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 <!-- JAL-3728 -->Jalview logos shown for Jalview Java
117 Console and other window widgets in taskbar and dock rather
118 than anonymous 'Java' icons
120 </ul> <em>JalviewJS</em>
123 <!-- JAL-3624 -->PDB structures mapped to Uniprot Sequences with
127 <!-- JAL-3208 -->setprop commandline argument reinstated for JalviewJS only
136 <!-- JAL-3163 -->Missing message bundle keys are only
137 reported once per key (avoids excessive log output in js
141 <!-- JAL-3168 -->Feature type is included in the title of
142 the Feature Settings' Colour Chooser dialog
145 </ul> <em>Development</em>
148 <!-- -->First integrated JalviewJS and Jalview release
150 <li>Updated building instructions</li>
152 <!-- JAL-3789, JAL-3679 -->Improved JalviewJS/Jalview build
153 process, added support for system package provided eclipse
156 <li>Install4j 9.0.x used for installer packaging</li>
157 <li>Notarized MacOS installer for compatibility with Big
158 Sur and Monterey</li>
160 <!-- JAL-3805 -->Uninstaller application for old
161 (InstallAnywhere based) Jalview installations removed from
165 <!-- JAL-3930 -->Improved use of installers for unattended
166 installation with a customizedId of "JALVIEW" in install4j's
176 <!-- JAL-3674 -->Slow structure commands can block Jalview
180 <!-- JAL-3904 -->Structure window's viewer-specific menu
181 disappears when only one structure is shown (and many
182 sequences:one chain mappings are present)
185 <!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
186 the first SEQUENCE_GROUP defined
191 <!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 -->Selections not
192 propagated between Linked CDS - Protein alignments and their
193 trees (known defect from 2.11.1.3)
196 <!-- JAL-3761 -->Not all codon positions highlighted for
197 overlapping exon splice sites (e.g due to RNA slippage)
200 <!-- JAL-3794 -->X was not being recognised as the unknown
201 base in DNA sequences
204 <!-- JAL-3915 -->Removed RNAview checkbox and logic from
205 Structure Preferences
208 <!-- JAL-3583 -->Tooltip behaviour improved (slightly)
211 <!-- JAL-3162 -->Can edit a feature so that start > end
214 <!-- JAL-2848 -->Cancel from Amend Features doesn't reset a
215 modified graduated colour
218 <!-- JAL-3788 -->New View with automatic 'Show Overview'
219 preference enabled results in Null Pointer Exceptions when
220 clustal colouring is enabled
223 <!-- JAL-3275 -->Can open multiple Preferences panels
226 <!-- JAL-3949 -->Standard out logging broken: messages only
227 routing to stderr and appear as a raw template
229 </ul> <em>JalviewJS</em>
232 <!-- JAL-3202 -->Consensus profile may include zero (rounded
233 down) percentage values causing a divide by zero
248 <!-- JAL-3762 -->JalviewJS doesn't honour arguments passed
249 via Info.args when there are arguments on the URL
252 <!-- JAL-3602 -->gradle closure-compiler not using UTF-8
255 <!-- JAL-3603 -->Annotation file fails to load from URL in
258 </ul> <em>Development</em>
262 <li>Fixed non-fatal gradle errors during build</li>
264 <!-- JAL-3745 -->Updated build.gradle for use with
274 <td width="60" align="center" nowrap><strong><a
275 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.7">.7</a><br />
276 <em>18/01/2022</em></strong></td>
278 <td align="left" valign="top">
281 <!-- JAL-3703, JAL-3935 -->Files open in Jalview cannot be
282 updated by Jalview or other applications (Windows, other non
285 </ul> <em>Security</em>
288 <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
294 <td width="60" align="center" nowrap><strong><a
295 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
296 <em>6/01/2022</em></strong></td>
298 <td align="left" valign="top"><em>Security</em>
301 <!-- JAL-3934 -->Version bump library dependency: Log4j
308 <td width="60" align="center" nowrap><strong><a
309 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
310 <em>20/12/2021</em></strong></td>
312 <td align="left" valign="top"><em>Security</em>
315 <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
317 </ul> <em>Development</em>
319 <li>Updated building instructions</li>
324 <!-- JAL-3840 -->Occupancy calculation is incorrect for
325 alignment columns with over -1+2^32 gaps (breaking filtering
329 <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
330 scale factors being set with buggy window-managers (linux
333 </ul> <em>Development</em>
335 <li>Fixed non-fatal gradle errors during build</li>
340 <td width="60" align="center" nowrap><strong><a
341 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
342 <em>09/03/2021</em></strong></td>
343 <td align="left" valign="top"><em>Improved control of
344 Jalview's use of network services via jalview_properties</em>
347 <!-- JAL-3814 -->New .jalview_properties token controlling
348 launch of the news browser (like -nonews argument)
351 <!-- JAL-3813 -->New .jalview_properties token controlling
352 download of linkout URLs from
353 www.jalview.org/services/identifiers
356 <!-- JAL-3812 -->New .jalview_properties token controlling
357 download of BIOJSHTML templates
360 <!-- JAL-3811 -->New 'Discover Web Services' option to
361 trigger a one off JABAWS discovery if autodiscovery was
365 <td align="left" valign="top">
368 <!-- JAL-3818 -->Intermittent deadlock opening structure in
371 </ul> <em>New Known defects</em>
374 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
375 always restored from project (since 2.10.3)
378 <!-- JAL-3806 -->Selections from tree built from CDS aren't
379 propagated to Protein alignment (since 2.11.1.3)
385 <td width="60" align="center" nowrap><strong><a
386 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
387 <em>29/10/2020</em></strong></td>
388 <td align="left" valign="top">
393 <td align="left" valign="top">
396 <!-- JAL-3765 -->Find doesn't always highlight all matching
397 positions in a sequence (bug introduced in 2.11.1.2)
400 <!-- JAL-3760 -->Alignments containing one or more protein
401 sequences can be classed as nucleotide
404 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
405 sequences after alignment of protein products (known defect
406 first reported for 2.11.1.0)
409 <!-- JAL-3725 -->No tooltip or popup menu for genomic
410 features outwith CDS shown overlaid on protein
413 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
414 correctly mapped by Jalview (e.g. affects viral CDS with
415 ribosomal slippage, since 2.9.0)
418 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
422 <!-- JAL-3700 -->Selections in CDS sequence panel don't
423 always select corresponding protein sequences
426 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
427 column selection doesn't always ignore hidden columns
429 </ul> <em>Installer</em>
432 <!-- JAL-3611 -->Space character in Jalview install path on
433 Windows prevents install4j launching getdown
435 </ul> <em>Development</em>
438 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
439 version numbers in doc/building.md
445 <td width="60" align="center" nowrap><strong><a
446 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
447 <em>25/09/2020</em></strong></td>
448 <td align="left" valign="top">
452 <td align="left" valign="top">
455 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
456 "Encountered problems opening
457 https://www.jalview.org/examples/exampleFile_2_7.jvp"
463 <td width="60" align="center" nowrap><strong><a
464 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
465 <em>17/09/2020</em></strong></td>
466 <td align="left" valign="top">
469 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
470 residue in cursor mode
473 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
474 HTSJDK from 2.12 to 2.23
477 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
478 optimisations and improvements suggested by Bob Hanson and
479 improved compatibility with JalviewJS
482 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
483 alignments from Pfam and Rfam
486 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
487 import (no longer based on .gz extension)
490 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
493 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
494 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
498 <!-- JAL-3667 -->Improved warning messages, debug logging
499 and fixed Retry action when Jalview encounters errors when
500 saving or making backup files.
503 <!-- JAL-3676 -->Enhanced Jalview Java Console:
505 <li>Jalview's logging level can be configured</li>
506 <li>Copy to Clipboard Buttion</li>
510 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
511 when running on Linux (Requires Java 11+)
513 </ul> <em>Launching Jalview</em>
516 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
517 through a system property
520 <!-- JAL-3477 -->Improved built-in documentation and command
521 line help for configuring Jalview's memory
525 <td align="left" valign="top">
528 <!-- JAL-3691 -->Conservation and Quality tracks are shown
529 but not calculated and no protein or DNA score models are
530 available for tree/PCA calculation when launched with
531 Turkish language locale
534 <!-- JAL-3493 -->Escape does not clear highlights on the
535 alignment (Since Jalview 2.10.3)
538 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
539 doesn't slide selected sequences, just sequence under cursor
542 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
543 sequence under the cursor
546 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
547 multiple EMBL gene products shown for a single contig
550 <!-- JAL-3696 -->Errors encountered when processing variants
551 from VCF files yield "Error processing VCF: Format specifier
555 <!-- JAL-3697 -->Count of features not shown can be wrong
556 when there are both local and complementary features mapped
557 to the position under the cursor
560 <!-- JAL-3673 -->Sequence ID for reference sequence is
561 clipped when Right align Sequence IDs enabled
564 <!-- JAL-2983 -->Slider with negative range values not
565 rendered correctly in VAqua4 (Since 2.10.4)
568 <!-- JAL-3685 -->Single quotes not displayed correctly in
569 internationalised text for some messages and log output
572 <!-- JAL-3490 -->Find doesn't report matches that span
573 hidden gapped columns
576 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
577 panels, Alignment viewport and annotation renderer.
580 <!-- JAL-3561 -->Jalview ignores file format parameter
581 specifying output format when exporting an alignment via the
585 <!-- JAL-3667 -->Windows 10: For a minority of users, if
586 backups are not enabled, Jalview sometimes fails to
587 overwrite an existing file and raises a warning dialog. (in
588 2.11.0, and 2.11.1.0, the workaround is to try to save the
589 file again, and if that fails, delete the original file and
593 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
597 <!-- JAL-3741 -->References to http://www.jalview.org in
598 program and documentation
600 </ul> <em>Launching Jalview</em>
603 <!-- JAL-3718 -->Jalview application fails when launched the
604 first time for a version that has different jars to the
605 previous launched version.
607 </ul> <em>Developing Jalview</em>
610 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
611 data, causing cloverReport gradle task to fail with an
615 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
616 monitor the release channel
618 </ul> <em>New Known defects</em>
621 <!-- JAL-3748 -->CDS shown in result of submitting proteins
622 in a CDS/Protein alignment to a web service is wrong when
623 proteins share a common transcript sequence (e.g. genome of
627 <!-- JAL-3576 -->Co-located features exported and
628 re-imported are ordered differently when shown on alignment
629 and in tooltips. (Also affects v2.11.1.0)
632 <!-- JAL-3702 -->Drag and drop of alignment file onto
633 alignment window when in a HiDPI scaled mode in Linux only
634 works for the top left quadrant of the alignment window
637 <!-- JAL-3701 -->Stale build data in jalview standalone jar
638 builds (only affects 2.11.1.1 branch)
641 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
642 when alignment view restored from project (since Jalview
646 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
647 protein products for certain ENA records are repeatedly
648 shown via Calculate->Show Cross Refs
654 <td width="60" align="center" nowrap><strong><a
655 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
656 <em>22/04/2020</em></strong></td>
657 <td align="left" valign="top">
660 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
661 'virtual' codon features shown on protein (or vice versa)
662 for display in alignments, on structure views (including
663 transfer to UCSF chimera), in feature reports and for
667 <!-- JAL-3121 -->Feature attributes from VCF files can be
668 exported and re-imported as GFF3 files
671 <!-- JAL-3376 -->Capture VCF "fixed column" values
672 POS, ID, QUAL, FILTER as Feature Attributes
675 <!-- JAL-3375 -->More robust VCF numeric data field
676 validation while parsing
679 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
683 <!-- JAL-3535 -->Feature Settings dialog title includes name
687 <!-- JAL-3538 -->Font anti-aliasing in alignment views
691 <!-- JAL-3468 -->Very long feature descriptions truncated in
695 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
696 with no feature types visible
699 <!-- JAL-3574 -->Improved support for filtering feature
700 attributes with large integer values
703 <em>Jalview Installer</em>
706 <!-- JAL-3449 -->Versions for install4j and getdown and
707 installer template version reported in console (may be null
708 when Jalview launched as executable jar or via conda)
711 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and
712 higher quality background images
715 <!-- JAL-3394 -->New installer/application launcher
716 generated with install4j 8.0.4
719 <!-- JAL-3420 -->Jalview File Associations shown for Unix
723 <!-- JAL-3477 -->Improved defaults for maximum memory
724 setting when running on large memory machines
726 </ul> <em>Release processes</em>
729 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
732 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier
733 access to test-release channel builds
735 </ul> <em>Build System</em>
738 <!-- JAL-3510 -->Clover updated to 4.4.1
741 <!-- JAL-3513 -->Test code included in Clover coverage
744 </ul> <em>Groovy Scripts</em>
747 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
748 to stdout containing the consensus sequence for each
749 alignment in a Jalview session
752 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
753 genomic sequence_variant annotation from CDS as
754 missense_variant or synonymous_variant on protein products.
758 <td align="left" valign="top">
761 <!-- JAL-3581 -->Hidden sequence markers still visible when
762 'Show hidden markers' option is not ticked
765 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
766 PNG output when 'Automatically set ID width' is set in
767 jalview preferences or properties file
770 <!-- JAL-3571 -->Feature Editor dialog can be opened when
771 'Show Sequence Features' option is not ticked
774 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
775 buttons in Feature Settings dialog are clicked when no
779 <!-- JAL-3412 -->ID margins for CDS and Protein views not
780 equal when split frame is first opened
783 <!-- JAL-3296 -->Sequence position numbers in status bar not
784 correct after editing a sequence's start position
787 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
788 with annotation and exceptions thrown when only a few
789 columns shown in wrapped mode
792 <!-- JAL-3386 -->Sequence IDs missing in headless export of
793 wrapped alignment figure with annotations
796 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
797 ID fails with ClassCastException
800 <!-- JAL-3389 -->Chimera session not restored from Jalview
804 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
805 feature settings dialog also selects columns
808 <!-- JAL-3473 -->SpinnerNumberModel causes
809 IllegalArgumentException in some circumstances
812 <!-- JAL-3534 -->Multiple feature settings dialogs can be
816 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
817 alignment window is closed
820 <!-- JAL-3406 -->Credits missing some authors in Jalview
821 help documentation for 2.11.0 release
824 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
825 includes Pfam ID as sequence's accession rather than its
828 </ul> <em>Java 11 Compatibility issues</em>
831 <!-- JAL-2987 -->OSX - Can't view some search results in
832 PDB/Uniprot search panel
834 </ul> <em>Installer</em>
837 <!-- JAL-3447 -->Jalview should not create file associations
838 for 3D structure files (.pdb, .mmcif. .cif)
840 </ul> <em>Repository and Source Release</em>
843 <!-- JAL-3474 -->removed obsolete .cvsignore files from
847 <!-- JAL-3541 -->Clover report generation running out of
850 </ul> <em>New Known Issues</em>
853 <!-- JAL-3523 -->OSX - Current working directory not
854 preserved when Jalview.app launched with parameters from
858 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
859 clipped in headless figure export when Right Align option
863 <!-- JAL-3542 -->Jalview Installation type always reports
864 'Source' in console output
867 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail
868 on jalview's bamboo server but run fine locally.
