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.2.11.2.1">.1</a><br />
62 <em>05/04/2022</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-3985 -->PDB FTS query results in error dialog
83 containing '414' [URL too long]
86 <!-- JAL-3980 JAL-3981 -->Sequence ID tooltip not shown during
87 long running retrieval/crossref operations (affects at least
91 <!-- JAL-3973 -->Cannot build Jalview 2.11.2.0 via gradle
92 from its source tarball
94 </ul> <em>New Known Issues</em>
97 <!-- JAL-3984 -->Keyboard mode (F2) stops working after
98 using the "Text Colour" dialog
101 <!-- JAL-3873 -->Colour by->all views doesn't allow
102 colouring same structure from different views (since
106 <!-- JAL-3981 --> Sequence Details report can take a long
107 time to be displayed for heavily annotated sequences (such
108 as single genome contigs for highly studied organisms)
111 <!-- JAL-3886 -->Pfam and Rfam alignment retrieval as
112 gzipped stockholm doesn't work on JalviewJS build of 2.11.2
115 <!-- JAL-3972 -->Java 11 Only: Jalview 2.11.2.0 OSX install
116 not working due to VAqua requiring
117 sun.awt.image.MultiResolutionImage
120 <!-- JAL-3981 -->Sequence Details can take a long time to be
121 displayed for heavily annotated sequences (all versions)
127 <td width="60" align="center" nowrap><strong><a
128 id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.0">.0</a><br />
129 <em>10/03/2022</em></strong></td>
130 <td align="left" valign="top">
133 <!-- JAL-3616 JAL-3551 JAL-2322 -->Support for viewing 3D
134 structures with ChimeraX and Pymol in addition to Jmol and
138 <!-- JAL-3829 -->Discover 3D structure data for sequences
139 with Uniprot references via 3D-Beacons
142 <!-- JAL-3391 -->Rank and select available structures for
143 Uniprot sequences according to number of residues in
144 structure mapped to positions involved in the alignment
147 <!-- JAL-2226 -->Structure annotation rows for all mapped
148 chains in 3D structures are included in the 'Reference
149 Annotation' for a sequence
152 <!-- JAL-1260 -->Import Genbank and EMBL format flatfiles
155 <!-- JAL-3821 -->ENA record's mol_type honoured so RNA
156 molecules imported from ENA records are shown as RNA
158 <!-- JAL-3863 -->Support for Canonical Uniprot IDs
161 <!-- JAL-3503 -->New Preferences tab for adjusting Jalview's
162 memory settings at launch
165 <!-- JAL-3881 -->Sequence IDs split on '_' as well as other
166 non-alphanumerics when discovering database references with
170 <!-- JAL-3884 -->Suppressed harmless exceptions output to
171 Console whilst discovering database references for a
175 <!-- JAL-3204 -->Updated Jalview bindings for Uniprot XML
179 <!-- JAL-3926 -->Uniprot and PDBe autosearch option is
183 <!-- JAL-3144 -->Reverted to Jalview 'classic' drop-down
184 menu for selecting which database to fetch from in sequence
188 <!-- JAL-3018 -->Updated Ensembl REST Client compatibility
189 to 15.2 and revised model organism names (rat, xenopus,
190 dmelanogaster now rattus_norvegicus, xenopus_tropicalis,
191 drosophila_melanogaster)
194 <!-- JAL-3530 -->-nowebservicediscovery command line
195 argument to prevent automatic discovery of analysis
196 webservices on launch
199 <!-- JAL-3618 -->Allow 'App' directories to be opened when
200 locating Chimera, ChimeraX or Pymol binaries via filechooser
201 opened by double clicking the Structure Preferences' path
205 <!-- JAL-3632 JAL-3633 -->support for HTTP/S access via
206 proxies that require authentication
209 <!-- JAL-3103 -->New mechanism for opening URLs with system
210 default browser (works on OSX and Linux as well as Windows)
213 <!-- JAL-3871 JAL-3874 -->Upgraded bundled version of Jmol
217 <!-- JAL-3837 -->GPL license info on splash screen and About
220 </ul> <em>Jalview Native App</em>
223 <!-- JAL-3830 -->New command line launcher scripts (.sh,
224 .ps1, .bat) usable on macOS, Linux/Unix, Windows and
225 documentation in Help. Installer wizard has option to add
226 this to PATH, or link to it in your PATH.<br /> <em>This
227 is the recommended workaround for known issue about
228 working directory preservation when running native
229 application from command line. <!-- JAL-3523 -->
232 <li>Notarized MacOS installer for compliance with latest
233 OSX releases (Monterey)</li>
235 <!-- JAL-3805 -->Uninstaller application for old
236 (InstallAnywhere based) Jalview installations removed from
240 <!-- JAL-3608 -->Options to allow user to choose the (Swing)
241 Look and Feel (LaF) used by Jalview
244 <!-- JAL-3552, JAL-3609 -->Metal LaF used to improved
245 operation on Linux Ubuntu with HiDPI display in Java 11
246 (still known issues with HiDPI screens in java 8 and 11. see
247 <a href="https://issues.jalview.org/browse/JAL-3137">JAL-3137</a>)
250 <!-- JAL-3633 -->Getdown launcher inherits HTTP/S proxy
251 configuration from jalview_properties
254 <!-- JAL- -->New Jalview Develop app - making it even easier
255 to get at Jalview's development builds
258 <!-- JAL-3594 -->New splashscreens for Jalview, Jalview Test
259 and Jalview Develop applications.
262 <!-- JAL-3728 -->Jalview logos shown for Jalview Java
263 Console and other window widgets in taskbar and dock rather
264 than anonymous 'Java' icons
266 </ul> <em>JalviewJS</em>
269 <!-- JAL-3624 -->PDB structures mapped to Uniprot Sequences
273 <!-- JAL-3208 -->setprop commandline argument reinstated for
277 <!-- JAL-3163 -->Missing message bundle keys are only
278 reported once per key (avoids excessive log output in js
282 <!-- JAL-3168 -->Feature type is included in the title of
283 the Feature Settings' Colour Chooser dialog
286 <!-- JAL-3279 -->Build details reported in About window
289 <!-- JAL-3038 JAL-3071 JAL-3263 JAL-3084 -->Numerous minor
290 GUI additions and improvements in sync with Java
293 </ul> <em>Development</em>
296 <!-- -->First integrated JalviewJS and Jalview release
299 <!-- JAL-3841,JAL-3248 -->Updated README and doc/building.md
302 <!-- JAL-3789, JAL-3679 -->Improved JalviewJS/Jalview build
303 process, added support for system package provided eclipse
306 <li>Install4j 9.0.x used for installer packaging</li>
308 <!-- JAL-3930 -->Improved use of installers for unattended
309 installation with a customizedId of "JALVIEW" in install4j's
313 <!-- JAL-3907 -->Improved compatibility of Jalview build
314 with Java 17 (next LTS target)
318 <td align="left" valign="top">
321 <!-- JAL-3674 -->Slow structure commands can block Jalview
325 <!-- JAL-3904 -->Structure window's viewer-specific menu
326 disappears when only one structure is shown (and many
327 sequences:one chain mappings are present)
330 <!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
331 the first SEQUENCE_GROUP defined
335 <!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 -->Selections not
336 propagated between Linked CDS - Protein alignments and their
337 trees (known defect from 2.11.1.3)
340 <!-- JAL-3761 -->Not all codon positions highlighted for
341 overlapping exon splice sites (e.g due to RNA slippage)
344 <!-- JAL-3794 -->X was not being recognised as the unknown
345 base in DNA sequences
348 <!-- JAL-3915 -->Removed RNAview checkbox and logic from
349 Structure Preferences
352 <!-- JAL-3583 -->Tooltip behaviour improved (slightly)
355 <!-- JAL-3162 -->Can edit a feature so that start > end
358 <!-- JAL-2848 -->Cancel from Amend Features doesn't reset a
359 modified graduated colour
362 <!-- JAL-3788 -->New View with automatic 'Show Overview'
363 preference enabled results in Null Pointer Exceptions when
364 clustal colouring is enabled
367 <!-- JAL-3275 -->Can open multiple Preferences panels
370 <!-- JAL-3633 -->Properly configure HTTPS proxy settings
374 <!-- JAL-3949 -->Standard out logging broken: messages only
375 routing to stderr and appear as a raw template
378 <!-- JAL-3739 -->Entering web service parameter values in
379 numerical field doesn't update the value of the parameter
380 until return is pressed.
383 <!-- JAL-3749 -->Resolved known issue (from 2.11.1.1)
384 concerning duplicate CDS sequences generated when protein
385 products for certain ENA records are repeatedly shown via
386 Calculate->Show Cross Refs
388 </ul> <em>JalviewJS</em>
391 <!-- JAL-3202 -->Consensus profile may include zero (rounded
392 down) percentage values causing a divide by zero
395 <!-- JAL-3762 -->JalviewJS doesn't honour arguments passed
396 via Info.args when there are arguments on the URL
399 <!-- JAL-3602 -->gradle closure-compiler not using UTF-8
402 <!-- JAL-3603 -->Annotation file fails to load from URL in
405 </ul> <em>Development</em>
409 <li>Fixed non-fatal gradle errors during build</li>
411 <!-- JAL-3745 -->Updated build.gradle for use with
417 </ul> <em>Known Issues</em>
420 <!-- JAL-3764 -->Display of RESNUM sequence features are not
421 suppressed when structures associated with a sequence are
422 viewed with an external viewer (Regression from 2.11.1
429 <td width="60" align="center" nowrap><strong><a
430 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.7">.7</a><br />
431 <em>18/01/2022</em></strong></td>
433 <td align="left" valign="top">
436 <!-- JAL-3703, JAL-3935 -->Files open in Jalview cannot be
437 updated by Jalview or other applications (Windows, other non
440 </ul> <em>Security</em>
443 <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
449 <td width="60" align="center" nowrap><strong><a
450 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
451 <em>6/01/2022</em></strong></td>
453 <td align="left" valign="top"><em>Security</em>
456 <!-- JAL-3934 -->Version bump library dependency: Log4j
463 <td width="60" align="center" nowrap><strong><a
464 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
465 <em>20/12/2021</em></strong></td>
467 <td align="left" valign="top"><em>Security</em>
470 <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
472 </ul> <em>Development</em>
474 <li>Updated building instructions</li>
479 <!-- JAL-3840 -->Occupancy calculation is incorrect for
480 alignment columns with over -1+2^32 gaps (breaking filtering
484 <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
485 scale factors being set with buggy window-managers (linux
488 </ul> <em>Development</em>
490 <li>Fixed non-fatal gradle errors during build</li>
495 <td width="60" align="center" nowrap><strong><a
496 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
497 <em>09/03/2021</em></strong></td>
498 <td align="left" valign="top"><em>Improved control of
499 Jalview's use of network services via jalview_properties</em>
502 <!-- JAL-3814 -->New .jalview_properties token controlling
503 launch of the news browser (like -nonews argument)
506 <!-- JAL-3813 -->New .jalview_properties token controlling
507 download of linkout URLs from
508 www.jalview.org/services/identifiers
511 <!-- JAL-3812 -->New .jalview_properties token controlling
512 download of BIOJSHTML templates
515 <!-- JAL-3811 -->New 'Discover Web Services' option to
516 trigger a one off JABAWS discovery if autodiscovery was
520 <td align="left" valign="top">
523 <!-- JAL-3818 -->Intermittent deadlock opening structure in
526 </ul> <em>New Known defects</em>
529 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
530 always restored from project (since 2.10.3)
533 <!-- JAL-3806 -->Selections from tree built from CDS aren't
534 propagated to Protein alignment (since 2.11.1.3)
540 <td width="60" align="center" nowrap><strong><a
541 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
542 <em>29/10/2020</em></strong></td>
543 <td align="left" valign="top">
548 <td align="left" valign="top">
551 <!-- JAL-3765 -->Find doesn't always highlight all matching
552 positions in a sequence (bug introduced in 2.11.1.2)
555 <!-- JAL-3760 -->Alignments containing one or more protein
556 sequences can be classed as nucleotide
559 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
560 sequences after alignment of protein products (known defect
561 first reported for 2.11.1.0)
564 <!-- JAL-3725 -->No tooltip or popup menu for genomic
565 features outwith CDS shown overlaid on protein
568 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
569 correctly mapped by Jalview (e.g. affects viral CDS with
570 ribosomal slippage, since 2.9.0)
573 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
577 <!-- JAL-3700 -->Selections in CDS sequence panel don't
578 always select corresponding protein sequences
581 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
582 column selection doesn't always ignore hidden columns
584 </ul> <em>Installer</em>
587 <!-- JAL-3611 -->Space character in Jalview install path on
588 Windows prevents install4j launching getdown
590 </ul> <em>Development</em>
593 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
594 version numbers in doc/building.md
600 <td width="60" align="center" nowrap><strong><a
601 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
602 <em>25/09/2020</em></strong></td>
603 <td align="left" valign="top">
607 <td align="left" valign="top">
610 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
611 "Encountered problems opening
612 https://www.jalview.org/examples/exampleFile_2_7.jvp"
618 <td width="60" align="center" nowrap><strong><a
619 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
620 <em>17/09/2020</em></strong></td>
621 <td align="left" valign="top">
624 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
625 residue in cursor mode
628 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
629 HTSJDK from 2.12 to 2.23
632 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
633 optimisations and improvements suggested by Bob Hanson and
634 improved compatibility with JalviewJS
637 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
638 alignments from Pfam and Rfam
641 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
642 import (no longer based on .gz extension)
645 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
648 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
649 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
653 <!-- JAL-3667 -->Improved warning messages, debug logging
654 and fixed Retry action when Jalview encounters errors when
655 saving or making backup files.
658 <!-- JAL-3676 -->Enhanced Jalview Java Console:
660 <li>Jalview's logging level can be configured</li>
661 <li>Copy to Clipboard Buttion</li>
665 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
666 when running on Linux (Requires Java 11+)
669 <!-- JAL-1842 JAL-3509 -->RESNUM sequence features (the
670 green ones) are not automatically displayed when associated
671 structures are displayed or for sequences retrieved from the
674 </ul> <em>Launching Jalview</em>
677 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
678 through a system property
681 <!-- JAL-3477 -->Improved built-in documentation and command
682 line help for configuring Jalview's memory
686 <td align="left" valign="top">
689 <!-- JAL-3691 -->Conservation and Quality tracks are shown
690 but not calculated and no protein or DNA score models are
691 available for tree/PCA calculation when launched with
692 Turkish language locale
695 <!-- JAL-3493 -->Escape does not clear highlights on the
696 alignment (Since Jalview 2.10.3)
699 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
700 doesn't slide selected sequences, just sequence under cursor
703 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
704 sequence under the cursor
707 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
708 multiple EMBL gene products shown for a single contig
711 <!-- JAL-3696 -->Errors encountered when processing variants
712 from VCF files yield "Error processing VCF: Format specifier
716 <!-- JAL-3697 -->Count of features not shown can be wrong
717 when there are both local and complementary features mapped
718 to the position under the cursor
721 <!-- JAL-3673 -->Sequence ID for reference sequence is
722 clipped when Right align Sequence IDs enabled
725 <!-- JAL-2983 -->Slider with negative range values not
726 rendered correctly in VAqua4 (Since 2.10.4)
729 <!-- JAL-3685 -->Single quotes not displayed correctly in
730 internationalised text for some messages and log output
733 <!-- JAL-3490 -->Find doesn't report matches that span
734 hidden gapped columns
737 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
738 panels, Alignment viewport and annotation renderer.
741 <!-- JAL-3561 -->Jalview ignores file format parameter
742 specifying output format when exporting an alignment via the
746 <!-- JAL-3667 -->Windows 10: For a minority of users, if
747 backups are not enabled, Jalview sometimes fails to
748 overwrite an existing file and raises a warning dialog. (in
749 2.11.0, and 2.11.1.0, the workaround is to try to save the
750 file again, and if that fails, delete the original file and
754 <!-- JAL-3509 -->Dragging a PDB file onto an alignment with
755 sequence features displayed causes displayed features to be
759 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
763 <!-- JAL-3741 -->References to http://www.jalview.org in
764 program and documentation
766 </ul> <em>Launching Jalview</em>
769 <!-- JAL-3718 -->Jalview application fails when launched the
770 first time for a version that has different jars to the
771 previous launched version.
