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>
130 <li>First integrated JalviewJS and Jalview release</li>
131 <li>Updated building instructions</li>
133 <!-- JAL-3679 -->Improved JalviewJS/Jalview build process
134 for system package provided eclipse installs on linux
136 <li>Install4j 9.0.x used for installer packaging</li>
137 <li>Notarized MacOS installer for compatibility with Big
138 Sur and Monterey</li>
140 <!-- JAL-3805 -->Uninstaller application for old
141 (InstallAnywhere based) Jalview installations removed from
145 <!-- JAL-3930 -->Improved use of installers for unattended
146 installation with a customizedId of "JALVIEW" in install4j's
156 <!-- JAL-3674 -->Slow structure commands can block Jalview
160 <!-- JAL-3904 -->Structure window's viewer-specific menu
161 disappears when only one structure is shown (and many
162 sequences:one chain mappings are present)
165 <!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
166 the first SEQUENCE_GROUP defined
171 <!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 -->Selections not
172 propagated between Linked CDS - Protein alignments and their
173 trees (known defect from 2.11.1.3)
176 <!-- JAL-3761 -->Not all codon positions highlighted for
177 overlapping exon splice sites (e.g due to RNA slippage)
180 <!-- JAL-3794 -->X was not being recognised as the unknown base
184 <!-- JAL-3915 -->Removed RNAview checkbox and logic from
185 Structure Preferences
188 <!-- JAL-3583 -->Tooltip behaviour improved (slightly)
191 <!-- JAL-3162 -->Can edit a feature so that start > end
194 <!-- JAL-2848 -->Cancel from Amend Features doesn't reset a
195 modified graduated colour
198 <!-- JAL-3788 -->New View with automatic 'Show Overview'
199 preference enabled results in Null Pointer Exceptions when
200 clustal colouring is enabled
202 <li><!-- JAL-3275 -->Can open multiple Preferences panels</li>
204 <!-- JAL-3949 -->Standard out logging broken: messages only
205 routing to stderr and appear as a raw template
207 </ul> <em>JalviewJS</em>
225 <!-- JAL-3762 -->JalviewJS doesn't honour arguments passed
226 via Info.args when there are arguments on the URL
229 <!-- JAL-3602 -->gradle closure-compiler not using UTF-8
232 <!-- JAL-3603 -->Annotation file fails to load from URL in
235 </ul> <em>Development</em>
239 <li>Fixed non-fatal gradle errors during build</li>
241 <!-- JAL-3745 -->Updated build.gradle for use with
251 <td width="60" align="center" nowrap><strong><a
252 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.7">.7</a><br />
253 <em>18/01/2022</em></strong></td>
255 <td align="left" valign="top">
258 <!-- JAL-3703, JAL-3935 -->Files open in Jalview cannot be
259 updated by Jalview or other applications (Windows, other non
262 </ul> <em>Security</em>
265 <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
271 <td width="60" align="center" nowrap><strong><a
272 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
273 <em>6/01/2022</em></strong></td>
275 <td align="left" valign="top"><em>Security</em>
278 <!-- JAL-3934 -->Version bump library dependency: Log4j 2.16.0 to 2.17.0.
285 <td width="60" align="center" nowrap><strong><a
286 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
287 <em>20/12/2021</em></strong></td>
289 <td align="left" valign="top"><em>Security</em>
292 <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
294 </ul> <em>Development</em>
296 <li>Updated building instructions</li>
301 <!-- JAL-3840 -->Occupancy calculation is incorrect for
302 alignment columns with over -1+2^32 gaps (breaking filtering
306 <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
307 scale factors being set with buggy window-managers (linux
310 </ul> <em>Development</em>
312 <li>Fixed non-fatal gradle errors during build</li>
317 <td width="60" align="center" nowrap><strong><a
318 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
319 <em>09/03/2021</em></strong></td>
320 <td align="left" valign="top"><em>Improved control of
321 Jalview's use of network services via jalview_properties</em>
324 <!-- JAL-3814 -->New .jalview_properties token controlling
325 launch of the news browser (like -nonews argument)
328 <!-- JAL-3813 -->New .jalview_properties token controlling
329 download of linkout URLs from
330 www.jalview.org/services/identifiers
333 <!-- JAL-3812 -->New .jalview_properties token controlling
334 download of BIOJSHTML templates
337 <!-- JAL-3811 -->New 'Discover Web Services' option to
338 trigger a one off JABAWS discovery if autodiscovery was
342 <td align="left" valign="top">
345 <!-- JAL-3818 -->Intermittent deadlock opening structure in
348 </ul> <em>New Known defects</em>
351 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
352 always restored from project (since 2.10.3)
355 <!-- JAL-3806 -->Selections from tree built from CDS aren't
356 propagated to Protein alignment (since 2.11.1.3)
362 <td width="60" align="center" nowrap><strong><a
363 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
364 <em>29/10/2020</em></strong></td>
365 <td align="left" valign="top">
370 <td align="left" valign="top">
373 <!-- JAL-3765 -->Find doesn't always highlight all matching
374 positions in a sequence (bug introduced in 2.11.1.2)
377 <!-- JAL-3760 -->Alignments containing one or more protein
378 sequences can be classed as nucleotide
381 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
382 sequences after alignment of protein products (known defect
383 first reported for 2.11.1.0)
386 <!-- JAL-3725 -->No tooltip or popup menu for genomic
387 features outwith CDS shown overlaid on protein
390 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
391 correctly mapped by Jalview (e.g. affects viral CDS with
392 ribosomal slippage, since 2.9.0)
395 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
399 <!-- JAL-3700 -->Selections in CDS sequence panel don't
400 always select corresponding protein sequences
403 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
404 column selection doesn't always ignore hidden columns
406 </ul> <em>Installer</em>
409 <!-- JAL-3611 -->Space character in Jalview install path on
410 Windows prevents install4j launching getdown
412 </ul> <em>Development</em>
415 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
416 version numbers in doc/building.md
422 <td width="60" align="center" nowrap><strong><a
423 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
424 <em>25/09/2020</em></strong></td>
425 <td align="left" valign="top">
429 <td align="left" valign="top">
432 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
433 "Encountered problems opening
434 https://www.jalview.org/examples/exampleFile_2_7.jvp"
440 <td width="60" align="center" nowrap><strong><a
441 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
442 <em>17/09/2020</em></strong></td>
443 <td align="left" valign="top">
446 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
447 residue in cursor mode
450 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
451 HTSJDK from 2.12 to 2.23
454 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
455 optimisations and improvements suggested by Bob Hanson and
456 improved compatibility with JalviewJS
459 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
460 alignments from Pfam and Rfam
463 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
464 import (no longer based on .gz extension)
467 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
470 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
471 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
475 <!-- JAL-3667 -->Improved warning messages, debug logging
476 and fixed Retry action when Jalview encounters errors when
477 saving or making backup files.
480 <!-- JAL-3676 -->Enhanced Jalview Java Console:
482 <li>Jalview's logging level can be configured</li>
483 <li>Copy to Clipboard Buttion</li>
487 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
488 when running on Linux (Requires Java 11+)
490 </ul> <em>Launching Jalview</em>
493 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
494 through a system property
497 <!-- JAL-3477 -->Improved built-in documentation and command
498 line help for configuring Jalview's memory
502 <td align="left" valign="top">
505 <!-- JAL-3691 -->Conservation and Quality tracks are shown
506 but not calculated and no protein or DNA score models are
507 available for tree/PCA calculation when launched with
508 Turkish language locale
511 <!-- JAL-3493 -->Escape does not clear highlights on the
512 alignment (Since Jalview 2.10.3)
515 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
516 doesn't slide selected sequences, just sequence under cursor
519 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
520 sequence under the cursor
523 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
524 multiple EMBL gene products shown for a single contig
527 <!-- JAL-3696 -->Errors encountered when processing variants
528 from VCF files yield "Error processing VCF: Format specifier
532 <!-- JAL-3697 -->Count of features not shown can be wrong
533 when there are both local and complementary features mapped
534 to the position under the cursor
537 <!-- JAL-3673 -->Sequence ID for reference sequence is
538 clipped when Right align Sequence IDs enabled
541 <!-- JAL-2983 -->Slider with negative range values not
542 rendered correctly in VAqua4 (Since 2.10.4)
545 <!-- JAL-3685 -->Single quotes not displayed correctly in
546 internationalised text for some messages and log output
549 <!-- JAL-3490 -->Find doesn't report matches that span
550 hidden gapped columns
553 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
554 panels, Alignment viewport and annotation renderer.
557 <!-- JAL-3561 -->Jalview ignores file format parameter
558 specifying output format when exporting an alignment via the
562 <!-- JAL-3667 -->Windows 10: For a minority of users, if
563 backups are not enabled, Jalview sometimes fails to
564 overwrite an existing file and raises a warning dialog. (in
565 2.11.0, and 2.11.1.0, the workaround is to try to save the
566 file again, and if that fails, delete the original file and
570 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
574 <!-- JAL-3741 -->References to http://www.jalview.org in
575 program and documentation
577 </ul> <em>Launching Jalview</em>
580 <!-- JAL-3718 -->Jalview application fails when launched the
581 first time for a version that has different jars to the
582 previous launched version.
584 </ul> <em>Developing Jalview</em>
587 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
588 data, causing cloverReport gradle task to fail with an
592 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
593 monitor the release channel
595 </ul> <em>New Known defects</em>
598 <!-- JAL-3748 -->CDS shown in result of submitting proteins
599 in a CDS/Protein alignment to a web service is wrong when
600 proteins share a common transcript sequence (e.g.
601 genome of RNA viruses)
604 <!-- JAL-3576 -->Co-located features exported and re-imported
605 are ordered differently when shown on alignment and in
606 tooltips. (Also affects v2.11.1.0)
609 <!-- JAL-3702 -->Drag and drop of alignment file onto
610 alignment window when in a HiDPI scaled mode in Linux only
611 works for the top left quadrant of the alignment window
614 <!-- JAL-3701 -->Stale build data in jalview standalone jar
615 builds (only affects 2.11.1.1 branch)
618 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
619 when alignment view restored from project (since Jalview 2.11.0)
622 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
623 protein products for certain ENA records are repeatedly
624 shown via Calculate->Show Cross Refs
630 <td width="60" align="center" nowrap><strong><a
631 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
632 <em>22/04/2020</em></strong></td>
633 <td align="left" valign="top">
636 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
637 'virtual' codon features shown on protein (or vice versa)
638 for display in alignments, on structure views (including
639 transfer to UCSF chimera), in feature reports and for
643 <!-- JAL-3121 -->Feature attributes from VCF files can be
644 exported and re-imported as GFF3 files
647 <!-- JAL-3376 -->Capture VCF "fixed column" values
648 POS, ID, QUAL, FILTER as Feature Attributes
651 <!-- JAL-3375 -->More robust VCF numeric data field
652 validation while parsing
655 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
659 <!-- JAL-3535 -->Feature Settings dialog title includes name
663 <!-- JAL-3538 -->Font anti-aliasing in alignment views
667 <!-- JAL-3468 -->Very long feature descriptions truncated in
671 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
672 with no feature types visible
675 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
677 </ul><em>Jalview Installer</em>
680 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
681 in console (may be null when Jalview launched as executable jar or via conda)
684 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
687 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
690 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
692 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
693 </ul> <em>Release processes</em>
696 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
699 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
701 </ul> <em>Build System</em>
704 <!-- JAL-3510 -->Clover updated to 4.4.1
707 <!-- JAL-3513 -->Test code included in Clover coverage
711 <em>Groovy Scripts</em>
714 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
715 to stdout containing the consensus sequence for each
716 alignment in a Jalview session
719 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
720 genomic sequence_variant annotation from CDS as
721 missense_variant or synonymous_variant on protein products.
725 <td align="left" valign="top">
728 <!-- JAL-3581 -->Hidden sequence markers still visible when
729 'Show hidden markers' option is not ticked
732 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
733 PNG output when 'Automatically set ID width' is set in
734 jalview preferences or properties file
737 <!-- JAL-3571 -->Feature Editor dialog can be opened when
738 'Show Sequence Features' option is not ticked
741 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
742 buttons in Feature Settings dialog are clicked when no
746 <!-- JAL-3412 -->ID margins for CDS and Protein views not
747 equal when split frame is first opened
750 <!-- JAL-3296 -->Sequence position numbers in status bar not
751 correct after editing a sequence's start position
754 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
755 with annotation and exceptions thrown when only a few
756 columns shown in wrapped mode
759 <!-- JAL-3386 -->Sequence IDs missing in headless export of
760 wrapped alignment figure with annotations
763 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
764 ID fails with ClassCastException
767 <!-- JAL-3389 -->Chimera session not restored from Jalview
771 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
772 feature settings dialog also selects columns
775 <!-- JAL-3473 -->SpinnerNumberModel causes
776 IllegalArgumentException in some circumstances
779 <!-- JAL-3534 -->Multiple feature settings dialogs can be
783 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
784 alignment window is closed
787 <!-- JAL-3406 -->Credits missing some authors in Jalview
788 help documentation for 2.11.0 release
791 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
792 includes Pfam ID as sequence's accession rather than its
795 </ul> <em>Java 11 Compatibility issues</em>
798 <!-- JAL-2987 -->OSX - Can't view some search results in
799 PDB/Uniprot search panel
801 </ul> <em>Installer</em>
804 <!-- JAL-3447 -->Jalview should not create file associations
805 for 3D structure files (.pdb, .mmcif. .cif)
807 </ul> <em>Repository and Source Release</em>
810 <!-- JAL-3474 -->removed obsolete .cvsignore files from
814 <!-- JAL-3541 -->Clover report generation running out of
817 </ul> <em>New Known Issues</em>
820 <!-- JAL-3523 -->OSX - Current working directory not
821 preserved when Jalview.app launched with parameters from
825 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
826 clipped in headless figure export when Right Align option
830 <!-- JAL-3542 -->Jalview Installation type always reports
831 'Source' in console output
834 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
835 bamboo server but run fine locally.