874 <td width="60" align="center" nowrap><strong><a
875 name="Jalview.2.11.0">2.11.0</a><br /> <em>04/07/2019</em></strong></td>
876 <td align="left" valign="top">
879 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native
880 Application and Installers built with <a
881 href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a>
882 (licensed to the Jalview open source project) rather than
886 <!-- JAL-1929 -->Jalview Launcher System to auto-configure
887 memory settings, receive over the air updates and launch
888 specific versions via (<a
889 href="https://github.com/threerings/getdown">Three
893 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations
894 for formats supported by Jalview (including .jvp project
898 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command
899 line arguments and switch between different getdown channels
902 <!-- JAL-3141 -->Backup files created when saving Jalview
903 project or alignment files
907 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF
911 <!-- JAL-2753 -->Version of HTSJDK shipped with Jalview
912 updated to version 2.12.0
915 <!-- JAL-2620 -->Alternative genetic code tables for
919 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0
921 <li><strong>Enhanced visualisation and analysis
922 of Sequence Features</strong>
925 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
926 implementation that allows updates) used for Sequence
930 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
931 features can be filtered and shaded according to any
932 associated attributes (e.g. variant attributes from VCF
933 file, or key-value pairs imported from column 9 of GFF
937 <!-- JAL-2879 -->Feature Attributes and shading schemes
938 stored and restored from Jalview Projects
941 <!-- JAL-3334 -->Use full Sequence Ontology (via
942 BioJava) to recognise variant features
945 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants
946 on peptide sequences (also coloured red by default)
949 <!-- JAL-2792 -->Popup window to show full report for a
950 selected sequence feature's details
953 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient
954 sequence feature render algorithm (Z-sort/transparency
958 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature
963 <!-- JAL-3205 -->Symmetric score matrices for faster tree
966 <li><strong>Principal Components Analysis Viewer</strong>
969 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis
970 results and Viewer state saved in Jalview Project
973 <!-- JAL-2962 -->'Change parameters' option removed from
974 viewer's drop-down menus
977 <!-- JAL-2975 -->Can use shift + arrow keys to rotate
978 PCA image incrementally
981 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
985 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
987 <li><strong>Speed and Efficiency</strong>
990 <!-- JAL-2185,JAL-3198 -->More efficient creation of
991 selections and multiple groups when working with large
995 <!-- JAL-3200 -->Speedier import of annotation rows when
996 parsing Stockholm files
999 <li><strong>User Interface</strong>
1002 <!-- JAL-2933 -->Finder panel remembers last position in
1006 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS
1007 (What you see is what is shown)<br />Only visible
1008 regions of alignment are shown by default (can be
1009 changed in user preferences)
1012 <!-- JAL-3169 -->File Chooser stays open after
1013 responding Cancel to the Overwrite Dialog
1016 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour
1017 when all sequences are hidden
1020 <!-- JAL-1244 -->Status bar shows bounds when dragging a
1021 selection region, and gap count when inserting or
1025 <!-- JAL-3132 -->Status bar updates over sequence and
1029 <!-- JAL-3093 -->Annotation tooltips and popup menus are
1030 shown when in wrapped mode
1033 <!-- JAL-3073 -->Can select columns by dragging
1034 left/right in a graph or histogram annotation
1037 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB
1041 <!-- JAL-2621 -->Cursor changes over draggable box in
1045 <!-- JAL-3181 -->Consistent ordering of links in
1046 sequence id popup menu
1049 <!-- JAL-3080 -->Red line indicating tree-cut position
1050 not shown if no subgroups are created
1053 <!-- JAL-3042 -->Removed ability to configure length of
1054 search history by right-clicking search box
1060 <!-- JAL-3232 -->Jalview Groovy Scripting Console updated to
1063 <li><strong>Java 11 Support (not yet on general
1067 <!-- -->OSX GUI integrations for App menu's 'About'
1068 entry and trapping CMD-Q
1071 </ul> <em>Deprecations</em>
1074 <!-- JAL-3035 -->DAS sequence retrieval and annotation
1075 capabilities removed from the Jalview Desktop
1078 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling
1079 and unmarshalling has been replaced by JAXB for Jalview
1080 projects and XML based data retrieval clients
1083 <!-- JAL-3311 -->Disable VAMSAS menu in preparation for
1087 <!-- -->Jalview Desktop no longer distributed via Java Web
1090 </ul> <em>Documentation</em>
1093 <!-- JAL-3003 -->Added remarks about transparent rendering
1094 effects not supported in EPS figure export
1097 <!-- JAL-2903 -->Typos in documentation for Preferences
1100 </ul> <em>Development and Release Processes</em>
1103 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated
1107 <!-- JAL-1424 -->Enhanced checks for missing and duplicated
1108 keys in Message bundles
1111 <!-- JAL-3225 -->Eclipse project configuration managed with
1115 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian Bamboo
1116 continuous integration for unattended Test Suite execution
1119 <!-- JAL-2864 -->Memory test suite to detect leaks in common
1123 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
1127 <!-- JAL-3248 -->Developer documentation migrated to
1128 markdown (with HTML rendering)
1131 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
1134 <!-- JAL-3289 -->New URLs for publishing development
1139 <td align="left" valign="top">
1142 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
1145 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
1146 superposition in Jmol fail on Windows
1149 <!-- JAL-3286 -->Blank error dialog is displayed when
1150 discovering structures for sequences with lots of PDB
1154 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export
1155 with monospaced font
1158 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
1159 Jalview project involving multiple views
1162 <!-- JAL-3164 -->Overview for complementary view in a linked
1163 CDS/Protein alignment is not updated when Hide Columns by
1164 Annotation dialog hides columns
1167 <!-- JAL-3158 -->Selection highlighting in the complement of
1168 a CDS/Protein alignment stops working after making a
1169 selection in one view, then making another selection in the
1173 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
1177 <!-- JAL-3154 -->Table Columns could be re-ordered in
1178 Feature Settings and Jalview Preferences panels
1181 <!-- JAL-2865 -->Jalview hangs when closing windows, or
1182 redrawing the overview with large alignments
1185 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
1186 region if columns were selected by dragging right-to-left
1187 and the mouse moved to the left of the first column
1190 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to
1191 a hidden column marker via scale popup menu
1194 <!-- JAL-2846 -->Error message for trying to load in invalid
1195 URLs doesn't tell users the invalid URL
1198 <!-- JAL-2816 -->Tooltips displayed for features filtered by
1202 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl
1203 during show cross references or Fetch Database References
1204 are shown in red in original view
1207 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown
1208 correctly on peptide sequence (computed variant shown as
1212 <!-- JAL-2060 -->'Graduated colour' option not offered for
1213 manually created features (where feature score is Float.NaN)
1216 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or
1217 printed when columns are hidden
1220 <!-- JAL-3082 -->Regular expression error for '(' in Select
1221 Columns by Annotation description
1224 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after
1225 dragging out of Scale or Annotation Panel
1228 <!-- JAL-3075 -->Column selection incorrect after scrolling
1232 <!-- JAL-3074 -->Left/right drag in annotation can scroll
1236 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal
1240 <!-- JAL-3002 -->Column display is out by one after Page
1241 Down, Page Up in wrapped mode
1244 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
1247 <!-- JAL-2932 -->Finder searches in minimised alignments
1250 <!-- JAL-2250 -->'Apply Colour to All Groups' not always
1251 selected on opening an alignment
1254 <!-- JAL-3180 -->'Colour by Annotation' not marked selected
1258 <!-- JAL-3201 -->Per-group Clustal colour scheme changes
1259 when different groups in the alignment are selected
1262 <!-- JAL-2717 -->Internationalised colour scheme names not
1263 shown correctly in menu
1266 <!-- JAL-3206 -->Colour by Annotation can go black at
1267 min/max threshold limit
1270 <!-- JAL-3125 -->Value input for graduated feature colour
1271 threshold gets 'unrounded'
1274 <!-- JAL-2982 -->PCA image export doesn't respect background
1278 <!-- JAL-2963 -->PCA points don't dim when rotated about y
1282 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
1285 <!-- JAL-3078 -->Cancel in Tree Font dialog resets
1286 alignment, not Tree font
1289 <!-- JAL-2964 -->Associate Tree with All Views not restored
1293 <!-- JAL-2915 -->Scrolling of split frame is sluggish if
1294 Overview shown in complementary view
1297 <!-- JAL-3313 -->Codon consensus incorrectly scaled when
1298 shown without normalisation
1301 <!-- JAL-3021 -->Sequence Details report should open
1302 positioned at top of report
1305 <!-- JAL-914 -->Help page can be opened twice
1308 <!-- JAL-3333 -->Fuzzy text in web service status menu on
1311 </ul> <em>Editing</em>
1314 <!-- JAL-2822 -->Start and End should be updated when
1315 sequence data at beginning or end of alignment added/removed
1319 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection
1320 doesn't relocate sequence features correctly when start of
1321 sequence is removed (Known defect since 2.10)
1324 <!-- JAL-2830 -->Inserting gap sequence via the Edit
1325 Sequence dialog corrupts dataset sequence
1328 <!-- JAL-868 -->Structure colours not updated when
1329 associated tree repartitions the alignment view (Regression
1332 </ul> <em>Datamodel</em>
1335 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
1336 sequence's End is greater than its length
1338 </ul> <em>Bugs fixed for Java 11 Support (not yet on general
1342 <!-- JAL-3288 -->Menus work properly in split-screen
1344 </ul> <em>New Known Defects</em>
1347 <!-- JAL-3340 -->Select columns containing feature by double
1348 clicking ignores bounds of an existing selected region
1351 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in
1352 gapped regions of protein alignment.
1355 <!-- JAL-2647 -->Input Data menu entry is greyed out when
1356 PCA View is restored from a Jalview 2.11 project
1359 <!-- JAL-3213 -->Alignment panel height can be too small
1363 <!-- JAL-3240 -->Display is incorrect after removing gapped
1364 columns within hidden columns
1367 <!-- JAL-3314 -->Rightmost selection is lost when mouse
1368 re-enters window after dragging left to select columns to
1369 left of visible region
1372 <!-- JAL-2876 -->Features coloured according to their
1373 description string and thresholded by score in earlier
1374 versions of Jalview are not shown as thresholded features in
1375 2.11. To workaround please create a Score filter instead.
1378 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't
1379 reset group visibility
1382 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in
1383 linked CDS/Protein view
1386 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1387 alignments with multiple views can close views unexpectedly
1389 </ul> <em>Java 11 Specific defects</em>
1392 <!-- JAL-3235 -->Jalview Properties file is not sorted
1393 alphabetically when saved
1399 <td width="60" nowrap>
1400 <div align="center">
1401 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1404 <td><div align="left">
1408 <!-- JAL-3101 -->Default memory for Jalview webstart and
1409 InstallAnywhere increased to 1G.
1412 <!-- JAL-247 -->Hidden sequence markers and representative
1413 sequence bolding included when exporting alignment as EPS,
1414 SVG, PNG or HTML. <em>Display is configured via the
1415 Format menu, or for command-line use via a Jalview
1416 properties file.</em>
1419 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1420 API and sequence data now imported as JSON.
1423 <!-- JAL-3065 -->Change in recommended way of starting
1424 Jalview via a Java command line: add jars in lib directory
1425 to CLASSPATH, rather than via the deprecated java.ext.dirs
1429 <em>Development</em>
1432 <!-- JAL-3047 -->Support added to execute test suite
1433 instrumented with <a href="http://openclover.org/">Open
1438 <td><div align="left">
1442 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1443 row shown in Feredoxin Structure alignment view of example
1447 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1448 annotation displayed.
1451 <!-- JAL-3107 -->Group conservation/consensus not shown
1452 for newly created group when 'Apply to all groups'
1456 <!-- JAL-3087 -->Corrupted display when switching to
1457 wrapped mode when sequence panel's vertical scrollbar is
1461 <!-- JAL-3003 -->Alignment is black in exported EPS file
1462 when sequences are selected in exported view.</em>
1465 <!-- JAL-3059 -->Groups with different coloured borders
1466 aren't rendered with correct colour.
1469 <!-- JAL-3092 -->Jalview could hang when importing certain
1470 types of knotted RNA secondary structure.
1473 <!-- JAL-3095 -->Sequence highlight and selection in
1474 trimmed VARNA 2D structure is incorrect for sequences that
1478 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1479 annotation when columns are inserted into an alignment,
1480 and when exporting as Stockholm flatfile.
1483 <!-- JAL-3053 -->Jalview annotation rows containing upper
1484 and lower-case 'E' and 'H' do not automatically get
1485 treated as RNA secondary structure.
1488 <!-- JAL-3106 -->.jvp should be used as default extension
1489 (not .jar) when saving a Jalview project file.
1492 <!-- JAL-3105 -->Mac Users: closing a window correctly
1493 transfers focus to previous window on OSX
1496 <em>Java 10 Issues Resolved</em>
1499 <!-- JAL-2988 -->OSX - Can't save new files via the File
1500 or export menus by typing in a name into the Save dialog
1504 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1505 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1506 'look and feel' which has improved compatibility with the
1507 latest version of OSX.
1513 <td width="60" nowrap>
1514 <div align="center">
1515 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1516 <em>7/06/2018</em></strong>
1519 <td><div align="left">
1523 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1524 annotation retrieved from Uniprot
1527 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1528 onto the Jalview Desktop
1532 <td><div align="left">
1536 <!-- JAL-3017 -->Cannot import features with multiple
1537 variant elements (blocks import of some Uniprot records)
1540 <!-- JAL-2997 -->Clustal files with sequence positions in
1541 right-hand column parsed correctly
1544 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1545 not alignment area in exported graphic
1548 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1549 window has input focus
1552 <!-- JAL-2992 -->Annotation panel set too high when
1553 annotation added to view (Windows)
1556 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1557 network connectivity is poor
1560 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1561 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1562 the currently open URL and links from a page viewed in
1563 Firefox or Chrome on Windows is now fully supported. If
1564 you are using Edge, only links in the page can be
1565 dragged, and with Internet Explorer, only the currently
1566 open URL in the browser can be dropped onto Jalview.</em>
1569 <em>New Known Defects</em>
1572 <!-- JAL-3083 -->Cancel option doesn't reset Colour by
1579 <td width="60" nowrap>
1580 <div align="center">
1581 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1584 <td><div align="left">
1588 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1589 for disabling automatic superposition of multiple
1590 structures and open structures in existing views
1593 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1594 ID and annotation area margins can be click-dragged to
1598 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1602 <!-- JAL-2759 -->Improved performance for large alignments
1603 and lots of hidden columns
1606 <!-- JAL-2593 -->Improved performance when rendering lots
1607 of features (particularly when transparency is disabled)
1610 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2
1611 for exchange of Jalview features and Chimera attributes
1612 made generally available
1616 <td><div align="left">
1619 <!-- JAL-2899 -->Structure and Overview aren't updated
1620 when Colour By Annotation threshold slider is adjusted
1623 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1624 overlapping alignment panel
1627 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1631 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1632 improved: CDS not handled correctly if transcript has no
1636 <!-- JAL-2321 -->Secondary structure and temperature
1637 factor annotation not added to sequence when local PDB
1638 file associated with it by drag'n'drop or structure
1642 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1643 dialog doesn't import PDB files dropped on an alignment
1646 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1647 scroll bar doesn't work for some CDS/Protein views
1650 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1651 Java 1.8u153 onwards and Java 1.9u4+.
