3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
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50 <strong>Release History</strong>
54 <th nowrap><em>Release</em></th>
55 <th><em>New Features</em></th>
56 <th><em>Issues Resolved</em></th>
59 <td width="60" align="center" nowrap><strong><a
60 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
61 <em>13/07/2020</em></strong></td>
62 <td align="left" valign="top">
67 <td align="left" valign="top">
69 <li><!-- JAL-3493 -->Escape does not clear highlights on the alignment (Since Jalview 2.10.3)</li>
74 <td width="60" align="center" nowrap><strong><a
75 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
76 <em>22/04/2020</em></strong></td>
77 <td align="left" valign="top">
80 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
81 'virtual' codon features shown on protein (or vice versa)
82 for display in alignments, on structure views (including
83 transfer to UCSF chimera), in feature reports and for
87 <!-- JAL-3121 -->Feature attributes from VCF files can be
88 exported and re-imported as GFF3 files
91 <!-- JAL-3376 -->Capture VCF "fixed column" values
92 POS, ID, QUAL, FILTER as Feature Attributes
95 <!-- JAL-3375 -->More robust VCF numeric data field
96 validation while parsing
99 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
103 <!-- JAL-3535 -->Feature Settings dialog title includes name
107 <!-- JAL-3538 -->Font anti-aliasing in alignment views
111 <!-- JAL-3468 -->Very long feature descriptions truncated in
115 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
116 with no feature types visible
119 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
121 </ul><em>Jalview Installer</em>
124 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
125 in console (may be null when Jalview launched as executable jar or via conda)
128 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
131 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
134 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
136 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
137 </ul> <em>Release processes</em>
140 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
143 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
145 </ul> <em>Build System</em>
148 <!-- JAL-3510 -->Clover updated to 4.4.1
151 <!-- JAL-3513 -->Test code included in Clover coverage
155 <em>Groovy Scripts</em>
158 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
159 to stdout containing the consensus sequence for each
160 alignment in a Jalview session
163 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
164 genomic sequence_variant annotation from CDS as
165 missense_variant or synonymous_variant on protein products.
169 <td align="left" valign="top">
172 <!-- JAL-3581 -->Hidden sequence markers still visible when
173 'Show hidden markers' option is not ticked
176 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
177 PNG output when 'Automatically set ID width' is set in
178 jalview preferences or properties file
181 <!-- JAL-3571 -->Feature Editor dialog can be opened when
182 'Show Sequence Features' option is not ticked
185 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
186 buttons in Feature Settings dialog are clicked when no
190 <!-- JAL-3412 -->ID margins for CDS and Protein views not
191 equal when split frame is first opened
194 <!-- JAL-3296 -->Sequence position numbers in status bar not
195 correct after editing a sequence's start position
198 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
199 with annotation and exceptions thrown when only a few
200 columns shown in wrapped mode
203 <!-- JAL-3386 -->Sequence IDs missing in headless export of
204 wrapped alignment figure with annotations
207 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
208 ID fails with ClassCastException
211 <!-- JAL-3389 -->Chimera session not restored from Jalview
215 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
216 feature settings dialog also selects columns
219 <!-- JAL-3473 -->SpinnerNumberModel causes
220 IllegalArgumentException in some circumstances
223 <!-- JAL-3534 -->Multiple feature settings dialogs can be
227 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
228 alignment window is closed
231 <!-- JAL-3406 -->Credits missing some authors in Jalview
232 help documentation for 2.11.0 release
235 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
236 includes Pfam ID as sequence's accession rather than its
239 </ul> <em>Java 11 Compatibility issues</em>
242 <!-- JAL-2987 -->OSX - Can't view some search results in
243 PDB/Uniprot search panel
245 </ul> <em>Installer</em>
248 <!-- JAL-3447 -->Jalview should not create file associations
249 for 3D structure files (.pdb, .mmcif. .cif)
251 </ul> <em>Repository and Source Release</em>
254 <!-- JAL-3474 -->removed obsolete .cvsignore files from
258 <!-- JAL-3541 -->Clover report generation running out of
261 </ul> <em>New Known Issues</em>
264 <!-- JAL-3523 -->OSX - Current working directory not
265 preserved when Jalview.app launched with parameters from
269 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
270 clipped in headless figure export when Right Align option
274 <!-- JAL-3542 -->Jalview Installation type always reports
275 'Source' in console output
278 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
279 bamboo server but run fine locally.
285 <td width="60" align="center" nowrap>
286 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
287 <em>04/07/2019</em></strong>
289 <td align="left" valign="top">
292 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
293 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
294 source project) rather than InstallAnywhere
297 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
298 settings, receive over the air updates and launch specific
299 versions via (<a href="https://github.com/threerings/getdown">Three
303 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
304 formats supported by Jalview (including .jvp project files)
307 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
308 arguments and switch between different getdown channels
311 <!-- JAL-3141 -->Backup files created when saving Jalview project
316 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
317 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
319 <!-- JAL-2620 -->Alternative genetic code tables for
320 'Translate as cDNA'</li>
322 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
323 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
326 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
327 implementation that allows updates) used for Sequence Feature collections</li>
329 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
330 features can be filtered and shaded according to any
331 associated attributes (e.g. variant attributes from VCF
332 file, or key-value pairs imported from column 9 of GFF
336 <!-- JAL-2879 -->Feature Attributes and shading schemes
337 stored and restored from Jalview Projects
340 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
341 recognise variant features
344 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
345 sequences (also coloured red by default)
348 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
352 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
353 algorithm (Z-sort/transparency and filter aware)
356 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
362 <!-- JAL-3205 -->Symmetric score matrices for faster
363 tree and PCA calculations
365 <li><strong>Principal Components Analysis Viewer</strong>
368 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
369 and Viewer state saved in Jalview Project
371 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
374 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
378 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
383 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
385 <li><strong>Speed and Efficiency</strong>
388 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
389 multiple groups when working with large alignments
392 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
396 <li><strong>User Interface</strong>
399 <!-- JAL-2933 -->Finder panel remembers last position in each
403 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
404 what is shown)<br />Only visible regions of alignment are shown by
405 default (can be changed in user preferences)
408 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
409 to the Overwrite Dialog
412 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
416 <!-- JAL-1244 -->Status bar shows bounds when dragging a
417 selection region, and gap count when inserting or deleting gaps
420 <!-- JAL-3132 -->Status bar updates over sequence and annotation
424 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
428 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
432 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
435 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
439 <!-- JAL-3181 -->Consistent ordering of links in sequence id
443 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
445 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
449 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
450 <li><strong>Java 11 Support (not yet on general release)</strong>
453 <!-- -->OSX GUI integrations for App menu's 'About' entry and
458 <em>Deprecations</em>
460 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
461 capabilities removed from the Jalview Desktop
463 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
464 unmarshalling has been replaced by JAXB for Jalview projects
465 and XML based data retrieval clients</li>
466 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
467 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
468 </ul> <em>Documentation</em>
470 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
471 not supported in EPS figure export
473 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
474 </ul> <em>Development and Release Processes</em>
477 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
480 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
482 <!-- JAL-3225 -->Eclipse project configuration managed with
486 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
487 Bamboo continuous integration for unattended Test Suite
491 <!-- JAL-2864 -->Memory test suite to detect leaks in common
495 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
499 <!-- JAL-3248 -->Developer documentation migrated to
500 markdown (with HTML rendering)
503 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
506 <!-- JAL-3289 -->New URLs for publishing development
511 <td align="left" valign="top">
514 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
517 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
518 superposition in Jmol fail on Windows
521 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
522 structures for sequences with lots of PDB structures
525 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
529 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
530 project involving multiple views
533 <!-- JAL-3164 -->Overview for complementary view in a linked
534 CDS/Protein alignment is not updated when Hide Columns by
535 Annotation dialog hides columns
538 <!-- JAL-3158 -->Selection highlighting in the complement of a
539 CDS/Protein alignment stops working after making a selection in
540 one view, then making another selection in the other view
543 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
547 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
548 Settings and Jalview Preferences panels
551 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
552 overview with large alignments
555 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
556 region if columns were selected by dragging right-to-left and the
557 mouse moved to the left of the first column
560 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
561 hidden column marker via scale popup menu
564 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
565 doesn't tell users the invalid URL
568 <!-- JAL-2816 -->Tooltips displayed for features filtered by
572 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
573 show cross references or Fetch Database References are shown in
577 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
578 peptide sequence (computed variant shown as p.Res.null)
581 <!-- JAL-2060 -->'Graduated colour' option not offered for
582 manually created features (where feature score is Float.NaN)
585 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
586 when columns are hidden
589 <!-- JAL-3082 -->Regular expression error for '(' in Select
590 Columns by Annotation description
593 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
594 out of Scale or Annotation Panel
597 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
601 <!-- JAL-3074 -->Left/right drag in annotation can scroll
605 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
609 <!-- JAL-3002 -->Column display is out by one after Page Down,
610 Page Up in wrapped mode
613 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
616 <!-- JAL-2932 -->Finder searches in minimised alignments
619 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
620 on opening an alignment
623 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
627 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
628 different groups in the alignment are selected
631 <!-- JAL-2717 -->Internationalised colour scheme names not shown
635 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
639 <!-- JAL-3125 -->Value input for graduated feature colour
640 threshold gets 'unrounded'
643 <!-- JAL-2982 -->PCA image export doesn't respect background
647 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
650 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
653 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
657 <!-- JAL-2964 -->Associate Tree with All Views not restored from
661 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
662 shown in complementary view
665 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
666 without normalisation
669 <!-- JAL-3021 -->Sequence Details report should open positioned at top
673 <!-- JAL-914 -->Help page can be opened twice
676 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
678 </ul> <em>Editing</em>
681 <!-- JAL-2822 -->Start and End should be updated when sequence
682 data at beginning or end of alignment added/removed via 'Edit'
686 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
687 relocate sequence features correctly when start of sequence is
688 removed (Known defect since 2.10)
691 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
692 dialog corrupts dataset sequence
695 <!-- JAL-868 -->Structure colours not updated when associated tree
696 repartitions the alignment view (Regression in 2.10.5)
698 </ul> <em>Datamodel</em>
701 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
702 sequence's End is greater than its length
704 </ul> <em>Bugs fixed for Java 11 Support (not yet on
705 general release)</em>
708 <!-- JAL-3288 -->Menus work properly in split-screen
710 </ul> <em>New Known Defects</em>
713 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
716 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
717 regions of protein alignment.
720 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
721 is restored from a Jalview 2.11 project
724 <!-- JAL-3213 -->Alignment panel height can be too small after
728 <!-- JAL-3240 -->Display is incorrect after removing gapped
729 columns within hidden columns
732 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
733 window after dragging left to select columns to left of visible
737 <!-- JAL-2876 -->Features coloured according to their description
738 string and thresholded by score in earlier versions of Jalview are
739 not shown as thresholded features in 2.11. To workaround please
740 create a Score filter instead.
743 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
745 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
748 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
749 alignments with multiple views can close views unexpectedly
752 <em>Java 11 Specific defects</em>
755 <!-- JAL-3235 -->Jalview Properties file is not sorted
756 alphabetically when saved
762 <td width="60" nowrap>
764 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
767 <td><div align="left">
771 <!-- JAL-3101 -->Default memory for Jalview webstart and
772 InstallAnywhere increased to 1G.
775 <!-- JAL-247 -->Hidden sequence markers and representative
776 sequence bolding included when exporting alignment as EPS,
777 SVG, PNG or HTML. <em>Display is configured via the
778 Format menu, or for command-line use via a Jalview
779 properties file.</em>
782 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
783 API and sequence data now imported as JSON.
786 <!-- JAL-3065 -->Change in recommended way of starting
787 Jalview via a Java command line: add jars in lib directory
788 to CLASSPATH, rather than via the deprecated java.ext.dirs
795 <!-- JAL-3047 -->Support added to execute test suite
796 instrumented with <a href="http://openclover.org/">Open
801 <td><div align="left">
805 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
806 row shown in Feredoxin Structure alignment view of example
810 <!-- JAL-2854 -->Annotation obscures sequences if lots of
811 annotation displayed.
