4 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
5 * Copyright (C) $$Year-Rel$$ The Jalview Authors
7 * This file is part of Jalview.
9 * Jalview is free software: you can redistribute it and/or
10 * modify it under the terms of the GNU General Public License
11 * as published by the Free Software Foundation, either version 3
12 * of the License, or (at your option) any later version.
14 * Jalview is distributed in the hope that it will be useful, but
15 * WITHOUT ANY WARRANTY; without even the implied warranty
16 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
17 * PURPOSE. See the GNU General Public License for more details.
19 * You should have received a copy of the GNU General Public License
20 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
21 * The Jalview Authors are detailed in the 'AUTHORS' file.
24 <title>Release History</title>
27 /* remove bullets, narrower indent */
28 list-style-type: none;
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51 <strong>Release History</strong>
55 <th nowrap><a id="Jalview.$$Version-Rel$$"><em>Release</em></th>
56 <th><em>New Features</em></th>
57 <th><em>Issues Resolved</em></th>
60 <td width="60" align="center" nowrap><strong><a
61 id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.0">.0</a><br />
62 <em>3/03/2022</em></strong></td>
63 <td align="left" valign="top">
66 <!-- JAL-3616 JAL-3551 JAL-2322 -->Support for viewing 3D
67 structures with ChimeraX and Pymol in addition to Jmol and
71 <!-- JAL-3829 -->Discover 3D structure data for sequences
72 with Uniprot references via 3D-Beacons
75 <!-- JAL-3391 -->Rank and select available structures for
76 Uniprot sequences according to number of residues in
77 structure mapped to positions involved in the alignment
80 <!-- JAL-3503 -->New Preferences tab for adjusting Jalview's
81 memory settings at launch
84 <!-- JAL-3144 -->Reverted to Jalview 'classic' drop-down
85 menu for selecting which database to fetch from in sequence
89 <!-- JAL-2226 -->Structure annotation rows for all mapped
90 chains in 3D structures are included in the 'Reference
91 Annotation' for a sequence
94 <!-- JAL-1260 -->Import Genbank and EMBL format flatfiles
97 <!-- JAL-3821 -->ENA record's mol_type honoured so RNA
98 molecules imported from ENA records are shown as RNA
100 <!-- JAL-3863 -->Support for Canonical Uniprot IDs
103 <!-- JAL-3204 -->Updated Jalview bindings for Uniprot XML
107 <!-- JAL-3926 -->Uniprot and PDBe autosearch option is
111 <!-- JAL-3530 -->-nowebservicediscovery command line
112 argument to prevent automatic discovery of analysis
113 webservices on launch
116 <!-- JAL-3618 -->Allow 'App' directories to be opened when
117 locating Chimera, ChimeraX or Pymol binaries via filechooser
118 opened by double clicking the Structure Preferences' path
122 <em>Jalview Native App</em>
125 <!-- JAL- -->New Jalview Develop app - making it even easier
126 to get at Jalview's development builds
129 <!-- JAL-3594 -->New splashscreens for Jalview, Jalview Test
130 and Jalview Develop applications.
133 <!-- JAL-3728 -->Jalview logos shown for Jalview Java
134 Console and other window widgets in taskbar and dock rather
135 than anonymous 'Java' icons
137 </ul> <em>JalviewJS</em>
140 <!-- JAL-3624 -->PDB structures mapped to Uniprot Sequences with
144 <!-- JAL-3208 -->setprop commandline argument reinstated for JalviewJS only
153 <!-- JAL-3163 -->Missing message bundle keys are only
154 reported once per key (avoids excessive log output in js
158 <!-- JAL-3168 -->Feature type is included in the title of
159 the Feature Settings' Colour Chooser dialog
162 </ul> <em>Development</em>
165 <!-- -->First integrated JalviewJS and Jalview release
167 <li>Updated building instructions</li>
169 <!-- JAL-3789, JAL-3679 -->Improved JalviewJS/Jalview build
170 process, added support for system package provided eclipse
173 <li>Install4j 9.0.x used for installer packaging</li>
174 <li>Notarized MacOS installer for compatibility with Big
175 Sur and Monterey</li>
177 <!-- JAL-3805 -->Uninstaller application for old
178 (InstallAnywhere based) Jalview installations removed from
182 <!-- JAL-3930 -->Improved use of installers for unattended
183 installation with a customizedId of "JALVIEW" in install4j's
187 <!-- JAL-3907 -->Improved compatibility of Jalview build
188 with Java 17 (next LTS target)
197 <!-- JAL-3674 -->Slow structure commands can block Jalview
201 <!-- JAL-3904 -->Structure window's viewer-specific menu
202 disappears when only one structure is shown (and many
203 sequences:one chain mappings are present)
206 <!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
207 the first SEQUENCE_GROUP defined
212 <!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 -->Selections not
213 propagated between Linked CDS - Protein alignments and their
214 trees (known defect from 2.11.1.3)
217 <!-- JAL-3761 -->Not all codon positions highlighted for
218 overlapping exon splice sites (e.g due to RNA slippage)
221 <!-- JAL-3794 -->X was not being recognised as the unknown
222 base in DNA sequences
225 <!-- JAL-3915 -->Removed RNAview checkbox and logic from
226 Structure Preferences
229 <!-- JAL-3583 -->Tooltip behaviour improved (slightly)
232 <!-- JAL-3162 -->Can edit a feature so that start > end
235 <!-- JAL-2848 -->Cancel from Amend Features doesn't reset a
236 modified graduated colour
239 <!-- JAL-3788 -->New View with automatic 'Show Overview'
240 preference enabled results in Null Pointer Exceptions when
241 clustal colouring is enabled
244 <!-- JAL-3275 -->Can open multiple Preferences panels
247 <!-- JAL-3949 -->Standard out logging broken: messages only
248 routing to stderr and appear as a raw template
250 </ul> <em>JalviewJS</em>
253 <!-- JAL-3202 -->Consensus profile may include zero (rounded
254 down) percentage values causing a divide by zero
269 <!-- JAL-3762 -->JalviewJS doesn't honour arguments passed
270 via Info.args when there are arguments on the URL
273 <!-- JAL-3602 -->gradle closure-compiler not using UTF-8
276 <!-- JAL-3603 -->Annotation file fails to load from URL in
279 </ul> <em>Development</em>
283 <li>Fixed non-fatal gradle errors during build</li>
285 <!-- JAL-3745 -->Updated build.gradle for use with
295 <td width="60" align="center" nowrap><strong><a
296 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.7">.7</a><br />
297 <em>18/01/2022</em></strong></td>
299 <td align="left" valign="top">
302 <!-- JAL-3703, JAL-3935 -->Files open in Jalview cannot be
303 updated by Jalview or other applications (Windows, other non
306 </ul> <em>Security</em>
309 <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
315 <td width="60" align="center" nowrap><strong><a
316 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
317 <em>6/01/2022</em></strong></td>
319 <td align="left" valign="top"><em>Security</em>
322 <!-- JAL-3934 -->Version bump library dependency: Log4j
329 <td width="60" align="center" nowrap><strong><a
330 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
331 <em>20/12/2021</em></strong></td>
333 <td align="left" valign="top"><em>Security</em>
336 <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
338 </ul> <em>Development</em>
340 <li>Updated building instructions</li>
345 <!-- JAL-3840 -->Occupancy calculation is incorrect for
346 alignment columns with over -1+2^32 gaps (breaking filtering
350 <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
351 scale factors being set with buggy window-managers (linux
354 </ul> <em>Development</em>
356 <li>Fixed non-fatal gradle errors during build</li>
361 <td width="60" align="center" nowrap><strong><a
362 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
363 <em>09/03/2021</em></strong></td>
364 <td align="left" valign="top"><em>Improved control of
365 Jalview's use of network services via jalview_properties</em>
368 <!-- JAL-3814 -->New .jalview_properties token controlling
369 launch of the news browser (like -nonews argument)
372 <!-- JAL-3813 -->New .jalview_properties token controlling
373 download of linkout URLs from
374 www.jalview.org/services/identifiers
377 <!-- JAL-3812 -->New .jalview_properties token controlling
378 download of BIOJSHTML templates
381 <!-- JAL-3811 -->New 'Discover Web Services' option to
382 trigger a one off JABAWS discovery if autodiscovery was
386 <td align="left" valign="top">
389 <!-- JAL-3818 -->Intermittent deadlock opening structure in
392 </ul> <em>New Known defects</em>
395 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
396 always restored from project (since 2.10.3)
399 <!-- JAL-3806 -->Selections from tree built from CDS aren't
400 propagated to Protein alignment (since 2.11.1.3)
406 <td width="60" align="center" nowrap><strong><a
407 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
408 <em>29/10/2020</em></strong></td>
409 <td align="left" valign="top">
414 <td align="left" valign="top">
417 <!-- JAL-3765 -->Find doesn't always highlight all matching
418 positions in a sequence (bug introduced in 2.11.1.2)
421 <!-- JAL-3760 -->Alignments containing one or more protein
422 sequences can be classed as nucleotide
425 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
426 sequences after alignment of protein products (known defect
427 first reported for 2.11.1.0)
430 <!-- JAL-3725 -->No tooltip or popup menu for genomic
431 features outwith CDS shown overlaid on protein
434 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
435 correctly mapped by Jalview (e.g. affects viral CDS with
436 ribosomal slippage, since 2.9.0)
439 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
443 <!-- JAL-3700 -->Selections in CDS sequence panel don't
444 always select corresponding protein sequences
447 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
448 column selection doesn't always ignore hidden columns
450 </ul> <em>Installer</em>
453 <!-- JAL-3611 -->Space character in Jalview install path on
454 Windows prevents install4j launching getdown
456 </ul> <em>Development</em>
459 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
460 version numbers in doc/building.md
466 <td width="60" align="center" nowrap><strong><a
467 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
468 <em>25/09/2020</em></strong></td>
469 <td align="left" valign="top">
473 <td align="left" valign="top">
476 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
477 "Encountered problems opening
478 https://www.jalview.org/examples/exampleFile_2_7.jvp"
484 <td width="60" align="center" nowrap><strong><a
485 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
486 <em>17/09/2020</em></strong></td>
487 <td align="left" valign="top">
490 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
491 residue in cursor mode
494 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
495 HTSJDK from 2.12 to 2.23
498 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
499 optimisations and improvements suggested by Bob Hanson and
500 improved compatibility with JalviewJS
503 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
504 alignments from Pfam and Rfam
507 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
508 import (no longer based on .gz extension)
511 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
514 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
515 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
519 <!-- JAL-3667 -->Improved warning messages, debug logging
520 and fixed Retry action when Jalview encounters errors when
521 saving or making backup files.
524 <!-- JAL-3676 -->Enhanced Jalview Java Console:
526 <li>Jalview's logging level can be configured</li>
527 <li>Copy to Clipboard Buttion</li>
531 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
532 when running on Linux (Requires Java 11+)
534 </ul> <em>Launching Jalview</em>
537 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
538 through a system property
541 <!-- JAL-3477 -->Improved built-in documentation and command
542 line help for configuring Jalview's memory
546 <td align="left" valign="top">
549 <!-- JAL-3691 -->Conservation and Quality tracks are shown
550 but not calculated and no protein or DNA score models are
551 available for tree/PCA calculation when launched with
552 Turkish language locale
555 <!-- JAL-3493 -->Escape does not clear highlights on the
556 alignment (Since Jalview 2.10.3)
559 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
560 doesn't slide selected sequences, just sequence under cursor
563 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
564 sequence under the cursor
567 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
568 multiple EMBL gene products shown for a single contig
571 <!-- JAL-3696 -->Errors encountered when processing variants
572 from VCF files yield "Error processing VCF: Format specifier
576 <!-- JAL-3697 -->Count of features not shown can be wrong
577 when there are both local and complementary features mapped
578 to the position under the cursor
581 <!-- JAL-3673 -->Sequence ID for reference sequence is
582 clipped when Right align Sequence IDs enabled
585 <!-- JAL-2983 -->Slider with negative range values not
586 rendered correctly in VAqua4 (Since 2.10.4)
589 <!-- JAL-3685 -->Single quotes not displayed correctly in
590 internationalised text for some messages and log output
593 <!-- JAL-3490 -->Find doesn't report matches that span
594 hidden gapped columns
597 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
598 panels, Alignment viewport and annotation renderer.
601 <!-- JAL-3561 -->Jalview ignores file format parameter
602 specifying output format when exporting an alignment via the
606 <!-- JAL-3667 -->Windows 10: For a minority of users, if
607 backups are not enabled, Jalview sometimes fails to
608 overwrite an existing file and raises a warning dialog. (in
609 2.11.0, and 2.11.1.0, the workaround is to try to save the
610 file again, and if that fails, delete the original file and
614 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
618 <!-- JAL-3741 -->References to http://www.jalview.org in
619 program and documentation
621 </ul> <em>Launching Jalview</em>
624 <!-- JAL-3718 -->Jalview application fails when launched the
625 first time for a version that has different jars to the
626 previous launched version.
628 </ul> <em>Developing Jalview</em>
631 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
632 data, causing cloverReport gradle task to fail with an
636 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
637 monitor the release channel
639 </ul> <em>New Known defects</em>
642 <!-- JAL-3748 -->CDS shown in result of submitting proteins
643 in a CDS/Protein alignment to a web service is wrong when
644 proteins share a common transcript sequence (e.g. genome of
648 <!-- JAL-3576 -->Co-located features exported and
649 re-imported are ordered differently when shown on alignment
650 and in tooltips. (Also affects v2.11.1.0)
653 <!-- JAL-3702 -->Drag and drop of alignment file onto
654 alignment window when in a HiDPI scaled mode in Linux only
655 works for the top left quadrant of the alignment window
658 <!-- JAL-3701 -->Stale build data in jalview standalone jar
659 builds (only affects 2.11.1.1 branch)
662 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
663 when alignment view restored from project (since Jalview
667 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
668 protein products for certain ENA records are repeatedly
669 shown via Calculate->Show Cross Refs
675 <td width="60" align="center" nowrap><strong><a
676 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
677 <em>22/04/2020</em></strong></td>
678 <td align="left" valign="top">
681 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
682 'virtual' codon features shown on protein (or vice versa)
683 for display in alignments, on structure views (including
684 transfer to UCSF chimera), in feature reports and for
688 <!-- JAL-3121 -->Feature attributes from VCF files can be
689 exported and re-imported as GFF3 files
692 <!-- JAL-3376 -->Capture VCF "fixed column" values
693 POS, ID, QUAL, FILTER as Feature Attributes
696 <!-- JAL-3375 -->More robust VCF numeric data field
697 validation while parsing
700 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
704 <!-- JAL-3535 -->Feature Settings dialog title includes name
708 <!-- JAL-3538 -->Font anti-aliasing in alignment views
712 <!-- JAL-3468 -->Very long feature descriptions truncated in
716 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
717 with no feature types visible
720 <!-- JAL-3574 -->Improved support for filtering feature
721 attributes with large integer values
724 <em>Jalview Installer</em>
727 <!-- JAL-3449 -->Versions for install4j and getdown and
728 installer template version reported in console (may be null
729 when Jalview launched as executable jar or via conda)
732 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and
733 higher quality background images
736 <!-- JAL-3394 -->New installer/application launcher
737 generated with install4j 8.0.4
740 <!-- JAL-3420 -->Jalview File Associations shown for Unix
744 <!-- JAL-3477 -->Improved defaults for maximum memory
745 setting when running on large memory machines
747 </ul> <em>Release processes</em>
750 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
753 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier
754 access to test-release channel builds
756 </ul> <em>Build System</em>
759 <!-- JAL-3510 -->Clover updated to 4.4.1
762 <!-- JAL-3513 -->Test code included in Clover coverage
765 </ul> <em>Groovy Scripts</em>
768 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
769 to stdout containing the consensus sequence for each
770 alignment in a Jalview session
773 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
774 genomic sequence_variant annotation from CDS as
775 missense_variant or synonymous_variant on protein products.
