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>24/02/2022</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
92 <!-- JAL-3863 -->Support for Canonical Uniprot IDs
95 <!-- JAL-3204 -->Updated Jalview bindings for Uniprot XML
98 </ul> <em>JalviewJS</em>
101 <!-- 3624 -->PDB structures mapped to Uniprot Sequences with
114 <!-- JAL-3163 -->Missing message bundle keys are only
115 reported once per key (avoids excessive log output in js
119 <!-- JAL-3168 -->Feature type is included in the title of
120 the Feature Settings' Colour Chooser dialog
123 </ul> <em>Development</em>
125 <li>First integrated JalviewJS and Jalview release</li>
126 <li>Updated building instructions</li>
128 <!-- JAL-3679 -->Improved JalviewJS/Jalview build process
129 for system package provided eclipse installs on linux
131 <li>Install4j 9.0.x used for installer packaging</li>
132 <li>Notarized MacOS installer for compatibility with Big
133 Sur and Monterey</li>
135 <!-- JAL-3805 -->Uninstaller application for old
136 (InstallAnywhere based) Jalview installations removed from
140 <!-- JAL-3930 -->Improved use of installers for unattended
141 installation with a customizedId of "JALVIEW" in install4j's
151 <!-- JAL-3674 -->Slow structure commands can block Jalview
155 <!-- JAL-3904 -->Structure window's viewer-specific menu
156 disappears when only one structure is shown (and many
157 sequences:one chain mappings are present)
160 <!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
161 the first SEQUENCE_GROUP defined
166 <!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 -->Selections not
167 propagated between Linked CDS - Protein alignments and their
168 trees (known defect from 2.11.1.3)
171 <!-- JAL-3761 -->Not all codon positions highlighted for
172 overlapping exon splice sites (e.g due to RNA slippage)
175 <!-- JAL-3794 -->X was not being recognised as the unknown base
179 <!-- JAL-3915 -->Removed RNAview checkbox and logic from
180 Structure Preferences
183 <!-- JAL-3583 -->Tooltip behaviour improved (slightly)
186 <!-- JAL-3162 -->Can edit a feature so that start > end
189 <!-- JAL-2848 -->Cancel from Amend Features doesn't reset a
190 modified graduated colour
193 <!-- JAL-3788 -->New View with automatic 'Show Overview'
194 preference enabled results in Null Pointer Exceptions when
195 clustal colouring is enabled
197 <li><!-- JAL-3275 -->Can open multiple Preferences panels</li>
199 <!-- JAL-3949 -->Standard out logging broken: messages only
200 routing to stderr and appear as a raw template
202 </ul> <em>JalviewJS</em>
220 <!-- JAL-3762 -->JalviewJS doesn't honour arguments passed
221 via Info.args when there are arguments on the URL
224 <!-- JAL-3602 -->gradle closure-compiler not using UTF-8
227 <!-- JAL-3603 -->Annotation file fails to load from URL in
230 </ul> <em>Development</em>
234 <li>Fixed non-fatal gradle errors during build</li>
236 <!-- JAL-3745 -->Updated build.gradle for use with
246 <td width="60" align="center" nowrap><strong><a
247 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.7">.7</a><br />
248 <em>18/01/2022</em></strong></td>
250 <td align="left" valign="top">
253 <!-- JAL-3703, JAL-3935 -->Files open in Jalview cannot be
254 updated by Jalview or other applications (Windows, other non
257 </ul> <em>Security</em>
260 <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
266 <td width="60" align="center" nowrap><strong><a
267 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
268 <em>6/01/2022</em></strong></td>
270 <td align="left" valign="top"><em>Security</em>
273 <!-- JAL-3934 -->Version bump library dependency: Log4j 2.16.0 to 2.17.0.
280 <td width="60" align="center" nowrap><strong><a
281 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
282 <em>20/12/2021</em></strong></td>
284 <td align="left" valign="top"><em>Security</em>
287 <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
289 </ul> <em>Development</em>
291 <li>Updated building instructions</li>
296 <!-- JAL-3840 -->Occupancy calculation is incorrect for
297 alignment columns with over -1+2^32 gaps (breaking filtering
301 <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
302 scale factors being set with buggy window-managers (linux
305 </ul> <em>Development</em>
307 <li>Fixed non-fatal gradle errors during build</li>
312 <td width="60" align="center" nowrap><strong><a
313 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
314 <em>09/03/2021</em></strong></td>
315 <td align="left" valign="top"><em>Improved control of
316 Jalview's use of network services via jalview_properties</em>
319 <!-- JAL-3814 -->New .jalview_properties token controlling
320 launch of the news browser (like -nonews argument)
323 <!-- JAL-3813 -->New .jalview_properties token controlling
324 download of linkout URLs from
325 www.jalview.org/services/identifiers
328 <!-- JAL-3812 -->New .jalview_properties token controlling
329 download of BIOJSHTML templates
332 <!-- JAL-3811 -->New 'Discover Web Services' option to
333 trigger a one off JABAWS discovery if autodiscovery was
337 <td align="left" valign="top">
340 <!-- JAL-3818 -->Intermittent deadlock opening structure in
343 </ul> <em>New Known defects</em>
346 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
347 always restored from project (since 2.10.3)
350 <!-- JAL-3806 -->Selections from tree built from CDS aren't
351 propagated to Protein alignment (since 2.11.1.3)
357 <td width="60" align="center" nowrap><strong><a
358 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
359 <em>29/10/2020</em></strong></td>
360 <td align="left" valign="top">
365 <td align="left" valign="top">
368 <!-- JAL-3765 -->Find doesn't always highlight all matching
369 positions in a sequence (bug introduced in 2.11.1.2)
372 <!-- JAL-3760 -->Alignments containing one or more protein
373 sequences can be classed as nucleotide
376 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
377 sequences after alignment of protein products (known defect
378 first reported for 2.11.1.0)
381 <!-- JAL-3725 -->No tooltip or popup menu for genomic
382 features outwith CDS shown overlaid on protein
385 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
386 correctly mapped by Jalview (e.g. affects viral CDS with
387 ribosomal slippage, since 2.9.0)
390 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
394 <!-- JAL-3700 -->Selections in CDS sequence panel don't
395 always select corresponding protein sequences
398 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
399 column selection doesn't always ignore hidden columns
401 </ul> <em>Installer</em>
404 <!-- JAL-3611 -->Space character in Jalview install path on
405 Windows prevents install4j launching getdown
407 </ul> <em>Development</em>
410 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
411 version numbers in doc/building.md
417 <td width="60" align="center" nowrap><strong><a
418 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
419 <em>25/09/2020</em></strong></td>
420 <td align="left" valign="top">
424 <td align="left" valign="top">
427 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
428 "Encountered problems opening
429 https://www.jalview.org/examples/exampleFile_2_7.jvp"
435 <td width="60" align="center" nowrap><strong><a
436 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
437 <em>17/09/2020</em></strong></td>
438 <td align="left" valign="top">
441 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
442 residue in cursor mode
445 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
446 HTSJDK from 2.12 to 2.23
449 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
450 optimisations and improvements suggested by Bob Hanson and
451 improved compatibility with JalviewJS
454 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
455 alignments from Pfam and Rfam
458 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
459 import (no longer based on .gz extension)
462 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
465 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
466 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
470 <!-- JAL-3667 -->Improved warning messages, debug logging
471 and fixed Retry action when Jalview encounters errors when
472 saving or making backup files.
475 <!-- JAL-3676 -->Enhanced Jalview Java Console:
477 <li>Jalview's logging level can be configured</li>
478 <li>Copy to Clipboard Buttion</li>
482 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
483 when running on Linux (Requires Java 11+)
485 </ul> <em>Launching Jalview</em>
488 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
489 through a system property
492 <!-- JAL-3477 -->Improved built-in documentation and command
493 line help for configuring Jalview's memory
497 <td align="left" valign="top">
500 <!-- JAL-3691 -->Conservation and Quality tracks are shown
501 but not calculated and no protein or DNA score models are
502 available for tree/PCA calculation when launched with
503 Turkish language locale
506 <!-- JAL-3493 -->Escape does not clear highlights on the
507 alignment (Since Jalview 2.10.3)
510 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
511 doesn't slide selected sequences, just sequence under cursor
514 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
515 sequence under the cursor
518 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
519 multiple EMBL gene products shown for a single contig
522 <!-- JAL-3696 -->Errors encountered when processing variants
523 from VCF files yield "Error processing VCF: Format specifier
527 <!-- JAL-3697 -->Count of features not shown can be wrong
528 when there are both local and complementary features mapped
529 to the position under the cursor
532 <!-- JAL-3673 -->Sequence ID for reference sequence is
533 clipped when Right align Sequence IDs enabled
536 <!-- JAL-2983 -->Slider with negative range values not
537 rendered correctly in VAqua4 (Since 2.10.4)
540 <!-- JAL-3685 -->Single quotes not displayed correctly in
541 internationalised text for some messages and log output
544 <!-- JAL-3490 -->Find doesn't report matches that span
545 hidden gapped columns
548 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
549 panels, Alignment viewport and annotation renderer.
552 <!-- JAL-3561 -->Jalview ignores file format parameter
553 specifying output format when exporting an alignment via the
557 <!-- JAL-3667 -->Windows 10: For a minority of users, if
558 backups are not enabled, Jalview sometimes fails to
559 overwrite an existing file and raises a warning dialog. (in
560 2.11.0, and 2.11.1.0, the workaround is to try to save the
561 file again, and if that fails, delete the original file and
565 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
569 <!-- JAL-3741 -->References to http://www.jalview.org in
570 program and documentation
572 </ul> <em>Launching Jalview</em>
575 <!-- JAL-3718 -->Jalview application fails when launched the
576 first time for a version that has different jars to the
577 previous launched version.
579 </ul> <em>Developing Jalview</em>
582 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
583 data, causing cloverReport gradle task to fail with an
587 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
588 monitor the release channel
590 </ul> <em>New Known defects</em>
593 <!-- JAL-3748 -->CDS shown in result of submitting proteins
594 in a CDS/Protein alignment to a web service is wrong when
595 proteins share a common transcript sequence (e.g.
596 genome of RNA viruses)
599 <!-- JAL-3576 -->Co-located features exported and re-imported
600 are ordered differently when shown on alignment and in
601 tooltips. (Also affects v2.11.1.0)
604 <!-- JAL-3702 -->Drag and drop of alignment file onto
605 alignment window when in a HiDPI scaled mode in Linux only
606 works for the top left quadrant of the alignment window
609 <!-- JAL-3701 -->Stale build data in jalview standalone jar
610 builds (only affects 2.11.1.1 branch)
613 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
614 when alignment view restored from project (since Jalview 2.11.0)
617 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
618 protein products for certain ENA records are repeatedly
619 shown via Calculate->Show Cross Refs
625 <td width="60" align="center" nowrap><strong><a
626 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
627 <em>22/04/2020</em></strong></td>
628 <td align="left" valign="top">
631 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
632 'virtual' codon features shown on protein (or vice versa)
633 for display in alignments, on structure views (including
634 transfer to UCSF chimera), in feature reports and for
638 <!-- JAL-3121 -->Feature attributes from VCF files can be
639 exported and re-imported as GFF3 files
642 <!-- JAL-3376 -->Capture VCF "fixed column" values
643 POS, ID, QUAL, FILTER as Feature Attributes
646 <!-- JAL-3375 -->More robust VCF numeric data field
647 validation while parsing
650 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
654 <!-- JAL-3535 -->Feature Settings dialog title includes name
658 <!-- JAL-3538 -->Font anti-aliasing in alignment views
662 <!-- JAL-3468 -->Very long feature descriptions truncated in
666 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
667 with no feature types visible
670 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
672 </ul><em>Jalview Installer</em>
675 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
676 in console (may be null when Jalview launched as executable jar or via conda)
679 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
682 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
685 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
687 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
688 </ul> <em>Release processes</em>
691 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
694 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
696 </ul> <em>Build System</em>
699 <!-- JAL-3510 -->Clover updated to 4.4.1
702 <!-- JAL-3513 -->Test code included in Clover coverage
706 <em>Groovy Scripts</em>
709 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
710 to stdout containing the consensus sequence for each
711 alignment in a Jalview session
714 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
715 genomic sequence_variant annotation from CDS as
716 missense_variant or synonymous_variant on protein products.
720 <td align="left" valign="top">
723 <!-- JAL-3581 -->Hidden sequence markers still visible when
724 'Show hidden markers' option is not ticked
727 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
728 PNG output when 'Automatically set ID width' is set in
729 jalview preferences or properties file
732 <!-- JAL-3571 -->Feature Editor dialog can be opened when
733 'Show Sequence Features' option is not ticked
736 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
737 buttons in Feature Settings dialog are clicked when no
741 <!-- JAL-3412 -->ID margins for CDS and Protein views not
742 equal when split frame is first opened
745 <!-- JAL-3296 -->Sequence position numbers in status bar not
746 correct after editing a sequence's start position
749 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
750 with annotation and exceptions thrown when only a few
751 columns shown in wrapped mode
754 <!-- JAL-3386 -->Sequence IDs missing in headless export of
755 wrapped alignment figure with annotations
758 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
759 ID fails with ClassCastException
762 <!-- JAL-3389 -->Chimera session not restored from Jalview
766 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
767 feature settings dialog also selects columns
770 <!-- JAL-3473 -->SpinnerNumberModel causes
771 IllegalArgumentException in some circumstances
774 <!-- JAL-3534 -->Multiple feature settings dialogs can be
778 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
779 alignment window is closed
782 <!-- JAL-3406 -->Credits missing some authors in Jalview
783 help documentation for 2.11.0 release
786 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
787 includes Pfam ID as sequence's accession rather than its
790 </ul> <em>Java 11 Compatibility issues</em>
793 <!-- JAL-2987 -->OSX - Can't view some search results in
794 PDB/Uniprot search panel
796 </ul> <em>Installer</em>
799 <!-- JAL-3447 -->Jalview should not create file associations
800 for 3D structure files (.pdb, .mmcif. .cif)
802 </ul> <em>Repository and Source Release</em>
805 <!-- JAL-3474 -->removed obsolete .cvsignore files from
809 <!-- JAL-3541 -->Clover report generation running out of
812 </ul> <em>New Known Issues</em>
815 <!-- JAL-3523 -->OSX - Current working directory not
816 preserved when Jalview.app launched with parameters from
820 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
821 clipped in headless figure export when Right Align option
825 <!-- JAL-3542 -->Jalview Installation type always reports
826 'Source' in console output
829 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
830 bamboo server but run fine locally.
