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>8/03/2022</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-3503 -->New Preferences tab for adjusting Jalview's
81 memory settings at launch
84 <!-- JAL-3144 -->Reverted to Jalview 'classic' drop-down
85 menu for selecting which database to fetch from in sequence
89 <!-- JAL-2226 -->Structure annotation rows for all mapped
90 chains in 3D structures are included in the 'Reference
91 Annotation' for a sequence
94 <!-- JAL-1260 -->Import Genbank and EMBL format flatfiles
97 <!-- JAL-3821 -->ENA record's mol_type honoured so RNA
98 molecules imported from ENA records are shown as RNA
100 <!-- JAL-3863 -->Support for Canonical Uniprot IDs
103 <!-- JAL-3018 -->Updated Ensembl REST Client compatibility
104 to 15.2 and revised model organism names (rat, xenopus, dmelanogaster now
105 rattus_norvegicus, xenopus_tropicalis, drosophila_melanogaster)
108 <!-- JAL-3881 -->Sequence IDs split on '_' as well as other
109 non-alphanumerics when discovering database references with
113 <!-- JAL-3884 -->Suppressed harmless exceptions output to
114 Console whilst discovering database references for a
118 <!-- JAL-3204 -->Updated Jalview bindings for Uniprot XML
122 <!-- JAL-3926 -->Uniprot and PDBe autosearch option is
126 <!-- JAL-3530 -->-nowebservicediscovery command line
127 argument to prevent automatic discovery of analysis
128 webservices on launch
131 <!-- JAL-3618 -->Allow 'App' directories to be opened when
132 locating Chimera, ChimeraX or Pymol binaries via filechooser
133 opened by double clicking the Structure Preferences' path
137 <!-- JAL-3632 JAL-3633 -->support for HTTP/S access via
138 proxies that require authentication
141 <!-- JAL-3103 -->New mechanism for opening URLs with system
142 default browser (works on OSX and Linux as well as Windows)
145 <!-- JAL-3837 -->GPL license info on splash screen and About
149 <em>Jalview Native App</em>
152 <!-- JAL- -->New Jalview Develop app - making it even easier
153 to get at Jalview's development builds
156 <!-- JAL-3594 -->New splashscreens for Jalview, Jalview Test
157 and Jalview Develop applications.
160 <!-- JAL-3728 -->Jalview logos shown for Jalview Java
161 Console and other window widgets in taskbar and dock rather
162 than anonymous 'Java' icons
165 <!-- JAL-3608 -->Options to allow user to choose the (Swing) Look and Feel (LaF) used by Jalview
168 <!-- JAL-3552, JAL-3609 -->Metal LaF used to improved operation on Linux Ubuntu with
169 HiDPI display in Java 11 (still known issues with HiDPI screens in java
171 href="https://issues.jalview.org/browse/JAL-3137">JAL-3137</a>)
174 <!-- JAL-3830 -->New command line launcher scripts (.sh, .ps1, .bat) usable on
175 macOS, Linux/Unix, Windows and documentation in Help. Installer wizard has option
176 to add this to PATH, or link to it in your PATH.
179 <!-- JAL-3633 -->Getdown launcher inherits HTTP/S proxy
180 configuration from jalview_properties
182 </ul> <em>JalviewJS</em>
185 <!-- JAL-3624 -->PDB structures mapped to Uniprot Sequences with
189 <!-- JAL-3208 -->setprop commandline argument reinstated for JalviewJS only
192 <!-- JAL-3163 -->Missing message bundle keys are only
193 reported once per key (avoids excessive log output in js
197 <!-- JAL-3168 -->Feature type is included in the title of
198 the Feature Settings' Colour Chooser dialog
201 </ul> <em>Development</em>
204 <!-- -->First integrated JalviewJS and Jalview release
206 <li>Updated building instructions</li>
208 <!-- JAL-3789, JAL-3679 -->Improved JalviewJS/Jalview build
209 process, added support for system package provided eclipse
212 <li>Install4j 9.0.x used for installer packaging</li>
213 <li>Notarized MacOS installer for compatibility with Big
214 Sur and Monterey</li>
216 <!-- JAL-3805 -->Uninstaller application for old
217 (InstallAnywhere based) Jalview installations removed from
221 <!-- JAL-3930 -->Improved use of installers for unattended
222 installation with a customizedId of "JALVIEW" in install4j's
226 <!-- JAL-3907 -->Improved compatibility of Jalview build
227 with Java 17 (next LTS target)
236 <!-- JAL-3674 -->Slow structure commands can block Jalview
240 <!-- JAL-3904 -->Structure window's viewer-specific menu
241 disappears when only one structure is shown (and many
242 sequences:one chain mappings are present)
245 <!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
246 the first SEQUENCE_GROUP defined
251 <!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 -->Selections not
252 propagated between Linked CDS - Protein alignments and their
253 trees (known defect from 2.11.1.3)
256 <!-- JAL-3761 -->Not all codon positions highlighted for
257 overlapping exon splice sites (e.g due to RNA slippage)
260 <!-- JAL-3794 -->X was not being recognised as the unknown
261 base in DNA sequences
264 <!-- JAL-3915 -->Removed RNAview checkbox and logic from
265 Structure Preferences
268 <!-- JAL-3583 -->Tooltip behaviour improved (slightly)
271 <!-- JAL-3162 -->Can edit a feature so that start > end
274 <!-- JAL-2848 -->Cancel from Amend Features doesn't reset a
275 modified graduated colour
278 <!-- JAL-3788 -->New View with automatic 'Show Overview'
279 preference enabled results in Null Pointer Exceptions when
280 clustal colouring is enabled
283 <!-- JAL-3275 -->Can open multiple Preferences panels
286 <!-- JAL-3633 -->Properly configure HTTPS proxy settings
290 <!-- JAL-3949 -->Standard out logging broken: messages only
291 routing to stderr and appear as a raw template
293 </ul> <em>JalviewJS</em>
296 <!-- JAL-3202 -->Consensus profile may include zero (rounded
297 down) percentage values causing a divide by zero
312 <!-- JAL-3762 -->JalviewJS doesn't honour arguments passed
313 via Info.args when there are arguments on the URL
316 <!-- JAL-3602 -->gradle closure-compiler not using UTF-8
319 <!-- JAL-3603 -->Annotation file fails to load from URL in
322 </ul> <em>Development</em>
326 <li>Fixed non-fatal gradle errors during build</li>
328 <!-- JAL-3745 -->Updated build.gradle for use with
335 <em>Known Issues</em>
338 <!-- JAL-3764 -->Display of RESNUM sequence features are not
339 suppressed when structures associated with a sequence are
340 viewed with an external viewer (Regression from 2.11.1 series)
346 <td width="60" align="center" nowrap><strong><a
347 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.7">.7</a><br />
348 <em>18/01/2022</em></strong></td>
350 <td align="left" valign="top">
353 <!-- JAL-3703, JAL-3935 -->Files open in Jalview cannot be
354 updated by Jalview or other applications (Windows, other non
357 </ul> <em>Security</em>
360 <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
366 <td width="60" align="center" nowrap><strong><a
367 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
368 <em>6/01/2022</em></strong></td>
370 <td align="left" valign="top"><em>Security</em>
373 <!-- JAL-3934 -->Version bump library dependency: Log4j
380 <td width="60" align="center" nowrap><strong><a
381 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
382 <em>20/12/2021</em></strong></td>
384 <td align="left" valign="top"><em>Security</em>
387 <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
389 </ul> <em>Development</em>
391 <li>Updated building instructions</li>
396 <!-- JAL-3840 -->Occupancy calculation is incorrect for
397 alignment columns with over -1+2^32 gaps (breaking filtering
401 <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
402 scale factors being set with buggy window-managers (linux
405 </ul> <em>Development</em>
407 <li>Fixed non-fatal gradle errors during build</li>
412 <td width="60" align="center" nowrap><strong><a
413 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
414 <em>09/03/2021</em></strong></td>
415 <td align="left" valign="top"><em>Improved control of
416 Jalview's use of network services via jalview_properties</em>
419 <!-- JAL-3814 -->New .jalview_properties token controlling
420 launch of the news browser (like -nonews argument)
423 <!-- JAL-3813 -->New .jalview_properties token controlling
424 download of linkout URLs from
425 www.jalview.org/services/identifiers
428 <!-- JAL-3812 -->New .jalview_properties token controlling
429 download of BIOJSHTML templates
432 <!-- JAL-3811 -->New 'Discover Web Services' option to
433 trigger a one off JABAWS discovery if autodiscovery was
437 <td align="left" valign="top">
440 <!-- JAL-3818 -->Intermittent deadlock opening structure in
443 </ul> <em>New Known defects</em>
446 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
447 always restored from project (since 2.10.3)
450 <!-- JAL-3806 -->Selections from tree built from CDS aren't
451 propagated to Protein alignment (since 2.11.1.3)
457 <td width="60" align="center" nowrap><strong><a
458 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
459 <em>29/10/2020</em></strong></td>
460 <td align="left" valign="top">
465 <td align="left" valign="top">
468 <!-- JAL-3765 -->Find doesn't always highlight all matching
469 positions in a sequence (bug introduced in 2.11.1.2)
472 <!-- JAL-3760 -->Alignments containing one or more protein
473 sequences can be classed as nucleotide
476 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
477 sequences after alignment of protein products (known defect
478 first reported for 2.11.1.0)
481 <!-- JAL-3725 -->No tooltip or popup menu for genomic
482 features outwith CDS shown overlaid on protein
485 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
486 correctly mapped by Jalview (e.g. affects viral CDS with
487 ribosomal slippage, since 2.9.0)
490 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
494 <!-- JAL-3700 -->Selections in CDS sequence panel don't
495 always select corresponding protein sequences
498 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
499 column selection doesn't always ignore hidden columns
501 </ul> <em>Installer</em>
504 <!-- JAL-3611 -->Space character in Jalview install path on
505 Windows prevents install4j launching getdown
507 </ul> <em>Development</em>
510 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
511 version numbers in doc/building.md
517 <td width="60" align="center" nowrap><strong><a
518 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
519 <em>25/09/2020</em></strong></td>
520 <td align="left" valign="top">
524 <td align="left" valign="top">
527 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
528 "Encountered problems opening
529 https://www.jalview.org/examples/exampleFile_2_7.jvp"
535 <td width="60" align="center" nowrap><strong><a
536 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
537 <em>17/09/2020</em></strong></td>
538 <td align="left" valign="top">
541 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
542 residue in cursor mode
545 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
546 HTSJDK from 2.12 to 2.23
549 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
550 optimisations and improvements suggested by Bob Hanson and
551 improved compatibility with JalviewJS
554 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
555 alignments from Pfam and Rfam
558 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
559 import (no longer based on .gz extension)
562 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
565 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
566 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
570 <!-- JAL-3667 -->Improved warning messages, debug logging
571 and fixed Retry action when Jalview encounters errors when
572 saving or making backup files.
575 <!-- JAL-3676 -->Enhanced Jalview Java Console:
577 <li>Jalview's logging level can be configured</li>
578 <li>Copy to Clipboard Buttion</li>
582 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
583 when running on Linux (Requires Java 11+)
586 <!-- JAL-1842 JAL-3509 -->RESNUM sequence features (the
587 green ones) are not automatically displayed when associated
588 structures are displayed or for sequences retrieved from the
591 </ul> <em>Launching Jalview</em>
594 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
595 through a system property
598 <!-- JAL-3477 -->Improved built-in documentation and command
599 line help for configuring Jalview's memory
603 <td align="left" valign="top">
606 <!-- JAL-3691 -->Conservation and Quality tracks are shown
607 but not calculated and no protein or DNA score models are
608 available for tree/PCA calculation when launched with
609 Turkish language locale
612 <!-- JAL-3493 -->Escape does not clear highlights on the
613 alignment (Since Jalview 2.10.3)
616 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
617 doesn't slide selected sequences, just sequence under cursor
620 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
621 sequence under the cursor
624 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
625 multiple EMBL gene products shown for a single contig
628 <!-- JAL-3696 -->Errors encountered when processing variants
629 from VCF files yield "Error processing VCF: Format specifier
633 <!-- JAL-3697 -->Count of features not shown can be wrong
634 when there are both local and complementary features mapped
635 to the position under the cursor
638 <!-- JAL-3673 -->Sequence ID for reference sequence is
639 clipped when Right align Sequence IDs enabled
642 <!-- JAL-2983 -->Slider with negative range values not
643 rendered correctly in VAqua4 (Since 2.10.4)
646 <!-- JAL-3685 -->Single quotes not displayed correctly in
647 internationalised text for some messages and log output
650 <!-- JAL-3490 -->Find doesn't report matches that span
651 hidden gapped columns
654 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
655 panels, Alignment viewport and annotation renderer.
658 <!-- JAL-3561 -->Jalview ignores file format parameter
659 specifying output format when exporting an alignment via the
663 <!-- JAL-3667 -->Windows 10: For a minority of users, if
664 backups are not enabled, Jalview sometimes fails to
665 overwrite an existing file and raises a warning dialog. (in
666 2.11.0, and 2.11.1.0, the workaround is to try to save the
667 file again, and if that fails, delete the original file and
671 <!-- JAL-3509 -->Dragging a PDB file onto an alignment with
672 sequence features displayed causes displayed features to be
676 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
680 <!-- JAL-3741 -->References to http://www.jalview.org in
681 program and documentation
683 </ul> <em>Launching Jalview</em>
686 <!-- JAL-3718 -->Jalview application fails when launched the
687 first time for a version that has different jars to the
688 previous launched version.
690 </ul> <em>Developing Jalview</em>
693 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
694 data, causing cloverReport gradle task to fail with an
698 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
699 monitor the release channel
701 </ul> <em>New Known defects</em>
704 <!-- JAL-3748 -->CDS shown in result of submitting proteins
705 in a CDS/Protein alignment to a web service is wrong when
706 proteins share a common transcript sequence (e.g. genome of
710 <!-- JAL-3576 -->Co-located features exported and
711 re-imported are ordered differently when shown on alignment
712 and in tooltips. (Also affects v2.11.1.0)
715 <!-- JAL-3702 -->Drag and drop of alignment file onto
716 alignment window when in a HiDPI scaled mode in Linux only
717 works for the top left quadrant of the alignment window
720 <!-- JAL-3701 -->Stale build data in jalview standalone jar
721 builds (only affects 2.11.1.1 branch)
724 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
725 when alignment view restored from project (since Jalview
729 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
730 protein products for certain ENA records are repeatedly
731 shown via Calculate->Show Cross Refs
737 <td width="60" align="center" nowrap><strong><a
738 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
739 <em>22/04/2020</em></strong></td>
740 <td align="left" valign="top">
743 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
744 'virtual' codon features shown on protein (or vice versa)
745 for display in alignments, on structure views (including
746 transfer to UCSF chimera), in feature reports and for
750 <!-- JAL-3121 -->Feature attributes from VCF files can be
751 exported and re-imported as GFF3 files
754 <!-- JAL-3376 -->Capture VCF "fixed column" values
755 POS, ID, QUAL, FILTER as Feature Attributes
758 <!-- JAL-3375 -->More robust VCF numeric data field
759 validation while parsing
762 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
766 <!-- JAL-3535 -->Feature Settings dialog title includes name
770 <!-- JAL-3538 -->Font anti-aliasing in alignment views
774 <!-- JAL-3468 -->Very long feature descriptions truncated in
778 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
779 with no feature types visible
782 <!-- JAL-3574 -->Improved support for filtering feature
783 attributes with large integer values
786 <em>Jalview Installer</em>
789 <!-- JAL-3449 -->Versions for install4j and getdown and
790 installer template version reported in console (may be null
791 when Jalview launched as executable jar or via conda)
794 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and
795 higher quality background images
798 <!-- JAL-3394 -->New installer/application launcher
799 generated with install4j 8.0.4
802 <!-- JAL-3420 -->Jalview File Associations shown for Unix
806 <!-- JAL-3477 -->Improved defaults for maximum memory
807 setting when running on large memory machines
809 </ul> <em>Release processes</em>
812 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
815 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier
816 access to test-release channel builds
818 </ul> <em>Build System</em>
821 <!-- JAL-3510 -->Clover updated to 4.4.1
824 <!-- JAL-3513 -->Test code included in Clover coverage
827 </ul> <em>Groovy Scripts</em>
830 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
831 to stdout containing the consensus sequence for each
832 alignment in a Jalview session
835 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
836 genomic sequence_variant annotation from CDS as
837 missense_variant or synonymous_variant on protein products.
