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 */
41 /* doesnt get processed in javahelp */
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>11/08/2020</em></strong></td>
62 <td align="left" valign="top">
66 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
67 residue in cursor mode
70 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
71 HTSJDK from 2.12 to 2.23
74 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
75 optimisations and improvements suggested by Bob Hanson and
76 improved compatibility with JalviewJS
79 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
80 alignments from Pfam and Rfam
83 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
84 import (no longer based on .gz extension)
87 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
90 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
91 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
95 <!-- JAL-3667 -->Improved warning messages, debug logging
96 and fixed Retry action when Jalview encounters errors when
97 saving or making backup files.
100 <!-- JAL-3676 -->Enhanced Jalview Java Console:
102 <li>Jalview's logging level can be configured</li>
103 <li>Copy to Clipboard Buttion</li>
107 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
108 when running on Linux (Requires Java 11+)
110 </ul> <em>Launching Jalview</em>
113 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
114 through a system property
117 <!-- JAL-3477 -->Improved built-in documentation and command
118 line help for configuring Jalview's memory
122 <td align="left" valign="top">
125 <!-- JAL-3493 -->Escape does not clear highlights on the
126 alignment (Since Jalview 2.10.3)
129 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
130 doesn't slide selected sequences, just sequence under cursor
133 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
134 multiple EMBL gene products shown forĀ a single contig
137 <!-- JAL-3696 -->Errors encountered when processing variants
138 from VCF files yield "Error processing VCF: Format specifier
142 <!-- JAL-3697 -->Count of features not shown can be wrong
143 when there are both local and complementary features mapped
144 to the position under the cursor
147 <!-- JAL-3673 -->Sequence ID for reference sequence is
148 clipped when Right align Sequence IDs enabled
151 <!-- JAL-2983 -->Slider with negative range values not
152 rendered correctly in VAqua4 (Since 2.10.4)
155 <!-- JAL-3685 -->Single quotes not displayed correctly in
156 internationalised text for some messages and log output
159 <!-- JAL-3490 -->Find doesn't report matches that span
160 hidden gapped columns
163 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
164 panels, Alignment viewport and annotation renderer.
166 </ul> <em>Developing Jalview</em>
169 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
170 data, causing cloverReport gradle task to fail with an
173 </ul> <em>New Known defects</em>
176 <!-- JAL-3576 -->Co-located features exported and re-imported
177 are ordered differently when shown on alignment and in
178 tooltips. (Also affects v2.11.1.0)
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.
184 Workaround is to try to save the file again, and if that
185 fails, delete the original file and save in place.
188 <!-- JAL-3702 -->Drag and drop of alignment file onto
189 alignment window not working correctly when in a HiDPI
193 <!-- JAL-3701 -->Stale build data in jalview standalone jar
194 builds (only affects 2.11.1.1 branch)
200 <td width="60" align="center" nowrap><strong><a
201 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
202 <em>22/04/2020</em></strong></td>
203 <td align="left" valign="top">
206 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
207 'virtual' codon features shown on protein (or vice versa)
208 for display in alignments, on structure views (including
209 transfer to UCSF chimera), in feature reports and for
213 <!-- JAL-3121 -->Feature attributes from VCF files can be
214 exported and re-imported as GFF3 files
217 <!-- JAL-3376 -->Capture VCF "fixed column" values
218 POS, ID, QUAL, FILTER as Feature Attributes
221 <!-- JAL-3375 -->More robust VCF numeric data field
222 validation while parsing
225 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
229 <!-- JAL-3535 -->Feature Settings dialog title includes name
233 <!-- JAL-3538 -->Font anti-aliasing in alignment views
237 <!-- JAL-3468 -->Very long feature descriptions truncated in
241 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
242 with no feature types visible
245 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
247 </ul><em>Jalview Installer</em>
250 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
251 in console (may be null when Jalview launched as executable jar or via conda)
254 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
257 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
260 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
262 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
263 </ul> <em>Release processes</em>
266 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
269 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
271 </ul> <em>Build System</em>
274 <!-- JAL-3510 -->Clover updated to 4.4.1
277 <!-- JAL-3513 -->Test code included in Clover coverage
281 <em>Groovy Scripts</em>
284 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
285 to stdout containing the consensus sequence for each
286 alignment in a Jalview session
289 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
290 genomic sequence_variant annotation from CDS as
291 missense_variant or synonymous_variant on protein products.
295 <td align="left" valign="top">
298 <!-- JAL-3581 -->Hidden sequence markers still visible when
299 'Show hidden markers' option is not ticked
302 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
303 PNG output when 'Automatically set ID width' is set in
304 jalview preferences or properties file
307 <!-- JAL-3571 -->Feature Editor dialog can be opened when
308 'Show Sequence Features' option is not ticked
311 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
312 buttons in Feature Settings dialog are clicked when no
316 <!-- JAL-3412 -->ID margins for CDS and Protein views not
317 equal when split frame is first opened
320 <!-- JAL-3296 -->Sequence position numbers in status bar not
321 correct after editing a sequence's start position
324 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
325 with annotation and exceptions thrown when only a few
326 columns shown in wrapped mode
329 <!-- JAL-3386 -->Sequence IDs missing in headless export of
330 wrapped alignment figure with annotations
333 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
334 ID fails with ClassCastException
337 <!-- JAL-3389 -->Chimera session not restored from Jalview
341 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
342 feature settings dialog also selects columns
345 <!-- JAL-3473 -->SpinnerNumberModel causes
346 IllegalArgumentException in some circumstances
349 <!-- JAL-3534 -->Multiple feature settings dialogs can be
353 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
354 alignment window is closed
357 <!-- JAL-3406 -->Credits missing some authors in Jalview
358 help documentation for 2.11.0 release
361 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
362 includes Pfam ID as sequence's accession rather than its
365 </ul> <em>Java 11 Compatibility issues</em>
368 <!-- JAL-2987 -->OSX - Can't view some search results in
369 PDB/Uniprot search panel
371 </ul> <em>Installer</em>
374 <!-- JAL-3447 -->Jalview should not create file associations
375 for 3D structure files (.pdb, .mmcif. .cif)
377 </ul> <em>Repository and Source Release</em>
380 <!-- JAL-3474 -->removed obsolete .cvsignore files from
384 <!-- JAL-3541 -->Clover report generation running out of
387 </ul> <em>New Known Issues</em>
390 <!-- JAL-3523 -->OSX - Current working directory not
391 preserved when Jalview.app launched with parameters from
395 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
396 clipped in headless figure export when Right Align option
400 <!-- JAL-3542 -->Jalview Installation type always reports
401 'Source' in console output
404 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
405 bamboo server but run fine locally.
411 <td width="60" align="center" nowrap>
412 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
413 <em>04/07/2019</em></strong>
415 <td align="left" valign="top">
418 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
419 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
420 source project) rather than InstallAnywhere
423 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
424 settings, receive over the air updates and launch specific
425 versions via (<a href="https://github.com/threerings/getdown">Three
429 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
430 formats supported by Jalview (including .jvp project files)
433 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
434 arguments and switch between different getdown channels
437 <!-- JAL-3141 -->Backup files created when saving Jalview project
442 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
443 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
445 <!-- JAL-2620 -->Alternative genetic code tables for
446 'Translate as cDNA'</li>
448 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
449 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
452 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
453 implementation that allows updates) used for Sequence Feature collections</li>
455 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
456 features can be filtered and shaded according to any
457 associated attributes (e.g. variant attributes from VCF
458 file, or key-value pairs imported from column 9 of GFF
462 <!-- JAL-2879 -->Feature Attributes and shading schemes
463 stored and restored from Jalview Projects
466 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
467 recognise variant features
470 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
471 sequences (also coloured red by default)
474 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
478 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
479 algorithm (Z-sort/transparency and filter aware)
482 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
488 <!-- JAL-3205 -->Symmetric score matrices for faster
489 tree and PCA calculations
491 <li><strong>Principal Components Analysis Viewer</strong>
494 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
495 and Viewer state saved in Jalview Project
497 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
500 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
504 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
509 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
511 <li><strong>Speed and Efficiency</strong>
514 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
515 multiple groups when working with large alignments
518 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
522 <li><strong>User Interface</strong>
525 <!-- JAL-2933 -->Finder panel remembers last position in each
529 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
530 what is shown)<br />Only visible regions of alignment are shown by
531 default (can be changed in user preferences)
534 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
535 to the Overwrite Dialog
538 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
542 <!-- JAL-1244 -->Status bar shows bounds when dragging a
543 selection region, and gap count when inserting or deleting gaps
546 <!-- JAL-3132 -->Status bar updates over sequence and annotation
550 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
554 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
558 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
561 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
565 <!-- JAL-3181 -->Consistent ordering of links in sequence id
569 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
571 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
575 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
576 <li><strong>Java 11 Support (not yet on general release)</strong>
579 <!-- -->OSX GUI integrations for App menu's 'About' entry and
584 <em>Deprecations</em>
586 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
587 capabilities removed from the Jalview Desktop
589 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
590 unmarshalling has been replaced by JAXB for Jalview projects
591 and XML based data retrieval clients</li>
592 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
593 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
594 </ul> <em>Documentation</em>
596 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
597 not supported in EPS figure export
599 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
600 </ul> <em>Development and Release Processes</em>
603 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
606 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
608 <!-- JAL-3225 -->Eclipse project configuration managed with
612 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
613 Bamboo continuous integration for unattended Test Suite
617 <!-- JAL-2864 -->Memory test suite to detect leaks in common
621 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
625 <!-- JAL-3248 -->Developer documentation migrated to
626 markdown (with HTML rendering)
629 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
632 <!-- JAL-3289 -->New URLs for publishing development
637 <td align="left" valign="top">
640 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
643 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
644 superposition in Jmol fail on Windows
647 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
648 structures for sequences with lots of PDB structures
651 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
655 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
656 project involving multiple views
659 <!-- JAL-3164 -->Overview for complementary view in a linked
660 CDS/Protein alignment is not updated when Hide Columns by
661 Annotation dialog hides columns
664 <!-- JAL-3158 -->Selection highlighting in the complement of a
665 CDS/Protein alignment stops working after making a selection in
666 one view, then making another selection in the other view
669 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
673 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
674 Settings and Jalview Preferences panels
677 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
678 overview with large alignments
681 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
682 region if columns were selected by dragging right-to-left and the
683 mouse moved to the left of the first column
686 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
687 hidden column marker via scale popup menu
690 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
691 doesn't tell users the invalid URL
694 <!-- JAL-2816 -->Tooltips displayed for features filtered by
698 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
699 show cross references or Fetch Database References are shown in
703 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
704 peptide sequence (computed variant shown as p.Res.null)
707 <!-- JAL-2060 -->'Graduated colour' option not offered for
708 manually created features (where feature score is Float.NaN)
711 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
712 when columns are hidden
715 <!-- JAL-3082 -->Regular expression error for '(' in Select
716 Columns by Annotation description
719 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
720 out of Scale or Annotation Panel
723 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
727 <!-- JAL-3074 -->Left/right drag in annotation can scroll
731 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
735 <!-- JAL-3002 -->Column display is out by one after Page Down,
736 Page Up in wrapped mode
739 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
742 <!-- JAL-2932 -->Finder searches in minimised alignments
745 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
746 on opening an alignment
749 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
753 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
754 different groups in the alignment are selected
757 <!-- JAL-2717 -->Internationalised colour scheme names not shown
761 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
765 <!-- JAL-3125 -->Value input for graduated feature colour
766 threshold gets 'unrounded'
769 <!-- JAL-2982 -->PCA image export doesn't respect background
773 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
776 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
779 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
783 <!-- JAL-2964 -->Associate Tree with All Views not restored from
787 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
788 shown in complementary view
791 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
792 without normalisation
795 <!-- JAL-3021 -->Sequence Details report should open positioned at top
799 <!-- JAL-914 -->Help page can be opened twice
802 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
804 </ul> <em>Editing</em>
807 <!-- JAL-2822 -->Start and End should be updated when sequence
808 data at beginning or end of alignment added/removed via 'Edit'
812 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
813 relocate sequence features correctly when start of sequence is
814 removed (Known defect since 2.10)
817 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
818 dialog corrupts dataset sequence
821 <!-- JAL-868 -->Structure colours not updated when associated tree
822 repartitions the alignment view (Regression in 2.10.5)
824 </ul> <em>Datamodel</em>
827 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
828 sequence's End is greater than its length
830 </ul> <em>Bugs fixed for Java 11 Support (not yet on
831 general release)</em>
834 <!-- JAL-3288 -->Menus work properly in split-screen
836 </ul> <em>New Known Defects</em>
839 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
842 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
843 regions of protein alignment.
846 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
847 is restored from a Jalview 2.11 project
850 <!-- JAL-3213 -->Alignment panel height can be too small after
854 <!-- JAL-3240 -->Display is incorrect after removing gapped
855 columns within hidden columns
858 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
859 window after dragging left to select columns to left of visible
863 <!-- JAL-2876 -->Features coloured according to their description
864 string and thresholded by score in earlier versions of Jalview are
865 not shown as thresholded features in 2.11. To workaround please
866 create a Score filter instead.
869 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
871 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
874 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
875 alignments with multiple views can close views unexpectedly
878 <em>Java 11 Specific defects</em>
881 <!-- JAL-3235 -->Jalview Properties file is not sorted
882 alphabetically when saved
888 <td width="60" nowrap>
890 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
893 <td><div align="left">
897 <!-- JAL-3101 -->Default memory for Jalview webstart and
898 InstallAnywhere increased to 1G.
901 <!-- JAL-247 -->Hidden sequence markers and representative
902 sequence bolding included when exporting alignment as EPS,
903 SVG, PNG or HTML. <em>Display is configured via the
904 Format menu, or for command-line use via a Jalview
905 properties file.</em>
908 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
909 API and sequence data now imported as JSON.
912 <!-- JAL-3065 -->Change in recommended way of starting
913 Jalview via a Java command line: add jars in lib directory
914 to CLASSPATH, rather than via the deprecated java.ext.dirs
921 <!-- JAL-3047 -->Support added to execute test suite
922 instrumented with <a href="http://openclover.org/">Open
927 <td><div align="left">
931 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
932 row shown in Feredoxin Structure alignment view of example
936 <!-- JAL-2854 -->Annotation obscures sequences if lots of
937 annotation displayed.
940 <!-- JAL-3107 -->Group conservation/consensus not shown
941 for newly created group when 'Apply to all groups'
945 <!-- JAL-3087 -->Corrupted display when switching to
946 wrapped mode when sequence panel's vertical scrollbar is
950 <!-- JAL-3003 -->Alignment is black in exported EPS file
951 when sequences are selected in exported view.</em>
954 <!-- JAL-3059 -->Groups with different coloured borders
955 aren't rendered with correct colour.