836 <td width="60" align="center" nowrap>
837 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
838 <em>04/07/2019</em></strong>
840 <td align="left" valign="top">
843 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
844 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
845 source project) rather than InstallAnywhere
848 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
849 settings, receive over the air updates and launch specific
850 versions via (<a href="https://github.com/threerings/getdown">Three
854 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
855 formats supported by Jalview (including .jvp project files)
858 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
859 arguments and switch between different getdown channels
862 <!-- JAL-3141 -->Backup files created when saving Jalview project
867 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
868 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
870 <!-- JAL-2620 -->Alternative genetic code tables for
871 'Translate as cDNA'</li>
873 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
874 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
877 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
878 implementation that allows updates) used for Sequence Feature collections</li>
880 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
881 features can be filtered and shaded according to any
882 associated attributes (e.g. variant attributes from VCF
883 file, or key-value pairs imported from column 9 of GFF
887 <!-- JAL-2879 -->Feature Attributes and shading schemes
888 stored and restored from Jalview Projects
891 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
892 recognise variant features
895 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
896 sequences (also coloured red by default)
899 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
903 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
904 algorithm (Z-sort/transparency and filter aware)
907 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
913 <!-- JAL-3205 -->Symmetric score matrices for faster
914 tree and PCA calculations
916 <li><strong>Principal Components Analysis Viewer</strong>
919 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
920 and Viewer state saved in Jalview Project
922 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
925 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
929 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
934 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
936 <li><strong>Speed and Efficiency</strong>
939 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
940 multiple groups when working with large alignments
943 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
947 <li><strong>User Interface</strong>
950 <!-- JAL-2933 -->Finder panel remembers last position in each
954 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
955 what is shown)<br />Only visible regions of alignment are shown by
956 default (can be changed in user preferences)
959 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
960 to the Overwrite Dialog
963 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
967 <!-- JAL-1244 -->Status bar shows bounds when dragging a
968 selection region, and gap count when inserting or deleting gaps
971 <!-- JAL-3132 -->Status bar updates over sequence and annotation
975 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
979 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
983 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
986 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
990 <!-- JAL-3181 -->Consistent ordering of links in sequence id
994 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
996 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
1000 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
1001 <li><strong>Java 11 Support (not yet on general release)</strong>
1004 <!-- -->OSX GUI integrations for App menu's 'About' entry and
1009 <em>Deprecations</em>
1011 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
1012 capabilities removed from the Jalview Desktop
1014 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
1015 unmarshalling has been replaced by JAXB for Jalview projects
1016 and XML based data retrieval clients</li>
1017 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
1018 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
1019 </ul> <em>Documentation</em>
1021 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
1022 not supported in EPS figure export
1024 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
1025 </ul> <em>Development and Release Processes</em>
1028 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
1031 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
1033 <!-- JAL-3225 -->Eclipse project configuration managed with
1037 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
1038 Bamboo continuous integration for unattended Test Suite
1042 <!-- JAL-2864 -->Memory test suite to detect leaks in common
1046 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
1050 <!-- JAL-3248 -->Developer documentation migrated to
1051 markdown (with HTML rendering)
1054 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
1057 <!-- JAL-3289 -->New URLs for publishing development
1062 <td align="left" valign="top">
1065 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
1068 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
1069 superposition in Jmol fail on Windows
1072 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
1073 structures for sequences with lots of PDB structures
1076 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
1080 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
1081 project involving multiple views
1084 <!-- JAL-3164 -->Overview for complementary view in a linked
1085 CDS/Protein alignment is not updated when Hide Columns by
1086 Annotation dialog hides columns
1089 <!-- JAL-3158 -->Selection highlighting in the complement of a
1090 CDS/Protein alignment stops working after making a selection in
1091 one view, then making another selection in the other view
1094 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
1098 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
1099 Settings and Jalview Preferences panels
1102 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
1103 overview with large alignments
1106 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
1107 region if columns were selected by dragging right-to-left and the
1108 mouse moved to the left of the first column
1111 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
1112 hidden column marker via scale popup menu
1115 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
1116 doesn't tell users the invalid URL
1119 <!-- JAL-2816 -->Tooltips displayed for features filtered by
1123 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
1124 show cross references or Fetch Database References are shown in
1125 red in original view
1128 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
1129 peptide sequence (computed variant shown as p.Res.null)
1132 <!-- JAL-2060 -->'Graduated colour' option not offered for
1133 manually created features (where feature score is Float.NaN)
1136 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
1137 when columns are hidden
1140 <!-- JAL-3082 -->Regular expression error for '(' in Select
1141 Columns by Annotation description
1144 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
1145 out of Scale or Annotation Panel
1148 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
1152 <!-- JAL-3074 -->Left/right drag in annotation can scroll
1156 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
1160 <!-- JAL-3002 -->Column display is out by one after Page Down,
1161 Page Up in wrapped mode
1164 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
1167 <!-- JAL-2932 -->Finder searches in minimised alignments
1170 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
1171 on opening an alignment
1174 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
1178 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
1179 different groups in the alignment are selected
1182 <!-- JAL-2717 -->Internationalised colour scheme names not shown
1186 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
1190 <!-- JAL-3125 -->Value input for graduated feature colour
1191 threshold gets 'unrounded'
1194 <!-- JAL-2982 -->PCA image export doesn't respect background
1198 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
1201 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
1204 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
1208 <!-- JAL-2964 -->Associate Tree with All Views not restored from
1212 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
1213 shown in complementary view
1216 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
1217 without normalisation
1220 <!-- JAL-3021 -->Sequence Details report should open positioned at top
1224 <!-- JAL-914 -->Help page can be opened twice
1227 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
1229 </ul> <em>Editing</em>
1232 <!-- JAL-2822 -->Start and End should be updated when sequence
1233 data at beginning or end of alignment added/removed via 'Edit'
1237 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
1238 relocate sequence features correctly when start of sequence is
1239 removed (Known defect since 2.10)
1242 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
1243 dialog corrupts dataset sequence
1246 <!-- JAL-868 -->Structure colours not updated when associated tree
1247 repartitions the alignment view (Regression in 2.10.5)
1249 </ul> <em>Datamodel</em>
1252 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
1253 sequence's End is greater than its length
1255 </ul> <em>Bugs fixed for Java 11 Support (not yet on
1256 general release)</em>
1259 <!-- JAL-3288 -->Menus work properly in split-screen
1261 </ul> <em>New Known Defects</em>
1264 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
1267 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
1268 regions of protein alignment.
1271 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
1272 is restored from a Jalview 2.11 project
1275 <!-- JAL-3213 -->Alignment panel height can be too small after
1279 <!-- JAL-3240 -->Display is incorrect after removing gapped
1280 columns within hidden columns
1283 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
1284 window after dragging left to select columns to left of visible
1288 <!-- JAL-2876 -->Features coloured according to their description
1289 string and thresholded by score in earlier versions of Jalview are
1290 not shown as thresholded features in 2.11. To workaround please
1291 create a Score filter instead.
1294 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
1296 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
1299 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1300 alignments with multiple views can close views unexpectedly
1303 <em>Java 11 Specific defects</em>
1306 <!-- JAL-3235 -->Jalview Properties file is not sorted
1307 alphabetically when saved
1313 <td width="60" nowrap>
1314 <div align="center">
1315 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1318 <td><div align="left">
1322 <!-- JAL-3101 -->Default memory for Jalview webstart and
1323 InstallAnywhere increased to 1G.
1326 <!-- JAL-247 -->Hidden sequence markers and representative
1327 sequence bolding included when exporting alignment as EPS,
1328 SVG, PNG or HTML. <em>Display is configured via the
1329 Format menu, or for command-line use via a Jalview
1330 properties file.</em>
1333 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1334 API and sequence data now imported as JSON.
1337 <!-- JAL-3065 -->Change in recommended way of starting
1338 Jalview via a Java command line: add jars in lib directory
1339 to CLASSPATH, rather than via the deprecated java.ext.dirs
1343 <em>Development</em>
1346 <!-- JAL-3047 -->Support added to execute test suite
1347 instrumented with <a href="http://openclover.org/">Open
1352 <td><div align="left">
1356 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1357 row shown in Feredoxin Structure alignment view of example
1361 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1362 annotation displayed.
1365 <!-- JAL-3107 -->Group conservation/consensus not shown
1366 for newly created group when 'Apply to all groups'
1370 <!-- JAL-3087 -->Corrupted display when switching to
1371 wrapped mode when sequence panel's vertical scrollbar is
1375 <!-- JAL-3003 -->Alignment is black in exported EPS file
1376 when sequences are selected in exported view.</em>
1379 <!-- JAL-3059 -->Groups with different coloured borders
1380 aren't rendered with correct colour.
1383 <!-- JAL-3092 -->Jalview could hang when importing certain
1384 types of knotted RNA secondary structure.
1387 <!-- JAL-3095 -->Sequence highlight and selection in
1388 trimmed VARNA 2D structure is incorrect for sequences that
1392 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1393 annotation when columns are inserted into an alignment,
1394 and when exporting as Stockholm flatfile.
1397 <!-- JAL-3053 -->Jalview annotation rows containing upper
1398 and lower-case 'E' and 'H' do not automatically get
1399 treated as RNA secondary structure.
1402 <!-- JAL-3106 -->.jvp should be used as default extension
1403 (not .jar) when saving a Jalview project file.
1406 <!-- JAL-3105 -->Mac Users: closing a window correctly
1407 transfers focus to previous window on OSX
1410 <em>Java 10 Issues Resolved</em>
1413 <!-- JAL-2988 -->OSX - Can't save new files via the File
1414 or export menus by typing in a name into the Save dialog
1418 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1419 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1420 'look and feel' which has improved compatibility with the
1421 latest version of OSX.
1428 <td width="60" nowrap>
1429 <div align="center">
1430 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1431 <em>7/06/2018</em></strong>
1434 <td><div align="left">
1438 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1439 annotation retrieved from Uniprot
1442 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1443 onto the Jalview Desktop
1447 <td><div align="left">
1451 <!-- JAL-3017 -->Cannot import features with multiple
1452 variant elements (blocks import of some Uniprot records)
1455 <!-- JAL-2997 -->Clustal files with sequence positions in
1456 right-hand column parsed correctly
1459 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1460 not alignment area in exported graphic
1463 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1464 window has input focus
1467 <!-- JAL-2992 -->Annotation panel set too high when
1468 annotation added to view (Windows)
1471 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1472 network connectivity is poor
1475 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1476 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1477 the currently open URL and links from a page viewed in
1478 Firefox or Chrome on Windows is now fully supported. If
1479 you are using Edge, only links in the page can be
1480 dragged, and with Internet Explorer, only the currently
1481 open URL in the browser can be dropped onto Jalview.</em>
1484 <em>New Known Defects</em>
1486 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1491 <td width="60" nowrap>
1492 <div align="center">
1493 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1496 <td><div align="left">
1500 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1501 for disabling automatic superposition of multiple
1502 structures and open structures in existing views
1505 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1506 ID and annotation area margins can be click-dragged to
1510 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1514 <!-- JAL-2759 -->Improved performance for large alignments
1515 and lots of hidden columns
1518 <!-- JAL-2593 -->Improved performance when rendering lots
1519 of features (particularly when transparency is disabled)
1522 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1523 exchange of Jalview features and Chimera attributes made
1529 <td><div align="left">
1532 <!-- JAL-2899 -->Structure and Overview aren't updated
1533 when Colour By Annotation threshold slider is adjusted
1536 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1537 overlapping alignment panel
1540 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1544 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1545 improved: CDS not handled correctly if transcript has no
1549 <!-- JAL-2321 -->Secondary structure and temperature
1550 factor annotation not added to sequence when local PDB
1551 file associated with it by drag'n'drop or structure
1555 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1556 dialog doesn't import PDB files dropped on an alignment
1559 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1560 scroll bar doesn't work for some CDS/Protein views
1563 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1564 Java 1.8u153 onwards and Java 1.9u4+.
1567 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1568 columns in annotation row
1571 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1572 honored in batch mode
1575 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1576 for structures added to existing Jmol view
1579 <!-- JAL-2223 -->'View Mappings' includes duplicate
1580 entries after importing project with multiple views
1583 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1584 protein sequences via SIFTS from associated PDB entries
1585 with negative residue numbers or missing residues fails
1588 <!-- JAL-2952 -->Exception when shading sequence with negative
1589 Temperature Factor values from annotated PDB files (e.g.
1590 as generated by CONSURF)
1593 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1594 tooltip doesn't include a text description of mutation
1597 <!-- JAL-2922 -->Invert displayed features very slow when
1598 structure and/or overview windows are also shown
1601 <!-- JAL-2954 -->Selecting columns from highlighted regions
1602 very slow for alignments with large numbers of sequences
1605 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1606 with 'StringIndexOutOfBounds'
1609 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1610 platforms running Java 10
1613 <!-- JAL-2960 -->Adding a structure to existing structure
1614 view appears to do nothing because the view is hidden behind the alignment view
1620 <!-- JAL-2926 -->Copy consensus sequence option in applet
1621 should copy the group consensus when popup is opened on it
1627 <!-- JAL-2913 -->Fixed ID width preference is not respected
1630 <em>New Known Defects</em>
1633 <!-- JAL-2973 --> Exceptions occasionally raised when
1634 editing a large alignment and overview is displayed
1637 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1638 repeatedly after a series of edits even when the overview
1639 is no longer reflecting updates
1642 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1643 structures for protein subsequence (if 'Trim Retrieved
1644 Sequences' enabled) or Ensembl isoforms (Workaround in
1645 2.10.4 is to fail back to N&W mapping)
1648 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1649 option gives blank output
1656 <td width="60" nowrap>
1657 <div align="center">
1658 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1661 <td><div align="left">
1662 <ul><li>Updated Certum Codesigning Certificate
1663 (Valid till 30th November 2018)</li></ul></div></td>
1664 <td><div align="left">
1665 <em>Desktop</em><ul>
1667 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1668 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1669 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1670 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1671 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1672 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1673 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1679 <td width="60" nowrap>
1680 <div align="center">
1681 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1684 <td><div align="left">
1688 <!-- JAL-2446 -->Faster and more efficient management and
1689 rendering of sequence features
1692 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1693 429 rate limit request hander
1696 <!-- JAL-2773 -->Structure views don't get updated unless
1697 their colours have changed
1700 <!-- JAL-2495 -->All linked sequences are highlighted for
1701 a structure mousover (Jmol) or selection (Chimera)
1704 <!-- JAL-2790 -->'Cancel' button in progress bar for
1705 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1708 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1709 view from Ensembl locus cross-references
1712 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1716 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1717 feature can be disabled
1720 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1721 PDB easier retrieval of sequences for lists of IDs
1724 <!-- JAL-2758 -->Short names for sequences retrieved from
1730 <li>Groovy interpreter updated to 2.4.12</li>
1731 <li>Example groovy script for generating a matrix of
1732 percent identity scores for current alignment.</li>
1734 <em>Testing and Deployment</em>
1737 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1741 <td><div align="left">
1745 <!-- JAL-2643 -->Pressing tab after updating the colour
1746 threshold text field doesn't trigger an update to the
1750 <!-- JAL-2682 -->Race condition when parsing sequence ID
1754 <!-- JAL-2608 -->Overview windows are also closed when
1755 alignment window is closed
1758 <!-- JAL-2548 -->Export of features doesn't always respect
1762 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1763 takes a long time in Cursor mode
1769 <!-- JAL-2777 -->Structures with whitespace chainCode
1770 cannot be viewed in Chimera
1773 <!-- JAL-2728 -->Protein annotation panel too high in
1777 <!-- JAL-2757 -->Can't edit the query after the server
1778 error warning icon is shown in Uniprot and PDB Free Text
1782 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1785 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1788 <!-- JAL-2739 -->Hidden column marker in last column not
1789 rendered when switching back from Wrapped to normal view
1792 <!-- JAL-2768 -->Annotation display corrupted when
1793 scrolling right in unwapped alignment view
1796 <!-- JAL-2542 -->Existing features on subsequence
1797 incorrectly relocated when full sequence retrieved from
1801 <!-- JAL-2733 -->Last reported memory still shown when
1802 Desktop->Show Memory is unticked (OSX only)
1805 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1806 features of same type and group to be selected for
1810 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1811 alignments when hidden columns are present
1814 <!-- JAL-2392 -->Jalview freezes when loading and
1815 displaying several structures
1818 <!-- JAL-2732 -->Black outlines left after resizing or
1822 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1823 within the Jalview desktop on OSX
1826 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1827 when in wrapped alignment mode
1830 <!-- JAL-2636 -->Scale mark not shown when close to right
1831 hand end of alignment
1834 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1835 each selected sequence do not have correct start/end
1839 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1840 after canceling the Alignment Window's Font dialog
1843 <!-- JAL-2036 -->Show cross-references not enabled after
1844 restoring project until a new view is created
1847 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1848 URL links appears when only default EMBL-EBI link is
1849 configured (since 2.10.2b2)
1852 <!-- JAL-2775 -->Overview redraws whole window when box
1853 position is adjusted
1856 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1857 in a multi-chain structure when viewing alignment
1858 involving more than one chain (since 2.10)
1861 <!-- JAL-2811 -->Double residue highlights in cursor mode
1862 if new selection moves alignment window
1865 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1866 arrow key in cursor mode to pass hidden column marker
1869 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1870 that produces correctly annotated transcripts and products
1873 <!-- JAL-2776 -->Toggling a feature group after first time
1874 doesn't update associated structure view
1877 <em>Applet</em><br />
1880 <!-- JAL-2687 -->Concurrent modification exception when
1881 closing alignment panel
1884 <em>BioJSON</em><br />
1887 <!-- JAL-2546 -->BioJSON export does not preserve
1888 non-positional features
1891 <em>New Known Issues</em>
1894 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1895 sequence features correctly (for many previous versions of
1899 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1900 using cursor in wrapped panel other than top
1903 <!-- JAL-2791 -->Select columns containing feature ignores
1904 graduated colour threshold
1907 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1908 always preserve numbering and sequence features
1911 <em>Known Java 9 Issues</em>
1914 <!-- JAL-2902 -->Groovy Console very slow to open and is
1915 not responsive when entering characters (Webstart, Java
1922 <td width="60" nowrap>
1923 <div align="center">
1924 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1925 <em>2/10/2017</em></strong>
1928 <td><div align="left">
1929 <em>New features in Jalview Desktop</em>
1932 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1934 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1938 <td><div align="left">
1942 <td width="60" nowrap>
1943 <div align="center">
1944 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1945 <em>7/9/2017</em></strong>
1948 <td><div align="left">
1952 <!-- JAL-2588 -->Show gaps in overview window by colouring
1953 in grey (sequences used to be coloured grey, and gaps were
1957 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1961 <!-- JAL-2587 -->Overview updates immediately on increase
1962 in size and progress bar shown as higher resolution
1963 overview is recalculated
1968 <td><div align="left">
1972 <!-- JAL-2664 -->Overview window redraws every hidden
1973 column region row by row
1976 <!-- JAL-2681 -->duplicate protein sequences shown after
1977 retrieving Ensembl crossrefs for sequences from Uniprot
1980 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1981 format setting is unticked
1984 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1985 if group has show boxes format setting unticked
1988 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1989 autoscrolling whilst dragging current selection group to
1990 include sequences and columns not currently displayed
1993 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1994 assemblies are imported via CIF file
1997 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1998 displayed when threshold or conservation colouring is also
2002 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
2006 <!-- JAL-2673 -->Jalview continues to scroll after
2007 dragging a selected region off the visible region of the
2011 <!-- JAL-2724 -->Cannot apply annotation based
2012 colourscheme to all groups in a view
2015 <!-- JAL-2511 -->IDs don't line up with sequences
2016 initially after font size change using the Font chooser or
2023 <td width="60" nowrap>
2024 <div align="center">
2025 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
2028 <td><div align="left">
2029 <em>Calculations</em>
2033 <!-- JAL-1933 -->Occupancy annotation row shows number of
2034 ungapped positions in each column of the alignment.
