</em>
1205 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1206 corrupted or unreadable alignment display when scrolling
1210 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1211 retrieval fails but progress bar continues for DAS retrieval
1212 with large number of ID
1215 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1216 flatfile output of visible region has incorrect sequence
1220 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1221 rna structure consensus doesn't update when secondary
1222 structure tracks are rearranged
1225 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1226 invalid rna structure positional highlighting does not
1227 highlight position of invalid base pairs
1230 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1231 out of memory errors are not raised when saving Jalview
1232 project from alignment window file menu
1235 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1236 Switching to RNA Helices colouring doesn't propagate to
1240 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1241 colour by RNA Helices not enabled when user created
1242 annotation added to alignment
1245 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1246 Jalview icon not shown on dock in Mountain Lion/Webstart
1248 </ul> <em>Applet Known Issues</em>
1251 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1252 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1255 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1256 Jalview and Jmol example not compatible with IE9
1259 <li>• Sort by annotation score doesn't reverse order
1265 <td><div align="center">
1266 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1269 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1272 <li>• Internationalisation of user interface (usually
1273 called i18n support) and translation for Spanish locale</li>
1274 <li>• Define/Undefine group on current selection with
1275 Ctrl-G/Shift Ctrl-G</li>
1276 <li>• Improved group creation/removal options in
1277 alignment/sequence Popup menu</li>
1278 <li>• Sensible precision for symbol distribution
1279 percentages shown in logo tooltip.</li>
1280 <li>• Annotation panel height set according to amount of
1281 annotation when alignment first opened</li>
1282 </ul> <em>Application</em>
1284 <li>• Interactive consensus RNA secondary structure
1285 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1286 <li>• Select columns containing particular features from
1287 Feature Settings dialog</li>
1288 <li>• View all 'representative' PDB structures for selected
1290 <li>• Update Jalview project format:
1292 <li>• New file extension for Jalview projects '.jvp'</li>
1293 <li>• Preserve sequence and annotation dataset (to
1294 store secondary structure annotation,etc)</li>
1295 <li>• Per group and alignment annotation and RNA helix
1299 <li>• New similarity measures for PCA and Tree calculation
1301 <li>• Experimental support for retrieval and viewing of
1302 flanking regions for an alignment</li>
1306 <!-- issues resolved --> <em>Application</em>
1308 <li>• logo keeps spinning and status remains at queued or
1309 running after job is cancelled</li>
1310 <li>• cannot export features from alignments imported from
1311 Jalview/VAMSAS projects</li>
1312 <li>• Buggy slider for web service parameters that take
1314 <li>• Newly created RNA secondary structure line doesn't
1315 have 'display all symbols' flag set</li>
1316 <li>• T-COFFEE alignment score shading scheme and other
1317 annotation shading not saved in Jalview project</li>
1318 <li>• Local file cannot be loaded in freshly downloaded
1320 <li>• Jalview icon not shown on dock in Mountain
1322 <li>• Load file from desktop file browser fails</li>
1323 <li>• Occasional NPE thrown when calculating large trees</li>
1324 <li>• Cannot reorder or slide sequences after dragging an
1325 alignment onto desktop</li>
1326 <li>• Colour by annotation dialog throws NPE after using
1327 'extract scores' function</li>
1328 <li>• Loading/cut'n'pasting an empty file leads to a grey
1329 alignment window</li>
1330 <li>• Disorder thresholds rendered incorrectly after
1331 performing IUPred disorder prediction</li>
1332 <li>• Multiple group annotated consensus rows shown when
1333 changing 'normalise logo' display setting</li>
1334 <li>• Find shows blank dialog after 'finished searching' if
1335 nothing matches query</li>
1336 <li>• Null Pointer Exceptions raised when sorting by
1337 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1339 <li>• Errors in Jmol console when structures in alignment
1340 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1342 <li>• Not all working JABAWS services are shown in
1344 <li>• JAVAWS version of Jalview fails to launch with
1345 'invalid literal/length code'</li>
1346 <li>• Annotation/RNA Helix colourschemes cannot be applied
1347 to alignment with groups (actually fixed in 2.8.0b1)</li>
1348 <li>• RNA Helices and T-Coffee Scores available as default
1351 </ul> <em>Applet</em>
1353 <li>• Remove group option is shown even when selection is
1355 <li>• Apply to all groups ticked but colourscheme changes
1356 don't affect groups</li>
1357 <li>• Documented RNA Helices and T-Coffee Scores as valid
1358 colourscheme name</li>
1359 <li>• Annotation labels drawn on sequence IDs when
1360 Annotation panel is not displayed</li>
1361 <li>• Increased font size for dropdown menus on OSX and
1362 embedded windows</li>
1363 </ul> <em>Other</em>
1365 <li>• Consensus sequence for alignments/groups with a
1366 single sequence were not calculated</li>
1367 <li>• annotation files that contain only groups imported as
1368 annotation and junk sequences</li>
1369 <li>• Fasta files with sequences containing '*' incorrectly
1370 recognised as PFAM or BLC</li>
1371 <li>• conservation/PID slider apply all groups option
1372 doesn't affect background (2.8.0b1)
1373 <li>• </li>
1374 <li>• redundancy highlighting is erratic at 0% and 100%</li>
1375 <li>• Remove gapped columns fails for sequences with ragged
1377 <li>• AMSA annotation row with leading spaces is not
1378 registered correctly on import</li>
1379 <li>• Jalview crashes when selecting PCA analysis for
1380 certain alignments</li>
1381 <li>• Opening the colour by annotation dialog for an
1382 existing annotation based 'use original colours'
1383 colourscheme loses original colours setting</li>
1388 <td><div align="center">
1389 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
1390 <em>30/1/2014</em></strong>
1394 <li>• Trusted certificates for JalviewLite applet and
1395 Jalview Desktop application<br />Certificate was donated by
1396 <a href="https://www.certum.eu">Certum</a> to the Jalview
1397 open source project).
