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 */
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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>3/03/2022</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-3881 -->Sequence IDs split on '_' as well as other
104 non-alphanumerics when discovering database references with
108 <!-- JAL-3884 -->Suppressed harmless exceptions output to
109 Console whilst discovering database references for a
113 <!-- JAL-3204 -->Updated Jalview bindings for Uniprot XML
117 <!-- JAL-3926 -->Uniprot and PDBe autosearch option is
121 <!-- JAL-3530 -->-nowebservicediscovery command line
122 argument to prevent automatic discovery of analysis
123 webservices on launch
126 <!-- JAL-3618 -->Allow 'App' directories to be opened when
127 locating Chimera, ChimeraX or Pymol binaries via filechooser
128 opened by double clicking the Structure Preferences' path
132 <!-- JAL-3632 JAL-3633 -->support for HTTP/S access via
133 proxies that require authentication
136 <!-- JAL-3103 -->New mechanism for opening URLs with system
137 default browser (works on OSX and Linux as well as Windows)
140 <!-- JAL-3837 -->GPL license info on splash screen and About
144 <em>Jalview Native App</em>
147 <!-- JAL- -->New Jalview Develop app - making it even easier
148 to get at Jalview's development builds
151 <!-- JAL-3594 -->New splashscreens for Jalview, Jalview Test
152 and Jalview Develop applications.
155 <!-- JAL-3728 -->Jalview logos shown for Jalview Java
156 Console and other window widgets in taskbar and dock rather
157 than anonymous 'Java' icons
160 <!-- JAL-3608 -->Options to allow user to choose the (Swing) Look and Feel (LaF) used by Jalview
163 <!-- JAL-3552, JAL-3609 -->Metal LaF used to improved operation on Linux Ubuntu with
164 HiDPI display in Java 11 (still known issues with HiDPI screens in java
166 href="https://issues.jalview.org/browse/JAL-3137">JAL-3137</a>)
169 <!-- JAL-3830 -->New command line launcher scripts (.sh, .ps1, .bat) usable on
170 macOS, Linux/Unix, Windows and documentation in Help. Installer wizard has option
171 to add this to PATH, or link to it in your PATH.
174 <!-- JAL-3633 -->Getdown launcher inherits HTTP/S proxy
175 configuration from jalview_properties
177 </ul> <em>JalviewJS</em>
180 <!-- JAL-3624 -->PDB structures mapped to Uniprot Sequences with
184 <!-- JAL-3208 -->setprop commandline argument reinstated for JalviewJS only
187 <!-- JAL-3163 -->Missing message bundle keys are only
188 reported once per key (avoids excessive log output in js
192 <!-- JAL-3168 -->Feature type is included in the title of
193 the Feature Settings' Colour Chooser dialog
196 </ul> <em>Development</em>
199 <!-- -->First integrated JalviewJS and Jalview release
201 <li>Updated building instructions</li>
203 <!-- JAL-3789, JAL-3679 -->Improved JalviewJS/Jalview build
204 process, added support for system package provided eclipse
207 <li>Install4j 9.0.x used for installer packaging</li>
208 <li>Notarized MacOS installer for compatibility with Big
209 Sur and Monterey</li>
211 <!-- JAL-3805 -->Uninstaller application for old
212 (InstallAnywhere based) Jalview installations removed from
216 <!-- JAL-3930 -->Improved use of installers for unattended
217 installation with a customizedId of "JALVIEW" in install4j's
221 <!-- JAL-3907 -->Improved compatibility of Jalview build
222 with Java 17 (next LTS target)
231 <!-- JAL-3674 -->Slow structure commands can block Jalview
235 <!-- JAL-3904 -->Structure window's viewer-specific menu
236 disappears when only one structure is shown (and many
237 sequences:one chain mappings are present)
240 <!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
241 the first SEQUENCE_GROUP defined
246 <!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 -->Selections not
247 propagated between Linked CDS - Protein alignments and their
248 trees (known defect from 2.11.1.3)
251 <!-- JAL-3761 -->Not all codon positions highlighted for
252 overlapping exon splice sites (e.g due to RNA slippage)
255 <!-- JAL-3794 -->X was not being recognised as the unknown
256 base in DNA sequences
259 <!-- JAL-3915 -->Removed RNAview checkbox and logic from
260 Structure Preferences
263 <!-- JAL-3583 -->Tooltip behaviour improved (slightly)
266 <!-- JAL-3162 -->Can edit a feature so that start > end
269 <!-- JAL-2848 -->Cancel from Amend Features doesn't reset a
270 modified graduated colour
273 <!-- JAL-3788 -->New View with automatic 'Show Overview'
274 preference enabled results in Null Pointer Exceptions when
275 clustal colouring is enabled
278 <!-- JAL-3275 -->Can open multiple Preferences panels
281 <!-- JAL-3633 -->Properly configure HTTPS proxy settings
285 <!-- JAL-3949 -->Standard out logging broken: messages only
286 routing to stderr and appear as a raw template
288 </ul> <em>JalviewJS</em>
291 <!-- JAL-3202 -->Consensus profile may include zero (rounded
292 down) percentage values causing a divide by zero
307 <!-- JAL-3762 -->JalviewJS doesn't honour arguments passed
308 via Info.args when there are arguments on the URL
311 <!-- JAL-3602 -->gradle closure-compiler not using UTF-8
314 <!-- JAL-3603 -->Annotation file fails to load from URL in
317 </ul> <em>Development</em>
321 <li>Fixed non-fatal gradle errors during build</li>
323 <!-- JAL-3745 -->Updated build.gradle for use with
330 <em>Known Issues</em>
333 <!-- JAL-3764 -->Display of RESNUM sequence features are not
334 suppressed when structures associated with a sequence are
335 viewed with an external viewer (Regression from 2.11.1 series)
341 <td width="60" align="center" nowrap><strong><a
342 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.7">.7</a><br />
343 <em>18/01/2022</em></strong></td>
345 <td align="left" valign="top">
348 <!-- JAL-3703, JAL-3935 -->Files open in Jalview cannot be
349 updated by Jalview or other applications (Windows, other non
352 </ul> <em>Security</em>
355 <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
361 <td width="60" align="center" nowrap><strong><a
362 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
363 <em>6/01/2022</em></strong></td>
365 <td align="left" valign="top"><em>Security</em>
368 <!-- JAL-3934 -->Version bump library dependency: Log4j
375 <td width="60" align="center" nowrap><strong><a
376 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
377 <em>20/12/2021</em></strong></td>
379 <td align="left" valign="top"><em>Security</em>
382 <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
384 </ul> <em>Development</em>
386 <li>Updated building instructions</li>
391 <!-- JAL-3840 -->Occupancy calculation is incorrect for
392 alignment columns with over -1+2^32 gaps (breaking filtering
396 <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
397 scale factors being set with buggy window-managers (linux
400 </ul> <em>Development</em>
402 <li>Fixed non-fatal gradle errors during build</li>
407 <td width="60" align="center" nowrap><strong><a
408 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
409 <em>09/03/2021</em></strong></td>
410 <td align="left" valign="top"><em>Improved control of
411 Jalview's use of network services via jalview_properties</em>
414 <!-- JAL-3814 -->New .jalview_properties token controlling
415 launch of the news browser (like -nonews argument)
418 <!-- JAL-3813 -->New .jalview_properties token controlling
419 download of linkout URLs from
420 www.jalview.org/services/identifiers
423 <!-- JAL-3812 -->New .jalview_properties token controlling
424 download of BIOJSHTML templates
427 <!-- JAL-3811 -->New 'Discover Web Services' option to
428 trigger a one off JABAWS discovery if autodiscovery was
432 <td align="left" valign="top">
435 <!-- JAL-3818 -->Intermittent deadlock opening structure in
438 </ul> <em>New Known defects</em>
441 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
442 always restored from project (since 2.10.3)
445 <!-- JAL-3806 -->Selections from tree built from CDS aren't
446 propagated to Protein alignment (since 2.11.1.3)
452 <td width="60" align="center" nowrap><strong><a
453 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
454 <em>29/10/2020</em></strong></td>
455 <td align="left" valign="top">
460 <td align="left" valign="top">
463 <!-- JAL-3765 -->Find doesn't always highlight all matching
464 positions in a sequence (bug introduced in 2.11.1.2)
467 <!-- JAL-3760 -->Alignments containing one or more protein
468 sequences can be classed as nucleotide
471 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
472 sequences after alignment of protein products (known defect
473 first reported for 2.11.1.0)
476 <!-- JAL-3725 -->No tooltip or popup menu for genomic
477 features outwith CDS shown overlaid on protein
480 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
481 correctly mapped by Jalview (e.g. affects viral CDS with
482 ribosomal slippage, since 2.9.0)
485 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
489 <!-- JAL-3700 -->Selections in CDS sequence panel don't
490 always select corresponding protein sequences
493 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
494 column selection doesn't always ignore hidden columns
496 </ul> <em>Installer</em>
499 <!-- JAL-3611 -->Space character in Jalview install path on
500 Windows prevents install4j launching getdown
502 </ul> <em>Development</em>
505 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
506 version numbers in doc/building.md
512 <td width="60" align="center" nowrap><strong><a
513 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
514 <em>25/09/2020</em></strong></td>
515 <td align="left" valign="top">
519 <td align="left" valign="top">
522 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
523 "Encountered problems opening
524 https://www.jalview.org/examples/exampleFile_2_7.jvp"
530 <td width="60" align="center" nowrap><strong><a
531 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
532 <em>17/09/2020</em></strong></td>
533 <td align="left" valign="top">
536 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
537 residue in cursor mode
540 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
541 HTSJDK from 2.12 to 2.23
544 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
545 optimisations and improvements suggested by Bob Hanson and
546 improved compatibility with JalviewJS
549 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
550 alignments from Pfam and Rfam
553 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
554 import (no longer based on .gz extension)
557 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
560 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
561 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
565 <!-- JAL-3667 -->Improved warning messages, debug logging
566 and fixed Retry action when Jalview encounters errors when
567 saving or making backup files.
570 <!-- JAL-3676 -->Enhanced Jalview Java Console:
572 <li>Jalview's logging level can be configured</li>
573 <li>Copy to Clipboard Buttion</li>
577 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
578 when running on Linux (Requires Java 11+)
581 <!-- JAL-1842 JAL-3509 -->RESNUM sequence features (the
582 green ones) are not automatically displayed when associated
583 structures are displayed or for sequences retrieved from the
586 </ul> <em>Launching Jalview</em>
589 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
590 through a system property
593 <!-- JAL-3477 -->Improved built-in documentation and command
594 line help for configuring Jalview's memory
598 <td align="left" valign="top">
601 <!-- JAL-3691 -->Conservation and Quality tracks are shown
602 but not calculated and no protein or DNA score models are
603 available for tree/PCA calculation when launched with
604 Turkish language locale
607 <!-- JAL-3493 -->Escape does not clear highlights on the
608 alignment (Since Jalview 2.10.3)
611 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
612 doesn't slide selected sequences, just sequence under cursor
615 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
616 sequence under the cursor
619 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
620 multiple EMBL gene products shown for a single contig
623 <!-- JAL-3696 -->Errors encountered when processing variants
624 from VCF files yield "Error processing VCF: Format specifier
628 <!-- JAL-3697 -->Count of features not shown can be wrong
629 when there are both local and complementary features mapped
630 to the position under the cursor
633 <!-- JAL-3673 -->Sequence ID for reference sequence is
634 clipped when Right align Sequence IDs enabled
637 <!-- JAL-2983 -->Slider with negative range values not
638 rendered correctly in VAqua4 (Since 2.10.4)
641 <!-- JAL-3685 -->Single quotes not displayed correctly in
642 internationalised text for some messages and log output
645 <!-- JAL-3490 -->Find doesn't report matches that span
646 hidden gapped columns
649 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
650 panels, Alignment viewport and annotation renderer.
653 <!-- JAL-3561 -->Jalview ignores file format parameter
654 specifying output format when exporting an alignment via the
658 <!-- JAL-3667 -->Windows 10: For a minority of users, if
659 backups are not enabled, Jalview sometimes fails to
660 overwrite an existing file and raises a warning dialog. (in
661 2.11.0, and 2.11.1.0, the workaround is to try to save the
662 file again, and if that fails, delete the original file and
666 <!-- JAL-3509 -->Dragging a PDB file onto an alignment with
667 sequence features displayed causes displayed features to be
671 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
675 <!-- JAL-3741 -->References to http://www.jalview.org in
676 program and documentation
678 </ul> <em>Launching Jalview</em>
681 <!-- JAL-3718 -->Jalview application fails when launched the
682 first time for a version that has different jars to the
683 previous launched version.
685 </ul> <em>Developing Jalview</em>
688 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
689 data, causing cloverReport gradle task to fail with an
693 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
694 monitor the release channel
696 </ul> <em>New Known defects</em>
699 <!-- JAL-3748 -->CDS shown in result of submitting proteins
700 in a CDS/Protein alignment to a web service is wrong when
701 proteins share a common transcript sequence (e.g. genome of
705 <!-- JAL-3576 -->Co-located features exported and
706 re-imported are ordered differently when shown on alignment
707 and in tooltips. (Also affects v2.11.1.0)
710 <!-- JAL-3702 -->Drag and drop of alignment file onto
711 alignment window when in a HiDPI scaled mode in Linux only
712 works for the top left quadrant of the alignment window
715 <!-- JAL-3701 -->Stale build data in jalview standalone jar
716 builds (only affects 2.11.1.1 branch)
719 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
720 when alignment view restored from project (since Jalview
724 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
725 protein products for certain ENA records are repeatedly
726 shown via Calculate->Show Cross Refs
732 <td width="60" align="center" nowrap><strong><a
733 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
734 <em>22/04/2020</em></strong></td>
735 <td align="left" valign="top">
738 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
739 'virtual' codon features shown on protein (or vice versa)
740 for display in alignments, on structure views (including
741 transfer to UCSF chimera), in feature reports and for
745 <!-- JAL-3121 -->Feature attributes from VCF files can be
746 exported and re-imported as GFF3 files
749 <!-- JAL-3376 -->Capture VCF "fixed column" values
750 POS, ID, QUAL, FILTER as Feature Attributes
753 <!-- JAL-3375 -->More robust VCF numeric data field
754 validation while parsing
757 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
761 <!-- JAL-3535 -->Feature Settings dialog title includes name
765 <!-- JAL-3538 -->Font anti-aliasing in alignment views
769 <!-- JAL-3468 -->Very long feature descriptions truncated in
773 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
774 with no feature types visible
777 <!-- JAL-3574 -->Improved support for filtering feature
778 attributes with large integer values
781 <em>Jalview Installer</em>
784 <!-- JAL-3449 -->Versions for install4j and getdown and
785 installer template version reported in console (may be null
786 when Jalview launched as executable jar or via conda)
789 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and
790 higher quality background images
793 <!-- JAL-3394 -->New installer/application launcher
794 generated with install4j 8.0.4
797 <!-- JAL-3420 -->Jalview File Associations shown for Unix
801 <!-- JAL-3477 -->Improved defaults for maximum memory
802 setting when running on large memory machines
804 </ul> <em>Release processes</em>
807 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
810 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier
811 access to test-release channel builds
813 </ul> <em>Build System</em>
816 <!-- JAL-3510 -->Clover updated to 4.4.1
819 <!-- JAL-3513 -->Test code included in Clover coverage
822 </ul> <em>Groovy Scripts</em>
825 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
826 to stdout containing the consensus sequence for each
827 alignment in a Jalview session
830 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
831 genomic sequence_variant annotation from CDS as
832 missense_variant or synonymous_variant on protein products.
836 <td align="left" valign="top">
839 <!-- JAL-3581 -->Hidden sequence markers still visible when
840 'Show hidden markers' option is not ticked
843 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
844 PNG output when 'Automatically set ID width' is set in
845 jalview preferences or properties file
848 <!-- JAL-3571 -->Feature Editor dialog can be opened when
849 'Show Sequence Features' option is not ticked
852 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
853 buttons in Feature Settings dialog are clicked when no
857 <!-- JAL-3412 -->ID margins for CDS and Protein views not
858 equal when split frame is first opened
861 <!-- JAL-3296 -->Sequence position numbers in status bar not
862 correct after editing a sequence's start position
865 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
866 with annotation and exceptions thrown when only a few
867 columns shown in wrapped mode
870 <!-- JAL-3386 -->Sequence IDs missing in headless export of
871 wrapped alignment figure with annotations
874 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
875 ID fails with ClassCastException
878 <!-- JAL-3389 -->Chimera session not restored from Jalview
882 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
883 feature settings dialog also selects columns
886 <!-- JAL-3473 -->SpinnerNumberModel causes
887 IllegalArgumentException in some circumstances
890 <!-- JAL-3534 -->Multiple feature settings dialogs can be
894 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
895 alignment window is closed
898 <!-- JAL-3406 -->Credits missing some authors in Jalview
899 help documentation for 2.11.0 release
902 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
903 includes Pfam ID as sequence's accession rather than its
906 </ul> <em>Java 11 Compatibility issues</em>
909 <!-- JAL-2987 -->OSX - Can't view some search results in
910 PDB/Uniprot search panel
912 </ul> <em>Installer</em>
915 <!-- JAL-3447 -->Jalview should not create file associations
916 for 3D structure files (.pdb, .mmcif. .cif)
918 </ul> <em>Repository and Source Release</em>
921 <!-- JAL-3474 -->removed obsolete .cvsignore files from
925 <!-- JAL-3541 -->Clover report generation running out of
928 </ul> <em>New Known Issues</em>
931 <!-- JAL-3523 -->OSX - Current working directory not
932 preserved when Jalview.app launched with parameters from
936 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
937 clipped in headless figure export when Right Align option
941 <!-- JAL-3542 -->Jalview Installation type always reports
942 'Source' in console output
945 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail
946 on jalview's bamboo server but run fine locally.
