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 <em>Jalview Native App</em>
119 <!-- JAL- -->New Jalview Develop app - making it even easier
120 to get at Jalview's development builds
123 <!-- JAL-3594 -->New splashscreens for Jalview, Jalview Test
124 and Jalview Develop applications.
127 <!-- JAL-3728 -->Jalview logos shown for Jalview Java
128 Console and other window widgets in taskbar and dock rather
129 than anonymous 'Java' icons
131 </ul> <em>JalviewJS</em>
134 <!-- JAL-3624 -->PDB structures mapped to Uniprot Sequences with
138 <!-- JAL-3208 -->setprop commandline argument reinstated for JalviewJS only
147 <!-- JAL-3163 -->Missing message bundle keys are only
148 reported once per key (avoids excessive log output in js
152 <!-- JAL-3168 -->Feature type is included in the title of
153 the Feature Settings' Colour Chooser dialog
156 </ul> <em>Development</em>
159 <!-- -->First integrated JalviewJS and Jalview release
161 <li>Updated building instructions</li>
163 <!-- JAL-3789, JAL-3679 -->Improved JalviewJS/Jalview build
164 process, added support for system package provided eclipse
167 <li>Install4j 9.0.x used for installer packaging</li>
168 <li>Notarized MacOS installer for compatibility with Big
169 Sur and Monterey</li>
171 <!-- JAL-3805 -->Uninstaller application for old
172 (InstallAnywhere based) Jalview installations removed from
176 <!-- JAL-3930 -->Improved use of installers for unattended
177 installation with a customizedId of "JALVIEW" in install4j's
187 <!-- JAL-3674 -->Slow structure commands can block Jalview
191 <!-- JAL-3904 -->Structure window's viewer-specific menu
192 disappears when only one structure is shown (and many
193 sequences:one chain mappings are present)
196 <!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
197 the first SEQUENCE_GROUP defined
202 <!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 -->Selections not
203 propagated between Linked CDS - Protein alignments and their
204 trees (known defect from 2.11.1.3)
207 <!-- JAL-3761 -->Not all codon positions highlighted for
208 overlapping exon splice sites (e.g due to RNA slippage)
211 <!-- JAL-3794 -->X was not being recognised as the unknown
212 base in DNA sequences
215 <!-- JAL-3915 -->Removed RNAview checkbox and logic from
216 Structure Preferences
219 <!-- JAL-3583 -->Tooltip behaviour improved (slightly)
222 <!-- JAL-3162 -->Can edit a feature so that start > end
225 <!-- JAL-2848 -->Cancel from Amend Features doesn't reset a
226 modified graduated colour
229 <!-- JAL-3788 -->New View with automatic 'Show Overview'
230 preference enabled results in Null Pointer Exceptions when
231 clustal colouring is enabled
234 <!-- JAL-3275 -->Can open multiple Preferences panels
237 <!-- JAL-3949 -->Standard out logging broken: messages only
238 routing to stderr and appear as a raw template
240 </ul> <em>JalviewJS</em>
243 <!-- JAL-3202 -->Consensus profile may include zero (rounded
244 down) percentage values causing a divide by zero
259 <!-- JAL-3762 -->JalviewJS doesn't honour arguments passed
260 via Info.args when there are arguments on the URL
263 <!-- JAL-3602 -->gradle closure-compiler not using UTF-8
266 <!-- JAL-3603 -->Annotation file fails to load from URL in
269 </ul> <em>Development</em>
273 <li>Fixed non-fatal gradle errors during build</li>
275 <!-- JAL-3745 -->Updated build.gradle for use with
285 <td width="60" align="center" nowrap><strong><a
286 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.7">.7</a><br />
287 <em>18/01/2022</em></strong></td>
289 <td align="left" valign="top">
292 <!-- JAL-3703, JAL-3935 -->Files open in Jalview cannot be
293 updated by Jalview or other applications (Windows, other non
296 </ul> <em>Security</em>
299 <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
305 <td width="60" align="center" nowrap><strong><a
306 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
307 <em>6/01/2022</em></strong></td>
309 <td align="left" valign="top"><em>Security</em>
312 <!-- JAL-3934 -->Version bump library dependency: Log4j
319 <td width="60" align="center" nowrap><strong><a
320 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
321 <em>20/12/2021</em></strong></td>
323 <td align="left" valign="top"><em>Security</em>
326 <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
328 </ul> <em>Development</em>
330 <li>Updated building instructions</li>
335 <!-- JAL-3840 -->Occupancy calculation is incorrect for
336 alignment columns with over -1+2^32 gaps (breaking filtering
340 <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
341 scale factors being set with buggy window-managers (linux
344 </ul> <em>Development</em>
346 <li>Fixed non-fatal gradle errors during build</li>
351 <td width="60" align="center" nowrap><strong><a
352 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
353 <em>09/03/2021</em></strong></td>
354 <td align="left" valign="top"><em>Improved control of
355 Jalview's use of network services via jalview_properties</em>
358 <!-- JAL-3814 -->New .jalview_properties token controlling
359 launch of the news browser (like -nonews argument)
362 <!-- JAL-3813 -->New .jalview_properties token controlling
363 download of linkout URLs from
364 www.jalview.org/services/identifiers
367 <!-- JAL-3812 -->New .jalview_properties token controlling
368 download of BIOJSHTML templates
371 <!-- JAL-3811 -->New 'Discover Web Services' option to
372 trigger a one off JABAWS discovery if autodiscovery was
376 <td align="left" valign="top">
379 <!-- JAL-3818 -->Intermittent deadlock opening structure in
382 </ul> <em>New Known defects</em>
385 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
386 always restored from project (since 2.10.3)
389 <!-- JAL-3806 -->Selections from tree built from CDS aren't
390 propagated to Protein alignment (since 2.11.1.3)
396 <td width="60" align="center" nowrap><strong><a
397 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
398 <em>29/10/2020</em></strong></td>
399 <td align="left" valign="top">
404 <td align="left" valign="top">
407 <!-- JAL-3765 -->Find doesn't always highlight all matching
408 positions in a sequence (bug introduced in 2.11.1.2)
411 <!-- JAL-3760 -->Alignments containing one or more protein
412 sequences can be classed as nucleotide
415 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
416 sequences after alignment of protein products (known defect
417 first reported for 2.11.1.0)
420 <!-- JAL-3725 -->No tooltip or popup menu for genomic
421 features outwith CDS shown overlaid on protein
424 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
425 correctly mapped by Jalview (e.g. affects viral CDS with
426 ribosomal slippage, since 2.9.0)
429 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
433 <!-- JAL-3700 -->Selections in CDS sequence panel don't
434 always select corresponding protein sequences
437 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
438 column selection doesn't always ignore hidden columns
440 </ul> <em>Installer</em>
443 <!-- JAL-3611 -->Space character in Jalview install path on
444 Windows prevents install4j launching getdown
446 </ul> <em>Development</em>
449 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
450 version numbers in doc/building.md
456 <td width="60" align="center" nowrap><strong><a
457 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
458 <em>25/09/2020</em></strong></td>
459 <td align="left" valign="top">
463 <td align="left" valign="top">
466 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
467 "Encountered problems opening
468 https://www.jalview.org/examples/exampleFile_2_7.jvp"
474 <td width="60" align="center" nowrap><strong><a
475 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
476 <em>17/09/2020</em></strong></td>
477 <td align="left" valign="top">
480 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
481 residue in cursor mode
484 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
485 HTSJDK from 2.12 to 2.23
488 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
489 optimisations and improvements suggested by Bob Hanson and
490 improved compatibility with JalviewJS
493 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
494 alignments from Pfam and Rfam
497 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
498 import (no longer based on .gz extension)
501 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
504 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
505 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
509 <!-- JAL-3667 -->Improved warning messages, debug logging
510 and fixed Retry action when Jalview encounters errors when
511 saving or making backup files.
514 <!-- JAL-3676 -->Enhanced Jalview Java Console:
516 <li>Jalview's logging level can be configured</li>
517 <li>Copy to Clipboard Buttion</li>
521 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
522 when running on Linux (Requires Java 11+)
524 </ul> <em>Launching Jalview</em>
527 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
528 through a system property
531 <!-- JAL-3477 -->Improved built-in documentation and command
532 line help for configuring Jalview's memory
536 <td align="left" valign="top">
539 <!-- JAL-3691 -->Conservation and Quality tracks are shown
540 but not calculated and no protein or DNA score models are
541 available for tree/PCA calculation when launched with
542 Turkish language locale
545 <!-- JAL-3493 -->Escape does not clear highlights on the
546 alignment (Since Jalview 2.10.3)
549 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
550 doesn't slide selected sequences, just sequence under cursor
553 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
554 sequence under the cursor
557 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
558 multiple EMBL gene products shown for a single contig
561 <!-- JAL-3696 -->Errors encountered when processing variants
562 from VCF files yield "Error processing VCF: Format specifier
566 <!-- JAL-3697 -->Count of features not shown can be wrong
567 when there are both local and complementary features mapped
568 to the position under the cursor
571 <!-- JAL-3673 -->Sequence ID for reference sequence is
572 clipped when Right align Sequence IDs enabled
575 <!-- JAL-2983 -->Slider with negative range values not
576 rendered correctly in VAqua4 (Since 2.10.4)
579 <!-- JAL-3685 -->Single quotes not displayed correctly in
580 internationalised text for some messages and log output
583 <!-- JAL-3490 -->Find doesn't report matches that span
584 hidden gapped columns
587 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
588 panels, Alignment viewport and annotation renderer.
591 <!-- JAL-3561 -->Jalview ignores file format parameter
592 specifying output format when exporting an alignment via the
596 <!-- JAL-3667 -->Windows 10: For a minority of users, if
597 backups are not enabled, Jalview sometimes fails to
598 overwrite an existing file and raises a warning dialog. (in
599 2.11.0, and 2.11.1.0, the workaround is to try to save the
600 file again, and if that fails, delete the original file and
604 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
608 <!-- JAL-3741 -->References to http://www.jalview.org in
609 program and documentation
611 </ul> <em>Launching Jalview</em>
614 <!-- JAL-3718 -->Jalview application fails when launched the
615 first time for a version that has different jars to the
616 previous launched version.
618 </ul> <em>Developing Jalview</em>
621 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
622 data, causing cloverReport gradle task to fail with an
626 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
627 monitor the release channel
629 </ul> <em>New Known defects</em>
632 <!-- JAL-3748 -->CDS shown in result of submitting proteins
633 in a CDS/Protein alignment to a web service is wrong when
634 proteins share a common transcript sequence (e.g. genome of
638 <!-- JAL-3576 -->Co-located features exported and
639 re-imported are ordered differently when shown on alignment
640 and in tooltips. (Also affects v2.11.1.0)
643 <!-- JAL-3702 -->Drag and drop of alignment file onto
644 alignment window when in a HiDPI scaled mode in Linux only
645 works for the top left quadrant of the alignment window
648 <!-- JAL-3701 -->Stale build data in jalview standalone jar
649 builds (only affects 2.11.1.1 branch)
652 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
653 when alignment view restored from project (since Jalview
657 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
658 protein products for certain ENA records are repeatedly
659 shown via Calculate->Show Cross Refs
665 <td width="60" align="center" nowrap><strong><a
666 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
667 <em>22/04/2020</em></strong></td>
668 <td align="left" valign="top">
671 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
672 'virtual' codon features shown on protein (or vice versa)
673 for display in alignments, on structure views (including
674 transfer to UCSF chimera), in feature reports and for
678 <!-- JAL-3121 -->Feature attributes from VCF files can be
679 exported and re-imported as GFF3 files
682 <!-- JAL-3376 -->Capture VCF "fixed column" values
683 POS, ID, QUAL, FILTER as Feature Attributes
686 <!-- JAL-3375 -->More robust VCF numeric data field
687 validation while parsing
690 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
694 <!-- JAL-3535 -->Feature Settings dialog title includes name
698 <!-- JAL-3538 -->Font anti-aliasing in alignment views
702 <!-- JAL-3468 -->Very long feature descriptions truncated in
706 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
707 with no feature types visible
710 <!-- JAL-3574 -->Improved support for filtering feature
711 attributes with large integer values
714 <em>Jalview Installer</em>
717 <!-- JAL-3449 -->Versions for install4j and getdown and
718 installer template version reported in console (may be null
719 when Jalview launched as executable jar or via conda)
722 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and
723 higher quality background images
726 <!-- JAL-3394 -->New installer/application launcher
727 generated with install4j 8.0.4
730 <!-- JAL-3420 -->Jalview File Associations shown for Unix
734 <!-- JAL-3477 -->Improved defaults for maximum memory
735 setting when running on large memory machines
737 </ul> <em>Release processes</em>
740 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
743 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier
744 access to test-release channel builds
746 </ul> <em>Build System</em>
749 <!-- JAL-3510 -->Clover updated to 4.4.1
752 <!-- JAL-3513 -->Test code included in Clover coverage
755 </ul> <em>Groovy Scripts</em>
758 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
759 to stdout containing the consensus sequence for each
760 alignment in a Jalview session
763 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
764 genomic sequence_variant annotation from CDS as
765 missense_variant or synonymous_variant on protein products.
769 <td align="left" valign="top">
772 <!-- JAL-3581 -->Hidden sequence markers still visible when
773 'Show hidden markers' option is not ticked
776 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
777 PNG output when 'Automatically set ID width' is set in
778 jalview preferences or properties file
781 <!-- JAL-3571 -->Feature Editor dialog can be opened when
782 'Show Sequence Features' option is not ticked
785 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
786 buttons in Feature Settings dialog are clicked when no
790 <!-- JAL-3412 -->ID margins for CDS and Protein views not
791 equal when split frame is first opened
794 <!-- JAL-3296 -->Sequence position numbers in status bar not
795 correct after editing a sequence's start position
798 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
799 with annotation and exceptions thrown when only a few
800 columns shown in wrapped mode
803 <!-- JAL-3386 -->Sequence IDs missing in headless export of
804 wrapped alignment figure with annotations
807 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
808 ID fails with ClassCastException
811 <!-- JAL-3389 -->Chimera session not restored from Jalview
815 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
816 feature settings dialog also selects columns
819 <!-- JAL-3473 -->SpinnerNumberModel causes
820 IllegalArgumentException in some circumstances
823 <!-- JAL-3534 -->Multiple feature settings dialogs can be
827 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
828 alignment window is closed
831 <!-- JAL-3406 -->Credits missing some authors in Jalview
832 help documentation for 2.11.0 release
835 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
836 includes Pfam ID as sequence's accession rather than its
839 </ul> <em>Java 11 Compatibility issues</em>
842 <!-- JAL-2987 -->OSX - Can't view some search results in
843 PDB/Uniprot search panel
845 </ul> <em>Installer</em>
848 <!-- JAL-3447 -->Jalview should not create file associations
849 for 3D structure files (.pdb, .mmcif. .cif)
851 </ul> <em>Repository and Source Release</em>
854 <!-- JAL-3474 -->removed obsolete .cvsignore files from
858 <!-- JAL-3541 -->Clover report generation running out of
861 </ul> <em>New Known Issues</em>
864 <!-- JAL-3523 -->OSX - Current working directory not
865 preserved when Jalview.app launched with parameters from
869 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
870 clipped in headless figure export when Right Align option
874 <!-- JAL-3542 -->Jalview Installation type always reports
875 'Source' in console output
878 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail
879 on jalview's bamboo server but run fine locally.
