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 used by Jalview
145 <!-- JAL-3830 -->New command line launcher scripts (.sh, .ps1, .bat) usable on
146 macOS, Linux/Unix, Windows and documentation in Help. Installer wizard has option
147 to add this to PATH, or link to it in your PATH.
150 </ul> <em>JalviewJS</em>
153 <!-- JAL-3624 -->PDB structures mapped to Uniprot Sequences with
157 <!-- JAL-3208 -->setprop commandline argument reinstated for JalviewJS only
160 <!-- JAL-3163 -->Missing message bundle keys are only
161 reported once per key (avoids excessive log output in js
165 <!-- JAL-3168 -->Feature type is included in the title of
166 the Feature Settings' Colour Chooser dialog
169 </ul> <em>Development</em>
172 <!-- -->First integrated JalviewJS and Jalview release
174 <li>Updated building instructions</li>
176 <!-- JAL-3789, JAL-3679 -->Improved JalviewJS/Jalview build
177 process, added support for system package provided eclipse
180 <li>Install4j 9.0.x used for installer packaging</li>
181 <li>Notarized MacOS installer for compatibility with Big
182 Sur and Monterey</li>
184 <!-- JAL-3805 -->Uninstaller application for old
185 (InstallAnywhere based) Jalview installations removed from
189 <!-- JAL-3930 -->Improved use of installers for unattended
190 installation with a customizedId of "JALVIEW" in install4j's
194 <!-- JAL-3907 -->Improved compatibility of Jalview build
195 with Java 17 (next LTS target)
204 <!-- JAL-3674 -->Slow structure commands can block Jalview
208 <!-- JAL-3904 -->Structure window's viewer-specific menu
209 disappears when only one structure is shown (and many
210 sequences:one chain mappings are present)
213 <!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
214 the first SEQUENCE_GROUP defined
219 <!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 -->Selections not
220 propagated between Linked CDS - Protein alignments and their
221 trees (known defect from 2.11.1.3)
224 <!-- JAL-3761 -->Not all codon positions highlighted for
225 overlapping exon splice sites (e.g due to RNA slippage)
228 <!-- JAL-3794 -->X was not being recognised as the unknown
229 base in DNA sequences
232 <!-- JAL-3915 -->Removed RNAview checkbox and logic from
233 Structure Preferences
236 <!-- JAL-3583 -->Tooltip behaviour improved (slightly)
239 <!-- JAL-3162 -->Can edit a feature so that start > end
242 <!-- JAL-2848 -->Cancel from Amend Features doesn't reset a
243 modified graduated colour
246 <!-- JAL-3788 -->New View with automatic 'Show Overview'
247 preference enabled results in Null Pointer Exceptions when
248 clustal colouring is enabled
251 <!-- JAL-3275 -->Can open multiple Preferences panels
254 <!-- JAL-3949 -->Standard out logging broken: messages only
255 routing to stderr and appear as a raw template
257 </ul> <em>JalviewJS</em>
260 <!-- JAL-3202 -->Consensus profile may include zero (rounded
261 down) percentage values causing a divide by zero
276 <!-- JAL-3762 -->JalviewJS doesn't honour arguments passed
277 via Info.args when there are arguments on the URL
280 <!-- JAL-3602 -->gradle closure-compiler not using UTF-8
283 <!-- JAL-3603 -->Annotation file fails to load from URL in
286 </ul> <em>Development</em>
290 <li>Fixed non-fatal gradle errors during build</li>
292 <!-- JAL-3745 -->Updated build.gradle for use with
302 <td width="60" align="center" nowrap><strong><a
303 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.7">.7</a><br />
304 <em>18/01/2022</em></strong></td>
306 <td align="left" valign="top">
309 <!-- JAL-3703, JAL-3935 -->Files open in Jalview cannot be
310 updated by Jalview or other applications (Windows, other non
313 </ul> <em>Security</em>
316 <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
322 <td width="60" align="center" nowrap><strong><a
323 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
324 <em>6/01/2022</em></strong></td>
326 <td align="left" valign="top"><em>Security</em>
329 <!-- JAL-3934 -->Version bump library dependency: Log4j
336 <td width="60" align="center" nowrap><strong><a
337 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
338 <em>20/12/2021</em></strong></td>
340 <td align="left" valign="top"><em>Security</em>
343 <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
345 </ul> <em>Development</em>
347 <li>Updated building instructions</li>
352 <!-- JAL-3840 -->Occupancy calculation is incorrect for
353 alignment columns with over -1+2^32 gaps (breaking filtering
357 <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
358 scale factors being set with buggy window-managers (linux
361 </ul> <em>Development</em>
363 <li>Fixed non-fatal gradle errors during build</li>
368 <td width="60" align="center" nowrap><strong><a
369 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
370 <em>09/03/2021</em></strong></td>
371 <td align="left" valign="top"><em>Improved control of
372 Jalview's use of network services via jalview_properties</em>
375 <!-- JAL-3814 -->New .jalview_properties token controlling
376 launch of the news browser (like -nonews argument)
379 <!-- JAL-3813 -->New .jalview_properties token controlling
380 download of linkout URLs from
381 www.jalview.org/services/identifiers
384 <!-- JAL-3812 -->New .jalview_properties token controlling
385 download of BIOJSHTML templates
388 <!-- JAL-3811 -->New 'Discover Web Services' option to
389 trigger a one off JABAWS discovery if autodiscovery was
393 <td align="left" valign="top">
396 <!-- JAL-3818 -->Intermittent deadlock opening structure in
399 </ul> <em>New Known defects</em>
402 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
403 always restored from project (since 2.10.3)
406 <!-- JAL-3806 -->Selections from tree built from CDS aren't
407 propagated to Protein alignment (since 2.11.1.3)
413 <td width="60" align="center" nowrap><strong><a
414 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
415 <em>29/10/2020</em></strong></td>
416 <td align="left" valign="top">
421 <td align="left" valign="top">
424 <!-- JAL-3765 -->Find doesn't always highlight all matching
425 positions in a sequence (bug introduced in 2.11.1.2)
428 <!-- JAL-3760 -->Alignments containing one or more protein
429 sequences can be classed as nucleotide
432 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
433 sequences after alignment of protein products (known defect
434 first reported for 2.11.1.0)
437 <!-- JAL-3725 -->No tooltip or popup menu for genomic
438 features outwith CDS shown overlaid on protein
441 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
442 correctly mapped by Jalview (e.g. affects viral CDS with
443 ribosomal slippage, since 2.9.0)
446 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
450 <!-- JAL-3700 -->Selections in CDS sequence panel don't
451 always select corresponding protein sequences
454 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
455 column selection doesn't always ignore hidden columns
457 </ul> <em>Installer</em>
460 <!-- JAL-3611 -->Space character in Jalview install path on
461 Windows prevents install4j launching getdown
463 </ul> <em>Development</em>
466 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
467 version numbers in doc/building.md
473 <td width="60" align="center" nowrap><strong><a
474 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
475 <em>25/09/2020</em></strong></td>
476 <td align="left" valign="top">
480 <td align="left" valign="top">
483 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
484 "Encountered problems opening
485 https://www.jalview.org/examples/exampleFile_2_7.jvp"
491 <td width="60" align="center" nowrap><strong><a
492 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
493 <em>17/09/2020</em></strong></td>
494 <td align="left" valign="top">
497 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
498 residue in cursor mode
501 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
502 HTSJDK from 2.12 to 2.23
505 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
506 optimisations and improvements suggested by Bob Hanson and
507 improved compatibility with JalviewJS
510 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
511 alignments from Pfam and Rfam
514 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
515 import (no longer based on .gz extension)
518 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
521 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
522 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
526 <!-- JAL-3667 -->Improved warning messages, debug logging
527 and fixed Retry action when Jalview encounters errors when
528 saving or making backup files.
531 <!-- JAL-3676 -->Enhanced Jalview Java Console:
533 <li>Jalview's logging level can be configured</li>
534 <li>Copy to Clipboard Buttion</li>
538 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
539 when running on Linux (Requires Java 11+)
541 </ul> <em>Launching Jalview</em>
544 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
545 through a system property
548 <!-- JAL-3477 -->Improved built-in documentation and command
549 line help for configuring Jalview's memory
553 <td align="left" valign="top">
556 <!-- JAL-3691 -->Conservation and Quality tracks are shown
557 but not calculated and no protein or DNA score models are
558 available for tree/PCA calculation when launched with
559 Turkish language locale
562 <!-- JAL-3493 -->Escape does not clear highlights on the
563 alignment (Since Jalview 2.10.3)
566 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
567 doesn't slide selected sequences, just sequence under cursor
570 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
571 sequence under the cursor
574 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
575 multiple EMBL gene products shown for a single contig
578 <!-- JAL-3696 -->Errors encountered when processing variants
579 from VCF files yield "Error processing VCF: Format specifier
583 <!-- JAL-3697 -->Count of features not shown can be wrong
584 when there are both local and complementary features mapped
585 to the position under the cursor
588 <!-- JAL-3673 -->Sequence ID for reference sequence is
589 clipped when Right align Sequence IDs enabled
592 <!-- JAL-2983 -->Slider with negative range values not
593 rendered correctly in VAqua4 (Since 2.10.4)
596 <!-- JAL-3685 -->Single quotes not displayed correctly in
597 internationalised text for some messages and log output
600 <!-- JAL-3490 -->Find doesn't report matches that span
601 hidden gapped columns
604 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
605 panels, Alignment viewport and annotation renderer.
608 <!-- JAL-3561 -->Jalview ignores file format parameter
609 specifying output format when exporting an alignment via the
613 <!-- JAL-3667 -->Windows 10: For a minority of users, if
614 backups are not enabled, Jalview sometimes fails to
615 overwrite an existing file and raises a warning dialog. (in
616 2.11.0, and 2.11.1.0, the workaround is to try to save the
617 file again, and if that fails, delete the original file and
621 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
625 <!-- JAL-3741 -->References to http://www.jalview.org in
626 program and documentation
628 </ul> <em>Launching Jalview</em>
631 <!-- JAL-3718 -->Jalview application fails when launched the
632 first time for a version that has different jars to the
633 previous launched version.
635 </ul> <em>Developing Jalview</em>
638 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
639 data, causing cloverReport gradle task to fail with an
643 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
644 monitor the release channel
646 </ul> <em>New Known defects</em>
649 <!-- JAL-3748 -->CDS shown in result of submitting proteins
650 in a CDS/Protein alignment to a web service is wrong when
651 proteins share a common transcript sequence (e.g. genome of
655 <!-- JAL-3576 -->Co-located features exported and
656 re-imported are ordered differently when shown on alignment
657 and in tooltips. (Also affects v2.11.1.0)
660 <!-- JAL-3702 -->Drag and drop of alignment file onto
661 alignment window when in a HiDPI scaled mode in Linux only
662 works for the top left quadrant of the alignment window
665 <!-- JAL-3701 -->Stale build data in jalview standalone jar
666 builds (only affects 2.11.1.1 branch)
669 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
670 when alignment view restored from project (since Jalview
674 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
675 protein products for certain ENA records are repeatedly
676 shown via Calculate->Show Cross Refs
682 <td width="60" align="center" nowrap><strong><a
683 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
684 <em>22/04/2020</em></strong></td>
685 <td align="left" valign="top">
688 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
689 'virtual' codon features shown on protein (or vice versa)
690 for display in alignments, on structure views (including
691 transfer to UCSF chimera), in feature reports and for
695 <!-- JAL-3121 -->Feature attributes from VCF files can be
696 exported and re-imported as GFF3 files
699 <!-- JAL-3376 -->Capture VCF "fixed column" values
700 POS, ID, QUAL, FILTER as Feature Attributes
703 <!-- JAL-3375 -->More robust VCF numeric data field
704 validation while parsing
707 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
711 <!-- JAL-3535 -->Feature Settings dialog title includes name
715 <!-- JAL-3538 -->Font anti-aliasing in alignment views
719 <!-- JAL-3468 -->Very long feature descriptions truncated in
723 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
724 with no feature types visible
727 <!-- JAL-3574 -->Improved support for filtering feature
728 attributes with large integer values
731 <em>Jalview Installer</em>
734 <!-- JAL-3449 -->Versions for install4j and getdown and
735 installer template version reported in console (may be null
736 when Jalview launched as executable jar or via conda)
739 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and
740 higher quality background images
743 <!-- JAL-3394 -->New installer/application launcher
744 generated with install4j 8.0.4
747 <!-- JAL-3420 -->Jalview File Associations shown for Unix
751 <!-- JAL-3477 -->Improved defaults for maximum memory
752 setting when running on large memory machines
754 </ul> <em>Release processes</em>
757 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
760 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier
761 access to test-release channel builds
763 </ul> <em>Build System</em>
766 <!-- JAL-3510 -->Clover updated to 4.4.1
769 <!-- JAL-3513 -->Test code included in Clover coverage
772 </ul> <em>Groovy Scripts</em>
775 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
776 to stdout containing the consensus sequence for each
777 alignment in a Jalview session
780 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
781 genomic sequence_variant annotation from CDS as
782 missense_variant or synonymous_variant on protein products.
786 <td align="left" valign="top">
789 <!-- JAL-3581 -->Hidden sequence markers still visible when
790 'Show hidden markers' option is not ticked
793 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
794 PNG output when 'Automatically set ID width' is set in
795 jalview preferences or properties file
798 <!-- JAL-3571 -->Feature Editor dialog can be opened when
799 'Show Sequence Features' option is not ticked
802 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
803 buttons in Feature Settings dialog are clicked when no
807 <!-- JAL-3412 -->ID margins for CDS and Protein views not
808 equal when split frame is first opened
811 <!-- JAL-3296 -->Sequence position numbers in status bar not
812 correct after editing a sequence's start position
815 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
816 with annotation and exceptions thrown when only a few
817 columns shown in wrapped mode
820 <!-- JAL-3386 -->Sequence IDs missing in headless export of
821 wrapped alignment figure with annotations
824 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
825 ID fails with ClassCastException
828 <!-- JAL-3389 -->Chimera session not restored from Jalview
832 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
833 feature settings dialog also selects columns
836 <!-- JAL-3473 -->SpinnerNumberModel causes
837 IllegalArgumentException in some circumstances
840 <!-- JAL-3534 -->Multiple feature settings dialogs can be
844 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
845 alignment window is closed
848 <!-- JAL-3406 -->Credits missing some authors in Jalview
849 help documentation for 2.11.0 release
852 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
853 includes Pfam ID as sequence's accession rather than its
856 </ul> <em>Java 11 Compatibility issues</em>
859 <!-- JAL-2987 -->OSX - Can't view some search results in
860 PDB/Uniprot search panel
862 </ul> <em>Installer</em>
865 <!-- JAL-3447 -->Jalview should not create file associations
866 for 3D structure files (.pdb, .mmcif. .cif)
868 </ul> <em>Repository and Source Release</em>
871 <!-- JAL-3474 -->removed obsolete .cvsignore files from
875 <!-- JAL-3541 -->Clover report generation running out of
878 </ul> <em>New Known Issues</em>
881 <!-- JAL-3523 -->OSX - Current working directory not
882 preserved when Jalview.app launched with parameters from
886 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
887 clipped in headless figure export when Right Align option
891 <!-- JAL-3542 -->Jalview Installation type always reports
892 'Source' in console output
895 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail
896 on jalview's bamboo server but run fine locally.
