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">
68 <td align="left" valign="top">
71 <!-- JAL-3975 -->Residue selection using keyboard input
72 stops working after first "Create sequence feature"
75 <!-- JAL-3976 -->3D Structure chooser fails to select
76 structures from 3D-beacons and pops up a 'null' dialog
79 <!-- JAL-3886 -->Pfam and Rfam alignment retrieval as
80 gzipped stockholm doesn't work on JalviewJS build of 2.11.2
83 <!-- JAL-3973 -->Cannot build Jalview 2.11.2.0 via gradle
84 from its source tarball
86 </ul> <em>New Known Issues</em>
89 <!-- JAL-3873 -->Colour by->all views doesn't allow
90 colouring same structure from different views (since
94 Sequence ID tooltip not showing during long running
95 retrieval/crossref operations (affects at least 2.11.1
99 <!-- JAL-3972 -->Java 11 Only: Jalview 2.11.2.0 OSX install
100 not working due to VAqua requiring
101 sun.awt.image.MultiResolutionImage
104 <!-- JAL-3981 -->Sequence Details can take a long time to be
105 displayed for heavily annotated sequences (all versions)
111 <td width="60" align="center" nowrap><strong><a
112 id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.0">.0</a><br />
113 <em>10/03/2022</em></strong></td>
114 <td align="left" valign="top">
117 <!-- JAL-3616 JAL-3551 JAL-2322 -->Support for viewing 3D
118 structures with ChimeraX and Pymol in addition to Jmol and
122 <!-- JAL-3829 -->Discover 3D structure data for sequences
123 with Uniprot references via 3D-Beacons
126 <!-- JAL-3391 -->Rank and select available structures for
127 Uniprot sequences according to number of residues in
128 structure mapped to positions involved in the alignment
131 <!-- JAL-2226 -->Structure annotation rows for all mapped
132 chains in 3D structures are included in the 'Reference
133 Annotation' for a sequence
136 <!-- JAL-1260 -->Import Genbank and EMBL format flatfiles
139 <!-- JAL-3821 -->ENA record's mol_type honoured so RNA
140 molecules imported from ENA records are shown as RNA
142 <!-- JAL-3863 -->Support for Canonical Uniprot IDs
145 <!-- JAL-3503 -->New Preferences tab for adjusting Jalview's
146 memory settings at launch
149 <!-- JAL-3881 -->Sequence IDs split on '_' as well as other
150 non-alphanumerics when discovering database references with
154 <!-- JAL-3884 -->Suppressed harmless exceptions output to
155 Console whilst discovering database references for a
159 <!-- JAL-3204 -->Updated Jalview bindings for Uniprot XML
163 <!-- JAL-3926 -->Uniprot and PDBe autosearch option is
167 <!-- JAL-3144 -->Reverted to Jalview 'classic' drop-down
168 menu for selecting which database to fetch from in sequence
172 <!-- JAL-3018 -->Updated Ensembl REST Client compatibility
173 to 15.2 and revised model organism names (rat, xenopus,
174 dmelanogaster now rattus_norvegicus, xenopus_tropicalis,
175 drosophila_melanogaster)
178 <!-- JAL-3530 -->-nowebservicediscovery command line
179 argument to prevent automatic discovery of analysis
180 webservices on launch
183 <!-- JAL-3618 -->Allow 'App' directories to be opened when
184 locating Chimera, ChimeraX or Pymol binaries via filechooser
185 opened by double clicking the Structure Preferences' path
189 <!-- JAL-3632 JAL-3633 -->support for HTTP/S access via
190 proxies that require authentication
193 <!-- JAL-3103 -->New mechanism for opening URLs with system
194 default browser (works on OSX and Linux as well as Windows)
197 <!-- JAL-3871 JAL-3874 -->Upgraded bundled version of Jmol
201 <!-- JAL-3837 -->GPL license info on splash screen and About
204 </ul> <em>Jalview Native App</em>
207 <!-- JAL-3830 -->New command line launcher scripts (.sh,
208 .ps1, .bat) usable on macOS, Linux/Unix, Windows and
209 documentation in Help. Installer wizard has option to add
210 this to PATH, or link to it in your PATH.<br /> <em>This
211 is the recommended workaround for known issue about
212 working directory preservation when running native
213 application from command line. <!-- JAL-3523 -->
216 <li>Notarized MacOS installer for compliance with latest
217 OSX releases (Monterey)</li>
219 <!-- JAL-3805 -->Uninstaller application for old
220 (InstallAnywhere based) Jalview installations removed from
224 <!-- JAL-3608 -->Options to allow user to choose the (Swing)
225 Look and Feel (LaF) used by Jalview
228 <!-- JAL-3552, JAL-3609 -->Metal LaF used to improved
229 operation on Linux Ubuntu with HiDPI display in Java 11
230 (still known issues with HiDPI screens in java 8 and 11. see
231 <a href="https://issues.jalview.org/browse/JAL-3137">JAL-3137</a>)
234 <!-- JAL-3633 -->Getdown launcher inherits HTTP/S proxy
235 configuration from jalview_properties
238 <!-- JAL- -->New Jalview Develop app - making it even easier
239 to get at Jalview's development builds
242 <!-- JAL-3594 -->New splashscreens for Jalview, Jalview Test
243 and Jalview Develop applications.
246 <!-- JAL-3728 -->Jalview logos shown for Jalview Java
247 Console and other window widgets in taskbar and dock rather
248 than anonymous 'Java' icons
250 </ul> <em>JalviewJS</em>
253 <!-- JAL-3624 -->PDB structures mapped to Uniprot Sequences
257 <!-- JAL-3208 -->setprop commandline argument reinstated for
261 <!-- JAL-3163 -->Missing message bundle keys are only
262 reported once per key (avoids excessive log output in js
266 <!-- JAL-3168 -->Feature type is included in the title of
267 the Feature Settings' Colour Chooser dialog
270 <!-- JAL-3279 -->Build details reported in About window
273 <!-- JAL-3038 JAL-3071 JAL-3263 JAL-3084 -->Numerous minor
274 GUI additions and improvements in sync with Java
277 </ul> <em>Development</em>
280 <!-- -->First integrated JalviewJS and Jalview release
283 <!-- JAL-3841,JAL-3248 -->Updated README and doc/building.md
286 <!-- JAL-3789, JAL-3679 -->Improved JalviewJS/Jalview build
287 process, added support for system package provided eclipse
290 <li>Install4j 9.0.x used for installer packaging</li>
292 <!-- JAL-3930 -->Improved use of installers for unattended
293 installation with a customizedId of "JALVIEW" in install4j's
297 <!-- JAL-3907 -->Improved compatibility of Jalview build
298 with Java 17 (next LTS target)
302 <td align="left" valign="top">
305 <!-- JAL-3674 -->Slow structure commands can block Jalview
309 <!-- JAL-3904 -->Structure window's viewer-specific menu
310 disappears when only one structure is shown (and many
311 sequences:one chain mappings are present)
314 <!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
315 the first SEQUENCE_GROUP defined
319 <!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 -->Selections not
320 propagated between Linked CDS - Protein alignments and their
321 trees (known defect from 2.11.1.3)
324 <!-- JAL-3761 -->Not all codon positions highlighted for
325 overlapping exon splice sites (e.g due to RNA slippage)
328 <!-- JAL-3794 -->X was not being recognised as the unknown
329 base in DNA sequences
332 <!-- JAL-3915 -->Removed RNAview checkbox and logic from
333 Structure Preferences
336 <!-- JAL-3583 -->Tooltip behaviour improved (slightly)
339 <!-- JAL-3162 -->Can edit a feature so that start > end
342 <!-- JAL-2848 -->Cancel from Amend Features doesn't reset a
343 modified graduated colour
346 <!-- JAL-3788 -->New View with automatic 'Show Overview'
347 preference enabled results in Null Pointer Exceptions when
348 clustal colouring is enabled
351 <!-- JAL-3275 -->Can open multiple Preferences panels
354 <!-- JAL-3633 -->Properly configure HTTPS proxy settings
358 <!-- JAL-3949 -->Standard out logging broken: messages only
359 routing to stderr and appear as a raw template
362 <!-- JAL-3739 -->Entering web service parameter values in
363 numerical field doesn't update the value of the parameter
364 until return is pressed.
367 <!-- JAL-3749 -->Resolved known issue (from 2.11.1.1)
368 concerning duplicate CDS sequences generated when protein
369 products for certain ENA records are repeatedly shown via
370 Calculate->Show Cross Refs
372 </ul> <em>JalviewJS</em>
375 <!-- JAL-3202 -->Consensus profile may include zero (rounded
376 down) percentage values causing a divide by zero
379 <!-- JAL-3762 -->JalviewJS doesn't honour arguments passed
380 via Info.args when there are arguments on the URL
383 <!-- JAL-3602 -->gradle closure-compiler not using UTF-8
386 <!-- JAL-3603 -->Annotation file fails to load from URL in
389 </ul> <em>Development</em>
393 <li>Fixed non-fatal gradle errors during build</li>
395 <!-- JAL-3745 -->Updated build.gradle for use with
401 </ul> <em>Known Issues</em>
404 <!-- JAL-3764 -->Display of RESNUM sequence features are not
405 suppressed when structures associated with a sequence are
406 viewed with an external viewer (Regression from 2.11.1
413 <td width="60" align="center" nowrap><strong><a
414 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.7">.7</a><br />
415 <em>18/01/2022</em></strong></td>
417 <td align="left" valign="top">
420 <!-- JAL-3703, JAL-3935 -->Files open in Jalview cannot be
421 updated by Jalview or other applications (Windows, other non
424 </ul> <em>Security</em>
427 <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
433 <td width="60" align="center" nowrap><strong><a
434 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
435 <em>6/01/2022</em></strong></td>
437 <td align="left" valign="top"><em>Security</em>
440 <!-- JAL-3934 -->Version bump library dependency: Log4j
447 <td width="60" align="center" nowrap><strong><a
448 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
449 <em>20/12/2021</em></strong></td>
451 <td align="left" valign="top"><em>Security</em>
454 <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
456 </ul> <em>Development</em>
458 <li>Updated building instructions</li>
463 <!-- JAL-3840 -->Occupancy calculation is incorrect for
464 alignment columns with over -1+2^32 gaps (breaking filtering
468 <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
469 scale factors being set with buggy window-managers (linux
472 </ul> <em>Development</em>
474 <li>Fixed non-fatal gradle errors during build</li>
479 <td width="60" align="center" nowrap><strong><a
480 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
481 <em>09/03/2021</em></strong></td>
482 <td align="left" valign="top"><em>Improved control of
483 Jalview's use of network services via jalview_properties</em>
486 <!-- JAL-3814 -->New .jalview_properties token controlling
487 launch of the news browser (like -nonews argument)
490 <!-- JAL-3813 -->New .jalview_properties token controlling
491 download of linkout URLs from
492 www.jalview.org/services/identifiers
495 <!-- JAL-3812 -->New .jalview_properties token controlling
496 download of BIOJSHTML templates
499 <!-- JAL-3811 -->New 'Discover Web Services' option to
500 trigger a one off JABAWS discovery if autodiscovery was
504 <td align="left" valign="top">
507 <!-- JAL-3818 -->Intermittent deadlock opening structure in
510 </ul> <em>New Known defects</em>
513 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
514 always restored from project (since 2.10.3)
517 <!-- JAL-3806 -->Selections from tree built from CDS aren't
518 propagated to Protein alignment (since 2.11.1.3)
524 <td width="60" align="center" nowrap><strong><a
525 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
526 <em>29/10/2020</em></strong></td>
527 <td align="left" valign="top">
532 <td align="left" valign="top">
535 <!-- JAL-3765 -->Find doesn't always highlight all matching
536 positions in a sequence (bug introduced in 2.11.1.2)
539 <!-- JAL-3760 -->Alignments containing one or more protein
540 sequences can be classed as nucleotide
543 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
544 sequences after alignment of protein products (known defect
545 first reported for 2.11.1.0)
548 <!-- JAL-3725 -->No tooltip or popup menu for genomic
549 features outwith CDS shown overlaid on protein
552 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
553 correctly mapped by Jalview (e.g. affects viral CDS with
554 ribosomal slippage, since 2.9.0)
557 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
561 <!-- JAL-3700 -->Selections in CDS sequence panel don't
562 always select corresponding protein sequences
565 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
566 column selection doesn't always ignore hidden columns
568 </ul> <em>Installer</em>
571 <!-- JAL-3611 -->Space character in Jalview install path on
572 Windows prevents install4j launching getdown
574 </ul> <em>Development</em>
577 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
578 version numbers in doc/building.md
584 <td width="60" align="center" nowrap><strong><a
585 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
586 <em>25/09/2020</em></strong></td>
587 <td align="left" valign="top">
591 <td align="left" valign="top">
594 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
595 "Encountered problems opening
596 https://www.jalview.org/examples/exampleFile_2_7.jvp"
602 <td width="60" align="center" nowrap><strong><a
603 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
604 <em>17/09/2020</em></strong></td>
605 <td align="left" valign="top">
608 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
609 residue in cursor mode
612 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
613 HTSJDK from 2.12 to 2.23
616 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
617 optimisations and improvements suggested by Bob Hanson and
618 improved compatibility with JalviewJS
621 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
622 alignments from Pfam and Rfam
625 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
626 import (no longer based on .gz extension)
629 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
632 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
633 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
637 <!-- JAL-3667 -->Improved warning messages, debug logging
638 and fixed Retry action when Jalview encounters errors when
639 saving or making backup files.
642 <!-- JAL-3676 -->Enhanced Jalview Java Console:
644 <li>Jalview's logging level can be configured</li>
645 <li>Copy to Clipboard Buttion</li>
649 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
650 when running on Linux (Requires Java 11+)
653 <!-- JAL-1842 JAL-3509 -->RESNUM sequence features (the
654 green ones) are not automatically displayed when associated
655 structures are displayed or for sequences retrieved from the
658 </ul> <em>Launching Jalview</em>
661 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
662 through a system property
665 <!-- JAL-3477 -->Improved built-in documentation and command
666 line help for configuring Jalview's memory
670 <td align="left" valign="top">
673 <!-- JAL-3691 -->Conservation and Quality tracks are shown
674 but not calculated and no protein or DNA score models are
675 available for tree/PCA calculation when launched with
676 Turkish language locale
679 <!-- JAL-3493 -->Escape does not clear highlights on the
680 alignment (Since Jalview 2.10.3)
683 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
684 doesn't slide selected sequences, just sequence under cursor
687 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
688 sequence under the cursor
691 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
692 multiple EMBL gene products shown for a single contig
695 <!-- JAL-3696 -->Errors encountered when processing variants
696 from VCF files yield "Error processing VCF: Format specifier
700 <!-- JAL-3697 -->Count of features not shown can be wrong
701 when there are both local and complementary features mapped
702 to the position under the cursor
705 <!-- JAL-3673 -->Sequence ID for reference sequence is
706 clipped when Right align Sequence IDs enabled
709 <!-- JAL-2983 -->Slider with negative range values not
710 rendered correctly in VAqua4 (Since 2.10.4)
713 <!-- JAL-3685 -->Single quotes not displayed correctly in
714 internationalised text for some messages and log output
717 <!-- JAL-3490 -->Find doesn't report matches that span
718 hidden gapped columns
721 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
722 panels, Alignment viewport and annotation renderer.
725 <!-- JAL-3561 -->Jalview ignores file format parameter
726 specifying output format when exporting an alignment via the
730 <!-- JAL-3667 -->Windows 10: For a minority of users, if
731 backups are not enabled, Jalview sometimes fails to
732 overwrite an existing file and raises a warning dialog. (in
733 2.11.0, and 2.11.1.0, the workaround is to try to save the
734 file again, and if that fails, delete the original file and
738 <!-- JAL-3509 -->Dragging a PDB file onto an alignment with
739 sequence features displayed causes displayed features to be
743 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
747 <!-- JAL-3741 -->References to http://www.jalview.org in
748 program and documentation
750 </ul> <em>Launching Jalview</em>
753 <!-- JAL-3718 -->Jalview application fails when launched the
754 first time for a version that has different jars to the
755 previous launched version.
