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">.0</a><br />
62 <em>10/03/2022</em></strong></td>
63 <td align="left" valign="top">
66 <!-- JAL-3616 JAL-3551 JAL-2322 -->Support for viewing 3D
67 structures with ChimeraX and Pymol in addition to Jmol and
71 <!-- JAL-3829 -->Discover 3D structure data for sequences
72 with Uniprot references via 3D-Beacons
75 <!-- JAL-3391 -->Rank and select available structures for
76 Uniprot sequences according to number of residues in
77 structure mapped to positions involved in the alignment
80 <!-- JAL-2226 -->Structure annotation rows for all mapped
81 chains in 3D structures are included in the 'Reference
82 Annotation' for a sequence
85 <!-- JAL-1260 -->Import Genbank and EMBL format flatfiles
88 <!-- JAL-3821 -->ENA record's mol_type honoured so RNA
89 molecules imported from ENA records are shown as RNA
91 <!-- JAL-3863 -->Support for Canonical Uniprot IDs
94 <!-- JAL-3503 -->New Preferences tab for adjusting Jalview's
95 memory settings at launch
98 <!-- JAL-3881 -->Sequence IDs split on '_' as well as other
99 non-alphanumerics when discovering database references with
103 <!-- JAL-3884 -->Suppressed harmless exceptions output to
104 Console whilst discovering database references for a
108 <!-- JAL-3204 -->Updated Jalview bindings for Uniprot XML
112 <!-- JAL-3926 -->Uniprot and PDBe autosearch option is
116 <!-- JAL-3144 -->Reverted to Jalview 'classic' drop-down
117 menu for selecting which database to fetch from in sequence
121 <!-- JAL-3018 -->Updated Ensembl REST Client compatibility
122 to 15.2 and revised model organism names (rat, xenopus,
123 dmelanogaster now rattus_norvegicus, xenopus_tropicalis,
124 drosophila_melanogaster)
127 <!-- JAL-3530 -->-nowebservicediscovery command line
128 argument to prevent automatic discovery of analysis
129 webservices on launch
132 <!-- JAL-3618 -->Allow 'App' directories to be opened when
133 locating Chimera, ChimeraX or Pymol binaries via filechooser
134 opened by double clicking the Structure Preferences' path
138 <!-- JAL-3632 JAL-3633 -->support for HTTP/S access via
139 proxies that require authentication
142 <!-- JAL-3103 -->New mechanism for opening URLs with system
143 default browser (works on OSX and Linux as well as Windows)
146 <!-- JAL-3871 JAL-3874 -->Upgraded bundled version of Jmol
150 <!-- JAL-3837 -->GPL license info on splash screen and About
153 </ul> <em>Jalview Native App</em>
156 <!-- JAL-3830 -->New command line launcher scripts (.sh,
157 .ps1, .bat) usable on macOS, Linux/Unix, Windows and
158 documentation in Help. Installer wizard has option to add
159 this to PATH, or link to it in your PATH.<br /> <em>This
160 is the recommended workaround for known issue about
161 working directory preservation when running native
162 application from command line. <!-- JAL-3523 -->
165 <li>Notarized MacOS installer for compliance with
166 latest OSX releases (Monterey)</li>
168 <!-- JAL-3805 -->Uninstaller application for old
169 (InstallAnywhere based) Jalview installations removed from
173 <!-- JAL-3608 -->Options to allow user to choose the (Swing)
174 Look and Feel (LaF) used by Jalview
177 <!-- JAL-3552, JAL-3609 -->Metal LaF used to improved
178 operation on Linux Ubuntu with HiDPI display in Java 11
179 (still known issues with HiDPI screens in java 8 and 11. see
180 <a href="https://issues.jalview.org/browse/JAL-3137">JAL-3137</a>)
183 <!-- JAL-3633 -->Getdown launcher inherits HTTP/S proxy
184 configuration from jalview_properties
187 <!-- JAL- -->New Jalview Develop app - making it even easier
188 to get at Jalview's development builds
191 <!-- JAL-3594 -->New splashscreens for Jalview, Jalview Test
192 and Jalview Develop applications.
195 <!-- JAL-3728 -->Jalview logos shown for Jalview Java
196 Console and other window widgets in taskbar and dock rather
197 than anonymous 'Java' icons
199 </ul> <em>JalviewJS</em>
202 <!-- JAL-3624 -->PDB structures mapped to Uniprot Sequences
206 <!-- JAL-3208 -->setprop commandline argument reinstated for
210 <!-- JAL-3163 -->Missing message bundle keys are only
211 reported once per key (avoids excessive log output in js
215 <!-- JAL-3168 -->Feature type is included in the title of
216 the Feature Settings' Colour Chooser dialog
219 <!-- JAL-3279 -->Build details reported in About window
222 <!-- JAL-3038 JAL-3071 JAL-3263 JAL-3084 -->Numerous minor
223 GUI additions and improvements in sync with Java
226 </ul> <em>Development</em>
229 <!-- -->First integrated JalviewJS and Jalview release
231 <li><!-- JAL-3841,JAL-3248 -->Updated README and doc/building.md</li>
233 <!-- JAL-3789, JAL-3679 -->Improved JalviewJS/Jalview build
234 process, added support for system package provided eclipse
237 <li>Install4j 9.0.x used for installer packaging</li>
239 <!-- JAL-3930 -->Improved use of installers for unattended
240 installation with a customizedId of "JALVIEW" in install4j's
244 <!-- JAL-3907 -->Improved compatibility of Jalview build
245 with Java 17 (next LTS target)
252 <!-- JAL-3674 -->Slow structure commands can block Jalview
256 <!-- JAL-3904 -->Structure window's viewer-specific menu
257 disappears when only one structure is shown (and many
258 sequences:one chain mappings are present)
261 <!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
262 the first SEQUENCE_GROUP defined
266 <!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 -->Selections not
267 propagated between Linked CDS - Protein alignments and their
268 trees (known defect from 2.11.1.3)
271 <!-- JAL-3761 -->Not all codon positions highlighted for
272 overlapping exon splice sites (e.g due to RNA slippage)
275 <!-- JAL-3794 -->X was not being recognised as the unknown
276 base in DNA sequences
279 <!-- JAL-3915 -->Removed RNAview checkbox and logic from
280 Structure Preferences
283 <!-- JAL-3583 -->Tooltip behaviour improved (slightly)
286 <!-- JAL-3162 -->Can edit a feature so that start > end
289 <!-- JAL-2848 -->Cancel from Amend Features doesn't reset a
290 modified graduated colour
293 <!-- JAL-3788 -->New View with automatic 'Show Overview'
294 preference enabled results in Null Pointer Exceptions when
295 clustal colouring is enabled
298 <!-- JAL-3275 -->Can open multiple Preferences panels
301 <!-- JAL-3633 -->Properly configure HTTPS proxy settings
305 <!-- JAL-3949 -->Standard out logging broken: messages only
306 routing to stderr and appear as a raw template
309 <!-- JAL-3739 -->Entering web service parameter values in
310 numerical field doesn't update the value of the parameter
311 until return is pressed.
314 <!-- JAL-3749 -->Resolved known issue (from 2.11.1.1)
315 concerning duplicate CDS sequences generated when protein
316 products for certain ENA records are repeatedly shown via
317 Calculate->Show Cross Refs
319 </ul> <em>JalviewJS</em>
322 <!-- JAL-3202 -->Consensus profile may include zero (rounded
323 down) percentage values causing a divide by zero
326 <!-- JAL-3762 -->JalviewJS doesn't honour arguments passed
327 via Info.args when there are arguments on the URL
330 <!-- JAL-3602 -->gradle closure-compiler not using UTF-8
333 <!-- JAL-3603 -->Annotation file fails to load from URL in
336 </ul> <em>Development</em>
340 <li>Fixed non-fatal gradle errors during build</li>
342 <!-- JAL-3745 -->Updated build.gradle for use with
348 </ul> <em>Known Issues</em>
351 <!-- JAL-3764 -->Display of RESNUM sequence features are not
352 suppressed when structures associated with a sequence are
353 viewed with an external viewer (Regression from 2.11.1
360 <td width="60" align="center" nowrap><strong><a
361 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.7">.7</a><br />
362 <em>18/01/2022</em></strong></td>
364 <td align="left" valign="top">
367 <!-- JAL-3703, JAL-3935 -->Files open in Jalview cannot be
368 updated by Jalview or other applications (Windows, other non
371 </ul> <em>Security</em>
374 <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
380 <td width="60" align="center" nowrap><strong><a
381 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
382 <em>6/01/2022</em></strong></td>
384 <td align="left" valign="top"><em>Security</em>
387 <!-- JAL-3934 -->Version bump library dependency: Log4j
394 <td width="60" align="center" nowrap><strong><a
395 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
396 <em>20/12/2021</em></strong></td>
398 <td align="left" valign="top"><em>Security</em>
401 <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
403 </ul> <em>Development</em>
405 <li>Updated building instructions</li>
410 <!-- JAL-3840 -->Occupancy calculation is incorrect for
411 alignment columns with over -1+2^32 gaps (breaking filtering
415 <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
416 scale factors being set with buggy window-managers (linux
419 </ul> <em>Development</em>
421 <li>Fixed non-fatal gradle errors during build</li>
426 <td width="60" align="center" nowrap><strong><a
427 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
428 <em>09/03/2021</em></strong></td>
429 <td align="left" valign="top"><em>Improved control of
430 Jalview's use of network services via jalview_properties</em>
433 <!-- JAL-3814 -->New .jalview_properties token controlling
434 launch of the news browser (like -nonews argument)
437 <!-- JAL-3813 -->New .jalview_properties token controlling
438 download of linkout URLs from
439 www.jalview.org/services/identifiers
442 <!-- JAL-3812 -->New .jalview_properties token controlling
443 download of BIOJSHTML templates
446 <!-- JAL-3811 -->New 'Discover Web Services' option to
447 trigger a one off JABAWS discovery if autodiscovery was
451 <td align="left" valign="top">
454 <!-- JAL-3818 -->Intermittent deadlock opening structure in
457 </ul> <em>New Known defects</em>
460 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
461 always restored from project (since 2.10.3)
464 <!-- JAL-3806 -->Selections from tree built from CDS aren't
465 propagated to Protein alignment (since 2.11.1.3)
471 <td width="60" align="center" nowrap><strong><a
472 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
473 <em>29/10/2020</em></strong></td>
474 <td align="left" valign="top">
479 <td align="left" valign="top">
482 <!-- JAL-3765 -->Find doesn't always highlight all matching
483 positions in a sequence (bug introduced in 2.11.1.2)
486 <!-- JAL-3760 -->Alignments containing one or more protein
487 sequences can be classed as nucleotide
490 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
491 sequences after alignment of protein products (known defect
492 first reported for 2.11.1.0)
495 <!-- JAL-3725 -->No tooltip or popup menu for genomic
496 features outwith CDS shown overlaid on protein
499 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
500 correctly mapped by Jalview (e.g. affects viral CDS with
501 ribosomal slippage, since 2.9.0)
504 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
508 <!-- JAL-3700 -->Selections in CDS sequence panel don't
509 always select corresponding protein sequences
512 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
513 column selection doesn't always ignore hidden columns
515 </ul> <em>Installer</em>
518 <!-- JAL-3611 -->Space character in Jalview install path on
519 Windows prevents install4j launching getdown
521 </ul> <em>Development</em>
524 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
525 version numbers in doc/building.md
531 <td width="60" align="center" nowrap><strong><a
532 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
533 <em>25/09/2020</em></strong></td>
534 <td align="left" valign="top">
538 <td align="left" valign="top">
541 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
542 "Encountered problems opening
543 https://www.jalview.org/examples/exampleFile_2_7.jvp"
549 <td width="60" align="center" nowrap><strong><a
550 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
551 <em>17/09/2020</em></strong></td>
552 <td align="left" valign="top">
555 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
556 residue in cursor mode
559 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
560 HTSJDK from 2.12 to 2.23
563 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
564 optimisations and improvements suggested by Bob Hanson and
565 improved compatibility with JalviewJS
568 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
569 alignments from Pfam and Rfam
572 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
573 import (no longer based on .gz extension)
576 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
579 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
580 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
584 <!-- JAL-3667 -->Improved warning messages, debug logging
585 and fixed Retry action when Jalview encounters errors when
586 saving or making backup files.
589 <!-- JAL-3676 -->Enhanced Jalview Java Console:
591 <li>Jalview's logging level can be configured</li>
592 <li>Copy to Clipboard Buttion</li>
596 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
597 when running on Linux (Requires Java 11+)
600 <!-- JAL-1842 JAL-3509 -->RESNUM sequence features (the
601 green ones) are not automatically displayed when associated
602 structures are displayed or for sequences retrieved from the
605 </ul> <em>Launching Jalview</em>
608 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
609 through a system property
612 <!-- JAL-3477 -->Improved built-in documentation and command
613 line help for configuring Jalview's memory
617 <td align="left" valign="top">
620 <!-- JAL-3691 -->Conservation and Quality tracks are shown
621 but not calculated and no protein or DNA score models are
622 available for tree/PCA calculation when launched with
623 Turkish language locale
626 <!-- JAL-3493 -->Escape does not clear highlights on the
627 alignment (Since Jalview 2.10.3)
630 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
631 doesn't slide selected sequences, just sequence under cursor
634 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
635 sequence under the cursor
638 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
639 multiple EMBL gene products shown for a single contig
642 <!-- JAL-3696 -->Errors encountered when processing variants
643 from VCF files yield "Error processing VCF: Format specifier
647 <!-- JAL-3697 -->Count of features not shown can be wrong
648 when there are both local and complementary features mapped
649 to the position under the cursor
652 <!-- JAL-3673 -->Sequence ID for reference sequence is
653 clipped when Right align Sequence IDs enabled
656 <!-- JAL-2983 -->Slider with negative range values not
657 rendered correctly in VAqua4 (Since 2.10.4)
660 <!-- JAL-3685 -->Single quotes not displayed correctly in
661 internationalised text for some messages and log output
664 <!-- JAL-3490 -->Find doesn't report matches that span
665 hidden gapped columns
668 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
669 panels, Alignment viewport and annotation renderer.
672 <!-- JAL-3561 -->Jalview ignores file format parameter
673 specifying output format when exporting an alignment via the
677 <!-- JAL-3667 -->Windows 10: For a minority of users, if
678 backups are not enabled, Jalview sometimes fails to
679 overwrite an existing file and raises a warning dialog. (in
680 2.11.0, and 2.11.1.0, the workaround is to try to save the
681 file again, and if that fails, delete the original file and
685 <!-- JAL-3509 -->Dragging a PDB file onto an alignment with
686 sequence features displayed causes displayed features to be
690 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
694 <!-- JAL-3741 -->References to http://www.jalview.org in
695 program and documentation
697 </ul> <em>Launching Jalview</em>
700 <!-- JAL-3718 -->Jalview application fails when launched the
701 first time for a version that has different jars to the
702 previous launched version.
704 </ul> <em>Developing Jalview</em>
707 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
708 data, causing cloverReport gradle task to fail with an
712 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
713 monitor the release channel
715 </ul> <em>New Known defects</em>
718 <!-- JAL-3748 -->CDS shown in result of submitting proteins
719 in a CDS/Protein alignment to a web service is wrong when
720 proteins share a common transcript sequence (e.g. genome of
724 <!-- JAL-3576 -->Co-located features exported and
725 re-imported are ordered differently when shown on alignment
726 and in tooltips. (Also affects v2.11.1.0)
729 <!-- JAL-3702 -->Drag and drop of alignment file onto
730 alignment window when in a HiDPI scaled mode in Linux only
731 works for the top left quadrant of the alignment window
734 <!-- JAL-3701 -->Stale build data in jalview standalone jar
735 builds (only affects 2.11.1.1 branch)
738 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
739 when alignment view restored from project (since Jalview
743 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
744 protein products for certain ENA records are repeatedly
745 shown via Calculate->Show Cross Refs
751 <td width="60" align="center" nowrap><strong><a
752 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
753 <em>22/04/2020</em></strong></td>
754 <td align="left" valign="top">
757 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
758 'virtual' codon features shown on protein (or vice versa)
759 for display in alignments, on structure views (including
760 transfer to UCSF chimera), in feature reports and for
764 <!-- JAL-3121 -->Feature attributes from VCF files can be
765 exported and re-imported as GFF3 files
768 <!-- JAL-3376 -->Capture VCF "fixed column" values
769 POS, ID, QUAL, FILTER as Feature Attributes
772 <!-- JAL-3375 -->More robust VCF numeric data field
773 validation while parsing
776 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
780 <!-- JAL-3535 -->Feature Settings dialog title includes name
784 <!-- JAL-3538 -->Font anti-aliasing in alignment views
788 <!-- JAL-3468 -->Very long feature descriptions truncated in
792 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
793 with no feature types visible
796 <!-- JAL-3574 -->Improved support for filtering feature
797 attributes with large integer values
800 <em>Jalview Installer</em>
803 <!-- JAL-3449 -->Versions for install4j and getdown and
804 installer template version reported in console (may be null
805 when Jalview launched as executable jar or via conda)
808 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and
809 higher quality background images
812 <!-- JAL-3394 -->New installer/application launcher
813 generated with install4j 8.0.4
816 <!-- JAL-3420 -->Jalview File Associations shown for Unix
820 <!-- JAL-3477 -->Improved defaults for maximum memory
821 setting when running on large memory machines
823 </ul> <em>Release processes</em>
826 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
829 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier
830 access to test-release channel builds
832 </ul> <em>Build System</em>
835 <!-- JAL-3510 -->Clover updated to 4.4.1
838 <!-- JAL-3513 -->Test code included in Clover coverage
841 </ul> <em>Groovy Scripts</em>
844 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
845 to stdout containing the consensus sequence for each
846 alignment in a Jalview session
849 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
850 genomic sequence_variant annotation from CDS as
851 missense_variant or synonymous_variant on protein products.