779 <td align="left" valign="top">
782 <!-- JAL-3581 -->Hidden sequence markers still visible when
783 'Show hidden markers' option is not ticked
786 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
787 PNG output when 'Automatically set ID width' is set in
788 jalview preferences or properties file
791 <!-- JAL-3571 -->Feature Editor dialog can be opened when
792 'Show Sequence Features' option is not ticked
795 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
796 buttons in Feature Settings dialog are clicked when no
800 <!-- JAL-3412 -->ID margins for CDS and Protein views not
801 equal when split frame is first opened
804 <!-- JAL-3296 -->Sequence position numbers in status bar not
805 correct after editing a sequence's start position
808 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
809 with annotation and exceptions thrown when only a few
810 columns shown in wrapped mode
813 <!-- JAL-3386 -->Sequence IDs missing in headless export of
814 wrapped alignment figure with annotations
817 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
818 ID fails with ClassCastException
821 <!-- JAL-3389 -->Chimera session not restored from Jalview
825 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
826 feature settings dialog also selects columns
829 <!-- JAL-3473 -->SpinnerNumberModel causes
830 IllegalArgumentException in some circumstances
833 <!-- JAL-3534 -->Multiple feature settings dialogs can be
837 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
838 alignment window is closed
841 <!-- JAL-3406 -->Credits missing some authors in Jalview
842 help documentation for 2.11.0 release
845 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
846 includes Pfam ID as sequence's accession rather than its
849 </ul> <em>Java 11 Compatibility issues</em>
852 <!-- JAL-2987 -->OSX - Can't view some search results in
853 PDB/Uniprot search panel
855 </ul> <em>Installer</em>
858 <!-- JAL-3447 -->Jalview should not create file associations
859 for 3D structure files (.pdb, .mmcif. .cif)
861 </ul> <em>Repository and Source Release</em>
864 <!-- JAL-3474 -->removed obsolete .cvsignore files from
868 <!-- JAL-3541 -->Clover report generation running out of
871 </ul> <em>New Known Issues</em>
874 <!-- JAL-3523 -->OSX - Current working directory not
875 preserved when Jalview.app launched with parameters from
879 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
880 clipped in headless figure export when Right Align option
884 <!-- JAL-3542 -->Jalview Installation type always reports
885 'Source' in console output
888 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail
889 on jalview's bamboo server but run fine locally.
895 <td width="60" align="center" nowrap><strong><a
896 name="Jalview.2.11.0">2.11.0</a><br /> <em>04/07/2019</em></strong></td>
897 <td align="left" valign="top">
900 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native
901 Application and Installers built with <a
902 href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a>
903 (licensed to the Jalview open source project) rather than
907 <!-- JAL-1929 -->Jalview Launcher System to auto-configure
908 memory settings, receive over the air updates and launch
909 specific versions via (<a
910 href="https://github.com/threerings/getdown">Three
914 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations
915 for formats supported by Jalview (including .jvp project
919 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command
920 line arguments and switch between different getdown channels
923 <!-- JAL-3141 -->Backup files created when saving Jalview
924 project or alignment files
928 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF
932 <!-- JAL-2753 -->Version of HTSJDK shipped with Jalview
933 updated to version 2.12.0
936 <!-- JAL-2620 -->Alternative genetic code tables for
940 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0
942 <li><strong>Enhanced visualisation and analysis
943 of Sequence Features</strong>
946 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
947 implementation that allows updates) used for Sequence
951 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
952 features can be filtered and shaded according to any
953 associated attributes (e.g. variant attributes from VCF
954 file, or key-value pairs imported from column 9 of GFF
958 <!-- JAL-2879 -->Feature Attributes and shading schemes
959 stored and restored from Jalview Projects
962 <!-- JAL-3334 -->Use full Sequence Ontology (via
963 BioJava) to recognise variant features
966 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants
967 on peptide sequences (also coloured red by default)
970 <!-- JAL-2792 -->Popup window to show full report for a
971 selected sequence feature's details
974 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient
975 sequence feature render algorithm (Z-sort/transparency
979 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature
984 <!-- JAL-3205 -->Symmetric score matrices for faster tree
987 <li><strong>Principal Components Analysis Viewer</strong>
990 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis
991 results and Viewer state saved in Jalview Project
994 <!-- JAL-2962 -->'Change parameters' option removed from
995 viewer's drop-down menus
998 <!-- JAL-2975 -->Can use shift + arrow keys to rotate
999 PCA image incrementally
1002 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
1006 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
1008 <li><strong>Speed and Efficiency</strong>
1011 <!-- JAL-2185,JAL-3198 -->More efficient creation of
1012 selections and multiple groups when working with large
1016 <!-- JAL-3200 -->Speedier import of annotation rows when
1017 parsing Stockholm files
1020 <li><strong>User Interface</strong>
1023 <!-- JAL-2933 -->Finder panel remembers last position in
1027 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS
1028 (What you see is what is shown)<br />Only visible
1029 regions of alignment are shown by default (can be
1030 changed in user preferences)
1033 <!-- JAL-3169 -->File Chooser stays open after
1034 responding Cancel to the Overwrite Dialog
1037 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour
1038 when all sequences are hidden
1041 <!-- JAL-1244 -->Status bar shows bounds when dragging a
1042 selection region, and gap count when inserting or
1046 <!-- JAL-3132 -->Status bar updates over sequence and
1050 <!-- JAL-3093 -->Annotation tooltips and popup menus are
1051 shown when in wrapped mode
1054 <!-- JAL-3073 -->Can select columns by dragging
1055 left/right in a graph or histogram annotation
1058 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB
1062 <!-- JAL-2621 -->Cursor changes over draggable box in
1066 <!-- JAL-3181 -->Consistent ordering of links in
1067 sequence id popup menu
1070 <!-- JAL-3080 -->Red line indicating tree-cut position
1071 not shown if no subgroups are created
1074 <!-- JAL-3042 -->Removed ability to configure length of
1075 search history by right-clicking search box
1081 <!-- JAL-3232 -->Jalview Groovy Scripting Console updated to
1084 <li><strong>Java 11 Support (not yet on general
1088 <!-- -->OSX GUI integrations for App menu's 'About'
1089 entry and trapping CMD-Q
1092 </ul> <em>Deprecations</em>
1095 <!-- JAL-3035 -->DAS sequence retrieval and annotation
1096 capabilities removed from the Jalview Desktop
1099 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling
1100 and unmarshalling has been replaced by JAXB for Jalview
1101 projects and XML based data retrieval clients
1104 <!-- JAL-3311 -->Disable VAMSAS menu in preparation for
1108 <!-- -->Jalview Desktop no longer distributed via Java Web
1111 </ul> <em>Documentation</em>
1114 <!-- JAL-3003 -->Added remarks about transparent rendering
1115 effects not supported in EPS figure export
1118 <!-- JAL-2903 -->Typos in documentation for Preferences
1121 </ul> <em>Development and Release Processes</em>
1124 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated
1128 <!-- JAL-1424 -->Enhanced checks for missing and duplicated
1129 keys in Message bundles
1132 <!-- JAL-3225 -->Eclipse project configuration managed with
1136 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian Bamboo
1137 continuous integration for unattended Test Suite execution
1140 <!-- JAL-2864 -->Memory test suite to detect leaks in common
1144 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
1148 <!-- JAL-3248 -->Developer documentation migrated to
1149 markdown (with HTML rendering)
1152 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
1155 <!-- JAL-3289 -->New URLs for publishing development
1160 <td align="left" valign="top">
1163 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
1166 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
1167 superposition in Jmol fail on Windows
1170 <!-- JAL-3286 -->Blank error dialog is displayed when
1171 discovering structures for sequences with lots of PDB
1175 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export
1176 with monospaced font
1179 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
1180 Jalview project involving multiple views
1183 <!-- JAL-3164 -->Overview for complementary view in a linked
1184 CDS/Protein alignment is not updated when Hide Columns by
1185 Annotation dialog hides columns
1188 <!-- JAL-3158 -->Selection highlighting in the complement of
1189 a CDS/Protein alignment stops working after making a
1190 selection in one view, then making another selection in the
1194 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
1198 <!-- JAL-3154 -->Table Columns could be re-ordered in
1199 Feature Settings and Jalview Preferences panels
1202 <!-- JAL-2865 -->Jalview hangs when closing windows, or
1203 redrawing the overview with large alignments
1206 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
1207 region if columns were selected by dragging right-to-left
1208 and the mouse moved to the left of the first column
1211 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to
1212 a hidden column marker via scale popup menu
1215 <!-- JAL-2846 -->Error message for trying to load in invalid
1216 URLs doesn't tell users the invalid URL
1219 <!-- JAL-2816 -->Tooltips displayed for features filtered by
1223 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl
1224 during show cross references or Fetch Database References
1225 are shown in red in original view
1228 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown
1229 correctly on peptide sequence (computed variant shown as
1233 <!-- JAL-2060 -->'Graduated colour' option not offered for
1234 manually created features (where feature score is Float.NaN)
1237 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or
1238 printed when columns are hidden
1241 <!-- JAL-3082 -->Regular expression error for '(' in Select
1242 Columns by Annotation description
1245 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after
1246 dragging out of Scale or Annotation Panel
1249 <!-- JAL-3075 -->Column selection incorrect after scrolling
1253 <!-- JAL-3074 -->Left/right drag in annotation can scroll
1257 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal
1261 <!-- JAL-3002 -->Column display is out by one after Page
1262 Down, Page Up in wrapped mode
1265 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
1268 <!-- JAL-2932 -->Finder searches in minimised alignments
1271 <!-- JAL-2250 -->'Apply Colour to All Groups' not always
1272 selected on opening an alignment
1275 <!-- JAL-3180 -->'Colour by Annotation' not marked selected
1279 <!-- JAL-3201 -->Per-group Clustal colour scheme changes
1280 when different groups in the alignment are selected
1283 <!-- JAL-2717 -->Internationalised colour scheme names not
1284 shown correctly in menu
1287 <!-- JAL-3206 -->Colour by Annotation can go black at
1288 min/max threshold limit
1291 <!-- JAL-3125 -->Value input for graduated feature colour
1292 threshold gets 'unrounded'
1295 <!-- JAL-2982 -->PCA image export doesn't respect background
1299 <!-- JAL-2963 -->PCA points don't dim when rotated about y
1303 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
1306 <!-- JAL-3078 -->Cancel in Tree Font dialog resets
1307 alignment, not Tree font
1310 <!-- JAL-2964 -->Associate Tree with All Views not restored
1314 <!-- JAL-2915 -->Scrolling of split frame is sluggish if
1315 Overview shown in complementary view
1318 <!-- JAL-3313 -->Codon consensus incorrectly scaled when
1319 shown without normalisation
1322 <!-- JAL-3021 -->Sequence Details report should open
1323 positioned at top of report
1326 <!-- JAL-914 -->Help page can be opened twice
1329 <!-- JAL-3333 -->Fuzzy text in web service status menu on
1332 </ul> <em>Editing</em>
1335 <!-- JAL-2822 -->Start and End should be updated when
1336 sequence data at beginning or end of alignment added/removed
1340 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection
1341 doesn't relocate sequence features correctly when start of
1342 sequence is removed (Known defect since 2.10)
1345 <!-- JAL-2830 -->Inserting gap sequence via the Edit
1346 Sequence dialog corrupts dataset sequence
1349 <!-- JAL-868 -->Structure colours not updated when
1350 associated tree repartitions the alignment view (Regression
1353 </ul> <em>Datamodel</em>
1356 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
1357 sequence's End is greater than its length
1359 </ul> <em>Bugs fixed for Java 11 Support (not yet on general
1363 <!-- JAL-3288 -->Menus work properly in split-screen
1365 </ul> <em>New Known Defects</em>
1368 <!-- JAL-3340 -->Select columns containing feature by double
1369 clicking ignores bounds of an existing selected region
1372 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in
1373 gapped regions of protein alignment.
1376 <!-- JAL-2647 -->Input Data menu entry is greyed out when
1377 PCA View is restored from a Jalview 2.11 project
1380 <!-- JAL-3213 -->Alignment panel height can be too small
1384 <!-- JAL-3240 -->Display is incorrect after removing gapped
1385 columns within hidden columns
1388 <!-- JAL-3314 -->Rightmost selection is lost when mouse
1389 re-enters window after dragging left to select columns to
1390 left of visible region
1393 <!-- JAL-2876 -->Features coloured according to their
1394 description string and thresholded by score in earlier
1395 versions of Jalview are not shown as thresholded features in
1396 2.11. To workaround please create a Score filter instead.
1399 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't
1400 reset group visibility
1403 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in
1404 linked CDS/Protein view
1407 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1408 alignments with multiple views can close views unexpectedly
1410 </ul> <em>Java 11 Specific defects</em>
1413 <!-- JAL-3235 -->Jalview Properties file is not sorted
1414 alphabetically when saved
1420 <td width="60" nowrap>
1421 <div align="center">
1422 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1425 <td><div align="left">
1429 <!-- JAL-3101 -->Default memory for Jalview webstart and
1430 InstallAnywhere increased to 1G.
1433 <!-- JAL-247 -->Hidden sequence markers and representative
1434 sequence bolding included when exporting alignment as EPS,
1435 SVG, PNG or HTML. <em>Display is configured via the
1436 Format menu, or for command-line use via a Jalview
1437 properties file.</em>
1440 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1441 API and sequence data now imported as JSON.
1444 <!-- JAL-3065 -->Change in recommended way of starting
1445 Jalview via a Java command line: add jars in lib directory
1446 to CLASSPATH, rather than via the deprecated java.ext.dirs
1450 <em>Development</em>
1453 <!-- JAL-3047 -->Support added to execute test suite
1454 instrumented with <a href="http://openclover.org/">Open
1459 <td><div align="left">
1463 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1464 row shown in Feredoxin Structure alignment view of example
1468 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1469 annotation displayed.
1472 <!-- JAL-3107 -->Group conservation/consensus not shown
1473 for newly created group when 'Apply to all groups'
1477 <!-- JAL-3087 -->Corrupted display when switching to
1478 wrapped mode when sequence panel's vertical scrollbar is
1482 <!-- JAL-3003 -->Alignment is black in exported EPS file
1483 when sequences are selected in exported view.</em>
1486 <!-- JAL-3059 -->Groups with different coloured borders
1487 aren't rendered with correct colour.
1490 <!-- JAL-3092 -->Jalview could hang when importing certain
1491 types of knotted RNA secondary structure.
1494 <!-- JAL-3095 -->Sequence highlight and selection in
1495 trimmed VARNA 2D structure is incorrect for sequences that
1499 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1500 annotation when columns are inserted into an alignment,
1501 and when exporting as Stockholm flatfile.
1504 <!-- JAL-3053 -->Jalview annotation rows containing upper
1505 and lower-case 'E' and 'H' do not automatically get
1506 treated as RNA secondary structure.
1509 <!-- JAL-3106 -->.jvp should be used as default extension
1510 (not .jar) when saving a Jalview project file.
1513 <!-- JAL-3105 -->Mac Users: closing a window correctly
1514 transfers focus to previous window on OSX
1517 <em>Java 10 Issues Resolved</em>
1520 <!-- JAL-2988 -->OSX - Can't save new files via the File
1521 or export menus by typing in a name into the Save dialog
1525 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1526 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1527 'look and feel' which has improved compatibility with the
1528 latest version of OSX.
1534 <td width="60" nowrap>
1535 <div align="center">
1536 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1537 <em>7/06/2018</em></strong>
1540 <td><div align="left">
1544 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1545 annotation retrieved from Uniprot
1548 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1549 onto the Jalview Desktop
1553 <td><div align="left">
1557 <!-- JAL-3017 -->Cannot import features with multiple
1558 variant elements (blocks import of some Uniprot records)
1561 <!-- JAL-2997 -->Clustal files with sequence positions in
1562 right-hand column parsed correctly
1565 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1566 not alignment area in exported graphic
1569 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1570 window has input focus
1573 <!-- JAL-2992 -->Annotation panel set too high when
1574 annotation added to view (Windows)
1577 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1578 network connectivity is poor
1581 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1582 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1583 the currently open URL and links from a page viewed in
1584 Firefox or Chrome on Windows is now fully supported. If
1585 you are using Edge, only links in the page can be
1586 dragged, and with Internet Explorer, only the currently
1587 open URL in the browser can be dropped onto Jalview.</em>
1590 <em>New Known Defects</em>
1593 <!-- JAL-3083 -->Cancel option doesn't reset Colour by
1600 <td width="60" nowrap>
1601 <div align="center">
1602 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1605 <td><div align="left">
1609 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1610 for disabling automatic superposition of multiple
1611 structures and open structures in existing views
1614 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1615 ID and annotation area margins can be click-dragged to
1619 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1623 <!-- JAL-2759 -->Improved performance for large alignments
1624 and lots of hidden columns
1627 <!-- JAL-2593 -->Improved performance when rendering lots
1628 of features (particularly when transparency is disabled)
1631 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2
1632 for exchange of Jalview features and Chimera attributes
1633 made generally available
1637 <td><div align="left">
1640 <!-- JAL-2899 -->Structure and Overview aren't updated
1641 when Colour By Annotation threshold slider is adjusted
1644 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1645 overlapping alignment panel
1648 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1652 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1653 improved: CDS not handled correctly if transcript has no
1657 <!-- JAL-2321 -->Secondary structure and temperature
1658 factor annotation not added to sequence when local PDB
1659 file associated with it by drag'n'drop or structure
1663 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1664 dialog doesn't import PDB files dropped on an alignment
1667 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1668 scroll bar doesn't work for some CDS/Protein views
1671 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1672 Java 1.8u153 onwards and Java 1.9u4+.