814 <!-- JAL-3107 -->Group conservation/consensus not shown
815 for newly created group when 'Apply to all groups'
819 <!-- JAL-3087 -->Corrupted display when switching to
820 wrapped mode when sequence panel's vertical scrollbar is
824 <!-- JAL-3003 -->Alignment is black in exported EPS file
825 when sequences are selected in exported view.</em>
828 <!-- JAL-3059 -->Groups with different coloured borders
829 aren't rendered with correct colour.
832 <!-- JAL-3092 -->Jalview could hang when importing certain
833 types of knotted RNA secondary structure.
836 <!-- JAL-3095 -->Sequence highlight and selection in
837 trimmed VARNA 2D structure is incorrect for sequences that
841 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
842 annotation when columns are inserted into an alignment,
843 and when exporting as Stockholm flatfile.
846 <!-- JAL-3053 -->Jalview annotation rows containing upper
847 and lower-case 'E' and 'H' do not automatically get
848 treated as RNA secondary structure.
851 <!-- JAL-3106 -->.jvp should be used as default extension
852 (not .jar) when saving a Jalview project file.
855 <!-- JAL-3105 -->Mac Users: closing a window correctly
856 transfers focus to previous window on OSX
859 <em>Java 10 Issues Resolved</em>
862 <!-- JAL-2988 -->OSX - Can't save new files via the File
863 or export menus by typing in a name into the Save dialog
867 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
868 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
869 'look and feel' which has improved compatibility with the
870 latest version of OSX.
877 <td width="60" nowrap>
879 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
880 <em>7/06/2018</em></strong>
883 <td><div align="left">
887 <!-- JAL-2920 -->Use HGVS nomenclature for variant
888 annotation retrieved from Uniprot
891 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
892 onto the Jalview Desktop
896 <td><div align="left">
900 <!-- JAL-3017 -->Cannot import features with multiple
901 variant elements (blocks import of some Uniprot records)
904 <!-- JAL-2997 -->Clustal files with sequence positions in
905 right-hand column parsed correctly
908 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
909 not alignment area in exported graphic
912 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
913 window has input focus
916 <!-- JAL-2992 -->Annotation panel set too high when
917 annotation added to view (Windows)
920 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
921 network connectivity is poor
924 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
925 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
926 the currently open URL and links from a page viewed in
927 Firefox or Chrome on Windows is now fully supported. If
928 you are using Edge, only links in the page can be
929 dragged, and with Internet Explorer, only the currently
930 open URL in the browser can be dropped onto Jalview.</em>
933 <em>New Known Defects</em>
935 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
940 <td width="60" nowrap>
942 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
945 <td><div align="left">
949 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
950 for disabling automatic superposition of multiple
951 structures and open structures in existing views
954 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
955 ID and annotation area margins can be click-dragged to
959 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
963 <!-- JAL-2759 -->Improved performance for large alignments
964 and lots of hidden columns
967 <!-- JAL-2593 -->Improved performance when rendering lots
968 of features (particularly when transparency is disabled)
971 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
972 exchange of Jalview features and Chimera attributes made
978 <td><div align="left">
981 <!-- JAL-2899 -->Structure and Overview aren't updated
982 when Colour By Annotation threshold slider is adjusted
985 <!-- JAL-2778 -->Slow redraw when Overview panel shown
986 overlapping alignment panel
989 <!-- JAL-2929 -->Overview doesn't show end of unpadded
993 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
994 improved: CDS not handled correctly if transcript has no
998 <!-- JAL-2321 -->Secondary structure and temperature
999 factor annotation not added to sequence when local PDB
1000 file associated with it by drag'n'drop or structure
1004 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1005 dialog doesn't import PDB files dropped on an alignment
1008 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1009 scroll bar doesn't work for some CDS/Protein views
1012 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1013 Java 1.8u153 onwards and Java 1.9u4+.
1016 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1017 columns in annotation row
1020 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1021 honored in batch mode
1024 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1025 for structures added to existing Jmol view
1028 <!-- JAL-2223 -->'View Mappings' includes duplicate
1029 entries after importing project with multiple views
1032 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1033 protein sequences via SIFTS from associated PDB entries
1034 with negative residue numbers or missing residues fails
1037 <!-- JAL-2952 -->Exception when shading sequence with negative
1038 Temperature Factor values from annotated PDB files (e.g.
1039 as generated by CONSURF)
1042 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1043 tooltip doesn't include a text description of mutation
1046 <!-- JAL-2922 -->Invert displayed features very slow when
1047 structure and/or overview windows are also shown
1050 <!-- JAL-2954 -->Selecting columns from highlighted regions
1051 very slow for alignments with large numbers of sequences
1054 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1055 with 'StringIndexOutOfBounds'
1058 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1059 platforms running Java 10
1062 <!-- JAL-2960 -->Adding a structure to existing structure
1063 view appears to do nothing because the view is hidden behind the alignment view
1069 <!-- JAL-2926 -->Copy consensus sequence option in applet
1070 should copy the group consensus when popup is opened on it
1076 <!-- JAL-2913 -->Fixed ID width preference is not respected
1079 <em>New Known Defects</em>
1082 <!-- JAL-2973 --> Exceptions occasionally raised when
1083 editing a large alignment and overview is displayed
1086 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1087 repeatedly after a series of edits even when the overview
1088 is no longer reflecting updates
1091 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1092 structures for protein subsequence (if 'Trim Retrieved
1093 Sequences' enabled) or Ensembl isoforms (Workaround in
1094 2.10.4 is to fail back to N&W mapping)
1097 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1098 option gives blank output
1105 <td width="60" nowrap>
1106 <div align="center">
1107 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1110 <td><div align="left">
1111 <ul><li>Updated Certum Codesigning Certificate
1112 (Valid till 30th November 2018)</li></ul></div></td>
1113 <td><div align="left">
1114 <em>Desktop</em><ul>
1116 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1117 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1118 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1119 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1120 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1121 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1122 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1128 <td width="60" nowrap>
1129 <div align="center">
1130 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1133 <td><div align="left">
1137 <!-- JAL-2446 -->Faster and more efficient management and
1138 rendering of sequence features
1141 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1142 429 rate limit request hander
1145 <!-- JAL-2773 -->Structure views don't get updated unless
1146 their colours have changed
1149 <!-- JAL-2495 -->All linked sequences are highlighted for
1150 a structure mousover (Jmol) or selection (Chimera)
1153 <!-- JAL-2790 -->'Cancel' button in progress bar for
1154 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1157 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1158 view from Ensembl locus cross-references
1161 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1165 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1166 feature can be disabled
1169 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1170 PDB easier retrieval of sequences for lists of IDs
1173 <!-- JAL-2758 -->Short names for sequences retrieved from
1179 <li>Groovy interpreter updated to 2.4.12</li>
1180 <li>Example groovy script for generating a matrix of
1181 percent identity scores for current alignment.</li>
1183 <em>Testing and Deployment</em>
1186 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1190 <td><div align="left">
1194 <!-- JAL-2643 -->Pressing tab after updating the colour
1195 threshold text field doesn't trigger an update to the
1199 <!-- JAL-2682 -->Race condition when parsing sequence ID
1203 <!-- JAL-2608 -->Overview windows are also closed when
1204 alignment window is closed
1207 <!-- JAL-2548 -->Export of features doesn't always respect
1211 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1212 takes a long time in Cursor mode
1218 <!-- JAL-2777 -->Structures with whitespace chainCode
1219 cannot be viewed in Chimera
1222 <!-- JAL-2728 -->Protein annotation panel too high in
1226 <!-- JAL-2757 -->Can't edit the query after the server
1227 error warning icon is shown in Uniprot and PDB Free Text
1231 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1234 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1237 <!-- JAL-2739 -->Hidden column marker in last column not
1238 rendered when switching back from Wrapped to normal view
1241 <!-- JAL-2768 -->Annotation display corrupted when
1242 scrolling right in unwapped alignment view
1245 <!-- JAL-2542 -->Existing features on subsequence
1246 incorrectly relocated when full sequence retrieved from
1250 <!-- JAL-2733 -->Last reported memory still shown when
1251 Desktop->Show Memory is unticked (OSX only)
1254 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1255 features of same type and group to be selected for
1259 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1260 alignments when hidden columns are present
1263 <!-- JAL-2392 -->Jalview freezes when loading and
1264 displaying several structures
1267 <!-- JAL-2732 -->Black outlines left after resizing or
1271 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1272 within the Jalview desktop on OSX
1275 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1276 when in wrapped alignment mode
1279 <!-- JAL-2636 -->Scale mark not shown when close to right
1280 hand end of alignment
1283 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1284 each selected sequence do not have correct start/end
1288 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1289 after canceling the Alignment Window's Font dialog
1292 <!-- JAL-2036 -->Show cross-references not enabled after
1293 restoring project until a new view is created
1296 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1297 URL links appears when only default EMBL-EBI link is
1298 configured (since 2.10.2b2)
1301 <!-- JAL-2775 -->Overview redraws whole window when box
1302 position is adjusted
1305 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1306 in a multi-chain structure when viewing alignment
1307 involving more than one chain (since 2.10)
1310 <!-- JAL-2811 -->Double residue highlights in cursor mode
1311 if new selection moves alignment window
1314 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1315 arrow key in cursor mode to pass hidden column marker
1318 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1319 that produces correctly annotated transcripts and products
1322 <!-- JAL-2776 -->Toggling a feature group after first time
1323 doesn't update associated structure view
1326 <em>Applet</em><br />
1329 <!-- JAL-2687 -->Concurrent modification exception when
1330 closing alignment panel
1333 <em>BioJSON</em><br />
1336 <!-- JAL-2546 -->BioJSON export does not preserve
1337 non-positional features
1340 <em>New Known Issues</em>
1343 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1344 sequence features correctly (for many previous versions of
1348 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1349 using cursor in wrapped panel other than top
1352 <!-- JAL-2791 -->Select columns containing feature ignores
1353 graduated colour threshold
1356 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1357 always preserve numbering and sequence features
1360 <em>Known Java 9 Issues</em>
1363 <!-- JAL-2902 -->Groovy Console very slow to open and is
1364 not responsive when entering characters (Webstart, Java
1371 <td width="60" nowrap>
1372 <div align="center">
1373 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1374 <em>2/10/2017</em></strong>
1377 <td><div align="left">
1378 <em>New features in Jalview Desktop</em>
1381 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1383 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1387 <td><div align="left">
1391 <td width="60" nowrap>
1392 <div align="center">
1393 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1394 <em>7/9/2017</em></strong>
1397 <td><div align="left">
1401 <!-- JAL-2588 -->Show gaps in overview window by colouring
1402 in grey (sequences used to be coloured grey, and gaps were
1406 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1410 <!-- JAL-2587 -->Overview updates immediately on increase
1411 in size and progress bar shown as higher resolution
1412 overview is recalculated
1417 <td><div align="left">
1421 <!-- JAL-2664 -->Overview window redraws every hidden
1422 column region row by row
1425 <!-- JAL-2681 -->duplicate protein sequences shown after
1426 retrieving Ensembl crossrefs for sequences from Uniprot
1429 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1430 format setting is unticked
1433 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1434 if group has show boxes format setting unticked
1437 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1438 autoscrolling whilst dragging current selection group to
1439 include sequences and columns not currently displayed
1442 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1443 assemblies are imported via CIF file
1446 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1447 displayed when threshold or conservation colouring is also
1451 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1455 <!-- JAL-2673 -->Jalview continues to scroll after
1456 dragging a selected region off the visible region of the
1460 <!-- JAL-2724 -->Cannot apply annotation based
1461 colourscheme to all groups in a view
1464 <!-- JAL-2511 -->IDs don't line up with sequences
1465 initially after font size change using the Font chooser or
1472 <td width="60" nowrap>
1473 <div align="center">
1474 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1477 <td><div align="left">
1478 <em>Calculations</em>
1482 <!-- JAL-1933 -->Occupancy annotation row shows number of
1483 ungapped positions in each column of the alignment.
