4 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
5 * Copyright (C) $$Year-Rel$$ The Jalview Authors
7 * This file is part of Jalview.
9 * Jalview is free software: you can redistribute it and/or
10 * modify it under the terms of the GNU General Public License
11 * as published by the Free Software Foundation, either version 3
12 * of the License, or (at your option) any later version.
14 * Jalview is distributed in the hope that it will be useful, but
15 * WITHOUT ANY WARRANTY; without even the implied warranty
16 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
17 * PURPOSE. See the GNU General Public License for more details.
19 * You should have received a copy of the GNU General Public License
20 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
21 * The Jalview Authors are detailed in the 'AUTHORS' file.
24 <title>Release History</title>
27 /* remove bullets, narrower indent */
28 list-style-type: none;
35 /* separate the items from eachother */
42 /* doesnt get processed in javahelp */
51 <strong>Release History</strong>
55 <th nowrap><a id="Jalview.$$Version-Rel$$"><em>Release</em></th>
56 <th><em>New Features</em></th>
57 <th><em>Issues Resolved</em></th>
60 <td width="60" align="center" nowrap><strong><a
61 id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.0">.1</a><br />
62 <em>31/03/2022</em></strong></td>
63 <td align="left" valign="top">
66 <!-- JAL-3973 -->Distribution Tarball includes git commit
71 <td align="left" valign="top">
74 <!-- JAL-3975 -->Keyboard mode (F2) stops working after
75 using the "Create sequence feature" dialog
78 <!-- JAL-3976 -->3D Structure chooser fails to select
79 structures from 3D-beacons and pops up a 'null' dialog
82 <!-- JAL-3973 -->Cannot build Jalview 2.11.2.0 via gradle
83 from its source tarball
85 </ul> <em>New Known Issues</em>
88 <!-- JAL-3873 -->Colour by->all views doesn't allow
89 colouring same structure from different views (since
93 <!-- JAL-3980 --> Sequence ID tooltip not showing during
94 long running retrieval/crossref operations (affects at least
98 <!-- JAL-3886 -->Pfam and Rfam alignment retrieval as
99 gzipped stockholm doesn't work on JalviewJS build of 2.11.2
102 <!-- JAL-3972 -->Java 11 Only: Jalview 2.11.2.0 OSX install
103 not working due to VAqua requiring
104 sun.awt.image.MultiResolutionImage
107 <!-- JAL-3981 -->Sequence Details can take a long time to be
108 displayed for heavily annotated sequences (all versions)
114 <td width="60" align="center" nowrap><strong><a
115 id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.0">.0</a><br />
116 <em>10/03/2022</em></strong></td>
117 <td align="left" valign="top">
120 <!-- JAL-3616 JAL-3551 JAL-2322 -->Support for viewing 3D
121 structures with ChimeraX and Pymol in addition to Jmol and
125 <!-- JAL-3829 -->Discover 3D structure data for sequences
126 with Uniprot references via 3D-Beacons
129 <!-- JAL-3391 -->Rank and select available structures for
130 Uniprot sequences according to number of residues in
131 structure mapped to positions involved in the alignment
134 <!-- JAL-2226 -->Structure annotation rows for all mapped
135 chains in 3D structures are included in the 'Reference
136 Annotation' for a sequence
139 <!-- JAL-1260 -->Import Genbank and EMBL format flatfiles
142 <!-- JAL-3821 -->ENA record's mol_type honoured so RNA
143 molecules imported from ENA records are shown as RNA
145 <!-- JAL-3863 -->Support for Canonical Uniprot IDs
148 <!-- JAL-3503 -->New Preferences tab for adjusting Jalview's
149 memory settings at launch
152 <!-- JAL-3881 -->Sequence IDs split on '_' as well as other
153 non-alphanumerics when discovering database references with
157 <!-- JAL-3884 -->Suppressed harmless exceptions output to
158 Console whilst discovering database references for a
162 <!-- JAL-3204 -->Updated Jalview bindings for Uniprot XML
166 <!-- JAL-3926 -->Uniprot and PDBe autosearch option is
170 <!-- JAL-3144 -->Reverted to Jalview 'classic' drop-down
171 menu for selecting which database to fetch from in sequence
175 <!-- JAL-3018 -->Updated Ensembl REST Client compatibility
176 to 15.2 and revised model organism names (rat, xenopus,
177 dmelanogaster now rattus_norvegicus, xenopus_tropicalis,
178 drosophila_melanogaster)
181 <!-- JAL-3530 -->-nowebservicediscovery command line
182 argument to prevent automatic discovery of analysis
183 webservices on launch
186 <!-- JAL-3618 -->Allow 'App' directories to be opened when
187 locating Chimera, ChimeraX or Pymol binaries via filechooser
188 opened by double clicking the Structure Preferences' path
192 <!-- JAL-3632 JAL-3633 -->support for HTTP/S access via
193 proxies that require authentication
196 <!-- JAL-3103 -->New mechanism for opening URLs with system
197 default browser (works on OSX and Linux as well as Windows)
200 <!-- JAL-3871 JAL-3874 -->Upgraded bundled version of Jmol
204 <!-- JAL-3837 -->GPL license info on splash screen and About
207 </ul> <em>Jalview Native App</em>
210 <!-- JAL-3830 -->New command line launcher scripts (.sh,
211 .ps1, .bat) usable on macOS, Linux/Unix, Windows and
212 documentation in Help. Installer wizard has option to add
213 this to PATH, or link to it in your PATH.<br /> <em>This
214 is the recommended workaround for known issue about
215 working directory preservation when running native
216 application from command line. <!-- JAL-3523 -->
219 <li>Notarized MacOS installer for compliance with latest
220 OSX releases (Monterey)</li>
222 <!-- JAL-3805 -->Uninstaller application for old
223 (InstallAnywhere based) Jalview installations removed from
227 <!-- JAL-3608 -->Options to allow user to choose the (Swing)
228 Look and Feel (LaF) used by Jalview
231 <!-- JAL-3552, JAL-3609 -->Metal LaF used to improved
232 operation on Linux Ubuntu with HiDPI display in Java 11
233 (still known issues with HiDPI screens in java 8 and 11. see
234 <a href="https://issues.jalview.org/browse/JAL-3137">JAL-3137</a>)
237 <!-- JAL-3633 -->Getdown launcher inherits HTTP/S proxy
238 configuration from jalview_properties
241 <!-- JAL- -->New Jalview Develop app - making it even easier
242 to get at Jalview's development builds
245 <!-- JAL-3594 -->New splashscreens for Jalview, Jalview Test
246 and Jalview Develop applications.
249 <!-- JAL-3728 -->Jalview logos shown for Jalview Java
250 Console and other window widgets in taskbar and dock rather
251 than anonymous 'Java' icons
253 </ul> <em>JalviewJS</em>
256 <!-- JAL-3624 -->PDB structures mapped to Uniprot Sequences
260 <!-- JAL-3208 -->setprop commandline argument reinstated for
264 <!-- JAL-3163 -->Missing message bundle keys are only
265 reported once per key (avoids excessive log output in js
269 <!-- JAL-3168 -->Feature type is included in the title of
270 the Feature Settings' Colour Chooser dialog
273 <!-- JAL-3279 -->Build details reported in About window
276 <!-- JAL-3038 JAL-3071 JAL-3263 JAL-3084 -->Numerous minor
277 GUI additions and improvements in sync with Java
280 </ul> <em>Development</em>
283 <!-- -->First integrated JalviewJS and Jalview release
286 <!-- JAL-3841,JAL-3248 -->Updated README and doc/building.md
289 <!-- JAL-3789, JAL-3679 -->Improved JalviewJS/Jalview build
290 process, added support for system package provided eclipse
293 <li>Install4j 9.0.x used for installer packaging</li>
295 <!-- JAL-3930 -->Improved use of installers for unattended
296 installation with a customizedId of "JALVIEW" in install4j's
300 <!-- JAL-3907 -->Improved compatibility of Jalview build
301 with Java 17 (next LTS target)
305 <td align="left" valign="top">
308 <!-- JAL-3674 -->Slow structure commands can block Jalview
312 <!-- JAL-3904 -->Structure window's viewer-specific menu
313 disappears when only one structure is shown (and many
314 sequences:one chain mappings are present)
317 <!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
318 the first SEQUENCE_GROUP defined
322 <!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 -->Selections not
323 propagated between Linked CDS - Protein alignments and their
324 trees (known defect from 2.11.1.3)
327 <!-- JAL-3761 -->Not all codon positions highlighted for
328 overlapping exon splice sites (e.g due to RNA slippage)
331 <!-- JAL-3794 -->X was not being recognised as the unknown
332 base in DNA sequences
335 <!-- JAL-3915 -->Removed RNAview checkbox and logic from
336 Structure Preferences
339 <!-- JAL-3583 -->Tooltip behaviour improved (slightly)
342 <!-- JAL-3162 -->Can edit a feature so that start > end
345 <!-- JAL-2848 -->Cancel from Amend Features doesn't reset a
346 modified graduated colour
349 <!-- JAL-3788 -->New View with automatic 'Show Overview'
350 preference enabled results in Null Pointer Exceptions when
351 clustal colouring is enabled
354 <!-- JAL-3275 -->Can open multiple Preferences panels
357 <!-- JAL-3633 -->Properly configure HTTPS proxy settings
361 <!-- JAL-3949 -->Standard out logging broken: messages only
362 routing to stderr and appear as a raw template
365 <!-- JAL-3739 -->Entering web service parameter values in
366 numerical field doesn't update the value of the parameter
367 until return is pressed.
370 <!-- JAL-3749 -->Resolved known issue (from 2.11.1.1)
371 concerning duplicate CDS sequences generated when protein
372 products for certain ENA records are repeatedly shown via
373 Calculate->Show Cross Refs
375 </ul> <em>JalviewJS</em>
378 <!-- JAL-3202 -->Consensus profile may include zero (rounded
379 down) percentage values causing a divide by zero
382 <!-- JAL-3762 -->JalviewJS doesn't honour arguments passed
383 via Info.args when there are arguments on the URL
386 <!-- JAL-3602 -->gradle closure-compiler not using UTF-8
389 <!-- JAL-3603 -->Annotation file fails to load from URL in
392 </ul> <em>Development</em>
396 <li>Fixed non-fatal gradle errors during build</li>
398 <!-- JAL-3745 -->Updated build.gradle for use with
404 </ul> <em>Known Issues</em>
407 <!-- JAL-3764 -->Display of RESNUM sequence features are not
408 suppressed when structures associated with a sequence are
409 viewed with an external viewer (Regression from 2.11.1
416 <td width="60" align="center" nowrap><strong><a
417 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.7">.7</a><br />
418 <em>18/01/2022</em></strong></td>
420 <td align="left" valign="top">
423 <!-- JAL-3703, JAL-3935 -->Files open in Jalview cannot be
424 updated by Jalview or other applications (Windows, other non
427 </ul> <em>Security</em>
430 <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
436 <td width="60" align="center" nowrap><strong><a
437 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
438 <em>6/01/2022</em></strong></td>
440 <td align="left" valign="top"><em>Security</em>
443 <!-- JAL-3934 -->Version bump library dependency: Log4j
450 <td width="60" align="center" nowrap><strong><a
451 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
452 <em>20/12/2021</em></strong></td>
454 <td align="left" valign="top"><em>Security</em>
457 <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
459 </ul> <em>Development</em>
461 <li>Updated building instructions</li>
466 <!-- JAL-3840 -->Occupancy calculation is incorrect for
467 alignment columns with over -1+2^32 gaps (breaking filtering
471 <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
472 scale factors being set with buggy window-managers (linux
475 </ul> <em>Development</em>
477 <li>Fixed non-fatal gradle errors during build</li>
482 <td width="60" align="center" nowrap><strong><a
483 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
484 <em>09/03/2021</em></strong></td>
485 <td align="left" valign="top"><em>Improved control of
486 Jalview's use of network services via jalview_properties</em>
489 <!-- JAL-3814 -->New .jalview_properties token controlling
490 launch of the news browser (like -nonews argument)
493 <!-- JAL-3813 -->New .jalview_properties token controlling
494 download of linkout URLs from
495 www.jalview.org/services/identifiers
498 <!-- JAL-3812 -->New .jalview_properties token controlling
499 download of BIOJSHTML templates
502 <!-- JAL-3811 -->New 'Discover Web Services' option to
503 trigger a one off JABAWS discovery if autodiscovery was
507 <td align="left" valign="top">
510 <!-- JAL-3818 -->Intermittent deadlock opening structure in
513 </ul> <em>New Known defects</em>
516 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
517 always restored from project (since 2.10.3)
520 <!-- JAL-3806 -->Selections from tree built from CDS aren't
521 propagated to Protein alignment (since 2.11.1.3)
527 <td width="60" align="center" nowrap><strong><a
528 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
529 <em>29/10/2020</em></strong></td>
530 <td align="left" valign="top">
535 <td align="left" valign="top">
538 <!-- JAL-3765 -->Find doesn't always highlight all matching
539 positions in a sequence (bug introduced in 2.11.1.2)
542 <!-- JAL-3760 -->Alignments containing one or more protein
543 sequences can be classed as nucleotide
546 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
547 sequences after alignment of protein products (known defect
548 first reported for 2.11.1.0)
551 <!-- JAL-3725 -->No tooltip or popup menu for genomic
552 features outwith CDS shown overlaid on protein
555 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
556 correctly mapped by Jalview (e.g. affects viral CDS with
557 ribosomal slippage, since 2.9.0)
560 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
564 <!-- JAL-3700 -->Selections in CDS sequence panel don't
565 always select corresponding protein sequences
568 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
569 column selection doesn't always ignore hidden columns
571 </ul> <em>Installer</em>
574 <!-- JAL-3611 -->Space character in Jalview install path on
575 Windows prevents install4j launching getdown
577 </ul> <em>Development</em>
580 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
581 version numbers in doc/building.md
587 <td width="60" align="center" nowrap><strong><a
588 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
589 <em>25/09/2020</em></strong></td>
590 <td align="left" valign="top">
594 <td align="left" valign="top">
597 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
598 "Encountered problems opening
599 https://www.jalview.org/examples/exampleFile_2_7.jvp"
605 <td width="60" align="center" nowrap><strong><a
606 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
607 <em>17/09/2020</em></strong></td>
608 <td align="left" valign="top">
611 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
612 residue in cursor mode
615 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
616 HTSJDK from 2.12 to 2.23
619 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
620 optimisations and improvements suggested by Bob Hanson and
621 improved compatibility with JalviewJS
624 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
625 alignments from Pfam and Rfam
628 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
629 import (no longer based on .gz extension)
632 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
635 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
636 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
640 <!-- JAL-3667 -->Improved warning messages, debug logging
641 and fixed Retry action when Jalview encounters errors when
642 saving or making backup files.
645 <!-- JAL-3676 -->Enhanced Jalview Java Console:
647 <li>Jalview's logging level can be configured</li>
648 <li>Copy to Clipboard Buttion</li>
652 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
653 when running on Linux (Requires Java 11+)
656 <!-- JAL-1842 JAL-3509 -->RESNUM sequence features (the
657 green ones) are not automatically displayed when associated
658 structures are displayed or for sequences retrieved from the
661 </ul> <em>Launching Jalview</em>
664 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
665 through a system property
668 <!-- JAL-3477 -->Improved built-in documentation and command
669 line help for configuring Jalview's memory
673 <td align="left" valign="top">
676 <!-- JAL-3691 -->Conservation and Quality tracks are shown
677 but not calculated and no protein or DNA score models are
678 available for tree/PCA calculation when launched with
679 Turkish language locale
682 <!-- JAL-3493 -->Escape does not clear highlights on the
683 alignment (Since Jalview 2.10.3)
686 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
687 doesn't slide selected sequences, just sequence under cursor
690 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
691 sequence under the cursor
694 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
695 multiple EMBL gene products shown for a single contig
698 <!-- JAL-3696 -->Errors encountered when processing variants
699 from VCF files yield "Error processing VCF: Format specifier
703 <!-- JAL-3697 -->Count of features not shown can be wrong
704 when there are both local and complementary features mapped
705 to the position under the cursor
708 <!-- JAL-3673 -->Sequence ID for reference sequence is
709 clipped when Right align Sequence IDs enabled
712 <!-- JAL-2983 -->Slider with negative range values not
713 rendered correctly in VAqua4 (Since 2.10.4)
716 <!-- JAL-3685 -->Single quotes not displayed correctly in
717 internationalised text for some messages and log output
720 <!-- JAL-3490 -->Find doesn't report matches that span
721 hidden gapped columns
724 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
725 panels, Alignment viewport and annotation renderer.
728 <!-- JAL-3561 -->Jalview ignores file format parameter
729 specifying output format when exporting an alignment via the
733 <!-- JAL-3667 -->Windows 10: For a minority of users, if
734 backups are not enabled, Jalview sometimes fails to
735 overwrite an existing file and raises a warning dialog. (in
736 2.11.0, and 2.11.1.0, the workaround is to try to save the
737 file again, and if that fails, delete the original file and
741 <!-- JAL-3509 -->Dragging a PDB file onto an alignment with
742 sequence features displayed causes displayed features to be
746 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
750 <!-- JAL-3741 -->References to http://www.jalview.org in
751 program and documentation
753 </ul> <em>Launching Jalview</em>
756 <!-- JAL-3718 -->Jalview application fails when launched the
757 first time for a version that has different jars to the
758 previous launched version.
