4 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
5 * Copyright (C) $$Year-Rel$$ The Jalview Authors
7 * This file is part of Jalview.
9 * Jalview is free software: you can redistribute it and/or
10 * modify it under the terms of the GNU General Public License
11 * as published by the Free Software Foundation, either version 3
12 * of the License, or (at your option) any later version.
14 * Jalview is distributed in the hope that it will be useful, but
15 * WITHOUT ANY WARRANTY; without even the implied warranty
16 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
17 * PURPOSE. See the GNU General Public License for more details.
19 * You should have received a copy of the GNU General Public License
20 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
21 * The Jalview Authors are detailed in the 'AUTHORS' file.
24 <title>Release History</title>
27 /* remove bullets, narrower indent */
28 list-style-type: none;
35 /* separate the items from eachother */
42 /* doesnt get processed in javahelp */
51 <strong>Release History</strong>
55 <th nowrap><a id="Jalview.$$Version-Rel$$"><em>Release</em></th>
56 <th><em>New Features</em></th>
57 <th><em>Issues Resolved</em></th>
60 <td width="60" align="center" nowrap><strong><a
61 id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.0">.0</a><br />
62 <em>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
112 argument to prevent automatic discovery of analysis
113 webservices on launch
116 <!-- JAL-3618 -->Allow 'App' directories to be opened when
117 locating Chimera, ChimeraX or Pymol binaries via filechooser
118 opened by double clicking the Structure Preferences' path
122 <!-- JAL-3837 -->GPL license info on splash screen and About
126 <em>Jalview Native App</em>
129 <!-- JAL- -->New Jalview Develop app - making it even easier
130 to get at Jalview's development builds
133 <!-- JAL-3594 -->New splashscreens for Jalview, Jalview Test
134 and Jalview Develop applications.
137 <!-- JAL-3728 -->Jalview logos shown for Jalview Java
138 Console and other window widgets in taskbar and dock rather
139 than anonymous 'Java' icons
141 </ul> <em>JalviewJS</em>
144 <!-- JAL-3624 -->PDB structures mapped to Uniprot Sequences with
148 <!-- JAL-3208 -->setprop commandline argument reinstated for JalviewJS only
151 <!-- JAL-3163 -->Missing message bundle keys are only
152 reported once per key (avoids excessive log output in js
156 <!-- JAL-3168 -->Feature type is included in the title of
157 the Feature Settings' Colour Chooser dialog
160 </ul> <em>Development</em>
163 <!-- -->First integrated JalviewJS and Jalview release
165 <li>Updated building instructions</li>
167 <!-- JAL-3789, JAL-3679 -->Improved JalviewJS/Jalview build
168 process, added support for system package provided eclipse
171 <li>Install4j 9.0.x used for installer packaging</li>
172 <li>Notarized MacOS installer for compatibility with Big
173 Sur and Monterey</li>
175 <!-- JAL-3805 -->Uninstaller application for old
176 (InstallAnywhere based) Jalview installations removed from
180 <!-- JAL-3930 -->Improved use of installers for unattended
181 installation with a customizedId of "JALVIEW" in install4j's
185 <!-- JAL-3907 -->Improved compatibility of Jalview build
186 with Java 17 (next LTS target)
195 <!-- JAL-3674 -->Slow structure commands can block Jalview
199 <!-- JAL-3904 -->Structure window's viewer-specific menu
200 disappears when only one structure is shown (and many
201 sequences:one chain mappings are present)
204 <!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
205 the first SEQUENCE_GROUP defined
210 <!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 -->Selections not
211 propagated between Linked CDS - Protein alignments and their
212 trees (known defect from 2.11.1.3)
215 <!-- JAL-3761 -->Not all codon positions highlighted for
216 overlapping exon splice sites (e.g due to RNA slippage)
219 <!-- JAL-3794 -->X was not being recognised as the unknown
220 base in DNA sequences
223 <!-- JAL-3915 -->Removed RNAview checkbox and logic from
224 Structure Preferences
227 <!-- JAL-3583 -->Tooltip behaviour improved (slightly)
230 <!-- JAL-3162 -->Can edit a feature so that start > end
233 <!-- JAL-2848 -->Cancel from Amend Features doesn't reset a
234 modified graduated colour
237 <!-- JAL-3788 -->New View with automatic 'Show Overview'
238 preference enabled results in Null Pointer Exceptions when
239 clustal colouring is enabled
242 <!-- JAL-3275 -->Can open multiple Preferences panels
245 <!-- JAL-3949 -->Standard out logging broken: messages only
246 routing to stderr and appear as a raw template
248 </ul> <em>JalviewJS</em>
251 <!-- JAL-3202 -->Consensus profile may include zero (rounded
252 down) percentage values causing a divide by zero
267 <!-- JAL-3762 -->JalviewJS doesn't honour arguments passed
268 via Info.args when there are arguments on the URL
271 <!-- JAL-3602 -->gradle closure-compiler not using UTF-8
274 <!-- JAL-3603 -->Annotation file fails to load from URL in
277 </ul> <em>Development</em>
281 <li>Fixed non-fatal gradle errors during build</li>
283 <!-- JAL-3745 -->Updated build.gradle for use with
293 <td width="60" align="center" nowrap><strong><a
294 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.7">.7</a><br />
295 <em>18/01/2022</em></strong></td>
297 <td align="left" valign="top">
300 <!-- JAL-3703, JAL-3935 -->Files open in Jalview cannot be
301 updated by Jalview or other applications (Windows, other non
304 </ul> <em>Security</em>
307 <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
313 <td width="60" align="center" nowrap><strong><a
314 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
315 <em>6/01/2022</em></strong></td>
317 <td align="left" valign="top"><em>Security</em>
320 <!-- JAL-3934 -->Version bump library dependency: Log4j
327 <td width="60" align="center" nowrap><strong><a
328 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
329 <em>20/12/2021</em></strong></td>
331 <td align="left" valign="top"><em>Security</em>
334 <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
336 </ul> <em>Development</em>
338 <li>Updated building instructions</li>
343 <!-- JAL-3840 -->Occupancy calculation is incorrect for
344 alignment columns with over -1+2^32 gaps (breaking filtering
348 <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
349 scale factors being set with buggy window-managers (linux
352 </ul> <em>Development</em>
354 <li>Fixed non-fatal gradle errors during build</li>
359 <td width="60" align="center" nowrap><strong><a
360 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
361 <em>09/03/2021</em></strong></td>
362 <td align="left" valign="top"><em>Improved control of
363 Jalview's use of network services via jalview_properties</em>
366 <!-- JAL-3814 -->New .jalview_properties token controlling
367 launch of the news browser (like -nonews argument)
370 <!-- JAL-3813 -->New .jalview_properties token controlling
371 download of linkout URLs from
372 www.jalview.org/services/identifiers
375 <!-- JAL-3812 -->New .jalview_properties token controlling
376 download of BIOJSHTML templates
379 <!-- JAL-3811 -->New 'Discover Web Services' option to
380 trigger a one off JABAWS discovery if autodiscovery was
384 <td align="left" valign="top">
387 <!-- JAL-3818 -->Intermittent deadlock opening structure in
390 </ul> <em>New Known defects</em>
393 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
394 always restored from project (since 2.10.3)
397 <!-- JAL-3806 -->Selections from tree built from CDS aren't
398 propagated to Protein alignment (since 2.11.1.3)
404 <td width="60" align="center" nowrap><strong><a
405 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
406 <em>29/10/2020</em></strong></td>
407 <td align="left" valign="top">
412 <td align="left" valign="top">
415 <!-- JAL-3765 -->Find doesn't always highlight all matching
416 positions in a sequence (bug introduced in 2.11.1.2)
419 <!-- JAL-3760 -->Alignments containing one or more protein
420 sequences can be classed as nucleotide
423 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
424 sequences after alignment of protein products (known defect
425 first reported for 2.11.1.0)
428 <!-- JAL-3725 -->No tooltip or popup menu for genomic
429 features outwith CDS shown overlaid on protein
432 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
433 correctly mapped by Jalview (e.g. affects viral CDS with
434 ribosomal slippage, since 2.9.0)
437 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
441 <!-- JAL-3700 -->Selections in CDS sequence panel don't
442 always select corresponding protein sequences
445 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
446 column selection doesn't always ignore hidden columns
448 </ul> <em>Installer</em>
451 <!-- JAL-3611 -->Space character in Jalview install path on
452 Windows prevents install4j launching getdown
454 </ul> <em>Development</em>
457 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
458 version numbers in doc/building.md
464 <td width="60" align="center" nowrap><strong><a
465 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
466 <em>25/09/2020</em></strong></td>
467 <td align="left" valign="top">
471 <td align="left" valign="top">
474 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
475 "Encountered problems opening
476 https://www.jalview.org/examples/exampleFile_2_7.jvp"
482 <td width="60" align="center" nowrap><strong><a
483 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
484 <em>17/09/2020</em></strong></td>
485 <td align="left" valign="top">
488 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
489 residue in cursor mode
492 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
493 HTSJDK from 2.12 to 2.23
496 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
497 optimisations and improvements suggested by Bob Hanson and
498 improved compatibility with JalviewJS
501 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
502 alignments from Pfam and Rfam
505 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
506 import (no longer based on .gz extension)
509 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
512 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
513 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
517 <!-- JAL-3667 -->Improved warning messages, debug logging
518 and fixed Retry action when Jalview encounters errors when
519 saving or making backup files.
522 <!-- JAL-3676 -->Enhanced Jalview Java Console:
524 <li>Jalview's logging level can be configured</li>
525 <li>Copy to Clipboard Buttion</li>
529 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
530 when running on Linux (Requires Java 11+)
532 </ul> <em>Launching Jalview</em>
535 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
536 through a system property
539 <!-- JAL-3477 -->Improved built-in documentation and command
540 line help for configuring Jalview's memory
544 <td align="left" valign="top">
547 <!-- JAL-3691 -->Conservation and Quality tracks are shown
548 but not calculated and no protein or DNA score models are
549 available for tree/PCA calculation when launched with
550 Turkish language locale
553 <!-- JAL-3493 -->Escape does not clear highlights on the
554 alignment (Since Jalview 2.10.3)
557 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
558 doesn't slide selected sequences, just sequence under cursor
561 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
562 sequence under the cursor
565 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
566 multiple EMBL gene products shown for a single contig
569 <!-- JAL-3696 -->Errors encountered when processing variants
570 from VCF files yield "Error processing VCF: Format specifier
574 <!-- JAL-3697 -->Count of features not shown can be wrong
575 when there are both local and complementary features mapped
576 to the position under the cursor
579 <!-- JAL-3673 -->Sequence ID for reference sequence is
580 clipped when Right align Sequence IDs enabled
583 <!-- JAL-2983 -->Slider with negative range values not
584 rendered correctly in VAqua4 (Since 2.10.4)
587 <!-- JAL-3685 -->Single quotes not displayed correctly in
588 internationalised text for some messages and log output
591 <!-- JAL-3490 -->Find doesn't report matches that span
592 hidden gapped columns
595 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
596 panels, Alignment viewport and annotation renderer.
599 <!-- JAL-3561 -->Jalview ignores file format parameter
600 specifying output format when exporting an alignment via the
604 <!-- JAL-3667 -->Windows 10: For a minority of users, if
605 backups are not enabled, Jalview sometimes fails to
606 overwrite an existing file and raises a warning dialog. (in
607 2.11.0, and 2.11.1.0, the workaround is to try to save the
608 file again, and if that fails, delete the original file and
612 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
616 <!-- JAL-3741 -->References to http://www.jalview.org in
617 program and documentation
619 </ul> <em>Launching Jalview</em>
622 <!-- JAL-3718 -->Jalview application fails when launched the
623 first time for a version that has different jars to the
624 previous launched version.
626 </ul> <em>Developing Jalview</em>
629 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
630 data, causing cloverReport gradle task to fail with an
634 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
635 monitor the release channel
637 </ul> <em>New Known defects</em>
640 <!-- JAL-3748 -->CDS shown in result of submitting proteins
641 in a CDS/Protein alignment to a web service is wrong when
642 proteins share a common transcript sequence (e.g. genome of
646 <!-- JAL-3576 -->Co-located features exported and
647 re-imported are ordered differently when shown on alignment
648 and in tooltips. (Also affects v2.11.1.0)
651 <!-- JAL-3702 -->Drag and drop of alignment file onto
652 alignment window when in a HiDPI scaled mode in Linux only
653 works for the top left quadrant of the alignment window
656 <!-- JAL-3701 -->Stale build data in jalview standalone jar
657 builds (only affects 2.11.1.1 branch)
660 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
661 when alignment view restored from project (since Jalview
665 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
666 protein products for certain ENA records are repeatedly
667 shown via Calculate->Show Cross Refs
673 <td width="60" align="center" nowrap><strong><a
674 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
675 <em>22/04/2020</em></strong></td>
676 <td align="left" valign="top">
679 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
680 'virtual' codon features shown on protein (or vice versa)
681 for display in alignments, on structure views (including
682 transfer to UCSF chimera), in feature reports and for
686 <!-- JAL-3121 -->Feature attributes from VCF files can be
687 exported and re-imported as GFF3 files
690 <!-- JAL-3376 -->Capture VCF "fixed column" values
691 POS, ID, QUAL, FILTER as Feature Attributes
694 <!-- JAL-3375 -->More robust VCF numeric data field
695 validation while parsing
698 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
702 <!-- JAL-3535 -->Feature Settings dialog title includes name
706 <!-- JAL-3538 -->Font anti-aliasing in alignment views
710 <!-- JAL-3468 -->Very long feature descriptions truncated in
714 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
715 with no feature types visible
718 <!-- JAL-3574 -->Improved support for filtering feature
719 attributes with large integer values
722 <em>Jalview Installer</em>
725 <!-- JAL-3449 -->Versions for install4j and getdown and
726 installer template version reported in console (may be null
727 when Jalview launched as executable jar or via conda)
730 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and
731 higher quality background images
734 <!-- JAL-3394 -->New installer/application launcher
735 generated with install4j 8.0.4
738 <!-- JAL-3420 -->Jalview File Associations shown for Unix
742 <!-- JAL-3477 -->Improved defaults for maximum memory
743 setting when running on large memory machines
745 </ul> <em>Release processes</em>
748 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
751 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier
752 access to test-release channel builds
754 </ul> <em>Build System</em>
757 <!-- JAL-3510 -->Clover updated to 4.4.1
760 <!-- JAL-3513 -->Test code included in Clover coverage
763 </ul> <em>Groovy Scripts</em>
766 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
767 to stdout containing the consensus sequence for each
768 alignment in a Jalview session
771 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
772 genomic sequence_variant annotation from CDS as
773 missense_variant or synonymous_variant on protein products.
777 <td align="left" valign="top">
780 <!-- JAL-3581 -->Hidden sequence markers still visible when
781 'Show hidden markers' option is not ticked
784 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
785 PNG output when 'Automatically set ID width' is set in
786 jalview preferences or properties file
789 <!-- JAL-3571 -->Feature Editor dialog can be opened when
790 'Show Sequence Features' option is not ticked
793 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
794 buttons in Feature Settings dialog are clicked when no
798 <!-- JAL-3412 -->ID margins for CDS and Protein views not
799 equal when split frame is first opened
802 <!-- JAL-3296 -->Sequence position numbers in status bar not
803 correct after editing a sequence's start position
806 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
807 with annotation and exceptions thrown when only a few
808 columns shown in wrapped mode
811 <!-- JAL-3386 -->Sequence IDs missing in headless export of
812 wrapped alignment figure with annotations
815 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
816 ID fails with ClassCastException
819 <!-- JAL-3389 -->Chimera session not restored from Jalview
823 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
824 feature settings dialog also selects columns
827 <!-- JAL-3473 -->SpinnerNumberModel causes
828 IllegalArgumentException in some circumstances
831 <!-- JAL-3534 -->Multiple feature settings dialogs can be
835 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
836 alignment window is closed
839 <!-- JAL-3406 -->Credits missing some authors in Jalview
840 help documentation for 2.11.0 release
843 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
844 includes Pfam ID as sequence's accession rather than its
847 </ul> <em>Java 11 Compatibility issues</em>
850 <!-- JAL-2987 -->OSX - Can't view some search results in
851 PDB/Uniprot search panel
853 </ul> <em>Installer</em>
856 <!-- JAL-3447 -->Jalview should not create file associations
857 for 3D structure files (.pdb, .mmcif. .cif)
859 </ul> <em>Repository and Source Release</em>
862 <!-- JAL-3474 -->removed obsolete .cvsignore files from
866 <!-- JAL-3541 -->Clover report generation running out of
869 </ul> <em>New Known Issues</em>
872 <!-- JAL-3523 -->OSX - Current working directory not
873 preserved when Jalview.app launched with parameters from
877 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
878 clipped in headless figure export when Right Align option
882 <!-- JAL-3542 -->Jalview Installation type always reports
883 'Source' in console output
886 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail
887 on jalview's bamboo server but run fine locally.