773 </ul> <em>Developing Jalview</em>
776 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
777 data, causing cloverReport gradle task to fail with an
781 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
782 monitor the release channel
784 </ul> <em>New Known defects</em>
787 <!-- JAL-3748 -->CDS shown in result of submitting proteins
788 in a CDS/Protein alignment to a web service is wrong when
789 proteins share a common transcript sequence (e.g. genome of
793 <!-- JAL-3576 -->Co-located features exported and
794 re-imported are ordered differently when shown on alignment
795 and in tooltips. (Also affects v2.11.1.0)
798 <!-- JAL-3702 -->Drag and drop of alignment file onto
799 alignment window when in a HiDPI scaled mode in Linux only
800 works for the top left quadrant of the alignment window
803 <!-- JAL-3701 -->Stale build data in jalview standalone jar
804 builds (only affects 2.11.1.1 branch)
807 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
808 when alignment view restored from project (since Jalview
812 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
813 protein products for certain ENA records are repeatedly
814 shown via Calculate->Show Cross Refs
820 <td width="60" align="center" nowrap><strong><a
821 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
822 <em>22/04/2020</em></strong></td>
823 <td align="left" valign="top">
826 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
827 'virtual' codon features shown on protein (or vice versa)
828 for display in alignments, on structure views (including
829 transfer to UCSF chimera), in feature reports and for
833 <!-- JAL-3121 -->Feature attributes from VCF files can be
834 exported and re-imported as GFF3 files
837 <!-- JAL-3376 -->Capture VCF "fixed column" values
838 POS, ID, QUAL, FILTER as Feature Attributes
841 <!-- JAL-3375 -->More robust VCF numeric data field
842 validation while parsing
845 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
849 <!-- JAL-3535 -->Feature Settings dialog title includes name
853 <!-- JAL-3538 -->Font anti-aliasing in alignment views
857 <!-- JAL-3468 -->Very long feature descriptions truncated in
861 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
862 with no feature types visible
865 <!-- JAL-3574 -->Improved support for filtering feature
866 attributes with large integer values
869 <em>Jalview Installer</em>
872 <!-- JAL-3449 -->Versions for install4j and getdown and
873 installer template version reported in console (may be null
874 when Jalview launched as executable jar or via conda)
877 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and
878 higher quality background images
881 <!-- JAL-3394 -->New installer/application launcher
882 generated with install4j 8.0.4
885 <!-- JAL-3420 -->Jalview File Associations shown for Unix
889 <!-- JAL-3477 -->Improved defaults for maximum memory
890 setting when running on large memory machines
892 </ul> <em>Release processes</em>
895 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
898 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier
899 access to test-release channel builds
901 </ul> <em>Build System</em>
904 <!-- JAL-3510 -->Clover updated to 4.4.1
907 <!-- JAL-3513 -->Test code included in Clover coverage
910 </ul> <em>Groovy Scripts</em>
913 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
914 to stdout containing the consensus sequence for each
915 alignment in a Jalview session
918 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
919 genomic sequence_variant annotation from CDS as
920 missense_variant or synonymous_variant on protein products.
924 <td align="left" valign="top">
927 <!-- JAL-3581 -->Hidden sequence markers still visible when
928 'Show hidden markers' option is not ticked
931 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
932 PNG output when 'Automatically set ID width' is set in
933 jalview preferences or properties file
936 <!-- JAL-3571 -->Feature Editor dialog can be opened when
937 'Show Sequence Features' option is not ticked
940 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
941 buttons in Feature Settings dialog are clicked when no
945 <!-- JAL-3412 -->ID margins for CDS and Protein views not
946 equal when split frame is first opened
949 <!-- JAL-3296 -->Sequence position numbers in status bar not
950 correct after editing a sequence's start position
953 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
954 with annotation and exceptions thrown when only a few
955 columns shown in wrapped mode
958 <!-- JAL-3386 -->Sequence IDs missing in headless export of
959 wrapped alignment figure with annotations
962 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
963 ID fails with ClassCastException
966 <!-- JAL-3389 -->Chimera session not restored from Jalview
970 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
971 feature settings dialog also selects columns
974 <!-- JAL-3473 -->SpinnerNumberModel causes
975 IllegalArgumentException in some circumstances
978 <!-- JAL-3534 -->Multiple feature settings dialogs can be
982 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
983 alignment window is closed
986 <!-- JAL-3406 -->Credits missing some authors in Jalview
987 help documentation for 2.11.0 release
990 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
991 includes Pfam ID as sequence's accession rather than its
994 </ul> <em>Java 11 Compatibility issues</em>
997 <!-- JAL-2987 -->OSX - Can't view some search results in
998 PDB/Uniprot search panel
1000 </ul> <em>Installer</em>
1003 <!-- JAL-3447 -->Jalview should not create file associations
1004 for 3D structure files (.pdb, .mmcif. .cif)
1006 </ul> <em>Repository and Source Release</em>
1009 <!-- JAL-3474 -->removed obsolete .cvsignore files from
1013 <!-- JAL-3541 -->Clover report generation running out of
1016 </ul> <em>New Known Issues</em>
1019 <!-- JAL-3523 -->OSX - Current working directory not
1020 preserved when Jalview.app launched with parameters from
1024 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
1025 clipped in headless figure export when Right Align option
1029 <!-- JAL-3542 -->Jalview Installation type always reports
1030 'Source' in console output
1033 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail
1034 on jalview's bamboo server but run fine locally.
1040 <td width="60" align="center" nowrap><strong><a
1041 name="Jalview.2.11.0">2.11.0</a><br /> <em>04/07/2019</em></strong></td>
1042 <td align="left" valign="top">
1045 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native
1046 Application and Installers built with <a
1047 href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a>
1048 (licensed to the Jalview open source project) rather than
1052 <!-- JAL-1929 -->Jalview Launcher System to auto-configure
1053 memory settings, receive over the air updates and launch
1054 specific versions via (<a
1055 href="https://github.com/threerings/getdown">Three
1059 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations
1060 for formats supported by Jalview (including .jvp project
1064 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command
1065 line arguments and switch between different getdown channels
1068 <!-- JAL-3141 -->Backup files created when saving Jalview
1069 project or alignment files
1073 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF
1077 <!-- JAL-2753 -->Version of HTSJDK shipped with Jalview
1078 updated to version 2.12.0
1081 <!-- JAL-2620 -->Alternative genetic code tables for
1085 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0
1087 <li><strong>Enhanced visualisation and analysis
1088 of Sequence Features</strong>
1091 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
1092 implementation that allows updates) used for Sequence
1096 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
1097 features can be filtered and shaded according to any
1098 associated attributes (e.g. variant attributes from VCF
1099 file, or key-value pairs imported from column 9 of GFF
1103 <!-- JAL-2879 -->Feature Attributes and shading schemes
1104 stored and restored from Jalview Projects
1107 <!-- JAL-3334 -->Use full Sequence Ontology (via
1108 BioJava) to recognise variant features
1111 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants
1112 on peptide sequences (also coloured red by default)
1115 <!-- JAL-2792 -->Popup window to show full report for a
1116 selected sequence feature's details
1119 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient
1120 sequence feature render algorithm (Z-sort/transparency
1124 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature
1129 <!-- JAL-3205 -->Symmetric score matrices for faster tree
1130 and PCA calculations
1132 <li><strong>Principal Components Analysis Viewer</strong>
1135 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis
1136 results and Viewer state saved in Jalview Project
1139 <!-- JAL-2962 -->'Change parameters' option removed from
1140 viewer's drop-down menus
1143 <!-- JAL-2975 -->Can use shift + arrow keys to rotate
1144 PCA image incrementally
1147 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
1151 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
1153 <li><strong>Speed and Efficiency</strong>
1156 <!-- JAL-2185,JAL-3198 -->More efficient creation of
1157 selections and multiple groups when working with large
1161 <!-- JAL-3200 -->Speedier import of annotation rows when
1162 parsing Stockholm files
1165 <li><strong>User Interface</strong>
1168 <!-- JAL-2933 -->Finder panel remembers last position in
1172 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS
1173 (What you see is what is shown)<br />Only visible
1174 regions of alignment are shown by default (can be
1175 changed in user preferences)
1178 <!-- JAL-3169 -->File Chooser stays open after
1179 responding Cancel to the Overwrite Dialog
1182 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour
1183 when all sequences are hidden
1186 <!-- JAL-1244 -->Status bar shows bounds when dragging a
1187 selection region, and gap count when inserting or
1191 <!-- JAL-3132 -->Status bar updates over sequence and
1195 <!-- JAL-3093 -->Annotation tooltips and popup menus are
1196 shown when in wrapped mode
1199 <!-- JAL-3073 -->Can select columns by dragging
1200 left/right in a graph or histogram annotation
1203 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB
1207 <!-- JAL-2621 -->Cursor changes over draggable box in
1211 <!-- JAL-3181 -->Consistent ordering of links in
1212 sequence id popup menu
1215 <!-- JAL-3080 -->Red line indicating tree-cut position
1216 not shown if no subgroups are created
1219 <!-- JAL-3042 -->Removed ability to configure length of
1220 search history by right-clicking search box
1226 <!-- JAL-3232 -->Jalview Groovy Scripting Console updated to
1229 <li><strong>Java 11 Support (not yet on general
1233 <!-- -->OSX GUI integrations for App menu's 'About'
1234 entry and trapping CMD-Q
1237 </ul> <em>Deprecations</em>
1240 <!-- JAL-3035 -->DAS sequence retrieval and annotation
1241 capabilities removed from the Jalview Desktop
1244 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling
1245 and unmarshalling has been replaced by JAXB for Jalview
1246 projects and XML based data retrieval clients
1249 <!-- JAL-3311 -->Disable VAMSAS menu in preparation for
1253 <!-- -->Jalview Desktop no longer distributed via Java Web
1256 </ul> <em>Documentation</em>
1259 <!-- JAL-3003 -->Added remarks about transparent rendering
1260 effects not supported in EPS figure export
1263 <!-- JAL-2903 -->Typos in documentation for Preferences
1266 </ul> <em>Development and Release Processes</em>
1269 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated
1273 <!-- JAL-1424 -->Enhanced checks for missing and duplicated
1274 keys in Message bundles
1277 <!-- JAL-3225 -->Eclipse project configuration managed with
1281 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian Bamboo
1282 continuous integration for unattended Test Suite execution
1285 <!-- JAL-2864 -->Memory test suite to detect leaks in common
1289 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
1293 <!-- JAL-3248 -->Developer documentation migrated to
1294 markdown (with HTML rendering)
1297 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
1300 <!-- JAL-3289 -->New URLs for publishing development
1305 <td align="left" valign="top">
1308 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
1311 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
1312 superposition in Jmol fail on Windows
1315 <!-- JAL-3286 -->Blank error dialog is displayed when
1316 discovering structures for sequences with lots of PDB
1320 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export
1321 with monospaced font
1324 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
1325 Jalview project involving multiple views
1328 <!-- JAL-3164 -->Overview for complementary view in a linked
1329 CDS/Protein alignment is not updated when Hide Columns by
1330 Annotation dialog hides columns
1333 <!-- JAL-3158 -->Selection highlighting in the complement of
1334 a CDS/Protein alignment stops working after making a
1335 selection in one view, then making another selection in the
1339 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
1343 <!-- JAL-3154 -->Table Columns could be re-ordered in
1344 Feature Settings and Jalview Preferences panels
1347 <!-- JAL-2865 -->Jalview hangs when closing windows, or
1348 redrawing the overview with large alignments
1351 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
1352 region if columns were selected by dragging right-to-left
1353 and the mouse moved to the left of the first column
1356 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to
1357 a hidden column marker via scale popup menu
1360 <!-- JAL-2846 -->Error message for trying to load in invalid
1361 URLs doesn't tell users the invalid URL
1364 <!-- JAL-2816 -->Tooltips displayed for features filtered by
1368 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl
1369 during show cross references or Fetch Database References
1370 are shown in red in original view
1373 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown
1374 correctly on peptide sequence (computed variant shown as
1378 <!-- JAL-2060 -->'Graduated colour' option not offered for
1379 manually created features (where feature score is Float.NaN)
1382 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or
1383 printed when columns are hidden
1386 <!-- JAL-3082 -->Regular expression error for '(' in Select
1387 Columns by Annotation description
1390 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after
1391 dragging out of Scale or Annotation Panel
1394 <!-- JAL-3075 -->Column selection incorrect after scrolling
1398 <!-- JAL-3074 -->Left/right drag in annotation can scroll
1402 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal
1406 <!-- JAL-3002 -->Column display is out by one after Page
1407 Down, Page Up in wrapped mode
1410 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
1413 <!-- JAL-2932 -->Finder searches in minimised alignments
1416 <!-- JAL-2250 -->'Apply Colour to All Groups' not always
1417 selected on opening an alignment
1420 <!-- JAL-3180 -->'Colour by Annotation' not marked selected
1424 <!-- JAL-3201 -->Per-group Clustal colour scheme changes
1425 when different groups in the alignment are selected
1428 <!-- JAL-2717 -->Internationalised colour scheme names not
1429 shown correctly in menu
1432 <!-- JAL-3206 -->Colour by Annotation can go black at
1433 min/max threshold limit
1436 <!-- JAL-3125 -->Value input for graduated feature colour
1437 threshold gets 'unrounded'
1440 <!-- JAL-2982 -->PCA image export doesn't respect background
1444 <!-- JAL-2963 -->PCA points don't dim when rotated about y
1448 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
1451 <!-- JAL-3078 -->Cancel in Tree Font dialog resets
1452 alignment, not Tree font
1455 <!-- JAL-2964 -->Associate Tree with All Views not restored
1459 <!-- JAL-2915 -->Scrolling of split frame is sluggish if
1460 Overview shown in complementary view
1463 <!-- JAL-3313 -->Codon consensus incorrectly scaled when
1464 shown without normalisation
1467 <!-- JAL-3021 -->Sequence Details report should open
1468 positioned at top of report
1471 <!-- JAL-914 -->Help page can be opened twice
1474 <!-- JAL-3333 -->Fuzzy text in web service status menu on
1477 </ul> <em>Editing</em>
1480 <!-- JAL-2822 -->Start and End should be updated when
1481 sequence data at beginning or end of alignment added/removed
1485 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection
1486 doesn't relocate sequence features correctly when start of
1487 sequence is removed (Known defect since 2.10)
1490 <!-- JAL-2830 -->Inserting gap sequence via the Edit
1491 Sequence dialog corrupts dataset sequence
1494 <!-- JAL-868 -->Structure colours not updated when
1495 associated tree repartitions the alignment view (Regression
1498 </ul> <em>Datamodel</em>
1501 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
1502 sequence's End is greater than its length
1504 </ul> <em>Bugs fixed for Java 11 Support (not yet on general
1508 <!-- JAL-3288 -->Menus work properly in split-screen
1510 </ul> <em>New Known Defects</em>
1513 <!-- JAL-3340 -->Select columns containing feature by double
1514 clicking ignores bounds of an existing selected region
1517 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in
1518 gapped regions of protein alignment.
1521 <!-- JAL-2647 -->Input Data menu entry is greyed out when
1522 PCA View is restored from a Jalview 2.11 project
1525 <!-- JAL-3213 -->Alignment panel height can be too small
1529 <!-- JAL-3240 -->Display is incorrect after removing gapped
1530 columns within hidden columns
1533 <!-- JAL-3314 -->Rightmost selection is lost when mouse
1534 re-enters window after dragging left to select columns to
1535 left of visible region
1538 <!-- JAL-2876 -->Features coloured according to their
1539 description string and thresholded by score in earlier
1540 versions of Jalview are not shown as thresholded features in
1541 2.11. To workaround please create a Score filter instead.
1544 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't
1545 reset group visibility
1548 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in
1549 linked CDS/Protein view
1552 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1553 alignments with multiple views can close views unexpectedly
1555 </ul> <em>Java 11 Specific defects</em>
1558 <!-- JAL-3235 -->Jalview Properties file is not sorted
1559 alphabetically when saved
1565 <td width="60" nowrap>
1566 <div align="center">
1567 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1570 <td><div align="left">
1574 <!-- JAL-3101 -->Default memory for Jalview webstart and
1575 InstallAnywhere increased to 1G.
1578 <!-- JAL-247 -->Hidden sequence markers and representative
1579 sequence bolding included when exporting alignment as EPS,
1580 SVG, PNG or HTML. <em>Display is configured via the
1581 Format menu, or for command-line use via a Jalview
1582 properties file.</em>
1585 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1586 API and sequence data now imported as JSON.
1589 <!-- JAL-3065 -->Change in recommended way of starting
1590 Jalview via a Java command line: add jars in lib directory
1591 to CLASSPATH, rather than via the deprecated java.ext.dirs
1595 <em>Development</em>
1598 <!-- JAL-3047 -->Support added to execute test suite
1599 instrumented with <a href="http://openclover.org/">Open
1604 <td><div align="left">
1608 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1609 row shown in Feredoxin Structure alignment view of example
1613 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1614 annotation displayed.
1617 <!-- JAL-3107 -->Group conservation/consensus not shown
1618 for newly created group when 'Apply to all groups'
1622 <!-- JAL-3087 -->Corrupted display when switching to
1623 wrapped mode when sequence panel's vertical scrollbar is
1627 <!-- JAL-3003 -->Alignment is black in exported EPS file
1628 when sequences are selected in exported view.</em>
1631 <!-- JAL-3059 -->Groups with different coloured borders
1632 aren't rendered with correct colour.
1635 <!-- JAL-3092 -->Jalview could hang when importing certain
1636 types of knotted RNA secondary structure.
1639 <!-- JAL-3095 -->Sequence highlight and selection in
1640 trimmed VARNA 2D structure is incorrect for sequences that
1644 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1645 annotation when columns are inserted into an alignment,
1646 and when exporting as Stockholm flatfile.
1649 <!-- JAL-3053 -->Jalview annotation rows containing upper
1650 and lower-case 'E' and 'H' do not automatically get
1651 treated as RNA secondary structure.
1654 <!-- JAL-3106 -->.jvp should be used as default extension
1655 (not .jar) when saving a Jalview project file.
1658 <!-- JAL-3105 -->Mac Users: closing a window correctly
1659 transfers focus to previous window on OSX
1662 <em>Java 10 Issues Resolved</em>
1665 <!-- JAL-2988 -->OSX - Can't save new files via the File
1666 or export menus by typing in a name into the Save dialog
1670 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1671 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1672 'look and feel' which has improved compatibility with the
1673 latest version of OSX.