760 </ul> <em>Developing Jalview</em>
763 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
764 data, causing cloverReport gradle task to fail with an
768 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
769 monitor the release channel
771 </ul> <em>New Known defects</em>
774 <!-- JAL-3748 -->CDS shown in result of submitting proteins
775 in a CDS/Protein alignment to a web service is wrong when
776 proteins share a common transcript sequence (e.g. genome of
780 <!-- JAL-3576 -->Co-located features exported and
781 re-imported are ordered differently when shown on alignment
782 and in tooltips. (Also affects v2.11.1.0)
785 <!-- JAL-3702 -->Drag and drop of alignment file onto
786 alignment window when in a HiDPI scaled mode in Linux only
787 works for the top left quadrant of the alignment window
790 <!-- JAL-3701 -->Stale build data in jalview standalone jar
791 builds (only affects 2.11.1.1 branch)
794 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
795 when alignment view restored from project (since Jalview
799 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
800 protein products for certain ENA records are repeatedly
801 shown via Calculate->Show Cross Refs
807 <td width="60" align="center" nowrap><strong><a
808 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
809 <em>22/04/2020</em></strong></td>
810 <td align="left" valign="top">
813 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
814 'virtual' codon features shown on protein (or vice versa)
815 for display in alignments, on structure views (including
816 transfer to UCSF chimera), in feature reports and for
820 <!-- JAL-3121 -->Feature attributes from VCF files can be
821 exported and re-imported as GFF3 files
824 <!-- JAL-3376 -->Capture VCF "fixed column" values
825 POS, ID, QUAL, FILTER as Feature Attributes
828 <!-- JAL-3375 -->More robust VCF numeric data field
829 validation while parsing
832 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
836 <!-- JAL-3535 -->Feature Settings dialog title includes name
840 <!-- JAL-3538 -->Font anti-aliasing in alignment views
844 <!-- JAL-3468 -->Very long feature descriptions truncated in
848 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
849 with no feature types visible
852 <!-- JAL-3574 -->Improved support for filtering feature
853 attributes with large integer values
856 <em>Jalview Installer</em>
859 <!-- JAL-3449 -->Versions for install4j and getdown and
860 installer template version reported in console (may be null
861 when Jalview launched as executable jar or via conda)
864 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and
865 higher quality background images
868 <!-- JAL-3394 -->New installer/application launcher
869 generated with install4j 8.0.4
872 <!-- JAL-3420 -->Jalview File Associations shown for Unix
876 <!-- JAL-3477 -->Improved defaults for maximum memory
877 setting when running on large memory machines
879 </ul> <em>Release processes</em>
882 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
885 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier
886 access to test-release channel builds
888 </ul> <em>Build System</em>
891 <!-- JAL-3510 -->Clover updated to 4.4.1
894 <!-- JAL-3513 -->Test code included in Clover coverage
897 </ul> <em>Groovy Scripts</em>
900 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
901 to stdout containing the consensus sequence for each
902 alignment in a Jalview session
905 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
906 genomic sequence_variant annotation from CDS as
907 missense_variant or synonymous_variant on protein products.
911 <td align="left" valign="top">
914 <!-- JAL-3581 -->Hidden sequence markers still visible when
915 'Show hidden markers' option is not ticked
918 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
919 PNG output when 'Automatically set ID width' is set in
920 jalview preferences or properties file
923 <!-- JAL-3571 -->Feature Editor dialog can be opened when
924 'Show Sequence Features' option is not ticked
927 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
928 buttons in Feature Settings dialog are clicked when no
932 <!-- JAL-3412 -->ID margins for CDS and Protein views not
933 equal when split frame is first opened
936 <!-- JAL-3296 -->Sequence position numbers in status bar not
937 correct after editing a sequence's start position
940 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
941 with annotation and exceptions thrown when only a few
942 columns shown in wrapped mode
945 <!-- JAL-3386 -->Sequence IDs missing in headless export of
946 wrapped alignment figure with annotations
949 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
950 ID fails with ClassCastException
953 <!-- JAL-3389 -->Chimera session not restored from Jalview
957 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
958 feature settings dialog also selects columns
961 <!-- JAL-3473 -->SpinnerNumberModel causes
962 IllegalArgumentException in some circumstances
965 <!-- JAL-3534 -->Multiple feature settings dialogs can be
969 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
970 alignment window is closed
973 <!-- JAL-3406 -->Credits missing some authors in Jalview
974 help documentation for 2.11.0 release
977 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
978 includes Pfam ID as sequence's accession rather than its
981 </ul> <em>Java 11 Compatibility issues</em>
984 <!-- JAL-2987 -->OSX - Can't view some search results in
985 PDB/Uniprot search panel
987 </ul> <em>Installer</em>
990 <!-- JAL-3447 -->Jalview should not create file associations
991 for 3D structure files (.pdb, .mmcif. .cif)
993 </ul> <em>Repository and Source Release</em>
996 <!-- JAL-3474 -->removed obsolete .cvsignore files from
1000 <!-- JAL-3541 -->Clover report generation running out of
1003 </ul> <em>New Known Issues</em>
1006 <!-- JAL-3523 -->OSX - Current working directory not
1007 preserved when Jalview.app launched with parameters from
1011 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
1012 clipped in headless figure export when Right Align option
1016 <!-- JAL-3542 -->Jalview Installation type always reports
1017 'Source' in console output
1020 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail
1021 on jalview's bamboo server but run fine locally.
1027 <td width="60" align="center" nowrap><strong><a
1028 name="Jalview.2.11.0">2.11.0</a><br /> <em>04/07/2019</em></strong></td>
1029 <td align="left" valign="top">
1032 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native
1033 Application and Installers built with <a
1034 href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a>
1035 (licensed to the Jalview open source project) rather than
1039 <!-- JAL-1929 -->Jalview Launcher System to auto-configure
1040 memory settings, receive over the air updates and launch
1041 specific versions via (<a
1042 href="https://github.com/threerings/getdown">Three
1046 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations
1047 for formats supported by Jalview (including .jvp project
1051 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command
1052 line arguments and switch between different getdown channels
1055 <!-- JAL-3141 -->Backup files created when saving Jalview
1056 project or alignment files
1060 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF
1064 <!-- JAL-2753 -->Version of HTSJDK shipped with Jalview
1065 updated to version 2.12.0
1068 <!-- JAL-2620 -->Alternative genetic code tables for
1072 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0
1074 <li><strong>Enhanced visualisation and analysis
1075 of Sequence Features</strong>
1078 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
1079 implementation that allows updates) used for Sequence
1083 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
1084 features can be filtered and shaded according to any
1085 associated attributes (e.g. variant attributes from VCF
1086 file, or key-value pairs imported from column 9 of GFF
1090 <!-- JAL-2879 -->Feature Attributes and shading schemes
1091 stored and restored from Jalview Projects
1094 <!-- JAL-3334 -->Use full Sequence Ontology (via
1095 BioJava) to recognise variant features
1098 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants
1099 on peptide sequences (also coloured red by default)
1102 <!-- JAL-2792 -->Popup window to show full report for a
1103 selected sequence feature's details
1106 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient
1107 sequence feature render algorithm (Z-sort/transparency
1111 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature
1116 <!-- JAL-3205 -->Symmetric score matrices for faster tree
1117 and PCA calculations
1119 <li><strong>Principal Components Analysis Viewer</strong>
1122 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis
1123 results and Viewer state saved in Jalview Project
1126 <!-- JAL-2962 -->'Change parameters' option removed from
1127 viewer's drop-down menus
1130 <!-- JAL-2975 -->Can use shift + arrow keys to rotate
1131 PCA image incrementally
1134 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
1138 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
1140 <li><strong>Speed and Efficiency</strong>
1143 <!-- JAL-2185,JAL-3198 -->More efficient creation of
1144 selections and multiple groups when working with large
1148 <!-- JAL-3200 -->Speedier import of annotation rows when
1149 parsing Stockholm files
1152 <li><strong>User Interface</strong>
1155 <!-- JAL-2933 -->Finder panel remembers last position in
1159 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS
1160 (What you see is what is shown)<br />Only visible
1161 regions of alignment are shown by default (can be
1162 changed in user preferences)
1165 <!-- JAL-3169 -->File Chooser stays open after
1166 responding Cancel to the Overwrite Dialog
1169 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour
1170 when all sequences are hidden
1173 <!-- JAL-1244 -->Status bar shows bounds when dragging a
1174 selection region, and gap count when inserting or
1178 <!-- JAL-3132 -->Status bar updates over sequence and
1182 <!-- JAL-3093 -->Annotation tooltips and popup menus are
1183 shown when in wrapped mode
1186 <!-- JAL-3073 -->Can select columns by dragging
1187 left/right in a graph or histogram annotation
1190 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB
1194 <!-- JAL-2621 -->Cursor changes over draggable box in
1198 <!-- JAL-3181 -->Consistent ordering of links in
1199 sequence id popup menu
1202 <!-- JAL-3080 -->Red line indicating tree-cut position
1203 not shown if no subgroups are created
1206 <!-- JAL-3042 -->Removed ability to configure length of
1207 search history by right-clicking search box
1213 <!-- JAL-3232 -->Jalview Groovy Scripting Console updated to
1216 <li><strong>Java 11 Support (not yet on general
1220 <!-- -->OSX GUI integrations for App menu's 'About'
1221 entry and trapping CMD-Q
1224 </ul> <em>Deprecations</em>
1227 <!-- JAL-3035 -->DAS sequence retrieval and annotation
1228 capabilities removed from the Jalview Desktop
1231 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling
1232 and unmarshalling has been replaced by JAXB for Jalview
1233 projects and XML based data retrieval clients
1236 <!-- JAL-3311 -->Disable VAMSAS menu in preparation for
1240 <!-- -->Jalview Desktop no longer distributed via Java Web
1243 </ul> <em>Documentation</em>
1246 <!-- JAL-3003 -->Added remarks about transparent rendering
1247 effects not supported in EPS figure export
1250 <!-- JAL-2903 -->Typos in documentation for Preferences
1253 </ul> <em>Development and Release Processes</em>
1256 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated
1260 <!-- JAL-1424 -->Enhanced checks for missing and duplicated
1261 keys in Message bundles
1264 <!-- JAL-3225 -->Eclipse project configuration managed with
1268 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian Bamboo
1269 continuous integration for unattended Test Suite execution
1272 <!-- JAL-2864 -->Memory test suite to detect leaks in common
1276 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
1280 <!-- JAL-3248 -->Developer documentation migrated to
1281 markdown (with HTML rendering)
1284 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
1287 <!-- JAL-3289 -->New URLs for publishing development
1292 <td align="left" valign="top">
1295 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
1298 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
1299 superposition in Jmol fail on Windows
1302 <!-- JAL-3286 -->Blank error dialog is displayed when
1303 discovering structures for sequences with lots of PDB
1307 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export
1308 with monospaced font
1311 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
1312 Jalview project involving multiple views
1315 <!-- JAL-3164 -->Overview for complementary view in a linked
1316 CDS/Protein alignment is not updated when Hide Columns by
1317 Annotation dialog hides columns
1320 <!-- JAL-3158 -->Selection highlighting in the complement of
1321 a CDS/Protein alignment stops working after making a
1322 selection in one view, then making another selection in the
1326 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
1330 <!-- JAL-3154 -->Table Columns could be re-ordered in
1331 Feature Settings and Jalview Preferences panels
1334 <!-- JAL-2865 -->Jalview hangs when closing windows, or
1335 redrawing the overview with large alignments
1338 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
1339 region if columns were selected by dragging right-to-left
1340 and the mouse moved to the left of the first column
1343 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to
1344 a hidden column marker via scale popup menu
1347 <!-- JAL-2846 -->Error message for trying to load in invalid
1348 URLs doesn't tell users the invalid URL
1351 <!-- JAL-2816 -->Tooltips displayed for features filtered by
1355 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl
1356 during show cross references or Fetch Database References
1357 are shown in red in original view
1360 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown
1361 correctly on peptide sequence (computed variant shown as
1365 <!-- JAL-2060 -->'Graduated colour' option not offered for
1366 manually created features (where feature score is Float.NaN)
1369 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or
1370 printed when columns are hidden
1373 <!-- JAL-3082 -->Regular expression error for '(' in Select
1374 Columns by Annotation description
1377 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after
1378 dragging out of Scale or Annotation Panel
1381 <!-- JAL-3075 -->Column selection incorrect after scrolling
1385 <!-- JAL-3074 -->Left/right drag in annotation can scroll
1389 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal
1393 <!-- JAL-3002 -->Column display is out by one after Page
1394 Down, Page Up in wrapped mode
1397 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
1400 <!-- JAL-2932 -->Finder searches in minimised alignments
1403 <!-- JAL-2250 -->'Apply Colour to All Groups' not always
1404 selected on opening an alignment
1407 <!-- JAL-3180 -->'Colour by Annotation' not marked selected
1411 <!-- JAL-3201 -->Per-group Clustal colour scheme changes
1412 when different groups in the alignment are selected
1415 <!-- JAL-2717 -->Internationalised colour scheme names not
1416 shown correctly in menu
1419 <!-- JAL-3206 -->Colour by Annotation can go black at
1420 min/max threshold limit
1423 <!-- JAL-3125 -->Value input for graduated feature colour
1424 threshold gets 'unrounded'
1427 <!-- JAL-2982 -->PCA image export doesn't respect background
1431 <!-- JAL-2963 -->PCA points don't dim when rotated about y
1435 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
1438 <!-- JAL-3078 -->Cancel in Tree Font dialog resets
1439 alignment, not Tree font
1442 <!-- JAL-2964 -->Associate Tree with All Views not restored
1446 <!-- JAL-2915 -->Scrolling of split frame is sluggish if
1447 Overview shown in complementary view
1450 <!-- JAL-3313 -->Codon consensus incorrectly scaled when
1451 shown without normalisation
1454 <!-- JAL-3021 -->Sequence Details report should open
1455 positioned at top of report
1458 <!-- JAL-914 -->Help page can be opened twice
1461 <!-- JAL-3333 -->Fuzzy text in web service status menu on
1464 </ul> <em>Editing</em>
1467 <!-- JAL-2822 -->Start and End should be updated when
1468 sequence data at beginning or end of alignment added/removed
1472 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection
1473 doesn't relocate sequence features correctly when start of
1474 sequence is removed (Known defect since 2.10)
1477 <!-- JAL-2830 -->Inserting gap sequence via the Edit
1478 Sequence dialog corrupts dataset sequence
1481 <!-- JAL-868 -->Structure colours not updated when
1482 associated tree repartitions the alignment view (Regression
1485 </ul> <em>Datamodel</em>
1488 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
1489 sequence's End is greater than its length
1491 </ul> <em>Bugs fixed for Java 11 Support (not yet on general
1495 <!-- JAL-3288 -->Menus work properly in split-screen
1497 </ul> <em>New Known Defects</em>
1500 <!-- JAL-3340 -->Select columns containing feature by double
1501 clicking ignores bounds of an existing selected region
1504 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in
1505 gapped regions of protein alignment.
1508 <!-- JAL-2647 -->Input Data menu entry is greyed out when
1509 PCA View is restored from a Jalview 2.11 project
1512 <!-- JAL-3213 -->Alignment panel height can be too small
1516 <!-- JAL-3240 -->Display is incorrect after removing gapped
1517 columns within hidden columns
1520 <!-- JAL-3314 -->Rightmost selection is lost when mouse
1521 re-enters window after dragging left to select columns to
1522 left of visible region
1525 <!-- JAL-2876 -->Features coloured according to their
1526 description string and thresholded by score in earlier
1527 versions of Jalview are not shown as thresholded features in
1528 2.11. To workaround please create a Score filter instead.
1531 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't
1532 reset group visibility
1535 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in
1536 linked CDS/Protein view
1539 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1540 alignments with multiple views can close views unexpectedly
1542 </ul> <em>Java 11 Specific defects</em>
1545 <!-- JAL-3235 -->Jalview Properties file is not sorted
1546 alphabetically when saved
1552 <td width="60" nowrap>
1553 <div align="center">
1554 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1557 <td><div align="left">
1561 <!-- JAL-3101 -->Default memory for Jalview webstart and
1562 InstallAnywhere increased to 1G.
1565 <!-- JAL-247 -->Hidden sequence markers and representative
1566 sequence bolding included when exporting alignment as EPS,
1567 SVG, PNG or HTML. <em>Display is configured via the
1568 Format menu, or for command-line use via a Jalview
1569 properties file.</em>
1572 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1573 API and sequence data now imported as JSON.
1576 <!-- JAL-3065 -->Change in recommended way of starting
1577 Jalview via a Java command line: add jars in lib directory
1578 to CLASSPATH, rather than via the deprecated java.ext.dirs
1582 <em>Development</em>
1585 <!-- JAL-3047 -->Support added to execute test suite
1586 instrumented with <a href="http://openclover.org/">Open
1591 <td><div align="left">
1595 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1596 row shown in Feredoxin Structure alignment view of example
1600 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1601 annotation displayed.
1604 <!-- JAL-3107 -->Group conservation/consensus not shown
1605 for newly created group when 'Apply to all groups'
1609 <!-- JAL-3087 -->Corrupted display when switching to
1610 wrapped mode when sequence panel's vertical scrollbar is
1614 <!-- JAL-3003 -->Alignment is black in exported EPS file
1615 when sequences are selected in exported view.</em>
1618 <!-- JAL-3059 -->Groups with different coloured borders
1619 aren't rendered with correct colour.
1622 <!-- JAL-3092 -->Jalview could hang when importing certain
1623 types of knotted RNA secondary structure.
1626 <!-- JAL-3095 -->Sequence highlight and selection in
1627 trimmed VARNA 2D structure is incorrect for sequences that
1631 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1632 annotation when columns are inserted into an alignment,
1633 and when exporting as Stockholm flatfile.
