4 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
5 * Copyright (C) $$Year-Rel$$ The Jalview Authors
7 * This file is part of Jalview.
9 * Jalview is free software: you can redistribute it and/or
10 * modify it under the terms of the GNU General Public License
11 * as published by the Free Software Foundation, either version 3
12 * of the License, or (at your option) any later version.
14 * Jalview is distributed in the hope that it will be useful, but
15 * WITHOUT ANY WARRANTY; without even the implied warranty
16 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
17 * PURPOSE. See the GNU General Public License for more details.
19 * You should have received a copy of the GNU General Public License
20 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
21 * The Jalview Authors are detailed in the 'AUTHORS' file.
24 <title>Release History</title>
27 /* remove bullets, narrower indent */
28 list-style-type: none;
35 /* separate the items from eachother */
42 /* doesnt get processed in javahelp */
51 <strong>Release History</strong>
55 <th nowrap><a id="Jalview.$$Version-Rel$$"><em>Release</em></th>
56 <th><em>New Features</em></th>
57 <th><em>Issues Resolved</em></th>
60 <td width="60" align="center" nowrap><strong><a
61 id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.3">.3</a><br />
62 <em>12/05/2022</em></strong></td>
63 <td align="left" valign="top">
65 <td align="left" valign="top">
68 <!-- JAL-4008 -->Validation fails when trying to configure custom JABAWS server
70 </ul> <!-- <em>New Known Issues</em>-->
74 <td width="60" align="center" nowrap><strong><a
75 id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.2">.2</a><br />
76 <em>19/04/2022</em></strong></td>
77 <td align="left" valign="top">
80 <!-- JAL-3992 -->Minor documentation fixes
84 <td align="left" valign="top">
87 <!-- JAL-3365 -->Secondary structure annotation from Pfam
88 not displayed correctly
91 <!-- JAL-3997 -->Null pointer exceptions when displaying
92 annotation tooltips whilst in wrapped mode
94 </ul> <!-- <em>New Known Issues</em>-->
98 <td width="60" align="center" nowrap><strong><a
99 id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.1">.1</a><br />
100 <em>05/04/2022</em></strong></td>
101 <td align="left" valign="top">
104 <!-- JAL-3973 -->Distribution Tarball includes git commit
109 <td align="left" valign="top">
112 <!-- JAL-3975 -->Keyboard mode (F2) stops working after
113 using the "Create sequence feature" dialog
116 <!-- JAL-3976 -->3D Structure chooser fails to select
117 structures from 3D-beacons and pops up a 'null' dialog
120 <!-- JAL-3985 -->PDB FTS query results in error dialog
121 containing '414' [URL too long]
124 <!-- JAL-3980 JAL-3981 -->Sequence ID tooltip not shown during
125 long running retrieval/crossref operations (affects at least
129 <!-- JAL-3973 -->Cannot build Jalview 2.11.2.0 via gradle
130 from its source tarball
132 </ul> <em>New Known Issues</em>
135 <!-- JAL-3984 -->Keyboard mode (F2) stops working after
136 using the "Text Colour" dialog
139 <!-- JAL-3873 -->Colour by->all views doesn't allow
140 colouring same structure from different views (since
144 <!-- JAL-3886 -->Pfam and Rfam alignment retrieval as
145 gzipped stockholm doesn't work on JalviewJS build of 2.11.2
148 <!-- JAL-3972 -->Java 11 Only: Jalview 2.11.2.0 OSX install
149 not working due to VAqua requiring
150 sun.awt.image.MultiResolutionImage
153 <!-- JAL-3981 -->Sequence Details can take a long time to be
154 displayed for heavily annotated sequences (all versions)
160 <td width="60" align="center" nowrap><strong><a
161 id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.0">.0</a><br />
162 <em>10/03/2022</em></strong></td>
163 <td align="left" valign="top">
166 <!-- JAL-3616 JAL-3551 JAL-2322 -->Support for viewing 3D
167 structures with ChimeraX and Pymol in addition to Jmol and
171 <!-- JAL-3829 -->Discover 3D structure data for sequences
172 with Uniprot references via 3D-Beacons
175 <!-- JAL-3391 -->Rank and select available structures for
176 Uniprot sequences according to number of residues in
177 structure mapped to positions involved in the alignment
180 <!-- JAL-2226 -->Structure annotation rows for all mapped
181 chains in 3D structures are included in the 'Reference
182 Annotation' for a sequence
185 <!-- JAL-1260 -->Import Genbank and EMBL format flatfiles
188 <!-- JAL-3821 -->ENA record's mol_type honoured so RNA
189 molecules imported from ENA records are shown as RNA
191 <!-- JAL-3863 -->Support for Canonical Uniprot IDs
194 <!-- JAL-3503 -->New Preferences tab for adjusting Jalview's
195 memory settings at launch
198 <!-- JAL-3881 -->Sequence IDs split on '_' as well as other
199 non-alphanumerics when discovering database references with
203 <!-- JAL-3884 -->Suppressed harmless exceptions output to
204 Console whilst discovering database references for a
208 <!-- JAL-3204 -->Updated Jalview bindings for Uniprot XML
212 <!-- JAL-3926 -->Uniprot and PDBe autosearch option is
216 <!-- JAL-3144 -->Reverted to Jalview 'classic' drop-down
217 menu for selecting which database to fetch from in sequence
221 <!-- JAL-3018 -->Updated Ensembl REST Client compatibility
222 to 15.2 and revised model organism names (rat, xenopus,
223 dmelanogaster now rattus_norvegicus, xenopus_tropicalis,
224 drosophila_melanogaster)
227 <!-- JAL-3530 -->-nowebservicediscovery command line
228 argument to prevent automatic discovery of analysis
229 webservices on launch
232 <!-- JAL-3618 -->Allow 'App' directories to be opened when
233 locating Chimera, ChimeraX or Pymol binaries via filechooser
234 opened by double clicking the Structure Preferences' path
238 <!-- JAL-3632 JAL-3633 -->support for HTTP/S access via
239 proxies that require authentication
242 <!-- JAL-3103 -->New mechanism for opening URLs with system
243 default browser (works on OSX and Linux as well as Windows)
246 <!-- JAL-3871 JAL-3874 -->Upgraded bundled version of Jmol
250 <!-- JAL-3837 -->GPL license info on splash screen and About
253 </ul> <em>Jalview Native App</em>
256 <!-- JAL-3830 -->New command line launcher scripts (.sh,
257 .ps1, .bat) usable on macOS, Linux/Unix, Windows and
258 documentation in Help. Installer wizard has option to add
259 this to PATH, or link to it in your PATH.<br /> <em>This
260 is the recommended workaround for known issue about
261 working directory preservation when running native
262 application from command line. <!-- JAL-3523 -->
265 <li>Notarized MacOS installer for compliance with latest
266 OSX releases (Monterey)</li>
268 <!-- JAL-3805 -->Uninstaller application for old
269 (InstallAnywhere based) Jalview installations removed from
273 <!-- JAL-3608 -->Options to allow user to choose the (Swing)
274 Look and Feel (LaF) used by Jalview
277 <!-- JAL-3552, JAL-3609 -->Metal LaF used to improved
278 operation on Linux Ubuntu with HiDPI display in Java 11
279 (still known issues with HiDPI screens in java 8 and 11. see
280 <a href="https://issues.jalview.org/browse/JAL-3137">JAL-3137</a>)
283 <!-- JAL-3633 -->Getdown launcher inherits HTTP/S proxy
284 configuration from jalview_properties
287 <!-- JAL- -->New Jalview Develop app - making it even easier
288 to get at Jalview's development builds
291 <!-- JAL-3594 -->New splashscreens for Jalview, Jalview Test
292 and Jalview Develop applications.
295 <!-- JAL-3728 -->Jalview logos shown for Jalview Java
296 Console and other window widgets in taskbar and dock rather
297 than anonymous 'Java' icons
299 </ul> <em>JalviewJS</em>
302 <!-- JAL-3624 -->PDB structures mapped to Uniprot Sequences
306 <!-- JAL-3208 -->setprop commandline argument reinstated for
310 <!-- JAL-3163 -->Missing message bundle keys are only
311 reported once per key (avoids excessive log output in js
315 <!-- JAL-3168 -->Feature type is included in the title of
316 the Feature Settings' Colour Chooser dialog
319 <!-- JAL-3279 -->Build details reported in About window
322 <!-- JAL-3038 JAL-3071 JAL-3263 JAL-3084 -->Numerous minor
323 GUI additions and improvements in sync with Java
326 </ul> <em>Development</em>
329 <!-- -->First integrated JalviewJS and Jalview release
332 <!-- JAL-3841,JAL-3248 -->Updated README and doc/building.md
335 <!-- JAL-3789, JAL-3679 -->Improved JalviewJS/Jalview build
336 process, added support for system package provided eclipse
339 <li>Install4j 9.0.x used for installer packaging</li>
341 <!-- JAL-3930 -->Improved use of installers for unattended
342 installation with a customizedId of "JALVIEW" in install4j's
346 <!-- JAL-3907 -->Improved compatibility of Jalview build
347 with Java 17 (next LTS target)
351 <td align="left" valign="top">
354 <!-- JAL-3674 -->Slow structure commands can block Jalview
358 <!-- JAL-3904 -->Structure window's viewer-specific menu
359 disappears when only one structure is shown (and many
360 sequences:one chain mappings are present)
363 <!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
364 the first SEQUENCE_GROUP defined
368 <!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 -->Selections not
369 propagated between Linked CDS - Protein alignments and their
370 trees (known defect from 2.11.1.3)
373 <!-- JAL-3761 -->Not all codon positions highlighted for
374 overlapping exon splice sites (e.g due to RNA slippage)
377 <!-- JAL-3794 -->X was not being recognised as the unknown
378 base in DNA sequences
381 <!-- JAL-3915 -->Removed RNAview checkbox and logic from
382 Structure Preferences
385 <!-- JAL-3583 -->Tooltip behaviour improved (slightly)
388 <!-- JAL-3162 -->Can edit a feature so that start > end
391 <!-- JAL-2848 -->Cancel from Amend Features doesn't reset a
392 modified graduated colour
395 <!-- JAL-3788 -->New View with automatic 'Show Overview'
396 preference enabled results in Null Pointer Exceptions when
397 clustal colouring is enabled
400 <!-- JAL-3275 -->Can open multiple Preferences panels
403 <!-- JAL-3633 -->Properly configure HTTPS proxy settings
407 <!-- JAL-3949 -->Standard out logging broken: messages only
408 routing to stderr and appear as a raw template
411 <!-- JAL-3739 -->Entering web service parameter values in
412 numerical field doesn't update the value of the parameter
413 until return is pressed.
416 <!-- JAL-3749 -->Resolved known issue (from 2.11.1.1)
417 concerning duplicate CDS sequences generated when protein
418 products for certain ENA records are repeatedly shown via
419 Calculate->Show Cross Refs
421 </ul> <em>JalviewJS</em>
424 <!-- JAL-3202 -->Consensus profile may include zero (rounded
425 down) percentage values causing a divide by zero
428 <!-- JAL-3762 -->JalviewJS doesn't honour arguments passed
429 via Info.args when there are arguments on the URL
432 <!-- JAL-3602 -->gradle closure-compiler not using UTF-8
435 <!-- JAL-3603 -->Annotation file fails to load from URL in
438 </ul> <em>Development</em>
442 <li>Fixed non-fatal gradle errors during build</li>
444 <!-- JAL-3745 -->Updated build.gradle for use with
450 </ul> <em>Known Issues</em>
453 <!-- JAL-3764 -->Display of RESNUM sequence features are not
454 suppressed when structures associated with a sequence are
455 viewed with an external viewer (Regression from 2.11.1
462 <td width="60" align="center" nowrap><strong><a
463 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.7">.7</a><br />
464 <em>18/01/2022</em></strong></td>
466 <td align="left" valign="top">
469 <!-- JAL-3703, JAL-3935 -->Files open in Jalview cannot be
470 updated by Jalview or other applications (Windows, other non
473 </ul> <em>Security</em>
476 <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
482 <td width="60" align="center" nowrap><strong><a
483 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
484 <em>6/01/2022</em></strong></td>
486 <td align="left" valign="top"><em>Security</em>
489 <!-- JAL-3934 -->Version bump library dependency: Log4j
496 <td width="60" align="center" nowrap><strong><a
497 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
498 <em>20/12/2021</em></strong></td>
500 <td align="left" valign="top"><em>Security</em>
503 <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
505 </ul> <em>Development</em>
507 <li>Updated building instructions</li>
512 <!-- JAL-3840 -->Occupancy calculation is incorrect for
513 alignment columns with over -1+2^32 gaps (breaking filtering
517 <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
518 scale factors being set with buggy window-managers (linux
521 </ul> <em>Development</em>
523 <li>Fixed non-fatal gradle errors during build</li>
528 <td width="60" align="center" nowrap><strong><a
529 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
530 <em>09/03/2021</em></strong></td>
531 <td align="left" valign="top"><em>Improved control of
532 Jalview's use of network services via jalview_properties</em>
535 <!-- JAL-3814 -->New .jalview_properties token controlling
536 launch of the news browser (like -nonews argument)
539 <!-- JAL-3813 -->New .jalview_properties token controlling
540 download of linkout URLs from
541 www.jalview.org/services/identifiers
544 <!-- JAL-3812 -->New .jalview_properties token controlling
545 download of BIOJSHTML templates
548 <!-- JAL-3811 -->New 'Discover Web Services' option to
549 trigger a one off JABAWS discovery if autodiscovery was
553 <td align="left" valign="top">
556 <!-- JAL-3818 -->Intermittent deadlock opening structure in
559 </ul> <em>New Known defects</em>
562 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
563 always restored from project (since 2.10.3)
566 <!-- JAL-3806 -->Selections from tree built from CDS aren't
567 propagated to Protein alignment (since 2.11.1.3)
573 <td width="60" align="center" nowrap><strong><a
574 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
575 <em>29/10/2020</em></strong></td>
576 <td align="left" valign="top">
581 <td align="left" valign="top">
584 <!-- JAL-3765 -->Find doesn't always highlight all matching
585 positions in a sequence (bug introduced in 2.11.1.2)
588 <!-- JAL-3760 -->Alignments containing one or more protein
589 sequences can be classed as nucleotide
592 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
593 sequences after alignment of protein products (known defect
594 first reported for 2.11.1.0)
597 <!-- JAL-3725 -->No tooltip or popup menu for genomic
598 features outwith CDS shown overlaid on protein
601 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
602 correctly mapped by Jalview (e.g. affects viral CDS with
603 ribosomal slippage, since 2.9.0)
606 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
610 <!-- JAL-3700 -->Selections in CDS sequence panel don't
611 always select corresponding protein sequences
614 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
615 column selection doesn't always ignore hidden columns
617 </ul> <em>Installer</em>
620 <!-- JAL-3611 -->Space character in Jalview install path on
621 Windows prevents install4j launching getdown
623 </ul> <em>Development</em>
626 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
627 version numbers in doc/building.md
633 <td width="60" align="center" nowrap><strong><a
634 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
635 <em>25/09/2020</em></strong></td>
636 <td align="left" valign="top">
640 <td align="left" valign="top">
643 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
644 "Encountered problems opening
645 https://www.jalview.org/examples/exampleFile_2_7.jvp"
651 <td width="60" align="center" nowrap><strong><a
652 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
653 <em>17/09/2020</em></strong></td>
654 <td align="left" valign="top">
657 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
658 residue in cursor mode
661 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
662 HTSJDK from 2.12 to 2.23
665 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
666 optimisations and improvements suggested by Bob Hanson and
667 improved compatibility with JalviewJS
670 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
671 alignments from Pfam and Rfam
674 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
675 import (no longer based on .gz extension)
678 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
681 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
682 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
686 <!-- JAL-3667 -->Improved warning messages, debug logging
687 and fixed Retry action when Jalview encounters errors when
688 saving or making backup files.
691 <!-- JAL-3676 -->Enhanced Jalview Java Console:
693 <li>Jalview's logging level can be configured</li>
694 <li>Copy to Clipboard Buttion</li>
698 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
699 when running on Linux (Requires Java 11+)
702 <!-- JAL-1842 JAL-3509 -->RESNUM sequence features (the
703 green ones) are not automatically displayed when associated
704 structures are displayed or for sequences retrieved from the
707 </ul> <em>Launching Jalview</em>
710 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
711 through a system property
714 <!-- JAL-3477 -->Improved built-in documentation and command
715 line help for configuring Jalview's memory
719 <td align="left" valign="top">
722 <!-- JAL-3691 -->Conservation and Quality tracks are shown
723 but not calculated and no protein or DNA score models are
724 available for tree/PCA calculation when launched with
725 Turkish language locale
728 <!-- JAL-3493 -->Escape does not clear highlights on the
729 alignment (Since Jalview 2.10.3)
732 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
733 doesn't slide selected sequences, just sequence under cursor
736 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
737 sequence under the cursor
740 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
741 multiple EMBL gene products shown for a single contig
744 <!-- JAL-3696 -->Errors encountered when processing variants
745 from VCF files yield "Error processing VCF: Format specifier
749 <!-- JAL-3697 -->Count of features not shown can be wrong
750 when there are both local and complementary features mapped
751 to the position under the cursor
754 <!-- JAL-3673 -->Sequence ID for reference sequence is
755 clipped when Right align Sequence IDs enabled
758 <!-- JAL-2983 -->Slider with negative range values not
759 rendered correctly in VAqua4 (Since 2.10.4)
762 <!-- JAL-3685 -->Single quotes not displayed correctly in
763 internationalised text for some messages and log output
766 <!-- JAL-3490 -->Find doesn't report matches that span
767 hidden gapped columns
770 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
771 panels, Alignment viewport and annotation renderer.
