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.2.11.2.0">.1</a><br />
62 <em>31/03/2022</em></strong></td>
63 <td align="left" valign="top">
66 <!-- JAL-3973 -->Distribution Tarball includes git commit
71 <td align="left" valign="top">
74 <!-- JAL-3975 -->Keyboard mode (F2) stops working after
75 using the "Create sequence feature" dialog
78 <!-- JAL-3976 -->3D Structure chooser fails to select
79 structures from 3D-beacons and pops up a 'null' dialog
82 <!-- JAL-3973 -->Cannot build Jalview 2.11.2.0 via gradle
83 from its source tarball
85 </ul> <em>New Known Issues</em>
88 <!-- JAL-3984 -->Keyboard mode (F2) stops working after
89 using the "Text Colour" dialog
92 <!-- JAL-3873 -->Colour by->all views doesn't allow
93 colouring same structure from different views (since
97 <!-- JAL-3980 --> Sequence ID tooltip not showing during
98 long running retrieval/crossref operations (affects at least
102 <!-- JAL-3886 -->Pfam and Rfam alignment retrieval as
103 gzipped stockholm doesn't work on JalviewJS build of 2.11.2
106 <!-- JAL-3972 -->Java 11 Only: Jalview 2.11.2.0 OSX install
107 not working due to VAqua requiring
108 sun.awt.image.MultiResolutionImage
111 <!-- JAL-3981 -->Sequence Details can take a long time to be
112 displayed for heavily annotated sequences (all versions)
118 <td width="60" align="center" nowrap><strong><a
119 id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.0">.0</a><br />
120 <em>10/03/2022</em></strong></td>
121 <td align="left" valign="top">
124 <!-- JAL-3616 JAL-3551 JAL-2322 -->Support for viewing 3D
125 structures with ChimeraX and Pymol in addition to Jmol and
129 <!-- JAL-3829 -->Discover 3D structure data for sequences
130 with Uniprot references via 3D-Beacons
133 <!-- JAL-3391 -->Rank and select available structures for
134 Uniprot sequences according to number of residues in
135 structure mapped to positions involved in the alignment
138 <!-- JAL-2226 -->Structure annotation rows for all mapped
139 chains in 3D structures are included in the 'Reference
140 Annotation' for a sequence
143 <!-- JAL-1260 -->Import Genbank and EMBL format flatfiles
146 <!-- JAL-3821 -->ENA record's mol_type honoured so RNA
147 molecules imported from ENA records are shown as RNA
149 <!-- JAL-3863 -->Support for Canonical Uniprot IDs
152 <!-- JAL-3503 -->New Preferences tab for adjusting Jalview's
153 memory settings at launch
156 <!-- JAL-3881 -->Sequence IDs split on '_' as well as other
157 non-alphanumerics when discovering database references with
161 <!-- JAL-3884 -->Suppressed harmless exceptions output to
162 Console whilst discovering database references for a
166 <!-- JAL-3204 -->Updated Jalview bindings for Uniprot XML
170 <!-- JAL-3926 -->Uniprot and PDBe autosearch option is
174 <!-- JAL-3144 -->Reverted to Jalview 'classic' drop-down
175 menu for selecting which database to fetch from in sequence
179 <!-- JAL-3018 -->Updated Ensembl REST Client compatibility
180 to 15.2 and revised model organism names (rat, xenopus,
181 dmelanogaster now rattus_norvegicus, xenopus_tropicalis,
182 drosophila_melanogaster)
185 <!-- JAL-3530 -->-nowebservicediscovery command line
186 argument to prevent automatic discovery of analysis
187 webservices on launch
190 <!-- JAL-3618 -->Allow 'App' directories to be opened when
191 locating Chimera, ChimeraX or Pymol binaries via filechooser
192 opened by double clicking the Structure Preferences' path
196 <!-- JAL-3632 JAL-3633 -->support for HTTP/S access via
197 proxies that require authentication
200 <!-- JAL-3103 -->New mechanism for opening URLs with system
201 default browser (works on OSX and Linux as well as Windows)
204 <!-- JAL-3871 JAL-3874 -->Upgraded bundled version of Jmol
208 <!-- JAL-3837 -->GPL license info on splash screen and About
211 </ul> <em>Jalview Native App</em>
214 <!-- JAL-3830 -->New command line launcher scripts (.sh,
215 .ps1, .bat) usable on macOS, Linux/Unix, Windows and
216 documentation in Help. Installer wizard has option to add
217 this to PATH, or link to it in your PATH.<br /> <em>This
218 is the recommended workaround for known issue about
219 working directory preservation when running native
220 application from command line. <!-- JAL-3523 -->
223 <li>Notarized MacOS installer for compliance with latest
224 OSX releases (Monterey)</li>
226 <!-- JAL-3805 -->Uninstaller application for old
227 (InstallAnywhere based) Jalview installations removed from
231 <!-- JAL-3608 -->Options to allow user to choose the (Swing)
232 Look and Feel (LaF) used by Jalview
235 <!-- JAL-3552, JAL-3609 -->Metal LaF used to improved
236 operation on Linux Ubuntu with HiDPI display in Java 11
237 (still known issues with HiDPI screens in java 8 and 11. see
238 <a href="https://issues.jalview.org/browse/JAL-3137">JAL-3137</a>)
241 <!-- JAL-3633 -->Getdown launcher inherits HTTP/S proxy
242 configuration from jalview_properties
245 <!-- JAL- -->New Jalview Develop app - making it even easier
246 to get at Jalview's development builds
249 <!-- JAL-3594 -->New splashscreens for Jalview, Jalview Test
250 and Jalview Develop applications.
253 <!-- JAL-3728 -->Jalview logos shown for Jalview Java
254 Console and other window widgets in taskbar and dock rather
255 than anonymous 'Java' icons
257 </ul> <em>JalviewJS</em>
260 <!-- JAL-3624 -->PDB structures mapped to Uniprot Sequences
264 <!-- JAL-3208 -->setprop commandline argument reinstated for
268 <!-- JAL-3163 -->Missing message bundle keys are only
269 reported once per key (avoids excessive log output in js
273 <!-- JAL-3168 -->Feature type is included in the title of
274 the Feature Settings' Colour Chooser dialog
277 <!-- JAL-3279 -->Build details reported in About window
280 <!-- JAL-3038 JAL-3071 JAL-3263 JAL-3084 -->Numerous minor
281 GUI additions and improvements in sync with Java
284 </ul> <em>Development</em>
287 <!-- -->First integrated JalviewJS and Jalview release
290 <!-- JAL-3841,JAL-3248 -->Updated README and doc/building.md
293 <!-- JAL-3789, JAL-3679 -->Improved JalviewJS/Jalview build
294 process, added support for system package provided eclipse
297 <li>Install4j 9.0.x used for installer packaging</li>
299 <!-- JAL-3930 -->Improved use of installers for unattended
300 installation with a customizedId of "JALVIEW" in install4j's
304 <!-- JAL-3907 -->Improved compatibility of Jalview build
305 with Java 17 (next LTS target)
309 <td align="left" valign="top">
312 <!-- JAL-3674 -->Slow structure commands can block Jalview
316 <!-- JAL-3904 -->Structure window's viewer-specific menu
317 disappears when only one structure is shown (and many
318 sequences:one chain mappings are present)
321 <!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
322 the first SEQUENCE_GROUP defined
326 <!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 -->Selections not
327 propagated between Linked CDS - Protein alignments and their
328 trees (known defect from 2.11.1.3)
331 <!-- JAL-3761 -->Not all codon positions highlighted for
332 overlapping exon splice sites (e.g due to RNA slippage)
335 <!-- JAL-3794 -->X was not being recognised as the unknown
336 base in DNA sequences
339 <!-- JAL-3915 -->Removed RNAview checkbox and logic from
340 Structure Preferences
343 <!-- JAL-3583 -->Tooltip behaviour improved (slightly)
346 <!-- JAL-3162 -->Can edit a feature so that start > end
349 <!-- JAL-2848 -->Cancel from Amend Features doesn't reset a
350 modified graduated colour
353 <!-- JAL-3788 -->New View with automatic 'Show Overview'
354 preference enabled results in Null Pointer Exceptions when
355 clustal colouring is enabled
358 <!-- JAL-3275 -->Can open multiple Preferences panels
361 <!-- JAL-3633 -->Properly configure HTTPS proxy settings
365 <!-- JAL-3949 -->Standard out logging broken: messages only
366 routing to stderr and appear as a raw template
369 <!-- JAL-3739 -->Entering web service parameter values in
370 numerical field doesn't update the value of the parameter
371 until return is pressed.
374 <!-- JAL-3749 -->Resolved known issue (from 2.11.1.1)
375 concerning duplicate CDS sequences generated when protein
376 products for certain ENA records are repeatedly shown via
377 Calculate->Show Cross Refs
379 </ul> <em>JalviewJS</em>
382 <!-- JAL-3202 -->Consensus profile may include zero (rounded
383 down) percentage values causing a divide by zero
386 <!-- JAL-3762 -->JalviewJS doesn't honour arguments passed
387 via Info.args when there are arguments on the URL
390 <!-- JAL-3602 -->gradle closure-compiler not using UTF-8
393 <!-- JAL-3603 -->Annotation file fails to load from URL in
396 </ul> <em>Development</em>
400 <li>Fixed non-fatal gradle errors during build</li>
402 <!-- JAL-3745 -->Updated build.gradle for use with
408 </ul> <em>Known Issues</em>
411 <!-- JAL-3764 -->Display of RESNUM sequence features are not
412 suppressed when structures associated with a sequence are
413 viewed with an external viewer (Regression from 2.11.1
420 <td width="60" align="center" nowrap><strong><a
421 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.7">.7</a><br />
422 <em>18/01/2022</em></strong></td>
424 <td align="left" valign="top">
427 <!-- JAL-3703, JAL-3935 -->Files open in Jalview cannot be
428 updated by Jalview or other applications (Windows, other non
431 </ul> <em>Security</em>
434 <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
440 <td width="60" align="center" nowrap><strong><a
441 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
442 <em>6/01/2022</em></strong></td>
444 <td align="left" valign="top"><em>Security</em>
447 <!-- JAL-3934 -->Version bump library dependency: Log4j
454 <td width="60" align="center" nowrap><strong><a
455 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
456 <em>20/12/2021</em></strong></td>
458 <td align="left" valign="top"><em>Security</em>
461 <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
463 </ul> <em>Development</em>
465 <li>Updated building instructions</li>
470 <!-- JAL-3840 -->Occupancy calculation is incorrect for
471 alignment columns with over -1+2^32 gaps (breaking filtering
475 <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
476 scale factors being set with buggy window-managers (linux
479 </ul> <em>Development</em>
481 <li>Fixed non-fatal gradle errors during build</li>
486 <td width="60" align="center" nowrap><strong><a
487 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
488 <em>09/03/2021</em></strong></td>
489 <td align="left" valign="top"><em>Improved control of
490 Jalview's use of network services via jalview_properties</em>
493 <!-- JAL-3814 -->New .jalview_properties token controlling
494 launch of the news browser (like -nonews argument)
497 <!-- JAL-3813 -->New .jalview_properties token controlling
498 download of linkout URLs from
499 www.jalview.org/services/identifiers
502 <!-- JAL-3812 -->New .jalview_properties token controlling
503 download of BIOJSHTML templates
506 <!-- JAL-3811 -->New 'Discover Web Services' option to
507 trigger a one off JABAWS discovery if autodiscovery was
511 <td align="left" valign="top">
514 <!-- JAL-3818 -->Intermittent deadlock opening structure in
517 </ul> <em>New Known defects</em>
520 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
521 always restored from project (since 2.10.3)
524 <!-- JAL-3806 -->Selections from tree built from CDS aren't
525 propagated to Protein alignment (since 2.11.1.3)
531 <td width="60" align="center" nowrap><strong><a
532 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
533 <em>29/10/2020</em></strong></td>
534 <td align="left" valign="top">
539 <td align="left" valign="top">
542 <!-- JAL-3765 -->Find doesn't always highlight all matching
543 positions in a sequence (bug introduced in 2.11.1.2)
546 <!-- JAL-3760 -->Alignments containing one or more protein
547 sequences can be classed as nucleotide
550 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
551 sequences after alignment of protein products (known defect
552 first reported for 2.11.1.0)
555 <!-- JAL-3725 -->No tooltip or popup menu for genomic
556 features outwith CDS shown overlaid on protein
559 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
560 correctly mapped by Jalview (e.g. affects viral CDS with
561 ribosomal slippage, since 2.9.0)
564 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
568 <!-- JAL-3700 -->Selections in CDS sequence panel don't
569 always select corresponding protein sequences
572 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
573 column selection doesn't always ignore hidden columns
575 </ul> <em>Installer</em>
578 <!-- JAL-3611 -->Space character in Jalview install path on
579 Windows prevents install4j launching getdown
581 </ul> <em>Development</em>
584 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
585 version numbers in doc/building.md
591 <td width="60" align="center" nowrap><strong><a
592 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
593 <em>25/09/2020</em></strong></td>
594 <td align="left" valign="top">
598 <td align="left" valign="top">
601 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
602 "Encountered problems opening
603 https://www.jalview.org/examples/exampleFile_2_7.jvp"
609 <td width="60" align="center" nowrap><strong><a
610 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
611 <em>17/09/2020</em></strong></td>
612 <td align="left" valign="top">
615 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
616 residue in cursor mode
619 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
620 HTSJDK from 2.12 to 2.23
623 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
624 optimisations and improvements suggested by Bob Hanson and
625 improved compatibility with JalviewJS
628 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
629 alignments from Pfam and Rfam
632 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
633 import (no longer based on .gz extension)
636 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
639 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
640 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
644 <!-- JAL-3667 -->Improved warning messages, debug logging
645 and fixed Retry action when Jalview encounters errors when
646 saving or making backup files.
649 <!-- JAL-3676 -->Enhanced Jalview Java Console:
651 <li>Jalview's logging level can be configured</li>
652 <li>Copy to Clipboard Buttion</li>
656 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
657 when running on Linux (Requires Java 11+)
660 <!-- JAL-1842 JAL-3509 -->RESNUM sequence features (the
661 green ones) are not automatically displayed when associated
662 structures are displayed or for sequences retrieved from the
665 </ul> <em>Launching Jalview</em>
668 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
669 through a system property
672 <!-- JAL-3477 -->Improved built-in documentation and command
673 line help for configuring Jalview's memory
677 <td align="left" valign="top">
680 <!-- JAL-3691 -->Conservation and Quality tracks are shown
681 but not calculated and no protein or DNA score models are
682 available for tree/PCA calculation when launched with
683 Turkish language locale
686 <!-- JAL-3493 -->Escape does not clear highlights on the
687 alignment (Since Jalview 2.10.3)
690 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
691 doesn't slide selected sequences, just sequence under cursor
694 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
695 sequence under the cursor
698 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
699 multiple EMBL gene products shown for a single contig
702 <!-- JAL-3696 -->Errors encountered when processing variants
703 from VCF files yield "Error processing VCF: Format specifier
707 <!-- JAL-3697 -->Count of features not shown can be wrong
708 when there are both local and complementary features mapped
709 to the position under the cursor
712 <!-- JAL-3673 -->Sequence ID for reference sequence is
713 clipped when Right align Sequence IDs enabled
716 <!-- JAL-2983 -->Slider with negative range values not
717 rendered correctly in VAqua4 (Since 2.10.4)
720 <!-- JAL-3685 -->Single quotes not displayed correctly in
721 internationalised text for some messages and log output
724 <!-- JAL-3490 -->Find doesn't report matches that span
725 hidden gapped columns
728 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
729 panels, Alignment viewport and annotation renderer.
732 <!-- JAL-3561 -->Jalview ignores file format parameter
733 specifying output format when exporting an alignment via the
737 <!-- JAL-3667 -->Windows 10: For a minority of users, if
738 backups are not enabled, Jalview sometimes fails to
739 overwrite an existing file and raises a warning dialog. (in
740 2.11.0, and 2.11.1.0, the workaround is to try to save the
741 file again, and if that fails, delete the original file and
745 <!-- JAL-3509 -->Dragging a PDB file onto an alignment with
746 sequence features displayed causes displayed features to be
750 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
754 <!-- JAL-3741 -->References to http://www.jalview.org in
755 program and documentation
757 </ul> <em>Launching Jalview</em>
760 <!-- JAL-3718 -->Jalview application fails when launched the
761 first time for a version that has different jars to the
762 previous launched version.
