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;
34 /* separate the items from eachother */
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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>17/09/2020</em></strong></td>
62 <td align="left" valign="top">
65 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
66 residue in cursor mode
69 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
70 HTSJDK from 2.12 to 2.23
73 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
74 optimisations and improvements suggested by Bob Hanson and
75 improved compatibility with JalviewJS
78 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
79 alignments from Pfam and Rfam
82 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
83 import (no longer based on .gz extension)
86 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
89 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
90 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
94 <!-- JAL-3667 -->Improved warning messages, debug logging
95 and fixed Retry action when Jalview encounters errors when
96 saving or making backup files.
99 <!-- JAL-3676 -->Enhanced Jalview Java Console:
101 <li>Jalview's logging level can be configured</li>
102 <li>Copy to Clipboard Buttion</li>
106 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
107 when running on Linux (Requires Java 11+)
109 </ul> <em>Launching Jalview</em>
112 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
113 through a system property
116 <!-- JAL-3477 -->Improved built-in documentation and command
117 line help for configuring Jalview's memory
121 <td align="left" valign="top">
124 <!-- JAL-3691 -->Conservation and Quality tracks are shown
125 but not calculated and no protein or DNA score models are
126 available for tree/PCA calculation when launched with
127 Turkish language locale
130 <!-- JAL-3493 -->Escape does not clear highlights on the
131 alignment (Since Jalview 2.10.3)
134 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
135 doesn't slide selected sequences, just sequence under cursor
138 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
139 sequence under the cursor
142 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
143 multiple EMBL gene products shown forĀ a single contig
146 <!-- JAL-3696 -->Errors encountered when processing variants
147 from VCF files yield "Error processing VCF: Format specifier
151 <!-- JAL-3697 -->Count of features not shown can be wrong
152 when there are both local and complementary features mapped
153 to the position under the cursor
156 <!-- JAL-3673 -->Sequence ID for reference sequence is
157 clipped when Right align Sequence IDs enabled
160 <!-- JAL-2983 -->Slider with negative range values not
161 rendered correctly in VAqua4 (Since 2.10.4)
164 <!-- JAL-3685 -->Single quotes not displayed correctly in
165 internationalised text for some messages and log output
168 <!-- JAL-3490 -->Find doesn't report matches that span
169 hidden gapped columns
172 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
173 panels, Alignment viewport and annotation renderer.
176 <!-- JAL-3561 -->Jalview ignores file format parameter
177 specifying output format when exporting an alignment via the
181 <!-- JAL-3667 -->Windows 10: For a minority of users, if
182 backups are not enabled, Jalview sometimes fails to
183 overwrite an existing file and raises a warning dialog. (in
184 2.11.0, and 2.11.1.0, the workaround is to try to save the
185 file again, and if that fails, delete the original file and
189 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
193 <!-- JAL-3741 -->References to http://www.jalview.org in
194 program and documentation
196 </ul> <em>Launching Jalview</em>
199 <!-- JAL-3718 -->Jalview application fails when launched the
200 first time for a version that has different jars to the
201 previous launched version.
203 </ul> <em>Developing Jalview</em>
206 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
207 data, causing cloverReport gradle task to fail with an
211 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
212 monitor the release channel
214 </ul> <em>New Known defects</em>
217 <!-- JAL-3748 -->CDS shown in result of submitting proteins
218 in a CDS/Protein alignment to a web service is wrong when
219 proteins share a common transcript sequence (e.g.
220 genome of RNA viruses)
223 <!-- JAL-3576 -->Co-located features exported and re-imported
224 are ordered differently when shown on alignment and in
225 tooltips. (Also affects v2.11.1.0)
228 <!-- JAL-3702 -->Drag and drop of alignment file onto
229 alignment window when in a HiDPI scaled mode in Linux only
230 works for the top left quadrant of the alignment window
233 <!-- JAL-3701 -->Stale build data in jalview standalone jar
234 builds (only affects 2.11.1.1 branch)
237 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
238 when alignment view restored from project (since Jalview 2.11.0)
244 <td width="60" align="center" nowrap><strong><a
245 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
246 <em>22/04/2020</em></strong></td>
247 <td align="left" valign="top">
250 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
251 'virtual' codon features shown on protein (or vice versa)
252 for display in alignments, on structure views (including
253 transfer to UCSF chimera), in feature reports and for
257 <!-- JAL-3121 -->Feature attributes from VCF files can be
258 exported and re-imported as GFF3 files
261 <!-- JAL-3376 -->Capture VCF "fixed column" values
262 POS, ID, QUAL, FILTER as Feature Attributes
265 <!-- JAL-3375 -->More robust VCF numeric data field
266 validation while parsing
269 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
273 <!-- JAL-3535 -->Feature Settings dialog title includes name
277 <!-- JAL-3538 -->Font anti-aliasing in alignment views
281 <!-- JAL-3468 -->Very long feature descriptions truncated in
285 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
286 with no feature types visible
289 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
291 </ul><em>Jalview Installer</em>
294 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
295 in console (may be null when Jalview launched as executable jar or via conda)
298 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
301 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
304 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
306 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
307 </ul> <em>Release processes</em>
310 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
313 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
315 </ul> <em>Build System</em>
318 <!-- JAL-3510 -->Clover updated to 4.4.1
321 <!-- JAL-3513 -->Test code included in Clover coverage
325 <em>Groovy Scripts</em>
328 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
329 to stdout containing the consensus sequence for each
330 alignment in a Jalview session
333 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
334 genomic sequence_variant annotation from CDS as
335 missense_variant or synonymous_variant on protein products.
339 <td align="left" valign="top">
342 <!-- JAL-3581 -->Hidden sequence markers still visible when
343 'Show hidden markers' option is not ticked
346 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
347 PNG output when 'Automatically set ID width' is set in
348 jalview preferences or properties file
351 <!-- JAL-3571 -->Feature Editor dialog can be opened when
352 'Show Sequence Features' option is not ticked
355 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
356 buttons in Feature Settings dialog are clicked when no
360 <!-- JAL-3412 -->ID margins for CDS and Protein views not
361 equal when split frame is first opened
364 <!-- JAL-3296 -->Sequence position numbers in status bar not
365 correct after editing a sequence's start position
368 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
369 with annotation and exceptions thrown when only a few
370 columns shown in wrapped mode
373 <!-- JAL-3386 -->Sequence IDs missing in headless export of
374 wrapped alignment figure with annotations
377 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
378 ID fails with ClassCastException
381 <!-- JAL-3389 -->Chimera session not restored from Jalview
385 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
386 feature settings dialog also selects columns
389 <!-- JAL-3473 -->SpinnerNumberModel causes
390 IllegalArgumentException in some circumstances
393 <!-- JAL-3534 -->Multiple feature settings dialogs can be
397 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
398 alignment window is closed
401 <!-- JAL-3406 -->Credits missing some authors in Jalview
402 help documentation for 2.11.0 release
405 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
406 includes Pfam ID as sequence's accession rather than its
409 </ul> <em>Java 11 Compatibility issues</em>
412 <!-- JAL-2987 -->OSX - Can't view some search results in
413 PDB/Uniprot search panel
415 </ul> <em>Installer</em>
418 <!-- JAL-3447 -->Jalview should not create file associations
419 for 3D structure files (.pdb, .mmcif. .cif)
421 </ul> <em>Repository and Source Release</em>
424 <!-- JAL-3474 -->removed obsolete .cvsignore files from
428 <!-- JAL-3541 -->Clover report generation running out of
431 </ul> <em>New Known Issues</em>
434 <!-- JAL-3523 -->OSX - Current working directory not
435 preserved when Jalview.app launched with parameters from
439 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
440 clipped in headless figure export when Right Align option
444 <!-- JAL-3542 -->Jalview Installation type always reports
445 'Source' in console output
448 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
449 bamboo server but run fine locally.
455 <td width="60" align="center" nowrap>
456 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
457 <em>04/07/2019</em></strong>
459 <td align="left" valign="top">
462 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
463 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
464 source project) rather than InstallAnywhere
467 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
468 settings, receive over the air updates and launch specific
469 versions via (<a href="https://github.com/threerings/getdown">Three
473 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
474 formats supported by Jalview (including .jvp project files)
477 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
478 arguments and switch between different getdown channels
481 <!-- JAL-3141 -->Backup files created when saving Jalview project
486 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
487 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
489 <!-- JAL-2620 -->Alternative genetic code tables for
490 'Translate as cDNA'</li>
492 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
493 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
496 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
497 implementation that allows updates) used for Sequence Feature collections</li>
499 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
500 features can be filtered and shaded according to any
501 associated attributes (e.g. variant attributes from VCF
502 file, or key-value pairs imported from column 9 of GFF
506 <!-- JAL-2879 -->Feature Attributes and shading schemes
507 stored and restored from Jalview Projects
510 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
511 recognise variant features
514 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
515 sequences (also coloured red by default)
518 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
522 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
523 algorithm (Z-sort/transparency and filter aware)
526 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
532 <!-- JAL-3205 -->Symmetric score matrices for faster
533 tree and PCA calculations
535 <li><strong>Principal Components Analysis Viewer</strong>
538 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
539 and Viewer state saved in Jalview Project
541 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
544 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
548 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
553 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
555 <li><strong>Speed and Efficiency</strong>
558 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
559 multiple groups when working with large alignments
562 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
566 <li><strong>User Interface</strong>
569 <!-- JAL-2933 -->Finder panel remembers last position in each
573 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
574 what is shown)<br />Only visible regions of alignment are shown by
575 default (can be changed in user preferences)
578 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
579 to the Overwrite Dialog
582 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
586 <!-- JAL-1244 -->Status bar shows bounds when dragging a
587 selection region, and gap count when inserting or deleting gaps
590 <!-- JAL-3132 -->Status bar updates over sequence and annotation
594 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
598 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
602 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
605 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
609 <!-- JAL-3181 -->Consistent ordering of links in sequence id
613 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
615 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
619 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
620 <li><strong>Java 11 Support (not yet on general release)</strong>
623 <!-- -->OSX GUI integrations for App menu's 'About' entry and
628 <em>Deprecations</em>
630 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
631 capabilities removed from the Jalview Desktop
633 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
634 unmarshalling has been replaced by JAXB for Jalview projects
635 and XML based data retrieval clients</li>
636 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
637 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
638 </ul> <em>Documentation</em>
640 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
641 not supported in EPS figure export
643 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
644 </ul> <em>Development and Release Processes</em>
647 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
650 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
652 <!-- JAL-3225 -->Eclipse project configuration managed with
656 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
657 Bamboo continuous integration for unattended Test Suite
661 <!-- JAL-2864 -->Memory test suite to detect leaks in common
665 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
669 <!-- JAL-3248 -->Developer documentation migrated to
670 markdown (with HTML rendering)
673 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
676 <!-- JAL-3289 -->New URLs for publishing development
681 <td align="left" valign="top">
684 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
687 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
688 superposition in Jmol fail on Windows
691 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
692 structures for sequences with lots of PDB structures
695 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
699 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
700 project involving multiple views
703 <!-- JAL-3164 -->Overview for complementary view in a linked
704 CDS/Protein alignment is not updated when Hide Columns by
705 Annotation dialog hides columns
708 <!-- JAL-3158 -->Selection highlighting in the complement of a
709 CDS/Protein alignment stops working after making a selection in
710 one view, then making another selection in the other view
713 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
717 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
718 Settings and Jalview Preferences panels
721 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
722 overview with large alignments
725 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
726 region if columns were selected by dragging right-to-left and the
727 mouse moved to the left of the first column
730 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
731 hidden column marker via scale popup menu
734 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
735 doesn't tell users the invalid URL
738 <!-- JAL-2816 -->Tooltips displayed for features filtered by
742 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
743 show cross references or Fetch Database References are shown in
747 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
748 peptide sequence (computed variant shown as p.Res.null)
751 <!-- JAL-2060 -->'Graduated colour' option not offered for
752 manually created features (where feature score is Float.NaN)
755 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
756 when columns are hidden
759 <!-- JAL-3082 -->Regular expression error for '(' in Select
760 Columns by Annotation description
763 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
764 out of Scale or Annotation Panel
767 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
771 <!-- JAL-3074 -->Left/right drag in annotation can scroll
775 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
779 <!-- JAL-3002 -->Column display is out by one after Page Down,
780 Page Up in wrapped mode
783 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
786 <!-- JAL-2932 -->Finder searches in minimised alignments
789 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
790 on opening an alignment
793 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
797 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
798 different groups in the alignment are selected
801 <!-- JAL-2717 -->Internationalised colour scheme names not shown
805 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
809 <!-- JAL-3125 -->Value input for graduated feature colour
810 threshold gets 'unrounded'
813 <!-- JAL-2982 -->PCA image export doesn't respect background
817 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
820 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
823 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
827 <!-- JAL-2964 -->Associate Tree with All Views not restored from
831 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
832 shown in complementary view
835 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
836 without normalisation
839 <!-- JAL-3021 -->Sequence Details report should open positioned at top
843 <!-- JAL-914 -->Help page can be opened twice
846 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
848 </ul> <em>Editing</em>
851 <!-- JAL-2822 -->Start and End should be updated when sequence
852 data at beginning or end of alignment added/removed via 'Edit'
856 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
857 relocate sequence features correctly when start of sequence is
858 removed (Known defect since 2.10)
861 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
862 dialog corrupts dataset sequence
865 <!-- JAL-868 -->Structure colours not updated when associated tree
866 repartitions the alignment view (Regression in 2.10.5)
868 </ul> <em>Datamodel</em>
871 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
872 sequence's End is greater than its length
874 </ul> <em>Bugs fixed for Java 11 Support (not yet on
875 general release)</em>
878 <!-- JAL-3288 -->Menus work properly in split-screen
880 </ul> <em>New Known Defects</em>
883 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
886 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
887 regions of protein alignment.
890 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
891 is restored from a Jalview 2.11 project
894 <!-- JAL-3213 -->Alignment panel height can be too small after
898 <!-- JAL-3240 -->Display is incorrect after removing gapped
899 columns within hidden columns
902 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
903 window after dragging left to select columns to left of visible
907 <!-- JAL-2876 -->Features coloured according to their description
908 string and thresholded by score in earlier versions of Jalview are
909 not shown as thresholded features in 2.11. To workaround please
910 create a Score filter instead.
913 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
915 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
918 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
919 alignments with multiple views can close views unexpectedly
922 <em>Java 11 Specific defects</em>
925 <!-- JAL-3235 -->Jalview Properties file is not sorted
926 alphabetically when saved
932 <td width="60" nowrap>
934 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
937 <td><div align="left">
941 <!-- JAL-3101 -->Default memory for Jalview webstart and
942 InstallAnywhere increased to 1G.
945 <!-- JAL-247 -->Hidden sequence markers and representative
946 sequence bolding included when exporting alignment as EPS,
947 SVG, PNG or HTML. <em>Display is configured via the
948 Format menu, or for command-line use via a Jalview
949 properties file.</em>
952 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
953 API and sequence data now imported as JSON.
956 <!-- JAL-3065 -->Change in recommended way of starting
957 Jalview via a Java command line: add jars in lib directory
958 to CLASSPATH, rather than via the deprecated java.ext.dirs
965 <!-- JAL-3047 -->Support added to execute test suite
966 instrumented with <a href="http://openclover.org/">Open
971 <td><div align="left">
975 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
976 row shown in Feredoxin Structure alignment view of example
980 <!-- JAL-2854 -->Annotation obscures sequences if lots of
981 annotation displayed.