885 <td width="60" align="center" nowrap><strong><a
886 name="Jalview.2.11.0">2.11.0</a><br /> <em>04/07/2019</em></strong></td>
887 <td align="left" valign="top">
890 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native
891 Application and Installers built with <a
892 href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a>
893 (licensed to the Jalview open source project) rather than
897 <!-- JAL-1929 -->Jalview Launcher System to auto-configure
898 memory settings, receive over the air updates and launch
899 specific versions via (<a
900 href="https://github.com/threerings/getdown">Three
904 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations
905 for formats supported by Jalview (including .jvp project
909 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command
910 line arguments and switch between different getdown channels
913 <!-- JAL-3141 -->Backup files created when saving Jalview
914 project or alignment files
918 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF
922 <!-- JAL-2753 -->Version of HTSJDK shipped with Jalview
923 updated to version 2.12.0
926 <!-- JAL-2620 -->Alternative genetic code tables for
930 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0
932 <li><strong>Enhanced visualisation and analysis
933 of Sequence Features</strong>
936 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
937 implementation that allows updates) used for Sequence
941 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
942 features can be filtered and shaded according to any
943 associated attributes (e.g. variant attributes from VCF
944 file, or key-value pairs imported from column 9 of GFF
948 <!-- JAL-2879 -->Feature Attributes and shading schemes
949 stored and restored from Jalview Projects
952 <!-- JAL-3334 -->Use full Sequence Ontology (via
953 BioJava) to recognise variant features
956 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants
957 on peptide sequences (also coloured red by default)
960 <!-- JAL-2792 -->Popup window to show full report for a
961 selected sequence feature's details
964 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient
965 sequence feature render algorithm (Z-sort/transparency
969 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature
974 <!-- JAL-3205 -->Symmetric score matrices for faster tree
977 <li><strong>Principal Components Analysis Viewer</strong>
980 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis
981 results and Viewer state saved in Jalview Project
984 <!-- JAL-2962 -->'Change parameters' option removed from
985 viewer's drop-down menus
988 <!-- JAL-2975 -->Can use shift + arrow keys to rotate
989 PCA image incrementally
992 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
996 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
998 <li><strong>Speed and Efficiency</strong>
1001 <!-- JAL-2185,JAL-3198 -->More efficient creation of
1002 selections and multiple groups when working with large
1006 <!-- JAL-3200 -->Speedier import of annotation rows when
1007 parsing Stockholm files
1010 <li><strong>User Interface</strong>
1013 <!-- JAL-2933 -->Finder panel remembers last position in
1017 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS
1018 (What you see is what is shown)<br />Only visible
1019 regions of alignment are shown by default (can be
1020 changed in user preferences)
1023 <!-- JAL-3169 -->File Chooser stays open after
1024 responding Cancel to the Overwrite Dialog
1027 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour
1028 when all sequences are hidden
1031 <!-- JAL-1244 -->Status bar shows bounds when dragging a
1032 selection region, and gap count when inserting or
1036 <!-- JAL-3132 -->Status bar updates over sequence and
1040 <!-- JAL-3093 -->Annotation tooltips and popup menus are
1041 shown when in wrapped mode
1044 <!-- JAL-3073 -->Can select columns by dragging
1045 left/right in a graph or histogram annotation
1048 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB
1052 <!-- JAL-2621 -->Cursor changes over draggable box in
1056 <!-- JAL-3181 -->Consistent ordering of links in
1057 sequence id popup menu
1060 <!-- JAL-3080 -->Red line indicating tree-cut position
1061 not shown if no subgroups are created
1064 <!-- JAL-3042 -->Removed ability to configure length of
1065 search history by right-clicking search box
1071 <!-- JAL-3232 -->Jalview Groovy Scripting Console updated to
1074 <li><strong>Java 11 Support (not yet on general
1078 <!-- -->OSX GUI integrations for App menu's 'About'
1079 entry and trapping CMD-Q
1082 </ul> <em>Deprecations</em>
1085 <!-- JAL-3035 -->DAS sequence retrieval and annotation
1086 capabilities removed from the Jalview Desktop
1089 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling
1090 and unmarshalling has been replaced by JAXB for Jalview
1091 projects and XML based data retrieval clients
1094 <!-- JAL-3311 -->Disable VAMSAS menu in preparation for
1098 <!-- -->Jalview Desktop no longer distributed via Java Web
1101 </ul> <em>Documentation</em>
1104 <!-- JAL-3003 -->Added remarks about transparent rendering
1105 effects not supported in EPS figure export
1108 <!-- JAL-2903 -->Typos in documentation for Preferences
1111 </ul> <em>Development and Release Processes</em>
1114 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated
1118 <!-- JAL-1424 -->Enhanced checks for missing and duplicated
1119 keys in Message bundles
1122 <!-- JAL-3225 -->Eclipse project configuration managed with
1126 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian Bamboo
1127 continuous integration for unattended Test Suite execution
1130 <!-- JAL-2864 -->Memory test suite to detect leaks in common
1134 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
1138 <!-- JAL-3248 -->Developer documentation migrated to
1139 markdown (with HTML rendering)
1142 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
1145 <!-- JAL-3289 -->New URLs for publishing development
1150 <td align="left" valign="top">
1153 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
1156 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
1157 superposition in Jmol fail on Windows
1160 <!-- JAL-3286 -->Blank error dialog is displayed when
1161 discovering structures for sequences with lots of PDB
1165 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export
1166 with monospaced font
1169 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
1170 Jalview project involving multiple views
1173 <!-- JAL-3164 -->Overview for complementary view in a linked
1174 CDS/Protein alignment is not updated when Hide Columns by
1175 Annotation dialog hides columns
1178 <!-- JAL-3158 -->Selection highlighting in the complement of
1179 a CDS/Protein alignment stops working after making a
1180 selection in one view, then making another selection in the
1184 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
1188 <!-- JAL-3154 -->Table Columns could be re-ordered in
1189 Feature Settings and Jalview Preferences panels
1192 <!-- JAL-2865 -->Jalview hangs when closing windows, or
1193 redrawing the overview with large alignments
1196 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
1197 region if columns were selected by dragging right-to-left
1198 and the mouse moved to the left of the first column
1201 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to
1202 a hidden column marker via scale popup menu
1205 <!-- JAL-2846 -->Error message for trying to load in invalid
1206 URLs doesn't tell users the invalid URL
1209 <!-- JAL-2816 -->Tooltips displayed for features filtered by
1213 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl
1214 during show cross references or Fetch Database References
1215 are shown in red in original view
1218 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown
1219 correctly on peptide sequence (computed variant shown as
1223 <!-- JAL-2060 -->'Graduated colour' option not offered for
1224 manually created features (where feature score is Float.NaN)
1227 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or
1228 printed when columns are hidden
1231 <!-- JAL-3082 -->Regular expression error for '(' in Select
1232 Columns by Annotation description
1235 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after
1236 dragging out of Scale or Annotation Panel
1239 <!-- JAL-3075 -->Column selection incorrect after scrolling
1243 <!-- JAL-3074 -->Left/right drag in annotation can scroll
1247 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal
1251 <!-- JAL-3002 -->Column display is out by one after Page
1252 Down, Page Up in wrapped mode
1255 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
1258 <!-- JAL-2932 -->Finder searches in minimised alignments
1261 <!-- JAL-2250 -->'Apply Colour to All Groups' not always
1262 selected on opening an alignment
1265 <!-- JAL-3180 -->'Colour by Annotation' not marked selected
1269 <!-- JAL-3201 -->Per-group Clustal colour scheme changes
1270 when different groups in the alignment are selected
1273 <!-- JAL-2717 -->Internationalised colour scheme names not
1274 shown correctly in menu
1277 <!-- JAL-3206 -->Colour by Annotation can go black at
1278 min/max threshold limit
1281 <!-- JAL-3125 -->Value input for graduated feature colour
1282 threshold gets 'unrounded'
1285 <!-- JAL-2982 -->PCA image export doesn't respect background
1289 <!-- JAL-2963 -->PCA points don't dim when rotated about y
1293 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
1296 <!-- JAL-3078 -->Cancel in Tree Font dialog resets
1297 alignment, not Tree font
1300 <!-- JAL-2964 -->Associate Tree with All Views not restored
1304 <!-- JAL-2915 -->Scrolling of split frame is sluggish if
1305 Overview shown in complementary view
1308 <!-- JAL-3313 -->Codon consensus incorrectly scaled when
1309 shown without normalisation
1312 <!-- JAL-3021 -->Sequence Details report should open
1313 positioned at top of report
1316 <!-- JAL-914 -->Help page can be opened twice
1319 <!-- JAL-3333 -->Fuzzy text in web service status menu on
1322 </ul> <em>Editing</em>
1325 <!-- JAL-2822 -->Start and End should be updated when
1326 sequence data at beginning or end of alignment added/removed
1330 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection
1331 doesn't relocate sequence features correctly when start of
1332 sequence is removed (Known defect since 2.10)
1335 <!-- JAL-2830 -->Inserting gap sequence via the Edit
1336 Sequence dialog corrupts dataset sequence
1339 <!-- JAL-868 -->Structure colours not updated when
1340 associated tree repartitions the alignment view (Regression
1343 </ul> <em>Datamodel</em>
1346 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
1347 sequence's End is greater than its length
1349 </ul> <em>Bugs fixed for Java 11 Support (not yet on general
1353 <!-- JAL-3288 -->Menus work properly in split-screen
1355 </ul> <em>New Known Defects</em>
1358 <!-- JAL-3340 -->Select columns containing feature by double
1359 clicking ignores bounds of an existing selected region
1362 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in
1363 gapped regions of protein alignment.
1366 <!-- JAL-2647 -->Input Data menu entry is greyed out when
1367 PCA View is restored from a Jalview 2.11 project
1370 <!-- JAL-3213 -->Alignment panel height can be too small
1374 <!-- JAL-3240 -->Display is incorrect after removing gapped
1375 columns within hidden columns
1378 <!-- JAL-3314 -->Rightmost selection is lost when mouse
1379 re-enters window after dragging left to select columns to
1380 left of visible region
1383 <!-- JAL-2876 -->Features coloured according to their
1384 description string and thresholded by score in earlier
1385 versions of Jalview are not shown as thresholded features in
1386 2.11. To workaround please create a Score filter instead.
1389 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't
1390 reset group visibility
1393 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in
1394 linked CDS/Protein view
1397 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1398 alignments with multiple views can close views unexpectedly
1400 </ul> <em>Java 11 Specific defects</em>
1403 <!-- JAL-3235 -->Jalview Properties file is not sorted
1404 alphabetically when saved
1410 <td width="60" nowrap>
1411 <div align="center">
1412 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1415 <td><div align="left">
1419 <!-- JAL-3101 -->Default memory for Jalview webstart and
1420 InstallAnywhere increased to 1G.
1423 <!-- JAL-247 -->Hidden sequence markers and representative
1424 sequence bolding included when exporting alignment as EPS,
1425 SVG, PNG or HTML. <em>Display is configured via the
1426 Format menu, or for command-line use via a Jalview
1427 properties file.</em>
1430 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1431 API and sequence data now imported as JSON.
1434 <!-- JAL-3065 -->Change in recommended way of starting
1435 Jalview via a Java command line: add jars in lib directory
1436 to CLASSPATH, rather than via the deprecated java.ext.dirs
1440 <em>Development</em>
1443 <!-- JAL-3047 -->Support added to execute test suite
1444 instrumented with <a href="http://openclover.org/">Open
1449 <td><div align="left">
1453 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1454 row shown in Feredoxin Structure alignment view of example
1458 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1459 annotation displayed.
1462 <!-- JAL-3107 -->Group conservation/consensus not shown
1463 for newly created group when 'Apply to all groups'
1467 <!-- JAL-3087 -->Corrupted display when switching to
1468 wrapped mode when sequence panel's vertical scrollbar is
1472 <!-- JAL-3003 -->Alignment is black in exported EPS file
1473 when sequences are selected in exported view.</em>
1476 <!-- JAL-3059 -->Groups with different coloured borders
1477 aren't rendered with correct colour.
1480 <!-- JAL-3092 -->Jalview could hang when importing certain
1481 types of knotted RNA secondary structure.
1484 <!-- JAL-3095 -->Sequence highlight and selection in
1485 trimmed VARNA 2D structure is incorrect for sequences that
1489 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1490 annotation when columns are inserted into an alignment,
1491 and when exporting as Stockholm flatfile.
1494 <!-- JAL-3053 -->Jalview annotation rows containing upper
1495 and lower-case 'E' and 'H' do not automatically get
1496 treated as RNA secondary structure.
1499 <!-- JAL-3106 -->.jvp should be used as default extension
1500 (not .jar) when saving a Jalview project file.
1503 <!-- JAL-3105 -->Mac Users: closing a window correctly
1504 transfers focus to previous window on OSX
1507 <em>Java 10 Issues Resolved</em>
1510 <!-- JAL-2988 -->OSX - Can't save new files via the File
1511 or export menus by typing in a name into the Save dialog
1515 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1516 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1517 'look and feel' which has improved compatibility with the
1518 latest version of OSX.
1524 <td width="60" nowrap>
1525 <div align="center">
1526 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1527 <em>7/06/2018</em></strong>
1530 <td><div align="left">
1534 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1535 annotation retrieved from Uniprot
1538 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1539 onto the Jalview Desktop
1543 <td><div align="left">
1547 <!-- JAL-3017 -->Cannot import features with multiple
1548 variant elements (blocks import of some Uniprot records)
1551 <!-- JAL-2997 -->Clustal files with sequence positions in
1552 right-hand column parsed correctly
1555 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1556 not alignment area in exported graphic
1559 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1560 window has input focus
1563 <!-- JAL-2992 -->Annotation panel set too high when
1564 annotation added to view (Windows)
1567 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1568 network connectivity is poor
1571 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1572 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1573 the currently open URL and links from a page viewed in
1574 Firefox or Chrome on Windows is now fully supported. If
1575 you are using Edge, only links in the page can be
1576 dragged, and with Internet Explorer, only the currently
1577 open URL in the browser can be dropped onto Jalview.</em>
1580 <em>New Known Defects</em>
1583 <!-- JAL-3083 -->Cancel option doesn't reset Colour by
1590 <td width="60" nowrap>
1591 <div align="center">
1592 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1595 <td><div align="left">
1599 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1600 for disabling automatic superposition of multiple
1601 structures and open structures in existing views
1604 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1605 ID and annotation area margins can be click-dragged to
1609 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1613 <!-- JAL-2759 -->Improved performance for large alignments
1614 and lots of hidden columns
1617 <!-- JAL-2593 -->Improved performance when rendering lots
1618 of features (particularly when transparency is disabled)
1621 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2
1622 for exchange of Jalview features and Chimera attributes
1623 made generally available
1627 <td><div align="left">
1630 <!-- JAL-2899 -->Structure and Overview aren't updated
1631 when Colour By Annotation threshold slider is adjusted
1634 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1635 overlapping alignment panel
1638 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1642 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1643 improved: CDS not handled correctly if transcript has no
1647 <!-- JAL-2321 -->Secondary structure and temperature
1648 factor annotation not added to sequence when local PDB
1649 file associated with it by drag'n'drop or structure
1653 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1654 dialog doesn't import PDB files dropped on an alignment
1657 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1658 scroll bar doesn't work for some CDS/Protein views
1661 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1662 Java 1.8u153 onwards and Java 1.9u4+.