952 <td width="60" align="center" nowrap><strong><a
953 name="Jalview.2.11.0">2.11.0</a><br /> <em>04/07/2019</em></strong></td>
954 <td align="left" valign="top">
957 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native
958 Application and Installers built with <a
959 href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a>
960 (licensed to the Jalview open source project) rather than
964 <!-- JAL-1929 -->Jalview Launcher System to auto-configure
965 memory settings, receive over the air updates and launch
966 specific versions via (<a
967 href="https://github.com/threerings/getdown">Three
971 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations
972 for formats supported by Jalview (including .jvp project
976 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command
977 line arguments and switch between different getdown channels
980 <!-- JAL-3141 -->Backup files created when saving Jalview
981 project or alignment files
985 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF
989 <!-- JAL-2753 -->Version of HTSJDK shipped with Jalview
990 updated to version 2.12.0
993 <!-- JAL-2620 -->Alternative genetic code tables for
997 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0
999 <li><strong>Enhanced visualisation and analysis
1000 of Sequence Features</strong>
1003 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
1004 implementation that allows updates) used for Sequence
1008 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
1009 features can be filtered and shaded according to any
1010 associated attributes (e.g. variant attributes from VCF
1011 file, or key-value pairs imported from column 9 of GFF
1015 <!-- JAL-2879 -->Feature Attributes and shading schemes
1016 stored and restored from Jalview Projects
1019 <!-- JAL-3334 -->Use full Sequence Ontology (via
1020 BioJava) to recognise variant features
1023 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants
1024 on peptide sequences (also coloured red by default)
1027 <!-- JAL-2792 -->Popup window to show full report for a
1028 selected sequence feature's details
1031 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient
1032 sequence feature render algorithm (Z-sort/transparency
1036 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature
1041 <!-- JAL-3205 -->Symmetric score matrices for faster tree
1042 and PCA calculations
1044 <li><strong>Principal Components Analysis Viewer</strong>
1047 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis
1048 results and Viewer state saved in Jalview Project
1051 <!-- JAL-2962 -->'Change parameters' option removed from
1052 viewer's drop-down menus
1055 <!-- JAL-2975 -->Can use shift + arrow keys to rotate
1056 PCA image incrementally
1059 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
1063 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
1065 <li><strong>Speed and Efficiency</strong>
1068 <!-- JAL-2185,JAL-3198 -->More efficient creation of
1069 selections and multiple groups when working with large
1073 <!-- JAL-3200 -->Speedier import of annotation rows when
1074 parsing Stockholm files
1077 <li><strong>User Interface</strong>
1080 <!-- JAL-2933 -->Finder panel remembers last position in
1084 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS
1085 (What you see is what is shown)<br />Only visible
1086 regions of alignment are shown by default (can be
1087 changed in user preferences)
1090 <!-- JAL-3169 -->File Chooser stays open after
1091 responding Cancel to the Overwrite Dialog
1094 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour
1095 when all sequences are hidden
1098 <!-- JAL-1244 -->Status bar shows bounds when dragging a
1099 selection region, and gap count when inserting or
1103 <!-- JAL-3132 -->Status bar updates over sequence and
1107 <!-- JAL-3093 -->Annotation tooltips and popup menus are
1108 shown when in wrapped mode
1111 <!-- JAL-3073 -->Can select columns by dragging
1112 left/right in a graph or histogram annotation
1115 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB
1119 <!-- JAL-2621 -->Cursor changes over draggable box in
1123 <!-- JAL-3181 -->Consistent ordering of links in
1124 sequence id popup menu
1127 <!-- JAL-3080 -->Red line indicating tree-cut position
1128 not shown if no subgroups are created
1131 <!-- JAL-3042 -->Removed ability to configure length of
1132 search history by right-clicking search box
1138 <!-- JAL-3232 -->Jalview Groovy Scripting Console updated to
1141 <li><strong>Java 11 Support (not yet on general
1145 <!-- -->OSX GUI integrations for App menu's 'About'
1146 entry and trapping CMD-Q
1149 </ul> <em>Deprecations</em>
1152 <!-- JAL-3035 -->DAS sequence retrieval and annotation
1153 capabilities removed from the Jalview Desktop
1156 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling
1157 and unmarshalling has been replaced by JAXB for Jalview
1158 projects and XML based data retrieval clients
1161 <!-- JAL-3311 -->Disable VAMSAS menu in preparation for
1165 <!-- -->Jalview Desktop no longer distributed via Java Web
1168 </ul> <em>Documentation</em>
1171 <!-- JAL-3003 -->Added remarks about transparent rendering
1172 effects not supported in EPS figure export
1175 <!-- JAL-2903 -->Typos in documentation for Preferences
1178 </ul> <em>Development and Release Processes</em>
1181 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated
1185 <!-- JAL-1424 -->Enhanced checks for missing and duplicated
1186 keys in Message bundles
1189 <!-- JAL-3225 -->Eclipse project configuration managed with
1193 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian Bamboo
1194 continuous integration for unattended Test Suite execution
1197 <!-- JAL-2864 -->Memory test suite to detect leaks in common
1201 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
1205 <!-- JAL-3248 -->Developer documentation migrated to
1206 markdown (with HTML rendering)
1209 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
1212 <!-- JAL-3289 -->New URLs for publishing development
1217 <td align="left" valign="top">
1220 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
1223 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
1224 superposition in Jmol fail on Windows
1227 <!-- JAL-3286 -->Blank error dialog is displayed when
1228 discovering structures for sequences with lots of PDB
1232 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export
1233 with monospaced font
1236 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
1237 Jalview project involving multiple views
1240 <!-- JAL-3164 -->Overview for complementary view in a linked
1241 CDS/Protein alignment is not updated when Hide Columns by
1242 Annotation dialog hides columns
1245 <!-- JAL-3158 -->Selection highlighting in the complement of
1246 a CDS/Protein alignment stops working after making a
1247 selection in one view, then making another selection in the
1251 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
1255 <!-- JAL-3154 -->Table Columns could be re-ordered in
1256 Feature Settings and Jalview Preferences panels
1259 <!-- JAL-2865 -->Jalview hangs when closing windows, or
1260 redrawing the overview with large alignments
1263 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
1264 region if columns were selected by dragging right-to-left
1265 and the mouse moved to the left of the first column
1268 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to
1269 a hidden column marker via scale popup menu
1272 <!-- JAL-2846 -->Error message for trying to load in invalid
1273 URLs doesn't tell users the invalid URL
1276 <!-- JAL-2816 -->Tooltips displayed for features filtered by
1280 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl
1281 during show cross references or Fetch Database References
1282 are shown in red in original view
1285 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown
1286 correctly on peptide sequence (computed variant shown as
1290 <!-- JAL-2060 -->'Graduated colour' option not offered for
1291 manually created features (where feature score is Float.NaN)
1294 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or
1295 printed when columns are hidden
1298 <!-- JAL-3082 -->Regular expression error for '(' in Select
1299 Columns by Annotation description
1302 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after
1303 dragging out of Scale or Annotation Panel
1306 <!-- JAL-3075 -->Column selection incorrect after scrolling
1310 <!-- JAL-3074 -->Left/right drag in annotation can scroll
1314 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal
1318 <!-- JAL-3002 -->Column display is out by one after Page
1319 Down, Page Up in wrapped mode
1322 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
1325 <!-- JAL-2932 -->Finder searches in minimised alignments
1328 <!-- JAL-2250 -->'Apply Colour to All Groups' not always
1329 selected on opening an alignment
1332 <!-- JAL-3180 -->'Colour by Annotation' not marked selected
1336 <!-- JAL-3201 -->Per-group Clustal colour scheme changes
1337 when different groups in the alignment are selected
1340 <!-- JAL-2717 -->Internationalised colour scheme names not
1341 shown correctly in menu
1344 <!-- JAL-3206 -->Colour by Annotation can go black at
1345 min/max threshold limit
1348 <!-- JAL-3125 -->Value input for graduated feature colour
1349 threshold gets 'unrounded'
1352 <!-- JAL-2982 -->PCA image export doesn't respect background
1356 <!-- JAL-2963 -->PCA points don't dim when rotated about y
1360 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
1363 <!-- JAL-3078 -->Cancel in Tree Font dialog resets
1364 alignment, not Tree font
1367 <!-- JAL-2964 -->Associate Tree with All Views not restored
1371 <!-- JAL-2915 -->Scrolling of split frame is sluggish if
1372 Overview shown in complementary view
1375 <!-- JAL-3313 -->Codon consensus incorrectly scaled when
1376 shown without normalisation
1379 <!-- JAL-3021 -->Sequence Details report should open
1380 positioned at top of report
1383 <!-- JAL-914 -->Help page can be opened twice
1386 <!-- JAL-3333 -->Fuzzy text in web service status menu on
1389 </ul> <em>Editing</em>
1392 <!-- JAL-2822 -->Start and End should be updated when
1393 sequence data at beginning or end of alignment added/removed
1397 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection
1398 doesn't relocate sequence features correctly when start of
1399 sequence is removed (Known defect since 2.10)
1402 <!-- JAL-2830 -->Inserting gap sequence via the Edit
1403 Sequence dialog corrupts dataset sequence
1406 <!-- JAL-868 -->Structure colours not updated when
1407 associated tree repartitions the alignment view (Regression
1410 </ul> <em>Datamodel</em>
1413 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
1414 sequence's End is greater than its length
1416 </ul> <em>Bugs fixed for Java 11 Support (not yet on general
1420 <!-- JAL-3288 -->Menus work properly in split-screen
1422 </ul> <em>New Known Defects</em>
1425 <!-- JAL-3340 -->Select columns containing feature by double
1426 clicking ignores bounds of an existing selected region
1429 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in
1430 gapped regions of protein alignment.
1433 <!-- JAL-2647 -->Input Data menu entry is greyed out when
1434 PCA View is restored from a Jalview 2.11 project
1437 <!-- JAL-3213 -->Alignment panel height can be too small
1441 <!-- JAL-3240 -->Display is incorrect after removing gapped
1442 columns within hidden columns
1445 <!-- JAL-3314 -->Rightmost selection is lost when mouse
1446 re-enters window after dragging left to select columns to
1447 left of visible region
1450 <!-- JAL-2876 -->Features coloured according to their
1451 description string and thresholded by score in earlier
1452 versions of Jalview are not shown as thresholded features in
1453 2.11. To workaround please create a Score filter instead.
1456 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't
1457 reset group visibility
1460 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in
1461 linked CDS/Protein view
1464 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1465 alignments with multiple views can close views unexpectedly
1467 </ul> <em>Java 11 Specific defects</em>
1470 <!-- JAL-3235 -->Jalview Properties file is not sorted
1471 alphabetically when saved
1477 <td width="60" nowrap>
1478 <div align="center">
1479 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1482 <td><div align="left">
1486 <!-- JAL-3101 -->Default memory for Jalview webstart and
1487 InstallAnywhere increased to 1G.
1490 <!-- JAL-247 -->Hidden sequence markers and representative
1491 sequence bolding included when exporting alignment as EPS,
1492 SVG, PNG or HTML. <em>Display is configured via the
1493 Format menu, or for command-line use via a Jalview
1494 properties file.</em>
1497 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1498 API and sequence data now imported as JSON.
1501 <!-- JAL-3065 -->Change in recommended way of starting
1502 Jalview via a Java command line: add jars in lib directory
1503 to CLASSPATH, rather than via the deprecated java.ext.dirs
1507 <em>Development</em>
1510 <!-- JAL-3047 -->Support added to execute test suite
1511 instrumented with <a href="http://openclover.org/">Open
1516 <td><div align="left">
1520 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1521 row shown in Feredoxin Structure alignment view of example
1525 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1526 annotation displayed.
1529 <!-- JAL-3107 -->Group conservation/consensus not shown
1530 for newly created group when 'Apply to all groups'
1534 <!-- JAL-3087 -->Corrupted display when switching to
1535 wrapped mode when sequence panel's vertical scrollbar is
1539 <!-- JAL-3003 -->Alignment is black in exported EPS file
1540 when sequences are selected in exported view.</em>
1543 <!-- JAL-3059 -->Groups with different coloured borders
1544 aren't rendered with correct colour.
1547 <!-- JAL-3092 -->Jalview could hang when importing certain
1548 types of knotted RNA secondary structure.
1551 <!-- JAL-3095 -->Sequence highlight and selection in
1552 trimmed VARNA 2D structure is incorrect for sequences that
1556 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1557 annotation when columns are inserted into an alignment,
1558 and when exporting as Stockholm flatfile.
1561 <!-- JAL-3053 -->Jalview annotation rows containing upper
1562 and lower-case 'E' and 'H' do not automatically get
1563 treated as RNA secondary structure.
1566 <!-- JAL-3106 -->.jvp should be used as default extension
1567 (not .jar) when saving a Jalview project file.
1570 <!-- JAL-3105 -->Mac Users: closing a window correctly
1571 transfers focus to previous window on OSX
1574 <em>Java 10 Issues Resolved</em>
1577 <!-- JAL-2988 -->OSX - Can't save new files via the File
1578 or export menus by typing in a name into the Save dialog
1582 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1583 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1584 'look and feel' which has improved compatibility with the
1585 latest version of OSX.
1591 <td width="60" nowrap>
1592 <div align="center">
1593 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1594 <em>7/06/2018</em></strong>
1597 <td><div align="left">
1601 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1602 annotation retrieved from Uniprot
1605 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1606 onto the Jalview Desktop
1610 <td><div align="left">
1614 <!-- JAL-3017 -->Cannot import features with multiple
1615 variant elements (blocks import of some Uniprot records)
1618 <!-- JAL-2997 -->Clustal files with sequence positions in
1619 right-hand column parsed correctly
1622 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1623 not alignment area in exported graphic
1626 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1627 window has input focus
1630 <!-- JAL-2992 -->Annotation panel set too high when
1631 annotation added to view (Windows)
1634 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1635 network connectivity is poor
1638 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1639 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1640 the currently open URL and links from a page viewed in
1641 Firefox or Chrome on Windows is now fully supported. If
1642 you are using Edge, only links in the page can be
1643 dragged, and with Internet Explorer, only the currently
1644 open URL in the browser can be dropped onto Jalview.</em>
1647 <em>New Known Defects</em>
1650 <!-- JAL-3083 -->Cancel option doesn't reset Colour by
1657 <td width="60" nowrap>
1658 <div align="center">
1659 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1662 <td><div align="left">
1666 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1667 for disabling automatic superposition of multiple
1668 structures and open structures in existing views
1671 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1672 ID and annotation area margins can be click-dragged to
1676 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1680 <!-- JAL-2759 -->Improved performance for large alignments
1681 and lots of hidden columns
1684 <!-- JAL-2593 -->Improved performance when rendering lots
1685 of features (particularly when transparency is disabled)
1688 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2
1689 for exchange of Jalview features and Chimera attributes
1690 made generally available
1694 <td><div align="left">
1697 <!-- JAL-2899 -->Structure and Overview aren't updated
1698 when Colour By Annotation threshold slider is adjusted
1701 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1702 overlapping alignment panel
1705 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1709 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1710 improved: CDS not handled correctly if transcript has no
1714 <!-- JAL-2321 -->Secondary structure and temperature
1715 factor annotation not added to sequence when local PDB
1716 file associated with it by drag'n'drop or structure
1720 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1721 dialog doesn't import PDB files dropped on an alignment
1724 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1725 scroll bar doesn't work for some CDS/Protein views
1728 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1729 Java 1.8u153 onwards and Java 1.9u4+.