855 <td align="left" valign="top">
858 <!-- JAL-3581 -->Hidden sequence markers still visible when
859 'Show hidden markers' option is not ticked
862 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
863 PNG output when 'Automatically set ID width' is set in
864 jalview preferences or properties file
867 <!-- JAL-3571 -->Feature Editor dialog can be opened when
868 'Show Sequence Features' option is not ticked
871 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
872 buttons in Feature Settings dialog are clicked when no
876 <!-- JAL-3412 -->ID margins for CDS and Protein views not
877 equal when split frame is first opened
880 <!-- JAL-3296 -->Sequence position numbers in status bar not
881 correct after editing a sequence's start position
884 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
885 with annotation and exceptions thrown when only a few
886 columns shown in wrapped mode
889 <!-- JAL-3386 -->Sequence IDs missing in headless export of
890 wrapped alignment figure with annotations
893 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
894 ID fails with ClassCastException
897 <!-- JAL-3389 -->Chimera session not restored from Jalview
901 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
902 feature settings dialog also selects columns
905 <!-- JAL-3473 -->SpinnerNumberModel causes
906 IllegalArgumentException in some circumstances
909 <!-- JAL-3534 -->Multiple feature settings dialogs can be
913 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
914 alignment window is closed
917 <!-- JAL-3406 -->Credits missing some authors in Jalview
918 help documentation for 2.11.0 release
921 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
922 includes Pfam ID as sequence's accession rather than its
925 </ul> <em>Java 11 Compatibility issues</em>
928 <!-- JAL-2987 -->OSX - Can't view some search results in
929 PDB/Uniprot search panel
931 </ul> <em>Installer</em>
934 <!-- JAL-3447 -->Jalview should not create file associations
935 for 3D structure files (.pdb, .mmcif. .cif)
937 </ul> <em>Repository and Source Release</em>
940 <!-- JAL-3474 -->removed obsolete .cvsignore files from
944 <!-- JAL-3541 -->Clover report generation running out of
947 </ul> <em>New Known Issues</em>
950 <!-- JAL-3523 -->OSX - Current working directory not
951 preserved when Jalview.app launched with parameters from
955 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
956 clipped in headless figure export when Right Align option
960 <!-- JAL-3542 -->Jalview Installation type always reports
961 'Source' in console output
964 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail
965 on jalview's bamboo server but run fine locally.
971 <td width="60" align="center" nowrap><strong><a
972 name="Jalview.2.11.0">2.11.0</a><br /> <em>04/07/2019</em></strong></td>
973 <td align="left" valign="top">
976 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native
977 Application and Installers built with <a
978 href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a>
979 (licensed to the Jalview open source project) rather than
983 <!-- JAL-1929 -->Jalview Launcher System to auto-configure
984 memory settings, receive over the air updates and launch
985 specific versions via (<a
986 href="https://github.com/threerings/getdown">Three
990 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations
991 for formats supported by Jalview (including .jvp project
995 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command
996 line arguments and switch between different getdown channels
999 <!-- JAL-3141 -->Backup files created when saving Jalview
1000 project or alignment files
1004 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF
1008 <!-- JAL-2753 -->Version of HTSJDK shipped with Jalview
1009 updated to version 2.12.0
1012 <!-- JAL-2620 -->Alternative genetic code tables for
1016 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0
1018 <li><strong>Enhanced visualisation and analysis
1019 of Sequence Features</strong>
1022 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
1023 implementation that allows updates) used for Sequence
1027 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
1028 features can be filtered and shaded according to any
1029 associated attributes (e.g. variant attributes from VCF
1030 file, or key-value pairs imported from column 9 of GFF
1034 <!-- JAL-2879 -->Feature Attributes and shading schemes
1035 stored and restored from Jalview Projects
1038 <!-- JAL-3334 -->Use full Sequence Ontology (via
1039 BioJava) to recognise variant features
1042 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants
1043 on peptide sequences (also coloured red by default)
1046 <!-- JAL-2792 -->Popup window to show full report for a
1047 selected sequence feature's details
1050 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient
1051 sequence feature render algorithm (Z-sort/transparency
1055 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature
1060 <!-- JAL-3205 -->Symmetric score matrices for faster tree
1061 and PCA calculations
1063 <li><strong>Principal Components Analysis Viewer</strong>
1066 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis
1067 results and Viewer state saved in Jalview Project
1070 <!-- JAL-2962 -->'Change parameters' option removed from
1071 viewer's drop-down menus
1074 <!-- JAL-2975 -->Can use shift + arrow keys to rotate
1075 PCA image incrementally
1078 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
1082 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
1084 <li><strong>Speed and Efficiency</strong>
1087 <!-- JAL-2185,JAL-3198 -->More efficient creation of
1088 selections and multiple groups when working with large
1092 <!-- JAL-3200 -->Speedier import of annotation rows when
1093 parsing Stockholm files
1096 <li><strong>User Interface</strong>
1099 <!-- JAL-2933 -->Finder panel remembers last position in
1103 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS
1104 (What you see is what is shown)<br />Only visible
1105 regions of alignment are shown by default (can be
1106 changed in user preferences)
1109 <!-- JAL-3169 -->File Chooser stays open after
1110 responding Cancel to the Overwrite Dialog
1113 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour
1114 when all sequences are hidden
1117 <!-- JAL-1244 -->Status bar shows bounds when dragging a
1118 selection region, and gap count when inserting or
1122 <!-- JAL-3132 -->Status bar updates over sequence and
1126 <!-- JAL-3093 -->Annotation tooltips and popup menus are
1127 shown when in wrapped mode
1130 <!-- JAL-3073 -->Can select columns by dragging
1131 left/right in a graph or histogram annotation
1134 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB
1138 <!-- JAL-2621 -->Cursor changes over draggable box in
1142 <!-- JAL-3181 -->Consistent ordering of links in
1143 sequence id popup menu
1146 <!-- JAL-3080 -->Red line indicating tree-cut position
1147 not shown if no subgroups are created
1150 <!-- JAL-3042 -->Removed ability to configure length of
1151 search history by right-clicking search box
1157 <!-- JAL-3232 -->Jalview Groovy Scripting Console updated to
1160 <li><strong>Java 11 Support (not yet on general
1164 <!-- -->OSX GUI integrations for App menu's 'About'
1165 entry and trapping CMD-Q
1168 </ul> <em>Deprecations</em>
1171 <!-- JAL-3035 -->DAS sequence retrieval and annotation
1172 capabilities removed from the Jalview Desktop
1175 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling
1176 and unmarshalling has been replaced by JAXB for Jalview
1177 projects and XML based data retrieval clients
1180 <!-- JAL-3311 -->Disable VAMSAS menu in preparation for
1184 <!-- -->Jalview Desktop no longer distributed via Java Web
1187 </ul> <em>Documentation</em>
1190 <!-- JAL-3003 -->Added remarks about transparent rendering
1191 effects not supported in EPS figure export
1194 <!-- JAL-2903 -->Typos in documentation for Preferences
1197 </ul> <em>Development and Release Processes</em>
1200 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated
1204 <!-- JAL-1424 -->Enhanced checks for missing and duplicated
1205 keys in Message bundles
1208 <!-- JAL-3225 -->Eclipse project configuration managed with
1212 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian Bamboo
1213 continuous integration for unattended Test Suite execution
1216 <!-- JAL-2864 -->Memory test suite to detect leaks in common
1220 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
1224 <!-- JAL-3248 -->Developer documentation migrated to
1225 markdown (with HTML rendering)
1228 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
1231 <!-- JAL-3289 -->New URLs for publishing development
1236 <td align="left" valign="top">
1239 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
1242 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
1243 superposition in Jmol fail on Windows
1246 <!-- JAL-3286 -->Blank error dialog is displayed when
1247 discovering structures for sequences with lots of PDB
1251 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export
1252 with monospaced font
1255 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
1256 Jalview project involving multiple views
1259 <!-- JAL-3164 -->Overview for complementary view in a linked
1260 CDS/Protein alignment is not updated when Hide Columns by
1261 Annotation dialog hides columns
1264 <!-- JAL-3158 -->Selection highlighting in the complement of
1265 a CDS/Protein alignment stops working after making a
1266 selection in one view, then making another selection in the
1270 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
1274 <!-- JAL-3154 -->Table Columns could be re-ordered in
1275 Feature Settings and Jalview Preferences panels
1278 <!-- JAL-2865 -->Jalview hangs when closing windows, or
1279 redrawing the overview with large alignments
1282 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
1283 region if columns were selected by dragging right-to-left
1284 and the mouse moved to the left of the first column
1287 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to
1288 a hidden column marker via scale popup menu
1291 <!-- JAL-2846 -->Error message for trying to load in invalid
1292 URLs doesn't tell users the invalid URL
1295 <!-- JAL-2816 -->Tooltips displayed for features filtered by
1299 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl
1300 during show cross references or Fetch Database References
1301 are shown in red in original view
1304 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown
1305 correctly on peptide sequence (computed variant shown as
1309 <!-- JAL-2060 -->'Graduated colour' option not offered for
1310 manually created features (where feature score is Float.NaN)
1313 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or
1314 printed when columns are hidden
1317 <!-- JAL-3082 -->Regular expression error for '(' in Select
1318 Columns by Annotation description
1321 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after
1322 dragging out of Scale or Annotation Panel
1325 <!-- JAL-3075 -->Column selection incorrect after scrolling
1329 <!-- JAL-3074 -->Left/right drag in annotation can scroll
1333 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal
1337 <!-- JAL-3002 -->Column display is out by one after Page
1338 Down, Page Up in wrapped mode
1341 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
1344 <!-- JAL-2932 -->Finder searches in minimised alignments
1347 <!-- JAL-2250 -->'Apply Colour to All Groups' not always
1348 selected on opening an alignment
1351 <!-- JAL-3180 -->'Colour by Annotation' not marked selected
1355 <!-- JAL-3201 -->Per-group Clustal colour scheme changes
1356 when different groups in the alignment are selected
1359 <!-- JAL-2717 -->Internationalised colour scheme names not
1360 shown correctly in menu
1363 <!-- JAL-3206 -->Colour by Annotation can go black at
1364 min/max threshold limit
1367 <!-- JAL-3125 -->Value input for graduated feature colour
1368 threshold gets 'unrounded'
1371 <!-- JAL-2982 -->PCA image export doesn't respect background
1375 <!-- JAL-2963 -->PCA points don't dim when rotated about y
1379 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
1382 <!-- JAL-3078 -->Cancel in Tree Font dialog resets
1383 alignment, not Tree font
1386 <!-- JAL-2964 -->Associate Tree with All Views not restored
1390 <!-- JAL-2915 -->Scrolling of split frame is sluggish if
1391 Overview shown in complementary view
1394 <!-- JAL-3313 -->Codon consensus incorrectly scaled when
1395 shown without normalisation
1398 <!-- JAL-3021 -->Sequence Details report should open
1399 positioned at top of report
1402 <!-- JAL-914 -->Help page can be opened twice
1405 <!-- JAL-3333 -->Fuzzy text in web service status menu on
1408 </ul> <em>Editing</em>
1411 <!-- JAL-2822 -->Start and End should be updated when
1412 sequence data at beginning or end of alignment added/removed
1416 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection
1417 doesn't relocate sequence features correctly when start of
1418 sequence is removed (Known defect since 2.10)
1421 <!-- JAL-2830 -->Inserting gap sequence via the Edit
1422 Sequence dialog corrupts dataset sequence
1425 <!-- JAL-868 -->Structure colours not updated when
1426 associated tree repartitions the alignment view (Regression
1429 </ul> <em>Datamodel</em>
1432 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
1433 sequence's End is greater than its length
1435 </ul> <em>Bugs fixed for Java 11 Support (not yet on general
1439 <!-- JAL-3288 -->Menus work properly in split-screen
1441 </ul> <em>New Known Defects</em>
1444 <!-- JAL-3340 -->Select columns containing feature by double
1445 clicking ignores bounds of an existing selected region
1448 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in
1449 gapped regions of protein alignment.
1452 <!-- JAL-2647 -->Input Data menu entry is greyed out when
1453 PCA View is restored from a Jalview 2.11 project
1456 <!-- JAL-3213 -->Alignment panel height can be too small
1460 <!-- JAL-3240 -->Display is incorrect after removing gapped
1461 columns within hidden columns
1464 <!-- JAL-3314 -->Rightmost selection is lost when mouse
1465 re-enters window after dragging left to select columns to
1466 left of visible region
1469 <!-- JAL-2876 -->Features coloured according to their
1470 description string and thresholded by score in earlier
1471 versions of Jalview are not shown as thresholded features in
1472 2.11. To workaround please create a Score filter instead.
1475 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't
1476 reset group visibility
1479 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in
1480 linked CDS/Protein view
1483 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1484 alignments with multiple views can close views unexpectedly
1486 </ul> <em>Java 11 Specific defects</em>
1489 <!-- JAL-3235 -->Jalview Properties file is not sorted
1490 alphabetically when saved
1496 <td width="60" nowrap>
1497 <div align="center">
1498 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1501 <td><div align="left">
1505 <!-- JAL-3101 -->Default memory for Jalview webstart and
1506 InstallAnywhere increased to 1G.
1509 <!-- JAL-247 -->Hidden sequence markers and representative
1510 sequence bolding included when exporting alignment as EPS,
1511 SVG, PNG or HTML. <em>Display is configured via the
1512 Format menu, or for command-line use via a Jalview
1513 properties file.</em>
1516 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1517 API and sequence data now imported as JSON.
1520 <!-- JAL-3065 -->Change in recommended way of starting
1521 Jalview via a Java command line: add jars in lib directory
1522 to CLASSPATH, rather than via the deprecated java.ext.dirs
1526 <em>Development</em>
1529 <!-- JAL-3047 -->Support added to execute test suite
1530 instrumented with <a href="http://openclover.org/">Open
1535 <td><div align="left">
1539 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1540 row shown in Feredoxin Structure alignment view of example
1544 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1545 annotation displayed.
1548 <!-- JAL-3107 -->Group conservation/consensus not shown
1549 for newly created group when 'Apply to all groups'
1553 <!-- JAL-3087 -->Corrupted display when switching to
1554 wrapped mode when sequence panel's vertical scrollbar is
1558 <!-- JAL-3003 -->Alignment is black in exported EPS file
1559 when sequences are selected in exported view.</em>
1562 <!-- JAL-3059 -->Groups with different coloured borders
1563 aren't rendered with correct colour.
1566 <!-- JAL-3092 -->Jalview could hang when importing certain
1567 types of knotted RNA secondary structure.
1570 <!-- JAL-3095 -->Sequence highlight and selection in
1571 trimmed VARNA 2D structure is incorrect for sequences that
1575 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1576 annotation when columns are inserted into an alignment,
1577 and when exporting as Stockholm flatfile.
1580 <!-- JAL-3053 -->Jalview annotation rows containing upper
1581 and lower-case 'E' and 'H' do not automatically get
1582 treated as RNA secondary structure.
1585 <!-- JAL-3106 -->.jvp should be used as default extension
1586 (not .jar) when saving a Jalview project file.
1589 <!-- JAL-3105 -->Mac Users: closing a window correctly
1590 transfers focus to previous window on OSX
1593 <em>Java 10 Issues Resolved</em>
1596 <!-- JAL-2988 -->OSX - Can't save new files via the File
1597 or export menus by typing in a name into the Save dialog
1601 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1602 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1603 'look and feel' which has improved compatibility with the
1604 latest version of OSX.
1610 <td width="60" nowrap>
1611 <div align="center">
1612 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1613 <em>7/06/2018</em></strong>
1616 <td><div align="left">
1620 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1621 annotation retrieved from Uniprot
1624 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1625 onto the Jalview Desktop
1629 <td><div align="left">
1633 <!-- JAL-3017 -->Cannot import features with multiple
1634 variant elements (blocks import of some Uniprot records)
1637 <!-- JAL-2997 -->Clustal files with sequence positions in
1638 right-hand column parsed correctly
1641 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1642 not alignment area in exported graphic
1645 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1646 window has input focus
1649 <!-- JAL-2992 -->Annotation panel set too high when
1650 annotation added to view (Windows)
1653 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1654 network connectivity is poor
1657 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1658 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1659 the currently open URL and links from a page viewed in
1660 Firefox or Chrome on Windows is now fully supported. If
1661 you are using Edge, only links in the page can be
1662 dragged, and with Internet Explorer, only the currently
1663 open URL in the browser can be dropped onto Jalview.</em>
1666 <em>New Known Defects</em>
1669 <!-- JAL-3083 -->Cancel option doesn't reset Colour by
1676 <td width="60" nowrap>
1677 <div align="center">
1678 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1681 <td><div align="left">
1685 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1686 for disabling automatic superposition of multiple
1687 structures and open structures in existing views
1690 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1691 ID and annotation area margins can be click-dragged to
1695 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1699 <!-- JAL-2759 -->Improved performance for large alignments
1700 and lots of hidden columns
1703 <!-- JAL-2593 -->Improved performance when rendering lots
1704 of features (particularly when transparency is disabled)
1707 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2
1708 for exchange of Jalview features and Chimera attributes
1709 made generally available
1713 <td><div align="left">
1716 <!-- JAL-2899 -->Structure and Overview aren't updated
1717 when Colour By Annotation threshold slider is adjusted
1720 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1721 overlapping alignment panel
1724 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1728 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1729 improved: CDS not handled correctly if transcript has no
1733 <!-- JAL-2321 -->Secondary structure and temperature
1734 factor annotation not added to sequence when local PDB
1735 file associated with it by drag'n'drop or structure
1739 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1740 dialog doesn't import PDB files dropped on an alignment
1743 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1744 scroll bar doesn't work for some CDS/Protein views
1747 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1748 Java 1.8u153 onwards and Java 1.9u4+.