764 </ul> <em>Developing Jalview</em>
767 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
768 data, causing cloverReport gradle task to fail with an
772 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
773 monitor the release channel
775 </ul> <em>New Known defects</em>
778 <!-- JAL-3748 -->CDS shown in result of submitting proteins
779 in a CDS/Protein alignment to a web service is wrong when
780 proteins share a common transcript sequence (e.g. genome of
784 <!-- JAL-3576 -->Co-located features exported and
785 re-imported are ordered differently when shown on alignment
786 and in tooltips. (Also affects v2.11.1.0)
789 <!-- JAL-3702 -->Drag and drop of alignment file onto
790 alignment window when in a HiDPI scaled mode in Linux only
791 works for the top left quadrant of the alignment window
794 <!-- JAL-3701 -->Stale build data in jalview standalone jar
795 builds (only affects 2.11.1.1 branch)
798 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
799 when alignment view restored from project (since Jalview
803 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
804 protein products for certain ENA records are repeatedly
805 shown via Calculate->Show Cross Refs
811 <td width="60" align="center" nowrap><strong><a
812 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
813 <em>22/04/2020</em></strong></td>
814 <td align="left" valign="top">
817 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
818 'virtual' codon features shown on protein (or vice versa)
819 for display in alignments, on structure views (including
820 transfer to UCSF chimera), in feature reports and for
824 <!-- JAL-3121 -->Feature attributes from VCF files can be
825 exported and re-imported as GFF3 files
828 <!-- JAL-3376 -->Capture VCF "fixed column" values
829 POS, ID, QUAL, FILTER as Feature Attributes
832 <!-- JAL-3375 -->More robust VCF numeric data field
833 validation while parsing
836 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
840 <!-- JAL-3535 -->Feature Settings dialog title includes name
844 <!-- JAL-3538 -->Font anti-aliasing in alignment views
848 <!-- JAL-3468 -->Very long feature descriptions truncated in
852 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
853 with no feature types visible
856 <!-- JAL-3574 -->Improved support for filtering feature
857 attributes with large integer values
860 <em>Jalview Installer</em>
863 <!-- JAL-3449 -->Versions for install4j and getdown and
864 installer template version reported in console (may be null
865 when Jalview launched as executable jar or via conda)
868 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and
869 higher quality background images
872 <!-- JAL-3394 -->New installer/application launcher
873 generated with install4j 8.0.4
876 <!-- JAL-3420 -->Jalview File Associations shown for Unix
880 <!-- JAL-3477 -->Improved defaults for maximum memory
881 setting when running on large memory machines
883 </ul> <em>Release processes</em>
886 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
889 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier
890 access to test-release channel builds
892 </ul> <em>Build System</em>
895 <!-- JAL-3510 -->Clover updated to 4.4.1
898 <!-- JAL-3513 -->Test code included in Clover coverage
901 </ul> <em>Groovy Scripts</em>
904 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
905 to stdout containing the consensus sequence for each
906 alignment in a Jalview session
909 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
910 genomic sequence_variant annotation from CDS as
911 missense_variant or synonymous_variant on protein products.
915 <td align="left" valign="top">
918 <!-- JAL-3581 -->Hidden sequence markers still visible when
919 'Show hidden markers' option is not ticked
922 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
923 PNG output when 'Automatically set ID width' is set in
924 jalview preferences or properties file
927 <!-- JAL-3571 -->Feature Editor dialog can be opened when
928 'Show Sequence Features' option is not ticked
931 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
932 buttons in Feature Settings dialog are clicked when no
936 <!-- JAL-3412 -->ID margins for CDS and Protein views not
937 equal when split frame is first opened
940 <!-- JAL-3296 -->Sequence position numbers in status bar not
941 correct after editing a sequence's start position
944 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
945 with annotation and exceptions thrown when only a few
946 columns shown in wrapped mode
949 <!-- JAL-3386 -->Sequence IDs missing in headless export of
950 wrapped alignment figure with annotations
953 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
954 ID fails with ClassCastException
957 <!-- JAL-3389 -->Chimera session not restored from Jalview
961 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
962 feature settings dialog also selects columns
965 <!-- JAL-3473 -->SpinnerNumberModel causes
966 IllegalArgumentException in some circumstances
969 <!-- JAL-3534 -->Multiple feature settings dialogs can be
973 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
974 alignment window is closed
977 <!-- JAL-3406 -->Credits missing some authors in Jalview
978 help documentation for 2.11.0 release
981 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
982 includes Pfam ID as sequence's accession rather than its
985 </ul> <em>Java 11 Compatibility issues</em>
988 <!-- JAL-2987 -->OSX - Can't view some search results in
989 PDB/Uniprot search panel
991 </ul> <em>Installer</em>
994 <!-- JAL-3447 -->Jalview should not create file associations
995 for 3D structure files (.pdb, .mmcif. .cif)
997 </ul> <em>Repository and Source Release</em>
1000 <!-- JAL-3474 -->removed obsolete .cvsignore files from
1004 <!-- JAL-3541 -->Clover report generation running out of
1007 </ul> <em>New Known Issues</em>
1010 <!-- JAL-3523 -->OSX - Current working directory not
1011 preserved when Jalview.app launched with parameters from
1015 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
1016 clipped in headless figure export when Right Align option
1020 <!-- JAL-3542 -->Jalview Installation type always reports
1021 'Source' in console output
1024 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail
1025 on jalview's bamboo server but run fine locally.
1031 <td width="60" align="center" nowrap><strong><a
1032 name="Jalview.2.11.0">2.11.0</a><br /> <em>04/07/2019</em></strong></td>
1033 <td align="left" valign="top">
1036 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native
1037 Application and Installers built with <a
1038 href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a>
1039 (licensed to the Jalview open source project) rather than
1043 <!-- JAL-1929 -->Jalview Launcher System to auto-configure
1044 memory settings, receive over the air updates and launch
1045 specific versions via (<a
1046 href="https://github.com/threerings/getdown">Three
1050 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations
1051 for formats supported by Jalview (including .jvp project
1055 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command
1056 line arguments and switch between different getdown channels
1059 <!-- JAL-3141 -->Backup files created when saving Jalview
1060 project or alignment files
1064 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF
1068 <!-- JAL-2753 -->Version of HTSJDK shipped with Jalview
1069 updated to version 2.12.0
1072 <!-- JAL-2620 -->Alternative genetic code tables for
1076 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0
1078 <li><strong>Enhanced visualisation and analysis
1079 of Sequence Features</strong>
1082 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
1083 implementation that allows updates) used for Sequence
1087 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
1088 features can be filtered and shaded according to any
1089 associated attributes (e.g. variant attributes from VCF
1090 file, or key-value pairs imported from column 9 of GFF
1094 <!-- JAL-2879 -->Feature Attributes and shading schemes
1095 stored and restored from Jalview Projects
1098 <!-- JAL-3334 -->Use full Sequence Ontology (via
1099 BioJava) to recognise variant features
1102 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants
1103 on peptide sequences (also coloured red by default)
1106 <!-- JAL-2792 -->Popup window to show full report for a
1107 selected sequence feature's details
1110 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient
1111 sequence feature render algorithm (Z-sort/transparency
1115 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature
1120 <!-- JAL-3205 -->Symmetric score matrices for faster tree
1121 and PCA calculations
1123 <li><strong>Principal Components Analysis Viewer</strong>
1126 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis
1127 results and Viewer state saved in Jalview Project
1130 <!-- JAL-2962 -->'Change parameters' option removed from
1131 viewer's drop-down menus
1134 <!-- JAL-2975 -->Can use shift + arrow keys to rotate
1135 PCA image incrementally
1138 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
1142 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
1144 <li><strong>Speed and Efficiency</strong>
1147 <!-- JAL-2185,JAL-3198 -->More efficient creation of
1148 selections and multiple groups when working with large
1152 <!-- JAL-3200 -->Speedier import of annotation rows when
1153 parsing Stockholm files
1156 <li><strong>User Interface</strong>
1159 <!-- JAL-2933 -->Finder panel remembers last position in
1163 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS
1164 (What you see is what is shown)<br />Only visible
1165 regions of alignment are shown by default (can be
1166 changed in user preferences)
1169 <!-- JAL-3169 -->File Chooser stays open after
1170 responding Cancel to the Overwrite Dialog
1173 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour
1174 when all sequences are hidden
1177 <!-- JAL-1244 -->Status bar shows bounds when dragging a
1178 selection region, and gap count when inserting or
1182 <!-- JAL-3132 -->Status bar updates over sequence and
1186 <!-- JAL-3093 -->Annotation tooltips and popup menus are
1187 shown when in wrapped mode
1190 <!-- JAL-3073 -->Can select columns by dragging
1191 left/right in a graph or histogram annotation
1194 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB
1198 <!-- JAL-2621 -->Cursor changes over draggable box in
1202 <!-- JAL-3181 -->Consistent ordering of links in
1203 sequence id popup menu
1206 <!-- JAL-3080 -->Red line indicating tree-cut position
1207 not shown if no subgroups are created
1210 <!-- JAL-3042 -->Removed ability to configure length of
1211 search history by right-clicking search box
1217 <!-- JAL-3232 -->Jalview Groovy Scripting Console updated to
1220 <li><strong>Java 11 Support (not yet on general
1224 <!-- -->OSX GUI integrations for App menu's 'About'
1225 entry and trapping CMD-Q
1228 </ul> <em>Deprecations</em>
1231 <!-- JAL-3035 -->DAS sequence retrieval and annotation
1232 capabilities removed from the Jalview Desktop
1235 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling
1236 and unmarshalling has been replaced by JAXB for Jalview
1237 projects and XML based data retrieval clients
1240 <!-- JAL-3311 -->Disable VAMSAS menu in preparation for
1244 <!-- -->Jalview Desktop no longer distributed via Java Web
1247 </ul> <em>Documentation</em>
1250 <!-- JAL-3003 -->Added remarks about transparent rendering
1251 effects not supported in EPS figure export
1254 <!-- JAL-2903 -->Typos in documentation for Preferences
1257 </ul> <em>Development and Release Processes</em>
1260 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated
1264 <!-- JAL-1424 -->Enhanced checks for missing and duplicated
1265 keys in Message bundles
1268 <!-- JAL-3225 -->Eclipse project configuration managed with
1272 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian Bamboo
1273 continuous integration for unattended Test Suite execution
1276 <!-- JAL-2864 -->Memory test suite to detect leaks in common
1280 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
1284 <!-- JAL-3248 -->Developer documentation migrated to
1285 markdown (with HTML rendering)
1288 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
1291 <!-- JAL-3289 -->New URLs for publishing development
1296 <td align="left" valign="top">
1299 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
1302 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
1303 superposition in Jmol fail on Windows
1306 <!-- JAL-3286 -->Blank error dialog is displayed when
1307 discovering structures for sequences with lots of PDB
1311 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export
1312 with monospaced font
1315 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
1316 Jalview project involving multiple views
1319 <!-- JAL-3164 -->Overview for complementary view in a linked
1320 CDS/Protein alignment is not updated when Hide Columns by
1321 Annotation dialog hides columns
1324 <!-- JAL-3158 -->Selection highlighting in the complement of
1325 a CDS/Protein alignment stops working after making a
1326 selection in one view, then making another selection in the
1330 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
1334 <!-- JAL-3154 -->Table Columns could be re-ordered in
1335 Feature Settings and Jalview Preferences panels
1338 <!-- JAL-2865 -->Jalview hangs when closing windows, or
1339 redrawing the overview with large alignments
1342 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
1343 region if columns were selected by dragging right-to-left
1344 and the mouse moved to the left of the first column
1347 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to
1348 a hidden column marker via scale popup menu
1351 <!-- JAL-2846 -->Error message for trying to load in invalid
1352 URLs doesn't tell users the invalid URL
1355 <!-- JAL-2816 -->Tooltips displayed for features filtered by
1359 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl
1360 during show cross references or Fetch Database References
1361 are shown in red in original view
1364 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown
1365 correctly on peptide sequence (computed variant shown as
1369 <!-- JAL-2060 -->'Graduated colour' option not offered for
1370 manually created features (where feature score is Float.NaN)
1373 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or
1374 printed when columns are hidden
1377 <!-- JAL-3082 -->Regular expression error for '(' in Select
1378 Columns by Annotation description
1381 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after
1382 dragging out of Scale or Annotation Panel
1385 <!-- JAL-3075 -->Column selection incorrect after scrolling
1389 <!-- JAL-3074 -->Left/right drag in annotation can scroll
1393 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal
1397 <!-- JAL-3002 -->Column display is out by one after Page
1398 Down, Page Up in wrapped mode
1401 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
1404 <!-- JAL-2932 -->Finder searches in minimised alignments
1407 <!-- JAL-2250 -->'Apply Colour to All Groups' not always
1408 selected on opening an alignment
1411 <!-- JAL-3180 -->'Colour by Annotation' not marked selected
1415 <!-- JAL-3201 -->Per-group Clustal colour scheme changes
1416 when different groups in the alignment are selected
1419 <!-- JAL-2717 -->Internationalised colour scheme names not
1420 shown correctly in menu
1423 <!-- JAL-3206 -->Colour by Annotation can go black at
1424 min/max threshold limit
1427 <!-- JAL-3125 -->Value input for graduated feature colour
1428 threshold gets 'unrounded'
1431 <!-- JAL-2982 -->PCA image export doesn't respect background
1435 <!-- JAL-2963 -->PCA points don't dim when rotated about y
1439 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
1442 <!-- JAL-3078 -->Cancel in Tree Font dialog resets
1443 alignment, not Tree font
1446 <!-- JAL-2964 -->Associate Tree with All Views not restored
1450 <!-- JAL-2915 -->Scrolling of split frame is sluggish if
1451 Overview shown in complementary view
1454 <!-- JAL-3313 -->Codon consensus incorrectly scaled when
1455 shown without normalisation
1458 <!-- JAL-3021 -->Sequence Details report should open
1459 positioned at top of report
1462 <!-- JAL-914 -->Help page can be opened twice
1465 <!-- JAL-3333 -->Fuzzy text in web service status menu on
1468 </ul> <em>Editing</em>
1471 <!-- JAL-2822 -->Start and End should be updated when
1472 sequence data at beginning or end of alignment added/removed
1476 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection
1477 doesn't relocate sequence features correctly when start of
1478 sequence is removed (Known defect since 2.10)
1481 <!-- JAL-2830 -->Inserting gap sequence via the Edit
1482 Sequence dialog corrupts dataset sequence
1485 <!-- JAL-868 -->Structure colours not updated when
1486 associated tree repartitions the alignment view (Regression
1489 </ul> <em>Datamodel</em>
1492 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
1493 sequence's End is greater than its length
1495 </ul> <em>Bugs fixed for Java 11 Support (not yet on general
1499 <!-- JAL-3288 -->Menus work properly in split-screen
1501 </ul> <em>New Known Defects</em>
1504 <!-- JAL-3340 -->Select columns containing feature by double
1505 clicking ignores bounds of an existing selected region
1508 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in
1509 gapped regions of protein alignment.
1512 <!-- JAL-2647 -->Input Data menu entry is greyed out when
1513 PCA View is restored from a Jalview 2.11 project
1516 <!-- JAL-3213 -->Alignment panel height can be too small
1520 <!-- JAL-3240 -->Display is incorrect after removing gapped
1521 columns within hidden columns
1524 <!-- JAL-3314 -->Rightmost selection is lost when mouse
1525 re-enters window after dragging left to select columns to
1526 left of visible region
1529 <!-- JAL-2876 -->Features coloured according to their
1530 description string and thresholded by score in earlier
1531 versions of Jalview are not shown as thresholded features in
1532 2.11. To workaround please create a Score filter instead.
1535 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't
1536 reset group visibility
1539 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in
1540 linked CDS/Protein view
1543 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1544 alignments with multiple views can close views unexpectedly
1546 </ul> <em>Java 11 Specific defects</em>
1549 <!-- JAL-3235 -->Jalview Properties file is not sorted
1550 alphabetically when saved
1556 <td width="60" nowrap>
1557 <div align="center">
1558 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1561 <td><div align="left">
1565 <!-- JAL-3101 -->Default memory for Jalview webstart and
1566 InstallAnywhere increased to 1G.
1569 <!-- JAL-247 -->Hidden sequence markers and representative
1570 sequence bolding included when exporting alignment as EPS,
1571 SVG, PNG or HTML. <em>Display is configured via the
1572 Format menu, or for command-line use via a Jalview
1573 properties file.</em>
1576 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1577 API and sequence data now imported as JSON.
1580 <!-- JAL-3065 -->Change in recommended way of starting
1581 Jalview via a Java command line: add jars in lib directory
1582 to CLASSPATH, rather than via the deprecated java.ext.dirs
1586 <em>Development</em>
1589 <!-- JAL-3047 -->Support added to execute test suite
1590 instrumented with <a href="http://openclover.org/">Open
1595 <td><div align="left">
1599 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1600 row shown in Feredoxin Structure alignment view of example
1604 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1605 annotation displayed.
1608 <!-- JAL-3107 -->Group conservation/consensus not shown
1609 for newly created group when 'Apply to all groups'
1613 <!-- JAL-3087 -->Corrupted display when switching to
1614 wrapped mode when sequence panel's vertical scrollbar is
1618 <!-- JAL-3003 -->Alignment is black in exported EPS file
1619 when sequences are selected in exported view.</em>
1622 <!-- JAL-3059 -->Groups with different coloured borders
1623 aren't rendered with correct colour.
1626 <!-- JAL-3092 -->Jalview could hang when importing certain
1627 types of knotted RNA secondary structure.
1630 <!-- JAL-3095 -->Sequence highlight and selection in
1631 trimmed VARNA 2D structure is incorrect for sequences that
1635 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1636 annotation when columns are inserted into an alignment,
1637 and when exporting as Stockholm flatfile.
1640 <!-- JAL-3053 -->Jalview annotation rows containing upper
1641 and lower-case 'E' and 'H' do not automatically get
1642 treated as RNA secondary structure.
1645 <!-- JAL-3106 -->.jvp should be used as default extension
1646 (not .jar) when saving a Jalview project file.
1649 <!-- JAL-3105 -->Mac Users: closing a window correctly
1650 transfers focus to previous window on OSX
1653 <em>Java 10 Issues Resolved</em>
1656 <!-- JAL-2988 -->OSX - Can't save new files via the File
1657 or export menus by typing in a name into the Save dialog
1661 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1662 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1663 'look and feel' which has improved compatibility with the
1664 latest version of OSX.