984 <!-- JAL-3107 -->Group conservation/consensus not shown
985 for newly created group when 'Apply to all groups'
989 <!-- JAL-3087 -->Corrupted display when switching to
990 wrapped mode when sequence panel's vertical scrollbar is
994 <!-- JAL-3003 -->Alignment is black in exported EPS file
995 when sequences are selected in exported view.</em>
998 <!-- JAL-3059 -->Groups with different coloured borders
999 aren't rendered with correct colour.
1002 <!-- JAL-3092 -->Jalview could hang when importing certain
1003 types of knotted RNA secondary structure.
1006 <!-- JAL-3095 -->Sequence highlight and selection in
1007 trimmed VARNA 2D structure is incorrect for sequences that
1011 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1012 annotation when columns are inserted into an alignment,
1013 and when exporting as Stockholm flatfile.
1016 <!-- JAL-3053 -->Jalview annotation rows containing upper
1017 and lower-case 'E' and 'H' do not automatically get
1018 treated as RNA secondary structure.
1021 <!-- JAL-3106 -->.jvp should be used as default extension
1022 (not .jar) when saving a Jalview project file.
1025 <!-- JAL-3105 -->Mac Users: closing a window correctly
1026 transfers focus to previous window on OSX
1029 <em>Java 10 Issues Resolved</em>
1032 <!-- JAL-2988 -->OSX - Can't save new files via the File
1033 or export menus by typing in a name into the Save dialog
1037 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1038 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1039 'look and feel' which has improved compatibility with the
1040 latest version of OSX.
1047 <td width="60" nowrap>
1048 <div align="center">
1049 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1050 <em>7/06/2018</em></strong>
1053 <td><div align="left">
1057 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1058 annotation retrieved from Uniprot
1061 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1062 onto the Jalview Desktop
1066 <td><div align="left">
1070 <!-- JAL-3017 -->Cannot import features with multiple
1071 variant elements (blocks import of some Uniprot records)
1074 <!-- JAL-2997 -->Clustal files with sequence positions in
1075 right-hand column parsed correctly
1078 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1079 not alignment area in exported graphic
1082 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1083 window has input focus
1086 <!-- JAL-2992 -->Annotation panel set too high when
1087 annotation added to view (Windows)
1090 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1091 network connectivity is poor
1094 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1095 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1096 the currently open URL and links from a page viewed in
1097 Firefox or Chrome on Windows is now fully supported. If
1098 you are using Edge, only links in the page can be
1099 dragged, and with Internet Explorer, only the currently
1100 open URL in the browser can be dropped onto Jalview.</em>
1103 <em>New Known Defects</em>
1105 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1110 <td width="60" nowrap>
1111 <div align="center">
1112 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1115 <td><div align="left">
1119 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1120 for disabling automatic superposition of multiple
1121 structures and open structures in existing views
1124 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1125 ID and annotation area margins can be click-dragged to
1129 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1133 <!-- JAL-2759 -->Improved performance for large alignments
1134 and lots of hidden columns
1137 <!-- JAL-2593 -->Improved performance when rendering lots
1138 of features (particularly when transparency is disabled)
1141 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1142 exchange of Jalview features and Chimera attributes made
1148 <td><div align="left">
1151 <!-- JAL-2899 -->Structure and Overview aren't updated
1152 when Colour By Annotation threshold slider is adjusted
1155 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1156 overlapping alignment panel
1159 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1163 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1164 improved: CDS not handled correctly if transcript has no
1168 <!-- JAL-2321 -->Secondary structure and temperature
1169 factor annotation not added to sequence when local PDB
1170 file associated with it by drag'n'drop or structure
1174 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1175 dialog doesn't import PDB files dropped on an alignment
1178 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1179 scroll bar doesn't work for some CDS/Protein views
1182 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1183 Java 1.8u153 onwards and Java 1.9u4+.
1186 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1187 columns in annotation row
1190 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1191 honored in batch mode
1194 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1195 for structures added to existing Jmol view
1198 <!-- JAL-2223 -->'View Mappings' includes duplicate
1199 entries after importing project with multiple views
1202 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1203 protein sequences via SIFTS from associated PDB entries
1204 with negative residue numbers or missing residues fails
1207 <!-- JAL-2952 -->Exception when shading sequence with negative
1208 Temperature Factor values from annotated PDB files (e.g.
1209 as generated by CONSURF)
1212 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1213 tooltip doesn't include a text description of mutation
1216 <!-- JAL-2922 -->Invert displayed features very slow when
1217 structure and/or overview windows are also shown
1220 <!-- JAL-2954 -->Selecting columns from highlighted regions
1221 very slow for alignments with large numbers of sequences
1224 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1225 with 'StringIndexOutOfBounds'
1228 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1229 platforms running Java 10
1232 <!-- JAL-2960 -->Adding a structure to existing structure
1233 view appears to do nothing because the view is hidden behind the alignment view
1239 <!-- JAL-2926 -->Copy consensus sequence option in applet
1240 should copy the group consensus when popup is opened on it
1246 <!-- JAL-2913 -->Fixed ID width preference is not respected
1249 <em>New Known Defects</em>
1252 <!-- JAL-2973 --> Exceptions occasionally raised when
1253 editing a large alignment and overview is displayed
1256 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1257 repeatedly after a series of edits even when the overview
1258 is no longer reflecting updates
1261 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1262 structures for protein subsequence (if 'Trim Retrieved
1263 Sequences' enabled) or Ensembl isoforms (Workaround in
1264 2.10.4 is to fail back to N&W mapping)
1267 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1268 option gives blank output
1275 <td width="60" nowrap>
1276 <div align="center">
1277 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1280 <td><div align="left">
1281 <ul><li>Updated Certum Codesigning Certificate
1282 (Valid till 30th November 2018)</li></ul></div></td>
1283 <td><div align="left">
1284 <em>Desktop</em><ul>
1286 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1287 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1288 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1289 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1290 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1291 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1292 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1298 <td width="60" nowrap>
1299 <div align="center">
1300 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1303 <td><div align="left">
1307 <!-- JAL-2446 -->Faster and more efficient management and
1308 rendering of sequence features
1311 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1312 429 rate limit request hander
1315 <!-- JAL-2773 -->Structure views don't get updated unless
1316 their colours have changed
1319 <!-- JAL-2495 -->All linked sequences are highlighted for
1320 a structure mousover (Jmol) or selection (Chimera)
1323 <!-- JAL-2790 -->'Cancel' button in progress bar for
1324 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1327 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1328 view from Ensembl locus cross-references
1331 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1335 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1336 feature can be disabled
1339 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1340 PDB easier retrieval of sequences for lists of IDs
1343 <!-- JAL-2758 -->Short names for sequences retrieved from
1349 <li>Groovy interpreter updated to 2.4.12</li>
1350 <li>Example groovy script for generating a matrix of
1351 percent identity scores for current alignment.</li>
1353 <em>Testing and Deployment</em>
1356 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1360 <td><div align="left">
1364 <!-- JAL-2643 -->Pressing tab after updating the colour
1365 threshold text field doesn't trigger an update to the
1369 <!-- JAL-2682 -->Race condition when parsing sequence ID
1373 <!-- JAL-2608 -->Overview windows are also closed when
1374 alignment window is closed
1377 <!-- JAL-2548 -->Export of features doesn't always respect
1381 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1382 takes a long time in Cursor mode
1388 <!-- JAL-2777 -->Structures with whitespace chainCode
1389 cannot be viewed in Chimera
1392 <!-- JAL-2728 -->Protein annotation panel too high in
1396 <!-- JAL-2757 -->Can't edit the query after the server
1397 error warning icon is shown in Uniprot and PDB Free Text
1401 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1404 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1407 <!-- JAL-2739 -->Hidden column marker in last column not
1408 rendered when switching back from Wrapped to normal view
1411 <!-- JAL-2768 -->Annotation display corrupted when
1412 scrolling right in unwapped alignment view
1415 <!-- JAL-2542 -->Existing features on subsequence
1416 incorrectly relocated when full sequence retrieved from
1420 <!-- JAL-2733 -->Last reported memory still shown when
1421 Desktop->Show Memory is unticked (OSX only)
1424 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1425 features of same type and group to be selected for
1429 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1430 alignments when hidden columns are present
1433 <!-- JAL-2392 -->Jalview freezes when loading and
1434 displaying several structures
1437 <!-- JAL-2732 -->Black outlines left after resizing or
1441 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1442 within the Jalview desktop on OSX
1445 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1446 when in wrapped alignment mode
1449 <!-- JAL-2636 -->Scale mark not shown when close to right
1450 hand end of alignment
1453 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1454 each selected sequence do not have correct start/end
1458 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1459 after canceling the Alignment Window's Font dialog
1462 <!-- JAL-2036 -->Show cross-references not enabled after
1463 restoring project until a new view is created
1466 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1467 URL links appears when only default EMBL-EBI link is
1468 configured (since 2.10.2b2)
1471 <!-- JAL-2775 -->Overview redraws whole window when box
1472 position is adjusted
1475 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1476 in a multi-chain structure when viewing alignment
1477 involving more than one chain (since 2.10)
1480 <!-- JAL-2811 -->Double residue highlights in cursor mode
1481 if new selection moves alignment window
1484 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1485 arrow key in cursor mode to pass hidden column marker
1488 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1489 that produces correctly annotated transcripts and products
1492 <!-- JAL-2776 -->Toggling a feature group after first time
1493 doesn't update associated structure view
1496 <em>Applet</em><br />
1499 <!-- JAL-2687 -->Concurrent modification exception when
1500 closing alignment panel
1503 <em>BioJSON</em><br />
1506 <!-- JAL-2546 -->BioJSON export does not preserve
1507 non-positional features
1510 <em>New Known Issues</em>
1513 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1514 sequence features correctly (for many previous versions of
1518 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1519 using cursor in wrapped panel other than top
1522 <!-- JAL-2791 -->Select columns containing feature ignores
1523 graduated colour threshold
1526 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1527 always preserve numbering and sequence features
1530 <em>Known Java 9 Issues</em>
1533 <!-- JAL-2902 -->Groovy Console very slow to open and is
1534 not responsive when entering characters (Webstart, Java
1541 <td width="60" nowrap>
1542 <div align="center">
1543 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1544 <em>2/10/2017</em></strong>
1547 <td><div align="left">
1548 <em>New features in Jalview Desktop</em>
1551 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1553 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1557 <td><div align="left">
1561 <td width="60" nowrap>
1562 <div align="center">
1563 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1564 <em>7/9/2017</em></strong>
1567 <td><div align="left">
1571 <!-- JAL-2588 -->Show gaps in overview window by colouring
1572 in grey (sequences used to be coloured grey, and gaps were
1576 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1580 <!-- JAL-2587 -->Overview updates immediately on increase
1581 in size and progress bar shown as higher resolution
1582 overview is recalculated
1587 <td><div align="left">
1591 <!-- JAL-2664 -->Overview window redraws every hidden
1592 column region row by row
1595 <!-- JAL-2681 -->duplicate protein sequences shown after
1596 retrieving Ensembl crossrefs for sequences from Uniprot
1599 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1600 format setting is unticked
1603 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1604 if group has show boxes format setting unticked
1607 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1608 autoscrolling whilst dragging current selection group to
1609 include sequences and columns not currently displayed
1612 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1613 assemblies are imported via CIF file
1616 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1617 displayed when threshold or conservation colouring is also
1621 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1625 <!-- JAL-2673 -->Jalview continues to scroll after
1626 dragging a selected region off the visible region of the
1630 <!-- JAL-2724 -->Cannot apply annotation based
1631 colourscheme to all groups in a view
1634 <!-- JAL-2511 -->IDs don't line up with sequences
1635 initially after font size change using the Font chooser or
1642 <td width="60" nowrap>
1643 <div align="center">
1644 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1647 <td><div align="left">
1648 <em>Calculations</em>
1652 <!-- JAL-1933 -->Occupancy annotation row shows number of
1653 ungapped positions in each column of the alignment.
1656 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1657 a calculation dialog box
1660 <!-- JAL-2379 -->Revised implementation of PCA for speed
1661 and memory efficiency (~30x faster)
1664 <!-- JAL-2403 -->Revised implementation of sequence
1665 similarity scores as used by Tree, PCA, Shading Consensus
1666 and other calculations
1669 <!-- JAL-2416 -->Score matrices are stored as resource
1670 files within the Jalview codebase
1673 <!-- JAL-2500 -->Trees computed on Sequence Feature
1674 Similarity may have different topology due to increased
1681 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1682 model for alignments and groups
1685 <!-- JAL-384 -->Custom shading schemes created via groovy
1692 <!-- JAL-2526 -->Efficiency improvements for interacting
1693 with alignment and overview windows
1696 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1700 <!-- JAL-2388 -->Hidden columns and sequences can be
1704 <!-- JAL-2611 -->Click-drag in visible area allows fine
1705 adjustment of visible position
1709 <em>Data import/export</em>
1712 <!-- JAL-2535 -->Posterior probability annotation from
1713 Stockholm files imported as sequence associated annotation
1716 <!-- JAL-2507 -->More robust per-sequence positional
1717 annotation input/output via stockholm flatfile
1720 <!-- JAL-2533 -->Sequence names don't include file
1721 extension when importing structure files without embedded
1722 names or PDB accessions
1725 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1726 format sequence substitution matrices
1729 <em>User Interface</em>
1732 <!-- JAL-2447 --> Experimental Features Checkbox in
1733 Desktop's Tools menu to hide or show untested features in
1737 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1738 via Overview or sequence motif search operations
1741 <!-- JAL-2547 -->Amend sequence features dialog box can be
1742 opened by double clicking gaps within sequence feature
1746 <!-- JAL-1476 -->Status bar message shown when not enough
1747 aligned positions were available to create a 3D structure
1751 <em>3D Structure</em>
1754 <!-- JAL-2430 -->Hidden regions in alignment views are not
1755 coloured in linked structure views
1758 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1759 file-based command exchange
1762 <!-- JAL-2375 -->Structure chooser automatically shows
1763 Cached Structures rather than querying the PDBe if
1764 structures are already available for sequences
1767 <!-- JAL-2520 -->Structures imported via URL are cached in
1768 the Jalview project rather than downloaded again when the
1769 project is reopened.