1751 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1752 columns in annotation row
1755 <!-- JAL-2913 -->Preferences panel's ID Width control is
1756 not honored in batch mode
1759 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1760 for structures added to existing Jmol view
1763 <!-- JAL-2223 -->'View Mappings' includes duplicate
1764 entries after importing project with multiple views
1767 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1768 protein sequences via SIFTS from associated PDB entries
1769 with negative residue numbers or missing residues fails
1772 <!-- JAL-2952 -->Exception when shading sequence with
1773 negative Temperature Factor values from annotated PDB
1774 files (e.g. as generated by CONSURF)
1777 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1778 tooltip doesn't include a text description of mutation
1781 <!-- JAL-2922 -->Invert displayed features very slow when
1782 structure and/or overview windows are also shown
1785 <!-- JAL-2954 -->Selecting columns from highlighted
1786 regions very slow for alignments with large numbers of
1790 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1791 with 'StringIndexOutOfBounds'
1794 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and
1795 Feel for OSX platforms running Java 10
1798 <!-- JAL-2960 -->Adding a structure to existing structure
1799 view appears to do nothing because the view is hidden
1800 behind the alignment view
1806 <!-- JAL-2926 -->Copy consensus sequence option in applet
1807 should copy the group consensus when popup is opened on it
1813 <!-- JAL-2913 -->Fixed ID width preference is not
1817 <em>New Known Defects</em>
1820 <!-- JAL-2973 --> Exceptions occasionally raised when
1821 editing a large alignment and overview is displayed
1824 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1825 repeatedly after a series of edits even when the overview
1826 is no longer reflecting updates
1829 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1830 structures for protein subsequence (if 'Trim Retrieved
1831 Sequences' enabled) or Ensembl isoforms (Workaround in
1832 2.10.4 is to fail back to N&W mapping)
1835 <!-- JAL-2990 -->Export Annotations from File Menu with
1836 CSV option gives blank output
1842 <td width="60" nowrap>
1843 <div align="center">
1844 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br />
1845 <em>24/1/2018</em></strong>
1848 <td><div align="left">
1850 <li>Updated Certum Codesigning Certificate (Valid till
1851 30th November 2018)</li>
1854 <td><div align="left">
1859 <!-- JAL-2859-->Only one structure is loaded when
1860 several sequences and structures are selected for
1864 <!-- JAL-2851-->Alignment doesn't appear to scroll
1865 vertically via trackpad and scrollwheel
1868 <!-- JAL-2842-->Jalview hangs if up/down arrows pressed
1869 in cursor mode when cursor lies in hidden region at
1873 <!-- JAL-2827-->Helix annotation has 'notches' when
1874 scrolled into view if columns are hidden
1877 <!-- JAL-2740-->Annotation column filter can be slow to
1878 reset (ie after hitting cancel) for large numbers of
1882 <!-- JAL-2849-->User preference for disabling inclusion
1883 of sequence limits when exporting as flat file has no
1887 <!-- JAL-2679-->Reproducible cross-reference
1888 relationships when retrieving sequences from
1895 <td width="60" nowrap>
1896 <div align="center">
1897 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1900 <td><div align="left">
1904 <!-- JAL-2446 -->Faster and more efficient management and
1905 rendering of sequence features
1908 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1909 429 rate limit request hander
1912 <!-- JAL-2773 -->Structure views don't get updated unless
1913 their colours have changed
1916 <!-- JAL-2495 -->All linked sequences are highlighted for
1917 a structure mousover (Jmol) or selection (Chimera)
1920 <!-- JAL-2790 -->'Cancel' button in progress bar for
1921 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1924 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1925 view from Ensembl locus cross-references
1928 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1932 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1933 feature can be disabled
1936 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1937 PDB easier retrieval of sequences for lists of IDs
1940 <!-- JAL-2758 -->Short names for sequences retrieved from
1946 <li>Groovy interpreter updated to 2.4.12</li>
1947 <li>Example groovy script for generating a matrix of
1948 percent identity scores for current alignment.</li>
1950 <em>Testing and Deployment</em>
1953 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1957 <td><div align="left">
1961 <!-- JAL-2643 -->Pressing tab after updating the colour
1962 threshold text field doesn't trigger an update to the
1966 <!-- JAL-2682 -->Race condition when parsing sequence ID
1970 <!-- JAL-2608 -->Overview windows are also closed when
1971 alignment window is closed
1974 <!-- JAL-2548 -->Export of features doesn't always respect
1978 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1979 takes a long time in Cursor mode
1985 <!-- JAL-2777 -->Structures with whitespace chainCode
1986 cannot be viewed in Chimera
1989 <!-- JAL-2728 -->Protein annotation panel too high in
1993 <!-- JAL-2757 -->Can't edit the query after the server
1994 error warning icon is shown in Uniprot and PDB Free Text
1998 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
2001 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
2004 <!-- JAL-2739 -->Hidden column marker in last column not
2005 rendered when switching back from Wrapped to normal view
2008 <!-- JAL-2768 -->Annotation display corrupted when
2009 scrolling right in unwapped alignment view
2012 <!-- JAL-2542 -->Existing features on subsequence
2013 incorrectly relocated when full sequence retrieved from
2017 <!-- JAL-2733 -->Last reported memory still shown when
2018 Desktop->Show Memory is unticked (OSX only)
2021 <!-- JAL-2658 -->Amend Features dialog doesn't allow
2022 features of same type and group to be selected for
2026 <!-- JAL-2524 -->Jalview becomes sluggish in wide
2027 alignments when hidden columns are present
2030 <!-- JAL-2392 -->Jalview freezes when loading and
2031 displaying several structures
2034 <!-- JAL-2732 -->Black outlines left after resizing or
2038 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
2039 within the Jalview desktop on OSX
2042 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
2043 when in wrapped alignment mode
2046 <!-- JAL-2636 -->Scale mark not shown when close to right
2047 hand end of alignment
2050 <!-- JAL-2684 -->Pairwise alignment of selected regions of
2051 each selected sequence do not have correct start/end
2055 <!-- JAL-2793 -->Alignment ruler height set incorrectly
2056 after canceling the Alignment Window's Font dialog
2059 <!-- JAL-2036 -->Show cross-references not enabled after
2060 restoring project until a new view is created
2063 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
2064 URL links appears when only default EMBL-EBI link is
2065 configured (since 2.10.2b2)
2068 <!-- JAL-2775 -->Overview redraws whole window when box
2069 position is adjusted
2072 <!-- JAL-2225 -->Structure viewer doesn't map all chains
2073 in a multi-chain structure when viewing alignment
2074 involving more than one chain (since 2.10)
2077 <!-- JAL-2811 -->Double residue highlights in cursor mode
2078 if new selection moves alignment window
2081 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
2082 arrow key in cursor mode to pass hidden column marker
2085 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
2086 that produces correctly annotated transcripts and products
2089 <!-- JAL-2776 -->Toggling a feature group after first time
2090 doesn't update associated structure view
2093 <em>Applet</em><br />
2096 <!-- JAL-2687 -->Concurrent modification exception when
2097 closing alignment panel
2100 <em>BioJSON</em><br />
2103 <!-- JAL-2546 -->BioJSON export does not preserve
2104 non-positional features
2107 <em>New Known Issues</em>
2110 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
2111 sequence features correctly (for many previous versions of
2115 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
2116 using cursor in wrapped panel other than top
2119 <!-- JAL-2791 -->Select columns containing feature ignores
2120 graduated colour threshold
2123 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
2124 always preserve numbering and sequence features
2127 <em>Known Java 9 Issues</em>
2130 <!-- JAL-2902 -->Groovy Console very slow to open and is
2131 not responsive when entering characters (Webstart, Java
2138 <td width="60" nowrap>
2139 <div align="center">
2140 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
2141 <em>2/10/2017</em></strong>
2144 <td><div align="left">
2145 <em>New features in Jalview Desktop</em>
2148 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API
2152 <!-- JAL-2745 -->HTTPS used for all connections to
2157 <td><div align="left"></div></td>
2160 <td width="60" nowrap>
2161 <div align="center">
2162 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
2163 <em>7/9/2017</em></strong>
2166 <td><div align="left">
2170 <!-- JAL-2588 -->Show gaps in overview window by colouring
2171 in grey (sequences used to be coloured grey, and gaps were
2175 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
2179 <!-- JAL-2587 -->Overview updates immediately on increase
2180 in size and progress bar shown as higher resolution
2181 overview is recalculated
2186 <td><div align="left">
2190 <!-- JAL-2664 -->Overview window redraws every hidden
2191 column region row by row
2194 <!-- JAL-2681 -->duplicate protein sequences shown after
2195 retrieving Ensembl crossrefs for sequences from Uniprot
2198 <!-- JAL-2603 -->Overview window throws NPE if show boxes
2199 format setting is unticked
2202 <!-- JAL-2610 -->Groups are coloured wrongly in overview
2203 if group has show boxes format setting unticked
2206 <!-- JAL-2672,JAL-2665 -->Redraw problems when
2207 autoscrolling whilst dragging current selection group to
2208 include sequences and columns not currently displayed
2211 <!-- JAL-2691 -->Not all chains are mapped when multimeric
2212 assemblies are imported via CIF file
2215 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
2216 displayed when threshold or conservation colouring is also
2220 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
2224 <!-- JAL-2673 -->Jalview continues to scroll after
2225 dragging a selected region off the visible region of the
2229 <!-- JAL-2724 -->Cannot apply annotation based
2230 colourscheme to all groups in a view
2233 <!-- JAL-2511 -->IDs don't line up with sequences
2234 initially after font size change using the Font chooser or
2241 <td width="60" nowrap>
2242 <div align="center">
2243 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
2246 <td><div align="left">
2247 <em>Calculations</em>
2251 <!-- JAL-1933 -->Occupancy annotation row shows number of
2252 ungapped positions in each column of the alignment.
2255 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
2256 a calculation dialog box
2259 <!-- JAL-2379 -->Revised implementation of PCA for speed
2260 and memory efficiency (~30x faster)
2263 <!-- JAL-2403 -->Revised implementation of sequence
2264 similarity scores as used by Tree, PCA, Shading Consensus
2265 and other calculations
2268 <!-- JAL-2416 -->Score matrices are stored as resource
2269 files within the Jalview codebase
2272 <!-- JAL-2500 -->Trees computed on Sequence Feature
2273 Similarity may have different topology due to increased
2280 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
2281 model for alignments and groups
2284 <!-- JAL-384 -->Custom shading schemes created via groovy
2291 <!-- JAL-2526 -->Efficiency improvements for interacting
2292 with alignment and overview windows
2295 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
2299 <!-- JAL-2388 -->Hidden columns and sequences can be
2303 <!-- JAL-2611 -->Click-drag in visible area allows fine
2304 adjustment of visible position
2308 <em>Data import/export</em>
2311 <!-- JAL-2535 -->Posterior probability annotation from
2312 Stockholm files imported as sequence associated annotation
2315 <!-- JAL-2507 -->More robust per-sequence positional
2316 annotation input/output via stockholm flatfile
2319 <!-- JAL-2533 -->Sequence names don't include file
2320 extension when importing structure files without embedded
2321 names or PDB accessions
2324 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
2325 format sequence substitution matrices
2328 <em>User Interface</em>
2331 <!-- JAL-2447 --> Experimental Features Checkbox in
2332 Desktop's Tools menu to hide or show untested features in
2336 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
2337 via Overview or sequence motif search operations
2340 <!-- JAL-2547 -->Amend sequence features dialog box can be
2341 opened by double clicking gaps within sequence feature
2345 <!-- JAL-1476 -->Status bar message shown when not enough
2346 aligned positions were available to create a 3D structure
2350 <em>3D Structure</em>
2353 <!-- JAL-2430 -->Hidden regions in alignment views are not
2354 coloured in linked structure views
2357 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
2358 file-based command exchange
2361 <!-- JAL-2375 -->Structure chooser automatically shows
2362 Cached Structures rather than querying the PDBe if
2363 structures are already available for sequences
2366 <!-- JAL-2520 -->Structures imported via URL are cached in
2367 the Jalview project rather than downloaded again when the
2368 project is reopened.
2371 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
2372 to transfer Chimera's structure attributes as Jalview
2373 features, and vice-versa (<strong>Experimental
2377 <em>Web Services</em>
2380 <!-- JAL-2549 -->Updated JABAWS client to v2.2
2383 <!-- JAL-2335 -->Filter non-standard amino acids and
2384 nucleotides when submitting to AACon and other MSA
2388 <!-- JAL-2316, -->URLs for viewing database
2389 cross-references provided by identifiers.org and the
2390 EMBL-EBI's MIRIAM DB
2397 <!-- JAL-2344 -->FileFormatI interface for describing and
2398 identifying file formats (instead of String constants)
2401 <!-- JAL-2228 -->FeatureCounter script refactored for
2402 efficiency when counting all displayed features (not
2403 backwards compatible with 2.10.1)
2406 <em>Example files</em>
2409 <!-- JAL-2631 -->Graduated feature colour style example
2410 included in the example feature file
2413 <em>Documentation</em>
2416 <!-- JAL-2339 -->Release notes reformatted for readability
2417 with the built-in Java help viewer
2420 <!-- JAL-1644 -->Find documentation updated with 'search
2421 sequence description' option
2427 <!-- JAL-2485, -->External service integration tests for
2428 Uniprot REST Free Text Search Client
2431 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
2434 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
2439 <td><div align="left">
2440 <em>Calculations</em>
2443 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
2444 matrix - C->R should be '-3'<br />Old matrix restored
2445 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
2447 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
2448 Jalview's treatment of gaps in PCA and substitution matrix
2449 based Tree calculations.<br /> <br />In earlier versions
2450 of Jalview, gaps matching gaps were penalised, and gaps
2451 matching non-gaps penalised even more. In the PCA
2452 calculation, gaps were actually treated as non-gaps - so
2453 different costs were applied, which meant Jalview's PCAs
2454 were different to those produced by SeqSpace.<br />Jalview
2455 now treats gaps in the same way as SeqSpace (ie it scores
2456 them as 0). <br /> <br />Enter the following in the
2457 Groovy console to restore pre-2.10.2 behaviour:<br />
2458 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
2459 // for 2.10.1 mode <br />
2460 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
2461 // to restore 2.10.2 mode <br /> <br /> <em>Note:
2462 these settings will affect all subsequent tree and PCA
2463 calculations (not recommended)</em></li>
2465 <!-- JAL-2424 -->Fixed off-by-one bug that affected
2466 scaling of branch lengths for trees computed using
2467 Sequence Feature Similarity.
2470 <!-- JAL-2377 -->PCA calculation could hang when
2471 generating output report when working with highly
2472 redundant alignments
2475 <!-- JAL-2544 --> Sort by features includes features to
2476 right of selected region when gaps present on right-hand
2480 <em>User Interface</em>
2483 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2484 doesn't reselect a specific sequence's associated
2485 annotation after it was used for colouring a view
2488 <!-- JAL-2419 -->Current selection lost if popup menu
2489 opened on a region of alignment without groups
2492 <!-- JAL-2374 -->Popup menu not always shown for regions
2493 of an alignment with overlapping groups
2496 <!-- JAL-2310 -->Finder double counts if both a sequence's
2497 name and description match
2500 <!-- JAL-2370 -->Hiding column selection containing two
2501 hidden regions results in incorrect hidden regions
2504 <!-- JAL-2386 -->'Apply to all groups' setting when
2505 changing colour does not apply Conservation slider value
2509 <!-- JAL-2373 -->Percentage identity and conservation menu
2510 items do not show a tick or allow shading to be disabled
2513 <!-- JAL-2385 -->Conservation shading or PID threshold
2514 lost when base colourscheme changed if slider not visible
2517 <!-- JAL-2547 -->Sequence features shown in tooltip for
2518 gaps before start of features
2521 <!-- JAL-2623 -->Graduated feature colour threshold not
2522 restored to UI when feature colour is edited
2525 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2526 a time when scrolling vertically in wrapped mode.