841 <td width="60" align="center" nowrap>
842 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
843 <em>04/07/2019</em></strong>
845 <td align="left" valign="top">
848 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
849 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
850 source project) rather than InstallAnywhere
853 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
854 settings, receive over the air updates and launch specific
855 versions via (<a href="https://github.com/threerings/getdown">Three
859 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
860 formats supported by Jalview (including .jvp project files)
863 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
864 arguments and switch between different getdown channels
867 <!-- JAL-3141 -->Backup files created when saving Jalview project
872 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
873 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
875 <!-- JAL-2620 -->Alternative genetic code tables for
876 'Translate as cDNA'</li>
878 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
879 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
882 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
883 implementation that allows updates) used for Sequence Feature collections</li>
885 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
886 features can be filtered and shaded according to any
887 associated attributes (e.g. variant attributes from VCF
888 file, or key-value pairs imported from column 9 of GFF
892 <!-- JAL-2879 -->Feature Attributes and shading schemes
893 stored and restored from Jalview Projects
896 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
897 recognise variant features
900 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
901 sequences (also coloured red by default)
904 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
908 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
909 algorithm (Z-sort/transparency and filter aware)
912 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
918 <!-- JAL-3205 -->Symmetric score matrices for faster
919 tree and PCA calculations
921 <li><strong>Principal Components Analysis Viewer</strong>
924 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
925 and Viewer state saved in Jalview Project
927 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
930 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
934 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
939 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
941 <li><strong>Speed and Efficiency</strong>
944 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
945 multiple groups when working with large alignments
948 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
952 <li><strong>User Interface</strong>
955 <!-- JAL-2933 -->Finder panel remembers last position in each
959 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
960 what is shown)<br />Only visible regions of alignment are shown by
961 default (can be changed in user preferences)
964 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
965 to the Overwrite Dialog
968 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
972 <!-- JAL-1244 -->Status bar shows bounds when dragging a
973 selection region, and gap count when inserting or deleting gaps
976 <!-- JAL-3132 -->Status bar updates over sequence and annotation
980 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
984 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
988 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
991 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
995 <!-- JAL-3181 -->Consistent ordering of links in sequence id
999 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
1001 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
1005 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
1006 <li><strong>Java 11 Support (not yet on general release)</strong>
1009 <!-- -->OSX GUI integrations for App menu's 'About' entry and
1014 <em>Deprecations</em>
1016 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
1017 capabilities removed from the Jalview Desktop
1019 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
1020 unmarshalling has been replaced by JAXB for Jalview projects
1021 and XML based data retrieval clients</li>
1022 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
1023 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
1024 </ul> <em>Documentation</em>
1026 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
1027 not supported in EPS figure export
1029 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
1030 </ul> <em>Development and Release Processes</em>
1033 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
1036 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
1038 <!-- JAL-3225 -->Eclipse project configuration managed with
1042 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
1043 Bamboo continuous integration for unattended Test Suite
1047 <!-- JAL-2864 -->Memory test suite to detect leaks in common
1051 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
1055 <!-- JAL-3248 -->Developer documentation migrated to
1056 markdown (with HTML rendering)
1059 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
1062 <!-- JAL-3289 -->New URLs for publishing development
1067 <td align="left" valign="top">
1070 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
1073 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
1074 superposition in Jmol fail on Windows
1077 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
1078 structures for sequences with lots of PDB structures
1081 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
1085 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
1086 project involving multiple views
1089 <!-- JAL-3164 -->Overview for complementary view in a linked
1090 CDS/Protein alignment is not updated when Hide Columns by
1091 Annotation dialog hides columns
1094 <!-- JAL-3158 -->Selection highlighting in the complement of a
1095 CDS/Protein alignment stops working after making a selection in
1096 one view, then making another selection in the other view
1099 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
1103 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
1104 Settings and Jalview Preferences panels
1107 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
1108 overview with large alignments
1111 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
1112 region if columns were selected by dragging right-to-left and the
1113 mouse moved to the left of the first column
1116 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
1117 hidden column marker via scale popup menu
1120 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
1121 doesn't tell users the invalid URL
1124 <!-- JAL-2816 -->Tooltips displayed for features filtered by
1128 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
1129 show cross references or Fetch Database References are shown in
1130 red in original view
1133 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
1134 peptide sequence (computed variant shown as p.Res.null)
1137 <!-- JAL-2060 -->'Graduated colour' option not offered for
1138 manually created features (where feature score is Float.NaN)
1141 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
1142 when columns are hidden
1145 <!-- JAL-3082 -->Regular expression error for '(' in Select
1146 Columns by Annotation description
1149 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
1150 out of Scale or Annotation Panel
1153 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
1157 <!-- JAL-3074 -->Left/right drag in annotation can scroll
1161 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
1165 <!-- JAL-3002 -->Column display is out by one after Page Down,
1166 Page Up in wrapped mode
1169 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
1172 <!-- JAL-2932 -->Finder searches in minimised alignments
1175 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
1176 on opening an alignment
1179 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
1183 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
1184 different groups in the alignment are selected
1187 <!-- JAL-2717 -->Internationalised colour scheme names not shown
1191 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
1195 <!-- JAL-3125 -->Value input for graduated feature colour
1196 threshold gets 'unrounded'
1199 <!-- JAL-2982 -->PCA image export doesn't respect background
1203 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
1206 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
1209 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
1213 <!-- JAL-2964 -->Associate Tree with All Views not restored from
1217 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
1218 shown in complementary view
1221 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
1222 without normalisation
1225 <!-- JAL-3021 -->Sequence Details report should open positioned at top
1229 <!-- JAL-914 -->Help page can be opened twice
1232 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
1234 </ul> <em>Editing</em>
1237 <!-- JAL-2822 -->Start and End should be updated when sequence
1238 data at beginning or end of alignment added/removed via 'Edit'
1242 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
1243 relocate sequence features correctly when start of sequence is
1244 removed (Known defect since 2.10)
1247 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
1248 dialog corrupts dataset sequence
1251 <!-- JAL-868 -->Structure colours not updated when associated tree
1252 repartitions the alignment view (Regression in 2.10.5)
1254 </ul> <em>Datamodel</em>
1257 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
1258 sequence's End is greater than its length
1260 </ul> <em>Bugs fixed for Java 11 Support (not yet on
1261 general release)</em>
1264 <!-- JAL-3288 -->Menus work properly in split-screen
1266 </ul> <em>New Known Defects</em>
1269 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
1272 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
1273 regions of protein alignment.
1276 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
1277 is restored from a Jalview 2.11 project
1280 <!-- JAL-3213 -->Alignment panel height can be too small after
1284 <!-- JAL-3240 -->Display is incorrect after removing gapped
1285 columns within hidden columns
1288 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
1289 window after dragging left to select columns to left of visible
1293 <!-- JAL-2876 -->Features coloured according to their description
1294 string and thresholded by score in earlier versions of Jalview are
1295 not shown as thresholded features in 2.11. To workaround please
1296 create a Score filter instead.
1299 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
1301 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
1304 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1305 alignments with multiple views can close views unexpectedly
1308 <em>Java 11 Specific defects</em>
1311 <!-- JAL-3235 -->Jalview Properties file is not sorted
1312 alphabetically when saved
1318 <td width="60" nowrap>
1319 <div align="center">
1320 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1323 <td><div align="left">
1327 <!-- JAL-3101 -->Default memory for Jalview webstart and
1328 InstallAnywhere increased to 1G.
1331 <!-- JAL-247 -->Hidden sequence markers and representative
1332 sequence bolding included when exporting alignment as EPS,
1333 SVG, PNG or HTML. <em>Display is configured via the
1334 Format menu, or for command-line use via a Jalview
1335 properties file.</em>
1338 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1339 API and sequence data now imported as JSON.
1342 <!-- JAL-3065 -->Change in recommended way of starting
1343 Jalview via a Java command line: add jars in lib directory
1344 to CLASSPATH, rather than via the deprecated java.ext.dirs
1348 <em>Development</em>
1351 <!-- JAL-3047 -->Support added to execute test suite
1352 instrumented with <a href="http://openclover.org/">Open
1357 <td><div align="left">
1361 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1362 row shown in Feredoxin Structure alignment view of example
1366 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1367 annotation displayed.
1370 <!-- JAL-3107 -->Group conservation/consensus not shown
1371 for newly created group when 'Apply to all groups'
1375 <!-- JAL-3087 -->Corrupted display when switching to
1376 wrapped mode when sequence panel's vertical scrollbar is
1380 <!-- JAL-3003 -->Alignment is black in exported EPS file
1381 when sequences are selected in exported view.</em>
1384 <!-- JAL-3059 -->Groups with different coloured borders
1385 aren't rendered with correct colour.
1388 <!-- JAL-3092 -->Jalview could hang when importing certain
1389 types of knotted RNA secondary structure.
1392 <!-- JAL-3095 -->Sequence highlight and selection in
1393 trimmed VARNA 2D structure is incorrect for sequences that
1397 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1398 annotation when columns are inserted into an alignment,
1399 and when exporting as Stockholm flatfile.
1402 <!-- JAL-3053 -->Jalview annotation rows containing upper
1403 and lower-case 'E' and 'H' do not automatically get
1404 treated as RNA secondary structure.
1407 <!-- JAL-3106 -->.jvp should be used as default extension
1408 (not .jar) when saving a Jalview project file.
1411 <!-- JAL-3105 -->Mac Users: closing a window correctly
1412 transfers focus to previous window on OSX
1415 <em>Java 10 Issues Resolved</em>
1418 <!-- JAL-2988 -->OSX - Can't save new files via the File
1419 or export menus by typing in a name into the Save dialog
1423 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1424 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1425 'look and feel' which has improved compatibility with the
1426 latest version of OSX.
1433 <td width="60" nowrap>
1434 <div align="center">
1435 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1436 <em>7/06/2018</em></strong>
1439 <td><div align="left">
1443 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1444 annotation retrieved from Uniprot
1447 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1448 onto the Jalview Desktop
1452 <td><div align="left">
1456 <!-- JAL-3017 -->Cannot import features with multiple
1457 variant elements (blocks import of some Uniprot records)
1460 <!-- JAL-2997 -->Clustal files with sequence positions in
1461 right-hand column parsed correctly
1464 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1465 not alignment area in exported graphic
1468 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1469 window has input focus
1472 <!-- JAL-2992 -->Annotation panel set too high when
1473 annotation added to view (Windows)
1476 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1477 network connectivity is poor
1480 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1481 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1482 the currently open URL and links from a page viewed in
1483 Firefox or Chrome on Windows is now fully supported. If
1484 you are using Edge, only links in the page can be
1485 dragged, and with Internet Explorer, only the currently
1486 open URL in the browser can be dropped onto Jalview.</em>
1489 <em>New Known Defects</em>
1491 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1496 <td width="60" nowrap>
1497 <div align="center">
1498 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1501 <td><div align="left">
1505 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1506 for disabling automatic superposition of multiple
1507 structures and open structures in existing views
1510 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1511 ID and annotation area margins can be click-dragged to
1515 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1519 <!-- JAL-2759 -->Improved performance for large alignments
1520 and lots of hidden columns
1523 <!-- JAL-2593 -->Improved performance when rendering lots
1524 of features (particularly when transparency is disabled)
1527 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1528 exchange of Jalview features and Chimera attributes made
1534 <td><div align="left">
1537 <!-- JAL-2899 -->Structure and Overview aren't updated
1538 when Colour By Annotation threshold slider is adjusted
1541 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1542 overlapping alignment panel
1545 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1549 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1550 improved: CDS not handled correctly if transcript has no
1554 <!-- JAL-2321 -->Secondary structure and temperature
1555 factor annotation not added to sequence when local PDB
1556 file associated with it by drag'n'drop or structure
1560 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1561 dialog doesn't import PDB files dropped on an alignment
1564 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1565 scroll bar doesn't work for some CDS/Protein views
1568 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1569 Java 1.8u153 onwards and Java 1.9u4+.
1572 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1573 columns in annotation row
1576 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1577 honored in batch mode
1580 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1581 for structures added to existing Jmol view
1584 <!-- JAL-2223 -->'View Mappings' includes duplicate
1585 entries after importing project with multiple views
1588 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1589 protein sequences via SIFTS from associated PDB entries
1590 with negative residue numbers or missing residues fails
1593 <!-- JAL-2952 -->Exception when shading sequence with negative
1594 Temperature Factor values from annotated PDB files (e.g.
1595 as generated by CONSURF)
1598 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1599 tooltip doesn't include a text description of mutation
1602 <!-- JAL-2922 -->Invert displayed features very slow when
1603 structure and/or overview windows are also shown
1606 <!-- JAL-2954 -->Selecting columns from highlighted regions
1607 very slow for alignments with large numbers of sequences
1610 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1611 with 'StringIndexOutOfBounds'
1614 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1615 platforms running Java 10
1618 <!-- JAL-2960 -->Adding a structure to existing structure
1619 view appears to do nothing because the view is hidden behind the alignment view
1625 <!-- JAL-2926 -->Copy consensus sequence option in applet
1626 should copy the group consensus when popup is opened on it
1632 <!-- JAL-2913 -->Fixed ID width preference is not respected
1635 <em>New Known Defects</em>
1638 <!-- JAL-2973 --> Exceptions occasionally raised when
1639 editing a large alignment and overview is displayed
1642 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1643 repeatedly after a series of edits even when the overview
1644 is no longer reflecting updates
1647 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1648 structures for protein subsequence (if 'Trim Retrieved
1649 Sequences' enabled) or Ensembl isoforms (Workaround in
1650 2.10.4 is to fail back to N&W mapping)
1653 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1654 option gives blank output
1661 <td width="60" nowrap>
1662 <div align="center">
1663 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1666 <td><div align="left">
1667 <ul><li>Updated Certum Codesigning Certificate
1668 (Valid till 30th November 2018)</li></ul></div></td>
1669 <td><div align="left">
1670 <em>Desktop</em><ul>
1672 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1673 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1674 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1675 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1676 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1677 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1678 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1684 <td width="60" nowrap>
1685 <div align="center">
1686 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1689 <td><div align="left">
1693 <!-- JAL-2446 -->Faster and more efficient management and
1694 rendering of sequence features
1697 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1698 429 rate limit request hander
1701 <!-- JAL-2773 -->Structure views don't get updated unless
1702 their colours have changed
1705 <!-- JAL-2495 -->All linked sequences are highlighted for
1706 a structure mousover (Jmol) or selection (Chimera)
1709 <!-- JAL-2790 -->'Cancel' button in progress bar for
1710 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1713 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1714 view from Ensembl locus cross-references
1717 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1721 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1722 feature can be disabled
1725 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1726 PDB easier retrieval of sequences for lists of IDs
1729 <!-- JAL-2758 -->Short names for sequences retrieved from
1735 <li>Groovy interpreter updated to 2.4.12</li>
1736 <li>Example groovy script for generating a matrix of
1737 percent identity scores for current alignment.</li>
1739 <em>Testing and Deployment</em>
1742 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1746 <td><div align="left">
1750 <!-- JAL-2643 -->Pressing tab after updating the colour
1751 threshold text field doesn't trigger an update to the
1755 <!-- JAL-2682 -->Race condition when parsing sequence ID
1759 <!-- JAL-2608 -->Overview windows are also closed when
1760 alignment window is closed
1763 <!-- JAL-2548 -->Export of features doesn't always respect
1767 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1768 takes a long time in Cursor mode
1774 <!-- JAL-2777 -->Structures with whitespace chainCode
1775 cannot be viewed in Chimera
1778 <!-- JAL-2728 -->Protein annotation panel too high in
1782 <!-- JAL-2757 -->Can't edit the query after the server
1783 error warning icon is shown in Uniprot and PDB Free Text
1787 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1790 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1793 <!-- JAL-2739 -->Hidden column marker in last column not
1794 rendered when switching back from Wrapped to normal view
1797 <!-- JAL-2768 -->Annotation display corrupted when
1798 scrolling right in unwapped alignment view
1801 <!-- JAL-2542 -->Existing features on subsequence
1802 incorrectly relocated when full sequence retrieved from
1806 <!-- JAL-2733 -->Last reported memory still shown when
1807 Desktop->Show Memory is unticked (OSX only)
1810 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1811 features of same type and group to be selected for
1815 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1816 alignments when hidden columns are present
1819 <!-- JAL-2392 -->Jalview freezes when loading and
1820 displaying several structures
1823 <!-- JAL-2732 -->Black outlines left after resizing or
1827 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1828 within the Jalview desktop on OSX
1831 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1832 when in wrapped alignment mode
1835 <!-- JAL-2636 -->Scale mark not shown when close to right
1836 hand end of alignment
1839 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1840 each selected sequence do not have correct start/end
1844 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1845 after canceling the Alignment Window's Font dialog
1848 <!-- JAL-2036 -->Show cross-references not enabled after
1849 restoring project until a new view is created
1852 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1853 URL links appears when only default EMBL-EBI link is
1854 configured (since 2.10.2b2)
1857 <!-- JAL-2775 -->Overview redraws whole window when box
1858 position is adjusted
1861 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1862 in a multi-chain structure when viewing alignment
1863 involving more than one chain (since 2.10)
1866 <!-- JAL-2811 -->Double residue highlights in cursor mode
1867 if new selection moves alignment window
1870 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1871 arrow key in cursor mode to pass hidden column marker
1874 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1875 that produces correctly annotated transcripts and products
1878 <!-- JAL-2776 -->Toggling a feature group after first time
1879 doesn't update associated structure view
1882 <em>Applet</em><br />
1885 <!-- JAL-2687 -->Concurrent modification exception when
1886 closing alignment panel
1889 <em>BioJSON</em><br />
1892 <!-- JAL-2546 -->BioJSON export does not preserve
1893 non-positional features
1896 <em>New Known Issues</em>
1899 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1900 sequence features correctly (for many previous versions of
1904 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1905 using cursor in wrapped panel other than top
1908 <!-- JAL-2791 -->Select columns containing feature ignores
1909 graduated colour threshold
1912 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1913 always preserve numbering and sequence features
1916 <em>Known Java 9 Issues</em>
1919 <!-- JAL-2902 -->Groovy Console very slow to open and is
1920 not responsive when entering characters (Webstart, Java
1927 <td width="60" nowrap>
1928 <div align="center">
1929 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1930 <em>2/10/2017</em></strong>
1933 <td><div align="left">
1934 <em>New features in Jalview Desktop</em>
1937 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1939 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1943 <td><div align="left">
1947 <td width="60" nowrap>
1948 <div align="center">
1949 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1950 <em>7/9/2017</em></strong>
1953 <td><div align="left">
1957 <!-- JAL-2588 -->Show gaps in overview window by colouring
1958 in grey (sequences used to be coloured grey, and gaps were
1962 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1966 <!-- JAL-2587 -->Overview updates immediately on increase
1967 in size and progress bar shown as higher resolution
1968 overview is recalculated
1973 <td><div align="left">
1977 <!-- JAL-2664 -->Overview window redraws every hidden
1978 column region row by row
1981 <!-- JAL-2681 -->duplicate protein sequences shown after
1982 retrieving Ensembl crossrefs for sequences from Uniprot
1985 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1986 format setting is unticked
1989 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1990 if group has show boxes format setting unticked
1993 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1994 autoscrolling whilst dragging current selection group to
1995 include sequences and columns not currently displayed
1998 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1999 assemblies are imported via CIF file
2002 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
2003 displayed when threshold or conservation colouring is also
2007 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
2011 <!-- JAL-2673 -->Jalview continues to scroll after
2012 dragging a selected region off the visible region of the
2016 <!-- JAL-2724 -->Cannot apply annotation based
2017 colourscheme to all groups in a view
2020 <!-- JAL-2511 -->IDs don't line up with sequences
2021 initially after font size change using the Font chooser or
2028 <td width="60" nowrap>
2029 <div align="center">
2030 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
2033 <td><div align="left">
2034 <em>Calculations</em>
2038 <!-- JAL-1933 -->Occupancy annotation row shows number of
2039 ungapped positions in each column of the alignment.