2037 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
2038 a calculation dialog box
2041 <!-- JAL-2379 -->Revised implementation of PCA for speed
2042 and memory efficiency (~30x faster)
2045 <!-- JAL-2403 -->Revised implementation of sequence
2046 similarity scores as used by Tree, PCA, Shading Consensus
2047 and other calculations
2050 <!-- JAL-2416 -->Score matrices are stored as resource
2051 files within the Jalview codebase
2054 <!-- JAL-2500 -->Trees computed on Sequence Feature
2055 Similarity may have different topology due to increased
2062 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
2063 model for alignments and groups
2066 <!-- JAL-384 -->Custom shading schemes created via groovy
2073 <!-- JAL-2526 -->Efficiency improvements for interacting
2074 with alignment and overview windows
2077 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
2081 <!-- JAL-2388 -->Hidden columns and sequences can be
2085 <!-- JAL-2611 -->Click-drag in visible area allows fine
2086 adjustment of visible position
2090 <em>Data import/export</em>
2093 <!-- JAL-2535 -->Posterior probability annotation from
2094 Stockholm files imported as sequence associated annotation
2097 <!-- JAL-2507 -->More robust per-sequence positional
2098 annotation input/output via stockholm flatfile
2101 <!-- JAL-2533 -->Sequence names don't include file
2102 extension when importing structure files without embedded
2103 names or PDB accessions
2106 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
2107 format sequence substitution matrices
2110 <em>User Interface</em>
2113 <!-- JAL-2447 --> Experimental Features Checkbox in
2114 Desktop's Tools menu to hide or show untested features in
2118 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
2119 via Overview or sequence motif search operations
2122 <!-- JAL-2547 -->Amend sequence features dialog box can be
2123 opened by double clicking gaps within sequence feature
2127 <!-- JAL-1476 -->Status bar message shown when not enough
2128 aligned positions were available to create a 3D structure
2132 <em>3D Structure</em>
2135 <!-- JAL-2430 -->Hidden regions in alignment views are not
2136 coloured in linked structure views
2139 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
2140 file-based command exchange
2143 <!-- JAL-2375 -->Structure chooser automatically shows
2144 Cached Structures rather than querying the PDBe if
2145 structures are already available for sequences
2148 <!-- JAL-2520 -->Structures imported via URL are cached in
2149 the Jalview project rather than downloaded again when the
2150 project is reopened.
2153 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
2154 to transfer Chimera's structure attributes as Jalview
2155 features, and vice-versa (<strong>Experimental
2159 <em>Web Services</em>
2162 <!-- JAL-2549 -->Updated JABAWS client to v2.2
2165 <!-- JAL-2335 -->Filter non-standard amino acids and
2166 nucleotides when submitting to AACon and other MSA
2170 <!-- JAL-2316, -->URLs for viewing database
2171 cross-references provided by identifiers.org and the
2172 EMBL-EBI's MIRIAM DB
2179 <!-- JAL-2344 -->FileFormatI interface for describing and
2180 identifying file formats (instead of String constants)
2183 <!-- JAL-2228 -->FeatureCounter script refactored for
2184 efficiency when counting all displayed features (not
2185 backwards compatible with 2.10.1)
2188 <em>Example files</em>
2191 <!-- JAL-2631 -->Graduated feature colour style example
2192 included in the example feature file
2195 <em>Documentation</em>
2198 <!-- JAL-2339 -->Release notes reformatted for readability
2199 with the built-in Java help viewer
2202 <!-- JAL-1644 -->Find documentation updated with 'search
2203 sequence description' option
2209 <!-- JAL-2485, -->External service integration tests for
2210 Uniprot REST Free Text Search Client
2213 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
2216 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
2221 <td><div align="left">
2222 <em>Calculations</em>
2225 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
2226 matrix - C->R should be '-3'<br />Old matrix restored
2227 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
2229 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
2230 Jalview's treatment of gaps in PCA and substitution matrix
2231 based Tree calculations.<br /> <br />In earlier versions
2232 of Jalview, gaps matching gaps were penalised, and gaps
2233 matching non-gaps penalised even more. In the PCA
2234 calculation, gaps were actually treated as non-gaps - so
2235 different costs were applied, which meant Jalview's PCAs
2236 were different to those produced by SeqSpace.<br />Jalview
2237 now treats gaps in the same way as SeqSpace (ie it scores
2238 them as 0). <br /> <br />Enter the following in the
2239 Groovy console to restore pre-2.10.2 behaviour:<br />
2240 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
2241 // for 2.10.1 mode <br />
2242 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
2243 // to restore 2.10.2 mode <br /> <br /> <em>Note:
2244 these settings will affect all subsequent tree and PCA
2245 calculations (not recommended)</em></li>
2247 <!-- JAL-2424 -->Fixed off-by-one bug that affected
2248 scaling of branch lengths for trees computed using
2249 Sequence Feature Similarity.
2252 <!-- JAL-2377 -->PCA calculation could hang when
2253 generating output report when working with highly
2254 redundant alignments
2257 <!-- JAL-2544 --> Sort by features includes features to
2258 right of selected region when gaps present on right-hand
2262 <em>User Interface</em>
2265 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2266 doesn't reselect a specific sequence's associated
2267 annotation after it was used for colouring a view
2270 <!-- JAL-2419 -->Current selection lost if popup menu
2271 opened on a region of alignment without groups
2274 <!-- JAL-2374 -->Popup menu not always shown for regions
2275 of an alignment with overlapping groups
2278 <!-- JAL-2310 -->Finder double counts if both a sequence's
2279 name and description match
2282 <!-- JAL-2370 -->Hiding column selection containing two
2283 hidden regions results in incorrect hidden regions
2286 <!-- JAL-2386 -->'Apply to all groups' setting when
2287 changing colour does not apply Conservation slider value
2291 <!-- JAL-2373 -->Percentage identity and conservation menu
2292 items do not show a tick or allow shading to be disabled
2295 <!-- JAL-2385 -->Conservation shading or PID threshold
2296 lost when base colourscheme changed if slider not visible
2299 <!-- JAL-2547 -->Sequence features shown in tooltip for
2300 gaps before start of features
2303 <!-- JAL-2623 -->Graduated feature colour threshold not
2304 restored to UI when feature colour is edited
2307 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2308 a time when scrolling vertically in wrapped mode.
2311 <!-- JAL-2630 -->Structure and alignment overview update
2312 as graduate feature colour settings are modified via the
2316 <!-- JAL-2034 -->Overview window doesn't always update
2317 when a group defined on the alignment is resized
2320 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2321 wrapped view result in positional status updates
2325 <!-- JAL-2563 -->Status bar doesn't show position for
2326 ambiguous amino acid and nucleotide symbols
2329 <!-- JAL-2602 -->Copy consensus sequence failed if
2330 alignment included gapped columns
2333 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2334 widgets don't permanently disappear
2337 <!-- JAL-2503 -->Cannot select or filter quantitative
2338 annotation that are shown only as column labels (e.g.
2339 T-Coffee column reliability scores)
2342 <!-- JAL-2594 -->Exception thrown if trying to create a
2343 sequence feature on gaps only
2346 <!-- JAL-2504 -->Features created with 'New feature'
2347 button from a Find inherit previously defined feature type
2348 rather than the Find query string
2351 <!-- JAL-2423 -->incorrect title in output window when
2352 exporting tree calculated in Jalview
2355 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2356 and then revealing them reorders sequences on the
2360 <!-- JAL-964 -->Group panel in sequence feature settings
2361 doesn't update to reflect available set of groups after
2362 interactively adding or modifying features
2365 <!-- JAL-2225 -->Sequence Database chooser unusable on
2369 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2370 only excluded gaps in current sequence and ignored
2377 <!-- JAL-2421 -->Overview window visible region moves
2378 erratically when hidden rows or columns are present
2381 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2382 Structure Viewer's colour menu don't correspond to
2386 <!-- JAL-2405 -->Protein specific colours only offered in
2387 colour and group colour menu for protein alignments
2390 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2391 reflect currently selected view or group's shading
2395 <!-- JAL-2624 -->Feature colour thresholds not respected
2396 when rendered on overview and structures when opacity at
2400 <!-- JAL-2589 -->User defined gap colour not shown in
2401 overview when features overlaid on alignment
2404 <!-- JAL-2567 -->Feature settings for different views not
2405 recovered correctly from Jalview project file
2408 <!-- JAL-2256 -->Feature colours in overview when first opened
2409 (automatically via preferences) are different to the main
2413 <em>Data import/export</em>
2416 <!-- JAL-2576 -->Very large alignments take a long time to
2420 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2421 added after a sequence was imported are not written to
2425 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2426 when importing RNA secondary structure via Stockholm
2429 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2430 not shown in correct direction for simple pseudoknots
2433 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2434 with lightGray or darkGray via features file (but can
2438 <!-- JAL-2383 -->Above PID colour threshold not recovered
2439 when alignment view imported from project
2442 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2443 structure and sequences extracted from structure files
2444 imported via URL and viewed in Jmol
2447 <!-- JAL-2520 -->Structures loaded via URL are saved in
2448 Jalview Projects rather than fetched via URL again when
2449 the project is loaded and the structure viewed
2452 <em>Web Services</em>
2455 <!-- JAL-2519 -->EnsemblGenomes example failing after
2456 release of Ensembl v.88
2459 <!-- JAL-2366 -->Proxy server address and port always
2460 appear enabled in Preferences->Connections
2463 <!-- JAL-2461 -->DAS registry not found exceptions
2464 removed from console output
2467 <!-- JAL-2582 -->Cannot retrieve protein products from
2468 Ensembl by Peptide ID
2471 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2472 created from SIFTs, and spurious 'Couldn't open structure
2473 in Chimera' errors raised after April 2017 update (problem
2474 due to 'null' string rather than empty string used for
2475 residues with no corresponding PDB mapping).
2478 <em>Application UI</em>
2481 <!-- JAL-2361 -->User Defined Colours not added to Colour
2485 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2486 case' residues (button in colourscheme editor debugged and
2487 new documentation and tooltips added)
2490 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2491 doesn't restore group-specific text colour thresholds
2494 <!-- JAL-2243 -->Feature settings panel does not update as
2495 new features are added to alignment
2498 <!-- JAL-2532 -->Cancel in feature settings reverts
2499 changes to feature colours via the Amend features dialog
2502 <!-- JAL-2506 -->Null pointer exception when attempting to
2503 edit graduated feature colour via amend features dialog
2507 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2508 selection menu changes colours of alignment views
2511 <!-- JAL-2426 -->Spurious exceptions in console raised
2512 from alignment calculation workers after alignment has
2516 <!-- JAL-1608 -->Typo in selection popup menu - Create
2517 groups now 'Create Group'
2520 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2521 Create/Undefine group doesn't always work
2524 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2525 shown again after pressing 'Cancel'
2528 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2529 adjusts start position in wrap mode
2532 <!-- JAL-2563 -->Status bar doesn't show positions for
2533 ambiguous amino acids
2536 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2537 CDS/Protein view after CDS sequences added for aligned
2541 <!-- JAL-2592 -->User defined colourschemes called 'User
2542 Defined' don't appear in Colours menu
2548 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2549 score models doesn't always result in an updated PCA plot
2552 <!-- JAL-2442 -->Features not rendered as transparent on
2553 overview or linked structure view
2556 <!-- JAL-2372 -->Colour group by conservation doesn't
2560 <!-- JAL-2517 -->Hitting Cancel after applying
2561 user-defined colourscheme doesn't restore original
2568 <!-- JAL-2314 -->Unit test failure:
2569 jalview.ws.jabaws.RNAStructExportImport setup fails
2572 <!-- JAL-2307 -->Unit test failure:
2573 jalview.ws.sifts.SiftsClientTest due to compatibility
2574 problems with deep array comparison equality asserts in
2575 successive versions of TestNG
2578 <!-- JAL-2479 -->Relocated StructureChooserTest and
2579 ParameterUtilsTest Unit tests to Network suite
2582 <em>New Known Issues</em>
2585 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2586 phase after a sequence motif find operation
2589 <!-- JAL-2550 -->Importing annotation file with rows
2590 containing just upper and lower case letters are
2591 interpreted as WUSS RNA secondary structure symbols
2594 <!-- JAL-2590 -->Cannot load and display Newick trees
2595 reliably from eggnog Ortholog database
2598 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2599 containing features of type Highlight' when 'B' is pressed
2600 to mark columns containing highlighted regions.
2603 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2604 doesn't always add secondary structure annotation.
2609 <td width="60" nowrap>
2610 <div align="center">
2611 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2614 <td><div align="left">
2618 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2619 for all consensus calculations
2622 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2625 <li>Updated Jalview's Certum code signing certificate
2628 <em>Application</em>
2631 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2632 set of database cross-references, sorted alphabetically
2635 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2636 from database cross references. Users with custom links
2637 will receive a <a href="webServices/urllinks.html#warning">warning
2638 dialog</a> asking them to update their preferences.