902 <td width="60" align="center" nowrap><strong><a
903 name="Jalview.2.11.0">2.11.0</a><br /> <em>04/07/2019</em></strong></td>
904 <td align="left" valign="top">
907 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native
908 Application and Installers built with <a
909 href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a>
910 (licensed to the Jalview open source project) rather than
914 <!-- JAL-1929 -->Jalview Launcher System to auto-configure
915 memory settings, receive over the air updates and launch
916 specific versions via (<a
917 href="https://github.com/threerings/getdown">Three
921 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations
922 for formats supported by Jalview (including .jvp project
926 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command
927 line arguments and switch between different getdown channels
930 <!-- JAL-3141 -->Backup files created when saving Jalview
931 project or alignment files
935 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF
939 <!-- JAL-2753 -->Version of HTSJDK shipped with Jalview
940 updated to version 2.12.0
943 <!-- JAL-2620 -->Alternative genetic code tables for
947 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0
949 <li><strong>Enhanced visualisation and analysis
950 of Sequence Features</strong>
953 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
954 implementation that allows updates) used for Sequence
958 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
959 features can be filtered and shaded according to any
960 associated attributes (e.g. variant attributes from VCF
961 file, or key-value pairs imported from column 9 of GFF
965 <!-- JAL-2879 -->Feature Attributes and shading schemes
966 stored and restored from Jalview Projects
969 <!-- JAL-3334 -->Use full Sequence Ontology (via
970 BioJava) to recognise variant features
973 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants
974 on peptide sequences (also coloured red by default)
977 <!-- JAL-2792 -->Popup window to show full report for a
978 selected sequence feature's details
981 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient
982 sequence feature render algorithm (Z-sort/transparency
986 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature
991 <!-- JAL-3205 -->Symmetric score matrices for faster tree
994 <li><strong>Principal Components Analysis Viewer</strong>
997 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis
998 results and Viewer state saved in Jalview Project
1001 <!-- JAL-2962 -->'Change parameters' option removed from
1002 viewer's drop-down menus
1005 <!-- JAL-2975 -->Can use shift + arrow keys to rotate
1006 PCA image incrementally
1009 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
1013 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
1015 <li><strong>Speed and Efficiency</strong>
1018 <!-- JAL-2185,JAL-3198 -->More efficient creation of
1019 selections and multiple groups when working with large
1023 <!-- JAL-3200 -->Speedier import of annotation rows when
1024 parsing Stockholm files
1027 <li><strong>User Interface</strong>
1030 <!-- JAL-2933 -->Finder panel remembers last position in
1034 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS
1035 (What you see is what is shown)<br />Only visible
1036 regions of alignment are shown by default (can be
1037 changed in user preferences)
1040 <!-- JAL-3169 -->File Chooser stays open after
1041 responding Cancel to the Overwrite Dialog
1044 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour
1045 when all sequences are hidden
1048 <!-- JAL-1244 -->Status bar shows bounds when dragging a
1049 selection region, and gap count when inserting or
1053 <!-- JAL-3132 -->Status bar updates over sequence and
1057 <!-- JAL-3093 -->Annotation tooltips and popup menus are
1058 shown when in wrapped mode
1061 <!-- JAL-3073 -->Can select columns by dragging
1062 left/right in a graph or histogram annotation
1065 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB
1069 <!-- JAL-2621 -->Cursor changes over draggable box in
1073 <!-- JAL-3181 -->Consistent ordering of links in
1074 sequence id popup menu
1077 <!-- JAL-3080 -->Red line indicating tree-cut position
1078 not shown if no subgroups are created
1081 <!-- JAL-3042 -->Removed ability to configure length of
1082 search history by right-clicking search box
1088 <!-- JAL-3232 -->Jalview Groovy Scripting Console updated to
1091 <li><strong>Java 11 Support (not yet on general
1095 <!-- -->OSX GUI integrations for App menu's 'About'
1096 entry and trapping CMD-Q
1099 </ul> <em>Deprecations</em>
1102 <!-- JAL-3035 -->DAS sequence retrieval and annotation
1103 capabilities removed from the Jalview Desktop
1106 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling
1107 and unmarshalling has been replaced by JAXB for Jalview
1108 projects and XML based data retrieval clients
1111 <!-- JAL-3311 -->Disable VAMSAS menu in preparation for
1115 <!-- -->Jalview Desktop no longer distributed via Java Web
1118 </ul> <em>Documentation</em>
1121 <!-- JAL-3003 -->Added remarks about transparent rendering
1122 effects not supported in EPS figure export
1125 <!-- JAL-2903 -->Typos in documentation for Preferences
1128 </ul> <em>Development and Release Processes</em>
1131 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated
1135 <!-- JAL-1424 -->Enhanced checks for missing and duplicated
1136 keys in Message bundles
1139 <!-- JAL-3225 -->Eclipse project configuration managed with
1143 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian Bamboo
1144 continuous integration for unattended Test Suite execution
1147 <!-- JAL-2864 -->Memory test suite to detect leaks in common
1151 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
1155 <!-- JAL-3248 -->Developer documentation migrated to
1156 markdown (with HTML rendering)
1159 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
1162 <!-- JAL-3289 -->New URLs for publishing development
1167 <td align="left" valign="top">
1170 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
1173 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
1174 superposition in Jmol fail on Windows
1177 <!-- JAL-3286 -->Blank error dialog is displayed when
1178 discovering structures for sequences with lots of PDB
1182 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export
1183 with monospaced font
1186 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
1187 Jalview project involving multiple views
1190 <!-- JAL-3164 -->Overview for complementary view in a linked
1191 CDS/Protein alignment is not updated when Hide Columns by
1192 Annotation dialog hides columns
1195 <!-- JAL-3158 -->Selection highlighting in the complement of
1196 a CDS/Protein alignment stops working after making a
1197 selection in one view, then making another selection in the
1201 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
1205 <!-- JAL-3154 -->Table Columns could be re-ordered in
1206 Feature Settings and Jalview Preferences panels
1209 <!-- JAL-2865 -->Jalview hangs when closing windows, or
1210 redrawing the overview with large alignments
1213 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
1214 region if columns were selected by dragging right-to-left
1215 and the mouse moved to the left of the first column
1218 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to
1219 a hidden column marker via scale popup menu
1222 <!-- JAL-2846 -->Error message for trying to load in invalid
1223 URLs doesn't tell users the invalid URL
1226 <!-- JAL-2816 -->Tooltips displayed for features filtered by
1230 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl
1231 during show cross references or Fetch Database References
1232 are shown in red in original view
1235 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown
1236 correctly on peptide sequence (computed variant shown as
1240 <!-- JAL-2060 -->'Graduated colour' option not offered for
1241 manually created features (where feature score is Float.NaN)
1244 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or
1245 printed when columns are hidden
1248 <!-- JAL-3082 -->Regular expression error for '(' in Select
1249 Columns by Annotation description
1252 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after
1253 dragging out of Scale or Annotation Panel
1256 <!-- JAL-3075 -->Column selection incorrect after scrolling
1260 <!-- JAL-3074 -->Left/right drag in annotation can scroll
1264 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal
1268 <!-- JAL-3002 -->Column display is out by one after Page
1269 Down, Page Up in wrapped mode
1272 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
1275 <!-- JAL-2932 -->Finder searches in minimised alignments
1278 <!-- JAL-2250 -->'Apply Colour to All Groups' not always
1279 selected on opening an alignment
1282 <!-- JAL-3180 -->'Colour by Annotation' not marked selected
1286 <!-- JAL-3201 -->Per-group Clustal colour scheme changes
1287 when different groups in the alignment are selected
1290 <!-- JAL-2717 -->Internationalised colour scheme names not
1291 shown correctly in menu
1294 <!-- JAL-3206 -->Colour by Annotation can go black at
1295 min/max threshold limit
1298 <!-- JAL-3125 -->Value input for graduated feature colour
1299 threshold gets 'unrounded'
1302 <!-- JAL-2982 -->PCA image export doesn't respect background
1306 <!-- JAL-2963 -->PCA points don't dim when rotated about y
1310 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
1313 <!-- JAL-3078 -->Cancel in Tree Font dialog resets
1314 alignment, not Tree font
1317 <!-- JAL-2964 -->Associate Tree with All Views not restored
1321 <!-- JAL-2915 -->Scrolling of split frame is sluggish if
1322 Overview shown in complementary view
1325 <!-- JAL-3313 -->Codon consensus incorrectly scaled when
1326 shown without normalisation
1329 <!-- JAL-3021 -->Sequence Details report should open
1330 positioned at top of report
1333 <!-- JAL-914 -->Help page can be opened twice
1336 <!-- JAL-3333 -->Fuzzy text in web service status menu on
1339 </ul> <em>Editing</em>
1342 <!-- JAL-2822 -->Start and End should be updated when
1343 sequence data at beginning or end of alignment added/removed
1347 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection
1348 doesn't relocate sequence features correctly when start of
1349 sequence is removed (Known defect since 2.10)
1352 <!-- JAL-2830 -->Inserting gap sequence via the Edit
1353 Sequence dialog corrupts dataset sequence
1356 <!-- JAL-868 -->Structure colours not updated when
1357 associated tree repartitions the alignment view (Regression
1360 </ul> <em>Datamodel</em>
1363 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
1364 sequence's End is greater than its length
1366 </ul> <em>Bugs fixed for Java 11 Support (not yet on general
1370 <!-- JAL-3288 -->Menus work properly in split-screen
1372 </ul> <em>New Known Defects</em>
1375 <!-- JAL-3340 -->Select columns containing feature by double
1376 clicking ignores bounds of an existing selected region
1379 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in
1380 gapped regions of protein alignment.
1383 <!-- JAL-2647 -->Input Data menu entry is greyed out when
1384 PCA View is restored from a Jalview 2.11 project
1387 <!-- JAL-3213 -->Alignment panel height can be too small
1391 <!-- JAL-3240 -->Display is incorrect after removing gapped
1392 columns within hidden columns
1395 <!-- JAL-3314 -->Rightmost selection is lost when mouse
1396 re-enters window after dragging left to select columns to
1397 left of visible region
1400 <!-- JAL-2876 -->Features coloured according to their
1401 description string and thresholded by score in earlier
1402 versions of Jalview are not shown as thresholded features in
1403 2.11. To workaround please create a Score filter instead.
1406 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't
1407 reset group visibility
1410 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in
1411 linked CDS/Protein view
1414 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1415 alignments with multiple views can close views unexpectedly
1417 </ul> <em>Java 11 Specific defects</em>
1420 <!-- JAL-3235 -->Jalview Properties file is not sorted
1421 alphabetically when saved
1427 <td width="60" nowrap>
1428 <div align="center">
1429 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1432 <td><div align="left">
1436 <!-- JAL-3101 -->Default memory for Jalview webstart and
1437 InstallAnywhere increased to 1G.
1440 <!-- JAL-247 -->Hidden sequence markers and representative
1441 sequence bolding included when exporting alignment as EPS,
1442 SVG, PNG or HTML. <em>Display is configured via the
1443 Format menu, or for command-line use via a Jalview
1444 properties file.</em>
1447 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1448 API and sequence data now imported as JSON.
1451 <!-- JAL-3065 -->Change in recommended way of starting
1452 Jalview via a Java command line: add jars in lib directory
1453 to CLASSPATH, rather than via the deprecated java.ext.dirs
1457 <em>Development</em>
1460 <!-- JAL-3047 -->Support added to execute test suite
1461 instrumented with <a href="http://openclover.org/">Open
1466 <td><div align="left">
1470 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1471 row shown in Feredoxin Structure alignment view of example
1475 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1476 annotation displayed.
1479 <!-- JAL-3107 -->Group conservation/consensus not shown
1480 for newly created group when 'Apply to all groups'
1484 <!-- JAL-3087 -->Corrupted display when switching to
1485 wrapped mode when sequence panel's vertical scrollbar is
1489 <!-- JAL-3003 -->Alignment is black in exported EPS file
1490 when sequences are selected in exported view.</em>
1493 <!-- JAL-3059 -->Groups with different coloured borders
1494 aren't rendered with correct colour.
1497 <!-- JAL-3092 -->Jalview could hang when importing certain
1498 types of knotted RNA secondary structure.
1501 <!-- JAL-3095 -->Sequence highlight and selection in
1502 trimmed VARNA 2D structure is incorrect for sequences that
1506 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1507 annotation when columns are inserted into an alignment,
1508 and when exporting as Stockholm flatfile.
1511 <!-- JAL-3053 -->Jalview annotation rows containing upper
1512 and lower-case 'E' and 'H' do not automatically get
1513 treated as RNA secondary structure.
1516 <!-- JAL-3106 -->.jvp should be used as default extension
1517 (not .jar) when saving a Jalview project file.
1520 <!-- JAL-3105 -->Mac Users: closing a window correctly
1521 transfers focus to previous window on OSX
1524 <em>Java 10 Issues Resolved</em>
1527 <!-- JAL-2988 -->OSX - Can't save new files via the File
1528 or export menus by typing in a name into the Save dialog
1532 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1533 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1534 'look and feel' which has improved compatibility with the
1535 latest version of OSX.
1541 <td width="60" nowrap>
1542 <div align="center">
1543 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1544 <em>7/06/2018</em></strong>
1547 <td><div align="left">
1551 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1552 annotation retrieved from Uniprot
1555 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1556 onto the Jalview Desktop
1560 <td><div align="left">
1564 <!-- JAL-3017 -->Cannot import features with multiple
1565 variant elements (blocks import of some Uniprot records)
1568 <!-- JAL-2997 -->Clustal files with sequence positions in
1569 right-hand column parsed correctly
1572 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1573 not alignment area in exported graphic
1576 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1577 window has input focus
1580 <!-- JAL-2992 -->Annotation panel set too high when
1581 annotation added to view (Windows)
1584 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1585 network connectivity is poor
1588 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1589 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1590 the currently open URL and links from a page viewed in
1591 Firefox or Chrome on Windows is now fully supported. If
1592 you are using Edge, only links in the page can be
1593 dragged, and with Internet Explorer, only the currently
1594 open URL in the browser can be dropped onto Jalview.</em>
1597 <em>New Known Defects</em>
1600 <!-- JAL-3083 -->Cancel option doesn't reset Colour by
1607 <td width="60" nowrap>
1608 <div align="center">
1609 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1612 <td><div align="left">
1616 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1617 for disabling automatic superposition of multiple
1618 structures and open structures in existing views
1621 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1622 ID and annotation area margins can be click-dragged to
1626 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1630 <!-- JAL-2759 -->Improved performance for large alignments
1631 and lots of hidden columns
1634 <!-- JAL-2593 -->Improved performance when rendering lots
1635 of features (particularly when transparency is disabled)
1638 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2
1639 for exchange of Jalview features and Chimera attributes
1640 made generally available
1644 <td><div align="left">
1647 <!-- JAL-2899 -->Structure and Overview aren't updated
1648 when Colour By Annotation threshold slider is adjusted
1651 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1652 overlapping alignment panel
1655 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1659 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1660 improved: CDS not handled correctly if transcript has no
1664 <!-- JAL-2321 -->Secondary structure and temperature
1665 factor annotation not added to sequence when local PDB
1666 file associated with it by drag'n'drop or structure
1670 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1671 dialog doesn't import PDB files dropped on an alignment
1674 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1675 scroll bar doesn't work for some CDS/Protein views
1678 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1679 Java 1.8u153 onwards and Java 1.9u4+.