893 <td width="60" align="center" nowrap><strong><a
894 name="Jalview.2.11.0">2.11.0</a><br /> <em>04/07/2019</em></strong></td>
895 <td align="left" valign="top">
898 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native
899 Application and Installers built with <a
900 href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a>
901 (licensed to the Jalview open source project) rather than
905 <!-- JAL-1929 -->Jalview Launcher System to auto-configure
906 memory settings, receive over the air updates and launch
907 specific versions via (<a
908 href="https://github.com/threerings/getdown">Three
912 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations
913 for formats supported by Jalview (including .jvp project
917 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command
918 line arguments and switch between different getdown channels
921 <!-- JAL-3141 -->Backup files created when saving Jalview
922 project or alignment files
926 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF
930 <!-- JAL-2753 -->Version of HTSJDK shipped with Jalview
931 updated to version 2.12.0
934 <!-- JAL-2620 -->Alternative genetic code tables for
938 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0
940 <li><strong>Enhanced visualisation and analysis
941 of Sequence Features</strong>
944 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
945 implementation that allows updates) used for Sequence
949 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
950 features can be filtered and shaded according to any
951 associated attributes (e.g. variant attributes from VCF
952 file, or key-value pairs imported from column 9 of GFF
956 <!-- JAL-2879 -->Feature Attributes and shading schemes
957 stored and restored from Jalview Projects
960 <!-- JAL-3334 -->Use full Sequence Ontology (via
961 BioJava) to recognise variant features
964 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants
965 on peptide sequences (also coloured red by default)
968 <!-- JAL-2792 -->Popup window to show full report for a
969 selected sequence feature's details
972 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient
973 sequence feature render algorithm (Z-sort/transparency
977 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature
982 <!-- JAL-3205 -->Symmetric score matrices for faster tree
985 <li><strong>Principal Components Analysis Viewer</strong>
988 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis
989 results and Viewer state saved in Jalview Project
992 <!-- JAL-2962 -->'Change parameters' option removed from
993 viewer's drop-down menus
996 <!-- JAL-2975 -->Can use shift + arrow keys to rotate
997 PCA image incrementally
1000 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
1004 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
1006 <li><strong>Speed and Efficiency</strong>
1009 <!-- JAL-2185,JAL-3198 -->More efficient creation of
1010 selections and multiple groups when working with large
1014 <!-- JAL-3200 -->Speedier import of annotation rows when
1015 parsing Stockholm files
1018 <li><strong>User Interface</strong>
1021 <!-- JAL-2933 -->Finder panel remembers last position in
1025 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS
1026 (What you see is what is shown)<br />Only visible
1027 regions of alignment are shown by default (can be
1028 changed in user preferences)
1031 <!-- JAL-3169 -->File Chooser stays open after
1032 responding Cancel to the Overwrite Dialog
1035 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour
1036 when all sequences are hidden
1039 <!-- JAL-1244 -->Status bar shows bounds when dragging a
1040 selection region, and gap count when inserting or
1044 <!-- JAL-3132 -->Status bar updates over sequence and
1048 <!-- JAL-3093 -->Annotation tooltips and popup menus are
1049 shown when in wrapped mode
1052 <!-- JAL-3073 -->Can select columns by dragging
1053 left/right in a graph or histogram annotation
1056 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB
1060 <!-- JAL-2621 -->Cursor changes over draggable box in
1064 <!-- JAL-3181 -->Consistent ordering of links in
1065 sequence id popup menu
1068 <!-- JAL-3080 -->Red line indicating tree-cut position
1069 not shown if no subgroups are created
1072 <!-- JAL-3042 -->Removed ability to configure length of
1073 search history by right-clicking search box
1079 <!-- JAL-3232 -->Jalview Groovy Scripting Console updated to
1082 <li><strong>Java 11 Support (not yet on general
1086 <!-- -->OSX GUI integrations for App menu's 'About'
1087 entry and trapping CMD-Q
1090 </ul> <em>Deprecations</em>
1093 <!-- JAL-3035 -->DAS sequence retrieval and annotation
1094 capabilities removed from the Jalview Desktop
1097 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling
1098 and unmarshalling has been replaced by JAXB for Jalview
1099 projects and XML based data retrieval clients
1102 <!-- JAL-3311 -->Disable VAMSAS menu in preparation for
1106 <!-- -->Jalview Desktop no longer distributed via Java Web
1109 </ul> <em>Documentation</em>
1112 <!-- JAL-3003 -->Added remarks about transparent rendering
1113 effects not supported in EPS figure export
1116 <!-- JAL-2903 -->Typos in documentation for Preferences
1119 </ul> <em>Development and Release Processes</em>
1122 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated
1126 <!-- JAL-1424 -->Enhanced checks for missing and duplicated
1127 keys in Message bundles
1130 <!-- JAL-3225 -->Eclipse project configuration managed with
1134 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian Bamboo
1135 continuous integration for unattended Test Suite execution
1138 <!-- JAL-2864 -->Memory test suite to detect leaks in common
1142 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
1146 <!-- JAL-3248 -->Developer documentation migrated to
1147 markdown (with HTML rendering)
1150 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
1153 <!-- JAL-3289 -->New URLs for publishing development
1158 <td align="left" valign="top">
1161 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
1164 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
1165 superposition in Jmol fail on Windows
1168 <!-- JAL-3286 -->Blank error dialog is displayed when
1169 discovering structures for sequences with lots of PDB
1173 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export
1174 with monospaced font
1177 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
1178 Jalview project involving multiple views
1181 <!-- JAL-3164 -->Overview for complementary view in a linked
1182 CDS/Protein alignment is not updated when Hide Columns by
1183 Annotation dialog hides columns
1186 <!-- JAL-3158 -->Selection highlighting in the complement of
1187 a CDS/Protein alignment stops working after making a
1188 selection in one view, then making another selection in the
1192 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
1196 <!-- JAL-3154 -->Table Columns could be re-ordered in
1197 Feature Settings and Jalview Preferences panels
1200 <!-- JAL-2865 -->Jalview hangs when closing windows, or
1201 redrawing the overview with large alignments
1204 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
1205 region if columns were selected by dragging right-to-left
1206 and the mouse moved to the left of the first column
1209 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to
1210 a hidden column marker via scale popup menu
1213 <!-- JAL-2846 -->Error message for trying to load in invalid
1214 URLs doesn't tell users the invalid URL
1217 <!-- JAL-2816 -->Tooltips displayed for features filtered by
1221 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl
1222 during show cross references or Fetch Database References
1223 are shown in red in original view
1226 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown
1227 correctly on peptide sequence (computed variant shown as
1231 <!-- JAL-2060 -->'Graduated colour' option not offered for
1232 manually created features (where feature score is Float.NaN)
1235 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or
1236 printed when columns are hidden
1239 <!-- JAL-3082 -->Regular expression error for '(' in Select
1240 Columns by Annotation description
1243 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after
1244 dragging out of Scale or Annotation Panel
1247 <!-- JAL-3075 -->Column selection incorrect after scrolling
1251 <!-- JAL-3074 -->Left/right drag in annotation can scroll
1255 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal
1259 <!-- JAL-3002 -->Column display is out by one after Page
1260 Down, Page Up in wrapped mode
1263 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
1266 <!-- JAL-2932 -->Finder searches in minimised alignments
1269 <!-- JAL-2250 -->'Apply Colour to All Groups' not always
1270 selected on opening an alignment
1273 <!-- JAL-3180 -->'Colour by Annotation' not marked selected
1277 <!-- JAL-3201 -->Per-group Clustal colour scheme changes
1278 when different groups in the alignment are selected
1281 <!-- JAL-2717 -->Internationalised colour scheme names not
1282 shown correctly in menu
1285 <!-- JAL-3206 -->Colour by Annotation can go black at
1286 min/max threshold limit
1289 <!-- JAL-3125 -->Value input for graduated feature colour
1290 threshold gets 'unrounded'
1293 <!-- JAL-2982 -->PCA image export doesn't respect background
1297 <!-- JAL-2963 -->PCA points don't dim when rotated about y
1301 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
1304 <!-- JAL-3078 -->Cancel in Tree Font dialog resets
1305 alignment, not Tree font
1308 <!-- JAL-2964 -->Associate Tree with All Views not restored
1312 <!-- JAL-2915 -->Scrolling of split frame is sluggish if
1313 Overview shown in complementary view
1316 <!-- JAL-3313 -->Codon consensus incorrectly scaled when
1317 shown without normalisation
1320 <!-- JAL-3021 -->Sequence Details report should open
1321 positioned at top of report
1324 <!-- JAL-914 -->Help page can be opened twice
1327 <!-- JAL-3333 -->Fuzzy text in web service status menu on
1330 </ul> <em>Editing</em>
1333 <!-- JAL-2822 -->Start and End should be updated when
1334 sequence data at beginning or end of alignment added/removed
1338 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection
1339 doesn't relocate sequence features correctly when start of
1340 sequence is removed (Known defect since 2.10)
1343 <!-- JAL-2830 -->Inserting gap sequence via the Edit
1344 Sequence dialog corrupts dataset sequence
1347 <!-- JAL-868 -->Structure colours not updated when
1348 associated tree repartitions the alignment view (Regression
1351 </ul> <em>Datamodel</em>
1354 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
1355 sequence's End is greater than its length
1357 </ul> <em>Bugs fixed for Java 11 Support (not yet on general
1361 <!-- JAL-3288 -->Menus work properly in split-screen
1363 </ul> <em>New Known Defects</em>
1366 <!-- JAL-3340 -->Select columns containing feature by double
1367 clicking ignores bounds of an existing selected region
1370 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in
1371 gapped regions of protein alignment.
1374 <!-- JAL-2647 -->Input Data menu entry is greyed out when
1375 PCA View is restored from a Jalview 2.11 project
1378 <!-- JAL-3213 -->Alignment panel height can be too small
1382 <!-- JAL-3240 -->Display is incorrect after removing gapped
1383 columns within hidden columns
1386 <!-- JAL-3314 -->Rightmost selection is lost when mouse
1387 re-enters window after dragging left to select columns to
1388 left of visible region
1391 <!-- JAL-2876 -->Features coloured according to their
1392 description string and thresholded by score in earlier
1393 versions of Jalview are not shown as thresholded features in
1394 2.11. To workaround please create a Score filter instead.
1397 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't
1398 reset group visibility
1401 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in
1402 linked CDS/Protein view
1405 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1406 alignments with multiple views can close views unexpectedly
1408 </ul> <em>Java 11 Specific defects</em>
1411 <!-- JAL-3235 -->Jalview Properties file is not sorted
1412 alphabetically when saved
1418 <td width="60" nowrap>
1419 <div align="center">
1420 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1423 <td><div align="left">
1427 <!-- JAL-3101 -->Default memory for Jalview webstart and
1428 InstallAnywhere increased to 1G.
1431 <!-- JAL-247 -->Hidden sequence markers and representative
1432 sequence bolding included when exporting alignment as EPS,
1433 SVG, PNG or HTML. <em>Display is configured via the
1434 Format menu, or for command-line use via a Jalview
1435 properties file.</em>
1438 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1439 API and sequence data now imported as JSON.
1442 <!-- JAL-3065 -->Change in recommended way of starting
1443 Jalview via a Java command line: add jars in lib directory
1444 to CLASSPATH, rather than via the deprecated java.ext.dirs
1448 <em>Development</em>
1451 <!-- JAL-3047 -->Support added to execute test suite
1452 instrumented with <a href="http://openclover.org/">Open
1457 <td><div align="left">
1461 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1462 row shown in Feredoxin Structure alignment view of example
1466 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1467 annotation displayed.
1470 <!-- JAL-3107 -->Group conservation/consensus not shown
1471 for newly created group when 'Apply to all groups'
1475 <!-- JAL-3087 -->Corrupted display when switching to
1476 wrapped mode when sequence panel's vertical scrollbar is
1480 <!-- JAL-3003 -->Alignment is black in exported EPS file
1481 when sequences are selected in exported view.</em>
1484 <!-- JAL-3059 -->Groups with different coloured borders
1485 aren't rendered with correct colour.
1488 <!-- JAL-3092 -->Jalview could hang when importing certain
1489 types of knotted RNA secondary structure.
1492 <!-- JAL-3095 -->Sequence highlight and selection in
1493 trimmed VARNA 2D structure is incorrect for sequences that
1497 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1498 annotation when columns are inserted into an alignment,
1499 and when exporting as Stockholm flatfile.
1502 <!-- JAL-3053 -->Jalview annotation rows containing upper
1503 and lower-case 'E' and 'H' do not automatically get
1504 treated as RNA secondary structure.
1507 <!-- JAL-3106 -->.jvp should be used as default extension
1508 (not .jar) when saving a Jalview project file.
1511 <!-- JAL-3105 -->Mac Users: closing a window correctly
1512 transfers focus to previous window on OSX
1515 <em>Java 10 Issues Resolved</em>
1518 <!-- JAL-2988 -->OSX - Can't save new files via the File
1519 or export menus by typing in a name into the Save dialog
1523 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1524 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1525 'look and feel' which has improved compatibility with the
1526 latest version of OSX.
1532 <td width="60" nowrap>
1533 <div align="center">
1534 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1535 <em>7/06/2018</em></strong>
1538 <td><div align="left">
1542 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1543 annotation retrieved from Uniprot
1546 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1547 onto the Jalview Desktop
1551 <td><div align="left">
1555 <!-- JAL-3017 -->Cannot import features with multiple
1556 variant elements (blocks import of some Uniprot records)
1559 <!-- JAL-2997 -->Clustal files with sequence positions in
1560 right-hand column parsed correctly
1563 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1564 not alignment area in exported graphic
1567 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1568 window has input focus
1571 <!-- JAL-2992 -->Annotation panel set too high when
1572 annotation added to view (Windows)
1575 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1576 network connectivity is poor
1579 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1580 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1581 the currently open URL and links from a page viewed in
1582 Firefox or Chrome on Windows is now fully supported. If
1583 you are using Edge, only links in the page can be
1584 dragged, and with Internet Explorer, only the currently
1585 open URL in the browser can be dropped onto Jalview.</em>
1588 <em>New Known Defects</em>
1591 <!-- JAL-3083 -->Cancel option doesn't reset Colour by
1598 <td width="60" nowrap>
1599 <div align="center">
1600 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1603 <td><div align="left">
1607 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1608 for disabling automatic superposition of multiple
1609 structures and open structures in existing views
1612 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1613 ID and annotation area margins can be click-dragged to
1617 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1621 <!-- JAL-2759 -->Improved performance for large alignments
1622 and lots of hidden columns
1625 <!-- JAL-2593 -->Improved performance when rendering lots
1626 of features (particularly when transparency is disabled)
1629 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2
1630 for exchange of Jalview features and Chimera attributes
1631 made generally available
1635 <td><div align="left">
1638 <!-- JAL-2899 -->Structure and Overview aren't updated
1639 when Colour By Annotation threshold slider is adjusted
1642 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1643 overlapping alignment panel
1646 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1650 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1651 improved: CDS not handled correctly if transcript has no
1655 <!-- JAL-2321 -->Secondary structure and temperature
1656 factor annotation not added to sequence when local PDB
1657 file associated with it by drag'n'drop or structure
1661 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1662 dialog doesn't import PDB files dropped on an alignment
1665 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1666 scroll bar doesn't work for some CDS/Protein views
1669 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1670 Java 1.8u153 onwards and Java 1.9u4+.