1399 <li>• Jalview SRS links replaced by UniProt and EBI-search
1401 <li>• Output in Stockholm format</li>
1402 <li>• Allow import of data from gzipped files</li>
1403 <li>• Export/import group and sequence associated line
1404 graph thresholds</li>
1405 <li>• Nucleotide substitution matrix that supports RNA and
1406 ambiguity codes</li>
1407 <li>• Allow disorder predictions to be made on the current
1408 selection (or visible selection) in the same way that JPred
1410 <li>• Groovy scripting for headless Jalview operation</li>
1411 </ul> <em>Other improvements</em>
1413 <li>• Upgrade desktop installer to InstallAnywhere 2013</li>
1414 <li>• COMBINE statement uses current SEQUENCE_REF and
1415 GROUP_REF scope to group annotation rows</li>
1416 <li>• Support '' style escaping of quotes in Newick
1418 <li>• Group options for JABAWS service by command line name</li>
1419 <li>• Empty tooltip shown for JABA service options with a
1420 link but no description</li>
1421 <li>• Select primary source when selecting authority in
1422 database fetcher GUI</li>
1423 <li>• Add .mfa to FASTA file extensions recognised by
1425 <li>• Annotation label tooltip text wrap</li>
1430 <li>• Slow scrolling when lots of annotation rows are
1432 <li>• Lots of NPE (and slowness) after creating RNA
1433 secondary structure annotation line</li>
1434 <li>• Sequence database accessions not imported when
1435 fetching alignments from Rfam</li>
1436 <li>• Incorrect SHMR submission for sequences with
1438 <li>• View all structures does not always superpose
1440 <li>• Option widgets in service parameters not updated to
1441 reflect user or preset settings</li>
1442 <li>• Null pointer exceptions for some services without
1443 presets or adjustable parameters</li>
1444 <li>• Discover PDB IDs entry in structure menu doesn't
1445 discover PDB xRefs</li>
1446 <li>• Exception encountered while trying to retrieve
1447 features with DAS</li>
1448 <li>• Lowest value in annotation row isn't coloured
1449 when colour by annotation (per sequence) is coloured</li>
1450 <li>• Keyboard mode P jumps to start of gapped region when
1451 residue follows a gap</li>
1452 <li>• Jalview appears to hang importing an alignment with
1453 Wrap as default or after enabling Wrap</li>
1454 <li>• 'Right click to add annotations' message
1455 shown in wrap mode when no annotations present</li>
1456 <li>• Disorder predictions fail with NPE if no automatic
1457 annotation already exists on alignment</li>
1458 <li>• oninit javascript function should be called after
1459 initialisation completes</li>
1460 <li>• Remove redundancy after disorder prediction corrupts
1461 alignment window display</li>
1462 <li>• Example annotation file in documentation is invalid</li>
1463 <li>• Grouped line graph annotation rows are not exported
1464 to annotation file</li>
1465 <li>• Multi-harmony analysis cannot be run when only two
1467 <li>• Cannot create multiple groups of line graphs with
1468 several 'combine' statements in annotation file</li>
1469 <li>• Pressing return several times causes Number Format
1470 exceptions in keyboard mode</li>
1471 <li>• Multi-harmony (SHMMR) method doesn't submit
1472 correct partitions for input data</li>
1473 <li>• Translation from DNA to Amino Acids fails</li>
1474 <li>• Jalview fail to load newick tree with quoted label</li>
1475 <li>• --headless flag isn't understood</li>
1476 <li>• ClassCastException when generating EPS in headless
1478 <li>• Adjusting sequence-associated shading threshold only
1479 changes one row's threshold</li>
1480 <li>• Preferences and Feature settings panel panel
1481 doesn't open</li>
1482 <li>• hide consensus histogram also hides conservation and
1483 quality histograms</li>
1488 <td><div align="center">
1489 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
1491 <td><em>Application</em>
1493 <li>• Support for JABAWS 2.0 Services (AACon alignment
1494 conservation, protein disorder and Clustal Omega)</li>
1495 <li>• JABAWS server status indicator in Web Services
1497 <li>• VARNA (http://varna.lri.fr) viewer for RNA structures
1498 in Jalview alignment window</li>
1499 <li>• Updated Jalview build and deploy framework for OSX
1500 mountain lion, windows 7, and 8</li>
1501 <li>• Nucleotide substitution matrix for PCA that supports
1502 RNA and ambiguity codes</li>
1504 <li>• Improved sequence database retrieval GUI</li>
1505 <li>• Support fetching and database reference look up
1506 against multiple DAS sources (Fetch all from in 'fetch db
1508 <li>• Jalview project improvements
1510 <li>• Store and retrieve the 'belowAlignment'
1511 flag for annotation</li>
1512 <li>• calcId attribute to group annotation rows on the
1514 <li>• Store AACon calculation settings for a view in
1515 Jalview project</li>
1519 <li>• horizontal scrolling gesture support</li>
1520 <li>• Visual progress indicator when PCA calculation is
1522 <li>• Simpler JABA web services menus</li>
1523 <li>• visual indication that web service results are still
1524 being retrieved from server</li>
1525 <li>• Serialise the dialogs that are shown when Jalview
1526 starts up for first time</li>
1527 <li>• Jalview user agent string for interacting with HTTP
1529 <li>• DAS 1.6 and DAS 2.0 source support using new JDAS
1531 <li>• Examples directory and Groovy library included in
1532 InstallAnywhere distribution</li>
1533 </ul> <em>Applet</em>
1535 <li>• RNA alignment and secondary structure annotation
1536 visualization applet example</li>
1537 </ul> <em>General</em>
1539 <li>• Normalise option for consensus sequence logo</li>
1540 <li>• Reset button in PCA window to return dimensions to
1542 <li>• Allow seqspace or Jalview variant of alignment PCA
1544 <li>• PCA with either nucleic acid and protein substitution
1546 <li>• Allow windows containing HTML reports to be exported
1548 <li>• Interactive display and editing of RNA secondary
1549 structure contacts</li>
1550 <li>• RNA Helix Alignment Colouring</li>
1551 <li>• RNA base pair logo consensus</li>
1552 <li>• Parse sequence associated secondary structure
1553 information in Stockholm files</li>
1554 <li>• HTML Export database accessions and annotation
1555 information presented in tooltip for sequences</li>
1556 <li>• Import secondary structure from LOCARNA clustalw
1557 style RNA alignment files</li>
1558 <li>• import and visualise T-COFFEE quality scores for an
1560 <li>• 'colour by annotation' per sequence option to
1561 shade each sequence according to its associated alignment
1563 <li>• New Jalview Logo</li>
1564 </ul> <em>Documentation and Development</em>
1566 <li>• documentation for score matrices used in Jalview</li>
1567 <li>• New Website!</li>
1569 <td><em>Application</em>
1571 <li>• PDB, Unprot and EMBL (ENA) databases retrieved via
1572 wsdbfetch REST service</li>
1573 <li>• Stop windows being moved outside desktop on OSX</li>
1574 <li>• Filetype associations not installed for webstart
1576 <li>• Jalview does not always retrieve progress of a JABAWS
1577 job execution in full once it is complete</li>
