3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
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50 <strong>Release History</strong>
54 <th nowrap><em>Release</em></th>
55 <th><em>New Features</em></th>
56 <th><em>Issues Resolved</em></th>
59 <td width="60" align="center" nowrap><strong><a
60 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
61 <em>8/09/2020</em></strong></td>
62 <td align="left" valign="top">
66 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
67 residue in cursor mode
70 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
71 HTSJDK from 2.12 to 2.23
74 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
75 optimisations and improvements suggested by Bob Hanson and
76 improved compatibility with JalviewJS
79 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
80 alignments from Pfam and Rfam
83 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
84 import (no longer based on .gz extension)
87 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
90 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
91 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
95 <!-- JAL-3667 -->Improved warning messages, debug logging
96 and fixed Retry action when Jalview encounters errors when
97 saving or making backup files.
100 <!-- JAL-3676 -->Enhanced Jalview Java Console:
102 <li>Jalview's logging level can be configured</li>
103 <li>Copy to Clipboard Buttion</li>
107 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
108 when running on Linux (Requires Java 11+)
110 </ul> <em>Launching Jalview</em>
113 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
114 through a system property
117 <!-- JAL-3477 -->Improved built-in documentation and command
118 line help for configuring Jalview's memory
122 <td align="left" valign="top">
125 <!-- JAL-3691 -->Conservation and Quality tracks are shown
126 but not calculated and no protein or DNA score models are
127 available for tree/PCA calculation when launched with
128 Turkish language locale
131 <!-- JAL-3493 -->Escape does not clear highlights on the
132 alignment (Since Jalview 2.10.3)
135 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
136 doesn't slide selected sequences, just sequence under cursor
139 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
140 multiple EMBL gene products shown forĀ a single contig
143 <!-- JAL-3696 -->Errors encountered when processing variants
144 from VCF files yield "Error processing VCF: Format specifier
148 <!-- JAL-3697 -->Count of features not shown can be wrong
149 when there are both local and complementary features mapped
150 to the position under the cursor
153 <!-- JAL-3673 -->Sequence ID for reference sequence is
154 clipped when Right align Sequence IDs enabled
157 <!-- JAL-2983 -->Slider with negative range values not
158 rendered correctly in VAqua4 (Since 2.10.4)
161 <!-- JAL-3685 -->Single quotes not displayed correctly in
162 internationalised text for some messages and log output
165 <!-- JAL-3490 -->Find doesn't report matches that span
166 hidden gapped columns
169 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
170 panels, Alignment viewport and annotation renderer.
173 <!-- JAL-3561 -->Jalview ignores file format parameter
174 specifying output format when exporting an alignment via the
178 <!-- JAL-3667 -->Windows 10: For a minority of users, if
179 backups are not enabled, Jalview sometimes fails to
180 overwrite an existing file and raises a warning dialog. (in
181 2.11.0, and 2.11.1.0, the workaround is to try to save the
182 file again, and if that fails, delete the original file and
185 </ul> <em>Developing Jalview</em>
188 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
189 data, causing cloverReport gradle task to fail with an
193 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
194 monitor the release channel
196 </ul> <em>New Known defects</em>
199 <!-- JAL-3576 -->Co-located features exported and re-imported
200 are ordered differently when shown on alignment and in
201 tooltips. (Also affects v2.11.1.0)
204 <!-- JAL-3702 -->Drag and drop of alignment file onto
205 alignment window when in a HiDPI scaled mode in Linux only
206 works for the top left quadrant of the alignment window
209 <!-- JAL-3701 -->Stale build data in jalview standalone jar
210 builds (only affects 2.11.1.1 branch)
213 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
214 when alignment view restored from project (since Jalview 2.11.0)
220 <td width="60" align="center" nowrap><strong><a
221 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
222 <em>22/04/2020</em></strong></td>
223 <td align="left" valign="top">
226 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
227 'virtual' codon features shown on protein (or vice versa)
228 for display in alignments, on structure views (including
229 transfer to UCSF chimera), in feature reports and for
233 <!-- JAL-3121 -->Feature attributes from VCF files can be
234 exported and re-imported as GFF3 files
237 <!-- JAL-3376 -->Capture VCF "fixed column" values
238 POS, ID, QUAL, FILTER as Feature Attributes
241 <!-- JAL-3375 -->More robust VCF numeric data field
242 validation while parsing
245 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
249 <!-- JAL-3535 -->Feature Settings dialog title includes name
253 <!-- JAL-3538 -->Font anti-aliasing in alignment views
257 <!-- JAL-3468 -->Very long feature descriptions truncated in
261 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
262 with no feature types visible
265 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
267 </ul><em>Jalview Installer</em>
270 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
271 in console (may be null when Jalview launched as executable jar or via conda)
274 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
277 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
280 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
282 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
283 </ul> <em>Release processes</em>
286 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
289 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
291 </ul> <em>Build System</em>
294 <!-- JAL-3510 -->Clover updated to 4.4.1
297 <!-- JAL-3513 -->Test code included in Clover coverage
301 <em>Groovy Scripts</em>
304 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
305 to stdout containing the consensus sequence for each
306 alignment in a Jalview session
309 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
310 genomic sequence_variant annotation from CDS as
311 missense_variant or synonymous_variant on protein products.
315 <td align="left" valign="top">
318 <!-- JAL-3581 -->Hidden sequence markers still visible when
319 'Show hidden markers' option is not ticked
322 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
323 PNG output when 'Automatically set ID width' is set in
324 jalview preferences or properties file
327 <!-- JAL-3571 -->Feature Editor dialog can be opened when
328 'Show Sequence Features' option is not ticked
331 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
332 buttons in Feature Settings dialog are clicked when no
336 <!-- JAL-3412 -->ID margins for CDS and Protein views not
337 equal when split frame is first opened
340 <!-- JAL-3296 -->Sequence position numbers in status bar not
341 correct after editing a sequence's start position
344 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
345 with annotation and exceptions thrown when only a few
346 columns shown in wrapped mode
349 <!-- JAL-3386 -->Sequence IDs missing in headless export of
350 wrapped alignment figure with annotations
353 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
354 ID fails with ClassCastException
357 <!-- JAL-3389 -->Chimera session not restored from Jalview
361 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
362 feature settings dialog also selects columns
365 <!-- JAL-3473 -->SpinnerNumberModel causes
366 IllegalArgumentException in some circumstances
369 <!-- JAL-3534 -->Multiple feature settings dialogs can be
373 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
374 alignment window is closed
377 <!-- JAL-3406 -->Credits missing some authors in Jalview
378 help documentation for 2.11.0 release
381 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
382 includes Pfam ID as sequence's accession rather than its
385 </ul> <em>Java 11 Compatibility issues</em>
388 <!-- JAL-2987 -->OSX - Can't view some search results in
389 PDB/Uniprot search panel
391 </ul> <em>Installer</em>
394 <!-- JAL-3447 -->Jalview should not create file associations
395 for 3D structure files (.pdb, .mmcif. .cif)
397 </ul> <em>Repository and Source Release</em>
400 <!-- JAL-3474 -->removed obsolete .cvsignore files from
404 <!-- JAL-3541 -->Clover report generation running out of
407 </ul> <em>New Known Issues</em>
410 <!-- JAL-3523 -->OSX - Current working directory not
411 preserved when Jalview.app launched with parameters from
415 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
416 clipped in headless figure export when Right Align option
420 <!-- JAL-3542 -->Jalview Installation type always reports
421 'Source' in console output
424 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
425 bamboo server but run fine locally.
431 <td width="60" align="center" nowrap>
432 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
433 <em>04/07/2019</em></strong>
435 <td align="left" valign="top">
438 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
439 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
440 source project) rather than InstallAnywhere
443 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
444 settings, receive over the air updates and launch specific
445 versions via (<a href="https://github.com/threerings/getdown">Three
449 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
450 formats supported by Jalview (including .jvp project files)
453 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
454 arguments and switch between different getdown channels
457 <!-- JAL-3141 -->Backup files created when saving Jalview project
462 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
463 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
465 <!-- JAL-2620 -->Alternative genetic code tables for
466 'Translate as cDNA'</li>
468 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
469 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
472 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
473 implementation that allows updates) used for Sequence Feature collections</li>
475 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
476 features can be filtered and shaded according to any
477 associated attributes (e.g. variant attributes from VCF
478 file, or key-value pairs imported from column 9 of GFF
482 <!-- JAL-2879 -->Feature Attributes and shading schemes
483 stored and restored from Jalview Projects
486 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
487 recognise variant features
490 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
491 sequences (also coloured red by default)
494 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
498 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
499 algorithm (Z-sort/transparency and filter aware)
502 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
508 <!-- JAL-3205 -->Symmetric score matrices for faster
509 tree and PCA calculations
511 <li><strong>Principal Components Analysis Viewer</strong>
514 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
515 and Viewer state saved in Jalview Project
517 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
520 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
524 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
529 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
531 <li><strong>Speed and Efficiency</strong>
534 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
535 multiple groups when working with large alignments
538 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
542 <li><strong>User Interface</strong>
545 <!-- JAL-2933 -->Finder panel remembers last position in each
549 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
550 what is shown)<br />Only visible regions of alignment are shown by
551 default (can be changed in user preferences)
554 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
555 to the Overwrite Dialog
558 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
562 <!-- JAL-1244 -->Status bar shows bounds when dragging a
563 selection region, and gap count when inserting or deleting gaps
566 <!-- JAL-3132 -->Status bar updates over sequence and annotation
570 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
574 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
578 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
581 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
585 <!-- JAL-3181 -->Consistent ordering of links in sequence id
589 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
591 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
595 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
596 <li><strong>Java 11 Support (not yet on general release)</strong>
599 <!-- -->OSX GUI integrations for App menu's 'About' entry and
604 <em>Deprecations</em>
606 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
607 capabilities removed from the Jalview Desktop
609 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
610 unmarshalling has been replaced by JAXB for Jalview projects
611 and XML based data retrieval clients</li>
612 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
613 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
614 </ul> <em>Documentation</em>
616 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
617 not supported in EPS figure export
619 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
620 </ul> <em>Development and Release Processes</em>
623 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
626 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
628 <!-- JAL-3225 -->Eclipse project configuration managed with
632 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
633 Bamboo continuous integration for unattended Test Suite
637 <!-- JAL-2864 -->Memory test suite to detect leaks in common
641 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
645 <!-- JAL-3248 -->Developer documentation migrated to
646 markdown (with HTML rendering)
649 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
652 <!-- JAL-3289 -->New URLs for publishing development
657 <td align="left" valign="top">
660 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
663 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
664 superposition in Jmol fail on Windows
667 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
668 structures for sequences with lots of PDB structures
671 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
675 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
676 project involving multiple views
679 <!-- JAL-3164 -->Overview for complementary view in a linked
680 CDS/Protein alignment is not updated when Hide Columns by
681 Annotation dialog hides columns
684 <!-- JAL-3158 -->Selection highlighting in the complement of a
685 CDS/Protein alignment stops working after making a selection in
686 one view, then making another selection in the other view
689 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
693 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
694 Settings and Jalview Preferences panels
697 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
698 overview with large alignments
701 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
702 region if columns were selected by dragging right-to-left and the
703 mouse moved to the left of the first column
706 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
707 hidden column marker via scale popup menu
710 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
711 doesn't tell users the invalid URL
714 <!-- JAL-2816 -->Tooltips displayed for features filtered by
718 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
719 show cross references or Fetch Database References are shown in
723 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
724 peptide sequence (computed variant shown as p.Res.null)
727 <!-- JAL-2060 -->'Graduated colour' option not offered for
728 manually created features (where feature score is Float.NaN)
731 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
732 when columns are hidden
735 <!-- JAL-3082 -->Regular expression error for '(' in Select
736 Columns by Annotation description
739 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
740 out of Scale or Annotation Panel
743 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
747 <!-- JAL-3074 -->Left/right drag in annotation can scroll
751 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
755 <!-- JAL-3002 -->Column display is out by one after Page Down,
756 Page Up in wrapped mode
759 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
762 <!-- JAL-2932 -->Finder searches in minimised alignments
765 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
766 on opening an alignment
769 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
773 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
774 different groups in the alignment are selected
777 <!-- JAL-2717 -->Internationalised colour scheme names not shown
781 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
785 <!-- JAL-3125 -->Value input for graduated feature colour
786 threshold gets 'unrounded'
789 <!-- JAL-2982 -->PCA image export doesn't respect background
793 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
796 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
799 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
803 <!-- JAL-2964 -->Associate Tree with All Views not restored from
807 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
808 shown in complementary view
811 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
812 without normalisation
815 <!-- JAL-3021 -->Sequence Details report should open positioned at top
819 <!-- JAL-914 -->Help page can be opened twice
822 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
824 </ul> <em>Editing</em>
827 <!-- JAL-2822 -->Start and End should be updated when sequence
828 data at beginning or end of alignment added/removed via 'Edit'
832 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
833 relocate sequence features correctly when start of sequence is
834 removed (Known defect since 2.10)
837 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
838 dialog corrupts dataset sequence
841 <!-- JAL-868 -->Structure colours not updated when associated tree
842 repartitions the alignment view (Regression in 2.10.5)
844 </ul> <em>Datamodel</em>
847 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
848 sequence's End is greater than its length
850 </ul> <em>Bugs fixed for Java 11 Support (not yet on
851 general release)</em>
854 <!-- JAL-3288 -->Menus work properly in split-screen
856 </ul> <em>New Known Defects</em>
859 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
862 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
863 regions of protein alignment.
866 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
867 is restored from a Jalview 2.11 project
870 <!-- JAL-3213 -->Alignment panel height can be too small after
874 <!-- JAL-3240 -->Display is incorrect after removing gapped
875 columns within hidden columns
878 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
879 window after dragging left to select columns to left of visible
883 <!-- JAL-2876 -->Features coloured according to their description
884 string and thresholded by score in earlier versions of Jalview are
885 not shown as thresholded features in 2.11. To workaround please
886 create a Score filter instead.
889 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
891 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
894 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
895 alignments with multiple views can close views unexpectedly
898 <em>Java 11 Specific defects</em>
901 <!-- JAL-3235 -->Jalview Properties file is not sorted
902 alphabetically when saved
908 <td width="60" nowrap>
910 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
913 <td><div align="left">
917 <!-- JAL-3101 -->Default memory for Jalview webstart and
918 InstallAnywhere increased to 1G.
921 <!-- JAL-247 -->Hidden sequence markers and representative
922 sequence bolding included when exporting alignment as EPS,
923 SVG, PNG or HTML. <em>Display is configured via the
924 Format menu, or for command-line use via a Jalview
925 properties file.</em>
928 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
929 API and sequence data now imported as JSON.
932 <!-- JAL-3065 -->Change in recommended way of starting
933 Jalview via a Java command line: add jars in lib directory
934 to CLASSPATH, rather than via the deprecated java.ext.dirs
941 <!-- JAL-3047 -->Support added to execute test suite
942 instrumented with <a href="http://openclover.org/">Open
947 <td><div align="left">
951 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
952 row shown in Feredoxin Structure alignment view of example
956 <!-- JAL-2854 -->Annotation obscures sequences if lots of
957 annotation displayed.