1636 <!-- JAL-3053 -->Jalview annotation rows containing upper
1637 and lower-case 'E' and 'H' do not automatically get
1638 treated as RNA secondary structure.
1641 <!-- JAL-3106 -->.jvp should be used as default extension
1642 (not .jar) when saving a Jalview project file.
1645 <!-- JAL-3105 -->Mac Users: closing a window correctly
1646 transfers focus to previous window on OSX
1649 <em>Java 10 Issues Resolved</em>
1652 <!-- JAL-2988 -->OSX - Can't save new files via the File
1653 or export menus by typing in a name into the Save dialog
1657 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1658 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1659 'look and feel' which has improved compatibility with the
1660 latest version of OSX.
1666 <td width="60" nowrap>
1667 <div align="center">
1668 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1669 <em>7/06/2018</em></strong>
1672 <td><div align="left">
1676 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1677 annotation retrieved from Uniprot
1680 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1681 onto the Jalview Desktop
1685 <td><div align="left">
1689 <!-- JAL-3017 -->Cannot import features with multiple
1690 variant elements (blocks import of some Uniprot records)
1693 <!-- JAL-2997 -->Clustal files with sequence positions in
1694 right-hand column parsed correctly
1697 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1698 not alignment area in exported graphic
1701 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1702 window has input focus
1705 <!-- JAL-2992 -->Annotation panel set too high when
1706 annotation added to view (Windows)
1709 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1710 network connectivity is poor
1713 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1714 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1715 the currently open URL and links from a page viewed in
1716 Firefox or Chrome on Windows is now fully supported. If
1717 you are using Edge, only links in the page can be
1718 dragged, and with Internet Explorer, only the currently
1719 open URL in the browser can be dropped onto Jalview.</em>
1722 <em>New Known Defects</em>
1725 <!-- JAL-3083 -->Cancel option doesn't reset Colour by
1732 <td width="60" nowrap>
1733 <div align="center">
1734 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1737 <td><div align="left">
1741 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1742 for disabling automatic superposition of multiple
1743 structures and open structures in existing views
1746 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1747 ID and annotation area margins can be click-dragged to
1751 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1755 <!-- JAL-2759 -->Improved performance for large alignments
1756 and lots of hidden columns
1759 <!-- JAL-2593 -->Improved performance when rendering lots
1760 of features (particularly when transparency is disabled)
1763 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2
1764 for exchange of Jalview features and Chimera attributes
1765 made generally available
1769 <td><div align="left">
1772 <!-- JAL-2899 -->Structure and Overview aren't updated
1773 when Colour By Annotation threshold slider is adjusted
1776 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1777 overlapping alignment panel
1780 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1784 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1785 improved: CDS not handled correctly if transcript has no
1789 <!-- JAL-2321 -->Secondary structure and temperature
1790 factor annotation not added to sequence when local PDB
1791 file associated with it by drag'n'drop or structure
1795 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1796 dialog doesn't import PDB files dropped on an alignment
1799 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1800 scroll bar doesn't work for some CDS/Protein views
1803 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1804 Java 1.8u153 onwards and Java 1.9u4+.
1807 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1808 columns in annotation row
1811 <!-- JAL-2913 -->Preferences panel's ID Width control is
1812 not honored in batch mode
1815 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1816 for structures added to existing Jmol view
1819 <!-- JAL-2223 -->'View Mappings' includes duplicate
1820 entries after importing project with multiple views
1823 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1824 protein sequences via SIFTS from associated PDB entries
1825 with negative residue numbers or missing residues fails
1828 <!-- JAL-2952 -->Exception when shading sequence with
1829 negative Temperature Factor values from annotated PDB
1830 files (e.g. as generated by CONSURF)
1833 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1834 tooltip doesn't include a text description of mutation
1837 <!-- JAL-2922 -->Invert displayed features very slow when
1838 structure and/or overview windows are also shown
1841 <!-- JAL-2954 -->Selecting columns from highlighted
1842 regions very slow for alignments with large numbers of
1846 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1847 with 'StringIndexOutOfBounds'
1850 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and
1851 Feel for OSX platforms running Java 10
1854 <!-- JAL-2960 -->Adding a structure to existing structure
1855 view appears to do nothing because the view is hidden
1856 behind the alignment view
1862 <!-- JAL-2926 -->Copy consensus sequence option in applet
1863 should copy the group consensus when popup is opened on it
1869 <!-- JAL-2913 -->Fixed ID width preference is not
1873 <em>New Known Defects</em>
1876 <!-- JAL-2973 --> Exceptions occasionally raised when
1877 editing a large alignment and overview is displayed
1880 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1881 repeatedly after a series of edits even when the overview
1882 is no longer reflecting updates
1885 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1886 structures for protein subsequence (if 'Trim Retrieved
1887 Sequences' enabled) or Ensembl isoforms (Workaround in
1888 2.10.4 is to fail back to N&W mapping)
1891 <!-- JAL-2990 -->Export Annotations from File Menu with
1892 CSV option gives blank output
1898 <td width="60" nowrap>
1899 <div align="center">
1900 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br />
1901 <em>24/1/2018</em></strong>
1904 <td><div align="left">
1906 <li>Updated Certum Codesigning Certificate (Valid till
1907 30th November 2018)</li>
1910 <td><div align="left">
1915 <!-- JAL-2859-->Only one structure is loaded when
1916 several sequences and structures are selected for
1920 <!-- JAL-2851-->Alignment doesn't appear to scroll
1921 vertically via trackpad and scrollwheel
1924 <!-- JAL-2842-->Jalview hangs if up/down arrows pressed
1925 in cursor mode when cursor lies in hidden region at
1929 <!-- JAL-2827-->Helix annotation has 'notches' when
1930 scrolled into view if columns are hidden
1933 <!-- JAL-2740-->Annotation column filter can be slow to
1934 reset (ie after hitting cancel) for large numbers of
1938 <!-- JAL-2849-->User preference for disabling inclusion
1939 of sequence limits when exporting as flat file has no
1943 <!-- JAL-2679-->Reproducible cross-reference
1944 relationships when retrieving sequences from
1951 <td width="60" nowrap>
1952 <div align="center">
1953 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1956 <td><div align="left">
1960 <!-- JAL-2446 -->Faster and more efficient management and
1961 rendering of sequence features
1964 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1965 429 rate limit request hander
1968 <!-- JAL-2773 -->Structure views don't get updated unless
1969 their colours have changed
1972 <!-- JAL-2495 -->All linked sequences are highlighted for
1973 a structure mousover (Jmol) or selection (Chimera)
1976 <!-- JAL-2790 -->'Cancel' button in progress bar for
1977 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1980 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1981 view from Ensembl locus cross-references
1984 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1988 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1989 feature can be disabled
1992 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1993 PDB easier retrieval of sequences for lists of IDs
1996 <!-- JAL-2758 -->Short names for sequences retrieved from
2002 <li>Groovy interpreter updated to 2.4.12</li>
2003 <li>Example groovy script for generating a matrix of
2004 percent identity scores for current alignment.</li>
2006 <em>Testing and Deployment</em>
2009 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
2013 <td><div align="left">
2017 <!-- JAL-2643 -->Pressing tab after updating the colour
2018 threshold text field doesn't trigger an update to the
2022 <!-- JAL-2682 -->Race condition when parsing sequence ID
2026 <!-- JAL-2608 -->Overview windows are also closed when
2027 alignment window is closed
2030 <!-- JAL-2548 -->Export of features doesn't always respect
2034 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
2035 takes a long time in Cursor mode
2041 <!-- JAL-2777 -->Structures with whitespace chainCode
2042 cannot be viewed in Chimera
2045 <!-- JAL-2728 -->Protein annotation panel too high in
2049 <!-- JAL-2757 -->Can't edit the query after the server
2050 error warning icon is shown in Uniprot and PDB Free Text
2054 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
2057 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
2060 <!-- JAL-2739 -->Hidden column marker in last column not
2061 rendered when switching back from Wrapped to normal view
2064 <!-- JAL-2768 -->Annotation display corrupted when
2065 scrolling right in unwapped alignment view
2068 <!-- JAL-2542 -->Existing features on subsequence
2069 incorrectly relocated when full sequence retrieved from
2073 <!-- JAL-2733 -->Last reported memory still shown when
2074 Desktop->Show Memory is unticked (OSX only)
2077 <!-- JAL-2658 -->Amend Features dialog doesn't allow
2078 features of same type and group to be selected for
2082 <!-- JAL-2524 -->Jalview becomes sluggish in wide
2083 alignments when hidden columns are present
2086 <!-- JAL-2392 -->Jalview freezes when loading and
2087 displaying several structures
2090 <!-- JAL-2732 -->Black outlines left after resizing or
2094 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
2095 within the Jalview desktop on OSX
2098 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
2099 when in wrapped alignment mode
2102 <!-- JAL-2636 -->Scale mark not shown when close to right
2103 hand end of alignment
2106 <!-- JAL-2684 -->Pairwise alignment of selected regions of
2107 each selected sequence do not have correct start/end
2111 <!-- JAL-2793 -->Alignment ruler height set incorrectly
2112 after canceling the Alignment Window's Font dialog
2115 <!-- JAL-2036 -->Show cross-references not enabled after
2116 restoring project until a new view is created
2119 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
2120 URL links appears when only default EMBL-EBI link is
2121 configured (since 2.10.2b2)
2124 <!-- JAL-2775 -->Overview redraws whole window when box
2125 position is adjusted
2128 <!-- JAL-2225 -->Structure viewer doesn't map all chains
2129 in a multi-chain structure when viewing alignment
2130 involving more than one chain (since 2.10)
2133 <!-- JAL-2811 -->Double residue highlights in cursor mode
2134 if new selection moves alignment window
2137 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
2138 arrow key in cursor mode to pass hidden column marker
2141 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
2142 that produces correctly annotated transcripts and products
2145 <!-- JAL-2776 -->Toggling a feature group after first time
2146 doesn't update associated structure view
2149 <em>Applet</em><br />
2152 <!-- JAL-2687 -->Concurrent modification exception when
2153 closing alignment panel
2156 <em>BioJSON</em><br />
2159 <!-- JAL-2546 -->BioJSON export does not preserve
2160 non-positional features
2163 <em>New Known Issues</em>
2166 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
2167 sequence features correctly (for many previous versions of
2171 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
2172 using cursor in wrapped panel other than top
2175 <!-- JAL-2791 -->Select columns containing feature ignores
2176 graduated colour threshold
2179 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
2180 always preserve numbering and sequence features
2183 <em>Known Java 9 Issues</em>
2186 <!-- JAL-2902 -->Groovy Console very slow to open and is
2187 not responsive when entering characters (Webstart, Java
2194 <td width="60" nowrap>
2195 <div align="center">
2196 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
2197 <em>2/10/2017</em></strong>
2200 <td><div align="left">
2201 <em>New features in Jalview Desktop</em>
2204 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API
2208 <!-- JAL-2745 -->HTTPS used for all connections to
2213 <td><div align="left"></div></td>
2216 <td width="60" nowrap>
2217 <div align="center">
2218 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
2219 <em>7/9/2017</em></strong>
2222 <td><div align="left">
2226 <!-- JAL-2588 -->Show gaps in overview window by colouring
2227 in grey (sequences used to be coloured grey, and gaps were
2231 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
2235 <!-- JAL-2587 -->Overview updates immediately on increase
2236 in size and progress bar shown as higher resolution
2237 overview is recalculated
2242 <td><div align="left">
2246 <!-- JAL-2664 -->Overview window redraws every hidden
2247 column region row by row
2250 <!-- JAL-2681 -->duplicate protein sequences shown after
2251 retrieving Ensembl crossrefs for sequences from Uniprot
2254 <!-- JAL-2603 -->Overview window throws NPE if show boxes
2255 format setting is unticked
2258 <!-- JAL-2610 -->Groups are coloured wrongly in overview
2259 if group has show boxes format setting unticked
2262 <!-- JAL-2672,JAL-2665 -->Redraw problems when
2263 autoscrolling whilst dragging current selection group to
2264 include sequences and columns not currently displayed
2267 <!-- JAL-2691 -->Not all chains are mapped when multimeric
2268 assemblies are imported via CIF file
2271 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
2272 displayed when threshold or conservation colouring is also
2276 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
2280 <!-- JAL-2673 -->Jalview continues to scroll after
2281 dragging a selected region off the visible region of the
2285 <!-- JAL-2724 -->Cannot apply annotation based
2286 colourscheme to all groups in a view
2289 <!-- JAL-2511 -->IDs don't line up with sequences
2290 initially after font size change using the Font chooser or
2297 <td width="60" nowrap>
2298 <div align="center">
2299 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
2302 <td><div align="left">
2303 <em>Calculations</em>
2307 <!-- JAL-1933 -->Occupancy annotation row shows number of
2308 ungapped positions in each column of the alignment.
2311 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
2312 a calculation dialog box
2315 <!-- JAL-2379 -->Revised implementation of PCA for speed
2316 and memory efficiency (~30x faster)
2319 <!-- JAL-2403 -->Revised implementation of sequence
2320 similarity scores as used by Tree, PCA, Shading Consensus
2321 and other calculations
2324 <!-- JAL-2416 -->Score matrices are stored as resource
2325 files within the Jalview codebase
2328 <!-- JAL-2500 -->Trees computed on Sequence Feature
2329 Similarity may have different topology due to increased
2336 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
2337 model for alignments and groups
2340 <!-- JAL-384 -->Custom shading schemes created via groovy
2347 <!-- JAL-2526 -->Efficiency improvements for interacting
2348 with alignment and overview windows
2351 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
2355 <!-- JAL-2388 -->Hidden columns and sequences can be
2359 <!-- JAL-2611 -->Click-drag in visible area allows fine
2360 adjustment of visible position
2364 <em>Data import/export</em>
2367 <!-- JAL-2535 -->Posterior probability annotation from
2368 Stockholm files imported as sequence associated annotation
2371 <!-- JAL-2507 -->More robust per-sequence positional
2372 annotation input/output via stockholm flatfile
2375 <!-- JAL-2533 -->Sequence names don't include file
2376 extension when importing structure files without embedded
2377 names or PDB accessions
2380 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
2381 format sequence substitution matrices
2384 <em>User Interface</em>
2387 <!-- JAL-2447 --> Experimental Features Checkbox in
2388 Desktop's Tools menu to hide or show untested features in
2392 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
2393 via Overview or sequence motif search operations
2396 <!-- JAL-2547 -->Amend sequence features dialog box can be
2397 opened by double clicking gaps within sequence feature
2401 <!-- JAL-1476 -->Status bar message shown when not enough
2402 aligned positions were available to create a 3D structure
2406 <em>3D Structure</em>
2409 <!-- JAL-2430 -->Hidden regions in alignment views are not
2410 coloured in linked structure views
2413 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
2414 file-based command exchange
2417 <!-- JAL-2375 -->Structure chooser automatically shows
2418 Cached Structures rather than querying the PDBe if
2419 structures are already available for sequences
2422 <!-- JAL-2520 -->Structures imported via URL are cached in
2423 the Jalview project rather than downloaded again when the
2424 project is reopened.
2427 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
2428 to transfer Chimera's structure attributes as Jalview
2429 features, and vice-versa (<strong>Experimental
2433 <em>Web Services</em>
2436 <!-- JAL-2549 -->Updated JABAWS client to v2.2
2439 <!-- JAL-2335 -->Filter non-standard amino acids and
2440 nucleotides when submitting to AACon and other MSA
2444 <!-- JAL-2316, -->URLs for viewing database
2445 cross-references provided by identifiers.org and the
2446 EMBL-EBI's MIRIAM DB
2453 <!-- JAL-2344 -->FileFormatI interface for describing and
2454 identifying file formats (instead of String constants)
2457 <!-- JAL-2228 -->FeatureCounter script refactored for
2458 efficiency when counting all displayed features (not
2459 backwards compatible with 2.10.1)
2462 <em>Example files</em>
2465 <!-- JAL-2631 -->Graduated feature colour style example
2466 included in the example feature file
2469 <em>Documentation</em>
2472 <!-- JAL-2339 -->Release notes reformatted for readability
2473 with the built-in Java help viewer
2476 <!-- JAL-1644 -->Find documentation updated with 'search
2477 sequence description' option
2483 <!-- JAL-2485, -->External service integration tests for
2484 Uniprot REST Free Text Search Client
2487 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
2490 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
2495 <td><div align="left">
2496 <em>Calculations</em>
2499 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
2500 matrix - C->R should be '-3'<br />Old matrix restored
2501 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
2503 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
2504 Jalview's treatment of gaps in PCA and substitution matrix
2505 based Tree calculations.<br /> <br />In earlier versions
2506 of Jalview, gaps matching gaps were penalised, and gaps
2507 matching non-gaps penalised even more. In the PCA
2508 calculation, gaps were actually treated as non-gaps - so
2509 different costs were applied, which meant Jalview's PCAs
2510 were different to those produced by SeqSpace.<br />Jalview
2511 now treats gaps in the same way as SeqSpace (ie it scores
2512 them as 0). <br /> <br />Enter the following in the
2513 Groovy console to restore pre-2.10.2 behaviour:<br />
2514 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
2515 // for 2.10.1 mode <br />
2516 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
2517 // to restore 2.10.2 mode <br /> <br /> <em>Note:
2518 these settings will affect all subsequent tree and PCA
2519 calculations (not recommended)</em></li>
2521 <!-- JAL-2424 -->Fixed off-by-one bug that affected
2522 scaling of branch lengths for trees computed using
2523 Sequence Feature Similarity.
2526 <!-- JAL-2377 -->PCA calculation could hang when
2527 generating output report when working with highly
2528 redundant alignments
2531 <!-- JAL-2544 --> Sort by features includes features to
2532 right of selected region when gaps present on right-hand
2536 <em>User Interface</em>
2539 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2540 doesn't reselect a specific sequence's associated
2541 annotation after it was used for colouring a view
2544 <!-- JAL-2419 -->Current selection lost if popup menu
2545 opened on a region of alignment without groups
2548 <!-- JAL-2374 -->Popup menu not always shown for regions
2549 of an alignment with overlapping groups
2552 <!-- JAL-2310 -->Finder double counts if both a sequence's
2553 name and description match
2556 <!-- JAL-2370 -->Hiding column selection containing two
2557 hidden regions results in incorrect hidden regions
2560 <!-- JAL-2386 -->'Apply to all groups' setting when
2561 changing colour does not apply Conservation slider value
2565 <!-- JAL-2373 -->Percentage identity and conservation menu
2566 items do not show a tick or allow shading to be disabled
2569 <!-- JAL-2385 -->Conservation shading or PID threshold
2570 lost when base colourscheme changed if slider not visible
2573 <!-- JAL-2547 -->Sequence features shown in tooltip for
2574 gaps before start of features
2577 <!-- JAL-2623 -->Graduated feature colour threshold not
2578 restored to UI when feature colour is edited
2581 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2582 a time when scrolling vertically in wrapped mode.