1578 <li>• revise SHMR RSBS definition to ensure alignment is
1579 uploaded via ali_file parameter</li>
1580 <li>• Jalview 2.7 is incompatible with Jmol-12.2.2</li>
1581 <li>• View all structures superposed fails with exception</li>
1582 <li>• Jnet job queues forever if a very short sequence is
1583 submitted for prediction</li>
1584 <li>• Cut and paste menu not opened when mouse clicked on
1586 <li>• Putting fractional value into integer text box in
1587 alignment parameter dialog causes Jalview to hang</li>
1588 <li>• Structure view highlighting doesn't work on
1590 <li>• View all structures fails with exception shown in
1592 <li>• Characters in filename associated with PDBEntry not
1593 escaped in a platform independent way</li>
1594 <li>• Jalview desktop fails to launch with exception when
1596 <li>• Tree calculation reports 'you must have 2 or more
1597 sequences selected' when selection is empty</li>
1598 <li>• Jalview desktop fails to launch with jar signature
1599 failure when java web start temporary file caching is
1601 <li>• DAS Sequence retrieval with range qualification
1602 results in sequence xref which includes range qualification</li>
1603 <li>• Errors during processing of command line arguments
1604 cause progress bar (JAL-898) to be removed</li>
1605 <li>• Replace comma for semi-colon option not disabled for
1606 DAS sources in sequence fetcher</li>
1607 <li>• Cannot close news reader when JABAWS server warning
1608 dialog is shown</li>
1609 <li>• Option widgets not updated to reflect user settings</li>
1610 <li>• Edited sequence not submitted to web service</li>
1611 <li>• Jalview 2.7 Webstart does not launch on mountain lion</li>
1612 <li>• InstallAnywhere installer doesn't unpack and run
1613 on OSX Mountain Lion</li>
1614 <li>• Annotation panel not given a scroll bar when
1615 sequences with alignment annotation are pasted into the
1617 <li>• Sequence associated annotation rows not associated
1618 when loaded from Jalview project</li>
1619 <li>• Browser launch fails with NPE on java 1.7</li>
1620 <li>• JABAWS alignment marked as finished when job was
1621 cancelled or job failed due to invalid input</li>
1622 <li>• NPE with v2.7 example when clicking on Tree
1623 associated with all views</li>
1624 <li>• Exceptions when copy/paste sequences with grouped
1625 annotation rows to new window</li>
1626 </ul> <em>Applet</em>
1628 <li>• Sequence features are momentarily displayed before
1629 they are hidden using hidefeaturegroups applet parameter</li>
1630 <li>• loading features via javascript API automatically
1631 enables feature display</li>
1632 <li>• scrollToColumnIn javascript API method doesn't
1634 </ul> <em>General</em>
1636 <li>• Redundancy removal fails for rna alignment</li>
1637 <li>• PCA calculation fails when sequence has been selected
1638 and then deselected</li>
1639 <li>• PCA window shows grey box when first opened on OSX</li>
1640 <li>• Letters coloured pink in sequence logo when alignment
1641 coloured with clustalx</li>
1642 <li>• Choosing fonts without letter symbols defined causes
1643 exceptions and redraw errors</li>
1644 <li>• Initial PCA plot view is not same as manually
1645 reconfigured view</li>
1646 <li>• Grouped annotation graph label has incorrect line
1648 <li>• Grouped annotation graph label display is corrupted
1649 for lots of labels</li>
1654 <div align="center">
1655 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
1658 <td><em>Application</em>
1660 <li>• Jalview Desktop News Reader</li>
1661 <li>• Tweaked default layout of web services menu</li>
1662 <li>• View/alignment association menu to enable user to
1663 easily specify which alignment a multi-structure view takes
1664 its colours/correspondences from</li>
1665 <li>• Allow properties file location to be specified as URL</li>
1666 <li>• Extend Jalview project to preserve associations
1667 between many alignment views and a single Jmol display</li>
1668 <li>• Store annotation row height in Jalview project file</li>
1669 <li>• Annotation row column label formatting attributes
1670 stored in project file</li>
1671 <li>• Annotation row order for auto-calculated annotation
1672 rows preserved in Jalview project file</li>
1673 <li>• Visual progress indication when Jalview state is
1674 saved using Desktop window menu</li>
1675 <li>• Visual indication that command line arguments are
1676 still being processed</li>
1677 <li>• Groovy script execution from URL</li>
1678 <li>• Colour by annotation default min and max colours in
1680 <li>• Automatically associate PDB files dragged onto an
1681 alignment with sequences that have high similarity and
1683 <li>• Update JGoogleAnalytics to latest release (0.3)</li>
1684 <li>• 'view structures' option to open many
1685 structures in same window</li>
1686 <li>• Sort associated views menu option for tree panel</li>
1687 <li>• Group all JABA and non-JABA services for a particular
1688 analysis function in its own submenu</li>
1689 </ul> <em>Applet</em>
1691 <li>• Userdefined and autogenerated annotation rows for
1693 <li>• Adjustment of alignment annotation pane height</li>
1694 <li>• Annotation scrollbar for annotation panel</li>
1695 <li>• Drag to reorder annotation rows in annotation panel</li>
1696 <li>• 'automaticScrolling' parameter</li>
1697 <li>• Allow sequences with partial ID string matches to be
1698 annotated from GFF/Jalview features files</li>
1699 <li>• Sequence logo annotation row in applet</li>
1700 <li>• Absolute paths relative to host server in applet
1701 parameters are treated as such</li>
1702 <li>• New in the JalviewLite javascript API:
1704 <li>• JalviewLite.js javascript library</li>
1705 <li>• Javascript callbacks for
1707 <li>• Applet initialisation</li>
1708 <li>• Sequence/alignment mouse-overs and selections</li>
1711 <li>• scrollTo row and column alignment scrolling
1713 <li>• Select sequence/alignment regions from javascript</li>
1714 <li>• javascript structure viewer harness to pass
1715 messages between Jmol and Jalview when running as
1716 distinct applets</li>
1717 <li>• sortBy method</li>
1718 <li>• Set of applet and application examples shipped
1719 with documentation</li>
1720 <li>• New example to demonstrate JalviewLite and Jmol
1721 javascript message exchange</li>
1723 </ul> <em>General</em>
1725 <li>• Enable Jmol displays to be associated with multiple
1726 multiple alignments</li>
1727 <li>• Option to automatically sort alignment with new tree</li>
1728 <li>• User configurable link to enable redirects to a
1729 www.Jalview.org mirror</li>
1730 <li>• Jmol colours option for Jmol displays</li>
1731 <li>• Configurable newline string when writing alignment
1732 and other flat files</li>
1733 <li>• Allow alignment annotation description lines to
1734 contain html tags</li>
1735 </ul> <em>Documentation and Development</em>
1737 <li>• Add groovy test harness for bulk load testing to
1739 <li>• Groovy script to load and align a set of sequences
1740 using a web service before displaying the result in the