1486 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1487 a calculation dialog box
1490 <!-- JAL-2379 -->Revised implementation of PCA for speed
1491 and memory efficiency (~30x faster)
1494 <!-- JAL-2403 -->Revised implementation of sequence
1495 similarity scores as used by Tree, PCA, Shading Consensus
1496 and other calculations
1499 <!-- JAL-2416 -->Score matrices are stored as resource
1500 files within the Jalview codebase
1503 <!-- JAL-2500 -->Trees computed on Sequence Feature
1504 Similarity may have different topology due to increased
1511 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1512 model for alignments and groups
1515 <!-- JAL-384 -->Custom shading schemes created via groovy
1522 <!-- JAL-2526 -->Efficiency improvements for interacting
1523 with alignment and overview windows
1526 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1530 <!-- JAL-2388 -->Hidden columns and sequences can be
1534 <!-- JAL-2611 -->Click-drag in visible area allows fine
1535 adjustment of visible position
1539 <em>Data import/export</em>
1542 <!-- JAL-2535 -->Posterior probability annotation from
1543 Stockholm files imported as sequence associated annotation
1546 <!-- JAL-2507 -->More robust per-sequence positional
1547 annotation input/output via stockholm flatfile
1550 <!-- JAL-2533 -->Sequence names don't include file
1551 extension when importing structure files without embedded
1552 names or PDB accessions
1555 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1556 format sequence substitution matrices
1559 <em>User Interface</em>
1562 <!-- JAL-2447 --> Experimental Features Checkbox in
1563 Desktop's Tools menu to hide or show untested features in
1567 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1568 via Overview or sequence motif search operations
1571 <!-- JAL-2547 -->Amend sequence features dialog box can be
1572 opened by double clicking gaps within sequence feature
1576 <!-- JAL-1476 -->Status bar message shown when not enough
1577 aligned positions were available to create a 3D structure
1581 <em>3D Structure</em>
1584 <!-- JAL-2430 -->Hidden regions in alignment views are not
1585 coloured in linked structure views
1588 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1589 file-based command exchange
1592 <!-- JAL-2375 -->Structure chooser automatically shows
1593 Cached Structures rather than querying the PDBe if
1594 structures are already available for sequences
1597 <!-- JAL-2520 -->Structures imported via URL are cached in
1598 the Jalview project rather than downloaded again when the
1599 project is reopened.
1602 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1603 to transfer Chimera's structure attributes as Jalview
1604 features, and vice-versa (<strong>Experimental
1608 <em>Web Services</em>
1611 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1614 <!-- JAL-2335 -->Filter non-standard amino acids and
1615 nucleotides when submitting to AACon and other MSA
1619 <!-- JAL-2316, -->URLs for viewing database
1620 cross-references provided by identifiers.org and the
1621 EMBL-EBI's MIRIAM DB
1628 <!-- JAL-2344 -->FileFormatI interface for describing and
1629 identifying file formats (instead of String constants)
1632 <!-- JAL-2228 -->FeatureCounter script refactored for
1633 efficiency when counting all displayed features (not
1634 backwards compatible with 2.10.1)
1637 <em>Example files</em>
1640 <!-- JAL-2631 -->Graduated feature colour style example
1641 included in the example feature file
1644 <em>Documentation</em>
1647 <!-- JAL-2339 -->Release notes reformatted for readability
1648 with the built-in Java help viewer
1651 <!-- JAL-1644 -->Find documentation updated with 'search
1652 sequence description' option
1658 <!-- JAL-2485, -->External service integration tests for
1659 Uniprot REST Free Text Search Client
1662 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1665 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1670 <td><div align="left">
1671 <em>Calculations</em>
1674 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1675 matrix - C->R should be '-3'<br />Old matrix restored
1676 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1678 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1679 Jalview's treatment of gaps in PCA and substitution matrix
1680 based Tree calculations.<br /> <br />In earlier versions
1681 of Jalview, gaps matching gaps were penalised, and gaps
1682 matching non-gaps penalised even more. In the PCA
1683 calculation, gaps were actually treated as non-gaps - so
1684 different costs were applied, which meant Jalview's PCAs
1685 were different to those produced by SeqSpace.<br />Jalview
1686 now treats gaps in the same way as SeqSpace (ie it scores
1687 them as 0). <br /> <br />Enter the following in the
1688 Groovy console to restore pre-2.10.2 behaviour:<br />
1689 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1690 // for 2.10.1 mode <br />
1691 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1692 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1693 these settings will affect all subsequent tree and PCA
1694 calculations (not recommended)</em></li>
1696 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1697 scaling of branch lengths for trees computed using
1698 Sequence Feature Similarity.
1701 <!-- JAL-2377 -->PCA calculation could hang when
1702 generating output report when working with highly
1703 redundant alignments
1706 <!-- JAL-2544 --> Sort by features includes features to
1707 right of selected region when gaps present on right-hand
1711 <em>User Interface</em>
1714 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1715 doesn't reselect a specific sequence's associated
1716 annotation after it was used for colouring a view
1719 <!-- JAL-2419 -->Current selection lost if popup menu
1720 opened on a region of alignment without groups
1723 <!-- JAL-2374 -->Popup menu not always shown for regions
1724 of an alignment with overlapping groups
1727 <!-- JAL-2310 -->Finder double counts if both a sequence's
1728 name and description match
1731 <!-- JAL-2370 -->Hiding column selection containing two
1732 hidden regions results in incorrect hidden regions
1735 <!-- JAL-2386 -->'Apply to all groups' setting when
1736 changing colour does not apply Conservation slider value
1740 <!-- JAL-2373 -->Percentage identity and conservation menu
1741 items do not show a tick or allow shading to be disabled
1744 <!-- JAL-2385 -->Conservation shading or PID threshold
1745 lost when base colourscheme changed if slider not visible
1748 <!-- JAL-2547 -->Sequence features shown in tooltip for
1749 gaps before start of features
1752 <!-- JAL-2623 -->Graduated feature colour threshold not
1753 restored to UI when feature colour is edited
1756 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1757 a time when scrolling vertically in wrapped mode.
1760 <!-- JAL-2630 -->Structure and alignment overview update
1761 as graduate feature colour settings are modified via the
1765 <!-- JAL-2034 -->Overview window doesn't always update
1766 when a group defined on the alignment is resized
1769 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1770 wrapped view result in positional status updates
1774 <!-- JAL-2563 -->Status bar doesn't show position for
1775 ambiguous amino acid and nucleotide symbols
1778 <!-- JAL-2602 -->Copy consensus sequence failed if
1779 alignment included gapped columns
1782 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1783 widgets don't permanently disappear
1786 <!-- JAL-2503 -->Cannot select or filter quantitative
1787 annotation that are shown only as column labels (e.g.
1788 T-Coffee column reliability scores)
1791 <!-- JAL-2594 -->Exception thrown if trying to create a
1792 sequence feature on gaps only
1795 <!-- JAL-2504 -->Features created with 'New feature'
1796 button from a Find inherit previously defined feature type
1797 rather than the Find query string
1800 <!-- JAL-2423 -->incorrect title in output window when
1801 exporting tree calculated in Jalview
1804 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1805 and then revealing them reorders sequences on the
1809 <!-- JAL-964 -->Group panel in sequence feature settings
1810 doesn't update to reflect available set of groups after
1811 interactively adding or modifying features
1814 <!-- JAL-2225 -->Sequence Database chooser unusable on
1818 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1819 only excluded gaps in current sequence and ignored
1826 <!-- JAL-2421 -->Overview window visible region moves
1827 erratically when hidden rows or columns are present
1830 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1831 Structure Viewer's colour menu don't correspond to
1835 <!-- JAL-2405 -->Protein specific colours only offered in
1836 colour and group colour menu for protein alignments
1839 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1840 reflect currently selected view or group's shading
1844 <!-- JAL-2624 -->Feature colour thresholds not respected
1845 when rendered on overview and structures when opacity at
1849 <!-- JAL-2589 -->User defined gap colour not shown in
1850 overview when features overlaid on alignment
1853 <!-- JAL-2567 -->Feature settings for different views not
1854 recovered correctly from Jalview project file
1857 <!-- JAL-2256 -->Feature colours in overview when first opened
1858 (automatically via preferences) are different to the main
1862 <em>Data import/export</em>
1865 <!-- JAL-2576 -->Very large alignments take a long time to
1869 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1870 added after a sequence was imported are not written to
1874 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1875 when importing RNA secondary structure via Stockholm
1878 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1879 not shown in correct direction for simple pseudoknots
1882 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1883 with lightGray or darkGray via features file (but can
1887 <!-- JAL-2383 -->Above PID colour threshold not recovered
1888 when alignment view imported from project
1891 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1892 structure and sequences extracted from structure files
1893 imported via URL and viewed in Jmol
1896 <!-- JAL-2520 -->Structures loaded via URL are saved in
1897 Jalview Projects rather than fetched via URL again when
1898 the project is loaded and the structure viewed
1901 <em>Web Services</em>
1904 <!-- JAL-2519 -->EnsemblGenomes example failing after
1905 release of Ensembl v.88
1908 <!-- JAL-2366 -->Proxy server address and port always
1909 appear enabled in Preferences->Connections
1912 <!-- JAL-2461 -->DAS registry not found exceptions
1913 removed from console output
1916 <!-- JAL-2582 -->Cannot retrieve protein products from
1917 Ensembl by Peptide ID
1920 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1921 created from SIFTs, and spurious 'Couldn't open structure
1922 in Chimera' errors raised after April 2017 update (problem
1923 due to 'null' string rather than empty string used for
1924 residues with no corresponding PDB mapping).
1927 <em>Application UI</em>
1930 <!-- JAL-2361 -->User Defined Colours not added to Colour
1934 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1935 case' residues (button in colourscheme editor debugged and
1936 new documentation and tooltips added)
1939 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1940 doesn't restore group-specific text colour thresholds
1943 <!-- JAL-2243 -->Feature settings panel does not update as
1944 new features are added to alignment
1947 <!-- JAL-2532 -->Cancel in feature settings reverts
1948 changes to feature colours via the Amend features dialog
1951 <!-- JAL-2506 -->Null pointer exception when attempting to
1952 edit graduated feature colour via amend features dialog
1956 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1957 selection menu changes colours of alignment views
1960 <!-- JAL-2426 -->Spurious exceptions in console raised
1961 from alignment calculation workers after alignment has
1965 <!-- JAL-1608 -->Typo in selection popup menu - Create
1966 groups now 'Create Group'
1969 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1970 Create/Undefine group doesn't always work
1973 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1974 shown again after pressing 'Cancel'
1977 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1978 adjusts start position in wrap mode
1981 <!-- JAL-2563 -->Status bar doesn't show positions for
1982 ambiguous amino acids
1985 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1986 CDS/Protein view after CDS sequences added for aligned
1990 <!-- JAL-2592 -->User defined colourschemes called 'User
1991 Defined' don't appear in Colours menu
1997 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1998 score models doesn't always result in an updated PCA plot
2001 <!-- JAL-2442 -->Features not rendered as transparent on
2002 overview or linked structure view
2005 <!-- JAL-2372 -->Colour group by conservation doesn't
2009 <!-- JAL-2517 -->Hitting Cancel after applying
2010 user-defined colourscheme doesn't restore original
2017 <!-- JAL-2314 -->Unit test failure:
2018 jalview.ws.jabaws.RNAStructExportImport setup fails
2021 <!-- JAL-2307 -->Unit test failure:
2022 jalview.ws.sifts.SiftsClientTest due to compatibility
2023 problems with deep array comparison equality asserts in
2024 successive versions of TestNG
2027 <!-- JAL-2479 -->Relocated StructureChooserTest and
2028 ParameterUtilsTest Unit tests to Network suite
2031 <em>New Known Issues</em>
2034 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2035 phase after a sequence motif find operation
2038 <!-- JAL-2550 -->Importing annotation file with rows
2039 containing just upper and lower case letters are
2040 interpreted as WUSS RNA secondary structure symbols
2043 <!-- JAL-2590 -->Cannot load and display Newick trees
2044 reliably from eggnog Ortholog database
2047 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2048 containing features of type Highlight' when 'B' is pressed
2049 to mark columns containing highlighted regions.
2052 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2053 doesn't always add secondary structure annotation.