757 </ul> <em>Developing Jalview</em>
760 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
761 data, causing cloverReport gradle task to fail with an
765 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
766 monitor the release channel
768 </ul> <em>New Known defects</em>
771 <!-- JAL-3748 -->CDS shown in result of submitting proteins
772 in a CDS/Protein alignment to a web service is wrong when
773 proteins share a common transcript sequence (e.g. genome of
777 <!-- JAL-3576 -->Co-located features exported and
778 re-imported are ordered differently when shown on alignment
779 and in tooltips. (Also affects v2.11.1.0)
782 <!-- JAL-3702 -->Drag and drop of alignment file onto
783 alignment window when in a HiDPI scaled mode in Linux only
784 works for the top left quadrant of the alignment window
787 <!-- JAL-3701 -->Stale build data in jalview standalone jar
788 builds (only affects 2.11.1.1 branch)
791 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
792 when alignment view restored from project (since Jalview
796 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
797 protein products for certain ENA records are repeatedly
798 shown via Calculate->Show Cross Refs
804 <td width="60" align="center" nowrap><strong><a
805 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
806 <em>22/04/2020</em></strong></td>
807 <td align="left" valign="top">
810 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
811 'virtual' codon features shown on protein (or vice versa)
812 for display in alignments, on structure views (including
813 transfer to UCSF chimera), in feature reports and for
817 <!-- JAL-3121 -->Feature attributes from VCF files can be
818 exported and re-imported as GFF3 files
821 <!-- JAL-3376 -->Capture VCF "fixed column" values
822 POS, ID, QUAL, FILTER as Feature Attributes
825 <!-- JAL-3375 -->More robust VCF numeric data field
826 validation while parsing
829 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
833 <!-- JAL-3535 -->Feature Settings dialog title includes name
837 <!-- JAL-3538 -->Font anti-aliasing in alignment views
841 <!-- JAL-3468 -->Very long feature descriptions truncated in
845 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
846 with no feature types visible
849 <!-- JAL-3574 -->Improved support for filtering feature
850 attributes with large integer values
853 <em>Jalview Installer</em>
856 <!-- JAL-3449 -->Versions for install4j and getdown and
857 installer template version reported in console (may be null
858 when Jalview launched as executable jar or via conda)
861 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and
862 higher quality background images
865 <!-- JAL-3394 -->New installer/application launcher
866 generated with install4j 8.0.4
869 <!-- JAL-3420 -->Jalview File Associations shown for Unix
873 <!-- JAL-3477 -->Improved defaults for maximum memory
874 setting when running on large memory machines
876 </ul> <em>Release processes</em>
879 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
882 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier
883 access to test-release channel builds
885 </ul> <em>Build System</em>
888 <!-- JAL-3510 -->Clover updated to 4.4.1
891 <!-- JAL-3513 -->Test code included in Clover coverage
894 </ul> <em>Groovy Scripts</em>
897 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
898 to stdout containing the consensus sequence for each
899 alignment in a Jalview session
902 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
903 genomic sequence_variant annotation from CDS as
904 missense_variant or synonymous_variant on protein products.
908 <td align="left" valign="top">
911 <!-- JAL-3581 -->Hidden sequence markers still visible when
912 'Show hidden markers' option is not ticked
915 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
916 PNG output when 'Automatically set ID width' is set in
917 jalview preferences or properties file
920 <!-- JAL-3571 -->Feature Editor dialog can be opened when
921 'Show Sequence Features' option is not ticked
924 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
925 buttons in Feature Settings dialog are clicked when no
929 <!-- JAL-3412 -->ID margins for CDS and Protein views not
930 equal when split frame is first opened
933 <!-- JAL-3296 -->Sequence position numbers in status bar not
934 correct after editing a sequence's start position
937 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
938 with annotation and exceptions thrown when only a few
939 columns shown in wrapped mode
942 <!-- JAL-3386 -->Sequence IDs missing in headless export of
943 wrapped alignment figure with annotations
946 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
947 ID fails with ClassCastException
950 <!-- JAL-3389 -->Chimera session not restored from Jalview
954 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
955 feature settings dialog also selects columns
958 <!-- JAL-3473 -->SpinnerNumberModel causes
959 IllegalArgumentException in some circumstances
962 <!-- JAL-3534 -->Multiple feature settings dialogs can be
966 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
967 alignment window is closed
970 <!-- JAL-3406 -->Credits missing some authors in Jalview
971 help documentation for 2.11.0 release
974 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
975 includes Pfam ID as sequence's accession rather than its
978 </ul> <em>Java 11 Compatibility issues</em>
981 <!-- JAL-2987 -->OSX - Can't view some search results in
982 PDB/Uniprot search panel
984 </ul> <em>Installer</em>
987 <!-- JAL-3447 -->Jalview should not create file associations
988 for 3D structure files (.pdb, .mmcif. .cif)
990 </ul> <em>Repository and Source Release</em>
993 <!-- JAL-3474 -->removed obsolete .cvsignore files from
997 <!-- JAL-3541 -->Clover report generation running out of
1000 </ul> <em>New Known Issues</em>
1003 <!-- JAL-3523 -->OSX - Current working directory not
1004 preserved when Jalview.app launched with parameters from
1008 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
1009 clipped in headless figure export when Right Align option
1013 <!-- JAL-3542 -->Jalview Installation type always reports
1014 'Source' in console output
1017 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail
1018 on jalview's bamboo server but run fine locally.
1024 <td width="60" align="center" nowrap><strong><a
1025 name="Jalview.2.11.0">2.11.0</a><br /> <em>04/07/2019</em></strong></td>
1026 <td align="left" valign="top">
1029 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native
1030 Application and Installers built with <a
1031 href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a>
1032 (licensed to the Jalview open source project) rather than
1036 <!-- JAL-1929 -->Jalview Launcher System to auto-configure
1037 memory settings, receive over the air updates and launch
1038 specific versions via (<a
1039 href="https://github.com/threerings/getdown">Three
1043 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations
1044 for formats supported by Jalview (including .jvp project
1048 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command
1049 line arguments and switch between different getdown channels
1052 <!-- JAL-3141 -->Backup files created when saving Jalview
1053 project or alignment files
1057 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF
1061 <!-- JAL-2753 -->Version of HTSJDK shipped with Jalview
1062 updated to version 2.12.0
1065 <!-- JAL-2620 -->Alternative genetic code tables for
1069 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0
1071 <li><strong>Enhanced visualisation and analysis
1072 of Sequence Features</strong>
1075 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
1076 implementation that allows updates) used for Sequence
1080 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
1081 features can be filtered and shaded according to any
1082 associated attributes (e.g. variant attributes from VCF
1083 file, or key-value pairs imported from column 9 of GFF
1087 <!-- JAL-2879 -->Feature Attributes and shading schemes
1088 stored and restored from Jalview Projects
1091 <!-- JAL-3334 -->Use full Sequence Ontology (via
1092 BioJava) to recognise variant features
1095 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants
1096 on peptide sequences (also coloured red by default)
1099 <!-- JAL-2792 -->Popup window to show full report for a
1100 selected sequence feature's details
1103 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient
1104 sequence feature render algorithm (Z-sort/transparency
1108 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature
1113 <!-- JAL-3205 -->Symmetric score matrices for faster tree
1114 and PCA calculations
1116 <li><strong>Principal Components Analysis Viewer</strong>
1119 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis
1120 results and Viewer state saved in Jalview Project
1123 <!-- JAL-2962 -->'Change parameters' option removed from
1124 viewer's drop-down menus
1127 <!-- JAL-2975 -->Can use shift + arrow keys to rotate
1128 PCA image incrementally
1131 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
1135 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
1137 <li><strong>Speed and Efficiency</strong>
1140 <!-- JAL-2185,JAL-3198 -->More efficient creation of
1141 selections and multiple groups when working with large
1145 <!-- JAL-3200 -->Speedier import of annotation rows when
1146 parsing Stockholm files
1149 <li><strong>User Interface</strong>
1152 <!-- JAL-2933 -->Finder panel remembers last position in
1156 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS
1157 (What you see is what is shown)<br />Only visible
1158 regions of alignment are shown by default (can be
1159 changed in user preferences)
1162 <!-- JAL-3169 -->File Chooser stays open after
1163 responding Cancel to the Overwrite Dialog
1166 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour
1167 when all sequences are hidden
1170 <!-- JAL-1244 -->Status bar shows bounds when dragging a
1171 selection region, and gap count when inserting or
1175 <!-- JAL-3132 -->Status bar updates over sequence and
1179 <!-- JAL-3093 -->Annotation tooltips and popup menus are
1180 shown when in wrapped mode
1183 <!-- JAL-3073 -->Can select columns by dragging
1184 left/right in a graph or histogram annotation
1187 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB
1191 <!-- JAL-2621 -->Cursor changes over draggable box in
1195 <!-- JAL-3181 -->Consistent ordering of links in
1196 sequence id popup menu
1199 <!-- JAL-3080 -->Red line indicating tree-cut position
1200 not shown if no subgroups are created
1203 <!-- JAL-3042 -->Removed ability to configure length of
1204 search history by right-clicking search box
1210 <!-- JAL-3232 -->Jalview Groovy Scripting Console updated to
1213 <li><strong>Java 11 Support (not yet on general
1217 <!-- -->OSX GUI integrations for App menu's 'About'
1218 entry and trapping CMD-Q
1221 </ul> <em>Deprecations</em>
1224 <!-- JAL-3035 -->DAS sequence retrieval and annotation
1225 capabilities removed from the Jalview Desktop
1228 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling
1229 and unmarshalling has been replaced by JAXB for Jalview
1230 projects and XML based data retrieval clients
1233 <!-- JAL-3311 -->Disable VAMSAS menu in preparation for
1237 <!-- -->Jalview Desktop no longer distributed via Java Web
1240 </ul> <em>Documentation</em>
1243 <!-- JAL-3003 -->Added remarks about transparent rendering
1244 effects not supported in EPS figure export
1247 <!-- JAL-2903 -->Typos in documentation for Preferences
1250 </ul> <em>Development and Release Processes</em>
1253 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated
1257 <!-- JAL-1424 -->Enhanced checks for missing and duplicated
1258 keys in Message bundles
1261 <!-- JAL-3225 -->Eclipse project configuration managed with
1265 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian Bamboo
1266 continuous integration for unattended Test Suite execution
1269 <!-- JAL-2864 -->Memory test suite to detect leaks in common
1273 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
1277 <!-- JAL-3248 -->Developer documentation migrated to
1278 markdown (with HTML rendering)
1281 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
1284 <!-- JAL-3289 -->New URLs for publishing development
1289 <td align="left" valign="top">
1292 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
1295 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
1296 superposition in Jmol fail on Windows
1299 <!-- JAL-3286 -->Blank error dialog is displayed when
1300 discovering structures for sequences with lots of PDB
1304 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export
1305 with monospaced font
1308 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
1309 Jalview project involving multiple views
1312 <!-- JAL-3164 -->Overview for complementary view in a linked
1313 CDS/Protein alignment is not updated when Hide Columns by
1314 Annotation dialog hides columns
1317 <!-- JAL-3158 -->Selection highlighting in the complement of
1318 a CDS/Protein alignment stops working after making a
1319 selection in one view, then making another selection in the
1323 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
1327 <!-- JAL-3154 -->Table Columns could be re-ordered in
1328 Feature Settings and Jalview Preferences panels
1331 <!-- JAL-2865 -->Jalview hangs when closing windows, or
1332 redrawing the overview with large alignments
1335 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
1336 region if columns were selected by dragging right-to-left
1337 and the mouse moved to the left of the first column
1340 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to
1341 a hidden column marker via scale popup menu
1344 <!-- JAL-2846 -->Error message for trying to load in invalid
1345 URLs doesn't tell users the invalid URL
1348 <!-- JAL-2816 -->Tooltips displayed for features filtered by
1352 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl
1353 during show cross references or Fetch Database References
1354 are shown in red in original view
1357 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown
1358 correctly on peptide sequence (computed variant shown as
1362 <!-- JAL-2060 -->'Graduated colour' option not offered for
1363 manually created features (where feature score is Float.NaN)
1366 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or
1367 printed when columns are hidden
1370 <!-- JAL-3082 -->Regular expression error for '(' in Select
1371 Columns by Annotation description
1374 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after
1375 dragging out of Scale or Annotation Panel
1378 <!-- JAL-3075 -->Column selection incorrect after scrolling
1382 <!-- JAL-3074 -->Left/right drag in annotation can scroll
1386 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal
1390 <!-- JAL-3002 -->Column display is out by one after Page
1391 Down, Page Up in wrapped mode
1394 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
1397 <!-- JAL-2932 -->Finder searches in minimised alignments
1400 <!-- JAL-2250 -->'Apply Colour to All Groups' not always
1401 selected on opening an alignment
1404 <!-- JAL-3180 -->'Colour by Annotation' not marked selected
1408 <!-- JAL-3201 -->Per-group Clustal colour scheme changes
1409 when different groups in the alignment are selected
1412 <!-- JAL-2717 -->Internationalised colour scheme names not
1413 shown correctly in menu
1416 <!-- JAL-3206 -->Colour by Annotation can go black at
1417 min/max threshold limit
1420 <!-- JAL-3125 -->Value input for graduated feature colour
1421 threshold gets 'unrounded'
1424 <!-- JAL-2982 -->PCA image export doesn't respect background
1428 <!-- JAL-2963 -->PCA points don't dim when rotated about y
1432 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
1435 <!-- JAL-3078 -->Cancel in Tree Font dialog resets
1436 alignment, not Tree font
1439 <!-- JAL-2964 -->Associate Tree with All Views not restored
1443 <!-- JAL-2915 -->Scrolling of split frame is sluggish if
1444 Overview shown in complementary view
1447 <!-- JAL-3313 -->Codon consensus incorrectly scaled when
1448 shown without normalisation
1451 <!-- JAL-3021 -->Sequence Details report should open
1452 positioned at top of report
1455 <!-- JAL-914 -->Help page can be opened twice
1458 <!-- JAL-3333 -->Fuzzy text in web service status menu on
1461 </ul> <em>Editing</em>
1464 <!-- JAL-2822 -->Start and End should be updated when
1465 sequence data at beginning or end of alignment added/removed
1469 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection
1470 doesn't relocate sequence features correctly when start of
1471 sequence is removed (Known defect since 2.10)
1474 <!-- JAL-2830 -->Inserting gap sequence via the Edit
1475 Sequence dialog corrupts dataset sequence
1478 <!-- JAL-868 -->Structure colours not updated when
1479 associated tree repartitions the alignment view (Regression
1482 </ul> <em>Datamodel</em>
1485 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
1486 sequence's End is greater than its length
1488 </ul> <em>Bugs fixed for Java 11 Support (not yet on general
1492 <!-- JAL-3288 -->Menus work properly in split-screen
1494 </ul> <em>New Known Defects</em>
1497 <!-- JAL-3340 -->Select columns containing feature by double
1498 clicking ignores bounds of an existing selected region
1501 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in
1502 gapped regions of protein alignment.
1505 <!-- JAL-2647 -->Input Data menu entry is greyed out when
1506 PCA View is restored from a Jalview 2.11 project
1509 <!-- JAL-3213 -->Alignment panel height can be too small
1513 <!-- JAL-3240 -->Display is incorrect after removing gapped
1514 columns within hidden columns
1517 <!-- JAL-3314 -->Rightmost selection is lost when mouse
1518 re-enters window after dragging left to select columns to
1519 left of visible region
1522 <!-- JAL-2876 -->Features coloured according to their
1523 description string and thresholded by score in earlier
1524 versions of Jalview are not shown as thresholded features in
1525 2.11. To workaround please create a Score filter instead.
1528 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't
1529 reset group visibility
1532 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in
1533 linked CDS/Protein view
1536 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1537 alignments with multiple views can close views unexpectedly
1539 </ul> <em>Java 11 Specific defects</em>
1542 <!-- JAL-3235 -->Jalview Properties file is not sorted
1543 alphabetically when saved
1549 <td width="60" nowrap>
1550 <div align="center">
1551 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1554 <td><div align="left">
1558 <!-- JAL-3101 -->Default memory for Jalview webstart and
1559 InstallAnywhere increased to 1G.
1562 <!-- JAL-247 -->Hidden sequence markers and representative
1563 sequence bolding included when exporting alignment as EPS,
1564 SVG, PNG or HTML. <em>Display is configured via the
1565 Format menu, or for command-line use via a Jalview
1566 properties file.</em>
1569 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1570 API and sequence data now imported as JSON.
1573 <!-- JAL-3065 -->Change in recommended way of starting
1574 Jalview via a Java command line: add jars in lib directory
1575 to CLASSPATH, rather than via the deprecated java.ext.dirs
1579 <em>Development</em>
1582 <!-- JAL-3047 -->Support added to execute test suite
1583 instrumented with <a href="http://openclover.org/">Open
1588 <td><div align="left">
1592 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1593 row shown in Feredoxin Structure alignment view of example
1597 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1598 annotation displayed.
1601 <!-- JAL-3107 -->Group conservation/consensus not shown
1602 for newly created group when 'Apply to all groups'
1606 <!-- JAL-3087 -->Corrupted display when switching to
1607 wrapped mode when sequence panel's vertical scrollbar is
1611 <!-- JAL-3003 -->Alignment is black in exported EPS file
1612 when sequences are selected in exported view.</em>
1615 <!-- JAL-3059 -->Groups with different coloured borders
1616 aren't rendered with correct colour.
1619 <!-- JAL-3092 -->Jalview could hang when importing certain
1620 types of knotted RNA secondary structure.
1623 <!-- JAL-3095 -->Sequence highlight and selection in
1624 trimmed VARNA 2D structure is incorrect for sequences that
1628 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1629 annotation when columns are inserted into an alignment,
1630 and when exporting as Stockholm flatfile.
1633 <!-- JAL-3053 -->Jalview annotation rows containing upper
1634 and lower-case 'E' and 'H' do not automatically get
1635 treated as RNA secondary structure.
1638 <!-- JAL-3106 -->.jvp should be used as default extension
1639 (not .jar) when saving a Jalview project file.
1642 <!-- JAL-3105 -->Mac Users: closing a window correctly
1643 transfers focus to previous window on OSX
1646 <em>Java 10 Issues Resolved</em>
1649 <!-- JAL-2988 -->OSX - Can't save new files via the File
1650 or export menus by typing in a name into the Save dialog
1654 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1655 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1656 'look and feel' which has improved compatibility with the
1657 latest version of OSX.