1670 <td width="60" nowrap>
1671 <div align="center">
1672 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1673 <em>7/06/2018</em></strong>
1676 <td><div align="left">
1680 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1681 annotation retrieved from Uniprot
1684 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1685 onto the Jalview Desktop
1689 <td><div align="left">
1693 <!-- JAL-3017 -->Cannot import features with multiple
1694 variant elements (blocks import of some Uniprot records)
1697 <!-- JAL-2997 -->Clustal files with sequence positions in
1698 right-hand column parsed correctly
1701 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1702 not alignment area in exported graphic
1705 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1706 window has input focus
1709 <!-- JAL-2992 -->Annotation panel set too high when
1710 annotation added to view (Windows)
1713 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1714 network connectivity is poor
1717 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1718 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1719 the currently open URL and links from a page viewed in
1720 Firefox or Chrome on Windows is now fully supported. If
1721 you are using Edge, only links in the page can be
1722 dragged, and with Internet Explorer, only the currently
1723 open URL in the browser can be dropped onto Jalview.</em>
1726 <em>New Known Defects</em>
1729 <!-- JAL-3083 -->Cancel option doesn't reset Colour by
1736 <td width="60" nowrap>
1737 <div align="center">
1738 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1741 <td><div align="left">
1745 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1746 for disabling automatic superposition of multiple
1747 structures and open structures in existing views
1750 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1751 ID and annotation area margins can be click-dragged to
1755 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1759 <!-- JAL-2759 -->Improved performance for large alignments
1760 and lots of hidden columns
1763 <!-- JAL-2593 -->Improved performance when rendering lots
1764 of features (particularly when transparency is disabled)
1767 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2
1768 for exchange of Jalview features and Chimera attributes
1769 made generally available
1773 <td><div align="left">
1776 <!-- JAL-2899 -->Structure and Overview aren't updated
1777 when Colour By Annotation threshold slider is adjusted
1780 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1781 overlapping alignment panel
1784 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1788 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1789 improved: CDS not handled correctly if transcript has no
1793 <!-- JAL-2321 -->Secondary structure and temperature
1794 factor annotation not added to sequence when local PDB
1795 file associated with it by drag'n'drop or structure
1799 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1800 dialog doesn't import PDB files dropped on an alignment
1803 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1804 scroll bar doesn't work for some CDS/Protein views
1807 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1808 Java 1.8u153 onwards and Java 1.9u4+.
1811 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1812 columns in annotation row
1815 <!-- JAL-2913 -->Preferences panel's ID Width control is
1816 not honored in batch mode
1819 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1820 for structures added to existing Jmol view
1823 <!-- JAL-2223 -->'View Mappings' includes duplicate
1824 entries after importing project with multiple views
1827 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1828 protein sequences via SIFTS from associated PDB entries
1829 with negative residue numbers or missing residues fails
1832 <!-- JAL-2952 -->Exception when shading sequence with
1833 negative Temperature Factor values from annotated PDB
1834 files (e.g. as generated by CONSURF)
1837 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1838 tooltip doesn't include a text description of mutation
1841 <!-- JAL-2922 -->Invert displayed features very slow when
1842 structure and/or overview windows are also shown
1845 <!-- JAL-2954 -->Selecting columns from highlighted
1846 regions very slow for alignments with large numbers of
1850 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1851 with 'StringIndexOutOfBounds'
1854 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and
1855 Feel for OSX platforms running Java 10
1858 <!-- JAL-2960 -->Adding a structure to existing structure
1859 view appears to do nothing because the view is hidden
1860 behind the alignment view
1866 <!-- JAL-2926 -->Copy consensus sequence option in applet
1867 should copy the group consensus when popup is opened on it
1873 <!-- JAL-2913 -->Fixed ID width preference is not
1877 <em>New Known Defects</em>
1880 <!-- JAL-2973 --> Exceptions occasionally raised when
1881 editing a large alignment and overview is displayed
1884 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1885 repeatedly after a series of edits even when the overview
1886 is no longer reflecting updates
1889 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1890 structures for protein subsequence (if 'Trim Retrieved
1891 Sequences' enabled) or Ensembl isoforms (Workaround in
1892 2.10.4 is to fail back to N&W mapping)
1895 <!-- JAL-2990 -->Export Annotations from File Menu with
1896 CSV option gives blank output
1902 <td width="60" nowrap>
1903 <div align="center">
1904 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br />
1905 <em>24/1/2018</em></strong>
1908 <td><div align="left">
1910 <li>Updated Certum Codesigning Certificate (Valid till
1911 30th November 2018)</li>
1914 <td><div align="left">
1919 <!-- JAL-2859-->Only one structure is loaded when
1920 several sequences and structures are selected for
1924 <!-- JAL-2851-->Alignment doesn't appear to scroll
1925 vertically via trackpad and scrollwheel
1928 <!-- JAL-2842-->Jalview hangs if up/down arrows pressed
1929 in cursor mode when cursor lies in hidden region at
1933 <!-- JAL-2827-->Helix annotation has 'notches' when
1934 scrolled into view if columns are hidden
1937 <!-- JAL-2740-->Annotation column filter can be slow to
1938 reset (ie after hitting cancel) for large numbers of
1942 <!-- JAL-2849-->User preference for disabling inclusion
1943 of sequence limits when exporting as flat file has no
1947 <!-- JAL-2679-->Reproducible cross-reference
1948 relationships when retrieving sequences from
1955 <td width="60" nowrap>
1956 <div align="center">
1957 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1960 <td><div align="left">
1964 <!-- JAL-2446 -->Faster and more efficient management and
1965 rendering of sequence features
1968 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1969 429 rate limit request hander
1972 <!-- JAL-2773 -->Structure views don't get updated unless
1973 their colours have changed
1976 <!-- JAL-2495 -->All linked sequences are highlighted for
1977 a structure mousover (Jmol) or selection (Chimera)
1980 <!-- JAL-2790 -->'Cancel' button in progress bar for
1981 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1984 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1985 view from Ensembl locus cross-references
1988 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1992 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1993 feature can be disabled
1996 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1997 PDB easier retrieval of sequences for lists of IDs
2000 <!-- JAL-2758 -->Short names for sequences retrieved from
2006 <li>Groovy interpreter updated to 2.4.12</li>
2007 <li>Example groovy script for generating a matrix of
2008 percent identity scores for current alignment.</li>
2010 <em>Testing and Deployment</em>
2013 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
2017 <td><div align="left">
2021 <!-- JAL-2643 -->Pressing tab after updating the colour
2022 threshold text field doesn't trigger an update to the
2026 <!-- JAL-2682 -->Race condition when parsing sequence ID
2030 <!-- JAL-2608 -->Overview windows are also closed when
2031 alignment window is closed
2034 <!-- JAL-2548 -->Export of features doesn't always respect
2038 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
2039 takes a long time in Cursor mode
2045 <!-- JAL-2777 -->Structures with whitespace chainCode
2046 cannot be viewed in Chimera
2049 <!-- JAL-2728 -->Protein annotation panel too high in
2053 <!-- JAL-2757 -->Can't edit the query after the server
2054 error warning icon is shown in Uniprot and PDB Free Text
2058 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
2061 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
2064 <!-- JAL-2739 -->Hidden column marker in last column not
2065 rendered when switching back from Wrapped to normal view
2068 <!-- JAL-2768 -->Annotation display corrupted when
2069 scrolling right in unwapped alignment view
2072 <!-- JAL-2542 -->Existing features on subsequence
2073 incorrectly relocated when full sequence retrieved from
2077 <!-- JAL-2733 -->Last reported memory still shown when
2078 Desktop->Show Memory is unticked (OSX only)
2081 <!-- JAL-2658 -->Amend Features dialog doesn't allow
2082 features of same type and group to be selected for
2086 <!-- JAL-2524 -->Jalview becomes sluggish in wide
2087 alignments when hidden columns are present
2090 <!-- JAL-2392 -->Jalview freezes when loading and
2091 displaying several structures
2094 <!-- JAL-2732 -->Black outlines left after resizing or
2098 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
2099 within the Jalview desktop on OSX
2102 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
2103 when in wrapped alignment mode
2106 <!-- JAL-2636 -->Scale mark not shown when close to right
2107 hand end of alignment
2110 <!-- JAL-2684 -->Pairwise alignment of selected regions of
2111 each selected sequence do not have correct start/end
2115 <!-- JAL-2793 -->Alignment ruler height set incorrectly
2116 after canceling the Alignment Window's Font dialog
2119 <!-- JAL-2036 -->Show cross-references not enabled after
2120 restoring project until a new view is created
2123 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
2124 URL links appears when only default EMBL-EBI link is
2125 configured (since 2.10.2b2)
2128 <!-- JAL-2775 -->Overview redraws whole window when box
2129 position is adjusted
2132 <!-- JAL-2225 -->Structure viewer doesn't map all chains
2133 in a multi-chain structure when viewing alignment
2134 involving more than one chain (since 2.10)
2137 <!-- JAL-2811 -->Double residue highlights in cursor mode
2138 if new selection moves alignment window
2141 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
2142 arrow key in cursor mode to pass hidden column marker
2145 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
2146 that produces correctly annotated transcripts and products
2149 <!-- JAL-2776 -->Toggling a feature group after first time
2150 doesn't update associated structure view
2153 <em>Applet</em><br />
2156 <!-- JAL-2687 -->Concurrent modification exception when
2157 closing alignment panel
2160 <em>BioJSON</em><br />
2163 <!-- JAL-2546 -->BioJSON export does not preserve
2164 non-positional features
2167 <em>New Known Issues</em>
2170 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
2171 sequence features correctly (for many previous versions of
2175 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
2176 using cursor in wrapped panel other than top
2179 <!-- JAL-2791 -->Select columns containing feature ignores
2180 graduated colour threshold
2183 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
2184 always preserve numbering and sequence features
2187 <em>Known Java 9 Issues</em>
2190 <!-- JAL-2902 -->Groovy Console very slow to open and is
2191 not responsive when entering characters (Webstart, Java
2198 <td width="60" nowrap>
2199 <div align="center">
2200 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
2201 <em>2/10/2017</em></strong>
2204 <td><div align="left">
2205 <em>New features in Jalview Desktop</em>
2208 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API
2212 <!-- JAL-2745 -->HTTPS used for all connections to
2217 <td><div align="left"></div></td>
2220 <td width="60" nowrap>
2221 <div align="center">
2222 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
2223 <em>7/9/2017</em></strong>
2226 <td><div align="left">
2230 <!-- JAL-2588 -->Show gaps in overview window by colouring
2231 in grey (sequences used to be coloured grey, and gaps were
2235 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
2239 <!-- JAL-2587 -->Overview updates immediately on increase
2240 in size and progress bar shown as higher resolution
2241 overview is recalculated
2246 <td><div align="left">
2250 <!-- JAL-2664 -->Overview window redraws every hidden
2251 column region row by row
2254 <!-- JAL-2681 -->duplicate protein sequences shown after
2255 retrieving Ensembl crossrefs for sequences from Uniprot
2258 <!-- JAL-2603 -->Overview window throws NPE if show boxes
2259 format setting is unticked
2262 <!-- JAL-2610 -->Groups are coloured wrongly in overview
2263 if group has show boxes format setting unticked
2266 <!-- JAL-2672,JAL-2665 -->Redraw problems when
2267 autoscrolling whilst dragging current selection group to
2268 include sequences and columns not currently displayed
2271 <!-- JAL-2691 -->Not all chains are mapped when multimeric
2272 assemblies are imported via CIF file
2275 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
2276 displayed when threshold or conservation colouring is also
2280 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
2284 <!-- JAL-2673 -->Jalview continues to scroll after
2285 dragging a selected region off the visible region of the
2289 <!-- JAL-2724 -->Cannot apply annotation based
2290 colourscheme to all groups in a view
2293 <!-- JAL-2511 -->IDs don't line up with sequences
2294 initially after font size change using the Font chooser or
2301 <td width="60" nowrap>
2302 <div align="center">
2303 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
2306 <td><div align="left">
2307 <em>Calculations</em>
2311 <!-- JAL-1933 -->Occupancy annotation row shows number of
2312 ungapped positions in each column of the alignment.
2315 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
2316 a calculation dialog box
2319 <!-- JAL-2379 -->Revised implementation of PCA for speed
2320 and memory efficiency (~30x faster)
2323 <!-- JAL-2403 -->Revised implementation of sequence
2324 similarity scores as used by Tree, PCA, Shading Consensus
2325 and other calculations
2328 <!-- JAL-2416 -->Score matrices are stored as resource
2329 files within the Jalview codebase
2332 <!-- JAL-2500 -->Trees computed on Sequence Feature
2333 Similarity may have different topology due to increased
2340 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
2341 model for alignments and groups
2344 <!-- JAL-384 -->Custom shading schemes created via groovy
2351 <!-- JAL-2526 -->Efficiency improvements for interacting
2352 with alignment and overview windows
2355 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
2359 <!-- JAL-2388 -->Hidden columns and sequences can be
2363 <!-- JAL-2611 -->Click-drag in visible area allows fine
2364 adjustment of visible position
2368 <em>Data import/export</em>
2371 <!-- JAL-2535 -->Posterior probability annotation from
2372 Stockholm files imported as sequence associated annotation
2375 <!-- JAL-2507 -->More robust per-sequence positional
2376 annotation input/output via stockholm flatfile
2379 <!-- JAL-2533 -->Sequence names don't include file
2380 extension when importing structure files without embedded
2381 names or PDB accessions
2384 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
2385 format sequence substitution matrices
2388 <em>User Interface</em>
2391 <!-- JAL-2447 --> Experimental Features Checkbox in
2392 Desktop's Tools menu to hide or show untested features in
2396 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
2397 via Overview or sequence motif search operations
2400 <!-- JAL-2547 -->Amend sequence features dialog box can be
2401 opened by double clicking gaps within sequence feature
2405 <!-- JAL-1476 -->Status bar message shown when not enough
2406 aligned positions were available to create a 3D structure
2410 <em>3D Structure</em>
2413 <!-- JAL-2430 -->Hidden regions in alignment views are not
2414 coloured in linked structure views
2417 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
2418 file-based command exchange
2421 <!-- JAL-2375 -->Structure chooser automatically shows
2422 Cached Structures rather than querying the PDBe if
2423 structures are already available for sequences
2426 <!-- JAL-2520 -->Structures imported via URL are cached in
2427 the Jalview project rather than downloaded again when the
2428 project is reopened.
2431 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
2432 to transfer Chimera's structure attributes as Jalview
2433 features, and vice-versa (<strong>Experimental
2437 <em>Web Services</em>
2440 <!-- JAL-2549 -->Updated JABAWS client to v2.2
2443 <!-- JAL-2335 -->Filter non-standard amino acids and
2444 nucleotides when submitting to AACon and other MSA
2448 <!-- JAL-2316, -->URLs for viewing database
2449 cross-references provided by identifiers.org and the
2450 EMBL-EBI's MIRIAM DB
2457 <!-- JAL-2344 -->FileFormatI interface for describing and
2458 identifying file formats (instead of String constants)
2461 <!-- JAL-2228 -->FeatureCounter script refactored for
2462 efficiency when counting all displayed features (not
2463 backwards compatible with 2.10.1)
2466 <em>Example files</em>
2469 <!-- JAL-2631 -->Graduated feature colour style example
2470 included in the example feature file
2473 <em>Documentation</em>
2476 <!-- JAL-2339 -->Release notes reformatted for readability
2477 with the built-in Java help viewer
2480 <!-- JAL-1644 -->Find documentation updated with 'search
2481 sequence description' option
2487 <!-- JAL-2485, -->External service integration tests for
2488 Uniprot REST Free Text Search Client
2491 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
2494 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
2499 <td><div align="left">
2500 <em>Calculations</em>
2503 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
2504 matrix - C->R should be '-3'<br />Old matrix restored
2505 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
2507 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
2508 Jalview's treatment of gaps in PCA and substitution matrix
2509 based Tree calculations.<br /> <br />In earlier versions
2510 of Jalview, gaps matching gaps were penalised, and gaps
2511 matching non-gaps penalised even more. In the PCA
2512 calculation, gaps were actually treated as non-gaps - so
2513 different costs were applied, which meant Jalview's PCAs
2514 were different to those produced by SeqSpace.<br />Jalview
2515 now treats gaps in the same way as SeqSpace (ie it scores
2516 them as 0). <br /> <br />Enter the following in the
2517 Groovy console to restore pre-2.10.2 behaviour:<br />
2518 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
2519 // for 2.10.1 mode <br />
2520 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
2521 // to restore 2.10.2 mode <br /> <br /> <em>Note:
2522 these settings will affect all subsequent tree and PCA
2523 calculations (not recommended)</em></li>
2525 <!-- JAL-2424 -->Fixed off-by-one bug that affected
2526 scaling of branch lengths for trees computed using
2527 Sequence Feature Similarity.
2530 <!-- JAL-2377 -->PCA calculation could hang when
2531 generating output report when working with highly
2532 redundant alignments
2535 <!-- JAL-2544 --> Sort by features includes features to
2536 right of selected region when gaps present on right-hand
2540 <em>User Interface</em>
2543 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2544 doesn't reselect a specific sequence's associated
2545 annotation after it was used for colouring a view
2548 <!-- JAL-2419 -->Current selection lost if popup menu
2549 opened on a region of alignment without groups
2552 <!-- JAL-2374 -->Popup menu not always shown for regions
2553 of an alignment with overlapping groups
2556 <!-- JAL-2310 -->Finder double counts if both a sequence's
2557 name and description match
2560 <!-- JAL-2370 -->Hiding column selection containing two
2561 hidden regions results in incorrect hidden regions
2564 <!-- JAL-2386 -->'Apply to all groups' setting when
2565 changing colour does not apply Conservation slider value
2569 <!-- JAL-2373 -->Percentage identity and conservation menu
2570 items do not show a tick or allow shading to be disabled
2573 <!-- JAL-2385 -->Conservation shading or PID threshold
2574 lost when base colourscheme changed if slider not visible
2577 <!-- JAL-2547 -->Sequence features shown in tooltip for
2578 gaps before start of features
2581 <!-- JAL-2623 -->Graduated feature colour threshold not
2582 restored to UI when feature colour is edited
2585 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2586 a time when scrolling vertically in wrapped mode.