1682 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1683 columns in annotation row
1686 <!-- JAL-2913 -->Preferences panel's ID Width control is
1687 not honored in batch mode
1690 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1691 for structures added to existing Jmol view
1694 <!-- JAL-2223 -->'View Mappings' includes duplicate
1695 entries after importing project with multiple views
1698 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1699 protein sequences via SIFTS from associated PDB entries
1700 with negative residue numbers or missing residues fails
1703 <!-- JAL-2952 -->Exception when shading sequence with
1704 negative Temperature Factor values from annotated PDB
1705 files (e.g. as generated by CONSURF)
1708 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1709 tooltip doesn't include a text description of mutation
1712 <!-- JAL-2922 -->Invert displayed features very slow when
1713 structure and/or overview windows are also shown
1716 <!-- JAL-2954 -->Selecting columns from highlighted
1717 regions very slow for alignments with large numbers of
1721 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1722 with 'StringIndexOutOfBounds'
1725 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and
1726 Feel for OSX platforms running Java 10
1729 <!-- JAL-2960 -->Adding a structure to existing structure
1730 view appears to do nothing because the view is hidden
1731 behind the alignment view
1737 <!-- JAL-2926 -->Copy consensus sequence option in applet
1738 should copy the group consensus when popup is opened on it
1744 <!-- JAL-2913 -->Fixed ID width preference is not
1748 <em>New Known Defects</em>
1751 <!-- JAL-2973 --> Exceptions occasionally raised when
1752 editing a large alignment and overview is displayed
1755 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1756 repeatedly after a series of edits even when the overview
1757 is no longer reflecting updates
1760 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1761 structures for protein subsequence (if 'Trim Retrieved
1762 Sequences' enabled) or Ensembl isoforms (Workaround in
1763 2.10.4 is to fail back to N&W mapping)
1766 <!-- JAL-2990 -->Export Annotations from File Menu with
1767 CSV option gives blank output
1773 <td width="60" nowrap>
1774 <div align="center">
1775 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br />
1776 <em>24/1/2018</em></strong>
1779 <td><div align="left">
1781 <li>Updated Certum Codesigning Certificate (Valid till
1782 30th November 2018)</li>
1785 <td><div align="left">
1790 <!-- JAL-2859-->Only one structure is loaded when
1791 several sequences and structures are selected for
1795 <!-- JAL-2851-->Alignment doesn't appear to scroll
1796 vertically via trackpad and scrollwheel
1799 <!-- JAL-2842-->Jalview hangs if up/down arrows pressed
1800 in cursor mode when cursor lies in hidden region at
1804 <!-- JAL-2827-->Helix annotation has 'notches' when
1805 scrolled into view if columns are hidden
1808 <!-- JAL-2740-->Annotation column filter can be slow to
1809 reset (ie after hitting cancel) for large numbers of
1813 <!-- JAL-2849-->User preference for disabling inclusion
1814 of sequence limits when exporting as flat file has no
1818 <!-- JAL-2679-->Reproducible cross-reference
1819 relationships when retrieving sequences from
1826 <td width="60" nowrap>
1827 <div align="center">
1828 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1831 <td><div align="left">
1835 <!-- JAL-2446 -->Faster and more efficient management and
1836 rendering of sequence features
1839 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1840 429 rate limit request hander
1843 <!-- JAL-2773 -->Structure views don't get updated unless
1844 their colours have changed
1847 <!-- JAL-2495 -->All linked sequences are highlighted for
1848 a structure mousover (Jmol) or selection (Chimera)
1851 <!-- JAL-2790 -->'Cancel' button in progress bar for
1852 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1855 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1856 view from Ensembl locus cross-references
1859 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1863 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1864 feature can be disabled
1867 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1868 PDB easier retrieval of sequences for lists of IDs
1871 <!-- JAL-2758 -->Short names for sequences retrieved from
1877 <li>Groovy interpreter updated to 2.4.12</li>
1878 <li>Example groovy script for generating a matrix of
1879 percent identity scores for current alignment.</li>
1881 <em>Testing and Deployment</em>
1884 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1888 <td><div align="left">
1892 <!-- JAL-2643 -->Pressing tab after updating the colour
1893 threshold text field doesn't trigger an update to the
1897 <!-- JAL-2682 -->Race condition when parsing sequence ID
1901 <!-- JAL-2608 -->Overview windows are also closed when
1902 alignment window is closed
1905 <!-- JAL-2548 -->Export of features doesn't always respect
1909 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1910 takes a long time in Cursor mode
1916 <!-- JAL-2777 -->Structures with whitespace chainCode
1917 cannot be viewed in Chimera
1920 <!-- JAL-2728 -->Protein annotation panel too high in
1924 <!-- JAL-2757 -->Can't edit the query after the server
1925 error warning icon is shown in Uniprot and PDB Free Text
1929 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1932 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1935 <!-- JAL-2739 -->Hidden column marker in last column not
1936 rendered when switching back from Wrapped to normal view
1939 <!-- JAL-2768 -->Annotation display corrupted when
1940 scrolling right in unwapped alignment view
1943 <!-- JAL-2542 -->Existing features on subsequence
1944 incorrectly relocated when full sequence retrieved from
1948 <!-- JAL-2733 -->Last reported memory still shown when
1949 Desktop->Show Memory is unticked (OSX only)
1952 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1953 features of same type and group to be selected for
1957 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1958 alignments when hidden columns are present
1961 <!-- JAL-2392 -->Jalview freezes when loading and
1962 displaying several structures
1965 <!-- JAL-2732 -->Black outlines left after resizing or
1969 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1970 within the Jalview desktop on OSX
1973 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1974 when in wrapped alignment mode
1977 <!-- JAL-2636 -->Scale mark not shown when close to right
1978 hand end of alignment
1981 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1982 each selected sequence do not have correct start/end
1986 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1987 after canceling the Alignment Window's Font dialog
1990 <!-- JAL-2036 -->Show cross-references not enabled after
1991 restoring project until a new view is created
1994 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1995 URL links appears when only default EMBL-EBI link is
1996 configured (since 2.10.2b2)
1999 <!-- JAL-2775 -->Overview redraws whole window when box
2000 position is adjusted
2003 <!-- JAL-2225 -->Structure viewer doesn't map all chains
2004 in a multi-chain structure when viewing alignment
2005 involving more than one chain (since 2.10)
2008 <!-- JAL-2811 -->Double residue highlights in cursor mode
2009 if new selection moves alignment window
2012 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
2013 arrow key in cursor mode to pass hidden column marker
2016 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
2017 that produces correctly annotated transcripts and products
2020 <!-- JAL-2776 -->Toggling a feature group after first time
2021 doesn't update associated structure view
2024 <em>Applet</em><br />
2027 <!-- JAL-2687 -->Concurrent modification exception when
2028 closing alignment panel
2031 <em>BioJSON</em><br />
2034 <!-- JAL-2546 -->BioJSON export does not preserve
2035 non-positional features
2038 <em>New Known Issues</em>
2041 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
2042 sequence features correctly (for many previous versions of
2046 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
2047 using cursor in wrapped panel other than top
2050 <!-- JAL-2791 -->Select columns containing feature ignores
2051 graduated colour threshold
2054 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
2055 always preserve numbering and sequence features
2058 <em>Known Java 9 Issues</em>
2061 <!-- JAL-2902 -->Groovy Console very slow to open and is
2062 not responsive when entering characters (Webstart, Java
2069 <td width="60" nowrap>
2070 <div align="center">
2071 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
2072 <em>2/10/2017</em></strong>
2075 <td><div align="left">
2076 <em>New features in Jalview Desktop</em>
2079 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API
2083 <!-- JAL-2745 -->HTTPS used for all connections to
2088 <td><div align="left"></div></td>
2091 <td width="60" nowrap>
2092 <div align="center">
2093 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
2094 <em>7/9/2017</em></strong>
2097 <td><div align="left">
2101 <!-- JAL-2588 -->Show gaps in overview window by colouring
2102 in grey (sequences used to be coloured grey, and gaps were
2106 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
2110 <!-- JAL-2587 -->Overview updates immediately on increase
2111 in size and progress bar shown as higher resolution
2112 overview is recalculated
2117 <td><div align="left">
2121 <!-- JAL-2664 -->Overview window redraws every hidden
2122 column region row by row
2125 <!-- JAL-2681 -->duplicate protein sequences shown after
2126 retrieving Ensembl crossrefs for sequences from Uniprot
2129 <!-- JAL-2603 -->Overview window throws NPE if show boxes
2130 format setting is unticked
2133 <!-- JAL-2610 -->Groups are coloured wrongly in overview
2134 if group has show boxes format setting unticked
2137 <!-- JAL-2672,JAL-2665 -->Redraw problems when
2138 autoscrolling whilst dragging current selection group to
2139 include sequences and columns not currently displayed
2142 <!-- JAL-2691 -->Not all chains are mapped when multimeric
2143 assemblies are imported via CIF file
2146 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
2147 displayed when threshold or conservation colouring is also
2151 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
2155 <!-- JAL-2673 -->Jalview continues to scroll after
2156 dragging a selected region off the visible region of the
2160 <!-- JAL-2724 -->Cannot apply annotation based
2161 colourscheme to all groups in a view
2164 <!-- JAL-2511 -->IDs don't line up with sequences
2165 initially after font size change using the Font chooser or
2172 <td width="60" nowrap>
2173 <div align="center">
2174 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
2177 <td><div align="left">
2178 <em>Calculations</em>
2182 <!-- JAL-1933 -->Occupancy annotation row shows number of
2183 ungapped positions in each column of the alignment.
2186 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
2187 a calculation dialog box
2190 <!-- JAL-2379 -->Revised implementation of PCA for speed
2191 and memory efficiency (~30x faster)
2194 <!-- JAL-2403 -->Revised implementation of sequence
2195 similarity scores as used by Tree, PCA, Shading Consensus
2196 and other calculations
2199 <!-- JAL-2416 -->Score matrices are stored as resource
2200 files within the Jalview codebase
2203 <!-- JAL-2500 -->Trees computed on Sequence Feature
2204 Similarity may have different topology due to increased
2211 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
2212 model for alignments and groups
2215 <!-- JAL-384 -->Custom shading schemes created via groovy
2222 <!-- JAL-2526 -->Efficiency improvements for interacting
2223 with alignment and overview windows
2226 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
2230 <!-- JAL-2388 -->Hidden columns and sequences can be
2234 <!-- JAL-2611 -->Click-drag in visible area allows fine
2235 adjustment of visible position
2239 <em>Data import/export</em>
2242 <!-- JAL-2535 -->Posterior probability annotation from
2243 Stockholm files imported as sequence associated annotation
2246 <!-- JAL-2507 -->More robust per-sequence positional
2247 annotation input/output via stockholm flatfile
2250 <!-- JAL-2533 -->Sequence names don't include file
2251 extension when importing structure files without embedded
2252 names or PDB accessions
2255 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
2256 format sequence substitution matrices
2259 <em>User Interface</em>
2262 <!-- JAL-2447 --> Experimental Features Checkbox in
2263 Desktop's Tools menu to hide or show untested features in
2267 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
2268 via Overview or sequence motif search operations
2271 <!-- JAL-2547 -->Amend sequence features dialog box can be
2272 opened by double clicking gaps within sequence feature
2276 <!-- JAL-1476 -->Status bar message shown when not enough
2277 aligned positions were available to create a 3D structure
2281 <em>3D Structure</em>
2284 <!-- JAL-2430 -->Hidden regions in alignment views are not
2285 coloured in linked structure views
2288 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
2289 file-based command exchange
2292 <!-- JAL-2375 -->Structure chooser automatically shows
2293 Cached Structures rather than querying the PDBe if
2294 structures are already available for sequences
2297 <!-- JAL-2520 -->Structures imported via URL are cached in
2298 the Jalview project rather than downloaded again when the
2299 project is reopened.
2302 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
2303 to transfer Chimera's structure attributes as Jalview
2304 features, and vice-versa (<strong>Experimental
2308 <em>Web Services</em>
2311 <!-- JAL-2549 -->Updated JABAWS client to v2.2
2314 <!-- JAL-2335 -->Filter non-standard amino acids and
2315 nucleotides when submitting to AACon and other MSA
2319 <!-- JAL-2316, -->URLs for viewing database
2320 cross-references provided by identifiers.org and the
2321 EMBL-EBI's MIRIAM DB
2328 <!-- JAL-2344 -->FileFormatI interface for describing and
2329 identifying file formats (instead of String constants)
2332 <!-- JAL-2228 -->FeatureCounter script refactored for
2333 efficiency when counting all displayed features (not
2334 backwards compatible with 2.10.1)
2337 <em>Example files</em>
2340 <!-- JAL-2631 -->Graduated feature colour style example
2341 included in the example feature file
2344 <em>Documentation</em>
2347 <!-- JAL-2339 -->Release notes reformatted for readability
2348 with the built-in Java help viewer
2351 <!-- JAL-1644 -->Find documentation updated with 'search
2352 sequence description' option
2358 <!-- JAL-2485, -->External service integration tests for
2359 Uniprot REST Free Text Search Client
2362 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
2365 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
2370 <td><div align="left">
2371 <em>Calculations</em>
2374 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
2375 matrix - C->R should be '-3'<br />Old matrix restored
2376 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
2378 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
2379 Jalview's treatment of gaps in PCA and substitution matrix
2380 based Tree calculations.<br /> <br />In earlier versions
2381 of Jalview, gaps matching gaps were penalised, and gaps
2382 matching non-gaps penalised even more. In the PCA
2383 calculation, gaps were actually treated as non-gaps - so
2384 different costs were applied, which meant Jalview's PCAs
2385 were different to those produced by SeqSpace.<br />Jalview
2386 now treats gaps in the same way as SeqSpace (ie it scores
2387 them as 0). <br /> <br />Enter the following in the
2388 Groovy console to restore pre-2.10.2 behaviour:<br />
2389 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
2390 // for 2.10.1 mode <br />
2391 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
2392 // to restore 2.10.2 mode <br /> <br /> <em>Note:
2393 these settings will affect all subsequent tree and PCA
2394 calculations (not recommended)</em></li>
2396 <!-- JAL-2424 -->Fixed off-by-one bug that affected
2397 scaling of branch lengths for trees computed using
2398 Sequence Feature Similarity.
2401 <!-- JAL-2377 -->PCA calculation could hang when
2402 generating output report when working with highly
2403 redundant alignments
2406 <!-- JAL-2544 --> Sort by features includes features to
2407 right of selected region when gaps present on right-hand
2411 <em>User Interface</em>
2414 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2415 doesn't reselect a specific sequence's associated
2416 annotation after it was used for colouring a view
2419 <!-- JAL-2419 -->Current selection lost if popup menu
2420 opened on a region of alignment without groups
2423 <!-- JAL-2374 -->Popup menu not always shown for regions
2424 of an alignment with overlapping groups
2427 <!-- JAL-2310 -->Finder double counts if both a sequence's
2428 name and description match
2431 <!-- JAL-2370 -->Hiding column selection containing two
2432 hidden regions results in incorrect hidden regions
2435 <!-- JAL-2386 -->'Apply to all groups' setting when
2436 changing colour does not apply Conservation slider value
2440 <!-- JAL-2373 -->Percentage identity and conservation menu
2441 items do not show a tick or allow shading to be disabled
2444 <!-- JAL-2385 -->Conservation shading or PID threshold
2445 lost when base colourscheme changed if slider not visible
2448 <!-- JAL-2547 -->Sequence features shown in tooltip for
2449 gaps before start of features
2452 <!-- JAL-2623 -->Graduated feature colour threshold not
2453 restored to UI when feature colour is edited
2456 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2457 a time when scrolling vertically in wrapped mode.
2460 <!-- JAL-2630 -->Structure and alignment overview update
2461 as graduate feature colour settings are modified via the
2465 <!-- JAL-2034 -->Overview window doesn't always update
2466 when a group defined on the alignment is resized
2469 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2470 wrapped view result in positional status updates
2474 <!-- JAL-2563 -->Status bar doesn't show position for
2475 ambiguous amino acid and nucleotide symbols
2478 <!-- JAL-2602 -->Copy consensus sequence failed if
2479 alignment included gapped columns
2482 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2483 widgets don't permanently disappear
2486 <!-- JAL-2503 -->Cannot select or filter quantitative
2487 annotation that are shown only as column labels (e.g.
2488 T-Coffee column reliability scores)
2491 <!-- JAL-2594 -->Exception thrown if trying to create a
2492 sequence feature on gaps only
2495 <!-- JAL-2504 -->Features created with 'New feature'
2496 button from a Find inherit previously defined feature type
2497 rather than the Find query string
2500 <!-- JAL-2423 -->incorrect title in output window when
2501 exporting tree calculated in Jalview
2504 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2505 and then revealing them reorders sequences on the
2509 <!-- JAL-964 -->Group panel in sequence feature settings
2510 doesn't update to reflect available set of groups after
2511 interactively adding or modifying features
2514 <!-- JAL-2225 -->Sequence Database chooser unusable on
2518 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2519 only excluded gaps in current sequence and ignored
2526 <!-- JAL-2421 -->Overview window visible region moves
2527 erratically when hidden rows or columns are present
2530 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2531 Structure Viewer's colour menu don't correspond to
2535 <!-- JAL-2405 -->Protein specific colours only offered in
2536 colour and group colour menu for protein alignments
2539 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2540 reflect currently selected view or group's shading
2544 <!-- JAL-2624 -->Feature colour thresholds not respected
2545 when rendered on overview and structures when opacity at
2549 <!-- JAL-2589 -->User defined gap colour not shown in
2550 overview when features overlaid on alignment
2553 <!-- JAL-2567 -->Feature settings for different views not
2554 recovered correctly from Jalview project file
2557 <!-- JAL-2256 -->Feature colours in overview when first
2558 opened (automatically via preferences) are different to
2559 the main alignment panel
2562 <em>Data import/export</em>
2565 <!-- JAL-2576 -->Very large alignments take a long time to
2569 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2570 added after a sequence was imported are not written to
2574 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2575 when importing RNA secondary structure via Stockholm
2578 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2579 not shown in correct direction for simple pseudoknots
2582 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2583 with lightGray or darkGray via features file (but can
2587 <!-- JAL-2383 -->Above PID colour threshold not recovered
2588 when alignment view imported from project
2591 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2592 structure and sequences extracted from structure files
2593 imported via URL and viewed in Jmol
2596 <!-- JAL-2520 -->Structures loaded via URL are saved in
2597 Jalview Projects rather than fetched via URL again when
2598 the project is loaded and the structure viewed
2601 <em>Web Services</em>
2604 <!-- JAL-2519 -->EnsemblGenomes example failing after
2605 release of Ensembl v.88
2608 <!-- JAL-2366 -->Proxy server address and port always
2609 appear enabled in Preferences->Connections
2612 <!-- JAL-2461 -->DAS registry not found exceptions
2613 removed from console output
2616 <!-- JAL-2582 -->Cannot retrieve protein products from
2617 Ensembl by Peptide ID
2620 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2621 created from SIFTs, and spurious 'Couldn't open structure
2622 in Chimera' errors raised after April 2017 update (problem
2623 due to 'null' string rather than empty string used for
2624 residues with no corresponding PDB mapping).