1663 <td width="60" nowrap>
1664 <div align="center">
1665 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1666 <em>7/06/2018</em></strong>
1669 <td><div align="left">
1673 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1674 annotation retrieved from Uniprot
1677 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1678 onto the Jalview Desktop
1682 <td><div align="left">
1686 <!-- JAL-3017 -->Cannot import features with multiple
1687 variant elements (blocks import of some Uniprot records)
1690 <!-- JAL-2997 -->Clustal files with sequence positions in
1691 right-hand column parsed correctly
1694 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1695 not alignment area in exported graphic
1698 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1699 window has input focus
1702 <!-- JAL-2992 -->Annotation panel set too high when
1703 annotation added to view (Windows)
1706 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1707 network connectivity is poor
1710 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1711 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1712 the currently open URL and links from a page viewed in
1713 Firefox or Chrome on Windows is now fully supported. If
1714 you are using Edge, only links in the page can be
1715 dragged, and with Internet Explorer, only the currently
1716 open URL in the browser can be dropped onto Jalview.</em>
1719 <em>New Known Defects</em>
1722 <!-- JAL-3083 -->Cancel option doesn't reset Colour by
1729 <td width="60" nowrap>
1730 <div align="center">
1731 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1734 <td><div align="left">
1738 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1739 for disabling automatic superposition of multiple
1740 structures and open structures in existing views
1743 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1744 ID and annotation area margins can be click-dragged to
1748 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1752 <!-- JAL-2759 -->Improved performance for large alignments
1753 and lots of hidden columns
1756 <!-- JAL-2593 -->Improved performance when rendering lots
1757 of features (particularly when transparency is disabled)
1760 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2
1761 for exchange of Jalview features and Chimera attributes
1762 made generally available
1766 <td><div align="left">
1769 <!-- JAL-2899 -->Structure and Overview aren't updated
1770 when Colour By Annotation threshold slider is adjusted
1773 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1774 overlapping alignment panel
1777 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1781 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1782 improved: CDS not handled correctly if transcript has no
1786 <!-- JAL-2321 -->Secondary structure and temperature
1787 factor annotation not added to sequence when local PDB
1788 file associated with it by drag'n'drop or structure
1792 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1793 dialog doesn't import PDB files dropped on an alignment
1796 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1797 scroll bar doesn't work for some CDS/Protein views
1800 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1801 Java 1.8u153 onwards and Java 1.9u4+.
1804 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1805 columns in annotation row
1808 <!-- JAL-2913 -->Preferences panel's ID Width control is
1809 not honored in batch mode
1812 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1813 for structures added to existing Jmol view
1816 <!-- JAL-2223 -->'View Mappings' includes duplicate
1817 entries after importing project with multiple views
1820 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1821 protein sequences via SIFTS from associated PDB entries
1822 with negative residue numbers or missing residues fails
1825 <!-- JAL-2952 -->Exception when shading sequence with
1826 negative Temperature Factor values from annotated PDB
1827 files (e.g. as generated by CONSURF)
1830 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1831 tooltip doesn't include a text description of mutation
1834 <!-- JAL-2922 -->Invert displayed features very slow when
1835 structure and/or overview windows are also shown
1838 <!-- JAL-2954 -->Selecting columns from highlighted
1839 regions very slow for alignments with large numbers of
1843 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1844 with 'StringIndexOutOfBounds'
1847 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and
1848 Feel for OSX platforms running Java 10
1851 <!-- JAL-2960 -->Adding a structure to existing structure
1852 view appears to do nothing because the view is hidden
1853 behind the alignment view
1859 <!-- JAL-2926 -->Copy consensus sequence option in applet
1860 should copy the group consensus when popup is opened on it
1866 <!-- JAL-2913 -->Fixed ID width preference is not
1870 <em>New Known Defects</em>
1873 <!-- JAL-2973 --> Exceptions occasionally raised when
1874 editing a large alignment and overview is displayed
1877 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1878 repeatedly after a series of edits even when the overview
1879 is no longer reflecting updates
1882 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1883 structures for protein subsequence (if 'Trim Retrieved
1884 Sequences' enabled) or Ensembl isoforms (Workaround in
1885 2.10.4 is to fail back to N&W mapping)
1888 <!-- JAL-2990 -->Export Annotations from File Menu with
1889 CSV option gives blank output
1895 <td width="60" nowrap>
1896 <div align="center">
1897 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br />
1898 <em>24/1/2018</em></strong>
1901 <td><div align="left">
1903 <li>Updated Certum Codesigning Certificate (Valid till
1904 30th November 2018)</li>
1907 <td><div align="left">
1912 <!-- JAL-2859-->Only one structure is loaded when
1913 several sequences and structures are selected for
1917 <!-- JAL-2851-->Alignment doesn't appear to scroll
1918 vertically via trackpad and scrollwheel
1921 <!-- JAL-2842-->Jalview hangs if up/down arrows pressed
1922 in cursor mode when cursor lies in hidden region at
1926 <!-- JAL-2827-->Helix annotation has 'notches' when
1927 scrolled into view if columns are hidden
1930 <!-- JAL-2740-->Annotation column filter can be slow to
1931 reset (ie after hitting cancel) for large numbers of
1935 <!-- JAL-2849-->User preference for disabling inclusion
1936 of sequence limits when exporting as flat file has no
1940 <!-- JAL-2679-->Reproducible cross-reference
1941 relationships when retrieving sequences from
1948 <td width="60" nowrap>
1949 <div align="center">
1950 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1953 <td><div align="left">
1957 <!-- JAL-2446 -->Faster and more efficient management and
1958 rendering of sequence features
1961 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1962 429 rate limit request hander
1965 <!-- JAL-2773 -->Structure views don't get updated unless
1966 their colours have changed
1969 <!-- JAL-2495 -->All linked sequences are highlighted for
1970 a structure mousover (Jmol) or selection (Chimera)
1973 <!-- JAL-2790 -->'Cancel' button in progress bar for
1974 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1977 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1978 view from Ensembl locus cross-references
1981 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1985 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1986 feature can be disabled
1989 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1990 PDB easier retrieval of sequences for lists of IDs
1993 <!-- JAL-2758 -->Short names for sequences retrieved from
1999 <li>Groovy interpreter updated to 2.4.12</li>
2000 <li>Example groovy script for generating a matrix of
2001 percent identity scores for current alignment.</li>
2003 <em>Testing and Deployment</em>
2006 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
2010 <td><div align="left">
2014 <!-- JAL-2643 -->Pressing tab after updating the colour
2015 threshold text field doesn't trigger an update to the
2019 <!-- JAL-2682 -->Race condition when parsing sequence ID
2023 <!-- JAL-2608 -->Overview windows are also closed when
2024 alignment window is closed
2027 <!-- JAL-2548 -->Export of features doesn't always respect
2031 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
2032 takes a long time in Cursor mode
2038 <!-- JAL-2777 -->Structures with whitespace chainCode
2039 cannot be viewed in Chimera
2042 <!-- JAL-2728 -->Protein annotation panel too high in
2046 <!-- JAL-2757 -->Can't edit the query after the server
2047 error warning icon is shown in Uniprot and PDB Free Text
2051 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
2054 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
2057 <!-- JAL-2739 -->Hidden column marker in last column not
2058 rendered when switching back from Wrapped to normal view
2061 <!-- JAL-2768 -->Annotation display corrupted when
2062 scrolling right in unwapped alignment view
2065 <!-- JAL-2542 -->Existing features on subsequence
2066 incorrectly relocated when full sequence retrieved from
2070 <!-- JAL-2733 -->Last reported memory still shown when
2071 Desktop->Show Memory is unticked (OSX only)
2074 <!-- JAL-2658 -->Amend Features dialog doesn't allow
2075 features of same type and group to be selected for
2079 <!-- JAL-2524 -->Jalview becomes sluggish in wide
2080 alignments when hidden columns are present
2083 <!-- JAL-2392 -->Jalview freezes when loading and
2084 displaying several structures
2087 <!-- JAL-2732 -->Black outlines left after resizing or
2091 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
2092 within the Jalview desktop on OSX
2095 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
2096 when in wrapped alignment mode
2099 <!-- JAL-2636 -->Scale mark not shown when close to right
2100 hand end of alignment
2103 <!-- JAL-2684 -->Pairwise alignment of selected regions of
2104 each selected sequence do not have correct start/end
2108 <!-- JAL-2793 -->Alignment ruler height set incorrectly
2109 after canceling the Alignment Window's Font dialog
2112 <!-- JAL-2036 -->Show cross-references not enabled after
2113 restoring project until a new view is created
2116 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
2117 URL links appears when only default EMBL-EBI link is
2118 configured (since 2.10.2b2)
2121 <!-- JAL-2775 -->Overview redraws whole window when box
2122 position is adjusted
2125 <!-- JAL-2225 -->Structure viewer doesn't map all chains
2126 in a multi-chain structure when viewing alignment
2127 involving more than one chain (since 2.10)
2130 <!-- JAL-2811 -->Double residue highlights in cursor mode
2131 if new selection moves alignment window
2134 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
2135 arrow key in cursor mode to pass hidden column marker
2138 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
2139 that produces correctly annotated transcripts and products
2142 <!-- JAL-2776 -->Toggling a feature group after first time
2143 doesn't update associated structure view
2146 <em>Applet</em><br />
2149 <!-- JAL-2687 -->Concurrent modification exception when
2150 closing alignment panel
2153 <em>BioJSON</em><br />
2156 <!-- JAL-2546 -->BioJSON export does not preserve
2157 non-positional features
2160 <em>New Known Issues</em>
2163 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
2164 sequence features correctly (for many previous versions of
2168 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
2169 using cursor in wrapped panel other than top
2172 <!-- JAL-2791 -->Select columns containing feature ignores
2173 graduated colour threshold
2176 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
2177 always preserve numbering and sequence features
2180 <em>Known Java 9 Issues</em>
2183 <!-- JAL-2902 -->Groovy Console very slow to open and is
2184 not responsive when entering characters (Webstart, Java
2191 <td width="60" nowrap>
2192 <div align="center">
2193 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
2194 <em>2/10/2017</em></strong>
2197 <td><div align="left">
2198 <em>New features in Jalview Desktop</em>
2201 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API
2205 <!-- JAL-2745 -->HTTPS used for all connections to
2210 <td><div align="left"></div></td>
2213 <td width="60" nowrap>
2214 <div align="center">
2215 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
2216 <em>7/9/2017</em></strong>
2219 <td><div align="left">
2223 <!-- JAL-2588 -->Show gaps in overview window by colouring
2224 in grey (sequences used to be coloured grey, and gaps were
2228 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
2232 <!-- JAL-2587 -->Overview updates immediately on increase
2233 in size and progress bar shown as higher resolution
2234 overview is recalculated
2239 <td><div align="left">
2243 <!-- JAL-2664 -->Overview window redraws every hidden
2244 column region row by row
2247 <!-- JAL-2681 -->duplicate protein sequences shown after
2248 retrieving Ensembl crossrefs for sequences from Uniprot
2251 <!-- JAL-2603 -->Overview window throws NPE if show boxes
2252 format setting is unticked
2255 <!-- JAL-2610 -->Groups are coloured wrongly in overview
2256 if group has show boxes format setting unticked
2259 <!-- JAL-2672,JAL-2665 -->Redraw problems when
2260 autoscrolling whilst dragging current selection group to
2261 include sequences and columns not currently displayed
2264 <!-- JAL-2691 -->Not all chains are mapped when multimeric
2265 assemblies are imported via CIF file
2268 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
2269 displayed when threshold or conservation colouring is also
2273 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
2277 <!-- JAL-2673 -->Jalview continues to scroll after
2278 dragging a selected region off the visible region of the
2282 <!-- JAL-2724 -->Cannot apply annotation based
2283 colourscheme to all groups in a view
2286 <!-- JAL-2511 -->IDs don't line up with sequences
2287 initially after font size change using the Font chooser or
2294 <td width="60" nowrap>
2295 <div align="center">
2296 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
2299 <td><div align="left">
2300 <em>Calculations</em>
2304 <!-- JAL-1933 -->Occupancy annotation row shows number of
2305 ungapped positions in each column of the alignment.
2308 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
2309 a calculation dialog box
2312 <!-- JAL-2379 -->Revised implementation of PCA for speed
2313 and memory efficiency (~30x faster)
2316 <!-- JAL-2403 -->Revised implementation of sequence
2317 similarity scores as used by Tree, PCA, Shading Consensus
2318 and other calculations
2321 <!-- JAL-2416 -->Score matrices are stored as resource
2322 files within the Jalview codebase
2325 <!-- JAL-2500 -->Trees computed on Sequence Feature
2326 Similarity may have different topology due to increased
2333 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
2334 model for alignments and groups
2337 <!-- JAL-384 -->Custom shading schemes created via groovy
2344 <!-- JAL-2526 -->Efficiency improvements for interacting
2345 with alignment and overview windows
2348 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
2352 <!-- JAL-2388 -->Hidden columns and sequences can be
2356 <!-- JAL-2611 -->Click-drag in visible area allows fine
2357 adjustment of visible position
2361 <em>Data import/export</em>
2364 <!-- JAL-2535 -->Posterior probability annotation from
2365 Stockholm files imported as sequence associated annotation
2368 <!-- JAL-2507 -->More robust per-sequence positional
2369 annotation input/output via stockholm flatfile
2372 <!-- JAL-2533 -->Sequence names don't include file
2373 extension when importing structure files without embedded
2374 names or PDB accessions
2377 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
2378 format sequence substitution matrices
2381 <em>User Interface</em>
2384 <!-- JAL-2447 --> Experimental Features Checkbox in
2385 Desktop's Tools menu to hide or show untested features in
2389 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
2390 via Overview or sequence motif search operations
2393 <!-- JAL-2547 -->Amend sequence features dialog box can be
2394 opened by double clicking gaps within sequence feature
2398 <!-- JAL-1476 -->Status bar message shown when not enough
2399 aligned positions were available to create a 3D structure
2403 <em>3D Structure</em>
2406 <!-- JAL-2430 -->Hidden regions in alignment views are not
2407 coloured in linked structure views
2410 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
2411 file-based command exchange
2414 <!-- JAL-2375 -->Structure chooser automatically shows
2415 Cached Structures rather than querying the PDBe if
2416 structures are already available for sequences
2419 <!-- JAL-2520 -->Structures imported via URL are cached in
2420 the Jalview project rather than downloaded again when the
2421 project is reopened.
2424 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
2425 to transfer Chimera's structure attributes as Jalview
2426 features, and vice-versa (<strong>Experimental
2430 <em>Web Services</em>
2433 <!-- JAL-2549 -->Updated JABAWS client to v2.2
2436 <!-- JAL-2335 -->Filter non-standard amino acids and
2437 nucleotides when submitting to AACon and other MSA
2441 <!-- JAL-2316, -->URLs for viewing database
2442 cross-references provided by identifiers.org and the
2443 EMBL-EBI's MIRIAM DB
2450 <!-- JAL-2344 -->FileFormatI interface for describing and
2451 identifying file formats (instead of String constants)
2454 <!-- JAL-2228 -->FeatureCounter script refactored for
2455 efficiency when counting all displayed features (not
2456 backwards compatible with 2.10.1)
2459 <em>Example files</em>
2462 <!-- JAL-2631 -->Graduated feature colour style example
2463 included in the example feature file
2466 <em>Documentation</em>
2469 <!-- JAL-2339 -->Release notes reformatted for readability
2470 with the built-in Java help viewer
2473 <!-- JAL-1644 -->Find documentation updated with 'search
2474 sequence description' option
2480 <!-- JAL-2485, -->External service integration tests for
2481 Uniprot REST Free Text Search Client
2484 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
2487 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
2492 <td><div align="left">
2493 <em>Calculations</em>
2496 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
2497 matrix - C->R should be '-3'<br />Old matrix restored
2498 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
2500 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
2501 Jalview's treatment of gaps in PCA and substitution matrix
2502 based Tree calculations.<br /> <br />In earlier versions
2503 of Jalview, gaps matching gaps were penalised, and gaps
2504 matching non-gaps penalised even more. In the PCA
2505 calculation, gaps were actually treated as non-gaps - so
2506 different costs were applied, which meant Jalview's PCAs
2507 were different to those produced by SeqSpace.<br />Jalview
2508 now treats gaps in the same way as SeqSpace (ie it scores
2509 them as 0). <br /> <br />Enter the following in the
2510 Groovy console to restore pre-2.10.2 behaviour:<br />
2511 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
2512 // for 2.10.1 mode <br />
2513 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
2514 // to restore 2.10.2 mode <br /> <br /> <em>Note:
2515 these settings will affect all subsequent tree and PCA
2516 calculations (not recommended)</em></li>
2518 <!-- JAL-2424 -->Fixed off-by-one bug that affected
2519 scaling of branch lengths for trees computed using
2520 Sequence Feature Similarity.
2523 <!-- JAL-2377 -->PCA calculation could hang when
2524 generating output report when working with highly
2525 redundant alignments
2528 <!-- JAL-2544 --> Sort by features includes features to
2529 right of selected region when gaps present on right-hand
2533 <em>User Interface</em>
2536 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2537 doesn't reselect a specific sequence's associated
2538 annotation after it was used for colouring a view
2541 <!-- JAL-2419 -->Current selection lost if popup menu
2542 opened on a region of alignment without groups
2545 <!-- JAL-2374 -->Popup menu not always shown for regions
2546 of an alignment with overlapping groups
2549 <!-- JAL-2310 -->Finder double counts if both a sequence's
2550 name and description match
2553 <!-- JAL-2370 -->Hiding column selection containing two
2554 hidden regions results in incorrect hidden regions
2557 <!-- JAL-2386 -->'Apply to all groups' setting when
2558 changing colour does not apply Conservation slider value
2562 <!-- JAL-2373 -->Percentage identity and conservation menu
2563 items do not show a tick or allow shading to be disabled
2566 <!-- JAL-2385 -->Conservation shading or PID threshold
2567 lost when base colourscheme changed if slider not visible
2570 <!-- JAL-2547 -->Sequence features shown in tooltip for
2571 gaps before start of features
2574 <!-- JAL-2623 -->Graduated feature colour threshold not
2575 restored to UI when feature colour is edited
2578 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2579 a time when scrolling vertically in wrapped mode.