1772 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1773 to transfer Chimera's structure attributes as Jalview
1774 features, and vice-versa (<strong>Experimental
1778 <em>Web Services</em>
1781 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1784 <!-- JAL-2335 -->Filter non-standard amino acids and
1785 nucleotides when submitting to AACon and other MSA
1789 <!-- JAL-2316, -->URLs for viewing database
1790 cross-references provided by identifiers.org and the
1791 EMBL-EBI's MIRIAM DB
1798 <!-- JAL-2344 -->FileFormatI interface for describing and
1799 identifying file formats (instead of String constants)
1802 <!-- JAL-2228 -->FeatureCounter script refactored for
1803 efficiency when counting all displayed features (not
1804 backwards compatible with 2.10.1)
1807 <em>Example files</em>
1810 <!-- JAL-2631 -->Graduated feature colour style example
1811 included in the example feature file
1814 <em>Documentation</em>
1817 <!-- JAL-2339 -->Release notes reformatted for readability
1818 with the built-in Java help viewer
1821 <!-- JAL-1644 -->Find documentation updated with 'search
1822 sequence description' option
1828 <!-- JAL-2485, -->External service integration tests for
1829 Uniprot REST Free Text Search Client
1832 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1835 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1840 <td><div align="left">
1841 <em>Calculations</em>
1844 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1845 matrix - C->R should be '-3'<br />Old matrix restored
1846 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1848 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1849 Jalview's treatment of gaps in PCA and substitution matrix
1850 based Tree calculations.<br /> <br />In earlier versions
1851 of Jalview, gaps matching gaps were penalised, and gaps
1852 matching non-gaps penalised even more. In the PCA
1853 calculation, gaps were actually treated as non-gaps - so
1854 different costs were applied, which meant Jalview's PCAs
1855 were different to those produced by SeqSpace.<br />Jalview
1856 now treats gaps in the same way as SeqSpace (ie it scores
1857 them as 0). <br /> <br />Enter the following in the
1858 Groovy console to restore pre-2.10.2 behaviour:<br />
1859 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1860 // for 2.10.1 mode <br />
1861 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1862 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1863 these settings will affect all subsequent tree and PCA
1864 calculations (not recommended)</em></li>
1866 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1867 scaling of branch lengths for trees computed using
1868 Sequence Feature Similarity.
1871 <!-- JAL-2377 -->PCA calculation could hang when
1872 generating output report when working with highly
1873 redundant alignments
1876 <!-- JAL-2544 --> Sort by features includes features to
1877 right of selected region when gaps present on right-hand
1881 <em>User Interface</em>
1884 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1885 doesn't reselect a specific sequence's associated
1886 annotation after it was used for colouring a view
1889 <!-- JAL-2419 -->Current selection lost if popup menu
1890 opened on a region of alignment without groups
1893 <!-- JAL-2374 -->Popup menu not always shown for regions
1894 of an alignment with overlapping groups
1897 <!-- JAL-2310 -->Finder double counts if both a sequence's
1898 name and description match
1901 <!-- JAL-2370 -->Hiding column selection containing two
1902 hidden regions results in incorrect hidden regions
1905 <!-- JAL-2386 -->'Apply to all groups' setting when
1906 changing colour does not apply Conservation slider value
1910 <!-- JAL-2373 -->Percentage identity and conservation menu
1911 items do not show a tick or allow shading to be disabled
1914 <!-- JAL-2385 -->Conservation shading or PID threshold
1915 lost when base colourscheme changed if slider not visible
1918 <!-- JAL-2547 -->Sequence features shown in tooltip for
1919 gaps before start of features
1922 <!-- JAL-2623 -->Graduated feature colour threshold not
1923 restored to UI when feature colour is edited
1926 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1927 a time when scrolling vertically in wrapped mode.
1930 <!-- JAL-2630 -->Structure and alignment overview update
1931 as graduate feature colour settings are modified via the
1935 <!-- JAL-2034 -->Overview window doesn't always update
1936 when a group defined on the alignment is resized
1939 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1940 wrapped view result in positional status updates
1944 <!-- JAL-2563 -->Status bar doesn't show position for
1945 ambiguous amino acid and nucleotide symbols
1948 <!-- JAL-2602 -->Copy consensus sequence failed if
1949 alignment included gapped columns
1952 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1953 widgets don't permanently disappear
1956 <!-- JAL-2503 -->Cannot select or filter quantitative
1957 annotation that are shown only as column labels (e.g.
1958 T-Coffee column reliability scores)
1961 <!-- JAL-2594 -->Exception thrown if trying to create a
1962 sequence feature on gaps only
1965 <!-- JAL-2504 -->Features created with 'New feature'
1966 button from a Find inherit previously defined feature type
1967 rather than the Find query string
1970 <!-- JAL-2423 -->incorrect title in output window when
1971 exporting tree calculated in Jalview
1974 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1975 and then revealing them reorders sequences on the
1979 <!-- JAL-964 -->Group panel in sequence feature settings
1980 doesn't update to reflect available set of groups after
1981 interactively adding or modifying features
1984 <!-- JAL-2225 -->Sequence Database chooser unusable on
1988 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1989 only excluded gaps in current sequence and ignored
1996 <!-- JAL-2421 -->Overview window visible region moves
1997 erratically when hidden rows or columns are present
2000 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2001 Structure Viewer's colour menu don't correspond to
2005 <!-- JAL-2405 -->Protein specific colours only offered in
2006 colour and group colour menu for protein alignments
2009 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2010 reflect currently selected view or group's shading
2014 <!-- JAL-2624 -->Feature colour thresholds not respected
2015 when rendered on overview and structures when opacity at
2019 <!-- JAL-2589 -->User defined gap colour not shown in
2020 overview when features overlaid on alignment
2023 <!-- JAL-2567 -->Feature settings for different views not
2024 recovered correctly from Jalview project file
2027 <!-- JAL-2256 -->Feature colours in overview when first opened
2028 (automatically via preferences) are different to the main
2032 <em>Data import/export</em>
2035 <!-- JAL-2576 -->Very large alignments take a long time to
2039 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2040 added after a sequence was imported are not written to
2044 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2045 when importing RNA secondary structure via Stockholm
2048 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2049 not shown in correct direction for simple pseudoknots
2052 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2053 with lightGray or darkGray via features file (but can
2057 <!-- JAL-2383 -->Above PID colour threshold not recovered
2058 when alignment view imported from project
2061 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2062 structure and sequences extracted from structure files
2063 imported via URL and viewed in Jmol
2066 <!-- JAL-2520 -->Structures loaded via URL are saved in
2067 Jalview Projects rather than fetched via URL again when
2068 the project is loaded and the structure viewed
2071 <em>Web Services</em>
2074 <!-- JAL-2519 -->EnsemblGenomes example failing after
2075 release of Ensembl v.88
2078 <!-- JAL-2366 -->Proxy server address and port always
2079 appear enabled in Preferences->Connections
2082 <!-- JAL-2461 -->DAS registry not found exceptions
2083 removed from console output
2086 <!-- JAL-2582 -->Cannot retrieve protein products from
2087 Ensembl by Peptide ID
2090 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2091 created from SIFTs, and spurious 'Couldn't open structure
2092 in Chimera' errors raised after April 2017 update (problem
2093 due to 'null' string rather than empty string used for
2094 residues with no corresponding PDB mapping).
2097 <em>Application UI</em>
2100 <!-- JAL-2361 -->User Defined Colours not added to Colour
2104 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2105 case' residues (button in colourscheme editor debugged and
2106 new documentation and tooltips added)
2109 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2110 doesn't restore group-specific text colour thresholds
2113 <!-- JAL-2243 -->Feature settings panel does not update as
2114 new features are added to alignment
2117 <!-- JAL-2532 -->Cancel in feature settings reverts
2118 changes to feature colours via the Amend features dialog
2121 <!-- JAL-2506 -->Null pointer exception when attempting to
2122 edit graduated feature colour via amend features dialog
2126 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2127 selection menu changes colours of alignment views
2130 <!-- JAL-2426 -->Spurious exceptions in console raised
2131 from alignment calculation workers after alignment has
2135 <!-- JAL-1608 -->Typo in selection popup menu - Create
2136 groups now 'Create Group'
2139 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2140 Create/Undefine group doesn't always work
2143 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2144 shown again after pressing 'Cancel'
2147 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2148 adjusts start position in wrap mode
2151 <!-- JAL-2563 -->Status bar doesn't show positions for
2152 ambiguous amino acids
2155 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2156 CDS/Protein view after CDS sequences added for aligned
2160 <!-- JAL-2592 -->User defined colourschemes called 'User
2161 Defined' don't appear in Colours menu
2167 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2168 score models doesn't always result in an updated PCA plot
2171 <!-- JAL-2442 -->Features not rendered as transparent on
2172 overview or linked structure view
2175 <!-- JAL-2372 -->Colour group by conservation doesn't
2179 <!-- JAL-2517 -->Hitting Cancel after applying
2180 user-defined colourscheme doesn't restore original
2187 <!-- JAL-2314 -->Unit test failure:
2188 jalview.ws.jabaws.RNAStructExportImport setup fails
2191 <!-- JAL-2307 -->Unit test failure:
2192 jalview.ws.sifts.SiftsClientTest due to compatibility
2193 problems with deep array comparison equality asserts in
2194 successive versions of TestNG
2197 <!-- JAL-2479 -->Relocated StructureChooserTest and
2198 ParameterUtilsTest Unit tests to Network suite
2201 <em>New Known Issues</em>
2204 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2205 phase after a sequence motif find operation
2208 <!-- JAL-2550 -->Importing annotation file with rows
2209 containing just upper and lower case letters are
2210 interpreted as WUSS RNA secondary structure symbols
2213 <!-- JAL-2590 -->Cannot load and display Newick trees
2214 reliably from eggnog Ortholog database
2217 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2218 containing features of type Highlight' when 'B' is pressed
2219 to mark columns containing highlighted regions.
2222 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2223 doesn't always add secondary structure annotation.
2228 <td width="60" nowrap>
2229 <div align="center">
2230 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2233 <td><div align="left">
2237 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2238 for all consensus calculations
2241 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2244 <li>Updated Jalview's Certum code signing certificate
2247 <em>Application</em>
2250 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2251 set of database cross-references, sorted alphabetically
2254 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2255 from database cross references. Users with custom links
2256 will receive a <a href="webServices/urllinks.html#warning">warning
2257 dialog</a> asking them to update their preferences.
2260 <!-- JAL-2287-->Cancel button and escape listener on
2261 dialog warning user about disconnecting Jalview from a
2265 <!-- JAL-2320-->Jalview's Chimera control window closes if
2266 the Chimera it is connected to is shut down
2269 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2270 columns menu item to mark columns containing highlighted
2271 regions (e.g. from structure selections or results of a
2275 <!-- JAL-2284-->Command line option for batch-generation
2276 of HTML pages rendering alignment data with the BioJS
2286 <!-- JAL-2286 -->Columns with more than one modal residue
2287 are not coloured or thresholded according to percent
2288 identity (first observed in Jalview 2.8.2)
2291 <!-- JAL-2301 -->Threonine incorrectly reported as not
2295 <!-- JAL-2318 -->Updates to documentation pages (above PID
2296 threshold, amino acid properties)
2299 <!-- JAL-2292 -->Lower case residues in sequences are not
2300 reported as mapped to residues in a structure file in the
2304 <!--JAL-2324 -->Identical features with non-numeric scores
2305 could be added multiple times to a sequence
2308 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2309 bond features shown as two highlighted residues rather
2310 than a range in linked structure views, and treated
2311 correctly when selecting and computing trees from features
2314 <!-- JAL-2281-->Custom URL links for database
2315 cross-references are matched to database name regardless
2320 <em>Application</em>
2323 <!-- JAL-2282-->Custom URL links for specific database
2324 names without regular expressions also offer links from
2328 <!-- JAL-2315-->Removing a single configured link in the
2329 URL links pane in Connections preferences doesn't actually
2330 update Jalview configuration
2333 <!-- JAL-2272-->CTRL-Click on a selected region to open
2334 the alignment area popup menu doesn't work on El-Capitan
2337 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2338 files with similarly named sequences if dropped onto the
2342 <!-- JAL-2312 -->Additional mappings are shown for PDB
2343 entries where more chains exist in the PDB accession than
2344 are reported in the SIFTS file
2347 <!-- JAL-2317-->Certain structures do not get mapped to
2348 the structure view when displayed with Chimera
2351 <!-- JAL-2317-->No chains shown in the Chimera view
2352 panel's View->Show Chains submenu
2355 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2356 work for wrapped alignment views
2359 <!--JAL-2197 -->Rename UI components for running JPred
2360 predictions from 'JNet' to 'JPred'
2363 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2364 corrupted when annotation panel vertical scroll is not at
2365 first annotation row
2368 <!--JAL-2332 -->Attempting to view structure for Hen
2369 lysozyme results in a PDB Client error dialog box
2372 <!-- JAL-2319 -->Structure View's mapping report switched
2373 ranges for PDB and sequence for SIFTS
2376 SIFTS 'Not_Observed' residues mapped to non-existant
2380 <!-- <em>New Known Issues</em>
2387 <td width="60" nowrap>
2388 <div align="center">
2389 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2390 <em>25/10/2016</em></strong>
2393 <td><em>Application</em>
2395 <li>3D Structure chooser opens with 'Cached structures'
2396 view if structures already loaded</li>
2397 <li>Progress bar reports models as they are loaded to
2398 structure views</li>
2404 <li>Colour by conservation always enabled and no tick
2405 shown in menu when BLOSUM or PID shading applied</li>
2406 <li>FER1_ARATH and FER2_ARATH labels were switched in
2407 example sequences/projects/trees</li>
2409 <em>Application</em>
2411 <li>Jalview projects with views of local PDB structure
2412 files saved on Windows cannot be opened on OSX</li>
2413 <li>Multiple structure views can be opened and superposed
2414 without timeout for structures with multiple models or
2415 multiple sequences in alignment</li>
2416 <li>Cannot import or associated local PDB files without a
2417 PDB ID HEADER line</li>
2418 <li>RMSD is not output in Jmol console when superposition
2420 <li>Drag and drop of URL from Browser fails for Linux and
2421 OSX versions earlier than El Capitan</li>
2422 <li>ENA client ignores invalid content from ENA server</li>
2423 <li>Exceptions are not raised in console when ENA client
2424 attempts to fetch non-existent IDs via Fetch DB Refs UI
2426 <li>Exceptions are not raised in console when a new view
2427 is created on the alignment</li>
2428 <li>OSX right-click fixed for group selections: CMD-click
2429 to insert/remove gaps in groups and CTRL-click to open group
2432 <em>Build and deployment</em>
2434 <li>URL link checker now copes with multi-line anchor
2437 <em>New Known Issues</em>
2439 <li>Drag and drop from URL links in browsers do not work
2446 <td width="60" nowrap>
2447 <div align="center">
2448 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2451 <td><em>General</em>
2454 <!-- JAL-2124 -->Updated Spanish translations.
