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-3503 -->New Preferences tab for adjusting Jalview's
72 memory settings at launch
75 <!-- JAL-3144 -->Reverted to Jalview 'classic' drop-down
76 menu for selecting which database to fetch from in sequence
86 <!-- JAL-2226 -->Structure annotation rows for all mapped
87 chains in 3D structures are included in the 'Reference
88 Annotation' for a sequence
91 <!-- JAL-1260 -->Import Genbank and EMBL format flatfiles
94 <!-- JAL-3821 -->ENA record's mol_type honoured so RNA
95 molecules imported from ENA records are shown as RNA
97 <!-- JAL-3863 -->Support for Canonical Uniprot IDs
100 <!-- JAL-3204 -->Updated Jalview bindings for Uniprot XML
103 </ul> <em>JalviewJS</em>
106 <!-- 3624 -->PDB structures mapped to Uniprot Sequences with
119 <!-- JAL-3163 -->Missing message bundle keys are only
120 reported once per key (avoids excessive log output in js
124 <!-- JAL-3168 -->Feature type is included in the title of
125 the Feature Settings' Colour Chooser dialog
128 </ul> <em>Development</em>
131 <!-- -->First integrated JalviewJS and Jalview release
133 <li>Updated building instructions</li>
135 <!-- JAL-3789, JAL-3679 -->Improved JalviewJS/Jalview build
136 process, added support for system package provided eclipse
139 <li>Install4j 9.0.x used for installer packaging</li>
140 <li>Notarized MacOS installer for compatibility with Big
141 Sur and Monterey</li>
143 <!-- JAL-3805 -->Uninstaller application for old
144 (InstallAnywhere based) Jalview installations removed from
148 <!-- JAL-3930 -->Improved use of installers for unattended
149 installation with a customizedId of "JALVIEW" in install4j's
159 <!-- JAL-3674 -->Slow structure commands can block Jalview
163 <!-- JAL-3904 -->Structure window's viewer-specific menu
164 disappears when only one structure is shown (and many
165 sequences:one chain mappings are present)
168 <!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
169 the first SEQUENCE_GROUP defined
174 <!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 -->Selections not
175 propagated between Linked CDS - Protein alignments and their
176 trees (known defect from 2.11.1.3)
179 <!-- JAL-3761 -->Not all codon positions highlighted for
180 overlapping exon splice sites (e.g due to RNA slippage)
183 <!-- JAL-3794 -->X was not being recognised as the unknown base
187 <!-- JAL-3915 -->Removed RNAview checkbox and logic from
188 Structure Preferences
191 <!-- JAL-3583 -->Tooltip behaviour improved (slightly)
194 <!-- JAL-3162 -->Can edit a feature so that start > end
197 <!-- JAL-2848 -->Cancel from Amend Features doesn't reset a
198 modified graduated colour
201 <!-- JAL-3788 -->New View with automatic 'Show Overview'
202 preference enabled results in Null Pointer Exceptions when
203 clustal colouring is enabled
205 <li><!-- JAL-3275 -->Can open multiple Preferences panels</li>
207 <!-- JAL-3949 -->Standard out logging broken: messages only
208 routing to stderr and appear as a raw template
210 </ul> <em>JalviewJS</em>
213 <!-- JAL-3202 -->Consensus profile may include zero (rounded
214 down) percentage values causing a divide by zero
229 <!-- JAL-3762 -->JalviewJS doesn't honour arguments passed
230 via Info.args when there are arguments on the URL
233 <!-- JAL-3602 -->gradle closure-compiler not using UTF-8
236 <!-- JAL-3603 -->Annotation file fails to load from URL in
239 </ul> <em>Development</em>
243 <li>Fixed non-fatal gradle errors during build</li>
245 <!-- JAL-3745 -->Updated build.gradle for use with
255 <td width="60" align="center" nowrap><strong><a
256 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.7">.7</a><br />
257 <em>18/01/2022</em></strong></td>
259 <td align="left" valign="top">
262 <!-- JAL-3703, JAL-3935 -->Files open in Jalview cannot be
263 updated by Jalview or other applications (Windows, other non
266 </ul> <em>Security</em>
269 <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
275 <td width="60" align="center" nowrap><strong><a
276 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
277 <em>6/01/2022</em></strong></td>
279 <td align="left" valign="top"><em>Security</em>
282 <!-- JAL-3934 -->Version bump library dependency: Log4j 2.16.0 to 2.17.0.
289 <td width="60" align="center" nowrap><strong><a
290 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
291 <em>20/12/2021</em></strong></td>
293 <td align="left" valign="top"><em>Security</em>
296 <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
298 </ul> <em>Development</em>
300 <li>Updated building instructions</li>
305 <!-- JAL-3840 -->Occupancy calculation is incorrect for
306 alignment columns with over -1+2^32 gaps (breaking filtering
310 <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
311 scale factors being set with buggy window-managers (linux
314 </ul> <em>Development</em>
316 <li>Fixed non-fatal gradle errors during build</li>
321 <td width="60" align="center" nowrap><strong><a
322 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
323 <em>09/03/2021</em></strong></td>
324 <td align="left" valign="top"><em>Improved control of
325 Jalview's use of network services via jalview_properties</em>
328 <!-- JAL-3814 -->New .jalview_properties token controlling
329 launch of the news browser (like -nonews argument)
332 <!-- JAL-3813 -->New .jalview_properties token controlling
333 download of linkout URLs from
334 www.jalview.org/services/identifiers
337 <!-- JAL-3812 -->New .jalview_properties token controlling
338 download of BIOJSHTML templates
341 <!-- JAL-3811 -->New 'Discover Web Services' option to
342 trigger a one off JABAWS discovery if autodiscovery was
346 <td align="left" valign="top">
349 <!-- JAL-3818 -->Intermittent deadlock opening structure in
352 </ul> <em>New Known defects</em>
355 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
356 always restored from project (since 2.10.3)
359 <!-- JAL-3806 -->Selections from tree built from CDS aren't
360 propagated to Protein alignment (since 2.11.1.3)
366 <td width="60" align="center" nowrap><strong><a
367 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
368 <em>29/10/2020</em></strong></td>
369 <td align="left" valign="top">
374 <td align="left" valign="top">
377 <!-- JAL-3765 -->Find doesn't always highlight all matching
378 positions in a sequence (bug introduced in 2.11.1.2)
381 <!-- JAL-3760 -->Alignments containing one or more protein
382 sequences can be classed as nucleotide
385 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
386 sequences after alignment of protein products (known defect
387 first reported for 2.11.1.0)
390 <!-- JAL-3725 -->No tooltip or popup menu for genomic
391 features outwith CDS shown overlaid on protein
394 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
395 correctly mapped by Jalview (e.g. affects viral CDS with
396 ribosomal slippage, since 2.9.0)
399 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
403 <!-- JAL-3700 -->Selections in CDS sequence panel don't
404 always select corresponding protein sequences
407 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
408 column selection doesn't always ignore hidden columns
410 </ul> <em>Installer</em>
413 <!-- JAL-3611 -->Space character in Jalview install path on
414 Windows prevents install4j launching getdown
416 </ul> <em>Development</em>
419 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
420 version numbers in doc/building.md
426 <td width="60" align="center" nowrap><strong><a
427 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
428 <em>25/09/2020</em></strong></td>
429 <td align="left" valign="top">
433 <td align="left" valign="top">
436 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
437 "Encountered problems opening
438 https://www.jalview.org/examples/exampleFile_2_7.jvp"
444 <td width="60" align="center" nowrap><strong><a
445 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
446 <em>17/09/2020</em></strong></td>
447 <td align="left" valign="top">
450 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
451 residue in cursor mode
454 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
455 HTSJDK from 2.12 to 2.23
458 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
459 optimisations and improvements suggested by Bob Hanson and
460 improved compatibility with JalviewJS
463 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
464 alignments from Pfam and Rfam
467 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
468 import (no longer based on .gz extension)
471 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
474 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
475 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
479 <!-- JAL-3667 -->Improved warning messages, debug logging
480 and fixed Retry action when Jalview encounters errors when
481 saving or making backup files.
484 <!-- JAL-3676 -->Enhanced Jalview Java Console:
486 <li>Jalview's logging level can be configured</li>
487 <li>Copy to Clipboard Buttion</li>
491 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
492 when running on Linux (Requires Java 11+)
494 </ul> <em>Launching Jalview</em>
497 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
498 through a system property
501 <!-- JAL-3477 -->Improved built-in documentation and command
502 line help for configuring Jalview's memory
506 <td align="left" valign="top">
509 <!-- JAL-3691 -->Conservation and Quality tracks are shown
510 but not calculated and no protein or DNA score models are
511 available for tree/PCA calculation when launched with
512 Turkish language locale
515 <!-- JAL-3493 -->Escape does not clear highlights on the
516 alignment (Since Jalview 2.10.3)
519 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
520 doesn't slide selected sequences, just sequence under cursor
523 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
524 sequence under the cursor
527 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
528 multiple EMBL gene products shown for a single contig
531 <!-- JAL-3696 -->Errors encountered when processing variants
532 from VCF files yield "Error processing VCF: Format specifier
536 <!-- JAL-3697 -->Count of features not shown can be wrong
537 when there are both local and complementary features mapped
538 to the position under the cursor
541 <!-- JAL-3673 -->Sequence ID for reference sequence is
542 clipped when Right align Sequence IDs enabled
545 <!-- JAL-2983 -->Slider with negative range values not
546 rendered correctly in VAqua4 (Since 2.10.4)
549 <!-- JAL-3685 -->Single quotes not displayed correctly in
550 internationalised text for some messages and log output
553 <!-- JAL-3490 -->Find doesn't report matches that span
554 hidden gapped columns
557 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
558 panels, Alignment viewport and annotation renderer.
561 <!-- JAL-3561 -->Jalview ignores file format parameter
562 specifying output format when exporting an alignment via the
566 <!-- JAL-3667 -->Windows 10: For a minority of users, if
567 backups are not enabled, Jalview sometimes fails to
568 overwrite an existing file and raises a warning dialog. (in
569 2.11.0, and 2.11.1.0, the workaround is to try to save the
570 file again, and if that fails, delete the original file and
574 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
578 <!-- JAL-3741 -->References to http://www.jalview.org in
579 program and documentation
581 </ul> <em>Launching Jalview</em>
584 <!-- JAL-3718 -->Jalview application fails when launched the
585 first time for a version that has different jars to the
586 previous launched version.
588 </ul> <em>Developing Jalview</em>
591 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
592 data, causing cloverReport gradle task to fail with an
596 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
597 monitor the release channel
599 </ul> <em>New Known defects</em>
602 <!-- JAL-3748 -->CDS shown in result of submitting proteins
603 in a CDS/Protein alignment to a web service is wrong when
604 proteins share a common transcript sequence (e.g.
605 genome of RNA viruses)
608 <!-- JAL-3576 -->Co-located features exported and re-imported
609 are ordered differently when shown on alignment and in
610 tooltips. (Also affects v2.11.1.0)
613 <!-- JAL-3702 -->Drag and drop of alignment file onto
614 alignment window when in a HiDPI scaled mode in Linux only
615 works for the top left quadrant of the alignment window
618 <!-- JAL-3701 -->Stale build data in jalview standalone jar
619 builds (only affects 2.11.1.1 branch)
622 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
623 when alignment view restored from project (since Jalview 2.11.0)
626 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
627 protein products for certain ENA records are repeatedly
628 shown via Calculate->Show Cross Refs
634 <td width="60" align="center" nowrap><strong><a
635 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
636 <em>22/04/2020</em></strong></td>
637 <td align="left" valign="top">
640 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
641 'virtual' codon features shown on protein (or vice versa)
642 for display in alignments, on structure views (including
643 transfer to UCSF chimera), in feature reports and for
647 <!-- JAL-3121 -->Feature attributes from VCF files can be
648 exported and re-imported as GFF3 files
651 <!-- JAL-3376 -->Capture VCF "fixed column" values
652 POS, ID, QUAL, FILTER as Feature Attributes
655 <!-- JAL-3375 -->More robust VCF numeric data field
656 validation while parsing
659 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
663 <!-- JAL-3535 -->Feature Settings dialog title includes name
667 <!-- JAL-3538 -->Font anti-aliasing in alignment views
671 <!-- JAL-3468 -->Very long feature descriptions truncated in
675 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
676 with no feature types visible
679 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
681 </ul><em>Jalview Installer</em>
684 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
685 in console (may be null when Jalview launched as executable jar or via conda)
688 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
691 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
694 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
696 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
697 </ul> <em>Release processes</em>
700 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
703 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
705 </ul> <em>Build System</em>
708 <!-- JAL-3510 -->Clover updated to 4.4.1
711 <!-- JAL-3513 -->Test code included in Clover coverage
715 <em>Groovy Scripts</em>
718 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
719 to stdout containing the consensus sequence for each
720 alignment in a Jalview session
723 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
724 genomic sequence_variant annotation from CDS as
725 missense_variant or synonymous_variant on protein products.
729 <td align="left" valign="top">
732 <!-- JAL-3581 -->Hidden sequence markers still visible when
733 'Show hidden markers' option is not ticked
736 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
737 PNG output when 'Automatically set ID width' is set in
738 jalview preferences or properties file
741 <!-- JAL-3571 -->Feature Editor dialog can be opened when
742 'Show Sequence Features' option is not ticked
745 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
746 buttons in Feature Settings dialog are clicked when no
750 <!-- JAL-3412 -->ID margins for CDS and Protein views not
751 equal when split frame is first opened
754 <!-- JAL-3296 -->Sequence position numbers in status bar not
755 correct after editing a sequence's start position
758 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
759 with annotation and exceptions thrown when only a few
760 columns shown in wrapped mode
763 <!-- JAL-3386 -->Sequence IDs missing in headless export of
764 wrapped alignment figure with annotations
767 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
768 ID fails with ClassCastException
771 <!-- JAL-3389 -->Chimera session not restored from Jalview
775 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
776 feature settings dialog also selects columns
779 <!-- JAL-3473 -->SpinnerNumberModel causes
780 IllegalArgumentException in some circumstances
783 <!-- JAL-3534 -->Multiple feature settings dialogs can be
787 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
788 alignment window is closed
791 <!-- JAL-3406 -->Credits missing some authors in Jalview
792 help documentation for 2.11.0 release
795 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
796 includes Pfam ID as sequence's accession rather than its
799 </ul> <em>Java 11 Compatibility issues</em>
802 <!-- JAL-2987 -->OSX - Can't view some search results in
803 PDB/Uniprot search panel
805 </ul> <em>Installer</em>
808 <!-- JAL-3447 -->Jalview should not create file associations
809 for 3D structure files (.pdb, .mmcif. .cif)
811 </ul> <em>Repository and Source Release</em>
814 <!-- JAL-3474 -->removed obsolete .cvsignore files from
818 <!-- JAL-3541 -->Clover report generation running out of
821 </ul> <em>New Known Issues</em>
824 <!-- JAL-3523 -->OSX - Current working directory not
825 preserved when Jalview.app launched with parameters from
829 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
830 clipped in headless figure export when Right Align option
834 <!-- JAL-3542 -->Jalview Installation type always reports
835 'Source' in console output
838 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
839 bamboo server but run fine locally.