1665 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1666 columns in annotation row
1669 <!-- JAL-2913 -->Preferences panel's ID Width control is
1670 not honored in batch mode
1673 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1674 for structures added to existing Jmol view
1677 <!-- JAL-2223 -->'View Mappings' includes duplicate
1678 entries after importing project with multiple views
1681 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1682 protein sequences via SIFTS from associated PDB entries
1683 with negative residue numbers or missing residues fails
1686 <!-- JAL-2952 -->Exception when shading sequence with
1687 negative Temperature Factor values from annotated PDB
1688 files (e.g. as generated by CONSURF)
1691 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1692 tooltip doesn't include a text description of mutation
1695 <!-- JAL-2922 -->Invert displayed features very slow when
1696 structure and/or overview windows are also shown
1699 <!-- JAL-2954 -->Selecting columns from highlighted
1700 regions very slow for alignments with large numbers of
1704 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1705 with 'StringIndexOutOfBounds'
1708 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and
1709 Feel for OSX platforms running Java 10
1712 <!-- JAL-2960 -->Adding a structure to existing structure
1713 view appears to do nothing because the view is hidden
1714 behind the alignment view
1720 <!-- JAL-2926 -->Copy consensus sequence option in applet
1721 should copy the group consensus when popup is opened on it
1727 <!-- JAL-2913 -->Fixed ID width preference is not
1731 <em>New Known Defects</em>
1734 <!-- JAL-2973 --> Exceptions occasionally raised when
1735 editing a large alignment and overview is displayed
1738 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1739 repeatedly after a series of edits even when the overview
1740 is no longer reflecting updates
1743 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1744 structures for protein subsequence (if 'Trim Retrieved
1745 Sequences' enabled) or Ensembl isoforms (Workaround in
1746 2.10.4 is to fail back to N&W mapping)
1749 <!-- JAL-2990 -->Export Annotations from File Menu with
1750 CSV option gives blank output
1756 <td width="60" nowrap>
1757 <div align="center">
1758 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br />
1759 <em>24/1/2018</em></strong>
1762 <td><div align="left">
1764 <li>Updated Certum Codesigning Certificate (Valid till
1765 30th November 2018)</li>
1768 <td><div align="left">
1773 <!-- JAL-2859-->Only one structure is loaded when
1774 several sequences and structures are selected for
1778 <!-- JAL-2851-->Alignment doesn't appear to scroll
1779 vertically via trackpad and scrollwheel
1782 <!-- JAL-2842-->Jalview hangs if up/down arrows pressed
1783 in cursor mode when cursor lies in hidden region at
1787 <!-- JAL-2827-->Helix annotation has 'notches' when
1788 scrolled into view if columns are hidden
1791 <!-- JAL-2740-->Annotation column filter can be slow to
1792 reset (ie after hitting cancel) for large numbers of
1796 <!-- JAL-2849-->User preference for disabling inclusion
1797 of sequence limits when exporting as flat file has no
1801 <!-- JAL-2679-->Reproducible cross-reference
1802 relationships when retrieving sequences from
1809 <td width="60" nowrap>
1810 <div align="center">
1811 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1814 <td><div align="left">
1818 <!-- JAL-2446 -->Faster and more efficient management and
1819 rendering of sequence features
1822 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1823 429 rate limit request hander
1826 <!-- JAL-2773 -->Structure views don't get updated unless
1827 their colours have changed
1830 <!-- JAL-2495 -->All linked sequences are highlighted for
1831 a structure mousover (Jmol) or selection (Chimera)
1834 <!-- JAL-2790 -->'Cancel' button in progress bar for
1835 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1838 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1839 view from Ensembl locus cross-references
1842 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1846 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1847 feature can be disabled
1850 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1851 PDB easier retrieval of sequences for lists of IDs
1854 <!-- JAL-2758 -->Short names for sequences retrieved from
1860 <li>Groovy interpreter updated to 2.4.12</li>
1861 <li>Example groovy script for generating a matrix of
1862 percent identity scores for current alignment.</li>
1864 <em>Testing and Deployment</em>
1867 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1871 <td><div align="left">
1875 <!-- JAL-2643 -->Pressing tab after updating the colour
1876 threshold text field doesn't trigger an update to the
1880 <!-- JAL-2682 -->Race condition when parsing sequence ID
1884 <!-- JAL-2608 -->Overview windows are also closed when
1885 alignment window is closed
1888 <!-- JAL-2548 -->Export of features doesn't always respect
1892 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1893 takes a long time in Cursor mode
1899 <!-- JAL-2777 -->Structures with whitespace chainCode
1900 cannot be viewed in Chimera
1903 <!-- JAL-2728 -->Protein annotation panel too high in
1907 <!-- JAL-2757 -->Can't edit the query after the server
1908 error warning icon is shown in Uniprot and PDB Free Text
1912 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1915 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1918 <!-- JAL-2739 -->Hidden column marker in last column not
1919 rendered when switching back from Wrapped to normal view
1922 <!-- JAL-2768 -->Annotation display corrupted when
1923 scrolling right in unwapped alignment view
1926 <!-- JAL-2542 -->Existing features on subsequence
1927 incorrectly relocated when full sequence retrieved from
1931 <!-- JAL-2733 -->Last reported memory still shown when
1932 Desktop->Show Memory is unticked (OSX only)
1935 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1936 features of same type and group to be selected for
1940 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1941 alignments when hidden columns are present
1944 <!-- JAL-2392 -->Jalview freezes when loading and
1945 displaying several structures
1948 <!-- JAL-2732 -->Black outlines left after resizing or
1952 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1953 within the Jalview desktop on OSX
1956 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1957 when in wrapped alignment mode
1960 <!-- JAL-2636 -->Scale mark not shown when close to right
1961 hand end of alignment
1964 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1965 each selected sequence do not have correct start/end
1969 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1970 after canceling the Alignment Window's Font dialog
1973 <!-- JAL-2036 -->Show cross-references not enabled after
1974 restoring project until a new view is created
1977 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1978 URL links appears when only default EMBL-EBI link is
1979 configured (since 2.10.2b2)
1982 <!-- JAL-2775 -->Overview redraws whole window when box
1983 position is adjusted
1986 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1987 in a multi-chain structure when viewing alignment
1988 involving more than one chain (since 2.10)
1991 <!-- JAL-2811 -->Double residue highlights in cursor mode
1992 if new selection moves alignment window
1995 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1996 arrow key in cursor mode to pass hidden column marker
1999 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
2000 that produces correctly annotated transcripts and products
2003 <!-- JAL-2776 -->Toggling a feature group after first time
2004 doesn't update associated structure view
2007 <em>Applet</em><br />
2010 <!-- JAL-2687 -->Concurrent modification exception when
2011 closing alignment panel
2014 <em>BioJSON</em><br />
2017 <!-- JAL-2546 -->BioJSON export does not preserve
2018 non-positional features
2021 <em>New Known Issues</em>
2024 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
2025 sequence features correctly (for many previous versions of
2029 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
2030 using cursor in wrapped panel other than top
2033 <!-- JAL-2791 -->Select columns containing feature ignores
2034 graduated colour threshold
2037 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
2038 always preserve numbering and sequence features
2041 <em>Known Java 9 Issues</em>
2044 <!-- JAL-2902 -->Groovy Console very slow to open and is
2045 not responsive when entering characters (Webstart, Java
2052 <td width="60" nowrap>
2053 <div align="center">
2054 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
2055 <em>2/10/2017</em></strong>
2058 <td><div align="left">
2059 <em>New features in Jalview Desktop</em>
2062 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API
2066 <!-- JAL-2745 -->HTTPS used for all connections to
2071 <td><div align="left"></div></td>
2074 <td width="60" nowrap>
2075 <div align="center">
2076 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
2077 <em>7/9/2017</em></strong>
2080 <td><div align="left">
2084 <!-- JAL-2588 -->Show gaps in overview window by colouring
2085 in grey (sequences used to be coloured grey, and gaps were
2089 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
2093 <!-- JAL-2587 -->Overview updates immediately on increase
2094 in size and progress bar shown as higher resolution
2095 overview is recalculated
2100 <td><div align="left">
2104 <!-- JAL-2664 -->Overview window redraws every hidden
2105 column region row by row
2108 <!-- JAL-2681 -->duplicate protein sequences shown after
2109 retrieving Ensembl crossrefs for sequences from Uniprot
2112 <!-- JAL-2603 -->Overview window throws NPE if show boxes
2113 format setting is unticked
2116 <!-- JAL-2610 -->Groups are coloured wrongly in overview
2117 if group has show boxes format setting unticked
2120 <!-- JAL-2672,JAL-2665 -->Redraw problems when
2121 autoscrolling whilst dragging current selection group to
2122 include sequences and columns not currently displayed
2125 <!-- JAL-2691 -->Not all chains are mapped when multimeric
2126 assemblies are imported via CIF file
2129 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
2130 displayed when threshold or conservation colouring is also
2134 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
2138 <!-- JAL-2673 -->Jalview continues to scroll after
2139 dragging a selected region off the visible region of the
2143 <!-- JAL-2724 -->Cannot apply annotation based
2144 colourscheme to all groups in a view
2147 <!-- JAL-2511 -->IDs don't line up with sequences
2148 initially after font size change using the Font chooser or
2155 <td width="60" nowrap>
2156 <div align="center">
2157 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
2160 <td><div align="left">
2161 <em>Calculations</em>
2165 <!-- JAL-1933 -->Occupancy annotation row shows number of
2166 ungapped positions in each column of the alignment.
2169 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
2170 a calculation dialog box
2173 <!-- JAL-2379 -->Revised implementation of PCA for speed
2174 and memory efficiency (~30x faster)
2177 <!-- JAL-2403 -->Revised implementation of sequence
2178 similarity scores as used by Tree, PCA, Shading Consensus
2179 and other calculations
2182 <!-- JAL-2416 -->Score matrices are stored as resource
2183 files within the Jalview codebase
2186 <!-- JAL-2500 -->Trees computed on Sequence Feature
2187 Similarity may have different topology due to increased
2194 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
2195 model for alignments and groups
2198 <!-- JAL-384 -->Custom shading schemes created via groovy
2205 <!-- JAL-2526 -->Efficiency improvements for interacting
2206 with alignment and overview windows
2209 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
2213 <!-- JAL-2388 -->Hidden columns and sequences can be
2217 <!-- JAL-2611 -->Click-drag in visible area allows fine
2218 adjustment of visible position
2222 <em>Data import/export</em>
2225 <!-- JAL-2535 -->Posterior probability annotation from
2226 Stockholm files imported as sequence associated annotation
2229 <!-- JAL-2507 -->More robust per-sequence positional
2230 annotation input/output via stockholm flatfile
2233 <!-- JAL-2533 -->Sequence names don't include file
2234 extension when importing structure files without embedded
2235 names or PDB accessions
2238 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
2239 format sequence substitution matrices
2242 <em>User Interface</em>
2245 <!-- JAL-2447 --> Experimental Features Checkbox in
2246 Desktop's Tools menu to hide or show untested features in
2250 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
2251 via Overview or sequence motif search operations
2254 <!-- JAL-2547 -->Amend sequence features dialog box can be
2255 opened by double clicking gaps within sequence feature
2259 <!-- JAL-1476 -->Status bar message shown when not enough
2260 aligned positions were available to create a 3D structure
2264 <em>3D Structure</em>
2267 <!-- JAL-2430 -->Hidden regions in alignment views are not
2268 coloured in linked structure views
2271 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
2272 file-based command exchange
2275 <!-- JAL-2375 -->Structure chooser automatically shows
2276 Cached Structures rather than querying the PDBe if
2277 structures are already available for sequences
2280 <!-- JAL-2520 -->Structures imported via URL are cached in
2281 the Jalview project rather than downloaded again when the
2282 project is reopened.
2285 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
2286 to transfer Chimera's structure attributes as Jalview
2287 features, and vice-versa (<strong>Experimental
2291 <em>Web Services</em>
2294 <!-- JAL-2549 -->Updated JABAWS client to v2.2
2297 <!-- JAL-2335 -->Filter non-standard amino acids and
2298 nucleotides when submitting to AACon and other MSA
2302 <!-- JAL-2316, -->URLs for viewing database
2303 cross-references provided by identifiers.org and the
2304 EMBL-EBI's MIRIAM DB
2311 <!-- JAL-2344 -->FileFormatI interface for describing and
2312 identifying file formats (instead of String constants)
2315 <!-- JAL-2228 -->FeatureCounter script refactored for
2316 efficiency when counting all displayed features (not
2317 backwards compatible with 2.10.1)
2320 <em>Example files</em>
2323 <!-- JAL-2631 -->Graduated feature colour style example
2324 included in the example feature file
2327 <em>Documentation</em>
2330 <!-- JAL-2339 -->Release notes reformatted for readability
2331 with the built-in Java help viewer
2334 <!-- JAL-1644 -->Find documentation updated with 'search
2335 sequence description' option
2341 <!-- JAL-2485, -->External service integration tests for
2342 Uniprot REST Free Text Search Client
2345 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
2348 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
2353 <td><div align="left">
2354 <em>Calculations</em>
2357 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
2358 matrix - C->R should be '-3'<br />Old matrix restored
2359 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
2361 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
2362 Jalview's treatment of gaps in PCA and substitution matrix
2363 based Tree calculations.<br /> <br />In earlier versions
2364 of Jalview, gaps matching gaps were penalised, and gaps
2365 matching non-gaps penalised even more. In the PCA
2366 calculation, gaps were actually treated as non-gaps - so
2367 different costs were applied, which meant Jalview's PCAs
2368 were different to those produced by SeqSpace.<br />Jalview
2369 now treats gaps in the same way as SeqSpace (ie it scores
2370 them as 0). <br /> <br />Enter the following in the
2371 Groovy console to restore pre-2.10.2 behaviour:<br />
2372 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
2373 // for 2.10.1 mode <br />
2374 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
2375 // to restore 2.10.2 mode <br /> <br /> <em>Note:
2376 these settings will affect all subsequent tree and PCA
2377 calculations (not recommended)</em></li>
2379 <!-- JAL-2424 -->Fixed off-by-one bug that affected
2380 scaling of branch lengths for trees computed using
2381 Sequence Feature Similarity.
2384 <!-- JAL-2377 -->PCA calculation could hang when
2385 generating output report when working with highly
2386 redundant alignments
2389 <!-- JAL-2544 --> Sort by features includes features to
2390 right of selected region when gaps present on right-hand
2394 <em>User Interface</em>
2397 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2398 doesn't reselect a specific sequence's associated
2399 annotation after it was used for colouring a view
2402 <!-- JAL-2419 -->Current selection lost if popup menu
2403 opened on a region of alignment without groups
2406 <!-- JAL-2374 -->Popup menu not always shown for regions
2407 of an alignment with overlapping groups
2410 <!-- JAL-2310 -->Finder double counts if both a sequence's
2411 name and description match
2414 <!-- JAL-2370 -->Hiding column selection containing two
2415 hidden regions results in incorrect hidden regions
2418 <!-- JAL-2386 -->'Apply to all groups' setting when
2419 changing colour does not apply Conservation slider value
2423 <!-- JAL-2373 -->Percentage identity and conservation menu
2424 items do not show a tick or allow shading to be disabled
2427 <!-- JAL-2385 -->Conservation shading or PID threshold
2428 lost when base colourscheme changed if slider not visible
2431 <!-- JAL-2547 -->Sequence features shown in tooltip for
2432 gaps before start of features
2435 <!-- JAL-2623 -->Graduated feature colour threshold not
2436 restored to UI when feature colour is edited
2439 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2440 a time when scrolling vertically in wrapped mode.
2443 <!-- JAL-2630 -->Structure and alignment overview update
2444 as graduate feature colour settings are modified via the
2448 <!-- JAL-2034 -->Overview window doesn't always update
2449 when a group defined on the alignment is resized
2452 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2453 wrapped view result in positional status updates
2457 <!-- JAL-2563 -->Status bar doesn't show position for
2458 ambiguous amino acid and nucleotide symbols
2461 <!-- JAL-2602 -->Copy consensus sequence failed if
2462 alignment included gapped columns
2465 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2466 widgets don't permanently disappear
2469 <!-- JAL-2503 -->Cannot select or filter quantitative
2470 annotation that are shown only as column labels (e.g.
2471 T-Coffee column reliability scores)
2474 <!-- JAL-2594 -->Exception thrown if trying to create a
2475 sequence feature on gaps only
2478 <!-- JAL-2504 -->Features created with 'New feature'
2479 button from a Find inherit previously defined feature type
2480 rather than the Find query string
2483 <!-- JAL-2423 -->incorrect title in output window when
2484 exporting tree calculated in Jalview
2487 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2488 and then revealing them reorders sequences on the
2492 <!-- JAL-964 -->Group panel in sequence feature settings
2493 doesn't update to reflect available set of groups after
2494 interactively adding or modifying features
2497 <!-- JAL-2225 -->Sequence Database chooser unusable on
2501 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2502 only excluded gaps in current sequence and ignored
2509 <!-- JAL-2421 -->Overview window visible region moves
2510 erratically when hidden rows or columns are present
2513 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2514 Structure Viewer's colour menu don't correspond to
2518 <!-- JAL-2405 -->Protein specific colours only offered in
2519 colour and group colour menu for protein alignments
2522 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2523 reflect currently selected view or group's shading
2527 <!-- JAL-2624 -->Feature colour thresholds not respected
2528 when rendered on overview and structures when opacity at
2532 <!-- JAL-2589 -->User defined gap colour not shown in
2533 overview when features overlaid on alignment
2536 <!-- JAL-2567 -->Feature settings for different views not
2537 recovered correctly from Jalview project file
2540 <!-- JAL-2256 -->Feature colours in overview when first
2541 opened (automatically via preferences) are different to
2542 the main alignment panel
2545 <em>Data import/export</em>
2548 <!-- JAL-2576 -->Very large alignments take a long time to
2552 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2553 added after a sequence was imported are not written to
2557 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2558 when importing RNA secondary structure via Stockholm
2561 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2562 not shown in correct direction for simple pseudoknots
2565 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2566 with lightGray or darkGray via features file (but can
2570 <!-- JAL-2383 -->Above PID colour threshold not recovered
2571 when alignment view imported from project
2574 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2575 structure and sequences extracted from structure files
2576 imported via URL and viewed in Jmol
2579 <!-- JAL-2520 -->Structures loaded via URL are saved in
2580 Jalview Projects rather than fetched via URL again when
2581 the project is loaded and the structure viewed
2584 <em>Web Services</em>
2587 <!-- JAL-2519 -->EnsemblGenomes example failing after
2588 release of Ensembl v.88
2591 <!-- JAL-2366 -->Proxy server address and port always
2592 appear enabled in Preferences->Connections
2595 <!-- JAL-2461 -->DAS registry not found exceptions
2596 removed from console output
2599 <!-- JAL-2582 -->Cannot retrieve protein products from
2600 Ensembl by Peptide ID
2603 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2604 created from SIFTs, and spurious 'Couldn't open structure
2605 in Chimera' errors raised after April 2017 update (problem
2606 due to 'null' string rather than empty string used for
2607 residues with no corresponding PDB mapping).