2585 <!-- JAL-2630 -->Structure and alignment overview update
2586 as graduate feature colour settings are modified via the
2590 <!-- JAL-2034 -->Overview window doesn't always update
2591 when a group defined on the alignment is resized
2594 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2595 wrapped view result in positional status updates
2599 <!-- JAL-2563 -->Status bar doesn't show position for
2600 ambiguous amino acid and nucleotide symbols
2603 <!-- JAL-2602 -->Copy consensus sequence failed if
2604 alignment included gapped columns
2607 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2608 widgets don't permanently disappear
2611 <!-- JAL-2503 -->Cannot select or filter quantitative
2612 annotation that are shown only as column labels (e.g.
2613 T-Coffee column reliability scores)
2616 <!-- JAL-2594 -->Exception thrown if trying to create a
2617 sequence feature on gaps only
2620 <!-- JAL-2504 -->Features created with 'New feature'
2621 button from a Find inherit previously defined feature type
2622 rather than the Find query string
2625 <!-- JAL-2423 -->incorrect title in output window when
2626 exporting tree calculated in Jalview
2629 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2630 and then revealing them reorders sequences on the
2634 <!-- JAL-964 -->Group panel in sequence feature settings
2635 doesn't update to reflect available set of groups after
2636 interactively adding or modifying features
2639 <!-- JAL-2225 -->Sequence Database chooser unusable on
2643 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2644 only excluded gaps in current sequence and ignored
2651 <!-- JAL-2421 -->Overview window visible region moves
2652 erratically when hidden rows or columns are present
2655 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2656 Structure Viewer's colour menu don't correspond to
2660 <!-- JAL-2405 -->Protein specific colours only offered in
2661 colour and group colour menu for protein alignments
2664 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2665 reflect currently selected view or group's shading
2669 <!-- JAL-2624 -->Feature colour thresholds not respected
2670 when rendered on overview and structures when opacity at
2674 <!-- JAL-2589 -->User defined gap colour not shown in
2675 overview when features overlaid on alignment
2678 <!-- JAL-2567 -->Feature settings for different views not
2679 recovered correctly from Jalview project file
2682 <!-- JAL-2256 -->Feature colours in overview when first
2683 opened (automatically via preferences) are different to
2684 the main alignment panel
2687 <em>Data import/export</em>
2690 <!-- JAL-2576 -->Very large alignments take a long time to
2694 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2695 added after a sequence was imported are not written to
2699 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2700 when importing RNA secondary structure via Stockholm
2703 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2704 not shown in correct direction for simple pseudoknots
2707 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2708 with lightGray or darkGray via features file (but can
2712 <!-- JAL-2383 -->Above PID colour threshold not recovered
2713 when alignment view imported from project
2716 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2717 structure and sequences extracted from structure files
2718 imported via URL and viewed in Jmol
2721 <!-- JAL-2520 -->Structures loaded via URL are saved in
2722 Jalview Projects rather than fetched via URL again when
2723 the project is loaded and the structure viewed
2726 <em>Web Services</em>
2729 <!-- JAL-2519 -->EnsemblGenomes example failing after
2730 release of Ensembl v.88
2733 <!-- JAL-2366 -->Proxy server address and port always
2734 appear enabled in Preferences->Connections
2737 <!-- JAL-2461 -->DAS registry not found exceptions
2738 removed from console output
2741 <!-- JAL-2582 -->Cannot retrieve protein products from
2742 Ensembl by Peptide ID
2745 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2746 created from SIFTs, and spurious 'Couldn't open structure
2747 in Chimera' errors raised after April 2017 update (problem
2748 due to 'null' string rather than empty string used for
2749 residues with no corresponding PDB mapping).
2752 <em>Application UI</em>
2755 <!-- JAL-2361 -->User Defined Colours not added to Colour
2759 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2760 case' residues (button in colourscheme editor debugged and
2761 new documentation and tooltips added)
2764 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2765 doesn't restore group-specific text colour thresholds
2768 <!-- JAL-2243 -->Feature settings panel does not update as
2769 new features are added to alignment
2772 <!-- JAL-2532 -->Cancel in feature settings reverts
2773 changes to feature colours via the Amend features dialog
2776 <!-- JAL-2506 -->Null pointer exception when attempting to
2777 edit graduated feature colour via amend features dialog
2781 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2782 selection menu changes colours of alignment views
2785 <!-- JAL-2426 -->Spurious exceptions in console raised
2786 from alignment calculation workers after alignment has
2790 <!-- JAL-1608 -->Typo in selection popup menu - Create
2791 groups now 'Create Group'
2794 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2795 Create/Undefine group doesn't always work
2798 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2799 shown again after pressing 'Cancel'
2802 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2803 adjusts start position in wrap mode
2806 <!-- JAL-2563 -->Status bar doesn't show positions for
2807 ambiguous amino acids
2810 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2811 CDS/Protein view after CDS sequences added for aligned
2815 <!-- JAL-2592 -->User defined colourschemes called 'User
2816 Defined' don't appear in Colours menu
2822 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2823 score models doesn't always result in an updated PCA plot
2826 <!-- JAL-2442 -->Features not rendered as transparent on
2827 overview or linked structure view
2830 <!-- JAL-2372 -->Colour group by conservation doesn't
2834 <!-- JAL-2517 -->Hitting Cancel after applying
2835 user-defined colourscheme doesn't restore original
2842 <!-- JAL-2314 -->Unit test failure:
2843 jalview.ws.jabaws.RNAStructExportImport setup fails
2846 <!-- JAL-2307 -->Unit test failure:
2847 jalview.ws.sifts.SiftsClientTest due to compatibility
2848 problems with deep array comparison equality asserts in
2849 successive versions of TestNG
2852 <!-- JAL-2479 -->Relocated StructureChooserTest and
2853 ParameterUtilsTest Unit tests to Network suite
2856 <em>New Known Issues</em>
2859 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2860 phase after a sequence motif find operation
2863 <!-- JAL-2550 -->Importing annotation file with rows
2864 containing just upper and lower case letters are
2865 interpreted as WUSS RNA secondary structure symbols
2868 <!-- JAL-2590 -->Cannot load and display Newick trees
2869 reliably from eggnog Ortholog database
2872 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2873 containing features of type Highlight' when 'B' is pressed
2874 to mark columns containing highlighted regions.
2877 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2878 doesn't always add secondary structure annotation.
2883 <td width="60" nowrap>
2884 <div align="center">
2885 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2888 <td><div align="left">
2892 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2893 for all consensus calculations
2896 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2899 <li>Updated Jalview's Certum code signing certificate
2902 <em>Application</em>
2905 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2906 set of database cross-references, sorted alphabetically
2909 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2910 from database cross references. Users with custom links
2911 will receive a <a href="webServices/urllinks.html#warning">warning
2912 dialog</a> asking them to update their preferences.
2915 <!-- JAL-2287-->Cancel button and escape listener on
2916 dialog warning user about disconnecting Jalview from a
2920 <!-- JAL-2320-->Jalview's Chimera control window closes if
2921 the Chimera it is connected to is shut down
2924 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2925 columns menu item to mark columns containing highlighted
2926 regions (e.g. from structure selections or results of a
2930 <!-- JAL-2284-->Command line option for batch-generation
2931 of HTML pages rendering alignment data with the BioJS
2941 <!-- JAL-2286 -->Columns with more than one modal residue
2942 are not coloured or thresholded according to percent
2943 identity (first observed in Jalview 2.8.2)
2946 <!-- JAL-2301 -->Threonine incorrectly reported as not
2950 <!-- JAL-2318 -->Updates to documentation pages (above PID
2951 threshold, amino acid properties)
2954 <!-- JAL-2292 -->Lower case residues in sequences are not
2955 reported as mapped to residues in a structure file in the
2959 <!--JAL-2324 -->Identical features with non-numeric scores
2960 could be added multiple times to a sequence
2963 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2964 bond features shown as two highlighted residues rather
2965 than a range in linked structure views, and treated
2966 correctly when selecting and computing trees from features
2969 <!-- JAL-2281-->Custom URL links for database
2970 cross-references are matched to database name regardless
2975 <em>Application</em>
2978 <!-- JAL-2282-->Custom URL links for specific database
2979 names without regular expressions also offer links from
2983 <!-- JAL-2315-->Removing a single configured link in the
2984 URL links pane in Connections preferences doesn't actually
2985 update Jalview configuration
2988 <!-- JAL-2272-->CTRL-Click on a selected region to open
2989 the alignment area popup menu doesn't work on El-Capitan
2992 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2993 files with similarly named sequences if dropped onto the
2997 <!-- JAL-2312 -->Additional mappings are shown for PDB
2998 entries where more chains exist in the PDB accession than
2999 are reported in the SIFTS file
3002 <!-- JAL-2317-->Certain structures do not get mapped to
3003 the structure view when displayed with Chimera
3006 <!-- JAL-2317-->No chains shown in the Chimera view
3007 panel's View->Show Chains submenu
3010 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
3011 work for wrapped alignment views
3014 <!--JAL-2197 -->Rename UI components for running JPred
3015 predictions from 'JNet' to 'JPred'
3018 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
3019 corrupted when annotation panel vertical scroll is not at
3020 first annotation row
3023 <!--JAL-2332 -->Attempting to view structure for Hen
3024 lysozyme results in a PDB Client error dialog box
3027 <!-- JAL-2319 -->Structure View's mapping report switched
3028 ranges for PDB and sequence for SIFTS
3031 SIFTS 'Not_Observed' residues mapped to non-existant
3035 <!-- <em>New Known Issues</em>
3042 <td width="60" nowrap>
3043 <div align="center">
3044 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
3045 <em>25/10/2016</em></strong>
3048 <td><em>Application</em>
3050 <li>3D Structure chooser opens with 'Cached structures'
3051 view if structures already loaded</li>
3052 <li>Progress bar reports models as they are loaded to
3053 structure views</li>
3059 <li>Colour by conservation always enabled and no tick
3060 shown in menu when BLOSUM or PID shading applied</li>
3061 <li>FER1_ARATH and FER2_ARATH labels were switched in
3062 example sequences/projects/trees</li>
3064 <em>Application</em>
3066 <li>Jalview projects with views of local PDB structure
3067 files saved on Windows cannot be opened on OSX</li>
3068 <li>Multiple structure views can be opened and superposed
3069 without timeout for structures with multiple models or
3070 multiple sequences in alignment</li>
3071 <li>Cannot import or associated local PDB files without a
3072 PDB ID HEADER line</li>
3073 <li>RMSD is not output in Jmol console when superposition
3075 <li>Drag and drop of URL from Browser fails for Linux and
3076 OSX versions earlier than El Capitan</li>
3077 <li>ENA client ignores invalid content from ENA server</li>
3078 <li>Exceptions are not raised in console when ENA client
3079 attempts to fetch non-existent IDs via Fetch DB Refs UI
3081 <li>Exceptions are not raised in console when a new view
3082 is created on the alignment</li>
3083 <li>OSX right-click fixed for group selections: CMD-click
3084 to insert/remove gaps in groups and CTRL-click to open group
3087 <em>Build and deployment</em>
3089 <li>URL link checker now copes with multi-line anchor
3092 <em>New Known Issues</em>
3094 <li>Drag and drop from URL links in browsers do not work
3101 <td width="60" nowrap>
3102 <div align="center">
3103 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
3106 <td><em>General</em>
3109 <!-- JAL-2124 -->Updated Spanish translations.
3112 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
3113 for importing structure data to Jalview. Enables mmCIF and
3117 <!-- JAL-192 --->Alignment ruler shows positions relative to
3121 <!-- JAL-2202 -->Position/residue shown in status bar when
3122 mousing over sequence associated annotation
3125 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
3129 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
3130 '()', canonical '[]' and invalid '{}' base pair populations
3134 <!-- JAL-2092 -->Feature settings popup menu options for
3135 showing or hiding columns containing a feature
3138 <!-- JAL-1557 -->Edit selected group by double clicking on
3139 group and sequence associated annotation labels
3142 <!-- JAL-2236 -->Sequence name added to annotation label in
3143 select/hide columns by annotation and colour by annotation
3147 </ul> <em>Application</em>
3150 <!-- JAL-2050-->Automatically hide introns when opening a
3151 gene/transcript view
3154 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
3158 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
3159 structure mappings with the EMBL-EBI PDBe SIFTS database
3162 <!-- JAL-2079 -->Updated download sites used for Rfam and
3163 Pfam sources to xfam.org
3166 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
3169 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
3170 over sequences in Jalview
3173 <!-- JAL-2027-->Support for reverse-complement coding
3174 regions in ENA and EMBL
3177 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
3178 for record retrieval via ENA rest API
3181 <!-- JAL-2027 -->Support for ENA CDS records with reverse
3185 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
3186 groovy script execution
3189 <!-- JAL-1812 -->New 'execute Groovy script' option in an
3190 alignment window's Calculate menu
3193 <!-- JAL-1812 -->Allow groovy scripts that call
3194 Jalview.getAlignFrames() to run in headless mode
3197 <!-- JAL-2068 -->Support for creating new alignment
3198 calculation workers from groovy scripts
3201 <!-- JAL-1369 --->Store/restore reference sequence in
3205 <!-- JAL-1803 -->Chain codes for a sequence's PDB
3206 associations are now saved/restored from project
3209 <!-- JAL-1993 -->Database selection dialog always shown
3210 before sequence fetcher is opened
3213 <!-- JAL-2183 -->Double click on an entry in Jalview's
3214 database chooser opens a sequence fetcher
3217 <!-- JAL-1563 -->Free-text search client for UniProt using
3218 the UniProt REST API
3221 <!-- JAL-2168 -->-nonews command line parameter to prevent
3222 the news reader opening
3225 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
3226 querying stored in preferences
3229 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
3233 <!-- JAL-1977-->Tooltips shown on database chooser
3236 <!-- JAL-391 -->Reverse complement function in calculate
3237 menu for nucleotide sequences
3240 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
3241 and feature counts preserves alignment ordering (and
3242 debugged for complex feature sets).
3245 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
3246 viewing structures with Jalview 2.10
3249 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
3250 genome, transcript CCDS and gene ids via the Ensembl and
3251 Ensembl Genomes REST API
3254 <!-- JAL-2049 -->Protein sequence variant annotation
3255 computed for 'sequence_variant' annotation on CDS regions
3259 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
3263 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
3264 Ref Fetcher fails to match, or otherwise updates sequence
3265 data from external database records.
3268 <!-- JAL-2154 -->Revised Jalview Project format for
3269 efficient recovery of sequence coding and alignment
3270 annotation relationships.