2457 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2458 for importing structure data to Jalview. Enables mmCIF and
2462 <!-- JAL-192 --->Alignment ruler shows positions relative to
2466 <!-- JAL-2202 -->Position/residue shown in status bar when
2467 mousing over sequence associated annotation
2470 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2474 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2475 '()', canonical '[]' and invalid '{}' base pair populations
2479 <!-- JAL-2092 -->Feature settings popup menu options for
2480 showing or hiding columns containing a feature
2483 <!-- JAL-1557 -->Edit selected group by double clicking on
2484 group and sequence associated annotation labels
2487 <!-- JAL-2236 -->Sequence name added to annotation label in
2488 select/hide columns by annotation and colour by annotation
2492 </ul> <em>Application</em>
2495 <!-- JAL-2050-->Automatically hide introns when opening a
2496 gene/transcript view
2499 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2503 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2504 structure mappings with the EMBL-EBI PDBe SIFTS database
2507 <!-- JAL-2079 -->Updated download sites used for Rfam and
2508 Pfam sources to xfam.org
2511 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2514 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2515 over sequences in Jalview
2518 <!-- JAL-2027-->Support for reverse-complement coding
2519 regions in ENA and EMBL
2522 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2523 for record retrieval via ENA rest API
2526 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2530 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2531 groovy script execution
2534 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2535 alignment window's Calculate menu
2538 <!-- JAL-1812 -->Allow groovy scripts that call
2539 Jalview.getAlignFrames() to run in headless mode
2542 <!-- JAL-2068 -->Support for creating new alignment
2543 calculation workers from groovy scripts
2546 <!-- JAL-1369 --->Store/restore reference sequence in
2550 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2551 associations are now saved/restored from project
2554 <!-- JAL-1993 -->Database selection dialog always shown
2555 before sequence fetcher is opened
2558 <!-- JAL-2183 -->Double click on an entry in Jalview's
2559 database chooser opens a sequence fetcher
2562 <!-- JAL-1563 -->Free-text search client for UniProt using
2563 the UniProt REST API
2566 <!-- JAL-2168 -->-nonews command line parameter to prevent
2567 the news reader opening
2570 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2571 querying stored in preferences
2574 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2578 <!-- JAL-1977-->Tooltips shown on database chooser
2581 <!-- JAL-391 -->Reverse complement function in calculate
2582 menu for nucleotide sequences
2585 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2586 and feature counts preserves alignment ordering (and
2587 debugged for complex feature sets).
2590 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2591 viewing structures with Jalview 2.10
2594 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2595 genome, transcript CCDS and gene ids via the Ensembl and
2596 Ensembl Genomes REST API
2599 <!-- JAL-2049 -->Protein sequence variant annotation
2600 computed for 'sequence_variant' annotation on CDS regions
2604 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2608 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2609 Ref Fetcher fails to match, or otherwise updates sequence
2610 data from external database records.
2613 <!-- JAL-2154 -->Revised Jalview Project format for
2614 efficient recovery of sequence coding and alignment
2615 annotation relationships.
2617 </ul> <!-- <em>Applet</em>
2628 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2632 <!-- JAL-2018-->Export features in Jalview format (again)
2633 includes graduated colourschemes
2636 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2637 working with big alignments and lots of hidden columns
2640 <!-- JAL-2053-->Hidden column markers not always rendered
2641 at right of alignment window
2644 <!-- JAL-2067 -->Tidied up links in help file table of
2648 <!-- JAL-2072 -->Feature based tree calculation not shown
2652 <!-- JAL-2075 -->Hidden columns ignored during feature
2653 based tree calculation
2656 <!-- JAL-2065 -->Alignment view stops updating when show
2657 unconserved enabled for group on alignment
2660 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2664 <!-- JAL-2146 -->Alignment column in status incorrectly
2665 shown as "Sequence position" when mousing over
2669 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2670 hidden columns present
2673 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2674 user created annotation added to alignment
2677 <!-- JAL-1841 -->RNA Structure consensus only computed for
2678 '()' base pair annotation
2681 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2682 in zero scores for all base pairs in RNA Structure
2686 <!-- JAL-2174-->Extend selection with columns containing
2690 <!-- JAL-2275 -->Pfam format writer puts extra space at
2691 beginning of sequence
2694 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2698 <!-- JAL-2238 -->Cannot create groups on an alignment from
2699 from a tree when t-coffee scores are shown
2702 <!-- JAL-1836,1967 -->Cannot import and view PDB
2703 structures with chains containing negative resnums (4q4h)
2706 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2710 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2711 to Clustal, PIR and PileUp output
2714 <!-- JAL-2008 -->Reordering sequence features that are
2715 not visible causes alignment window to repaint
2718 <!-- JAL-2006 -->Threshold sliders don't work in
2719 graduated colour and colour by annotation row for e-value
2720 scores associated with features and annotation rows
2723 <!-- JAL-1797 -->amino acid physicochemical conservation
2724 calculation should be case independent
2727 <!-- JAL-2173 -->Remove annotation also updates hidden
2731 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2732 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2733 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2736 <!-- JAL-2065 -->Null pointer exceptions and redraw
2737 problems when reference sequence defined and 'show
2738 non-conserved' enabled
2741 <!-- JAL-1306 -->Quality and Conservation are now shown on
2742 load even when Consensus calculation is disabled
2745 <!-- JAL-1932 -->Remove right on penultimate column of
2746 alignment does nothing
2749 <em>Application</em>
2752 <!-- JAL-1552-->URLs and links can't be imported by
2753 drag'n'drop on OSX when launched via webstart (note - not
2754 yet fixed for El Capitan)
2757 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2758 output when running on non-gb/us i18n platforms
2761 <!-- JAL-1944 -->Error thrown when exporting a view with
2762 hidden sequences as flat-file alignment
2765 <!-- JAL-2030-->InstallAnywhere distribution fails when
2769 <!-- JAL-2080-->Jalview very slow to launch via webstart
2770 (also hotfix for 2.9.0b2)
2773 <!-- JAL-2085 -->Cannot save project when view has a
2774 reference sequence defined
2777 <!-- JAL-1011 -->Columns are suddenly selected in other
2778 alignments and views when revealing hidden columns
2781 <!-- JAL-1989 -->Hide columns not mirrored in complement
2782 view in a cDNA/Protein splitframe
2785 <!-- JAL-1369 -->Cannot save/restore representative
2786 sequence from project when only one sequence is
2790 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2791 in Structure Chooser
2794 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2795 structure consensus didn't refresh annotation panel
2798 <!-- JAL-1962 -->View mapping in structure view shows
2799 mappings between sequence and all chains in a PDB file
2802 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2803 dialogs format columns correctly, don't display array
2804 data, sort columns according to type
2807 <!-- JAL-1975 -->Export complete shown after destination
2808 file chooser is cancelled during an image export
2811 <!-- JAL-2025 -->Error when querying PDB Service with
2812 sequence name containing special characters
2815 <!-- JAL-2024 -->Manual PDB structure querying should be
2819 <!-- JAL-2104 -->Large tooltips with broken HTML
2820 formatting don't wrap
2823 <!-- JAL-1128 -->Figures exported from wrapped view are
2824 truncated so L looks like I in consensus annotation
2827 <!-- JAL-2003 -->Export features should only export the
2828 currently displayed features for the current selection or
2832 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2833 after fetching cross-references, and restoring from
2837 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2838 followed in the structure viewer
2841 <!-- JAL-2163 -->Titles for individual alignments in
2842 splitframe not restored from project
2845 <!-- JAL-2145 -->missing autocalculated annotation at
2846 trailing end of protein alignment in transcript/product
2847 splitview when pad-gaps not enabled by default
2850 <!-- JAL-1797 -->amino acid physicochemical conservation
2854 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2855 article has been read (reopened issue due to
2856 internationalisation problems)
2859 <!-- JAL-1960 -->Only offer PDB structures in structure
2860 viewer based on sequence name, PDB and UniProt
2865 <!-- JAL-1976 -->No progress bar shown during export of
2869 <!-- JAL-2213 -->Structures not always superimposed after
2870 multiple structures are shown for one or more sequences.
2873 <!-- JAL-1370 -->Reference sequence characters should not
2874 be replaced with '.' when 'Show unconserved' format option
2878 <!-- JAL-1823 -->Cannot specify chain code when entering
2879 specific PDB id for sequence
2882 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2883 'Export hidden sequences' is enabled, but 'export hidden
2884 columns' is disabled.
2887 <!--JAL-2026-->Best Quality option in structure chooser
2888 selects lowest rather than highest resolution structures
2892 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2893 to sequence mapping in 'View Mappings' report
2896 <!-- JAL-2284 -->Unable to read old Jalview projects that
2897 contain non-XML data added after Jalvew wrote project.
2900 <!-- JAL-2118 -->Newly created annotation row reorders
2901 after clicking on it to create new annotation for a
2905 <!-- JAL-1980 -->Null Pointer Exception raised when
2906 pressing Add on an orphaned cut'n'paste window.
2908 <!-- may exclude, this is an external service stability issue JAL-1941
2909 -- > RNA 3D structure not added via DSSR service</li> -->
2914 <!-- JAL-2151 -->Incorrect columns are selected when
2915 hidden columns present before start of sequence
2918 <!-- JAL-1986 -->Missing dependencies on applet pages
2922 <!-- JAL-1947 -->Overview pixel size changes when
2923 sequences are hidden in applet
2926 <!-- JAL-1996 -->Updated instructions for applet
2927 deployment on examples pages.
2934 <td width="60" nowrap>
2935 <div align="center">
2936 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2937 <em>16/10/2015</em></strong>
2940 <td><em>General</em>
2942 <li>Time stamps for signed Jalview application and applet
2947 <em>Application</em>
2949 <li>Duplicate group consensus and conservation rows
2950 shown when tree is partitioned</li>
2951 <li>Erratic behaviour when tree partitions made with
2952 multiple cDNA/Protein split views</li>
2958 <td width="60" nowrap>
2959 <div align="center">
2960 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2961 <em>8/10/2015</em></strong>
2964 <td><em>General</em>
2966 <li>Updated Spanish translations of localized text for
2968 </ul> <em>Application</em>
2970 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2971 <li>Signed OSX InstallAnywhere installer<br></li>
2972 <li>Support for per-sequence based annotations in BioJSON</li>
2973 </ul> <em>Applet</em>
2975 <li>Split frame example added to applet examples page</li>
2976 </ul> <em>Build and Deployment</em>
2979 <!-- JAL-1888 -->New ant target for running Jalview's test
2987 <li>Mapping of cDNA to protein in split frames
2988 incorrect when sequence start > 1</li>
2989 <li>Broken images in filter column by annotation dialog
2991 <li>Feature colours not parsed from features file</li>
2992 <li>Exceptions and incomplete link URLs recovered when
2993 loading a features file containing HTML tags in feature
2997 <em>Application</em>
2999 <li>Annotations corrupted after BioJS export and
3001 <li>Incorrect sequence limits after Fetch DB References
3002 with 'trim retrieved sequences'</li>
3003 <li>Incorrect warning about deleting all data when
3004 deleting selected columns</li>
3005 <li>Patch to build system for shipping properly signed
3006 JNLP templates for webstart launch</li>
3007 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3008 unreleased structures for download or viewing</li>
3009 <li>Tab/space/return keystroke operation of EMBL-PDBe
3010 fetcher/viewer dialogs works correctly</li>
3011 <li>Disabled 'minimise' button on Jalview windows
3012 running on OSX to workaround redraw hang bug</li>
3013 <li>Split cDNA/Protein view position and geometry not
3014 recovered from jalview project</li>
3015 <li>Initial enabled/disabled state of annotation menu
3016 sorter 'show autocalculated first/last' corresponds to
3018 <li>Restoring of Clustal, RNA Helices and T-Coffee
3019 color schemes from BioJSON</li>
3023 <li>Reorder sequences mirrored in cDNA/Protein split
3025 <li>Applet with Jmol examples not loading correctly</li>
3031 <td><div align="center">
3032 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3034 <td><em>General</em>
3036 <li>Linked visualisation and analysis of DNA and Protein
3039 <li>Translated cDNA alignments shown as split protein
3040 and DNA alignment views</li>
3041 <li>Codon consensus annotation for linked protein and
3042 cDNA alignment views</li>
3043 <li>Link cDNA or Protein product sequences by loading
3044 them onto Protein or cDNA alignments</li>
3045 <li>Reconstruct linked cDNA alignment from aligned
3046 protein sequences</li>
3049 <li>Jmol integration updated to Jmol v14.2.14</li>
3050 <li>Import and export of Jalview alignment views as <a
3051 href="features/bioJsonFormat.html">BioJSON</a></li>
3052 <li>New alignment annotation file statements for
3053 reference sequences and marking hidden columns</li>
3054 <li>Reference sequence based alignment shading to
3055 highlight variation</li>
3056 <li>Select or hide columns according to alignment
3058 <li>Find option for locating sequences by description</li>
3059 <li>Conserved physicochemical properties shown in amino
3060 acid conservation row</li>
3061 <li>Alignments can be sorted by number of RNA helices</li>
3062 </ul> <em>Application</em>
3064 <li>New cDNA/Protein analysis capabilities
3066 <li>Get Cross-References should open a Split Frame
3067 view with cDNA/Protein</li>
3068 <li>Detect when nucleotide sequences and protein
3069 sequences are placed in the same alignment</li>
3070 <li>Split cDNA/Protein views are saved in Jalview
3075 <li>Use REST API to talk to Chimera</li>
3076 <li>Selected regions in Chimera are highlighted in linked
3077 Jalview windows</li>
3079 <li>VARNA RNA viewer updated to v3.93</li>
3080 <li>VARNA views are saved in Jalview Projects</li>
3081 <li>Pseudoknots displayed as Jalview RNA annotation can
3082 be shown in VARNA</li>
3084 <li>Make groups for selection uses marked columns as well
3085 as the active selected region</li>
3087 <li>Calculate UPGMA and NJ trees using sequence feature
3089 <li>New Export options
3091 <li>New Export Settings dialog to control hidden
3092 region export in flat file generation</li>
3094 <li>Export alignment views for display with the <a
3095 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3097 <li>Export scrollable SVG in HTML page</li>
3098 <li>Optional embedding of BioJSON data when exporting
3099 alignment figures to HTML</li>
3101 <li>3D structure retrieval and display
3103 <li>Free text and structured queries with the PDBe
3105 <li>PDBe Search API based discovery and selection of
3106 PDB structures for a sequence set</li>
3110 <li>JPred4 employed for protein secondary structure
3112 <li>Hide Insertions menu option to hide unaligned columns
3113 for one or a group of sequences</li>
3114 <li>Automatically hide insertions in alignments imported
3115 from the JPred4 web server</li>
3116 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3117 system on OSX<br />LGPL libraries courtesy of <a