1679 <td width="60" nowrap>
1680 <div align="center">
1681 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1682 <em>7/06/2018</em></strong>
1685 <td><div align="left">
1689 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1690 annotation retrieved from Uniprot
1693 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1694 onto the Jalview Desktop
1698 <td><div align="left">
1702 <!-- JAL-3017 -->Cannot import features with multiple
1703 variant elements (blocks import of some Uniprot records)
1706 <!-- JAL-2997 -->Clustal files with sequence positions in
1707 right-hand column parsed correctly
1710 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1711 not alignment area in exported graphic
1714 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1715 window has input focus
1718 <!-- JAL-2992 -->Annotation panel set too high when
1719 annotation added to view (Windows)
1722 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1723 network connectivity is poor
1726 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1727 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1728 the currently open URL and links from a page viewed in
1729 Firefox or Chrome on Windows is now fully supported. If
1730 you are using Edge, only links in the page can be
1731 dragged, and with Internet Explorer, only the currently
1732 open URL in the browser can be dropped onto Jalview.</em>
1735 <em>New Known Defects</em>
1738 <!-- JAL-3083 -->Cancel option doesn't reset Colour by
1745 <td width="60" nowrap>
1746 <div align="center">
1747 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1750 <td><div align="left">
1754 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1755 for disabling automatic superposition of multiple
1756 structures and open structures in existing views
1759 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1760 ID and annotation area margins can be click-dragged to
1764 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1768 <!-- JAL-2759 -->Improved performance for large alignments
1769 and lots of hidden columns
1772 <!-- JAL-2593 -->Improved performance when rendering lots
1773 of features (particularly when transparency is disabled)
1776 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2
1777 for exchange of Jalview features and Chimera attributes
1778 made generally available
1782 <td><div align="left">
1785 <!-- JAL-2899 -->Structure and Overview aren't updated
1786 when Colour By Annotation threshold slider is adjusted
1789 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1790 overlapping alignment panel
1793 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1797 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1798 improved: CDS not handled correctly if transcript has no
1802 <!-- JAL-2321 -->Secondary structure and temperature
1803 factor annotation not added to sequence when local PDB
1804 file associated with it by drag'n'drop or structure
1808 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1809 dialog doesn't import PDB files dropped on an alignment
1812 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1813 scroll bar doesn't work for some CDS/Protein views
1816 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1817 Java 1.8u153 onwards and Java 1.9u4+.
1820 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1821 columns in annotation row
1824 <!-- JAL-2913 -->Preferences panel's ID Width control is
1825 not honored in batch mode
1828 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1829 for structures added to existing Jmol view
1832 <!-- JAL-2223 -->'View Mappings' includes duplicate
1833 entries after importing project with multiple views
1836 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1837 protein sequences via SIFTS from associated PDB entries
1838 with negative residue numbers or missing residues fails
1841 <!-- JAL-2952 -->Exception when shading sequence with
1842 negative Temperature Factor values from annotated PDB
1843 files (e.g. as generated by CONSURF)
1846 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1847 tooltip doesn't include a text description of mutation
1850 <!-- JAL-2922 -->Invert displayed features very slow when
1851 structure and/or overview windows are also shown
1854 <!-- JAL-2954 -->Selecting columns from highlighted
1855 regions very slow for alignments with large numbers of
1859 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1860 with 'StringIndexOutOfBounds'
1863 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and
1864 Feel for OSX platforms running Java 10
1867 <!-- JAL-2960 -->Adding a structure to existing structure
1868 view appears to do nothing because the view is hidden
1869 behind the alignment view
1875 <!-- JAL-2926 -->Copy consensus sequence option in applet
1876 should copy the group consensus when popup is opened on it
1882 <!-- JAL-2913 -->Fixed ID width preference is not
1886 <em>New Known Defects</em>
1889 <!-- JAL-2973 --> Exceptions occasionally raised when
1890 editing a large alignment and overview is displayed
1893 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1894 repeatedly after a series of edits even when the overview
1895 is no longer reflecting updates
1898 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1899 structures for protein subsequence (if 'Trim Retrieved
1900 Sequences' enabled) or Ensembl isoforms (Workaround in
1901 2.10.4 is to fail back to N&W mapping)
1904 <!-- JAL-2990 -->Export Annotations from File Menu with
1905 CSV option gives blank output
1911 <td width="60" nowrap>
1912 <div align="center">
1913 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br />
1914 <em>24/1/2018</em></strong>
1917 <td><div align="left">
1919 <li>Updated Certum Codesigning Certificate (Valid till
1920 30th November 2018)</li>
1923 <td><div align="left">
1928 <!-- JAL-2859-->Only one structure is loaded when
1929 several sequences and structures are selected for
1933 <!-- JAL-2851-->Alignment doesn't appear to scroll
1934 vertically via trackpad and scrollwheel
1937 <!-- JAL-2842-->Jalview hangs if up/down arrows pressed
1938 in cursor mode when cursor lies in hidden region at
1942 <!-- JAL-2827-->Helix annotation has 'notches' when
1943 scrolled into view if columns are hidden
1946 <!-- JAL-2740-->Annotation column filter can be slow to
1947 reset (ie after hitting cancel) for large numbers of
1951 <!-- JAL-2849-->User preference for disabling inclusion
1952 of sequence limits when exporting as flat file has no
1956 <!-- JAL-2679-->Reproducible cross-reference
1957 relationships when retrieving sequences from
1964 <td width="60" nowrap>
1965 <div align="center">
1966 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1969 <td><div align="left">
1973 <!-- JAL-2446 -->Faster and more efficient management and
1974 rendering of sequence features
1977 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1978 429 rate limit request hander
1981 <!-- JAL-2773 -->Structure views don't get updated unless
1982 their colours have changed
1985 <!-- JAL-2495 -->All linked sequences are highlighted for
1986 a structure mousover (Jmol) or selection (Chimera)
1989 <!-- JAL-2790 -->'Cancel' button in progress bar for
1990 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1993 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1994 view from Ensembl locus cross-references
1997 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
2001 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
2002 feature can be disabled
2005 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
2006 PDB easier retrieval of sequences for lists of IDs
2009 <!-- JAL-2758 -->Short names for sequences retrieved from
2015 <li>Groovy interpreter updated to 2.4.12</li>
2016 <li>Example groovy script for generating a matrix of
2017 percent identity scores for current alignment.</li>
2019 <em>Testing and Deployment</em>
2022 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
2026 <td><div align="left">
2030 <!-- JAL-2643 -->Pressing tab after updating the colour
2031 threshold text field doesn't trigger an update to the
2035 <!-- JAL-2682 -->Race condition when parsing sequence ID
2039 <!-- JAL-2608 -->Overview windows are also closed when
2040 alignment window is closed
2043 <!-- JAL-2548 -->Export of features doesn't always respect
2047 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
2048 takes a long time in Cursor mode
2054 <!-- JAL-2777 -->Structures with whitespace chainCode
2055 cannot be viewed in Chimera
2058 <!-- JAL-2728 -->Protein annotation panel too high in
2062 <!-- JAL-2757 -->Can't edit the query after the server
2063 error warning icon is shown in Uniprot and PDB Free Text
2067 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
2070 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
2073 <!-- JAL-2739 -->Hidden column marker in last column not
2074 rendered when switching back from Wrapped to normal view
2077 <!-- JAL-2768 -->Annotation display corrupted when
2078 scrolling right in unwapped alignment view
2081 <!-- JAL-2542 -->Existing features on subsequence
2082 incorrectly relocated when full sequence retrieved from
2086 <!-- JAL-2733 -->Last reported memory still shown when
2087 Desktop->Show Memory is unticked (OSX only)
2090 <!-- JAL-2658 -->Amend Features dialog doesn't allow
2091 features of same type and group to be selected for
2095 <!-- JAL-2524 -->Jalview becomes sluggish in wide
2096 alignments when hidden columns are present
2099 <!-- JAL-2392 -->Jalview freezes when loading and
2100 displaying several structures
2103 <!-- JAL-2732 -->Black outlines left after resizing or
2107 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
2108 within the Jalview desktop on OSX
2111 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
2112 when in wrapped alignment mode
2115 <!-- JAL-2636 -->Scale mark not shown when close to right
2116 hand end of alignment
2119 <!-- JAL-2684 -->Pairwise alignment of selected regions of
2120 each selected sequence do not have correct start/end
2124 <!-- JAL-2793 -->Alignment ruler height set incorrectly
2125 after canceling the Alignment Window's Font dialog
2128 <!-- JAL-2036 -->Show cross-references not enabled after
2129 restoring project until a new view is created
2132 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
2133 URL links appears when only default EMBL-EBI link is
2134 configured (since 2.10.2b2)
2137 <!-- JAL-2775 -->Overview redraws whole window when box
2138 position is adjusted
2141 <!-- JAL-2225 -->Structure viewer doesn't map all chains
2142 in a multi-chain structure when viewing alignment
2143 involving more than one chain (since 2.10)
2146 <!-- JAL-2811 -->Double residue highlights in cursor mode
2147 if new selection moves alignment window
2150 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
2151 arrow key in cursor mode to pass hidden column marker
2154 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
2155 that produces correctly annotated transcripts and products
2158 <!-- JAL-2776 -->Toggling a feature group after first time
2159 doesn't update associated structure view
2162 <em>Applet</em><br />
2165 <!-- JAL-2687 -->Concurrent modification exception when
2166 closing alignment panel
2169 <em>BioJSON</em><br />
2172 <!-- JAL-2546 -->BioJSON export does not preserve
2173 non-positional features
2176 <em>New Known Issues</em>
2179 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
2180 sequence features correctly (for many previous versions of
2184 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
2185 using cursor in wrapped panel other than top
2188 <!-- JAL-2791 -->Select columns containing feature ignores
2189 graduated colour threshold
2192 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
2193 always preserve numbering and sequence features
2196 <em>Known Java 9 Issues</em>
2199 <!-- JAL-2902 -->Groovy Console very slow to open and is
2200 not responsive when entering characters (Webstart, Java
2207 <td width="60" nowrap>
2208 <div align="center">
2209 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
2210 <em>2/10/2017</em></strong>
2213 <td><div align="left">
2214 <em>New features in Jalview Desktop</em>
2217 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API
2221 <!-- JAL-2745 -->HTTPS used for all connections to
2226 <td><div align="left"></div></td>
2229 <td width="60" nowrap>
2230 <div align="center">
2231 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
2232 <em>7/9/2017</em></strong>
2235 <td><div align="left">
2239 <!-- JAL-2588 -->Show gaps in overview window by colouring
2240 in grey (sequences used to be coloured grey, and gaps were
2244 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
2248 <!-- JAL-2587 -->Overview updates immediately on increase
2249 in size and progress bar shown as higher resolution
2250 overview is recalculated
2255 <td><div align="left">
2259 <!-- JAL-2664 -->Overview window redraws every hidden
2260 column region row by row
2263 <!-- JAL-2681 -->duplicate protein sequences shown after
2264 retrieving Ensembl crossrefs for sequences from Uniprot
2267 <!-- JAL-2603 -->Overview window throws NPE if show boxes
2268 format setting is unticked
2271 <!-- JAL-2610 -->Groups are coloured wrongly in overview
2272 if group has show boxes format setting unticked
2275 <!-- JAL-2672,JAL-2665 -->Redraw problems when
2276 autoscrolling whilst dragging current selection group to
2277 include sequences and columns not currently displayed
2280 <!-- JAL-2691 -->Not all chains are mapped when multimeric
2281 assemblies are imported via CIF file
2284 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
2285 displayed when threshold or conservation colouring is also
2289 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
2293 <!-- JAL-2673 -->Jalview continues to scroll after
2294 dragging a selected region off the visible region of the
2298 <!-- JAL-2724 -->Cannot apply annotation based
2299 colourscheme to all groups in a view
2302 <!-- JAL-2511 -->IDs don't line up with sequences
2303 initially after font size change using the Font chooser or
2310 <td width="60" nowrap>
2311 <div align="center">
2312 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
2315 <td><div align="left">
2316 <em>Calculations</em>
2320 <!-- JAL-1933 -->Occupancy annotation row shows number of
2321 ungapped positions in each column of the alignment.
2324 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
2325 a calculation dialog box
2328 <!-- JAL-2379 -->Revised implementation of PCA for speed
2329 and memory efficiency (~30x faster)
2332 <!-- JAL-2403 -->Revised implementation of sequence
2333 similarity scores as used by Tree, PCA, Shading Consensus
2334 and other calculations
2337 <!-- JAL-2416 -->Score matrices are stored as resource
2338 files within the Jalview codebase
2341 <!-- JAL-2500 -->Trees computed on Sequence Feature
2342 Similarity may have different topology due to increased
2349 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
2350 model for alignments and groups
2353 <!-- JAL-384 -->Custom shading schemes created via groovy
2360 <!-- JAL-2526 -->Efficiency improvements for interacting
2361 with alignment and overview windows
2364 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
2368 <!-- JAL-2388 -->Hidden columns and sequences can be
2372 <!-- JAL-2611 -->Click-drag in visible area allows fine
2373 adjustment of visible position
2377 <em>Data import/export</em>
2380 <!-- JAL-2535 -->Posterior probability annotation from
2381 Stockholm files imported as sequence associated annotation
2384 <!-- JAL-2507 -->More robust per-sequence positional
2385 annotation input/output via stockholm flatfile
2388 <!-- JAL-2533 -->Sequence names don't include file
2389 extension when importing structure files without embedded
2390 names or PDB accessions
2393 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
2394 format sequence substitution matrices
2397 <em>User Interface</em>
2400 <!-- JAL-2447 --> Experimental Features Checkbox in
2401 Desktop's Tools menu to hide or show untested features in
2405 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
2406 via Overview or sequence motif search operations
2409 <!-- JAL-2547 -->Amend sequence features dialog box can be
2410 opened by double clicking gaps within sequence feature
2414 <!-- JAL-1476 -->Status bar message shown when not enough
2415 aligned positions were available to create a 3D structure
2419 <em>3D Structure</em>
2422 <!-- JAL-2430 -->Hidden regions in alignment views are not
2423 coloured in linked structure views
2426 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
2427 file-based command exchange
2430 <!-- JAL-2375 -->Structure chooser automatically shows
2431 Cached Structures rather than querying the PDBe if
2432 structures are already available for sequences
2435 <!-- JAL-2520 -->Structures imported via URL are cached in
2436 the Jalview project rather than downloaded again when the
2437 project is reopened.
2440 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
2441 to transfer Chimera's structure attributes as Jalview
2442 features, and vice-versa (<strong>Experimental
2446 <em>Web Services</em>
2449 <!-- JAL-2549 -->Updated JABAWS client to v2.2
2452 <!-- JAL-2335 -->Filter non-standard amino acids and
2453 nucleotides when submitting to AACon and other MSA
2457 <!-- JAL-2316, -->URLs for viewing database
2458 cross-references provided by identifiers.org and the
2459 EMBL-EBI's MIRIAM DB
2466 <!-- JAL-2344 -->FileFormatI interface for describing and
2467 identifying file formats (instead of String constants)
2470 <!-- JAL-2228 -->FeatureCounter script refactored for
2471 efficiency when counting all displayed features (not
2472 backwards compatible with 2.10.1)
2475 <em>Example files</em>
2478 <!-- JAL-2631 -->Graduated feature colour style example
2479 included in the example feature file
2482 <em>Documentation</em>
2485 <!-- JAL-2339 -->Release notes reformatted for readability
2486 with the built-in Java help viewer
2489 <!-- JAL-1644 -->Find documentation updated with 'search
2490 sequence description' option
2496 <!-- JAL-2485, -->External service integration tests for
2497 Uniprot REST Free Text Search Client
2500 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
2503 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
2508 <td><div align="left">
2509 <em>Calculations</em>
2512 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
2513 matrix - C->R should be '-3'<br />Old matrix restored
2514 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
2516 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
2517 Jalview's treatment of gaps in PCA and substitution matrix
2518 based Tree calculations.<br /> <br />In earlier versions
2519 of Jalview, gaps matching gaps were penalised, and gaps
2520 matching non-gaps penalised even more. In the PCA
2521 calculation, gaps were actually treated as non-gaps - so
2522 different costs were applied, which meant Jalview's PCAs
2523 were different to those produced by SeqSpace.<br />Jalview
2524 now treats gaps in the same way as SeqSpace (ie it scores
2525 them as 0). <br /> <br />Enter the following in the
2526 Groovy console to restore pre-2.10.2 behaviour:<br />
2527 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
2528 // for 2.10.1 mode <br />
2529 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
2530 // to restore 2.10.2 mode <br /> <br /> <em>Note:
2531 these settings will affect all subsequent tree and PCA
2532 calculations (not recommended)</em></li>
2534 <!-- JAL-2424 -->Fixed off-by-one bug that affected
2535 scaling of branch lengths for trees computed using
2536 Sequence Feature Similarity.
2539 <!-- JAL-2377 -->PCA calculation could hang when
2540 generating output report when working with highly
2541 redundant alignments
2544 <!-- JAL-2544 --> Sort by features includes features to
2545 right of selected region when gaps present on right-hand
2549 <em>User Interface</em>
2552 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2553 doesn't reselect a specific sequence's associated
2554 annotation after it was used for colouring a view
2557 <!-- JAL-2419 -->Current selection lost if popup menu
2558 opened on a region of alignment without groups
2561 <!-- JAL-2374 -->Popup menu not always shown for regions
2562 of an alignment with overlapping groups
2565 <!-- JAL-2310 -->Finder double counts if both a sequence's
2566 name and description match
2569 <!-- JAL-2370 -->Hiding column selection containing two
2570 hidden regions results in incorrect hidden regions
2573 <!-- JAL-2386 -->'Apply to all groups' setting when
2574 changing colour does not apply Conservation slider value
2578 <!-- JAL-2373 -->Percentage identity and conservation menu
2579 items do not show a tick or allow shading to be disabled
2582 <!-- JAL-2385 -->Conservation shading or PID threshold
2583 lost when base colourscheme changed if slider not visible
2586 <!-- JAL-2547 -->Sequence features shown in tooltip for
2587 gaps before start of features
2590 <!-- JAL-2623 -->Graduated feature colour threshold not
2591 restored to UI when feature colour is edited
2594 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2595 a time when scrolling vertically in wrapped mode.
