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;
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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-3204 -->Updated Jalview bindings for Uniprot XML
107 <!-- JAL-3926 -->Uniprot and PDBe autosearch option is
111 <!-- JAL-3530 -->-nowebservicediscovery command line argument to
112 prevent automatic discovery of analysis webservices on
116 </ul> <em>JalviewJS</em>
119 <!-- 3624 -->PDB structures mapped to Uniprot Sequences with
132 <!-- JAL-3163 -->Missing message bundle keys are only
133 reported once per key (avoids excessive log output in js
137 <!-- JAL-3168 -->Feature type is included in the title of
138 the Feature Settings' Colour Chooser dialog
141 </ul> <em>Development</em>
144 <!-- -->First integrated JalviewJS and Jalview release
146 <li>Updated building instructions</li>
148 <!-- JAL-3789, JAL-3679 -->Improved JalviewJS/Jalview build
149 process, added support for system package provided eclipse
152 <li>Install4j 9.0.x used for installer packaging</li>
153 <li>Notarized MacOS installer for compatibility with Big
154 Sur and Monterey</li>
156 <!-- JAL-3805 -->Uninstaller application for old
157 (InstallAnywhere based) Jalview installations removed from
161 <!-- JAL-3930 -->Improved use of installers for unattended
162 installation with a customizedId of "JALVIEW" in install4j's
172 <!-- JAL-3674 -->Slow structure commands can block Jalview
176 <!-- JAL-3904 -->Structure window's viewer-specific menu
177 disappears when only one structure is shown (and many
178 sequences:one chain mappings are present)
181 <!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
182 the first SEQUENCE_GROUP defined
187 <!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 -->Selections not
188 propagated between Linked CDS - Protein alignments and their
189 trees (known defect from 2.11.1.3)
192 <!-- JAL-3761 -->Not all codon positions highlighted for
193 overlapping exon splice sites (e.g due to RNA slippage)
196 <!-- JAL-3794 -->X was not being recognised as the unknown
197 base in DNA sequences
200 <!-- JAL-3915 -->Removed RNAview checkbox and logic from
201 Structure Preferences
204 <!-- JAL-3583 -->Tooltip behaviour improved (slightly)
207 <!-- JAL-3162 -->Can edit a feature so that start > end
210 <!-- JAL-2848 -->Cancel from Amend Features doesn't reset a
211 modified graduated colour
214 <!-- JAL-3788 -->New View with automatic 'Show Overview'
215 preference enabled results in Null Pointer Exceptions when
216 clustal colouring is enabled
219 <!-- JAL-3275 -->Can open multiple Preferences panels
222 <!-- JAL-3949 -->Standard out logging broken: messages only
223 routing to stderr and appear as a raw template
225 </ul> <em>JalviewJS</em>
228 <!-- JAL-3202 -->Consensus profile may include zero (rounded
229 down) percentage values causing a divide by zero
244 <!-- JAL-3762 -->JalviewJS doesn't honour arguments passed
245 via Info.args when there are arguments on the URL
248 <!-- JAL-3602 -->gradle closure-compiler not using UTF-8
251 <!-- JAL-3603 -->Annotation file fails to load from URL in
254 </ul> <em>Development</em>
258 <li>Fixed non-fatal gradle errors during build</li>
260 <!-- JAL-3745 -->Updated build.gradle for use with
270 <td width="60" align="center" nowrap><strong><a
271 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.7">.7</a><br />
272 <em>18/01/2022</em></strong></td>
274 <td align="left" valign="top">
277 <!-- JAL-3703, JAL-3935 -->Files open in Jalview cannot be
278 updated by Jalview or other applications (Windows, other non
281 </ul> <em>Security</em>
284 <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
290 <td width="60" align="center" nowrap><strong><a
291 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
292 <em>6/01/2022</em></strong></td>
294 <td align="left" valign="top"><em>Security</em>
297 <!-- JAL-3934 -->Version bump library dependency: Log4j
304 <td width="60" align="center" nowrap><strong><a
305 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
306 <em>20/12/2021</em></strong></td>
308 <td align="left" valign="top"><em>Security</em>
311 <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
313 </ul> <em>Development</em>
315 <li>Updated building instructions</li>
320 <!-- JAL-3840 -->Occupancy calculation is incorrect for
321 alignment columns with over -1+2^32 gaps (breaking filtering
325 <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
326 scale factors being set with buggy window-managers (linux
329 </ul> <em>Development</em>
331 <li>Fixed non-fatal gradle errors during build</li>
336 <td width="60" align="center" nowrap><strong><a
337 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
338 <em>09/03/2021</em></strong></td>
339 <td align="left" valign="top"><em>Improved control of
340 Jalview's use of network services via jalview_properties</em>
343 <!-- JAL-3814 -->New .jalview_properties token controlling
344 launch of the news browser (like -nonews argument)
347 <!-- JAL-3813 -->New .jalview_properties token controlling
348 download of linkout URLs from
349 www.jalview.org/services/identifiers
352 <!-- JAL-3812 -->New .jalview_properties token controlling
353 download of BIOJSHTML templates
356 <!-- JAL-3811 -->New 'Discover Web Services' option to
357 trigger a one off JABAWS discovery if autodiscovery was
361 <td align="left" valign="top">
364 <!-- JAL-3818 -->Intermittent deadlock opening structure in
367 </ul> <em>New Known defects</em>
370 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
371 always restored from project (since 2.10.3)
374 <!-- JAL-3806 -->Selections from tree built from CDS aren't
375 propagated to Protein alignment (since 2.11.1.3)
381 <td width="60" align="center" nowrap><strong><a
382 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
383 <em>29/10/2020</em></strong></td>
384 <td align="left" valign="top">
389 <td align="left" valign="top">
392 <!-- JAL-3765 -->Find doesn't always highlight all matching
393 positions in a sequence (bug introduced in 2.11.1.2)
396 <!-- JAL-3760 -->Alignments containing one or more protein
397 sequences can be classed as nucleotide
400 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
401 sequences after alignment of protein products (known defect
402 first reported for 2.11.1.0)
405 <!-- JAL-3725 -->No tooltip or popup menu for genomic
406 features outwith CDS shown overlaid on protein
409 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
410 correctly mapped by Jalview (e.g. affects viral CDS with
411 ribosomal slippage, since 2.9.0)
414 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
418 <!-- JAL-3700 -->Selections in CDS sequence panel don't
419 always select corresponding protein sequences
422 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
423 column selection doesn't always ignore hidden columns
425 </ul> <em>Installer</em>
428 <!-- JAL-3611 -->Space character in Jalview install path on
429 Windows prevents install4j launching getdown
431 </ul> <em>Development</em>
434 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
435 version numbers in doc/building.md
441 <td width="60" align="center" nowrap><strong><a
442 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
443 <em>25/09/2020</em></strong></td>
444 <td align="left" valign="top">
448 <td align="left" valign="top">
451 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
452 "Encountered problems opening
453 https://www.jalview.org/examples/exampleFile_2_7.jvp"
459 <td width="60" align="center" nowrap><strong><a
460 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
461 <em>17/09/2020</em></strong></td>
462 <td align="left" valign="top">
465 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
466 residue in cursor mode
469 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
470 HTSJDK from 2.12 to 2.23
473 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
474 optimisations and improvements suggested by Bob Hanson and
475 improved compatibility with JalviewJS
478 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
479 alignments from Pfam and Rfam
482 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
483 import (no longer based on .gz extension)
486 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
489 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
490 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
494 <!-- JAL-3667 -->Improved warning messages, debug logging
495 and fixed Retry action when Jalview encounters errors when
496 saving or making backup files.
499 <!-- JAL-3676 -->Enhanced Jalview Java Console:
501 <li>Jalview's logging level can be configured</li>
502 <li>Copy to Clipboard Buttion</li>
506 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
507 when running on Linux (Requires Java 11+)
509 </ul> <em>Launching Jalview</em>
512 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
513 through a system property
516 <!-- JAL-3477 -->Improved built-in documentation and command
517 line help for configuring Jalview's memory
521 <td align="left" valign="top">
524 <!-- JAL-3691 -->Conservation and Quality tracks are shown
525 but not calculated and no protein or DNA score models are
526 available for tree/PCA calculation when launched with
527 Turkish language locale
530 <!-- JAL-3493 -->Escape does not clear highlights on the
531 alignment (Since Jalview 2.10.3)
534 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
535 doesn't slide selected sequences, just sequence under cursor
538 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
539 sequence under the cursor
542 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
543 multiple EMBL gene products shown for a single contig
546 <!-- JAL-3696 -->Errors encountered when processing variants
547 from VCF files yield "Error processing VCF: Format specifier
551 <!-- JAL-3697 -->Count of features not shown can be wrong
552 when there are both local and complementary features mapped
553 to the position under the cursor
556 <!-- JAL-3673 -->Sequence ID for reference sequence is
557 clipped when Right align Sequence IDs enabled
560 <!-- JAL-2983 -->Slider with negative range values not
561 rendered correctly in VAqua4 (Since 2.10.4)
564 <!-- JAL-3685 -->Single quotes not displayed correctly in
565 internationalised text for some messages and log output
568 <!-- JAL-3490 -->Find doesn't report matches that span
569 hidden gapped columns
572 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
573 panels, Alignment viewport and annotation renderer.
576 <!-- JAL-3561 -->Jalview ignores file format parameter
577 specifying output format when exporting an alignment via the
581 <!-- JAL-3667 -->Windows 10: For a minority of users, if
582 backups are not enabled, Jalview sometimes fails to
583 overwrite an existing file and raises a warning dialog. (in
584 2.11.0, and 2.11.1.0, the workaround is to try to save the
585 file again, and if that fails, delete the original file and
589 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
593 <!-- JAL-3741 -->References to http://www.jalview.org in
594 program and documentation
596 </ul> <em>Launching Jalview</em>
599 <!-- JAL-3718 -->Jalview application fails when launched the
600 first time for a version that has different jars to the
601 previous launched version.
603 </ul> <em>Developing Jalview</em>
606 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
607 data, causing cloverReport gradle task to fail with an
611 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
612 monitor the release channel
614 </ul> <em>New Known defects</em>
617 <!-- JAL-3748 -->CDS shown in result of submitting proteins
618 in a CDS/Protein alignment to a web service is wrong when
619 proteins share a common transcript sequence (e.g. genome of
623 <!-- JAL-3576 -->Co-located features exported and
624 re-imported are ordered differently when shown on alignment
625 and in tooltips. (Also affects v2.11.1.0)
628 <!-- JAL-3702 -->Drag and drop of alignment file onto
629 alignment window when in a HiDPI scaled mode in Linux only
630 works for the top left quadrant of the alignment window
633 <!-- JAL-3701 -->Stale build data in jalview standalone jar
634 builds (only affects 2.11.1.1 branch)
637 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
638 when alignment view restored from project (since Jalview
642 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
643 protein products for certain ENA records are repeatedly
644 shown via Calculate->Show Cross Refs
650 <td width="60" align="center" nowrap><strong><a
651 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
652 <em>22/04/2020</em></strong></td>
653 <td align="left" valign="top">
656 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
657 'virtual' codon features shown on protein (or vice versa)
658 for display in alignments, on structure views (including
659 transfer to UCSF chimera), in feature reports and for
663 <!-- JAL-3121 -->Feature attributes from VCF files can be
664 exported and re-imported as GFF3 files
667 <!-- JAL-3376 -->Capture VCF "fixed column" values
668 POS, ID, QUAL, FILTER as Feature Attributes
671 <!-- JAL-3375 -->More robust VCF numeric data field
672 validation while parsing
675 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
679 <!-- JAL-3535 -->Feature Settings dialog title includes name
683 <!-- JAL-3538 -->Font anti-aliasing in alignment views
687 <!-- JAL-3468 -->Very long feature descriptions truncated in
691 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
692 with no feature types visible
695 <!-- JAL-3574 -->Improved support for filtering feature
696 attributes with large integer values
699 <em>Jalview Installer</em>
702 <!-- JAL-3449 -->Versions for install4j and getdown and
703 installer template version reported in console (may be null
704 when Jalview launched as executable jar or via conda)
707 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and
708 higher quality background images
711 <!-- JAL-3394 -->New installer/application launcher
712 generated with install4j 8.0.4
715 <!-- JAL-3420 -->Jalview File Associations shown for Unix
719 <!-- JAL-3477 -->Improved defaults for maximum memory
720 setting when running on large memory machines
722 </ul> <em>Release processes</em>
725 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
728 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier
729 access to test-release channel builds
731 </ul> <em>Build System</em>
734 <!-- JAL-3510 -->Clover updated to 4.4.1
737 <!-- JAL-3513 -->Test code included in Clover coverage
740 </ul> <em>Groovy Scripts</em>
743 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
744 to stdout containing the consensus sequence for each
745 alignment in a Jalview session
748 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
749 genomic sequence_variant annotation from CDS as
750 missense_variant or synonymous_variant on protein products.
754 <td align="left" valign="top">
757 <!-- JAL-3581 -->Hidden sequence markers still visible when
758 'Show hidden markers' option is not ticked
761 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
762 PNG output when 'Automatically set ID width' is set in
763 jalview preferences or properties file
766 <!-- JAL-3571 -->Feature Editor dialog can be opened when
767 'Show Sequence Features' option is not ticked
770 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
771 buttons in Feature Settings dialog are clicked when no
775 <!-- JAL-3412 -->ID margins for CDS and Protein views not
776 equal when split frame is first opened
779 <!-- JAL-3296 -->Sequence position numbers in status bar not
780 correct after editing a sequence's start position
783 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
784 with annotation and exceptions thrown when only a few
785 columns shown in wrapped mode
788 <!-- JAL-3386 -->Sequence IDs missing in headless export of
789 wrapped alignment figure with annotations
792 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
793 ID fails with ClassCastException
796 <!-- JAL-3389 -->Chimera session not restored from Jalview
800 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
801 feature settings dialog also selects columns
804 <!-- JAL-3473 -->SpinnerNumberModel causes
805 IllegalArgumentException in some circumstances
808 <!-- JAL-3534 -->Multiple feature settings dialogs can be
812 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
813 alignment window is closed
816 <!-- JAL-3406 -->Credits missing some authors in Jalview
817 help documentation for 2.11.0 release
820 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
821 includes Pfam ID as sequence's accession rather than its
824 </ul> <em>Java 11 Compatibility issues</em>
827 <!-- JAL-2987 -->OSX - Can't view some search results in
828 PDB/Uniprot search panel
830 </ul> <em>Installer</em>
833 <!-- JAL-3447 -->Jalview should not create file associations
834 for 3D structure files (.pdb, .mmcif. .cif)
836 </ul> <em>Repository and Source Release</em>
839 <!-- JAL-3474 -->removed obsolete .cvsignore files from
843 <!-- JAL-3541 -->Clover report generation running out of
846 </ul> <em>New Known Issues</em>
849 <!-- JAL-3523 -->OSX - Current working directory not
850 preserved when Jalview.app launched with parameters from
854 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
855 clipped in headless figure export when Right Align option
859 <!-- JAL-3542 -->Jalview Installation type always reports
860 'Source' in console output
863 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail
864 on jalview's bamboo server but run fine locally.