2582 <!-- JAL-2630 -->Structure and alignment overview update
2583 as graduate feature colour settings are modified via the
2587 <!-- JAL-2034 -->Overview window doesn't always update
2588 when a group defined on the alignment is resized
2591 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2592 wrapped view result in positional status updates
2596 <!-- JAL-2563 -->Status bar doesn't show position for
2597 ambiguous amino acid and nucleotide symbols
2600 <!-- JAL-2602 -->Copy consensus sequence failed if
2601 alignment included gapped columns
2604 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2605 widgets don't permanently disappear
2608 <!-- JAL-2503 -->Cannot select or filter quantitative
2609 annotation that are shown only as column labels (e.g.
2610 T-Coffee column reliability scores)
2613 <!-- JAL-2594 -->Exception thrown if trying to create a
2614 sequence feature on gaps only
2617 <!-- JAL-2504 -->Features created with 'New feature'
2618 button from a Find inherit previously defined feature type
2619 rather than the Find query string
2622 <!-- JAL-2423 -->incorrect title in output window when
2623 exporting tree calculated in Jalview
2626 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2627 and then revealing them reorders sequences on the
2631 <!-- JAL-964 -->Group panel in sequence feature settings
2632 doesn't update to reflect available set of groups after
2633 interactively adding or modifying features
2636 <!-- JAL-2225 -->Sequence Database chooser unusable on
2640 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2641 only excluded gaps in current sequence and ignored
2648 <!-- JAL-2421 -->Overview window visible region moves
2649 erratically when hidden rows or columns are present
2652 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2653 Structure Viewer's colour menu don't correspond to
2657 <!-- JAL-2405 -->Protein specific colours only offered in
2658 colour and group colour menu for protein alignments
2661 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2662 reflect currently selected view or group's shading
2666 <!-- JAL-2624 -->Feature colour thresholds not respected
2667 when rendered on overview and structures when opacity at
2671 <!-- JAL-2589 -->User defined gap colour not shown in
2672 overview when features overlaid on alignment
2675 <!-- JAL-2567 -->Feature settings for different views not
2676 recovered correctly from Jalview project file
2679 <!-- JAL-2256 -->Feature colours in overview when first
2680 opened (automatically via preferences) are different to
2681 the main alignment panel
2684 <em>Data import/export</em>
2687 <!-- JAL-2576 -->Very large alignments take a long time to
2691 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2692 added after a sequence was imported are not written to
2696 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2697 when importing RNA secondary structure via Stockholm
2700 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2701 not shown in correct direction for simple pseudoknots
2704 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2705 with lightGray or darkGray via features file (but can
2709 <!-- JAL-2383 -->Above PID colour threshold not recovered
2710 when alignment view imported from project
2713 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2714 structure and sequences extracted from structure files
2715 imported via URL and viewed in Jmol
2718 <!-- JAL-2520 -->Structures loaded via URL are saved in
2719 Jalview Projects rather than fetched via URL again when
2720 the project is loaded and the structure viewed
2723 <em>Web Services</em>
2726 <!-- JAL-2519 -->EnsemblGenomes example failing after
2727 release of Ensembl v.88
2730 <!-- JAL-2366 -->Proxy server address and port always
2731 appear enabled in Preferences->Connections
2734 <!-- JAL-2461 -->DAS registry not found exceptions
2735 removed from console output
2738 <!-- JAL-2582 -->Cannot retrieve protein products from
2739 Ensembl by Peptide ID
2742 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2743 created from SIFTs, and spurious 'Couldn't open structure
2744 in Chimera' errors raised after April 2017 update (problem
2745 due to 'null' string rather than empty string used for
2746 residues with no corresponding PDB mapping).
2749 <em>Application UI</em>
2752 <!-- JAL-2361 -->User Defined Colours not added to Colour
2756 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2757 case' residues (button in colourscheme editor debugged and
2758 new documentation and tooltips added)
2761 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2762 doesn't restore group-specific text colour thresholds
2765 <!-- JAL-2243 -->Feature settings panel does not update as
2766 new features are added to alignment
2769 <!-- JAL-2532 -->Cancel in feature settings reverts
2770 changes to feature colours via the Amend features dialog
2773 <!-- JAL-2506 -->Null pointer exception when attempting to
2774 edit graduated feature colour via amend features dialog
2778 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2779 selection menu changes colours of alignment views
2782 <!-- JAL-2426 -->Spurious exceptions in console raised
2783 from alignment calculation workers after alignment has
2787 <!-- JAL-1608 -->Typo in selection popup menu - Create
2788 groups now 'Create Group'
2791 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2792 Create/Undefine group doesn't always work
2795 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2796 shown again after pressing 'Cancel'
2799 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2800 adjusts start position in wrap mode
2803 <!-- JAL-2563 -->Status bar doesn't show positions for
2804 ambiguous amino acids
2807 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2808 CDS/Protein view after CDS sequences added for aligned
2812 <!-- JAL-2592 -->User defined colourschemes called 'User
2813 Defined' don't appear in Colours menu
2819 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2820 score models doesn't always result in an updated PCA plot
2823 <!-- JAL-2442 -->Features not rendered as transparent on
2824 overview or linked structure view
2827 <!-- JAL-2372 -->Colour group by conservation doesn't
2831 <!-- JAL-2517 -->Hitting Cancel after applying
2832 user-defined colourscheme doesn't restore original
2839 <!-- JAL-2314 -->Unit test failure:
2840 jalview.ws.jabaws.RNAStructExportImport setup fails
2843 <!-- JAL-2307 -->Unit test failure:
2844 jalview.ws.sifts.SiftsClientTest due to compatibility
2845 problems with deep array comparison equality asserts in
2846 successive versions of TestNG
2849 <!-- JAL-2479 -->Relocated StructureChooserTest and
2850 ParameterUtilsTest Unit tests to Network suite
2853 <em>New Known Issues</em>
2856 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2857 phase after a sequence motif find operation
2860 <!-- JAL-2550 -->Importing annotation file with rows
2861 containing just upper and lower case letters are
2862 interpreted as WUSS RNA secondary structure symbols
2865 <!-- JAL-2590 -->Cannot load and display Newick trees
2866 reliably from eggnog Ortholog database
2869 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2870 containing features of type Highlight' when 'B' is pressed
2871 to mark columns containing highlighted regions.
2874 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2875 doesn't always add secondary structure annotation.
2880 <td width="60" nowrap>
2881 <div align="center">
2882 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2885 <td><div align="left">
2889 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2890 for all consensus calculations
2893 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2896 <li>Updated Jalview's Certum code signing certificate
2899 <em>Application</em>
2902 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2903 set of database cross-references, sorted alphabetically
2906 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2907 from database cross references. Users with custom links
2908 will receive a <a href="webServices/urllinks.html#warning">warning
2909 dialog</a> asking them to update their preferences.
2912 <!-- JAL-2287-->Cancel button and escape listener on
2913 dialog warning user about disconnecting Jalview from a
2917 <!-- JAL-2320-->Jalview's Chimera control window closes if
2918 the Chimera it is connected to is shut down
2921 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2922 columns menu item to mark columns containing highlighted
2923 regions (e.g. from structure selections or results of a
2927 <!-- JAL-2284-->Command line option for batch-generation
2928 of HTML pages rendering alignment data with the BioJS
2938 <!-- JAL-2286 -->Columns with more than one modal residue
2939 are not coloured or thresholded according to percent
2940 identity (first observed in Jalview 2.8.2)
2943 <!-- JAL-2301 -->Threonine incorrectly reported as not
2947 <!-- JAL-2318 -->Updates to documentation pages (above PID
2948 threshold, amino acid properties)
2951 <!-- JAL-2292 -->Lower case residues in sequences are not
2952 reported as mapped to residues in a structure file in the
2956 <!--JAL-2324 -->Identical features with non-numeric scores
2957 could be added multiple times to a sequence
2960 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2961 bond features shown as two highlighted residues rather
2962 than a range in linked structure views, and treated
2963 correctly when selecting and computing trees from features
2966 <!-- JAL-2281-->Custom URL links for database
2967 cross-references are matched to database name regardless
2972 <em>Application</em>
2975 <!-- JAL-2282-->Custom URL links for specific database
2976 names without regular expressions also offer links from
2980 <!-- JAL-2315-->Removing a single configured link in the
2981 URL links pane in Connections preferences doesn't actually
2982 update Jalview configuration
2985 <!-- JAL-2272-->CTRL-Click on a selected region to open
2986 the alignment area popup menu doesn't work on El-Capitan
2989 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2990 files with similarly named sequences if dropped onto the
2994 <!-- JAL-2312 -->Additional mappings are shown for PDB
2995 entries where more chains exist in the PDB accession than
2996 are reported in the SIFTS file
2999 <!-- JAL-2317-->Certain structures do not get mapped to
3000 the structure view when displayed with Chimera
3003 <!-- JAL-2317-->No chains shown in the Chimera view
3004 panel's View->Show Chains submenu
3007 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
3008 work for wrapped alignment views
3011 <!--JAL-2197 -->Rename UI components for running JPred
3012 predictions from 'JNet' to 'JPred'
3015 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
3016 corrupted when annotation panel vertical scroll is not at
3017 first annotation row
3020 <!--JAL-2332 -->Attempting to view structure for Hen
3021 lysozyme results in a PDB Client error dialog box
3024 <!-- JAL-2319 -->Structure View's mapping report switched
3025 ranges for PDB and sequence for SIFTS
3028 SIFTS 'Not_Observed' residues mapped to non-existant
3032 <!-- <em>New Known Issues</em>
3039 <td width="60" nowrap>
3040 <div align="center">
3041 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
3042 <em>25/10/2016</em></strong>
3045 <td><em>Application</em>
3047 <li>3D Structure chooser opens with 'Cached structures'
3048 view if structures already loaded</li>
3049 <li>Progress bar reports models as they are loaded to
3050 structure views</li>
3056 <li>Colour by conservation always enabled and no tick
3057 shown in menu when BLOSUM or PID shading applied</li>
3058 <li>FER1_ARATH and FER2_ARATH labels were switched in
3059 example sequences/projects/trees</li>
3061 <em>Application</em>
3063 <li>Jalview projects with views of local PDB structure
3064 files saved on Windows cannot be opened on OSX</li>
3065 <li>Multiple structure views can be opened and superposed
3066 without timeout for structures with multiple models or
3067 multiple sequences in alignment</li>
3068 <li>Cannot import or associated local PDB files without a
3069 PDB ID HEADER line</li>
3070 <li>RMSD is not output in Jmol console when superposition
3072 <li>Drag and drop of URL from Browser fails for Linux and
3073 OSX versions earlier than El Capitan</li>
3074 <li>ENA client ignores invalid content from ENA server</li>
3075 <li>Exceptions are not raised in console when ENA client
3076 attempts to fetch non-existent IDs via Fetch DB Refs UI
3078 <li>Exceptions are not raised in console when a new view
3079 is created on the alignment</li>
3080 <li>OSX right-click fixed for group selections: CMD-click
3081 to insert/remove gaps in groups and CTRL-click to open group
3084 <em>Build and deployment</em>
3086 <li>URL link checker now copes with multi-line anchor
3089 <em>New Known Issues</em>
3091 <li>Drag and drop from URL links in browsers do not work
3098 <td width="60" nowrap>
3099 <div align="center">
3100 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
3103 <td><em>General</em>
3106 <!-- JAL-2124 -->Updated Spanish translations.
3109 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
3110 for importing structure data to Jalview. Enables mmCIF and
3114 <!-- JAL-192 --->Alignment ruler shows positions relative to
3118 <!-- JAL-2202 -->Position/residue shown in status bar when
3119 mousing over sequence associated annotation
3122 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
3126 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
3127 '()', canonical '[]' and invalid '{}' base pair populations
3131 <!-- JAL-2092 -->Feature settings popup menu options for
3132 showing or hiding columns containing a feature
3135 <!-- JAL-1557 -->Edit selected group by double clicking on
3136 group and sequence associated annotation labels
3139 <!-- JAL-2236 -->Sequence name added to annotation label in
3140 select/hide columns by annotation and colour by annotation
3144 </ul> <em>Application</em>
3147 <!-- JAL-2050-->Automatically hide introns when opening a
3148 gene/transcript view
3151 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
3155 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
3156 structure mappings with the EMBL-EBI PDBe SIFTS database
3159 <!-- JAL-2079 -->Updated download sites used for Rfam and
3160 Pfam sources to xfam.org
3163 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
3166 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
3167 over sequences in Jalview
3170 <!-- JAL-2027-->Support for reverse-complement coding
3171 regions in ENA and EMBL
3174 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
3175 for record retrieval via ENA rest API
3178 <!-- JAL-2027 -->Support for ENA CDS records with reverse
3182 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
3183 groovy script execution
3186 <!-- JAL-1812 -->New 'execute Groovy script' option in an
3187 alignment window's Calculate menu
3190 <!-- JAL-1812 -->Allow groovy scripts that call
3191 Jalview.getAlignFrames() to run in headless mode
3194 <!-- JAL-2068 -->Support for creating new alignment
3195 calculation workers from groovy scripts
3198 <!-- JAL-1369 --->Store/restore reference sequence in
3202 <!-- JAL-1803 -->Chain codes for a sequence's PDB
3203 associations are now saved/restored from project
3206 <!-- JAL-1993 -->Database selection dialog always shown
3207 before sequence fetcher is opened
3210 <!-- JAL-2183 -->Double click on an entry in Jalview's
3211 database chooser opens a sequence fetcher
3214 <!-- JAL-1563 -->Free-text search client for UniProt using
3215 the UniProt REST API
3218 <!-- JAL-2168 -->-nonews command line parameter to prevent
3219 the news reader opening
3222 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
3223 querying stored in preferences
3226 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
3230 <!-- JAL-1977-->Tooltips shown on database chooser
3233 <!-- JAL-391 -->Reverse complement function in calculate
3234 menu for nucleotide sequences
3237 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
3238 and feature counts preserves alignment ordering (and
3239 debugged for complex feature sets).
3242 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
3243 viewing structures with Jalview 2.10
3246 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
3247 genome, transcript CCDS and gene ids via the Ensembl and
3248 Ensembl Genomes REST API
3251 <!-- JAL-2049 -->Protein sequence variant annotation
3252 computed for 'sequence_variant' annotation on CDS regions
3256 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
3260 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
3261 Ref Fetcher fails to match, or otherwise updates sequence
3262 data from external database records.
3265 <!-- JAL-2154 -->Revised Jalview Project format for
3266 efficient recovery of sequence coding and alignment
3267 annotation relationships.