841 <td align="left" valign="top">
844 <!-- JAL-3581 -->Hidden sequence markers still visible when
845 'Show hidden markers' option is not ticked
848 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
849 PNG output when 'Automatically set ID width' is set in
850 jalview preferences or properties file
853 <!-- JAL-3571 -->Feature Editor dialog can be opened when
854 'Show Sequence Features' option is not ticked
857 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
858 buttons in Feature Settings dialog are clicked when no
862 <!-- JAL-3412 -->ID margins for CDS and Protein views not
863 equal when split frame is first opened
866 <!-- JAL-3296 -->Sequence position numbers in status bar not
867 correct after editing a sequence's start position
870 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
871 with annotation and exceptions thrown when only a few
872 columns shown in wrapped mode
875 <!-- JAL-3386 -->Sequence IDs missing in headless export of
876 wrapped alignment figure with annotations
879 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
880 ID fails with ClassCastException
883 <!-- JAL-3389 -->Chimera session not restored from Jalview
887 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
888 feature settings dialog also selects columns
891 <!-- JAL-3473 -->SpinnerNumberModel causes
892 IllegalArgumentException in some circumstances
895 <!-- JAL-3534 -->Multiple feature settings dialogs can be
899 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
900 alignment window is closed
903 <!-- JAL-3406 -->Credits missing some authors in Jalview
904 help documentation for 2.11.0 release
907 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
908 includes Pfam ID as sequence's accession rather than its
911 </ul> <em>Java 11 Compatibility issues</em>
914 <!-- JAL-2987 -->OSX - Can't view some search results in
915 PDB/Uniprot search panel
917 </ul> <em>Installer</em>
920 <!-- JAL-3447 -->Jalview should not create file associations
921 for 3D structure files (.pdb, .mmcif. .cif)
923 </ul> <em>Repository and Source Release</em>
926 <!-- JAL-3474 -->removed obsolete .cvsignore files from
930 <!-- JAL-3541 -->Clover report generation running out of
933 </ul> <em>New Known Issues</em>
936 <!-- JAL-3523 -->OSX - Current working directory not
937 preserved when Jalview.app launched with parameters from
941 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
942 clipped in headless figure export when Right Align option
946 <!-- JAL-3542 -->Jalview Installation type always reports
947 'Source' in console output
950 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail
951 on jalview's bamboo server but run fine locally.
957 <td width="60" align="center" nowrap><strong><a
958 name="Jalview.2.11.0">2.11.0</a><br /> <em>04/07/2019</em></strong></td>
959 <td align="left" valign="top">
962 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native
963 Application and Installers built with <a
964 href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a>
965 (licensed to the Jalview open source project) rather than
969 <!-- JAL-1929 -->Jalview Launcher System to auto-configure
970 memory settings, receive over the air updates and launch
971 specific versions via (<a
972 href="https://github.com/threerings/getdown">Three
976 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations
977 for formats supported by Jalview (including .jvp project
981 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command
982 line arguments and switch between different getdown channels
985 <!-- JAL-3141 -->Backup files created when saving Jalview
986 project or alignment files
990 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF
994 <!-- JAL-2753 -->Version of HTSJDK shipped with Jalview
995 updated to version 2.12.0
998 <!-- JAL-2620 -->Alternative genetic code tables for
1002 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0
1004 <li><strong>Enhanced visualisation and analysis
1005 of Sequence Features</strong>
1008 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
1009 implementation that allows updates) used for Sequence
1013 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
1014 features can be filtered and shaded according to any
1015 associated attributes (e.g. variant attributes from VCF
1016 file, or key-value pairs imported from column 9 of GFF
1020 <!-- JAL-2879 -->Feature Attributes and shading schemes
1021 stored and restored from Jalview Projects
1024 <!-- JAL-3334 -->Use full Sequence Ontology (via
1025 BioJava) to recognise variant features
1028 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants
1029 on peptide sequences (also coloured red by default)
1032 <!-- JAL-2792 -->Popup window to show full report for a
1033 selected sequence feature's details
1036 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient
1037 sequence feature render algorithm (Z-sort/transparency
1041 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature
1046 <!-- JAL-3205 -->Symmetric score matrices for faster tree
1047 and PCA calculations
1049 <li><strong>Principal Components Analysis Viewer</strong>
1052 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis
1053 results and Viewer state saved in Jalview Project
1056 <!-- JAL-2962 -->'Change parameters' option removed from
1057 viewer's drop-down menus
1060 <!-- JAL-2975 -->Can use shift + arrow keys to rotate
1061 PCA image incrementally
1064 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
1068 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
1070 <li><strong>Speed and Efficiency</strong>
1073 <!-- JAL-2185,JAL-3198 -->More efficient creation of
1074 selections and multiple groups when working with large
1078 <!-- JAL-3200 -->Speedier import of annotation rows when
1079 parsing Stockholm files
1082 <li><strong>User Interface</strong>
1085 <!-- JAL-2933 -->Finder panel remembers last position in
1089 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS
1090 (What you see is what is shown)<br />Only visible
1091 regions of alignment are shown by default (can be
1092 changed in user preferences)
1095 <!-- JAL-3169 -->File Chooser stays open after
1096 responding Cancel to the Overwrite Dialog
1099 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour
1100 when all sequences are hidden
1103 <!-- JAL-1244 -->Status bar shows bounds when dragging a
1104 selection region, and gap count when inserting or
1108 <!-- JAL-3132 -->Status bar updates over sequence and
1112 <!-- JAL-3093 -->Annotation tooltips and popup menus are
1113 shown when in wrapped mode
1116 <!-- JAL-3073 -->Can select columns by dragging
1117 left/right in a graph or histogram annotation
1120 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB
1124 <!-- JAL-2621 -->Cursor changes over draggable box in
1128 <!-- JAL-3181 -->Consistent ordering of links in
1129 sequence id popup menu
1132 <!-- JAL-3080 -->Red line indicating tree-cut position
1133 not shown if no subgroups are created
1136 <!-- JAL-3042 -->Removed ability to configure length of
1137 search history by right-clicking search box
1143 <!-- JAL-3232 -->Jalview Groovy Scripting Console updated to
1146 <li><strong>Java 11 Support (not yet on general
1150 <!-- -->OSX GUI integrations for App menu's 'About'
1151 entry and trapping CMD-Q
1154 </ul> <em>Deprecations</em>
1157 <!-- JAL-3035 -->DAS sequence retrieval and annotation
1158 capabilities removed from the Jalview Desktop
1161 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling
1162 and unmarshalling has been replaced by JAXB for Jalview
1163 projects and XML based data retrieval clients
1166 <!-- JAL-3311 -->Disable VAMSAS menu in preparation for
1170 <!-- -->Jalview Desktop no longer distributed via Java Web
1173 </ul> <em>Documentation</em>
1176 <!-- JAL-3003 -->Added remarks about transparent rendering
1177 effects not supported in EPS figure export
1180 <!-- JAL-2903 -->Typos in documentation for Preferences
1183 </ul> <em>Development and Release Processes</em>
1186 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated
1190 <!-- JAL-1424 -->Enhanced checks for missing and duplicated
1191 keys in Message bundles
1194 <!-- JAL-3225 -->Eclipse project configuration managed with
1198 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian Bamboo
1199 continuous integration for unattended Test Suite execution
1202 <!-- JAL-2864 -->Memory test suite to detect leaks in common
1206 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
1210 <!-- JAL-3248 -->Developer documentation migrated to
1211 markdown (with HTML rendering)
1214 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
1217 <!-- JAL-3289 -->New URLs for publishing development
1222 <td align="left" valign="top">
1225 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
1228 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
1229 superposition in Jmol fail on Windows
1232 <!-- JAL-3286 -->Blank error dialog is displayed when
1233 discovering structures for sequences with lots of PDB
1237 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export
1238 with monospaced font
1241 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
1242 Jalview project involving multiple views
1245 <!-- JAL-3164 -->Overview for complementary view in a linked
1246 CDS/Protein alignment is not updated when Hide Columns by
1247 Annotation dialog hides columns
1250 <!-- JAL-3158 -->Selection highlighting in the complement of
1251 a CDS/Protein alignment stops working after making a
1252 selection in one view, then making another selection in the
1256 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
1260 <!-- JAL-3154 -->Table Columns could be re-ordered in
1261 Feature Settings and Jalview Preferences panels
1264 <!-- JAL-2865 -->Jalview hangs when closing windows, or
1265 redrawing the overview with large alignments
1268 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
1269 region if columns were selected by dragging right-to-left
1270 and the mouse moved to the left of the first column
1273 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to
1274 a hidden column marker via scale popup menu
1277 <!-- JAL-2846 -->Error message for trying to load in invalid
1278 URLs doesn't tell users the invalid URL
1281 <!-- JAL-2816 -->Tooltips displayed for features filtered by
1285 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl
1286 during show cross references or Fetch Database References
1287 are shown in red in original view
1290 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown
1291 correctly on peptide sequence (computed variant shown as
1295 <!-- JAL-2060 -->'Graduated colour' option not offered for
1296 manually created features (where feature score is Float.NaN)
1299 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or
1300 printed when columns are hidden
1303 <!-- JAL-3082 -->Regular expression error for '(' in Select
1304 Columns by Annotation description
1307 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after
1308 dragging out of Scale or Annotation Panel
1311 <!-- JAL-3075 -->Column selection incorrect after scrolling
1315 <!-- JAL-3074 -->Left/right drag in annotation can scroll
1319 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal
1323 <!-- JAL-3002 -->Column display is out by one after Page
1324 Down, Page Up in wrapped mode
1327 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
1330 <!-- JAL-2932 -->Finder searches in minimised alignments
1333 <!-- JAL-2250 -->'Apply Colour to All Groups' not always
1334 selected on opening an alignment
1337 <!-- JAL-3180 -->'Colour by Annotation' not marked selected
1341 <!-- JAL-3201 -->Per-group Clustal colour scheme changes
1342 when different groups in the alignment are selected
1345 <!-- JAL-2717 -->Internationalised colour scheme names not
1346 shown correctly in menu
1349 <!-- JAL-3206 -->Colour by Annotation can go black at
1350 min/max threshold limit
1353 <!-- JAL-3125 -->Value input for graduated feature colour
1354 threshold gets 'unrounded'
1357 <!-- JAL-2982 -->PCA image export doesn't respect background
1361 <!-- JAL-2963 -->PCA points don't dim when rotated about y
1365 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
1368 <!-- JAL-3078 -->Cancel in Tree Font dialog resets
1369 alignment, not Tree font
1372 <!-- JAL-2964 -->Associate Tree with All Views not restored
1376 <!-- JAL-2915 -->Scrolling of split frame is sluggish if
1377 Overview shown in complementary view
1380 <!-- JAL-3313 -->Codon consensus incorrectly scaled when
1381 shown without normalisation
1384 <!-- JAL-3021 -->Sequence Details report should open
1385 positioned at top of report
1388 <!-- JAL-914 -->Help page can be opened twice
1391 <!-- JAL-3333 -->Fuzzy text in web service status menu on
1394 </ul> <em>Editing</em>
1397 <!-- JAL-2822 -->Start and End should be updated when
1398 sequence data at beginning or end of alignment added/removed
1402 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection
1403 doesn't relocate sequence features correctly when start of
1404 sequence is removed (Known defect since 2.10)
1407 <!-- JAL-2830 -->Inserting gap sequence via the Edit
1408 Sequence dialog corrupts dataset sequence
1411 <!-- JAL-868 -->Structure colours not updated when
1412 associated tree repartitions the alignment view (Regression
1415 </ul> <em>Datamodel</em>
1418 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
1419 sequence's End is greater than its length
1421 </ul> <em>Bugs fixed for Java 11 Support (not yet on general
1425 <!-- JAL-3288 -->Menus work properly in split-screen
1427 </ul> <em>New Known Defects</em>
1430 <!-- JAL-3340 -->Select columns containing feature by double
1431 clicking ignores bounds of an existing selected region
1434 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in
1435 gapped regions of protein alignment.
1438 <!-- JAL-2647 -->Input Data menu entry is greyed out when
1439 PCA View is restored from a Jalview 2.11 project
1442 <!-- JAL-3213 -->Alignment panel height can be too small
1446 <!-- JAL-3240 -->Display is incorrect after removing gapped
1447 columns within hidden columns
1450 <!-- JAL-3314 -->Rightmost selection is lost when mouse
1451 re-enters window after dragging left to select columns to
1452 left of visible region
1455 <!-- JAL-2876 -->Features coloured according to their
1456 description string and thresholded by score in earlier
1457 versions of Jalview are not shown as thresholded features in
1458 2.11. To workaround please create a Score filter instead.
1461 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't
1462 reset group visibility
1465 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in
1466 linked CDS/Protein view
1469 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1470 alignments with multiple views can close views unexpectedly
1472 </ul> <em>Java 11 Specific defects</em>
1475 <!-- JAL-3235 -->Jalview Properties file is not sorted
1476 alphabetically when saved
1482 <td width="60" nowrap>
1483 <div align="center">
1484 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1487 <td><div align="left">
1491 <!-- JAL-3101 -->Default memory for Jalview webstart and
1492 InstallAnywhere increased to 1G.
1495 <!-- JAL-247 -->Hidden sequence markers and representative
1496 sequence bolding included when exporting alignment as EPS,
1497 SVG, PNG or HTML. <em>Display is configured via the
1498 Format menu, or for command-line use via a Jalview
1499 properties file.</em>
1502 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1503 API and sequence data now imported as JSON.
1506 <!-- JAL-3065 -->Change in recommended way of starting
1507 Jalview via a Java command line: add jars in lib directory
1508 to CLASSPATH, rather than via the deprecated java.ext.dirs
1512 <em>Development</em>
1515 <!-- JAL-3047 -->Support added to execute test suite
1516 instrumented with <a href="http://openclover.org/">Open
1521 <td><div align="left">
1525 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1526 row shown in Feredoxin Structure alignment view of example
1530 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1531 annotation displayed.
1534 <!-- JAL-3107 -->Group conservation/consensus not shown
1535 for newly created group when 'Apply to all groups'
1539 <!-- JAL-3087 -->Corrupted display when switching to
1540 wrapped mode when sequence panel's vertical scrollbar is
1544 <!-- JAL-3003 -->Alignment is black in exported EPS file
1545 when sequences are selected in exported view.</em>
1548 <!-- JAL-3059 -->Groups with different coloured borders
1549 aren't rendered with correct colour.
1552 <!-- JAL-3092 -->Jalview could hang when importing certain
1553 types of knotted RNA secondary structure.
1556 <!-- JAL-3095 -->Sequence highlight and selection in
1557 trimmed VARNA 2D structure is incorrect for sequences that
1561 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1562 annotation when columns are inserted into an alignment,
1563 and when exporting as Stockholm flatfile.
1566 <!-- JAL-3053 -->Jalview annotation rows containing upper
1567 and lower-case 'E' and 'H' do not automatically get
1568 treated as RNA secondary structure.
1571 <!-- JAL-3106 -->.jvp should be used as default extension
1572 (not .jar) when saving a Jalview project file.
1575 <!-- JAL-3105 -->Mac Users: closing a window correctly
1576 transfers focus to previous window on OSX
1579 <em>Java 10 Issues Resolved</em>
1582 <!-- JAL-2988 -->OSX - Can't save new files via the File
1583 or export menus by typing in a name into the Save dialog
1587 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1588 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1589 'look and feel' which has improved compatibility with the
1590 latest version of OSX.
1596 <td width="60" nowrap>
1597 <div align="center">
1598 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1599 <em>7/06/2018</em></strong>
1602 <td><div align="left">
1606 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1607 annotation retrieved from Uniprot
1610 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1611 onto the Jalview Desktop
1615 <td><div align="left">
1619 <!-- JAL-3017 -->Cannot import features with multiple
1620 variant elements (blocks import of some Uniprot records)
1623 <!-- JAL-2997 -->Clustal files with sequence positions in
1624 right-hand column parsed correctly
1627 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1628 not alignment area in exported graphic
1631 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1632 window has input focus
1635 <!-- JAL-2992 -->Annotation panel set too high when
1636 annotation added to view (Windows)
1639 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1640 network connectivity is poor
1643 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1644 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1645 the currently open URL and links from a page viewed in
1646 Firefox or Chrome on Windows is now fully supported. If
1647 you are using Edge, only links in the page can be
1648 dragged, and with Internet Explorer, only the currently
1649 open URL in the browser can be dropped onto Jalview.</em>
1652 <em>New Known Defects</em>
1655 <!-- JAL-3083 -->Cancel option doesn't reset Colour by
1662 <td width="60" nowrap>
1663 <div align="center">
1664 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1667 <td><div align="left">
1671 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1672 for disabling automatic superposition of multiple
1673 structures and open structures in existing views
1676 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1677 ID and annotation area margins can be click-dragged to
1681 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1685 <!-- JAL-2759 -->Improved performance for large alignments
1686 and lots of hidden columns
1689 <!-- JAL-2593 -->Improved performance when rendering lots
1690 of features (particularly when transparency is disabled)
1693 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2
1694 for exchange of Jalview features and Chimera attributes
1695 made generally available
1699 <td><div align="left">
1702 <!-- JAL-2899 -->Structure and Overview aren't updated
1703 when Colour By Annotation threshold slider is adjusted
1706 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1707 overlapping alignment panel
1710 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1714 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1715 improved: CDS not handled correctly if transcript has no
1719 <!-- JAL-2321 -->Secondary structure and temperature
1720 factor annotation not added to sequence when local PDB
1721 file associated with it by drag'n'drop or structure
1725 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1726 dialog doesn't import PDB files dropped on an alignment
1729 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1730 scroll bar doesn't work for some CDS/Protein views
1733 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1734 Java 1.8u153 onwards and Java 1.9u4+.