845 <td width="60" align="center" nowrap>
846 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
847 <em>04/07/2019</em></strong>
849 <td align="left" valign="top">
852 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
853 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
854 source project) rather than InstallAnywhere
857 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
858 settings, receive over the air updates and launch specific
859 versions via (<a href="https://github.com/threerings/getdown">Three
863 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
864 formats supported by Jalview (including .jvp project files)
867 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
868 arguments and switch between different getdown channels
871 <!-- JAL-3141 -->Backup files created when saving Jalview project
876 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
877 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
879 <!-- JAL-2620 -->Alternative genetic code tables for
880 'Translate as cDNA'</li>
882 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
883 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
886 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
887 implementation that allows updates) used for Sequence Feature collections</li>
889 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
890 features can be filtered and shaded according to any
891 associated attributes (e.g. variant attributes from VCF
892 file, or key-value pairs imported from column 9 of GFF
896 <!-- JAL-2879 -->Feature Attributes and shading schemes
897 stored and restored from Jalview Projects
900 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
901 recognise variant features
904 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
905 sequences (also coloured red by default)
908 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
912 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
913 algorithm (Z-sort/transparency and filter aware)
916 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
922 <!-- JAL-3205 -->Symmetric score matrices for faster
923 tree and PCA calculations
925 <li><strong>Principal Components Analysis Viewer</strong>
928 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
929 and Viewer state saved in Jalview Project
931 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
934 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
938 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
943 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
945 <li><strong>Speed and Efficiency</strong>
948 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
949 multiple groups when working with large alignments
952 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
956 <li><strong>User Interface</strong>
959 <!-- JAL-2933 -->Finder panel remembers last position in each
963 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
964 what is shown)<br />Only visible regions of alignment are shown by
965 default (can be changed in user preferences)
968 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
969 to the Overwrite Dialog
972 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
976 <!-- JAL-1244 -->Status bar shows bounds when dragging a
977 selection region, and gap count when inserting or deleting gaps
980 <!-- JAL-3132 -->Status bar updates over sequence and annotation
984 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
988 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
992 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
995 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
999 <!-- JAL-3181 -->Consistent ordering of links in sequence id
1003 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
1005 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
1009 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
1010 <li><strong>Java 11 Support (not yet on general release)</strong>
1013 <!-- -->OSX GUI integrations for App menu's 'About' entry and
1018 <em>Deprecations</em>
1020 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
1021 capabilities removed from the Jalview Desktop
1023 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
1024 unmarshalling has been replaced by JAXB for Jalview projects
1025 and XML based data retrieval clients</li>
1026 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
1027 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
1028 </ul> <em>Documentation</em>
1030 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
1031 not supported in EPS figure export
1033 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
1034 </ul> <em>Development and Release Processes</em>
1037 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
1040 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
1042 <!-- JAL-3225 -->Eclipse project configuration managed with
1046 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
1047 Bamboo continuous integration for unattended Test Suite
1051 <!-- JAL-2864 -->Memory test suite to detect leaks in common
1055 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
1059 <!-- JAL-3248 -->Developer documentation migrated to
1060 markdown (with HTML rendering)
1063 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
1066 <!-- JAL-3289 -->New URLs for publishing development
1071 <td align="left" valign="top">
1074 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
1077 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
1078 superposition in Jmol fail on Windows
1081 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
1082 structures for sequences with lots of PDB structures
1085 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
1089 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
1090 project involving multiple views
1093 <!-- JAL-3164 -->Overview for complementary view in a linked
1094 CDS/Protein alignment is not updated when Hide Columns by
1095 Annotation dialog hides columns
1098 <!-- JAL-3158 -->Selection highlighting in the complement of a
1099 CDS/Protein alignment stops working after making a selection in
1100 one view, then making another selection in the other view
1103 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
1107 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
1108 Settings and Jalview Preferences panels
1111 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
1112 overview with large alignments
1115 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
1116 region if columns were selected by dragging right-to-left and the
1117 mouse moved to the left of the first column
1120 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
1121 hidden column marker via scale popup menu
1124 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
1125 doesn't tell users the invalid URL
1128 <!-- JAL-2816 -->Tooltips displayed for features filtered by
1132 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
1133 show cross references or Fetch Database References are shown in
1134 red in original view
1137 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
1138 peptide sequence (computed variant shown as p.Res.null)
1141 <!-- JAL-2060 -->'Graduated colour' option not offered for
1142 manually created features (where feature score is Float.NaN)
1145 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
1146 when columns are hidden
1149 <!-- JAL-3082 -->Regular expression error for '(' in Select
1150 Columns by Annotation description
1153 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
1154 out of Scale or Annotation Panel
1157 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
1161 <!-- JAL-3074 -->Left/right drag in annotation can scroll
1165 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
1169 <!-- JAL-3002 -->Column display is out by one after Page Down,
1170 Page Up in wrapped mode
1173 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
1176 <!-- JAL-2932 -->Finder searches in minimised alignments
1179 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
1180 on opening an alignment
1183 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
1187 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
1188 different groups in the alignment are selected
1191 <!-- JAL-2717 -->Internationalised colour scheme names not shown
1195 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
1199 <!-- JAL-3125 -->Value input for graduated feature colour
1200 threshold gets 'unrounded'
1203 <!-- JAL-2982 -->PCA image export doesn't respect background
1207 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
1210 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
1213 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
1217 <!-- JAL-2964 -->Associate Tree with All Views not restored from
1221 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
1222 shown in complementary view
1225 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
1226 without normalisation
1229 <!-- JAL-3021 -->Sequence Details report should open positioned at top
1233 <!-- JAL-914 -->Help page can be opened twice
1236 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
1238 </ul> <em>Editing</em>
1241 <!-- JAL-2822 -->Start and End should be updated when sequence
1242 data at beginning or end of alignment added/removed via 'Edit'
1246 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
1247 relocate sequence features correctly when start of sequence is
1248 removed (Known defect since 2.10)
1251 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
1252 dialog corrupts dataset sequence
1255 <!-- JAL-868 -->Structure colours not updated when associated tree
1256 repartitions the alignment view (Regression in 2.10.5)
1258 </ul> <em>Datamodel</em>
1261 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
1262 sequence's End is greater than its length
1264 </ul> <em>Bugs fixed for Java 11 Support (not yet on
1265 general release)</em>
1268 <!-- JAL-3288 -->Menus work properly in split-screen
1270 </ul> <em>New Known Defects</em>
1273 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
1276 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
1277 regions of protein alignment.
1280 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
1281 is restored from a Jalview 2.11 project
1284 <!-- JAL-3213 -->Alignment panel height can be too small after
1288 <!-- JAL-3240 -->Display is incorrect after removing gapped
1289 columns within hidden columns
1292 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
1293 window after dragging left to select columns to left of visible
1297 <!-- JAL-2876 -->Features coloured according to their description
1298 string and thresholded by score in earlier versions of Jalview are
1299 not shown as thresholded features in 2.11. To workaround please
1300 create a Score filter instead.
1303 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
1305 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
1308 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1309 alignments with multiple views can close views unexpectedly
1312 <em>Java 11 Specific defects</em>
1315 <!-- JAL-3235 -->Jalview Properties file is not sorted
1316 alphabetically when saved
1322 <td width="60" nowrap>
1323 <div align="center">
1324 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1327 <td><div align="left">
1331 <!-- JAL-3101 -->Default memory for Jalview webstart and
1332 InstallAnywhere increased to 1G.
1335 <!-- JAL-247 -->Hidden sequence markers and representative
1336 sequence bolding included when exporting alignment as EPS,
1337 SVG, PNG or HTML. <em>Display is configured via the
1338 Format menu, or for command-line use via a Jalview
1339 properties file.</em>
1342 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1343 API and sequence data now imported as JSON.
1346 <!-- JAL-3065 -->Change in recommended way of starting
1347 Jalview via a Java command line: add jars in lib directory
1348 to CLASSPATH, rather than via the deprecated java.ext.dirs
1352 <em>Development</em>
1355 <!-- JAL-3047 -->Support added to execute test suite
1356 instrumented with <a href="http://openclover.org/">Open
1361 <td><div align="left">
1365 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1366 row shown in Feredoxin Structure alignment view of example
1370 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1371 annotation displayed.
1374 <!-- JAL-3107 -->Group conservation/consensus not shown
1375 for newly created group when 'Apply to all groups'
1379 <!-- JAL-3087 -->Corrupted display when switching to
1380 wrapped mode when sequence panel's vertical scrollbar is
1384 <!-- JAL-3003 -->Alignment is black in exported EPS file
1385 when sequences are selected in exported view.</em>
1388 <!-- JAL-3059 -->Groups with different coloured borders
1389 aren't rendered with correct colour.
1392 <!-- JAL-3092 -->Jalview could hang when importing certain
1393 types of knotted RNA secondary structure.
1396 <!-- JAL-3095 -->Sequence highlight and selection in
1397 trimmed VARNA 2D structure is incorrect for sequences that
1401 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1402 annotation when columns are inserted into an alignment,
1403 and when exporting as Stockholm flatfile.
1406 <!-- JAL-3053 -->Jalview annotation rows containing upper
1407 and lower-case 'E' and 'H' do not automatically get
1408 treated as RNA secondary structure.
1411 <!-- JAL-3106 -->.jvp should be used as default extension
1412 (not .jar) when saving a Jalview project file.
1415 <!-- JAL-3105 -->Mac Users: closing a window correctly
1416 transfers focus to previous window on OSX
1419 <em>Java 10 Issues Resolved</em>
1422 <!-- JAL-2988 -->OSX - Can't save new files via the File
1423 or export menus by typing in a name into the Save dialog
1427 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1428 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1429 'look and feel' which has improved compatibility with the
1430 latest version of OSX.
1437 <td width="60" nowrap>
1438 <div align="center">
1439 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1440 <em>7/06/2018</em></strong>
1443 <td><div align="left">
1447 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1448 annotation retrieved from Uniprot
1451 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1452 onto the Jalview Desktop
1456 <td><div align="left">
1460 <!-- JAL-3017 -->Cannot import features with multiple
1461 variant elements (blocks import of some Uniprot records)
1464 <!-- JAL-2997 -->Clustal files with sequence positions in
1465 right-hand column parsed correctly
1468 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1469 not alignment area in exported graphic
1472 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1473 window has input focus
1476 <!-- JAL-2992 -->Annotation panel set too high when
1477 annotation added to view (Windows)
1480 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1481 network connectivity is poor
1484 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1485 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1486 the currently open URL and links from a page viewed in
1487 Firefox or Chrome on Windows is now fully supported. If
1488 you are using Edge, only links in the page can be
1489 dragged, and with Internet Explorer, only the currently
1490 open URL in the browser can be dropped onto Jalview.</em>
1493 <em>New Known Defects</em>
1495 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1500 <td width="60" nowrap>
1501 <div align="center">
1502 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1505 <td><div align="left">
1509 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1510 for disabling automatic superposition of multiple
1511 structures and open structures in existing views
1514 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1515 ID and annotation area margins can be click-dragged to
1519 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1523 <!-- JAL-2759 -->Improved performance for large alignments
1524 and lots of hidden columns
1527 <!-- JAL-2593 -->Improved performance when rendering lots
1528 of features (particularly when transparency is disabled)
1531 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1532 exchange of Jalview features and Chimera attributes made
1538 <td><div align="left">
1541 <!-- JAL-2899 -->Structure and Overview aren't updated
1542 when Colour By Annotation threshold slider is adjusted
1545 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1546 overlapping alignment panel
1549 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1553 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1554 improved: CDS not handled correctly if transcript has no
1558 <!-- JAL-2321 -->Secondary structure and temperature
1559 factor annotation not added to sequence when local PDB
1560 file associated with it by drag'n'drop or structure
1564 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1565 dialog doesn't import PDB files dropped on an alignment
1568 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1569 scroll bar doesn't work for some CDS/Protein views
1572 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1573 Java 1.8u153 onwards and Java 1.9u4+.
1576 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1577 columns in annotation row
1580 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1581 honored in batch mode
1584 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1585 for structures added to existing Jmol view
1588 <!-- JAL-2223 -->'View Mappings' includes duplicate
1589 entries after importing project with multiple views
1592 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1593 protein sequences via SIFTS from associated PDB entries
1594 with negative residue numbers or missing residues fails
1597 <!-- JAL-2952 -->Exception when shading sequence with negative
1598 Temperature Factor values from annotated PDB files (e.g.
1599 as generated by CONSURF)
1602 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1603 tooltip doesn't include a text description of mutation
1606 <!-- JAL-2922 -->Invert displayed features very slow when
1607 structure and/or overview windows are also shown
1610 <!-- JAL-2954 -->Selecting columns from highlighted regions
1611 very slow for alignments with large numbers of sequences
1614 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1615 with 'StringIndexOutOfBounds'
1618 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1619 platforms running Java 10
1622 <!-- JAL-2960 -->Adding a structure to existing structure
1623 view appears to do nothing because the view is hidden behind the alignment view
1629 <!-- JAL-2926 -->Copy consensus sequence option in applet
1630 should copy the group consensus when popup is opened on it
1636 <!-- JAL-2913 -->Fixed ID width preference is not respected
1639 <em>New Known Defects</em>
1642 <!-- JAL-2973 --> Exceptions occasionally raised when
1643 editing a large alignment and overview is displayed
1646 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1647 repeatedly after a series of edits even when the overview
1648 is no longer reflecting updates
1651 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1652 structures for protein subsequence (if 'Trim Retrieved
1653 Sequences' enabled) or Ensembl isoforms (Workaround in
1654 2.10.4 is to fail back to N&W mapping)
1657 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1658 option gives blank output
1665 <td width="60" nowrap>
1666 <div align="center">
1667 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1670 <td><div align="left">
1671 <ul><li>Updated Certum Codesigning Certificate
1672 (Valid till 30th November 2018)</li></ul></div></td>
1673 <td><div align="left">
1674 <em>Desktop</em><ul>
1676 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1677 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1678 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1679 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1680 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1681 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1682 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1688 <td width="60" nowrap>
1689 <div align="center">
1690 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1693 <td><div align="left">
1697 <!-- JAL-2446 -->Faster and more efficient management and
1698 rendering of sequence features
1701 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1702 429 rate limit request hander
1705 <!-- JAL-2773 -->Structure views don't get updated unless
1706 their colours have changed
1709 <!-- JAL-2495 -->All linked sequences are highlighted for
1710 a structure mousover (Jmol) or selection (Chimera)
1713 <!-- JAL-2790 -->'Cancel' button in progress bar for
1714 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1717 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1718 view from Ensembl locus cross-references
1721 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1725 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1726 feature can be disabled
1729 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1730 PDB easier retrieval of sequences for lists of IDs
1733 <!-- JAL-2758 -->Short names for sequences retrieved from
1739 <li>Groovy interpreter updated to 2.4.12</li>
1740 <li>Example groovy script for generating a matrix of
1741 percent identity scores for current alignment.</li>
1743 <em>Testing and Deployment</em>
1746 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1750 <td><div align="left">
1754 <!-- JAL-2643 -->Pressing tab after updating the colour
1755 threshold text field doesn't trigger an update to the
1759 <!-- JAL-2682 -->Race condition when parsing sequence ID
1763 <!-- JAL-2608 -->Overview windows are also closed when
1764 alignment window is closed
1767 <!-- JAL-2548 -->Export of features doesn't always respect
1771 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1772 takes a long time in Cursor mode
1778 <!-- JAL-2777 -->Structures with whitespace chainCode
1779 cannot be viewed in Chimera
1782 <!-- JAL-2728 -->Protein annotation panel too high in
1786 <!-- JAL-2757 -->Can't edit the query after the server
1787 error warning icon is shown in Uniprot and PDB Free Text
1791 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1794 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1797 <!-- JAL-2739 -->Hidden column marker in last column not
1798 rendered when switching back from Wrapped to normal view
1801 <!-- JAL-2768 -->Annotation display corrupted when
1802 scrolling right in unwapped alignment view
1805 <!-- JAL-2542 -->Existing features on subsequence
1806 incorrectly relocated when full sequence retrieved from
1810 <!-- JAL-2733 -->Last reported memory still shown when
1811 Desktop->Show Memory is unticked (OSX only)
1814 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1815 features of same type and group to be selected for
1819 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1820 alignments when hidden columns are present
1823 <!-- JAL-2392 -->Jalview freezes when loading and
1824 displaying several structures
1827 <!-- JAL-2732 -->Black outlines left after resizing or
1831 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1832 within the Jalview desktop on OSX
1835 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1836 when in wrapped alignment mode
1839 <!-- JAL-2636 -->Scale mark not shown when close to right
1840 hand end of alignment
1843 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1844 each selected sequence do not have correct start/end
1848 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1849 after canceling the Alignment Window's Font dialog
1852 <!-- JAL-2036 -->Show cross-references not enabled after
1853 restoring project until a new view is created
1856 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1857 URL links appears when only default EMBL-EBI link is
1858 configured (since 2.10.2b2)
1861 <!-- JAL-2775 -->Overview redraws whole window when box
1862 position is adjusted
1865 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1866 in a multi-chain structure when viewing alignment
1867 involving more than one chain (since 2.10)
1870 <!-- JAL-2811 -->Double residue highlights in cursor mode
1871 if new selection moves alignment window
1874 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1875 arrow key in cursor mode to pass hidden column marker
1878 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1879 that produces correctly annotated transcripts and products
1882 <!-- JAL-2776 -->Toggling a feature group after first time
1883 doesn't update associated structure view
1886 <em>Applet</em><br />
1889 <!-- JAL-2687 -->Concurrent modification exception when
1890 closing alignment panel
1893 <em>BioJSON</em><br />
1896 <!-- JAL-2546 -->BioJSON export does not preserve
1897 non-positional features
1900 <em>New Known Issues</em>
1903 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1904 sequence features correctly (for many previous versions of
1908 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1909 using cursor in wrapped panel other than top
1912 <!-- JAL-2791 -->Select columns containing feature ignores
1913 graduated colour threshold
1916 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1917 always preserve numbering and sequence features
1920 <em>Known Java 9 Issues</em>
1923 <!-- JAL-2902 -->Groovy Console very slow to open and is
1924 not responsive when entering characters (Webstart, Java
1931 <td width="60" nowrap>
1932 <div align="center">
1933 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1934 <em>2/10/2017</em></strong>
1937 <td><div align="left">
1938 <em>New features in Jalview Desktop</em>
1941 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1943 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1947 <td><div align="left">
1951 <td width="60" nowrap>
1952 <div align="center">
1953 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1954 <em>7/9/2017</em></strong>
1957 <td><div align="left">
1961 <!-- JAL-2588 -->Show gaps in overview window by colouring
1962 in grey (sequences used to be coloured grey, and gaps were
1966 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1970 <!-- JAL-2587 -->Overview updates immediately on increase
1971 in size and progress bar shown as higher resolution
1972 overview is recalculated
1977 <td><div align="left">
1981 <!-- JAL-2664 -->Overview window redraws every hidden
1982 column region row by row
1985 <!-- JAL-2681 -->duplicate protein sequences shown after
1986 retrieving Ensembl crossrefs for sequences from Uniprot
1989 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1990 format setting is unticked
1993 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1994 if group has show boxes format setting unticked
1997 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1998 autoscrolling whilst dragging current selection group to
1999 include sequences and columns not currently displayed
2002 <!-- JAL-2691 -->Not all chains are mapped when multimeric
2003 assemblies are imported via CIF file
2006 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
2007 displayed when threshold or conservation colouring is also
2011 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
2015 <!-- JAL-2673 -->Jalview continues to scroll after
2016 dragging a selected region off the visible region of the
2020 <!-- JAL-2724 -->Cannot apply annotation based
2021 colourscheme to all groups in a view
2024 <!-- JAL-2511 -->IDs don't line up with sequences
2025 initially after font size change using the Font chooser or
2032 <td width="60" nowrap>
2033 <div align="center">
2034 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
2037 <td><div align="left">
2038 <em>Calculations</em>
2042 <!-- JAL-1933 -->Occupancy annotation row shows number of
2043 ungapped positions in each column of the alignment.