1732 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1733 columns in annotation row
1736 <!-- JAL-2913 -->Preferences panel's ID Width control is
1737 not honored in batch mode
1740 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1741 for structures added to existing Jmol view
1744 <!-- JAL-2223 -->'View Mappings' includes duplicate
1745 entries after importing project with multiple views
1748 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1749 protein sequences via SIFTS from associated PDB entries
1750 with negative residue numbers or missing residues fails
1753 <!-- JAL-2952 -->Exception when shading sequence with
1754 negative Temperature Factor values from annotated PDB
1755 files (e.g. as generated by CONSURF)
1758 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1759 tooltip doesn't include a text description of mutation
1762 <!-- JAL-2922 -->Invert displayed features very slow when
1763 structure and/or overview windows are also shown
1766 <!-- JAL-2954 -->Selecting columns from highlighted
1767 regions very slow for alignments with large numbers of
1771 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1772 with 'StringIndexOutOfBounds'
1775 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and
1776 Feel for OSX platforms running Java 10
1779 <!-- JAL-2960 -->Adding a structure to existing structure
1780 view appears to do nothing because the view is hidden
1781 behind the alignment view
1787 <!-- JAL-2926 -->Copy consensus sequence option in applet
1788 should copy the group consensus when popup is opened on it
1794 <!-- JAL-2913 -->Fixed ID width preference is not
1798 <em>New Known Defects</em>
1801 <!-- JAL-2973 --> Exceptions occasionally raised when
1802 editing a large alignment and overview is displayed
1805 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1806 repeatedly after a series of edits even when the overview
1807 is no longer reflecting updates
1810 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1811 structures for protein subsequence (if 'Trim Retrieved
1812 Sequences' enabled) or Ensembl isoforms (Workaround in
1813 2.10.4 is to fail back to N&W mapping)
1816 <!-- JAL-2990 -->Export Annotations from File Menu with
1817 CSV option gives blank output
1823 <td width="60" nowrap>
1824 <div align="center">
1825 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br />
1826 <em>24/1/2018</em></strong>
1829 <td><div align="left">
1831 <li>Updated Certum Codesigning Certificate (Valid till
1832 30th November 2018)</li>
1835 <td><div align="left">
1840 <!-- JAL-2859-->Only one structure is loaded when
1841 several sequences and structures are selected for
1845 <!-- JAL-2851-->Alignment doesn't appear to scroll
1846 vertically via trackpad and scrollwheel
1849 <!-- JAL-2842-->Jalview hangs if up/down arrows pressed
1850 in cursor mode when cursor lies in hidden region at
1854 <!-- JAL-2827-->Helix annotation has 'notches' when
1855 scrolled into view if columns are hidden
1858 <!-- JAL-2740-->Annotation column filter can be slow to
1859 reset (ie after hitting cancel) for large numbers of
1863 <!-- JAL-2849-->User preference for disabling inclusion
1864 of sequence limits when exporting as flat file has no
1868 <!-- JAL-2679-->Reproducible cross-reference
1869 relationships when retrieving sequences from
1876 <td width="60" nowrap>
1877 <div align="center">
1878 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1881 <td><div align="left">
1885 <!-- JAL-2446 -->Faster and more efficient management and
1886 rendering of sequence features
1889 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1890 429 rate limit request hander
1893 <!-- JAL-2773 -->Structure views don't get updated unless
1894 their colours have changed
1897 <!-- JAL-2495 -->All linked sequences are highlighted for
1898 a structure mousover (Jmol) or selection (Chimera)
1901 <!-- JAL-2790 -->'Cancel' button in progress bar for
1902 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1905 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1906 view from Ensembl locus cross-references
1909 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1913 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1914 feature can be disabled
1917 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1918 PDB easier retrieval of sequences for lists of IDs
1921 <!-- JAL-2758 -->Short names for sequences retrieved from
1927 <li>Groovy interpreter updated to 2.4.12</li>
1928 <li>Example groovy script for generating a matrix of
1929 percent identity scores for current alignment.</li>
1931 <em>Testing and Deployment</em>
1934 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1938 <td><div align="left">
1942 <!-- JAL-2643 -->Pressing tab after updating the colour
1943 threshold text field doesn't trigger an update to the
1947 <!-- JAL-2682 -->Race condition when parsing sequence ID
1951 <!-- JAL-2608 -->Overview windows are also closed when
1952 alignment window is closed
1955 <!-- JAL-2548 -->Export of features doesn't always respect
1959 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1960 takes a long time in Cursor mode
1966 <!-- JAL-2777 -->Structures with whitespace chainCode
1967 cannot be viewed in Chimera
1970 <!-- JAL-2728 -->Protein annotation panel too high in
1974 <!-- JAL-2757 -->Can't edit the query after the server
1975 error warning icon is shown in Uniprot and PDB Free Text
1979 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1982 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1985 <!-- JAL-2739 -->Hidden column marker in last column not
1986 rendered when switching back from Wrapped to normal view
1989 <!-- JAL-2768 -->Annotation display corrupted when
1990 scrolling right in unwapped alignment view
1993 <!-- JAL-2542 -->Existing features on subsequence
1994 incorrectly relocated when full sequence retrieved from
1998 <!-- JAL-2733 -->Last reported memory still shown when
1999 Desktop->Show Memory is unticked (OSX only)
2002 <!-- JAL-2658 -->Amend Features dialog doesn't allow
2003 features of same type and group to be selected for
2007 <!-- JAL-2524 -->Jalview becomes sluggish in wide
2008 alignments when hidden columns are present
2011 <!-- JAL-2392 -->Jalview freezes when loading and
2012 displaying several structures
2015 <!-- JAL-2732 -->Black outlines left after resizing or
2019 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
2020 within the Jalview desktop on OSX
2023 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
2024 when in wrapped alignment mode
2027 <!-- JAL-2636 -->Scale mark not shown when close to right
2028 hand end of alignment
2031 <!-- JAL-2684 -->Pairwise alignment of selected regions of
2032 each selected sequence do not have correct start/end
2036 <!-- JAL-2793 -->Alignment ruler height set incorrectly
2037 after canceling the Alignment Window's Font dialog
2040 <!-- JAL-2036 -->Show cross-references not enabled after
2041 restoring project until a new view is created
2044 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
2045 URL links appears when only default EMBL-EBI link is
2046 configured (since 2.10.2b2)
2049 <!-- JAL-2775 -->Overview redraws whole window when box
2050 position is adjusted
2053 <!-- JAL-2225 -->Structure viewer doesn't map all chains
2054 in a multi-chain structure when viewing alignment
2055 involving more than one chain (since 2.10)
2058 <!-- JAL-2811 -->Double residue highlights in cursor mode
2059 if new selection moves alignment window
2062 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
2063 arrow key in cursor mode to pass hidden column marker
2066 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
2067 that produces correctly annotated transcripts and products
2070 <!-- JAL-2776 -->Toggling a feature group after first time
2071 doesn't update associated structure view
2074 <em>Applet</em><br />
2077 <!-- JAL-2687 -->Concurrent modification exception when
2078 closing alignment panel
2081 <em>BioJSON</em><br />
2084 <!-- JAL-2546 -->BioJSON export does not preserve
2085 non-positional features
2088 <em>New Known Issues</em>
2091 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
2092 sequence features correctly (for many previous versions of
2096 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
2097 using cursor in wrapped panel other than top
2100 <!-- JAL-2791 -->Select columns containing feature ignores
2101 graduated colour threshold
2104 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
2105 always preserve numbering and sequence features
2108 <em>Known Java 9 Issues</em>
2111 <!-- JAL-2902 -->Groovy Console very slow to open and is
2112 not responsive when entering characters (Webstart, Java
2119 <td width="60" nowrap>
2120 <div align="center">
2121 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
2122 <em>2/10/2017</em></strong>
2125 <td><div align="left">
2126 <em>New features in Jalview Desktop</em>
2129 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API
2133 <!-- JAL-2745 -->HTTPS used for all connections to
2138 <td><div align="left"></div></td>
2141 <td width="60" nowrap>
2142 <div align="center">
2143 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
2144 <em>7/9/2017</em></strong>
2147 <td><div align="left">
2151 <!-- JAL-2588 -->Show gaps in overview window by colouring
2152 in grey (sequences used to be coloured grey, and gaps were
2156 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
2160 <!-- JAL-2587 -->Overview updates immediately on increase
2161 in size and progress bar shown as higher resolution
2162 overview is recalculated
2167 <td><div align="left">
2171 <!-- JAL-2664 -->Overview window redraws every hidden
2172 column region row by row
2175 <!-- JAL-2681 -->duplicate protein sequences shown after
2176 retrieving Ensembl crossrefs for sequences from Uniprot
2179 <!-- JAL-2603 -->Overview window throws NPE if show boxes
2180 format setting is unticked
2183 <!-- JAL-2610 -->Groups are coloured wrongly in overview
2184 if group has show boxes format setting unticked
2187 <!-- JAL-2672,JAL-2665 -->Redraw problems when
2188 autoscrolling whilst dragging current selection group to
2189 include sequences and columns not currently displayed
2192 <!-- JAL-2691 -->Not all chains are mapped when multimeric
2193 assemblies are imported via CIF file
2196 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
2197 displayed when threshold or conservation colouring is also
2201 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
2205 <!-- JAL-2673 -->Jalview continues to scroll after
2206 dragging a selected region off the visible region of the
2210 <!-- JAL-2724 -->Cannot apply annotation based
2211 colourscheme to all groups in a view
2214 <!-- JAL-2511 -->IDs don't line up with sequences
2215 initially after font size change using the Font chooser or
2222 <td width="60" nowrap>
2223 <div align="center">
2224 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
2227 <td><div align="left">
2228 <em>Calculations</em>
2232 <!-- JAL-1933 -->Occupancy annotation row shows number of
2233 ungapped positions in each column of the alignment.
2236 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
2237 a calculation dialog box
2240 <!-- JAL-2379 -->Revised implementation of PCA for speed
2241 and memory efficiency (~30x faster)
2244 <!-- JAL-2403 -->Revised implementation of sequence
2245 similarity scores as used by Tree, PCA, Shading Consensus
2246 and other calculations
2249 <!-- JAL-2416 -->Score matrices are stored as resource
2250 files within the Jalview codebase
2253 <!-- JAL-2500 -->Trees computed on Sequence Feature
2254 Similarity may have different topology due to increased
2261 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
2262 model for alignments and groups
2265 <!-- JAL-384 -->Custom shading schemes created via groovy
2272 <!-- JAL-2526 -->Efficiency improvements for interacting
2273 with alignment and overview windows
2276 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
2280 <!-- JAL-2388 -->Hidden columns and sequences can be
2284 <!-- JAL-2611 -->Click-drag in visible area allows fine
2285 adjustment of visible position
2289 <em>Data import/export</em>
2292 <!-- JAL-2535 -->Posterior probability annotation from
2293 Stockholm files imported as sequence associated annotation
2296 <!-- JAL-2507 -->More robust per-sequence positional
2297 annotation input/output via stockholm flatfile
2300 <!-- JAL-2533 -->Sequence names don't include file
2301 extension when importing structure files without embedded
2302 names or PDB accessions
2305 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
2306 format sequence substitution matrices
2309 <em>User Interface</em>
2312 <!-- JAL-2447 --> Experimental Features Checkbox in
2313 Desktop's Tools menu to hide or show untested features in
2317 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
2318 via Overview or sequence motif search operations
2321 <!-- JAL-2547 -->Amend sequence features dialog box can be
2322 opened by double clicking gaps within sequence feature
2326 <!-- JAL-1476 -->Status bar message shown when not enough
2327 aligned positions were available to create a 3D structure
2331 <em>3D Structure</em>
2334 <!-- JAL-2430 -->Hidden regions in alignment views are not
2335 coloured in linked structure views
2338 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
2339 file-based command exchange
2342 <!-- JAL-2375 -->Structure chooser automatically shows
2343 Cached Structures rather than querying the PDBe if
2344 structures are already available for sequences
2347 <!-- JAL-2520 -->Structures imported via URL are cached in
2348 the Jalview project rather than downloaded again when the
2349 project is reopened.
2352 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
2353 to transfer Chimera's structure attributes as Jalview
2354 features, and vice-versa (<strong>Experimental
2358 <em>Web Services</em>
2361 <!-- JAL-2549 -->Updated JABAWS client to v2.2
2364 <!-- JAL-2335 -->Filter non-standard amino acids and
2365 nucleotides when submitting to AACon and other MSA
2369 <!-- JAL-2316, -->URLs for viewing database
2370 cross-references provided by identifiers.org and the
2371 EMBL-EBI's MIRIAM DB
2378 <!-- JAL-2344 -->FileFormatI interface for describing and
2379 identifying file formats (instead of String constants)
2382 <!-- JAL-2228 -->FeatureCounter script refactored for
2383 efficiency when counting all displayed features (not
2384 backwards compatible with 2.10.1)
2387 <em>Example files</em>
2390 <!-- JAL-2631 -->Graduated feature colour style example
2391 included in the example feature file
2394 <em>Documentation</em>
2397 <!-- JAL-2339 -->Release notes reformatted for readability
2398 with the built-in Java help viewer
2401 <!-- JAL-1644 -->Find documentation updated with 'search
2402 sequence description' option
2408 <!-- JAL-2485, -->External service integration tests for
2409 Uniprot REST Free Text Search Client
2412 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
2415 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
2420 <td><div align="left">
2421 <em>Calculations</em>
2424 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
2425 matrix - C->R should be '-3'<br />Old matrix restored
2426 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
2428 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
2429 Jalview's treatment of gaps in PCA and substitution matrix
2430 based Tree calculations.<br /> <br />In earlier versions
2431 of Jalview, gaps matching gaps were penalised, and gaps
2432 matching non-gaps penalised even more. In the PCA
2433 calculation, gaps were actually treated as non-gaps - so
2434 different costs were applied, which meant Jalview's PCAs
2435 were different to those produced by SeqSpace.<br />Jalview
2436 now treats gaps in the same way as SeqSpace (ie it scores
2437 them as 0). <br /> <br />Enter the following in the
2438 Groovy console to restore pre-2.10.2 behaviour:<br />
2439 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
2440 // for 2.10.1 mode <br />
2441 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
2442 // to restore 2.10.2 mode <br /> <br /> <em>Note:
2443 these settings will affect all subsequent tree and PCA
2444 calculations (not recommended)</em></li>
2446 <!-- JAL-2424 -->Fixed off-by-one bug that affected
2447 scaling of branch lengths for trees computed using
2448 Sequence Feature Similarity.
2451 <!-- JAL-2377 -->PCA calculation could hang when
2452 generating output report when working with highly
2453 redundant alignments
2456 <!-- JAL-2544 --> Sort by features includes features to
2457 right of selected region when gaps present on right-hand
2461 <em>User Interface</em>
2464 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2465 doesn't reselect a specific sequence's associated
2466 annotation after it was used for colouring a view
2469 <!-- JAL-2419 -->Current selection lost if popup menu
2470 opened on a region of alignment without groups
2473 <!-- JAL-2374 -->Popup menu not always shown for regions
2474 of an alignment with overlapping groups
2477 <!-- JAL-2310 -->Finder double counts if both a sequence's
2478 name and description match
2481 <!-- JAL-2370 -->Hiding column selection containing two
2482 hidden regions results in incorrect hidden regions
2485 <!-- JAL-2386 -->'Apply to all groups' setting when
2486 changing colour does not apply Conservation slider value
2490 <!-- JAL-2373 -->Percentage identity and conservation menu
2491 items do not show a tick or allow shading to be disabled
2494 <!-- JAL-2385 -->Conservation shading or PID threshold
2495 lost when base colourscheme changed if slider not visible
2498 <!-- JAL-2547 -->Sequence features shown in tooltip for
2499 gaps before start of features
2502 <!-- JAL-2623 -->Graduated feature colour threshold not
2503 restored to UI when feature colour is edited
2506 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2507 a time when scrolling vertically in wrapped mode.
2510 <!-- JAL-2630 -->Structure and alignment overview update
2511 as graduate feature colour settings are modified via the
2515 <!-- JAL-2034 -->Overview window doesn't always update
2516 when a group defined on the alignment is resized
2519 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2520 wrapped view result in positional status updates
2524 <!-- JAL-2563 -->Status bar doesn't show position for
2525 ambiguous amino acid and nucleotide symbols
2528 <!-- JAL-2602 -->Copy consensus sequence failed if
2529 alignment included gapped columns
2532 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2533 widgets don't permanently disappear
2536 <!-- JAL-2503 -->Cannot select or filter quantitative
2537 annotation that are shown only as column labels (e.g.