870 <td width="60" align="center" nowrap><strong><a
871 name="Jalview.2.11.0">2.11.0</a><br /> <em>04/07/2019</em></strong></td>
872 <td align="left" valign="top">
875 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native
876 Application and Installers built with <a
877 href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a>
878 (licensed to the Jalview open source project) rather than
882 <!-- JAL-1929 -->Jalview Launcher System to auto-configure
883 memory settings, receive over the air updates and launch
884 specific versions via (<a
885 href="https://github.com/threerings/getdown">Three
889 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations
890 for formats supported by Jalview (including .jvp project
894 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command
895 line arguments and switch between different getdown channels
898 <!-- JAL-3141 -->Backup files created when saving Jalview
899 project or alignment files
903 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF
907 <!-- JAL-2753 -->Version of HTSJDK shipped with Jalview
908 updated to version 2.12.0
911 <!-- JAL-2620 -->Alternative genetic code tables for
915 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0
917 <li><strong>Enhanced visualisation and analysis
918 of Sequence Features</strong>
921 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
922 implementation that allows updates) used for Sequence
926 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
927 features can be filtered and shaded according to any
928 associated attributes (e.g. variant attributes from VCF
929 file, or key-value pairs imported from column 9 of GFF
933 <!-- JAL-2879 -->Feature Attributes and shading schemes
934 stored and restored from Jalview Projects
937 <!-- JAL-3334 -->Use full Sequence Ontology (via
938 BioJava) to recognise variant features
941 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants
942 on peptide sequences (also coloured red by default)
945 <!-- JAL-2792 -->Popup window to show full report for a
946 selected sequence feature's details
949 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient
950 sequence feature render algorithm (Z-sort/transparency
954 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature
959 <!-- JAL-3205 -->Symmetric score matrices for faster tree
962 <li><strong>Principal Components Analysis Viewer</strong>
965 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis
966 results and Viewer state saved in Jalview Project
969 <!-- JAL-2962 -->'Change parameters' option removed from
970 viewer's drop-down menus
973 <!-- JAL-2975 -->Can use shift + arrow keys to rotate
974 PCA image incrementally
977 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
981 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
983 <li><strong>Speed and Efficiency</strong>
986 <!-- JAL-2185,JAL-3198 -->More efficient creation of
987 selections and multiple groups when working with large
991 <!-- JAL-3200 -->Speedier import of annotation rows when
992 parsing Stockholm files
995 <li><strong>User Interface</strong>
998 <!-- JAL-2933 -->Finder panel remembers last position in
1002 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS
1003 (What you see is what is shown)<br />Only visible
1004 regions of alignment are shown by default (can be
1005 changed in user preferences)
1008 <!-- JAL-3169 -->File Chooser stays open after
1009 responding Cancel to the Overwrite Dialog
1012 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour
1013 when all sequences are hidden
1016 <!-- JAL-1244 -->Status bar shows bounds when dragging a
1017 selection region, and gap count when inserting or
1021 <!-- JAL-3132 -->Status bar updates over sequence and
1025 <!-- JAL-3093 -->Annotation tooltips and popup menus are
1026 shown when in wrapped mode
1029 <!-- JAL-3073 -->Can select columns by dragging
1030 left/right in a graph or histogram annotation
1033 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB
1037 <!-- JAL-2621 -->Cursor changes over draggable box in
1041 <!-- JAL-3181 -->Consistent ordering of links in
1042 sequence id popup menu
1045 <!-- JAL-3080 -->Red line indicating tree-cut position
1046 not shown if no subgroups are created
1049 <!-- JAL-3042 -->Removed ability to configure length of
1050 search history by right-clicking search box
1056 <!-- JAL-3232 -->Jalview Groovy Scripting Console updated to
1059 <li><strong>Java 11 Support (not yet on general
1063 <!-- -->OSX GUI integrations for App menu's 'About'
1064 entry and trapping CMD-Q
1067 </ul> <em>Deprecations</em>
1070 <!-- JAL-3035 -->DAS sequence retrieval and annotation
1071 capabilities removed from the Jalview Desktop
1074 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling
1075 and unmarshalling has been replaced by JAXB for Jalview
1076 projects and XML based data retrieval clients
1079 <!-- JAL-3311 -->Disable VAMSAS menu in preparation for
1083 <!-- -->Jalview Desktop no longer distributed via Java Web
1086 </ul> <em>Documentation</em>
1089 <!-- JAL-3003 -->Added remarks about transparent rendering
1090 effects not supported in EPS figure export
1093 <!-- JAL-2903 -->Typos in documentation for Preferences
1096 </ul> <em>Development and Release Processes</em>
1099 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated
1103 <!-- JAL-1424 -->Enhanced checks for missing and duplicated
1104 keys in Message bundles
1107 <!-- JAL-3225 -->Eclipse project configuration managed with
1111 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian Bamboo
1112 continuous integration for unattended Test Suite execution
1115 <!-- JAL-2864 -->Memory test suite to detect leaks in common
1119 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
1123 <!-- JAL-3248 -->Developer documentation migrated to
1124 markdown (with HTML rendering)
1127 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
1130 <!-- JAL-3289 -->New URLs for publishing development
1135 <td align="left" valign="top">
1138 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
1141 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
1142 superposition in Jmol fail on Windows
1145 <!-- JAL-3286 -->Blank error dialog is displayed when
1146 discovering structures for sequences with lots of PDB
1150 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export
1151 with monospaced font
1154 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
1155 Jalview project involving multiple views
1158 <!-- JAL-3164 -->Overview for complementary view in a linked
1159 CDS/Protein alignment is not updated when Hide Columns by
1160 Annotation dialog hides columns
1163 <!-- JAL-3158 -->Selection highlighting in the complement of
1164 a CDS/Protein alignment stops working after making a
1165 selection in one view, then making another selection in the
1169 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
1173 <!-- JAL-3154 -->Table Columns could be re-ordered in
1174 Feature Settings and Jalview Preferences panels
1177 <!-- JAL-2865 -->Jalview hangs when closing windows, or
1178 redrawing the overview with large alignments
1181 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
1182 region if columns were selected by dragging right-to-left
1183 and the mouse moved to the left of the first column
1186 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to
1187 a hidden column marker via scale popup menu
1190 <!-- JAL-2846 -->Error message for trying to load in invalid
1191 URLs doesn't tell users the invalid URL
1194 <!-- JAL-2816 -->Tooltips displayed for features filtered by
1198 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl
1199 during show cross references or Fetch Database References
1200 are shown in red in original view
1203 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown
1204 correctly on peptide sequence (computed variant shown as
1208 <!-- JAL-2060 -->'Graduated colour' option not offered for
1209 manually created features (where feature score is Float.NaN)
1212 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or
1213 printed when columns are hidden
1216 <!-- JAL-3082 -->Regular expression error for '(' in Select
1217 Columns by Annotation description
1220 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after
1221 dragging out of Scale or Annotation Panel
1224 <!-- JAL-3075 -->Column selection incorrect after scrolling
1228 <!-- JAL-3074 -->Left/right drag in annotation can scroll
1232 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal
1236 <!-- JAL-3002 -->Column display is out by one after Page
1237 Down, Page Up in wrapped mode
1240 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
1243 <!-- JAL-2932 -->Finder searches in minimised alignments
1246 <!-- JAL-2250 -->'Apply Colour to All Groups' not always
1247 selected on opening an alignment
1250 <!-- JAL-3180 -->'Colour by Annotation' not marked selected
1254 <!-- JAL-3201 -->Per-group Clustal colour scheme changes
1255 when different groups in the alignment are selected
1258 <!-- JAL-2717 -->Internationalised colour scheme names not
1259 shown correctly in menu
1262 <!-- JAL-3206 -->Colour by Annotation can go black at
1263 min/max threshold limit
1266 <!-- JAL-3125 -->Value input for graduated feature colour
1267 threshold gets 'unrounded'
1270 <!-- JAL-2982 -->PCA image export doesn't respect background
1274 <!-- JAL-2963 -->PCA points don't dim when rotated about y
1278 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
1281 <!-- JAL-3078 -->Cancel in Tree Font dialog resets
1282 alignment, not Tree font
1285 <!-- JAL-2964 -->Associate Tree with All Views not restored
1289 <!-- JAL-2915 -->Scrolling of split frame is sluggish if
1290 Overview shown in complementary view
1293 <!-- JAL-3313 -->Codon consensus incorrectly scaled when
1294 shown without normalisation
1297 <!-- JAL-3021 -->Sequence Details report should open
1298 positioned at top of report
1301 <!-- JAL-914 -->Help page can be opened twice
1304 <!-- JAL-3333 -->Fuzzy text in web service status menu on
1307 </ul> <em>Editing</em>
1310 <!-- JAL-2822 -->Start and End should be updated when
1311 sequence data at beginning or end of alignment added/removed
1315 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection
1316 doesn't relocate sequence features correctly when start of
1317 sequence is removed (Known defect since 2.10)
1320 <!-- JAL-2830 -->Inserting gap sequence via the Edit
1321 Sequence dialog corrupts dataset sequence
1324 <!-- JAL-868 -->Structure colours not updated when
1325 associated tree repartitions the alignment view (Regression
1328 </ul> <em>Datamodel</em>
1331 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
1332 sequence's End is greater than its length
1334 </ul> <em>Bugs fixed for Java 11 Support (not yet on general
1338 <!-- JAL-3288 -->Menus work properly in split-screen
1340 </ul> <em>New Known Defects</em>
1343 <!-- JAL-3340 -->Select columns containing feature by double
1344 clicking ignores bounds of an existing selected region
1347 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in
1348 gapped regions of protein alignment.
1351 <!-- JAL-2647 -->Input Data menu entry is greyed out when
1352 PCA View is restored from a Jalview 2.11 project
1355 <!-- JAL-3213 -->Alignment panel height can be too small
1359 <!-- JAL-3240 -->Display is incorrect after removing gapped
1360 columns within hidden columns
1363 <!-- JAL-3314 -->Rightmost selection is lost when mouse
1364 re-enters window after dragging left to select columns to
1365 left of visible region
1368 <!-- JAL-2876 -->Features coloured according to their
1369 description string and thresholded by score in earlier
1370 versions of Jalview are not shown as thresholded features in
1371 2.11. To workaround please create a Score filter instead.
1374 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't
1375 reset group visibility
1378 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in
1379 linked CDS/Protein view
1382 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1383 alignments with multiple views can close views unexpectedly
1385 </ul> <em>Java 11 Specific defects</em>
1388 <!-- JAL-3235 -->Jalview Properties file is not sorted
1389 alphabetically when saved
1395 <td width="60" nowrap>
1396 <div align="center">
1397 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1400 <td><div align="left">
1404 <!-- JAL-3101 -->Default memory for Jalview webstart and
1405 InstallAnywhere increased to 1G.
1408 <!-- JAL-247 -->Hidden sequence markers and representative
1409 sequence bolding included when exporting alignment as EPS,
1410 SVG, PNG or HTML. <em>Display is configured via the
1411 Format menu, or for command-line use via a Jalview
1412 properties file.</em>
1415 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1416 API and sequence data now imported as JSON.
1419 <!-- JAL-3065 -->Change in recommended way of starting
1420 Jalview via a Java command line: add jars in lib directory
1421 to CLASSPATH, rather than via the deprecated java.ext.dirs
1425 <em>Development</em>
1428 <!-- JAL-3047 -->Support added to execute test suite
1429 instrumented with <a href="http://openclover.org/">Open
1434 <td><div align="left">
1438 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1439 row shown in Feredoxin Structure alignment view of example
1443 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1444 annotation displayed.
1447 <!-- JAL-3107 -->Group conservation/consensus not shown
1448 for newly created group when 'Apply to all groups'
1452 <!-- JAL-3087 -->Corrupted display when switching to
1453 wrapped mode when sequence panel's vertical scrollbar is
1457 <!-- JAL-3003 -->Alignment is black in exported EPS file
1458 when sequences are selected in exported view.</em>
1461 <!-- JAL-3059 -->Groups with different coloured borders
1462 aren't rendered with correct colour.
1465 <!-- JAL-3092 -->Jalview could hang when importing certain
1466 types of knotted RNA secondary structure.
1469 <!-- JAL-3095 -->Sequence highlight and selection in
1470 trimmed VARNA 2D structure is incorrect for sequences that
1474 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1475 annotation when columns are inserted into an alignment,
1476 and when exporting as Stockholm flatfile.
1479 <!-- JAL-3053 -->Jalview annotation rows containing upper
1480 and lower-case 'E' and 'H' do not automatically get
1481 treated as RNA secondary structure.
1484 <!-- JAL-3106 -->.jvp should be used as default extension
1485 (not .jar) when saving a Jalview project file.
1488 <!-- JAL-3105 -->Mac Users: closing a window correctly
1489 transfers focus to previous window on OSX
1492 <em>Java 10 Issues Resolved</em>
1495 <!-- JAL-2988 -->OSX - Can't save new files via the File
1496 or export menus by typing in a name into the Save dialog
1500 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1501 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1502 'look and feel' which has improved compatibility with the
1503 latest version of OSX.
1509 <td width="60" nowrap>
1510 <div align="center">
1511 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1512 <em>7/06/2018</em></strong>
1515 <td><div align="left">
1519 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1520 annotation retrieved from Uniprot
1523 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1524 onto the Jalview Desktop
1528 <td><div align="left">
1532 <!-- JAL-3017 -->Cannot import features with multiple
1533 variant elements (blocks import of some Uniprot records)
1536 <!-- JAL-2997 -->Clustal files with sequence positions in
1537 right-hand column parsed correctly
1540 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1541 not alignment area in exported graphic
1544 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1545 window has input focus
1548 <!-- JAL-2992 -->Annotation panel set too high when
1549 annotation added to view (Windows)
1552 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1553 network connectivity is poor
1556 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1557 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1558 the currently open URL and links from a page viewed in
1559 Firefox or Chrome on Windows is now fully supported. If
1560 you are using Edge, only links in the page can be
1561 dragged, and with Internet Explorer, only the currently
1562 open URL in the browser can be dropped onto Jalview.</em>
1565 <em>New Known Defects</em>
1568 <!-- JAL-3083 -->Cancel option doesn't reset Colour by
1575 <td width="60" nowrap>
1576 <div align="center">
1577 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1580 <td><div align="left">
1584 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1585 for disabling automatic superposition of multiple
1586 structures and open structures in existing views
1589 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1590 ID and annotation area margins can be click-dragged to
1594 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1598 <!-- JAL-2759 -->Improved performance for large alignments
1599 and lots of hidden columns
1602 <!-- JAL-2593 -->Improved performance when rendering lots
1603 of features (particularly when transparency is disabled)
1606 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2
1607 for exchange of Jalview features and Chimera attributes
1608 made generally available
1612 <td><div align="left">
1615 <!-- JAL-2899 -->Structure and Overview aren't updated
1616 when Colour By Annotation threshold slider is adjusted
1619 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1620 overlapping alignment panel
1623 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1627 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1628 improved: CDS not handled correctly if transcript has no
1632 <!-- JAL-2321 -->Secondary structure and temperature
1633 factor annotation not added to sequence when local PDB
1634 file associated with it by drag'n'drop or structure
1638 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1639 dialog doesn't import PDB files dropped on an alignment
1642 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1643 scroll bar doesn't work for some CDS/Protein views
1646 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1647 Java 1.8u153 onwards and Java 1.9u4+.