960 <!-- JAL-3107 -->Group conservation/consensus not shown
961 for newly created group when 'Apply to all groups'
965 <!-- JAL-3087 -->Corrupted display when switching to
966 wrapped mode when sequence panel's vertical scrollbar is
970 <!-- JAL-3003 -->Alignment is black in exported EPS file
971 when sequences are selected in exported view.</em>
974 <!-- JAL-3059 -->Groups with different coloured borders
975 aren't rendered with correct colour.
978 <!-- JAL-3092 -->Jalview could hang when importing certain
979 types of knotted RNA secondary structure.
982 <!-- JAL-3095 -->Sequence highlight and selection in
983 trimmed VARNA 2D structure is incorrect for sequences that
987 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
988 annotation when columns are inserted into an alignment,
989 and when exporting as Stockholm flatfile.
992 <!-- JAL-3053 -->Jalview annotation rows containing upper
993 and lower-case 'E' and 'H' do not automatically get
994 treated as RNA secondary structure.
997 <!-- JAL-3106 -->.jvp should be used as default extension
998 (not .jar) when saving a Jalview project file.
1001 <!-- JAL-3105 -->Mac Users: closing a window correctly
1002 transfers focus to previous window on OSX
1005 <em>Java 10 Issues Resolved</em>
1008 <!-- JAL-2988 -->OSX - Can't save new files via the File
1009 or export menus by typing in a name into the Save dialog
1013 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1014 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1015 'look and feel' which has improved compatibility with the
1016 latest version of OSX.
1023 <td width="60" nowrap>
1024 <div align="center">
1025 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1026 <em>7/06/2018</em></strong>
1029 <td><div align="left">
1033 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1034 annotation retrieved from Uniprot
1037 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1038 onto the Jalview Desktop
1042 <td><div align="left">
1046 <!-- JAL-3017 -->Cannot import features with multiple
1047 variant elements (blocks import of some Uniprot records)
1050 <!-- JAL-2997 -->Clustal files with sequence positions in
1051 right-hand column parsed correctly
1054 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1055 not alignment area in exported graphic
1058 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1059 window has input focus
1062 <!-- JAL-2992 -->Annotation panel set too high when
1063 annotation added to view (Windows)
1066 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1067 network connectivity is poor
1070 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1071 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1072 the currently open URL and links from a page viewed in
1073 Firefox or Chrome on Windows is now fully supported. If
1074 you are using Edge, only links in the page can be
1075 dragged, and with Internet Explorer, only the currently
1076 open URL in the browser can be dropped onto Jalview.</em>
1079 <em>New Known Defects</em>
1081 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1086 <td width="60" nowrap>
1087 <div align="center">
1088 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1091 <td><div align="left">
1095 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1096 for disabling automatic superposition of multiple
1097 structures and open structures in existing views
1100 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1101 ID and annotation area margins can be click-dragged to
1105 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1109 <!-- JAL-2759 -->Improved performance for large alignments
1110 and lots of hidden columns
1113 <!-- JAL-2593 -->Improved performance when rendering lots
1114 of features (particularly when transparency is disabled)
1117 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1118 exchange of Jalview features and Chimera attributes made
1124 <td><div align="left">
1127 <!-- JAL-2899 -->Structure and Overview aren't updated
1128 when Colour By Annotation threshold slider is adjusted
1131 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1132 overlapping alignment panel
1135 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1139 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1140 improved: CDS not handled correctly if transcript has no
1144 <!-- JAL-2321 -->Secondary structure and temperature
1145 factor annotation not added to sequence when local PDB
1146 file associated with it by drag'n'drop or structure
1150 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1151 dialog doesn't import PDB files dropped on an alignment
1154 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1155 scroll bar doesn't work for some CDS/Protein views
1158 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1159 Java 1.8u153 onwards and Java 1.9u4+.
1162 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1163 columns in annotation row
1166 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1167 honored in batch mode
1170 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1171 for structures added to existing Jmol view
1174 <!-- JAL-2223 -->'View Mappings' includes duplicate
1175 entries after importing project with multiple views
1178 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1179 protein sequences via SIFTS from associated PDB entries
1180 with negative residue numbers or missing residues fails
1183 <!-- JAL-2952 -->Exception when shading sequence with negative
1184 Temperature Factor values from annotated PDB files (e.g.
1185 as generated by CONSURF)
1188 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1189 tooltip doesn't include a text description of mutation
1192 <!-- JAL-2922 -->Invert displayed features very slow when
1193 structure and/or overview windows are also shown
1196 <!-- JAL-2954 -->Selecting columns from highlighted regions
1197 very slow for alignments with large numbers of sequences
1200 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1201 with 'StringIndexOutOfBounds'
1204 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1205 platforms running Java 10
1208 <!-- JAL-2960 -->Adding a structure to existing structure
1209 view appears to do nothing because the view is hidden behind the alignment view
1215 <!-- JAL-2926 -->Copy consensus sequence option in applet
1216 should copy the group consensus when popup is opened on it
1222 <!-- JAL-2913 -->Fixed ID width preference is not respected
1225 <em>New Known Defects</em>
1228 <!-- JAL-2973 --> Exceptions occasionally raised when
1229 editing a large alignment and overview is displayed
1232 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1233 repeatedly after a series of edits even when the overview
1234 is no longer reflecting updates
1237 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1238 structures for protein subsequence (if 'Trim Retrieved
1239 Sequences' enabled) or Ensembl isoforms (Workaround in
1240 2.10.4 is to fail back to N&W mapping)
1243 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1244 option gives blank output
1251 <td width="60" nowrap>
1252 <div align="center">
1253 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1256 <td><div align="left">
1257 <ul><li>Updated Certum Codesigning Certificate
1258 (Valid till 30th November 2018)</li></ul></div></td>
1259 <td><div align="left">
1260 <em>Desktop</em><ul>
1262 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1263 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1264 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1265 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1266 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1267 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1268 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1274 <td width="60" nowrap>
1275 <div align="center">
1276 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1279 <td><div align="left">
1283 <!-- JAL-2446 -->Faster and more efficient management and
1284 rendering of sequence features
1287 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1288 429 rate limit request hander
1291 <!-- JAL-2773 -->Structure views don't get updated unless
1292 their colours have changed
1295 <!-- JAL-2495 -->All linked sequences are highlighted for
1296 a structure mousover (Jmol) or selection (Chimera)
1299 <!-- JAL-2790 -->'Cancel' button in progress bar for
1300 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1303 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1304 view from Ensembl locus cross-references
1307 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1311 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1312 feature can be disabled
1315 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1316 PDB easier retrieval of sequences for lists of IDs
1319 <!-- JAL-2758 -->Short names for sequences retrieved from
1325 <li>Groovy interpreter updated to 2.4.12</li>
1326 <li>Example groovy script for generating a matrix of
1327 percent identity scores for current alignment.</li>
1329 <em>Testing and Deployment</em>
1332 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1336 <td><div align="left">
1340 <!-- JAL-2643 -->Pressing tab after updating the colour
1341 threshold text field doesn't trigger an update to the
1345 <!-- JAL-2682 -->Race condition when parsing sequence ID
1349 <!-- JAL-2608 -->Overview windows are also closed when
1350 alignment window is closed
1353 <!-- JAL-2548 -->Export of features doesn't always respect
1357 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1358 takes a long time in Cursor mode
1364 <!-- JAL-2777 -->Structures with whitespace chainCode
1365 cannot be viewed in Chimera
1368 <!-- JAL-2728 -->Protein annotation panel too high in
1372 <!-- JAL-2757 -->Can't edit the query after the server
1373 error warning icon is shown in Uniprot and PDB Free Text
1377 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1380 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1383 <!-- JAL-2739 -->Hidden column marker in last column not
1384 rendered when switching back from Wrapped to normal view
1387 <!-- JAL-2768 -->Annotation display corrupted when
1388 scrolling right in unwapped alignment view
1391 <!-- JAL-2542 -->Existing features on subsequence
1392 incorrectly relocated when full sequence retrieved from
1396 <!-- JAL-2733 -->Last reported memory still shown when
1397 Desktop->Show Memory is unticked (OSX only)
1400 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1401 features of same type and group to be selected for
1405 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1406 alignments when hidden columns are present
1409 <!-- JAL-2392 -->Jalview freezes when loading and
1410 displaying several structures
1413 <!-- JAL-2732 -->Black outlines left after resizing or
1417 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1418 within the Jalview desktop on OSX
1421 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1422 when in wrapped alignment mode
1425 <!-- JAL-2636 -->Scale mark not shown when close to right
1426 hand end of alignment
1429 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1430 each selected sequence do not have correct start/end
1434 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1435 after canceling the Alignment Window's Font dialog
1438 <!-- JAL-2036 -->Show cross-references not enabled after
1439 restoring project until a new view is created
1442 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1443 URL links appears when only default EMBL-EBI link is
1444 configured (since 2.10.2b2)
1447 <!-- JAL-2775 -->Overview redraws whole window when box
1448 position is adjusted
1451 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1452 in a multi-chain structure when viewing alignment
1453 involving more than one chain (since 2.10)
1456 <!-- JAL-2811 -->Double residue highlights in cursor mode
1457 if new selection moves alignment window
1460 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1461 arrow key in cursor mode to pass hidden column marker
1464 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1465 that produces correctly annotated transcripts and products
1468 <!-- JAL-2776 -->Toggling a feature group after first time
1469 doesn't update associated structure view
1472 <em>Applet</em><br />
1475 <!-- JAL-2687 -->Concurrent modification exception when
1476 closing alignment panel
1479 <em>BioJSON</em><br />
1482 <!-- JAL-2546 -->BioJSON export does not preserve
1483 non-positional features
1486 <em>New Known Issues</em>
1489 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1490 sequence features correctly (for many previous versions of
1494 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1495 using cursor in wrapped panel other than top
1498 <!-- JAL-2791 -->Select columns containing feature ignores
1499 graduated colour threshold
1502 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1503 always preserve numbering and sequence features
1506 <em>Known Java 9 Issues</em>
1509 <!-- JAL-2902 -->Groovy Console very slow to open and is
1510 not responsive when entering characters (Webstart, Java
1517 <td width="60" nowrap>
1518 <div align="center">
1519 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1520 <em>2/10/2017</em></strong>
1523 <td><div align="left">
1524 <em>New features in Jalview Desktop</em>
1527 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1529 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1533 <td><div align="left">
1537 <td width="60" nowrap>
1538 <div align="center">
1539 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1540 <em>7/9/2017</em></strong>
1543 <td><div align="left">
1547 <!-- JAL-2588 -->Show gaps in overview window by colouring
1548 in grey (sequences used to be coloured grey, and gaps were
1552 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1556 <!-- JAL-2587 -->Overview updates immediately on increase
1557 in size and progress bar shown as higher resolution
1558 overview is recalculated
1563 <td><div align="left">
1567 <!-- JAL-2664 -->Overview window redraws every hidden
1568 column region row by row
1571 <!-- JAL-2681 -->duplicate protein sequences shown after
1572 retrieving Ensembl crossrefs for sequences from Uniprot
1575 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1576 format setting is unticked
1579 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1580 if group has show boxes format setting unticked
1583 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1584 autoscrolling whilst dragging current selection group to
1585 include sequences and columns not currently displayed
1588 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1589 assemblies are imported via CIF file
1592 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1593 displayed when threshold or conservation colouring is also
1597 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1601 <!-- JAL-2673 -->Jalview continues to scroll after
1602 dragging a selected region off the visible region of the
1606 <!-- JAL-2724 -->Cannot apply annotation based
1607 colourscheme to all groups in a view
1610 <!-- JAL-2511 -->IDs don't line up with sequences
1611 initially after font size change using the Font chooser or
1618 <td width="60" nowrap>
1619 <div align="center">
1620 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1623 <td><div align="left">
1624 <em>Calculations</em>
1628 <!-- JAL-1933 -->Occupancy annotation row shows number of
1629 ungapped positions in each column of the alignment.
1632 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1633 a calculation dialog box
1636 <!-- JAL-2379 -->Revised implementation of PCA for speed
1637 and memory efficiency (~30x faster)
1640 <!-- JAL-2403 -->Revised implementation of sequence
1641 similarity scores as used by Tree, PCA, Shading Consensus
1642 and other calculations
1645 <!-- JAL-2416 -->Score matrices are stored as resource
1646 files within the Jalview codebase
1649 <!-- JAL-2500 -->Trees computed on Sequence Feature
1650 Similarity may have different topology due to increased
1657 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1658 model for alignments and groups
1661 <!-- JAL-384 -->Custom shading schemes created via groovy
1668 <!-- JAL-2526 -->Efficiency improvements for interacting
1669 with alignment and overview windows
1672 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1676 <!-- JAL-2388 -->Hidden columns and sequences can be
1680 <!-- JAL-2611 -->Click-drag in visible area allows fine
1681 adjustment of visible position
1685 <em>Data import/export</em>
1688 <!-- JAL-2535 -->Posterior probability annotation from
1689 Stockholm files imported as sequence associated annotation
1692 <!-- JAL-2507 -->More robust per-sequence positional
1693 annotation input/output via stockholm flatfile
1696 <!-- JAL-2533 -->Sequence names don't include file
1697 extension when importing structure files without embedded
1698 names or PDB accessions
1701 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1702 format sequence substitution matrices
1705 <em>User Interface</em>
1708 <!-- JAL-2447 --> Experimental Features Checkbox in
1709 Desktop's Tools menu to hide or show untested features in
1713 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1714 via Overview or sequence motif search operations
1717 <!-- JAL-2547 -->Amend sequence features dialog box can be
1718 opened by double clicking gaps within sequence feature
1722 <!-- JAL-1476 -->Status bar message shown when not enough
1723 aligned positions were available to create a 3D structure
1727 <em>3D Structure</em>
1730 <!-- JAL-2430 -->Hidden regions in alignment views are not
1731 coloured in linked structure views
1734 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1735 file-based command exchange
1738 <!-- JAL-2375 -->Structure chooser automatically shows
1739 Cached Structures rather than querying the PDBe if
1740 structures are already available for sequences
1743 <!-- JAL-2520 -->Structures imported via URL are cached in
1744 the Jalview project rather than downloaded again when the
1745 project is reopened.