2641 <!-- JAL-2287-->Cancel button and escape listener on
2642 dialog warning user about disconnecting Jalview from a
2646 <!-- JAL-2320-->Jalview's Chimera control window closes if
2647 the Chimera it is connected to is shut down
2650 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2651 columns menu item to mark columns containing highlighted
2652 regions (e.g. from structure selections or results of a
2656 <!-- JAL-2284-->Command line option for batch-generation
2657 of HTML pages rendering alignment data with the BioJS
2667 <!-- JAL-2286 -->Columns with more than one modal residue
2668 are not coloured or thresholded according to percent
2669 identity (first observed in Jalview 2.8.2)
2672 <!-- JAL-2301 -->Threonine incorrectly reported as not
2676 <!-- JAL-2318 -->Updates to documentation pages (above PID
2677 threshold, amino acid properties)
2680 <!-- JAL-2292 -->Lower case residues in sequences are not
2681 reported as mapped to residues in a structure file in the
2685 <!--JAL-2324 -->Identical features with non-numeric scores
2686 could be added multiple times to a sequence
2689 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2690 bond features shown as two highlighted residues rather
2691 than a range in linked structure views, and treated
2692 correctly when selecting and computing trees from features
2695 <!-- JAL-2281-->Custom URL links for database
2696 cross-references are matched to database name regardless
2701 <em>Application</em>
2704 <!-- JAL-2282-->Custom URL links for specific database
2705 names without regular expressions also offer links from
2709 <!-- JAL-2315-->Removing a single configured link in the
2710 URL links pane in Connections preferences doesn't actually
2711 update Jalview configuration
2714 <!-- JAL-2272-->CTRL-Click on a selected region to open
2715 the alignment area popup menu doesn't work on El-Capitan
2718 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2719 files with similarly named sequences if dropped onto the
2723 <!-- JAL-2312 -->Additional mappings are shown for PDB
2724 entries where more chains exist in the PDB accession than
2725 are reported in the SIFTS file
2728 <!-- JAL-2317-->Certain structures do not get mapped to
2729 the structure view when displayed with Chimera
2732 <!-- JAL-2317-->No chains shown in the Chimera view
2733 panel's View->Show Chains submenu
2736 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2737 work for wrapped alignment views
2740 <!--JAL-2197 -->Rename UI components for running JPred
2741 predictions from 'JNet' to 'JPred'
2744 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2745 corrupted when annotation panel vertical scroll is not at
2746 first annotation row
2749 <!--JAL-2332 -->Attempting to view structure for Hen
2750 lysozyme results in a PDB Client error dialog box
2753 <!-- JAL-2319 -->Structure View's mapping report switched
2754 ranges for PDB and sequence for SIFTS
2757 SIFTS 'Not_Observed' residues mapped to non-existant
2761 <!-- <em>New Known Issues</em>
2768 <td width="60" nowrap>
2769 <div align="center">
2770 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2771 <em>25/10/2016</em></strong>
2774 <td><em>Application</em>
2776 <li>3D Structure chooser opens with 'Cached structures'
2777 view if structures already loaded</li>
2778 <li>Progress bar reports models as they are loaded to
2779 structure views</li>
2785 <li>Colour by conservation always enabled and no tick
2786 shown in menu when BLOSUM or PID shading applied</li>
2787 <li>FER1_ARATH and FER2_ARATH labels were switched in
2788 example sequences/projects/trees</li>
2790 <em>Application</em>
2792 <li>Jalview projects with views of local PDB structure
2793 files saved on Windows cannot be opened on OSX</li>
2794 <li>Multiple structure views can be opened and superposed
2795 without timeout for structures with multiple models or
2796 multiple sequences in alignment</li>
2797 <li>Cannot import or associated local PDB files without a
2798 PDB ID HEADER line</li>
2799 <li>RMSD is not output in Jmol console when superposition
2801 <li>Drag and drop of URL from Browser fails for Linux and
2802 OSX versions earlier than El Capitan</li>
2803 <li>ENA client ignores invalid content from ENA server</li>
2804 <li>Exceptions are not raised in console when ENA client
2805 attempts to fetch non-existent IDs via Fetch DB Refs UI
2807 <li>Exceptions are not raised in console when a new view
2808 is created on the alignment</li>
2809 <li>OSX right-click fixed for group selections: CMD-click
2810 to insert/remove gaps in groups and CTRL-click to open group
2813 <em>Build and deployment</em>
2815 <li>URL link checker now copes with multi-line anchor
2818 <em>New Known Issues</em>
2820 <li>Drag and drop from URL links in browsers do not work
2827 <td width="60" nowrap>
2828 <div align="center">
2829 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2832 <td><em>General</em>
2835 <!-- JAL-2124 -->Updated Spanish translations.
2838 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2839 for importing structure data to Jalview. Enables mmCIF and
2843 <!-- JAL-192 --->Alignment ruler shows positions relative to
2847 <!-- JAL-2202 -->Position/residue shown in status bar when
2848 mousing over sequence associated annotation
2851 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2855 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2856 '()', canonical '[]' and invalid '{}' base pair populations
2860 <!-- JAL-2092 -->Feature settings popup menu options for
2861 showing or hiding columns containing a feature
2864 <!-- JAL-1557 -->Edit selected group by double clicking on
2865 group and sequence associated annotation labels
2868 <!-- JAL-2236 -->Sequence name added to annotation label in
2869 select/hide columns by annotation and colour by annotation
2873 </ul> <em>Application</em>
2876 <!-- JAL-2050-->Automatically hide introns when opening a
2877 gene/transcript view
2880 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2884 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2885 structure mappings with the EMBL-EBI PDBe SIFTS database
2888 <!-- JAL-2079 -->Updated download sites used for Rfam and
2889 Pfam sources to xfam.org
2892 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2895 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2896 over sequences in Jalview
2899 <!-- JAL-2027-->Support for reverse-complement coding
2900 regions in ENA and EMBL
2903 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2904 for record retrieval via ENA rest API
2907 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2911 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2912 groovy script execution
2915 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2916 alignment window's Calculate menu
2919 <!-- JAL-1812 -->Allow groovy scripts that call
2920 Jalview.getAlignFrames() to run in headless mode
2923 <!-- JAL-2068 -->Support for creating new alignment
2924 calculation workers from groovy scripts
2927 <!-- JAL-1369 --->Store/restore reference sequence in
2931 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2932 associations are now saved/restored from project
2935 <!-- JAL-1993 -->Database selection dialog always shown
2936 before sequence fetcher is opened
2939 <!-- JAL-2183 -->Double click on an entry in Jalview's
2940 database chooser opens a sequence fetcher
2943 <!-- JAL-1563 -->Free-text search client for UniProt using
2944 the UniProt REST API
2947 <!-- JAL-2168 -->-nonews command line parameter to prevent
2948 the news reader opening
2951 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2952 querying stored in preferences
2955 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2959 <!-- JAL-1977-->Tooltips shown on database chooser
2962 <!-- JAL-391 -->Reverse complement function in calculate
2963 menu for nucleotide sequences
2966 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2967 and feature counts preserves alignment ordering (and
2968 debugged for complex feature sets).
2971 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2972 viewing structures with Jalview 2.10
2975 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2976 genome, transcript CCDS and gene ids via the Ensembl and
2977 Ensembl Genomes REST API
2980 <!-- JAL-2049 -->Protein sequence variant annotation
2981 computed for 'sequence_variant' annotation on CDS regions
2985 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2989 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2990 Ref Fetcher fails to match, or otherwise updates sequence
2991 data from external database records.
2994 <!-- JAL-2154 -->Revised Jalview Project format for
2995 efficient recovery of sequence coding and alignment
2996 annotation relationships.
2998 </ul> <!-- <em>Applet</em>
3009 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
3013 <!-- JAL-2018-->Export features in Jalview format (again)
3014 includes graduated colourschemes
3017 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
3018 working with big alignments and lots of hidden columns
3021 <!-- JAL-2053-->Hidden column markers not always rendered
3022 at right of alignment window
3025 <!-- JAL-2067 -->Tidied up links in help file table of
3029 <!-- JAL-2072 -->Feature based tree calculation not shown
3033 <!-- JAL-2075 -->Hidden columns ignored during feature
3034 based tree calculation
3037 <!-- JAL-2065 -->Alignment view stops updating when show
3038 unconserved enabled for group on alignment
3041 <!-- JAL-2086 -->Cannot insert gaps into sequence when
3045 <!-- JAL-2146 -->Alignment column in status incorrectly
3046 shown as "Sequence position" when mousing over
3050 <!-- JAL-2099 -->Incorrect column numbers in ruler when
3051 hidden columns present
3054 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
3055 user created annotation added to alignment
3058 <!-- JAL-1841 -->RNA Structure consensus only computed for
3059 '()' base pair annotation
3062 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
3063 in zero scores for all base pairs in RNA Structure
3067 <!-- JAL-2174-->Extend selection with columns containing
3071 <!-- JAL-2275 -->Pfam format writer puts extra space at
3072 beginning of sequence
3075 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
3079 <!-- JAL-2238 -->Cannot create groups on an alignment from
3080 from a tree when t-coffee scores are shown
3083 <!-- JAL-1836,1967 -->Cannot import and view PDB
3084 structures with chains containing negative resnums (4q4h)
3087 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
3091 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
3092 to Clustal, PIR and PileUp output
3095 <!-- JAL-2008 -->Reordering sequence features that are
3096 not visible causes alignment window to repaint
3099 <!-- JAL-2006 -->Threshold sliders don't work in
3100 graduated colour and colour by annotation row for e-value
3101 scores associated with features and annotation rows
3104 <!-- JAL-1797 -->amino acid physicochemical conservation
3105 calculation should be case independent
3108 <!-- JAL-2173 -->Remove annotation also updates hidden
3112 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
3113 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
3114 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
3117 <!-- JAL-2065 -->Null pointer exceptions and redraw
3118 problems when reference sequence defined and 'show
3119 non-conserved' enabled
3122 <!-- JAL-1306 -->Quality and Conservation are now shown on
3123 load even when Consensus calculation is disabled
3126 <!-- JAL-1932 -->Remove right on penultimate column of
3127 alignment does nothing
3130 <em>Application</em>
3133 <!-- JAL-1552-->URLs and links can't be imported by
3134 drag'n'drop on OSX when launched via webstart (note - not
3135 yet fixed for El Capitan)
3138 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
3139 output when running on non-gb/us i18n platforms
3142 <!-- JAL-1944 -->Error thrown when exporting a view with
3143 hidden sequences as flat-file alignment
3146 <!-- JAL-2030-->InstallAnywhere distribution fails when
3150 <!-- JAL-2080-->Jalview very slow to launch via webstart
3151 (also hotfix for 2.9.0b2)
3154 <!-- JAL-2085 -->Cannot save project when view has a
3155 reference sequence defined
3158 <!-- JAL-1011 -->Columns are suddenly selected in other
3159 alignments and views when revealing hidden columns
3162 <!-- JAL-1989 -->Hide columns not mirrored in complement
3163 view in a cDNA/Protein splitframe
3166 <!-- JAL-1369 -->Cannot save/restore representative
3167 sequence from project when only one sequence is
3171 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
3172 in Structure Chooser
3175 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
3176 structure consensus didn't refresh annotation panel
3179 <!-- JAL-1962 -->View mapping in structure view shows
3180 mappings between sequence and all chains in a PDB file
3183 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
3184 dialogs format columns correctly, don't display array
3185 data, sort columns according to type
3188 <!-- JAL-1975 -->Export complete shown after destination
3189 file chooser is cancelled during an image export
3192 <!-- JAL-2025 -->Error when querying PDB Service with
3193 sequence name containing special characters
3196 <!-- JAL-2024 -->Manual PDB structure querying should be
3200 <!-- JAL-2104 -->Large tooltips with broken HTML
3201 formatting don't wrap
3204 <!-- JAL-1128 -->Figures exported from wrapped view are
3205 truncated so L looks like I in consensus annotation
3208 <!-- JAL-2003 -->Export features should only export the
3209 currently displayed features for the current selection or
3213 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
3214 after fetching cross-references, and restoring from
3218 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
3219 followed in the structure viewer
3222 <!-- JAL-2163 -->Titles for individual alignments in
3223 splitframe not restored from project
3226 <!-- JAL-2145 -->missing autocalculated annotation at
3227 trailing end of protein alignment in transcript/product
3228 splitview when pad-gaps not enabled by default
3231 <!-- JAL-1797 -->amino acid physicochemical conservation
3235 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
3236 article has been read (reopened issue due to
3237 internationalisation problems)
3240 <!-- JAL-1960 -->Only offer PDB structures in structure
3241 viewer based on sequence name, PDB and UniProt
3246 <!-- JAL-1976 -->No progress bar shown during export of
3250 <!-- JAL-2213 -->Structures not always superimposed after
3251 multiple structures are shown for one or more sequences.
3254 <!-- JAL-1370 -->Reference sequence characters should not
3255 be replaced with '.' when 'Show unconserved' format option
3259 <!-- JAL-1823 -->Cannot specify chain code when entering
3260 specific PDB id for sequence
3263 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3264 'Export hidden sequences' is enabled, but 'export hidden
3265 columns' is disabled.
3268 <!--JAL-2026-->Best Quality option in structure chooser
3269 selects lowest rather than highest resolution structures
3273 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3274 to sequence mapping in 'View Mappings' report
3277 <!-- JAL-2284 -->Unable to read old Jalview projects that
3278 contain non-XML data added after Jalvew wrote project.
3281 <!-- JAL-2118 -->Newly created annotation row reorders
3282 after clicking on it to create new annotation for a
3286 <!-- JAL-1980 -->Null Pointer Exception raised when
3287 pressing Add on an orphaned cut'n'paste window.
3289 <!-- may exclude, this is an external service stability issue JAL-1941
3290 -- > RNA 3D structure not added via DSSR service</li> -->
3295 <!-- JAL-2151 -->Incorrect columns are selected when
3296 hidden columns present before start of sequence
3299 <!-- JAL-1986 -->Missing dependencies on applet pages
3303 <!-- JAL-1947 -->Overview pixel size changes when
3304 sequences are hidden in applet
3307 <!-- JAL-1996 -->Updated instructions for applet
3308 deployment on examples pages.