1650 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1651 columns in annotation row
1654 <!-- JAL-2913 -->Preferences panel's ID Width control is
1655 not honored in batch mode
1658 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1659 for structures added to existing Jmol view
1662 <!-- JAL-2223 -->'View Mappings' includes duplicate
1663 entries after importing project with multiple views
1666 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1667 protein sequences via SIFTS from associated PDB entries
1668 with negative residue numbers or missing residues fails
1671 <!-- JAL-2952 -->Exception when shading sequence with
1672 negative Temperature Factor values from annotated PDB
1673 files (e.g. as generated by CONSURF)
1676 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1677 tooltip doesn't include a text description of mutation
1680 <!-- JAL-2922 -->Invert displayed features very slow when
1681 structure and/or overview windows are also shown
1684 <!-- JAL-2954 -->Selecting columns from highlighted
1685 regions very slow for alignments with large numbers of
1689 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1690 with 'StringIndexOutOfBounds'
1693 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and
1694 Feel for OSX platforms running Java 10
1697 <!-- JAL-2960 -->Adding a structure to existing structure
1698 view appears to do nothing because the view is hidden
1699 behind the alignment view
1705 <!-- JAL-2926 -->Copy consensus sequence option in applet
1706 should copy the group consensus when popup is opened on it
1712 <!-- JAL-2913 -->Fixed ID width preference is not
1716 <em>New Known Defects</em>
1719 <!-- JAL-2973 --> Exceptions occasionally raised when
1720 editing a large alignment and overview is displayed
1723 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1724 repeatedly after a series of edits even when the overview
1725 is no longer reflecting updates
1728 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1729 structures for protein subsequence (if 'Trim Retrieved
1730 Sequences' enabled) or Ensembl isoforms (Workaround in
1731 2.10.4 is to fail back to N&W mapping)
1734 <!-- JAL-2990 -->Export Annotations from File Menu with
1735 CSV option gives blank output
1741 <td width="60" nowrap>
1742 <div align="center">
1743 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br />
1744 <em>24/1/2018</em></strong>
1747 <td><div align="left">
1749 <li>Updated Certum Codesigning Certificate (Valid till
1750 30th November 2018)</li>
1753 <td><div align="left">
1758 <!-- JAL-2859-->Only one structure is loaded when
1759 several sequences and structures are selected for
1763 <!-- JAL-2851-->Alignment doesn't appear to scroll
1764 vertically via trackpad and scrollwheel
1767 <!-- JAL-2842-->Jalview hangs if up/down arrows pressed
1768 in cursor mode when cursor lies in hidden region at
1772 <!-- JAL-2827-->Helix annotation has 'notches' when
1773 scrolled into view if columns are hidden
1776 <!-- JAL-2740-->Annotation column filter can be slow to
1777 reset (ie after hitting cancel) for large numbers of
1781 <!-- JAL-2849-->User preference for disabling inclusion
1782 of sequence limits when exporting as flat file has no
1786 <!-- JAL-2679-->Reproducible cross-reference
1787 relationships when retrieving sequences from
1794 <td width="60" nowrap>
1795 <div align="center">
1796 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1799 <td><div align="left">
1803 <!-- JAL-2446 -->Faster and more efficient management and
1804 rendering of sequence features
1807 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1808 429 rate limit request hander
1811 <!-- JAL-2773 -->Structure views don't get updated unless
1812 their colours have changed
1815 <!-- JAL-2495 -->All linked sequences are highlighted for
1816 a structure mousover (Jmol) or selection (Chimera)
1819 <!-- JAL-2790 -->'Cancel' button in progress bar for
1820 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1823 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1824 view from Ensembl locus cross-references
1827 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1831 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1832 feature can be disabled
1835 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1836 PDB easier retrieval of sequences for lists of IDs
1839 <!-- JAL-2758 -->Short names for sequences retrieved from
1845 <li>Groovy interpreter updated to 2.4.12</li>
1846 <li>Example groovy script for generating a matrix of
1847 percent identity scores for current alignment.</li>
1849 <em>Testing and Deployment</em>
1852 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1856 <td><div align="left">
1860 <!-- JAL-2643 -->Pressing tab after updating the colour
1861 threshold text field doesn't trigger an update to the
1865 <!-- JAL-2682 -->Race condition when parsing sequence ID
1869 <!-- JAL-2608 -->Overview windows are also closed when
1870 alignment window is closed
1873 <!-- JAL-2548 -->Export of features doesn't always respect
1877 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1878 takes a long time in Cursor mode
1884 <!-- JAL-2777 -->Structures with whitespace chainCode
1885 cannot be viewed in Chimera
1888 <!-- JAL-2728 -->Protein annotation panel too high in
1892 <!-- JAL-2757 -->Can't edit the query after the server
1893 error warning icon is shown in Uniprot and PDB Free Text
1897 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1900 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1903 <!-- JAL-2739 -->Hidden column marker in last column not
1904 rendered when switching back from Wrapped to normal view
1907 <!-- JAL-2768 -->Annotation display corrupted when
1908 scrolling right in unwapped alignment view
1911 <!-- JAL-2542 -->Existing features on subsequence
1912 incorrectly relocated when full sequence retrieved from
1916 <!-- JAL-2733 -->Last reported memory still shown when
1917 Desktop->Show Memory is unticked (OSX only)
1920 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1921 features of same type and group to be selected for
1925 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1926 alignments when hidden columns are present
1929 <!-- JAL-2392 -->Jalview freezes when loading and
1930 displaying several structures
1933 <!-- JAL-2732 -->Black outlines left after resizing or
1937 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1938 within the Jalview desktop on OSX
1941 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1942 when in wrapped alignment mode
1945 <!-- JAL-2636 -->Scale mark not shown when close to right
1946 hand end of alignment
1949 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1950 each selected sequence do not have correct start/end
1954 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1955 after canceling the Alignment Window's Font dialog
1958 <!-- JAL-2036 -->Show cross-references not enabled after
1959 restoring project until a new view is created
1962 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1963 URL links appears when only default EMBL-EBI link is
1964 configured (since 2.10.2b2)
1967 <!-- JAL-2775 -->Overview redraws whole window when box
1968 position is adjusted
1971 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1972 in a multi-chain structure when viewing alignment
1973 involving more than one chain (since 2.10)
1976 <!-- JAL-2811 -->Double residue highlights in cursor mode
1977 if new selection moves alignment window
1980 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1981 arrow key in cursor mode to pass hidden column marker
1984 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1985 that produces correctly annotated transcripts and products
1988 <!-- JAL-2776 -->Toggling a feature group after first time
1989 doesn't update associated structure view
1992 <em>Applet</em><br />
1995 <!-- JAL-2687 -->Concurrent modification exception when
1996 closing alignment panel
1999 <em>BioJSON</em><br />
2002 <!-- JAL-2546 -->BioJSON export does not preserve
2003 non-positional features
2006 <em>New Known Issues</em>
2009 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
2010 sequence features correctly (for many previous versions of
2014 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
2015 using cursor in wrapped panel other than top
2018 <!-- JAL-2791 -->Select columns containing feature ignores
2019 graduated colour threshold
2022 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
2023 always preserve numbering and sequence features
2026 <em>Known Java 9 Issues</em>
2029 <!-- JAL-2902 -->Groovy Console very slow to open and is
2030 not responsive when entering characters (Webstart, Java
2037 <td width="60" nowrap>
2038 <div align="center">
2039 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
2040 <em>2/10/2017</em></strong>
2043 <td><div align="left">
2044 <em>New features in Jalview Desktop</em>
2047 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API
2051 <!-- JAL-2745 -->HTTPS used for all connections to
2056 <td><div align="left"></div></td>
2059 <td width="60" nowrap>
2060 <div align="center">
2061 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
2062 <em>7/9/2017</em></strong>
2065 <td><div align="left">
2069 <!-- JAL-2588 -->Show gaps in overview window by colouring
2070 in grey (sequences used to be coloured grey, and gaps were
2074 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
2078 <!-- JAL-2587 -->Overview updates immediately on increase
2079 in size and progress bar shown as higher resolution
2080 overview is recalculated
2085 <td><div align="left">
2089 <!-- JAL-2664 -->Overview window redraws every hidden
2090 column region row by row
2093 <!-- JAL-2681 -->duplicate protein sequences shown after
2094 retrieving Ensembl crossrefs for sequences from Uniprot
2097 <!-- JAL-2603 -->Overview window throws NPE if show boxes
2098 format setting is unticked
2101 <!-- JAL-2610 -->Groups are coloured wrongly in overview
2102 if group has show boxes format setting unticked
2105 <!-- JAL-2672,JAL-2665 -->Redraw problems when
2106 autoscrolling whilst dragging current selection group to
2107 include sequences and columns not currently displayed
2110 <!-- JAL-2691 -->Not all chains are mapped when multimeric
2111 assemblies are imported via CIF file
2114 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
2115 displayed when threshold or conservation colouring is also
2119 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
2123 <!-- JAL-2673 -->Jalview continues to scroll after
2124 dragging a selected region off the visible region of the
2128 <!-- JAL-2724 -->Cannot apply annotation based
2129 colourscheme to all groups in a view
2132 <!-- JAL-2511 -->IDs don't line up with sequences
2133 initially after font size change using the Font chooser or
2140 <td width="60" nowrap>
2141 <div align="center">
2142 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
2145 <td><div align="left">
2146 <em>Calculations</em>
2150 <!-- JAL-1933 -->Occupancy annotation row shows number of
2151 ungapped positions in each column of the alignment.
2154 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
2155 a calculation dialog box
2158 <!-- JAL-2379 -->Revised implementation of PCA for speed
2159 and memory efficiency (~30x faster)
2162 <!-- JAL-2403 -->Revised implementation of sequence
2163 similarity scores as used by Tree, PCA, Shading Consensus
2164 and other calculations
2167 <!-- JAL-2416 -->Score matrices are stored as resource
2168 files within the Jalview codebase
2171 <!-- JAL-2500 -->Trees computed on Sequence Feature
2172 Similarity may have different topology due to increased
2179 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
2180 model for alignments and groups
2183 <!-- JAL-384 -->Custom shading schemes created via groovy
2190 <!-- JAL-2526 -->Efficiency improvements for interacting
2191 with alignment and overview windows
2194 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
2198 <!-- JAL-2388 -->Hidden columns and sequences can be
2202 <!-- JAL-2611 -->Click-drag in visible area allows fine
2203 adjustment of visible position
2207 <em>Data import/export</em>
2210 <!-- JAL-2535 -->Posterior probability annotation from
2211 Stockholm files imported as sequence associated annotation
2214 <!-- JAL-2507 -->More robust per-sequence positional
2215 annotation input/output via stockholm flatfile
2218 <!-- JAL-2533 -->Sequence names don't include file
2219 extension when importing structure files without embedded
2220 names or PDB accessions
2223 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
2224 format sequence substitution matrices
2227 <em>User Interface</em>
2230 <!-- JAL-2447 --> Experimental Features Checkbox in
2231 Desktop's Tools menu to hide or show untested features in
2235 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
2236 via Overview or sequence motif search operations
2239 <!-- JAL-2547 -->Amend sequence features dialog box can be
2240 opened by double clicking gaps within sequence feature
2244 <!-- JAL-1476 -->Status bar message shown when not enough
2245 aligned positions were available to create a 3D structure
2249 <em>3D Structure</em>
2252 <!-- JAL-2430 -->Hidden regions in alignment views are not
2253 coloured in linked structure views
2256 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
2257 file-based command exchange
2260 <!-- JAL-2375 -->Structure chooser automatically shows
2261 Cached Structures rather than querying the PDBe if
2262 structures are already available for sequences
2265 <!-- JAL-2520 -->Structures imported via URL are cached in
2266 the Jalview project rather than downloaded again when the
2267 project is reopened.
2270 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
2271 to transfer Chimera's structure attributes as Jalview
2272 features, and vice-versa (<strong>Experimental
2276 <em>Web Services</em>
2279 <!-- JAL-2549 -->Updated JABAWS client to v2.2
2282 <!-- JAL-2335 -->Filter non-standard amino acids and
2283 nucleotides when submitting to AACon and other MSA
2287 <!-- JAL-2316, -->URLs for viewing database
2288 cross-references provided by identifiers.org and the
2289 EMBL-EBI's MIRIAM DB
2296 <!-- JAL-2344 -->FileFormatI interface for describing and
2297 identifying file formats (instead of String constants)
2300 <!-- JAL-2228 -->FeatureCounter script refactored for
2301 efficiency when counting all displayed features (not
2302 backwards compatible with 2.10.1)
2305 <em>Example files</em>
2308 <!-- JAL-2631 -->Graduated feature colour style example
2309 included in the example feature file
2312 <em>Documentation</em>
2315 <!-- JAL-2339 -->Release notes reformatted for readability
2316 with the built-in Java help viewer
2319 <!-- JAL-1644 -->Find documentation updated with 'search
2320 sequence description' option
2326 <!-- JAL-2485, -->External service integration tests for
2327 Uniprot REST Free Text Search Client
2330 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
2333 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
2338 <td><div align="left">
2339 <em>Calculations</em>
2342 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
2343 matrix - C->R should be '-3'<br />Old matrix restored
2344 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
2346 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
2347 Jalview's treatment of gaps in PCA and substitution matrix
2348 based Tree calculations.<br /> <br />In earlier versions
2349 of Jalview, gaps matching gaps were penalised, and gaps
2350 matching non-gaps penalised even more. In the PCA
2351 calculation, gaps were actually treated as non-gaps - so
2352 different costs were applied, which meant Jalview's PCAs
2353 were different to those produced by SeqSpace.<br />Jalview
2354 now treats gaps in the same way as SeqSpace (ie it scores
2355 them as 0). <br /> <br />Enter the following in the
2356 Groovy console to restore pre-2.10.2 behaviour:<br />
2357 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
2358 // for 2.10.1 mode <br />
2359 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
2360 // to restore 2.10.2 mode <br /> <br /> <em>Note:
2361 these settings will affect all subsequent tree and PCA
2362 calculations (not recommended)</em></li>
2364 <!-- JAL-2424 -->Fixed off-by-one bug that affected
2365 scaling of branch lengths for trees computed using
2366 Sequence Feature Similarity.
2369 <!-- JAL-2377 -->PCA calculation could hang when
2370 generating output report when working with highly
2371 redundant alignments
2374 <!-- JAL-2544 --> Sort by features includes features to
2375 right of selected region when gaps present on right-hand
2379 <em>User Interface</em>
2382 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2383 doesn't reselect a specific sequence's associated
2384 annotation after it was used for colouring a view
2387 <!-- JAL-2419 -->Current selection lost if popup menu
2388 opened on a region of alignment without groups
2391 <!-- JAL-2374 -->Popup menu not always shown for regions
2392 of an alignment with overlapping groups
2395 <!-- JAL-2310 -->Finder double counts if both a sequence's
2396 name and description match
2399 <!-- JAL-2370 -->Hiding column selection containing two
2400 hidden regions results in incorrect hidden regions
2403 <!-- JAL-2386 -->'Apply to all groups' setting when
2404 changing colour does not apply Conservation slider value
2408 <!-- JAL-2373 -->Percentage identity and conservation menu
2409 items do not show a tick or allow shading to be disabled
2412 <!-- JAL-2385 -->Conservation shading or PID threshold
2413 lost when base colourscheme changed if slider not visible
2416 <!-- JAL-2547 -->Sequence features shown in tooltip for
2417 gaps before start of features
2420 <!-- JAL-2623 -->Graduated feature colour threshold not
2421 restored to UI when feature colour is edited
2424 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2425 a time when scrolling vertically in wrapped mode.
2428 <!-- JAL-2630 -->Structure and alignment overview update
2429 as graduate feature colour settings are modified via the
2433 <!-- JAL-2034 -->Overview window doesn't always update
2434 when a group defined on the alignment is resized
2437 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2438 wrapped view result in positional status updates
2442 <!-- JAL-2563 -->Status bar doesn't show position for
2443 ambiguous amino acid and nucleotide symbols
2446 <!-- JAL-2602 -->Copy consensus sequence failed if
2447 alignment included gapped columns
2450 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2451 widgets don't permanently disappear
2454 <!-- JAL-2503 -->Cannot select or filter quantitative
2455 annotation that are shown only as column labels (e.g.
2456 T-Coffee column reliability scores)
2459 <!-- JAL-2594 -->Exception thrown if trying to create a
2460 sequence feature on gaps only
2463 <!-- JAL-2504 -->Features created with 'New feature'
2464 button from a Find inherit previously defined feature type
2465 rather than the Find query string
2468 <!-- JAL-2423 -->incorrect title in output window when
2469 exporting tree calculated in Jalview
2472 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2473 and then revealing them reorders sequences on the
2477 <!-- JAL-964 -->Group panel in sequence feature settings
2478 doesn't update to reflect available set of groups after
2479 interactively adding or modifying features
2482 <!-- JAL-2225 -->Sequence Database chooser unusable on
2486 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2487 only excluded gaps in current sequence and ignored
2494 <!-- JAL-2421 -->Overview window visible region moves
2495 erratically when hidden rows or columns are present
2498 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2499 Structure Viewer's colour menu don't correspond to
2503 <!-- JAL-2405 -->Protein specific colours only offered in
2504 colour and group colour menu for protein alignments
2507 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2508 reflect currently selected view or group's shading
2512 <!-- JAL-2624 -->Feature colour thresholds not respected
2513 when rendered on overview and structures when opacity at
2517 <!-- JAL-2589 -->User defined gap colour not shown in
2518 overview when features overlaid on alignment
2521 <!-- JAL-2567 -->Feature settings for different views not
2522 recovered correctly from Jalview project file
2525 <!-- JAL-2256 -->Feature colours in overview when first
2526 opened (automatically via preferences) are different to
2527 the main alignment panel
2530 <em>Data import/export</em>
2533 <!-- JAL-2576 -->Very large alignments take a long time to
2537 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2538 added after a sequence was imported are not written to
2542 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2543 when importing RNA secondary structure via Stockholm
2546 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2547 not shown in correct direction for simple pseudoknots
2550 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2551 with lightGray or darkGray via features file (but can
2555 <!-- JAL-2383 -->Above PID colour threshold not recovered
2556 when alignment view imported from project
2559 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2560 structure and sequences extracted from structure files
2561 imported via URL and viewed in Jmol
2564 <!-- JAL-2520 -->Structures loaded via URL are saved in
2565 Jalview Projects rather than fetched via URL again when
2566 the project is loaded and the structure viewed
2569 <em>Web Services</em>
2572 <!-- JAL-2519 -->EnsemblGenomes example failing after
2573 release of Ensembl v.88
2576 <!-- JAL-2366 -->Proxy server address and port always
2577 appear enabled in Preferences->Connections
2580 <!-- JAL-2461 -->DAS registry not found exceptions
2581 removed from console output
2584 <!-- JAL-2582 -->Cannot retrieve protein products from
2585 Ensembl by Peptide ID
2588 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2589 created from SIFTs, and spurious 'Couldn't open structure
2590 in Chimera' errors raised after April 2017 update (problem
2591 due to 'null' string rather than empty string used for
2592 residues with no corresponding PDB mapping).