1673 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1674 columns in annotation row
1677 <!-- JAL-2913 -->Preferences panel's ID Width control is
1678 not honored in batch mode
1681 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1682 for structures added to existing Jmol view
1685 <!-- JAL-2223 -->'View Mappings' includes duplicate
1686 entries after importing project with multiple views
1689 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1690 protein sequences via SIFTS from associated PDB entries
1691 with negative residue numbers or missing residues fails
1694 <!-- JAL-2952 -->Exception when shading sequence with
1695 negative Temperature Factor values from annotated PDB
1696 files (e.g. as generated by CONSURF)
1699 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1700 tooltip doesn't include a text description of mutation
1703 <!-- JAL-2922 -->Invert displayed features very slow when
1704 structure and/or overview windows are also shown
1707 <!-- JAL-2954 -->Selecting columns from highlighted
1708 regions very slow for alignments with large numbers of
1712 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1713 with 'StringIndexOutOfBounds'
1716 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and
1717 Feel for OSX platforms running Java 10
1720 <!-- JAL-2960 -->Adding a structure to existing structure
1721 view appears to do nothing because the view is hidden
1722 behind the alignment view
1728 <!-- JAL-2926 -->Copy consensus sequence option in applet
1729 should copy the group consensus when popup is opened on it
1735 <!-- JAL-2913 -->Fixed ID width preference is not
1739 <em>New Known Defects</em>
1742 <!-- JAL-2973 --> Exceptions occasionally raised when
1743 editing a large alignment and overview is displayed
1746 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1747 repeatedly after a series of edits even when the overview
1748 is no longer reflecting updates
1751 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1752 structures for protein subsequence (if 'Trim Retrieved
1753 Sequences' enabled) or Ensembl isoforms (Workaround in
1754 2.10.4 is to fail back to N&W mapping)
1757 <!-- JAL-2990 -->Export Annotations from File Menu with
1758 CSV option gives blank output
1764 <td width="60" nowrap>
1765 <div align="center">
1766 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br />
1767 <em>24/1/2018</em></strong>
1770 <td><div align="left">
1772 <li>Updated Certum Codesigning Certificate (Valid till
1773 30th November 2018)</li>
1776 <td><div align="left">
1781 <!-- JAL-2859-->Only one structure is loaded when
1782 several sequences and structures are selected for
1786 <!-- JAL-2851-->Alignment doesn't appear to scroll
1787 vertically via trackpad and scrollwheel
1790 <!-- JAL-2842-->Jalview hangs if up/down arrows pressed
1791 in cursor mode when cursor lies in hidden region at
1795 <!-- JAL-2827-->Helix annotation has 'notches' when
1796 scrolled into view if columns are hidden
1799 <!-- JAL-2740-->Annotation column filter can be slow to
1800 reset (ie after hitting cancel) for large numbers of
1804 <!-- JAL-2849-->User preference for disabling inclusion
1805 of sequence limits when exporting as flat file has no
1809 <!-- JAL-2679-->Reproducible cross-reference
1810 relationships when retrieving sequences from
1817 <td width="60" nowrap>
1818 <div align="center">
1819 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1822 <td><div align="left">
1826 <!-- JAL-2446 -->Faster and more efficient management and
1827 rendering of sequence features
1830 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1831 429 rate limit request hander
1834 <!-- JAL-2773 -->Structure views don't get updated unless
1835 their colours have changed
1838 <!-- JAL-2495 -->All linked sequences are highlighted for
1839 a structure mousover (Jmol) or selection (Chimera)
1842 <!-- JAL-2790 -->'Cancel' button in progress bar for
1843 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1846 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1847 view from Ensembl locus cross-references
1850 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1854 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1855 feature can be disabled
1858 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1859 PDB easier retrieval of sequences for lists of IDs
1862 <!-- JAL-2758 -->Short names for sequences retrieved from
1868 <li>Groovy interpreter updated to 2.4.12</li>
1869 <li>Example groovy script for generating a matrix of
1870 percent identity scores for current alignment.</li>
1872 <em>Testing and Deployment</em>
1875 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1879 <td><div align="left">
1883 <!-- JAL-2643 -->Pressing tab after updating the colour
1884 threshold text field doesn't trigger an update to the
1888 <!-- JAL-2682 -->Race condition when parsing sequence ID
1892 <!-- JAL-2608 -->Overview windows are also closed when
1893 alignment window is closed
1896 <!-- JAL-2548 -->Export of features doesn't always respect
1900 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1901 takes a long time in Cursor mode
1907 <!-- JAL-2777 -->Structures with whitespace chainCode
1908 cannot be viewed in Chimera
1911 <!-- JAL-2728 -->Protein annotation panel too high in
1915 <!-- JAL-2757 -->Can't edit the query after the server
1916 error warning icon is shown in Uniprot and PDB Free Text
1920 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1923 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1926 <!-- JAL-2739 -->Hidden column marker in last column not
1927 rendered when switching back from Wrapped to normal view
1930 <!-- JAL-2768 -->Annotation display corrupted when
1931 scrolling right in unwapped alignment view
1934 <!-- JAL-2542 -->Existing features on subsequence
1935 incorrectly relocated when full sequence retrieved from
1939 <!-- JAL-2733 -->Last reported memory still shown when
1940 Desktop->Show Memory is unticked (OSX only)
1943 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1944 features of same type and group to be selected for
1948 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1949 alignments when hidden columns are present
1952 <!-- JAL-2392 -->Jalview freezes when loading and
1953 displaying several structures
1956 <!-- JAL-2732 -->Black outlines left after resizing or
1960 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1961 within the Jalview desktop on OSX
1964 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1965 when in wrapped alignment mode
1968 <!-- JAL-2636 -->Scale mark not shown when close to right
1969 hand end of alignment
1972 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1973 each selected sequence do not have correct start/end
1977 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1978 after canceling the Alignment Window's Font dialog
1981 <!-- JAL-2036 -->Show cross-references not enabled after
1982 restoring project until a new view is created
1985 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1986 URL links appears when only default EMBL-EBI link is
1987 configured (since 2.10.2b2)
1990 <!-- JAL-2775 -->Overview redraws whole window when box
1991 position is adjusted
1994 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1995 in a multi-chain structure when viewing alignment
1996 involving more than one chain (since 2.10)
1999 <!-- JAL-2811 -->Double residue highlights in cursor mode
2000 if new selection moves alignment window
2003 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
2004 arrow key in cursor mode to pass hidden column marker
2007 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
2008 that produces correctly annotated transcripts and products
2011 <!-- JAL-2776 -->Toggling a feature group after first time
2012 doesn't update associated structure view
2015 <em>Applet</em><br />
2018 <!-- JAL-2687 -->Concurrent modification exception when
2019 closing alignment panel
2022 <em>BioJSON</em><br />
2025 <!-- JAL-2546 -->BioJSON export does not preserve
2026 non-positional features
2029 <em>New Known Issues</em>
2032 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
2033 sequence features correctly (for many previous versions of
2037 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
2038 using cursor in wrapped panel other than top
2041 <!-- JAL-2791 -->Select columns containing feature ignores
2042 graduated colour threshold
2045 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
2046 always preserve numbering and sequence features
2049 <em>Known Java 9 Issues</em>
2052 <!-- JAL-2902 -->Groovy Console very slow to open and is
2053 not responsive when entering characters (Webstart, Java
2060 <td width="60" nowrap>
2061 <div align="center">
2062 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
2063 <em>2/10/2017</em></strong>
2066 <td><div align="left">
2067 <em>New features in Jalview Desktop</em>
2070 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API
2074 <!-- JAL-2745 -->HTTPS used for all connections to
2079 <td><div align="left"></div></td>
2082 <td width="60" nowrap>
2083 <div align="center">
2084 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
2085 <em>7/9/2017</em></strong>
2088 <td><div align="left">
2092 <!-- JAL-2588 -->Show gaps in overview window by colouring
2093 in grey (sequences used to be coloured grey, and gaps were
2097 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
2101 <!-- JAL-2587 -->Overview updates immediately on increase
2102 in size and progress bar shown as higher resolution
2103 overview is recalculated
2108 <td><div align="left">
2112 <!-- JAL-2664 -->Overview window redraws every hidden
2113 column region row by row
2116 <!-- JAL-2681 -->duplicate protein sequences shown after
2117 retrieving Ensembl crossrefs for sequences from Uniprot
2120 <!-- JAL-2603 -->Overview window throws NPE if show boxes
2121 format setting is unticked
2124 <!-- JAL-2610 -->Groups are coloured wrongly in overview
2125 if group has show boxes format setting unticked
2128 <!-- JAL-2672,JAL-2665 -->Redraw problems when
2129 autoscrolling whilst dragging current selection group to
2130 include sequences and columns not currently displayed
2133 <!-- JAL-2691 -->Not all chains are mapped when multimeric
2134 assemblies are imported via CIF file
2137 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
2138 displayed when threshold or conservation colouring is also
2142 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
2146 <!-- JAL-2673 -->Jalview continues to scroll after
2147 dragging a selected region off the visible region of the
2151 <!-- JAL-2724 -->Cannot apply annotation based
2152 colourscheme to all groups in a view
2155 <!-- JAL-2511 -->IDs don't line up with sequences
2156 initially after font size change using the Font chooser or
2163 <td width="60" nowrap>
2164 <div align="center">
2165 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
2168 <td><div align="left">
2169 <em>Calculations</em>
2173 <!-- JAL-1933 -->Occupancy annotation row shows number of
2174 ungapped positions in each column of the alignment.
2177 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
2178 a calculation dialog box
2181 <!-- JAL-2379 -->Revised implementation of PCA for speed
2182 and memory efficiency (~30x faster)
2185 <!-- JAL-2403 -->Revised implementation of sequence
2186 similarity scores as used by Tree, PCA, Shading Consensus
2187 and other calculations
2190 <!-- JAL-2416 -->Score matrices are stored as resource
2191 files within the Jalview codebase
2194 <!-- JAL-2500 -->Trees computed on Sequence Feature
2195 Similarity may have different topology due to increased
2202 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
2203 model for alignments and groups
2206 <!-- JAL-384 -->Custom shading schemes created via groovy
2213 <!-- JAL-2526 -->Efficiency improvements for interacting
2214 with alignment and overview windows
2217 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
2221 <!-- JAL-2388 -->Hidden columns and sequences can be
2225 <!-- JAL-2611 -->Click-drag in visible area allows fine
2226 adjustment of visible position
2230 <em>Data import/export</em>
2233 <!-- JAL-2535 -->Posterior probability annotation from
2234 Stockholm files imported as sequence associated annotation
2237 <!-- JAL-2507 -->More robust per-sequence positional
2238 annotation input/output via stockholm flatfile
2241 <!-- JAL-2533 -->Sequence names don't include file
2242 extension when importing structure files without embedded
2243 names or PDB accessions
2246 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
2247 format sequence substitution matrices
2250 <em>User Interface</em>
2253 <!-- JAL-2447 --> Experimental Features Checkbox in
2254 Desktop's Tools menu to hide or show untested features in
2258 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
2259 via Overview or sequence motif search operations
2262 <!-- JAL-2547 -->Amend sequence features dialog box can be
2263 opened by double clicking gaps within sequence feature
2267 <!-- JAL-1476 -->Status bar message shown when not enough
2268 aligned positions were available to create a 3D structure
2272 <em>3D Structure</em>
2275 <!-- JAL-2430 -->Hidden regions in alignment views are not
2276 coloured in linked structure views
2279 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
2280 file-based command exchange
2283 <!-- JAL-2375 -->Structure chooser automatically shows
2284 Cached Structures rather than querying the PDBe if
2285 structures are already available for sequences
2288 <!-- JAL-2520 -->Structures imported via URL are cached in
2289 the Jalview project rather than downloaded again when the
2290 project is reopened.
2293 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
2294 to transfer Chimera's structure attributes as Jalview
2295 features, and vice-versa (<strong>Experimental
2299 <em>Web Services</em>
2302 <!-- JAL-2549 -->Updated JABAWS client to v2.2
2305 <!-- JAL-2335 -->Filter non-standard amino acids and
2306 nucleotides when submitting to AACon and other MSA
2310 <!-- JAL-2316, -->URLs for viewing database
2311 cross-references provided by identifiers.org and the
2312 EMBL-EBI's MIRIAM DB
2319 <!-- JAL-2344 -->FileFormatI interface for describing and
2320 identifying file formats (instead of String constants)
2323 <!-- JAL-2228 -->FeatureCounter script refactored for
2324 efficiency when counting all displayed features (not
2325 backwards compatible with 2.10.1)
2328 <em>Example files</em>
2331 <!-- JAL-2631 -->Graduated feature colour style example
2332 included in the example feature file
2335 <em>Documentation</em>
2338 <!-- JAL-2339 -->Release notes reformatted for readability
2339 with the built-in Java help viewer
2342 <!-- JAL-1644 -->Find documentation updated with 'search
2343 sequence description' option
2349 <!-- JAL-2485, -->External service integration tests for
2350 Uniprot REST Free Text Search Client
2353 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
2356 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
2361 <td><div align="left">
2362 <em>Calculations</em>
2365 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
2366 matrix - C->R should be '-3'<br />Old matrix restored
2367 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
2369 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
2370 Jalview's treatment of gaps in PCA and substitution matrix
2371 based Tree calculations.<br /> <br />In earlier versions
2372 of Jalview, gaps matching gaps were penalised, and gaps
2373 matching non-gaps penalised even more. In the PCA
2374 calculation, gaps were actually treated as non-gaps - so
2375 different costs were applied, which meant Jalview's PCAs
2376 were different to those produced by SeqSpace.<br />Jalview
2377 now treats gaps in the same way as SeqSpace (ie it scores
2378 them as 0). <br /> <br />Enter the following in the
2379 Groovy console to restore pre-2.10.2 behaviour:<br />
2380 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
2381 // for 2.10.1 mode <br />
2382 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
2383 // to restore 2.10.2 mode <br /> <br /> <em>Note:
2384 these settings will affect all subsequent tree and PCA
2385 calculations (not recommended)</em></li>
2387 <!-- JAL-2424 -->Fixed off-by-one bug that affected
2388 scaling of branch lengths for trees computed using
2389 Sequence Feature Similarity.
2392 <!-- JAL-2377 -->PCA calculation could hang when
2393 generating output report when working with highly
2394 redundant alignments
2397 <!-- JAL-2544 --> Sort by features includes features to
2398 right of selected region when gaps present on right-hand
2402 <em>User Interface</em>
2405 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2406 doesn't reselect a specific sequence's associated
2407 annotation after it was used for colouring a view
2410 <!-- JAL-2419 -->Current selection lost if popup menu
2411 opened on a region of alignment without groups
2414 <!-- JAL-2374 -->Popup menu not always shown for regions
2415 of an alignment with overlapping groups
2418 <!-- JAL-2310 -->Finder double counts if both a sequence's
2419 name and description match
2422 <!-- JAL-2370 -->Hiding column selection containing two
2423 hidden regions results in incorrect hidden regions
2426 <!-- JAL-2386 -->'Apply to all groups' setting when
2427 changing colour does not apply Conservation slider value
2431 <!-- JAL-2373 -->Percentage identity and conservation menu
2432 items do not show a tick or allow shading to be disabled
2435 <!-- JAL-2385 -->Conservation shading or PID threshold
2436 lost when base colourscheme changed if slider not visible
2439 <!-- JAL-2547 -->Sequence features shown in tooltip for
2440 gaps before start of features
2443 <!-- JAL-2623 -->Graduated feature colour threshold not
2444 restored to UI when feature colour is edited
2447 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2448 a time when scrolling vertically in wrapped mode.
2451 <!-- JAL-2630 -->Structure and alignment overview update
2452 as graduate feature colour settings are modified via the
2456 <!-- JAL-2034 -->Overview window doesn't always update
2457 when a group defined on the alignment is resized
2460 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2461 wrapped view result in positional status updates
2465 <!-- JAL-2563 -->Status bar doesn't show position for
2466 ambiguous amino acid and nucleotide symbols
2469 <!-- JAL-2602 -->Copy consensus sequence failed if
2470 alignment included gapped columns
2473 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2474 widgets don't permanently disappear
2477 <!-- JAL-2503 -->Cannot select or filter quantitative
2478 annotation that are shown only as column labels (e.g.
2479 T-Coffee column reliability scores)
2482 <!-- JAL-2594 -->Exception thrown if trying to create a
2483 sequence feature on gaps only
2486 <!-- JAL-2504 -->Features created with 'New feature'
2487 button from a Find inherit previously defined feature type
2488 rather than the Find query string
2491 <!-- JAL-2423 -->incorrect title in output window when
2492 exporting tree calculated in Jalview
2495 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2496 and then revealing them reorders sequences on the
2500 <!-- JAL-964 -->Group panel in sequence feature settings
2501 doesn't update to reflect available set of groups after
2502 interactively adding or modifying features
2505 <!-- JAL-2225 -->Sequence Database chooser unusable on
2509 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2510 only excluded gaps in current sequence and ignored
2517 <!-- JAL-2421 -->Overview window visible region moves
2518 erratically when hidden rows or columns are present
2521 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2522 Structure Viewer's colour menu don't correspond to
2526 <!-- JAL-2405 -->Protein specific colours only offered in
2527 colour and group colour menu for protein alignments
2530 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2531 reflect currently selected view or group's shading
2535 <!-- JAL-2624 -->Feature colour thresholds not respected
2536 when rendered on overview and structures when opacity at
2540 <!-- JAL-2589 -->User defined gap colour not shown in
2541 overview when features overlaid on alignment
2544 <!-- JAL-2567 -->Feature settings for different views not
2545 recovered correctly from Jalview project file
2548 <!-- JAL-2256 -->Feature colours in overview when first
2549 opened (automatically via preferences) are different to
2550 the main alignment panel
2553 <em>Data import/export</em>
2556 <!-- JAL-2576 -->Very large alignments take a long time to
2560 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2561 added after a sequence was imported are not written to
2565 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2566 when importing RNA secondary structure via Stockholm
2569 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2570 not shown in correct direction for simple pseudoknots
2573 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2574 with lightGray or darkGray via features file (but can
2578 <!-- JAL-2383 -->Above PID colour threshold not recovered
2579 when alignment view imported from project
2582 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2583 structure and sequences extracted from structure files
2584 imported via URL and viewed in Jmol
2587 <!-- JAL-2520 -->Structures loaded via URL are saved in
2588 Jalview Projects rather than fetched via URL again when
2589 the project is loaded and the structure viewed
2592 <em>Web Services</em>
2595 <!-- JAL-2519 -->EnsemblGenomes example failing after
2596 release of Ensembl v.88
2599 <!-- JAL-2366 -->Proxy server address and port always
2600 appear enabled in Preferences->Connections
2603 <!-- JAL-2461 -->DAS registry not found exceptions
2604 removed from console output
2607 <!-- JAL-2582 -->Cannot retrieve protein products from
2608 Ensembl by Peptide ID
2611 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2612 created from SIFTs, and spurious 'Couldn't open structure
2613 in Chimera' errors raised after April 2017 update (problem
2614 due to 'null' string rather than empty string used for
2615 residues with no corresponding PDB mapping).
