4 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
5 * Copyright (C) $$Year-Rel$$ The Jalview Authors
7 * This file is part of Jalview.
9 * Jalview is free software: you can redistribute it and/or
10 * modify it under the terms of the GNU General Public License
11 * as published by the Free Software Foundation, either version 3
12 * of the License, or (at your option) any later version.
14 * Jalview is distributed in the hope that it will be useful, but
15 * WITHOUT ANY WARRANTY; without even the implied warranty
16 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
17 * PURPOSE. See the GNU General Public License for more details.
19 * You should have received a copy of the GNU General Public License
20 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
21 * The Jalview Authors are detailed in the 'AUTHORS' file.
24 <title>Release History</title>
27 /* remove bullets, narrower indent */
28 list-style-type: none;
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51 <strong>Release History</strong>
55 <th nowrap><a id="Jalview.$$Version-Rel$$"><em>Release</em></th>
56 <th><em>New Features</em></th>
57 <th><em>Issues Resolved</em></th>
60 <td width="60" align="center" nowrap><strong><a
61 id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.0">.0</a><br />
62 <em>3/03/2022</em></strong></td>
63 <td align="left" valign="top">
66 <!-- JAL-3616 JAL-3551 JAL-2322 -->Support for viewing 3D
67 structures with ChimeraX and Pymol in addition to Jmol and
71 <!-- JAL-3829 -->Discover 3D structure data for sequences
72 with Uniprot references via 3D-Beacons
75 <!-- JAL-3391 -->Rank and select available structures for
76 Uniprot sequences according to number of residues in
77 structure mapped to positions involved in the alignment
80 <!-- JAL-3503 -->New Preferences tab for adjusting Jalview's
81 memory settings at launch
84 <!-- JAL-3144 -->Reverted to Jalview 'classic' drop-down
85 menu for selecting which database to fetch from in sequence
89 <!-- JAL-2226 -->Structure annotation rows for all mapped
90 chains in 3D structures are included in the 'Reference
91 Annotation' for a sequence
94 <!-- JAL-1260 -->Import Genbank and EMBL format flatfiles
97 <!-- JAL-3821 -->ENA record's mol_type honoured so RNA
98 molecules imported from ENA records are shown as RNA
100 <!-- JAL-3863 -->Support for Canonical Uniprot IDs
103 <!-- JAL-3204 -->Updated Jalview bindings for Uniprot XML
107 <!-- JAL-3926 -->Uniprot and PDBe autosearch option is
111 <!-- JAL-3530 -->-nowebservicediscovery command line
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
142 <!-- JAL-3608 -->Options to allow user to choose the (Swing) Look and Feel (LaF) used by Jalview
145 <!-- JAL-3552, JAL-3609 -->Metal LaF used to improved operation on Linux Ubuntu with
146 HiDPI display in Java 11 (still known issues with HiDPI screens in java
148 href="https://issues.jalview.org/browse/JAL-3137">JAL-3137</a>)
151 <!-- JAL-3830 -->New command line launcher scripts (.sh, .ps1, .bat) usable on
152 macOS, Linux/Unix, Windows and documentation in Help. Installer wizard has option
153 to add this to PATH, or link to it in your PATH.
156 </ul> <em>JalviewJS</em>
159 <!-- JAL-3624 -->PDB structures mapped to Uniprot Sequences with
163 <!-- JAL-3208 -->setprop commandline argument reinstated for JalviewJS only
166 <!-- JAL-3163 -->Missing message bundle keys are only
167 reported once per key (avoids excessive log output in js
171 <!-- JAL-3168 -->Feature type is included in the title of
172 the Feature Settings' Colour Chooser dialog
175 </ul> <em>Development</em>
178 <!-- -->First integrated JalviewJS and Jalview release
180 <li>Updated building instructions</li>
182 <!-- JAL-3789, JAL-3679 -->Improved JalviewJS/Jalview build
183 process, added support for system package provided eclipse
186 <li>Install4j 9.0.x used for installer packaging</li>
187 <li>Notarized MacOS installer for compatibility with Big
188 Sur and Monterey</li>
190 <!-- JAL-3805 -->Uninstaller application for old
191 (InstallAnywhere based) Jalview installations removed from
195 <!-- JAL-3930 -->Improved use of installers for unattended
196 installation with a customizedId of "JALVIEW" in install4j's
200 <!-- JAL-3907 -->Improved compatibility of Jalview build
201 with Java 17 (next LTS target)
210 <!-- JAL-3674 -->Slow structure commands can block Jalview
214 <!-- JAL-3904 -->Structure window's viewer-specific menu
215 disappears when only one structure is shown (and many
216 sequences:one chain mappings are present)
219 <!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
220 the first SEQUENCE_GROUP defined
225 <!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 -->Selections not
226 propagated between Linked CDS - Protein alignments and their
227 trees (known defect from 2.11.1.3)
230 <!-- JAL-3761 -->Not all codon positions highlighted for
231 overlapping exon splice sites (e.g due to RNA slippage)
234 <!-- JAL-3794 -->X was not being recognised as the unknown
235 base in DNA sequences
238 <!-- JAL-3915 -->Removed RNAview checkbox and logic from
239 Structure Preferences
242 <!-- JAL-3583 -->Tooltip behaviour improved (slightly)
245 <!-- JAL-3162 -->Can edit a feature so that start > end
248 <!-- JAL-2848 -->Cancel from Amend Features doesn't reset a
249 modified graduated colour
252 <!-- JAL-3788 -->New View with automatic 'Show Overview'
253 preference enabled results in Null Pointer Exceptions when
254 clustal colouring is enabled
257 <!-- JAL-3275 -->Can open multiple Preferences panels
260 <!-- JAL-3949 -->Standard out logging broken: messages only
261 routing to stderr and appear as a raw template
263 </ul> <em>JalviewJS</em>
266 <!-- JAL-3202 -->Consensus profile may include zero (rounded
267 down) percentage values causing a divide by zero
282 <!-- JAL-3762 -->JalviewJS doesn't honour arguments passed
283 via Info.args when there are arguments on the URL
286 <!-- JAL-3602 -->gradle closure-compiler not using UTF-8
289 <!-- JAL-3603 -->Annotation file fails to load from URL in
292 </ul> <em>Development</em>
296 <li>Fixed non-fatal gradle errors during build</li>
298 <!-- JAL-3745 -->Updated build.gradle for use with
308 <td width="60" align="center" nowrap><strong><a
309 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.7">.7</a><br />
310 <em>18/01/2022</em></strong></td>
312 <td align="left" valign="top">
315 <!-- JAL-3703, JAL-3935 -->Files open in Jalview cannot be
316 updated by Jalview or other applications (Windows, other non
319 </ul> <em>Security</em>
322 <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
328 <td width="60" align="center" nowrap><strong><a
329 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
330 <em>6/01/2022</em></strong></td>
332 <td align="left" valign="top"><em>Security</em>
335 <!-- JAL-3934 -->Version bump library dependency: Log4j
342 <td width="60" align="center" nowrap><strong><a
343 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
344 <em>20/12/2021</em></strong></td>
346 <td align="left" valign="top"><em>Security</em>
349 <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
351 </ul> <em>Development</em>
353 <li>Updated building instructions</li>
358 <!-- JAL-3840 -->Occupancy calculation is incorrect for
359 alignment columns with over -1+2^32 gaps (breaking filtering
363 <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
364 scale factors being set with buggy window-managers (linux
367 </ul> <em>Development</em>
369 <li>Fixed non-fatal gradle errors during build</li>
374 <td width="60" align="center" nowrap><strong><a
375 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
376 <em>09/03/2021</em></strong></td>
377 <td align="left" valign="top"><em>Improved control of
378 Jalview's use of network services via jalview_properties</em>
381 <!-- JAL-3814 -->New .jalview_properties token controlling
382 launch of the news browser (like -nonews argument)
385 <!-- JAL-3813 -->New .jalview_properties token controlling
386 download of linkout URLs from
387 www.jalview.org/services/identifiers
390 <!-- JAL-3812 -->New .jalview_properties token controlling
391 download of BIOJSHTML templates
394 <!-- JAL-3811 -->New 'Discover Web Services' option to
395 trigger a one off JABAWS discovery if autodiscovery was
399 <td align="left" valign="top">
402 <!-- JAL-3818 -->Intermittent deadlock opening structure in
405 </ul> <em>New Known defects</em>
408 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
409 always restored from project (since 2.10.3)
412 <!-- JAL-3806 -->Selections from tree built from CDS aren't
413 propagated to Protein alignment (since 2.11.1.3)
419 <td width="60" align="center" nowrap><strong><a
420 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
421 <em>29/10/2020</em></strong></td>
422 <td align="left" valign="top">
427 <td align="left" valign="top">
430 <!-- JAL-3765 -->Find doesn't always highlight all matching
431 positions in a sequence (bug introduced in 2.11.1.2)
434 <!-- JAL-3760 -->Alignments containing one or more protein
435 sequences can be classed as nucleotide
438 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
439 sequences after alignment of protein products (known defect
440 first reported for 2.11.1.0)
443 <!-- JAL-3725 -->No tooltip or popup menu for genomic
444 features outwith CDS shown overlaid on protein
447 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
448 correctly mapped by Jalview (e.g. affects viral CDS with
449 ribosomal slippage, since 2.9.0)
452 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
456 <!-- JAL-3700 -->Selections in CDS sequence panel don't
457 always select corresponding protein sequences
460 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
461 column selection doesn't always ignore hidden columns
463 </ul> <em>Installer</em>
466 <!-- JAL-3611 -->Space character in Jalview install path on
467 Windows prevents install4j launching getdown
469 </ul> <em>Development</em>
472 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
473 version numbers in doc/building.md
479 <td width="60" align="center" nowrap><strong><a
480 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
481 <em>25/09/2020</em></strong></td>
482 <td align="left" valign="top">
486 <td align="left" valign="top">
489 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
490 "Encountered problems opening
491 https://www.jalview.org/examples/exampleFile_2_7.jvp"
497 <td width="60" align="center" nowrap><strong><a
498 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
499 <em>17/09/2020</em></strong></td>
500 <td align="left" valign="top">
503 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
504 residue in cursor mode
507 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
508 HTSJDK from 2.12 to 2.23
511 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
512 optimisations and improvements suggested by Bob Hanson and
513 improved compatibility with JalviewJS
516 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
517 alignments from Pfam and Rfam
520 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
521 import (no longer based on .gz extension)
524 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
527 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
528 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
532 <!-- JAL-3667 -->Improved warning messages, debug logging
533 and fixed Retry action when Jalview encounters errors when
534 saving or making backup files.
537 <!-- JAL-3676 -->Enhanced Jalview Java Console:
539 <li>Jalview's logging level can be configured</li>
540 <li>Copy to Clipboard Buttion</li>
544 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
545 when running on Linux (Requires Java 11+)
547 </ul> <em>Launching Jalview</em>
550 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
551 through a system property
554 <!-- JAL-3477 -->Improved built-in documentation and command
555 line help for configuring Jalview's memory
559 <td align="left" valign="top">
562 <!-- JAL-3691 -->Conservation and Quality tracks are shown
563 but not calculated and no protein or DNA score models are
564 available for tree/PCA calculation when launched with
565 Turkish language locale
568 <!-- JAL-3493 -->Escape does not clear highlights on the
569 alignment (Since Jalview 2.10.3)
572 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
573 doesn't slide selected sequences, just sequence under cursor
576 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
577 sequence under the cursor
580 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
581 multiple EMBL gene products shown for a single contig
584 <!-- JAL-3696 -->Errors encountered when processing variants
585 from VCF files yield "Error processing VCF: Format specifier
589 <!-- JAL-3697 -->Count of features not shown can be wrong
590 when there are both local and complementary features mapped
591 to the position under the cursor
594 <!-- JAL-3673 -->Sequence ID for reference sequence is
595 clipped when Right align Sequence IDs enabled
598 <!-- JAL-2983 -->Slider with negative range values not
599 rendered correctly in VAqua4 (Since 2.10.4)
602 <!-- JAL-3685 -->Single quotes not displayed correctly in
603 internationalised text for some messages and log output
606 <!-- JAL-3490 -->Find doesn't report matches that span
607 hidden gapped columns
610 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
611 panels, Alignment viewport and annotation renderer.
614 <!-- JAL-3561 -->Jalview ignores file format parameter
615 specifying output format when exporting an alignment via the
619 <!-- JAL-3667 -->Windows 10: For a minority of users, if
620 backups are not enabled, Jalview sometimes fails to
621 overwrite an existing file and raises a warning dialog. (in
622 2.11.0, and 2.11.1.0, the workaround is to try to save the
623 file again, and if that fails, delete the original file and
627 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
631 <!-- JAL-3741 -->References to http://www.jalview.org in
632 program and documentation
634 </ul> <em>Launching Jalview</em>
637 <!-- JAL-3718 -->Jalview application fails when launched the
638 first time for a version that has different jars to the
639 previous launched version.
641 </ul> <em>Developing Jalview</em>
644 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
645 data, causing cloverReport gradle task to fail with an
649 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
650 monitor the release channel
652 </ul> <em>New Known defects</em>
655 <!-- JAL-3748 -->CDS shown in result of submitting proteins
656 in a CDS/Protein alignment to a web service is wrong when
657 proteins share a common transcript sequence (e.g. genome of
661 <!-- JAL-3576 -->Co-located features exported and
662 re-imported are ordered differently when shown on alignment
663 and in tooltips. (Also affects v2.11.1.0)
666 <!-- JAL-3702 -->Drag and drop of alignment file onto
667 alignment window when in a HiDPI scaled mode in Linux only
668 works for the top left quadrant of the alignment window
671 <!-- JAL-3701 -->Stale build data in jalview standalone jar
672 builds (only affects 2.11.1.1 branch)
675 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
676 when alignment view restored from project (since Jalview
680 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
681 protein products for certain ENA records are repeatedly
682 shown via Calculate->Show Cross Refs
688 <td width="60" align="center" nowrap><strong><a
689 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
690 <em>22/04/2020</em></strong></td>
691 <td align="left" valign="top">
694 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
695 'virtual' codon features shown on protein (or vice versa)
696 for display in alignments, on structure views (including
697 transfer to UCSF chimera), in feature reports and for
701 <!-- JAL-3121 -->Feature attributes from VCF files can be
702 exported and re-imported as GFF3 files
705 <!-- JAL-3376 -->Capture VCF "fixed column" values
706 POS, ID, QUAL, FILTER as Feature Attributes
709 <!-- JAL-3375 -->More robust VCF numeric data field
710 validation while parsing
713 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
717 <!-- JAL-3535 -->Feature Settings dialog title includes name
721 <!-- JAL-3538 -->Font anti-aliasing in alignment views
725 <!-- JAL-3468 -->Very long feature descriptions truncated in
729 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
730 with no feature types visible
733 <!-- JAL-3574 -->Improved support for filtering feature
734 attributes with large integer values
737 <em>Jalview Installer</em>
740 <!-- JAL-3449 -->Versions for install4j and getdown and
741 installer template version reported in console (may be null
742 when Jalview launched as executable jar or via conda)
745 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and
746 higher quality background images
749 <!-- JAL-3394 -->New installer/application launcher
750 generated with install4j 8.0.4
753 <!-- JAL-3420 -->Jalview File Associations shown for Unix
757 <!-- JAL-3477 -->Improved defaults for maximum memory
758 setting when running on large memory machines
760 </ul> <em>Release processes</em>
763 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
766 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier
767 access to test-release channel builds
769 </ul> <em>Build System</em>
772 <!-- JAL-3510 -->Clover updated to 4.4.1
775 <!-- JAL-3513 -->Test code included in Clover coverage
778 </ul> <em>Groovy Scripts</em>
781 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
782 to stdout containing the consensus sequence for each
783 alignment in a Jalview session
786 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
787 genomic sequence_variant annotation from CDS as
788 missense_variant or synonymous_variant on protein products.