1741 Jalview desktop</li>
1742 <li>• Restructured javascript and applet api documentation</li>
1743 <li>• Ant target to publish example html files with applet
1745 <li>• Netbeans project for building Jalview from source</li>
1746 <li>• ant task to create online javadoc for Jalview source</li>
1748 <td><em>Application</em>
1750 <li>• User defined colourscheme throws exception when
1751 current built in colourscheme is saved as new scheme</li>
1752 <li>• AlignFrame->Save in application pops up save
1753 dialog for valid filename/format</li>
1754 <li>• Cannot view associated structure for UniProt sequence</li>
1755 <li>• PDB file association breaks for UniProt sequence
1757 <li>• Associate PDB from file dialog does not tell you
1758 which sequence is to be associated with the file</li>
1759 <li>• Find All raises null pointer exception when query
1760 only matches sequence IDs</li>
1761 <li>• Pre 2.6 Jalview project cannot be loaded into v2.6</li>
1762 <li>• Jalview project with Jmol views created with Jalview
1763 2.4 cannot be loaded</li>
1764 <li>• Filetype associations not installed for webstart
1766 <li>• Two or more chains in a single PDB file associated
1767 with sequences in different alignments do not get coloured
1768 by their associated sequence</li>
1769 <li>• Visibility status of autocalculated annotation row
1770 not preserved when project is loaded</li>
1771 <li>• Annotation row height and visibility attributes not
1772 stored in Jalview project</li>
1773 <li>• Tree bootstraps are not preserved when saved as a
1774 Jalview project</li>
1775 <li>• Envision2 workflow tooltips are corrupted</li>
1776 <li>• Enabling show group conservation also enables colour
1777 by conservation</li>
1778 <li>• Duplicate group associated conservation or consensus
1779 created on new view</li>
1780 <li>• Annotation scrollbar not displayed after 'show
1781 all hidden annotation rows' option selected</li>
1782 <li>• Alignment quality not updated after alignment
1783 annotation row is hidden then shown</li>
1784 <li>• Preserve colouring of structures coloured by
1785 sequences in pre Jalview 2.7 projects</li>
1786 <li>• Web service job parameter dialog is not laid out
1788 <li>• Web services menu not refreshed after 'reset
1789 services' button is pressed in preferences</li>
1790 <li>• Annotation off by one in Jalview v2_3 example project</li>
1791 <li>• Structures imported from file and saved in project
1792 get name like jalview_pdb1234.txt when reloaded</li>
1793 <li>• Jalview does not always retrieve progress of a JABAWS
1794 job execution in full once it is complete</li>
1795 </ul> <em>Applet</em>
1797 <li>• Alignment height set incorrectly when lots of
1798 annotation rows are displayed</li>
1799 <li>• Relative URLs in feature HTML text not resolved to
1801 <li>• View follows highlighting does not work for positions
1803 <li>• <= shown as = in tooltip</li>
1804 <li>• Export features raises exception when no features
1806 <li>• Separator string used for serialising lists of IDs
1807 for javascript api is modified when separator string
1808 provided as parameter</li>
1809 <li>• Null pointer exception when selecting tree leaves for
1810 alignment with no existing selection</li>
1811 <li>• Relative URLs for datasources assumed to be relative
1812 to applet's codebase</li>
1813 <li>• Status bar not updated after finished searching and
1814 search wraps around to first result</li>
1815 <li>• StructureSelectionManager instance shared between
1816 several Jalview applets causes race conditions and memory
1818 <li>• Hover tooltip and mouseover of position on structure
1819 not sent from Jmol in applet</li>
1820 <li>• Certain sequences of javascript method calls to
1821 applet API fatally hang browser</li>
1822 </ul> <em>General</em>
1824 <li>• View follows structure mouseover scrolls beyond
1825 position with wrapped view and hidden regions</li>
1826 <li>• Find sequence position moves to wrong residue
1827 with/without hidden columns</li>
1828 <li>• Sequence length given in alignment properties window
1830 <li>• InvalidNumberFormat exceptions thrown when trying to
1831 import PDB like structure files</li>
1832 <li>• Positional search results are only highlighted
1833 between user-supplied sequence start/end bounds</li>
1834 <li>• End attribute of sequence is not validated</li>
1835 <li>• Find dialog only finds first sequence containing a
1836 given sequence position</li>
1837 <li>• Sequence numbering not preserved in MSF alignment
1839 <li>• Jalview PDB file reader does not extract sequence
1840 from nucleotide chains correctly</li>
1841 <li>• Structure colours not updated when tree partition
1842 changed in alignment</li>
1843 <li>• Sequence associated secondary structure not correctly
1844 parsed in interleaved stockholm</li>
1845 <li>• Colour by annotation dialog does not restore current
1847 <li>• Hiding (nearly) all sequences doesn't work
1849 <li>• Sequences containing lowercase letters are not
1850 properly associated with their pdb files</li>
1851 </ul> <em>Documentation and Development</em>
1853 <li>• schemas/JalviewWsParamSet.xsd corrupted by
1854 ApplyCopyright tool</li>
1859 <div align="center">
1860 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
1863 <td><em>Application</em>
1865 <li>• New warning dialog when the Jalview Desktop cannot
1866 contact web services</li>
1867 <li>• JABA service parameters for a preset are shown in
1868 service job window</li>
1869 <li>• JABA Service menu entries reworded</li>
1873 <li>• Modeller PIR IO broken - cannot correctly import a
1874 pir file emitted by Jalview</li>
1875 <li>• Existing feature settings transferred to new
1876 alignment view created from cut'n'paste</li>
1877 <li>• Improved test for mixed amino/nucleotide chains when
1878 parsing PDB files</li>
1879 <li>• Consensus and conservation annotation rows
1880 occasionally become blank for all new windows</li>
1881 <li>• Exception raised when right clicking above sequences
1882 in wrapped view mode</li>
1883 </ul> <em>Application</em>
1885 <li>• multiple multiply aligned structure views cause cpu
1886 usage to hit 100% and computer to hang</li>
1887 <li>• Web Service parameter layout breaks for long user
1888 parameter names</li>
1889 <li>• Jaba service discovery hangs desktop if Jaba server
1896 <div align="center">
1897 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
1900 <td><em>Application</em>
1902 <li>• Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
1903 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
1906 <li>• Web Services preference tab</li>
1907 <li>• Analysis parameters dialog box and user defined
1909 <li>• Improved speed and layout of Envision2 service menu</li>
1910 <li>• Superpose structures using associated sequence
1912 <li>• Export coordinates and projection as CSV from PCA
1914 </ul> <em>Applet</em>
1916 <li>• enable javascript: execution by the applet via the
1917 link out mechanism</li>
1918 </ul> <em>Other</em>
1920 <li>• Updated the Jmol Jalview interface to work with Jmol