958 <!-- JAL-3092 -->Jalview could hang when importing certain
959 types of knotted RNA secondary structure.
962 <!-- JAL-3095 -->Sequence highlight and selection in
963 trimmed VARNA 2D structure is incorrect for sequences that
967 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
968 annotation when columns are inserted into an alignment,
969 and when exporting as Stockholm flatfile.
972 <!-- JAL-3053 -->Jalview annotation rows containing upper
973 and lower-case 'E' and 'H' do not automatically get
974 treated as RNA secondary structure.
977 <!-- JAL-3106 -->.jvp should be used as default extension
978 (not .jar) when saving a Jalview project file.
981 <!-- JAL-3105 -->Mac Users: closing a window correctly
982 transfers focus to previous window on OSX
985 <em>Java 10 Issues Resolved</em>
988 <!-- JAL-2988 -->OSX - Can't save new files via the File
989 or export menus by typing in a name into the Save dialog
993 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
994 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
995 'look and feel' which has improved compatibility with the
996 latest version of OSX.
1003 <td width="60" nowrap>
1004 <div align="center">
1005 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1006 <em>7/06/2018</em></strong>
1009 <td><div align="left">
1013 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1014 annotation retrieved from Uniprot
1017 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1018 onto the Jalview Desktop
1022 <td><div align="left">
1026 <!-- JAL-3017 -->Cannot import features with multiple
1027 variant elements (blocks import of some Uniprot records)
1030 <!-- JAL-2997 -->Clustal files with sequence positions in
1031 right-hand column parsed correctly
1034 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1035 not alignment area in exported graphic
1038 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1039 window has input focus
1042 <!-- JAL-2992 -->Annotation panel set too high when
1043 annotation added to view (Windows)
1046 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1047 network connectivity is poor
1050 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1051 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1052 the currently open URL and links from a page viewed in
1053 Firefox or Chrome on Windows is now fully supported. If
1054 you are using Edge, only links in the page can be
1055 dragged, and with Internet Explorer, only the currently
1056 open URL in the browser can be dropped onto Jalview.</em>
1059 <em>New Known Defects</em>
1061 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1066 <td width="60" nowrap>
1067 <div align="center">
1068 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1071 <td><div align="left">
1075 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1076 for disabling automatic superposition of multiple
1077 structures and open structures in existing views
1080 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1081 ID and annotation area margins can be click-dragged to
1085 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1089 <!-- JAL-2759 -->Improved performance for large alignments
1090 and lots of hidden columns
1093 <!-- JAL-2593 -->Improved performance when rendering lots
1094 of features (particularly when transparency is disabled)
1097 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1098 exchange of Jalview features and Chimera attributes made
1104 <td><div align="left">
1107 <!-- JAL-2899 -->Structure and Overview aren't updated
1108 when Colour By Annotation threshold slider is adjusted
1111 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1112 overlapping alignment panel
1115 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1119 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1120 improved: CDS not handled correctly if transcript has no
1124 <!-- JAL-2321 -->Secondary structure and temperature
1125 factor annotation not added to sequence when local PDB
1126 file associated with it by drag'n'drop or structure
1130 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1131 dialog doesn't import PDB files dropped on an alignment
1134 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1135 scroll bar doesn't work for some CDS/Protein views
1138 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1139 Java 1.8u153 onwards and Java 1.9u4+.
1142 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1143 columns in annotation row
1146 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1147 honored in batch mode
1150 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1151 for structures added to existing Jmol view
1154 <!-- JAL-2223 -->'View Mappings' includes duplicate
1155 entries after importing project with multiple views
1158 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1159 protein sequences via SIFTS from associated PDB entries
1160 with negative residue numbers or missing residues fails
1163 <!-- JAL-2952 -->Exception when shading sequence with negative
1164 Temperature Factor values from annotated PDB files (e.g.
1165 as generated by CONSURF)
1168 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1169 tooltip doesn't include a text description of mutation
1172 <!-- JAL-2922 -->Invert displayed features very slow when
1173 structure and/or overview windows are also shown
1176 <!-- JAL-2954 -->Selecting columns from highlighted regions
1177 very slow for alignments with large numbers of sequences
1180 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1181 with 'StringIndexOutOfBounds'
1184 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1185 platforms running Java 10
1188 <!-- JAL-2960 -->Adding a structure to existing structure
1189 view appears to do nothing because the view is hidden behind the alignment view
1195 <!-- JAL-2926 -->Copy consensus sequence option in applet
1196 should copy the group consensus when popup is opened on it
1202 <!-- JAL-2913 -->Fixed ID width preference is not respected
1205 <em>New Known Defects</em>
1208 <!-- JAL-2973 --> Exceptions occasionally raised when
1209 editing a large alignment and overview is displayed
1212 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1213 repeatedly after a series of edits even when the overview
1214 is no longer reflecting updates
1217 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1218 structures for protein subsequence (if 'Trim Retrieved
1219 Sequences' enabled) or Ensembl isoforms (Workaround in
1220 2.10.4 is to fail back to N&W mapping)
1223 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1224 option gives blank output
1231 <td width="60" nowrap>
1232 <div align="center">
1233 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1236 <td><div align="left">
1237 <ul><li>Updated Certum Codesigning Certificate
1238 (Valid till 30th November 2018)</li></ul></div></td>
1239 <td><div align="left">
1240 <em>Desktop</em><ul>
1242 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1243 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1244 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1245 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1246 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1247 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1248 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1254 <td width="60" nowrap>
1255 <div align="center">
1256 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1259 <td><div align="left">
1263 <!-- JAL-2446 -->Faster and more efficient management and
1264 rendering of sequence features
1267 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1268 429 rate limit request hander
1271 <!-- JAL-2773 -->Structure views don't get updated unless
1272 their colours have changed
1275 <!-- JAL-2495 -->All linked sequences are highlighted for
1276 a structure mousover (Jmol) or selection (Chimera)
1279 <!-- JAL-2790 -->'Cancel' button in progress bar for
1280 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1283 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1284 view from Ensembl locus cross-references
1287 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1291 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1292 feature can be disabled
1295 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1296 PDB easier retrieval of sequences for lists of IDs
1299 <!-- JAL-2758 -->Short names for sequences retrieved from
1305 <li>Groovy interpreter updated to 2.4.12</li>
1306 <li>Example groovy script for generating a matrix of
1307 percent identity scores for current alignment.</li>
1309 <em>Testing and Deployment</em>
1312 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1316 <td><div align="left">
1320 <!-- JAL-2643 -->Pressing tab after updating the colour
1321 threshold text field doesn't trigger an update to the
1325 <!-- JAL-2682 -->Race condition when parsing sequence ID
1329 <!-- JAL-2608 -->Overview windows are also closed when
1330 alignment window is closed
1333 <!-- JAL-2548 -->Export of features doesn't always respect
1337 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1338 takes a long time in Cursor mode
1344 <!-- JAL-2777 -->Structures with whitespace chainCode
1345 cannot be viewed in Chimera
1348 <!-- JAL-2728 -->Protein annotation panel too high in
1352 <!-- JAL-2757 -->Can't edit the query after the server
1353 error warning icon is shown in Uniprot and PDB Free Text
1357 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1360 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1363 <!-- JAL-2739 -->Hidden column marker in last column not
1364 rendered when switching back from Wrapped to normal view
1367 <!-- JAL-2768 -->Annotation display corrupted when
1368 scrolling right in unwapped alignment view
1371 <!-- JAL-2542 -->Existing features on subsequence
1372 incorrectly relocated when full sequence retrieved from
1376 <!-- JAL-2733 -->Last reported memory still shown when
1377 Desktop->Show Memory is unticked (OSX only)
1380 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1381 features of same type and group to be selected for
1385 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1386 alignments when hidden columns are present
1389 <!-- JAL-2392 -->Jalview freezes when loading and
1390 displaying several structures
1393 <!-- JAL-2732 -->Black outlines left after resizing or
1397 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1398 within the Jalview desktop on OSX
1401 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1402 when in wrapped alignment mode
1405 <!-- JAL-2636 -->Scale mark not shown when close to right
1406 hand end of alignment
1409 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1410 each selected sequence do not have correct start/end
1414 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1415 after canceling the Alignment Window's Font dialog
1418 <!-- JAL-2036 -->Show cross-references not enabled after
1419 restoring project until a new view is created
1422 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1423 URL links appears when only default EMBL-EBI link is
1424 configured (since 2.10.2b2)
1427 <!-- JAL-2775 -->Overview redraws whole window when box
1428 position is adjusted
1431 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1432 in a multi-chain structure when viewing alignment
1433 involving more than one chain (since 2.10)
1436 <!-- JAL-2811 -->Double residue highlights in cursor mode
1437 if new selection moves alignment window
1440 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1441 arrow key in cursor mode to pass hidden column marker
1444 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1445 that produces correctly annotated transcripts and products
1448 <!-- JAL-2776 -->Toggling a feature group after first time
1449 doesn't update associated structure view
1452 <em>Applet</em><br />
1455 <!-- JAL-2687 -->Concurrent modification exception when
1456 closing alignment panel
1459 <em>BioJSON</em><br />
1462 <!-- JAL-2546 -->BioJSON export does not preserve
1463 non-positional features
1466 <em>New Known Issues</em>
1469 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1470 sequence features correctly (for many previous versions of
1474 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1475 using cursor in wrapped panel other than top
1478 <!-- JAL-2791 -->Select columns containing feature ignores
1479 graduated colour threshold
1482 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1483 always preserve numbering and sequence features
1486 <em>Known Java 9 Issues</em>
1489 <!-- JAL-2902 -->Groovy Console very slow to open and is
1490 not responsive when entering characters (Webstart, Java
1497 <td width="60" nowrap>
1498 <div align="center">
1499 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1500 <em>2/10/2017</em></strong>
1503 <td><div align="left">
1504 <em>New features in Jalview Desktop</em>
1507 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1509 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1513 <td><div align="left">
1517 <td width="60" nowrap>
1518 <div align="center">
1519 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1520 <em>7/9/2017</em></strong>
1523 <td><div align="left">
1527 <!-- JAL-2588 -->Show gaps in overview window by colouring
1528 in grey (sequences used to be coloured grey, and gaps were
1532 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1536 <!-- JAL-2587 -->Overview updates immediately on increase
1537 in size and progress bar shown as higher resolution
1538 overview is recalculated
1543 <td><div align="left">
1547 <!-- JAL-2664 -->Overview window redraws every hidden
1548 column region row by row
1551 <!-- JAL-2681 -->duplicate protein sequences shown after
1552 retrieving Ensembl crossrefs for sequences from Uniprot
1555 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1556 format setting is unticked
1559 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1560 if group has show boxes format setting unticked
1563 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1564 autoscrolling whilst dragging current selection group to
1565 include sequences and columns not currently displayed
1568 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1569 assemblies are imported via CIF file
1572 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1573 displayed when threshold or conservation colouring is also
1577 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1581 <!-- JAL-2673 -->Jalview continues to scroll after
1582 dragging a selected region off the visible region of the
1586 <!-- JAL-2724 -->Cannot apply annotation based
1587 colourscheme to all groups in a view
1590 <!-- JAL-2511 -->IDs don't line up with sequences
1591 initially after font size change using the Font chooser or
1598 <td width="60" nowrap>
1599 <div align="center">
1600 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1603 <td><div align="left">
1604 <em>Calculations</em>
1608 <!-- JAL-1933 -->Occupancy annotation row shows number of
1609 ungapped positions in each column of the alignment.
1612 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1613 a calculation dialog box
1616 <!-- JAL-2379 -->Revised implementation of PCA for speed
1617 and memory efficiency (~30x faster)
1620 <!-- JAL-2403 -->Revised implementation of sequence
1621 similarity scores as used by Tree, PCA, Shading Consensus
1622 and other calculations
1625 <!-- JAL-2416 -->Score matrices are stored as resource
1626 files within the Jalview codebase
1629 <!-- JAL-2500 -->Trees computed on Sequence Feature
1630 Similarity may have different topology due to increased
1637 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1638 model for alignments and groups
1641 <!-- JAL-384 -->Custom shading schemes created via groovy
1648 <!-- JAL-2526 -->Efficiency improvements for interacting
1649 with alignment and overview windows
1652 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1656 <!-- JAL-2388 -->Hidden columns and sequences can be
1660 <!-- JAL-2611 -->Click-drag in visible area allows fine
1661 adjustment of visible position
1665 <em>Data import/export</em>
1668 <!-- JAL-2535 -->Posterior probability annotation from
1669 Stockholm files imported as sequence associated annotation
1672 <!-- JAL-2507 -->More robust per-sequence positional
1673 annotation input/output via stockholm flatfile
1676 <!-- JAL-2533 -->Sequence names don't include file
1677 extension when importing structure files without embedded
1678 names or PDB accessions
1681 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1682 format sequence substitution matrices
1685 <em>User Interface</em>
1688 <!-- JAL-2447 --> Experimental Features Checkbox in
1689 Desktop's Tools menu to hide or show untested features in
1693 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1694 via Overview or sequence motif search operations
1697 <!-- JAL-2547 -->Amend sequence features dialog box can be
1698 opened by double clicking gaps within sequence feature
1702 <!-- JAL-1476 -->Status bar message shown when not enough
1703 aligned positions were available to create a 3D structure
1707 <em>3D Structure</em>
1710 <!-- JAL-2430 -->Hidden regions in alignment views are not
1711 coloured in linked structure views
1714 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1715 file-based command exchange
1718 <!-- JAL-2375 -->Structure chooser automatically shows
1719 Cached Structures rather than querying the PDBe if
1720 structures are already available for sequences
1723 <!-- JAL-2520 -->Structures imported via URL are cached in
1724 the Jalview project rather than downloaded again when the
1725 project is reopened.