2042 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
2043 a calculation dialog box
2046 <!-- JAL-2379 -->Revised implementation of PCA for speed
2047 and memory efficiency (~30x faster)
2050 <!-- JAL-2403 -->Revised implementation of sequence
2051 similarity scores as used by Tree, PCA, Shading Consensus
2052 and other calculations
2055 <!-- JAL-2416 -->Score matrices are stored as resource
2056 files within the Jalview codebase
2059 <!-- JAL-2500 -->Trees computed on Sequence Feature
2060 Similarity may have different topology due to increased
2067 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
2068 model for alignments and groups
2071 <!-- JAL-384 -->Custom shading schemes created via groovy
2078 <!-- JAL-2526 -->Efficiency improvements for interacting
2079 with alignment and overview windows
2082 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
2086 <!-- JAL-2388 -->Hidden columns and sequences can be
2090 <!-- JAL-2611 -->Click-drag in visible area allows fine
2091 adjustment of visible position
2095 <em>Data import/export</em>
2098 <!-- JAL-2535 -->Posterior probability annotation from
2099 Stockholm files imported as sequence associated annotation
2102 <!-- JAL-2507 -->More robust per-sequence positional
2103 annotation input/output via stockholm flatfile
2106 <!-- JAL-2533 -->Sequence names don't include file
2107 extension when importing structure files without embedded
2108 names or PDB accessions
2111 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
2112 format sequence substitution matrices
2115 <em>User Interface</em>
2118 <!-- JAL-2447 --> Experimental Features Checkbox in
2119 Desktop's Tools menu to hide or show untested features in
2123 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
2124 via Overview or sequence motif search operations
2127 <!-- JAL-2547 -->Amend sequence features dialog box can be
2128 opened by double clicking gaps within sequence feature
2132 <!-- JAL-1476 -->Status bar message shown when not enough
2133 aligned positions were available to create a 3D structure
2137 <em>3D Structure</em>
2140 <!-- JAL-2430 -->Hidden regions in alignment views are not
2141 coloured in linked structure views
2144 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
2145 file-based command exchange
2148 <!-- JAL-2375 -->Structure chooser automatically shows
2149 Cached Structures rather than querying the PDBe if
2150 structures are already available for sequences
2153 <!-- JAL-2520 -->Structures imported via URL are cached in
2154 the Jalview project rather than downloaded again when the
2155 project is reopened.
2158 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
2159 to transfer Chimera's structure attributes as Jalview
2160 features, and vice-versa (<strong>Experimental
2164 <em>Web Services</em>
2167 <!-- JAL-2549 -->Updated JABAWS client to v2.2
2170 <!-- JAL-2335 -->Filter non-standard amino acids and
2171 nucleotides when submitting to AACon and other MSA
2175 <!-- JAL-2316, -->URLs for viewing database
2176 cross-references provided by identifiers.org and the
2177 EMBL-EBI's MIRIAM DB
2184 <!-- JAL-2344 -->FileFormatI interface for describing and
2185 identifying file formats (instead of String constants)
2188 <!-- JAL-2228 -->FeatureCounter script refactored for
2189 efficiency when counting all displayed features (not
2190 backwards compatible with 2.10.1)
2193 <em>Example files</em>
2196 <!-- JAL-2631 -->Graduated feature colour style example
2197 included in the example feature file
2200 <em>Documentation</em>
2203 <!-- JAL-2339 -->Release notes reformatted for readability
2204 with the built-in Java help viewer
2207 <!-- JAL-1644 -->Find documentation updated with 'search
2208 sequence description' option
2214 <!-- JAL-2485, -->External service integration tests for
2215 Uniprot REST Free Text Search Client
2218 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
2221 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
2226 <td><div align="left">
2227 <em>Calculations</em>
2230 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
2231 matrix - C->R should be '-3'<br />Old matrix restored
2232 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
2234 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
2235 Jalview's treatment of gaps in PCA and substitution matrix
2236 based Tree calculations.<br /> <br />In earlier versions
2237 of Jalview, gaps matching gaps were penalised, and gaps
2238 matching non-gaps penalised even more. In the PCA
2239 calculation, gaps were actually treated as non-gaps - so
2240 different costs were applied, which meant Jalview's PCAs
2241 were different to those produced by SeqSpace.<br />Jalview
2242 now treats gaps in the same way as SeqSpace (ie it scores
2243 them as 0). <br /> <br />Enter the following in the
2244 Groovy console to restore pre-2.10.2 behaviour:<br />
2245 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
2246 // for 2.10.1 mode <br />
2247 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
2248 // to restore 2.10.2 mode <br /> <br /> <em>Note:
2249 these settings will affect all subsequent tree and PCA
2250 calculations (not recommended)</em></li>
2252 <!-- JAL-2424 -->Fixed off-by-one bug that affected
2253 scaling of branch lengths for trees computed using
2254 Sequence Feature Similarity.
2257 <!-- JAL-2377 -->PCA calculation could hang when
2258 generating output report when working with highly
2259 redundant alignments
2262 <!-- JAL-2544 --> Sort by features includes features to
2263 right of selected region when gaps present on right-hand
2267 <em>User Interface</em>
2270 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2271 doesn't reselect a specific sequence's associated
2272 annotation after it was used for colouring a view
2275 <!-- JAL-2419 -->Current selection lost if popup menu
2276 opened on a region of alignment without groups
2279 <!-- JAL-2374 -->Popup menu not always shown for regions
2280 of an alignment with overlapping groups
2283 <!-- JAL-2310 -->Finder double counts if both a sequence's
2284 name and description match
2287 <!-- JAL-2370 -->Hiding column selection containing two
2288 hidden regions results in incorrect hidden regions
2291 <!-- JAL-2386 -->'Apply to all groups' setting when
2292 changing colour does not apply Conservation slider value
2296 <!-- JAL-2373 -->Percentage identity and conservation menu
2297 items do not show a tick or allow shading to be disabled
2300 <!-- JAL-2385 -->Conservation shading or PID threshold
2301 lost when base colourscheme changed if slider not visible
2304 <!-- JAL-2547 -->Sequence features shown in tooltip for
2305 gaps before start of features
2308 <!-- JAL-2623 -->Graduated feature colour threshold not
2309 restored to UI when feature colour is edited
2312 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2313 a time when scrolling vertically in wrapped mode.
2316 <!-- JAL-2630 -->Structure and alignment overview update
2317 as graduate feature colour settings are modified via the
2321 <!-- JAL-2034 -->Overview window doesn't always update
2322 when a group defined on the alignment is resized
2325 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2326 wrapped view result in positional status updates
2330 <!-- JAL-2563 -->Status bar doesn't show position for
2331 ambiguous amino acid and nucleotide symbols
2334 <!-- JAL-2602 -->Copy consensus sequence failed if
2335 alignment included gapped columns
2338 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2339 widgets don't permanently disappear
2342 <!-- JAL-2503 -->Cannot select or filter quantitative
2343 annotation that are shown only as column labels (e.g.
2344 T-Coffee column reliability scores)
2347 <!-- JAL-2594 -->Exception thrown if trying to create a
2348 sequence feature on gaps only
2351 <!-- JAL-2504 -->Features created with 'New feature'
2352 button from a Find inherit previously defined feature type
2353 rather than the Find query string
2356 <!-- JAL-2423 -->incorrect title in output window when
2357 exporting tree calculated in Jalview
2360 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2361 and then revealing them reorders sequences on the
2365 <!-- JAL-964 -->Group panel in sequence feature settings
2366 doesn't update to reflect available set of groups after
2367 interactively adding or modifying features
2370 <!-- JAL-2225 -->Sequence Database chooser unusable on
2374 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2375 only excluded gaps in current sequence and ignored
2382 <!-- JAL-2421 -->Overview window visible region moves
2383 erratically when hidden rows or columns are present
2386 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2387 Structure Viewer's colour menu don't correspond to
2391 <!-- JAL-2405 -->Protein specific colours only offered in
2392 colour and group colour menu for protein alignments
2395 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2396 reflect currently selected view or group's shading
2400 <!-- JAL-2624 -->Feature colour thresholds not respected
2401 when rendered on overview and structures when opacity at
2405 <!-- JAL-2589 -->User defined gap colour not shown in
2406 overview when features overlaid on alignment
2409 <!-- JAL-2567 -->Feature settings for different views not
2410 recovered correctly from Jalview project file
2413 <!-- JAL-2256 -->Feature colours in overview when first opened
2414 (automatically via preferences) are different to the main
2418 <em>Data import/export</em>
2421 <!-- JAL-2576 -->Very large alignments take a long time to
2425 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2426 added after a sequence was imported are not written to
2430 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2431 when importing RNA secondary structure via Stockholm
2434 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2435 not shown in correct direction for simple pseudoknots
2438 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2439 with lightGray or darkGray via features file (but can
2443 <!-- JAL-2383 -->Above PID colour threshold not recovered
2444 when alignment view imported from project
2447 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2448 structure and sequences extracted from structure files
2449 imported via URL and viewed in Jmol
2452 <!-- JAL-2520 -->Structures loaded via URL are saved in
2453 Jalview Projects rather than fetched via URL again when
2454 the project is loaded and the structure viewed
2457 <em>Web Services</em>
2460 <!-- JAL-2519 -->EnsemblGenomes example failing after
2461 release of Ensembl v.88
2464 <!-- JAL-2366 -->Proxy server address and port always
2465 appear enabled in Preferences->Connections
2468 <!-- JAL-2461 -->DAS registry not found exceptions
2469 removed from console output
2472 <!-- JAL-2582 -->Cannot retrieve protein products from
2473 Ensembl by Peptide ID
2476 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2477 created from SIFTs, and spurious 'Couldn't open structure
2478 in Chimera' errors raised after April 2017 update (problem
2479 due to 'null' string rather than empty string used for
2480 residues with no corresponding PDB mapping).
2483 <em>Application UI</em>
2486 <!-- JAL-2361 -->User Defined Colours not added to Colour
2490 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2491 case' residues (button in colourscheme editor debugged and
2492 new documentation and tooltips added)
2495 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2496 doesn't restore group-specific text colour thresholds
2499 <!-- JAL-2243 -->Feature settings panel does not update as
2500 new features are added to alignment
2503 <!-- JAL-2532 -->Cancel in feature settings reverts
2504 changes to feature colours via the Amend features dialog
2507 <!-- JAL-2506 -->Null pointer exception when attempting to
2508 edit graduated feature colour via amend features dialog
2512 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2513 selection menu changes colours of alignment views
2516 <!-- JAL-2426 -->Spurious exceptions in console raised
2517 from alignment calculation workers after alignment has
2521 <!-- JAL-1608 -->Typo in selection popup menu - Create
2522 groups now 'Create Group'
2525 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2526 Create/Undefine group doesn't always work
2529 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2530 shown again after pressing 'Cancel'
2533 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2534 adjusts start position in wrap mode
2537 <!-- JAL-2563 -->Status bar doesn't show positions for
2538 ambiguous amino acids
2541 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2542 CDS/Protein view after CDS sequences added for aligned
2546 <!-- JAL-2592 -->User defined colourschemes called 'User
2547 Defined' don't appear in Colours menu
2553 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2554 score models doesn't always result in an updated PCA plot
2557 <!-- JAL-2442 -->Features not rendered as transparent on
2558 overview or linked structure view
2561 <!-- JAL-2372 -->Colour group by conservation doesn't
2565 <!-- JAL-2517 -->Hitting Cancel after applying
2566 user-defined colourscheme doesn't restore original
2573 <!-- JAL-2314 -->Unit test failure:
2574 jalview.ws.jabaws.RNAStructExportImport setup fails
2577 <!-- JAL-2307 -->Unit test failure:
2578 jalview.ws.sifts.SiftsClientTest due to compatibility
2579 problems with deep array comparison equality asserts in
2580 successive versions of TestNG
2583 <!-- JAL-2479 -->Relocated StructureChooserTest and
2584 ParameterUtilsTest Unit tests to Network suite
2587 <em>New Known Issues</em>
2590 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2591 phase after a sequence motif find operation
2594 <!-- JAL-2550 -->Importing annotation file with rows
2595 containing just upper and lower case letters are
2596 interpreted as WUSS RNA secondary structure symbols
2599 <!-- JAL-2590 -->Cannot load and display Newick trees
2600 reliably from eggnog Ortholog database
2603 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2604 containing features of type Highlight' when 'B' is pressed
2605 to mark columns containing highlighted regions.
2608 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2609 doesn't always add secondary structure annotation.
2614 <td width="60" nowrap>
2615 <div align="center">
2616 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2619 <td><div align="left">
2623 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2624 for all consensus calculations
2627 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2630 <li>Updated Jalview's Certum code signing certificate
2633 <em>Application</em>
2636 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2637 set of database cross-references, sorted alphabetically
2640 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2641 from database cross references. Users with custom links
2642 will receive a <a href="webServices/urllinks.html#warning">warning
2643 dialog</a> asking them to update their preferences.