2610 <em>Application UI</em>
2613 <!-- JAL-2361 -->User Defined Colours not added to Colour
2617 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2618 case' residues (button in colourscheme editor debugged and
2619 new documentation and tooltips added)
2622 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2623 doesn't restore group-specific text colour thresholds
2626 <!-- JAL-2243 -->Feature settings panel does not update as
2627 new features are added to alignment
2630 <!-- JAL-2532 -->Cancel in feature settings reverts
2631 changes to feature colours via the Amend features dialog
2634 <!-- JAL-2506 -->Null pointer exception when attempting to
2635 edit graduated feature colour via amend features dialog
2639 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2640 selection menu changes colours of alignment views
2643 <!-- JAL-2426 -->Spurious exceptions in console raised
2644 from alignment calculation workers after alignment has
2648 <!-- JAL-1608 -->Typo in selection popup menu - Create
2649 groups now 'Create Group'
2652 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2653 Create/Undefine group doesn't always work
2656 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2657 shown again after pressing 'Cancel'
2660 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2661 adjusts start position in wrap mode
2664 <!-- JAL-2563 -->Status bar doesn't show positions for
2665 ambiguous amino acids
2668 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2669 CDS/Protein view after CDS sequences added for aligned
2673 <!-- JAL-2592 -->User defined colourschemes called 'User
2674 Defined' don't appear in Colours menu
2680 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2681 score models doesn't always result in an updated PCA plot
2684 <!-- JAL-2442 -->Features not rendered as transparent on
2685 overview or linked structure view
2688 <!-- JAL-2372 -->Colour group by conservation doesn't
2692 <!-- JAL-2517 -->Hitting Cancel after applying
2693 user-defined colourscheme doesn't restore original
2700 <!-- JAL-2314 -->Unit test failure:
2701 jalview.ws.jabaws.RNAStructExportImport setup fails
2704 <!-- JAL-2307 -->Unit test failure:
2705 jalview.ws.sifts.SiftsClientTest due to compatibility
2706 problems with deep array comparison equality asserts in
2707 successive versions of TestNG
2710 <!-- JAL-2479 -->Relocated StructureChooserTest and
2711 ParameterUtilsTest Unit tests to Network suite
2714 <em>New Known Issues</em>
2717 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2718 phase after a sequence motif find operation
2721 <!-- JAL-2550 -->Importing annotation file with rows
2722 containing just upper and lower case letters are
2723 interpreted as WUSS RNA secondary structure symbols
2726 <!-- JAL-2590 -->Cannot load and display Newick trees
2727 reliably from eggnog Ortholog database
2730 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2731 containing features of type Highlight' when 'B' is pressed
2732 to mark columns containing highlighted regions.
2735 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2736 doesn't always add secondary structure annotation.
2741 <td width="60" nowrap>
2742 <div align="center">
2743 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2746 <td><div align="left">
2750 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2751 for all consensus calculations
2754 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2757 <li>Updated Jalview's Certum code signing certificate
2760 <em>Application</em>
2763 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2764 set of database cross-references, sorted alphabetically
2767 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2768 from database cross references. Users with custom links
2769 will receive a <a href="webServices/urllinks.html#warning">warning
2770 dialog</a> asking them to update their preferences.
2773 <!-- JAL-2287-->Cancel button and escape listener on
2774 dialog warning user about disconnecting Jalview from a
2778 <!-- JAL-2320-->Jalview's Chimera control window closes if
2779 the Chimera it is connected to is shut down
2782 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2783 columns menu item to mark columns containing highlighted
2784 regions (e.g. from structure selections or results of a
2788 <!-- JAL-2284-->Command line option for batch-generation
2789 of HTML pages rendering alignment data with the BioJS
2799 <!-- JAL-2286 -->Columns with more than one modal residue
2800 are not coloured or thresholded according to percent
2801 identity (first observed in Jalview 2.8.2)
2804 <!-- JAL-2301 -->Threonine incorrectly reported as not
2808 <!-- JAL-2318 -->Updates to documentation pages (above PID
2809 threshold, amino acid properties)
2812 <!-- JAL-2292 -->Lower case residues in sequences are not
2813 reported as mapped to residues in a structure file in the
2817 <!--JAL-2324 -->Identical features with non-numeric scores
2818 could be added multiple times to a sequence
2821 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2822 bond features shown as two highlighted residues rather
2823 than a range in linked structure views, and treated
2824 correctly when selecting and computing trees from features
2827 <!-- JAL-2281-->Custom URL links for database
2828 cross-references are matched to database name regardless
2833 <em>Application</em>
2836 <!-- JAL-2282-->Custom URL links for specific database
2837 names without regular expressions also offer links from
2841 <!-- JAL-2315-->Removing a single configured link in the
2842 URL links pane in Connections preferences doesn't actually
2843 update Jalview configuration
2846 <!-- JAL-2272-->CTRL-Click on a selected region to open
2847 the alignment area popup menu doesn't work on El-Capitan
2850 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2851 files with similarly named sequences if dropped onto the
2855 <!-- JAL-2312 -->Additional mappings are shown for PDB
2856 entries where more chains exist in the PDB accession than
2857 are reported in the SIFTS file
2860 <!-- JAL-2317-->Certain structures do not get mapped to
2861 the structure view when displayed with Chimera
2864 <!-- JAL-2317-->No chains shown in the Chimera view
2865 panel's View->Show Chains submenu
2868 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2869 work for wrapped alignment views
2872 <!--JAL-2197 -->Rename UI components for running JPred
2873 predictions from 'JNet' to 'JPred'
2876 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2877 corrupted when annotation panel vertical scroll is not at
2878 first annotation row
2881 <!--JAL-2332 -->Attempting to view structure for Hen
2882 lysozyme results in a PDB Client error dialog box
2885 <!-- JAL-2319 -->Structure View's mapping report switched
2886 ranges for PDB and sequence for SIFTS
2889 SIFTS 'Not_Observed' residues mapped to non-existant
2893 <!-- <em>New Known Issues</em>
2900 <td width="60" nowrap>
2901 <div align="center">
2902 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2903 <em>25/10/2016</em></strong>
2906 <td><em>Application</em>
2908 <li>3D Structure chooser opens with 'Cached structures'
2909 view if structures already loaded</li>
2910 <li>Progress bar reports models as they are loaded to
2911 structure views</li>
2917 <li>Colour by conservation always enabled and no tick
2918 shown in menu when BLOSUM or PID shading applied</li>
2919 <li>FER1_ARATH and FER2_ARATH labels were switched in
2920 example sequences/projects/trees</li>
2922 <em>Application</em>
2924 <li>Jalview projects with views of local PDB structure
2925 files saved on Windows cannot be opened on OSX</li>
2926 <li>Multiple structure views can be opened and superposed
2927 without timeout for structures with multiple models or
2928 multiple sequences in alignment</li>
2929 <li>Cannot import or associated local PDB files without a
2930 PDB ID HEADER line</li>
2931 <li>RMSD is not output in Jmol console when superposition
2933 <li>Drag and drop of URL from Browser fails for Linux and
2934 OSX versions earlier than El Capitan</li>
2935 <li>ENA client ignores invalid content from ENA server</li>
2936 <li>Exceptions are not raised in console when ENA client
2937 attempts to fetch non-existent IDs via Fetch DB Refs UI
2939 <li>Exceptions are not raised in console when a new view
2940 is created on the alignment</li>
2941 <li>OSX right-click fixed for group selections: CMD-click
2942 to insert/remove gaps in groups and CTRL-click to open group
2945 <em>Build and deployment</em>
2947 <li>URL link checker now copes with multi-line anchor
2950 <em>New Known Issues</em>
2952 <li>Drag and drop from URL links in browsers do not work
2959 <td width="60" nowrap>
2960 <div align="center">
2961 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2964 <td><em>General</em>
2967 <!-- JAL-2124 -->Updated Spanish translations.
2970 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2971 for importing structure data to Jalview. Enables mmCIF and
2975 <!-- JAL-192 --->Alignment ruler shows positions relative to
2979 <!-- JAL-2202 -->Position/residue shown in status bar when
2980 mousing over sequence associated annotation
2983 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2987 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2988 '()', canonical '[]' and invalid '{}' base pair populations
2992 <!-- JAL-2092 -->Feature settings popup menu options for
2993 showing or hiding columns containing a feature
2996 <!-- JAL-1557 -->Edit selected group by double clicking on
2997 group and sequence associated annotation labels
3000 <!-- JAL-2236 -->Sequence name added to annotation label in
3001 select/hide columns by annotation and colour by annotation
3005 </ul> <em>Application</em>
3008 <!-- JAL-2050-->Automatically hide introns when opening a
3009 gene/transcript view
3012 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
3016 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
3017 structure mappings with the EMBL-EBI PDBe SIFTS database
3020 <!-- JAL-2079 -->Updated download sites used for Rfam and
3021 Pfam sources to xfam.org
3024 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
3027 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
3028 over sequences in Jalview
3031 <!-- JAL-2027-->Support for reverse-complement coding
3032 regions in ENA and EMBL
3035 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
3036 for record retrieval via ENA rest API
3039 <!-- JAL-2027 -->Support for ENA CDS records with reverse
3043 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
3044 groovy script execution
3047 <!-- JAL-1812 -->New 'execute Groovy script' option in an
3048 alignment window's Calculate menu
3051 <!-- JAL-1812 -->Allow groovy scripts that call
3052 Jalview.getAlignFrames() to run in headless mode
3055 <!-- JAL-2068 -->Support for creating new alignment
3056 calculation workers from groovy scripts
3059 <!-- JAL-1369 --->Store/restore reference sequence in
3063 <!-- JAL-1803 -->Chain codes for a sequence's PDB
3064 associations are now saved/restored from project
3067 <!-- JAL-1993 -->Database selection dialog always shown
3068 before sequence fetcher is opened
3071 <!-- JAL-2183 -->Double click on an entry in Jalview's
3072 database chooser opens a sequence fetcher
3075 <!-- JAL-1563 -->Free-text search client for UniProt using
3076 the UniProt REST API
3079 <!-- JAL-2168 -->-nonews command line parameter to prevent
3080 the news reader opening
3083 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
3084 querying stored in preferences
3087 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
3091 <!-- JAL-1977-->Tooltips shown on database chooser
3094 <!-- JAL-391 -->Reverse complement function in calculate
3095 menu for nucleotide sequences
3098 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
3099 and feature counts preserves alignment ordering (and
3100 debugged for complex feature sets).
3103 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
3104 viewing structures with Jalview 2.10
3107 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
3108 genome, transcript CCDS and gene ids via the Ensembl and
3109 Ensembl Genomes REST API
3112 <!-- JAL-2049 -->Protein sequence variant annotation
3113 computed for 'sequence_variant' annotation on CDS regions
3117 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
3121 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
3122 Ref Fetcher fails to match, or otherwise updates sequence
3123 data from external database records.
3126 <!-- JAL-2154 -->Revised Jalview Project format for
3127 efficient recovery of sequence coding and alignment
3128 annotation relationships.
3130 </ul> <!-- <em>Applet</em>
3141 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
3145 <!-- JAL-2018-->Export features in Jalview format (again)
3146 includes graduated colourschemes
3149 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
3150 working with big alignments and lots of hidden columns
3153 <!-- JAL-2053-->Hidden column markers not always rendered
3154 at right of alignment window
3157 <!-- JAL-2067 -->Tidied up links in help file table of
3161 <!-- JAL-2072 -->Feature based tree calculation not shown
3165 <!-- JAL-2075 -->Hidden columns ignored during feature
3166 based tree calculation
3169 <!-- JAL-2065 -->Alignment view stops updating when show
3170 unconserved enabled for group on alignment
3173 <!-- JAL-2086 -->Cannot insert gaps into sequence when
3177 <!-- JAL-2146 -->Alignment column in status incorrectly
3178 shown as "Sequence position" when mousing over
3182 <!-- JAL-2099 -->Incorrect column numbers in ruler when
3183 hidden columns present
3186 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
3187 user created annotation added to alignment
3190 <!-- JAL-1841 -->RNA Structure consensus only computed for
3191 '()' base pair annotation
3194 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
3195 in zero scores for all base pairs in RNA Structure
3199 <!-- JAL-2174-->Extend selection with columns containing
3203 <!-- JAL-2275 -->Pfam format writer puts extra space at
3204 beginning of sequence
3207 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
3211 <!-- JAL-2238 -->Cannot create groups on an alignment from
3212 from a tree when t-coffee scores are shown
3215 <!-- JAL-1836,1967 -->Cannot import and view PDB
3216 structures with chains containing negative resnums (4q4h)
3219 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
3223 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
3224 to Clustal, PIR and PileUp output
3227 <!-- JAL-2008 -->Reordering sequence features that are
3228 not visible causes alignment window to repaint
3231 <!-- JAL-2006 -->Threshold sliders don't work in
3232 graduated colour and colour by annotation row for e-value
3233 scores associated with features and annotation rows
3236 <!-- JAL-1797 -->amino acid physicochemical conservation
3237 calculation should be case independent
3240 <!-- JAL-2173 -->Remove annotation also updates hidden
3244 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
3245 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
3246 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
3249 <!-- JAL-2065 -->Null pointer exceptions and redraw
3250 problems when reference sequence defined and 'show
3251 non-conserved' enabled
3254 <!-- JAL-1306 -->Quality and Conservation are now shown on
3255 load even when Consensus calculation is disabled
3258 <!-- JAL-1932 -->Remove right on penultimate column of
3259 alignment does nothing
3262 <em>Application</em>
3265 <!-- JAL-1552-->URLs and links can't be imported by
3266 drag'n'drop on OSX when launched via webstart (note - not
3267 yet fixed for El Capitan)
3270 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
3271 output when running on non-gb/us i18n platforms
3274 <!-- JAL-1944 -->Error thrown when exporting a view with
3275 hidden sequences as flat-file alignment
3278 <!-- JAL-2030-->InstallAnywhere distribution fails when
3282 <!-- JAL-2080-->Jalview very slow to launch via webstart
3283 (also hotfix for 2.9.0b2)
3286 <!-- JAL-2085 -->Cannot save project when view has a
3287 reference sequence defined
3290 <!-- JAL-1011 -->Columns are suddenly selected in other
3291 alignments and views when revealing hidden columns
3294 <!-- JAL-1989 -->Hide columns not mirrored in complement
3295 view in a cDNA/Protein splitframe
3298 <!-- JAL-1369 -->Cannot save/restore representative
3299 sequence from project when only one sequence is
3303 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
3304 in Structure Chooser
3307 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
3308 structure consensus didn't refresh annotation panel
3311 <!-- JAL-1962 -->View mapping in structure view shows
3312 mappings between sequence and all chains in a PDB file
3315 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
3316 dialogs format columns correctly, don't display array
3317 data, sort columns according to type
3320 <!-- JAL-1975 -->Export complete shown after destination
3321 file chooser is cancelled during an image export
3324 <!-- JAL-2025 -->Error when querying PDB Service with
3325 sequence name containing special characters
3328 <!-- JAL-2024 -->Manual PDB structure querying should be
3332 <!-- JAL-2104 -->Large tooltips with broken HTML
3333 formatting don't wrap
3336 <!-- JAL-1128 -->Figures exported from wrapped view are
3337 truncated so L looks like I in consensus annotation
3340 <!-- JAL-2003 -->Export features should only export the
3341 currently displayed features for the current selection or
3345 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
3346 after fetching cross-references, and restoring from
3350 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
3351 followed in the structure viewer
3354 <!-- JAL-2163 -->Titles for individual alignments in
3355 splitframe not restored from project
3358 <!-- JAL-2145 -->missing autocalculated annotation at
3359 trailing end of protein alignment in transcript/product
3360 splitview when pad-gaps not enabled by default
3363 <!-- JAL-1797 -->amino acid physicochemical conservation
3367 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
3368 article has been read (reopened issue due to
3369 internationalisation problems)
3372 <!-- JAL-1960 -->Only offer PDB structures in structure
3373 viewer based on sequence name, PDB and UniProt
3378 <!-- JAL-1976 -->No progress bar shown during export of
3382 <!-- JAL-2213 -->Structures not always superimposed after
3383 multiple structures are shown for one or more sequences.
3386 <!-- JAL-1370 -->Reference sequence characters should not
3387 be replaced with '.' when 'Show unconserved' format option
3391 <!-- JAL-1823 -->Cannot specify chain code when entering
3392 specific PDB id for sequence
3395 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3396 'Export hidden sequences' is enabled, but 'export hidden
3397 columns' is disabled.