774 <!-- JAL-3561 -->Jalview ignores file format parameter
775 specifying output format when exporting an alignment via the
779 <!-- JAL-3667 -->Windows 10: For a minority of users, if
780 backups are not enabled, Jalview sometimes fails to
781 overwrite an existing file and raises a warning dialog. (in
782 2.11.0, and 2.11.1.0, the workaround is to try to save the
783 file again, and if that fails, delete the original file and
787 <!-- JAL-3509 -->Dragging a PDB file onto an alignment with
788 sequence features displayed causes displayed features to be
792 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
796 <!-- JAL-3741 -->References to http://www.jalview.org in
797 program and documentation
799 </ul> <em>Launching Jalview</em>
802 <!-- JAL-3718 -->Jalview application fails when launched the
803 first time for a version that has different jars to the
804 previous launched version.
806 </ul> <em>Developing Jalview</em>
809 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
810 data, causing cloverReport gradle task to fail with an
814 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
815 monitor the release channel
817 </ul> <em>New Known defects</em>
820 <!-- JAL-3748 -->CDS shown in result of submitting proteins
821 in a CDS/Protein alignment to a web service is wrong when
822 proteins share a common transcript sequence (e.g. genome of
826 <!-- JAL-3576 -->Co-located features exported and
827 re-imported are ordered differently when shown on alignment
828 and in tooltips. (Also affects v2.11.1.0)
831 <!-- JAL-3702 -->Drag and drop of alignment file onto
832 alignment window when in a HiDPI scaled mode in Linux only
833 works for the top left quadrant of the alignment window
836 <!-- JAL-3701 -->Stale build data in jalview standalone jar
837 builds (only affects 2.11.1.1 branch)
840 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
841 when alignment view restored from project (since Jalview
845 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
846 protein products for certain ENA records are repeatedly
847 shown via Calculate->Show Cross Refs
853 <td width="60" align="center" nowrap><strong><a
854 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
855 <em>22/04/2020</em></strong></td>
856 <td align="left" valign="top">
859 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
860 'virtual' codon features shown on protein (or vice versa)
861 for display in alignments, on structure views (including
862 transfer to UCSF chimera), in feature reports and for
866 <!-- JAL-3121 -->Feature attributes from VCF files can be
867 exported and re-imported as GFF3 files
870 <!-- JAL-3376 -->Capture VCF "fixed column" values
871 POS, ID, QUAL, FILTER as Feature Attributes
874 <!-- JAL-3375 -->More robust VCF numeric data field
875 validation while parsing
878 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
882 <!-- JAL-3535 -->Feature Settings dialog title includes name
886 <!-- JAL-3538 -->Font anti-aliasing in alignment views
890 <!-- JAL-3468 -->Very long feature descriptions truncated in
894 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
895 with no feature types visible
898 <!-- JAL-3574 -->Improved support for filtering feature
899 attributes with large integer values
902 <em>Jalview Installer</em>
905 <!-- JAL-3449 -->Versions for install4j and getdown and
906 installer template version reported in console (may be null
907 when Jalview launched as executable jar or via conda)
910 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and
911 higher quality background images
914 <!-- JAL-3394 -->New installer/application launcher
915 generated with install4j 8.0.4
918 <!-- JAL-3420 -->Jalview File Associations shown for Unix
922 <!-- JAL-3477 -->Improved defaults for maximum memory
923 setting when running on large memory machines
925 </ul> <em>Release processes</em>
928 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
931 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier
932 access to test-release channel builds
934 </ul> <em>Build System</em>
937 <!-- JAL-3510 -->Clover updated to 4.4.1
940 <!-- JAL-3513 -->Test code included in Clover coverage
943 </ul> <em>Groovy Scripts</em>
946 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
947 to stdout containing the consensus sequence for each
948 alignment in a Jalview session
951 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
952 genomic sequence_variant annotation from CDS as
953 missense_variant or synonymous_variant on protein products.
957 <td align="left" valign="top">
960 <!-- JAL-3581 -->Hidden sequence markers still visible when
961 'Show hidden markers' option is not ticked
964 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
965 PNG output when 'Automatically set ID width' is set in
966 jalview preferences or properties file
969 <!-- JAL-3571 -->Feature Editor dialog can be opened when
970 'Show Sequence Features' option is not ticked
973 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
974 buttons in Feature Settings dialog are clicked when no
978 <!-- JAL-3412 -->ID margins for CDS and Protein views not
979 equal when split frame is first opened
982 <!-- JAL-3296 -->Sequence position numbers in status bar not
983 correct after editing a sequence's start position
986 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
987 with annotation and exceptions thrown when only a few
988 columns shown in wrapped mode
991 <!-- JAL-3386 -->Sequence IDs missing in headless export of
992 wrapped alignment figure with annotations
995 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
996 ID fails with ClassCastException
999 <!-- JAL-3389 -->Chimera session not restored from Jalview
1003 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
1004 feature settings dialog also selects columns
1007 <!-- JAL-3473 -->SpinnerNumberModel causes
1008 IllegalArgumentException in some circumstances
1011 <!-- JAL-3534 -->Multiple feature settings dialogs can be
1015 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
1016 alignment window is closed
1019 <!-- JAL-3406 -->Credits missing some authors in Jalview
1020 help documentation for 2.11.0 release
1023 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
1024 includes Pfam ID as sequence's accession rather than its
1027 </ul> <em>Java 11 Compatibility issues</em>
1030 <!-- JAL-2987 -->OSX - Can't view some search results in
1031 PDB/Uniprot search panel
1033 </ul> <em>Installer</em>
1036 <!-- JAL-3447 -->Jalview should not create file associations
1037 for 3D structure files (.pdb, .mmcif. .cif)
1039 </ul> <em>Repository and Source Release</em>
1042 <!-- JAL-3474 -->removed obsolete .cvsignore files from
1046 <!-- JAL-3541 -->Clover report generation running out of
1049 </ul> <em>New Known Issues</em>
1052 <!-- JAL-3523 -->OSX - Current working directory not
1053 preserved when Jalview.app launched with parameters from
1057 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
1058 clipped in headless figure export when Right Align option
1062 <!-- JAL-3542 -->Jalview Installation type always reports
1063 'Source' in console output
1066 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail
1067 on jalview's bamboo server but run fine locally.
1073 <td width="60" align="center" nowrap><strong><a
1074 name="Jalview.2.11.0">2.11.0</a><br /> <em>04/07/2019</em></strong></td>
1075 <td align="left" valign="top">
1078 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native
1079 Application and Installers built with <a
1080 href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a>
1081 (licensed to the Jalview open source project) rather than
1085 <!-- JAL-1929 -->Jalview Launcher System to auto-configure
1086 memory settings, receive over the air updates and launch
1087 specific versions via (<a
1088 href="https://github.com/threerings/getdown">Three
1092 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations
1093 for formats supported by Jalview (including .jvp project
1097 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command
1098 line arguments and switch between different getdown channels
1101 <!-- JAL-3141 -->Backup files created when saving Jalview
1102 project or alignment files
1106 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF
1110 <!-- JAL-2753 -->Version of HTSJDK shipped with Jalview
1111 updated to version 2.12.0
1114 <!-- JAL-2620 -->Alternative genetic code tables for
1118 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0
1120 <li><strong>Enhanced visualisation and analysis
1121 of Sequence Features</strong>
1124 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
1125 implementation that allows updates) used for Sequence
1129 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
1130 features can be filtered and shaded according to any
1131 associated attributes (e.g. variant attributes from VCF
1132 file, or key-value pairs imported from column 9 of GFF
1136 <!-- JAL-2879 -->Feature Attributes and shading schemes
1137 stored and restored from Jalview Projects
1140 <!-- JAL-3334 -->Use full Sequence Ontology (via
1141 BioJava) to recognise variant features
1144 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants
1145 on peptide sequences (also coloured red by default)
1148 <!-- JAL-2792 -->Popup window to show full report for a
1149 selected sequence feature's details
1152 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient
1153 sequence feature render algorithm (Z-sort/transparency
1157 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature
1162 <!-- JAL-3205 -->Symmetric score matrices for faster tree
1163 and PCA calculations
1165 <li><strong>Principal Components Analysis Viewer</strong>
1168 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis
1169 results and Viewer state saved in Jalview Project
1172 <!-- JAL-2962 -->'Change parameters' option removed from
1173 viewer's drop-down menus
1176 <!-- JAL-2975 -->Can use shift + arrow keys to rotate
1177 PCA image incrementally
1180 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
1184 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
1186 <li><strong>Speed and Efficiency</strong>
1189 <!-- JAL-2185,JAL-3198 -->More efficient creation of
1190 selections and multiple groups when working with large
1194 <!-- JAL-3200 -->Speedier import of annotation rows when
1195 parsing Stockholm files
1198 <li><strong>User Interface</strong>
1201 <!-- JAL-2933 -->Finder panel remembers last position in
1205 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS
1206 (What you see is what is shown)<br />Only visible
1207 regions of alignment are shown by default (can be
1208 changed in user preferences)
1211 <!-- JAL-3169 -->File Chooser stays open after
1212 responding Cancel to the Overwrite Dialog
1215 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour
1216 when all sequences are hidden
1219 <!-- JAL-1244 -->Status bar shows bounds when dragging a
1220 selection region, and gap count when inserting or
1224 <!-- JAL-3132 -->Status bar updates over sequence and
1228 <!-- JAL-3093 -->Annotation tooltips and popup menus are
1229 shown when in wrapped mode
1232 <!-- JAL-3073 -->Can select columns by dragging
1233 left/right in a graph or histogram annotation
1236 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB
1240 <!-- JAL-2621 -->Cursor changes over draggable box in
1244 <!-- JAL-3181 -->Consistent ordering of links in
1245 sequence id popup menu
1248 <!-- JAL-3080 -->Red line indicating tree-cut position
1249 not shown if no subgroups are created
1252 <!-- JAL-3042 -->Removed ability to configure length of
1253 search history by right-clicking search box
1259 <!-- JAL-3232 -->Jalview Groovy Scripting Console updated to
1262 <li><strong>Java 11 Support (not yet on general
1266 <!-- -->OSX GUI integrations for App menu's 'About'
1267 entry and trapping CMD-Q
1270 </ul> <em>Deprecations</em>
1273 <!-- JAL-3035 -->DAS sequence retrieval and annotation
1274 capabilities removed from the Jalview Desktop
1277 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling
1278 and unmarshalling has been replaced by JAXB for Jalview
1279 projects and XML based data retrieval clients
1282 <!-- JAL-3311 -->Disable VAMSAS menu in preparation for
1286 <!-- -->Jalview Desktop no longer distributed via Java Web
1289 </ul> <em>Documentation</em>
1292 <!-- JAL-3003 -->Added remarks about transparent rendering
1293 effects not supported in EPS figure export
1296 <!-- JAL-2903 -->Typos in documentation for Preferences
1299 </ul> <em>Development and Release Processes</em>
1302 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated
1306 <!-- JAL-1424 -->Enhanced checks for missing and duplicated
1307 keys in Message bundles
1310 <!-- JAL-3225 -->Eclipse project configuration managed with
1314 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian Bamboo
1315 continuous integration for unattended Test Suite execution
1318 <!-- JAL-2864 -->Memory test suite to detect leaks in common
1322 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
1326 <!-- JAL-3248 -->Developer documentation migrated to
1327 markdown (with HTML rendering)
1330 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
1333 <!-- JAL-3289 -->New URLs for publishing development
1338 <td align="left" valign="top">
1341 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
1344 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
1345 superposition in Jmol fail on Windows
1348 <!-- JAL-3286 -->Blank error dialog is displayed when
1349 discovering structures for sequences with lots of PDB
1353 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export
1354 with monospaced font
1357 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
1358 Jalview project involving multiple views
1361 <!-- JAL-3164 -->Overview for complementary view in a linked
1362 CDS/Protein alignment is not updated when Hide Columns by
1363 Annotation dialog hides columns
1366 <!-- JAL-3158 -->Selection highlighting in the complement of
1367 a CDS/Protein alignment stops working after making a
1368 selection in one view, then making another selection in the
1372 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
1376 <!-- JAL-3154 -->Table Columns could be re-ordered in
1377 Feature Settings and Jalview Preferences panels
1380 <!-- JAL-2865 -->Jalview hangs when closing windows, or
1381 redrawing the overview with large alignments
1384 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
1385 region if columns were selected by dragging right-to-left
1386 and the mouse moved to the left of the first column
1389 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to
1390 a hidden column marker via scale popup menu
1393 <!-- JAL-2846 -->Error message for trying to load in invalid
1394 URLs doesn't tell users the invalid URL
1397 <!-- JAL-2816 -->Tooltips displayed for features filtered by
1401 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl
1402 during show cross references or Fetch Database References
1403 are shown in red in original view
1406 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown
1407 correctly on peptide sequence (computed variant shown as
1411 <!-- JAL-2060 -->'Graduated colour' option not offered for
1412 manually created features (where feature score is Float.NaN)
1415 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or
1416 printed when columns are hidden
1419 <!-- JAL-3082 -->Regular expression error for '(' in Select
1420 Columns by Annotation description
1423 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after
1424 dragging out of Scale or Annotation Panel
1427 <!-- JAL-3075 -->Column selection incorrect after scrolling
1431 <!-- JAL-3074 -->Left/right drag in annotation can scroll
1435 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal
1439 <!-- JAL-3002 -->Column display is out by one after Page
1440 Down, Page Up in wrapped mode
1443 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
1446 <!-- JAL-2932 -->Finder searches in minimised alignments
1449 <!-- JAL-2250 -->'Apply Colour to All Groups' not always
1450 selected on opening an alignment
1453 <!-- JAL-3180 -->'Colour by Annotation' not marked selected
1457 <!-- JAL-3201 -->Per-group Clustal colour scheme changes
1458 when different groups in the alignment are selected
1461 <!-- JAL-2717 -->Internationalised colour scheme names not
1462 shown correctly in menu
1465 <!-- JAL-3206 -->Colour by Annotation can go black at
1466 min/max threshold limit
1469 <!-- JAL-3125 -->Value input for graduated feature colour
1470 threshold gets 'unrounded'
1473 <!-- JAL-2982 -->PCA image export doesn't respect background
1477 <!-- JAL-2963 -->PCA points don't dim when rotated about y
1481 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
1484 <!-- JAL-3078 -->Cancel in Tree Font dialog resets
1485 alignment, not Tree font
1488 <!-- JAL-2964 -->Associate Tree with All Views not restored
1492 <!-- JAL-2915 -->Scrolling of split frame is sluggish if
1493 Overview shown in complementary view
1496 <!-- JAL-3313 -->Codon consensus incorrectly scaled when
1497 shown without normalisation
1500 <!-- JAL-3021 -->Sequence Details report should open
1501 positioned at top of report
1504 <!-- JAL-914 -->Help page can be opened twice
1507 <!-- JAL-3333 -->Fuzzy text in web service status menu on
1510 </ul> <em>Editing</em>
1513 <!-- JAL-2822 -->Start and End should be updated when
1514 sequence data at beginning or end of alignment added/removed
1518 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection
1519 doesn't relocate sequence features correctly when start of
1520 sequence is removed (Known defect since 2.10)
1523 <!-- JAL-2830 -->Inserting gap sequence via the Edit
1524 Sequence dialog corrupts dataset sequence
1527 <!-- JAL-868 -->Structure colours not updated when
1528 associated tree repartitions the alignment view (Regression
1531 </ul> <em>Datamodel</em>
1534 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
1535 sequence's End is greater than its length
1537 </ul> <em>Bugs fixed for Java 11 Support (not yet on general
1541 <!-- JAL-3288 -->Menus work properly in split-screen
1543 </ul> <em>New Known Defects</em>
1546 <!-- JAL-3340 -->Select columns containing feature by double
1547 clicking ignores bounds of an existing selected region
1550 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in
1551 gapped regions of protein alignment.
1554 <!-- JAL-2647 -->Input Data menu entry is greyed out when
1555 PCA View is restored from a Jalview 2.11 project
1558 <!-- JAL-3213 -->Alignment panel height can be too small
1562 <!-- JAL-3240 -->Display is incorrect after removing gapped
1563 columns within hidden columns
1566 <!-- JAL-3314 -->Rightmost selection is lost when mouse
1567 re-enters window after dragging left to select columns to
1568 left of visible region
1571 <!-- JAL-2876 -->Features coloured according to their
1572 description string and thresholded by score in earlier
1573 versions of Jalview are not shown as thresholded features in
1574 2.11. To workaround please create a Score filter instead.
1577 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't
1578 reset group visibility
1581 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in
1582 linked CDS/Protein view
1585 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1586 alignments with multiple views can close views unexpectedly
1588 </ul> <em>Java 11 Specific defects</em>
1591 <!-- JAL-3235 -->Jalview Properties file is not sorted
1592 alphabetically when saved
1598 <td width="60" nowrap>
1599 <div align="center">
1600 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1603 <td><div align="left">
1607 <!-- JAL-3101 -->Default memory for Jalview webstart and
1608 InstallAnywhere increased to 1G.
1611 <!-- JAL-247 -->Hidden sequence markers and representative
1612 sequence bolding included when exporting alignment as EPS,
1613 SVG, PNG or HTML. <em>Display is configured via the
1614 Format menu, or for command-line use via a Jalview
1615 properties file.</em>
1618 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1619 API and sequence data now imported as JSON.
1622 <!-- JAL-3065 -->Change in recommended way of starting
1623 Jalview via a Java command line: add jars in lib directory
1624 to CLASSPATH, rather than via the deprecated java.ext.dirs
1628 <em>Development</em>
1631 <!-- JAL-3047 -->Support added to execute test suite
1632 instrumented with <a href="http://openclover.org/">Open
1637 <td><div align="left">
1641 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1642 row shown in Feredoxin Structure alignment view of example
1646 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1647 annotation displayed.