1675 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1676 columns in annotation row
1679 <!-- JAL-2913 -->Preferences panel's ID Width control is
1680 not honored in batch mode
1683 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1684 for structures added to existing Jmol view
1687 <!-- JAL-2223 -->'View Mappings' includes duplicate
1688 entries after importing project with multiple views
1691 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1692 protein sequences via SIFTS from associated PDB entries
1693 with negative residue numbers or missing residues fails
1696 <!-- JAL-2952 -->Exception when shading sequence with
1697 negative Temperature Factor values from annotated PDB
1698 files (e.g. as generated by CONSURF)
1701 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1702 tooltip doesn't include a text description of mutation
1705 <!-- JAL-2922 -->Invert displayed features very slow when
1706 structure and/or overview windows are also shown
1709 <!-- JAL-2954 -->Selecting columns from highlighted
1710 regions very slow for alignments with large numbers of
1714 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1715 with 'StringIndexOutOfBounds'
1718 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and
1719 Feel for OSX platforms running Java 10
1722 <!-- JAL-2960 -->Adding a structure to existing structure
1723 view appears to do nothing because the view is hidden
1724 behind the alignment view
1730 <!-- JAL-2926 -->Copy consensus sequence option in applet
1731 should copy the group consensus when popup is opened on it
1737 <!-- JAL-2913 -->Fixed ID width preference is not
1741 <em>New Known Defects</em>
1744 <!-- JAL-2973 --> Exceptions occasionally raised when
1745 editing a large alignment and overview is displayed
1748 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1749 repeatedly after a series of edits even when the overview
1750 is no longer reflecting updates
1753 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1754 structures for protein subsequence (if 'Trim Retrieved
1755 Sequences' enabled) or Ensembl isoforms (Workaround in
1756 2.10.4 is to fail back to N&W mapping)
1759 <!-- JAL-2990 -->Export Annotations from File Menu with
1760 CSV option gives blank output
1766 <td width="60" nowrap>
1767 <div align="center">
1768 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br />
1769 <em>24/1/2018</em></strong>
1772 <td><div align="left">
1774 <li>Updated Certum Codesigning Certificate (Valid till
1775 30th November 2018)</li>
1778 <td><div align="left">
1783 <!-- JAL-2859-->Only one structure is loaded when
1784 several sequences and structures are selected for
1788 <!-- JAL-2851-->Alignment doesn't appear to scroll
1789 vertically via trackpad and scrollwheel
1792 <!-- JAL-2842-->Jalview hangs if up/down arrows pressed
1793 in cursor mode when cursor lies in hidden region at
1797 <!-- JAL-2827-->Helix annotation has 'notches' when
1798 scrolled into view if columns are hidden
1801 <!-- JAL-2740-->Annotation column filter can be slow to
1802 reset (ie after hitting cancel) for large numbers of
1806 <!-- JAL-2849-->User preference for disabling inclusion
1807 of sequence limits when exporting as flat file has no
1811 <!-- JAL-2679-->Reproducible cross-reference
1812 relationships when retrieving sequences from
1819 <td width="60" nowrap>
1820 <div align="center">
1821 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1824 <td><div align="left">
1828 <!-- JAL-2446 -->Faster and more efficient management and
1829 rendering of sequence features
1832 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1833 429 rate limit request hander
1836 <!-- JAL-2773 -->Structure views don't get updated unless
1837 their colours have changed
1840 <!-- JAL-2495 -->All linked sequences are highlighted for
1841 a structure mousover (Jmol) or selection (Chimera)
1844 <!-- JAL-2790 -->'Cancel' button in progress bar for
1845 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1848 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1849 view from Ensembl locus cross-references
1852 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1856 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1857 feature can be disabled
1860 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1861 PDB easier retrieval of sequences for lists of IDs
1864 <!-- JAL-2758 -->Short names for sequences retrieved from
1870 <li>Groovy interpreter updated to 2.4.12</li>
1871 <li>Example groovy script for generating a matrix of
1872 percent identity scores for current alignment.</li>
1874 <em>Testing and Deployment</em>
1877 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1881 <td><div align="left">
1885 <!-- JAL-2643 -->Pressing tab after updating the colour
1886 threshold text field doesn't trigger an update to the
1890 <!-- JAL-2682 -->Race condition when parsing sequence ID
1894 <!-- JAL-2608 -->Overview windows are also closed when
1895 alignment window is closed
1898 <!-- JAL-2548 -->Export of features doesn't always respect
1902 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1903 takes a long time in Cursor mode
1909 <!-- JAL-2777 -->Structures with whitespace chainCode
1910 cannot be viewed in Chimera
1913 <!-- JAL-2728 -->Protein annotation panel too high in
1917 <!-- JAL-2757 -->Can't edit the query after the server
1918 error warning icon is shown in Uniprot and PDB Free Text
1922 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1925 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1928 <!-- JAL-2739 -->Hidden column marker in last column not
1929 rendered when switching back from Wrapped to normal view
1932 <!-- JAL-2768 -->Annotation display corrupted when
1933 scrolling right in unwapped alignment view
1936 <!-- JAL-2542 -->Existing features on subsequence
1937 incorrectly relocated when full sequence retrieved from
1941 <!-- JAL-2733 -->Last reported memory still shown when
1942 Desktop->Show Memory is unticked (OSX only)
1945 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1946 features of same type and group to be selected for
1950 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1951 alignments when hidden columns are present
1954 <!-- JAL-2392 -->Jalview freezes when loading and
1955 displaying several structures
1958 <!-- JAL-2732 -->Black outlines left after resizing or
1962 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1963 within the Jalview desktop on OSX
1966 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1967 when in wrapped alignment mode
1970 <!-- JAL-2636 -->Scale mark not shown when close to right
1971 hand end of alignment
1974 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1975 each selected sequence do not have correct start/end
1979 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1980 after canceling the Alignment Window's Font dialog
1983 <!-- JAL-2036 -->Show cross-references not enabled after
1984 restoring project until a new view is created
1987 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1988 URL links appears when only default EMBL-EBI link is
1989 configured (since 2.10.2b2)
1992 <!-- JAL-2775 -->Overview redraws whole window when box
1993 position is adjusted
1996 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1997 in a multi-chain structure when viewing alignment
1998 involving more than one chain (since 2.10)
2001 <!-- JAL-2811 -->Double residue highlights in cursor mode
2002 if new selection moves alignment window
2005 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
2006 arrow key in cursor mode to pass hidden column marker
2009 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
2010 that produces correctly annotated transcripts and products
2013 <!-- JAL-2776 -->Toggling a feature group after first time
2014 doesn't update associated structure view
2017 <em>Applet</em><br />
2020 <!-- JAL-2687 -->Concurrent modification exception when
2021 closing alignment panel
2024 <em>BioJSON</em><br />
2027 <!-- JAL-2546 -->BioJSON export does not preserve
2028 non-positional features
2031 <em>New Known Issues</em>
2034 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
2035 sequence features correctly (for many previous versions of
2039 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
2040 using cursor in wrapped panel other than top
2043 <!-- JAL-2791 -->Select columns containing feature ignores
2044 graduated colour threshold
2047 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
2048 always preserve numbering and sequence features
2051 <em>Known Java 9 Issues</em>
2054 <!-- JAL-2902 -->Groovy Console very slow to open and is
2055 not responsive when entering characters (Webstart, Java
2062 <td width="60" nowrap>
2063 <div align="center">
2064 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
2065 <em>2/10/2017</em></strong>
2068 <td><div align="left">
2069 <em>New features in Jalview Desktop</em>
2072 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API
2076 <!-- JAL-2745 -->HTTPS used for all connections to
2081 <td><div align="left"></div></td>
2084 <td width="60" nowrap>
2085 <div align="center">
2086 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
2087 <em>7/9/2017</em></strong>
2090 <td><div align="left">
2094 <!-- JAL-2588 -->Show gaps in overview window by colouring
2095 in grey (sequences used to be coloured grey, and gaps were
2099 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
2103 <!-- JAL-2587 -->Overview updates immediately on increase
2104 in size and progress bar shown as higher resolution
2105 overview is recalculated
2110 <td><div align="left">
2114 <!-- JAL-2664 -->Overview window redraws every hidden
2115 column region row by row
2118 <!-- JAL-2681 -->duplicate protein sequences shown after
2119 retrieving Ensembl crossrefs for sequences from Uniprot
2122 <!-- JAL-2603 -->Overview window throws NPE if show boxes
2123 format setting is unticked
2126 <!-- JAL-2610 -->Groups are coloured wrongly in overview
2127 if group has show boxes format setting unticked
2130 <!-- JAL-2672,JAL-2665 -->Redraw problems when
2131 autoscrolling whilst dragging current selection group to
2132 include sequences and columns not currently displayed
2135 <!-- JAL-2691 -->Not all chains are mapped when multimeric
2136 assemblies are imported via CIF file
2139 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
2140 displayed when threshold or conservation colouring is also
2144 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
2148 <!-- JAL-2673 -->Jalview continues to scroll after
2149 dragging a selected region off the visible region of the
2153 <!-- JAL-2724 -->Cannot apply annotation based
2154 colourscheme to all groups in a view
2157 <!-- JAL-2511 -->IDs don't line up with sequences
2158 initially after font size change using the Font chooser or
2165 <td width="60" nowrap>
2166 <div align="center">
2167 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
2170 <td><div align="left">
2171 <em>Calculations</em>
2175 <!-- JAL-1933 -->Occupancy annotation row shows number of
2176 ungapped positions in each column of the alignment.
2179 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
2180 a calculation dialog box
2183 <!-- JAL-2379 -->Revised implementation of PCA for speed
2184 and memory efficiency (~30x faster)
2187 <!-- JAL-2403 -->Revised implementation of sequence
2188 similarity scores as used by Tree, PCA, Shading Consensus
2189 and other calculations
2192 <!-- JAL-2416 -->Score matrices are stored as resource
2193 files within the Jalview codebase
2196 <!-- JAL-2500 -->Trees computed on Sequence Feature
2197 Similarity may have different topology due to increased
2204 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
2205 model for alignments and groups
2208 <!-- JAL-384 -->Custom shading schemes created via groovy
2215 <!-- JAL-2526 -->Efficiency improvements for interacting
2216 with alignment and overview windows
2219 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
2223 <!-- JAL-2388 -->Hidden columns and sequences can be
2227 <!-- JAL-2611 -->Click-drag in visible area allows fine
2228 adjustment of visible position
2232 <em>Data import/export</em>
2235 <!-- JAL-2535 -->Posterior probability annotation from
2236 Stockholm files imported as sequence associated annotation
2239 <!-- JAL-2507 -->More robust per-sequence positional
2240 annotation input/output via stockholm flatfile
2243 <!-- JAL-2533 -->Sequence names don't include file
2244 extension when importing structure files without embedded
2245 names or PDB accessions
2248 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
2249 format sequence substitution matrices
2252 <em>User Interface</em>
2255 <!-- JAL-2447 --> Experimental Features Checkbox in
2256 Desktop's Tools menu to hide or show untested features in
2260 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
2261 via Overview or sequence motif search operations
2264 <!-- JAL-2547 -->Amend sequence features dialog box can be
2265 opened by double clicking gaps within sequence feature
2269 <!-- JAL-1476 -->Status bar message shown when not enough
2270 aligned positions were available to create a 3D structure
2274 <em>3D Structure</em>
2277 <!-- JAL-2430 -->Hidden regions in alignment views are not
2278 coloured in linked structure views
2281 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
2282 file-based command exchange
2285 <!-- JAL-2375 -->Structure chooser automatically shows
2286 Cached Structures rather than querying the PDBe if
2287 structures are already available for sequences
2290 <!-- JAL-2520 -->Structures imported via URL are cached in
2291 the Jalview project rather than downloaded again when the
2292 project is reopened.
2295 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
2296 to transfer Chimera's structure attributes as Jalview
2297 features, and vice-versa (<strong>Experimental
2301 <em>Web Services</em>
2304 <!-- JAL-2549 -->Updated JABAWS client to v2.2
2307 <!-- JAL-2335 -->Filter non-standard amino acids and
2308 nucleotides when submitting to AACon and other MSA
2312 <!-- JAL-2316, -->URLs for viewing database
2313 cross-references provided by identifiers.org and the
2314 EMBL-EBI's MIRIAM DB
2321 <!-- JAL-2344 -->FileFormatI interface for describing and
2322 identifying file formats (instead of String constants)
2325 <!-- JAL-2228 -->FeatureCounter script refactored for
2326 efficiency when counting all displayed features (not
2327 backwards compatible with 2.10.1)
2330 <em>Example files</em>
2333 <!-- JAL-2631 -->Graduated feature colour style example
2334 included in the example feature file
2337 <em>Documentation</em>
2340 <!-- JAL-2339 -->Release notes reformatted for readability
2341 with the built-in Java help viewer
2344 <!-- JAL-1644 -->Find documentation updated with 'search
2345 sequence description' option
2351 <!-- JAL-2485, -->External service integration tests for
2352 Uniprot REST Free Text Search Client
2355 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
2358 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
2363 <td><div align="left">
2364 <em>Calculations</em>
2367 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
2368 matrix - C->R should be '-3'<br />Old matrix restored
2369 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
2371 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
2372 Jalview's treatment of gaps in PCA and substitution matrix
2373 based Tree calculations.<br /> <br />In earlier versions
2374 of Jalview, gaps matching gaps were penalised, and gaps
2375 matching non-gaps penalised even more. In the PCA
2376 calculation, gaps were actually treated as non-gaps - so
2377 different costs were applied, which meant Jalview's PCAs
2378 were different to those produced by SeqSpace.<br />Jalview
2379 now treats gaps in the same way as SeqSpace (ie it scores
2380 them as 0). <br /> <br />Enter the following in the
2381 Groovy console to restore pre-2.10.2 behaviour:<br />
2382 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
2383 // for 2.10.1 mode <br />
2384 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
2385 // to restore 2.10.2 mode <br /> <br /> <em>Note:
2386 these settings will affect all subsequent tree and PCA
2387 calculations (not recommended)</em></li>
2389 <!-- JAL-2424 -->Fixed off-by-one bug that affected
2390 scaling of branch lengths for trees computed using
2391 Sequence Feature Similarity.
2394 <!-- JAL-2377 -->PCA calculation could hang when
2395 generating output report when working with highly
2396 redundant alignments
2399 <!-- JAL-2544 --> Sort by features includes features to
2400 right of selected region when gaps present on right-hand
2404 <em>User Interface</em>
2407 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2408 doesn't reselect a specific sequence's associated
2409 annotation after it was used for colouring a view
2412 <!-- JAL-2419 -->Current selection lost if popup menu
2413 opened on a region of alignment without groups
2416 <!-- JAL-2374 -->Popup menu not always shown for regions
2417 of an alignment with overlapping groups
2420 <!-- JAL-2310 -->Finder double counts if both a sequence's
2421 name and description match
2424 <!-- JAL-2370 -->Hiding column selection containing two
2425 hidden regions results in incorrect hidden regions
2428 <!-- JAL-2386 -->'Apply to all groups' setting when
2429 changing colour does not apply Conservation slider value
2433 <!-- JAL-2373 -->Percentage identity and conservation menu
2434 items do not show a tick or allow shading to be disabled
2437 <!-- JAL-2385 -->Conservation shading or PID threshold
2438 lost when base colourscheme changed if slider not visible
2441 <!-- JAL-2547 -->Sequence features shown in tooltip for
2442 gaps before start of features
2445 <!-- JAL-2623 -->Graduated feature colour threshold not
2446 restored to UI when feature colour is edited
2449 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2450 a time when scrolling vertically in wrapped mode.
2453 <!-- JAL-2630 -->Structure and alignment overview update
2454 as graduate feature colour settings are modified via the
2458 <!-- JAL-2034 -->Overview window doesn't always update
2459 when a group defined on the alignment is resized
2462 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2463 wrapped view result in positional status updates
2467 <!-- JAL-2563 -->Status bar doesn't show position for
2468 ambiguous amino acid and nucleotide symbols
2471 <!-- JAL-2602 -->Copy consensus sequence failed if
2472 alignment included gapped columns
2475 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2476 widgets don't permanently disappear
2479 <!-- JAL-2503 -->Cannot select or filter quantitative
2480 annotation that are shown only as column labels (e.g.