2538 T-Coffee column reliability scores)
2541 <!-- JAL-2594 -->Exception thrown if trying to create a
2542 sequence feature on gaps only
2545 <!-- JAL-2504 -->Features created with 'New feature'
2546 button from a Find inherit previously defined feature type
2547 rather than the Find query string
2550 <!-- JAL-2423 -->incorrect title in output window when
2551 exporting tree calculated in Jalview
2554 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2555 and then revealing them reorders sequences on the
2559 <!-- JAL-964 -->Group panel in sequence feature settings
2560 doesn't update to reflect available set of groups after
2561 interactively adding or modifying features
2564 <!-- JAL-2225 -->Sequence Database chooser unusable on
2568 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2569 only excluded gaps in current sequence and ignored
2576 <!-- JAL-2421 -->Overview window visible region moves
2577 erratically when hidden rows or columns are present
2580 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2581 Structure Viewer's colour menu don't correspond to
2585 <!-- JAL-2405 -->Protein specific colours only offered in
2586 colour and group colour menu for protein alignments
2589 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2590 reflect currently selected view or group's shading
2594 <!-- JAL-2624 -->Feature colour thresholds not respected
2595 when rendered on overview and structures when opacity at
2599 <!-- JAL-2589 -->User defined gap colour not shown in
2600 overview when features overlaid on alignment
2603 <!-- JAL-2567 -->Feature settings for different views not
2604 recovered correctly from Jalview project file
2607 <!-- JAL-2256 -->Feature colours in overview when first
2608 opened (automatically via preferences) are different to
2609 the main alignment panel
2612 <em>Data import/export</em>
2615 <!-- JAL-2576 -->Very large alignments take a long time to
2619 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2620 added after a sequence was imported are not written to
2624 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2625 when importing RNA secondary structure via Stockholm
2628 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2629 not shown in correct direction for simple pseudoknots
2632 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2633 with lightGray or darkGray via features file (but can
2637 <!-- JAL-2383 -->Above PID colour threshold not recovered
2638 when alignment view imported from project
2641 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2642 structure and sequences extracted from structure files
2643 imported via URL and viewed in Jmol
2646 <!-- JAL-2520 -->Structures loaded via URL are saved in
2647 Jalview Projects rather than fetched via URL again when
2648 the project is loaded and the structure viewed
2651 <em>Web Services</em>
2654 <!-- JAL-2519 -->EnsemblGenomes example failing after
2655 release of Ensembl v.88
2658 <!-- JAL-2366 -->Proxy server address and port always
2659 appear enabled in Preferences->Connections
2662 <!-- JAL-2461 -->DAS registry not found exceptions
2663 removed from console output
2666 <!-- JAL-2582 -->Cannot retrieve protein products from
2667 Ensembl by Peptide ID
2670 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2671 created from SIFTs, and spurious 'Couldn't open structure
2672 in Chimera' errors raised after April 2017 update (problem
2673 due to 'null' string rather than empty string used for
2674 residues with no corresponding PDB mapping).
2677 <em>Application UI</em>
2680 <!-- JAL-2361 -->User Defined Colours not added to Colour
2684 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2685 case' residues (button in colourscheme editor debugged and
2686 new documentation and tooltips added)
2689 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2690 doesn't restore group-specific text colour thresholds
2693 <!-- JAL-2243 -->Feature settings panel does not update as
2694 new features are added to alignment
2697 <!-- JAL-2532 -->Cancel in feature settings reverts
2698 changes to feature colours via the Amend features dialog
2701 <!-- JAL-2506 -->Null pointer exception when attempting to
2702 edit graduated feature colour via amend features dialog
2706 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2707 selection menu changes colours of alignment views
2710 <!-- JAL-2426 -->Spurious exceptions in console raised
2711 from alignment calculation workers after alignment has
2715 <!-- JAL-1608 -->Typo in selection popup menu - Create
2716 groups now 'Create Group'
2719 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2720 Create/Undefine group doesn't always work
2723 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2724 shown again after pressing 'Cancel'
2727 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2728 adjusts start position in wrap mode
2731 <!-- JAL-2563 -->Status bar doesn't show positions for
2732 ambiguous amino acids
2735 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2736 CDS/Protein view after CDS sequences added for aligned
2740 <!-- JAL-2592 -->User defined colourschemes called 'User
2741 Defined' don't appear in Colours menu
2747 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2748 score models doesn't always result in an updated PCA plot
2751 <!-- JAL-2442 -->Features not rendered as transparent on
2752 overview or linked structure view
2755 <!-- JAL-2372 -->Colour group by conservation doesn't
2759 <!-- JAL-2517 -->Hitting Cancel after applying
2760 user-defined colourscheme doesn't restore original
2767 <!-- JAL-2314 -->Unit test failure:
2768 jalview.ws.jabaws.RNAStructExportImport setup fails
2771 <!-- JAL-2307 -->Unit test failure:
2772 jalview.ws.sifts.SiftsClientTest due to compatibility
2773 problems with deep array comparison equality asserts in
2774 successive versions of TestNG
2777 <!-- JAL-2479 -->Relocated StructureChooserTest and
2778 ParameterUtilsTest Unit tests to Network suite
2781 <em>New Known Issues</em>
2784 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2785 phase after a sequence motif find operation
2788 <!-- JAL-2550 -->Importing annotation file with rows
2789 containing just upper and lower case letters are
2790 interpreted as WUSS RNA secondary structure symbols
2793 <!-- JAL-2590 -->Cannot load and display Newick trees
2794 reliably from eggnog Ortholog database
2797 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2798 containing features of type Highlight' when 'B' is pressed
2799 to mark columns containing highlighted regions.
2802 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2803 doesn't always add secondary structure annotation.
2808 <td width="60" nowrap>
2809 <div align="center">
2810 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2813 <td><div align="left">
2817 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2818 for all consensus calculations
2821 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2824 <li>Updated Jalview's Certum code signing certificate
2827 <em>Application</em>
2830 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2831 set of database cross-references, sorted alphabetically
2834 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2835 from database cross references. Users with custom links
2836 will receive a <a href="webServices/urllinks.html#warning">warning
2837 dialog</a> asking them to update their preferences.
2840 <!-- JAL-2287-->Cancel button and escape listener on
2841 dialog warning user about disconnecting Jalview from a
2845 <!-- JAL-2320-->Jalview's Chimera control window closes if
2846 the Chimera it is connected to is shut down
2849 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2850 columns menu item to mark columns containing highlighted
2851 regions (e.g. from structure selections or results of a
2855 <!-- JAL-2284-->Command line option for batch-generation
2856 of HTML pages rendering alignment data with the BioJS
2866 <!-- JAL-2286 -->Columns with more than one modal residue
2867 are not coloured or thresholded according to percent
2868 identity (first observed in Jalview 2.8.2)
2871 <!-- JAL-2301 -->Threonine incorrectly reported as not
2875 <!-- JAL-2318 -->Updates to documentation pages (above PID
2876 threshold, amino acid properties)
2879 <!-- JAL-2292 -->Lower case residues in sequences are not
2880 reported as mapped to residues in a structure file in the
2884 <!--JAL-2324 -->Identical features with non-numeric scores
2885 could be added multiple times to a sequence
2888 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2889 bond features shown as two highlighted residues rather
2890 than a range in linked structure views, and treated
2891 correctly when selecting and computing trees from features
2894 <!-- JAL-2281-->Custom URL links for database
2895 cross-references are matched to database name regardless
2900 <em>Application</em>
2903 <!-- JAL-2282-->Custom URL links for specific database
2904 names without regular expressions also offer links from
2908 <!-- JAL-2315-->Removing a single configured link in the
2909 URL links pane in Connections preferences doesn't actually
2910 update Jalview configuration
2913 <!-- JAL-2272-->CTRL-Click on a selected region to open
2914 the alignment area popup menu doesn't work on El-Capitan
2917 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2918 files with similarly named sequences if dropped onto the
2922 <!-- JAL-2312 -->Additional mappings are shown for PDB
2923 entries where more chains exist in the PDB accession than
2924 are reported in the SIFTS file
2927 <!-- JAL-2317-->Certain structures do not get mapped to
2928 the structure view when displayed with Chimera
2931 <!-- JAL-2317-->No chains shown in the Chimera view
2932 panel's View->Show Chains submenu
2935 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2936 work for wrapped alignment views
2939 <!--JAL-2197 -->Rename UI components for running JPred
2940 predictions from 'JNet' to 'JPred'
2943 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2944 corrupted when annotation panel vertical scroll is not at
2945 first annotation row
2948 <!--JAL-2332 -->Attempting to view structure for Hen
2949 lysozyme results in a PDB Client error dialog box
2952 <!-- JAL-2319 -->Structure View's mapping report switched
2953 ranges for PDB and sequence for SIFTS
2956 SIFTS 'Not_Observed' residues mapped to non-existant
2960 <!-- <em>New Known Issues</em>
2967 <td width="60" nowrap>
2968 <div align="center">
2969 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2970 <em>25/10/2016</em></strong>
2973 <td><em>Application</em>
2975 <li>3D Structure chooser opens with 'Cached structures'
2976 view if structures already loaded</li>
2977 <li>Progress bar reports models as they are loaded to
2978 structure views</li>
2984 <li>Colour by conservation always enabled and no tick
2985 shown in menu when BLOSUM or PID shading applied</li>
2986 <li>FER1_ARATH and FER2_ARATH labels were switched in
2987 example sequences/projects/trees</li>
2989 <em>Application</em>
2991 <li>Jalview projects with views of local PDB structure
2992 files saved on Windows cannot be opened on OSX</li>
2993 <li>Multiple structure views can be opened and superposed
2994 without timeout for structures with multiple models or
2995 multiple sequences in alignment</li>
2996 <li>Cannot import or associated local PDB files without a
2997 PDB ID HEADER line</li>
2998 <li>RMSD is not output in Jmol console when superposition
3000 <li>Drag and drop of URL from Browser fails for Linux and
3001 OSX versions earlier than El Capitan</li>
3002 <li>ENA client ignores invalid content from ENA server</li>
3003 <li>Exceptions are not raised in console when ENA client
3004 attempts to fetch non-existent IDs via Fetch DB Refs UI
3006 <li>Exceptions are not raised in console when a new view
3007 is created on the alignment</li>
3008 <li>OSX right-click fixed for group selections: CMD-click
3009 to insert/remove gaps in groups and CTRL-click to open group
3012 <em>Build and deployment</em>
3014 <li>URL link checker now copes with multi-line anchor
3017 <em>New Known Issues</em>
3019 <li>Drag and drop from URL links in browsers do not work
3026 <td width="60" nowrap>
3027 <div align="center">
3028 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
3031 <td><em>General</em>
3034 <!-- JAL-2124 -->Updated Spanish translations.
3037 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
3038 for importing structure data to Jalview. Enables mmCIF and
3042 <!-- JAL-192 --->Alignment ruler shows positions relative to
3046 <!-- JAL-2202 -->Position/residue shown in status bar when
3047 mousing over sequence associated annotation
3050 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
3054 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
3055 '()', canonical '[]' and invalid '{}' base pair populations
3059 <!-- JAL-2092 -->Feature settings popup menu options for
3060 showing or hiding columns containing a feature
3063 <!-- JAL-1557 -->Edit selected group by double clicking on
3064 group and sequence associated annotation labels
3067 <!-- JAL-2236 -->Sequence name added to annotation label in
3068 select/hide columns by annotation and colour by annotation
3072 </ul> <em>Application</em>
3075 <!-- JAL-2050-->Automatically hide introns when opening a
3076 gene/transcript view
3079 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
3083 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
3084 structure mappings with the EMBL-EBI PDBe SIFTS database
3087 <!-- JAL-2079 -->Updated download sites used for Rfam and
3088 Pfam sources to xfam.org
3091 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
3094 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
3095 over sequences in Jalview
3098 <!-- JAL-2027-->Support for reverse-complement coding
3099 regions in ENA and EMBL
3102 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
3103 for record retrieval via ENA rest API
3106 <!-- JAL-2027 -->Support for ENA CDS records with reverse
3110 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
3111 groovy script execution
3114 <!-- JAL-1812 -->New 'execute Groovy script' option in an
3115 alignment window's Calculate menu
3118 <!-- JAL-1812 -->Allow groovy scripts that call
3119 Jalview.getAlignFrames() to run in headless mode
3122 <!-- JAL-2068 -->Support for creating new alignment
3123 calculation workers from groovy scripts
3126 <!-- JAL-1369 --->Store/restore reference sequence in
3130 <!-- JAL-1803 -->Chain codes for a sequence's PDB
3131 associations are now saved/restored from project
3134 <!-- JAL-1993 -->Database selection dialog always shown
3135 before sequence fetcher is opened
3138 <!-- JAL-2183 -->Double click on an entry in Jalview's
3139 database chooser opens a sequence fetcher
3142 <!-- JAL-1563 -->Free-text search client for UniProt using
3143 the UniProt REST API
3146 <!-- JAL-2168 -->-nonews command line parameter to prevent
3147 the news reader opening
3150 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
3151 querying stored in preferences
3154 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
3158 <!-- JAL-1977-->Tooltips shown on database chooser
3161 <!-- JAL-391 -->Reverse complement function in calculate
3162 menu for nucleotide sequences
3165 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
3166 and feature counts preserves alignment ordering (and
3167 debugged for complex feature sets).
3170 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
3171 viewing structures with Jalview 2.10
3174 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
3175 genome, transcript CCDS and gene ids via the Ensembl and
3176 Ensembl Genomes REST API
3179 <!-- JAL-2049 -->Protein sequence variant annotation
3180 computed for 'sequence_variant' annotation on CDS regions
3184 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
3188 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
3189 Ref Fetcher fails to match, or otherwise updates sequence
3190 data from external database records.
3193 <!-- JAL-2154 -->Revised Jalview Project format for
3194 efficient recovery of sequence coding and alignment
3195 annotation relationships.
3197 </ul> <!-- <em>Applet</em>
3208 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
3212 <!-- JAL-2018-->Export features in Jalview format (again)
3213 includes graduated colourschemes
3216 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
3217 working with big alignments and lots of hidden columns
3220 <!-- JAL-2053-->Hidden column markers not always rendered
3221 at right of alignment window
3224 <!-- JAL-2067 -->Tidied up links in help file table of
3228 <!-- JAL-2072 -->Feature based tree calculation not shown
3232 <!-- JAL-2075 -->Hidden columns ignored during feature
3233 based tree calculation
3236 <!-- JAL-2065 -->Alignment view stops updating when show
3237 unconserved enabled for group on alignment
3240 <!-- JAL-2086 -->Cannot insert gaps into sequence when
3244 <!-- JAL-2146 -->Alignment column in status incorrectly
3245 shown as "Sequence position" when mousing over
3249 <!-- JAL-2099 -->Incorrect column numbers in ruler when
3250 hidden columns present
3253 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
3254 user created annotation added to alignment
3257 <!-- JAL-1841 -->RNA Structure consensus only computed for
3258 '()' base pair annotation
3261 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
3262 in zero scores for all base pairs in RNA Structure
3266 <!-- JAL-2174-->Extend selection with columns containing
3270 <!-- JAL-2275 -->Pfam format writer puts extra space at
3271 beginning of sequence
3274 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
3278 <!-- JAL-2238 -->Cannot create groups on an alignment from
3279 from a tree when t-coffee scores are shown
3282 <!-- JAL-1836,1967 -->Cannot import and view PDB
3283 structures with chains containing negative resnums (4q4h)
3286 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
3290 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
3291 to Clustal, PIR and PileUp output
3294 <!-- JAL-2008 -->Reordering sequence features that are
3295 not visible causes alignment window to repaint
3298 <!-- JAL-2006 -->Threshold sliders don't work in
3299 graduated colour and colour by annotation row for e-value
3300 scores associated with features and annotation rows
3303 <!-- JAL-1797 -->amino acid physicochemical conservation
3304 calculation should be case independent
3307 <!-- JAL-2173 -->Remove annotation also updates hidden
3311 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
3312 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
3313 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
3316 <!-- JAL-2065 -->Null pointer exceptions and redraw
3317 problems when reference sequence defined and 'show
3318 non-conserved' enabled
3321 <!-- JAL-1306 -->Quality and Conservation are now shown on
3322 load even when Consensus calculation is disabled
3325 <!-- JAL-1932 -->Remove right on penultimate column of
3326 alignment does nothing
3329 <em>Application</em>
3332 <!-- JAL-1552-->URLs and links can't be imported by
3333 drag'n'drop on OSX when launched via webstart (note - not
3334 yet fixed for El Capitan)
3337 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
3338 output when running on non-gb/us i18n platforms
3341 <!-- JAL-1944 -->Error thrown when exporting a view with
3342 hidden sequences as flat-file alignment
3345 <!-- JAL-2030-->InstallAnywhere distribution fails when
3349 <!-- JAL-2080-->Jalview very slow to launch via webstart
3350 (also hotfix for 2.9.0b2)
3353 <!-- JAL-2085 -->Cannot save project when view has a
3354 reference sequence defined
3357 <!-- JAL-1011 -->Columns are suddenly selected in other
3358 alignments and views when revealing hidden columns
3361 <!-- JAL-1989 -->Hide columns not mirrored in complement
3362 view in a cDNA/Protein splitframe
3365 <!-- JAL-1369 -->Cannot save/restore representative
3366 sequence from project when only one sequence is
3370 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
3371 in Structure Chooser
3374 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
3375 structure consensus didn't refresh annotation panel
3378 <!-- JAL-1962 -->View mapping in structure view shows
3379 mappings between sequence and all chains in a PDB file
3382 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
3383 dialogs format columns correctly, don't display array
3384 data, sort columns according to type
3387 <!-- JAL-1975 -->Export complete shown after destination
3388 file chooser is cancelled during an image export
3391 <!-- JAL-2025 -->Error when querying PDB Service with
3392 sequence name containing special characters
3395 <!-- JAL-2024 -->Manual PDB structure querying should be
3399 <!-- JAL-2104 -->Large tooltips with broken HTML
3400 formatting don't wrap
3403 <!-- JAL-1128 -->Figures exported from wrapped view are
3404 truncated so L looks like I in consensus annotation
3407 <!-- JAL-2003 -->Export features should only export the
3408 currently displayed features for the current selection or
3412 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
3413 after fetching cross-references, and restoring from
3417 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
3418 followed in the structure viewer
3421 <!-- JAL-2163 -->Titles for individual alignments in
3422 splitframe not restored from project
3425 <!-- JAL-2145 -->missing autocalculated annotation at
3426 trailing end of protein alignment in transcript/product
3427 splitview when pad-gaps not enabled by default
3430 <!-- JAL-1797 -->amino acid physicochemical conservation
3434 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
3435 article has been read (reopened issue due to
3436 internationalisation problems)
3439 <!-- JAL-1960 -->Only offer PDB structures in structure
3440 viewer based on sequence name, PDB and UniProt
3445 <!-- JAL-1976 -->No progress bar shown during export of
3449 <!-- JAL-2213 -->Structures not always superimposed after
3450 multiple structures are shown for one or more sequences.