1650 <!-- JAL-3107 -->Group conservation/consensus not shown
1651 for newly created group when 'Apply to all groups'
1655 <!-- JAL-3087 -->Corrupted display when switching to
1656 wrapped mode when sequence panel's vertical scrollbar is
1660 <!-- JAL-3003 -->Alignment is black in exported EPS file
1661 when sequences are selected in exported view.</em>
1664 <!-- JAL-3059 -->Groups with different coloured borders
1665 aren't rendered with correct colour.
1668 <!-- JAL-3092 -->Jalview could hang when importing certain
1669 types of knotted RNA secondary structure.
1672 <!-- JAL-3095 -->Sequence highlight and selection in
1673 trimmed VARNA 2D structure is incorrect for sequences that
1677 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1678 annotation when columns are inserted into an alignment,
1679 and when exporting as Stockholm flatfile.
1682 <!-- JAL-3053 -->Jalview annotation rows containing upper
1683 and lower-case 'E' and 'H' do not automatically get
1684 treated as RNA secondary structure.
1687 <!-- JAL-3106 -->.jvp should be used as default extension
1688 (not .jar) when saving a Jalview project file.
1691 <!-- JAL-3105 -->Mac Users: closing a window correctly
1692 transfers focus to previous window on OSX
1695 <em>Java 10 Issues Resolved</em>
1698 <!-- JAL-2988 -->OSX - Can't save new files via the File
1699 or export menus by typing in a name into the Save dialog
1703 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1704 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1705 'look and feel' which has improved compatibility with the
1706 latest version of OSX.
1712 <td width="60" nowrap>
1713 <div align="center">
1714 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1715 <em>7/06/2018</em></strong>
1718 <td><div align="left">
1722 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1723 annotation retrieved from Uniprot
1726 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1727 onto the Jalview Desktop
1731 <td><div align="left">
1735 <!-- JAL-3017 -->Cannot import features with multiple
1736 variant elements (blocks import of some Uniprot records)
1739 <!-- JAL-2997 -->Clustal files with sequence positions in
1740 right-hand column parsed correctly
1743 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1744 not alignment area in exported graphic
1747 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1748 window has input focus
1751 <!-- JAL-2992 -->Annotation panel set too high when
1752 annotation added to view (Windows)
1755 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1756 network connectivity is poor
1759 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1760 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1761 the currently open URL and links from a page viewed in
1762 Firefox or Chrome on Windows is now fully supported. If
1763 you are using Edge, only links in the page can be
1764 dragged, and with Internet Explorer, only the currently
1765 open URL in the browser can be dropped onto Jalview.</em>
1768 <em>New Known Defects</em>
1771 <!-- JAL-3083 -->Cancel option doesn't reset Colour by
1778 <td width="60" nowrap>
1779 <div align="center">
1780 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1783 <td><div align="left">
1787 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1788 for disabling automatic superposition of multiple
1789 structures and open structures in existing views
1792 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1793 ID and annotation area margins can be click-dragged to
1797 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1801 <!-- JAL-2759 -->Improved performance for large alignments
1802 and lots of hidden columns
1805 <!-- JAL-2593 -->Improved performance when rendering lots
1806 of features (particularly when transparency is disabled)
1809 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2
1810 for exchange of Jalview features and Chimera attributes
1811 made generally available
1815 <td><div align="left">
1818 <!-- JAL-2899 -->Structure and Overview aren't updated
1819 when Colour By Annotation threshold slider is adjusted
1822 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1823 overlapping alignment panel
1826 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1830 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1831 improved: CDS not handled correctly if transcript has no
1835 <!-- JAL-2321 -->Secondary structure and temperature
1836 factor annotation not added to sequence when local PDB
1837 file associated with it by drag'n'drop or structure
1841 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1842 dialog doesn't import PDB files dropped on an alignment
1845 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1846 scroll bar doesn't work for some CDS/Protein views
1849 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1850 Java 1.8u153 onwards and Java 1.9u4+.
1853 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1854 columns in annotation row
1857 <!-- JAL-2913 -->Preferences panel's ID Width control is
1858 not honored in batch mode
1861 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1862 for structures added to existing Jmol view
1865 <!-- JAL-2223 -->'View Mappings' includes duplicate
1866 entries after importing project with multiple views
1869 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1870 protein sequences via SIFTS from associated PDB entries
1871 with negative residue numbers or missing residues fails
1874 <!-- JAL-2952 -->Exception when shading sequence with
1875 negative Temperature Factor values from annotated PDB
1876 files (e.g. as generated by CONSURF)
1879 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1880 tooltip doesn't include a text description of mutation
1883 <!-- JAL-2922 -->Invert displayed features very slow when
1884 structure and/or overview windows are also shown
1887 <!-- JAL-2954 -->Selecting columns from highlighted
1888 regions very slow for alignments with large numbers of
1892 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1893 with 'StringIndexOutOfBounds'
1896 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and
1897 Feel for OSX platforms running Java 10
1900 <!-- JAL-2960 -->Adding a structure to existing structure
1901 view appears to do nothing because the view is hidden
1902 behind the alignment view
1908 <!-- JAL-2926 -->Copy consensus sequence option in applet
1909 should copy the group consensus when popup is opened on it
1915 <!-- JAL-2913 -->Fixed ID width preference is not
1919 <em>New Known Defects</em>
1922 <!-- JAL-2973 --> Exceptions occasionally raised when
1923 editing a large alignment and overview is displayed
1926 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1927 repeatedly after a series of edits even when the overview
1928 is no longer reflecting updates
1931 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1932 structures for protein subsequence (if 'Trim Retrieved
1933 Sequences' enabled) or Ensembl isoforms (Workaround in
1934 2.10.4 is to fail back to N&W mapping)
1937 <!-- JAL-2990 -->Export Annotations from File Menu with
1938 CSV option gives blank output
1944 <td width="60" nowrap>
1945 <div align="center">
1946 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br />
1947 <em>24/1/2018</em></strong>
1950 <td><div align="left">
1952 <li>Updated Certum Codesigning Certificate (Valid till
1953 30th November 2018)</li>
1956 <td><div align="left">
1961 <!-- JAL-2859-->Only one structure is loaded when
1962 several sequences and structures are selected for
1966 <!-- JAL-2851-->Alignment doesn't appear to scroll
1967 vertically via trackpad and scrollwheel
1970 <!-- JAL-2842-->Jalview hangs if up/down arrows pressed
1971 in cursor mode when cursor lies in hidden region at
1975 <!-- JAL-2827-->Helix annotation has 'notches' when
1976 scrolled into view if columns are hidden
1979 <!-- JAL-2740-->Annotation column filter can be slow to
1980 reset (ie after hitting cancel) for large numbers of
1984 <!-- JAL-2849-->User preference for disabling inclusion
1985 of sequence limits when exporting as flat file has no
1989 <!-- JAL-2679-->Reproducible cross-reference
1990 relationships when retrieving sequences from
1997 <td width="60" nowrap>
1998 <div align="center">
1999 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
2002 <td><div align="left">
2006 <!-- JAL-2446 -->Faster and more efficient management and
2007 rendering of sequence features
2010 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
2011 429 rate limit request hander
2014 <!-- JAL-2773 -->Structure views don't get updated unless
2015 their colours have changed
2018 <!-- JAL-2495 -->All linked sequences are highlighted for
2019 a structure mousover (Jmol) or selection (Chimera)
2022 <!-- JAL-2790 -->'Cancel' button in progress bar for
2023 JABAWS AACon, RNAAliFold and Disorder prediction jobs
2026 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
2027 view from Ensembl locus cross-references
2030 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
2034 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
2035 feature can be disabled
2038 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
2039 PDB easier retrieval of sequences for lists of IDs
2042 <!-- JAL-2758 -->Short names for sequences retrieved from
2048 <li>Groovy interpreter updated to 2.4.12</li>
2049 <li>Example groovy script for generating a matrix of
2050 percent identity scores for current alignment.</li>
2052 <em>Testing and Deployment</em>
2055 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
2059 <td><div align="left">
2063 <!-- JAL-2643 -->Pressing tab after updating the colour
2064 threshold text field doesn't trigger an update to the
2068 <!-- JAL-2682 -->Race condition when parsing sequence ID
2072 <!-- JAL-2608 -->Overview windows are also closed when
2073 alignment window is closed
2076 <!-- JAL-2548 -->Export of features doesn't always respect
2080 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
2081 takes a long time in Cursor mode
2087 <!-- JAL-2777 -->Structures with whitespace chainCode
2088 cannot be viewed in Chimera
2091 <!-- JAL-2728 -->Protein annotation panel too high in
2095 <!-- JAL-2757 -->Can't edit the query after the server
2096 error warning icon is shown in Uniprot and PDB Free Text
2100 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
2103 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
2106 <!-- JAL-2739 -->Hidden column marker in last column not
2107 rendered when switching back from Wrapped to normal view
2110 <!-- JAL-2768 -->Annotation display corrupted when
2111 scrolling right in unwapped alignment view
2114 <!-- JAL-2542 -->Existing features on subsequence
2115 incorrectly relocated when full sequence retrieved from
2119 <!-- JAL-2733 -->Last reported memory still shown when
2120 Desktop->Show Memory is unticked (OSX only)
2123 <!-- JAL-2658 -->Amend Features dialog doesn't allow
2124 features of same type and group to be selected for
2128 <!-- JAL-2524 -->Jalview becomes sluggish in wide
2129 alignments when hidden columns are present
2132 <!-- JAL-2392 -->Jalview freezes when loading and
2133 displaying several structures
2136 <!-- JAL-2732 -->Black outlines left after resizing or
2140 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
2141 within the Jalview desktop on OSX
2144 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
2145 when in wrapped alignment mode
2148 <!-- JAL-2636 -->Scale mark not shown when close to right
2149 hand end of alignment
2152 <!-- JAL-2684 -->Pairwise alignment of selected regions of
2153 each selected sequence do not have correct start/end
2157 <!-- JAL-2793 -->Alignment ruler height set incorrectly
2158 after canceling the Alignment Window's Font dialog
2161 <!-- JAL-2036 -->Show cross-references not enabled after
2162 restoring project until a new view is created
2165 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
2166 URL links appears when only default EMBL-EBI link is
2167 configured (since 2.10.2b2)
2170 <!-- JAL-2775 -->Overview redraws whole window when box
2171 position is adjusted
2174 <!-- JAL-2225 -->Structure viewer doesn't map all chains
2175 in a multi-chain structure when viewing alignment
2176 involving more than one chain (since 2.10)
2179 <!-- JAL-2811 -->Double residue highlights in cursor mode
2180 if new selection moves alignment window
2183 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
2184 arrow key in cursor mode to pass hidden column marker
2187 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
2188 that produces correctly annotated transcripts and products
2191 <!-- JAL-2776 -->Toggling a feature group after first time
2192 doesn't update associated structure view
2195 <em>Applet</em><br />
2198 <!-- JAL-2687 -->Concurrent modification exception when
2199 closing alignment panel
2202 <em>BioJSON</em><br />
2205 <!-- JAL-2546 -->BioJSON export does not preserve
2206 non-positional features
2209 <em>New Known Issues</em>
2212 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
2213 sequence features correctly (for many previous versions of
2217 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
2218 using cursor in wrapped panel other than top
2221 <!-- JAL-2791 -->Select columns containing feature ignores
2222 graduated colour threshold
2225 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
2226 always preserve numbering and sequence features
2229 <em>Known Java 9 Issues</em>
2232 <!-- JAL-2902 -->Groovy Console very slow to open and is
2233 not responsive when entering characters (Webstart, Java
2240 <td width="60" nowrap>
2241 <div align="center">
2242 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
2243 <em>2/10/2017</em></strong>
2246 <td><div align="left">
2247 <em>New features in Jalview Desktop</em>
2250 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API
2254 <!-- JAL-2745 -->HTTPS used for all connections to
2259 <td><div align="left"></div></td>
2262 <td width="60" nowrap>
2263 <div align="center">
2264 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
2265 <em>7/9/2017</em></strong>
2268 <td><div align="left">
2272 <!-- JAL-2588 -->Show gaps in overview window by colouring
2273 in grey (sequences used to be coloured grey, and gaps were
2277 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
2281 <!-- JAL-2587 -->Overview updates immediately on increase
2282 in size and progress bar shown as higher resolution
2283 overview is recalculated
2288 <td><div align="left">
2292 <!-- JAL-2664 -->Overview window redraws every hidden
2293 column region row by row
2296 <!-- JAL-2681 -->duplicate protein sequences shown after
2297 retrieving Ensembl crossrefs for sequences from Uniprot
2300 <!-- JAL-2603 -->Overview window throws NPE if show boxes
2301 format setting is unticked
2304 <!-- JAL-2610 -->Groups are coloured wrongly in overview
2305 if group has show boxes format setting unticked
2308 <!-- JAL-2672,JAL-2665 -->Redraw problems when
2309 autoscrolling whilst dragging current selection group to
2310 include sequences and columns not currently displayed
2313 <!-- JAL-2691 -->Not all chains are mapped when multimeric
2314 assemblies are imported via CIF file
2317 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
2318 displayed when threshold or conservation colouring is also
2322 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
2326 <!-- JAL-2673 -->Jalview continues to scroll after
2327 dragging a selected region off the visible region of the
2331 <!-- JAL-2724 -->Cannot apply annotation based
2332 colourscheme to all groups in a view
2335 <!-- JAL-2511 -->IDs don't line up with sequences
2336 initially after font size change using the Font chooser or
2343 <td width="60" nowrap>
2344 <div align="center">
2345 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
2348 <td><div align="left">
2349 <em>Calculations</em>
2353 <!-- JAL-1933 -->Occupancy annotation row shows number of
2354 ungapped positions in each column of the alignment.
2357 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
2358 a calculation dialog box
2361 <!-- JAL-2379 -->Revised implementation of PCA for speed
2362 and memory efficiency (~30x faster)
2365 <!-- JAL-2403 -->Revised implementation of sequence
2366 similarity scores as used by Tree, PCA, Shading Consensus
2367 and other calculations
2370 <!-- JAL-2416 -->Score matrices are stored as resource
2371 files within the Jalview codebase
2374 <!-- JAL-2500 -->Trees computed on Sequence Feature
2375 Similarity may have different topology due to increased
2382 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
2383 model for alignments and groups
2386 <!-- JAL-384 -->Custom shading schemes created via groovy
2393 <!-- JAL-2526 -->Efficiency improvements for interacting
2394 with alignment and overview windows
2397 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
2401 <!-- JAL-2388 -->Hidden columns and sequences can be
2405 <!-- JAL-2611 -->Click-drag in visible area allows fine
2406 adjustment of visible position
2410 <em>Data import/export</em>
2413 <!-- JAL-2535 -->Posterior probability annotation from
2414 Stockholm files imported as sequence associated annotation
2417 <!-- JAL-2507 -->More robust per-sequence positional
2418 annotation input/output via stockholm flatfile
2421 <!-- JAL-2533 -->Sequence names don't include file
2422 extension when importing structure files without embedded
2423 names or PDB accessions
2426 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
2427 format sequence substitution matrices
2430 <em>User Interface</em>
2433 <!-- JAL-2447 --> Experimental Features Checkbox in
2434 Desktop's Tools menu to hide or show untested features in
2438 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
2439 via Overview or sequence motif search operations
2442 <!-- JAL-2547 -->Amend sequence features dialog box can be
2443 opened by double clicking gaps within sequence feature
2447 <!-- JAL-1476 -->Status bar message shown when not enough
2448 aligned positions were available to create a 3D structure
2452 <em>3D Structure</em>
2455 <!-- JAL-2430 -->Hidden regions in alignment views are not
2456 coloured in linked structure views
2459 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
2460 file-based command exchange
2463 <!-- JAL-2375 -->Structure chooser automatically shows
2464 Cached Structures rather than querying the PDBe if
2465 structures are already available for sequences
2468 <!-- JAL-2520 -->Structures imported via URL are cached in
2469 the Jalview project rather than downloaded again when the
2470 project is reopened.