2046 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
2047 a calculation dialog box
2050 <!-- JAL-2379 -->Revised implementation of PCA for speed
2051 and memory efficiency (~30x faster)
2054 <!-- JAL-2403 -->Revised implementation of sequence
2055 similarity scores as used by Tree, PCA, Shading Consensus
2056 and other calculations
2059 <!-- JAL-2416 -->Score matrices are stored as resource
2060 files within the Jalview codebase
2063 <!-- JAL-2500 -->Trees computed on Sequence Feature
2064 Similarity may have different topology due to increased
2071 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
2072 model for alignments and groups
2075 <!-- JAL-384 -->Custom shading schemes created via groovy
2082 <!-- JAL-2526 -->Efficiency improvements for interacting
2083 with alignment and overview windows
2086 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
2090 <!-- JAL-2388 -->Hidden columns and sequences can be
2094 <!-- JAL-2611 -->Click-drag in visible area allows fine
2095 adjustment of visible position
2099 <em>Data import/export</em>
2102 <!-- JAL-2535 -->Posterior probability annotation from
2103 Stockholm files imported as sequence associated annotation
2106 <!-- JAL-2507 -->More robust per-sequence positional
2107 annotation input/output via stockholm flatfile
2110 <!-- JAL-2533 -->Sequence names don't include file
2111 extension when importing structure files without embedded
2112 names or PDB accessions
2115 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
2116 format sequence substitution matrices
2119 <em>User Interface</em>
2122 <!-- JAL-2447 --> Experimental Features Checkbox in
2123 Desktop's Tools menu to hide or show untested features in
2127 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
2128 via Overview or sequence motif search operations
2131 <!-- JAL-2547 -->Amend sequence features dialog box can be
2132 opened by double clicking gaps within sequence feature
2136 <!-- JAL-1476 -->Status bar message shown when not enough
2137 aligned positions were available to create a 3D structure
2141 <em>3D Structure</em>
2144 <!-- JAL-2430 -->Hidden regions in alignment views are not
2145 coloured in linked structure views
2148 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
2149 file-based command exchange
2152 <!-- JAL-2375 -->Structure chooser automatically shows
2153 Cached Structures rather than querying the PDBe if
2154 structures are already available for sequences
2157 <!-- JAL-2520 -->Structures imported via URL are cached in
2158 the Jalview project rather than downloaded again when the
2159 project is reopened.
2162 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
2163 to transfer Chimera's structure attributes as Jalview
2164 features, and vice-versa (<strong>Experimental
2168 <em>Web Services</em>
2171 <!-- JAL-2549 -->Updated JABAWS client to v2.2
2174 <!-- JAL-2335 -->Filter non-standard amino acids and
2175 nucleotides when submitting to AACon and other MSA
2179 <!-- JAL-2316, -->URLs for viewing database
2180 cross-references provided by identifiers.org and the
2181 EMBL-EBI's MIRIAM DB
2188 <!-- JAL-2344 -->FileFormatI interface for describing and
2189 identifying file formats (instead of String constants)
2192 <!-- JAL-2228 -->FeatureCounter script refactored for
2193 efficiency when counting all displayed features (not
2194 backwards compatible with 2.10.1)
2197 <em>Example files</em>
2200 <!-- JAL-2631 -->Graduated feature colour style example
2201 included in the example feature file
2204 <em>Documentation</em>
2207 <!-- JAL-2339 -->Release notes reformatted for readability
2208 with the built-in Java help viewer
2211 <!-- JAL-1644 -->Find documentation updated with 'search
2212 sequence description' option
2218 <!-- JAL-2485, -->External service integration tests for
2219 Uniprot REST Free Text Search Client
2222 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
2225 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
2230 <td><div align="left">
2231 <em>Calculations</em>
2234 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
2235 matrix - C->R should be '-3'<br />Old matrix restored
2236 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
2238 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
2239 Jalview's treatment of gaps in PCA and substitution matrix
2240 based Tree calculations.<br /> <br />In earlier versions
2241 of Jalview, gaps matching gaps were penalised, and gaps
2242 matching non-gaps penalised even more. In the PCA
2243 calculation, gaps were actually treated as non-gaps - so
2244 different costs were applied, which meant Jalview's PCAs
2245 were different to those produced by SeqSpace.<br />Jalview
2246 now treats gaps in the same way as SeqSpace (ie it scores
2247 them as 0). <br /> <br />Enter the following in the
2248 Groovy console to restore pre-2.10.2 behaviour:<br />
2249 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
2250 // for 2.10.1 mode <br />
2251 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
2252 // to restore 2.10.2 mode <br /> <br /> <em>Note:
2253 these settings will affect all subsequent tree and PCA
2254 calculations (not recommended)</em></li>
2256 <!-- JAL-2424 -->Fixed off-by-one bug that affected
2257 scaling of branch lengths for trees computed using
2258 Sequence Feature Similarity.
2261 <!-- JAL-2377 -->PCA calculation could hang when
2262 generating output report when working with highly
2263 redundant alignments
2266 <!-- JAL-2544 --> Sort by features includes features to
2267 right of selected region when gaps present on right-hand
2271 <em>User Interface</em>
2274 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2275 doesn't reselect a specific sequence's associated
2276 annotation after it was used for colouring a view
2279 <!-- JAL-2419 -->Current selection lost if popup menu
2280 opened on a region of alignment without groups
2283 <!-- JAL-2374 -->Popup menu not always shown for regions
2284 of an alignment with overlapping groups
2287 <!-- JAL-2310 -->Finder double counts if both a sequence's
2288 name and description match
2291 <!-- JAL-2370 -->Hiding column selection containing two
2292 hidden regions results in incorrect hidden regions
2295 <!-- JAL-2386 -->'Apply to all groups' setting when
2296 changing colour does not apply Conservation slider value
2300 <!-- JAL-2373 -->Percentage identity and conservation menu
2301 items do not show a tick or allow shading to be disabled
2304 <!-- JAL-2385 -->Conservation shading or PID threshold
2305 lost when base colourscheme changed if slider not visible
2308 <!-- JAL-2547 -->Sequence features shown in tooltip for
2309 gaps before start of features
2312 <!-- JAL-2623 -->Graduated feature colour threshold not
2313 restored to UI when feature colour is edited
2316 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2317 a time when scrolling vertically in wrapped mode.
2320 <!-- JAL-2630 -->Structure and alignment overview update
2321 as graduate feature colour settings are modified via the
2325 <!-- JAL-2034 -->Overview window doesn't always update
2326 when a group defined on the alignment is resized
2329 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2330 wrapped view result in positional status updates
2334 <!-- JAL-2563 -->Status bar doesn't show position for
2335 ambiguous amino acid and nucleotide symbols
2338 <!-- JAL-2602 -->Copy consensus sequence failed if
2339 alignment included gapped columns
2342 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2343 widgets don't permanently disappear
2346 <!-- JAL-2503 -->Cannot select or filter quantitative
2347 annotation that are shown only as column labels (e.g.
2348 T-Coffee column reliability scores)
2351 <!-- JAL-2594 -->Exception thrown if trying to create a
2352 sequence feature on gaps only
2355 <!-- JAL-2504 -->Features created with 'New feature'
2356 button from a Find inherit previously defined feature type
2357 rather than the Find query string
2360 <!-- JAL-2423 -->incorrect title in output window when
2361 exporting tree calculated in Jalview
2364 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2365 and then revealing them reorders sequences on the
2369 <!-- JAL-964 -->Group panel in sequence feature settings
2370 doesn't update to reflect available set of groups after
2371 interactively adding or modifying features
2374 <!-- JAL-2225 -->Sequence Database chooser unusable on
2378 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2379 only excluded gaps in current sequence and ignored
2386 <!-- JAL-2421 -->Overview window visible region moves
2387 erratically when hidden rows or columns are present
2390 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2391 Structure Viewer's colour menu don't correspond to
2395 <!-- JAL-2405 -->Protein specific colours only offered in
2396 colour and group colour menu for protein alignments
2399 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2400 reflect currently selected view or group's shading
2404 <!-- JAL-2624 -->Feature colour thresholds not respected
2405 when rendered on overview and structures when opacity at
2409 <!-- JAL-2589 -->User defined gap colour not shown in
2410 overview when features overlaid on alignment
2413 <!-- JAL-2567 -->Feature settings for different views not
2414 recovered correctly from Jalview project file
2417 <!-- JAL-2256 -->Feature colours in overview when first opened
2418 (automatically via preferences) are different to the main
2422 <em>Data import/export</em>
2425 <!-- JAL-2576 -->Very large alignments take a long time to
2429 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2430 added after a sequence was imported are not written to
2434 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2435 when importing RNA secondary structure via Stockholm
2438 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2439 not shown in correct direction for simple pseudoknots
2442 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2443 with lightGray or darkGray via features file (but can
2447 <!-- JAL-2383 -->Above PID colour threshold not recovered
2448 when alignment view imported from project
2451 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2452 structure and sequences extracted from structure files
2453 imported via URL and viewed in Jmol
2456 <!-- JAL-2520 -->Structures loaded via URL are saved in
2457 Jalview Projects rather than fetched via URL again when
2458 the project is loaded and the structure viewed
2461 <em>Web Services</em>
2464 <!-- JAL-2519 -->EnsemblGenomes example failing after
2465 release of Ensembl v.88
2468 <!-- JAL-2366 -->Proxy server address and port always
2469 appear enabled in Preferences->Connections
2472 <!-- JAL-2461 -->DAS registry not found exceptions
2473 removed from console output
2476 <!-- JAL-2582 -->Cannot retrieve protein products from
2477 Ensembl by Peptide ID
2480 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2481 created from SIFTs, and spurious 'Couldn't open structure
2482 in Chimera' errors raised after April 2017 update (problem
2483 due to 'null' string rather than empty string used for
2484 residues with no corresponding PDB mapping).
2487 <em>Application UI</em>
2490 <!-- JAL-2361 -->User Defined Colours not added to Colour
2494 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2495 case' residues (button in colourscheme editor debugged and
2496 new documentation and tooltips added)
2499 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2500 doesn't restore group-specific text colour thresholds
2503 <!-- JAL-2243 -->Feature settings panel does not update as
2504 new features are added to alignment
2507 <!-- JAL-2532 -->Cancel in feature settings reverts
2508 changes to feature colours via the Amend features dialog
2511 <!-- JAL-2506 -->Null pointer exception when attempting to
2512 edit graduated feature colour via amend features dialog
2516 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2517 selection menu changes colours of alignment views
2520 <!-- JAL-2426 -->Spurious exceptions in console raised
2521 from alignment calculation workers after alignment has
2525 <!-- JAL-1608 -->Typo in selection popup menu - Create
2526 groups now 'Create Group'
2529 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2530 Create/Undefine group doesn't always work
2533 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2534 shown again after pressing 'Cancel'
2537 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2538 adjusts start position in wrap mode
2541 <!-- JAL-2563 -->Status bar doesn't show positions for
2542 ambiguous amino acids
2545 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2546 CDS/Protein view after CDS sequences added for aligned
2550 <!-- JAL-2592 -->User defined colourschemes called 'User
2551 Defined' don't appear in Colours menu
2557 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2558 score models doesn't always result in an updated PCA plot
2561 <!-- JAL-2442 -->Features not rendered as transparent on
2562 overview or linked structure view
2565 <!-- JAL-2372 -->Colour group by conservation doesn't
2569 <!-- JAL-2517 -->Hitting Cancel after applying
2570 user-defined colourscheme doesn't restore original
2577 <!-- JAL-2314 -->Unit test failure:
2578 jalview.ws.jabaws.RNAStructExportImport setup fails
2581 <!-- JAL-2307 -->Unit test failure:
2582 jalview.ws.sifts.SiftsClientTest due to compatibility
2583 problems with deep array comparison equality asserts in
2584 successive versions of TestNG
2587 <!-- JAL-2479 -->Relocated StructureChooserTest and
2588 ParameterUtilsTest Unit tests to Network suite
2591 <em>New Known Issues</em>
2594 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2595 phase after a sequence motif find operation
2598 <!-- JAL-2550 -->Importing annotation file with rows
2599 containing just upper and lower case letters are
2600 interpreted as WUSS RNA secondary structure symbols
2603 <!-- JAL-2590 -->Cannot load and display Newick trees
2604 reliably from eggnog Ortholog database
2607 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2608 containing features of type Highlight' when 'B' is pressed
2609 to mark columns containing highlighted regions.
2612 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2613 doesn't always add secondary structure annotation.
2618 <td width="60" nowrap>
2619 <div align="center">
2620 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2623 <td><div align="left">
2627 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2628 for all consensus calculations
2631 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2634 <li>Updated Jalview's Certum code signing certificate
2637 <em>Application</em>
2640 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2641 set of database cross-references, sorted alphabetically
2644 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2645 from database cross references. Users with custom links
2646 will receive a <a href="webServices/urllinks.html#warning">warning
2647 dialog</a> asking them to update their preferences.