2058 <td width="60" nowrap>
2059 <div align="center">
2060 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2063 <td><div align="left">
2067 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2068 for all consensus calculations
2071 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2074 <li>Updated Jalview's Certum code signing certificate
2077 <em>Application</em>
2080 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2081 set of database cross-references, sorted alphabetically
2084 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2085 from database cross references. Users with custom links
2086 will receive a <a href="webServices/urllinks.html#warning">warning
2087 dialog</a> asking them to update their preferences.
2090 <!-- JAL-2287-->Cancel button and escape listener on
2091 dialog warning user about disconnecting Jalview from a
2095 <!-- JAL-2320-->Jalview's Chimera control window closes if
2096 the Chimera it is connected to is shut down
2099 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2100 columns menu item to mark columns containing highlighted
2101 regions (e.g. from structure selections or results of a
2105 <!-- JAL-2284-->Command line option for batch-generation
2106 of HTML pages rendering alignment data with the BioJS
2116 <!-- JAL-2286 -->Columns with more than one modal residue
2117 are not coloured or thresholded according to percent
2118 identity (first observed in Jalview 2.8.2)
2121 <!-- JAL-2301 -->Threonine incorrectly reported as not
2125 <!-- JAL-2318 -->Updates to documentation pages (above PID
2126 threshold, amino acid properties)
2129 <!-- JAL-2292 -->Lower case residues in sequences are not
2130 reported as mapped to residues in a structure file in the
2134 <!--JAL-2324 -->Identical features with non-numeric scores
2135 could be added multiple times to a sequence
2138 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2139 bond features shown as two highlighted residues rather
2140 than a range in linked structure views, and treated
2141 correctly when selecting and computing trees from features
2144 <!-- JAL-2281-->Custom URL links for database
2145 cross-references are matched to database name regardless
2150 <em>Application</em>
2153 <!-- JAL-2282-->Custom URL links for specific database
2154 names without regular expressions also offer links from
2158 <!-- JAL-2315-->Removing a single configured link in the
2159 URL links pane in Connections preferences doesn't actually
2160 update Jalview configuration
2163 <!-- JAL-2272-->CTRL-Click on a selected region to open
2164 the alignment area popup menu doesn't work on El-Capitan
2167 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2168 files with similarly named sequences if dropped onto the
2172 <!-- JAL-2312 -->Additional mappings are shown for PDB
2173 entries where more chains exist in the PDB accession than
2174 are reported in the SIFTS file
2177 <!-- JAL-2317-->Certain structures do not get mapped to
2178 the structure view when displayed with Chimera
2181 <!-- JAL-2317-->No chains shown in the Chimera view
2182 panel's View->Show Chains submenu
2185 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2186 work for wrapped alignment views
2189 <!--JAL-2197 -->Rename UI components for running JPred
2190 predictions from 'JNet' to 'JPred'
2193 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2194 corrupted when annotation panel vertical scroll is not at
2195 first annotation row
2198 <!--JAL-2332 -->Attempting to view structure for Hen
2199 lysozyme results in a PDB Client error dialog box
2202 <!-- JAL-2319 -->Structure View's mapping report switched
2203 ranges for PDB and sequence for SIFTS
2206 SIFTS 'Not_Observed' residues mapped to non-existant
2210 <!-- <em>New Known Issues</em>
2217 <td width="60" nowrap>
2218 <div align="center">
2219 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2220 <em>25/10/2016</em></strong>
2223 <td><em>Application</em>
2225 <li>3D Structure chooser opens with 'Cached structures'
2226 view if structures already loaded</li>
2227 <li>Progress bar reports models as they are loaded to
2228 structure views</li>
2234 <li>Colour by conservation always enabled and no tick
2235 shown in menu when BLOSUM or PID shading applied</li>
2236 <li>FER1_ARATH and FER2_ARATH labels were switched in
2237 example sequences/projects/trees</li>
2239 <em>Application</em>
2241 <li>Jalview projects with views of local PDB structure
2242 files saved on Windows cannot be opened on OSX</li>
2243 <li>Multiple structure views can be opened and superposed
2244 without timeout for structures with multiple models or
2245 multiple sequences in alignment</li>
2246 <li>Cannot import or associated local PDB files without a
2247 PDB ID HEADER line</li>
2248 <li>RMSD is not output in Jmol console when superposition
2250 <li>Drag and drop of URL from Browser fails for Linux and
2251 OSX versions earlier than El Capitan</li>
2252 <li>ENA client ignores invalid content from ENA server</li>
2253 <li>Exceptions are not raised in console when ENA client
2254 attempts to fetch non-existent IDs via Fetch DB Refs UI
2256 <li>Exceptions are not raised in console when a new view
2257 is created on the alignment</li>
2258 <li>OSX right-click fixed for group selections: CMD-click
2259 to insert/remove gaps in groups and CTRL-click to open group
2262 <em>Build and deployment</em>
2264 <li>URL link checker now copes with multi-line anchor
2267 <em>New Known Issues</em>
2269 <li>Drag and drop from URL links in browsers do not work
2276 <td width="60" nowrap>
2277 <div align="center">
2278 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2281 <td><em>General</em>
2284 <!-- JAL-2124 -->Updated Spanish translations.
2287 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2288 for importing structure data to Jalview. Enables mmCIF and
2292 <!-- JAL-192 --->Alignment ruler shows positions relative to
2296 <!-- JAL-2202 -->Position/residue shown in status bar when
2297 mousing over sequence associated annotation
2300 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2304 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2305 '()', canonical '[]' and invalid '{}' base pair populations
2309 <!-- JAL-2092 -->Feature settings popup menu options for
2310 showing or hiding columns containing a feature
2313 <!-- JAL-1557 -->Edit selected group by double clicking on
2314 group and sequence associated annotation labels
2317 <!-- JAL-2236 -->Sequence name added to annotation label in
2318 select/hide columns by annotation and colour by annotation
2322 </ul> <em>Application</em>
2325 <!-- JAL-2050-->Automatically hide introns when opening a
2326 gene/transcript view
2329 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2333 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2334 structure mappings with the EMBL-EBI PDBe SIFTS database
2337 <!-- JAL-2079 -->Updated download sites used for Rfam and
2338 Pfam sources to xfam.org
2341 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2344 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2345 over sequences in Jalview
2348 <!-- JAL-2027-->Support for reverse-complement coding
2349 regions in ENA and EMBL
2352 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2353 for record retrieval via ENA rest API
2356 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2360 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2361 groovy script execution
2364 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2365 alignment window's Calculate menu
2368 <!-- JAL-1812 -->Allow groovy scripts that call
2369 Jalview.getAlignFrames() to run in headless mode
2372 <!-- JAL-2068 -->Support for creating new alignment
2373 calculation workers from groovy scripts
2376 <!-- JAL-1369 --->Store/restore reference sequence in
2380 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2381 associations are now saved/restored from project
2384 <!-- JAL-1993 -->Database selection dialog always shown
2385 before sequence fetcher is opened
2388 <!-- JAL-2183 -->Double click on an entry in Jalview's
2389 database chooser opens a sequence fetcher
2392 <!-- JAL-1563 -->Free-text search client for UniProt using
2393 the UniProt REST API
2396 <!-- JAL-2168 -->-nonews command line parameter to prevent
2397 the news reader opening
2400 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2401 querying stored in preferences
2404 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2408 <!-- JAL-1977-->Tooltips shown on database chooser
2411 <!-- JAL-391 -->Reverse complement function in calculate
2412 menu for nucleotide sequences
2415 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2416 and feature counts preserves alignment ordering (and
2417 debugged for complex feature sets).
2420 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2421 viewing structures with Jalview 2.10
2424 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2425 genome, transcript CCDS and gene ids via the Ensembl and
2426 Ensembl Genomes REST API
2429 <!-- JAL-2049 -->Protein sequence variant annotation
2430 computed for 'sequence_variant' annotation on CDS regions
2434 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2438 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2439 Ref Fetcher fails to match, or otherwise updates sequence
2440 data from external database records.
2443 <!-- JAL-2154 -->Revised Jalview Project format for
2444 efficient recovery of sequence coding and alignment
2445 annotation relationships.
2447 </ul> <!-- <em>Applet</em>
2458 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2462 <!-- JAL-2018-->Export features in Jalview format (again)
2463 includes graduated colourschemes
2466 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2467 working with big alignments and lots of hidden columns
2470 <!-- JAL-2053-->Hidden column markers not always rendered
2471 at right of alignment window
2474 <!-- JAL-2067 -->Tidied up links in help file table of
2478 <!-- JAL-2072 -->Feature based tree calculation not shown
2482 <!-- JAL-2075 -->Hidden columns ignored during feature
2483 based tree calculation
2486 <!-- JAL-2065 -->Alignment view stops updating when show
2487 unconserved enabled for group on alignment
2490 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2494 <!-- JAL-2146 -->Alignment column in status incorrectly
2495 shown as "Sequence position" when mousing over
2499 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2500 hidden columns present
2503 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2504 user created annotation added to alignment
2507 <!-- JAL-1841 -->RNA Structure consensus only computed for
2508 '()' base pair annotation
2511 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2512 in zero scores for all base pairs in RNA Structure
2516 <!-- JAL-2174-->Extend selection with columns containing
2520 <!-- JAL-2275 -->Pfam format writer puts extra space at
2521 beginning of sequence
2524 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2528 <!-- JAL-2238 -->Cannot create groups on an alignment from
2529 from a tree when t-coffee scores are shown
2532 <!-- JAL-1836,1967 -->Cannot import and view PDB
2533 structures with chains containing negative resnums (4q4h)
2536 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2540 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2541 to Clustal, PIR and PileUp output
2544 <!-- JAL-2008 -->Reordering sequence features that are
2545 not visible causes alignment window to repaint
2548 <!-- JAL-2006 -->Threshold sliders don't work in
2549 graduated colour and colour by annotation row for e-value
2550 scores associated with features and annotation rows
2553 <!-- JAL-1797 -->amino acid physicochemical conservation
2554 calculation should be case independent
2557 <!-- JAL-2173 -->Remove annotation also updates hidden
2561 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2562 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2563 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2566 <!-- JAL-2065 -->Null pointer exceptions and redraw
2567 problems when reference sequence defined and 'show
2568 non-conserved' enabled
2571 <!-- JAL-1306 -->Quality and Conservation are now shown on
2572 load even when Consensus calculation is disabled
2575 <!-- JAL-1932 -->Remove right on penultimate column of
2576 alignment does nothing
2579 <em>Application</em>
2582 <!-- JAL-1552-->URLs and links can't be imported by
2583 drag'n'drop on OSX when launched via webstart (note - not
2584 yet fixed for El Capitan)
2587 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2588 output when running on non-gb/us i18n platforms
2591 <!-- JAL-1944 -->Error thrown when exporting a view with
2592 hidden sequences as flat-file alignment
2595 <!-- JAL-2030-->InstallAnywhere distribution fails when
2599 <!-- JAL-2080-->Jalview very slow to launch via webstart
2600 (also hotfix for 2.9.0b2)
2603 <!-- JAL-2085 -->Cannot save project when view has a
2604 reference sequence defined
2607 <!-- JAL-1011 -->Columns are suddenly selected in other
2608 alignments and views when revealing hidden columns
2611 <!-- JAL-1989 -->Hide columns not mirrored in complement
2612 view in a cDNA/Protein splitframe
2615 <!-- JAL-1369 -->Cannot save/restore representative
2616 sequence from project when only one sequence is
2620 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2621 in Structure Chooser
2624 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2625 structure consensus didn't refresh annotation panel
2628 <!-- JAL-1962 -->View mapping in structure view shows
2629 mappings between sequence and all chains in a PDB file
2632 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2633 dialogs format columns correctly, don't display array
2634 data, sort columns according to type
2637 <!-- JAL-1975 -->Export complete shown after destination
2638 file chooser is cancelled during an image export
2641 <!-- JAL-2025 -->Error when querying PDB Service with
2642 sequence name containing special characters
2645 <!-- JAL-2024 -->Manual PDB structure querying should be
2649 <!-- JAL-2104 -->Large tooltips with broken HTML
2650 formatting don't wrap
2653 <!-- JAL-1128 -->Figures exported from wrapped view are
2654 truncated so L looks like I in consensus annotation
2657 <!-- JAL-2003 -->Export features should only export the
2658 currently displayed features for the current selection or
2662 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2663 after fetching cross-references, and restoring from
2667 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2668 followed in the structure viewer
2671 <!-- JAL-2163 -->Titles for individual alignments in
2672 splitframe not restored from project
2675 <!-- JAL-2145 -->missing autocalculated annotation at
2676 trailing end of protein alignment in transcript/product
2677 splitview when pad-gaps not enabled by default
2680 <!-- JAL-1797 -->amino acid physicochemical conservation
2684 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2685 article has been read (reopened issue due to
2686 internationalisation problems)
2689 <!-- JAL-1960 -->Only offer PDB structures in structure
2690 viewer based on sequence name, PDB and UniProt
2695 <!-- JAL-1976 -->No progress bar shown during export of
2699 <!-- JAL-2213 -->Structures not always superimposed after
2700 multiple structures are shown for one or more sequences.