2473 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
2474 to transfer Chimera's structure attributes as Jalview
2475 features, and vice-versa (<strong>Experimental
2479 <em>Web Services</em>
2482 <!-- JAL-2549 -->Updated JABAWS client to v2.2
2485 <!-- JAL-2335 -->Filter non-standard amino acids and
2486 nucleotides when submitting to AACon and other MSA
2490 <!-- JAL-2316, -->URLs for viewing database
2491 cross-references provided by identifiers.org and the
2492 EMBL-EBI's MIRIAM DB
2499 <!-- JAL-2344 -->FileFormatI interface for describing and
2500 identifying file formats (instead of String constants)
2503 <!-- JAL-2228 -->FeatureCounter script refactored for
2504 efficiency when counting all displayed features (not
2505 backwards compatible with 2.10.1)
2508 <em>Example files</em>
2511 <!-- JAL-2631 -->Graduated feature colour style example
2512 included in the example feature file
2515 <em>Documentation</em>
2518 <!-- JAL-2339 -->Release notes reformatted for readability
2519 with the built-in Java help viewer
2522 <!-- JAL-1644 -->Find documentation updated with 'search
2523 sequence description' option
2529 <!-- JAL-2485, -->External service integration tests for
2530 Uniprot REST Free Text Search Client
2533 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
2536 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
2541 <td><div align="left">
2542 <em>Calculations</em>
2545 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
2546 matrix - C->R should be '-3'<br />Old matrix restored
2547 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
2549 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
2550 Jalview's treatment of gaps in PCA and substitution matrix
2551 based Tree calculations.<br /> <br />In earlier versions
2552 of Jalview, gaps matching gaps were penalised, and gaps
2553 matching non-gaps penalised even more. In the PCA
2554 calculation, gaps were actually treated as non-gaps - so
2555 different costs were applied, which meant Jalview's PCAs
2556 were different to those produced by SeqSpace.<br />Jalview
2557 now treats gaps in the same way as SeqSpace (ie it scores
2558 them as 0). <br /> <br />Enter the following in the
2559 Groovy console to restore pre-2.10.2 behaviour:<br />
2560 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
2561 // for 2.10.1 mode <br />
2562 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
2563 // to restore 2.10.2 mode <br /> <br /> <em>Note:
2564 these settings will affect all subsequent tree and PCA
2565 calculations (not recommended)</em></li>
2567 <!-- JAL-2424 -->Fixed off-by-one bug that affected
2568 scaling of branch lengths for trees computed using
2569 Sequence Feature Similarity.
2572 <!-- JAL-2377 -->PCA calculation could hang when
2573 generating output report when working with highly
2574 redundant alignments
2577 <!-- JAL-2544 --> Sort by features includes features to
2578 right of selected region when gaps present on right-hand
2582 <em>User Interface</em>
2585 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2586 doesn't reselect a specific sequence's associated
2587 annotation after it was used for colouring a view
2590 <!-- JAL-2419 -->Current selection lost if popup menu
2591 opened on a region of alignment without groups
2594 <!-- JAL-2374 -->Popup menu not always shown for regions
2595 of an alignment with overlapping groups
2598 <!-- JAL-2310 -->Finder double counts if both a sequence's
2599 name and description match
2602 <!-- JAL-2370 -->Hiding column selection containing two
2603 hidden regions results in incorrect hidden regions
2606 <!-- JAL-2386 -->'Apply to all groups' setting when
2607 changing colour does not apply Conservation slider value
2611 <!-- JAL-2373 -->Percentage identity and conservation menu
2612 items do not show a tick or allow shading to be disabled
2615 <!-- JAL-2385 -->Conservation shading or PID threshold
2616 lost when base colourscheme changed if slider not visible
2619 <!-- JAL-2547 -->Sequence features shown in tooltip for
2620 gaps before start of features
2623 <!-- JAL-2623 -->Graduated feature colour threshold not
2624 restored to UI when feature colour is edited
2627 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2628 a time when scrolling vertically in wrapped mode.
2631 <!-- JAL-2630 -->Structure and alignment overview update
2632 as graduate feature colour settings are modified via the
2636 <!-- JAL-2034 -->Overview window doesn't always update
2637 when a group defined on the alignment is resized
2640 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2641 wrapped view result in positional status updates
2645 <!-- JAL-2563 -->Status bar doesn't show position for
2646 ambiguous amino acid and nucleotide symbols
2649 <!-- JAL-2602 -->Copy consensus sequence failed if
2650 alignment included gapped columns
2653 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2654 widgets don't permanently disappear
2657 <!-- JAL-2503 -->Cannot select or filter quantitative
2658 annotation that are shown only as column labels (e.g.
2659 T-Coffee column reliability scores)
2662 <!-- JAL-2594 -->Exception thrown if trying to create a
2663 sequence feature on gaps only
2666 <!-- JAL-2504 -->Features created with 'New feature'
2667 button from a Find inherit previously defined feature type
2668 rather than the Find query string
2671 <!-- JAL-2423 -->incorrect title in output window when
2672 exporting tree calculated in Jalview
2675 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2676 and then revealing them reorders sequences on the
2680 <!-- JAL-964 -->Group panel in sequence feature settings
2681 doesn't update to reflect available set of groups after
2682 interactively adding or modifying features
2685 <!-- JAL-2225 -->Sequence Database chooser unusable on
2689 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2690 only excluded gaps in current sequence and ignored
2697 <!-- JAL-2421 -->Overview window visible region moves
2698 erratically when hidden rows or columns are present
2701 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2702 Structure Viewer's colour menu don't correspond to
2706 <!-- JAL-2405 -->Protein specific colours only offered in
2707 colour and group colour menu for protein alignments
2710 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2711 reflect currently selected view or group's shading
2715 <!-- JAL-2624 -->Feature colour thresholds not respected
2716 when rendered on overview and structures when opacity at
2720 <!-- JAL-2589 -->User defined gap colour not shown in
2721 overview when features overlaid on alignment
2724 <!-- JAL-2567 -->Feature settings for different views not
2725 recovered correctly from Jalview project file
2728 <!-- JAL-2256 -->Feature colours in overview when first
2729 opened (automatically via preferences) are different to
2730 the main alignment panel
2733 <em>Data import/export</em>
2736 <!-- JAL-2576 -->Very large alignments take a long time to
2740 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2741 added after a sequence was imported are not written to
2745 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2746 when importing RNA secondary structure via Stockholm
2749 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2750 not shown in correct direction for simple pseudoknots
2753 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2754 with lightGray or darkGray via features file (but can
2758 <!-- JAL-2383 -->Above PID colour threshold not recovered
2759 when alignment view imported from project
2762 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2763 structure and sequences extracted from structure files
2764 imported via URL and viewed in Jmol
2767 <!-- JAL-2520 -->Structures loaded via URL are saved in
2768 Jalview Projects rather than fetched via URL again when
2769 the project is loaded and the structure viewed
2772 <em>Web Services</em>
2775 <!-- JAL-2519 -->EnsemblGenomes example failing after
2776 release of Ensembl v.88
2779 <!-- JAL-2366 -->Proxy server address and port always
2780 appear enabled in Preferences->Connections
2783 <!-- JAL-2461 -->DAS registry not found exceptions
2784 removed from console output
2787 <!-- JAL-2582 -->Cannot retrieve protein products from
2788 Ensembl by Peptide ID
2791 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2792 created from SIFTs, and spurious 'Couldn't open structure
2793 in Chimera' errors raised after April 2017 update (problem
2794 due to 'null' string rather than empty string used for
2795 residues with no corresponding PDB mapping).
2798 <em>Application UI</em>
2801 <!-- JAL-2361 -->User Defined Colours not added to Colour
2805 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2806 case' residues (button in colourscheme editor debugged and
2807 new documentation and tooltips added)
2810 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2811 doesn't restore group-specific text colour thresholds
2814 <!-- JAL-2243 -->Feature settings panel does not update as
2815 new features are added to alignment
2818 <!-- JAL-2532 -->Cancel in feature settings reverts
2819 changes to feature colours via the Amend features dialog
2822 <!-- JAL-2506 -->Null pointer exception when attempting to
2823 edit graduated feature colour via amend features dialog
2827 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2828 selection menu changes colours of alignment views
2831 <!-- JAL-2426 -->Spurious exceptions in console raised
2832 from alignment calculation workers after alignment has
2836 <!-- JAL-1608 -->Typo in selection popup menu - Create
2837 groups now 'Create Group'
2840 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2841 Create/Undefine group doesn't always work
2844 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2845 shown again after pressing 'Cancel'
2848 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2849 adjusts start position in wrap mode
2852 <!-- JAL-2563 -->Status bar doesn't show positions for
2853 ambiguous amino acids
2856 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2857 CDS/Protein view after CDS sequences added for aligned
2861 <!-- JAL-2592 -->User defined colourschemes called 'User
2862 Defined' don't appear in Colours menu
2868 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2869 score models doesn't always result in an updated PCA plot
2872 <!-- JAL-2442 -->Features not rendered as transparent on
2873 overview or linked structure view
2876 <!-- JAL-2372 -->Colour group by conservation doesn't
2880 <!-- JAL-2517 -->Hitting Cancel after applying
2881 user-defined colourscheme doesn't restore original
2888 <!-- JAL-2314 -->Unit test failure:
2889 jalview.ws.jabaws.RNAStructExportImport setup fails
2892 <!-- JAL-2307 -->Unit test failure:
2893 jalview.ws.sifts.SiftsClientTest due to compatibility
2894 problems with deep array comparison equality asserts in
2895 successive versions of TestNG
2898 <!-- JAL-2479 -->Relocated StructureChooserTest and
2899 ParameterUtilsTest Unit tests to Network suite
2902 <em>New Known Issues</em>
2905 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2906 phase after a sequence motif find operation
2909 <!-- JAL-2550 -->Importing annotation file with rows
2910 containing just upper and lower case letters are
2911 interpreted as WUSS RNA secondary structure symbols
2914 <!-- JAL-2590 -->Cannot load and display Newick trees
2915 reliably from eggnog Ortholog database
2918 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2919 containing features of type Highlight' when 'B' is pressed
2920 to mark columns containing highlighted regions.
2923 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2924 doesn't always add secondary structure annotation.
2929 <td width="60" nowrap>
2930 <div align="center">
2931 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2934 <td><div align="left">
2938 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2939 for all consensus calculations
2942 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2945 <li>Updated Jalview's Certum code signing certificate
2948 <em>Application</em>
2951 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2952 set of database cross-references, sorted alphabetically
2955 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2956 from database cross references. Users with custom links
2957 will receive a <a href="webServices/urllinks.html#warning">warning
2958 dialog</a> asking them to update their preferences.
2961 <!-- JAL-2287-->Cancel button and escape listener on
2962 dialog warning user about disconnecting Jalview from a
2966 <!-- JAL-2320-->Jalview's Chimera control window closes if
2967 the Chimera it is connected to is shut down
2970 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2971 columns menu item to mark columns containing highlighted
2972 regions (e.g. from structure selections or results of a
2976 <!-- JAL-2284-->Command line option for batch-generation
2977 of HTML pages rendering alignment data with the BioJS
2987 <!-- JAL-2286 -->Columns with more than one modal residue
2988 are not coloured or thresholded according to percent
2989 identity (first observed in Jalview 2.8.2)
2992 <!-- JAL-2301 -->Threonine incorrectly reported as not
2996 <!-- JAL-2318 -->Updates to documentation pages (above PID
2997 threshold, amino acid properties)
3000 <!-- JAL-2292 -->Lower case residues in sequences are not
3001 reported as mapped to residues in a structure file in the
3005 <!--JAL-2324 -->Identical features with non-numeric scores
3006 could be added multiple times to a sequence
3009 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
3010 bond features shown as two highlighted residues rather
3011 than a range in linked structure views, and treated
3012 correctly when selecting and computing trees from features
3015 <!-- JAL-2281-->Custom URL links for database
3016 cross-references are matched to database name regardless
3021 <em>Application</em>
3024 <!-- JAL-2282-->Custom URL links for specific database
3025 names without regular expressions also offer links from
3029 <!-- JAL-2315-->Removing a single configured link in the
3030 URL links pane in Connections preferences doesn't actually
3031 update Jalview configuration
3034 <!-- JAL-2272-->CTRL-Click on a selected region to open
3035 the alignment area popup menu doesn't work on El-Capitan
3038 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
3039 files with similarly named sequences if dropped onto the
3043 <!-- JAL-2312 -->Additional mappings are shown for PDB
3044 entries where more chains exist in the PDB accession than
3045 are reported in the SIFTS file
3048 <!-- JAL-2317-->Certain structures do not get mapped to
3049 the structure view when displayed with Chimera
3052 <!-- JAL-2317-->No chains shown in the Chimera view
3053 panel's View->Show Chains submenu
3056 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
3057 work for wrapped alignment views
3060 <!--JAL-2197 -->Rename UI components for running JPred
3061 predictions from 'JNet' to 'JPred'
3064 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
3065 corrupted when annotation panel vertical scroll is not at
3066 first annotation row
3069 <!--JAL-2332 -->Attempting to view structure for Hen
3070 lysozyme results in a PDB Client error dialog box
3073 <!-- JAL-2319 -->Structure View's mapping report switched
3074 ranges for PDB and sequence for SIFTS
3077 SIFTS 'Not_Observed' residues mapped to non-existant
3081 <!-- <em>New Known Issues</em>
3088 <td width="60" nowrap>
3089 <div align="center">
3090 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
3091 <em>25/10/2016</em></strong>
3094 <td><em>Application</em>
3096 <li>3D Structure chooser opens with 'Cached structures'
3097 view if structures already loaded</li>
3098 <li>Progress bar reports models as they are loaded to
3099 structure views</li>
3105 <li>Colour by conservation always enabled and no tick
3106 shown in menu when BLOSUM or PID shading applied</li>
3107 <li>FER1_ARATH and FER2_ARATH labels were switched in
3108 example sequences/projects/trees</li>
3110 <em>Application</em>
3112 <li>Jalview projects with views of local PDB structure
3113 files saved on Windows cannot be opened on OSX</li>
3114 <li>Multiple structure views can be opened and superposed
3115 without timeout for structures with multiple models or
3116 multiple sequences in alignment</li>
3117 <li>Cannot import or associated local PDB files without a
3118 PDB ID HEADER line</li>
3119 <li>RMSD is not output in Jmol console when superposition
3121 <li>Drag and drop of URL from Browser fails for Linux and
3122 OSX versions earlier than El Capitan</li>
3123 <li>ENA client ignores invalid content from ENA server</li>
3124 <li>Exceptions are not raised in console when ENA client
3125 attempts to fetch non-existent IDs via Fetch DB Refs UI
3127 <li>Exceptions are not raised in console when a new view
3128 is created on the alignment</li>
3129 <li>OSX right-click fixed for group selections: CMD-click
3130 to insert/remove gaps in groups and CTRL-click to open group
3133 <em>Build and deployment</em>
3135 <li>URL link checker now copes with multi-line anchor
3138 <em>New Known Issues</em>
3140 <li>Drag and drop from URL links in browsers do not work
3147 <td width="60" nowrap>
3148 <div align="center">
3149 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
3152 <td><em>General</em>
3155 <!-- JAL-2124 -->Updated Spanish translations.
3158 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
3159 for importing structure data to Jalview. Enables mmCIF and
3163 <!-- JAL-192 --->Alignment ruler shows positions relative to
3167 <!-- JAL-2202 -->Position/residue shown in status bar when
3168 mousing over sequence associated annotation
3171 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
3175 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
3176 '()', canonical '[]' and invalid '{}' base pair populations
3180 <!-- JAL-2092 -->Feature settings popup menu options for
3181 showing or hiding columns containing a feature
3184 <!-- JAL-1557 -->Edit selected group by double clicking on
3185 group and sequence associated annotation labels
3188 <!-- JAL-2236 -->Sequence name added to annotation label in
3189 select/hide columns by annotation and colour by annotation
3193 </ul> <em>Application</em>
3196 <!-- JAL-2050-->Automatically hide introns when opening a
3197 gene/transcript view
3200 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
3204 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
3205 structure mappings with the EMBL-EBI PDBe SIFTS database
3208 <!-- JAL-2079 -->Updated download sites used for Rfam and
3209 Pfam sources to xfam.org
3212 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
3215 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
3216 over sequences in Jalview
3219 <!-- JAL-2027-->Support for reverse-complement coding
3220 regions in ENA and EMBL
3223 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
3224 for record retrieval via ENA rest API
3227 <!-- JAL-2027 -->Support for ENA CDS records with reverse
3231 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
3232 groovy script execution
3235 <!-- JAL-1812 -->New 'execute Groovy script' option in an
3236 alignment window's Calculate menu
3239 <!-- JAL-1812 -->Allow groovy scripts that call
3240 Jalview.getAlignFrames() to run in headless mode
3243 <!-- JAL-2068 -->Support for creating new alignment
3244 calculation workers from groovy scripts
3247 <!-- JAL-1369 --->Store/restore reference sequence in
3251 <!-- JAL-1803 -->Chain codes for a sequence's PDB
3252 associations are now saved/restored from project
3255 <!-- JAL-1993 -->Database selection dialog always shown
3256 before sequence fetcher is opened
3259 <!-- JAL-2183 -->Double click on an entry in Jalview's
3260 database chooser opens a sequence fetcher
3263 <!-- JAL-1563 -->Free-text search client for UniProt using
3264 the UniProt REST API
3267 <!-- JAL-2168 -->-nonews command line parameter to prevent
3268 the news reader opening
3271 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
3272 querying stored in preferences
3275 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
3279 <!-- JAL-1977-->Tooltips shown on database chooser
3282 <!-- JAL-391 -->Reverse complement function in calculate
3283 menu for nucleotide sequences
3286 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
3287 and feature counts preserves alignment ordering (and
3288 debugged for complex feature sets).
3291 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
3292 viewing structures with Jalview 2.10
3295 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
3296 genome, transcript CCDS and gene ids via the Ensembl and
3297 Ensembl Genomes REST API
3300 <!-- JAL-2049 -->Protein sequence variant annotation
3301 computed for 'sequence_variant' annotation on CDS regions
3305 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
3309 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
3310 Ref Fetcher fails to match, or otherwise updates sequence
3311 data from external database records.
3314 <!-- JAL-2154 -->Revised Jalview Project format for
3315 efficient recovery of sequence coding and alignment
3316 annotation relationships.