2481 T-Coffee column reliability scores)
2484 <!-- JAL-2594 -->Exception thrown if trying to create a
2485 sequence feature on gaps only
2488 <!-- JAL-2504 -->Features created with 'New feature'
2489 button from a Find inherit previously defined feature type
2490 rather than the Find query string
2493 <!-- JAL-2423 -->incorrect title in output window when
2494 exporting tree calculated in Jalview
2497 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2498 and then revealing them reorders sequences on the
2502 <!-- JAL-964 -->Group panel in sequence feature settings
2503 doesn't update to reflect available set of groups after
2504 interactively adding or modifying features
2507 <!-- JAL-2225 -->Sequence Database chooser unusable on
2511 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2512 only excluded gaps in current sequence and ignored
2519 <!-- JAL-2421 -->Overview window visible region moves
2520 erratically when hidden rows or columns are present
2523 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2524 Structure Viewer's colour menu don't correspond to
2528 <!-- JAL-2405 -->Protein specific colours only offered in
2529 colour and group colour menu for protein alignments
2532 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2533 reflect currently selected view or group's shading
2537 <!-- JAL-2624 -->Feature colour thresholds not respected
2538 when rendered on overview and structures when opacity at
2542 <!-- JAL-2589 -->User defined gap colour not shown in
2543 overview when features overlaid on alignment
2546 <!-- JAL-2567 -->Feature settings for different views not
2547 recovered correctly from Jalview project file
2550 <!-- JAL-2256 -->Feature colours in overview when first
2551 opened (automatically via preferences) are different to
2552 the main alignment panel
2555 <em>Data import/export</em>
2558 <!-- JAL-2576 -->Very large alignments take a long time to
2562 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2563 added after a sequence was imported are not written to
2567 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2568 when importing RNA secondary structure via Stockholm
2571 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2572 not shown in correct direction for simple pseudoknots
2575 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2576 with lightGray or darkGray via features file (but can
2580 <!-- JAL-2383 -->Above PID colour threshold not recovered
2581 when alignment view imported from project
2584 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2585 structure and sequences extracted from structure files
2586 imported via URL and viewed in Jmol
2589 <!-- JAL-2520 -->Structures loaded via URL are saved in
2590 Jalview Projects rather than fetched via URL again when
2591 the project is loaded and the structure viewed
2594 <em>Web Services</em>
2597 <!-- JAL-2519 -->EnsemblGenomes example failing after
2598 release of Ensembl v.88
2601 <!-- JAL-2366 -->Proxy server address and port always
2602 appear enabled in Preferences->Connections
2605 <!-- JAL-2461 -->DAS registry not found exceptions
2606 removed from console output
2609 <!-- JAL-2582 -->Cannot retrieve protein products from
2610 Ensembl by Peptide ID
2613 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2614 created from SIFTs, and spurious 'Couldn't open structure
2615 in Chimera' errors raised after April 2017 update (problem
2616 due to 'null' string rather than empty string used for
2617 residues with no corresponding PDB mapping).
2620 <em>Application UI</em>
2623 <!-- JAL-2361 -->User Defined Colours not added to Colour
2627 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2628 case' residues (button in colourscheme editor debugged and
2629 new documentation and tooltips added)
2632 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2633 doesn't restore group-specific text colour thresholds
2636 <!-- JAL-2243 -->Feature settings panel does not update as
2637 new features are added to alignment
2640 <!-- JAL-2532 -->Cancel in feature settings reverts
2641 changes to feature colours via the Amend features dialog
2644 <!-- JAL-2506 -->Null pointer exception when attempting to
2645 edit graduated feature colour via amend features dialog
2649 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2650 selection menu changes colours of alignment views
2653 <!-- JAL-2426 -->Spurious exceptions in console raised
2654 from alignment calculation workers after alignment has
2658 <!-- JAL-1608 -->Typo in selection popup menu - Create
2659 groups now 'Create Group'
2662 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2663 Create/Undefine group doesn't always work
2666 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2667 shown again after pressing 'Cancel'
2670 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2671 adjusts start position in wrap mode
2674 <!-- JAL-2563 -->Status bar doesn't show positions for
2675 ambiguous amino acids
2678 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2679 CDS/Protein view after CDS sequences added for aligned
2683 <!-- JAL-2592 -->User defined colourschemes called 'User
2684 Defined' don't appear in Colours menu
2690 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2691 score models doesn't always result in an updated PCA plot
2694 <!-- JAL-2442 -->Features not rendered as transparent on
2695 overview or linked structure view
2698 <!-- JAL-2372 -->Colour group by conservation doesn't
2702 <!-- JAL-2517 -->Hitting Cancel after applying
2703 user-defined colourscheme doesn't restore original
2710 <!-- JAL-2314 -->Unit test failure:
2711 jalview.ws.jabaws.RNAStructExportImport setup fails
2714 <!-- JAL-2307 -->Unit test failure:
2715 jalview.ws.sifts.SiftsClientTest due to compatibility
2716 problems with deep array comparison equality asserts in
2717 successive versions of TestNG
2720 <!-- JAL-2479 -->Relocated StructureChooserTest and
2721 ParameterUtilsTest Unit tests to Network suite
2724 <em>New Known Issues</em>
2727 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2728 phase after a sequence motif find operation
2731 <!-- JAL-2550 -->Importing annotation file with rows
2732 containing just upper and lower case letters are
2733 interpreted as WUSS RNA secondary structure symbols
2736 <!-- JAL-2590 -->Cannot load and display Newick trees
2737 reliably from eggnog Ortholog database
2740 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2741 containing features of type Highlight' when 'B' is pressed
2742 to mark columns containing highlighted regions.
2745 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2746 doesn't always add secondary structure annotation.
2751 <td width="60" nowrap>
2752 <div align="center">
2753 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2756 <td><div align="left">
2760 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2761 for all consensus calculations
2764 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2767 <li>Updated Jalview's Certum code signing certificate
2770 <em>Application</em>
2773 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2774 set of database cross-references, sorted alphabetically
2777 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2778 from database cross references. Users with custom links
2779 will receive a <a href="webServices/urllinks.html#warning">warning
2780 dialog</a> asking them to update their preferences.
2783 <!-- JAL-2287-->Cancel button and escape listener on
2784 dialog warning user about disconnecting Jalview from a
2788 <!-- JAL-2320-->Jalview's Chimera control window closes if
2789 the Chimera it is connected to is shut down
2792 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2793 columns menu item to mark columns containing highlighted
2794 regions (e.g. from structure selections or results of a
2798 <!-- JAL-2284-->Command line option for batch-generation
2799 of HTML pages rendering alignment data with the BioJS
2809 <!-- JAL-2286 -->Columns with more than one modal residue
2810 are not coloured or thresholded according to percent
2811 identity (first observed in Jalview 2.8.2)
2814 <!-- JAL-2301 -->Threonine incorrectly reported as not
2818 <!-- JAL-2318 -->Updates to documentation pages (above PID
2819 threshold, amino acid properties)
2822 <!-- JAL-2292 -->Lower case residues in sequences are not
2823 reported as mapped to residues in a structure file in the
2827 <!--JAL-2324 -->Identical features with non-numeric scores
2828 could be added multiple times to a sequence
2831 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2832 bond features shown as two highlighted residues rather
2833 than a range in linked structure views, and treated
2834 correctly when selecting and computing trees from features
2837 <!-- JAL-2281-->Custom URL links for database
2838 cross-references are matched to database name regardless
2843 <em>Application</em>
2846 <!-- JAL-2282-->Custom URL links for specific database
2847 names without regular expressions also offer links from
2851 <!-- JAL-2315-->Removing a single configured link in the
2852 URL links pane in Connections preferences doesn't actually
2853 update Jalview configuration
2856 <!-- JAL-2272-->CTRL-Click on a selected region to open
2857 the alignment area popup menu doesn't work on El-Capitan
2860 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2861 files with similarly named sequences if dropped onto the
2865 <!-- JAL-2312 -->Additional mappings are shown for PDB
2866 entries where more chains exist in the PDB accession than
2867 are reported in the SIFTS file
2870 <!-- JAL-2317-->Certain structures do not get mapped to
2871 the structure view when displayed with Chimera
2874 <!-- JAL-2317-->No chains shown in the Chimera view
2875 panel's View->Show Chains submenu
2878 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2879 work for wrapped alignment views
2882 <!--JAL-2197 -->Rename UI components for running JPred
2883 predictions from 'JNet' to 'JPred'
2886 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2887 corrupted when annotation panel vertical scroll is not at
2888 first annotation row
2891 <!--JAL-2332 -->Attempting to view structure for Hen
2892 lysozyme results in a PDB Client error dialog box
2895 <!-- JAL-2319 -->Structure View's mapping report switched
2896 ranges for PDB and sequence for SIFTS
2899 SIFTS 'Not_Observed' residues mapped to non-existant
2903 <!-- <em>New Known Issues</em>
2910 <td width="60" nowrap>
2911 <div align="center">
2912 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2913 <em>25/10/2016</em></strong>
2916 <td><em>Application</em>
2918 <li>3D Structure chooser opens with 'Cached structures'
2919 view if structures already loaded</li>
2920 <li>Progress bar reports models as they are loaded to
2921 structure views</li>
2927 <li>Colour by conservation always enabled and no tick
2928 shown in menu when BLOSUM or PID shading applied</li>
2929 <li>FER1_ARATH and FER2_ARATH labels were switched in
2930 example sequences/projects/trees</li>
2932 <em>Application</em>
2934 <li>Jalview projects with views of local PDB structure
2935 files saved on Windows cannot be opened on OSX</li>
2936 <li>Multiple structure views can be opened and superposed
2937 without timeout for structures with multiple models or
2938 multiple sequences in alignment</li>
2939 <li>Cannot import or associated local PDB files without a
2940 PDB ID HEADER line</li>
2941 <li>RMSD is not output in Jmol console when superposition
2943 <li>Drag and drop of URL from Browser fails for Linux and
2944 OSX versions earlier than El Capitan</li>
2945 <li>ENA client ignores invalid content from ENA server</li>
2946 <li>Exceptions are not raised in console when ENA client
2947 attempts to fetch non-existent IDs via Fetch DB Refs UI
2949 <li>Exceptions are not raised in console when a new view
2950 is created on the alignment</li>
2951 <li>OSX right-click fixed for group selections: CMD-click
2952 to insert/remove gaps in groups and CTRL-click to open group
2955 <em>Build and deployment</em>
2957 <li>URL link checker now copes with multi-line anchor
2960 <em>New Known Issues</em>
2962 <li>Drag and drop from URL links in browsers do not work
2969 <td width="60" nowrap>
2970 <div align="center">
2971 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2974 <td><em>General</em>
2977 <!-- JAL-2124 -->Updated Spanish translations.
2980 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2981 for importing structure data to Jalview. Enables mmCIF and
2985 <!-- JAL-192 --->Alignment ruler shows positions relative to
2989 <!-- JAL-2202 -->Position/residue shown in status bar when
2990 mousing over sequence associated annotation
2993 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2997 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2998 '()', canonical '[]' and invalid '{}' base pair populations
3002 <!-- JAL-2092 -->Feature settings popup menu options for
3003 showing or hiding columns containing a feature
3006 <!-- JAL-1557 -->Edit selected group by double clicking on
3007 group and sequence associated annotation labels
3010 <!-- JAL-2236 -->Sequence name added to annotation label in
3011 select/hide columns by annotation and colour by annotation
3015 </ul> <em>Application</em>
3018 <!-- JAL-2050-->Automatically hide introns when opening a
3019 gene/transcript view
3022 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
3026 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
3027 structure mappings with the EMBL-EBI PDBe SIFTS database
3030 <!-- JAL-2079 -->Updated download sites used for Rfam and
3031 Pfam sources to xfam.org
3034 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
3037 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
3038 over sequences in Jalview
3041 <!-- JAL-2027-->Support for reverse-complement coding
3042 regions in ENA and EMBL
3045 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
3046 for record retrieval via ENA rest API
3049 <!-- JAL-2027 -->Support for ENA CDS records with reverse
3053 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
3054 groovy script execution
3057 <!-- JAL-1812 -->New 'execute Groovy script' option in an
3058 alignment window's Calculate menu
3061 <!-- JAL-1812 -->Allow groovy scripts that call
3062 Jalview.getAlignFrames() to run in headless mode
3065 <!-- JAL-2068 -->Support for creating new alignment
3066 calculation workers from groovy scripts
3069 <!-- JAL-1369 --->Store/restore reference sequence in
3073 <!-- JAL-1803 -->Chain codes for a sequence's PDB
3074 associations are now saved/restored from project
3077 <!-- JAL-1993 -->Database selection dialog always shown
3078 before sequence fetcher is opened
3081 <!-- JAL-2183 -->Double click on an entry in Jalview's
3082 database chooser opens a sequence fetcher
3085 <!-- JAL-1563 -->Free-text search client for UniProt using
3086 the UniProt REST API
3089 <!-- JAL-2168 -->-nonews command line parameter to prevent
3090 the news reader opening
3093 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
3094 querying stored in preferences
3097 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
3101 <!-- JAL-1977-->Tooltips shown on database chooser
3104 <!-- JAL-391 -->Reverse complement function in calculate
3105 menu for nucleotide sequences
3108 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
3109 and feature counts preserves alignment ordering (and
3110 debugged for complex feature sets).
3113 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
3114 viewing structures with Jalview 2.10
3117 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
3118 genome, transcript CCDS and gene ids via the Ensembl and
3119 Ensembl Genomes REST API
3122 <!-- JAL-2049 -->Protein sequence variant annotation
3123 computed for 'sequence_variant' annotation on CDS regions
3127 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
3131 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
3132 Ref Fetcher fails to match, or otherwise updates sequence
3133 data from external database records.
3136 <!-- JAL-2154 -->Revised Jalview Project format for
3137 efficient recovery of sequence coding and alignment
3138 annotation relationships.
3140 </ul> <!-- <em>Applet</em>
3151 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
3155 <!-- JAL-2018-->Export features in Jalview format (again)
3156 includes graduated colourschemes
3159 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
3160 working with big alignments and lots of hidden columns
3163 <!-- JAL-2053-->Hidden column markers not always rendered
3164 at right of alignment window
3167 <!-- JAL-2067 -->Tidied up links in help file table of
3171 <!-- JAL-2072 -->Feature based tree calculation not shown
3175 <!-- JAL-2075 -->Hidden columns ignored during feature
3176 based tree calculation
3179 <!-- JAL-2065 -->Alignment view stops updating when show
3180 unconserved enabled for group on alignment
3183 <!-- JAL-2086 -->Cannot insert gaps into sequence when
3187 <!-- JAL-2146 -->Alignment column in status incorrectly
3188 shown as "Sequence position" when mousing over
3192 <!-- JAL-2099 -->Incorrect column numbers in ruler when
3193 hidden columns present
3196 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
3197 user created annotation added to alignment
3200 <!-- JAL-1841 -->RNA Structure consensus only computed for
3201 '()' base pair annotation
3204 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
3205 in zero scores for all base pairs in RNA Structure
3209 <!-- JAL-2174-->Extend selection with columns containing
3213 <!-- JAL-2275 -->Pfam format writer puts extra space at
3214 beginning of sequence
3217 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
3221 <!-- JAL-2238 -->Cannot create groups on an alignment from
3222 from a tree when t-coffee scores are shown
3225 <!-- JAL-1836,1967 -->Cannot import and view PDB
3226 structures with chains containing negative resnums (4q4h)
3229 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
3233 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
3234 to Clustal, PIR and PileUp output
3237 <!-- JAL-2008 -->Reordering sequence features that are
3238 not visible causes alignment window to repaint
3241 <!-- JAL-2006 -->Threshold sliders don't work in
3242 graduated colour and colour by annotation row for e-value
3243 scores associated with features and annotation rows
3246 <!-- JAL-1797 -->amino acid physicochemical conservation
3247 calculation should be case independent
3250 <!-- JAL-2173 -->Remove annotation also updates hidden
3254 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
3255 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
3256 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
3259 <!-- JAL-2065 -->Null pointer exceptions and redraw
3260 problems when reference sequence defined and 'show
3261 non-conserved' enabled
3264 <!-- JAL-1306 -->Quality and Conservation are now shown on
3265 load even when Consensus calculation is disabled
3268 <!-- JAL-1932 -->Remove right on penultimate column of
3269 alignment does nothing
3272 <em>Application</em>
3275 <!-- JAL-1552-->URLs and links can't be imported by
3276 drag'n'drop on OSX when launched via webstart (note - not
3277 yet fixed for El Capitan)
3280 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
3281 output when running on non-gb/us i18n platforms
3284 <!-- JAL-1944 -->Error thrown when exporting a view with
3285 hidden sequences as flat-file alignment
3288 <!-- JAL-2030-->InstallAnywhere distribution fails when
3292 <!-- JAL-2080-->Jalview very slow to launch via webstart
3293 (also hotfix for 2.9.0b2)
3296 <!-- JAL-2085 -->Cannot save project when view has a
3297 reference sequence defined
3300 <!-- JAL-1011 -->Columns are suddenly selected in other
3301 alignments and views when revealing hidden columns
3304 <!-- JAL-1989 -->Hide columns not mirrored in complement
3305 view in a cDNA/Protein splitframe
3308 <!-- JAL-1369 -->Cannot save/restore representative
3309 sequence from project when only one sequence is
3313 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
3314 in Structure Chooser
3317 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
3318 structure consensus didn't refresh annotation panel
3321 <!-- JAL-1962 -->View mapping in structure view shows
3322 mappings between sequence and all chains in a PDB file
3325 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
3326 dialogs format columns correctly, don't display array
3327 data, sort columns according to type
3330 <!-- JAL-1975 -->Export complete shown after destination
3331 file chooser is cancelled during an image export
3334 <!-- JAL-2025 -->Error when querying PDB Service with
3335 sequence name containing special characters
3338 <!-- JAL-2024 -->Manual PDB structure querying should be
3342 <!-- JAL-2104 -->Large tooltips with broken HTML
3343 formatting don't wrap
3346 <!-- JAL-1128 -->Figures exported from wrapped view are
3347 truncated so L looks like I in consensus annotation
3350 <!-- JAL-2003 -->Export features should only export the
3351 currently displayed features for the current selection or
3355 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
3356 after fetching cross-references, and restoring from
3360 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
3361 followed in the structure viewer
3364 <!-- JAL-2163 -->Titles for individual alignments in
3365 splitframe not restored from project
3368 <!-- JAL-2145 -->missing autocalculated annotation at
3369 trailing end of protein alignment in transcript/product
3370 splitview when pad-gaps not enabled by default
3373 <!-- JAL-1797 -->amino acid physicochemical conservation
3377 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
3378 article has been read (reopened issue due to
3379 internationalisation problems)
3382 <!-- JAL-1960 -->Only offer PDB structures in structure
3383 viewer based on sequence name, PDB and UniProt
3388 <!-- JAL-1976 -->No progress bar shown during export of
3392 <!-- JAL-2213 -->Structures not always superimposed after
3393 multiple structures are shown for one or more sequences.