1737 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1738 columns in annotation row
1741 <!-- JAL-2913 -->Preferences panel's ID Width control is
1742 not honored in batch mode
1745 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1746 for structures added to existing Jmol view
1749 <!-- JAL-2223 -->'View Mappings' includes duplicate
1750 entries after importing project with multiple views
1753 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1754 protein sequences via SIFTS from associated PDB entries
1755 with negative residue numbers or missing residues fails
1758 <!-- JAL-2952 -->Exception when shading sequence with
1759 negative Temperature Factor values from annotated PDB
1760 files (e.g. as generated by CONSURF)
1763 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1764 tooltip doesn't include a text description of mutation
1767 <!-- JAL-2922 -->Invert displayed features very slow when
1768 structure and/or overview windows are also shown
1771 <!-- JAL-2954 -->Selecting columns from highlighted
1772 regions very slow for alignments with large numbers of
1776 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1777 with 'StringIndexOutOfBounds'
1780 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and
1781 Feel for OSX platforms running Java 10
1784 <!-- JAL-2960 -->Adding a structure to existing structure
1785 view appears to do nothing because the view is hidden
1786 behind the alignment view
1792 <!-- JAL-2926 -->Copy consensus sequence option in applet
1793 should copy the group consensus when popup is opened on it
1799 <!-- JAL-2913 -->Fixed ID width preference is not
1803 <em>New Known Defects</em>
1806 <!-- JAL-2973 --> Exceptions occasionally raised when
1807 editing a large alignment and overview is displayed
1810 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1811 repeatedly after a series of edits even when the overview
1812 is no longer reflecting updates
1815 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1816 structures for protein subsequence (if 'Trim Retrieved
1817 Sequences' enabled) or Ensembl isoforms (Workaround in
1818 2.10.4 is to fail back to N&W mapping)
1821 <!-- JAL-2990 -->Export Annotations from File Menu with
1822 CSV option gives blank output
1828 <td width="60" nowrap>
1829 <div align="center">
1830 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br />
1831 <em>24/1/2018</em></strong>
1834 <td><div align="left">
1836 <li>Updated Certum Codesigning Certificate (Valid till
1837 30th November 2018)</li>
1840 <td><div align="left">
1845 <!-- JAL-2859-->Only one structure is loaded when
1846 several sequences and structures are selected for
1850 <!-- JAL-2851-->Alignment doesn't appear to scroll
1851 vertically via trackpad and scrollwheel
1854 <!-- JAL-2842-->Jalview hangs if up/down arrows pressed
1855 in cursor mode when cursor lies in hidden region at
1859 <!-- JAL-2827-->Helix annotation has 'notches' when
1860 scrolled into view if columns are hidden
1863 <!-- JAL-2740-->Annotation column filter can be slow to
1864 reset (ie after hitting cancel) for large numbers of
1868 <!-- JAL-2849-->User preference for disabling inclusion
1869 of sequence limits when exporting as flat file has no
1873 <!-- JAL-2679-->Reproducible cross-reference
1874 relationships when retrieving sequences from
1881 <td width="60" nowrap>
1882 <div align="center">
1883 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1886 <td><div align="left">
1890 <!-- JAL-2446 -->Faster and more efficient management and
1891 rendering of sequence features
1894 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1895 429 rate limit request hander
1898 <!-- JAL-2773 -->Structure views don't get updated unless
1899 their colours have changed
1902 <!-- JAL-2495 -->All linked sequences are highlighted for
1903 a structure mousover (Jmol) or selection (Chimera)
1906 <!-- JAL-2790 -->'Cancel' button in progress bar for
1907 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1910 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1911 view from Ensembl locus cross-references
1914 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1918 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1919 feature can be disabled
1922 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1923 PDB easier retrieval of sequences for lists of IDs
1926 <!-- JAL-2758 -->Short names for sequences retrieved from
1932 <li>Groovy interpreter updated to 2.4.12</li>
1933 <li>Example groovy script for generating a matrix of
1934 percent identity scores for current alignment.</li>
1936 <em>Testing and Deployment</em>
1939 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1943 <td><div align="left">
1947 <!-- JAL-2643 -->Pressing tab after updating the colour
1948 threshold text field doesn't trigger an update to the
1952 <!-- JAL-2682 -->Race condition when parsing sequence ID
1956 <!-- JAL-2608 -->Overview windows are also closed when
1957 alignment window is closed
1960 <!-- JAL-2548 -->Export of features doesn't always respect
1964 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1965 takes a long time in Cursor mode
1971 <!-- JAL-2777 -->Structures with whitespace chainCode
1972 cannot be viewed in Chimera
1975 <!-- JAL-2728 -->Protein annotation panel too high in
1979 <!-- JAL-2757 -->Can't edit the query after the server
1980 error warning icon is shown in Uniprot and PDB Free Text
1984 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1987 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1990 <!-- JAL-2739 -->Hidden column marker in last column not
1991 rendered when switching back from Wrapped to normal view
1994 <!-- JAL-2768 -->Annotation display corrupted when
1995 scrolling right in unwapped alignment view
1998 <!-- JAL-2542 -->Existing features on subsequence
1999 incorrectly relocated when full sequence retrieved from
2003 <!-- JAL-2733 -->Last reported memory still shown when
2004 Desktop->Show Memory is unticked (OSX only)
2007 <!-- JAL-2658 -->Amend Features dialog doesn't allow
2008 features of same type and group to be selected for
2012 <!-- JAL-2524 -->Jalview becomes sluggish in wide
2013 alignments when hidden columns are present
2016 <!-- JAL-2392 -->Jalview freezes when loading and
2017 displaying several structures
2020 <!-- JAL-2732 -->Black outlines left after resizing or
2024 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
2025 within the Jalview desktop on OSX
2028 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
2029 when in wrapped alignment mode
2032 <!-- JAL-2636 -->Scale mark not shown when close to right
2033 hand end of alignment
2036 <!-- JAL-2684 -->Pairwise alignment of selected regions of
2037 each selected sequence do not have correct start/end
2041 <!-- JAL-2793 -->Alignment ruler height set incorrectly
2042 after canceling the Alignment Window's Font dialog
2045 <!-- JAL-2036 -->Show cross-references not enabled after
2046 restoring project until a new view is created
2049 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
2050 URL links appears when only default EMBL-EBI link is
2051 configured (since 2.10.2b2)
2054 <!-- JAL-2775 -->Overview redraws whole window when box
2055 position is adjusted
2058 <!-- JAL-2225 -->Structure viewer doesn't map all chains
2059 in a multi-chain structure when viewing alignment
2060 involving more than one chain (since 2.10)
2063 <!-- JAL-2811 -->Double residue highlights in cursor mode
2064 if new selection moves alignment window
2067 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
2068 arrow key in cursor mode to pass hidden column marker
2071 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
2072 that produces correctly annotated transcripts and products
2075 <!-- JAL-2776 -->Toggling a feature group after first time
2076 doesn't update associated structure view
2079 <em>Applet</em><br />
2082 <!-- JAL-2687 -->Concurrent modification exception when
2083 closing alignment panel
2086 <em>BioJSON</em><br />
2089 <!-- JAL-2546 -->BioJSON export does not preserve
2090 non-positional features
2093 <em>New Known Issues</em>
2096 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
2097 sequence features correctly (for many previous versions of
2101 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
2102 using cursor in wrapped panel other than top
2105 <!-- JAL-2791 -->Select columns containing feature ignores
2106 graduated colour threshold
2109 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
2110 always preserve numbering and sequence features
2113 <em>Known Java 9 Issues</em>
2116 <!-- JAL-2902 -->Groovy Console very slow to open and is
2117 not responsive when entering characters (Webstart, Java
2124 <td width="60" nowrap>
2125 <div align="center">
2126 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
2127 <em>2/10/2017</em></strong>
2130 <td><div align="left">
2131 <em>New features in Jalview Desktop</em>
2134 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API
2138 <!-- JAL-2745 -->HTTPS used for all connections to
2143 <td><div align="left"></div></td>
2146 <td width="60" nowrap>
2147 <div align="center">
2148 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
2149 <em>7/9/2017</em></strong>
2152 <td><div align="left">
2156 <!-- JAL-2588 -->Show gaps in overview window by colouring
2157 in grey (sequences used to be coloured grey, and gaps were
2161 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
2165 <!-- JAL-2587 -->Overview updates immediately on increase
2166 in size and progress bar shown as higher resolution
2167 overview is recalculated
2172 <td><div align="left">
2176 <!-- JAL-2664 -->Overview window redraws every hidden
2177 column region row by row
2180 <!-- JAL-2681 -->duplicate protein sequences shown after
2181 retrieving Ensembl crossrefs for sequences from Uniprot
2184 <!-- JAL-2603 -->Overview window throws NPE if show boxes
2185 format setting is unticked
2188 <!-- JAL-2610 -->Groups are coloured wrongly in overview
2189 if group has show boxes format setting unticked
2192 <!-- JAL-2672,JAL-2665 -->Redraw problems when
2193 autoscrolling whilst dragging current selection group to
2194 include sequences and columns not currently displayed
2197 <!-- JAL-2691 -->Not all chains are mapped when multimeric
2198 assemblies are imported via CIF file
2201 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
2202 displayed when threshold or conservation colouring is also
2206 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
2210 <!-- JAL-2673 -->Jalview continues to scroll after
2211 dragging a selected region off the visible region of the
2215 <!-- JAL-2724 -->Cannot apply annotation based
2216 colourscheme to all groups in a view
2219 <!-- JAL-2511 -->IDs don't line up with sequences
2220 initially after font size change using the Font chooser or
2227 <td width="60" nowrap>
2228 <div align="center">
2229 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
2232 <td><div align="left">
2233 <em>Calculations</em>
2237 <!-- JAL-1933 -->Occupancy annotation row shows number of
2238 ungapped positions in each column of the alignment.
2241 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
2242 a calculation dialog box
2245 <!-- JAL-2379 -->Revised implementation of PCA for speed
2246 and memory efficiency (~30x faster)
2249 <!-- JAL-2403 -->Revised implementation of sequence
2250 similarity scores as used by Tree, PCA, Shading Consensus
2251 and other calculations
2254 <!-- JAL-2416 -->Score matrices are stored as resource
2255 files within the Jalview codebase
2258 <!-- JAL-2500 -->Trees computed on Sequence Feature
2259 Similarity may have different topology due to increased
2266 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
2267 model for alignments and groups
2270 <!-- JAL-384 -->Custom shading schemes created via groovy
2277 <!-- JAL-2526 -->Efficiency improvements for interacting
2278 with alignment and overview windows
2281 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
2285 <!-- JAL-2388 -->Hidden columns and sequences can be
2289 <!-- JAL-2611 -->Click-drag in visible area allows fine
2290 adjustment of visible position
2294 <em>Data import/export</em>
2297 <!-- JAL-2535 -->Posterior probability annotation from
2298 Stockholm files imported as sequence associated annotation
2301 <!-- JAL-2507 -->More robust per-sequence positional
2302 annotation input/output via stockholm flatfile
2305 <!-- JAL-2533 -->Sequence names don't include file
2306 extension when importing structure files without embedded
2307 names or PDB accessions
2310 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
2311 format sequence substitution matrices
2314 <em>User Interface</em>
2317 <!-- JAL-2447 --> Experimental Features Checkbox in
2318 Desktop's Tools menu to hide or show untested features in
2322 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
2323 via Overview or sequence motif search operations
2326 <!-- JAL-2547 -->Amend sequence features dialog box can be
2327 opened by double clicking gaps within sequence feature
2331 <!-- JAL-1476 -->Status bar message shown when not enough
2332 aligned positions were available to create a 3D structure
2336 <em>3D Structure</em>
2339 <!-- JAL-2430 -->Hidden regions in alignment views are not
2340 coloured in linked structure views
2343 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
2344 file-based command exchange
2347 <!-- JAL-2375 -->Structure chooser automatically shows
2348 Cached Structures rather than querying the PDBe if
2349 structures are already available for sequences
2352 <!-- JAL-2520 -->Structures imported via URL are cached in
2353 the Jalview project rather than downloaded again when the
2354 project is reopened.
2357 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
2358 to transfer Chimera's structure attributes as Jalview
2359 features, and vice-versa (<strong>Experimental
2363 <em>Web Services</em>
2366 <!-- JAL-2549 -->Updated JABAWS client to v2.2
2369 <!-- JAL-2335 -->Filter non-standard amino acids and
2370 nucleotides when submitting to AACon and other MSA
2374 <!-- JAL-2316, -->URLs for viewing database
2375 cross-references provided by identifiers.org and the
2376 EMBL-EBI's MIRIAM DB
2383 <!-- JAL-2344 -->FileFormatI interface for describing and
2384 identifying file formats (instead of String constants)
2387 <!-- JAL-2228 -->FeatureCounter script refactored for
2388 efficiency when counting all displayed features (not
2389 backwards compatible with 2.10.1)
2392 <em>Example files</em>
2395 <!-- JAL-2631 -->Graduated feature colour style example
2396 included in the example feature file
2399 <em>Documentation</em>
2402 <!-- JAL-2339 -->Release notes reformatted for readability
2403 with the built-in Java help viewer
2406 <!-- JAL-1644 -->Find documentation updated with 'search
2407 sequence description' option
2413 <!-- JAL-2485, -->External service integration tests for
2414 Uniprot REST Free Text Search Client
2417 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
2420 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
2425 <td><div align="left">
2426 <em>Calculations</em>
2429 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
2430 matrix - C->R should be '-3'<br />Old matrix restored
2431 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
2433 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
2434 Jalview's treatment of gaps in PCA and substitution matrix
2435 based Tree calculations.<br /> <br />In earlier versions
2436 of Jalview, gaps matching gaps were penalised, and gaps
2437 matching non-gaps penalised even more. In the PCA
2438 calculation, gaps were actually treated as non-gaps - so
2439 different costs were applied, which meant Jalview's PCAs
2440 were different to those produced by SeqSpace.<br />Jalview
2441 now treats gaps in the same way as SeqSpace (ie it scores
2442 them as 0). <br /> <br />Enter the following in the
2443 Groovy console to restore pre-2.10.2 behaviour:<br />
2444 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
2445 // for 2.10.1 mode <br />
2446 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
2447 // to restore 2.10.2 mode <br /> <br /> <em>Note:
2448 these settings will affect all subsequent tree and PCA
2449 calculations (not recommended)</em></li>
2451 <!-- JAL-2424 -->Fixed off-by-one bug that affected
2452 scaling of branch lengths for trees computed using
2453 Sequence Feature Similarity.
2456 <!-- JAL-2377 -->PCA calculation could hang when
2457 generating output report when working with highly
2458 redundant alignments
2461 <!-- JAL-2544 --> Sort by features includes features to
2462 right of selected region when gaps present on right-hand
2466 <em>User Interface</em>
2469 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2470 doesn't reselect a specific sequence's associated
2471 annotation after it was used for colouring a view
2474 <!-- JAL-2419 -->Current selection lost if popup menu
2475 opened on a region of alignment without groups
2478 <!-- JAL-2374 -->Popup menu not always shown for regions
2479 of an alignment with overlapping groups
2482 <!-- JAL-2310 -->Finder double counts if both a sequence's
2483 name and description match
2486 <!-- JAL-2370 -->Hiding column selection containing two
2487 hidden regions results in incorrect hidden regions
2490 <!-- JAL-2386 -->'Apply to all groups' setting when
2491 changing colour does not apply Conservation slider value
2495 <!-- JAL-2373 -->Percentage identity and conservation menu
2496 items do not show a tick or allow shading to be disabled
2499 <!-- JAL-2385 -->Conservation shading or PID threshold
2500 lost when base colourscheme changed if slider not visible
2503 <!-- JAL-2547 -->Sequence features shown in tooltip for
2504 gaps before start of features
2507 <!-- JAL-2623 -->Graduated feature colour threshold not
2508 restored to UI when feature colour is edited
2511 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2512 a time when scrolling vertically in wrapped mode.
2515 <!-- JAL-2630 -->Structure and alignment overview update
2516 as graduate feature colour settings are modified via the
2520 <!-- JAL-2034 -->Overview window doesn't always update
2521 when a group defined on the alignment is resized
2524 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2525 wrapped view result in positional status updates
2529 <!-- JAL-2563 -->Status bar doesn't show position for
2530 ambiguous amino acid and nucleotide symbols
2533 <!-- JAL-2602 -->Copy consensus sequence failed if
2534 alignment included gapped columns
2537 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2538 widgets don't permanently disappear
2541 <!-- JAL-2503 -->Cannot select or filter quantitative
2542 annotation that are shown only as column labels (e.g.