792 <td align="left" valign="top">
795 <!-- JAL-3581 -->Hidden sequence markers still visible when
796 'Show hidden markers' option is not ticked
799 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
800 PNG output when 'Automatically set ID width' is set in
801 jalview preferences or properties file
804 <!-- JAL-3571 -->Feature Editor dialog can be opened when
805 'Show Sequence Features' option is not ticked
808 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
809 buttons in Feature Settings dialog are clicked when no
813 <!-- JAL-3412 -->ID margins for CDS and Protein views not
814 equal when split frame is first opened
817 <!-- JAL-3296 -->Sequence position numbers in status bar not
818 correct after editing a sequence's start position
821 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
822 with annotation and exceptions thrown when only a few
823 columns shown in wrapped mode
826 <!-- JAL-3386 -->Sequence IDs missing in headless export of
827 wrapped alignment figure with annotations
830 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
831 ID fails with ClassCastException
834 <!-- JAL-3389 -->Chimera session not restored from Jalview
838 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
839 feature settings dialog also selects columns
842 <!-- JAL-3473 -->SpinnerNumberModel causes
843 IllegalArgumentException in some circumstances
846 <!-- JAL-3534 -->Multiple feature settings dialogs can be
850 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
851 alignment window is closed
854 <!-- JAL-3406 -->Credits missing some authors in Jalview
855 help documentation for 2.11.0 release
858 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
859 includes Pfam ID as sequence's accession rather than its
862 </ul> <em>Java 11 Compatibility issues</em>
865 <!-- JAL-2987 -->OSX - Can't view some search results in
866 PDB/Uniprot search panel
868 </ul> <em>Installer</em>
871 <!-- JAL-3447 -->Jalview should not create file associations
872 for 3D structure files (.pdb, .mmcif. .cif)
874 </ul> <em>Repository and Source Release</em>
877 <!-- JAL-3474 -->removed obsolete .cvsignore files from
881 <!-- JAL-3541 -->Clover report generation running out of
884 </ul> <em>New Known Issues</em>
887 <!-- JAL-3523 -->OSX - Current working directory not
888 preserved when Jalview.app launched with parameters from
892 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
893 clipped in headless figure export when Right Align option
897 <!-- JAL-3542 -->Jalview Installation type always reports
898 'Source' in console output
901 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail
902 on jalview's bamboo server but run fine locally.
908 <td width="60" align="center" nowrap><strong><a
909 name="Jalview.2.11.0">2.11.0</a><br /> <em>04/07/2019</em></strong></td>
910 <td align="left" valign="top">
913 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native
914 Application and Installers built with <a
915 href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a>
916 (licensed to the Jalview open source project) rather than
920 <!-- JAL-1929 -->Jalview Launcher System to auto-configure
921 memory settings, receive over the air updates and launch
922 specific versions via (<a
923 href="https://github.com/threerings/getdown">Three
927 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations
928 for formats supported by Jalview (including .jvp project
932 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command
933 line arguments and switch between different getdown channels
936 <!-- JAL-3141 -->Backup files created when saving Jalview
937 project or alignment files
941 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF
945 <!-- JAL-2753 -->Version of HTSJDK shipped with Jalview
946 updated to version 2.12.0
949 <!-- JAL-2620 -->Alternative genetic code tables for
953 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0
955 <li><strong>Enhanced visualisation and analysis
956 of Sequence Features</strong>
959 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
960 implementation that allows updates) used for Sequence
964 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
965 features can be filtered and shaded according to any
966 associated attributes (e.g. variant attributes from VCF
967 file, or key-value pairs imported from column 9 of GFF
971 <!-- JAL-2879 -->Feature Attributes and shading schemes
972 stored and restored from Jalview Projects
975 <!-- JAL-3334 -->Use full Sequence Ontology (via
976 BioJava) to recognise variant features
979 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants
980 on peptide sequences (also coloured red by default)
983 <!-- JAL-2792 -->Popup window to show full report for a
984 selected sequence feature's details
987 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient
988 sequence feature render algorithm (Z-sort/transparency
992 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature
997 <!-- JAL-3205 -->Symmetric score matrices for faster tree
1000 <li><strong>Principal Components Analysis Viewer</strong>
1003 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis
1004 results and Viewer state saved in Jalview Project
1007 <!-- JAL-2962 -->'Change parameters' option removed from
1008 viewer's drop-down menus
1011 <!-- JAL-2975 -->Can use shift + arrow keys to rotate
1012 PCA image incrementally
1015 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
1019 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
1021 <li><strong>Speed and Efficiency</strong>
1024 <!-- JAL-2185,JAL-3198 -->More efficient creation of
1025 selections and multiple groups when working with large
1029 <!-- JAL-3200 -->Speedier import of annotation rows when
1030 parsing Stockholm files
1033 <li><strong>User Interface</strong>
1036 <!-- JAL-2933 -->Finder panel remembers last position in
1040 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS
1041 (What you see is what is shown)<br />Only visible
1042 regions of alignment are shown by default (can be
1043 changed in user preferences)
1046 <!-- JAL-3169 -->File Chooser stays open after
1047 responding Cancel to the Overwrite Dialog
1050 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour
1051 when all sequences are hidden
1054 <!-- JAL-1244 -->Status bar shows bounds when dragging a
1055 selection region, and gap count when inserting or
1059 <!-- JAL-3132 -->Status bar updates over sequence and
1063 <!-- JAL-3093 -->Annotation tooltips and popup menus are
1064 shown when in wrapped mode
1067 <!-- JAL-3073 -->Can select columns by dragging
1068 left/right in a graph or histogram annotation
1071 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB
1075 <!-- JAL-2621 -->Cursor changes over draggable box in
1079 <!-- JAL-3181 -->Consistent ordering of links in
1080 sequence id popup menu
1083 <!-- JAL-3080 -->Red line indicating tree-cut position
1084 not shown if no subgroups are created
1087 <!-- JAL-3042 -->Removed ability to configure length of
1088 search history by right-clicking search box
1094 <!-- JAL-3232 -->Jalview Groovy Scripting Console updated to
1097 <li><strong>Java 11 Support (not yet on general
1101 <!-- -->OSX GUI integrations for App menu's 'About'
1102 entry and trapping CMD-Q
1105 </ul> <em>Deprecations</em>
1108 <!-- JAL-3035 -->DAS sequence retrieval and annotation
1109 capabilities removed from the Jalview Desktop
1112 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling
1113 and unmarshalling has been replaced by JAXB for Jalview
1114 projects and XML based data retrieval clients
1117 <!-- JAL-3311 -->Disable VAMSAS menu in preparation for
1121 <!-- -->Jalview Desktop no longer distributed via Java Web
1124 </ul> <em>Documentation</em>
1127 <!-- JAL-3003 -->Added remarks about transparent rendering
1128 effects not supported in EPS figure export
1131 <!-- JAL-2903 -->Typos in documentation for Preferences
1134 </ul> <em>Development and Release Processes</em>
1137 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated
1141 <!-- JAL-1424 -->Enhanced checks for missing and duplicated
1142 keys in Message bundles
1145 <!-- JAL-3225 -->Eclipse project configuration managed with
1149 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian Bamboo
1150 continuous integration for unattended Test Suite execution
1153 <!-- JAL-2864 -->Memory test suite to detect leaks in common
1157 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
1161 <!-- JAL-3248 -->Developer documentation migrated to
1162 markdown (with HTML rendering)
1165 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
1168 <!-- JAL-3289 -->New URLs for publishing development
1173 <td align="left" valign="top">
1176 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
1179 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
1180 superposition in Jmol fail on Windows
1183 <!-- JAL-3286 -->Blank error dialog is displayed when
1184 discovering structures for sequences with lots of PDB
1188 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export
1189 with monospaced font
1192 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
1193 Jalview project involving multiple views
1196 <!-- JAL-3164 -->Overview for complementary view in a linked
1197 CDS/Protein alignment is not updated when Hide Columns by
1198 Annotation dialog hides columns
1201 <!-- JAL-3158 -->Selection highlighting in the complement of
1202 a CDS/Protein alignment stops working after making a
1203 selection in one view, then making another selection in the
1207 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
1211 <!-- JAL-3154 -->Table Columns could be re-ordered in
1212 Feature Settings and Jalview Preferences panels
1215 <!-- JAL-2865 -->Jalview hangs when closing windows, or
1216 redrawing the overview with large alignments
1219 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
1220 region if columns were selected by dragging right-to-left
1221 and the mouse moved to the left of the first column
1224 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to
1225 a hidden column marker via scale popup menu
1228 <!-- JAL-2846 -->Error message for trying to load in invalid
1229 URLs doesn't tell users the invalid URL
1232 <!-- JAL-2816 -->Tooltips displayed for features filtered by
1236 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl
1237 during show cross references or Fetch Database References
1238 are shown in red in original view
1241 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown
1242 correctly on peptide sequence (computed variant shown as
1246 <!-- JAL-2060 -->'Graduated colour' option not offered for
1247 manually created features (where feature score is Float.NaN)
1250 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or
1251 printed when columns are hidden
1254 <!-- JAL-3082 -->Regular expression error for '(' in Select
1255 Columns by Annotation description
1258 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after
1259 dragging out of Scale or Annotation Panel
1262 <!-- JAL-3075 -->Column selection incorrect after scrolling
1266 <!-- JAL-3074 -->Left/right drag in annotation can scroll
1270 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal
1274 <!-- JAL-3002 -->Column display is out by one after Page
1275 Down, Page Up in wrapped mode
1278 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
1281 <!-- JAL-2932 -->Finder searches in minimised alignments
1284 <!-- JAL-2250 -->'Apply Colour to All Groups' not always
1285 selected on opening an alignment
1288 <!-- JAL-3180 -->'Colour by Annotation' not marked selected
1292 <!-- JAL-3201 -->Per-group Clustal colour scheme changes
1293 when different groups in the alignment are selected
1296 <!-- JAL-2717 -->Internationalised colour scheme names not
1297 shown correctly in menu
1300 <!-- JAL-3206 -->Colour by Annotation can go black at
1301 min/max threshold limit
1304 <!-- JAL-3125 -->Value input for graduated feature colour
1305 threshold gets 'unrounded'
1308 <!-- JAL-2982 -->PCA image export doesn't respect background
1312 <!-- JAL-2963 -->PCA points don't dim when rotated about y
1316 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
1319 <!-- JAL-3078 -->Cancel in Tree Font dialog resets
1320 alignment, not Tree font
1323 <!-- JAL-2964 -->Associate Tree with All Views not restored
1327 <!-- JAL-2915 -->Scrolling of split frame is sluggish if
1328 Overview shown in complementary view
1331 <!-- JAL-3313 -->Codon consensus incorrectly scaled when
1332 shown without normalisation
1335 <!-- JAL-3021 -->Sequence Details report should open
1336 positioned at top of report
1339 <!-- JAL-914 -->Help page can be opened twice
1342 <!-- JAL-3333 -->Fuzzy text in web service status menu on
1345 </ul> <em>Editing</em>
1348 <!-- JAL-2822 -->Start and End should be updated when
1349 sequence data at beginning or end of alignment added/removed
1353 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection
1354 doesn't relocate sequence features correctly when start of
1355 sequence is removed (Known defect since 2.10)
1358 <!-- JAL-2830 -->Inserting gap sequence via the Edit
1359 Sequence dialog corrupts dataset sequence
1362 <!-- JAL-868 -->Structure colours not updated when
1363 associated tree repartitions the alignment view (Regression
1366 </ul> <em>Datamodel</em>
1369 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
1370 sequence's End is greater than its length
1372 </ul> <em>Bugs fixed for Java 11 Support (not yet on general
1376 <!-- JAL-3288 -->Menus work properly in split-screen
1378 </ul> <em>New Known Defects</em>
1381 <!-- JAL-3340 -->Select columns containing feature by double
1382 clicking ignores bounds of an existing selected region
1385 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in
1386 gapped regions of protein alignment.
1389 <!-- JAL-2647 -->Input Data menu entry is greyed out when
1390 PCA View is restored from a Jalview 2.11 project
1393 <!-- JAL-3213 -->Alignment panel height can be too small
1397 <!-- JAL-3240 -->Display is incorrect after removing gapped
1398 columns within hidden columns
1401 <!-- JAL-3314 -->Rightmost selection is lost when mouse
1402 re-enters window after dragging left to select columns to
1403 left of visible region
1406 <!-- JAL-2876 -->Features coloured according to their
1407 description string and thresholded by score in earlier
1408 versions of Jalview are not shown as thresholded features in
1409 2.11. To workaround please create a Score filter instead.
1412 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't
1413 reset group visibility
1416 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in
1417 linked CDS/Protein view
1420 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1421 alignments with multiple views can close views unexpectedly
1423 </ul> <em>Java 11 Specific defects</em>
1426 <!-- JAL-3235 -->Jalview Properties file is not sorted
1427 alphabetically when saved
1433 <td width="60" nowrap>
1434 <div align="center">
1435 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1438 <td><div align="left">
1442 <!-- JAL-3101 -->Default memory for Jalview webstart and
1443 InstallAnywhere increased to 1G.
1446 <!-- JAL-247 -->Hidden sequence markers and representative
1447 sequence bolding included when exporting alignment as EPS,
1448 SVG, PNG or HTML. <em>Display is configured via the
1449 Format menu, or for command-line use via a Jalview
1450 properties file.</em>
1453 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1454 API and sequence data now imported as JSON.
1457 <!-- JAL-3065 -->Change in recommended way of starting
1458 Jalview via a Java command line: add jars in lib directory
1459 to CLASSPATH, rather than via the deprecated java.ext.dirs
1463 <em>Development</em>
1466 <!-- JAL-3047 -->Support added to execute test suite
1467 instrumented with <a href="http://openclover.org/">Open
1472 <td><div align="left">
1476 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1477 row shown in Feredoxin Structure alignment view of example
1481 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1482 annotation displayed.
1485 <!-- JAL-3107 -->Group conservation/consensus not shown
1486 for newly created group when 'Apply to all groups'
1490 <!-- JAL-3087 -->Corrupted display when switching to
1491 wrapped mode when sequence panel's vertical scrollbar is
1495 <!-- JAL-3003 -->Alignment is black in exported EPS file
1496 when sequences are selected in exported view.</em>
1499 <!-- JAL-3059 -->Groups with different coloured borders
1500 aren't rendered with correct colour.
1503 <!-- JAL-3092 -->Jalview could hang when importing certain
1504 types of knotted RNA secondary structure.
1507 <!-- JAL-3095 -->Sequence highlight and selection in
1508 trimmed VARNA 2D structure is incorrect for sequences that
1512 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1513 annotation when columns are inserted into an alignment,
1514 and when exporting as Stockholm flatfile.
1517 <!-- JAL-3053 -->Jalview annotation rows containing upper
1518 and lower-case 'E' and 'H' do not automatically get
1519 treated as RNA secondary structure.
1522 <!-- JAL-3106 -->.jvp should be used as default extension
1523 (not .jar) when saving a Jalview project file.
1526 <!-- JAL-3105 -->Mac Users: closing a window correctly
1527 transfers focus to previous window on OSX
1530 <em>Java 10 Issues Resolved</em>
1533 <!-- JAL-2988 -->OSX - Can't save new files via the File
1534 or export menus by typing in a name into the Save dialog
1538 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1539 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1540 'look and feel' which has improved compatibility with the
1541 latest version of OSX.
1547 <td width="60" nowrap>
1548 <div align="center">
1549 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1550 <em>7/06/2018</em></strong>
1553 <td><div align="left">
1557 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1558 annotation retrieved from Uniprot
1561 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1562 onto the Jalview Desktop
1566 <td><div align="left">
1570 <!-- JAL-3017 -->Cannot import features with multiple
1571 variant elements (blocks import of some Uniprot records)
1574 <!-- JAL-2997 -->Clustal files with sequence positions in
1575 right-hand column parsed correctly
1578 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1579 not alignment area in exported graphic
1582 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1583 window has input focus
1586 <!-- JAL-2992 -->Annotation panel set too high when
1587 annotation added to view (Windows)
1590 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1591 network connectivity is poor
1594 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1595 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1596 the currently open URL and links from a page viewed in
1597 Firefox or Chrome on Windows is now fully supported. If
1598 you are using Edge, only links in the page can be
1599 dragged, and with Internet Explorer, only the currently
1600 open URL in the browser can be dropped onto Jalview.</em>
1603 <em>New Known Defects</em>
1606 <!-- JAL-3083 -->Cancel option doesn't reset Colour by
1613 <td width="60" nowrap>
1614 <div align="center">
1615 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1618 <td><div align="left">
1622 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1623 for disabling automatic superposition of multiple
1624 structures and open structures in existing views
1627 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1628 ID and annotation area margins can be click-dragged to
1632 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1636 <!-- JAL-2759 -->Improved performance for large alignments
1637 and lots of hidden columns
1640 <!-- JAL-2593 -->Improved performance when rendering lots
1641 of features (particularly when transparency is disabled)
1644 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2
1645 for exchange of Jalview features and Chimera attributes
1646 made generally available
1650 <td><div align="left">
1653 <!-- JAL-2899 -->Structure and Overview aren't updated
1654 when Colour By Annotation threshold slider is adjusted
1657 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1658 overlapping alignment panel
1661 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1665 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1666 improved: CDS not handled correctly if transcript has no
1670 <!-- JAL-2321 -->Secondary structure and temperature
1671 factor annotation not added to sequence when local PDB
1672 file associated with it by drag'n'drop or structure
1676 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1677 dialog doesn't import PDB files dropped on an alignment
1680 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1681 scroll bar doesn't work for some CDS/Protein views
1684 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1685 Java 1.8u153 onwards and Java 1.9u4+.