1922 <li>• The Jalview Desktop and JalviewLite applet now
1923 require Java 1.5</li>
1924 <li>• Allow Jalview feature colour specification for GFF
1925 sequence annotation files</li>
1926 <li>• New 'colour by label' keword in Jalview feature file
1927 type colour specification</li>
1928 <li>• New Jalview Desktop Groovy API method that allows a
1929 script to check if it being run in an interactive session or
1930 in a batch operation from the Jalview command line</li>
1934 <li>• clustalx colourscheme colours Ds preferentially when
1935 both D+E are present in over 50% of the column</li>
1936 </ul> <em>Application</em>
1938 <li>• typo in AlignmentFrame->View->Hide->all but
1939 selected Regions menu item</li>
1940 <li>• sequence fetcher replaces ',' for ';' when the ',' is
1941 part of a valid accession ID</li>
1942 <li>• fatal OOM if object retrieved by sequence fetcher
1943 runs out of memory</li>
1944 <li>• unhandled Out of Memory Error when viewing pca
1945 analysis results</li>
1946 <li>• InstallAnywhere builds fail to launch on OS X java
1947 10.5 update 4 (due to apple Java 1.6 update)</li>
1948 <li>• Installanywhere Jalview silently fails to launch</li>
1949 </ul> <em>Applet</em>
1951 <li>• Jalview.getFeatureGroups() raises an
1952 ArrayIndexOutOfBoundsException if no feature groups are
1959 <div align="center">
1960 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
1966 <li>• Alignment prettyprinter doesn't cope with long
1968 <li>• clustalx colourscheme colours Ds preferentially when
1969 both D+E are present in over 50% of the column</li>
1970 <li>• nucleic acid structures retrieved from PDB do not
1971 import correctly</li>
1972 <li>• More columns get selected than were clicked on when a
1973 number of columns are hidden</li>
1974 <li>• annotation label popup menu not providing correct
1975 add/hide/show options when rows are hidden or none are
1977 <li>• Stockholm format shown in list of readable formats,
1978 and parser copes better with alignments from RFAM.</li>
1979 <li>• CSV output of consensus only includes the percentage
1980 of all symbols if sequence logo display is enabled</li>
1982 </ul> <em>Applet</em>
1984 <li>• annotation panel disappears when annotation is
1986 </ul> <em>Application</em>
1988 <li>• Alignment view not redrawn properly when new
1989 alignment opened where annotation panel is visible but no
1990 annotations are present on alignment</li>
1991 <li>• pasted region containing hidden columns is
1992 incorrectly displayed in new alignment window</li>
1993 <li>• Jalview slow to complete operations when stdout is
1994 flooded (fix is to close the Jalview console)</li>
1995 <li>• typo in AlignmentFrame->View->Hide->all but
1996 selected Rregions menu item.</li>
1997 <li>• inconsistent group submenu and Format submenu entry
1998 'Un' or 'Non'conserved</li>
1999 <li>• Sequence feature settings are being shared by
2000 multiple distinct alignments</li>
2001 <li>• group annotation not recreated when tree partition is
2003 <li>• double click on group annotation to select sequences
2004 does not propagate to associated trees</li>
2005 <li>• Mac OSX specific issues:
2007 <li>• exception raised when mouse clicked on desktop
2008 window background</li>
2009 <li>• Desktop menu placed on menu bar and application
2010 name set correctly</li>
2011 <li>• sequence feature settings not wide enough for the
2012 save feature colourscheme button</li>
2021 <div align="center">
2022 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2025 <td><em>New Capabilities</em>
2027 <li>• URL links generated from description line for
2028 regular-expression based URL links (applet and application)
2035 <li>• Non-positional feature URL links are shown in link
2037 <li>• Linked viewing of nucleic acid sequences and
2039 <li>• Automatic Scrolling option in View menu to display
2040 the currently highlighted region of an alignment.</li>
2041 <li>• Order an alignment by sequence length, or using the
2042 average score or total feature count for each sequence.</li>
2043 <li>• Shading features by score or associated description</li>
2044 <li>• Subdivide alignment and groups based on identity of
2045 selected subsequence (Make Groups from Selection).</li>
2046 <li>• New hide/show options including Shift+Control+H to
2047 hide everything but the currently selected region.</li>
2048 <!-- introduced but not yet documented <li>• Experimental blast report parser</li> -->
2049 </ul> <em>Application</em>
2051 <li>• Fetch DB References capabilities and UI expanded to
2052 support retrieval from DAS sequence sources</li>
2053 <li>• Local DAS Sequence sources can be added via the
2054 command line or via the Add local source dialog box.</li>
2055 <li>• DAS Dbref and DbxRef feature types are parsed as
2056 database references and protein_name is parsed as
2057 description line (BioSapiens terms).</li>
2058 <li>• Enable or disable non-positional feature and database
2059 references in sequence ID tooltip from View menu in
2061 <!-- <li>• New hidden columns and rows and representatives capabilities
2062 in annotations file (in progress - not yet fully implemented)</li> -->
2063 <li>• Group-associated consensus, sequence logos and
2064 conservation plots</li>
2065 <li>• Symbol distributions for each column can be exported
2066 and visualized as sequence logos</li>
2067 <li>• Optionally scale multi-character column labels to fit
2068 within each column of annotation row<!-- todo for applet -->
2070 <li>• Optional automatic sort of associated alignment view
2071 when a new tree is opened.</li>
2072 <li>• Jalview Java Console</li>
2073 <li>• Better placement of desktop window when moving
2074 between different screens.</li>
2075 <li>• New preference items for sequence ID tooltip and
2076 consensus annotation</li>
2077 <li>• Client to submit sequences and IDs to Envision2
2079 <li>• <em>Vamsas Capabilities</em>
2081 <li>• Improved VAMSAS synchronization (Jalview archive
2082 used to preserve views, structures, and tree display
2084 <li>• Import of vamsas documents from disk or URL via
2086 <li>• Sharing of selected regions between views and
2087 with other VAMSAS applications (Experimental feature!)</li>
2088 <li>• Updated API to VAMSAS version 0.2</li>
2090 </ul> <em>Applet</em>
2092 <li>• Middle button resizes annotation row height</li>
2093 <li>• New Parameters
2095 <li>• sortByTree (true/false) - automatically sort the
2096 associated alignment view by the tree when a new tree is
2098 <li>• showTreeBootstraps (true/false) - show or hide
2099 branch bootstraps (default is to show them if available)</li>
2100 <li>• showTreeDistances (true/false) - show or hide
2101 branch lengths (default is to show them if available)</li>
2102 <li>• showUnlinkedTreeNodes (true/false) - indicate if
2103 unassociated nodes should be highlighted in the tree
2105 <li>• heightScale and widthScale (1.0 or more) -
2106 increase the height or width of a cell in the alignment
2107 grid relative to the current font size.</li>