2543 T-Coffee column reliability scores)
2546 <!-- JAL-2594 -->Exception thrown if trying to create a
2547 sequence feature on gaps only
2550 <!-- JAL-2504 -->Features created with 'New feature'
2551 button from a Find inherit previously defined feature type
2552 rather than the Find query string
2555 <!-- JAL-2423 -->incorrect title in output window when
2556 exporting tree calculated in Jalview
2559 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2560 and then revealing them reorders sequences on the
2564 <!-- JAL-964 -->Group panel in sequence feature settings
2565 doesn't update to reflect available set of groups after
2566 interactively adding or modifying features
2569 <!-- JAL-2225 -->Sequence Database chooser unusable on
2573 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2574 only excluded gaps in current sequence and ignored
2581 <!-- JAL-2421 -->Overview window visible region moves
2582 erratically when hidden rows or columns are present
2585 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2586 Structure Viewer's colour menu don't correspond to
2590 <!-- JAL-2405 -->Protein specific colours only offered in
2591 colour and group colour menu for protein alignments
2594 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2595 reflect currently selected view or group's shading
2599 <!-- JAL-2624 -->Feature colour thresholds not respected
2600 when rendered on overview and structures when opacity at
2604 <!-- JAL-2589 -->User defined gap colour not shown in
2605 overview when features overlaid on alignment
2608 <!-- JAL-2567 -->Feature settings for different views not
2609 recovered correctly from Jalview project file
2612 <!-- JAL-2256 -->Feature colours in overview when first
2613 opened (automatically via preferences) are different to
2614 the main alignment panel
2617 <em>Data import/export</em>
2620 <!-- JAL-2576 -->Very large alignments take a long time to
2624 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2625 added after a sequence was imported are not written to
2629 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2630 when importing RNA secondary structure via Stockholm
2633 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2634 not shown in correct direction for simple pseudoknots
2637 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2638 with lightGray or darkGray via features file (but can
2642 <!-- JAL-2383 -->Above PID colour threshold not recovered
2643 when alignment view imported from project
2646 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2647 structure and sequences extracted from structure files
2648 imported via URL and viewed in Jmol
2651 <!-- JAL-2520 -->Structures loaded via URL are saved in
2652 Jalview Projects rather than fetched via URL again when
2653 the project is loaded and the structure viewed
2656 <em>Web Services</em>
2659 <!-- JAL-2519 -->EnsemblGenomes example failing after
2660 release of Ensembl v.88
2663 <!-- JAL-2366 -->Proxy server address and port always
2664 appear enabled in Preferences->Connections
2667 <!-- JAL-2461 -->DAS registry not found exceptions
2668 removed from console output
2671 <!-- JAL-2582 -->Cannot retrieve protein products from
2672 Ensembl by Peptide ID
2675 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2676 created from SIFTs, and spurious 'Couldn't open structure
2677 in Chimera' errors raised after April 2017 update (problem
2678 due to 'null' string rather than empty string used for
2679 residues with no corresponding PDB mapping).
2682 <em>Application UI</em>
2685 <!-- JAL-2361 -->User Defined Colours not added to Colour
2689 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2690 case' residues (button in colourscheme editor debugged and
2691 new documentation and tooltips added)
2694 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2695 doesn't restore group-specific text colour thresholds
2698 <!-- JAL-2243 -->Feature settings panel does not update as
2699 new features are added to alignment
2702 <!-- JAL-2532 -->Cancel in feature settings reverts
2703 changes to feature colours via the Amend features dialog
2706 <!-- JAL-2506 -->Null pointer exception when attempting to
2707 edit graduated feature colour via amend features dialog
2711 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2712 selection menu changes colours of alignment views
2715 <!-- JAL-2426 -->Spurious exceptions in console raised
2716 from alignment calculation workers after alignment has
2720 <!-- JAL-1608 -->Typo in selection popup menu - Create
2721 groups now 'Create Group'
2724 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2725 Create/Undefine group doesn't always work
2728 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2729 shown again after pressing 'Cancel'
2732 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2733 adjusts start position in wrap mode
2736 <!-- JAL-2563 -->Status bar doesn't show positions for
2737 ambiguous amino acids
2740 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2741 CDS/Protein view after CDS sequences added for aligned
2745 <!-- JAL-2592 -->User defined colourschemes called 'User
2746 Defined' don't appear in Colours menu
2752 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2753 score models doesn't always result in an updated PCA plot
2756 <!-- JAL-2442 -->Features not rendered as transparent on
2757 overview or linked structure view
2760 <!-- JAL-2372 -->Colour group by conservation doesn't
2764 <!-- JAL-2517 -->Hitting Cancel after applying
2765 user-defined colourscheme doesn't restore original
2772 <!-- JAL-2314 -->Unit test failure:
2773 jalview.ws.jabaws.RNAStructExportImport setup fails
2776 <!-- JAL-2307 -->Unit test failure:
2777 jalview.ws.sifts.SiftsClientTest due to compatibility
2778 problems with deep array comparison equality asserts in
2779 successive versions of TestNG
2782 <!-- JAL-2479 -->Relocated StructureChooserTest and
2783 ParameterUtilsTest Unit tests to Network suite
2786 <em>New Known Issues</em>
2789 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2790 phase after a sequence motif find operation
2793 <!-- JAL-2550 -->Importing annotation file with rows
2794 containing just upper and lower case letters are
2795 interpreted as WUSS RNA secondary structure symbols
2798 <!-- JAL-2590 -->Cannot load and display Newick trees
2799 reliably from eggnog Ortholog database
2802 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2803 containing features of type Highlight' when 'B' is pressed
2804 to mark columns containing highlighted regions.
2807 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2808 doesn't always add secondary structure annotation.
2813 <td width="60" nowrap>
2814 <div align="center">
2815 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2818 <td><div align="left">
2822 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2823 for all consensus calculations
2826 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2829 <li>Updated Jalview's Certum code signing certificate
2832 <em>Application</em>
2835 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2836 set of database cross-references, sorted alphabetically
2839 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2840 from database cross references. Users with custom links
2841 will receive a <a href="webServices/urllinks.html#warning">warning
2842 dialog</a> asking them to update their preferences.
2845 <!-- JAL-2287-->Cancel button and escape listener on
2846 dialog warning user about disconnecting Jalview from a
2850 <!-- JAL-2320-->Jalview's Chimera control window closes if
2851 the Chimera it is connected to is shut down
2854 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2855 columns menu item to mark columns containing highlighted
2856 regions (e.g. from structure selections or results of a
2860 <!-- JAL-2284-->Command line option for batch-generation
2861 of HTML pages rendering alignment data with the BioJS
2871 <!-- JAL-2286 -->Columns with more than one modal residue
2872 are not coloured or thresholded according to percent
2873 identity (first observed in Jalview 2.8.2)
2876 <!-- JAL-2301 -->Threonine incorrectly reported as not
2880 <!-- JAL-2318 -->Updates to documentation pages (above PID
2881 threshold, amino acid properties)
2884 <!-- JAL-2292 -->Lower case residues in sequences are not
2885 reported as mapped to residues in a structure file in the
2889 <!--JAL-2324 -->Identical features with non-numeric scores
2890 could be added multiple times to a sequence
2893 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2894 bond features shown as two highlighted residues rather
2895 than a range in linked structure views, and treated
2896 correctly when selecting and computing trees from features
2899 <!-- JAL-2281-->Custom URL links for database
2900 cross-references are matched to database name regardless
2905 <em>Application</em>
2908 <!-- JAL-2282-->Custom URL links for specific database
2909 names without regular expressions also offer links from
2913 <!-- JAL-2315-->Removing a single configured link in the
2914 URL links pane in Connections preferences doesn't actually
2915 update Jalview configuration
2918 <!-- JAL-2272-->CTRL-Click on a selected region to open
2919 the alignment area popup menu doesn't work on El-Capitan
2922 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2923 files with similarly named sequences if dropped onto the
2927 <!-- JAL-2312 -->Additional mappings are shown for PDB
2928 entries where more chains exist in the PDB accession than
2929 are reported in the SIFTS file
2932 <!-- JAL-2317-->Certain structures do not get mapped to
2933 the structure view when displayed with Chimera
2936 <!-- JAL-2317-->No chains shown in the Chimera view
2937 panel's View->Show Chains submenu
2940 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2941 work for wrapped alignment views
2944 <!--JAL-2197 -->Rename UI components for running JPred
2945 predictions from 'JNet' to 'JPred'
2948 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2949 corrupted when annotation panel vertical scroll is not at
2950 first annotation row
2953 <!--JAL-2332 -->Attempting to view structure for Hen
2954 lysozyme results in a PDB Client error dialog box
2957 <!-- JAL-2319 -->Structure View's mapping report switched
2958 ranges for PDB and sequence for SIFTS
2961 SIFTS 'Not_Observed' residues mapped to non-existant
2965 <!-- <em>New Known Issues</em>
2972 <td width="60" nowrap>
2973 <div align="center">
2974 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2975 <em>25/10/2016</em></strong>
2978 <td><em>Application</em>
2980 <li>3D Structure chooser opens with 'Cached structures'
2981 view if structures already loaded</li>
2982 <li>Progress bar reports models as they are loaded to
2983 structure views</li>
2989 <li>Colour by conservation always enabled and no tick
2990 shown in menu when BLOSUM or PID shading applied</li>
2991 <li>FER1_ARATH and FER2_ARATH labels were switched in
2992 example sequences/projects/trees</li>
2994 <em>Application</em>
2996 <li>Jalview projects with views of local PDB structure
2997 files saved on Windows cannot be opened on OSX</li>
2998 <li>Multiple structure views can be opened and superposed
2999 without timeout for structures with multiple models or
3000 multiple sequences in alignment</li>
3001 <li>Cannot import or associated local PDB files without a
3002 PDB ID HEADER line</li>
3003 <li>RMSD is not output in Jmol console when superposition
3005 <li>Drag and drop of URL from Browser fails for Linux and
3006 OSX versions earlier than El Capitan</li>
3007 <li>ENA client ignores invalid content from ENA server</li>
3008 <li>Exceptions are not raised in console when ENA client
3009 attempts to fetch non-existent IDs via Fetch DB Refs UI
3011 <li>Exceptions are not raised in console when a new view
3012 is created on the alignment</li>
3013 <li>OSX right-click fixed for group selections: CMD-click
3014 to insert/remove gaps in groups and CTRL-click to open group
3017 <em>Build and deployment</em>
3019 <li>URL link checker now copes with multi-line anchor
3022 <em>New Known Issues</em>
3024 <li>Drag and drop from URL links in browsers do not work
3031 <td width="60" nowrap>
3032 <div align="center">
3033 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
3036 <td><em>General</em>
3039 <!-- JAL-2124 -->Updated Spanish translations.
3042 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
3043 for importing structure data to Jalview. Enables mmCIF and
3047 <!-- JAL-192 --->Alignment ruler shows positions relative to
3051 <!-- JAL-2202 -->Position/residue shown in status bar when
3052 mousing over sequence associated annotation
3055 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
3059 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
3060 '()', canonical '[]' and invalid '{}' base pair populations
3064 <!-- JAL-2092 -->Feature settings popup menu options for
3065 showing or hiding columns containing a feature
3068 <!-- JAL-1557 -->Edit selected group by double clicking on
3069 group and sequence associated annotation labels
3072 <!-- JAL-2236 -->Sequence name added to annotation label in
3073 select/hide columns by annotation and colour by annotation
3077 </ul> <em>Application</em>
3080 <!-- JAL-2050-->Automatically hide introns when opening a
3081 gene/transcript view
3084 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
3088 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
3089 structure mappings with the EMBL-EBI PDBe SIFTS database
3092 <!-- JAL-2079 -->Updated download sites used for Rfam and
3093 Pfam sources to xfam.org
3096 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
3099 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
3100 over sequences in Jalview
3103 <!-- JAL-2027-->Support for reverse-complement coding
3104 regions in ENA and EMBL
3107 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
3108 for record retrieval via ENA rest API
3111 <!-- JAL-2027 -->Support for ENA CDS records with reverse
3115 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
3116 groovy script execution
3119 <!-- JAL-1812 -->New 'execute Groovy script' option in an
3120 alignment window's Calculate menu
3123 <!-- JAL-1812 -->Allow groovy scripts that call
3124 Jalview.getAlignFrames() to run in headless mode
3127 <!-- JAL-2068 -->Support for creating new alignment
3128 calculation workers from groovy scripts
3131 <!-- JAL-1369 --->Store/restore reference sequence in
3135 <!-- JAL-1803 -->Chain codes for a sequence's PDB
3136 associations are now saved/restored from project
3139 <!-- JAL-1993 -->Database selection dialog always shown
3140 before sequence fetcher is opened
3143 <!-- JAL-2183 -->Double click on an entry in Jalview's
3144 database chooser opens a sequence fetcher
3147 <!-- JAL-1563 -->Free-text search client for UniProt using
3148 the UniProt REST API
3151 <!-- JAL-2168 -->-nonews command line parameter to prevent
3152 the news reader opening
3155 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
3156 querying stored in preferences
3159 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
3163 <!-- JAL-1977-->Tooltips shown on database chooser
3166 <!-- JAL-391 -->Reverse complement function in calculate
3167 menu for nucleotide sequences
3170 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
3171 and feature counts preserves alignment ordering (and
3172 debugged for complex feature sets).
3175 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
3176 viewing structures with Jalview 2.10
3179 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
3180 genome, transcript CCDS and gene ids via the Ensembl and
3181 Ensembl Genomes REST API
3184 <!-- JAL-2049 -->Protein sequence variant annotation
3185 computed for 'sequence_variant' annotation on CDS regions
3189 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
3193 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
3194 Ref Fetcher fails to match, or otherwise updates sequence
3195 data from external database records.
3198 <!-- JAL-2154 -->Revised Jalview Project format for
3199 efficient recovery of sequence coding and alignment
3200 annotation relationships.
3202 </ul> <!-- <em>Applet</em>
3213 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
3217 <!-- JAL-2018-->Export features in Jalview format (again)
3218 includes graduated colourschemes
3221 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
3222 working with big alignments and lots of hidden columns
3225 <!-- JAL-2053-->Hidden column markers not always rendered
3226 at right of alignment window
3229 <!-- JAL-2067 -->Tidied up links in help file table of
3233 <!-- JAL-2072 -->Feature based tree calculation not shown
3237 <!-- JAL-2075 -->Hidden columns ignored during feature
3238 based tree calculation
3241 <!-- JAL-2065 -->Alignment view stops updating when show
3242 unconserved enabled for group on alignment
3245 <!-- JAL-2086 -->Cannot insert gaps into sequence when
3249 <!-- JAL-2146 -->Alignment column in status incorrectly
3250 shown as "Sequence position" when mousing over
3254 <!-- JAL-2099 -->Incorrect column numbers in ruler when
3255 hidden columns present
3258 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
3259 user created annotation added to alignment
3262 <!-- JAL-1841 -->RNA Structure consensus only computed for
3263 '()' base pair annotation
3266 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
3267 in zero scores for all base pairs in RNA Structure
3271 <!-- JAL-2174-->Extend selection with columns containing
3275 <!-- JAL-2275 -->Pfam format writer puts extra space at
3276 beginning of sequence
3279 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
3283 <!-- JAL-2238 -->Cannot create groups on an alignment from
3284 from a tree when t-coffee scores are shown
3287 <!-- JAL-1836,1967 -->Cannot import and view PDB
3288 structures with chains containing negative resnums (4q4h)
3291 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
3295 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
3296 to Clustal, PIR and PileUp output
3299 <!-- JAL-2008 -->Reordering sequence features that are
3300 not visible causes alignment window to repaint
3303 <!-- JAL-2006 -->Threshold sliders don't work in
3304 graduated colour and colour by annotation row for e-value
3305 scores associated with features and annotation rows
3308 <!-- JAL-1797 -->amino acid physicochemical conservation
3309 calculation should be case independent
3312 <!-- JAL-2173 -->Remove annotation also updates hidden
3316 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
3317 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
3318 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
3321 <!-- JAL-2065 -->Null pointer exceptions and redraw
3322 problems when reference sequence defined and 'show
3323 non-conserved' enabled
3326 <!-- JAL-1306 -->Quality and Conservation are now shown on
3327 load even when Consensus calculation is disabled
3330 <!-- JAL-1932 -->Remove right on penultimate column of
3331 alignment does nothing
3334 <em>Application</em>
3337 <!-- JAL-1552-->URLs and links can't be imported by
3338 drag'n'drop on OSX when launched via webstart (note - not
3339 yet fixed for El Capitan)
3342 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
3343 output when running on non-gb/us i18n platforms
3346 <!-- JAL-1944 -->Error thrown when exporting a view with
3347 hidden sequences as flat-file alignment
3350 <!-- JAL-2030-->InstallAnywhere distribution fails when
3354 <!-- JAL-2080-->Jalview very slow to launch via webstart
3355 (also hotfix for 2.9.0b2)
3358 <!-- JAL-2085 -->Cannot save project when view has a
3359 reference sequence defined
3362 <!-- JAL-1011 -->Columns are suddenly selected in other
3363 alignments and views when revealing hidden columns
3366 <!-- JAL-1989 -->Hide columns not mirrored in complement
3367 view in a cDNA/Protein splitframe
3370 <!-- JAL-1369 -->Cannot save/restore representative
3371 sequence from project when only one sequence is
3375 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
3376 in Structure Chooser
3379 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
3380 structure consensus didn't refresh annotation panel
3383 <!-- JAL-1962 -->View mapping in structure view shows
3384 mappings between sequence and all chains in a PDB file
3387 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
3388 dialogs format columns correctly, don't display array
3389 data, sort columns according to type
3392 <!-- JAL-1975 -->Export complete shown after destination
3393 file chooser is cancelled during an image export
3396 <!-- JAL-2025 -->Error when querying PDB Service with
3397 sequence name containing special characters
3400 <!-- JAL-2024 -->Manual PDB structure querying should be
3404 <!-- JAL-2104 -->Large tooltips with broken HTML
3405 formatting don't wrap
3408 <!-- JAL-1128 -->Figures exported from wrapped view are
3409 truncated so L looks like I in consensus annotation
3412 <!-- JAL-2003 -->Export features should only export the
3413 currently displayed features for the current selection or
3417 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
3418 after fetching cross-references, and restoring from
3422 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
3423 followed in the structure viewer
3426 <!-- JAL-2163 -->Titles for individual alignments in
3427 splitframe not restored from project
3430 <!-- JAL-2145 -->missing autocalculated annotation at
3431 trailing end of protein alignment in transcript/product
3432 splitview when pad-gaps not enabled by default
3435 <!-- JAL-1797 -->amino acid physicochemical conservation
3439 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
3440 article has been read (reopened issue due to
3441 internationalisation problems)
3444 <!-- JAL-1960 -->Only offer PDB structures in structure
3445 viewer based on sequence name, PDB and UniProt
3450 <!-- JAL-1976 -->No progress bar shown during export of
3454 <!-- JAL-2213 -->Structures not always superimposed after
3455 multiple structures are shown for one or more sequences.