2595 <em>Application UI</em>
2598 <!-- JAL-2361 -->User Defined Colours not added to Colour
2602 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2603 case' residues (button in colourscheme editor debugged and
2604 new documentation and tooltips added)
2607 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2608 doesn't restore group-specific text colour thresholds
2611 <!-- JAL-2243 -->Feature settings panel does not update as
2612 new features are added to alignment
2615 <!-- JAL-2532 -->Cancel in feature settings reverts
2616 changes to feature colours via the Amend features dialog
2619 <!-- JAL-2506 -->Null pointer exception when attempting to
2620 edit graduated feature colour via amend features dialog
2624 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2625 selection menu changes colours of alignment views
2628 <!-- JAL-2426 -->Spurious exceptions in console raised
2629 from alignment calculation workers after alignment has
2633 <!-- JAL-1608 -->Typo in selection popup menu - Create
2634 groups now 'Create Group'
2637 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2638 Create/Undefine group doesn't always work
2641 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2642 shown again after pressing 'Cancel'
2645 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2646 adjusts start position in wrap mode
2649 <!-- JAL-2563 -->Status bar doesn't show positions for
2650 ambiguous amino acids
2653 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2654 CDS/Protein view after CDS sequences added for aligned
2658 <!-- JAL-2592 -->User defined colourschemes called 'User
2659 Defined' don't appear in Colours menu
2665 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2666 score models doesn't always result in an updated PCA plot
2669 <!-- JAL-2442 -->Features not rendered as transparent on
2670 overview or linked structure view
2673 <!-- JAL-2372 -->Colour group by conservation doesn't
2677 <!-- JAL-2517 -->Hitting Cancel after applying
2678 user-defined colourscheme doesn't restore original
2685 <!-- JAL-2314 -->Unit test failure:
2686 jalview.ws.jabaws.RNAStructExportImport setup fails
2689 <!-- JAL-2307 -->Unit test failure:
2690 jalview.ws.sifts.SiftsClientTest due to compatibility
2691 problems with deep array comparison equality asserts in
2692 successive versions of TestNG
2695 <!-- JAL-2479 -->Relocated StructureChooserTest and
2696 ParameterUtilsTest Unit tests to Network suite
2699 <em>New Known Issues</em>
2702 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2703 phase after a sequence motif find operation
2706 <!-- JAL-2550 -->Importing annotation file with rows
2707 containing just upper and lower case letters are
2708 interpreted as WUSS RNA secondary structure symbols
2711 <!-- JAL-2590 -->Cannot load and display Newick trees
2712 reliably from eggnog Ortholog database
2715 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2716 containing features of type Highlight' when 'B' is pressed
2717 to mark columns containing highlighted regions.
2720 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2721 doesn't always add secondary structure annotation.
2726 <td width="60" nowrap>
2727 <div align="center">
2728 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2731 <td><div align="left">
2735 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2736 for all consensus calculations
2739 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2742 <li>Updated Jalview's Certum code signing certificate
2745 <em>Application</em>
2748 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2749 set of database cross-references, sorted alphabetically
2752 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2753 from database cross references. Users with custom links
2754 will receive a <a href="webServices/urllinks.html#warning">warning
2755 dialog</a> asking them to update their preferences.
2758 <!-- JAL-2287-->Cancel button and escape listener on
2759 dialog warning user about disconnecting Jalview from a
2763 <!-- JAL-2320-->Jalview's Chimera control window closes if
2764 the Chimera it is connected to is shut down
2767 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2768 columns menu item to mark columns containing highlighted
2769 regions (e.g. from structure selections or results of a
2773 <!-- JAL-2284-->Command line option for batch-generation
2774 of HTML pages rendering alignment data with the BioJS
2784 <!-- JAL-2286 -->Columns with more than one modal residue
2785 are not coloured or thresholded according to percent
2786 identity (first observed in Jalview 2.8.2)
2789 <!-- JAL-2301 -->Threonine incorrectly reported as not
2793 <!-- JAL-2318 -->Updates to documentation pages (above PID
2794 threshold, amino acid properties)
2797 <!-- JAL-2292 -->Lower case residues in sequences are not
2798 reported as mapped to residues in a structure file in the
2802 <!--JAL-2324 -->Identical features with non-numeric scores
2803 could be added multiple times to a sequence
2806 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2807 bond features shown as two highlighted residues rather
2808 than a range in linked structure views, and treated
2809 correctly when selecting and computing trees from features
2812 <!-- JAL-2281-->Custom URL links for database
2813 cross-references are matched to database name regardless
2818 <em>Application</em>
2821 <!-- JAL-2282-->Custom URL links for specific database
2822 names without regular expressions also offer links from
2826 <!-- JAL-2315-->Removing a single configured link in the
2827 URL links pane in Connections preferences doesn't actually
2828 update Jalview configuration
2831 <!-- JAL-2272-->CTRL-Click on a selected region to open
2832 the alignment area popup menu doesn't work on El-Capitan
2835 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2836 files with similarly named sequences if dropped onto the
2840 <!-- JAL-2312 -->Additional mappings are shown for PDB
2841 entries where more chains exist in the PDB accession than
2842 are reported in the SIFTS file
2845 <!-- JAL-2317-->Certain structures do not get mapped to
2846 the structure view when displayed with Chimera
2849 <!-- JAL-2317-->No chains shown in the Chimera view
2850 panel's View->Show Chains submenu
2853 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2854 work for wrapped alignment views
2857 <!--JAL-2197 -->Rename UI components for running JPred
2858 predictions from 'JNet' to 'JPred'
2861 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2862 corrupted when annotation panel vertical scroll is not at
2863 first annotation row
2866 <!--JAL-2332 -->Attempting to view structure for Hen
2867 lysozyme results in a PDB Client error dialog box
2870 <!-- JAL-2319 -->Structure View's mapping report switched
2871 ranges for PDB and sequence for SIFTS
2874 SIFTS 'Not_Observed' residues mapped to non-existant
2878 <!-- <em>New Known Issues</em>
2885 <td width="60" nowrap>
2886 <div align="center">
2887 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2888 <em>25/10/2016</em></strong>
2891 <td><em>Application</em>
2893 <li>3D Structure chooser opens with 'Cached structures'
2894 view if structures already loaded</li>
2895 <li>Progress bar reports models as they are loaded to
2896 structure views</li>
2902 <li>Colour by conservation always enabled and no tick
2903 shown in menu when BLOSUM or PID shading applied</li>
2904 <li>FER1_ARATH and FER2_ARATH labels were switched in
2905 example sequences/projects/trees</li>
2907 <em>Application</em>
2909 <li>Jalview projects with views of local PDB structure
2910 files saved on Windows cannot be opened on OSX</li>
2911 <li>Multiple structure views can be opened and superposed
2912 without timeout for structures with multiple models or
2913 multiple sequences in alignment</li>
2914 <li>Cannot import or associated local PDB files without a
2915 PDB ID HEADER line</li>
2916 <li>RMSD is not output in Jmol console when superposition
2918 <li>Drag and drop of URL from Browser fails for Linux and
2919 OSX versions earlier than El Capitan</li>
2920 <li>ENA client ignores invalid content from ENA server</li>
2921 <li>Exceptions are not raised in console when ENA client
2922 attempts to fetch non-existent IDs via Fetch DB Refs UI
2924 <li>Exceptions are not raised in console when a new view
2925 is created on the alignment</li>
2926 <li>OSX right-click fixed for group selections: CMD-click
2927 to insert/remove gaps in groups and CTRL-click to open group
2930 <em>Build and deployment</em>
2932 <li>URL link checker now copes with multi-line anchor
2935 <em>New Known Issues</em>
2937 <li>Drag and drop from URL links in browsers do not work
2944 <td width="60" nowrap>
2945 <div align="center">
2946 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2949 <td><em>General</em>
2952 <!-- JAL-2124 -->Updated Spanish translations.
2955 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2956 for importing structure data to Jalview. Enables mmCIF and
2960 <!-- JAL-192 --->Alignment ruler shows positions relative to
2964 <!-- JAL-2202 -->Position/residue shown in status bar when
2965 mousing over sequence associated annotation
2968 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2972 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2973 '()', canonical '[]' and invalid '{}' base pair populations
2977 <!-- JAL-2092 -->Feature settings popup menu options for
2978 showing or hiding columns containing a feature
2981 <!-- JAL-1557 -->Edit selected group by double clicking on
2982 group and sequence associated annotation labels
2985 <!-- JAL-2236 -->Sequence name added to annotation label in
2986 select/hide columns by annotation and colour by annotation
2990 </ul> <em>Application</em>
2993 <!-- JAL-2050-->Automatically hide introns when opening a
2994 gene/transcript view
2997 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
3001 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
3002 structure mappings with the EMBL-EBI PDBe SIFTS database
3005 <!-- JAL-2079 -->Updated download sites used for Rfam and
3006 Pfam sources to xfam.org
3009 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
3012 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
3013 over sequences in Jalview
3016 <!-- JAL-2027-->Support for reverse-complement coding
3017 regions in ENA and EMBL
3020 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
3021 for record retrieval via ENA rest API
3024 <!-- JAL-2027 -->Support for ENA CDS records with reverse
3028 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
3029 groovy script execution
3032 <!-- JAL-1812 -->New 'execute Groovy script' option in an
3033 alignment window's Calculate menu
3036 <!-- JAL-1812 -->Allow groovy scripts that call
3037 Jalview.getAlignFrames() to run in headless mode
3040 <!-- JAL-2068 -->Support for creating new alignment
3041 calculation workers from groovy scripts
3044 <!-- JAL-1369 --->Store/restore reference sequence in
3048 <!-- JAL-1803 -->Chain codes for a sequence's PDB
3049 associations are now saved/restored from project
3052 <!-- JAL-1993 -->Database selection dialog always shown
3053 before sequence fetcher is opened
3056 <!-- JAL-2183 -->Double click on an entry in Jalview's
3057 database chooser opens a sequence fetcher
3060 <!-- JAL-1563 -->Free-text search client for UniProt using
3061 the UniProt REST API
3064 <!-- JAL-2168 -->-nonews command line parameter to prevent
3065 the news reader opening
3068 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
3069 querying stored in preferences
3072 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
3076 <!-- JAL-1977-->Tooltips shown on database chooser
3079 <!-- JAL-391 -->Reverse complement function in calculate
3080 menu for nucleotide sequences
3083 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
3084 and feature counts preserves alignment ordering (and
3085 debugged for complex feature sets).
3088 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
3089 viewing structures with Jalview 2.10
3092 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
3093 genome, transcript CCDS and gene ids via the Ensembl and
3094 Ensembl Genomes REST API
3097 <!-- JAL-2049 -->Protein sequence variant annotation
3098 computed for 'sequence_variant' annotation on CDS regions
3102 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
3106 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
3107 Ref Fetcher fails to match, or otherwise updates sequence
3108 data from external database records.
3111 <!-- JAL-2154 -->Revised Jalview Project format for
3112 efficient recovery of sequence coding and alignment
3113 annotation relationships.
3115 </ul> <!-- <em>Applet</em>
3126 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
3130 <!-- JAL-2018-->Export features in Jalview format (again)
3131 includes graduated colourschemes
3134 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
3135 working with big alignments and lots of hidden columns
3138 <!-- JAL-2053-->Hidden column markers not always rendered
3139 at right of alignment window
3142 <!-- JAL-2067 -->Tidied up links in help file table of
3146 <!-- JAL-2072 -->Feature based tree calculation not shown
3150 <!-- JAL-2075 -->Hidden columns ignored during feature
3151 based tree calculation
3154 <!-- JAL-2065 -->Alignment view stops updating when show
3155 unconserved enabled for group on alignment
3158 <!-- JAL-2086 -->Cannot insert gaps into sequence when
3162 <!-- JAL-2146 -->Alignment column in status incorrectly
3163 shown as "Sequence position" when mousing over
3167 <!-- JAL-2099 -->Incorrect column numbers in ruler when
3168 hidden columns present
3171 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
3172 user created annotation added to alignment
3175 <!-- JAL-1841 -->RNA Structure consensus only computed for
3176 '()' base pair annotation
3179 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
3180 in zero scores for all base pairs in RNA Structure
3184 <!-- JAL-2174-->Extend selection with columns containing
3188 <!-- JAL-2275 -->Pfam format writer puts extra space at
3189 beginning of sequence
3192 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
3196 <!-- JAL-2238 -->Cannot create groups on an alignment from
3197 from a tree when t-coffee scores are shown
3200 <!-- JAL-1836,1967 -->Cannot import and view PDB
3201 structures with chains containing negative resnums (4q4h)
3204 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
3208 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
3209 to Clustal, PIR and PileUp output
3212 <!-- JAL-2008 -->Reordering sequence features that are
3213 not visible causes alignment window to repaint
3216 <!-- JAL-2006 -->Threshold sliders don't work in
3217 graduated colour and colour by annotation row for e-value
3218 scores associated with features and annotation rows
3221 <!-- JAL-1797 -->amino acid physicochemical conservation
3222 calculation should be case independent
3225 <!-- JAL-2173 -->Remove annotation also updates hidden
3229 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
3230 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
3231 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
3234 <!-- JAL-2065 -->Null pointer exceptions and redraw
3235 problems when reference sequence defined and 'show
3236 non-conserved' enabled
3239 <!-- JAL-1306 -->Quality and Conservation are now shown on
3240 load even when Consensus calculation is disabled
3243 <!-- JAL-1932 -->Remove right on penultimate column of
3244 alignment does nothing
3247 <em>Application</em>
3250 <!-- JAL-1552-->URLs and links can't be imported by
3251 drag'n'drop on OSX when launched via webstart (note - not
3252 yet fixed for El Capitan)
3255 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
3256 output when running on non-gb/us i18n platforms
3259 <!-- JAL-1944 -->Error thrown when exporting a view with
3260 hidden sequences as flat-file alignment
3263 <!-- JAL-2030-->InstallAnywhere distribution fails when
3267 <!-- JAL-2080-->Jalview very slow to launch via webstart
3268 (also hotfix for 2.9.0b2)
3271 <!-- JAL-2085 -->Cannot save project when view has a
3272 reference sequence defined
3275 <!-- JAL-1011 -->Columns are suddenly selected in other
3276 alignments and views when revealing hidden columns
3279 <!-- JAL-1989 -->Hide columns not mirrored in complement
3280 view in a cDNA/Protein splitframe
3283 <!-- JAL-1369 -->Cannot save/restore representative
3284 sequence from project when only one sequence is
3288 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
3289 in Structure Chooser
3292 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
3293 structure consensus didn't refresh annotation panel
3296 <!-- JAL-1962 -->View mapping in structure view shows
3297 mappings between sequence and all chains in a PDB file
3300 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
3301 dialogs format columns correctly, don't display array
3302 data, sort columns according to type
3305 <!-- JAL-1975 -->Export complete shown after destination
3306 file chooser is cancelled during an image export
3309 <!-- JAL-2025 -->Error when querying PDB Service with
3310 sequence name containing special characters
3313 <!-- JAL-2024 -->Manual PDB structure querying should be
3317 <!-- JAL-2104 -->Large tooltips with broken HTML
3318 formatting don't wrap
3321 <!-- JAL-1128 -->Figures exported from wrapped view are
3322 truncated so L looks like I in consensus annotation
3325 <!-- JAL-2003 -->Export features should only export the
3326 currently displayed features for the current selection or
3330 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
3331 after fetching cross-references, and restoring from
3335 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
3336 followed in the structure viewer
3339 <!-- JAL-2163 -->Titles for individual alignments in
3340 splitframe not restored from project
3343 <!-- JAL-2145 -->missing autocalculated annotation at
3344 trailing end of protein alignment in transcript/product
3345 splitview when pad-gaps not enabled by default
3348 <!-- JAL-1797 -->amino acid physicochemical conservation
3352 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
3353 article has been read (reopened issue due to
3354 internationalisation problems)
3357 <!-- JAL-1960 -->Only offer PDB structures in structure
3358 viewer based on sequence name, PDB and UniProt
3363 <!-- JAL-1976 -->No progress bar shown during export of
3367 <!-- JAL-2213 -->Structures not always superimposed after
3368 multiple structures are shown for one or more sequences.
3371 <!-- JAL-1370 -->Reference sequence characters should not
3372 be replaced with '.' when 'Show unconserved' format option
3376 <!-- JAL-1823 -->Cannot specify chain code when entering
3377 specific PDB id for sequence
3380 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3381 'Export hidden sequences' is enabled, but 'export hidden
3382 columns' is disabled.
3385 <!--JAL-2026-->Best Quality option in structure chooser
3386 selects lowest rather than highest resolution structures
3390 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3391 to sequence mapping in 'View Mappings' report
3394 <!-- JAL-2284 -->Unable to read old Jalview projects that
3395 contain non-XML data added after Jalvew wrote project.