2529 <!-- JAL-2630 -->Structure and alignment overview update
2530 as graduate feature colour settings are modified via the
2534 <!-- JAL-2034 -->Overview window doesn't always update
2535 when a group defined on the alignment is resized
2538 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2539 wrapped view result in positional status updates
2543 <!-- JAL-2563 -->Status bar doesn't show position for
2544 ambiguous amino acid and nucleotide symbols
2547 <!-- JAL-2602 -->Copy consensus sequence failed if
2548 alignment included gapped columns
2551 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2552 widgets don't permanently disappear
2555 <!-- JAL-2503 -->Cannot select or filter quantitative
2556 annotation that are shown only as column labels (e.g.
2557 T-Coffee column reliability scores)
2560 <!-- JAL-2594 -->Exception thrown if trying to create a
2561 sequence feature on gaps only
2564 <!-- JAL-2504 -->Features created with 'New feature'
2565 button from a Find inherit previously defined feature type
2566 rather than the Find query string
2569 <!-- JAL-2423 -->incorrect title in output window when
2570 exporting tree calculated in Jalview
2573 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2574 and then revealing them reorders sequences on the
2578 <!-- JAL-964 -->Group panel in sequence feature settings
2579 doesn't update to reflect available set of groups after
2580 interactively adding or modifying features
2583 <!-- JAL-2225 -->Sequence Database chooser unusable on
2587 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2588 only excluded gaps in current sequence and ignored
2595 <!-- JAL-2421 -->Overview window visible region moves
2596 erratically when hidden rows or columns are present
2599 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2600 Structure Viewer's colour menu don't correspond to
2604 <!-- JAL-2405 -->Protein specific colours only offered in
2605 colour and group colour menu for protein alignments
2608 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2609 reflect currently selected view or group's shading
2613 <!-- JAL-2624 -->Feature colour thresholds not respected
2614 when rendered on overview and structures when opacity at
2618 <!-- JAL-2589 -->User defined gap colour not shown in
2619 overview when features overlaid on alignment
2622 <!-- JAL-2567 -->Feature settings for different views not
2623 recovered correctly from Jalview project file
2626 <!-- JAL-2256 -->Feature colours in overview when first
2627 opened (automatically via preferences) are different to
2628 the main alignment panel
2631 <em>Data import/export</em>
2634 <!-- JAL-2576 -->Very large alignments take a long time to
2638 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2639 added after a sequence was imported are not written to
2643 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2644 when importing RNA secondary structure via Stockholm
2647 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2648 not shown in correct direction for simple pseudoknots
2651 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2652 with lightGray or darkGray via features file (but can
2656 <!-- JAL-2383 -->Above PID colour threshold not recovered
2657 when alignment view imported from project
2660 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2661 structure and sequences extracted from structure files
2662 imported via URL and viewed in Jmol
2665 <!-- JAL-2520 -->Structures loaded via URL are saved in
2666 Jalview Projects rather than fetched via URL again when
2667 the project is loaded and the structure viewed
2670 <em>Web Services</em>
2673 <!-- JAL-2519 -->EnsemblGenomes example failing after
2674 release of Ensembl v.88
2677 <!-- JAL-2366 -->Proxy server address and port always
2678 appear enabled in Preferences->Connections
2681 <!-- JAL-2461 -->DAS registry not found exceptions
2682 removed from console output
2685 <!-- JAL-2582 -->Cannot retrieve protein products from
2686 Ensembl by Peptide ID
2689 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2690 created from SIFTs, and spurious 'Couldn't open structure
2691 in Chimera' errors raised after April 2017 update (problem
2692 due to 'null' string rather than empty string used for
2693 residues with no corresponding PDB mapping).
2696 <em>Application UI</em>
2699 <!-- JAL-2361 -->User Defined Colours not added to Colour
2703 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2704 case' residues (button in colourscheme editor debugged and
2705 new documentation and tooltips added)
2708 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2709 doesn't restore group-specific text colour thresholds
2712 <!-- JAL-2243 -->Feature settings panel does not update as
2713 new features are added to alignment
2716 <!-- JAL-2532 -->Cancel in feature settings reverts
2717 changes to feature colours via the Amend features dialog
2720 <!-- JAL-2506 -->Null pointer exception when attempting to
2721 edit graduated feature colour via amend features dialog
2725 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2726 selection menu changes colours of alignment views
2729 <!-- JAL-2426 -->Spurious exceptions in console raised
2730 from alignment calculation workers after alignment has
2734 <!-- JAL-1608 -->Typo in selection popup menu - Create
2735 groups now 'Create Group'
2738 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2739 Create/Undefine group doesn't always work
2742 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2743 shown again after pressing 'Cancel'
2746 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2747 adjusts start position in wrap mode
2750 <!-- JAL-2563 -->Status bar doesn't show positions for
2751 ambiguous amino acids
2754 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2755 CDS/Protein view after CDS sequences added for aligned
2759 <!-- JAL-2592 -->User defined colourschemes called 'User
2760 Defined' don't appear in Colours menu
2766 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2767 score models doesn't always result in an updated PCA plot
2770 <!-- JAL-2442 -->Features not rendered as transparent on
2771 overview or linked structure view
2774 <!-- JAL-2372 -->Colour group by conservation doesn't
2778 <!-- JAL-2517 -->Hitting Cancel after applying
2779 user-defined colourscheme doesn't restore original
2786 <!-- JAL-2314 -->Unit test failure:
2787 jalview.ws.jabaws.RNAStructExportImport setup fails
2790 <!-- JAL-2307 -->Unit test failure:
2791 jalview.ws.sifts.SiftsClientTest due to compatibility
2792 problems with deep array comparison equality asserts in
2793 successive versions of TestNG
2796 <!-- JAL-2479 -->Relocated StructureChooserTest and
2797 ParameterUtilsTest Unit tests to Network suite
2800 <em>New Known Issues</em>
2803 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2804 phase after a sequence motif find operation
2807 <!-- JAL-2550 -->Importing annotation file with rows
2808 containing just upper and lower case letters are
2809 interpreted as WUSS RNA secondary structure symbols
2812 <!-- JAL-2590 -->Cannot load and display Newick trees
2813 reliably from eggnog Ortholog database
2816 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2817 containing features of type Highlight' when 'B' is pressed
2818 to mark columns containing highlighted regions.
2821 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2822 doesn't always add secondary structure annotation.
2827 <td width="60" nowrap>
2828 <div align="center">
2829 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2832 <td><div align="left">
2836 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2837 for all consensus calculations
2840 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2843 <li>Updated Jalview's Certum code signing certificate
2846 <em>Application</em>
2849 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2850 set of database cross-references, sorted alphabetically
2853 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2854 from database cross references. Users with custom links
2855 will receive a <a href="webServices/urllinks.html#warning">warning
2856 dialog</a> asking them to update their preferences.
2859 <!-- JAL-2287-->Cancel button and escape listener on
2860 dialog warning user about disconnecting Jalview from a
2864 <!-- JAL-2320-->Jalview's Chimera control window closes if
2865 the Chimera it is connected to is shut down
2868 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2869 columns menu item to mark columns containing highlighted
2870 regions (e.g. from structure selections or results of a
2874 <!-- JAL-2284-->Command line option for batch-generation
2875 of HTML pages rendering alignment data with the BioJS
2885 <!-- JAL-2286 -->Columns with more than one modal residue
2886 are not coloured or thresholded according to percent
2887 identity (first observed in Jalview 2.8.2)
2890 <!-- JAL-2301 -->Threonine incorrectly reported as not
2894 <!-- JAL-2318 -->Updates to documentation pages (above PID
2895 threshold, amino acid properties)
2898 <!-- JAL-2292 -->Lower case residues in sequences are not
2899 reported as mapped to residues in a structure file in the
2903 <!--JAL-2324 -->Identical features with non-numeric scores
2904 could be added multiple times to a sequence
2907 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2908 bond features shown as two highlighted residues rather
2909 than a range in linked structure views, and treated
2910 correctly when selecting and computing trees from features
2913 <!-- JAL-2281-->Custom URL links for database
2914 cross-references are matched to database name regardless
2919 <em>Application</em>
2922 <!-- JAL-2282-->Custom URL links for specific database
2923 names without regular expressions also offer links from
2927 <!-- JAL-2315-->Removing a single configured link in the
2928 URL links pane in Connections preferences doesn't actually
2929 update Jalview configuration
2932 <!-- JAL-2272-->CTRL-Click on a selected region to open
2933 the alignment area popup menu doesn't work on El-Capitan
2936 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2937 files with similarly named sequences if dropped onto the
2941 <!-- JAL-2312 -->Additional mappings are shown for PDB
2942 entries where more chains exist in the PDB accession than
2943 are reported in the SIFTS file
2946 <!-- JAL-2317-->Certain structures do not get mapped to
2947 the structure view when displayed with Chimera
2950 <!-- JAL-2317-->No chains shown in the Chimera view
2951 panel's View->Show Chains submenu
2954 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2955 work for wrapped alignment views
2958 <!--JAL-2197 -->Rename UI components for running JPred
2959 predictions from 'JNet' to 'JPred'
2962 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2963 corrupted when annotation panel vertical scroll is not at
2964 first annotation row
2967 <!--JAL-2332 -->Attempting to view structure for Hen
2968 lysozyme results in a PDB Client error dialog box
2971 <!-- JAL-2319 -->Structure View's mapping report switched
2972 ranges for PDB and sequence for SIFTS
2975 SIFTS 'Not_Observed' residues mapped to non-existant
2979 <!-- <em>New Known Issues</em>
2986 <td width="60" nowrap>
2987 <div align="center">
2988 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2989 <em>25/10/2016</em></strong>
2992 <td><em>Application</em>
2994 <li>3D Structure chooser opens with 'Cached structures'
2995 view if structures already loaded</li>
2996 <li>Progress bar reports models as they are loaded to
2997 structure views</li>
3003 <li>Colour by conservation always enabled and no tick
3004 shown in menu when BLOSUM or PID shading applied</li>
3005 <li>FER1_ARATH and FER2_ARATH labels were switched in
3006 example sequences/projects/trees</li>
3008 <em>Application</em>
3010 <li>Jalview projects with views of local PDB structure
3011 files saved on Windows cannot be opened on OSX</li>
3012 <li>Multiple structure views can be opened and superposed
3013 without timeout for structures with multiple models or
3014 multiple sequences in alignment</li>
3015 <li>Cannot import or associated local PDB files without a
3016 PDB ID HEADER line</li>
3017 <li>RMSD is not output in Jmol console when superposition
3019 <li>Drag and drop of URL from Browser fails for Linux and
3020 OSX versions earlier than El Capitan</li>
3021 <li>ENA client ignores invalid content from ENA server</li>
3022 <li>Exceptions are not raised in console when ENA client
3023 attempts to fetch non-existent IDs via Fetch DB Refs UI
3025 <li>Exceptions are not raised in console when a new view
3026 is created on the alignment</li>
3027 <li>OSX right-click fixed for group selections: CMD-click
3028 to insert/remove gaps in groups and CTRL-click to open group
3031 <em>Build and deployment</em>
3033 <li>URL link checker now copes with multi-line anchor
3036 <em>New Known Issues</em>
3038 <li>Drag and drop from URL links in browsers do not work
3045 <td width="60" nowrap>
3046 <div align="center">
3047 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
3050 <td><em>General</em>
3053 <!-- JAL-2124 -->Updated Spanish translations.
3056 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
3057 for importing structure data to Jalview. Enables mmCIF and
3061 <!-- JAL-192 --->Alignment ruler shows positions relative to
3065 <!-- JAL-2202 -->Position/residue shown in status bar when
3066 mousing over sequence associated annotation
3069 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
3073 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
3074 '()', canonical '[]' and invalid '{}' base pair populations
3078 <!-- JAL-2092 -->Feature settings popup menu options for
3079 showing or hiding columns containing a feature
3082 <!-- JAL-1557 -->Edit selected group by double clicking on
3083 group and sequence associated annotation labels
3086 <!-- JAL-2236 -->Sequence name added to annotation label in
3087 select/hide columns by annotation and colour by annotation
3091 </ul> <em>Application</em>
3094 <!-- JAL-2050-->Automatically hide introns when opening a
3095 gene/transcript view
3098 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
3102 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
3103 structure mappings with the EMBL-EBI PDBe SIFTS database
3106 <!-- JAL-2079 -->Updated download sites used for Rfam and
3107 Pfam sources to xfam.org
3110 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
3113 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
3114 over sequences in Jalview
3117 <!-- JAL-2027-->Support for reverse-complement coding
3118 regions in ENA and EMBL
3121 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
3122 for record retrieval via ENA rest API
3125 <!-- JAL-2027 -->Support for ENA CDS records with reverse
3129 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
3130 groovy script execution
3133 <!-- JAL-1812 -->New 'execute Groovy script' option in an
3134 alignment window's Calculate menu
3137 <!-- JAL-1812 -->Allow groovy scripts that call
3138 Jalview.getAlignFrames() to run in headless mode
3141 <!-- JAL-2068 -->Support for creating new alignment
3142 calculation workers from groovy scripts
3145 <!-- JAL-1369 --->Store/restore reference sequence in
3149 <!-- JAL-1803 -->Chain codes for a sequence's PDB
3150 associations are now saved/restored from project
3153 <!-- JAL-1993 -->Database selection dialog always shown
3154 before sequence fetcher is opened
3157 <!-- JAL-2183 -->Double click on an entry in Jalview's
3158 database chooser opens a sequence fetcher
3161 <!-- JAL-1563 -->Free-text search client for UniProt using
3162 the UniProt REST API
3165 <!-- JAL-2168 -->-nonews command line parameter to prevent
3166 the news reader opening
3169 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
3170 querying stored in preferences
3173 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
3177 <!-- JAL-1977-->Tooltips shown on database chooser
3180 <!-- JAL-391 -->Reverse complement function in calculate
3181 menu for nucleotide sequences
3184 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
3185 and feature counts preserves alignment ordering (and
3186 debugged for complex feature sets).
3189 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
3190 viewing structures with Jalview 2.10
3193 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
3194 genome, transcript CCDS and gene ids via the Ensembl and
3195 Ensembl Genomes REST API
3198 <!-- JAL-2049 -->Protein sequence variant annotation
3199 computed for 'sequence_variant' annotation on CDS regions
3203 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
3207 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
3208 Ref Fetcher fails to match, or otherwise updates sequence
3209 data from external database records.
3212 <!-- JAL-2154 -->Revised Jalview Project format for
3213 efficient recovery of sequence coding and alignment
3214 annotation relationships.
3216 </ul> <!-- <em>Applet</em>
3227 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
3231 <!-- JAL-2018-->Export features in Jalview format (again)
3232 includes graduated colourschemes
3235 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
3236 working with big alignments and lots of hidden columns
3239 <!-- JAL-2053-->Hidden column markers not always rendered
3240 at right of alignment window
3243 <!-- JAL-2067 -->Tidied up links in help file table of
3247 <!-- JAL-2072 -->Feature based tree calculation not shown
3251 <!-- JAL-2075 -->Hidden columns ignored during feature
3252 based tree calculation
3255 <!-- JAL-2065 -->Alignment view stops updating when show
3256 unconserved enabled for group on alignment
3259 <!-- JAL-2086 -->Cannot insert gaps into sequence when
3263 <!-- JAL-2146 -->Alignment column in status incorrectly
3264 shown as "Sequence position" when mousing over
3268 <!-- JAL-2099 -->Incorrect column numbers in ruler when
3269 hidden columns present
3272 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
3273 user created annotation added to alignment
3276 <!-- JAL-1841 -->RNA Structure consensus only computed for
3277 '()' base pair annotation
3280 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
3281 in zero scores for all base pairs in RNA Structure
3285 <!-- JAL-2174-->Extend selection with columns containing
3289 <!-- JAL-2275 -->Pfam format writer puts extra space at
3290 beginning of sequence
3293 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
3297 <!-- JAL-2238 -->Cannot create groups on an alignment from
3298 from a tree when t-coffee scores are shown
3301 <!-- JAL-1836,1967 -->Cannot import and view PDB
3302 structures with chains containing negative resnums (4q4h)
3305 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
3309 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
3310 to Clustal, PIR and PileUp output
3313 <!-- JAL-2008 -->Reordering sequence features that are
3314 not visible causes alignment window to repaint
3317 <!-- JAL-2006 -->Threshold sliders don't work in
3318 graduated colour and colour by annotation row for e-value
3319 scores associated with features and annotation rows
3322 <!-- JAL-1797 -->amino acid physicochemical conservation
3323 calculation should be case independent
3326 <!-- JAL-2173 -->Remove annotation also updates hidden
3330 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
3331 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
3332 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
3335 <!-- JAL-2065 -->Null pointer exceptions and redraw
3336 problems when reference sequence defined and 'show
3337 non-conserved' enabled
3340 <!-- JAL-1306 -->Quality and Conservation are now shown on
3341 load even when Consensus calculation is disabled
3344 <!-- JAL-1932 -->Remove right on penultimate column of
3345 alignment does nothing
3348 <em>Application</em>
3351 <!-- JAL-1552-->URLs and links can't be imported by
3352 drag'n'drop on OSX when launched via webstart (note - not
3353 yet fixed for El Capitan)
3356 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
3357 output when running on non-gb/us i18n platforms
3360 <!-- JAL-1944 -->Error thrown when exporting a view with
3361 hidden sequences as flat-file alignment
3364 <!-- JAL-2030-->InstallAnywhere distribution fails when
3368 <!-- JAL-2080-->Jalview very slow to launch via webstart
3369 (also hotfix for 2.9.0b2)
3372 <!-- JAL-2085 -->Cannot save project when view has a
3373 reference sequence defined
3376 <!-- JAL-1011 -->Columns are suddenly selected in other
3377 alignments and views when revealing hidden columns
3380 <!-- JAL-1989 -->Hide columns not mirrored in complement
3381 view in a cDNA/Protein splitframe
3384 <!-- JAL-1369 -->Cannot save/restore representative
3385 sequence from project when only one sequence is
3389 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
3390 in Structure Chooser
3393 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
3394 structure consensus didn't refresh annotation panel
3397 <!-- JAL-1962 -->View mapping in structure view shows
3398 mappings between sequence and all chains in a PDB file
3401 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
3402 dialogs format columns correctly, don't display array
3403 data, sort columns according to type
3406 <!-- JAL-1975 -->Export complete shown after destination
3407 file chooser is cancelled during an image export
3410 <!-- JAL-2025 -->Error when querying PDB Service with
3411 sequence name containing special characters
3414 <!-- JAL-2024 -->Manual PDB structure querying should be
3418 <!-- JAL-2104 -->Large tooltips with broken HTML
3419 formatting don't wrap
3422 <!-- JAL-1128 -->Figures exported from wrapped view are
3423 truncated so L looks like I in consensus annotation
3426 <!-- JAL-2003 -->Export features should only export the
3427 currently displayed features for the current selection or
3431 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
3432 after fetching cross-references, and restoring from
3436 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
3437 followed in the structure viewer
3440 <!-- JAL-2163 -->Titles for individual alignments in
3441 splitframe not restored from project
3444 <!-- JAL-2145 -->missing autocalculated annotation at
3445 trailing end of protein alignment in transcript/product
3446 splitview when pad-gaps not enabled by default
3449 <!-- JAL-1797 -->amino acid physicochemical conservation
3453 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
3454 article has been read (reopened issue due to
3455 internationalisation problems)
3458 <!-- JAL-1960 -->Only offer PDB structures in structure
3459 viewer based on sequence name, PDB and UniProt
3464 <!-- JAL-1976 -->No progress bar shown during export of
3468 <!-- JAL-2213 -->Structures not always superimposed after
3469 multiple structures are shown for one or more sequences.