2589 <!-- JAL-2630 -->Structure and alignment overview update
2590 as graduate feature colour settings are modified via the
2594 <!-- JAL-2034 -->Overview window doesn't always update
2595 when a group defined on the alignment is resized
2598 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2599 wrapped view result in positional status updates
2603 <!-- JAL-2563 -->Status bar doesn't show position for
2604 ambiguous amino acid and nucleotide symbols
2607 <!-- JAL-2602 -->Copy consensus sequence failed if
2608 alignment included gapped columns
2611 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2612 widgets don't permanently disappear
2615 <!-- JAL-2503 -->Cannot select or filter quantitative
2616 annotation that are shown only as column labels (e.g.
2617 T-Coffee column reliability scores)
2620 <!-- JAL-2594 -->Exception thrown if trying to create a
2621 sequence feature on gaps only
2624 <!-- JAL-2504 -->Features created with 'New feature'
2625 button from a Find inherit previously defined feature type
2626 rather than the Find query string
2629 <!-- JAL-2423 -->incorrect title in output window when
2630 exporting tree calculated in Jalview
2633 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2634 and then revealing them reorders sequences on the
2638 <!-- JAL-964 -->Group panel in sequence feature settings
2639 doesn't update to reflect available set of groups after
2640 interactively adding or modifying features
2643 <!-- JAL-2225 -->Sequence Database chooser unusable on
2647 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2648 only excluded gaps in current sequence and ignored
2655 <!-- JAL-2421 -->Overview window visible region moves
2656 erratically when hidden rows or columns are present
2659 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2660 Structure Viewer's colour menu don't correspond to
2664 <!-- JAL-2405 -->Protein specific colours only offered in
2665 colour and group colour menu for protein alignments
2668 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2669 reflect currently selected view or group's shading
2673 <!-- JAL-2624 -->Feature colour thresholds not respected
2674 when rendered on overview and structures when opacity at
2678 <!-- JAL-2589 -->User defined gap colour not shown in
2679 overview when features overlaid on alignment
2682 <!-- JAL-2567 -->Feature settings for different views not
2683 recovered correctly from Jalview project file
2686 <!-- JAL-2256 -->Feature colours in overview when first
2687 opened (automatically via preferences) are different to
2688 the main alignment panel
2691 <em>Data import/export</em>
2694 <!-- JAL-2576 -->Very large alignments take a long time to
2698 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2699 added after a sequence was imported are not written to
2703 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2704 when importing RNA secondary structure via Stockholm
2707 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2708 not shown in correct direction for simple pseudoknots
2711 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2712 with lightGray or darkGray via features file (but can
2716 <!-- JAL-2383 -->Above PID colour threshold not recovered
2717 when alignment view imported from project
2720 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2721 structure and sequences extracted from structure files
2722 imported via URL and viewed in Jmol
2725 <!-- JAL-2520 -->Structures loaded via URL are saved in
2726 Jalview Projects rather than fetched via URL again when
2727 the project is loaded and the structure viewed
2730 <em>Web Services</em>
2733 <!-- JAL-2519 -->EnsemblGenomes example failing after
2734 release of Ensembl v.88
2737 <!-- JAL-2366 -->Proxy server address and port always
2738 appear enabled in Preferences->Connections
2741 <!-- JAL-2461 -->DAS registry not found exceptions
2742 removed from console output
2745 <!-- JAL-2582 -->Cannot retrieve protein products from
2746 Ensembl by Peptide ID
2749 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2750 created from SIFTs, and spurious 'Couldn't open structure
2751 in Chimera' errors raised after April 2017 update (problem
2752 due to 'null' string rather than empty string used for
2753 residues with no corresponding PDB mapping).
2756 <em>Application UI</em>
2759 <!-- JAL-2361 -->User Defined Colours not added to Colour
2763 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2764 case' residues (button in colourscheme editor debugged and
2765 new documentation and tooltips added)
2768 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2769 doesn't restore group-specific text colour thresholds
2772 <!-- JAL-2243 -->Feature settings panel does not update as
2773 new features are added to alignment
2776 <!-- JAL-2532 -->Cancel in feature settings reverts
2777 changes to feature colours via the Amend features dialog
2780 <!-- JAL-2506 -->Null pointer exception when attempting to
2781 edit graduated feature colour via amend features dialog
2785 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2786 selection menu changes colours of alignment views
2789 <!-- JAL-2426 -->Spurious exceptions in console raised
2790 from alignment calculation workers after alignment has
2794 <!-- JAL-1608 -->Typo in selection popup menu - Create
2795 groups now 'Create Group'
2798 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2799 Create/Undefine group doesn't always work
2802 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2803 shown again after pressing 'Cancel'
2806 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2807 adjusts start position in wrap mode
2810 <!-- JAL-2563 -->Status bar doesn't show positions for
2811 ambiguous amino acids
2814 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2815 CDS/Protein view after CDS sequences added for aligned
2819 <!-- JAL-2592 -->User defined colourschemes called 'User
2820 Defined' don't appear in Colours menu
2826 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2827 score models doesn't always result in an updated PCA plot
2830 <!-- JAL-2442 -->Features not rendered as transparent on
2831 overview or linked structure view
2834 <!-- JAL-2372 -->Colour group by conservation doesn't
2838 <!-- JAL-2517 -->Hitting Cancel after applying
2839 user-defined colourscheme doesn't restore original
2846 <!-- JAL-2314 -->Unit test failure:
2847 jalview.ws.jabaws.RNAStructExportImport setup fails
2850 <!-- JAL-2307 -->Unit test failure:
2851 jalview.ws.sifts.SiftsClientTest due to compatibility
2852 problems with deep array comparison equality asserts in
2853 successive versions of TestNG
2856 <!-- JAL-2479 -->Relocated StructureChooserTest and
2857 ParameterUtilsTest Unit tests to Network suite
2860 <em>New Known Issues</em>
2863 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2864 phase after a sequence motif find operation
2867 <!-- JAL-2550 -->Importing annotation file with rows
2868 containing just upper and lower case letters are
2869 interpreted as WUSS RNA secondary structure symbols
2872 <!-- JAL-2590 -->Cannot load and display Newick trees
2873 reliably from eggnog Ortholog database
2876 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2877 containing features of type Highlight' when 'B' is pressed
2878 to mark columns containing highlighted regions.
2881 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2882 doesn't always add secondary structure annotation.
2887 <td width="60" nowrap>
2888 <div align="center">
2889 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2892 <td><div align="left">
2896 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2897 for all consensus calculations
2900 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2903 <li>Updated Jalview's Certum code signing certificate
2906 <em>Application</em>
2909 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2910 set of database cross-references, sorted alphabetically
2913 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2914 from database cross references. Users with custom links
2915 will receive a <a href="webServices/urllinks.html#warning">warning
2916 dialog</a> asking them to update their preferences.
2919 <!-- JAL-2287-->Cancel button and escape listener on
2920 dialog warning user about disconnecting Jalview from a
2924 <!-- JAL-2320-->Jalview's Chimera control window closes if
2925 the Chimera it is connected to is shut down
2928 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2929 columns menu item to mark columns containing highlighted
2930 regions (e.g. from structure selections or results of a
2934 <!-- JAL-2284-->Command line option for batch-generation
2935 of HTML pages rendering alignment data with the BioJS
2945 <!-- JAL-2286 -->Columns with more than one modal residue
2946 are not coloured or thresholded according to percent
2947 identity (first observed in Jalview 2.8.2)
2950 <!-- JAL-2301 -->Threonine incorrectly reported as not
2954 <!-- JAL-2318 -->Updates to documentation pages (above PID
2955 threshold, amino acid properties)
2958 <!-- JAL-2292 -->Lower case residues in sequences are not
2959 reported as mapped to residues in a structure file in the
2963 <!--JAL-2324 -->Identical features with non-numeric scores
2964 could be added multiple times to a sequence
2967 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2968 bond features shown as two highlighted residues rather
2969 than a range in linked structure views, and treated
2970 correctly when selecting and computing trees from features
2973 <!-- JAL-2281-->Custom URL links for database
2974 cross-references are matched to database name regardless
2979 <em>Application</em>
2982 <!-- JAL-2282-->Custom URL links for specific database
2983 names without regular expressions also offer links from
2987 <!-- JAL-2315-->Removing a single configured link in the
2988 URL links pane in Connections preferences doesn't actually
2989 update Jalview configuration
2992 <!-- JAL-2272-->CTRL-Click on a selected region to open
2993 the alignment area popup menu doesn't work on El-Capitan
2996 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2997 files with similarly named sequences if dropped onto the
3001 <!-- JAL-2312 -->Additional mappings are shown for PDB
3002 entries where more chains exist in the PDB accession than
3003 are reported in the SIFTS file
3006 <!-- JAL-2317-->Certain structures do not get mapped to
3007 the structure view when displayed with Chimera
3010 <!-- JAL-2317-->No chains shown in the Chimera view
3011 panel's View->Show Chains submenu
3014 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
3015 work for wrapped alignment views
3018 <!--JAL-2197 -->Rename UI components for running JPred
3019 predictions from 'JNet' to 'JPred'
3022 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
3023 corrupted when annotation panel vertical scroll is not at
3024 first annotation row
3027 <!--JAL-2332 -->Attempting to view structure for Hen
3028 lysozyme results in a PDB Client error dialog box
3031 <!-- JAL-2319 -->Structure View's mapping report switched
3032 ranges for PDB and sequence for SIFTS
3035 SIFTS 'Not_Observed' residues mapped to non-existant
3039 <!-- <em>New Known Issues</em>
3046 <td width="60" nowrap>
3047 <div align="center">
3048 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
3049 <em>25/10/2016</em></strong>
3052 <td><em>Application</em>
3054 <li>3D Structure chooser opens with 'Cached structures'
3055 view if structures already loaded</li>
3056 <li>Progress bar reports models as they are loaded to
3057 structure views</li>
3063 <li>Colour by conservation always enabled and no tick
3064 shown in menu when BLOSUM or PID shading applied</li>
3065 <li>FER1_ARATH and FER2_ARATH labels were switched in
3066 example sequences/projects/trees</li>
3068 <em>Application</em>
3070 <li>Jalview projects with views of local PDB structure
3071 files saved on Windows cannot be opened on OSX</li>
3072 <li>Multiple structure views can be opened and superposed
3073 without timeout for structures with multiple models or
3074 multiple sequences in alignment</li>
3075 <li>Cannot import or associated local PDB files without a
3076 PDB ID HEADER line</li>
3077 <li>RMSD is not output in Jmol console when superposition
3079 <li>Drag and drop of URL from Browser fails for Linux and
3080 OSX versions earlier than El Capitan</li>
3081 <li>ENA client ignores invalid content from ENA server</li>
3082 <li>Exceptions are not raised in console when ENA client
3083 attempts to fetch non-existent IDs via Fetch DB Refs UI
3085 <li>Exceptions are not raised in console when a new view
3086 is created on the alignment</li>
3087 <li>OSX right-click fixed for group selections: CMD-click
3088 to insert/remove gaps in groups and CTRL-click to open group
3091 <em>Build and deployment</em>
3093 <li>URL link checker now copes with multi-line anchor
3096 <em>New Known Issues</em>
3098 <li>Drag and drop from URL links in browsers do not work
3105 <td width="60" nowrap>
3106 <div align="center">
3107 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
3110 <td><em>General</em>
3113 <!-- JAL-2124 -->Updated Spanish translations.
3116 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
3117 for importing structure data to Jalview. Enables mmCIF and
3121 <!-- JAL-192 --->Alignment ruler shows positions relative to
3125 <!-- JAL-2202 -->Position/residue shown in status bar when
3126 mousing over sequence associated annotation
3129 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
3133 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
3134 '()', canonical '[]' and invalid '{}' base pair populations
3138 <!-- JAL-2092 -->Feature settings popup menu options for
3139 showing or hiding columns containing a feature
3142 <!-- JAL-1557 -->Edit selected group by double clicking on
3143 group and sequence associated annotation labels
3146 <!-- JAL-2236 -->Sequence name added to annotation label in
3147 select/hide columns by annotation and colour by annotation
3151 </ul> <em>Application</em>
3154 <!-- JAL-2050-->Automatically hide introns when opening a
3155 gene/transcript view
3158 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
3162 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
3163 structure mappings with the EMBL-EBI PDBe SIFTS database
3166 <!-- JAL-2079 -->Updated download sites used for Rfam and
3167 Pfam sources to xfam.org
3170 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
3173 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
3174 over sequences in Jalview
3177 <!-- JAL-2027-->Support for reverse-complement coding
3178 regions in ENA and EMBL
3181 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
3182 for record retrieval via ENA rest API
3185 <!-- JAL-2027 -->Support for ENA CDS records with reverse
3189 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
3190 groovy script execution
3193 <!-- JAL-1812 -->New 'execute Groovy script' option in an
3194 alignment window's Calculate menu
3197 <!-- JAL-1812 -->Allow groovy scripts that call
3198 Jalview.getAlignFrames() to run in headless mode
3201 <!-- JAL-2068 -->Support for creating new alignment
3202 calculation workers from groovy scripts
3205 <!-- JAL-1369 --->Store/restore reference sequence in
3209 <!-- JAL-1803 -->Chain codes for a sequence's PDB
3210 associations are now saved/restored from project
3213 <!-- JAL-1993 -->Database selection dialog always shown
3214 before sequence fetcher is opened
3217 <!-- JAL-2183 -->Double click on an entry in Jalview's
3218 database chooser opens a sequence fetcher
3221 <!-- JAL-1563 -->Free-text search client for UniProt using
3222 the UniProt REST API
3225 <!-- JAL-2168 -->-nonews command line parameter to prevent
3226 the news reader opening
3229 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
3230 querying stored in preferences
3233 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
3237 <!-- JAL-1977-->Tooltips shown on database chooser
3240 <!-- JAL-391 -->Reverse complement function in calculate
3241 menu for nucleotide sequences
3244 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
3245 and feature counts preserves alignment ordering (and
3246 debugged for complex feature sets).
3249 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
3250 viewing structures with Jalview 2.10
3253 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
3254 genome, transcript CCDS and gene ids via the Ensembl and
3255 Ensembl Genomes REST API
3258 <!-- JAL-2049 -->Protein sequence variant annotation
3259 computed for 'sequence_variant' annotation on CDS regions
3263 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
3267 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
3268 Ref Fetcher fails to match, or otherwise updates sequence
3269 data from external database records.
3272 <!-- JAL-2154 -->Revised Jalview Project format for
3273 efficient recovery of sequence coding and alignment
3274 annotation relationships.