2598 <!-- JAL-2630 -->Structure and alignment overview update
2599 as graduate feature colour settings are modified via the
2603 <!-- JAL-2034 -->Overview window doesn't always update
2604 when a group defined on the alignment is resized
2607 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2608 wrapped view result in positional status updates
2612 <!-- JAL-2563 -->Status bar doesn't show position for
2613 ambiguous amino acid and nucleotide symbols
2616 <!-- JAL-2602 -->Copy consensus sequence failed if
2617 alignment included gapped columns
2620 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2621 widgets don't permanently disappear
2624 <!-- JAL-2503 -->Cannot select or filter quantitative
2625 annotation that are shown only as column labels (e.g.
2626 T-Coffee column reliability scores)
2629 <!-- JAL-2594 -->Exception thrown if trying to create a
2630 sequence feature on gaps only
2633 <!-- JAL-2504 -->Features created with 'New feature'
2634 button from a Find inherit previously defined feature type
2635 rather than the Find query string
2638 <!-- JAL-2423 -->incorrect title in output window when
2639 exporting tree calculated in Jalview
2642 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2643 and then revealing them reorders sequences on the
2647 <!-- JAL-964 -->Group panel in sequence feature settings
2648 doesn't update to reflect available set of groups after
2649 interactively adding or modifying features
2652 <!-- JAL-2225 -->Sequence Database chooser unusable on
2656 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2657 only excluded gaps in current sequence and ignored
2664 <!-- JAL-2421 -->Overview window visible region moves
2665 erratically when hidden rows or columns are present
2668 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2669 Structure Viewer's colour menu don't correspond to
2673 <!-- JAL-2405 -->Protein specific colours only offered in
2674 colour and group colour menu for protein alignments
2677 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2678 reflect currently selected view or group's shading
2682 <!-- JAL-2624 -->Feature colour thresholds not respected
2683 when rendered on overview and structures when opacity at
2687 <!-- JAL-2589 -->User defined gap colour not shown in
2688 overview when features overlaid on alignment
2691 <!-- JAL-2567 -->Feature settings for different views not
2692 recovered correctly from Jalview project file
2695 <!-- JAL-2256 -->Feature colours in overview when first
2696 opened (automatically via preferences) are different to
2697 the main alignment panel
2700 <em>Data import/export</em>
2703 <!-- JAL-2576 -->Very large alignments take a long time to
2707 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2708 added after a sequence was imported are not written to
2712 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2713 when importing RNA secondary structure via Stockholm
2716 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2717 not shown in correct direction for simple pseudoknots
2720 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2721 with lightGray or darkGray via features file (but can
2725 <!-- JAL-2383 -->Above PID colour threshold not recovered
2726 when alignment view imported from project
2729 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2730 structure and sequences extracted from structure files
2731 imported via URL and viewed in Jmol
2734 <!-- JAL-2520 -->Structures loaded via URL are saved in
2735 Jalview Projects rather than fetched via URL again when
2736 the project is loaded and the structure viewed
2739 <em>Web Services</em>
2742 <!-- JAL-2519 -->EnsemblGenomes example failing after
2743 release of Ensembl v.88
2746 <!-- JAL-2366 -->Proxy server address and port always
2747 appear enabled in Preferences->Connections
2750 <!-- JAL-2461 -->DAS registry not found exceptions
2751 removed from console output
2754 <!-- JAL-2582 -->Cannot retrieve protein products from
2755 Ensembl by Peptide ID
2758 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2759 created from SIFTs, and spurious 'Couldn't open structure
2760 in Chimera' errors raised after April 2017 update (problem
2761 due to 'null' string rather than empty string used for
2762 residues with no corresponding PDB mapping).
2765 <em>Application UI</em>
2768 <!-- JAL-2361 -->User Defined Colours not added to Colour
2772 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2773 case' residues (button in colourscheme editor debugged and
2774 new documentation and tooltips added)
2777 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2778 doesn't restore group-specific text colour thresholds
2781 <!-- JAL-2243 -->Feature settings panel does not update as
2782 new features are added to alignment
2785 <!-- JAL-2532 -->Cancel in feature settings reverts
2786 changes to feature colours via the Amend features dialog
2789 <!-- JAL-2506 -->Null pointer exception when attempting to
2790 edit graduated feature colour via amend features dialog
2794 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2795 selection menu changes colours of alignment views
2798 <!-- JAL-2426 -->Spurious exceptions in console raised
2799 from alignment calculation workers after alignment has
2803 <!-- JAL-1608 -->Typo in selection popup menu - Create
2804 groups now 'Create Group'
2807 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2808 Create/Undefine group doesn't always work
2811 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2812 shown again after pressing 'Cancel'
2815 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2816 adjusts start position in wrap mode
2819 <!-- JAL-2563 -->Status bar doesn't show positions for
2820 ambiguous amino acids
2823 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2824 CDS/Protein view after CDS sequences added for aligned
2828 <!-- JAL-2592 -->User defined colourschemes called 'User
2829 Defined' don't appear in Colours menu
2835 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2836 score models doesn't always result in an updated PCA plot
2839 <!-- JAL-2442 -->Features not rendered as transparent on
2840 overview or linked structure view
2843 <!-- JAL-2372 -->Colour group by conservation doesn't
2847 <!-- JAL-2517 -->Hitting Cancel after applying
2848 user-defined colourscheme doesn't restore original
2855 <!-- JAL-2314 -->Unit test failure:
2856 jalview.ws.jabaws.RNAStructExportImport setup fails
2859 <!-- JAL-2307 -->Unit test failure:
2860 jalview.ws.sifts.SiftsClientTest due to compatibility
2861 problems with deep array comparison equality asserts in
2862 successive versions of TestNG
2865 <!-- JAL-2479 -->Relocated StructureChooserTest and
2866 ParameterUtilsTest Unit tests to Network suite
2869 <em>New Known Issues</em>
2872 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2873 phase after a sequence motif find operation
2876 <!-- JAL-2550 -->Importing annotation file with rows
2877 containing just upper and lower case letters are
2878 interpreted as WUSS RNA secondary structure symbols
2881 <!-- JAL-2590 -->Cannot load and display Newick trees
2882 reliably from eggnog Ortholog database
2885 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2886 containing features of type Highlight' when 'B' is pressed
2887 to mark columns containing highlighted regions.
2890 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2891 doesn't always add secondary structure annotation.
2896 <td width="60" nowrap>
2897 <div align="center">
2898 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2901 <td><div align="left">
2905 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2906 for all consensus calculations
2909 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2912 <li>Updated Jalview's Certum code signing certificate
2915 <em>Application</em>
2918 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2919 set of database cross-references, sorted alphabetically
2922 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2923 from database cross references. Users with custom links
2924 will receive a <a href="webServices/urllinks.html#warning">warning
2925 dialog</a> asking them to update their preferences.
2928 <!-- JAL-2287-->Cancel button and escape listener on
2929 dialog warning user about disconnecting Jalview from a
2933 <!-- JAL-2320-->Jalview's Chimera control window closes if
2934 the Chimera it is connected to is shut down
2937 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2938 columns menu item to mark columns containing highlighted
2939 regions (e.g. from structure selections or results of a
2943 <!-- JAL-2284-->Command line option for batch-generation
2944 of HTML pages rendering alignment data with the BioJS
2954 <!-- JAL-2286 -->Columns with more than one modal residue
2955 are not coloured or thresholded according to percent
2956 identity (first observed in Jalview 2.8.2)
2959 <!-- JAL-2301 -->Threonine incorrectly reported as not
2963 <!-- JAL-2318 -->Updates to documentation pages (above PID
2964 threshold, amino acid properties)
2967 <!-- JAL-2292 -->Lower case residues in sequences are not
2968 reported as mapped to residues in a structure file in the
2972 <!--JAL-2324 -->Identical features with non-numeric scores
2973 could be added multiple times to a sequence
2976 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2977 bond features shown as two highlighted residues rather
2978 than a range in linked structure views, and treated
2979 correctly when selecting and computing trees from features
2982 <!-- JAL-2281-->Custom URL links for database
2983 cross-references are matched to database name regardless
2988 <em>Application</em>
2991 <!-- JAL-2282-->Custom URL links for specific database
2992 names without regular expressions also offer links from
2996 <!-- JAL-2315-->Removing a single configured link in the
2997 URL links pane in Connections preferences doesn't actually
2998 update Jalview configuration
3001 <!-- JAL-2272-->CTRL-Click on a selected region to open
3002 the alignment area popup menu doesn't work on El-Capitan
3005 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
3006 files with similarly named sequences if dropped onto the
3010 <!-- JAL-2312 -->Additional mappings are shown for PDB
3011 entries where more chains exist in the PDB accession than
3012 are reported in the SIFTS file
3015 <!-- JAL-2317-->Certain structures do not get mapped to
3016 the structure view when displayed with Chimera
3019 <!-- JAL-2317-->No chains shown in the Chimera view
3020 panel's View->Show Chains submenu
3023 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
3024 work for wrapped alignment views
3027 <!--JAL-2197 -->Rename UI components for running JPred
3028 predictions from 'JNet' to 'JPred'
3031 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
3032 corrupted when annotation panel vertical scroll is not at
3033 first annotation row
3036 <!--JAL-2332 -->Attempting to view structure for Hen
3037 lysozyme results in a PDB Client error dialog box
3040 <!-- JAL-2319 -->Structure View's mapping report switched
3041 ranges for PDB and sequence for SIFTS
3044 SIFTS 'Not_Observed' residues mapped to non-existant
3048 <!-- <em>New Known Issues</em>
3055 <td width="60" nowrap>
3056 <div align="center">
3057 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
3058 <em>25/10/2016</em></strong>
3061 <td><em>Application</em>
3063 <li>3D Structure chooser opens with 'Cached structures'
3064 view if structures already loaded</li>
3065 <li>Progress bar reports models as they are loaded to
3066 structure views</li>
3072 <li>Colour by conservation always enabled and no tick
3073 shown in menu when BLOSUM or PID shading applied</li>
3074 <li>FER1_ARATH and FER2_ARATH labels were switched in
3075 example sequences/projects/trees</li>
3077 <em>Application</em>
3079 <li>Jalview projects with views of local PDB structure
3080 files saved on Windows cannot be opened on OSX</li>
3081 <li>Multiple structure views can be opened and superposed
3082 without timeout for structures with multiple models or
3083 multiple sequences in alignment</li>
3084 <li>Cannot import or associated local PDB files without a
3085 PDB ID HEADER line</li>
3086 <li>RMSD is not output in Jmol console when superposition
3088 <li>Drag and drop of URL from Browser fails for Linux and
3089 OSX versions earlier than El Capitan</li>
3090 <li>ENA client ignores invalid content from ENA server</li>
3091 <li>Exceptions are not raised in console when ENA client
3092 attempts to fetch non-existent IDs via Fetch DB Refs UI
3094 <li>Exceptions are not raised in console when a new view
3095 is created on the alignment</li>
3096 <li>OSX right-click fixed for group selections: CMD-click
3097 to insert/remove gaps in groups and CTRL-click to open group
3100 <em>Build and deployment</em>
3102 <li>URL link checker now copes with multi-line anchor
3105 <em>New Known Issues</em>
3107 <li>Drag and drop from URL links in browsers do not work
3114 <td width="60" nowrap>
3115 <div align="center">
3116 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
3119 <td><em>General</em>
3122 <!-- JAL-2124 -->Updated Spanish translations.
3125 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
3126 for importing structure data to Jalview. Enables mmCIF and
3130 <!-- JAL-192 --->Alignment ruler shows positions relative to
3134 <!-- JAL-2202 -->Position/residue shown in status bar when
3135 mousing over sequence associated annotation
3138 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
3142 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
3143 '()', canonical '[]' and invalid '{}' base pair populations
3147 <!-- JAL-2092 -->Feature settings popup menu options for
3148 showing or hiding columns containing a feature
3151 <!-- JAL-1557 -->Edit selected group by double clicking on
3152 group and sequence associated annotation labels
3155 <!-- JAL-2236 -->Sequence name added to annotation label in
3156 select/hide columns by annotation and colour by annotation
3160 </ul> <em>Application</em>
3163 <!-- JAL-2050-->Automatically hide introns when opening a
3164 gene/transcript view
3167 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
3171 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
3172 structure mappings with the EMBL-EBI PDBe SIFTS database
3175 <!-- JAL-2079 -->Updated download sites used for Rfam and
3176 Pfam sources to xfam.org
3179 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
3182 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
3183 over sequences in Jalview
3186 <!-- JAL-2027-->Support for reverse-complement coding
3187 regions in ENA and EMBL
3190 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
3191 for record retrieval via ENA rest API
3194 <!-- JAL-2027 -->Support for ENA CDS records with reverse
3198 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
3199 groovy script execution
3202 <!-- JAL-1812 -->New 'execute Groovy script' option in an
3203 alignment window's Calculate menu
3206 <!-- JAL-1812 -->Allow groovy scripts that call
3207 Jalview.getAlignFrames() to run in headless mode
3210 <!-- JAL-2068 -->Support for creating new alignment
3211 calculation workers from groovy scripts
3214 <!-- JAL-1369 --->Store/restore reference sequence in
3218 <!-- JAL-1803 -->Chain codes for a sequence's PDB
3219 associations are now saved/restored from project
3222 <!-- JAL-1993 -->Database selection dialog always shown
3223 before sequence fetcher is opened
3226 <!-- JAL-2183 -->Double click on an entry in Jalview's
3227 database chooser opens a sequence fetcher
3230 <!-- JAL-1563 -->Free-text search client for UniProt using
3231 the UniProt REST API
3234 <!-- JAL-2168 -->-nonews command line parameter to prevent
3235 the news reader opening
3238 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
3239 querying stored in preferences
3242 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
3246 <!-- JAL-1977-->Tooltips shown on database chooser
3249 <!-- JAL-391 -->Reverse complement function in calculate
3250 menu for nucleotide sequences
3253 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
3254 and feature counts preserves alignment ordering (and
3255 debugged for complex feature sets).
3258 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
3259 viewing structures with Jalview 2.10
3262 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
3263 genome, transcript CCDS and gene ids via the Ensembl and
3264 Ensembl Genomes REST API
3267 <!-- JAL-2049 -->Protein sequence variant annotation
3268 computed for 'sequence_variant' annotation on CDS regions
3272 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
3276 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
3277 Ref Fetcher fails to match, or otherwise updates sequence
3278 data from external database records.
3281 <!-- JAL-2154 -->Revised Jalview Project format for
3282 efficient recovery of sequence coding and alignment
3283 annotation relationships.