3472 <!-- JAL-1370 -->Reference sequence characters should not
3473 be replaced with '.' when 'Show unconserved' format option
3477 <!-- JAL-1823 -->Cannot specify chain code when entering
3478 specific PDB id for sequence
3481 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3482 'Export hidden sequences' is enabled, but 'export hidden
3483 columns' is disabled.
3486 <!--JAL-2026-->Best Quality option in structure chooser
3487 selects lowest rather than highest resolution structures
3491 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3492 to sequence mapping in 'View Mappings' report
3495 <!-- JAL-2284 -->Unable to read old Jalview projects that
3496 contain non-XML data added after Jalvew wrote project.
3499 <!-- JAL-2118 -->Newly created annotation row reorders
3500 after clicking on it to create new annotation for a
3504 <!-- JAL-1980 -->Null Pointer Exception raised when
3505 pressing Add on an orphaned cut'n'paste window.
3507 <!-- may exclude, this is an external service stability issue JAL-1941
3508 -- > RNA 3D structure not added via DSSR service</li> -->
3513 <!-- JAL-2151 -->Incorrect columns are selected when
3514 hidden columns present before start of sequence
3517 <!-- JAL-1986 -->Missing dependencies on applet pages
3521 <!-- JAL-1947 -->Overview pixel size changes when
3522 sequences are hidden in applet
3525 <!-- JAL-1996 -->Updated instructions for applet
3526 deployment on examples pages.
3533 <td width="60" nowrap>
3534 <div align="center">
3535 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3536 <em>16/10/2015</em></strong>
3539 <td><em>General</em>
3541 <li>Time stamps for signed Jalview application and applet
3546 <em>Application</em>
3548 <li>Duplicate group consensus and conservation rows
3549 shown when tree is partitioned</li>
3550 <li>Erratic behaviour when tree partitions made with
3551 multiple cDNA/Protein split views</li>
3557 <td width="60" nowrap>
3558 <div align="center">
3559 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3560 <em>8/10/2015</em></strong>
3563 <td><em>General</em>
3565 <li>Updated Spanish translations of localized text for
3567 </ul> <em>Application</em>
3569 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3570 <li>Signed OSX InstallAnywhere installer<br></li>
3571 <li>Support for per-sequence based annotations in BioJSON</li>
3572 </ul> <em>Applet</em>
3574 <li>Split frame example added to applet examples page</li>
3575 </ul> <em>Build and Deployment</em>
3578 <!-- JAL-1888 -->New ant target for running Jalview's test
3586 <li>Mapping of cDNA to protein in split frames
3587 incorrect when sequence start > 1</li>
3588 <li>Broken images in filter column by annotation dialog
3590 <li>Feature colours not parsed from features file</li>
3591 <li>Exceptions and incomplete link URLs recovered when
3592 loading a features file containing HTML tags in feature
3596 <em>Application</em>
3598 <li>Annotations corrupted after BioJS export and
3600 <li>Incorrect sequence limits after Fetch DB References
3601 with 'trim retrieved sequences'</li>
3602 <li>Incorrect warning about deleting all data when
3603 deleting selected columns</li>
3604 <li>Patch to build system for shipping properly signed
3605 JNLP templates for webstart launch</li>
3606 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3607 unreleased structures for download or viewing</li>
3608 <li>Tab/space/return keystroke operation of EMBL-PDBe
3609 fetcher/viewer dialogs works correctly</li>
3610 <li>Disabled 'minimise' button on Jalview windows
3611 running on OSX to workaround redraw hang bug</li>
3612 <li>Split cDNA/Protein view position and geometry not
3613 recovered from jalview project</li>
3614 <li>Initial enabled/disabled state of annotation menu
3615 sorter 'show autocalculated first/last' corresponds to
3617 <li>Restoring of Clustal, RNA Helices and T-Coffee
3618 color schemes from BioJSON</li>
3622 <li>Reorder sequences mirrored in cDNA/Protein split
3624 <li>Applet with Jmol examples not loading correctly</li>
3630 <td><div align="center">
3631 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3633 <td><em>General</em>
3635 <li>Linked visualisation and analysis of DNA and Protein
3638 <li>Translated cDNA alignments shown as split protein
3639 and DNA alignment views</li>
3640 <li>Codon consensus annotation for linked protein and
3641 cDNA alignment views</li>
3642 <li>Link cDNA or Protein product sequences by loading
3643 them onto Protein or cDNA alignments</li>
3644 <li>Reconstruct linked cDNA alignment from aligned
3645 protein sequences</li>
3648 <li>Jmol integration updated to Jmol v14.2.14</li>
3649 <li>Import and export of Jalview alignment views as <a
3650 href="features/bioJsonFormat.html">BioJSON</a></li>
3651 <li>New alignment annotation file statements for
3652 reference sequences and marking hidden columns</li>
3653 <li>Reference sequence based alignment shading to
3654 highlight variation</li>
3655 <li>Select or hide columns according to alignment
3657 <li>Find option for locating sequences by description</li>
3658 <li>Conserved physicochemical properties shown in amino
3659 acid conservation row</li>
3660 <li>Alignments can be sorted by number of RNA helices</li>
3661 </ul> <em>Application</em>
3663 <li>New cDNA/Protein analysis capabilities
3665 <li>Get Cross-References should open a Split Frame
3666 view with cDNA/Protein</li>
3667 <li>Detect when nucleotide sequences and protein
3668 sequences are placed in the same alignment</li>
3669 <li>Split cDNA/Protein views are saved in Jalview
3674 <li>Use REST API to talk to Chimera</li>
3675 <li>Selected regions in Chimera are highlighted in linked
3676 Jalview windows</li>
3678 <li>VARNA RNA viewer updated to v3.93</li>
3679 <li>VARNA views are saved in Jalview Projects</li>
3680 <li>Pseudoknots displayed as Jalview RNA annotation can
3681 be shown in VARNA</li>
3683 <li>Make groups for selection uses marked columns as well
3684 as the active selected region</li>
3686 <li>Calculate UPGMA and NJ trees using sequence feature
3688 <li>New Export options
3690 <li>New Export Settings dialog to control hidden
3691 region export in flat file generation</li>
3693 <li>Export alignment views for display with the <a
3694 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3696 <li>Export scrollable SVG in HTML page</li>
3697 <li>Optional embedding of BioJSON data when exporting
3698 alignment figures to HTML</li>
3700 <li>3D structure retrieval and display
3702 <li>Free text and structured queries with the PDBe
3704 <li>PDBe Search API based discovery and selection of
3705 PDB structures for a sequence set</li>
3709 <li>JPred4 employed for protein secondary structure
3711 <li>Hide Insertions menu option to hide unaligned columns
3712 for one or a group of sequences</li>
3713 <li>Automatically hide insertions in alignments imported
3714 from the JPred4 web server</li>
3715 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3716 system on OSX<br />LGPL libraries courtesy of <a
3717 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3719 <li>changed 'View nucleotide structure' submenu to 'View
3720 VARNA 2D Structure'</li>
3721 <li>change "View protein structure" menu option to "3D
3724 </ul> <em>Applet</em>
3726 <li>New layout for applet example pages</li>
3727 <li>New parameters to enable SplitFrame view
3728 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3729 <li>New example demonstrating linked viewing of cDNA and
3730 Protein alignments</li>
3731 </ul> <em>Development and deployment</em>
3733 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3734 <li>Include installation type and git revision in build
3735 properties and console log output</li>
3736 <li>Jalview Github organisation, and new github site for
3737 storing BioJsMSA Templates</li>
3738 <li>Jalview's unit tests now managed with TestNG</li>
3741 <!-- <em>General</em>
3743 </ul> --> <!-- issues resolved --> <em>Application</em>
3745 <li>Escape should close any open find dialogs</li>
3746 <li>Typo in select-by-features status report</li>
3747 <li>Consensus RNA secondary secondary structure
3748 predictions are not highlighted in amber</li>
3749 <li>Missing gap character in v2.7 example file means
3750 alignment appears unaligned when pad-gaps is not enabled</li>
3751 <li>First switch to RNA Helices colouring doesn't colour
3752 associated structure views</li>
3753 <li>ID width preference option is greyed out when auto
3754 width checkbox not enabled</li>
3755 <li>Stopped a warning dialog from being shown when
3756 creating user defined colours</li>
3757 <li>'View Mapping' in structure viewer shows sequence
3758 mappings for just that viewer's sequences</li>
3759 <li>Workaround for superposing PDB files containing
3760 multiple models in Chimera</li>
3761 <li>Report sequence position in status bar when hovering
3762 over Jmol structure</li>
3763 <li>Cannot output gaps as '.' symbols with Selection ->
3764 output to text box</li>
3765 <li>Flat file exports of alignments with hidden columns
3766 have incorrect sequence start/end</li>
3767 <li>'Aligning' a second chain to a Chimera structure from
3769 <li>Colour schemes applied to structure viewers don't
3770 work for nucleotide</li>
3771 <li>Loading/cut'n'pasting an empty or invalid file leads
3772 to a grey/invisible alignment window</li>
3773 <li>Exported Jpred annotation from a sequence region
3774 imports to different position</li>
3775 <li>Space at beginning of sequence feature tooltips shown
3776 on some platforms</li>
3777 <li>Chimera viewer 'View | Show Chain' menu is not
3779 <li>'New View' fails with a Null Pointer Exception in
3780 console if Chimera has been opened</li>
3781 <li>Mouseover to Chimera not working</li>
3782 <li>Miscellaneous ENA XML feature qualifiers not
3784 <li>NPE in annotation renderer after 'Extract Scores'</li>
3785 <li>If two structures in one Chimera window, mouseover of
3786 either sequence shows on first structure</li>
3787 <li>'Show annotations' options should not make
3788 non-positional annotations visible</li>
3789 <li>Subsequence secondary structure annotation not shown
3790 in right place after 'view flanking regions'</li>
3791 <li>File Save As type unset when current file format is
3793 <li>Save as '.jar' option removed for saving Jalview
3795 <li>Colour by Sequence colouring in Chimera more
3797 <li>Cannot 'add reference annotation' for a sequence in
3798 several views on same alignment</li>
3799 <li>Cannot show linked products for EMBL / ENA records</li>
3800 <li>Jalview's tooltip wraps long texts containing no
3802 </ul> <em>Applet</em>
3804 <li>Jmol to JalviewLite mouseover/link not working</li>
3805 <li>JalviewLite can't import sequences with ID
3806 descriptions containing angle brackets</li>
3807 </ul> <em>General</em>
3809 <li>Cannot export and reimport RNA secondary structure
3810 via jalview annotation file</li>
3811 <li>Random helix colour palette for colour by annotation
3812 with RNA secondary structure</li>
3813 <li>Mouseover to cDNA from STOP residue in protein
3814 translation doesn't work.</li>
3815 <li>hints when using the select by annotation dialog box</li>
3816 <li>Jmol alignment incorrect if PDB file has alternate CA
3818 <li>FontChooser message dialog appears to hang after
3819 choosing 1pt font</li>
3820 <li>Peptide secondary structure incorrectly imported from
3821 annotation file when annotation display text includes 'e' or
3823 <li>Cannot set colour of new feature type whilst creating
3825 <li>cDNA translation alignment should not be sequence
3826 order dependent</li>
3827 <li>'Show unconserved' doesn't work for lower case
3829 <li>Nucleotide ambiguity codes involving R not recognised</li>
3830 </ul> <em>Deployment and Documentation</em>
3832 <li>Applet example pages appear different to the rest of
3833 www.jalview.org</li>
3834 </ul> <em>Application Known issues</em>
3836 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3837 <li>Misleading message appears after trying to delete
3839 <li>Jalview icon not shown in dock after InstallAnywhere
3840 version launches</li>
3841 <li>Fetching EMBL reference for an RNA sequence results
3842 fails with a sequence mismatch</li>
3843 <li>Corrupted or unreadable alignment display when
3844 scrolling alignment to right</li>
3845 <li>ArrayIndexOutOfBoundsException thrown when remove
3846 empty columns called on alignment with ragged gapped ends</li>
3847 <li>auto calculated alignment annotation rows do not get
3848 placed above or below non-autocalculated rows</li>
3849 <li>Jalview dekstop becomes sluggish at full screen in
3850 ultra-high resolution</li>
3851 <li>Cannot disable consensus calculation independently of
3852 quality and conservation</li>
3853 <li>Mouseover highlighting between cDNA and protein can
3854 become sluggish with more than one splitframe shown</li>
3855 </ul> <em>Applet Known Issues</em>
3857 <li>Core PDB parsing code requires Jmol</li>
3858 <li>Sequence canvas panel goes white when alignment
3859 window is being resized</li>
3865 <td><div align="center">
3866 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3868 <td><em>General</em>
3870 <li>Updated Java code signing certificate donated by
3872 <li>Features and annotation preserved when performing
3873 pairwise alignment</li>
3874 <li>RNA pseudoknot annotation can be
3875 imported/exported/displayed</li>
3876 <li>'colour by annotation' can colour by RNA and
3877 protein secondary structure</li>
3878 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3879 post-hoc with 2.9 release</em>)
3882 </ul> <em>Application</em>
3884 <li>Extract and display secondary structure for sequences
3885 with 3D structures</li>
3886 <li>Support for parsing RNAML</li>
3887 <li>Annotations menu for layout
3889 <li>sort sequence annotation rows by alignment</li>
3890 <li>place sequence annotation above/below alignment
3893 <li>Output in Stockholm format</li>
3894 <li>Internationalisation: improved Spanish (es)
3896 <li>Structure viewer preferences tab</li>
3897 <li>Disorder and Secondary Structure annotation tracks
3898 shared between alignments</li>
3899 <li>UCSF Chimera launch and linked highlighting from
3901 <li>Show/hide all sequence associated annotation rows for
3902 all or current selection</li>
3903 <li>disorder and secondary structure predictions
3904 available as dataset annotation</li>
3905 <li>Per-sequence rna helices colouring</li>
3908 <li>Sequence database accessions imported when fetching
3909 alignments from Rfam</li>
3910 <li>update VARNA version to 3.91</li>
3912 <li>New groovy scripts for exporting aligned positions,
3913 conservation values, and calculating sum of pairs scores.</li>
3914 <li>Command line argument to set default JABAWS server</li>
3915 <li>include installation type in build properties and
3916 console log output</li>
3917 <li>Updated Jalview project format to preserve dataset
3921 <!-- issues resolved --> <em>Application</em>
3923 <li>Distinguish alignment and sequence associated RNA
3924 structure in structure->view->VARNA</li>
3925 <li>Raise dialog box if user deletes all sequences in an
3927 <li>Pressing F1 results in documentation opening twice</li>
3928 <li>Sequence feature tooltip is wrapped</li>
3929 <li>Double click on sequence associated annotation
3930 selects only first column</li>
3931 <li>Redundancy removal doesn't result in unlinked
3932 leaves shown in tree</li>
3933 <li>Undos after several redundancy removals don't undo
3935 <li>Hide sequence doesn't hide associated annotation</li>
3936 <li>User defined colours dialog box too big to fit on
3937 screen and buttons not visible</li>
3938 <li>author list isn't updated if already written to
3939 Jalview properties</li>
3940 <li>Popup menu won't open after retrieving sequence
3942 <li>File open window for associate PDB doesn't open</li>
3943 <li>Left-then-right click on a sequence id opens a
3944 browser search window</li>
3945 <li>Cannot open sequence feature shading/sort popup menu
3946 in feature settings dialog</li>
3947 <li>better tooltip placement for some areas of Jalview
3949 <li>Allow addition of JABAWS Server which doesn't
3950 pass validation</li>
3951 <li>Web services parameters dialog box is too large to
3953 <li>Muscle nucleotide alignment preset obscured by
3955 <li>JABAWS preset submenus don't contain newly
3956 defined user preset</li>
3957 <li>MSA web services warns user if they were launched
3958 with invalid input</li>
3959 <li>Jalview cannot contact DAS Registy when running on
3962 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3963 'Superpose with' submenu not shown when new view
3967 </ul> <!-- <em>Applet</em>
3969 </ul> <em>General</em>
3971 </ul>--> <em>Deployment and Documentation</em>
3973 <li>2G and 1G options in launchApp have no effect on
3974 memory allocation</li>
3975 <li>launchApp service doesn't automatically open
3976 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3978 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3979 InstallAnywhere reports cannot find valid JVM when Java
3980 1.7_055 is available
3982 </ul> <em>Application Known issues</em>
3985 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3986 corrupted or unreadable alignment display when scrolling
3990 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3991 retrieval fails but progress bar continues for DAS retrieval
3992 with large number of ID
3995 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3996 flatfile output of visible region has incorrect sequence
4000 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
4001 rna structure consensus doesn't update when secondary