1688 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1689 columns in annotation row
1692 <!-- JAL-2913 -->Preferences panel's ID Width control is
1693 not honored in batch mode
1696 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1697 for structures added to existing Jmol view
1700 <!-- JAL-2223 -->'View Mappings' includes duplicate
1701 entries after importing project with multiple views
1704 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1705 protein sequences via SIFTS from associated PDB entries
1706 with negative residue numbers or missing residues fails
1709 <!-- JAL-2952 -->Exception when shading sequence with
1710 negative Temperature Factor values from annotated PDB
1711 files (e.g. as generated by CONSURF)
1714 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1715 tooltip doesn't include a text description of mutation
1718 <!-- JAL-2922 -->Invert displayed features very slow when
1719 structure and/or overview windows are also shown
1722 <!-- JAL-2954 -->Selecting columns from highlighted
1723 regions very slow for alignments with large numbers of
1727 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1728 with 'StringIndexOutOfBounds'
1731 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and
1732 Feel for OSX platforms running Java 10
1735 <!-- JAL-2960 -->Adding a structure to existing structure
1736 view appears to do nothing because the view is hidden
1737 behind the alignment view
1743 <!-- JAL-2926 -->Copy consensus sequence option in applet
1744 should copy the group consensus when popup is opened on it
1750 <!-- JAL-2913 -->Fixed ID width preference is not
1754 <em>New Known Defects</em>
1757 <!-- JAL-2973 --> Exceptions occasionally raised when
1758 editing a large alignment and overview is displayed
1761 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1762 repeatedly after a series of edits even when the overview
1763 is no longer reflecting updates
1766 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1767 structures for protein subsequence (if 'Trim Retrieved
1768 Sequences' enabled) or Ensembl isoforms (Workaround in
1769 2.10.4 is to fail back to N&W mapping)
1772 <!-- JAL-2990 -->Export Annotations from File Menu with
1773 CSV option gives blank output
1779 <td width="60" nowrap>
1780 <div align="center">
1781 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br />
1782 <em>24/1/2018</em></strong>
1785 <td><div align="left">
1787 <li>Updated Certum Codesigning Certificate (Valid till
1788 30th November 2018)</li>
1791 <td><div align="left">
1796 <!-- JAL-2859-->Only one structure is loaded when
1797 several sequences and structures are selected for
1801 <!-- JAL-2851-->Alignment doesn't appear to scroll
1802 vertically via trackpad and scrollwheel
1805 <!-- JAL-2842-->Jalview hangs if up/down arrows pressed
1806 in cursor mode when cursor lies in hidden region at
1810 <!-- JAL-2827-->Helix annotation has 'notches' when
1811 scrolled into view if columns are hidden
1814 <!-- JAL-2740-->Annotation column filter can be slow to
1815 reset (ie after hitting cancel) for large numbers of
1819 <!-- JAL-2849-->User preference for disabling inclusion
1820 of sequence limits when exporting as flat file has no
1824 <!-- JAL-2679-->Reproducible cross-reference
1825 relationships when retrieving sequences from
1832 <td width="60" nowrap>
1833 <div align="center">
1834 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1837 <td><div align="left">
1841 <!-- JAL-2446 -->Faster and more efficient management and
1842 rendering of sequence features
1845 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1846 429 rate limit request hander
1849 <!-- JAL-2773 -->Structure views don't get updated unless
1850 their colours have changed
1853 <!-- JAL-2495 -->All linked sequences are highlighted for
1854 a structure mousover (Jmol) or selection (Chimera)
1857 <!-- JAL-2790 -->'Cancel' button in progress bar for
1858 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1861 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1862 view from Ensembl locus cross-references
1865 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1869 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1870 feature can be disabled
1873 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1874 PDB easier retrieval of sequences for lists of IDs
1877 <!-- JAL-2758 -->Short names for sequences retrieved from
1883 <li>Groovy interpreter updated to 2.4.12</li>
1884 <li>Example groovy script for generating a matrix of
1885 percent identity scores for current alignment.</li>
1887 <em>Testing and Deployment</em>
1890 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1894 <td><div align="left">
1898 <!-- JAL-2643 -->Pressing tab after updating the colour
1899 threshold text field doesn't trigger an update to the
1903 <!-- JAL-2682 -->Race condition when parsing sequence ID
1907 <!-- JAL-2608 -->Overview windows are also closed when
1908 alignment window is closed
1911 <!-- JAL-2548 -->Export of features doesn't always respect
1915 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1916 takes a long time in Cursor mode
1922 <!-- JAL-2777 -->Structures with whitespace chainCode
1923 cannot be viewed in Chimera
1926 <!-- JAL-2728 -->Protein annotation panel too high in
1930 <!-- JAL-2757 -->Can't edit the query after the server
1931 error warning icon is shown in Uniprot and PDB Free Text
1935 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1938 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1941 <!-- JAL-2739 -->Hidden column marker in last column not
1942 rendered when switching back from Wrapped to normal view
1945 <!-- JAL-2768 -->Annotation display corrupted when
1946 scrolling right in unwapped alignment view
1949 <!-- JAL-2542 -->Existing features on subsequence
1950 incorrectly relocated when full sequence retrieved from
1954 <!-- JAL-2733 -->Last reported memory still shown when
1955 Desktop->Show Memory is unticked (OSX only)
1958 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1959 features of same type and group to be selected for
1963 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1964 alignments when hidden columns are present
1967 <!-- JAL-2392 -->Jalview freezes when loading and
1968 displaying several structures
1971 <!-- JAL-2732 -->Black outlines left after resizing or
1975 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1976 within the Jalview desktop on OSX
1979 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1980 when in wrapped alignment mode
1983 <!-- JAL-2636 -->Scale mark not shown when close to right
1984 hand end of alignment
1987 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1988 each selected sequence do not have correct start/end
1992 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1993 after canceling the Alignment Window's Font dialog
1996 <!-- JAL-2036 -->Show cross-references not enabled after
1997 restoring project until a new view is created
2000 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
2001 URL links appears when only default EMBL-EBI link is
2002 configured (since 2.10.2b2)
2005 <!-- JAL-2775 -->Overview redraws whole window when box
2006 position is adjusted
2009 <!-- JAL-2225 -->Structure viewer doesn't map all chains
2010 in a multi-chain structure when viewing alignment
2011 involving more than one chain (since 2.10)
2014 <!-- JAL-2811 -->Double residue highlights in cursor mode
2015 if new selection moves alignment window
2018 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
2019 arrow key in cursor mode to pass hidden column marker
2022 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
2023 that produces correctly annotated transcripts and products
2026 <!-- JAL-2776 -->Toggling a feature group after first time
2027 doesn't update associated structure view
2030 <em>Applet</em><br />
2033 <!-- JAL-2687 -->Concurrent modification exception when
2034 closing alignment panel
2037 <em>BioJSON</em><br />
2040 <!-- JAL-2546 -->BioJSON export does not preserve
2041 non-positional features
2044 <em>New Known Issues</em>
2047 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
2048 sequence features correctly (for many previous versions of
2052 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
2053 using cursor in wrapped panel other than top
2056 <!-- JAL-2791 -->Select columns containing feature ignores
2057 graduated colour threshold
2060 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
2061 always preserve numbering and sequence features
2064 <em>Known Java 9 Issues</em>
2067 <!-- JAL-2902 -->Groovy Console very slow to open and is
2068 not responsive when entering characters (Webstart, Java
2075 <td width="60" nowrap>
2076 <div align="center">
2077 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
2078 <em>2/10/2017</em></strong>
2081 <td><div align="left">
2082 <em>New features in Jalview Desktop</em>
2085 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API
2089 <!-- JAL-2745 -->HTTPS used for all connections to
2094 <td><div align="left"></div></td>
2097 <td width="60" nowrap>
2098 <div align="center">
2099 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
2100 <em>7/9/2017</em></strong>
2103 <td><div align="left">
2107 <!-- JAL-2588 -->Show gaps in overview window by colouring
2108 in grey (sequences used to be coloured grey, and gaps were
2112 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
2116 <!-- JAL-2587 -->Overview updates immediately on increase
2117 in size and progress bar shown as higher resolution
2118 overview is recalculated
2123 <td><div align="left">
2127 <!-- JAL-2664 -->Overview window redraws every hidden
2128 column region row by row
2131 <!-- JAL-2681 -->duplicate protein sequences shown after
2132 retrieving Ensembl crossrefs for sequences from Uniprot
2135 <!-- JAL-2603 -->Overview window throws NPE if show boxes
2136 format setting is unticked
2139 <!-- JAL-2610 -->Groups are coloured wrongly in overview
2140 if group has show boxes format setting unticked
2143 <!-- JAL-2672,JAL-2665 -->Redraw problems when
2144 autoscrolling whilst dragging current selection group to
2145 include sequences and columns not currently displayed
2148 <!-- JAL-2691 -->Not all chains are mapped when multimeric
2149 assemblies are imported via CIF file
2152 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
2153 displayed when threshold or conservation colouring is also
2157 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
2161 <!-- JAL-2673 -->Jalview continues to scroll after
2162 dragging a selected region off the visible region of the
2166 <!-- JAL-2724 -->Cannot apply annotation based
2167 colourscheme to all groups in a view
2170 <!-- JAL-2511 -->IDs don't line up with sequences
2171 initially after font size change using the Font chooser or
2178 <td width="60" nowrap>
2179 <div align="center">
2180 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
2183 <td><div align="left">
2184 <em>Calculations</em>
2188 <!-- JAL-1933 -->Occupancy annotation row shows number of
2189 ungapped positions in each column of the alignment.
2192 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
2193 a calculation dialog box
2196 <!-- JAL-2379 -->Revised implementation of PCA for speed
2197 and memory efficiency (~30x faster)
2200 <!-- JAL-2403 -->Revised implementation of sequence
2201 similarity scores as used by Tree, PCA, Shading Consensus
2202 and other calculations
2205 <!-- JAL-2416 -->Score matrices are stored as resource
2206 files within the Jalview codebase
2209 <!-- JAL-2500 -->Trees computed on Sequence Feature
2210 Similarity may have different topology due to increased
2217 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
2218 model for alignments and groups
2221 <!-- JAL-384 -->Custom shading schemes created via groovy
2228 <!-- JAL-2526 -->Efficiency improvements for interacting
2229 with alignment and overview windows
2232 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
2236 <!-- JAL-2388 -->Hidden columns and sequences can be
2240 <!-- JAL-2611 -->Click-drag in visible area allows fine
2241 adjustment of visible position
2245 <em>Data import/export</em>
2248 <!-- JAL-2535 -->Posterior probability annotation from
2249 Stockholm files imported as sequence associated annotation
2252 <!-- JAL-2507 -->More robust per-sequence positional
2253 annotation input/output via stockholm flatfile
2256 <!-- JAL-2533 -->Sequence names don't include file
2257 extension when importing structure files without embedded
2258 names or PDB accessions
2261 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
2262 format sequence substitution matrices
2265 <em>User Interface</em>
2268 <!-- JAL-2447 --> Experimental Features Checkbox in
2269 Desktop's Tools menu to hide or show untested features in
2273 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
2274 via Overview or sequence motif search operations
2277 <!-- JAL-2547 -->Amend sequence features dialog box can be
2278 opened by double clicking gaps within sequence feature
2282 <!-- JAL-1476 -->Status bar message shown when not enough
2283 aligned positions were available to create a 3D structure
2287 <em>3D Structure</em>
2290 <!-- JAL-2430 -->Hidden regions in alignment views are not
2291 coloured in linked structure views
2294 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
2295 file-based command exchange
2298 <!-- JAL-2375 -->Structure chooser automatically shows
2299 Cached Structures rather than querying the PDBe if
2300 structures are already available for sequences
2303 <!-- JAL-2520 -->Structures imported via URL are cached in
2304 the Jalview project rather than downloaded again when the
2305 project is reopened.
2308 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
2309 to transfer Chimera's structure attributes as Jalview
2310 features, and vice-versa (<strong>Experimental
2314 <em>Web Services</em>
2317 <!-- JAL-2549 -->Updated JABAWS client to v2.2
2320 <!-- JAL-2335 -->Filter non-standard amino acids and
2321 nucleotides when submitting to AACon and other MSA
2325 <!-- JAL-2316, -->URLs for viewing database
2326 cross-references provided by identifiers.org and the
2327 EMBL-EBI's MIRIAM DB
2334 <!-- JAL-2344 -->FileFormatI interface for describing and
2335 identifying file formats (instead of String constants)
2338 <!-- JAL-2228 -->FeatureCounter script refactored for
2339 efficiency when counting all displayed features (not
2340 backwards compatible with 2.10.1)
2343 <em>Example files</em>
2346 <!-- JAL-2631 -->Graduated feature colour style example
2347 included in the example feature file
2350 <em>Documentation</em>
2353 <!-- JAL-2339 -->Release notes reformatted for readability
2354 with the built-in Java help viewer
2357 <!-- JAL-1644 -->Find documentation updated with 'search
2358 sequence description' option
2364 <!-- JAL-2485, -->External service integration tests for
2365 Uniprot REST Free Text Search Client
2368 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
2371 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
2376 <td><div align="left">
2377 <em>Calculations</em>
2380 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
2381 matrix - C->R should be '-3'<br />Old matrix restored
2382 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
2384 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
2385 Jalview's treatment of gaps in PCA and substitution matrix
2386 based Tree calculations.<br /> <br />In earlier versions
2387 of Jalview, gaps matching gaps were penalised, and gaps
2388 matching non-gaps penalised even more. In the PCA
2389 calculation, gaps were actually treated as non-gaps - so
2390 different costs were applied, which meant Jalview's PCAs
2391 were different to those produced by SeqSpace.<br />Jalview
2392 now treats gaps in the same way as SeqSpace (ie it scores
2393 them as 0). <br /> <br />Enter the following in the
2394 Groovy console to restore pre-2.10.2 behaviour:<br />
2395 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
2396 // for 2.10.1 mode <br />
2397 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
2398 // to restore 2.10.2 mode <br /> <br /> <em>Note:
2399 these settings will affect all subsequent tree and PCA
2400 calculations (not recommended)</em></li>
2402 <!-- JAL-2424 -->Fixed off-by-one bug that affected
2403 scaling of branch lengths for trees computed using
2404 Sequence Feature Similarity.
2407 <!-- JAL-2377 -->PCA calculation could hang when
2408 generating output report when working with highly
2409 redundant alignments
2412 <!-- JAL-2544 --> Sort by features includes features to
2413 right of selected region when gaps present on right-hand
2417 <em>User Interface</em>
2420 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2421 doesn't reselect a specific sequence's associated
2422 annotation after it was used for colouring a view
2425 <!-- JAL-2419 -->Current selection lost if popup menu
2426 opened on a region of alignment without groups
2429 <!-- JAL-2374 -->Popup menu not always shown for regions
2430 of an alignment with overlapping groups
2433 <!-- JAL-2310 -->Finder double counts if both a sequence's
2434 name and description match
2437 <!-- JAL-2370 -->Hiding column selection containing two
2438 hidden regions results in incorrect hidden regions
2441 <!-- JAL-2386 -->'Apply to all groups' setting when
2442 changing colour does not apply Conservation slider value
2446 <!-- JAL-2373 -->Percentage identity and conservation menu
2447 items do not show a tick or allow shading to be disabled
2450 <!-- JAL-2385 -->Conservation shading or PID threshold
2451 lost when base colourscheme changed if slider not visible
2454 <!-- JAL-2547 -->Sequence features shown in tooltip for
2455 gaps before start of features
2458 <!-- JAL-2623 -->Graduated feature colour threshold not
2459 restored to UI when feature colour is edited
2462 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2463 a time when scrolling vertically in wrapped mode.
2466 <!-- JAL-2630 -->Structure and alignment overview update
2467 as graduate feature colour settings are modified via the
2471 <!-- JAL-2034 -->Overview window doesn't always update
2472 when a group defined on the alignment is resized
2475 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2476 wrapped view result in positional status updates
2480 <!-- JAL-2563 -->Status bar doesn't show position for
2481 ambiguous amino acid and nucleotide symbols
2484 <!-- JAL-2602 -->Copy consensus sequence failed if
2485 alignment included gapped columns
2488 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2489 widgets don't permanently disappear
2492 <!-- JAL-2503 -->Cannot select or filter quantitative
2493 annotation that are shown only as column labels (e.g.