2646 <!-- JAL-2287-->Cancel button and escape listener on
2647 dialog warning user about disconnecting Jalview from a
2651 <!-- JAL-2320-->Jalview's Chimera control window closes if
2652 the Chimera it is connected to is shut down
2655 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2656 columns menu item to mark columns containing highlighted
2657 regions (e.g. from structure selections or results of a
2661 <!-- JAL-2284-->Command line option for batch-generation
2662 of HTML pages rendering alignment data with the BioJS
2672 <!-- JAL-2286 -->Columns with more than one modal residue
2673 are not coloured or thresholded according to percent
2674 identity (first observed in Jalview 2.8.2)
2677 <!-- JAL-2301 -->Threonine incorrectly reported as not
2681 <!-- JAL-2318 -->Updates to documentation pages (above PID
2682 threshold, amino acid properties)
2685 <!-- JAL-2292 -->Lower case residues in sequences are not
2686 reported as mapped to residues in a structure file in the
2690 <!--JAL-2324 -->Identical features with non-numeric scores
2691 could be added multiple times to a sequence
2694 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2695 bond features shown as two highlighted residues rather
2696 than a range in linked structure views, and treated
2697 correctly when selecting and computing trees from features
2700 <!-- JAL-2281-->Custom URL links for database
2701 cross-references are matched to database name regardless
2706 <em>Application</em>
2709 <!-- JAL-2282-->Custom URL links for specific database
2710 names without regular expressions also offer links from
2714 <!-- JAL-2315-->Removing a single configured link in the
2715 URL links pane in Connections preferences doesn't actually
2716 update Jalview configuration
2719 <!-- JAL-2272-->CTRL-Click on a selected region to open
2720 the alignment area popup menu doesn't work on El-Capitan
2723 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2724 files with similarly named sequences if dropped onto the
2728 <!-- JAL-2312 -->Additional mappings are shown for PDB
2729 entries where more chains exist in the PDB accession than
2730 are reported in the SIFTS file
2733 <!-- JAL-2317-->Certain structures do not get mapped to
2734 the structure view when displayed with Chimera
2737 <!-- JAL-2317-->No chains shown in the Chimera view
2738 panel's View->Show Chains submenu
2741 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2742 work for wrapped alignment views
2745 <!--JAL-2197 -->Rename UI components for running JPred
2746 predictions from 'JNet' to 'JPred'
2749 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2750 corrupted when annotation panel vertical scroll is not at
2751 first annotation row
2754 <!--JAL-2332 -->Attempting to view structure for Hen
2755 lysozyme results in a PDB Client error dialog box
2758 <!-- JAL-2319 -->Structure View's mapping report switched
2759 ranges for PDB and sequence for SIFTS
2762 SIFTS 'Not_Observed' residues mapped to non-existant
2766 <!-- <em>New Known Issues</em>
2773 <td width="60" nowrap>
2774 <div align="center">
2775 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2776 <em>25/10/2016</em></strong>
2779 <td><em>Application</em>
2781 <li>3D Structure chooser opens with 'Cached structures'
2782 view if structures already loaded</li>
2783 <li>Progress bar reports models as they are loaded to
2784 structure views</li>
2790 <li>Colour by conservation always enabled and no tick
2791 shown in menu when BLOSUM or PID shading applied</li>
2792 <li>FER1_ARATH and FER2_ARATH labels were switched in
2793 example sequences/projects/trees</li>
2795 <em>Application</em>
2797 <li>Jalview projects with views of local PDB structure
2798 files saved on Windows cannot be opened on OSX</li>
2799 <li>Multiple structure views can be opened and superposed
2800 without timeout for structures with multiple models or
2801 multiple sequences in alignment</li>
2802 <li>Cannot import or associated local PDB files without a
2803 PDB ID HEADER line</li>
2804 <li>RMSD is not output in Jmol console when superposition
2806 <li>Drag and drop of URL from Browser fails for Linux and
2807 OSX versions earlier than El Capitan</li>
2808 <li>ENA client ignores invalid content from ENA server</li>
2809 <li>Exceptions are not raised in console when ENA client
2810 attempts to fetch non-existent IDs via Fetch DB Refs UI
2812 <li>Exceptions are not raised in console when a new view
2813 is created on the alignment</li>
2814 <li>OSX right-click fixed for group selections: CMD-click
2815 to insert/remove gaps in groups and CTRL-click to open group
2818 <em>Build and deployment</em>
2820 <li>URL link checker now copes with multi-line anchor
2823 <em>New Known Issues</em>
2825 <li>Drag and drop from URL links in browsers do not work
2832 <td width="60" nowrap>
2833 <div align="center">
2834 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2837 <td><em>General</em>
2840 <!-- JAL-2124 -->Updated Spanish translations.
2843 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2844 for importing structure data to Jalview. Enables mmCIF and
2848 <!-- JAL-192 --->Alignment ruler shows positions relative to
2852 <!-- JAL-2202 -->Position/residue shown in status bar when
2853 mousing over sequence associated annotation
2856 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2860 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2861 '()', canonical '[]' and invalid '{}' base pair populations
2865 <!-- JAL-2092 -->Feature settings popup menu options for
2866 showing or hiding columns containing a feature
2869 <!-- JAL-1557 -->Edit selected group by double clicking on
2870 group and sequence associated annotation labels
2873 <!-- JAL-2236 -->Sequence name added to annotation label in
2874 select/hide columns by annotation and colour by annotation
2878 </ul> <em>Application</em>
2881 <!-- JAL-2050-->Automatically hide introns when opening a
2882 gene/transcript view
2885 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2889 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2890 structure mappings with the EMBL-EBI PDBe SIFTS database
2893 <!-- JAL-2079 -->Updated download sites used for Rfam and
2894 Pfam sources to xfam.org
2897 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2900 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2901 over sequences in Jalview
2904 <!-- JAL-2027-->Support for reverse-complement coding
2905 regions in ENA and EMBL
2908 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2909 for record retrieval via ENA rest API
2912 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2916 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2917 groovy script execution
2920 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2921 alignment window's Calculate menu
2924 <!-- JAL-1812 -->Allow groovy scripts that call
2925 Jalview.getAlignFrames() to run in headless mode
2928 <!-- JAL-2068 -->Support for creating new alignment
2929 calculation workers from groovy scripts
2932 <!-- JAL-1369 --->Store/restore reference sequence in
2936 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2937 associations are now saved/restored from project
2940 <!-- JAL-1993 -->Database selection dialog always shown
2941 before sequence fetcher is opened
2944 <!-- JAL-2183 -->Double click on an entry in Jalview's
2945 database chooser opens a sequence fetcher
2948 <!-- JAL-1563 -->Free-text search client for UniProt using
2949 the UniProt REST API
2952 <!-- JAL-2168 -->-nonews command line parameter to prevent
2953 the news reader opening
2956 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2957 querying stored in preferences
2960 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2964 <!-- JAL-1977-->Tooltips shown on database chooser
2967 <!-- JAL-391 -->Reverse complement function in calculate
2968 menu for nucleotide sequences
2971 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2972 and feature counts preserves alignment ordering (and
2973 debugged for complex feature sets).
2976 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2977 viewing structures with Jalview 2.10
2980 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2981 genome, transcript CCDS and gene ids via the Ensembl and
2982 Ensembl Genomes REST API
2985 <!-- JAL-2049 -->Protein sequence variant annotation
2986 computed for 'sequence_variant' annotation on CDS regions
2990 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2994 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2995 Ref Fetcher fails to match, or otherwise updates sequence
2996 data from external database records.
2999 <!-- JAL-2154 -->Revised Jalview Project format for
3000 efficient recovery of sequence coding and alignment
3001 annotation relationships.
3003 </ul> <!-- <em>Applet</em>
3014 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
3018 <!-- JAL-2018-->Export features in Jalview format (again)
3019 includes graduated colourschemes
3022 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
3023 working with big alignments and lots of hidden columns
3026 <!-- JAL-2053-->Hidden column markers not always rendered
3027 at right of alignment window
3030 <!-- JAL-2067 -->Tidied up links in help file table of
3034 <!-- JAL-2072 -->Feature based tree calculation not shown
3038 <!-- JAL-2075 -->Hidden columns ignored during feature
3039 based tree calculation
3042 <!-- JAL-2065 -->Alignment view stops updating when show
3043 unconserved enabled for group on alignment
3046 <!-- JAL-2086 -->Cannot insert gaps into sequence when
3050 <!-- JAL-2146 -->Alignment column in status incorrectly
3051 shown as "Sequence position" when mousing over
3055 <!-- JAL-2099 -->Incorrect column numbers in ruler when
3056 hidden columns present
3059 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
3060 user created annotation added to alignment
3063 <!-- JAL-1841 -->RNA Structure consensus only computed for
3064 '()' base pair annotation
3067 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
3068 in zero scores for all base pairs in RNA Structure
3072 <!-- JAL-2174-->Extend selection with columns containing
3076 <!-- JAL-2275 -->Pfam format writer puts extra space at
3077 beginning of sequence
3080 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
3084 <!-- JAL-2238 -->Cannot create groups on an alignment from
3085 from a tree when t-coffee scores are shown
3088 <!-- JAL-1836,1967 -->Cannot import and view PDB
3089 structures with chains containing negative resnums (4q4h)
3092 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
3096 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
3097 to Clustal, PIR and PileUp output
3100 <!-- JAL-2008 -->Reordering sequence features that are
3101 not visible causes alignment window to repaint
3104 <!-- JAL-2006 -->Threshold sliders don't work in
3105 graduated colour and colour by annotation row for e-value
3106 scores associated with features and annotation rows
3109 <!-- JAL-1797 -->amino acid physicochemical conservation
3110 calculation should be case independent
3113 <!-- JAL-2173 -->Remove annotation also updates hidden
3117 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
3118 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
3119 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
3122 <!-- JAL-2065 -->Null pointer exceptions and redraw
3123 problems when reference sequence defined and 'show
3124 non-conserved' enabled
3127 <!-- JAL-1306 -->Quality and Conservation are now shown on
3128 load even when Consensus calculation is disabled
3131 <!-- JAL-1932 -->Remove right on penultimate column of
3132 alignment does nothing
3135 <em>Application</em>
3138 <!-- JAL-1552-->URLs and links can't be imported by
3139 drag'n'drop on OSX when launched via webstart (note - not
3140 yet fixed for El Capitan)
3143 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
3144 output when running on non-gb/us i18n platforms
3147 <!-- JAL-1944 -->Error thrown when exporting a view with
3148 hidden sequences as flat-file alignment
3151 <!-- JAL-2030-->InstallAnywhere distribution fails when
3155 <!-- JAL-2080-->Jalview very slow to launch via webstart
3156 (also hotfix for 2.9.0b2)
3159 <!-- JAL-2085 -->Cannot save project when view has a
3160 reference sequence defined
3163 <!-- JAL-1011 -->Columns are suddenly selected in other
3164 alignments and views when revealing hidden columns
3167 <!-- JAL-1989 -->Hide columns not mirrored in complement
3168 view in a cDNA/Protein splitframe
3171 <!-- JAL-1369 -->Cannot save/restore representative
3172 sequence from project when only one sequence is
3176 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
3177 in Structure Chooser
3180 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
3181 structure consensus didn't refresh annotation panel
3184 <!-- JAL-1962 -->View mapping in structure view shows
3185 mappings between sequence and all chains in a PDB file
3188 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
3189 dialogs format columns correctly, don't display array
3190 data, sort columns according to type
3193 <!-- JAL-1975 -->Export complete shown after destination
3194 file chooser is cancelled during an image export
3197 <!-- JAL-2025 -->Error when querying PDB Service with
3198 sequence name containing special characters
3201 <!-- JAL-2024 -->Manual PDB structure querying should be
3205 <!-- JAL-2104 -->Large tooltips with broken HTML
3206 formatting don't wrap
3209 <!-- JAL-1128 -->Figures exported from wrapped view are
3210 truncated so L looks like I in consensus annotation
3213 <!-- JAL-2003 -->Export features should only export the
3214 currently displayed features for the current selection or
3218 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
3219 after fetching cross-references, and restoring from
3223 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
3224 followed in the structure viewer
3227 <!-- JAL-2163 -->Titles for individual alignments in
3228 splitframe not restored from project
3231 <!-- JAL-2145 -->missing autocalculated annotation at
3232 trailing end of protein alignment in transcript/product
3233 splitview when pad-gaps not enabled by default
3236 <!-- JAL-1797 -->amino acid physicochemical conservation
3240 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
3241 article has been read (reopened issue due to
3242 internationalisation problems)
3245 <!-- JAL-1960 -->Only offer PDB structures in structure
3246 viewer based on sequence name, PDB and UniProt
3251 <!-- JAL-1976 -->No progress bar shown during export of
3255 <!-- JAL-2213 -->Structures not always superimposed after
3256 multiple structures are shown for one or more sequences.
3259 <!-- JAL-1370 -->Reference sequence characters should not
3260 be replaced with '.' when 'Show unconserved' format option
3264 <!-- JAL-1823 -->Cannot specify chain code when entering
3265 specific PDB id for sequence
3268 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3269 'Export hidden sequences' is enabled, but 'export hidden
3270 columns' is disabled.
3273 <!--JAL-2026-->Best Quality option in structure chooser
3274 selects lowest rather than highest resolution structures
3278 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3279 to sequence mapping in 'View Mappings' report
3282 <!-- JAL-2284 -->Unable to read old Jalview projects that
3283 contain non-XML data added after Jalvew wrote project.
3286 <!-- JAL-2118 -->Newly created annotation row reorders
3287 after clicking on it to create new annotation for a
3291 <!-- JAL-1980 -->Null Pointer Exception raised when
3292 pressing Add on an orphaned cut'n'paste window.
3294 <!-- may exclude, this is an external service stability issue JAL-1941
3295 -- > RNA 3D structure not added via DSSR service</li> -->
3300 <!-- JAL-2151 -->Incorrect columns are selected when
3301 hidden columns present before start of sequence
3304 <!-- JAL-1986 -->Missing dependencies on applet pages
3308 <!-- JAL-1947 -->Overview pixel size changes when
3309 sequences are hidden in applet
3312 <!-- JAL-1996 -->Updated instructions for applet
3313 deployment on examples pages.