2627 <em>Application UI</em>
2630 <!-- JAL-2361 -->User Defined Colours not added to Colour
2634 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2635 case' residues (button in colourscheme editor debugged and
2636 new documentation and tooltips added)
2639 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2640 doesn't restore group-specific text colour thresholds
2643 <!-- JAL-2243 -->Feature settings panel does not update as
2644 new features are added to alignment
2647 <!-- JAL-2532 -->Cancel in feature settings reverts
2648 changes to feature colours via the Amend features dialog
2651 <!-- JAL-2506 -->Null pointer exception when attempting to
2652 edit graduated feature colour via amend features dialog
2656 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2657 selection menu changes colours of alignment views
2660 <!-- JAL-2426 -->Spurious exceptions in console raised
2661 from alignment calculation workers after alignment has
2665 <!-- JAL-1608 -->Typo in selection popup menu - Create
2666 groups now 'Create Group'
2669 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2670 Create/Undefine group doesn't always work
2673 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2674 shown again after pressing 'Cancel'
2677 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2678 adjusts start position in wrap mode
2681 <!-- JAL-2563 -->Status bar doesn't show positions for
2682 ambiguous amino acids
2685 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2686 CDS/Protein view after CDS sequences added for aligned
2690 <!-- JAL-2592 -->User defined colourschemes called 'User
2691 Defined' don't appear in Colours menu
2697 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2698 score models doesn't always result in an updated PCA plot
2701 <!-- JAL-2442 -->Features not rendered as transparent on
2702 overview or linked structure view
2705 <!-- JAL-2372 -->Colour group by conservation doesn't
2709 <!-- JAL-2517 -->Hitting Cancel after applying
2710 user-defined colourscheme doesn't restore original
2717 <!-- JAL-2314 -->Unit test failure:
2718 jalview.ws.jabaws.RNAStructExportImport setup fails
2721 <!-- JAL-2307 -->Unit test failure:
2722 jalview.ws.sifts.SiftsClientTest due to compatibility
2723 problems with deep array comparison equality asserts in
2724 successive versions of TestNG
2727 <!-- JAL-2479 -->Relocated StructureChooserTest and
2728 ParameterUtilsTest Unit tests to Network suite
2731 <em>New Known Issues</em>
2734 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2735 phase after a sequence motif find operation
2738 <!-- JAL-2550 -->Importing annotation file with rows
2739 containing just upper and lower case letters are
2740 interpreted as WUSS RNA secondary structure symbols
2743 <!-- JAL-2590 -->Cannot load and display Newick trees
2744 reliably from eggnog Ortholog database
2747 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2748 containing features of type Highlight' when 'B' is pressed
2749 to mark columns containing highlighted regions.
2752 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2753 doesn't always add secondary structure annotation.
2758 <td width="60" nowrap>
2759 <div align="center">
2760 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2763 <td><div align="left">
2767 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2768 for all consensus calculations
2771 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2774 <li>Updated Jalview's Certum code signing certificate
2777 <em>Application</em>
2780 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2781 set of database cross-references, sorted alphabetically
2784 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2785 from database cross references. Users with custom links
2786 will receive a <a href="webServices/urllinks.html#warning">warning
2787 dialog</a> asking them to update their preferences.
2790 <!-- JAL-2287-->Cancel button and escape listener on
2791 dialog warning user about disconnecting Jalview from a
2795 <!-- JAL-2320-->Jalview's Chimera control window closes if
2796 the Chimera it is connected to is shut down
2799 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2800 columns menu item to mark columns containing highlighted
2801 regions (e.g. from structure selections or results of a
2805 <!-- JAL-2284-->Command line option for batch-generation
2806 of HTML pages rendering alignment data with the BioJS
2816 <!-- JAL-2286 -->Columns with more than one modal residue
2817 are not coloured or thresholded according to percent
2818 identity (first observed in Jalview 2.8.2)
2821 <!-- JAL-2301 -->Threonine incorrectly reported as not
2825 <!-- JAL-2318 -->Updates to documentation pages (above PID
2826 threshold, amino acid properties)
2829 <!-- JAL-2292 -->Lower case residues in sequences are not
2830 reported as mapped to residues in a structure file in the
2834 <!--JAL-2324 -->Identical features with non-numeric scores
2835 could be added multiple times to a sequence
2838 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2839 bond features shown as two highlighted residues rather
2840 than a range in linked structure views, and treated
2841 correctly when selecting and computing trees from features
2844 <!-- JAL-2281-->Custom URL links for database
2845 cross-references are matched to database name regardless
2850 <em>Application</em>
2853 <!-- JAL-2282-->Custom URL links for specific database
2854 names without regular expressions also offer links from
2858 <!-- JAL-2315-->Removing a single configured link in the
2859 URL links pane in Connections preferences doesn't actually
2860 update Jalview configuration
2863 <!-- JAL-2272-->CTRL-Click on a selected region to open
2864 the alignment area popup menu doesn't work on El-Capitan
2867 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2868 files with similarly named sequences if dropped onto the
2872 <!-- JAL-2312 -->Additional mappings are shown for PDB
2873 entries where more chains exist in the PDB accession than
2874 are reported in the SIFTS file
2877 <!-- JAL-2317-->Certain structures do not get mapped to
2878 the structure view when displayed with Chimera
2881 <!-- JAL-2317-->No chains shown in the Chimera view
2882 panel's View->Show Chains submenu
2885 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2886 work for wrapped alignment views
2889 <!--JAL-2197 -->Rename UI components for running JPred
2890 predictions from 'JNet' to 'JPred'
2893 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2894 corrupted when annotation panel vertical scroll is not at
2895 first annotation row
2898 <!--JAL-2332 -->Attempting to view structure for Hen
2899 lysozyme results in a PDB Client error dialog box
2902 <!-- JAL-2319 -->Structure View's mapping report switched
2903 ranges for PDB and sequence for SIFTS
2906 SIFTS 'Not_Observed' residues mapped to non-existant
2910 <!-- <em>New Known Issues</em>
2917 <td width="60" nowrap>
2918 <div align="center">
2919 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2920 <em>25/10/2016</em></strong>
2923 <td><em>Application</em>
2925 <li>3D Structure chooser opens with 'Cached structures'
2926 view if structures already loaded</li>
2927 <li>Progress bar reports models as they are loaded to
2928 structure views</li>
2934 <li>Colour by conservation always enabled and no tick
2935 shown in menu when BLOSUM or PID shading applied</li>
2936 <li>FER1_ARATH and FER2_ARATH labels were switched in
2937 example sequences/projects/trees</li>
2939 <em>Application</em>
2941 <li>Jalview projects with views of local PDB structure
2942 files saved on Windows cannot be opened on OSX</li>
2943 <li>Multiple structure views can be opened and superposed
2944 without timeout for structures with multiple models or
2945 multiple sequences in alignment</li>
2946 <li>Cannot import or associated local PDB files without a
2947 PDB ID HEADER line</li>
2948 <li>RMSD is not output in Jmol console when superposition
2950 <li>Drag and drop of URL from Browser fails for Linux and
2951 OSX versions earlier than El Capitan</li>
2952 <li>ENA client ignores invalid content from ENA server</li>
2953 <li>Exceptions are not raised in console when ENA client
2954 attempts to fetch non-existent IDs via Fetch DB Refs UI
2956 <li>Exceptions are not raised in console when a new view
2957 is created on the alignment</li>
2958 <li>OSX right-click fixed for group selections: CMD-click
2959 to insert/remove gaps in groups and CTRL-click to open group
2962 <em>Build and deployment</em>
2964 <li>URL link checker now copes with multi-line anchor
2967 <em>New Known Issues</em>
2969 <li>Drag and drop from URL links in browsers do not work
2976 <td width="60" nowrap>
2977 <div align="center">
2978 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2981 <td><em>General</em>
2984 <!-- JAL-2124 -->Updated Spanish translations.
2987 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2988 for importing structure data to Jalview. Enables mmCIF and
2992 <!-- JAL-192 --->Alignment ruler shows positions relative to
2996 <!-- JAL-2202 -->Position/residue shown in status bar when
2997 mousing over sequence associated annotation
3000 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
3004 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
3005 '()', canonical '[]' and invalid '{}' base pair populations
3009 <!-- JAL-2092 -->Feature settings popup menu options for
3010 showing or hiding columns containing a feature
3013 <!-- JAL-1557 -->Edit selected group by double clicking on
3014 group and sequence associated annotation labels
3017 <!-- JAL-2236 -->Sequence name added to annotation label in
3018 select/hide columns by annotation and colour by annotation
3022 </ul> <em>Application</em>
3025 <!-- JAL-2050-->Automatically hide introns when opening a
3026 gene/transcript view
3029 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
3033 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
3034 structure mappings with the EMBL-EBI PDBe SIFTS database
3037 <!-- JAL-2079 -->Updated download sites used for Rfam and
3038 Pfam sources to xfam.org
3041 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
3044 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
3045 over sequences in Jalview
3048 <!-- JAL-2027-->Support for reverse-complement coding
3049 regions in ENA and EMBL
3052 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
3053 for record retrieval via ENA rest API
3056 <!-- JAL-2027 -->Support for ENA CDS records with reverse
3060 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
3061 groovy script execution
3064 <!-- JAL-1812 -->New 'execute Groovy script' option in an
3065 alignment window's Calculate menu
3068 <!-- JAL-1812 -->Allow groovy scripts that call
3069 Jalview.getAlignFrames() to run in headless mode
3072 <!-- JAL-2068 -->Support for creating new alignment
3073 calculation workers from groovy scripts
3076 <!-- JAL-1369 --->Store/restore reference sequence in
3080 <!-- JAL-1803 -->Chain codes for a sequence's PDB
3081 associations are now saved/restored from project
3084 <!-- JAL-1993 -->Database selection dialog always shown
3085 before sequence fetcher is opened
3088 <!-- JAL-2183 -->Double click on an entry in Jalview's
3089 database chooser opens a sequence fetcher
3092 <!-- JAL-1563 -->Free-text search client for UniProt using
3093 the UniProt REST API
3096 <!-- JAL-2168 -->-nonews command line parameter to prevent
3097 the news reader opening
3100 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
3101 querying stored in preferences
3104 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
3108 <!-- JAL-1977-->Tooltips shown on database chooser
3111 <!-- JAL-391 -->Reverse complement function in calculate
3112 menu for nucleotide sequences
3115 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
3116 and feature counts preserves alignment ordering (and
3117 debugged for complex feature sets).
3120 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
3121 viewing structures with Jalview 2.10
3124 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
3125 genome, transcript CCDS and gene ids via the Ensembl and
3126 Ensembl Genomes REST API
3129 <!-- JAL-2049 -->Protein sequence variant annotation
3130 computed for 'sequence_variant' annotation on CDS regions
3134 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
3138 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
3139 Ref Fetcher fails to match, or otherwise updates sequence
3140 data from external database records.
3143 <!-- JAL-2154 -->Revised Jalview Project format for
3144 efficient recovery of sequence coding and alignment
3145 annotation relationships.
3147 </ul> <!-- <em>Applet</em>
3158 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
3162 <!-- JAL-2018-->Export features in Jalview format (again)
3163 includes graduated colourschemes
3166 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
3167 working with big alignments and lots of hidden columns
3170 <!-- JAL-2053-->Hidden column markers not always rendered
3171 at right of alignment window
3174 <!-- JAL-2067 -->Tidied up links in help file table of
3178 <!-- JAL-2072 -->Feature based tree calculation not shown
3182 <!-- JAL-2075 -->Hidden columns ignored during feature
3183 based tree calculation
3186 <!-- JAL-2065 -->Alignment view stops updating when show
3187 unconserved enabled for group on alignment
3190 <!-- JAL-2086 -->Cannot insert gaps into sequence when
3194 <!-- JAL-2146 -->Alignment column in status incorrectly
3195 shown as "Sequence position" when mousing over
3199 <!-- JAL-2099 -->Incorrect column numbers in ruler when
3200 hidden columns present
3203 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
3204 user created annotation added to alignment
3207 <!-- JAL-1841 -->RNA Structure consensus only computed for
3208 '()' base pair annotation
3211 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
3212 in zero scores for all base pairs in RNA Structure
3216 <!-- JAL-2174-->Extend selection with columns containing
3220 <!-- JAL-2275 -->Pfam format writer puts extra space at
3221 beginning of sequence
3224 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
3228 <!-- JAL-2238 -->Cannot create groups on an alignment from
3229 from a tree when t-coffee scores are shown
3232 <!-- JAL-1836,1967 -->Cannot import and view PDB
3233 structures with chains containing negative resnums (4q4h)
3236 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
3240 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
3241 to Clustal, PIR and PileUp output
3244 <!-- JAL-2008 -->Reordering sequence features that are
3245 not visible causes alignment window to repaint
3248 <!-- JAL-2006 -->Threshold sliders don't work in
3249 graduated colour and colour by annotation row for e-value
3250 scores associated with features and annotation rows
3253 <!-- JAL-1797 -->amino acid physicochemical conservation
3254 calculation should be case independent
3257 <!-- JAL-2173 -->Remove annotation also updates hidden
3261 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
3262 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
3263 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
3266 <!-- JAL-2065 -->Null pointer exceptions and redraw
3267 problems when reference sequence defined and 'show
3268 non-conserved' enabled
3271 <!-- JAL-1306 -->Quality and Conservation are now shown on
3272 load even when Consensus calculation is disabled
3275 <!-- JAL-1932 -->Remove right on penultimate column of
3276 alignment does nothing
3279 <em>Application</em>
3282 <!-- JAL-1552-->URLs and links can't be imported by
3283 drag'n'drop on OSX when launched via webstart (note - not
3284 yet fixed for El Capitan)
3287 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
3288 output when running on non-gb/us i18n platforms
3291 <!-- JAL-1944 -->Error thrown when exporting a view with
3292 hidden sequences as flat-file alignment
3295 <!-- JAL-2030-->InstallAnywhere distribution fails when
3299 <!-- JAL-2080-->Jalview very slow to launch via webstart
3300 (also hotfix for 2.9.0b2)
3303 <!-- JAL-2085 -->Cannot save project when view has a
3304 reference sequence defined
3307 <!-- JAL-1011 -->Columns are suddenly selected in other
3308 alignments and views when revealing hidden columns
3311 <!-- JAL-1989 -->Hide columns not mirrored in complement
3312 view in a cDNA/Protein splitframe
3315 <!-- JAL-1369 -->Cannot save/restore representative
3316 sequence from project when only one sequence is
3320 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
3321 in Structure Chooser
3324 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
3325 structure consensus didn't refresh annotation panel
3328 <!-- JAL-1962 -->View mapping in structure view shows
3329 mappings between sequence and all chains in a PDB file
3332 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
3333 dialogs format columns correctly, don't display array
3334 data, sort columns according to type
3337 <!-- JAL-1975 -->Export complete shown after destination
3338 file chooser is cancelled during an image export
3341 <!-- JAL-2025 -->Error when querying PDB Service with
3342 sequence name containing special characters
3345 <!-- JAL-2024 -->Manual PDB structure querying should be
3349 <!-- JAL-2104 -->Large tooltips with broken HTML
3350 formatting don't wrap
3353 <!-- JAL-1128 -->Figures exported from wrapped view are
3354 truncated so L looks like I in consensus annotation
3357 <!-- JAL-2003 -->Export features should only export the
3358 currently displayed features for the current selection or
3362 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
3363 after fetching cross-references, and restoring from
3367 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
3368 followed in the structure viewer
3371 <!-- JAL-2163 -->Titles for individual alignments in
3372 splitframe not restored from project
3375 <!-- JAL-2145 -->missing autocalculated annotation at
3376 trailing end of protein alignment in transcript/product
3377 splitview when pad-gaps not enabled by default
3380 <!-- JAL-1797 -->amino acid physicochemical conservation
3384 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
3385 article has been read (reopened issue due to
3386 internationalisation problems)
3389 <!-- JAL-1960 -->Only offer PDB structures in structure
3390 viewer based on sequence name, PDB and UniProt
3395 <!-- JAL-1976 -->No progress bar shown during export of
3399 <!-- JAL-2213 -->Structures not always superimposed after
3400 multiple structures are shown for one or more sequences.
3403 <!-- JAL-1370 -->Reference sequence characters should not
3404 be replaced with '.' when 'Show unconserved' format option
3408 <!-- JAL-1823 -->Cannot specify chain code when entering
3409 specific PDB id for sequence
3412 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3413 'Export hidden sequences' is enabled, but 'export hidden
3414 columns' is disabled.