3118 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3120 <li>changed 'View nucleotide structure' submenu to 'View
3121 VARNA 2D Structure'</li>
3122 <li>change "View protein structure" menu option to "3D
3125 </ul> <em>Applet</em>
3127 <li>New layout for applet example pages</li>
3128 <li>New parameters to enable SplitFrame view
3129 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3130 <li>New example demonstrating linked viewing of cDNA and
3131 Protein alignments</li>
3132 </ul> <em>Development and deployment</em>
3134 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3135 <li>Include installation type and git revision in build
3136 properties and console log output</li>
3137 <li>Jalview Github organisation, and new github site for
3138 storing BioJsMSA Templates</li>
3139 <li>Jalview's unit tests now managed with TestNG</li>
3142 <!-- <em>General</em>
3144 </ul> --> <!-- issues resolved --> <em>Application</em>
3146 <li>Escape should close any open find dialogs</li>
3147 <li>Typo in select-by-features status report</li>
3148 <li>Consensus RNA secondary secondary structure
3149 predictions are not highlighted in amber</li>
3150 <li>Missing gap character in v2.7 example file means
3151 alignment appears unaligned when pad-gaps is not enabled</li>
3152 <li>First switch to RNA Helices colouring doesn't colour
3153 associated structure views</li>
3154 <li>ID width preference option is greyed out when auto
3155 width checkbox not enabled</li>
3156 <li>Stopped a warning dialog from being shown when
3157 creating user defined colours</li>
3158 <li>'View Mapping' in structure viewer shows sequence
3159 mappings for just that viewer's sequences</li>
3160 <li>Workaround for superposing PDB files containing
3161 multiple models in Chimera</li>
3162 <li>Report sequence position in status bar when hovering
3163 over Jmol structure</li>
3164 <li>Cannot output gaps as '.' symbols with Selection ->
3165 output to text box</li>
3166 <li>Flat file exports of alignments with hidden columns
3167 have incorrect sequence start/end</li>
3168 <li>'Aligning' a second chain to a Chimera structure from
3170 <li>Colour schemes applied to structure viewers don't
3171 work for nucleotide</li>
3172 <li>Loading/cut'n'pasting an empty or invalid file leads
3173 to a grey/invisible alignment window</li>
3174 <li>Exported Jpred annotation from a sequence region
3175 imports to different position</li>
3176 <li>Space at beginning of sequence feature tooltips shown
3177 on some platforms</li>
3178 <li>Chimera viewer 'View | Show Chain' menu is not
3180 <li>'New View' fails with a Null Pointer Exception in
3181 console if Chimera has been opened</li>
3182 <li>Mouseover to Chimera not working</li>
3183 <li>Miscellaneous ENA XML feature qualifiers not
3185 <li>NPE in annotation renderer after 'Extract Scores'</li>
3186 <li>If two structures in one Chimera window, mouseover of
3187 either sequence shows on first structure</li>
3188 <li>'Show annotations' options should not make
3189 non-positional annotations visible</li>
3190 <li>Subsequence secondary structure annotation not shown
3191 in right place after 'view flanking regions'</li>
3192 <li>File Save As type unset when current file format is
3194 <li>Save as '.jar' option removed for saving Jalview
3196 <li>Colour by Sequence colouring in Chimera more
3198 <li>Cannot 'add reference annotation' for a sequence in
3199 several views on same alignment</li>
3200 <li>Cannot show linked products for EMBL / ENA records</li>
3201 <li>Jalview's tooltip wraps long texts containing no
3203 </ul> <em>Applet</em>
3205 <li>Jmol to JalviewLite mouseover/link not working</li>
3206 <li>JalviewLite can't import sequences with ID
3207 descriptions containing angle brackets</li>
3208 </ul> <em>General</em>
3210 <li>Cannot export and reimport RNA secondary structure
3211 via jalview annotation file</li>
3212 <li>Random helix colour palette for colour by annotation
3213 with RNA secondary structure</li>
3214 <li>Mouseover to cDNA from STOP residue in protein
3215 translation doesn't work.</li>
3216 <li>hints when using the select by annotation dialog box</li>
3217 <li>Jmol alignment incorrect if PDB file has alternate CA
3219 <li>FontChooser message dialog appears to hang after
3220 choosing 1pt font</li>
3221 <li>Peptide secondary structure incorrectly imported from
3222 annotation file when annotation display text includes 'e' or
3224 <li>Cannot set colour of new feature type whilst creating
3226 <li>cDNA translation alignment should not be sequence
3227 order dependent</li>
3228 <li>'Show unconserved' doesn't work for lower case
3230 <li>Nucleotide ambiguity codes involving R not recognised</li>
3231 </ul> <em>Deployment and Documentation</em>
3233 <li>Applet example pages appear different to the rest of
3234 www.jalview.org</li>
3235 </ul> <em>Application Known issues</em>
3237 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3238 <li>Misleading message appears after trying to delete
3240 <li>Jalview icon not shown in dock after InstallAnywhere
3241 version launches</li>
3242 <li>Fetching EMBL reference for an RNA sequence results
3243 fails with a sequence mismatch</li>
3244 <li>Corrupted or unreadable alignment display when
3245 scrolling alignment to right</li>
3246 <li>ArrayIndexOutOfBoundsException thrown when remove
3247 empty columns called on alignment with ragged gapped ends</li>
3248 <li>auto calculated alignment annotation rows do not get
3249 placed above or below non-autocalculated rows</li>
3250 <li>Jalview dekstop becomes sluggish at full screen in
3251 ultra-high resolution</li>
3252 <li>Cannot disable consensus calculation independently of
3253 quality and conservation</li>
3254 <li>Mouseover highlighting between cDNA and protein can
3255 become sluggish with more than one splitframe shown</li>
3256 </ul> <em>Applet Known Issues</em>
3258 <li>Core PDB parsing code requires Jmol</li>
3259 <li>Sequence canvas panel goes white when alignment
3260 window is being resized</li>
3266 <td><div align="center">
3267 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3269 <td><em>General</em>
3271 <li>Updated Java code signing certificate donated by
3273 <li>Features and annotation preserved when performing
3274 pairwise alignment</li>
3275 <li>RNA pseudoknot annotation can be
3276 imported/exported/displayed</li>
3277 <li>'colour by annotation' can colour by RNA and
3278 protein secondary structure</li>
3279 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3280 post-hoc with 2.9 release</em>)
3283 </ul> <em>Application</em>
3285 <li>Extract and display secondary structure for sequences
3286 with 3D structures</li>
3287 <li>Support for parsing RNAML</li>
3288 <li>Annotations menu for layout
3290 <li>sort sequence annotation rows by alignment</li>
3291 <li>place sequence annotation above/below alignment
3294 <li>Output in Stockholm format</li>
3295 <li>Internationalisation: improved Spanish (es)
3297 <li>Structure viewer preferences tab</li>
3298 <li>Disorder and Secondary Structure annotation tracks
3299 shared between alignments</li>
3300 <li>UCSF Chimera launch and linked highlighting from
3302 <li>Show/hide all sequence associated annotation rows for
3303 all or current selection</li>
3304 <li>disorder and secondary structure predictions
3305 available as dataset annotation</li>
3306 <li>Per-sequence rna helices colouring</li>
3309 <li>Sequence database accessions imported when fetching
3310 alignments from Rfam</li>
3311 <li>update VARNA version to 3.91</li>
3313 <li>New groovy scripts for exporting aligned positions,
3314 conservation values, and calculating sum of pairs scores.</li>
3315 <li>Command line argument to set default JABAWS server</li>
3316 <li>include installation type in build properties and
3317 console log output</li>
3318 <li>Updated Jalview project format to preserve dataset
3322 <!-- issues resolved --> <em>Application</em>
3324 <li>Distinguish alignment and sequence associated RNA
3325 structure in structure->view->VARNA</li>
3326 <li>Raise dialog box if user deletes all sequences in an
3328 <li>Pressing F1 results in documentation opening twice</li>
3329 <li>Sequence feature tooltip is wrapped</li>
3330 <li>Double click on sequence associated annotation
3331 selects only first column</li>
3332 <li>Redundancy removal doesn't result in unlinked
3333 leaves shown in tree</li>
3334 <li>Undos after several redundancy removals don't undo
3336 <li>Hide sequence doesn't hide associated annotation</li>
3337 <li>User defined colours dialog box too big to fit on
3338 screen and buttons not visible</li>
3339 <li>author list isn't updated if already written to
3340 Jalview properties</li>
3341 <li>Popup menu won't open after retrieving sequence
3343 <li>File open window for associate PDB doesn't open</li>
3344 <li>Left-then-right click on a sequence id opens a
3345 browser search window</li>
3346 <li>Cannot open sequence feature shading/sort popup menu
3347 in feature settings dialog</li>
3348 <li>better tooltip placement for some areas of Jalview
3350 <li>Allow addition of JABAWS Server which doesn't
3351 pass validation</li>
3352 <li>Web services parameters dialog box is too large to
3354 <li>Muscle nucleotide alignment preset obscured by
3356 <li>JABAWS preset submenus don't contain newly
3357 defined user preset</li>
3358 <li>MSA web services warns user if they were launched
3359 with invalid input</li>
3360 <li>Jalview cannot contact DAS Registy when running on
3363 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3364 'Superpose with' submenu not shown when new view
3368 </ul> <!-- <em>Applet</em>
3370 </ul> <em>General</em>
3372 </ul>--> <em>Deployment and Documentation</em>
3374 <li>2G and 1G options in launchApp have no effect on
3375 memory allocation</li>
3376 <li>launchApp service doesn't automatically open
3377 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3379 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3380 InstallAnywhere reports cannot find valid JVM when Java
3381 1.7_055 is available
3383 </ul> <em>Application Known issues</em>
3386 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3387 corrupted or unreadable alignment display when scrolling
3391 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3392 retrieval fails but progress bar continues for DAS retrieval
3393 with large number of ID
3396 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3397 flatfile output of visible region has incorrect sequence
3401 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3402 rna structure consensus doesn't update when secondary
3403 structure tracks are rearranged
3406 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3407 invalid rna structure positional highlighting does not
3408 highlight position of invalid base pairs
3411 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3412 out of memory errors are not raised when saving Jalview
3413 project from alignment window file menu
3416 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3417 Switching to RNA Helices colouring doesn't propagate to
3421 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3422 colour by RNA Helices not enabled when user created
3423 annotation added to alignment
3426 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3427 Jalview icon not shown on dock in Mountain Lion/Webstart
3429 </ul> <em>Applet Known Issues</em>
3432 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3433 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3436 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3437 Jalview and Jmol example not compatible with IE9
3440 <li>Sort by annotation score doesn't reverse order
3446 <td><div align="center">
3447 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3450 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3453 <li>Internationalisation of user interface (usually
3454 called i18n support) and translation for Spanish locale</li>
3455 <li>Define/Undefine group on current selection with
3456 Ctrl-G/Shift Ctrl-G</li>
3457 <li>Improved group creation/removal options in
3458 alignment/sequence Popup menu</li>
3459 <li>Sensible precision for symbol distribution
3460 percentages shown in logo tooltip.</li>
3461 <li>Annotation panel height set according to amount of
3462 annotation when alignment first opened</li>
3463 </ul> <em>Application</em>
3465 <li>Interactive consensus RNA secondary structure
3466 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3467 <li>Select columns containing particular features from
3468 Feature Settings dialog</li>
3469 <li>View all 'representative' PDB structures for selected
3471 <li>Update Jalview project format:
3473 <li>New file extension for Jalview projects '.jvp'</li>
3474 <li>Preserve sequence and annotation dataset (to
3475 store secondary structure annotation,etc)</li>
3476 <li>Per group and alignment annotation and RNA helix
3480 <li>New similarity measures for PCA and Tree calculation
3482 <li>Experimental support for retrieval and viewing of
3483 flanking regions for an alignment</li>
3487 <!-- issues resolved --> <em>Application</em>
3489 <li>logo keeps spinning and status remains at queued or
3490 running after job is cancelled</li>
3491 <li>cannot export features from alignments imported from
3492 Jalview/VAMSAS projects</li>
3493 <li>Buggy slider for web service parameters that take
3495 <li>Newly created RNA secondary structure line doesn't
3496 have 'display all symbols' flag set</li>
3497 <li>T-COFFEE alignment score shading scheme and other
3498 annotation shading not saved in Jalview project</li>
3499 <li>Local file cannot be loaded in freshly downloaded
3501 <li>Jalview icon not shown on dock in Mountain
3503 <li>Load file from desktop file browser fails</li>
3504 <li>Occasional NPE thrown when calculating large trees</li>
3505 <li>Cannot reorder or slide sequences after dragging an
3506 alignment onto desktop</li>
3507 <li>Colour by annotation dialog throws NPE after using
3508 'extract scores' function</li>
3509 <li>Loading/cut'n'pasting an empty file leads to a grey
3510 alignment window</li>
3511 <li>Disorder thresholds rendered incorrectly after
3512 performing IUPred disorder prediction</li>
3513 <li>Multiple group annotated consensus rows shown when
3514 changing 'normalise logo' display setting</li>
3515 <li>Find shows blank dialog after 'finished searching' if
3516 nothing matches query</li>
3517 <li>Null Pointer Exceptions raised when sorting by
3518 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3520 <li>Errors in Jmol console when structures in alignment
3521 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3523 <li>Not all working JABAWS services are shown in
3525 <li>JAVAWS version of Jalview fails to launch with
3526 'invalid literal/length code'</li>
3527 <li>Annotation/RNA Helix colourschemes cannot be applied
3528 to alignment with groups (actually fixed in 2.8.0b1)</li>
3529 <li>RNA Helices and T-Coffee Scores available as default
3532 </ul> <em>Applet</em>
3534 <li>Remove group option is shown even when selection is
3536 <li>Apply to all groups ticked but colourscheme changes
3537 don't affect groups</li>
3538 <li>Documented RNA Helices and T-Coffee Scores as valid
3539 colourscheme name</li>
3540 <li>Annotation labels drawn on sequence IDs when
3541 Annotation panel is not displayed</li>
3542 <li>Increased font size for dropdown menus on OSX and
3543 embedded windows</li>
3544 </ul> <em>Other</em>
3546 <li>Consensus sequence for alignments/groups with a
3547 single sequence were not calculated</li>
3548 <li>annotation files that contain only groups imported as
3549 annotation and junk sequences</li>
3550 <li>Fasta files with sequences containing '*' incorrectly
3551 recognised as PFAM or BLC</li>
3552 <li>conservation/PID slider apply all groups option
3553 doesn't affect background (2.8.0b1)
3555 <li>redundancy highlighting is erratic at 0% and 100%</li>
3556 <li>Remove gapped columns fails for sequences with ragged
3558 <li>AMSA annotation row with leading spaces is not
3559 registered correctly on import</li>
3560 <li>Jalview crashes when selecting PCA analysis for
3561 certain alignments</li>
3562 <li>Opening the colour by annotation dialog for an
3563 existing annotation based 'use original colours'
3564 colourscheme loses original colours setting</li>
3569 <td><div align="center">
3570 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3571 <em>30/1/2014</em></strong>
3575 <li>Trusted certificates for JalviewLite applet and
3576 Jalview Desktop application<br />Certificate was donated by
3577 <a href="https://www.certum.eu">Certum</a> to the Jalview
3578 open source project).