3269 </ul> <!-- <em>Applet</em>
3280 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
3284 <!-- JAL-2018-->Export features in Jalview format (again)
3285 includes graduated colourschemes
3288 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
3289 working with big alignments and lots of hidden columns
3292 <!-- JAL-2053-->Hidden column markers not always rendered
3293 at right of alignment window
3296 <!-- JAL-2067 -->Tidied up links in help file table of
3300 <!-- JAL-2072 -->Feature based tree calculation not shown
3304 <!-- JAL-2075 -->Hidden columns ignored during feature
3305 based tree calculation
3308 <!-- JAL-2065 -->Alignment view stops updating when show
3309 unconserved enabled for group on alignment
3312 <!-- JAL-2086 -->Cannot insert gaps into sequence when
3316 <!-- JAL-2146 -->Alignment column in status incorrectly
3317 shown as "Sequence position" when mousing over
3321 <!-- JAL-2099 -->Incorrect column numbers in ruler when
3322 hidden columns present
3325 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
3326 user created annotation added to alignment
3329 <!-- JAL-1841 -->RNA Structure consensus only computed for
3330 '()' base pair annotation
3333 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
3334 in zero scores for all base pairs in RNA Structure
3338 <!-- JAL-2174-->Extend selection with columns containing
3342 <!-- JAL-2275 -->Pfam format writer puts extra space at
3343 beginning of sequence
3346 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
3350 <!-- JAL-2238 -->Cannot create groups on an alignment from
3351 from a tree when t-coffee scores are shown
3354 <!-- JAL-1836,1967 -->Cannot import and view PDB
3355 structures with chains containing negative resnums (4q4h)
3358 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
3362 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
3363 to Clustal, PIR and PileUp output
3366 <!-- JAL-2008 -->Reordering sequence features that are
3367 not visible causes alignment window to repaint
3370 <!-- JAL-2006 -->Threshold sliders don't work in
3371 graduated colour and colour by annotation row for e-value
3372 scores associated with features and annotation rows
3375 <!-- JAL-1797 -->amino acid physicochemical conservation
3376 calculation should be case independent
3379 <!-- JAL-2173 -->Remove annotation also updates hidden
3383 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
3384 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
3385 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
3388 <!-- JAL-2065 -->Null pointer exceptions and redraw
3389 problems when reference sequence defined and 'show
3390 non-conserved' enabled
3393 <!-- JAL-1306 -->Quality and Conservation are now shown on
3394 load even when Consensus calculation is disabled
3397 <!-- JAL-1932 -->Remove right on penultimate column of
3398 alignment does nothing
3401 <em>Application</em>
3404 <!-- JAL-1552-->URLs and links can't be imported by
3405 drag'n'drop on OSX when launched via webstart (note - not
3406 yet fixed for El Capitan)
3409 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
3410 output when running on non-gb/us i18n platforms
3413 <!-- JAL-1944 -->Error thrown when exporting a view with
3414 hidden sequences as flat-file alignment
3417 <!-- JAL-2030-->InstallAnywhere distribution fails when
3421 <!-- JAL-2080-->Jalview very slow to launch via webstart
3422 (also hotfix for 2.9.0b2)
3425 <!-- JAL-2085 -->Cannot save project when view has a
3426 reference sequence defined
3429 <!-- JAL-1011 -->Columns are suddenly selected in other
3430 alignments and views when revealing hidden columns
3433 <!-- JAL-1989 -->Hide columns not mirrored in complement
3434 view in a cDNA/Protein splitframe
3437 <!-- JAL-1369 -->Cannot save/restore representative
3438 sequence from project when only one sequence is
3442 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
3443 in Structure Chooser
3446 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
3447 structure consensus didn't refresh annotation panel
3450 <!-- JAL-1962 -->View mapping in structure view shows
3451 mappings between sequence and all chains in a PDB file
3454 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
3455 dialogs format columns correctly, don't display array
3456 data, sort columns according to type
3459 <!-- JAL-1975 -->Export complete shown after destination
3460 file chooser is cancelled during an image export
3463 <!-- JAL-2025 -->Error when querying PDB Service with
3464 sequence name containing special characters
3467 <!-- JAL-2024 -->Manual PDB structure querying should be
3471 <!-- JAL-2104 -->Large tooltips with broken HTML
3472 formatting don't wrap
3475 <!-- JAL-1128 -->Figures exported from wrapped view are
3476 truncated so L looks like I in consensus annotation
3479 <!-- JAL-2003 -->Export features should only export the
3480 currently displayed features for the current selection or
3484 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
3485 after fetching cross-references, and restoring from
3489 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
3490 followed in the structure viewer
3493 <!-- JAL-2163 -->Titles for individual alignments in
3494 splitframe not restored from project
3497 <!-- JAL-2145 -->missing autocalculated annotation at
3498 trailing end of protein alignment in transcript/product
3499 splitview when pad-gaps not enabled by default
3502 <!-- JAL-1797 -->amino acid physicochemical conservation
3506 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
3507 article has been read (reopened issue due to
3508 internationalisation problems)
3511 <!-- JAL-1960 -->Only offer PDB structures in structure
3512 viewer based on sequence name, PDB and UniProt
3517 <!-- JAL-1976 -->No progress bar shown during export of
3521 <!-- JAL-2213 -->Structures not always superimposed after
3522 multiple structures are shown for one or more sequences.
3525 <!-- JAL-1370 -->Reference sequence characters should not
3526 be replaced with '.' when 'Show unconserved' format option
3530 <!-- JAL-1823 -->Cannot specify chain code when entering
3531 specific PDB id for sequence
3534 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3535 'Export hidden sequences' is enabled, but 'export hidden
3536 columns' is disabled.
3539 <!--JAL-2026-->Best Quality option in structure chooser
3540 selects lowest rather than highest resolution structures
3544 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3545 to sequence mapping in 'View Mappings' report
3548 <!-- JAL-2284 -->Unable to read old Jalview projects that
3549 contain non-XML data added after Jalvew wrote project.
3552 <!-- JAL-2118 -->Newly created annotation row reorders
3553 after clicking on it to create new annotation for a
3557 <!-- JAL-1980 -->Null Pointer Exception raised when
3558 pressing Add on an orphaned cut'n'paste window.
3560 <!-- may exclude, this is an external service stability issue JAL-1941
3561 -- > RNA 3D structure not added via DSSR service</li> -->
3566 <!-- JAL-2151 -->Incorrect columns are selected when
3567 hidden columns present before start of sequence
3570 <!-- JAL-1986 -->Missing dependencies on applet pages
3574 <!-- JAL-1947 -->Overview pixel size changes when
3575 sequences are hidden in applet
3578 <!-- JAL-1996 -->Updated instructions for applet
3579 deployment on examples pages.
3586 <td width="60" nowrap>
3587 <div align="center">
3588 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3589 <em>16/10/2015</em></strong>
3592 <td><em>General</em>
3594 <li>Time stamps for signed Jalview application and applet
3599 <em>Application</em>
3601 <li>Duplicate group consensus and conservation rows
3602 shown when tree is partitioned</li>
3603 <li>Erratic behaviour when tree partitions made with
3604 multiple cDNA/Protein split views</li>
3610 <td width="60" nowrap>
3611 <div align="center">
3612 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3613 <em>8/10/2015</em></strong>
3616 <td><em>General</em>
3618 <li>Updated Spanish translations of localized text for
3620 </ul> <em>Application</em>
3622 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3623 <li>Signed OSX InstallAnywhere installer<br></li>
3624 <li>Support for per-sequence based annotations in BioJSON</li>
3625 </ul> <em>Applet</em>
3627 <li>Split frame example added to applet examples page</li>
3628 </ul> <em>Build and Deployment</em>
3631 <!-- JAL-1888 -->New ant target for running Jalview's test
3639 <li>Mapping of cDNA to protein in split frames
3640 incorrect when sequence start > 1</li>
3641 <li>Broken images in filter column by annotation dialog
3643 <li>Feature colours not parsed from features file</li>
3644 <li>Exceptions and incomplete link URLs recovered when
3645 loading a features file containing HTML tags in feature
3649 <em>Application</em>
3651 <li>Annotations corrupted after BioJS export and
3653 <li>Incorrect sequence limits after Fetch DB References
3654 with 'trim retrieved sequences'</li>
3655 <li>Incorrect warning about deleting all data when
3656 deleting selected columns</li>
3657 <li>Patch to build system for shipping properly signed
3658 JNLP templates for webstart launch</li>
3659 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3660 unreleased structures for download or viewing</li>
3661 <li>Tab/space/return keystroke operation of EMBL-PDBe
3662 fetcher/viewer dialogs works correctly</li>
3663 <li>Disabled 'minimise' button on Jalview windows
3664 running on OSX to workaround redraw hang bug</li>
3665 <li>Split cDNA/Protein view position and geometry not
3666 recovered from jalview project</li>
3667 <li>Initial enabled/disabled state of annotation menu
3668 sorter 'show autocalculated first/last' corresponds to
3670 <li>Restoring of Clustal, RNA Helices and T-Coffee
3671 color schemes from BioJSON</li>
3675 <li>Reorder sequences mirrored in cDNA/Protein split
3677 <li>Applet with Jmol examples not loading correctly</li>
3683 <td><div align="center">
3684 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3686 <td><em>General</em>
3688 <li>Linked visualisation and analysis of DNA and Protein
3691 <li>Translated cDNA alignments shown as split protein
3692 and DNA alignment views</li>
3693 <li>Codon consensus annotation for linked protein and
3694 cDNA alignment views</li>
3695 <li>Link cDNA or Protein product sequences by loading
3696 them onto Protein or cDNA alignments</li>
3697 <li>Reconstruct linked cDNA alignment from aligned
3698 protein sequences</li>
3701 <li>Jmol integration updated to Jmol v14.2.14</li>
3702 <li>Import and export of Jalview alignment views as <a
3703 href="features/bioJsonFormat.html">BioJSON</a></li>
3704 <li>New alignment annotation file statements for
3705 reference sequences and marking hidden columns</li>
3706 <li>Reference sequence based alignment shading to
3707 highlight variation</li>
3708 <li>Select or hide columns according to alignment
3710 <li>Find option for locating sequences by description</li>
3711 <li>Conserved physicochemical properties shown in amino
3712 acid conservation row</li>
3713 <li>Alignments can be sorted by number of RNA helices</li>
3714 </ul> <em>Application</em>
3716 <li>New cDNA/Protein analysis capabilities
3718 <li>Get Cross-References should open a Split Frame
3719 view with cDNA/Protein</li>
3720 <li>Detect when nucleotide sequences and protein
3721 sequences are placed in the same alignment</li>
3722 <li>Split cDNA/Protein views are saved in Jalview
3727 <li>Use REST API to talk to Chimera</li>
3728 <li>Selected regions in Chimera are highlighted in linked
3729 Jalview windows</li>
3731 <li>VARNA RNA viewer updated to v3.93</li>
3732 <li>VARNA views are saved in Jalview Projects</li>
3733 <li>Pseudoknots displayed as Jalview RNA annotation can
3734 be shown in VARNA</li>
3736 <li>Make groups for selection uses marked columns as well
3737 as the active selected region</li>
3739 <li>Calculate UPGMA and NJ trees using sequence feature
3741 <li>New Export options
3743 <li>New Export Settings dialog to control hidden
3744 region export in flat file generation</li>
3746 <li>Export alignment views for display with the <a
3747 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3749 <li>Export scrollable SVG in HTML page</li>
3750 <li>Optional embedding of BioJSON data when exporting
3751 alignment figures to HTML</li>
3753 <li>3D structure retrieval and display
3755 <li>Free text and structured queries with the PDBe
3757 <li>PDBe Search API based discovery and selection of
3758 PDB structures for a sequence set</li>
3762 <li>JPred4 employed for protein secondary structure
3764 <li>Hide Insertions menu option to hide unaligned columns
3765 for one or a group of sequences</li>
3766 <li>Automatically hide insertions in alignments imported
3767 from the JPred4 web server</li>
3768 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3769 system on OSX<br />LGPL libraries courtesy of <a
3770 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3772 <li>changed 'View nucleotide structure' submenu to 'View
3773 VARNA 2D Structure'</li>
3774 <li>change "View protein structure" menu option to "3D
3777 </ul> <em>Applet</em>
3779 <li>New layout for applet example pages</li>
3780 <li>New parameters to enable SplitFrame view
3781 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3782 <li>New example demonstrating linked viewing of cDNA and
3783 Protein alignments</li>
3784 </ul> <em>Development and deployment</em>
3786 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3787 <li>Include installation type and git revision in build
3788 properties and console log output</li>
3789 <li>Jalview Github organisation, and new github site for
3790 storing BioJsMSA Templates</li>
3791 <li>Jalview's unit tests now managed with TestNG</li>
3794 <!-- <em>General</em>
3796 </ul> --> <!-- issues resolved --> <em>Application</em>
3798 <li>Escape should close any open find dialogs</li>
3799 <li>Typo in select-by-features status report</li>
3800 <li>Consensus RNA secondary secondary structure
3801 predictions are not highlighted in amber</li>
3802 <li>Missing gap character in v2.7 example file means
3803 alignment appears unaligned when pad-gaps is not enabled</li>
3804 <li>First switch to RNA Helices colouring doesn't colour
3805 associated structure views</li>
3806 <li>ID width preference option is greyed out when auto
3807 width checkbox not enabled</li>
3808 <li>Stopped a warning dialog from being shown when
3809 creating user defined colours</li>
3810 <li>'View Mapping' in structure viewer shows sequence
3811 mappings for just that viewer's sequences</li>
3812 <li>Workaround for superposing PDB files containing
3813 multiple models in Chimera</li>
3814 <li>Report sequence position in status bar when hovering
3815 over Jmol structure</li>
3816 <li>Cannot output gaps as '.' symbols with Selection ->
3817 output to text box</li>
3818 <li>Flat file exports of alignments with hidden columns
3819 have incorrect sequence start/end</li>
3820 <li>'Aligning' a second chain to a Chimera structure from
3822 <li>Colour schemes applied to structure viewers don't
3823 work for nucleotide</li>
3824 <li>Loading/cut'n'pasting an empty or invalid file leads
3825 to a grey/invisible alignment window</li>
3826 <li>Exported Jpred annotation from a sequence region
3827 imports to different position</li>
3828 <li>Space at beginning of sequence feature tooltips shown
3829 on some platforms</li>
3830 <li>Chimera viewer 'View | Show Chain' menu is not
3832 <li>'New View' fails with a Null Pointer Exception in
3833 console if Chimera has been opened</li>
3834 <li>Mouseover to Chimera not working</li>
3835 <li>Miscellaneous ENA XML feature qualifiers not
3837 <li>NPE in annotation renderer after 'Extract Scores'</li>
3838 <li>If two structures in one Chimera window, mouseover of
3839 either sequence shows on first structure</li>
3840 <li>'Show annotations' options should not make
3841 non-positional annotations visible</li>
3842 <li>Subsequence secondary structure annotation not shown
3843 in right place after 'view flanking regions'</li>
3844 <li>File Save As type unset when current file format is
3846 <li>Save as '.jar' option removed for saving Jalview
3848 <li>Colour by Sequence colouring in Chimera more
3850 <li>Cannot 'add reference annotation' for a sequence in
3851 several views on same alignment</li>
3852 <li>Cannot show linked products for EMBL / ENA records</li>
3853 <li>Jalview's tooltip wraps long texts containing no
3855 </ul> <em>Applet</em>
3857 <li>Jmol to JalviewLite mouseover/link not working</li>
3858 <li>JalviewLite can't import sequences with ID
3859 descriptions containing angle brackets</li>
3860 </ul> <em>General</em>
3862 <li>Cannot export and reimport RNA secondary structure
3863 via jalview annotation file</li>
3864 <li>Random helix colour palette for colour by annotation
3865 with RNA secondary structure</li>
3866 <li>Mouseover to cDNA from STOP residue in protein
3867 translation doesn't work.</li>
3868 <li>hints when using the select by annotation dialog box</li>
3869 <li>Jmol alignment incorrect if PDB file has alternate CA
3871 <li>FontChooser message dialog appears to hang after
3872 choosing 1pt font</li>
3873 <li>Peptide secondary structure incorrectly imported from
3874 annotation file when annotation display text includes 'e' or
3876 <li>Cannot set colour of new feature type whilst creating
3878 <li>cDNA translation alignment should not be sequence
3879 order dependent</li>
3880 <li>'Show unconserved' doesn't work for lower case
3882 <li>Nucleotide ambiguity codes involving R not recognised</li>
3883 </ul> <em>Deployment and Documentation</em>
3885 <li>Applet example pages appear different to the rest of
3886 www.jalview.org</li>
3887 </ul> <em>Application Known issues</em>
3889 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3890 <li>Misleading message appears after trying to delete
3892 <li>Jalview icon not shown in dock after InstallAnywhere
3893 version launches</li>
3894 <li>Fetching EMBL reference for an RNA sequence results
3895 fails with a sequence mismatch</li>
3896 <li>Corrupted or unreadable alignment display when
3897 scrolling alignment to right</li>
3898 <li>ArrayIndexOutOfBoundsException thrown when remove
3899 empty columns called on alignment with ragged gapped ends</li>
3900 <li>auto calculated alignment annotation rows do not get
3901 placed above or below non-autocalculated rows</li>
3902 <li>Jalview dekstop becomes sluggish at full screen in
3903 ultra-high resolution</li>
3904 <li>Cannot disable consensus calculation independently of
3905 quality and conservation</li>
3906 <li>Mouseover highlighting between cDNA and protein can
3907 become sluggish with more than one splitframe shown</li>
3908 </ul> <em>Applet Known Issues</em>
3910 <li>Core PDB parsing code requires Jmol</li>
3911 <li>Sequence canvas panel goes white when alignment
3912 window is being resized</li>
3918 <td><div align="center">
3919 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3921 <td><em>General</em>
3923 <li>Updated Java code signing certificate donated by