3272 </ul> <!-- <em>Applet</em>
3283 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
3287 <!-- JAL-2018-->Export features in Jalview format (again)
3288 includes graduated colourschemes
3291 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
3292 working with big alignments and lots of hidden columns
3295 <!-- JAL-2053-->Hidden column markers not always rendered
3296 at right of alignment window
3299 <!-- JAL-2067 -->Tidied up links in help file table of
3303 <!-- JAL-2072 -->Feature based tree calculation not shown
3307 <!-- JAL-2075 -->Hidden columns ignored during feature
3308 based tree calculation
3311 <!-- JAL-2065 -->Alignment view stops updating when show
3312 unconserved enabled for group on alignment
3315 <!-- JAL-2086 -->Cannot insert gaps into sequence when
3319 <!-- JAL-2146 -->Alignment column in status incorrectly
3320 shown as "Sequence position" when mousing over
3324 <!-- JAL-2099 -->Incorrect column numbers in ruler when
3325 hidden columns present
3328 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
3329 user created annotation added to alignment
3332 <!-- JAL-1841 -->RNA Structure consensus only computed for
3333 '()' base pair annotation
3336 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
3337 in zero scores for all base pairs in RNA Structure
3341 <!-- JAL-2174-->Extend selection with columns containing
3345 <!-- JAL-2275 -->Pfam format writer puts extra space at
3346 beginning of sequence
3349 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
3353 <!-- JAL-2238 -->Cannot create groups on an alignment from
3354 from a tree when t-coffee scores are shown
3357 <!-- JAL-1836,1967 -->Cannot import and view PDB
3358 structures with chains containing negative resnums (4q4h)
3361 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
3365 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
3366 to Clustal, PIR and PileUp output
3369 <!-- JAL-2008 -->Reordering sequence features that are
3370 not visible causes alignment window to repaint
3373 <!-- JAL-2006 -->Threshold sliders don't work in
3374 graduated colour and colour by annotation row for e-value
3375 scores associated with features and annotation rows
3378 <!-- JAL-1797 -->amino acid physicochemical conservation
3379 calculation should be case independent
3382 <!-- JAL-2173 -->Remove annotation also updates hidden
3386 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
3387 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
3388 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
3391 <!-- JAL-2065 -->Null pointer exceptions and redraw
3392 problems when reference sequence defined and 'show
3393 non-conserved' enabled
3396 <!-- JAL-1306 -->Quality and Conservation are now shown on
3397 load even when Consensus calculation is disabled
3400 <!-- JAL-1932 -->Remove right on penultimate column of
3401 alignment does nothing
3404 <em>Application</em>
3407 <!-- JAL-1552-->URLs and links can't be imported by
3408 drag'n'drop on OSX when launched via webstart (note - not
3409 yet fixed for El Capitan)
3412 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
3413 output when running on non-gb/us i18n platforms
3416 <!-- JAL-1944 -->Error thrown when exporting a view with
3417 hidden sequences as flat-file alignment
3420 <!-- JAL-2030-->InstallAnywhere distribution fails when
3424 <!-- JAL-2080-->Jalview very slow to launch via webstart
3425 (also hotfix for 2.9.0b2)
3428 <!-- JAL-2085 -->Cannot save project when view has a
3429 reference sequence defined
3432 <!-- JAL-1011 -->Columns are suddenly selected in other
3433 alignments and views when revealing hidden columns
3436 <!-- JAL-1989 -->Hide columns not mirrored in complement
3437 view in a cDNA/Protein splitframe
3440 <!-- JAL-1369 -->Cannot save/restore representative
3441 sequence from project when only one sequence is
3445 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
3446 in Structure Chooser
3449 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
3450 structure consensus didn't refresh annotation panel
3453 <!-- JAL-1962 -->View mapping in structure view shows
3454 mappings between sequence and all chains in a PDB file
3457 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
3458 dialogs format columns correctly, don't display array
3459 data, sort columns according to type
3462 <!-- JAL-1975 -->Export complete shown after destination
3463 file chooser is cancelled during an image export
3466 <!-- JAL-2025 -->Error when querying PDB Service with
3467 sequence name containing special characters
3470 <!-- JAL-2024 -->Manual PDB structure querying should be
3474 <!-- JAL-2104 -->Large tooltips with broken HTML
3475 formatting don't wrap
3478 <!-- JAL-1128 -->Figures exported from wrapped view are
3479 truncated so L looks like I in consensus annotation
3482 <!-- JAL-2003 -->Export features should only export the
3483 currently displayed features for the current selection or
3487 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
3488 after fetching cross-references, and restoring from
3492 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
3493 followed in the structure viewer
3496 <!-- JAL-2163 -->Titles for individual alignments in
3497 splitframe not restored from project
3500 <!-- JAL-2145 -->missing autocalculated annotation at
3501 trailing end of protein alignment in transcript/product
3502 splitview when pad-gaps not enabled by default
3505 <!-- JAL-1797 -->amino acid physicochemical conservation
3509 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
3510 article has been read (reopened issue due to
3511 internationalisation problems)
3514 <!-- JAL-1960 -->Only offer PDB structures in structure
3515 viewer based on sequence name, PDB and UniProt
3520 <!-- JAL-1976 -->No progress bar shown during export of
3524 <!-- JAL-2213 -->Structures not always superimposed after
3525 multiple structures are shown for one or more sequences.
3528 <!-- JAL-1370 -->Reference sequence characters should not
3529 be replaced with '.' when 'Show unconserved' format option
3533 <!-- JAL-1823 -->Cannot specify chain code when entering
3534 specific PDB id for sequence
3537 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3538 'Export hidden sequences' is enabled, but 'export hidden
3539 columns' is disabled.
3542 <!--JAL-2026-->Best Quality option in structure chooser
3543 selects lowest rather than highest resolution structures
3547 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3548 to sequence mapping in 'View Mappings' report
3551 <!-- JAL-2284 -->Unable to read old Jalview projects that
3552 contain non-XML data added after Jalvew wrote project.
3555 <!-- JAL-2118 -->Newly created annotation row reorders
3556 after clicking on it to create new annotation for a
3560 <!-- JAL-1980 -->Null Pointer Exception raised when
3561 pressing Add on an orphaned cut'n'paste window.
3563 <!-- may exclude, this is an external service stability issue JAL-1941
3564 -- > RNA 3D structure not added via DSSR service</li> -->
3569 <!-- JAL-2151 -->Incorrect columns are selected when
3570 hidden columns present before start of sequence
3573 <!-- JAL-1986 -->Missing dependencies on applet pages
3577 <!-- JAL-1947 -->Overview pixel size changes when
3578 sequences are hidden in applet
3581 <!-- JAL-1996 -->Updated instructions for applet
3582 deployment on examples pages.
3589 <td width="60" nowrap>
3590 <div align="center">
3591 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3592 <em>16/10/2015</em></strong>
3595 <td><em>General</em>
3597 <li>Time stamps for signed Jalview application and applet
3602 <em>Application</em>
3604 <li>Duplicate group consensus and conservation rows
3605 shown when tree is partitioned</li>
3606 <li>Erratic behaviour when tree partitions made with
3607 multiple cDNA/Protein split views</li>
3613 <td width="60" nowrap>
3614 <div align="center">
3615 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3616 <em>8/10/2015</em></strong>
3619 <td><em>General</em>
3621 <li>Updated Spanish translations of localized text for
3623 </ul> <em>Application</em>
3625 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3626 <li>Signed OSX InstallAnywhere installer<br></li>
3627 <li>Support for per-sequence based annotations in BioJSON</li>
3628 </ul> <em>Applet</em>
3630 <li>Split frame example added to applet examples page</li>
3631 </ul> <em>Build and Deployment</em>
3634 <!-- JAL-1888 -->New ant target for running Jalview's test
3642 <li>Mapping of cDNA to protein in split frames
3643 incorrect when sequence start > 1</li>
3644 <li>Broken images in filter column by annotation dialog
3646 <li>Feature colours not parsed from features file</li>
3647 <li>Exceptions and incomplete link URLs recovered when
3648 loading a features file containing HTML tags in feature
3652 <em>Application</em>
3654 <li>Annotations corrupted after BioJS export and
3656 <li>Incorrect sequence limits after Fetch DB References
3657 with 'trim retrieved sequences'</li>
3658 <li>Incorrect warning about deleting all data when
3659 deleting selected columns</li>
3660 <li>Patch to build system for shipping properly signed
3661 JNLP templates for webstart launch</li>
3662 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3663 unreleased structures for download or viewing</li>
3664 <li>Tab/space/return keystroke operation of EMBL-PDBe
3665 fetcher/viewer dialogs works correctly</li>
3666 <li>Disabled 'minimise' button on Jalview windows
3667 running on OSX to workaround redraw hang bug</li>
3668 <li>Split cDNA/Protein view position and geometry not
3669 recovered from jalview project</li>
3670 <li>Initial enabled/disabled state of annotation menu
3671 sorter 'show autocalculated first/last' corresponds to
3673 <li>Restoring of Clustal, RNA Helices and T-Coffee
3674 color schemes from BioJSON</li>
3678 <li>Reorder sequences mirrored in cDNA/Protein split
3680 <li>Applet with Jmol examples not loading correctly</li>
3686 <td><div align="center">
3687 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3689 <td><em>General</em>
3691 <li>Linked visualisation and analysis of DNA and Protein
3694 <li>Translated cDNA alignments shown as split protein
3695 and DNA alignment views</li>
3696 <li>Codon consensus annotation for linked protein and
3697 cDNA alignment views</li>
3698 <li>Link cDNA or Protein product sequences by loading
3699 them onto Protein or cDNA alignments</li>
3700 <li>Reconstruct linked cDNA alignment from aligned
3701 protein sequences</li>
3704 <li>Jmol integration updated to Jmol v14.2.14</li>
3705 <li>Import and export of Jalview alignment views as <a
3706 href="features/bioJsonFormat.html">BioJSON</a></li>
3707 <li>New alignment annotation file statements for
3708 reference sequences and marking hidden columns</li>
3709 <li>Reference sequence based alignment shading to
3710 highlight variation</li>
3711 <li>Select or hide columns according to alignment
3713 <li>Find option for locating sequences by description</li>
3714 <li>Conserved physicochemical properties shown in amino
3715 acid conservation row</li>
3716 <li>Alignments can be sorted by number of RNA helices</li>
3717 </ul> <em>Application</em>
3719 <li>New cDNA/Protein analysis capabilities
3721 <li>Get Cross-References should open a Split Frame
3722 view with cDNA/Protein</li>
3723 <li>Detect when nucleotide sequences and protein
3724 sequences are placed in the same alignment</li>
3725 <li>Split cDNA/Protein views are saved in Jalview
3730 <li>Use REST API to talk to Chimera</li>
3731 <li>Selected regions in Chimera are highlighted in linked
3732 Jalview windows</li>
3734 <li>VARNA RNA viewer updated to v3.93</li>
3735 <li>VARNA views are saved in Jalview Projects</li>
3736 <li>Pseudoknots displayed as Jalview RNA annotation can
3737 be shown in VARNA</li>
3739 <li>Make groups for selection uses marked columns as well
3740 as the active selected region</li>
3742 <li>Calculate UPGMA and NJ trees using sequence feature
3744 <li>New Export options
3746 <li>New Export Settings dialog to control hidden
3747 region export in flat file generation</li>
3749 <li>Export alignment views for display with the <a
3750 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3752 <li>Export scrollable SVG in HTML page</li>
3753 <li>Optional embedding of BioJSON data when exporting
3754 alignment figures to HTML</li>
3756 <li>3D structure retrieval and display
3758 <li>Free text and structured queries with the PDBe
3760 <li>PDBe Search API based discovery and selection of
3761 PDB structures for a sequence set</li>
3765 <li>JPred4 employed for protein secondary structure
3767 <li>Hide Insertions menu option to hide unaligned columns
3768 for one or a group of sequences</li>
3769 <li>Automatically hide insertions in alignments imported
3770 from the JPred4 web server</li>
3771 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3772 system on OSX<br />LGPL libraries courtesy of <a
3773 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3775 <li>changed 'View nucleotide structure' submenu to 'View
3776 VARNA 2D Structure'</li>
3777 <li>change "View protein structure" menu option to "3D
3780 </ul> <em>Applet</em>
3782 <li>New layout for applet example pages</li>
3783 <li>New parameters to enable SplitFrame view
3784 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3785 <li>New example demonstrating linked viewing of cDNA and
3786 Protein alignments</li>
3787 </ul> <em>Development and deployment</em>
3789 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3790 <li>Include installation type and git revision in build
3791 properties and console log output</li>
3792 <li>Jalview Github organisation, and new github site for
3793 storing BioJsMSA Templates</li>
3794 <li>Jalview's unit tests now managed with TestNG</li>
3797 <!-- <em>General</em>
3799 </ul> --> <!-- issues resolved --> <em>Application</em>
3801 <li>Escape should close any open find dialogs</li>
3802 <li>Typo in select-by-features status report</li>
3803 <li>Consensus RNA secondary secondary structure
3804 predictions are not highlighted in amber</li>
3805 <li>Missing gap character in v2.7 example file means
3806 alignment appears unaligned when pad-gaps is not enabled</li>
3807 <li>First switch to RNA Helices colouring doesn't colour
3808 associated structure views</li>
3809 <li>ID width preference option is greyed out when auto
3810 width checkbox not enabled</li>
3811 <li>Stopped a warning dialog from being shown when
3812 creating user defined colours</li>
3813 <li>'View Mapping' in structure viewer shows sequence
3814 mappings for just that viewer's sequences</li>
3815 <li>Workaround for superposing PDB files containing
3816 multiple models in Chimera</li>
3817 <li>Report sequence position in status bar when hovering
3818 over Jmol structure</li>
3819 <li>Cannot output gaps as '.' symbols with Selection ->
3820 output to text box</li>
3821 <li>Flat file exports of alignments with hidden columns
3822 have incorrect sequence start/end</li>
3823 <li>'Aligning' a second chain to a Chimera structure from
3825 <li>Colour schemes applied to structure viewers don't
3826 work for nucleotide</li>
3827 <li>Loading/cut'n'pasting an empty or invalid file leads
3828 to a grey/invisible alignment window</li>
3829 <li>Exported Jpred annotation from a sequence region
3830 imports to different position</li>
3831 <li>Space at beginning of sequence feature tooltips shown
3832 on some platforms</li>
3833 <li>Chimera viewer 'View | Show Chain' menu is not
3835 <li>'New View' fails with a Null Pointer Exception in
3836 console if Chimera has been opened</li>
3837 <li>Mouseover to Chimera not working</li>
3838 <li>Miscellaneous ENA XML feature qualifiers not
3840 <li>NPE in annotation renderer after 'Extract Scores'</li>
3841 <li>If two structures in one Chimera window, mouseover of
3842 either sequence shows on first structure</li>
3843 <li>'Show annotations' options should not make
3844 non-positional annotations visible</li>
3845 <li>Subsequence secondary structure annotation not shown
3846 in right place after 'view flanking regions'</li>
3847 <li>File Save As type unset when current file format is
3849 <li>Save as '.jar' option removed for saving Jalview
3851 <li>Colour by Sequence colouring in Chimera more
3853 <li>Cannot 'add reference annotation' for a sequence in
3854 several views on same alignment</li>
3855 <li>Cannot show linked products for EMBL / ENA records</li>
3856 <li>Jalview's tooltip wraps long texts containing no
3858 </ul> <em>Applet</em>
3860 <li>Jmol to JalviewLite mouseover/link not working</li>
3861 <li>JalviewLite can't import sequences with ID
3862 descriptions containing angle brackets</li>
3863 </ul> <em>General</em>
3865 <li>Cannot export and reimport RNA secondary structure
3866 via jalview annotation file</li>
3867 <li>Random helix colour palette for colour by annotation
3868 with RNA secondary structure</li>
3869 <li>Mouseover to cDNA from STOP residue in protein
3870 translation doesn't work.</li>
3871 <li>hints when using the select by annotation dialog box</li>
3872 <li>Jmol alignment incorrect if PDB file has alternate CA
3874 <li>FontChooser message dialog appears to hang after
3875 choosing 1pt font</li>
3876 <li>Peptide secondary structure incorrectly imported from
3877 annotation file when annotation display text includes 'e' or
3879 <li>Cannot set colour of new feature type whilst creating
3881 <li>cDNA translation alignment should not be sequence
3882 order dependent</li>
3883 <li>'Show unconserved' doesn't work for lower case
3885 <li>Nucleotide ambiguity codes involving R not recognised</li>
3886 </ul> <em>Deployment and Documentation</em>
3888 <li>Applet example pages appear different to the rest of
3889 www.jalview.org</li>
3890 </ul> <em>Application Known issues</em>
3892 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3893 <li>Misleading message appears after trying to delete
3895 <li>Jalview icon not shown in dock after InstallAnywhere
3896 version launches</li>
3897 <li>Fetching EMBL reference for an RNA sequence results
3898 fails with a sequence mismatch</li>
3899 <li>Corrupted or unreadable alignment display when
3900 scrolling alignment to right</li>
3901 <li>ArrayIndexOutOfBoundsException thrown when remove
3902 empty columns called on alignment with ragged gapped ends</li>
3903 <li>auto calculated alignment annotation rows do not get
3904 placed above or below non-autocalculated rows</li>
3905 <li>Jalview dekstop becomes sluggish at full screen in
3906 ultra-high resolution</li>
3907 <li>Cannot disable consensus calculation independently of
3908 quality and conservation</li>
3909 <li>Mouseover highlighting between cDNA and protein can
3910 become sluggish with more than one splitframe shown</li>
3911 </ul> <em>Applet Known Issues</em>
3913 <li>Core PDB parsing code requires Jmol</li>
3914 <li>Sequence canvas panel goes white when alignment
3915 window is being resized</li>
3921 <td><div align="center">
3922 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3924 <td><em>General</em>
3926 <li>Updated Java code signing certificate donated by