2110 <li>• Non-positional features displayed in sequence ID
2112 </ul> <em>Other</em>
2114 <li>• Features format: graduated colour definitions and
2115 specification of feature scores</li>
2116 <li>• Alignment Annotations format: new keywords for group
2117 associated annotation (GROUP_REF) and annotation row display
2118 properties (ROW_PROPERTIES)</li>
2119 <li>• XML formats extended to support graduated feature
2120 colourschemes, group associated annotation, and profile
2121 visualization settings.</li></td>
2124 <li>• Source field in GFF files parsed as feature source
2125 rather than description</li>
2126 <li>• Non-positional features are now included in sequence
2127 feature and gff files (controlled via non-positional feature
2128 visibility in tooltip).</li>
2129 <li>• URL links generated for all feature links (bugfix)</li>
2130 <li>• Added URL embedding instructions to features file
2132 <li>• Codons containing ambiguous nucleotides translated as
2133 'X' in peptide product</li>
2134 <li>• Match case switch in find dialog box works for both
2135 sequence ID and sequence string and query strings do not
2136 have to be in upper case to match case-insensitively.</li>
2137 <li>• AMSA files only contain first column of
2138 multi-character column annotation labels</li>
2139 <li>• Jalview Annotation File generation/parsing consistent
2140 with documentation (e.g. Stockholm annotation can be
2141 exported and re-imported)</li>
2142 <li>• PDB files without embedded PDB IDs given a friendly
2144 <li>• Find incrementally searches ID string matches as well
2145 as subsequence matches, and correctly reports total number
2147 <li>• Application:
2149 <li>• Better handling of exceptions during sequence
2151 <li>• Dasobert generated non-positional feature URL
2152 link text excludes the start_end suffix</li>
2153 <li>• DAS feature and source retrieval buttons disabled
2154 when fetch or registry operations in progress.</li>
2155 <li>• PDB files retrieved from URLs are cached properly</li>
2156 <li>• Sequence description lines properly shared via
2158 <li>• Sequence fetcher fetches multiple records for all
2160 <li>• Ensured that command line das feature retrieval
2161 completes before alignment figures are generated.</li>
2162 <li>• Reduced time taken when opening file browser for
2164 <li>• isAligned check prior to calculating tree, PCA or
2165 submitting an MSA to JNet now excludes hidden sequences.</li>
2166 <li>• User defined group colours properly recovered
2167 from Jalview projects.</li>
2176 <div align="center">
2177 <strong>2.4.0.b2</strong><br> 28/10/2009
2182 <li>• Experimental support for google analytics usage
2184 <li>• Jalview privacy settings (user preferences and docs).</li>
2189 <li>• Race condition in applet preventing startup in
2191 <li>• Exception when feature created from selection beyond
2192 length of sequence.</li>
2193 <li>• Allow synthetic PDB files to be imported gracefully</li>
2194 <li>• Sequence associated annotation rows associate with
2195 all sequences with a given id</li>
2196 <li>• Find function matches case-insensitively for sequence
2197 ID string searches</li>
2198 <li>• Non-standard characters do not cause pairwise
2199 alignment to fail with exception</li>
2200 </ul> <em>Application Issues</em>
2202 <li>• Sequences are now validated against EMBL database</li>
2203 <li>• Sequence fetcher fetches multiple records for all
2205 </ul> <em>InstallAnywhere Issues</em>
2207 <li>• Dock icon works for Mac OS X java (Mac 1.6 update
2208 issue with installAnywhere mechanism)</li>
2209 <li>• Command line launching of JARs from InstallAnywhere
2210 version (java class versioning error fixed)</li>
2217 <div align="center">
2218 <strong>2.4</strong><br> 27/8/2008
2221 <td><em>User Interface</em>
2223 <li>• Linked highlighting of codon and amino acid from
2224 translation and protein products</li>
2225 <li>• Linked highlighting of structure associated with
2226 residue mapping to codon position</li>
2227 <li>• Sequence Fetcher provides example accession numbers
2228 and 'clear' button</li>
2229 <li>• MemoryMonitor added as an option under Desktop's
2231 <li>• Extract score function to parse whitespace separated
2232 numeric data in description line</li>
2233 <li>• Column labels in alignment annotation can be centred.</li>
2234 <li>• Tooltip for sequence associated annotation give name
2236 </ul> <em>Web Services and URL fetching</em>
2238 <li>• JPred3 web service</li>
2239 <li>• Prototype sequence search client (no public services
2241 <li>• Fetch either seed alignment or full alignment from
2243 <li>• URL Links created for matching database cross
2244 references as well as sequence ID</li>
2245 <li>• URL Links can be created using regular-expressions</li>
2246 </ul> <em>Sequence Database Connectivity</em>
2248 <li>• Retrieval of cross-referenced sequences from other
2250 <li>• Generalised database reference retrieval and
2251 validation to all fetchable databases</li>
2252 <li>• Fetch sequences from DAS sources supporting the
2253 sequence command</li>
2254 </ul> <em>Import and Export</em>
2255 <li>• export annotation rows as CSV for spreadsheet import</li>
2256 <li>• Jalview projects record alignment dataset associations,
2257 EMBL products, and cDNA sequence mappings</li>
2258 <li>• Sequence Group colour can be specified in Annotation
2260 <li>• Ad-hoc colouring of group in Annotation File using RGB
2261 triplet as name of colourscheme</li>
2262 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2264 <li>• treenode binding for VAMSAS tree exchange</li>
2265 <li>• local editing and update of sequences in VAMSAS
2266 alignments (experimental)</li>
2267 <li>• Create new or select existing session to join</li>
2268 <li>• load and save of vamsas documents</li>
2269 </ul> <em>Application command line</em>
2271 <li>• -tree parameter to open trees (introduced for passing
2273 <li>• -fetchfrom command line argument to specify nicknames
2274 of DAS servers to query for alignment features</li>
2275 <li>• -dasserver command line argument to add new servers
2276 that are also automatically queried for features</li>
2277 <li>• -groovy command line argument executes a given groovy
2278 script after all input data has been loaded and parsed</li>
2279 </ul> <em>Applet-Application data exchange</em>
2281 <li>• Trees passed as applet parameters can be passed to
2282 application (when using "View in full
2283 application")</li>
2284 </ul> <em>Applet Parameters</em>
2286 <li>• feature group display control parameter</li>
2287 <li>• debug parameter</li>
2288 <li>• showbutton parameter</li>
2289 </ul> <em>Applet API methods</em>
2291 <li>• newView public method</li>
2292 <li>• Window (current view) specific get/set public methods</li>
2293 <li>• Feature display control methods</li>
2294 <li>• get list of currently selected sequences</li>
2295 </ul> <em>New Jalview distribution features</em>
2297 <li>• InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2298 <li>• RELEASE file gives build properties for the latest