2494 T-Coffee column reliability scores)
2497 <!-- JAL-2594 -->Exception thrown if trying to create a
2498 sequence feature on gaps only
2501 <!-- JAL-2504 -->Features created with 'New feature'
2502 button from a Find inherit previously defined feature type
2503 rather than the Find query string
2506 <!-- JAL-2423 -->incorrect title in output window when
2507 exporting tree calculated in Jalview
2510 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2511 and then revealing them reorders sequences on the
2515 <!-- JAL-964 -->Group panel in sequence feature settings
2516 doesn't update to reflect available set of groups after
2517 interactively adding or modifying features
2520 <!-- JAL-2225 -->Sequence Database chooser unusable on
2524 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2525 only excluded gaps in current sequence and ignored
2532 <!-- JAL-2421 -->Overview window visible region moves
2533 erratically when hidden rows or columns are present
2536 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2537 Structure Viewer's colour menu don't correspond to
2541 <!-- JAL-2405 -->Protein specific colours only offered in
2542 colour and group colour menu for protein alignments
2545 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2546 reflect currently selected view or group's shading
2550 <!-- JAL-2624 -->Feature colour thresholds not respected
2551 when rendered on overview and structures when opacity at
2555 <!-- JAL-2589 -->User defined gap colour not shown in
2556 overview when features overlaid on alignment
2559 <!-- JAL-2567 -->Feature settings for different views not
2560 recovered correctly from Jalview project file
2563 <!-- JAL-2256 -->Feature colours in overview when first
2564 opened (automatically via preferences) are different to
2565 the main alignment panel
2568 <em>Data import/export</em>
2571 <!-- JAL-2576 -->Very large alignments take a long time to
2575 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2576 added after a sequence was imported are not written to
2580 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2581 when importing RNA secondary structure via Stockholm
2584 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2585 not shown in correct direction for simple pseudoknots
2588 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2589 with lightGray or darkGray via features file (but can
2593 <!-- JAL-2383 -->Above PID colour threshold not recovered
2594 when alignment view imported from project
2597 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2598 structure and sequences extracted from structure files
2599 imported via URL and viewed in Jmol
2602 <!-- JAL-2520 -->Structures loaded via URL are saved in
2603 Jalview Projects rather than fetched via URL again when
2604 the project is loaded and the structure viewed
2607 <em>Web Services</em>
2610 <!-- JAL-2519 -->EnsemblGenomes example failing after
2611 release of Ensembl v.88
2614 <!-- JAL-2366 -->Proxy server address and port always
2615 appear enabled in Preferences->Connections
2618 <!-- JAL-2461 -->DAS registry not found exceptions
2619 removed from console output
2622 <!-- JAL-2582 -->Cannot retrieve protein products from
2623 Ensembl by Peptide ID
2626 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2627 created from SIFTs, and spurious 'Couldn't open structure
2628 in Chimera' errors raised after April 2017 update (problem
2629 due to 'null' string rather than empty string used for
2630 residues with no corresponding PDB mapping).
2633 <em>Application UI</em>
2636 <!-- JAL-2361 -->User Defined Colours not added to Colour
2640 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2641 case' residues (button in colourscheme editor debugged and
2642 new documentation and tooltips added)
2645 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2646 doesn't restore group-specific text colour thresholds
2649 <!-- JAL-2243 -->Feature settings panel does not update as
2650 new features are added to alignment
2653 <!-- JAL-2532 -->Cancel in feature settings reverts
2654 changes to feature colours via the Amend features dialog
2657 <!-- JAL-2506 -->Null pointer exception when attempting to
2658 edit graduated feature colour via amend features dialog
2662 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2663 selection menu changes colours of alignment views
2666 <!-- JAL-2426 -->Spurious exceptions in console raised
2667 from alignment calculation workers after alignment has
2671 <!-- JAL-1608 -->Typo in selection popup menu - Create
2672 groups now 'Create Group'
2675 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2676 Create/Undefine group doesn't always work
2679 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2680 shown again after pressing 'Cancel'
2683 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2684 adjusts start position in wrap mode
2687 <!-- JAL-2563 -->Status bar doesn't show positions for
2688 ambiguous amino acids
2691 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2692 CDS/Protein view after CDS sequences added for aligned
2696 <!-- JAL-2592 -->User defined colourschemes called 'User
2697 Defined' don't appear in Colours menu
2703 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2704 score models doesn't always result in an updated PCA plot
2707 <!-- JAL-2442 -->Features not rendered as transparent on
2708 overview or linked structure view
2711 <!-- JAL-2372 -->Colour group by conservation doesn't
2715 <!-- JAL-2517 -->Hitting Cancel after applying
2716 user-defined colourscheme doesn't restore original
2723 <!-- JAL-2314 -->Unit test failure:
2724 jalview.ws.jabaws.RNAStructExportImport setup fails
2727 <!-- JAL-2307 -->Unit test failure:
2728 jalview.ws.sifts.SiftsClientTest due to compatibility
2729 problems with deep array comparison equality asserts in
2730 successive versions of TestNG
2733 <!-- JAL-2479 -->Relocated StructureChooserTest and
2734 ParameterUtilsTest Unit tests to Network suite
2737 <em>New Known Issues</em>
2740 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2741 phase after a sequence motif find operation
2744 <!-- JAL-2550 -->Importing annotation file with rows
2745 containing just upper and lower case letters are
2746 interpreted as WUSS RNA secondary structure symbols
2749 <!-- JAL-2590 -->Cannot load and display Newick trees
2750 reliably from eggnog Ortholog database
2753 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2754 containing features of type Highlight' when 'B' is pressed
2755 to mark columns containing highlighted regions.
2758 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2759 doesn't always add secondary structure annotation.
2764 <td width="60" nowrap>
2765 <div align="center">
2766 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2769 <td><div align="left">
2773 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2774 for all consensus calculations
2777 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2780 <li>Updated Jalview's Certum code signing certificate
2783 <em>Application</em>
2786 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2787 set of database cross-references, sorted alphabetically
2790 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2791 from database cross references. Users with custom links
2792 will receive a <a href="webServices/urllinks.html#warning">warning
2793 dialog</a> asking them to update their preferences.
2796 <!-- JAL-2287-->Cancel button and escape listener on
2797 dialog warning user about disconnecting Jalview from a
2801 <!-- JAL-2320-->Jalview's Chimera control window closes if
2802 the Chimera it is connected to is shut down
2805 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2806 columns menu item to mark columns containing highlighted
2807 regions (e.g. from structure selections or results of a
2811 <!-- JAL-2284-->Command line option for batch-generation
2812 of HTML pages rendering alignment data with the BioJS
2822 <!-- JAL-2286 -->Columns with more than one modal residue
2823 are not coloured or thresholded according to percent
2824 identity (first observed in Jalview 2.8.2)
2827 <!-- JAL-2301 -->Threonine incorrectly reported as not
2831 <!-- JAL-2318 -->Updates to documentation pages (above PID
2832 threshold, amino acid properties)
2835 <!-- JAL-2292 -->Lower case residues in sequences are not
2836 reported as mapped to residues in a structure file in the
2840 <!--JAL-2324 -->Identical features with non-numeric scores
2841 could be added multiple times to a sequence
2844 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2845 bond features shown as two highlighted residues rather
2846 than a range in linked structure views, and treated
2847 correctly when selecting and computing trees from features
2850 <!-- JAL-2281-->Custom URL links for database
2851 cross-references are matched to database name regardless
2856 <em>Application</em>
2859 <!-- JAL-2282-->Custom URL links for specific database
2860 names without regular expressions also offer links from
2864 <!-- JAL-2315-->Removing a single configured link in the
2865 URL links pane in Connections preferences doesn't actually
2866 update Jalview configuration
2869 <!-- JAL-2272-->CTRL-Click on a selected region to open
2870 the alignment area popup menu doesn't work on El-Capitan
2873 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2874 files with similarly named sequences if dropped onto the
2878 <!-- JAL-2312 -->Additional mappings are shown for PDB
2879 entries where more chains exist in the PDB accession than
2880 are reported in the SIFTS file
2883 <!-- JAL-2317-->Certain structures do not get mapped to
2884 the structure view when displayed with Chimera
2887 <!-- JAL-2317-->No chains shown in the Chimera view
2888 panel's View->Show Chains submenu
2891 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2892 work for wrapped alignment views
2895 <!--JAL-2197 -->Rename UI components for running JPred
2896 predictions from 'JNet' to 'JPred'
2899 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2900 corrupted when annotation panel vertical scroll is not at
2901 first annotation row
2904 <!--JAL-2332 -->Attempting to view structure for Hen
2905 lysozyme results in a PDB Client error dialog box
2908 <!-- JAL-2319 -->Structure View's mapping report switched
2909 ranges for PDB and sequence for SIFTS
2912 SIFTS 'Not_Observed' residues mapped to non-existant
2916 <!-- <em>New Known Issues</em>
2923 <td width="60" nowrap>
2924 <div align="center">
2925 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2926 <em>25/10/2016</em></strong>
2929 <td><em>Application</em>
2931 <li>3D Structure chooser opens with 'Cached structures'
2932 view if structures already loaded</li>
2933 <li>Progress bar reports models as they are loaded to
2934 structure views</li>
2940 <li>Colour by conservation always enabled and no tick
2941 shown in menu when BLOSUM or PID shading applied</li>
2942 <li>FER1_ARATH and FER2_ARATH labels were switched in
2943 example sequences/projects/trees</li>
2945 <em>Application</em>
2947 <li>Jalview projects with views of local PDB structure
2948 files saved on Windows cannot be opened on OSX</li>
2949 <li>Multiple structure views can be opened and superposed
2950 without timeout for structures with multiple models or
2951 multiple sequences in alignment</li>
2952 <li>Cannot import or associated local PDB files without a
2953 PDB ID HEADER line</li>
2954 <li>RMSD is not output in Jmol console when superposition
2956 <li>Drag and drop of URL from Browser fails for Linux and
2957 OSX versions earlier than El Capitan</li>
2958 <li>ENA client ignores invalid content from ENA server</li>
2959 <li>Exceptions are not raised in console when ENA client
2960 attempts to fetch non-existent IDs via Fetch DB Refs UI
2962 <li>Exceptions are not raised in console when a new view
2963 is created on the alignment</li>
2964 <li>OSX right-click fixed for group selections: CMD-click
2965 to insert/remove gaps in groups and CTRL-click to open group
2968 <em>Build and deployment</em>
2970 <li>URL link checker now copes with multi-line anchor
2973 <em>New Known Issues</em>
2975 <li>Drag and drop from URL links in browsers do not work
2982 <td width="60" nowrap>
2983 <div align="center">
2984 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2987 <td><em>General</em>
2990 <!-- JAL-2124 -->Updated Spanish translations.
2993 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2994 for importing structure data to Jalview. Enables mmCIF and
2998 <!-- JAL-192 --->Alignment ruler shows positions relative to
3002 <!-- JAL-2202 -->Position/residue shown in status bar when
3003 mousing over sequence associated annotation
3006 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
3010 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
3011 '()', canonical '[]' and invalid '{}' base pair populations
3015 <!-- JAL-2092 -->Feature settings popup menu options for
3016 showing or hiding columns containing a feature
3019 <!-- JAL-1557 -->Edit selected group by double clicking on
3020 group and sequence associated annotation labels
3023 <!-- JAL-2236 -->Sequence name added to annotation label in
3024 select/hide columns by annotation and colour by annotation
3028 </ul> <em>Application</em>
3031 <!-- JAL-2050-->Automatically hide introns when opening a
3032 gene/transcript view
3035 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
3039 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
3040 structure mappings with the EMBL-EBI PDBe SIFTS database
3043 <!-- JAL-2079 -->Updated download sites used for Rfam and
3044 Pfam sources to xfam.org
3047 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
3050 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
3051 over sequences in Jalview
3054 <!-- JAL-2027-->Support for reverse-complement coding
3055 regions in ENA and EMBL
3058 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
3059 for record retrieval via ENA rest API
3062 <!-- JAL-2027 -->Support for ENA CDS records with reverse
3066 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
3067 groovy script execution
3070 <!-- JAL-1812 -->New 'execute Groovy script' option in an
3071 alignment window's Calculate menu
3074 <!-- JAL-1812 -->Allow groovy scripts that call
3075 Jalview.getAlignFrames() to run in headless mode
3078 <!-- JAL-2068 -->Support for creating new alignment
3079 calculation workers from groovy scripts
3082 <!-- JAL-1369 --->Store/restore reference sequence in
3086 <!-- JAL-1803 -->Chain codes for a sequence's PDB
3087 associations are now saved/restored from project
3090 <!-- JAL-1993 -->Database selection dialog always shown
3091 before sequence fetcher is opened
3094 <!-- JAL-2183 -->Double click on an entry in Jalview's
3095 database chooser opens a sequence fetcher
3098 <!-- JAL-1563 -->Free-text search client for UniProt using
3099 the UniProt REST API
3102 <!-- JAL-2168 -->-nonews command line parameter to prevent
3103 the news reader opening
3106 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
3107 querying stored in preferences
3110 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
3114 <!-- JAL-1977-->Tooltips shown on database chooser
3117 <!-- JAL-391 -->Reverse complement function in calculate
3118 menu for nucleotide sequences
3121 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
3122 and feature counts preserves alignment ordering (and
3123 debugged for complex feature sets).
3126 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
3127 viewing structures with Jalview 2.10
3130 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
3131 genome, transcript CCDS and gene ids via the Ensembl and
3132 Ensembl Genomes REST API
3135 <!-- JAL-2049 -->Protein sequence variant annotation
3136 computed for 'sequence_variant' annotation on CDS regions
3140 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
3144 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
3145 Ref Fetcher fails to match, or otherwise updates sequence
3146 data from external database records.
3149 <!-- JAL-2154 -->Revised Jalview Project format for
3150 efficient recovery of sequence coding and alignment
3151 annotation relationships.
3153 </ul> <!-- <em>Applet</em>
3164 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
3168 <!-- JAL-2018-->Export features in Jalview format (again)
3169 includes graduated colourschemes
3172 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
3173 working with big alignments and lots of hidden columns
3176 <!-- JAL-2053-->Hidden column markers not always rendered
3177 at right of alignment window
3180 <!-- JAL-2067 -->Tidied up links in help file table of
3184 <!-- JAL-2072 -->Feature based tree calculation not shown
3188 <!-- JAL-2075 -->Hidden columns ignored during feature
3189 based tree calculation
3192 <!-- JAL-2065 -->Alignment view stops updating when show
3193 unconserved enabled for group on alignment
3196 <!-- JAL-2086 -->Cannot insert gaps into sequence when
3200 <!-- JAL-2146 -->Alignment column in status incorrectly
3201 shown as "Sequence position" when mousing over
3205 <!-- JAL-2099 -->Incorrect column numbers in ruler when
3206 hidden columns present
3209 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
3210 user created annotation added to alignment
3213 <!-- JAL-1841 -->RNA Structure consensus only computed for
3214 '()' base pair annotation
3217 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
3218 in zero scores for all base pairs in RNA Structure
3222 <!-- JAL-2174-->Extend selection with columns containing
3226 <!-- JAL-2275 -->Pfam format writer puts extra space at
3227 beginning of sequence
3230 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
3234 <!-- JAL-2238 -->Cannot create groups on an alignment from
3235 from a tree when t-coffee scores are shown
3238 <!-- JAL-1836,1967 -->Cannot import and view PDB
3239 structures with chains containing negative resnums (4q4h)
3242 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
3246 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
3247 to Clustal, PIR and PileUp output
3250 <!-- JAL-2008 -->Reordering sequence features that are
3251 not visible causes alignment window to repaint
3254 <!-- JAL-2006 -->Threshold sliders don't work in
3255 graduated colour and colour by annotation row for e-value
3256 scores associated with features and annotation rows
3259 <!-- JAL-1797 -->amino acid physicochemical conservation
3260 calculation should be case independent
3263 <!-- JAL-2173 -->Remove annotation also updates hidden
3267 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
3268 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
3269 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
3272 <!-- JAL-2065 -->Null pointer exceptions and redraw
3273 problems when reference sequence defined and 'show
3274 non-conserved' enabled
3277 <!-- JAL-1306 -->Quality and Conservation are now shown on
3278 load even when Consensus calculation is disabled
3281 <!-- JAL-1932 -->Remove right on penultimate column of
3282 alignment does nothing
3285 <em>Application</em>
3288 <!-- JAL-1552-->URLs and links can't be imported by
3289 drag'n'drop on OSX when launched via webstart (note - not
3290 yet fixed for El Capitan)
3293 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
3294 output when running on non-gb/us i18n platforms
3297 <!-- JAL-1944 -->Error thrown when exporting a view with
3298 hidden sequences as flat-file alignment
3301 <!-- JAL-2030-->InstallAnywhere distribution fails when
3305 <!-- JAL-2080-->Jalview very slow to launch via webstart
3306 (also hotfix for 2.9.0b2)
3309 <!-- JAL-2085 -->Cannot save project when view has a
3310 reference sequence defined
3313 <!-- JAL-1011 -->Columns are suddenly selected in other
3314 alignments and views when revealing hidden columns
3317 <!-- JAL-1989 -->Hide columns not mirrored in complement
3318 view in a cDNA/Protein splitframe
3321 <!-- JAL-1369 -->Cannot save/restore representative
3322 sequence from project when only one sequence is
3326 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
3327 in Structure Chooser
3330 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
3331 structure consensus didn't refresh annotation panel
3334 <!-- JAL-1962 -->View mapping in structure view shows
3335 mappings between sequence and all chains in a PDB file
3338 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
3339 dialogs format columns correctly, don't display array
3340 data, sort columns according to type
3343 <!-- JAL-1975 -->Export complete shown after destination
3344 file chooser is cancelled during an image export
3347 <!-- JAL-2025 -->Error when querying PDB Service with
3348 sequence name containing special characters
3351 <!-- JAL-2024 -->Manual PDB structure querying should be
3355 <!-- JAL-2104 -->Large tooltips with broken HTML
3356 formatting don't wrap
3359 <!-- JAL-1128 -->Figures exported from wrapped view are
3360 truncated so L looks like I in consensus annotation
3363 <!-- JAL-2003 -->Export features should only export the
3364 currently displayed features for the current selection or
3368 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
3369 after fetching cross-references, and restoring from
3373 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
3374 followed in the structure viewer
3377 <!-- JAL-2163 -->Titles for individual alignments in
3378 splitframe not restored from project
3381 <!-- JAL-2145 -->missing autocalculated annotation at
3382 trailing end of protein alignment in transcript/product
3383 splitview when pad-gaps not enabled by default
3386 <!-- JAL-1797 -->amino acid physicochemical conservation
3390 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
3391 article has been read (reopened issue due to
3392 internationalisation problems)
3395 <!-- JAL-1960 -->Only offer PDB structures in structure
3396 viewer based on sequence name, PDB and UniProt
3401 <!-- JAL-1976 -->No progress bar shown during export of
3405 <!-- JAL-2213 -->Structures not always superimposed after
3406 multiple structures are shown for one or more sequences.