3396 <!-- JAL-1370 -->Reference sequence characters should not
3397 be replaced with '.' when 'Show unconserved' format option
3401 <!-- JAL-1823 -->Cannot specify chain code when entering
3402 specific PDB id for sequence
3405 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3406 'Export hidden sequences' is enabled, but 'export hidden
3407 columns' is disabled.
3410 <!--JAL-2026-->Best Quality option in structure chooser
3411 selects lowest rather than highest resolution structures
3415 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3416 to sequence mapping in 'View Mappings' report
3419 <!-- JAL-2284 -->Unable to read old Jalview projects that
3420 contain non-XML data added after Jalvew wrote project.
3423 <!-- JAL-2118 -->Newly created annotation row reorders
3424 after clicking on it to create new annotation for a
3428 <!-- JAL-1980 -->Null Pointer Exception raised when
3429 pressing Add on an orphaned cut'n'paste window.
3431 <!-- may exclude, this is an external service stability issue JAL-1941
3432 -- > RNA 3D structure not added via DSSR service</li> -->
3437 <!-- JAL-2151 -->Incorrect columns are selected when
3438 hidden columns present before start of sequence
3441 <!-- JAL-1986 -->Missing dependencies on applet pages
3445 <!-- JAL-1947 -->Overview pixel size changes when
3446 sequences are hidden in applet
3449 <!-- JAL-1996 -->Updated instructions for applet
3450 deployment on examples pages.
3457 <td width="60" nowrap>
3458 <div align="center">
3459 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3460 <em>16/10/2015</em></strong>
3463 <td><em>General</em>
3465 <li>Time stamps for signed Jalview application and applet
3470 <em>Application</em>
3472 <li>Duplicate group consensus and conservation rows
3473 shown when tree is partitioned</li>
3474 <li>Erratic behaviour when tree partitions made with
3475 multiple cDNA/Protein split views</li>
3481 <td width="60" nowrap>
3482 <div align="center">
3483 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3484 <em>8/10/2015</em></strong>
3487 <td><em>General</em>
3489 <li>Updated Spanish translations of localized text for
3491 </ul> <em>Application</em>
3493 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3494 <li>Signed OSX InstallAnywhere installer<br></li>
3495 <li>Support for per-sequence based annotations in BioJSON</li>
3496 </ul> <em>Applet</em>
3498 <li>Split frame example added to applet examples page</li>
3499 </ul> <em>Build and Deployment</em>
3502 <!-- JAL-1888 -->New ant target for running Jalview's test
3510 <li>Mapping of cDNA to protein in split frames
3511 incorrect when sequence start > 1</li>
3512 <li>Broken images in filter column by annotation dialog
3514 <li>Feature colours not parsed from features file</li>
3515 <li>Exceptions and incomplete link URLs recovered when
3516 loading a features file containing HTML tags in feature
3520 <em>Application</em>
3522 <li>Annotations corrupted after BioJS export and
3524 <li>Incorrect sequence limits after Fetch DB References
3525 with 'trim retrieved sequences'</li>
3526 <li>Incorrect warning about deleting all data when
3527 deleting selected columns</li>
3528 <li>Patch to build system for shipping properly signed
3529 JNLP templates for webstart launch</li>
3530 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3531 unreleased structures for download or viewing</li>
3532 <li>Tab/space/return keystroke operation of EMBL-PDBe
3533 fetcher/viewer dialogs works correctly</li>
3534 <li>Disabled 'minimise' button on Jalview windows
3535 running on OSX to workaround redraw hang bug</li>
3536 <li>Split cDNA/Protein view position and geometry not
3537 recovered from jalview project</li>
3538 <li>Initial enabled/disabled state of annotation menu
3539 sorter 'show autocalculated first/last' corresponds to
3541 <li>Restoring of Clustal, RNA Helices and T-Coffee
3542 color schemes from BioJSON</li>
3546 <li>Reorder sequences mirrored in cDNA/Protein split
3548 <li>Applet with Jmol examples not loading correctly</li>
3554 <td><div align="center">
3555 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3557 <td><em>General</em>
3559 <li>Linked visualisation and analysis of DNA and Protein
3562 <li>Translated cDNA alignments shown as split protein
3563 and DNA alignment views</li>
3564 <li>Codon consensus annotation for linked protein and
3565 cDNA alignment views</li>
3566 <li>Link cDNA or Protein product sequences by loading
3567 them onto Protein or cDNA alignments</li>
3568 <li>Reconstruct linked cDNA alignment from aligned
3569 protein sequences</li>
3572 <li>Jmol integration updated to Jmol v14.2.14</li>
3573 <li>Import and export of Jalview alignment views as <a
3574 href="features/bioJsonFormat.html">BioJSON</a></li>
3575 <li>New alignment annotation file statements for
3576 reference sequences and marking hidden columns</li>
3577 <li>Reference sequence based alignment shading to
3578 highlight variation</li>
3579 <li>Select or hide columns according to alignment
3581 <li>Find option for locating sequences by description</li>
3582 <li>Conserved physicochemical properties shown in amino
3583 acid conservation row</li>
3584 <li>Alignments can be sorted by number of RNA helices</li>
3585 </ul> <em>Application</em>
3587 <li>New cDNA/Protein analysis capabilities
3589 <li>Get Cross-References should open a Split Frame
3590 view with cDNA/Protein</li>
3591 <li>Detect when nucleotide sequences and protein
3592 sequences are placed in the same alignment</li>
3593 <li>Split cDNA/Protein views are saved in Jalview
3598 <li>Use REST API to talk to Chimera</li>
3599 <li>Selected regions in Chimera are highlighted in linked
3600 Jalview windows</li>
3602 <li>VARNA RNA viewer updated to v3.93</li>
3603 <li>VARNA views are saved in Jalview Projects</li>
3604 <li>Pseudoknots displayed as Jalview RNA annotation can
3605 be shown in VARNA</li>
3607 <li>Make groups for selection uses marked columns as well
3608 as the active selected region</li>
3610 <li>Calculate UPGMA and NJ trees using sequence feature
3612 <li>New Export options
3614 <li>New Export Settings dialog to control hidden
3615 region export in flat file generation</li>
3617 <li>Export alignment views for display with the <a
3618 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3620 <li>Export scrollable SVG in HTML page</li>
3621 <li>Optional embedding of BioJSON data when exporting
3622 alignment figures to HTML</li>
3624 <li>3D structure retrieval and display
3626 <li>Free text and structured queries with the PDBe
3628 <li>PDBe Search API based discovery and selection of
3629 PDB structures for a sequence set</li>
3633 <li>JPred4 employed for protein secondary structure
3635 <li>Hide Insertions menu option to hide unaligned columns
3636 for one or a group of sequences</li>
3637 <li>Automatically hide insertions in alignments imported
3638 from the JPred4 web server</li>
3639 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3640 system on OSX<br />LGPL libraries courtesy of <a
3641 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3643 <li>changed 'View nucleotide structure' submenu to 'View
3644 VARNA 2D Structure'</li>
3645 <li>change "View protein structure" menu option to "3D
3648 </ul> <em>Applet</em>
3650 <li>New layout for applet example pages</li>
3651 <li>New parameters to enable SplitFrame view
3652 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3653 <li>New example demonstrating linked viewing of cDNA and
3654 Protein alignments</li>
3655 </ul> <em>Development and deployment</em>
3657 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3658 <li>Include installation type and git revision in build
3659 properties and console log output</li>
3660 <li>Jalview Github organisation, and new github site for
3661 storing BioJsMSA Templates</li>
3662 <li>Jalview's unit tests now managed with TestNG</li>
3665 <!-- <em>General</em>
3667 </ul> --> <!-- issues resolved --> <em>Application</em>
3669 <li>Escape should close any open find dialogs</li>
3670 <li>Typo in select-by-features status report</li>
3671 <li>Consensus RNA secondary secondary structure
3672 predictions are not highlighted in amber</li>
3673 <li>Missing gap character in v2.7 example file means
3674 alignment appears unaligned when pad-gaps is not enabled</li>
3675 <li>First switch to RNA Helices colouring doesn't colour
3676 associated structure views</li>
3677 <li>ID width preference option is greyed out when auto
3678 width checkbox not enabled</li>
3679 <li>Stopped a warning dialog from being shown when
3680 creating user defined colours</li>
3681 <li>'View Mapping' in structure viewer shows sequence
3682 mappings for just that viewer's sequences</li>
3683 <li>Workaround for superposing PDB files containing
3684 multiple models in Chimera</li>
3685 <li>Report sequence position in status bar when hovering
3686 over Jmol structure</li>
3687 <li>Cannot output gaps as '.' symbols with Selection ->
3688 output to text box</li>
3689 <li>Flat file exports of alignments with hidden columns
3690 have incorrect sequence start/end</li>
3691 <li>'Aligning' a second chain to a Chimera structure from
3693 <li>Colour schemes applied to structure viewers don't
3694 work for nucleotide</li>
3695 <li>Loading/cut'n'pasting an empty or invalid file leads
3696 to a grey/invisible alignment window</li>
3697 <li>Exported Jpred annotation from a sequence region
3698 imports to different position</li>
3699 <li>Space at beginning of sequence feature tooltips shown
3700 on some platforms</li>
3701 <li>Chimera viewer 'View | Show Chain' menu is not
3703 <li>'New View' fails with a Null Pointer Exception in
3704 console if Chimera has been opened</li>
3705 <li>Mouseover to Chimera not working</li>
3706 <li>Miscellaneous ENA XML feature qualifiers not
3708 <li>NPE in annotation renderer after 'Extract Scores'</li>
3709 <li>If two structures in one Chimera window, mouseover of
3710 either sequence shows on first structure</li>
3711 <li>'Show annotations' options should not make
3712 non-positional annotations visible</li>
3713 <li>Subsequence secondary structure annotation not shown
3714 in right place after 'view flanking regions'</li>
3715 <li>File Save As type unset when current file format is
3717 <li>Save as '.jar' option removed for saving Jalview
3719 <li>Colour by Sequence colouring in Chimera more
3721 <li>Cannot 'add reference annotation' for a sequence in
3722 several views on same alignment</li>
3723 <li>Cannot show linked products for EMBL / ENA records</li>
3724 <li>Jalview's tooltip wraps long texts containing no
3726 </ul> <em>Applet</em>
3728 <li>Jmol to JalviewLite mouseover/link not working</li>
3729 <li>JalviewLite can't import sequences with ID
3730 descriptions containing angle brackets</li>
3731 </ul> <em>General</em>
3733 <li>Cannot export and reimport RNA secondary structure
3734 via jalview annotation file</li>
3735 <li>Random helix colour palette for colour by annotation
3736 with RNA secondary structure</li>
3737 <li>Mouseover to cDNA from STOP residue in protein
3738 translation doesn't work.</li>
3739 <li>hints when using the select by annotation dialog box</li>
3740 <li>Jmol alignment incorrect if PDB file has alternate CA
3742 <li>FontChooser message dialog appears to hang after
3743 choosing 1pt font</li>
3744 <li>Peptide secondary structure incorrectly imported from
3745 annotation file when annotation display text includes 'e' or
3747 <li>Cannot set colour of new feature type whilst creating
3749 <li>cDNA translation alignment should not be sequence
3750 order dependent</li>
3751 <li>'Show unconserved' doesn't work for lower case
3753 <li>Nucleotide ambiguity codes involving R not recognised</li>
3754 </ul> <em>Deployment and Documentation</em>
3756 <li>Applet example pages appear different to the rest of
3757 www.jalview.org</li>
3758 </ul> <em>Application Known issues</em>
3760 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3761 <li>Misleading message appears after trying to delete
3763 <li>Jalview icon not shown in dock after InstallAnywhere
3764 version launches</li>
3765 <li>Fetching EMBL reference for an RNA sequence results
3766 fails with a sequence mismatch</li>
3767 <li>Corrupted or unreadable alignment display when
3768 scrolling alignment to right</li>
3769 <li>ArrayIndexOutOfBoundsException thrown when remove
3770 empty columns called on alignment with ragged gapped ends</li>
3771 <li>auto calculated alignment annotation rows do not get
3772 placed above or below non-autocalculated rows</li>
3773 <li>Jalview dekstop becomes sluggish at full screen in
3774 ultra-high resolution</li>
3775 <li>Cannot disable consensus calculation independently of
3776 quality and conservation</li>
3777 <li>Mouseover highlighting between cDNA and protein can
3778 become sluggish with more than one splitframe shown</li>
3779 </ul> <em>Applet Known Issues</em>
3781 <li>Core PDB parsing code requires Jmol</li>
3782 <li>Sequence canvas panel goes white when alignment
3783 window is being resized</li>
3789 <td><div align="center">
3790 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3792 <td><em>General</em>
3794 <li>Updated Java code signing certificate donated by
3796 <li>Features and annotation preserved when performing
3797 pairwise alignment</li>
3798 <li>RNA pseudoknot annotation can be
3799 imported/exported/displayed</li>
3800 <li>'colour by annotation' can colour by RNA and
3801 protein secondary structure</li>
3802 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3803 post-hoc with 2.9 release</em>)
3806 </ul> <em>Application</em>
3808 <li>Extract and display secondary structure for sequences
3809 with 3D structures</li>
3810 <li>Support for parsing RNAML</li>
3811 <li>Annotations menu for layout
3813 <li>sort sequence annotation rows by alignment</li>
3814 <li>place sequence annotation above/below alignment
3817 <li>Output in Stockholm format</li>
3818 <li>Internationalisation: improved Spanish (es)
3820 <li>Structure viewer preferences tab</li>
3821 <li>Disorder and Secondary Structure annotation tracks
3822 shared between alignments</li>
3823 <li>UCSF Chimera launch and linked highlighting from
3825 <li>Show/hide all sequence associated annotation rows for
3826 all or current selection</li>
3827 <li>disorder and secondary structure predictions
3828 available as dataset annotation</li>
3829 <li>Per-sequence rna helices colouring</li>
3832 <li>Sequence database accessions imported when fetching
3833 alignments from Rfam</li>
3834 <li>update VARNA version to 3.91</li>
3836 <li>New groovy scripts for exporting aligned positions,
3837 conservation values, and calculating sum of pairs scores.</li>
3838 <li>Command line argument to set default JABAWS server</li>
3839 <li>include installation type in build properties and
3840 console log output</li>
3841 <li>Updated Jalview project format to preserve dataset
3845 <!-- issues resolved --> <em>Application</em>
3847 <li>Distinguish alignment and sequence associated RNA
3848 structure in structure->view->VARNA</li>
3849 <li>Raise dialog box if user deletes all sequences in an
3851 <li>Pressing F1 results in documentation opening twice</li>
3852 <li>Sequence feature tooltip is wrapped</li>
3853 <li>Double click on sequence associated annotation
3854 selects only first column</li>
3855 <li>Redundancy removal doesn't result in unlinked
3856 leaves shown in tree</li>
3857 <li>Undos after several redundancy removals don't undo
3859 <li>Hide sequence doesn't hide associated annotation</li>
3860 <li>User defined colours dialog box too big to fit on
3861 screen and buttons not visible</li>
3862 <li>author list isn't updated if already written to
3863 Jalview properties</li>
3864 <li>Popup menu won't open after retrieving sequence
3866 <li>File open window for associate PDB doesn't open</li>
3867 <li>Left-then-right click on a sequence id opens a
3868 browser search window</li>
3869 <li>Cannot open sequence feature shading/sort popup menu
3870 in feature settings dialog</li>
3871 <li>better tooltip placement for some areas of Jalview
3873 <li>Allow addition of JABAWS Server which doesn't
3874 pass validation</li>
3875 <li>Web services parameters dialog box is too large to
3877 <li>Muscle nucleotide alignment preset obscured by
3879 <li>JABAWS preset submenus don't contain newly
3880 defined user preset</li>
3881 <li>MSA web services warns user if they were launched
3882 with invalid input</li>
3883 <li>Jalview cannot contact DAS Registy when running on
3886 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3887 'Superpose with' submenu not shown when new view
3891 </ul> <!-- <em>Applet</em>
3893 </ul> <em>General</em>
3895 </ul>--> <em>Deployment and Documentation</em>
3897 <li>2G and 1G options in launchApp have no effect on
3898 memory allocation</li>
3899 <li>launchApp service doesn't automatically open
3900 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3902 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3903 InstallAnywhere reports cannot find valid JVM when Java
3904 1.7_055 is available
3906 </ul> <em>Application Known issues</em>
3909 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3910 corrupted or unreadable alignment display when scrolling
3914 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3915 retrieval fails but progress bar continues for DAS retrieval
3916 with large number of ID
3919 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3920 flatfile output of visible region has incorrect sequence
3924 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3925 rna structure consensus doesn't update when secondary