2618 <em>Application UI</em>
2621 <!-- JAL-2361 -->User Defined Colours not added to Colour
2625 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2626 case' residues (button in colourscheme editor debugged and
2627 new documentation and tooltips added)
2630 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2631 doesn't restore group-specific text colour thresholds
2634 <!-- JAL-2243 -->Feature settings panel does not update as
2635 new features are added to alignment
2638 <!-- JAL-2532 -->Cancel in feature settings reverts
2639 changes to feature colours via the Amend features dialog
2642 <!-- JAL-2506 -->Null pointer exception when attempting to
2643 edit graduated feature colour via amend features dialog
2647 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2648 selection menu changes colours of alignment views
2651 <!-- JAL-2426 -->Spurious exceptions in console raised
2652 from alignment calculation workers after alignment has
2656 <!-- JAL-1608 -->Typo in selection popup menu - Create
2657 groups now 'Create Group'
2660 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2661 Create/Undefine group doesn't always work
2664 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2665 shown again after pressing 'Cancel'
2668 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2669 adjusts start position in wrap mode
2672 <!-- JAL-2563 -->Status bar doesn't show positions for
2673 ambiguous amino acids
2676 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2677 CDS/Protein view after CDS sequences added for aligned
2681 <!-- JAL-2592 -->User defined colourschemes called 'User
2682 Defined' don't appear in Colours menu
2688 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2689 score models doesn't always result in an updated PCA plot
2692 <!-- JAL-2442 -->Features not rendered as transparent on
2693 overview or linked structure view
2696 <!-- JAL-2372 -->Colour group by conservation doesn't
2700 <!-- JAL-2517 -->Hitting Cancel after applying
2701 user-defined colourscheme doesn't restore original
2708 <!-- JAL-2314 -->Unit test failure:
2709 jalview.ws.jabaws.RNAStructExportImport setup fails
2712 <!-- JAL-2307 -->Unit test failure:
2713 jalview.ws.sifts.SiftsClientTest due to compatibility
2714 problems with deep array comparison equality asserts in
2715 successive versions of TestNG
2718 <!-- JAL-2479 -->Relocated StructureChooserTest and
2719 ParameterUtilsTest Unit tests to Network suite
2722 <em>New Known Issues</em>
2725 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2726 phase after a sequence motif find operation
2729 <!-- JAL-2550 -->Importing annotation file with rows
2730 containing just upper and lower case letters are
2731 interpreted as WUSS RNA secondary structure symbols
2734 <!-- JAL-2590 -->Cannot load and display Newick trees
2735 reliably from eggnog Ortholog database
2738 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2739 containing features of type Highlight' when 'B' is pressed
2740 to mark columns containing highlighted regions.
2743 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2744 doesn't always add secondary structure annotation.
2749 <td width="60" nowrap>
2750 <div align="center">
2751 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2754 <td><div align="left">
2758 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2759 for all consensus calculations
2762 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2765 <li>Updated Jalview's Certum code signing certificate
2768 <em>Application</em>
2771 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2772 set of database cross-references, sorted alphabetically
2775 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2776 from database cross references. Users with custom links
2777 will receive a <a href="webServices/urllinks.html#warning">warning
2778 dialog</a> asking them to update their preferences.
2781 <!-- JAL-2287-->Cancel button and escape listener on
2782 dialog warning user about disconnecting Jalview from a
2786 <!-- JAL-2320-->Jalview's Chimera control window closes if
2787 the Chimera it is connected to is shut down
2790 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2791 columns menu item to mark columns containing highlighted
2792 regions (e.g. from structure selections or results of a
2796 <!-- JAL-2284-->Command line option for batch-generation
2797 of HTML pages rendering alignment data with the BioJS
2807 <!-- JAL-2286 -->Columns with more than one modal residue
2808 are not coloured or thresholded according to percent
2809 identity (first observed in Jalview 2.8.2)
2812 <!-- JAL-2301 -->Threonine incorrectly reported as not
2816 <!-- JAL-2318 -->Updates to documentation pages (above PID
2817 threshold, amino acid properties)
2820 <!-- JAL-2292 -->Lower case residues in sequences are not
2821 reported as mapped to residues in a structure file in the
2825 <!--JAL-2324 -->Identical features with non-numeric scores
2826 could be added multiple times to a sequence
2829 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2830 bond features shown as two highlighted residues rather
2831 than a range in linked structure views, and treated
2832 correctly when selecting and computing trees from features
2835 <!-- JAL-2281-->Custom URL links for database
2836 cross-references are matched to database name regardless
2841 <em>Application</em>
2844 <!-- JAL-2282-->Custom URL links for specific database
2845 names without regular expressions also offer links from
2849 <!-- JAL-2315-->Removing a single configured link in the
2850 URL links pane in Connections preferences doesn't actually
2851 update Jalview configuration
2854 <!-- JAL-2272-->CTRL-Click on a selected region to open
2855 the alignment area popup menu doesn't work on El-Capitan
2858 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2859 files with similarly named sequences if dropped onto the
2863 <!-- JAL-2312 -->Additional mappings are shown for PDB
2864 entries where more chains exist in the PDB accession than
2865 are reported in the SIFTS file
2868 <!-- JAL-2317-->Certain structures do not get mapped to
2869 the structure view when displayed with Chimera
2872 <!-- JAL-2317-->No chains shown in the Chimera view
2873 panel's View->Show Chains submenu
2876 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2877 work for wrapped alignment views
2880 <!--JAL-2197 -->Rename UI components for running JPred
2881 predictions from 'JNet' to 'JPred'
2884 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2885 corrupted when annotation panel vertical scroll is not at
2886 first annotation row
2889 <!--JAL-2332 -->Attempting to view structure for Hen
2890 lysozyme results in a PDB Client error dialog box
2893 <!-- JAL-2319 -->Structure View's mapping report switched
2894 ranges for PDB and sequence for SIFTS
2897 SIFTS 'Not_Observed' residues mapped to non-existant
2901 <!-- <em>New Known Issues</em>
2908 <td width="60" nowrap>
2909 <div align="center">
2910 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2911 <em>25/10/2016</em></strong>
2914 <td><em>Application</em>
2916 <li>3D Structure chooser opens with 'Cached structures'
2917 view if structures already loaded</li>
2918 <li>Progress bar reports models as they are loaded to
2919 structure views</li>
2925 <li>Colour by conservation always enabled and no tick
2926 shown in menu when BLOSUM or PID shading applied</li>
2927 <li>FER1_ARATH and FER2_ARATH labels were switched in
2928 example sequences/projects/trees</li>
2930 <em>Application</em>
2932 <li>Jalview projects with views of local PDB structure
2933 files saved on Windows cannot be opened on OSX</li>
2934 <li>Multiple structure views can be opened and superposed
2935 without timeout for structures with multiple models or
2936 multiple sequences in alignment</li>
2937 <li>Cannot import or associated local PDB files without a
2938 PDB ID HEADER line</li>
2939 <li>RMSD is not output in Jmol console when superposition
2941 <li>Drag and drop of URL from Browser fails for Linux and
2942 OSX versions earlier than El Capitan</li>
2943 <li>ENA client ignores invalid content from ENA server</li>
2944 <li>Exceptions are not raised in console when ENA client
2945 attempts to fetch non-existent IDs via Fetch DB Refs UI
2947 <li>Exceptions are not raised in console when a new view
2948 is created on the alignment</li>
2949 <li>OSX right-click fixed for group selections: CMD-click
2950 to insert/remove gaps in groups and CTRL-click to open group
2953 <em>Build and deployment</em>
2955 <li>URL link checker now copes with multi-line anchor
2958 <em>New Known Issues</em>
2960 <li>Drag and drop from URL links in browsers do not work
2967 <td width="60" nowrap>
2968 <div align="center">
2969 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2972 <td><em>General</em>
2975 <!-- JAL-2124 -->Updated Spanish translations.
2978 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2979 for importing structure data to Jalview. Enables mmCIF and
2983 <!-- JAL-192 --->Alignment ruler shows positions relative to
2987 <!-- JAL-2202 -->Position/residue shown in status bar when
2988 mousing over sequence associated annotation
2991 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2995 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2996 '()', canonical '[]' and invalid '{}' base pair populations
3000 <!-- JAL-2092 -->Feature settings popup menu options for
3001 showing or hiding columns containing a feature
3004 <!-- JAL-1557 -->Edit selected group by double clicking on
3005 group and sequence associated annotation labels
3008 <!-- JAL-2236 -->Sequence name added to annotation label in
3009 select/hide columns by annotation and colour by annotation
3013 </ul> <em>Application</em>
3016 <!-- JAL-2050-->Automatically hide introns when opening a
3017 gene/transcript view
3020 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
3024 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
3025 structure mappings with the EMBL-EBI PDBe SIFTS database
3028 <!-- JAL-2079 -->Updated download sites used for Rfam and
3029 Pfam sources to xfam.org
3032 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
3035 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
3036 over sequences in Jalview
3039 <!-- JAL-2027-->Support for reverse-complement coding
3040 regions in ENA and EMBL
3043 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
3044 for record retrieval via ENA rest API
3047 <!-- JAL-2027 -->Support for ENA CDS records with reverse
3051 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
3052 groovy script execution
3055 <!-- JAL-1812 -->New 'execute Groovy script' option in an
3056 alignment window's Calculate menu
3059 <!-- JAL-1812 -->Allow groovy scripts that call
3060 Jalview.getAlignFrames() to run in headless mode
3063 <!-- JAL-2068 -->Support for creating new alignment
3064 calculation workers from groovy scripts
3067 <!-- JAL-1369 --->Store/restore reference sequence in
3071 <!-- JAL-1803 -->Chain codes for a sequence's PDB
3072 associations are now saved/restored from project
3075 <!-- JAL-1993 -->Database selection dialog always shown
3076 before sequence fetcher is opened
3079 <!-- JAL-2183 -->Double click on an entry in Jalview's
3080 database chooser opens a sequence fetcher
3083 <!-- JAL-1563 -->Free-text search client for UniProt using
3084 the UniProt REST API
3087 <!-- JAL-2168 -->-nonews command line parameter to prevent
3088 the news reader opening
3091 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
3092 querying stored in preferences
3095 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
3099 <!-- JAL-1977-->Tooltips shown on database chooser
3102 <!-- JAL-391 -->Reverse complement function in calculate
3103 menu for nucleotide sequences
3106 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
3107 and feature counts preserves alignment ordering (and
3108 debugged for complex feature sets).
3111 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
3112 viewing structures with Jalview 2.10
3115 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
3116 genome, transcript CCDS and gene ids via the Ensembl and
3117 Ensembl Genomes REST API
3120 <!-- JAL-2049 -->Protein sequence variant annotation
3121 computed for 'sequence_variant' annotation on CDS regions
3125 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
3129 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
3130 Ref Fetcher fails to match, or otherwise updates sequence
3131 data from external database records.
3134 <!-- JAL-2154 -->Revised Jalview Project format for
3135 efficient recovery of sequence coding and alignment
3136 annotation relationships.
3138 </ul> <!-- <em>Applet</em>
3149 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
3153 <!-- JAL-2018-->Export features in Jalview format (again)
3154 includes graduated colourschemes
3157 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
3158 working with big alignments and lots of hidden columns
3161 <!-- JAL-2053-->Hidden column markers not always rendered
3162 at right of alignment window
3165 <!-- JAL-2067 -->Tidied up links in help file table of
3169 <!-- JAL-2072 -->Feature based tree calculation not shown
3173 <!-- JAL-2075 -->Hidden columns ignored during feature
3174 based tree calculation
3177 <!-- JAL-2065 -->Alignment view stops updating when show
3178 unconserved enabled for group on alignment
3181 <!-- JAL-2086 -->Cannot insert gaps into sequence when
3185 <!-- JAL-2146 -->Alignment column in status incorrectly
3186 shown as "Sequence position" when mousing over
3190 <!-- JAL-2099 -->Incorrect column numbers in ruler when
3191 hidden columns present
3194 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
3195 user created annotation added to alignment
3198 <!-- JAL-1841 -->RNA Structure consensus only computed for
3199 '()' base pair annotation
3202 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
3203 in zero scores for all base pairs in RNA Structure
3207 <!-- JAL-2174-->Extend selection with columns containing
3211 <!-- JAL-2275 -->Pfam format writer puts extra space at
3212 beginning of sequence
3215 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
3219 <!-- JAL-2238 -->Cannot create groups on an alignment from
3220 from a tree when t-coffee scores are shown
3223 <!-- JAL-1836,1967 -->Cannot import and view PDB
3224 structures with chains containing negative resnums (4q4h)
3227 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
3231 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
3232 to Clustal, PIR and PileUp output
3235 <!-- JAL-2008 -->Reordering sequence features that are
3236 not visible causes alignment window to repaint
3239 <!-- JAL-2006 -->Threshold sliders don't work in
3240 graduated colour and colour by annotation row for e-value
3241 scores associated with features and annotation rows
3244 <!-- JAL-1797 -->amino acid physicochemical conservation
3245 calculation should be case independent
3248 <!-- JAL-2173 -->Remove annotation also updates hidden
3252 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
3253 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
3254 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
3257 <!-- JAL-2065 -->Null pointer exceptions and redraw
3258 problems when reference sequence defined and 'show
3259 non-conserved' enabled
3262 <!-- JAL-1306 -->Quality and Conservation are now shown on
3263 load even when Consensus calculation is disabled
3266 <!-- JAL-1932 -->Remove right on penultimate column of
3267 alignment does nothing
3270 <em>Application</em>
3273 <!-- JAL-1552-->URLs and links can't be imported by
3274 drag'n'drop on OSX when launched via webstart (note - not
3275 yet fixed for El Capitan)
3278 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
3279 output when running on non-gb/us i18n platforms
3282 <!-- JAL-1944 -->Error thrown when exporting a view with
3283 hidden sequences as flat-file alignment
3286 <!-- JAL-2030-->InstallAnywhere distribution fails when
3290 <!-- JAL-2080-->Jalview very slow to launch via webstart
3291 (also hotfix for 2.9.0b2)
3294 <!-- JAL-2085 -->Cannot save project when view has a
3295 reference sequence defined
3298 <!-- JAL-1011 -->Columns are suddenly selected in other
3299 alignments and views when revealing hidden columns
3302 <!-- JAL-1989 -->Hide columns not mirrored in complement
3303 view in a cDNA/Protein splitframe
3306 <!-- JAL-1369 -->Cannot save/restore representative
3307 sequence from project when only one sequence is
3311 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
3312 in Structure Chooser
3315 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
3316 structure consensus didn't refresh annotation panel
3319 <!-- JAL-1962 -->View mapping in structure view shows
3320 mappings between sequence and all chains in a PDB file
3323 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
3324 dialogs format columns correctly, don't display array
3325 data, sort columns according to type
3328 <!-- JAL-1975 -->Export complete shown after destination
3329 file chooser is cancelled during an image export
3332 <!-- JAL-2025 -->Error when querying PDB Service with
3333 sequence name containing special characters
3336 <!-- JAL-2024 -->Manual PDB structure querying should be
3340 <!-- JAL-2104 -->Large tooltips with broken HTML
3341 formatting don't wrap
3344 <!-- JAL-1128 -->Figures exported from wrapped view are
3345 truncated so L looks like I in consensus annotation
3348 <!-- JAL-2003 -->Export features should only export the
3349 currently displayed features for the current selection or
3353 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
3354 after fetching cross-references, and restoring from
3358 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
3359 followed in the structure viewer
3362 <!-- JAL-2163 -->Titles for individual alignments in
3363 splitframe not restored from project
3366 <!-- JAL-2145 -->missing autocalculated annotation at
3367 trailing end of protein alignment in transcript/product
3368 splitview when pad-gaps not enabled by default
3371 <!-- JAL-1797 -->amino acid physicochemical conservation
3375 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
3376 article has been read (reopened issue due to
3377 internationalisation problems)
3380 <!-- JAL-1960 -->Only offer PDB structures in structure
3381 viewer based on sequence name, PDB and UniProt
3386 <!-- JAL-1976 -->No progress bar shown during export of
3390 <!-- JAL-2213 -->Structures not always superimposed after
3391 multiple structures are shown for one or more sequences.