3458 <!-- JAL-1370 -->Reference sequence characters should not
3459 be replaced with '.' when 'Show unconserved' format option
3463 <!-- JAL-1823 -->Cannot specify chain code when entering
3464 specific PDB id for sequence
3467 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3468 'Export hidden sequences' is enabled, but 'export hidden
3469 columns' is disabled.
3472 <!--JAL-2026-->Best Quality option in structure chooser
3473 selects lowest rather than highest resolution structures
3477 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3478 to sequence mapping in 'View Mappings' report
3481 <!-- JAL-2284 -->Unable to read old Jalview projects that
3482 contain non-XML data added after Jalvew wrote project.
3485 <!-- JAL-2118 -->Newly created annotation row reorders
3486 after clicking on it to create new annotation for a
3490 <!-- JAL-1980 -->Null Pointer Exception raised when
3491 pressing Add on an orphaned cut'n'paste window.
3493 <!-- may exclude, this is an external service stability issue JAL-1941
3494 -- > RNA 3D structure not added via DSSR service</li> -->
3499 <!-- JAL-2151 -->Incorrect columns are selected when
3500 hidden columns present before start of sequence
3503 <!-- JAL-1986 -->Missing dependencies on applet pages
3507 <!-- JAL-1947 -->Overview pixel size changes when
3508 sequences are hidden in applet
3511 <!-- JAL-1996 -->Updated instructions for applet
3512 deployment on examples pages.
3519 <td width="60" nowrap>
3520 <div align="center">
3521 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3522 <em>16/10/2015</em></strong>
3525 <td><em>General</em>
3527 <li>Time stamps for signed Jalview application and applet
3532 <em>Application</em>
3534 <li>Duplicate group consensus and conservation rows
3535 shown when tree is partitioned</li>
3536 <li>Erratic behaviour when tree partitions made with
3537 multiple cDNA/Protein split views</li>
3543 <td width="60" nowrap>
3544 <div align="center">
3545 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3546 <em>8/10/2015</em></strong>
3549 <td><em>General</em>
3551 <li>Updated Spanish translations of localized text for
3553 </ul> <em>Application</em>
3555 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3556 <li>Signed OSX InstallAnywhere installer<br></li>
3557 <li>Support for per-sequence based annotations in BioJSON</li>
3558 </ul> <em>Applet</em>
3560 <li>Split frame example added to applet examples page</li>
3561 </ul> <em>Build and Deployment</em>
3564 <!-- JAL-1888 -->New ant target for running Jalview's test
3572 <li>Mapping of cDNA to protein in split frames
3573 incorrect when sequence start > 1</li>
3574 <li>Broken images in filter column by annotation dialog
3576 <li>Feature colours not parsed from features file</li>
3577 <li>Exceptions and incomplete link URLs recovered when
3578 loading a features file containing HTML tags in feature
3582 <em>Application</em>
3584 <li>Annotations corrupted after BioJS export and
3586 <li>Incorrect sequence limits after Fetch DB References
3587 with 'trim retrieved sequences'</li>
3588 <li>Incorrect warning about deleting all data when
3589 deleting selected columns</li>
3590 <li>Patch to build system for shipping properly signed
3591 JNLP templates for webstart launch</li>
3592 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3593 unreleased structures for download or viewing</li>
3594 <li>Tab/space/return keystroke operation of EMBL-PDBe
3595 fetcher/viewer dialogs works correctly</li>
3596 <li>Disabled 'minimise' button on Jalview windows
3597 running on OSX to workaround redraw hang bug</li>
3598 <li>Split cDNA/Protein view position and geometry not
3599 recovered from jalview project</li>
3600 <li>Initial enabled/disabled state of annotation menu
3601 sorter 'show autocalculated first/last' corresponds to
3603 <li>Restoring of Clustal, RNA Helices and T-Coffee
3604 color schemes from BioJSON</li>
3608 <li>Reorder sequences mirrored in cDNA/Protein split
3610 <li>Applet with Jmol examples not loading correctly</li>
3616 <td><div align="center">
3617 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3619 <td><em>General</em>
3621 <li>Linked visualisation and analysis of DNA and Protein
3624 <li>Translated cDNA alignments shown as split protein
3625 and DNA alignment views</li>
3626 <li>Codon consensus annotation for linked protein and
3627 cDNA alignment views</li>
3628 <li>Link cDNA or Protein product sequences by loading
3629 them onto Protein or cDNA alignments</li>
3630 <li>Reconstruct linked cDNA alignment from aligned
3631 protein sequences</li>
3634 <li>Jmol integration updated to Jmol v14.2.14</li>
3635 <li>Import and export of Jalview alignment views as <a
3636 href="features/bioJsonFormat.html">BioJSON</a></li>
3637 <li>New alignment annotation file statements for
3638 reference sequences and marking hidden columns</li>
3639 <li>Reference sequence based alignment shading to
3640 highlight variation</li>
3641 <li>Select or hide columns according to alignment
3643 <li>Find option for locating sequences by description</li>
3644 <li>Conserved physicochemical properties shown in amino
3645 acid conservation row</li>
3646 <li>Alignments can be sorted by number of RNA helices</li>
3647 </ul> <em>Application</em>
3649 <li>New cDNA/Protein analysis capabilities
3651 <li>Get Cross-References should open a Split Frame
3652 view with cDNA/Protein</li>
3653 <li>Detect when nucleotide sequences and protein
3654 sequences are placed in the same alignment</li>
3655 <li>Split cDNA/Protein views are saved in Jalview
3660 <li>Use REST API to talk to Chimera</li>
3661 <li>Selected regions in Chimera are highlighted in linked
3662 Jalview windows</li>
3664 <li>VARNA RNA viewer updated to v3.93</li>
3665 <li>VARNA views are saved in Jalview Projects</li>
3666 <li>Pseudoknots displayed as Jalview RNA annotation can
3667 be shown in VARNA</li>
3669 <li>Make groups for selection uses marked columns as well
3670 as the active selected region</li>
3672 <li>Calculate UPGMA and NJ trees using sequence feature
3674 <li>New Export options
3676 <li>New Export Settings dialog to control hidden
3677 region export in flat file generation</li>
3679 <li>Export alignment views for display with the <a
3680 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3682 <li>Export scrollable SVG in HTML page</li>
3683 <li>Optional embedding of BioJSON data when exporting
3684 alignment figures to HTML</li>
3686 <li>3D structure retrieval and display
3688 <li>Free text and structured queries with the PDBe
3690 <li>PDBe Search API based discovery and selection of
3691 PDB structures for a sequence set</li>
3695 <li>JPred4 employed for protein secondary structure
3697 <li>Hide Insertions menu option to hide unaligned columns
3698 for one or a group of sequences</li>
3699 <li>Automatically hide insertions in alignments imported
3700 from the JPred4 web server</li>
3701 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3702 system on OSX<br />LGPL libraries courtesy of <a
3703 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3705 <li>changed 'View nucleotide structure' submenu to 'View
3706 VARNA 2D Structure'</li>
3707 <li>change "View protein structure" menu option to "3D
3710 </ul> <em>Applet</em>
3712 <li>New layout for applet example pages</li>
3713 <li>New parameters to enable SplitFrame view
3714 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3715 <li>New example demonstrating linked viewing of cDNA and
3716 Protein alignments</li>
3717 </ul> <em>Development and deployment</em>
3719 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3720 <li>Include installation type and git revision in build
3721 properties and console log output</li>
3722 <li>Jalview Github organisation, and new github site for
3723 storing BioJsMSA Templates</li>
3724 <li>Jalview's unit tests now managed with TestNG</li>
3727 <!-- <em>General</em>
3729 </ul> --> <!-- issues resolved --> <em>Application</em>
3731 <li>Escape should close any open find dialogs</li>
3732 <li>Typo in select-by-features status report</li>
3733 <li>Consensus RNA secondary secondary structure
3734 predictions are not highlighted in amber</li>
3735 <li>Missing gap character in v2.7 example file means
3736 alignment appears unaligned when pad-gaps is not enabled</li>
3737 <li>First switch to RNA Helices colouring doesn't colour
3738 associated structure views</li>
3739 <li>ID width preference option is greyed out when auto
3740 width checkbox not enabled</li>
3741 <li>Stopped a warning dialog from being shown when
3742 creating user defined colours</li>
3743 <li>'View Mapping' in structure viewer shows sequence
3744 mappings for just that viewer's sequences</li>
3745 <li>Workaround for superposing PDB files containing
3746 multiple models in Chimera</li>
3747 <li>Report sequence position in status bar when hovering
3748 over Jmol structure</li>
3749 <li>Cannot output gaps as '.' symbols with Selection ->
3750 output to text box</li>
3751 <li>Flat file exports of alignments with hidden columns
3752 have incorrect sequence start/end</li>
3753 <li>'Aligning' a second chain to a Chimera structure from
3755 <li>Colour schemes applied to structure viewers don't
3756 work for nucleotide</li>
3757 <li>Loading/cut'n'pasting an empty or invalid file leads
3758 to a grey/invisible alignment window</li>
3759 <li>Exported Jpred annotation from a sequence region
3760 imports to different position</li>
3761 <li>Space at beginning of sequence feature tooltips shown
3762 on some platforms</li>
3763 <li>Chimera viewer 'View | Show Chain' menu is not
3765 <li>'New View' fails with a Null Pointer Exception in
3766 console if Chimera has been opened</li>
3767 <li>Mouseover to Chimera not working</li>
3768 <li>Miscellaneous ENA XML feature qualifiers not
3770 <li>NPE in annotation renderer after 'Extract Scores'</li>
3771 <li>If two structures in one Chimera window, mouseover of
3772 either sequence shows on first structure</li>
3773 <li>'Show annotations' options should not make
3774 non-positional annotations visible</li>
3775 <li>Subsequence secondary structure annotation not shown
3776 in right place after 'view flanking regions'</li>
3777 <li>File Save As type unset when current file format is
3779 <li>Save as '.jar' option removed for saving Jalview
3781 <li>Colour by Sequence colouring in Chimera more
3783 <li>Cannot 'add reference annotation' for a sequence in
3784 several views on same alignment</li>
3785 <li>Cannot show linked products for EMBL / ENA records</li>
3786 <li>Jalview's tooltip wraps long texts containing no
3788 </ul> <em>Applet</em>
3790 <li>Jmol to JalviewLite mouseover/link not working</li>
3791 <li>JalviewLite can't import sequences with ID
3792 descriptions containing angle brackets</li>
3793 </ul> <em>General</em>
3795 <li>Cannot export and reimport RNA secondary structure
3796 via jalview annotation file</li>
3797 <li>Random helix colour palette for colour by annotation
3798 with RNA secondary structure</li>
3799 <li>Mouseover to cDNA from STOP residue in protein
3800 translation doesn't work.</li>
3801 <li>hints when using the select by annotation dialog box</li>
3802 <li>Jmol alignment incorrect if PDB file has alternate CA
3804 <li>FontChooser message dialog appears to hang after
3805 choosing 1pt font</li>
3806 <li>Peptide secondary structure incorrectly imported from
3807 annotation file when annotation display text includes 'e' or
3809 <li>Cannot set colour of new feature type whilst creating
3811 <li>cDNA translation alignment should not be sequence
3812 order dependent</li>
3813 <li>'Show unconserved' doesn't work for lower case
3815 <li>Nucleotide ambiguity codes involving R not recognised</li>
3816 </ul> <em>Deployment and Documentation</em>
3818 <li>Applet example pages appear different to the rest of
3819 www.jalview.org</li>
3820 </ul> <em>Application Known issues</em>
3822 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3823 <li>Misleading message appears after trying to delete
3825 <li>Jalview icon not shown in dock after InstallAnywhere
3826 version launches</li>
3827 <li>Fetching EMBL reference for an RNA sequence results
3828 fails with a sequence mismatch</li>
3829 <li>Corrupted or unreadable alignment display when
3830 scrolling alignment to right</li>
3831 <li>ArrayIndexOutOfBoundsException thrown when remove
3832 empty columns called on alignment with ragged gapped ends</li>
3833 <li>auto calculated alignment annotation rows do not get
3834 placed above or below non-autocalculated rows</li>
3835 <li>Jalview dekstop becomes sluggish at full screen in
3836 ultra-high resolution</li>
3837 <li>Cannot disable consensus calculation independently of
3838 quality and conservation</li>
3839 <li>Mouseover highlighting between cDNA and protein can
3840 become sluggish with more than one splitframe shown</li>
3841 </ul> <em>Applet Known Issues</em>
3843 <li>Core PDB parsing code requires Jmol</li>
3844 <li>Sequence canvas panel goes white when alignment
3845 window is being resized</li>
3851 <td><div align="center">
3852 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3854 <td><em>General</em>
3856 <li>Updated Java code signing certificate donated by
3858 <li>Features and annotation preserved when performing
3859 pairwise alignment</li>
3860 <li>RNA pseudoknot annotation can be
3861 imported/exported/displayed</li>
3862 <li>'colour by annotation' can colour by RNA and
3863 protein secondary structure</li>
3864 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3865 post-hoc with 2.9 release</em>)
3868 </ul> <em>Application</em>
3870 <li>Extract and display secondary structure for sequences
3871 with 3D structures</li>
3872 <li>Support for parsing RNAML</li>
3873 <li>Annotations menu for layout
3875 <li>sort sequence annotation rows by alignment</li>
3876 <li>place sequence annotation above/below alignment
3879 <li>Output in Stockholm format</li>
3880 <li>Internationalisation: improved Spanish (es)
3882 <li>Structure viewer preferences tab</li>
3883 <li>Disorder and Secondary Structure annotation tracks
3884 shared between alignments</li>
3885 <li>UCSF Chimera launch and linked highlighting from
3887 <li>Show/hide all sequence associated annotation rows for
3888 all or current selection</li>
3889 <li>disorder and secondary structure predictions
3890 available as dataset annotation</li>
3891 <li>Per-sequence rna helices colouring</li>
3894 <li>Sequence database accessions imported when fetching
3895 alignments from Rfam</li>
3896 <li>update VARNA version to 3.91</li>
3898 <li>New groovy scripts for exporting aligned positions,
3899 conservation values, and calculating sum of pairs scores.</li>
3900 <li>Command line argument to set default JABAWS server</li>
3901 <li>include installation type in build properties and
3902 console log output</li>
3903 <li>Updated Jalview project format to preserve dataset
3907 <!-- issues resolved --> <em>Application</em>
3909 <li>Distinguish alignment and sequence associated RNA
3910 structure in structure->view->VARNA</li>
3911 <li>Raise dialog box if user deletes all sequences in an
3913 <li>Pressing F1 results in documentation opening twice</li>
3914 <li>Sequence feature tooltip is wrapped</li>
3915 <li>Double click on sequence associated annotation
3916 selects only first column</li>
3917 <li>Redundancy removal doesn't result in unlinked
3918 leaves shown in tree</li>
3919 <li>Undos after several redundancy removals don't undo
3921 <li>Hide sequence doesn't hide associated annotation</li>
3922 <li>User defined colours dialog box too big to fit on
3923 screen and buttons not visible</li>
3924 <li>author list isn't updated if already written to
3925 Jalview properties</li>
3926 <li>Popup menu won't open after retrieving sequence
3928 <li>File open window for associate PDB doesn't open</li>
3929 <li>Left-then-right click on a sequence id opens a
3930 browser search window</li>
3931 <li>Cannot open sequence feature shading/sort popup menu
3932 in feature settings dialog</li>
3933 <li>better tooltip placement for some areas of Jalview
3935 <li>Allow addition of JABAWS Server which doesn't
3936 pass validation</li>
3937 <li>Web services parameters dialog box is too large to
3939 <li>Muscle nucleotide alignment preset obscured by
3941 <li>JABAWS preset submenus don't contain newly
3942 defined user preset</li>
3943 <li>MSA web services warns user if they were launched
3944 with invalid input</li>
3945 <li>Jalview cannot contact DAS Registy when running on
3948 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3949 'Superpose with' submenu not shown when new view
3953 </ul> <!-- <em>Applet</em>
3955 </ul> <em>General</em>
3957 </ul>--> <em>Deployment and Documentation</em>
3959 <li>2G and 1G options in launchApp have no effect on
3960 memory allocation</li>
3961 <li>launchApp service doesn't automatically open
3962 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3964 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3965 InstallAnywhere reports cannot find valid JVM when Java
3966 1.7_055 is available
3968 </ul> <em>Application Known issues</em>
3971 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3972 corrupted or unreadable alignment display when scrolling
3976 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3977 retrieval fails but progress bar continues for DAS retrieval
3978 with large number of ID
3981 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3982 flatfile output of visible region has incorrect sequence
3986 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3987 rna structure consensus doesn't update when secondary