2650 <!-- JAL-2287-->Cancel button and escape listener on
2651 dialog warning user about disconnecting Jalview from a
2655 <!-- JAL-2320-->Jalview's Chimera control window closes if
2656 the Chimera it is connected to is shut down
2659 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2660 columns menu item to mark columns containing highlighted
2661 regions (e.g. from structure selections or results of a
2665 <!-- JAL-2284-->Command line option for batch-generation
2666 of HTML pages rendering alignment data with the BioJS
2676 <!-- JAL-2286 -->Columns with more than one modal residue
2677 are not coloured or thresholded according to percent
2678 identity (first observed in Jalview 2.8.2)
2681 <!-- JAL-2301 -->Threonine incorrectly reported as not
2685 <!-- JAL-2318 -->Updates to documentation pages (above PID
2686 threshold, amino acid properties)
2689 <!-- JAL-2292 -->Lower case residues in sequences are not
2690 reported as mapped to residues in a structure file in the
2694 <!--JAL-2324 -->Identical features with non-numeric scores
2695 could be added multiple times to a sequence
2698 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2699 bond features shown as two highlighted residues rather
2700 than a range in linked structure views, and treated
2701 correctly when selecting and computing trees from features
2704 <!-- JAL-2281-->Custom URL links for database
2705 cross-references are matched to database name regardless
2710 <em>Application</em>
2713 <!-- JAL-2282-->Custom URL links for specific database
2714 names without regular expressions also offer links from
2718 <!-- JAL-2315-->Removing a single configured link in the
2719 URL links pane in Connections preferences doesn't actually
2720 update Jalview configuration
2723 <!-- JAL-2272-->CTRL-Click on a selected region to open
2724 the alignment area popup menu doesn't work on El-Capitan
2727 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2728 files with similarly named sequences if dropped onto the
2732 <!-- JAL-2312 -->Additional mappings are shown for PDB
2733 entries where more chains exist in the PDB accession than
2734 are reported in the SIFTS file
2737 <!-- JAL-2317-->Certain structures do not get mapped to
2738 the structure view when displayed with Chimera
2741 <!-- JAL-2317-->No chains shown in the Chimera view
2742 panel's View->Show Chains submenu
2745 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2746 work for wrapped alignment views
2749 <!--JAL-2197 -->Rename UI components for running JPred
2750 predictions from 'JNet' to 'JPred'
2753 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2754 corrupted when annotation panel vertical scroll is not at
2755 first annotation row
2758 <!--JAL-2332 -->Attempting to view structure for Hen
2759 lysozyme results in a PDB Client error dialog box
2762 <!-- JAL-2319 -->Structure View's mapping report switched
2763 ranges for PDB and sequence for SIFTS
2766 SIFTS 'Not_Observed' residues mapped to non-existant
2770 <!-- <em>New Known Issues</em>
2777 <td width="60" nowrap>
2778 <div align="center">
2779 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2780 <em>25/10/2016</em></strong>
2783 <td><em>Application</em>
2785 <li>3D Structure chooser opens with 'Cached structures'
2786 view if structures already loaded</li>
2787 <li>Progress bar reports models as they are loaded to
2788 structure views</li>
2794 <li>Colour by conservation always enabled and no tick
2795 shown in menu when BLOSUM or PID shading applied</li>
2796 <li>FER1_ARATH and FER2_ARATH labels were switched in
2797 example sequences/projects/trees</li>
2799 <em>Application</em>
2801 <li>Jalview projects with views of local PDB structure
2802 files saved on Windows cannot be opened on OSX</li>
2803 <li>Multiple structure views can be opened and superposed
2804 without timeout for structures with multiple models or
2805 multiple sequences in alignment</li>
2806 <li>Cannot import or associated local PDB files without a
2807 PDB ID HEADER line</li>
2808 <li>RMSD is not output in Jmol console when superposition
2810 <li>Drag and drop of URL from Browser fails for Linux and
2811 OSX versions earlier than El Capitan</li>
2812 <li>ENA client ignores invalid content from ENA server</li>
2813 <li>Exceptions are not raised in console when ENA client
2814 attempts to fetch non-existent IDs via Fetch DB Refs UI
2816 <li>Exceptions are not raised in console when a new view
2817 is created on the alignment</li>
2818 <li>OSX right-click fixed for group selections: CMD-click
2819 to insert/remove gaps in groups and CTRL-click to open group
2822 <em>Build and deployment</em>
2824 <li>URL link checker now copes with multi-line anchor
2827 <em>New Known Issues</em>
2829 <li>Drag and drop from URL links in browsers do not work
2836 <td width="60" nowrap>
2837 <div align="center">
2838 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2841 <td><em>General</em>
2844 <!-- JAL-2124 -->Updated Spanish translations.
2847 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2848 for importing structure data to Jalview. Enables mmCIF and
2852 <!-- JAL-192 --->Alignment ruler shows positions relative to
2856 <!-- JAL-2202 -->Position/residue shown in status bar when
2857 mousing over sequence associated annotation
2860 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2864 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2865 '()', canonical '[]' and invalid '{}' base pair populations
2869 <!-- JAL-2092 -->Feature settings popup menu options for
2870 showing or hiding columns containing a feature
2873 <!-- JAL-1557 -->Edit selected group by double clicking on
2874 group and sequence associated annotation labels
2877 <!-- JAL-2236 -->Sequence name added to annotation label in
2878 select/hide columns by annotation and colour by annotation
2882 </ul> <em>Application</em>
2885 <!-- JAL-2050-->Automatically hide introns when opening a
2886 gene/transcript view
2889 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2893 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2894 structure mappings with the EMBL-EBI PDBe SIFTS database
2897 <!-- JAL-2079 -->Updated download sites used for Rfam and
2898 Pfam sources to xfam.org
2901 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2904 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2905 over sequences in Jalview
2908 <!-- JAL-2027-->Support for reverse-complement coding
2909 regions in ENA and EMBL
2912 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2913 for record retrieval via ENA rest API
2916 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2920 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2921 groovy script execution
2924 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2925 alignment window's Calculate menu
2928 <!-- JAL-1812 -->Allow groovy scripts that call
2929 Jalview.getAlignFrames() to run in headless mode
2932 <!-- JAL-2068 -->Support for creating new alignment
2933 calculation workers from groovy scripts
2936 <!-- JAL-1369 --->Store/restore reference sequence in
2940 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2941 associations are now saved/restored from project
2944 <!-- JAL-1993 -->Database selection dialog always shown
2945 before sequence fetcher is opened
2948 <!-- JAL-2183 -->Double click on an entry in Jalview's
2949 database chooser opens a sequence fetcher
2952 <!-- JAL-1563 -->Free-text search client for UniProt using
2953 the UniProt REST API
2956 <!-- JAL-2168 -->-nonews command line parameter to prevent
2957 the news reader opening
2960 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2961 querying stored in preferences
2964 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2968 <!-- JAL-1977-->Tooltips shown on database chooser
2971 <!-- JAL-391 -->Reverse complement function in calculate
2972 menu for nucleotide sequences
2975 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2976 and feature counts preserves alignment ordering (and
2977 debugged for complex feature sets).
2980 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2981 viewing structures with Jalview 2.10
2984 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2985 genome, transcript CCDS and gene ids via the Ensembl and
2986 Ensembl Genomes REST API
2989 <!-- JAL-2049 -->Protein sequence variant annotation
2990 computed for 'sequence_variant' annotation on CDS regions
2994 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2998 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2999 Ref Fetcher fails to match, or otherwise updates sequence
3000 data from external database records.
3003 <!-- JAL-2154 -->Revised Jalview Project format for
3004 efficient recovery of sequence coding and alignment
3005 annotation relationships.
3007 </ul> <!-- <em>Applet</em>
3018 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
3022 <!-- JAL-2018-->Export features in Jalview format (again)
3023 includes graduated colourschemes
3026 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
3027 working with big alignments and lots of hidden columns
3030 <!-- JAL-2053-->Hidden column markers not always rendered
3031 at right of alignment window
3034 <!-- JAL-2067 -->Tidied up links in help file table of
3038 <!-- JAL-2072 -->Feature based tree calculation not shown
3042 <!-- JAL-2075 -->Hidden columns ignored during feature
3043 based tree calculation
3046 <!-- JAL-2065 -->Alignment view stops updating when show
3047 unconserved enabled for group on alignment
3050 <!-- JAL-2086 -->Cannot insert gaps into sequence when
3054 <!-- JAL-2146 -->Alignment column in status incorrectly
3055 shown as "Sequence position" when mousing over
3059 <!-- JAL-2099 -->Incorrect column numbers in ruler when
3060 hidden columns present
3063 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
3064 user created annotation added to alignment
3067 <!-- JAL-1841 -->RNA Structure consensus only computed for
3068 '()' base pair annotation
3071 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
3072 in zero scores for all base pairs in RNA Structure
3076 <!-- JAL-2174-->Extend selection with columns containing
3080 <!-- JAL-2275 -->Pfam format writer puts extra space at
3081 beginning of sequence
3084 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
3088 <!-- JAL-2238 -->Cannot create groups on an alignment from
3089 from a tree when t-coffee scores are shown
3092 <!-- JAL-1836,1967 -->Cannot import and view PDB
3093 structures with chains containing negative resnums (4q4h)
3096 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
3100 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
3101 to Clustal, PIR and PileUp output
3104 <!-- JAL-2008 -->Reordering sequence features that are
3105 not visible causes alignment window to repaint
3108 <!-- JAL-2006 -->Threshold sliders don't work in
3109 graduated colour and colour by annotation row for e-value
3110 scores associated with features and annotation rows
3113 <!-- JAL-1797 -->amino acid physicochemical conservation
3114 calculation should be case independent
3117 <!-- JAL-2173 -->Remove annotation also updates hidden
3121 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
3122 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
3123 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
3126 <!-- JAL-2065 -->Null pointer exceptions and redraw
3127 problems when reference sequence defined and 'show
3128 non-conserved' enabled
3131 <!-- JAL-1306 -->Quality and Conservation are now shown on
3132 load even when Consensus calculation is disabled
3135 <!-- JAL-1932 -->Remove right on penultimate column of
3136 alignment does nothing
3139 <em>Application</em>
3142 <!-- JAL-1552-->URLs and links can't be imported by
3143 drag'n'drop on OSX when launched via webstart (note - not
3144 yet fixed for El Capitan)
3147 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
3148 output when running on non-gb/us i18n platforms
3151 <!-- JAL-1944 -->Error thrown when exporting a view with
3152 hidden sequences as flat-file alignment
3155 <!-- JAL-2030-->InstallAnywhere distribution fails when
3159 <!-- JAL-2080-->Jalview very slow to launch via webstart
3160 (also hotfix for 2.9.0b2)
3163 <!-- JAL-2085 -->Cannot save project when view has a
3164 reference sequence defined
3167 <!-- JAL-1011 -->Columns are suddenly selected in other
3168 alignments and views when revealing hidden columns
3171 <!-- JAL-1989 -->Hide columns not mirrored in complement
3172 view in a cDNA/Protein splitframe
3175 <!-- JAL-1369 -->Cannot save/restore representative
3176 sequence from project when only one sequence is
3180 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
3181 in Structure Chooser
3184 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
3185 structure consensus didn't refresh annotation panel
3188 <!-- JAL-1962 -->View mapping in structure view shows
3189 mappings between sequence and all chains in a PDB file
3192 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
3193 dialogs format columns correctly, don't display array
3194 data, sort columns according to type
3197 <!-- JAL-1975 -->Export complete shown after destination
3198 file chooser is cancelled during an image export
3201 <!-- JAL-2025 -->Error when querying PDB Service with
3202 sequence name containing special characters
3205 <!-- JAL-2024 -->Manual PDB structure querying should be
3209 <!-- JAL-2104 -->Large tooltips with broken HTML
3210 formatting don't wrap
3213 <!-- JAL-1128 -->Figures exported from wrapped view are
3214 truncated so L looks like I in consensus annotation
3217 <!-- JAL-2003 -->Export features should only export the
3218 currently displayed features for the current selection or
3222 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
3223 after fetching cross-references, and restoring from
3227 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
3228 followed in the structure viewer
3231 <!-- JAL-2163 -->Titles for individual alignments in
3232 splitframe not restored from project
3235 <!-- JAL-2145 -->missing autocalculated annotation at
3236 trailing end of protein alignment in transcript/product
3237 splitview when pad-gaps not enabled by default
3240 <!-- JAL-1797 -->amino acid physicochemical conservation
3244 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
3245 article has been read (reopened issue due to
3246 internationalisation problems)
3249 <!-- JAL-1960 -->Only offer PDB structures in structure
3250 viewer based on sequence name, PDB and UniProt
3255 <!-- JAL-1976 -->No progress bar shown during export of
3259 <!-- JAL-2213 -->Structures not always superimposed after
3260 multiple structures are shown for one or more sequences.
3263 <!-- JAL-1370 -->Reference sequence characters should not
3264 be replaced with '.' when 'Show unconserved' format option
3268 <!-- JAL-1823 -->Cannot specify chain code when entering
3269 specific PDB id for sequence
3272 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3273 'Export hidden sequences' is enabled, but 'export hidden
3274 columns' is disabled.
3277 <!--JAL-2026-->Best Quality option in structure chooser
3278 selects lowest rather than highest resolution structures
3282 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3283 to sequence mapping in 'View Mappings' report
3286 <!-- JAL-2284 -->Unable to read old Jalview projects that
3287 contain non-XML data added after Jalvew wrote project.
3290 <!-- JAL-2118 -->Newly created annotation row reorders
3291 after clicking on it to create new annotation for a
3295 <!-- JAL-1980 -->Null Pointer Exception raised when
3296 pressing Add on an orphaned cut'n'paste window.
3298 <!-- may exclude, this is an external service stability issue JAL-1941
3299 -- > RNA 3D structure not added via DSSR service</li> -->
3304 <!-- JAL-2151 -->Incorrect columns are selected when
3305 hidden columns present before start of sequence
3308 <!-- JAL-1986 -->Missing dependencies on applet pages
3312 <!-- JAL-1947 -->Overview pixel size changes when
3313 sequences are hidden in applet
3316 <!-- JAL-1996 -->Updated instructions for applet
3317 deployment on examples pages.