1728 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1729 to transfer Chimera's structure attributes as Jalview
1730 features, and vice-versa (<strong>Experimental
1734 <em>Web Services</em>
1737 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1740 <!-- JAL-2335 -->Filter non-standard amino acids and
1741 nucleotides when submitting to AACon and other MSA
1745 <!-- JAL-2316, -->URLs for viewing database
1746 cross-references provided by identifiers.org and the
1747 EMBL-EBI's MIRIAM DB
1754 <!-- JAL-2344 -->FileFormatI interface for describing and
1755 identifying file formats (instead of String constants)
1758 <!-- JAL-2228 -->FeatureCounter script refactored for
1759 efficiency when counting all displayed features (not
1760 backwards compatible with 2.10.1)
1763 <em>Example files</em>
1766 <!-- JAL-2631 -->Graduated feature colour style example
1767 included in the example feature file
1770 <em>Documentation</em>
1773 <!-- JAL-2339 -->Release notes reformatted for readability
1774 with the built-in Java help viewer
1777 <!-- JAL-1644 -->Find documentation updated with 'search
1778 sequence description' option
1784 <!-- JAL-2485, -->External service integration tests for
1785 Uniprot REST Free Text Search Client
1788 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1791 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1796 <td><div align="left">
1797 <em>Calculations</em>
1800 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1801 matrix - C->R should be '-3'<br />Old matrix restored
1802 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1804 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1805 Jalview's treatment of gaps in PCA and substitution matrix
1806 based Tree calculations.<br /> <br />In earlier versions
1807 of Jalview, gaps matching gaps were penalised, and gaps
1808 matching non-gaps penalised even more. In the PCA
1809 calculation, gaps were actually treated as non-gaps - so
1810 different costs were applied, which meant Jalview's PCAs
1811 were different to those produced by SeqSpace.<br />Jalview
1812 now treats gaps in the same way as SeqSpace (ie it scores
1813 them as 0). <br /> <br />Enter the following in the
1814 Groovy console to restore pre-2.10.2 behaviour:<br />
1815 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1816 // for 2.10.1 mode <br />
1817 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1818 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1819 these settings will affect all subsequent tree and PCA
1820 calculations (not recommended)</em></li>
1822 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1823 scaling of branch lengths for trees computed using
1824 Sequence Feature Similarity.
1827 <!-- JAL-2377 -->PCA calculation could hang when
1828 generating output report when working with highly
1829 redundant alignments
1832 <!-- JAL-2544 --> Sort by features includes features to
1833 right of selected region when gaps present on right-hand
1837 <em>User Interface</em>
1840 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1841 doesn't reselect a specific sequence's associated
1842 annotation after it was used for colouring a view
1845 <!-- JAL-2419 -->Current selection lost if popup menu
1846 opened on a region of alignment without groups
1849 <!-- JAL-2374 -->Popup menu not always shown for regions
1850 of an alignment with overlapping groups
1853 <!-- JAL-2310 -->Finder double counts if both a sequence's
1854 name and description match
1857 <!-- JAL-2370 -->Hiding column selection containing two
1858 hidden regions results in incorrect hidden regions
1861 <!-- JAL-2386 -->'Apply to all groups' setting when
1862 changing colour does not apply Conservation slider value
1866 <!-- JAL-2373 -->Percentage identity and conservation menu
1867 items do not show a tick or allow shading to be disabled
1870 <!-- JAL-2385 -->Conservation shading or PID threshold
1871 lost when base colourscheme changed if slider not visible
1874 <!-- JAL-2547 -->Sequence features shown in tooltip for
1875 gaps before start of features
1878 <!-- JAL-2623 -->Graduated feature colour threshold not
1879 restored to UI when feature colour is edited
1882 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1883 a time when scrolling vertically in wrapped mode.
1886 <!-- JAL-2630 -->Structure and alignment overview update
1887 as graduate feature colour settings are modified via the
1891 <!-- JAL-2034 -->Overview window doesn't always update
1892 when a group defined on the alignment is resized
1895 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1896 wrapped view result in positional status updates
1900 <!-- JAL-2563 -->Status bar doesn't show position for
1901 ambiguous amino acid and nucleotide symbols
1904 <!-- JAL-2602 -->Copy consensus sequence failed if
1905 alignment included gapped columns
1908 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1909 widgets don't permanently disappear
1912 <!-- JAL-2503 -->Cannot select or filter quantitative
1913 annotation that are shown only as column labels (e.g.
1914 T-Coffee column reliability scores)
1917 <!-- JAL-2594 -->Exception thrown if trying to create a
1918 sequence feature on gaps only
1921 <!-- JAL-2504 -->Features created with 'New feature'
1922 button from a Find inherit previously defined feature type
1923 rather than the Find query string
1926 <!-- JAL-2423 -->incorrect title in output window when
1927 exporting tree calculated in Jalview
1930 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1931 and then revealing them reorders sequences on the
1935 <!-- JAL-964 -->Group panel in sequence feature settings
1936 doesn't update to reflect available set of groups after
1937 interactively adding or modifying features
1940 <!-- JAL-2225 -->Sequence Database chooser unusable on
1944 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1945 only excluded gaps in current sequence and ignored
1952 <!-- JAL-2421 -->Overview window visible region moves
1953 erratically when hidden rows or columns are present
1956 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1957 Structure Viewer's colour menu don't correspond to
1961 <!-- JAL-2405 -->Protein specific colours only offered in
1962 colour and group colour menu for protein alignments
1965 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1966 reflect currently selected view or group's shading
1970 <!-- JAL-2624 -->Feature colour thresholds not respected
1971 when rendered on overview and structures when opacity at
1975 <!-- JAL-2589 -->User defined gap colour not shown in
1976 overview when features overlaid on alignment
1979 <!-- JAL-2567 -->Feature settings for different views not
1980 recovered correctly from Jalview project file
1983 <!-- JAL-2256 -->Feature colours in overview when first opened
1984 (automatically via preferences) are different to the main
1988 <em>Data import/export</em>
1991 <!-- JAL-2576 -->Very large alignments take a long time to
1995 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1996 added after a sequence was imported are not written to
2000 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2001 when importing RNA secondary structure via Stockholm
2004 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2005 not shown in correct direction for simple pseudoknots
2008 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2009 with lightGray or darkGray via features file (but can
2013 <!-- JAL-2383 -->Above PID colour threshold not recovered
2014 when alignment view imported from project
2017 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2018 structure and sequences extracted from structure files
2019 imported via URL and viewed in Jmol
2022 <!-- JAL-2520 -->Structures loaded via URL are saved in
2023 Jalview Projects rather than fetched via URL again when
2024 the project is loaded and the structure viewed
2027 <em>Web Services</em>
2030 <!-- JAL-2519 -->EnsemblGenomes example failing after
2031 release of Ensembl v.88
2034 <!-- JAL-2366 -->Proxy server address and port always
2035 appear enabled in Preferences->Connections
2038 <!-- JAL-2461 -->DAS registry not found exceptions
2039 removed from console output
2042 <!-- JAL-2582 -->Cannot retrieve protein products from
2043 Ensembl by Peptide ID
2046 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2047 created from SIFTs, and spurious 'Couldn't open structure
2048 in Chimera' errors raised after April 2017 update (problem
2049 due to 'null' string rather than empty string used for
2050 residues with no corresponding PDB mapping).
2053 <em>Application UI</em>
2056 <!-- JAL-2361 -->User Defined Colours not added to Colour
2060 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2061 case' residues (button in colourscheme editor debugged and
2062 new documentation and tooltips added)
2065 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2066 doesn't restore group-specific text colour thresholds
2069 <!-- JAL-2243 -->Feature settings panel does not update as
2070 new features are added to alignment
2073 <!-- JAL-2532 -->Cancel in feature settings reverts
2074 changes to feature colours via the Amend features dialog
2077 <!-- JAL-2506 -->Null pointer exception when attempting to
2078 edit graduated feature colour via amend features dialog
2082 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2083 selection menu changes colours of alignment views
2086 <!-- JAL-2426 -->Spurious exceptions in console raised
2087 from alignment calculation workers after alignment has
2091 <!-- JAL-1608 -->Typo in selection popup menu - Create
2092 groups now 'Create Group'
2095 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2096 Create/Undefine group doesn't always work
2099 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2100 shown again after pressing 'Cancel'
2103 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2104 adjusts start position in wrap mode
2107 <!-- JAL-2563 -->Status bar doesn't show positions for
2108 ambiguous amino acids
2111 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2112 CDS/Protein view after CDS sequences added for aligned
2116 <!-- JAL-2592 -->User defined colourschemes called 'User
2117 Defined' don't appear in Colours menu
2123 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2124 score models doesn't always result in an updated PCA plot
2127 <!-- JAL-2442 -->Features not rendered as transparent on
2128 overview or linked structure view
2131 <!-- JAL-2372 -->Colour group by conservation doesn't
2135 <!-- JAL-2517 -->Hitting Cancel after applying
2136 user-defined colourscheme doesn't restore original
2143 <!-- JAL-2314 -->Unit test failure:
2144 jalview.ws.jabaws.RNAStructExportImport setup fails
2147 <!-- JAL-2307 -->Unit test failure:
2148 jalview.ws.sifts.SiftsClientTest due to compatibility
2149 problems with deep array comparison equality asserts in
2150 successive versions of TestNG
2153 <!-- JAL-2479 -->Relocated StructureChooserTest and
2154 ParameterUtilsTest Unit tests to Network suite
2157 <em>New Known Issues</em>
2160 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2161 phase after a sequence motif find operation
2164 <!-- JAL-2550 -->Importing annotation file with rows
2165 containing just upper and lower case letters are
2166 interpreted as WUSS RNA secondary structure symbols
2169 <!-- JAL-2590 -->Cannot load and display Newick trees
2170 reliably from eggnog Ortholog database
2173 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2174 containing features of type Highlight' when 'B' is pressed
2175 to mark columns containing highlighted regions.
2178 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2179 doesn't always add secondary structure annotation.
2184 <td width="60" nowrap>
2185 <div align="center">
2186 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2189 <td><div align="left">
2193 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2194 for all consensus calculations
2197 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2200 <li>Updated Jalview's Certum code signing certificate
2203 <em>Application</em>
2206 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2207 set of database cross-references, sorted alphabetically
2210 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2211 from database cross references. Users with custom links
2212 will receive a <a href="webServices/urllinks.html#warning">warning
2213 dialog</a> asking them to update their preferences.
2216 <!-- JAL-2287-->Cancel button and escape listener on
2217 dialog warning user about disconnecting Jalview from a
2221 <!-- JAL-2320-->Jalview's Chimera control window closes if
2222 the Chimera it is connected to is shut down
2225 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2226 columns menu item to mark columns containing highlighted
2227 regions (e.g. from structure selections or results of a
2231 <!-- JAL-2284-->Command line option for batch-generation
2232 of HTML pages rendering alignment data with the BioJS
2242 <!-- JAL-2286 -->Columns with more than one modal residue
2243 are not coloured or thresholded according to percent
2244 identity (first observed in Jalview 2.8.2)
2247 <!-- JAL-2301 -->Threonine incorrectly reported as not
2251 <!-- JAL-2318 -->Updates to documentation pages (above PID
2252 threshold, amino acid properties)
2255 <!-- JAL-2292 -->Lower case residues in sequences are not
2256 reported as mapped to residues in a structure file in the
2260 <!--JAL-2324 -->Identical features with non-numeric scores
2261 could be added multiple times to a sequence
2264 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2265 bond features shown as two highlighted residues rather
2266 than a range in linked structure views, and treated
2267 correctly when selecting and computing trees from features
2270 <!-- JAL-2281-->Custom URL links for database
2271 cross-references are matched to database name regardless
2276 <em>Application</em>
2279 <!-- JAL-2282-->Custom URL links for specific database
2280 names without regular expressions also offer links from
2284 <!-- JAL-2315-->Removing a single configured link in the
2285 URL links pane in Connections preferences doesn't actually
2286 update Jalview configuration
2289 <!-- JAL-2272-->CTRL-Click on a selected region to open
2290 the alignment area popup menu doesn't work on El-Capitan
2293 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2294 files with similarly named sequences if dropped onto the
2298 <!-- JAL-2312 -->Additional mappings are shown for PDB
2299 entries where more chains exist in the PDB accession than
2300 are reported in the SIFTS file
2303 <!-- JAL-2317-->Certain structures do not get mapped to
2304 the structure view when displayed with Chimera
2307 <!-- JAL-2317-->No chains shown in the Chimera view
2308 panel's View->Show Chains submenu
2311 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2312 work for wrapped alignment views
2315 <!--JAL-2197 -->Rename UI components for running JPred
2316 predictions from 'JNet' to 'JPred'
2319 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2320 corrupted when annotation panel vertical scroll is not at
2321 first annotation row
2324 <!--JAL-2332 -->Attempting to view structure for Hen
2325 lysozyme results in a PDB Client error dialog box
2328 <!-- JAL-2319 -->Structure View's mapping report switched
2329 ranges for PDB and sequence for SIFTS
2332 SIFTS 'Not_Observed' residues mapped to non-existant
2336 <!-- <em>New Known Issues</em>
2343 <td width="60" nowrap>
2344 <div align="center">
2345 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2346 <em>25/10/2016</em></strong>
2349 <td><em>Application</em>
2351 <li>3D Structure chooser opens with 'Cached structures'
2352 view if structures already loaded</li>
2353 <li>Progress bar reports models as they are loaded to
2354 structure views</li>
2360 <li>Colour by conservation always enabled and no tick
2361 shown in menu when BLOSUM or PID shading applied</li>
2362 <li>FER1_ARATH and FER2_ARATH labels were switched in
2363 example sequences/projects/trees</li>
2365 <em>Application</em>
2367 <li>Jalview projects with views of local PDB structure
2368 files saved on Windows cannot be opened on OSX</li>
2369 <li>Multiple structure views can be opened and superposed
2370 without timeout for structures with multiple models or
2371 multiple sequences in alignment</li>
2372 <li>Cannot import or associated local PDB files without a
2373 PDB ID HEADER line</li>
2374 <li>RMSD is not output in Jmol console when superposition
2376 <li>Drag and drop of URL from Browser fails for Linux and
2377 OSX versions earlier than El Capitan</li>
2378 <li>ENA client ignores invalid content from ENA server</li>
2379 <li>Exceptions are not raised in console when ENA client
2380 attempts to fetch non-existent IDs via Fetch DB Refs UI
2382 <li>Exceptions are not raised in console when a new view
2383 is created on the alignment</li>
2384 <li>OSX right-click fixed for group selections: CMD-click
2385 to insert/remove gaps in groups and CTRL-click to open group
2388 <em>Build and deployment</em>
2390 <li>URL link checker now copes with multi-line anchor
2393 <em>New Known Issues</em>
2395 <li>Drag and drop from URL links in browsers do not work
2402 <td width="60" nowrap>
2403 <div align="center">
2404 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2407 <td><em>General</em>
2410 <!-- JAL-2124 -->Updated Spanish translations.