1748 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1749 to transfer Chimera's structure attributes as Jalview
1750 features, and vice-versa (<strong>Experimental
1754 <em>Web Services</em>
1757 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1760 <!-- JAL-2335 -->Filter non-standard amino acids and
1761 nucleotides when submitting to AACon and other MSA
1765 <!-- JAL-2316, -->URLs for viewing database
1766 cross-references provided by identifiers.org and the
1767 EMBL-EBI's MIRIAM DB
1774 <!-- JAL-2344 -->FileFormatI interface for describing and
1775 identifying file formats (instead of String constants)
1778 <!-- JAL-2228 -->FeatureCounter script refactored for
1779 efficiency when counting all displayed features (not
1780 backwards compatible with 2.10.1)
1783 <em>Example files</em>
1786 <!-- JAL-2631 -->Graduated feature colour style example
1787 included in the example feature file
1790 <em>Documentation</em>
1793 <!-- JAL-2339 -->Release notes reformatted for readability
1794 with the built-in Java help viewer
1797 <!-- JAL-1644 -->Find documentation updated with 'search
1798 sequence description' option
1804 <!-- JAL-2485, -->External service integration tests for
1805 Uniprot REST Free Text Search Client
1808 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1811 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1816 <td><div align="left">
1817 <em>Calculations</em>
1820 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1821 matrix - C->R should be '-3'<br />Old matrix restored
1822 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1824 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1825 Jalview's treatment of gaps in PCA and substitution matrix
1826 based Tree calculations.<br /> <br />In earlier versions
1827 of Jalview, gaps matching gaps were penalised, and gaps
1828 matching non-gaps penalised even more. In the PCA
1829 calculation, gaps were actually treated as non-gaps - so
1830 different costs were applied, which meant Jalview's PCAs
1831 were different to those produced by SeqSpace.<br />Jalview
1832 now treats gaps in the same way as SeqSpace (ie it scores
1833 them as 0). <br /> <br />Enter the following in the
1834 Groovy console to restore pre-2.10.2 behaviour:<br />
1835 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1836 // for 2.10.1 mode <br />
1837 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1838 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1839 these settings will affect all subsequent tree and PCA
1840 calculations (not recommended)</em></li>
1842 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1843 scaling of branch lengths for trees computed using
1844 Sequence Feature Similarity.
1847 <!-- JAL-2377 -->PCA calculation could hang when
1848 generating output report when working with highly
1849 redundant alignments
1852 <!-- JAL-2544 --> Sort by features includes features to
1853 right of selected region when gaps present on right-hand
1857 <em>User Interface</em>
1860 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1861 doesn't reselect a specific sequence's associated
1862 annotation after it was used for colouring a view
1865 <!-- JAL-2419 -->Current selection lost if popup menu
1866 opened on a region of alignment without groups
1869 <!-- JAL-2374 -->Popup menu not always shown for regions
1870 of an alignment with overlapping groups
1873 <!-- JAL-2310 -->Finder double counts if both a sequence's
1874 name and description match
1877 <!-- JAL-2370 -->Hiding column selection containing two
1878 hidden regions results in incorrect hidden regions
1881 <!-- JAL-2386 -->'Apply to all groups' setting when
1882 changing colour does not apply Conservation slider value
1886 <!-- JAL-2373 -->Percentage identity and conservation menu
1887 items do not show a tick or allow shading to be disabled
1890 <!-- JAL-2385 -->Conservation shading or PID threshold
1891 lost when base colourscheme changed if slider not visible
1894 <!-- JAL-2547 -->Sequence features shown in tooltip for
1895 gaps before start of features
1898 <!-- JAL-2623 -->Graduated feature colour threshold not
1899 restored to UI when feature colour is edited
1902 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1903 a time when scrolling vertically in wrapped mode.
1906 <!-- JAL-2630 -->Structure and alignment overview update
1907 as graduate feature colour settings are modified via the
1911 <!-- JAL-2034 -->Overview window doesn't always update
1912 when a group defined on the alignment is resized
1915 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1916 wrapped view result in positional status updates
1920 <!-- JAL-2563 -->Status bar doesn't show position for
1921 ambiguous amino acid and nucleotide symbols
1924 <!-- JAL-2602 -->Copy consensus sequence failed if
1925 alignment included gapped columns
1928 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1929 widgets don't permanently disappear
1932 <!-- JAL-2503 -->Cannot select or filter quantitative
1933 annotation that are shown only as column labels (e.g.
1934 T-Coffee column reliability scores)
1937 <!-- JAL-2594 -->Exception thrown if trying to create a
1938 sequence feature on gaps only
1941 <!-- JAL-2504 -->Features created with 'New feature'
1942 button from a Find inherit previously defined feature type
1943 rather than the Find query string
1946 <!-- JAL-2423 -->incorrect title in output window when
1947 exporting tree calculated in Jalview
1950 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1951 and then revealing them reorders sequences on the
1955 <!-- JAL-964 -->Group panel in sequence feature settings
1956 doesn't update to reflect available set of groups after
1957 interactively adding or modifying features
1960 <!-- JAL-2225 -->Sequence Database chooser unusable on
1964 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1965 only excluded gaps in current sequence and ignored
1972 <!-- JAL-2421 -->Overview window visible region moves
1973 erratically when hidden rows or columns are present
1976 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1977 Structure Viewer's colour menu don't correspond to
1981 <!-- JAL-2405 -->Protein specific colours only offered in
1982 colour and group colour menu for protein alignments
1985 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1986 reflect currently selected view or group's shading
1990 <!-- JAL-2624 -->Feature colour thresholds not respected
1991 when rendered on overview and structures when opacity at
1995 <!-- JAL-2589 -->User defined gap colour not shown in
1996 overview when features overlaid on alignment
1999 <!-- JAL-2567 -->Feature settings for different views not
2000 recovered correctly from Jalview project file
2003 <!-- JAL-2256 -->Feature colours in overview when first opened
2004 (automatically via preferences) are different to the main
2008 <em>Data import/export</em>
2011 <!-- JAL-2576 -->Very large alignments take a long time to
2015 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2016 added after a sequence was imported are not written to
2020 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2021 when importing RNA secondary structure via Stockholm
2024 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2025 not shown in correct direction for simple pseudoknots
2028 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2029 with lightGray or darkGray via features file (but can
2033 <!-- JAL-2383 -->Above PID colour threshold not recovered
2034 when alignment view imported from project
2037 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2038 structure and sequences extracted from structure files
2039 imported via URL and viewed in Jmol
2042 <!-- JAL-2520 -->Structures loaded via URL are saved in
2043 Jalview Projects rather than fetched via URL again when
2044 the project is loaded and the structure viewed
2047 <em>Web Services</em>
2050 <!-- JAL-2519 -->EnsemblGenomes example failing after
2051 release of Ensembl v.88
2054 <!-- JAL-2366 -->Proxy server address and port always
2055 appear enabled in Preferences->Connections
2058 <!-- JAL-2461 -->DAS registry not found exceptions
2059 removed from console output
2062 <!-- JAL-2582 -->Cannot retrieve protein products from
2063 Ensembl by Peptide ID
2066 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2067 created from SIFTs, and spurious 'Couldn't open structure
2068 in Chimera' errors raised after April 2017 update (problem
2069 due to 'null' string rather than empty string used for
2070 residues with no corresponding PDB mapping).
2073 <em>Application UI</em>
2076 <!-- JAL-2361 -->User Defined Colours not added to Colour
2080 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2081 case' residues (button in colourscheme editor debugged and
2082 new documentation and tooltips added)
2085 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2086 doesn't restore group-specific text colour thresholds
2089 <!-- JAL-2243 -->Feature settings panel does not update as
2090 new features are added to alignment
2093 <!-- JAL-2532 -->Cancel in feature settings reverts
2094 changes to feature colours via the Amend features dialog
2097 <!-- JAL-2506 -->Null pointer exception when attempting to
2098 edit graduated feature colour via amend features dialog
2102 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2103 selection menu changes colours of alignment views
2106 <!-- JAL-2426 -->Spurious exceptions in console raised
2107 from alignment calculation workers after alignment has
2111 <!-- JAL-1608 -->Typo in selection popup menu - Create
2112 groups now 'Create Group'
2115 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2116 Create/Undefine group doesn't always work
2119 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2120 shown again after pressing 'Cancel'
2123 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2124 adjusts start position in wrap mode
2127 <!-- JAL-2563 -->Status bar doesn't show positions for
2128 ambiguous amino acids
2131 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2132 CDS/Protein view after CDS sequences added for aligned
2136 <!-- JAL-2592 -->User defined colourschemes called 'User
2137 Defined' don't appear in Colours menu
2143 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2144 score models doesn't always result in an updated PCA plot
2147 <!-- JAL-2442 -->Features not rendered as transparent on
2148 overview or linked structure view
2151 <!-- JAL-2372 -->Colour group by conservation doesn't
2155 <!-- JAL-2517 -->Hitting Cancel after applying
2156 user-defined colourscheme doesn't restore original
2163 <!-- JAL-2314 -->Unit test failure:
2164 jalview.ws.jabaws.RNAStructExportImport setup fails
2167 <!-- JAL-2307 -->Unit test failure:
2168 jalview.ws.sifts.SiftsClientTest due to compatibility
2169 problems with deep array comparison equality asserts in
2170 successive versions of TestNG
2173 <!-- JAL-2479 -->Relocated StructureChooserTest and
2174 ParameterUtilsTest Unit tests to Network suite
2177 <em>New Known Issues</em>
2180 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2181 phase after a sequence motif find operation
2184 <!-- JAL-2550 -->Importing annotation file with rows
2185 containing just upper and lower case letters are
2186 interpreted as WUSS RNA secondary structure symbols
2189 <!-- JAL-2590 -->Cannot load and display Newick trees
2190 reliably from eggnog Ortholog database
2193 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2194 containing features of type Highlight' when 'B' is pressed
2195 to mark columns containing highlighted regions.
2198 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2199 doesn't always add secondary structure annotation.
2204 <td width="60" nowrap>
2205 <div align="center">
2206 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2209 <td><div align="left">
2213 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2214 for all consensus calculations
2217 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2220 <li>Updated Jalview's Certum code signing certificate
2223 <em>Application</em>
2226 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2227 set of database cross-references, sorted alphabetically
2230 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2231 from database cross references. Users with custom links
2232 will receive a <a href="webServices/urllinks.html#warning">warning
2233 dialog</a> asking them to update their preferences.
2236 <!-- JAL-2287-->Cancel button and escape listener on
2237 dialog warning user about disconnecting Jalview from a
2241 <!-- JAL-2320-->Jalview's Chimera control window closes if
2242 the Chimera it is connected to is shut down
2245 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2246 columns menu item to mark columns containing highlighted
2247 regions (e.g. from structure selections or results of a
2251 <!-- JAL-2284-->Command line option for batch-generation
2252 of HTML pages rendering alignment data with the BioJS
2262 <!-- JAL-2286 -->Columns with more than one modal residue
2263 are not coloured or thresholded according to percent
2264 identity (first observed in Jalview 2.8.2)
2267 <!-- JAL-2301 -->Threonine incorrectly reported as not
2271 <!-- JAL-2318 -->Updates to documentation pages (above PID
2272 threshold, amino acid properties)
2275 <!-- JAL-2292 -->Lower case residues in sequences are not
2276 reported as mapped to residues in a structure file in the
2280 <!--JAL-2324 -->Identical features with non-numeric scores
2281 could be added multiple times to a sequence
2284 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2285 bond features shown as two highlighted residues rather
2286 than a range in linked structure views, and treated
2287 correctly when selecting and computing trees from features
2290 <!-- JAL-2281-->Custom URL links for database
2291 cross-references are matched to database name regardless
2296 <em>Application</em>
2299 <!-- JAL-2282-->Custom URL links for specific database
2300 names without regular expressions also offer links from
2304 <!-- JAL-2315-->Removing a single configured link in the
2305 URL links pane in Connections preferences doesn't actually
2306 update Jalview configuration
2309 <!-- JAL-2272-->CTRL-Click on a selected region to open
2310 the alignment area popup menu doesn't work on El-Capitan
2313 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2314 files with similarly named sequences if dropped onto the
2318 <!-- JAL-2312 -->Additional mappings are shown for PDB
2319 entries where more chains exist in the PDB accession than
2320 are reported in the SIFTS file
2323 <!-- JAL-2317-->Certain structures do not get mapped to
2324 the structure view when displayed with Chimera
2327 <!-- JAL-2317-->No chains shown in the Chimera view
2328 panel's View->Show Chains submenu
2331 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2332 work for wrapped alignment views
2335 <!--JAL-2197 -->Rename UI components for running JPred
2336 predictions from 'JNet' to 'JPred'
2339 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2340 corrupted when annotation panel vertical scroll is not at
2341 first annotation row
2344 <!--JAL-2332 -->Attempting to view structure for Hen
2345 lysozyme results in a PDB Client error dialog box
2348 <!-- JAL-2319 -->Structure View's mapping report switched
2349 ranges for PDB and sequence for SIFTS
2352 SIFTS 'Not_Observed' residues mapped to non-existant
2356 <!-- <em>New Known Issues</em>
2363 <td width="60" nowrap>
2364 <div align="center">
2365 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2366 <em>25/10/2016</em></strong>
2369 <td><em>Application</em>
2371 <li>3D Structure chooser opens with 'Cached structures'
2372 view if structures already loaded</li>
2373 <li>Progress bar reports models as they are loaded to
2374 structure views</li>
2380 <li>Colour by conservation always enabled and no tick
2381 shown in menu when BLOSUM or PID shading applied</li>
2382 <li>FER1_ARATH and FER2_ARATH labels were switched in
2383 example sequences/projects/trees</li>
2385 <em>Application</em>
2387 <li>Jalview projects with views of local PDB structure
2388 files saved on Windows cannot be opened on OSX</li>
2389 <li>Multiple structure views can be opened and superposed
2390 without timeout for structures with multiple models or
2391 multiple sequences in alignment</li>
2392 <li>Cannot import or associated local PDB files without a
2393 PDB ID HEADER line</li>
2394 <li>RMSD is not output in Jmol console when superposition
2396 <li>Drag and drop of URL from Browser fails for Linux and
2397 OSX versions earlier than El Capitan</li>
2398 <li>ENA client ignores invalid content from ENA server</li>
2399 <li>Exceptions are not raised in console when ENA client
2400 attempts to fetch non-existent IDs via Fetch DB Refs UI
2402 <li>Exceptions are not raised in console when a new view
2403 is created on the alignment</li>
2404 <li>OSX right-click fixed for group selections: CMD-click
2405 to insert/remove gaps in groups and CTRL-click to open group
2408 <em>Build and deployment</em>
2410 <li>URL link checker now copes with multi-line anchor
2413 <em>New Known Issues</em>
2415 <li>Drag and drop from URL links in browsers do not work
2422 <td width="60" nowrap>
2423 <div align="center">
2424 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2427 <td><em>General</em>
2430 <!-- JAL-2124 -->Updated Spanish translations.