3417 <!--JAL-2026-->Best Quality option in structure chooser
3418 selects lowest rather than highest resolution structures
3422 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3423 to sequence mapping in 'View Mappings' report
3426 <!-- JAL-2284 -->Unable to read old Jalview projects that
3427 contain non-XML data added after Jalvew wrote project.
3430 <!-- JAL-2118 -->Newly created annotation row reorders
3431 after clicking on it to create new annotation for a
3435 <!-- JAL-1980 -->Null Pointer Exception raised when
3436 pressing Add on an orphaned cut'n'paste window.
3438 <!-- may exclude, this is an external service stability issue JAL-1941
3439 -- > RNA 3D structure not added via DSSR service</li> -->
3444 <!-- JAL-2151 -->Incorrect columns are selected when
3445 hidden columns present before start of sequence
3448 <!-- JAL-1986 -->Missing dependencies on applet pages
3452 <!-- JAL-1947 -->Overview pixel size changes when
3453 sequences are hidden in applet
3456 <!-- JAL-1996 -->Updated instructions for applet
3457 deployment on examples pages.
3464 <td width="60" nowrap>
3465 <div align="center">
3466 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3467 <em>16/10/2015</em></strong>
3470 <td><em>General</em>
3472 <li>Time stamps for signed Jalview application and applet
3477 <em>Application</em>
3479 <li>Duplicate group consensus and conservation rows
3480 shown when tree is partitioned</li>
3481 <li>Erratic behaviour when tree partitions made with
3482 multiple cDNA/Protein split views</li>
3488 <td width="60" nowrap>
3489 <div align="center">
3490 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3491 <em>8/10/2015</em></strong>
3494 <td><em>General</em>
3496 <li>Updated Spanish translations of localized text for
3498 </ul> <em>Application</em>
3500 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3501 <li>Signed OSX InstallAnywhere installer<br></li>
3502 <li>Support for per-sequence based annotations in BioJSON</li>
3503 </ul> <em>Applet</em>
3505 <li>Split frame example added to applet examples page</li>
3506 </ul> <em>Build and Deployment</em>
3509 <!-- JAL-1888 -->New ant target for running Jalview's test
3517 <li>Mapping of cDNA to protein in split frames
3518 incorrect when sequence start > 1</li>
3519 <li>Broken images in filter column by annotation dialog
3521 <li>Feature colours not parsed from features file</li>
3522 <li>Exceptions and incomplete link URLs recovered when
3523 loading a features file containing HTML tags in feature
3527 <em>Application</em>
3529 <li>Annotations corrupted after BioJS export and
3531 <li>Incorrect sequence limits after Fetch DB References
3532 with 'trim retrieved sequences'</li>
3533 <li>Incorrect warning about deleting all data when
3534 deleting selected columns</li>
3535 <li>Patch to build system for shipping properly signed
3536 JNLP templates for webstart launch</li>
3537 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3538 unreleased structures for download or viewing</li>
3539 <li>Tab/space/return keystroke operation of EMBL-PDBe
3540 fetcher/viewer dialogs works correctly</li>
3541 <li>Disabled 'minimise' button on Jalview windows
3542 running on OSX to workaround redraw hang bug</li>
3543 <li>Split cDNA/Protein view position and geometry not
3544 recovered from jalview project</li>
3545 <li>Initial enabled/disabled state of annotation menu
3546 sorter 'show autocalculated first/last' corresponds to
3548 <li>Restoring of Clustal, RNA Helices and T-Coffee
3549 color schemes from BioJSON</li>
3553 <li>Reorder sequences mirrored in cDNA/Protein split
3555 <li>Applet with Jmol examples not loading correctly</li>
3561 <td><div align="center">
3562 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3564 <td><em>General</em>
3566 <li>Linked visualisation and analysis of DNA and Protein
3569 <li>Translated cDNA alignments shown as split protein
3570 and DNA alignment views</li>
3571 <li>Codon consensus annotation for linked protein and
3572 cDNA alignment views</li>
3573 <li>Link cDNA or Protein product sequences by loading
3574 them onto Protein or cDNA alignments</li>
3575 <li>Reconstruct linked cDNA alignment from aligned
3576 protein sequences</li>
3579 <li>Jmol integration updated to Jmol v14.2.14</li>
3580 <li>Import and export of Jalview alignment views as <a
3581 href="features/bioJsonFormat.html">BioJSON</a></li>
3582 <li>New alignment annotation file statements for
3583 reference sequences and marking hidden columns</li>
3584 <li>Reference sequence based alignment shading to
3585 highlight variation</li>
3586 <li>Select or hide columns according to alignment
3588 <li>Find option for locating sequences by description</li>
3589 <li>Conserved physicochemical properties shown in amino
3590 acid conservation row</li>
3591 <li>Alignments can be sorted by number of RNA helices</li>
3592 </ul> <em>Application</em>
3594 <li>New cDNA/Protein analysis capabilities
3596 <li>Get Cross-References should open a Split Frame
3597 view with cDNA/Protein</li>
3598 <li>Detect when nucleotide sequences and protein
3599 sequences are placed in the same alignment</li>
3600 <li>Split cDNA/Protein views are saved in Jalview
3605 <li>Use REST API to talk to Chimera</li>
3606 <li>Selected regions in Chimera are highlighted in linked
3607 Jalview windows</li>
3609 <li>VARNA RNA viewer updated to v3.93</li>
3610 <li>VARNA views are saved in Jalview Projects</li>
3611 <li>Pseudoknots displayed as Jalview RNA annotation can
3612 be shown in VARNA</li>
3614 <li>Make groups for selection uses marked columns as well
3615 as the active selected region</li>
3617 <li>Calculate UPGMA and NJ trees using sequence feature
3619 <li>New Export options
3621 <li>New Export Settings dialog to control hidden
3622 region export in flat file generation</li>
3624 <li>Export alignment views for display with the <a
3625 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3627 <li>Export scrollable SVG in HTML page</li>
3628 <li>Optional embedding of BioJSON data when exporting
3629 alignment figures to HTML</li>
3631 <li>3D structure retrieval and display
3633 <li>Free text and structured queries with the PDBe
3635 <li>PDBe Search API based discovery and selection of
3636 PDB structures for a sequence set</li>
3640 <li>JPred4 employed for protein secondary structure
3642 <li>Hide Insertions menu option to hide unaligned columns
3643 for one or a group of sequences</li>
3644 <li>Automatically hide insertions in alignments imported
3645 from the JPred4 web server</li>
3646 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3647 system on OSX<br />LGPL libraries courtesy of <a
3648 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3650 <li>changed 'View nucleotide structure' submenu to 'View
3651 VARNA 2D Structure'</li>
3652 <li>change "View protein structure" menu option to "3D
3655 </ul> <em>Applet</em>
3657 <li>New layout for applet example pages</li>
3658 <li>New parameters to enable SplitFrame view
3659 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3660 <li>New example demonstrating linked viewing of cDNA and
3661 Protein alignments</li>
3662 </ul> <em>Development and deployment</em>
3664 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3665 <li>Include installation type and git revision in build
3666 properties and console log output</li>
3667 <li>Jalview Github organisation, and new github site for
3668 storing BioJsMSA Templates</li>
3669 <li>Jalview's unit tests now managed with TestNG</li>
3672 <!-- <em>General</em>
3674 </ul> --> <!-- issues resolved --> <em>Application</em>
3676 <li>Escape should close any open find dialogs</li>
3677 <li>Typo in select-by-features status report</li>
3678 <li>Consensus RNA secondary secondary structure
3679 predictions are not highlighted in amber</li>
3680 <li>Missing gap character in v2.7 example file means
3681 alignment appears unaligned when pad-gaps is not enabled</li>
3682 <li>First switch to RNA Helices colouring doesn't colour
3683 associated structure views</li>
3684 <li>ID width preference option is greyed out when auto
3685 width checkbox not enabled</li>
3686 <li>Stopped a warning dialog from being shown when
3687 creating user defined colours</li>
3688 <li>'View Mapping' in structure viewer shows sequence
3689 mappings for just that viewer's sequences</li>
3690 <li>Workaround for superposing PDB files containing
3691 multiple models in Chimera</li>
3692 <li>Report sequence position in status bar when hovering
3693 over Jmol structure</li>
3694 <li>Cannot output gaps as '.' symbols with Selection ->
3695 output to text box</li>
3696 <li>Flat file exports of alignments with hidden columns
3697 have incorrect sequence start/end</li>
3698 <li>'Aligning' a second chain to a Chimera structure from
3700 <li>Colour schemes applied to structure viewers don't
3701 work for nucleotide</li>
3702 <li>Loading/cut'n'pasting an empty or invalid file leads
3703 to a grey/invisible alignment window</li>
3704 <li>Exported Jpred annotation from a sequence region
3705 imports to different position</li>
3706 <li>Space at beginning of sequence feature tooltips shown
3707 on some platforms</li>
3708 <li>Chimera viewer 'View | Show Chain' menu is not
3710 <li>'New View' fails with a Null Pointer Exception in
3711 console if Chimera has been opened</li>
3712 <li>Mouseover to Chimera not working</li>
3713 <li>Miscellaneous ENA XML feature qualifiers not
3715 <li>NPE in annotation renderer after 'Extract Scores'</li>
3716 <li>If two structures in one Chimera window, mouseover of
3717 either sequence shows on first structure</li>
3718 <li>'Show annotations' options should not make
3719 non-positional annotations visible</li>
3720 <li>Subsequence secondary structure annotation not shown
3721 in right place after 'view flanking regions'</li>
3722 <li>File Save As type unset when current file format is
3724 <li>Save as '.jar' option removed for saving Jalview
3726 <li>Colour by Sequence colouring in Chimera more
3728 <li>Cannot 'add reference annotation' for a sequence in
3729 several views on same alignment</li>
3730 <li>Cannot show linked products for EMBL / ENA records</li>
3731 <li>Jalview's tooltip wraps long texts containing no
3733 </ul> <em>Applet</em>
3735 <li>Jmol to JalviewLite mouseover/link not working</li>
3736 <li>JalviewLite can't import sequences with ID
3737 descriptions containing angle brackets</li>
3738 </ul> <em>General</em>
3740 <li>Cannot export and reimport RNA secondary structure
3741 via jalview annotation file</li>
3742 <li>Random helix colour palette for colour by annotation
3743 with RNA secondary structure</li>
3744 <li>Mouseover to cDNA from STOP residue in protein
3745 translation doesn't work.</li>
3746 <li>hints when using the select by annotation dialog box</li>
3747 <li>Jmol alignment incorrect if PDB file has alternate CA
3749 <li>FontChooser message dialog appears to hang after
3750 choosing 1pt font</li>
3751 <li>Peptide secondary structure incorrectly imported from
3752 annotation file when annotation display text includes 'e' or
3754 <li>Cannot set colour of new feature type whilst creating
3756 <li>cDNA translation alignment should not be sequence
3757 order dependent</li>
3758 <li>'Show unconserved' doesn't work for lower case
3760 <li>Nucleotide ambiguity codes involving R not recognised</li>
3761 </ul> <em>Deployment and Documentation</em>
3763 <li>Applet example pages appear different to the rest of
3764 www.jalview.org</li>
3765 </ul> <em>Application Known issues</em>
3767 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3768 <li>Misleading message appears after trying to delete
3770 <li>Jalview icon not shown in dock after InstallAnywhere
3771 version launches</li>
3772 <li>Fetching EMBL reference for an RNA sequence results
3773 fails with a sequence mismatch</li>
3774 <li>Corrupted or unreadable alignment display when
3775 scrolling alignment to right</li>
3776 <li>ArrayIndexOutOfBoundsException thrown when remove
3777 empty columns called on alignment with ragged gapped ends</li>
3778 <li>auto calculated alignment annotation rows do not get
3779 placed above or below non-autocalculated rows</li>
3780 <li>Jalview dekstop becomes sluggish at full screen in
3781 ultra-high resolution</li>
3782 <li>Cannot disable consensus calculation independently of
3783 quality and conservation</li>
3784 <li>Mouseover highlighting between cDNA and protein can
3785 become sluggish with more than one splitframe shown</li>
3786 </ul> <em>Applet Known Issues</em>
3788 <li>Core PDB parsing code requires Jmol</li>
3789 <li>Sequence canvas panel goes white when alignment
3790 window is being resized</li>
3796 <td><div align="center">
3797 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3799 <td><em>General</em>
3801 <li>Updated Java code signing certificate donated by
3803 <li>Features and annotation preserved when performing
3804 pairwise alignment</li>
3805 <li>RNA pseudoknot annotation can be
3806 imported/exported/displayed</li>
3807 <li>'colour by annotation' can colour by RNA and
3808 protein secondary structure</li>
3809 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3810 post-hoc with 2.9 release</em>)
3813 </ul> <em>Application</em>
3815 <li>Extract and display secondary structure for sequences
3816 with 3D structures</li>
3817 <li>Support for parsing RNAML</li>
3818 <li>Annotations menu for layout
3820 <li>sort sequence annotation rows by alignment</li>
3821 <li>place sequence annotation above/below alignment
3824 <li>Output in Stockholm format</li>
3825 <li>Internationalisation: improved Spanish (es)
3827 <li>Structure viewer preferences tab</li>
3828 <li>Disorder and Secondary Structure annotation tracks
3829 shared between alignments</li>
3830 <li>UCSF Chimera launch and linked highlighting from
3832 <li>Show/hide all sequence associated annotation rows for
3833 all or current selection</li>
3834 <li>disorder and secondary structure predictions
3835 available as dataset annotation</li>
3836 <li>Per-sequence rna helices colouring</li>
3839 <li>Sequence database accessions imported when fetching
3840 alignments from Rfam</li>
3841 <li>update VARNA version to 3.91</li>
3843 <li>New groovy scripts for exporting aligned positions,
3844 conservation values, and calculating sum of pairs scores.</li>
3845 <li>Command line argument to set default JABAWS server</li>
3846 <li>include installation type in build properties and
3847 console log output</li>
3848 <li>Updated Jalview project format to preserve dataset
3852 <!-- issues resolved --> <em>Application</em>
3854 <li>Distinguish alignment and sequence associated RNA
3855 structure in structure->view->VARNA</li>
3856 <li>Raise dialog box if user deletes all sequences in an
3858 <li>Pressing F1 results in documentation opening twice</li>
3859 <li>Sequence feature tooltip is wrapped</li>
3860 <li>Double click on sequence associated annotation
3861 selects only first column</li>
3862 <li>Redundancy removal doesn't result in unlinked
3863 leaves shown in tree</li>
3864 <li>Undos after several redundancy removals don't undo
3866 <li>Hide sequence doesn't hide associated annotation</li>
3867 <li>User defined colours dialog box too big to fit on
3868 screen and buttons not visible</li>
3869 <li>author list isn't updated if already written to
3870 Jalview properties</li>
3871 <li>Popup menu won't open after retrieving sequence
3873 <li>File open window for associate PDB doesn't open</li>
3874 <li>Left-then-right click on a sequence id opens a
3875 browser search window</li>
3876 <li>Cannot open sequence feature shading/sort popup menu
3877 in feature settings dialog</li>
3878 <li>better tooltip placement for some areas of Jalview
3880 <li>Allow addition of JABAWS Server which doesn't
3881 pass validation</li>
3882 <li>Web services parameters dialog box is too large to
3884 <li>Muscle nucleotide alignment preset obscured by
3886 <li>JABAWS preset submenus don't contain newly
3887 defined user preset</li>
3888 <li>MSA web services warns user if they were launched
3889 with invalid input</li>
3890 <li>Jalview cannot contact DAS Registy when running on
3893 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3894 'Superpose with' submenu not shown when new view
3898 </ul> <!-- <em>Applet</em>
3900 </ul> <em>General</em>
3902 </ul>--> <em>Deployment and Documentation</em>
3904 <li>2G and 1G options in launchApp have no effect on
3905 memory allocation</li>
3906 <li>launchApp service doesn't automatically open
3907 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3909 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3910 InstallAnywhere reports cannot find valid JVM when Java
3911 1.7_055 is available
3913 </ul> <em>Application Known issues</em>
3916 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3917 corrupted or unreadable alignment display when scrolling
3921 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3922 retrieval fails but progress bar continues for DAS retrieval
3923 with large number of ID
3926 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3927 flatfile output of visible region has incorrect sequence
3931 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3932 rna structure consensus doesn't update when secondary
3933 structure tracks are rearranged
3936 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3937 invalid rna structure positional highlighting does not
3938 highlight position of invalid base pairs
3941 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3942 out of memory errors are not raised when saving Jalview