2413 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2414 for importing structure data to Jalview. Enables mmCIF and
2418 <!-- JAL-192 --->Alignment ruler shows positions relative to
2422 <!-- JAL-2202 -->Position/residue shown in status bar when
2423 mousing over sequence associated annotation
2426 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2430 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2431 '()', canonical '[]' and invalid '{}' base pair populations
2435 <!-- JAL-2092 -->Feature settings popup menu options for
2436 showing or hiding columns containing a feature
2439 <!-- JAL-1557 -->Edit selected group by double clicking on
2440 group and sequence associated annotation labels
2443 <!-- JAL-2236 -->Sequence name added to annotation label in
2444 select/hide columns by annotation and colour by annotation
2448 </ul> <em>Application</em>
2451 <!-- JAL-2050-->Automatically hide introns when opening a
2452 gene/transcript view
2455 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2459 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2460 structure mappings with the EMBL-EBI PDBe SIFTS database
2463 <!-- JAL-2079 -->Updated download sites used for Rfam and
2464 Pfam sources to xfam.org
2467 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2470 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2471 over sequences in Jalview
2474 <!-- JAL-2027-->Support for reverse-complement coding
2475 regions in ENA and EMBL
2478 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2479 for record retrieval via ENA rest API
2482 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2486 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2487 groovy script execution
2490 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2491 alignment window's Calculate menu
2494 <!-- JAL-1812 -->Allow groovy scripts that call
2495 Jalview.getAlignFrames() to run in headless mode
2498 <!-- JAL-2068 -->Support for creating new alignment
2499 calculation workers from groovy scripts
2502 <!-- JAL-1369 --->Store/restore reference sequence in
2506 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2507 associations are now saved/restored from project
2510 <!-- JAL-1993 -->Database selection dialog always shown
2511 before sequence fetcher is opened
2514 <!-- JAL-2183 -->Double click on an entry in Jalview's
2515 database chooser opens a sequence fetcher
2518 <!-- JAL-1563 -->Free-text search client for UniProt using
2519 the UniProt REST API
2522 <!-- JAL-2168 -->-nonews command line parameter to prevent
2523 the news reader opening
2526 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2527 querying stored in preferences
2530 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2534 <!-- JAL-1977-->Tooltips shown on database chooser
2537 <!-- JAL-391 -->Reverse complement function in calculate
2538 menu for nucleotide sequences
2541 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2542 and feature counts preserves alignment ordering (and
2543 debugged for complex feature sets).
2546 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2547 viewing structures with Jalview 2.10
2550 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2551 genome, transcript CCDS and gene ids via the Ensembl and
2552 Ensembl Genomes REST API
2555 <!-- JAL-2049 -->Protein sequence variant annotation
2556 computed for 'sequence_variant' annotation on CDS regions
2560 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2564 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2565 Ref Fetcher fails to match, or otherwise updates sequence
2566 data from external database records.
2569 <!-- JAL-2154 -->Revised Jalview Project format for
2570 efficient recovery of sequence coding and alignment
2571 annotation relationships.
2573 </ul> <!-- <em>Applet</em>
2584 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2588 <!-- JAL-2018-->Export features in Jalview format (again)
2589 includes graduated colourschemes
2592 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2593 working with big alignments and lots of hidden columns
2596 <!-- JAL-2053-->Hidden column markers not always rendered
2597 at right of alignment window
2600 <!-- JAL-2067 -->Tidied up links in help file table of
2604 <!-- JAL-2072 -->Feature based tree calculation not shown
2608 <!-- JAL-2075 -->Hidden columns ignored during feature
2609 based tree calculation
2612 <!-- JAL-2065 -->Alignment view stops updating when show
2613 unconserved enabled for group on alignment
2616 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2620 <!-- JAL-2146 -->Alignment column in status incorrectly
2621 shown as "Sequence position" when mousing over
2625 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2626 hidden columns present
2629 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2630 user created annotation added to alignment
2633 <!-- JAL-1841 -->RNA Structure consensus only computed for
2634 '()' base pair annotation
2637 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2638 in zero scores for all base pairs in RNA Structure
2642 <!-- JAL-2174-->Extend selection with columns containing
2646 <!-- JAL-2275 -->Pfam format writer puts extra space at
2647 beginning of sequence
2650 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2654 <!-- JAL-2238 -->Cannot create groups on an alignment from
2655 from a tree when t-coffee scores are shown
2658 <!-- JAL-1836,1967 -->Cannot import and view PDB
2659 structures with chains containing negative resnums (4q4h)
2662 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2666 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2667 to Clustal, PIR and PileUp output
2670 <!-- JAL-2008 -->Reordering sequence features that are
2671 not visible causes alignment window to repaint
2674 <!-- JAL-2006 -->Threshold sliders don't work in
2675 graduated colour and colour by annotation row for e-value
2676 scores associated with features and annotation rows
2679 <!-- JAL-1797 -->amino acid physicochemical conservation
2680 calculation should be case independent
2683 <!-- JAL-2173 -->Remove annotation also updates hidden
2687 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2688 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2689 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2692 <!-- JAL-2065 -->Null pointer exceptions and redraw
2693 problems when reference sequence defined and 'show
2694 non-conserved' enabled
2697 <!-- JAL-1306 -->Quality and Conservation are now shown on
2698 load even when Consensus calculation is disabled
2701 <!-- JAL-1932 -->Remove right on penultimate column of
2702 alignment does nothing
2705 <em>Application</em>
2708 <!-- JAL-1552-->URLs and links can't be imported by
2709 drag'n'drop on OSX when launched via webstart (note - not
2710 yet fixed for El Capitan)
2713 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2714 output when running on non-gb/us i18n platforms
2717 <!-- JAL-1944 -->Error thrown when exporting a view with
2718 hidden sequences as flat-file alignment
2721 <!-- JAL-2030-->InstallAnywhere distribution fails when
2725 <!-- JAL-2080-->Jalview very slow to launch via webstart
2726 (also hotfix for 2.9.0b2)
2729 <!-- JAL-2085 -->Cannot save project when view has a
2730 reference sequence defined
2733 <!-- JAL-1011 -->Columns are suddenly selected in other
2734 alignments and views when revealing hidden columns
2737 <!-- JAL-1989 -->Hide columns not mirrored in complement
2738 view in a cDNA/Protein splitframe
2741 <!-- JAL-1369 -->Cannot save/restore representative
2742 sequence from project when only one sequence is
2746 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2747 in Structure Chooser
2750 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2751 structure consensus didn't refresh annotation panel
2754 <!-- JAL-1962 -->View mapping in structure view shows
2755 mappings between sequence and all chains in a PDB file
2758 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2759 dialogs format columns correctly, don't display array
2760 data, sort columns according to type
2763 <!-- JAL-1975 -->Export complete shown after destination
2764 file chooser is cancelled during an image export
2767 <!-- JAL-2025 -->Error when querying PDB Service with
2768 sequence name containing special characters
2771 <!-- JAL-2024 -->Manual PDB structure querying should be
2775 <!-- JAL-2104 -->Large tooltips with broken HTML
2776 formatting don't wrap
2779 <!-- JAL-1128 -->Figures exported from wrapped view are
2780 truncated so L looks like I in consensus annotation
2783 <!-- JAL-2003 -->Export features should only export the
2784 currently displayed features for the current selection or
2788 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2789 after fetching cross-references, and restoring from
2793 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2794 followed in the structure viewer
2797 <!-- JAL-2163 -->Titles for individual alignments in
2798 splitframe not restored from project
2801 <!-- JAL-2145 -->missing autocalculated annotation at
2802 trailing end of protein alignment in transcript/product
2803 splitview when pad-gaps not enabled by default
2806 <!-- JAL-1797 -->amino acid physicochemical conservation
2810 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2811 article has been read (reopened issue due to
2812 internationalisation problems)
2815 <!-- JAL-1960 -->Only offer PDB structures in structure
2816 viewer based on sequence name, PDB and UniProt
2821 <!-- JAL-1976 -->No progress bar shown during export of
2825 <!-- JAL-2213 -->Structures not always superimposed after
2826 multiple structures are shown for one or more sequences.
2829 <!-- JAL-1370 -->Reference sequence characters should not
2830 be replaced with '.' when 'Show unconserved' format option
2834 <!-- JAL-1823 -->Cannot specify chain code when entering
2835 specific PDB id for sequence
2838 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2839 'Export hidden sequences' is enabled, but 'export hidden
2840 columns' is disabled.
2843 <!--JAL-2026-->Best Quality option in structure chooser
2844 selects lowest rather than highest resolution structures
2848 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2849 to sequence mapping in 'View Mappings' report
2852 <!-- JAL-2284 -->Unable to read old Jalview projects that
2853 contain non-XML data added after Jalvew wrote project.
2856 <!-- JAL-2118 -->Newly created annotation row reorders
2857 after clicking on it to create new annotation for a
2861 <!-- JAL-1980 -->Null Pointer Exception raised when
2862 pressing Add on an orphaned cut'n'paste window.
2864 <!-- may exclude, this is an external service stability issue JAL-1941
2865 -- > RNA 3D structure not added via DSSR service</li> -->
2870 <!-- JAL-2151 -->Incorrect columns are selected when
2871 hidden columns present before start of sequence
2874 <!-- JAL-1986 -->Missing dependencies on applet pages
2878 <!-- JAL-1947 -->Overview pixel size changes when
2879 sequences are hidden in applet
2882 <!-- JAL-1996 -->Updated instructions for applet
2883 deployment on examples pages.
2890 <td width="60" nowrap>
2891 <div align="center">
2892 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2893 <em>16/10/2015</em></strong>
2896 <td><em>General</em>
2898 <li>Time stamps for signed Jalview application and applet
2903 <em>Application</em>
2905 <li>Duplicate group consensus and conservation rows
2906 shown when tree is partitioned</li>
2907 <li>Erratic behaviour when tree partitions made with
2908 multiple cDNA/Protein split views</li>
2914 <td width="60" nowrap>
2915 <div align="center">
2916 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2917 <em>8/10/2015</em></strong>
2920 <td><em>General</em>
2922 <li>Updated Spanish translations of localized text for
2924 </ul> <em>Application</em>
2926 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2927 <li>Signed OSX InstallAnywhere installer<br></li>
2928 <li>Support for per-sequence based annotations in BioJSON</li>
2929 </ul> <em>Applet</em>
2931 <li>Split frame example added to applet examples page</li>
2932 </ul> <em>Build and Deployment</em>
2935 <!-- JAL-1888 -->New ant target for running Jalview's test
2943 <li>Mapping of cDNA to protein in split frames
2944 incorrect when sequence start > 1</li>
2945 <li>Broken images in filter column by annotation dialog
2947 <li>Feature colours not parsed from features file</li>
2948 <li>Exceptions and incomplete link URLs recovered when
2949 loading a features file containing HTML tags in feature
2953 <em>Application</em>
2955 <li>Annotations corrupted after BioJS export and
2957 <li>Incorrect sequence limits after Fetch DB References
2958 with 'trim retrieved sequences'</li>
2959 <li>Incorrect warning about deleting all data when
2960 deleting selected columns</li>
2961 <li>Patch to build system for shipping properly signed
2962 JNLP templates for webstart launch</li>
2963 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2964 unreleased structures for download or viewing</li>
2965 <li>Tab/space/return keystroke operation of EMBL-PDBe
2966 fetcher/viewer dialogs works correctly</li>
2967 <li>Disabled 'minimise' button on Jalview windows
2968 running on OSX to workaround redraw hang bug</li>
2969 <li>Split cDNA/Protein view position and geometry not
2970 recovered from jalview project</li>
2971 <li>Initial enabled/disabled state of annotation menu
2972 sorter 'show autocalculated first/last' corresponds to
2974 <li>Restoring of Clustal, RNA Helices and T-Coffee
2975 color schemes from BioJSON</li>
2979 <li>Reorder sequences mirrored in cDNA/Protein split
2981 <li>Applet with Jmol examples not loading correctly</li>
2987 <td><div align="center">
2988 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2990 <td><em>General</em>
2992 <li>Linked visualisation and analysis of DNA and Protein
2995 <li>Translated cDNA alignments shown as split protein
2996 and DNA alignment views</li>
2997 <li>Codon consensus annotation for linked protein and
2998 cDNA alignment views</li>
2999 <li>Link cDNA or Protein product sequences by loading
3000 them onto Protein or cDNA alignments</li>
3001 <li>Reconstruct linked cDNA alignment from aligned
3002 protein sequences</li>
3005 <li>Jmol integration updated to Jmol v14.2.14</li>
3006 <li>Import and export of Jalview alignment views as <a
3007 href="features/bioJsonFormat.html">BioJSON</a></li>
3008 <li>New alignment annotation file statements for
3009 reference sequences and marking hidden columns</li>
3010 <li>Reference sequence based alignment shading to
3011 highlight variation</li>
3012 <li>Select or hide columns according to alignment
3014 <li>Find option for locating sequences by description</li>
3015 <li>Conserved physicochemical properties shown in amino
3016 acid conservation row</li>
3017 <li>Alignments can be sorted by number of RNA helices</li>
3018 </ul> <em>Application</em>
3020 <li>New cDNA/Protein analysis capabilities
3022 <li>Get Cross-References should open a Split Frame
3023 view with cDNA/Protein</li>
3024 <li>Detect when nucleotide sequences and protein
3025 sequences are placed in the same alignment</li>
3026 <li>Split cDNA/Protein views are saved in Jalview
3031 <li>Use REST API to talk to Chimera</li>
3032 <li>Selected regions in Chimera are highlighted in linked
3033 Jalview windows</li>
3035 <li>VARNA RNA viewer updated to v3.93</li>
3036 <li>VARNA views are saved in Jalview Projects</li>
3037 <li>Pseudoknots displayed as Jalview RNA annotation can
3038 be shown in VARNA</li>
3040 <li>Make groups for selection uses marked columns as well
3041 as the active selected region</li>
3043 <li>Calculate UPGMA and NJ trees using sequence feature
3045 <li>New Export options
3047 <li>New Export Settings dialog to control hidden
3048 region export in flat file generation</li>
3050 <li>Export alignment views for display with the <a
3051 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3053 <li>Export scrollable SVG in HTML page</li>
3054 <li>Optional embedding of BioJSON data when exporting
3055 alignment figures to HTML</li>
3057 <li>3D structure retrieval and display
3059 <li>Free text and structured queries with the PDBe
3061 <li>PDBe Search API based discovery and selection of
3062 PDB structures for a sequence set</li>
3066 <li>JPred4 employed for protein secondary structure
3068 <li>Hide Insertions menu option to hide unaligned columns
3069 for one or a group of sequences</li>
3070 <li>Automatically hide insertions in alignments imported
3071 from the JPred4 web server</li>
3072 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3073 system on OSX<br />LGPL libraries courtesy of <a