3580 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3581 <li>Output in Stockholm format</li>
3582 <li>Allow import of data from gzipped files</li>
3583 <li>Export/import group and sequence associated line
3584 graph thresholds</li>
3585 <li>Nucleotide substitution matrix that supports RNA and
3586 ambiguity codes</li>
3587 <li>Allow disorder predictions to be made on the current
3588 selection (or visible selection) in the same way that JPred
3590 <li>Groovy scripting for headless Jalview operation</li>
3591 </ul> <em>Other improvements</em>
3593 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3594 <li>COMBINE statement uses current SEQUENCE_REF and
3595 GROUP_REF scope to group annotation rows</li>
3596 <li>Support '' style escaping of quotes in Newick
3598 <li>Group options for JABAWS service by command line name</li>
3599 <li>Empty tooltip shown for JABA service options with a
3600 link but no description</li>
3601 <li>Select primary source when selecting authority in
3602 database fetcher GUI</li>
3603 <li>Add .mfa to FASTA file extensions recognised by
3605 <li>Annotation label tooltip text wrap</li>
3610 <li>Slow scrolling when lots of annotation rows are
3612 <li>Lots of NPE (and slowness) after creating RNA
3613 secondary structure annotation line</li>
3614 <li>Sequence database accessions not imported when
3615 fetching alignments from Rfam</li>
3616 <li>Incorrect SHMR submission for sequences with
3618 <li>View all structures does not always superpose
3620 <li>Option widgets in service parameters not updated to
3621 reflect user or preset settings</li>
3622 <li>Null pointer exceptions for some services without
3623 presets or adjustable parameters</li>
3624 <li>Discover PDB IDs entry in structure menu doesn't
3625 discover PDB xRefs</li>
3626 <li>Exception encountered while trying to retrieve
3627 features with DAS</li>
3628 <li>Lowest value in annotation row isn't coloured
3629 when colour by annotation (per sequence) is coloured</li>
3630 <li>Keyboard mode P jumps to start of gapped region when
3631 residue follows a gap</li>
3632 <li>Jalview appears to hang importing an alignment with
3633 Wrap as default or after enabling Wrap</li>
3634 <li>'Right click to add annotations' message
3635 shown in wrap mode when no annotations present</li>
3636 <li>Disorder predictions fail with NPE if no automatic
3637 annotation already exists on alignment</li>
3638 <li>oninit javascript function should be called after
3639 initialisation completes</li>
3640 <li>Remove redundancy after disorder prediction corrupts
3641 alignment window display</li>
3642 <li>Example annotation file in documentation is invalid</li>
3643 <li>Grouped line graph annotation rows are not exported
3644 to annotation file</li>
3645 <li>Multi-harmony analysis cannot be run when only two
3647 <li>Cannot create multiple groups of line graphs with
3648 several 'combine' statements in annotation file</li>
3649 <li>Pressing return several times causes Number Format
3650 exceptions in keyboard mode</li>
3651 <li>Multi-harmony (SHMMR) method doesn't submit
3652 correct partitions for input data</li>
3653 <li>Translation from DNA to Amino Acids fails</li>
3654 <li>Jalview fail to load newick tree with quoted label</li>
3655 <li>--headless flag isn't understood</li>
3656 <li>ClassCastException when generating EPS in headless
3658 <li>Adjusting sequence-associated shading threshold only
3659 changes one row's threshold</li>
3660 <li>Preferences and Feature settings panel panel
3661 doesn't open</li>
3662 <li>hide consensus histogram also hides conservation and
3663 quality histograms</li>
3668 <td><div align="center">
3669 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3671 <td><em>Application</em>
3673 <li>Support for JABAWS 2.0 Services (AACon alignment
3674 conservation, protein disorder and Clustal Omega)</li>
3675 <li>JABAWS server status indicator in Web Services
3677 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3678 in Jalview alignment window</li>
3679 <li>Updated Jalview build and deploy framework for OSX
3680 mountain lion, windows 7, and 8</li>
3681 <li>Nucleotide substitution matrix for PCA that supports
3682 RNA and ambiguity codes</li>
3684 <li>Improved sequence database retrieval GUI</li>
3685 <li>Support fetching and database reference look up
3686 against multiple DAS sources (Fetch all from in 'fetch db
3688 <li>Jalview project improvements
3690 <li>Store and retrieve the 'belowAlignment'
3691 flag for annotation</li>
3692 <li>calcId attribute to group annotation rows on the
3694 <li>Store AACon calculation settings for a view in
3695 Jalview project</li>
3699 <li>horizontal scrolling gesture support</li>
3700 <li>Visual progress indicator when PCA calculation is
3702 <li>Simpler JABA web services menus</li>
3703 <li>visual indication that web service results are still
3704 being retrieved from server</li>
3705 <li>Serialise the dialogs that are shown when Jalview
3706 starts up for first time</li>
3707 <li>Jalview user agent string for interacting with HTTP
3709 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3711 <li>Examples directory and Groovy library included in
3712 InstallAnywhere distribution</li>
3713 </ul> <em>Applet</em>
3715 <li>RNA alignment and secondary structure annotation
3716 visualization applet example</li>
3717 </ul> <em>General</em>
3719 <li>Normalise option for consensus sequence logo</li>
3720 <li>Reset button in PCA window to return dimensions to
3722 <li>Allow seqspace or Jalview variant of alignment PCA
3724 <li>PCA with either nucleic acid and protein substitution
3726 <li>Allow windows containing HTML reports to be exported
3728 <li>Interactive display and editing of RNA secondary
3729 structure contacts</li>
3730 <li>RNA Helix Alignment Colouring</li>
3731 <li>RNA base pair logo consensus</li>
3732 <li>Parse sequence associated secondary structure
3733 information in Stockholm files</li>
3734 <li>HTML Export database accessions and annotation
3735 information presented in tooltip for sequences</li>
3736 <li>Import secondary structure from LOCARNA clustalw
3737 style RNA alignment files</li>
3738 <li>import and visualise T-COFFEE quality scores for an
3740 <li>'colour by annotation' per sequence option to
3741 shade each sequence according to its associated alignment
3743 <li>New Jalview Logo</li>
3744 </ul> <em>Documentation and Development</em>
3746 <li>documentation for score matrices used in Jalview</li>
3747 <li>New Website!</li>
3749 <td><em>Application</em>
3751 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3752 wsdbfetch REST service</li>
3753 <li>Stop windows being moved outside desktop on OSX</li>
3754 <li>Filetype associations not installed for webstart
3756 <li>Jalview does not always retrieve progress of a JABAWS
3757 job execution in full once it is complete</li>
3758 <li>revise SHMR RSBS definition to ensure alignment is
3759 uploaded via ali_file parameter</li>
3760 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3761 <li>View all structures superposed fails with exception</li>
3762 <li>Jnet job queues forever if a very short sequence is
3763 submitted for prediction</li>
3764 <li>Cut and paste menu not opened when mouse clicked on
3766 <li>Putting fractional value into integer text box in
3767 alignment parameter dialog causes Jalview to hang</li>
3768 <li>Structure view highlighting doesn't work on
3770 <li>View all structures fails with exception shown in
3772 <li>Characters in filename associated with PDBEntry not
3773 escaped in a platform independent way</li>
3774 <li>Jalview desktop fails to launch with exception when
3776 <li>Tree calculation reports 'you must have 2 or more
3777 sequences selected' when selection is empty</li>
3778 <li>Jalview desktop fails to launch with jar signature
3779 failure when java web start temporary file caching is
3781 <li>DAS Sequence retrieval with range qualification
3782 results in sequence xref which includes range qualification</li>
3783 <li>Errors during processing of command line arguments
3784 cause progress bar (JAL-898) to be removed</li>
3785 <li>Replace comma for semi-colon option not disabled for
3786 DAS sources in sequence fetcher</li>
3787 <li>Cannot close news reader when JABAWS server warning
3788 dialog is shown</li>
3789 <li>Option widgets not updated to reflect user settings</li>
3790 <li>Edited sequence not submitted to web service</li>
3791 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3792 <li>InstallAnywhere installer doesn't unpack and run
3793 on OSX Mountain Lion</li>
3794 <li>Annotation panel not given a scroll bar when
3795 sequences with alignment annotation are pasted into the
3797 <li>Sequence associated annotation rows not associated
3798 when loaded from Jalview project</li>
3799 <li>Browser launch fails with NPE on java 1.7</li>
3800 <li>JABAWS alignment marked as finished when job was
3801 cancelled or job failed due to invalid input</li>
3802 <li>NPE with v2.7 example when clicking on Tree
3803 associated with all views</li>
3804 <li>Exceptions when copy/paste sequences with grouped
3805 annotation rows to new window</li>
3806 </ul> <em>Applet</em>
3808 <li>Sequence features are momentarily displayed before
3809 they are hidden using hidefeaturegroups applet parameter</li>
3810 <li>loading features via javascript API automatically
3811 enables feature display</li>
3812 <li>scrollToColumnIn javascript API method doesn't
3814 </ul> <em>General</em>
3816 <li>Redundancy removal fails for rna alignment</li>
3817 <li>PCA calculation fails when sequence has been selected
3818 and then deselected</li>
3819 <li>PCA window shows grey box when first opened on OSX</li>
3820 <li>Letters coloured pink in sequence logo when alignment
3821 coloured with clustalx</li>
3822 <li>Choosing fonts without letter symbols defined causes
3823 exceptions and redraw errors</li>
3824 <li>Initial PCA plot view is not same as manually
3825 reconfigured view</li>
3826 <li>Grouped annotation graph label has incorrect line
3828 <li>Grouped annotation graph label display is corrupted
3829 for lots of labels</li>
3834 <div align="center">
3835 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3838 <td><em>Application</em>
3840 <li>Jalview Desktop News Reader</li>
3841 <li>Tweaked default layout of web services menu</li>
3842 <li>View/alignment association menu to enable user to
3843 easily specify which alignment a multi-structure view takes
3844 its colours/correspondences from</li>
3845 <li>Allow properties file location to be specified as URL</li>
3846 <li>Extend Jalview project to preserve associations
3847 between many alignment views and a single Jmol display</li>
3848 <li>Store annotation row height in Jalview project file</li>
3849 <li>Annotation row column label formatting attributes
3850 stored in project file</li>
3851 <li>Annotation row order for auto-calculated annotation
3852 rows preserved in Jalview project file</li>
3853 <li>Visual progress indication when Jalview state is
3854 saved using Desktop window menu</li>
3855 <li>Visual indication that command line arguments are
3856 still being processed</li>
3857 <li>Groovy script execution from URL</li>
3858 <li>Colour by annotation default min and max colours in
3860 <li>Automatically associate PDB files dragged onto an
3861 alignment with sequences that have high similarity and
3863 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3864 <li>'view structures' option to open many
3865 structures in same window</li>
3866 <li>Sort associated views menu option for tree panel</li>
3867 <li>Group all JABA and non-JABA services for a particular
3868 analysis function in its own submenu</li>
3869 </ul> <em>Applet</em>
3871 <li>Userdefined and autogenerated annotation rows for
3873 <li>Adjustment of alignment annotation pane height</li>
3874 <li>Annotation scrollbar for annotation panel</li>
3875 <li>Drag to reorder annotation rows in annotation panel</li>
3876 <li>'automaticScrolling' parameter</li>
3877 <li>Allow sequences with partial ID string matches to be
3878 annotated from GFF/Jalview features files</li>
3879 <li>Sequence logo annotation row in applet</li>
3880 <li>Absolute paths relative to host server in applet
3881 parameters are treated as such</li>
3882 <li>New in the JalviewLite javascript API:
3884 <li>JalviewLite.js javascript library</li>
3885 <li>Javascript callbacks for
3887 <li>Applet initialisation</li>
3888 <li>Sequence/alignment mouse-overs and selections</li>
3891 <li>scrollTo row and column alignment scrolling
3893 <li>Select sequence/alignment regions from javascript</li>
3894 <li>javascript structure viewer harness to pass
3895 messages between Jmol and Jalview when running as
3896 distinct applets</li>
3897 <li>sortBy method</li>
3898 <li>Set of applet and application examples shipped
3899 with documentation</li>
3900 <li>New example to demonstrate JalviewLite and Jmol
3901 javascript message exchange</li>
3903 </ul> <em>General</em>
3905 <li>Enable Jmol displays to be associated with multiple
3906 multiple alignments</li>
3907 <li>Option to automatically sort alignment with new tree</li>
3908 <li>User configurable link to enable redirects to a
3909 www.Jalview.org mirror</li>
3910 <li>Jmol colours option for Jmol displays</li>
3911 <li>Configurable newline string when writing alignment
3912 and other flat files</li>
3913 <li>Allow alignment annotation description lines to
3914 contain html tags</li>
3915 </ul> <em>Documentation and Development</em>
3917 <li>Add groovy test harness for bulk load testing to
3919 <li>Groovy script to load and align a set of sequences
3920 using a web service before displaying the result in the
3921 Jalview desktop</li>
3922 <li>Restructured javascript and applet api documentation</li>
3923 <li>Ant target to publish example html files with applet
3925 <li>Netbeans project for building Jalview from source</li>
3926 <li>ant task to create online javadoc for Jalview source</li>
3928 <td><em>Application</em>
3930 <li>User defined colourscheme throws exception when
3931 current built in colourscheme is saved as new scheme</li>
3932 <li>AlignFrame->Save in application pops up save
3933 dialog for valid filename/format</li>
3934 <li>Cannot view associated structure for UniProt sequence</li>
3935 <li>PDB file association breaks for UniProt sequence
3937 <li>Associate PDB from file dialog does not tell you
3938 which sequence is to be associated with the file</li>
3939 <li>Find All raises null pointer exception when query
3940 only matches sequence IDs</li>
3941 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3942 <li>Jalview project with Jmol views created with Jalview
3943 2.4 cannot be loaded</li>
3944 <li>Filetype associations not installed for webstart
3946 <li>Two or more chains in a single PDB file associated
3947 with sequences in different alignments do not get coloured
3948 by their associated sequence</li>
3949 <li>Visibility status of autocalculated annotation row
3950 not preserved when project is loaded</li>
3951 <li>Annotation row height and visibility attributes not
3952 stored in Jalview project</li>
3953 <li>Tree bootstraps are not preserved when saved as a
3954 Jalview project</li>
3955 <li>Envision2 workflow tooltips are corrupted</li>
3956 <li>Enabling show group conservation also enables colour
3957 by conservation</li>
3958 <li>Duplicate group associated conservation or consensus
3959 created on new view</li>
3960 <li>Annotation scrollbar not displayed after 'show
3961 all hidden annotation rows' option selected</li>