1654 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1655 columns in annotation row
1658 <!-- JAL-2913 -->Preferences panel's ID Width control is
1659 not honored in batch mode
1662 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1663 for structures added to existing Jmol view
1666 <!-- JAL-2223 -->'View Mappings' includes duplicate
1667 entries after importing project with multiple views
1670 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1671 protein sequences via SIFTS from associated PDB entries
1672 with negative residue numbers or missing residues fails
1675 <!-- JAL-2952 -->Exception when shading sequence with
1676 negative Temperature Factor values from annotated PDB
1677 files (e.g. as generated by CONSURF)
1680 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1681 tooltip doesn't include a text description of mutation
1684 <!-- JAL-2922 -->Invert displayed features very slow when
1685 structure and/or overview windows are also shown
1688 <!-- JAL-2954 -->Selecting columns from highlighted
1689 regions very slow for alignments with large numbers of
1693 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1694 with 'StringIndexOutOfBounds'
1697 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and
1698 Feel for OSX platforms running Java 10
1701 <!-- JAL-2960 -->Adding a structure to existing structure
1702 view appears to do nothing because the view is hidden
1703 behind the alignment view
1709 <!-- JAL-2926 -->Copy consensus sequence option in applet
1710 should copy the group consensus when popup is opened on it
1716 <!-- JAL-2913 -->Fixed ID width preference is not
1720 <em>New Known Defects</em>
1723 <!-- JAL-2973 --> Exceptions occasionally raised when
1724 editing a large alignment and overview is displayed
1727 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1728 repeatedly after a series of edits even when the overview
1729 is no longer reflecting updates
1732 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1733 structures for protein subsequence (if 'Trim Retrieved
1734 Sequences' enabled) or Ensembl isoforms (Workaround in
1735 2.10.4 is to fail back to N&W mapping)
1738 <!-- JAL-2990 -->Export Annotations from File Menu with
1739 CSV option gives blank output
1745 <td width="60" nowrap>
1746 <div align="center">
1747 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br />
1748 <em>24/1/2018</em></strong>
1751 <td><div align="left">
1753 <li>Updated Certum Codesigning Certificate (Valid till
1754 30th November 2018)</li>
1757 <td><div align="left">
1762 <!-- JAL-2859-->Only one structure is loaded when
1763 several sequences and structures are selected for
1767 <!-- JAL-2851-->Alignment doesn't appear to scroll
1768 vertically via trackpad and scrollwheel
1771 <!-- JAL-2842-->Jalview hangs if up/down arrows pressed
1772 in cursor mode when cursor lies in hidden region at
1776 <!-- JAL-2827-->Helix annotation has 'notches' when
1777 scrolled into view if columns are hidden
1780 <!-- JAL-2740-->Annotation column filter can be slow to
1781 reset (ie after hitting cancel) for large numbers of
1785 <!-- JAL-2849-->User preference for disabling inclusion
1786 of sequence limits when exporting as flat file has no
1790 <!-- JAL-2679-->Reproducible cross-reference
1791 relationships when retrieving sequences from
1798 <td width="60" nowrap>
1799 <div align="center">
1800 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1803 <td><div align="left">
1807 <!-- JAL-2446 -->Faster and more efficient management and
1808 rendering of sequence features
1811 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1812 429 rate limit request hander
1815 <!-- JAL-2773 -->Structure views don't get updated unless
1816 their colours have changed
1819 <!-- JAL-2495 -->All linked sequences are highlighted for
1820 a structure mousover (Jmol) or selection (Chimera)
1823 <!-- JAL-2790 -->'Cancel' button in progress bar for
1824 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1827 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1828 view from Ensembl locus cross-references
1831 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1835 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1836 feature can be disabled
1839 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1840 PDB easier retrieval of sequences for lists of IDs
1843 <!-- JAL-2758 -->Short names for sequences retrieved from
1849 <li>Groovy interpreter updated to 2.4.12</li>
1850 <li>Example groovy script for generating a matrix of
1851 percent identity scores for current alignment.</li>
1853 <em>Testing and Deployment</em>
1856 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1860 <td><div align="left">
1864 <!-- JAL-2643 -->Pressing tab after updating the colour
1865 threshold text field doesn't trigger an update to the
1869 <!-- JAL-2682 -->Race condition when parsing sequence ID
1873 <!-- JAL-2608 -->Overview windows are also closed when
1874 alignment window is closed
1877 <!-- JAL-2548 -->Export of features doesn't always respect
1881 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1882 takes a long time in Cursor mode
1888 <!-- JAL-2777 -->Structures with whitespace chainCode
1889 cannot be viewed in Chimera
1892 <!-- JAL-2728 -->Protein annotation panel too high in
1896 <!-- JAL-2757 -->Can't edit the query after the server
1897 error warning icon is shown in Uniprot and PDB Free Text
1901 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1904 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1907 <!-- JAL-2739 -->Hidden column marker in last column not
1908 rendered when switching back from Wrapped to normal view
1911 <!-- JAL-2768 -->Annotation display corrupted when
1912 scrolling right in unwapped alignment view
1915 <!-- JAL-2542 -->Existing features on subsequence
1916 incorrectly relocated when full sequence retrieved from
1920 <!-- JAL-2733 -->Last reported memory still shown when
1921 Desktop->Show Memory is unticked (OSX only)
1924 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1925 features of same type and group to be selected for
1929 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1930 alignments when hidden columns are present
1933 <!-- JAL-2392 -->Jalview freezes when loading and
1934 displaying several structures
1937 <!-- JAL-2732 -->Black outlines left after resizing or
1941 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1942 within the Jalview desktop on OSX
1945 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1946 when in wrapped alignment mode
1949 <!-- JAL-2636 -->Scale mark not shown when close to right
1950 hand end of alignment
1953 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1954 each selected sequence do not have correct start/end
1958 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1959 after canceling the Alignment Window's Font dialog
1962 <!-- JAL-2036 -->Show cross-references not enabled after
1963 restoring project until a new view is created
1966 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1967 URL links appears when only default EMBL-EBI link is
1968 configured (since 2.10.2b2)
1971 <!-- JAL-2775 -->Overview redraws whole window when box
1972 position is adjusted
1975 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1976 in a multi-chain structure when viewing alignment
1977 involving more than one chain (since 2.10)
1980 <!-- JAL-2811 -->Double residue highlights in cursor mode
1981 if new selection moves alignment window
1984 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1985 arrow key in cursor mode to pass hidden column marker
1988 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1989 that produces correctly annotated transcripts and products
1992 <!-- JAL-2776 -->Toggling a feature group after first time
1993 doesn't update associated structure view
1996 <em>Applet</em><br />
1999 <!-- JAL-2687 -->Concurrent modification exception when
2000 closing alignment panel
2003 <em>BioJSON</em><br />
2006 <!-- JAL-2546 -->BioJSON export does not preserve
2007 non-positional features
2010 <em>New Known Issues</em>
2013 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
2014 sequence features correctly (for many previous versions of
2018 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
2019 using cursor in wrapped panel other than top
2022 <!-- JAL-2791 -->Select columns containing feature ignores
2023 graduated colour threshold
2026 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
2027 always preserve numbering and sequence features
2030 <em>Known Java 9 Issues</em>
2033 <!-- JAL-2902 -->Groovy Console very slow to open and is
2034 not responsive when entering characters (Webstart, Java
2041 <td width="60" nowrap>
2042 <div align="center">
2043 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
2044 <em>2/10/2017</em></strong>
2047 <td><div align="left">
2048 <em>New features in Jalview Desktop</em>
2051 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API
2055 <!-- JAL-2745 -->HTTPS used for all connections to
2060 <td><div align="left"></div></td>
2063 <td width="60" nowrap>
2064 <div align="center">
2065 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
2066 <em>7/9/2017</em></strong>
2069 <td><div align="left">
2073 <!-- JAL-2588 -->Show gaps in overview window by colouring
2074 in grey (sequences used to be coloured grey, and gaps were
2078 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
2082 <!-- JAL-2587 -->Overview updates immediately on increase
2083 in size and progress bar shown as higher resolution
2084 overview is recalculated
2089 <td><div align="left">
2093 <!-- JAL-2664 -->Overview window redraws every hidden
2094 column region row by row
2097 <!-- JAL-2681 -->duplicate protein sequences shown after
2098 retrieving Ensembl crossrefs for sequences from Uniprot
2101 <!-- JAL-2603 -->Overview window throws NPE if show boxes
2102 format setting is unticked
2105 <!-- JAL-2610 -->Groups are coloured wrongly in overview
2106 if group has show boxes format setting unticked
2109 <!-- JAL-2672,JAL-2665 -->Redraw problems when
2110 autoscrolling whilst dragging current selection group to
2111 include sequences and columns not currently displayed
2114 <!-- JAL-2691 -->Not all chains are mapped when multimeric
2115 assemblies are imported via CIF file
2118 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
2119 displayed when threshold or conservation colouring is also
2123 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
2127 <!-- JAL-2673 -->Jalview continues to scroll after
2128 dragging a selected region off the visible region of the
2132 <!-- JAL-2724 -->Cannot apply annotation based
2133 colourscheme to all groups in a view
2136 <!-- JAL-2511 -->IDs don't line up with sequences
2137 initially after font size change using the Font chooser or
2144 <td width="60" nowrap>
2145 <div align="center">
2146 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
2149 <td><div align="left">
2150 <em>Calculations</em>
2154 <!-- JAL-1933 -->Occupancy annotation row shows number of
2155 ungapped positions in each column of the alignment.
2158 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
2159 a calculation dialog box
2162 <!-- JAL-2379 -->Revised implementation of PCA for speed
2163 and memory efficiency (~30x faster)
2166 <!-- JAL-2403 -->Revised implementation of sequence
2167 similarity scores as used by Tree, PCA, Shading Consensus
2168 and other calculations
2171 <!-- JAL-2416 -->Score matrices are stored as resource
2172 files within the Jalview codebase
2175 <!-- JAL-2500 -->Trees computed on Sequence Feature
2176 Similarity may have different topology due to increased
2183 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
2184 model for alignments and groups
2187 <!-- JAL-384 -->Custom shading schemes created via groovy
2194 <!-- JAL-2526 -->Efficiency improvements for interacting
2195 with alignment and overview windows
2198 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
2202 <!-- JAL-2388 -->Hidden columns and sequences can be
2206 <!-- JAL-2611 -->Click-drag in visible area allows fine
2207 adjustment of visible position
2211 <em>Data import/export</em>
2214 <!-- JAL-2535 -->Posterior probability annotation from
2215 Stockholm files imported as sequence associated annotation
2218 <!-- JAL-2507 -->More robust per-sequence positional
2219 annotation input/output via stockholm flatfile
2222 <!-- JAL-2533 -->Sequence names don't include file
2223 extension when importing structure files without embedded
2224 names or PDB accessions
2227 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
2228 format sequence substitution matrices
2231 <em>User Interface</em>
2234 <!-- JAL-2447 --> Experimental Features Checkbox in
2235 Desktop's Tools menu to hide or show untested features in
2239 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
2240 via Overview or sequence motif search operations
2243 <!-- JAL-2547 -->Amend sequence features dialog box can be
2244 opened by double clicking gaps within sequence feature
2248 <!-- JAL-1476 -->Status bar message shown when not enough
2249 aligned positions were available to create a 3D structure
2253 <em>3D Structure</em>
2256 <!-- JAL-2430 -->Hidden regions in alignment views are not
2257 coloured in linked structure views
2260 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
2261 file-based command exchange
2264 <!-- JAL-2375 -->Structure chooser automatically shows
2265 Cached Structures rather than querying the PDBe if
2266 structures are already available for sequences
2269 <!-- JAL-2520 -->Structures imported via URL are cached in
2270 the Jalview project rather than downloaded again when the
2271 project is reopened.
2274 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
2275 to transfer Chimera's structure attributes as Jalview
2276 features, and vice-versa (<strong>Experimental
2280 <em>Web Services</em>
2283 <!-- JAL-2549 -->Updated JABAWS client to v2.2
2286 <!-- JAL-2335 -->Filter non-standard amino acids and
2287 nucleotides when submitting to AACon and other MSA
2291 <!-- JAL-2316, -->URLs for viewing database
2292 cross-references provided by identifiers.org and the
2293 EMBL-EBI's MIRIAM DB
2300 <!-- JAL-2344 -->FileFormatI interface for describing and
2301 identifying file formats (instead of String constants)
2304 <!-- JAL-2228 -->FeatureCounter script refactored for
2305 efficiency when counting all displayed features (not
2306 backwards compatible with 2.10.1)
2309 <em>Example files</em>
2312 <!-- JAL-2631 -->Graduated feature colour style example
2313 included in the example feature file
2316 <em>Documentation</em>
2319 <!-- JAL-2339 -->Release notes reformatted for readability
2320 with the built-in Java help viewer
2323 <!-- JAL-1644 -->Find documentation updated with 'search
2324 sequence description' option
2330 <!-- JAL-2485, -->External service integration tests for
2331 Uniprot REST Free Text Search Client
2334 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
2337 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
2342 <td><div align="left">
2343 <em>Calculations</em>
2346 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
2347 matrix - C->R should be '-3'<br />Old matrix restored
2348 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
2350 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
2351 Jalview's treatment of gaps in PCA and substitution matrix
2352 based Tree calculations.<br /> <br />In earlier versions
2353 of Jalview, gaps matching gaps were penalised, and gaps
2354 matching non-gaps penalised even more. In the PCA
2355 calculation, gaps were actually treated as non-gaps - so
2356 different costs were applied, which meant Jalview's PCAs
2357 were different to those produced by SeqSpace.<br />Jalview
2358 now treats gaps in the same way as SeqSpace (ie it scores
2359 them as 0). <br /> <br />Enter the following in the
2360 Groovy console to restore pre-2.10.2 behaviour:<br />
2361 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
2362 // for 2.10.1 mode <br />
2363 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
2364 // to restore 2.10.2 mode <br /> <br /> <em>Note:
2365 these settings will affect all subsequent tree and PCA
2366 calculations (not recommended)</em></li>
2368 <!-- JAL-2424 -->Fixed off-by-one bug that affected
2369 scaling of branch lengths for trees computed using
2370 Sequence Feature Similarity.
2373 <!-- JAL-2377 -->PCA calculation could hang when
2374 generating output report when working with highly
2375 redundant alignments
2378 <!-- JAL-2544 --> Sort by features includes features to
2379 right of selected region when gaps present on right-hand
2383 <em>User Interface</em>
2386 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2387 doesn't reselect a specific sequence's associated
2388 annotation after it was used for colouring a view
2391 <!-- JAL-2419 -->Current selection lost if popup menu
2392 opened on a region of alignment without groups
2395 <!-- JAL-2374 -->Popup menu not always shown for regions
2396 of an alignment with overlapping groups
2399 <!-- JAL-2310 -->Finder double counts if both a sequence's
2400 name and description match
2403 <!-- JAL-2370 -->Hiding column selection containing two
2404 hidden regions results in incorrect hidden regions
2407 <!-- JAL-2386 -->'Apply to all groups' setting when
2408 changing colour does not apply Conservation slider value
2412 <!-- JAL-2373 -->Percentage identity and conservation menu
2413 items do not show a tick or allow shading to be disabled
2416 <!-- JAL-2385 -->Conservation shading or PID threshold
2417 lost when base colourscheme changed if slider not visible
2420 <!-- JAL-2547 -->Sequence features shown in tooltip for
2421 gaps before start of features
2424 <!-- JAL-2623 -->Graduated feature colour threshold not
2425 restored to UI when feature colour is edited
2428 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2429 a time when scrolling vertically in wrapped mode.
2432 <!-- JAL-2630 -->Structure and alignment overview update
2433 as graduate feature colour settings are modified via the
2437 <!-- JAL-2034 -->Overview window doesn't always update
2438 when a group defined on the alignment is resized
2441 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2442 wrapped view result in positional status updates
2446 <!-- JAL-2563 -->Status bar doesn't show position for
2447 ambiguous amino acid and nucleotide symbols
2450 <!-- JAL-2602 -->Copy consensus sequence failed if
2451 alignment included gapped columns
2454 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2455 widgets don't permanently disappear
2458 <!-- JAL-2503 -->Cannot select or filter quantitative
2459 annotation that are shown only as column labels (e.g.
2460 T-Coffee column reliability scores)
2463 <!-- JAL-2594 -->Exception thrown if trying to create a
2464 sequence feature on gaps only
2467 <!-- JAL-2504 -->Features created with 'New feature'
2468 button from a Find inherit previously defined feature type
2469 rather than the Find query string
2472 <!-- JAL-2423 -->incorrect title in output window when
2473 exporting tree calculated in Jalview
2476 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2477 and then revealing them reorders sequences on the
2481 <!-- JAL-964 -->Group panel in sequence feature settings
2482 doesn't update to reflect available set of groups after
2483 interactively adding or modifying features
2486 <!-- JAL-2225 -->Sequence Database chooser unusable on
2490 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2491 only excluded gaps in current sequence and ignored
2498 <!-- JAL-2421 -->Overview window visible region moves
2499 erratically when hidden rows or columns are present
2502 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2503 Structure Viewer's colour menu don't correspond to
2507 <!-- JAL-2405 -->Protein specific colours only offered in
2508 colour and group colour menu for protein alignments
2511 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2512 reflect currently selected view or group's shading
2516 <!-- JAL-2624 -->Feature colour thresholds not respected
2517 when rendered on overview and structures when opacity at
2521 <!-- JAL-2589 -->User defined gap colour not shown in
2522 overview when features overlaid on alignment
2525 <!-- JAL-2567 -->Feature settings for different views not
2526 recovered correctly from Jalview project file
2529 <!-- JAL-2256 -->Feature colours in overview when first
2530 opened (automatically via preferences) are different to
2531 the main alignment panel
2534 <em>Data import/export</em>
2537 <!-- JAL-2576 -->Very large alignments take a long time to
2541 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2542 added after a sequence was imported are not written to
2546 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2547 when importing RNA secondary structure via Stockholm
2550 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2551 not shown in correct direction for simple pseudoknots
2554 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2555 with lightGray or darkGray via features file (but can
2559 <!-- JAL-2383 -->Above PID colour threshold not recovered
2560 when alignment view imported from project
2563 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2564 structure and sequences extracted from structure files
2565 imported via URL and viewed in Jmol
2568 <!-- JAL-2520 -->Structures loaded via URL are saved in
2569 Jalview Projects rather than fetched via URL again when
2570 the project is loaded and the structure viewed
2573 <em>Web Services</em>
2576 <!-- JAL-2519 -->EnsemblGenomes example failing after
2577 release of Ensembl v.88
2580 <!-- JAL-2366 -->Proxy server address and port always
2581 appear enabled in Preferences->Connections
2584 <!-- JAL-2461 -->DAS registry not found exceptions
2585 removed from console output
2588 <!-- JAL-2582 -->Cannot retrieve protein products from
2589 Ensembl by Peptide ID
2592 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2593 created from SIFTs, and spurious 'Couldn't open structure
2594 in Chimera' errors raised after April 2017 update (problem
2595 due to 'null' string rather than empty string used for
2596 residues with no corresponding PDB mapping).