3928 <li>Features and annotation preserved when performing
3929 pairwise alignment</li>
3930 <li>RNA pseudoknot annotation can be
3931 imported/exported/displayed</li>
3932 <li>'colour by annotation' can colour by RNA and
3933 protein secondary structure</li>
3934 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3935 post-hoc with 2.9 release</em>)
3938 </ul> <em>Application</em>
3940 <li>Extract and display secondary structure for sequences
3941 with 3D structures</li>
3942 <li>Support for parsing RNAML</li>
3943 <li>Annotations menu for layout
3945 <li>sort sequence annotation rows by alignment</li>
3946 <li>place sequence annotation above/below alignment
3949 <li>Output in Stockholm format</li>
3950 <li>Internationalisation: improved Spanish (es)
3952 <li>Structure viewer preferences tab</li>
3953 <li>Disorder and Secondary Structure annotation tracks
3954 shared between alignments</li>
3955 <li>UCSF Chimera launch and linked highlighting from
3957 <li>Show/hide all sequence associated annotation rows for
3958 all or current selection</li>
3959 <li>disorder and secondary structure predictions
3960 available as dataset annotation</li>
3961 <li>Per-sequence rna helices colouring</li>
3964 <li>Sequence database accessions imported when fetching
3965 alignments from Rfam</li>
3966 <li>update VARNA version to 3.91</li>
3968 <li>New groovy scripts for exporting aligned positions,
3969 conservation values, and calculating sum of pairs scores.</li>
3970 <li>Command line argument to set default JABAWS server</li>
3971 <li>include installation type in build properties and
3972 console log output</li>
3973 <li>Updated Jalview project format to preserve dataset
3977 <!-- issues resolved --> <em>Application</em>
3979 <li>Distinguish alignment and sequence associated RNA
3980 structure in structure->view->VARNA</li>
3981 <li>Raise dialog box if user deletes all sequences in an
3983 <li>Pressing F1 results in documentation opening twice</li>
3984 <li>Sequence feature tooltip is wrapped</li>
3985 <li>Double click on sequence associated annotation
3986 selects only first column</li>
3987 <li>Redundancy removal doesn't result in unlinked
3988 leaves shown in tree</li>
3989 <li>Undos after several redundancy removals don't undo
3991 <li>Hide sequence doesn't hide associated annotation</li>
3992 <li>User defined colours dialog box too big to fit on
3993 screen and buttons not visible</li>
3994 <li>author list isn't updated if already written to
3995 Jalview properties</li>
3996 <li>Popup menu won't open after retrieving sequence
3998 <li>File open window for associate PDB doesn't open</li>
3999 <li>Left-then-right click on a sequence id opens a
4000 browser search window</li>
4001 <li>Cannot open sequence feature shading/sort popup menu
4002 in feature settings dialog</li>
4003 <li>better tooltip placement for some areas of Jalview
4005 <li>Allow addition of JABAWS Server which doesn't
4006 pass validation</li>
4007 <li>Web services parameters dialog box is too large to
4009 <li>Muscle nucleotide alignment preset obscured by
4011 <li>JABAWS preset submenus don't contain newly
4012 defined user preset</li>
4013 <li>MSA web services warns user if they were launched
4014 with invalid input</li>
4015 <li>Jalview cannot contact DAS Registy when running on
4018 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
4019 'Superpose with' submenu not shown when new view
4023 </ul> <!-- <em>Applet</em>
4025 </ul> <em>General</em>
4027 </ul>--> <em>Deployment and Documentation</em>
4029 <li>2G and 1G options in launchApp have no effect on
4030 memory allocation</li>
4031 <li>launchApp service doesn't automatically open
4032 www.jalview.org/examples/exampleFile.jar if no file is given</li>
4034 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
4035 InstallAnywhere reports cannot find valid JVM when Java
4036 1.7_055 is available
4038 </ul> <em>Application Known issues</em>
4041 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
4042 corrupted or unreadable alignment display when scrolling
4046 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
4047 retrieval fails but progress bar continues for DAS retrieval
4048 with large number of ID
4051 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
4052 flatfile output of visible region has incorrect sequence
4056 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
4057 rna structure consensus doesn't update when secondary
4058 structure tracks are rearranged
4061 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
4062 invalid rna structure positional highlighting does not
4063 highlight position of invalid base pairs
4066 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
4067 out of memory errors are not raised when saving Jalview
4068 project from alignment window file menu
4071 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
4072 Switching to RNA Helices colouring doesn't propagate to
4076 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
4077 colour by RNA Helices not enabled when user created
4078 annotation added to alignment
4081 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
4082 Jalview icon not shown on dock in Mountain Lion/Webstart
4084 </ul> <em>Applet Known Issues</em>
4087 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
4088 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
4091 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
4092 Jalview and Jmol example not compatible with IE9
4095 <li>Sort by annotation score doesn't reverse order
4101 <td><div align="center">
4102 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
4105 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
4108 <li>Internationalisation of user interface (usually
4109 called i18n support) and translation for Spanish locale</li>
4110 <li>Define/Undefine group on current selection with
4111 Ctrl-G/Shift Ctrl-G</li>
4112 <li>Improved group creation/removal options in
4113 alignment/sequence Popup menu</li>
4114 <li>Sensible precision for symbol distribution
4115 percentages shown in logo tooltip.</li>
4116 <li>Annotation panel height set according to amount of
4117 annotation when alignment first opened</li>
4118 </ul> <em>Application</em>
4120 <li>Interactive consensus RNA secondary structure
4121 prediction VIENNA RNAAliFold JABA 2.1 service</li>
4122 <li>Select columns containing particular features from
4123 Feature Settings dialog</li>
4124 <li>View all 'representative' PDB structures for selected
4126 <li>Update Jalview project format:
4128 <li>New file extension for Jalview projects '.jvp'</li>
4129 <li>Preserve sequence and annotation dataset (to
4130 store secondary structure annotation,etc)</li>
4131 <li>Per group and alignment annotation and RNA helix
4135 <li>New similarity measures for PCA and Tree calculation
4137 <li>Experimental support for retrieval and viewing of
4138 flanking regions for an alignment</li>
4142 <!-- issues resolved --> <em>Application</em>
4144 <li>logo keeps spinning and status remains at queued or
4145 running after job is cancelled</li>
4146 <li>cannot export features from alignments imported from
4147 Jalview/VAMSAS projects</li>
4148 <li>Buggy slider for web service parameters that take
4150 <li>Newly created RNA secondary structure line doesn't
4151 have 'display all symbols' flag set</li>
4152 <li>T-COFFEE alignment score shading scheme and other
4153 annotation shading not saved in Jalview project</li>
4154 <li>Local file cannot be loaded in freshly downloaded
4156 <li>Jalview icon not shown on dock in Mountain
4158 <li>Load file from desktop file browser fails</li>
4159 <li>Occasional NPE thrown when calculating large trees</li>
4160 <li>Cannot reorder or slide sequences after dragging an
4161 alignment onto desktop</li>
4162 <li>Colour by annotation dialog throws NPE after using
4163 'extract scores' function</li>
4164 <li>Loading/cut'n'pasting an empty file leads to a grey
4165 alignment window</li>
4166 <li>Disorder thresholds rendered incorrectly after
4167 performing IUPred disorder prediction</li>
4168 <li>Multiple group annotated consensus rows shown when
4169 changing 'normalise logo' display setting</li>
4170 <li>Find shows blank dialog after 'finished searching' if
4171 nothing matches query</li>
4172 <li>Null Pointer Exceptions raised when sorting by
4173 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
4175 <li>Errors in Jmol console when structures in alignment
4176 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
4178 <li>Not all working JABAWS services are shown in
4180 <li>JAVAWS version of Jalview fails to launch with
4181 'invalid literal/length code'</li>
4182 <li>Annotation/RNA Helix colourschemes cannot be applied
4183 to alignment with groups (actually fixed in 2.8.0b1)</li>
4184 <li>RNA Helices and T-Coffee Scores available as default
4187 </ul> <em>Applet</em>
4189 <li>Remove group option is shown even when selection is
4191 <li>Apply to all groups ticked but colourscheme changes
4192 don't affect groups</li>
4193 <li>Documented RNA Helices and T-Coffee Scores as valid
4194 colourscheme name</li>
4195 <li>Annotation labels drawn on sequence IDs when
4196 Annotation panel is not displayed</li>
4197 <li>Increased font size for dropdown menus on OSX and
4198 embedded windows</li>
4199 </ul> <em>Other</em>
4201 <li>Consensus sequence for alignments/groups with a
4202 single sequence were not calculated</li>
4203 <li>annotation files that contain only groups imported as
4204 annotation and junk sequences</li>
4205 <li>Fasta files with sequences containing '*' incorrectly
4206 recognised as PFAM or BLC</li>
4207 <li>conservation/PID slider apply all groups option
4208 doesn't affect background (2.8.0b1)
4210 <li>redundancy highlighting is erratic at 0% and 100%</li>
4211 <li>Remove gapped columns fails for sequences with ragged
4213 <li>AMSA annotation row with leading spaces is not
4214 registered correctly on import</li>
4215 <li>Jalview crashes when selecting PCA analysis for
4216 certain alignments</li>
4217 <li>Opening the colour by annotation dialog for an
4218 existing annotation based 'use original colours'
4219 colourscheme loses original colours setting</li>
4224 <td><div align="center">
4225 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
4226 <em>30/1/2014</em></strong>
4230 <li>Trusted certificates for JalviewLite applet and
4231 Jalview Desktop application<br />Certificate was donated by
4232 <a href="https://www.certum.eu">Certum</a> to the Jalview
4233 open source project).
4235 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
4236 <li>Output in Stockholm format</li>
4237 <li>Allow import of data from gzipped files</li>
4238 <li>Export/import group and sequence associated line
4239 graph thresholds</li>
4240 <li>Nucleotide substitution matrix that supports RNA and
4241 ambiguity codes</li>
4242 <li>Allow disorder predictions to be made on the current
4243 selection (or visible selection) in the same way that JPred
4245 <li>Groovy scripting for headless Jalview operation</li>
4246 </ul> <em>Other improvements</em>
4248 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
4249 <li>COMBINE statement uses current SEQUENCE_REF and
4250 GROUP_REF scope to group annotation rows</li>
4251 <li>Support '' style escaping of quotes in Newick
4253 <li>Group options for JABAWS service by command line name</li>
4254 <li>Empty tooltip shown for JABA service options with a
4255 link but no description</li>
4256 <li>Select primary source when selecting authority in
4257 database fetcher GUI</li>
4258 <li>Add .mfa to FASTA file extensions recognised by
4260 <li>Annotation label tooltip text wrap</li>
4265 <li>Slow scrolling when lots of annotation rows are
4267 <li>Lots of NPE (and slowness) after creating RNA
4268 secondary structure annotation line</li>
4269 <li>Sequence database accessions not imported when
4270 fetching alignments from Rfam</li>
4271 <li>Incorrect SHMR submission for sequences with
4273 <li>View all structures does not always superpose
4275 <li>Option widgets in service parameters not updated to
4276 reflect user or preset settings</li>
4277 <li>Null pointer exceptions for some services without
4278 presets or adjustable parameters</li>
4279 <li>Discover PDB IDs entry in structure menu doesn't
4280 discover PDB xRefs</li>
4281 <li>Exception encountered while trying to retrieve
4282 features with DAS</li>
4283 <li>Lowest value in annotation row isn't coloured
4284 when colour by annotation (per sequence) is coloured</li>
4285 <li>Keyboard mode P jumps to start of gapped region when
4286 residue follows a gap</li>
4287 <li>Jalview appears to hang importing an alignment with
4288 Wrap as default or after enabling Wrap</li>
4289 <li>'Right click to add annotations' message
4290 shown in wrap mode when no annotations present</li>
4291 <li>Disorder predictions fail with NPE if no automatic
4292 annotation already exists on alignment</li>
4293 <li>oninit javascript function should be called after
4294 initialisation completes</li>
4295 <li>Remove redundancy after disorder prediction corrupts
4296 alignment window display</li>
4297 <li>Example annotation file in documentation is invalid</li>
4298 <li>Grouped line graph annotation rows are not exported
4299 to annotation file</li>
4300 <li>Multi-harmony analysis cannot be run when only two
4302 <li>Cannot create multiple groups of line graphs with
4303 several 'combine' statements in annotation file</li>
4304 <li>Pressing return several times causes Number Format
4305 exceptions in keyboard mode</li>
4306 <li>Multi-harmony (SHMMR) method doesn't submit
4307 correct partitions for input data</li>
4308 <li>Translation from DNA to Amino Acids fails</li>
4309 <li>Jalview fail to load newick tree with quoted label</li>
4310 <li>--headless flag isn't understood</li>
4311 <li>ClassCastException when generating EPS in headless
4313 <li>Adjusting sequence-associated shading threshold only
4314 changes one row's threshold</li>
4315 <li>Preferences and Feature settings panel panel
4316 doesn't open</li>
4317 <li>hide consensus histogram also hides conservation and
4318 quality histograms</li>
4323 <td><div align="center">
4324 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
4326 <td><em>Application</em>
4328 <li>Support for JABAWS 2.0 Services (AACon alignment
4329 conservation, protein disorder and Clustal Omega)</li>
4330 <li>JABAWS server status indicator in Web Services
4332 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
4333 in Jalview alignment window</li>
4334 <li>Updated Jalview build and deploy framework for OSX
4335 mountain lion, windows 7, and 8</li>
4336 <li>Nucleotide substitution matrix for PCA that supports
4337 RNA and ambiguity codes</li>
4339 <li>Improved sequence database retrieval GUI</li>
4340 <li>Support fetching and database reference look up
4341 against multiple DAS sources (Fetch all from in 'fetch db
4343 <li>Jalview project improvements
4345 <li>Store and retrieve the 'belowAlignment'
4346 flag for annotation</li>
4347 <li>calcId attribute to group annotation rows on the
4349 <li>Store AACon calculation settings for a view in
4350 Jalview project</li>
4354 <li>horizontal scrolling gesture support</li>
4355 <li>Visual progress indicator when PCA calculation is
4357 <li>Simpler JABA web services menus</li>
4358 <li>visual indication that web service results are still
4359 being retrieved from server</li>
4360 <li>Serialise the dialogs that are shown when Jalview
4361 starts up for first time</li>
4362 <li>Jalview user agent string for interacting with HTTP
4364 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
4366 <li>Examples directory and Groovy library included in
4367 InstallAnywhere distribution</li>
4368 </ul> <em>Applet</em>
4370 <li>RNA alignment and secondary structure annotation
4371 visualization applet example</li>
4372 </ul> <em>General</em>
4374 <li>Normalise option for consensus sequence logo</li>
4375 <li>Reset button in PCA window to return dimensions to
4377 <li>Allow seqspace or Jalview variant of alignment PCA
4379 <li>PCA with either nucleic acid and protein substitution
4381 <li>Allow windows containing HTML reports to be exported
4383 <li>Interactive display and editing of RNA secondary
4384 structure contacts</li>
4385 <li>RNA Helix Alignment Colouring</li>
4386 <li>RNA base pair logo consensus</li>
4387 <li>Parse sequence associated secondary structure
4388 information in Stockholm files</li>
4389 <li>HTML Export database accessions and annotation
4390 information presented in tooltip for sequences</li>
4391 <li>Import secondary structure from LOCARNA clustalw
4392 style RNA alignment files</li>
4393 <li>import and visualise T-COFFEE quality scores for an
4395 <li>'colour by annotation' per sequence option to
4396 shade each sequence according to its associated alignment
4398 <li>New Jalview Logo</li>
4399 </ul> <em>Documentation and Development</em>
4401 <li>documentation for score matrices used in Jalview</li>
4402 <li>New Website!</li>
4404 <td><em>Application</em>
4406 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
4407 wsdbfetch REST service</li>
4408 <li>Stop windows being moved outside desktop on OSX</li>
4409 <li>Filetype associations not installed for webstart
4411 <li>Jalview does not always retrieve progress of a JABAWS
4412 job execution in full once it is complete</li>
4413 <li>revise SHMR RSBS definition to ensure alignment is
4414 uploaded via ali_file parameter</li>
4415 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
4416 <li>View all structures superposed fails with exception</li>
4417 <li>Jnet job queues forever if a very short sequence is
4418 submitted for prediction</li>
4419 <li>Cut and paste menu not opened when mouse clicked on
4421 <li>Putting fractional value into integer text box in
4422 alignment parameter dialog causes Jalview to hang</li>
4423 <li>Structure view highlighting doesn't work on
4425 <li>View all structures fails with exception shown in
4427 <li>Characters in filename associated with PDBEntry not
4428 escaped in a platform independent way</li>
4429 <li>Jalview desktop fails to launch with exception when
4431 <li>Tree calculation reports 'you must have 2 or more
4432 sequences selected' when selection is empty</li>
4433 <li>Jalview desktop fails to launch with jar signature
4434 failure when java web start temporary file caching is
4436 <li>DAS Sequence retrieval with range qualification
4437 results in sequence xref which includes range qualification</li>
4438 <li>Errors during processing of command line arguments
4439 cause progress bar (JAL-898) to be removed</li>
4440 <li>Replace comma for semi-colon option not disabled for
4441 DAS sources in sequence fetcher</li>
4442 <li>Cannot close news reader when JABAWS server warning
4443 dialog is shown</li>
4444 <li>Option widgets not updated to reflect user settings</li>
4445 <li>Edited sequence not submitted to web service</li>
4446 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
4447 <li>InstallAnywhere installer doesn't unpack and run
4448 on OSX Mountain Lion</li>