3409 <!-- JAL-1370 -->Reference sequence characters should not
3410 be replaced with '.' when 'Show unconserved' format option
3414 <!-- JAL-1823 -->Cannot specify chain code when entering
3415 specific PDB id for sequence
3418 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3419 'Export hidden sequences' is enabled, but 'export hidden
3420 columns' is disabled.
3423 <!--JAL-2026-->Best Quality option in structure chooser
3424 selects lowest rather than highest resolution structures
3428 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3429 to sequence mapping in 'View Mappings' report
3432 <!-- JAL-2284 -->Unable to read old Jalview projects that
3433 contain non-XML data added after Jalvew wrote project.
3436 <!-- JAL-2118 -->Newly created annotation row reorders
3437 after clicking on it to create new annotation for a
3441 <!-- JAL-1980 -->Null Pointer Exception raised when
3442 pressing Add on an orphaned cut'n'paste window.
3444 <!-- may exclude, this is an external service stability issue JAL-1941
3445 -- > RNA 3D structure not added via DSSR service</li> -->
3450 <!-- JAL-2151 -->Incorrect columns are selected when
3451 hidden columns present before start of sequence
3454 <!-- JAL-1986 -->Missing dependencies on applet pages
3458 <!-- JAL-1947 -->Overview pixel size changes when
3459 sequences are hidden in applet
3462 <!-- JAL-1996 -->Updated instructions for applet
3463 deployment on examples pages.
3470 <td width="60" nowrap>
3471 <div align="center">
3472 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3473 <em>16/10/2015</em></strong>
3476 <td><em>General</em>
3478 <li>Time stamps for signed Jalview application and applet
3483 <em>Application</em>
3485 <li>Duplicate group consensus and conservation rows
3486 shown when tree is partitioned</li>
3487 <li>Erratic behaviour when tree partitions made with
3488 multiple cDNA/Protein split views</li>
3494 <td width="60" nowrap>
3495 <div align="center">
3496 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3497 <em>8/10/2015</em></strong>
3500 <td><em>General</em>
3502 <li>Updated Spanish translations of localized text for
3504 </ul> <em>Application</em>
3506 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3507 <li>Signed OSX InstallAnywhere installer<br></li>
3508 <li>Support for per-sequence based annotations in BioJSON</li>
3509 </ul> <em>Applet</em>
3511 <li>Split frame example added to applet examples page</li>
3512 </ul> <em>Build and Deployment</em>
3515 <!-- JAL-1888 -->New ant target for running Jalview's test
3523 <li>Mapping of cDNA to protein in split frames
3524 incorrect when sequence start > 1</li>
3525 <li>Broken images in filter column by annotation dialog
3527 <li>Feature colours not parsed from features file</li>
3528 <li>Exceptions and incomplete link URLs recovered when
3529 loading a features file containing HTML tags in feature
3533 <em>Application</em>
3535 <li>Annotations corrupted after BioJS export and
3537 <li>Incorrect sequence limits after Fetch DB References
3538 with 'trim retrieved sequences'</li>
3539 <li>Incorrect warning about deleting all data when
3540 deleting selected columns</li>
3541 <li>Patch to build system for shipping properly signed
3542 JNLP templates for webstart launch</li>
3543 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3544 unreleased structures for download or viewing</li>
3545 <li>Tab/space/return keystroke operation of EMBL-PDBe
3546 fetcher/viewer dialogs works correctly</li>
3547 <li>Disabled 'minimise' button on Jalview windows
3548 running on OSX to workaround redraw hang bug</li>
3549 <li>Split cDNA/Protein view position and geometry not
3550 recovered from jalview project</li>
3551 <li>Initial enabled/disabled state of annotation menu
3552 sorter 'show autocalculated first/last' corresponds to
3554 <li>Restoring of Clustal, RNA Helices and T-Coffee
3555 color schemes from BioJSON</li>
3559 <li>Reorder sequences mirrored in cDNA/Protein split
3561 <li>Applet with Jmol examples not loading correctly</li>
3567 <td><div align="center">
3568 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3570 <td><em>General</em>
3572 <li>Linked visualisation and analysis of DNA and Protein
3575 <li>Translated cDNA alignments shown as split protein
3576 and DNA alignment views</li>
3577 <li>Codon consensus annotation for linked protein and
3578 cDNA alignment views</li>
3579 <li>Link cDNA or Protein product sequences by loading
3580 them onto Protein or cDNA alignments</li>
3581 <li>Reconstruct linked cDNA alignment from aligned
3582 protein sequences</li>
3585 <li>Jmol integration updated to Jmol v14.2.14</li>
3586 <li>Import and export of Jalview alignment views as <a
3587 href="features/bioJsonFormat.html">BioJSON</a></li>
3588 <li>New alignment annotation file statements for
3589 reference sequences and marking hidden columns</li>
3590 <li>Reference sequence based alignment shading to
3591 highlight variation</li>
3592 <li>Select or hide columns according to alignment
3594 <li>Find option for locating sequences by description</li>
3595 <li>Conserved physicochemical properties shown in amino
3596 acid conservation row</li>
3597 <li>Alignments can be sorted by number of RNA helices</li>
3598 </ul> <em>Application</em>
3600 <li>New cDNA/Protein analysis capabilities
3602 <li>Get Cross-References should open a Split Frame
3603 view with cDNA/Protein</li>
3604 <li>Detect when nucleotide sequences and protein
3605 sequences are placed in the same alignment</li>
3606 <li>Split cDNA/Protein views are saved in Jalview
3611 <li>Use REST API to talk to Chimera</li>
3612 <li>Selected regions in Chimera are highlighted in linked
3613 Jalview windows</li>
3615 <li>VARNA RNA viewer updated to v3.93</li>
3616 <li>VARNA views are saved in Jalview Projects</li>
3617 <li>Pseudoknots displayed as Jalview RNA annotation can
3618 be shown in VARNA</li>
3620 <li>Make groups for selection uses marked columns as well
3621 as the active selected region</li>
3623 <li>Calculate UPGMA and NJ trees using sequence feature
3625 <li>New Export options
3627 <li>New Export Settings dialog to control hidden
3628 region export in flat file generation</li>
3630 <li>Export alignment views for display with the <a
3631 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3633 <li>Export scrollable SVG in HTML page</li>
3634 <li>Optional embedding of BioJSON data when exporting
3635 alignment figures to HTML</li>
3637 <li>3D structure retrieval and display
3639 <li>Free text and structured queries with the PDBe
3641 <li>PDBe Search API based discovery and selection of
3642 PDB structures for a sequence set</li>
3646 <li>JPred4 employed for protein secondary structure
3648 <li>Hide Insertions menu option to hide unaligned columns
3649 for one or a group of sequences</li>
3650 <li>Automatically hide insertions in alignments imported
3651 from the JPred4 web server</li>
3652 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3653 system on OSX<br />LGPL libraries courtesy of <a
3654 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3656 <li>changed 'View nucleotide structure' submenu to 'View
3657 VARNA 2D Structure'</li>
3658 <li>change "View protein structure" menu option to "3D
3661 </ul> <em>Applet</em>
3663 <li>New layout for applet example pages</li>
3664 <li>New parameters to enable SplitFrame view
3665 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3666 <li>New example demonstrating linked viewing of cDNA and
3667 Protein alignments</li>
3668 </ul> <em>Development and deployment</em>
3670 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3671 <li>Include installation type and git revision in build
3672 properties and console log output</li>
3673 <li>Jalview Github organisation, and new github site for
3674 storing BioJsMSA Templates</li>
3675 <li>Jalview's unit tests now managed with TestNG</li>
3678 <!-- <em>General</em>
3680 </ul> --> <!-- issues resolved --> <em>Application</em>
3682 <li>Escape should close any open find dialogs</li>
3683 <li>Typo in select-by-features status report</li>
3684 <li>Consensus RNA secondary secondary structure
3685 predictions are not highlighted in amber</li>
3686 <li>Missing gap character in v2.7 example file means
3687 alignment appears unaligned when pad-gaps is not enabled</li>
3688 <li>First switch to RNA Helices colouring doesn't colour
3689 associated structure views</li>
3690 <li>ID width preference option is greyed out when auto
3691 width checkbox not enabled</li>
3692 <li>Stopped a warning dialog from being shown when
3693 creating user defined colours</li>
3694 <li>'View Mapping' in structure viewer shows sequence
3695 mappings for just that viewer's sequences</li>
3696 <li>Workaround for superposing PDB files containing
3697 multiple models in Chimera</li>
3698 <li>Report sequence position in status bar when hovering
3699 over Jmol structure</li>
3700 <li>Cannot output gaps as '.' symbols with Selection ->
3701 output to text box</li>
3702 <li>Flat file exports of alignments with hidden columns
3703 have incorrect sequence start/end</li>
3704 <li>'Aligning' a second chain to a Chimera structure from
3706 <li>Colour schemes applied to structure viewers don't
3707 work for nucleotide</li>
3708 <li>Loading/cut'n'pasting an empty or invalid file leads
3709 to a grey/invisible alignment window</li>
3710 <li>Exported Jpred annotation from a sequence region
3711 imports to different position</li>
3712 <li>Space at beginning of sequence feature tooltips shown
3713 on some platforms</li>
3714 <li>Chimera viewer 'View | Show Chain' menu is not
3716 <li>'New View' fails with a Null Pointer Exception in
3717 console if Chimera has been opened</li>
3718 <li>Mouseover to Chimera not working</li>
3719 <li>Miscellaneous ENA XML feature qualifiers not
3721 <li>NPE in annotation renderer after 'Extract Scores'</li>
3722 <li>If two structures in one Chimera window, mouseover of
3723 either sequence shows on first structure</li>
3724 <li>'Show annotations' options should not make
3725 non-positional annotations visible</li>
3726 <li>Subsequence secondary structure annotation not shown
3727 in right place after 'view flanking regions'</li>
3728 <li>File Save As type unset when current file format is
3730 <li>Save as '.jar' option removed for saving Jalview
3732 <li>Colour by Sequence colouring in Chimera more
3734 <li>Cannot 'add reference annotation' for a sequence in
3735 several views on same alignment</li>
3736 <li>Cannot show linked products for EMBL / ENA records</li>
3737 <li>Jalview's tooltip wraps long texts containing no
3739 </ul> <em>Applet</em>
3741 <li>Jmol to JalviewLite mouseover/link not working</li>
3742 <li>JalviewLite can't import sequences with ID
3743 descriptions containing angle brackets</li>
3744 </ul> <em>General</em>
3746 <li>Cannot export and reimport RNA secondary structure
3747 via jalview annotation file</li>
3748 <li>Random helix colour palette for colour by annotation
3749 with RNA secondary structure</li>
3750 <li>Mouseover to cDNA from STOP residue in protein
3751 translation doesn't work.</li>
3752 <li>hints when using the select by annotation dialog box</li>
3753 <li>Jmol alignment incorrect if PDB file has alternate CA
3755 <li>FontChooser message dialog appears to hang after
3756 choosing 1pt font</li>
3757 <li>Peptide secondary structure incorrectly imported from
3758 annotation file when annotation display text includes 'e' or
3760 <li>Cannot set colour of new feature type whilst creating
3762 <li>cDNA translation alignment should not be sequence
3763 order dependent</li>
3764 <li>'Show unconserved' doesn't work for lower case
3766 <li>Nucleotide ambiguity codes involving R not recognised</li>
3767 </ul> <em>Deployment and Documentation</em>
3769 <li>Applet example pages appear different to the rest of
3770 www.jalview.org</li>
3771 </ul> <em>Application Known issues</em>
3773 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3774 <li>Misleading message appears after trying to delete
3776 <li>Jalview icon not shown in dock after InstallAnywhere
3777 version launches</li>
3778 <li>Fetching EMBL reference for an RNA sequence results
3779 fails with a sequence mismatch</li>
3780 <li>Corrupted or unreadable alignment display when
3781 scrolling alignment to right</li>
3782 <li>ArrayIndexOutOfBoundsException thrown when remove
3783 empty columns called on alignment with ragged gapped ends</li>
3784 <li>auto calculated alignment annotation rows do not get
3785 placed above or below non-autocalculated rows</li>
3786 <li>Jalview dekstop becomes sluggish at full screen in
3787 ultra-high resolution</li>
3788 <li>Cannot disable consensus calculation independently of
3789 quality and conservation</li>
3790 <li>Mouseover highlighting between cDNA and protein can
3791 become sluggish with more than one splitframe shown</li>
3792 </ul> <em>Applet Known Issues</em>
3794 <li>Core PDB parsing code requires Jmol</li>
3795 <li>Sequence canvas panel goes white when alignment
3796 window is being resized</li>
3802 <td><div align="center">
3803 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3805 <td><em>General</em>
3807 <li>Updated Java code signing certificate donated by
3809 <li>Features and annotation preserved when performing
3810 pairwise alignment</li>
3811 <li>RNA pseudoknot annotation can be
3812 imported/exported/displayed</li>
3813 <li>'colour by annotation' can colour by RNA and
3814 protein secondary structure</li>
3815 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3816 post-hoc with 2.9 release</em>)
3819 </ul> <em>Application</em>
3821 <li>Extract and display secondary structure for sequences
3822 with 3D structures</li>
3823 <li>Support for parsing RNAML</li>
3824 <li>Annotations menu for layout
3826 <li>sort sequence annotation rows by alignment</li>
3827 <li>place sequence annotation above/below alignment
3830 <li>Output in Stockholm format</li>
3831 <li>Internationalisation: improved Spanish (es)
3833 <li>Structure viewer preferences tab</li>
3834 <li>Disorder and Secondary Structure annotation tracks
3835 shared between alignments</li>
3836 <li>UCSF Chimera launch and linked highlighting from
3838 <li>Show/hide all sequence associated annotation rows for
3839 all or current selection</li>
3840 <li>disorder and secondary structure predictions
3841 available as dataset annotation</li>
3842 <li>Per-sequence rna helices colouring</li>
3845 <li>Sequence database accessions imported when fetching
3846 alignments from Rfam</li>
3847 <li>update VARNA version to 3.91</li>
3849 <li>New groovy scripts for exporting aligned positions,
3850 conservation values, and calculating sum of pairs scores.</li>
3851 <li>Command line argument to set default JABAWS server</li>
3852 <li>include installation type in build properties and
3853 console log output</li>
3854 <li>Updated Jalview project format to preserve dataset
3858 <!-- issues resolved --> <em>Application</em>
3860 <li>Distinguish alignment and sequence associated RNA
3861 structure in structure->view->VARNA</li>
3862 <li>Raise dialog box if user deletes all sequences in an
3864 <li>Pressing F1 results in documentation opening twice</li>
3865 <li>Sequence feature tooltip is wrapped</li>
3866 <li>Double click on sequence associated annotation
3867 selects only first column</li>
3868 <li>Redundancy removal doesn't result in unlinked
3869 leaves shown in tree</li>
3870 <li>Undos after several redundancy removals don't undo
3872 <li>Hide sequence doesn't hide associated annotation</li>
3873 <li>User defined colours dialog box too big to fit on
3874 screen and buttons not visible</li>
3875 <li>author list isn't updated if already written to
3876 Jalview properties</li>
3877 <li>Popup menu won't open after retrieving sequence
3879 <li>File open window for associate PDB doesn't open</li>
3880 <li>Left-then-right click on a sequence id opens a
3881 browser search window</li>
3882 <li>Cannot open sequence feature shading/sort popup menu
3883 in feature settings dialog</li>
3884 <li>better tooltip placement for some areas of Jalview
3886 <li>Allow addition of JABAWS Server which doesn't
3887 pass validation</li>
3888 <li>Web services parameters dialog box is too large to
3890 <li>Muscle nucleotide alignment preset obscured by
3892 <li>JABAWS preset submenus don't contain newly
3893 defined user preset</li>
3894 <li>MSA web services warns user if they were launched
3895 with invalid input</li>
3896 <li>Jalview cannot contact DAS Registy when running on
3899 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3900 'Superpose with' submenu not shown when new view
3904 </ul> <!-- <em>Applet</em>
3906 </ul> <em>General</em>
3908 </ul>--> <em>Deployment and Documentation</em>
3910 <li>2G and 1G options in launchApp have no effect on
3911 memory allocation</li>
3912 <li>launchApp service doesn't automatically open
3913 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3915 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3916 InstallAnywhere reports cannot find valid JVM when Java
3917 1.7_055 is available
3919 </ul> <em>Application Known issues</em>
3922 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3923 corrupted or unreadable alignment display when scrolling
3927 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3928 retrieval fails but progress bar continues for DAS retrieval
3929 with large number of ID
3932 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3933 flatfile output of visible region has incorrect sequence
3937 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3938 rna structure consensus doesn't update when secondary