2599 <em>Application UI</em>
2602 <!-- JAL-2361 -->User Defined Colours not added to Colour
2606 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2607 case' residues (button in colourscheme editor debugged and
2608 new documentation and tooltips added)
2611 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2612 doesn't restore group-specific text colour thresholds
2615 <!-- JAL-2243 -->Feature settings panel does not update as
2616 new features are added to alignment
2619 <!-- JAL-2532 -->Cancel in feature settings reverts
2620 changes to feature colours via the Amend features dialog
2623 <!-- JAL-2506 -->Null pointer exception when attempting to
2624 edit graduated feature colour via amend features dialog
2628 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2629 selection menu changes colours of alignment views
2632 <!-- JAL-2426 -->Spurious exceptions in console raised
2633 from alignment calculation workers after alignment has
2637 <!-- JAL-1608 -->Typo in selection popup menu - Create
2638 groups now 'Create Group'
2641 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2642 Create/Undefine group doesn't always work
2645 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2646 shown again after pressing 'Cancel'
2649 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2650 adjusts start position in wrap mode
2653 <!-- JAL-2563 -->Status bar doesn't show positions for
2654 ambiguous amino acids
2657 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2658 CDS/Protein view after CDS sequences added for aligned
2662 <!-- JAL-2592 -->User defined colourschemes called 'User
2663 Defined' don't appear in Colours menu
2669 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2670 score models doesn't always result in an updated PCA plot
2673 <!-- JAL-2442 -->Features not rendered as transparent on
2674 overview or linked structure view
2677 <!-- JAL-2372 -->Colour group by conservation doesn't
2681 <!-- JAL-2517 -->Hitting Cancel after applying
2682 user-defined colourscheme doesn't restore original
2689 <!-- JAL-2314 -->Unit test failure:
2690 jalview.ws.jabaws.RNAStructExportImport setup fails
2693 <!-- JAL-2307 -->Unit test failure:
2694 jalview.ws.sifts.SiftsClientTest due to compatibility
2695 problems with deep array comparison equality asserts in
2696 successive versions of TestNG
2699 <!-- JAL-2479 -->Relocated StructureChooserTest and
2700 ParameterUtilsTest Unit tests to Network suite
2703 <em>New Known Issues</em>
2706 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2707 phase after a sequence motif find operation
2710 <!-- JAL-2550 -->Importing annotation file with rows
2711 containing just upper and lower case letters are
2712 interpreted as WUSS RNA secondary structure symbols
2715 <!-- JAL-2590 -->Cannot load and display Newick trees
2716 reliably from eggnog Ortholog database
2719 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2720 containing features of type Highlight' when 'B' is pressed
2721 to mark columns containing highlighted regions.
2724 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2725 doesn't always add secondary structure annotation.
2730 <td width="60" nowrap>
2731 <div align="center">
2732 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2735 <td><div align="left">
2739 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2740 for all consensus calculations
2743 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2746 <li>Updated Jalview's Certum code signing certificate
2749 <em>Application</em>
2752 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2753 set of database cross-references, sorted alphabetically
2756 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2757 from database cross references. Users with custom links
2758 will receive a <a href="webServices/urllinks.html#warning">warning
2759 dialog</a> asking them to update their preferences.
2762 <!-- JAL-2287-->Cancel button and escape listener on
2763 dialog warning user about disconnecting Jalview from a
2767 <!-- JAL-2320-->Jalview's Chimera control window closes if
2768 the Chimera it is connected to is shut down
2771 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2772 columns menu item to mark columns containing highlighted
2773 regions (e.g. from structure selections or results of a
2777 <!-- JAL-2284-->Command line option for batch-generation
2778 of HTML pages rendering alignment data with the BioJS
2788 <!-- JAL-2286 -->Columns with more than one modal residue
2789 are not coloured or thresholded according to percent
2790 identity (first observed in Jalview 2.8.2)
2793 <!-- JAL-2301 -->Threonine incorrectly reported as not
2797 <!-- JAL-2318 -->Updates to documentation pages (above PID
2798 threshold, amino acid properties)
2801 <!-- JAL-2292 -->Lower case residues in sequences are not
2802 reported as mapped to residues in a structure file in the
2806 <!--JAL-2324 -->Identical features with non-numeric scores
2807 could be added multiple times to a sequence
2810 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2811 bond features shown as two highlighted residues rather
2812 than a range in linked structure views, and treated
2813 correctly when selecting and computing trees from features
2816 <!-- JAL-2281-->Custom URL links for database
2817 cross-references are matched to database name regardless
2822 <em>Application</em>
2825 <!-- JAL-2282-->Custom URL links for specific database
2826 names without regular expressions also offer links from
2830 <!-- JAL-2315-->Removing a single configured link in the
2831 URL links pane in Connections preferences doesn't actually
2832 update Jalview configuration
2835 <!-- JAL-2272-->CTRL-Click on a selected region to open
2836 the alignment area popup menu doesn't work on El-Capitan
2839 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2840 files with similarly named sequences if dropped onto the
2844 <!-- JAL-2312 -->Additional mappings are shown for PDB
2845 entries where more chains exist in the PDB accession than
2846 are reported in the SIFTS file
2849 <!-- JAL-2317-->Certain structures do not get mapped to
2850 the structure view when displayed with Chimera
2853 <!-- JAL-2317-->No chains shown in the Chimera view
2854 panel's View->Show Chains submenu
2857 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2858 work for wrapped alignment views
2861 <!--JAL-2197 -->Rename UI components for running JPred
2862 predictions from 'JNet' to 'JPred'
2865 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2866 corrupted when annotation panel vertical scroll is not at
2867 first annotation row
2870 <!--JAL-2332 -->Attempting to view structure for Hen
2871 lysozyme results in a PDB Client error dialog box
2874 <!-- JAL-2319 -->Structure View's mapping report switched
2875 ranges for PDB and sequence for SIFTS
2878 SIFTS 'Not_Observed' residues mapped to non-existant
2882 <!-- <em>New Known Issues</em>
2889 <td width="60" nowrap>
2890 <div align="center">
2891 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2892 <em>25/10/2016</em></strong>
2895 <td><em>Application</em>
2897 <li>3D Structure chooser opens with 'Cached structures'
2898 view if structures already loaded</li>
2899 <li>Progress bar reports models as they are loaded to
2900 structure views</li>
2906 <li>Colour by conservation always enabled and no tick
2907 shown in menu when BLOSUM or PID shading applied</li>
2908 <li>FER1_ARATH and FER2_ARATH labels were switched in
2909 example sequences/projects/trees</li>
2911 <em>Application</em>
2913 <li>Jalview projects with views of local PDB structure
2914 files saved on Windows cannot be opened on OSX</li>
2915 <li>Multiple structure views can be opened and superposed
2916 without timeout for structures with multiple models or
2917 multiple sequences in alignment</li>
2918 <li>Cannot import or associated local PDB files without a
2919 PDB ID HEADER line</li>
2920 <li>RMSD is not output in Jmol console when superposition
2922 <li>Drag and drop of URL from Browser fails for Linux and
2923 OSX versions earlier than El Capitan</li>
2924 <li>ENA client ignores invalid content from ENA server</li>
2925 <li>Exceptions are not raised in console when ENA client
2926 attempts to fetch non-existent IDs via Fetch DB Refs UI
2928 <li>Exceptions are not raised in console when a new view
2929 is created on the alignment</li>
2930 <li>OSX right-click fixed for group selections: CMD-click
2931 to insert/remove gaps in groups and CTRL-click to open group
2934 <em>Build and deployment</em>
2936 <li>URL link checker now copes with multi-line anchor
2939 <em>New Known Issues</em>
2941 <li>Drag and drop from URL links in browsers do not work
2948 <td width="60" nowrap>
2949 <div align="center">
2950 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2953 <td><em>General</em>
2956 <!-- JAL-2124 -->Updated Spanish translations.
2959 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2960 for importing structure data to Jalview. Enables mmCIF and
2964 <!-- JAL-192 --->Alignment ruler shows positions relative to
2968 <!-- JAL-2202 -->Position/residue shown in status bar when
2969 mousing over sequence associated annotation
2972 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2976 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2977 '()', canonical '[]' and invalid '{}' base pair populations
2981 <!-- JAL-2092 -->Feature settings popup menu options for
2982 showing or hiding columns containing a feature
2985 <!-- JAL-1557 -->Edit selected group by double clicking on
2986 group and sequence associated annotation labels
2989 <!-- JAL-2236 -->Sequence name added to annotation label in
2990 select/hide columns by annotation and colour by annotation
2994 </ul> <em>Application</em>
2997 <!-- JAL-2050-->Automatically hide introns when opening a
2998 gene/transcript view
3001 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
3005 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
3006 structure mappings with the EMBL-EBI PDBe SIFTS database
3009 <!-- JAL-2079 -->Updated download sites used for Rfam and
3010 Pfam sources to xfam.org
3013 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
3016 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
3017 over sequences in Jalview
3020 <!-- JAL-2027-->Support for reverse-complement coding
3021 regions in ENA and EMBL
3024 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
3025 for record retrieval via ENA rest API
3028 <!-- JAL-2027 -->Support for ENA CDS records with reverse
3032 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
3033 groovy script execution
3036 <!-- JAL-1812 -->New 'execute Groovy script' option in an
3037 alignment window's Calculate menu
3040 <!-- JAL-1812 -->Allow groovy scripts that call
3041 Jalview.getAlignFrames() to run in headless mode
3044 <!-- JAL-2068 -->Support for creating new alignment
3045 calculation workers from groovy scripts
3048 <!-- JAL-1369 --->Store/restore reference sequence in
3052 <!-- JAL-1803 -->Chain codes for a sequence's PDB
3053 associations are now saved/restored from project
3056 <!-- JAL-1993 -->Database selection dialog always shown
3057 before sequence fetcher is opened
3060 <!-- JAL-2183 -->Double click on an entry in Jalview's
3061 database chooser opens a sequence fetcher
3064 <!-- JAL-1563 -->Free-text search client for UniProt using
3065 the UniProt REST API
3068 <!-- JAL-2168 -->-nonews command line parameter to prevent
3069 the news reader opening
3072 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
3073 querying stored in preferences
3076 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
3080 <!-- JAL-1977-->Tooltips shown on database chooser
3083 <!-- JAL-391 -->Reverse complement function in calculate
3084 menu for nucleotide sequences
3087 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
3088 and feature counts preserves alignment ordering (and
3089 debugged for complex feature sets).
3092 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
3093 viewing structures with Jalview 2.10
3096 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
3097 genome, transcript CCDS and gene ids via the Ensembl and
3098 Ensembl Genomes REST API
3101 <!-- JAL-2049 -->Protein sequence variant annotation
3102 computed for 'sequence_variant' annotation on CDS regions
3106 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
3110 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
3111 Ref Fetcher fails to match, or otherwise updates sequence
3112 data from external database records.
3115 <!-- JAL-2154 -->Revised Jalview Project format for
3116 efficient recovery of sequence coding and alignment
3117 annotation relationships.
3119 </ul> <!-- <em>Applet</em>
3130 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
3134 <!-- JAL-2018-->Export features in Jalview format (again)
3135 includes graduated colourschemes
3138 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
3139 working with big alignments and lots of hidden columns
3142 <!-- JAL-2053-->Hidden column markers not always rendered
3143 at right of alignment window
3146 <!-- JAL-2067 -->Tidied up links in help file table of
3150 <!-- JAL-2072 -->Feature based tree calculation not shown
3154 <!-- JAL-2075 -->Hidden columns ignored during feature
3155 based tree calculation
3158 <!-- JAL-2065 -->Alignment view stops updating when show
3159 unconserved enabled for group on alignment
3162 <!-- JAL-2086 -->Cannot insert gaps into sequence when
3166 <!-- JAL-2146 -->Alignment column in status incorrectly
3167 shown as "Sequence position" when mousing over
3171 <!-- JAL-2099 -->Incorrect column numbers in ruler when
3172 hidden columns present
3175 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
3176 user created annotation added to alignment
3179 <!-- JAL-1841 -->RNA Structure consensus only computed for
3180 '()' base pair annotation
3183 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
3184 in zero scores for all base pairs in RNA Structure
3188 <!-- JAL-2174-->Extend selection with columns containing
3192 <!-- JAL-2275 -->Pfam format writer puts extra space at
3193 beginning of sequence
3196 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
3200 <!-- JAL-2238 -->Cannot create groups on an alignment from
3201 from a tree when t-coffee scores are shown
3204 <!-- JAL-1836,1967 -->Cannot import and view PDB
3205 structures with chains containing negative resnums (4q4h)
3208 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
3212 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
3213 to Clustal, PIR and PileUp output
3216 <!-- JAL-2008 -->Reordering sequence features that are
3217 not visible causes alignment window to repaint
3220 <!-- JAL-2006 -->Threshold sliders don't work in
3221 graduated colour and colour by annotation row for e-value
3222 scores associated with features and annotation rows
3225 <!-- JAL-1797 -->amino acid physicochemical conservation
3226 calculation should be case independent
3229 <!-- JAL-2173 -->Remove annotation also updates hidden
3233 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
3234 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
3235 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
3238 <!-- JAL-2065 -->Null pointer exceptions and redraw
3239 problems when reference sequence defined and 'show
3240 non-conserved' enabled
3243 <!-- JAL-1306 -->Quality and Conservation are now shown on
3244 load even when Consensus calculation is disabled
3247 <!-- JAL-1932 -->Remove right on penultimate column of
3248 alignment does nothing
3251 <em>Application</em>
3254 <!-- JAL-1552-->URLs and links can't be imported by
3255 drag'n'drop on OSX when launched via webstart (note - not
3256 yet fixed for El Capitan)
3259 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
3260 output when running on non-gb/us i18n platforms
3263 <!-- JAL-1944 -->Error thrown when exporting a view with
3264 hidden sequences as flat-file alignment
3267 <!-- JAL-2030-->InstallAnywhere distribution fails when
3271 <!-- JAL-2080-->Jalview very slow to launch via webstart
3272 (also hotfix for 2.9.0b2)
3275 <!-- JAL-2085 -->Cannot save project when view has a
3276 reference sequence defined
3279 <!-- JAL-1011 -->Columns are suddenly selected in other
3280 alignments and views when revealing hidden columns
3283 <!-- JAL-1989 -->Hide columns not mirrored in complement
3284 view in a cDNA/Protein splitframe
3287 <!-- JAL-1369 -->Cannot save/restore representative
3288 sequence from project when only one sequence is
3292 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
3293 in Structure Chooser
3296 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
3297 structure consensus didn't refresh annotation panel
3300 <!-- JAL-1962 -->View mapping in structure view shows
3301 mappings between sequence and all chains in a PDB file
3304 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
3305 dialogs format columns correctly, don't display array
3306 data, sort columns according to type
3309 <!-- JAL-1975 -->Export complete shown after destination
3310 file chooser is cancelled during an image export
3313 <!-- JAL-2025 -->Error when querying PDB Service with
3314 sequence name containing special characters
3317 <!-- JAL-2024 -->Manual PDB structure querying should be
3321 <!-- JAL-2104 -->Large tooltips with broken HTML
3322 formatting don't wrap
3325 <!-- JAL-1128 -->Figures exported from wrapped view are
3326 truncated so L looks like I in consensus annotation
3329 <!-- JAL-2003 -->Export features should only export the
3330 currently displayed features for the current selection or
3334 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
3335 after fetching cross-references, and restoring from
3339 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
3340 followed in the structure viewer
3343 <!-- JAL-2163 -->Titles for individual alignments in
3344 splitframe not restored from project
3347 <!-- JAL-2145 -->missing autocalculated annotation at
3348 trailing end of protein alignment in transcript/product
3349 splitview when pad-gaps not enabled by default
3352 <!-- JAL-1797 -->amino acid physicochemical conservation
3356 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
3357 article has been read (reopened issue due to
3358 internationalisation problems)
3361 <!-- JAL-1960 -->Only offer PDB structures in structure
3362 viewer based on sequence name, PDB and UniProt
3367 <!-- JAL-1976 -->No progress bar shown during export of
3371 <!-- JAL-2213 -->Structures not always superimposed after
3372 multiple structures are shown for one or more sequences.
3375 <!-- JAL-1370 -->Reference sequence characters should not
3376 be replaced with '.' when 'Show unconserved' format option
3380 <!-- JAL-1823 -->Cannot specify chain code when entering
3381 specific PDB id for sequence
3384 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3385 'Export hidden sequences' is enabled, but 'export hidden
3386 columns' is disabled.
3389 <!--JAL-2026-->Best Quality option in structure chooser
3390 selects lowest rather than highest resolution structures
3394 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3395 to sequence mapping in 'View Mappings' report
3398 <!-- JAL-2284 -->Unable to read old Jalview projects that
3399 contain non-XML data added after Jalvew wrote project.