3453 <!-- JAL-1370 -->Reference sequence characters should not
3454 be replaced with '.' when 'Show unconserved' format option
3458 <!-- JAL-1823 -->Cannot specify chain code when entering
3459 specific PDB id for sequence
3462 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3463 'Export hidden sequences' is enabled, but 'export hidden
3464 columns' is disabled.
3467 <!--JAL-2026-->Best Quality option in structure chooser
3468 selects lowest rather than highest resolution structures
3472 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3473 to sequence mapping in 'View Mappings' report
3476 <!-- JAL-2284 -->Unable to read old Jalview projects that
3477 contain non-XML data added after Jalvew wrote project.
3480 <!-- JAL-2118 -->Newly created annotation row reorders
3481 after clicking on it to create new annotation for a
3485 <!-- JAL-1980 -->Null Pointer Exception raised when
3486 pressing Add on an orphaned cut'n'paste window.
3488 <!-- may exclude, this is an external service stability issue JAL-1941
3489 -- > RNA 3D structure not added via DSSR service</li> -->
3494 <!-- JAL-2151 -->Incorrect columns are selected when
3495 hidden columns present before start of sequence
3498 <!-- JAL-1986 -->Missing dependencies on applet pages
3502 <!-- JAL-1947 -->Overview pixel size changes when
3503 sequences are hidden in applet
3506 <!-- JAL-1996 -->Updated instructions for applet
3507 deployment on examples pages.
3514 <td width="60" nowrap>
3515 <div align="center">
3516 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3517 <em>16/10/2015</em></strong>
3520 <td><em>General</em>
3522 <li>Time stamps for signed Jalview application and applet
3527 <em>Application</em>
3529 <li>Duplicate group consensus and conservation rows
3530 shown when tree is partitioned</li>
3531 <li>Erratic behaviour when tree partitions made with
3532 multiple cDNA/Protein split views</li>
3538 <td width="60" nowrap>
3539 <div align="center">
3540 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3541 <em>8/10/2015</em></strong>
3544 <td><em>General</em>
3546 <li>Updated Spanish translations of localized text for
3548 </ul> <em>Application</em>
3550 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3551 <li>Signed OSX InstallAnywhere installer<br></li>
3552 <li>Support for per-sequence based annotations in BioJSON</li>
3553 </ul> <em>Applet</em>
3555 <li>Split frame example added to applet examples page</li>
3556 </ul> <em>Build and Deployment</em>
3559 <!-- JAL-1888 -->New ant target for running Jalview's test
3567 <li>Mapping of cDNA to protein in split frames
3568 incorrect when sequence start > 1</li>
3569 <li>Broken images in filter column by annotation dialog
3571 <li>Feature colours not parsed from features file</li>
3572 <li>Exceptions and incomplete link URLs recovered when
3573 loading a features file containing HTML tags in feature
3577 <em>Application</em>
3579 <li>Annotations corrupted after BioJS export and
3581 <li>Incorrect sequence limits after Fetch DB References
3582 with 'trim retrieved sequences'</li>
3583 <li>Incorrect warning about deleting all data when
3584 deleting selected columns</li>
3585 <li>Patch to build system for shipping properly signed
3586 JNLP templates for webstart launch</li>
3587 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3588 unreleased structures for download or viewing</li>
3589 <li>Tab/space/return keystroke operation of EMBL-PDBe
3590 fetcher/viewer dialogs works correctly</li>
3591 <li>Disabled 'minimise' button on Jalview windows
3592 running on OSX to workaround redraw hang bug</li>
3593 <li>Split cDNA/Protein view position and geometry not
3594 recovered from jalview project</li>
3595 <li>Initial enabled/disabled state of annotation menu
3596 sorter 'show autocalculated first/last' corresponds to
3598 <li>Restoring of Clustal, RNA Helices and T-Coffee
3599 color schemes from BioJSON</li>
3603 <li>Reorder sequences mirrored in cDNA/Protein split
3605 <li>Applet with Jmol examples not loading correctly</li>
3611 <td><div align="center">
3612 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3614 <td><em>General</em>
3616 <li>Linked visualisation and analysis of DNA and Protein
3619 <li>Translated cDNA alignments shown as split protein
3620 and DNA alignment views</li>
3621 <li>Codon consensus annotation for linked protein and
3622 cDNA alignment views</li>
3623 <li>Link cDNA or Protein product sequences by loading
3624 them onto Protein or cDNA alignments</li>
3625 <li>Reconstruct linked cDNA alignment from aligned
3626 protein sequences</li>
3629 <li>Jmol integration updated to Jmol v14.2.14</li>
3630 <li>Import and export of Jalview alignment views as <a
3631 href="features/bioJsonFormat.html">BioJSON</a></li>
3632 <li>New alignment annotation file statements for
3633 reference sequences and marking hidden columns</li>
3634 <li>Reference sequence based alignment shading to
3635 highlight variation</li>
3636 <li>Select or hide columns according to alignment
3638 <li>Find option for locating sequences by description</li>
3639 <li>Conserved physicochemical properties shown in amino
3640 acid conservation row</li>
3641 <li>Alignments can be sorted by number of RNA helices</li>
3642 </ul> <em>Application</em>
3644 <li>New cDNA/Protein analysis capabilities
3646 <li>Get Cross-References should open a Split Frame
3647 view with cDNA/Protein</li>
3648 <li>Detect when nucleotide sequences and protein
3649 sequences are placed in the same alignment</li>
3650 <li>Split cDNA/Protein views are saved in Jalview
3655 <li>Use REST API to talk to Chimera</li>
3656 <li>Selected regions in Chimera are highlighted in linked
3657 Jalview windows</li>
3659 <li>VARNA RNA viewer updated to v3.93</li>
3660 <li>VARNA views are saved in Jalview Projects</li>
3661 <li>Pseudoknots displayed as Jalview RNA annotation can
3662 be shown in VARNA</li>
3664 <li>Make groups for selection uses marked columns as well
3665 as the active selected region</li>
3667 <li>Calculate UPGMA and NJ trees using sequence feature
3669 <li>New Export options
3671 <li>New Export Settings dialog to control hidden
3672 region export in flat file generation</li>
3674 <li>Export alignment views for display with the <a
3675 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3677 <li>Export scrollable SVG in HTML page</li>
3678 <li>Optional embedding of BioJSON data when exporting
3679 alignment figures to HTML</li>
3681 <li>3D structure retrieval and display
3683 <li>Free text and structured queries with the PDBe
3685 <li>PDBe Search API based discovery and selection of
3686 PDB structures for a sequence set</li>
3690 <li>JPred4 employed for protein secondary structure
3692 <li>Hide Insertions menu option to hide unaligned columns
3693 for one or a group of sequences</li>
3694 <li>Automatically hide insertions in alignments imported
3695 from the JPred4 web server</li>
3696 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3697 system on OSX<br />LGPL libraries courtesy of <a
3698 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3700 <li>changed 'View nucleotide structure' submenu to 'View
3701 VARNA 2D Structure'</li>
3702 <li>change "View protein structure" menu option to "3D
3705 </ul> <em>Applet</em>
3707 <li>New layout for applet example pages</li>
3708 <li>New parameters to enable SplitFrame view
3709 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3710 <li>New example demonstrating linked viewing of cDNA and
3711 Protein alignments</li>
3712 </ul> <em>Development and deployment</em>
3714 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3715 <li>Include installation type and git revision in build
3716 properties and console log output</li>
3717 <li>Jalview Github organisation, and new github site for
3718 storing BioJsMSA Templates</li>
3719 <li>Jalview's unit tests now managed with TestNG</li>
3722 <!-- <em>General</em>
3724 </ul> --> <!-- issues resolved --> <em>Application</em>
3726 <li>Escape should close any open find dialogs</li>
3727 <li>Typo in select-by-features status report</li>
3728 <li>Consensus RNA secondary secondary structure
3729 predictions are not highlighted in amber</li>
3730 <li>Missing gap character in v2.7 example file means
3731 alignment appears unaligned when pad-gaps is not enabled</li>
3732 <li>First switch to RNA Helices colouring doesn't colour
3733 associated structure views</li>
3734 <li>ID width preference option is greyed out when auto
3735 width checkbox not enabled</li>
3736 <li>Stopped a warning dialog from being shown when
3737 creating user defined colours</li>
3738 <li>'View Mapping' in structure viewer shows sequence
3739 mappings for just that viewer's sequences</li>
3740 <li>Workaround for superposing PDB files containing
3741 multiple models in Chimera</li>
3742 <li>Report sequence position in status bar when hovering
3743 over Jmol structure</li>
3744 <li>Cannot output gaps as '.' symbols with Selection ->
3745 output to text box</li>
3746 <li>Flat file exports of alignments with hidden columns
3747 have incorrect sequence start/end</li>
3748 <li>'Aligning' a second chain to a Chimera structure from
3750 <li>Colour schemes applied to structure viewers don't
3751 work for nucleotide</li>
3752 <li>Loading/cut'n'pasting an empty or invalid file leads
3753 to a grey/invisible alignment window</li>
3754 <li>Exported Jpred annotation from a sequence region
3755 imports to different position</li>
3756 <li>Space at beginning of sequence feature tooltips shown
3757 on some platforms</li>
3758 <li>Chimera viewer 'View | Show Chain' menu is not
3760 <li>'New View' fails with a Null Pointer Exception in
3761 console if Chimera has been opened</li>
3762 <li>Mouseover to Chimera not working</li>
3763 <li>Miscellaneous ENA XML feature qualifiers not
3765 <li>NPE in annotation renderer after 'Extract Scores'</li>
3766 <li>If two structures in one Chimera window, mouseover of
3767 either sequence shows on first structure</li>
3768 <li>'Show annotations' options should not make
3769 non-positional annotations visible</li>
3770 <li>Subsequence secondary structure annotation not shown
3771 in right place after 'view flanking regions'</li>
3772 <li>File Save As type unset when current file format is
3774 <li>Save as '.jar' option removed for saving Jalview
3776 <li>Colour by Sequence colouring in Chimera more
3778 <li>Cannot 'add reference annotation' for a sequence in
3779 several views on same alignment</li>
3780 <li>Cannot show linked products for EMBL / ENA records</li>
3781 <li>Jalview's tooltip wraps long texts containing no
3783 </ul> <em>Applet</em>
3785 <li>Jmol to JalviewLite mouseover/link not working</li>
3786 <li>JalviewLite can't import sequences with ID
3787 descriptions containing angle brackets</li>
3788 </ul> <em>General</em>
3790 <li>Cannot export and reimport RNA secondary structure
3791 via jalview annotation file</li>
3792 <li>Random helix colour palette for colour by annotation
3793 with RNA secondary structure</li>
3794 <li>Mouseover to cDNA from STOP residue in protein
3795 translation doesn't work.</li>
3796 <li>hints when using the select by annotation dialog box</li>
3797 <li>Jmol alignment incorrect if PDB file has alternate CA
3799 <li>FontChooser message dialog appears to hang after
3800 choosing 1pt font</li>
3801 <li>Peptide secondary structure incorrectly imported from
3802 annotation file when annotation display text includes 'e' or
3804 <li>Cannot set colour of new feature type whilst creating
3806 <li>cDNA translation alignment should not be sequence
3807 order dependent</li>
3808 <li>'Show unconserved' doesn't work for lower case
3810 <li>Nucleotide ambiguity codes involving R not recognised</li>
3811 </ul> <em>Deployment and Documentation</em>
3813 <li>Applet example pages appear different to the rest of
3814 www.jalview.org</li>
3815 </ul> <em>Application Known issues</em>
3817 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3818 <li>Misleading message appears after trying to delete
3820 <li>Jalview icon not shown in dock after InstallAnywhere
3821 version launches</li>
3822 <li>Fetching EMBL reference for an RNA sequence results
3823 fails with a sequence mismatch</li>
3824 <li>Corrupted or unreadable alignment display when
3825 scrolling alignment to right</li>
3826 <li>ArrayIndexOutOfBoundsException thrown when remove
3827 empty columns called on alignment with ragged gapped ends</li>
3828 <li>auto calculated alignment annotation rows do not get
3829 placed above or below non-autocalculated rows</li>
3830 <li>Jalview dekstop becomes sluggish at full screen in
3831 ultra-high resolution</li>
3832 <li>Cannot disable consensus calculation independently of
3833 quality and conservation</li>
3834 <li>Mouseover highlighting between cDNA and protein can
3835 become sluggish with more than one splitframe shown</li>
3836 </ul> <em>Applet Known Issues</em>
3838 <li>Core PDB parsing code requires Jmol</li>
3839 <li>Sequence canvas panel goes white when alignment
3840 window is being resized</li>
3846 <td><div align="center">
3847 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3849 <td><em>General</em>
3851 <li>Updated Java code signing certificate donated by
3853 <li>Features and annotation preserved when performing
3854 pairwise alignment</li>
3855 <li>RNA pseudoknot annotation can be
3856 imported/exported/displayed</li>
3857 <li>'colour by annotation' can colour by RNA and
3858 protein secondary structure</li>
3859 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3860 post-hoc with 2.9 release</em>)
3863 </ul> <em>Application</em>
3865 <li>Extract and display secondary structure for sequences
3866 with 3D structures</li>
3867 <li>Support for parsing RNAML</li>
3868 <li>Annotations menu for layout
3870 <li>sort sequence annotation rows by alignment</li>
3871 <li>place sequence annotation above/below alignment
3874 <li>Output in Stockholm format</li>
3875 <li>Internationalisation: improved Spanish (es)
3877 <li>Structure viewer preferences tab</li>
3878 <li>Disorder and Secondary Structure annotation tracks
3879 shared between alignments</li>
3880 <li>UCSF Chimera launch and linked highlighting from
3882 <li>Show/hide all sequence associated annotation rows for
3883 all or current selection</li>
3884 <li>disorder and secondary structure predictions
3885 available as dataset annotation</li>
3886 <li>Per-sequence rna helices colouring</li>
3889 <li>Sequence database accessions imported when fetching
3890 alignments from Rfam</li>
3891 <li>update VARNA version to 3.91</li>
3893 <li>New groovy scripts for exporting aligned positions,
3894 conservation values, and calculating sum of pairs scores.</li>
3895 <li>Command line argument to set default JABAWS server</li>
3896 <li>include installation type in build properties and
3897 console log output</li>
3898 <li>Updated Jalview project format to preserve dataset
3902 <!-- issues resolved --> <em>Application</em>
3904 <li>Distinguish alignment and sequence associated RNA
3905 structure in structure->view->VARNA</li>
3906 <li>Raise dialog box if user deletes all sequences in an
3908 <li>Pressing F1 results in documentation opening twice</li>
3909 <li>Sequence feature tooltip is wrapped</li>
3910 <li>Double click on sequence associated annotation
3911 selects only first column</li>
3912 <li>Redundancy removal doesn't result in unlinked
3913 leaves shown in tree</li>
3914 <li>Undos after several redundancy removals don't undo
3916 <li>Hide sequence doesn't hide associated annotation</li>
3917 <li>User defined colours dialog box too big to fit on
3918 screen and buttons not visible</li>
3919 <li>author list isn't updated if already written to
3920 Jalview properties</li>
3921 <li>Popup menu won't open after retrieving sequence
3923 <li>File open window for associate PDB doesn't open</li>
3924 <li>Left-then-right click on a sequence id opens a
3925 browser search window</li>
3926 <li>Cannot open sequence feature shading/sort popup menu
3927 in feature settings dialog</li>
3928 <li>better tooltip placement for some areas of Jalview
3930 <li>Allow addition of JABAWS Server which doesn't
3931 pass validation</li>
3932 <li>Web services parameters dialog box is too large to
3934 <li>Muscle nucleotide alignment preset obscured by
3936 <li>JABAWS preset submenus don't contain newly
3937 defined user preset</li>
3938 <li>MSA web services warns user if they were launched
3939 with invalid input</li>
3940 <li>Jalview cannot contact DAS Registy when running on
3943 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3944 'Superpose with' submenu not shown when new view
3948 </ul> <!-- <em>Applet</em>
3950 </ul> <em>General</em>
3952 </ul>--> <em>Deployment and Documentation</em>
3954 <li>2G and 1G options in launchApp have no effect on
3955 memory allocation</li>
3956 <li>launchApp service doesn't automatically open
3957 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3959 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3960 InstallAnywhere reports cannot find valid JVM when Java
3961 1.7_055 is available
3963 </ul> <em>Application Known issues</em>
3966 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3967 corrupted or unreadable alignment display when scrolling
3971 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3972 retrieval fails but progress bar continues for DAS retrieval
3973 with large number of ID
3976 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3977 flatfile output of visible region has incorrect sequence
3981 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3982 rna structure consensus doesn't update when secondary