3285 </ul> <!-- <em>Applet</em>
3296 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
3300 <!-- JAL-2018-->Export features in Jalview format (again)
3301 includes graduated colourschemes
3304 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
3305 working with big alignments and lots of hidden columns
3308 <!-- JAL-2053-->Hidden column markers not always rendered
3309 at right of alignment window
3312 <!-- JAL-2067 -->Tidied up links in help file table of
3316 <!-- JAL-2072 -->Feature based tree calculation not shown
3320 <!-- JAL-2075 -->Hidden columns ignored during feature
3321 based tree calculation
3324 <!-- JAL-2065 -->Alignment view stops updating when show
3325 unconserved enabled for group on alignment
3328 <!-- JAL-2086 -->Cannot insert gaps into sequence when
3332 <!-- JAL-2146 -->Alignment column in status incorrectly
3333 shown as "Sequence position" when mousing over
3337 <!-- JAL-2099 -->Incorrect column numbers in ruler when
3338 hidden columns present
3341 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
3342 user created annotation added to alignment
3345 <!-- JAL-1841 -->RNA Structure consensus only computed for
3346 '()' base pair annotation
3349 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
3350 in zero scores for all base pairs in RNA Structure
3354 <!-- JAL-2174-->Extend selection with columns containing
3358 <!-- JAL-2275 -->Pfam format writer puts extra space at
3359 beginning of sequence
3362 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
3366 <!-- JAL-2238 -->Cannot create groups on an alignment from
3367 from a tree when t-coffee scores are shown
3370 <!-- JAL-1836,1967 -->Cannot import and view PDB
3371 structures with chains containing negative resnums (4q4h)
3374 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
3378 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
3379 to Clustal, PIR and PileUp output
3382 <!-- JAL-2008 -->Reordering sequence features that are
3383 not visible causes alignment window to repaint
3386 <!-- JAL-2006 -->Threshold sliders don't work in
3387 graduated colour and colour by annotation row for e-value
3388 scores associated with features and annotation rows
3391 <!-- JAL-1797 -->amino acid physicochemical conservation
3392 calculation should be case independent
3395 <!-- JAL-2173 -->Remove annotation also updates hidden
3399 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
3400 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
3401 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
3404 <!-- JAL-2065 -->Null pointer exceptions and redraw
3405 problems when reference sequence defined and 'show
3406 non-conserved' enabled
3409 <!-- JAL-1306 -->Quality and Conservation are now shown on
3410 load even when Consensus calculation is disabled
3413 <!-- JAL-1932 -->Remove right on penultimate column of
3414 alignment does nothing
3417 <em>Application</em>
3420 <!-- JAL-1552-->URLs and links can't be imported by
3421 drag'n'drop on OSX when launched via webstart (note - not
3422 yet fixed for El Capitan)
3425 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
3426 output when running on non-gb/us i18n platforms
3429 <!-- JAL-1944 -->Error thrown when exporting a view with
3430 hidden sequences as flat-file alignment
3433 <!-- JAL-2030-->InstallAnywhere distribution fails when
3437 <!-- JAL-2080-->Jalview very slow to launch via webstart
3438 (also hotfix for 2.9.0b2)
3441 <!-- JAL-2085 -->Cannot save project when view has a
3442 reference sequence defined
3445 <!-- JAL-1011 -->Columns are suddenly selected in other
3446 alignments and views when revealing hidden columns
3449 <!-- JAL-1989 -->Hide columns not mirrored in complement
3450 view in a cDNA/Protein splitframe
3453 <!-- JAL-1369 -->Cannot save/restore representative
3454 sequence from project when only one sequence is
3458 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
3459 in Structure Chooser
3462 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
3463 structure consensus didn't refresh annotation panel
3466 <!-- JAL-1962 -->View mapping in structure view shows
3467 mappings between sequence and all chains in a PDB file
3470 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
3471 dialogs format columns correctly, don't display array
3472 data, sort columns according to type
3475 <!-- JAL-1975 -->Export complete shown after destination
3476 file chooser is cancelled during an image export
3479 <!-- JAL-2025 -->Error when querying PDB Service with
3480 sequence name containing special characters
3483 <!-- JAL-2024 -->Manual PDB structure querying should be
3487 <!-- JAL-2104 -->Large tooltips with broken HTML
3488 formatting don't wrap
3491 <!-- JAL-1128 -->Figures exported from wrapped view are
3492 truncated so L looks like I in consensus annotation
3495 <!-- JAL-2003 -->Export features should only export the
3496 currently displayed features for the current selection or
3500 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
3501 after fetching cross-references, and restoring from
3505 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
3506 followed in the structure viewer
3509 <!-- JAL-2163 -->Titles for individual alignments in
3510 splitframe not restored from project
3513 <!-- JAL-2145 -->missing autocalculated annotation at
3514 trailing end of protein alignment in transcript/product
3515 splitview when pad-gaps not enabled by default
3518 <!-- JAL-1797 -->amino acid physicochemical conservation
3522 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
3523 article has been read (reopened issue due to
3524 internationalisation problems)
3527 <!-- JAL-1960 -->Only offer PDB structures in structure
3528 viewer based on sequence name, PDB and UniProt
3533 <!-- JAL-1976 -->No progress bar shown during export of
3537 <!-- JAL-2213 -->Structures not always superimposed after
3538 multiple structures are shown for one or more sequences.
3541 <!-- JAL-1370 -->Reference sequence characters should not
3542 be replaced with '.' when 'Show unconserved' format option
3546 <!-- JAL-1823 -->Cannot specify chain code when entering
3547 specific PDB id for sequence
3550 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3551 'Export hidden sequences' is enabled, but 'export hidden
3552 columns' is disabled.
3555 <!--JAL-2026-->Best Quality option in structure chooser
3556 selects lowest rather than highest resolution structures
3560 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3561 to sequence mapping in 'View Mappings' report
3564 <!-- JAL-2284 -->Unable to read old Jalview projects that
3565 contain non-XML data added after Jalvew wrote project.
3568 <!-- JAL-2118 -->Newly created annotation row reorders
3569 after clicking on it to create new annotation for a
3573 <!-- JAL-1980 -->Null Pointer Exception raised when
3574 pressing Add on an orphaned cut'n'paste window.
3576 <!-- may exclude, this is an external service stability issue JAL-1941
3577 -- > RNA 3D structure not added via DSSR service</li> -->
3582 <!-- JAL-2151 -->Incorrect columns are selected when
3583 hidden columns present before start of sequence
3586 <!-- JAL-1986 -->Missing dependencies on applet pages
3590 <!-- JAL-1947 -->Overview pixel size changes when
3591 sequences are hidden in applet
3594 <!-- JAL-1996 -->Updated instructions for applet
3595 deployment on examples pages.
3602 <td width="60" nowrap>
3603 <div align="center">
3604 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3605 <em>16/10/2015</em></strong>
3608 <td><em>General</em>
3610 <li>Time stamps for signed Jalview application and applet
3615 <em>Application</em>
3617 <li>Duplicate group consensus and conservation rows
3618 shown when tree is partitioned</li>
3619 <li>Erratic behaviour when tree partitions made with
3620 multiple cDNA/Protein split views</li>
3626 <td width="60" nowrap>
3627 <div align="center">
3628 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3629 <em>8/10/2015</em></strong>
3632 <td><em>General</em>
3634 <li>Updated Spanish translations of localized text for
3636 </ul> <em>Application</em>
3638 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3639 <li>Signed OSX InstallAnywhere installer<br></li>
3640 <li>Support for per-sequence based annotations in BioJSON</li>
3641 </ul> <em>Applet</em>
3643 <li>Split frame example added to applet examples page</li>
3644 </ul> <em>Build and Deployment</em>
3647 <!-- JAL-1888 -->New ant target for running Jalview's test
3655 <li>Mapping of cDNA to protein in split frames
3656 incorrect when sequence start > 1</li>
3657 <li>Broken images in filter column by annotation dialog
3659 <li>Feature colours not parsed from features file</li>
3660 <li>Exceptions and incomplete link URLs recovered when
3661 loading a features file containing HTML tags in feature
3665 <em>Application</em>
3667 <li>Annotations corrupted after BioJS export and
3669 <li>Incorrect sequence limits after Fetch DB References
3670 with 'trim retrieved sequences'</li>
3671 <li>Incorrect warning about deleting all data when
3672 deleting selected columns</li>
3673 <li>Patch to build system for shipping properly signed
3674 JNLP templates for webstart launch</li>
3675 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3676 unreleased structures for download or viewing</li>
3677 <li>Tab/space/return keystroke operation of EMBL-PDBe
3678 fetcher/viewer dialogs works correctly</li>
3679 <li>Disabled 'minimise' button on Jalview windows
3680 running on OSX to workaround redraw hang bug</li>
3681 <li>Split cDNA/Protein view position and geometry not
3682 recovered from jalview project</li>
3683 <li>Initial enabled/disabled state of annotation menu
3684 sorter 'show autocalculated first/last' corresponds to
3686 <li>Restoring of Clustal, RNA Helices and T-Coffee
3687 color schemes from BioJSON</li>
3691 <li>Reorder sequences mirrored in cDNA/Protein split
3693 <li>Applet with Jmol examples not loading correctly</li>
3699 <td><div align="center">
3700 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3702 <td><em>General</em>
3704 <li>Linked visualisation and analysis of DNA and Protein
3707 <li>Translated cDNA alignments shown as split protein
3708 and DNA alignment views</li>
3709 <li>Codon consensus annotation for linked protein and
3710 cDNA alignment views</li>
3711 <li>Link cDNA or Protein product sequences by loading
3712 them onto Protein or cDNA alignments</li>
3713 <li>Reconstruct linked cDNA alignment from aligned
3714 protein sequences</li>
3717 <li>Jmol integration updated to Jmol v14.2.14</li>
3718 <li>Import and export of Jalview alignment views as <a
3719 href="features/bioJsonFormat.html">BioJSON</a></li>
3720 <li>New alignment annotation file statements for
3721 reference sequences and marking hidden columns</li>
3722 <li>Reference sequence based alignment shading to
3723 highlight variation</li>
3724 <li>Select or hide columns according to alignment
3726 <li>Find option for locating sequences by description</li>
3727 <li>Conserved physicochemical properties shown in amino
3728 acid conservation row</li>
3729 <li>Alignments can be sorted by number of RNA helices</li>
3730 </ul> <em>Application</em>
3732 <li>New cDNA/Protein analysis capabilities
3734 <li>Get Cross-References should open a Split Frame
3735 view with cDNA/Protein</li>
3736 <li>Detect when nucleotide sequences and protein
3737 sequences are placed in the same alignment</li>
3738 <li>Split cDNA/Protein views are saved in Jalview
3743 <li>Use REST API to talk to Chimera</li>
3744 <li>Selected regions in Chimera are highlighted in linked
3745 Jalview windows</li>
3747 <li>VARNA RNA viewer updated to v3.93</li>
3748 <li>VARNA views are saved in Jalview Projects</li>
3749 <li>Pseudoknots displayed as Jalview RNA annotation can
3750 be shown in VARNA</li>
3752 <li>Make groups for selection uses marked columns as well
3753 as the active selected region</li>
3755 <li>Calculate UPGMA and NJ trees using sequence feature
3757 <li>New Export options
3759 <li>New Export Settings dialog to control hidden
3760 region export in flat file generation</li>
3762 <li>Export alignment views for display with the <a
3763 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3765 <li>Export scrollable SVG in HTML page</li>
3766 <li>Optional embedding of BioJSON data when exporting
3767 alignment figures to HTML</li>
3769 <li>3D structure retrieval and display
3771 <li>Free text and structured queries with the PDBe
3773 <li>PDBe Search API based discovery and selection of
3774 PDB structures for a sequence set</li>
3778 <li>JPred4 employed for protein secondary structure
3780 <li>Hide Insertions menu option to hide unaligned columns
3781 for one or a group of sequences</li>
3782 <li>Automatically hide insertions in alignments imported
3783 from the JPred4 web server</li>
3784 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3785 system on OSX<br />LGPL libraries courtesy of <a
3786 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3788 <li>changed 'View nucleotide structure' submenu to 'View
3789 VARNA 2D Structure'</li>
3790 <li>change "View protein structure" menu option to "3D
3793 </ul> <em>Applet</em>
3795 <li>New layout for applet example pages</li>
3796 <li>New parameters to enable SplitFrame view
3797 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3798 <li>New example demonstrating linked viewing of cDNA and
3799 Protein alignments</li>
3800 </ul> <em>Development and deployment</em>
3802 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3803 <li>Include installation type and git revision in build
3804 properties and console log output</li>
3805 <li>Jalview Github organisation, and new github site for
3806 storing BioJsMSA Templates</li>
3807 <li>Jalview's unit tests now managed with TestNG</li>
3810 <!-- <em>General</em>
3812 </ul> --> <!-- issues resolved --> <em>Application</em>
3814 <li>Escape should close any open find dialogs</li>
3815 <li>Typo in select-by-features status report</li>
3816 <li>Consensus RNA secondary secondary structure
3817 predictions are not highlighted in amber</li>
3818 <li>Missing gap character in v2.7 example file means
3819 alignment appears unaligned when pad-gaps is not enabled</li>
3820 <li>First switch to RNA Helices colouring doesn't colour
3821 associated structure views</li>
3822 <li>ID width preference option is greyed out when auto
3823 width checkbox not enabled</li>
3824 <li>Stopped a warning dialog from being shown when
3825 creating user defined colours</li>
3826 <li>'View Mapping' in structure viewer shows sequence
3827 mappings for just that viewer's sequences</li>
3828 <li>Workaround for superposing PDB files containing
3829 multiple models in Chimera</li>
3830 <li>Report sequence position in status bar when hovering
3831 over Jmol structure</li>
3832 <li>Cannot output gaps as '.' symbols with Selection ->
3833 output to text box</li>
3834 <li>Flat file exports of alignments with hidden columns
3835 have incorrect sequence start/end</li>
3836 <li>'Aligning' a second chain to a Chimera structure from
3838 <li>Colour schemes applied to structure viewers don't
3839 work for nucleotide</li>
3840 <li>Loading/cut'n'pasting an empty or invalid file leads
3841 to a grey/invisible alignment window</li>
3842 <li>Exported Jpred annotation from a sequence region
3843 imports to different position</li>
3844 <li>Space at beginning of sequence feature tooltips shown
3845 on some platforms</li>
3846 <li>Chimera viewer 'View | Show Chain' menu is not
3848 <li>'New View' fails with a Null Pointer Exception in
3849 console if Chimera has been opened</li>
3850 <li>Mouseover to Chimera not working</li>
3851 <li>Miscellaneous ENA XML feature qualifiers not
3853 <li>NPE in annotation renderer after 'Extract Scores'</li>
3854 <li>If two structures in one Chimera window, mouseover of
3855 either sequence shows on first structure</li>
3856 <li>'Show annotations' options should not make
3857 non-positional annotations visible</li>
3858 <li>Subsequence secondary structure annotation not shown
3859 in right place after 'view flanking regions'</li>
3860 <li>File Save As type unset when current file format is
3862 <li>Save as '.jar' option removed for saving Jalview
3864 <li>Colour by Sequence colouring in Chimera more
3866 <li>Cannot 'add reference annotation' for a sequence in
3867 several views on same alignment</li>
3868 <li>Cannot show linked products for EMBL / ENA records</li>
3869 <li>Jalview's tooltip wraps long texts containing no
3871 </ul> <em>Applet</em>
3873 <li>Jmol to JalviewLite mouseover/link not working</li>
3874 <li>JalviewLite can't import sequences with ID
3875 descriptions containing angle brackets</li>
3876 </ul> <em>General</em>
3878 <li>Cannot export and reimport RNA secondary structure
3879 via jalview annotation file</li>
3880 <li>Random helix colour palette for colour by annotation
3881 with RNA secondary structure</li>
3882 <li>Mouseover to cDNA from STOP residue in protein
3883 translation doesn't work.</li>
3884 <li>hints when using the select by annotation dialog box</li>
3885 <li>Jmol alignment incorrect if PDB file has alternate CA
3887 <li>FontChooser message dialog appears to hang after
3888 choosing 1pt font</li>
3889 <li>Peptide secondary structure incorrectly imported from
3890 annotation file when annotation display text includes 'e' or
3892 <li>Cannot set colour of new feature type whilst creating
3894 <li>cDNA translation alignment should not be sequence
3895 order dependent</li>
3896 <li>'Show unconserved' doesn't work for lower case
3898 <li>Nucleotide ambiguity codes involving R not recognised</li>
3899 </ul> <em>Deployment and Documentation</em>
3901 <li>Applet example pages appear different to the rest of
3902 www.jalview.org</li>
3903 </ul> <em>Application Known issues</em>
3905 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3906 <li>Misleading message appears after trying to delete
3908 <li>Jalview icon not shown in dock after InstallAnywhere
3909 version launches</li>
3910 <li>Fetching EMBL reference for an RNA sequence results
3911 fails with a sequence mismatch</li>
3912 <li>Corrupted or unreadable alignment display when
3913 scrolling alignment to right</li>
3914 <li>ArrayIndexOutOfBoundsException thrown when remove
3915 empty columns called on alignment with ragged gapped ends</li>
3916 <li>auto calculated alignment annotation rows do not get
3917 placed above or below non-autocalculated rows</li>
3918 <li>Jalview dekstop becomes sluggish at full screen in
3919 ultra-high resolution</li>
3920 <li>Cannot disable consensus calculation independently of
3921 quality and conservation</li>
3922 <li>Mouseover highlighting between cDNA and protein can
3923 become sluggish with more than one splitframe shown</li>
3924 </ul> <em>Applet Known Issues</em>
3926 <li>Core PDB parsing code requires Jmol</li>
3927 <li>Sequence canvas panel goes white when alignment
3928 window is being resized</li>
3934 <td><div align="center">
3935 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3937 <td><em>General</em>
3939 <li>Updated Java code signing certificate donated by