3318 </ul> <!-- <em>Applet</em>
3329 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
3333 <!-- JAL-2018-->Export features in Jalview format (again)
3334 includes graduated colourschemes
3337 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
3338 working with big alignments and lots of hidden columns
3341 <!-- JAL-2053-->Hidden column markers not always rendered
3342 at right of alignment window
3345 <!-- JAL-2067 -->Tidied up links in help file table of
3349 <!-- JAL-2072 -->Feature based tree calculation not shown
3353 <!-- JAL-2075 -->Hidden columns ignored during feature
3354 based tree calculation
3357 <!-- JAL-2065 -->Alignment view stops updating when show
3358 unconserved enabled for group on alignment
3361 <!-- JAL-2086 -->Cannot insert gaps into sequence when
3365 <!-- JAL-2146 -->Alignment column in status incorrectly
3366 shown as "Sequence position" when mousing over
3370 <!-- JAL-2099 -->Incorrect column numbers in ruler when
3371 hidden columns present
3374 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
3375 user created annotation added to alignment
3378 <!-- JAL-1841 -->RNA Structure consensus only computed for
3379 '()' base pair annotation
3382 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
3383 in zero scores for all base pairs in RNA Structure
3387 <!-- JAL-2174-->Extend selection with columns containing
3391 <!-- JAL-2275 -->Pfam format writer puts extra space at
3392 beginning of sequence
3395 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
3399 <!-- JAL-2238 -->Cannot create groups on an alignment from
3400 from a tree when t-coffee scores are shown
3403 <!-- JAL-1836,1967 -->Cannot import and view PDB
3404 structures with chains containing negative resnums (4q4h)
3407 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
3411 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
3412 to Clustal, PIR and PileUp output
3415 <!-- JAL-2008 -->Reordering sequence features that are
3416 not visible causes alignment window to repaint
3419 <!-- JAL-2006 -->Threshold sliders don't work in
3420 graduated colour and colour by annotation row for e-value
3421 scores associated with features and annotation rows
3424 <!-- JAL-1797 -->amino acid physicochemical conservation
3425 calculation should be case independent
3428 <!-- JAL-2173 -->Remove annotation also updates hidden
3432 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
3433 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
3434 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
3437 <!-- JAL-2065 -->Null pointer exceptions and redraw
3438 problems when reference sequence defined and 'show
3439 non-conserved' enabled
3442 <!-- JAL-1306 -->Quality and Conservation are now shown on
3443 load even when Consensus calculation is disabled
3446 <!-- JAL-1932 -->Remove right on penultimate column of
3447 alignment does nothing
3450 <em>Application</em>
3453 <!-- JAL-1552-->URLs and links can't be imported by
3454 drag'n'drop on OSX when launched via webstart (note - not
3455 yet fixed for El Capitan)
3458 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
3459 output when running on non-gb/us i18n platforms
3462 <!-- JAL-1944 -->Error thrown when exporting a view with
3463 hidden sequences as flat-file alignment
3466 <!-- JAL-2030-->InstallAnywhere distribution fails when
3470 <!-- JAL-2080-->Jalview very slow to launch via webstart
3471 (also hotfix for 2.9.0b2)
3474 <!-- JAL-2085 -->Cannot save project when view has a
3475 reference sequence defined
3478 <!-- JAL-1011 -->Columns are suddenly selected in other
3479 alignments and views when revealing hidden columns
3482 <!-- JAL-1989 -->Hide columns not mirrored in complement
3483 view in a cDNA/Protein splitframe
3486 <!-- JAL-1369 -->Cannot save/restore representative
3487 sequence from project when only one sequence is
3491 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
3492 in Structure Chooser
3495 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
3496 structure consensus didn't refresh annotation panel
3499 <!-- JAL-1962 -->View mapping in structure view shows
3500 mappings between sequence and all chains in a PDB file
3503 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
3504 dialogs format columns correctly, don't display array
3505 data, sort columns according to type
3508 <!-- JAL-1975 -->Export complete shown after destination
3509 file chooser is cancelled during an image export
3512 <!-- JAL-2025 -->Error when querying PDB Service with
3513 sequence name containing special characters
3516 <!-- JAL-2024 -->Manual PDB structure querying should be
3520 <!-- JAL-2104 -->Large tooltips with broken HTML
3521 formatting don't wrap
3524 <!-- JAL-1128 -->Figures exported from wrapped view are
3525 truncated so L looks like I in consensus annotation
3528 <!-- JAL-2003 -->Export features should only export the
3529 currently displayed features for the current selection or
3533 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
3534 after fetching cross-references, and restoring from
3538 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
3539 followed in the structure viewer
3542 <!-- JAL-2163 -->Titles for individual alignments in
3543 splitframe not restored from project
3546 <!-- JAL-2145 -->missing autocalculated annotation at
3547 trailing end of protein alignment in transcript/product
3548 splitview when pad-gaps not enabled by default
3551 <!-- JAL-1797 -->amino acid physicochemical conservation
3555 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
3556 article has been read (reopened issue due to
3557 internationalisation problems)
3560 <!-- JAL-1960 -->Only offer PDB structures in structure
3561 viewer based on sequence name, PDB and UniProt
3566 <!-- JAL-1976 -->No progress bar shown during export of
3570 <!-- JAL-2213 -->Structures not always superimposed after
3571 multiple structures are shown for one or more sequences.
3574 <!-- JAL-1370 -->Reference sequence characters should not
3575 be replaced with '.' when 'Show unconserved' format option
3579 <!-- JAL-1823 -->Cannot specify chain code when entering
3580 specific PDB id for sequence
3583 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3584 'Export hidden sequences' is enabled, but 'export hidden
3585 columns' is disabled.
3588 <!--JAL-2026-->Best Quality option in structure chooser
3589 selects lowest rather than highest resolution structures
3593 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3594 to sequence mapping in 'View Mappings' report
3597 <!-- JAL-2284 -->Unable to read old Jalview projects that
3598 contain non-XML data added after Jalvew wrote project.
3601 <!-- JAL-2118 -->Newly created annotation row reorders
3602 after clicking on it to create new annotation for a
3606 <!-- JAL-1980 -->Null Pointer Exception raised when
3607 pressing Add on an orphaned cut'n'paste window.
3609 <!-- may exclude, this is an external service stability issue JAL-1941
3610 -- > RNA 3D structure not added via DSSR service</li> -->
3615 <!-- JAL-2151 -->Incorrect columns are selected when
3616 hidden columns present before start of sequence
3619 <!-- JAL-1986 -->Missing dependencies on applet pages
3623 <!-- JAL-1947 -->Overview pixel size changes when
3624 sequences are hidden in applet
3627 <!-- JAL-1996 -->Updated instructions for applet
3628 deployment on examples pages.
3635 <td width="60" nowrap>
3636 <div align="center">
3637 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3638 <em>16/10/2015</em></strong>
3641 <td><em>General</em>
3643 <li>Time stamps for signed Jalview application and applet
3648 <em>Application</em>
3650 <li>Duplicate group consensus and conservation rows
3651 shown when tree is partitioned</li>
3652 <li>Erratic behaviour when tree partitions made with
3653 multiple cDNA/Protein split views</li>
3659 <td width="60" nowrap>
3660 <div align="center">
3661 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3662 <em>8/10/2015</em></strong>
3665 <td><em>General</em>
3667 <li>Updated Spanish translations of localized text for
3669 </ul> <em>Application</em>
3671 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3672 <li>Signed OSX InstallAnywhere installer<br></li>
3673 <li>Support for per-sequence based annotations in BioJSON</li>
3674 </ul> <em>Applet</em>
3676 <li>Split frame example added to applet examples page</li>
3677 </ul> <em>Build and Deployment</em>
3680 <!-- JAL-1888 -->New ant target for running Jalview's test
3688 <li>Mapping of cDNA to protein in split frames
3689 incorrect when sequence start > 1</li>
3690 <li>Broken images in filter column by annotation dialog
3692 <li>Feature colours not parsed from features file</li>
3693 <li>Exceptions and incomplete link URLs recovered when
3694 loading a features file containing HTML tags in feature
3698 <em>Application</em>
3700 <li>Annotations corrupted after BioJS export and
3702 <li>Incorrect sequence limits after Fetch DB References
3703 with 'trim retrieved sequences'</li>
3704 <li>Incorrect warning about deleting all data when
3705 deleting selected columns</li>
3706 <li>Patch to build system for shipping properly signed
3707 JNLP templates for webstart launch</li>
3708 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3709 unreleased structures for download or viewing</li>
3710 <li>Tab/space/return keystroke operation of EMBL-PDBe
3711 fetcher/viewer dialogs works correctly</li>
3712 <li>Disabled 'minimise' button on Jalview windows
3713 running on OSX to workaround redraw hang bug</li>
3714 <li>Split cDNA/Protein view position and geometry not
3715 recovered from jalview project</li>
3716 <li>Initial enabled/disabled state of annotation menu
3717 sorter 'show autocalculated first/last' corresponds to
3719 <li>Restoring of Clustal, RNA Helices and T-Coffee
3720 color schemes from BioJSON</li>
3724 <li>Reorder sequences mirrored in cDNA/Protein split
3726 <li>Applet with Jmol examples not loading correctly</li>
3732 <td><div align="center">
3733 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3735 <td><em>General</em>
3737 <li>Linked visualisation and analysis of DNA and Protein
3740 <li>Translated cDNA alignments shown as split protein
3741 and DNA alignment views</li>
3742 <li>Codon consensus annotation for linked protein and
3743 cDNA alignment views</li>
3744 <li>Link cDNA or Protein product sequences by loading
3745 them onto Protein or cDNA alignments</li>
3746 <li>Reconstruct linked cDNA alignment from aligned
3747 protein sequences</li>
3750 <li>Jmol integration updated to Jmol v14.2.14</li>
3751 <li>Import and export of Jalview alignment views as <a
3752 href="features/bioJsonFormat.html">BioJSON</a></li>
3753 <li>New alignment annotation file statements for
3754 reference sequences and marking hidden columns</li>
3755 <li>Reference sequence based alignment shading to
3756 highlight variation</li>
3757 <li>Select or hide columns according to alignment
3759 <li>Find option for locating sequences by description</li>
3760 <li>Conserved physicochemical properties shown in amino
3761 acid conservation row</li>
3762 <li>Alignments can be sorted by number of RNA helices</li>
3763 </ul> <em>Application</em>
3765 <li>New cDNA/Protein analysis capabilities
3767 <li>Get Cross-References should open a Split Frame
3768 view with cDNA/Protein</li>
3769 <li>Detect when nucleotide sequences and protein
3770 sequences are placed in the same alignment</li>
3771 <li>Split cDNA/Protein views are saved in Jalview
3776 <li>Use REST API to talk to Chimera</li>
3777 <li>Selected regions in Chimera are highlighted in linked
3778 Jalview windows</li>
3780 <li>VARNA RNA viewer updated to v3.93</li>
3781 <li>VARNA views are saved in Jalview Projects</li>
3782 <li>Pseudoknots displayed as Jalview RNA annotation can
3783 be shown in VARNA</li>
3785 <li>Make groups for selection uses marked columns as well
3786 as the active selected region</li>
3788 <li>Calculate UPGMA and NJ trees using sequence feature
3790 <li>New Export options
3792 <li>New Export Settings dialog to control hidden
3793 region export in flat file generation</li>
3795 <li>Export alignment views for display with the <a
3796 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3798 <li>Export scrollable SVG in HTML page</li>
3799 <li>Optional embedding of BioJSON data when exporting
3800 alignment figures to HTML</li>
3802 <li>3D structure retrieval and display
3804 <li>Free text and structured queries with the PDBe
3806 <li>PDBe Search API based discovery and selection of
3807 PDB structures for a sequence set</li>
3811 <li>JPred4 employed for protein secondary structure
3813 <li>Hide Insertions menu option to hide unaligned columns
3814 for one or a group of sequences</li>
3815 <li>Automatically hide insertions in alignments imported
3816 from the JPred4 web server</li>
3817 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3818 system on OSX<br />LGPL libraries courtesy of <a
3819 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3821 <li>changed 'View nucleotide structure' submenu to 'View
3822 VARNA 2D Structure'</li>
3823 <li>change "View protein structure" menu option to "3D
3826 </ul> <em>Applet</em>
3828 <li>New layout for applet example pages</li>
3829 <li>New parameters to enable SplitFrame view
3830 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3831 <li>New example demonstrating linked viewing of cDNA and
3832 Protein alignments</li>
3833 </ul> <em>Development and deployment</em>
3835 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3836 <li>Include installation type and git revision in build
3837 properties and console log output</li>
3838 <li>Jalview Github organisation, and new github site for
3839 storing BioJsMSA Templates</li>
3840 <li>Jalview's unit tests now managed with TestNG</li>
3843 <!-- <em>General</em>
3845 </ul> --> <!-- issues resolved --> <em>Application</em>
3847 <li>Escape should close any open find dialogs</li>
3848 <li>Typo in select-by-features status report</li>
3849 <li>Consensus RNA secondary secondary structure
3850 predictions are not highlighted in amber</li>
3851 <li>Missing gap character in v2.7 example file means
3852 alignment appears unaligned when pad-gaps is not enabled</li>
3853 <li>First switch to RNA Helices colouring doesn't colour
3854 associated structure views</li>
3855 <li>ID width preference option is greyed out when auto
3856 width checkbox not enabled</li>
3857 <li>Stopped a warning dialog from being shown when
3858 creating user defined colours</li>
3859 <li>'View Mapping' in structure viewer shows sequence
3860 mappings for just that viewer's sequences</li>
3861 <li>Workaround for superposing PDB files containing
3862 multiple models in Chimera</li>
3863 <li>Report sequence position in status bar when hovering
3864 over Jmol structure</li>
3865 <li>Cannot output gaps as '.' symbols with Selection ->
3866 output to text box</li>
3867 <li>Flat file exports of alignments with hidden columns
3868 have incorrect sequence start/end</li>
3869 <li>'Aligning' a second chain to a Chimera structure from
3871 <li>Colour schemes applied to structure viewers don't
3872 work for nucleotide</li>
3873 <li>Loading/cut'n'pasting an empty or invalid file leads
3874 to a grey/invisible alignment window</li>
3875 <li>Exported Jpred annotation from a sequence region
3876 imports to different position</li>
3877 <li>Space at beginning of sequence feature tooltips shown
3878 on some platforms</li>
3879 <li>Chimera viewer 'View | Show Chain' menu is not
3881 <li>'New View' fails with a Null Pointer Exception in
3882 console if Chimera has been opened</li>
3883 <li>Mouseover to Chimera not working</li>
3884 <li>Miscellaneous ENA XML feature qualifiers not
3886 <li>NPE in annotation renderer after 'Extract Scores'</li>
3887 <li>If two structures in one Chimera window, mouseover of
3888 either sequence shows on first structure</li>
3889 <li>'Show annotations' options should not make
3890 non-positional annotations visible</li>
3891 <li>Subsequence secondary structure annotation not shown
3892 in right place after 'view flanking regions'</li>
3893 <li>File Save As type unset when current file format is
3895 <li>Save as '.jar' option removed for saving Jalview
3897 <li>Colour by Sequence colouring in Chimera more
3899 <li>Cannot 'add reference annotation' for a sequence in
3900 several views on same alignment</li>
3901 <li>Cannot show linked products for EMBL / ENA records</li>
3902 <li>Jalview's tooltip wraps long texts containing no
3904 </ul> <em>Applet</em>
3906 <li>Jmol to JalviewLite mouseover/link not working</li>
3907 <li>JalviewLite can't import sequences with ID
3908 descriptions containing angle brackets</li>
3909 </ul> <em>General</em>
3911 <li>Cannot export and reimport RNA secondary structure
3912 via jalview annotation file</li>
3913 <li>Random helix colour palette for colour by annotation
3914 with RNA secondary structure</li>
3915 <li>Mouseover to cDNA from STOP residue in protein
3916 translation doesn't work.</li>
3917 <li>hints when using the select by annotation dialog box</li>
3918 <li>Jmol alignment incorrect if PDB file has alternate CA
3920 <li>FontChooser message dialog appears to hang after
3921 choosing 1pt font</li>
3922 <li>Peptide secondary structure incorrectly imported from
3923 annotation file when annotation display text includes 'e' or
3925 <li>Cannot set colour of new feature type whilst creating
3927 <li>cDNA translation alignment should not be sequence
3928 order dependent</li>
3929 <li>'Show unconserved' doesn't work for lower case
3931 <li>Nucleotide ambiguity codes involving R not recognised</li>
3932 </ul> <em>Deployment and Documentation</em>
3934 <li>Applet example pages appear different to the rest of
3935 www.jalview.org</li>
3936 </ul> <em>Application Known issues</em>
3938 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3939 <li>Misleading message appears after trying to delete
3941 <li>Jalview icon not shown in dock after InstallAnywhere
3942 version launches</li>
3943 <li>Fetching EMBL reference for an RNA sequence results
3944 fails with a sequence mismatch</li>
3945 <li>Corrupted or unreadable alignment display when
3946 scrolling alignment to right</li>
3947 <li>ArrayIndexOutOfBoundsException thrown when remove
3948 empty columns called on alignment with ragged gapped ends</li>
3949 <li>auto calculated alignment annotation rows do not get
3950 placed above or below non-autocalculated rows</li>
3951 <li>Jalview dekstop becomes sluggish at full screen in
3952 ultra-high resolution</li>
3953 <li>Cannot disable consensus calculation independently of
3954 quality and conservation</li>
3955 <li>Mouseover highlighting between cDNA and protein can
3956 become sluggish with more than one splitframe shown</li>
3957 </ul> <em>Applet Known Issues</em>
3959 <li>Core PDB parsing code requires Jmol</li>
3960 <li>Sequence canvas panel goes white when alignment
3961 window is being resized</li>
3967 <td><div align="center">
3968 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3970 <td><em>General</em>
3972 <li>Updated Java code signing certificate donated by