3074 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3076 <li>changed 'View nucleotide structure' submenu to 'View
3077 VARNA 2D Structure'</li>
3078 <li>change "View protein structure" menu option to "3D
3081 </ul> <em>Applet</em>
3083 <li>New layout for applet example pages</li>
3084 <li>New parameters to enable SplitFrame view
3085 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3086 <li>New example demonstrating linked viewing of cDNA and
3087 Protein alignments</li>
3088 </ul> <em>Development and deployment</em>
3090 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3091 <li>Include installation type and git revision in build
3092 properties and console log output</li>
3093 <li>Jalview Github organisation, and new github site for
3094 storing BioJsMSA Templates</li>
3095 <li>Jalview's unit tests now managed with TestNG</li>
3098 <!-- <em>General</em>
3100 </ul> --> <!-- issues resolved --> <em>Application</em>
3102 <li>Escape should close any open find dialogs</li>
3103 <li>Typo in select-by-features status report</li>
3104 <li>Consensus RNA secondary secondary structure
3105 predictions are not highlighted in amber</li>
3106 <li>Missing gap character in v2.7 example file means
3107 alignment appears unaligned when pad-gaps is not enabled</li>
3108 <li>First switch to RNA Helices colouring doesn't colour
3109 associated structure views</li>
3110 <li>ID width preference option is greyed out when auto
3111 width checkbox not enabled</li>
3112 <li>Stopped a warning dialog from being shown when
3113 creating user defined colours</li>
3114 <li>'View Mapping' in structure viewer shows sequence
3115 mappings for just that viewer's sequences</li>
3116 <li>Workaround for superposing PDB files containing
3117 multiple models in Chimera</li>
3118 <li>Report sequence position in status bar when hovering
3119 over Jmol structure</li>
3120 <li>Cannot output gaps as '.' symbols with Selection ->
3121 output to text box</li>
3122 <li>Flat file exports of alignments with hidden columns
3123 have incorrect sequence start/end</li>
3124 <li>'Aligning' a second chain to a Chimera structure from
3126 <li>Colour schemes applied to structure viewers don't
3127 work for nucleotide</li>
3128 <li>Loading/cut'n'pasting an empty or invalid file leads
3129 to a grey/invisible alignment window</li>
3130 <li>Exported Jpred annotation from a sequence region
3131 imports to different position</li>
3132 <li>Space at beginning of sequence feature tooltips shown
3133 on some platforms</li>
3134 <li>Chimera viewer 'View | Show Chain' menu is not
3136 <li>'New View' fails with a Null Pointer Exception in
3137 console if Chimera has been opened</li>
3138 <li>Mouseover to Chimera not working</li>
3139 <li>Miscellaneous ENA XML feature qualifiers not
3141 <li>NPE in annotation renderer after 'Extract Scores'</li>
3142 <li>If two structures in one Chimera window, mouseover of
3143 either sequence shows on first structure</li>
3144 <li>'Show annotations' options should not make
3145 non-positional annotations visible</li>
3146 <li>Subsequence secondary structure annotation not shown
3147 in right place after 'view flanking regions'</li>
3148 <li>File Save As type unset when current file format is
3150 <li>Save as '.jar' option removed for saving Jalview
3152 <li>Colour by Sequence colouring in Chimera more
3154 <li>Cannot 'add reference annotation' for a sequence in
3155 several views on same alignment</li>
3156 <li>Cannot show linked products for EMBL / ENA records</li>
3157 <li>Jalview's tooltip wraps long texts containing no
3159 </ul> <em>Applet</em>
3161 <li>Jmol to JalviewLite mouseover/link not working</li>
3162 <li>JalviewLite can't import sequences with ID
3163 descriptions containing angle brackets</li>
3164 </ul> <em>General</em>
3166 <li>Cannot export and reimport RNA secondary structure
3167 via jalview annotation file</li>
3168 <li>Random helix colour palette for colour by annotation
3169 with RNA secondary structure</li>
3170 <li>Mouseover to cDNA from STOP residue in protein
3171 translation doesn't work.</li>
3172 <li>hints when using the select by annotation dialog box</li>
3173 <li>Jmol alignment incorrect if PDB file has alternate CA
3175 <li>FontChooser message dialog appears to hang after
3176 choosing 1pt font</li>
3177 <li>Peptide secondary structure incorrectly imported from
3178 annotation file when annotation display text includes 'e' or
3180 <li>Cannot set colour of new feature type whilst creating
3182 <li>cDNA translation alignment should not be sequence
3183 order dependent</li>
3184 <li>'Show unconserved' doesn't work for lower case
3186 <li>Nucleotide ambiguity codes involving R not recognised</li>
3187 </ul> <em>Deployment and Documentation</em>
3189 <li>Applet example pages appear different to the rest of
3190 www.jalview.org</li>
3191 </ul> <em>Application Known issues</em>
3193 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3194 <li>Misleading message appears after trying to delete
3196 <li>Jalview icon not shown in dock after InstallAnywhere
3197 version launches</li>
3198 <li>Fetching EMBL reference for an RNA sequence results
3199 fails with a sequence mismatch</li>
3200 <li>Corrupted or unreadable alignment display when
3201 scrolling alignment to right</li>
3202 <li>ArrayIndexOutOfBoundsException thrown when remove
3203 empty columns called on alignment with ragged gapped ends</li>
3204 <li>auto calculated alignment annotation rows do not get
3205 placed above or below non-autocalculated rows</li>
3206 <li>Jalview dekstop becomes sluggish at full screen in
3207 ultra-high resolution</li>
3208 <li>Cannot disable consensus calculation independently of
3209 quality and conservation</li>
3210 <li>Mouseover highlighting between cDNA and protein can
3211 become sluggish with more than one splitframe shown</li>
3212 </ul> <em>Applet Known Issues</em>
3214 <li>Core PDB parsing code requires Jmol</li>
3215 <li>Sequence canvas panel goes white when alignment
3216 window is being resized</li>
3222 <td><div align="center">
3223 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3225 <td><em>General</em>
3227 <li>Updated Java code signing certificate donated by
3229 <li>Features and annotation preserved when performing
3230 pairwise alignment</li>
3231 <li>RNA pseudoknot annotation can be
3232 imported/exported/displayed</li>
3233 <li>'colour by annotation' can colour by RNA and
3234 protein secondary structure</li>
3235 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3236 post-hoc with 2.9 release</em>)
3239 </ul> <em>Application</em>
3241 <li>Extract and display secondary structure for sequences
3242 with 3D structures</li>
3243 <li>Support for parsing RNAML</li>
3244 <li>Annotations menu for layout
3246 <li>sort sequence annotation rows by alignment</li>
3247 <li>place sequence annotation above/below alignment
3250 <li>Output in Stockholm format</li>
3251 <li>Internationalisation: improved Spanish (es)
3253 <li>Structure viewer preferences tab</li>
3254 <li>Disorder and Secondary Structure annotation tracks
3255 shared between alignments</li>
3256 <li>UCSF Chimera launch and linked highlighting from
3258 <li>Show/hide all sequence associated annotation rows for
3259 all or current selection</li>
3260 <li>disorder and secondary structure predictions
3261 available as dataset annotation</li>
3262 <li>Per-sequence rna helices colouring</li>
3265 <li>Sequence database accessions imported when fetching
3266 alignments from Rfam</li>
3267 <li>update VARNA version to 3.91</li>
3269 <li>New groovy scripts for exporting aligned positions,
3270 conservation values, and calculating sum of pairs scores.</li>
3271 <li>Command line argument to set default JABAWS server</li>
3272 <li>include installation type in build properties and
3273 console log output</li>
3274 <li>Updated Jalview project format to preserve dataset
3278 <!-- issues resolved --> <em>Application</em>
3280 <li>Distinguish alignment and sequence associated RNA
3281 structure in structure->view->VARNA</li>
3282 <li>Raise dialog box if user deletes all sequences in an
3284 <li>Pressing F1 results in documentation opening twice</li>
3285 <li>Sequence feature tooltip is wrapped</li>
3286 <li>Double click on sequence associated annotation
3287 selects only first column</li>
3288 <li>Redundancy removal doesn't result in unlinked
3289 leaves shown in tree</li>
3290 <li>Undos after several redundancy removals don't undo
3292 <li>Hide sequence doesn't hide associated annotation</li>
3293 <li>User defined colours dialog box too big to fit on
3294 screen and buttons not visible</li>
3295 <li>author list isn't updated if already written to
3296 Jalview properties</li>
3297 <li>Popup menu won't open after retrieving sequence
3299 <li>File open window for associate PDB doesn't open</li>
3300 <li>Left-then-right click on a sequence id opens a
3301 browser search window</li>
3302 <li>Cannot open sequence feature shading/sort popup menu
3303 in feature settings dialog</li>
3304 <li>better tooltip placement for some areas of Jalview
3306 <li>Allow addition of JABAWS Server which doesn't
3307 pass validation</li>
3308 <li>Web services parameters dialog box is too large to
3310 <li>Muscle nucleotide alignment preset obscured by
3312 <li>JABAWS preset submenus don't contain newly
3313 defined user preset</li>
3314 <li>MSA web services warns user if they were launched
3315 with invalid input</li>
3316 <li>Jalview cannot contact DAS Registy when running on
3319 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3320 'Superpose with' submenu not shown when new view
3324 </ul> <!-- <em>Applet</em>
3326 </ul> <em>General</em>
3328 </ul>--> <em>Deployment and Documentation</em>
3330 <li>2G and 1G options in launchApp have no effect on
3331 memory allocation</li>
3332 <li>launchApp service doesn't automatically open
3333 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3335 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3336 InstallAnywhere reports cannot find valid JVM when Java
3337 1.7_055 is available
3339 </ul> <em>Application Known issues</em>
3342 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3343 corrupted or unreadable alignment display when scrolling
3347 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3348 retrieval fails but progress bar continues for DAS retrieval
3349 with large number of ID
3352 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3353 flatfile output of visible region has incorrect sequence
3357 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3358 rna structure consensus doesn't update when secondary
3359 structure tracks are rearranged
3362 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3363 invalid rna structure positional highlighting does not
3364 highlight position of invalid base pairs
3367 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3368 out of memory errors are not raised when saving Jalview
3369 project from alignment window file menu
3372 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3373 Switching to RNA Helices colouring doesn't propagate to
3377 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3378 colour by RNA Helices not enabled when user created
3379 annotation added to alignment
3382 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3383 Jalview icon not shown on dock in Mountain Lion/Webstart
3385 </ul> <em>Applet Known Issues</em>
3388 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3389 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3392 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3393 Jalview and Jmol example not compatible with IE9
3396 <li>Sort by annotation score doesn't reverse order
3402 <td><div align="center">
3403 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3406 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3409 <li>Internationalisation of user interface (usually
3410 called i18n support) and translation for Spanish locale</li>
3411 <li>Define/Undefine group on current selection with
3412 Ctrl-G/Shift Ctrl-G</li>
3413 <li>Improved group creation/removal options in
3414 alignment/sequence Popup menu</li>
3415 <li>Sensible precision for symbol distribution
3416 percentages shown in logo tooltip.</li>
3417 <li>Annotation panel height set according to amount of
3418 annotation when alignment first opened</li>
3419 </ul> <em>Application</em>
3421 <li>Interactive consensus RNA secondary structure
3422 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3423 <li>Select columns containing particular features from
3424 Feature Settings dialog</li>
3425 <li>View all 'representative' PDB structures for selected
3427 <li>Update Jalview project format:
3429 <li>New file extension for Jalview projects '.jvp'</li>
3430 <li>Preserve sequence and annotation dataset (to
3431 store secondary structure annotation,etc)</li>
3432 <li>Per group and alignment annotation and RNA helix
3436 <li>New similarity measures for PCA and Tree calculation
3438 <li>Experimental support for retrieval and viewing of
3439 flanking regions for an alignment</li>
3443 <!-- issues resolved --> <em>Application</em>
3445 <li>logo keeps spinning and status remains at queued or
3446 running after job is cancelled</li>
3447 <li>cannot export features from alignments imported from
3448 Jalview/VAMSAS projects</li>
3449 <li>Buggy slider for web service parameters that take
3451 <li>Newly created RNA secondary structure line doesn't
3452 have 'display all symbols' flag set</li>
3453 <li>T-COFFEE alignment score shading scheme and other
3454 annotation shading not saved in Jalview project</li>
3455 <li>Local file cannot be loaded in freshly downloaded
3457 <li>Jalview icon not shown on dock in Mountain
3459 <li>Load file from desktop file browser fails</li>
3460 <li>Occasional NPE thrown when calculating large trees</li>
3461 <li>Cannot reorder or slide sequences after dragging an
3462 alignment onto desktop</li>
3463 <li>Colour by annotation dialog throws NPE after using
3464 'extract scores' function</li>
3465 <li>Loading/cut'n'pasting an empty file leads to a grey
3466 alignment window</li>
3467 <li>Disorder thresholds rendered incorrectly after
3468 performing IUPred disorder prediction</li>
3469 <li>Multiple group annotated consensus rows shown when
3470 changing 'normalise logo' display setting</li>
3471 <li>Find shows blank dialog after 'finished searching' if
3472 nothing matches query</li>
3473 <li>Null Pointer Exceptions raised when sorting by
3474 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3476 <li>Errors in Jmol console when structures in alignment
3477 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3479 <li>Not all working JABAWS services are shown in
3481 <li>JAVAWS version of Jalview fails to launch with
3482 'invalid literal/length code'</li>
3483 <li>Annotation/RNA Helix colourschemes cannot be applied
3484 to alignment with groups (actually fixed in 2.8.0b1)</li>
3485 <li>RNA Helices and T-Coffee Scores available as default
3488 </ul> <em>Applet</em>
3490 <li>Remove group option is shown even when selection is
3492 <li>Apply to all groups ticked but colourscheme changes
3493 don't affect groups</li>
3494 <li>Documented RNA Helices and T-Coffee Scores as valid
3495 colourscheme name</li>
3496 <li>Annotation labels drawn on sequence IDs when
3497 Annotation panel is not displayed</li>
3498 <li>Increased font size for dropdown menus on OSX and
3499 embedded windows</li>
3500 </ul> <em>Other</em>
3502 <li>Consensus sequence for alignments/groups with a
3503 single sequence were not calculated</li>
3504 <li>annotation files that contain only groups imported as
3505 annotation and junk sequences</li>
3506 <li>Fasta files with sequences containing '*' incorrectly
3507 recognised as PFAM or BLC</li>
3508 <li>conservation/PID slider apply all groups option
3509 doesn't affect background (2.8.0b1)
3511 <li>redundancy highlighting is erratic at 0% and 100%</li>
3512 <li>Remove gapped columns fails for sequences with ragged
3514 <li>AMSA annotation row with leading spaces is not
3515 registered correctly on import</li>
3516 <li>Jalview crashes when selecting PCA analysis for
3517 certain alignments</li>
3518 <li>Opening the colour by annotation dialog for an
3519 existing annotation based 'use original colours'
3520 colourscheme loses original colours setting</li>
3525 <td><div align="center">
3526 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3527 <em>30/1/2014</em></strong>
3531 <li>Trusted certificates for JalviewLite applet and
3532 Jalview Desktop application<br />Certificate was donated by
3533 <a href="https://www.certum.eu">Certum</a> to the Jalview
3534 open source project).