2433 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2434 for importing structure data to Jalview. Enables mmCIF and
2438 <!-- JAL-192 --->Alignment ruler shows positions relative to
2442 <!-- JAL-2202 -->Position/residue shown in status bar when
2443 mousing over sequence associated annotation
2446 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2450 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2451 '()', canonical '[]' and invalid '{}' base pair populations
2455 <!-- JAL-2092 -->Feature settings popup menu options for
2456 showing or hiding columns containing a feature
2459 <!-- JAL-1557 -->Edit selected group by double clicking on
2460 group and sequence associated annotation labels
2463 <!-- JAL-2236 -->Sequence name added to annotation label in
2464 select/hide columns by annotation and colour by annotation
2468 </ul> <em>Application</em>
2471 <!-- JAL-2050-->Automatically hide introns when opening a
2472 gene/transcript view
2475 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2479 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2480 structure mappings with the EMBL-EBI PDBe SIFTS database
2483 <!-- JAL-2079 -->Updated download sites used for Rfam and
2484 Pfam sources to xfam.org
2487 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2490 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2491 over sequences in Jalview
2494 <!-- JAL-2027-->Support for reverse-complement coding
2495 regions in ENA and EMBL
2498 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2499 for record retrieval via ENA rest API
2502 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2506 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2507 groovy script execution
2510 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2511 alignment window's Calculate menu
2514 <!-- JAL-1812 -->Allow groovy scripts that call
2515 Jalview.getAlignFrames() to run in headless mode
2518 <!-- JAL-2068 -->Support for creating new alignment
2519 calculation workers from groovy scripts
2522 <!-- JAL-1369 --->Store/restore reference sequence in
2526 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2527 associations are now saved/restored from project
2530 <!-- JAL-1993 -->Database selection dialog always shown
2531 before sequence fetcher is opened
2534 <!-- JAL-2183 -->Double click on an entry in Jalview's
2535 database chooser opens a sequence fetcher
2538 <!-- JAL-1563 -->Free-text search client for UniProt using
2539 the UniProt REST API
2542 <!-- JAL-2168 -->-nonews command line parameter to prevent
2543 the news reader opening
2546 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2547 querying stored in preferences
2550 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2554 <!-- JAL-1977-->Tooltips shown on database chooser
2557 <!-- JAL-391 -->Reverse complement function in calculate
2558 menu for nucleotide sequences
2561 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2562 and feature counts preserves alignment ordering (and
2563 debugged for complex feature sets).
2566 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2567 viewing structures with Jalview 2.10
2570 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2571 genome, transcript CCDS and gene ids via the Ensembl and
2572 Ensembl Genomes REST API
2575 <!-- JAL-2049 -->Protein sequence variant annotation
2576 computed for 'sequence_variant' annotation on CDS regions
2580 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2584 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2585 Ref Fetcher fails to match, or otherwise updates sequence
2586 data from external database records.
2589 <!-- JAL-2154 -->Revised Jalview Project format for
2590 efficient recovery of sequence coding and alignment
2591 annotation relationships.
2593 </ul> <!-- <em>Applet</em>
2604 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2608 <!-- JAL-2018-->Export features in Jalview format (again)
2609 includes graduated colourschemes
2612 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2613 working with big alignments and lots of hidden columns
2616 <!-- JAL-2053-->Hidden column markers not always rendered
2617 at right of alignment window
2620 <!-- JAL-2067 -->Tidied up links in help file table of
2624 <!-- JAL-2072 -->Feature based tree calculation not shown
2628 <!-- JAL-2075 -->Hidden columns ignored during feature
2629 based tree calculation
2632 <!-- JAL-2065 -->Alignment view stops updating when show
2633 unconserved enabled for group on alignment
2636 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2640 <!-- JAL-2146 -->Alignment column in status incorrectly
2641 shown as "Sequence position" when mousing over
2645 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2646 hidden columns present
2649 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2650 user created annotation added to alignment
2653 <!-- JAL-1841 -->RNA Structure consensus only computed for
2654 '()' base pair annotation
2657 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2658 in zero scores for all base pairs in RNA Structure
2662 <!-- JAL-2174-->Extend selection with columns containing
2666 <!-- JAL-2275 -->Pfam format writer puts extra space at
2667 beginning of sequence
2670 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2674 <!-- JAL-2238 -->Cannot create groups on an alignment from
2675 from a tree when t-coffee scores are shown
2678 <!-- JAL-1836,1967 -->Cannot import and view PDB
2679 structures with chains containing negative resnums (4q4h)
2682 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2686 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2687 to Clustal, PIR and PileUp output
2690 <!-- JAL-2008 -->Reordering sequence features that are
2691 not visible causes alignment window to repaint
2694 <!-- JAL-2006 -->Threshold sliders don't work in
2695 graduated colour and colour by annotation row for e-value
2696 scores associated with features and annotation rows
2699 <!-- JAL-1797 -->amino acid physicochemical conservation
2700 calculation should be case independent
2703 <!-- JAL-2173 -->Remove annotation also updates hidden
2707 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2708 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2709 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2712 <!-- JAL-2065 -->Null pointer exceptions and redraw
2713 problems when reference sequence defined and 'show
2714 non-conserved' enabled
2717 <!-- JAL-1306 -->Quality and Conservation are now shown on
2718 load even when Consensus calculation is disabled
2721 <!-- JAL-1932 -->Remove right on penultimate column of
2722 alignment does nothing
2725 <em>Application</em>
2728 <!-- JAL-1552-->URLs and links can't be imported by
2729 drag'n'drop on OSX when launched via webstart (note - not
2730 yet fixed for El Capitan)
2733 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2734 output when running on non-gb/us i18n platforms
2737 <!-- JAL-1944 -->Error thrown when exporting a view with
2738 hidden sequences as flat-file alignment
2741 <!-- JAL-2030-->InstallAnywhere distribution fails when
2745 <!-- JAL-2080-->Jalview very slow to launch via webstart
2746 (also hotfix for 2.9.0b2)
2749 <!-- JAL-2085 -->Cannot save project when view has a
2750 reference sequence defined
2753 <!-- JAL-1011 -->Columns are suddenly selected in other
2754 alignments and views when revealing hidden columns
2757 <!-- JAL-1989 -->Hide columns not mirrored in complement
2758 view in a cDNA/Protein splitframe
2761 <!-- JAL-1369 -->Cannot save/restore representative
2762 sequence from project when only one sequence is
2766 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2767 in Structure Chooser
2770 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2771 structure consensus didn't refresh annotation panel
2774 <!-- JAL-1962 -->View mapping in structure view shows
2775 mappings between sequence and all chains in a PDB file
2778 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2779 dialogs format columns correctly, don't display array
2780 data, sort columns according to type
2783 <!-- JAL-1975 -->Export complete shown after destination
2784 file chooser is cancelled during an image export
2787 <!-- JAL-2025 -->Error when querying PDB Service with
2788 sequence name containing special characters
2791 <!-- JAL-2024 -->Manual PDB structure querying should be
2795 <!-- JAL-2104 -->Large tooltips with broken HTML
2796 formatting don't wrap
2799 <!-- JAL-1128 -->Figures exported from wrapped view are
2800 truncated so L looks like I in consensus annotation
2803 <!-- JAL-2003 -->Export features should only export the
2804 currently displayed features for the current selection or
2808 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2809 after fetching cross-references, and restoring from
2813 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2814 followed in the structure viewer
2817 <!-- JAL-2163 -->Titles for individual alignments in
2818 splitframe not restored from project
2821 <!-- JAL-2145 -->missing autocalculated annotation at
2822 trailing end of protein alignment in transcript/product
2823 splitview when pad-gaps not enabled by default
2826 <!-- JAL-1797 -->amino acid physicochemical conservation
2830 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2831 article has been read (reopened issue due to
2832 internationalisation problems)
2835 <!-- JAL-1960 -->Only offer PDB structures in structure
2836 viewer based on sequence name, PDB and UniProt
2841 <!-- JAL-1976 -->No progress bar shown during export of
2845 <!-- JAL-2213 -->Structures not always superimposed after
2846 multiple structures are shown for one or more sequences.
2849 <!-- JAL-1370 -->Reference sequence characters should not
2850 be replaced with '.' when 'Show unconserved' format option
2854 <!-- JAL-1823 -->Cannot specify chain code when entering
2855 specific PDB id for sequence
2858 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2859 'Export hidden sequences' is enabled, but 'export hidden
2860 columns' is disabled.
2863 <!--JAL-2026-->Best Quality option in structure chooser
2864 selects lowest rather than highest resolution structures
2868 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2869 to sequence mapping in 'View Mappings' report
2872 <!-- JAL-2284 -->Unable to read old Jalview projects that
2873 contain non-XML data added after Jalvew wrote project.
2876 <!-- JAL-2118 -->Newly created annotation row reorders
2877 after clicking on it to create new annotation for a
2881 <!-- JAL-1980 -->Null Pointer Exception raised when
2882 pressing Add on an orphaned cut'n'paste window.
2884 <!-- may exclude, this is an external service stability issue JAL-1941
2885 -- > RNA 3D structure not added via DSSR service</li> -->
2890 <!-- JAL-2151 -->Incorrect columns are selected when
2891 hidden columns present before start of sequence
2894 <!-- JAL-1986 -->Missing dependencies on applet pages
2898 <!-- JAL-1947 -->Overview pixel size changes when
2899 sequences are hidden in applet
2902 <!-- JAL-1996 -->Updated instructions for applet
2903 deployment on examples pages.
2910 <td width="60" nowrap>
2911 <div align="center">
2912 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2913 <em>16/10/2015</em></strong>
2916 <td><em>General</em>
2918 <li>Time stamps for signed Jalview application and applet
2923 <em>Application</em>
2925 <li>Duplicate group consensus and conservation rows
2926 shown when tree is partitioned</li>
2927 <li>Erratic behaviour when tree partitions made with
2928 multiple cDNA/Protein split views</li>
2934 <td width="60" nowrap>
2935 <div align="center">
2936 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2937 <em>8/10/2015</em></strong>
2940 <td><em>General</em>
2942 <li>Updated Spanish translations of localized text for
2944 </ul> <em>Application</em>
2946 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2947 <li>Signed OSX InstallAnywhere installer<br></li>
2948 <li>Support for per-sequence based annotations in BioJSON</li>
2949 </ul> <em>Applet</em>
2951 <li>Split frame example added to applet examples page</li>
2952 </ul> <em>Build and Deployment</em>
2955 <!-- JAL-1888 -->New ant target for running Jalview's test
2963 <li>Mapping of cDNA to protein in split frames
2964 incorrect when sequence start > 1</li>
2965 <li>Broken images in filter column by annotation dialog
2967 <li>Feature colours not parsed from features file</li>
2968 <li>Exceptions and incomplete link URLs recovered when
2969 loading a features file containing HTML tags in feature
2973 <em>Application</em>
2975 <li>Annotations corrupted after BioJS export and
2977 <li>Incorrect sequence limits after Fetch DB References
2978 with 'trim retrieved sequences'</li>
2979 <li>Incorrect warning about deleting all data when
2980 deleting selected columns</li>
2981 <li>Patch to build system for shipping properly signed
2982 JNLP templates for webstart launch</li>
2983 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2984 unreleased structures for download or viewing</li>
2985 <li>Tab/space/return keystroke operation of EMBL-PDBe
2986 fetcher/viewer dialogs works correctly</li>
2987 <li>Disabled 'minimise' button on Jalview windows
2988 running on OSX to workaround redraw hang bug</li>
2989 <li>Split cDNA/Protein view position and geometry not
2990 recovered from jalview project</li>
2991 <li>Initial enabled/disabled state of annotation menu
2992 sorter 'show autocalculated first/last' corresponds to
2994 <li>Restoring of Clustal, RNA Helices and T-Coffee
2995 color schemes from BioJSON</li>
2999 <li>Reorder sequences mirrored in cDNA/Protein split
3001 <li>Applet with Jmol examples not loading correctly</li>
3007 <td><div align="center">
3008 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3010 <td><em>General</em>
3012 <li>Linked visualisation and analysis of DNA and Protein
3015 <li>Translated cDNA alignments shown as split protein
3016 and DNA alignment views</li>
3017 <li>Codon consensus annotation for linked protein and
3018 cDNA alignment views</li>
3019 <li>Link cDNA or Protein product sequences by loading
3020 them onto Protein or cDNA alignments</li>
3021 <li>Reconstruct linked cDNA alignment from aligned
3022 protein sequences</li>
3025 <li>Jmol integration updated to Jmol v14.2.14</li>
3026 <li>Import and export of Jalview alignment views as <a
3027 href="features/bioJsonFormat.html">BioJSON</a></li>
3028 <li>New alignment annotation file statements for
3029 reference sequences and marking hidden columns</li>
3030 <li>Reference sequence based alignment shading to
3031 highlight variation</li>
3032 <li>Select or hide columns according to alignment
3034 <li>Find option for locating sequences by description</li>
3035 <li>Conserved physicochemical properties shown in amino
3036 acid conservation row</li>
3037 <li>Alignments can be sorted by number of RNA helices</li>
3038 </ul> <em>Application</em>
3040 <li>New cDNA/Protein analysis capabilities
3042 <li>Get Cross-References should open a Split Frame
3043 view with cDNA/Protein</li>
3044 <li>Detect when nucleotide sequences and protein
3045 sequences are placed in the same alignment</li>
3046 <li>Split cDNA/Protein views are saved in Jalview
3051 <li>Use REST API to talk to Chimera</li>
3052 <li>Selected regions in Chimera are highlighted in linked
3053 Jalview windows</li>
3055 <li>VARNA RNA viewer updated to v3.93</li>
3056 <li>VARNA views are saved in Jalview Projects</li>
3057 <li>Pseudoknots displayed as Jalview RNA annotation can
3058 be shown in VARNA</li>
3060 <li>Make groups for selection uses marked columns as well
3061 as the active selected region</li>
3063 <li>Calculate UPGMA and NJ trees using sequence feature
3065 <li>New Export options
3067 <li>New Export Settings dialog to control hidden
3068 region export in flat file generation</li>
3070 <li>Export alignment views for display with the <a
3071 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3073 <li>Export scrollable SVG in HTML page</li>
3074 <li>Optional embedding of BioJSON data when exporting
3075 alignment figures to HTML</li>
3077 <li>3D structure retrieval and display
3079 <li>Free text and structured queries with the PDBe
3081 <li>PDBe Search API based discovery and selection of
3082 PDB structures for a sequence set</li>
3086 <li>JPred4 employed for protein secondary structure
3088 <li>Hide Insertions menu option to hide unaligned columns
3089 for one or a group of sequences</li>
3090 <li>Automatically hide insertions in alignments imported
3091 from the JPred4 web server</li>
3092 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3093 system on OSX<br />LGPL libraries courtesy of <a