3276 </ul> <!-- <em>Applet</em>
3287 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
3291 <!-- JAL-2018-->Export features in Jalview format (again)
3292 includes graduated colourschemes
3295 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
3296 working with big alignments and lots of hidden columns
3299 <!-- JAL-2053-->Hidden column markers not always rendered
3300 at right of alignment window
3303 <!-- JAL-2067 -->Tidied up links in help file table of
3307 <!-- JAL-2072 -->Feature based tree calculation not shown
3311 <!-- JAL-2075 -->Hidden columns ignored during feature
3312 based tree calculation
3315 <!-- JAL-2065 -->Alignment view stops updating when show
3316 unconserved enabled for group on alignment
3319 <!-- JAL-2086 -->Cannot insert gaps into sequence when
3323 <!-- JAL-2146 -->Alignment column in status incorrectly
3324 shown as "Sequence position" when mousing over
3328 <!-- JAL-2099 -->Incorrect column numbers in ruler when
3329 hidden columns present
3332 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
3333 user created annotation added to alignment
3336 <!-- JAL-1841 -->RNA Structure consensus only computed for
3337 '()' base pair annotation
3340 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
3341 in zero scores for all base pairs in RNA Structure
3345 <!-- JAL-2174-->Extend selection with columns containing
3349 <!-- JAL-2275 -->Pfam format writer puts extra space at
3350 beginning of sequence
3353 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
3357 <!-- JAL-2238 -->Cannot create groups on an alignment from
3358 from a tree when t-coffee scores are shown
3361 <!-- JAL-1836,1967 -->Cannot import and view PDB
3362 structures with chains containing negative resnums (4q4h)
3365 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
3369 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
3370 to Clustal, PIR and PileUp output
3373 <!-- JAL-2008 -->Reordering sequence features that are
3374 not visible causes alignment window to repaint
3377 <!-- JAL-2006 -->Threshold sliders don't work in
3378 graduated colour and colour by annotation row for e-value
3379 scores associated with features and annotation rows
3382 <!-- JAL-1797 -->amino acid physicochemical conservation
3383 calculation should be case independent
3386 <!-- JAL-2173 -->Remove annotation also updates hidden
3390 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
3391 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
3392 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
3395 <!-- JAL-2065 -->Null pointer exceptions and redraw
3396 problems when reference sequence defined and 'show
3397 non-conserved' enabled
3400 <!-- JAL-1306 -->Quality and Conservation are now shown on
3401 load even when Consensus calculation is disabled
3404 <!-- JAL-1932 -->Remove right on penultimate column of
3405 alignment does nothing
3408 <em>Application</em>
3411 <!-- JAL-1552-->URLs and links can't be imported by
3412 drag'n'drop on OSX when launched via webstart (note - not
3413 yet fixed for El Capitan)
3416 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
3417 output when running on non-gb/us i18n platforms
3420 <!-- JAL-1944 -->Error thrown when exporting a view with
3421 hidden sequences as flat-file alignment
3424 <!-- JAL-2030-->InstallAnywhere distribution fails when
3428 <!-- JAL-2080-->Jalview very slow to launch via webstart
3429 (also hotfix for 2.9.0b2)
3432 <!-- JAL-2085 -->Cannot save project when view has a
3433 reference sequence defined
3436 <!-- JAL-1011 -->Columns are suddenly selected in other
3437 alignments and views when revealing hidden columns
3440 <!-- JAL-1989 -->Hide columns not mirrored in complement
3441 view in a cDNA/Protein splitframe
3444 <!-- JAL-1369 -->Cannot save/restore representative
3445 sequence from project when only one sequence is
3449 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
3450 in Structure Chooser
3453 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
3454 structure consensus didn't refresh annotation panel
3457 <!-- JAL-1962 -->View mapping in structure view shows
3458 mappings between sequence and all chains in a PDB file
3461 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
3462 dialogs format columns correctly, don't display array
3463 data, sort columns according to type
3466 <!-- JAL-1975 -->Export complete shown after destination
3467 file chooser is cancelled during an image export
3470 <!-- JAL-2025 -->Error when querying PDB Service with
3471 sequence name containing special characters
3474 <!-- JAL-2024 -->Manual PDB structure querying should be
3478 <!-- JAL-2104 -->Large tooltips with broken HTML
3479 formatting don't wrap
3482 <!-- JAL-1128 -->Figures exported from wrapped view are
3483 truncated so L looks like I in consensus annotation
3486 <!-- JAL-2003 -->Export features should only export the
3487 currently displayed features for the current selection or
3491 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
3492 after fetching cross-references, and restoring from
3496 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
3497 followed in the structure viewer
3500 <!-- JAL-2163 -->Titles for individual alignments in
3501 splitframe not restored from project
3504 <!-- JAL-2145 -->missing autocalculated annotation at
3505 trailing end of protein alignment in transcript/product
3506 splitview when pad-gaps not enabled by default
3509 <!-- JAL-1797 -->amino acid physicochemical conservation
3513 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
3514 article has been read (reopened issue due to
3515 internationalisation problems)
3518 <!-- JAL-1960 -->Only offer PDB structures in structure
3519 viewer based on sequence name, PDB and UniProt
3524 <!-- JAL-1976 -->No progress bar shown during export of
3528 <!-- JAL-2213 -->Structures not always superimposed after
3529 multiple structures are shown for one or more sequences.
3532 <!-- JAL-1370 -->Reference sequence characters should not
3533 be replaced with '.' when 'Show unconserved' format option
3537 <!-- JAL-1823 -->Cannot specify chain code when entering
3538 specific PDB id for sequence
3541 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3542 'Export hidden sequences' is enabled, but 'export hidden
3543 columns' is disabled.
3546 <!--JAL-2026-->Best Quality option in structure chooser
3547 selects lowest rather than highest resolution structures
3551 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3552 to sequence mapping in 'View Mappings' report
3555 <!-- JAL-2284 -->Unable to read old Jalview projects that
3556 contain non-XML data added after Jalvew wrote project.
3559 <!-- JAL-2118 -->Newly created annotation row reorders
3560 after clicking on it to create new annotation for a
3564 <!-- JAL-1980 -->Null Pointer Exception raised when
3565 pressing Add on an orphaned cut'n'paste window.
3567 <!-- may exclude, this is an external service stability issue JAL-1941
3568 -- > RNA 3D structure not added via DSSR service</li> -->
3573 <!-- JAL-2151 -->Incorrect columns are selected when
3574 hidden columns present before start of sequence
3577 <!-- JAL-1986 -->Missing dependencies on applet pages
3581 <!-- JAL-1947 -->Overview pixel size changes when
3582 sequences are hidden in applet
3585 <!-- JAL-1996 -->Updated instructions for applet
3586 deployment on examples pages.
3593 <td width="60" nowrap>
3594 <div align="center">
3595 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3596 <em>16/10/2015</em></strong>
3599 <td><em>General</em>
3601 <li>Time stamps for signed Jalview application and applet
3606 <em>Application</em>
3608 <li>Duplicate group consensus and conservation rows
3609 shown when tree is partitioned</li>
3610 <li>Erratic behaviour when tree partitions made with
3611 multiple cDNA/Protein split views</li>
3617 <td width="60" nowrap>
3618 <div align="center">
3619 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3620 <em>8/10/2015</em></strong>
3623 <td><em>General</em>
3625 <li>Updated Spanish translations of localized text for
3627 </ul> <em>Application</em>
3629 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3630 <li>Signed OSX InstallAnywhere installer<br></li>
3631 <li>Support for per-sequence based annotations in BioJSON</li>
3632 </ul> <em>Applet</em>
3634 <li>Split frame example added to applet examples page</li>
3635 </ul> <em>Build and Deployment</em>
3638 <!-- JAL-1888 -->New ant target for running Jalview's test
3646 <li>Mapping of cDNA to protein in split frames
3647 incorrect when sequence start > 1</li>
3648 <li>Broken images in filter column by annotation dialog
3650 <li>Feature colours not parsed from features file</li>
3651 <li>Exceptions and incomplete link URLs recovered when
3652 loading a features file containing HTML tags in feature
3656 <em>Application</em>
3658 <li>Annotations corrupted after BioJS export and
3660 <li>Incorrect sequence limits after Fetch DB References
3661 with 'trim retrieved sequences'</li>
3662 <li>Incorrect warning about deleting all data when
3663 deleting selected columns</li>
3664 <li>Patch to build system for shipping properly signed
3665 JNLP templates for webstart launch</li>
3666 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3667 unreleased structures for download or viewing</li>
3668 <li>Tab/space/return keystroke operation of EMBL-PDBe
3669 fetcher/viewer dialogs works correctly</li>
3670 <li>Disabled 'minimise' button on Jalview windows
3671 running on OSX to workaround redraw hang bug</li>
3672 <li>Split cDNA/Protein view position and geometry not
3673 recovered from jalview project</li>
3674 <li>Initial enabled/disabled state of annotation menu
3675 sorter 'show autocalculated first/last' corresponds to
3677 <li>Restoring of Clustal, RNA Helices and T-Coffee
3678 color schemes from BioJSON</li>
3682 <li>Reorder sequences mirrored in cDNA/Protein split
3684 <li>Applet with Jmol examples not loading correctly</li>
3690 <td><div align="center">
3691 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3693 <td><em>General</em>
3695 <li>Linked visualisation and analysis of DNA and Protein
3698 <li>Translated cDNA alignments shown as split protein
3699 and DNA alignment views</li>
3700 <li>Codon consensus annotation for linked protein and
3701 cDNA alignment views</li>
3702 <li>Link cDNA or Protein product sequences by loading
3703 them onto Protein or cDNA alignments</li>
3704 <li>Reconstruct linked cDNA alignment from aligned
3705 protein sequences</li>
3708 <li>Jmol integration updated to Jmol v14.2.14</li>
3709 <li>Import and export of Jalview alignment views as <a
3710 href="features/bioJsonFormat.html">BioJSON</a></li>
3711 <li>New alignment annotation file statements for
3712 reference sequences and marking hidden columns</li>
3713 <li>Reference sequence based alignment shading to
3714 highlight variation</li>
3715 <li>Select or hide columns according to alignment
3717 <li>Find option for locating sequences by description</li>
3718 <li>Conserved physicochemical properties shown in amino
3719 acid conservation row</li>
3720 <li>Alignments can be sorted by number of RNA helices</li>
3721 </ul> <em>Application</em>
3723 <li>New cDNA/Protein analysis capabilities
3725 <li>Get Cross-References should open a Split Frame
3726 view with cDNA/Protein</li>
3727 <li>Detect when nucleotide sequences and protein
3728 sequences are placed in the same alignment</li>
3729 <li>Split cDNA/Protein views are saved in Jalview
3734 <li>Use REST API to talk to Chimera</li>
3735 <li>Selected regions in Chimera are highlighted in linked
3736 Jalview windows</li>
3738 <li>VARNA RNA viewer updated to v3.93</li>
3739 <li>VARNA views are saved in Jalview Projects</li>
3740 <li>Pseudoknots displayed as Jalview RNA annotation can
3741 be shown in VARNA</li>
3743 <li>Make groups for selection uses marked columns as well
3744 as the active selected region</li>
3746 <li>Calculate UPGMA and NJ trees using sequence feature
3748 <li>New Export options
3750 <li>New Export Settings dialog to control hidden
3751 region export in flat file generation</li>
3753 <li>Export alignment views for display with the <a
3754 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3756 <li>Export scrollable SVG in HTML page</li>
3757 <li>Optional embedding of BioJSON data when exporting
3758 alignment figures to HTML</li>
3760 <li>3D structure retrieval and display
3762 <li>Free text and structured queries with the PDBe
3764 <li>PDBe Search API based discovery and selection of
3765 PDB structures for a sequence set</li>
3769 <li>JPred4 employed for protein secondary structure
3771 <li>Hide Insertions menu option to hide unaligned columns
3772 for one or a group of sequences</li>
3773 <li>Automatically hide insertions in alignments imported
3774 from the JPred4 web server</li>
3775 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3776 system on OSX<br />LGPL libraries courtesy of <a
3777 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3779 <li>changed 'View nucleotide structure' submenu to 'View
3780 VARNA 2D Structure'</li>
3781 <li>change "View protein structure" menu option to "3D
3784 </ul> <em>Applet</em>
3786 <li>New layout for applet example pages</li>
3787 <li>New parameters to enable SplitFrame view
3788 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3789 <li>New example demonstrating linked viewing of cDNA and
3790 Protein alignments</li>
3791 </ul> <em>Development and deployment</em>
3793 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3794 <li>Include installation type and git revision in build
3795 properties and console log output</li>
3796 <li>Jalview Github organisation, and new github site for
3797 storing BioJsMSA Templates</li>
3798 <li>Jalview's unit tests now managed with TestNG</li>
3801 <!-- <em>General</em>
3803 </ul> --> <!-- issues resolved --> <em>Application</em>
3805 <li>Escape should close any open find dialogs</li>
3806 <li>Typo in select-by-features status report</li>
3807 <li>Consensus RNA secondary secondary structure
3808 predictions are not highlighted in amber</li>
3809 <li>Missing gap character in v2.7 example file means
3810 alignment appears unaligned when pad-gaps is not enabled</li>
3811 <li>First switch to RNA Helices colouring doesn't colour
3812 associated structure views</li>
3813 <li>ID width preference option is greyed out when auto
3814 width checkbox not enabled</li>
3815 <li>Stopped a warning dialog from being shown when
3816 creating user defined colours</li>
3817 <li>'View Mapping' in structure viewer shows sequence
3818 mappings for just that viewer's sequences</li>
3819 <li>Workaround for superposing PDB files containing
3820 multiple models in Chimera</li>
3821 <li>Report sequence position in status bar when hovering
3822 over Jmol structure</li>
3823 <li>Cannot output gaps as '.' symbols with Selection ->
3824 output to text box</li>
3825 <li>Flat file exports of alignments with hidden columns
3826 have incorrect sequence start/end</li>
3827 <li>'Aligning' a second chain to a Chimera structure from
3829 <li>Colour schemes applied to structure viewers don't
3830 work for nucleotide</li>
3831 <li>Loading/cut'n'pasting an empty or invalid file leads
3832 to a grey/invisible alignment window</li>
3833 <li>Exported Jpred annotation from a sequence region
3834 imports to different position</li>
3835 <li>Space at beginning of sequence feature tooltips shown
3836 on some platforms</li>
3837 <li>Chimera viewer 'View | Show Chain' menu is not
3839 <li>'New View' fails with a Null Pointer Exception in
3840 console if Chimera has been opened</li>
3841 <li>Mouseover to Chimera not working</li>
3842 <li>Miscellaneous ENA XML feature qualifiers not
3844 <li>NPE in annotation renderer after 'Extract Scores'</li>
3845 <li>If two structures in one Chimera window, mouseover of
3846 either sequence shows on first structure</li>
3847 <li>'Show annotations' options should not make
3848 non-positional annotations visible</li>
3849 <li>Subsequence secondary structure annotation not shown
3850 in right place after 'view flanking regions'</li>
3851 <li>File Save As type unset when current file format is
3853 <li>Save as '.jar' option removed for saving Jalview
3855 <li>Colour by Sequence colouring in Chimera more
3857 <li>Cannot 'add reference annotation' for a sequence in
3858 several views on same alignment</li>
3859 <li>Cannot show linked products for EMBL / ENA records</li>
3860 <li>Jalview's tooltip wraps long texts containing no
3862 </ul> <em>Applet</em>
3864 <li>Jmol to JalviewLite mouseover/link not working</li>
3865 <li>JalviewLite can't import sequences with ID
3866 descriptions containing angle brackets</li>
3867 </ul> <em>General</em>
3869 <li>Cannot export and reimport RNA secondary structure
3870 via jalview annotation file</li>
3871 <li>Random helix colour palette for colour by annotation
3872 with RNA secondary structure</li>
3873 <li>Mouseover to cDNA from STOP residue in protein
3874 translation doesn't work.</li>
3875 <li>hints when using the select by annotation dialog box</li>
3876 <li>Jmol alignment incorrect if PDB file has alternate CA
3878 <li>FontChooser message dialog appears to hang after
3879 choosing 1pt font</li>
3880 <li>Peptide secondary structure incorrectly imported from
3881 annotation file when annotation display text includes 'e' or
3883 <li>Cannot set colour of new feature type whilst creating
3885 <li>cDNA translation alignment should not be sequence
3886 order dependent</li>
3887 <li>'Show unconserved' doesn't work for lower case
3889 <li>Nucleotide ambiguity codes involving R not recognised</li>
3890 </ul> <em>Deployment and Documentation</em>
3892 <li>Applet example pages appear different to the rest of
3893 www.jalview.org</li>
3894 </ul> <em>Application Known issues</em>
3896 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3897 <li>Misleading message appears after trying to delete
3899 <li>Jalview icon not shown in dock after InstallAnywhere
3900 version launches</li>
3901 <li>Fetching EMBL reference for an RNA sequence results
3902 fails with a sequence mismatch</li>
3903 <li>Corrupted or unreadable alignment display when
3904 scrolling alignment to right</li>
3905 <li>ArrayIndexOutOfBoundsException thrown when remove
3906 empty columns called on alignment with ragged gapped ends</li>
3907 <li>auto calculated alignment annotation rows do not get
3908 placed above or below non-autocalculated rows</li>
3909 <li>Jalview dekstop becomes sluggish at full screen in
3910 ultra-high resolution</li>
3911 <li>Cannot disable consensus calculation independently of
3912 quality and conservation</li>
3913 <li>Mouseover highlighting between cDNA and protein can
3914 become sluggish with more than one splitframe shown</li>
3915 </ul> <em>Applet Known Issues</em>
3917 <li>Core PDB parsing code requires Jmol</li>
3918 <li>Sequence canvas panel goes white when alignment
3919 window is being resized</li>
3925 <td><div align="center">
3926 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3928 <td><em>General</em>
3930 <li>Updated Java code signing certificate donated by