3536 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3537 <li>Output in Stockholm format</li>
3538 <li>Allow import of data from gzipped files</li>
3539 <li>Export/import group and sequence associated line
3540 graph thresholds</li>
3541 <li>Nucleotide substitution matrix that supports RNA and
3542 ambiguity codes</li>
3543 <li>Allow disorder predictions to be made on the current
3544 selection (or visible selection) in the same way that JPred
3546 <li>Groovy scripting for headless Jalview operation</li>
3547 </ul> <em>Other improvements</em>
3549 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3550 <li>COMBINE statement uses current SEQUENCE_REF and
3551 GROUP_REF scope to group annotation rows</li>
3552 <li>Support '' style escaping of quotes in Newick
3554 <li>Group options for JABAWS service by command line name</li>
3555 <li>Empty tooltip shown for JABA service options with a
3556 link but no description</li>
3557 <li>Select primary source when selecting authority in
3558 database fetcher GUI</li>
3559 <li>Add .mfa to FASTA file extensions recognised by
3561 <li>Annotation label tooltip text wrap</li>
3566 <li>Slow scrolling when lots of annotation rows are
3568 <li>Lots of NPE (and slowness) after creating RNA
3569 secondary structure annotation line</li>
3570 <li>Sequence database accessions not imported when
3571 fetching alignments from Rfam</li>
3572 <li>Incorrect SHMR submission for sequences with
3574 <li>View all structures does not always superpose
3576 <li>Option widgets in service parameters not updated to
3577 reflect user or preset settings</li>
3578 <li>Null pointer exceptions for some services without
3579 presets or adjustable parameters</li>
3580 <li>Discover PDB IDs entry in structure menu doesn't
3581 discover PDB xRefs</li>
3582 <li>Exception encountered while trying to retrieve
3583 features with DAS</li>
3584 <li>Lowest value in annotation row isn't coloured
3585 when colour by annotation (per sequence) is coloured</li>
3586 <li>Keyboard mode P jumps to start of gapped region when
3587 residue follows a gap</li>
3588 <li>Jalview appears to hang importing an alignment with
3589 Wrap as default or after enabling Wrap</li>
3590 <li>'Right click to add annotations' message
3591 shown in wrap mode when no annotations present</li>
3592 <li>Disorder predictions fail with NPE if no automatic
3593 annotation already exists on alignment</li>
3594 <li>oninit javascript function should be called after
3595 initialisation completes</li>
3596 <li>Remove redundancy after disorder prediction corrupts
3597 alignment window display</li>
3598 <li>Example annotation file in documentation is invalid</li>
3599 <li>Grouped line graph annotation rows are not exported
3600 to annotation file</li>
3601 <li>Multi-harmony analysis cannot be run when only two
3603 <li>Cannot create multiple groups of line graphs with
3604 several 'combine' statements in annotation file</li>
3605 <li>Pressing return several times causes Number Format
3606 exceptions in keyboard mode</li>
3607 <li>Multi-harmony (SHMMR) method doesn't submit
3608 correct partitions for input data</li>
3609 <li>Translation from DNA to Amino Acids fails</li>
3610 <li>Jalview fail to load newick tree with quoted label</li>
3611 <li>--headless flag isn't understood</li>
3612 <li>ClassCastException when generating EPS in headless
3614 <li>Adjusting sequence-associated shading threshold only
3615 changes one row's threshold</li>
3616 <li>Preferences and Feature settings panel panel
3617 doesn't open</li>
3618 <li>hide consensus histogram also hides conservation and
3619 quality histograms</li>
3624 <td><div align="center">
3625 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3627 <td><em>Application</em>
3629 <li>Support for JABAWS 2.0 Services (AACon alignment
3630 conservation, protein disorder and Clustal Omega)</li>
3631 <li>JABAWS server status indicator in Web Services
3633 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3634 in Jalview alignment window</li>
3635 <li>Updated Jalview build and deploy framework for OSX
3636 mountain lion, windows 7, and 8</li>
3637 <li>Nucleotide substitution matrix for PCA that supports
3638 RNA and ambiguity codes</li>
3640 <li>Improved sequence database retrieval GUI</li>
3641 <li>Support fetching and database reference look up
3642 against multiple DAS sources (Fetch all from in 'fetch db
3644 <li>Jalview project improvements
3646 <li>Store and retrieve the 'belowAlignment'
3647 flag for annotation</li>
3648 <li>calcId attribute to group annotation rows on the
3650 <li>Store AACon calculation settings for a view in
3651 Jalview project</li>
3655 <li>horizontal scrolling gesture support</li>
3656 <li>Visual progress indicator when PCA calculation is
3658 <li>Simpler JABA web services menus</li>
3659 <li>visual indication that web service results are still
3660 being retrieved from server</li>
3661 <li>Serialise the dialogs that are shown when Jalview
3662 starts up for first time</li>
3663 <li>Jalview user agent string for interacting with HTTP
3665 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3667 <li>Examples directory and Groovy library included in
3668 InstallAnywhere distribution</li>
3669 </ul> <em>Applet</em>
3671 <li>RNA alignment and secondary structure annotation
3672 visualization applet example</li>
3673 </ul> <em>General</em>
3675 <li>Normalise option for consensus sequence logo</li>
3676 <li>Reset button in PCA window to return dimensions to
3678 <li>Allow seqspace or Jalview variant of alignment PCA
3680 <li>PCA with either nucleic acid and protein substitution
3682 <li>Allow windows containing HTML reports to be exported
3684 <li>Interactive display and editing of RNA secondary
3685 structure contacts</li>
3686 <li>RNA Helix Alignment Colouring</li>
3687 <li>RNA base pair logo consensus</li>
3688 <li>Parse sequence associated secondary structure
3689 information in Stockholm files</li>
3690 <li>HTML Export database accessions and annotation
3691 information presented in tooltip for sequences</li>
3692 <li>Import secondary structure from LOCARNA clustalw
3693 style RNA alignment files</li>
3694 <li>import and visualise T-COFFEE quality scores for an
3696 <li>'colour by annotation' per sequence option to
3697 shade each sequence according to its associated alignment
3699 <li>New Jalview Logo</li>
3700 </ul> <em>Documentation and Development</em>
3702 <li>documentation for score matrices used in Jalview</li>
3703 <li>New Website!</li>
3705 <td><em>Application</em>
3707 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3708 wsdbfetch REST service</li>
3709 <li>Stop windows being moved outside desktop on OSX</li>
3710 <li>Filetype associations not installed for webstart
3712 <li>Jalview does not always retrieve progress of a JABAWS
3713 job execution in full once it is complete</li>
3714 <li>revise SHMR RSBS definition to ensure alignment is
3715 uploaded via ali_file parameter</li>
3716 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3717 <li>View all structures superposed fails with exception</li>
3718 <li>Jnet job queues forever if a very short sequence is
3719 submitted for prediction</li>
3720 <li>Cut and paste menu not opened when mouse clicked on
3722 <li>Putting fractional value into integer text box in
3723 alignment parameter dialog causes Jalview to hang</li>
3724 <li>Structure view highlighting doesn't work on
3726 <li>View all structures fails with exception shown in
3728 <li>Characters in filename associated with PDBEntry not
3729 escaped in a platform independent way</li>
3730 <li>Jalview desktop fails to launch with exception when
3732 <li>Tree calculation reports 'you must have 2 or more
3733 sequences selected' when selection is empty</li>
3734 <li>Jalview desktop fails to launch with jar signature
3735 failure when java web start temporary file caching is
3737 <li>DAS Sequence retrieval with range qualification
3738 results in sequence xref which includes range qualification</li>
3739 <li>Errors during processing of command line arguments
3740 cause progress bar (JAL-898) to be removed</li>
3741 <li>Replace comma for semi-colon option not disabled for
3742 DAS sources in sequence fetcher</li>
3743 <li>Cannot close news reader when JABAWS server warning
3744 dialog is shown</li>
3745 <li>Option widgets not updated to reflect user settings</li>
3746 <li>Edited sequence not submitted to web service</li>
3747 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3748 <li>InstallAnywhere installer doesn't unpack and run
3749 on OSX Mountain Lion</li>
3750 <li>Annotation panel not given a scroll bar when
3751 sequences with alignment annotation are pasted into the
3753 <li>Sequence associated annotation rows not associated
3754 when loaded from Jalview project</li>
3755 <li>Browser launch fails with NPE on java 1.7</li>
3756 <li>JABAWS alignment marked as finished when job was
3757 cancelled or job failed due to invalid input</li>
3758 <li>NPE with v2.7 example when clicking on Tree
3759 associated with all views</li>
3760 <li>Exceptions when copy/paste sequences with grouped
3761 annotation rows to new window</li>
3762 </ul> <em>Applet</em>
3764 <li>Sequence features are momentarily displayed before
3765 they are hidden using hidefeaturegroups applet parameter</li>
3766 <li>loading features via javascript API automatically
3767 enables feature display</li>
3768 <li>scrollToColumnIn javascript API method doesn't
3770 </ul> <em>General</em>
3772 <li>Redundancy removal fails for rna alignment</li>
3773 <li>PCA calculation fails when sequence has been selected
3774 and then deselected</li>
3775 <li>PCA window shows grey box when first opened on OSX</li>
3776 <li>Letters coloured pink in sequence logo when alignment
3777 coloured with clustalx</li>
3778 <li>Choosing fonts without letter symbols defined causes
3779 exceptions and redraw errors</li>
3780 <li>Initial PCA plot view is not same as manually
3781 reconfigured view</li>
3782 <li>Grouped annotation graph label has incorrect line
3784 <li>Grouped annotation graph label display is corrupted
3785 for lots of labels</li>
3790 <div align="center">
3791 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3794 <td><em>Application</em>
3796 <li>Jalview Desktop News Reader</li>
3797 <li>Tweaked default layout of web services menu</li>
3798 <li>View/alignment association menu to enable user to
3799 easily specify which alignment a multi-structure view takes
3800 its colours/correspondences from</li>
3801 <li>Allow properties file location to be specified as URL</li>
3802 <li>Extend Jalview project to preserve associations
3803 between many alignment views and a single Jmol display</li>
3804 <li>Store annotation row height in Jalview project file</li>
3805 <li>Annotation row column label formatting attributes
3806 stored in project file</li>
3807 <li>Annotation row order for auto-calculated annotation
3808 rows preserved in Jalview project file</li>
3809 <li>Visual progress indication when Jalview state is
3810 saved using Desktop window menu</li>
3811 <li>Visual indication that command line arguments are
3812 still being processed</li>
3813 <li>Groovy script execution from URL</li>
3814 <li>Colour by annotation default min and max colours in
3816 <li>Automatically associate PDB files dragged onto an
3817 alignment with sequences that have high similarity and
3819 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3820 <li>'view structures' option to open many
3821 structures in same window</li>
3822 <li>Sort associated views menu option for tree panel</li>
3823 <li>Group all JABA and non-JABA services for a particular
3824 analysis function in its own submenu</li>
3825 </ul> <em>Applet</em>
3827 <li>Userdefined and autogenerated annotation rows for
3829 <li>Adjustment of alignment annotation pane height</li>
3830 <li>Annotation scrollbar for annotation panel</li>
3831 <li>Drag to reorder annotation rows in annotation panel</li>
3832 <li>'automaticScrolling' parameter</li>
3833 <li>Allow sequences with partial ID string matches to be
3834 annotated from GFF/Jalview features files</li>
3835 <li>Sequence logo annotation row in applet</li>
3836 <li>Absolute paths relative to host server in applet
3837 parameters are treated as such</li>
3838 <li>New in the JalviewLite javascript API:
3840 <li>JalviewLite.js javascript library</li>
3841 <li>Javascript callbacks for
3843 <li>Applet initialisation</li>
3844 <li>Sequence/alignment mouse-overs and selections</li>
3847 <li>scrollTo row and column alignment scrolling
3849 <li>Select sequence/alignment regions from javascript</li>
3850 <li>javascript structure viewer harness to pass
3851 messages between Jmol and Jalview when running as
3852 distinct applets</li>
3853 <li>sortBy method</li>
3854 <li>Set of applet and application examples shipped
3855 with documentation</li>
3856 <li>New example to demonstrate JalviewLite and Jmol
3857 javascript message exchange</li>
3859 </ul> <em>General</em>
3861 <li>Enable Jmol displays to be associated with multiple
3862 multiple alignments</li>
3863 <li>Option to automatically sort alignment with new tree</li>
3864 <li>User configurable link to enable redirects to a
3865 www.Jalview.org mirror</li>
3866 <li>Jmol colours option for Jmol displays</li>
3867 <li>Configurable newline string when writing alignment
3868 and other flat files</li>
3869 <li>Allow alignment annotation description lines to
3870 contain html tags</li>
3871 </ul> <em>Documentation and Development</em>
3873 <li>Add groovy test harness for bulk load testing to
3875 <li>Groovy script to load and align a set of sequences
3876 using a web service before displaying the result in the
3877 Jalview desktop</li>
3878 <li>Restructured javascript and applet api documentation</li>
3879 <li>Ant target to publish example html files with applet
3881 <li>Netbeans project for building Jalview from source</li>
3882 <li>ant task to create online javadoc for Jalview source</li>
3884 <td><em>Application</em>
3886 <li>User defined colourscheme throws exception when
3887 current built in colourscheme is saved as new scheme</li>
3888 <li>AlignFrame->Save in application pops up save
3889 dialog for valid filename/format</li>
3890 <li>Cannot view associated structure for UniProt sequence</li>
3891 <li>PDB file association breaks for UniProt sequence
3893 <li>Associate PDB from file dialog does not tell you
3894 which sequence is to be associated with the file</li>
3895 <li>Find All raises null pointer exception when query
3896 only matches sequence IDs</li>
3897 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3898 <li>Jalview project with Jmol views created with Jalview
3899 2.4 cannot be loaded</li>
3900 <li>Filetype associations not installed for webstart
3902 <li>Two or more chains in a single PDB file associated
3903 with sequences in different alignments do not get coloured
3904 by their associated sequence</li>
3905 <li>Visibility status of autocalculated annotation row
3906 not preserved when project is loaded</li>
3907 <li>Annotation row height and visibility attributes not
3908 stored in Jalview project</li>
3909 <li>Tree bootstraps are not preserved when saved as a
3910 Jalview project</li>
3911 <li>Envision2 workflow tooltips are corrupted</li>
3912 <li>Enabling show group conservation also enables colour
3913 by conservation</li>
3914 <li>Duplicate group associated conservation or consensus
3915 created on new view</li>
3916 <li>Annotation scrollbar not displayed after 'show
3917 all hidden annotation rows' option selected</li>