3962 <li>Alignment quality not updated after alignment
3963 annotation row is hidden then shown</li>
3964 <li>Preserve colouring of structures coloured by
3965 sequences in pre Jalview 2.7 projects</li>
3966 <li>Web service job parameter dialog is not laid out
3968 <li>Web services menu not refreshed after 'reset
3969 services' button is pressed in preferences</li>
3970 <li>Annotation off by one in Jalview v2_3 example project</li>
3971 <li>Structures imported from file and saved in project
3972 get name like jalview_pdb1234.txt when reloaded</li>
3973 <li>Jalview does not always retrieve progress of a JABAWS
3974 job execution in full once it is complete</li>
3975 </ul> <em>Applet</em>
3977 <li>Alignment height set incorrectly when lots of
3978 annotation rows are displayed</li>
3979 <li>Relative URLs in feature HTML text not resolved to
3981 <li>View follows highlighting does not work for positions
3983 <li><= shown as = in tooltip</li>
3984 <li>Export features raises exception when no features
3986 <li>Separator string used for serialising lists of IDs
3987 for javascript api is modified when separator string
3988 provided as parameter</li>
3989 <li>Null pointer exception when selecting tree leaves for
3990 alignment with no existing selection</li>
3991 <li>Relative URLs for datasources assumed to be relative
3992 to applet's codebase</li>
3993 <li>Status bar not updated after finished searching and
3994 search wraps around to first result</li>
3995 <li>StructureSelectionManager instance shared between
3996 several Jalview applets causes race conditions and memory
3998 <li>Hover tooltip and mouseover of position on structure
3999 not sent from Jmol in applet</li>
4000 <li>Certain sequences of javascript method calls to
4001 applet API fatally hang browser</li>
4002 </ul> <em>General</em>
4004 <li>View follows structure mouseover scrolls beyond
4005 position with wrapped view and hidden regions</li>
4006 <li>Find sequence position moves to wrong residue
4007 with/without hidden columns</li>
4008 <li>Sequence length given in alignment properties window
4010 <li>InvalidNumberFormat exceptions thrown when trying to
4011 import PDB like structure files</li>
4012 <li>Positional search results are only highlighted
4013 between user-supplied sequence start/end bounds</li>
4014 <li>End attribute of sequence is not validated</li>
4015 <li>Find dialog only finds first sequence containing a
4016 given sequence position</li>
4017 <li>Sequence numbering not preserved in MSF alignment
4019 <li>Jalview PDB file reader does not extract sequence
4020 from nucleotide chains correctly</li>
4021 <li>Structure colours not updated when tree partition
4022 changed in alignment</li>
4023 <li>Sequence associated secondary structure not correctly
4024 parsed in interleaved stockholm</li>
4025 <li>Colour by annotation dialog does not restore current
4027 <li>Hiding (nearly) all sequences doesn't work
4029 <li>Sequences containing lowercase letters are not
4030 properly associated with their pdb files</li>
4031 </ul> <em>Documentation and Development</em>
4033 <li>schemas/JalviewWsParamSet.xsd corrupted by
4034 ApplyCopyright tool</li>
4039 <div align="center">
4040 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4043 <td><em>Application</em>
4045 <li>New warning dialog when the Jalview Desktop cannot
4046 contact web services</li>
4047 <li>JABA service parameters for a preset are shown in
4048 service job window</li>
4049 <li>JABA Service menu entries reworded</li>
4053 <li>Modeller PIR IO broken - cannot correctly import a
4054 pir file emitted by Jalview</li>
4055 <li>Existing feature settings transferred to new
4056 alignment view created from cut'n'paste</li>
4057 <li>Improved test for mixed amino/nucleotide chains when
4058 parsing PDB files</li>
4059 <li>Consensus and conservation annotation rows
4060 occasionally become blank for all new windows</li>
4061 <li>Exception raised when right clicking above sequences
4062 in wrapped view mode</li>
4063 </ul> <em>Application</em>
4065 <li>multiple multiply aligned structure views cause cpu
4066 usage to hit 100% and computer to hang</li>
4067 <li>Web Service parameter layout breaks for long user
4068 parameter names</li>
4069 <li>Jaba service discovery hangs desktop if Jaba server
4076 <div align="center">
4077 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4080 <td><em>Application</em>
4082 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4083 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4086 <li>Web Services preference tab</li>
4087 <li>Analysis parameters dialog box and user defined
4089 <li>Improved speed and layout of Envision2 service menu</li>
4090 <li>Superpose structures using associated sequence
4092 <li>Export coordinates and projection as CSV from PCA
4094 </ul> <em>Applet</em>
4096 <li>enable javascript: execution by the applet via the
4097 link out mechanism</li>
4098 </ul> <em>Other</em>
4100 <li>Updated the Jmol Jalview interface to work with Jmol
4102 <li>The Jalview Desktop and JalviewLite applet now
4103 require Java 1.5</li>
4104 <li>Allow Jalview feature colour specification for GFF
4105 sequence annotation files</li>
4106 <li>New 'colour by label' keword in Jalview feature file
4107 type colour specification</li>
4108 <li>New Jalview Desktop Groovy API method that allows a
4109 script to check if it being run in an interactive session or
4110 in a batch operation from the Jalview command line</li>
4114 <li>clustalx colourscheme colours Ds preferentially when
4115 both D+E are present in over 50% of the column</li>
4116 </ul> <em>Application</em>
4118 <li>typo in AlignmentFrame->View->Hide->all but
4119 selected Regions menu item</li>
4120 <li>sequence fetcher replaces ',' for ';' when the ',' is
4121 part of a valid accession ID</li>
4122 <li>fatal OOM if object retrieved by sequence fetcher
4123 runs out of memory</li>
4124 <li>unhandled Out of Memory Error when viewing pca
4125 analysis results</li>
4126 <li>InstallAnywhere builds fail to launch on OS X java
4127 10.5 update 4 (due to apple Java 1.6 update)</li>
4128 <li>Installanywhere Jalview silently fails to launch</li>
4129 </ul> <em>Applet</em>
4131 <li>Jalview.getFeatureGroups() raises an
4132 ArrayIndexOutOfBoundsException if no feature groups are
4139 <div align="center">
4140 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4146 <li>Alignment prettyprinter doesn't cope with long
4148 <li>clustalx colourscheme colours Ds preferentially when
4149 both D+E are present in over 50% of the column</li>
4150 <li>nucleic acid structures retrieved from PDB do not
4151 import correctly</li>
4152 <li>More columns get selected than were clicked on when a
4153 number of columns are hidden</li>
4154 <li>annotation label popup menu not providing correct
4155 add/hide/show options when rows are hidden or none are
4157 <li>Stockholm format shown in list of readable formats,
4158 and parser copes better with alignments from RFAM.</li>
4159 <li>CSV output of consensus only includes the percentage
4160 of all symbols if sequence logo display is enabled</li>
4162 </ul> <em>Applet</em>
4164 <li>annotation panel disappears when annotation is
4166 </ul> <em>Application</em>
4168 <li>Alignment view not redrawn properly when new
4169 alignment opened where annotation panel is visible but no
4170 annotations are present on alignment</li>
4171 <li>pasted region containing hidden columns is
4172 incorrectly displayed in new alignment window</li>
4173 <li>Jalview slow to complete operations when stdout is
4174 flooded (fix is to close the Jalview console)</li>
4175 <li>typo in AlignmentFrame->View->Hide->all but
4176 selected Rregions menu item.</li>
4177 <li>inconsistent group submenu and Format submenu entry
4178 'Un' or 'Non'conserved</li>
4179 <li>Sequence feature settings are being shared by
4180 multiple distinct alignments</li>
4181 <li>group annotation not recreated when tree partition is
4183 <li>double click on group annotation to select sequences
4184 does not propagate to associated trees</li>
4185 <li>Mac OSX specific issues:
4187 <li>exception raised when mouse clicked on desktop
4188 window background</li>
4189 <li>Desktop menu placed on menu bar and application
4190 name set correctly</li>
4191 <li>sequence feature settings not wide enough for the
4192 save feature colourscheme button</li>
4201 <div align="center">
4202 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4205 <td><em>New Capabilities</em>
4207 <li>URL links generated from description line for
4208 regular-expression based URL links (applet and application)
4210 <li>Non-positional feature URL links are shown in link
4212 <li>Linked viewing of nucleic acid sequences and
4214 <li>Automatic Scrolling option in View menu to display
4215 the currently highlighted region of an alignment.</li>
4216 <li>Order an alignment by sequence length, or using the
4217 average score or total feature count for each sequence.</li>
4218 <li>Shading features by score or associated description</li>
4219 <li>Subdivide alignment and groups based on identity of
4220 selected subsequence (Make Groups from Selection).</li>
4221 <li>New hide/show options including Shift+Control+H to
4222 hide everything but the currently selected region.</li>
4223 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4224 </ul> <em>Application</em>
4226 <li>Fetch DB References capabilities and UI expanded to
4227 support retrieval from DAS sequence sources</li>
4228 <li>Local DAS Sequence sources can be added via the
4229 command line or via the Add local source dialog box.</li>
4230 <li>DAS Dbref and DbxRef feature types are parsed as
4231 database references and protein_name is parsed as
4232 description line (BioSapiens terms).</li>
4233 <li>Enable or disable non-positional feature and database
4234 references in sequence ID tooltip from View menu in
4236 <!-- <li>New hidden columns and rows and representatives capabilities
4237 in annotations file (in progress - not yet fully implemented)</li> -->
4238 <li>Group-associated consensus, sequence logos and
4239 conservation plots</li>
4240 <li>Symbol distributions for each column can be exported
4241 and visualized as sequence logos</li>
4242 <li>Optionally scale multi-character column labels to fit
4243 within each column of annotation row<!-- todo for applet -->
4245 <li>Optional automatic sort of associated alignment view
4246 when a new tree is opened.</li>
4247 <li>Jalview Java Console</li>
4248 <li>Better placement of desktop window when moving
4249 between different screens.</li>
4250 <li>New preference items for sequence ID tooltip and
4251 consensus annotation</li>
4252 <li>Client to submit sequences and IDs to Envision2
4254 <li><em>Vamsas Capabilities</em>
4256 <li>Improved VAMSAS synchronization (Jalview archive
4257 used to preserve views, structures, and tree display
4259 <li>Import of vamsas documents from disk or URL via
4261 <li>Sharing of selected regions between views and
4262 with other VAMSAS applications (Experimental feature!)</li>
4263 <li>Updated API to VAMSAS version 0.2</li>
4265 </ul> <em>Applet</em>
4267 <li>Middle button resizes annotation row height</li>
4270 <li>sortByTree (true/false) - automatically sort the
4271 associated alignment view by the tree when a new tree is
4273 <li>showTreeBootstraps (true/false) - show or hide
4274 branch bootstraps (default is to show them if available)</li>
4275 <li>showTreeDistances (true/false) - show or hide
4276 branch lengths (default is to show them if available)</li>
4277 <li>showUnlinkedTreeNodes (true/false) - indicate if
4278 unassociated nodes should be highlighted in the tree
4280 <li>heightScale and widthScale (1.0 or more) -
4281 increase the height or width of a cell in the alignment
4282 grid relative to the current font size.</li>
4285 <li>Non-positional features displayed in sequence ID
4287 </ul> <em>Other</em>
4289 <li>Features format: graduated colour definitions and
4290 specification of feature scores</li>
4291 <li>Alignment Annotations format: new keywords for group
4292 associated annotation (GROUP_REF) and annotation row display
4293 properties (ROW_PROPERTIES)</li>
4294 <li>XML formats extended to support graduated feature
4295 colourschemes, group associated annotation, and profile
4296 visualization settings.</li></td>
4299 <li>Source field in GFF files parsed as feature source
4300 rather than description</li>
4301 <li>Non-positional features are now included in sequence
4302 feature and gff files (controlled via non-positional feature
4303 visibility in tooltip).</li>
4304 <li>URL links generated for all feature links (bugfix)</li>
4305 <li>Added URL embedding instructions to features file
4307 <li>Codons containing ambiguous nucleotides translated as
4308 'X' in peptide product</li>
4309 <li>Match case switch in find dialog box works for both
4310 sequence ID and sequence string and query strings do not
4311 have to be in upper case to match case-insensitively.</li>
4312 <li>AMSA files only contain first column of
4313 multi-character column annotation labels</li>
4314 <li>Jalview Annotation File generation/parsing consistent
4315 with documentation (e.g. Stockholm annotation can be
4316 exported and re-imported)</li>
4317 <li>PDB files without embedded PDB IDs given a friendly
4319 <li>Find incrementally searches ID string matches as well
4320 as subsequence matches, and correctly reports total number
4324 <li>Better handling of exceptions during sequence
4326 <li>Dasobert generated non-positional feature URL
4327 link text excludes the start_end suffix</li>
4328 <li>DAS feature and source retrieval buttons disabled
4329 when fetch or registry operations in progress.</li>
4330 <li>PDB files retrieved from URLs are cached properly</li>
4331 <li>Sequence description lines properly shared via
4333 <li>Sequence fetcher fetches multiple records for all
4335 <li>Ensured that command line das feature retrieval
4336 completes before alignment figures are generated.</li>
4337 <li>Reduced time taken when opening file browser for
4339 <li>isAligned check prior to calculating tree, PCA or
4340 submitting an MSA to JNet now excludes hidden sequences.</li>
4341 <li>User defined group colours properly recovered
4342 from Jalview projects.</li>
4351 <div align="center">
4352 <strong>2.4.0.b2</strong><br> 28/10/2009
4357 <li>Experimental support for google analytics usage
4359 <li>Jalview privacy settings (user preferences and docs).</li>
4364 <li>Race condition in applet preventing startup in
4366 <li>Exception when feature created from selection beyond
4367 length of sequence.</li>
4368 <li>Allow synthetic PDB files to be imported gracefully</li>
4369 <li>Sequence associated annotation rows associate with
4370 all sequences with a given id</li>
4371 <li>Find function matches case-insensitively for sequence
4372 ID string searches</li>
4373 <li>Non-standard characters do not cause pairwise
4374 alignment to fail with exception</li>
4375 </ul> <em>Application Issues</em>
4377 <li>Sequences are now validated against EMBL database</li>
4378 <li>Sequence fetcher fetches multiple records for all
4380 </ul> <em>InstallAnywhere Issues</em>
4382 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4383 issue with installAnywhere mechanism)</li>
4384 <li>Command line launching of JARs from InstallAnywhere
4385 version (java class versioning error fixed)</li>
4392 <div align="center">
4393 <strong>2.4</strong><br> 27/8/2008
4396 <td><em>User Interface</em>
4398 <li>Linked highlighting of codon and amino acid from
4399 translation and protein products</li>