2299 Jalview release.</li>
2300 <li>• Java 1.1 Applet build made easier and donotobfuscate
2301 property controls execution of obfuscator</li>
2302 <li>• Build target for generating source distribution</li>
2303 <li>• Debug flag for javacc</li>
2304 <li>• .jalview_properties file is documented (slightly) in
2305 jalview.bin.Cache</li>
2306 <li>• Continuous Build Integration for stable and
2307 development version of Application, Applet and source
2312 <li>• selected region output includes visible annotations
2313 (for certain formats)</li>
2314 <li>• edit label/displaychar contains existing label/char
2316 <li>• update PDBEntries when DBRefEntries change (vamsas)</li>
2317 <li>• shorter peptide product names from EMBL records</li>
2318 <li>• Newick string generator makes compact representations</li>
2319 <li>• bootstrap values parsed correctly for tree files with
2321 <li>• pathological filechooser bug avoided by not allowing
2322 filenames containing a ':'</li>
2323 <li>• Fixed exception when parsing GFF files containing
2324 global sequence features</li>
2325 <li>• Alignment datasets are finalized only when number of
2326 references from alignment sequences goes to zero</li>
2327 <li>• Close of tree branch colour box without colour
2328 selection causes cascading exceptions</li>
2329 <li>• occasional negative imgwidth exceptions</li>
2330 <li>• better reporting of non-fatal warnings to user when
2331 file parsing fails.</li>
2332 <li>• Save works when Jalview project is default format</li>
2333 <li>• Save as dialog opened if current alignment format is
2334 not a valid output format</li>
2335 <li>• UniProt canonical names introduced for both das and
2337 <li>• Histidine should be midblue (not pink!) in Zappo</li>
2338 <li>• error messages passed up and output when data read
2340 <li>• edit undo recovers previous dataset sequence when
2341 sequence is edited</li>
2342 <li>• allow PDB files without pdb ID HEADER lines (like
2343 those generated by MODELLER) to be read in properly</li>
2344 <li>• allow reading of JPred concise files as a normal
2346 <li>• Stockholm annotation parsing and alignment properties
2347 import fixed for PFAM records</li>
2348 <li>• Structure view windows have correct name in Desktop
2350 <li>• annotation consisting of sequence associated scores
2351 can be read and written correctly to annotation file</li>
2352 <li>• Aligned cDNA translation to aligned peptide works
2354 <li>• Fixed display of hidden sequence markers and
2355 non-italic font for representatives in Applet</li>
2356 <li>• Applet Menus are always embedded in applet window on
2358 <li>• Newly shown features appear at top of stack (in
2360 <li>• Annotations added via parameter not drawn properly
2361 due to null pointer exceptions</li>
2362 <li>• Secondary structure lines are drawn starting from
2363 first column of alignment</li>
2364 <li>• UniProt XML import updated for new schema release in
2366 <li>• Sequence feature to sequence ID match for Features
2367 file is case-insensitive</li>
2368 <li>• Sequence features read from Features file appended to
2369 all sequences with matching IDs</li>
2370 <li>• PDB structure coloured correctly for associated views
2371 containing a sub-sequence</li>
2372 <li>• PDB files can be retrieved by applet from Jar files</li>
2373 <li>• feature and annotation file applet parameters
2374 referring to different directories are retrieved correctly</li>
2375 <!--<li>• DAS Histogram Features display ( (Prlic et al) </li>-->
2376 <li>• Fixed application hang whilst waiting for
2377 splash-screen version check to complete</li>
2378 <li>• Applet properly URLencodes input parameter values
2379 when passing them to the launchApp service</li>
2380 <li>• display name and local features preserved in results
2381 retrieved from web service</li>
2382 <li>• Visual delay indication for sequence retrieval and
2383 sequence fetcher initialisation</li>
2384 <li>• updated Application to use DAS 1.53e version of
2385 dasobert DAS client</li>
2386 <li>• Re-instated Full AMSA support and .amsa file
2388 <li>• Fixed parsing of JNet Concise annotation <em>sans</em>
2396 <div align="center">
2397 <strong>2.3</strong><br> 9/5/07
2402 <li>• Jmol 11.0.2 integration</li>
2403 <li>• PDB views stored in Jalview XML files</li>
2404 <li>• Slide sequences</li>
2405 <li>• Edit sequence in place</li>
2406 <li>• EMBL CDS features</li>
2407 <li>• DAS Feature mapping</li>
2408 <li>• Feature ordering</li>
2409 <li>• Alignment Properties</li>
2410 <li>• Annotation Scores</li>
2411 <li>• Sort by scores</li>
2412 <li>• Feature/annotation editing in applet</li>
2417 <li>• Headless state operation in 2.2.1</li>
2418 <li>• Incorrect and unstable DNA pairwise alignment</li>
2419 <li>• Cut and paste of sequences with annotation</li>
2420 <li>• Feature group display state in XML</li>
2421 <li>• Feature ordering in XML</li>
2422 <li>• blc file iteration selection using filename # suffix</li>
2423 <li>• Stockholm alignment properties</li>
2424 <li>• Stockhom alignment secondary structure annotation</li>
2425 <li>• 2.2.1 applet had no feature transparency</li>
2426 <li>• Number pad keys can be used in cursor mode</li>
2427 <li>• Structure Viewer mirror image resolved</li>
2434 <div align="center">
2435 <strong>2.2.1</strong><br> 12/2/07
2440 <li>• Non standard characters can be read and displayed
2441 <li>• Annotations/Features can be imported/exported to the
2443 <li>• Applet allows editing of sequence/annotation/group
2444 name & description
2445 <li>• Preference setting to display sequence name in
2447 <li>• Annotation file format extended to allow
2448 Sequence_groups to be defined
2449 <li>• Default opening of alignment overview panel can be
2450 specified in preferences
2451 <li>• PDB residue numbering annotation added to associated
2457 <li>• Applet crash under certain Linux OS with Java 1.6
2459 <li>• Annotation file export / import bugs fixed
2460 <li>• PNG / EPS image output bugs fixed
2466 <div align="center">
2467 <strong>2.2</strong><br> 27/11/06
2472 <li>• Multiple views on alignment
2473 <li>• Sequence feature editing
2474 <li>• "Reload" alignment
2475 <li>• "Save" to current filename
2476 <li>• Background dependent text colour
2477 <li>• Right align sequence ids
2478 <li>• User-defined lower case residue colours
2479 <li>• Format Menu
2480 <li>• Select Menu
2481 <li>• Menu item accelerator keys
2482 <li>• Control-V pastes to current alignment
2483 <li>• Cancel button for DAS Feature Fetching
2484 <li>• PCA and PDB Viewers zoom via mouse roller
2485 <li>• User-defined sub-tree colours and sub-tree selection
2492 <li>• 'New Window' button on the 'Output to Text box'
2497 <li>• New memory efficient Undo/Redo System
2498 <li>• Optimised symbol lookups and conservation/consensus
2500 <li>• Region Conservation/Consensus recalculated after
2502 <li>• Fixed Remove Empty Columns Bug (empty columns at end
2504 <li>• Slowed DAS Feature Fetching for increased robustness.