3324 <td width="60" nowrap>
3325 <div align="center">
3326 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3327 <em>16/10/2015</em></strong>
3330 <td><em>General</em>
3332 <li>Time stamps for signed Jalview application and applet
3337 <em>Application</em>
3339 <li>Duplicate group consensus and conservation rows
3340 shown when tree is partitioned</li>
3341 <li>Erratic behaviour when tree partitions made with
3342 multiple cDNA/Protein split views</li>
3348 <td width="60" nowrap>
3349 <div align="center">
3350 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3351 <em>8/10/2015</em></strong>
3354 <td><em>General</em>
3356 <li>Updated Spanish translations of localized text for
3358 </ul> <em>Application</em>
3360 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3361 <li>Signed OSX InstallAnywhere installer<br></li>
3362 <li>Support for per-sequence based annotations in BioJSON</li>
3363 </ul> <em>Applet</em>
3365 <li>Split frame example added to applet examples page</li>
3366 </ul> <em>Build and Deployment</em>
3369 <!-- JAL-1888 -->New ant target for running Jalview's test
3377 <li>Mapping of cDNA to protein in split frames
3378 incorrect when sequence start > 1</li>
3379 <li>Broken images in filter column by annotation dialog
3381 <li>Feature colours not parsed from features file</li>
3382 <li>Exceptions and incomplete link URLs recovered when
3383 loading a features file containing HTML tags in feature
3387 <em>Application</em>
3389 <li>Annotations corrupted after BioJS export and
3391 <li>Incorrect sequence limits after Fetch DB References
3392 with 'trim retrieved sequences'</li>
3393 <li>Incorrect warning about deleting all data when
3394 deleting selected columns</li>
3395 <li>Patch to build system for shipping properly signed
3396 JNLP templates for webstart launch</li>
3397 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3398 unreleased structures for download or viewing</li>
3399 <li>Tab/space/return keystroke operation of EMBL-PDBe
3400 fetcher/viewer dialogs works correctly</li>
3401 <li>Disabled 'minimise' button on Jalview windows
3402 running on OSX to workaround redraw hang bug</li>
3403 <li>Split cDNA/Protein view position and geometry not
3404 recovered from jalview project</li>
3405 <li>Initial enabled/disabled state of annotation menu
3406 sorter 'show autocalculated first/last' corresponds to
3408 <li>Restoring of Clustal, RNA Helices and T-Coffee
3409 color schemes from BioJSON</li>
3413 <li>Reorder sequences mirrored in cDNA/Protein split
3415 <li>Applet with Jmol examples not loading correctly</li>
3421 <td><div align="center">
3422 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3424 <td><em>General</em>
3426 <li>Linked visualisation and analysis of DNA and Protein
3429 <li>Translated cDNA alignments shown as split protein
3430 and DNA alignment views</li>
3431 <li>Codon consensus annotation for linked protein and
3432 cDNA alignment views</li>
3433 <li>Link cDNA or Protein product sequences by loading
3434 them onto Protein or cDNA alignments</li>
3435 <li>Reconstruct linked cDNA alignment from aligned
3436 protein sequences</li>
3439 <li>Jmol integration updated to Jmol v14.2.14</li>
3440 <li>Import and export of Jalview alignment views as <a
3441 href="features/bioJsonFormat.html">BioJSON</a></li>
3442 <li>New alignment annotation file statements for
3443 reference sequences and marking hidden columns</li>
3444 <li>Reference sequence based alignment shading to
3445 highlight variation</li>
3446 <li>Select or hide columns according to alignment
3448 <li>Find option for locating sequences by description</li>
3449 <li>Conserved physicochemical properties shown in amino
3450 acid conservation row</li>
3451 <li>Alignments can be sorted by number of RNA helices</li>
3452 </ul> <em>Application</em>
3454 <li>New cDNA/Protein analysis capabilities
3456 <li>Get Cross-References should open a Split Frame
3457 view with cDNA/Protein</li>
3458 <li>Detect when nucleotide sequences and protein
3459 sequences are placed in the same alignment</li>
3460 <li>Split cDNA/Protein views are saved in Jalview
3465 <li>Use REST API to talk to Chimera</li>
3466 <li>Selected regions in Chimera are highlighted in linked
3467 Jalview windows</li>
3469 <li>VARNA RNA viewer updated to v3.93</li>
3470 <li>VARNA views are saved in Jalview Projects</li>
3471 <li>Pseudoknots displayed as Jalview RNA annotation can
3472 be shown in VARNA</li>
3474 <li>Make groups for selection uses marked columns as well
3475 as the active selected region</li>
3477 <li>Calculate UPGMA and NJ trees using sequence feature
3479 <li>New Export options
3481 <li>New Export Settings dialog to control hidden
3482 region export in flat file generation</li>
3484 <li>Export alignment views for display with the <a
3485 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3487 <li>Export scrollable SVG in HTML page</li>
3488 <li>Optional embedding of BioJSON data when exporting
3489 alignment figures to HTML</li>
3491 <li>3D structure retrieval and display
3493 <li>Free text and structured queries with the PDBe
3495 <li>PDBe Search API based discovery and selection of
3496 PDB structures for a sequence set</li>
3500 <li>JPred4 employed for protein secondary structure
3502 <li>Hide Insertions menu option to hide unaligned columns
3503 for one or a group of sequences</li>
3504 <li>Automatically hide insertions in alignments imported
3505 from the JPred4 web server</li>
3506 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3507 system on OSX<br />LGPL libraries courtesy of <a
3508 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3510 <li>changed 'View nucleotide structure' submenu to 'View
3511 VARNA 2D Structure'</li>
3512 <li>change "View protein structure" menu option to "3D
3515 </ul> <em>Applet</em>
3517 <li>New layout for applet example pages</li>
3518 <li>New parameters to enable SplitFrame view
3519 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3520 <li>New example demonstrating linked viewing of cDNA and
3521 Protein alignments</li>
3522 </ul> <em>Development and deployment</em>
3524 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3525 <li>Include installation type and git revision in build
3526 properties and console log output</li>
3527 <li>Jalview Github organisation, and new github site for
3528 storing BioJsMSA Templates</li>
3529 <li>Jalview's unit tests now managed with TestNG</li>
3532 <!-- <em>General</em>
3534 </ul> --> <!-- issues resolved --> <em>Application</em>
3536 <li>Escape should close any open find dialogs</li>
3537 <li>Typo in select-by-features status report</li>
3538 <li>Consensus RNA secondary secondary structure
3539 predictions are not highlighted in amber</li>
3540 <li>Missing gap character in v2.7 example file means
3541 alignment appears unaligned when pad-gaps is not enabled</li>
3542 <li>First switch to RNA Helices colouring doesn't colour
3543 associated structure views</li>
3544 <li>ID width preference option is greyed out when auto
3545 width checkbox not enabled</li>
3546 <li>Stopped a warning dialog from being shown when
3547 creating user defined colours</li>
3548 <li>'View Mapping' in structure viewer shows sequence
3549 mappings for just that viewer's sequences</li>
3550 <li>Workaround for superposing PDB files containing
3551 multiple models in Chimera</li>
3552 <li>Report sequence position in status bar when hovering
3553 over Jmol structure</li>
3554 <li>Cannot output gaps as '.' symbols with Selection ->
3555 output to text box</li>
3556 <li>Flat file exports of alignments with hidden columns
3557 have incorrect sequence start/end</li>
3558 <li>'Aligning' a second chain to a Chimera structure from
3560 <li>Colour schemes applied to structure viewers don't
3561 work for nucleotide</li>
3562 <li>Loading/cut'n'pasting an empty or invalid file leads
3563 to a grey/invisible alignment window</li>
3564 <li>Exported Jpred annotation from a sequence region
3565 imports to different position</li>
3566 <li>Space at beginning of sequence feature tooltips shown
3567 on some platforms</li>
3568 <li>Chimera viewer 'View | Show Chain' menu is not
3570 <li>'New View' fails with a Null Pointer Exception in
3571 console if Chimera has been opened</li>
3572 <li>Mouseover to Chimera not working</li>
3573 <li>Miscellaneous ENA XML feature qualifiers not
3575 <li>NPE in annotation renderer after 'Extract Scores'</li>
3576 <li>If two structures in one Chimera window, mouseover of
3577 either sequence shows on first structure</li>
3578 <li>'Show annotations' options should not make
3579 non-positional annotations visible</li>
3580 <li>Subsequence secondary structure annotation not shown
3581 in right place after 'view flanking regions'</li>
3582 <li>File Save As type unset when current file format is
3584 <li>Save as '.jar' option removed for saving Jalview
3586 <li>Colour by Sequence colouring in Chimera more
3588 <li>Cannot 'add reference annotation' for a sequence in
3589 several views on same alignment</li>
3590 <li>Cannot show linked products for EMBL / ENA records</li>
3591 <li>Jalview's tooltip wraps long texts containing no
3593 </ul> <em>Applet</em>
3595 <li>Jmol to JalviewLite mouseover/link not working</li>
3596 <li>JalviewLite can't import sequences with ID
3597 descriptions containing angle brackets</li>
3598 </ul> <em>General</em>
3600 <li>Cannot export and reimport RNA secondary structure
3601 via jalview annotation file</li>
3602 <li>Random helix colour palette for colour by annotation
3603 with RNA secondary structure</li>
3604 <li>Mouseover to cDNA from STOP residue in protein
3605 translation doesn't work.</li>
3606 <li>hints when using the select by annotation dialog box</li>
3607 <li>Jmol alignment incorrect if PDB file has alternate CA
3609 <li>FontChooser message dialog appears to hang after
3610 choosing 1pt font</li>
3611 <li>Peptide secondary structure incorrectly imported from
3612 annotation file when annotation display text includes 'e' or
3614 <li>Cannot set colour of new feature type whilst creating
3616 <li>cDNA translation alignment should not be sequence
3617 order dependent</li>
3618 <li>'Show unconserved' doesn't work for lower case
3620 <li>Nucleotide ambiguity codes involving R not recognised</li>
3621 </ul> <em>Deployment and Documentation</em>
3623 <li>Applet example pages appear different to the rest of
3624 www.jalview.org</li>
3625 </ul> <em>Application Known issues</em>
3627 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3628 <li>Misleading message appears after trying to delete
3630 <li>Jalview icon not shown in dock after InstallAnywhere
3631 version launches</li>
3632 <li>Fetching EMBL reference for an RNA sequence results
3633 fails with a sequence mismatch</li>
3634 <li>Corrupted or unreadable alignment display when
3635 scrolling alignment to right</li>
3636 <li>ArrayIndexOutOfBoundsException thrown when remove
3637 empty columns called on alignment with ragged gapped ends</li>
3638 <li>auto calculated alignment annotation rows do not get
3639 placed above or below non-autocalculated rows</li>
3640 <li>Jalview dekstop becomes sluggish at full screen in
3641 ultra-high resolution</li>
3642 <li>Cannot disable consensus calculation independently of
3643 quality and conservation</li>
3644 <li>Mouseover highlighting between cDNA and protein can
3645 become sluggish with more than one splitframe shown</li>
3646 </ul> <em>Applet Known Issues</em>
3648 <li>Core PDB parsing code requires Jmol</li>
3649 <li>Sequence canvas panel goes white when alignment
3650 window is being resized</li>
3656 <td><div align="center">
3657 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3659 <td><em>General</em>
3661 <li>Updated Java code signing certificate donated by
3663 <li>Features and annotation preserved when performing
3664 pairwise alignment</li>
3665 <li>RNA pseudoknot annotation can be
3666 imported/exported/displayed</li>
3667 <li>'colour by annotation' can colour by RNA and
3668 protein secondary structure</li>
3669 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3670 post-hoc with 2.9 release</em>)
3673 </ul> <em>Application</em>
3675 <li>Extract and display secondary structure for sequences
3676 with 3D structures</li>
3677 <li>Support for parsing RNAML</li>
3678 <li>Annotations menu for layout
3680 <li>sort sequence annotation rows by alignment</li>
3681 <li>place sequence annotation above/below alignment
3684 <li>Output in Stockholm format</li>
3685 <li>Internationalisation: improved Spanish (es)
3687 <li>Structure viewer preferences tab</li>
3688 <li>Disorder and Secondary Structure annotation tracks
3689 shared between alignments</li>
3690 <li>UCSF Chimera launch and linked highlighting from
3692 <li>Show/hide all sequence associated annotation rows for
3693 all or current selection</li>
3694 <li>disorder and secondary structure predictions
3695 available as dataset annotation</li>
3696 <li>Per-sequence rna helices colouring</li>
3699 <li>Sequence database accessions imported when fetching
3700 alignments from Rfam</li>
3701 <li>update VARNA version to 3.91</li>
3703 <li>New groovy scripts for exporting aligned positions,
3704 conservation values, and calculating sum of pairs scores.</li>
3705 <li>Command line argument to set default JABAWS server</li>
3706 <li>include installation type in build properties and
3707 console log output</li>
3708 <li>Updated Jalview project format to preserve dataset
3712 <!-- issues resolved --> <em>Application</em>
3714 <li>Distinguish alignment and sequence associated RNA
3715 structure in structure->view->VARNA</li>
3716 <li>Raise dialog box if user deletes all sequences in an
3718 <li>Pressing F1 results in documentation opening twice</li>
3719 <li>Sequence feature tooltip is wrapped</li>
3720 <li>Double click on sequence associated annotation
3721 selects only first column</li>
3722 <li>Redundancy removal doesn't result in unlinked
3723 leaves shown in tree</li>
3724 <li>Undos after several redundancy removals don't undo
3726 <li>Hide sequence doesn't hide associated annotation</li>
3727 <li>User defined colours dialog box too big to fit on
3728 screen and buttons not visible</li>
3729 <li>author list isn't updated if already written to
3730 Jalview properties</li>
3731 <li>Popup menu won't open after retrieving sequence
3733 <li>File open window for associate PDB doesn't open</li>
3734 <li>Left-then-right click on a sequence id opens a
3735 browser search window</li>
3736 <li>Cannot open sequence feature shading/sort popup menu
3737 in feature settings dialog</li>
3738 <li>better tooltip placement for some areas of Jalview
3740 <li>Allow addition of JABAWS Server which doesn't
3741 pass validation</li>
3742 <li>Web services parameters dialog box is too large to
3744 <li>Muscle nucleotide alignment preset obscured by
3746 <li>JABAWS preset submenus don't contain newly
3747 defined user preset</li>
3748 <li>MSA web services warns user if they were launched
3749 with invalid input</li>
3750 <li>Jalview cannot contact DAS Registy when running on
3753 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3754 'Superpose with' submenu not shown when new view
3758 </ul> <!-- <em>Applet</em>
3760 </ul> <em>General</em>
3762 </ul>--> <em>Deployment and Documentation</em>
3764 <li>2G and 1G options in launchApp have no effect on
3765 memory allocation</li>
3766 <li>launchApp service doesn't automatically open
3767 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3769 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3770 InstallAnywhere reports cannot find valid JVM when Java
3771 1.7_055 is available
3773 </ul> <em>Application Known issues</em>
3776 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3777 corrupted or unreadable alignment display when scrolling
3781 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3782 retrieval fails but progress bar continues for DAS retrieval
3783 with large number of ID
3786 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3787 flatfile output of visible region has incorrect sequence
3791 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3792 rna structure consensus doesn't update when secondary
3793 structure tracks are rearranged
3796 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3797 invalid rna structure positional highlighting does not
3798 highlight position of invalid base pairs
3801 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3802 out of memory errors are not raised when saving Jalview
3803 project from alignment window file menu
3806 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3807 Switching to RNA Helices colouring doesn't propagate to
3811 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3812 colour by RNA Helices not enabled when user created
3813 annotation added to alignment
3816 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3817 Jalview icon not shown on dock in Mountain Lion/Webstart
3819 </ul> <em>Applet Known Issues</em>
3822 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3823 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3826 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3827 Jalview and Jmol example not compatible with IE9
3830 <li>Sort by annotation score doesn't reverse order
3836 <td><div align="center">
3837 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3840 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3843 <li>Internationalisation of user interface (usually
3844 called i18n support) and translation for Spanish locale</li>
3845 <li>Define/Undefine group on current selection with
3846 Ctrl-G/Shift Ctrl-G</li>
3847 <li>Improved group creation/removal options in
3848 alignment/sequence Popup menu</li>
3849 <li>Sensible precision for symbol distribution
3850 percentages shown in logo tooltip.</li>
3851 <li>Annotation panel height set according to amount of
3852 annotation when alignment first opened</li>
3853 </ul> <em>Application</em>
3855 <li>Interactive consensus RNA secondary structure
3856 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3857 <li>Select columns containing particular features from
3858 Feature Settings dialog</li>
3859 <li>View all 'representative' PDB structures for selected
3861 <li>Update Jalview project format:
3863 <li>New file extension for Jalview projects '.jvp'</li>
3864 <li>Preserve sequence and annotation dataset (to
3865 store secondary structure annotation,etc)</li>
3866 <li>Per group and alignment annotation and RNA helix
3870 <li>New similarity measures for PCA and Tree calculation
3872 <li>Experimental support for retrieval and viewing of
3873 flanking regions for an alignment</li>
3877 <!-- issues resolved --> <em>Application</em>
3879 <li>logo keeps spinning and status remains at queued or
3880 running after job is cancelled</li>
3881 <li>cannot export features from alignments imported from
3882 Jalview/VAMSAS projects</li>
3883 <li>Buggy slider for web service parameters that take
3885 <li>Newly created RNA secondary structure line doesn't
3886 have 'display all symbols' flag set</li>
3887 <li>T-COFFEE alignment score shading scheme and other
3888 annotation shading not saved in Jalview project</li>
3889 <li>Local file cannot be loaded in freshly downloaded
3891 <li>Jalview icon not shown on dock in Mountain
3893 <li>Load file from desktop file browser fails</li>
3894 <li>Occasional NPE thrown when calculating large trees</li>
3895 <li>Cannot reorder or slide sequences after dragging an
3896 alignment onto desktop</li>
3897 <li>Colour by annotation dialog throws NPE after using
3898 'extract scores' function</li>
3899 <li>Loading/cut'n'pasting an empty file leads to a grey
3900 alignment window</li>
3901 <li>Disorder thresholds rendered incorrectly after
3902 performing IUPred disorder prediction</li>
3903 <li>Multiple group annotated consensus rows shown when
3904 changing 'normalise logo' display setting</li>
3905 <li>Find shows blank dialog after 'finished searching' if
3906 nothing matches query</li>
3907 <li>Null Pointer Exceptions raised when sorting by
3908 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3910 <li>Errors in Jmol console when structures in alignment
3911 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3913 <li>Not all working JABAWS services are shown in
3915 <li>JAVAWS version of Jalview fails to launch with
3916 'invalid literal/length code'</li>
3917 <li>Annotation/RNA Helix colourschemes cannot be applied
3918 to alignment with groups (actually fixed in 2.8.0b1)</li>
3919 <li>RNA Helices and T-Coffee Scores available as default
3922 </ul> <em>Applet</em>
3924 <li>Remove group option is shown even when selection is
3926 <li>Apply to all groups ticked but colourscheme changes
3927 don't affect groups</li>
3928 <li>Documented RNA Helices and T-Coffee Scores as valid
3929 colourscheme name</li>
3930 <li>Annotation labels drawn on sequence IDs when
3931 Annotation panel is not displayed</li>
3932 <li>Increased font size for dropdown menus on OSX and
3933 embedded windows</li>
3934 </ul> <em>Other</em>
3936 <li>Consensus sequence for alignments/groups with a
3937 single sequence were not calculated</li>
3938 <li>annotation files that contain only groups imported as
3939 annotation and junk sequences</li>
3940 <li>Fasta files with sequences containing '*' incorrectly
3941 recognised as PFAM or BLC</li>
3942 <li>conservation/PID slider apply all groups option
3943 doesn't affect background (2.8.0b1)
3945 <li>redundancy highlighting is erratic at 0% and 100%</li>
3946 <li>Remove gapped columns fails for sequences with ragged
3948 <li>AMSA annotation row with leading spaces is not
3949 registered correctly on import</li>
3950 <li>Jalview crashes when selecting PCA analysis for
3951 certain alignments</li>
3952 <li>Opening the colour by annotation dialog for an
3953 existing annotation based 'use original colours'
3954 colourscheme loses original colours setting</li>
3959 <td><div align="center">
3960 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3961 <em>30/1/2014</em></strong>
3965 <li>Trusted certificates for JalviewLite applet and
3966 Jalview Desktop application<br />Certificate was donated by
3967 <a href="https://www.certum.eu">Certum</a> to the Jalview
3968 open source project).