3394 <!-- JAL-1370 -->Reference sequence characters should not
3395 be replaced with '.' when 'Show unconserved' format option
3399 <!-- JAL-1823 -->Cannot specify chain code when entering
3400 specific PDB id for sequence
3403 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3404 'Export hidden sequences' is enabled, but 'export hidden
3405 columns' is disabled.
3408 <!--JAL-2026-->Best Quality option in structure chooser
3409 selects lowest rather than highest resolution structures
3413 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3414 to sequence mapping in 'View Mappings' report
3417 <!-- JAL-2284 -->Unable to read old Jalview projects that
3418 contain non-XML data added after Jalvew wrote project.
3421 <!-- JAL-2118 -->Newly created annotation row reorders
3422 after clicking on it to create new annotation for a
3426 <!-- JAL-1980 -->Null Pointer Exception raised when
3427 pressing Add on an orphaned cut'n'paste window.
3429 <!-- may exclude, this is an external service stability issue JAL-1941
3430 -- > RNA 3D structure not added via DSSR service</li> -->
3435 <!-- JAL-2151 -->Incorrect columns are selected when
3436 hidden columns present before start of sequence
3439 <!-- JAL-1986 -->Missing dependencies on applet pages
3443 <!-- JAL-1947 -->Overview pixel size changes when
3444 sequences are hidden in applet
3447 <!-- JAL-1996 -->Updated instructions for applet
3448 deployment on examples pages.
3455 <td width="60" nowrap>
3456 <div align="center">
3457 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3458 <em>16/10/2015</em></strong>
3461 <td><em>General</em>
3463 <li>Time stamps for signed Jalview application and applet
3468 <em>Application</em>
3470 <li>Duplicate group consensus and conservation rows
3471 shown when tree is partitioned</li>
3472 <li>Erratic behaviour when tree partitions made with
3473 multiple cDNA/Protein split views</li>
3479 <td width="60" nowrap>
3480 <div align="center">
3481 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3482 <em>8/10/2015</em></strong>
3485 <td><em>General</em>
3487 <li>Updated Spanish translations of localized text for
3489 </ul> <em>Application</em>
3491 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3492 <li>Signed OSX InstallAnywhere installer<br></li>
3493 <li>Support for per-sequence based annotations in BioJSON</li>
3494 </ul> <em>Applet</em>
3496 <li>Split frame example added to applet examples page</li>
3497 </ul> <em>Build and Deployment</em>
3500 <!-- JAL-1888 -->New ant target for running Jalview's test
3508 <li>Mapping of cDNA to protein in split frames
3509 incorrect when sequence start > 1</li>
3510 <li>Broken images in filter column by annotation dialog
3512 <li>Feature colours not parsed from features file</li>
3513 <li>Exceptions and incomplete link URLs recovered when
3514 loading a features file containing HTML tags in feature
3518 <em>Application</em>
3520 <li>Annotations corrupted after BioJS export and
3522 <li>Incorrect sequence limits after Fetch DB References
3523 with 'trim retrieved sequences'</li>
3524 <li>Incorrect warning about deleting all data when
3525 deleting selected columns</li>
3526 <li>Patch to build system for shipping properly signed
3527 JNLP templates for webstart launch</li>
3528 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3529 unreleased structures for download or viewing</li>
3530 <li>Tab/space/return keystroke operation of EMBL-PDBe
3531 fetcher/viewer dialogs works correctly</li>
3532 <li>Disabled 'minimise' button on Jalview windows
3533 running on OSX to workaround redraw hang bug</li>
3534 <li>Split cDNA/Protein view position and geometry not
3535 recovered from jalview project</li>
3536 <li>Initial enabled/disabled state of annotation menu
3537 sorter 'show autocalculated first/last' corresponds to
3539 <li>Restoring of Clustal, RNA Helices and T-Coffee
3540 color schemes from BioJSON</li>
3544 <li>Reorder sequences mirrored in cDNA/Protein split
3546 <li>Applet with Jmol examples not loading correctly</li>
3552 <td><div align="center">
3553 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3555 <td><em>General</em>
3557 <li>Linked visualisation and analysis of DNA and Protein
3560 <li>Translated cDNA alignments shown as split protein
3561 and DNA alignment views</li>
3562 <li>Codon consensus annotation for linked protein and
3563 cDNA alignment views</li>
3564 <li>Link cDNA or Protein product sequences by loading
3565 them onto Protein or cDNA alignments</li>
3566 <li>Reconstruct linked cDNA alignment from aligned
3567 protein sequences</li>
3570 <li>Jmol integration updated to Jmol v14.2.14</li>
3571 <li>Import and export of Jalview alignment views as <a
3572 href="features/bioJsonFormat.html">BioJSON</a></li>
3573 <li>New alignment annotation file statements for
3574 reference sequences and marking hidden columns</li>
3575 <li>Reference sequence based alignment shading to
3576 highlight variation</li>
3577 <li>Select or hide columns according to alignment
3579 <li>Find option for locating sequences by description</li>
3580 <li>Conserved physicochemical properties shown in amino
3581 acid conservation row</li>
3582 <li>Alignments can be sorted by number of RNA helices</li>
3583 </ul> <em>Application</em>
3585 <li>New cDNA/Protein analysis capabilities
3587 <li>Get Cross-References should open a Split Frame
3588 view with cDNA/Protein</li>
3589 <li>Detect when nucleotide sequences and protein
3590 sequences are placed in the same alignment</li>
3591 <li>Split cDNA/Protein views are saved in Jalview
3596 <li>Use REST API to talk to Chimera</li>
3597 <li>Selected regions in Chimera are highlighted in linked
3598 Jalview windows</li>
3600 <li>VARNA RNA viewer updated to v3.93</li>
3601 <li>VARNA views are saved in Jalview Projects</li>
3602 <li>Pseudoknots displayed as Jalview RNA annotation can
3603 be shown in VARNA</li>
3605 <li>Make groups for selection uses marked columns as well
3606 as the active selected region</li>
3608 <li>Calculate UPGMA and NJ trees using sequence feature
3610 <li>New Export options
3612 <li>New Export Settings dialog to control hidden
3613 region export in flat file generation</li>
3615 <li>Export alignment views for display with the <a
3616 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3618 <li>Export scrollable SVG in HTML page</li>
3619 <li>Optional embedding of BioJSON data when exporting
3620 alignment figures to HTML</li>
3622 <li>3D structure retrieval and display
3624 <li>Free text and structured queries with the PDBe
3626 <li>PDBe Search API based discovery and selection of
3627 PDB structures for a sequence set</li>
3631 <li>JPred4 employed for protein secondary structure
3633 <li>Hide Insertions menu option to hide unaligned columns
3634 for one or a group of sequences</li>
3635 <li>Automatically hide insertions in alignments imported
3636 from the JPred4 web server</li>
3637 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3638 system on OSX<br />LGPL libraries courtesy of <a
3639 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3641 <li>changed 'View nucleotide structure' submenu to 'View
3642 VARNA 2D Structure'</li>
3643 <li>change "View protein structure" menu option to "3D
3646 </ul> <em>Applet</em>
3648 <li>New layout for applet example pages</li>
3649 <li>New parameters to enable SplitFrame view
3650 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3651 <li>New example demonstrating linked viewing of cDNA and
3652 Protein alignments</li>
3653 </ul> <em>Development and deployment</em>
3655 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3656 <li>Include installation type and git revision in build
3657 properties and console log output</li>
3658 <li>Jalview Github organisation, and new github site for
3659 storing BioJsMSA Templates</li>
3660 <li>Jalview's unit tests now managed with TestNG</li>
3663 <!-- <em>General</em>
3665 </ul> --> <!-- issues resolved --> <em>Application</em>
3667 <li>Escape should close any open find dialogs</li>
3668 <li>Typo in select-by-features status report</li>
3669 <li>Consensus RNA secondary secondary structure
3670 predictions are not highlighted in amber</li>
3671 <li>Missing gap character in v2.7 example file means
3672 alignment appears unaligned when pad-gaps is not enabled</li>
3673 <li>First switch to RNA Helices colouring doesn't colour
3674 associated structure views</li>
3675 <li>ID width preference option is greyed out when auto
3676 width checkbox not enabled</li>
3677 <li>Stopped a warning dialog from being shown when
3678 creating user defined colours</li>
3679 <li>'View Mapping' in structure viewer shows sequence
3680 mappings for just that viewer's sequences</li>
3681 <li>Workaround for superposing PDB files containing
3682 multiple models in Chimera</li>
3683 <li>Report sequence position in status bar when hovering
3684 over Jmol structure</li>
3685 <li>Cannot output gaps as '.' symbols with Selection ->
3686 output to text box</li>
3687 <li>Flat file exports of alignments with hidden columns
3688 have incorrect sequence start/end</li>
3689 <li>'Aligning' a second chain to a Chimera structure from
3691 <li>Colour schemes applied to structure viewers don't
3692 work for nucleotide</li>
3693 <li>Loading/cut'n'pasting an empty or invalid file leads
3694 to a grey/invisible alignment window</li>
3695 <li>Exported Jpred annotation from a sequence region
3696 imports to different position</li>
3697 <li>Space at beginning of sequence feature tooltips shown
3698 on some platforms</li>
3699 <li>Chimera viewer 'View | Show Chain' menu is not
3701 <li>'New View' fails with a Null Pointer Exception in
3702 console if Chimera has been opened</li>
3703 <li>Mouseover to Chimera not working</li>
3704 <li>Miscellaneous ENA XML feature qualifiers not
3706 <li>NPE in annotation renderer after 'Extract Scores'</li>
3707 <li>If two structures in one Chimera window, mouseover of
3708 either sequence shows on first structure</li>
3709 <li>'Show annotations' options should not make
3710 non-positional annotations visible</li>
3711 <li>Subsequence secondary structure annotation not shown
3712 in right place after 'view flanking regions'</li>
3713 <li>File Save As type unset when current file format is
3715 <li>Save as '.jar' option removed for saving Jalview
3717 <li>Colour by Sequence colouring in Chimera more
3719 <li>Cannot 'add reference annotation' for a sequence in
3720 several views on same alignment</li>
3721 <li>Cannot show linked products for EMBL / ENA records</li>
3722 <li>Jalview's tooltip wraps long texts containing no
3724 </ul> <em>Applet</em>
3726 <li>Jmol to JalviewLite mouseover/link not working</li>
3727 <li>JalviewLite can't import sequences with ID
3728 descriptions containing angle brackets</li>
3729 </ul> <em>General</em>
3731 <li>Cannot export and reimport RNA secondary structure
3732 via jalview annotation file</li>
3733 <li>Random helix colour palette for colour by annotation
3734 with RNA secondary structure</li>
3735 <li>Mouseover to cDNA from STOP residue in protein
3736 translation doesn't work.</li>
3737 <li>hints when using the select by annotation dialog box</li>
3738 <li>Jmol alignment incorrect if PDB file has alternate CA
3740 <li>FontChooser message dialog appears to hang after
3741 choosing 1pt font</li>
3742 <li>Peptide secondary structure incorrectly imported from
3743 annotation file when annotation display text includes 'e' or
3745 <li>Cannot set colour of new feature type whilst creating
3747 <li>cDNA translation alignment should not be sequence
3748 order dependent</li>
3749 <li>'Show unconserved' doesn't work for lower case
3751 <li>Nucleotide ambiguity codes involving R not recognised</li>
3752 </ul> <em>Deployment and Documentation</em>
3754 <li>Applet example pages appear different to the rest of
3755 www.jalview.org</li>
3756 </ul> <em>Application Known issues</em>
3758 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3759 <li>Misleading message appears after trying to delete
3761 <li>Jalview icon not shown in dock after InstallAnywhere
3762 version launches</li>
3763 <li>Fetching EMBL reference for an RNA sequence results
3764 fails with a sequence mismatch</li>
3765 <li>Corrupted or unreadable alignment display when
3766 scrolling alignment to right</li>
3767 <li>ArrayIndexOutOfBoundsException thrown when remove
3768 empty columns called on alignment with ragged gapped ends</li>
3769 <li>auto calculated alignment annotation rows do not get
3770 placed above or below non-autocalculated rows</li>
3771 <li>Jalview dekstop becomes sluggish at full screen in
3772 ultra-high resolution</li>
3773 <li>Cannot disable consensus calculation independently of
3774 quality and conservation</li>
3775 <li>Mouseover highlighting between cDNA and protein can
3776 become sluggish with more than one splitframe shown</li>
3777 </ul> <em>Applet Known Issues</em>
3779 <li>Core PDB parsing code requires Jmol</li>
3780 <li>Sequence canvas panel goes white when alignment
3781 window is being resized</li>
3787 <td><div align="center">
3788 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3790 <td><em>General</em>
3792 <li>Updated Java code signing certificate donated by
3794 <li>Features and annotation preserved when performing
3795 pairwise alignment</li>
3796 <li>RNA pseudoknot annotation can be
3797 imported/exported/displayed</li>
3798 <li>'colour by annotation' can colour by RNA and
3799 protein secondary structure</li>
3800 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3801 post-hoc with 2.9 release</em>)
3804 </ul> <em>Application</em>
3806 <li>Extract and display secondary structure for sequences
3807 with 3D structures</li>
3808 <li>Support for parsing RNAML</li>
3809 <li>Annotations menu for layout
3811 <li>sort sequence annotation rows by alignment</li>
3812 <li>place sequence annotation above/below alignment
3815 <li>Output in Stockholm format</li>
3816 <li>Internationalisation: improved Spanish (es)
3818 <li>Structure viewer preferences tab</li>
3819 <li>Disorder and Secondary Structure annotation tracks
3820 shared between alignments</li>
3821 <li>UCSF Chimera launch and linked highlighting from
3823 <li>Show/hide all sequence associated annotation rows for
3824 all or current selection</li>
3825 <li>disorder and secondary structure predictions
3826 available as dataset annotation</li>
3827 <li>Per-sequence rna helices colouring</li>
3830 <li>Sequence database accessions imported when fetching
3831 alignments from Rfam</li>
3832 <li>update VARNA version to 3.91</li>
3834 <li>New groovy scripts for exporting aligned positions,
3835 conservation values, and calculating sum of pairs scores.</li>
3836 <li>Command line argument to set default JABAWS server</li>
3837 <li>include installation type in build properties and
3838 console log output</li>
3839 <li>Updated Jalview project format to preserve dataset
3843 <!-- issues resolved --> <em>Application</em>
3845 <li>Distinguish alignment and sequence associated RNA
3846 structure in structure->view->VARNA</li>
3847 <li>Raise dialog box if user deletes all sequences in an
3849 <li>Pressing F1 results in documentation opening twice</li>
3850 <li>Sequence feature tooltip is wrapped</li>
3851 <li>Double click on sequence associated annotation
3852 selects only first column</li>
3853 <li>Redundancy removal doesn't result in unlinked
3854 leaves shown in tree</li>
3855 <li>Undos after several redundancy removals don't undo
3857 <li>Hide sequence doesn't hide associated annotation</li>
3858 <li>User defined colours dialog box too big to fit on
3859 screen and buttons not visible</li>
3860 <li>author list isn't updated if already written to
3861 Jalview properties</li>
3862 <li>Popup menu won't open after retrieving sequence
3864 <li>File open window for associate PDB doesn't open</li>
3865 <li>Left-then-right click on a sequence id opens a
3866 browser search window</li>
3867 <li>Cannot open sequence feature shading/sort popup menu
3868 in feature settings dialog</li>
3869 <li>better tooltip placement for some areas of Jalview
3871 <li>Allow addition of JABAWS Server which doesn't
3872 pass validation</li>
3873 <li>Web services parameters dialog box is too large to
3875 <li>Muscle nucleotide alignment preset obscured by
3877 <li>JABAWS preset submenus don't contain newly
3878 defined user preset</li>
3879 <li>MSA web services warns user if they were launched
3880 with invalid input</li>
3881 <li>Jalview cannot contact DAS Registy when running on
3884 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3885 'Superpose with' submenu not shown when new view
3889 </ul> <!-- <em>Applet</em>
3891 </ul> <em>General</em>
3893 </ul>--> <em>Deployment and Documentation</em>
3895 <li>2G and 1G options in launchApp have no effect on
3896 memory allocation</li>
3897 <li>launchApp service doesn't automatically open
3898 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3900 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3901 InstallAnywhere reports cannot find valid JVM when Java
3902 1.7_055 is available
3904 </ul> <em>Application Known issues</em>
3907 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3908 corrupted or unreadable alignment display when scrolling
3912 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3913 retrieval fails but progress bar continues for DAS retrieval
3914 with large number of ID
3917 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3918 flatfile output of visible region has incorrect sequence
3922 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3923 rna structure consensus doesn't update when secondary