3918 <li>Alignment quality not updated after alignment
3919 annotation row is hidden then shown</li>
3920 <li>Preserve colouring of structures coloured by
3921 sequences in pre Jalview 2.7 projects</li>
3922 <li>Web service job parameter dialog is not laid out
3924 <li>Web services menu not refreshed after 'reset
3925 services' button is pressed in preferences</li>
3926 <li>Annotation off by one in Jalview v2_3 example project</li>
3927 <li>Structures imported from file and saved in project
3928 get name like jalview_pdb1234.txt when reloaded</li>
3929 <li>Jalview does not always retrieve progress of a JABAWS
3930 job execution in full once it is complete</li>
3931 </ul> <em>Applet</em>
3933 <li>Alignment height set incorrectly when lots of
3934 annotation rows are displayed</li>
3935 <li>Relative URLs in feature HTML text not resolved to
3937 <li>View follows highlighting does not work for positions
3939 <li><= shown as = in tooltip</li>
3940 <li>Export features raises exception when no features
3942 <li>Separator string used for serialising lists of IDs
3943 for javascript api is modified when separator string
3944 provided as parameter</li>
3945 <li>Null pointer exception when selecting tree leaves for
3946 alignment with no existing selection</li>
3947 <li>Relative URLs for datasources assumed to be relative
3948 to applet's codebase</li>
3949 <li>Status bar not updated after finished searching and
3950 search wraps around to first result</li>
3951 <li>StructureSelectionManager instance shared between
3952 several Jalview applets causes race conditions and memory
3954 <li>Hover tooltip and mouseover of position on structure
3955 not sent from Jmol in applet</li>
3956 <li>Certain sequences of javascript method calls to
3957 applet API fatally hang browser</li>
3958 </ul> <em>General</em>
3960 <li>View follows structure mouseover scrolls beyond
3961 position with wrapped view and hidden regions</li>
3962 <li>Find sequence position moves to wrong residue
3963 with/without hidden columns</li>
3964 <li>Sequence length given in alignment properties window
3966 <li>InvalidNumberFormat exceptions thrown when trying to
3967 import PDB like structure files</li>
3968 <li>Positional search results are only highlighted
3969 between user-supplied sequence start/end bounds</li>
3970 <li>End attribute of sequence is not validated</li>
3971 <li>Find dialog only finds first sequence containing a
3972 given sequence position</li>
3973 <li>Sequence numbering not preserved in MSF alignment
3975 <li>Jalview PDB file reader does not extract sequence
3976 from nucleotide chains correctly</li>
3977 <li>Structure colours not updated when tree partition
3978 changed in alignment</li>
3979 <li>Sequence associated secondary structure not correctly
3980 parsed in interleaved stockholm</li>
3981 <li>Colour by annotation dialog does not restore current
3983 <li>Hiding (nearly) all sequences doesn't work
3985 <li>Sequences containing lowercase letters are not
3986 properly associated with their pdb files</li>
3987 </ul> <em>Documentation and Development</em>
3989 <li>schemas/JalviewWsParamSet.xsd corrupted by
3990 ApplyCopyright tool</li>
3995 <div align="center">
3996 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3999 <td><em>Application</em>
4001 <li>New warning dialog when the Jalview Desktop cannot
4002 contact web services</li>
4003 <li>JABA service parameters for a preset are shown in
4004 service job window</li>
4005 <li>JABA Service menu entries reworded</li>
4009 <li>Modeller PIR IO broken - cannot correctly import a
4010 pir file emitted by Jalview</li>
4011 <li>Existing feature settings transferred to new
4012 alignment view created from cut'n'paste</li>
4013 <li>Improved test for mixed amino/nucleotide chains when
4014 parsing PDB files</li>
4015 <li>Consensus and conservation annotation rows
4016 occasionally become blank for all new windows</li>
4017 <li>Exception raised when right clicking above sequences
4018 in wrapped view mode</li>
4019 </ul> <em>Application</em>
4021 <li>multiple multiply aligned structure views cause cpu
4022 usage to hit 100% and computer to hang</li>
4023 <li>Web Service parameter layout breaks for long user
4024 parameter names</li>
4025 <li>Jaba service discovery hangs desktop if Jaba server
4032 <div align="center">
4033 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4036 <td><em>Application</em>
4038 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4039 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4042 <li>Web Services preference tab</li>
4043 <li>Analysis parameters dialog box and user defined
4045 <li>Improved speed and layout of Envision2 service menu</li>
4046 <li>Superpose structures using associated sequence
4048 <li>Export coordinates and projection as CSV from PCA
4050 </ul> <em>Applet</em>
4052 <li>enable javascript: execution by the applet via the
4053 link out mechanism</li>
4054 </ul> <em>Other</em>
4056 <li>Updated the Jmol Jalview interface to work with Jmol
4058 <li>The Jalview Desktop and JalviewLite applet now
4059 require Java 1.5</li>
4060 <li>Allow Jalview feature colour specification for GFF
4061 sequence annotation files</li>
4062 <li>New 'colour by label' keword in Jalview feature file
4063 type colour specification</li>
4064 <li>New Jalview Desktop Groovy API method that allows a
4065 script to check if it being run in an interactive session or
4066 in a batch operation from the Jalview command line</li>
4070 <li>clustalx colourscheme colours Ds preferentially when
4071 both D+E are present in over 50% of the column</li>
4072 </ul> <em>Application</em>
4074 <li>typo in AlignmentFrame->View->Hide->all but
4075 selected Regions menu item</li>
4076 <li>sequence fetcher replaces ',' for ';' when the ',' is
4077 part of a valid accession ID</li>
4078 <li>fatal OOM if object retrieved by sequence fetcher
4079 runs out of memory</li>
4080 <li>unhandled Out of Memory Error when viewing pca
4081 analysis results</li>
4082 <li>InstallAnywhere builds fail to launch on OS X java
4083 10.5 update 4 (due to apple Java 1.6 update)</li>
4084 <li>Installanywhere Jalview silently fails to launch</li>
4085 </ul> <em>Applet</em>
4087 <li>Jalview.getFeatureGroups() raises an
4088 ArrayIndexOutOfBoundsException if no feature groups are
4095 <div align="center">
4096 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4102 <li>Alignment prettyprinter doesn't cope with long
4104 <li>clustalx colourscheme colours Ds preferentially when
4105 both D+E are present in over 50% of the column</li>
4106 <li>nucleic acid structures retrieved from PDB do not
4107 import correctly</li>
4108 <li>More columns get selected than were clicked on when a
4109 number of columns are hidden</li>
4110 <li>annotation label popup menu not providing correct
4111 add/hide/show options when rows are hidden or none are
4113 <li>Stockholm format shown in list of readable formats,
4114 and parser copes better with alignments from RFAM.</li>
4115 <li>CSV output of consensus only includes the percentage
4116 of all symbols if sequence logo display is enabled</li>
4118 </ul> <em>Applet</em>
4120 <li>annotation panel disappears when annotation is
4122 </ul> <em>Application</em>
4124 <li>Alignment view not redrawn properly when new
4125 alignment opened where annotation panel is visible but no
4126 annotations are present on alignment</li>
4127 <li>pasted region containing hidden columns is
4128 incorrectly displayed in new alignment window</li>
4129 <li>Jalview slow to complete operations when stdout is
4130 flooded (fix is to close the Jalview console)</li>
4131 <li>typo in AlignmentFrame->View->Hide->all but
4132 selected Rregions menu item.</li>
4133 <li>inconsistent group submenu and Format submenu entry
4134 'Un' or 'Non'conserved</li>
4135 <li>Sequence feature settings are being shared by
4136 multiple distinct alignments</li>
4137 <li>group annotation not recreated when tree partition is
4139 <li>double click on group annotation to select sequences
4140 does not propagate to associated trees</li>
4141 <li>Mac OSX specific issues:
4143 <li>exception raised when mouse clicked on desktop
4144 window background</li>
4145 <li>Desktop menu placed on menu bar and application
4146 name set correctly</li>
4147 <li>sequence feature settings not wide enough for the
4148 save feature colourscheme button</li>
4157 <div align="center">
4158 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4161 <td><em>New Capabilities</em>
4163 <li>URL links generated from description line for
4164 regular-expression based URL links (applet and application)
4166 <li>Non-positional feature URL links are shown in link
4168 <li>Linked viewing of nucleic acid sequences and
4170 <li>Automatic Scrolling option in View menu to display
4171 the currently highlighted region of an alignment.</li>
4172 <li>Order an alignment by sequence length, or using the
4173 average score or total feature count for each sequence.</li>
4174 <li>Shading features by score or associated description</li>
4175 <li>Subdivide alignment and groups based on identity of
4176 selected subsequence (Make Groups from Selection).</li>
4177 <li>New hide/show options including Shift+Control+H to
4178 hide everything but the currently selected region.</li>
4179 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4180 </ul> <em>Application</em>
4182 <li>Fetch DB References capabilities and UI expanded to
4183 support retrieval from DAS sequence sources</li>
4184 <li>Local DAS Sequence sources can be added via the
4185 command line or via the Add local source dialog box.</li>
4186 <li>DAS Dbref and DbxRef feature types are parsed as
4187 database references and protein_name is parsed as
4188 description line (BioSapiens terms).</li>
4189 <li>Enable or disable non-positional feature and database
4190 references in sequence ID tooltip from View menu in
4192 <!-- <li>New hidden columns and rows and representatives capabilities
4193 in annotations file (in progress - not yet fully implemented)</li> -->
4194 <li>Group-associated consensus, sequence logos and
4195 conservation plots</li>
4196 <li>Symbol distributions for each column can be exported
4197 and visualized as sequence logos</li>
4198 <li>Optionally scale multi-character column labels to fit
4199 within each column of annotation row<!-- todo for applet -->
4201 <li>Optional automatic sort of associated alignment view
4202 when a new tree is opened.</li>
4203 <li>Jalview Java Console</li>
4204 <li>Better placement of desktop window when moving
4205 between different screens.</li>
4206 <li>New preference items for sequence ID tooltip and
4207 consensus annotation</li>
4208 <li>Client to submit sequences and IDs to Envision2
4210 <li><em>Vamsas Capabilities</em>
4212 <li>Improved VAMSAS synchronization (Jalview archive
4213 used to preserve views, structures, and tree display
4215 <li>Import of vamsas documents from disk or URL via
4217 <li>Sharing of selected regions between views and
4218 with other VAMSAS applications (Experimental feature!)</li>
4219 <li>Updated API to VAMSAS version 0.2</li>
4221 </ul> <em>Applet</em>
4223 <li>Middle button resizes annotation row height</li>
4226 <li>sortByTree (true/false) - automatically sort the
4227 associated alignment view by the tree when a new tree is
4229 <li>showTreeBootstraps (true/false) - show or hide
4230 branch bootstraps (default is to show them if available)</li>
4231 <li>showTreeDistances (true/false) - show or hide
4232 branch lengths (default is to show them if available)</li>
4233 <li>showUnlinkedTreeNodes (true/false) - indicate if
4234 unassociated nodes should be highlighted in the tree
4236 <li>heightScale and widthScale (1.0 or more) -
4237 increase the height or width of a cell in the alignment
4238 grid relative to the current font size.</li>
4241 <li>Non-positional features displayed in sequence ID
4243 </ul> <em>Other</em>
4245 <li>Features format: graduated colour definitions and
4246 specification of feature scores</li>
4247 <li>Alignment Annotations format: new keywords for group
4248 associated annotation (GROUP_REF) and annotation row display
4249 properties (ROW_PROPERTIES)</li>
4250 <li>XML formats extended to support graduated feature
4251 colourschemes, group associated annotation, and profile
4252 visualization settings.</li></td>
4255 <li>Source field in GFF files parsed as feature source
4256 rather than description</li>
4257 <li>Non-positional features are now included in sequence
4258 feature and gff files (controlled via non-positional feature
4259 visibility in tooltip).</li>
4260 <li>URL links generated for all feature links (bugfix)</li>
4261 <li>Added URL embedding instructions to features file
4263 <li>Codons containing ambiguous nucleotides translated as
4264 'X' in peptide product</li>
4265 <li>Match case switch in find dialog box works for both
4266 sequence ID and sequence string and query strings do not
4267 have to be in upper case to match case-insensitively.</li>
4268 <li>AMSA files only contain first column of
4269 multi-character column annotation labels</li>
4270 <li>Jalview Annotation File generation/parsing consistent
4271 with documentation (e.g. Stockholm annotation can be
4272 exported and re-imported)</li>
4273 <li>PDB files without embedded PDB IDs given a friendly
4275 <li>Find incrementally searches ID string matches as well
4276 as subsequence matches, and correctly reports total number
4280 <li>Better handling of exceptions during sequence
4282 <li>Dasobert generated non-positional feature URL
4283 link text excludes the start_end suffix</li>
4284 <li>DAS feature and source retrieval buttons disabled
4285 when fetch or registry operations in progress.</li>
4286 <li>PDB files retrieved from URLs are cached properly</li>
4287 <li>Sequence description lines properly shared via
4289 <li>Sequence fetcher fetches multiple records for all
4291 <li>Ensured that command line das feature retrieval
4292 completes before alignment figures are generated.</li>
4293 <li>Reduced time taken when opening file browser for
4295 <li>isAligned check prior to calculating tree, PCA or
4296 submitting an MSA to JNet now excludes hidden sequences.</li>
4297 <li>User defined group colours properly recovered
4298 from Jalview projects.</li>
4307 <div align="center">
4308 <strong>2.4.0.b2</strong><br> 28/10/2009
4313 <li>Experimental support for google analytics usage
4315 <li>Jalview privacy settings (user preferences and docs).</li>
4320 <li>Race condition in applet preventing startup in
4322 <li>Exception when feature created from selection beyond
4323 length of sequence.</li>
4324 <li>Allow synthetic PDB files to be imported gracefully</li>
4325 <li>Sequence associated annotation rows associate with
4326 all sequences with a given id</li>
4327 <li>Find function matches case-insensitively for sequence
4328 ID string searches</li>
4329 <li>Non-standard characters do not cause pairwise
4330 alignment to fail with exception</li>
4331 </ul> <em>Application Issues</em>
4333 <li>Sequences are now validated against EMBL database</li>
4334 <li>Sequence fetcher fetches multiple records for all
4336 </ul> <em>InstallAnywhere Issues</em>
4338 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4339 issue with installAnywhere mechanism)</li>
4340 <li>Command line launching of JARs from InstallAnywhere
4341 version (java class versioning error fixed)</li>
4348 <div align="center">
4349 <strong>2.4</strong><br> 27/8/2008
4352 <td><em>User Interface</em>
4354 <li>Linked highlighting of codon and amino acid from
4355 translation and protein products</li>