4002 structure tracks are rearranged
4005 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
4006 invalid rna structure positional highlighting does not
4007 highlight position of invalid base pairs
4010 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
4011 out of memory errors are not raised when saving Jalview
4012 project from alignment window file menu
4015 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
4016 Switching to RNA Helices colouring doesn't propagate to
4020 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
4021 colour by RNA Helices not enabled when user created
4022 annotation added to alignment
4025 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
4026 Jalview icon not shown on dock in Mountain Lion/Webstart
4028 </ul> <em>Applet Known Issues</em>
4031 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
4032 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
4035 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
4036 Jalview and Jmol example not compatible with IE9
4039 <li>Sort by annotation score doesn't reverse order
4045 <td><div align="center">
4046 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
4049 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
4052 <li>Internationalisation of user interface (usually
4053 called i18n support) and translation for Spanish locale</li>
4054 <li>Define/Undefine group on current selection with
4055 Ctrl-G/Shift Ctrl-G</li>
4056 <li>Improved group creation/removal options in
4057 alignment/sequence Popup menu</li>
4058 <li>Sensible precision for symbol distribution
4059 percentages shown in logo tooltip.</li>
4060 <li>Annotation panel height set according to amount of
4061 annotation when alignment first opened</li>
4062 </ul> <em>Application</em>
4064 <li>Interactive consensus RNA secondary structure
4065 prediction VIENNA RNAAliFold JABA 2.1 service</li>
4066 <li>Select columns containing particular features from
4067 Feature Settings dialog</li>
4068 <li>View all 'representative' PDB structures for selected
4070 <li>Update Jalview project format:
4072 <li>New file extension for Jalview projects '.jvp'</li>
4073 <li>Preserve sequence and annotation dataset (to
4074 store secondary structure annotation,etc)</li>
4075 <li>Per group and alignment annotation and RNA helix
4079 <li>New similarity measures for PCA and Tree calculation
4081 <li>Experimental support for retrieval and viewing of
4082 flanking regions for an alignment</li>
4086 <!-- issues resolved --> <em>Application</em>
4088 <li>logo keeps spinning and status remains at queued or
4089 running after job is cancelled</li>
4090 <li>cannot export features from alignments imported from
4091 Jalview/VAMSAS projects</li>
4092 <li>Buggy slider for web service parameters that take
4094 <li>Newly created RNA secondary structure line doesn't
4095 have 'display all symbols' flag set</li>
4096 <li>T-COFFEE alignment score shading scheme and other
4097 annotation shading not saved in Jalview project</li>
4098 <li>Local file cannot be loaded in freshly downloaded
4100 <li>Jalview icon not shown on dock in Mountain
4102 <li>Load file from desktop file browser fails</li>
4103 <li>Occasional NPE thrown when calculating large trees</li>
4104 <li>Cannot reorder or slide sequences after dragging an
4105 alignment onto desktop</li>
4106 <li>Colour by annotation dialog throws NPE after using
4107 'extract scores' function</li>
4108 <li>Loading/cut'n'pasting an empty file leads to a grey
4109 alignment window</li>
4110 <li>Disorder thresholds rendered incorrectly after
4111 performing IUPred disorder prediction</li>
4112 <li>Multiple group annotated consensus rows shown when
4113 changing 'normalise logo' display setting</li>
4114 <li>Find shows blank dialog after 'finished searching' if
4115 nothing matches query</li>
4116 <li>Null Pointer Exceptions raised when sorting by
4117 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
4119 <li>Errors in Jmol console when structures in alignment
4120 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
4122 <li>Not all working JABAWS services are shown in
4124 <li>JAVAWS version of Jalview fails to launch with
4125 'invalid literal/length code'</li>
4126 <li>Annotation/RNA Helix colourschemes cannot be applied
4127 to alignment with groups (actually fixed in 2.8.0b1)</li>
4128 <li>RNA Helices and T-Coffee Scores available as default
4131 </ul> <em>Applet</em>
4133 <li>Remove group option is shown even when selection is
4135 <li>Apply to all groups ticked but colourscheme changes
4136 don't affect groups</li>
4137 <li>Documented RNA Helices and T-Coffee Scores as valid
4138 colourscheme name</li>
4139 <li>Annotation labels drawn on sequence IDs when
4140 Annotation panel is not displayed</li>
4141 <li>Increased font size for dropdown menus on OSX and
4142 embedded windows</li>
4143 </ul> <em>Other</em>
4145 <li>Consensus sequence for alignments/groups with a
4146 single sequence were not calculated</li>
4147 <li>annotation files that contain only groups imported as
4148 annotation and junk sequences</li>
4149 <li>Fasta files with sequences containing '*' incorrectly
4150 recognised as PFAM or BLC</li>
4151 <li>conservation/PID slider apply all groups option
4152 doesn't affect background (2.8.0b1)
4154 <li>redundancy highlighting is erratic at 0% and 100%</li>
4155 <li>Remove gapped columns fails for sequences with ragged
4157 <li>AMSA annotation row with leading spaces is not
4158 registered correctly on import</li>
4159 <li>Jalview crashes when selecting PCA analysis for
4160 certain alignments</li>
4161 <li>Opening the colour by annotation dialog for an
4162 existing annotation based 'use original colours'
4163 colourscheme loses original colours setting</li>
4168 <td><div align="center">
4169 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
4170 <em>30/1/2014</em></strong>
4174 <li>Trusted certificates for JalviewLite applet and
4175 Jalview Desktop application<br />Certificate was donated by
4176 <a href="https://www.certum.eu">Certum</a> to the Jalview
4177 open source project).
4179 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
4180 <li>Output in Stockholm format</li>
4181 <li>Allow import of data from gzipped files</li>
4182 <li>Export/import group and sequence associated line
4183 graph thresholds</li>
4184 <li>Nucleotide substitution matrix that supports RNA and
4185 ambiguity codes</li>
4186 <li>Allow disorder predictions to be made on the current
4187 selection (or visible selection) in the same way that JPred
4189 <li>Groovy scripting for headless Jalview operation</li>
4190 </ul> <em>Other improvements</em>
4192 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
4193 <li>COMBINE statement uses current SEQUENCE_REF and
4194 GROUP_REF scope to group annotation rows</li>
4195 <li>Support '' style escaping of quotes in Newick
4197 <li>Group options for JABAWS service by command line name</li>
4198 <li>Empty tooltip shown for JABA service options with a
4199 link but no description</li>
4200 <li>Select primary source when selecting authority in
4201 database fetcher GUI</li>
4202 <li>Add .mfa to FASTA file extensions recognised by
4204 <li>Annotation label tooltip text wrap</li>
4209 <li>Slow scrolling when lots of annotation rows are
4211 <li>Lots of NPE (and slowness) after creating RNA
4212 secondary structure annotation line</li>
4213 <li>Sequence database accessions not imported when
4214 fetching alignments from Rfam</li>
4215 <li>Incorrect SHMR submission for sequences with
4217 <li>View all structures does not always superpose
4219 <li>Option widgets in service parameters not updated to
4220 reflect user or preset settings</li>
4221 <li>Null pointer exceptions for some services without
4222 presets or adjustable parameters</li>
4223 <li>Discover PDB IDs entry in structure menu doesn't
4224 discover PDB xRefs</li>
4225 <li>Exception encountered while trying to retrieve
4226 features with DAS</li>
4227 <li>Lowest value in annotation row isn't coloured
4228 when colour by annotation (per sequence) is coloured</li>
4229 <li>Keyboard mode P jumps to start of gapped region when
4230 residue follows a gap</li>
4231 <li>Jalview appears to hang importing an alignment with
4232 Wrap as default or after enabling Wrap</li>
4233 <li>'Right click to add annotations' message
4234 shown in wrap mode when no annotations present</li>
4235 <li>Disorder predictions fail with NPE if no automatic
4236 annotation already exists on alignment</li>
4237 <li>oninit javascript function should be called after
4238 initialisation completes</li>
4239 <li>Remove redundancy after disorder prediction corrupts
4240 alignment window display</li>
4241 <li>Example annotation file in documentation is invalid</li>
4242 <li>Grouped line graph annotation rows are not exported
4243 to annotation file</li>
4244 <li>Multi-harmony analysis cannot be run when only two
4246 <li>Cannot create multiple groups of line graphs with
4247 several 'combine' statements in annotation file</li>
4248 <li>Pressing return several times causes Number Format
4249 exceptions in keyboard mode</li>
4250 <li>Multi-harmony (SHMMR) method doesn't submit
4251 correct partitions for input data</li>
4252 <li>Translation from DNA to Amino Acids fails</li>
4253 <li>Jalview fail to load newick tree with quoted label</li>
4254 <li>--headless flag isn't understood</li>
4255 <li>ClassCastException when generating EPS in headless
4257 <li>Adjusting sequence-associated shading threshold only
4258 changes one row's threshold</li>
4259 <li>Preferences and Feature settings panel panel
4260 doesn't open</li>
4261 <li>hide consensus histogram also hides conservation and
4262 quality histograms</li>
4267 <td><div align="center">
4268 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
4270 <td><em>Application</em>
4272 <li>Support for JABAWS 2.0 Services (AACon alignment
4273 conservation, protein disorder and Clustal Omega)</li>
4274 <li>JABAWS server status indicator in Web Services
4276 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
4277 in Jalview alignment window</li>
4278 <li>Updated Jalview build and deploy framework for OSX
4279 mountain lion, windows 7, and 8</li>
4280 <li>Nucleotide substitution matrix for PCA that supports
4281 RNA and ambiguity codes</li>
4283 <li>Improved sequence database retrieval GUI</li>
4284 <li>Support fetching and database reference look up
4285 against multiple DAS sources (Fetch all from in 'fetch db
4287 <li>Jalview project improvements
4289 <li>Store and retrieve the 'belowAlignment'
4290 flag for annotation</li>
4291 <li>calcId attribute to group annotation rows on the
4293 <li>Store AACon calculation settings for a view in
4294 Jalview project</li>
4298 <li>horizontal scrolling gesture support</li>
4299 <li>Visual progress indicator when PCA calculation is
4301 <li>Simpler JABA web services menus</li>
4302 <li>visual indication that web service results are still
4303 being retrieved from server</li>
4304 <li>Serialise the dialogs that are shown when Jalview
4305 starts up for first time</li>
4306 <li>Jalview user agent string for interacting with HTTP
4308 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
4310 <li>Examples directory and Groovy library included in
4311 InstallAnywhere distribution</li>
4312 </ul> <em>Applet</em>
4314 <li>RNA alignment and secondary structure annotation
4315 visualization applet example</li>
4316 </ul> <em>General</em>
4318 <li>Normalise option for consensus sequence logo</li>
4319 <li>Reset button in PCA window to return dimensions to
4321 <li>Allow seqspace or Jalview variant of alignment PCA
4323 <li>PCA with either nucleic acid and protein substitution
4325 <li>Allow windows containing HTML reports to be exported
4327 <li>Interactive display and editing of RNA secondary
4328 structure contacts</li>
4329 <li>RNA Helix Alignment Colouring</li>
4330 <li>RNA base pair logo consensus</li>
4331 <li>Parse sequence associated secondary structure
4332 information in Stockholm files</li>
4333 <li>HTML Export database accessions and annotation
4334 information presented in tooltip for sequences</li>
4335 <li>Import secondary structure from LOCARNA clustalw
4336 style RNA alignment files</li>
4337 <li>import and visualise T-COFFEE quality scores for an
4339 <li>'colour by annotation' per sequence option to
4340 shade each sequence according to its associated alignment
4342 <li>New Jalview Logo</li>
4343 </ul> <em>Documentation and Development</em>
4345 <li>documentation for score matrices used in Jalview</li>
4346 <li>New Website!</li>
4348 <td><em>Application</em>
4350 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
4351 wsdbfetch REST service</li>
4352 <li>Stop windows being moved outside desktop on OSX</li>
4353 <li>Filetype associations not installed for webstart
4355 <li>Jalview does not always retrieve progress of a JABAWS
4356 job execution in full once it is complete</li>
4357 <li>revise SHMR RSBS definition to ensure alignment is
4358 uploaded via ali_file parameter</li>
4359 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
4360 <li>View all structures superposed fails with exception</li>
4361 <li>Jnet job queues forever if a very short sequence is
4362 submitted for prediction</li>
4363 <li>Cut and paste menu not opened when mouse clicked on
4365 <li>Putting fractional value into integer text box in
4366 alignment parameter dialog causes Jalview to hang</li>
4367 <li>Structure view highlighting doesn't work on
4369 <li>View all structures fails with exception shown in
4371 <li>Characters in filename associated with PDBEntry not
4372 escaped in a platform independent way</li>
4373 <li>Jalview desktop fails to launch with exception when
4375 <li>Tree calculation reports 'you must have 2 or more
4376 sequences selected' when selection is empty</li>
4377 <li>Jalview desktop fails to launch with jar signature
4378 failure when java web start temporary file caching is
4380 <li>DAS Sequence retrieval with range qualification
4381 results in sequence xref which includes range qualification</li>
4382 <li>Errors during processing of command line arguments
4383 cause progress bar (JAL-898) to be removed</li>
4384 <li>Replace comma for semi-colon option not disabled for
4385 DAS sources in sequence fetcher</li>
4386 <li>Cannot close news reader when JABAWS server warning
4387 dialog is shown</li>
4388 <li>Option widgets not updated to reflect user settings</li>
4389 <li>Edited sequence not submitted to web service</li>
4390 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
4391 <li>InstallAnywhere installer doesn't unpack and run
4392 on OSX Mountain Lion</li>
4393 <li>Annotation panel not given a scroll bar when
4394 sequences with alignment annotation are pasted into the
4396 <li>Sequence associated annotation rows not associated
4397 when loaded from Jalview project</li>
4398 <li>Browser launch fails with NPE on java 1.7</li>
4399 <li>JABAWS alignment marked as finished when job was
4400 cancelled or job failed due to invalid input</li>
4401 <li>NPE with v2.7 example when clicking on Tree
4402 associated with all views</li>
4403 <li>Exceptions when copy/paste sequences with grouped
4404 annotation rows to new window</li>
4405 </ul> <em>Applet</em>
4407 <li>Sequence features are momentarily displayed before
4408 they are hidden using hidefeaturegroups applet parameter</li>
4409 <li>loading features via javascript API automatically
4410 enables feature display</li>
4411 <li>scrollToColumnIn javascript API method doesn't
4413 </ul> <em>General</em>
4415 <li>Redundancy removal fails for rna alignment</li>
4416 <li>PCA calculation fails when sequence has been selected
4417 and then deselected</li>
4418 <li>PCA window shows grey box when first opened on OSX</li>
4419 <li>Letters coloured pink in sequence logo when alignment
4420 coloured with clustalx</li>
4421 <li>Choosing fonts without letter symbols defined causes
4422 exceptions and redraw errors</li>
4423 <li>Initial PCA plot view is not same as manually
4424 reconfigured view</li>
4425 <li>Grouped annotation graph label has incorrect line
4427 <li>Grouped annotation graph label display is corrupted
4428 for lots of labels</li>
4433 <div align="center">
4434 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
4437 <td><em>Application</em>
4439 <li>Jalview Desktop News Reader</li>
4440 <li>Tweaked default layout of web services menu</li>
4441 <li>View/alignment association menu to enable user to
4442 easily specify which alignment a multi-structure view takes
4443 its colours/correspondences from</li>
4444 <li>Allow properties file location to be specified as URL</li>
4445 <li>Extend Jalview project to preserve associations
4446 between many alignment views and a single Jmol display</li>
4447 <li>Store annotation row height in Jalview project file</li>
4448 <li>Annotation row column label formatting attributes
4449 stored in project file</li>
4450 <li>Annotation row order for auto-calculated annotation
4451 rows preserved in Jalview project file</li>
4452 <li>Visual progress indication when Jalview state is
4453 saved using Desktop window menu</li>
4454 <li>Visual indication that command line arguments are
4455 still being processed</li>
4456 <li>Groovy script execution from URL</li>
4457 <li>Colour by annotation default min and max colours in
4459 <li>Automatically associate PDB files dragged onto an
4460 alignment with sequences that have high similarity and
4462 <li>Update JGoogleAnalytics to latest release (0.3)</li>
4463 <li>'view structures' option to open many
4464 structures in same window</li>