4400 <li>Linked highlighting of structure associated with
4401 residue mapping to codon position</li>
4402 <li>Sequence Fetcher provides example accession numbers
4403 and 'clear' button</li>
4404 <li>MemoryMonitor added as an option under Desktop's
4406 <li>Extract score function to parse whitespace separated
4407 numeric data in description line</li>
4408 <li>Column labels in alignment annotation can be centred.</li>
4409 <li>Tooltip for sequence associated annotation give name
4411 </ul> <em>Web Services and URL fetching</em>
4413 <li>JPred3 web service</li>
4414 <li>Prototype sequence search client (no public services
4416 <li>Fetch either seed alignment or full alignment from
4418 <li>URL Links created for matching database cross
4419 references as well as sequence ID</li>
4420 <li>URL Links can be created using regular-expressions</li>
4421 </ul> <em>Sequence Database Connectivity</em>
4423 <li>Retrieval of cross-referenced sequences from other
4425 <li>Generalised database reference retrieval and
4426 validation to all fetchable databases</li>
4427 <li>Fetch sequences from DAS sources supporting the
4428 sequence command</li>
4429 </ul> <em>Import and Export</em>
4430 <li>export annotation rows as CSV for spreadsheet import</li>
4431 <li>Jalview projects record alignment dataset associations,
4432 EMBL products, and cDNA sequence mappings</li>
4433 <li>Sequence Group colour can be specified in Annotation
4435 <li>Ad-hoc colouring of group in Annotation File using RGB
4436 triplet as name of colourscheme</li>
4437 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4439 <li>treenode binding for VAMSAS tree exchange</li>
4440 <li>local editing and update of sequences in VAMSAS
4441 alignments (experimental)</li>
4442 <li>Create new or select existing session to join</li>
4443 <li>load and save of vamsas documents</li>
4444 </ul> <em>Application command line</em>
4446 <li>-tree parameter to open trees (introduced for passing
4448 <li>-fetchfrom command line argument to specify nicknames
4449 of DAS servers to query for alignment features</li>
4450 <li>-dasserver command line argument to add new servers
4451 that are also automatically queried for features</li>
4452 <li>-groovy command line argument executes a given groovy
4453 script after all input data has been loaded and parsed</li>
4454 </ul> <em>Applet-Application data exchange</em>
4456 <li>Trees passed as applet parameters can be passed to
4457 application (when using "View in full
4458 application")</li>
4459 </ul> <em>Applet Parameters</em>
4461 <li>feature group display control parameter</li>
4462 <li>debug parameter</li>
4463 <li>showbutton parameter</li>
4464 </ul> <em>Applet API methods</em>
4466 <li>newView public method</li>
4467 <li>Window (current view) specific get/set public methods</li>
4468 <li>Feature display control methods</li>
4469 <li>get list of currently selected sequences</li>
4470 </ul> <em>New Jalview distribution features</em>
4472 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4473 <li>RELEASE file gives build properties for the latest
4474 Jalview release.</li>
4475 <li>Java 1.1 Applet build made easier and donotobfuscate
4476 property controls execution of obfuscator</li>
4477 <li>Build target for generating source distribution</li>
4478 <li>Debug flag for javacc</li>
4479 <li>.jalview_properties file is documented (slightly) in
4480 jalview.bin.Cache</li>
4481 <li>Continuous Build Integration for stable and
4482 development version of Application, Applet and source
4487 <li>selected region output includes visible annotations
4488 (for certain formats)</li>
4489 <li>edit label/displaychar contains existing label/char
4491 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4492 <li>shorter peptide product names from EMBL records</li>
4493 <li>Newick string generator makes compact representations</li>
4494 <li>bootstrap values parsed correctly for tree files with
4496 <li>pathological filechooser bug avoided by not allowing
4497 filenames containing a ':'</li>
4498 <li>Fixed exception when parsing GFF files containing
4499 global sequence features</li>
4500 <li>Alignment datasets are finalized only when number of
4501 references from alignment sequences goes to zero</li>
4502 <li>Close of tree branch colour box without colour
4503 selection causes cascading exceptions</li>
4504 <li>occasional negative imgwidth exceptions</li>
4505 <li>better reporting of non-fatal warnings to user when
4506 file parsing fails.</li>
4507 <li>Save works when Jalview project is default format</li>
4508 <li>Save as dialog opened if current alignment format is
4509 not a valid output format</li>
4510 <li>UniProt canonical names introduced for both das and
4512 <li>Histidine should be midblue (not pink!) in Zappo</li>
4513 <li>error messages passed up and output when data read
4515 <li>edit undo recovers previous dataset sequence when
4516 sequence is edited</li>
4517 <li>allow PDB files without pdb ID HEADER lines (like
4518 those generated by MODELLER) to be read in properly</li>
4519 <li>allow reading of JPred concise files as a normal
4521 <li>Stockholm annotation parsing and alignment properties
4522 import fixed for PFAM records</li>
4523 <li>Structure view windows have correct name in Desktop
4525 <li>annotation consisting of sequence associated scores
4526 can be read and written correctly to annotation file</li>
4527 <li>Aligned cDNA translation to aligned peptide works
4529 <li>Fixed display of hidden sequence markers and
4530 non-italic font for representatives in Applet</li>
4531 <li>Applet Menus are always embedded in applet window on
4533 <li>Newly shown features appear at top of stack (in
4535 <li>Annotations added via parameter not drawn properly
4536 due to null pointer exceptions</li>
4537 <li>Secondary structure lines are drawn starting from
4538 first column of alignment</li>
4539 <li>UniProt XML import updated for new schema release in
4541 <li>Sequence feature to sequence ID match for Features
4542 file is case-insensitive</li>
4543 <li>Sequence features read from Features file appended to
4544 all sequences with matching IDs</li>
4545 <li>PDB structure coloured correctly for associated views
4546 containing a sub-sequence</li>
4547 <li>PDB files can be retrieved by applet from Jar files</li>
4548 <li>feature and annotation file applet parameters
4549 referring to different directories are retrieved correctly</li>
4550 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4551 <li>Fixed application hang whilst waiting for
4552 splash-screen version check to complete</li>
4553 <li>Applet properly URLencodes input parameter values
4554 when passing them to the launchApp service</li>
4555 <li>display name and local features preserved in results
4556 retrieved from web service</li>
4557 <li>Visual delay indication for sequence retrieval and
4558 sequence fetcher initialisation</li>
4559 <li>updated Application to use DAS 1.53e version of
4560 dasobert DAS client</li>
4561 <li>Re-instated Full AMSA support and .amsa file
4563 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4571 <div align="center">
4572 <strong>2.3</strong><br> 9/5/07
4577 <li>Jmol 11.0.2 integration</li>
4578 <li>PDB views stored in Jalview XML files</li>
4579 <li>Slide sequences</li>
4580 <li>Edit sequence in place</li>
4581 <li>EMBL CDS features</li>
4582 <li>DAS Feature mapping</li>
4583 <li>Feature ordering</li>
4584 <li>Alignment Properties</li>
4585 <li>Annotation Scores</li>
4586 <li>Sort by scores</li>
4587 <li>Feature/annotation editing in applet</li>
4592 <li>Headless state operation in 2.2.1</li>
4593 <li>Incorrect and unstable DNA pairwise alignment</li>
4594 <li>Cut and paste of sequences with annotation</li>
4595 <li>Feature group display state in XML</li>
4596 <li>Feature ordering in XML</li>
4597 <li>blc file iteration selection using filename # suffix</li>
4598 <li>Stockholm alignment properties</li>
4599 <li>Stockhom alignment secondary structure annotation</li>
4600 <li>2.2.1 applet had no feature transparency</li>
4601 <li>Number pad keys can be used in cursor mode</li>
4602 <li>Structure Viewer mirror image resolved</li>
4609 <div align="center">
4610 <strong>2.2.1</strong><br> 12/2/07
4615 <li>Non standard characters can be read and displayed
4616 <li>Annotations/Features can be imported/exported to the
4618 <li>Applet allows editing of sequence/annotation/group
4619 name & description
4620 <li>Preference setting to display sequence name in
4622 <li>Annotation file format extended to allow
4623 Sequence_groups to be defined
4624 <li>Default opening of alignment overview panel can be
4625 specified in preferences
4626 <li>PDB residue numbering annotation added to associated
4632 <li>Applet crash under certain Linux OS with Java 1.6
4634 <li>Annotation file export / import bugs fixed
4635 <li>PNG / EPS image output bugs fixed
4641 <div align="center">
4642 <strong>2.2</strong><br> 27/11/06
4647 <li>Multiple views on alignment
4648 <li>Sequence feature editing
4649 <li>"Reload" alignment
4650 <li>"Save" to current filename
4651 <li>Background dependent text colour
4652 <li>Right align sequence ids
4653 <li>User-defined lower case residue colours
4656 <li>Menu item accelerator keys
4657 <li>Control-V pastes to current alignment
4658 <li>Cancel button for DAS Feature Fetching
4659 <li>PCA and PDB Viewers zoom via mouse roller
4660 <li>User-defined sub-tree colours and sub-tree selection
4662 <li>'New Window' button on the 'Output to Text box'
4667 <li>New memory efficient Undo/Redo System
4668 <li>Optimised symbol lookups and conservation/consensus
4670 <li>Region Conservation/Consensus recalculated after
4672 <li>Fixed Remove Empty Columns Bug (empty columns at end
4674 <li>Slowed DAS Feature Fetching for increased robustness.
4676 <li>Made angle brackets in ASCII feature descriptions
4678 <li>Re-instated Zoom function for PCA
4679 <li>Sequence descriptions conserved in web service
4681 <li>UniProt ID discoverer uses any word separated by
4683 <li>WsDbFetch query/result association resolved
4684 <li>Tree leaf to sequence mapping improved
4685 <li>Smooth fonts switch moved to FontChooser dialog box.
4692 <div align="center">
4693 <strong>2.1.1</strong><br> 12/9/06
4698 <li>Copy consensus sequence to clipboard</li>
4703 <li>Image output - rightmost residues are rendered if
4704 sequence id panel has been resized</li>
4705 <li>Image output - all offscreen group boundaries are
4707 <li>Annotation files with sequence references - all
4708 elements in file are relative to sequence position</li>
4709 <li>Mac Applet users can use Alt key for group editing</li>
4715 <div align="center">
4716 <strong>2.1</strong><br> 22/8/06
4721 <li>MAFFT Multiple Alignment in default Web Service list</li>
4722 <li>DAS Feature fetching</li>
4723 <li>Hide sequences and columns</li>
4724 <li>Export Annotations and Features</li>
4725 <li>GFF file reading / writing</li>
4726 <li>Associate structures with sequences from local PDB
4728 <li>Add sequences to exisiting alignment</li>
4729 <li>Recently opened files / URL lists</li>
4730 <li>Applet can launch the full application</li>
4731 <li>Applet has transparency for features (Java 1.2
4733 <li>Applet has user defined colours parameter</li>
4734 <li>Applet can load sequences from parameter
4735 "sequence<em>x</em>"
4741 <li>Redundancy Panel reinstalled in the Applet</li>
4742 <li>Monospaced font - EPS / rescaling bug fixed</li>
4743 <li>Annotation files with sequence references bug fixed</li>
4749 <div align="center">
4750 <strong>2.08.1</strong><br> 2/5/06
4755 <li>Change case of selected region from Popup menu</li>
4756 <li>Choose to match case when searching</li>
4757 <li>Middle mouse button and mouse movement can compress /
4758 expand the visible width and height of the alignment</li>
4763 <li>Annotation Panel displays complete JNet results</li>
4769 <div align="center">
4770 <strong>2.08b</strong><br> 18/4/06
4776 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4777 <li>Righthand label on wrapped alignments shows correct
4784 <div align="center">
4785 <strong>2.08</strong><br> 10/4/06
4790 <li>Editing can be locked to the selection area</li>
4791 <li>Keyboard editing</li>
4792 <li>Create sequence features from searches</li>
4793 <li>Precalculated annotations can be loaded onto
4795 <li>Features file allows grouping of features</li>
4796 <li>Annotation Colouring scheme added</li>
4797 <li>Smooth fonts off by default - Faster rendering</li>
4798 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4803 <li>Drag & Drop fixed on Linux</li>
4804 <li>Jalview Archive file faster to load/save, sequence
4805 descriptions saved.</li>
4811 <div align="center">
4812 <strong>2.07</strong><br> 12/12/05
4817 <li>PDB Structure Viewer enhanced</li>
4818 <li>Sequence Feature retrieval and display enhanced</li>
4819 <li>Choose to output sequence start-end after sequence
4820 name for file output</li>
4821 <li>Sequence Fetcher WSDBFetch@EBI</li>
4822 <li>Applet can read feature files, PDB files and can be
4823 used for HTML form input</li>
4828 <li>HTML output writes groups and features</li>
4829 <li>Group editing is Control and mouse click</li>
4830 <li>File IO bugs</li>
4836 <div align="center">
4837 <strong>2.06</strong><br> 28/9/05
4842 <li>View annotations in wrapped mode</li>
4843 <li>More options for PCA viewer</li>
4848 <li>GUI bugs resolved</li>
4849 <li>Runs with -nodisplay from command line</li>
4855 <div align="center">
4856 <strong>2.05b</strong><br> 15/9/05
4861 <li>Choose EPS export as lineart or text</li>
4862 <li>Jar files are executable</li>
4863 <li>Can read in Uracil - maps to unknown residue</li>
4868 <li>Known OutOfMemory errors give warning message</li>
4869 <li>Overview window calculated more efficiently</li>
4870 <li>Several GUI bugs resolved</li>
4876 <div align="center">
4877 <strong>2.05</strong><br> 30/8/05
4882 <li>Edit and annotate in "Wrapped" view</li>
4887 <li>Several GUI bugs resolved</li>
4893 <div align="center">
4894 <strong>2.04</strong><br> 24/8/05
4899 <li>Hold down mouse wheel & scroll to change font
4905 <li>Improved JPred client reliability</li>
4906 <li>Improved loading of Jalview files</li>
4912 <div align="center">
4913 <strong>2.03</strong><br> 18/8/05
4918 <li>Set Proxy server name and port in preferences</li>
4919 <li>Multiple URL links from sequence ids</li>
4920 <li>User Defined Colours can have a scheme name and added
4922 <li>Choose to ignore gaps in consensus calculation</li>
4923 <li>Unix users can set default web browser</li>
4924 <li>Runs without GUI for batch processing</li>
4925 <li>Dynamically generated Web Service Menus</li>
4930 <li>InstallAnywhere download for Sparc Solaris</li>
4936 <div align="center">
4937 <strong>2.02</strong><br> 18/7/05
4943 <li>Copy & Paste order of sequences maintains
4944 alignment order.</li>
4950 <div align="center">
4951 <strong>2.01</strong><br> 12/7/05
4956 <li>Use delete key for deleting selection.</li>
4957 <li>Use Mouse wheel to scroll sequences.</li>
4958 <li>Help file updated to describe how to add alignment
4960 <li>Version and build date written to build properties
4962 <li>InstallAnywhere installation will check for updates
4963 at launch of Jalview.</li>
4968 <li>Delete gaps bug fixed.</li>
4969 <li>FileChooser sorts columns.</li>
4970 <li>Can remove groups one by one.</li>
4971 <li>Filechooser icons installed.</li>
4972 <li>Finder ignores return character when searching.
4973 Return key will initiate a search.<br>
4980 <div align="center">
4981 <strong>2.0</strong><br> 20/6/05
4986 <li>New codebase</li>