2511 <li>• Made angle brackets in ASCII feature descriptions
2513 <li>• Re-instated Zoom function for PCA
2514 <li>• Sequence descriptions conserved in web service
2516 <li>• UniProt ID discoverer uses any word separated by
2518 <li>• WsDbFetch query/result association resolved
2519 <li>• Tree leaf to sequence mapping improved
2520 <li>• Smooth fonts switch moved to FontChooser dialog box.
2532 <div align="center">
2533 <strong>2.1.1</strong><br> 12/9/06
2538 <li>• Copy consensus sequence to clipboard</li>
2543 <li>• Image output - rightmost residues are rendered if
2544 sequence id panel has been resized</li>
2545 <li>• Image output - all offscreen group boundaries are
2547 <li>• Annotation files with sequence references - all
2548 elements in file are relative to sequence position</li>
2549 <li>• Mac Applet users can use Alt key for group editing</li>
2555 <div align="center">
2556 <strong>2.1</strong><br> 22/8/06
2561 <li>• MAFFT Multiple Alignment in default Web Service list</li>
2562 <li>• DAS Feature fetching</li>
2563 <li>• Hide sequences and columns</li>
2564 <li>• Export Annotations and Features</li>
2565 <li>• GFF file reading / writing</li>
2566 <li>• Associate structures with sequences from local PDB
2568 <li>• Add sequences to exisiting alignment</li>
2569 <li>• Recently opened files / URL lists</li>
2570 <li>• Applet can launch the full application</li>
2571 <li>• Applet has transparency for features (Java 1.2
2573 <li>• Applet has user defined colours parameter</li>
2574 <li>• Applet can load sequences from parameter
2575 "sequence<em>x</em>"
2581 <li>• Redundancy Panel reinstalled in the Applet</li>
2582 <li>• Monospaced font - EPS / rescaling bug fixed</li>
2583 <li>• Annotation files with sequence references bug fixed</li>
2589 <div align="center">
2590 <strong>2.08.1</strong><br> 2/5/06
2595 <li>• Change case of selected region from Popup menu</li>
2596 <li>• Choose to match case when searching</li>
2597 <li>• Middle mouse button and mouse movement can compress /
2598 expand the visible width and height of the alignment</li>
2603 <li>• Annotation Panel displays complete JNet results</li>
2609 <div align="center">
2610 <strong>2.08b</strong><br> 18/4/06
2616 <li>• Java 1.5 bug - InternalMessageDialog fix for threads</li>
2617 <li>• Righthand label on wrapped alignments shows correct
2624 <div align="center">
2625 <strong>2.08</strong><br> 10/4/06
2630 <li>• Editing can be locked to the selection area</li>
2631 <li>• Keyboard editing</li>
2632 <li>• Create sequence features from searches</li>
2633 <li>• Precalculated annotations can be loaded onto
2635 <li>• Features file allows grouping of features</li>
2636 <li>• Annotation Colouring scheme added</li>
2637 <li>• Smooth fonts off by default - Faster rendering</li>
2638 <li>• Choose to toggle Autocalculate Consensus On/Off</li>
2643 <li>• Drag & Drop fixed on Linux</li>
2644 <li>• Jalview Archive file faster to load/save, sequence
2645 descriptions saved.</li>
2651 <div align="center">
2652 <strong>2.07</strong><br> 12/12/05
2657 <li>• PDB Structure Viewer enhanced</li>
2658 <li>• Sequence Feature retrieval and display enhanced</li>
2659 <li>• Choose to output sequence start-end after sequence
2660 name for file output</li>
2661 <li>• Sequence Fetcher WSDBFetch@EBI</li>
2662 <li>• Applet can read feature files, PDB files and can be
2663 used for HTML form input</li>
2668 <li>• HTML output writes groups and features</li>
2669 <li>• Group editing is Control and mouse click</li>
2670 <li>• File IO bugs</li>
2676 <div align="center">
2677 <strong>2.06</strong><br> 28/9/05
2682 <li>• View annotations in wrapped mode</li>
2683 <li>• More options for PCA viewer</li>
2688 <li>• GUI bugs resolved</li>
2689 <li>• Runs with -nodisplay from command line</li>
2695 <div align="center">
2696 <strong>2.05b</strong><br> 15/9/05
2701 <li>• Choose EPS export as lineart or text</li>
2702 <li>• Jar files are executable</li>
2703 <li>• Can read in Uracil - maps to unknown residue</li>
2708 <li>• Known OutOfMemory errors give warning message</li>
2709 <li>• Overview window calculated more efficiently</li>
2710 <li>• Several GUI bugs resolved</li>
2716 <div align="center">
2717 <strong>2.05</strong><br> 30/8/05
2722 <li>• Edit and annotate in "Wrapped" view</li>
2727 <li>• Several GUI bugs resolved</li>
2733 <div align="center">
2734 <strong>2.04</strong><br> 24/8/05
2739 <li>• Hold down mouse wheel & scroll to change font
2745 <li>• Improved JPred client reliability</li>
2746 <li>• Improved loading of Jalview files</li>
2752 <div align="center">
2753 <strong>2.03</strong><br> 18/8/05
2758 <li>• Set Proxy server name and port in preferences</li>
2759 <li>• Multiple URL links from sequence ids</li>
2760 <li>• User Defined Colours can have a scheme name and added
2762 <li>• Choose to ignore gaps in consensus calculation</li>
2763 <li>• Unix users can set default web browser</li>
2764 <li>• Runs without GUI for batch processing</li>
2765 <li>• Dynamically generated Web Service Menus</li>
2770 <li>• InstallAnywhere download for Sparc Solaris</li>
2776 <div align="center">
2777 <strong>2.02</strong><br> 18/7/05
2783 <li>• Copy & Paste order of sequences maintains
2784 alignment order.</li>
2790 <div align="center">
2791 <strong>2.01</strong><br> 12/7/05
2796 <li>• Use delete key for deleting selection.</li>
2797 <li>• Use Mouse wheel to scroll sequences.</li>
2798 <li>• Help file updated to describe how to add alignment
2800 <li>• Version and build date written to build properties
2802 <li>• InstallAnywhere installation will check for updates
2803 at launch of Jalview.</li>
2808 <li>• Delete gaps bug fixed.</li>
2809 <li>• FileChooser sorts columns.</li>
2810 <li>• Can remove groups one by one.</li>
2811 <li>• Filechooser icons installed.</li>
2812 <li>• Finder ignores return character when searching.
2813 Return key will initiate a search.<br>
2820 <div align="center">
2821 <strong>2.0</strong><br> 20/6/05
2826 <li>• New codebase</li>
git://source.jalview.org / jalview.git / blob