3941 <li>Features and annotation preserved when performing
3942 pairwise alignment</li>
3943 <li>RNA pseudoknot annotation can be
3944 imported/exported/displayed</li>
3945 <li>'colour by annotation' can colour by RNA and
3946 protein secondary structure</li>
3947 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3948 post-hoc with 2.9 release</em>)
3951 </ul> <em>Application</em>
3953 <li>Extract and display secondary structure for sequences
3954 with 3D structures</li>
3955 <li>Support for parsing RNAML</li>
3956 <li>Annotations menu for layout
3958 <li>sort sequence annotation rows by alignment</li>
3959 <li>place sequence annotation above/below alignment
3962 <li>Output in Stockholm format</li>
3963 <li>Internationalisation: improved Spanish (es)
3965 <li>Structure viewer preferences tab</li>
3966 <li>Disorder and Secondary Structure annotation tracks
3967 shared between alignments</li>
3968 <li>UCSF Chimera launch and linked highlighting from
3970 <li>Show/hide all sequence associated annotation rows for
3971 all or current selection</li>
3972 <li>disorder and secondary structure predictions
3973 available as dataset annotation</li>
3974 <li>Per-sequence rna helices colouring</li>
3977 <li>Sequence database accessions imported when fetching
3978 alignments from Rfam</li>
3979 <li>update VARNA version to 3.91</li>
3981 <li>New groovy scripts for exporting aligned positions,
3982 conservation values, and calculating sum of pairs scores.</li>
3983 <li>Command line argument to set default JABAWS server</li>
3984 <li>include installation type in build properties and
3985 console log output</li>
3986 <li>Updated Jalview project format to preserve dataset
3990 <!-- issues resolved --> <em>Application</em>
3992 <li>Distinguish alignment and sequence associated RNA
3993 structure in structure->view->VARNA</li>
3994 <li>Raise dialog box if user deletes all sequences in an
3996 <li>Pressing F1 results in documentation opening twice</li>
3997 <li>Sequence feature tooltip is wrapped</li>
3998 <li>Double click on sequence associated annotation
3999 selects only first column</li>
4000 <li>Redundancy removal doesn't result in unlinked
4001 leaves shown in tree</li>
4002 <li>Undos after several redundancy removals don't undo
4004 <li>Hide sequence doesn't hide associated annotation</li>
4005 <li>User defined colours dialog box too big to fit on
4006 screen and buttons not visible</li>
4007 <li>author list isn't updated if already written to
4008 Jalview properties</li>
4009 <li>Popup menu won't open after retrieving sequence
4011 <li>File open window for associate PDB doesn't open</li>
4012 <li>Left-then-right click on a sequence id opens a
4013 browser search window</li>
4014 <li>Cannot open sequence feature shading/sort popup menu
4015 in feature settings dialog</li>
4016 <li>better tooltip placement for some areas of Jalview
4018 <li>Allow addition of JABAWS Server which doesn't
4019 pass validation</li>
4020 <li>Web services parameters dialog box is too large to
4022 <li>Muscle nucleotide alignment preset obscured by
4024 <li>JABAWS preset submenus don't contain newly
4025 defined user preset</li>
4026 <li>MSA web services warns user if they were launched
4027 with invalid input</li>
4028 <li>Jalview cannot contact DAS Registy when running on
4031 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
4032 'Superpose with' submenu not shown when new view
4036 </ul> <!-- <em>Applet</em>
4038 </ul> <em>General</em>
4040 </ul>--> <em>Deployment and Documentation</em>
4042 <li>2G and 1G options in launchApp have no effect on
4043 memory allocation</li>
4044 <li>launchApp service doesn't automatically open
4045 www.jalview.org/examples/exampleFile.jar if no file is given</li>
4047 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
4048 InstallAnywhere reports cannot find valid JVM when Java
4049 1.7_055 is available
4051 </ul> <em>Application Known issues</em>
4054 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
4055 corrupted or unreadable alignment display when scrolling
4059 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
4060 retrieval fails but progress bar continues for DAS retrieval
4061 with large number of ID
4064 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
4065 flatfile output of visible region has incorrect sequence
4069 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
4070 rna structure consensus doesn't update when secondary
4071 structure tracks are rearranged
4074 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
4075 invalid rna structure positional highlighting does not
4076 highlight position of invalid base pairs
4079 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
4080 out of memory errors are not raised when saving Jalview
4081 project from alignment window file menu
4084 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
4085 Switching to RNA Helices colouring doesn't propagate to
4089 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
4090 colour by RNA Helices not enabled when user created
4091 annotation added to alignment
4094 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
4095 Jalview icon not shown on dock in Mountain Lion/Webstart
4097 </ul> <em>Applet Known Issues</em>
4100 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
4101 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
4104 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
4105 Jalview and Jmol example not compatible with IE9
4108 <li>Sort by annotation score doesn't reverse order
4114 <td><div align="center">
4115 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
4118 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
4121 <li>Internationalisation of user interface (usually
4122 called i18n support) and translation for Spanish locale</li>
4123 <li>Define/Undefine group on current selection with
4124 Ctrl-G/Shift Ctrl-G</li>
4125 <li>Improved group creation/removal options in
4126 alignment/sequence Popup menu</li>
4127 <li>Sensible precision for symbol distribution
4128 percentages shown in logo tooltip.</li>
4129 <li>Annotation panel height set according to amount of
4130 annotation when alignment first opened</li>
4131 </ul> <em>Application</em>
4133 <li>Interactive consensus RNA secondary structure
4134 prediction VIENNA RNAAliFold JABA 2.1 service</li>
4135 <li>Select columns containing particular features from
4136 Feature Settings dialog</li>
4137 <li>View all 'representative' PDB structures for selected
4139 <li>Update Jalview project format:
4141 <li>New file extension for Jalview projects '.jvp'</li>
4142 <li>Preserve sequence and annotation dataset (to
4143 store secondary structure annotation,etc)</li>
4144 <li>Per group and alignment annotation and RNA helix
4148 <li>New similarity measures for PCA and Tree calculation
4150 <li>Experimental support for retrieval and viewing of
4151 flanking regions for an alignment</li>
4155 <!-- issues resolved --> <em>Application</em>
4157 <li>logo keeps spinning and status remains at queued or
4158 running after job is cancelled</li>
4159 <li>cannot export features from alignments imported from
4160 Jalview/VAMSAS projects</li>
4161 <li>Buggy slider for web service parameters that take
4163 <li>Newly created RNA secondary structure line doesn't
4164 have 'display all symbols' flag set</li>
4165 <li>T-COFFEE alignment score shading scheme and other
4166 annotation shading not saved in Jalview project</li>
4167 <li>Local file cannot be loaded in freshly downloaded
4169 <li>Jalview icon not shown on dock in Mountain
4171 <li>Load file from desktop file browser fails</li>
4172 <li>Occasional NPE thrown when calculating large trees</li>
4173 <li>Cannot reorder or slide sequences after dragging an
4174 alignment onto desktop</li>
4175 <li>Colour by annotation dialog throws NPE after using
4176 'extract scores' function</li>
4177 <li>Loading/cut'n'pasting an empty file leads to a grey
4178 alignment window</li>
4179 <li>Disorder thresholds rendered incorrectly after
4180 performing IUPred disorder prediction</li>
4181 <li>Multiple group annotated consensus rows shown when
4182 changing 'normalise logo' display setting</li>
4183 <li>Find shows blank dialog after 'finished searching' if
4184 nothing matches query</li>
4185 <li>Null Pointer Exceptions raised when sorting by
4186 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
4188 <li>Errors in Jmol console when structures in alignment
4189 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
4191 <li>Not all working JABAWS services are shown in
4193 <li>JAVAWS version of Jalview fails to launch with
4194 'invalid literal/length code'</li>
4195 <li>Annotation/RNA Helix colourschemes cannot be applied
4196 to alignment with groups (actually fixed in 2.8.0b1)</li>
4197 <li>RNA Helices and T-Coffee Scores available as default
4200 </ul> <em>Applet</em>
4202 <li>Remove group option is shown even when selection is
4204 <li>Apply to all groups ticked but colourscheme changes
4205 don't affect groups</li>
4206 <li>Documented RNA Helices and T-Coffee Scores as valid
4207 colourscheme name</li>
4208 <li>Annotation labels drawn on sequence IDs when
4209 Annotation panel is not displayed</li>
4210 <li>Increased font size for dropdown menus on OSX and
4211 embedded windows</li>
4212 </ul> <em>Other</em>
4214 <li>Consensus sequence for alignments/groups with a
4215 single sequence were not calculated</li>
4216 <li>annotation files that contain only groups imported as
4217 annotation and junk sequences</li>
4218 <li>Fasta files with sequences containing '*' incorrectly
4219 recognised as PFAM or BLC</li>
4220 <li>conservation/PID slider apply all groups option
4221 doesn't affect background (2.8.0b1)
4223 <li>redundancy highlighting is erratic at 0% and 100%</li>
4224 <li>Remove gapped columns fails for sequences with ragged
4226 <li>AMSA annotation row with leading spaces is not
4227 registered correctly on import</li>
4228 <li>Jalview crashes when selecting PCA analysis for
4229 certain alignments</li>
4230 <li>Opening the colour by annotation dialog for an
4231 existing annotation based 'use original colours'
4232 colourscheme loses original colours setting</li>
4237 <td><div align="center">
4238 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
4239 <em>30/1/2014</em></strong>
4243 <li>Trusted certificates for JalviewLite applet and
4244 Jalview Desktop application<br />Certificate was donated by
4245 <a href="https://www.certum.eu">Certum</a> to the Jalview
4246 open source project).
4248 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
4249 <li>Output in Stockholm format</li>
4250 <li>Allow import of data from gzipped files</li>
4251 <li>Export/import group and sequence associated line
4252 graph thresholds</li>
4253 <li>Nucleotide substitution matrix that supports RNA and
4254 ambiguity codes</li>
4255 <li>Allow disorder predictions to be made on the current
4256 selection (or visible selection) in the same way that JPred
4258 <li>Groovy scripting for headless Jalview operation</li>
4259 </ul> <em>Other improvements</em>
4261 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
4262 <li>COMBINE statement uses current SEQUENCE_REF and
4263 GROUP_REF scope to group annotation rows</li>
4264 <li>Support '' style escaping of quotes in Newick
4266 <li>Group options for JABAWS service by command line name</li>
4267 <li>Empty tooltip shown for JABA service options with a
4268 link but no description</li>
4269 <li>Select primary source when selecting authority in
4270 database fetcher GUI</li>
4271 <li>Add .mfa to FASTA file extensions recognised by
4273 <li>Annotation label tooltip text wrap</li>
4278 <li>Slow scrolling when lots of annotation rows are
4280 <li>Lots of NPE (and slowness) after creating RNA
4281 secondary structure annotation line</li>
4282 <li>Sequence database accessions not imported when
4283 fetching alignments from Rfam</li>
4284 <li>Incorrect SHMR submission for sequences with
4286 <li>View all structures does not always superpose
4288 <li>Option widgets in service parameters not updated to
4289 reflect user or preset settings</li>
4290 <li>Null pointer exceptions for some services without
4291 presets or adjustable parameters</li>
4292 <li>Discover PDB IDs entry in structure menu doesn't
4293 discover PDB xRefs</li>
4294 <li>Exception encountered while trying to retrieve
4295 features with DAS</li>
4296 <li>Lowest value in annotation row isn't coloured
4297 when colour by annotation (per sequence) is coloured</li>
4298 <li>Keyboard mode P jumps to start of gapped region when
4299 residue follows a gap</li>
4300 <li>Jalview appears to hang importing an alignment with
4301 Wrap as default or after enabling Wrap</li>
4302 <li>'Right click to add annotations' message
4303 shown in wrap mode when no annotations present</li>
4304 <li>Disorder predictions fail with NPE if no automatic
4305 annotation already exists on alignment</li>
4306 <li>oninit javascript function should be called after
4307 initialisation completes</li>
4308 <li>Remove redundancy after disorder prediction corrupts
4309 alignment window display</li>
4310 <li>Example annotation file in documentation is invalid</li>
4311 <li>Grouped line graph annotation rows are not exported
4312 to annotation file</li>
4313 <li>Multi-harmony analysis cannot be run when only two
4315 <li>Cannot create multiple groups of line graphs with
4316 several 'combine' statements in annotation file</li>
4317 <li>Pressing return several times causes Number Format
4318 exceptions in keyboard mode</li>
4319 <li>Multi-harmony (SHMMR) method doesn't submit
4320 correct partitions for input data</li>
4321 <li>Translation from DNA to Amino Acids fails</li>
4322 <li>Jalview fail to load newick tree with quoted label</li>
4323 <li>--headless flag isn't understood</li>
4324 <li>ClassCastException when generating EPS in headless
4326 <li>Adjusting sequence-associated shading threshold only
4327 changes one row's threshold</li>
4328 <li>Preferences and Feature settings panel panel
4329 doesn't open</li>
4330 <li>hide consensus histogram also hides conservation and
4331 quality histograms</li>
4336 <td><div align="center">
4337 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
4339 <td><em>Application</em>
4341 <li>Support for JABAWS 2.0 Services (AACon alignment
4342 conservation, protein disorder and Clustal Omega)</li>
4343 <li>JABAWS server status indicator in Web Services
4345 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
4346 in Jalview alignment window</li>
4347 <li>Updated Jalview build and deploy framework for OSX
4348 mountain lion, windows 7, and 8</li>
4349 <li>Nucleotide substitution matrix for PCA that supports
4350 RNA and ambiguity codes</li>
4352 <li>Improved sequence database retrieval GUI</li>
4353 <li>Support fetching and database reference look up
4354 against multiple DAS sources (Fetch all from in 'fetch db
4356 <li>Jalview project improvements
4358 <li>Store and retrieve the 'belowAlignment'
4359 flag for annotation</li>
4360 <li>calcId attribute to group annotation rows on the
4362 <li>Store AACon calculation settings for a view in
4363 Jalview project</li>
4367 <li>horizontal scrolling gesture support</li>
4368 <li>Visual progress indicator when PCA calculation is
4370 <li>Simpler JABA web services menus</li>
4371 <li>visual indication that web service results are still
4372 being retrieved from server</li>
4373 <li>Serialise the dialogs that are shown when Jalview
4374 starts up for first time</li>
4375 <li>Jalview user agent string for interacting with HTTP
4377 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
4379 <li>Examples directory and Groovy library included in
4380 InstallAnywhere distribution</li>
4381 </ul> <em>Applet</em>
4383 <li>RNA alignment and secondary structure annotation
4384 visualization applet example</li>
4385 </ul> <em>General</em>
4387 <li>Normalise option for consensus sequence logo</li>
4388 <li>Reset button in PCA window to return dimensions to
4390 <li>Allow seqspace or Jalview variant of alignment PCA
4392 <li>PCA with either nucleic acid and protein substitution
4394 <li>Allow windows containing HTML reports to be exported
4396 <li>Interactive display and editing of RNA secondary
4397 structure contacts</li>
4398 <li>RNA Helix Alignment Colouring</li>
4399 <li>RNA base pair logo consensus</li>
4400 <li>Parse sequence associated secondary structure
4401 information in Stockholm files</li>
4402 <li>HTML Export database accessions and annotation
4403 information presented in tooltip for sequences</li>
4404 <li>Import secondary structure from LOCARNA clustalw
4405 style RNA alignment files</li>
4406 <li>import and visualise T-COFFEE quality scores for an
4408 <li>'colour by annotation' per sequence option to
4409 shade each sequence according to its associated alignment
4411 <li>New Jalview Logo</li>
4412 </ul> <em>Documentation and Development</em>
4414 <li>documentation for score matrices used in Jalview</li>
4415 <li>New Website!</li>
4417 <td><em>Application</em>
4419 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
4420 wsdbfetch REST service</li>
4421 <li>Stop windows being moved outside desktop on OSX</li>
4422 <li>Filetype associations not installed for webstart
4424 <li>Jalview does not always retrieve progress of a JABAWS
4425 job execution in full once it is complete</li>
4426 <li>revise SHMR RSBS definition to ensure alignment is
4427 uploaded via ali_file parameter</li>
4428 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
4429 <li>View all structures superposed fails with exception</li>
4430 <li>Jnet job queues forever if a very short sequence is
4431 submitted for prediction</li>
4432 <li>Cut and paste menu not opened when mouse clicked on
4434 <li>Putting fractional value into integer text box in
4435 alignment parameter dialog causes Jalview to hang</li>
4436 <li>Structure view highlighting doesn't work on
4438 <li>View all structures fails with exception shown in
4440 <li>Characters in filename associated with PDBEntry not
4441 escaped in a platform independent way</li>
4442 <li>Jalview desktop fails to launch with exception when
4444 <li>Tree calculation reports 'you must have 2 or more
4445 sequences selected' when selection is empty</li>
4446 <li>Jalview desktop fails to launch with jar signature
4447 failure when java web start temporary file caching is
4449 <li>DAS Sequence retrieval with range qualification
4450 results in sequence xref which includes range qualification</li>
4451 <li>Errors during processing of command line arguments
4452 cause progress bar (JAL-898) to be removed</li>
4453 <li>Replace comma for semi-colon option not disabled for
4454 DAS sources in sequence fetcher</li>
4455 <li>Cannot close news reader when JABAWS server warning
4456 dialog is shown</li>
4457 <li>Option widgets not updated to reflect user settings</li>
4458 <li>Edited sequence not submitted to web service</li>
4459 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
4460 <li>InstallAnywhere installer doesn't unpack and run
4461 on OSX Mountain Lion</li>