4465 <li>Sort associated views menu option for tree panel</li>
4466 <li>Group all JABA and non-JABA services for a particular
4467 analysis function in its own submenu</li>
4468 </ul> <em>Applet</em>
4470 <li>Userdefined and autogenerated annotation rows for
4472 <li>Adjustment of alignment annotation pane height</li>
4473 <li>Annotation scrollbar for annotation panel</li>
4474 <li>Drag to reorder annotation rows in annotation panel</li>
4475 <li>'automaticScrolling' parameter</li>
4476 <li>Allow sequences with partial ID string matches to be
4477 annotated from GFF/Jalview features files</li>
4478 <li>Sequence logo annotation row in applet</li>
4479 <li>Absolute paths relative to host server in applet
4480 parameters are treated as such</li>
4481 <li>New in the JalviewLite javascript API:
4483 <li>JalviewLite.js javascript library</li>
4484 <li>Javascript callbacks for
4486 <li>Applet initialisation</li>
4487 <li>Sequence/alignment mouse-overs and selections</li>
4490 <li>scrollTo row and column alignment scrolling
4492 <li>Select sequence/alignment regions from javascript</li>
4493 <li>javascript structure viewer harness to pass
4494 messages between Jmol and Jalview when running as
4495 distinct applets</li>
4496 <li>sortBy method</li>
4497 <li>Set of applet and application examples shipped
4498 with documentation</li>
4499 <li>New example to demonstrate JalviewLite and Jmol
4500 javascript message exchange</li>
4502 </ul> <em>General</em>
4504 <li>Enable Jmol displays to be associated with multiple
4505 multiple alignments</li>
4506 <li>Option to automatically sort alignment with new tree</li>
4507 <li>User configurable link to enable redirects to a
4508 www.Jalview.org mirror</li>
4509 <li>Jmol colours option for Jmol displays</li>
4510 <li>Configurable newline string when writing alignment
4511 and other flat files</li>
4512 <li>Allow alignment annotation description lines to
4513 contain html tags</li>
4514 </ul> <em>Documentation and Development</em>
4516 <li>Add groovy test harness for bulk load testing to
4518 <li>Groovy script to load and align a set of sequences
4519 using a web service before displaying the result in the
4520 Jalview desktop</li>
4521 <li>Restructured javascript and applet api documentation</li>
4522 <li>Ant target to publish example html files with applet
4524 <li>Netbeans project for building Jalview from source</li>
4525 <li>ant task to create online javadoc for Jalview source</li>
4527 <td><em>Application</em>
4529 <li>User defined colourscheme throws exception when
4530 current built in colourscheme is saved as new scheme</li>
4531 <li>AlignFrame->Save in application pops up save
4532 dialog for valid filename/format</li>
4533 <li>Cannot view associated structure for UniProt sequence</li>
4534 <li>PDB file association breaks for UniProt sequence
4536 <li>Associate PDB from file dialog does not tell you
4537 which sequence is to be associated with the file</li>
4538 <li>Find All raises null pointer exception when query
4539 only matches sequence IDs</li>
4540 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4541 <li>Jalview project with Jmol views created with Jalview
4542 2.4 cannot be loaded</li>
4543 <li>Filetype associations not installed for webstart
4545 <li>Two or more chains in a single PDB file associated
4546 with sequences in different alignments do not get coloured
4547 by their associated sequence</li>
4548 <li>Visibility status of autocalculated annotation row
4549 not preserved when project is loaded</li>
4550 <li>Annotation row height and visibility attributes not
4551 stored in Jalview project</li>
4552 <li>Tree bootstraps are not preserved when saved as a
4553 Jalview project</li>
4554 <li>Envision2 workflow tooltips are corrupted</li>
4555 <li>Enabling show group conservation also enables colour
4556 by conservation</li>
4557 <li>Duplicate group associated conservation or consensus
4558 created on new view</li>
4559 <li>Annotation scrollbar not displayed after 'show
4560 all hidden annotation rows' option selected</li>
4561 <li>Alignment quality not updated after alignment
4562 annotation row is hidden then shown</li>
4563 <li>Preserve colouring of structures coloured by
4564 sequences in pre Jalview 2.7 projects</li>
4565 <li>Web service job parameter dialog is not laid out
4567 <li>Web services menu not refreshed after 'reset
4568 services' button is pressed in preferences</li>
4569 <li>Annotation off by one in Jalview v2_3 example project</li>
4570 <li>Structures imported from file and saved in project
4571 get name like jalview_pdb1234.txt when reloaded</li>
4572 <li>Jalview does not always retrieve progress of a JABAWS
4573 job execution in full once it is complete</li>
4574 </ul> <em>Applet</em>
4576 <li>Alignment height set incorrectly when lots of
4577 annotation rows are displayed</li>
4578 <li>Relative URLs in feature HTML text not resolved to
4580 <li>View follows highlighting does not work for positions
4582 <li><= shown as = in tooltip</li>
4583 <li>Export features raises exception when no features
4585 <li>Separator string used for serialising lists of IDs
4586 for javascript api is modified when separator string
4587 provided as parameter</li>
4588 <li>Null pointer exception when selecting tree leaves for
4589 alignment with no existing selection</li>
4590 <li>Relative URLs for datasources assumed to be relative
4591 to applet's codebase</li>
4592 <li>Status bar not updated after finished searching and
4593 search wraps around to first result</li>
4594 <li>StructureSelectionManager instance shared between
4595 several Jalview applets causes race conditions and memory
4597 <li>Hover tooltip and mouseover of position on structure
4598 not sent from Jmol in applet</li>
4599 <li>Certain sequences of javascript method calls to
4600 applet API fatally hang browser</li>
4601 </ul> <em>General</em>
4603 <li>View follows structure mouseover scrolls beyond
4604 position with wrapped view and hidden regions</li>
4605 <li>Find sequence position moves to wrong residue
4606 with/without hidden columns</li>
4607 <li>Sequence length given in alignment properties window
4609 <li>InvalidNumberFormat exceptions thrown when trying to
4610 import PDB like structure files</li>
4611 <li>Positional search results are only highlighted
4612 between user-supplied sequence start/end bounds</li>
4613 <li>End attribute of sequence is not validated</li>
4614 <li>Find dialog only finds first sequence containing a
4615 given sequence position</li>
4616 <li>Sequence numbering not preserved in MSF alignment
4618 <li>Jalview PDB file reader does not extract sequence
4619 from nucleotide chains correctly</li>
4620 <li>Structure colours not updated when tree partition
4621 changed in alignment</li>
4622 <li>Sequence associated secondary structure not correctly
4623 parsed in interleaved stockholm</li>
4624 <li>Colour by annotation dialog does not restore current
4626 <li>Hiding (nearly) all sequences doesn't work
4628 <li>Sequences containing lowercase letters are not
4629 properly associated with their pdb files</li>
4630 </ul> <em>Documentation and Development</em>
4632 <li>schemas/JalviewWsParamSet.xsd corrupted by
4633 ApplyCopyright tool</li>
4638 <div align="center">
4639 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4642 <td><em>Application</em>
4644 <li>New warning dialog when the Jalview Desktop cannot
4645 contact web services</li>
4646 <li>JABA service parameters for a preset are shown in
4647 service job window</li>
4648 <li>JABA Service menu entries reworded</li>
4652 <li>Modeller PIR IO broken - cannot correctly import a
4653 pir file emitted by Jalview</li>
4654 <li>Existing feature settings transferred to new
4655 alignment view created from cut'n'paste</li>
4656 <li>Improved test for mixed amino/nucleotide chains when
4657 parsing PDB files</li>
4658 <li>Consensus and conservation annotation rows
4659 occasionally become blank for all new windows</li>
4660 <li>Exception raised when right clicking above sequences
4661 in wrapped view mode</li>
4662 </ul> <em>Application</em>
4664 <li>multiple multiply aligned structure views cause cpu
4665 usage to hit 100% and computer to hang</li>
4666 <li>Web Service parameter layout breaks for long user
4667 parameter names</li>
4668 <li>Jaba service discovery hangs desktop if Jaba server
4675 <div align="center">
4676 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4679 <td><em>Application</em>
4681 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4682 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4685 <li>Web Services preference tab</li>
4686 <li>Analysis parameters dialog box and user defined
4688 <li>Improved speed and layout of Envision2 service menu</li>
4689 <li>Superpose structures using associated sequence
4691 <li>Export coordinates and projection as CSV from PCA
4693 </ul> <em>Applet</em>
4695 <li>enable javascript: execution by the applet via the
4696 link out mechanism</li>
4697 </ul> <em>Other</em>
4699 <li>Updated the Jmol Jalview interface to work with Jmol
4701 <li>The Jalview Desktop and JalviewLite applet now
4702 require Java 1.5</li>
4703 <li>Allow Jalview feature colour specification for GFF
4704 sequence annotation files</li>
4705 <li>New 'colour by label' keword in Jalview feature file
4706 type colour specification</li>
4707 <li>New Jalview Desktop Groovy API method that allows a
4708 script to check if it being run in an interactive session or
4709 in a batch operation from the Jalview command line</li>
4713 <li>clustalx colourscheme colours Ds preferentially when
4714 both D+E are present in over 50% of the column</li>
4715 </ul> <em>Application</em>
4717 <li>typo in AlignmentFrame->View->Hide->all but
4718 selected Regions menu item</li>
4719 <li>sequence fetcher replaces ',' for ';' when the ',' is
4720 part of a valid accession ID</li>
4721 <li>fatal OOM if object retrieved by sequence fetcher
4722 runs out of memory</li>
4723 <li>unhandled Out of Memory Error when viewing pca
4724 analysis results</li>
4725 <li>InstallAnywhere builds fail to launch on OS X java
4726 10.5 update 4 (due to apple Java 1.6 update)</li>
4727 <li>Installanywhere Jalview silently fails to launch</li>
4728 </ul> <em>Applet</em>
4730 <li>Jalview.getFeatureGroups() raises an
4731 ArrayIndexOutOfBoundsException if no feature groups are
4738 <div align="center">
4739 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4745 <li>Alignment prettyprinter doesn't cope with long
4747 <li>clustalx colourscheme colours Ds preferentially when
4748 both D+E are present in over 50% of the column</li>
4749 <li>nucleic acid structures retrieved from PDB do not
4750 import correctly</li>
4751 <li>More columns get selected than were clicked on when a
4752 number of columns are hidden</li>
4753 <li>annotation label popup menu not providing correct
4754 add/hide/show options when rows are hidden or none are
4756 <li>Stockholm format shown in list of readable formats,
4757 and parser copes better with alignments from RFAM.</li>
4758 <li>CSV output of consensus only includes the percentage
4759 of all symbols if sequence logo display is enabled</li>
4761 </ul> <em>Applet</em>
4763 <li>annotation panel disappears when annotation is
4765 </ul> <em>Application</em>
4767 <li>Alignment view not redrawn properly when new
4768 alignment opened where annotation panel is visible but no
4769 annotations are present on alignment</li>
4770 <li>pasted region containing hidden columns is
4771 incorrectly displayed in new alignment window</li>
4772 <li>Jalview slow to complete operations when stdout is
4773 flooded (fix is to close the Jalview console)</li>
4774 <li>typo in AlignmentFrame->View->Hide->all but
4775 selected Rregions menu item.</li>
4776 <li>inconsistent group submenu and Format submenu entry
4777 'Un' or 'Non'conserved</li>
4778 <li>Sequence feature settings are being shared by
4779 multiple distinct alignments</li>
4780 <li>group annotation not recreated when tree partition is
4782 <li>double click on group annotation to select sequences
4783 does not propagate to associated trees</li>
4784 <li>Mac OSX specific issues:
4786 <li>exception raised when mouse clicked on desktop
4787 window background</li>
4788 <li>Desktop menu placed on menu bar and application
4789 name set correctly</li>
4790 <li>sequence feature settings not wide enough for the
4791 save feature colourscheme button</li>
4800 <div align="center">
4801 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4804 <td><em>New Capabilities</em>
4806 <li>URL links generated from description line for
4807 regular-expression based URL links (applet and application)
4810 <li>Non-positional feature URL links are shown in link
4812 <li>Linked viewing of nucleic acid sequences and
4814 <li>Automatic Scrolling option in View menu to display
4815 the currently highlighted region of an alignment.</li>
4816 <li>Order an alignment by sequence length, or using the
4817 average score or total feature count for each sequence.</li>
4818 <li>Shading features by score or associated description</li>
4819 <li>Subdivide alignment and groups based on identity of
4820 selected subsequence (Make Groups from Selection).</li>
4821 <li>New hide/show options including Shift+Control+H to
4822 hide everything but the currently selected region.</li>
4823 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4824 </ul> <em>Application</em>
4826 <li>Fetch DB References capabilities and UI expanded to
4827 support retrieval from DAS sequence sources</li>
4828 <li>Local DAS Sequence sources can be added via the
4829 command line or via the Add local source dialog box.</li>
4830 <li>DAS Dbref and DbxRef feature types are parsed as
4831 database references and protein_name is parsed as
4832 description line (BioSapiens terms).</li>
4833 <li>Enable or disable non-positional feature and database
4834 references in sequence ID tooltip from View menu in
4836 <!-- <li>New hidden columns and rows and representatives capabilities
4837 in annotations file (in progress - not yet fully implemented)</li> -->
4838 <li>Group-associated consensus, sequence logos and
4839 conservation plots</li>
4840 <li>Symbol distributions for each column can be exported
4841 and visualized as sequence logos</li>
4842 <li>Optionally scale multi-character column labels to fit
4843 within each column of annotation row<!-- todo for applet -->
4845 <li>Optional automatic sort of associated alignment view
4846 when a new tree is opened.</li>
4847 <li>Jalview Java Console</li>
4848 <li>Better placement of desktop window when moving
4849 between different screens.</li>
4850 <li>New preference items for sequence ID tooltip and
4851 consensus annotation</li>
4852 <li>Client to submit sequences and IDs to Envision2
4854 <li><em>Vamsas Capabilities</em>
4856 <li>Improved VAMSAS synchronization (Jalview archive
4857 used to preserve views, structures, and tree display
4859 <li>Import of vamsas documents from disk or URL via
4861 <li>Sharing of selected regions between views and
4862 with other VAMSAS applications (Experimental feature!)</li>
4863 <li>Updated API to VAMSAS version 0.2</li>
4865 </ul> <em>Applet</em>
4867 <li>Middle button resizes annotation row height</li>
4870 <li>sortByTree (true/false) - automatically sort the
4871 associated alignment view by the tree when a new tree is
4873 <li>showTreeBootstraps (true/false) - show or hide
4874 branch bootstraps (default is to show them if available)</li>
4875 <li>showTreeDistances (true/false) - show or hide
4876 branch lengths (default is to show them if available)</li>
4877 <li>showUnlinkedTreeNodes (true/false) - indicate if
4878 unassociated nodes should be highlighted in the tree
4880 <li>heightScale and widthScale (1.0 or more) -
4881 increase the height or width of a cell in the alignment
4882 grid relative to the current font size.</li>
4885 <li>Non-positional features displayed in sequence ID
4887 </ul> <em>Other</em>
4889 <li>Features format: graduated colour definitions and
4890 specification of feature scores</li>
4891 <li>Alignment Annotations format: new keywords for group
4892 associated annotation (GROUP_REF) and annotation row display
4893 properties (ROW_PROPERTIES)</li>
4894 <li>XML formats extended to support graduated feature
4895 colourschemes, group associated annotation, and profile
4896 visualization settings.</li></td>
4899 <li>Source field in GFF files parsed as feature source
4900 rather than description</li>
4901 <li>Non-positional features are now included in sequence
4902 feature and gff files (controlled via non-positional feature
4903 visibility in tooltip).</li>
4904 <li>URL links generated for all feature links (bugfix)</li>
4905 <li>Added URL embedding instructions to features file
4907 <li>Codons containing ambiguous nucleotides translated as
4908 'X' in peptide product</li>
4909 <li>Match case switch in find dialog box works for both
4910 sequence ID and sequence string and query strings do not
4911 have to be in upper case to match case-insensitively.</li>
4912 <li>AMSA files only contain first column of
4913 multi-character column annotation labels</li>
4914 <li>Jalview Annotation File generation/parsing consistent
4915 with documentation (e.g. Stockholm annotation can be
4916 exported and re-imported)</li>
4917 <li>PDB files without embedded PDB IDs given a friendly
4919 <li>Find incrementally searches ID string matches as well
4920 as subsequence matches, and correctly reports total number
4924 <li>Better handling of exceptions during sequence
4926 <li>Dasobert generated non-positional feature URL
4927 link text excludes the start_end suffix</li>