3398 <!-- JAL-2118 -->Newly created annotation row reorders
3399 after clicking on it to create new annotation for a
3403 <!-- JAL-1980 -->Null Pointer Exception raised when
3404 pressing Add on an orphaned cut'n'paste window.
3406 <!-- may exclude, this is an external service stability issue JAL-1941
3407 -- > RNA 3D structure not added via DSSR service</li> -->
3412 <!-- JAL-2151 -->Incorrect columns are selected when
3413 hidden columns present before start of sequence
3416 <!-- JAL-1986 -->Missing dependencies on applet pages
3420 <!-- JAL-1947 -->Overview pixel size changes when
3421 sequences are hidden in applet
3424 <!-- JAL-1996 -->Updated instructions for applet
3425 deployment on examples pages.
3432 <td width="60" nowrap>
3433 <div align="center">
3434 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3435 <em>16/10/2015</em></strong>
3438 <td><em>General</em>
3440 <li>Time stamps for signed Jalview application and applet
3445 <em>Application</em>
3447 <li>Duplicate group consensus and conservation rows
3448 shown when tree is partitioned</li>
3449 <li>Erratic behaviour when tree partitions made with
3450 multiple cDNA/Protein split views</li>
3456 <td width="60" nowrap>
3457 <div align="center">
3458 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3459 <em>8/10/2015</em></strong>
3462 <td><em>General</em>
3464 <li>Updated Spanish translations of localized text for
3466 </ul> <em>Application</em>
3468 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3469 <li>Signed OSX InstallAnywhere installer<br></li>
3470 <li>Support for per-sequence based annotations in BioJSON</li>
3471 </ul> <em>Applet</em>
3473 <li>Split frame example added to applet examples page</li>
3474 </ul> <em>Build and Deployment</em>
3477 <!-- JAL-1888 -->New ant target for running Jalview's test
3485 <li>Mapping of cDNA to protein in split frames
3486 incorrect when sequence start > 1</li>
3487 <li>Broken images in filter column by annotation dialog
3489 <li>Feature colours not parsed from features file</li>
3490 <li>Exceptions and incomplete link URLs recovered when
3491 loading a features file containing HTML tags in feature
3495 <em>Application</em>
3497 <li>Annotations corrupted after BioJS export and
3499 <li>Incorrect sequence limits after Fetch DB References
3500 with 'trim retrieved sequences'</li>
3501 <li>Incorrect warning about deleting all data when
3502 deleting selected columns</li>
3503 <li>Patch to build system for shipping properly signed
3504 JNLP templates for webstart launch</li>
3505 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3506 unreleased structures for download or viewing</li>
3507 <li>Tab/space/return keystroke operation of EMBL-PDBe
3508 fetcher/viewer dialogs works correctly</li>
3509 <li>Disabled 'minimise' button on Jalview windows
3510 running on OSX to workaround redraw hang bug</li>
3511 <li>Split cDNA/Protein view position and geometry not
3512 recovered from jalview project</li>
3513 <li>Initial enabled/disabled state of annotation menu
3514 sorter 'show autocalculated first/last' corresponds to
3516 <li>Restoring of Clustal, RNA Helices and T-Coffee
3517 color schemes from BioJSON</li>
3521 <li>Reorder sequences mirrored in cDNA/Protein split
3523 <li>Applet with Jmol examples not loading correctly</li>
3529 <td><div align="center">
3530 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3532 <td><em>General</em>
3534 <li>Linked visualisation and analysis of DNA and Protein
3537 <li>Translated cDNA alignments shown as split protein
3538 and DNA alignment views</li>
3539 <li>Codon consensus annotation for linked protein and
3540 cDNA alignment views</li>
3541 <li>Link cDNA or Protein product sequences by loading
3542 them onto Protein or cDNA alignments</li>
3543 <li>Reconstruct linked cDNA alignment from aligned
3544 protein sequences</li>
3547 <li>Jmol integration updated to Jmol v14.2.14</li>
3548 <li>Import and export of Jalview alignment views as <a
3549 href="features/bioJsonFormat.html">BioJSON</a></li>
3550 <li>New alignment annotation file statements for
3551 reference sequences and marking hidden columns</li>
3552 <li>Reference sequence based alignment shading to
3553 highlight variation</li>
3554 <li>Select or hide columns according to alignment
3556 <li>Find option for locating sequences by description</li>
3557 <li>Conserved physicochemical properties shown in amino
3558 acid conservation row</li>
3559 <li>Alignments can be sorted by number of RNA helices</li>
3560 </ul> <em>Application</em>
3562 <li>New cDNA/Protein analysis capabilities
3564 <li>Get Cross-References should open a Split Frame
3565 view with cDNA/Protein</li>
3566 <li>Detect when nucleotide sequences and protein
3567 sequences are placed in the same alignment</li>
3568 <li>Split cDNA/Protein views are saved in Jalview
3573 <li>Use REST API to talk to Chimera</li>
3574 <li>Selected regions in Chimera are highlighted in linked
3575 Jalview windows</li>
3577 <li>VARNA RNA viewer updated to v3.93</li>
3578 <li>VARNA views are saved in Jalview Projects</li>
3579 <li>Pseudoknots displayed as Jalview RNA annotation can
3580 be shown in VARNA</li>
3582 <li>Make groups for selection uses marked columns as well
3583 as the active selected region</li>
3585 <li>Calculate UPGMA and NJ trees using sequence feature
3587 <li>New Export options
3589 <li>New Export Settings dialog to control hidden
3590 region export in flat file generation</li>
3592 <li>Export alignment views for display with the <a
3593 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3595 <li>Export scrollable SVG in HTML page</li>
3596 <li>Optional embedding of BioJSON data when exporting
3597 alignment figures to HTML</li>
3599 <li>3D structure retrieval and display
3601 <li>Free text and structured queries with the PDBe
3603 <li>PDBe Search API based discovery and selection of
3604 PDB structures for a sequence set</li>
3608 <li>JPred4 employed for protein secondary structure
3610 <li>Hide Insertions menu option to hide unaligned columns
3611 for one or a group of sequences</li>
3612 <li>Automatically hide insertions in alignments imported
3613 from the JPred4 web server</li>
3614 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3615 system on OSX<br />LGPL libraries courtesy of <a
3616 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3618 <li>changed 'View nucleotide structure' submenu to 'View
3619 VARNA 2D Structure'</li>
3620 <li>change "View protein structure" menu option to "3D
3623 </ul> <em>Applet</em>
3625 <li>New layout for applet example pages</li>
3626 <li>New parameters to enable SplitFrame view
3627 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3628 <li>New example demonstrating linked viewing of cDNA and
3629 Protein alignments</li>
3630 </ul> <em>Development and deployment</em>
3632 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3633 <li>Include installation type and git revision in build
3634 properties and console log output</li>
3635 <li>Jalview Github organisation, and new github site for
3636 storing BioJsMSA Templates</li>
3637 <li>Jalview's unit tests now managed with TestNG</li>
3640 <!-- <em>General</em>
3642 </ul> --> <!-- issues resolved --> <em>Application</em>
3644 <li>Escape should close any open find dialogs</li>
3645 <li>Typo in select-by-features status report</li>
3646 <li>Consensus RNA secondary secondary structure
3647 predictions are not highlighted in amber</li>
3648 <li>Missing gap character in v2.7 example file means
3649 alignment appears unaligned when pad-gaps is not enabled</li>
3650 <li>First switch to RNA Helices colouring doesn't colour
3651 associated structure views</li>
3652 <li>ID width preference option is greyed out when auto
3653 width checkbox not enabled</li>
3654 <li>Stopped a warning dialog from being shown when
3655 creating user defined colours</li>
3656 <li>'View Mapping' in structure viewer shows sequence
3657 mappings for just that viewer's sequences</li>
3658 <li>Workaround for superposing PDB files containing
3659 multiple models in Chimera</li>
3660 <li>Report sequence position in status bar when hovering
3661 over Jmol structure</li>
3662 <li>Cannot output gaps as '.' symbols with Selection ->
3663 output to text box</li>
3664 <li>Flat file exports of alignments with hidden columns
3665 have incorrect sequence start/end</li>
3666 <li>'Aligning' a second chain to a Chimera structure from
3668 <li>Colour schemes applied to structure viewers don't
3669 work for nucleotide</li>
3670 <li>Loading/cut'n'pasting an empty or invalid file leads
3671 to a grey/invisible alignment window</li>
3672 <li>Exported Jpred annotation from a sequence region
3673 imports to different position</li>
3674 <li>Space at beginning of sequence feature tooltips shown
3675 on some platforms</li>
3676 <li>Chimera viewer 'View | Show Chain' menu is not
3678 <li>'New View' fails with a Null Pointer Exception in
3679 console if Chimera has been opened</li>
3680 <li>Mouseover to Chimera not working</li>
3681 <li>Miscellaneous ENA XML feature qualifiers not
3683 <li>NPE in annotation renderer after 'Extract Scores'</li>
3684 <li>If two structures in one Chimera window, mouseover of
3685 either sequence shows on first structure</li>
3686 <li>'Show annotations' options should not make
3687 non-positional annotations visible</li>
3688 <li>Subsequence secondary structure annotation not shown
3689 in right place after 'view flanking regions'</li>
3690 <li>File Save As type unset when current file format is
3692 <li>Save as '.jar' option removed for saving Jalview
3694 <li>Colour by Sequence colouring in Chimera more
3696 <li>Cannot 'add reference annotation' for a sequence in
3697 several views on same alignment</li>
3698 <li>Cannot show linked products for EMBL / ENA records</li>
3699 <li>Jalview's tooltip wraps long texts containing no
3701 </ul> <em>Applet</em>
3703 <li>Jmol to JalviewLite mouseover/link not working</li>
3704 <li>JalviewLite can't import sequences with ID
3705 descriptions containing angle brackets</li>
3706 </ul> <em>General</em>
3708 <li>Cannot export and reimport RNA secondary structure
3709 via jalview annotation file</li>
3710 <li>Random helix colour palette for colour by annotation
3711 with RNA secondary structure</li>
3712 <li>Mouseover to cDNA from STOP residue in protein
3713 translation doesn't work.</li>
3714 <li>hints when using the select by annotation dialog box</li>
3715 <li>Jmol alignment incorrect if PDB file has alternate CA
3717 <li>FontChooser message dialog appears to hang after
3718 choosing 1pt font</li>
3719 <li>Peptide secondary structure incorrectly imported from
3720 annotation file when annotation display text includes 'e' or
3722 <li>Cannot set colour of new feature type whilst creating
3724 <li>cDNA translation alignment should not be sequence
3725 order dependent</li>
3726 <li>'Show unconserved' doesn't work for lower case
3728 <li>Nucleotide ambiguity codes involving R not recognised</li>
3729 </ul> <em>Deployment and Documentation</em>
3731 <li>Applet example pages appear different to the rest of
3732 www.jalview.org</li>
3733 </ul> <em>Application Known issues</em>
3735 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3736 <li>Misleading message appears after trying to delete
3738 <li>Jalview icon not shown in dock after InstallAnywhere
3739 version launches</li>
3740 <li>Fetching EMBL reference for an RNA sequence results
3741 fails with a sequence mismatch</li>
3742 <li>Corrupted or unreadable alignment display when
3743 scrolling alignment to right</li>
3744 <li>ArrayIndexOutOfBoundsException thrown when remove
3745 empty columns called on alignment with ragged gapped ends</li>
3746 <li>auto calculated alignment annotation rows do not get
3747 placed above or below non-autocalculated rows</li>
3748 <li>Jalview dekstop becomes sluggish at full screen in
3749 ultra-high resolution</li>
3750 <li>Cannot disable consensus calculation independently of
3751 quality and conservation</li>
3752 <li>Mouseover highlighting between cDNA and protein can
3753 become sluggish with more than one splitframe shown</li>
3754 </ul> <em>Applet Known Issues</em>
3756 <li>Core PDB parsing code requires Jmol</li>
3757 <li>Sequence canvas panel goes white when alignment
3758 window is being resized</li>
3764 <td><div align="center">
3765 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3767 <td><em>General</em>
3769 <li>Updated Java code signing certificate donated by
3771 <li>Features and annotation preserved when performing
3772 pairwise alignment</li>
3773 <li>RNA pseudoknot annotation can be
3774 imported/exported/displayed</li>
3775 <li>'colour by annotation' can colour by RNA and
3776 protein secondary structure</li>
3777 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3778 post-hoc with 2.9 release</em>)
3781 </ul> <em>Application</em>
3783 <li>Extract and display secondary structure for sequences
3784 with 3D structures</li>
3785 <li>Support for parsing RNAML</li>
3786 <li>Annotations menu for layout
3788 <li>sort sequence annotation rows by alignment</li>
3789 <li>place sequence annotation above/below alignment
3792 <li>Output in Stockholm format</li>
3793 <li>Internationalisation: improved Spanish (es)
3795 <li>Structure viewer preferences tab</li>
3796 <li>Disorder and Secondary Structure annotation tracks
3797 shared between alignments</li>
3798 <li>UCSF Chimera launch and linked highlighting from
3800 <li>Show/hide all sequence associated annotation rows for
3801 all or current selection</li>
3802 <li>disorder and secondary structure predictions
3803 available as dataset annotation</li>
3804 <li>Per-sequence rna helices colouring</li>
3807 <li>Sequence database accessions imported when fetching
3808 alignments from Rfam</li>
3809 <li>update VARNA version to 3.91</li>
3811 <li>New groovy scripts for exporting aligned positions,
3812 conservation values, and calculating sum of pairs scores.</li>
3813 <li>Command line argument to set default JABAWS server</li>
3814 <li>include installation type in build properties and
3815 console log output</li>
3816 <li>Updated Jalview project format to preserve dataset
3820 <!-- issues resolved --> <em>Application</em>
3822 <li>Distinguish alignment and sequence associated RNA
3823 structure in structure->view->VARNA</li>
3824 <li>Raise dialog box if user deletes all sequences in an
3826 <li>Pressing F1 results in documentation opening twice</li>
3827 <li>Sequence feature tooltip is wrapped</li>
3828 <li>Double click on sequence associated annotation
3829 selects only first column</li>
3830 <li>Redundancy removal doesn't result in unlinked
3831 leaves shown in tree</li>
3832 <li>Undos after several redundancy removals don't undo
3834 <li>Hide sequence doesn't hide associated annotation</li>
3835 <li>User defined colours dialog box too big to fit on
3836 screen and buttons not visible</li>
3837 <li>author list isn't updated if already written to
3838 Jalview properties</li>
3839 <li>Popup menu won't open after retrieving sequence
3841 <li>File open window for associate PDB doesn't open</li>
3842 <li>Left-then-right click on a sequence id opens a
3843 browser search window</li>
3844 <li>Cannot open sequence feature shading/sort popup menu
3845 in feature settings dialog</li>
3846 <li>better tooltip placement for some areas of Jalview
3848 <li>Allow addition of JABAWS Server which doesn't
3849 pass validation</li>
3850 <li>Web services parameters dialog box is too large to
3852 <li>Muscle nucleotide alignment preset obscured by
3854 <li>JABAWS preset submenus don't contain newly
3855 defined user preset</li>
3856 <li>MSA web services warns user if they were launched
3857 with invalid input</li>
3858 <li>Jalview cannot contact DAS Registy when running on
3861 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3862 'Superpose with' submenu not shown when new view
3866 </ul> <!-- <em>Applet</em>
3868 </ul> <em>General</em>
3870 </ul>--> <em>Deployment and Documentation</em>
3872 <li>2G and 1G options in launchApp have no effect on
3873 memory allocation</li>
3874 <li>launchApp service doesn't automatically open
3875 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3877 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3878 InstallAnywhere reports cannot find valid JVM when Java
3879 1.7_055 is available
3881 </ul> <em>Application Known issues</em>
3884 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3885 corrupted or unreadable alignment display when scrolling
3889 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3890 retrieval fails but progress bar continues for DAS retrieval
3891 with large number of ID
3894 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3895 flatfile output of visible region has incorrect sequence
3899 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3900 rna structure consensus doesn't update when secondary
3901 structure tracks are rearranged
3904 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3905 invalid rna structure positional highlighting does not
3906 highlight position of invalid base pairs
3909 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3910 out of memory errors are not raised when saving Jalview
3911 project from alignment window file menu
3914 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3915 Switching to RNA Helices colouring doesn't propagate to
3919 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3920 colour by RNA Helices not enabled when user created
3921 annotation added to alignment
3924 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3925 Jalview icon not shown on dock in Mountain Lion/Webstart
3927 </ul> <em>Applet Known Issues</em>
3930 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3931 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3934 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3935 Jalview and Jmol example not compatible with IE9
3938 <li>Sort by annotation score doesn't reverse order
3944 <td><div align="center">
3945 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3948 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3951 <li>Internationalisation of user interface (usually
3952 called i18n support) and translation for Spanish locale</li>
3953 <li>Define/Undefine group on current selection with
3954 Ctrl-G/Shift Ctrl-G</li>
3955 <li>Improved group creation/removal options in
3956 alignment/sequence Popup menu</li>
3957 <li>Sensible precision for symbol distribution
3958 percentages shown in logo tooltip.</li>
3959 <li>Annotation panel height set according to amount of
3960 annotation when alignment first opened</li>
3961 </ul> <em>Application</em>
3963 <li>Interactive consensus RNA secondary structure
3964 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3965 <li>Select columns containing particular features from
3966 Feature Settings dialog</li>
3967 <li>View all 'representative' PDB structures for selected
3969 <li>Update Jalview project format:
3971 <li>New file extension for Jalview projects '.jvp'</li>
3972 <li>Preserve sequence and annotation dataset (to
3973 store secondary structure annotation,etc)</li>
3974 <li>Per group and alignment annotation and RNA helix
3978 <li>New similarity measures for PCA and Tree calculation
3980 <li>Experimental support for retrieval and viewing of
3981 flanking regions for an alignment</li>
3985 <!-- issues resolved --> <em>Application</em>
3987 <li>logo keeps spinning and status remains at queued or
3988 running after job is cancelled</li>
3989 <li>cannot export features from alignments imported from
3990 Jalview/VAMSAS projects</li>
3991 <li>Buggy slider for web service parameters that take
3993 <li>Newly created RNA secondary structure line doesn't
3994 have 'display all symbols' flag set</li>
3995 <li>T-COFFEE alignment score shading scheme and other
3996 annotation shading not saved in Jalview project</li>
3997 <li>Local file cannot be loaded in freshly downloaded
3999 <li>Jalview icon not shown on dock in Mountain
4001 <li>Load file from desktop file browser fails</li>
4002 <li>Occasional NPE thrown when calculating large trees</li>
4003 <li>Cannot reorder or slide sequences after dragging an
4004 alignment onto desktop</li>
4005 <li>Colour by annotation dialog throws NPE after using
4006 'extract scores' function</li>
4007 <li>Loading/cut'n'pasting an empty file leads to a grey
4008 alignment window</li>
4009 <li>Disorder thresholds rendered incorrectly after
4010 performing IUPred disorder prediction</li>
4011 <li>Multiple group annotated consensus rows shown when
4012 changing 'normalise logo' display setting</li>
4013 <li>Find shows blank dialog after 'finished searching' if
4014 nothing matches query</li>
4015 <li>Null Pointer Exceptions raised when sorting by
4016 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
4018 <li>Errors in Jmol console when structures in alignment
4019 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
4021 <li>Not all working JABAWS services are shown in
4023 <li>JAVAWS version of Jalview fails to launch with
4024 'invalid literal/length code'</li>
4025 <li>Annotation/RNA Helix colourschemes cannot be applied
4026 to alignment with groups (actually fixed in 2.8.0b1)</li>
4027 <li>RNA Helices and T-Coffee Scores available as default
4030 </ul> <em>Applet</em>
4032 <li>Remove group option is shown even when selection is
4034 <li>Apply to all groups ticked but colourscheme changes
4035 don't affect groups</li>
4036 <li>Documented RNA Helices and T-Coffee Scores as valid
4037 colourscheme name</li>
4038 <li>Annotation labels drawn on sequence IDs when
4039 Annotation panel is not displayed</li>
4040 <li>Increased font size for dropdown menus on OSX and
4041 embedded windows</li>
4042 </ul> <em>Other</em>
4044 <li>Consensus sequence for alignments/groups with a
4045 single sequence were not calculated</li>
4046 <li>annotation files that contain only groups imported as
4047 annotation and junk sequences</li>
4048 <li>Fasta files with sequences containing '*' incorrectly
4049 recognised as PFAM or BLC</li>
4050 <li>conservation/PID slider apply all groups option
4051 doesn't affect background (2.8.0b1)
4053 <li>redundancy highlighting is erratic at 0% and 100%</li>
4054 <li>Remove gapped columns fails for sequences with ragged
4056 <li>AMSA annotation row with leading spaces is not
4057 registered correctly on import</li>
4058 <li>Jalview crashes when selecting PCA analysis for
4059 certain alignments</li>
4060 <li>Opening the colour by annotation dialog for an
4061 existing annotation based 'use original colours'
4062 colourscheme loses original colours setting</li>
4067 <td><div align="center">
4068 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
4069 <em>30/1/2014</em></strong>
4073 <li>Trusted certificates for JalviewLite applet and
4074 Jalview Desktop application<br />Certificate was donated by
4075 <a href="https://www.certum.eu">Certum</a> to the Jalview
4076 open source project).