3970 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3971 <li>Output in Stockholm format</li>
3972 <li>Allow import of data from gzipped files</li>
3973 <li>Export/import group and sequence associated line
3974 graph thresholds</li>
3975 <li>Nucleotide substitution matrix that supports RNA and
3976 ambiguity codes</li>
3977 <li>Allow disorder predictions to be made on the current
3978 selection (or visible selection) in the same way that JPred
3980 <li>Groovy scripting for headless Jalview operation</li>
3981 </ul> <em>Other improvements</em>
3983 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3984 <li>COMBINE statement uses current SEQUENCE_REF and
3985 GROUP_REF scope to group annotation rows</li>
3986 <li>Support '' style escaping of quotes in Newick
3988 <li>Group options for JABAWS service by command line name</li>
3989 <li>Empty tooltip shown for JABA service options with a
3990 link but no description</li>
3991 <li>Select primary source when selecting authority in
3992 database fetcher GUI</li>
3993 <li>Add .mfa to FASTA file extensions recognised by
3995 <li>Annotation label tooltip text wrap</li>
4000 <li>Slow scrolling when lots of annotation rows are
4002 <li>Lots of NPE (and slowness) after creating RNA
4003 secondary structure annotation line</li>
4004 <li>Sequence database accessions not imported when
4005 fetching alignments from Rfam</li>
4006 <li>Incorrect SHMR submission for sequences with
4008 <li>View all structures does not always superpose
4010 <li>Option widgets in service parameters not updated to
4011 reflect user or preset settings</li>
4012 <li>Null pointer exceptions for some services without
4013 presets or adjustable parameters</li>
4014 <li>Discover PDB IDs entry in structure menu doesn't
4015 discover PDB xRefs</li>
4016 <li>Exception encountered while trying to retrieve
4017 features with DAS</li>
4018 <li>Lowest value in annotation row isn't coloured
4019 when colour by annotation (per sequence) is coloured</li>
4020 <li>Keyboard mode P jumps to start of gapped region when
4021 residue follows a gap</li>
4022 <li>Jalview appears to hang importing an alignment with
4023 Wrap as default or after enabling Wrap</li>
4024 <li>'Right click to add annotations' message
4025 shown in wrap mode when no annotations present</li>
4026 <li>Disorder predictions fail with NPE if no automatic
4027 annotation already exists on alignment</li>
4028 <li>oninit javascript function should be called after
4029 initialisation completes</li>
4030 <li>Remove redundancy after disorder prediction corrupts
4031 alignment window display</li>
4032 <li>Example annotation file in documentation is invalid</li>
4033 <li>Grouped line graph annotation rows are not exported
4034 to annotation file</li>
4035 <li>Multi-harmony analysis cannot be run when only two
4037 <li>Cannot create multiple groups of line graphs with
4038 several 'combine' statements in annotation file</li>
4039 <li>Pressing return several times causes Number Format
4040 exceptions in keyboard mode</li>
4041 <li>Multi-harmony (SHMMR) method doesn't submit
4042 correct partitions for input data</li>
4043 <li>Translation from DNA to Amino Acids fails</li>
4044 <li>Jalview fail to load newick tree with quoted label</li>
4045 <li>--headless flag isn't understood</li>
4046 <li>ClassCastException when generating EPS in headless
4048 <li>Adjusting sequence-associated shading threshold only
4049 changes one row's threshold</li>
4050 <li>Preferences and Feature settings panel panel
4051 doesn't open</li>
4052 <li>hide consensus histogram also hides conservation and
4053 quality histograms</li>
4058 <td><div align="center">
4059 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
4061 <td><em>Application</em>
4063 <li>Support for JABAWS 2.0 Services (AACon alignment
4064 conservation, protein disorder and Clustal Omega)</li>
4065 <li>JABAWS server status indicator in Web Services
4067 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
4068 in Jalview alignment window</li>
4069 <li>Updated Jalview build and deploy framework for OSX
4070 mountain lion, windows 7, and 8</li>
4071 <li>Nucleotide substitution matrix for PCA that supports
4072 RNA and ambiguity codes</li>
4074 <li>Improved sequence database retrieval GUI</li>
4075 <li>Support fetching and database reference look up
4076 against multiple DAS sources (Fetch all from in 'fetch db
4078 <li>Jalview project improvements
4080 <li>Store and retrieve the 'belowAlignment'
4081 flag for annotation</li>
4082 <li>calcId attribute to group annotation rows on the
4084 <li>Store AACon calculation settings for a view in
4085 Jalview project</li>
4089 <li>horizontal scrolling gesture support</li>
4090 <li>Visual progress indicator when PCA calculation is
4092 <li>Simpler JABA web services menus</li>
4093 <li>visual indication that web service results are still
4094 being retrieved from server</li>
4095 <li>Serialise the dialogs that are shown when Jalview
4096 starts up for first time</li>
4097 <li>Jalview user agent string for interacting with HTTP
4099 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
4101 <li>Examples directory and Groovy library included in
4102 InstallAnywhere distribution</li>
4103 </ul> <em>Applet</em>
4105 <li>RNA alignment and secondary structure annotation
4106 visualization applet example</li>
4107 </ul> <em>General</em>
4109 <li>Normalise option for consensus sequence logo</li>
4110 <li>Reset button in PCA window to return dimensions to
4112 <li>Allow seqspace or Jalview variant of alignment PCA
4114 <li>PCA with either nucleic acid and protein substitution
4116 <li>Allow windows containing HTML reports to be exported
4118 <li>Interactive display and editing of RNA secondary
4119 structure contacts</li>
4120 <li>RNA Helix Alignment Colouring</li>
4121 <li>RNA base pair logo consensus</li>
4122 <li>Parse sequence associated secondary structure
4123 information in Stockholm files</li>
4124 <li>HTML Export database accessions and annotation
4125 information presented in tooltip for sequences</li>
4126 <li>Import secondary structure from LOCARNA clustalw
4127 style RNA alignment files</li>
4128 <li>import and visualise T-COFFEE quality scores for an
4130 <li>'colour by annotation' per sequence option to
4131 shade each sequence according to its associated alignment
4133 <li>New Jalview Logo</li>
4134 </ul> <em>Documentation and Development</em>
4136 <li>documentation for score matrices used in Jalview</li>
4137 <li>New Website!</li>
4139 <td><em>Application</em>
4141 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
4142 wsdbfetch REST service</li>
4143 <li>Stop windows being moved outside desktop on OSX</li>
4144 <li>Filetype associations not installed for webstart
4146 <li>Jalview does not always retrieve progress of a JABAWS
4147 job execution in full once it is complete</li>
4148 <li>revise SHMR RSBS definition to ensure alignment is
4149 uploaded via ali_file parameter</li>
4150 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
4151 <li>View all structures superposed fails with exception</li>
4152 <li>Jnet job queues forever if a very short sequence is
4153 submitted for prediction</li>
4154 <li>Cut and paste menu not opened when mouse clicked on
4156 <li>Putting fractional value into integer text box in
4157 alignment parameter dialog causes Jalview to hang</li>
4158 <li>Structure view highlighting doesn't work on
4160 <li>View all structures fails with exception shown in
4162 <li>Characters in filename associated with PDBEntry not
4163 escaped in a platform independent way</li>
4164 <li>Jalview desktop fails to launch with exception when
4166 <li>Tree calculation reports 'you must have 2 or more
4167 sequences selected' when selection is empty</li>
4168 <li>Jalview desktop fails to launch with jar signature
4169 failure when java web start temporary file caching is
4171 <li>DAS Sequence retrieval with range qualification
4172 results in sequence xref which includes range qualification</li>
4173 <li>Errors during processing of command line arguments
4174 cause progress bar (JAL-898) to be removed</li>
4175 <li>Replace comma for semi-colon option not disabled for
4176 DAS sources in sequence fetcher</li>
4177 <li>Cannot close news reader when JABAWS server warning
4178 dialog is shown</li>
4179 <li>Option widgets not updated to reflect user settings</li>
4180 <li>Edited sequence not submitted to web service</li>
4181 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
4182 <li>InstallAnywhere installer doesn't unpack and run
4183 on OSX Mountain Lion</li>
4184 <li>Annotation panel not given a scroll bar when
4185 sequences with alignment annotation are pasted into the
4187 <li>Sequence associated annotation rows not associated
4188 when loaded from Jalview project</li>
4189 <li>Browser launch fails with NPE on java 1.7</li>
4190 <li>JABAWS alignment marked as finished when job was
4191 cancelled or job failed due to invalid input</li>
4192 <li>NPE with v2.7 example when clicking on Tree
4193 associated with all views</li>
4194 <li>Exceptions when copy/paste sequences with grouped
4195 annotation rows to new window</li>
4196 </ul> <em>Applet</em>
4198 <li>Sequence features are momentarily displayed before
4199 they are hidden using hidefeaturegroups applet parameter</li>
4200 <li>loading features via javascript API automatically
4201 enables feature display</li>
4202 <li>scrollToColumnIn javascript API method doesn't
4204 </ul> <em>General</em>
4206 <li>Redundancy removal fails for rna alignment</li>
4207 <li>PCA calculation fails when sequence has been selected
4208 and then deselected</li>
4209 <li>PCA window shows grey box when first opened on OSX</li>
4210 <li>Letters coloured pink in sequence logo when alignment
4211 coloured with clustalx</li>
4212 <li>Choosing fonts without letter symbols defined causes
4213 exceptions and redraw errors</li>
4214 <li>Initial PCA plot view is not same as manually
4215 reconfigured view</li>
4216 <li>Grouped annotation graph label has incorrect line
4218 <li>Grouped annotation graph label display is corrupted
4219 for lots of labels</li>
4224 <div align="center">
4225 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
4228 <td><em>Application</em>
4230 <li>Jalview Desktop News Reader</li>
4231 <li>Tweaked default layout of web services menu</li>
4232 <li>View/alignment association menu to enable user to
4233 easily specify which alignment a multi-structure view takes
4234 its colours/correspondences from</li>
4235 <li>Allow properties file location to be specified as URL</li>
4236 <li>Extend Jalview project to preserve associations
4237 between many alignment views and a single Jmol display</li>
4238 <li>Store annotation row height in Jalview project file</li>
4239 <li>Annotation row column label formatting attributes
4240 stored in project file</li>
4241 <li>Annotation row order for auto-calculated annotation
4242 rows preserved in Jalview project file</li>
4243 <li>Visual progress indication when Jalview state is
4244 saved using Desktop window menu</li>
4245 <li>Visual indication that command line arguments are
4246 still being processed</li>
4247 <li>Groovy script execution from URL</li>
4248 <li>Colour by annotation default min and max colours in
4250 <li>Automatically associate PDB files dragged onto an
4251 alignment with sequences that have high similarity and
4253 <li>Update JGoogleAnalytics to latest release (0.3)</li>
4254 <li>'view structures' option to open many
4255 structures in same window</li>
4256 <li>Sort associated views menu option for tree panel</li>
4257 <li>Group all JABA and non-JABA services for a particular
4258 analysis function in its own submenu</li>
4259 </ul> <em>Applet</em>
4261 <li>Userdefined and autogenerated annotation rows for
4263 <li>Adjustment of alignment annotation pane height</li>
4264 <li>Annotation scrollbar for annotation panel</li>
4265 <li>Drag to reorder annotation rows in annotation panel</li>
4266 <li>'automaticScrolling' parameter</li>
4267 <li>Allow sequences with partial ID string matches to be
4268 annotated from GFF/Jalview features files</li>
4269 <li>Sequence logo annotation row in applet</li>
4270 <li>Absolute paths relative to host server in applet
4271 parameters are treated as such</li>
4272 <li>New in the JalviewLite javascript API:
4274 <li>JalviewLite.js javascript library</li>
4275 <li>Javascript callbacks for
4277 <li>Applet initialisation</li>
4278 <li>Sequence/alignment mouse-overs and selections</li>
4281 <li>scrollTo row and column alignment scrolling
4283 <li>Select sequence/alignment regions from javascript</li>
4284 <li>javascript structure viewer harness to pass
4285 messages between Jmol and Jalview when running as
4286 distinct applets</li>
4287 <li>sortBy method</li>
4288 <li>Set of applet and application examples shipped
4289 with documentation</li>
4290 <li>New example to demonstrate JalviewLite and Jmol
4291 javascript message exchange</li>
4293 </ul> <em>General</em>
4295 <li>Enable Jmol displays to be associated with multiple
4296 multiple alignments</li>
4297 <li>Option to automatically sort alignment with new tree</li>
4298 <li>User configurable link to enable redirects to a
4299 www.Jalview.org mirror</li>
4300 <li>Jmol colours option for Jmol displays</li>
4301 <li>Configurable newline string when writing alignment
4302 and other flat files</li>
4303 <li>Allow alignment annotation description lines to
4304 contain html tags</li>
4305 </ul> <em>Documentation and Development</em>
4307 <li>Add groovy test harness for bulk load testing to
4309 <li>Groovy script to load and align a set of sequences
4310 using a web service before displaying the result in the
4311 Jalview desktop</li>
4312 <li>Restructured javascript and applet api documentation</li>
4313 <li>Ant target to publish example html files with applet
4315 <li>Netbeans project for building Jalview from source</li>
4316 <li>ant task to create online javadoc for Jalview source</li>
4318 <td><em>Application</em>
4320 <li>User defined colourscheme throws exception when
4321 current built in colourscheme is saved as new scheme</li>
4322 <li>AlignFrame->Save in application pops up save
4323 dialog for valid filename/format</li>
4324 <li>Cannot view associated structure for UniProt sequence</li>
4325 <li>PDB file association breaks for UniProt sequence
4327 <li>Associate PDB from file dialog does not tell you
4328 which sequence is to be associated with the file</li>
4329 <li>Find All raises null pointer exception when query
4330 only matches sequence IDs</li>
4331 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4332 <li>Jalview project with Jmol views created with Jalview
4333 2.4 cannot be loaded</li>
4334 <li>Filetype associations not installed for webstart
4336 <li>Two or more chains in a single PDB file associated
4337 with sequences in different alignments do not get coloured
4338 by their associated sequence</li>
4339 <li>Visibility status of autocalculated annotation row
4340 not preserved when project is loaded</li>
4341 <li>Annotation row height and visibility attributes not
4342 stored in Jalview project</li>
4343 <li>Tree bootstraps are not preserved when saved as a
4344 Jalview project</li>
4345 <li>Envision2 workflow tooltips are corrupted</li>
4346 <li>Enabling show group conservation also enables colour
4347 by conservation</li>
4348 <li>Duplicate group associated conservation or consensus
4349 created on new view</li>
4350 <li>Annotation scrollbar not displayed after 'show
4351 all hidden annotation rows' option selected</li>