3315 <td width="60" nowrap>
3316 <div align="center">
3317 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3318 <em>16/10/2015</em></strong>
3321 <td><em>General</em>
3323 <li>Time stamps for signed Jalview application and applet
3328 <em>Application</em>
3330 <li>Duplicate group consensus and conservation rows
3331 shown when tree is partitioned</li>
3332 <li>Erratic behaviour when tree partitions made with
3333 multiple cDNA/Protein split views</li>
3339 <td width="60" nowrap>
3340 <div align="center">
3341 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3342 <em>8/10/2015</em></strong>
3345 <td><em>General</em>
3347 <li>Updated Spanish translations of localized text for
3349 </ul> <em>Application</em>
3351 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3352 <li>Signed OSX InstallAnywhere installer<br></li>
3353 <li>Support for per-sequence based annotations in BioJSON</li>
3354 </ul> <em>Applet</em>
3356 <li>Split frame example added to applet examples page</li>
3357 </ul> <em>Build and Deployment</em>
3360 <!-- JAL-1888 -->New ant target for running Jalview's test
3368 <li>Mapping of cDNA to protein in split frames
3369 incorrect when sequence start > 1</li>
3370 <li>Broken images in filter column by annotation dialog
3372 <li>Feature colours not parsed from features file</li>
3373 <li>Exceptions and incomplete link URLs recovered when
3374 loading a features file containing HTML tags in feature
3378 <em>Application</em>
3380 <li>Annotations corrupted after BioJS export and
3382 <li>Incorrect sequence limits after Fetch DB References
3383 with 'trim retrieved sequences'</li>
3384 <li>Incorrect warning about deleting all data when
3385 deleting selected columns</li>
3386 <li>Patch to build system for shipping properly signed
3387 JNLP templates for webstart launch</li>
3388 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3389 unreleased structures for download or viewing</li>
3390 <li>Tab/space/return keystroke operation of EMBL-PDBe
3391 fetcher/viewer dialogs works correctly</li>
3392 <li>Disabled 'minimise' button on Jalview windows
3393 running on OSX to workaround redraw hang bug</li>
3394 <li>Split cDNA/Protein view position and geometry not
3395 recovered from jalview project</li>
3396 <li>Initial enabled/disabled state of annotation menu
3397 sorter 'show autocalculated first/last' corresponds to
3399 <li>Restoring of Clustal, RNA Helices and T-Coffee
3400 color schemes from BioJSON</li>
3404 <li>Reorder sequences mirrored in cDNA/Protein split
3406 <li>Applet with Jmol examples not loading correctly</li>
3412 <td><div align="center">
3413 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3415 <td><em>General</em>
3417 <li>Linked visualisation and analysis of DNA and Protein
3420 <li>Translated cDNA alignments shown as split protein
3421 and DNA alignment views</li>
3422 <li>Codon consensus annotation for linked protein and
3423 cDNA alignment views</li>
3424 <li>Link cDNA or Protein product sequences by loading
3425 them onto Protein or cDNA alignments</li>
3426 <li>Reconstruct linked cDNA alignment from aligned
3427 protein sequences</li>
3430 <li>Jmol integration updated to Jmol v14.2.14</li>
3431 <li>Import and export of Jalview alignment views as <a
3432 href="features/bioJsonFormat.html">BioJSON</a></li>
3433 <li>New alignment annotation file statements for
3434 reference sequences and marking hidden columns</li>
3435 <li>Reference sequence based alignment shading to
3436 highlight variation</li>
3437 <li>Select or hide columns according to alignment
3439 <li>Find option for locating sequences by description</li>
3440 <li>Conserved physicochemical properties shown in amino
3441 acid conservation row</li>
3442 <li>Alignments can be sorted by number of RNA helices</li>
3443 </ul> <em>Application</em>
3445 <li>New cDNA/Protein analysis capabilities
3447 <li>Get Cross-References should open a Split Frame
3448 view with cDNA/Protein</li>
3449 <li>Detect when nucleotide sequences and protein
3450 sequences are placed in the same alignment</li>
3451 <li>Split cDNA/Protein views are saved in Jalview
3456 <li>Use REST API to talk to Chimera</li>
3457 <li>Selected regions in Chimera are highlighted in linked
3458 Jalview windows</li>
3460 <li>VARNA RNA viewer updated to v3.93</li>
3461 <li>VARNA views are saved in Jalview Projects</li>
3462 <li>Pseudoknots displayed as Jalview RNA annotation can
3463 be shown in VARNA</li>
3465 <li>Make groups for selection uses marked columns as well
3466 as the active selected region</li>
3468 <li>Calculate UPGMA and NJ trees using sequence feature
3470 <li>New Export options
3472 <li>New Export Settings dialog to control hidden
3473 region export in flat file generation</li>
3475 <li>Export alignment views for display with the <a
3476 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3478 <li>Export scrollable SVG in HTML page</li>
3479 <li>Optional embedding of BioJSON data when exporting
3480 alignment figures to HTML</li>
3482 <li>3D structure retrieval and display
3484 <li>Free text and structured queries with the PDBe
3486 <li>PDBe Search API based discovery and selection of
3487 PDB structures for a sequence set</li>
3491 <li>JPred4 employed for protein secondary structure
3493 <li>Hide Insertions menu option to hide unaligned columns
3494 for one or a group of sequences</li>
3495 <li>Automatically hide insertions in alignments imported
3496 from the JPred4 web server</li>
3497 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3498 system on OSX<br />LGPL libraries courtesy of <a
3499 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3501 <li>changed 'View nucleotide structure' submenu to 'View
3502 VARNA 2D Structure'</li>
3503 <li>change "View protein structure" menu option to "3D
3506 </ul> <em>Applet</em>
3508 <li>New layout for applet example pages</li>
3509 <li>New parameters to enable SplitFrame view
3510 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3511 <li>New example demonstrating linked viewing of cDNA and
3512 Protein alignments</li>
3513 </ul> <em>Development and deployment</em>
3515 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3516 <li>Include installation type and git revision in build
3517 properties and console log output</li>
3518 <li>Jalview Github organisation, and new github site for
3519 storing BioJsMSA Templates</li>
3520 <li>Jalview's unit tests now managed with TestNG</li>
3523 <!-- <em>General</em>
3525 </ul> --> <!-- issues resolved --> <em>Application</em>
3527 <li>Escape should close any open find dialogs</li>
3528 <li>Typo in select-by-features status report</li>
3529 <li>Consensus RNA secondary secondary structure
3530 predictions are not highlighted in amber</li>
3531 <li>Missing gap character in v2.7 example file means
3532 alignment appears unaligned when pad-gaps is not enabled</li>
3533 <li>First switch to RNA Helices colouring doesn't colour
3534 associated structure views</li>
3535 <li>ID width preference option is greyed out when auto
3536 width checkbox not enabled</li>
3537 <li>Stopped a warning dialog from being shown when
3538 creating user defined colours</li>
3539 <li>'View Mapping' in structure viewer shows sequence
3540 mappings for just that viewer's sequences</li>
3541 <li>Workaround for superposing PDB files containing
3542 multiple models in Chimera</li>
3543 <li>Report sequence position in status bar when hovering
3544 over Jmol structure</li>
3545 <li>Cannot output gaps as '.' symbols with Selection ->
3546 output to text box</li>
3547 <li>Flat file exports of alignments with hidden columns
3548 have incorrect sequence start/end</li>
3549 <li>'Aligning' a second chain to a Chimera structure from
3551 <li>Colour schemes applied to structure viewers don't
3552 work for nucleotide</li>
3553 <li>Loading/cut'n'pasting an empty or invalid file leads
3554 to a grey/invisible alignment window</li>
3555 <li>Exported Jpred annotation from a sequence region
3556 imports to different position</li>
3557 <li>Space at beginning of sequence feature tooltips shown
3558 on some platforms</li>
3559 <li>Chimera viewer 'View | Show Chain' menu is not
3561 <li>'New View' fails with a Null Pointer Exception in
3562 console if Chimera has been opened</li>
3563 <li>Mouseover to Chimera not working</li>
3564 <li>Miscellaneous ENA XML feature qualifiers not
3566 <li>NPE in annotation renderer after 'Extract Scores'</li>
3567 <li>If two structures in one Chimera window, mouseover of
3568 either sequence shows on first structure</li>
3569 <li>'Show annotations' options should not make
3570 non-positional annotations visible</li>
3571 <li>Subsequence secondary structure annotation not shown
3572 in right place after 'view flanking regions'</li>
3573 <li>File Save As type unset when current file format is
3575 <li>Save as '.jar' option removed for saving Jalview
3577 <li>Colour by Sequence colouring in Chimera more
3579 <li>Cannot 'add reference annotation' for a sequence in
3580 several views on same alignment</li>
3581 <li>Cannot show linked products for EMBL / ENA records</li>
3582 <li>Jalview's tooltip wraps long texts containing no
3584 </ul> <em>Applet</em>
3586 <li>Jmol to JalviewLite mouseover/link not working</li>
3587 <li>JalviewLite can't import sequences with ID
3588 descriptions containing angle brackets</li>
3589 </ul> <em>General</em>
3591 <li>Cannot export and reimport RNA secondary structure
3592 via jalview annotation file</li>
3593 <li>Random helix colour palette for colour by annotation
3594 with RNA secondary structure</li>
3595 <li>Mouseover to cDNA from STOP residue in protein
3596 translation doesn't work.</li>
3597 <li>hints when using the select by annotation dialog box</li>
3598 <li>Jmol alignment incorrect if PDB file has alternate CA
3600 <li>FontChooser message dialog appears to hang after
3601 choosing 1pt font</li>
3602 <li>Peptide secondary structure incorrectly imported from
3603 annotation file when annotation display text includes 'e' or
3605 <li>Cannot set colour of new feature type whilst creating
3607 <li>cDNA translation alignment should not be sequence
3608 order dependent</li>
3609 <li>'Show unconserved' doesn't work for lower case
3611 <li>Nucleotide ambiguity codes involving R not recognised</li>
3612 </ul> <em>Deployment and Documentation</em>
3614 <li>Applet example pages appear different to the rest of
3615 www.jalview.org</li>
3616 </ul> <em>Application Known issues</em>
3618 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3619 <li>Misleading message appears after trying to delete
3621 <li>Jalview icon not shown in dock after InstallAnywhere
3622 version launches</li>
3623 <li>Fetching EMBL reference for an RNA sequence results
3624 fails with a sequence mismatch</li>
3625 <li>Corrupted or unreadable alignment display when
3626 scrolling alignment to right</li>
3627 <li>ArrayIndexOutOfBoundsException thrown when remove
3628 empty columns called on alignment with ragged gapped ends</li>
3629 <li>auto calculated alignment annotation rows do not get
3630 placed above or below non-autocalculated rows</li>
3631 <li>Jalview dekstop becomes sluggish at full screen in
3632 ultra-high resolution</li>
3633 <li>Cannot disable consensus calculation independently of
3634 quality and conservation</li>
3635 <li>Mouseover highlighting between cDNA and protein can
3636 become sluggish with more than one splitframe shown</li>
3637 </ul> <em>Applet Known Issues</em>
3639 <li>Core PDB parsing code requires Jmol</li>
3640 <li>Sequence canvas panel goes white when alignment
3641 window is being resized</li>
3647 <td><div align="center">
3648 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3650 <td><em>General</em>
3652 <li>Updated Java code signing certificate donated by
3654 <li>Features and annotation preserved when performing
3655 pairwise alignment</li>
3656 <li>RNA pseudoknot annotation can be
3657 imported/exported/displayed</li>
3658 <li>'colour by annotation' can colour by RNA and
3659 protein secondary structure</li>
3660 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3661 post-hoc with 2.9 release</em>)
3664 </ul> <em>Application</em>
3666 <li>Extract and display secondary structure for sequences
3667 with 3D structures</li>
3668 <li>Support for parsing RNAML</li>
3669 <li>Annotations menu for layout
3671 <li>sort sequence annotation rows by alignment</li>
3672 <li>place sequence annotation above/below alignment
3675 <li>Output in Stockholm format</li>
3676 <li>Internationalisation: improved Spanish (es)
3678 <li>Structure viewer preferences tab</li>
3679 <li>Disorder and Secondary Structure annotation tracks
3680 shared between alignments</li>
3681 <li>UCSF Chimera launch and linked highlighting from
3683 <li>Show/hide all sequence associated annotation rows for
3684 all or current selection</li>
3685 <li>disorder and secondary structure predictions
3686 available as dataset annotation</li>
3687 <li>Per-sequence rna helices colouring</li>
3690 <li>Sequence database accessions imported when fetching
3691 alignments from Rfam</li>
3692 <li>update VARNA version to 3.91</li>
3694 <li>New groovy scripts for exporting aligned positions,
3695 conservation values, and calculating sum of pairs scores.</li>
3696 <li>Command line argument to set default JABAWS server</li>
3697 <li>include installation type in build properties and
3698 console log output</li>
3699 <li>Updated Jalview project format to preserve dataset
3703 <!-- issues resolved --> <em>Application</em>
3705 <li>Distinguish alignment and sequence associated RNA
3706 structure in structure->view->VARNA</li>
3707 <li>Raise dialog box if user deletes all sequences in an
3709 <li>Pressing F1 results in documentation opening twice</li>
3710 <li>Sequence feature tooltip is wrapped</li>
3711 <li>Double click on sequence associated annotation
3712 selects only first column</li>
3713 <li>Redundancy removal doesn't result in unlinked
3714 leaves shown in tree</li>
3715 <li>Undos after several redundancy removals don't undo
3717 <li>Hide sequence doesn't hide associated annotation</li>
3718 <li>User defined colours dialog box too big to fit on
3719 screen and buttons not visible</li>
3720 <li>author list isn't updated if already written to
3721 Jalview properties</li>
3722 <li>Popup menu won't open after retrieving sequence
3724 <li>File open window for associate PDB doesn't open</li>
3725 <li>Left-then-right click on a sequence id opens a
3726 browser search window</li>
3727 <li>Cannot open sequence feature shading/sort popup menu
3728 in feature settings dialog</li>
3729 <li>better tooltip placement for some areas of Jalview
3731 <li>Allow addition of JABAWS Server which doesn't
3732 pass validation</li>
3733 <li>Web services parameters dialog box is too large to
3735 <li>Muscle nucleotide alignment preset obscured by
3737 <li>JABAWS preset submenus don't contain newly
3738 defined user preset</li>
3739 <li>MSA web services warns user if they were launched
3740 with invalid input</li>
3741 <li>Jalview cannot contact DAS Registy when running on
3744 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3745 'Superpose with' submenu not shown when new view
3749 </ul> <!-- <em>Applet</em>
3751 </ul> <em>General</em>
3753 </ul>--> <em>Deployment and Documentation</em>
3755 <li>2G and 1G options in launchApp have no effect on
3756 memory allocation</li>
3757 <li>launchApp service doesn't automatically open
3758 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3760 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3761 InstallAnywhere reports cannot find valid JVM when Java
3762 1.7_055 is available
3764 </ul> <em>Application Known issues</em>
3767 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3768 corrupted or unreadable alignment display when scrolling
3772 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3773 retrieval fails but progress bar continues for DAS retrieval
3774 with large number of ID
3777 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3778 flatfile output of visible region has incorrect sequence
3782 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3783 rna structure consensus doesn't update when secondary
3784 structure tracks are rearranged
3787 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3788 invalid rna structure positional highlighting does not
3789 highlight position of invalid base pairs
3792 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3793 out of memory errors are not raised when saving Jalview
3794 project from alignment window file menu
3797 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3798 Switching to RNA Helices colouring doesn't propagate to
3802 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3803 colour by RNA Helices not enabled when user created
3804 annotation added to alignment
3807 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3808 Jalview icon not shown on dock in Mountain Lion/Webstart
3810 </ul> <em>Applet Known Issues</em>
3813 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3814 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3817 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3818 Jalview and Jmol example not compatible with IE9
3821 <li>Sort by annotation score doesn't reverse order
3827 <td><div align="center">
3828 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3831 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3834 <li>Internationalisation of user interface (usually
3835 called i18n support) and translation for Spanish locale</li>
3836 <li>Define/Undefine group on current selection with
3837 Ctrl-G/Shift Ctrl-G</li>
3838 <li>Improved group creation/removal options in
3839 alignment/sequence Popup menu</li>
3840 <li>Sensible precision for symbol distribution
3841 percentages shown in logo tooltip.</li>
3842 <li>Annotation panel height set according to amount of
3843 annotation when alignment first opened</li>
3844 </ul> <em>Application</em>
3846 <li>Interactive consensus RNA secondary structure
3847 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3848 <li>Select columns containing particular features from
3849 Feature Settings dialog</li>
3850 <li>View all 'representative' PDB structures for selected
3852 <li>Update Jalview project format:
3854 <li>New file extension for Jalview projects '.jvp'</li>
3855 <li>Preserve sequence and annotation dataset (to
3856 store secondary structure annotation,etc)</li>
3857 <li>Per group and alignment annotation and RNA helix
3861 <li>New similarity measures for PCA and Tree calculation
3863 <li>Experimental support for retrieval and viewing of
3864 flanking regions for an alignment</li>
3868 <!-- issues resolved --> <em>Application</em>
3870 <li>logo keeps spinning and status remains at queued or
3871 running after job is cancelled</li>
3872 <li>cannot export features from alignments imported from
3873 Jalview/VAMSAS projects</li>
3874 <li>Buggy slider for web service parameters that take
3876 <li>Newly created RNA secondary structure line doesn't
3877 have 'display all symbols' flag set</li>
3878 <li>T-COFFEE alignment score shading scheme and other
3879 annotation shading not saved in Jalview project</li>
3880 <li>Local file cannot be loaded in freshly downloaded
3882 <li>Jalview icon not shown on dock in Mountain
3884 <li>Load file from desktop file browser fails</li>
3885 <li>Occasional NPE thrown when calculating large trees</li>
3886 <li>Cannot reorder or slide sequences after dragging an
3887 alignment onto desktop</li>
3888 <li>Colour by annotation dialog throws NPE after using
3889 'extract scores' function</li>
3890 <li>Loading/cut'n'pasting an empty file leads to a grey
3891 alignment window</li>
3892 <li>Disorder thresholds rendered incorrectly after
3893 performing IUPred disorder prediction</li>
3894 <li>Multiple group annotated consensus rows shown when
3895 changing 'normalise logo' display setting</li>
3896 <li>Find shows blank dialog after 'finished searching' if
3897 nothing matches query</li>
3898 <li>Null Pointer Exceptions raised when sorting by
3899 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3901 <li>Errors in Jmol console when structures in alignment
3902 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3904 <li>Not all working JABAWS services are shown in
3906 <li>JAVAWS version of Jalview fails to launch with
3907 'invalid literal/length code'</li>
3908 <li>Annotation/RNA Helix colourschemes cannot be applied
3909 to alignment with groups (actually fixed in 2.8.0b1)</li>
3910 <li>RNA Helices and T-Coffee Scores available as default
3913 </ul> <em>Applet</em>
3915 <li>Remove group option is shown even when selection is
3917 <li>Apply to all groups ticked but colourscheme changes
3918 don't affect groups</li>
3919 <li>Documented RNA Helices and T-Coffee Scores as valid
3920 colourscheme name</li>
3921 <li>Annotation labels drawn on sequence IDs when
3922 Annotation panel is not displayed</li>
3923 <li>Increased font size for dropdown menus on OSX and
3924 embedded windows</li>
3925 </ul> <em>Other</em>
3927 <li>Consensus sequence for alignments/groups with a
3928 single sequence were not calculated</li>
3929 <li>annotation files that contain only groups imported as
3930 annotation and junk sequences</li>
3931 <li>Fasta files with sequences containing '*' incorrectly
3932 recognised as PFAM or BLC</li>
3933 <li>conservation/PID slider apply all groups option
3934 doesn't affect background (2.8.0b1)
3936 <li>redundancy highlighting is erratic at 0% and 100%</li>
3937 <li>Remove gapped columns fails for sequences with ragged
3939 <li>AMSA annotation row with leading spaces is not
3940 registered correctly on import</li>
3941 <li>Jalview crashes when selecting PCA analysis for
3942 certain alignments</li>
3943 <li>Opening the colour by annotation dialog for an
3944 existing annotation based 'use original colours'
3945 colourscheme loses original colours setting</li>
3950 <td><div align="center">
3951 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3952 <em>30/1/2014</em></strong>
3956 <li>Trusted certificates for JalviewLite applet and
3957 Jalview Desktop application<br />Certificate was donated by
3958 <a href="https://www.certum.eu">Certum</a> to the Jalview
3959 open source project).