4449 <li>Annotation panel not given a scroll bar when
4450 sequences with alignment annotation are pasted into the
4452 <li>Sequence associated annotation rows not associated
4453 when loaded from Jalview project</li>
4454 <li>Browser launch fails with NPE on java 1.7</li>
4455 <li>JABAWS alignment marked as finished when job was
4456 cancelled or job failed due to invalid input</li>
4457 <li>NPE with v2.7 example when clicking on Tree
4458 associated with all views</li>
4459 <li>Exceptions when copy/paste sequences with grouped
4460 annotation rows to new window</li>
4461 </ul> <em>Applet</em>
4463 <li>Sequence features are momentarily displayed before
4464 they are hidden using hidefeaturegroups applet parameter</li>
4465 <li>loading features via javascript API automatically
4466 enables feature display</li>
4467 <li>scrollToColumnIn javascript API method doesn't
4469 </ul> <em>General</em>
4471 <li>Redundancy removal fails for rna alignment</li>
4472 <li>PCA calculation fails when sequence has been selected
4473 and then deselected</li>
4474 <li>PCA window shows grey box when first opened on OSX</li>
4475 <li>Letters coloured pink in sequence logo when alignment
4476 coloured with clustalx</li>
4477 <li>Choosing fonts without letter symbols defined causes
4478 exceptions and redraw errors</li>
4479 <li>Initial PCA plot view is not same as manually
4480 reconfigured view</li>
4481 <li>Grouped annotation graph label has incorrect line
4483 <li>Grouped annotation graph label display is corrupted
4484 for lots of labels</li>
4489 <div align="center">
4490 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
4493 <td><em>Application</em>
4495 <li>Jalview Desktop News Reader</li>
4496 <li>Tweaked default layout of web services menu</li>
4497 <li>View/alignment association menu to enable user to
4498 easily specify which alignment a multi-structure view takes
4499 its colours/correspondences from</li>
4500 <li>Allow properties file location to be specified as URL</li>
4501 <li>Extend Jalview project to preserve associations
4502 between many alignment views and a single Jmol display</li>
4503 <li>Store annotation row height in Jalview project file</li>
4504 <li>Annotation row column label formatting attributes
4505 stored in project file</li>
4506 <li>Annotation row order for auto-calculated annotation
4507 rows preserved in Jalview project file</li>
4508 <li>Visual progress indication when Jalview state is
4509 saved using Desktop window menu</li>
4510 <li>Visual indication that command line arguments are
4511 still being processed</li>
4512 <li>Groovy script execution from URL</li>
4513 <li>Colour by annotation default min and max colours in
4515 <li>Automatically associate PDB files dragged onto an
4516 alignment with sequences that have high similarity and
4518 <li>Update JGoogleAnalytics to latest release (0.3)</li>
4519 <li>'view structures' option to open many
4520 structures in same window</li>
4521 <li>Sort associated views menu option for tree panel</li>
4522 <li>Group all JABA and non-JABA services for a particular
4523 analysis function in its own submenu</li>
4524 </ul> <em>Applet</em>
4526 <li>Userdefined and autogenerated annotation rows for
4528 <li>Adjustment of alignment annotation pane height</li>
4529 <li>Annotation scrollbar for annotation panel</li>
4530 <li>Drag to reorder annotation rows in annotation panel</li>
4531 <li>'automaticScrolling' parameter</li>
4532 <li>Allow sequences with partial ID string matches to be
4533 annotated from GFF/Jalview features files</li>
4534 <li>Sequence logo annotation row in applet</li>
4535 <li>Absolute paths relative to host server in applet
4536 parameters are treated as such</li>
4537 <li>New in the JalviewLite javascript API:
4539 <li>JalviewLite.js javascript library</li>
4540 <li>Javascript callbacks for
4542 <li>Applet initialisation</li>
4543 <li>Sequence/alignment mouse-overs and selections</li>
4546 <li>scrollTo row and column alignment scrolling
4548 <li>Select sequence/alignment regions from javascript</li>
4549 <li>javascript structure viewer harness to pass
4550 messages between Jmol and Jalview when running as
4551 distinct applets</li>
4552 <li>sortBy method</li>
4553 <li>Set of applet and application examples shipped
4554 with documentation</li>
4555 <li>New example to demonstrate JalviewLite and Jmol
4556 javascript message exchange</li>
4558 </ul> <em>General</em>
4560 <li>Enable Jmol displays to be associated with multiple
4561 multiple alignments</li>
4562 <li>Option to automatically sort alignment with new tree</li>
4563 <li>User configurable link to enable redirects to a
4564 www.Jalview.org mirror</li>
4565 <li>Jmol colours option for Jmol displays</li>
4566 <li>Configurable newline string when writing alignment
4567 and other flat files</li>
4568 <li>Allow alignment annotation description lines to
4569 contain html tags</li>
4570 </ul> <em>Documentation and Development</em>
4572 <li>Add groovy test harness for bulk load testing to
4574 <li>Groovy script to load and align a set of sequences
4575 using a web service before displaying the result in the
4576 Jalview desktop</li>
4577 <li>Restructured javascript and applet api documentation</li>
4578 <li>Ant target to publish example html files with applet
4580 <li>Netbeans project for building Jalview from source</li>
4581 <li>ant task to create online javadoc for Jalview source</li>
4583 <td><em>Application</em>
4585 <li>User defined colourscheme throws exception when
4586 current built in colourscheme is saved as new scheme</li>
4587 <li>AlignFrame->Save in application pops up save
4588 dialog for valid filename/format</li>
4589 <li>Cannot view associated structure for UniProt sequence</li>
4590 <li>PDB file association breaks for UniProt sequence
4592 <li>Associate PDB from file dialog does not tell you
4593 which sequence is to be associated with the file</li>
4594 <li>Find All raises null pointer exception when query
4595 only matches sequence IDs</li>
4596 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4597 <li>Jalview project with Jmol views created with Jalview
4598 2.4 cannot be loaded</li>
4599 <li>Filetype associations not installed for webstart
4601 <li>Two or more chains in a single PDB file associated
4602 with sequences in different alignments do not get coloured
4603 by their associated sequence</li>
4604 <li>Visibility status of autocalculated annotation row
4605 not preserved when project is loaded</li>
4606 <li>Annotation row height and visibility attributes not
4607 stored in Jalview project</li>
4608 <li>Tree bootstraps are not preserved when saved as a
4609 Jalview project</li>
4610 <li>Envision2 workflow tooltips are corrupted</li>
4611 <li>Enabling show group conservation also enables colour
4612 by conservation</li>
4613 <li>Duplicate group associated conservation or consensus
4614 created on new view</li>
4615 <li>Annotation scrollbar not displayed after 'show
4616 all hidden annotation rows' option selected</li>
4617 <li>Alignment quality not updated after alignment
4618 annotation row is hidden then shown</li>
4619 <li>Preserve colouring of structures coloured by
4620 sequences in pre Jalview 2.7 projects</li>
4621 <li>Web service job parameter dialog is not laid out
4623 <li>Web services menu not refreshed after 'reset
4624 services' button is pressed in preferences</li>
4625 <li>Annotation off by one in Jalview v2_3 example project</li>
4626 <li>Structures imported from file and saved in project
4627 get name like jalview_pdb1234.txt when reloaded</li>
4628 <li>Jalview does not always retrieve progress of a JABAWS
4629 job execution in full once it is complete</li>
4630 </ul> <em>Applet</em>
4632 <li>Alignment height set incorrectly when lots of
4633 annotation rows are displayed</li>
4634 <li>Relative URLs in feature HTML text not resolved to
4636 <li>View follows highlighting does not work for positions
4638 <li><= shown as = in tooltip</li>
4639 <li>Export features raises exception when no features
4641 <li>Separator string used for serialising lists of IDs
4642 for javascript api is modified when separator string
4643 provided as parameter</li>
4644 <li>Null pointer exception when selecting tree leaves for
4645 alignment with no existing selection</li>
4646 <li>Relative URLs for datasources assumed to be relative
4647 to applet's codebase</li>
4648 <li>Status bar not updated after finished searching and
4649 search wraps around to first result</li>
4650 <li>StructureSelectionManager instance shared between
4651 several Jalview applets causes race conditions and memory
4653 <li>Hover tooltip and mouseover of position on structure
4654 not sent from Jmol in applet</li>
4655 <li>Certain sequences of javascript method calls to
4656 applet API fatally hang browser</li>
4657 </ul> <em>General</em>
4659 <li>View follows structure mouseover scrolls beyond
4660 position with wrapped view and hidden regions</li>
4661 <li>Find sequence position moves to wrong residue
4662 with/without hidden columns</li>
4663 <li>Sequence length given in alignment properties window
4665 <li>InvalidNumberFormat exceptions thrown when trying to
4666 import PDB like structure files</li>
4667 <li>Positional search results are only highlighted
4668 between user-supplied sequence start/end bounds</li>
4669 <li>End attribute of sequence is not validated</li>
4670 <li>Find dialog only finds first sequence containing a
4671 given sequence position</li>
4672 <li>Sequence numbering not preserved in MSF alignment
4674 <li>Jalview PDB file reader does not extract sequence
4675 from nucleotide chains correctly</li>
4676 <li>Structure colours not updated when tree partition
4677 changed in alignment</li>
4678 <li>Sequence associated secondary structure not correctly
4679 parsed in interleaved stockholm</li>
4680 <li>Colour by annotation dialog does not restore current
4682 <li>Hiding (nearly) all sequences doesn't work
4684 <li>Sequences containing lowercase letters are not
4685 properly associated with their pdb files</li>
4686 </ul> <em>Documentation and Development</em>
4688 <li>schemas/JalviewWsParamSet.xsd corrupted by
4689 ApplyCopyright tool</li>
4694 <div align="center">
4695 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4698 <td><em>Application</em>
4700 <li>New warning dialog when the Jalview Desktop cannot
4701 contact web services</li>
4702 <li>JABA service parameters for a preset are shown in
4703 service job window</li>
4704 <li>JABA Service menu entries reworded</li>
4708 <li>Modeller PIR IO broken - cannot correctly import a
4709 pir file emitted by Jalview</li>
4710 <li>Existing feature settings transferred to new
4711 alignment view created from cut'n'paste</li>
4712 <li>Improved test for mixed amino/nucleotide chains when
4713 parsing PDB files</li>
4714 <li>Consensus and conservation annotation rows
4715 occasionally become blank for all new windows</li>
4716 <li>Exception raised when right clicking above sequences
4717 in wrapped view mode</li>
4718 </ul> <em>Application</em>
4720 <li>multiple multiply aligned structure views cause cpu
4721 usage to hit 100% and computer to hang</li>
4722 <li>Web Service parameter layout breaks for long user
4723 parameter names</li>
4724 <li>Jaba service discovery hangs desktop if Jaba server
4731 <div align="center">
4732 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4735 <td><em>Application</em>
4737 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4738 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4741 <li>Web Services preference tab</li>
4742 <li>Analysis parameters dialog box and user defined
4744 <li>Improved speed and layout of Envision2 service menu</li>
4745 <li>Superpose structures using associated sequence
4747 <li>Export coordinates and projection as CSV from PCA
4749 </ul> <em>Applet</em>
4751 <li>enable javascript: execution by the applet via the
4752 link out mechanism</li>
4753 </ul> <em>Other</em>
4755 <li>Updated the Jmol Jalview interface to work with Jmol
4757 <li>The Jalview Desktop and JalviewLite applet now
4758 require Java 1.5</li>
4759 <li>Allow Jalview feature colour specification for GFF
4760 sequence annotation files</li>
4761 <li>New 'colour by label' keword in Jalview feature file
4762 type colour specification</li>
4763 <li>New Jalview Desktop Groovy API method that allows a
4764 script to check if it being run in an interactive session or
4765 in a batch operation from the Jalview command line</li>
4769 <li>clustalx colourscheme colours Ds preferentially when
4770 both D+E are present in over 50% of the column</li>
4771 </ul> <em>Application</em>
4773 <li>typo in AlignmentFrame->View->Hide->all but
4774 selected Regions menu item</li>
4775 <li>sequence fetcher replaces ',' for ';' when the ',' is
4776 part of a valid accession ID</li>
4777 <li>fatal OOM if object retrieved by sequence fetcher
4778 runs out of memory</li>
4779 <li>unhandled Out of Memory Error when viewing pca
4780 analysis results</li>
4781 <li>InstallAnywhere builds fail to launch on OS X java
4782 10.5 update 4 (due to apple Java 1.6 update)</li>
4783 <li>Installanywhere Jalview silently fails to launch</li>
4784 </ul> <em>Applet</em>
4786 <li>Jalview.getFeatureGroups() raises an
4787 ArrayIndexOutOfBoundsException if no feature groups are
4794 <div align="center">
4795 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4801 <li>Alignment prettyprinter doesn't cope with long
4803 <li>clustalx colourscheme colours Ds preferentially when
4804 both D+E are present in over 50% of the column</li>
4805 <li>nucleic acid structures retrieved from PDB do not
4806 import correctly</li>
4807 <li>More columns get selected than were clicked on when a
4808 number of columns are hidden</li>
4809 <li>annotation label popup menu not providing correct
4810 add/hide/show options when rows are hidden or none are
4812 <li>Stockholm format shown in list of readable formats,
4813 and parser copes better with alignments from RFAM.</li>
4814 <li>CSV output of consensus only includes the percentage
4815 of all symbols if sequence logo display is enabled</li>
4817 </ul> <em>Applet</em>
4819 <li>annotation panel disappears when annotation is
4821 </ul> <em>Application</em>
4823 <li>Alignment view not redrawn properly when new
4824 alignment opened where annotation panel is visible but no
4825 annotations are present on alignment</li>
4826 <li>pasted region containing hidden columns is
4827 incorrectly displayed in new alignment window</li>
4828 <li>Jalview slow to complete operations when stdout is
4829 flooded (fix is to close the Jalview console)</li>
4830 <li>typo in AlignmentFrame->View->Hide->all but
4831 selected Rregions menu item.</li>
4832 <li>inconsistent group submenu and Format submenu entry
4833 'Un' or 'Non'conserved</li>
4834 <li>Sequence feature settings are being shared by
4835 multiple distinct alignments</li>
4836 <li>group annotation not recreated when tree partition is
4838 <li>double click on group annotation to select sequences
4839 does not propagate to associated trees</li>
4840 <li>Mac OSX specific issues:
4842 <li>exception raised when mouse clicked on desktop
4843 window background</li>
4844 <li>Desktop menu placed on menu bar and application
4845 name set correctly</li>
4846 <li>sequence feature settings not wide enough for the
4847 save feature colourscheme button</li>
4856 <div align="center">
4857 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4860 <td><em>New Capabilities</em>
4862 <li>URL links generated from description line for
4863 regular-expression based URL links (applet and application)
4866 <li>Non-positional feature URL links are shown in link
4868 <li>Linked viewing of nucleic acid sequences and
4870 <li>Automatic Scrolling option in View menu to display
4871 the currently highlighted region of an alignment.</li>
4872 <li>Order an alignment by sequence length, or using the
4873 average score or total feature count for each sequence.</li>
4874 <li>Shading features by score or associated description</li>
4875 <li>Subdivide alignment and groups based on identity of
4876 selected subsequence (Make Groups from Selection).</li>
4877 <li>New hide/show options including Shift+Control+H to
4878 hide everything but the currently selected region.</li>
4879 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4880 </ul> <em>Application</em>
4882 <li>Fetch DB References capabilities and UI expanded to
4883 support retrieval from DAS sequence sources</li>
4884 <li>Local DAS Sequence sources can be added via the
4885 command line or via the Add local source dialog box.</li>
4886 <li>DAS Dbref and DbxRef feature types are parsed as
4887 database references and protein_name is parsed as
4888 description line (BioSapiens terms).</li>
4889 <li>Enable or disable non-positional feature and database
4890 references in sequence ID tooltip from View menu in
4892 <!-- <li>New hidden columns and rows and representatives capabilities
4893 in annotations file (in progress - not yet fully implemented)</li> -->
4894 <li>Group-associated consensus, sequence logos and
4895 conservation plots</li>
4896 <li>Symbol distributions for each column can be exported
4897 and visualized as sequence logos</li>
4898 <li>Optionally scale multi-character column labels to fit
4899 within each column of annotation row<!-- todo for applet -->
4901 <li>Optional automatic sort of associated alignment view
4902 when a new tree is opened.</li>
4903 <li>Jalview Java Console</li>
4904 <li>Better placement of desktop window when moving
4905 between different screens.</li>
4906 <li>New preference items for sequence ID tooltip and
4907 consensus annotation</li>
4908 <li>Client to submit sequences and IDs to Envision2
4910 <li><em>Vamsas Capabilities</em>
4912 <li>Improved VAMSAS synchronization (Jalview archive
4913 used to preserve views, structures, and tree display
4915 <li>Import of vamsas documents from disk or URL via
4917 <li>Sharing of selected regions between views and
4918 with other VAMSAS applications (Experimental feature!)</li>
4919 <li>Updated API to VAMSAS version 0.2</li>
4921 </ul> <em>Applet</em>
4923 <li>Middle button resizes annotation row height</li>
4926 <li>sortByTree (true/false) - automatically sort the
4927 associated alignment view by the tree when a new tree is
4929 <li>showTreeBootstraps (true/false) - show or hide
4930 branch bootstraps (default is to show them if available)</li>
4931 <li>showTreeDistances (true/false) - show or hide
4932 branch lengths (default is to show them if available)</li>
4933 <li>showUnlinkedTreeNodes (true/false) - indicate if
4934 unassociated nodes should be highlighted in the tree
4936 <li>heightScale and widthScale (1.0 or more) -
4937 increase the height or width of a cell in the alignment
4938 grid relative to the current font size.</li>
4941 <li>Non-positional features displayed in sequence ID
4943 </ul> <em>Other</em>
4945 <li>Features format: graduated colour definitions and
4946 specification of feature scores</li>
4947 <li>Alignment Annotations format: new keywords for group
4948 associated annotation (GROUP_REF) and annotation row display