3094 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3096 <li>changed 'View nucleotide structure' submenu to 'View
3097 VARNA 2D Structure'</li>
3098 <li>change "View protein structure" menu option to "3D
3101 </ul> <em>Applet</em>
3103 <li>New layout for applet example pages</li>
3104 <li>New parameters to enable SplitFrame view
3105 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3106 <li>New example demonstrating linked viewing of cDNA and
3107 Protein alignments</li>
3108 </ul> <em>Development and deployment</em>
3110 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3111 <li>Include installation type and git revision in build
3112 properties and console log output</li>
3113 <li>Jalview Github organisation, and new github site for
3114 storing BioJsMSA Templates</li>
3115 <li>Jalview's unit tests now managed with TestNG</li>
3118 <!-- <em>General</em>
3120 </ul> --> <!-- issues resolved --> <em>Application</em>
3122 <li>Escape should close any open find dialogs</li>
3123 <li>Typo in select-by-features status report</li>
3124 <li>Consensus RNA secondary secondary structure
3125 predictions are not highlighted in amber</li>
3126 <li>Missing gap character in v2.7 example file means
3127 alignment appears unaligned when pad-gaps is not enabled</li>
3128 <li>First switch to RNA Helices colouring doesn't colour
3129 associated structure views</li>
3130 <li>ID width preference option is greyed out when auto
3131 width checkbox not enabled</li>
3132 <li>Stopped a warning dialog from being shown when
3133 creating user defined colours</li>
3134 <li>'View Mapping' in structure viewer shows sequence
3135 mappings for just that viewer's sequences</li>
3136 <li>Workaround for superposing PDB files containing
3137 multiple models in Chimera</li>
3138 <li>Report sequence position in status bar when hovering
3139 over Jmol structure</li>
3140 <li>Cannot output gaps as '.' symbols with Selection ->
3141 output to text box</li>
3142 <li>Flat file exports of alignments with hidden columns
3143 have incorrect sequence start/end</li>
3144 <li>'Aligning' a second chain to a Chimera structure from
3146 <li>Colour schemes applied to structure viewers don't
3147 work for nucleotide</li>
3148 <li>Loading/cut'n'pasting an empty or invalid file leads
3149 to a grey/invisible alignment window</li>
3150 <li>Exported Jpred annotation from a sequence region
3151 imports to different position</li>
3152 <li>Space at beginning of sequence feature tooltips shown
3153 on some platforms</li>
3154 <li>Chimera viewer 'View | Show Chain' menu is not
3156 <li>'New View' fails with a Null Pointer Exception in
3157 console if Chimera has been opened</li>
3158 <li>Mouseover to Chimera not working</li>
3159 <li>Miscellaneous ENA XML feature qualifiers not
3161 <li>NPE in annotation renderer after 'Extract Scores'</li>
3162 <li>If two structures in one Chimera window, mouseover of
3163 either sequence shows on first structure</li>
3164 <li>'Show annotations' options should not make
3165 non-positional annotations visible</li>
3166 <li>Subsequence secondary structure annotation not shown
3167 in right place after 'view flanking regions'</li>
3168 <li>File Save As type unset when current file format is
3170 <li>Save as '.jar' option removed for saving Jalview
3172 <li>Colour by Sequence colouring in Chimera more
3174 <li>Cannot 'add reference annotation' for a sequence in
3175 several views on same alignment</li>
3176 <li>Cannot show linked products for EMBL / ENA records</li>
3177 <li>Jalview's tooltip wraps long texts containing no
3179 </ul> <em>Applet</em>
3181 <li>Jmol to JalviewLite mouseover/link not working</li>
3182 <li>JalviewLite can't import sequences with ID
3183 descriptions containing angle brackets</li>
3184 </ul> <em>General</em>
3186 <li>Cannot export and reimport RNA secondary structure
3187 via jalview annotation file</li>
3188 <li>Random helix colour palette for colour by annotation
3189 with RNA secondary structure</li>
3190 <li>Mouseover to cDNA from STOP residue in protein
3191 translation doesn't work.</li>
3192 <li>hints when using the select by annotation dialog box</li>
3193 <li>Jmol alignment incorrect if PDB file has alternate CA
3195 <li>FontChooser message dialog appears to hang after
3196 choosing 1pt font</li>
3197 <li>Peptide secondary structure incorrectly imported from
3198 annotation file when annotation display text includes 'e' or
3200 <li>Cannot set colour of new feature type whilst creating
3202 <li>cDNA translation alignment should not be sequence
3203 order dependent</li>
3204 <li>'Show unconserved' doesn't work for lower case
3206 <li>Nucleotide ambiguity codes involving R not recognised</li>
3207 </ul> <em>Deployment and Documentation</em>
3209 <li>Applet example pages appear different to the rest of
3210 www.jalview.org</li>
3211 </ul> <em>Application Known issues</em>
3213 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3214 <li>Misleading message appears after trying to delete
3216 <li>Jalview icon not shown in dock after InstallAnywhere
3217 version launches</li>
3218 <li>Fetching EMBL reference for an RNA sequence results
3219 fails with a sequence mismatch</li>
3220 <li>Corrupted or unreadable alignment display when
3221 scrolling alignment to right</li>
3222 <li>ArrayIndexOutOfBoundsException thrown when remove
3223 empty columns called on alignment with ragged gapped ends</li>
3224 <li>auto calculated alignment annotation rows do not get
3225 placed above or below non-autocalculated rows</li>
3226 <li>Jalview dekstop becomes sluggish at full screen in
3227 ultra-high resolution</li>
3228 <li>Cannot disable consensus calculation independently of
3229 quality and conservation</li>
3230 <li>Mouseover highlighting between cDNA and protein can
3231 become sluggish with more than one splitframe shown</li>
3232 </ul> <em>Applet Known Issues</em>
3234 <li>Core PDB parsing code requires Jmol</li>
3235 <li>Sequence canvas panel goes white when alignment
3236 window is being resized</li>
3242 <td><div align="center">
3243 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3245 <td><em>General</em>
3247 <li>Updated Java code signing certificate donated by
3249 <li>Features and annotation preserved when performing
3250 pairwise alignment</li>
3251 <li>RNA pseudoknot annotation can be
3252 imported/exported/displayed</li>
3253 <li>'colour by annotation' can colour by RNA and
3254 protein secondary structure</li>
3255 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3256 post-hoc with 2.9 release</em>)
3259 </ul> <em>Application</em>
3261 <li>Extract and display secondary structure for sequences
3262 with 3D structures</li>
3263 <li>Support for parsing RNAML</li>
3264 <li>Annotations menu for layout
3266 <li>sort sequence annotation rows by alignment</li>
3267 <li>place sequence annotation above/below alignment
3270 <li>Output in Stockholm format</li>
3271 <li>Internationalisation: improved Spanish (es)
3273 <li>Structure viewer preferences tab</li>
3274 <li>Disorder and Secondary Structure annotation tracks
3275 shared between alignments</li>
3276 <li>UCSF Chimera launch and linked highlighting from
3278 <li>Show/hide all sequence associated annotation rows for
3279 all or current selection</li>
3280 <li>disorder and secondary structure predictions
3281 available as dataset annotation</li>
3282 <li>Per-sequence rna helices colouring</li>
3285 <li>Sequence database accessions imported when fetching
3286 alignments from Rfam</li>
3287 <li>update VARNA version to 3.91</li>
3289 <li>New groovy scripts for exporting aligned positions,
3290 conservation values, and calculating sum of pairs scores.</li>
3291 <li>Command line argument to set default JABAWS server</li>
3292 <li>include installation type in build properties and
3293 console log output</li>
3294 <li>Updated Jalview project format to preserve dataset
3298 <!-- issues resolved --> <em>Application</em>
3300 <li>Distinguish alignment and sequence associated RNA
3301 structure in structure->view->VARNA</li>
3302 <li>Raise dialog box if user deletes all sequences in an
3304 <li>Pressing F1 results in documentation opening twice</li>
3305 <li>Sequence feature tooltip is wrapped</li>
3306 <li>Double click on sequence associated annotation
3307 selects only first column</li>
3308 <li>Redundancy removal doesn't result in unlinked
3309 leaves shown in tree</li>
3310 <li>Undos after several redundancy removals don't undo
3312 <li>Hide sequence doesn't hide associated annotation</li>
3313 <li>User defined colours dialog box too big to fit on
3314 screen and buttons not visible</li>
3315 <li>author list isn't updated if already written to
3316 Jalview properties</li>
3317 <li>Popup menu won't open after retrieving sequence
3319 <li>File open window for associate PDB doesn't open</li>
3320 <li>Left-then-right click on a sequence id opens a
3321 browser search window</li>
3322 <li>Cannot open sequence feature shading/sort popup menu
3323 in feature settings dialog</li>
3324 <li>better tooltip placement for some areas of Jalview
3326 <li>Allow addition of JABAWS Server which doesn't
3327 pass validation</li>
3328 <li>Web services parameters dialog box is too large to
3330 <li>Muscle nucleotide alignment preset obscured by
3332 <li>JABAWS preset submenus don't contain newly
3333 defined user preset</li>
3334 <li>MSA web services warns user if they were launched
3335 with invalid input</li>
3336 <li>Jalview cannot contact DAS Registy when running on
3339 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3340 'Superpose with' submenu not shown when new view
3344 </ul> <!-- <em>Applet</em>
3346 </ul> <em>General</em>
3348 </ul>--> <em>Deployment and Documentation</em>
3350 <li>2G and 1G options in launchApp have no effect on
3351 memory allocation</li>
3352 <li>launchApp service doesn't automatically open
3353 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3355 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3356 InstallAnywhere reports cannot find valid JVM when Java
3357 1.7_055 is available
3359 </ul> <em>Application Known issues</em>
3362 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3363 corrupted or unreadable alignment display when scrolling
3367 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3368 retrieval fails but progress bar continues for DAS retrieval
3369 with large number of ID
3372 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3373 flatfile output of visible region has incorrect sequence
3377 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3378 rna structure consensus doesn't update when secondary
3379 structure tracks are rearranged
3382 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3383 invalid rna structure positional highlighting does not
3384 highlight position of invalid base pairs
3387 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3388 out of memory errors are not raised when saving Jalview
3389 project from alignment window file menu
3392 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3393 Switching to RNA Helices colouring doesn't propagate to
3397 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3398 colour by RNA Helices not enabled when user created
3399 annotation added to alignment
3402 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3403 Jalview icon not shown on dock in Mountain Lion/Webstart
3405 </ul> <em>Applet Known Issues</em>
3408 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3409 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3412 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3413 Jalview and Jmol example not compatible with IE9
3416 <li>Sort by annotation score doesn't reverse order
3422 <td><div align="center">
3423 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3426 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3429 <li>Internationalisation of user interface (usually
3430 called i18n support) and translation for Spanish locale</li>
3431 <li>Define/Undefine group on current selection with
3432 Ctrl-G/Shift Ctrl-G</li>
3433 <li>Improved group creation/removal options in
3434 alignment/sequence Popup menu</li>
3435 <li>Sensible precision for symbol distribution
3436 percentages shown in logo tooltip.</li>
3437 <li>Annotation panel height set according to amount of
3438 annotation when alignment first opened</li>
3439 </ul> <em>Application</em>
3441 <li>Interactive consensus RNA secondary structure
3442 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3443 <li>Select columns containing particular features from
3444 Feature Settings dialog</li>
3445 <li>View all 'representative' PDB structures for selected
3447 <li>Update Jalview project format:
3449 <li>New file extension for Jalview projects '.jvp'</li>
3450 <li>Preserve sequence and annotation dataset (to
3451 store secondary structure annotation,etc)</li>
3452 <li>Per group and alignment annotation and RNA helix
3456 <li>New similarity measures for PCA and Tree calculation
3458 <li>Experimental support for retrieval and viewing of
3459 flanking regions for an alignment</li>
3463 <!-- issues resolved --> <em>Application</em>
3465 <li>logo keeps spinning and status remains at queued or
3466 running after job is cancelled</li>
3467 <li>cannot export features from alignments imported from
3468 Jalview/VAMSAS projects</li>
3469 <li>Buggy slider for web service parameters that take
3471 <li>Newly created RNA secondary structure line doesn't
3472 have 'display all symbols' flag set</li>
3473 <li>T-COFFEE alignment score shading scheme and other
3474 annotation shading not saved in Jalview project</li>
3475 <li>Local file cannot be loaded in freshly downloaded
3477 <li>Jalview icon not shown on dock in Mountain
3479 <li>Load file from desktop file browser fails</li>
3480 <li>Occasional NPE thrown when calculating large trees</li>
3481 <li>Cannot reorder or slide sequences after dragging an
3482 alignment onto desktop</li>
3483 <li>Colour by annotation dialog throws NPE after using
3484 'extract scores' function</li>
3485 <li>Loading/cut'n'pasting an empty file leads to a grey
3486 alignment window</li>
3487 <li>Disorder thresholds rendered incorrectly after
3488 performing IUPred disorder prediction</li>
3489 <li>Multiple group annotated consensus rows shown when
3490 changing 'normalise logo' display setting</li>
3491 <li>Find shows blank dialog after 'finished searching' if
3492 nothing matches query</li>
3493 <li>Null Pointer Exceptions raised when sorting by
3494 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3496 <li>Errors in Jmol console when structures in alignment
3497 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3499 <li>Not all working JABAWS services are shown in
3501 <li>JAVAWS version of Jalview fails to launch with
3502 'invalid literal/length code'</li>
3503 <li>Annotation/RNA Helix colourschemes cannot be applied
3504 to alignment with groups (actually fixed in 2.8.0b1)</li>
3505 <li>RNA Helices and T-Coffee Scores available as default
3508 </ul> <em>Applet</em>
3510 <li>Remove group option is shown even when selection is
3512 <li>Apply to all groups ticked but colourscheme changes
3513 don't affect groups</li>
3514 <li>Documented RNA Helices and T-Coffee Scores as valid
3515 colourscheme name</li>
3516 <li>Annotation labels drawn on sequence IDs when
3517 Annotation panel is not displayed</li>
3518 <li>Increased font size for dropdown menus on OSX and
3519 embedded windows</li>
3520 </ul> <em>Other</em>
3522 <li>Consensus sequence for alignments/groups with a
3523 single sequence were not calculated</li>
3524 <li>annotation files that contain only groups imported as
3525 annotation and junk sequences</li>
3526 <li>Fasta files with sequences containing '*' incorrectly
3527 recognised as PFAM or BLC</li>
3528 <li>conservation/PID slider apply all groups option
3529 doesn't affect background (2.8.0b1)
3531 <li>redundancy highlighting is erratic at 0% and 100%</li>
3532 <li>Remove gapped columns fails for sequences with ragged
3534 <li>AMSA annotation row with leading spaces is not
3535 registered correctly on import</li>
3536 <li>Jalview crashes when selecting PCA analysis for
3537 certain alignments</li>
3538 <li>Opening the colour by annotation dialog for an
3539 existing annotation based 'use original colours'
3540 colourscheme loses original colours setting</li>
3545 <td><div align="center">
3546 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3547 <em>30/1/2014</em></strong>
3551 <li>Trusted certificates for JalviewLite applet and
3552 Jalview Desktop application<br />Certificate was donated by
3553 <a href="https://www.certum.eu">Certum</a> to the Jalview
3554 open source project).