4078 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
4079 <li>Output in Stockholm format</li>
4080 <li>Allow import of data from gzipped files</li>
4081 <li>Export/import group and sequence associated line
4082 graph thresholds</li>
4083 <li>Nucleotide substitution matrix that supports RNA and
4084 ambiguity codes</li>
4085 <li>Allow disorder predictions to be made on the current
4086 selection (or visible selection) in the same way that JPred
4088 <li>Groovy scripting for headless Jalview operation</li>
4089 </ul> <em>Other improvements</em>
4091 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
4092 <li>COMBINE statement uses current SEQUENCE_REF and
4093 GROUP_REF scope to group annotation rows</li>
4094 <li>Support '' style escaping of quotes in Newick
4096 <li>Group options for JABAWS service by command line name</li>
4097 <li>Empty tooltip shown for JABA service options with a
4098 link but no description</li>
4099 <li>Select primary source when selecting authority in
4100 database fetcher GUI</li>
4101 <li>Add .mfa to FASTA file extensions recognised by
4103 <li>Annotation label tooltip text wrap</li>
4108 <li>Slow scrolling when lots of annotation rows are
4110 <li>Lots of NPE (and slowness) after creating RNA
4111 secondary structure annotation line</li>
4112 <li>Sequence database accessions not imported when
4113 fetching alignments from Rfam</li>
4114 <li>Incorrect SHMR submission for sequences with
4116 <li>View all structures does not always superpose
4118 <li>Option widgets in service parameters not updated to
4119 reflect user or preset settings</li>
4120 <li>Null pointer exceptions for some services without
4121 presets or adjustable parameters</li>
4122 <li>Discover PDB IDs entry in structure menu doesn't
4123 discover PDB xRefs</li>
4124 <li>Exception encountered while trying to retrieve
4125 features with DAS</li>
4126 <li>Lowest value in annotation row isn't coloured
4127 when colour by annotation (per sequence) is coloured</li>
4128 <li>Keyboard mode P jumps to start of gapped region when
4129 residue follows a gap</li>
4130 <li>Jalview appears to hang importing an alignment with
4131 Wrap as default or after enabling Wrap</li>
4132 <li>'Right click to add annotations' message
4133 shown in wrap mode when no annotations present</li>
4134 <li>Disorder predictions fail with NPE if no automatic
4135 annotation already exists on alignment</li>
4136 <li>oninit javascript function should be called after
4137 initialisation completes</li>
4138 <li>Remove redundancy after disorder prediction corrupts
4139 alignment window display</li>
4140 <li>Example annotation file in documentation is invalid</li>
4141 <li>Grouped line graph annotation rows are not exported
4142 to annotation file</li>
4143 <li>Multi-harmony analysis cannot be run when only two
4145 <li>Cannot create multiple groups of line graphs with
4146 several 'combine' statements in annotation file</li>
4147 <li>Pressing return several times causes Number Format
4148 exceptions in keyboard mode</li>
4149 <li>Multi-harmony (SHMMR) method doesn't submit
4150 correct partitions for input data</li>
4151 <li>Translation from DNA to Amino Acids fails</li>
4152 <li>Jalview fail to load newick tree with quoted label</li>
4153 <li>--headless flag isn't understood</li>
4154 <li>ClassCastException when generating EPS in headless
4156 <li>Adjusting sequence-associated shading threshold only
4157 changes one row's threshold</li>
4158 <li>Preferences and Feature settings panel panel
4159 doesn't open</li>
4160 <li>hide consensus histogram also hides conservation and
4161 quality histograms</li>
4166 <td><div align="center">
4167 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
4169 <td><em>Application</em>
4171 <li>Support for JABAWS 2.0 Services (AACon alignment
4172 conservation, protein disorder and Clustal Omega)</li>
4173 <li>JABAWS server status indicator in Web Services
4175 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
4176 in Jalview alignment window</li>
4177 <li>Updated Jalview build and deploy framework for OSX
4178 mountain lion, windows 7, and 8</li>
4179 <li>Nucleotide substitution matrix for PCA that supports
4180 RNA and ambiguity codes</li>
4182 <li>Improved sequence database retrieval GUI</li>
4183 <li>Support fetching and database reference look up
4184 against multiple DAS sources (Fetch all from in 'fetch db
4186 <li>Jalview project improvements
4188 <li>Store and retrieve the 'belowAlignment'
4189 flag for annotation</li>
4190 <li>calcId attribute to group annotation rows on the
4192 <li>Store AACon calculation settings for a view in
4193 Jalview project</li>
4197 <li>horizontal scrolling gesture support</li>
4198 <li>Visual progress indicator when PCA calculation is
4200 <li>Simpler JABA web services menus</li>
4201 <li>visual indication that web service results are still
4202 being retrieved from server</li>
4203 <li>Serialise the dialogs that are shown when Jalview
4204 starts up for first time</li>
4205 <li>Jalview user agent string for interacting with HTTP
4207 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
4209 <li>Examples directory and Groovy library included in
4210 InstallAnywhere distribution</li>
4211 </ul> <em>Applet</em>
4213 <li>RNA alignment and secondary structure annotation
4214 visualization applet example</li>
4215 </ul> <em>General</em>
4217 <li>Normalise option for consensus sequence logo</li>
4218 <li>Reset button in PCA window to return dimensions to
4220 <li>Allow seqspace or Jalview variant of alignment PCA
4222 <li>PCA with either nucleic acid and protein substitution
4224 <li>Allow windows containing HTML reports to be exported
4226 <li>Interactive display and editing of RNA secondary
4227 structure contacts</li>
4228 <li>RNA Helix Alignment Colouring</li>
4229 <li>RNA base pair logo consensus</li>
4230 <li>Parse sequence associated secondary structure
4231 information in Stockholm files</li>
4232 <li>HTML Export database accessions and annotation
4233 information presented in tooltip for sequences</li>
4234 <li>Import secondary structure from LOCARNA clustalw
4235 style RNA alignment files</li>
4236 <li>import and visualise T-COFFEE quality scores for an
4238 <li>'colour by annotation' per sequence option to
4239 shade each sequence according to its associated alignment
4241 <li>New Jalview Logo</li>
4242 </ul> <em>Documentation and Development</em>
4244 <li>documentation for score matrices used in Jalview</li>
4245 <li>New Website!</li>
4247 <td><em>Application</em>
4249 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
4250 wsdbfetch REST service</li>
4251 <li>Stop windows being moved outside desktop on OSX</li>
4252 <li>Filetype associations not installed for webstart
4254 <li>Jalview does not always retrieve progress of a JABAWS
4255 job execution in full once it is complete</li>
4256 <li>revise SHMR RSBS definition to ensure alignment is
4257 uploaded via ali_file parameter</li>
4258 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
4259 <li>View all structures superposed fails with exception</li>
4260 <li>Jnet job queues forever if a very short sequence is
4261 submitted for prediction</li>
4262 <li>Cut and paste menu not opened when mouse clicked on
4264 <li>Putting fractional value into integer text box in
4265 alignment parameter dialog causes Jalview to hang</li>
4266 <li>Structure view highlighting doesn't work on
4268 <li>View all structures fails with exception shown in
4270 <li>Characters in filename associated with PDBEntry not
4271 escaped in a platform independent way</li>
4272 <li>Jalview desktop fails to launch with exception when
4274 <li>Tree calculation reports 'you must have 2 or more
4275 sequences selected' when selection is empty</li>
4276 <li>Jalview desktop fails to launch with jar signature
4277 failure when java web start temporary file caching is
4279 <li>DAS Sequence retrieval with range qualification
4280 results in sequence xref which includes range qualification</li>
4281 <li>Errors during processing of command line arguments
4282 cause progress bar (JAL-898) to be removed</li>
4283 <li>Replace comma for semi-colon option not disabled for
4284 DAS sources in sequence fetcher</li>
4285 <li>Cannot close news reader when JABAWS server warning
4286 dialog is shown</li>
4287 <li>Option widgets not updated to reflect user settings</li>
4288 <li>Edited sequence not submitted to web service</li>
4289 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
4290 <li>InstallAnywhere installer doesn't unpack and run
4291 on OSX Mountain Lion</li>
4292 <li>Annotation panel not given a scroll bar when
4293 sequences with alignment annotation are pasted into the
4295 <li>Sequence associated annotation rows not associated
4296 when loaded from Jalview project</li>
4297 <li>Browser launch fails with NPE on java 1.7</li>
4298 <li>JABAWS alignment marked as finished when job was
4299 cancelled or job failed due to invalid input</li>
4300 <li>NPE with v2.7 example when clicking on Tree
4301 associated with all views</li>
4302 <li>Exceptions when copy/paste sequences with grouped
4303 annotation rows to new window</li>
4304 </ul> <em>Applet</em>
4306 <li>Sequence features are momentarily displayed before
4307 they are hidden using hidefeaturegroups applet parameter</li>
4308 <li>loading features via javascript API automatically
4309 enables feature display</li>
4310 <li>scrollToColumnIn javascript API method doesn't
4312 </ul> <em>General</em>
4314 <li>Redundancy removal fails for rna alignment</li>
4315 <li>PCA calculation fails when sequence has been selected
4316 and then deselected</li>
4317 <li>PCA window shows grey box when first opened on OSX</li>
4318 <li>Letters coloured pink in sequence logo when alignment
4319 coloured with clustalx</li>
4320 <li>Choosing fonts without letter symbols defined causes
4321 exceptions and redraw errors</li>
4322 <li>Initial PCA plot view is not same as manually
4323 reconfigured view</li>
4324 <li>Grouped annotation graph label has incorrect line
4326 <li>Grouped annotation graph label display is corrupted
4327 for lots of labels</li>
4332 <div align="center">
4333 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
4336 <td><em>Application</em>
4338 <li>Jalview Desktop News Reader</li>
4339 <li>Tweaked default layout of web services menu</li>
4340 <li>View/alignment association menu to enable user to
4341 easily specify which alignment a multi-structure view takes
4342 its colours/correspondences from</li>
4343 <li>Allow properties file location to be specified as URL</li>
4344 <li>Extend Jalview project to preserve associations
4345 between many alignment views and a single Jmol display</li>
4346 <li>Store annotation row height in Jalview project file</li>
4347 <li>Annotation row column label formatting attributes
4348 stored in project file</li>
4349 <li>Annotation row order for auto-calculated annotation
4350 rows preserved in Jalview project file</li>
4351 <li>Visual progress indication when Jalview state is
4352 saved using Desktop window menu</li>
4353 <li>Visual indication that command line arguments are
4354 still being processed</li>
4355 <li>Groovy script execution from URL</li>
4356 <li>Colour by annotation default min and max colours in
4358 <li>Automatically associate PDB files dragged onto an
4359 alignment with sequences that have high similarity and
4361 <li>Update JGoogleAnalytics to latest release (0.3)</li>
4362 <li>'view structures' option to open many
4363 structures in same window</li>
4364 <li>Sort associated views menu option for tree panel</li>
4365 <li>Group all JABA and non-JABA services for a particular
4366 analysis function in its own submenu</li>
4367 </ul> <em>Applet</em>
4369 <li>Userdefined and autogenerated annotation rows for
4371 <li>Adjustment of alignment annotation pane height</li>
4372 <li>Annotation scrollbar for annotation panel</li>
4373 <li>Drag to reorder annotation rows in annotation panel</li>
4374 <li>'automaticScrolling' parameter</li>
4375 <li>Allow sequences with partial ID string matches to be
4376 annotated from GFF/Jalview features files</li>
4377 <li>Sequence logo annotation row in applet</li>
4378 <li>Absolute paths relative to host server in applet
4379 parameters are treated as such</li>
4380 <li>New in the JalviewLite javascript API:
4382 <li>JalviewLite.js javascript library</li>
4383 <li>Javascript callbacks for
4385 <li>Applet initialisation</li>
4386 <li>Sequence/alignment mouse-overs and selections</li>
4389 <li>scrollTo row and column alignment scrolling
4391 <li>Select sequence/alignment regions from javascript</li>
4392 <li>javascript structure viewer harness to pass
4393 messages between Jmol and Jalview when running as
4394 distinct applets</li>
4395 <li>sortBy method</li>
4396 <li>Set of applet and application examples shipped
4397 with documentation</li>
4398 <li>New example to demonstrate JalviewLite and Jmol
4399 javascript message exchange</li>
4401 </ul> <em>General</em>
4403 <li>Enable Jmol displays to be associated with multiple
4404 multiple alignments</li>
4405 <li>Option to automatically sort alignment with new tree</li>
4406 <li>User configurable link to enable redirects to a
4407 www.Jalview.org mirror</li>
4408 <li>Jmol colours option for Jmol displays</li>
4409 <li>Configurable newline string when writing alignment
4410 and other flat files</li>
4411 <li>Allow alignment annotation description lines to
4412 contain html tags</li>
4413 </ul> <em>Documentation and Development</em>
4415 <li>Add groovy test harness for bulk load testing to
4417 <li>Groovy script to load and align a set of sequences
4418 using a web service before displaying the result in the
4419 Jalview desktop</li>
4420 <li>Restructured javascript and applet api documentation</li>
4421 <li>Ant target to publish example html files with applet
4423 <li>Netbeans project for building Jalview from source</li>
4424 <li>ant task to create online javadoc for Jalview source</li>
4426 <td><em>Application</em>
4428 <li>User defined colourscheme throws exception when
4429 current built in colourscheme is saved as new scheme</li>
4430 <li>AlignFrame->Save in application pops up save
4431 dialog for valid filename/format</li>
4432 <li>Cannot view associated structure for UniProt sequence</li>
4433 <li>PDB file association breaks for UniProt sequence
4435 <li>Associate PDB from file dialog does not tell you
4436 which sequence is to be associated with the file</li>
4437 <li>Find All raises null pointer exception when query
4438 only matches sequence IDs</li>
4439 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4440 <li>Jalview project with Jmol views created with Jalview
4441 2.4 cannot be loaded</li>
4442 <li>Filetype associations not installed for webstart
4444 <li>Two or more chains in a single PDB file associated
4445 with sequences in different alignments do not get coloured
4446 by their associated sequence</li>
4447 <li>Visibility status of autocalculated annotation row
4448 not preserved when project is loaded</li>
4449 <li>Annotation row height and visibility attributes not
4450 stored in Jalview project</li>
4451 <li>Tree bootstraps are not preserved when saved as a
4452 Jalview project</li>
4453 <li>Envision2 workflow tooltips are corrupted</li>
4454 <li>Enabling show group conservation also enables colour
4455 by conservation</li>
4456 <li>Duplicate group associated conservation or consensus
4457 created on new view</li>
4458 <li>Annotation scrollbar not displayed after 'show
4459 all hidden annotation rows' option selected</li>