3932 <li>Features and annotation preserved when performing
3933 pairwise alignment</li>
3934 <li>RNA pseudoknot annotation can be
3935 imported/exported/displayed</li>
3936 <li>'colour by annotation' can colour by RNA and
3937 protein secondary structure</li>
3938 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3939 post-hoc with 2.9 release</em>)
3942 </ul> <em>Application</em>
3944 <li>Extract and display secondary structure for sequences
3945 with 3D structures</li>
3946 <li>Support for parsing RNAML</li>
3947 <li>Annotations menu for layout
3949 <li>sort sequence annotation rows by alignment</li>
3950 <li>place sequence annotation above/below alignment
3953 <li>Output in Stockholm format</li>
3954 <li>Internationalisation: improved Spanish (es)
3956 <li>Structure viewer preferences tab</li>
3957 <li>Disorder and Secondary Structure annotation tracks
3958 shared between alignments</li>
3959 <li>UCSF Chimera launch and linked highlighting from
3961 <li>Show/hide all sequence associated annotation rows for
3962 all or current selection</li>
3963 <li>disorder and secondary structure predictions
3964 available as dataset annotation</li>
3965 <li>Per-sequence rna helices colouring</li>
3968 <li>Sequence database accessions imported when fetching
3969 alignments from Rfam</li>
3970 <li>update VARNA version to 3.91</li>
3972 <li>New groovy scripts for exporting aligned positions,
3973 conservation values, and calculating sum of pairs scores.</li>
3974 <li>Command line argument to set default JABAWS server</li>
3975 <li>include installation type in build properties and
3976 console log output</li>
3977 <li>Updated Jalview project format to preserve dataset
3981 <!-- issues resolved --> <em>Application</em>
3983 <li>Distinguish alignment and sequence associated RNA
3984 structure in structure->view->VARNA</li>
3985 <li>Raise dialog box if user deletes all sequences in an
3987 <li>Pressing F1 results in documentation opening twice</li>
3988 <li>Sequence feature tooltip is wrapped</li>
3989 <li>Double click on sequence associated annotation
3990 selects only first column</li>
3991 <li>Redundancy removal doesn't result in unlinked
3992 leaves shown in tree</li>
3993 <li>Undos after several redundancy removals don't undo
3995 <li>Hide sequence doesn't hide associated annotation</li>
3996 <li>User defined colours dialog box too big to fit on
3997 screen and buttons not visible</li>
3998 <li>author list isn't updated if already written to
3999 Jalview properties</li>
4000 <li>Popup menu won't open after retrieving sequence
4002 <li>File open window for associate PDB doesn't open</li>
4003 <li>Left-then-right click on a sequence id opens a
4004 browser search window</li>
4005 <li>Cannot open sequence feature shading/sort popup menu
4006 in feature settings dialog</li>
4007 <li>better tooltip placement for some areas of Jalview
4009 <li>Allow addition of JABAWS Server which doesn't
4010 pass validation</li>
4011 <li>Web services parameters dialog box is too large to
4013 <li>Muscle nucleotide alignment preset obscured by
4015 <li>JABAWS preset submenus don't contain newly
4016 defined user preset</li>
4017 <li>MSA web services warns user if they were launched
4018 with invalid input</li>
4019 <li>Jalview cannot contact DAS Registy when running on
4022 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
4023 'Superpose with' submenu not shown when new view
4027 </ul> <!-- <em>Applet</em>
4029 </ul> <em>General</em>
4031 </ul>--> <em>Deployment and Documentation</em>
4033 <li>2G and 1G options in launchApp have no effect on
4034 memory allocation</li>
4035 <li>launchApp service doesn't automatically open
4036 www.jalview.org/examples/exampleFile.jar if no file is given</li>
4038 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
4039 InstallAnywhere reports cannot find valid JVM when Java
4040 1.7_055 is available
4042 </ul> <em>Application Known issues</em>
4045 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
4046 corrupted or unreadable alignment display when scrolling
4050 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
4051 retrieval fails but progress bar continues for DAS retrieval
4052 with large number of ID
4055 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
4056 flatfile output of visible region has incorrect sequence
4060 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
4061 rna structure consensus doesn't update when secondary
4062 structure tracks are rearranged
4065 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
4066 invalid rna structure positional highlighting does not
4067 highlight position of invalid base pairs
4070 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
4071 out of memory errors are not raised when saving Jalview
4072 project from alignment window file menu
4075 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
4076 Switching to RNA Helices colouring doesn't propagate to
4080 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
4081 colour by RNA Helices not enabled when user created
4082 annotation added to alignment
4085 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
4086 Jalview icon not shown on dock in Mountain Lion/Webstart
4088 </ul> <em>Applet Known Issues</em>
4091 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
4092 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
4095 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
4096 Jalview and Jmol example not compatible with IE9
4099 <li>Sort by annotation score doesn't reverse order
4105 <td><div align="center">
4106 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
4109 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
4112 <li>Internationalisation of user interface (usually
4113 called i18n support) and translation for Spanish locale</li>
4114 <li>Define/Undefine group on current selection with
4115 Ctrl-G/Shift Ctrl-G</li>
4116 <li>Improved group creation/removal options in
4117 alignment/sequence Popup menu</li>
4118 <li>Sensible precision for symbol distribution
4119 percentages shown in logo tooltip.</li>
4120 <li>Annotation panel height set according to amount of
4121 annotation when alignment first opened</li>
4122 </ul> <em>Application</em>
4124 <li>Interactive consensus RNA secondary structure
4125 prediction VIENNA RNAAliFold JABA 2.1 service</li>
4126 <li>Select columns containing particular features from
4127 Feature Settings dialog</li>
4128 <li>View all 'representative' PDB structures for selected
4130 <li>Update Jalview project format:
4132 <li>New file extension for Jalview projects '.jvp'</li>
4133 <li>Preserve sequence and annotation dataset (to
4134 store secondary structure annotation,etc)</li>
4135 <li>Per group and alignment annotation and RNA helix
4139 <li>New similarity measures for PCA and Tree calculation
4141 <li>Experimental support for retrieval and viewing of
4142 flanking regions for an alignment</li>
4146 <!-- issues resolved --> <em>Application</em>
4148 <li>logo keeps spinning and status remains at queued or
4149 running after job is cancelled</li>
4150 <li>cannot export features from alignments imported from
4151 Jalview/VAMSAS projects</li>
4152 <li>Buggy slider for web service parameters that take
4154 <li>Newly created RNA secondary structure line doesn't
4155 have 'display all symbols' flag set</li>
4156 <li>T-COFFEE alignment score shading scheme and other
4157 annotation shading not saved in Jalview project</li>
4158 <li>Local file cannot be loaded in freshly downloaded
4160 <li>Jalview icon not shown on dock in Mountain
4162 <li>Load file from desktop file browser fails</li>
4163 <li>Occasional NPE thrown when calculating large trees</li>
4164 <li>Cannot reorder or slide sequences after dragging an
4165 alignment onto desktop</li>
4166 <li>Colour by annotation dialog throws NPE after using
4167 'extract scores' function</li>
4168 <li>Loading/cut'n'pasting an empty file leads to a grey
4169 alignment window</li>
4170 <li>Disorder thresholds rendered incorrectly after
4171 performing IUPred disorder prediction</li>
4172 <li>Multiple group annotated consensus rows shown when
4173 changing 'normalise logo' display setting</li>
4174 <li>Find shows blank dialog after 'finished searching' if
4175 nothing matches query</li>
4176 <li>Null Pointer Exceptions raised when sorting by
4177 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
4179 <li>Errors in Jmol console when structures in alignment
4180 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
4182 <li>Not all working JABAWS services are shown in
4184 <li>JAVAWS version of Jalview fails to launch with
4185 'invalid literal/length code'</li>
4186 <li>Annotation/RNA Helix colourschemes cannot be applied
4187 to alignment with groups (actually fixed in 2.8.0b1)</li>
4188 <li>RNA Helices and T-Coffee Scores available as default
4191 </ul> <em>Applet</em>
4193 <li>Remove group option is shown even when selection is
4195 <li>Apply to all groups ticked but colourscheme changes
4196 don't affect groups</li>
4197 <li>Documented RNA Helices and T-Coffee Scores as valid
4198 colourscheme name</li>
4199 <li>Annotation labels drawn on sequence IDs when
4200 Annotation panel is not displayed</li>
4201 <li>Increased font size for dropdown menus on OSX and
4202 embedded windows</li>
4203 </ul> <em>Other</em>
4205 <li>Consensus sequence for alignments/groups with a
4206 single sequence were not calculated</li>
4207 <li>annotation files that contain only groups imported as
4208 annotation and junk sequences</li>
4209 <li>Fasta files with sequences containing '*' incorrectly
4210 recognised as PFAM or BLC</li>
4211 <li>conservation/PID slider apply all groups option
4212 doesn't affect background (2.8.0b1)
4214 <li>redundancy highlighting is erratic at 0% and 100%</li>
4215 <li>Remove gapped columns fails for sequences with ragged
4217 <li>AMSA annotation row with leading spaces is not
4218 registered correctly on import</li>
4219 <li>Jalview crashes when selecting PCA analysis for
4220 certain alignments</li>
4221 <li>Opening the colour by annotation dialog for an
4222 existing annotation based 'use original colours'
4223 colourscheme loses original colours setting</li>
4228 <td><div align="center">
4229 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
4230 <em>30/1/2014</em></strong>
4234 <li>Trusted certificates for JalviewLite applet and
4235 Jalview Desktop application<br />Certificate was donated by
4236 <a href="https://www.certum.eu">Certum</a> to the Jalview
4237 open source project).
4239 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
4240 <li>Output in Stockholm format</li>
4241 <li>Allow import of data from gzipped files</li>
4242 <li>Export/import group and sequence associated line
4243 graph thresholds</li>
4244 <li>Nucleotide substitution matrix that supports RNA and
4245 ambiguity codes</li>
4246 <li>Allow disorder predictions to be made on the current
4247 selection (or visible selection) in the same way that JPred
4249 <li>Groovy scripting for headless Jalview operation</li>
4250 </ul> <em>Other improvements</em>
4252 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
4253 <li>COMBINE statement uses current SEQUENCE_REF and
4254 GROUP_REF scope to group annotation rows</li>
4255 <li>Support '' style escaping of quotes in Newick
4257 <li>Group options for JABAWS service by command line name</li>
4258 <li>Empty tooltip shown for JABA service options with a
4259 link but no description</li>
4260 <li>Select primary source when selecting authority in
4261 database fetcher GUI</li>
4262 <li>Add .mfa to FASTA file extensions recognised by
4264 <li>Annotation label tooltip text wrap</li>
4269 <li>Slow scrolling when lots of annotation rows are
4271 <li>Lots of NPE (and slowness) after creating RNA
4272 secondary structure annotation line</li>
4273 <li>Sequence database accessions not imported when
4274 fetching alignments from Rfam</li>
4275 <li>Incorrect SHMR submission for sequences with
4277 <li>View all structures does not always superpose
4279 <li>Option widgets in service parameters not updated to
4280 reflect user or preset settings</li>
4281 <li>Null pointer exceptions for some services without
4282 presets or adjustable parameters</li>
4283 <li>Discover PDB IDs entry in structure menu doesn't
4284 discover PDB xRefs</li>
4285 <li>Exception encountered while trying to retrieve
4286 features with DAS</li>
4287 <li>Lowest value in annotation row isn't coloured
4288 when colour by annotation (per sequence) is coloured</li>
4289 <li>Keyboard mode P jumps to start of gapped region when
4290 residue follows a gap</li>
4291 <li>Jalview appears to hang importing an alignment with
4292 Wrap as default or after enabling Wrap</li>
4293 <li>'Right click to add annotations' message
4294 shown in wrap mode when no annotations present</li>
4295 <li>Disorder predictions fail with NPE if no automatic
4296 annotation already exists on alignment</li>
4297 <li>oninit javascript function should be called after
4298 initialisation completes</li>
4299 <li>Remove redundancy after disorder prediction corrupts
4300 alignment window display</li>
4301 <li>Example annotation file in documentation is invalid</li>
4302 <li>Grouped line graph annotation rows are not exported
4303 to annotation file</li>
4304 <li>Multi-harmony analysis cannot be run when only two
4306 <li>Cannot create multiple groups of line graphs with
4307 several 'combine' statements in annotation file</li>
4308 <li>Pressing return several times causes Number Format
4309 exceptions in keyboard mode</li>
4310 <li>Multi-harmony (SHMMR) method doesn't submit
4311 correct partitions for input data</li>
4312 <li>Translation from DNA to Amino Acids fails</li>
4313 <li>Jalview fail to load newick tree with quoted label</li>
4314 <li>--headless flag isn't understood</li>
4315 <li>ClassCastException when generating EPS in headless
4317 <li>Adjusting sequence-associated shading threshold only
4318 changes one row's threshold</li>
4319 <li>Preferences and Feature settings panel panel
4320 doesn't open</li>
4321 <li>hide consensus histogram also hides conservation and
4322 quality histograms</li>
4327 <td><div align="center">
4328 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
4330 <td><em>Application</em>
4332 <li>Support for JABAWS 2.0 Services (AACon alignment
4333 conservation, protein disorder and Clustal Omega)</li>
4334 <li>JABAWS server status indicator in Web Services
4336 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
4337 in Jalview alignment window</li>
4338 <li>Updated Jalview build and deploy framework for OSX
4339 mountain lion, windows 7, and 8</li>
4340 <li>Nucleotide substitution matrix for PCA that supports
4341 RNA and ambiguity codes</li>
4343 <li>Improved sequence database retrieval GUI</li>
4344 <li>Support fetching and database reference look up
4345 against multiple DAS sources (Fetch all from in 'fetch db
4347 <li>Jalview project improvements
4349 <li>Store and retrieve the 'belowAlignment'
4350 flag for annotation</li>
4351 <li>calcId attribute to group annotation rows on the
4353 <li>Store AACon calculation settings for a view in
4354 Jalview project</li>
4358 <li>horizontal scrolling gesture support</li>
4359 <li>Visual progress indicator when PCA calculation is
4361 <li>Simpler JABA web services menus</li>
4362 <li>visual indication that web service results are still
4363 being retrieved from server</li>
4364 <li>Serialise the dialogs that are shown when Jalview
4365 starts up for first time</li>
4366 <li>Jalview user agent string for interacting with HTTP
4368 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
4370 <li>Examples directory and Groovy library included in
4371 InstallAnywhere distribution</li>
4372 </ul> <em>Applet</em>
4374 <li>RNA alignment and secondary structure annotation
4375 visualization applet example</li>
4376 </ul> <em>General</em>
4378 <li>Normalise option for consensus sequence logo</li>
4379 <li>Reset button in PCA window to return dimensions to
4381 <li>Allow seqspace or Jalview variant of alignment PCA
4383 <li>PCA with either nucleic acid and protein substitution
4385 <li>Allow windows containing HTML reports to be exported
4387 <li>Interactive display and editing of RNA secondary
4388 structure contacts</li>
4389 <li>RNA Helix Alignment Colouring</li>
4390 <li>RNA base pair logo consensus</li>
4391 <li>Parse sequence associated secondary structure
4392 information in Stockholm files</li>
4393 <li>HTML Export database accessions and annotation
4394 information presented in tooltip for sequences</li>
4395 <li>Import secondary structure from LOCARNA clustalw
4396 style RNA alignment files</li>
4397 <li>import and visualise T-COFFEE quality scores for an
4399 <li>'colour by annotation' per sequence option to
4400 shade each sequence according to its associated alignment
4402 <li>New Jalview Logo</li>
4403 </ul> <em>Documentation and Development</em>
4405 <li>documentation for score matrices used in Jalview</li>
4406 <li>New Website!</li>
4408 <td><em>Application</em>
4410 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
4411 wsdbfetch REST service</li>
4412 <li>Stop windows being moved outside desktop on OSX</li>
4413 <li>Filetype associations not installed for webstart
4415 <li>Jalview does not always retrieve progress of a JABAWS
4416 job execution in full once it is complete</li>
4417 <li>revise SHMR RSBS definition to ensure alignment is
4418 uploaded via ali_file parameter</li>
4419 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
4420 <li>View all structures superposed fails with exception</li>
4421 <li>Jnet job queues forever if a very short sequence is
4422 submitted for prediction</li>
4423 <li>Cut and paste menu not opened when mouse clicked on
4425 <li>Putting fractional value into integer text box in
4426 alignment parameter dialog causes Jalview to hang</li>
4427 <li>Structure view highlighting doesn't work on
4429 <li>View all structures fails with exception shown in
4431 <li>Characters in filename associated with PDBEntry not
4432 escaped in a platform independent way</li>
4433 <li>Jalview desktop fails to launch with exception when
4435 <li>Tree calculation reports 'you must have 2 or more
4436 sequences selected' when selection is empty</li>
4437 <li>Jalview desktop fails to launch with jar signature
4438 failure when java web start temporary file caching is
4440 <li>DAS Sequence retrieval with range qualification
4441 results in sequence xref which includes range qualification</li>
4442 <li>Errors during processing of command line arguments
4443 cause progress bar (JAL-898) to be removed</li>
4444 <li>Replace comma for semi-colon option not disabled for
4445 DAS sources in sequence fetcher</li>
4446 <li>Cannot close news reader when JABAWS server warning
4447 dialog is shown</li>
4448 <li>Option widgets not updated to reflect user settings</li>
4449 <li>Edited sequence not submitted to web service</li>
4450 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
4451 <li>InstallAnywhere installer doesn't unpack and run
4452 on OSX Mountain Lion</li>