2703 <!-- JAL-1370 -->Reference sequence characters should not
2704 be replaced with '.' when 'Show unconserved' format option
2708 <!-- JAL-1823 -->Cannot specify chain code when entering
2709 specific PDB id for sequence
2712 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2713 'Export hidden sequences' is enabled, but 'export hidden
2714 columns' is disabled.
2717 <!--JAL-2026-->Best Quality option in structure chooser
2718 selects lowest rather than highest resolution structures
2722 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2723 to sequence mapping in 'View Mappings' report
2726 <!-- JAL-2284 -->Unable to read old Jalview projects that
2727 contain non-XML data added after Jalvew wrote project.
2730 <!-- JAL-2118 -->Newly created annotation row reorders
2731 after clicking on it to create new annotation for a
2735 <!-- JAL-1980 -->Null Pointer Exception raised when
2736 pressing Add on an orphaned cut'n'paste window.
2738 <!-- may exclude, this is an external service stability issue JAL-1941
2739 -- > RNA 3D structure not added via DSSR service</li> -->
2744 <!-- JAL-2151 -->Incorrect columns are selected when
2745 hidden columns present before start of sequence
2748 <!-- JAL-1986 -->Missing dependencies on applet pages
2752 <!-- JAL-1947 -->Overview pixel size changes when
2753 sequences are hidden in applet
2756 <!-- JAL-1996 -->Updated instructions for applet
2757 deployment on examples pages.
2764 <td width="60" nowrap>
2765 <div align="center">
2766 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2767 <em>16/10/2015</em></strong>
2770 <td><em>General</em>
2772 <li>Time stamps for signed Jalview application and applet
2777 <em>Application</em>
2779 <li>Duplicate group consensus and conservation rows
2780 shown when tree is partitioned</li>
2781 <li>Erratic behaviour when tree partitions made with
2782 multiple cDNA/Protein split views</li>
2788 <td width="60" nowrap>
2789 <div align="center">
2790 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2791 <em>8/10/2015</em></strong>
2794 <td><em>General</em>
2796 <li>Updated Spanish translations of localized text for
2798 </ul> <em>Application</em>
2800 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2801 <li>Signed OSX InstallAnywhere installer<br></li>
2802 <li>Support for per-sequence based annotations in BioJSON</li>
2803 </ul> <em>Applet</em>
2805 <li>Split frame example added to applet examples page</li>
2806 </ul> <em>Build and Deployment</em>
2809 <!-- JAL-1888 -->New ant target for running Jalview's test
2817 <li>Mapping of cDNA to protein in split frames
2818 incorrect when sequence start > 1</li>
2819 <li>Broken images in filter column by annotation dialog
2821 <li>Feature colours not parsed from features file</li>
2822 <li>Exceptions and incomplete link URLs recovered when
2823 loading a features file containing HTML tags in feature
2827 <em>Application</em>
2829 <li>Annotations corrupted after BioJS export and
2831 <li>Incorrect sequence limits after Fetch DB References
2832 with 'trim retrieved sequences'</li>
2833 <li>Incorrect warning about deleting all data when
2834 deleting selected columns</li>
2835 <li>Patch to build system for shipping properly signed
2836 JNLP templates for webstart launch</li>
2837 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2838 unreleased structures for download or viewing</li>
2839 <li>Tab/space/return keystroke operation of EMBL-PDBe
2840 fetcher/viewer dialogs works correctly</li>
2841 <li>Disabled 'minimise' button on Jalview windows
2842 running on OSX to workaround redraw hang bug</li>
2843 <li>Split cDNA/Protein view position and geometry not
2844 recovered from jalview project</li>
2845 <li>Initial enabled/disabled state of annotation menu
2846 sorter 'show autocalculated first/last' corresponds to
2848 <li>Restoring of Clustal, RNA Helices and T-Coffee
2849 color schemes from BioJSON</li>
2853 <li>Reorder sequences mirrored in cDNA/Protein split
2855 <li>Applet with Jmol examples not loading correctly</li>
2861 <td><div align="center">
2862 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2864 <td><em>General</em>
2866 <li>Linked visualisation and analysis of DNA and Protein
2869 <li>Translated cDNA alignments shown as split protein
2870 and DNA alignment views</li>
2871 <li>Codon consensus annotation for linked protein and
2872 cDNA alignment views</li>
2873 <li>Link cDNA or Protein product sequences by loading
2874 them onto Protein or cDNA alignments</li>
2875 <li>Reconstruct linked cDNA alignment from aligned
2876 protein sequences</li>
2879 <li>Jmol integration updated to Jmol v14.2.14</li>
2880 <li>Import and export of Jalview alignment views as <a
2881 href="features/bioJsonFormat.html">BioJSON</a></li>
2882 <li>New alignment annotation file statements for
2883 reference sequences and marking hidden columns</li>
2884 <li>Reference sequence based alignment shading to
2885 highlight variation</li>
2886 <li>Select or hide columns according to alignment
2888 <li>Find option for locating sequences by description</li>
2889 <li>Conserved physicochemical properties shown in amino
2890 acid conservation row</li>
2891 <li>Alignments can be sorted by number of RNA helices</li>
2892 </ul> <em>Application</em>
2894 <li>New cDNA/Protein analysis capabilities
2896 <li>Get Cross-References should open a Split Frame
2897 view with cDNA/Protein</li>
2898 <li>Detect when nucleotide sequences and protein
2899 sequences are placed in the same alignment</li>
2900 <li>Split cDNA/Protein views are saved in Jalview
2905 <li>Use REST API to talk to Chimera</li>
2906 <li>Selected regions in Chimera are highlighted in linked
2907 Jalview windows</li>
2909 <li>VARNA RNA viewer updated to v3.93</li>
2910 <li>VARNA views are saved in Jalview Projects</li>
2911 <li>Pseudoknots displayed as Jalview RNA annotation can
2912 be shown in VARNA</li>
2914 <li>Make groups for selection uses marked columns as well
2915 as the active selected region</li>
2917 <li>Calculate UPGMA and NJ trees using sequence feature
2919 <li>New Export options
2921 <li>New Export Settings dialog to control hidden
2922 region export in flat file generation</li>
2924 <li>Export alignment views for display with the <a
2925 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2927 <li>Export scrollable SVG in HTML page</li>
2928 <li>Optional embedding of BioJSON data when exporting
2929 alignment figures to HTML</li>
2931 <li>3D structure retrieval and display
2933 <li>Free text and structured queries with the PDBe
2935 <li>PDBe Search API based discovery and selection of
2936 PDB structures for a sequence set</li>
2940 <li>JPred4 employed for protein secondary structure
2942 <li>Hide Insertions menu option to hide unaligned columns
2943 for one or a group of sequences</li>
2944 <li>Automatically hide insertions in alignments imported
2945 from the JPred4 web server</li>
2946 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2947 system on OSX<br />LGPL libraries courtesy of <a
2948 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2950 <li>changed 'View nucleotide structure' submenu to 'View
2951 VARNA 2D Structure'</li>
2952 <li>change "View protein structure" menu option to "3D
2955 </ul> <em>Applet</em>
2957 <li>New layout for applet example pages</li>
2958 <li>New parameters to enable SplitFrame view
2959 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2960 <li>New example demonstrating linked viewing of cDNA and
2961 Protein alignments</li>
2962 </ul> <em>Development and deployment</em>
2964 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2965 <li>Include installation type and git revision in build
2966 properties and console log output</li>
2967 <li>Jalview Github organisation, and new github site for
2968 storing BioJsMSA Templates</li>
2969 <li>Jalview's unit tests now managed with TestNG</li>
2972 <!-- <em>General</em>
2974 </ul> --> <!-- issues resolved --> <em>Application</em>
2976 <li>Escape should close any open find dialogs</li>
2977 <li>Typo in select-by-features status report</li>
2978 <li>Consensus RNA secondary secondary structure
2979 predictions are not highlighted in amber</li>
2980 <li>Missing gap character in v2.7 example file means
2981 alignment appears unaligned when pad-gaps is not enabled</li>
2982 <li>First switch to RNA Helices colouring doesn't colour
2983 associated structure views</li>
2984 <li>ID width preference option is greyed out when auto
2985 width checkbox not enabled</li>
2986 <li>Stopped a warning dialog from being shown when
2987 creating user defined colours</li>
2988 <li>'View Mapping' in structure viewer shows sequence
2989 mappings for just that viewer's sequences</li>
2990 <li>Workaround for superposing PDB files containing
2991 multiple models in Chimera</li>
2992 <li>Report sequence position in status bar when hovering
2993 over Jmol structure</li>
2994 <li>Cannot output gaps as '.' symbols with Selection ->
2995 output to text box</li>
2996 <li>Flat file exports of alignments with hidden columns
2997 have incorrect sequence start/end</li>
2998 <li>'Aligning' a second chain to a Chimera structure from
3000 <li>Colour schemes applied to structure viewers don't
3001 work for nucleotide</li>
3002 <li>Loading/cut'n'pasting an empty or invalid file leads
3003 to a grey/invisible alignment window</li>
3004 <li>Exported Jpred annotation from a sequence region
3005 imports to different position</li>
3006 <li>Space at beginning of sequence feature tooltips shown
3007 on some platforms</li>
3008 <li>Chimera viewer 'View | Show Chain' menu is not
3010 <li>'New View' fails with a Null Pointer Exception in
3011 console if Chimera has been opened</li>
3012 <li>Mouseover to Chimera not working</li>
3013 <li>Miscellaneous ENA XML feature qualifiers not
3015 <li>NPE in annotation renderer after 'Extract Scores'</li>
3016 <li>If two structures in one Chimera window, mouseover of
3017 either sequence shows on first structure</li>
3018 <li>'Show annotations' options should not make
3019 non-positional annotations visible</li>
3020 <li>Subsequence secondary structure annotation not shown
3021 in right place after 'view flanking regions'</li>
3022 <li>File Save As type unset when current file format is
3024 <li>Save as '.jar' option removed for saving Jalview
3026 <li>Colour by Sequence colouring in Chimera more
3028 <li>Cannot 'add reference annotation' for a sequence in
3029 several views on same alignment</li>
3030 <li>Cannot show linked products for EMBL / ENA records</li>
3031 <li>Jalview's tooltip wraps long texts containing no
3033 </ul> <em>Applet</em>
3035 <li>Jmol to JalviewLite mouseover/link not working</li>
3036 <li>JalviewLite can't import sequences with ID
3037 descriptions containing angle brackets</li>
3038 </ul> <em>General</em>
3040 <li>Cannot export and reimport RNA secondary structure
3041 via jalview annotation file</li>
3042 <li>Random helix colour palette for colour by annotation
3043 with RNA secondary structure</li>
3044 <li>Mouseover to cDNA from STOP residue in protein
3045 translation doesn't work.</li>
3046 <li>hints when using the select by annotation dialog box</li>
3047 <li>Jmol alignment incorrect if PDB file has alternate CA
3049 <li>FontChooser message dialog appears to hang after
3050 choosing 1pt font</li>
3051 <li>Peptide secondary structure incorrectly imported from
3052 annotation file when annotation display text includes 'e' or
3054 <li>Cannot set colour of new feature type whilst creating
3056 <li>cDNA translation alignment should not be sequence
3057 order dependent</li>
3058 <li>'Show unconserved' doesn't work for lower case
3060 <li>Nucleotide ambiguity codes involving R not recognised</li>
3061 </ul> <em>Deployment and Documentation</em>
3063 <li>Applet example pages appear different to the rest of
3064 www.jalview.org</li>