4928 <li>DAS feature and source retrieval buttons disabled
4929 when fetch or registry operations in progress.</li>
4930 <li>PDB files retrieved from URLs are cached properly</li>
4931 <li>Sequence description lines properly shared via
4933 <li>Sequence fetcher fetches multiple records for all
4935 <li>Ensured that command line das feature retrieval
4936 completes before alignment figures are generated.</li>
4937 <li>Reduced time taken when opening file browser for
4939 <li>isAligned check prior to calculating tree, PCA or
4940 submitting an MSA to JNet now excludes hidden sequences.</li>
4941 <li>User defined group colours properly recovered
4942 from Jalview projects.</li>
4951 <div align="center">
4952 <strong>2.4.0.b2</strong><br> 28/10/2009
4957 <li>Experimental support for google analytics usage
4959 <li>Jalview privacy settings (user preferences and docs).</li>
4964 <li>Race condition in applet preventing startup in
4966 <li>Exception when feature created from selection beyond
4967 length of sequence.</li>
4968 <li>Allow synthetic PDB files to be imported gracefully</li>
4969 <li>Sequence associated annotation rows associate with
4970 all sequences with a given id</li>
4971 <li>Find function matches case-insensitively for sequence
4972 ID string searches</li>
4973 <li>Non-standard characters do not cause pairwise
4974 alignment to fail with exception</li>
4975 </ul> <em>Application Issues</em>
4977 <li>Sequences are now validated against EMBL database</li>
4978 <li>Sequence fetcher fetches multiple records for all
4980 </ul> <em>InstallAnywhere Issues</em>
4982 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4983 issue with installAnywhere mechanism)</li>
4984 <li>Command line launching of JARs from InstallAnywhere
4985 version (java class versioning error fixed)</li>
4992 <div align="center">
4993 <strong>2.4</strong><br> 27/8/2008
4996 <td><em>User Interface</em>
4998 <li>Linked highlighting of codon and amino acid from
4999 translation and protein products</li>
5000 <li>Linked highlighting of structure associated with
5001 residue mapping to codon position</li>
5002 <li>Sequence Fetcher provides example accession numbers
5003 and 'clear' button</li>
5004 <li>MemoryMonitor added as an option under Desktop's
5006 <li>Extract score function to parse whitespace separated
5007 numeric data in description line</li>
5008 <li>Column labels in alignment annotation can be centred.</li>
5009 <li>Tooltip for sequence associated annotation give name
5011 </ul> <em>Web Services and URL fetching</em>
5013 <li>JPred3 web service</li>
5014 <li>Prototype sequence search client (no public services
5016 <li>Fetch either seed alignment or full alignment from
5018 <li>URL Links created for matching database cross
5019 references as well as sequence ID</li>
5020 <li>URL Links can be created using regular-expressions</li>
5021 </ul> <em>Sequence Database Connectivity</em>
5023 <li>Retrieval of cross-referenced sequences from other
5025 <li>Generalised database reference retrieval and
5026 validation to all fetchable databases</li>
5027 <li>Fetch sequences from DAS sources supporting the
5028 sequence command</li>
5029 </ul> <em>Import and Export</em>
5030 <li>export annotation rows as CSV for spreadsheet import</li>
5031 <li>Jalview projects record alignment dataset associations,
5032 EMBL products, and cDNA sequence mappings</li>
5033 <li>Sequence Group colour can be specified in Annotation
5035 <li>Ad-hoc colouring of group in Annotation File using RGB
5036 triplet as name of colourscheme</li>
5037 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
5039 <li>treenode binding for VAMSAS tree exchange</li>
5040 <li>local editing and update of sequences in VAMSAS
5041 alignments (experimental)</li>
5042 <li>Create new or select existing session to join</li>
5043 <li>load and save of vamsas documents</li>
5044 </ul> <em>Application command line</em>
5046 <li>-tree parameter to open trees (introduced for passing
5048 <li>-fetchfrom command line argument to specify nicknames
5049 of DAS servers to query for alignment features</li>
5050 <li>-dasserver command line argument to add new servers
5051 that are also automatically queried for features</li>
5052 <li>-groovy command line argument executes a given groovy
5053 script after all input data has been loaded and parsed</li>
5054 </ul> <em>Applet-Application data exchange</em>
5056 <li>Trees passed as applet parameters can be passed to
5057 application (when using "View in full
5058 application")</li>
5059 </ul> <em>Applet Parameters</em>
5061 <li>feature group display control parameter</li>
5062 <li>debug parameter</li>
5063 <li>showbutton parameter</li>
5064 </ul> <em>Applet API methods</em>
5066 <li>newView public method</li>
5067 <li>Window (current view) specific get/set public methods</li>
5068 <li>Feature display control methods</li>
5069 <li>get list of currently selected sequences</li>
5070 </ul> <em>New Jalview distribution features</em>
5072 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
5073 <li>RELEASE file gives build properties for the latest
5074 Jalview release.</li>
5075 <li>Java 1.1 Applet build made easier and donotobfuscate
5076 property controls execution of obfuscator</li>
5077 <li>Build target for generating source distribution</li>
5078 <li>Debug flag for javacc</li>
5079 <li>.jalview_properties file is documented (slightly) in
5080 jalview.bin.Cache</li>
5081 <li>Continuous Build Integration for stable and
5082 development version of Application, Applet and source
5087 <li>selected region output includes visible annotations
5088 (for certain formats)</li>
5089 <li>edit label/displaychar contains existing label/char
5091 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
5092 <li>shorter peptide product names from EMBL records</li>
5093 <li>Newick string generator makes compact representations</li>
5094 <li>bootstrap values parsed correctly for tree files with
5096 <li>pathological filechooser bug avoided by not allowing
5097 filenames containing a ':'</li>
5098 <li>Fixed exception when parsing GFF files containing
5099 global sequence features</li>
5100 <li>Alignment datasets are finalized only when number of
5101 references from alignment sequences goes to zero</li>
5102 <li>Close of tree branch colour box without colour
5103 selection causes cascading exceptions</li>
5104 <li>occasional negative imgwidth exceptions</li>
5105 <li>better reporting of non-fatal warnings to user when
5106 file parsing fails.</li>
5107 <li>Save works when Jalview project is default format</li>
5108 <li>Save as dialog opened if current alignment format is
5109 not a valid output format</li>
5110 <li>UniProt canonical names introduced for both das and
5112 <li>Histidine should be midblue (not pink!) in Zappo</li>
5113 <li>error messages passed up and output when data read
5115 <li>edit undo recovers previous dataset sequence when
5116 sequence is edited</li>
5117 <li>allow PDB files without pdb ID HEADER lines (like
5118 those generated by MODELLER) to be read in properly</li>
5119 <li>allow reading of JPred concise files as a normal
5121 <li>Stockholm annotation parsing and alignment properties
5122 import fixed for PFAM records</li>
5123 <li>Structure view windows have correct name in Desktop
5125 <li>annotation consisting of sequence associated scores
5126 can be read and written correctly to annotation file</li>
5127 <li>Aligned cDNA translation to aligned peptide works
5129 <li>Fixed display of hidden sequence markers and
5130 non-italic font for representatives in Applet</li>
5131 <li>Applet Menus are always embedded in applet window on
5133 <li>Newly shown features appear at top of stack (in
5135 <li>Annotations added via parameter not drawn properly
5136 due to null pointer exceptions</li>
5137 <li>Secondary structure lines are drawn starting from
5138 first column of alignment</li>
5139 <li>UniProt XML import updated for new schema release in
5141 <li>Sequence feature to sequence ID match for Features
5142 file is case-insensitive</li>
5143 <li>Sequence features read from Features file appended to
5144 all sequences with matching IDs</li>
5145 <li>PDB structure coloured correctly for associated views
5146 containing a sub-sequence</li>
5147 <li>PDB files can be retrieved by applet from Jar files</li>
5148 <li>feature and annotation file applet parameters
5149 referring to different directories are retrieved correctly</li>
5150 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
5151 <li>Fixed application hang whilst waiting for
5152 splash-screen version check to complete</li>
5153 <li>Applet properly URLencodes input parameter values
5154 when passing them to the launchApp service</li>
5155 <li>display name and local features preserved in results
5156 retrieved from web service</li>
5157 <li>Visual delay indication for sequence retrieval and
5158 sequence fetcher initialisation</li>
5159 <li>updated Application to use DAS 1.53e version of
5160 dasobert DAS client</li>
5161 <li>Re-instated Full AMSA support and .amsa file
5163 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
5171 <div align="center">
5172 <strong>2.3</strong><br> 9/5/07
5177 <li>Jmol 11.0.2 integration</li>
5178 <li>PDB views stored in Jalview XML files</li>
5179 <li>Slide sequences</li>
5180 <li>Edit sequence in place</li>
5181 <li>EMBL CDS features</li>
5182 <li>DAS Feature mapping</li>
5183 <li>Feature ordering</li>
5184 <li>Alignment Properties</li>
5185 <li>Annotation Scores</li>
5186 <li>Sort by scores</li>
5187 <li>Feature/annotation editing in applet</li>
5192 <li>Headless state operation in 2.2.1</li>
5193 <li>Incorrect and unstable DNA pairwise alignment</li>
5194 <li>Cut and paste of sequences with annotation</li>
5195 <li>Feature group display state in XML</li>
5196 <li>Feature ordering in XML</li>
5197 <li>blc file iteration selection using filename # suffix</li>
5198 <li>Stockholm alignment properties</li>
5199 <li>Stockhom alignment secondary structure annotation</li>
5200 <li>2.2.1 applet had no feature transparency</li>
5201 <li>Number pad keys can be used in cursor mode</li>
5202 <li>Structure Viewer mirror image resolved</li>
5209 <div align="center">
5210 <strong>2.2.1</strong><br> 12/2/07
5215 <li>Non standard characters can be read and displayed
5216 <li>Annotations/Features can be imported/exported to the
5218 <li>Applet allows editing of sequence/annotation/group
5219 name & description
5220 <li>Preference setting to display sequence name in
5222 <li>Annotation file format extended to allow
5223 Sequence_groups to be defined
5224 <li>Default opening of alignment overview panel can be
5225 specified in preferences
5226 <li>PDB residue numbering annotation added to associated
5232 <li>Applet crash under certain Linux OS with Java 1.6
5234 <li>Annotation file export / import bugs fixed
5235 <li>PNG / EPS image output bugs fixed
5241 <div align="center">
5242 <strong>2.2</strong><br> 27/11/06
5247 <li>Multiple views on alignment
5248 <li>Sequence feature editing
5249 <li>"Reload" alignment
5250 <li>"Save" to current filename
5251 <li>Background dependent text colour
5252 <li>Right align sequence ids
5253 <li>User-defined lower case residue colours
5256 <li>Menu item accelerator keys
5257 <li>Control-V pastes to current alignment
5258 <li>Cancel button for DAS Feature Fetching
5259 <li>PCA and PDB Viewers zoom via mouse roller
5260 <li>User-defined sub-tree colours and sub-tree selection
5263 <li>'New Window' button on the 'Output to Text box'
5268 <li>New memory efficient Undo/Redo System
5269 <li>Optimised symbol lookups and conservation/consensus
5271 <li>Region Conservation/Consensus recalculated after
5273 <li>Fixed Remove Empty Columns Bug (empty columns at end
5275 <li>Slowed DAS Feature Fetching for increased robustness.
5278 <li>Made angle brackets in ASCII feature descriptions
5280 <li>Re-instated Zoom function for PCA
5281 <li>Sequence descriptions conserved in web service
5283 <li>UniProt ID discoverer uses any word separated by
5285 <li>WsDbFetch query/result association resolved
5286 <li>Tree leaf to sequence mapping improved
5287 <li>Smooth fonts switch moved to FontChooser dialog box.
5295 <div align="center">
5296 <strong>2.1.1</strong><br> 12/9/06
5301 <li>Copy consensus sequence to clipboard</li>
5306 <li>Image output - rightmost residues are rendered if
5307 sequence id panel has been resized</li>
5308 <li>Image output - all offscreen group boundaries are
5310 <li>Annotation files with sequence references - all
5311 elements in file are relative to sequence position</li>
5312 <li>Mac Applet users can use Alt key for group editing</li>
5318 <div align="center">
5319 <strong>2.1</strong><br> 22/8/06
5324 <li>MAFFT Multiple Alignment in default Web Service list</li>
5325 <li>DAS Feature fetching</li>
5326 <li>Hide sequences and columns</li>
5327 <li>Export Annotations and Features</li>
5328 <li>GFF file reading / writing</li>
5329 <li>Associate structures with sequences from local PDB
5331 <li>Add sequences to exisiting alignment</li>
5332 <li>Recently opened files / URL lists</li>
5333 <li>Applet can launch the full application</li>
5334 <li>Applet has transparency for features (Java 1.2
5336 <li>Applet has user defined colours parameter</li>
5337 <li>Applet can load sequences from parameter
5338 "sequence<em>x</em>"
5344 <li>Redundancy Panel reinstalled in the Applet</li>
5345 <li>Monospaced font - EPS / rescaling bug fixed</li>
5346 <li>Annotation files with sequence references bug fixed</li>
5352 <div align="center">
5353 <strong>2.08.1</strong><br> 2/5/06
5358 <li>Change case of selected region from Popup menu</li>
5359 <li>Choose to match case when searching</li>
5360 <li>Middle mouse button and mouse movement can compress /
5361 expand the visible width and height of the alignment</li>
5366 <li>Annotation Panel displays complete JNet results</li>
5372 <div align="center">
5373 <strong>2.08b</strong><br> 18/4/06
5379 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
5380 <li>Righthand label on wrapped alignments shows correct
5387 <div align="center">
5388 <strong>2.08</strong><br> 10/4/06
5393 <li>Editing can be locked to the selection area</li>
5394 <li>Keyboard editing</li>
5395 <li>Create sequence features from searches</li>
5396 <li>Precalculated annotations can be loaded onto
5398 <li>Features file allows grouping of features</li>
5399 <li>Annotation Colouring scheme added</li>
5400 <li>Smooth fonts off by default - Faster rendering</li>
5401 <li>Choose to toggle Autocalculate Consensus On/Off</li>
5406 <li>Drag & Drop fixed on Linux</li>
5407 <li>Jalview Archive file faster to load/save, sequence
5408 descriptions saved.</li>
5414 <div align="center">
5415 <strong>2.07</strong><br> 12/12/05
5420 <li>PDB Structure Viewer enhanced</li>
5421 <li>Sequence Feature retrieval and display enhanced</li>
5422 <li>Choose to output sequence start-end after sequence
5423 name for file output</li>
5424 <li>Sequence Fetcher WSDBFetch@EBI</li>
5425 <li>Applet can read feature files, PDB files and can be
5426 used for HTML form input</li>
5431 <li>HTML output writes groups and features</li>
5432 <li>Group editing is Control and mouse click</li>
5433 <li>File IO bugs</li>
5439 <div align="center">
5440 <strong>2.06</strong><br> 28/9/05
5445 <li>View annotations in wrapped mode</li>
5446 <li>More options for PCA viewer</li>
5451 <li>GUI bugs resolved</li>
5452 <li>Runs with -nodisplay from command line</li>
5458 <div align="center">
5459 <strong>2.05b</strong><br> 15/9/05
5464 <li>Choose EPS export as lineart or text</li>
5465 <li>Jar files are executable</li>
5466 <li>Can read in Uracil - maps to unknown residue</li>
5471 <li>Known OutOfMemory errors give warning message</li>
5472 <li>Overview window calculated more efficiently</li>
5473 <li>Several GUI bugs resolved</li>
5479 <div align="center">
5480 <strong>2.05</strong><br> 30/8/05
5485 <li>Edit and annotate in "Wrapped" view</li>
5490 <li>Several GUI bugs resolved</li>
5496 <div align="center">
5497 <strong>2.04</strong><br> 24/8/05
5502 <li>Hold down mouse wheel & scroll to change font
5508 <li>Improved JPred client reliability</li>
5509 <li>Improved loading of Jalview files</li>
5515 <div align="center">
5516 <strong>2.03</strong><br> 18/8/05
5521 <li>Set Proxy server name and port in preferences</li>
5522 <li>Multiple URL links from sequence ids</li>
5523 <li>User Defined Colours can have a scheme name and added
5525 <li>Choose to ignore gaps in consensus calculation</li>
5526 <li>Unix users can set default web browser</li>
5527 <li>Runs without GUI for batch processing</li>
5528 <li>Dynamically generated Web Service Menus</li>
5533 <li>InstallAnywhere download for Sparc Solaris</li>
5539 <div align="center">
5540 <strong>2.02</strong><br> 18/7/05
5546 <li>Copy & Paste order of sequences maintains
5547 alignment order.</li>
5553 <div align="center">
5554 <strong>2.01</strong><br> 12/7/05
5559 <li>Use delete key for deleting selection.</li>
5560 <li>Use Mouse wheel to scroll sequences.</li>
5561 <li>Help file updated to describe how to add alignment
5563 <li>Version and build date written to build properties
5565 <li>InstallAnywhere installation will check for updates
5566 at launch of Jalview.</li>
5571 <li>Delete gaps bug fixed.</li>
5572 <li>FileChooser sorts columns.</li>
5573 <li>Can remove groups one by one.</li>
5574 <li>Filechooser icons installed.</li>
5575 <li>Finder ignores return character when searching.
5576 Return key will initiate a search.<br>
5583 <div align="center">
5584 <strong>2.0</strong><br> 20/6/05
5589 <li>New codebase</li>