3400 <!--JAL-2026-->Best Quality option in structure chooser
3401 selects lowest rather than highest resolution structures
3405 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3406 to sequence mapping in 'View Mappings' report
3409 <!-- JAL-2284 -->Unable to read old Jalview projects that
3410 contain non-XML data added after Jalvew wrote project.
3413 <!-- JAL-2118 -->Newly created annotation row reorders
3414 after clicking on it to create new annotation for a
3418 <!-- JAL-1980 -->Null Pointer Exception raised when
3419 pressing Add on an orphaned cut'n'paste window.
3421 <!-- may exclude, this is an external service stability issue JAL-1941
3422 -- > RNA 3D structure not added via DSSR service</li> -->
3427 <!-- JAL-2151 -->Incorrect columns are selected when
3428 hidden columns present before start of sequence
3431 <!-- JAL-1986 -->Missing dependencies on applet pages
3435 <!-- JAL-1947 -->Overview pixel size changes when
3436 sequences are hidden in applet
3439 <!-- JAL-1996 -->Updated instructions for applet
3440 deployment on examples pages.
3447 <td width="60" nowrap>
3448 <div align="center">
3449 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3450 <em>16/10/2015</em></strong>
3453 <td><em>General</em>
3455 <li>Time stamps for signed Jalview application and applet
3460 <em>Application</em>
3462 <li>Duplicate group consensus and conservation rows
3463 shown when tree is partitioned</li>
3464 <li>Erratic behaviour when tree partitions made with
3465 multiple cDNA/Protein split views</li>
3471 <td width="60" nowrap>
3472 <div align="center">
3473 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3474 <em>8/10/2015</em></strong>
3477 <td><em>General</em>
3479 <li>Updated Spanish translations of localized text for
3481 </ul> <em>Application</em>
3483 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3484 <li>Signed OSX InstallAnywhere installer<br></li>
3485 <li>Support for per-sequence based annotations in BioJSON</li>
3486 </ul> <em>Applet</em>
3488 <li>Split frame example added to applet examples page</li>
3489 </ul> <em>Build and Deployment</em>
3492 <!-- JAL-1888 -->New ant target for running Jalview's test
3500 <li>Mapping of cDNA to protein in split frames
3501 incorrect when sequence start > 1</li>
3502 <li>Broken images in filter column by annotation dialog
3504 <li>Feature colours not parsed from features file</li>
3505 <li>Exceptions and incomplete link URLs recovered when
3506 loading a features file containing HTML tags in feature
3510 <em>Application</em>
3512 <li>Annotations corrupted after BioJS export and
3514 <li>Incorrect sequence limits after Fetch DB References
3515 with 'trim retrieved sequences'</li>
3516 <li>Incorrect warning about deleting all data when
3517 deleting selected columns</li>
3518 <li>Patch to build system for shipping properly signed
3519 JNLP templates for webstart launch</li>
3520 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3521 unreleased structures for download or viewing</li>
3522 <li>Tab/space/return keystroke operation of EMBL-PDBe
3523 fetcher/viewer dialogs works correctly</li>
3524 <li>Disabled 'minimise' button on Jalview windows
3525 running on OSX to workaround redraw hang bug</li>
3526 <li>Split cDNA/Protein view position and geometry not
3527 recovered from jalview project</li>
3528 <li>Initial enabled/disabled state of annotation menu
3529 sorter 'show autocalculated first/last' corresponds to
3531 <li>Restoring of Clustal, RNA Helices and T-Coffee
3532 color schemes from BioJSON</li>
3536 <li>Reorder sequences mirrored in cDNA/Protein split
3538 <li>Applet with Jmol examples not loading correctly</li>
3544 <td><div align="center">
3545 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3547 <td><em>General</em>
3549 <li>Linked visualisation and analysis of DNA and Protein
3552 <li>Translated cDNA alignments shown as split protein
3553 and DNA alignment views</li>
3554 <li>Codon consensus annotation for linked protein and
3555 cDNA alignment views</li>
3556 <li>Link cDNA or Protein product sequences by loading
3557 them onto Protein or cDNA alignments</li>
3558 <li>Reconstruct linked cDNA alignment from aligned
3559 protein sequences</li>
3562 <li>Jmol integration updated to Jmol v14.2.14</li>
3563 <li>Import and export of Jalview alignment views as <a
3564 href="features/bioJsonFormat.html">BioJSON</a></li>
3565 <li>New alignment annotation file statements for
3566 reference sequences and marking hidden columns</li>
3567 <li>Reference sequence based alignment shading to
3568 highlight variation</li>
3569 <li>Select or hide columns according to alignment
3571 <li>Find option for locating sequences by description</li>
3572 <li>Conserved physicochemical properties shown in amino
3573 acid conservation row</li>
3574 <li>Alignments can be sorted by number of RNA helices</li>
3575 </ul> <em>Application</em>
3577 <li>New cDNA/Protein analysis capabilities
3579 <li>Get Cross-References should open a Split Frame
3580 view with cDNA/Protein</li>
3581 <li>Detect when nucleotide sequences and protein
3582 sequences are placed in the same alignment</li>
3583 <li>Split cDNA/Protein views are saved in Jalview
3588 <li>Use REST API to talk to Chimera</li>
3589 <li>Selected regions in Chimera are highlighted in linked
3590 Jalview windows</li>
3592 <li>VARNA RNA viewer updated to v3.93</li>
3593 <li>VARNA views are saved in Jalview Projects</li>
3594 <li>Pseudoknots displayed as Jalview RNA annotation can
3595 be shown in VARNA</li>
3597 <li>Make groups for selection uses marked columns as well
3598 as the active selected region</li>
3600 <li>Calculate UPGMA and NJ trees using sequence feature
3602 <li>New Export options
3604 <li>New Export Settings dialog to control hidden
3605 region export in flat file generation</li>
3607 <li>Export alignment views for display with the <a
3608 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3610 <li>Export scrollable SVG in HTML page</li>
3611 <li>Optional embedding of BioJSON data when exporting
3612 alignment figures to HTML</li>
3614 <li>3D structure retrieval and display
3616 <li>Free text and structured queries with the PDBe
3618 <li>PDBe Search API based discovery and selection of
3619 PDB structures for a sequence set</li>
3623 <li>JPred4 employed for protein secondary structure
3625 <li>Hide Insertions menu option to hide unaligned columns
3626 for one or a group of sequences</li>
3627 <li>Automatically hide insertions in alignments imported
3628 from the JPred4 web server</li>
3629 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3630 system on OSX<br />LGPL libraries courtesy of <a
3631 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3633 <li>changed 'View nucleotide structure' submenu to 'View
3634 VARNA 2D Structure'</li>
3635 <li>change "View protein structure" menu option to "3D
3638 </ul> <em>Applet</em>
3640 <li>New layout for applet example pages</li>
3641 <li>New parameters to enable SplitFrame view
3642 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3643 <li>New example demonstrating linked viewing of cDNA and
3644 Protein alignments</li>
3645 </ul> <em>Development and deployment</em>
3647 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3648 <li>Include installation type and git revision in build
3649 properties and console log output</li>
3650 <li>Jalview Github organisation, and new github site for
3651 storing BioJsMSA Templates</li>
3652 <li>Jalview's unit tests now managed with TestNG</li>
3655 <!-- <em>General</em>
3657 </ul> --> <!-- issues resolved --> <em>Application</em>
3659 <li>Escape should close any open find dialogs</li>
3660 <li>Typo in select-by-features status report</li>
3661 <li>Consensus RNA secondary secondary structure
3662 predictions are not highlighted in amber</li>
3663 <li>Missing gap character in v2.7 example file means
3664 alignment appears unaligned when pad-gaps is not enabled</li>
3665 <li>First switch to RNA Helices colouring doesn't colour
3666 associated structure views</li>
3667 <li>ID width preference option is greyed out when auto
3668 width checkbox not enabled</li>
3669 <li>Stopped a warning dialog from being shown when
3670 creating user defined colours</li>
3671 <li>'View Mapping' in structure viewer shows sequence
3672 mappings for just that viewer's sequences</li>
3673 <li>Workaround for superposing PDB files containing
3674 multiple models in Chimera</li>
3675 <li>Report sequence position in status bar when hovering
3676 over Jmol structure</li>
3677 <li>Cannot output gaps as '.' symbols with Selection ->
3678 output to text box</li>
3679 <li>Flat file exports of alignments with hidden columns
3680 have incorrect sequence start/end</li>
3681 <li>'Aligning' a second chain to a Chimera structure from
3683 <li>Colour schemes applied to structure viewers don't
3684 work for nucleotide</li>
3685 <li>Loading/cut'n'pasting an empty or invalid file leads
3686 to a grey/invisible alignment window</li>
3687 <li>Exported Jpred annotation from a sequence region
3688 imports to different position</li>
3689 <li>Space at beginning of sequence feature tooltips shown
3690 on some platforms</li>
3691 <li>Chimera viewer 'View | Show Chain' menu is not
3693 <li>'New View' fails with a Null Pointer Exception in
3694 console if Chimera has been opened</li>
3695 <li>Mouseover to Chimera not working</li>
3696 <li>Miscellaneous ENA XML feature qualifiers not
3698 <li>NPE in annotation renderer after 'Extract Scores'</li>
3699 <li>If two structures in one Chimera window, mouseover of
3700 either sequence shows on first structure</li>
3701 <li>'Show annotations' options should not make
3702 non-positional annotations visible</li>
3703 <li>Subsequence secondary structure annotation not shown
3704 in right place after 'view flanking regions'</li>
3705 <li>File Save As type unset when current file format is
3707 <li>Save as '.jar' option removed for saving Jalview
3709 <li>Colour by Sequence colouring in Chimera more
3711 <li>Cannot 'add reference annotation' for a sequence in
3712 several views on same alignment</li>
3713 <li>Cannot show linked products for EMBL / ENA records</li>
3714 <li>Jalview's tooltip wraps long texts containing no
3716 </ul> <em>Applet</em>
3718 <li>Jmol to JalviewLite mouseover/link not working</li>
3719 <li>JalviewLite can't import sequences with ID
3720 descriptions containing angle brackets</li>
3721 </ul> <em>General</em>
3723 <li>Cannot export and reimport RNA secondary structure
3724 via jalview annotation file</li>
3725 <li>Random helix colour palette for colour by annotation
3726 with RNA secondary structure</li>
3727 <li>Mouseover to cDNA from STOP residue in protein
3728 translation doesn't work.</li>
3729 <li>hints when using the select by annotation dialog box</li>
3730 <li>Jmol alignment incorrect if PDB file has alternate CA
3732 <li>FontChooser message dialog appears to hang after
3733 choosing 1pt font</li>
3734 <li>Peptide secondary structure incorrectly imported from
3735 annotation file when annotation display text includes 'e' or
3737 <li>Cannot set colour of new feature type whilst creating
3739 <li>cDNA translation alignment should not be sequence
3740 order dependent</li>
3741 <li>'Show unconserved' doesn't work for lower case
3743 <li>Nucleotide ambiguity codes involving R not recognised</li>
3744 </ul> <em>Deployment and Documentation</em>
3746 <li>Applet example pages appear different to the rest of
3747 www.jalview.org</li>
3748 </ul> <em>Application Known issues</em>
3750 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3751 <li>Misleading message appears after trying to delete
3753 <li>Jalview icon not shown in dock after InstallAnywhere
3754 version launches</li>
3755 <li>Fetching EMBL reference for an RNA sequence results
3756 fails with a sequence mismatch</li>
3757 <li>Corrupted or unreadable alignment display when
3758 scrolling alignment to right</li>
3759 <li>ArrayIndexOutOfBoundsException thrown when remove
3760 empty columns called on alignment with ragged gapped ends</li>
3761 <li>auto calculated alignment annotation rows do not get
3762 placed above or below non-autocalculated rows</li>
3763 <li>Jalview dekstop becomes sluggish at full screen in
3764 ultra-high resolution</li>
3765 <li>Cannot disable consensus calculation independently of
3766 quality and conservation</li>
3767 <li>Mouseover highlighting between cDNA and protein can
3768 become sluggish with more than one splitframe shown</li>
3769 </ul> <em>Applet Known Issues</em>
3771 <li>Core PDB parsing code requires Jmol</li>
3772 <li>Sequence canvas panel goes white when alignment
3773 window is being resized</li>
3779 <td><div align="center">
3780 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3782 <td><em>General</em>
3784 <li>Updated Java code signing certificate donated by
3786 <li>Features and annotation preserved when performing
3787 pairwise alignment</li>
3788 <li>RNA pseudoknot annotation can be
3789 imported/exported/displayed</li>
3790 <li>'colour by annotation' can colour by RNA and
3791 protein secondary structure</li>
3792 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3793 post-hoc with 2.9 release</em>)
3796 </ul> <em>Application</em>
3798 <li>Extract and display secondary structure for sequences
3799 with 3D structures</li>
3800 <li>Support for parsing RNAML</li>
3801 <li>Annotations menu for layout
3803 <li>sort sequence annotation rows by alignment</li>
3804 <li>place sequence annotation above/below alignment
3807 <li>Output in Stockholm format</li>
3808 <li>Internationalisation: improved Spanish (es)
3810 <li>Structure viewer preferences tab</li>
3811 <li>Disorder and Secondary Structure annotation tracks
3812 shared between alignments</li>
3813 <li>UCSF Chimera launch and linked highlighting from
3815 <li>Show/hide all sequence associated annotation rows for
3816 all or current selection</li>
3817 <li>disorder and secondary structure predictions
3818 available as dataset annotation</li>
3819 <li>Per-sequence rna helices colouring</li>
3822 <li>Sequence database accessions imported when fetching
3823 alignments from Rfam</li>
3824 <li>update VARNA version to 3.91</li>
3826 <li>New groovy scripts for exporting aligned positions,
3827 conservation values, and calculating sum of pairs scores.</li>
3828 <li>Command line argument to set default JABAWS server</li>
3829 <li>include installation type in build properties and
3830 console log output</li>
3831 <li>Updated Jalview project format to preserve dataset
3835 <!-- issues resolved --> <em>Application</em>
3837 <li>Distinguish alignment and sequence associated RNA
3838 structure in structure->view->VARNA</li>
3839 <li>Raise dialog box if user deletes all sequences in an
3841 <li>Pressing F1 results in documentation opening twice</li>
3842 <li>Sequence feature tooltip is wrapped</li>
3843 <li>Double click on sequence associated annotation
3844 selects only first column</li>
3845 <li>Redundancy removal doesn't result in unlinked
3846 leaves shown in tree</li>
3847 <li>Undos after several redundancy removals don't undo
3849 <li>Hide sequence doesn't hide associated annotation</li>
3850 <li>User defined colours dialog box too big to fit on
3851 screen and buttons not visible</li>
3852 <li>author list isn't updated if already written to
3853 Jalview properties</li>
3854 <li>Popup menu won't open after retrieving sequence
3856 <li>File open window for associate PDB doesn't open</li>
3857 <li>Left-then-right click on a sequence id opens a
3858 browser search window</li>
3859 <li>Cannot open sequence feature shading/sort popup menu
3860 in feature settings dialog</li>
3861 <li>better tooltip placement for some areas of Jalview
3863 <li>Allow addition of JABAWS Server which doesn't
3864 pass validation</li>
3865 <li>Web services parameters dialog box is too large to
3867 <li>Muscle nucleotide alignment preset obscured by
3869 <li>JABAWS preset submenus don't contain newly
3870 defined user preset</li>
3871 <li>MSA web services warns user if they were launched
3872 with invalid input</li>
3873 <li>Jalview cannot contact DAS Registy when running on
3876 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3877 'Superpose with' submenu not shown when new view
3881 </ul> <!-- <em>Applet</em>
3883 </ul> <em>General</em>
3885 </ul>--> <em>Deployment and Documentation</em>
3887 <li>2G and 1G options in launchApp have no effect on
3888 memory allocation</li>
3889 <li>launchApp service doesn't automatically open
3890 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3892 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3893 InstallAnywhere reports cannot find valid JVM when Java
3894 1.7_055 is available
3896 </ul> <em>Application Known issues</em>
3899 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3900 corrupted or unreadable alignment display when scrolling
3904 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3905 retrieval fails but progress bar continues for DAS retrieval
3906 with large number of ID
3909 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3910 flatfile output of visible region has incorrect sequence
3914 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3915 rna structure consensus doesn't update when secondary
3916 structure tracks are rearranged
3919 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3920 invalid rna structure positional highlighting does not
3921 highlight position of invalid base pairs
3924 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3925 out of memory errors are not raised when saving Jalview