3065 </ul> <em>Application Known issues</em>
3067 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3068 <li>Misleading message appears after trying to delete
3070 <li>Jalview icon not shown in dock after InstallAnywhere
3071 version launches</li>
3072 <li>Fetching EMBL reference for an RNA sequence results
3073 fails with a sequence mismatch</li>
3074 <li>Corrupted or unreadable alignment display when
3075 scrolling alignment to right</li>
3076 <li>ArrayIndexOutOfBoundsException thrown when remove
3077 empty columns called on alignment with ragged gapped ends</li>
3078 <li>auto calculated alignment annotation rows do not get
3079 placed above or below non-autocalculated rows</li>
3080 <li>Jalview dekstop becomes sluggish at full screen in
3081 ultra-high resolution</li>
3082 <li>Cannot disable consensus calculation independently of
3083 quality and conservation</li>
3084 <li>Mouseover highlighting between cDNA and protein can
3085 become sluggish with more than one splitframe shown</li>
3086 </ul> <em>Applet Known Issues</em>
3088 <li>Core PDB parsing code requires Jmol</li>
3089 <li>Sequence canvas panel goes white when alignment
3090 window is being resized</li>
3096 <td><div align="center">
3097 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3099 <td><em>General</em>
3101 <li>Updated Java code signing certificate donated by
3103 <li>Features and annotation preserved when performing
3104 pairwise alignment</li>
3105 <li>RNA pseudoknot annotation can be
3106 imported/exported/displayed</li>
3107 <li>'colour by annotation' can colour by RNA and
3108 protein secondary structure</li>
3109 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3110 post-hoc with 2.9 release</em>)
3113 </ul> <em>Application</em>
3115 <li>Extract and display secondary structure for sequences
3116 with 3D structures</li>
3117 <li>Support for parsing RNAML</li>
3118 <li>Annotations menu for layout
3120 <li>sort sequence annotation rows by alignment</li>
3121 <li>place sequence annotation above/below alignment
3124 <li>Output in Stockholm format</li>
3125 <li>Internationalisation: improved Spanish (es)
3127 <li>Structure viewer preferences tab</li>
3128 <li>Disorder and Secondary Structure annotation tracks
3129 shared between alignments</li>
3130 <li>UCSF Chimera launch and linked highlighting from
3132 <li>Show/hide all sequence associated annotation rows for
3133 all or current selection</li>
3134 <li>disorder and secondary structure predictions
3135 available as dataset annotation</li>
3136 <li>Per-sequence rna helices colouring</li>
3139 <li>Sequence database accessions imported when fetching
3140 alignments from Rfam</li>
3141 <li>update VARNA version to 3.91</li>
3143 <li>New groovy scripts for exporting aligned positions,
3144 conservation values, and calculating sum of pairs scores.</li>
3145 <li>Command line argument to set default JABAWS server</li>
3146 <li>include installation type in build properties and
3147 console log output</li>
3148 <li>Updated Jalview project format to preserve dataset
3152 <!-- issues resolved --> <em>Application</em>
3154 <li>Distinguish alignment and sequence associated RNA
3155 structure in structure->view->VARNA</li>
3156 <li>Raise dialog box if user deletes all sequences in an
3158 <li>Pressing F1 results in documentation opening twice</li>
3159 <li>Sequence feature tooltip is wrapped</li>
3160 <li>Double click on sequence associated annotation
3161 selects only first column</li>
3162 <li>Redundancy removal doesn't result in unlinked
3163 leaves shown in tree</li>
3164 <li>Undos after several redundancy removals don't undo
3166 <li>Hide sequence doesn't hide associated annotation</li>
3167 <li>User defined colours dialog box too big to fit on
3168 screen and buttons not visible</li>
3169 <li>author list isn't updated if already written to
3170 Jalview properties</li>
3171 <li>Popup menu won't open after retrieving sequence
3173 <li>File open window for associate PDB doesn't open</li>
3174 <li>Left-then-right click on a sequence id opens a
3175 browser search window</li>
3176 <li>Cannot open sequence feature shading/sort popup menu
3177 in feature settings dialog</li>
3178 <li>better tooltip placement for some areas of Jalview
3180 <li>Allow addition of JABAWS Server which doesn't
3181 pass validation</li>
3182 <li>Web services parameters dialog box is too large to
3184 <li>Muscle nucleotide alignment preset obscured by
3186 <li>JABAWS preset submenus don't contain newly
3187 defined user preset</li>
3188 <li>MSA web services warns user if they were launched
3189 with invalid input</li>
3190 <li>Jalview cannot contact DAS Registy when running on
3193 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3194 'Superpose with' submenu not shown when new view
3198 </ul> <!-- <em>Applet</em>
3200 </ul> <em>General</em>
3202 </ul>--> <em>Deployment and Documentation</em>
3204 <li>2G and 1G options in launchApp have no effect on
3205 memory allocation</li>
3206 <li>launchApp service doesn't automatically open
3207 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3209 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3210 InstallAnywhere reports cannot find valid JVM when Java
3211 1.7_055 is available
3213 </ul> <em>Application Known issues</em>
3216 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3217 corrupted or unreadable alignment display when scrolling
3221 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3222 retrieval fails but progress bar continues for DAS retrieval
3223 with large number of ID
3226 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3227 flatfile output of visible region has incorrect sequence
3231 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3232 rna structure consensus doesn't update when secondary
3233 structure tracks are rearranged
3236 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3237 invalid rna structure positional highlighting does not
3238 highlight position of invalid base pairs
3241 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3242 out of memory errors are not raised when saving Jalview
3243 project from alignment window file menu
3246 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3247 Switching to RNA Helices colouring doesn't propagate to
3251 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3252 colour by RNA Helices not enabled when user created
3253 annotation added to alignment
3256 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3257 Jalview icon not shown on dock in Mountain Lion/Webstart
3259 </ul> <em>Applet Known Issues</em>
3262 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3263 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3266 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3267 Jalview and Jmol example not compatible with IE9
3270 <li>Sort by annotation score doesn't reverse order
3276 <td><div align="center">
3277 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3280 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3283 <li>Internationalisation of user interface (usually
3284 called i18n support) and translation for Spanish locale</li>
3285 <li>Define/Undefine group on current selection with
3286 Ctrl-G/Shift Ctrl-G</li>
3287 <li>Improved group creation/removal options in
3288 alignment/sequence Popup menu</li>
3289 <li>Sensible precision for symbol distribution
3290 percentages shown in logo tooltip.</li>
3291 <li>Annotation panel height set according to amount of
3292 annotation when alignment first opened</li>
3293 </ul> <em>Application</em>
3295 <li>Interactive consensus RNA secondary structure
3296 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3297 <li>Select columns containing particular features from
3298 Feature Settings dialog</li>
3299 <li>View all 'representative' PDB structures for selected
3301 <li>Update Jalview project format:
3303 <li>New file extension for Jalview projects '.jvp'</li>
3304 <li>Preserve sequence and annotation dataset (to
3305 store secondary structure annotation,etc)</li>
3306 <li>Per group and alignment annotation and RNA helix
3310 <li>New similarity measures for PCA and Tree calculation
3312 <li>Experimental support for retrieval and viewing of
3313 flanking regions for an alignment</li>
3317 <!-- issues resolved --> <em>Application</em>
3319 <li>logo keeps spinning and status remains at queued or
3320 running after job is cancelled</li>
3321 <li>cannot export features from alignments imported from
3322 Jalview/VAMSAS projects</li>
3323 <li>Buggy slider for web service parameters that take
3325 <li>Newly created RNA secondary structure line doesn't
3326 have 'display all symbols' flag set</li>
3327 <li>T-COFFEE alignment score shading scheme and other
3328 annotation shading not saved in Jalview project</li>
3329 <li>Local file cannot be loaded in freshly downloaded
3331 <li>Jalview icon not shown on dock in Mountain
3333 <li>Load file from desktop file browser fails</li>
3334 <li>Occasional NPE thrown when calculating large trees</li>
3335 <li>Cannot reorder or slide sequences after dragging an
3336 alignment onto desktop</li>
3337 <li>Colour by annotation dialog throws NPE after using
3338 'extract scores' function</li>
3339 <li>Loading/cut'n'pasting an empty file leads to a grey
3340 alignment window</li>
3341 <li>Disorder thresholds rendered incorrectly after
3342 performing IUPred disorder prediction</li>
3343 <li>Multiple group annotated consensus rows shown when
3344 changing 'normalise logo' display setting</li>
3345 <li>Find shows blank dialog after 'finished searching' if
3346 nothing matches query</li>
3347 <li>Null Pointer Exceptions raised when sorting by
3348 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3350 <li>Errors in Jmol console when structures in alignment
3351 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3353 <li>Not all working JABAWS services are shown in
3355 <li>JAVAWS version of Jalview fails to launch with
3356 'invalid literal/length code'</li>
3357 <li>Annotation/RNA Helix colourschemes cannot be applied
3358 to alignment with groups (actually fixed in 2.8.0b1)</li>
3359 <li>RNA Helices and T-Coffee Scores available as default
3362 </ul> <em>Applet</em>
3364 <li>Remove group option is shown even when selection is
3366 <li>Apply to all groups ticked but colourscheme changes
3367 don't affect groups</li>
3368 <li>Documented RNA Helices and T-Coffee Scores as valid
3369 colourscheme name</li>
3370 <li>Annotation labels drawn on sequence IDs when
3371 Annotation panel is not displayed</li>
3372 <li>Increased font size for dropdown menus on OSX and
3373 embedded windows</li>
3374 </ul> <em>Other</em>
3376 <li>Consensus sequence for alignments/groups with a
3377 single sequence were not calculated</li>
3378 <li>annotation files that contain only groups imported as
3379 annotation and junk sequences</li>
3380 <li>Fasta files with sequences containing '*' incorrectly
3381 recognised as PFAM or BLC</li>
3382 <li>conservation/PID slider apply all groups option
3383 doesn't affect background (2.8.0b1)
3385 <li>redundancy highlighting is erratic at 0% and 100%</li>
3386 <li>Remove gapped columns fails for sequences with ragged
3388 <li>AMSA annotation row with leading spaces is not
3389 registered correctly on import</li>
3390 <li>Jalview crashes when selecting PCA analysis for
3391 certain alignments</li>
3392 <li>Opening the colour by annotation dialog for an
3393 existing annotation based 'use original colours'
3394 colourscheme loses original colours setting</li>
3399 <td><div align="center">
3400 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3401 <em>30/1/2014</em></strong>
3405 <li>Trusted certificates for JalviewLite applet and
3406 Jalview Desktop application<br />Certificate was donated by
3407 <a href="https://www.certum.eu">Certum</a> to the Jalview
3408 open source project).