3939 structure tracks are rearranged
3942 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3943 invalid rna structure positional highlighting does not
3944 highlight position of invalid base pairs
3947 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3948 out of memory errors are not raised when saving Jalview
3949 project from alignment window file menu
3952 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3953 Switching to RNA Helices colouring doesn't propagate to
3957 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3958 colour by RNA Helices not enabled when user created
3959 annotation added to alignment
3962 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3963 Jalview icon not shown on dock in Mountain Lion/Webstart
3965 </ul> <em>Applet Known Issues</em>
3968 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3969 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3972 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3973 Jalview and Jmol example not compatible with IE9
3976 <li>Sort by annotation score doesn't reverse order
3982 <td><div align="center">
3983 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3986 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3989 <li>Internationalisation of user interface (usually
3990 called i18n support) and translation for Spanish locale</li>
3991 <li>Define/Undefine group on current selection with
3992 Ctrl-G/Shift Ctrl-G</li>
3993 <li>Improved group creation/removal options in
3994 alignment/sequence Popup menu</li>
3995 <li>Sensible precision for symbol distribution
3996 percentages shown in logo tooltip.</li>
3997 <li>Annotation panel height set according to amount of
3998 annotation when alignment first opened</li>
3999 </ul> <em>Application</em>
4001 <li>Interactive consensus RNA secondary structure
4002 prediction VIENNA RNAAliFold JABA 2.1 service</li>
4003 <li>Select columns containing particular features from
4004 Feature Settings dialog</li>
4005 <li>View all 'representative' PDB structures for selected
4007 <li>Update Jalview project format:
4009 <li>New file extension for Jalview projects '.jvp'</li>
4010 <li>Preserve sequence and annotation dataset (to
4011 store secondary structure annotation,etc)</li>
4012 <li>Per group and alignment annotation and RNA helix
4016 <li>New similarity measures for PCA and Tree calculation
4018 <li>Experimental support for retrieval and viewing of
4019 flanking regions for an alignment</li>
4023 <!-- issues resolved --> <em>Application</em>
4025 <li>logo keeps spinning and status remains at queued or
4026 running after job is cancelled</li>
4027 <li>cannot export features from alignments imported from
4028 Jalview/VAMSAS projects</li>
4029 <li>Buggy slider for web service parameters that take
4031 <li>Newly created RNA secondary structure line doesn't
4032 have 'display all symbols' flag set</li>
4033 <li>T-COFFEE alignment score shading scheme and other
4034 annotation shading not saved in Jalview project</li>
4035 <li>Local file cannot be loaded in freshly downloaded
4037 <li>Jalview icon not shown on dock in Mountain
4039 <li>Load file from desktop file browser fails</li>
4040 <li>Occasional NPE thrown when calculating large trees</li>
4041 <li>Cannot reorder or slide sequences after dragging an
4042 alignment onto desktop</li>
4043 <li>Colour by annotation dialog throws NPE after using
4044 'extract scores' function</li>
4045 <li>Loading/cut'n'pasting an empty file leads to a grey
4046 alignment window</li>
4047 <li>Disorder thresholds rendered incorrectly after
4048 performing IUPred disorder prediction</li>
4049 <li>Multiple group annotated consensus rows shown when
4050 changing 'normalise logo' display setting</li>
4051 <li>Find shows blank dialog after 'finished searching' if
4052 nothing matches query</li>
4053 <li>Null Pointer Exceptions raised when sorting by
4054 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
4056 <li>Errors in Jmol console when structures in alignment
4057 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
4059 <li>Not all working JABAWS services are shown in
4061 <li>JAVAWS version of Jalview fails to launch with
4062 'invalid literal/length code'</li>
4063 <li>Annotation/RNA Helix colourschemes cannot be applied
4064 to alignment with groups (actually fixed in 2.8.0b1)</li>
4065 <li>RNA Helices and T-Coffee Scores available as default
4068 </ul> <em>Applet</em>
4070 <li>Remove group option is shown even when selection is
4072 <li>Apply to all groups ticked but colourscheme changes
4073 don't affect groups</li>
4074 <li>Documented RNA Helices and T-Coffee Scores as valid
4075 colourscheme name</li>
4076 <li>Annotation labels drawn on sequence IDs when
4077 Annotation panel is not displayed</li>
4078 <li>Increased font size for dropdown menus on OSX and
4079 embedded windows</li>
4080 </ul> <em>Other</em>
4082 <li>Consensus sequence for alignments/groups with a
4083 single sequence were not calculated</li>
4084 <li>annotation files that contain only groups imported as
4085 annotation and junk sequences</li>
4086 <li>Fasta files with sequences containing '*' incorrectly
4087 recognised as PFAM or BLC</li>
4088 <li>conservation/PID slider apply all groups option
4089 doesn't affect background (2.8.0b1)
4091 <li>redundancy highlighting is erratic at 0% and 100%</li>
4092 <li>Remove gapped columns fails for sequences with ragged
4094 <li>AMSA annotation row with leading spaces is not
4095 registered correctly on import</li>
4096 <li>Jalview crashes when selecting PCA analysis for
4097 certain alignments</li>
4098 <li>Opening the colour by annotation dialog for an
4099 existing annotation based 'use original colours'
4100 colourscheme loses original colours setting</li>
4105 <td><div align="center">
4106 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
4107 <em>30/1/2014</em></strong>
4111 <li>Trusted certificates for JalviewLite applet and
4112 Jalview Desktop application<br />Certificate was donated by
4113 <a href="https://www.certum.eu">Certum</a> to the Jalview
4114 open source project).
4116 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
4117 <li>Output in Stockholm format</li>
4118 <li>Allow import of data from gzipped files</li>
4119 <li>Export/import group and sequence associated line
4120 graph thresholds</li>
4121 <li>Nucleotide substitution matrix that supports RNA and
4122 ambiguity codes</li>
4123 <li>Allow disorder predictions to be made on the current
4124 selection (or visible selection) in the same way that JPred
4126 <li>Groovy scripting for headless Jalview operation</li>
4127 </ul> <em>Other improvements</em>
4129 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
4130 <li>COMBINE statement uses current SEQUENCE_REF and
4131 GROUP_REF scope to group annotation rows</li>
4132 <li>Support '' style escaping of quotes in Newick
4134 <li>Group options for JABAWS service by command line name</li>
4135 <li>Empty tooltip shown for JABA service options with a
4136 link but no description</li>
4137 <li>Select primary source when selecting authority in
4138 database fetcher GUI</li>
4139 <li>Add .mfa to FASTA file extensions recognised by
4141 <li>Annotation label tooltip text wrap</li>
4146 <li>Slow scrolling when lots of annotation rows are
4148 <li>Lots of NPE (and slowness) after creating RNA
4149 secondary structure annotation line</li>
4150 <li>Sequence database accessions not imported when
4151 fetching alignments from Rfam</li>
4152 <li>Incorrect SHMR submission for sequences with
4154 <li>View all structures does not always superpose
4156 <li>Option widgets in service parameters not updated to
4157 reflect user or preset settings</li>
4158 <li>Null pointer exceptions for some services without
4159 presets or adjustable parameters</li>
4160 <li>Discover PDB IDs entry in structure menu doesn't
4161 discover PDB xRefs</li>
4162 <li>Exception encountered while trying to retrieve
4163 features with DAS</li>
4164 <li>Lowest value in annotation row isn't coloured
4165 when colour by annotation (per sequence) is coloured</li>
4166 <li>Keyboard mode P jumps to start of gapped region when
4167 residue follows a gap</li>
4168 <li>Jalview appears to hang importing an alignment with
4169 Wrap as default or after enabling Wrap</li>
4170 <li>'Right click to add annotations' message
4171 shown in wrap mode when no annotations present</li>
4172 <li>Disorder predictions fail with NPE if no automatic
4173 annotation already exists on alignment</li>
4174 <li>oninit javascript function should be called after
4175 initialisation completes</li>
4176 <li>Remove redundancy after disorder prediction corrupts
4177 alignment window display</li>
4178 <li>Example annotation file in documentation is invalid</li>
4179 <li>Grouped line graph annotation rows are not exported
4180 to annotation file</li>
4181 <li>Multi-harmony analysis cannot be run when only two
4183 <li>Cannot create multiple groups of line graphs with
4184 several 'combine' statements in annotation file</li>
4185 <li>Pressing return several times causes Number Format
4186 exceptions in keyboard mode</li>
4187 <li>Multi-harmony (SHMMR) method doesn't submit
4188 correct partitions for input data</li>
4189 <li>Translation from DNA to Amino Acids fails</li>
4190 <li>Jalview fail to load newick tree with quoted label</li>
4191 <li>--headless flag isn't understood</li>
4192 <li>ClassCastException when generating EPS in headless
4194 <li>Adjusting sequence-associated shading threshold only
4195 changes one row's threshold</li>
4196 <li>Preferences and Feature settings panel panel
4197 doesn't open</li>
4198 <li>hide consensus histogram also hides conservation and
4199 quality histograms</li>
4204 <td><div align="center">
4205 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
4207 <td><em>Application</em>
4209 <li>Support for JABAWS 2.0 Services (AACon alignment
4210 conservation, protein disorder and Clustal Omega)</li>
4211 <li>JABAWS server status indicator in Web Services
4213 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
4214 in Jalview alignment window</li>
4215 <li>Updated Jalview build and deploy framework for OSX
4216 mountain lion, windows 7, and 8</li>
4217 <li>Nucleotide substitution matrix for PCA that supports
4218 RNA and ambiguity codes</li>
4220 <li>Improved sequence database retrieval GUI</li>
4221 <li>Support fetching and database reference look up
4222 against multiple DAS sources (Fetch all from in 'fetch db
4224 <li>Jalview project improvements
4226 <li>Store and retrieve the 'belowAlignment'
4227 flag for annotation</li>
4228 <li>calcId attribute to group annotation rows on the
4230 <li>Store AACon calculation settings for a view in
4231 Jalview project</li>
4235 <li>horizontal scrolling gesture support</li>
4236 <li>Visual progress indicator when PCA calculation is
4238 <li>Simpler JABA web services menus</li>
4239 <li>visual indication that web service results are still
4240 being retrieved from server</li>
4241 <li>Serialise the dialogs that are shown when Jalview
4242 starts up for first time</li>
4243 <li>Jalview user agent string for interacting with HTTP
4245 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
4247 <li>Examples directory and Groovy library included in
4248 InstallAnywhere distribution</li>
4249 </ul> <em>Applet</em>
4251 <li>RNA alignment and secondary structure annotation
4252 visualization applet example</li>
4253 </ul> <em>General</em>
4255 <li>Normalise option for consensus sequence logo</li>
4256 <li>Reset button in PCA window to return dimensions to
4258 <li>Allow seqspace or Jalview variant of alignment PCA
4260 <li>PCA with either nucleic acid and protein substitution
4262 <li>Allow windows containing HTML reports to be exported
4264 <li>Interactive display and editing of RNA secondary
4265 structure contacts</li>
4266 <li>RNA Helix Alignment Colouring</li>
4267 <li>RNA base pair logo consensus</li>
4268 <li>Parse sequence associated secondary structure
4269 information in Stockholm files</li>
4270 <li>HTML Export database accessions and annotation
4271 information presented in tooltip for sequences</li>
4272 <li>Import secondary structure from LOCARNA clustalw
4273 style RNA alignment files</li>
4274 <li>import and visualise T-COFFEE quality scores for an
4276 <li>'colour by annotation' per sequence option to
4277 shade each sequence according to its associated alignment
4279 <li>New Jalview Logo</li>
4280 </ul> <em>Documentation and Development</em>
4282 <li>documentation for score matrices used in Jalview</li>
4283 <li>New Website!</li>
4285 <td><em>Application</em>
4287 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
4288 wsdbfetch REST service</li>
4289 <li>Stop windows being moved outside desktop on OSX</li>
4290 <li>Filetype associations not installed for webstart
4292 <li>Jalview does not always retrieve progress of a JABAWS
4293 job execution in full once it is complete</li>
4294 <li>revise SHMR RSBS definition to ensure alignment is
4295 uploaded via ali_file parameter</li>
4296 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
4297 <li>View all structures superposed fails with exception</li>
4298 <li>Jnet job queues forever if a very short sequence is
4299 submitted for prediction</li>
4300 <li>Cut and paste menu not opened when mouse clicked on
4302 <li>Putting fractional value into integer text box in
4303 alignment parameter dialog causes Jalview to hang</li>
4304 <li>Structure view highlighting doesn't work on
4306 <li>View all structures fails with exception shown in
4308 <li>Characters in filename associated with PDBEntry not
4309 escaped in a platform independent way</li>
4310 <li>Jalview desktop fails to launch with exception when
4312 <li>Tree calculation reports 'you must have 2 or more
4313 sequences selected' when selection is empty</li>
4314 <li>Jalview desktop fails to launch with jar signature
4315 failure when java web start temporary file caching is
4317 <li>DAS Sequence retrieval with range qualification
4318 results in sequence xref which includes range qualification</li>
4319 <li>Errors during processing of command line arguments
4320 cause progress bar (JAL-898) to be removed</li>
4321 <li>Replace comma for semi-colon option not disabled for
4322 DAS sources in sequence fetcher</li>
4323 <li>Cannot close news reader when JABAWS server warning
4324 dialog is shown</li>
4325 <li>Option widgets not updated to reflect user settings</li>
4326 <li>Edited sequence not submitted to web service</li>
4327 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
4328 <li>InstallAnywhere installer doesn't unpack and run
4329 on OSX Mountain Lion</li>
4330 <li>Annotation panel not given a scroll bar when
4331 sequences with alignment annotation are pasted into the
4333 <li>Sequence associated annotation rows not associated
4334 when loaded from Jalview project</li>
4335 <li>Browser launch fails with NPE on java 1.7</li>
4336 <li>JABAWS alignment marked as finished when job was
4337 cancelled or job failed due to invalid input</li>
4338 <li>NPE with v2.7 example when clicking on Tree
4339 associated with all views</li>
4340 <li>Exceptions when copy/paste sequences with grouped
4341 annotation rows to new window</li>
4342 </ul> <em>Applet</em>
4344 <li>Sequence features are momentarily displayed before
4345 they are hidden using hidefeaturegroups applet parameter</li>
4346 <li>loading features via javascript API automatically
4347 enables feature display</li>
4348 <li>scrollToColumnIn javascript API method doesn't
4350 </ul> <em>General</em>
4352 <li>Redundancy removal fails for rna alignment</li>
4353 <li>PCA calculation fails when sequence has been selected
4354 and then deselected</li>
4355 <li>PCA window shows grey box when first opened on OSX</li>
4356 <li>Letters coloured pink in sequence logo when alignment
4357 coloured with clustalx</li>
4358 <li>Choosing fonts without letter symbols defined causes
4359 exceptions and redraw errors</li>
4360 <li>Initial PCA plot view is not same as manually
4361 reconfigured view</li>
4362 <li>Grouped annotation graph label has incorrect line
4364 <li>Grouped annotation graph label display is corrupted
4365 for lots of labels</li>
4370 <div align="center">
4371 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
4374 <td><em>Application</em>
4376 <li>Jalview Desktop News Reader</li>
4377 <li>Tweaked default layout of web services menu</li>
4378 <li>View/alignment association menu to enable user to
4379 easily specify which alignment a multi-structure view takes
4380 its colours/correspondences from</li>
4381 <li>Allow properties file location to be specified as URL</li>
4382 <li>Extend Jalview project to preserve associations
4383 between many alignment views and a single Jmol display</li>
4384 <li>Store annotation row height in Jalview project file</li>
4385 <li>Annotation row column label formatting attributes
4386 stored in project file</li>
4387 <li>Annotation row order for auto-calculated annotation
4388 rows preserved in Jalview project file</li>
4389 <li>Visual progress indication when Jalview state is
4390 saved using Desktop window menu</li>
4391 <li>Visual indication that command line arguments are
4392 still being processed</li>
4393 <li>Groovy script execution from URL</li>
4394 <li>Colour by annotation default min and max colours in
4396 <li>Automatically associate PDB files dragged onto an
4397 alignment with sequences that have high similarity and
4399 <li>Update JGoogleAnalytics to latest release (0.3)</li>
4400 <li>'view structures' option to open many
4401 structures in same window</li>