3402 <!-- JAL-2118 -->Newly created annotation row reorders
3403 after clicking on it to create new annotation for a
3407 <!-- JAL-1980 -->Null Pointer Exception raised when
3408 pressing Add on an orphaned cut'n'paste window.
3410 <!-- may exclude, this is an external service stability issue JAL-1941
3411 -- > RNA 3D structure not added via DSSR service</li> -->
3416 <!-- JAL-2151 -->Incorrect columns are selected when
3417 hidden columns present before start of sequence
3420 <!-- JAL-1986 -->Missing dependencies on applet pages
3424 <!-- JAL-1947 -->Overview pixel size changes when
3425 sequences are hidden in applet
3428 <!-- JAL-1996 -->Updated instructions for applet
3429 deployment on examples pages.
3436 <td width="60" nowrap>
3437 <div align="center">
3438 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3439 <em>16/10/2015</em></strong>
3442 <td><em>General</em>
3444 <li>Time stamps for signed Jalview application and applet
3449 <em>Application</em>
3451 <li>Duplicate group consensus and conservation rows
3452 shown when tree is partitioned</li>
3453 <li>Erratic behaviour when tree partitions made with
3454 multiple cDNA/Protein split views</li>
3460 <td width="60" nowrap>
3461 <div align="center">
3462 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3463 <em>8/10/2015</em></strong>
3466 <td><em>General</em>
3468 <li>Updated Spanish translations of localized text for
3470 </ul> <em>Application</em>
3472 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3473 <li>Signed OSX InstallAnywhere installer<br></li>
3474 <li>Support for per-sequence based annotations in BioJSON</li>
3475 </ul> <em>Applet</em>
3477 <li>Split frame example added to applet examples page</li>
3478 </ul> <em>Build and Deployment</em>
3481 <!-- JAL-1888 -->New ant target for running Jalview's test
3489 <li>Mapping of cDNA to protein in split frames
3490 incorrect when sequence start > 1</li>
3491 <li>Broken images in filter column by annotation dialog
3493 <li>Feature colours not parsed from features file</li>
3494 <li>Exceptions and incomplete link URLs recovered when
3495 loading a features file containing HTML tags in feature
3499 <em>Application</em>
3501 <li>Annotations corrupted after BioJS export and
3503 <li>Incorrect sequence limits after Fetch DB References
3504 with 'trim retrieved sequences'</li>
3505 <li>Incorrect warning about deleting all data when
3506 deleting selected columns</li>
3507 <li>Patch to build system for shipping properly signed
3508 JNLP templates for webstart launch</li>
3509 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3510 unreleased structures for download or viewing</li>
3511 <li>Tab/space/return keystroke operation of EMBL-PDBe
3512 fetcher/viewer dialogs works correctly</li>
3513 <li>Disabled 'minimise' button on Jalview windows
3514 running on OSX to workaround redraw hang bug</li>
3515 <li>Split cDNA/Protein view position and geometry not
3516 recovered from jalview project</li>
3517 <li>Initial enabled/disabled state of annotation menu
3518 sorter 'show autocalculated first/last' corresponds to
3520 <li>Restoring of Clustal, RNA Helices and T-Coffee
3521 color schemes from BioJSON</li>
3525 <li>Reorder sequences mirrored in cDNA/Protein split
3527 <li>Applet with Jmol examples not loading correctly</li>
3533 <td><div align="center">
3534 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3536 <td><em>General</em>
3538 <li>Linked visualisation and analysis of DNA and Protein
3541 <li>Translated cDNA alignments shown as split protein
3542 and DNA alignment views</li>
3543 <li>Codon consensus annotation for linked protein and
3544 cDNA alignment views</li>
3545 <li>Link cDNA or Protein product sequences by loading
3546 them onto Protein or cDNA alignments</li>
3547 <li>Reconstruct linked cDNA alignment from aligned
3548 protein sequences</li>
3551 <li>Jmol integration updated to Jmol v14.2.14</li>
3552 <li>Import and export of Jalview alignment views as <a
3553 href="features/bioJsonFormat.html">BioJSON</a></li>
3554 <li>New alignment annotation file statements for
3555 reference sequences and marking hidden columns</li>
3556 <li>Reference sequence based alignment shading to
3557 highlight variation</li>
3558 <li>Select or hide columns according to alignment
3560 <li>Find option for locating sequences by description</li>
3561 <li>Conserved physicochemical properties shown in amino
3562 acid conservation row</li>
3563 <li>Alignments can be sorted by number of RNA helices</li>
3564 </ul> <em>Application</em>
3566 <li>New cDNA/Protein analysis capabilities
3568 <li>Get Cross-References should open a Split Frame
3569 view with cDNA/Protein</li>
3570 <li>Detect when nucleotide sequences and protein
3571 sequences are placed in the same alignment</li>
3572 <li>Split cDNA/Protein views are saved in Jalview
3577 <li>Use REST API to talk to Chimera</li>
3578 <li>Selected regions in Chimera are highlighted in linked
3579 Jalview windows</li>
3581 <li>VARNA RNA viewer updated to v3.93</li>
3582 <li>VARNA views are saved in Jalview Projects</li>
3583 <li>Pseudoknots displayed as Jalview RNA annotation can
3584 be shown in VARNA</li>
3586 <li>Make groups for selection uses marked columns as well
3587 as the active selected region</li>
3589 <li>Calculate UPGMA and NJ trees using sequence feature
3591 <li>New Export options
3593 <li>New Export Settings dialog to control hidden
3594 region export in flat file generation</li>
3596 <li>Export alignment views for display with the <a
3597 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3599 <li>Export scrollable SVG in HTML page</li>
3600 <li>Optional embedding of BioJSON data when exporting
3601 alignment figures to HTML</li>
3603 <li>3D structure retrieval and display
3605 <li>Free text and structured queries with the PDBe
3607 <li>PDBe Search API based discovery and selection of
3608 PDB structures for a sequence set</li>
3612 <li>JPred4 employed for protein secondary structure
3614 <li>Hide Insertions menu option to hide unaligned columns
3615 for one or a group of sequences</li>
3616 <li>Automatically hide insertions in alignments imported
3617 from the JPred4 web server</li>
3618 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3619 system on OSX<br />LGPL libraries courtesy of <a
3620 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3622 <li>changed 'View nucleotide structure' submenu to 'View
3623 VARNA 2D Structure'</li>
3624 <li>change "View protein structure" menu option to "3D
3627 </ul> <em>Applet</em>
3629 <li>New layout for applet example pages</li>
3630 <li>New parameters to enable SplitFrame view
3631 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3632 <li>New example demonstrating linked viewing of cDNA and
3633 Protein alignments</li>
3634 </ul> <em>Development and deployment</em>
3636 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3637 <li>Include installation type and git revision in build
3638 properties and console log output</li>
3639 <li>Jalview Github organisation, and new github site for
3640 storing BioJsMSA Templates</li>
3641 <li>Jalview's unit tests now managed with TestNG</li>
3644 <!-- <em>General</em>
3646 </ul> --> <!-- issues resolved --> <em>Application</em>
3648 <li>Escape should close any open find dialogs</li>
3649 <li>Typo in select-by-features status report</li>
3650 <li>Consensus RNA secondary secondary structure
3651 predictions are not highlighted in amber</li>
3652 <li>Missing gap character in v2.7 example file means
3653 alignment appears unaligned when pad-gaps is not enabled</li>
3654 <li>First switch to RNA Helices colouring doesn't colour
3655 associated structure views</li>
3656 <li>ID width preference option is greyed out when auto
3657 width checkbox not enabled</li>
3658 <li>Stopped a warning dialog from being shown when
3659 creating user defined colours</li>
3660 <li>'View Mapping' in structure viewer shows sequence
3661 mappings for just that viewer's sequences</li>
3662 <li>Workaround for superposing PDB files containing
3663 multiple models in Chimera</li>
3664 <li>Report sequence position in status bar when hovering
3665 over Jmol structure</li>
3666 <li>Cannot output gaps as '.' symbols with Selection ->
3667 output to text box</li>
3668 <li>Flat file exports of alignments with hidden columns
3669 have incorrect sequence start/end</li>
3670 <li>'Aligning' a second chain to a Chimera structure from
3672 <li>Colour schemes applied to structure viewers don't
3673 work for nucleotide</li>
3674 <li>Loading/cut'n'pasting an empty or invalid file leads
3675 to a grey/invisible alignment window</li>
3676 <li>Exported Jpred annotation from a sequence region
3677 imports to different position</li>
3678 <li>Space at beginning of sequence feature tooltips shown
3679 on some platforms</li>
3680 <li>Chimera viewer 'View | Show Chain' menu is not
3682 <li>'New View' fails with a Null Pointer Exception in
3683 console if Chimera has been opened</li>
3684 <li>Mouseover to Chimera not working</li>
3685 <li>Miscellaneous ENA XML feature qualifiers not
3687 <li>NPE in annotation renderer after 'Extract Scores'</li>
3688 <li>If two structures in one Chimera window, mouseover of
3689 either sequence shows on first structure</li>
3690 <li>'Show annotations' options should not make
3691 non-positional annotations visible</li>
3692 <li>Subsequence secondary structure annotation not shown
3693 in right place after 'view flanking regions'</li>
3694 <li>File Save As type unset when current file format is
3696 <li>Save as '.jar' option removed for saving Jalview
3698 <li>Colour by Sequence colouring in Chimera more
3700 <li>Cannot 'add reference annotation' for a sequence in
3701 several views on same alignment</li>
3702 <li>Cannot show linked products for EMBL / ENA records</li>
3703 <li>Jalview's tooltip wraps long texts containing no
3705 </ul> <em>Applet</em>
3707 <li>Jmol to JalviewLite mouseover/link not working</li>
3708 <li>JalviewLite can't import sequences with ID
3709 descriptions containing angle brackets</li>
3710 </ul> <em>General</em>
3712 <li>Cannot export and reimport RNA secondary structure
3713 via jalview annotation file</li>
3714 <li>Random helix colour palette for colour by annotation
3715 with RNA secondary structure</li>
3716 <li>Mouseover to cDNA from STOP residue in protein
3717 translation doesn't work.</li>
3718 <li>hints when using the select by annotation dialog box</li>
3719 <li>Jmol alignment incorrect if PDB file has alternate CA
3721 <li>FontChooser message dialog appears to hang after
3722 choosing 1pt font</li>
3723 <li>Peptide secondary structure incorrectly imported from
3724 annotation file when annotation display text includes 'e' or
3726 <li>Cannot set colour of new feature type whilst creating
3728 <li>cDNA translation alignment should not be sequence
3729 order dependent</li>
3730 <li>'Show unconserved' doesn't work for lower case
3732 <li>Nucleotide ambiguity codes involving R not recognised</li>
3733 </ul> <em>Deployment and Documentation</em>
3735 <li>Applet example pages appear different to the rest of
3736 www.jalview.org</li>
3737 </ul> <em>Application Known issues</em>
3739 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3740 <li>Misleading message appears after trying to delete
3742 <li>Jalview icon not shown in dock after InstallAnywhere
3743 version launches</li>
3744 <li>Fetching EMBL reference for an RNA sequence results
3745 fails with a sequence mismatch</li>
3746 <li>Corrupted or unreadable alignment display when
3747 scrolling alignment to right</li>
3748 <li>ArrayIndexOutOfBoundsException thrown when remove
3749 empty columns called on alignment with ragged gapped ends</li>
3750 <li>auto calculated alignment annotation rows do not get
3751 placed above or below non-autocalculated rows</li>
3752 <li>Jalview dekstop becomes sluggish at full screen in
3753 ultra-high resolution</li>
3754 <li>Cannot disable consensus calculation independently of
3755 quality and conservation</li>
3756 <li>Mouseover highlighting between cDNA and protein can
3757 become sluggish with more than one splitframe shown</li>
3758 </ul> <em>Applet Known Issues</em>
3760 <li>Core PDB parsing code requires Jmol</li>
3761 <li>Sequence canvas panel goes white when alignment
3762 window is being resized</li>
3768 <td><div align="center">
3769 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3771 <td><em>General</em>
3773 <li>Updated Java code signing certificate donated by
3775 <li>Features and annotation preserved when performing
3776 pairwise alignment</li>
3777 <li>RNA pseudoknot annotation can be
3778 imported/exported/displayed</li>
3779 <li>'colour by annotation' can colour by RNA and
3780 protein secondary structure</li>
3781 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3782 post-hoc with 2.9 release</em>)
3785 </ul> <em>Application</em>
3787 <li>Extract and display secondary structure for sequences
3788 with 3D structures</li>
3789 <li>Support for parsing RNAML</li>
3790 <li>Annotations menu for layout
3792 <li>sort sequence annotation rows by alignment</li>
3793 <li>place sequence annotation above/below alignment
3796 <li>Output in Stockholm format</li>
3797 <li>Internationalisation: improved Spanish (es)
3799 <li>Structure viewer preferences tab</li>
3800 <li>Disorder and Secondary Structure annotation tracks
3801 shared between alignments</li>
3802 <li>UCSF Chimera launch and linked highlighting from
3804 <li>Show/hide all sequence associated annotation rows for
3805 all or current selection</li>
3806 <li>disorder and secondary structure predictions
3807 available as dataset annotation</li>
3808 <li>Per-sequence rna helices colouring</li>
3811 <li>Sequence database accessions imported when fetching
3812 alignments from Rfam</li>
3813 <li>update VARNA version to 3.91</li>
3815 <li>New groovy scripts for exporting aligned positions,
3816 conservation values, and calculating sum of pairs scores.</li>
3817 <li>Command line argument to set default JABAWS server</li>
3818 <li>include installation type in build properties and
3819 console log output</li>
3820 <li>Updated Jalview project format to preserve dataset
3824 <!-- issues resolved --> <em>Application</em>
3826 <li>Distinguish alignment and sequence associated RNA
3827 structure in structure->view->VARNA</li>
3828 <li>Raise dialog box if user deletes all sequences in an
3830 <li>Pressing F1 results in documentation opening twice</li>
3831 <li>Sequence feature tooltip is wrapped</li>
3832 <li>Double click on sequence associated annotation
3833 selects only first column</li>
3834 <li>Redundancy removal doesn't result in unlinked
3835 leaves shown in tree</li>
3836 <li>Undos after several redundancy removals don't undo
3838 <li>Hide sequence doesn't hide associated annotation</li>
3839 <li>User defined colours dialog box too big to fit on
3840 screen and buttons not visible</li>
3841 <li>author list isn't updated if already written to
3842 Jalview properties</li>
3843 <li>Popup menu won't open after retrieving sequence
3845 <li>File open window for associate PDB doesn't open</li>
3846 <li>Left-then-right click on a sequence id opens a
3847 browser search window</li>
3848 <li>Cannot open sequence feature shading/sort popup menu
3849 in feature settings dialog</li>
3850 <li>better tooltip placement for some areas of Jalview
3852 <li>Allow addition of JABAWS Server which doesn't
3853 pass validation</li>
3854 <li>Web services parameters dialog box is too large to
3856 <li>Muscle nucleotide alignment preset obscured by
3858 <li>JABAWS preset submenus don't contain newly
3859 defined user preset</li>
3860 <li>MSA web services warns user if they were launched
3861 with invalid input</li>
3862 <li>Jalview cannot contact DAS Registy when running on
3865 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3866 'Superpose with' submenu not shown when new view
3870 </ul> <!-- <em>Applet</em>
3872 </ul> <em>General</em>
3874 </ul>--> <em>Deployment and Documentation</em>
3876 <li>2G and 1G options in launchApp have no effect on
3877 memory allocation</li>
3878 <li>launchApp service doesn't automatically open
3879 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3881 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3882 InstallAnywhere reports cannot find valid JVM when Java
3883 1.7_055 is available
3885 </ul> <em>Application Known issues</em>
3888 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3889 corrupted or unreadable alignment display when scrolling
3893 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3894 retrieval fails but progress bar continues for DAS retrieval
3895 with large number of ID
3898 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3899 flatfile output of visible region has incorrect sequence
3903 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3904 rna structure consensus doesn't update when secondary
3905 structure tracks are rearranged
3908 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3909 invalid rna structure positional highlighting does not
3910 highlight position of invalid base pairs
3913 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3914 out of memory errors are not raised when saving Jalview
3915 project from alignment window file menu
3918 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3919 Switching to RNA Helices colouring doesn't propagate to
3923 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3924 colour by RNA Helices not enabled when user created
3925 annotation added to alignment
3928 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3929 Jalview icon not shown on dock in Mountain Lion/Webstart
3931 </ul> <em>Applet Known Issues</em>
3934 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3935 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3938 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3939 Jalview and Jmol example not compatible with IE9
3942 <li>Sort by annotation score doesn't reverse order
3948 <td><div align="center">
3949 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3952 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3955 <li>Internationalisation of user interface (usually
3956 called i18n support) and translation for Spanish locale</li>
3957 <li>Define/Undefine group on current selection with
3958 Ctrl-G/Shift Ctrl-G</li>
3959 <li>Improved group creation/removal options in
3960 alignment/sequence Popup menu</li>
3961 <li>Sensible precision for symbol distribution
3962 percentages shown in logo tooltip.</li>
3963 <li>Annotation panel height set according to amount of
3964 annotation when alignment first opened</li>
3965 </ul> <em>Application</em>
3967 <li>Interactive consensus RNA secondary structure
3968 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3969 <li>Select columns containing particular features from
3970 Feature Settings dialog</li>
3971 <li>View all 'representative' PDB structures for selected
3973 <li>Update Jalview project format:
3975 <li>New file extension for Jalview projects '.jvp'</li>
3976 <li>Preserve sequence and annotation dataset (to
3977 store secondary structure annotation,etc)</li>
3978 <li>Per group and alignment annotation and RNA helix
3982 <li>New similarity measures for PCA and Tree calculation
3984 <li>Experimental support for retrieval and viewing of
3985 flanking regions for an alignment</li>
3989 <!-- issues resolved --> <em>Application</em>
3991 <li>logo keeps spinning and status remains at queued or
3992 running after job is cancelled</li>
3993 <li>cannot export features from alignments imported from
3994 Jalview/VAMSAS projects</li>
3995 <li>Buggy slider for web service parameters that take
3997 <li>Newly created RNA secondary structure line doesn't
3998 have 'display all symbols' flag set</li>
3999 <li>T-COFFEE alignment score shading scheme and other
4000 annotation shading not saved in Jalview project</li>
4001 <li>Local file cannot be loaded in freshly downloaded
4003 <li>Jalview icon not shown on dock in Mountain
4005 <li>Load file from desktop file browser fails</li>
4006 <li>Occasional NPE thrown when calculating large trees</li>
4007 <li>Cannot reorder or slide sequences after dragging an
4008 alignment onto desktop</li>
4009 <li>Colour by annotation dialog throws NPE after using
4010 'extract scores' function</li>
4011 <li>Loading/cut'n'pasting an empty file leads to a grey
4012 alignment window</li>
4013 <li>Disorder thresholds rendered incorrectly after
4014 performing IUPred disorder prediction</li>
4015 <li>Multiple group annotated consensus rows shown when
4016 changing 'normalise logo' display setting</li>
4017 <li>Find shows blank dialog after 'finished searching' if
4018 nothing matches query</li>
4019 <li>Null Pointer Exceptions raised when sorting by
4020 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
4022 <li>Errors in Jmol console when structures in alignment
4023 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
4025 <li>Not all working JABAWS services are shown in
4027 <li>JAVAWS version of Jalview fails to launch with
4028 'invalid literal/length code'</li>
4029 <li>Annotation/RNA Helix colourschemes cannot be applied
4030 to alignment with groups (actually fixed in 2.8.0b1)</li>
4031 <li>RNA Helices and T-Coffee Scores available as default
4034 </ul> <em>Applet</em>
4036 <li>Remove group option is shown even when selection is
4038 <li>Apply to all groups ticked but colourscheme changes
4039 don't affect groups</li>
4040 <li>Documented RNA Helices and T-Coffee Scores as valid
4041 colourscheme name</li>
4042 <li>Annotation labels drawn on sequence IDs when
4043 Annotation panel is not displayed</li>
4044 <li>Increased font size for dropdown menus on OSX and
4045 embedded windows</li>
4046 </ul> <em>Other</em>
4048 <li>Consensus sequence for alignments/groups with a
4049 single sequence were not calculated</li>
4050 <li>annotation files that contain only groups imported as
4051 annotation and junk sequences</li>
4052 <li>Fasta files with sequences containing '*' incorrectly
4053 recognised as PFAM or BLC</li>
4054 <li>conservation/PID slider apply all groups option
4055 doesn't affect background (2.8.0b1)
4057 <li>redundancy highlighting is erratic at 0% and 100%</li>
4058 <li>Remove gapped columns fails for sequences with ragged
4060 <li>AMSA annotation row with leading spaces is not
4061 registered correctly on import</li>
4062 <li>Jalview crashes when selecting PCA analysis for
4063 certain alignments</li>
4064 <li>Opening the colour by annotation dialog for an
4065 existing annotation based 'use original colours'
4066 colourscheme loses original colours setting</li>
4071 <td><div align="center">
4072 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
4073 <em>30/1/2014</em></strong>
4077 <li>Trusted certificates for JalviewLite applet and
4078 Jalview Desktop application<br />Certificate was donated by
4079 <a href="https://www.certum.eu">Certum</a> to the Jalview
4080 open source project).