3556 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3557 <li>Output in Stockholm format</li>
3558 <li>Allow import of data from gzipped files</li>
3559 <li>Export/import group and sequence associated line
3560 graph thresholds</li>
3561 <li>Nucleotide substitution matrix that supports RNA and
3562 ambiguity codes</li>
3563 <li>Allow disorder predictions to be made on the current
3564 selection (or visible selection) in the same way that JPred
3566 <li>Groovy scripting for headless Jalview operation</li>
3567 </ul> <em>Other improvements</em>
3569 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3570 <li>COMBINE statement uses current SEQUENCE_REF and
3571 GROUP_REF scope to group annotation rows</li>
3572 <li>Support '' style escaping of quotes in Newick
3574 <li>Group options for JABAWS service by command line name</li>
3575 <li>Empty tooltip shown for JABA service options with a
3576 link but no description</li>
3577 <li>Select primary source when selecting authority in
3578 database fetcher GUI</li>
3579 <li>Add .mfa to FASTA file extensions recognised by
3581 <li>Annotation label tooltip text wrap</li>
3586 <li>Slow scrolling when lots of annotation rows are
3588 <li>Lots of NPE (and slowness) after creating RNA
3589 secondary structure annotation line</li>
3590 <li>Sequence database accessions not imported when
3591 fetching alignments from Rfam</li>
3592 <li>Incorrect SHMR submission for sequences with
3594 <li>View all structures does not always superpose
3596 <li>Option widgets in service parameters not updated to
3597 reflect user or preset settings</li>
3598 <li>Null pointer exceptions for some services without
3599 presets or adjustable parameters</li>
3600 <li>Discover PDB IDs entry in structure menu doesn't
3601 discover PDB xRefs</li>
3602 <li>Exception encountered while trying to retrieve
3603 features with DAS</li>
3604 <li>Lowest value in annotation row isn't coloured
3605 when colour by annotation (per sequence) is coloured</li>
3606 <li>Keyboard mode P jumps to start of gapped region when
3607 residue follows a gap</li>
3608 <li>Jalview appears to hang importing an alignment with
3609 Wrap as default or after enabling Wrap</li>
3610 <li>'Right click to add annotations' message
3611 shown in wrap mode when no annotations present</li>
3612 <li>Disorder predictions fail with NPE if no automatic
3613 annotation already exists on alignment</li>
3614 <li>oninit javascript function should be called after
3615 initialisation completes</li>
3616 <li>Remove redundancy after disorder prediction corrupts
3617 alignment window display</li>
3618 <li>Example annotation file in documentation is invalid</li>
3619 <li>Grouped line graph annotation rows are not exported
3620 to annotation file</li>
3621 <li>Multi-harmony analysis cannot be run when only two
3623 <li>Cannot create multiple groups of line graphs with
3624 several 'combine' statements in annotation file</li>
3625 <li>Pressing return several times causes Number Format
3626 exceptions in keyboard mode</li>
3627 <li>Multi-harmony (SHMMR) method doesn't submit
3628 correct partitions for input data</li>
3629 <li>Translation from DNA to Amino Acids fails</li>
3630 <li>Jalview fail to load newick tree with quoted label</li>
3631 <li>--headless flag isn't understood</li>
3632 <li>ClassCastException when generating EPS in headless
3634 <li>Adjusting sequence-associated shading threshold only
3635 changes one row's threshold</li>
3636 <li>Preferences and Feature settings panel panel
3637 doesn't open</li>
3638 <li>hide consensus histogram also hides conservation and
3639 quality histograms</li>
3644 <td><div align="center">
3645 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3647 <td><em>Application</em>
3649 <li>Support for JABAWS 2.0 Services (AACon alignment
3650 conservation, protein disorder and Clustal Omega)</li>
3651 <li>JABAWS server status indicator in Web Services
3653 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3654 in Jalview alignment window</li>
3655 <li>Updated Jalview build and deploy framework for OSX
3656 mountain lion, windows 7, and 8</li>
3657 <li>Nucleotide substitution matrix for PCA that supports
3658 RNA and ambiguity codes</li>
3660 <li>Improved sequence database retrieval GUI</li>
3661 <li>Support fetching and database reference look up
3662 against multiple DAS sources (Fetch all from in 'fetch db
3664 <li>Jalview project improvements
3666 <li>Store and retrieve the 'belowAlignment'
3667 flag for annotation</li>
3668 <li>calcId attribute to group annotation rows on the
3670 <li>Store AACon calculation settings for a view in
3671 Jalview project</li>
3675 <li>horizontal scrolling gesture support</li>
3676 <li>Visual progress indicator when PCA calculation is
3678 <li>Simpler JABA web services menus</li>
3679 <li>visual indication that web service results are still
3680 being retrieved from server</li>
3681 <li>Serialise the dialogs that are shown when Jalview
3682 starts up for first time</li>
3683 <li>Jalview user agent string for interacting with HTTP
3685 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3687 <li>Examples directory and Groovy library included in
3688 InstallAnywhere distribution</li>
3689 </ul> <em>Applet</em>
3691 <li>RNA alignment and secondary structure annotation
3692 visualization applet example</li>
3693 </ul> <em>General</em>
3695 <li>Normalise option for consensus sequence logo</li>
3696 <li>Reset button in PCA window to return dimensions to
3698 <li>Allow seqspace or Jalview variant of alignment PCA
3700 <li>PCA with either nucleic acid and protein substitution
3702 <li>Allow windows containing HTML reports to be exported
3704 <li>Interactive display and editing of RNA secondary
3705 structure contacts</li>
3706 <li>RNA Helix Alignment Colouring</li>
3707 <li>RNA base pair logo consensus</li>
3708 <li>Parse sequence associated secondary structure
3709 information in Stockholm files</li>
3710 <li>HTML Export database accessions and annotation
3711 information presented in tooltip for sequences</li>
3712 <li>Import secondary structure from LOCARNA clustalw
3713 style RNA alignment files</li>
3714 <li>import and visualise T-COFFEE quality scores for an
3716 <li>'colour by annotation' per sequence option to
3717 shade each sequence according to its associated alignment
3719 <li>New Jalview Logo</li>
3720 </ul> <em>Documentation and Development</em>
3722 <li>documentation for score matrices used in Jalview</li>
3723 <li>New Website!</li>
3725 <td><em>Application</em>
3727 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3728 wsdbfetch REST service</li>
3729 <li>Stop windows being moved outside desktop on OSX</li>
3730 <li>Filetype associations not installed for webstart
3732 <li>Jalview does not always retrieve progress of a JABAWS
3733 job execution in full once it is complete</li>
3734 <li>revise SHMR RSBS definition to ensure alignment is
3735 uploaded via ali_file parameter</li>
3736 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3737 <li>View all structures superposed fails with exception</li>
3738 <li>Jnet job queues forever if a very short sequence is
3739 submitted for prediction</li>
3740 <li>Cut and paste menu not opened when mouse clicked on
3742 <li>Putting fractional value into integer text box in
3743 alignment parameter dialog causes Jalview to hang</li>
3744 <li>Structure view highlighting doesn't work on
3746 <li>View all structures fails with exception shown in
3748 <li>Characters in filename associated with PDBEntry not
3749 escaped in a platform independent way</li>
3750 <li>Jalview desktop fails to launch with exception when
3752 <li>Tree calculation reports 'you must have 2 or more
3753 sequences selected' when selection is empty</li>
3754 <li>Jalview desktop fails to launch with jar signature
3755 failure when java web start temporary file caching is
3757 <li>DAS Sequence retrieval with range qualification
3758 results in sequence xref which includes range qualification</li>
3759 <li>Errors during processing of command line arguments
3760 cause progress bar (JAL-898) to be removed</li>
3761 <li>Replace comma for semi-colon option not disabled for
3762 DAS sources in sequence fetcher</li>
3763 <li>Cannot close news reader when JABAWS server warning
3764 dialog is shown</li>
3765 <li>Option widgets not updated to reflect user settings</li>
3766 <li>Edited sequence not submitted to web service</li>
3767 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3768 <li>InstallAnywhere installer doesn't unpack and run
3769 on OSX Mountain Lion</li>
3770 <li>Annotation panel not given a scroll bar when
3771 sequences with alignment annotation are pasted into the
3773 <li>Sequence associated annotation rows not associated
3774 when loaded from Jalview project</li>
3775 <li>Browser launch fails with NPE on java 1.7</li>
3776 <li>JABAWS alignment marked as finished when job was
3777 cancelled or job failed due to invalid input</li>
3778 <li>NPE with v2.7 example when clicking on Tree
3779 associated with all views</li>
3780 <li>Exceptions when copy/paste sequences with grouped
3781 annotation rows to new window</li>
3782 </ul> <em>Applet</em>
3784 <li>Sequence features are momentarily displayed before
3785 they are hidden using hidefeaturegroups applet parameter</li>
3786 <li>loading features via javascript API automatically
3787 enables feature display</li>
3788 <li>scrollToColumnIn javascript API method doesn't
3790 </ul> <em>General</em>
3792 <li>Redundancy removal fails for rna alignment</li>
3793 <li>PCA calculation fails when sequence has been selected
3794 and then deselected</li>
3795 <li>PCA window shows grey box when first opened on OSX</li>
3796 <li>Letters coloured pink in sequence logo when alignment
3797 coloured with clustalx</li>
3798 <li>Choosing fonts without letter symbols defined causes
3799 exceptions and redraw errors</li>
3800 <li>Initial PCA plot view is not same as manually
3801 reconfigured view</li>
3802 <li>Grouped annotation graph label has incorrect line
3804 <li>Grouped annotation graph label display is corrupted
3805 for lots of labels</li>
3810 <div align="center">
3811 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3814 <td><em>Application</em>
3816 <li>Jalview Desktop News Reader</li>
3817 <li>Tweaked default layout of web services menu</li>
3818 <li>View/alignment association menu to enable user to
3819 easily specify which alignment a multi-structure view takes
3820 its colours/correspondences from</li>
3821 <li>Allow properties file location to be specified as URL</li>
3822 <li>Extend Jalview project to preserve associations
3823 between many alignment views and a single Jmol display</li>
3824 <li>Store annotation row height in Jalview project file</li>
3825 <li>Annotation row column label formatting attributes
3826 stored in project file</li>
3827 <li>Annotation row order for auto-calculated annotation
3828 rows preserved in Jalview project file</li>
3829 <li>Visual progress indication when Jalview state is
3830 saved using Desktop window menu</li>
3831 <li>Visual indication that command line arguments are
3832 still being processed</li>
3833 <li>Groovy script execution from URL</li>
3834 <li>Colour by annotation default min and max colours in
3836 <li>Automatically associate PDB files dragged onto an
3837 alignment with sequences that have high similarity and
3839 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3840 <li>'view structures' option to open many
3841 structures in same window</li>
3842 <li>Sort associated views menu option for tree panel</li>
3843 <li>Group all JABA and non-JABA services for a particular
3844 analysis function in its own submenu</li>
3845 </ul> <em>Applet</em>
3847 <li>Userdefined and autogenerated annotation rows for
3849 <li>Adjustment of alignment annotation pane height</li>
3850 <li>Annotation scrollbar for annotation panel</li>
3851 <li>Drag to reorder annotation rows in annotation panel</li>
3852 <li>'automaticScrolling' parameter</li>
3853 <li>Allow sequences with partial ID string matches to be
3854 annotated from GFF/Jalview features files</li>
3855 <li>Sequence logo annotation row in applet</li>
3856 <li>Absolute paths relative to host server in applet
3857 parameters are treated as such</li>
3858 <li>New in the JalviewLite javascript API:
3860 <li>JalviewLite.js javascript library</li>
3861 <li>Javascript callbacks for
3863 <li>Applet initialisation</li>
3864 <li>Sequence/alignment mouse-overs and selections</li>
3867 <li>scrollTo row and column alignment scrolling
3869 <li>Select sequence/alignment regions from javascript</li>
3870 <li>javascript structure viewer harness to pass
3871 messages between Jmol and Jalview when running as
3872 distinct applets</li>
3873 <li>sortBy method</li>
3874 <li>Set of applet and application examples shipped
3875 with documentation</li>
3876 <li>New example to demonstrate JalviewLite and Jmol
3877 javascript message exchange</li>
3879 </ul> <em>General</em>
3881 <li>Enable Jmol displays to be associated with multiple
3882 multiple alignments</li>
3883 <li>Option to automatically sort alignment with new tree</li>
3884 <li>User configurable link to enable redirects to a
3885 www.Jalview.org mirror</li>
3886 <li>Jmol colours option for Jmol displays</li>
3887 <li>Configurable newline string when writing alignment
3888 and other flat files</li>
3889 <li>Allow alignment annotation description lines to
3890 contain html tags</li>
3891 </ul> <em>Documentation and Development</em>
3893 <li>Add groovy test harness for bulk load testing to
3895 <li>Groovy script to load and align a set of sequences
3896 using a web service before displaying the result in the
3897 Jalview desktop</li>
3898 <li>Restructured javascript and applet api documentation</li>
3899 <li>Ant target to publish example html files with applet
3901 <li>Netbeans project for building Jalview from source</li>
3902 <li>ant task to create online javadoc for Jalview source</li>
3904 <td><em>Application</em>
3906 <li>User defined colourscheme throws exception when
3907 current built in colourscheme is saved as new scheme</li>
3908 <li>AlignFrame->Save in application pops up save
3909 dialog for valid filename/format</li>
3910 <li>Cannot view associated structure for UniProt sequence</li>
3911 <li>PDB file association breaks for UniProt sequence
3913 <li>Associate PDB from file dialog does not tell you
3914 which sequence is to be associated with the file</li>
3915 <li>Find All raises null pointer exception when query
3916 only matches sequence IDs</li>
3917 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3918 <li>Jalview project with Jmol views created with Jalview
3919 2.4 cannot be loaded</li>
3920 <li>Filetype associations not installed for webstart
3922 <li>Two or more chains in a single PDB file associated
3923 with sequences in different alignments do not get coloured
3924 by their associated sequence</li>
3925 <li>Visibility status of autocalculated annotation row
3926 not preserved when project is loaded</li>
3927 <li>Annotation row height and visibility attributes not
3928 stored in Jalview project</li>
3929 <li>Tree bootstraps are not preserved when saved as a
3930 Jalview project</li>
3931 <li>Envision2 workflow tooltips are corrupted</li>
3932 <li>Enabling show group conservation also enables colour
3933 by conservation</li>
3934 <li>Duplicate group associated conservation or consensus
3935 created on new view</li>
3936 <li>Annotation scrollbar not displayed after 'show
3937 all hidden annotation rows' option selected</li>