4352 <li>Alignment quality not updated after alignment
4353 annotation row is hidden then shown</li>
4354 <li>Preserve colouring of structures coloured by
4355 sequences in pre Jalview 2.7 projects</li>
4356 <li>Web service job parameter dialog is not laid out
4358 <li>Web services menu not refreshed after 'reset
4359 services' button is pressed in preferences</li>
4360 <li>Annotation off by one in Jalview v2_3 example project</li>
4361 <li>Structures imported from file and saved in project
4362 get name like jalview_pdb1234.txt when reloaded</li>
4363 <li>Jalview does not always retrieve progress of a JABAWS
4364 job execution in full once it is complete</li>
4365 </ul> <em>Applet</em>
4367 <li>Alignment height set incorrectly when lots of
4368 annotation rows are displayed</li>
4369 <li>Relative URLs in feature HTML text not resolved to
4371 <li>View follows highlighting does not work for positions
4373 <li><= shown as = in tooltip</li>
4374 <li>Export features raises exception when no features
4376 <li>Separator string used for serialising lists of IDs
4377 for javascript api is modified when separator string
4378 provided as parameter</li>
4379 <li>Null pointer exception when selecting tree leaves for
4380 alignment with no existing selection</li>
4381 <li>Relative URLs for datasources assumed to be relative
4382 to applet's codebase</li>
4383 <li>Status bar not updated after finished searching and
4384 search wraps around to first result</li>
4385 <li>StructureSelectionManager instance shared between
4386 several Jalview applets causes race conditions and memory
4388 <li>Hover tooltip and mouseover of position on structure
4389 not sent from Jmol in applet</li>
4390 <li>Certain sequences of javascript method calls to
4391 applet API fatally hang browser</li>
4392 </ul> <em>General</em>
4394 <li>View follows structure mouseover scrolls beyond
4395 position with wrapped view and hidden regions</li>
4396 <li>Find sequence position moves to wrong residue
4397 with/without hidden columns</li>
4398 <li>Sequence length given in alignment properties window
4400 <li>InvalidNumberFormat exceptions thrown when trying to
4401 import PDB like structure files</li>
4402 <li>Positional search results are only highlighted
4403 between user-supplied sequence start/end bounds</li>
4404 <li>End attribute of sequence is not validated</li>
4405 <li>Find dialog only finds first sequence containing a
4406 given sequence position</li>
4407 <li>Sequence numbering not preserved in MSF alignment
4409 <li>Jalview PDB file reader does not extract sequence
4410 from nucleotide chains correctly</li>
4411 <li>Structure colours not updated when tree partition
4412 changed in alignment</li>
4413 <li>Sequence associated secondary structure not correctly
4414 parsed in interleaved stockholm</li>
4415 <li>Colour by annotation dialog does not restore current
4417 <li>Hiding (nearly) all sequences doesn't work
4419 <li>Sequences containing lowercase letters are not
4420 properly associated with their pdb files</li>
4421 </ul> <em>Documentation and Development</em>
4423 <li>schemas/JalviewWsParamSet.xsd corrupted by
4424 ApplyCopyright tool</li>
4429 <div align="center">
4430 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4433 <td><em>Application</em>
4435 <li>New warning dialog when the Jalview Desktop cannot
4436 contact web services</li>
4437 <li>JABA service parameters for a preset are shown in
4438 service job window</li>
4439 <li>JABA Service menu entries reworded</li>
4443 <li>Modeller PIR IO broken - cannot correctly import a
4444 pir file emitted by Jalview</li>
4445 <li>Existing feature settings transferred to new
4446 alignment view created from cut'n'paste</li>
4447 <li>Improved test for mixed amino/nucleotide chains when
4448 parsing PDB files</li>
4449 <li>Consensus and conservation annotation rows
4450 occasionally become blank for all new windows</li>
4451 <li>Exception raised when right clicking above sequences
4452 in wrapped view mode</li>
4453 </ul> <em>Application</em>
4455 <li>multiple multiply aligned structure views cause cpu
4456 usage to hit 100% and computer to hang</li>
4457 <li>Web Service parameter layout breaks for long user
4458 parameter names</li>
4459 <li>Jaba service discovery hangs desktop if Jaba server
4466 <div align="center">
4467 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4470 <td><em>Application</em>
4472 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4473 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4476 <li>Web Services preference tab</li>
4477 <li>Analysis parameters dialog box and user defined
4479 <li>Improved speed and layout of Envision2 service menu</li>
4480 <li>Superpose structures using associated sequence
4482 <li>Export coordinates and projection as CSV from PCA
4484 </ul> <em>Applet</em>
4486 <li>enable javascript: execution by the applet via the
4487 link out mechanism</li>
4488 </ul> <em>Other</em>
4490 <li>Updated the Jmol Jalview interface to work with Jmol
4492 <li>The Jalview Desktop and JalviewLite applet now
4493 require Java 1.5</li>
4494 <li>Allow Jalview feature colour specification for GFF
4495 sequence annotation files</li>
4496 <li>New 'colour by label' keword in Jalview feature file
4497 type colour specification</li>
4498 <li>New Jalview Desktop Groovy API method that allows a
4499 script to check if it being run in an interactive session or
4500 in a batch operation from the Jalview command line</li>
4504 <li>clustalx colourscheme colours Ds preferentially when
4505 both D+E are present in over 50% of the column</li>
4506 </ul> <em>Application</em>
4508 <li>typo in AlignmentFrame->View->Hide->all but
4509 selected Regions menu item</li>
4510 <li>sequence fetcher replaces ',' for ';' when the ',' is
4511 part of a valid accession ID</li>
4512 <li>fatal OOM if object retrieved by sequence fetcher
4513 runs out of memory</li>
4514 <li>unhandled Out of Memory Error when viewing pca
4515 analysis results</li>
4516 <li>InstallAnywhere builds fail to launch on OS X java
4517 10.5 update 4 (due to apple Java 1.6 update)</li>
4518 <li>Installanywhere Jalview silently fails to launch</li>
4519 </ul> <em>Applet</em>
4521 <li>Jalview.getFeatureGroups() raises an
4522 ArrayIndexOutOfBoundsException if no feature groups are
4529 <div align="center">
4530 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4536 <li>Alignment prettyprinter doesn't cope with long
4538 <li>clustalx colourscheme colours Ds preferentially when
4539 both D+E are present in over 50% of the column</li>
4540 <li>nucleic acid structures retrieved from PDB do not
4541 import correctly</li>
4542 <li>More columns get selected than were clicked on when a
4543 number of columns are hidden</li>
4544 <li>annotation label popup menu not providing correct
4545 add/hide/show options when rows are hidden or none are
4547 <li>Stockholm format shown in list of readable formats,
4548 and parser copes better with alignments from RFAM.</li>
4549 <li>CSV output of consensus only includes the percentage
4550 of all symbols if sequence logo display is enabled</li>
4552 </ul> <em>Applet</em>
4554 <li>annotation panel disappears when annotation is
4556 </ul> <em>Application</em>
4558 <li>Alignment view not redrawn properly when new
4559 alignment opened where annotation panel is visible but no
4560 annotations are present on alignment</li>
4561 <li>pasted region containing hidden columns is
4562 incorrectly displayed in new alignment window</li>
4563 <li>Jalview slow to complete operations when stdout is
4564 flooded (fix is to close the Jalview console)</li>
4565 <li>typo in AlignmentFrame->View->Hide->all but
4566 selected Rregions menu item.</li>
4567 <li>inconsistent group submenu and Format submenu entry
4568 'Un' or 'Non'conserved</li>
4569 <li>Sequence feature settings are being shared by
4570 multiple distinct alignments</li>
4571 <li>group annotation not recreated when tree partition is
4573 <li>double click on group annotation to select sequences
4574 does not propagate to associated trees</li>
4575 <li>Mac OSX specific issues:
4577 <li>exception raised when mouse clicked on desktop
4578 window background</li>
4579 <li>Desktop menu placed on menu bar and application
4580 name set correctly</li>
4581 <li>sequence feature settings not wide enough for the
4582 save feature colourscheme button</li>
4591 <div align="center">
4592 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4595 <td><em>New Capabilities</em>
4597 <li>URL links generated from description line for
4598 regular-expression based URL links (applet and application)
4600 <li>Non-positional feature URL links are shown in link
4602 <li>Linked viewing of nucleic acid sequences and
4604 <li>Automatic Scrolling option in View menu to display
4605 the currently highlighted region of an alignment.</li>
4606 <li>Order an alignment by sequence length, or using the
4607 average score or total feature count for each sequence.</li>
4608 <li>Shading features by score or associated description</li>
4609 <li>Subdivide alignment and groups based on identity of
4610 selected subsequence (Make Groups from Selection).</li>
4611 <li>New hide/show options including Shift+Control+H to
4612 hide everything but the currently selected region.</li>
4613 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4614 </ul> <em>Application</em>
4616 <li>Fetch DB References capabilities and UI expanded to
4617 support retrieval from DAS sequence sources</li>
4618 <li>Local DAS Sequence sources can be added via the
4619 command line or via the Add local source dialog box.</li>
4620 <li>DAS Dbref and DbxRef feature types are parsed as
4621 database references and protein_name is parsed as
4622 description line (BioSapiens terms).</li>
4623 <li>Enable or disable non-positional feature and database
4624 references in sequence ID tooltip from View menu in
4626 <!-- <li>New hidden columns and rows and representatives capabilities
4627 in annotations file (in progress - not yet fully implemented)</li> -->
4628 <li>Group-associated consensus, sequence logos and
4629 conservation plots</li>
4630 <li>Symbol distributions for each column can be exported
4631 and visualized as sequence logos</li>
4632 <li>Optionally scale multi-character column labels to fit
4633 within each column of annotation row<!-- todo for applet -->
4635 <li>Optional automatic sort of associated alignment view
4636 when a new tree is opened.</li>
4637 <li>Jalview Java Console</li>
4638 <li>Better placement of desktop window when moving
4639 between different screens.</li>
4640 <li>New preference items for sequence ID tooltip and
4641 consensus annotation</li>
4642 <li>Client to submit sequences and IDs to Envision2
4644 <li><em>Vamsas Capabilities</em>
4646 <li>Improved VAMSAS synchronization (Jalview archive
4647 used to preserve views, structures, and tree display
4649 <li>Import of vamsas documents from disk or URL via
4651 <li>Sharing of selected regions between views and
4652 with other VAMSAS applications (Experimental feature!)</li>
4653 <li>Updated API to VAMSAS version 0.2</li>
4655 </ul> <em>Applet</em>
4657 <li>Middle button resizes annotation row height</li>
4660 <li>sortByTree (true/false) - automatically sort the
4661 associated alignment view by the tree when a new tree is
4663 <li>showTreeBootstraps (true/false) - show or hide
4664 branch bootstraps (default is to show them if available)</li>
4665 <li>showTreeDistances (true/false) - show or hide
4666 branch lengths (default is to show them if available)</li>
4667 <li>showUnlinkedTreeNodes (true/false) - indicate if
4668 unassociated nodes should be highlighted in the tree
4670 <li>heightScale and widthScale (1.0 or more) -
4671 increase the height or width of a cell in the alignment
4672 grid relative to the current font size.</li>
4675 <li>Non-positional features displayed in sequence ID
4677 </ul> <em>Other</em>
4679 <li>Features format: graduated colour definitions and
4680 specification of feature scores</li>
4681 <li>Alignment Annotations format: new keywords for group
4682 associated annotation (GROUP_REF) and annotation row display
4683 properties (ROW_PROPERTIES)</li>
4684 <li>XML formats extended to support graduated feature
4685 colourschemes, group associated annotation, and profile
4686 visualization settings.</li></td>
4689 <li>Source field in GFF files parsed as feature source
4690 rather than description</li>
4691 <li>Non-positional features are now included in sequence
4692 feature and gff files (controlled via non-positional feature
4693 visibility in tooltip).</li>
4694 <li>URL links generated for all feature links (bugfix)</li>
4695 <li>Added URL embedding instructions to features file
4697 <li>Codons containing ambiguous nucleotides translated as
4698 'X' in peptide product</li>
4699 <li>Match case switch in find dialog box works for both
4700 sequence ID and sequence string and query strings do not
4701 have to be in upper case to match case-insensitively.</li>
4702 <li>AMSA files only contain first column of
4703 multi-character column annotation labels</li>
4704 <li>Jalview Annotation File generation/parsing consistent
4705 with documentation (e.g. Stockholm annotation can be
4706 exported and re-imported)</li>
4707 <li>PDB files without embedded PDB IDs given a friendly
4709 <li>Find incrementally searches ID string matches as well
4710 as subsequence matches, and correctly reports total number
4714 <li>Better handling of exceptions during sequence
4716 <li>Dasobert generated non-positional feature URL
4717 link text excludes the start_end suffix</li>
4718 <li>DAS feature and source retrieval buttons disabled
4719 when fetch or registry operations in progress.</li>
4720 <li>PDB files retrieved from URLs are cached properly</li>
4721 <li>Sequence description lines properly shared via
4723 <li>Sequence fetcher fetches multiple records for all
4725 <li>Ensured that command line das feature retrieval
4726 completes before alignment figures are generated.</li>
4727 <li>Reduced time taken when opening file browser for
4729 <li>isAligned check prior to calculating tree, PCA or
4730 submitting an MSA to JNet now excludes hidden sequences.</li>
4731 <li>User defined group colours properly recovered
4732 from Jalview projects.</li>
4741 <div align="center">
4742 <strong>2.4.0.b2</strong><br> 28/10/2009
4747 <li>Experimental support for google analytics usage
4749 <li>Jalview privacy settings (user preferences and docs).</li>
4754 <li>Race condition in applet preventing startup in
4756 <li>Exception when feature created from selection beyond
4757 length of sequence.</li>
4758 <li>Allow synthetic PDB files to be imported gracefully</li>
4759 <li>Sequence associated annotation rows associate with
4760 all sequences with a given id</li>
4761 <li>Find function matches case-insensitively for sequence
4762 ID string searches</li>
4763 <li>Non-standard characters do not cause pairwise
4764 alignment to fail with exception</li>
4765 </ul> <em>Application Issues</em>
4767 <li>Sequences are now validated against EMBL database</li>
4768 <li>Sequence fetcher fetches multiple records for all
4770 </ul> <em>InstallAnywhere Issues</em>
4772 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4773 issue with installAnywhere mechanism)</li>
4774 <li>Command line launching of JARs from InstallAnywhere
4775 version (java class versioning error fixed)</li>
4782 <div align="center">
4783 <strong>2.4</strong><br> 27/8/2008
4786 <td><em>User Interface</em>
4788 <li>Linked highlighting of codon and amino acid from
4789 translation and protein products</li>