4462 <li>Annotation panel not given a scroll bar when
4463 sequences with alignment annotation are pasted into the
4465 <li>Sequence associated annotation rows not associated
4466 when loaded from Jalview project</li>
4467 <li>Browser launch fails with NPE on java 1.7</li>
4468 <li>JABAWS alignment marked as finished when job was
4469 cancelled or job failed due to invalid input</li>
4470 <li>NPE with v2.7 example when clicking on Tree
4471 associated with all views</li>
4472 <li>Exceptions when copy/paste sequences with grouped
4473 annotation rows to new window</li>
4474 </ul> <em>Applet</em>
4476 <li>Sequence features are momentarily displayed before
4477 they are hidden using hidefeaturegroups applet parameter</li>
4478 <li>loading features via javascript API automatically
4479 enables feature display</li>
4480 <li>scrollToColumnIn javascript API method doesn't
4482 </ul> <em>General</em>
4484 <li>Redundancy removal fails for rna alignment</li>
4485 <li>PCA calculation fails when sequence has been selected
4486 and then deselected</li>
4487 <li>PCA window shows grey box when first opened on OSX</li>
4488 <li>Letters coloured pink in sequence logo when alignment
4489 coloured with clustalx</li>
4490 <li>Choosing fonts without letter symbols defined causes
4491 exceptions and redraw errors</li>
4492 <li>Initial PCA plot view is not same as manually
4493 reconfigured view</li>
4494 <li>Grouped annotation graph label has incorrect line
4496 <li>Grouped annotation graph label display is corrupted
4497 for lots of labels</li>
4502 <div align="center">
4503 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
4506 <td><em>Application</em>
4508 <li>Jalview Desktop News Reader</li>
4509 <li>Tweaked default layout of web services menu</li>
4510 <li>View/alignment association menu to enable user to
4511 easily specify which alignment a multi-structure view takes
4512 its colours/correspondences from</li>
4513 <li>Allow properties file location to be specified as URL</li>
4514 <li>Extend Jalview project to preserve associations
4515 between many alignment views and a single Jmol display</li>
4516 <li>Store annotation row height in Jalview project file</li>
4517 <li>Annotation row column label formatting attributes
4518 stored in project file</li>
4519 <li>Annotation row order for auto-calculated annotation
4520 rows preserved in Jalview project file</li>
4521 <li>Visual progress indication when Jalview state is
4522 saved using Desktop window menu</li>
4523 <li>Visual indication that command line arguments are
4524 still being processed</li>
4525 <li>Groovy script execution from URL</li>
4526 <li>Colour by annotation default min and max colours in
4528 <li>Automatically associate PDB files dragged onto an
4529 alignment with sequences that have high similarity and
4531 <li>Update JGoogleAnalytics to latest release (0.3)</li>
4532 <li>'view structures' option to open many
4533 structures in same window</li>
4534 <li>Sort associated views menu option for tree panel</li>
4535 <li>Group all JABA and non-JABA services for a particular
4536 analysis function in its own submenu</li>
4537 </ul> <em>Applet</em>
4539 <li>Userdefined and autogenerated annotation rows for
4541 <li>Adjustment of alignment annotation pane height</li>
4542 <li>Annotation scrollbar for annotation panel</li>
4543 <li>Drag to reorder annotation rows in annotation panel</li>
4544 <li>'automaticScrolling' parameter</li>
4545 <li>Allow sequences with partial ID string matches to be
4546 annotated from GFF/Jalview features files</li>
4547 <li>Sequence logo annotation row in applet</li>
4548 <li>Absolute paths relative to host server in applet
4549 parameters are treated as such</li>
4550 <li>New in the JalviewLite javascript API:
4552 <li>JalviewLite.js javascript library</li>
4553 <li>Javascript callbacks for
4555 <li>Applet initialisation</li>
4556 <li>Sequence/alignment mouse-overs and selections</li>
4559 <li>scrollTo row and column alignment scrolling
4561 <li>Select sequence/alignment regions from javascript</li>
4562 <li>javascript structure viewer harness to pass
4563 messages between Jmol and Jalview when running as
4564 distinct applets</li>
4565 <li>sortBy method</li>
4566 <li>Set of applet and application examples shipped
4567 with documentation</li>
4568 <li>New example to demonstrate JalviewLite and Jmol
4569 javascript message exchange</li>
4571 </ul> <em>General</em>
4573 <li>Enable Jmol displays to be associated with multiple
4574 multiple alignments</li>
4575 <li>Option to automatically sort alignment with new tree</li>
4576 <li>User configurable link to enable redirects to a
4577 www.Jalview.org mirror</li>
4578 <li>Jmol colours option for Jmol displays</li>
4579 <li>Configurable newline string when writing alignment
4580 and other flat files</li>
4581 <li>Allow alignment annotation description lines to
4582 contain html tags</li>
4583 </ul> <em>Documentation and Development</em>
4585 <li>Add groovy test harness for bulk load testing to
4587 <li>Groovy script to load and align a set of sequences
4588 using a web service before displaying the result in the
4589 Jalview desktop</li>
4590 <li>Restructured javascript and applet api documentation</li>
4591 <li>Ant target to publish example html files with applet
4593 <li>Netbeans project for building Jalview from source</li>
4594 <li>ant task to create online javadoc for Jalview source</li>
4596 <td><em>Application</em>
4598 <li>User defined colourscheme throws exception when
4599 current built in colourscheme is saved as new scheme</li>
4600 <li>AlignFrame->Save in application pops up save
4601 dialog for valid filename/format</li>
4602 <li>Cannot view associated structure for UniProt sequence</li>
4603 <li>PDB file association breaks for UniProt sequence
4605 <li>Associate PDB from file dialog does not tell you
4606 which sequence is to be associated with the file</li>
4607 <li>Find All raises null pointer exception when query
4608 only matches sequence IDs</li>
4609 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4610 <li>Jalview project with Jmol views created with Jalview
4611 2.4 cannot be loaded</li>
4612 <li>Filetype associations not installed for webstart
4614 <li>Two or more chains in a single PDB file associated
4615 with sequences in different alignments do not get coloured
4616 by their associated sequence</li>
4617 <li>Visibility status of autocalculated annotation row
4618 not preserved when project is loaded</li>
4619 <li>Annotation row height and visibility attributes not
4620 stored in Jalview project</li>
4621 <li>Tree bootstraps are not preserved when saved as a
4622 Jalview project</li>
4623 <li>Envision2 workflow tooltips are corrupted</li>
4624 <li>Enabling show group conservation also enables colour
4625 by conservation</li>
4626 <li>Duplicate group associated conservation or consensus
4627 created on new view</li>
4628 <li>Annotation scrollbar not displayed after 'show
4629 all hidden annotation rows' option selected</li>
4630 <li>Alignment quality not updated after alignment
4631 annotation row is hidden then shown</li>
4632 <li>Preserve colouring of structures coloured by
4633 sequences in pre Jalview 2.7 projects</li>
4634 <li>Web service job parameter dialog is not laid out
4636 <li>Web services menu not refreshed after 'reset
4637 services' button is pressed in preferences</li>
4638 <li>Annotation off by one in Jalview v2_3 example project</li>
4639 <li>Structures imported from file and saved in project
4640 get name like jalview_pdb1234.txt when reloaded</li>
4641 <li>Jalview does not always retrieve progress of a JABAWS
4642 job execution in full once it is complete</li>
4643 </ul> <em>Applet</em>
4645 <li>Alignment height set incorrectly when lots of
4646 annotation rows are displayed</li>
4647 <li>Relative URLs in feature HTML text not resolved to
4649 <li>View follows highlighting does not work for positions
4651 <li><= shown as = in tooltip</li>
4652 <li>Export features raises exception when no features
4654 <li>Separator string used for serialising lists of IDs
4655 for javascript api is modified when separator string
4656 provided as parameter</li>
4657 <li>Null pointer exception when selecting tree leaves for
4658 alignment with no existing selection</li>
4659 <li>Relative URLs for datasources assumed to be relative
4660 to applet's codebase</li>
4661 <li>Status bar not updated after finished searching and
4662 search wraps around to first result</li>
4663 <li>StructureSelectionManager instance shared between
4664 several Jalview applets causes race conditions and memory
4666 <li>Hover tooltip and mouseover of position on structure
4667 not sent from Jmol in applet</li>
4668 <li>Certain sequences of javascript method calls to
4669 applet API fatally hang browser</li>
4670 </ul> <em>General</em>
4672 <li>View follows structure mouseover scrolls beyond
4673 position with wrapped view and hidden regions</li>
4674 <li>Find sequence position moves to wrong residue
4675 with/without hidden columns</li>
4676 <li>Sequence length given in alignment properties window
4678 <li>InvalidNumberFormat exceptions thrown when trying to
4679 import PDB like structure files</li>
4680 <li>Positional search results are only highlighted
4681 between user-supplied sequence start/end bounds</li>
4682 <li>End attribute of sequence is not validated</li>
4683 <li>Find dialog only finds first sequence containing a
4684 given sequence position</li>
4685 <li>Sequence numbering not preserved in MSF alignment
4687 <li>Jalview PDB file reader does not extract sequence
4688 from nucleotide chains correctly</li>
4689 <li>Structure colours not updated when tree partition
4690 changed in alignment</li>
4691 <li>Sequence associated secondary structure not correctly
4692 parsed in interleaved stockholm</li>
4693 <li>Colour by annotation dialog does not restore current
4695 <li>Hiding (nearly) all sequences doesn't work
4697 <li>Sequences containing lowercase letters are not
4698 properly associated with their pdb files</li>
4699 </ul> <em>Documentation and Development</em>
4701 <li>schemas/JalviewWsParamSet.xsd corrupted by
4702 ApplyCopyright tool</li>
4707 <div align="center">
4708 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4711 <td><em>Application</em>
4713 <li>New warning dialog when the Jalview Desktop cannot
4714 contact web services</li>
4715 <li>JABA service parameters for a preset are shown in
4716 service job window</li>
4717 <li>JABA Service menu entries reworded</li>
4721 <li>Modeller PIR IO broken - cannot correctly import a
4722 pir file emitted by Jalview</li>
4723 <li>Existing feature settings transferred to new
4724 alignment view created from cut'n'paste</li>
4725 <li>Improved test for mixed amino/nucleotide chains when
4726 parsing PDB files</li>
4727 <li>Consensus and conservation annotation rows
4728 occasionally become blank for all new windows</li>
4729 <li>Exception raised when right clicking above sequences
4730 in wrapped view mode</li>
4731 </ul> <em>Application</em>
4733 <li>multiple multiply aligned structure views cause cpu
4734 usage to hit 100% and computer to hang</li>
4735 <li>Web Service parameter layout breaks for long user
4736 parameter names</li>
4737 <li>Jaba service discovery hangs desktop if Jaba server
4744 <div align="center">
4745 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4748 <td><em>Application</em>
4750 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4751 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4754 <li>Web Services preference tab</li>
4755 <li>Analysis parameters dialog box and user defined
4757 <li>Improved speed and layout of Envision2 service menu</li>
4758 <li>Superpose structures using associated sequence
4760 <li>Export coordinates and projection as CSV from PCA
4762 </ul> <em>Applet</em>
4764 <li>enable javascript: execution by the applet via the
4765 link out mechanism</li>
4766 </ul> <em>Other</em>
4768 <li>Updated the Jmol Jalview interface to work with Jmol
4770 <li>The Jalview Desktop and JalviewLite applet now
4771 require Java 1.5</li>
4772 <li>Allow Jalview feature colour specification for GFF
4773 sequence annotation files</li>
4774 <li>New 'colour by label' keword in Jalview feature file
4775 type colour specification</li>
4776 <li>New Jalview Desktop Groovy API method that allows a
4777 script to check if it being run in an interactive session or
4778 in a batch operation from the Jalview command line</li>
4782 <li>clustalx colourscheme colours Ds preferentially when
4783 both D+E are present in over 50% of the column</li>
4784 </ul> <em>Application</em>
4786 <li>typo in AlignmentFrame->View->Hide->all but
4787 selected Regions menu item</li>
4788 <li>sequence fetcher replaces ',' for ';' when the ',' is
4789 part of a valid accession ID</li>
4790 <li>fatal OOM if object retrieved by sequence fetcher
4791 runs out of memory</li>
4792 <li>unhandled Out of Memory Error when viewing pca
4793 analysis results</li>
4794 <li>InstallAnywhere builds fail to launch on OS X java
4795 10.5 update 4 (due to apple Java 1.6 update)</li>
4796 <li>Installanywhere Jalview silently fails to launch</li>
4797 </ul> <em>Applet</em>
4799 <li>Jalview.getFeatureGroups() raises an
4800 ArrayIndexOutOfBoundsException if no feature groups are
4807 <div align="center">
4808 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4814 <li>Alignment prettyprinter doesn't cope with long
4816 <li>clustalx colourscheme colours Ds preferentially when
4817 both D+E are present in over 50% of the column</li>
4818 <li>nucleic acid structures retrieved from PDB do not
4819 import correctly</li>
4820 <li>More columns get selected than were clicked on when a
4821 number of columns are hidden</li>
4822 <li>annotation label popup menu not providing correct
4823 add/hide/show options when rows are hidden or none are
4825 <li>Stockholm format shown in list of readable formats,
4826 and parser copes better with alignments from RFAM.</li>
4827 <li>CSV output of consensus only includes the percentage
4828 of all symbols if sequence logo display is enabled</li>
4830 </ul> <em>Applet</em>
4832 <li>annotation panel disappears when annotation is
4834 </ul> <em>Application</em>
4836 <li>Alignment view not redrawn properly when new
4837 alignment opened where annotation panel is visible but no
4838 annotations are present on alignment</li>
4839 <li>pasted region containing hidden columns is
4840 incorrectly displayed in new alignment window</li>
4841 <li>Jalview slow to complete operations when stdout is
4842 flooded (fix is to close the Jalview console)</li>
4843 <li>typo in AlignmentFrame->View->Hide->all but
4844 selected Rregions menu item.</li>
4845 <li>inconsistent group submenu and Format submenu entry
4846 'Un' or 'Non'conserved</li>
4847 <li>Sequence feature settings are being shared by
4848 multiple distinct alignments</li>
4849 <li>group annotation not recreated when tree partition is
4851 <li>double click on group annotation to select sequences
4852 does not propagate to associated trees</li>
4853 <li>Mac OSX specific issues:
4855 <li>exception raised when mouse clicked on desktop
4856 window background</li>
4857 <li>Desktop menu placed on menu bar and application
4858 name set correctly</li>
4859 <li>sequence feature settings not wide enough for the
4860 save feature colourscheme button</li>
4869 <div align="center">
4870 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4873 <td><em>New Capabilities</em>
4875 <li>URL links generated from description line for
4876 regular-expression based URL links (applet and application)
4879 <li>Non-positional feature URL links are shown in link
4881 <li>Linked viewing of nucleic acid sequences and
4883 <li>Automatic Scrolling option in View menu to display
4884 the currently highlighted region of an alignment.</li>
4885 <li>Order an alignment by sequence length, or using the
4886 average score or total feature count for each sequence.</li>
4887 <li>Shading features by score or associated description</li>
4888 <li>Subdivide alignment and groups based on identity of
4889 selected subsequence (Make Groups from Selection).</li>
4890 <li>New hide/show options including Shift+Control+H to
4891 hide everything but the currently selected region.</li>
4892 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4893 </ul> <em>Application</em>
4895 <li>Fetch DB References capabilities and UI expanded to
4896 support retrieval from DAS sequence sources</li>
4897 <li>Local DAS Sequence sources can be added via the
4898 command line or via the Add local source dialog box.</li>
4899 <li>DAS Dbref and DbxRef feature types are parsed as
4900 database references and protein_name is parsed as
4901 description line (BioSapiens terms).</li>
4902 <li>Enable or disable non-positional feature and database
4903 references in sequence ID tooltip from View menu in
4905 <!-- <li>New hidden columns and rows and representatives capabilities
4906 in annotations file (in progress - not yet fully implemented)</li> -->
4907 <li>Group-associated consensus, sequence logos and
4908 conservation plots</li>
4909 <li>Symbol distributions for each column can be exported
4910 and visualized as sequence logos</li>
4911 <li>Optionally scale multi-character column labels to fit
4912 within each column of annotation row<!-- todo for applet -->
4914 <li>Optional automatic sort of associated alignment view
4915 when a new tree is opened.</li>
4916 <li>Jalview Java Console</li>
4917 <li>Better placement of desktop window when moving
4918 between different screens.</li>
4919 <li>New preference items for sequence ID tooltip and
4920 consensus annotation</li>
4921 <li>Client to submit sequences and IDs to Envision2
4923 <li><em>Vamsas Capabilities</em>
4925 <li>Improved VAMSAS synchronization (Jalview archive
4926 used to preserve views, structures, and tree display
4928 <li>Import of vamsas documents from disk or URL via
4930 <li>Sharing of selected regions between views and
4931 with other VAMSAS applications (Experimental feature!)</li>
4932 <li>Updated API to VAMSAS version 0.2</li>
4934 </ul> <em>Applet</em>
4936 <li>Middle button resizes annotation row height</li>
4939 <li>sortByTree (true/false) - automatically sort the
4940 associated alignment view by the tree when a new tree is
4942 <li>showTreeBootstraps (true/false) - show or hide
4943 branch bootstraps (default is to show them if available)</li>
4944 <li>showTreeDistances (true/false) - show or hide
4945 branch lengths (default is to show them if available)</li>
4946 <li>showUnlinkedTreeNodes (true/false) - indicate if
4947 unassociated nodes should be highlighted in the tree
4949 <li>heightScale and widthScale (1.0 or more) -
4950 increase the height or width of a cell in the alignment
4951 grid relative to the current font size.</li>
4954 <li>Non-positional features displayed in sequence ID
4956 </ul> <em>Other</em>
4958 <li>Features format: graduated colour definitions and
4959 specification of feature scores</li>
4960 <li>Alignment Annotations format: new keywords for group
4961 associated annotation (GROUP_REF) and annotation row display