3925 <li>Features and annotation preserved when performing
3926 pairwise alignment</li>
3927 <li>RNA pseudoknot annotation can be
3928 imported/exported/displayed</li>
3929 <li>'colour by annotation' can colour by RNA and
3930 protein secondary structure</li>
3931 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3932 post-hoc with 2.9 release</em>)
3935 </ul> <em>Application</em>
3937 <li>Extract and display secondary structure for sequences
3938 with 3D structures</li>
3939 <li>Support for parsing RNAML</li>
3940 <li>Annotations menu for layout
3942 <li>sort sequence annotation rows by alignment</li>
3943 <li>place sequence annotation above/below alignment
3946 <li>Output in Stockholm format</li>
3947 <li>Internationalisation: improved Spanish (es)
3949 <li>Structure viewer preferences tab</li>
3950 <li>Disorder and Secondary Structure annotation tracks
3951 shared between alignments</li>
3952 <li>UCSF Chimera launch and linked highlighting from
3954 <li>Show/hide all sequence associated annotation rows for
3955 all or current selection</li>
3956 <li>disorder and secondary structure predictions
3957 available as dataset annotation</li>
3958 <li>Per-sequence rna helices colouring</li>
3961 <li>Sequence database accessions imported when fetching
3962 alignments from Rfam</li>
3963 <li>update VARNA version to 3.91</li>
3965 <li>New groovy scripts for exporting aligned positions,
3966 conservation values, and calculating sum of pairs scores.</li>
3967 <li>Command line argument to set default JABAWS server</li>
3968 <li>include installation type in build properties and
3969 console log output</li>
3970 <li>Updated Jalview project format to preserve dataset
3974 <!-- issues resolved --> <em>Application</em>
3976 <li>Distinguish alignment and sequence associated RNA
3977 structure in structure->view->VARNA</li>
3978 <li>Raise dialog box if user deletes all sequences in an
3980 <li>Pressing F1 results in documentation opening twice</li>
3981 <li>Sequence feature tooltip is wrapped</li>
3982 <li>Double click on sequence associated annotation
3983 selects only first column</li>
3984 <li>Redundancy removal doesn't result in unlinked
3985 leaves shown in tree</li>
3986 <li>Undos after several redundancy removals don't undo
3988 <li>Hide sequence doesn't hide associated annotation</li>
3989 <li>User defined colours dialog box too big to fit on
3990 screen and buttons not visible</li>
3991 <li>author list isn't updated if already written to
3992 Jalview properties</li>
3993 <li>Popup menu won't open after retrieving sequence
3995 <li>File open window for associate PDB doesn't open</li>
3996 <li>Left-then-right click on a sequence id opens a
3997 browser search window</li>
3998 <li>Cannot open sequence feature shading/sort popup menu
3999 in feature settings dialog</li>
4000 <li>better tooltip placement for some areas of Jalview
4002 <li>Allow addition of JABAWS Server which doesn't
4003 pass validation</li>
4004 <li>Web services parameters dialog box is too large to
4006 <li>Muscle nucleotide alignment preset obscured by
4008 <li>JABAWS preset submenus don't contain newly
4009 defined user preset</li>
4010 <li>MSA web services warns user if they were launched
4011 with invalid input</li>
4012 <li>Jalview cannot contact DAS Registy when running on
4015 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
4016 'Superpose with' submenu not shown when new view
4020 </ul> <!-- <em>Applet</em>
4022 </ul> <em>General</em>
4024 </ul>--> <em>Deployment and Documentation</em>
4026 <li>2G and 1G options in launchApp have no effect on
4027 memory allocation</li>
4028 <li>launchApp service doesn't automatically open
4029 www.jalview.org/examples/exampleFile.jar if no file is given</li>
4031 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
4032 InstallAnywhere reports cannot find valid JVM when Java
4033 1.7_055 is available
4035 </ul> <em>Application Known issues</em>
4038 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
4039 corrupted or unreadable alignment display when scrolling
4043 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
4044 retrieval fails but progress bar continues for DAS retrieval
4045 with large number of ID
4048 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
4049 flatfile output of visible region has incorrect sequence
4053 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
4054 rna structure consensus doesn't update when secondary
4055 structure tracks are rearranged
4058 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
4059 invalid rna structure positional highlighting does not
4060 highlight position of invalid base pairs
4063 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
4064 out of memory errors are not raised when saving Jalview
4065 project from alignment window file menu
4068 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
4069 Switching to RNA Helices colouring doesn't propagate to
4073 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
4074 colour by RNA Helices not enabled when user created
4075 annotation added to alignment
4078 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
4079 Jalview icon not shown on dock in Mountain Lion/Webstart
4081 </ul> <em>Applet Known Issues</em>
4084 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
4085 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
4088 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
4089 Jalview and Jmol example not compatible with IE9
4092 <li>Sort by annotation score doesn't reverse order
4098 <td><div align="center">
4099 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
4102 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
4105 <li>Internationalisation of user interface (usually
4106 called i18n support) and translation for Spanish locale</li>
4107 <li>Define/Undefine group on current selection with
4108 Ctrl-G/Shift Ctrl-G</li>
4109 <li>Improved group creation/removal options in
4110 alignment/sequence Popup menu</li>
4111 <li>Sensible precision for symbol distribution
4112 percentages shown in logo tooltip.</li>
4113 <li>Annotation panel height set according to amount of
4114 annotation when alignment first opened</li>
4115 </ul> <em>Application</em>
4117 <li>Interactive consensus RNA secondary structure
4118 prediction VIENNA RNAAliFold JABA 2.1 service</li>
4119 <li>Select columns containing particular features from
4120 Feature Settings dialog</li>
4121 <li>View all 'representative' PDB structures for selected
4123 <li>Update Jalview project format:
4125 <li>New file extension for Jalview projects '.jvp'</li>
4126 <li>Preserve sequence and annotation dataset (to
4127 store secondary structure annotation,etc)</li>
4128 <li>Per group and alignment annotation and RNA helix
4132 <li>New similarity measures for PCA and Tree calculation
4134 <li>Experimental support for retrieval and viewing of
4135 flanking regions for an alignment</li>
4139 <!-- issues resolved --> <em>Application</em>
4141 <li>logo keeps spinning and status remains at queued or
4142 running after job is cancelled</li>
4143 <li>cannot export features from alignments imported from
4144 Jalview/VAMSAS projects</li>
4145 <li>Buggy slider for web service parameters that take
4147 <li>Newly created RNA secondary structure line doesn't
4148 have 'display all symbols' flag set</li>
4149 <li>T-COFFEE alignment score shading scheme and other
4150 annotation shading not saved in Jalview project</li>
4151 <li>Local file cannot be loaded in freshly downloaded
4153 <li>Jalview icon not shown on dock in Mountain
4155 <li>Load file from desktop file browser fails</li>
4156 <li>Occasional NPE thrown when calculating large trees</li>
4157 <li>Cannot reorder or slide sequences after dragging an
4158 alignment onto desktop</li>
4159 <li>Colour by annotation dialog throws NPE after using
4160 'extract scores' function</li>
4161 <li>Loading/cut'n'pasting an empty file leads to a grey
4162 alignment window</li>
4163 <li>Disorder thresholds rendered incorrectly after
4164 performing IUPred disorder prediction</li>
4165 <li>Multiple group annotated consensus rows shown when
4166 changing 'normalise logo' display setting</li>
4167 <li>Find shows blank dialog after 'finished searching' if
4168 nothing matches query</li>
4169 <li>Null Pointer Exceptions raised when sorting by
4170 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
4172 <li>Errors in Jmol console when structures in alignment
4173 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
4175 <li>Not all working JABAWS services are shown in
4177 <li>JAVAWS version of Jalview fails to launch with
4178 'invalid literal/length code'</li>
4179 <li>Annotation/RNA Helix colourschemes cannot be applied
4180 to alignment with groups (actually fixed in 2.8.0b1)</li>
4181 <li>RNA Helices and T-Coffee Scores available as default
4184 </ul> <em>Applet</em>
4186 <li>Remove group option is shown even when selection is
4188 <li>Apply to all groups ticked but colourscheme changes
4189 don't affect groups</li>
4190 <li>Documented RNA Helices and T-Coffee Scores as valid
4191 colourscheme name</li>
4192 <li>Annotation labels drawn on sequence IDs when
4193 Annotation panel is not displayed</li>
4194 <li>Increased font size for dropdown menus on OSX and
4195 embedded windows</li>
4196 </ul> <em>Other</em>
4198 <li>Consensus sequence for alignments/groups with a
4199 single sequence were not calculated</li>
4200 <li>annotation files that contain only groups imported as
4201 annotation and junk sequences</li>
4202 <li>Fasta files with sequences containing '*' incorrectly
4203 recognised as PFAM or BLC</li>
4204 <li>conservation/PID slider apply all groups option
4205 doesn't affect background (2.8.0b1)
4207 <li>redundancy highlighting is erratic at 0% and 100%</li>
4208 <li>Remove gapped columns fails for sequences with ragged
4210 <li>AMSA annotation row with leading spaces is not
4211 registered correctly on import</li>
4212 <li>Jalview crashes when selecting PCA analysis for
4213 certain alignments</li>
4214 <li>Opening the colour by annotation dialog for an
4215 existing annotation based 'use original colours'
4216 colourscheme loses original colours setting</li>
4221 <td><div align="center">
4222 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
4223 <em>30/1/2014</em></strong>
4227 <li>Trusted certificates for JalviewLite applet and
4228 Jalview Desktop application<br />Certificate was donated by
4229 <a href="https://www.certum.eu">Certum</a> to the Jalview
4230 open source project).
4232 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
4233 <li>Output in Stockholm format</li>
4234 <li>Allow import of data from gzipped files</li>
4235 <li>Export/import group and sequence associated line
4236 graph thresholds</li>
4237 <li>Nucleotide substitution matrix that supports RNA and
4238 ambiguity codes</li>
4239 <li>Allow disorder predictions to be made on the current
4240 selection (or visible selection) in the same way that JPred
4242 <li>Groovy scripting for headless Jalview operation</li>
4243 </ul> <em>Other improvements</em>
4245 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
4246 <li>COMBINE statement uses current SEQUENCE_REF and
4247 GROUP_REF scope to group annotation rows</li>
4248 <li>Support '' style escaping of quotes in Newick
4250 <li>Group options for JABAWS service by command line name</li>
4251 <li>Empty tooltip shown for JABA service options with a
4252 link but no description</li>
4253 <li>Select primary source when selecting authority in
4254 database fetcher GUI</li>
4255 <li>Add .mfa to FASTA file extensions recognised by
4257 <li>Annotation label tooltip text wrap</li>
4262 <li>Slow scrolling when lots of annotation rows are
4264 <li>Lots of NPE (and slowness) after creating RNA
4265 secondary structure annotation line</li>
4266 <li>Sequence database accessions not imported when
4267 fetching alignments from Rfam</li>
4268 <li>Incorrect SHMR submission for sequences with
4270 <li>View all structures does not always superpose
4272 <li>Option widgets in service parameters not updated to
4273 reflect user or preset settings</li>
4274 <li>Null pointer exceptions for some services without
4275 presets or adjustable parameters</li>
4276 <li>Discover PDB IDs entry in structure menu doesn't
4277 discover PDB xRefs</li>
4278 <li>Exception encountered while trying to retrieve
4279 features with DAS</li>
4280 <li>Lowest value in annotation row isn't coloured
4281 when colour by annotation (per sequence) is coloured</li>
4282 <li>Keyboard mode P jumps to start of gapped region when
4283 residue follows a gap</li>
4284 <li>Jalview appears to hang importing an alignment with
4285 Wrap as default or after enabling Wrap</li>
4286 <li>'Right click to add annotations' message
4287 shown in wrap mode when no annotations present</li>
4288 <li>Disorder predictions fail with NPE if no automatic
4289 annotation already exists on alignment</li>
4290 <li>oninit javascript function should be called after
4291 initialisation completes</li>
4292 <li>Remove redundancy after disorder prediction corrupts
4293 alignment window display</li>
4294 <li>Example annotation file in documentation is invalid</li>
4295 <li>Grouped line graph annotation rows are not exported
4296 to annotation file</li>
4297 <li>Multi-harmony analysis cannot be run when only two
4299 <li>Cannot create multiple groups of line graphs with
4300 several 'combine' statements in annotation file</li>
4301 <li>Pressing return several times causes Number Format
4302 exceptions in keyboard mode</li>
4303 <li>Multi-harmony (SHMMR) method doesn't submit
4304 correct partitions for input data</li>
4305 <li>Translation from DNA to Amino Acids fails</li>
4306 <li>Jalview fail to load newick tree with quoted label</li>
4307 <li>--headless flag isn't understood</li>
4308 <li>ClassCastException when generating EPS in headless
4310 <li>Adjusting sequence-associated shading threshold only
4311 changes one row's threshold</li>
4312 <li>Preferences and Feature settings panel panel
4313 doesn't open</li>
4314 <li>hide consensus histogram also hides conservation and
4315 quality histograms</li>
4320 <td><div align="center">
4321 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
4323 <td><em>Application</em>
4325 <li>Support for JABAWS 2.0 Services (AACon alignment
4326 conservation, protein disorder and Clustal Omega)</li>
4327 <li>JABAWS server status indicator in Web Services
4329 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
4330 in Jalview alignment window</li>
4331 <li>Updated Jalview build and deploy framework for OSX
4332 mountain lion, windows 7, and 8</li>
4333 <li>Nucleotide substitution matrix for PCA that supports
4334 RNA and ambiguity codes</li>
4336 <li>Improved sequence database retrieval GUI</li>
4337 <li>Support fetching and database reference look up
4338 against multiple DAS sources (Fetch all from in 'fetch db
4340 <li>Jalview project improvements
4342 <li>Store and retrieve the 'belowAlignment'
4343 flag for annotation</li>
4344 <li>calcId attribute to group annotation rows on the
4346 <li>Store AACon calculation settings for a view in
4347 Jalview project</li>
4351 <li>horizontal scrolling gesture support</li>
4352 <li>Visual progress indicator when PCA calculation is
4354 <li>Simpler JABA web services menus</li>
4355 <li>visual indication that web service results are still
4356 being retrieved from server</li>
4357 <li>Serialise the dialogs that are shown when Jalview
4358 starts up for first time</li>
4359 <li>Jalview user agent string for interacting with HTTP
4361 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
4363 <li>Examples directory and Groovy library included in
4364 InstallAnywhere distribution</li>
4365 </ul> <em>Applet</em>
4367 <li>RNA alignment and secondary structure annotation
4368 visualization applet example</li>
4369 </ul> <em>General</em>
4371 <li>Normalise option for consensus sequence logo</li>
4372 <li>Reset button in PCA window to return dimensions to
4374 <li>Allow seqspace or Jalview variant of alignment PCA
4376 <li>PCA with either nucleic acid and protein substitution
4378 <li>Allow windows containing HTML reports to be exported
4380 <li>Interactive display and editing of RNA secondary
4381 structure contacts</li>
4382 <li>RNA Helix Alignment Colouring</li>
4383 <li>RNA base pair logo consensus</li>
4384 <li>Parse sequence associated secondary structure
4385 information in Stockholm files</li>
4386 <li>HTML Export database accessions and annotation
4387 information presented in tooltip for sequences</li>
4388 <li>Import secondary structure from LOCARNA clustalw
4389 style RNA alignment files</li>
4390 <li>import and visualise T-COFFEE quality scores for an
4392 <li>'colour by annotation' per sequence option to
4393 shade each sequence according to its associated alignment
4395 <li>New Jalview Logo</li>
4396 </ul> <em>Documentation and Development</em>
4398 <li>documentation for score matrices used in Jalview</li>
4399 <li>New Website!</li>
4401 <td><em>Application</em>
4403 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
4404 wsdbfetch REST service</li>
4405 <li>Stop windows being moved outside desktop on OSX</li>
4406 <li>Filetype associations not installed for webstart
4408 <li>Jalview does not always retrieve progress of a JABAWS
4409 job execution in full once it is complete</li>
4410 <li>revise SHMR RSBS definition to ensure alignment is
4411 uploaded via ali_file parameter</li>
4412 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
4413 <li>View all structures superposed fails with exception</li>
4414 <li>Jnet job queues forever if a very short sequence is
4415 submitted for prediction</li>
4416 <li>Cut and paste menu not opened when mouse clicked on
4418 <li>Putting fractional value into integer text box in
4419 alignment parameter dialog causes Jalview to hang</li>
4420 <li>Structure view highlighting doesn't work on
4422 <li>View all structures fails with exception shown in
4424 <li>Characters in filename associated with PDBEntry not
4425 escaped in a platform independent way</li>
4426 <li>Jalview desktop fails to launch with exception when
4428 <li>Tree calculation reports 'you must have 2 or more
4429 sequences selected' when selection is empty</li>
4430 <li>Jalview desktop fails to launch with jar signature
4431 failure when java web start temporary file caching is
4433 <li>DAS Sequence retrieval with range qualification
4434 results in sequence xref which includes range qualification</li>
4435 <li>Errors during processing of command line arguments
4436 cause progress bar (JAL-898) to be removed</li>
4437 <li>Replace comma for semi-colon option not disabled for
4438 DAS sources in sequence fetcher</li>
4439 <li>Cannot close news reader when JABAWS server warning
4440 dialog is shown</li>
4441 <li>Option widgets not updated to reflect user settings</li>
4442 <li>Edited sequence not submitted to web service</li>
4443 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
4444 <li>InstallAnywhere installer doesn't unpack and run
4445 on OSX Mountain Lion</li>