3974 <li>Features and annotation preserved when performing
3975 pairwise alignment</li>
3976 <li>RNA pseudoknot annotation can be
3977 imported/exported/displayed</li>
3978 <li>'colour by annotation' can colour by RNA and
3979 protein secondary structure</li>
3980 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3981 post-hoc with 2.9 release</em>)
3984 </ul> <em>Application</em>
3986 <li>Extract and display secondary structure for sequences
3987 with 3D structures</li>
3988 <li>Support for parsing RNAML</li>
3989 <li>Annotations menu for layout
3991 <li>sort sequence annotation rows by alignment</li>
3992 <li>place sequence annotation above/below alignment
3995 <li>Output in Stockholm format</li>
3996 <li>Internationalisation: improved Spanish (es)
3998 <li>Structure viewer preferences tab</li>
3999 <li>Disorder and Secondary Structure annotation tracks
4000 shared between alignments</li>
4001 <li>UCSF Chimera launch and linked highlighting from
4003 <li>Show/hide all sequence associated annotation rows for
4004 all or current selection</li>
4005 <li>disorder and secondary structure predictions
4006 available as dataset annotation</li>
4007 <li>Per-sequence rna helices colouring</li>
4010 <li>Sequence database accessions imported when fetching
4011 alignments from Rfam</li>
4012 <li>update VARNA version to 3.91</li>
4014 <li>New groovy scripts for exporting aligned positions,
4015 conservation values, and calculating sum of pairs scores.</li>
4016 <li>Command line argument to set default JABAWS server</li>
4017 <li>include installation type in build properties and
4018 console log output</li>
4019 <li>Updated Jalview project format to preserve dataset
4023 <!-- issues resolved --> <em>Application</em>
4025 <li>Distinguish alignment and sequence associated RNA
4026 structure in structure->view->VARNA</li>
4027 <li>Raise dialog box if user deletes all sequences in an
4029 <li>Pressing F1 results in documentation opening twice</li>
4030 <li>Sequence feature tooltip is wrapped</li>
4031 <li>Double click on sequence associated annotation
4032 selects only first column</li>
4033 <li>Redundancy removal doesn't result in unlinked
4034 leaves shown in tree</li>
4035 <li>Undos after several redundancy removals don't undo
4037 <li>Hide sequence doesn't hide associated annotation</li>
4038 <li>User defined colours dialog box too big to fit on
4039 screen and buttons not visible</li>
4040 <li>author list isn't updated if already written to
4041 Jalview properties</li>
4042 <li>Popup menu won't open after retrieving sequence
4044 <li>File open window for associate PDB doesn't open</li>
4045 <li>Left-then-right click on a sequence id opens a
4046 browser search window</li>
4047 <li>Cannot open sequence feature shading/sort popup menu
4048 in feature settings dialog</li>
4049 <li>better tooltip placement for some areas of Jalview
4051 <li>Allow addition of JABAWS Server which doesn't
4052 pass validation</li>
4053 <li>Web services parameters dialog box is too large to
4055 <li>Muscle nucleotide alignment preset obscured by
4057 <li>JABAWS preset submenus don't contain newly
4058 defined user preset</li>
4059 <li>MSA web services warns user if they were launched
4060 with invalid input</li>
4061 <li>Jalview cannot contact DAS Registy when running on
4064 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
4065 'Superpose with' submenu not shown when new view
4069 </ul> <!-- <em>Applet</em>
4071 </ul> <em>General</em>
4073 </ul>--> <em>Deployment and Documentation</em>
4075 <li>2G and 1G options in launchApp have no effect on
4076 memory allocation</li>
4077 <li>launchApp service doesn't automatically open
4078 www.jalview.org/examples/exampleFile.jar if no file is given</li>
4080 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
4081 InstallAnywhere reports cannot find valid JVM when Java
4082 1.7_055 is available
4084 </ul> <em>Application Known issues</em>
4087 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
4088 corrupted or unreadable alignment display when scrolling
4092 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
4093 retrieval fails but progress bar continues for DAS retrieval
4094 with large number of ID
4097 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
4098 flatfile output of visible region has incorrect sequence
4102 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
4103 rna structure consensus doesn't update when secondary
4104 structure tracks are rearranged
4107 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
4108 invalid rna structure positional highlighting does not
4109 highlight position of invalid base pairs
4112 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
4113 out of memory errors are not raised when saving Jalview
4114 project from alignment window file menu
4117 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
4118 Switching to RNA Helices colouring doesn't propagate to
4122 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
4123 colour by RNA Helices not enabled when user created
4124 annotation added to alignment
4127 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
4128 Jalview icon not shown on dock in Mountain Lion/Webstart
4130 </ul> <em>Applet Known Issues</em>
4133 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
4134 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
4137 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
4138 Jalview and Jmol example not compatible with IE9
4141 <li>Sort by annotation score doesn't reverse order
4147 <td><div align="center">
4148 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
4151 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
4154 <li>Internationalisation of user interface (usually
4155 called i18n support) and translation for Spanish locale</li>
4156 <li>Define/Undefine group on current selection with
4157 Ctrl-G/Shift Ctrl-G</li>
4158 <li>Improved group creation/removal options in
4159 alignment/sequence Popup menu</li>
4160 <li>Sensible precision for symbol distribution
4161 percentages shown in logo tooltip.</li>
4162 <li>Annotation panel height set according to amount of
4163 annotation when alignment first opened</li>
4164 </ul> <em>Application</em>
4166 <li>Interactive consensus RNA secondary structure
4167 prediction VIENNA RNAAliFold JABA 2.1 service</li>
4168 <li>Select columns containing particular features from
4169 Feature Settings dialog</li>
4170 <li>View all 'representative' PDB structures for selected
4172 <li>Update Jalview project format:
4174 <li>New file extension for Jalview projects '.jvp'</li>
4175 <li>Preserve sequence and annotation dataset (to
4176 store secondary structure annotation,etc)</li>
4177 <li>Per group and alignment annotation and RNA helix
4181 <li>New similarity measures for PCA and Tree calculation
4183 <li>Experimental support for retrieval and viewing of
4184 flanking regions for an alignment</li>
4188 <!-- issues resolved --> <em>Application</em>
4190 <li>logo keeps spinning and status remains at queued or
4191 running after job is cancelled</li>
4192 <li>cannot export features from alignments imported from
4193 Jalview/VAMSAS projects</li>
4194 <li>Buggy slider for web service parameters that take
4196 <li>Newly created RNA secondary structure line doesn't
4197 have 'display all symbols' flag set</li>
4198 <li>T-COFFEE alignment score shading scheme and other
4199 annotation shading not saved in Jalview project</li>
4200 <li>Local file cannot be loaded in freshly downloaded
4202 <li>Jalview icon not shown on dock in Mountain
4204 <li>Load file from desktop file browser fails</li>
4205 <li>Occasional NPE thrown when calculating large trees</li>
4206 <li>Cannot reorder or slide sequences after dragging an
4207 alignment onto desktop</li>
4208 <li>Colour by annotation dialog throws NPE after using
4209 'extract scores' function</li>
4210 <li>Loading/cut'n'pasting an empty file leads to a grey
4211 alignment window</li>
4212 <li>Disorder thresholds rendered incorrectly after
4213 performing IUPred disorder prediction</li>
4214 <li>Multiple group annotated consensus rows shown when
4215 changing 'normalise logo' display setting</li>
4216 <li>Find shows blank dialog after 'finished searching' if
4217 nothing matches query</li>
4218 <li>Null Pointer Exceptions raised when sorting by
4219 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
4221 <li>Errors in Jmol console when structures in alignment
4222 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
4224 <li>Not all working JABAWS services are shown in
4226 <li>JAVAWS version of Jalview fails to launch with
4227 'invalid literal/length code'</li>
4228 <li>Annotation/RNA Helix colourschemes cannot be applied
4229 to alignment with groups (actually fixed in 2.8.0b1)</li>
4230 <li>RNA Helices and T-Coffee Scores available as default
4233 </ul> <em>Applet</em>
4235 <li>Remove group option is shown even when selection is
4237 <li>Apply to all groups ticked but colourscheme changes
4238 don't affect groups</li>
4239 <li>Documented RNA Helices and T-Coffee Scores as valid
4240 colourscheme name</li>
4241 <li>Annotation labels drawn on sequence IDs when
4242 Annotation panel is not displayed</li>
4243 <li>Increased font size for dropdown menus on OSX and
4244 embedded windows</li>
4245 </ul> <em>Other</em>
4247 <li>Consensus sequence for alignments/groups with a
4248 single sequence were not calculated</li>
4249 <li>annotation files that contain only groups imported as
4250 annotation and junk sequences</li>
4251 <li>Fasta files with sequences containing '*' incorrectly
4252 recognised as PFAM or BLC</li>
4253 <li>conservation/PID slider apply all groups option
4254 doesn't affect background (2.8.0b1)
4256 <li>redundancy highlighting is erratic at 0% and 100%</li>
4257 <li>Remove gapped columns fails for sequences with ragged
4259 <li>AMSA annotation row with leading spaces is not
4260 registered correctly on import</li>
4261 <li>Jalview crashes when selecting PCA analysis for
4262 certain alignments</li>
4263 <li>Opening the colour by annotation dialog for an
4264 existing annotation based 'use original colours'
4265 colourscheme loses original colours setting</li>
4270 <td><div align="center">
4271 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
4272 <em>30/1/2014</em></strong>
4276 <li>Trusted certificates for JalviewLite applet and
4277 Jalview Desktop application<br />Certificate was donated by
4278 <a href="https://www.certum.eu">Certum</a> to the Jalview
4279 open source project).
4281 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
4282 <li>Output in Stockholm format</li>
4283 <li>Allow import of data from gzipped files</li>
4284 <li>Export/import group and sequence associated line
4285 graph thresholds</li>
4286 <li>Nucleotide substitution matrix that supports RNA and
4287 ambiguity codes</li>
4288 <li>Allow disorder predictions to be made on the current
4289 selection (or visible selection) in the same way that JPred
4291 <li>Groovy scripting for headless Jalview operation</li>
4292 </ul> <em>Other improvements</em>
4294 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
4295 <li>COMBINE statement uses current SEQUENCE_REF and
4296 GROUP_REF scope to group annotation rows</li>
4297 <li>Support '' style escaping of quotes in Newick
4299 <li>Group options for JABAWS service by command line name</li>
4300 <li>Empty tooltip shown for JABA service options with a
4301 link but no description</li>
4302 <li>Select primary source when selecting authority in
4303 database fetcher GUI</li>
4304 <li>Add .mfa to FASTA file extensions recognised by
4306 <li>Annotation label tooltip text wrap</li>
4311 <li>Slow scrolling when lots of annotation rows are
4313 <li>Lots of NPE (and slowness) after creating RNA
4314 secondary structure annotation line</li>
4315 <li>Sequence database accessions not imported when
4316 fetching alignments from Rfam</li>
4317 <li>Incorrect SHMR submission for sequences with
4319 <li>View all structures does not always superpose
4321 <li>Option widgets in service parameters not updated to
4322 reflect user or preset settings</li>
4323 <li>Null pointer exceptions for some services without
4324 presets or adjustable parameters</li>
4325 <li>Discover PDB IDs entry in structure menu doesn't
4326 discover PDB xRefs</li>
4327 <li>Exception encountered while trying to retrieve
4328 features with DAS</li>
4329 <li>Lowest value in annotation row isn't coloured
4330 when colour by annotation (per sequence) is coloured</li>
4331 <li>Keyboard mode P jumps to start of gapped region when
4332 residue follows a gap</li>
4333 <li>Jalview appears to hang importing an alignment with
4334 Wrap as default or after enabling Wrap</li>
4335 <li>'Right click to add annotations' message
4336 shown in wrap mode when no annotations present</li>
4337 <li>Disorder predictions fail with NPE if no automatic
4338 annotation already exists on alignment</li>
4339 <li>oninit javascript function should be called after
4340 initialisation completes</li>
4341 <li>Remove redundancy after disorder prediction corrupts
4342 alignment window display</li>
4343 <li>Example annotation file in documentation is invalid</li>
4344 <li>Grouped line graph annotation rows are not exported
4345 to annotation file</li>
4346 <li>Multi-harmony analysis cannot be run when only two
4348 <li>Cannot create multiple groups of line graphs with
4349 several 'combine' statements in annotation file</li>
4350 <li>Pressing return several times causes Number Format
4351 exceptions in keyboard mode</li>
4352 <li>Multi-harmony (SHMMR) method doesn't submit
4353 correct partitions for input data</li>
4354 <li>Translation from DNA to Amino Acids fails</li>
4355 <li>Jalview fail to load newick tree with quoted label</li>
4356 <li>--headless flag isn't understood</li>
4357 <li>ClassCastException when generating EPS in headless
4359 <li>Adjusting sequence-associated shading threshold only
4360 changes one row's threshold</li>
4361 <li>Preferences and Feature settings panel panel
4362 doesn't open</li>
4363 <li>hide consensus histogram also hides conservation and
4364 quality histograms</li>
4369 <td><div align="center">
4370 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
4372 <td><em>Application</em>
4374 <li>Support for JABAWS 2.0 Services (AACon alignment
4375 conservation, protein disorder and Clustal Omega)</li>
4376 <li>JABAWS server status indicator in Web Services
4378 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
4379 in Jalview alignment window</li>
4380 <li>Updated Jalview build and deploy framework for OSX
4381 mountain lion, windows 7, and 8</li>
4382 <li>Nucleotide substitution matrix for PCA that supports
4383 RNA and ambiguity codes</li>
4385 <li>Improved sequence database retrieval GUI</li>
4386 <li>Support fetching and database reference look up
4387 against multiple DAS sources (Fetch all from in 'fetch db
4389 <li>Jalview project improvements
4391 <li>Store and retrieve the 'belowAlignment'
4392 flag for annotation</li>
4393 <li>calcId attribute to group annotation rows on the
4395 <li>Store AACon calculation settings for a view in
4396 Jalview project</li>
4400 <li>horizontal scrolling gesture support</li>
4401 <li>Visual progress indicator when PCA calculation is
4403 <li>Simpler JABA web services menus</li>
4404 <li>visual indication that web service results are still
4405 being retrieved from server</li>
4406 <li>Serialise the dialogs that are shown when Jalview
4407 starts up for first time</li>
4408 <li>Jalview user agent string for interacting with HTTP
4410 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
4412 <li>Examples directory and Groovy library included in
4413 InstallAnywhere distribution</li>
4414 </ul> <em>Applet</em>
4416 <li>RNA alignment and secondary structure annotation
4417 visualization applet example</li>
4418 </ul> <em>General</em>
4420 <li>Normalise option for consensus sequence logo</li>
4421 <li>Reset button in PCA window to return dimensions to
4423 <li>Allow seqspace or Jalview variant of alignment PCA
4425 <li>PCA with either nucleic acid and protein substitution
4427 <li>Allow windows containing HTML reports to be exported
4429 <li>Interactive display and editing of RNA secondary
4430 structure contacts</li>
4431 <li>RNA Helix Alignment Colouring</li>
4432 <li>RNA base pair logo consensus</li>
4433 <li>Parse sequence associated secondary structure
4434 information in Stockholm files</li>
4435 <li>HTML Export database accessions and annotation
4436 information presented in tooltip for sequences</li>
4437 <li>Import secondary structure from LOCARNA clustalw
4438 style RNA alignment files</li>
4439 <li>import and visualise T-COFFEE quality scores for an
4441 <li>'colour by annotation' per sequence option to
4442 shade each sequence according to its associated alignment
4444 <li>New Jalview Logo</li>
4445 </ul> <em>Documentation and Development</em>
4447 <li>documentation for score matrices used in Jalview</li>
4448 <li>New Website!</li>
4450 <td><em>Application</em>
4452 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
4453 wsdbfetch REST service</li>
4454 <li>Stop windows being moved outside desktop on OSX</li>
4455 <li>Filetype associations not installed for webstart
4457 <li>Jalview does not always retrieve progress of a JABAWS
4458 job execution in full once it is complete</li>
4459 <li>revise SHMR RSBS definition to ensure alignment is
4460 uploaded via ali_file parameter</li>
4461 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
4462 <li>View all structures superposed fails with exception</li>
4463 <li>Jnet job queues forever if a very short sequence is
4464 submitted for prediction</li>
4465 <li>Cut and paste menu not opened when mouse clicked on
4467 <li>Putting fractional value into integer text box in
4468 alignment parameter dialog causes Jalview to hang</li>
4469 <li>Structure view highlighting doesn't work on
4471 <li>View all structures fails with exception shown in
4473 <li>Characters in filename associated with PDBEntry not
4474 escaped in a platform independent way</li>
4475 <li>Jalview desktop fails to launch with exception when
4477 <li>Tree calculation reports 'you must have 2 or more
4478 sequences selected' when selection is empty</li>
4479 <li>Jalview desktop fails to launch with jar signature
4480 failure when java web start temporary file caching is
4482 <li>DAS Sequence retrieval with range qualification
4483 results in sequence xref which includes range qualification</li>
4484 <li>Errors during processing of command line arguments
4485 cause progress bar (JAL-898) to be removed</li>
4486 <li>Replace comma for semi-colon option not disabled for
4487 DAS sources in sequence fetcher</li>
4488 <li>Cannot close news reader when JABAWS server warning
4489 dialog is shown</li>
4490 <li>Option widgets not updated to reflect user settings</li>
4491 <li>Edited sequence not submitted to web service</li>
4492 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
4493 <li>InstallAnywhere installer doesn't unpack and run
4494 on OSX Mountain Lion</li>