3926 structure tracks are rearranged
3929 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3930 invalid rna structure positional highlighting does not
3931 highlight position of invalid base pairs
3934 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3935 out of memory errors are not raised when saving Jalview
3936 project from alignment window file menu
3939 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3940 Switching to RNA Helices colouring doesn't propagate to
3944 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3945 colour by RNA Helices not enabled when user created
3946 annotation added to alignment
3949 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3950 Jalview icon not shown on dock in Mountain Lion/Webstart
3952 </ul> <em>Applet Known Issues</em>
3955 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3956 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3959 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3960 Jalview and Jmol example not compatible with IE9
3963 <li>Sort by annotation score doesn't reverse order
3969 <td><div align="center">
3970 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3973 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3976 <li>Internationalisation of user interface (usually
3977 called i18n support) and translation for Spanish locale</li>
3978 <li>Define/Undefine group on current selection with
3979 Ctrl-G/Shift Ctrl-G</li>
3980 <li>Improved group creation/removal options in
3981 alignment/sequence Popup menu</li>
3982 <li>Sensible precision for symbol distribution
3983 percentages shown in logo tooltip.</li>
3984 <li>Annotation panel height set according to amount of
3985 annotation when alignment first opened</li>
3986 </ul> <em>Application</em>
3988 <li>Interactive consensus RNA secondary structure
3989 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3990 <li>Select columns containing particular features from
3991 Feature Settings dialog</li>
3992 <li>View all 'representative' PDB structures for selected
3994 <li>Update Jalview project format:
3996 <li>New file extension for Jalview projects '.jvp'</li>
3997 <li>Preserve sequence and annotation dataset (to
3998 store secondary structure annotation,etc)</li>
3999 <li>Per group and alignment annotation and RNA helix
4003 <li>New similarity measures for PCA and Tree calculation
4005 <li>Experimental support for retrieval and viewing of
4006 flanking regions for an alignment</li>
4010 <!-- issues resolved --> <em>Application</em>
4012 <li>logo keeps spinning and status remains at queued or
4013 running after job is cancelled</li>
4014 <li>cannot export features from alignments imported from
4015 Jalview/VAMSAS projects</li>
4016 <li>Buggy slider for web service parameters that take
4018 <li>Newly created RNA secondary structure line doesn't
4019 have 'display all symbols' flag set</li>
4020 <li>T-COFFEE alignment score shading scheme and other
4021 annotation shading not saved in Jalview project</li>
4022 <li>Local file cannot be loaded in freshly downloaded
4024 <li>Jalview icon not shown on dock in Mountain
4026 <li>Load file from desktop file browser fails</li>
4027 <li>Occasional NPE thrown when calculating large trees</li>
4028 <li>Cannot reorder or slide sequences after dragging an
4029 alignment onto desktop</li>
4030 <li>Colour by annotation dialog throws NPE after using
4031 'extract scores' function</li>
4032 <li>Loading/cut'n'pasting an empty file leads to a grey
4033 alignment window</li>
4034 <li>Disorder thresholds rendered incorrectly after
4035 performing IUPred disorder prediction</li>
4036 <li>Multiple group annotated consensus rows shown when
4037 changing 'normalise logo' display setting</li>
4038 <li>Find shows blank dialog after 'finished searching' if
4039 nothing matches query</li>
4040 <li>Null Pointer Exceptions raised when sorting by
4041 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
4043 <li>Errors in Jmol console when structures in alignment
4044 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
4046 <li>Not all working JABAWS services are shown in
4048 <li>JAVAWS version of Jalview fails to launch with
4049 'invalid literal/length code'</li>
4050 <li>Annotation/RNA Helix colourschemes cannot be applied
4051 to alignment with groups (actually fixed in 2.8.0b1)</li>
4052 <li>RNA Helices and T-Coffee Scores available as default
4055 </ul> <em>Applet</em>
4057 <li>Remove group option is shown even when selection is
4059 <li>Apply to all groups ticked but colourscheme changes
4060 don't affect groups</li>
4061 <li>Documented RNA Helices and T-Coffee Scores as valid
4062 colourscheme name</li>
4063 <li>Annotation labels drawn on sequence IDs when
4064 Annotation panel is not displayed</li>
4065 <li>Increased font size for dropdown menus on OSX and
4066 embedded windows</li>
4067 </ul> <em>Other</em>
4069 <li>Consensus sequence for alignments/groups with a
4070 single sequence were not calculated</li>
4071 <li>annotation files that contain only groups imported as
4072 annotation and junk sequences</li>
4073 <li>Fasta files with sequences containing '*' incorrectly
4074 recognised as PFAM or BLC</li>
4075 <li>conservation/PID slider apply all groups option
4076 doesn't affect background (2.8.0b1)
4078 <li>redundancy highlighting is erratic at 0% and 100%</li>
4079 <li>Remove gapped columns fails for sequences with ragged
4081 <li>AMSA annotation row with leading spaces is not
4082 registered correctly on import</li>
4083 <li>Jalview crashes when selecting PCA analysis for
4084 certain alignments</li>
4085 <li>Opening the colour by annotation dialog for an
4086 existing annotation based 'use original colours'
4087 colourscheme loses original colours setting</li>
4092 <td><div align="center">
4093 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
4094 <em>30/1/2014</em></strong>
4098 <li>Trusted certificates for JalviewLite applet and
4099 Jalview Desktop application<br />Certificate was donated by
4100 <a href="https://www.certum.eu">Certum</a> to the Jalview
4101 open source project).
4103 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
4104 <li>Output in Stockholm format</li>
4105 <li>Allow import of data from gzipped files</li>
4106 <li>Export/import group and sequence associated line
4107 graph thresholds</li>
4108 <li>Nucleotide substitution matrix that supports RNA and
4109 ambiguity codes</li>
4110 <li>Allow disorder predictions to be made on the current
4111 selection (or visible selection) in the same way that JPred
4113 <li>Groovy scripting for headless Jalview operation</li>
4114 </ul> <em>Other improvements</em>
4116 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
4117 <li>COMBINE statement uses current SEQUENCE_REF and
4118 GROUP_REF scope to group annotation rows</li>
4119 <li>Support '' style escaping of quotes in Newick
4121 <li>Group options for JABAWS service by command line name</li>
4122 <li>Empty tooltip shown for JABA service options with a
4123 link but no description</li>
4124 <li>Select primary source when selecting authority in
4125 database fetcher GUI</li>
4126 <li>Add .mfa to FASTA file extensions recognised by
4128 <li>Annotation label tooltip text wrap</li>
4133 <li>Slow scrolling when lots of annotation rows are
4135 <li>Lots of NPE (and slowness) after creating RNA
4136 secondary structure annotation line</li>
4137 <li>Sequence database accessions not imported when
4138 fetching alignments from Rfam</li>
4139 <li>Incorrect SHMR submission for sequences with
4141 <li>View all structures does not always superpose
4143 <li>Option widgets in service parameters not updated to
4144 reflect user or preset settings</li>
4145 <li>Null pointer exceptions for some services without
4146 presets or adjustable parameters</li>
4147 <li>Discover PDB IDs entry in structure menu doesn't
4148 discover PDB xRefs</li>
4149 <li>Exception encountered while trying to retrieve
4150 features with DAS</li>
4151 <li>Lowest value in annotation row isn't coloured
4152 when colour by annotation (per sequence) is coloured</li>
4153 <li>Keyboard mode P jumps to start of gapped region when
4154 residue follows a gap</li>
4155 <li>Jalview appears to hang importing an alignment with
4156 Wrap as default or after enabling Wrap</li>
4157 <li>'Right click to add annotations' message
4158 shown in wrap mode when no annotations present</li>
4159 <li>Disorder predictions fail with NPE if no automatic
4160 annotation already exists on alignment</li>
4161 <li>oninit javascript function should be called after
4162 initialisation completes</li>
4163 <li>Remove redundancy after disorder prediction corrupts
4164 alignment window display</li>
4165 <li>Example annotation file in documentation is invalid</li>
4166 <li>Grouped line graph annotation rows are not exported
4167 to annotation file</li>
4168 <li>Multi-harmony analysis cannot be run when only two
4170 <li>Cannot create multiple groups of line graphs with
4171 several 'combine' statements in annotation file</li>
4172 <li>Pressing return several times causes Number Format
4173 exceptions in keyboard mode</li>
4174 <li>Multi-harmony (SHMMR) method doesn't submit
4175 correct partitions for input data</li>
4176 <li>Translation from DNA to Amino Acids fails</li>
4177 <li>Jalview fail to load newick tree with quoted label</li>
4178 <li>--headless flag isn't understood</li>
4179 <li>ClassCastException when generating EPS in headless
4181 <li>Adjusting sequence-associated shading threshold only
4182 changes one row's threshold</li>
4183 <li>Preferences and Feature settings panel panel
4184 doesn't open</li>
4185 <li>hide consensus histogram also hides conservation and
4186 quality histograms</li>
4191 <td><div align="center">
4192 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
4194 <td><em>Application</em>
4196 <li>Support for JABAWS 2.0 Services (AACon alignment
4197 conservation, protein disorder and Clustal Omega)</li>
4198 <li>JABAWS server status indicator in Web Services
4200 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
4201 in Jalview alignment window</li>
4202 <li>Updated Jalview build and deploy framework for OSX
4203 mountain lion, windows 7, and 8</li>
4204 <li>Nucleotide substitution matrix for PCA that supports
4205 RNA and ambiguity codes</li>
4207 <li>Improved sequence database retrieval GUI</li>
4208 <li>Support fetching and database reference look up
4209 against multiple DAS sources (Fetch all from in 'fetch db
4211 <li>Jalview project improvements
4213 <li>Store and retrieve the 'belowAlignment'
4214 flag for annotation</li>
4215 <li>calcId attribute to group annotation rows on the
4217 <li>Store AACon calculation settings for a view in
4218 Jalview project</li>
4222 <li>horizontal scrolling gesture support</li>
4223 <li>Visual progress indicator when PCA calculation is
4225 <li>Simpler JABA web services menus</li>
4226 <li>visual indication that web service results are still
4227 being retrieved from server</li>
4228 <li>Serialise the dialogs that are shown when Jalview
4229 starts up for first time</li>
4230 <li>Jalview user agent string for interacting with HTTP
4232 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
4234 <li>Examples directory and Groovy library included in
4235 InstallAnywhere distribution</li>
4236 </ul> <em>Applet</em>
4238 <li>RNA alignment and secondary structure annotation
4239 visualization applet example</li>
4240 </ul> <em>General</em>
4242 <li>Normalise option for consensus sequence logo</li>
4243 <li>Reset button in PCA window to return dimensions to
4245 <li>Allow seqspace or Jalview variant of alignment PCA
4247 <li>PCA with either nucleic acid and protein substitution
4249 <li>Allow windows containing HTML reports to be exported
4251 <li>Interactive display and editing of RNA secondary
4252 structure contacts</li>
4253 <li>RNA Helix Alignment Colouring</li>
4254 <li>RNA base pair logo consensus</li>
4255 <li>Parse sequence associated secondary structure
4256 information in Stockholm files</li>
4257 <li>HTML Export database accessions and annotation
4258 information presented in tooltip for sequences</li>
4259 <li>Import secondary structure from LOCARNA clustalw
4260 style RNA alignment files</li>
4261 <li>import and visualise T-COFFEE quality scores for an
4263 <li>'colour by annotation' per sequence option to
4264 shade each sequence according to its associated alignment
4266 <li>New Jalview Logo</li>
4267 </ul> <em>Documentation and Development</em>
4269 <li>documentation for score matrices used in Jalview</li>
4270 <li>New Website!</li>
4272 <td><em>Application</em>
4274 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
4275 wsdbfetch REST service</li>
4276 <li>Stop windows being moved outside desktop on OSX</li>
4277 <li>Filetype associations not installed for webstart
4279 <li>Jalview does not always retrieve progress of a JABAWS
4280 job execution in full once it is complete</li>
4281 <li>revise SHMR RSBS definition to ensure alignment is
4282 uploaded via ali_file parameter</li>
4283 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
4284 <li>View all structures superposed fails with exception</li>
4285 <li>Jnet job queues forever if a very short sequence is
4286 submitted for prediction</li>
4287 <li>Cut and paste menu not opened when mouse clicked on
4289 <li>Putting fractional value into integer text box in
4290 alignment parameter dialog causes Jalview to hang</li>
4291 <li>Structure view highlighting doesn't work on
4293 <li>View all structures fails with exception shown in
4295 <li>Characters in filename associated with PDBEntry not
4296 escaped in a platform independent way</li>
4297 <li>Jalview desktop fails to launch with exception when
4299 <li>Tree calculation reports 'you must have 2 or more
4300 sequences selected' when selection is empty</li>
4301 <li>Jalview desktop fails to launch with jar signature
4302 failure when java web start temporary file caching is
4304 <li>DAS Sequence retrieval with range qualification
4305 results in sequence xref which includes range qualification</li>
4306 <li>Errors during processing of command line arguments
4307 cause progress bar (JAL-898) to be removed</li>
4308 <li>Replace comma for semi-colon option not disabled for
4309 DAS sources in sequence fetcher</li>
4310 <li>Cannot close news reader when JABAWS server warning
4311 dialog is shown</li>
4312 <li>Option widgets not updated to reflect user settings</li>
4313 <li>Edited sequence not submitted to web service</li>
4314 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
4315 <li>InstallAnywhere installer doesn't unpack and run
4316 on OSX Mountain Lion</li>
4317 <li>Annotation panel not given a scroll bar when
4318 sequences with alignment annotation are pasted into the
4320 <li>Sequence associated annotation rows not associated
4321 when loaded from Jalview project</li>
4322 <li>Browser launch fails with NPE on java 1.7</li>
4323 <li>JABAWS alignment marked as finished when job was
4324 cancelled or job failed due to invalid input</li>
4325 <li>NPE with v2.7 example when clicking on Tree
4326 associated with all views</li>
4327 <li>Exceptions when copy/paste sequences with grouped
4328 annotation rows to new window</li>
4329 </ul> <em>Applet</em>
4331 <li>Sequence features are momentarily displayed before
4332 they are hidden using hidefeaturegroups applet parameter</li>
4333 <li>loading features via javascript API automatically
4334 enables feature display</li>
4335 <li>scrollToColumnIn javascript API method doesn't
4337 </ul> <em>General</em>
4339 <li>Redundancy removal fails for rna alignment</li>
4340 <li>PCA calculation fails when sequence has been selected
4341 and then deselected</li>
4342 <li>PCA window shows grey box when first opened on OSX</li>
4343 <li>Letters coloured pink in sequence logo when alignment
4344 coloured with clustalx</li>
4345 <li>Choosing fonts without letter symbols defined causes
4346 exceptions and redraw errors</li>
4347 <li>Initial PCA plot view is not same as manually
4348 reconfigured view</li>
4349 <li>Grouped annotation graph label has incorrect line
4351 <li>Grouped annotation graph label display is corrupted
4352 for lots of labels</li>
4357 <div align="center">
4358 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
4361 <td><em>Application</em>
4363 <li>Jalview Desktop News Reader</li>
4364 <li>Tweaked default layout of web services menu</li>
4365 <li>View/alignment association menu to enable user to
4366 easily specify which alignment a multi-structure view takes
4367 its colours/correspondences from</li>
4368 <li>Allow properties file location to be specified as URL</li>
4369 <li>Extend Jalview project to preserve associations
4370 between many alignment views and a single Jmol display</li>
4371 <li>Store annotation row height in Jalview project file</li>
4372 <li>Annotation row column label formatting attributes
4373 stored in project file</li>
4374 <li>Annotation row order for auto-calculated annotation
4375 rows preserved in Jalview project file</li>
4376 <li>Visual progress indication when Jalview state is
4377 saved using Desktop window menu</li>
4378 <li>Visual indication that command line arguments are
4379 still being processed</li>
4380 <li>Groovy script execution from URL</li>
4381 <li>Colour by annotation default min and max colours in
4383 <li>Automatically associate PDB files dragged onto an
4384 alignment with sequences that have high similarity and
4386 <li>Update JGoogleAnalytics to latest release (0.3)</li>
4387 <li>'view structures' option to open many
4388 structures in same window</li>