3320 <td width="60" nowrap>
3321 <div align="center">
3322 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3323 <em>16/10/2015</em></strong>
3326 <td><em>General</em>
3328 <li>Time stamps for signed Jalview application and applet
3333 <em>Application</em>
3335 <li>Duplicate group consensus and conservation rows
3336 shown when tree is partitioned</li>
3337 <li>Erratic behaviour when tree partitions made with
3338 multiple cDNA/Protein split views</li>
3344 <td width="60" nowrap>
3345 <div align="center">
3346 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3347 <em>8/10/2015</em></strong>
3350 <td><em>General</em>
3352 <li>Updated Spanish translations of localized text for
3354 </ul> <em>Application</em>
3356 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3357 <li>Signed OSX InstallAnywhere installer<br></li>
3358 <li>Support for per-sequence based annotations in BioJSON</li>
3359 </ul> <em>Applet</em>
3361 <li>Split frame example added to applet examples page</li>
3362 </ul> <em>Build and Deployment</em>
3365 <!-- JAL-1888 -->New ant target for running Jalview's test
3373 <li>Mapping of cDNA to protein in split frames
3374 incorrect when sequence start > 1</li>
3375 <li>Broken images in filter column by annotation dialog
3377 <li>Feature colours not parsed from features file</li>
3378 <li>Exceptions and incomplete link URLs recovered when
3379 loading a features file containing HTML tags in feature
3383 <em>Application</em>
3385 <li>Annotations corrupted after BioJS export and
3387 <li>Incorrect sequence limits after Fetch DB References
3388 with 'trim retrieved sequences'</li>
3389 <li>Incorrect warning about deleting all data when
3390 deleting selected columns</li>
3391 <li>Patch to build system for shipping properly signed
3392 JNLP templates for webstart launch</li>
3393 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3394 unreleased structures for download or viewing</li>
3395 <li>Tab/space/return keystroke operation of EMBL-PDBe
3396 fetcher/viewer dialogs works correctly</li>
3397 <li>Disabled 'minimise' button on Jalview windows
3398 running on OSX to workaround redraw hang bug</li>
3399 <li>Split cDNA/Protein view position and geometry not
3400 recovered from jalview project</li>
3401 <li>Initial enabled/disabled state of annotation menu
3402 sorter 'show autocalculated first/last' corresponds to
3404 <li>Restoring of Clustal, RNA Helices and T-Coffee
3405 color schemes from BioJSON</li>
3409 <li>Reorder sequences mirrored in cDNA/Protein split
3411 <li>Applet with Jmol examples not loading correctly</li>
3417 <td><div align="center">
3418 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3420 <td><em>General</em>
3422 <li>Linked visualisation and analysis of DNA and Protein
3425 <li>Translated cDNA alignments shown as split protein
3426 and DNA alignment views</li>
3427 <li>Codon consensus annotation for linked protein and
3428 cDNA alignment views</li>
3429 <li>Link cDNA or Protein product sequences by loading
3430 them onto Protein or cDNA alignments</li>
3431 <li>Reconstruct linked cDNA alignment from aligned
3432 protein sequences</li>
3435 <li>Jmol integration updated to Jmol v14.2.14</li>
3436 <li>Import and export of Jalview alignment views as <a
3437 href="features/bioJsonFormat.html">BioJSON</a></li>
3438 <li>New alignment annotation file statements for
3439 reference sequences and marking hidden columns</li>
3440 <li>Reference sequence based alignment shading to
3441 highlight variation</li>
3442 <li>Select or hide columns according to alignment
3444 <li>Find option for locating sequences by description</li>
3445 <li>Conserved physicochemical properties shown in amino
3446 acid conservation row</li>
3447 <li>Alignments can be sorted by number of RNA helices</li>
3448 </ul> <em>Application</em>
3450 <li>New cDNA/Protein analysis capabilities
3452 <li>Get Cross-References should open a Split Frame
3453 view with cDNA/Protein</li>
3454 <li>Detect when nucleotide sequences and protein
3455 sequences are placed in the same alignment</li>
3456 <li>Split cDNA/Protein views are saved in Jalview
3461 <li>Use REST API to talk to Chimera</li>
3462 <li>Selected regions in Chimera are highlighted in linked
3463 Jalview windows</li>
3465 <li>VARNA RNA viewer updated to v3.93</li>
3466 <li>VARNA views are saved in Jalview Projects</li>
3467 <li>Pseudoknots displayed as Jalview RNA annotation can
3468 be shown in VARNA</li>
3470 <li>Make groups for selection uses marked columns as well
3471 as the active selected region</li>
3473 <li>Calculate UPGMA and NJ trees using sequence feature
3475 <li>New Export options
3477 <li>New Export Settings dialog to control hidden
3478 region export in flat file generation</li>
3480 <li>Export alignment views for display with the <a
3481 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3483 <li>Export scrollable SVG in HTML page</li>
3484 <li>Optional embedding of BioJSON data when exporting
3485 alignment figures to HTML</li>
3487 <li>3D structure retrieval and display
3489 <li>Free text and structured queries with the PDBe
3491 <li>PDBe Search API based discovery and selection of
3492 PDB structures for a sequence set</li>
3496 <li>JPred4 employed for protein secondary structure
3498 <li>Hide Insertions menu option to hide unaligned columns
3499 for one or a group of sequences</li>
3500 <li>Automatically hide insertions in alignments imported
3501 from the JPred4 web server</li>
3502 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3503 system on OSX<br />LGPL libraries courtesy of <a
3504 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3506 <li>changed 'View nucleotide structure' submenu to 'View
3507 VARNA 2D Structure'</li>
3508 <li>change "View protein structure" menu option to "3D
3511 </ul> <em>Applet</em>
3513 <li>New layout for applet example pages</li>
3514 <li>New parameters to enable SplitFrame view
3515 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3516 <li>New example demonstrating linked viewing of cDNA and
3517 Protein alignments</li>
3518 </ul> <em>Development and deployment</em>
3520 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3521 <li>Include installation type and git revision in build
3522 properties and console log output</li>
3523 <li>Jalview Github organisation, and new github site for
3524 storing BioJsMSA Templates</li>
3525 <li>Jalview's unit tests now managed with TestNG</li>
3528 <!-- <em>General</em>
3530 </ul> --> <!-- issues resolved --> <em>Application</em>
3532 <li>Escape should close any open find dialogs</li>
3533 <li>Typo in select-by-features status report</li>
3534 <li>Consensus RNA secondary secondary structure
3535 predictions are not highlighted in amber</li>
3536 <li>Missing gap character in v2.7 example file means
3537 alignment appears unaligned when pad-gaps is not enabled</li>
3538 <li>First switch to RNA Helices colouring doesn't colour
3539 associated structure views</li>
3540 <li>ID width preference option is greyed out when auto
3541 width checkbox not enabled</li>
3542 <li>Stopped a warning dialog from being shown when
3543 creating user defined colours</li>
3544 <li>'View Mapping' in structure viewer shows sequence
3545 mappings for just that viewer's sequences</li>
3546 <li>Workaround for superposing PDB files containing
3547 multiple models in Chimera</li>
3548 <li>Report sequence position in status bar when hovering
3549 over Jmol structure</li>
3550 <li>Cannot output gaps as '.' symbols with Selection ->
3551 output to text box</li>
3552 <li>Flat file exports of alignments with hidden columns
3553 have incorrect sequence start/end</li>
3554 <li>'Aligning' a second chain to a Chimera structure from
3556 <li>Colour schemes applied to structure viewers don't
3557 work for nucleotide</li>
3558 <li>Loading/cut'n'pasting an empty or invalid file leads
3559 to a grey/invisible alignment window</li>
3560 <li>Exported Jpred annotation from a sequence region
3561 imports to different position</li>
3562 <li>Space at beginning of sequence feature tooltips shown
3563 on some platforms</li>
3564 <li>Chimera viewer 'View | Show Chain' menu is not
3566 <li>'New View' fails with a Null Pointer Exception in
3567 console if Chimera has been opened</li>
3568 <li>Mouseover to Chimera not working</li>
3569 <li>Miscellaneous ENA XML feature qualifiers not
3571 <li>NPE in annotation renderer after 'Extract Scores'</li>
3572 <li>If two structures in one Chimera window, mouseover of
3573 either sequence shows on first structure</li>
3574 <li>'Show annotations' options should not make
3575 non-positional annotations visible</li>
3576 <li>Subsequence secondary structure annotation not shown
3577 in right place after 'view flanking regions'</li>
3578 <li>File Save As type unset when current file format is
3580 <li>Save as '.jar' option removed for saving Jalview
3582 <li>Colour by Sequence colouring in Chimera more
3584 <li>Cannot 'add reference annotation' for a sequence in
3585 several views on same alignment</li>
3586 <li>Cannot show linked products for EMBL / ENA records</li>
3587 <li>Jalview's tooltip wraps long texts containing no
3589 </ul> <em>Applet</em>
3591 <li>Jmol to JalviewLite mouseover/link not working</li>
3592 <li>JalviewLite can't import sequences with ID
3593 descriptions containing angle brackets</li>
3594 </ul> <em>General</em>
3596 <li>Cannot export and reimport RNA secondary structure
3597 via jalview annotation file</li>
3598 <li>Random helix colour palette for colour by annotation
3599 with RNA secondary structure</li>
3600 <li>Mouseover to cDNA from STOP residue in protein
3601 translation doesn't work.</li>
3602 <li>hints when using the select by annotation dialog box</li>
3603 <li>Jmol alignment incorrect if PDB file has alternate CA
3605 <li>FontChooser message dialog appears to hang after
3606 choosing 1pt font</li>
3607 <li>Peptide secondary structure incorrectly imported from
3608 annotation file when annotation display text includes 'e' or
3610 <li>Cannot set colour of new feature type whilst creating
3612 <li>cDNA translation alignment should not be sequence
3613 order dependent</li>
3614 <li>'Show unconserved' doesn't work for lower case
3616 <li>Nucleotide ambiguity codes involving R not recognised</li>
3617 </ul> <em>Deployment and Documentation</em>
3619 <li>Applet example pages appear different to the rest of
3620 www.jalview.org</li>
3621 </ul> <em>Application Known issues</em>
3623 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3624 <li>Misleading message appears after trying to delete
3626 <li>Jalview icon not shown in dock after InstallAnywhere
3627 version launches</li>
3628 <li>Fetching EMBL reference for an RNA sequence results
3629 fails with a sequence mismatch</li>
3630 <li>Corrupted or unreadable alignment display when
3631 scrolling alignment to right</li>
3632 <li>ArrayIndexOutOfBoundsException thrown when remove
3633 empty columns called on alignment with ragged gapped ends</li>
3634 <li>auto calculated alignment annotation rows do not get
3635 placed above or below non-autocalculated rows</li>
3636 <li>Jalview dekstop becomes sluggish at full screen in
3637 ultra-high resolution</li>
3638 <li>Cannot disable consensus calculation independently of
3639 quality and conservation</li>
3640 <li>Mouseover highlighting between cDNA and protein can
3641 become sluggish with more than one splitframe shown</li>
3642 </ul> <em>Applet Known Issues</em>
3644 <li>Core PDB parsing code requires Jmol</li>
3645 <li>Sequence canvas panel goes white when alignment
3646 window is being resized</li>
3652 <td><div align="center">
3653 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3655 <td><em>General</em>
3657 <li>Updated Java code signing certificate donated by
3659 <li>Features and annotation preserved when performing
3660 pairwise alignment</li>
3661 <li>RNA pseudoknot annotation can be
3662 imported/exported/displayed</li>
3663 <li>'colour by annotation' can colour by RNA and
3664 protein secondary structure</li>
3665 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3666 post-hoc with 2.9 release</em>)
3669 </ul> <em>Application</em>
3671 <li>Extract and display secondary structure for sequences
3672 with 3D structures</li>
3673 <li>Support for parsing RNAML</li>
3674 <li>Annotations menu for layout
3676 <li>sort sequence annotation rows by alignment</li>
3677 <li>place sequence annotation above/below alignment
3680 <li>Output in Stockholm format</li>
3681 <li>Internationalisation: improved Spanish (es)
3683 <li>Structure viewer preferences tab</li>
3684 <li>Disorder and Secondary Structure annotation tracks
3685 shared between alignments</li>
3686 <li>UCSF Chimera launch and linked highlighting from
3688 <li>Show/hide all sequence associated annotation rows for
3689 all or current selection</li>
3690 <li>disorder and secondary structure predictions
3691 available as dataset annotation</li>
3692 <li>Per-sequence rna helices colouring</li>
3695 <li>Sequence database accessions imported when fetching
3696 alignments from Rfam</li>
3697 <li>update VARNA version to 3.91</li>
3699 <li>New groovy scripts for exporting aligned positions,
3700 conservation values, and calculating sum of pairs scores.</li>
3701 <li>Command line argument to set default JABAWS server</li>
3702 <li>include installation type in build properties and
3703 console log output</li>
3704 <li>Updated Jalview project format to preserve dataset
3708 <!-- issues resolved --> <em>Application</em>
3710 <li>Distinguish alignment and sequence associated RNA
3711 structure in structure->view->VARNA</li>
3712 <li>Raise dialog box if user deletes all sequences in an
3714 <li>Pressing F1 results in documentation opening twice</li>
3715 <li>Sequence feature tooltip is wrapped</li>
3716 <li>Double click on sequence associated annotation
3717 selects only first column</li>
3718 <li>Redundancy removal doesn't result in unlinked
3719 leaves shown in tree</li>
3720 <li>Undos after several redundancy removals don't undo
3722 <li>Hide sequence doesn't hide associated annotation</li>
3723 <li>User defined colours dialog box too big to fit on
3724 screen and buttons not visible</li>
3725 <li>author list isn't updated if already written to
3726 Jalview properties</li>
3727 <li>Popup menu won't open after retrieving sequence
3729 <li>File open window for associate PDB doesn't open</li>
3730 <li>Left-then-right click on a sequence id opens a
3731 browser search window</li>
3732 <li>Cannot open sequence feature shading/sort popup menu
3733 in feature settings dialog</li>
3734 <li>better tooltip placement for some areas of Jalview
3736 <li>Allow addition of JABAWS Server which doesn't
3737 pass validation</li>
3738 <li>Web services parameters dialog box is too large to
3740 <li>Muscle nucleotide alignment preset obscured by
3742 <li>JABAWS preset submenus don't contain newly
3743 defined user preset</li>
3744 <li>MSA web services warns user if they were launched
3745 with invalid input</li>
3746 <li>Jalview cannot contact DAS Registy when running on
3749 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3750 'Superpose with' submenu not shown when new view
3754 </ul> <!-- <em>Applet</em>
3756 </ul> <em>General</em>
3758 </ul>--> <em>Deployment and Documentation</em>
3760 <li>2G and 1G options in launchApp have no effect on
3761 memory allocation</li>
3762 <li>launchApp service doesn't automatically open
3763 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3765 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3766 InstallAnywhere reports cannot find valid JVM when Java
3767 1.7_055 is available
3769 </ul> <em>Application Known issues</em>
3772 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3773 corrupted or unreadable alignment display when scrolling
3777 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3778 retrieval fails but progress bar continues for DAS retrieval
3779 with large number of ID
3782 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3783 flatfile output of visible region has incorrect sequence
3787 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3788 rna structure consensus doesn't update when secondary
3789 structure tracks are rearranged
3792 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3793 invalid rna structure positional highlighting does not
3794 highlight position of invalid base pairs
3797 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3798 out of memory errors are not raised when saving Jalview
3799 project from alignment window file menu
3802 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3803 Switching to RNA Helices colouring doesn't propagate to
3807 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3808 colour by RNA Helices not enabled when user created
3809 annotation added to alignment
3812 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3813 Jalview icon not shown on dock in Mountain Lion/Webstart
3815 </ul> <em>Applet Known Issues</em>
3818 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3819 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3822 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3823 Jalview and Jmol example not compatible with IE9
3826 <li>Sort by annotation score doesn't reverse order
3832 <td><div align="center">
3833 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3836 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3839 <li>Internationalisation of user interface (usually
3840 called i18n support) and translation for Spanish locale</li>
3841 <li>Define/Undefine group on current selection with
3842 Ctrl-G/Shift Ctrl-G</li>
3843 <li>Improved group creation/removal options in
3844 alignment/sequence Popup menu</li>
3845 <li>Sensible precision for symbol distribution
3846 percentages shown in logo tooltip.</li>
3847 <li>Annotation panel height set according to amount of
3848 annotation when alignment first opened</li>
3849 </ul> <em>Application</em>
3851 <li>Interactive consensus RNA secondary structure
3852 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3853 <li>Select columns containing particular features from
3854 Feature Settings dialog</li>
3855 <li>View all 'representative' PDB structures for selected
3857 <li>Update Jalview project format:
3859 <li>New file extension for Jalview projects '.jvp'</li>
3860 <li>Preserve sequence and annotation dataset (to
3861 store secondary structure annotation,etc)</li>
3862 <li>Per group and alignment annotation and RNA helix
3866 <li>New similarity measures for PCA and Tree calculation
3868 <li>Experimental support for retrieval and viewing of
3869 flanking regions for an alignment</li>
3873 <!-- issues resolved --> <em>Application</em>
3875 <li>logo keeps spinning and status remains at queued or
3876 running after job is cancelled</li>
3877 <li>cannot export features from alignments imported from
3878 Jalview/VAMSAS projects</li>
3879 <li>Buggy slider for web service parameters that take
3881 <li>Newly created RNA secondary structure line doesn't
3882 have 'display all symbols' flag set</li>
3883 <li>T-COFFEE alignment score shading scheme and other
3884 annotation shading not saved in Jalview project</li>
3885 <li>Local file cannot be loaded in freshly downloaded
3887 <li>Jalview icon not shown on dock in Mountain
3889 <li>Load file from desktop file browser fails</li>
3890 <li>Occasional NPE thrown when calculating large trees</li>
3891 <li>Cannot reorder or slide sequences after dragging an
3892 alignment onto desktop</li>
3893 <li>Colour by annotation dialog throws NPE after using
3894 'extract scores' function</li>
3895 <li>Loading/cut'n'pasting an empty file leads to a grey
3896 alignment window</li>
3897 <li>Disorder thresholds rendered incorrectly after
3898 performing IUPred disorder prediction</li>
3899 <li>Multiple group annotated consensus rows shown when
3900 changing 'normalise logo' display setting</li>
3901 <li>Find shows blank dialog after 'finished searching' if
3902 nothing matches query</li>
3903 <li>Null Pointer Exceptions raised when sorting by
3904 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3906 <li>Errors in Jmol console when structures in alignment
3907 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3909 <li>Not all working JABAWS services are shown in
3911 <li>JAVAWS version of Jalview fails to launch with
3912 'invalid literal/length code'</li>
3913 <li>Annotation/RNA Helix colourschemes cannot be applied
3914 to alignment with groups (actually fixed in 2.8.0b1)</li>
3915 <li>RNA Helices and T-Coffee Scores available as default
3918 </ul> <em>Applet</em>
3920 <li>Remove group option is shown even when selection is
3922 <li>Apply to all groups ticked but colourscheme changes
3923 don't affect groups</li>
3924 <li>Documented RNA Helices and T-Coffee Scores as valid
3925 colourscheme name</li>
3926 <li>Annotation labels drawn on sequence IDs when
3927 Annotation panel is not displayed</li>
3928 <li>Increased font size for dropdown menus on OSX and
3929 embedded windows</li>
3930 </ul> <em>Other</em>
3932 <li>Consensus sequence for alignments/groups with a
3933 single sequence were not calculated</li>
3934 <li>annotation files that contain only groups imported as
3935 annotation and junk sequences</li>
3936 <li>Fasta files with sequences containing '*' incorrectly
3937 recognised as PFAM or BLC</li>
3938 <li>conservation/PID slider apply all groups option
3939 doesn't affect background (2.8.0b1)
3941 <li>redundancy highlighting is erratic at 0% and 100%</li>
3942 <li>Remove gapped columns fails for sequences with ragged
3944 <li>AMSA annotation row with leading spaces is not
3945 registered correctly on import</li>
3946 <li>Jalview crashes when selecting PCA analysis for
3947 certain alignments</li>
3948 <li>Opening the colour by annotation dialog for an
3949 existing annotation based 'use original colours'
3950 colourscheme loses original colours setting</li>
3955 <td><div align="center">
3956 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3957 <em>30/1/2014</em></strong>
3961 <li>Trusted certificates for JalviewLite applet and
3962 Jalview Desktop application<br />Certificate was donated by
3963 <a href="https://www.certum.eu">Certum</a> to the Jalview
3964 open source project).