3410 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3411 <li>Output in Stockholm format</li>
3412 <li>Allow import of data from gzipped files</li>
3413 <li>Export/import group and sequence associated line
3414 graph thresholds</li>
3415 <li>Nucleotide substitution matrix that supports RNA and
3416 ambiguity codes</li>
3417 <li>Allow disorder predictions to be made on the current
3418 selection (or visible selection) in the same way that JPred
3420 <li>Groovy scripting for headless Jalview operation</li>
3421 </ul> <em>Other improvements</em>
3423 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3424 <li>COMBINE statement uses current SEQUENCE_REF and
3425 GROUP_REF scope to group annotation rows</li>
3426 <li>Support '' style escaping of quotes in Newick
3428 <li>Group options for JABAWS service by command line name</li>
3429 <li>Empty tooltip shown for JABA service options with a
3430 link but no description</li>
3431 <li>Select primary source when selecting authority in
3432 database fetcher GUI</li>
3433 <li>Add .mfa to FASTA file extensions recognised by
3435 <li>Annotation label tooltip text wrap</li>
3440 <li>Slow scrolling when lots of annotation rows are
3442 <li>Lots of NPE (and slowness) after creating RNA
3443 secondary structure annotation line</li>
3444 <li>Sequence database accessions not imported when
3445 fetching alignments from Rfam</li>
3446 <li>Incorrect SHMR submission for sequences with
3448 <li>View all structures does not always superpose
3450 <li>Option widgets in service parameters not updated to
3451 reflect user or preset settings</li>
3452 <li>Null pointer exceptions for some services without
3453 presets or adjustable parameters</li>
3454 <li>Discover PDB IDs entry in structure menu doesn't
3455 discover PDB xRefs</li>
3456 <li>Exception encountered while trying to retrieve
3457 features with DAS</li>
3458 <li>Lowest value in annotation row isn't coloured
3459 when colour by annotation (per sequence) is coloured</li>
3460 <li>Keyboard mode P jumps to start of gapped region when
3461 residue follows a gap</li>
3462 <li>Jalview appears to hang importing an alignment with
3463 Wrap as default or after enabling Wrap</li>
3464 <li>'Right click to add annotations' message
3465 shown in wrap mode when no annotations present</li>
3466 <li>Disorder predictions fail with NPE if no automatic
3467 annotation already exists on alignment</li>
3468 <li>oninit javascript function should be called after
3469 initialisation completes</li>
3470 <li>Remove redundancy after disorder prediction corrupts
3471 alignment window display</li>
3472 <li>Example annotation file in documentation is invalid</li>
3473 <li>Grouped line graph annotation rows are not exported
3474 to annotation file</li>
3475 <li>Multi-harmony analysis cannot be run when only two
3477 <li>Cannot create multiple groups of line graphs with
3478 several 'combine' statements in annotation file</li>
3479 <li>Pressing return several times causes Number Format
3480 exceptions in keyboard mode</li>
3481 <li>Multi-harmony (SHMMR) method doesn't submit
3482 correct partitions for input data</li>
3483 <li>Translation from DNA to Amino Acids fails</li>
3484 <li>Jalview fail to load newick tree with quoted label</li>
3485 <li>--headless flag isn't understood</li>
3486 <li>ClassCastException when generating EPS in headless
3488 <li>Adjusting sequence-associated shading threshold only
3489 changes one row's threshold</li>
3490 <li>Preferences and Feature settings panel panel
3491 doesn't open</li>
3492 <li>hide consensus histogram also hides conservation and
3493 quality histograms</li>
3498 <td><div align="center">
3499 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3501 <td><em>Application</em>
3503 <li>Support for JABAWS 2.0 Services (AACon alignment
3504 conservation, protein disorder and Clustal Omega)</li>
3505 <li>JABAWS server status indicator in Web Services
3507 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3508 in Jalview alignment window</li>
3509 <li>Updated Jalview build and deploy framework for OSX
3510 mountain lion, windows 7, and 8</li>
3511 <li>Nucleotide substitution matrix for PCA that supports
3512 RNA and ambiguity codes</li>
3514 <li>Improved sequence database retrieval GUI</li>
3515 <li>Support fetching and database reference look up
3516 against multiple DAS sources (Fetch all from in 'fetch db
3518 <li>Jalview project improvements
3520 <li>Store and retrieve the 'belowAlignment'
3521 flag for annotation</li>
3522 <li>calcId attribute to group annotation rows on the
3524 <li>Store AACon calculation settings for a view in
3525 Jalview project</li>
3529 <li>horizontal scrolling gesture support</li>
3530 <li>Visual progress indicator when PCA calculation is
3532 <li>Simpler JABA web services menus</li>
3533 <li>visual indication that web service results are still
3534 being retrieved from server</li>
3535 <li>Serialise the dialogs that are shown when Jalview
3536 starts up for first time</li>
3537 <li>Jalview user agent string for interacting with HTTP
3539 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3541 <li>Examples directory and Groovy library included in
3542 InstallAnywhere distribution</li>
3543 </ul> <em>Applet</em>
3545 <li>RNA alignment and secondary structure annotation
3546 visualization applet example</li>
3547 </ul> <em>General</em>
3549 <li>Normalise option for consensus sequence logo</li>
3550 <li>Reset button in PCA window to return dimensions to
3552 <li>Allow seqspace or Jalview variant of alignment PCA
3554 <li>PCA with either nucleic acid and protein substitution
3556 <li>Allow windows containing HTML reports to be exported
3558 <li>Interactive display and editing of RNA secondary
3559 structure contacts</li>
3560 <li>RNA Helix Alignment Colouring</li>
3561 <li>RNA base pair logo consensus</li>
3562 <li>Parse sequence associated secondary structure
3563 information in Stockholm files</li>
3564 <li>HTML Export database accessions and annotation
3565 information presented in tooltip for sequences</li>
3566 <li>Import secondary structure from LOCARNA clustalw
3567 style RNA alignment files</li>
3568 <li>import and visualise T-COFFEE quality scores for an
3570 <li>'colour by annotation' per sequence option to
3571 shade each sequence according to its associated alignment
3573 <li>New Jalview Logo</li>
3574 </ul> <em>Documentation and Development</em>
3576 <li>documentation for score matrices used in Jalview</li>
3577 <li>New Website!</li>
3579 <td><em>Application</em>
3581 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3582 wsdbfetch REST service</li>
3583 <li>Stop windows being moved outside desktop on OSX</li>
3584 <li>Filetype associations not installed for webstart
3586 <li>Jalview does not always retrieve progress of a JABAWS
3587 job execution in full once it is complete</li>
3588 <li>revise SHMR RSBS definition to ensure alignment is
3589 uploaded via ali_file parameter</li>
3590 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3591 <li>View all structures superposed fails with exception</li>
3592 <li>Jnet job queues forever if a very short sequence is
3593 submitted for prediction</li>
3594 <li>Cut and paste menu not opened when mouse clicked on
3596 <li>Putting fractional value into integer text box in
3597 alignment parameter dialog causes Jalview to hang</li>
3598 <li>Structure view highlighting doesn't work on
3600 <li>View all structures fails with exception shown in
3602 <li>Characters in filename associated with PDBEntry not
3603 escaped in a platform independent way</li>
3604 <li>Jalview desktop fails to launch with exception when
3606 <li>Tree calculation reports 'you must have 2 or more
3607 sequences selected' when selection is empty</li>
3608 <li>Jalview desktop fails to launch with jar signature
3609 failure when java web start temporary file caching is
3611 <li>DAS Sequence retrieval with range qualification
3612 results in sequence xref which includes range qualification</li>
3613 <li>Errors during processing of command line arguments
3614 cause progress bar (JAL-898) to be removed</li>
3615 <li>Replace comma for semi-colon option not disabled for
3616 DAS sources in sequence fetcher</li>
3617 <li>Cannot close news reader when JABAWS server warning
3618 dialog is shown</li>
3619 <li>Option widgets not updated to reflect user settings</li>
3620 <li>Edited sequence not submitted to web service</li>
3621 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3622 <li>InstallAnywhere installer doesn't unpack and run
3623 on OSX Mountain Lion</li>
3624 <li>Annotation panel not given a scroll bar when
3625 sequences with alignment annotation are pasted into the
3627 <li>Sequence associated annotation rows not associated
3628 when loaded from Jalview project</li>
3629 <li>Browser launch fails with NPE on java 1.7</li>
3630 <li>JABAWS alignment marked as finished when job was
3631 cancelled or job failed due to invalid input</li>
3632 <li>NPE with v2.7 example when clicking on Tree
3633 associated with all views</li>
3634 <li>Exceptions when copy/paste sequences with grouped
3635 annotation rows to new window</li>
3636 </ul> <em>Applet</em>
3638 <li>Sequence features are momentarily displayed before
3639 they are hidden using hidefeaturegroups applet parameter</li>
3640 <li>loading features via javascript API automatically
3641 enables feature display</li>
3642 <li>scrollToColumnIn javascript API method doesn't
3644 </ul> <em>General</em>
3646 <li>Redundancy removal fails for rna alignment</li>
3647 <li>PCA calculation fails when sequence has been selected
3648 and then deselected</li>
3649 <li>PCA window shows grey box when first opened on OSX</li>
3650 <li>Letters coloured pink in sequence logo when alignment
3651 coloured with clustalx</li>
3652 <li>Choosing fonts without letter symbols defined causes
3653 exceptions and redraw errors</li>
3654 <li>Initial PCA plot view is not same as manually
3655 reconfigured view</li>
3656 <li>Grouped annotation graph label has incorrect line
3658 <li>Grouped annotation graph label display is corrupted
3659 for lots of labels</li>
3664 <div align="center">
3665 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3668 <td><em>Application</em>
3670 <li>Jalview Desktop News Reader</li>
3671 <li>Tweaked default layout of web services menu</li>
3672 <li>View/alignment association menu to enable user to
3673 easily specify which alignment a multi-structure view takes
3674 its colours/correspondences from</li>
3675 <li>Allow properties file location to be specified as URL</li>
3676 <li>Extend Jalview project to preserve associations
3677 between many alignment views and a single Jmol display</li>
3678 <li>Store annotation row height in Jalview project file</li>
3679 <li>Annotation row column label formatting attributes
3680 stored in project file</li>
3681 <li>Annotation row order for auto-calculated annotation
3682 rows preserved in Jalview project file</li>
3683 <li>Visual progress indication when Jalview state is
3684 saved using Desktop window menu</li>
3685 <li>Visual indication that command line arguments are
3686 still being processed</li>
3687 <li>Groovy script execution from URL</li>
3688 <li>Colour by annotation default min and max colours in
3690 <li>Automatically associate PDB files dragged onto an
3691 alignment with sequences that have high similarity and
3693 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3694 <li>'view structures' option to open many
3695 structures in same window</li>
3696 <li>Sort associated views menu option for tree panel</li>
3697 <li>Group all JABA and non-JABA services for a particular
3698 analysis function in its own submenu</li>
3699 </ul> <em>Applet</em>
3701 <li>Userdefined and autogenerated annotation rows for
3703 <li>Adjustment of alignment annotation pane height</li>
3704 <li>Annotation scrollbar for annotation panel</li>
3705 <li>Drag to reorder annotation rows in annotation panel</li>
3706 <li>'automaticScrolling' parameter</li>
3707 <li>Allow sequences with partial ID string matches to be
3708 annotated from GFF/Jalview features files</li>
3709 <li>Sequence logo annotation row in applet</li>
3710 <li>Absolute paths relative to host server in applet
3711 parameters are treated as such</li>
3712 <li>New in the JalviewLite javascript API:
3714 <li>JalviewLite.js javascript library</li>
3715 <li>Javascript callbacks for
3717 <li>Applet initialisation</li>
3718 <li>Sequence/alignment mouse-overs and selections</li>
3721 <li>scrollTo row and column alignment scrolling
3723 <li>Select sequence/alignment regions from javascript</li>
3724 <li>javascript structure viewer harness to pass
3725 messages between Jmol and Jalview when running as
3726 distinct applets</li>
3727 <li>sortBy method</li>
3728 <li>Set of applet and application examples shipped
3729 with documentation</li>
3730 <li>New example to demonstrate JalviewLite and Jmol
3731 javascript message exchange</li>
3733 </ul> <em>General</em>
3735 <li>Enable Jmol displays to be associated with multiple
3736 multiple alignments</li>
3737 <li>Option to automatically sort alignment with new tree</li>
3738 <li>User configurable link to enable redirects to a
3739 www.Jalview.org mirror</li>
3740 <li>Jmol colours option for Jmol displays</li>
3741 <li>Configurable newline string when writing alignment
3742 and other flat files</li>
3743 <li>Allow alignment annotation description lines to