3938 <li>Alignment quality not updated after alignment
3939 annotation row is hidden then shown</li>
3940 <li>Preserve colouring of structures coloured by
3941 sequences in pre Jalview 2.7 projects</li>
3942 <li>Web service job parameter dialog is not laid out
3944 <li>Web services menu not refreshed after 'reset
3945 services' button is pressed in preferences</li>
3946 <li>Annotation off by one in Jalview v2_3 example project</li>
3947 <li>Structures imported from file and saved in project
3948 get name like jalview_pdb1234.txt when reloaded</li>
3949 <li>Jalview does not always retrieve progress of a JABAWS
3950 job execution in full once it is complete</li>
3951 </ul> <em>Applet</em>
3953 <li>Alignment height set incorrectly when lots of
3954 annotation rows are displayed</li>
3955 <li>Relative URLs in feature HTML text not resolved to
3957 <li>View follows highlighting does not work for positions
3959 <li><= shown as = in tooltip</li>
3960 <li>Export features raises exception when no features
3962 <li>Separator string used for serialising lists of IDs
3963 for javascript api is modified when separator string
3964 provided as parameter</li>
3965 <li>Null pointer exception when selecting tree leaves for
3966 alignment with no existing selection</li>
3967 <li>Relative URLs for datasources assumed to be relative
3968 to applet's codebase</li>
3969 <li>Status bar not updated after finished searching and
3970 search wraps around to first result</li>
3971 <li>StructureSelectionManager instance shared between
3972 several Jalview applets causes race conditions and memory
3974 <li>Hover tooltip and mouseover of position on structure
3975 not sent from Jmol in applet</li>
3976 <li>Certain sequences of javascript method calls to
3977 applet API fatally hang browser</li>
3978 </ul> <em>General</em>
3980 <li>View follows structure mouseover scrolls beyond
3981 position with wrapped view and hidden regions</li>
3982 <li>Find sequence position moves to wrong residue
3983 with/without hidden columns</li>
3984 <li>Sequence length given in alignment properties window
3986 <li>InvalidNumberFormat exceptions thrown when trying to
3987 import PDB like structure files</li>
3988 <li>Positional search results are only highlighted
3989 between user-supplied sequence start/end bounds</li>
3990 <li>End attribute of sequence is not validated</li>
3991 <li>Find dialog only finds first sequence containing a
3992 given sequence position</li>
3993 <li>Sequence numbering not preserved in MSF alignment
3995 <li>Jalview PDB file reader does not extract sequence
3996 from nucleotide chains correctly</li>
3997 <li>Structure colours not updated when tree partition
3998 changed in alignment</li>
3999 <li>Sequence associated secondary structure not correctly
4000 parsed in interleaved stockholm</li>
4001 <li>Colour by annotation dialog does not restore current
4003 <li>Hiding (nearly) all sequences doesn't work
4005 <li>Sequences containing lowercase letters are not
4006 properly associated with their pdb files</li>
4007 </ul> <em>Documentation and Development</em>
4009 <li>schemas/JalviewWsParamSet.xsd corrupted by
4010 ApplyCopyright tool</li>
4015 <div align="center">
4016 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4019 <td><em>Application</em>
4021 <li>New warning dialog when the Jalview Desktop cannot
4022 contact web services</li>
4023 <li>JABA service parameters for a preset are shown in
4024 service job window</li>
4025 <li>JABA Service menu entries reworded</li>
4029 <li>Modeller PIR IO broken - cannot correctly import a
4030 pir file emitted by Jalview</li>
4031 <li>Existing feature settings transferred to new
4032 alignment view created from cut'n'paste</li>
4033 <li>Improved test for mixed amino/nucleotide chains when
4034 parsing PDB files</li>
4035 <li>Consensus and conservation annotation rows
4036 occasionally become blank for all new windows</li>
4037 <li>Exception raised when right clicking above sequences
4038 in wrapped view mode</li>
4039 </ul> <em>Application</em>
4041 <li>multiple multiply aligned structure views cause cpu
4042 usage to hit 100% and computer to hang</li>
4043 <li>Web Service parameter layout breaks for long user
4044 parameter names</li>
4045 <li>Jaba service discovery hangs desktop if Jaba server
4052 <div align="center">
4053 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4056 <td><em>Application</em>
4058 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4059 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4062 <li>Web Services preference tab</li>
4063 <li>Analysis parameters dialog box and user defined
4065 <li>Improved speed and layout of Envision2 service menu</li>
4066 <li>Superpose structures using associated sequence
4068 <li>Export coordinates and projection as CSV from PCA
4070 </ul> <em>Applet</em>
4072 <li>enable javascript: execution by the applet via the
4073 link out mechanism</li>
4074 </ul> <em>Other</em>
4076 <li>Updated the Jmol Jalview interface to work with Jmol
4078 <li>The Jalview Desktop and JalviewLite applet now
4079 require Java 1.5</li>
4080 <li>Allow Jalview feature colour specification for GFF
4081 sequence annotation files</li>
4082 <li>New 'colour by label' keword in Jalview feature file
4083 type colour specification</li>
4084 <li>New Jalview Desktop Groovy API method that allows a
4085 script to check if it being run in an interactive session or
4086 in a batch operation from the Jalview command line</li>
4090 <li>clustalx colourscheme colours Ds preferentially when
4091 both D+E are present in over 50% of the column</li>
4092 </ul> <em>Application</em>
4094 <li>typo in AlignmentFrame->View->Hide->all but
4095 selected Regions menu item</li>
4096 <li>sequence fetcher replaces ',' for ';' when the ',' is
4097 part of a valid accession ID</li>
4098 <li>fatal OOM if object retrieved by sequence fetcher
4099 runs out of memory</li>
4100 <li>unhandled Out of Memory Error when viewing pca
4101 analysis results</li>
4102 <li>InstallAnywhere builds fail to launch on OS X java
4103 10.5 update 4 (due to apple Java 1.6 update)</li>
4104 <li>Installanywhere Jalview silently fails to launch</li>
4105 </ul> <em>Applet</em>
4107 <li>Jalview.getFeatureGroups() raises an
4108 ArrayIndexOutOfBoundsException if no feature groups are
4115 <div align="center">
4116 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4122 <li>Alignment prettyprinter doesn't cope with long
4124 <li>clustalx colourscheme colours Ds preferentially when
4125 both D+E are present in over 50% of the column</li>
4126 <li>nucleic acid structures retrieved from PDB do not
4127 import correctly</li>
4128 <li>More columns get selected than were clicked on when a
4129 number of columns are hidden</li>
4130 <li>annotation label popup menu not providing correct
4131 add/hide/show options when rows are hidden or none are
4133 <li>Stockholm format shown in list of readable formats,
4134 and parser copes better with alignments from RFAM.</li>
4135 <li>CSV output of consensus only includes the percentage
4136 of all symbols if sequence logo display is enabled</li>
4138 </ul> <em>Applet</em>
4140 <li>annotation panel disappears when annotation is
4142 </ul> <em>Application</em>
4144 <li>Alignment view not redrawn properly when new
4145 alignment opened where annotation panel is visible but no
4146 annotations are present on alignment</li>
4147 <li>pasted region containing hidden columns is
4148 incorrectly displayed in new alignment window</li>
4149 <li>Jalview slow to complete operations when stdout is
4150 flooded (fix is to close the Jalview console)</li>
4151 <li>typo in AlignmentFrame->View->Hide->all but
4152 selected Rregions menu item.</li>
4153 <li>inconsistent group submenu and Format submenu entry
4154 'Un' or 'Non'conserved</li>
4155 <li>Sequence feature settings are being shared by
4156 multiple distinct alignments</li>
4157 <li>group annotation not recreated when tree partition is
4159 <li>double click on group annotation to select sequences
4160 does not propagate to associated trees</li>
4161 <li>Mac OSX specific issues:
4163 <li>exception raised when mouse clicked on desktop
4164 window background</li>
4165 <li>Desktop menu placed on menu bar and application
4166 name set correctly</li>
4167 <li>sequence feature settings not wide enough for the
4168 save feature colourscheme button</li>
4177 <div align="center">
4178 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4181 <td><em>New Capabilities</em>
4183 <li>URL links generated from description line for
4184 regular-expression based URL links (applet and application)
4186 <li>Non-positional feature URL links are shown in link
4188 <li>Linked viewing of nucleic acid sequences and
4190 <li>Automatic Scrolling option in View menu to display
4191 the currently highlighted region of an alignment.</li>
4192 <li>Order an alignment by sequence length, or using the
4193 average score or total feature count for each sequence.</li>
4194 <li>Shading features by score or associated description</li>
4195 <li>Subdivide alignment and groups based on identity of
4196 selected subsequence (Make Groups from Selection).</li>
4197 <li>New hide/show options including Shift+Control+H to
4198 hide everything but the currently selected region.</li>
4199 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4200 </ul> <em>Application</em>
4202 <li>Fetch DB References capabilities and UI expanded to
4203 support retrieval from DAS sequence sources</li>
4204 <li>Local DAS Sequence sources can be added via the
4205 command line or via the Add local source dialog box.</li>
4206 <li>DAS Dbref and DbxRef feature types are parsed as
4207 database references and protein_name is parsed as
4208 description line (BioSapiens terms).</li>
4209 <li>Enable or disable non-positional feature and database
4210 references in sequence ID tooltip from View menu in
4212 <!-- <li>New hidden columns and rows and representatives capabilities
4213 in annotations file (in progress - not yet fully implemented)</li> -->
4214 <li>Group-associated consensus, sequence logos and
4215 conservation plots</li>
4216 <li>Symbol distributions for each column can be exported
4217 and visualized as sequence logos</li>
4218 <li>Optionally scale multi-character column labels to fit
4219 within each column of annotation row<!-- todo for applet -->
4221 <li>Optional automatic sort of associated alignment view
4222 when a new tree is opened.</li>
4223 <li>Jalview Java Console</li>
4224 <li>Better placement of desktop window when moving
4225 between different screens.</li>
4226 <li>New preference items for sequence ID tooltip and
4227 consensus annotation</li>
4228 <li>Client to submit sequences and IDs to Envision2
4230 <li><em>Vamsas Capabilities</em>
4232 <li>Improved VAMSAS synchronization (Jalview archive
4233 used to preserve views, structures, and tree display
4235 <li>Import of vamsas documents from disk or URL via
4237 <li>Sharing of selected regions between views and
4238 with other VAMSAS applications (Experimental feature!)</li>
4239 <li>Updated API to VAMSAS version 0.2</li>
4241 </ul> <em>Applet</em>
4243 <li>Middle button resizes annotation row height</li>
4246 <li>sortByTree (true/false) - automatically sort the
4247 associated alignment view by the tree when a new tree is
4249 <li>showTreeBootstraps (true/false) - show or hide
4250 branch bootstraps (default is to show them if available)</li>
4251 <li>showTreeDistances (true/false) - show or hide
4252 branch lengths (default is to show them if available)</li>
4253 <li>showUnlinkedTreeNodes (true/false) - indicate if
4254 unassociated nodes should be highlighted in the tree
4256 <li>heightScale and widthScale (1.0 or more) -
4257 increase the height or width of a cell in the alignment
4258 grid relative to the current font size.</li>
4261 <li>Non-positional features displayed in sequence ID
4263 </ul> <em>Other</em>
4265 <li>Features format: graduated colour definitions and
4266 specification of feature scores</li>
4267 <li>Alignment Annotations format: new keywords for group
4268 associated annotation (GROUP_REF) and annotation row display
4269 properties (ROW_PROPERTIES)</li>
4270 <li>XML formats extended to support graduated feature
4271 colourschemes, group associated annotation, and profile
4272 visualization settings.</li></td>
4275 <li>Source field in GFF files parsed as feature source
4276 rather than description</li>
4277 <li>Non-positional features are now included in sequence
4278 feature and gff files (controlled via non-positional feature
4279 visibility in tooltip).</li>
4280 <li>URL links generated for all feature links (bugfix)</li>
4281 <li>Added URL embedding instructions to features file
4283 <li>Codons containing ambiguous nucleotides translated as
4284 'X' in peptide product</li>
4285 <li>Match case switch in find dialog box works for both
4286 sequence ID and sequence string and query strings do not
4287 have to be in upper case to match case-insensitively.</li>
4288 <li>AMSA files only contain first column of
4289 multi-character column annotation labels</li>
4290 <li>Jalview Annotation File generation/parsing consistent
4291 with documentation (e.g. Stockholm annotation can be
4292 exported and re-imported)</li>
4293 <li>PDB files without embedded PDB IDs given a friendly
4295 <li>Find incrementally searches ID string matches as well
4296 as subsequence matches, and correctly reports total number
4300 <li>Better handling of exceptions during sequence
4302 <li>Dasobert generated non-positional feature URL
4303 link text excludes the start_end suffix</li>
4304 <li>DAS feature and source retrieval buttons disabled
4305 when fetch or registry operations in progress.</li>
4306 <li>PDB files retrieved from URLs are cached properly</li>
4307 <li>Sequence description lines properly shared via
4309 <li>Sequence fetcher fetches multiple records for all
4311 <li>Ensured that command line das feature retrieval
4312 completes before alignment figures are generated.</li>
4313 <li>Reduced time taken when opening file browser for
4315 <li>isAligned check prior to calculating tree, PCA or
4316 submitting an MSA to JNet now excludes hidden sequences.</li>
4317 <li>User defined group colours properly recovered
4318 from Jalview projects.</li>
4327 <div align="center">
4328 <strong>2.4.0.b2</strong><br> 28/10/2009
4333 <li>Experimental support for google analytics usage
4335 <li>Jalview privacy settings (user preferences and docs).</li>
4340 <li>Race condition in applet preventing startup in
4342 <li>Exception when feature created from selection beyond
4343 length of sequence.</li>
4344 <li>Allow synthetic PDB files to be imported gracefully</li>
4345 <li>Sequence associated annotation rows associate with
4346 all sequences with a given id</li>
4347 <li>Find function matches case-insensitively for sequence
4348 ID string searches</li>
4349 <li>Non-standard characters do not cause pairwise
4350 alignment to fail with exception</li>
4351 </ul> <em>Application Issues</em>
4353 <li>Sequences are now validated against EMBL database</li>
4354 <li>Sequence fetcher fetches multiple records for all
4356 </ul> <em>InstallAnywhere Issues</em>
4358 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4359 issue with installAnywhere mechanism)</li>
4360 <li>Command line launching of JARs from InstallAnywhere
4361 version (java class versioning error fixed)</li>
4368 <div align="center">
4369 <strong>2.4</strong><br> 27/8/2008
4372 <td><em>User Interface</em>
4374 <li>Linked highlighting of codon and amino acid from
4375 translation and protein products</li>