3983 structure tracks are rearranged
3986 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3987 invalid rna structure positional highlighting does not
3988 highlight position of invalid base pairs
3991 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3992 out of memory errors are not raised when saving Jalview
3993 project from alignment window file menu
3996 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3997 Switching to RNA Helices colouring doesn't propagate to
4001 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
4002 colour by RNA Helices not enabled when user created
4003 annotation added to alignment
4006 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
4007 Jalview icon not shown on dock in Mountain Lion/Webstart
4009 </ul> <em>Applet Known Issues</em>
4012 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
4013 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
4016 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
4017 Jalview and Jmol example not compatible with IE9
4020 <li>Sort by annotation score doesn't reverse order
4026 <td><div align="center">
4027 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
4030 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
4033 <li>Internationalisation of user interface (usually
4034 called i18n support) and translation for Spanish locale</li>
4035 <li>Define/Undefine group on current selection with
4036 Ctrl-G/Shift Ctrl-G</li>
4037 <li>Improved group creation/removal options in
4038 alignment/sequence Popup menu</li>
4039 <li>Sensible precision for symbol distribution
4040 percentages shown in logo tooltip.</li>
4041 <li>Annotation panel height set according to amount of
4042 annotation when alignment first opened</li>
4043 </ul> <em>Application</em>
4045 <li>Interactive consensus RNA secondary structure
4046 prediction VIENNA RNAAliFold JABA 2.1 service</li>
4047 <li>Select columns containing particular features from
4048 Feature Settings dialog</li>
4049 <li>View all 'representative' PDB structures for selected
4051 <li>Update Jalview project format:
4053 <li>New file extension for Jalview projects '.jvp'</li>
4054 <li>Preserve sequence and annotation dataset (to
4055 store secondary structure annotation,etc)</li>
4056 <li>Per group and alignment annotation and RNA helix
4060 <li>New similarity measures for PCA and Tree calculation
4062 <li>Experimental support for retrieval and viewing of
4063 flanking regions for an alignment</li>
4067 <!-- issues resolved --> <em>Application</em>
4069 <li>logo keeps spinning and status remains at queued or
4070 running after job is cancelled</li>
4071 <li>cannot export features from alignments imported from
4072 Jalview/VAMSAS projects</li>
4073 <li>Buggy slider for web service parameters that take
4075 <li>Newly created RNA secondary structure line doesn't
4076 have 'display all symbols' flag set</li>
4077 <li>T-COFFEE alignment score shading scheme and other
4078 annotation shading not saved in Jalview project</li>
4079 <li>Local file cannot be loaded in freshly downloaded
4081 <li>Jalview icon not shown on dock in Mountain
4083 <li>Load file from desktop file browser fails</li>
4084 <li>Occasional NPE thrown when calculating large trees</li>
4085 <li>Cannot reorder or slide sequences after dragging an
4086 alignment onto desktop</li>
4087 <li>Colour by annotation dialog throws NPE after using
4088 'extract scores' function</li>
4089 <li>Loading/cut'n'pasting an empty file leads to a grey
4090 alignment window</li>
4091 <li>Disorder thresholds rendered incorrectly after
4092 performing IUPred disorder prediction</li>
4093 <li>Multiple group annotated consensus rows shown when
4094 changing 'normalise logo' display setting</li>
4095 <li>Find shows blank dialog after 'finished searching' if
4096 nothing matches query</li>
4097 <li>Null Pointer Exceptions raised when sorting by
4098 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
4100 <li>Errors in Jmol console when structures in alignment
4101 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
4103 <li>Not all working JABAWS services are shown in
4105 <li>JAVAWS version of Jalview fails to launch with
4106 'invalid literal/length code'</li>
4107 <li>Annotation/RNA Helix colourschemes cannot be applied
4108 to alignment with groups (actually fixed in 2.8.0b1)</li>
4109 <li>RNA Helices and T-Coffee Scores available as default
4112 </ul> <em>Applet</em>
4114 <li>Remove group option is shown even when selection is
4116 <li>Apply to all groups ticked but colourscheme changes
4117 don't affect groups</li>
4118 <li>Documented RNA Helices and T-Coffee Scores as valid
4119 colourscheme name</li>
4120 <li>Annotation labels drawn on sequence IDs when
4121 Annotation panel is not displayed</li>
4122 <li>Increased font size for dropdown menus on OSX and
4123 embedded windows</li>
4124 </ul> <em>Other</em>
4126 <li>Consensus sequence for alignments/groups with a
4127 single sequence were not calculated</li>
4128 <li>annotation files that contain only groups imported as
4129 annotation and junk sequences</li>
4130 <li>Fasta files with sequences containing '*' incorrectly
4131 recognised as PFAM or BLC</li>
4132 <li>conservation/PID slider apply all groups option
4133 doesn't affect background (2.8.0b1)
4135 <li>redundancy highlighting is erratic at 0% and 100%</li>
4136 <li>Remove gapped columns fails for sequences with ragged
4138 <li>AMSA annotation row with leading spaces is not
4139 registered correctly on import</li>
4140 <li>Jalview crashes when selecting PCA analysis for
4141 certain alignments</li>
4142 <li>Opening the colour by annotation dialog for an
4143 existing annotation based 'use original colours'
4144 colourscheme loses original colours setting</li>
4149 <td><div align="center">
4150 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
4151 <em>30/1/2014</em></strong>
4155 <li>Trusted certificates for JalviewLite applet and
4156 Jalview Desktop application<br />Certificate was donated by
4157 <a href="https://www.certum.eu">Certum</a> to the Jalview
4158 open source project).
4160 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
4161 <li>Output in Stockholm format</li>
4162 <li>Allow import of data from gzipped files</li>
4163 <li>Export/import group and sequence associated line
4164 graph thresholds</li>
4165 <li>Nucleotide substitution matrix that supports RNA and
4166 ambiguity codes</li>
4167 <li>Allow disorder predictions to be made on the current
4168 selection (or visible selection) in the same way that JPred
4170 <li>Groovy scripting for headless Jalview operation</li>
4171 </ul> <em>Other improvements</em>
4173 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
4174 <li>COMBINE statement uses current SEQUENCE_REF and
4175 GROUP_REF scope to group annotation rows</li>
4176 <li>Support '' style escaping of quotes in Newick
4178 <li>Group options for JABAWS service by command line name</li>
4179 <li>Empty tooltip shown for JABA service options with a
4180 link but no description</li>
4181 <li>Select primary source when selecting authority in
4182 database fetcher GUI</li>
4183 <li>Add .mfa to FASTA file extensions recognised by
4185 <li>Annotation label tooltip text wrap</li>
4190 <li>Slow scrolling when lots of annotation rows are
4192 <li>Lots of NPE (and slowness) after creating RNA
4193 secondary structure annotation line</li>
4194 <li>Sequence database accessions not imported when
4195 fetching alignments from Rfam</li>
4196 <li>Incorrect SHMR submission for sequences with
4198 <li>View all structures does not always superpose
4200 <li>Option widgets in service parameters not updated to
4201 reflect user or preset settings</li>
4202 <li>Null pointer exceptions for some services without
4203 presets or adjustable parameters</li>
4204 <li>Discover PDB IDs entry in structure menu doesn't
4205 discover PDB xRefs</li>
4206 <li>Exception encountered while trying to retrieve
4207 features with DAS</li>
4208 <li>Lowest value in annotation row isn't coloured
4209 when colour by annotation (per sequence) is coloured</li>
4210 <li>Keyboard mode P jumps to start of gapped region when
4211 residue follows a gap</li>
4212 <li>Jalview appears to hang importing an alignment with
4213 Wrap as default or after enabling Wrap</li>
4214 <li>'Right click to add annotations' message
4215 shown in wrap mode when no annotations present</li>
4216 <li>Disorder predictions fail with NPE if no automatic
4217 annotation already exists on alignment</li>
4218 <li>oninit javascript function should be called after
4219 initialisation completes</li>
4220 <li>Remove redundancy after disorder prediction corrupts
4221 alignment window display</li>
4222 <li>Example annotation file in documentation is invalid</li>
4223 <li>Grouped line graph annotation rows are not exported
4224 to annotation file</li>
4225 <li>Multi-harmony analysis cannot be run when only two
4227 <li>Cannot create multiple groups of line graphs with
4228 several 'combine' statements in annotation file</li>
4229 <li>Pressing return several times causes Number Format
4230 exceptions in keyboard mode</li>
4231 <li>Multi-harmony (SHMMR) method doesn't submit
4232 correct partitions for input data</li>
4233 <li>Translation from DNA to Amino Acids fails</li>
4234 <li>Jalview fail to load newick tree with quoted label</li>
4235 <li>--headless flag isn't understood</li>
4236 <li>ClassCastException when generating EPS in headless
4238 <li>Adjusting sequence-associated shading threshold only
4239 changes one row's threshold</li>
4240 <li>Preferences and Feature settings panel panel
4241 doesn't open</li>
4242 <li>hide consensus histogram also hides conservation and
4243 quality histograms</li>
4248 <td><div align="center">
4249 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
4251 <td><em>Application</em>
4253 <li>Support for JABAWS 2.0 Services (AACon alignment
4254 conservation, protein disorder and Clustal Omega)</li>
4255 <li>JABAWS server status indicator in Web Services
4257 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
4258 in Jalview alignment window</li>
4259 <li>Updated Jalview build and deploy framework for OSX
4260 mountain lion, windows 7, and 8</li>
4261 <li>Nucleotide substitution matrix for PCA that supports
4262 RNA and ambiguity codes</li>
4264 <li>Improved sequence database retrieval GUI</li>
4265 <li>Support fetching and database reference look up
4266 against multiple DAS sources (Fetch all from in 'fetch db
4268 <li>Jalview project improvements
4270 <li>Store and retrieve the 'belowAlignment'
4271 flag for annotation</li>
4272 <li>calcId attribute to group annotation rows on the
4274 <li>Store AACon calculation settings for a view in
4275 Jalview project</li>
4279 <li>horizontal scrolling gesture support</li>
4280 <li>Visual progress indicator when PCA calculation is
4282 <li>Simpler JABA web services menus</li>
4283 <li>visual indication that web service results are still
4284 being retrieved from server</li>
4285 <li>Serialise the dialogs that are shown when Jalview
4286 starts up for first time</li>
4287 <li>Jalview user agent string for interacting with HTTP
4289 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
4291 <li>Examples directory and Groovy library included in
4292 InstallAnywhere distribution</li>
4293 </ul> <em>Applet</em>
4295 <li>RNA alignment and secondary structure annotation
4296 visualization applet example</li>
4297 </ul> <em>General</em>
4299 <li>Normalise option for consensus sequence logo</li>
4300 <li>Reset button in PCA window to return dimensions to
4302 <li>Allow seqspace or Jalview variant of alignment PCA
4304 <li>PCA with either nucleic acid and protein substitution
4306 <li>Allow windows containing HTML reports to be exported
4308 <li>Interactive display and editing of RNA secondary
4309 structure contacts</li>
4310 <li>RNA Helix Alignment Colouring</li>
4311 <li>RNA base pair logo consensus</li>
4312 <li>Parse sequence associated secondary structure
4313 information in Stockholm files</li>
4314 <li>HTML Export database accessions and annotation
4315 information presented in tooltip for sequences</li>
4316 <li>Import secondary structure from LOCARNA clustalw
4317 style RNA alignment files</li>
4318 <li>import and visualise T-COFFEE quality scores for an
4320 <li>'colour by annotation' per sequence option to
4321 shade each sequence according to its associated alignment
4323 <li>New Jalview Logo</li>
4324 </ul> <em>Documentation and Development</em>
4326 <li>documentation for score matrices used in Jalview</li>
4327 <li>New Website!</li>
4329 <td><em>Application</em>
4331 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
4332 wsdbfetch REST service</li>
4333 <li>Stop windows being moved outside desktop on OSX</li>
4334 <li>Filetype associations not installed for webstart
4336 <li>Jalview does not always retrieve progress of a JABAWS
4337 job execution in full once it is complete</li>
4338 <li>revise SHMR RSBS definition to ensure alignment is
4339 uploaded via ali_file parameter</li>
4340 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
4341 <li>View all structures superposed fails with exception</li>
4342 <li>Jnet job queues forever if a very short sequence is
4343 submitted for prediction</li>
4344 <li>Cut and paste menu not opened when mouse clicked on
4346 <li>Putting fractional value into integer text box in
4347 alignment parameter dialog causes Jalview to hang</li>
4348 <li>Structure view highlighting doesn't work on
4350 <li>View all structures fails with exception shown in
4352 <li>Characters in filename associated with PDBEntry not
4353 escaped in a platform independent way</li>
4354 <li>Jalview desktop fails to launch with exception when
4356 <li>Tree calculation reports 'you must have 2 or more
4357 sequences selected' when selection is empty</li>
4358 <li>Jalview desktop fails to launch with jar signature
4359 failure when java web start temporary file caching is
4361 <li>DAS Sequence retrieval with range qualification
4362 results in sequence xref which includes range qualification</li>
4363 <li>Errors during processing of command line arguments
4364 cause progress bar (JAL-898) to be removed</li>
4365 <li>Replace comma for semi-colon option not disabled for
4366 DAS sources in sequence fetcher</li>
4367 <li>Cannot close news reader when JABAWS server warning
4368 dialog is shown</li>
4369 <li>Option widgets not updated to reflect user settings</li>
4370 <li>Edited sequence not submitted to web service</li>
4371 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
4372 <li>InstallAnywhere installer doesn't unpack and run
4373 on OSX Mountain Lion</li>
4374 <li>Annotation panel not given a scroll bar when
4375 sequences with alignment annotation are pasted into the
4377 <li>Sequence associated annotation rows not associated
4378 when loaded from Jalview project</li>
4379 <li>Browser launch fails with NPE on java 1.7</li>
4380 <li>JABAWS alignment marked as finished when job was
4381 cancelled or job failed due to invalid input</li>
4382 <li>NPE with v2.7 example when clicking on Tree
4383 associated with all views</li>
4384 <li>Exceptions when copy/paste sequences with grouped
4385 annotation rows to new window</li>
4386 </ul> <em>Applet</em>
4388 <li>Sequence features are momentarily displayed before
4389 they are hidden using hidefeaturegroups applet parameter</li>
4390 <li>loading features via javascript API automatically
4391 enables feature display</li>
4392 <li>scrollToColumnIn javascript API method doesn't
4394 </ul> <em>General</em>
4396 <li>Redundancy removal fails for rna alignment</li>
4397 <li>PCA calculation fails when sequence has been selected
4398 and then deselected</li>
4399 <li>PCA window shows grey box when first opened on OSX</li>
4400 <li>Letters coloured pink in sequence logo when alignment
4401 coloured with clustalx</li>
4402 <li>Choosing fonts without letter symbols defined causes
4403 exceptions and redraw errors</li>
4404 <li>Initial PCA plot view is not same as manually
4405 reconfigured view</li>
4406 <li>Grouped annotation graph label has incorrect line
4408 <li>Grouped annotation graph label display is corrupted
4409 for lots of labels</li>
4414 <div align="center">
4415 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
4418 <td><em>Application</em>
4420 <li>Jalview Desktop News Reader</li>
4421 <li>Tweaked default layout of web services menu</li>
4422 <li>View/alignment association menu to enable user to
4423 easily specify which alignment a multi-structure view takes
4424 its colours/correspondences from</li>
4425 <li>Allow properties file location to be specified as URL</li>
4426 <li>Extend Jalview project to preserve associations
4427 between many alignment views and a single Jmol display</li>
4428 <li>Store annotation row height in Jalview project file</li>
4429 <li>Annotation row column label formatting attributes
4430 stored in project file</li>
4431 <li>Annotation row order for auto-calculated annotation
4432 rows preserved in Jalview project file</li>
4433 <li>Visual progress indication when Jalview state is
4434 saved using Desktop window menu</li>
4435 <li>Visual indication that command line arguments are
4436 still being processed</li>
4437 <li>Groovy script execution from URL</li>
4438 <li>Colour by annotation default min and max colours in
4440 <li>Automatically associate PDB files dragged onto an
4441 alignment with sequences that have high similarity and
4443 <li>Update JGoogleAnalytics to latest release (0.3)</li>
4444 <li>'view structures' option to open many
4445 structures in same window</li>