3926 project from alignment window file menu
3929 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3930 Switching to RNA Helices colouring doesn't propagate to
3934 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3935 colour by RNA Helices not enabled when user created
3936 annotation added to alignment
3939 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3940 Jalview icon not shown on dock in Mountain Lion/Webstart
3942 </ul> <em>Applet Known Issues</em>
3945 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3946 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3949 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3950 Jalview and Jmol example not compatible with IE9
3953 <li>Sort by annotation score doesn't reverse order
3959 <td><div align="center">
3960 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3963 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3966 <li>Internationalisation of user interface (usually
3967 called i18n support) and translation for Spanish locale</li>
3968 <li>Define/Undefine group on current selection with
3969 Ctrl-G/Shift Ctrl-G</li>
3970 <li>Improved group creation/removal options in
3971 alignment/sequence Popup menu</li>
3972 <li>Sensible precision for symbol distribution
3973 percentages shown in logo tooltip.</li>
3974 <li>Annotation panel height set according to amount of
3975 annotation when alignment first opened</li>
3976 </ul> <em>Application</em>
3978 <li>Interactive consensus RNA secondary structure
3979 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3980 <li>Select columns containing particular features from
3981 Feature Settings dialog</li>
3982 <li>View all 'representative' PDB structures for selected
3984 <li>Update Jalview project format:
3986 <li>New file extension for Jalview projects '.jvp'</li>
3987 <li>Preserve sequence and annotation dataset (to
3988 store secondary structure annotation,etc)</li>
3989 <li>Per group and alignment annotation and RNA helix
3993 <li>New similarity measures for PCA and Tree calculation
3995 <li>Experimental support for retrieval and viewing of
3996 flanking regions for an alignment</li>
4000 <!-- issues resolved --> <em>Application</em>
4002 <li>logo keeps spinning and status remains at queued or
4003 running after job is cancelled</li>
4004 <li>cannot export features from alignments imported from
4005 Jalview/VAMSAS projects</li>
4006 <li>Buggy slider for web service parameters that take
4008 <li>Newly created RNA secondary structure line doesn't
4009 have 'display all symbols' flag set</li>
4010 <li>T-COFFEE alignment score shading scheme and other
4011 annotation shading not saved in Jalview project</li>
4012 <li>Local file cannot be loaded in freshly downloaded
4014 <li>Jalview icon not shown on dock in Mountain
4016 <li>Load file from desktop file browser fails</li>
4017 <li>Occasional NPE thrown when calculating large trees</li>
4018 <li>Cannot reorder or slide sequences after dragging an
4019 alignment onto desktop</li>
4020 <li>Colour by annotation dialog throws NPE after using
4021 'extract scores' function</li>
4022 <li>Loading/cut'n'pasting an empty file leads to a grey
4023 alignment window</li>
4024 <li>Disorder thresholds rendered incorrectly after
4025 performing IUPred disorder prediction</li>
4026 <li>Multiple group annotated consensus rows shown when
4027 changing 'normalise logo' display setting</li>
4028 <li>Find shows blank dialog after 'finished searching' if
4029 nothing matches query</li>
4030 <li>Null Pointer Exceptions raised when sorting by
4031 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
4033 <li>Errors in Jmol console when structures in alignment
4034 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
4036 <li>Not all working JABAWS services are shown in
4038 <li>JAVAWS version of Jalview fails to launch with
4039 'invalid literal/length code'</li>
4040 <li>Annotation/RNA Helix colourschemes cannot be applied
4041 to alignment with groups (actually fixed in 2.8.0b1)</li>
4042 <li>RNA Helices and T-Coffee Scores available as default
4045 </ul> <em>Applet</em>
4047 <li>Remove group option is shown even when selection is
4049 <li>Apply to all groups ticked but colourscheme changes
4050 don't affect groups</li>
4051 <li>Documented RNA Helices and T-Coffee Scores as valid
4052 colourscheme name</li>
4053 <li>Annotation labels drawn on sequence IDs when
4054 Annotation panel is not displayed</li>
4055 <li>Increased font size for dropdown menus on OSX and
4056 embedded windows</li>
4057 </ul> <em>Other</em>
4059 <li>Consensus sequence for alignments/groups with a
4060 single sequence were not calculated</li>
4061 <li>annotation files that contain only groups imported as
4062 annotation and junk sequences</li>
4063 <li>Fasta files with sequences containing '*' incorrectly
4064 recognised as PFAM or BLC</li>
4065 <li>conservation/PID slider apply all groups option
4066 doesn't affect background (2.8.0b1)
4068 <li>redundancy highlighting is erratic at 0% and 100%</li>
4069 <li>Remove gapped columns fails for sequences with ragged
4071 <li>AMSA annotation row with leading spaces is not
4072 registered correctly on import</li>
4073 <li>Jalview crashes when selecting PCA analysis for
4074 certain alignments</li>
4075 <li>Opening the colour by annotation dialog for an
4076 existing annotation based 'use original colours'
4077 colourscheme loses original colours setting</li>
4082 <td><div align="center">
4083 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
4084 <em>30/1/2014</em></strong>
4088 <li>Trusted certificates for JalviewLite applet and
4089 Jalview Desktop application<br />Certificate was donated by
4090 <a href="https://www.certum.eu">Certum</a> to the Jalview
4091 open source project).
4093 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
4094 <li>Output in Stockholm format</li>
4095 <li>Allow import of data from gzipped files</li>
4096 <li>Export/import group and sequence associated line
4097 graph thresholds</li>
4098 <li>Nucleotide substitution matrix that supports RNA and
4099 ambiguity codes</li>
4100 <li>Allow disorder predictions to be made on the current
4101 selection (or visible selection) in the same way that JPred
4103 <li>Groovy scripting for headless Jalview operation</li>
4104 </ul> <em>Other improvements</em>
4106 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
4107 <li>COMBINE statement uses current SEQUENCE_REF and
4108 GROUP_REF scope to group annotation rows</li>
4109 <li>Support '' style escaping of quotes in Newick
4111 <li>Group options for JABAWS service by command line name</li>
4112 <li>Empty tooltip shown for JABA service options with a
4113 link but no description</li>
4114 <li>Select primary source when selecting authority in
4115 database fetcher GUI</li>
4116 <li>Add .mfa to FASTA file extensions recognised by
4118 <li>Annotation label tooltip text wrap</li>
4123 <li>Slow scrolling when lots of annotation rows are
4125 <li>Lots of NPE (and slowness) after creating RNA
4126 secondary structure annotation line</li>
4127 <li>Sequence database accessions not imported when
4128 fetching alignments from Rfam</li>
4129 <li>Incorrect SHMR submission for sequences with
4131 <li>View all structures does not always superpose
4133 <li>Option widgets in service parameters not updated to
4134 reflect user or preset settings</li>
4135 <li>Null pointer exceptions for some services without
4136 presets or adjustable parameters</li>
4137 <li>Discover PDB IDs entry in structure menu doesn't
4138 discover PDB xRefs</li>
4139 <li>Exception encountered while trying to retrieve
4140 features with DAS</li>
4141 <li>Lowest value in annotation row isn't coloured
4142 when colour by annotation (per sequence) is coloured</li>
4143 <li>Keyboard mode P jumps to start of gapped region when
4144 residue follows a gap</li>
4145 <li>Jalview appears to hang importing an alignment with
4146 Wrap as default or after enabling Wrap</li>
4147 <li>'Right click to add annotations' message
4148 shown in wrap mode when no annotations present</li>
4149 <li>Disorder predictions fail with NPE if no automatic
4150 annotation already exists on alignment</li>
4151 <li>oninit javascript function should be called after
4152 initialisation completes</li>
4153 <li>Remove redundancy after disorder prediction corrupts
4154 alignment window display</li>
4155 <li>Example annotation file in documentation is invalid</li>
4156 <li>Grouped line graph annotation rows are not exported
4157 to annotation file</li>
4158 <li>Multi-harmony analysis cannot be run when only two
4160 <li>Cannot create multiple groups of line graphs with
4161 several 'combine' statements in annotation file</li>
4162 <li>Pressing return several times causes Number Format
4163 exceptions in keyboard mode</li>
4164 <li>Multi-harmony (SHMMR) method doesn't submit
4165 correct partitions for input data</li>
4166 <li>Translation from DNA to Amino Acids fails</li>
4167 <li>Jalview fail to load newick tree with quoted label</li>
4168 <li>--headless flag isn't understood</li>
4169 <li>ClassCastException when generating EPS in headless
4171 <li>Adjusting sequence-associated shading threshold only
4172 changes one row's threshold</li>
4173 <li>Preferences and Feature settings panel panel
4174 doesn't open</li>
4175 <li>hide consensus histogram also hides conservation and
4176 quality histograms</li>
4181 <td><div align="center">
4182 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
4184 <td><em>Application</em>
4186 <li>Support for JABAWS 2.0 Services (AACon alignment
4187 conservation, protein disorder and Clustal Omega)</li>
4188 <li>JABAWS server status indicator in Web Services
4190 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
4191 in Jalview alignment window</li>
4192 <li>Updated Jalview build and deploy framework for OSX
4193 mountain lion, windows 7, and 8</li>
4194 <li>Nucleotide substitution matrix for PCA that supports
4195 RNA and ambiguity codes</li>
4197 <li>Improved sequence database retrieval GUI</li>
4198 <li>Support fetching and database reference look up
4199 against multiple DAS sources (Fetch all from in 'fetch db
4201 <li>Jalview project improvements
4203 <li>Store and retrieve the 'belowAlignment'
4204 flag for annotation</li>
4205 <li>calcId attribute to group annotation rows on the
4207 <li>Store AACon calculation settings for a view in
4208 Jalview project</li>
4212 <li>horizontal scrolling gesture support</li>
4213 <li>Visual progress indicator when PCA calculation is
4215 <li>Simpler JABA web services menus</li>
4216 <li>visual indication that web service results are still
4217 being retrieved from server</li>
4218 <li>Serialise the dialogs that are shown when Jalview
4219 starts up for first time</li>
4220 <li>Jalview user agent string for interacting with HTTP
4222 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
4224 <li>Examples directory and Groovy library included in
4225 InstallAnywhere distribution</li>
4226 </ul> <em>Applet</em>
4228 <li>RNA alignment and secondary structure annotation
4229 visualization applet example</li>
4230 </ul> <em>General</em>
4232 <li>Normalise option for consensus sequence logo</li>
4233 <li>Reset button in PCA window to return dimensions to
4235 <li>Allow seqspace or Jalview variant of alignment PCA
4237 <li>PCA with either nucleic acid and protein substitution
4239 <li>Allow windows containing HTML reports to be exported
4241 <li>Interactive display and editing of RNA secondary
4242 structure contacts</li>
4243 <li>RNA Helix Alignment Colouring</li>
4244 <li>RNA base pair logo consensus</li>
4245 <li>Parse sequence associated secondary structure
4246 information in Stockholm files</li>
4247 <li>HTML Export database accessions and annotation
4248 information presented in tooltip for sequences</li>
4249 <li>Import secondary structure from LOCARNA clustalw
4250 style RNA alignment files</li>
4251 <li>import and visualise T-COFFEE quality scores for an
4253 <li>'colour by annotation' per sequence option to
4254 shade each sequence according to its associated alignment
4256 <li>New Jalview Logo</li>
4257 </ul> <em>Documentation and Development</em>
4259 <li>documentation for score matrices used in Jalview</li>
4260 <li>New Website!</li>
4262 <td><em>Application</em>
4264 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
4265 wsdbfetch REST service</li>
4266 <li>Stop windows being moved outside desktop on OSX</li>
4267 <li>Filetype associations not installed for webstart
4269 <li>Jalview does not always retrieve progress of a JABAWS
4270 job execution in full once it is complete</li>
4271 <li>revise SHMR RSBS definition to ensure alignment is
4272 uploaded via ali_file parameter</li>
4273 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
4274 <li>View all structures superposed fails with exception</li>
4275 <li>Jnet job queues forever if a very short sequence is
4276 submitted for prediction</li>
4277 <li>Cut and paste menu not opened when mouse clicked on
4279 <li>Putting fractional value into integer text box in
4280 alignment parameter dialog causes Jalview to hang</li>
4281 <li>Structure view highlighting doesn't work on
4283 <li>View all structures fails with exception shown in
4285 <li>Characters in filename associated with PDBEntry not
4286 escaped in a platform independent way</li>
4287 <li>Jalview desktop fails to launch with exception when
4289 <li>Tree calculation reports 'you must have 2 or more
4290 sequences selected' when selection is empty</li>
4291 <li>Jalview desktop fails to launch with jar signature
4292 failure when java web start temporary file caching is
4294 <li>DAS Sequence retrieval with range qualification
4295 results in sequence xref which includes range qualification</li>
4296 <li>Errors during processing of command line arguments
4297 cause progress bar (JAL-898) to be removed</li>
4298 <li>Replace comma for semi-colon option not disabled for
4299 DAS sources in sequence fetcher</li>
4300 <li>Cannot close news reader when JABAWS server warning
4301 dialog is shown</li>
4302 <li>Option widgets not updated to reflect user settings</li>
4303 <li>Edited sequence not submitted to web service</li>
4304 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
4305 <li>InstallAnywhere installer doesn't unpack and run
4306 on OSX Mountain Lion</li>
4307 <li>Annotation panel not given a scroll bar when
4308 sequences with alignment annotation are pasted into the
4310 <li>Sequence associated annotation rows not associated
4311 when loaded from Jalview project</li>
4312 <li>Browser launch fails with NPE on java 1.7</li>
4313 <li>JABAWS alignment marked as finished when job was
4314 cancelled or job failed due to invalid input</li>
4315 <li>NPE with v2.7 example when clicking on Tree
4316 associated with all views</li>
4317 <li>Exceptions when copy/paste sequences with grouped
4318 annotation rows to new window</li>
4319 </ul> <em>Applet</em>
4321 <li>Sequence features are momentarily displayed before
4322 they are hidden using hidefeaturegroups applet parameter</li>
4323 <li>loading features via javascript API automatically
4324 enables feature display</li>
4325 <li>scrollToColumnIn javascript API method doesn't
4327 </ul> <em>General</em>
4329 <li>Redundancy removal fails for rna alignment</li>
4330 <li>PCA calculation fails when sequence has been selected
4331 and then deselected</li>
4332 <li>PCA window shows grey box when first opened on OSX</li>
4333 <li>Letters coloured pink in sequence logo when alignment
4334 coloured with clustalx</li>
4335 <li>Choosing fonts without letter symbols defined causes
4336 exceptions and redraw errors</li>
4337 <li>Initial PCA plot view is not same as manually
4338 reconfigured view</li>
4339 <li>Grouped annotation graph label has incorrect line
4341 <li>Grouped annotation graph label display is corrupted
4342 for lots of labels</li>
4347 <div align="center">
4348 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
4351 <td><em>Application</em>
4353 <li>Jalview Desktop News Reader</li>
4354 <li>Tweaked default layout of web services menu</li>
4355 <li>View/alignment association menu to enable user to
4356 easily specify which alignment a multi-structure view takes
4357 its colours/correspondences from</li>
4358 <li>Allow properties file location to be specified as URL</li>
4359 <li>Extend Jalview project to preserve associations
4360 between many alignment views and a single Jmol display</li>
4361 <li>Store annotation row height in Jalview project file</li>
4362 <li>Annotation row column label formatting attributes
4363 stored in project file</li>
4364 <li>Annotation row order for auto-calculated annotation
4365 rows preserved in Jalview project file</li>
4366 <li>Visual progress indication when Jalview state is
4367 saved using Desktop window menu</li>
4368 <li>Visual indication that command line arguments are
4369 still being processed</li>
4370 <li>Groovy script execution from URL</li>
4371 <li>Colour by annotation default min and max colours in
4373 <li>Automatically associate PDB files dragged onto an
4374 alignment with sequences that have high similarity and
4376 <li>Update JGoogleAnalytics to latest release (0.3)</li>
4377 <li>'view structures' option to open many
4378 structures in same window</li>
4379 <li>Sort associated views menu option for tree panel</li>
4380 <li>Group all JABA and non-JABA services for a particular
4381 analysis function in its own submenu</li>
4382 </ul> <em>Applet</em>