3961 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3962 <li>Output in Stockholm format</li>
3963 <li>Allow import of data from gzipped files</li>
3964 <li>Export/import group and sequence associated line
3965 graph thresholds</li>
3966 <li>Nucleotide substitution matrix that supports RNA and
3967 ambiguity codes</li>
3968 <li>Allow disorder predictions to be made on the current
3969 selection (or visible selection) in the same way that JPred
3971 <li>Groovy scripting for headless Jalview operation</li>
3972 </ul> <em>Other improvements</em>
3974 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3975 <li>COMBINE statement uses current SEQUENCE_REF and
3976 GROUP_REF scope to group annotation rows</li>
3977 <li>Support '' style escaping of quotes in Newick
3979 <li>Group options for JABAWS service by command line name</li>
3980 <li>Empty tooltip shown for JABA service options with a
3981 link but no description</li>
3982 <li>Select primary source when selecting authority in
3983 database fetcher GUI</li>
3984 <li>Add .mfa to FASTA file extensions recognised by
3986 <li>Annotation label tooltip text wrap</li>
3991 <li>Slow scrolling when lots of annotation rows are
3993 <li>Lots of NPE (and slowness) after creating RNA
3994 secondary structure annotation line</li>
3995 <li>Sequence database accessions not imported when
3996 fetching alignments from Rfam</li>
3997 <li>Incorrect SHMR submission for sequences with
3999 <li>View all structures does not always superpose
4001 <li>Option widgets in service parameters not updated to
4002 reflect user or preset settings</li>
4003 <li>Null pointer exceptions for some services without
4004 presets or adjustable parameters</li>
4005 <li>Discover PDB IDs entry in structure menu doesn't
4006 discover PDB xRefs</li>
4007 <li>Exception encountered while trying to retrieve
4008 features with DAS</li>
4009 <li>Lowest value in annotation row isn't coloured
4010 when colour by annotation (per sequence) is coloured</li>
4011 <li>Keyboard mode P jumps to start of gapped region when
4012 residue follows a gap</li>
4013 <li>Jalview appears to hang importing an alignment with
4014 Wrap as default or after enabling Wrap</li>
4015 <li>'Right click to add annotations' message
4016 shown in wrap mode when no annotations present</li>
4017 <li>Disorder predictions fail with NPE if no automatic
4018 annotation already exists on alignment</li>
4019 <li>oninit javascript function should be called after
4020 initialisation completes</li>
4021 <li>Remove redundancy after disorder prediction corrupts
4022 alignment window display</li>
4023 <li>Example annotation file in documentation is invalid</li>
4024 <li>Grouped line graph annotation rows are not exported
4025 to annotation file</li>
4026 <li>Multi-harmony analysis cannot be run when only two
4028 <li>Cannot create multiple groups of line graphs with
4029 several 'combine' statements in annotation file</li>
4030 <li>Pressing return several times causes Number Format
4031 exceptions in keyboard mode</li>
4032 <li>Multi-harmony (SHMMR) method doesn't submit
4033 correct partitions for input data</li>
4034 <li>Translation from DNA to Amino Acids fails</li>
4035 <li>Jalview fail to load newick tree with quoted label</li>
4036 <li>--headless flag isn't understood</li>
4037 <li>ClassCastException when generating EPS in headless
4039 <li>Adjusting sequence-associated shading threshold only
4040 changes one row's threshold</li>
4041 <li>Preferences and Feature settings panel panel
4042 doesn't open</li>
4043 <li>hide consensus histogram also hides conservation and
4044 quality histograms</li>
4049 <td><div align="center">
4050 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
4052 <td><em>Application</em>
4054 <li>Support for JABAWS 2.0 Services (AACon alignment
4055 conservation, protein disorder and Clustal Omega)</li>
4056 <li>JABAWS server status indicator in Web Services
4058 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
4059 in Jalview alignment window</li>
4060 <li>Updated Jalview build and deploy framework for OSX
4061 mountain lion, windows 7, and 8</li>
4062 <li>Nucleotide substitution matrix for PCA that supports
4063 RNA and ambiguity codes</li>
4065 <li>Improved sequence database retrieval GUI</li>
4066 <li>Support fetching and database reference look up
4067 against multiple DAS sources (Fetch all from in 'fetch db
4069 <li>Jalview project improvements
4071 <li>Store and retrieve the 'belowAlignment'
4072 flag for annotation</li>
4073 <li>calcId attribute to group annotation rows on the
4075 <li>Store AACon calculation settings for a view in
4076 Jalview project</li>
4080 <li>horizontal scrolling gesture support</li>
4081 <li>Visual progress indicator when PCA calculation is
4083 <li>Simpler JABA web services menus</li>
4084 <li>visual indication that web service results are still
4085 being retrieved from server</li>
4086 <li>Serialise the dialogs that are shown when Jalview
4087 starts up for first time</li>
4088 <li>Jalview user agent string for interacting with HTTP
4090 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
4092 <li>Examples directory and Groovy library included in
4093 InstallAnywhere distribution</li>
4094 </ul> <em>Applet</em>
4096 <li>RNA alignment and secondary structure annotation
4097 visualization applet example</li>
4098 </ul> <em>General</em>
4100 <li>Normalise option for consensus sequence logo</li>
4101 <li>Reset button in PCA window to return dimensions to
4103 <li>Allow seqspace or Jalview variant of alignment PCA
4105 <li>PCA with either nucleic acid and protein substitution
4107 <li>Allow windows containing HTML reports to be exported
4109 <li>Interactive display and editing of RNA secondary
4110 structure contacts</li>
4111 <li>RNA Helix Alignment Colouring</li>
4112 <li>RNA base pair logo consensus</li>
4113 <li>Parse sequence associated secondary structure
4114 information in Stockholm files</li>
4115 <li>HTML Export database accessions and annotation
4116 information presented in tooltip for sequences</li>
4117 <li>Import secondary structure from LOCARNA clustalw
4118 style RNA alignment files</li>
4119 <li>import and visualise T-COFFEE quality scores for an
4121 <li>'colour by annotation' per sequence option to
4122 shade each sequence according to its associated alignment
4124 <li>New Jalview Logo</li>
4125 </ul> <em>Documentation and Development</em>
4127 <li>documentation for score matrices used in Jalview</li>
4128 <li>New Website!</li>
4130 <td><em>Application</em>
4132 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
4133 wsdbfetch REST service</li>
4134 <li>Stop windows being moved outside desktop on OSX</li>
4135 <li>Filetype associations not installed for webstart
4137 <li>Jalview does not always retrieve progress of a JABAWS
4138 job execution in full once it is complete</li>
4139 <li>revise SHMR RSBS definition to ensure alignment is
4140 uploaded via ali_file parameter</li>
4141 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
4142 <li>View all structures superposed fails with exception</li>
4143 <li>Jnet job queues forever if a very short sequence is
4144 submitted for prediction</li>
4145 <li>Cut and paste menu not opened when mouse clicked on
4147 <li>Putting fractional value into integer text box in
4148 alignment parameter dialog causes Jalview to hang</li>
4149 <li>Structure view highlighting doesn't work on
4151 <li>View all structures fails with exception shown in
4153 <li>Characters in filename associated with PDBEntry not
4154 escaped in a platform independent way</li>
4155 <li>Jalview desktop fails to launch with exception when
4157 <li>Tree calculation reports 'you must have 2 or more
4158 sequences selected' when selection is empty</li>
4159 <li>Jalview desktop fails to launch with jar signature
4160 failure when java web start temporary file caching is
4162 <li>DAS Sequence retrieval with range qualification
4163 results in sequence xref which includes range qualification</li>
4164 <li>Errors during processing of command line arguments
4165 cause progress bar (JAL-898) to be removed</li>
4166 <li>Replace comma for semi-colon option not disabled for
4167 DAS sources in sequence fetcher</li>
4168 <li>Cannot close news reader when JABAWS server warning
4169 dialog is shown</li>
4170 <li>Option widgets not updated to reflect user settings</li>
4171 <li>Edited sequence not submitted to web service</li>
4172 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
4173 <li>InstallAnywhere installer doesn't unpack and run
4174 on OSX Mountain Lion</li>
4175 <li>Annotation panel not given a scroll bar when
4176 sequences with alignment annotation are pasted into the
4178 <li>Sequence associated annotation rows not associated
4179 when loaded from Jalview project</li>
4180 <li>Browser launch fails with NPE on java 1.7</li>
4181 <li>JABAWS alignment marked as finished when job was
4182 cancelled or job failed due to invalid input</li>
4183 <li>NPE with v2.7 example when clicking on Tree
4184 associated with all views</li>
4185 <li>Exceptions when copy/paste sequences with grouped
4186 annotation rows to new window</li>
4187 </ul> <em>Applet</em>
4189 <li>Sequence features are momentarily displayed before
4190 they are hidden using hidefeaturegroups applet parameter</li>
4191 <li>loading features via javascript API automatically
4192 enables feature display</li>
4193 <li>scrollToColumnIn javascript API method doesn't
4195 </ul> <em>General</em>
4197 <li>Redundancy removal fails for rna alignment</li>
4198 <li>PCA calculation fails when sequence has been selected
4199 and then deselected</li>
4200 <li>PCA window shows grey box when first opened on OSX</li>
4201 <li>Letters coloured pink in sequence logo when alignment
4202 coloured with clustalx</li>
4203 <li>Choosing fonts without letter symbols defined causes
4204 exceptions and redraw errors</li>
4205 <li>Initial PCA plot view is not same as manually
4206 reconfigured view</li>
4207 <li>Grouped annotation graph label has incorrect line
4209 <li>Grouped annotation graph label display is corrupted
4210 for lots of labels</li>
4215 <div align="center">
4216 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
4219 <td><em>Application</em>
4221 <li>Jalview Desktop News Reader</li>
4222 <li>Tweaked default layout of web services menu</li>
4223 <li>View/alignment association menu to enable user to
4224 easily specify which alignment a multi-structure view takes
4225 its colours/correspondences from</li>
4226 <li>Allow properties file location to be specified as URL</li>
4227 <li>Extend Jalview project to preserve associations
4228 between many alignment views and a single Jmol display</li>
4229 <li>Store annotation row height in Jalview project file</li>
4230 <li>Annotation row column label formatting attributes
4231 stored in project file</li>
4232 <li>Annotation row order for auto-calculated annotation
4233 rows preserved in Jalview project file</li>
4234 <li>Visual progress indication when Jalview state is
4235 saved using Desktop window menu</li>
4236 <li>Visual indication that command line arguments are
4237 still being processed</li>
4238 <li>Groovy script execution from URL</li>
4239 <li>Colour by annotation default min and max colours in
4241 <li>Automatically associate PDB files dragged onto an
4242 alignment with sequences that have high similarity and
4244 <li>Update JGoogleAnalytics to latest release (0.3)</li>
4245 <li>'view structures' option to open many
4246 structures in same window</li>
4247 <li>Sort associated views menu option for tree panel</li>
4248 <li>Group all JABA and non-JABA services for a particular
4249 analysis function in its own submenu</li>
4250 </ul> <em>Applet</em>
4252 <li>Userdefined and autogenerated annotation rows for
4254 <li>Adjustment of alignment annotation pane height</li>
4255 <li>Annotation scrollbar for annotation panel</li>
4256 <li>Drag to reorder annotation rows in annotation panel</li>
4257 <li>'automaticScrolling' parameter</li>
4258 <li>Allow sequences with partial ID string matches to be
4259 annotated from GFF/Jalview features files</li>
4260 <li>Sequence logo annotation row in applet</li>
4261 <li>Absolute paths relative to host server in applet
4262 parameters are treated as such</li>
4263 <li>New in the JalviewLite javascript API:
4265 <li>JalviewLite.js javascript library</li>
4266 <li>Javascript callbacks for
4268 <li>Applet initialisation</li>
4269 <li>Sequence/alignment mouse-overs and selections</li>
4272 <li>scrollTo row and column alignment scrolling
4274 <li>Select sequence/alignment regions from javascript</li>
4275 <li>javascript structure viewer harness to pass
4276 messages between Jmol and Jalview when running as
4277 distinct applets</li>
4278 <li>sortBy method</li>
4279 <li>Set of applet and application examples shipped
4280 with documentation</li>
4281 <li>New example to demonstrate JalviewLite and Jmol
4282 javascript message exchange</li>
4284 </ul> <em>General</em>
4286 <li>Enable Jmol displays to be associated with multiple
4287 multiple alignments</li>
4288 <li>Option to automatically sort alignment with new tree</li>
4289 <li>User configurable link to enable redirects to a
4290 www.Jalview.org mirror</li>
4291 <li>Jmol colours option for Jmol displays</li>
4292 <li>Configurable newline string when writing alignment
4293 and other flat files</li>
4294 <li>Allow alignment annotation description lines to
4295 contain html tags</li>
4296 </ul> <em>Documentation and Development</em>
4298 <li>Add groovy test harness for bulk load testing to
4300 <li>Groovy script to load and align a set of sequences
4301 using a web service before displaying the result in the
4302 Jalview desktop</li>
4303 <li>Restructured javascript and applet api documentation</li>
4304 <li>Ant target to publish example html files with applet
4306 <li>Netbeans project for building Jalview from source</li>
4307 <li>ant task to create online javadoc for Jalview source</li>
4309 <td><em>Application</em>
4311 <li>User defined colourscheme throws exception when
4312 current built in colourscheme is saved as new scheme</li>
4313 <li>AlignFrame->Save in application pops up save
4314 dialog for valid filename/format</li>
4315 <li>Cannot view associated structure for UniProt sequence</li>
4316 <li>PDB file association breaks for UniProt sequence
4318 <li>Associate PDB from file dialog does not tell you
4319 which sequence is to be associated with the file</li>
4320 <li>Find All raises null pointer exception when query
4321 only matches sequence IDs</li>
4322 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4323 <li>Jalview project with Jmol views created with Jalview
4324 2.4 cannot be loaded</li>
4325 <li>Filetype associations not installed for webstart
4327 <li>Two or more chains in a single PDB file associated
4328 with sequences in different alignments do not get coloured
4329 by their associated sequence</li>
4330 <li>Visibility status of autocalculated annotation row
4331 not preserved when project is loaded</li>
4332 <li>Annotation row height and visibility attributes not
4333 stored in Jalview project</li>
4334 <li>Tree bootstraps are not preserved when saved as a
4335 Jalview project</li>
4336 <li>Envision2 workflow tooltips are corrupted</li>
4337 <li>Enabling show group conservation also enables colour
4338 by conservation</li>
4339 <li>Duplicate group associated conservation or consensus
4340 created on new view</li>
4341 <li>Annotation scrollbar not displayed after 'show
4342 all hidden annotation rows' option selected</li>