4402 <li>Sort associated views menu option for tree panel</li>
4403 <li>Group all JABA and non-JABA services for a particular
4404 analysis function in its own submenu</li>
4405 </ul> <em>Applet</em>
4407 <li>Userdefined and autogenerated annotation rows for
4409 <li>Adjustment of alignment annotation pane height</li>
4410 <li>Annotation scrollbar for annotation panel</li>
4411 <li>Drag to reorder annotation rows in annotation panel</li>
4412 <li>'automaticScrolling' parameter</li>
4413 <li>Allow sequences with partial ID string matches to be
4414 annotated from GFF/Jalview features files</li>
4415 <li>Sequence logo annotation row in applet</li>
4416 <li>Absolute paths relative to host server in applet
4417 parameters are treated as such</li>
4418 <li>New in the JalviewLite javascript API:
4420 <li>JalviewLite.js javascript library</li>
4421 <li>Javascript callbacks for
4423 <li>Applet initialisation</li>
4424 <li>Sequence/alignment mouse-overs and selections</li>
4427 <li>scrollTo row and column alignment scrolling
4429 <li>Select sequence/alignment regions from javascript</li>
4430 <li>javascript structure viewer harness to pass
4431 messages between Jmol and Jalview when running as
4432 distinct applets</li>
4433 <li>sortBy method</li>
4434 <li>Set of applet and application examples shipped
4435 with documentation</li>
4436 <li>New example to demonstrate JalviewLite and Jmol
4437 javascript message exchange</li>
4439 </ul> <em>General</em>
4441 <li>Enable Jmol displays to be associated with multiple
4442 multiple alignments</li>
4443 <li>Option to automatically sort alignment with new tree</li>
4444 <li>User configurable link to enable redirects to a
4445 www.Jalview.org mirror</li>
4446 <li>Jmol colours option for Jmol displays</li>
4447 <li>Configurable newline string when writing alignment
4448 and other flat files</li>
4449 <li>Allow alignment annotation description lines to
4450 contain html tags</li>
4451 </ul> <em>Documentation and Development</em>
4453 <li>Add groovy test harness for bulk load testing to
4455 <li>Groovy script to load and align a set of sequences
4456 using a web service before displaying the result in the
4457 Jalview desktop</li>
4458 <li>Restructured javascript and applet api documentation</li>
4459 <li>Ant target to publish example html files with applet
4461 <li>Netbeans project for building Jalview from source</li>
4462 <li>ant task to create online javadoc for Jalview source</li>
4464 <td><em>Application</em>
4466 <li>User defined colourscheme throws exception when
4467 current built in colourscheme is saved as new scheme</li>
4468 <li>AlignFrame->Save in application pops up save
4469 dialog for valid filename/format</li>
4470 <li>Cannot view associated structure for UniProt sequence</li>
4471 <li>PDB file association breaks for UniProt sequence
4473 <li>Associate PDB from file dialog does not tell you
4474 which sequence is to be associated with the file</li>
4475 <li>Find All raises null pointer exception when query
4476 only matches sequence IDs</li>
4477 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4478 <li>Jalview project with Jmol views created with Jalview
4479 2.4 cannot be loaded</li>
4480 <li>Filetype associations not installed for webstart
4482 <li>Two or more chains in a single PDB file associated
4483 with sequences in different alignments do not get coloured
4484 by their associated sequence</li>
4485 <li>Visibility status of autocalculated annotation row
4486 not preserved when project is loaded</li>
4487 <li>Annotation row height and visibility attributes not
4488 stored in Jalview project</li>
4489 <li>Tree bootstraps are not preserved when saved as a
4490 Jalview project</li>
4491 <li>Envision2 workflow tooltips are corrupted</li>
4492 <li>Enabling show group conservation also enables colour
4493 by conservation</li>
4494 <li>Duplicate group associated conservation or consensus
4495 created on new view</li>
4496 <li>Annotation scrollbar not displayed after 'show
4497 all hidden annotation rows' option selected</li>
4498 <li>Alignment quality not updated after alignment
4499 annotation row is hidden then shown</li>
4500 <li>Preserve colouring of structures coloured by
4501 sequences in pre Jalview 2.7 projects</li>
4502 <li>Web service job parameter dialog is not laid out
4504 <li>Web services menu not refreshed after 'reset
4505 services' button is pressed in preferences</li>
4506 <li>Annotation off by one in Jalview v2_3 example project</li>
4507 <li>Structures imported from file and saved in project
4508 get name like jalview_pdb1234.txt when reloaded</li>
4509 <li>Jalview does not always retrieve progress of a JABAWS
4510 job execution in full once it is complete</li>
4511 </ul> <em>Applet</em>
4513 <li>Alignment height set incorrectly when lots of
4514 annotation rows are displayed</li>
4515 <li>Relative URLs in feature HTML text not resolved to
4517 <li>View follows highlighting does not work for positions
4519 <li><= shown as = in tooltip</li>
4520 <li>Export features raises exception when no features
4522 <li>Separator string used for serialising lists of IDs
4523 for javascript api is modified when separator string
4524 provided as parameter</li>
4525 <li>Null pointer exception when selecting tree leaves for
4526 alignment with no existing selection</li>
4527 <li>Relative URLs for datasources assumed to be relative
4528 to applet's codebase</li>
4529 <li>Status bar not updated after finished searching and
4530 search wraps around to first result</li>
4531 <li>StructureSelectionManager instance shared between
4532 several Jalview applets causes race conditions and memory
4534 <li>Hover tooltip and mouseover of position on structure
4535 not sent from Jmol in applet</li>
4536 <li>Certain sequences of javascript method calls to
4537 applet API fatally hang browser</li>
4538 </ul> <em>General</em>
4540 <li>View follows structure mouseover scrolls beyond
4541 position with wrapped view and hidden regions</li>
4542 <li>Find sequence position moves to wrong residue
4543 with/without hidden columns</li>
4544 <li>Sequence length given in alignment properties window
4546 <li>InvalidNumberFormat exceptions thrown when trying to
4547 import PDB like structure files</li>
4548 <li>Positional search results are only highlighted
4549 between user-supplied sequence start/end bounds</li>
4550 <li>End attribute of sequence is not validated</li>
4551 <li>Find dialog only finds first sequence containing a
4552 given sequence position</li>
4553 <li>Sequence numbering not preserved in MSF alignment
4555 <li>Jalview PDB file reader does not extract sequence
4556 from nucleotide chains correctly</li>
4557 <li>Structure colours not updated when tree partition
4558 changed in alignment</li>
4559 <li>Sequence associated secondary structure not correctly
4560 parsed in interleaved stockholm</li>
4561 <li>Colour by annotation dialog does not restore current
4563 <li>Hiding (nearly) all sequences doesn't work
4565 <li>Sequences containing lowercase letters are not
4566 properly associated with their pdb files</li>
4567 </ul> <em>Documentation and Development</em>
4569 <li>schemas/JalviewWsParamSet.xsd corrupted by
4570 ApplyCopyright tool</li>
4575 <div align="center">
4576 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4579 <td><em>Application</em>
4581 <li>New warning dialog when the Jalview Desktop cannot
4582 contact web services</li>
4583 <li>JABA service parameters for a preset are shown in
4584 service job window</li>
4585 <li>JABA Service menu entries reworded</li>
4589 <li>Modeller PIR IO broken - cannot correctly import a
4590 pir file emitted by Jalview</li>
4591 <li>Existing feature settings transferred to new
4592 alignment view created from cut'n'paste</li>
4593 <li>Improved test for mixed amino/nucleotide chains when
4594 parsing PDB files</li>
4595 <li>Consensus and conservation annotation rows
4596 occasionally become blank for all new windows</li>
4597 <li>Exception raised when right clicking above sequences
4598 in wrapped view mode</li>
4599 </ul> <em>Application</em>
4601 <li>multiple multiply aligned structure views cause cpu
4602 usage to hit 100% and computer to hang</li>
4603 <li>Web Service parameter layout breaks for long user
4604 parameter names</li>
4605 <li>Jaba service discovery hangs desktop if Jaba server
4612 <div align="center">
4613 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4616 <td><em>Application</em>
4618 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4619 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4622 <li>Web Services preference tab</li>
4623 <li>Analysis parameters dialog box and user defined
4625 <li>Improved speed and layout of Envision2 service menu</li>
4626 <li>Superpose structures using associated sequence
4628 <li>Export coordinates and projection as CSV from PCA
4630 </ul> <em>Applet</em>
4632 <li>enable javascript: execution by the applet via the
4633 link out mechanism</li>
4634 </ul> <em>Other</em>
4636 <li>Updated the Jmol Jalview interface to work with Jmol
4638 <li>The Jalview Desktop and JalviewLite applet now
4639 require Java 1.5</li>
4640 <li>Allow Jalview feature colour specification for GFF
4641 sequence annotation files</li>
4642 <li>New 'colour by label' keword in Jalview feature file
4643 type colour specification</li>
4644 <li>New Jalview Desktop Groovy API method that allows a
4645 script to check if it being run in an interactive session or
4646 in a batch operation from the Jalview command line</li>
4650 <li>clustalx colourscheme colours Ds preferentially when
4651 both D+E are present in over 50% of the column</li>
4652 </ul> <em>Application</em>
4654 <li>typo in AlignmentFrame->View->Hide->all but
4655 selected Regions menu item</li>
4656 <li>sequence fetcher replaces ',' for ';' when the ',' is
4657 part of a valid accession ID</li>
4658 <li>fatal OOM if object retrieved by sequence fetcher
4659 runs out of memory</li>
4660 <li>unhandled Out of Memory Error when viewing pca
4661 analysis results</li>
4662 <li>InstallAnywhere builds fail to launch on OS X java
4663 10.5 update 4 (due to apple Java 1.6 update)</li>
4664 <li>Installanywhere Jalview silently fails to launch</li>
4665 </ul> <em>Applet</em>
4667 <li>Jalview.getFeatureGroups() raises an
4668 ArrayIndexOutOfBoundsException if no feature groups are
4675 <div align="center">
4676 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4682 <li>Alignment prettyprinter doesn't cope with long
4684 <li>clustalx colourscheme colours Ds preferentially when
4685 both D+E are present in over 50% of the column</li>
4686 <li>nucleic acid structures retrieved from PDB do not
4687 import correctly</li>
4688 <li>More columns get selected than were clicked on when a
4689 number of columns are hidden</li>
4690 <li>annotation label popup menu not providing correct
4691 add/hide/show options when rows are hidden or none are
4693 <li>Stockholm format shown in list of readable formats,
4694 and parser copes better with alignments from RFAM.</li>
4695 <li>CSV output of consensus only includes the percentage
4696 of all symbols if sequence logo display is enabled</li>
4698 </ul> <em>Applet</em>
4700 <li>annotation panel disappears when annotation is
4702 </ul> <em>Application</em>
4704 <li>Alignment view not redrawn properly when new
4705 alignment opened where annotation panel is visible but no
4706 annotations are present on alignment</li>
4707 <li>pasted region containing hidden columns is
4708 incorrectly displayed in new alignment window</li>
4709 <li>Jalview slow to complete operations when stdout is
4710 flooded (fix is to close the Jalview console)</li>
4711 <li>typo in AlignmentFrame->View->Hide->all but
4712 selected Rregions menu item.</li>
4713 <li>inconsistent group submenu and Format submenu entry
4714 'Un' or 'Non'conserved</li>
4715 <li>Sequence feature settings are being shared by
4716 multiple distinct alignments</li>
4717 <li>group annotation not recreated when tree partition is
4719 <li>double click on group annotation to select sequences
4720 does not propagate to associated trees</li>
4721 <li>Mac OSX specific issues:
4723 <li>exception raised when mouse clicked on desktop
4724 window background</li>
4725 <li>Desktop menu placed on menu bar and application
4726 name set correctly</li>
4727 <li>sequence feature settings not wide enough for the
4728 save feature colourscheme button</li>
4737 <div align="center">
4738 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4741 <td><em>New Capabilities</em>
4743 <li>URL links generated from description line for
4744 regular-expression based URL links (applet and application)
4747 <li>Non-positional feature URL links are shown in link
4749 <li>Linked viewing of nucleic acid sequences and
4751 <li>Automatic Scrolling option in View menu to display
4752 the currently highlighted region of an alignment.</li>
4753 <li>Order an alignment by sequence length, or using the
4754 average score or total feature count for each sequence.</li>
4755 <li>Shading features by score or associated description</li>
4756 <li>Subdivide alignment and groups based on identity of
4757 selected subsequence (Make Groups from Selection).</li>
4758 <li>New hide/show options including Shift+Control+H to
4759 hide everything but the currently selected region.</li>
4760 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4761 </ul> <em>Application</em>
4763 <li>Fetch DB References capabilities and UI expanded to
4764 support retrieval from DAS sequence sources</li>
4765 <li>Local DAS Sequence sources can be added via the
4766 command line or via the Add local source dialog box.</li>
4767 <li>DAS Dbref and DbxRef feature types are parsed as
4768 database references and protein_name is parsed as
4769 description line (BioSapiens terms).</li>
4770 <li>Enable or disable non-positional feature and database
4771 references in sequence ID tooltip from View menu in
4773 <!-- <li>New hidden columns and rows and representatives capabilities
4774 in annotations file (in progress - not yet fully implemented)</li> -->
4775 <li>Group-associated consensus, sequence logos and
4776 conservation plots</li>
4777 <li>Symbol distributions for each column can be exported
4778 and visualized as sequence logos</li>
4779 <li>Optionally scale multi-character column labels to fit
4780 within each column of annotation row<!-- todo for applet -->
4782 <li>Optional automatic sort of associated alignment view
4783 when a new tree is opened.</li>
4784 <li>Jalview Java Console</li>
4785 <li>Better placement of desktop window when moving
4786 between different screens.</li>
4787 <li>New preference items for sequence ID tooltip and
4788 consensus annotation</li>
4789 <li>Client to submit sequences and IDs to Envision2
4791 <li><em>Vamsas Capabilities</em>
4793 <li>Improved VAMSAS synchronization (Jalview archive
4794 used to preserve views, structures, and tree display
4796 <li>Import of vamsas documents from disk or URL via
4798 <li>Sharing of selected regions between views and
4799 with other VAMSAS applications (Experimental feature!)</li>
4800 <li>Updated API to VAMSAS version 0.2</li>
4802 </ul> <em>Applet</em>
4804 <li>Middle button resizes annotation row height</li>
4807 <li>sortByTree (true/false) - automatically sort the
4808 associated alignment view by the tree when a new tree is
4810 <li>showTreeBootstraps (true/false) - show or hide
4811 branch bootstraps (default is to show them if available)</li>
4812 <li>showTreeDistances (true/false) - show or hide
4813 branch lengths (default is to show them if available)</li>
4814 <li>showUnlinkedTreeNodes (true/false) - indicate if
4815 unassociated nodes should be highlighted in the tree
4817 <li>heightScale and widthScale (1.0 or more) -
4818 increase the height or width of a cell in the alignment
4819 grid relative to the current font size.</li>
4822 <li>Non-positional features displayed in sequence ID
4824 </ul> <em>Other</em>
4826 <li>Features format: graduated colour definitions and
4827 specification of feature scores</li>
4828 <li>Alignment Annotations format: new keywords for group
4829 associated annotation (GROUP_REF) and annotation row display
4830 properties (ROW_PROPERTIES)</li>
4831 <li>XML formats extended to support graduated feature
4832 colourschemes, group associated annotation, and profile
4833 visualization settings.</li></td>
4836 <li>Source field in GFF files parsed as feature source
4837 rather than description</li>
4838 <li>Non-positional features are now included in sequence
4839 feature and gff files (controlled via non-positional feature
4840 visibility in tooltip).</li>
4841 <li>URL links generated for all feature links (bugfix)</li>
4842 <li>Added URL embedding instructions to features file
4844 <li>Codons containing ambiguous nucleotides translated as
4845 'X' in peptide product</li>
4846 <li>Match case switch in find dialog box works for both
4847 sequence ID and sequence string and query strings do not
4848 have to be in upper case to match case-insensitively.</li>
4849 <li>AMSA files only contain first column of
4850 multi-character column annotation labels</li>
4851 <li>Jalview Annotation File generation/parsing consistent
4852 with documentation (e.g. Stockholm annotation can be
4853 exported and re-imported)</li>
4854 <li>PDB files without embedded PDB IDs given a friendly
4856 <li>Find incrementally searches ID string matches as well
4857 as subsequence matches, and correctly reports total number
4861 <li>Better handling of exceptions during sequence
4863 <li>Dasobert generated non-positional feature URL
4864 link text excludes the start_end suffix</li>