3988 structure tracks are rearranged
3991 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3992 invalid rna structure positional highlighting does not
3993 highlight position of invalid base pairs
3996 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3997 out of memory errors are not raised when saving Jalview
3998 project from alignment window file menu
4001 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
4002 Switching to RNA Helices colouring doesn't propagate to
4006 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
4007 colour by RNA Helices not enabled when user created
4008 annotation added to alignment
4011 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
4012 Jalview icon not shown on dock in Mountain Lion/Webstart
4014 </ul> <em>Applet Known Issues</em>
4017 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
4018 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
4021 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
4022 Jalview and Jmol example not compatible with IE9
4025 <li>Sort by annotation score doesn't reverse order
4031 <td><div align="center">
4032 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
4035 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
4038 <li>Internationalisation of user interface (usually
4039 called i18n support) and translation for Spanish locale</li>
4040 <li>Define/Undefine group on current selection with
4041 Ctrl-G/Shift Ctrl-G</li>
4042 <li>Improved group creation/removal options in
4043 alignment/sequence Popup menu</li>
4044 <li>Sensible precision for symbol distribution
4045 percentages shown in logo tooltip.</li>
4046 <li>Annotation panel height set according to amount of
4047 annotation when alignment first opened</li>
4048 </ul> <em>Application</em>
4050 <li>Interactive consensus RNA secondary structure
4051 prediction VIENNA RNAAliFold JABA 2.1 service</li>
4052 <li>Select columns containing particular features from
4053 Feature Settings dialog</li>
4054 <li>View all 'representative' PDB structures for selected
4056 <li>Update Jalview project format:
4058 <li>New file extension for Jalview projects '.jvp'</li>
4059 <li>Preserve sequence and annotation dataset (to
4060 store secondary structure annotation,etc)</li>
4061 <li>Per group and alignment annotation and RNA helix
4065 <li>New similarity measures for PCA and Tree calculation
4067 <li>Experimental support for retrieval and viewing of
4068 flanking regions for an alignment</li>
4072 <!-- issues resolved --> <em>Application</em>
4074 <li>logo keeps spinning and status remains at queued or
4075 running after job is cancelled</li>
4076 <li>cannot export features from alignments imported from
4077 Jalview/VAMSAS projects</li>
4078 <li>Buggy slider for web service parameters that take
4080 <li>Newly created RNA secondary structure line doesn't
4081 have 'display all symbols' flag set</li>
4082 <li>T-COFFEE alignment score shading scheme and other
4083 annotation shading not saved in Jalview project</li>
4084 <li>Local file cannot be loaded in freshly downloaded
4086 <li>Jalview icon not shown on dock in Mountain
4088 <li>Load file from desktop file browser fails</li>
4089 <li>Occasional NPE thrown when calculating large trees</li>
4090 <li>Cannot reorder or slide sequences after dragging an
4091 alignment onto desktop</li>
4092 <li>Colour by annotation dialog throws NPE after using
4093 'extract scores' function</li>
4094 <li>Loading/cut'n'pasting an empty file leads to a grey
4095 alignment window</li>
4096 <li>Disorder thresholds rendered incorrectly after
4097 performing IUPred disorder prediction</li>
4098 <li>Multiple group annotated consensus rows shown when
4099 changing 'normalise logo' display setting</li>
4100 <li>Find shows blank dialog after 'finished searching' if
4101 nothing matches query</li>
4102 <li>Null Pointer Exceptions raised when sorting by
4103 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
4105 <li>Errors in Jmol console when structures in alignment
4106 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
4108 <li>Not all working JABAWS services are shown in
4110 <li>JAVAWS version of Jalview fails to launch with
4111 'invalid literal/length code'</li>
4112 <li>Annotation/RNA Helix colourschemes cannot be applied
4113 to alignment with groups (actually fixed in 2.8.0b1)</li>
4114 <li>RNA Helices and T-Coffee Scores available as default
4117 </ul> <em>Applet</em>
4119 <li>Remove group option is shown even when selection is
4121 <li>Apply to all groups ticked but colourscheme changes
4122 don't affect groups</li>
4123 <li>Documented RNA Helices and T-Coffee Scores as valid
4124 colourscheme name</li>
4125 <li>Annotation labels drawn on sequence IDs when
4126 Annotation panel is not displayed</li>
4127 <li>Increased font size for dropdown menus on OSX and
4128 embedded windows</li>
4129 </ul> <em>Other</em>
4131 <li>Consensus sequence for alignments/groups with a
4132 single sequence were not calculated</li>
4133 <li>annotation files that contain only groups imported as
4134 annotation and junk sequences</li>
4135 <li>Fasta files with sequences containing '*' incorrectly
4136 recognised as PFAM or BLC</li>
4137 <li>conservation/PID slider apply all groups option
4138 doesn't affect background (2.8.0b1)
4140 <li>redundancy highlighting is erratic at 0% and 100%</li>
4141 <li>Remove gapped columns fails for sequences with ragged
4143 <li>AMSA annotation row with leading spaces is not
4144 registered correctly on import</li>
4145 <li>Jalview crashes when selecting PCA analysis for
4146 certain alignments</li>
4147 <li>Opening the colour by annotation dialog for an
4148 existing annotation based 'use original colours'
4149 colourscheme loses original colours setting</li>
4154 <td><div align="center">
4155 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
4156 <em>30/1/2014</em></strong>
4160 <li>Trusted certificates for JalviewLite applet and
4161 Jalview Desktop application<br />Certificate was donated by
4162 <a href="https://www.certum.eu">Certum</a> to the Jalview
4163 open source project).
4165 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
4166 <li>Output in Stockholm format</li>
4167 <li>Allow import of data from gzipped files</li>
4168 <li>Export/import group and sequence associated line
4169 graph thresholds</li>
4170 <li>Nucleotide substitution matrix that supports RNA and
4171 ambiguity codes</li>
4172 <li>Allow disorder predictions to be made on the current
4173 selection (or visible selection) in the same way that JPred
4175 <li>Groovy scripting for headless Jalview operation</li>
4176 </ul> <em>Other improvements</em>
4178 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
4179 <li>COMBINE statement uses current SEQUENCE_REF and
4180 GROUP_REF scope to group annotation rows</li>
4181 <li>Support '' style escaping of quotes in Newick
4183 <li>Group options for JABAWS service by command line name</li>
4184 <li>Empty tooltip shown for JABA service options with a
4185 link but no description</li>
4186 <li>Select primary source when selecting authority in
4187 database fetcher GUI</li>
4188 <li>Add .mfa to FASTA file extensions recognised by
4190 <li>Annotation label tooltip text wrap</li>
4195 <li>Slow scrolling when lots of annotation rows are
4197 <li>Lots of NPE (and slowness) after creating RNA
4198 secondary structure annotation line</li>
4199 <li>Sequence database accessions not imported when
4200 fetching alignments from Rfam</li>
4201 <li>Incorrect SHMR submission for sequences with
4203 <li>View all structures does not always superpose
4205 <li>Option widgets in service parameters not updated to
4206 reflect user or preset settings</li>
4207 <li>Null pointer exceptions for some services without
4208 presets or adjustable parameters</li>
4209 <li>Discover PDB IDs entry in structure menu doesn't
4210 discover PDB xRefs</li>
4211 <li>Exception encountered while trying to retrieve
4212 features with DAS</li>
4213 <li>Lowest value in annotation row isn't coloured
4214 when colour by annotation (per sequence) is coloured</li>
4215 <li>Keyboard mode P jumps to start of gapped region when
4216 residue follows a gap</li>
4217 <li>Jalview appears to hang importing an alignment with
4218 Wrap as default or after enabling Wrap</li>
4219 <li>'Right click to add annotations' message
4220 shown in wrap mode when no annotations present</li>
4221 <li>Disorder predictions fail with NPE if no automatic
4222 annotation already exists on alignment</li>
4223 <li>oninit javascript function should be called after
4224 initialisation completes</li>
4225 <li>Remove redundancy after disorder prediction corrupts
4226 alignment window display</li>
4227 <li>Example annotation file in documentation is invalid</li>
4228 <li>Grouped line graph annotation rows are not exported
4229 to annotation file</li>
4230 <li>Multi-harmony analysis cannot be run when only two
4232 <li>Cannot create multiple groups of line graphs with
4233 several 'combine' statements in annotation file</li>
4234 <li>Pressing return several times causes Number Format
4235 exceptions in keyboard mode</li>
4236 <li>Multi-harmony (SHMMR) method doesn't submit
4237 correct partitions for input data</li>
4238 <li>Translation from DNA to Amino Acids fails</li>
4239 <li>Jalview fail to load newick tree with quoted label</li>
4240 <li>--headless flag isn't understood</li>
4241 <li>ClassCastException when generating EPS in headless
4243 <li>Adjusting sequence-associated shading threshold only
4244 changes one row's threshold</li>
4245 <li>Preferences and Feature settings panel panel
4246 doesn't open</li>
4247 <li>hide consensus histogram also hides conservation and
4248 quality histograms</li>
4253 <td><div align="center">
4254 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
4256 <td><em>Application</em>
4258 <li>Support for JABAWS 2.0 Services (AACon alignment
4259 conservation, protein disorder and Clustal Omega)</li>
4260 <li>JABAWS server status indicator in Web Services
4262 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
4263 in Jalview alignment window</li>
4264 <li>Updated Jalview build and deploy framework for OSX
4265 mountain lion, windows 7, and 8</li>
4266 <li>Nucleotide substitution matrix for PCA that supports
4267 RNA and ambiguity codes</li>
4269 <li>Improved sequence database retrieval GUI</li>
4270 <li>Support fetching and database reference look up
4271 against multiple DAS sources (Fetch all from in 'fetch db
4273 <li>Jalview project improvements
4275 <li>Store and retrieve the 'belowAlignment'
4276 flag for annotation</li>
4277 <li>calcId attribute to group annotation rows on the
4279 <li>Store AACon calculation settings for a view in
4280 Jalview project</li>
4284 <li>horizontal scrolling gesture support</li>
4285 <li>Visual progress indicator when PCA calculation is
4287 <li>Simpler JABA web services menus</li>
4288 <li>visual indication that web service results are still
4289 being retrieved from server</li>
4290 <li>Serialise the dialogs that are shown when Jalview
4291 starts up for first time</li>
4292 <li>Jalview user agent string for interacting with HTTP
4294 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
4296 <li>Examples directory and Groovy library included in
4297 InstallAnywhere distribution</li>
4298 </ul> <em>Applet</em>
4300 <li>RNA alignment and secondary structure annotation
4301 visualization applet example</li>
4302 </ul> <em>General</em>
4304 <li>Normalise option for consensus sequence logo</li>
4305 <li>Reset button in PCA window to return dimensions to
4307 <li>Allow seqspace or Jalview variant of alignment PCA
4309 <li>PCA with either nucleic acid and protein substitution
4311 <li>Allow windows containing HTML reports to be exported
4313 <li>Interactive display and editing of RNA secondary
4314 structure contacts</li>
4315 <li>RNA Helix Alignment Colouring</li>
4316 <li>RNA base pair logo consensus</li>
4317 <li>Parse sequence associated secondary structure
4318 information in Stockholm files</li>
4319 <li>HTML Export database accessions and annotation
4320 information presented in tooltip for sequences</li>
4321 <li>Import secondary structure from LOCARNA clustalw
4322 style RNA alignment files</li>
4323 <li>import and visualise T-COFFEE quality scores for an
4325 <li>'colour by annotation' per sequence option to
4326 shade each sequence according to its associated alignment
4328 <li>New Jalview Logo</li>
4329 </ul> <em>Documentation and Development</em>
4331 <li>documentation for score matrices used in Jalview</li>
4332 <li>New Website!</li>
4334 <td><em>Application</em>
4336 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
4337 wsdbfetch REST service</li>
4338 <li>Stop windows being moved outside desktop on OSX</li>
4339 <li>Filetype associations not installed for webstart
4341 <li>Jalview does not always retrieve progress of a JABAWS
4342 job execution in full once it is complete</li>
4343 <li>revise SHMR RSBS definition to ensure alignment is
4344 uploaded via ali_file parameter</li>
4345 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
4346 <li>View all structures superposed fails with exception</li>
4347 <li>Jnet job queues forever if a very short sequence is
4348 submitted for prediction</li>
4349 <li>Cut and paste menu not opened when mouse clicked on
4351 <li>Putting fractional value into integer text box in
4352 alignment parameter dialog causes Jalview to hang</li>
4353 <li>Structure view highlighting doesn't work on
4355 <li>View all structures fails with exception shown in
4357 <li>Characters in filename associated with PDBEntry not
4358 escaped in a platform independent way</li>
4359 <li>Jalview desktop fails to launch with exception when
4361 <li>Tree calculation reports 'you must have 2 or more
4362 sequences selected' when selection is empty</li>
4363 <li>Jalview desktop fails to launch with jar signature
4364 failure when java web start temporary file caching is
4366 <li>DAS Sequence retrieval with range qualification
4367 results in sequence xref which includes range qualification</li>
4368 <li>Errors during processing of command line arguments
4369 cause progress bar (JAL-898) to be removed</li>
4370 <li>Replace comma for semi-colon option not disabled for
4371 DAS sources in sequence fetcher</li>
4372 <li>Cannot close news reader when JABAWS server warning
4373 dialog is shown</li>
4374 <li>Option widgets not updated to reflect user settings</li>
4375 <li>Edited sequence not submitted to web service</li>
4376 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
4377 <li>InstallAnywhere installer doesn't unpack and run
4378 on OSX Mountain Lion</li>
4379 <li>Annotation panel not given a scroll bar when
4380 sequences with alignment annotation are pasted into the
4382 <li>Sequence associated annotation rows not associated
4383 when loaded from Jalview project</li>
4384 <li>Browser launch fails with NPE on java 1.7</li>
4385 <li>JABAWS alignment marked as finished when job was
4386 cancelled or job failed due to invalid input</li>
4387 <li>NPE with v2.7 example when clicking on Tree
4388 associated with all views</li>
4389 <li>Exceptions when copy/paste sequences with grouped
4390 annotation rows to new window</li>
4391 </ul> <em>Applet</em>
4393 <li>Sequence features are momentarily displayed before
4394 they are hidden using hidefeaturegroups applet parameter</li>
4395 <li>loading features via javascript API automatically
4396 enables feature display</li>
4397 <li>scrollToColumnIn javascript API method doesn't
4399 </ul> <em>General</em>
4401 <li>Redundancy removal fails for rna alignment</li>
4402 <li>PCA calculation fails when sequence has been selected
4403 and then deselected</li>
4404 <li>PCA window shows grey box when first opened on OSX</li>
4405 <li>Letters coloured pink in sequence logo when alignment
4406 coloured with clustalx</li>
4407 <li>Choosing fonts without letter symbols defined causes
4408 exceptions and redraw errors</li>
4409 <li>Initial PCA plot view is not same as manually
4410 reconfigured view</li>
4411 <li>Grouped annotation graph label has incorrect line
4413 <li>Grouped annotation graph label display is corrupted
4414 for lots of labels</li>
4419 <div align="center">
4420 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
4423 <td><em>Application</em>
4425 <li>Jalview Desktop News Reader</li>
4426 <li>Tweaked default layout of web services menu</li>
4427 <li>View/alignment association menu to enable user to
4428 easily specify which alignment a multi-structure view takes
4429 its colours/correspondences from</li>
4430 <li>Allow properties file location to be specified as URL</li>
4431 <li>Extend Jalview project to preserve associations
4432 between many alignment views and a single Jmol display</li>
4433 <li>Store annotation row height in Jalview project file</li>
4434 <li>Annotation row column label formatting attributes
4435 stored in project file</li>
4436 <li>Annotation row order for auto-calculated annotation
4437 rows preserved in Jalview project file</li>
4438 <li>Visual progress indication when Jalview state is
4439 saved using Desktop window menu</li>
4440 <li>Visual indication that command line arguments are
4441 still being processed</li>
4442 <li>Groovy script execution from URL</li>
4443 <li>Colour by annotation default min and max colours in
4445 <li>Automatically associate PDB files dragged onto an
4446 alignment with sequences that have high similarity and
4448 <li>Update JGoogleAnalytics to latest release (0.3)</li>
4449 <li>'view structures' option to open many
4450 structures in same window</li>