4082 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
4083 <li>Output in Stockholm format</li>
4084 <li>Allow import of data from gzipped files</li>
4085 <li>Export/import group and sequence associated line
4086 graph thresholds</li>
4087 <li>Nucleotide substitution matrix that supports RNA and
4088 ambiguity codes</li>
4089 <li>Allow disorder predictions to be made on the current
4090 selection (or visible selection) in the same way that JPred
4092 <li>Groovy scripting for headless Jalview operation</li>
4093 </ul> <em>Other improvements</em>
4095 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
4096 <li>COMBINE statement uses current SEQUENCE_REF and
4097 GROUP_REF scope to group annotation rows</li>
4098 <li>Support '' style escaping of quotes in Newick
4100 <li>Group options for JABAWS service by command line name</li>
4101 <li>Empty tooltip shown for JABA service options with a
4102 link but no description</li>
4103 <li>Select primary source when selecting authority in
4104 database fetcher GUI</li>
4105 <li>Add .mfa to FASTA file extensions recognised by
4107 <li>Annotation label tooltip text wrap</li>
4112 <li>Slow scrolling when lots of annotation rows are
4114 <li>Lots of NPE (and slowness) after creating RNA
4115 secondary structure annotation line</li>
4116 <li>Sequence database accessions not imported when
4117 fetching alignments from Rfam</li>
4118 <li>Incorrect SHMR submission for sequences with
4120 <li>View all structures does not always superpose
4122 <li>Option widgets in service parameters not updated to
4123 reflect user or preset settings</li>
4124 <li>Null pointer exceptions for some services without
4125 presets or adjustable parameters</li>
4126 <li>Discover PDB IDs entry in structure menu doesn't
4127 discover PDB xRefs</li>
4128 <li>Exception encountered while trying to retrieve
4129 features with DAS</li>
4130 <li>Lowest value in annotation row isn't coloured
4131 when colour by annotation (per sequence) is coloured</li>
4132 <li>Keyboard mode P jumps to start of gapped region when
4133 residue follows a gap</li>
4134 <li>Jalview appears to hang importing an alignment with
4135 Wrap as default or after enabling Wrap</li>
4136 <li>'Right click to add annotations' message
4137 shown in wrap mode when no annotations present</li>
4138 <li>Disorder predictions fail with NPE if no automatic
4139 annotation already exists on alignment</li>
4140 <li>oninit javascript function should be called after
4141 initialisation completes</li>
4142 <li>Remove redundancy after disorder prediction corrupts
4143 alignment window display</li>
4144 <li>Example annotation file in documentation is invalid</li>
4145 <li>Grouped line graph annotation rows are not exported
4146 to annotation file</li>
4147 <li>Multi-harmony analysis cannot be run when only two
4149 <li>Cannot create multiple groups of line graphs with
4150 several 'combine' statements in annotation file</li>
4151 <li>Pressing return several times causes Number Format
4152 exceptions in keyboard mode</li>
4153 <li>Multi-harmony (SHMMR) method doesn't submit
4154 correct partitions for input data</li>
4155 <li>Translation from DNA to Amino Acids fails</li>
4156 <li>Jalview fail to load newick tree with quoted label</li>
4157 <li>--headless flag isn't understood</li>
4158 <li>ClassCastException when generating EPS in headless
4160 <li>Adjusting sequence-associated shading threshold only
4161 changes one row's threshold</li>
4162 <li>Preferences and Feature settings panel panel
4163 doesn't open</li>
4164 <li>hide consensus histogram also hides conservation and
4165 quality histograms</li>
4170 <td><div align="center">
4171 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
4173 <td><em>Application</em>
4175 <li>Support for JABAWS 2.0 Services (AACon alignment
4176 conservation, protein disorder and Clustal Omega)</li>
4177 <li>JABAWS server status indicator in Web Services
4179 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
4180 in Jalview alignment window</li>
4181 <li>Updated Jalview build and deploy framework for OSX
4182 mountain lion, windows 7, and 8</li>
4183 <li>Nucleotide substitution matrix for PCA that supports
4184 RNA and ambiguity codes</li>
4186 <li>Improved sequence database retrieval GUI</li>
4187 <li>Support fetching and database reference look up
4188 against multiple DAS sources (Fetch all from in 'fetch db
4190 <li>Jalview project improvements
4192 <li>Store and retrieve the 'belowAlignment'
4193 flag for annotation</li>
4194 <li>calcId attribute to group annotation rows on the
4196 <li>Store AACon calculation settings for a view in
4197 Jalview project</li>
4201 <li>horizontal scrolling gesture support</li>
4202 <li>Visual progress indicator when PCA calculation is
4204 <li>Simpler JABA web services menus</li>
4205 <li>visual indication that web service results are still
4206 being retrieved from server</li>
4207 <li>Serialise the dialogs that are shown when Jalview
4208 starts up for first time</li>
4209 <li>Jalview user agent string for interacting with HTTP
4211 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
4213 <li>Examples directory and Groovy library included in
4214 InstallAnywhere distribution</li>
4215 </ul> <em>Applet</em>
4217 <li>RNA alignment and secondary structure annotation
4218 visualization applet example</li>
4219 </ul> <em>General</em>
4221 <li>Normalise option for consensus sequence logo</li>
4222 <li>Reset button in PCA window to return dimensions to
4224 <li>Allow seqspace or Jalview variant of alignment PCA
4226 <li>PCA with either nucleic acid and protein substitution
4228 <li>Allow windows containing HTML reports to be exported
4230 <li>Interactive display and editing of RNA secondary
4231 structure contacts</li>
4232 <li>RNA Helix Alignment Colouring</li>
4233 <li>RNA base pair logo consensus</li>
4234 <li>Parse sequence associated secondary structure
4235 information in Stockholm files</li>
4236 <li>HTML Export database accessions and annotation
4237 information presented in tooltip for sequences</li>
4238 <li>Import secondary structure from LOCARNA clustalw
4239 style RNA alignment files</li>
4240 <li>import and visualise T-COFFEE quality scores for an
4242 <li>'colour by annotation' per sequence option to
4243 shade each sequence according to its associated alignment
4245 <li>New Jalview Logo</li>
4246 </ul> <em>Documentation and Development</em>
4248 <li>documentation for score matrices used in Jalview</li>
4249 <li>New Website!</li>
4251 <td><em>Application</em>
4253 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
4254 wsdbfetch REST service</li>
4255 <li>Stop windows being moved outside desktop on OSX</li>
4256 <li>Filetype associations not installed for webstart
4258 <li>Jalview does not always retrieve progress of a JABAWS
4259 job execution in full once it is complete</li>
4260 <li>revise SHMR RSBS definition to ensure alignment is
4261 uploaded via ali_file parameter</li>
4262 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
4263 <li>View all structures superposed fails with exception</li>
4264 <li>Jnet job queues forever if a very short sequence is
4265 submitted for prediction</li>
4266 <li>Cut and paste menu not opened when mouse clicked on
4268 <li>Putting fractional value into integer text box in
4269 alignment parameter dialog causes Jalview to hang</li>
4270 <li>Structure view highlighting doesn't work on
4272 <li>View all structures fails with exception shown in
4274 <li>Characters in filename associated with PDBEntry not
4275 escaped in a platform independent way</li>
4276 <li>Jalview desktop fails to launch with exception when
4278 <li>Tree calculation reports 'you must have 2 or more
4279 sequences selected' when selection is empty</li>
4280 <li>Jalview desktop fails to launch with jar signature
4281 failure when java web start temporary file caching is
4283 <li>DAS Sequence retrieval with range qualification
4284 results in sequence xref which includes range qualification</li>
4285 <li>Errors during processing of command line arguments
4286 cause progress bar (JAL-898) to be removed</li>
4287 <li>Replace comma for semi-colon option not disabled for
4288 DAS sources in sequence fetcher</li>
4289 <li>Cannot close news reader when JABAWS server warning
4290 dialog is shown</li>
4291 <li>Option widgets not updated to reflect user settings</li>
4292 <li>Edited sequence not submitted to web service</li>
4293 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
4294 <li>InstallAnywhere installer doesn't unpack and run
4295 on OSX Mountain Lion</li>
4296 <li>Annotation panel not given a scroll bar when
4297 sequences with alignment annotation are pasted into the
4299 <li>Sequence associated annotation rows not associated
4300 when loaded from Jalview project</li>
4301 <li>Browser launch fails with NPE on java 1.7</li>
4302 <li>JABAWS alignment marked as finished when job was
4303 cancelled or job failed due to invalid input</li>
4304 <li>NPE with v2.7 example when clicking on Tree
4305 associated with all views</li>
4306 <li>Exceptions when copy/paste sequences with grouped
4307 annotation rows to new window</li>
4308 </ul> <em>Applet</em>
4310 <li>Sequence features are momentarily displayed before
4311 they are hidden using hidefeaturegroups applet parameter</li>
4312 <li>loading features via javascript API automatically
4313 enables feature display</li>
4314 <li>scrollToColumnIn javascript API method doesn't
4316 </ul> <em>General</em>
4318 <li>Redundancy removal fails for rna alignment</li>
4319 <li>PCA calculation fails when sequence has been selected
4320 and then deselected</li>
4321 <li>PCA window shows grey box when first opened on OSX</li>
4322 <li>Letters coloured pink in sequence logo when alignment
4323 coloured with clustalx</li>
4324 <li>Choosing fonts without letter symbols defined causes
4325 exceptions and redraw errors</li>
4326 <li>Initial PCA plot view is not same as manually
4327 reconfigured view</li>
4328 <li>Grouped annotation graph label has incorrect line
4330 <li>Grouped annotation graph label display is corrupted
4331 for lots of labels</li>
4336 <div align="center">
4337 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
4340 <td><em>Application</em>
4342 <li>Jalview Desktop News Reader</li>
4343 <li>Tweaked default layout of web services menu</li>
4344 <li>View/alignment association menu to enable user to
4345 easily specify which alignment a multi-structure view takes
4346 its colours/correspondences from</li>
4347 <li>Allow properties file location to be specified as URL</li>
4348 <li>Extend Jalview project to preserve associations
4349 between many alignment views and a single Jmol display</li>
4350 <li>Store annotation row height in Jalview project file</li>
4351 <li>Annotation row column label formatting attributes
4352 stored in project file</li>
4353 <li>Annotation row order for auto-calculated annotation
4354 rows preserved in Jalview project file</li>
4355 <li>Visual progress indication when Jalview state is
4356 saved using Desktop window menu</li>
4357 <li>Visual indication that command line arguments are
4358 still being processed</li>
4359 <li>Groovy script execution from URL</li>
4360 <li>Colour by annotation default min and max colours in
4362 <li>Automatically associate PDB files dragged onto an
4363 alignment with sequences that have high similarity and
4365 <li>Update JGoogleAnalytics to latest release (0.3)</li>
4366 <li>'view structures' option to open many
4367 structures in same window</li>
4368 <li>Sort associated views menu option for tree panel</li>
4369 <li>Group all JABA and non-JABA services for a particular
4370 analysis function in its own submenu</li>
4371 </ul> <em>Applet</em>
4373 <li>Userdefined and autogenerated annotation rows for
4375 <li>Adjustment of alignment annotation pane height</li>
4376 <li>Annotation scrollbar for annotation panel</li>
4377 <li>Drag to reorder annotation rows in annotation panel</li>
4378 <li>'automaticScrolling' parameter</li>
4379 <li>Allow sequences with partial ID string matches to be
4380 annotated from GFF/Jalview features files</li>
4381 <li>Sequence logo annotation row in applet</li>
4382 <li>Absolute paths relative to host server in applet
4383 parameters are treated as such</li>
4384 <li>New in the JalviewLite javascript API:
4386 <li>JalviewLite.js javascript library</li>
4387 <li>Javascript callbacks for
4389 <li>Applet initialisation</li>
4390 <li>Sequence/alignment mouse-overs and selections</li>
4393 <li>scrollTo row and column alignment scrolling
4395 <li>Select sequence/alignment regions from javascript</li>
4396 <li>javascript structure viewer harness to pass
4397 messages between Jmol and Jalview when running as
4398 distinct applets</li>
4399 <li>sortBy method</li>
4400 <li>Set of applet and application examples shipped
4401 with documentation</li>
4402 <li>New example to demonstrate JalviewLite and Jmol
4403 javascript message exchange</li>
4405 </ul> <em>General</em>
4407 <li>Enable Jmol displays to be associated with multiple
4408 multiple alignments</li>
4409 <li>Option to automatically sort alignment with new tree</li>
4410 <li>User configurable link to enable redirects to a
4411 www.Jalview.org mirror</li>
4412 <li>Jmol colours option for Jmol displays</li>
4413 <li>Configurable newline string when writing alignment
4414 and other flat files</li>
4415 <li>Allow alignment annotation description lines to
4416 contain html tags</li>
4417 </ul> <em>Documentation and Development</em>
4419 <li>Add groovy test harness for bulk load testing to
4421 <li>Groovy script to load and align a set of sequences
4422 using a web service before displaying the result in the
4423 Jalview desktop</li>
4424 <li>Restructured javascript and applet api documentation</li>
4425 <li>Ant target to publish example html files with applet
4427 <li>Netbeans project for building Jalview from source</li>
4428 <li>ant task to create online javadoc for Jalview source</li>
4430 <td><em>Application</em>
4432 <li>User defined colourscheme throws exception when
4433 current built in colourscheme is saved as new scheme</li>
4434 <li>AlignFrame->Save in application pops up save
4435 dialog for valid filename/format</li>
4436 <li>Cannot view associated structure for UniProt sequence</li>
4437 <li>PDB file association breaks for UniProt sequence
4439 <li>Associate PDB from file dialog does not tell you
4440 which sequence is to be associated with the file</li>
4441 <li>Find All raises null pointer exception when query
4442 only matches sequence IDs</li>
4443 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4444 <li>Jalview project with Jmol views created with Jalview
4445 2.4 cannot be loaded</li>
4446 <li>Filetype associations not installed for webstart
4448 <li>Two or more chains in a single PDB file associated
4449 with sequences in different alignments do not get coloured
4450 by their associated sequence</li>
4451 <li>Visibility status of autocalculated annotation row
4452 not preserved when project is loaded</li>
4453 <li>Annotation row height and visibility attributes not
4454 stored in Jalview project</li>
4455 <li>Tree bootstraps are not preserved when saved as a
4456 Jalview project</li>
4457 <li>Envision2 workflow tooltips are corrupted</li>
4458 <li>Enabling show group conservation also enables colour
4459 by conservation</li>
4460 <li>Duplicate group associated conservation or consensus
4461 created on new view</li>
4462 <li>Annotation scrollbar not displayed after 'show
4463 all hidden annotation rows' option selected</li>