3924 structure tracks are rearranged
3927 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3928 invalid rna structure positional highlighting does not
3929 highlight position of invalid base pairs
3932 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3933 out of memory errors are not raised when saving Jalview
3934 project from alignment window file menu
3937 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3938 Switching to RNA Helices colouring doesn't propagate to
3942 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3943 colour by RNA Helices not enabled when user created
3944 annotation added to alignment
3947 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3948 Jalview icon not shown on dock in Mountain Lion/Webstart
3950 </ul> <em>Applet Known Issues</em>
3953 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3954 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3957 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3958 Jalview and Jmol example not compatible with IE9
3961 <li>Sort by annotation score doesn't reverse order
3967 <td><div align="center">
3968 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3971 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3974 <li>Internationalisation of user interface (usually
3975 called i18n support) and translation for Spanish locale</li>
3976 <li>Define/Undefine group on current selection with
3977 Ctrl-G/Shift Ctrl-G</li>
3978 <li>Improved group creation/removal options in
3979 alignment/sequence Popup menu</li>
3980 <li>Sensible precision for symbol distribution
3981 percentages shown in logo tooltip.</li>
3982 <li>Annotation panel height set according to amount of
3983 annotation when alignment first opened</li>
3984 </ul> <em>Application</em>
3986 <li>Interactive consensus RNA secondary structure
3987 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3988 <li>Select columns containing particular features from
3989 Feature Settings dialog</li>
3990 <li>View all 'representative' PDB structures for selected
3992 <li>Update Jalview project format:
3994 <li>New file extension for Jalview projects '.jvp'</li>
3995 <li>Preserve sequence and annotation dataset (to
3996 store secondary structure annotation,etc)</li>
3997 <li>Per group and alignment annotation and RNA helix
4001 <li>New similarity measures for PCA and Tree calculation
4003 <li>Experimental support for retrieval and viewing of
4004 flanking regions for an alignment</li>
4008 <!-- issues resolved --> <em>Application</em>
4010 <li>logo keeps spinning and status remains at queued or
4011 running after job is cancelled</li>
4012 <li>cannot export features from alignments imported from
4013 Jalview/VAMSAS projects</li>
4014 <li>Buggy slider for web service parameters that take
4016 <li>Newly created RNA secondary structure line doesn't
4017 have 'display all symbols' flag set</li>
4018 <li>T-COFFEE alignment score shading scheme and other
4019 annotation shading not saved in Jalview project</li>
4020 <li>Local file cannot be loaded in freshly downloaded
4022 <li>Jalview icon not shown on dock in Mountain
4024 <li>Load file from desktop file browser fails</li>
4025 <li>Occasional NPE thrown when calculating large trees</li>
4026 <li>Cannot reorder or slide sequences after dragging an
4027 alignment onto desktop</li>
4028 <li>Colour by annotation dialog throws NPE after using
4029 'extract scores' function</li>
4030 <li>Loading/cut'n'pasting an empty file leads to a grey
4031 alignment window</li>
4032 <li>Disorder thresholds rendered incorrectly after
4033 performing IUPred disorder prediction</li>
4034 <li>Multiple group annotated consensus rows shown when
4035 changing 'normalise logo' display setting</li>
4036 <li>Find shows blank dialog after 'finished searching' if
4037 nothing matches query</li>
4038 <li>Null Pointer Exceptions raised when sorting by
4039 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
4041 <li>Errors in Jmol console when structures in alignment
4042 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
4044 <li>Not all working JABAWS services are shown in
4046 <li>JAVAWS version of Jalview fails to launch with
4047 'invalid literal/length code'</li>
4048 <li>Annotation/RNA Helix colourschemes cannot be applied
4049 to alignment with groups (actually fixed in 2.8.0b1)</li>
4050 <li>RNA Helices and T-Coffee Scores available as default
4053 </ul> <em>Applet</em>
4055 <li>Remove group option is shown even when selection is
4057 <li>Apply to all groups ticked but colourscheme changes
4058 don't affect groups</li>
4059 <li>Documented RNA Helices and T-Coffee Scores as valid
4060 colourscheme name</li>
4061 <li>Annotation labels drawn on sequence IDs when
4062 Annotation panel is not displayed</li>
4063 <li>Increased font size for dropdown menus on OSX and
4064 embedded windows</li>
4065 </ul> <em>Other</em>
4067 <li>Consensus sequence for alignments/groups with a
4068 single sequence were not calculated</li>
4069 <li>annotation files that contain only groups imported as
4070 annotation and junk sequences</li>
4071 <li>Fasta files with sequences containing '*' incorrectly
4072 recognised as PFAM or BLC</li>
4073 <li>conservation/PID slider apply all groups option
4074 doesn't affect background (2.8.0b1)
4076 <li>redundancy highlighting is erratic at 0% and 100%</li>
4077 <li>Remove gapped columns fails for sequences with ragged
4079 <li>AMSA annotation row with leading spaces is not
4080 registered correctly on import</li>
4081 <li>Jalview crashes when selecting PCA analysis for
4082 certain alignments</li>
4083 <li>Opening the colour by annotation dialog for an
4084 existing annotation based 'use original colours'
4085 colourscheme loses original colours setting</li>
4090 <td><div align="center">
4091 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
4092 <em>30/1/2014</em></strong>
4096 <li>Trusted certificates for JalviewLite applet and
4097 Jalview Desktop application<br />Certificate was donated by
4098 <a href="https://www.certum.eu">Certum</a> to the Jalview
4099 open source project).
4101 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
4102 <li>Output in Stockholm format</li>
4103 <li>Allow import of data from gzipped files</li>
4104 <li>Export/import group and sequence associated line
4105 graph thresholds</li>
4106 <li>Nucleotide substitution matrix that supports RNA and
4107 ambiguity codes</li>
4108 <li>Allow disorder predictions to be made on the current
4109 selection (or visible selection) in the same way that JPred
4111 <li>Groovy scripting for headless Jalview operation</li>
4112 </ul> <em>Other improvements</em>
4114 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
4115 <li>COMBINE statement uses current SEQUENCE_REF and
4116 GROUP_REF scope to group annotation rows</li>
4117 <li>Support '' style escaping of quotes in Newick
4119 <li>Group options for JABAWS service by command line name</li>
4120 <li>Empty tooltip shown for JABA service options with a
4121 link but no description</li>
4122 <li>Select primary source when selecting authority in
4123 database fetcher GUI</li>
4124 <li>Add .mfa to FASTA file extensions recognised by
4126 <li>Annotation label tooltip text wrap</li>
4131 <li>Slow scrolling when lots of annotation rows are
4133 <li>Lots of NPE (and slowness) after creating RNA
4134 secondary structure annotation line</li>
4135 <li>Sequence database accessions not imported when
4136 fetching alignments from Rfam</li>
4137 <li>Incorrect SHMR submission for sequences with
4139 <li>View all structures does not always superpose
4141 <li>Option widgets in service parameters not updated to
4142 reflect user or preset settings</li>
4143 <li>Null pointer exceptions for some services without
4144 presets or adjustable parameters</li>
4145 <li>Discover PDB IDs entry in structure menu doesn't
4146 discover PDB xRefs</li>
4147 <li>Exception encountered while trying to retrieve
4148 features with DAS</li>
4149 <li>Lowest value in annotation row isn't coloured
4150 when colour by annotation (per sequence) is coloured</li>
4151 <li>Keyboard mode P jumps to start of gapped region when
4152 residue follows a gap</li>
4153 <li>Jalview appears to hang importing an alignment with
4154 Wrap as default or after enabling Wrap</li>
4155 <li>'Right click to add annotations' message
4156 shown in wrap mode when no annotations present</li>
4157 <li>Disorder predictions fail with NPE if no automatic
4158 annotation already exists on alignment</li>
4159 <li>oninit javascript function should be called after
4160 initialisation completes</li>
4161 <li>Remove redundancy after disorder prediction corrupts
4162 alignment window display</li>
4163 <li>Example annotation file in documentation is invalid</li>
4164 <li>Grouped line graph annotation rows are not exported
4165 to annotation file</li>
4166 <li>Multi-harmony analysis cannot be run when only two
4168 <li>Cannot create multiple groups of line graphs with
4169 several 'combine' statements in annotation file</li>
4170 <li>Pressing return several times causes Number Format
4171 exceptions in keyboard mode</li>
4172 <li>Multi-harmony (SHMMR) method doesn't submit
4173 correct partitions for input data</li>
4174 <li>Translation from DNA to Amino Acids fails</li>
4175 <li>Jalview fail to load newick tree with quoted label</li>
4176 <li>--headless flag isn't understood</li>
4177 <li>ClassCastException when generating EPS in headless
4179 <li>Adjusting sequence-associated shading threshold only
4180 changes one row's threshold</li>
4181 <li>Preferences and Feature settings panel panel
4182 doesn't open</li>
4183 <li>hide consensus histogram also hides conservation and
4184 quality histograms</li>
4189 <td><div align="center">
4190 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
4192 <td><em>Application</em>
4194 <li>Support for JABAWS 2.0 Services (AACon alignment
4195 conservation, protein disorder and Clustal Omega)</li>
4196 <li>JABAWS server status indicator in Web Services
4198 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
4199 in Jalview alignment window</li>
4200 <li>Updated Jalview build and deploy framework for OSX
4201 mountain lion, windows 7, and 8</li>
4202 <li>Nucleotide substitution matrix for PCA that supports
4203 RNA and ambiguity codes</li>
4205 <li>Improved sequence database retrieval GUI</li>
4206 <li>Support fetching and database reference look up
4207 against multiple DAS sources (Fetch all from in 'fetch db
4209 <li>Jalview project improvements
4211 <li>Store and retrieve the 'belowAlignment'
4212 flag for annotation</li>
4213 <li>calcId attribute to group annotation rows on the
4215 <li>Store AACon calculation settings for a view in
4216 Jalview project</li>
4220 <li>horizontal scrolling gesture support</li>
4221 <li>Visual progress indicator when PCA calculation is
4223 <li>Simpler JABA web services menus</li>
4224 <li>visual indication that web service results are still
4225 being retrieved from server</li>
4226 <li>Serialise the dialogs that are shown when Jalview
4227 starts up for first time</li>
4228 <li>Jalview user agent string for interacting with HTTP
4230 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
4232 <li>Examples directory and Groovy library included in
4233 InstallAnywhere distribution</li>
4234 </ul> <em>Applet</em>
4236 <li>RNA alignment and secondary structure annotation
4237 visualization applet example</li>
4238 </ul> <em>General</em>
4240 <li>Normalise option for consensus sequence logo</li>
4241 <li>Reset button in PCA window to return dimensions to
4243 <li>Allow seqspace or Jalview variant of alignment PCA
4245 <li>PCA with either nucleic acid and protein substitution
4247 <li>Allow windows containing HTML reports to be exported
4249 <li>Interactive display and editing of RNA secondary
4250 structure contacts</li>
4251 <li>RNA Helix Alignment Colouring</li>
4252 <li>RNA base pair logo consensus</li>
4253 <li>Parse sequence associated secondary structure
4254 information in Stockholm files</li>
4255 <li>HTML Export database accessions and annotation
4256 information presented in tooltip for sequences</li>
4257 <li>Import secondary structure from LOCARNA clustalw
4258 style RNA alignment files</li>
4259 <li>import and visualise T-COFFEE quality scores for an
4261 <li>'colour by annotation' per sequence option to
4262 shade each sequence according to its associated alignment
4264 <li>New Jalview Logo</li>
4265 </ul> <em>Documentation and Development</em>
4267 <li>documentation for score matrices used in Jalview</li>
4268 <li>New Website!</li>
4270 <td><em>Application</em>
4272 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
4273 wsdbfetch REST service</li>
4274 <li>Stop windows being moved outside desktop on OSX</li>
4275 <li>Filetype associations not installed for webstart
4277 <li>Jalview does not always retrieve progress of a JABAWS
4278 job execution in full once it is complete</li>
4279 <li>revise SHMR RSBS definition to ensure alignment is
4280 uploaded via ali_file parameter</li>
4281 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
4282 <li>View all structures superposed fails with exception</li>
4283 <li>Jnet job queues forever if a very short sequence is
4284 submitted for prediction</li>
4285 <li>Cut and paste menu not opened when mouse clicked on
4287 <li>Putting fractional value into integer text box in
4288 alignment parameter dialog causes Jalview to hang</li>
4289 <li>Structure view highlighting doesn't work on
4291 <li>View all structures fails with exception shown in
4293 <li>Characters in filename associated with PDBEntry not
4294 escaped in a platform independent way</li>
4295 <li>Jalview desktop fails to launch with exception when
4297 <li>Tree calculation reports 'you must have 2 or more
4298 sequences selected' when selection is empty</li>
4299 <li>Jalview desktop fails to launch with jar signature
4300 failure when java web start temporary file caching is
4302 <li>DAS Sequence retrieval with range qualification
4303 results in sequence xref which includes range qualification</li>
4304 <li>Errors during processing of command line arguments
4305 cause progress bar (JAL-898) to be removed</li>
4306 <li>Replace comma for semi-colon option not disabled for
4307 DAS sources in sequence fetcher</li>
4308 <li>Cannot close news reader when JABAWS server warning
4309 dialog is shown</li>
4310 <li>Option widgets not updated to reflect user settings</li>
4311 <li>Edited sequence not submitted to web service</li>
4312 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
4313 <li>InstallAnywhere installer doesn't unpack and run
4314 on OSX Mountain Lion</li>
4315 <li>Annotation panel not given a scroll bar when
4316 sequences with alignment annotation are pasted into the
4318 <li>Sequence associated annotation rows not associated
4319 when loaded from Jalview project</li>
4320 <li>Browser launch fails with NPE on java 1.7</li>
4321 <li>JABAWS alignment marked as finished when job was
4322 cancelled or job failed due to invalid input</li>
4323 <li>NPE with v2.7 example when clicking on Tree
4324 associated with all views</li>
4325 <li>Exceptions when copy/paste sequences with grouped
4326 annotation rows to new window</li>
4327 </ul> <em>Applet</em>
4329 <li>Sequence features are momentarily displayed before
4330 they are hidden using hidefeaturegroups applet parameter</li>
4331 <li>loading features via javascript API automatically
4332 enables feature display</li>
4333 <li>scrollToColumnIn javascript API method doesn't
4335 </ul> <em>General</em>
4337 <li>Redundancy removal fails for rna alignment</li>
4338 <li>PCA calculation fails when sequence has been selected
4339 and then deselected</li>
4340 <li>PCA window shows grey box when first opened on OSX</li>
4341 <li>Letters coloured pink in sequence logo when alignment
4342 coloured with clustalx</li>
4343 <li>Choosing fonts without letter symbols defined causes
4344 exceptions and redraw errors</li>
4345 <li>Initial PCA plot view is not same as manually
4346 reconfigured view</li>
4347 <li>Grouped annotation graph label has incorrect line
4349 <li>Grouped annotation graph label display is corrupted
4350 for lots of labels</li>
4355 <div align="center">
4356 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
4359 <td><em>Application</em>
4361 <li>Jalview Desktop News Reader</li>
4362 <li>Tweaked default layout of web services menu</li>
4363 <li>View/alignment association menu to enable user to
4364 easily specify which alignment a multi-structure view takes
4365 its colours/correspondences from</li>
4366 <li>Allow properties file location to be specified as URL</li>
4367 <li>Extend Jalview project to preserve associations
4368 between many alignment views and a single Jmol display</li>
4369 <li>Store annotation row height in Jalview project file</li>
4370 <li>Annotation row column label formatting attributes
4371 stored in project file</li>
4372 <li>Annotation row order for auto-calculated annotation
4373 rows preserved in Jalview project file</li>
4374 <li>Visual progress indication when Jalview state is
4375 saved using Desktop window menu</li>
4376 <li>Visual indication that command line arguments are
4377 still being processed</li>
4378 <li>Groovy script execution from URL</li>
4379 <li>Colour by annotation default min and max colours in
4381 <li>Automatically associate PDB files dragged onto an
4382 alignment with sequences that have high similarity and
4384 <li>Update JGoogleAnalytics to latest release (0.3)</li>
4385 <li>'view structures' option to open many
4386 structures in same window</li>