4451 <li>Sort associated views menu option for tree panel</li>
4452 <li>Group all JABA and non-JABA services for a particular
4453 analysis function in its own submenu</li>
4454 </ul> <em>Applet</em>
4456 <li>Userdefined and autogenerated annotation rows for
4458 <li>Adjustment of alignment annotation pane height</li>
4459 <li>Annotation scrollbar for annotation panel</li>
4460 <li>Drag to reorder annotation rows in annotation panel</li>
4461 <li>'automaticScrolling' parameter</li>
4462 <li>Allow sequences with partial ID string matches to be
4463 annotated from GFF/Jalview features files</li>
4464 <li>Sequence logo annotation row in applet</li>
4465 <li>Absolute paths relative to host server in applet
4466 parameters are treated as such</li>
4467 <li>New in the JalviewLite javascript API:
4469 <li>JalviewLite.js javascript library</li>
4470 <li>Javascript callbacks for
4472 <li>Applet initialisation</li>
4473 <li>Sequence/alignment mouse-overs and selections</li>
4476 <li>scrollTo row and column alignment scrolling
4478 <li>Select sequence/alignment regions from javascript</li>
4479 <li>javascript structure viewer harness to pass
4480 messages between Jmol and Jalview when running as
4481 distinct applets</li>
4482 <li>sortBy method</li>
4483 <li>Set of applet and application examples shipped
4484 with documentation</li>
4485 <li>New example to demonstrate JalviewLite and Jmol
4486 javascript message exchange</li>
4488 </ul> <em>General</em>
4490 <li>Enable Jmol displays to be associated with multiple
4491 multiple alignments</li>
4492 <li>Option to automatically sort alignment with new tree</li>
4493 <li>User configurable link to enable redirects to a
4494 www.Jalview.org mirror</li>
4495 <li>Jmol colours option for Jmol displays</li>
4496 <li>Configurable newline string when writing alignment
4497 and other flat files</li>
4498 <li>Allow alignment annotation description lines to
4499 contain html tags</li>
4500 </ul> <em>Documentation and Development</em>
4502 <li>Add groovy test harness for bulk load testing to
4504 <li>Groovy script to load and align a set of sequences
4505 using a web service before displaying the result in the
4506 Jalview desktop</li>
4507 <li>Restructured javascript and applet api documentation</li>
4508 <li>Ant target to publish example html files with applet
4510 <li>Netbeans project for building Jalview from source</li>
4511 <li>ant task to create online javadoc for Jalview source</li>
4513 <td><em>Application</em>
4515 <li>User defined colourscheme throws exception when
4516 current built in colourscheme is saved as new scheme</li>
4517 <li>AlignFrame->Save in application pops up save
4518 dialog for valid filename/format</li>
4519 <li>Cannot view associated structure for UniProt sequence</li>
4520 <li>PDB file association breaks for UniProt sequence
4522 <li>Associate PDB from file dialog does not tell you
4523 which sequence is to be associated with the file</li>
4524 <li>Find All raises null pointer exception when query
4525 only matches sequence IDs</li>
4526 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4527 <li>Jalview project with Jmol views created with Jalview
4528 2.4 cannot be loaded</li>
4529 <li>Filetype associations not installed for webstart
4531 <li>Two or more chains in a single PDB file associated
4532 with sequences in different alignments do not get coloured
4533 by their associated sequence</li>
4534 <li>Visibility status of autocalculated annotation row
4535 not preserved when project is loaded</li>
4536 <li>Annotation row height and visibility attributes not
4537 stored in Jalview project</li>
4538 <li>Tree bootstraps are not preserved when saved as a
4539 Jalview project</li>
4540 <li>Envision2 workflow tooltips are corrupted</li>
4541 <li>Enabling show group conservation also enables colour
4542 by conservation</li>
4543 <li>Duplicate group associated conservation or consensus
4544 created on new view</li>
4545 <li>Annotation scrollbar not displayed after 'show
4546 all hidden annotation rows' option selected</li>
4547 <li>Alignment quality not updated after alignment
4548 annotation row is hidden then shown</li>
4549 <li>Preserve colouring of structures coloured by
4550 sequences in pre Jalview 2.7 projects</li>
4551 <li>Web service job parameter dialog is not laid out
4553 <li>Web services menu not refreshed after 'reset
4554 services' button is pressed in preferences</li>
4555 <li>Annotation off by one in Jalview v2_3 example project</li>
4556 <li>Structures imported from file and saved in project
4557 get name like jalview_pdb1234.txt when reloaded</li>
4558 <li>Jalview does not always retrieve progress of a JABAWS
4559 job execution in full once it is complete</li>
4560 </ul> <em>Applet</em>
4562 <li>Alignment height set incorrectly when lots of
4563 annotation rows are displayed</li>
4564 <li>Relative URLs in feature HTML text not resolved to
4566 <li>View follows highlighting does not work for positions
4568 <li><= shown as = in tooltip</li>
4569 <li>Export features raises exception when no features
4571 <li>Separator string used for serialising lists of IDs
4572 for javascript api is modified when separator string
4573 provided as parameter</li>
4574 <li>Null pointer exception when selecting tree leaves for
4575 alignment with no existing selection</li>
4576 <li>Relative URLs for datasources assumed to be relative
4577 to applet's codebase</li>
4578 <li>Status bar not updated after finished searching and
4579 search wraps around to first result</li>
4580 <li>StructureSelectionManager instance shared between
4581 several Jalview applets causes race conditions and memory
4583 <li>Hover tooltip and mouseover of position on structure
4584 not sent from Jmol in applet</li>
4585 <li>Certain sequences of javascript method calls to
4586 applet API fatally hang browser</li>
4587 </ul> <em>General</em>
4589 <li>View follows structure mouseover scrolls beyond
4590 position with wrapped view and hidden regions</li>
4591 <li>Find sequence position moves to wrong residue
4592 with/without hidden columns</li>
4593 <li>Sequence length given in alignment properties window
4595 <li>InvalidNumberFormat exceptions thrown when trying to
4596 import PDB like structure files</li>
4597 <li>Positional search results are only highlighted
4598 between user-supplied sequence start/end bounds</li>
4599 <li>End attribute of sequence is not validated</li>
4600 <li>Find dialog only finds first sequence containing a
4601 given sequence position</li>
4602 <li>Sequence numbering not preserved in MSF alignment
4604 <li>Jalview PDB file reader does not extract sequence
4605 from nucleotide chains correctly</li>
4606 <li>Structure colours not updated when tree partition
4607 changed in alignment</li>
4608 <li>Sequence associated secondary structure not correctly
4609 parsed in interleaved stockholm</li>
4610 <li>Colour by annotation dialog does not restore current
4612 <li>Hiding (nearly) all sequences doesn't work
4614 <li>Sequences containing lowercase letters are not
4615 properly associated with their pdb files</li>
4616 </ul> <em>Documentation and Development</em>
4618 <li>schemas/JalviewWsParamSet.xsd corrupted by
4619 ApplyCopyright tool</li>
4624 <div align="center">
4625 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4628 <td><em>Application</em>
4630 <li>New warning dialog when the Jalview Desktop cannot
4631 contact web services</li>
4632 <li>JABA service parameters for a preset are shown in
4633 service job window</li>
4634 <li>JABA Service menu entries reworded</li>
4638 <li>Modeller PIR IO broken - cannot correctly import a
4639 pir file emitted by Jalview</li>
4640 <li>Existing feature settings transferred to new
4641 alignment view created from cut'n'paste</li>
4642 <li>Improved test for mixed amino/nucleotide chains when
4643 parsing PDB files</li>
4644 <li>Consensus and conservation annotation rows
4645 occasionally become blank for all new windows</li>
4646 <li>Exception raised when right clicking above sequences
4647 in wrapped view mode</li>
4648 </ul> <em>Application</em>
4650 <li>multiple multiply aligned structure views cause cpu
4651 usage to hit 100% and computer to hang</li>
4652 <li>Web Service parameter layout breaks for long user
4653 parameter names</li>
4654 <li>Jaba service discovery hangs desktop if Jaba server
4661 <div align="center">
4662 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4665 <td><em>Application</em>
4667 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4668 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4671 <li>Web Services preference tab</li>
4672 <li>Analysis parameters dialog box and user defined
4674 <li>Improved speed and layout of Envision2 service menu</li>
4675 <li>Superpose structures using associated sequence
4677 <li>Export coordinates and projection as CSV from PCA
4679 </ul> <em>Applet</em>
4681 <li>enable javascript: execution by the applet via the
4682 link out mechanism</li>
4683 </ul> <em>Other</em>
4685 <li>Updated the Jmol Jalview interface to work with Jmol
4687 <li>The Jalview Desktop and JalviewLite applet now
4688 require Java 1.5</li>
4689 <li>Allow Jalview feature colour specification for GFF
4690 sequence annotation files</li>
4691 <li>New 'colour by label' keword in Jalview feature file
4692 type colour specification</li>
4693 <li>New Jalview Desktop Groovy API method that allows a
4694 script to check if it being run in an interactive session or
4695 in a batch operation from the Jalview command line</li>
4699 <li>clustalx colourscheme colours Ds preferentially when
4700 both D+E are present in over 50% of the column</li>
4701 </ul> <em>Application</em>
4703 <li>typo in AlignmentFrame->View->Hide->all but
4704 selected Regions menu item</li>
4705 <li>sequence fetcher replaces ',' for ';' when the ',' is
4706 part of a valid accession ID</li>
4707 <li>fatal OOM if object retrieved by sequence fetcher
4708 runs out of memory</li>
4709 <li>unhandled Out of Memory Error when viewing pca
4710 analysis results</li>
4711 <li>InstallAnywhere builds fail to launch on OS X java
4712 10.5 update 4 (due to apple Java 1.6 update)</li>
4713 <li>Installanywhere Jalview silently fails to launch</li>
4714 </ul> <em>Applet</em>
4716 <li>Jalview.getFeatureGroups() raises an
4717 ArrayIndexOutOfBoundsException if no feature groups are
4724 <div align="center">
4725 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4731 <li>Alignment prettyprinter doesn't cope with long
4733 <li>clustalx colourscheme colours Ds preferentially when
4734 both D+E are present in over 50% of the column</li>
4735 <li>nucleic acid structures retrieved from PDB do not
4736 import correctly</li>
4737 <li>More columns get selected than were clicked on when a
4738 number of columns are hidden</li>
4739 <li>annotation label popup menu not providing correct
4740 add/hide/show options when rows are hidden or none are
4742 <li>Stockholm format shown in list of readable formats,
4743 and parser copes better with alignments from RFAM.</li>
4744 <li>CSV output of consensus only includes the percentage
4745 of all symbols if sequence logo display is enabled</li>
4747 </ul> <em>Applet</em>
4749 <li>annotation panel disappears when annotation is
4751 </ul> <em>Application</em>
4753 <li>Alignment view not redrawn properly when new
4754 alignment opened where annotation panel is visible but no
4755 annotations are present on alignment</li>
4756 <li>pasted region containing hidden columns is
4757 incorrectly displayed in new alignment window</li>
4758 <li>Jalview slow to complete operations when stdout is
4759 flooded (fix is to close the Jalview console)</li>
4760 <li>typo in AlignmentFrame->View->Hide->all but
4761 selected Rregions menu item.</li>
4762 <li>inconsistent group submenu and Format submenu entry
4763 'Un' or 'Non'conserved</li>
4764 <li>Sequence feature settings are being shared by
4765 multiple distinct alignments</li>
4766 <li>group annotation not recreated when tree partition is
4768 <li>double click on group annotation to select sequences
4769 does not propagate to associated trees</li>
4770 <li>Mac OSX specific issues:
4772 <li>exception raised when mouse clicked on desktop
4773 window background</li>
4774 <li>Desktop menu placed on menu bar and application
4775 name set correctly</li>
4776 <li>sequence feature settings not wide enough for the
4777 save feature colourscheme button</li>
4786 <div align="center">
4787 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4790 <td><em>New Capabilities</em>
4792 <li>URL links generated from description line for
4793 regular-expression based URL links (applet and application)
4796 <li>Non-positional feature URL links are shown in link
4798 <li>Linked viewing of nucleic acid sequences and
4800 <li>Automatic Scrolling option in View menu to display
4801 the currently highlighted region of an alignment.</li>
4802 <li>Order an alignment by sequence length, or using the
4803 average score or total feature count for each sequence.</li>
4804 <li>Shading features by score or associated description</li>
4805 <li>Subdivide alignment and groups based on identity of
4806 selected subsequence (Make Groups from Selection).</li>
4807 <li>New hide/show options including Shift+Control+H to
4808 hide everything but the currently selected region.</li>
4809 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4810 </ul> <em>Application</em>
4812 <li>Fetch DB References capabilities and UI expanded to
4813 support retrieval from DAS sequence sources</li>
4814 <li>Local DAS Sequence sources can be added via the
4815 command line or via the Add local source dialog box.</li>
4816 <li>DAS Dbref and DbxRef feature types are parsed as
4817 database references and protein_name is parsed as
4818 description line (BioSapiens terms).</li>
4819 <li>Enable or disable non-positional feature and database
4820 references in sequence ID tooltip from View menu in
4822 <!-- <li>New hidden columns and rows and representatives capabilities
4823 in annotations file (in progress - not yet fully implemented)</li> -->
4824 <li>Group-associated consensus, sequence logos and
4825 conservation plots</li>
4826 <li>Symbol distributions for each column can be exported
4827 and visualized as sequence logos</li>
4828 <li>Optionally scale multi-character column labels to fit
4829 within each column of annotation row<!-- todo for applet -->
4831 <li>Optional automatic sort of associated alignment view
4832 when a new tree is opened.</li>
4833 <li>Jalview Java Console</li>
4834 <li>Better placement of desktop window when moving
4835 between different screens.</li>
4836 <li>New preference items for sequence ID tooltip and
4837 consensus annotation</li>
4838 <li>Client to submit sequences and IDs to Envision2
4840 <li><em>Vamsas Capabilities</em>
4842 <li>Improved VAMSAS synchronization (Jalview archive
4843 used to preserve views, structures, and tree display
4845 <li>Import of vamsas documents from disk or URL via
4847 <li>Sharing of selected regions between views and
4848 with other VAMSAS applications (Experimental feature!)</li>
4849 <li>Updated API to VAMSAS version 0.2</li>
4851 </ul> <em>Applet</em>
4853 <li>Middle button resizes annotation row height</li>
4856 <li>sortByTree (true/false) - automatically sort the
4857 associated alignment view by the tree when a new tree is
4859 <li>showTreeBootstraps (true/false) - show or hide
4860 branch bootstraps (default is to show them if available)</li>
4861 <li>showTreeDistances (true/false) - show or hide
4862 branch lengths (default is to show them if available)</li>
4863 <li>showUnlinkedTreeNodes (true/false) - indicate if
4864 unassociated nodes should be highlighted in the tree
4866 <li>heightScale and widthScale (1.0 or more) -
4867 increase the height or width of a cell in the alignment
4868 grid relative to the current font size.</li>
4871 <li>Non-positional features displayed in sequence ID
4873 </ul> <em>Other</em>
4875 <li>Features format: graduated colour definitions and
4876 specification of feature scores</li>
4877 <li>Alignment Annotations format: new keywords for group
4878 associated annotation (GROUP_REF) and annotation row display
4879 properties (ROW_PROPERTIES)</li>
4880 <li>XML formats extended to support graduated feature
4881 colourschemes, group associated annotation, and profile
4882 visualization settings.</li></td>
4885 <li>Source field in GFF files parsed as feature source
4886 rather than description</li>
4887 <li>Non-positional features are now included in sequence
4888 feature and gff files (controlled via non-positional feature
4889 visibility in tooltip).</li>
4890 <li>URL links generated for all feature links (bugfix)</li>
4891 <li>Added URL embedding instructions to features file
4893 <li>Codons containing ambiguous nucleotides translated as
4894 'X' in peptide product</li>
4895 <li>Match case switch in find dialog box works for both
4896 sequence ID and sequence string and query strings do not
4897 have to be in upper case to match case-insensitively.</li>
4898 <li>AMSA files only contain first column of
4899 multi-character column annotation labels</li>
4900 <li>Jalview Annotation File generation/parsing consistent
4901 with documentation (e.g. Stockholm annotation can be
4902 exported and re-imported)</li>
4903 <li>PDB files without embedded PDB IDs given a friendly
4905 <li>Find incrementally searches ID string matches as well
4906 as subsequence matches, and correctly reports total number
4910 <li>Better handling of exceptions during sequence
4912 <li>Dasobert generated non-positional feature URL
4913 link text excludes the start_end suffix</li>