4464 <li>Alignment quality not updated after alignment
4465 annotation row is hidden then shown</li>
4466 <li>Preserve colouring of structures coloured by
4467 sequences in pre Jalview 2.7 projects</li>
4468 <li>Web service job parameter dialog is not laid out
4470 <li>Web services menu not refreshed after 'reset
4471 services' button is pressed in preferences</li>
4472 <li>Annotation off by one in Jalview v2_3 example project</li>
4473 <li>Structures imported from file and saved in project
4474 get name like jalview_pdb1234.txt when reloaded</li>
4475 <li>Jalview does not always retrieve progress of a JABAWS
4476 job execution in full once it is complete</li>
4477 </ul> <em>Applet</em>
4479 <li>Alignment height set incorrectly when lots of
4480 annotation rows are displayed</li>
4481 <li>Relative URLs in feature HTML text not resolved to
4483 <li>View follows highlighting does not work for positions
4485 <li><= shown as = in tooltip</li>
4486 <li>Export features raises exception when no features
4488 <li>Separator string used for serialising lists of IDs
4489 for javascript api is modified when separator string
4490 provided as parameter</li>
4491 <li>Null pointer exception when selecting tree leaves for
4492 alignment with no existing selection</li>
4493 <li>Relative URLs for datasources assumed to be relative
4494 to applet's codebase</li>
4495 <li>Status bar not updated after finished searching and
4496 search wraps around to first result</li>
4497 <li>StructureSelectionManager instance shared between
4498 several Jalview applets causes race conditions and memory
4500 <li>Hover tooltip and mouseover of position on structure
4501 not sent from Jmol in applet</li>
4502 <li>Certain sequences of javascript method calls to
4503 applet API fatally hang browser</li>
4504 </ul> <em>General</em>
4506 <li>View follows structure mouseover scrolls beyond
4507 position with wrapped view and hidden regions</li>
4508 <li>Find sequence position moves to wrong residue
4509 with/without hidden columns</li>
4510 <li>Sequence length given in alignment properties window
4512 <li>InvalidNumberFormat exceptions thrown when trying to
4513 import PDB like structure files</li>
4514 <li>Positional search results are only highlighted
4515 between user-supplied sequence start/end bounds</li>
4516 <li>End attribute of sequence is not validated</li>
4517 <li>Find dialog only finds first sequence containing a
4518 given sequence position</li>
4519 <li>Sequence numbering not preserved in MSF alignment
4521 <li>Jalview PDB file reader does not extract sequence
4522 from nucleotide chains correctly</li>
4523 <li>Structure colours not updated when tree partition
4524 changed in alignment</li>
4525 <li>Sequence associated secondary structure not correctly
4526 parsed in interleaved stockholm</li>
4527 <li>Colour by annotation dialog does not restore current
4529 <li>Hiding (nearly) all sequences doesn't work
4531 <li>Sequences containing lowercase letters are not
4532 properly associated with their pdb files</li>
4533 </ul> <em>Documentation and Development</em>
4535 <li>schemas/JalviewWsParamSet.xsd corrupted by
4536 ApplyCopyright tool</li>
4541 <div align="center">
4542 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4545 <td><em>Application</em>
4547 <li>New warning dialog when the Jalview Desktop cannot
4548 contact web services</li>
4549 <li>JABA service parameters for a preset are shown in
4550 service job window</li>
4551 <li>JABA Service menu entries reworded</li>
4555 <li>Modeller PIR IO broken - cannot correctly import a
4556 pir file emitted by Jalview</li>
4557 <li>Existing feature settings transferred to new
4558 alignment view created from cut'n'paste</li>
4559 <li>Improved test for mixed amino/nucleotide chains when
4560 parsing PDB files</li>
4561 <li>Consensus and conservation annotation rows
4562 occasionally become blank for all new windows</li>
4563 <li>Exception raised when right clicking above sequences
4564 in wrapped view mode</li>
4565 </ul> <em>Application</em>
4567 <li>multiple multiply aligned structure views cause cpu
4568 usage to hit 100% and computer to hang</li>
4569 <li>Web Service parameter layout breaks for long user
4570 parameter names</li>
4571 <li>Jaba service discovery hangs desktop if Jaba server
4578 <div align="center">
4579 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4582 <td><em>Application</em>
4584 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4585 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4588 <li>Web Services preference tab</li>
4589 <li>Analysis parameters dialog box and user defined
4591 <li>Improved speed and layout of Envision2 service menu</li>
4592 <li>Superpose structures using associated sequence
4594 <li>Export coordinates and projection as CSV from PCA
4596 </ul> <em>Applet</em>
4598 <li>enable javascript: execution by the applet via the
4599 link out mechanism</li>
4600 </ul> <em>Other</em>
4602 <li>Updated the Jmol Jalview interface to work with Jmol
4604 <li>The Jalview Desktop and JalviewLite applet now
4605 require Java 1.5</li>
4606 <li>Allow Jalview feature colour specification for GFF
4607 sequence annotation files</li>
4608 <li>New 'colour by label' keword in Jalview feature file
4609 type colour specification</li>
4610 <li>New Jalview Desktop Groovy API method that allows a
4611 script to check if it being run in an interactive session or
4612 in a batch operation from the Jalview command line</li>
4616 <li>clustalx colourscheme colours Ds preferentially when
4617 both D+E are present in over 50% of the column</li>
4618 </ul> <em>Application</em>
4620 <li>typo in AlignmentFrame->View->Hide->all but
4621 selected Regions menu item</li>
4622 <li>sequence fetcher replaces ',' for ';' when the ',' is
4623 part of a valid accession ID</li>
4624 <li>fatal OOM if object retrieved by sequence fetcher
4625 runs out of memory</li>
4626 <li>unhandled Out of Memory Error when viewing pca
4627 analysis results</li>
4628 <li>InstallAnywhere builds fail to launch on OS X java
4629 10.5 update 4 (due to apple Java 1.6 update)</li>
4630 <li>Installanywhere Jalview silently fails to launch</li>
4631 </ul> <em>Applet</em>
4633 <li>Jalview.getFeatureGroups() raises an
4634 ArrayIndexOutOfBoundsException if no feature groups are
4641 <div align="center">
4642 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4648 <li>Alignment prettyprinter doesn't cope with long
4650 <li>clustalx colourscheme colours Ds preferentially when
4651 both D+E are present in over 50% of the column</li>
4652 <li>nucleic acid structures retrieved from PDB do not
4653 import correctly</li>
4654 <li>More columns get selected than were clicked on when a
4655 number of columns are hidden</li>
4656 <li>annotation label popup menu not providing correct
4657 add/hide/show options when rows are hidden or none are
4659 <li>Stockholm format shown in list of readable formats,
4660 and parser copes better with alignments from RFAM.</li>
4661 <li>CSV output of consensus only includes the percentage
4662 of all symbols if sequence logo display is enabled</li>
4664 </ul> <em>Applet</em>
4666 <li>annotation panel disappears when annotation is
4668 </ul> <em>Application</em>
4670 <li>Alignment view not redrawn properly when new
4671 alignment opened where annotation panel is visible but no
4672 annotations are present on alignment</li>
4673 <li>pasted region containing hidden columns is
4674 incorrectly displayed in new alignment window</li>
4675 <li>Jalview slow to complete operations when stdout is
4676 flooded (fix is to close the Jalview console)</li>
4677 <li>typo in AlignmentFrame->View->Hide->all but
4678 selected Rregions menu item.</li>
4679 <li>inconsistent group submenu and Format submenu entry
4680 'Un' or 'Non'conserved</li>
4681 <li>Sequence feature settings are being shared by
4682 multiple distinct alignments</li>
4683 <li>group annotation not recreated when tree partition is
4685 <li>double click on group annotation to select sequences
4686 does not propagate to associated trees</li>
4687 <li>Mac OSX specific issues:
4689 <li>exception raised when mouse clicked on desktop
4690 window background</li>
4691 <li>Desktop menu placed on menu bar and application
4692 name set correctly</li>
4693 <li>sequence feature settings not wide enough for the
4694 save feature colourscheme button</li>
4703 <div align="center">
4704 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4707 <td><em>New Capabilities</em>
4709 <li>URL links generated from description line for
4710 regular-expression based URL links (applet and application)
4713 <li>Non-positional feature URL links are shown in link
4715 <li>Linked viewing of nucleic acid sequences and
4717 <li>Automatic Scrolling option in View menu to display
4718 the currently highlighted region of an alignment.</li>
4719 <li>Order an alignment by sequence length, or using the
4720 average score or total feature count for each sequence.</li>
4721 <li>Shading features by score or associated description</li>
4722 <li>Subdivide alignment and groups based on identity of
4723 selected subsequence (Make Groups from Selection).</li>
4724 <li>New hide/show options including Shift+Control+H to
4725 hide everything but the currently selected region.</li>
4726 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4727 </ul> <em>Application</em>
4729 <li>Fetch DB References capabilities and UI expanded to
4730 support retrieval from DAS sequence sources</li>
4731 <li>Local DAS Sequence sources can be added via the
4732 command line or via the Add local source dialog box.</li>
4733 <li>DAS Dbref and DbxRef feature types are parsed as
4734 database references and protein_name is parsed as
4735 description line (BioSapiens terms).</li>
4736 <li>Enable or disable non-positional feature and database
4737 references in sequence ID tooltip from View menu in
4739 <!-- <li>New hidden columns and rows and representatives capabilities
4740 in annotations file (in progress - not yet fully implemented)</li> -->
4741 <li>Group-associated consensus, sequence logos and
4742 conservation plots</li>
4743 <li>Symbol distributions for each column can be exported
4744 and visualized as sequence logos</li>
4745 <li>Optionally scale multi-character column labels to fit
4746 within each column of annotation row<!-- todo for applet -->
4748 <li>Optional automatic sort of associated alignment view
4749 when a new tree is opened.</li>
4750 <li>Jalview Java Console</li>
4751 <li>Better placement of desktop window when moving
4752 between different screens.</li>
4753 <li>New preference items for sequence ID tooltip and
4754 consensus annotation</li>
4755 <li>Client to submit sequences and IDs to Envision2
4757 <li><em>Vamsas Capabilities</em>
4759 <li>Improved VAMSAS synchronization (Jalview archive
4760 used to preserve views, structures, and tree display
4762 <li>Import of vamsas documents from disk or URL via
4764 <li>Sharing of selected regions between views and
4765 with other VAMSAS applications (Experimental feature!)</li>
4766 <li>Updated API to VAMSAS version 0.2</li>
4768 </ul> <em>Applet</em>
4770 <li>Middle button resizes annotation row height</li>
4773 <li>sortByTree (true/false) - automatically sort the
4774 associated alignment view by the tree when a new tree is
4776 <li>showTreeBootstraps (true/false) - show or hide
4777 branch bootstraps (default is to show them if available)</li>
4778 <li>showTreeDistances (true/false) - show or hide
4779 branch lengths (default is to show them if available)</li>
4780 <li>showUnlinkedTreeNodes (true/false) - indicate if
4781 unassociated nodes should be highlighted in the tree
4783 <li>heightScale and widthScale (1.0 or more) -
4784 increase the height or width of a cell in the alignment
4785 grid relative to the current font size.</li>
4788 <li>Non-positional features displayed in sequence ID
4790 </ul> <em>Other</em>
4792 <li>Features format: graduated colour definitions and
4793 specification of feature scores</li>
4794 <li>Alignment Annotations format: new keywords for group
4795 associated annotation (GROUP_REF) and annotation row display
4796 properties (ROW_PROPERTIES)</li>
4797 <li>XML formats extended to support graduated feature
4798 colourschemes, group associated annotation, and profile
4799 visualization settings.</li></td>
4802 <li>Source field in GFF files parsed as feature source
4803 rather than description</li>
4804 <li>Non-positional features are now included in sequence
4805 feature and gff files (controlled via non-positional feature
4806 visibility in tooltip).</li>
4807 <li>URL links generated for all feature links (bugfix)</li>
4808 <li>Added URL embedding instructions to features file
4810 <li>Codons containing ambiguous nucleotides translated as
4811 'X' in peptide product</li>
4812 <li>Match case switch in find dialog box works for both
4813 sequence ID and sequence string and query strings do not
4814 have to be in upper case to match case-insensitively.</li>
4815 <li>AMSA files only contain first column of
4816 multi-character column annotation labels</li>
4817 <li>Jalview Annotation File generation/parsing consistent
4818 with documentation (e.g. Stockholm annotation can be
4819 exported and re-imported)</li>
4820 <li>PDB files without embedded PDB IDs given a friendly
4822 <li>Find incrementally searches ID string matches as well
4823 as subsequence matches, and correctly reports total number
4827 <li>Better handling of exceptions during sequence
4829 <li>Dasobert generated non-positional feature URL
4830 link text excludes the start_end suffix</li>
4831 <li>DAS feature and source retrieval buttons disabled
4832 when fetch or registry operations in progress.</li>
4833 <li>PDB files retrieved from URLs are cached properly</li>
4834 <li>Sequence description lines properly shared via
4836 <li>Sequence fetcher fetches multiple records for all
4838 <li>Ensured that command line das feature retrieval
4839 completes before alignment figures are generated.</li>
4840 <li>Reduced time taken when opening file browser for
4842 <li>isAligned check prior to calculating tree, PCA or
4843 submitting an MSA to JNet now excludes hidden sequences.</li>
4844 <li>User defined group colours properly recovered
4845 from Jalview projects.</li>
4854 <div align="center">
4855 <strong>2.4.0.b2</strong><br> 28/10/2009
4860 <li>Experimental support for google analytics usage
4862 <li>Jalview privacy settings (user preferences and docs).</li>
4867 <li>Race condition in applet preventing startup in
4869 <li>Exception when feature created from selection beyond
4870 length of sequence.</li>
4871 <li>Allow synthetic PDB files to be imported gracefully</li>
4872 <li>Sequence associated annotation rows associate with
4873 all sequences with a given id</li>
4874 <li>Find function matches case-insensitively for sequence
4875 ID string searches</li>
4876 <li>Non-standard characters do not cause pairwise
4877 alignment to fail with exception</li>
4878 </ul> <em>Application Issues</em>
4880 <li>Sequences are now validated against EMBL database</li>
4881 <li>Sequence fetcher fetches multiple records for all
4883 </ul> <em>InstallAnywhere Issues</em>
4885 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4886 issue with installAnywhere mechanism)</li>
4887 <li>Command line launching of JARs from InstallAnywhere
4888 version (java class versioning error fixed)</li>
4895 <div align="center">
4896 <strong>2.4</strong><br> 27/8/2008
4899 <td><em>User Interface</em>
4901 <li>Linked highlighting of codon and amino acid from
4902 translation and protein products</li>