3943 project from alignment window file menu
3946 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3947 Switching to RNA Helices colouring doesn't propagate to
3951 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3952 colour by RNA Helices not enabled when user created
3953 annotation added to alignment
3956 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3957 Jalview icon not shown on dock in Mountain Lion/Webstart
3959 </ul> <em>Applet Known Issues</em>
3962 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3963 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3966 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3967 Jalview and Jmol example not compatible with IE9
3970 <li>Sort by annotation score doesn't reverse order
3976 <td><div align="center">
3977 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3980 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3983 <li>Internationalisation of user interface (usually
3984 called i18n support) and translation for Spanish locale</li>
3985 <li>Define/Undefine group on current selection with
3986 Ctrl-G/Shift Ctrl-G</li>
3987 <li>Improved group creation/removal options in
3988 alignment/sequence Popup menu</li>
3989 <li>Sensible precision for symbol distribution
3990 percentages shown in logo tooltip.</li>
3991 <li>Annotation panel height set according to amount of
3992 annotation when alignment first opened</li>
3993 </ul> <em>Application</em>
3995 <li>Interactive consensus RNA secondary structure
3996 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3997 <li>Select columns containing particular features from
3998 Feature Settings dialog</li>
3999 <li>View all 'representative' PDB structures for selected
4001 <li>Update Jalview project format:
4003 <li>New file extension for Jalview projects '.jvp'</li>
4004 <li>Preserve sequence and annotation dataset (to
4005 store secondary structure annotation,etc)</li>
4006 <li>Per group and alignment annotation and RNA helix
4010 <li>New similarity measures for PCA and Tree calculation
4012 <li>Experimental support for retrieval and viewing of
4013 flanking regions for an alignment</li>
4017 <!-- issues resolved --> <em>Application</em>
4019 <li>logo keeps spinning and status remains at queued or
4020 running after job is cancelled</li>
4021 <li>cannot export features from alignments imported from
4022 Jalview/VAMSAS projects</li>
4023 <li>Buggy slider for web service parameters that take
4025 <li>Newly created RNA secondary structure line doesn't
4026 have 'display all symbols' flag set</li>
4027 <li>T-COFFEE alignment score shading scheme and other
4028 annotation shading not saved in Jalview project</li>
4029 <li>Local file cannot be loaded in freshly downloaded
4031 <li>Jalview icon not shown on dock in Mountain
4033 <li>Load file from desktop file browser fails</li>
4034 <li>Occasional NPE thrown when calculating large trees</li>
4035 <li>Cannot reorder or slide sequences after dragging an
4036 alignment onto desktop</li>
4037 <li>Colour by annotation dialog throws NPE after using
4038 'extract scores' function</li>
4039 <li>Loading/cut'n'pasting an empty file leads to a grey
4040 alignment window</li>
4041 <li>Disorder thresholds rendered incorrectly after
4042 performing IUPred disorder prediction</li>
4043 <li>Multiple group annotated consensus rows shown when
4044 changing 'normalise logo' display setting</li>
4045 <li>Find shows blank dialog after 'finished searching' if
4046 nothing matches query</li>
4047 <li>Null Pointer Exceptions raised when sorting by
4048 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
4050 <li>Errors in Jmol console when structures in alignment
4051 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
4053 <li>Not all working JABAWS services are shown in
4055 <li>JAVAWS version of Jalview fails to launch with
4056 'invalid literal/length code'</li>
4057 <li>Annotation/RNA Helix colourschemes cannot be applied
4058 to alignment with groups (actually fixed in 2.8.0b1)</li>
4059 <li>RNA Helices and T-Coffee Scores available as default
4062 </ul> <em>Applet</em>
4064 <li>Remove group option is shown even when selection is
4066 <li>Apply to all groups ticked but colourscheme changes
4067 don't affect groups</li>
4068 <li>Documented RNA Helices and T-Coffee Scores as valid
4069 colourscheme name</li>
4070 <li>Annotation labels drawn on sequence IDs when
4071 Annotation panel is not displayed</li>
4072 <li>Increased font size for dropdown menus on OSX and
4073 embedded windows</li>
4074 </ul> <em>Other</em>
4076 <li>Consensus sequence for alignments/groups with a
4077 single sequence were not calculated</li>
4078 <li>annotation files that contain only groups imported as
4079 annotation and junk sequences</li>
4080 <li>Fasta files with sequences containing '*' incorrectly
4081 recognised as PFAM or BLC</li>
4082 <li>conservation/PID slider apply all groups option
4083 doesn't affect background (2.8.0b1)
4085 <li>redundancy highlighting is erratic at 0% and 100%</li>
4086 <li>Remove gapped columns fails for sequences with ragged
4088 <li>AMSA annotation row with leading spaces is not
4089 registered correctly on import</li>
4090 <li>Jalview crashes when selecting PCA analysis for
4091 certain alignments</li>
4092 <li>Opening the colour by annotation dialog for an
4093 existing annotation based 'use original colours'
4094 colourscheme loses original colours setting</li>
4099 <td><div align="center">
4100 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
4101 <em>30/1/2014</em></strong>
4105 <li>Trusted certificates for JalviewLite applet and
4106 Jalview Desktop application<br />Certificate was donated by
4107 <a href="https://www.certum.eu">Certum</a> to the Jalview
4108 open source project).
4110 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
4111 <li>Output in Stockholm format</li>
4112 <li>Allow import of data from gzipped files</li>
4113 <li>Export/import group and sequence associated line
4114 graph thresholds</li>
4115 <li>Nucleotide substitution matrix that supports RNA and
4116 ambiguity codes</li>
4117 <li>Allow disorder predictions to be made on the current
4118 selection (or visible selection) in the same way that JPred
4120 <li>Groovy scripting for headless Jalview operation</li>
4121 </ul> <em>Other improvements</em>
4123 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
4124 <li>COMBINE statement uses current SEQUENCE_REF and
4125 GROUP_REF scope to group annotation rows</li>
4126 <li>Support '' style escaping of quotes in Newick
4128 <li>Group options for JABAWS service by command line name</li>
4129 <li>Empty tooltip shown for JABA service options with a
4130 link but no description</li>
4131 <li>Select primary source when selecting authority in
4132 database fetcher GUI</li>
4133 <li>Add .mfa to FASTA file extensions recognised by
4135 <li>Annotation label tooltip text wrap</li>
4140 <li>Slow scrolling when lots of annotation rows are
4142 <li>Lots of NPE (and slowness) after creating RNA
4143 secondary structure annotation line</li>
4144 <li>Sequence database accessions not imported when
4145 fetching alignments from Rfam</li>
4146 <li>Incorrect SHMR submission for sequences with
4148 <li>View all structures does not always superpose
4150 <li>Option widgets in service parameters not updated to
4151 reflect user or preset settings</li>
4152 <li>Null pointer exceptions for some services without
4153 presets or adjustable parameters</li>
4154 <li>Discover PDB IDs entry in structure menu doesn't
4155 discover PDB xRefs</li>
4156 <li>Exception encountered while trying to retrieve
4157 features with DAS</li>
4158 <li>Lowest value in annotation row isn't coloured
4159 when colour by annotation (per sequence) is coloured</li>
4160 <li>Keyboard mode P jumps to start of gapped region when
4161 residue follows a gap</li>
4162 <li>Jalview appears to hang importing an alignment with
4163 Wrap as default or after enabling Wrap</li>
4164 <li>'Right click to add annotations' message
4165 shown in wrap mode when no annotations present</li>
4166 <li>Disorder predictions fail with NPE if no automatic
4167 annotation already exists on alignment</li>
4168 <li>oninit javascript function should be called after
4169 initialisation completes</li>
4170 <li>Remove redundancy after disorder prediction corrupts
4171 alignment window display</li>
4172 <li>Example annotation file in documentation is invalid</li>
4173 <li>Grouped line graph annotation rows are not exported
4174 to annotation file</li>
4175 <li>Multi-harmony analysis cannot be run when only two
4177 <li>Cannot create multiple groups of line graphs with
4178 several 'combine' statements in annotation file</li>
4179 <li>Pressing return several times causes Number Format
4180 exceptions in keyboard mode</li>
4181 <li>Multi-harmony (SHMMR) method doesn't submit
4182 correct partitions for input data</li>
4183 <li>Translation from DNA to Amino Acids fails</li>
4184 <li>Jalview fail to load newick tree with quoted label</li>
4185 <li>--headless flag isn't understood</li>
4186 <li>ClassCastException when generating EPS in headless
4188 <li>Adjusting sequence-associated shading threshold only
4189 changes one row's threshold</li>
4190 <li>Preferences and Feature settings panel panel
4191 doesn't open</li>
4192 <li>hide consensus histogram also hides conservation and
4193 quality histograms</li>
4198 <td><div align="center">
4199 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
4201 <td><em>Application</em>
4203 <li>Support for JABAWS 2.0 Services (AACon alignment
4204 conservation, protein disorder and Clustal Omega)</li>
4205 <li>JABAWS server status indicator in Web Services
4207 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
4208 in Jalview alignment window</li>
4209 <li>Updated Jalview build and deploy framework for OSX
4210 mountain lion, windows 7, and 8</li>
4211 <li>Nucleotide substitution matrix for PCA that supports
4212 RNA and ambiguity codes</li>
4214 <li>Improved sequence database retrieval GUI</li>
4215 <li>Support fetching and database reference look up
4216 against multiple DAS sources (Fetch all from in 'fetch db
4218 <li>Jalview project improvements
4220 <li>Store and retrieve the 'belowAlignment'
4221 flag for annotation</li>
4222 <li>calcId attribute to group annotation rows on the
4224 <li>Store AACon calculation settings for a view in
4225 Jalview project</li>
4229 <li>horizontal scrolling gesture support</li>
4230 <li>Visual progress indicator when PCA calculation is
4232 <li>Simpler JABA web services menus</li>
4233 <li>visual indication that web service results are still
4234 being retrieved from server</li>
4235 <li>Serialise the dialogs that are shown when Jalview
4236 starts up for first time</li>
4237 <li>Jalview user agent string for interacting with HTTP
4239 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
4241 <li>Examples directory and Groovy library included in
4242 InstallAnywhere distribution</li>
4243 </ul> <em>Applet</em>
4245 <li>RNA alignment and secondary structure annotation
4246 visualization applet example</li>
4247 </ul> <em>General</em>
4249 <li>Normalise option for consensus sequence logo</li>
4250 <li>Reset button in PCA window to return dimensions to
4252 <li>Allow seqspace or Jalview variant of alignment PCA
4254 <li>PCA with either nucleic acid and protein substitution
4256 <li>Allow windows containing HTML reports to be exported
4258 <li>Interactive display and editing of RNA secondary
4259 structure contacts</li>
4260 <li>RNA Helix Alignment Colouring</li>
4261 <li>RNA base pair logo consensus</li>
4262 <li>Parse sequence associated secondary structure
4263 information in Stockholm files</li>
4264 <li>HTML Export database accessions and annotation
4265 information presented in tooltip for sequences</li>
4266 <li>Import secondary structure from LOCARNA clustalw
4267 style RNA alignment files</li>
4268 <li>import and visualise T-COFFEE quality scores for an
4270 <li>'colour by annotation' per sequence option to
4271 shade each sequence according to its associated alignment
4273 <li>New Jalview Logo</li>
4274 </ul> <em>Documentation and Development</em>
4276 <li>documentation for score matrices used in Jalview</li>
4277 <li>New Website!</li>
4279 <td><em>Application</em>
4281 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
4282 wsdbfetch REST service</li>
4283 <li>Stop windows being moved outside desktop on OSX</li>
4284 <li>Filetype associations not installed for webstart
4286 <li>Jalview does not always retrieve progress of a JABAWS
4287 job execution in full once it is complete</li>
4288 <li>revise SHMR RSBS definition to ensure alignment is
4289 uploaded via ali_file parameter</li>
4290 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
4291 <li>View all structures superposed fails with exception</li>
4292 <li>Jnet job queues forever if a very short sequence is
4293 submitted for prediction</li>
4294 <li>Cut and paste menu not opened when mouse clicked on
4296 <li>Putting fractional value into integer text box in
4297 alignment parameter dialog causes Jalview to hang</li>
4298 <li>Structure view highlighting doesn't work on
4300 <li>View all structures fails with exception shown in
4302 <li>Characters in filename associated with PDBEntry not
4303 escaped in a platform independent way</li>
4304 <li>Jalview desktop fails to launch with exception when
4306 <li>Tree calculation reports 'you must have 2 or more
4307 sequences selected' when selection is empty</li>
4308 <li>Jalview desktop fails to launch with jar signature
4309 failure when java web start temporary file caching is
4311 <li>DAS Sequence retrieval with range qualification
4312 results in sequence xref which includes range qualification</li>
4313 <li>Errors during processing of command line arguments
4314 cause progress bar (JAL-898) to be removed</li>
4315 <li>Replace comma for semi-colon option not disabled for
4316 DAS sources in sequence fetcher</li>
4317 <li>Cannot close news reader when JABAWS server warning
4318 dialog is shown</li>
4319 <li>Option widgets not updated to reflect user settings</li>
4320 <li>Edited sequence not submitted to web service</li>
4321 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
4322 <li>InstallAnywhere installer doesn't unpack and run
4323 on OSX Mountain Lion</li>
4324 <li>Annotation panel not given a scroll bar when
4325 sequences with alignment annotation are pasted into the
4327 <li>Sequence associated annotation rows not associated
4328 when loaded from Jalview project</li>
4329 <li>Browser launch fails with NPE on java 1.7</li>
4330 <li>JABAWS alignment marked as finished when job was
4331 cancelled or job failed due to invalid input</li>
4332 <li>NPE with v2.7 example when clicking on Tree
4333 associated with all views</li>
4334 <li>Exceptions when copy/paste sequences with grouped
4335 annotation rows to new window</li>
4336 </ul> <em>Applet</em>
4338 <li>Sequence features are momentarily displayed before
4339 they are hidden using hidefeaturegroups applet parameter</li>
4340 <li>loading features via javascript API automatically
4341 enables feature display</li>
4342 <li>scrollToColumnIn javascript API method doesn't
4344 </ul> <em>General</em>
4346 <li>Redundancy removal fails for rna alignment</li>
4347 <li>PCA calculation fails when sequence has been selected
4348 and then deselected</li>
4349 <li>PCA window shows grey box when first opened on OSX</li>
4350 <li>Letters coloured pink in sequence logo when alignment
4351 coloured with clustalx</li>
4352 <li>Choosing fonts without letter symbols defined causes
4353 exceptions and redraw errors</li>
4354 <li>Initial PCA plot view is not same as manually
4355 reconfigured view</li>
4356 <li>Grouped annotation graph label has incorrect line
4358 <li>Grouped annotation graph label display is corrupted
4359 for lots of labels</li>
4364 <div align="center">
4365 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
4368 <td><em>Application</em>
4370 <li>Jalview Desktop News Reader</li>
4371 <li>Tweaked default layout of web services menu</li>
4372 <li>View/alignment association menu to enable user to
4373 easily specify which alignment a multi-structure view takes
4374 its colours/correspondences from</li>
4375 <li>Allow properties file location to be specified as URL</li>
4376 <li>Extend Jalview project to preserve associations
4377 between many alignment views and a single Jmol display</li>
4378 <li>Store annotation row height in Jalview project file</li>
4379 <li>Annotation row column label formatting attributes
4380 stored in project file</li>
4381 <li>Annotation row order for auto-calculated annotation
4382 rows preserved in Jalview project file</li>
4383 <li>Visual progress indication when Jalview state is
4384 saved using Desktop window menu</li>
4385 <li>Visual indication that command line arguments are
4386 still being processed</li>
4387 <li>Groovy script execution from URL</li>
4388 <li>Colour by annotation default min and max colours in
4390 <li>Automatically associate PDB files dragged onto an
4391 alignment with sequences that have high similarity and
4393 <li>Update JGoogleAnalytics to latest release (0.3)</li>
4394 <li>'view structures' option to open many
4395 structures in same window</li>
4396 <li>Sort associated views menu option for tree panel</li>
4397 <li>Group all JABA and non-JABA services for a particular
4398 analysis function in its own submenu</li>
4399 </ul> <em>Applet</em>