4914 <li>DAS feature and source retrieval buttons disabled
4915 when fetch or registry operations in progress.</li>
4916 <li>PDB files retrieved from URLs are cached properly</li>
4917 <li>Sequence description lines properly shared via
4919 <li>Sequence fetcher fetches multiple records for all
4921 <li>Ensured that command line das feature retrieval
4922 completes before alignment figures are generated.</li>
4923 <li>Reduced time taken when opening file browser for
4925 <li>isAligned check prior to calculating tree, PCA or
4926 submitting an MSA to JNet now excludes hidden sequences.</li>
4927 <li>User defined group colours properly recovered
4928 from Jalview projects.</li>
4937 <div align="center">
4938 <strong>2.4.0.b2</strong><br> 28/10/2009
4943 <li>Experimental support for google analytics usage
4945 <li>Jalview privacy settings (user preferences and docs).</li>
4950 <li>Race condition in applet preventing startup in
4952 <li>Exception when feature created from selection beyond
4953 length of sequence.</li>
4954 <li>Allow synthetic PDB files to be imported gracefully</li>
4955 <li>Sequence associated annotation rows associate with
4956 all sequences with a given id</li>
4957 <li>Find function matches case-insensitively for sequence
4958 ID string searches</li>
4959 <li>Non-standard characters do not cause pairwise
4960 alignment to fail with exception</li>
4961 </ul> <em>Application Issues</em>
4963 <li>Sequences are now validated against EMBL database</li>
4964 <li>Sequence fetcher fetches multiple records for all
4966 </ul> <em>InstallAnywhere Issues</em>
4968 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4969 issue with installAnywhere mechanism)</li>
4970 <li>Command line launching of JARs from InstallAnywhere
4971 version (java class versioning error fixed)</li>
4978 <div align="center">
4979 <strong>2.4</strong><br> 27/8/2008
4982 <td><em>User Interface</em>
4984 <li>Linked highlighting of codon and amino acid from
4985 translation and protein products</li>
4986 <li>Linked highlighting of structure associated with
4987 residue mapping to codon position</li>
4988 <li>Sequence Fetcher provides example accession numbers
4989 and 'clear' button</li>
4990 <li>MemoryMonitor added as an option under Desktop's
4992 <li>Extract score function to parse whitespace separated
4993 numeric data in description line</li>
4994 <li>Column labels in alignment annotation can be centred.</li>
4995 <li>Tooltip for sequence associated annotation give name
4997 </ul> <em>Web Services and URL fetching</em>
4999 <li>JPred3 web service</li>
5000 <li>Prototype sequence search client (no public services
5002 <li>Fetch either seed alignment or full alignment from
5004 <li>URL Links created for matching database cross
5005 references as well as sequence ID</li>
5006 <li>URL Links can be created using regular-expressions</li>
5007 </ul> <em>Sequence Database Connectivity</em>
5009 <li>Retrieval of cross-referenced sequences from other
5011 <li>Generalised database reference retrieval and
5012 validation to all fetchable databases</li>
5013 <li>Fetch sequences from DAS sources supporting the
5014 sequence command</li>
5015 </ul> <em>Import and Export</em>
5016 <li>export annotation rows as CSV for spreadsheet import</li>
5017 <li>Jalview projects record alignment dataset associations,
5018 EMBL products, and cDNA sequence mappings</li>
5019 <li>Sequence Group colour can be specified in Annotation
5021 <li>Ad-hoc colouring of group in Annotation File using RGB
5022 triplet as name of colourscheme</li>
5023 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
5025 <li>treenode binding for VAMSAS tree exchange</li>
5026 <li>local editing and update of sequences in VAMSAS
5027 alignments (experimental)</li>
5028 <li>Create new or select existing session to join</li>
5029 <li>load and save of vamsas documents</li>
5030 </ul> <em>Application command line</em>
5032 <li>-tree parameter to open trees (introduced for passing
5034 <li>-fetchfrom command line argument to specify nicknames
5035 of DAS servers to query for alignment features</li>
5036 <li>-dasserver command line argument to add new servers
5037 that are also automatically queried for features</li>
5038 <li>-groovy command line argument executes a given groovy
5039 script after all input data has been loaded and parsed</li>
5040 </ul> <em>Applet-Application data exchange</em>
5042 <li>Trees passed as applet parameters can be passed to
5043 application (when using "View in full
5044 application")</li>
5045 </ul> <em>Applet Parameters</em>
5047 <li>feature group display control parameter</li>
5048 <li>debug parameter</li>
5049 <li>showbutton parameter</li>
5050 </ul> <em>Applet API methods</em>
5052 <li>newView public method</li>
5053 <li>Window (current view) specific get/set public methods</li>
5054 <li>Feature display control methods</li>
5055 <li>get list of currently selected sequences</li>
5056 </ul> <em>New Jalview distribution features</em>
5058 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
5059 <li>RELEASE file gives build properties for the latest
5060 Jalview release.</li>
5061 <li>Java 1.1 Applet build made easier and donotobfuscate
5062 property controls execution of obfuscator</li>
5063 <li>Build target for generating source distribution</li>
5064 <li>Debug flag for javacc</li>
5065 <li>.jalview_properties file is documented (slightly) in
5066 jalview.bin.Cache</li>
5067 <li>Continuous Build Integration for stable and
5068 development version of Application, Applet and source
5073 <li>selected region output includes visible annotations
5074 (for certain formats)</li>
5075 <li>edit label/displaychar contains existing label/char
5077 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
5078 <li>shorter peptide product names from EMBL records</li>
5079 <li>Newick string generator makes compact representations</li>
5080 <li>bootstrap values parsed correctly for tree files with
5082 <li>pathological filechooser bug avoided by not allowing
5083 filenames containing a ':'</li>
5084 <li>Fixed exception when parsing GFF files containing
5085 global sequence features</li>
5086 <li>Alignment datasets are finalized only when number of
5087 references from alignment sequences goes to zero</li>
5088 <li>Close of tree branch colour box without colour
5089 selection causes cascading exceptions</li>
5090 <li>occasional negative imgwidth exceptions</li>
5091 <li>better reporting of non-fatal warnings to user when
5092 file parsing fails.</li>
5093 <li>Save works when Jalview project is default format</li>
5094 <li>Save as dialog opened if current alignment format is
5095 not a valid output format</li>
5096 <li>UniProt canonical names introduced for both das and
5098 <li>Histidine should be midblue (not pink!) in Zappo</li>
5099 <li>error messages passed up and output when data read
5101 <li>edit undo recovers previous dataset sequence when
5102 sequence is edited</li>
5103 <li>allow PDB files without pdb ID HEADER lines (like
5104 those generated by MODELLER) to be read in properly</li>
5105 <li>allow reading of JPred concise files as a normal
5107 <li>Stockholm annotation parsing and alignment properties
5108 import fixed for PFAM records</li>
5109 <li>Structure view windows have correct name in Desktop
5111 <li>annotation consisting of sequence associated scores
5112 can be read and written correctly to annotation file</li>
5113 <li>Aligned cDNA translation to aligned peptide works
5115 <li>Fixed display of hidden sequence markers and
5116 non-italic font for representatives in Applet</li>
5117 <li>Applet Menus are always embedded in applet window on
5119 <li>Newly shown features appear at top of stack (in
5121 <li>Annotations added via parameter not drawn properly
5122 due to null pointer exceptions</li>
5123 <li>Secondary structure lines are drawn starting from
5124 first column of alignment</li>
5125 <li>UniProt XML import updated for new schema release in
5127 <li>Sequence feature to sequence ID match for Features
5128 file is case-insensitive</li>
5129 <li>Sequence features read from Features file appended to
5130 all sequences with matching IDs</li>
5131 <li>PDB structure coloured correctly for associated views
5132 containing a sub-sequence</li>
5133 <li>PDB files can be retrieved by applet from Jar files</li>
5134 <li>feature and annotation file applet parameters
5135 referring to different directories are retrieved correctly</li>
5136 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
5137 <li>Fixed application hang whilst waiting for
5138 splash-screen version check to complete</li>
5139 <li>Applet properly URLencodes input parameter values
5140 when passing them to the launchApp service</li>
5141 <li>display name and local features preserved in results
5142 retrieved from web service</li>
5143 <li>Visual delay indication for sequence retrieval and
5144 sequence fetcher initialisation</li>
5145 <li>updated Application to use DAS 1.53e version of
5146 dasobert DAS client</li>
5147 <li>Re-instated Full AMSA support and .amsa file
5149 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
5157 <div align="center">
5158 <strong>2.3</strong><br> 9/5/07
5163 <li>Jmol 11.0.2 integration</li>
5164 <li>PDB views stored in Jalview XML files</li>
5165 <li>Slide sequences</li>
5166 <li>Edit sequence in place</li>
5167 <li>EMBL CDS features</li>
5168 <li>DAS Feature mapping</li>
5169 <li>Feature ordering</li>
5170 <li>Alignment Properties</li>
5171 <li>Annotation Scores</li>
5172 <li>Sort by scores</li>
5173 <li>Feature/annotation editing in applet</li>
5178 <li>Headless state operation in 2.2.1</li>
5179 <li>Incorrect and unstable DNA pairwise alignment</li>
5180 <li>Cut and paste of sequences with annotation</li>
5181 <li>Feature group display state in XML</li>
5182 <li>Feature ordering in XML</li>
5183 <li>blc file iteration selection using filename # suffix</li>
5184 <li>Stockholm alignment properties</li>
5185 <li>Stockhom alignment secondary structure annotation</li>
5186 <li>2.2.1 applet had no feature transparency</li>
5187 <li>Number pad keys can be used in cursor mode</li>
5188 <li>Structure Viewer mirror image resolved</li>
5195 <div align="center">
5196 <strong>2.2.1</strong><br> 12/2/07
5201 <li>Non standard characters can be read and displayed
5202 <li>Annotations/Features can be imported/exported to the
5204 <li>Applet allows editing of sequence/annotation/group
5205 name & description
5206 <li>Preference setting to display sequence name in
5208 <li>Annotation file format extended to allow
5209 Sequence_groups to be defined
5210 <li>Default opening of alignment overview panel can be
5211 specified in preferences
5212 <li>PDB residue numbering annotation added to associated
5218 <li>Applet crash under certain Linux OS with Java 1.6
5220 <li>Annotation file export / import bugs fixed
5221 <li>PNG / EPS image output bugs fixed
5227 <div align="center">
5228 <strong>2.2</strong><br> 27/11/06
5233 <li>Multiple views on alignment
5234 <li>Sequence feature editing
5235 <li>"Reload" alignment
5236 <li>"Save" to current filename
5237 <li>Background dependent text colour
5238 <li>Right align sequence ids
5239 <li>User-defined lower case residue colours
5242 <li>Menu item accelerator keys
5243 <li>Control-V pastes to current alignment
5244 <li>Cancel button for DAS Feature Fetching
5245 <li>PCA and PDB Viewers zoom via mouse roller
5246 <li>User-defined sub-tree colours and sub-tree selection
5249 <li>'New Window' button on the 'Output to Text box'
5254 <li>New memory efficient Undo/Redo System
5255 <li>Optimised symbol lookups and conservation/consensus
5257 <li>Region Conservation/Consensus recalculated after
5259 <li>Fixed Remove Empty Columns Bug (empty columns at end
5261 <li>Slowed DAS Feature Fetching for increased robustness.
5264 <li>Made angle brackets in ASCII feature descriptions
5266 <li>Re-instated Zoom function for PCA
5267 <li>Sequence descriptions conserved in web service
5269 <li>UniProt ID discoverer uses any word separated by
5271 <li>WsDbFetch query/result association resolved
5272 <li>Tree leaf to sequence mapping improved
5273 <li>Smooth fonts switch moved to FontChooser dialog box.
5281 <div align="center">
5282 <strong>2.1.1</strong><br> 12/9/06
5287 <li>Copy consensus sequence to clipboard</li>
5292 <li>Image output - rightmost residues are rendered if
5293 sequence id panel has been resized</li>
5294 <li>Image output - all offscreen group boundaries are
5296 <li>Annotation files with sequence references - all
5297 elements in file are relative to sequence position</li>
5298 <li>Mac Applet users can use Alt key for group editing</li>
5304 <div align="center">
5305 <strong>2.1</strong><br> 22/8/06
5310 <li>MAFFT Multiple Alignment in default Web Service list</li>
5311 <li>DAS Feature fetching</li>
5312 <li>Hide sequences and columns</li>
5313 <li>Export Annotations and Features</li>
5314 <li>GFF file reading / writing</li>
5315 <li>Associate structures with sequences from local PDB
5317 <li>Add sequences to exisiting alignment</li>
5318 <li>Recently opened files / URL lists</li>
5319 <li>Applet can launch the full application</li>
5320 <li>Applet has transparency for features (Java 1.2
5322 <li>Applet has user defined colours parameter</li>
5323 <li>Applet can load sequences from parameter
5324 "sequence<em>x</em>"
5330 <li>Redundancy Panel reinstalled in the Applet</li>
5331 <li>Monospaced font - EPS / rescaling bug fixed</li>
5332 <li>Annotation files with sequence references bug fixed</li>
5338 <div align="center">
5339 <strong>2.08.1</strong><br> 2/5/06
5344 <li>Change case of selected region from Popup menu</li>
5345 <li>Choose to match case when searching</li>
5346 <li>Middle mouse button and mouse movement can compress /
5347 expand the visible width and height of the alignment</li>
5352 <li>Annotation Panel displays complete JNet results</li>
5358 <div align="center">
5359 <strong>2.08b</strong><br> 18/4/06
5365 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
5366 <li>Righthand label on wrapped alignments shows correct
5373 <div align="center">
5374 <strong>2.08</strong><br> 10/4/06
5379 <li>Editing can be locked to the selection area</li>
5380 <li>Keyboard editing</li>
5381 <li>Create sequence features from searches</li>
5382 <li>Precalculated annotations can be loaded onto
5384 <li>Features file allows grouping of features</li>
5385 <li>Annotation Colouring scheme added</li>
5386 <li>Smooth fonts off by default - Faster rendering</li>
5387 <li>Choose to toggle Autocalculate Consensus On/Off</li>
5392 <li>Drag & Drop fixed on Linux</li>
5393 <li>Jalview Archive file faster to load/save, sequence
5394 descriptions saved.</li>
5400 <div align="center">
5401 <strong>2.07</strong><br> 12/12/05
5406 <li>PDB Structure Viewer enhanced</li>
5407 <li>Sequence Feature retrieval and display enhanced</li>
5408 <li>Choose to output sequence start-end after sequence
5409 name for file output</li>
5410 <li>Sequence Fetcher WSDBFetch@EBI</li>
5411 <li>Applet can read feature files, PDB files and can be
5412 used for HTML form input</li>
5417 <li>HTML output writes groups and features</li>
5418 <li>Group editing is Control and mouse click</li>
5419 <li>File IO bugs</li>
5425 <div align="center">
5426 <strong>2.06</strong><br> 28/9/05
5431 <li>View annotations in wrapped mode</li>
5432 <li>More options for PCA viewer</li>
5437 <li>GUI bugs resolved</li>
5438 <li>Runs with -nodisplay from command line</li>
5444 <div align="center">
5445 <strong>2.05b</strong><br> 15/9/05
5450 <li>Choose EPS export as lineart or text</li>
5451 <li>Jar files are executable</li>
5452 <li>Can read in Uracil - maps to unknown residue</li>
5457 <li>Known OutOfMemory errors give warning message</li>
5458 <li>Overview window calculated more efficiently</li>
5459 <li>Several GUI bugs resolved</li>
5465 <div align="center">
5466 <strong>2.05</strong><br> 30/8/05
5471 <li>Edit and annotate in "Wrapped" view</li>
5476 <li>Several GUI bugs resolved</li>
5482 <div align="center">
5483 <strong>2.04</strong><br> 24/8/05
5488 <li>Hold down mouse wheel & scroll to change font
5494 <li>Improved JPred client reliability</li>
5495 <li>Improved loading of Jalview files</li>
5501 <div align="center">
5502 <strong>2.03</strong><br> 18/8/05
5507 <li>Set Proxy server name and port in preferences</li>
5508 <li>Multiple URL links from sequence ids</li>
5509 <li>User Defined Colours can have a scheme name and added
5511 <li>Choose to ignore gaps in consensus calculation</li>
5512 <li>Unix users can set default web browser</li>
5513 <li>Runs without GUI for batch processing</li>
5514 <li>Dynamically generated Web Service Menus</li>
5519 <li>InstallAnywhere download for Sparc Solaris</li>
5525 <div align="center">
5526 <strong>2.02</strong><br> 18/7/05
5532 <li>Copy & Paste order of sequences maintains
5533 alignment order.</li>
5539 <div align="center">
5540 <strong>2.01</strong><br> 12/7/05
5545 <li>Use delete key for deleting selection.</li>
5546 <li>Use Mouse wheel to scroll sequences.</li>
5547 <li>Help file updated to describe how to add alignment
5549 <li>Version and build date written to build properties
5551 <li>InstallAnywhere installation will check for updates
5552 at launch of Jalview.</li>
5557 <li>Delete gaps bug fixed.</li>
5558 <li>FileChooser sorts columns.</li>
5559 <li>Can remove groups one by one.</li>
5560 <li>Filechooser icons installed.</li>
5561 <li>Finder ignores return character when searching.
5562 Return key will initiate a search.<br>
5569 <div align="center">
5570 <strong>2.0</strong><br> 20/6/05
5575 <li>New codebase</li>