4453 <li>Annotation panel not given a scroll bar when
4454 sequences with alignment annotation are pasted into the
4456 <li>Sequence associated annotation rows not associated
4457 when loaded from Jalview project</li>
4458 <li>Browser launch fails with NPE on java 1.7</li>
4459 <li>JABAWS alignment marked as finished when job was
4460 cancelled or job failed due to invalid input</li>
4461 <li>NPE with v2.7 example when clicking on Tree
4462 associated with all views</li>
4463 <li>Exceptions when copy/paste sequences with grouped
4464 annotation rows to new window</li>
4465 </ul> <em>Applet</em>
4467 <li>Sequence features are momentarily displayed before
4468 they are hidden using hidefeaturegroups applet parameter</li>
4469 <li>loading features via javascript API automatically
4470 enables feature display</li>
4471 <li>scrollToColumnIn javascript API method doesn't
4473 </ul> <em>General</em>
4475 <li>Redundancy removal fails for rna alignment</li>
4476 <li>PCA calculation fails when sequence has been selected
4477 and then deselected</li>
4478 <li>PCA window shows grey box when first opened on OSX</li>
4479 <li>Letters coloured pink in sequence logo when alignment
4480 coloured with clustalx</li>
4481 <li>Choosing fonts without letter symbols defined causes
4482 exceptions and redraw errors</li>
4483 <li>Initial PCA plot view is not same as manually
4484 reconfigured view</li>
4485 <li>Grouped annotation graph label has incorrect line
4487 <li>Grouped annotation graph label display is corrupted
4488 for lots of labels</li>
4493 <div align="center">
4494 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
4497 <td><em>Application</em>
4499 <li>Jalview Desktop News Reader</li>
4500 <li>Tweaked default layout of web services menu</li>
4501 <li>View/alignment association menu to enable user to
4502 easily specify which alignment a multi-structure view takes
4503 its colours/correspondences from</li>
4504 <li>Allow properties file location to be specified as URL</li>
4505 <li>Extend Jalview project to preserve associations
4506 between many alignment views and a single Jmol display</li>
4507 <li>Store annotation row height in Jalview project file</li>
4508 <li>Annotation row column label formatting attributes
4509 stored in project file</li>
4510 <li>Annotation row order for auto-calculated annotation
4511 rows preserved in Jalview project file</li>
4512 <li>Visual progress indication when Jalview state is
4513 saved using Desktop window menu</li>
4514 <li>Visual indication that command line arguments are
4515 still being processed</li>
4516 <li>Groovy script execution from URL</li>
4517 <li>Colour by annotation default min and max colours in
4519 <li>Automatically associate PDB files dragged onto an
4520 alignment with sequences that have high similarity and
4522 <li>Update JGoogleAnalytics to latest release (0.3)</li>
4523 <li>'view structures' option to open many
4524 structures in same window</li>
4525 <li>Sort associated views menu option for tree panel</li>
4526 <li>Group all JABA and non-JABA services for a particular
4527 analysis function in its own submenu</li>
4528 </ul> <em>Applet</em>
4530 <li>Userdefined and autogenerated annotation rows for
4532 <li>Adjustment of alignment annotation pane height</li>
4533 <li>Annotation scrollbar for annotation panel</li>
4534 <li>Drag to reorder annotation rows in annotation panel</li>
4535 <li>'automaticScrolling' parameter</li>
4536 <li>Allow sequences with partial ID string matches to be
4537 annotated from GFF/Jalview features files</li>
4538 <li>Sequence logo annotation row in applet</li>
4539 <li>Absolute paths relative to host server in applet
4540 parameters are treated as such</li>
4541 <li>New in the JalviewLite javascript API:
4543 <li>JalviewLite.js javascript library</li>
4544 <li>Javascript callbacks for
4546 <li>Applet initialisation</li>
4547 <li>Sequence/alignment mouse-overs and selections</li>
4550 <li>scrollTo row and column alignment scrolling
4552 <li>Select sequence/alignment regions from javascript</li>
4553 <li>javascript structure viewer harness to pass
4554 messages between Jmol and Jalview when running as
4555 distinct applets</li>
4556 <li>sortBy method</li>
4557 <li>Set of applet and application examples shipped
4558 with documentation</li>
4559 <li>New example to demonstrate JalviewLite and Jmol
4560 javascript message exchange</li>
4562 </ul> <em>General</em>
4564 <li>Enable Jmol displays to be associated with multiple
4565 multiple alignments</li>
4566 <li>Option to automatically sort alignment with new tree</li>
4567 <li>User configurable link to enable redirects to a
4568 www.Jalview.org mirror</li>
4569 <li>Jmol colours option for Jmol displays</li>
4570 <li>Configurable newline string when writing alignment
4571 and other flat files</li>
4572 <li>Allow alignment annotation description lines to
4573 contain html tags</li>
4574 </ul> <em>Documentation and Development</em>
4576 <li>Add groovy test harness for bulk load testing to
4578 <li>Groovy script to load and align a set of sequences
4579 using a web service before displaying the result in the
4580 Jalview desktop</li>
4581 <li>Restructured javascript and applet api documentation</li>
4582 <li>Ant target to publish example html files with applet
4584 <li>Netbeans project for building Jalview from source</li>
4585 <li>ant task to create online javadoc for Jalview source</li>
4587 <td><em>Application</em>
4589 <li>User defined colourscheme throws exception when
4590 current built in colourscheme is saved as new scheme</li>
4591 <li>AlignFrame->Save in application pops up save
4592 dialog for valid filename/format</li>
4593 <li>Cannot view associated structure for UniProt sequence</li>
4594 <li>PDB file association breaks for UniProt sequence
4596 <li>Associate PDB from file dialog does not tell you
4597 which sequence is to be associated with the file</li>
4598 <li>Find All raises null pointer exception when query
4599 only matches sequence IDs</li>
4600 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4601 <li>Jalview project with Jmol views created with Jalview
4602 2.4 cannot be loaded</li>
4603 <li>Filetype associations not installed for webstart
4605 <li>Two or more chains in a single PDB file associated
4606 with sequences in different alignments do not get coloured
4607 by their associated sequence</li>
4608 <li>Visibility status of autocalculated annotation row
4609 not preserved when project is loaded</li>
4610 <li>Annotation row height and visibility attributes not
4611 stored in Jalview project</li>
4612 <li>Tree bootstraps are not preserved when saved as a
4613 Jalview project</li>
4614 <li>Envision2 workflow tooltips are corrupted</li>
4615 <li>Enabling show group conservation also enables colour
4616 by conservation</li>
4617 <li>Duplicate group associated conservation or consensus
4618 created on new view</li>
4619 <li>Annotation scrollbar not displayed after 'show
4620 all hidden annotation rows' option selected</li>
4621 <li>Alignment quality not updated after alignment
4622 annotation row is hidden then shown</li>
4623 <li>Preserve colouring of structures coloured by
4624 sequences in pre Jalview 2.7 projects</li>
4625 <li>Web service job parameter dialog is not laid out
4627 <li>Web services menu not refreshed after 'reset
4628 services' button is pressed in preferences</li>
4629 <li>Annotation off by one in Jalview v2_3 example project</li>
4630 <li>Structures imported from file and saved in project
4631 get name like jalview_pdb1234.txt when reloaded</li>
4632 <li>Jalview does not always retrieve progress of a JABAWS
4633 job execution in full once it is complete</li>
4634 </ul> <em>Applet</em>
4636 <li>Alignment height set incorrectly when lots of
4637 annotation rows are displayed</li>
4638 <li>Relative URLs in feature HTML text not resolved to
4640 <li>View follows highlighting does not work for positions
4642 <li><= shown as = in tooltip</li>
4643 <li>Export features raises exception when no features
4645 <li>Separator string used for serialising lists of IDs
4646 for javascript api is modified when separator string
4647 provided as parameter</li>
4648 <li>Null pointer exception when selecting tree leaves for
4649 alignment with no existing selection</li>
4650 <li>Relative URLs for datasources assumed to be relative
4651 to applet's codebase</li>
4652 <li>Status bar not updated after finished searching and
4653 search wraps around to first result</li>
4654 <li>StructureSelectionManager instance shared between
4655 several Jalview applets causes race conditions and memory
4657 <li>Hover tooltip and mouseover of position on structure
4658 not sent from Jmol in applet</li>
4659 <li>Certain sequences of javascript method calls to
4660 applet API fatally hang browser</li>
4661 </ul> <em>General</em>
4663 <li>View follows structure mouseover scrolls beyond
4664 position with wrapped view and hidden regions</li>
4665 <li>Find sequence position moves to wrong residue
4666 with/without hidden columns</li>
4667 <li>Sequence length given in alignment properties window
4669 <li>InvalidNumberFormat exceptions thrown when trying to
4670 import PDB like structure files</li>
4671 <li>Positional search results are only highlighted
4672 between user-supplied sequence start/end bounds</li>
4673 <li>End attribute of sequence is not validated</li>
4674 <li>Find dialog only finds first sequence containing a
4675 given sequence position</li>
4676 <li>Sequence numbering not preserved in MSF alignment
4678 <li>Jalview PDB file reader does not extract sequence
4679 from nucleotide chains correctly</li>
4680 <li>Structure colours not updated when tree partition
4681 changed in alignment</li>
4682 <li>Sequence associated secondary structure not correctly
4683 parsed in interleaved stockholm</li>
4684 <li>Colour by annotation dialog does not restore current
4686 <li>Hiding (nearly) all sequences doesn't work
4688 <li>Sequences containing lowercase letters are not
4689 properly associated with their pdb files</li>
4690 </ul> <em>Documentation and Development</em>
4692 <li>schemas/JalviewWsParamSet.xsd corrupted by
4693 ApplyCopyright tool</li>
4698 <div align="center">
4699 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4702 <td><em>Application</em>
4704 <li>New warning dialog when the Jalview Desktop cannot
4705 contact web services</li>
4706 <li>JABA service parameters for a preset are shown in
4707 service job window</li>
4708 <li>JABA Service menu entries reworded</li>
4712 <li>Modeller PIR IO broken - cannot correctly import a
4713 pir file emitted by Jalview</li>
4714 <li>Existing feature settings transferred to new
4715 alignment view created from cut'n'paste</li>
4716 <li>Improved test for mixed amino/nucleotide chains when
4717 parsing PDB files</li>
4718 <li>Consensus and conservation annotation rows
4719 occasionally become blank for all new windows</li>
4720 <li>Exception raised when right clicking above sequences
4721 in wrapped view mode</li>
4722 </ul> <em>Application</em>
4724 <li>multiple multiply aligned structure views cause cpu
4725 usage to hit 100% and computer to hang</li>
4726 <li>Web Service parameter layout breaks for long user
4727 parameter names</li>
4728 <li>Jaba service discovery hangs desktop if Jaba server
4735 <div align="center">
4736 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4739 <td><em>Application</em>
4741 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4742 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4745 <li>Web Services preference tab</li>
4746 <li>Analysis parameters dialog box and user defined
4748 <li>Improved speed and layout of Envision2 service menu</li>
4749 <li>Superpose structures using associated sequence
4751 <li>Export coordinates and projection as CSV from PCA
4753 </ul> <em>Applet</em>
4755 <li>enable javascript: execution by the applet via the
4756 link out mechanism</li>
4757 </ul> <em>Other</em>
4759 <li>Updated the Jmol Jalview interface to work with Jmol
4761 <li>The Jalview Desktop and JalviewLite applet now
4762 require Java 1.5</li>
4763 <li>Allow Jalview feature colour specification for GFF
4764 sequence annotation files</li>
4765 <li>New 'colour by label' keword in Jalview feature file
4766 type colour specification</li>
4767 <li>New Jalview Desktop Groovy API method that allows a
4768 script to check if it being run in an interactive session or
4769 in a batch operation from the Jalview command line</li>
4773 <li>clustalx colourscheme colours Ds preferentially when
4774 both D+E are present in over 50% of the column</li>
4775 </ul> <em>Application</em>
4777 <li>typo in AlignmentFrame->View->Hide->all but
4778 selected Regions menu item</li>
4779 <li>sequence fetcher replaces ',' for ';' when the ',' is
4780 part of a valid accession ID</li>
4781 <li>fatal OOM if object retrieved by sequence fetcher
4782 runs out of memory</li>
4783 <li>unhandled Out of Memory Error when viewing pca
4784 analysis results</li>
4785 <li>InstallAnywhere builds fail to launch on OS X java
4786 10.5 update 4 (due to apple Java 1.6 update)</li>
4787 <li>Installanywhere Jalview silently fails to launch</li>
4788 </ul> <em>Applet</em>
4790 <li>Jalview.getFeatureGroups() raises an
4791 ArrayIndexOutOfBoundsException if no feature groups are
4798 <div align="center">
4799 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4805 <li>Alignment prettyprinter doesn't cope with long
4807 <li>clustalx colourscheme colours Ds preferentially when
4808 both D+E are present in over 50% of the column</li>
4809 <li>nucleic acid structures retrieved from PDB do not
4810 import correctly</li>
4811 <li>More columns get selected than were clicked on when a
4812 number of columns are hidden</li>
4813 <li>annotation label popup menu not providing correct
4814 add/hide/show options when rows are hidden or none are
4816 <li>Stockholm format shown in list of readable formats,
4817 and parser copes better with alignments from RFAM.</li>
4818 <li>CSV output of consensus only includes the percentage
4819 of all symbols if sequence logo display is enabled</li>
4821 </ul> <em>Applet</em>
4823 <li>annotation panel disappears when annotation is
4825 </ul> <em>Application</em>
4827 <li>Alignment view not redrawn properly when new
4828 alignment opened where annotation panel is visible but no
4829 annotations are present on alignment</li>
4830 <li>pasted region containing hidden columns is
4831 incorrectly displayed in new alignment window</li>
4832 <li>Jalview slow to complete operations when stdout is
4833 flooded (fix is to close the Jalview console)</li>
4834 <li>typo in AlignmentFrame->View->Hide->all but
4835 selected Rregions menu item.</li>
4836 <li>inconsistent group submenu and Format submenu entry
4837 'Un' or 'Non'conserved</li>
4838 <li>Sequence feature settings are being shared by
4839 multiple distinct alignments</li>
4840 <li>group annotation not recreated when tree partition is
4842 <li>double click on group annotation to select sequences
4843 does not propagate to associated trees</li>
4844 <li>Mac OSX specific issues:
4846 <li>exception raised when mouse clicked on desktop
4847 window background</li>
4848 <li>Desktop menu placed on menu bar and application
4849 name set correctly</li>
4850 <li>sequence feature settings not wide enough for the
4851 save feature colourscheme button</li>
4860 <div align="center">
4861 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4864 <td><em>New Capabilities</em>
4866 <li>URL links generated from description line for
4867 regular-expression based URL links (applet and application)
4870 <li>Non-positional feature URL links are shown in link
4872 <li>Linked viewing of nucleic acid sequences and
4874 <li>Automatic Scrolling option in View menu to display
4875 the currently highlighted region of an alignment.</li>
4876 <li>Order an alignment by sequence length, or using the
4877 average score or total feature count for each sequence.</li>
4878 <li>Shading features by score or associated description</li>
4879 <li>Subdivide alignment and groups based on identity of
4880 selected subsequence (Make Groups from Selection).</li>
4881 <li>New hide/show options including Shift+Control+H to
4882 hide everything but the currently selected region.</li>
4883 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4884 </ul> <em>Application</em>
4886 <li>Fetch DB References capabilities and UI expanded to
4887 support retrieval from DAS sequence sources</li>
4888 <li>Local DAS Sequence sources can be added via the
4889 command line or via the Add local source dialog box.</li>
4890 <li>DAS Dbref and DbxRef feature types are parsed as
4891 database references and protein_name is parsed as
4892 description line (BioSapiens terms).</li>
4893 <li>Enable or disable non-positional feature and database
4894 references in sequence ID tooltip from View menu in
4896 <!-- <li>New hidden columns and rows and representatives capabilities
4897 in annotations file (in progress - not yet fully implemented)</li> -->
4898 <li>Group-associated consensus, sequence logos and
4899 conservation plots</li>
4900 <li>Symbol distributions for each column can be exported
4901 and visualized as sequence logos</li>
4902 <li>Optionally scale multi-character column labels to fit
4903 within each column of annotation row<!-- todo for applet -->
4905 <li>Optional automatic sort of associated alignment view
4906 when a new tree is opened.</li>
4907 <li>Jalview Java Console</li>
4908 <li>Better placement of desktop window when moving
4909 between different screens.</li>
4910 <li>New preference items for sequence ID tooltip and
4911 consensus annotation</li>
4912 <li>Client to submit sequences and IDs to Envision2
4914 <li><em>Vamsas Capabilities</em>
4916 <li>Improved VAMSAS synchronization (Jalview archive
4917 used to preserve views, structures, and tree display
4919 <li>Import of vamsas documents from disk or URL via
4921 <li>Sharing of selected regions between views and
4922 with other VAMSAS applications (Experimental feature!)</li>
4923 <li>Updated API to VAMSAS version 0.2</li>
4925 </ul> <em>Applet</em>
4927 <li>Middle button resizes annotation row height</li>
4930 <li>sortByTree (true/false) - automatically sort the
4931 associated alignment view by the tree when a new tree is
4933 <li>showTreeBootstraps (true/false) - show or hide
4934 branch bootstraps (default is to show them if available)</li>
4935 <li>showTreeDistances (true/false) - show or hide
4936 branch lengths (default is to show them if available)</li>
4937 <li>showUnlinkedTreeNodes (true/false) - indicate if
4938 unassociated nodes should be highlighted in the tree
4940 <li>heightScale and widthScale (1.0 or more) -
4941 increase the height or width of a cell in the alignment
4942 grid relative to the current font size.</li>
4945 <li>Non-positional features displayed in sequence ID
4947 </ul> <em>Other</em>
4949 <li>Features format: graduated colour definitions and
4950 specification of feature scores</li>
4951 <li>Alignment Annotations format: new keywords for group
4952 associated annotation (GROUP_REF) and annotation row display