3966 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3967 <li>Output in Stockholm format</li>
3968 <li>Allow import of data from gzipped files</li>
3969 <li>Export/import group and sequence associated line
3970 graph thresholds</li>
3971 <li>Nucleotide substitution matrix that supports RNA and
3972 ambiguity codes</li>
3973 <li>Allow disorder predictions to be made on the current
3974 selection (or visible selection) in the same way that JPred
3976 <li>Groovy scripting for headless Jalview operation</li>
3977 </ul> <em>Other improvements</em>
3979 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3980 <li>COMBINE statement uses current SEQUENCE_REF and
3981 GROUP_REF scope to group annotation rows</li>
3982 <li>Support '' style escaping of quotes in Newick
3984 <li>Group options for JABAWS service by command line name</li>
3985 <li>Empty tooltip shown for JABA service options with a
3986 link but no description</li>
3987 <li>Select primary source when selecting authority in
3988 database fetcher GUI</li>
3989 <li>Add .mfa to FASTA file extensions recognised by
3991 <li>Annotation label tooltip text wrap</li>
3996 <li>Slow scrolling when lots of annotation rows are
3998 <li>Lots of NPE (and slowness) after creating RNA
3999 secondary structure annotation line</li>
4000 <li>Sequence database accessions not imported when
4001 fetching alignments from Rfam</li>
4002 <li>Incorrect SHMR submission for sequences with
4004 <li>View all structures does not always superpose
4006 <li>Option widgets in service parameters not updated to
4007 reflect user or preset settings</li>
4008 <li>Null pointer exceptions for some services without
4009 presets or adjustable parameters</li>
4010 <li>Discover PDB IDs entry in structure menu doesn't
4011 discover PDB xRefs</li>
4012 <li>Exception encountered while trying to retrieve
4013 features with DAS</li>
4014 <li>Lowest value in annotation row isn't coloured
4015 when colour by annotation (per sequence) is coloured</li>
4016 <li>Keyboard mode P jumps to start of gapped region when
4017 residue follows a gap</li>
4018 <li>Jalview appears to hang importing an alignment with
4019 Wrap as default or after enabling Wrap</li>
4020 <li>'Right click to add annotations' message
4021 shown in wrap mode when no annotations present</li>
4022 <li>Disorder predictions fail with NPE if no automatic
4023 annotation already exists on alignment</li>
4024 <li>oninit javascript function should be called after
4025 initialisation completes</li>
4026 <li>Remove redundancy after disorder prediction corrupts
4027 alignment window display</li>
4028 <li>Example annotation file in documentation is invalid</li>
4029 <li>Grouped line graph annotation rows are not exported
4030 to annotation file</li>
4031 <li>Multi-harmony analysis cannot be run when only two
4033 <li>Cannot create multiple groups of line graphs with
4034 several 'combine' statements in annotation file</li>
4035 <li>Pressing return several times causes Number Format
4036 exceptions in keyboard mode</li>
4037 <li>Multi-harmony (SHMMR) method doesn't submit
4038 correct partitions for input data</li>
4039 <li>Translation from DNA to Amino Acids fails</li>
4040 <li>Jalview fail to load newick tree with quoted label</li>
4041 <li>--headless flag isn't understood</li>
4042 <li>ClassCastException when generating EPS in headless
4044 <li>Adjusting sequence-associated shading threshold only
4045 changes one row's threshold</li>
4046 <li>Preferences and Feature settings panel panel
4047 doesn't open</li>
4048 <li>hide consensus histogram also hides conservation and
4049 quality histograms</li>
4054 <td><div align="center">
4055 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
4057 <td><em>Application</em>
4059 <li>Support for JABAWS 2.0 Services (AACon alignment
4060 conservation, protein disorder and Clustal Omega)</li>
4061 <li>JABAWS server status indicator in Web Services
4063 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
4064 in Jalview alignment window</li>
4065 <li>Updated Jalview build and deploy framework for OSX
4066 mountain lion, windows 7, and 8</li>
4067 <li>Nucleotide substitution matrix for PCA that supports
4068 RNA and ambiguity codes</li>
4070 <li>Improved sequence database retrieval GUI</li>
4071 <li>Support fetching and database reference look up
4072 against multiple DAS sources (Fetch all from in 'fetch db
4074 <li>Jalview project improvements
4076 <li>Store and retrieve the 'belowAlignment'
4077 flag for annotation</li>
4078 <li>calcId attribute to group annotation rows on the
4080 <li>Store AACon calculation settings for a view in
4081 Jalview project</li>
4085 <li>horizontal scrolling gesture support</li>
4086 <li>Visual progress indicator when PCA calculation is
4088 <li>Simpler JABA web services menus</li>
4089 <li>visual indication that web service results are still
4090 being retrieved from server</li>
4091 <li>Serialise the dialogs that are shown when Jalview
4092 starts up for first time</li>
4093 <li>Jalview user agent string for interacting with HTTP
4095 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
4097 <li>Examples directory and Groovy library included in
4098 InstallAnywhere distribution</li>
4099 </ul> <em>Applet</em>
4101 <li>RNA alignment and secondary structure annotation
4102 visualization applet example</li>
4103 </ul> <em>General</em>
4105 <li>Normalise option for consensus sequence logo</li>
4106 <li>Reset button in PCA window to return dimensions to
4108 <li>Allow seqspace or Jalview variant of alignment PCA
4110 <li>PCA with either nucleic acid and protein substitution
4112 <li>Allow windows containing HTML reports to be exported
4114 <li>Interactive display and editing of RNA secondary
4115 structure contacts</li>
4116 <li>RNA Helix Alignment Colouring</li>
4117 <li>RNA base pair logo consensus</li>
4118 <li>Parse sequence associated secondary structure
4119 information in Stockholm files</li>
4120 <li>HTML Export database accessions and annotation
4121 information presented in tooltip for sequences</li>
4122 <li>Import secondary structure from LOCARNA clustalw
4123 style RNA alignment files</li>
4124 <li>import and visualise T-COFFEE quality scores for an
4126 <li>'colour by annotation' per sequence option to
4127 shade each sequence according to its associated alignment
4129 <li>New Jalview Logo</li>
4130 </ul> <em>Documentation and Development</em>
4132 <li>documentation for score matrices used in Jalview</li>
4133 <li>New Website!</li>
4135 <td><em>Application</em>
4137 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
4138 wsdbfetch REST service</li>
4139 <li>Stop windows being moved outside desktop on OSX</li>
4140 <li>Filetype associations not installed for webstart
4142 <li>Jalview does not always retrieve progress of a JABAWS
4143 job execution in full once it is complete</li>
4144 <li>revise SHMR RSBS definition to ensure alignment is
4145 uploaded via ali_file parameter</li>
4146 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
4147 <li>View all structures superposed fails with exception</li>
4148 <li>Jnet job queues forever if a very short sequence is
4149 submitted for prediction</li>
4150 <li>Cut and paste menu not opened when mouse clicked on
4152 <li>Putting fractional value into integer text box in
4153 alignment parameter dialog causes Jalview to hang</li>
4154 <li>Structure view highlighting doesn't work on
4156 <li>View all structures fails with exception shown in
4158 <li>Characters in filename associated with PDBEntry not
4159 escaped in a platform independent way</li>
4160 <li>Jalview desktop fails to launch with exception when
4162 <li>Tree calculation reports 'you must have 2 or more
4163 sequences selected' when selection is empty</li>
4164 <li>Jalview desktop fails to launch with jar signature
4165 failure when java web start temporary file caching is
4167 <li>DAS Sequence retrieval with range qualification
4168 results in sequence xref which includes range qualification</li>
4169 <li>Errors during processing of command line arguments
4170 cause progress bar (JAL-898) to be removed</li>
4171 <li>Replace comma for semi-colon option not disabled for
4172 DAS sources in sequence fetcher</li>
4173 <li>Cannot close news reader when JABAWS server warning
4174 dialog is shown</li>
4175 <li>Option widgets not updated to reflect user settings</li>
4176 <li>Edited sequence not submitted to web service</li>
4177 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
4178 <li>InstallAnywhere installer doesn't unpack and run
4179 on OSX Mountain Lion</li>
4180 <li>Annotation panel not given a scroll bar when
4181 sequences with alignment annotation are pasted into the
4183 <li>Sequence associated annotation rows not associated
4184 when loaded from Jalview project</li>
4185 <li>Browser launch fails with NPE on java 1.7</li>
4186 <li>JABAWS alignment marked as finished when job was
4187 cancelled or job failed due to invalid input</li>
4188 <li>NPE with v2.7 example when clicking on Tree
4189 associated with all views</li>
4190 <li>Exceptions when copy/paste sequences with grouped
4191 annotation rows to new window</li>
4192 </ul> <em>Applet</em>
4194 <li>Sequence features are momentarily displayed before
4195 they are hidden using hidefeaturegroups applet parameter</li>
4196 <li>loading features via javascript API automatically
4197 enables feature display</li>
4198 <li>scrollToColumnIn javascript API method doesn't
4200 </ul> <em>General</em>
4202 <li>Redundancy removal fails for rna alignment</li>
4203 <li>PCA calculation fails when sequence has been selected
4204 and then deselected</li>
4205 <li>PCA window shows grey box when first opened on OSX</li>
4206 <li>Letters coloured pink in sequence logo when alignment
4207 coloured with clustalx</li>
4208 <li>Choosing fonts without letter symbols defined causes
4209 exceptions and redraw errors</li>
4210 <li>Initial PCA plot view is not same as manually
4211 reconfigured view</li>
4212 <li>Grouped annotation graph label has incorrect line
4214 <li>Grouped annotation graph label display is corrupted
4215 for lots of labels</li>
4220 <div align="center">
4221 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
4224 <td><em>Application</em>
4226 <li>Jalview Desktop News Reader</li>
4227 <li>Tweaked default layout of web services menu</li>
4228 <li>View/alignment association menu to enable user to
4229 easily specify which alignment a multi-structure view takes
4230 its colours/correspondences from</li>
4231 <li>Allow properties file location to be specified as URL</li>
4232 <li>Extend Jalview project to preserve associations
4233 between many alignment views and a single Jmol display</li>
4234 <li>Store annotation row height in Jalview project file</li>
4235 <li>Annotation row column label formatting attributes
4236 stored in project file</li>
4237 <li>Annotation row order for auto-calculated annotation
4238 rows preserved in Jalview project file</li>
4239 <li>Visual progress indication when Jalview state is
4240 saved using Desktop window menu</li>
4241 <li>Visual indication that command line arguments are
4242 still being processed</li>
4243 <li>Groovy script execution from URL</li>
4244 <li>Colour by annotation default min and max colours in
4246 <li>Automatically associate PDB files dragged onto an
4247 alignment with sequences that have high similarity and
4249 <li>Update JGoogleAnalytics to latest release (0.3)</li>
4250 <li>'view structures' option to open many
4251 structures in same window</li>
4252 <li>Sort associated views menu option for tree panel</li>
4253 <li>Group all JABA and non-JABA services for a particular
4254 analysis function in its own submenu</li>
4255 </ul> <em>Applet</em>
4257 <li>Userdefined and autogenerated annotation rows for
4259 <li>Adjustment of alignment annotation pane height</li>
4260 <li>Annotation scrollbar for annotation panel</li>
4261 <li>Drag to reorder annotation rows in annotation panel</li>
4262 <li>'automaticScrolling' parameter</li>
4263 <li>Allow sequences with partial ID string matches to be
4264 annotated from GFF/Jalview features files</li>
4265 <li>Sequence logo annotation row in applet</li>
4266 <li>Absolute paths relative to host server in applet
4267 parameters are treated as such</li>
4268 <li>New in the JalviewLite javascript API:
4270 <li>JalviewLite.js javascript library</li>
4271 <li>Javascript callbacks for
4273 <li>Applet initialisation</li>
4274 <li>Sequence/alignment mouse-overs and selections</li>
4277 <li>scrollTo row and column alignment scrolling
4279 <li>Select sequence/alignment regions from javascript</li>
4280 <li>javascript structure viewer harness to pass
4281 messages between Jmol and Jalview when running as
4282 distinct applets</li>
4283 <li>sortBy method</li>
4284 <li>Set of applet and application examples shipped
4285 with documentation</li>
4286 <li>New example to demonstrate JalviewLite and Jmol
4287 javascript message exchange</li>
4289 </ul> <em>General</em>
4291 <li>Enable Jmol displays to be associated with multiple
4292 multiple alignments</li>
4293 <li>Option to automatically sort alignment with new tree</li>
4294 <li>User configurable link to enable redirects to a
4295 www.Jalview.org mirror</li>
4296 <li>Jmol colours option for Jmol displays</li>
4297 <li>Configurable newline string when writing alignment
4298 and other flat files</li>
4299 <li>Allow alignment annotation description lines to
4300 contain html tags</li>
4301 </ul> <em>Documentation and Development</em>
4303 <li>Add groovy test harness for bulk load testing to
4305 <li>Groovy script to load and align a set of sequences
4306 using a web service before displaying the result in the
4307 Jalview desktop</li>
4308 <li>Restructured javascript and applet api documentation</li>
4309 <li>Ant target to publish example html files with applet
4311 <li>Netbeans project for building Jalview from source</li>
4312 <li>ant task to create online javadoc for Jalview source</li>
4314 <td><em>Application</em>
4316 <li>User defined colourscheme throws exception when
4317 current built in colourscheme is saved as new scheme</li>
4318 <li>AlignFrame->Save in application pops up save
4319 dialog for valid filename/format</li>
4320 <li>Cannot view associated structure for UniProt sequence</li>
4321 <li>PDB file association breaks for UniProt sequence
4323 <li>Associate PDB from file dialog does not tell you
4324 which sequence is to be associated with the file</li>
4325 <li>Find All raises null pointer exception when query
4326 only matches sequence IDs</li>
4327 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4328 <li>Jalview project with Jmol views created with Jalview
4329 2.4 cannot be loaded</li>
4330 <li>Filetype associations not installed for webstart
4332 <li>Two or more chains in a single PDB file associated
4333 with sequences in different alignments do not get coloured
4334 by their associated sequence</li>
4335 <li>Visibility status of autocalculated annotation row
4336 not preserved when project is loaded</li>
4337 <li>Annotation row height and visibility attributes not
4338 stored in Jalview project</li>
4339 <li>Tree bootstraps are not preserved when saved as a
4340 Jalview project</li>
4341 <li>Envision2 workflow tooltips are corrupted</li>
4342 <li>Enabling show group conservation also enables colour
4343 by conservation</li>
4344 <li>Duplicate group associated conservation or consensus
4345 created on new view</li>
4346 <li>Annotation scrollbar not displayed after 'show
4347 all hidden annotation rows' option selected</li>