4949 properties (ROW_PROPERTIES)</li>
4950 <li>XML formats extended to support graduated feature
4951 colourschemes, group associated annotation, and profile
4952 visualization settings.</li></td>
4955 <li>Source field in GFF files parsed as feature source
4956 rather than description</li>
4957 <li>Non-positional features are now included in sequence
4958 feature and gff files (controlled via non-positional feature
4959 visibility in tooltip).</li>
4960 <li>URL links generated for all feature links (bugfix)</li>
4961 <li>Added URL embedding instructions to features file
4963 <li>Codons containing ambiguous nucleotides translated as
4964 'X' in peptide product</li>
4965 <li>Match case switch in find dialog box works for both
4966 sequence ID and sequence string and query strings do not
4967 have to be in upper case to match case-insensitively.</li>
4968 <li>AMSA files only contain first column of
4969 multi-character column annotation labels</li>
4970 <li>Jalview Annotation File generation/parsing consistent
4971 with documentation (e.g. Stockholm annotation can be
4972 exported and re-imported)</li>
4973 <li>PDB files without embedded PDB IDs given a friendly
4975 <li>Find incrementally searches ID string matches as well
4976 as subsequence matches, and correctly reports total number
4980 <li>Better handling of exceptions during sequence
4982 <li>Dasobert generated non-positional feature URL
4983 link text excludes the start_end suffix</li>
4984 <li>DAS feature and source retrieval buttons disabled
4985 when fetch or registry operations in progress.</li>
4986 <li>PDB files retrieved from URLs are cached properly</li>
4987 <li>Sequence description lines properly shared via
4989 <li>Sequence fetcher fetches multiple records for all
4991 <li>Ensured that command line das feature retrieval
4992 completes before alignment figures are generated.</li>
4993 <li>Reduced time taken when opening file browser for
4995 <li>isAligned check prior to calculating tree, PCA or
4996 submitting an MSA to JNet now excludes hidden sequences.</li>
4997 <li>User defined group colours properly recovered
4998 from Jalview projects.</li>
5007 <div align="center">
5008 <strong>2.4.0.b2</strong><br> 28/10/2009
5013 <li>Experimental support for google analytics usage
5015 <li>Jalview privacy settings (user preferences and docs).</li>
5020 <li>Race condition in applet preventing startup in
5022 <li>Exception when feature created from selection beyond
5023 length of sequence.</li>
5024 <li>Allow synthetic PDB files to be imported gracefully</li>
5025 <li>Sequence associated annotation rows associate with
5026 all sequences with a given id</li>
5027 <li>Find function matches case-insensitively for sequence
5028 ID string searches</li>
5029 <li>Non-standard characters do not cause pairwise
5030 alignment to fail with exception</li>
5031 </ul> <em>Application Issues</em>
5033 <li>Sequences are now validated against EMBL database</li>
5034 <li>Sequence fetcher fetches multiple records for all
5036 </ul> <em>InstallAnywhere Issues</em>
5038 <li>Dock icon works for Mac OS X java (Mac 1.6 update
5039 issue with installAnywhere mechanism)</li>
5040 <li>Command line launching of JARs from InstallAnywhere
5041 version (java class versioning error fixed)</li>
5048 <div align="center">
5049 <strong>2.4</strong><br> 27/8/2008
5052 <td><em>User Interface</em>
5054 <li>Linked highlighting of codon and amino acid from
5055 translation and protein products</li>
5056 <li>Linked highlighting of structure associated with
5057 residue mapping to codon position</li>
5058 <li>Sequence Fetcher provides example accession numbers
5059 and 'clear' button</li>
5060 <li>MemoryMonitor added as an option under Desktop's
5062 <li>Extract score function to parse whitespace separated
5063 numeric data in description line</li>
5064 <li>Column labels in alignment annotation can be centred.</li>
5065 <li>Tooltip for sequence associated annotation give name
5067 </ul> <em>Web Services and URL fetching</em>
5069 <li>JPred3 web service</li>
5070 <li>Prototype sequence search client (no public services
5072 <li>Fetch either seed alignment or full alignment from
5074 <li>URL Links created for matching database cross
5075 references as well as sequence ID</li>
5076 <li>URL Links can be created using regular-expressions</li>
5077 </ul> <em>Sequence Database Connectivity</em>
5079 <li>Retrieval of cross-referenced sequences from other
5081 <li>Generalised database reference retrieval and
5082 validation to all fetchable databases</li>
5083 <li>Fetch sequences from DAS sources supporting the
5084 sequence command</li>
5085 </ul> <em>Import and Export</em>
5086 <li>export annotation rows as CSV for spreadsheet import</li>
5087 <li>Jalview projects record alignment dataset associations,
5088 EMBL products, and cDNA sequence mappings</li>
5089 <li>Sequence Group colour can be specified in Annotation
5091 <li>Ad-hoc colouring of group in Annotation File using RGB
5092 triplet as name of colourscheme</li>
5093 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
5095 <li>treenode binding for VAMSAS tree exchange</li>
5096 <li>local editing and update of sequences in VAMSAS
5097 alignments (experimental)</li>
5098 <li>Create new or select existing session to join</li>
5099 <li>load and save of vamsas documents</li>
5100 </ul> <em>Application command line</em>
5102 <li>-tree parameter to open trees (introduced for passing
5104 <li>-fetchfrom command line argument to specify nicknames
5105 of DAS servers to query for alignment features</li>
5106 <li>-dasserver command line argument to add new servers
5107 that are also automatically queried for features</li>
5108 <li>-groovy command line argument executes a given groovy
5109 script after all input data has been loaded and parsed</li>
5110 </ul> <em>Applet-Application data exchange</em>
5112 <li>Trees passed as applet parameters can be passed to
5113 application (when using "View in full
5114 application")</li>
5115 </ul> <em>Applet Parameters</em>
5117 <li>feature group display control parameter</li>
5118 <li>debug parameter</li>
5119 <li>showbutton parameter</li>
5120 </ul> <em>Applet API methods</em>
5122 <li>newView public method</li>
5123 <li>Window (current view) specific get/set public methods</li>
5124 <li>Feature display control methods</li>
5125 <li>get list of currently selected sequences</li>
5126 </ul> <em>New Jalview distribution features</em>
5128 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
5129 <li>RELEASE file gives build properties for the latest
5130 Jalview release.</li>
5131 <li>Java 1.1 Applet build made easier and donotobfuscate
5132 property controls execution of obfuscator</li>
5133 <li>Build target for generating source distribution</li>
5134 <li>Debug flag for javacc</li>
5135 <li>.jalview_properties file is documented (slightly) in
5136 jalview.bin.Cache</li>
5137 <li>Continuous Build Integration for stable and
5138 development version of Application, Applet and source
5143 <li>selected region output includes visible annotations
5144 (for certain formats)</li>
5145 <li>edit label/displaychar contains existing label/char
5147 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
5148 <li>shorter peptide product names from EMBL records</li>
5149 <li>Newick string generator makes compact representations</li>
5150 <li>bootstrap values parsed correctly for tree files with
5152 <li>pathological filechooser bug avoided by not allowing
5153 filenames containing a ':'</li>
5154 <li>Fixed exception when parsing GFF files containing
5155 global sequence features</li>
5156 <li>Alignment datasets are finalized only when number of
5157 references from alignment sequences goes to zero</li>
5158 <li>Close of tree branch colour box without colour
5159 selection causes cascading exceptions</li>
5160 <li>occasional negative imgwidth exceptions</li>
5161 <li>better reporting of non-fatal warnings to user when
5162 file parsing fails.</li>
5163 <li>Save works when Jalview project is default format</li>
5164 <li>Save as dialog opened if current alignment format is
5165 not a valid output format</li>
5166 <li>UniProt canonical names introduced for both das and
5168 <li>Histidine should be midblue (not pink!) in Zappo</li>
5169 <li>error messages passed up and output when data read
5171 <li>edit undo recovers previous dataset sequence when
5172 sequence is edited</li>
5173 <li>allow PDB files without pdb ID HEADER lines (like
5174 those generated by MODELLER) to be read in properly</li>
5175 <li>allow reading of JPred concise files as a normal
5177 <li>Stockholm annotation parsing and alignment properties
5178 import fixed for PFAM records</li>
5179 <li>Structure view windows have correct name in Desktop
5181 <li>annotation consisting of sequence associated scores
5182 can be read and written correctly to annotation file</li>
5183 <li>Aligned cDNA translation to aligned peptide works
5185 <li>Fixed display of hidden sequence markers and
5186 non-italic font for representatives in Applet</li>
5187 <li>Applet Menus are always embedded in applet window on
5189 <li>Newly shown features appear at top of stack (in
5191 <li>Annotations added via parameter not drawn properly
5192 due to null pointer exceptions</li>
5193 <li>Secondary structure lines are drawn starting from
5194 first column of alignment</li>
5195 <li>UniProt XML import updated for new schema release in
5197 <li>Sequence feature to sequence ID match for Features
5198 file is case-insensitive</li>
5199 <li>Sequence features read from Features file appended to
5200 all sequences with matching IDs</li>
5201 <li>PDB structure coloured correctly for associated views
5202 containing a sub-sequence</li>
5203 <li>PDB files can be retrieved by applet from Jar files</li>
5204 <li>feature and annotation file applet parameters
5205 referring to different directories are retrieved correctly</li>
5206 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
5207 <li>Fixed application hang whilst waiting for
5208 splash-screen version check to complete</li>
5209 <li>Applet properly URLencodes input parameter values
5210 when passing them to the launchApp service</li>
5211 <li>display name and local features preserved in results
5212 retrieved from web service</li>
5213 <li>Visual delay indication for sequence retrieval and
5214 sequence fetcher initialisation</li>
5215 <li>updated Application to use DAS 1.53e version of
5216 dasobert DAS client</li>
5217 <li>Re-instated Full AMSA support and .amsa file
5219 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
5227 <div align="center">
5228 <strong>2.3</strong><br> 9/5/07
5233 <li>Jmol 11.0.2 integration</li>
5234 <li>PDB views stored in Jalview XML files</li>
5235 <li>Slide sequences</li>
5236 <li>Edit sequence in place</li>
5237 <li>EMBL CDS features</li>
5238 <li>DAS Feature mapping</li>
5239 <li>Feature ordering</li>
5240 <li>Alignment Properties</li>
5241 <li>Annotation Scores</li>
5242 <li>Sort by scores</li>
5243 <li>Feature/annotation editing in applet</li>
5248 <li>Headless state operation in 2.2.1</li>
5249 <li>Incorrect and unstable DNA pairwise alignment</li>
5250 <li>Cut and paste of sequences with annotation</li>
5251 <li>Feature group display state in XML</li>
5252 <li>Feature ordering in XML</li>
5253 <li>blc file iteration selection using filename # suffix</li>
5254 <li>Stockholm alignment properties</li>
5255 <li>Stockhom alignment secondary structure annotation</li>
5256 <li>2.2.1 applet had no feature transparency</li>
5257 <li>Number pad keys can be used in cursor mode</li>
5258 <li>Structure Viewer mirror image resolved</li>
5265 <div align="center">
5266 <strong>2.2.1</strong><br> 12/2/07
5271 <li>Non standard characters can be read and displayed
5272 <li>Annotations/Features can be imported/exported to the
5274 <li>Applet allows editing of sequence/annotation/group
5275 name & description
5276 <li>Preference setting to display sequence name in
5278 <li>Annotation file format extended to allow
5279 Sequence_groups to be defined
5280 <li>Default opening of alignment overview panel can be
5281 specified in preferences
5282 <li>PDB residue numbering annotation added to associated
5288 <li>Applet crash under certain Linux OS with Java 1.6
5290 <li>Annotation file export / import bugs fixed
5291 <li>PNG / EPS image output bugs fixed
5297 <div align="center">
5298 <strong>2.2</strong><br> 27/11/06
5303 <li>Multiple views on alignment
5304 <li>Sequence feature editing
5305 <li>"Reload" alignment
5306 <li>"Save" to current filename
5307 <li>Background dependent text colour
5308 <li>Right align sequence ids
5309 <li>User-defined lower case residue colours
5312 <li>Menu item accelerator keys
5313 <li>Control-V pastes to current alignment
5314 <li>Cancel button for DAS Feature Fetching
5315 <li>PCA and PDB Viewers zoom via mouse roller
5316 <li>User-defined sub-tree colours and sub-tree selection
5319 <li>'New Window' button on the 'Output to Text box'
5324 <li>New memory efficient Undo/Redo System
5325 <li>Optimised symbol lookups and conservation/consensus
5327 <li>Region Conservation/Consensus recalculated after
5329 <li>Fixed Remove Empty Columns Bug (empty columns at end
5331 <li>Slowed DAS Feature Fetching for increased robustness.
5334 <li>Made angle brackets in ASCII feature descriptions
5336 <li>Re-instated Zoom function for PCA
5337 <li>Sequence descriptions conserved in web service
5339 <li>UniProt ID discoverer uses any word separated by
5341 <li>WsDbFetch query/result association resolved
5342 <li>Tree leaf to sequence mapping improved
5343 <li>Smooth fonts switch moved to FontChooser dialog box.
5351 <div align="center">
5352 <strong>2.1.1</strong><br> 12/9/06
5357 <li>Copy consensus sequence to clipboard</li>
5362 <li>Image output - rightmost residues are rendered if
5363 sequence id panel has been resized</li>
5364 <li>Image output - all offscreen group boundaries are
5366 <li>Annotation files with sequence references - all
5367 elements in file are relative to sequence position</li>
5368 <li>Mac Applet users can use Alt key for group editing</li>
5374 <div align="center">
5375 <strong>2.1</strong><br> 22/8/06
5380 <li>MAFFT Multiple Alignment in default Web Service list</li>
5381 <li>DAS Feature fetching</li>
5382 <li>Hide sequences and columns</li>
5383 <li>Export Annotations and Features</li>
5384 <li>GFF file reading / writing</li>
5385 <li>Associate structures with sequences from local PDB
5387 <li>Add sequences to exisiting alignment</li>
5388 <li>Recently opened files / URL lists</li>
5389 <li>Applet can launch the full application</li>
5390 <li>Applet has transparency for features (Java 1.2
5392 <li>Applet has user defined colours parameter</li>
5393 <li>Applet can load sequences from parameter
5394 "sequence<em>x</em>"
5400 <li>Redundancy Panel reinstalled in the Applet</li>
5401 <li>Monospaced font - EPS / rescaling bug fixed</li>
5402 <li>Annotation files with sequence references bug fixed</li>
5408 <div align="center">
5409 <strong>2.08.1</strong><br> 2/5/06
5414 <li>Change case of selected region from Popup menu</li>
5415 <li>Choose to match case when searching</li>
5416 <li>Middle mouse button and mouse movement can compress /
5417 expand the visible width and height of the alignment</li>
5422 <li>Annotation Panel displays complete JNet results</li>
5428 <div align="center">
5429 <strong>2.08b</strong><br> 18/4/06
5435 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
5436 <li>Righthand label on wrapped alignments shows correct
5443 <div align="center">
5444 <strong>2.08</strong><br> 10/4/06
5449 <li>Editing can be locked to the selection area</li>
5450 <li>Keyboard editing</li>
5451 <li>Create sequence features from searches</li>
5452 <li>Precalculated annotations can be loaded onto
5454 <li>Features file allows grouping of features</li>
5455 <li>Annotation Colouring scheme added</li>
5456 <li>Smooth fonts off by default - Faster rendering</li>
5457 <li>Choose to toggle Autocalculate Consensus On/Off</li>
5462 <li>Drag & Drop fixed on Linux</li>
5463 <li>Jalview Archive file faster to load/save, sequence
5464 descriptions saved.</li>
5470 <div align="center">
5471 <strong>2.07</strong><br> 12/12/05
5476 <li>PDB Structure Viewer enhanced</li>
5477 <li>Sequence Feature retrieval and display enhanced</li>
5478 <li>Choose to output sequence start-end after sequence
5479 name for file output</li>
5480 <li>Sequence Fetcher WSDBFetch@EBI</li>
5481 <li>Applet can read feature files, PDB files and can be
5482 used for HTML form input</li>
5487 <li>HTML output writes groups and features</li>
5488 <li>Group editing is Control and mouse click</li>
5489 <li>File IO bugs</li>
5495 <div align="center">
5496 <strong>2.06</strong><br> 28/9/05
5501 <li>View annotations in wrapped mode</li>
5502 <li>More options for PCA viewer</li>
5507 <li>GUI bugs resolved</li>
5508 <li>Runs with -nodisplay from command line</li>
5514 <div align="center">
5515 <strong>2.05b</strong><br> 15/9/05
5520 <li>Choose EPS export as lineart or text</li>
5521 <li>Jar files are executable</li>
5522 <li>Can read in Uracil - maps to unknown residue</li>
5527 <li>Known OutOfMemory errors give warning message</li>
5528 <li>Overview window calculated more efficiently</li>
5529 <li>Several GUI bugs resolved</li>
5535 <div align="center">
5536 <strong>2.05</strong><br> 30/8/05
5541 <li>Edit and annotate in "Wrapped" view</li>
5546 <li>Several GUI bugs resolved</li>
5552 <div align="center">
5553 <strong>2.04</strong><br> 24/8/05
5558 <li>Hold down mouse wheel & scroll to change font
5564 <li>Improved JPred client reliability</li>
5565 <li>Improved loading of Jalview files</li>
5571 <div align="center">
5572 <strong>2.03</strong><br> 18/8/05
5577 <li>Set Proxy server name and port in preferences</li>
5578 <li>Multiple URL links from sequence ids</li>
5579 <li>User Defined Colours can have a scheme name and added
5581 <li>Choose to ignore gaps in consensus calculation</li>
5582 <li>Unix users can set default web browser</li>
5583 <li>Runs without GUI for batch processing</li>
5584 <li>Dynamically generated Web Service Menus</li>
5589 <li>InstallAnywhere download for Sparc Solaris</li>
5595 <div align="center">
5596 <strong>2.02</strong><br> 18/7/05
5602 <li>Copy & Paste order of sequences maintains
5603 alignment order.</li>
5609 <div align="center">
5610 <strong>2.01</strong><br> 12/7/05
5615 <li>Use delete key for deleting selection.</li>
5616 <li>Use Mouse wheel to scroll sequences.</li>
5617 <li>Help file updated to describe how to add alignment
5619 <li>Version and build date written to build properties
5621 <li>InstallAnywhere installation will check for updates
5622 at launch of Jalview.</li>
5627 <li>Delete gaps bug fixed.</li>
5628 <li>FileChooser sorts columns.</li>
5629 <li>Can remove groups one by one.</li>
5630 <li>Filechooser icons installed.</li>
5631 <li>Finder ignores return character when searching.
5632 Return key will initiate a search.<br>
5639 <div align="center">
5640 <strong>2.0</strong><br> 20/6/05
5645 <li>New codebase</li>