4376 <li>Linked highlighting of structure associated with
4377 residue mapping to codon position</li>
4378 <li>Sequence Fetcher provides example accession numbers
4379 and 'clear' button</li>
4380 <li>MemoryMonitor added as an option under Desktop's
4382 <li>Extract score function to parse whitespace separated
4383 numeric data in description line</li>
4384 <li>Column labels in alignment annotation can be centred.</li>
4385 <li>Tooltip for sequence associated annotation give name
4387 </ul> <em>Web Services and URL fetching</em>
4389 <li>JPred3 web service</li>
4390 <li>Prototype sequence search client (no public services
4392 <li>Fetch either seed alignment or full alignment from
4394 <li>URL Links created for matching database cross
4395 references as well as sequence ID</li>
4396 <li>URL Links can be created using regular-expressions</li>
4397 </ul> <em>Sequence Database Connectivity</em>
4399 <li>Retrieval of cross-referenced sequences from other
4401 <li>Generalised database reference retrieval and
4402 validation to all fetchable databases</li>
4403 <li>Fetch sequences from DAS sources supporting the
4404 sequence command</li>
4405 </ul> <em>Import and Export</em>
4406 <li>export annotation rows as CSV for spreadsheet import</li>
4407 <li>Jalview projects record alignment dataset associations,
4408 EMBL products, and cDNA sequence mappings</li>
4409 <li>Sequence Group colour can be specified in Annotation
4411 <li>Ad-hoc colouring of group in Annotation File using RGB
4412 triplet as name of colourscheme</li>
4413 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4415 <li>treenode binding for VAMSAS tree exchange</li>
4416 <li>local editing and update of sequences in VAMSAS
4417 alignments (experimental)</li>
4418 <li>Create new or select existing session to join</li>
4419 <li>load and save of vamsas documents</li>
4420 </ul> <em>Application command line</em>
4422 <li>-tree parameter to open trees (introduced for passing
4424 <li>-fetchfrom command line argument to specify nicknames
4425 of DAS servers to query for alignment features</li>
4426 <li>-dasserver command line argument to add new servers
4427 that are also automatically queried for features</li>
4428 <li>-groovy command line argument executes a given groovy
4429 script after all input data has been loaded and parsed</li>
4430 </ul> <em>Applet-Application data exchange</em>
4432 <li>Trees passed as applet parameters can be passed to
4433 application (when using "View in full
4434 application")</li>
4435 </ul> <em>Applet Parameters</em>
4437 <li>feature group display control parameter</li>
4438 <li>debug parameter</li>
4439 <li>showbutton parameter</li>
4440 </ul> <em>Applet API methods</em>
4442 <li>newView public method</li>
4443 <li>Window (current view) specific get/set public methods</li>
4444 <li>Feature display control methods</li>
4445 <li>get list of currently selected sequences</li>
4446 </ul> <em>New Jalview distribution features</em>
4448 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4449 <li>RELEASE file gives build properties for the latest
4450 Jalview release.</li>
4451 <li>Java 1.1 Applet build made easier and donotobfuscate
4452 property controls execution of obfuscator</li>
4453 <li>Build target for generating source distribution</li>
4454 <li>Debug flag for javacc</li>
4455 <li>.jalview_properties file is documented (slightly) in
4456 jalview.bin.Cache</li>
4457 <li>Continuous Build Integration for stable and
4458 development version of Application, Applet and source
4463 <li>selected region output includes visible annotations
4464 (for certain formats)</li>
4465 <li>edit label/displaychar contains existing label/char
4467 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4468 <li>shorter peptide product names from EMBL records</li>
4469 <li>Newick string generator makes compact representations</li>
4470 <li>bootstrap values parsed correctly for tree files with
4472 <li>pathological filechooser bug avoided by not allowing
4473 filenames containing a ':'</li>
4474 <li>Fixed exception when parsing GFF files containing
4475 global sequence features</li>
4476 <li>Alignment datasets are finalized only when number of
4477 references from alignment sequences goes to zero</li>
4478 <li>Close of tree branch colour box without colour
4479 selection causes cascading exceptions</li>
4480 <li>occasional negative imgwidth exceptions</li>
4481 <li>better reporting of non-fatal warnings to user when
4482 file parsing fails.</li>
4483 <li>Save works when Jalview project is default format</li>
4484 <li>Save as dialog opened if current alignment format is
4485 not a valid output format</li>
4486 <li>UniProt canonical names introduced for both das and
4488 <li>Histidine should be midblue (not pink!) in Zappo</li>
4489 <li>error messages passed up and output when data read
4491 <li>edit undo recovers previous dataset sequence when
4492 sequence is edited</li>
4493 <li>allow PDB files without pdb ID HEADER lines (like
4494 those generated by MODELLER) to be read in properly</li>
4495 <li>allow reading of JPred concise files as a normal
4497 <li>Stockholm annotation parsing and alignment properties
4498 import fixed for PFAM records</li>
4499 <li>Structure view windows have correct name in Desktop
4501 <li>annotation consisting of sequence associated scores
4502 can be read and written correctly to annotation file</li>
4503 <li>Aligned cDNA translation to aligned peptide works
4505 <li>Fixed display of hidden sequence markers and
4506 non-italic font for representatives in Applet</li>
4507 <li>Applet Menus are always embedded in applet window on
4509 <li>Newly shown features appear at top of stack (in
4511 <li>Annotations added via parameter not drawn properly
4512 due to null pointer exceptions</li>
4513 <li>Secondary structure lines are drawn starting from
4514 first column of alignment</li>
4515 <li>UniProt XML import updated for new schema release in
4517 <li>Sequence feature to sequence ID match for Features
4518 file is case-insensitive</li>
4519 <li>Sequence features read from Features file appended to
4520 all sequences with matching IDs</li>
4521 <li>PDB structure coloured correctly for associated views
4522 containing a sub-sequence</li>
4523 <li>PDB files can be retrieved by applet from Jar files</li>
4524 <li>feature and annotation file applet parameters
4525 referring to different directories are retrieved correctly</li>
4526 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4527 <li>Fixed application hang whilst waiting for
4528 splash-screen version check to complete</li>
4529 <li>Applet properly URLencodes input parameter values
4530 when passing them to the launchApp service</li>
4531 <li>display name and local features preserved in results
4532 retrieved from web service</li>
4533 <li>Visual delay indication for sequence retrieval and
4534 sequence fetcher initialisation</li>
4535 <li>updated Application to use DAS 1.53e version of
4536 dasobert DAS client</li>
4537 <li>Re-instated Full AMSA support and .amsa file
4539 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4547 <div align="center">
4548 <strong>2.3</strong><br> 9/5/07
4553 <li>Jmol 11.0.2 integration</li>
4554 <li>PDB views stored in Jalview XML files</li>
4555 <li>Slide sequences</li>
4556 <li>Edit sequence in place</li>
4557 <li>EMBL CDS features</li>
4558 <li>DAS Feature mapping</li>
4559 <li>Feature ordering</li>
4560 <li>Alignment Properties</li>
4561 <li>Annotation Scores</li>
4562 <li>Sort by scores</li>
4563 <li>Feature/annotation editing in applet</li>
4568 <li>Headless state operation in 2.2.1</li>
4569 <li>Incorrect and unstable DNA pairwise alignment</li>
4570 <li>Cut and paste of sequences with annotation</li>
4571 <li>Feature group display state in XML</li>
4572 <li>Feature ordering in XML</li>
4573 <li>blc file iteration selection using filename # suffix</li>
4574 <li>Stockholm alignment properties</li>
4575 <li>Stockhom alignment secondary structure annotation</li>
4576 <li>2.2.1 applet had no feature transparency</li>
4577 <li>Number pad keys can be used in cursor mode</li>
4578 <li>Structure Viewer mirror image resolved</li>
4585 <div align="center">
4586 <strong>2.2.1</strong><br> 12/2/07
4591 <li>Non standard characters can be read and displayed
4592 <li>Annotations/Features can be imported/exported to the
4594 <li>Applet allows editing of sequence/annotation/group
4595 name & description
4596 <li>Preference setting to display sequence name in
4598 <li>Annotation file format extended to allow
4599 Sequence_groups to be defined
4600 <li>Default opening of alignment overview panel can be
4601 specified in preferences
4602 <li>PDB residue numbering annotation added to associated
4608 <li>Applet crash under certain Linux OS with Java 1.6
4610 <li>Annotation file export / import bugs fixed
4611 <li>PNG / EPS image output bugs fixed
4617 <div align="center">
4618 <strong>2.2</strong><br> 27/11/06
4623 <li>Multiple views on alignment
4624 <li>Sequence feature editing
4625 <li>"Reload" alignment
4626 <li>"Save" to current filename
4627 <li>Background dependent text colour
4628 <li>Right align sequence ids
4629 <li>User-defined lower case residue colours
4632 <li>Menu item accelerator keys
4633 <li>Control-V pastes to current alignment
4634 <li>Cancel button for DAS Feature Fetching
4635 <li>PCA and PDB Viewers zoom via mouse roller
4636 <li>User-defined sub-tree colours and sub-tree selection
4638 <li>'New Window' button on the 'Output to Text box'
4643 <li>New memory efficient Undo/Redo System
4644 <li>Optimised symbol lookups and conservation/consensus
4646 <li>Region Conservation/Consensus recalculated after
4648 <li>Fixed Remove Empty Columns Bug (empty columns at end
4650 <li>Slowed DAS Feature Fetching for increased robustness.
4652 <li>Made angle brackets in ASCII feature descriptions
4654 <li>Re-instated Zoom function for PCA
4655 <li>Sequence descriptions conserved in web service
4657 <li>UniProt ID discoverer uses any word separated by
4659 <li>WsDbFetch query/result association resolved
4660 <li>Tree leaf to sequence mapping improved
4661 <li>Smooth fonts switch moved to FontChooser dialog box.
4668 <div align="center">
4669 <strong>2.1.1</strong><br> 12/9/06
4674 <li>Copy consensus sequence to clipboard</li>
4679 <li>Image output - rightmost residues are rendered if
4680 sequence id panel has been resized</li>
4681 <li>Image output - all offscreen group boundaries are
4683 <li>Annotation files with sequence references - all
4684 elements in file are relative to sequence position</li>
4685 <li>Mac Applet users can use Alt key for group editing</li>
4691 <div align="center">
4692 <strong>2.1</strong><br> 22/8/06
4697 <li>MAFFT Multiple Alignment in default Web Service list</li>
4698 <li>DAS Feature fetching</li>
4699 <li>Hide sequences and columns</li>
4700 <li>Export Annotations and Features</li>
4701 <li>GFF file reading / writing</li>
4702 <li>Associate structures with sequences from local PDB
4704 <li>Add sequences to exisiting alignment</li>
4705 <li>Recently opened files / URL lists</li>
4706 <li>Applet can launch the full application</li>
4707 <li>Applet has transparency for features (Java 1.2
4709 <li>Applet has user defined colours parameter</li>
4710 <li>Applet can load sequences from parameter
4711 "sequence<em>x</em>"
4717 <li>Redundancy Panel reinstalled in the Applet</li>
4718 <li>Monospaced font - EPS / rescaling bug fixed</li>
4719 <li>Annotation files with sequence references bug fixed</li>
4725 <div align="center">
4726 <strong>2.08.1</strong><br> 2/5/06
4731 <li>Change case of selected region from Popup menu</li>
4732 <li>Choose to match case when searching</li>
4733 <li>Middle mouse button and mouse movement can compress /
4734 expand the visible width and height of the alignment</li>
4739 <li>Annotation Panel displays complete JNet results</li>
4745 <div align="center">
4746 <strong>2.08b</strong><br> 18/4/06
4752 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4753 <li>Righthand label on wrapped alignments shows correct
4760 <div align="center">
4761 <strong>2.08</strong><br> 10/4/06
4766 <li>Editing can be locked to the selection area</li>
4767 <li>Keyboard editing</li>
4768 <li>Create sequence features from searches</li>
4769 <li>Precalculated annotations can be loaded onto
4771 <li>Features file allows grouping of features</li>
4772 <li>Annotation Colouring scheme added</li>
4773 <li>Smooth fonts off by default - Faster rendering</li>
4774 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4779 <li>Drag & Drop fixed on Linux</li>
4780 <li>Jalview Archive file faster to load/save, sequence
4781 descriptions saved.</li>
4787 <div align="center">
4788 <strong>2.07</strong><br> 12/12/05
4793 <li>PDB Structure Viewer enhanced</li>
4794 <li>Sequence Feature retrieval and display enhanced</li>
4795 <li>Choose to output sequence start-end after sequence
4796 name for file output</li>
4797 <li>Sequence Fetcher WSDBFetch@EBI</li>
4798 <li>Applet can read feature files, PDB files and can be
4799 used for HTML form input</li>
4804 <li>HTML output writes groups and features</li>
4805 <li>Group editing is Control and mouse click</li>
4806 <li>File IO bugs</li>
4812 <div align="center">
4813 <strong>2.06</strong><br> 28/9/05
4818 <li>View annotations in wrapped mode</li>
4819 <li>More options for PCA viewer</li>
4824 <li>GUI bugs resolved</li>
4825 <li>Runs with -nodisplay from command line</li>
4831 <div align="center">
4832 <strong>2.05b</strong><br> 15/9/05
4837 <li>Choose EPS export as lineart or text</li>
4838 <li>Jar files are executable</li>
4839 <li>Can read in Uracil - maps to unknown residue</li>
4844 <li>Known OutOfMemory errors give warning message</li>
4845 <li>Overview window calculated more efficiently</li>
4846 <li>Several GUI bugs resolved</li>
4852 <div align="center">
4853 <strong>2.05</strong><br> 30/8/05
4858 <li>Edit and annotate in "Wrapped" view</li>
4863 <li>Several GUI bugs resolved</li>
4869 <div align="center">
4870 <strong>2.04</strong><br> 24/8/05
4875 <li>Hold down mouse wheel & scroll to change font
4881 <li>Improved JPred client reliability</li>
4882 <li>Improved loading of Jalview files</li>
4888 <div align="center">
4889 <strong>2.03</strong><br> 18/8/05
4894 <li>Set Proxy server name and port in preferences</li>
4895 <li>Multiple URL links from sequence ids</li>
4896 <li>User Defined Colours can have a scheme name and added
4898 <li>Choose to ignore gaps in consensus calculation</li>
4899 <li>Unix users can set default web browser</li>
4900 <li>Runs without GUI for batch processing</li>
4901 <li>Dynamically generated Web Service Menus</li>
4906 <li>InstallAnywhere download for Sparc Solaris</li>
4912 <div align="center">
4913 <strong>2.02</strong><br> 18/7/05
4919 <li>Copy & Paste order of sequences maintains
4920 alignment order.</li>
4926 <div align="center">
4927 <strong>2.01</strong><br> 12/7/05
4932 <li>Use delete key for deleting selection.</li>
4933 <li>Use Mouse wheel to scroll sequences.</li>
4934 <li>Help file updated to describe how to add alignment
4936 <li>Version and build date written to build properties
4938 <li>InstallAnywhere installation will check for updates
4939 at launch of Jalview.</li>
4944 <li>Delete gaps bug fixed.</li>
4945 <li>FileChooser sorts columns.</li>
4946 <li>Can remove groups one by one.</li>
4947 <li>Filechooser icons installed.</li>
4948 <li>Finder ignores return character when searching.
4949 Return key will initiate a search.<br>
4956 <div align="center">
4957 <strong>2.0</strong><br> 20/6/05
4962 <li>New codebase</li>