4348 <li>Alignment quality not updated after alignment
4349 annotation row is hidden then shown</li>
4350 <li>Preserve colouring of structures coloured by
4351 sequences in pre Jalview 2.7 projects</li>
4352 <li>Web service job parameter dialog is not laid out
4354 <li>Web services menu not refreshed after 'reset
4355 services' button is pressed in preferences</li>
4356 <li>Annotation off by one in Jalview v2_3 example project</li>
4357 <li>Structures imported from file and saved in project
4358 get name like jalview_pdb1234.txt when reloaded</li>
4359 <li>Jalview does not always retrieve progress of a JABAWS
4360 job execution in full once it is complete</li>
4361 </ul> <em>Applet</em>
4363 <li>Alignment height set incorrectly when lots of
4364 annotation rows are displayed</li>
4365 <li>Relative URLs in feature HTML text not resolved to
4367 <li>View follows highlighting does not work for positions
4369 <li><= shown as = in tooltip</li>
4370 <li>Export features raises exception when no features
4372 <li>Separator string used for serialising lists of IDs
4373 for javascript api is modified when separator string
4374 provided as parameter</li>
4375 <li>Null pointer exception when selecting tree leaves for
4376 alignment with no existing selection</li>
4377 <li>Relative URLs for datasources assumed to be relative
4378 to applet's codebase</li>
4379 <li>Status bar not updated after finished searching and
4380 search wraps around to first result</li>
4381 <li>StructureSelectionManager instance shared between
4382 several Jalview applets causes race conditions and memory
4384 <li>Hover tooltip and mouseover of position on structure
4385 not sent from Jmol in applet</li>
4386 <li>Certain sequences of javascript method calls to
4387 applet API fatally hang browser</li>
4388 </ul> <em>General</em>
4390 <li>View follows structure mouseover scrolls beyond
4391 position with wrapped view and hidden regions</li>
4392 <li>Find sequence position moves to wrong residue
4393 with/without hidden columns</li>
4394 <li>Sequence length given in alignment properties window
4396 <li>InvalidNumberFormat exceptions thrown when trying to
4397 import PDB like structure files</li>
4398 <li>Positional search results are only highlighted
4399 between user-supplied sequence start/end bounds</li>
4400 <li>End attribute of sequence is not validated</li>
4401 <li>Find dialog only finds first sequence containing a
4402 given sequence position</li>
4403 <li>Sequence numbering not preserved in MSF alignment
4405 <li>Jalview PDB file reader does not extract sequence
4406 from nucleotide chains correctly</li>
4407 <li>Structure colours not updated when tree partition
4408 changed in alignment</li>
4409 <li>Sequence associated secondary structure not correctly
4410 parsed in interleaved stockholm</li>
4411 <li>Colour by annotation dialog does not restore current
4413 <li>Hiding (nearly) all sequences doesn't work
4415 <li>Sequences containing lowercase letters are not
4416 properly associated with their pdb files</li>
4417 </ul> <em>Documentation and Development</em>
4419 <li>schemas/JalviewWsParamSet.xsd corrupted by
4420 ApplyCopyright tool</li>
4425 <div align="center">
4426 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4429 <td><em>Application</em>
4431 <li>New warning dialog when the Jalview Desktop cannot
4432 contact web services</li>
4433 <li>JABA service parameters for a preset are shown in
4434 service job window</li>
4435 <li>JABA Service menu entries reworded</li>
4439 <li>Modeller PIR IO broken - cannot correctly import a
4440 pir file emitted by Jalview</li>
4441 <li>Existing feature settings transferred to new
4442 alignment view created from cut'n'paste</li>
4443 <li>Improved test for mixed amino/nucleotide chains when
4444 parsing PDB files</li>
4445 <li>Consensus and conservation annotation rows
4446 occasionally become blank for all new windows</li>
4447 <li>Exception raised when right clicking above sequences
4448 in wrapped view mode</li>
4449 </ul> <em>Application</em>
4451 <li>multiple multiply aligned structure views cause cpu
4452 usage to hit 100% and computer to hang</li>
4453 <li>Web Service parameter layout breaks for long user
4454 parameter names</li>
4455 <li>Jaba service discovery hangs desktop if Jaba server
4462 <div align="center">
4463 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4466 <td><em>Application</em>
4468 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4469 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4472 <li>Web Services preference tab</li>
4473 <li>Analysis parameters dialog box and user defined
4475 <li>Improved speed and layout of Envision2 service menu</li>
4476 <li>Superpose structures using associated sequence
4478 <li>Export coordinates and projection as CSV from PCA
4480 </ul> <em>Applet</em>
4482 <li>enable javascript: execution by the applet via the
4483 link out mechanism</li>
4484 </ul> <em>Other</em>
4486 <li>Updated the Jmol Jalview interface to work with Jmol
4488 <li>The Jalview Desktop and JalviewLite applet now
4489 require Java 1.5</li>
4490 <li>Allow Jalview feature colour specification for GFF
4491 sequence annotation files</li>
4492 <li>New 'colour by label' keword in Jalview feature file
4493 type colour specification</li>
4494 <li>New Jalview Desktop Groovy API method that allows a
4495 script to check if it being run in an interactive session or
4496 in a batch operation from the Jalview command line</li>
4500 <li>clustalx colourscheme colours Ds preferentially when
4501 both D+E are present in over 50% of the column</li>
4502 </ul> <em>Application</em>
4504 <li>typo in AlignmentFrame->View->Hide->all but
4505 selected Regions menu item</li>
4506 <li>sequence fetcher replaces ',' for ';' when the ',' is
4507 part of a valid accession ID</li>
4508 <li>fatal OOM if object retrieved by sequence fetcher
4509 runs out of memory</li>
4510 <li>unhandled Out of Memory Error when viewing pca
4511 analysis results</li>
4512 <li>InstallAnywhere builds fail to launch on OS X java
4513 10.5 update 4 (due to apple Java 1.6 update)</li>
4514 <li>Installanywhere Jalview silently fails to launch</li>
4515 </ul> <em>Applet</em>
4517 <li>Jalview.getFeatureGroups() raises an
4518 ArrayIndexOutOfBoundsException if no feature groups are
4525 <div align="center">
4526 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4532 <li>Alignment prettyprinter doesn't cope with long
4534 <li>clustalx colourscheme colours Ds preferentially when
4535 both D+E are present in over 50% of the column</li>
4536 <li>nucleic acid structures retrieved from PDB do not
4537 import correctly</li>
4538 <li>More columns get selected than were clicked on when a
4539 number of columns are hidden</li>
4540 <li>annotation label popup menu not providing correct
4541 add/hide/show options when rows are hidden or none are
4543 <li>Stockholm format shown in list of readable formats,
4544 and parser copes better with alignments from RFAM.</li>
4545 <li>CSV output of consensus only includes the percentage
4546 of all symbols if sequence logo display is enabled</li>
4548 </ul> <em>Applet</em>
4550 <li>annotation panel disappears when annotation is
4552 </ul> <em>Application</em>
4554 <li>Alignment view not redrawn properly when new
4555 alignment opened where annotation panel is visible but no
4556 annotations are present on alignment</li>
4557 <li>pasted region containing hidden columns is
4558 incorrectly displayed in new alignment window</li>
4559 <li>Jalview slow to complete operations when stdout is
4560 flooded (fix is to close the Jalview console)</li>
4561 <li>typo in AlignmentFrame->View->Hide->all but
4562 selected Rregions menu item.</li>
4563 <li>inconsistent group submenu and Format submenu entry
4564 'Un' or 'Non'conserved</li>
4565 <li>Sequence feature settings are being shared by
4566 multiple distinct alignments</li>
4567 <li>group annotation not recreated when tree partition is
4569 <li>double click on group annotation to select sequences
4570 does not propagate to associated trees</li>
4571 <li>Mac OSX specific issues:
4573 <li>exception raised when mouse clicked on desktop
4574 window background</li>
4575 <li>Desktop menu placed on menu bar and application
4576 name set correctly</li>
4577 <li>sequence feature settings not wide enough for the
4578 save feature colourscheme button</li>
4587 <div align="center">
4588 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4591 <td><em>New Capabilities</em>
4593 <li>URL links generated from description line for
4594 regular-expression based URL links (applet and application)
4596 <li>Non-positional feature URL links are shown in link
4598 <li>Linked viewing of nucleic acid sequences and
4600 <li>Automatic Scrolling option in View menu to display
4601 the currently highlighted region of an alignment.</li>
4602 <li>Order an alignment by sequence length, or using the
4603 average score or total feature count for each sequence.</li>
4604 <li>Shading features by score or associated description</li>
4605 <li>Subdivide alignment and groups based on identity of
4606 selected subsequence (Make Groups from Selection).</li>
4607 <li>New hide/show options including Shift+Control+H to
4608 hide everything but the currently selected region.</li>
4609 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4610 </ul> <em>Application</em>
4612 <li>Fetch DB References capabilities and UI expanded to
4613 support retrieval from DAS sequence sources</li>
4614 <li>Local DAS Sequence sources can be added via the
4615 command line or via the Add local source dialog box.</li>
4616 <li>DAS Dbref and DbxRef feature types are parsed as
4617 database references and protein_name is parsed as
4618 description line (BioSapiens terms).</li>
4619 <li>Enable or disable non-positional feature and database
4620 references in sequence ID tooltip from View menu in
4622 <!-- <li>New hidden columns and rows and representatives capabilities
4623 in annotations file (in progress - not yet fully implemented)</li> -->
4624 <li>Group-associated consensus, sequence logos and
4625 conservation plots</li>
4626 <li>Symbol distributions for each column can be exported
4627 and visualized as sequence logos</li>
4628 <li>Optionally scale multi-character column labels to fit
4629 within each column of annotation row<!-- todo for applet -->
4631 <li>Optional automatic sort of associated alignment view
4632 when a new tree is opened.</li>
4633 <li>Jalview Java Console</li>
4634 <li>Better placement of desktop window when moving
4635 between different screens.</li>
4636 <li>New preference items for sequence ID tooltip and
4637 consensus annotation</li>
4638 <li>Client to submit sequences and IDs to Envision2
4640 <li><em>Vamsas Capabilities</em>
4642 <li>Improved VAMSAS synchronization (Jalview archive
4643 used to preserve views, structures, and tree display
4645 <li>Import of vamsas documents from disk or URL via
4647 <li>Sharing of selected regions between views and
4648 with other VAMSAS applications (Experimental feature!)</li>
4649 <li>Updated API to VAMSAS version 0.2</li>
4651 </ul> <em>Applet</em>
4653 <li>Middle button resizes annotation row height</li>
4656 <li>sortByTree (true/false) - automatically sort the
4657 associated alignment view by the tree when a new tree is
4659 <li>showTreeBootstraps (true/false) - show or hide
4660 branch bootstraps (default is to show them if available)</li>
4661 <li>showTreeDistances (true/false) - show or hide
4662 branch lengths (default is to show them if available)</li>
4663 <li>showUnlinkedTreeNodes (true/false) - indicate if
4664 unassociated nodes should be highlighted in the tree
4666 <li>heightScale and widthScale (1.0 or more) -
4667 increase the height or width of a cell in the alignment
4668 grid relative to the current font size.</li>
4671 <li>Non-positional features displayed in sequence ID
4673 </ul> <em>Other</em>
4675 <li>Features format: graduated colour definitions and
4676 specification of feature scores</li>
4677 <li>Alignment Annotations format: new keywords for group
4678 associated annotation (GROUP_REF) and annotation row display
4679 properties (ROW_PROPERTIES)</li>
4680 <li>XML formats extended to support graduated feature
4681 colourschemes, group associated annotation, and profile
4682 visualization settings.</li></td>
4685 <li>Source field in GFF files parsed as feature source
4686 rather than description</li>
4687 <li>Non-positional features are now included in sequence
4688 feature and gff files (controlled via non-positional feature
4689 visibility in tooltip).</li>
4690 <li>URL links generated for all feature links (bugfix)</li>
4691 <li>Added URL embedding instructions to features file
4693 <li>Codons containing ambiguous nucleotides translated as
4694 'X' in peptide product</li>
4695 <li>Match case switch in find dialog box works for both
4696 sequence ID and sequence string and query strings do not
4697 have to be in upper case to match case-insensitively.</li>
4698 <li>AMSA files only contain first column of
4699 multi-character column annotation labels</li>
4700 <li>Jalview Annotation File generation/parsing consistent
4701 with documentation (e.g. Stockholm annotation can be
4702 exported and re-imported)</li>
4703 <li>PDB files without embedded PDB IDs given a friendly
4705 <li>Find incrementally searches ID string matches as well
4706 as subsequence matches, and correctly reports total number
4710 <li>Better handling of exceptions during sequence
4712 <li>Dasobert generated non-positional feature URL
4713 link text excludes the start_end suffix</li>
4714 <li>DAS feature and source retrieval buttons disabled
4715 when fetch or registry operations in progress.</li>
4716 <li>PDB files retrieved from URLs are cached properly</li>
4717 <li>Sequence description lines properly shared via
4719 <li>Sequence fetcher fetches multiple records for all
4721 <li>Ensured that command line das feature retrieval
4722 completes before alignment figures are generated.</li>
4723 <li>Reduced time taken when opening file browser for
4725 <li>isAligned check prior to calculating tree, PCA or
4726 submitting an MSA to JNet now excludes hidden sequences.</li>
4727 <li>User defined group colours properly recovered
4728 from Jalview projects.</li>
4737 <div align="center">
4738 <strong>2.4.0.b2</strong><br> 28/10/2009
4743 <li>Experimental support for google analytics usage
4745 <li>Jalview privacy settings (user preferences and docs).</li>
4750 <li>Race condition in applet preventing startup in
4752 <li>Exception when feature created from selection beyond
4753 length of sequence.</li>
4754 <li>Allow synthetic PDB files to be imported gracefully</li>
4755 <li>Sequence associated annotation rows associate with
4756 all sequences with a given id</li>
4757 <li>Find function matches case-insensitively for sequence
4758 ID string searches</li>
4759 <li>Non-standard characters do not cause pairwise
4760 alignment to fail with exception</li>
4761 </ul> <em>Application Issues</em>
4763 <li>Sequences are now validated against EMBL database</li>
4764 <li>Sequence fetcher fetches multiple records for all
4766 </ul> <em>InstallAnywhere Issues</em>
4768 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4769 issue with installAnywhere mechanism)</li>
4770 <li>Command line launching of JARs from InstallAnywhere
4771 version (java class versioning error fixed)</li>
4778 <div align="center">
4779 <strong>2.4</strong><br> 27/8/2008
4782 <td><em>User Interface</em>
4784 <li>Linked highlighting of codon and amino acid from
4785 translation and protein products</li>