4446 <li>Annotation panel not given a scroll bar when
4447 sequences with alignment annotation are pasted into the
4449 <li>Sequence associated annotation rows not associated
4450 when loaded from Jalview project</li>
4451 <li>Browser launch fails with NPE on java 1.7</li>
4452 <li>JABAWS alignment marked as finished when job was
4453 cancelled or job failed due to invalid input</li>
4454 <li>NPE with v2.7 example when clicking on Tree
4455 associated with all views</li>
4456 <li>Exceptions when copy/paste sequences with grouped
4457 annotation rows to new window</li>
4458 </ul> <em>Applet</em>
4460 <li>Sequence features are momentarily displayed before
4461 they are hidden using hidefeaturegroups applet parameter</li>
4462 <li>loading features via javascript API automatically
4463 enables feature display</li>
4464 <li>scrollToColumnIn javascript API method doesn't
4466 </ul> <em>General</em>
4468 <li>Redundancy removal fails for rna alignment</li>
4469 <li>PCA calculation fails when sequence has been selected
4470 and then deselected</li>
4471 <li>PCA window shows grey box when first opened on OSX</li>
4472 <li>Letters coloured pink in sequence logo when alignment
4473 coloured with clustalx</li>
4474 <li>Choosing fonts without letter symbols defined causes
4475 exceptions and redraw errors</li>
4476 <li>Initial PCA plot view is not same as manually
4477 reconfigured view</li>
4478 <li>Grouped annotation graph label has incorrect line
4480 <li>Grouped annotation graph label display is corrupted
4481 for lots of labels</li>
4486 <div align="center">
4487 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
4490 <td><em>Application</em>
4492 <li>Jalview Desktop News Reader</li>
4493 <li>Tweaked default layout of web services menu</li>
4494 <li>View/alignment association menu to enable user to
4495 easily specify which alignment a multi-structure view takes
4496 its colours/correspondences from</li>
4497 <li>Allow properties file location to be specified as URL</li>
4498 <li>Extend Jalview project to preserve associations
4499 between many alignment views and a single Jmol display</li>
4500 <li>Store annotation row height in Jalview project file</li>
4501 <li>Annotation row column label formatting attributes
4502 stored in project file</li>
4503 <li>Annotation row order for auto-calculated annotation
4504 rows preserved in Jalview project file</li>
4505 <li>Visual progress indication when Jalview state is
4506 saved using Desktop window menu</li>
4507 <li>Visual indication that command line arguments are
4508 still being processed</li>
4509 <li>Groovy script execution from URL</li>
4510 <li>Colour by annotation default min and max colours in
4512 <li>Automatically associate PDB files dragged onto an
4513 alignment with sequences that have high similarity and
4515 <li>Update JGoogleAnalytics to latest release (0.3)</li>
4516 <li>'view structures' option to open many
4517 structures in same window</li>
4518 <li>Sort associated views menu option for tree panel</li>
4519 <li>Group all JABA and non-JABA services for a particular
4520 analysis function in its own submenu</li>
4521 </ul> <em>Applet</em>
4523 <li>Userdefined and autogenerated annotation rows for
4525 <li>Adjustment of alignment annotation pane height</li>
4526 <li>Annotation scrollbar for annotation panel</li>
4527 <li>Drag to reorder annotation rows in annotation panel</li>
4528 <li>'automaticScrolling' parameter</li>
4529 <li>Allow sequences with partial ID string matches to be
4530 annotated from GFF/Jalview features files</li>
4531 <li>Sequence logo annotation row in applet</li>
4532 <li>Absolute paths relative to host server in applet
4533 parameters are treated as such</li>
4534 <li>New in the JalviewLite javascript API:
4536 <li>JalviewLite.js javascript library</li>
4537 <li>Javascript callbacks for
4539 <li>Applet initialisation</li>
4540 <li>Sequence/alignment mouse-overs and selections</li>
4543 <li>scrollTo row and column alignment scrolling
4545 <li>Select sequence/alignment regions from javascript</li>
4546 <li>javascript structure viewer harness to pass
4547 messages between Jmol and Jalview when running as
4548 distinct applets</li>
4549 <li>sortBy method</li>
4550 <li>Set of applet and application examples shipped
4551 with documentation</li>
4552 <li>New example to demonstrate JalviewLite and Jmol
4553 javascript message exchange</li>
4555 </ul> <em>General</em>
4557 <li>Enable Jmol displays to be associated with multiple
4558 multiple alignments</li>
4559 <li>Option to automatically sort alignment with new tree</li>
4560 <li>User configurable link to enable redirects to a
4561 www.Jalview.org mirror</li>
4562 <li>Jmol colours option for Jmol displays</li>
4563 <li>Configurable newline string when writing alignment
4564 and other flat files</li>
4565 <li>Allow alignment annotation description lines to
4566 contain html tags</li>
4567 </ul> <em>Documentation and Development</em>
4569 <li>Add groovy test harness for bulk load testing to
4571 <li>Groovy script to load and align a set of sequences
4572 using a web service before displaying the result in the
4573 Jalview desktop</li>
4574 <li>Restructured javascript and applet api documentation</li>
4575 <li>Ant target to publish example html files with applet
4577 <li>Netbeans project for building Jalview from source</li>
4578 <li>ant task to create online javadoc for Jalview source</li>
4580 <td><em>Application</em>
4582 <li>User defined colourscheme throws exception when
4583 current built in colourscheme is saved as new scheme</li>
4584 <li>AlignFrame->Save in application pops up save
4585 dialog for valid filename/format</li>
4586 <li>Cannot view associated structure for UniProt sequence</li>
4587 <li>PDB file association breaks for UniProt sequence
4589 <li>Associate PDB from file dialog does not tell you
4590 which sequence is to be associated with the file</li>
4591 <li>Find All raises null pointer exception when query
4592 only matches sequence IDs</li>
4593 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4594 <li>Jalview project with Jmol views created with Jalview
4595 2.4 cannot be loaded</li>
4596 <li>Filetype associations not installed for webstart
4598 <li>Two or more chains in a single PDB file associated
4599 with sequences in different alignments do not get coloured
4600 by their associated sequence</li>
4601 <li>Visibility status of autocalculated annotation row
4602 not preserved when project is loaded</li>
4603 <li>Annotation row height and visibility attributes not
4604 stored in Jalview project</li>
4605 <li>Tree bootstraps are not preserved when saved as a
4606 Jalview project</li>
4607 <li>Envision2 workflow tooltips are corrupted</li>
4608 <li>Enabling show group conservation also enables colour
4609 by conservation</li>
4610 <li>Duplicate group associated conservation or consensus
4611 created on new view</li>
4612 <li>Annotation scrollbar not displayed after 'show
4613 all hidden annotation rows' option selected</li>
4614 <li>Alignment quality not updated after alignment
4615 annotation row is hidden then shown</li>
4616 <li>Preserve colouring of structures coloured by
4617 sequences in pre Jalview 2.7 projects</li>
4618 <li>Web service job parameter dialog is not laid out
4620 <li>Web services menu not refreshed after 'reset
4621 services' button is pressed in preferences</li>
4622 <li>Annotation off by one in Jalview v2_3 example project</li>
4623 <li>Structures imported from file and saved in project
4624 get name like jalview_pdb1234.txt when reloaded</li>
4625 <li>Jalview does not always retrieve progress of a JABAWS
4626 job execution in full once it is complete</li>
4627 </ul> <em>Applet</em>
4629 <li>Alignment height set incorrectly when lots of
4630 annotation rows are displayed</li>
4631 <li>Relative URLs in feature HTML text not resolved to
4633 <li>View follows highlighting does not work for positions
4635 <li><= shown as = in tooltip</li>
4636 <li>Export features raises exception when no features
4638 <li>Separator string used for serialising lists of IDs
4639 for javascript api is modified when separator string
4640 provided as parameter</li>
4641 <li>Null pointer exception when selecting tree leaves for
4642 alignment with no existing selection</li>
4643 <li>Relative URLs for datasources assumed to be relative
4644 to applet's codebase</li>
4645 <li>Status bar not updated after finished searching and
4646 search wraps around to first result</li>
4647 <li>StructureSelectionManager instance shared between
4648 several Jalview applets causes race conditions and memory
4650 <li>Hover tooltip and mouseover of position on structure
4651 not sent from Jmol in applet</li>
4652 <li>Certain sequences of javascript method calls to
4653 applet API fatally hang browser</li>
4654 </ul> <em>General</em>
4656 <li>View follows structure mouseover scrolls beyond
4657 position with wrapped view and hidden regions</li>
4658 <li>Find sequence position moves to wrong residue
4659 with/without hidden columns</li>
4660 <li>Sequence length given in alignment properties window
4662 <li>InvalidNumberFormat exceptions thrown when trying to
4663 import PDB like structure files</li>
4664 <li>Positional search results are only highlighted
4665 between user-supplied sequence start/end bounds</li>
4666 <li>End attribute of sequence is not validated</li>
4667 <li>Find dialog only finds first sequence containing a
4668 given sequence position</li>
4669 <li>Sequence numbering not preserved in MSF alignment
4671 <li>Jalview PDB file reader does not extract sequence
4672 from nucleotide chains correctly</li>
4673 <li>Structure colours not updated when tree partition
4674 changed in alignment</li>
4675 <li>Sequence associated secondary structure not correctly
4676 parsed in interleaved stockholm</li>
4677 <li>Colour by annotation dialog does not restore current
4679 <li>Hiding (nearly) all sequences doesn't work
4681 <li>Sequences containing lowercase letters are not
4682 properly associated with their pdb files</li>
4683 </ul> <em>Documentation and Development</em>
4685 <li>schemas/JalviewWsParamSet.xsd corrupted by
4686 ApplyCopyright tool</li>
4691 <div align="center">
4692 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4695 <td><em>Application</em>
4697 <li>New warning dialog when the Jalview Desktop cannot
4698 contact web services</li>
4699 <li>JABA service parameters for a preset are shown in
4700 service job window</li>
4701 <li>JABA Service menu entries reworded</li>
4705 <li>Modeller PIR IO broken - cannot correctly import a
4706 pir file emitted by Jalview</li>
4707 <li>Existing feature settings transferred to new
4708 alignment view created from cut'n'paste</li>
4709 <li>Improved test for mixed amino/nucleotide chains when
4710 parsing PDB files</li>
4711 <li>Consensus and conservation annotation rows
4712 occasionally become blank for all new windows</li>
4713 <li>Exception raised when right clicking above sequences
4714 in wrapped view mode</li>
4715 </ul> <em>Application</em>
4717 <li>multiple multiply aligned structure views cause cpu
4718 usage to hit 100% and computer to hang</li>
4719 <li>Web Service parameter layout breaks for long user
4720 parameter names</li>
4721 <li>Jaba service discovery hangs desktop if Jaba server
4728 <div align="center">
4729 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4732 <td><em>Application</em>
4734 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4735 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4738 <li>Web Services preference tab</li>
4739 <li>Analysis parameters dialog box and user defined
4741 <li>Improved speed and layout of Envision2 service menu</li>
4742 <li>Superpose structures using associated sequence
4744 <li>Export coordinates and projection as CSV from PCA
4746 </ul> <em>Applet</em>
4748 <li>enable javascript: execution by the applet via the
4749 link out mechanism</li>
4750 </ul> <em>Other</em>
4752 <li>Updated the Jmol Jalview interface to work with Jmol
4754 <li>The Jalview Desktop and JalviewLite applet now
4755 require Java 1.5</li>
4756 <li>Allow Jalview feature colour specification for GFF
4757 sequence annotation files</li>
4758 <li>New 'colour by label' keword in Jalview feature file
4759 type colour specification</li>
4760 <li>New Jalview Desktop Groovy API method that allows a
4761 script to check if it being run in an interactive session or
4762 in a batch operation from the Jalview command line</li>
4766 <li>clustalx colourscheme colours Ds preferentially when
4767 both D+E are present in over 50% of the column</li>
4768 </ul> <em>Application</em>
4770 <li>typo in AlignmentFrame->View->Hide->all but
4771 selected Regions menu item</li>
4772 <li>sequence fetcher replaces ',' for ';' when the ',' is
4773 part of a valid accession ID</li>
4774 <li>fatal OOM if object retrieved by sequence fetcher
4775 runs out of memory</li>
4776 <li>unhandled Out of Memory Error when viewing pca
4777 analysis results</li>
4778 <li>InstallAnywhere builds fail to launch on OS X java
4779 10.5 update 4 (due to apple Java 1.6 update)</li>
4780 <li>Installanywhere Jalview silently fails to launch</li>
4781 </ul> <em>Applet</em>
4783 <li>Jalview.getFeatureGroups() raises an
4784 ArrayIndexOutOfBoundsException if no feature groups are
4791 <div align="center">
4792 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4798 <li>Alignment prettyprinter doesn't cope with long
4800 <li>clustalx colourscheme colours Ds preferentially when
4801 both D+E are present in over 50% of the column</li>
4802 <li>nucleic acid structures retrieved from PDB do not
4803 import correctly</li>
4804 <li>More columns get selected than were clicked on when a
4805 number of columns are hidden</li>
4806 <li>annotation label popup menu not providing correct
4807 add/hide/show options when rows are hidden or none are
4809 <li>Stockholm format shown in list of readable formats,
4810 and parser copes better with alignments from RFAM.</li>
4811 <li>CSV output of consensus only includes the percentage
4812 of all symbols if sequence logo display is enabled</li>
4814 </ul> <em>Applet</em>
4816 <li>annotation panel disappears when annotation is
4818 </ul> <em>Application</em>
4820 <li>Alignment view not redrawn properly when new
4821 alignment opened where annotation panel is visible but no
4822 annotations are present on alignment</li>
4823 <li>pasted region containing hidden columns is
4824 incorrectly displayed in new alignment window</li>
4825 <li>Jalview slow to complete operations when stdout is
4826 flooded (fix is to close the Jalview console)</li>
4827 <li>typo in AlignmentFrame->View->Hide->all but
4828 selected Rregions menu item.</li>
4829 <li>inconsistent group submenu and Format submenu entry
4830 'Un' or 'Non'conserved</li>
4831 <li>Sequence feature settings are being shared by
4832 multiple distinct alignments</li>
4833 <li>group annotation not recreated when tree partition is
4835 <li>double click on group annotation to select sequences
4836 does not propagate to associated trees</li>
4837 <li>Mac OSX specific issues:
4839 <li>exception raised when mouse clicked on desktop
4840 window background</li>
4841 <li>Desktop menu placed on menu bar and application
4842 name set correctly</li>
4843 <li>sequence feature settings not wide enough for the
4844 save feature colourscheme button</li>
4853 <div align="center">
4854 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4857 <td><em>New Capabilities</em>
4859 <li>URL links generated from description line for
4860 regular-expression based URL links (applet and application)
4863 <li>Non-positional feature URL links are shown in link
4865 <li>Linked viewing of nucleic acid sequences and
4867 <li>Automatic Scrolling option in View menu to display
4868 the currently highlighted region of an alignment.</li>
4869 <li>Order an alignment by sequence length, or using the
4870 average score or total feature count for each sequence.</li>
4871 <li>Shading features by score or associated description</li>
4872 <li>Subdivide alignment and groups based on identity of
4873 selected subsequence (Make Groups from Selection).</li>
4874 <li>New hide/show options including Shift+Control+H to
4875 hide everything but the currently selected region.</li>
4876 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4877 </ul> <em>Application</em>
4879 <li>Fetch DB References capabilities and UI expanded to
4880 support retrieval from DAS sequence sources</li>
4881 <li>Local DAS Sequence sources can be added via the
4882 command line or via the Add local source dialog box.</li>
4883 <li>DAS Dbref and DbxRef feature types are parsed as
4884 database references and protein_name is parsed as
4885 description line (BioSapiens terms).</li>
4886 <li>Enable or disable non-positional feature and database
4887 references in sequence ID tooltip from View menu in
4889 <!-- <li>New hidden columns and rows and representatives capabilities
4890 in annotations file (in progress - not yet fully implemented)</li> -->
4891 <li>Group-associated consensus, sequence logos and
4892 conservation plots</li>
4893 <li>Symbol distributions for each column can be exported
4894 and visualized as sequence logos</li>
4895 <li>Optionally scale multi-character column labels to fit
4896 within each column of annotation row<!-- todo for applet -->
4898 <li>Optional automatic sort of associated alignment view
4899 when a new tree is opened.</li>
4900 <li>Jalview Java Console</li>
4901 <li>Better placement of desktop window when moving
4902 between different screens.</li>
4903 <li>New preference items for sequence ID tooltip and
4904 consensus annotation</li>
4905 <li>Client to submit sequences and IDs to Envision2
4907 <li><em>Vamsas Capabilities</em>
4909 <li>Improved VAMSAS synchronization (Jalview archive
4910 used to preserve views, structures, and tree display
4912 <li>Import of vamsas documents from disk or URL via
4914 <li>Sharing of selected regions between views and
4915 with other VAMSAS applications (Experimental feature!)</li>
4916 <li>Updated API to VAMSAS version 0.2</li>
4918 </ul> <em>Applet</em>
4920 <li>Middle button resizes annotation row height</li>
4923 <li>sortByTree (true/false) - automatically sort the
4924 associated alignment view by the tree when a new tree is
4926 <li>showTreeBootstraps (true/false) - show or hide
4927 branch bootstraps (default is to show them if available)</li>
4928 <li>showTreeDistances (true/false) - show or hide
4929 branch lengths (default is to show them if available)</li>
4930 <li>showUnlinkedTreeNodes (true/false) - indicate if
4931 unassociated nodes should be highlighted in the tree
4933 <li>heightScale and widthScale (1.0 or more) -
4934 increase the height or width of a cell in the alignment
4935 grid relative to the current font size.</li>
4938 <li>Non-positional features displayed in sequence ID
4940 </ul> <em>Other</em>
4942 <li>Features format: graduated colour definitions and
4943 specification of feature scores</li>
4944 <li>Alignment Annotations format: new keywords for group
4945 associated annotation (GROUP_REF) and annotation row display