4401 <li>Userdefined and autogenerated annotation rows for
4403 <li>Adjustment of alignment annotation pane height</li>
4404 <li>Annotation scrollbar for annotation panel</li>
4405 <li>Drag to reorder annotation rows in annotation panel</li>
4406 <li>'automaticScrolling' parameter</li>
4407 <li>Allow sequences with partial ID string matches to be
4408 annotated from GFF/Jalview features files</li>
4409 <li>Sequence logo annotation row in applet</li>
4410 <li>Absolute paths relative to host server in applet
4411 parameters are treated as such</li>
4412 <li>New in the JalviewLite javascript API:
4414 <li>JalviewLite.js javascript library</li>
4415 <li>Javascript callbacks for
4417 <li>Applet initialisation</li>
4418 <li>Sequence/alignment mouse-overs and selections</li>
4421 <li>scrollTo row and column alignment scrolling
4423 <li>Select sequence/alignment regions from javascript</li>
4424 <li>javascript structure viewer harness to pass
4425 messages between Jmol and Jalview when running as
4426 distinct applets</li>
4427 <li>sortBy method</li>
4428 <li>Set of applet and application examples shipped
4429 with documentation</li>
4430 <li>New example to demonstrate JalviewLite and Jmol
4431 javascript message exchange</li>
4433 </ul> <em>General</em>
4435 <li>Enable Jmol displays to be associated with multiple
4436 multiple alignments</li>
4437 <li>Option to automatically sort alignment with new tree</li>
4438 <li>User configurable link to enable redirects to a
4439 www.Jalview.org mirror</li>
4440 <li>Jmol colours option for Jmol displays</li>
4441 <li>Configurable newline string when writing alignment
4442 and other flat files</li>
4443 <li>Allow alignment annotation description lines to
4444 contain html tags</li>
4445 </ul> <em>Documentation and Development</em>
4447 <li>Add groovy test harness for bulk load testing to
4449 <li>Groovy script to load and align a set of sequences
4450 using a web service before displaying the result in the
4451 Jalview desktop</li>
4452 <li>Restructured javascript and applet api documentation</li>
4453 <li>Ant target to publish example html files with applet
4455 <li>Netbeans project for building Jalview from source</li>
4456 <li>ant task to create online javadoc for Jalview source</li>
4458 <td><em>Application</em>
4460 <li>User defined colourscheme throws exception when
4461 current built in colourscheme is saved as new scheme</li>
4462 <li>AlignFrame->Save in application pops up save
4463 dialog for valid filename/format</li>
4464 <li>Cannot view associated structure for UniProt sequence</li>
4465 <li>PDB file association breaks for UniProt sequence
4467 <li>Associate PDB from file dialog does not tell you
4468 which sequence is to be associated with the file</li>
4469 <li>Find All raises null pointer exception when query
4470 only matches sequence IDs</li>
4471 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4472 <li>Jalview project with Jmol views created with Jalview
4473 2.4 cannot be loaded</li>
4474 <li>Filetype associations not installed for webstart
4476 <li>Two or more chains in a single PDB file associated
4477 with sequences in different alignments do not get coloured
4478 by their associated sequence</li>
4479 <li>Visibility status of autocalculated annotation row
4480 not preserved when project is loaded</li>
4481 <li>Annotation row height and visibility attributes not
4482 stored in Jalview project</li>
4483 <li>Tree bootstraps are not preserved when saved as a
4484 Jalview project</li>
4485 <li>Envision2 workflow tooltips are corrupted</li>
4486 <li>Enabling show group conservation also enables colour
4487 by conservation</li>
4488 <li>Duplicate group associated conservation or consensus
4489 created on new view</li>
4490 <li>Annotation scrollbar not displayed after 'show
4491 all hidden annotation rows' option selected</li>
4492 <li>Alignment quality not updated after alignment
4493 annotation row is hidden then shown</li>
4494 <li>Preserve colouring of structures coloured by
4495 sequences in pre Jalview 2.7 projects</li>
4496 <li>Web service job parameter dialog is not laid out
4498 <li>Web services menu not refreshed after 'reset
4499 services' button is pressed in preferences</li>
4500 <li>Annotation off by one in Jalview v2_3 example project</li>
4501 <li>Structures imported from file and saved in project
4502 get name like jalview_pdb1234.txt when reloaded</li>
4503 <li>Jalview does not always retrieve progress of a JABAWS
4504 job execution in full once it is complete</li>
4505 </ul> <em>Applet</em>
4507 <li>Alignment height set incorrectly when lots of
4508 annotation rows are displayed</li>
4509 <li>Relative URLs in feature HTML text not resolved to
4511 <li>View follows highlighting does not work for positions
4513 <li><= shown as = in tooltip</li>
4514 <li>Export features raises exception when no features
4516 <li>Separator string used for serialising lists of IDs
4517 for javascript api is modified when separator string
4518 provided as parameter</li>
4519 <li>Null pointer exception when selecting tree leaves for
4520 alignment with no existing selection</li>
4521 <li>Relative URLs for datasources assumed to be relative
4522 to applet's codebase</li>
4523 <li>Status bar not updated after finished searching and
4524 search wraps around to first result</li>
4525 <li>StructureSelectionManager instance shared between
4526 several Jalview applets causes race conditions and memory
4528 <li>Hover tooltip and mouseover of position on structure
4529 not sent from Jmol in applet</li>
4530 <li>Certain sequences of javascript method calls to
4531 applet API fatally hang browser</li>
4532 </ul> <em>General</em>
4534 <li>View follows structure mouseover scrolls beyond
4535 position with wrapped view and hidden regions</li>
4536 <li>Find sequence position moves to wrong residue
4537 with/without hidden columns</li>
4538 <li>Sequence length given in alignment properties window
4540 <li>InvalidNumberFormat exceptions thrown when trying to
4541 import PDB like structure files</li>
4542 <li>Positional search results are only highlighted
4543 between user-supplied sequence start/end bounds</li>
4544 <li>End attribute of sequence is not validated</li>
4545 <li>Find dialog only finds first sequence containing a
4546 given sequence position</li>
4547 <li>Sequence numbering not preserved in MSF alignment
4549 <li>Jalview PDB file reader does not extract sequence
4550 from nucleotide chains correctly</li>
4551 <li>Structure colours not updated when tree partition
4552 changed in alignment</li>
4553 <li>Sequence associated secondary structure not correctly
4554 parsed in interleaved stockholm</li>
4555 <li>Colour by annotation dialog does not restore current
4557 <li>Hiding (nearly) all sequences doesn't work
4559 <li>Sequences containing lowercase letters are not
4560 properly associated with their pdb files</li>
4561 </ul> <em>Documentation and Development</em>
4563 <li>schemas/JalviewWsParamSet.xsd corrupted by
4564 ApplyCopyright tool</li>
4569 <div align="center">
4570 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4573 <td><em>Application</em>
4575 <li>New warning dialog when the Jalview Desktop cannot
4576 contact web services</li>
4577 <li>JABA service parameters for a preset are shown in
4578 service job window</li>
4579 <li>JABA Service menu entries reworded</li>
4583 <li>Modeller PIR IO broken - cannot correctly import a
4584 pir file emitted by Jalview</li>
4585 <li>Existing feature settings transferred to new
4586 alignment view created from cut'n'paste</li>
4587 <li>Improved test for mixed amino/nucleotide chains when
4588 parsing PDB files</li>
4589 <li>Consensus and conservation annotation rows
4590 occasionally become blank for all new windows</li>
4591 <li>Exception raised when right clicking above sequences
4592 in wrapped view mode</li>
4593 </ul> <em>Application</em>
4595 <li>multiple multiply aligned structure views cause cpu
4596 usage to hit 100% and computer to hang</li>
4597 <li>Web Service parameter layout breaks for long user
4598 parameter names</li>
4599 <li>Jaba service discovery hangs desktop if Jaba server
4606 <div align="center">
4607 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4610 <td><em>Application</em>
4612 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4613 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4616 <li>Web Services preference tab</li>
4617 <li>Analysis parameters dialog box and user defined
4619 <li>Improved speed and layout of Envision2 service menu</li>
4620 <li>Superpose structures using associated sequence
4622 <li>Export coordinates and projection as CSV from PCA
4624 </ul> <em>Applet</em>
4626 <li>enable javascript: execution by the applet via the
4627 link out mechanism</li>
4628 </ul> <em>Other</em>
4630 <li>Updated the Jmol Jalview interface to work with Jmol
4632 <li>The Jalview Desktop and JalviewLite applet now
4633 require Java 1.5</li>
4634 <li>Allow Jalview feature colour specification for GFF
4635 sequence annotation files</li>
4636 <li>New 'colour by label' keword in Jalview feature file
4637 type colour specification</li>
4638 <li>New Jalview Desktop Groovy API method that allows a
4639 script to check if it being run in an interactive session or
4640 in a batch operation from the Jalview command line</li>
4644 <li>clustalx colourscheme colours Ds preferentially when
4645 both D+E are present in over 50% of the column</li>
4646 </ul> <em>Application</em>
4648 <li>typo in AlignmentFrame->View->Hide->all but
4649 selected Regions menu item</li>
4650 <li>sequence fetcher replaces ',' for ';' when the ',' is
4651 part of a valid accession ID</li>
4652 <li>fatal OOM if object retrieved by sequence fetcher
4653 runs out of memory</li>
4654 <li>unhandled Out of Memory Error when viewing pca
4655 analysis results</li>
4656 <li>InstallAnywhere builds fail to launch on OS X java
4657 10.5 update 4 (due to apple Java 1.6 update)</li>
4658 <li>Installanywhere Jalview silently fails to launch</li>
4659 </ul> <em>Applet</em>
4661 <li>Jalview.getFeatureGroups() raises an
4662 ArrayIndexOutOfBoundsException if no feature groups are
4669 <div align="center">
4670 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4676 <li>Alignment prettyprinter doesn't cope with long
4678 <li>clustalx colourscheme colours Ds preferentially when
4679 both D+E are present in over 50% of the column</li>
4680 <li>nucleic acid structures retrieved from PDB do not
4681 import correctly</li>
4682 <li>More columns get selected than were clicked on when a
4683 number of columns are hidden</li>
4684 <li>annotation label popup menu not providing correct
4685 add/hide/show options when rows are hidden or none are
4687 <li>Stockholm format shown in list of readable formats,
4688 and parser copes better with alignments from RFAM.</li>
4689 <li>CSV output of consensus only includes the percentage
4690 of all symbols if sequence logo display is enabled</li>
4692 </ul> <em>Applet</em>
4694 <li>annotation panel disappears when annotation is
4696 </ul> <em>Application</em>
4698 <li>Alignment view not redrawn properly when new
4699 alignment opened where annotation panel is visible but no
4700 annotations are present on alignment</li>
4701 <li>pasted region containing hidden columns is
4702 incorrectly displayed in new alignment window</li>
4703 <li>Jalview slow to complete operations when stdout is
4704 flooded (fix is to close the Jalview console)</li>
4705 <li>typo in AlignmentFrame->View->Hide->all but
4706 selected Rregions menu item.</li>
4707 <li>inconsistent group submenu and Format submenu entry
4708 'Un' or 'Non'conserved</li>
4709 <li>Sequence feature settings are being shared by
4710 multiple distinct alignments</li>
4711 <li>group annotation not recreated when tree partition is
4713 <li>double click on group annotation to select sequences
4714 does not propagate to associated trees</li>
4715 <li>Mac OSX specific issues:
4717 <li>exception raised when mouse clicked on desktop
4718 window background</li>
4719 <li>Desktop menu placed on menu bar and application
4720 name set correctly</li>
4721 <li>sequence feature settings not wide enough for the
4722 save feature colourscheme button</li>
4731 <div align="center">
4732 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4735 <td><em>New Capabilities</em>
4737 <li>URL links generated from description line for
4738 regular-expression based URL links (applet and application)
4741 <li>Non-positional feature URL links are shown in link
4743 <li>Linked viewing of nucleic acid sequences and
4745 <li>Automatic Scrolling option in View menu to display
4746 the currently highlighted region of an alignment.</li>
4747 <li>Order an alignment by sequence length, or using the
4748 average score or total feature count for each sequence.</li>
4749 <li>Shading features by score or associated description</li>
4750 <li>Subdivide alignment and groups based on identity of
4751 selected subsequence (Make Groups from Selection).</li>
4752 <li>New hide/show options including Shift+Control+H to
4753 hide everything but the currently selected region.</li>
4754 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4755 </ul> <em>Application</em>
4757 <li>Fetch DB References capabilities and UI expanded to
4758 support retrieval from DAS sequence sources</li>
4759 <li>Local DAS Sequence sources can be added via the
4760 command line or via the Add local source dialog box.</li>
4761 <li>DAS Dbref and DbxRef feature types are parsed as
4762 database references and protein_name is parsed as
4763 description line (BioSapiens terms).</li>
4764 <li>Enable or disable non-positional feature and database
4765 references in sequence ID tooltip from View menu in
4767 <!-- <li>New hidden columns and rows and representatives capabilities
4768 in annotations file (in progress - not yet fully implemented)</li> -->
4769 <li>Group-associated consensus, sequence logos and
4770 conservation plots</li>
4771 <li>Symbol distributions for each column can be exported
4772 and visualized as sequence logos</li>
4773 <li>Optionally scale multi-character column labels to fit
4774 within each column of annotation row<!-- todo for applet -->
4776 <li>Optional automatic sort of associated alignment view
4777 when a new tree is opened.</li>
4778 <li>Jalview Java Console</li>
4779 <li>Better placement of desktop window when moving
4780 between different screens.</li>
4781 <li>New preference items for sequence ID tooltip and
4782 consensus annotation</li>
4783 <li>Client to submit sequences and IDs to Envision2
4785 <li><em>Vamsas Capabilities</em>
4787 <li>Improved VAMSAS synchronization (Jalview archive
4788 used to preserve views, structures, and tree display
4790 <li>Import of vamsas documents from disk or URL via
4792 <li>Sharing of selected regions between views and
4793 with other VAMSAS applications (Experimental feature!)</li>
4794 <li>Updated API to VAMSAS version 0.2</li>
4796 </ul> <em>Applet</em>
4798 <li>Middle button resizes annotation row height</li>
4801 <li>sortByTree (true/false) - automatically sort the
4802 associated alignment view by the tree when a new tree is
4804 <li>showTreeBootstraps (true/false) - show or hide
4805 branch bootstraps (default is to show them if available)</li>
4806 <li>showTreeDistances (true/false) - show or hide
4807 branch lengths (default is to show them if available)</li>
4808 <li>showUnlinkedTreeNodes (true/false) - indicate if
4809 unassociated nodes should be highlighted in the tree
4811 <li>heightScale and widthScale (1.0 or more) -
4812 increase the height or width of a cell in the alignment
4813 grid relative to the current font size.</li>
4816 <li>Non-positional features displayed in sequence ID
4818 </ul> <em>Other</em>
4820 <li>Features format: graduated colour definitions and
4821 specification of feature scores</li>
4822 <li>Alignment Annotations format: new keywords for group
4823 associated annotation (GROUP_REF) and annotation row display
4824 properties (ROW_PROPERTIES)</li>
4825 <li>XML formats extended to support graduated feature
4826 colourschemes, group associated annotation, and profile
4827 visualization settings.</li></td>
4830 <li>Source field in GFF files parsed as feature source
4831 rather than description</li>
4832 <li>Non-positional features are now included in sequence
4833 feature and gff files (controlled via non-positional feature
4834 visibility in tooltip).</li>
4835 <li>URL links generated for all feature links (bugfix)</li>
4836 <li>Added URL embedding instructions to features file
4838 <li>Codons containing ambiguous nucleotides translated as
4839 'X' in peptide product</li>
4840 <li>Match case switch in find dialog box works for both
4841 sequence ID and sequence string and query strings do not
4842 have to be in upper case to match case-insensitively.</li>
4843 <li>AMSA files only contain first column of
4844 multi-character column annotation labels</li>
4845 <li>Jalview Annotation File generation/parsing consistent
4846 with documentation (e.g. Stockholm annotation can be
4847 exported and re-imported)</li>
4848 <li>PDB files without embedded PDB IDs given a friendly
4850 <li>Find incrementally searches ID string matches as well
4851 as subsequence matches, and correctly reports total number
4855 <li>Better handling of exceptions during sequence
4857 <li>Dasobert generated non-positional feature URL
4858 link text excludes the start_end suffix</li>
4859 <li>DAS feature and source retrieval buttons disabled