4356 <li>Linked highlighting of structure associated with
4357 residue mapping to codon position</li>
4358 <li>Sequence Fetcher provides example accession numbers
4359 and 'clear' button</li>
4360 <li>MemoryMonitor added as an option under Desktop's
4362 <li>Extract score function to parse whitespace separated
4363 numeric data in description line</li>
4364 <li>Column labels in alignment annotation can be centred.</li>
4365 <li>Tooltip for sequence associated annotation give name
4367 </ul> <em>Web Services and URL fetching</em>
4369 <li>JPred3 web service</li>
4370 <li>Prototype sequence search client (no public services
4372 <li>Fetch either seed alignment or full alignment from
4374 <li>URL Links created for matching database cross
4375 references as well as sequence ID</li>
4376 <li>URL Links can be created using regular-expressions</li>
4377 </ul> <em>Sequence Database Connectivity</em>
4379 <li>Retrieval of cross-referenced sequences from other
4381 <li>Generalised database reference retrieval and
4382 validation to all fetchable databases</li>
4383 <li>Fetch sequences from DAS sources supporting the
4384 sequence command</li>
4385 </ul> <em>Import and Export</em>
4386 <li>export annotation rows as CSV for spreadsheet import</li>
4387 <li>Jalview projects record alignment dataset associations,
4388 EMBL products, and cDNA sequence mappings</li>
4389 <li>Sequence Group colour can be specified in Annotation
4391 <li>Ad-hoc colouring of group in Annotation File using RGB
4392 triplet as name of colourscheme</li>
4393 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4395 <li>treenode binding for VAMSAS tree exchange</li>
4396 <li>local editing and update of sequences in VAMSAS
4397 alignments (experimental)</li>
4398 <li>Create new or select existing session to join</li>
4399 <li>load and save of vamsas documents</li>
4400 </ul> <em>Application command line</em>
4402 <li>-tree parameter to open trees (introduced for passing
4404 <li>-fetchfrom command line argument to specify nicknames
4405 of DAS servers to query for alignment features</li>
4406 <li>-dasserver command line argument to add new servers
4407 that are also automatically queried for features</li>
4408 <li>-groovy command line argument executes a given groovy
4409 script after all input data has been loaded and parsed</li>
4410 </ul> <em>Applet-Application data exchange</em>
4412 <li>Trees passed as applet parameters can be passed to
4413 application (when using "View in full
4414 application")</li>
4415 </ul> <em>Applet Parameters</em>
4417 <li>feature group display control parameter</li>
4418 <li>debug parameter</li>
4419 <li>showbutton parameter</li>
4420 </ul> <em>Applet API methods</em>
4422 <li>newView public method</li>
4423 <li>Window (current view) specific get/set public methods</li>
4424 <li>Feature display control methods</li>
4425 <li>get list of currently selected sequences</li>
4426 </ul> <em>New Jalview distribution features</em>
4428 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4429 <li>RELEASE file gives build properties for the latest
4430 Jalview release.</li>
4431 <li>Java 1.1 Applet build made easier and donotobfuscate
4432 property controls execution of obfuscator</li>
4433 <li>Build target for generating source distribution</li>
4434 <li>Debug flag for javacc</li>
4435 <li>.jalview_properties file is documented (slightly) in
4436 jalview.bin.Cache</li>
4437 <li>Continuous Build Integration for stable and
4438 development version of Application, Applet and source
4443 <li>selected region output includes visible annotations
4444 (for certain formats)</li>
4445 <li>edit label/displaychar contains existing label/char
4447 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4448 <li>shorter peptide product names from EMBL records</li>
4449 <li>Newick string generator makes compact representations</li>
4450 <li>bootstrap values parsed correctly for tree files with
4452 <li>pathological filechooser bug avoided by not allowing
4453 filenames containing a ':'</li>
4454 <li>Fixed exception when parsing GFF files containing
4455 global sequence features</li>
4456 <li>Alignment datasets are finalized only when number of
4457 references from alignment sequences goes to zero</li>
4458 <li>Close of tree branch colour box without colour
4459 selection causes cascading exceptions</li>
4460 <li>occasional negative imgwidth exceptions</li>
4461 <li>better reporting of non-fatal warnings to user when
4462 file parsing fails.</li>
4463 <li>Save works when Jalview project is default format</li>
4464 <li>Save as dialog opened if current alignment format is
4465 not a valid output format</li>
4466 <li>UniProt canonical names introduced for both das and
4468 <li>Histidine should be midblue (not pink!) in Zappo</li>
4469 <li>error messages passed up and output when data read
4471 <li>edit undo recovers previous dataset sequence when
4472 sequence is edited</li>
4473 <li>allow PDB files without pdb ID HEADER lines (like
4474 those generated by MODELLER) to be read in properly</li>
4475 <li>allow reading of JPred concise files as a normal
4477 <li>Stockholm annotation parsing and alignment properties
4478 import fixed for PFAM records</li>
4479 <li>Structure view windows have correct name in Desktop
4481 <li>annotation consisting of sequence associated scores
4482 can be read and written correctly to annotation file</li>
4483 <li>Aligned cDNA translation to aligned peptide works
4485 <li>Fixed display of hidden sequence markers and
4486 non-italic font for representatives in Applet</li>
4487 <li>Applet Menus are always embedded in applet window on
4489 <li>Newly shown features appear at top of stack (in
4491 <li>Annotations added via parameter not drawn properly
4492 due to null pointer exceptions</li>
4493 <li>Secondary structure lines are drawn starting from
4494 first column of alignment</li>
4495 <li>UniProt XML import updated for new schema release in
4497 <li>Sequence feature to sequence ID match for Features
4498 file is case-insensitive</li>
4499 <li>Sequence features read from Features file appended to
4500 all sequences with matching IDs</li>
4501 <li>PDB structure coloured correctly for associated views
4502 containing a sub-sequence</li>
4503 <li>PDB files can be retrieved by applet from Jar files</li>
4504 <li>feature and annotation file applet parameters
4505 referring to different directories are retrieved correctly</li>
4506 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4507 <li>Fixed application hang whilst waiting for
4508 splash-screen version check to complete</li>
4509 <li>Applet properly URLencodes input parameter values
4510 when passing them to the launchApp service</li>
4511 <li>display name and local features preserved in results
4512 retrieved from web service</li>
4513 <li>Visual delay indication for sequence retrieval and
4514 sequence fetcher initialisation</li>
4515 <li>updated Application to use DAS 1.53e version of
4516 dasobert DAS client</li>
4517 <li>Re-instated Full AMSA support and .amsa file
4519 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4527 <div align="center">
4528 <strong>2.3</strong><br> 9/5/07
4533 <li>Jmol 11.0.2 integration</li>
4534 <li>PDB views stored in Jalview XML files</li>
4535 <li>Slide sequences</li>
4536 <li>Edit sequence in place</li>
4537 <li>EMBL CDS features</li>
4538 <li>DAS Feature mapping</li>
4539 <li>Feature ordering</li>
4540 <li>Alignment Properties</li>
4541 <li>Annotation Scores</li>
4542 <li>Sort by scores</li>
4543 <li>Feature/annotation editing in applet</li>
4548 <li>Headless state operation in 2.2.1</li>
4549 <li>Incorrect and unstable DNA pairwise alignment</li>
4550 <li>Cut and paste of sequences with annotation</li>
4551 <li>Feature group display state in XML</li>
4552 <li>Feature ordering in XML</li>
4553 <li>blc file iteration selection using filename # suffix</li>
4554 <li>Stockholm alignment properties</li>
4555 <li>Stockhom alignment secondary structure annotation</li>
4556 <li>2.2.1 applet had no feature transparency</li>
4557 <li>Number pad keys can be used in cursor mode</li>
4558 <li>Structure Viewer mirror image resolved</li>
4565 <div align="center">
4566 <strong>2.2.1</strong><br> 12/2/07
4571 <li>Non standard characters can be read and displayed
4572 <li>Annotations/Features can be imported/exported to the
4574 <li>Applet allows editing of sequence/annotation/group
4575 name & description
4576 <li>Preference setting to display sequence name in
4578 <li>Annotation file format extended to allow
4579 Sequence_groups to be defined
4580 <li>Default opening of alignment overview panel can be
4581 specified in preferences
4582 <li>PDB residue numbering annotation added to associated
4588 <li>Applet crash under certain Linux OS with Java 1.6
4590 <li>Annotation file export / import bugs fixed
4591 <li>PNG / EPS image output bugs fixed
4597 <div align="center">
4598 <strong>2.2</strong><br> 27/11/06
4603 <li>Multiple views on alignment
4604 <li>Sequence feature editing
4605 <li>"Reload" alignment
4606 <li>"Save" to current filename
4607 <li>Background dependent text colour
4608 <li>Right align sequence ids
4609 <li>User-defined lower case residue colours
4612 <li>Menu item accelerator keys
4613 <li>Control-V pastes to current alignment
4614 <li>Cancel button for DAS Feature Fetching
4615 <li>PCA and PDB Viewers zoom via mouse roller
4616 <li>User-defined sub-tree colours and sub-tree selection
4618 <li>'New Window' button on the 'Output to Text box'
4623 <li>New memory efficient Undo/Redo System
4624 <li>Optimised symbol lookups and conservation/consensus
4626 <li>Region Conservation/Consensus recalculated after
4628 <li>Fixed Remove Empty Columns Bug (empty columns at end
4630 <li>Slowed DAS Feature Fetching for increased robustness.
4632 <li>Made angle brackets in ASCII feature descriptions
4634 <li>Re-instated Zoom function for PCA
4635 <li>Sequence descriptions conserved in web service
4637 <li>UniProt ID discoverer uses any word separated by
4639 <li>WsDbFetch query/result association resolved
4640 <li>Tree leaf to sequence mapping improved
4641 <li>Smooth fonts switch moved to FontChooser dialog box.
4648 <div align="center">
4649 <strong>2.1.1</strong><br> 12/9/06
4654 <li>Copy consensus sequence to clipboard</li>
4659 <li>Image output - rightmost residues are rendered if
4660 sequence id panel has been resized</li>
4661 <li>Image output - all offscreen group boundaries are
4663 <li>Annotation files with sequence references - all
4664 elements in file are relative to sequence position</li>
4665 <li>Mac Applet users can use Alt key for group editing</li>
4671 <div align="center">
4672 <strong>2.1</strong><br> 22/8/06
4677 <li>MAFFT Multiple Alignment in default Web Service list</li>
4678 <li>DAS Feature fetching</li>
4679 <li>Hide sequences and columns</li>
4680 <li>Export Annotations and Features</li>
4681 <li>GFF file reading / writing</li>
4682 <li>Associate structures with sequences from local PDB
4684 <li>Add sequences to exisiting alignment</li>
4685 <li>Recently opened files / URL lists</li>
4686 <li>Applet can launch the full application</li>
4687 <li>Applet has transparency for features (Java 1.2
4689 <li>Applet has user defined colours parameter</li>
4690 <li>Applet can load sequences from parameter
4691 "sequence<em>x</em>"
4697 <li>Redundancy Panel reinstalled in the Applet</li>
4698 <li>Monospaced font - EPS / rescaling bug fixed</li>
4699 <li>Annotation files with sequence references bug fixed</li>
4705 <div align="center">
4706 <strong>2.08.1</strong><br> 2/5/06
4711 <li>Change case of selected region from Popup menu</li>
4712 <li>Choose to match case when searching</li>
4713 <li>Middle mouse button and mouse movement can compress /
4714 expand the visible width and height of the alignment</li>
4719 <li>Annotation Panel displays complete JNet results</li>
4725 <div align="center">
4726 <strong>2.08b</strong><br> 18/4/06
4732 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4733 <li>Righthand label on wrapped alignments shows correct
4740 <div align="center">
4741 <strong>2.08</strong><br> 10/4/06
4746 <li>Editing can be locked to the selection area</li>
4747 <li>Keyboard editing</li>
4748 <li>Create sequence features from searches</li>
4749 <li>Precalculated annotations can be loaded onto
4751 <li>Features file allows grouping of features</li>
4752 <li>Annotation Colouring scheme added</li>
4753 <li>Smooth fonts off by default - Faster rendering</li>
4754 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4759 <li>Drag & Drop fixed on Linux</li>
4760 <li>Jalview Archive file faster to load/save, sequence
4761 descriptions saved.</li>
4767 <div align="center">
4768 <strong>2.07</strong><br> 12/12/05
4773 <li>PDB Structure Viewer enhanced</li>
4774 <li>Sequence Feature retrieval and display enhanced</li>
4775 <li>Choose to output sequence start-end after sequence
4776 name for file output</li>
4777 <li>Sequence Fetcher WSDBFetch@EBI</li>
4778 <li>Applet can read feature files, PDB files and can be
4779 used for HTML form input</li>
4784 <li>HTML output writes groups and features</li>
4785 <li>Group editing is Control and mouse click</li>
4786 <li>File IO bugs</li>
4792 <div align="center">
4793 <strong>2.06</strong><br> 28/9/05
4798 <li>View annotations in wrapped mode</li>
4799 <li>More options for PCA viewer</li>
4804 <li>GUI bugs resolved</li>
4805 <li>Runs with -nodisplay from command line</li>
4811 <div align="center">
4812 <strong>2.05b</strong><br> 15/9/05
4817 <li>Choose EPS export as lineart or text</li>
4818 <li>Jar files are executable</li>
4819 <li>Can read in Uracil - maps to unknown residue</li>
4824 <li>Known OutOfMemory errors give warning message</li>
4825 <li>Overview window calculated more efficiently</li>
4826 <li>Several GUI bugs resolved</li>
4832 <div align="center">
4833 <strong>2.05</strong><br> 30/8/05
4838 <li>Edit and annotate in "Wrapped" view</li>
4843 <li>Several GUI bugs resolved</li>
4849 <div align="center">
4850 <strong>2.04</strong><br> 24/8/05
4855 <li>Hold down mouse wheel & scroll to change font
4861 <li>Improved JPred client reliability</li>
4862 <li>Improved loading of Jalview files</li>
4868 <div align="center">
4869 <strong>2.03</strong><br> 18/8/05
4874 <li>Set Proxy server name and port in preferences</li>
4875 <li>Multiple URL links from sequence ids</li>
4876 <li>User Defined Colours can have a scheme name and added
4878 <li>Choose to ignore gaps in consensus calculation</li>
4879 <li>Unix users can set default web browser</li>
4880 <li>Runs without GUI for batch processing</li>
4881 <li>Dynamically generated Web Service Menus</li>
4886 <li>InstallAnywhere download for Sparc Solaris</li>
4892 <div align="center">
4893 <strong>2.02</strong><br> 18/7/05
4899 <li>Copy & Paste order of sequences maintains
4900 alignment order.</li>
4906 <div align="center">
4907 <strong>2.01</strong><br> 12/7/05
4912 <li>Use delete key for deleting selection.</li>
4913 <li>Use Mouse wheel to scroll sequences.</li>
4914 <li>Help file updated to describe how to add alignment
4916 <li>Version and build date written to build properties
4918 <li>InstallAnywhere installation will check for updates
4919 at launch of Jalview.</li>
4924 <li>Delete gaps bug fixed.</li>
4925 <li>FileChooser sorts columns.</li>
4926 <li>Can remove groups one by one.</li>
4927 <li>Filechooser icons installed.</li>
4928 <li>Finder ignores return character when searching.
4929 Return key will initiate a search.<br>
4936 <div align="center">
4937 <strong>2.0</strong><br> 20/6/05
4942 <li>New codebase</li>