4460 <li>Alignment quality not updated after alignment
4461 annotation row is hidden then shown</li>
4462 <li>Preserve colouring of structures coloured by
4463 sequences in pre Jalview 2.7 projects</li>
4464 <li>Web service job parameter dialog is not laid out
4466 <li>Web services menu not refreshed after 'reset
4467 services' button is pressed in preferences</li>
4468 <li>Annotation off by one in Jalview v2_3 example project</li>
4469 <li>Structures imported from file and saved in project
4470 get name like jalview_pdb1234.txt when reloaded</li>
4471 <li>Jalview does not always retrieve progress of a JABAWS
4472 job execution in full once it is complete</li>
4473 </ul> <em>Applet</em>
4475 <li>Alignment height set incorrectly when lots of
4476 annotation rows are displayed</li>
4477 <li>Relative URLs in feature HTML text not resolved to
4479 <li>View follows highlighting does not work for positions
4481 <li><= shown as = in tooltip</li>
4482 <li>Export features raises exception when no features
4484 <li>Separator string used for serialising lists of IDs
4485 for javascript api is modified when separator string
4486 provided as parameter</li>
4487 <li>Null pointer exception when selecting tree leaves for
4488 alignment with no existing selection</li>
4489 <li>Relative URLs for datasources assumed to be relative
4490 to applet's codebase</li>
4491 <li>Status bar not updated after finished searching and
4492 search wraps around to first result</li>
4493 <li>StructureSelectionManager instance shared between
4494 several Jalview applets causes race conditions and memory
4496 <li>Hover tooltip and mouseover of position on structure
4497 not sent from Jmol in applet</li>
4498 <li>Certain sequences of javascript method calls to
4499 applet API fatally hang browser</li>
4500 </ul> <em>General</em>
4502 <li>View follows structure mouseover scrolls beyond
4503 position with wrapped view and hidden regions</li>
4504 <li>Find sequence position moves to wrong residue
4505 with/without hidden columns</li>
4506 <li>Sequence length given in alignment properties window
4508 <li>InvalidNumberFormat exceptions thrown when trying to
4509 import PDB like structure files</li>
4510 <li>Positional search results are only highlighted
4511 between user-supplied sequence start/end bounds</li>
4512 <li>End attribute of sequence is not validated</li>
4513 <li>Find dialog only finds first sequence containing a
4514 given sequence position</li>
4515 <li>Sequence numbering not preserved in MSF alignment
4517 <li>Jalview PDB file reader does not extract sequence
4518 from nucleotide chains correctly</li>
4519 <li>Structure colours not updated when tree partition
4520 changed in alignment</li>
4521 <li>Sequence associated secondary structure not correctly
4522 parsed in interleaved stockholm</li>
4523 <li>Colour by annotation dialog does not restore current
4525 <li>Hiding (nearly) all sequences doesn't work
4527 <li>Sequences containing lowercase letters are not
4528 properly associated with their pdb files</li>
4529 </ul> <em>Documentation and Development</em>
4531 <li>schemas/JalviewWsParamSet.xsd corrupted by
4532 ApplyCopyright tool</li>
4537 <div align="center">
4538 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4541 <td><em>Application</em>
4543 <li>New warning dialog when the Jalview Desktop cannot
4544 contact web services</li>
4545 <li>JABA service parameters for a preset are shown in
4546 service job window</li>
4547 <li>JABA Service menu entries reworded</li>
4551 <li>Modeller PIR IO broken - cannot correctly import a
4552 pir file emitted by Jalview</li>
4553 <li>Existing feature settings transferred to new
4554 alignment view created from cut'n'paste</li>
4555 <li>Improved test for mixed amino/nucleotide chains when
4556 parsing PDB files</li>
4557 <li>Consensus and conservation annotation rows
4558 occasionally become blank for all new windows</li>
4559 <li>Exception raised when right clicking above sequences
4560 in wrapped view mode</li>
4561 </ul> <em>Application</em>
4563 <li>multiple multiply aligned structure views cause cpu
4564 usage to hit 100% and computer to hang</li>
4565 <li>Web Service parameter layout breaks for long user
4566 parameter names</li>
4567 <li>Jaba service discovery hangs desktop if Jaba server
4574 <div align="center">
4575 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4578 <td><em>Application</em>
4580 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4581 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4584 <li>Web Services preference tab</li>
4585 <li>Analysis parameters dialog box and user defined
4587 <li>Improved speed and layout of Envision2 service menu</li>
4588 <li>Superpose structures using associated sequence
4590 <li>Export coordinates and projection as CSV from PCA
4592 </ul> <em>Applet</em>
4594 <li>enable javascript: execution by the applet via the
4595 link out mechanism</li>
4596 </ul> <em>Other</em>
4598 <li>Updated the Jmol Jalview interface to work with Jmol
4600 <li>The Jalview Desktop and JalviewLite applet now
4601 require Java 1.5</li>
4602 <li>Allow Jalview feature colour specification for GFF
4603 sequence annotation files</li>
4604 <li>New 'colour by label' keword in Jalview feature file
4605 type colour specification</li>
4606 <li>New Jalview Desktop Groovy API method that allows a
4607 script to check if it being run in an interactive session or
4608 in a batch operation from the Jalview command line</li>
4612 <li>clustalx colourscheme colours Ds preferentially when
4613 both D+E are present in over 50% of the column</li>
4614 </ul> <em>Application</em>
4616 <li>typo in AlignmentFrame->View->Hide->all but
4617 selected Regions menu item</li>
4618 <li>sequence fetcher replaces ',' for ';' when the ',' is
4619 part of a valid accession ID</li>
4620 <li>fatal OOM if object retrieved by sequence fetcher
4621 runs out of memory</li>
4622 <li>unhandled Out of Memory Error when viewing pca
4623 analysis results</li>
4624 <li>InstallAnywhere builds fail to launch on OS X java
4625 10.5 update 4 (due to apple Java 1.6 update)</li>
4626 <li>Installanywhere Jalview silently fails to launch</li>
4627 </ul> <em>Applet</em>
4629 <li>Jalview.getFeatureGroups() raises an
4630 ArrayIndexOutOfBoundsException if no feature groups are
4637 <div align="center">
4638 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4644 <li>Alignment prettyprinter doesn't cope with long
4646 <li>clustalx colourscheme colours Ds preferentially when
4647 both D+E are present in over 50% of the column</li>
4648 <li>nucleic acid structures retrieved from PDB do not
4649 import correctly</li>
4650 <li>More columns get selected than were clicked on when a
4651 number of columns are hidden</li>
4652 <li>annotation label popup menu not providing correct
4653 add/hide/show options when rows are hidden or none are
4655 <li>Stockholm format shown in list of readable formats,
4656 and parser copes better with alignments from RFAM.</li>
4657 <li>CSV output of consensus only includes the percentage
4658 of all symbols if sequence logo display is enabled</li>
4660 </ul> <em>Applet</em>
4662 <li>annotation panel disappears when annotation is
4664 </ul> <em>Application</em>
4666 <li>Alignment view not redrawn properly when new
4667 alignment opened where annotation panel is visible but no
4668 annotations are present on alignment</li>
4669 <li>pasted region containing hidden columns is
4670 incorrectly displayed in new alignment window</li>
4671 <li>Jalview slow to complete operations when stdout is
4672 flooded (fix is to close the Jalview console)</li>
4673 <li>typo in AlignmentFrame->View->Hide->all but
4674 selected Rregions menu item.</li>
4675 <li>inconsistent group submenu and Format submenu entry
4676 'Un' or 'Non'conserved</li>
4677 <li>Sequence feature settings are being shared by
4678 multiple distinct alignments</li>
4679 <li>group annotation not recreated when tree partition is
4681 <li>double click on group annotation to select sequences
4682 does not propagate to associated trees</li>
4683 <li>Mac OSX specific issues:
4685 <li>exception raised when mouse clicked on desktop
4686 window background</li>
4687 <li>Desktop menu placed on menu bar and application
4688 name set correctly</li>
4689 <li>sequence feature settings not wide enough for the
4690 save feature colourscheme button</li>
4699 <div align="center">
4700 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4703 <td><em>New Capabilities</em>
4705 <li>URL links generated from description line for
4706 regular-expression based URL links (applet and application)
4709 <li>Non-positional feature URL links are shown in link
4711 <li>Linked viewing of nucleic acid sequences and
4713 <li>Automatic Scrolling option in View menu to display
4714 the currently highlighted region of an alignment.</li>
4715 <li>Order an alignment by sequence length, or using the
4716 average score or total feature count for each sequence.</li>
4717 <li>Shading features by score or associated description</li>
4718 <li>Subdivide alignment and groups based on identity of
4719 selected subsequence (Make Groups from Selection).</li>
4720 <li>New hide/show options including Shift+Control+H to
4721 hide everything but the currently selected region.</li>
4722 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4723 </ul> <em>Application</em>
4725 <li>Fetch DB References capabilities and UI expanded to
4726 support retrieval from DAS sequence sources</li>
4727 <li>Local DAS Sequence sources can be added via the
4728 command line or via the Add local source dialog box.</li>
4729 <li>DAS Dbref and DbxRef feature types are parsed as
4730 database references and protein_name is parsed as
4731 description line (BioSapiens terms).</li>
4732 <li>Enable or disable non-positional feature and database
4733 references in sequence ID tooltip from View menu in
4735 <!-- <li>New hidden columns and rows and representatives capabilities
4736 in annotations file (in progress - not yet fully implemented)</li> -->
4737 <li>Group-associated consensus, sequence logos and
4738 conservation plots</li>
4739 <li>Symbol distributions for each column can be exported
4740 and visualized as sequence logos</li>
4741 <li>Optionally scale multi-character column labels to fit
4742 within each column of annotation row<!-- todo for applet -->
4744 <li>Optional automatic sort of associated alignment view
4745 when a new tree is opened.</li>
4746 <li>Jalview Java Console</li>
4747 <li>Better placement of desktop window when moving
4748 between different screens.</li>
4749 <li>New preference items for sequence ID tooltip and
4750 consensus annotation</li>
4751 <li>Client to submit sequences and IDs to Envision2
4753 <li><em>Vamsas Capabilities</em>
4755 <li>Improved VAMSAS synchronization (Jalview archive
4756 used to preserve views, structures, and tree display
4758 <li>Import of vamsas documents from disk or URL via
4760 <li>Sharing of selected regions between views and
4761 with other VAMSAS applications (Experimental feature!)</li>
4762 <li>Updated API to VAMSAS version 0.2</li>
4764 </ul> <em>Applet</em>
4766 <li>Middle button resizes annotation row height</li>
4769 <li>sortByTree (true/false) - automatically sort the
4770 associated alignment view by the tree when a new tree is
4772 <li>showTreeBootstraps (true/false) - show or hide
4773 branch bootstraps (default is to show them if available)</li>
4774 <li>showTreeDistances (true/false) - show or hide
4775 branch lengths (default is to show them if available)</li>
4776 <li>showUnlinkedTreeNodes (true/false) - indicate if
4777 unassociated nodes should be highlighted in the tree
4779 <li>heightScale and widthScale (1.0 or more) -
4780 increase the height or width of a cell in the alignment
4781 grid relative to the current font size.</li>
4784 <li>Non-positional features displayed in sequence ID
4786 </ul> <em>Other</em>
4788 <li>Features format: graduated colour definitions and
4789 specification of feature scores</li>
4790 <li>Alignment Annotations format: new keywords for group
4791 associated annotation (GROUP_REF) and annotation row display
4792 properties (ROW_PROPERTIES)</li>
4793 <li>XML formats extended to support graduated feature
4794 colourschemes, group associated annotation, and profile
4795 visualization settings.</li></td>
4798 <li>Source field in GFF files parsed as feature source
4799 rather than description</li>
4800 <li>Non-positional features are now included in sequence
4801 feature and gff files (controlled via non-positional feature
4802 visibility in tooltip).</li>
4803 <li>URL links generated for all feature links (bugfix)</li>
4804 <li>Added URL embedding instructions to features file
4806 <li>Codons containing ambiguous nucleotides translated as
4807 'X' in peptide product</li>
4808 <li>Match case switch in find dialog box works for both
4809 sequence ID and sequence string and query strings do not
4810 have to be in upper case to match case-insensitively.</li>
4811 <li>AMSA files only contain first column of
4812 multi-character column annotation labels</li>
4813 <li>Jalview Annotation File generation/parsing consistent
4814 with documentation (e.g. Stockholm annotation can be
4815 exported and re-imported)</li>
4816 <li>PDB files without embedded PDB IDs given a friendly
4818 <li>Find incrementally searches ID string matches as well
4819 as subsequence matches, and correctly reports total number
4823 <li>Better handling of exceptions during sequence
4825 <li>Dasobert generated non-positional feature URL
4826 link text excludes the start_end suffix</li>
4827 <li>DAS feature and source retrieval buttons disabled
4828 when fetch or registry operations in progress.</li>
4829 <li>PDB files retrieved from URLs are cached properly</li>
4830 <li>Sequence description lines properly shared via
4832 <li>Sequence fetcher fetches multiple records for all
4834 <li>Ensured that command line das feature retrieval
4835 completes before alignment figures are generated.</li>
4836 <li>Reduced time taken when opening file browser for
4838 <li>isAligned check prior to calculating tree, PCA or
4839 submitting an MSA to JNet now excludes hidden sequences.</li>
4840 <li>User defined group colours properly recovered
4841 from Jalview projects.</li>
4850 <div align="center">
4851 <strong>2.4.0.b2</strong><br> 28/10/2009
4856 <li>Experimental support for google analytics usage
4858 <li>Jalview privacy settings (user preferences and docs).</li>
4863 <li>Race condition in applet preventing startup in
4865 <li>Exception when feature created from selection beyond
4866 length of sequence.</li>
4867 <li>Allow synthetic PDB files to be imported gracefully</li>
4868 <li>Sequence associated annotation rows associate with
4869 all sequences with a given id</li>
4870 <li>Find function matches case-insensitively for sequence
4871 ID string searches</li>
4872 <li>Non-standard characters do not cause pairwise
4873 alignment to fail with exception</li>
4874 </ul> <em>Application Issues</em>
4876 <li>Sequences are now validated against EMBL database</li>
4877 <li>Sequence fetcher fetches multiple records for all
4879 </ul> <em>InstallAnywhere Issues</em>
4881 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4882 issue with installAnywhere mechanism)</li>
4883 <li>Command line launching of JARs from InstallAnywhere
4884 version (java class versioning error fixed)</li>
4891 <div align="center">
4892 <strong>2.4</strong><br> 27/8/2008
4895 <td><em>User Interface</em>
4897 <li>Linked highlighting of codon and amino acid from
4898 translation and protein products</li>