4387 <li>Sort associated views menu option for tree panel</li>
4388 <li>Group all JABA and non-JABA services for a particular
4389 analysis function in its own submenu</li>
4390 </ul> <em>Applet</em>
4392 <li>Userdefined and autogenerated annotation rows for
4394 <li>Adjustment of alignment annotation pane height</li>
4395 <li>Annotation scrollbar for annotation panel</li>
4396 <li>Drag to reorder annotation rows in annotation panel</li>
4397 <li>'automaticScrolling' parameter</li>
4398 <li>Allow sequences with partial ID string matches to be
4399 annotated from GFF/Jalview features files</li>
4400 <li>Sequence logo annotation row in applet</li>
4401 <li>Absolute paths relative to host server in applet
4402 parameters are treated as such</li>
4403 <li>New in the JalviewLite javascript API:
4405 <li>JalviewLite.js javascript library</li>
4406 <li>Javascript callbacks for
4408 <li>Applet initialisation</li>
4409 <li>Sequence/alignment mouse-overs and selections</li>
4412 <li>scrollTo row and column alignment scrolling
4414 <li>Select sequence/alignment regions from javascript</li>
4415 <li>javascript structure viewer harness to pass
4416 messages between Jmol and Jalview when running as
4417 distinct applets</li>
4418 <li>sortBy method</li>
4419 <li>Set of applet and application examples shipped
4420 with documentation</li>
4421 <li>New example to demonstrate JalviewLite and Jmol
4422 javascript message exchange</li>
4424 </ul> <em>General</em>
4426 <li>Enable Jmol displays to be associated with multiple
4427 multiple alignments</li>
4428 <li>Option to automatically sort alignment with new tree</li>
4429 <li>User configurable link to enable redirects to a
4430 www.Jalview.org mirror</li>
4431 <li>Jmol colours option for Jmol displays</li>
4432 <li>Configurable newline string when writing alignment
4433 and other flat files</li>
4434 <li>Allow alignment annotation description lines to
4435 contain html tags</li>
4436 </ul> <em>Documentation and Development</em>
4438 <li>Add groovy test harness for bulk load testing to
4440 <li>Groovy script to load and align a set of sequences
4441 using a web service before displaying the result in the
4442 Jalview desktop</li>
4443 <li>Restructured javascript and applet api documentation</li>
4444 <li>Ant target to publish example html files with applet
4446 <li>Netbeans project for building Jalview from source</li>
4447 <li>ant task to create online javadoc for Jalview source</li>
4449 <td><em>Application</em>
4451 <li>User defined colourscheme throws exception when
4452 current built in colourscheme is saved as new scheme</li>
4453 <li>AlignFrame->Save in application pops up save
4454 dialog for valid filename/format</li>
4455 <li>Cannot view associated structure for UniProt sequence</li>
4456 <li>PDB file association breaks for UniProt sequence
4458 <li>Associate PDB from file dialog does not tell you
4459 which sequence is to be associated with the file</li>
4460 <li>Find All raises null pointer exception when query
4461 only matches sequence IDs</li>
4462 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4463 <li>Jalview project with Jmol views created with Jalview
4464 2.4 cannot be loaded</li>
4465 <li>Filetype associations not installed for webstart
4467 <li>Two or more chains in a single PDB file associated
4468 with sequences in different alignments do not get coloured
4469 by their associated sequence</li>
4470 <li>Visibility status of autocalculated annotation row
4471 not preserved when project is loaded</li>
4472 <li>Annotation row height and visibility attributes not
4473 stored in Jalview project</li>
4474 <li>Tree bootstraps are not preserved when saved as a
4475 Jalview project</li>
4476 <li>Envision2 workflow tooltips are corrupted</li>
4477 <li>Enabling show group conservation also enables colour
4478 by conservation</li>
4479 <li>Duplicate group associated conservation or consensus
4480 created on new view</li>
4481 <li>Annotation scrollbar not displayed after 'show
4482 all hidden annotation rows' option selected</li>
4483 <li>Alignment quality not updated after alignment
4484 annotation row is hidden then shown</li>
4485 <li>Preserve colouring of structures coloured by
4486 sequences in pre Jalview 2.7 projects</li>
4487 <li>Web service job parameter dialog is not laid out
4489 <li>Web services menu not refreshed after 'reset
4490 services' button is pressed in preferences</li>
4491 <li>Annotation off by one in Jalview v2_3 example project</li>
4492 <li>Structures imported from file and saved in project
4493 get name like jalview_pdb1234.txt when reloaded</li>
4494 <li>Jalview does not always retrieve progress of a JABAWS
4495 job execution in full once it is complete</li>
4496 </ul> <em>Applet</em>
4498 <li>Alignment height set incorrectly when lots of
4499 annotation rows are displayed</li>
4500 <li>Relative URLs in feature HTML text not resolved to
4502 <li>View follows highlighting does not work for positions
4504 <li><= shown as = in tooltip</li>
4505 <li>Export features raises exception when no features
4507 <li>Separator string used for serialising lists of IDs
4508 for javascript api is modified when separator string
4509 provided as parameter</li>
4510 <li>Null pointer exception when selecting tree leaves for
4511 alignment with no existing selection</li>
4512 <li>Relative URLs for datasources assumed to be relative
4513 to applet's codebase</li>
4514 <li>Status bar not updated after finished searching and
4515 search wraps around to first result</li>
4516 <li>StructureSelectionManager instance shared between
4517 several Jalview applets causes race conditions and memory
4519 <li>Hover tooltip and mouseover of position on structure
4520 not sent from Jmol in applet</li>
4521 <li>Certain sequences of javascript method calls to
4522 applet API fatally hang browser</li>
4523 </ul> <em>General</em>
4525 <li>View follows structure mouseover scrolls beyond
4526 position with wrapped view and hidden regions</li>
4527 <li>Find sequence position moves to wrong residue
4528 with/without hidden columns</li>
4529 <li>Sequence length given in alignment properties window
4531 <li>InvalidNumberFormat exceptions thrown when trying to
4532 import PDB like structure files</li>
4533 <li>Positional search results are only highlighted
4534 between user-supplied sequence start/end bounds</li>
4535 <li>End attribute of sequence is not validated</li>
4536 <li>Find dialog only finds first sequence containing a
4537 given sequence position</li>
4538 <li>Sequence numbering not preserved in MSF alignment
4540 <li>Jalview PDB file reader does not extract sequence
4541 from nucleotide chains correctly</li>
4542 <li>Structure colours not updated when tree partition
4543 changed in alignment</li>
4544 <li>Sequence associated secondary structure not correctly
4545 parsed in interleaved stockholm</li>
4546 <li>Colour by annotation dialog does not restore current
4548 <li>Hiding (nearly) all sequences doesn't work
4550 <li>Sequences containing lowercase letters are not
4551 properly associated with their pdb files</li>
4552 </ul> <em>Documentation and Development</em>
4554 <li>schemas/JalviewWsParamSet.xsd corrupted by
4555 ApplyCopyright tool</li>
4560 <div align="center">
4561 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4564 <td><em>Application</em>
4566 <li>New warning dialog when the Jalview Desktop cannot
4567 contact web services</li>
4568 <li>JABA service parameters for a preset are shown in
4569 service job window</li>
4570 <li>JABA Service menu entries reworded</li>
4574 <li>Modeller PIR IO broken - cannot correctly import a
4575 pir file emitted by Jalview</li>
4576 <li>Existing feature settings transferred to new
4577 alignment view created from cut'n'paste</li>
4578 <li>Improved test for mixed amino/nucleotide chains when
4579 parsing PDB files</li>
4580 <li>Consensus and conservation annotation rows
4581 occasionally become blank for all new windows</li>
4582 <li>Exception raised when right clicking above sequences
4583 in wrapped view mode</li>
4584 </ul> <em>Application</em>
4586 <li>multiple multiply aligned structure views cause cpu
4587 usage to hit 100% and computer to hang</li>
4588 <li>Web Service parameter layout breaks for long user
4589 parameter names</li>
4590 <li>Jaba service discovery hangs desktop if Jaba server
4597 <div align="center">
4598 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4601 <td><em>Application</em>
4603 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4604 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4607 <li>Web Services preference tab</li>
4608 <li>Analysis parameters dialog box and user defined
4610 <li>Improved speed and layout of Envision2 service menu</li>
4611 <li>Superpose structures using associated sequence
4613 <li>Export coordinates and projection as CSV from PCA
4615 </ul> <em>Applet</em>
4617 <li>enable javascript: execution by the applet via the
4618 link out mechanism</li>
4619 </ul> <em>Other</em>
4621 <li>Updated the Jmol Jalview interface to work with Jmol
4623 <li>The Jalview Desktop and JalviewLite applet now
4624 require Java 1.5</li>
4625 <li>Allow Jalview feature colour specification for GFF
4626 sequence annotation files</li>
4627 <li>New 'colour by label' keword in Jalview feature file
4628 type colour specification</li>
4629 <li>New Jalview Desktop Groovy API method that allows a
4630 script to check if it being run in an interactive session or
4631 in a batch operation from the Jalview command line</li>
4635 <li>clustalx colourscheme colours Ds preferentially when
4636 both D+E are present in over 50% of the column</li>
4637 </ul> <em>Application</em>
4639 <li>typo in AlignmentFrame->View->Hide->all but
4640 selected Regions menu item</li>
4641 <li>sequence fetcher replaces ',' for ';' when the ',' is
4642 part of a valid accession ID</li>
4643 <li>fatal OOM if object retrieved by sequence fetcher
4644 runs out of memory</li>
4645 <li>unhandled Out of Memory Error when viewing pca
4646 analysis results</li>
4647 <li>InstallAnywhere builds fail to launch on OS X java
4648 10.5 update 4 (due to apple Java 1.6 update)</li>
4649 <li>Installanywhere Jalview silently fails to launch</li>
4650 </ul> <em>Applet</em>
4652 <li>Jalview.getFeatureGroups() raises an
4653 ArrayIndexOutOfBoundsException if no feature groups are
4660 <div align="center">
4661 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4667 <li>Alignment prettyprinter doesn't cope with long
4669 <li>clustalx colourscheme colours Ds preferentially when
4670 both D+E are present in over 50% of the column</li>
4671 <li>nucleic acid structures retrieved from PDB do not
4672 import correctly</li>
4673 <li>More columns get selected than were clicked on when a
4674 number of columns are hidden</li>
4675 <li>annotation label popup menu not providing correct
4676 add/hide/show options when rows are hidden or none are
4678 <li>Stockholm format shown in list of readable formats,
4679 and parser copes better with alignments from RFAM.</li>
4680 <li>CSV output of consensus only includes the percentage
4681 of all symbols if sequence logo display is enabled</li>
4683 </ul> <em>Applet</em>
4685 <li>annotation panel disappears when annotation is
4687 </ul> <em>Application</em>
4689 <li>Alignment view not redrawn properly when new
4690 alignment opened where annotation panel is visible but no
4691 annotations are present on alignment</li>
4692 <li>pasted region containing hidden columns is
4693 incorrectly displayed in new alignment window</li>
4694 <li>Jalview slow to complete operations when stdout is
4695 flooded (fix is to close the Jalview console)</li>
4696 <li>typo in AlignmentFrame->View->Hide->all but
4697 selected Rregions menu item.</li>
4698 <li>inconsistent group submenu and Format submenu entry
4699 'Un' or 'Non'conserved</li>
4700 <li>Sequence feature settings are being shared by
4701 multiple distinct alignments</li>
4702 <li>group annotation not recreated when tree partition is
4704 <li>double click on group annotation to select sequences
4705 does not propagate to associated trees</li>
4706 <li>Mac OSX specific issues:
4708 <li>exception raised when mouse clicked on desktop
4709 window background</li>
4710 <li>Desktop menu placed on menu bar and application
4711 name set correctly</li>
4712 <li>sequence feature settings not wide enough for the
4713 save feature colourscheme button</li>
4722 <div align="center">
4723 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4726 <td><em>New Capabilities</em>
4728 <li>URL links generated from description line for
4729 regular-expression based URL links (applet and application)
4732 <li>Non-positional feature URL links are shown in link
4734 <li>Linked viewing of nucleic acid sequences and
4736 <li>Automatic Scrolling option in View menu to display
4737 the currently highlighted region of an alignment.</li>
4738 <li>Order an alignment by sequence length, or using the
4739 average score or total feature count for each sequence.</li>
4740 <li>Shading features by score or associated description</li>
4741 <li>Subdivide alignment and groups based on identity of
4742 selected subsequence (Make Groups from Selection).</li>
4743 <li>New hide/show options including Shift+Control+H to
4744 hide everything but the currently selected region.</li>
4745 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4746 </ul> <em>Application</em>
4748 <li>Fetch DB References capabilities and UI expanded to
4749 support retrieval from DAS sequence sources</li>
4750 <li>Local DAS Sequence sources can be added via the
4751 command line or via the Add local source dialog box.</li>
4752 <li>DAS Dbref and DbxRef feature types are parsed as
4753 database references and protein_name is parsed as
4754 description line (BioSapiens terms).</li>
4755 <li>Enable or disable non-positional feature and database
4756 references in sequence ID tooltip from View menu in
4758 <!-- <li>New hidden columns and rows and representatives capabilities
4759 in annotations file (in progress - not yet fully implemented)</li> -->
4760 <li>Group-associated consensus, sequence logos and
4761 conservation plots</li>
4762 <li>Symbol distributions for each column can be exported
4763 and visualized as sequence logos</li>
4764 <li>Optionally scale multi-character column labels to fit
4765 within each column of annotation row<!-- todo for applet -->
4767 <li>Optional automatic sort of associated alignment view
4768 when a new tree is opened.</li>
4769 <li>Jalview Java Console</li>
4770 <li>Better placement of desktop window when moving
4771 between different screens.</li>
4772 <li>New preference items for sequence ID tooltip and
4773 consensus annotation</li>
4774 <li>Client to submit sequences and IDs to Envision2
4776 <li><em>Vamsas Capabilities</em>
4778 <li>Improved VAMSAS synchronization (Jalview archive
4779 used to preserve views, structures, and tree display
4781 <li>Import of vamsas documents from disk or URL via
4783 <li>Sharing of selected regions between views and
4784 with other VAMSAS applications (Experimental feature!)</li>
4785 <li>Updated API to VAMSAS version 0.2</li>
4787 </ul> <em>Applet</em>
4789 <li>Middle button resizes annotation row height</li>
4792 <li>sortByTree (true/false) - automatically sort the
4793 associated alignment view by the tree when a new tree is
4795 <li>showTreeBootstraps (true/false) - show or hide
4796 branch bootstraps (default is to show them if available)</li>
4797 <li>showTreeDistances (true/false) - show or hide
4798 branch lengths (default is to show them if available)</li>
4799 <li>showUnlinkedTreeNodes (true/false) - indicate if
4800 unassociated nodes should be highlighted in the tree
4802 <li>heightScale and widthScale (1.0 or more) -
4803 increase the height or width of a cell in the alignment
4804 grid relative to the current font size.</li>
4807 <li>Non-positional features displayed in sequence ID
4809 </ul> <em>Other</em>
4811 <li>Features format: graduated colour definitions and
4812 specification of feature scores</li>
4813 <li>Alignment Annotations format: new keywords for group
4814 associated annotation (GROUP_REF) and annotation row display
4815 properties (ROW_PROPERTIES)</li>
4816 <li>XML formats extended to support graduated feature
4817 colourschemes, group associated annotation, and profile
4818 visualization settings.</li></td>
4821 <li>Source field in GFF files parsed as feature source
4822 rather than description</li>
4823 <li>Non-positional features are now included in sequence
4824 feature and gff files (controlled via non-positional feature
4825 visibility in tooltip).</li>
4826 <li>URL links generated for all feature links (bugfix)</li>
4827 <li>Added URL embedding instructions to features file
4829 <li>Codons containing ambiguous nucleotides translated as
4830 'X' in peptide product</li>
4831 <li>Match case switch in find dialog box works for both
4832 sequence ID and sequence string and query strings do not
4833 have to be in upper case to match case-insensitively.</li>
4834 <li>AMSA files only contain first column of
4835 multi-character column annotation labels</li>
4836 <li>Jalview Annotation File generation/parsing consistent
4837 with documentation (e.g. Stockholm annotation can be
4838 exported and re-imported)</li>
4839 <li>PDB files without embedded PDB IDs given a friendly
4841 <li>Find incrementally searches ID string matches as well
4842 as subsequence matches, and correctly reports total number
4846 <li>Better handling of exceptions during sequence
4848 <li>Dasobert generated non-positional feature URL
4849 link text excludes the start_end suffix</li>