4384 <li>Userdefined and autogenerated annotation rows for
4386 <li>Adjustment of alignment annotation pane height</li>
4387 <li>Annotation scrollbar for annotation panel</li>
4388 <li>Drag to reorder annotation rows in annotation panel</li>
4389 <li>'automaticScrolling' parameter</li>
4390 <li>Allow sequences with partial ID string matches to be
4391 annotated from GFF/Jalview features files</li>
4392 <li>Sequence logo annotation row in applet</li>
4393 <li>Absolute paths relative to host server in applet
4394 parameters are treated as such</li>
4395 <li>New in the JalviewLite javascript API:
4397 <li>JalviewLite.js javascript library</li>
4398 <li>Javascript callbacks for
4400 <li>Applet initialisation</li>
4401 <li>Sequence/alignment mouse-overs and selections</li>
4404 <li>scrollTo row and column alignment scrolling
4406 <li>Select sequence/alignment regions from javascript</li>
4407 <li>javascript structure viewer harness to pass
4408 messages between Jmol and Jalview when running as
4409 distinct applets</li>
4410 <li>sortBy method</li>
4411 <li>Set of applet and application examples shipped
4412 with documentation</li>
4413 <li>New example to demonstrate JalviewLite and Jmol
4414 javascript message exchange</li>
4416 </ul> <em>General</em>
4418 <li>Enable Jmol displays to be associated with multiple
4419 multiple alignments</li>
4420 <li>Option to automatically sort alignment with new tree</li>
4421 <li>User configurable link to enable redirects to a
4422 www.Jalview.org mirror</li>
4423 <li>Jmol colours option for Jmol displays</li>
4424 <li>Configurable newline string when writing alignment
4425 and other flat files</li>
4426 <li>Allow alignment annotation description lines to
4427 contain html tags</li>
4428 </ul> <em>Documentation and Development</em>
4430 <li>Add groovy test harness for bulk load testing to
4432 <li>Groovy script to load and align a set of sequences
4433 using a web service before displaying the result in the
4434 Jalview desktop</li>
4435 <li>Restructured javascript and applet api documentation</li>
4436 <li>Ant target to publish example html files with applet
4438 <li>Netbeans project for building Jalview from source</li>
4439 <li>ant task to create online javadoc for Jalview source</li>
4441 <td><em>Application</em>
4443 <li>User defined colourscheme throws exception when
4444 current built in colourscheme is saved as new scheme</li>
4445 <li>AlignFrame->Save in application pops up save
4446 dialog for valid filename/format</li>
4447 <li>Cannot view associated structure for UniProt sequence</li>
4448 <li>PDB file association breaks for UniProt sequence
4450 <li>Associate PDB from file dialog does not tell you
4451 which sequence is to be associated with the file</li>
4452 <li>Find All raises null pointer exception when query
4453 only matches sequence IDs</li>
4454 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4455 <li>Jalview project with Jmol views created with Jalview
4456 2.4 cannot be loaded</li>
4457 <li>Filetype associations not installed for webstart
4459 <li>Two or more chains in a single PDB file associated
4460 with sequences in different alignments do not get coloured
4461 by their associated sequence</li>
4462 <li>Visibility status of autocalculated annotation row
4463 not preserved when project is loaded</li>
4464 <li>Annotation row height and visibility attributes not
4465 stored in Jalview project</li>
4466 <li>Tree bootstraps are not preserved when saved as a
4467 Jalview project</li>
4468 <li>Envision2 workflow tooltips are corrupted</li>
4469 <li>Enabling show group conservation also enables colour
4470 by conservation</li>
4471 <li>Duplicate group associated conservation or consensus
4472 created on new view</li>
4473 <li>Annotation scrollbar not displayed after 'show
4474 all hidden annotation rows' option selected</li>
4475 <li>Alignment quality not updated after alignment
4476 annotation row is hidden then shown</li>
4477 <li>Preserve colouring of structures coloured by
4478 sequences in pre Jalview 2.7 projects</li>
4479 <li>Web service job parameter dialog is not laid out
4481 <li>Web services menu not refreshed after 'reset
4482 services' button is pressed in preferences</li>
4483 <li>Annotation off by one in Jalview v2_3 example project</li>
4484 <li>Structures imported from file and saved in project
4485 get name like jalview_pdb1234.txt when reloaded</li>
4486 <li>Jalview does not always retrieve progress of a JABAWS
4487 job execution in full once it is complete</li>
4488 </ul> <em>Applet</em>
4490 <li>Alignment height set incorrectly when lots of
4491 annotation rows are displayed</li>
4492 <li>Relative URLs in feature HTML text not resolved to
4494 <li>View follows highlighting does not work for positions
4496 <li><= shown as = in tooltip</li>
4497 <li>Export features raises exception when no features
4499 <li>Separator string used for serialising lists of IDs
4500 for javascript api is modified when separator string
4501 provided as parameter</li>
4502 <li>Null pointer exception when selecting tree leaves for
4503 alignment with no existing selection</li>
4504 <li>Relative URLs for datasources assumed to be relative
4505 to applet's codebase</li>
4506 <li>Status bar not updated after finished searching and
4507 search wraps around to first result</li>
4508 <li>StructureSelectionManager instance shared between
4509 several Jalview applets causes race conditions and memory
4511 <li>Hover tooltip and mouseover of position on structure
4512 not sent from Jmol in applet</li>
4513 <li>Certain sequences of javascript method calls to
4514 applet API fatally hang browser</li>
4515 </ul> <em>General</em>
4517 <li>View follows structure mouseover scrolls beyond
4518 position with wrapped view and hidden regions</li>
4519 <li>Find sequence position moves to wrong residue
4520 with/without hidden columns</li>
4521 <li>Sequence length given in alignment properties window
4523 <li>InvalidNumberFormat exceptions thrown when trying to
4524 import PDB like structure files</li>
4525 <li>Positional search results are only highlighted
4526 between user-supplied sequence start/end bounds</li>
4527 <li>End attribute of sequence is not validated</li>
4528 <li>Find dialog only finds first sequence containing a
4529 given sequence position</li>
4530 <li>Sequence numbering not preserved in MSF alignment
4532 <li>Jalview PDB file reader does not extract sequence
4533 from nucleotide chains correctly</li>
4534 <li>Structure colours not updated when tree partition
4535 changed in alignment</li>
4536 <li>Sequence associated secondary structure not correctly
4537 parsed in interleaved stockholm</li>
4538 <li>Colour by annotation dialog does not restore current
4540 <li>Hiding (nearly) all sequences doesn't work
4542 <li>Sequences containing lowercase letters are not
4543 properly associated with their pdb files</li>
4544 </ul> <em>Documentation and Development</em>
4546 <li>schemas/JalviewWsParamSet.xsd corrupted by
4547 ApplyCopyright tool</li>
4552 <div align="center">
4553 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4556 <td><em>Application</em>
4558 <li>New warning dialog when the Jalview Desktop cannot
4559 contact web services</li>
4560 <li>JABA service parameters for a preset are shown in
4561 service job window</li>
4562 <li>JABA Service menu entries reworded</li>
4566 <li>Modeller PIR IO broken - cannot correctly import a
4567 pir file emitted by Jalview</li>
4568 <li>Existing feature settings transferred to new
4569 alignment view created from cut'n'paste</li>
4570 <li>Improved test for mixed amino/nucleotide chains when
4571 parsing PDB files</li>
4572 <li>Consensus and conservation annotation rows
4573 occasionally become blank for all new windows</li>
4574 <li>Exception raised when right clicking above sequences
4575 in wrapped view mode</li>
4576 </ul> <em>Application</em>
4578 <li>multiple multiply aligned structure views cause cpu
4579 usage to hit 100% and computer to hang</li>
4580 <li>Web Service parameter layout breaks for long user
4581 parameter names</li>
4582 <li>Jaba service discovery hangs desktop if Jaba server
4589 <div align="center">
4590 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4593 <td><em>Application</em>
4595 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4596 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4599 <li>Web Services preference tab</li>
4600 <li>Analysis parameters dialog box and user defined
4602 <li>Improved speed and layout of Envision2 service menu</li>
4603 <li>Superpose structures using associated sequence
4605 <li>Export coordinates and projection as CSV from PCA
4607 </ul> <em>Applet</em>
4609 <li>enable javascript: execution by the applet via the
4610 link out mechanism</li>
4611 </ul> <em>Other</em>
4613 <li>Updated the Jmol Jalview interface to work with Jmol
4615 <li>The Jalview Desktop and JalviewLite applet now
4616 require Java 1.5</li>
4617 <li>Allow Jalview feature colour specification for GFF
4618 sequence annotation files</li>
4619 <li>New 'colour by label' keword in Jalview feature file
4620 type colour specification</li>
4621 <li>New Jalview Desktop Groovy API method that allows a
4622 script to check if it being run in an interactive session or
4623 in a batch operation from the Jalview command line</li>
4627 <li>clustalx colourscheme colours Ds preferentially when
4628 both D+E are present in over 50% of the column</li>
4629 </ul> <em>Application</em>
4631 <li>typo in AlignmentFrame->View->Hide->all but
4632 selected Regions menu item</li>
4633 <li>sequence fetcher replaces ',' for ';' when the ',' is
4634 part of a valid accession ID</li>
4635 <li>fatal OOM if object retrieved by sequence fetcher
4636 runs out of memory</li>
4637 <li>unhandled Out of Memory Error when viewing pca
4638 analysis results</li>
4639 <li>InstallAnywhere builds fail to launch on OS X java
4640 10.5 update 4 (due to apple Java 1.6 update)</li>
4641 <li>Installanywhere Jalview silently fails to launch</li>
4642 </ul> <em>Applet</em>
4644 <li>Jalview.getFeatureGroups() raises an
4645 ArrayIndexOutOfBoundsException if no feature groups are
4652 <div align="center">
4653 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4659 <li>Alignment prettyprinter doesn't cope with long
4661 <li>clustalx colourscheme colours Ds preferentially when
4662 both D+E are present in over 50% of the column</li>
4663 <li>nucleic acid structures retrieved from PDB do not
4664 import correctly</li>
4665 <li>More columns get selected than were clicked on when a
4666 number of columns are hidden</li>
4667 <li>annotation label popup menu not providing correct
4668 add/hide/show options when rows are hidden or none are
4670 <li>Stockholm format shown in list of readable formats,
4671 and parser copes better with alignments from RFAM.</li>
4672 <li>CSV output of consensus only includes the percentage
4673 of all symbols if sequence logo display is enabled</li>
4675 </ul> <em>Applet</em>
4677 <li>annotation panel disappears when annotation is
4679 </ul> <em>Application</em>
4681 <li>Alignment view not redrawn properly when new
4682 alignment opened where annotation panel is visible but no
4683 annotations are present on alignment</li>
4684 <li>pasted region containing hidden columns is
4685 incorrectly displayed in new alignment window</li>
4686 <li>Jalview slow to complete operations when stdout is
4687 flooded (fix is to close the Jalview console)</li>
4688 <li>typo in AlignmentFrame->View->Hide->all but
4689 selected Rregions menu item.</li>
4690 <li>inconsistent group submenu and Format submenu entry
4691 'Un' or 'Non'conserved</li>
4692 <li>Sequence feature settings are being shared by
4693 multiple distinct alignments</li>
4694 <li>group annotation not recreated when tree partition is
4696 <li>double click on group annotation to select sequences
4697 does not propagate to associated trees</li>
4698 <li>Mac OSX specific issues:
4700 <li>exception raised when mouse clicked on desktop
4701 window background</li>
4702 <li>Desktop menu placed on menu bar and application
4703 name set correctly</li>
4704 <li>sequence feature settings not wide enough for the
4705 save feature colourscheme button</li>
4714 <div align="center">
4715 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4718 <td><em>New Capabilities</em>
4720 <li>URL links generated from description line for
4721 regular-expression based URL links (applet and application)
4724 <li>Non-positional feature URL links are shown in link
4726 <li>Linked viewing of nucleic acid sequences and
4728 <li>Automatic Scrolling option in View menu to display
4729 the currently highlighted region of an alignment.</li>
4730 <li>Order an alignment by sequence length, or using the
4731 average score or total feature count for each sequence.</li>
4732 <li>Shading features by score or associated description</li>
4733 <li>Subdivide alignment and groups based on identity of
4734 selected subsequence (Make Groups from Selection).</li>
4735 <li>New hide/show options including Shift+Control+H to
4736 hide everything but the currently selected region.</li>
4737 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4738 </ul> <em>Application</em>
4740 <li>Fetch DB References capabilities and UI expanded to
4741 support retrieval from DAS sequence sources</li>
4742 <li>Local DAS Sequence sources can be added via the
4743 command line or via the Add local source dialog box.</li>
4744 <li>DAS Dbref and DbxRef feature types are parsed as
4745 database references and protein_name is parsed as
4746 description line (BioSapiens terms).</li>
4747 <li>Enable or disable non-positional feature and database
4748 references in sequence ID tooltip from View menu in
4750 <!-- <li>New hidden columns and rows and representatives capabilities
4751 in annotations file (in progress - not yet fully implemented)</li> -->
4752 <li>Group-associated consensus, sequence logos and
4753 conservation plots</li>
4754 <li>Symbol distributions for each column can be exported
4755 and visualized as sequence logos</li>
4756 <li>Optionally scale multi-character column labels to fit
4757 within each column of annotation row<!-- todo for applet -->
4759 <li>Optional automatic sort of associated alignment view
4760 when a new tree is opened.</li>
4761 <li>Jalview Java Console</li>
4762 <li>Better placement of desktop window when moving
4763 between different screens.</li>
4764 <li>New preference items for sequence ID tooltip and
4765 consensus annotation</li>
4766 <li>Client to submit sequences and IDs to Envision2
4768 <li><em>Vamsas Capabilities</em>
4770 <li>Improved VAMSAS synchronization (Jalview archive
4771 used to preserve views, structures, and tree display
4773 <li>Import of vamsas documents from disk or URL via
4775 <li>Sharing of selected regions between views and
4776 with other VAMSAS applications (Experimental feature!)</li>
4777 <li>Updated API to VAMSAS version 0.2</li>
4779 </ul> <em>Applet</em>
4781 <li>Middle button resizes annotation row height</li>
4784 <li>sortByTree (true/false) - automatically sort the
4785 associated alignment view by the tree when a new tree is
4787 <li>showTreeBootstraps (true/false) - show or hide
4788 branch bootstraps (default is to show them if available)</li>
4789 <li>showTreeDistances (true/false) - show or hide
4790 branch lengths (default is to show them if available)</li>
4791 <li>showUnlinkedTreeNodes (true/false) - indicate if
4792 unassociated nodes should be highlighted in the tree
4794 <li>heightScale and widthScale (1.0 or more) -
4795 increase the height or width of a cell in the alignment
4796 grid relative to the current font size.</li>
4799 <li>Non-positional features displayed in sequence ID
4801 </ul> <em>Other</em>
4803 <li>Features format: graduated colour definitions and
4804 specification of feature scores</li>
4805 <li>Alignment Annotations format: new keywords for group
4806 associated annotation (GROUP_REF) and annotation row display
4807 properties (ROW_PROPERTIES)</li>
4808 <li>XML formats extended to support graduated feature
4809 colourschemes, group associated annotation, and profile
4810 visualization settings.</li></td>
4813 <li>Source field in GFF files parsed as feature source
4814 rather than description</li>
4815 <li>Non-positional features are now included in sequence
4816 feature and gff files (controlled via non-positional feature
4817 visibility in tooltip).</li>
4818 <li>URL links generated for all feature links (bugfix)</li>
4819 <li>Added URL embedding instructions to features file
4821 <li>Codons containing ambiguous nucleotides translated as
4822 'X' in peptide product</li>
4823 <li>Match case switch in find dialog box works for both
4824 sequence ID and sequence string and query strings do not
4825 have to be in upper case to match case-insensitively.</li>
4826 <li>AMSA files only contain first column of
4827 multi-character column annotation labels</li>
4828 <li>Jalview Annotation File generation/parsing consistent
4829 with documentation (e.g. Stockholm annotation can be
4830 exported and re-imported)</li>
4831 <li>PDB files without embedded PDB IDs given a friendly
4833 <li>Find incrementally searches ID string matches as well
4834 as subsequence matches, and correctly reports total number
4838 <li>Better handling of exceptions during sequence
4840 <li>Dasobert generated non-positional feature URL
4841 link text excludes the start_end suffix</li>
4842 <li>DAS feature and source retrieval buttons disabled