4495 <li>Annotation panel not given a scroll bar when
4496 sequences with alignment annotation are pasted into the
4498 <li>Sequence associated annotation rows not associated
4499 when loaded from Jalview project</li>
4500 <li>Browser launch fails with NPE on java 1.7</li>
4501 <li>JABAWS alignment marked as finished when job was
4502 cancelled or job failed due to invalid input</li>
4503 <li>NPE with v2.7 example when clicking on Tree
4504 associated with all views</li>
4505 <li>Exceptions when copy/paste sequences with grouped
4506 annotation rows to new window</li>
4507 </ul> <em>Applet</em>
4509 <li>Sequence features are momentarily displayed before
4510 they are hidden using hidefeaturegroups applet parameter</li>
4511 <li>loading features via javascript API automatically
4512 enables feature display</li>
4513 <li>scrollToColumnIn javascript API method doesn't
4515 </ul> <em>General</em>
4517 <li>Redundancy removal fails for rna alignment</li>
4518 <li>PCA calculation fails when sequence has been selected
4519 and then deselected</li>
4520 <li>PCA window shows grey box when first opened on OSX</li>
4521 <li>Letters coloured pink in sequence logo when alignment
4522 coloured with clustalx</li>
4523 <li>Choosing fonts without letter symbols defined causes
4524 exceptions and redraw errors</li>
4525 <li>Initial PCA plot view is not same as manually
4526 reconfigured view</li>
4527 <li>Grouped annotation graph label has incorrect line
4529 <li>Grouped annotation graph label display is corrupted
4530 for lots of labels</li>
4535 <div align="center">
4536 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
4539 <td><em>Application</em>
4541 <li>Jalview Desktop News Reader</li>
4542 <li>Tweaked default layout of web services menu</li>
4543 <li>View/alignment association menu to enable user to
4544 easily specify which alignment a multi-structure view takes
4545 its colours/correspondences from</li>
4546 <li>Allow properties file location to be specified as URL</li>
4547 <li>Extend Jalview project to preserve associations
4548 between many alignment views and a single Jmol display</li>
4549 <li>Store annotation row height in Jalview project file</li>
4550 <li>Annotation row column label formatting attributes
4551 stored in project file</li>
4552 <li>Annotation row order for auto-calculated annotation
4553 rows preserved in Jalview project file</li>
4554 <li>Visual progress indication when Jalview state is
4555 saved using Desktop window menu</li>
4556 <li>Visual indication that command line arguments are
4557 still being processed</li>
4558 <li>Groovy script execution from URL</li>
4559 <li>Colour by annotation default min and max colours in
4561 <li>Automatically associate PDB files dragged onto an
4562 alignment with sequences that have high similarity and
4564 <li>Update JGoogleAnalytics to latest release (0.3)</li>
4565 <li>'view structures' option to open many
4566 structures in same window</li>
4567 <li>Sort associated views menu option for tree panel</li>
4568 <li>Group all JABA and non-JABA services for a particular
4569 analysis function in its own submenu</li>
4570 </ul> <em>Applet</em>
4572 <li>Userdefined and autogenerated annotation rows for
4574 <li>Adjustment of alignment annotation pane height</li>
4575 <li>Annotation scrollbar for annotation panel</li>
4576 <li>Drag to reorder annotation rows in annotation panel</li>
4577 <li>'automaticScrolling' parameter</li>
4578 <li>Allow sequences with partial ID string matches to be
4579 annotated from GFF/Jalview features files</li>
4580 <li>Sequence logo annotation row in applet</li>
4581 <li>Absolute paths relative to host server in applet
4582 parameters are treated as such</li>
4583 <li>New in the JalviewLite javascript API:
4585 <li>JalviewLite.js javascript library</li>
4586 <li>Javascript callbacks for
4588 <li>Applet initialisation</li>
4589 <li>Sequence/alignment mouse-overs and selections</li>
4592 <li>scrollTo row and column alignment scrolling
4594 <li>Select sequence/alignment regions from javascript</li>
4595 <li>javascript structure viewer harness to pass
4596 messages between Jmol and Jalview when running as
4597 distinct applets</li>
4598 <li>sortBy method</li>
4599 <li>Set of applet and application examples shipped
4600 with documentation</li>
4601 <li>New example to demonstrate JalviewLite and Jmol
4602 javascript message exchange</li>
4604 </ul> <em>General</em>
4606 <li>Enable Jmol displays to be associated with multiple
4607 multiple alignments</li>
4608 <li>Option to automatically sort alignment with new tree</li>
4609 <li>User configurable link to enable redirects to a
4610 www.Jalview.org mirror</li>
4611 <li>Jmol colours option for Jmol displays</li>
4612 <li>Configurable newline string when writing alignment
4613 and other flat files</li>
4614 <li>Allow alignment annotation description lines to
4615 contain html tags</li>
4616 </ul> <em>Documentation and Development</em>
4618 <li>Add groovy test harness for bulk load testing to
4620 <li>Groovy script to load and align a set of sequences
4621 using a web service before displaying the result in the
4622 Jalview desktop</li>
4623 <li>Restructured javascript and applet api documentation</li>
4624 <li>Ant target to publish example html files with applet
4626 <li>Netbeans project for building Jalview from source</li>
4627 <li>ant task to create online javadoc for Jalview source</li>
4629 <td><em>Application</em>
4631 <li>User defined colourscheme throws exception when
4632 current built in colourscheme is saved as new scheme</li>
4633 <li>AlignFrame->Save in application pops up save
4634 dialog for valid filename/format</li>
4635 <li>Cannot view associated structure for UniProt sequence</li>
4636 <li>PDB file association breaks for UniProt sequence
4638 <li>Associate PDB from file dialog does not tell you
4639 which sequence is to be associated with the file</li>
4640 <li>Find All raises null pointer exception when query
4641 only matches sequence IDs</li>
4642 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4643 <li>Jalview project with Jmol views created with Jalview
4644 2.4 cannot be loaded</li>
4645 <li>Filetype associations not installed for webstart
4647 <li>Two or more chains in a single PDB file associated
4648 with sequences in different alignments do not get coloured
4649 by their associated sequence</li>
4650 <li>Visibility status of autocalculated annotation row
4651 not preserved when project is loaded</li>
4652 <li>Annotation row height and visibility attributes not
4653 stored in Jalview project</li>
4654 <li>Tree bootstraps are not preserved when saved as a
4655 Jalview project</li>
4656 <li>Envision2 workflow tooltips are corrupted</li>
4657 <li>Enabling show group conservation also enables colour
4658 by conservation</li>
4659 <li>Duplicate group associated conservation or consensus
4660 created on new view</li>
4661 <li>Annotation scrollbar not displayed after 'show
4662 all hidden annotation rows' option selected</li>
4663 <li>Alignment quality not updated after alignment
4664 annotation row is hidden then shown</li>
4665 <li>Preserve colouring of structures coloured by
4666 sequences in pre Jalview 2.7 projects</li>
4667 <li>Web service job parameter dialog is not laid out
4669 <li>Web services menu not refreshed after 'reset
4670 services' button is pressed in preferences</li>
4671 <li>Annotation off by one in Jalview v2_3 example project</li>
4672 <li>Structures imported from file and saved in project
4673 get name like jalview_pdb1234.txt when reloaded</li>
4674 <li>Jalview does not always retrieve progress of a JABAWS
4675 job execution in full once it is complete</li>
4676 </ul> <em>Applet</em>
4678 <li>Alignment height set incorrectly when lots of
4679 annotation rows are displayed</li>
4680 <li>Relative URLs in feature HTML text not resolved to
4682 <li>View follows highlighting does not work for positions
4684 <li><= shown as = in tooltip</li>
4685 <li>Export features raises exception when no features
4687 <li>Separator string used for serialising lists of IDs
4688 for javascript api is modified when separator string
4689 provided as parameter</li>
4690 <li>Null pointer exception when selecting tree leaves for
4691 alignment with no existing selection</li>
4692 <li>Relative URLs for datasources assumed to be relative
4693 to applet's codebase</li>
4694 <li>Status bar not updated after finished searching and
4695 search wraps around to first result</li>
4696 <li>StructureSelectionManager instance shared between
4697 several Jalview applets causes race conditions and memory
4699 <li>Hover tooltip and mouseover of position on structure
4700 not sent from Jmol in applet</li>
4701 <li>Certain sequences of javascript method calls to
4702 applet API fatally hang browser</li>
4703 </ul> <em>General</em>
4705 <li>View follows structure mouseover scrolls beyond
4706 position with wrapped view and hidden regions</li>
4707 <li>Find sequence position moves to wrong residue
4708 with/without hidden columns</li>
4709 <li>Sequence length given in alignment properties window
4711 <li>InvalidNumberFormat exceptions thrown when trying to
4712 import PDB like structure files</li>
4713 <li>Positional search results are only highlighted
4714 between user-supplied sequence start/end bounds</li>
4715 <li>End attribute of sequence is not validated</li>
4716 <li>Find dialog only finds first sequence containing a
4717 given sequence position</li>
4718 <li>Sequence numbering not preserved in MSF alignment
4720 <li>Jalview PDB file reader does not extract sequence
4721 from nucleotide chains correctly</li>
4722 <li>Structure colours not updated when tree partition
4723 changed in alignment</li>
4724 <li>Sequence associated secondary structure not correctly
4725 parsed in interleaved stockholm</li>
4726 <li>Colour by annotation dialog does not restore current
4728 <li>Hiding (nearly) all sequences doesn't work
4730 <li>Sequences containing lowercase letters are not
4731 properly associated with their pdb files</li>
4732 </ul> <em>Documentation and Development</em>
4734 <li>schemas/JalviewWsParamSet.xsd corrupted by
4735 ApplyCopyright tool</li>
4740 <div align="center">
4741 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4744 <td><em>Application</em>
4746 <li>New warning dialog when the Jalview Desktop cannot
4747 contact web services</li>
4748 <li>JABA service parameters for a preset are shown in
4749 service job window</li>
4750 <li>JABA Service menu entries reworded</li>
4754 <li>Modeller PIR IO broken - cannot correctly import a
4755 pir file emitted by Jalview</li>
4756 <li>Existing feature settings transferred to new
4757 alignment view created from cut'n'paste</li>
4758 <li>Improved test for mixed amino/nucleotide chains when
4759 parsing PDB files</li>
4760 <li>Consensus and conservation annotation rows
4761 occasionally become blank for all new windows</li>
4762 <li>Exception raised when right clicking above sequences
4763 in wrapped view mode</li>
4764 </ul> <em>Application</em>
4766 <li>multiple multiply aligned structure views cause cpu
4767 usage to hit 100% and computer to hang</li>
4768 <li>Web Service parameter layout breaks for long user
4769 parameter names</li>
4770 <li>Jaba service discovery hangs desktop if Jaba server
4777 <div align="center">
4778 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4781 <td><em>Application</em>
4783 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4784 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4787 <li>Web Services preference tab</li>
4788 <li>Analysis parameters dialog box and user defined
4790 <li>Improved speed and layout of Envision2 service menu</li>
4791 <li>Superpose structures using associated sequence
4793 <li>Export coordinates and projection as CSV from PCA
4795 </ul> <em>Applet</em>
4797 <li>enable javascript: execution by the applet via the
4798 link out mechanism</li>
4799 </ul> <em>Other</em>
4801 <li>Updated the Jmol Jalview interface to work with Jmol
4803 <li>The Jalview Desktop and JalviewLite applet now
4804 require Java 1.5</li>
4805 <li>Allow Jalview feature colour specification for GFF
4806 sequence annotation files</li>
4807 <li>New 'colour by label' keword in Jalview feature file
4808 type colour specification</li>
4809 <li>New Jalview Desktop Groovy API method that allows a
4810 script to check if it being run in an interactive session or
4811 in a batch operation from the Jalview command line</li>
4815 <li>clustalx colourscheme colours Ds preferentially when
4816 both D+E are present in over 50% of the column</li>
4817 </ul> <em>Application</em>
4819 <li>typo in AlignmentFrame->View->Hide->all but
4820 selected Regions menu item</li>
4821 <li>sequence fetcher replaces ',' for ';' when the ',' is
4822 part of a valid accession ID</li>
4823 <li>fatal OOM if object retrieved by sequence fetcher
4824 runs out of memory</li>
4825 <li>unhandled Out of Memory Error when viewing pca
4826 analysis results</li>
4827 <li>InstallAnywhere builds fail to launch on OS X java
4828 10.5 update 4 (due to apple Java 1.6 update)</li>
4829 <li>Installanywhere Jalview silently fails to launch</li>
4830 </ul> <em>Applet</em>
4832 <li>Jalview.getFeatureGroups() raises an
4833 ArrayIndexOutOfBoundsException if no feature groups are
4840 <div align="center">
4841 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4847 <li>Alignment prettyprinter doesn't cope with long
4849 <li>clustalx colourscheme colours Ds preferentially when
4850 both D+E are present in over 50% of the column</li>
4851 <li>nucleic acid structures retrieved from PDB do not
4852 import correctly</li>
4853 <li>More columns get selected than were clicked on when a
4854 number of columns are hidden</li>
4855 <li>annotation label popup menu not providing correct
4856 add/hide/show options when rows are hidden or none are
4858 <li>Stockholm format shown in list of readable formats,
4859 and parser copes better with alignments from RFAM.</li>
4860 <li>CSV output of consensus only includes the percentage
4861 of all symbols if sequence logo display is enabled</li>
4863 </ul> <em>Applet</em>
4865 <li>annotation panel disappears when annotation is
4867 </ul> <em>Application</em>
4869 <li>Alignment view not redrawn properly when new
4870 alignment opened where annotation panel is visible but no
4871 annotations are present on alignment</li>
4872 <li>pasted region containing hidden columns is
4873 incorrectly displayed in new alignment window</li>
4874 <li>Jalview slow to complete operations when stdout is
4875 flooded (fix is to close the Jalview console)</li>
4876 <li>typo in AlignmentFrame->View->Hide->all but
4877 selected Rregions menu item.</li>
4878 <li>inconsistent group submenu and Format submenu entry
4879 'Un' or 'Non'conserved</li>
4880 <li>Sequence feature settings are being shared by
4881 multiple distinct alignments</li>
4882 <li>group annotation not recreated when tree partition is
4884 <li>double click on group annotation to select sequences
4885 does not propagate to associated trees</li>
4886 <li>Mac OSX specific issues:
4888 <li>exception raised when mouse clicked on desktop
4889 window background</li>
4890 <li>Desktop menu placed on menu bar and application
4891 name set correctly</li>
4892 <li>sequence feature settings not wide enough for the
4893 save feature colourscheme button</li>
4902 <div align="center">
4903 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4906 <td><em>New Capabilities</em>
4908 <li>URL links generated from description line for
4909 regular-expression based URL links (applet and application)
4912 <li>Non-positional feature URL links are shown in link
4914 <li>Linked viewing of nucleic acid sequences and
4916 <li>Automatic Scrolling option in View menu to display
4917 the currently highlighted region of an alignment.</li>
4918 <li>Order an alignment by sequence length, or using the
4919 average score or total feature count for each sequence.</li>
4920 <li>Shading features by score or associated description</li>
4921 <li>Subdivide alignment and groups based on identity of
4922 selected subsequence (Make Groups from Selection).</li>
4923 <li>New hide/show options including Shift+Control+H to
4924 hide everything but the currently selected region.</li>
4925 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4926 </ul> <em>Application</em>
4928 <li>Fetch DB References capabilities and UI expanded to
4929 support retrieval from DAS sequence sources</li>
4930 <li>Local DAS Sequence sources can be added via the
4931 command line or via the Add local source dialog box.</li>
4932 <li>DAS Dbref and DbxRef feature types are parsed as
4933 database references and protein_name is parsed as
4934 description line (BioSapiens terms).</li>
4935 <li>Enable or disable non-positional feature and database
4936 references in sequence ID tooltip from View menu in
4938 <!-- <li>New hidden columns and rows and representatives capabilities
4939 in annotations file (in progress - not yet fully implemented)</li> -->
4940 <li>Group-associated consensus, sequence logos and
4941 conservation plots</li>
4942 <li>Symbol distributions for each column can be exported
4943 and visualized as sequence logos</li>
4944 <li>Optionally scale multi-character column labels to fit
4945 within each column of annotation row<!-- todo for applet -->
4947 <li>Optional automatic sort of associated alignment view
4948 when a new tree is opened.</li>
4949 <li>Jalview Java Console</li>
4950 <li>Better placement of desktop window when moving
4951 between different screens.</li>
4952 <li>New preference items for sequence ID tooltip and
4953 consensus annotation</li>
4954 <li>Client to submit sequences and IDs to Envision2
4956 <li><em>Vamsas Capabilities</em>
4958 <li>Improved VAMSAS synchronization (Jalview archive
4959 used to preserve views, structures, and tree display
4961 <li>Import of vamsas documents from disk or URL via
4963 <li>Sharing of selected regions between views and
4964 with other VAMSAS applications (Experimental feature!)</li>
4965 <li>Updated API to VAMSAS version 0.2</li>
4967 </ul> <em>Applet</em>
4969 <li>Middle button resizes annotation row height</li>
4972 <li>sortByTree (true/false) - automatically sort the
4973 associated alignment view by the tree when a new tree is
4975 <li>showTreeBootstraps (true/false) - show or hide
4976 branch bootstraps (default is to show them if available)</li>
4977 <li>showTreeDistances (true/false) - show or hide
4978 branch lengths (default is to show them if available)</li>
4979 <li>showUnlinkedTreeNodes (true/false) - indicate if
4980 unassociated nodes should be highlighted in the tree
4982 <li>heightScale and widthScale (1.0 or more) -
4983 increase the height or width of a cell in the alignment
4984 grid relative to the current font size.</li>
4987 <li>Non-positional features displayed in sequence ID
4989 </ul> <em>Other</em>
4991 <li>Features format: graduated colour definitions and
4992 specification of feature scores</li>
4993 <li>Alignment Annotations format: new keywords for group
4994 associated annotation (GROUP_REF) and annotation row display