4790 <li>Linked highlighting of structure associated with
4791 residue mapping to codon position</li>
4792 <li>Sequence Fetcher provides example accession numbers
4793 and 'clear' button</li>
4794 <li>MemoryMonitor added as an option under Desktop's
4796 <li>Extract score function to parse whitespace separated
4797 numeric data in description line</li>
4798 <li>Column labels in alignment annotation can be centred.</li>
4799 <li>Tooltip for sequence associated annotation give name
4801 </ul> <em>Web Services and URL fetching</em>
4803 <li>JPred3 web service</li>
4804 <li>Prototype sequence search client (no public services
4806 <li>Fetch either seed alignment or full alignment from
4808 <li>URL Links created for matching database cross
4809 references as well as sequence ID</li>
4810 <li>URL Links can be created using regular-expressions</li>
4811 </ul> <em>Sequence Database Connectivity</em>
4813 <li>Retrieval of cross-referenced sequences from other
4815 <li>Generalised database reference retrieval and
4816 validation to all fetchable databases</li>
4817 <li>Fetch sequences from DAS sources supporting the
4818 sequence command</li>
4819 </ul> <em>Import and Export</em>
4820 <li>export annotation rows as CSV for spreadsheet import</li>
4821 <li>Jalview projects record alignment dataset associations,
4822 EMBL products, and cDNA sequence mappings</li>
4823 <li>Sequence Group colour can be specified in Annotation
4825 <li>Ad-hoc colouring of group in Annotation File using RGB
4826 triplet as name of colourscheme</li>
4827 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4829 <li>treenode binding for VAMSAS tree exchange</li>
4830 <li>local editing and update of sequences in VAMSAS
4831 alignments (experimental)</li>
4832 <li>Create new or select existing session to join</li>
4833 <li>load and save of vamsas documents</li>
4834 </ul> <em>Application command line</em>
4836 <li>-tree parameter to open trees (introduced for passing
4838 <li>-fetchfrom command line argument to specify nicknames
4839 of DAS servers to query for alignment features</li>
4840 <li>-dasserver command line argument to add new servers
4841 that are also automatically queried for features</li>
4842 <li>-groovy command line argument executes a given groovy
4843 script after all input data has been loaded and parsed</li>
4844 </ul> <em>Applet-Application data exchange</em>
4846 <li>Trees passed as applet parameters can be passed to
4847 application (when using "View in full
4848 application")</li>
4849 </ul> <em>Applet Parameters</em>
4851 <li>feature group display control parameter</li>
4852 <li>debug parameter</li>
4853 <li>showbutton parameter</li>
4854 </ul> <em>Applet API methods</em>
4856 <li>newView public method</li>
4857 <li>Window (current view) specific get/set public methods</li>
4858 <li>Feature display control methods</li>
4859 <li>get list of currently selected sequences</li>
4860 </ul> <em>New Jalview distribution features</em>
4862 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4863 <li>RELEASE file gives build properties for the latest
4864 Jalview release.</li>
4865 <li>Java 1.1 Applet build made easier and donotobfuscate
4866 property controls execution of obfuscator</li>
4867 <li>Build target for generating source distribution</li>
4868 <li>Debug flag for javacc</li>
4869 <li>.jalview_properties file is documented (slightly) in
4870 jalview.bin.Cache</li>
4871 <li>Continuous Build Integration for stable and
4872 development version of Application, Applet and source
4877 <li>selected region output includes visible annotations
4878 (for certain formats)</li>
4879 <li>edit label/displaychar contains existing label/char
4881 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4882 <li>shorter peptide product names from EMBL records</li>
4883 <li>Newick string generator makes compact representations</li>
4884 <li>bootstrap values parsed correctly for tree files with
4886 <li>pathological filechooser bug avoided by not allowing
4887 filenames containing a ':'</li>
4888 <li>Fixed exception when parsing GFF files containing
4889 global sequence features</li>
4890 <li>Alignment datasets are finalized only when number of
4891 references from alignment sequences goes to zero</li>
4892 <li>Close of tree branch colour box without colour
4893 selection causes cascading exceptions</li>
4894 <li>occasional negative imgwidth exceptions</li>
4895 <li>better reporting of non-fatal warnings to user when
4896 file parsing fails.</li>
4897 <li>Save works when Jalview project is default format</li>
4898 <li>Save as dialog opened if current alignment format is
4899 not a valid output format</li>
4900 <li>UniProt canonical names introduced for both das and
4902 <li>Histidine should be midblue (not pink!) in Zappo</li>
4903 <li>error messages passed up and output when data read
4905 <li>edit undo recovers previous dataset sequence when
4906 sequence is edited</li>
4907 <li>allow PDB files without pdb ID HEADER lines (like
4908 those generated by MODELLER) to be read in properly</li>
4909 <li>allow reading of JPred concise files as a normal
4911 <li>Stockholm annotation parsing and alignment properties
4912 import fixed for PFAM records</li>
4913 <li>Structure view windows have correct name in Desktop
4915 <li>annotation consisting of sequence associated scores
4916 can be read and written correctly to annotation file</li>
4917 <li>Aligned cDNA translation to aligned peptide works
4919 <li>Fixed display of hidden sequence markers and
4920 non-italic font for representatives in Applet</li>
4921 <li>Applet Menus are always embedded in applet window on
4923 <li>Newly shown features appear at top of stack (in
4925 <li>Annotations added via parameter not drawn properly
4926 due to null pointer exceptions</li>
4927 <li>Secondary structure lines are drawn starting from
4928 first column of alignment</li>
4929 <li>UniProt XML import updated for new schema release in
4931 <li>Sequence feature to sequence ID match for Features
4932 file is case-insensitive</li>
4933 <li>Sequence features read from Features file appended to
4934 all sequences with matching IDs</li>
4935 <li>PDB structure coloured correctly for associated views
4936 containing a sub-sequence</li>
4937 <li>PDB files can be retrieved by applet from Jar files</li>
4938 <li>feature and annotation file applet parameters
4939 referring to different directories are retrieved correctly</li>
4940 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4941 <li>Fixed application hang whilst waiting for
4942 splash-screen version check to complete</li>
4943 <li>Applet properly URLencodes input parameter values
4944 when passing them to the launchApp service</li>
4945 <li>display name and local features preserved in results
4946 retrieved from web service</li>
4947 <li>Visual delay indication for sequence retrieval and
4948 sequence fetcher initialisation</li>
4949 <li>updated Application to use DAS 1.53e version of
4950 dasobert DAS client</li>
4951 <li>Re-instated Full AMSA support and .amsa file
4953 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4961 <div align="center">
4962 <strong>2.3</strong><br> 9/5/07
4967 <li>Jmol 11.0.2 integration</li>
4968 <li>PDB views stored in Jalview XML files</li>
4969 <li>Slide sequences</li>
4970 <li>Edit sequence in place</li>
4971 <li>EMBL CDS features</li>
4972 <li>DAS Feature mapping</li>
4973 <li>Feature ordering</li>
4974 <li>Alignment Properties</li>
4975 <li>Annotation Scores</li>
4976 <li>Sort by scores</li>
4977 <li>Feature/annotation editing in applet</li>
4982 <li>Headless state operation in 2.2.1</li>
4983 <li>Incorrect and unstable DNA pairwise alignment</li>
4984 <li>Cut and paste of sequences with annotation</li>
4985 <li>Feature group display state in XML</li>
4986 <li>Feature ordering in XML</li>
4987 <li>blc file iteration selection using filename # suffix</li>
4988 <li>Stockholm alignment properties</li>
4989 <li>Stockhom alignment secondary structure annotation</li>
4990 <li>2.2.1 applet had no feature transparency</li>
4991 <li>Number pad keys can be used in cursor mode</li>
4992 <li>Structure Viewer mirror image resolved</li>
4999 <div align="center">
5000 <strong>2.2.1</strong><br> 12/2/07
5005 <li>Non standard characters can be read and displayed
5006 <li>Annotations/Features can be imported/exported to the
5008 <li>Applet allows editing of sequence/annotation/group
5009 name & description
5010 <li>Preference setting to display sequence name in
5012 <li>Annotation file format extended to allow
5013 Sequence_groups to be defined
5014 <li>Default opening of alignment overview panel can be
5015 specified in preferences
5016 <li>PDB residue numbering annotation added to associated
5022 <li>Applet crash under certain Linux OS with Java 1.6
5024 <li>Annotation file export / import bugs fixed
5025 <li>PNG / EPS image output bugs fixed
5031 <div align="center">
5032 <strong>2.2</strong><br> 27/11/06
5037 <li>Multiple views on alignment
5038 <li>Sequence feature editing
5039 <li>"Reload" alignment
5040 <li>"Save" to current filename
5041 <li>Background dependent text colour
5042 <li>Right align sequence ids
5043 <li>User-defined lower case residue colours
5046 <li>Menu item accelerator keys
5047 <li>Control-V pastes to current alignment
5048 <li>Cancel button for DAS Feature Fetching
5049 <li>PCA and PDB Viewers zoom via mouse roller
5050 <li>User-defined sub-tree colours and sub-tree selection
5052 <li>'New Window' button on the 'Output to Text box'
5057 <li>New memory efficient Undo/Redo System
5058 <li>Optimised symbol lookups and conservation/consensus
5060 <li>Region Conservation/Consensus recalculated after
5062 <li>Fixed Remove Empty Columns Bug (empty columns at end
5064 <li>Slowed DAS Feature Fetching for increased robustness.
5066 <li>Made angle brackets in ASCII feature descriptions
5068 <li>Re-instated Zoom function for PCA
5069 <li>Sequence descriptions conserved in web service
5071 <li>UniProt ID discoverer uses any word separated by
5073 <li>WsDbFetch query/result association resolved
5074 <li>Tree leaf to sequence mapping improved
5075 <li>Smooth fonts switch moved to FontChooser dialog box.
5082 <div align="center">
5083 <strong>2.1.1</strong><br> 12/9/06
5088 <li>Copy consensus sequence to clipboard</li>
5093 <li>Image output - rightmost residues are rendered if
5094 sequence id panel has been resized</li>
5095 <li>Image output - all offscreen group boundaries are
5097 <li>Annotation files with sequence references - all
5098 elements in file are relative to sequence position</li>
5099 <li>Mac Applet users can use Alt key for group editing</li>
5105 <div align="center">
5106 <strong>2.1</strong><br> 22/8/06
5111 <li>MAFFT Multiple Alignment in default Web Service list</li>
5112 <li>DAS Feature fetching</li>
5113 <li>Hide sequences and columns</li>
5114 <li>Export Annotations and Features</li>
5115 <li>GFF file reading / writing</li>
5116 <li>Associate structures with sequences from local PDB
5118 <li>Add sequences to exisiting alignment</li>
5119 <li>Recently opened files / URL lists</li>
5120 <li>Applet can launch the full application</li>
5121 <li>Applet has transparency for features (Java 1.2
5123 <li>Applet has user defined colours parameter</li>
5124 <li>Applet can load sequences from parameter
5125 "sequence<em>x</em>"
5131 <li>Redundancy Panel reinstalled in the Applet</li>
5132 <li>Monospaced font - EPS / rescaling bug fixed</li>
5133 <li>Annotation files with sequence references bug fixed</li>
5139 <div align="center">
5140 <strong>2.08.1</strong><br> 2/5/06
5145 <li>Change case of selected region from Popup menu</li>
5146 <li>Choose to match case when searching</li>
5147 <li>Middle mouse button and mouse movement can compress /
5148 expand the visible width and height of the alignment</li>
5153 <li>Annotation Panel displays complete JNet results</li>
5159 <div align="center">
5160 <strong>2.08b</strong><br> 18/4/06
5166 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
5167 <li>Righthand label on wrapped alignments shows correct
5174 <div align="center">
5175 <strong>2.08</strong><br> 10/4/06
5180 <li>Editing can be locked to the selection area</li>
5181 <li>Keyboard editing</li>
5182 <li>Create sequence features from searches</li>
5183 <li>Precalculated annotations can be loaded onto
5185 <li>Features file allows grouping of features</li>
5186 <li>Annotation Colouring scheme added</li>
5187 <li>Smooth fonts off by default - Faster rendering</li>
5188 <li>Choose to toggle Autocalculate Consensus On/Off</li>
5193 <li>Drag & Drop fixed on Linux</li>
5194 <li>Jalview Archive file faster to load/save, sequence
5195 descriptions saved.</li>
5201 <div align="center">
5202 <strong>2.07</strong><br> 12/12/05
5207 <li>PDB Structure Viewer enhanced</li>
5208 <li>Sequence Feature retrieval and display enhanced</li>
5209 <li>Choose to output sequence start-end after sequence
5210 name for file output</li>
5211 <li>Sequence Fetcher WSDBFetch@EBI</li>
5212 <li>Applet can read feature files, PDB files and can be
5213 used for HTML form input</li>
5218 <li>HTML output writes groups and features</li>
5219 <li>Group editing is Control and mouse click</li>
5220 <li>File IO bugs</li>
5226 <div align="center">
5227 <strong>2.06</strong><br> 28/9/05
5232 <li>View annotations in wrapped mode</li>
5233 <li>More options for PCA viewer</li>
5238 <li>GUI bugs resolved</li>
5239 <li>Runs with -nodisplay from command line</li>
5245 <div align="center">
5246 <strong>2.05b</strong><br> 15/9/05
5251 <li>Choose EPS export as lineart or text</li>
5252 <li>Jar files are executable</li>
5253 <li>Can read in Uracil - maps to unknown residue</li>
5258 <li>Known OutOfMemory errors give warning message</li>
5259 <li>Overview window calculated more efficiently</li>
5260 <li>Several GUI bugs resolved</li>
5266 <div align="center">
5267 <strong>2.05</strong><br> 30/8/05
5272 <li>Edit and annotate in "Wrapped" view</li>
5277 <li>Several GUI bugs resolved</li>
5283 <div align="center">
5284 <strong>2.04</strong><br> 24/8/05
5289 <li>Hold down mouse wheel & scroll to change font
5295 <li>Improved JPred client reliability</li>
5296 <li>Improved loading of Jalview files</li>
5302 <div align="center">
5303 <strong>2.03</strong><br> 18/8/05
5308 <li>Set Proxy server name and port in preferences</li>
5309 <li>Multiple URL links from sequence ids</li>
5310 <li>User Defined Colours can have a scheme name and added
5312 <li>Choose to ignore gaps in consensus calculation</li>
5313 <li>Unix users can set default web browser</li>
5314 <li>Runs without GUI for batch processing</li>
5315 <li>Dynamically generated Web Service Menus</li>
5320 <li>InstallAnywhere download for Sparc Solaris</li>
5326 <div align="center">
5327 <strong>2.02</strong><br> 18/7/05
5333 <li>Copy & Paste order of sequences maintains
5334 alignment order.</li>
5340 <div align="center">
5341 <strong>2.01</strong><br> 12/7/05
5346 <li>Use delete key for deleting selection.</li>
5347 <li>Use Mouse wheel to scroll sequences.</li>
5348 <li>Help file updated to describe how to add alignment
5350 <li>Version and build date written to build properties
5352 <li>InstallAnywhere installation will check for updates
5353 at launch of Jalview.</li>
5358 <li>Delete gaps bug fixed.</li>
5359 <li>FileChooser sorts columns.</li>
5360 <li>Can remove groups one by one.</li>
5361 <li>Filechooser icons installed.</li>
5362 <li>Finder ignores return character when searching.
5363 Return key will initiate a search.<br>
5370 <div align="center">
5371 <strong>2.0</strong><br> 20/6/05
5376 <li>New codebase</li>