4850 <li>DAS feature and source retrieval buttons disabled
4851 when fetch or registry operations in progress.</li>
4852 <li>PDB files retrieved from URLs are cached properly</li>
4853 <li>Sequence description lines properly shared via
4855 <li>Sequence fetcher fetches multiple records for all
4857 <li>Ensured that command line das feature retrieval
4858 completes before alignment figures are generated.</li>
4859 <li>Reduced time taken when opening file browser for
4861 <li>isAligned check prior to calculating tree, PCA or
4862 submitting an MSA to JNet now excludes hidden sequences.</li>
4863 <li>User defined group colours properly recovered
4864 from Jalview projects.</li>
4873 <div align="center">
4874 <strong>2.4.0.b2</strong><br> 28/10/2009
4879 <li>Experimental support for google analytics usage
4881 <li>Jalview privacy settings (user preferences and docs).</li>
4886 <li>Race condition in applet preventing startup in
4888 <li>Exception when feature created from selection beyond
4889 length of sequence.</li>
4890 <li>Allow synthetic PDB files to be imported gracefully</li>
4891 <li>Sequence associated annotation rows associate with
4892 all sequences with a given id</li>
4893 <li>Find function matches case-insensitively for sequence
4894 ID string searches</li>
4895 <li>Non-standard characters do not cause pairwise
4896 alignment to fail with exception</li>
4897 </ul> <em>Application Issues</em>
4899 <li>Sequences are now validated against EMBL database</li>
4900 <li>Sequence fetcher fetches multiple records for all
4902 </ul> <em>InstallAnywhere Issues</em>
4904 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4905 issue with installAnywhere mechanism)</li>
4906 <li>Command line launching of JARs from InstallAnywhere
4907 version (java class versioning error fixed)</li>
4914 <div align="center">
4915 <strong>2.4</strong><br> 27/8/2008
4918 <td><em>User Interface</em>
4920 <li>Linked highlighting of codon and amino acid from
4921 translation and protein products</li>
4922 <li>Linked highlighting of structure associated with
4923 residue mapping to codon position</li>
4924 <li>Sequence Fetcher provides example accession numbers
4925 and 'clear' button</li>
4926 <li>MemoryMonitor added as an option under Desktop's
4928 <li>Extract score function to parse whitespace separated
4929 numeric data in description line</li>
4930 <li>Column labels in alignment annotation can be centred.</li>
4931 <li>Tooltip for sequence associated annotation give name
4933 </ul> <em>Web Services and URL fetching</em>
4935 <li>JPred3 web service</li>
4936 <li>Prototype sequence search client (no public services
4938 <li>Fetch either seed alignment or full alignment from
4940 <li>URL Links created for matching database cross
4941 references as well as sequence ID</li>
4942 <li>URL Links can be created using regular-expressions</li>
4943 </ul> <em>Sequence Database Connectivity</em>
4945 <li>Retrieval of cross-referenced sequences from other
4947 <li>Generalised database reference retrieval and
4948 validation to all fetchable databases</li>
4949 <li>Fetch sequences from DAS sources supporting the
4950 sequence command</li>
4951 </ul> <em>Import and Export</em>
4952 <li>export annotation rows as CSV for spreadsheet import</li>
4953 <li>Jalview projects record alignment dataset associations,
4954 EMBL products, and cDNA sequence mappings</li>
4955 <li>Sequence Group colour can be specified in Annotation
4957 <li>Ad-hoc colouring of group in Annotation File using RGB
4958 triplet as name of colourscheme</li>
4959 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4961 <li>treenode binding for VAMSAS tree exchange</li>
4962 <li>local editing and update of sequences in VAMSAS
4963 alignments (experimental)</li>
4964 <li>Create new or select existing session to join</li>
4965 <li>load and save of vamsas documents</li>
4966 </ul> <em>Application command line</em>
4968 <li>-tree parameter to open trees (introduced for passing
4970 <li>-fetchfrom command line argument to specify nicknames
4971 of DAS servers to query for alignment features</li>
4972 <li>-dasserver command line argument to add new servers
4973 that are also automatically queried for features</li>
4974 <li>-groovy command line argument executes a given groovy
4975 script after all input data has been loaded and parsed</li>
4976 </ul> <em>Applet-Application data exchange</em>
4978 <li>Trees passed as applet parameters can be passed to
4979 application (when using "View in full
4980 application")</li>
4981 </ul> <em>Applet Parameters</em>
4983 <li>feature group display control parameter</li>
4984 <li>debug parameter</li>
4985 <li>showbutton parameter</li>
4986 </ul> <em>Applet API methods</em>
4988 <li>newView public method</li>
4989 <li>Window (current view) specific get/set public methods</li>
4990 <li>Feature display control methods</li>
4991 <li>get list of currently selected sequences</li>
4992 </ul> <em>New Jalview distribution features</em>
4994 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4995 <li>RELEASE file gives build properties for the latest
4996 Jalview release.</li>
4997 <li>Java 1.1 Applet build made easier and donotobfuscate
4998 property controls execution of obfuscator</li>
4999 <li>Build target for generating source distribution</li>
5000 <li>Debug flag for javacc</li>
5001 <li>.jalview_properties file is documented (slightly) in
5002 jalview.bin.Cache</li>
5003 <li>Continuous Build Integration for stable and
5004 development version of Application, Applet and source
5009 <li>selected region output includes visible annotations
5010 (for certain formats)</li>
5011 <li>edit label/displaychar contains existing label/char
5013 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
5014 <li>shorter peptide product names from EMBL records</li>
5015 <li>Newick string generator makes compact representations</li>
5016 <li>bootstrap values parsed correctly for tree files with
5018 <li>pathological filechooser bug avoided by not allowing
5019 filenames containing a ':'</li>
5020 <li>Fixed exception when parsing GFF files containing
5021 global sequence features</li>
5022 <li>Alignment datasets are finalized only when number of
5023 references from alignment sequences goes to zero</li>
5024 <li>Close of tree branch colour box without colour
5025 selection causes cascading exceptions</li>
5026 <li>occasional negative imgwidth exceptions</li>
5027 <li>better reporting of non-fatal warnings to user when
5028 file parsing fails.</li>
5029 <li>Save works when Jalview project is default format</li>
5030 <li>Save as dialog opened if current alignment format is
5031 not a valid output format</li>
5032 <li>UniProt canonical names introduced for both das and
5034 <li>Histidine should be midblue (not pink!) in Zappo</li>
5035 <li>error messages passed up and output when data read
5037 <li>edit undo recovers previous dataset sequence when
5038 sequence is edited</li>
5039 <li>allow PDB files without pdb ID HEADER lines (like
5040 those generated by MODELLER) to be read in properly</li>
5041 <li>allow reading of JPred concise files as a normal
5043 <li>Stockholm annotation parsing and alignment properties
5044 import fixed for PFAM records</li>
5045 <li>Structure view windows have correct name in Desktop
5047 <li>annotation consisting of sequence associated scores
5048 can be read and written correctly to annotation file</li>
5049 <li>Aligned cDNA translation to aligned peptide works
5051 <li>Fixed display of hidden sequence markers and
5052 non-italic font for representatives in Applet</li>
5053 <li>Applet Menus are always embedded in applet window on
5055 <li>Newly shown features appear at top of stack (in
5057 <li>Annotations added via parameter not drawn properly
5058 due to null pointer exceptions</li>
5059 <li>Secondary structure lines are drawn starting from
5060 first column of alignment</li>
5061 <li>UniProt XML import updated for new schema release in
5063 <li>Sequence feature to sequence ID match for Features
5064 file is case-insensitive</li>
5065 <li>Sequence features read from Features file appended to
5066 all sequences with matching IDs</li>
5067 <li>PDB structure coloured correctly for associated views
5068 containing a sub-sequence</li>
5069 <li>PDB files can be retrieved by applet from Jar files</li>
5070 <li>feature and annotation file applet parameters
5071 referring to different directories are retrieved correctly</li>
5072 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
5073 <li>Fixed application hang whilst waiting for
5074 splash-screen version check to complete</li>
5075 <li>Applet properly URLencodes input parameter values
5076 when passing them to the launchApp service</li>
5077 <li>display name and local features preserved in results
5078 retrieved from web service</li>
5079 <li>Visual delay indication for sequence retrieval and
5080 sequence fetcher initialisation</li>
5081 <li>updated Application to use DAS 1.53e version of
5082 dasobert DAS client</li>
5083 <li>Re-instated Full AMSA support and .amsa file
5085 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
5093 <div align="center">
5094 <strong>2.3</strong><br> 9/5/07
5099 <li>Jmol 11.0.2 integration</li>
5100 <li>PDB views stored in Jalview XML files</li>
5101 <li>Slide sequences</li>
5102 <li>Edit sequence in place</li>
5103 <li>EMBL CDS features</li>
5104 <li>DAS Feature mapping</li>
5105 <li>Feature ordering</li>
5106 <li>Alignment Properties</li>
5107 <li>Annotation Scores</li>
5108 <li>Sort by scores</li>
5109 <li>Feature/annotation editing in applet</li>
5114 <li>Headless state operation in 2.2.1</li>
5115 <li>Incorrect and unstable DNA pairwise alignment</li>
5116 <li>Cut and paste of sequences with annotation</li>
5117 <li>Feature group display state in XML</li>
5118 <li>Feature ordering in XML</li>
5119 <li>blc file iteration selection using filename # suffix</li>
5120 <li>Stockholm alignment properties</li>
5121 <li>Stockhom alignment secondary structure annotation</li>
5122 <li>2.2.1 applet had no feature transparency</li>
5123 <li>Number pad keys can be used in cursor mode</li>
5124 <li>Structure Viewer mirror image resolved</li>
5131 <div align="center">
5132 <strong>2.2.1</strong><br> 12/2/07
5137 <li>Non standard characters can be read and displayed
5138 <li>Annotations/Features can be imported/exported to the
5140 <li>Applet allows editing of sequence/annotation/group
5141 name & description
5142 <li>Preference setting to display sequence name in
5144 <li>Annotation file format extended to allow
5145 Sequence_groups to be defined
5146 <li>Default opening of alignment overview panel can be
5147 specified in preferences
5148 <li>PDB residue numbering annotation added to associated
5154 <li>Applet crash under certain Linux OS with Java 1.6
5156 <li>Annotation file export / import bugs fixed
5157 <li>PNG / EPS image output bugs fixed
5163 <div align="center">
5164 <strong>2.2</strong><br> 27/11/06
5169 <li>Multiple views on alignment
5170 <li>Sequence feature editing
5171 <li>"Reload" alignment
5172 <li>"Save" to current filename
5173 <li>Background dependent text colour
5174 <li>Right align sequence ids
5175 <li>User-defined lower case residue colours
5178 <li>Menu item accelerator keys
5179 <li>Control-V pastes to current alignment
5180 <li>Cancel button for DAS Feature Fetching
5181 <li>PCA and PDB Viewers zoom via mouse roller
5182 <li>User-defined sub-tree colours and sub-tree selection
5185 <li>'New Window' button on the 'Output to Text box'
5190 <li>New memory efficient Undo/Redo System
5191 <li>Optimised symbol lookups and conservation/consensus
5193 <li>Region Conservation/Consensus recalculated after
5195 <li>Fixed Remove Empty Columns Bug (empty columns at end
5197 <li>Slowed DAS Feature Fetching for increased robustness.
5200 <li>Made angle brackets in ASCII feature descriptions
5202 <li>Re-instated Zoom function for PCA
5203 <li>Sequence descriptions conserved in web service
5205 <li>UniProt ID discoverer uses any word separated by
5207 <li>WsDbFetch query/result association resolved
5208 <li>Tree leaf to sequence mapping improved
5209 <li>Smooth fonts switch moved to FontChooser dialog box.
5217 <div align="center">
5218 <strong>2.1.1</strong><br> 12/9/06
5223 <li>Copy consensus sequence to clipboard</li>
5228 <li>Image output - rightmost residues are rendered if
5229 sequence id panel has been resized</li>
5230 <li>Image output - all offscreen group boundaries are
5232 <li>Annotation files with sequence references - all
5233 elements in file are relative to sequence position</li>
5234 <li>Mac Applet users can use Alt key for group editing</li>
5240 <div align="center">
5241 <strong>2.1</strong><br> 22/8/06
5246 <li>MAFFT Multiple Alignment in default Web Service list</li>
5247 <li>DAS Feature fetching</li>
5248 <li>Hide sequences and columns</li>
5249 <li>Export Annotations and Features</li>
5250 <li>GFF file reading / writing</li>
5251 <li>Associate structures with sequences from local PDB
5253 <li>Add sequences to exisiting alignment</li>
5254 <li>Recently opened files / URL lists</li>
5255 <li>Applet can launch the full application</li>
5256 <li>Applet has transparency for features (Java 1.2
5258 <li>Applet has user defined colours parameter</li>
5259 <li>Applet can load sequences from parameter
5260 "sequence<em>x</em>"
5266 <li>Redundancy Panel reinstalled in the Applet</li>
5267 <li>Monospaced font - EPS / rescaling bug fixed</li>
5268 <li>Annotation files with sequence references bug fixed</li>
5274 <div align="center">
5275 <strong>2.08.1</strong><br> 2/5/06
5280 <li>Change case of selected region from Popup menu</li>
5281 <li>Choose to match case when searching</li>
5282 <li>Middle mouse button and mouse movement can compress /
5283 expand the visible width and height of the alignment</li>
5288 <li>Annotation Panel displays complete JNet results</li>
5294 <div align="center">
5295 <strong>2.08b</strong><br> 18/4/06
5301 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
5302 <li>Righthand label on wrapped alignments shows correct
5309 <div align="center">
5310 <strong>2.08</strong><br> 10/4/06
5315 <li>Editing can be locked to the selection area</li>
5316 <li>Keyboard editing</li>
5317 <li>Create sequence features from searches</li>
5318 <li>Precalculated annotations can be loaded onto
5320 <li>Features file allows grouping of features</li>
5321 <li>Annotation Colouring scheme added</li>
5322 <li>Smooth fonts off by default - Faster rendering</li>
5323 <li>Choose to toggle Autocalculate Consensus On/Off</li>
5328 <li>Drag & Drop fixed on Linux</li>
5329 <li>Jalview Archive file faster to load/save, sequence
5330 descriptions saved.</li>
5336 <div align="center">
5337 <strong>2.07</strong><br> 12/12/05
5342 <li>PDB Structure Viewer enhanced</li>
5343 <li>Sequence Feature retrieval and display enhanced</li>
5344 <li>Choose to output sequence start-end after sequence
5345 name for file output</li>
5346 <li>Sequence Fetcher WSDBFetch@EBI</li>
5347 <li>Applet can read feature files, PDB files and can be
5348 used for HTML form input</li>
5353 <li>HTML output writes groups and features</li>
5354 <li>Group editing is Control and mouse click</li>
5355 <li>File IO bugs</li>
5361 <div align="center">
5362 <strong>2.06</strong><br> 28/9/05
5367 <li>View annotations in wrapped mode</li>
5368 <li>More options for PCA viewer</li>
5373 <li>GUI bugs resolved</li>
5374 <li>Runs with -nodisplay from command line</li>
5380 <div align="center">
5381 <strong>2.05b</strong><br> 15/9/05
5386 <li>Choose EPS export as lineart or text</li>
5387 <li>Jar files are executable</li>
5388 <li>Can read in Uracil - maps to unknown residue</li>
5393 <li>Known OutOfMemory errors give warning message</li>
5394 <li>Overview window calculated more efficiently</li>
5395 <li>Several GUI bugs resolved</li>
5401 <div align="center">
5402 <strong>2.05</strong><br> 30/8/05
5407 <li>Edit and annotate in "Wrapped" view</li>
5412 <li>Several GUI bugs resolved</li>
5418 <div align="center">
5419 <strong>2.04</strong><br> 24/8/05
5424 <li>Hold down mouse wheel & scroll to change font
5430 <li>Improved JPred client reliability</li>
5431 <li>Improved loading of Jalview files</li>
5437 <div align="center">
5438 <strong>2.03</strong><br> 18/8/05
5443 <li>Set Proxy server name and port in preferences</li>
5444 <li>Multiple URL links from sequence ids</li>
5445 <li>User Defined Colours can have a scheme name and added
5447 <li>Choose to ignore gaps in consensus calculation</li>
5448 <li>Unix users can set default web browser</li>
5449 <li>Runs without GUI for batch processing</li>
5450 <li>Dynamically generated Web Service Menus</li>
5455 <li>InstallAnywhere download for Sparc Solaris</li>
5461 <div align="center">
5462 <strong>2.02</strong><br> 18/7/05
5468 <li>Copy & Paste order of sequences maintains
5469 alignment order.</li>
5475 <div align="center">
5476 <strong>2.01</strong><br> 12/7/05
5481 <li>Use delete key for deleting selection.</li>
5482 <li>Use Mouse wheel to scroll sequences.</li>
5483 <li>Help file updated to describe how to add alignment
5485 <li>Version and build date written to build properties
5487 <li>InstallAnywhere installation will check for updates
5488 at launch of Jalview.</li>
5493 <li>Delete gaps bug fixed.</li>
5494 <li>FileChooser sorts columns.</li>
5495 <li>Can remove groups one by one.</li>
5496 <li>Filechooser icons installed.</li>
5497 <li>Finder ignores return character when searching.
5498 Return key will initiate a search.<br>
5505 <div align="center">
5506 <strong>2.0</strong><br> 20/6/05
5511 <li>New codebase</li>