4343 <li>Alignment quality not updated after alignment
4344 annotation row is hidden then shown</li>
4345 <li>Preserve colouring of structures coloured by
4346 sequences in pre Jalview 2.7 projects</li>
4347 <li>Web service job parameter dialog is not laid out
4349 <li>Web services menu not refreshed after 'reset
4350 services' button is pressed in preferences</li>
4351 <li>Annotation off by one in Jalview v2_3 example project</li>
4352 <li>Structures imported from file and saved in project
4353 get name like jalview_pdb1234.txt when reloaded</li>
4354 <li>Jalview does not always retrieve progress of a JABAWS
4355 job execution in full once it is complete</li>
4356 </ul> <em>Applet</em>
4358 <li>Alignment height set incorrectly when lots of
4359 annotation rows are displayed</li>
4360 <li>Relative URLs in feature HTML text not resolved to
4362 <li>View follows highlighting does not work for positions
4364 <li><= shown as = in tooltip</li>
4365 <li>Export features raises exception when no features
4367 <li>Separator string used for serialising lists of IDs
4368 for javascript api is modified when separator string
4369 provided as parameter</li>
4370 <li>Null pointer exception when selecting tree leaves for
4371 alignment with no existing selection</li>
4372 <li>Relative URLs for datasources assumed to be relative
4373 to applet's codebase</li>
4374 <li>Status bar not updated after finished searching and
4375 search wraps around to first result</li>
4376 <li>StructureSelectionManager instance shared between
4377 several Jalview applets causes race conditions and memory
4379 <li>Hover tooltip and mouseover of position on structure
4380 not sent from Jmol in applet</li>
4381 <li>Certain sequences of javascript method calls to
4382 applet API fatally hang browser</li>
4383 </ul> <em>General</em>
4385 <li>View follows structure mouseover scrolls beyond
4386 position with wrapped view and hidden regions</li>
4387 <li>Find sequence position moves to wrong residue
4388 with/without hidden columns</li>
4389 <li>Sequence length given in alignment properties window
4391 <li>InvalidNumberFormat exceptions thrown when trying to
4392 import PDB like structure files</li>
4393 <li>Positional search results are only highlighted
4394 between user-supplied sequence start/end bounds</li>
4395 <li>End attribute of sequence is not validated</li>
4396 <li>Find dialog only finds first sequence containing a
4397 given sequence position</li>
4398 <li>Sequence numbering not preserved in MSF alignment
4400 <li>Jalview PDB file reader does not extract sequence
4401 from nucleotide chains correctly</li>
4402 <li>Structure colours not updated when tree partition
4403 changed in alignment</li>
4404 <li>Sequence associated secondary structure not correctly
4405 parsed in interleaved stockholm</li>
4406 <li>Colour by annotation dialog does not restore current
4408 <li>Hiding (nearly) all sequences doesn't work
4410 <li>Sequences containing lowercase letters are not
4411 properly associated with their pdb files</li>
4412 </ul> <em>Documentation and Development</em>
4414 <li>schemas/JalviewWsParamSet.xsd corrupted by
4415 ApplyCopyright tool</li>
4420 <div align="center">
4421 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4424 <td><em>Application</em>
4426 <li>New warning dialog when the Jalview Desktop cannot
4427 contact web services</li>
4428 <li>JABA service parameters for a preset are shown in
4429 service job window</li>
4430 <li>JABA Service menu entries reworded</li>
4434 <li>Modeller PIR IO broken - cannot correctly import a
4435 pir file emitted by Jalview</li>
4436 <li>Existing feature settings transferred to new
4437 alignment view created from cut'n'paste</li>
4438 <li>Improved test for mixed amino/nucleotide chains when
4439 parsing PDB files</li>
4440 <li>Consensus and conservation annotation rows
4441 occasionally become blank for all new windows</li>
4442 <li>Exception raised when right clicking above sequences
4443 in wrapped view mode</li>
4444 </ul> <em>Application</em>
4446 <li>multiple multiply aligned structure views cause cpu
4447 usage to hit 100% and computer to hang</li>
4448 <li>Web Service parameter layout breaks for long user
4449 parameter names</li>
4450 <li>Jaba service discovery hangs desktop if Jaba server
4457 <div align="center">
4458 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4461 <td><em>Application</em>
4463 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4464 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4467 <li>Web Services preference tab</li>
4468 <li>Analysis parameters dialog box and user defined
4470 <li>Improved speed and layout of Envision2 service menu</li>
4471 <li>Superpose structures using associated sequence
4473 <li>Export coordinates and projection as CSV from PCA
4475 </ul> <em>Applet</em>
4477 <li>enable javascript: execution by the applet via the
4478 link out mechanism</li>
4479 </ul> <em>Other</em>
4481 <li>Updated the Jmol Jalview interface to work with Jmol
4483 <li>The Jalview Desktop and JalviewLite applet now
4484 require Java 1.5</li>
4485 <li>Allow Jalview feature colour specification for GFF
4486 sequence annotation files</li>
4487 <li>New 'colour by label' keword in Jalview feature file
4488 type colour specification</li>
4489 <li>New Jalview Desktop Groovy API method that allows a
4490 script to check if it being run in an interactive session or
4491 in a batch operation from the Jalview command line</li>
4495 <li>clustalx colourscheme colours Ds preferentially when
4496 both D+E are present in over 50% of the column</li>
4497 </ul> <em>Application</em>
4499 <li>typo in AlignmentFrame->View->Hide->all but
4500 selected Regions menu item</li>
4501 <li>sequence fetcher replaces ',' for ';' when the ',' is
4502 part of a valid accession ID</li>
4503 <li>fatal OOM if object retrieved by sequence fetcher
4504 runs out of memory</li>
4505 <li>unhandled Out of Memory Error when viewing pca
4506 analysis results</li>
4507 <li>InstallAnywhere builds fail to launch on OS X java
4508 10.5 update 4 (due to apple Java 1.6 update)</li>
4509 <li>Installanywhere Jalview silently fails to launch</li>
4510 </ul> <em>Applet</em>
4512 <li>Jalview.getFeatureGroups() raises an
4513 ArrayIndexOutOfBoundsException if no feature groups are
4520 <div align="center">
4521 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4527 <li>Alignment prettyprinter doesn't cope with long
4529 <li>clustalx colourscheme colours Ds preferentially when
4530 both D+E are present in over 50% of the column</li>
4531 <li>nucleic acid structures retrieved from PDB do not
4532 import correctly</li>
4533 <li>More columns get selected than were clicked on when a
4534 number of columns are hidden</li>
4535 <li>annotation label popup menu not providing correct
4536 add/hide/show options when rows are hidden or none are
4538 <li>Stockholm format shown in list of readable formats,
4539 and parser copes better with alignments from RFAM.</li>
4540 <li>CSV output of consensus only includes the percentage
4541 of all symbols if sequence logo display is enabled</li>
4543 </ul> <em>Applet</em>
4545 <li>annotation panel disappears when annotation is
4547 </ul> <em>Application</em>
4549 <li>Alignment view not redrawn properly when new
4550 alignment opened where annotation panel is visible but no
4551 annotations are present on alignment</li>
4552 <li>pasted region containing hidden columns is
4553 incorrectly displayed in new alignment window</li>
4554 <li>Jalview slow to complete operations when stdout is
4555 flooded (fix is to close the Jalview console)</li>
4556 <li>typo in AlignmentFrame->View->Hide->all but
4557 selected Rregions menu item.</li>
4558 <li>inconsistent group submenu and Format submenu entry
4559 'Un' or 'Non'conserved</li>
4560 <li>Sequence feature settings are being shared by
4561 multiple distinct alignments</li>
4562 <li>group annotation not recreated when tree partition is
4564 <li>double click on group annotation to select sequences
4565 does not propagate to associated trees</li>
4566 <li>Mac OSX specific issues:
4568 <li>exception raised when mouse clicked on desktop
4569 window background</li>
4570 <li>Desktop menu placed on menu bar and application
4571 name set correctly</li>
4572 <li>sequence feature settings not wide enough for the
4573 save feature colourscheme button</li>
4582 <div align="center">
4583 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4586 <td><em>New Capabilities</em>
4588 <li>URL links generated from description line for
4589 regular-expression based URL links (applet and application)
4591 <li>Non-positional feature URL links are shown in link
4593 <li>Linked viewing of nucleic acid sequences and
4595 <li>Automatic Scrolling option in View menu to display
4596 the currently highlighted region of an alignment.</li>
4597 <li>Order an alignment by sequence length, or using the
4598 average score or total feature count for each sequence.</li>
4599 <li>Shading features by score or associated description</li>
4600 <li>Subdivide alignment and groups based on identity of
4601 selected subsequence (Make Groups from Selection).</li>
4602 <li>New hide/show options including Shift+Control+H to
4603 hide everything but the currently selected region.</li>
4604 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4605 </ul> <em>Application</em>
4607 <li>Fetch DB References capabilities and UI expanded to
4608 support retrieval from DAS sequence sources</li>
4609 <li>Local DAS Sequence sources can be added via the
4610 command line or via the Add local source dialog box.</li>
4611 <li>DAS Dbref and DbxRef feature types are parsed as
4612 database references and protein_name is parsed as
4613 description line (BioSapiens terms).</li>
4614 <li>Enable or disable non-positional feature and database
4615 references in sequence ID tooltip from View menu in
4617 <!-- <li>New hidden columns and rows and representatives capabilities
4618 in annotations file (in progress - not yet fully implemented)</li> -->
4619 <li>Group-associated consensus, sequence logos and
4620 conservation plots</li>
4621 <li>Symbol distributions for each column can be exported
4622 and visualized as sequence logos</li>
4623 <li>Optionally scale multi-character column labels to fit
4624 within each column of annotation row<!-- todo for applet -->
4626 <li>Optional automatic sort of associated alignment view
4627 when a new tree is opened.</li>
4628 <li>Jalview Java Console</li>
4629 <li>Better placement of desktop window when moving
4630 between different screens.</li>
4631 <li>New preference items for sequence ID tooltip and
4632 consensus annotation</li>
4633 <li>Client to submit sequences and IDs to Envision2
4635 <li><em>Vamsas Capabilities</em>
4637 <li>Improved VAMSAS synchronization (Jalview archive
4638 used to preserve views, structures, and tree display
4640 <li>Import of vamsas documents from disk or URL via
4642 <li>Sharing of selected regions between views and
4643 with other VAMSAS applications (Experimental feature!)</li>
4644 <li>Updated API to VAMSAS version 0.2</li>
4646 </ul> <em>Applet</em>
4648 <li>Middle button resizes annotation row height</li>
4651 <li>sortByTree (true/false) - automatically sort the
4652 associated alignment view by the tree when a new tree is
4654 <li>showTreeBootstraps (true/false) - show or hide
4655 branch bootstraps (default is to show them if available)</li>
4656 <li>showTreeDistances (true/false) - show or hide
4657 branch lengths (default is to show them if available)</li>
4658 <li>showUnlinkedTreeNodes (true/false) - indicate if
4659 unassociated nodes should be highlighted in the tree
4661 <li>heightScale and widthScale (1.0 or more) -
4662 increase the height or width of a cell in the alignment
4663 grid relative to the current font size.</li>
4666 <li>Non-positional features displayed in sequence ID
4668 </ul> <em>Other</em>
4670 <li>Features format: graduated colour definitions and
4671 specification of feature scores</li>
4672 <li>Alignment Annotations format: new keywords for group
4673 associated annotation (GROUP_REF) and annotation row display
4674 properties (ROW_PROPERTIES)</li>
4675 <li>XML formats extended to support graduated feature
4676 colourschemes, group associated annotation, and profile
4677 visualization settings.</li></td>
4680 <li>Source field in GFF files parsed as feature source
4681 rather than description</li>
4682 <li>Non-positional features are now included in sequence
4683 feature and gff files (controlled via non-positional feature
4684 visibility in tooltip).</li>
4685 <li>URL links generated for all feature links (bugfix)</li>
4686 <li>Added URL embedding instructions to features file
4688 <li>Codons containing ambiguous nucleotides translated as
4689 'X' in peptide product</li>
4690 <li>Match case switch in find dialog box works for both
4691 sequence ID and sequence string and query strings do not
4692 have to be in upper case to match case-insensitively.</li>
4693 <li>AMSA files only contain first column of
4694 multi-character column annotation labels</li>
4695 <li>Jalview Annotation File generation/parsing consistent
4696 with documentation (e.g. Stockholm annotation can be
4697 exported and re-imported)</li>
4698 <li>PDB files without embedded PDB IDs given a friendly
4700 <li>Find incrementally searches ID string matches as well
4701 as subsequence matches, and correctly reports total number
4705 <li>Better handling of exceptions during sequence
4707 <li>Dasobert generated non-positional feature URL
4708 link text excludes the start_end suffix</li>
4709 <li>DAS feature and source retrieval buttons disabled
4710 when fetch or registry operations in progress.</li>
4711 <li>PDB files retrieved from URLs are cached properly</li>
4712 <li>Sequence description lines properly shared via
4714 <li>Sequence fetcher fetches multiple records for all
4716 <li>Ensured that command line das feature retrieval
4717 completes before alignment figures are generated.</li>
4718 <li>Reduced time taken when opening file browser for
4720 <li>isAligned check prior to calculating tree, PCA or
4721 submitting an MSA to JNet now excludes hidden sequences.</li>
4722 <li>User defined group colours properly recovered
4723 from Jalview projects.</li>
4732 <div align="center">
4733 <strong>2.4.0.b2</strong><br> 28/10/2009
4738 <li>Experimental support for google analytics usage
4740 <li>Jalview privacy settings (user preferences and docs).</li>
4745 <li>Race condition in applet preventing startup in
4747 <li>Exception when feature created from selection beyond
4748 length of sequence.</li>
4749 <li>Allow synthetic PDB files to be imported gracefully</li>
4750 <li>Sequence associated annotation rows associate with
4751 all sequences with a given id</li>
4752 <li>Find function matches case-insensitively for sequence
4753 ID string searches</li>
4754 <li>Non-standard characters do not cause pairwise
4755 alignment to fail with exception</li>
4756 </ul> <em>Application Issues</em>
4758 <li>Sequences are now validated against EMBL database</li>
4759 <li>Sequence fetcher fetches multiple records for all
4761 </ul> <em>InstallAnywhere Issues</em>
4763 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4764 issue with installAnywhere mechanism)</li>
4765 <li>Command line launching of JARs from InstallAnywhere
4766 version (java class versioning error fixed)</li>
4773 <div align="center">
4774 <strong>2.4</strong><br> 27/8/2008
4777 <td><em>User Interface</em>
4779 <li>Linked highlighting of codon and amino acid from
4780 translation and protein products</li>