4843 when fetch or registry operations in progress.</li>
4844 <li>PDB files retrieved from URLs are cached properly</li>
4845 <li>Sequence description lines properly shared via
4847 <li>Sequence fetcher fetches multiple records for all
4849 <li>Ensured that command line das feature retrieval
4850 completes before alignment figures are generated.</li>
4851 <li>Reduced time taken when opening file browser for
4853 <li>isAligned check prior to calculating tree, PCA or
4854 submitting an MSA to JNet now excludes hidden sequences.</li>
4855 <li>User defined group colours properly recovered
4856 from Jalview projects.</li>
4865 <div align="center">
4866 <strong>2.4.0.b2</strong><br> 28/10/2009
4871 <li>Experimental support for google analytics usage
4873 <li>Jalview privacy settings (user preferences and docs).</li>
4878 <li>Race condition in applet preventing startup in
4880 <li>Exception when feature created from selection beyond
4881 length of sequence.</li>
4882 <li>Allow synthetic PDB files to be imported gracefully</li>
4883 <li>Sequence associated annotation rows associate with
4884 all sequences with a given id</li>
4885 <li>Find function matches case-insensitively for sequence
4886 ID string searches</li>
4887 <li>Non-standard characters do not cause pairwise
4888 alignment to fail with exception</li>
4889 </ul> <em>Application Issues</em>
4891 <li>Sequences are now validated against EMBL database</li>
4892 <li>Sequence fetcher fetches multiple records for all
4894 </ul> <em>InstallAnywhere Issues</em>
4896 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4897 issue with installAnywhere mechanism)</li>
4898 <li>Command line launching of JARs from InstallAnywhere
4899 version (java class versioning error fixed)</li>
4906 <div align="center">
4907 <strong>2.4</strong><br> 27/8/2008
4910 <td><em>User Interface</em>
4912 <li>Linked highlighting of codon and amino acid from
4913 translation and protein products</li>
4914 <li>Linked highlighting of structure associated with
4915 residue mapping to codon position</li>
4916 <li>Sequence Fetcher provides example accession numbers
4917 and 'clear' button</li>
4918 <li>MemoryMonitor added as an option under Desktop's
4920 <li>Extract score function to parse whitespace separated
4921 numeric data in description line</li>
4922 <li>Column labels in alignment annotation can be centred.</li>
4923 <li>Tooltip for sequence associated annotation give name
4925 </ul> <em>Web Services and URL fetching</em>
4927 <li>JPred3 web service</li>
4928 <li>Prototype sequence search client (no public services
4930 <li>Fetch either seed alignment or full alignment from
4932 <li>URL Links created for matching database cross
4933 references as well as sequence ID</li>
4934 <li>URL Links can be created using regular-expressions</li>
4935 </ul> <em>Sequence Database Connectivity</em>
4937 <li>Retrieval of cross-referenced sequences from other
4939 <li>Generalised database reference retrieval and
4940 validation to all fetchable databases</li>
4941 <li>Fetch sequences from DAS sources supporting the
4942 sequence command</li>
4943 </ul> <em>Import and Export</em>
4944 <li>export annotation rows as CSV for spreadsheet import</li>
4945 <li>Jalview projects record alignment dataset associations,
4946 EMBL products, and cDNA sequence mappings</li>
4947 <li>Sequence Group colour can be specified in Annotation
4949 <li>Ad-hoc colouring of group in Annotation File using RGB
4950 triplet as name of colourscheme</li>
4951 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4953 <li>treenode binding for VAMSAS tree exchange</li>
4954 <li>local editing and update of sequences in VAMSAS
4955 alignments (experimental)</li>
4956 <li>Create new or select existing session to join</li>
4957 <li>load and save of vamsas documents</li>
4958 </ul> <em>Application command line</em>
4960 <li>-tree parameter to open trees (introduced for passing
4962 <li>-fetchfrom command line argument to specify nicknames
4963 of DAS servers to query for alignment features</li>
4964 <li>-dasserver command line argument to add new servers
4965 that are also automatically queried for features</li>
4966 <li>-groovy command line argument executes a given groovy
4967 script after all input data has been loaded and parsed</li>
4968 </ul> <em>Applet-Application data exchange</em>
4970 <li>Trees passed as applet parameters can be passed to
4971 application (when using "View in full
4972 application")</li>
4973 </ul> <em>Applet Parameters</em>
4975 <li>feature group display control parameter</li>
4976 <li>debug parameter</li>
4977 <li>showbutton parameter</li>
4978 </ul> <em>Applet API methods</em>
4980 <li>newView public method</li>
4981 <li>Window (current view) specific get/set public methods</li>
4982 <li>Feature display control methods</li>
4983 <li>get list of currently selected sequences</li>
4984 </ul> <em>New Jalview distribution features</em>
4986 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4987 <li>RELEASE file gives build properties for the latest
4988 Jalview release.</li>
4989 <li>Java 1.1 Applet build made easier and donotobfuscate
4990 property controls execution of obfuscator</li>
4991 <li>Build target for generating source distribution</li>
4992 <li>Debug flag for javacc</li>
4993 <li>.jalview_properties file is documented (slightly) in
4994 jalview.bin.Cache</li>
4995 <li>Continuous Build Integration for stable and
4996 development version of Application, Applet and source
5001 <li>selected region output includes visible annotations
5002 (for certain formats)</li>
5003 <li>edit label/displaychar contains existing label/char
5005 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
5006 <li>shorter peptide product names from EMBL records</li>
5007 <li>Newick string generator makes compact representations</li>
5008 <li>bootstrap values parsed correctly for tree files with
5010 <li>pathological filechooser bug avoided by not allowing
5011 filenames containing a ':'</li>
5012 <li>Fixed exception when parsing GFF files containing
5013 global sequence features</li>
5014 <li>Alignment datasets are finalized only when number of
5015 references from alignment sequences goes to zero</li>
5016 <li>Close of tree branch colour box without colour
5017 selection causes cascading exceptions</li>
5018 <li>occasional negative imgwidth exceptions</li>
5019 <li>better reporting of non-fatal warnings to user when
5020 file parsing fails.</li>
5021 <li>Save works when Jalview project is default format</li>
5022 <li>Save as dialog opened if current alignment format is
5023 not a valid output format</li>
5024 <li>UniProt canonical names introduced for both das and
5026 <li>Histidine should be midblue (not pink!) in Zappo</li>
5027 <li>error messages passed up and output when data read
5029 <li>edit undo recovers previous dataset sequence when
5030 sequence is edited</li>
5031 <li>allow PDB files without pdb ID HEADER lines (like
5032 those generated by MODELLER) to be read in properly</li>
5033 <li>allow reading of JPred concise files as a normal
5035 <li>Stockholm annotation parsing and alignment properties
5036 import fixed for PFAM records</li>
5037 <li>Structure view windows have correct name in Desktop
5039 <li>annotation consisting of sequence associated scores
5040 can be read and written correctly to annotation file</li>
5041 <li>Aligned cDNA translation to aligned peptide works
5043 <li>Fixed display of hidden sequence markers and
5044 non-italic font for representatives in Applet</li>
5045 <li>Applet Menus are always embedded in applet window on
5047 <li>Newly shown features appear at top of stack (in
5049 <li>Annotations added via parameter not drawn properly
5050 due to null pointer exceptions</li>
5051 <li>Secondary structure lines are drawn starting from
5052 first column of alignment</li>
5053 <li>UniProt XML import updated for new schema release in
5055 <li>Sequence feature to sequence ID match for Features
5056 file is case-insensitive</li>
5057 <li>Sequence features read from Features file appended to
5058 all sequences with matching IDs</li>
5059 <li>PDB structure coloured correctly for associated views
5060 containing a sub-sequence</li>
5061 <li>PDB files can be retrieved by applet from Jar files</li>
5062 <li>feature and annotation file applet parameters
5063 referring to different directories are retrieved correctly</li>
5064 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
5065 <li>Fixed application hang whilst waiting for
5066 splash-screen version check to complete</li>
5067 <li>Applet properly URLencodes input parameter values
5068 when passing them to the launchApp service</li>
5069 <li>display name and local features preserved in results
5070 retrieved from web service</li>
5071 <li>Visual delay indication for sequence retrieval and
5072 sequence fetcher initialisation</li>
5073 <li>updated Application to use DAS 1.53e version of
5074 dasobert DAS client</li>
5075 <li>Re-instated Full AMSA support and .amsa file
5077 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
5085 <div align="center">
5086 <strong>2.3</strong><br> 9/5/07
5091 <li>Jmol 11.0.2 integration</li>
5092 <li>PDB views stored in Jalview XML files</li>
5093 <li>Slide sequences</li>
5094 <li>Edit sequence in place</li>
5095 <li>EMBL CDS features</li>
5096 <li>DAS Feature mapping</li>
5097 <li>Feature ordering</li>
5098 <li>Alignment Properties</li>
5099 <li>Annotation Scores</li>
5100 <li>Sort by scores</li>
5101 <li>Feature/annotation editing in applet</li>
5106 <li>Headless state operation in 2.2.1</li>
5107 <li>Incorrect and unstable DNA pairwise alignment</li>
5108 <li>Cut and paste of sequences with annotation</li>
5109 <li>Feature group display state in XML</li>
5110 <li>Feature ordering in XML</li>
5111 <li>blc file iteration selection using filename # suffix</li>
5112 <li>Stockholm alignment properties</li>
5113 <li>Stockhom alignment secondary structure annotation</li>
5114 <li>2.2.1 applet had no feature transparency</li>
5115 <li>Number pad keys can be used in cursor mode</li>
5116 <li>Structure Viewer mirror image resolved</li>
5123 <div align="center">
5124 <strong>2.2.1</strong><br> 12/2/07
5129 <li>Non standard characters can be read and displayed
5130 <li>Annotations/Features can be imported/exported to the
5132 <li>Applet allows editing of sequence/annotation/group
5133 name & description
5134 <li>Preference setting to display sequence name in
5136 <li>Annotation file format extended to allow
5137 Sequence_groups to be defined
5138 <li>Default opening of alignment overview panel can be
5139 specified in preferences
5140 <li>PDB residue numbering annotation added to associated
5146 <li>Applet crash under certain Linux OS with Java 1.6
5148 <li>Annotation file export / import bugs fixed
5149 <li>PNG / EPS image output bugs fixed
5155 <div align="center">
5156 <strong>2.2</strong><br> 27/11/06
5161 <li>Multiple views on alignment
5162 <li>Sequence feature editing
5163 <li>"Reload" alignment
5164 <li>"Save" to current filename
5165 <li>Background dependent text colour
5166 <li>Right align sequence ids
5167 <li>User-defined lower case residue colours
5170 <li>Menu item accelerator keys
5171 <li>Control-V pastes to current alignment
5172 <li>Cancel button for DAS Feature Fetching
5173 <li>PCA and PDB Viewers zoom via mouse roller
5174 <li>User-defined sub-tree colours and sub-tree selection
5177 <li>'New Window' button on the 'Output to Text box'
5182 <li>New memory efficient Undo/Redo System
5183 <li>Optimised symbol lookups and conservation/consensus
5185 <li>Region Conservation/Consensus recalculated after
5187 <li>Fixed Remove Empty Columns Bug (empty columns at end
5189 <li>Slowed DAS Feature Fetching for increased robustness.
5192 <li>Made angle brackets in ASCII feature descriptions
5194 <li>Re-instated Zoom function for PCA
5195 <li>Sequence descriptions conserved in web service
5197 <li>UniProt ID discoverer uses any word separated by
5199 <li>WsDbFetch query/result association resolved
5200 <li>Tree leaf to sequence mapping improved
5201 <li>Smooth fonts switch moved to FontChooser dialog box.
5209 <div align="center">
5210 <strong>2.1.1</strong><br> 12/9/06
5215 <li>Copy consensus sequence to clipboard</li>
5220 <li>Image output - rightmost residues are rendered if
5221 sequence id panel has been resized</li>
5222 <li>Image output - all offscreen group boundaries are
5224 <li>Annotation files with sequence references - all
5225 elements in file are relative to sequence position</li>
5226 <li>Mac Applet users can use Alt key for group editing</li>
5232 <div align="center">
5233 <strong>2.1</strong><br> 22/8/06
5238 <li>MAFFT Multiple Alignment in default Web Service list</li>
5239 <li>DAS Feature fetching</li>
5240 <li>Hide sequences and columns</li>
5241 <li>Export Annotations and Features</li>
5242 <li>GFF file reading / writing</li>
5243 <li>Associate structures with sequences from local PDB
5245 <li>Add sequences to exisiting alignment</li>
5246 <li>Recently opened files / URL lists</li>
5247 <li>Applet can launch the full application</li>
5248 <li>Applet has transparency for features (Java 1.2
5250 <li>Applet has user defined colours parameter</li>
5251 <li>Applet can load sequences from parameter
5252 "sequence<em>x</em>"
5258 <li>Redundancy Panel reinstalled in the Applet</li>
5259 <li>Monospaced font - EPS / rescaling bug fixed</li>
5260 <li>Annotation files with sequence references bug fixed</li>
5266 <div align="center">
5267 <strong>2.08.1</strong><br> 2/5/06
5272 <li>Change case of selected region from Popup menu</li>
5273 <li>Choose to match case when searching</li>
5274 <li>Middle mouse button and mouse movement can compress /
5275 expand the visible width and height of the alignment</li>
5280 <li>Annotation Panel displays complete JNet results</li>
5286 <div align="center">
5287 <strong>2.08b</strong><br> 18/4/06
5293 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
5294 <li>Righthand label on wrapped alignments shows correct
5301 <div align="center">
5302 <strong>2.08</strong><br> 10/4/06
5307 <li>Editing can be locked to the selection area</li>
5308 <li>Keyboard editing</li>
5309 <li>Create sequence features from searches</li>
5310 <li>Precalculated annotations can be loaded onto
5312 <li>Features file allows grouping of features</li>
5313 <li>Annotation Colouring scheme added</li>
5314 <li>Smooth fonts off by default - Faster rendering</li>
5315 <li>Choose to toggle Autocalculate Consensus On/Off</li>
5320 <li>Drag & Drop fixed on Linux</li>
5321 <li>Jalview Archive file faster to load/save, sequence
5322 descriptions saved.</li>
5328 <div align="center">
5329 <strong>2.07</strong><br> 12/12/05
5334 <li>PDB Structure Viewer enhanced</li>
5335 <li>Sequence Feature retrieval and display enhanced</li>
5336 <li>Choose to output sequence start-end after sequence
5337 name for file output</li>
5338 <li>Sequence Fetcher WSDBFetch@EBI</li>
5339 <li>Applet can read feature files, PDB files and can be
5340 used for HTML form input</li>
5345 <li>HTML output writes groups and features</li>
5346 <li>Group editing is Control and mouse click</li>
5347 <li>File IO bugs</li>
5353 <div align="center">
5354 <strong>2.06</strong><br> 28/9/05
5359 <li>View annotations in wrapped mode</li>
5360 <li>More options for PCA viewer</li>
5365 <li>GUI bugs resolved</li>
5366 <li>Runs with -nodisplay from command line</li>
5372 <div align="center">
5373 <strong>2.05b</strong><br> 15/9/05
5378 <li>Choose EPS export as lineart or text</li>
5379 <li>Jar files are executable</li>
5380 <li>Can read in Uracil - maps to unknown residue</li>
5385 <li>Known OutOfMemory errors give warning message</li>
5386 <li>Overview window calculated more efficiently</li>
5387 <li>Several GUI bugs resolved</li>
5393 <div align="center">
5394 <strong>2.05</strong><br> 30/8/05
5399 <li>Edit and annotate in "Wrapped" view</li>
5404 <li>Several GUI bugs resolved</li>
5410 <div align="center">
5411 <strong>2.04</strong><br> 24/8/05
5416 <li>Hold down mouse wheel & scroll to change font
5422 <li>Improved JPred client reliability</li>
5423 <li>Improved loading of Jalview files</li>
5429 <div align="center">
5430 <strong>2.03</strong><br> 18/8/05
5435 <li>Set Proxy server name and port in preferences</li>
5436 <li>Multiple URL links from sequence ids</li>
5437 <li>User Defined Colours can have a scheme name and added
5439 <li>Choose to ignore gaps in consensus calculation</li>
5440 <li>Unix users can set default web browser</li>
5441 <li>Runs without GUI for batch processing</li>
5442 <li>Dynamically generated Web Service Menus</li>
5447 <li>InstallAnywhere download for Sparc Solaris</li>
5453 <div align="center">
5454 <strong>2.02</strong><br> 18/7/05
5460 <li>Copy & Paste order of sequences maintains
5461 alignment order.</li>
5467 <div align="center">
5468 <strong>2.01</strong><br> 12/7/05
5473 <li>Use delete key for deleting selection.</li>
5474 <li>Use Mouse wheel to scroll sequences.</li>
5475 <li>Help file updated to describe how to add alignment
5477 <li>Version and build date written to build properties
5479 <li>InstallAnywhere installation will check for updates
5480 at launch of Jalview.</li>
5485 <li>Delete gaps bug fixed.</li>
5486 <li>FileChooser sorts columns.</li>
5487 <li>Can remove groups one by one.</li>
5488 <li>Filechooser icons installed.</li>
5489 <li>Finder ignores return character when searching.
5490 Return key will initiate a search.<br>
5497 <div align="center">
5498 <strong>2.0</strong><br> 20/6/05
5503 <li>New codebase</li>