4786 <li>Linked highlighting of structure associated with
4787 residue mapping to codon position</li>
4788 <li>Sequence Fetcher provides example accession numbers
4789 and 'clear' button</li>
4790 <li>MemoryMonitor added as an option under Desktop's
4792 <li>Extract score function to parse whitespace separated
4793 numeric data in description line</li>
4794 <li>Column labels in alignment annotation can be centred.</li>
4795 <li>Tooltip for sequence associated annotation give name
4797 </ul> <em>Web Services and URL fetching</em>
4799 <li>JPred3 web service</li>
4800 <li>Prototype sequence search client (no public services
4802 <li>Fetch either seed alignment or full alignment from
4804 <li>URL Links created for matching database cross
4805 references as well as sequence ID</li>
4806 <li>URL Links can be created using regular-expressions</li>
4807 </ul> <em>Sequence Database Connectivity</em>
4809 <li>Retrieval of cross-referenced sequences from other
4811 <li>Generalised database reference retrieval and
4812 validation to all fetchable databases</li>
4813 <li>Fetch sequences from DAS sources supporting the
4814 sequence command</li>
4815 </ul> <em>Import and Export</em>
4816 <li>export annotation rows as CSV for spreadsheet import</li>
4817 <li>Jalview projects record alignment dataset associations,
4818 EMBL products, and cDNA sequence mappings</li>
4819 <li>Sequence Group colour can be specified in Annotation
4821 <li>Ad-hoc colouring of group in Annotation File using RGB
4822 triplet as name of colourscheme</li>
4823 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4825 <li>treenode binding for VAMSAS tree exchange</li>
4826 <li>local editing and update of sequences in VAMSAS
4827 alignments (experimental)</li>
4828 <li>Create new or select existing session to join</li>
4829 <li>load and save of vamsas documents</li>
4830 </ul> <em>Application command line</em>
4832 <li>-tree parameter to open trees (introduced for passing
4834 <li>-fetchfrom command line argument to specify nicknames
4835 of DAS servers to query for alignment features</li>
4836 <li>-dasserver command line argument to add new servers
4837 that are also automatically queried for features</li>
4838 <li>-groovy command line argument executes a given groovy
4839 script after all input data has been loaded and parsed</li>
4840 </ul> <em>Applet-Application data exchange</em>
4842 <li>Trees passed as applet parameters can be passed to
4843 application (when using "View in full
4844 application")</li>
4845 </ul> <em>Applet Parameters</em>
4847 <li>feature group display control parameter</li>
4848 <li>debug parameter</li>
4849 <li>showbutton parameter</li>
4850 </ul> <em>Applet API methods</em>
4852 <li>newView public method</li>
4853 <li>Window (current view) specific get/set public methods</li>
4854 <li>Feature display control methods</li>
4855 <li>get list of currently selected sequences</li>
4856 </ul> <em>New Jalview distribution features</em>
4858 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4859 <li>RELEASE file gives build properties for the latest
4860 Jalview release.</li>
4861 <li>Java 1.1 Applet build made easier and donotobfuscate
4862 property controls execution of obfuscator</li>
4863 <li>Build target for generating source distribution</li>
4864 <li>Debug flag for javacc</li>
4865 <li>.jalview_properties file is documented (slightly) in
4866 jalview.bin.Cache</li>
4867 <li>Continuous Build Integration for stable and
4868 development version of Application, Applet and source
4873 <li>selected region output includes visible annotations
4874 (for certain formats)</li>
4875 <li>edit label/displaychar contains existing label/char
4877 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4878 <li>shorter peptide product names from EMBL records</li>
4879 <li>Newick string generator makes compact representations</li>
4880 <li>bootstrap values parsed correctly for tree files with
4882 <li>pathological filechooser bug avoided by not allowing
4883 filenames containing a ':'</li>
4884 <li>Fixed exception when parsing GFF files containing
4885 global sequence features</li>
4886 <li>Alignment datasets are finalized only when number of
4887 references from alignment sequences goes to zero</li>
4888 <li>Close of tree branch colour box without colour
4889 selection causes cascading exceptions</li>
4890 <li>occasional negative imgwidth exceptions</li>
4891 <li>better reporting of non-fatal warnings to user when
4892 file parsing fails.</li>
4893 <li>Save works when Jalview project is default format</li>
4894 <li>Save as dialog opened if current alignment format is
4895 not a valid output format</li>
4896 <li>UniProt canonical names introduced for both das and
4898 <li>Histidine should be midblue (not pink!) in Zappo</li>
4899 <li>error messages passed up and output when data read
4901 <li>edit undo recovers previous dataset sequence when
4902 sequence is edited</li>
4903 <li>allow PDB files without pdb ID HEADER lines (like
4904 those generated by MODELLER) to be read in properly</li>
4905 <li>allow reading of JPred concise files as a normal
4907 <li>Stockholm annotation parsing and alignment properties
4908 import fixed for PFAM records</li>
4909 <li>Structure view windows have correct name in Desktop
4911 <li>annotation consisting of sequence associated scores
4912 can be read and written correctly to annotation file</li>
4913 <li>Aligned cDNA translation to aligned peptide works
4915 <li>Fixed display of hidden sequence markers and
4916 non-italic font for representatives in Applet</li>
4917 <li>Applet Menus are always embedded in applet window on
4919 <li>Newly shown features appear at top of stack (in
4921 <li>Annotations added via parameter not drawn properly
4922 due to null pointer exceptions</li>
4923 <li>Secondary structure lines are drawn starting from
4924 first column of alignment</li>
4925 <li>UniProt XML import updated for new schema release in
4927 <li>Sequence feature to sequence ID match for Features
4928 file is case-insensitive</li>
4929 <li>Sequence features read from Features file appended to
4930 all sequences with matching IDs</li>
4931 <li>PDB structure coloured correctly for associated views
4932 containing a sub-sequence</li>
4933 <li>PDB files can be retrieved by applet from Jar files</li>
4934 <li>feature and annotation file applet parameters
4935 referring to different directories are retrieved correctly</li>
4936 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4937 <li>Fixed application hang whilst waiting for
4938 splash-screen version check to complete</li>
4939 <li>Applet properly URLencodes input parameter values
4940 when passing them to the launchApp service</li>
4941 <li>display name and local features preserved in results
4942 retrieved from web service</li>
4943 <li>Visual delay indication for sequence retrieval and
4944 sequence fetcher initialisation</li>
4945 <li>updated Application to use DAS 1.53e version of
4946 dasobert DAS client</li>
4947 <li>Re-instated Full AMSA support and .amsa file
4949 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4957 <div align="center">
4958 <strong>2.3</strong><br> 9/5/07
4963 <li>Jmol 11.0.2 integration</li>
4964 <li>PDB views stored in Jalview XML files</li>
4965 <li>Slide sequences</li>
4966 <li>Edit sequence in place</li>
4967 <li>EMBL CDS features</li>
4968 <li>DAS Feature mapping</li>
4969 <li>Feature ordering</li>
4970 <li>Alignment Properties</li>
4971 <li>Annotation Scores</li>
4972 <li>Sort by scores</li>
4973 <li>Feature/annotation editing in applet</li>
4978 <li>Headless state operation in 2.2.1</li>
4979 <li>Incorrect and unstable DNA pairwise alignment</li>
4980 <li>Cut and paste of sequences with annotation</li>
4981 <li>Feature group display state in XML</li>
4982 <li>Feature ordering in XML</li>
4983 <li>blc file iteration selection using filename # suffix</li>
4984 <li>Stockholm alignment properties</li>
4985 <li>Stockhom alignment secondary structure annotation</li>
4986 <li>2.2.1 applet had no feature transparency</li>
4987 <li>Number pad keys can be used in cursor mode</li>
4988 <li>Structure Viewer mirror image resolved</li>
4995 <div align="center">
4996 <strong>2.2.1</strong><br> 12/2/07
5001 <li>Non standard characters can be read and displayed
5002 <li>Annotations/Features can be imported/exported to the
5004 <li>Applet allows editing of sequence/annotation/group
5005 name & description
5006 <li>Preference setting to display sequence name in
5008 <li>Annotation file format extended to allow
5009 Sequence_groups to be defined
5010 <li>Default opening of alignment overview panel can be
5011 specified in preferences
5012 <li>PDB residue numbering annotation added to associated
5018 <li>Applet crash under certain Linux OS with Java 1.6
5020 <li>Annotation file export / import bugs fixed
5021 <li>PNG / EPS image output bugs fixed
5027 <div align="center">
5028 <strong>2.2</strong><br> 27/11/06
5033 <li>Multiple views on alignment
5034 <li>Sequence feature editing
5035 <li>"Reload" alignment
5036 <li>"Save" to current filename
5037 <li>Background dependent text colour
5038 <li>Right align sequence ids
5039 <li>User-defined lower case residue colours
5042 <li>Menu item accelerator keys
5043 <li>Control-V pastes to current alignment
5044 <li>Cancel button for DAS Feature Fetching
5045 <li>PCA and PDB Viewers zoom via mouse roller
5046 <li>User-defined sub-tree colours and sub-tree selection
5048 <li>'New Window' button on the 'Output to Text box'
5053 <li>New memory efficient Undo/Redo System
5054 <li>Optimised symbol lookups and conservation/consensus
5056 <li>Region Conservation/Consensus recalculated after
5058 <li>Fixed Remove Empty Columns Bug (empty columns at end
5060 <li>Slowed DAS Feature Fetching for increased robustness.
5062 <li>Made angle brackets in ASCII feature descriptions
5064 <li>Re-instated Zoom function for PCA
5065 <li>Sequence descriptions conserved in web service
5067 <li>UniProt ID discoverer uses any word separated by
5069 <li>WsDbFetch query/result association resolved
5070 <li>Tree leaf to sequence mapping improved
5071 <li>Smooth fonts switch moved to FontChooser dialog box.
5078 <div align="center">
5079 <strong>2.1.1</strong><br> 12/9/06
5084 <li>Copy consensus sequence to clipboard</li>
5089 <li>Image output - rightmost residues are rendered if
5090 sequence id panel has been resized</li>
5091 <li>Image output - all offscreen group boundaries are
5093 <li>Annotation files with sequence references - all
5094 elements in file are relative to sequence position</li>
5095 <li>Mac Applet users can use Alt key for group editing</li>
5101 <div align="center">
5102 <strong>2.1</strong><br> 22/8/06
5107 <li>MAFFT Multiple Alignment in default Web Service list</li>
5108 <li>DAS Feature fetching</li>
5109 <li>Hide sequences and columns</li>
5110 <li>Export Annotations and Features</li>
5111 <li>GFF file reading / writing</li>
5112 <li>Associate structures with sequences from local PDB
5114 <li>Add sequences to exisiting alignment</li>
5115 <li>Recently opened files / URL lists</li>
5116 <li>Applet can launch the full application</li>
5117 <li>Applet has transparency for features (Java 1.2
5119 <li>Applet has user defined colours parameter</li>
5120 <li>Applet can load sequences from parameter
5121 "sequence<em>x</em>"
5127 <li>Redundancy Panel reinstalled in the Applet</li>
5128 <li>Monospaced font - EPS / rescaling bug fixed</li>
5129 <li>Annotation files with sequence references bug fixed</li>
5135 <div align="center">
5136 <strong>2.08.1</strong><br> 2/5/06
5141 <li>Change case of selected region from Popup menu</li>
5142 <li>Choose to match case when searching</li>
5143 <li>Middle mouse button and mouse movement can compress /
5144 expand the visible width and height of the alignment</li>
5149 <li>Annotation Panel displays complete JNet results</li>
5155 <div align="center">
5156 <strong>2.08b</strong><br> 18/4/06
5162 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
5163 <li>Righthand label on wrapped alignments shows correct
5170 <div align="center">
5171 <strong>2.08</strong><br> 10/4/06
5176 <li>Editing can be locked to the selection area</li>
5177 <li>Keyboard editing</li>
5178 <li>Create sequence features from searches</li>
5179 <li>Precalculated annotations can be loaded onto
5181 <li>Features file allows grouping of features</li>
5182 <li>Annotation Colouring scheme added</li>
5183 <li>Smooth fonts off by default - Faster rendering</li>
5184 <li>Choose to toggle Autocalculate Consensus On/Off</li>
5189 <li>Drag & Drop fixed on Linux</li>
5190 <li>Jalview Archive file faster to load/save, sequence
5191 descriptions saved.</li>
5197 <div align="center">
5198 <strong>2.07</strong><br> 12/12/05
5203 <li>PDB Structure Viewer enhanced</li>
5204 <li>Sequence Feature retrieval and display enhanced</li>
5205 <li>Choose to output sequence start-end after sequence
5206 name for file output</li>
5207 <li>Sequence Fetcher WSDBFetch@EBI</li>
5208 <li>Applet can read feature files, PDB files and can be
5209 used for HTML form input</li>
5214 <li>HTML output writes groups and features</li>
5215 <li>Group editing is Control and mouse click</li>
5216 <li>File IO bugs</li>
5222 <div align="center">
5223 <strong>2.06</strong><br> 28/9/05
5228 <li>View annotations in wrapped mode</li>
5229 <li>More options for PCA viewer</li>
5234 <li>GUI bugs resolved</li>
5235 <li>Runs with -nodisplay from command line</li>
5241 <div align="center">
5242 <strong>2.05b</strong><br> 15/9/05
5247 <li>Choose EPS export as lineart or text</li>
5248 <li>Jar files are executable</li>
5249 <li>Can read in Uracil - maps to unknown residue</li>
5254 <li>Known OutOfMemory errors give warning message</li>
5255 <li>Overview window calculated more efficiently</li>
5256 <li>Several GUI bugs resolved</li>
5262 <div align="center">
5263 <strong>2.05</strong><br> 30/8/05
5268 <li>Edit and annotate in "Wrapped" view</li>
5273 <li>Several GUI bugs resolved</li>
5279 <div align="center">
5280 <strong>2.04</strong><br> 24/8/05
5285 <li>Hold down mouse wheel & scroll to change font
5291 <li>Improved JPred client reliability</li>
5292 <li>Improved loading of Jalview files</li>
5298 <div align="center">
5299 <strong>2.03</strong><br> 18/8/05
5304 <li>Set Proxy server name and port in preferences</li>
5305 <li>Multiple URL links from sequence ids</li>
5306 <li>User Defined Colours can have a scheme name and added
5308 <li>Choose to ignore gaps in consensus calculation</li>
5309 <li>Unix users can set default web browser</li>
5310 <li>Runs without GUI for batch processing</li>
5311 <li>Dynamically generated Web Service Menus</li>
5316 <li>InstallAnywhere download for Sparc Solaris</li>
5322 <div align="center">
5323 <strong>2.02</strong><br> 18/7/05
5329 <li>Copy & Paste order of sequences maintains
5330 alignment order.</li>
5336 <div align="center">
5337 <strong>2.01</strong><br> 12/7/05
5342 <li>Use delete key for deleting selection.</li>
5343 <li>Use Mouse wheel to scroll sequences.</li>
5344 <li>Help file updated to describe how to add alignment
5346 <li>Version and build date written to build properties
5348 <li>InstallAnywhere installation will check for updates
5349 at launch of Jalview.</li>
5354 <li>Delete gaps bug fixed.</li>
5355 <li>FileChooser sorts columns.</li>
5356 <li>Can remove groups one by one.</li>
5357 <li>Filechooser icons installed.</li>
5358 <li>Finder ignores return character when searching.
5359 Return key will initiate a search.<br>
5366 <div align="center">
5367 <strong>2.0</strong><br> 20/6/05
5372 <li>New codebase</li>