4781 <li>Linked highlighting of structure associated with
4782 residue mapping to codon position</li>
4783 <li>Sequence Fetcher provides example accession numbers
4784 and 'clear' button</li>
4785 <li>MemoryMonitor added as an option under Desktop's
4787 <li>Extract score function to parse whitespace separated
4788 numeric data in description line</li>
4789 <li>Column labels in alignment annotation can be centred.</li>
4790 <li>Tooltip for sequence associated annotation give name
4792 </ul> <em>Web Services and URL fetching</em>
4794 <li>JPred3 web service</li>
4795 <li>Prototype sequence search client (no public services
4797 <li>Fetch either seed alignment or full alignment from
4799 <li>URL Links created for matching database cross
4800 references as well as sequence ID</li>
4801 <li>URL Links can be created using regular-expressions</li>
4802 </ul> <em>Sequence Database Connectivity</em>
4804 <li>Retrieval of cross-referenced sequences from other
4806 <li>Generalised database reference retrieval and
4807 validation to all fetchable databases</li>
4808 <li>Fetch sequences from DAS sources supporting the
4809 sequence command</li>
4810 </ul> <em>Import and Export</em>
4811 <li>export annotation rows as CSV for spreadsheet import</li>
4812 <li>Jalview projects record alignment dataset associations,
4813 EMBL products, and cDNA sequence mappings</li>
4814 <li>Sequence Group colour can be specified in Annotation
4816 <li>Ad-hoc colouring of group in Annotation File using RGB
4817 triplet as name of colourscheme</li>
4818 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4820 <li>treenode binding for VAMSAS tree exchange</li>
4821 <li>local editing and update of sequences in VAMSAS
4822 alignments (experimental)</li>
4823 <li>Create new or select existing session to join</li>
4824 <li>load and save of vamsas documents</li>
4825 </ul> <em>Application command line</em>
4827 <li>-tree parameter to open trees (introduced for passing
4829 <li>-fetchfrom command line argument to specify nicknames
4830 of DAS servers to query for alignment features</li>
4831 <li>-dasserver command line argument to add new servers
4832 that are also automatically queried for features</li>
4833 <li>-groovy command line argument executes a given groovy
4834 script after all input data has been loaded and parsed</li>
4835 </ul> <em>Applet-Application data exchange</em>
4837 <li>Trees passed as applet parameters can be passed to
4838 application (when using "View in full
4839 application")</li>
4840 </ul> <em>Applet Parameters</em>
4842 <li>feature group display control parameter</li>
4843 <li>debug parameter</li>
4844 <li>showbutton parameter</li>
4845 </ul> <em>Applet API methods</em>
4847 <li>newView public method</li>
4848 <li>Window (current view) specific get/set public methods</li>
4849 <li>Feature display control methods</li>
4850 <li>get list of currently selected sequences</li>
4851 </ul> <em>New Jalview distribution features</em>
4853 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4854 <li>RELEASE file gives build properties for the latest
4855 Jalview release.</li>
4856 <li>Java 1.1 Applet build made easier and donotobfuscate
4857 property controls execution of obfuscator</li>
4858 <li>Build target for generating source distribution</li>
4859 <li>Debug flag for javacc</li>
4860 <li>.jalview_properties file is documented (slightly) in
4861 jalview.bin.Cache</li>
4862 <li>Continuous Build Integration for stable and
4863 development version of Application, Applet and source
4868 <li>selected region output includes visible annotations
4869 (for certain formats)</li>
4870 <li>edit label/displaychar contains existing label/char
4872 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4873 <li>shorter peptide product names from EMBL records</li>
4874 <li>Newick string generator makes compact representations</li>
4875 <li>bootstrap values parsed correctly for tree files with
4877 <li>pathological filechooser bug avoided by not allowing
4878 filenames containing a ':'</li>
4879 <li>Fixed exception when parsing GFF files containing
4880 global sequence features</li>
4881 <li>Alignment datasets are finalized only when number of
4882 references from alignment sequences goes to zero</li>
4883 <li>Close of tree branch colour box without colour
4884 selection causes cascading exceptions</li>
4885 <li>occasional negative imgwidth exceptions</li>
4886 <li>better reporting of non-fatal warnings to user when
4887 file parsing fails.</li>
4888 <li>Save works when Jalview project is default format</li>
4889 <li>Save as dialog opened if current alignment format is
4890 not a valid output format</li>
4891 <li>UniProt canonical names introduced for both das and
4893 <li>Histidine should be midblue (not pink!) in Zappo</li>
4894 <li>error messages passed up and output when data read
4896 <li>edit undo recovers previous dataset sequence when
4897 sequence is edited</li>
4898 <li>allow PDB files without pdb ID HEADER lines (like
4899 those generated by MODELLER) to be read in properly</li>
4900 <li>allow reading of JPred concise files as a normal
4902 <li>Stockholm annotation parsing and alignment properties
4903 import fixed for PFAM records</li>
4904 <li>Structure view windows have correct name in Desktop
4906 <li>annotation consisting of sequence associated scores
4907 can be read and written correctly to annotation file</li>
4908 <li>Aligned cDNA translation to aligned peptide works
4910 <li>Fixed display of hidden sequence markers and
4911 non-italic font for representatives in Applet</li>
4912 <li>Applet Menus are always embedded in applet window on
4914 <li>Newly shown features appear at top of stack (in
4916 <li>Annotations added via parameter not drawn properly
4917 due to null pointer exceptions</li>
4918 <li>Secondary structure lines are drawn starting from
4919 first column of alignment</li>
4920 <li>UniProt XML import updated for new schema release in
4922 <li>Sequence feature to sequence ID match for Features
4923 file is case-insensitive</li>
4924 <li>Sequence features read from Features file appended to
4925 all sequences with matching IDs</li>
4926 <li>PDB structure coloured correctly for associated views
4927 containing a sub-sequence</li>
4928 <li>PDB files can be retrieved by applet from Jar files</li>
4929 <li>feature and annotation file applet parameters
4930 referring to different directories are retrieved correctly</li>
4931 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4932 <li>Fixed application hang whilst waiting for
4933 splash-screen version check to complete</li>
4934 <li>Applet properly URLencodes input parameter values
4935 when passing them to the launchApp service</li>
4936 <li>display name and local features preserved in results
4937 retrieved from web service</li>
4938 <li>Visual delay indication for sequence retrieval and
4939 sequence fetcher initialisation</li>
4940 <li>updated Application to use DAS 1.53e version of
4941 dasobert DAS client</li>
4942 <li>Re-instated Full AMSA support and .amsa file
4944 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4952 <div align="center">
4953 <strong>2.3</strong><br> 9/5/07
4958 <li>Jmol 11.0.2 integration</li>
4959 <li>PDB views stored in Jalview XML files</li>
4960 <li>Slide sequences</li>
4961 <li>Edit sequence in place</li>
4962 <li>EMBL CDS features</li>
4963 <li>DAS Feature mapping</li>
4964 <li>Feature ordering</li>
4965 <li>Alignment Properties</li>
4966 <li>Annotation Scores</li>
4967 <li>Sort by scores</li>
4968 <li>Feature/annotation editing in applet</li>
4973 <li>Headless state operation in 2.2.1</li>
4974 <li>Incorrect and unstable DNA pairwise alignment</li>
4975 <li>Cut and paste of sequences with annotation</li>
4976 <li>Feature group display state in XML</li>
4977 <li>Feature ordering in XML</li>
4978 <li>blc file iteration selection using filename # suffix</li>
4979 <li>Stockholm alignment properties</li>
4980 <li>Stockhom alignment secondary structure annotation</li>
4981 <li>2.2.1 applet had no feature transparency</li>
4982 <li>Number pad keys can be used in cursor mode</li>
4983 <li>Structure Viewer mirror image resolved</li>
4990 <div align="center">
4991 <strong>2.2.1</strong><br> 12/2/07
4996 <li>Non standard characters can be read and displayed
4997 <li>Annotations/Features can be imported/exported to the
4999 <li>Applet allows editing of sequence/annotation/group
5000 name & description
5001 <li>Preference setting to display sequence name in
5003 <li>Annotation file format extended to allow
5004 Sequence_groups to be defined
5005 <li>Default opening of alignment overview panel can be
5006 specified in preferences
5007 <li>PDB residue numbering annotation added to associated
5013 <li>Applet crash under certain Linux OS with Java 1.6
5015 <li>Annotation file export / import bugs fixed
5016 <li>PNG / EPS image output bugs fixed
5022 <div align="center">
5023 <strong>2.2</strong><br> 27/11/06
5028 <li>Multiple views on alignment
5029 <li>Sequence feature editing
5030 <li>"Reload" alignment
5031 <li>"Save" to current filename
5032 <li>Background dependent text colour
5033 <li>Right align sequence ids
5034 <li>User-defined lower case residue colours
5037 <li>Menu item accelerator keys
5038 <li>Control-V pastes to current alignment
5039 <li>Cancel button for DAS Feature Fetching
5040 <li>PCA and PDB Viewers zoom via mouse roller
5041 <li>User-defined sub-tree colours and sub-tree selection
5043 <li>'New Window' button on the 'Output to Text box'
5048 <li>New memory efficient Undo/Redo System
5049 <li>Optimised symbol lookups and conservation/consensus
5051 <li>Region Conservation/Consensus recalculated after
5053 <li>Fixed Remove Empty Columns Bug (empty columns at end
5055 <li>Slowed DAS Feature Fetching for increased robustness.
5057 <li>Made angle brackets in ASCII feature descriptions
5059 <li>Re-instated Zoom function for PCA
5060 <li>Sequence descriptions conserved in web service
5062 <li>UniProt ID discoverer uses any word separated by
5064 <li>WsDbFetch query/result association resolved
5065 <li>Tree leaf to sequence mapping improved
5066 <li>Smooth fonts switch moved to FontChooser dialog box.
5073 <div align="center">
5074 <strong>2.1.1</strong><br> 12/9/06
5079 <li>Copy consensus sequence to clipboard</li>
5084 <li>Image output - rightmost residues are rendered if
5085 sequence id panel has been resized</li>
5086 <li>Image output - all offscreen group boundaries are
5088 <li>Annotation files with sequence references - all
5089 elements in file are relative to sequence position</li>
5090 <li>Mac Applet users can use Alt key for group editing</li>
5096 <div align="center">
5097 <strong>2.1</strong><br> 22/8/06
5102 <li>MAFFT Multiple Alignment in default Web Service list</li>
5103 <li>DAS Feature fetching</li>
5104 <li>Hide sequences and columns</li>
5105 <li>Export Annotations and Features</li>
5106 <li>GFF file reading / writing</li>
5107 <li>Associate structures with sequences from local PDB
5109 <li>Add sequences to exisiting alignment</li>
5110 <li>Recently opened files / URL lists</li>
5111 <li>Applet can launch the full application</li>
5112 <li>Applet has transparency for features (Java 1.2
5114 <li>Applet has user defined colours parameter</li>
5115 <li>Applet can load sequences from parameter
5116 "sequence<em>x</em>"
5122 <li>Redundancy Panel reinstalled in the Applet</li>
5123 <li>Monospaced font - EPS / rescaling bug fixed</li>
5124 <li>Annotation files with sequence references bug fixed</li>
5130 <div align="center">
5131 <strong>2.08.1</strong><br> 2/5/06
5136 <li>Change case of selected region from Popup menu</li>
5137 <li>Choose to match case when searching</li>
5138 <li>Middle mouse button and mouse movement can compress /
5139 expand the visible width and height of the alignment</li>
5144 <li>Annotation Panel displays complete JNet results</li>
5150 <div align="center">
5151 <strong>2.08b</strong><br> 18/4/06
5157 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
5158 <li>Righthand label on wrapped alignments shows correct
5165 <div align="center">
5166 <strong>2.08</strong><br> 10/4/06
5171 <li>Editing can be locked to the selection area</li>
5172 <li>Keyboard editing</li>
5173 <li>Create sequence features from searches</li>
5174 <li>Precalculated annotations can be loaded onto
5176 <li>Features file allows grouping of features</li>
5177 <li>Annotation Colouring scheme added</li>
5178 <li>Smooth fonts off by default - Faster rendering</li>
5179 <li>Choose to toggle Autocalculate Consensus On/Off</li>
5184 <li>Drag & Drop fixed on Linux</li>
5185 <li>Jalview Archive file faster to load/save, sequence
5186 descriptions saved.</li>
5192 <div align="center">
5193 <strong>2.07</strong><br> 12/12/05
5198 <li>PDB Structure Viewer enhanced</li>
5199 <li>Sequence Feature retrieval and display enhanced</li>
5200 <li>Choose to output sequence start-end after sequence
5201 name for file output</li>
5202 <li>Sequence Fetcher WSDBFetch@EBI</li>
5203 <li>Applet can read feature files, PDB files and can be
5204 used for HTML form input</li>
5209 <li>HTML output writes groups and features</li>
5210 <li>Group editing is Control and mouse click</li>
5211 <li>File IO bugs</li>
5217 <div align="center">
5218 <strong>2.06</strong><br> 28/9/05
5223 <li>View annotations in wrapped mode</li>
5224 <li>More options for PCA viewer</li>
5229 <li>GUI bugs resolved</li>
5230 <li>Runs with -nodisplay from command line</li>
5236 <div align="center">
5237 <strong>2.05b</strong><br> 15/9/05
5242 <li>Choose EPS export as lineart or text</li>
5243 <li>Jar files are executable</li>
5244 <li>Can read in Uracil - maps to unknown residue</li>
5249 <li>Known OutOfMemory errors give warning message</li>
5250 <li>Overview window calculated more efficiently</li>
5251 <li>Several GUI bugs resolved</li>
5257 <div align="center">
5258 <strong>2.05</strong><br> 30/8/05
5263 <li>Edit and annotate in "Wrapped" view</li>
5268 <li>Several GUI bugs resolved</li>
5274 <div align="center">
5275 <strong>2.04</strong><br> 24/8/05
5280 <li>Hold down mouse wheel & scroll to change font
5286 <li>Improved JPred client reliability</li>
5287 <li>Improved loading of Jalview files</li>
5293 <div align="center">
5294 <strong>2.03</strong><br> 18/8/05
5299 <li>Set Proxy server name and port in preferences</li>
5300 <li>Multiple URL links from sequence ids</li>
5301 <li>User Defined Colours can have a scheme name and added
5303 <li>Choose to ignore gaps in consensus calculation</li>
5304 <li>Unix users can set default web browser</li>
5305 <li>Runs without GUI for batch processing</li>
5306 <li>Dynamically generated Web Service Menus</li>
5311 <li>InstallAnywhere download for Sparc Solaris</li>
5317 <div align="center">
5318 <strong>2.02</strong><br> 18/7/05
5324 <li>Copy & Paste order of sequences maintains
5325 alignment order.</li>
5331 <div align="center">
5332 <strong>2.01</strong><br> 12/7/05
5337 <li>Use delete key for deleting selection.</li>
5338 <li>Use Mouse wheel to scroll sequences.</li>
5339 <li>Help file updated to describe how to add alignment
5341 <li>Version and build date written to build properties
5343 <li>InstallAnywhere installation will check for updates
5344 at launch of Jalview.</li>
5349 <li>Delete gaps bug fixed.</li>
5350 <li>FileChooser sorts columns.</li>
5351 <li>Can remove groups one by one.</li>
5352 <li>Filechooser icons installed.</li>
5353 <li>Finder ignores return character when searching.
5354 Return key will initiate a search.<br>
5361 <div align="center">
5362 <strong>2.0</strong><br> 20/6/05
5367 <li>New codebase</li>