4962 properties (ROW_PROPERTIES)</li>
4963 <li>XML formats extended to support graduated feature
4964 colourschemes, group associated annotation, and profile
4965 visualization settings.</li></td>
4968 <li>Source field in GFF files parsed as feature source
4969 rather than description</li>
4970 <li>Non-positional features are now included in sequence
4971 feature and gff files (controlled via non-positional feature
4972 visibility in tooltip).</li>
4973 <li>URL links generated for all feature links (bugfix)</li>
4974 <li>Added URL embedding instructions to features file
4976 <li>Codons containing ambiguous nucleotides translated as
4977 'X' in peptide product</li>
4978 <li>Match case switch in find dialog box works for both
4979 sequence ID and sequence string and query strings do not
4980 have to be in upper case to match case-insensitively.</li>
4981 <li>AMSA files only contain first column of
4982 multi-character column annotation labels</li>
4983 <li>Jalview Annotation File generation/parsing consistent
4984 with documentation (e.g. Stockholm annotation can be
4985 exported and re-imported)</li>
4986 <li>PDB files without embedded PDB IDs given a friendly
4988 <li>Find incrementally searches ID string matches as well
4989 as subsequence matches, and correctly reports total number
4993 <li>Better handling of exceptions during sequence
4995 <li>Dasobert generated non-positional feature URL
4996 link text excludes the start_end suffix</li>
4997 <li>DAS feature and source retrieval buttons disabled
4998 when fetch or registry operations in progress.</li>
4999 <li>PDB files retrieved from URLs are cached properly</li>
5000 <li>Sequence description lines properly shared via
5002 <li>Sequence fetcher fetches multiple records for all
5004 <li>Ensured that command line das feature retrieval
5005 completes before alignment figures are generated.</li>
5006 <li>Reduced time taken when opening file browser for
5008 <li>isAligned check prior to calculating tree, PCA or
5009 submitting an MSA to JNet now excludes hidden sequences.</li>
5010 <li>User defined group colours properly recovered
5011 from Jalview projects.</li>
5020 <div align="center">
5021 <strong>2.4.0.b2</strong><br> 28/10/2009
5026 <li>Experimental support for google analytics usage
5028 <li>Jalview privacy settings (user preferences and docs).</li>
5033 <li>Race condition in applet preventing startup in
5035 <li>Exception when feature created from selection beyond
5036 length of sequence.</li>
5037 <li>Allow synthetic PDB files to be imported gracefully</li>
5038 <li>Sequence associated annotation rows associate with
5039 all sequences with a given id</li>
5040 <li>Find function matches case-insensitively for sequence
5041 ID string searches</li>
5042 <li>Non-standard characters do not cause pairwise
5043 alignment to fail with exception</li>
5044 </ul> <em>Application Issues</em>
5046 <li>Sequences are now validated against EMBL database</li>
5047 <li>Sequence fetcher fetches multiple records for all
5049 </ul> <em>InstallAnywhere Issues</em>
5051 <li>Dock icon works for Mac OS X java (Mac 1.6 update
5052 issue with installAnywhere mechanism)</li>
5053 <li>Command line launching of JARs from InstallAnywhere
5054 version (java class versioning error fixed)</li>
5061 <div align="center">
5062 <strong>2.4</strong><br> 27/8/2008
5065 <td><em>User Interface</em>
5067 <li>Linked highlighting of codon and amino acid from
5068 translation and protein products</li>
5069 <li>Linked highlighting of structure associated with
5070 residue mapping to codon position</li>
5071 <li>Sequence Fetcher provides example accession numbers
5072 and 'clear' button</li>
5073 <li>MemoryMonitor added as an option under Desktop's
5075 <li>Extract score function to parse whitespace separated
5076 numeric data in description line</li>
5077 <li>Column labels in alignment annotation can be centred.</li>
5078 <li>Tooltip for sequence associated annotation give name
5080 </ul> <em>Web Services and URL fetching</em>
5082 <li>JPred3 web service</li>
5083 <li>Prototype sequence search client (no public services
5085 <li>Fetch either seed alignment or full alignment from
5087 <li>URL Links created for matching database cross
5088 references as well as sequence ID</li>
5089 <li>URL Links can be created using regular-expressions</li>
5090 </ul> <em>Sequence Database Connectivity</em>
5092 <li>Retrieval of cross-referenced sequences from other
5094 <li>Generalised database reference retrieval and
5095 validation to all fetchable databases</li>
5096 <li>Fetch sequences from DAS sources supporting the
5097 sequence command</li>
5098 </ul> <em>Import and Export</em>
5099 <li>export annotation rows as CSV for spreadsheet import</li>
5100 <li>Jalview projects record alignment dataset associations,
5101 EMBL products, and cDNA sequence mappings</li>
5102 <li>Sequence Group colour can be specified in Annotation
5104 <li>Ad-hoc colouring of group in Annotation File using RGB
5105 triplet as name of colourscheme</li>
5106 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
5108 <li>treenode binding for VAMSAS tree exchange</li>
5109 <li>local editing and update of sequences in VAMSAS
5110 alignments (experimental)</li>
5111 <li>Create new or select existing session to join</li>
5112 <li>load and save of vamsas documents</li>
5113 </ul> <em>Application command line</em>
5115 <li>-tree parameter to open trees (introduced for passing
5117 <li>-fetchfrom command line argument to specify nicknames
5118 of DAS servers to query for alignment features</li>
5119 <li>-dasserver command line argument to add new servers
5120 that are also automatically queried for features</li>
5121 <li>-groovy command line argument executes a given groovy
5122 script after all input data has been loaded and parsed</li>
5123 </ul> <em>Applet-Application data exchange</em>
5125 <li>Trees passed as applet parameters can be passed to
5126 application (when using "View in full
5127 application")</li>
5128 </ul> <em>Applet Parameters</em>
5130 <li>feature group display control parameter</li>
5131 <li>debug parameter</li>
5132 <li>showbutton parameter</li>
5133 </ul> <em>Applet API methods</em>
5135 <li>newView public method</li>
5136 <li>Window (current view) specific get/set public methods</li>
5137 <li>Feature display control methods</li>
5138 <li>get list of currently selected sequences</li>
5139 </ul> <em>New Jalview distribution features</em>
5141 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
5142 <li>RELEASE file gives build properties for the latest
5143 Jalview release.</li>
5144 <li>Java 1.1 Applet build made easier and donotobfuscate
5145 property controls execution of obfuscator</li>
5146 <li>Build target for generating source distribution</li>
5147 <li>Debug flag for javacc</li>
5148 <li>.jalview_properties file is documented (slightly) in
5149 jalview.bin.Cache</li>
5150 <li>Continuous Build Integration for stable and
5151 development version of Application, Applet and source
5156 <li>selected region output includes visible annotations
5157 (for certain formats)</li>
5158 <li>edit label/displaychar contains existing label/char
5160 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
5161 <li>shorter peptide product names from EMBL records</li>
5162 <li>Newick string generator makes compact representations</li>
5163 <li>bootstrap values parsed correctly for tree files with
5165 <li>pathological filechooser bug avoided by not allowing
5166 filenames containing a ':'</li>
5167 <li>Fixed exception when parsing GFF files containing
5168 global sequence features</li>
5169 <li>Alignment datasets are finalized only when number of
5170 references from alignment sequences goes to zero</li>
5171 <li>Close of tree branch colour box without colour
5172 selection causes cascading exceptions</li>
5173 <li>occasional negative imgwidth exceptions</li>
5174 <li>better reporting of non-fatal warnings to user when
5175 file parsing fails.</li>
5176 <li>Save works when Jalview project is default format</li>
5177 <li>Save as dialog opened if current alignment format is
5178 not a valid output format</li>
5179 <li>UniProt canonical names introduced for both das and
5181 <li>Histidine should be midblue (not pink!) in Zappo</li>
5182 <li>error messages passed up and output when data read
5184 <li>edit undo recovers previous dataset sequence when
5185 sequence is edited</li>
5186 <li>allow PDB files without pdb ID HEADER lines (like
5187 those generated by MODELLER) to be read in properly</li>
5188 <li>allow reading of JPred concise files as a normal
5190 <li>Stockholm annotation parsing and alignment properties
5191 import fixed for PFAM records</li>
5192 <li>Structure view windows have correct name in Desktop
5194 <li>annotation consisting of sequence associated scores
5195 can be read and written correctly to annotation file</li>
5196 <li>Aligned cDNA translation to aligned peptide works
5198 <li>Fixed display of hidden sequence markers and
5199 non-italic font for representatives in Applet</li>
5200 <li>Applet Menus are always embedded in applet window on
5202 <li>Newly shown features appear at top of stack (in
5204 <li>Annotations added via parameter not drawn properly
5205 due to null pointer exceptions</li>
5206 <li>Secondary structure lines are drawn starting from
5207 first column of alignment</li>
5208 <li>UniProt XML import updated for new schema release in
5210 <li>Sequence feature to sequence ID match for Features
5211 file is case-insensitive</li>
5212 <li>Sequence features read from Features file appended to
5213 all sequences with matching IDs</li>
5214 <li>PDB structure coloured correctly for associated views
5215 containing a sub-sequence</li>
5216 <li>PDB files can be retrieved by applet from Jar files</li>
5217 <li>feature and annotation file applet parameters
5218 referring to different directories are retrieved correctly</li>
5219 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
5220 <li>Fixed application hang whilst waiting for
5221 splash-screen version check to complete</li>
5222 <li>Applet properly URLencodes input parameter values
5223 when passing them to the launchApp service</li>
5224 <li>display name and local features preserved in results
5225 retrieved from web service</li>
5226 <li>Visual delay indication for sequence retrieval and
5227 sequence fetcher initialisation</li>
5228 <li>updated Application to use DAS 1.53e version of
5229 dasobert DAS client</li>
5230 <li>Re-instated Full AMSA support and .amsa file
5232 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
5240 <div align="center">
5241 <strong>2.3</strong><br> 9/5/07
5246 <li>Jmol 11.0.2 integration</li>
5247 <li>PDB views stored in Jalview XML files</li>
5248 <li>Slide sequences</li>
5249 <li>Edit sequence in place</li>
5250 <li>EMBL CDS features</li>
5251 <li>DAS Feature mapping</li>
5252 <li>Feature ordering</li>
5253 <li>Alignment Properties</li>
5254 <li>Annotation Scores</li>
5255 <li>Sort by scores</li>
5256 <li>Feature/annotation editing in applet</li>
5261 <li>Headless state operation in 2.2.1</li>
5262 <li>Incorrect and unstable DNA pairwise alignment</li>
5263 <li>Cut and paste of sequences with annotation</li>
5264 <li>Feature group display state in XML</li>
5265 <li>Feature ordering in XML</li>
5266 <li>blc file iteration selection using filename # suffix</li>
5267 <li>Stockholm alignment properties</li>
5268 <li>Stockhom alignment secondary structure annotation</li>
5269 <li>2.2.1 applet had no feature transparency</li>
5270 <li>Number pad keys can be used in cursor mode</li>
5271 <li>Structure Viewer mirror image resolved</li>
5278 <div align="center">
5279 <strong>2.2.1</strong><br> 12/2/07
5284 <li>Non standard characters can be read and displayed
5285 <li>Annotations/Features can be imported/exported to the
5287 <li>Applet allows editing of sequence/annotation/group
5288 name & description
5289 <li>Preference setting to display sequence name in
5291 <li>Annotation file format extended to allow
5292 Sequence_groups to be defined
5293 <li>Default opening of alignment overview panel can be
5294 specified in preferences
5295 <li>PDB residue numbering annotation added to associated
5301 <li>Applet crash under certain Linux OS with Java 1.6
5303 <li>Annotation file export / import bugs fixed
5304 <li>PNG / EPS image output bugs fixed
5310 <div align="center">
5311 <strong>2.2</strong><br> 27/11/06
5316 <li>Multiple views on alignment
5317 <li>Sequence feature editing
5318 <li>"Reload" alignment
5319 <li>"Save" to current filename
5320 <li>Background dependent text colour
5321 <li>Right align sequence ids
5322 <li>User-defined lower case residue colours
5325 <li>Menu item accelerator keys
5326 <li>Control-V pastes to current alignment
5327 <li>Cancel button for DAS Feature Fetching
5328 <li>PCA and PDB Viewers zoom via mouse roller
5329 <li>User-defined sub-tree colours and sub-tree selection
5332 <li>'New Window' button on the 'Output to Text box'
5337 <li>New memory efficient Undo/Redo System
5338 <li>Optimised symbol lookups and conservation/consensus
5340 <li>Region Conservation/Consensus recalculated after
5342 <li>Fixed Remove Empty Columns Bug (empty columns at end
5344 <li>Slowed DAS Feature Fetching for increased robustness.
5347 <li>Made angle brackets in ASCII feature descriptions
5349 <li>Re-instated Zoom function for PCA
5350 <li>Sequence descriptions conserved in web service
5352 <li>UniProt ID discoverer uses any word separated by
5354 <li>WsDbFetch query/result association resolved
5355 <li>Tree leaf to sequence mapping improved
5356 <li>Smooth fonts switch moved to FontChooser dialog box.
5364 <div align="center">
5365 <strong>2.1.1</strong><br> 12/9/06
5370 <li>Copy consensus sequence to clipboard</li>
5375 <li>Image output - rightmost residues are rendered if
5376 sequence id panel has been resized</li>
5377 <li>Image output - all offscreen group boundaries are
5379 <li>Annotation files with sequence references - all
5380 elements in file are relative to sequence position</li>
5381 <li>Mac Applet users can use Alt key for group editing</li>
5387 <div align="center">
5388 <strong>2.1</strong><br> 22/8/06
5393 <li>MAFFT Multiple Alignment in default Web Service list</li>
5394 <li>DAS Feature fetching</li>
5395 <li>Hide sequences and columns</li>
5396 <li>Export Annotations and Features</li>
5397 <li>GFF file reading / writing</li>
5398 <li>Associate structures with sequences from local PDB
5400 <li>Add sequences to exisiting alignment</li>
5401 <li>Recently opened files / URL lists</li>
5402 <li>Applet can launch the full application</li>
5403 <li>Applet has transparency for features (Java 1.2
5405 <li>Applet has user defined colours parameter</li>
5406 <li>Applet can load sequences from parameter
5407 "sequence<em>x</em>"
5413 <li>Redundancy Panel reinstalled in the Applet</li>
5414 <li>Monospaced font - EPS / rescaling bug fixed</li>
5415 <li>Annotation files with sequence references bug fixed</li>
5421 <div align="center">
5422 <strong>2.08.1</strong><br> 2/5/06
5427 <li>Change case of selected region from Popup menu</li>
5428 <li>Choose to match case when searching</li>
5429 <li>Middle mouse button and mouse movement can compress /
5430 expand the visible width and height of the alignment</li>
5435 <li>Annotation Panel displays complete JNet results</li>
5441 <div align="center">
5442 <strong>2.08b</strong><br> 18/4/06
5448 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
5449 <li>Righthand label on wrapped alignments shows correct
5456 <div align="center">
5457 <strong>2.08</strong><br> 10/4/06
5462 <li>Editing can be locked to the selection area</li>
5463 <li>Keyboard editing</li>
5464 <li>Create sequence features from searches</li>
5465 <li>Precalculated annotations can be loaded onto
5467 <li>Features file allows grouping of features</li>
5468 <li>Annotation Colouring scheme added</li>
5469 <li>Smooth fonts off by default - Faster rendering</li>
5470 <li>Choose to toggle Autocalculate Consensus On/Off</li>
5475 <li>Drag & Drop fixed on Linux</li>
5476 <li>Jalview Archive file faster to load/save, sequence
5477 descriptions saved.</li>
5483 <div align="center">
5484 <strong>2.07</strong><br> 12/12/05
5489 <li>PDB Structure Viewer enhanced</li>
5490 <li>Sequence Feature retrieval and display enhanced</li>
5491 <li>Choose to output sequence start-end after sequence
5492 name for file output</li>
5493 <li>Sequence Fetcher WSDBFetch@EBI</li>
5494 <li>Applet can read feature files, PDB files and can be
5495 used for HTML form input</li>
5500 <li>HTML output writes groups and features</li>
5501 <li>Group editing is Control and mouse click</li>
5502 <li>File IO bugs</li>
5508 <div align="center">
5509 <strong>2.06</strong><br> 28/9/05
5514 <li>View annotations in wrapped mode</li>
5515 <li>More options for PCA viewer</li>
5520 <li>GUI bugs resolved</li>
5521 <li>Runs with -nodisplay from command line</li>
5527 <div align="center">
5528 <strong>2.05b</strong><br> 15/9/05
5533 <li>Choose EPS export as lineart or text</li>
5534 <li>Jar files are executable</li>
5535 <li>Can read in Uracil - maps to unknown residue</li>
5540 <li>Known OutOfMemory errors give warning message</li>
5541 <li>Overview window calculated more efficiently</li>
5542 <li>Several GUI bugs resolved</li>
5548 <div align="center">
5549 <strong>2.05</strong><br> 30/8/05
5554 <li>Edit and annotate in "Wrapped" view</li>
5559 <li>Several GUI bugs resolved</li>
5565 <div align="center">
5566 <strong>2.04</strong><br> 24/8/05
5571 <li>Hold down mouse wheel & scroll to change font
5577 <li>Improved JPred client reliability</li>
5578 <li>Improved loading of Jalview files</li>
5584 <div align="center">
5585 <strong>2.03</strong><br> 18/8/05
5590 <li>Set Proxy server name and port in preferences</li>
5591 <li>Multiple URL links from sequence ids</li>
5592 <li>User Defined Colours can have a scheme name and added
5594 <li>Choose to ignore gaps in consensus calculation</li>
5595 <li>Unix users can set default web browser</li>
5596 <li>Runs without GUI for batch processing</li>
5597 <li>Dynamically generated Web Service Menus</li>
5602 <li>InstallAnywhere download for Sparc Solaris</li>
5608 <div align="center">
5609 <strong>2.02</strong><br> 18/7/05
5615 <li>Copy & Paste order of sequences maintains
5616 alignment order.</li>
5622 <div align="center">
5623 <strong>2.01</strong><br> 12/7/05
5628 <li>Use delete key for deleting selection.</li>
5629 <li>Use Mouse wheel to scroll sequences.</li>
5630 <li>Help file updated to describe how to add alignment
5632 <li>Version and build date written to build properties
5634 <li>InstallAnywhere installation will check for updates
5635 at launch of Jalview.</li>
5640 <li>Delete gaps bug fixed.</li>
5641 <li>FileChooser sorts columns.</li>
5642 <li>Can remove groups one by one.</li>
5643 <li>Filechooser icons installed.</li>
5644 <li>Finder ignores return character when searching.
5645 Return key will initiate a search.<br>
5652 <div align="center">
5653 <strong>2.0</strong><br> 20/6/05
5658 <li>New codebase</li>