4946 properties (ROW_PROPERTIES)</li>
4947 <li>XML formats extended to support graduated feature
4948 colourschemes, group associated annotation, and profile
4949 visualization settings.</li></td>
4952 <li>Source field in GFF files parsed as feature source
4953 rather than description</li>
4954 <li>Non-positional features are now included in sequence
4955 feature and gff files (controlled via non-positional feature
4956 visibility in tooltip).</li>
4957 <li>URL links generated for all feature links (bugfix)</li>
4958 <li>Added URL embedding instructions to features file
4960 <li>Codons containing ambiguous nucleotides translated as
4961 'X' in peptide product</li>
4962 <li>Match case switch in find dialog box works for both
4963 sequence ID and sequence string and query strings do not
4964 have to be in upper case to match case-insensitively.</li>
4965 <li>AMSA files only contain first column of
4966 multi-character column annotation labels</li>
4967 <li>Jalview Annotation File generation/parsing consistent
4968 with documentation (e.g. Stockholm annotation can be
4969 exported and re-imported)</li>
4970 <li>PDB files without embedded PDB IDs given a friendly
4972 <li>Find incrementally searches ID string matches as well
4973 as subsequence matches, and correctly reports total number
4977 <li>Better handling of exceptions during sequence
4979 <li>Dasobert generated non-positional feature URL
4980 link text excludes the start_end suffix</li>
4981 <li>DAS feature and source retrieval buttons disabled
4982 when fetch or registry operations in progress.</li>
4983 <li>PDB files retrieved from URLs are cached properly</li>
4984 <li>Sequence description lines properly shared via
4986 <li>Sequence fetcher fetches multiple records for all
4988 <li>Ensured that command line das feature retrieval
4989 completes before alignment figures are generated.</li>
4990 <li>Reduced time taken when opening file browser for
4992 <li>isAligned check prior to calculating tree, PCA or
4993 submitting an MSA to JNet now excludes hidden sequences.</li>
4994 <li>User defined group colours properly recovered
4995 from Jalview projects.</li>
5004 <div align="center">
5005 <strong>2.4.0.b2</strong><br> 28/10/2009
5010 <li>Experimental support for google analytics usage
5012 <li>Jalview privacy settings (user preferences and docs).</li>
5017 <li>Race condition in applet preventing startup in
5019 <li>Exception when feature created from selection beyond
5020 length of sequence.</li>
5021 <li>Allow synthetic PDB files to be imported gracefully</li>
5022 <li>Sequence associated annotation rows associate with
5023 all sequences with a given id</li>
5024 <li>Find function matches case-insensitively for sequence
5025 ID string searches</li>
5026 <li>Non-standard characters do not cause pairwise
5027 alignment to fail with exception</li>
5028 </ul> <em>Application Issues</em>
5030 <li>Sequences are now validated against EMBL database</li>
5031 <li>Sequence fetcher fetches multiple records for all
5033 </ul> <em>InstallAnywhere Issues</em>
5035 <li>Dock icon works for Mac OS X java (Mac 1.6 update
5036 issue with installAnywhere mechanism)</li>
5037 <li>Command line launching of JARs from InstallAnywhere
5038 version (java class versioning error fixed)</li>
5045 <div align="center">
5046 <strong>2.4</strong><br> 27/8/2008
5049 <td><em>User Interface</em>
5051 <li>Linked highlighting of codon and amino acid from
5052 translation and protein products</li>
5053 <li>Linked highlighting of structure associated with
5054 residue mapping to codon position</li>
5055 <li>Sequence Fetcher provides example accession numbers
5056 and 'clear' button</li>
5057 <li>MemoryMonitor added as an option under Desktop's
5059 <li>Extract score function to parse whitespace separated
5060 numeric data in description line</li>
5061 <li>Column labels in alignment annotation can be centred.</li>
5062 <li>Tooltip for sequence associated annotation give name
5064 </ul> <em>Web Services and URL fetching</em>
5066 <li>JPred3 web service</li>
5067 <li>Prototype sequence search client (no public services
5069 <li>Fetch either seed alignment or full alignment from
5071 <li>URL Links created for matching database cross
5072 references as well as sequence ID</li>
5073 <li>URL Links can be created using regular-expressions</li>
5074 </ul> <em>Sequence Database Connectivity</em>
5076 <li>Retrieval of cross-referenced sequences from other
5078 <li>Generalised database reference retrieval and
5079 validation to all fetchable databases</li>
5080 <li>Fetch sequences from DAS sources supporting the
5081 sequence command</li>
5082 </ul> <em>Import and Export</em>
5083 <li>export annotation rows as CSV for spreadsheet import</li>
5084 <li>Jalview projects record alignment dataset associations,
5085 EMBL products, and cDNA sequence mappings</li>
5086 <li>Sequence Group colour can be specified in Annotation
5088 <li>Ad-hoc colouring of group in Annotation File using RGB
5089 triplet as name of colourscheme</li>
5090 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
5092 <li>treenode binding for VAMSAS tree exchange</li>
5093 <li>local editing and update of sequences in VAMSAS
5094 alignments (experimental)</li>
5095 <li>Create new or select existing session to join</li>
5096 <li>load and save of vamsas documents</li>
5097 </ul> <em>Application command line</em>
5099 <li>-tree parameter to open trees (introduced for passing
5101 <li>-fetchfrom command line argument to specify nicknames
5102 of DAS servers to query for alignment features</li>
5103 <li>-dasserver command line argument to add new servers
5104 that are also automatically queried for features</li>
5105 <li>-groovy command line argument executes a given groovy
5106 script after all input data has been loaded and parsed</li>
5107 </ul> <em>Applet-Application data exchange</em>
5109 <li>Trees passed as applet parameters can be passed to
5110 application (when using "View in full
5111 application")</li>
5112 </ul> <em>Applet Parameters</em>
5114 <li>feature group display control parameter</li>
5115 <li>debug parameter</li>
5116 <li>showbutton parameter</li>
5117 </ul> <em>Applet API methods</em>
5119 <li>newView public method</li>
5120 <li>Window (current view) specific get/set public methods</li>
5121 <li>Feature display control methods</li>
5122 <li>get list of currently selected sequences</li>
5123 </ul> <em>New Jalview distribution features</em>
5125 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
5126 <li>RELEASE file gives build properties for the latest
5127 Jalview release.</li>
5128 <li>Java 1.1 Applet build made easier and donotobfuscate
5129 property controls execution of obfuscator</li>
5130 <li>Build target for generating source distribution</li>
5131 <li>Debug flag for javacc</li>
5132 <li>.jalview_properties file is documented (slightly) in
5133 jalview.bin.Cache</li>
5134 <li>Continuous Build Integration for stable and
5135 development version of Application, Applet and source
5140 <li>selected region output includes visible annotations
5141 (for certain formats)</li>
5142 <li>edit label/displaychar contains existing label/char
5144 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
5145 <li>shorter peptide product names from EMBL records</li>
5146 <li>Newick string generator makes compact representations</li>
5147 <li>bootstrap values parsed correctly for tree files with
5149 <li>pathological filechooser bug avoided by not allowing
5150 filenames containing a ':'</li>
5151 <li>Fixed exception when parsing GFF files containing
5152 global sequence features</li>
5153 <li>Alignment datasets are finalized only when number of
5154 references from alignment sequences goes to zero</li>
5155 <li>Close of tree branch colour box without colour
5156 selection causes cascading exceptions</li>
5157 <li>occasional negative imgwidth exceptions</li>
5158 <li>better reporting of non-fatal warnings to user when
5159 file parsing fails.</li>
5160 <li>Save works when Jalview project is default format</li>
5161 <li>Save as dialog opened if current alignment format is
5162 not a valid output format</li>
5163 <li>UniProt canonical names introduced for both das and
5165 <li>Histidine should be midblue (not pink!) in Zappo</li>
5166 <li>error messages passed up and output when data read
5168 <li>edit undo recovers previous dataset sequence when
5169 sequence is edited</li>
5170 <li>allow PDB files without pdb ID HEADER lines (like
5171 those generated by MODELLER) to be read in properly</li>
5172 <li>allow reading of JPred concise files as a normal
5174 <li>Stockholm annotation parsing and alignment properties
5175 import fixed for PFAM records</li>
5176 <li>Structure view windows have correct name in Desktop
5178 <li>annotation consisting of sequence associated scores
5179 can be read and written correctly to annotation file</li>
5180 <li>Aligned cDNA translation to aligned peptide works
5182 <li>Fixed display of hidden sequence markers and
5183 non-italic font for representatives in Applet</li>
5184 <li>Applet Menus are always embedded in applet window on
5186 <li>Newly shown features appear at top of stack (in
5188 <li>Annotations added via parameter not drawn properly
5189 due to null pointer exceptions</li>
5190 <li>Secondary structure lines are drawn starting from
5191 first column of alignment</li>
5192 <li>UniProt XML import updated for new schema release in
5194 <li>Sequence feature to sequence ID match for Features
5195 file is case-insensitive</li>
5196 <li>Sequence features read from Features file appended to
5197 all sequences with matching IDs</li>
5198 <li>PDB structure coloured correctly for associated views
5199 containing a sub-sequence</li>
5200 <li>PDB files can be retrieved by applet from Jar files</li>
5201 <li>feature and annotation file applet parameters
5202 referring to different directories are retrieved correctly</li>
5203 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
5204 <li>Fixed application hang whilst waiting for
5205 splash-screen version check to complete</li>
5206 <li>Applet properly URLencodes input parameter values
5207 when passing them to the launchApp service</li>
5208 <li>display name and local features preserved in results
5209 retrieved from web service</li>
5210 <li>Visual delay indication for sequence retrieval and
5211 sequence fetcher initialisation</li>
5212 <li>updated Application to use DAS 1.53e version of
5213 dasobert DAS client</li>
5214 <li>Re-instated Full AMSA support and .amsa file
5216 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
5224 <div align="center">
5225 <strong>2.3</strong><br> 9/5/07
5230 <li>Jmol 11.0.2 integration</li>
5231 <li>PDB views stored in Jalview XML files</li>
5232 <li>Slide sequences</li>
5233 <li>Edit sequence in place</li>
5234 <li>EMBL CDS features</li>
5235 <li>DAS Feature mapping</li>
5236 <li>Feature ordering</li>
5237 <li>Alignment Properties</li>
5238 <li>Annotation Scores</li>
5239 <li>Sort by scores</li>
5240 <li>Feature/annotation editing in applet</li>
5245 <li>Headless state operation in 2.2.1</li>
5246 <li>Incorrect and unstable DNA pairwise alignment</li>
5247 <li>Cut and paste of sequences with annotation</li>
5248 <li>Feature group display state in XML</li>
5249 <li>Feature ordering in XML</li>
5250 <li>blc file iteration selection using filename # suffix</li>
5251 <li>Stockholm alignment properties</li>
5252 <li>Stockhom alignment secondary structure annotation</li>
5253 <li>2.2.1 applet had no feature transparency</li>
5254 <li>Number pad keys can be used in cursor mode</li>
5255 <li>Structure Viewer mirror image resolved</li>
5262 <div align="center">
5263 <strong>2.2.1</strong><br> 12/2/07
5268 <li>Non standard characters can be read and displayed
5269 <li>Annotations/Features can be imported/exported to the
5271 <li>Applet allows editing of sequence/annotation/group
5272 name & description
5273 <li>Preference setting to display sequence name in
5275 <li>Annotation file format extended to allow
5276 Sequence_groups to be defined
5277 <li>Default opening of alignment overview panel can be
5278 specified in preferences
5279 <li>PDB residue numbering annotation added to associated
5285 <li>Applet crash under certain Linux OS with Java 1.6
5287 <li>Annotation file export / import bugs fixed
5288 <li>PNG / EPS image output bugs fixed
5294 <div align="center">
5295 <strong>2.2</strong><br> 27/11/06
5300 <li>Multiple views on alignment
5301 <li>Sequence feature editing
5302 <li>"Reload" alignment
5303 <li>"Save" to current filename
5304 <li>Background dependent text colour
5305 <li>Right align sequence ids
5306 <li>User-defined lower case residue colours
5309 <li>Menu item accelerator keys
5310 <li>Control-V pastes to current alignment
5311 <li>Cancel button for DAS Feature Fetching
5312 <li>PCA and PDB Viewers zoom via mouse roller
5313 <li>User-defined sub-tree colours and sub-tree selection
5316 <li>'New Window' button on the 'Output to Text box'
5321 <li>New memory efficient Undo/Redo System
5322 <li>Optimised symbol lookups and conservation/consensus
5324 <li>Region Conservation/Consensus recalculated after
5326 <li>Fixed Remove Empty Columns Bug (empty columns at end
5328 <li>Slowed DAS Feature Fetching for increased robustness.
5331 <li>Made angle brackets in ASCII feature descriptions
5333 <li>Re-instated Zoom function for PCA
5334 <li>Sequence descriptions conserved in web service
5336 <li>UniProt ID discoverer uses any word separated by
5338 <li>WsDbFetch query/result association resolved
5339 <li>Tree leaf to sequence mapping improved
5340 <li>Smooth fonts switch moved to FontChooser dialog box.
5348 <div align="center">
5349 <strong>2.1.1</strong><br> 12/9/06
5354 <li>Copy consensus sequence to clipboard</li>
5359 <li>Image output - rightmost residues are rendered if
5360 sequence id panel has been resized</li>
5361 <li>Image output - all offscreen group boundaries are
5363 <li>Annotation files with sequence references - all
5364 elements in file are relative to sequence position</li>
5365 <li>Mac Applet users can use Alt key for group editing</li>
5371 <div align="center">
5372 <strong>2.1</strong><br> 22/8/06
5377 <li>MAFFT Multiple Alignment in default Web Service list</li>
5378 <li>DAS Feature fetching</li>
5379 <li>Hide sequences and columns</li>
5380 <li>Export Annotations and Features</li>
5381 <li>GFF file reading / writing</li>
5382 <li>Associate structures with sequences from local PDB
5384 <li>Add sequences to exisiting alignment</li>
5385 <li>Recently opened files / URL lists</li>
5386 <li>Applet can launch the full application</li>
5387 <li>Applet has transparency for features (Java 1.2
5389 <li>Applet has user defined colours parameter</li>
5390 <li>Applet can load sequences from parameter
5391 "sequence<em>x</em>"
5397 <li>Redundancy Panel reinstalled in the Applet</li>
5398 <li>Monospaced font - EPS / rescaling bug fixed</li>
5399 <li>Annotation files with sequence references bug fixed</li>
5405 <div align="center">
5406 <strong>2.08.1</strong><br> 2/5/06
5411 <li>Change case of selected region from Popup menu</li>
5412 <li>Choose to match case when searching</li>
5413 <li>Middle mouse button and mouse movement can compress /
5414 expand the visible width and height of the alignment</li>
5419 <li>Annotation Panel displays complete JNet results</li>
5425 <div align="center">
5426 <strong>2.08b</strong><br> 18/4/06
5432 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
5433 <li>Righthand label on wrapped alignments shows correct
5440 <div align="center">
5441 <strong>2.08</strong><br> 10/4/06
5446 <li>Editing can be locked to the selection area</li>
5447 <li>Keyboard editing</li>
5448 <li>Create sequence features from searches</li>
5449 <li>Precalculated annotations can be loaded onto
5451 <li>Features file allows grouping of features</li>
5452 <li>Annotation Colouring scheme added</li>
5453 <li>Smooth fonts off by default - Faster rendering</li>
5454 <li>Choose to toggle Autocalculate Consensus On/Off</li>
5459 <li>Drag & Drop fixed on Linux</li>
5460 <li>Jalview Archive file faster to load/save, sequence
5461 descriptions saved.</li>
5467 <div align="center">
5468 <strong>2.07</strong><br> 12/12/05
5473 <li>PDB Structure Viewer enhanced</li>
5474 <li>Sequence Feature retrieval and display enhanced</li>
5475 <li>Choose to output sequence start-end after sequence
5476 name for file output</li>
5477 <li>Sequence Fetcher WSDBFetch@EBI</li>
5478 <li>Applet can read feature files, PDB files and can be
5479 used for HTML form input</li>
5484 <li>HTML output writes groups and features</li>
5485 <li>Group editing is Control and mouse click</li>
5486 <li>File IO bugs</li>
5492 <div align="center">
5493 <strong>2.06</strong><br> 28/9/05
5498 <li>View annotations in wrapped mode</li>
5499 <li>More options for PCA viewer</li>
5504 <li>GUI bugs resolved</li>
5505 <li>Runs with -nodisplay from command line</li>
5511 <div align="center">
5512 <strong>2.05b</strong><br> 15/9/05
5517 <li>Choose EPS export as lineart or text</li>
5518 <li>Jar files are executable</li>
5519 <li>Can read in Uracil - maps to unknown residue</li>
5524 <li>Known OutOfMemory errors give warning message</li>
5525 <li>Overview window calculated more efficiently</li>
5526 <li>Several GUI bugs resolved</li>
5532 <div align="center">
5533 <strong>2.05</strong><br> 30/8/05
5538 <li>Edit and annotate in "Wrapped" view</li>
5543 <li>Several GUI bugs resolved</li>
5549 <div align="center">
5550 <strong>2.04</strong><br> 24/8/05
5555 <li>Hold down mouse wheel & scroll to change font
5561 <li>Improved JPred client reliability</li>
5562 <li>Improved loading of Jalview files</li>
5568 <div align="center">
5569 <strong>2.03</strong><br> 18/8/05
5574 <li>Set Proxy server name and port in preferences</li>
5575 <li>Multiple URL links from sequence ids</li>
5576 <li>User Defined Colours can have a scheme name and added
5578 <li>Choose to ignore gaps in consensus calculation</li>
5579 <li>Unix users can set default web browser</li>
5580 <li>Runs without GUI for batch processing</li>
5581 <li>Dynamically generated Web Service Menus</li>
5586 <li>InstallAnywhere download for Sparc Solaris</li>
5592 <div align="center">
5593 <strong>2.02</strong><br> 18/7/05
5599 <li>Copy & Paste order of sequences maintains
5600 alignment order.</li>
5606 <div align="center">
5607 <strong>2.01</strong><br> 12/7/05
5612 <li>Use delete key for deleting selection.</li>
5613 <li>Use Mouse wheel to scroll sequences.</li>
5614 <li>Help file updated to describe how to add alignment
5616 <li>Version and build date written to build properties
5618 <li>InstallAnywhere installation will check for updates
5619 at launch of Jalview.</li>
5624 <li>Delete gaps bug fixed.</li>
5625 <li>FileChooser sorts columns.</li>
5626 <li>Can remove groups one by one.</li>
5627 <li>Filechooser icons installed.</li>
5628 <li>Finder ignores return character when searching.
5629 Return key will initiate a search.<br>
5636 <div align="center">
5637 <strong>2.0</strong><br> 20/6/05
5642 <li>New codebase</li>