4953 properties (ROW_PROPERTIES)</li>
4954 <li>XML formats extended to support graduated feature
4955 colourschemes, group associated annotation, and profile
4956 visualization settings.</li></td>
4959 <li>Source field in GFF files parsed as feature source
4960 rather than description</li>
4961 <li>Non-positional features are now included in sequence
4962 feature and gff files (controlled via non-positional feature
4963 visibility in tooltip).</li>
4964 <li>URL links generated for all feature links (bugfix)</li>
4965 <li>Added URL embedding instructions to features file
4967 <li>Codons containing ambiguous nucleotides translated as
4968 'X' in peptide product</li>
4969 <li>Match case switch in find dialog box works for both
4970 sequence ID and sequence string and query strings do not
4971 have to be in upper case to match case-insensitively.</li>
4972 <li>AMSA files only contain first column of
4973 multi-character column annotation labels</li>
4974 <li>Jalview Annotation File generation/parsing consistent
4975 with documentation (e.g. Stockholm annotation can be
4976 exported and re-imported)</li>
4977 <li>PDB files without embedded PDB IDs given a friendly
4979 <li>Find incrementally searches ID string matches as well
4980 as subsequence matches, and correctly reports total number
4984 <li>Better handling of exceptions during sequence
4986 <li>Dasobert generated non-positional feature URL
4987 link text excludes the start_end suffix</li>
4988 <li>DAS feature and source retrieval buttons disabled
4989 when fetch or registry operations in progress.</li>
4990 <li>PDB files retrieved from URLs are cached properly</li>
4991 <li>Sequence description lines properly shared via
4993 <li>Sequence fetcher fetches multiple records for all
4995 <li>Ensured that command line das feature retrieval
4996 completes before alignment figures are generated.</li>
4997 <li>Reduced time taken when opening file browser for
4999 <li>isAligned check prior to calculating tree, PCA or
5000 submitting an MSA to JNet now excludes hidden sequences.</li>
5001 <li>User defined group colours properly recovered
5002 from Jalview projects.</li>
5011 <div align="center">
5012 <strong>2.4.0.b2</strong><br> 28/10/2009
5017 <li>Experimental support for google analytics usage
5019 <li>Jalview privacy settings (user preferences and docs).</li>
5024 <li>Race condition in applet preventing startup in
5026 <li>Exception when feature created from selection beyond
5027 length of sequence.</li>
5028 <li>Allow synthetic PDB files to be imported gracefully</li>
5029 <li>Sequence associated annotation rows associate with
5030 all sequences with a given id</li>
5031 <li>Find function matches case-insensitively for sequence
5032 ID string searches</li>
5033 <li>Non-standard characters do not cause pairwise
5034 alignment to fail with exception</li>
5035 </ul> <em>Application Issues</em>
5037 <li>Sequences are now validated against EMBL database</li>
5038 <li>Sequence fetcher fetches multiple records for all
5040 </ul> <em>InstallAnywhere Issues</em>
5042 <li>Dock icon works for Mac OS X java (Mac 1.6 update
5043 issue with installAnywhere mechanism)</li>
5044 <li>Command line launching of JARs from InstallAnywhere
5045 version (java class versioning error fixed)</li>
5052 <div align="center">
5053 <strong>2.4</strong><br> 27/8/2008
5056 <td><em>User Interface</em>
5058 <li>Linked highlighting of codon and amino acid from
5059 translation and protein products</li>
5060 <li>Linked highlighting of structure associated with
5061 residue mapping to codon position</li>
5062 <li>Sequence Fetcher provides example accession numbers
5063 and 'clear' button</li>
5064 <li>MemoryMonitor added as an option under Desktop's
5066 <li>Extract score function to parse whitespace separated
5067 numeric data in description line</li>
5068 <li>Column labels in alignment annotation can be centred.</li>
5069 <li>Tooltip for sequence associated annotation give name
5071 </ul> <em>Web Services and URL fetching</em>
5073 <li>JPred3 web service</li>
5074 <li>Prototype sequence search client (no public services
5076 <li>Fetch either seed alignment or full alignment from
5078 <li>URL Links created for matching database cross
5079 references as well as sequence ID</li>
5080 <li>URL Links can be created using regular-expressions</li>
5081 </ul> <em>Sequence Database Connectivity</em>
5083 <li>Retrieval of cross-referenced sequences from other
5085 <li>Generalised database reference retrieval and
5086 validation to all fetchable databases</li>
5087 <li>Fetch sequences from DAS sources supporting the
5088 sequence command</li>
5089 </ul> <em>Import and Export</em>
5090 <li>export annotation rows as CSV for spreadsheet import</li>
5091 <li>Jalview projects record alignment dataset associations,
5092 EMBL products, and cDNA sequence mappings</li>
5093 <li>Sequence Group colour can be specified in Annotation
5095 <li>Ad-hoc colouring of group in Annotation File using RGB
5096 triplet as name of colourscheme</li>
5097 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
5099 <li>treenode binding for VAMSAS tree exchange</li>
5100 <li>local editing and update of sequences in VAMSAS
5101 alignments (experimental)</li>
5102 <li>Create new or select existing session to join</li>
5103 <li>load and save of vamsas documents</li>
5104 </ul> <em>Application command line</em>
5106 <li>-tree parameter to open trees (introduced for passing
5108 <li>-fetchfrom command line argument to specify nicknames
5109 of DAS servers to query for alignment features</li>
5110 <li>-dasserver command line argument to add new servers
5111 that are also automatically queried for features</li>
5112 <li>-groovy command line argument executes a given groovy
5113 script after all input data has been loaded and parsed</li>
5114 </ul> <em>Applet-Application data exchange</em>
5116 <li>Trees passed as applet parameters can be passed to
5117 application (when using "View in full
5118 application")</li>
5119 </ul> <em>Applet Parameters</em>
5121 <li>feature group display control parameter</li>
5122 <li>debug parameter</li>
5123 <li>showbutton parameter</li>
5124 </ul> <em>Applet API methods</em>
5126 <li>newView public method</li>
5127 <li>Window (current view) specific get/set public methods</li>
5128 <li>Feature display control methods</li>
5129 <li>get list of currently selected sequences</li>
5130 </ul> <em>New Jalview distribution features</em>
5132 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
5133 <li>RELEASE file gives build properties for the latest
5134 Jalview release.</li>
5135 <li>Java 1.1 Applet build made easier and donotobfuscate
5136 property controls execution of obfuscator</li>
5137 <li>Build target for generating source distribution</li>
5138 <li>Debug flag for javacc</li>
5139 <li>.jalview_properties file is documented (slightly) in
5140 jalview.bin.Cache</li>
5141 <li>Continuous Build Integration for stable and
5142 development version of Application, Applet and source
5147 <li>selected region output includes visible annotations
5148 (for certain formats)</li>
5149 <li>edit label/displaychar contains existing label/char
5151 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
5152 <li>shorter peptide product names from EMBL records</li>
5153 <li>Newick string generator makes compact representations</li>
5154 <li>bootstrap values parsed correctly for tree files with
5156 <li>pathological filechooser bug avoided by not allowing
5157 filenames containing a ':'</li>
5158 <li>Fixed exception when parsing GFF files containing
5159 global sequence features</li>
5160 <li>Alignment datasets are finalized only when number of
5161 references from alignment sequences goes to zero</li>
5162 <li>Close of tree branch colour box without colour
5163 selection causes cascading exceptions</li>
5164 <li>occasional negative imgwidth exceptions</li>
5165 <li>better reporting of non-fatal warnings to user when
5166 file parsing fails.</li>
5167 <li>Save works when Jalview project is default format</li>
5168 <li>Save as dialog opened if current alignment format is
5169 not a valid output format</li>
5170 <li>UniProt canonical names introduced for both das and
5172 <li>Histidine should be midblue (not pink!) in Zappo</li>
5173 <li>error messages passed up and output when data read
5175 <li>edit undo recovers previous dataset sequence when
5176 sequence is edited</li>
5177 <li>allow PDB files without pdb ID HEADER lines (like
5178 those generated by MODELLER) to be read in properly</li>
5179 <li>allow reading of JPred concise files as a normal
5181 <li>Stockholm annotation parsing and alignment properties
5182 import fixed for PFAM records</li>
5183 <li>Structure view windows have correct name in Desktop
5185 <li>annotation consisting of sequence associated scores
5186 can be read and written correctly to annotation file</li>
5187 <li>Aligned cDNA translation to aligned peptide works
5189 <li>Fixed display of hidden sequence markers and
5190 non-italic font for representatives in Applet</li>
5191 <li>Applet Menus are always embedded in applet window on
5193 <li>Newly shown features appear at top of stack (in
5195 <li>Annotations added via parameter not drawn properly
5196 due to null pointer exceptions</li>
5197 <li>Secondary structure lines are drawn starting from
5198 first column of alignment</li>
5199 <li>UniProt XML import updated for new schema release in
5201 <li>Sequence feature to sequence ID match for Features
5202 file is case-insensitive</li>
5203 <li>Sequence features read from Features file appended to
5204 all sequences with matching IDs</li>
5205 <li>PDB structure coloured correctly for associated views
5206 containing a sub-sequence</li>
5207 <li>PDB files can be retrieved by applet from Jar files</li>
5208 <li>feature and annotation file applet parameters
5209 referring to different directories are retrieved correctly</li>
5210 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
5211 <li>Fixed application hang whilst waiting for
5212 splash-screen version check to complete</li>
5213 <li>Applet properly URLencodes input parameter values
5214 when passing them to the launchApp service</li>
5215 <li>display name and local features preserved in results
5216 retrieved from web service</li>
5217 <li>Visual delay indication for sequence retrieval and
5218 sequence fetcher initialisation</li>
5219 <li>updated Application to use DAS 1.53e version of
5220 dasobert DAS client</li>
5221 <li>Re-instated Full AMSA support and .amsa file
5223 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
5231 <div align="center">
5232 <strong>2.3</strong><br> 9/5/07
5237 <li>Jmol 11.0.2 integration</li>
5238 <li>PDB views stored in Jalview XML files</li>
5239 <li>Slide sequences</li>
5240 <li>Edit sequence in place</li>
5241 <li>EMBL CDS features</li>
5242 <li>DAS Feature mapping</li>
5243 <li>Feature ordering</li>
5244 <li>Alignment Properties</li>
5245 <li>Annotation Scores</li>
5246 <li>Sort by scores</li>
5247 <li>Feature/annotation editing in applet</li>
5252 <li>Headless state operation in 2.2.1</li>
5253 <li>Incorrect and unstable DNA pairwise alignment</li>
5254 <li>Cut and paste of sequences with annotation</li>
5255 <li>Feature group display state in XML</li>
5256 <li>Feature ordering in XML</li>
5257 <li>blc file iteration selection using filename # suffix</li>
5258 <li>Stockholm alignment properties</li>
5259 <li>Stockhom alignment secondary structure annotation</li>
5260 <li>2.2.1 applet had no feature transparency</li>
5261 <li>Number pad keys can be used in cursor mode</li>
5262 <li>Structure Viewer mirror image resolved</li>
5269 <div align="center">
5270 <strong>2.2.1</strong><br> 12/2/07
5275 <li>Non standard characters can be read and displayed
5276 <li>Annotations/Features can be imported/exported to the
5278 <li>Applet allows editing of sequence/annotation/group
5279 name & description
5280 <li>Preference setting to display sequence name in
5282 <li>Annotation file format extended to allow
5283 Sequence_groups to be defined
5284 <li>Default opening of alignment overview panel can be
5285 specified in preferences
5286 <li>PDB residue numbering annotation added to associated
5292 <li>Applet crash under certain Linux OS with Java 1.6
5294 <li>Annotation file export / import bugs fixed
5295 <li>PNG / EPS image output bugs fixed
5301 <div align="center">
5302 <strong>2.2</strong><br> 27/11/06
5307 <li>Multiple views on alignment
5308 <li>Sequence feature editing
5309 <li>"Reload" alignment
5310 <li>"Save" to current filename
5311 <li>Background dependent text colour
5312 <li>Right align sequence ids
5313 <li>User-defined lower case residue colours
5316 <li>Menu item accelerator keys
5317 <li>Control-V pastes to current alignment
5318 <li>Cancel button for DAS Feature Fetching
5319 <li>PCA and PDB Viewers zoom via mouse roller
5320 <li>User-defined sub-tree colours and sub-tree selection
5323 <li>'New Window' button on the 'Output to Text box'
5328 <li>New memory efficient Undo/Redo System
5329 <li>Optimised symbol lookups and conservation/consensus
5331 <li>Region Conservation/Consensus recalculated after
5333 <li>Fixed Remove Empty Columns Bug (empty columns at end
5335 <li>Slowed DAS Feature Fetching for increased robustness.
5338 <li>Made angle brackets in ASCII feature descriptions
5340 <li>Re-instated Zoom function for PCA
5341 <li>Sequence descriptions conserved in web service
5343 <li>UniProt ID discoverer uses any word separated by
5345 <li>WsDbFetch query/result association resolved
5346 <li>Tree leaf to sequence mapping improved
5347 <li>Smooth fonts switch moved to FontChooser dialog box.
5355 <div align="center">
5356 <strong>2.1.1</strong><br> 12/9/06
5361 <li>Copy consensus sequence to clipboard</li>
5366 <li>Image output - rightmost residues are rendered if
5367 sequence id panel has been resized</li>
5368 <li>Image output - all offscreen group boundaries are
5370 <li>Annotation files with sequence references - all
5371 elements in file are relative to sequence position</li>
5372 <li>Mac Applet users can use Alt key for group editing</li>
5378 <div align="center">
5379 <strong>2.1</strong><br> 22/8/06
5384 <li>MAFFT Multiple Alignment in default Web Service list</li>
5385 <li>DAS Feature fetching</li>
5386 <li>Hide sequences and columns</li>
5387 <li>Export Annotations and Features</li>
5388 <li>GFF file reading / writing</li>
5389 <li>Associate structures with sequences from local PDB
5391 <li>Add sequences to exisiting alignment</li>
5392 <li>Recently opened files / URL lists</li>
5393 <li>Applet can launch the full application</li>
5394 <li>Applet has transparency for features (Java 1.2
5396 <li>Applet has user defined colours parameter</li>
5397 <li>Applet can load sequences from parameter
5398 "sequence<em>x</em>"
5404 <li>Redundancy Panel reinstalled in the Applet</li>
5405 <li>Monospaced font - EPS / rescaling bug fixed</li>
5406 <li>Annotation files with sequence references bug fixed</li>
5412 <div align="center">
5413 <strong>2.08.1</strong><br> 2/5/06
5418 <li>Change case of selected region from Popup menu</li>
5419 <li>Choose to match case when searching</li>
5420 <li>Middle mouse button and mouse movement can compress /
5421 expand the visible width and height of the alignment</li>
5426 <li>Annotation Panel displays complete JNet results</li>
5432 <div align="center">
5433 <strong>2.08b</strong><br> 18/4/06
5439 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
5440 <li>Righthand label on wrapped alignments shows correct
5447 <div align="center">
5448 <strong>2.08</strong><br> 10/4/06
5453 <li>Editing can be locked to the selection area</li>
5454 <li>Keyboard editing</li>
5455 <li>Create sequence features from searches</li>
5456 <li>Precalculated annotations can be loaded onto
5458 <li>Features file allows grouping of features</li>
5459 <li>Annotation Colouring scheme added</li>
5460 <li>Smooth fonts off by default - Faster rendering</li>
5461 <li>Choose to toggle Autocalculate Consensus On/Off</li>
5466 <li>Drag & Drop fixed on Linux</li>
5467 <li>Jalview Archive file faster to load/save, sequence
5468 descriptions saved.</li>
5474 <div align="center">
5475 <strong>2.07</strong><br> 12/12/05
5480 <li>PDB Structure Viewer enhanced</li>
5481 <li>Sequence Feature retrieval and display enhanced</li>
5482 <li>Choose to output sequence start-end after sequence
5483 name for file output</li>
5484 <li>Sequence Fetcher WSDBFetch@EBI</li>
5485 <li>Applet can read feature files, PDB files and can be
5486 used for HTML form input</li>
5491 <li>HTML output writes groups and features</li>
5492 <li>Group editing is Control and mouse click</li>
5493 <li>File IO bugs</li>
5499 <div align="center">
5500 <strong>2.06</strong><br> 28/9/05
5505 <li>View annotations in wrapped mode</li>
5506 <li>More options for PCA viewer</li>
5511 <li>GUI bugs resolved</li>
5512 <li>Runs with -nodisplay from command line</li>
5518 <div align="center">
5519 <strong>2.05b</strong><br> 15/9/05
5524 <li>Choose EPS export as lineart or text</li>
5525 <li>Jar files are executable</li>
5526 <li>Can read in Uracil - maps to unknown residue</li>
5531 <li>Known OutOfMemory errors give warning message</li>
5532 <li>Overview window calculated more efficiently</li>
5533 <li>Several GUI bugs resolved</li>
5539 <div align="center">
5540 <strong>2.05</strong><br> 30/8/05
5545 <li>Edit and annotate in "Wrapped" view</li>
5550 <li>Several GUI bugs resolved</li>
5556 <div align="center">
5557 <strong>2.04</strong><br> 24/8/05
5562 <li>Hold down mouse wheel & scroll to change font
5568 <li>Improved JPred client reliability</li>
5569 <li>Improved loading of Jalview files</li>
5575 <div align="center">
5576 <strong>2.03</strong><br> 18/8/05
5581 <li>Set Proxy server name and port in preferences</li>
5582 <li>Multiple URL links from sequence ids</li>
5583 <li>User Defined Colours can have a scheme name and added
5585 <li>Choose to ignore gaps in consensus calculation</li>
5586 <li>Unix users can set default web browser</li>
5587 <li>Runs without GUI for batch processing</li>
5588 <li>Dynamically generated Web Service Menus</li>
5593 <li>InstallAnywhere download for Sparc Solaris</li>
5599 <div align="center">
5600 <strong>2.02</strong><br> 18/7/05
5606 <li>Copy & Paste order of sequences maintains
5607 alignment order.</li>
5613 <div align="center">
5614 <strong>2.01</strong><br> 12/7/05
5619 <li>Use delete key for deleting selection.</li>
5620 <li>Use Mouse wheel to scroll sequences.</li>
5621 <li>Help file updated to describe how to add alignment
5623 <li>Version and build date written to build properties
5625 <li>InstallAnywhere installation will check for updates
5626 at launch of Jalview.</li>
5631 <li>Delete gaps bug fixed.</li>
5632 <li>FileChooser sorts columns.</li>
5633 <li>Can remove groups one by one.</li>
5634 <li>Filechooser icons installed.</li>
5635 <li>Finder ignores return character when searching.
5636 Return key will initiate a search.<br>
5643 <div align="center">
5644 <strong>2.0</strong><br> 20/6/05
5649 <li>New codebase</li>