4865 <li>DAS feature and source retrieval buttons disabled
4866 when fetch or registry operations in progress.</li>
4867 <li>PDB files retrieved from URLs are cached properly</li>
4868 <li>Sequence description lines properly shared via
4870 <li>Sequence fetcher fetches multiple records for all
4872 <li>Ensured that command line das feature retrieval
4873 completes before alignment figures are generated.</li>
4874 <li>Reduced time taken when opening file browser for
4876 <li>isAligned check prior to calculating tree, PCA or
4877 submitting an MSA to JNet now excludes hidden sequences.</li>
4878 <li>User defined group colours properly recovered
4879 from Jalview projects.</li>
4888 <div align="center">
4889 <strong>2.4.0.b2</strong><br> 28/10/2009
4894 <li>Experimental support for google analytics usage
4896 <li>Jalview privacy settings (user preferences and docs).</li>
4901 <li>Race condition in applet preventing startup in
4903 <li>Exception when feature created from selection beyond
4904 length of sequence.</li>
4905 <li>Allow synthetic PDB files to be imported gracefully</li>
4906 <li>Sequence associated annotation rows associate with
4907 all sequences with a given id</li>
4908 <li>Find function matches case-insensitively for sequence
4909 ID string searches</li>
4910 <li>Non-standard characters do not cause pairwise
4911 alignment to fail with exception</li>
4912 </ul> <em>Application Issues</em>
4914 <li>Sequences are now validated against EMBL database</li>
4915 <li>Sequence fetcher fetches multiple records for all
4917 </ul> <em>InstallAnywhere Issues</em>
4919 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4920 issue with installAnywhere mechanism)</li>
4921 <li>Command line launching of JARs from InstallAnywhere
4922 version (java class versioning error fixed)</li>
4929 <div align="center">
4930 <strong>2.4</strong><br> 27/8/2008
4933 <td><em>User Interface</em>
4935 <li>Linked highlighting of codon and amino acid from
4936 translation and protein products</li>
4937 <li>Linked highlighting of structure associated with
4938 residue mapping to codon position</li>
4939 <li>Sequence Fetcher provides example accession numbers
4940 and 'clear' button</li>
4941 <li>MemoryMonitor added as an option under Desktop's
4943 <li>Extract score function to parse whitespace separated
4944 numeric data in description line</li>
4945 <li>Column labels in alignment annotation can be centred.</li>
4946 <li>Tooltip for sequence associated annotation give name
4948 </ul> <em>Web Services and URL fetching</em>
4950 <li>JPred3 web service</li>
4951 <li>Prototype sequence search client (no public services
4953 <li>Fetch either seed alignment or full alignment from
4955 <li>URL Links created for matching database cross
4956 references as well as sequence ID</li>
4957 <li>URL Links can be created using regular-expressions</li>
4958 </ul> <em>Sequence Database Connectivity</em>
4960 <li>Retrieval of cross-referenced sequences from other
4962 <li>Generalised database reference retrieval and
4963 validation to all fetchable databases</li>
4964 <li>Fetch sequences from DAS sources supporting the
4965 sequence command</li>
4966 </ul> <em>Import and Export</em>
4967 <li>export annotation rows as CSV for spreadsheet import</li>
4968 <li>Jalview projects record alignment dataset associations,
4969 EMBL products, and cDNA sequence mappings</li>
4970 <li>Sequence Group colour can be specified in Annotation
4972 <li>Ad-hoc colouring of group in Annotation File using RGB
4973 triplet as name of colourscheme</li>
4974 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4976 <li>treenode binding for VAMSAS tree exchange</li>
4977 <li>local editing and update of sequences in VAMSAS
4978 alignments (experimental)</li>
4979 <li>Create new or select existing session to join</li>
4980 <li>load and save of vamsas documents</li>
4981 </ul> <em>Application command line</em>
4983 <li>-tree parameter to open trees (introduced for passing
4985 <li>-fetchfrom command line argument to specify nicknames
4986 of DAS servers to query for alignment features</li>
4987 <li>-dasserver command line argument to add new servers
4988 that are also automatically queried for features</li>
4989 <li>-groovy command line argument executes a given groovy
4990 script after all input data has been loaded and parsed</li>
4991 </ul> <em>Applet-Application data exchange</em>
4993 <li>Trees passed as applet parameters can be passed to
4994 application (when using "View in full
4995 application")</li>
4996 </ul> <em>Applet Parameters</em>
4998 <li>feature group display control parameter</li>
4999 <li>debug parameter</li>
5000 <li>showbutton parameter</li>
5001 </ul> <em>Applet API methods</em>
5003 <li>newView public method</li>
5004 <li>Window (current view) specific get/set public methods</li>
5005 <li>Feature display control methods</li>
5006 <li>get list of currently selected sequences</li>
5007 </ul> <em>New Jalview distribution features</em>
5009 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
5010 <li>RELEASE file gives build properties for the latest
5011 Jalview release.</li>
5012 <li>Java 1.1 Applet build made easier and donotobfuscate
5013 property controls execution of obfuscator</li>
5014 <li>Build target for generating source distribution</li>
5015 <li>Debug flag for javacc</li>
5016 <li>.jalview_properties file is documented (slightly) in
5017 jalview.bin.Cache</li>
5018 <li>Continuous Build Integration for stable and
5019 development version of Application, Applet and source
5024 <li>selected region output includes visible annotations
5025 (for certain formats)</li>
5026 <li>edit label/displaychar contains existing label/char
5028 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
5029 <li>shorter peptide product names from EMBL records</li>
5030 <li>Newick string generator makes compact representations</li>
5031 <li>bootstrap values parsed correctly for tree files with
5033 <li>pathological filechooser bug avoided by not allowing
5034 filenames containing a ':'</li>
5035 <li>Fixed exception when parsing GFF files containing
5036 global sequence features</li>
5037 <li>Alignment datasets are finalized only when number of
5038 references from alignment sequences goes to zero</li>
5039 <li>Close of tree branch colour box without colour
5040 selection causes cascading exceptions</li>
5041 <li>occasional negative imgwidth exceptions</li>
5042 <li>better reporting of non-fatal warnings to user when
5043 file parsing fails.</li>
5044 <li>Save works when Jalview project is default format</li>
5045 <li>Save as dialog opened if current alignment format is
5046 not a valid output format</li>
5047 <li>UniProt canonical names introduced for both das and
5049 <li>Histidine should be midblue (not pink!) in Zappo</li>
5050 <li>error messages passed up and output when data read
5052 <li>edit undo recovers previous dataset sequence when
5053 sequence is edited</li>
5054 <li>allow PDB files without pdb ID HEADER lines (like
5055 those generated by MODELLER) to be read in properly</li>
5056 <li>allow reading of JPred concise files as a normal
5058 <li>Stockholm annotation parsing and alignment properties
5059 import fixed for PFAM records</li>
5060 <li>Structure view windows have correct name in Desktop
5062 <li>annotation consisting of sequence associated scores
5063 can be read and written correctly to annotation file</li>
5064 <li>Aligned cDNA translation to aligned peptide works
5066 <li>Fixed display of hidden sequence markers and
5067 non-italic font for representatives in Applet</li>
5068 <li>Applet Menus are always embedded in applet window on
5070 <li>Newly shown features appear at top of stack (in
5072 <li>Annotations added via parameter not drawn properly
5073 due to null pointer exceptions</li>
5074 <li>Secondary structure lines are drawn starting from
5075 first column of alignment</li>
5076 <li>UniProt XML import updated for new schema release in
5078 <li>Sequence feature to sequence ID match for Features
5079 file is case-insensitive</li>
5080 <li>Sequence features read from Features file appended to
5081 all sequences with matching IDs</li>
5082 <li>PDB structure coloured correctly for associated views
5083 containing a sub-sequence</li>
5084 <li>PDB files can be retrieved by applet from Jar files</li>
5085 <li>feature and annotation file applet parameters
5086 referring to different directories are retrieved correctly</li>
5087 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
5088 <li>Fixed application hang whilst waiting for
5089 splash-screen version check to complete</li>
5090 <li>Applet properly URLencodes input parameter values
5091 when passing them to the launchApp service</li>
5092 <li>display name and local features preserved in results
5093 retrieved from web service</li>
5094 <li>Visual delay indication for sequence retrieval and
5095 sequence fetcher initialisation</li>
5096 <li>updated Application to use DAS 1.53e version of
5097 dasobert DAS client</li>
5098 <li>Re-instated Full AMSA support and .amsa file
5100 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
5108 <div align="center">
5109 <strong>2.3</strong><br> 9/5/07
5114 <li>Jmol 11.0.2 integration</li>
5115 <li>PDB views stored in Jalview XML files</li>
5116 <li>Slide sequences</li>
5117 <li>Edit sequence in place</li>
5118 <li>EMBL CDS features</li>
5119 <li>DAS Feature mapping</li>
5120 <li>Feature ordering</li>
5121 <li>Alignment Properties</li>
5122 <li>Annotation Scores</li>
5123 <li>Sort by scores</li>
5124 <li>Feature/annotation editing in applet</li>
5129 <li>Headless state operation in 2.2.1</li>
5130 <li>Incorrect and unstable DNA pairwise alignment</li>
5131 <li>Cut and paste of sequences with annotation</li>
5132 <li>Feature group display state in XML</li>
5133 <li>Feature ordering in XML</li>
5134 <li>blc file iteration selection using filename # suffix</li>
5135 <li>Stockholm alignment properties</li>
5136 <li>Stockhom alignment secondary structure annotation</li>
5137 <li>2.2.1 applet had no feature transparency</li>
5138 <li>Number pad keys can be used in cursor mode</li>
5139 <li>Structure Viewer mirror image resolved</li>
5146 <div align="center">
5147 <strong>2.2.1</strong><br> 12/2/07
5152 <li>Non standard characters can be read and displayed
5153 <li>Annotations/Features can be imported/exported to the
5155 <li>Applet allows editing of sequence/annotation/group
5156 name & description
5157 <li>Preference setting to display sequence name in
5159 <li>Annotation file format extended to allow
5160 Sequence_groups to be defined
5161 <li>Default opening of alignment overview panel can be
5162 specified in preferences
5163 <li>PDB residue numbering annotation added to associated
5169 <li>Applet crash under certain Linux OS with Java 1.6
5171 <li>Annotation file export / import bugs fixed
5172 <li>PNG / EPS image output bugs fixed
5178 <div align="center">
5179 <strong>2.2</strong><br> 27/11/06
5184 <li>Multiple views on alignment
5185 <li>Sequence feature editing
5186 <li>"Reload" alignment
5187 <li>"Save" to current filename
5188 <li>Background dependent text colour
5189 <li>Right align sequence ids
5190 <li>User-defined lower case residue colours
5193 <li>Menu item accelerator keys
5194 <li>Control-V pastes to current alignment
5195 <li>Cancel button for DAS Feature Fetching
5196 <li>PCA and PDB Viewers zoom via mouse roller
5197 <li>User-defined sub-tree colours and sub-tree selection
5200 <li>'New Window' button on the 'Output to Text box'
5205 <li>New memory efficient Undo/Redo System
5206 <li>Optimised symbol lookups and conservation/consensus
5208 <li>Region Conservation/Consensus recalculated after
5210 <li>Fixed Remove Empty Columns Bug (empty columns at end
5212 <li>Slowed DAS Feature Fetching for increased robustness.
5215 <li>Made angle brackets in ASCII feature descriptions
5217 <li>Re-instated Zoom function for PCA
5218 <li>Sequence descriptions conserved in web service
5220 <li>UniProt ID discoverer uses any word separated by
5222 <li>WsDbFetch query/result association resolved
5223 <li>Tree leaf to sequence mapping improved
5224 <li>Smooth fonts switch moved to FontChooser dialog box.
5232 <div align="center">
5233 <strong>2.1.1</strong><br> 12/9/06
5238 <li>Copy consensus sequence to clipboard</li>
5243 <li>Image output - rightmost residues are rendered if
5244 sequence id panel has been resized</li>
5245 <li>Image output - all offscreen group boundaries are
5247 <li>Annotation files with sequence references - all
5248 elements in file are relative to sequence position</li>
5249 <li>Mac Applet users can use Alt key for group editing</li>
5255 <div align="center">
5256 <strong>2.1</strong><br> 22/8/06
5261 <li>MAFFT Multiple Alignment in default Web Service list</li>
5262 <li>DAS Feature fetching</li>
5263 <li>Hide sequences and columns</li>
5264 <li>Export Annotations and Features</li>
5265 <li>GFF file reading / writing</li>
5266 <li>Associate structures with sequences from local PDB
5268 <li>Add sequences to exisiting alignment</li>
5269 <li>Recently opened files / URL lists</li>
5270 <li>Applet can launch the full application</li>
5271 <li>Applet has transparency for features (Java 1.2
5273 <li>Applet has user defined colours parameter</li>
5274 <li>Applet can load sequences from parameter
5275 "sequence<em>x</em>"
5281 <li>Redundancy Panel reinstalled in the Applet</li>
5282 <li>Monospaced font - EPS / rescaling bug fixed</li>
5283 <li>Annotation files with sequence references bug fixed</li>
5289 <div align="center">
5290 <strong>2.08.1</strong><br> 2/5/06
5295 <li>Change case of selected region from Popup menu</li>
5296 <li>Choose to match case when searching</li>
5297 <li>Middle mouse button and mouse movement can compress /
5298 expand the visible width and height of the alignment</li>
5303 <li>Annotation Panel displays complete JNet results</li>
5309 <div align="center">
5310 <strong>2.08b</strong><br> 18/4/06
5316 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
5317 <li>Righthand label on wrapped alignments shows correct
5324 <div align="center">
5325 <strong>2.08</strong><br> 10/4/06
5330 <li>Editing can be locked to the selection area</li>
5331 <li>Keyboard editing</li>
5332 <li>Create sequence features from searches</li>
5333 <li>Precalculated annotations can be loaded onto
5335 <li>Features file allows grouping of features</li>
5336 <li>Annotation Colouring scheme added</li>
5337 <li>Smooth fonts off by default - Faster rendering</li>
5338 <li>Choose to toggle Autocalculate Consensus On/Off</li>
5343 <li>Drag & Drop fixed on Linux</li>
5344 <li>Jalview Archive file faster to load/save, sequence
5345 descriptions saved.</li>
5351 <div align="center">
5352 <strong>2.07</strong><br> 12/12/05
5357 <li>PDB Structure Viewer enhanced</li>
5358 <li>Sequence Feature retrieval and display enhanced</li>
5359 <li>Choose to output sequence start-end after sequence
5360 name for file output</li>
5361 <li>Sequence Fetcher WSDBFetch@EBI</li>
5362 <li>Applet can read feature files, PDB files and can be
5363 used for HTML form input</li>
5368 <li>HTML output writes groups and features</li>
5369 <li>Group editing is Control and mouse click</li>
5370 <li>File IO bugs</li>
5376 <div align="center">
5377 <strong>2.06</strong><br> 28/9/05
5382 <li>View annotations in wrapped mode</li>
5383 <li>More options for PCA viewer</li>
5388 <li>GUI bugs resolved</li>
5389 <li>Runs with -nodisplay from command line</li>
5395 <div align="center">
5396 <strong>2.05b</strong><br> 15/9/05
5401 <li>Choose EPS export as lineart or text</li>
5402 <li>Jar files are executable</li>
5403 <li>Can read in Uracil - maps to unknown residue</li>
5408 <li>Known OutOfMemory errors give warning message</li>
5409 <li>Overview window calculated more efficiently</li>
5410 <li>Several GUI bugs resolved</li>
5416 <div align="center">
5417 <strong>2.05</strong><br> 30/8/05
5422 <li>Edit and annotate in "Wrapped" view</li>
5427 <li>Several GUI bugs resolved</li>
5433 <div align="center">
5434 <strong>2.04</strong><br> 24/8/05
5439 <li>Hold down mouse wheel & scroll to change font
5445 <li>Improved JPred client reliability</li>
5446 <li>Improved loading of Jalview files</li>
5452 <div align="center">
5453 <strong>2.03</strong><br> 18/8/05
5458 <li>Set Proxy server name and port in preferences</li>
5459 <li>Multiple URL links from sequence ids</li>
5460 <li>User Defined Colours can have a scheme name and added
5462 <li>Choose to ignore gaps in consensus calculation</li>
5463 <li>Unix users can set default web browser</li>
5464 <li>Runs without GUI for batch processing</li>
5465 <li>Dynamically generated Web Service Menus</li>
5470 <li>InstallAnywhere download for Sparc Solaris</li>
5476 <div align="center">
5477 <strong>2.02</strong><br> 18/7/05
5483 <li>Copy & Paste order of sequences maintains
5484 alignment order.</li>
5490 <div align="center">
5491 <strong>2.01</strong><br> 12/7/05
5496 <li>Use delete key for deleting selection.</li>
5497 <li>Use Mouse wheel to scroll sequences.</li>
5498 <li>Help file updated to describe how to add alignment
5500 <li>Version and build date written to build properties
5502 <li>InstallAnywhere installation will check for updates
5503 at launch of Jalview.</li>
5508 <li>Delete gaps bug fixed.</li>
5509 <li>FileChooser sorts columns.</li>
5510 <li>Can remove groups one by one.</li>
5511 <li>Filechooser icons installed.</li>
5512 <li>Finder ignores return character when searching.
5513 Return key will initiate a search.<br>
5520 <div align="center">
5521 <strong>2.0</strong><br> 20/6/05
5526 <li>New codebase</li>