4860 when fetch or registry operations in progress.</li>
4861 <li>PDB files retrieved from URLs are cached properly</li>
4862 <li>Sequence description lines properly shared via
4864 <li>Sequence fetcher fetches multiple records for all
4866 <li>Ensured that command line das feature retrieval
4867 completes before alignment figures are generated.</li>
4868 <li>Reduced time taken when opening file browser for
4870 <li>isAligned check prior to calculating tree, PCA or
4871 submitting an MSA to JNet now excludes hidden sequences.</li>
4872 <li>User defined group colours properly recovered
4873 from Jalview projects.</li>
4882 <div align="center">
4883 <strong>2.4.0.b2</strong><br> 28/10/2009
4888 <li>Experimental support for google analytics usage
4890 <li>Jalview privacy settings (user preferences and docs).</li>
4895 <li>Race condition in applet preventing startup in
4897 <li>Exception when feature created from selection beyond
4898 length of sequence.</li>
4899 <li>Allow synthetic PDB files to be imported gracefully</li>
4900 <li>Sequence associated annotation rows associate with
4901 all sequences with a given id</li>
4902 <li>Find function matches case-insensitively for sequence
4903 ID string searches</li>
4904 <li>Non-standard characters do not cause pairwise
4905 alignment to fail with exception</li>
4906 </ul> <em>Application Issues</em>
4908 <li>Sequences are now validated against EMBL database</li>
4909 <li>Sequence fetcher fetches multiple records for all
4911 </ul> <em>InstallAnywhere Issues</em>
4913 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4914 issue with installAnywhere mechanism)</li>
4915 <li>Command line launching of JARs from InstallAnywhere
4916 version (java class versioning error fixed)</li>
4923 <div align="center">
4924 <strong>2.4</strong><br> 27/8/2008
4927 <td><em>User Interface</em>
4929 <li>Linked highlighting of codon and amino acid from
4930 translation and protein products</li>
4931 <li>Linked highlighting of structure associated with
4932 residue mapping to codon position</li>
4933 <li>Sequence Fetcher provides example accession numbers
4934 and 'clear' button</li>
4935 <li>MemoryMonitor added as an option under Desktop's
4937 <li>Extract score function to parse whitespace separated
4938 numeric data in description line</li>
4939 <li>Column labels in alignment annotation can be centred.</li>
4940 <li>Tooltip for sequence associated annotation give name
4942 </ul> <em>Web Services and URL fetching</em>
4944 <li>JPred3 web service</li>
4945 <li>Prototype sequence search client (no public services
4947 <li>Fetch either seed alignment or full alignment from
4949 <li>URL Links created for matching database cross
4950 references as well as sequence ID</li>
4951 <li>URL Links can be created using regular-expressions</li>
4952 </ul> <em>Sequence Database Connectivity</em>
4954 <li>Retrieval of cross-referenced sequences from other
4956 <li>Generalised database reference retrieval and
4957 validation to all fetchable databases</li>
4958 <li>Fetch sequences from DAS sources supporting the
4959 sequence command</li>
4960 </ul> <em>Import and Export</em>
4961 <li>export annotation rows as CSV for spreadsheet import</li>
4962 <li>Jalview projects record alignment dataset associations,
4963 EMBL products, and cDNA sequence mappings</li>
4964 <li>Sequence Group colour can be specified in Annotation
4966 <li>Ad-hoc colouring of group in Annotation File using RGB
4967 triplet as name of colourscheme</li>
4968 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4970 <li>treenode binding for VAMSAS tree exchange</li>
4971 <li>local editing and update of sequences in VAMSAS
4972 alignments (experimental)</li>
4973 <li>Create new or select existing session to join</li>
4974 <li>load and save of vamsas documents</li>
4975 </ul> <em>Application command line</em>
4977 <li>-tree parameter to open trees (introduced for passing
4979 <li>-fetchfrom command line argument to specify nicknames
4980 of DAS servers to query for alignment features</li>
4981 <li>-dasserver command line argument to add new servers
4982 that are also automatically queried for features</li>
4983 <li>-groovy command line argument executes a given groovy
4984 script after all input data has been loaded and parsed</li>
4985 </ul> <em>Applet-Application data exchange</em>
4987 <li>Trees passed as applet parameters can be passed to
4988 application (when using "View in full
4989 application")</li>
4990 </ul> <em>Applet Parameters</em>
4992 <li>feature group display control parameter</li>
4993 <li>debug parameter</li>
4994 <li>showbutton parameter</li>
4995 </ul> <em>Applet API methods</em>
4997 <li>newView public method</li>
4998 <li>Window (current view) specific get/set public methods</li>
4999 <li>Feature display control methods</li>
5000 <li>get list of currently selected sequences</li>
5001 </ul> <em>New Jalview distribution features</em>
5003 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
5004 <li>RELEASE file gives build properties for the latest
5005 Jalview release.</li>
5006 <li>Java 1.1 Applet build made easier and donotobfuscate
5007 property controls execution of obfuscator</li>
5008 <li>Build target for generating source distribution</li>
5009 <li>Debug flag for javacc</li>
5010 <li>.jalview_properties file is documented (slightly) in
5011 jalview.bin.Cache</li>
5012 <li>Continuous Build Integration for stable and
5013 development version of Application, Applet and source
5018 <li>selected region output includes visible annotations
5019 (for certain formats)</li>
5020 <li>edit label/displaychar contains existing label/char
5022 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
5023 <li>shorter peptide product names from EMBL records</li>
5024 <li>Newick string generator makes compact representations</li>
5025 <li>bootstrap values parsed correctly for tree files with
5027 <li>pathological filechooser bug avoided by not allowing
5028 filenames containing a ':'</li>
5029 <li>Fixed exception when parsing GFF files containing
5030 global sequence features</li>
5031 <li>Alignment datasets are finalized only when number of
5032 references from alignment sequences goes to zero</li>
5033 <li>Close of tree branch colour box without colour
5034 selection causes cascading exceptions</li>
5035 <li>occasional negative imgwidth exceptions</li>
5036 <li>better reporting of non-fatal warnings to user when
5037 file parsing fails.</li>
5038 <li>Save works when Jalview project is default format</li>
5039 <li>Save as dialog opened if current alignment format is
5040 not a valid output format</li>
5041 <li>UniProt canonical names introduced for both das and
5043 <li>Histidine should be midblue (not pink!) in Zappo</li>
5044 <li>error messages passed up and output when data read
5046 <li>edit undo recovers previous dataset sequence when
5047 sequence is edited</li>
5048 <li>allow PDB files without pdb ID HEADER lines (like
5049 those generated by MODELLER) to be read in properly</li>
5050 <li>allow reading of JPred concise files as a normal
5052 <li>Stockholm annotation parsing and alignment properties
5053 import fixed for PFAM records</li>
5054 <li>Structure view windows have correct name in Desktop
5056 <li>annotation consisting of sequence associated scores
5057 can be read and written correctly to annotation file</li>
5058 <li>Aligned cDNA translation to aligned peptide works
5060 <li>Fixed display of hidden sequence markers and
5061 non-italic font for representatives in Applet</li>
5062 <li>Applet Menus are always embedded in applet window on
5064 <li>Newly shown features appear at top of stack (in
5066 <li>Annotations added via parameter not drawn properly
5067 due to null pointer exceptions</li>
5068 <li>Secondary structure lines are drawn starting from
5069 first column of alignment</li>
5070 <li>UniProt XML import updated for new schema release in
5072 <li>Sequence feature to sequence ID match for Features
5073 file is case-insensitive</li>
5074 <li>Sequence features read from Features file appended to
5075 all sequences with matching IDs</li>
5076 <li>PDB structure coloured correctly for associated views
5077 containing a sub-sequence</li>
5078 <li>PDB files can be retrieved by applet from Jar files</li>
5079 <li>feature and annotation file applet parameters
5080 referring to different directories are retrieved correctly</li>
5081 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
5082 <li>Fixed application hang whilst waiting for
5083 splash-screen version check to complete</li>
5084 <li>Applet properly URLencodes input parameter values
5085 when passing them to the launchApp service</li>
5086 <li>display name and local features preserved in results
5087 retrieved from web service</li>
5088 <li>Visual delay indication for sequence retrieval and
5089 sequence fetcher initialisation</li>
5090 <li>updated Application to use DAS 1.53e version of
5091 dasobert DAS client</li>
5092 <li>Re-instated Full AMSA support and .amsa file
5094 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
5102 <div align="center">
5103 <strong>2.3</strong><br> 9/5/07
5108 <li>Jmol 11.0.2 integration</li>
5109 <li>PDB views stored in Jalview XML files</li>
5110 <li>Slide sequences</li>
5111 <li>Edit sequence in place</li>
5112 <li>EMBL CDS features</li>
5113 <li>DAS Feature mapping</li>
5114 <li>Feature ordering</li>
5115 <li>Alignment Properties</li>
5116 <li>Annotation Scores</li>
5117 <li>Sort by scores</li>
5118 <li>Feature/annotation editing in applet</li>
5123 <li>Headless state operation in 2.2.1</li>
5124 <li>Incorrect and unstable DNA pairwise alignment</li>
5125 <li>Cut and paste of sequences with annotation</li>
5126 <li>Feature group display state in XML</li>
5127 <li>Feature ordering in XML</li>
5128 <li>blc file iteration selection using filename # suffix</li>
5129 <li>Stockholm alignment properties</li>
5130 <li>Stockhom alignment secondary structure annotation</li>
5131 <li>2.2.1 applet had no feature transparency</li>
5132 <li>Number pad keys can be used in cursor mode</li>
5133 <li>Structure Viewer mirror image resolved</li>
5140 <div align="center">
5141 <strong>2.2.1</strong><br> 12/2/07
5146 <li>Non standard characters can be read and displayed
5147 <li>Annotations/Features can be imported/exported to the
5149 <li>Applet allows editing of sequence/annotation/group
5150 name & description
5151 <li>Preference setting to display sequence name in
5153 <li>Annotation file format extended to allow
5154 Sequence_groups to be defined
5155 <li>Default opening of alignment overview panel can be
5156 specified in preferences
5157 <li>PDB residue numbering annotation added to associated
5163 <li>Applet crash under certain Linux OS with Java 1.6
5165 <li>Annotation file export / import bugs fixed
5166 <li>PNG / EPS image output bugs fixed
5172 <div align="center">
5173 <strong>2.2</strong><br> 27/11/06
5178 <li>Multiple views on alignment
5179 <li>Sequence feature editing
5180 <li>"Reload" alignment
5181 <li>"Save" to current filename
5182 <li>Background dependent text colour
5183 <li>Right align sequence ids
5184 <li>User-defined lower case residue colours
5187 <li>Menu item accelerator keys
5188 <li>Control-V pastes to current alignment
5189 <li>Cancel button for DAS Feature Fetching
5190 <li>PCA and PDB Viewers zoom via mouse roller
5191 <li>User-defined sub-tree colours and sub-tree selection
5194 <li>'New Window' button on the 'Output to Text box'
5199 <li>New memory efficient Undo/Redo System
5200 <li>Optimised symbol lookups and conservation/consensus
5202 <li>Region Conservation/Consensus recalculated after
5204 <li>Fixed Remove Empty Columns Bug (empty columns at end
5206 <li>Slowed DAS Feature Fetching for increased robustness.
5209 <li>Made angle brackets in ASCII feature descriptions
5211 <li>Re-instated Zoom function for PCA
5212 <li>Sequence descriptions conserved in web service
5214 <li>UniProt ID discoverer uses any word separated by
5216 <li>WsDbFetch query/result association resolved
5217 <li>Tree leaf to sequence mapping improved
5218 <li>Smooth fonts switch moved to FontChooser dialog box.
5226 <div align="center">
5227 <strong>2.1.1</strong><br> 12/9/06
5232 <li>Copy consensus sequence to clipboard</li>
5237 <li>Image output - rightmost residues are rendered if
5238 sequence id panel has been resized</li>
5239 <li>Image output - all offscreen group boundaries are
5241 <li>Annotation files with sequence references - all
5242 elements in file are relative to sequence position</li>
5243 <li>Mac Applet users can use Alt key for group editing</li>
5249 <div align="center">
5250 <strong>2.1</strong><br> 22/8/06
5255 <li>MAFFT Multiple Alignment in default Web Service list</li>
5256 <li>DAS Feature fetching</li>
5257 <li>Hide sequences and columns</li>
5258 <li>Export Annotations and Features</li>
5259 <li>GFF file reading / writing</li>
5260 <li>Associate structures with sequences from local PDB
5262 <li>Add sequences to exisiting alignment</li>
5263 <li>Recently opened files / URL lists</li>
5264 <li>Applet can launch the full application</li>
5265 <li>Applet has transparency for features (Java 1.2
5267 <li>Applet has user defined colours parameter</li>
5268 <li>Applet can load sequences from parameter
5269 "sequence<em>x</em>"
5275 <li>Redundancy Panel reinstalled in the Applet</li>
5276 <li>Monospaced font - EPS / rescaling bug fixed</li>
5277 <li>Annotation files with sequence references bug fixed</li>
5283 <div align="center">
5284 <strong>2.08.1</strong><br> 2/5/06
5289 <li>Change case of selected region from Popup menu</li>
5290 <li>Choose to match case when searching</li>
5291 <li>Middle mouse button and mouse movement can compress /
5292 expand the visible width and height of the alignment</li>
5297 <li>Annotation Panel displays complete JNet results</li>
5303 <div align="center">
5304 <strong>2.08b</strong><br> 18/4/06
5310 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
5311 <li>Righthand label on wrapped alignments shows correct
5318 <div align="center">
5319 <strong>2.08</strong><br> 10/4/06
5324 <li>Editing can be locked to the selection area</li>
5325 <li>Keyboard editing</li>
5326 <li>Create sequence features from searches</li>
5327 <li>Precalculated annotations can be loaded onto
5329 <li>Features file allows grouping of features</li>
5330 <li>Annotation Colouring scheme added</li>
5331 <li>Smooth fonts off by default - Faster rendering</li>
5332 <li>Choose to toggle Autocalculate Consensus On/Off</li>
5337 <li>Drag & Drop fixed on Linux</li>
5338 <li>Jalview Archive file faster to load/save, sequence
5339 descriptions saved.</li>
5345 <div align="center">
5346 <strong>2.07</strong><br> 12/12/05
5351 <li>PDB Structure Viewer enhanced</li>
5352 <li>Sequence Feature retrieval and display enhanced</li>
5353 <li>Choose to output sequence start-end after sequence
5354 name for file output</li>
5355 <li>Sequence Fetcher WSDBFetch@EBI</li>
5356 <li>Applet can read feature files, PDB files and can be
5357 used for HTML form input</li>
5362 <li>HTML output writes groups and features</li>
5363 <li>Group editing is Control and mouse click</li>
5364 <li>File IO bugs</li>
5370 <div align="center">
5371 <strong>2.06</strong><br> 28/9/05
5376 <li>View annotations in wrapped mode</li>
5377 <li>More options for PCA viewer</li>
5382 <li>GUI bugs resolved</li>
5383 <li>Runs with -nodisplay from command line</li>
5389 <div align="center">
5390 <strong>2.05b</strong><br> 15/9/05
5395 <li>Choose EPS export as lineart or text</li>
5396 <li>Jar files are executable</li>
5397 <li>Can read in Uracil - maps to unknown residue</li>
5402 <li>Known OutOfMemory errors give warning message</li>
5403 <li>Overview window calculated more efficiently</li>
5404 <li>Several GUI bugs resolved</li>
5410 <div align="center">
5411 <strong>2.05</strong><br> 30/8/05
5416 <li>Edit and annotate in "Wrapped" view</li>
5421 <li>Several GUI bugs resolved</li>
5427 <div align="center">
5428 <strong>2.04</strong><br> 24/8/05
5433 <li>Hold down mouse wheel & scroll to change font
5439 <li>Improved JPred client reliability</li>
5440 <li>Improved loading of Jalview files</li>
5446 <div align="center">
5447 <strong>2.03</strong><br> 18/8/05
5452 <li>Set Proxy server name and port in preferences</li>
5453 <li>Multiple URL links from sequence ids</li>
5454 <li>User Defined Colours can have a scheme name and added
5456 <li>Choose to ignore gaps in consensus calculation</li>
5457 <li>Unix users can set default web browser</li>
5458 <li>Runs without GUI for batch processing</li>
5459 <li>Dynamically generated Web Service Menus</li>
5464 <li>InstallAnywhere download for Sparc Solaris</li>
5470 <div align="center">
5471 <strong>2.02</strong><br> 18/7/05
5477 <li>Copy & Paste order of sequences maintains
5478 alignment order.</li>
5484 <div align="center">
5485 <strong>2.01</strong><br> 12/7/05
5490 <li>Use delete key for deleting selection.</li>
5491 <li>Use Mouse wheel to scroll sequences.</li>
5492 <li>Help file updated to describe how to add alignment
5494 <li>Version and build date written to build properties
5496 <li>InstallAnywhere installation will check for updates
5497 at launch of Jalview.</li>
5502 <li>Delete gaps bug fixed.</li>
5503 <li>FileChooser sorts columns.</li>
5504 <li>Can remove groups one by one.</li>
5505 <li>Filechooser icons installed.</li>
5506 <li>Finder ignores return character when searching.
5507 Return key will initiate a search.<br>
5514 <div align="center">
5515 <strong>2.0</strong><br> 20/6/05
5520 <li>New codebase</li>