4446 <li>Sort associated views menu option for tree panel</li>
4447 <li>Group all JABA and non-JABA services for a particular
4448 analysis function in its own submenu</li>
4449 </ul> <em>Applet</em>
4451 <li>Userdefined and autogenerated annotation rows for
4453 <li>Adjustment of alignment annotation pane height</li>
4454 <li>Annotation scrollbar for annotation panel</li>
4455 <li>Drag to reorder annotation rows in annotation panel</li>
4456 <li>'automaticScrolling' parameter</li>
4457 <li>Allow sequences with partial ID string matches to be
4458 annotated from GFF/Jalview features files</li>
4459 <li>Sequence logo annotation row in applet</li>
4460 <li>Absolute paths relative to host server in applet
4461 parameters are treated as such</li>
4462 <li>New in the JalviewLite javascript API:
4464 <li>JalviewLite.js javascript library</li>
4465 <li>Javascript callbacks for
4467 <li>Applet initialisation</li>
4468 <li>Sequence/alignment mouse-overs and selections</li>
4471 <li>scrollTo row and column alignment scrolling
4473 <li>Select sequence/alignment regions from javascript</li>
4474 <li>javascript structure viewer harness to pass
4475 messages between Jmol and Jalview when running as
4476 distinct applets</li>
4477 <li>sortBy method</li>
4478 <li>Set of applet and application examples shipped
4479 with documentation</li>
4480 <li>New example to demonstrate JalviewLite and Jmol
4481 javascript message exchange</li>
4483 </ul> <em>General</em>
4485 <li>Enable Jmol displays to be associated with multiple
4486 multiple alignments</li>
4487 <li>Option to automatically sort alignment with new tree</li>
4488 <li>User configurable link to enable redirects to a
4489 www.Jalview.org mirror</li>
4490 <li>Jmol colours option for Jmol displays</li>
4491 <li>Configurable newline string when writing alignment
4492 and other flat files</li>
4493 <li>Allow alignment annotation description lines to
4494 contain html tags</li>
4495 </ul> <em>Documentation and Development</em>
4497 <li>Add groovy test harness for bulk load testing to
4499 <li>Groovy script to load and align a set of sequences
4500 using a web service before displaying the result in the
4501 Jalview desktop</li>
4502 <li>Restructured javascript and applet api documentation</li>
4503 <li>Ant target to publish example html files with applet
4505 <li>Netbeans project for building Jalview from source</li>
4506 <li>ant task to create online javadoc for Jalview source</li>
4508 <td><em>Application</em>
4510 <li>User defined colourscheme throws exception when
4511 current built in colourscheme is saved as new scheme</li>
4512 <li>AlignFrame->Save in application pops up save
4513 dialog for valid filename/format</li>
4514 <li>Cannot view associated structure for UniProt sequence</li>
4515 <li>PDB file association breaks for UniProt sequence
4517 <li>Associate PDB from file dialog does not tell you
4518 which sequence is to be associated with the file</li>
4519 <li>Find All raises null pointer exception when query
4520 only matches sequence IDs</li>
4521 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4522 <li>Jalview project with Jmol views created with Jalview
4523 2.4 cannot be loaded</li>
4524 <li>Filetype associations not installed for webstart
4526 <li>Two or more chains in a single PDB file associated
4527 with sequences in different alignments do not get coloured
4528 by their associated sequence</li>
4529 <li>Visibility status of autocalculated annotation row
4530 not preserved when project is loaded</li>
4531 <li>Annotation row height and visibility attributes not
4532 stored in Jalview project</li>
4533 <li>Tree bootstraps are not preserved when saved as a
4534 Jalview project</li>
4535 <li>Envision2 workflow tooltips are corrupted</li>
4536 <li>Enabling show group conservation also enables colour
4537 by conservation</li>
4538 <li>Duplicate group associated conservation or consensus
4539 created on new view</li>
4540 <li>Annotation scrollbar not displayed after 'show
4541 all hidden annotation rows' option selected</li>
4542 <li>Alignment quality not updated after alignment
4543 annotation row is hidden then shown</li>
4544 <li>Preserve colouring of structures coloured by
4545 sequences in pre Jalview 2.7 projects</li>
4546 <li>Web service job parameter dialog is not laid out
4548 <li>Web services menu not refreshed after 'reset
4549 services' button is pressed in preferences</li>
4550 <li>Annotation off by one in Jalview v2_3 example project</li>
4551 <li>Structures imported from file and saved in project
4552 get name like jalview_pdb1234.txt when reloaded</li>
4553 <li>Jalview does not always retrieve progress of a JABAWS
4554 job execution in full once it is complete</li>
4555 </ul> <em>Applet</em>
4557 <li>Alignment height set incorrectly when lots of
4558 annotation rows are displayed</li>
4559 <li>Relative URLs in feature HTML text not resolved to
4561 <li>View follows highlighting does not work for positions
4563 <li><= shown as = in tooltip</li>
4564 <li>Export features raises exception when no features
4566 <li>Separator string used for serialising lists of IDs
4567 for javascript api is modified when separator string
4568 provided as parameter</li>
4569 <li>Null pointer exception when selecting tree leaves for
4570 alignment with no existing selection</li>
4571 <li>Relative URLs for datasources assumed to be relative
4572 to applet's codebase</li>
4573 <li>Status bar not updated after finished searching and
4574 search wraps around to first result</li>
4575 <li>StructureSelectionManager instance shared between
4576 several Jalview applets causes race conditions and memory
4578 <li>Hover tooltip and mouseover of position on structure
4579 not sent from Jmol in applet</li>
4580 <li>Certain sequences of javascript method calls to
4581 applet API fatally hang browser</li>
4582 </ul> <em>General</em>
4584 <li>View follows structure mouseover scrolls beyond
4585 position with wrapped view and hidden regions</li>
4586 <li>Find sequence position moves to wrong residue
4587 with/without hidden columns</li>
4588 <li>Sequence length given in alignment properties window
4590 <li>InvalidNumberFormat exceptions thrown when trying to
4591 import PDB like structure files</li>
4592 <li>Positional search results are only highlighted
4593 between user-supplied sequence start/end bounds</li>
4594 <li>End attribute of sequence is not validated</li>
4595 <li>Find dialog only finds first sequence containing a
4596 given sequence position</li>
4597 <li>Sequence numbering not preserved in MSF alignment
4599 <li>Jalview PDB file reader does not extract sequence
4600 from nucleotide chains correctly</li>
4601 <li>Structure colours not updated when tree partition
4602 changed in alignment</li>
4603 <li>Sequence associated secondary structure not correctly
4604 parsed in interleaved stockholm</li>
4605 <li>Colour by annotation dialog does not restore current
4607 <li>Hiding (nearly) all sequences doesn't work
4609 <li>Sequences containing lowercase letters are not
4610 properly associated with their pdb files</li>
4611 </ul> <em>Documentation and Development</em>
4613 <li>schemas/JalviewWsParamSet.xsd corrupted by
4614 ApplyCopyright tool</li>
4619 <div align="center">
4620 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4623 <td><em>Application</em>
4625 <li>New warning dialog when the Jalview Desktop cannot
4626 contact web services</li>
4627 <li>JABA service parameters for a preset are shown in
4628 service job window</li>
4629 <li>JABA Service menu entries reworded</li>
4633 <li>Modeller PIR IO broken - cannot correctly import a
4634 pir file emitted by Jalview</li>
4635 <li>Existing feature settings transferred to new
4636 alignment view created from cut'n'paste</li>
4637 <li>Improved test for mixed amino/nucleotide chains when
4638 parsing PDB files</li>
4639 <li>Consensus and conservation annotation rows
4640 occasionally become blank for all new windows</li>
4641 <li>Exception raised when right clicking above sequences
4642 in wrapped view mode</li>
4643 </ul> <em>Application</em>
4645 <li>multiple multiply aligned structure views cause cpu
4646 usage to hit 100% and computer to hang</li>
4647 <li>Web Service parameter layout breaks for long user
4648 parameter names</li>
4649 <li>Jaba service discovery hangs desktop if Jaba server
4656 <div align="center">
4657 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4660 <td><em>Application</em>
4662 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4663 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4666 <li>Web Services preference tab</li>
4667 <li>Analysis parameters dialog box and user defined
4669 <li>Improved speed and layout of Envision2 service menu</li>
4670 <li>Superpose structures using associated sequence
4672 <li>Export coordinates and projection as CSV from PCA
4674 </ul> <em>Applet</em>
4676 <li>enable javascript: execution by the applet via the
4677 link out mechanism</li>
4678 </ul> <em>Other</em>
4680 <li>Updated the Jmol Jalview interface to work with Jmol
4682 <li>The Jalview Desktop and JalviewLite applet now
4683 require Java 1.5</li>
4684 <li>Allow Jalview feature colour specification for GFF
4685 sequence annotation files</li>
4686 <li>New 'colour by label' keword in Jalview feature file
4687 type colour specification</li>
4688 <li>New Jalview Desktop Groovy API method that allows a
4689 script to check if it being run in an interactive session or
4690 in a batch operation from the Jalview command line</li>
4694 <li>clustalx colourscheme colours Ds preferentially when
4695 both D+E are present in over 50% of the column</li>
4696 </ul> <em>Application</em>
4698 <li>typo in AlignmentFrame->View->Hide->all but
4699 selected Regions menu item</li>
4700 <li>sequence fetcher replaces ',' for ';' when the ',' is
4701 part of a valid accession ID</li>
4702 <li>fatal OOM if object retrieved by sequence fetcher
4703 runs out of memory</li>
4704 <li>unhandled Out of Memory Error when viewing pca
4705 analysis results</li>
4706 <li>InstallAnywhere builds fail to launch on OS X java
4707 10.5 update 4 (due to apple Java 1.6 update)</li>
4708 <li>Installanywhere Jalview silently fails to launch</li>
4709 </ul> <em>Applet</em>
4711 <li>Jalview.getFeatureGroups() raises an
4712 ArrayIndexOutOfBoundsException if no feature groups are
4719 <div align="center">
4720 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4726 <li>Alignment prettyprinter doesn't cope with long
4728 <li>clustalx colourscheme colours Ds preferentially when
4729 both D+E are present in over 50% of the column</li>
4730 <li>nucleic acid structures retrieved from PDB do not
4731 import correctly</li>
4732 <li>More columns get selected than were clicked on when a
4733 number of columns are hidden</li>
4734 <li>annotation label popup menu not providing correct
4735 add/hide/show options when rows are hidden or none are
4737 <li>Stockholm format shown in list of readable formats,
4738 and parser copes better with alignments from RFAM.</li>
4739 <li>CSV output of consensus only includes the percentage
4740 of all symbols if sequence logo display is enabled</li>
4742 </ul> <em>Applet</em>
4744 <li>annotation panel disappears when annotation is
4746 </ul> <em>Application</em>
4748 <li>Alignment view not redrawn properly when new
4749 alignment opened where annotation panel is visible but no
4750 annotations are present on alignment</li>
4751 <li>pasted region containing hidden columns is
4752 incorrectly displayed in new alignment window</li>
4753 <li>Jalview slow to complete operations when stdout is
4754 flooded (fix is to close the Jalview console)</li>
4755 <li>typo in AlignmentFrame->View->Hide->all but
4756 selected Rregions menu item.</li>
4757 <li>inconsistent group submenu and Format submenu entry
4758 'Un' or 'Non'conserved</li>
4759 <li>Sequence feature settings are being shared by
4760 multiple distinct alignments</li>
4761 <li>group annotation not recreated when tree partition is
4763 <li>double click on group annotation to select sequences
4764 does not propagate to associated trees</li>
4765 <li>Mac OSX specific issues:
4767 <li>exception raised when mouse clicked on desktop
4768 window background</li>
4769 <li>Desktop menu placed on menu bar and application
4770 name set correctly</li>
4771 <li>sequence feature settings not wide enough for the
4772 save feature colourscheme button</li>
4781 <div align="center">
4782 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4785 <td><em>New Capabilities</em>
4787 <li>URL links generated from description line for
4788 regular-expression based URL links (applet and application)
4791 <li>Non-positional feature URL links are shown in link
4793 <li>Linked viewing of nucleic acid sequences and
4795 <li>Automatic Scrolling option in View menu to display
4796 the currently highlighted region of an alignment.</li>
4797 <li>Order an alignment by sequence length, or using the
4798 average score or total feature count for each sequence.</li>
4799 <li>Shading features by score or associated description</li>
4800 <li>Subdivide alignment and groups based on identity of
4801 selected subsequence (Make Groups from Selection).</li>
4802 <li>New hide/show options including Shift+Control+H to
4803 hide everything but the currently selected region.</li>
4804 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4805 </ul> <em>Application</em>
4807 <li>Fetch DB References capabilities and UI expanded to
4808 support retrieval from DAS sequence sources</li>
4809 <li>Local DAS Sequence sources can be added via the
4810 command line or via the Add local source dialog box.</li>
4811 <li>DAS Dbref and DbxRef feature types are parsed as
4812 database references and protein_name is parsed as
4813 description line (BioSapiens terms).</li>
4814 <li>Enable or disable non-positional feature and database
4815 references in sequence ID tooltip from View menu in
4817 <!-- <li>New hidden columns and rows and representatives capabilities
4818 in annotations file (in progress - not yet fully implemented)</li> -->
4819 <li>Group-associated consensus, sequence logos and
4820 conservation plots</li>
4821 <li>Symbol distributions for each column can be exported
4822 and visualized as sequence logos</li>
4823 <li>Optionally scale multi-character column labels to fit
4824 within each column of annotation row<!-- todo for applet -->
4826 <li>Optional automatic sort of associated alignment view
4827 when a new tree is opened.</li>
4828 <li>Jalview Java Console</li>
4829 <li>Better placement of desktop window when moving
4830 between different screens.</li>
4831 <li>New preference items for sequence ID tooltip and
4832 consensus annotation</li>
4833 <li>Client to submit sequences and IDs to Envision2
4835 <li><em>Vamsas Capabilities</em>
4837 <li>Improved VAMSAS synchronization (Jalview archive
4838 used to preserve views, structures, and tree display
4840 <li>Import of vamsas documents from disk or URL via
4842 <li>Sharing of selected regions between views and
4843 with other VAMSAS applications (Experimental feature!)</li>
4844 <li>Updated API to VAMSAS version 0.2</li>
4846 </ul> <em>Applet</em>
4848 <li>Middle button resizes annotation row height</li>
4851 <li>sortByTree (true/false) - automatically sort the
4852 associated alignment view by the tree when a new tree is
4854 <li>showTreeBootstraps (true/false) - show or hide
4855 branch bootstraps (default is to show them if available)</li>
4856 <li>showTreeDistances (true/false) - show or hide
4857 branch lengths (default is to show them if available)</li>
4858 <li>showUnlinkedTreeNodes (true/false) - indicate if
4859 unassociated nodes should be highlighted in the tree
4861 <li>heightScale and widthScale (1.0 or more) -
4862 increase the height or width of a cell in the alignment
4863 grid relative to the current font size.</li>
4866 <li>Non-positional features displayed in sequence ID
4868 </ul> <em>Other</em>
4870 <li>Features format: graduated colour definitions and
4871 specification of feature scores</li>
4872 <li>Alignment Annotations format: new keywords for group
4873 associated annotation (GROUP_REF) and annotation row display
4874 properties (ROW_PROPERTIES)</li>
4875 <li>XML formats extended to support graduated feature
4876 colourschemes, group associated annotation, and profile
4877 visualization settings.</li></td>
4880 <li>Source field in GFF files parsed as feature source
4881 rather than description</li>
4882 <li>Non-positional features are now included in sequence
4883 feature and gff files (controlled via non-positional feature
4884 visibility in tooltip).</li>
4885 <li>URL links generated for all feature links (bugfix)</li>
4886 <li>Added URL embedding instructions to features file
4888 <li>Codons containing ambiguous nucleotides translated as
4889 'X' in peptide product</li>
4890 <li>Match case switch in find dialog box works for both
4891 sequence ID and sequence string and query strings do not
4892 have to be in upper case to match case-insensitively.</li>
4893 <li>AMSA files only contain first column of
4894 multi-character column annotation labels</li>
4895 <li>Jalview Annotation File generation/parsing consistent
4896 with documentation (e.g. Stockholm annotation can be
4897 exported and re-imported)</li>
4898 <li>PDB files without embedded PDB IDs given a friendly
4900 <li>Find incrementally searches ID string matches as well
4901 as subsequence matches, and correctly reports total number
4905 <li>Better handling of exceptions during sequence
4907 <li>Dasobert generated non-positional feature URL
4908 link text excludes the start_end suffix</li>