4903 <li>Linked highlighting of structure associated with
4904 residue mapping to codon position</li>
4905 <li>Sequence Fetcher provides example accession numbers
4906 and 'clear' button</li>
4907 <li>MemoryMonitor added as an option under Desktop's
4909 <li>Extract score function to parse whitespace separated
4910 numeric data in description line</li>
4911 <li>Column labels in alignment annotation can be centred.</li>
4912 <li>Tooltip for sequence associated annotation give name
4914 </ul> <em>Web Services and URL fetching</em>
4916 <li>JPred3 web service</li>
4917 <li>Prototype sequence search client (no public services
4919 <li>Fetch either seed alignment or full alignment from
4921 <li>URL Links created for matching database cross
4922 references as well as sequence ID</li>
4923 <li>URL Links can be created using regular-expressions</li>
4924 </ul> <em>Sequence Database Connectivity</em>
4926 <li>Retrieval of cross-referenced sequences from other
4928 <li>Generalised database reference retrieval and
4929 validation to all fetchable databases</li>
4930 <li>Fetch sequences from DAS sources supporting the
4931 sequence command</li>
4932 </ul> <em>Import and Export</em>
4933 <li>export annotation rows as CSV for spreadsheet import</li>
4934 <li>Jalview projects record alignment dataset associations,
4935 EMBL products, and cDNA sequence mappings</li>
4936 <li>Sequence Group colour can be specified in Annotation
4938 <li>Ad-hoc colouring of group in Annotation File using RGB
4939 triplet as name of colourscheme</li>
4940 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4942 <li>treenode binding for VAMSAS tree exchange</li>
4943 <li>local editing and update of sequences in VAMSAS
4944 alignments (experimental)</li>
4945 <li>Create new or select existing session to join</li>
4946 <li>load and save of vamsas documents</li>
4947 </ul> <em>Application command line</em>
4949 <li>-tree parameter to open trees (introduced for passing
4951 <li>-fetchfrom command line argument to specify nicknames
4952 of DAS servers to query for alignment features</li>
4953 <li>-dasserver command line argument to add new servers
4954 that are also automatically queried for features</li>
4955 <li>-groovy command line argument executes a given groovy
4956 script after all input data has been loaded and parsed</li>
4957 </ul> <em>Applet-Application data exchange</em>
4959 <li>Trees passed as applet parameters can be passed to
4960 application (when using "View in full
4961 application")</li>
4962 </ul> <em>Applet Parameters</em>
4964 <li>feature group display control parameter</li>
4965 <li>debug parameter</li>
4966 <li>showbutton parameter</li>
4967 </ul> <em>Applet API methods</em>
4969 <li>newView public method</li>
4970 <li>Window (current view) specific get/set public methods</li>
4971 <li>Feature display control methods</li>
4972 <li>get list of currently selected sequences</li>
4973 </ul> <em>New Jalview distribution features</em>
4975 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4976 <li>RELEASE file gives build properties for the latest
4977 Jalview release.</li>
4978 <li>Java 1.1 Applet build made easier and donotobfuscate
4979 property controls execution of obfuscator</li>
4980 <li>Build target for generating source distribution</li>
4981 <li>Debug flag for javacc</li>
4982 <li>.jalview_properties file is documented (slightly) in
4983 jalview.bin.Cache</li>
4984 <li>Continuous Build Integration for stable and
4985 development version of Application, Applet and source
4990 <li>selected region output includes visible annotations
4991 (for certain formats)</li>
4992 <li>edit label/displaychar contains existing label/char
4994 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4995 <li>shorter peptide product names from EMBL records</li>
4996 <li>Newick string generator makes compact representations</li>
4997 <li>bootstrap values parsed correctly for tree files with
4999 <li>pathological filechooser bug avoided by not allowing
5000 filenames containing a ':'</li>
5001 <li>Fixed exception when parsing GFF files containing
5002 global sequence features</li>
5003 <li>Alignment datasets are finalized only when number of
5004 references from alignment sequences goes to zero</li>
5005 <li>Close of tree branch colour box without colour
5006 selection causes cascading exceptions</li>
5007 <li>occasional negative imgwidth exceptions</li>
5008 <li>better reporting of non-fatal warnings to user when
5009 file parsing fails.</li>
5010 <li>Save works when Jalview project is default format</li>
5011 <li>Save as dialog opened if current alignment format is
5012 not a valid output format</li>
5013 <li>UniProt canonical names introduced for both das and
5015 <li>Histidine should be midblue (not pink!) in Zappo</li>
5016 <li>error messages passed up and output when data read
5018 <li>edit undo recovers previous dataset sequence when
5019 sequence is edited</li>
5020 <li>allow PDB files without pdb ID HEADER lines (like
5021 those generated by MODELLER) to be read in properly</li>
5022 <li>allow reading of JPred concise files as a normal
5024 <li>Stockholm annotation parsing and alignment properties
5025 import fixed for PFAM records</li>
5026 <li>Structure view windows have correct name in Desktop
5028 <li>annotation consisting of sequence associated scores
5029 can be read and written correctly to annotation file</li>
5030 <li>Aligned cDNA translation to aligned peptide works
5032 <li>Fixed display of hidden sequence markers and
5033 non-italic font for representatives in Applet</li>
5034 <li>Applet Menus are always embedded in applet window on
5036 <li>Newly shown features appear at top of stack (in
5038 <li>Annotations added via parameter not drawn properly
5039 due to null pointer exceptions</li>
5040 <li>Secondary structure lines are drawn starting from
5041 first column of alignment</li>
5042 <li>UniProt XML import updated for new schema release in
5044 <li>Sequence feature to sequence ID match for Features
5045 file is case-insensitive</li>
5046 <li>Sequence features read from Features file appended to
5047 all sequences with matching IDs</li>
5048 <li>PDB structure coloured correctly for associated views
5049 containing a sub-sequence</li>
5050 <li>PDB files can be retrieved by applet from Jar files</li>
5051 <li>feature and annotation file applet parameters
5052 referring to different directories are retrieved correctly</li>
5053 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
5054 <li>Fixed application hang whilst waiting for
5055 splash-screen version check to complete</li>
5056 <li>Applet properly URLencodes input parameter values
5057 when passing them to the launchApp service</li>
5058 <li>display name and local features preserved in results
5059 retrieved from web service</li>
5060 <li>Visual delay indication for sequence retrieval and
5061 sequence fetcher initialisation</li>
5062 <li>updated Application to use DAS 1.53e version of
5063 dasobert DAS client</li>
5064 <li>Re-instated Full AMSA support and .amsa file
5066 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
5074 <div align="center">
5075 <strong>2.3</strong><br> 9/5/07
5080 <li>Jmol 11.0.2 integration</li>
5081 <li>PDB views stored in Jalview XML files</li>
5082 <li>Slide sequences</li>
5083 <li>Edit sequence in place</li>
5084 <li>EMBL CDS features</li>
5085 <li>DAS Feature mapping</li>
5086 <li>Feature ordering</li>
5087 <li>Alignment Properties</li>
5088 <li>Annotation Scores</li>
5089 <li>Sort by scores</li>
5090 <li>Feature/annotation editing in applet</li>
5095 <li>Headless state operation in 2.2.1</li>
5096 <li>Incorrect and unstable DNA pairwise alignment</li>
5097 <li>Cut and paste of sequences with annotation</li>
5098 <li>Feature group display state in XML</li>
5099 <li>Feature ordering in XML</li>
5100 <li>blc file iteration selection using filename # suffix</li>
5101 <li>Stockholm alignment properties</li>
5102 <li>Stockhom alignment secondary structure annotation</li>
5103 <li>2.2.1 applet had no feature transparency</li>
5104 <li>Number pad keys can be used in cursor mode</li>
5105 <li>Structure Viewer mirror image resolved</li>
5112 <div align="center">
5113 <strong>2.2.1</strong><br> 12/2/07
5118 <li>Non standard characters can be read and displayed
5119 <li>Annotations/Features can be imported/exported to the
5121 <li>Applet allows editing of sequence/annotation/group
5122 name & description
5123 <li>Preference setting to display sequence name in
5125 <li>Annotation file format extended to allow
5126 Sequence_groups to be defined
5127 <li>Default opening of alignment overview panel can be
5128 specified in preferences
5129 <li>PDB residue numbering annotation added to associated
5135 <li>Applet crash under certain Linux OS with Java 1.6
5137 <li>Annotation file export / import bugs fixed
5138 <li>PNG / EPS image output bugs fixed
5144 <div align="center">
5145 <strong>2.2</strong><br> 27/11/06
5150 <li>Multiple views on alignment
5151 <li>Sequence feature editing
5152 <li>"Reload" alignment
5153 <li>"Save" to current filename
5154 <li>Background dependent text colour
5155 <li>Right align sequence ids
5156 <li>User-defined lower case residue colours
5159 <li>Menu item accelerator keys
5160 <li>Control-V pastes to current alignment
5161 <li>Cancel button for DAS Feature Fetching
5162 <li>PCA and PDB Viewers zoom via mouse roller
5163 <li>User-defined sub-tree colours and sub-tree selection
5166 <li>'New Window' button on the 'Output to Text box'
5171 <li>New memory efficient Undo/Redo System
5172 <li>Optimised symbol lookups and conservation/consensus
5174 <li>Region Conservation/Consensus recalculated after
5176 <li>Fixed Remove Empty Columns Bug (empty columns at end
5178 <li>Slowed DAS Feature Fetching for increased robustness.
5181 <li>Made angle brackets in ASCII feature descriptions
5183 <li>Re-instated Zoom function for PCA
5184 <li>Sequence descriptions conserved in web service
5186 <li>UniProt ID discoverer uses any word separated by
5188 <li>WsDbFetch query/result association resolved
5189 <li>Tree leaf to sequence mapping improved
5190 <li>Smooth fonts switch moved to FontChooser dialog box.
5198 <div align="center">
5199 <strong>2.1.1</strong><br> 12/9/06
5204 <li>Copy consensus sequence to clipboard</li>
5209 <li>Image output - rightmost residues are rendered if
5210 sequence id panel has been resized</li>
5211 <li>Image output - all offscreen group boundaries are
5213 <li>Annotation files with sequence references - all
5214 elements in file are relative to sequence position</li>
5215 <li>Mac Applet users can use Alt key for group editing</li>
5221 <div align="center">
5222 <strong>2.1</strong><br> 22/8/06
5227 <li>MAFFT Multiple Alignment in default Web Service list</li>
5228 <li>DAS Feature fetching</li>
5229 <li>Hide sequences and columns</li>
5230 <li>Export Annotations and Features</li>
5231 <li>GFF file reading / writing</li>
5232 <li>Associate structures with sequences from local PDB
5234 <li>Add sequences to exisiting alignment</li>
5235 <li>Recently opened files / URL lists</li>
5236 <li>Applet can launch the full application</li>
5237 <li>Applet has transparency for features (Java 1.2
5239 <li>Applet has user defined colours parameter</li>
5240 <li>Applet can load sequences from parameter
5241 "sequence<em>x</em>"
5247 <li>Redundancy Panel reinstalled in the Applet</li>
5248 <li>Monospaced font - EPS / rescaling bug fixed</li>
5249 <li>Annotation files with sequence references bug fixed</li>
5255 <div align="center">
5256 <strong>2.08.1</strong><br> 2/5/06
5261 <li>Change case of selected region from Popup menu</li>
5262 <li>Choose to match case when searching</li>
5263 <li>Middle mouse button and mouse movement can compress /
5264 expand the visible width and height of the alignment</li>
5269 <li>Annotation Panel displays complete JNet results</li>
5275 <div align="center">
5276 <strong>2.08b</strong><br> 18/4/06
5282 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
5283 <li>Righthand label on wrapped alignments shows correct
5290 <div align="center">
5291 <strong>2.08</strong><br> 10/4/06
5296 <li>Editing can be locked to the selection area</li>
5297 <li>Keyboard editing</li>
5298 <li>Create sequence features from searches</li>
5299 <li>Precalculated annotations can be loaded onto
5301 <li>Features file allows grouping of features</li>
5302 <li>Annotation Colouring scheme added</li>
5303 <li>Smooth fonts off by default - Faster rendering</li>
5304 <li>Choose to toggle Autocalculate Consensus On/Off</li>
5309 <li>Drag & Drop fixed on Linux</li>
5310 <li>Jalview Archive file faster to load/save, sequence
5311 descriptions saved.</li>
5317 <div align="center">
5318 <strong>2.07</strong><br> 12/12/05
5323 <li>PDB Structure Viewer enhanced</li>
5324 <li>Sequence Feature retrieval and display enhanced</li>
5325 <li>Choose to output sequence start-end after sequence
5326 name for file output</li>
5327 <li>Sequence Fetcher WSDBFetch@EBI</li>
5328 <li>Applet can read feature files, PDB files and can be
5329 used for HTML form input</li>
5334 <li>HTML output writes groups and features</li>
5335 <li>Group editing is Control and mouse click</li>
5336 <li>File IO bugs</li>
5342 <div align="center">
5343 <strong>2.06</strong><br> 28/9/05
5348 <li>View annotations in wrapped mode</li>
5349 <li>More options for PCA viewer</li>
5354 <li>GUI bugs resolved</li>
5355 <li>Runs with -nodisplay from command line</li>
5361 <div align="center">
5362 <strong>2.05b</strong><br> 15/9/05
5367 <li>Choose EPS export as lineart or text</li>
5368 <li>Jar files are executable</li>
5369 <li>Can read in Uracil - maps to unknown residue</li>
5374 <li>Known OutOfMemory errors give warning message</li>
5375 <li>Overview window calculated more efficiently</li>
5376 <li>Several GUI bugs resolved</li>
5382 <div align="center">
5383 <strong>2.05</strong><br> 30/8/05
5388 <li>Edit and annotate in "Wrapped" view</li>
5393 <li>Several GUI bugs resolved</li>
5399 <div align="center">
5400 <strong>2.04</strong><br> 24/8/05
5405 <li>Hold down mouse wheel & scroll to change font
5411 <li>Improved JPred client reliability</li>
5412 <li>Improved loading of Jalview files</li>
5418 <div align="center">
5419 <strong>2.03</strong><br> 18/8/05
5424 <li>Set Proxy server name and port in preferences</li>
5425 <li>Multiple URL links from sequence ids</li>
5426 <li>User Defined Colours can have a scheme name and added
5428 <li>Choose to ignore gaps in consensus calculation</li>
5429 <li>Unix users can set default web browser</li>
5430 <li>Runs without GUI for batch processing</li>
5431 <li>Dynamically generated Web Service Menus</li>
5436 <li>InstallAnywhere download for Sparc Solaris</li>
5442 <div align="center">
5443 <strong>2.02</strong><br> 18/7/05
5449 <li>Copy & Paste order of sequences maintains
5450 alignment order.</li>
5456 <div align="center">
5457 <strong>2.01</strong><br> 12/7/05
5462 <li>Use delete key for deleting selection.</li>
5463 <li>Use Mouse wheel to scroll sequences.</li>
5464 <li>Help file updated to describe how to add alignment
5466 <li>Version and build date written to build properties
5468 <li>InstallAnywhere installation will check for updates
5469 at launch of Jalview.</li>
5474 <li>Delete gaps bug fixed.</li>
5475 <li>FileChooser sorts columns.</li>
5476 <li>Can remove groups one by one.</li>
5477 <li>Filechooser icons installed.</li>
5478 <li>Finder ignores return character when searching.
5479 Return key will initiate a search.<br>
5486 <div align="center">
5487 <strong>2.0</strong><br> 20/6/05
5492 <li>New codebase</li>