4899 <li>Linked highlighting of structure associated with
4900 residue mapping to codon position</li>
4901 <li>Sequence Fetcher provides example accession numbers
4902 and 'clear' button</li>
4903 <li>MemoryMonitor added as an option under Desktop's
4905 <li>Extract score function to parse whitespace separated
4906 numeric data in description line</li>
4907 <li>Column labels in alignment annotation can be centred.</li>
4908 <li>Tooltip for sequence associated annotation give name
4910 </ul> <em>Web Services and URL fetching</em>
4912 <li>JPred3 web service</li>
4913 <li>Prototype sequence search client (no public services
4915 <li>Fetch either seed alignment or full alignment from
4917 <li>URL Links created for matching database cross
4918 references as well as sequence ID</li>
4919 <li>URL Links can be created using regular-expressions</li>
4920 </ul> <em>Sequence Database Connectivity</em>
4922 <li>Retrieval of cross-referenced sequences from other
4924 <li>Generalised database reference retrieval and
4925 validation to all fetchable databases</li>
4926 <li>Fetch sequences from DAS sources supporting the
4927 sequence command</li>
4928 </ul> <em>Import and Export</em>
4929 <li>export annotation rows as CSV for spreadsheet import</li>
4930 <li>Jalview projects record alignment dataset associations,
4931 EMBL products, and cDNA sequence mappings</li>
4932 <li>Sequence Group colour can be specified in Annotation
4934 <li>Ad-hoc colouring of group in Annotation File using RGB
4935 triplet as name of colourscheme</li>
4936 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4938 <li>treenode binding for VAMSAS tree exchange</li>
4939 <li>local editing and update of sequences in VAMSAS
4940 alignments (experimental)</li>
4941 <li>Create new or select existing session to join</li>
4942 <li>load and save of vamsas documents</li>
4943 </ul> <em>Application command line</em>
4945 <li>-tree parameter to open trees (introduced for passing
4947 <li>-fetchfrom command line argument to specify nicknames
4948 of DAS servers to query for alignment features</li>
4949 <li>-dasserver command line argument to add new servers
4950 that are also automatically queried for features</li>
4951 <li>-groovy command line argument executes a given groovy
4952 script after all input data has been loaded and parsed</li>
4953 </ul> <em>Applet-Application data exchange</em>
4955 <li>Trees passed as applet parameters can be passed to
4956 application (when using "View in full
4957 application")</li>
4958 </ul> <em>Applet Parameters</em>
4960 <li>feature group display control parameter</li>
4961 <li>debug parameter</li>
4962 <li>showbutton parameter</li>
4963 </ul> <em>Applet API methods</em>
4965 <li>newView public method</li>
4966 <li>Window (current view) specific get/set public methods</li>
4967 <li>Feature display control methods</li>
4968 <li>get list of currently selected sequences</li>
4969 </ul> <em>New Jalview distribution features</em>
4971 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4972 <li>RELEASE file gives build properties for the latest
4973 Jalview release.</li>
4974 <li>Java 1.1 Applet build made easier and donotobfuscate
4975 property controls execution of obfuscator</li>
4976 <li>Build target for generating source distribution</li>
4977 <li>Debug flag for javacc</li>
4978 <li>.jalview_properties file is documented (slightly) in
4979 jalview.bin.Cache</li>
4980 <li>Continuous Build Integration for stable and
4981 development version of Application, Applet and source
4986 <li>selected region output includes visible annotations
4987 (for certain formats)</li>
4988 <li>edit label/displaychar contains existing label/char
4990 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4991 <li>shorter peptide product names from EMBL records</li>
4992 <li>Newick string generator makes compact representations</li>
4993 <li>bootstrap values parsed correctly for tree files with
4995 <li>pathological filechooser bug avoided by not allowing
4996 filenames containing a ':'</li>
4997 <li>Fixed exception when parsing GFF files containing
4998 global sequence features</li>
4999 <li>Alignment datasets are finalized only when number of
5000 references from alignment sequences goes to zero</li>
5001 <li>Close of tree branch colour box without colour
5002 selection causes cascading exceptions</li>
5003 <li>occasional negative imgwidth exceptions</li>
5004 <li>better reporting of non-fatal warnings to user when
5005 file parsing fails.</li>
5006 <li>Save works when Jalview project is default format</li>
5007 <li>Save as dialog opened if current alignment format is
5008 not a valid output format</li>
5009 <li>UniProt canonical names introduced for both das and
5011 <li>Histidine should be midblue (not pink!) in Zappo</li>
5012 <li>error messages passed up and output when data read
5014 <li>edit undo recovers previous dataset sequence when
5015 sequence is edited</li>
5016 <li>allow PDB files without pdb ID HEADER lines (like
5017 those generated by MODELLER) to be read in properly</li>
5018 <li>allow reading of JPred concise files as a normal
5020 <li>Stockholm annotation parsing and alignment properties
5021 import fixed for PFAM records</li>
5022 <li>Structure view windows have correct name in Desktop
5024 <li>annotation consisting of sequence associated scores
5025 can be read and written correctly to annotation file</li>
5026 <li>Aligned cDNA translation to aligned peptide works
5028 <li>Fixed display of hidden sequence markers and
5029 non-italic font for representatives in Applet</li>
5030 <li>Applet Menus are always embedded in applet window on
5032 <li>Newly shown features appear at top of stack (in
5034 <li>Annotations added via parameter not drawn properly
5035 due to null pointer exceptions</li>
5036 <li>Secondary structure lines are drawn starting from
5037 first column of alignment</li>
5038 <li>UniProt XML import updated for new schema release in
5040 <li>Sequence feature to sequence ID match for Features
5041 file is case-insensitive</li>
5042 <li>Sequence features read from Features file appended to
5043 all sequences with matching IDs</li>
5044 <li>PDB structure coloured correctly for associated views
5045 containing a sub-sequence</li>
5046 <li>PDB files can be retrieved by applet from Jar files</li>
5047 <li>feature and annotation file applet parameters
5048 referring to different directories are retrieved correctly</li>
5049 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
5050 <li>Fixed application hang whilst waiting for
5051 splash-screen version check to complete</li>
5052 <li>Applet properly URLencodes input parameter values
5053 when passing them to the launchApp service</li>
5054 <li>display name and local features preserved in results
5055 retrieved from web service</li>
5056 <li>Visual delay indication for sequence retrieval and
5057 sequence fetcher initialisation</li>
5058 <li>updated Application to use DAS 1.53e version of
5059 dasobert DAS client</li>
5060 <li>Re-instated Full AMSA support and .amsa file
5062 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
5070 <div align="center">
5071 <strong>2.3</strong><br> 9/5/07
5076 <li>Jmol 11.0.2 integration</li>
5077 <li>PDB views stored in Jalview XML files</li>
5078 <li>Slide sequences</li>
5079 <li>Edit sequence in place</li>
5080 <li>EMBL CDS features</li>
5081 <li>DAS Feature mapping</li>
5082 <li>Feature ordering</li>
5083 <li>Alignment Properties</li>
5084 <li>Annotation Scores</li>
5085 <li>Sort by scores</li>
5086 <li>Feature/annotation editing in applet</li>
5091 <li>Headless state operation in 2.2.1</li>
5092 <li>Incorrect and unstable DNA pairwise alignment</li>
5093 <li>Cut and paste of sequences with annotation</li>
5094 <li>Feature group display state in XML</li>
5095 <li>Feature ordering in XML</li>
5096 <li>blc file iteration selection using filename # suffix</li>
5097 <li>Stockholm alignment properties</li>
5098 <li>Stockhom alignment secondary structure annotation</li>
5099 <li>2.2.1 applet had no feature transparency</li>
5100 <li>Number pad keys can be used in cursor mode</li>
5101 <li>Structure Viewer mirror image resolved</li>
5108 <div align="center">
5109 <strong>2.2.1</strong><br> 12/2/07
5114 <li>Non standard characters can be read and displayed
5115 <li>Annotations/Features can be imported/exported to the
5117 <li>Applet allows editing of sequence/annotation/group
5118 name & description
5119 <li>Preference setting to display sequence name in
5121 <li>Annotation file format extended to allow
5122 Sequence_groups to be defined
5123 <li>Default opening of alignment overview panel can be
5124 specified in preferences
5125 <li>PDB residue numbering annotation added to associated
5131 <li>Applet crash under certain Linux OS with Java 1.6
5133 <li>Annotation file export / import bugs fixed
5134 <li>PNG / EPS image output bugs fixed
5140 <div align="center">
5141 <strong>2.2</strong><br> 27/11/06
5146 <li>Multiple views on alignment
5147 <li>Sequence feature editing
5148 <li>"Reload" alignment
5149 <li>"Save" to current filename
5150 <li>Background dependent text colour
5151 <li>Right align sequence ids
5152 <li>User-defined lower case residue colours
5155 <li>Menu item accelerator keys
5156 <li>Control-V pastes to current alignment
5157 <li>Cancel button for DAS Feature Fetching
5158 <li>PCA and PDB Viewers zoom via mouse roller
5159 <li>User-defined sub-tree colours and sub-tree selection
5162 <li>'New Window' button on the 'Output to Text box'
5167 <li>New memory efficient Undo/Redo System
5168 <li>Optimised symbol lookups and conservation/consensus
5170 <li>Region Conservation/Consensus recalculated after
5172 <li>Fixed Remove Empty Columns Bug (empty columns at end
5174 <li>Slowed DAS Feature Fetching for increased robustness.
5177 <li>Made angle brackets in ASCII feature descriptions
5179 <li>Re-instated Zoom function for PCA
5180 <li>Sequence descriptions conserved in web service
5182 <li>UniProt ID discoverer uses any word separated by
5184 <li>WsDbFetch query/result association resolved
5185 <li>Tree leaf to sequence mapping improved
5186 <li>Smooth fonts switch moved to FontChooser dialog box.
5194 <div align="center">
5195 <strong>2.1.1</strong><br> 12/9/06
5200 <li>Copy consensus sequence to clipboard</li>
5205 <li>Image output - rightmost residues are rendered if
5206 sequence id panel has been resized</li>
5207 <li>Image output - all offscreen group boundaries are
5209 <li>Annotation files with sequence references - all
5210 elements in file are relative to sequence position</li>
5211 <li>Mac Applet users can use Alt key for group editing</li>
5217 <div align="center">
5218 <strong>2.1</strong><br> 22/8/06
5223 <li>MAFFT Multiple Alignment in default Web Service list</li>
5224 <li>DAS Feature fetching</li>
5225 <li>Hide sequences and columns</li>
5226 <li>Export Annotations and Features</li>
5227 <li>GFF file reading / writing</li>
5228 <li>Associate structures with sequences from local PDB
5230 <li>Add sequences to exisiting alignment</li>
5231 <li>Recently opened files / URL lists</li>
5232 <li>Applet can launch the full application</li>
5233 <li>Applet has transparency for features (Java 1.2
5235 <li>Applet has user defined colours parameter</li>
5236 <li>Applet can load sequences from parameter
5237 "sequence<em>x</em>"
5243 <li>Redundancy Panel reinstalled in the Applet</li>
5244 <li>Monospaced font - EPS / rescaling bug fixed</li>
5245 <li>Annotation files with sequence references bug fixed</li>
5251 <div align="center">
5252 <strong>2.08.1</strong><br> 2/5/06
5257 <li>Change case of selected region from Popup menu</li>
5258 <li>Choose to match case when searching</li>
5259 <li>Middle mouse button and mouse movement can compress /
5260 expand the visible width and height of the alignment</li>
5265 <li>Annotation Panel displays complete JNet results</li>
5271 <div align="center">
5272 <strong>2.08b</strong><br> 18/4/06
5278 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
5279 <li>Righthand label on wrapped alignments shows correct
5286 <div align="center">
5287 <strong>2.08</strong><br> 10/4/06
5292 <li>Editing can be locked to the selection area</li>
5293 <li>Keyboard editing</li>
5294 <li>Create sequence features from searches</li>
5295 <li>Precalculated annotations can be loaded onto
5297 <li>Features file allows grouping of features</li>
5298 <li>Annotation Colouring scheme added</li>
5299 <li>Smooth fonts off by default - Faster rendering</li>
5300 <li>Choose to toggle Autocalculate Consensus On/Off</li>
5305 <li>Drag & Drop fixed on Linux</li>
5306 <li>Jalview Archive file faster to load/save, sequence
5307 descriptions saved.</li>
5313 <div align="center">
5314 <strong>2.07</strong><br> 12/12/05
5319 <li>PDB Structure Viewer enhanced</li>
5320 <li>Sequence Feature retrieval and display enhanced</li>
5321 <li>Choose to output sequence start-end after sequence
5322 name for file output</li>
5323 <li>Sequence Fetcher WSDBFetch@EBI</li>
5324 <li>Applet can read feature files, PDB files and can be
5325 used for HTML form input</li>
5330 <li>HTML output writes groups and features</li>
5331 <li>Group editing is Control and mouse click</li>
5332 <li>File IO bugs</li>
5338 <div align="center">
5339 <strong>2.06</strong><br> 28/9/05
5344 <li>View annotations in wrapped mode</li>
5345 <li>More options for PCA viewer</li>
5350 <li>GUI bugs resolved</li>
5351 <li>Runs with -nodisplay from command line</li>
5357 <div align="center">
5358 <strong>2.05b</strong><br> 15/9/05
5363 <li>Choose EPS export as lineart or text</li>
5364 <li>Jar files are executable</li>
5365 <li>Can read in Uracil - maps to unknown residue</li>
5370 <li>Known OutOfMemory errors give warning message</li>
5371 <li>Overview window calculated more efficiently</li>
5372 <li>Several GUI bugs resolved</li>
5378 <div align="center">
5379 <strong>2.05</strong><br> 30/8/05
5384 <li>Edit and annotate in "Wrapped" view</li>
5389 <li>Several GUI bugs resolved</li>
5395 <div align="center">
5396 <strong>2.04</strong><br> 24/8/05
5401 <li>Hold down mouse wheel & scroll to change font
5407 <li>Improved JPred client reliability</li>
5408 <li>Improved loading of Jalview files</li>
5414 <div align="center">
5415 <strong>2.03</strong><br> 18/8/05
5420 <li>Set Proxy server name and port in preferences</li>
5421 <li>Multiple URL links from sequence ids</li>
5422 <li>User Defined Colours can have a scheme name and added
5424 <li>Choose to ignore gaps in consensus calculation</li>
5425 <li>Unix users can set default web browser</li>
5426 <li>Runs without GUI for batch processing</li>
5427 <li>Dynamically generated Web Service Menus</li>
5432 <li>InstallAnywhere download for Sparc Solaris</li>
5438 <div align="center">
5439 <strong>2.02</strong><br> 18/7/05
5445 <li>Copy & Paste order of sequences maintains
5446 alignment order.</li>
5452 <div align="center">
5453 <strong>2.01</strong><br> 12/7/05
5458 <li>Use delete key for deleting selection.</li>
5459 <li>Use Mouse wheel to scroll sequences.</li>
5460 <li>Help file updated to describe how to add alignment
5462 <li>Version and build date written to build properties
5464 <li>InstallAnywhere installation will check for updates
5465 at launch of Jalview.</li>
5470 <li>Delete gaps bug fixed.</li>
5471 <li>FileChooser sorts columns.</li>
5472 <li>Can remove groups one by one.</li>
5473 <li>Filechooser icons installed.</li>
5474 <li>Finder ignores return character when searching.
5475 Return key will initiate a search.<br>
5482 <div align="center">
5483 <strong>2.0</strong><br> 20/6/05
5488 <li>New codebase</li>