4389 <li>Sort associated views menu option for tree panel</li>
4390 <li>Group all JABA and non-JABA services for a particular
4391 analysis function in its own submenu</li>
4392 </ul> <em>Applet</em>
4394 <li>Userdefined and autogenerated annotation rows for
4396 <li>Adjustment of alignment annotation pane height</li>
4397 <li>Annotation scrollbar for annotation panel</li>
4398 <li>Drag to reorder annotation rows in annotation panel</li>
4399 <li>'automaticScrolling' parameter</li>
4400 <li>Allow sequences with partial ID string matches to be
4401 annotated from GFF/Jalview features files</li>
4402 <li>Sequence logo annotation row in applet</li>
4403 <li>Absolute paths relative to host server in applet
4404 parameters are treated as such</li>
4405 <li>New in the JalviewLite javascript API:
4407 <li>JalviewLite.js javascript library</li>
4408 <li>Javascript callbacks for
4410 <li>Applet initialisation</li>
4411 <li>Sequence/alignment mouse-overs and selections</li>
4414 <li>scrollTo row and column alignment scrolling
4416 <li>Select sequence/alignment regions from javascript</li>
4417 <li>javascript structure viewer harness to pass
4418 messages between Jmol and Jalview when running as
4419 distinct applets</li>
4420 <li>sortBy method</li>
4421 <li>Set of applet and application examples shipped
4422 with documentation</li>
4423 <li>New example to demonstrate JalviewLite and Jmol
4424 javascript message exchange</li>
4426 </ul> <em>General</em>
4428 <li>Enable Jmol displays to be associated with multiple
4429 multiple alignments</li>
4430 <li>Option to automatically sort alignment with new tree</li>
4431 <li>User configurable link to enable redirects to a
4432 www.Jalview.org mirror</li>
4433 <li>Jmol colours option for Jmol displays</li>
4434 <li>Configurable newline string when writing alignment
4435 and other flat files</li>
4436 <li>Allow alignment annotation description lines to
4437 contain html tags</li>
4438 </ul> <em>Documentation and Development</em>
4440 <li>Add groovy test harness for bulk load testing to
4442 <li>Groovy script to load and align a set of sequences
4443 using a web service before displaying the result in the
4444 Jalview desktop</li>
4445 <li>Restructured javascript and applet api documentation</li>
4446 <li>Ant target to publish example html files with applet
4448 <li>Netbeans project for building Jalview from source</li>
4449 <li>ant task to create online javadoc for Jalview source</li>
4451 <td><em>Application</em>
4453 <li>User defined colourscheme throws exception when
4454 current built in colourscheme is saved as new scheme</li>
4455 <li>AlignFrame->Save in application pops up save
4456 dialog for valid filename/format</li>
4457 <li>Cannot view associated structure for UniProt sequence</li>
4458 <li>PDB file association breaks for UniProt sequence
4460 <li>Associate PDB from file dialog does not tell you
4461 which sequence is to be associated with the file</li>
4462 <li>Find All raises null pointer exception when query
4463 only matches sequence IDs</li>
4464 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4465 <li>Jalview project with Jmol views created with Jalview
4466 2.4 cannot be loaded</li>
4467 <li>Filetype associations not installed for webstart
4469 <li>Two or more chains in a single PDB file associated
4470 with sequences in different alignments do not get coloured
4471 by their associated sequence</li>
4472 <li>Visibility status of autocalculated annotation row
4473 not preserved when project is loaded</li>
4474 <li>Annotation row height and visibility attributes not
4475 stored in Jalview project</li>
4476 <li>Tree bootstraps are not preserved when saved as a
4477 Jalview project</li>
4478 <li>Envision2 workflow tooltips are corrupted</li>
4479 <li>Enabling show group conservation also enables colour
4480 by conservation</li>
4481 <li>Duplicate group associated conservation or consensus
4482 created on new view</li>
4483 <li>Annotation scrollbar not displayed after 'show
4484 all hidden annotation rows' option selected</li>
4485 <li>Alignment quality not updated after alignment
4486 annotation row is hidden then shown</li>
4487 <li>Preserve colouring of structures coloured by
4488 sequences in pre Jalview 2.7 projects</li>
4489 <li>Web service job parameter dialog is not laid out
4491 <li>Web services menu not refreshed after 'reset
4492 services' button is pressed in preferences</li>
4493 <li>Annotation off by one in Jalview v2_3 example project</li>
4494 <li>Structures imported from file and saved in project
4495 get name like jalview_pdb1234.txt when reloaded</li>
4496 <li>Jalview does not always retrieve progress of a JABAWS
4497 job execution in full once it is complete</li>
4498 </ul> <em>Applet</em>
4500 <li>Alignment height set incorrectly when lots of
4501 annotation rows are displayed</li>
4502 <li>Relative URLs in feature HTML text not resolved to
4504 <li>View follows highlighting does not work for positions
4506 <li><= shown as = in tooltip</li>
4507 <li>Export features raises exception when no features
4509 <li>Separator string used for serialising lists of IDs
4510 for javascript api is modified when separator string
4511 provided as parameter</li>
4512 <li>Null pointer exception when selecting tree leaves for
4513 alignment with no existing selection</li>
4514 <li>Relative URLs for datasources assumed to be relative
4515 to applet's codebase</li>
4516 <li>Status bar not updated after finished searching and
4517 search wraps around to first result</li>
4518 <li>StructureSelectionManager instance shared between
4519 several Jalview applets causes race conditions and memory
4521 <li>Hover tooltip and mouseover of position on structure
4522 not sent from Jmol in applet</li>
4523 <li>Certain sequences of javascript method calls to
4524 applet API fatally hang browser</li>
4525 </ul> <em>General</em>
4527 <li>View follows structure mouseover scrolls beyond
4528 position with wrapped view and hidden regions</li>
4529 <li>Find sequence position moves to wrong residue
4530 with/without hidden columns</li>
4531 <li>Sequence length given in alignment properties window
4533 <li>InvalidNumberFormat exceptions thrown when trying to
4534 import PDB like structure files</li>
4535 <li>Positional search results are only highlighted
4536 between user-supplied sequence start/end bounds</li>
4537 <li>End attribute of sequence is not validated</li>
4538 <li>Find dialog only finds first sequence containing a
4539 given sequence position</li>
4540 <li>Sequence numbering not preserved in MSF alignment
4542 <li>Jalview PDB file reader does not extract sequence
4543 from nucleotide chains correctly</li>
4544 <li>Structure colours not updated when tree partition
4545 changed in alignment</li>
4546 <li>Sequence associated secondary structure not correctly
4547 parsed in interleaved stockholm</li>
4548 <li>Colour by annotation dialog does not restore current
4550 <li>Hiding (nearly) all sequences doesn't work
4552 <li>Sequences containing lowercase letters are not
4553 properly associated with their pdb files</li>
4554 </ul> <em>Documentation and Development</em>
4556 <li>schemas/JalviewWsParamSet.xsd corrupted by
4557 ApplyCopyright tool</li>
4562 <div align="center">
4563 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4566 <td><em>Application</em>
4568 <li>New warning dialog when the Jalview Desktop cannot
4569 contact web services</li>
4570 <li>JABA service parameters for a preset are shown in
4571 service job window</li>
4572 <li>JABA Service menu entries reworded</li>
4576 <li>Modeller PIR IO broken - cannot correctly import a
4577 pir file emitted by Jalview</li>
4578 <li>Existing feature settings transferred to new
4579 alignment view created from cut'n'paste</li>
4580 <li>Improved test for mixed amino/nucleotide chains when
4581 parsing PDB files</li>
4582 <li>Consensus and conservation annotation rows
4583 occasionally become blank for all new windows</li>
4584 <li>Exception raised when right clicking above sequences
4585 in wrapped view mode</li>
4586 </ul> <em>Application</em>
4588 <li>multiple multiply aligned structure views cause cpu
4589 usage to hit 100% and computer to hang</li>
4590 <li>Web Service parameter layout breaks for long user
4591 parameter names</li>
4592 <li>Jaba service discovery hangs desktop if Jaba server
4599 <div align="center">
4600 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4603 <td><em>Application</em>
4605 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4606 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4609 <li>Web Services preference tab</li>
4610 <li>Analysis parameters dialog box and user defined
4612 <li>Improved speed and layout of Envision2 service menu</li>
4613 <li>Superpose structures using associated sequence
4615 <li>Export coordinates and projection as CSV from PCA
4617 </ul> <em>Applet</em>
4619 <li>enable javascript: execution by the applet via the
4620 link out mechanism</li>
4621 </ul> <em>Other</em>
4623 <li>Updated the Jmol Jalview interface to work with Jmol
4625 <li>The Jalview Desktop and JalviewLite applet now
4626 require Java 1.5</li>
4627 <li>Allow Jalview feature colour specification for GFF
4628 sequence annotation files</li>
4629 <li>New 'colour by label' keword in Jalview feature file
4630 type colour specification</li>
4631 <li>New Jalview Desktop Groovy API method that allows a
4632 script to check if it being run in an interactive session or
4633 in a batch operation from the Jalview command line</li>
4637 <li>clustalx colourscheme colours Ds preferentially when
4638 both D+E are present in over 50% of the column</li>
4639 </ul> <em>Application</em>
4641 <li>typo in AlignmentFrame->View->Hide->all but
4642 selected Regions menu item</li>
4643 <li>sequence fetcher replaces ',' for ';' when the ',' is
4644 part of a valid accession ID</li>
4645 <li>fatal OOM if object retrieved by sequence fetcher
4646 runs out of memory</li>
4647 <li>unhandled Out of Memory Error when viewing pca
4648 analysis results</li>
4649 <li>InstallAnywhere builds fail to launch on OS X java
4650 10.5 update 4 (due to apple Java 1.6 update)</li>
4651 <li>Installanywhere Jalview silently fails to launch</li>
4652 </ul> <em>Applet</em>
4654 <li>Jalview.getFeatureGroups() raises an
4655 ArrayIndexOutOfBoundsException if no feature groups are
4662 <div align="center">
4663 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4669 <li>Alignment prettyprinter doesn't cope with long
4671 <li>clustalx colourscheme colours Ds preferentially when
4672 both D+E are present in over 50% of the column</li>
4673 <li>nucleic acid structures retrieved from PDB do not
4674 import correctly</li>
4675 <li>More columns get selected than were clicked on when a
4676 number of columns are hidden</li>
4677 <li>annotation label popup menu not providing correct
4678 add/hide/show options when rows are hidden or none are
4680 <li>Stockholm format shown in list of readable formats,
4681 and parser copes better with alignments from RFAM.</li>
4682 <li>CSV output of consensus only includes the percentage
4683 of all symbols if sequence logo display is enabled</li>
4685 </ul> <em>Applet</em>
4687 <li>annotation panel disappears when annotation is
4689 </ul> <em>Application</em>
4691 <li>Alignment view not redrawn properly when new
4692 alignment opened where annotation panel is visible but no
4693 annotations are present on alignment</li>
4694 <li>pasted region containing hidden columns is
4695 incorrectly displayed in new alignment window</li>
4696 <li>Jalview slow to complete operations when stdout is
4697 flooded (fix is to close the Jalview console)</li>
4698 <li>typo in AlignmentFrame->View->Hide->all but
4699 selected Rregions menu item.</li>
4700 <li>inconsistent group submenu and Format submenu entry
4701 'Un' or 'Non'conserved</li>
4702 <li>Sequence feature settings are being shared by
4703 multiple distinct alignments</li>
4704 <li>group annotation not recreated when tree partition is
4706 <li>double click on group annotation to select sequences
4707 does not propagate to associated trees</li>
4708 <li>Mac OSX specific issues:
4710 <li>exception raised when mouse clicked on desktop
4711 window background</li>
4712 <li>Desktop menu placed on menu bar and application
4713 name set correctly</li>
4714 <li>sequence feature settings not wide enough for the
4715 save feature colourscheme button</li>
4724 <div align="center">
4725 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4728 <td><em>New Capabilities</em>
4730 <li>URL links generated from description line for
4731 regular-expression based URL links (applet and application)
4734 <li>Non-positional feature URL links are shown in link
4736 <li>Linked viewing of nucleic acid sequences and
4738 <li>Automatic Scrolling option in View menu to display
4739 the currently highlighted region of an alignment.</li>
4740 <li>Order an alignment by sequence length, or using the
4741 average score or total feature count for each sequence.</li>
4742 <li>Shading features by score or associated description</li>
4743 <li>Subdivide alignment and groups based on identity of
4744 selected subsequence (Make Groups from Selection).</li>
4745 <li>New hide/show options including Shift+Control+H to
4746 hide everything but the currently selected region.</li>
4747 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4748 </ul> <em>Application</em>
4750 <li>Fetch DB References capabilities and UI expanded to
4751 support retrieval from DAS sequence sources</li>
4752 <li>Local DAS Sequence sources can be added via the
4753 command line or via the Add local source dialog box.</li>
4754 <li>DAS Dbref and DbxRef feature types are parsed as
4755 database references and protein_name is parsed as
4756 description line (BioSapiens terms).</li>
4757 <li>Enable or disable non-positional feature and database
4758 references in sequence ID tooltip from View menu in
4760 <!-- <li>New hidden columns and rows and representatives capabilities
4761 in annotations file (in progress - not yet fully implemented)</li> -->
4762 <li>Group-associated consensus, sequence logos and
4763 conservation plots</li>
4764 <li>Symbol distributions for each column can be exported
4765 and visualized as sequence logos</li>
4766 <li>Optionally scale multi-character column labels to fit
4767 within each column of annotation row<!-- todo for applet -->
4769 <li>Optional automatic sort of associated alignment view
4770 when a new tree is opened.</li>
4771 <li>Jalview Java Console</li>
4772 <li>Better placement of desktop window when moving
4773 between different screens.</li>
4774 <li>New preference items for sequence ID tooltip and
4775 consensus annotation</li>
4776 <li>Client to submit sequences and IDs to Envision2
4778 <li><em>Vamsas Capabilities</em>
4780 <li>Improved VAMSAS synchronization (Jalview archive
4781 used to preserve views, structures, and tree display
4783 <li>Import of vamsas documents from disk or URL via
4785 <li>Sharing of selected regions between views and
4786 with other VAMSAS applications (Experimental feature!)</li>
4787 <li>Updated API to VAMSAS version 0.2</li>
4789 </ul> <em>Applet</em>
4791 <li>Middle button resizes annotation row height</li>
4794 <li>sortByTree (true/false) - automatically sort the
4795 associated alignment view by the tree when a new tree is
4797 <li>showTreeBootstraps (true/false) - show or hide
4798 branch bootstraps (default is to show them if available)</li>
4799 <li>showTreeDistances (true/false) - show or hide
4800 branch lengths (default is to show them if available)</li>
4801 <li>showUnlinkedTreeNodes (true/false) - indicate if
4802 unassociated nodes should be highlighted in the tree
4804 <li>heightScale and widthScale (1.0 or more) -
4805 increase the height or width of a cell in the alignment
4806 grid relative to the current font size.</li>
4809 <li>Non-positional features displayed in sequence ID
4811 </ul> <em>Other</em>
4813 <li>Features format: graduated colour definitions and
4814 specification of feature scores</li>
4815 <li>Alignment Annotations format: new keywords for group
4816 associated annotation (GROUP_REF) and annotation row display
4817 properties (ROW_PROPERTIES)</li>
4818 <li>XML formats extended to support graduated feature
4819 colourschemes, group associated annotation, and profile
4820 visualization settings.</li></td>
4823 <li>Source field in GFF files parsed as feature source
4824 rather than description</li>
4825 <li>Non-positional features are now included in sequence
4826 feature and gff files (controlled via non-positional feature
4827 visibility in tooltip).</li>
4828 <li>URL links generated for all feature links (bugfix)</li>
4829 <li>Added URL embedding instructions to features file
4831 <li>Codons containing ambiguous nucleotides translated as
4832 'X' in peptide product</li>
4833 <li>Match case switch in find dialog box works for both
4834 sequence ID and sequence string and query strings do not
4835 have to be in upper case to match case-insensitively.</li>
4836 <li>AMSA files only contain first column of
4837 multi-character column annotation labels</li>
4838 <li>Jalview Annotation File generation/parsing consistent
4839 with documentation (e.g. Stockholm annotation can be
4840 exported and re-imported)</li>
4841 <li>PDB files without embedded PDB IDs given a friendly
4843 <li>Find incrementally searches ID string matches as well
4844 as subsequence matches, and correctly reports total number
4848 <li>Better handling of exceptions during sequence
4850 <li>Dasobert generated non-positional feature URL
4851 link text excludes the start_end suffix</li>