4909 <li>DAS feature and source retrieval buttons disabled
4910 when fetch or registry operations in progress.</li>
4911 <li>PDB files retrieved from URLs are cached properly</li>
4912 <li>Sequence description lines properly shared via
4914 <li>Sequence fetcher fetches multiple records for all
4916 <li>Ensured that command line das feature retrieval
4917 completes before alignment figures are generated.</li>
4918 <li>Reduced time taken when opening file browser for
4920 <li>isAligned check prior to calculating tree, PCA or
4921 submitting an MSA to JNet now excludes hidden sequences.</li>
4922 <li>User defined group colours properly recovered
4923 from Jalview projects.</li>
4932 <div align="center">
4933 <strong>2.4.0.b2</strong><br> 28/10/2009
4938 <li>Experimental support for google analytics usage
4940 <li>Jalview privacy settings (user preferences and docs).</li>
4945 <li>Race condition in applet preventing startup in
4947 <li>Exception when feature created from selection beyond
4948 length of sequence.</li>
4949 <li>Allow synthetic PDB files to be imported gracefully</li>
4950 <li>Sequence associated annotation rows associate with
4951 all sequences with a given id</li>
4952 <li>Find function matches case-insensitively for sequence
4953 ID string searches</li>
4954 <li>Non-standard characters do not cause pairwise
4955 alignment to fail with exception</li>
4956 </ul> <em>Application Issues</em>
4958 <li>Sequences are now validated against EMBL database</li>
4959 <li>Sequence fetcher fetches multiple records for all
4961 </ul> <em>InstallAnywhere Issues</em>
4963 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4964 issue with installAnywhere mechanism)</li>
4965 <li>Command line launching of JARs from InstallAnywhere
4966 version (java class versioning error fixed)</li>
4973 <div align="center">
4974 <strong>2.4</strong><br> 27/8/2008
4977 <td><em>User Interface</em>
4979 <li>Linked highlighting of codon and amino acid from
4980 translation and protein products</li>
4981 <li>Linked highlighting of structure associated with
4982 residue mapping to codon position</li>
4983 <li>Sequence Fetcher provides example accession numbers
4984 and 'clear' button</li>
4985 <li>MemoryMonitor added as an option under Desktop's
4987 <li>Extract score function to parse whitespace separated
4988 numeric data in description line</li>
4989 <li>Column labels in alignment annotation can be centred.</li>
4990 <li>Tooltip for sequence associated annotation give name
4992 </ul> <em>Web Services and URL fetching</em>
4994 <li>JPred3 web service</li>
4995 <li>Prototype sequence search client (no public services
4997 <li>Fetch either seed alignment or full alignment from
4999 <li>URL Links created for matching database cross
5000 references as well as sequence ID</li>
5001 <li>URL Links can be created using regular-expressions</li>
5002 </ul> <em>Sequence Database Connectivity</em>
5004 <li>Retrieval of cross-referenced sequences from other
5006 <li>Generalised database reference retrieval and
5007 validation to all fetchable databases</li>
5008 <li>Fetch sequences from DAS sources supporting the
5009 sequence command</li>
5010 </ul> <em>Import and Export</em>
5011 <li>export annotation rows as CSV for spreadsheet import</li>
5012 <li>Jalview projects record alignment dataset associations,
5013 EMBL products, and cDNA sequence mappings</li>
5014 <li>Sequence Group colour can be specified in Annotation
5016 <li>Ad-hoc colouring of group in Annotation File using RGB
5017 triplet as name of colourscheme</li>
5018 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
5020 <li>treenode binding for VAMSAS tree exchange</li>
5021 <li>local editing and update of sequences in VAMSAS
5022 alignments (experimental)</li>
5023 <li>Create new or select existing session to join</li>
5024 <li>load and save of vamsas documents</li>
5025 </ul> <em>Application command line</em>
5027 <li>-tree parameter to open trees (introduced for passing
5029 <li>-fetchfrom command line argument to specify nicknames
5030 of DAS servers to query for alignment features</li>
5031 <li>-dasserver command line argument to add new servers
5032 that are also automatically queried for features</li>
5033 <li>-groovy command line argument executes a given groovy
5034 script after all input data has been loaded and parsed</li>
5035 </ul> <em>Applet-Application data exchange</em>
5037 <li>Trees passed as applet parameters can be passed to
5038 application (when using "View in full
5039 application")</li>
5040 </ul> <em>Applet Parameters</em>
5042 <li>feature group display control parameter</li>
5043 <li>debug parameter</li>
5044 <li>showbutton parameter</li>
5045 </ul> <em>Applet API methods</em>
5047 <li>newView public method</li>
5048 <li>Window (current view) specific get/set public methods</li>
5049 <li>Feature display control methods</li>
5050 <li>get list of currently selected sequences</li>
5051 </ul> <em>New Jalview distribution features</em>
5053 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
5054 <li>RELEASE file gives build properties for the latest
5055 Jalview release.</li>
5056 <li>Java 1.1 Applet build made easier and donotobfuscate
5057 property controls execution of obfuscator</li>
5058 <li>Build target for generating source distribution</li>
5059 <li>Debug flag for javacc</li>
5060 <li>.jalview_properties file is documented (slightly) in
5061 jalview.bin.Cache</li>
5062 <li>Continuous Build Integration for stable and
5063 development version of Application, Applet and source
5068 <li>selected region output includes visible annotations
5069 (for certain formats)</li>
5070 <li>edit label/displaychar contains existing label/char
5072 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
5073 <li>shorter peptide product names from EMBL records</li>
5074 <li>Newick string generator makes compact representations</li>
5075 <li>bootstrap values parsed correctly for tree files with
5077 <li>pathological filechooser bug avoided by not allowing
5078 filenames containing a ':'</li>
5079 <li>Fixed exception when parsing GFF files containing
5080 global sequence features</li>
5081 <li>Alignment datasets are finalized only when number of
5082 references from alignment sequences goes to zero</li>
5083 <li>Close of tree branch colour box without colour
5084 selection causes cascading exceptions</li>
5085 <li>occasional negative imgwidth exceptions</li>
5086 <li>better reporting of non-fatal warnings to user when
5087 file parsing fails.</li>
5088 <li>Save works when Jalview project is default format</li>
5089 <li>Save as dialog opened if current alignment format is
5090 not a valid output format</li>
5091 <li>UniProt canonical names introduced for both das and
5093 <li>Histidine should be midblue (not pink!) in Zappo</li>
5094 <li>error messages passed up and output when data read
5096 <li>edit undo recovers previous dataset sequence when
5097 sequence is edited</li>
5098 <li>allow PDB files without pdb ID HEADER lines (like
5099 those generated by MODELLER) to be read in properly</li>
5100 <li>allow reading of JPred concise files as a normal
5102 <li>Stockholm annotation parsing and alignment properties
5103 import fixed for PFAM records</li>
5104 <li>Structure view windows have correct name in Desktop
5106 <li>annotation consisting of sequence associated scores
5107 can be read and written correctly to annotation file</li>
5108 <li>Aligned cDNA translation to aligned peptide works
5110 <li>Fixed display of hidden sequence markers and
5111 non-italic font for representatives in Applet</li>
5112 <li>Applet Menus are always embedded in applet window on
5114 <li>Newly shown features appear at top of stack (in
5116 <li>Annotations added via parameter not drawn properly
5117 due to null pointer exceptions</li>
5118 <li>Secondary structure lines are drawn starting from
5119 first column of alignment</li>
5120 <li>UniProt XML import updated for new schema release in
5122 <li>Sequence feature to sequence ID match for Features
5123 file is case-insensitive</li>
5124 <li>Sequence features read from Features file appended to
5125 all sequences with matching IDs</li>
5126 <li>PDB structure coloured correctly for associated views
5127 containing a sub-sequence</li>
5128 <li>PDB files can be retrieved by applet from Jar files</li>
5129 <li>feature and annotation file applet parameters
5130 referring to different directories are retrieved correctly</li>
5131 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
5132 <li>Fixed application hang whilst waiting for
5133 splash-screen version check to complete</li>
5134 <li>Applet properly URLencodes input parameter values
5135 when passing them to the launchApp service</li>
5136 <li>display name and local features preserved in results
5137 retrieved from web service</li>
5138 <li>Visual delay indication for sequence retrieval and
5139 sequence fetcher initialisation</li>
5140 <li>updated Application to use DAS 1.53e version of
5141 dasobert DAS client</li>
5142 <li>Re-instated Full AMSA support and .amsa file
5144 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
5152 <div align="center">
5153 <strong>2.3</strong><br> 9/5/07
5158 <li>Jmol 11.0.2 integration</li>
5159 <li>PDB views stored in Jalview XML files</li>
5160 <li>Slide sequences</li>
5161 <li>Edit sequence in place</li>
5162 <li>EMBL CDS features</li>
5163 <li>DAS Feature mapping</li>
5164 <li>Feature ordering</li>
5165 <li>Alignment Properties</li>
5166 <li>Annotation Scores</li>
5167 <li>Sort by scores</li>
5168 <li>Feature/annotation editing in applet</li>
5173 <li>Headless state operation in 2.2.1</li>
5174 <li>Incorrect and unstable DNA pairwise alignment</li>
5175 <li>Cut and paste of sequences with annotation</li>
5176 <li>Feature group display state in XML</li>
5177 <li>Feature ordering in XML</li>
5178 <li>blc file iteration selection using filename # suffix</li>
5179 <li>Stockholm alignment properties</li>
5180 <li>Stockhom alignment secondary structure annotation</li>
5181 <li>2.2.1 applet had no feature transparency</li>
5182 <li>Number pad keys can be used in cursor mode</li>
5183 <li>Structure Viewer mirror image resolved</li>
5190 <div align="center">
5191 <strong>2.2.1</strong><br> 12/2/07
5196 <li>Non standard characters can be read and displayed
5197 <li>Annotations/Features can be imported/exported to the
5199 <li>Applet allows editing of sequence/annotation/group
5200 name & description
5201 <li>Preference setting to display sequence name in
5203 <li>Annotation file format extended to allow
5204 Sequence_groups to be defined
5205 <li>Default opening of alignment overview panel can be
5206 specified in preferences
5207 <li>PDB residue numbering annotation added to associated
5213 <li>Applet crash under certain Linux OS with Java 1.6
5215 <li>Annotation file export / import bugs fixed
5216 <li>PNG / EPS image output bugs fixed
5222 <div align="center">
5223 <strong>2.2</strong><br> 27/11/06
5228 <li>Multiple views on alignment
5229 <li>Sequence feature editing
5230 <li>"Reload" alignment
5231 <li>"Save" to current filename
5232 <li>Background dependent text colour
5233 <li>Right align sequence ids
5234 <li>User-defined lower case residue colours
5237 <li>Menu item accelerator keys
5238 <li>Control-V pastes to current alignment
5239 <li>Cancel button for DAS Feature Fetching
5240 <li>PCA and PDB Viewers zoom via mouse roller
5241 <li>User-defined sub-tree colours and sub-tree selection
5244 <li>'New Window' button on the 'Output to Text box'
5249 <li>New memory efficient Undo/Redo System
5250 <li>Optimised symbol lookups and conservation/consensus
5252 <li>Region Conservation/Consensus recalculated after
5254 <li>Fixed Remove Empty Columns Bug (empty columns at end
5256 <li>Slowed DAS Feature Fetching for increased robustness.
5259 <li>Made angle brackets in ASCII feature descriptions
5261 <li>Re-instated Zoom function for PCA
5262 <li>Sequence descriptions conserved in web service
5264 <li>UniProt ID discoverer uses any word separated by
5266 <li>WsDbFetch query/result association resolved
5267 <li>Tree leaf to sequence mapping improved
5268 <li>Smooth fonts switch moved to FontChooser dialog box.
5276 <div align="center">
5277 <strong>2.1.1</strong><br> 12/9/06
5282 <li>Copy consensus sequence to clipboard</li>
5287 <li>Image output - rightmost residues are rendered if
5288 sequence id panel has been resized</li>
5289 <li>Image output - all offscreen group boundaries are
5291 <li>Annotation files with sequence references - all
5292 elements in file are relative to sequence position</li>
5293 <li>Mac Applet users can use Alt key for group editing</li>
5299 <div align="center">
5300 <strong>2.1</strong><br> 22/8/06
5305 <li>MAFFT Multiple Alignment in default Web Service list</li>
5306 <li>DAS Feature fetching</li>
5307 <li>Hide sequences and columns</li>
5308 <li>Export Annotations and Features</li>
5309 <li>GFF file reading / writing</li>
5310 <li>Associate structures with sequences from local PDB
5312 <li>Add sequences to exisiting alignment</li>
5313 <li>Recently opened files / URL lists</li>
5314 <li>Applet can launch the full application</li>
5315 <li>Applet has transparency for features (Java 1.2
5317 <li>Applet has user defined colours parameter</li>
5318 <li>Applet can load sequences from parameter
5319 "sequence<em>x</em>"
5325 <li>Redundancy Panel reinstalled in the Applet</li>
5326 <li>Monospaced font - EPS / rescaling bug fixed</li>
5327 <li>Annotation files with sequence references bug fixed</li>
5333 <div align="center">
5334 <strong>2.08.1</strong><br> 2/5/06
5339 <li>Change case of selected region from Popup menu</li>
5340 <li>Choose to match case when searching</li>
5341 <li>Middle mouse button and mouse movement can compress /
5342 expand the visible width and height of the alignment</li>
5347 <li>Annotation Panel displays complete JNet results</li>
5353 <div align="center">
5354 <strong>2.08b</strong><br> 18/4/06
5360 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
5361 <li>Righthand label on wrapped alignments shows correct
5368 <div align="center">
5369 <strong>2.08</strong><br> 10/4/06
5374 <li>Editing can be locked to the selection area</li>
5375 <li>Keyboard editing</li>
5376 <li>Create sequence features from searches</li>
5377 <li>Precalculated annotations can be loaded onto
5379 <li>Features file allows grouping of features</li>
5380 <li>Annotation Colouring scheme added</li>
5381 <li>Smooth fonts off by default - Faster rendering</li>
5382 <li>Choose to toggle Autocalculate Consensus On/Off</li>
5387 <li>Drag & Drop fixed on Linux</li>
5388 <li>Jalview Archive file faster to load/save, sequence
5389 descriptions saved.</li>
5395 <div align="center">
5396 <strong>2.07</strong><br> 12/12/05
5401 <li>PDB Structure Viewer enhanced</li>
5402 <li>Sequence Feature retrieval and display enhanced</li>
5403 <li>Choose to output sequence start-end after sequence
5404 name for file output</li>
5405 <li>Sequence Fetcher WSDBFetch@EBI</li>
5406 <li>Applet can read feature files, PDB files and can be
5407 used for HTML form input</li>
5412 <li>HTML output writes groups and features</li>
5413 <li>Group editing is Control and mouse click</li>
5414 <li>File IO bugs</li>
5420 <div align="center">
5421 <strong>2.06</strong><br> 28/9/05
5426 <li>View annotations in wrapped mode</li>
5427 <li>More options for PCA viewer</li>
5432 <li>GUI bugs resolved</li>
5433 <li>Runs with -nodisplay from command line</li>
5439 <div align="center">
5440 <strong>2.05b</strong><br> 15/9/05
5445 <li>Choose EPS export as lineart or text</li>
5446 <li>Jar files are executable</li>
5447 <li>Can read in Uracil - maps to unknown residue</li>
5452 <li>Known OutOfMemory errors give warning message</li>
5453 <li>Overview window calculated more efficiently</li>
5454 <li>Several GUI bugs resolved</li>
5460 <div align="center">
5461 <strong>2.05</strong><br> 30/8/05
5466 <li>Edit and annotate in "Wrapped" view</li>
5471 <li>Several GUI bugs resolved</li>
5477 <div align="center">
5478 <strong>2.04</strong><br> 24/8/05
5483 <li>Hold down mouse wheel & scroll to change font
5489 <li>Improved JPred client reliability</li>
5490 <li>Improved loading of Jalview files</li>
5496 <div align="center">
5497 <strong>2.03</strong><br> 18/8/05
5502 <li>Set Proxy server name and port in preferences</li>
5503 <li>Multiple URL links from sequence ids</li>
5504 <li>User Defined Colours can have a scheme name and added
5506 <li>Choose to ignore gaps in consensus calculation</li>
5507 <li>Unix users can set default web browser</li>
5508 <li>Runs without GUI for batch processing</li>
5509 <li>Dynamically generated Web Service Menus</li>
5514 <li>InstallAnywhere download for Sparc Solaris</li>
5520 <div align="center">
5521 <strong>2.02</strong><br> 18/7/05
5527 <li>Copy & Paste order of sequences maintains
5528 alignment order.</li>
5534 <div align="center">
5535 <strong>2.01</strong><br> 12/7/05
5540 <li>Use delete key for deleting selection.</li>
5541 <li>Use Mouse wheel to scroll sequences.</li>
5542 <li>Help file updated to describe how to add alignment
5544 <li>Version and build date written to build properties
5546 <li>InstallAnywhere installation will check for updates
5547 at launch of Jalview.</li>
5552 <li>Delete gaps bug fixed.</li>
5553 <li>FileChooser sorts columns.</li>
5554 <li>Can remove groups one by one.</li>
5555 <li>Filechooser icons installed.</li>
5556 <li>Finder ignores return character when searching.
5557 Return key will initiate a search.<br>
5564 <div align="center">
5565 <strong>2.0</strong><br> 20/6/05
5570 <li>New codebase</li>