4995 properties (ROW_PROPERTIES)</li>
4996 <li>XML formats extended to support graduated feature
4997 colourschemes, group associated annotation, and profile
4998 visualization settings.</li></td>
5001 <li>Source field in GFF files parsed as feature source
5002 rather than description</li>
5003 <li>Non-positional features are now included in sequence
5004 feature and gff files (controlled via non-positional feature
5005 visibility in tooltip).</li>
5006 <li>URL links generated for all feature links (bugfix)</li>
5007 <li>Added URL embedding instructions to features file
5009 <li>Codons containing ambiguous nucleotides translated as
5010 'X' in peptide product</li>
5011 <li>Match case switch in find dialog box works for both
5012 sequence ID and sequence string and query strings do not
5013 have to be in upper case to match case-insensitively.</li>
5014 <li>AMSA files only contain first column of
5015 multi-character column annotation labels</li>
5016 <li>Jalview Annotation File generation/parsing consistent
5017 with documentation (e.g. Stockholm annotation can be
5018 exported and re-imported)</li>
5019 <li>PDB files without embedded PDB IDs given a friendly
5021 <li>Find incrementally searches ID string matches as well
5022 as subsequence matches, and correctly reports total number
5026 <li>Better handling of exceptions during sequence
5028 <li>Dasobert generated non-positional feature URL
5029 link text excludes the start_end suffix</li>
5030 <li>DAS feature and source retrieval buttons disabled
5031 when fetch or registry operations in progress.</li>
5032 <li>PDB files retrieved from URLs are cached properly</li>
5033 <li>Sequence description lines properly shared via
5035 <li>Sequence fetcher fetches multiple records for all
5037 <li>Ensured that command line das feature retrieval
5038 completes before alignment figures are generated.</li>
5039 <li>Reduced time taken when opening file browser for
5041 <li>isAligned check prior to calculating tree, PCA or
5042 submitting an MSA to JNet now excludes hidden sequences.</li>
5043 <li>User defined group colours properly recovered
5044 from Jalview projects.</li>
5053 <div align="center">
5054 <strong>2.4.0.b2</strong><br> 28/10/2009
5059 <li>Experimental support for google analytics usage
5061 <li>Jalview privacy settings (user preferences and docs).</li>
5066 <li>Race condition in applet preventing startup in
5068 <li>Exception when feature created from selection beyond
5069 length of sequence.</li>
5070 <li>Allow synthetic PDB files to be imported gracefully</li>
5071 <li>Sequence associated annotation rows associate with
5072 all sequences with a given id</li>
5073 <li>Find function matches case-insensitively for sequence
5074 ID string searches</li>
5075 <li>Non-standard characters do not cause pairwise
5076 alignment to fail with exception</li>
5077 </ul> <em>Application Issues</em>
5079 <li>Sequences are now validated against EMBL database</li>
5080 <li>Sequence fetcher fetches multiple records for all
5082 </ul> <em>InstallAnywhere Issues</em>
5084 <li>Dock icon works for Mac OS X java (Mac 1.6 update
5085 issue with installAnywhere mechanism)</li>
5086 <li>Command line launching of JARs from InstallAnywhere
5087 version (java class versioning error fixed)</li>
5094 <div align="center">
5095 <strong>2.4</strong><br> 27/8/2008
5098 <td><em>User Interface</em>
5100 <li>Linked highlighting of codon and amino acid from
5101 translation and protein products</li>
5102 <li>Linked highlighting of structure associated with
5103 residue mapping to codon position</li>
5104 <li>Sequence Fetcher provides example accession numbers
5105 and 'clear' button</li>
5106 <li>MemoryMonitor added as an option under Desktop's
5108 <li>Extract score function to parse whitespace separated
5109 numeric data in description line</li>
5110 <li>Column labels in alignment annotation can be centred.</li>
5111 <li>Tooltip for sequence associated annotation give name
5113 </ul> <em>Web Services and URL fetching</em>
5115 <li>JPred3 web service</li>
5116 <li>Prototype sequence search client (no public services
5118 <li>Fetch either seed alignment or full alignment from
5120 <li>URL Links created for matching database cross
5121 references as well as sequence ID</li>
5122 <li>URL Links can be created using regular-expressions</li>
5123 </ul> <em>Sequence Database Connectivity</em>
5125 <li>Retrieval of cross-referenced sequences from other
5127 <li>Generalised database reference retrieval and
5128 validation to all fetchable databases</li>
5129 <li>Fetch sequences from DAS sources supporting the
5130 sequence command</li>
5131 </ul> <em>Import and Export</em>
5132 <li>export annotation rows as CSV for spreadsheet import</li>
5133 <li>Jalview projects record alignment dataset associations,
5134 EMBL products, and cDNA sequence mappings</li>
5135 <li>Sequence Group colour can be specified in Annotation
5137 <li>Ad-hoc colouring of group in Annotation File using RGB
5138 triplet as name of colourscheme</li>
5139 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
5141 <li>treenode binding for VAMSAS tree exchange</li>
5142 <li>local editing and update of sequences in VAMSAS
5143 alignments (experimental)</li>
5144 <li>Create new or select existing session to join</li>
5145 <li>load and save of vamsas documents</li>
5146 </ul> <em>Application command line</em>
5148 <li>-tree parameter to open trees (introduced for passing
5150 <li>-fetchfrom command line argument to specify nicknames
5151 of DAS servers to query for alignment features</li>
5152 <li>-dasserver command line argument to add new servers
5153 that are also automatically queried for features</li>
5154 <li>-groovy command line argument executes a given groovy
5155 script after all input data has been loaded and parsed</li>
5156 </ul> <em>Applet-Application data exchange</em>
5158 <li>Trees passed as applet parameters can be passed to
5159 application (when using "View in full
5160 application")</li>
5161 </ul> <em>Applet Parameters</em>
5163 <li>feature group display control parameter</li>
5164 <li>debug parameter</li>
5165 <li>showbutton parameter</li>
5166 </ul> <em>Applet API methods</em>
5168 <li>newView public method</li>
5169 <li>Window (current view) specific get/set public methods</li>
5170 <li>Feature display control methods</li>
5171 <li>get list of currently selected sequences</li>
5172 </ul> <em>New Jalview distribution features</em>
5174 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
5175 <li>RELEASE file gives build properties for the latest
5176 Jalview release.</li>
5177 <li>Java 1.1 Applet build made easier and donotobfuscate
5178 property controls execution of obfuscator</li>
5179 <li>Build target for generating source distribution</li>
5180 <li>Debug flag for javacc</li>
5181 <li>.jalview_properties file is documented (slightly) in
5182 jalview.bin.Cache</li>
5183 <li>Continuous Build Integration for stable and
5184 development version of Application, Applet and source
5189 <li>selected region output includes visible annotations
5190 (for certain formats)</li>
5191 <li>edit label/displaychar contains existing label/char
5193 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
5194 <li>shorter peptide product names from EMBL records</li>
5195 <li>Newick string generator makes compact representations</li>
5196 <li>bootstrap values parsed correctly for tree files with
5198 <li>pathological filechooser bug avoided by not allowing
5199 filenames containing a ':'</li>
5200 <li>Fixed exception when parsing GFF files containing
5201 global sequence features</li>
5202 <li>Alignment datasets are finalized only when number of
5203 references from alignment sequences goes to zero</li>
5204 <li>Close of tree branch colour box without colour
5205 selection causes cascading exceptions</li>
5206 <li>occasional negative imgwidth exceptions</li>
5207 <li>better reporting of non-fatal warnings to user when
5208 file parsing fails.</li>
5209 <li>Save works when Jalview project is default format</li>
5210 <li>Save as dialog opened if current alignment format is
5211 not a valid output format</li>
5212 <li>UniProt canonical names introduced for both das and
5214 <li>Histidine should be midblue (not pink!) in Zappo</li>
5215 <li>error messages passed up and output when data read
5217 <li>edit undo recovers previous dataset sequence when
5218 sequence is edited</li>
5219 <li>allow PDB files without pdb ID HEADER lines (like
5220 those generated by MODELLER) to be read in properly</li>
5221 <li>allow reading of JPred concise files as a normal
5223 <li>Stockholm annotation parsing and alignment properties
5224 import fixed for PFAM records</li>
5225 <li>Structure view windows have correct name in Desktop
5227 <li>annotation consisting of sequence associated scores
5228 can be read and written correctly to annotation file</li>
5229 <li>Aligned cDNA translation to aligned peptide works
5231 <li>Fixed display of hidden sequence markers and
5232 non-italic font for representatives in Applet</li>
5233 <li>Applet Menus are always embedded in applet window on
5235 <li>Newly shown features appear at top of stack (in
5237 <li>Annotations added via parameter not drawn properly
5238 due to null pointer exceptions</li>
5239 <li>Secondary structure lines are drawn starting from
5240 first column of alignment</li>
5241 <li>UniProt XML import updated for new schema release in
5243 <li>Sequence feature to sequence ID match for Features
5244 file is case-insensitive</li>
5245 <li>Sequence features read from Features file appended to
5246 all sequences with matching IDs</li>
5247 <li>PDB structure coloured correctly for associated views
5248 containing a sub-sequence</li>
5249 <li>PDB files can be retrieved by applet from Jar files</li>
5250 <li>feature and annotation file applet parameters
5251 referring to different directories are retrieved correctly</li>
5252 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
5253 <li>Fixed application hang whilst waiting for
5254 splash-screen version check to complete</li>
5255 <li>Applet properly URLencodes input parameter values
5256 when passing them to the launchApp service</li>
5257 <li>display name and local features preserved in results
5258 retrieved from web service</li>
5259 <li>Visual delay indication for sequence retrieval and
5260 sequence fetcher initialisation</li>
5261 <li>updated Application to use DAS 1.53e version of
5262 dasobert DAS client</li>
5263 <li>Re-instated Full AMSA support and .amsa file
5265 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
5273 <div align="center">
5274 <strong>2.3</strong><br> 9/5/07
5279 <li>Jmol 11.0.2 integration</li>
5280 <li>PDB views stored in Jalview XML files</li>
5281 <li>Slide sequences</li>
5282 <li>Edit sequence in place</li>
5283 <li>EMBL CDS features</li>
5284 <li>DAS Feature mapping</li>
5285 <li>Feature ordering</li>
5286 <li>Alignment Properties</li>
5287 <li>Annotation Scores</li>
5288 <li>Sort by scores</li>
5289 <li>Feature/annotation editing in applet</li>
5294 <li>Headless state operation in 2.2.1</li>
5295 <li>Incorrect and unstable DNA pairwise alignment</li>
5296 <li>Cut and paste of sequences with annotation</li>
5297 <li>Feature group display state in XML</li>
5298 <li>Feature ordering in XML</li>
5299 <li>blc file iteration selection using filename # suffix</li>
5300 <li>Stockholm alignment properties</li>
5301 <li>Stockhom alignment secondary structure annotation</li>
5302 <li>2.2.1 applet had no feature transparency</li>
5303 <li>Number pad keys can be used in cursor mode</li>
5304 <li>Structure Viewer mirror image resolved</li>
5311 <div align="center">
5312 <strong>2.2.1</strong><br> 12/2/07
5317 <li>Non standard characters can be read and displayed
5318 <li>Annotations/Features can be imported/exported to the
5320 <li>Applet allows editing of sequence/annotation/group
5321 name & description
5322 <li>Preference setting to display sequence name in
5324 <li>Annotation file format extended to allow
5325 Sequence_groups to be defined
5326 <li>Default opening of alignment overview panel can be
5327 specified in preferences
5328 <li>PDB residue numbering annotation added to associated
5334 <li>Applet crash under certain Linux OS with Java 1.6
5336 <li>Annotation file export / import bugs fixed
5337 <li>PNG / EPS image output bugs fixed
5343 <div align="center">
5344 <strong>2.2</strong><br> 27/11/06
5349 <li>Multiple views on alignment
5350 <li>Sequence feature editing
5351 <li>"Reload" alignment
5352 <li>"Save" to current filename
5353 <li>Background dependent text colour
5354 <li>Right align sequence ids
5355 <li>User-defined lower case residue colours
5358 <li>Menu item accelerator keys
5359 <li>Control-V pastes to current alignment
5360 <li>Cancel button for DAS Feature Fetching
5361 <li>PCA and PDB Viewers zoom via mouse roller
5362 <li>User-defined sub-tree colours and sub-tree selection
5365 <li>'New Window' button on the 'Output to Text box'
5370 <li>New memory efficient Undo/Redo System
5371 <li>Optimised symbol lookups and conservation/consensus
5373 <li>Region Conservation/Consensus recalculated after
5375 <li>Fixed Remove Empty Columns Bug (empty columns at end
5377 <li>Slowed DAS Feature Fetching for increased robustness.
5380 <li>Made angle brackets in ASCII feature descriptions
5382 <li>Re-instated Zoom function for PCA
5383 <li>Sequence descriptions conserved in web service
5385 <li>UniProt ID discoverer uses any word separated by
5387 <li>WsDbFetch query/result association resolved
5388 <li>Tree leaf to sequence mapping improved
5389 <li>Smooth fonts switch moved to FontChooser dialog box.
5397 <div align="center">
5398 <strong>2.1.1</strong><br> 12/9/06
5403 <li>Copy consensus sequence to clipboard</li>
5408 <li>Image output - rightmost residues are rendered if
5409 sequence id panel has been resized</li>
5410 <li>Image output - all offscreen group boundaries are
5412 <li>Annotation files with sequence references - all
5413 elements in file are relative to sequence position</li>
5414 <li>Mac Applet users can use Alt key for group editing</li>
5420 <div align="center">
5421 <strong>2.1</strong><br> 22/8/06
5426 <li>MAFFT Multiple Alignment in default Web Service list</li>
5427 <li>DAS Feature fetching</li>
5428 <li>Hide sequences and columns</li>
5429 <li>Export Annotations and Features</li>
5430 <li>GFF file reading / writing</li>
5431 <li>Associate structures with sequences from local PDB
5433 <li>Add sequences to exisiting alignment</li>
5434 <li>Recently opened files / URL lists</li>
5435 <li>Applet can launch the full application</li>
5436 <li>Applet has transparency for features (Java 1.2
5438 <li>Applet has user defined colours parameter</li>
5439 <li>Applet can load sequences from parameter
5440 "sequence<em>x</em>"
5446 <li>Redundancy Panel reinstalled in the Applet</li>
5447 <li>Monospaced font - EPS / rescaling bug fixed</li>
5448 <li>Annotation files with sequence references bug fixed</li>
5454 <div align="center">
5455 <strong>2.08.1</strong><br> 2/5/06
5460 <li>Change case of selected region from Popup menu</li>
5461 <li>Choose to match case when searching</li>
5462 <li>Middle mouse button and mouse movement can compress /
5463 expand the visible width and height of the alignment</li>
5468 <li>Annotation Panel displays complete JNet results</li>
5474 <div align="center">
5475 <strong>2.08b</strong><br> 18/4/06
5481 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
5482 <li>Righthand label on wrapped alignments shows correct
5489 <div align="center">
5490 <strong>2.08</strong><br> 10/4/06
5495 <li>Editing can be locked to the selection area</li>
5496 <li>Keyboard editing</li>
5497 <li>Create sequence features from searches</li>
5498 <li>Precalculated annotations can be loaded onto
5500 <li>Features file allows grouping of features</li>
5501 <li>Annotation Colouring scheme added</li>
5502 <li>Smooth fonts off by default - Faster rendering</li>
5503 <li>Choose to toggle Autocalculate Consensus On/Off</li>
5508 <li>Drag & Drop fixed on Linux</li>
5509 <li>Jalview Archive file faster to load/save, sequence
5510 descriptions saved.</li>
5516 <div align="center">
5517 <strong>2.07</strong><br> 12/12/05
5522 <li>PDB Structure Viewer enhanced</li>
5523 <li>Sequence Feature retrieval and display enhanced</li>
5524 <li>Choose to output sequence start-end after sequence
5525 name for file output</li>
5526 <li>Sequence Fetcher WSDBFetch@EBI</li>
5527 <li>Applet can read feature files, PDB files and can be
5528 used for HTML form input</li>
5533 <li>HTML output writes groups and features</li>
5534 <li>Group editing is Control and mouse click</li>
5535 <li>File IO bugs</li>
5541 <div align="center">
5542 <strong>2.06</strong><br> 28/9/05
5547 <li>View annotations in wrapped mode</li>
5548 <li>More options for PCA viewer</li>
5553 <li>GUI bugs resolved</li>
5554 <li>Runs with -nodisplay from command line</li>
5560 <div align="center">
5561 <strong>2.05b</strong><br> 15/9/05
5566 <li>Choose EPS export as lineart or text</li>
5567 <li>Jar files are executable</li>
5568 <li>Can read in Uracil - maps to unknown residue</li>
5573 <li>Known OutOfMemory errors give warning message</li>
5574 <li>Overview window calculated more efficiently</li>
5575 <li>Several GUI bugs resolved</li>
5581 <div align="center">
5582 <strong>2.05</strong><br> 30/8/05
5587 <li>Edit and annotate in "Wrapped" view</li>
5592 <li>Several GUI bugs resolved</li>
5598 <div align="center">
5599 <strong>2.04</strong><br> 24/8/05
5604 <li>Hold down mouse wheel & scroll to change font
5610 <li>Improved JPred client reliability</li>
5611 <li>Improved loading of Jalview files</li>
5617 <div align="center">
5618 <strong>2.03</strong><br> 18/8/05
5623 <li>Set Proxy server name and port in preferences</li>
5624 <li>Multiple URL links from sequence ids</li>
5625 <li>User Defined Colours can have a scheme name and added
5627 <li>Choose to ignore gaps in consensus calculation</li>
5628 <li>Unix users can set default web browser</li>
5629 <li>Runs without GUI for batch processing</li>
5630 <li>Dynamically generated Web Service Menus</li>
5635 <li>InstallAnywhere download for Sparc Solaris</li>
5641 <div align="center">
5642 <strong>2.02</strong><br> 18/7/05
5648 <li>Copy & Paste order of sequences maintains
5649 alignment order.</li>
5655 <div align="center">
5656 <strong>2.01</strong><br> 12/7/05
5661 <li>Use delete key for deleting selection.</li>
5662 <li>Use Mouse wheel to scroll sequences.</li>
5663 <li>Help file updated to describe how to add alignment
5665 <li>Version and build date written to build properties
5667 <li>InstallAnywhere installation will check for updates
5668 at launch of Jalview.</li>
5673 <li>Delete gaps bug fixed.</li>
5674 <li>FileChooser sorts columns.</li>
5675 <li>Can remove groups one by one.</li>
5676 <li>Filechooser icons installed.</li>
5677 <li>Finder ignores return character when searching.
5678 Return key will initiate a search.<br>
5685 <div align="center">
5686 <strong>2.0</strong><br> 20/6/05
5691 <li>New codebase</li>