4852 <li>DAS feature and source retrieval buttons disabled
4853 when fetch or registry operations in progress.</li>
4854 <li>PDB files retrieved from URLs are cached properly</li>
4855 <li>Sequence description lines properly shared via
4857 <li>Sequence fetcher fetches multiple records for all
4859 <li>Ensured that command line das feature retrieval
4860 completes before alignment figures are generated.</li>
4861 <li>Reduced time taken when opening file browser for
4863 <li>isAligned check prior to calculating tree, PCA or
4864 submitting an MSA to JNet now excludes hidden sequences.</li>
4865 <li>User defined group colours properly recovered
4866 from Jalview projects.</li>
4875 <div align="center">
4876 <strong>2.4.0.b2</strong><br> 28/10/2009
4881 <li>Experimental support for google analytics usage
4883 <li>Jalview privacy settings (user preferences and docs).</li>
4888 <li>Race condition in applet preventing startup in
4890 <li>Exception when feature created from selection beyond
4891 length of sequence.</li>
4892 <li>Allow synthetic PDB files to be imported gracefully</li>
4893 <li>Sequence associated annotation rows associate with
4894 all sequences with a given id</li>
4895 <li>Find function matches case-insensitively for sequence
4896 ID string searches</li>
4897 <li>Non-standard characters do not cause pairwise
4898 alignment to fail with exception</li>
4899 </ul> <em>Application Issues</em>
4901 <li>Sequences are now validated against EMBL database</li>
4902 <li>Sequence fetcher fetches multiple records for all
4904 </ul> <em>InstallAnywhere Issues</em>
4906 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4907 issue with installAnywhere mechanism)</li>
4908 <li>Command line launching of JARs from InstallAnywhere
4909 version (java class versioning error fixed)</li>
4916 <div align="center">
4917 <strong>2.4</strong><br> 27/8/2008
4920 <td><em>User Interface</em>
4922 <li>Linked highlighting of codon and amino acid from
4923 translation and protein products</li>
4924 <li>Linked highlighting of structure associated with
4925 residue mapping to codon position</li>
4926 <li>Sequence Fetcher provides example accession numbers
4927 and 'clear' button</li>
4928 <li>MemoryMonitor added as an option under Desktop's
4930 <li>Extract score function to parse whitespace separated
4931 numeric data in description line</li>
4932 <li>Column labels in alignment annotation can be centred.</li>
4933 <li>Tooltip for sequence associated annotation give name
4935 </ul> <em>Web Services and URL fetching</em>
4937 <li>JPred3 web service</li>
4938 <li>Prototype sequence search client (no public services
4940 <li>Fetch either seed alignment or full alignment from
4942 <li>URL Links created for matching database cross
4943 references as well as sequence ID</li>
4944 <li>URL Links can be created using regular-expressions</li>
4945 </ul> <em>Sequence Database Connectivity</em>
4947 <li>Retrieval of cross-referenced sequences from other
4949 <li>Generalised database reference retrieval and
4950 validation to all fetchable databases</li>
4951 <li>Fetch sequences from DAS sources supporting the
4952 sequence command</li>
4953 </ul> <em>Import and Export</em>
4954 <li>export annotation rows as CSV for spreadsheet import</li>
4955 <li>Jalview projects record alignment dataset associations,
4956 EMBL products, and cDNA sequence mappings</li>
4957 <li>Sequence Group colour can be specified in Annotation
4959 <li>Ad-hoc colouring of group in Annotation File using RGB
4960 triplet as name of colourscheme</li>
4961 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4963 <li>treenode binding for VAMSAS tree exchange</li>
4964 <li>local editing and update of sequences in VAMSAS
4965 alignments (experimental)</li>
4966 <li>Create new or select existing session to join</li>
4967 <li>load and save of vamsas documents</li>
4968 </ul> <em>Application command line</em>
4970 <li>-tree parameter to open trees (introduced for passing
4972 <li>-fetchfrom command line argument to specify nicknames
4973 of DAS servers to query for alignment features</li>
4974 <li>-dasserver command line argument to add new servers
4975 that are also automatically queried for features</li>
4976 <li>-groovy command line argument executes a given groovy
4977 script after all input data has been loaded and parsed</li>
4978 </ul> <em>Applet-Application data exchange</em>
4980 <li>Trees passed as applet parameters can be passed to
4981 application (when using "View in full
4982 application")</li>
4983 </ul> <em>Applet Parameters</em>
4985 <li>feature group display control parameter</li>
4986 <li>debug parameter</li>
4987 <li>showbutton parameter</li>
4988 </ul> <em>Applet API methods</em>
4990 <li>newView public method</li>
4991 <li>Window (current view) specific get/set public methods</li>
4992 <li>Feature display control methods</li>
4993 <li>get list of currently selected sequences</li>
4994 </ul> <em>New Jalview distribution features</em>
4996 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4997 <li>RELEASE file gives build properties for the latest
4998 Jalview release.</li>
4999 <li>Java 1.1 Applet build made easier and donotobfuscate
5000 property controls execution of obfuscator</li>
5001 <li>Build target for generating source distribution</li>
5002 <li>Debug flag for javacc</li>
5003 <li>.jalview_properties file is documented (slightly) in
5004 jalview.bin.Cache</li>
5005 <li>Continuous Build Integration for stable and
5006 development version of Application, Applet and source
5011 <li>selected region output includes visible annotations
5012 (for certain formats)</li>
5013 <li>edit label/displaychar contains existing label/char
5015 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
5016 <li>shorter peptide product names from EMBL records</li>
5017 <li>Newick string generator makes compact representations</li>
5018 <li>bootstrap values parsed correctly for tree files with
5020 <li>pathological filechooser bug avoided by not allowing
5021 filenames containing a ':'</li>
5022 <li>Fixed exception when parsing GFF files containing
5023 global sequence features</li>
5024 <li>Alignment datasets are finalized only when number of
5025 references from alignment sequences goes to zero</li>
5026 <li>Close of tree branch colour box without colour
5027 selection causes cascading exceptions</li>
5028 <li>occasional negative imgwidth exceptions</li>
5029 <li>better reporting of non-fatal warnings to user when
5030 file parsing fails.</li>
5031 <li>Save works when Jalview project is default format</li>
5032 <li>Save as dialog opened if current alignment format is
5033 not a valid output format</li>
5034 <li>UniProt canonical names introduced for both das and
5036 <li>Histidine should be midblue (not pink!) in Zappo</li>
5037 <li>error messages passed up and output when data read
5039 <li>edit undo recovers previous dataset sequence when
5040 sequence is edited</li>
5041 <li>allow PDB files without pdb ID HEADER lines (like
5042 those generated by MODELLER) to be read in properly</li>
5043 <li>allow reading of JPred concise files as a normal
5045 <li>Stockholm annotation parsing and alignment properties
5046 import fixed for PFAM records</li>
5047 <li>Structure view windows have correct name in Desktop
5049 <li>annotation consisting of sequence associated scores
5050 can be read and written correctly to annotation file</li>
5051 <li>Aligned cDNA translation to aligned peptide works
5053 <li>Fixed display of hidden sequence markers and
5054 non-italic font for representatives in Applet</li>
5055 <li>Applet Menus are always embedded in applet window on
5057 <li>Newly shown features appear at top of stack (in
5059 <li>Annotations added via parameter not drawn properly
5060 due to null pointer exceptions</li>
5061 <li>Secondary structure lines are drawn starting from
5062 first column of alignment</li>
5063 <li>UniProt XML import updated for new schema release in
5065 <li>Sequence feature to sequence ID match for Features
5066 file is case-insensitive</li>
5067 <li>Sequence features read from Features file appended to
5068 all sequences with matching IDs</li>
5069 <li>PDB structure coloured correctly for associated views
5070 containing a sub-sequence</li>
5071 <li>PDB files can be retrieved by applet from Jar files</li>
5072 <li>feature and annotation file applet parameters
5073 referring to different directories are retrieved correctly</li>
5074 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
5075 <li>Fixed application hang whilst waiting for
5076 splash-screen version check to complete</li>
5077 <li>Applet properly URLencodes input parameter values
5078 when passing them to the launchApp service</li>
5079 <li>display name and local features preserved in results
5080 retrieved from web service</li>
5081 <li>Visual delay indication for sequence retrieval and
5082 sequence fetcher initialisation</li>
5083 <li>updated Application to use DAS 1.53e version of
5084 dasobert DAS client</li>
5085 <li>Re-instated Full AMSA support and .amsa file
5087 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
5095 <div align="center">
5096 <strong>2.3</strong><br> 9/5/07
5101 <li>Jmol 11.0.2 integration</li>
5102 <li>PDB views stored in Jalview XML files</li>
5103 <li>Slide sequences</li>
5104 <li>Edit sequence in place</li>
5105 <li>EMBL CDS features</li>
5106 <li>DAS Feature mapping</li>
5107 <li>Feature ordering</li>
5108 <li>Alignment Properties</li>
5109 <li>Annotation Scores</li>
5110 <li>Sort by scores</li>
5111 <li>Feature/annotation editing in applet</li>
5116 <li>Headless state operation in 2.2.1</li>
5117 <li>Incorrect and unstable DNA pairwise alignment</li>
5118 <li>Cut and paste of sequences with annotation</li>
5119 <li>Feature group display state in XML</li>
5120 <li>Feature ordering in XML</li>
5121 <li>blc file iteration selection using filename # suffix</li>
5122 <li>Stockholm alignment properties</li>
5123 <li>Stockhom alignment secondary structure annotation</li>
5124 <li>2.2.1 applet had no feature transparency</li>
5125 <li>Number pad keys can be used in cursor mode</li>
5126 <li>Structure Viewer mirror image resolved</li>
5133 <div align="center">
5134 <strong>2.2.1</strong><br> 12/2/07
5139 <li>Non standard characters can be read and displayed
5140 <li>Annotations/Features can be imported/exported to the
5142 <li>Applet allows editing of sequence/annotation/group
5143 name & description
5144 <li>Preference setting to display sequence name in
5146 <li>Annotation file format extended to allow
5147 Sequence_groups to be defined
5148 <li>Default opening of alignment overview panel can be
5149 specified in preferences
5150 <li>PDB residue numbering annotation added to associated
5156 <li>Applet crash under certain Linux OS with Java 1.6
5158 <li>Annotation file export / import bugs fixed
5159 <li>PNG / EPS image output bugs fixed
5165 <div align="center">
5166 <strong>2.2</strong><br> 27/11/06
5171 <li>Multiple views on alignment
5172 <li>Sequence feature editing
5173 <li>"Reload" alignment
5174 <li>"Save" to current filename
5175 <li>Background dependent text colour
5176 <li>Right align sequence ids
5177 <li>User-defined lower case residue colours
5180 <li>Menu item accelerator keys
5181 <li>Control-V pastes to current alignment
5182 <li>Cancel button for DAS Feature Fetching
5183 <li>PCA and PDB Viewers zoom via mouse roller
5184 <li>User-defined sub-tree colours and sub-tree selection
5187 <li>'New Window' button on the 'Output to Text box'
5192 <li>New memory efficient Undo/Redo System
5193 <li>Optimised symbol lookups and conservation/consensus
5195 <li>Region Conservation/Consensus recalculated after
5197 <li>Fixed Remove Empty Columns Bug (empty columns at end
5199 <li>Slowed DAS Feature Fetching for increased robustness.
5202 <li>Made angle brackets in ASCII feature descriptions
5204 <li>Re-instated Zoom function for PCA
5205 <li>Sequence descriptions conserved in web service
5207 <li>UniProt ID discoverer uses any word separated by
5209 <li>WsDbFetch query/result association resolved
5210 <li>Tree leaf to sequence mapping improved
5211 <li>Smooth fonts switch moved to FontChooser dialog box.
5219 <div align="center">
5220 <strong>2.1.1</strong><br> 12/9/06
5225 <li>Copy consensus sequence to clipboard</li>
5230 <li>Image output - rightmost residues are rendered if
5231 sequence id panel has been resized</li>
5232 <li>Image output - all offscreen group boundaries are
5234 <li>Annotation files with sequence references - all
5235 elements in file are relative to sequence position</li>
5236 <li>Mac Applet users can use Alt key for group editing</li>
5242 <div align="center">
5243 <strong>2.1</strong><br> 22/8/06
5248 <li>MAFFT Multiple Alignment in default Web Service list</li>
5249 <li>DAS Feature fetching</li>
5250 <li>Hide sequences and columns</li>
5251 <li>Export Annotations and Features</li>
5252 <li>GFF file reading / writing</li>
5253 <li>Associate structures with sequences from local PDB
5255 <li>Add sequences to exisiting alignment</li>
5256 <li>Recently opened files / URL lists</li>
5257 <li>Applet can launch the full application</li>
5258 <li>Applet has transparency for features (Java 1.2
5260 <li>Applet has user defined colours parameter</li>
5261 <li>Applet can load sequences from parameter
5262 "sequence<em>x</em>"
5268 <li>Redundancy Panel reinstalled in the Applet</li>
5269 <li>Monospaced font - EPS / rescaling bug fixed</li>
5270 <li>Annotation files with sequence references bug fixed</li>
5276 <div align="center">
5277 <strong>2.08.1</strong><br> 2/5/06
5282 <li>Change case of selected region from Popup menu</li>
5283 <li>Choose to match case when searching</li>
5284 <li>Middle mouse button and mouse movement can compress /
5285 expand the visible width and height of the alignment</li>
5290 <li>Annotation Panel displays complete JNet results</li>
5296 <div align="center">
5297 <strong>2.08b</strong><br> 18/4/06
5303 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
5304 <li>Righthand label on wrapped alignments shows correct
5311 <div align="center">
5312 <strong>2.08</strong><br> 10/4/06
5317 <li>Editing can be locked to the selection area</li>
5318 <li>Keyboard editing</li>
5319 <li>Create sequence features from searches</li>
5320 <li>Precalculated annotations can be loaded onto
5322 <li>Features file allows grouping of features</li>
5323 <li>Annotation Colouring scheme added</li>
5324 <li>Smooth fonts off by default - Faster rendering</li>
5325 <li>Choose to toggle Autocalculate Consensus On/Off</li>
5330 <li>Drag & Drop fixed on Linux</li>
5331 <li>Jalview Archive file faster to load/save, sequence
5332 descriptions saved.</li>
5338 <div align="center">
5339 <strong>2.07</strong><br> 12/12/05
5344 <li>PDB Structure Viewer enhanced</li>
5345 <li>Sequence Feature retrieval and display enhanced</li>
5346 <li>Choose to output sequence start-end after sequence
5347 name for file output</li>
5348 <li>Sequence Fetcher WSDBFetch@EBI</li>
5349 <li>Applet can read feature files, PDB files and can be
5350 used for HTML form input</li>
5355 <li>HTML output writes groups and features</li>
5356 <li>Group editing is Control and mouse click</li>
5357 <li>File IO bugs</li>
5363 <div align="center">
5364 <strong>2.06</strong><br> 28/9/05
5369 <li>View annotations in wrapped mode</li>
5370 <li>More options for PCA viewer</li>
5375 <li>GUI bugs resolved</li>
5376 <li>Runs with -nodisplay from command line</li>
5382 <div align="center">
5383 <strong>2.05b</strong><br> 15/9/05
5388 <li>Choose EPS export as lineart or text</li>
5389 <li>Jar files are executable</li>
5390 <li>Can read in Uracil - maps to unknown residue</li>
5395 <li>Known OutOfMemory errors give warning message</li>
5396 <li>Overview window calculated more efficiently</li>
5397 <li>Several GUI bugs resolved</li>
5403 <div align="center">
5404 <strong>2.05</strong><br> 30/8/05
5409 <li>Edit and annotate in "Wrapped" view</li>
5414 <li>Several GUI bugs resolved</li>
5420 <div align="center">
5421 <strong>2.04</strong><br> 24/8/05
5426 <li>Hold down mouse wheel & scroll to change font
5432 <li>Improved JPred client reliability</li>
5433 <li>Improved loading of Jalview files</li>
5439 <div align="center">
5440 <strong>2.03</strong><br> 18/8/05
5445 <li>Set Proxy server name and port in preferences</li>
5446 <li>Multiple URL links from sequence ids</li>
5447 <li>User Defined Colours can have a scheme name and added
5449 <li>Choose to ignore gaps in consensus calculation</li>
5450 <li>Unix users can set default web browser</li>
5451 <li>Runs without GUI for batch processing</li>
5452 <li>Dynamically generated Web Service Menus</li>
5457 <li>InstallAnywhere download for Sparc Solaris</li>
5463 <div align="center">
5464 <strong>2.02</strong><br> 18/7/05
5470 <li>Copy & Paste order of sequences maintains
5471 alignment order.</li>
5477 <div align="center">
5478 <strong>2.01</strong><br> 12/7/05
5483 <li>Use delete key for deleting selection.</li>
5484 <li>Use Mouse wheel to scroll sequences.</li>
5485 <li>Help file updated to describe how to add alignment
5487 <li>Version and build date written to build properties
5489 <li>InstallAnywhere installation will check for updates
5490 at launch of Jalview.</li>
5495 <li>Delete gaps bug fixed.</li>
5496 <li>FileChooser sorts columns.</li>
5497 <li>Can remove groups one by one.</li>
5498 <li>Filechooser icons installed.</li>
5499 <li>Finder ignores return character when searching.
5500 Return key will initiate a search.<br>
5507 <div align="center">
5508 <strong>2.0</strong><br> 20/6/05
5513 <li>New codebase</li>