3744 contain html tags</li>
3745 </ul> <em>Documentation and Development</em>
3747 <li>Add groovy test harness for bulk load testing to
3749 <li>Groovy script to load and align a set of sequences
3750 using a web service before displaying the result in the
3751 Jalview desktop</li>
3752 <li>Restructured javascript and applet api documentation</li>
3753 <li>Ant target to publish example html files with applet
3755 <li>Netbeans project for building Jalview from source</li>
3756 <li>ant task to create online javadoc for Jalview source</li>
3758 <td><em>Application</em>
3760 <li>User defined colourscheme throws exception when
3761 current built in colourscheme is saved as new scheme</li>
3762 <li>AlignFrame->Save in application pops up save
3763 dialog for valid filename/format</li>
3764 <li>Cannot view associated structure for UniProt sequence</li>
3765 <li>PDB file association breaks for UniProt sequence
3767 <li>Associate PDB from file dialog does not tell you
3768 which sequence is to be associated with the file</li>
3769 <li>Find All raises null pointer exception when query
3770 only matches sequence IDs</li>
3771 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3772 <li>Jalview project with Jmol views created with Jalview
3773 2.4 cannot be loaded</li>
3774 <li>Filetype associations not installed for webstart
3776 <li>Two or more chains in a single PDB file associated
3777 with sequences in different alignments do not get coloured
3778 by their associated sequence</li>
3779 <li>Visibility status of autocalculated annotation row
3780 not preserved when project is loaded</li>
3781 <li>Annotation row height and visibility attributes not
3782 stored in Jalview project</li>
3783 <li>Tree bootstraps are not preserved when saved as a
3784 Jalview project</li>
3785 <li>Envision2 workflow tooltips are corrupted</li>
3786 <li>Enabling show group conservation also enables colour
3787 by conservation</li>
3788 <li>Duplicate group associated conservation or consensus
3789 created on new view</li>
3790 <li>Annotation scrollbar not displayed after 'show
3791 all hidden annotation rows' option selected</li>
3792 <li>Alignment quality not updated after alignment
3793 annotation row is hidden then shown</li>
3794 <li>Preserve colouring of structures coloured by
3795 sequences in pre Jalview 2.7 projects</li>
3796 <li>Web service job parameter dialog is not laid out
3798 <li>Web services menu not refreshed after 'reset
3799 services' button is pressed in preferences</li>
3800 <li>Annotation off by one in Jalview v2_3 example project</li>
3801 <li>Structures imported from file and saved in project
3802 get name like jalview_pdb1234.txt when reloaded</li>
3803 <li>Jalview does not always retrieve progress of a JABAWS
3804 job execution in full once it is complete</li>
3805 </ul> <em>Applet</em>
3807 <li>Alignment height set incorrectly when lots of
3808 annotation rows are displayed</li>
3809 <li>Relative URLs in feature HTML text not resolved to
3811 <li>View follows highlighting does not work for positions
3813 <li><= shown as = in tooltip</li>
3814 <li>Export features raises exception when no features
3816 <li>Separator string used for serialising lists of IDs
3817 for javascript api is modified when separator string
3818 provided as parameter</li>
3819 <li>Null pointer exception when selecting tree leaves for
3820 alignment with no existing selection</li>
3821 <li>Relative URLs for datasources assumed to be relative
3822 to applet's codebase</li>
3823 <li>Status bar not updated after finished searching and
3824 search wraps around to first result</li>
3825 <li>StructureSelectionManager instance shared between
3826 several Jalview applets causes race conditions and memory
3828 <li>Hover tooltip and mouseover of position on structure
3829 not sent from Jmol in applet</li>
3830 <li>Certain sequences of javascript method calls to
3831 applet API fatally hang browser</li>
3832 </ul> <em>General</em>
3834 <li>View follows structure mouseover scrolls beyond
3835 position with wrapped view and hidden regions</li>
3836 <li>Find sequence position moves to wrong residue
3837 with/without hidden columns</li>
3838 <li>Sequence length given in alignment properties window
3840 <li>InvalidNumberFormat exceptions thrown when trying to
3841 import PDB like structure files</li>
3842 <li>Positional search results are only highlighted
3843 between user-supplied sequence start/end bounds</li>
3844 <li>End attribute of sequence is not validated</li>
3845 <li>Find dialog only finds first sequence containing a
3846 given sequence position</li>
3847 <li>Sequence numbering not preserved in MSF alignment
3849 <li>Jalview PDB file reader does not extract sequence
3850 from nucleotide chains correctly</li>
3851 <li>Structure colours not updated when tree partition
3852 changed in alignment</li>
3853 <li>Sequence associated secondary structure not correctly
3854 parsed in interleaved stockholm</li>
3855 <li>Colour by annotation dialog does not restore current
3857 <li>Hiding (nearly) all sequences doesn't work
3859 <li>Sequences containing lowercase letters are not
3860 properly associated with their pdb files</li>
3861 </ul> <em>Documentation and Development</em>
3863 <li>schemas/JalviewWsParamSet.xsd corrupted by
3864 ApplyCopyright tool</li>
3869 <div align="center">
3870 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3873 <td><em>Application</em>
3875 <li>New warning dialog when the Jalview Desktop cannot
3876 contact web services</li>
3877 <li>JABA service parameters for a preset are shown in
3878 service job window</li>
3879 <li>JABA Service menu entries reworded</li>
3883 <li>Modeller PIR IO broken - cannot correctly import a
3884 pir file emitted by Jalview</li>
3885 <li>Existing feature settings transferred to new
3886 alignment view created from cut'n'paste</li>
3887 <li>Improved test for mixed amino/nucleotide chains when
3888 parsing PDB files</li>
3889 <li>Consensus and conservation annotation rows
3890 occasionally become blank for all new windows</li>
3891 <li>Exception raised when right clicking above sequences
3892 in wrapped view mode</li>
3893 </ul> <em>Application</em>
3895 <li>multiple multiply aligned structure views cause cpu
3896 usage to hit 100% and computer to hang</li>
3897 <li>Web Service parameter layout breaks for long user
3898 parameter names</li>
3899 <li>Jaba service discovery hangs desktop if Jaba server
3906 <div align="center">
3907 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3910 <td><em>Application</em>
3912 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3913 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3916 <li>Web Services preference tab</li>
3917 <li>Analysis parameters dialog box and user defined
3919 <li>Improved speed and layout of Envision2 service menu</li>
3920 <li>Superpose structures using associated sequence
3922 <li>Export coordinates and projection as CSV from PCA
3924 </ul> <em>Applet</em>
3926 <li>enable javascript: execution by the applet via the
3927 link out mechanism</li>
3928 </ul> <em>Other</em>
3930 <li>Updated the Jmol Jalview interface to work with Jmol
3932 <li>The Jalview Desktop and JalviewLite applet now
3933 require Java 1.5</li>
3934 <li>Allow Jalview feature colour specification for GFF
3935 sequence annotation files</li>
3936 <li>New 'colour by label' keword in Jalview feature file
3937 type colour specification</li>
3938 <li>New Jalview Desktop Groovy API method that allows a
3939 script to check if it being run in an interactive session or
3940 in a batch operation from the Jalview command line</li>
3944 <li>clustalx colourscheme colours Ds preferentially when
3945 both D+E are present in over 50% of the column</li>
3946 </ul> <em>Application</em>
3948 <li>typo in AlignmentFrame->View->Hide->all but
3949 selected Regions menu item</li>
3950 <li>sequence fetcher replaces ',' for ';' when the ',' is
3951 part of a valid accession ID</li>
3952 <li>fatal OOM if object retrieved by sequence fetcher
3953 runs out of memory</li>
3954 <li>unhandled Out of Memory Error when viewing pca
3955 analysis results</li>
3956 <li>InstallAnywhere builds fail to launch on OS X java
3957 10.5 update 4 (due to apple Java 1.6 update)</li>
3958 <li>Installanywhere Jalview silently fails to launch</li>
3959 </ul> <em>Applet</em>
3961 <li>Jalview.getFeatureGroups() raises an
3962 ArrayIndexOutOfBoundsException if no feature groups are
3969 <div align="center">
3970 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3976 <li>Alignment prettyprinter doesn't cope with long
3978 <li>clustalx colourscheme colours Ds preferentially when
3979 both D+E are present in over 50% of the column</li>
3980 <li>nucleic acid structures retrieved from PDB do not
3981 import correctly</li>
3982 <li>More columns get selected than were clicked on when a
3983 number of columns are hidden</li>
3984 <li>annotation label popup menu not providing correct
3985 add/hide/show options when rows are hidden or none are
3987 <li>Stockholm format shown in list of readable formats,
3988 and parser copes better with alignments from RFAM.</li>
3989 <li>CSV output of consensus only includes the percentage
3990 of all symbols if sequence logo display is enabled</li>
3992 </ul> <em>Applet</em>
3994 <li>annotation panel disappears when annotation is
3996 </ul> <em>Application</em>
3998 <li>Alignment view not redrawn properly when new
3999 alignment opened where annotation panel is visible but no
4000 annotations are present on alignment</li>
4001 <li>pasted region containing hidden columns is
4002 incorrectly displayed in new alignment window</li>
4003 <li>Jalview slow to complete operations when stdout is
4004 flooded (fix is to close the Jalview console)</li>
4005 <li>typo in AlignmentFrame->View->Hide->all but
4006 selected Rregions menu item.</li>
4007 <li>inconsistent group submenu and Format submenu entry
4008 'Un' or 'Non'conserved</li>
4009 <li>Sequence feature settings are being shared by
4010 multiple distinct alignments</li>
4011 <li>group annotation not recreated when tree partition is
4013 <li>double click on group annotation to select sequences
4014 does not propagate to associated trees</li>
4015 <li>Mac OSX specific issues:
4017 <li>exception raised when mouse clicked on desktop
4018 window background</li>
4019 <li>Desktop menu placed on menu bar and application
4020 name set correctly</li>
4021 <li>sequence feature settings not wide enough for the
4022 save feature colourscheme button</li>
4031 <div align="center">
4032 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4035 <td><em>New Capabilities</em>
4037 <li>URL links generated from description line for
4038 regular-expression based URL links (applet and application)
4040 <li>Non-positional feature URL links are shown in link
4042 <li>Linked viewing of nucleic acid sequences and
4044 <li>Automatic Scrolling option in View menu to display
4045 the currently highlighted region of an alignment.</li>
4046 <li>Order an alignment by sequence length, or using the
4047 average score or total feature count for each sequence.</li>
4048 <li>Shading features by score or associated description</li>
4049 <li>Subdivide alignment and groups based on identity of
4050 selected subsequence (Make Groups from Selection).</li>
4051 <li>New hide/show options including Shift+Control+H to
4052 hide everything but the currently selected region.</li>
4053 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4054 </ul> <em>Application</em>
4056 <li>Fetch DB References capabilities and UI expanded to
4057 support retrieval from DAS sequence sources</li>
4058 <li>Local DAS Sequence sources can be added via the
4059 command line or via the Add local source dialog box.</li>
4060 <li>DAS Dbref and DbxRef feature types are parsed as
4061 database references and protein_name is parsed as
4062 description line (BioSapiens terms).</li>
4063 <li>Enable or disable non-positional feature and database
4064 references in sequence ID tooltip from View menu in
4066 <!-- <li>New hidden columns and rows and representatives capabilities
4067 in annotations file (in progress - not yet fully implemented)</li> -->
4068 <li>Group-associated consensus, sequence logos and
4069 conservation plots</li>
4070 <li>Symbol distributions for each column can be exported
4071 and visualized as sequence logos</li>
4072 <li>Optionally scale multi-character column labels to fit
4073 within each column of annotation row<!-- todo for applet -->
4075 <li>Optional automatic sort of associated alignment view
4076 when a new tree is opened.</li>
4077 <li>Jalview Java Console</li>
4078 <li>Better placement of desktop window when moving
4079 between different screens.</li>
4080 <li>New preference items for sequence ID tooltip and
4081 consensus annotation</li>
4082 <li>Client to submit sequences and IDs to Envision2
4084 <li><em>Vamsas Capabilities</em>
4086 <li>Improved VAMSAS synchronization (Jalview archive
4087 used to preserve views, structures, and tree display
4089 <li>Import of vamsas documents from disk or URL via
4091 <li>Sharing of selected regions between views and
4092 with other VAMSAS applications (Experimental feature!)</li>
4093 <li>Updated API to VAMSAS version 0.2</li>
4095 </ul> <em>Applet</em>
4097 <li>Middle button resizes annotation row height</li>
4100 <li>sortByTree (true/false) - automatically sort the
4101 associated alignment view by the tree when a new tree is
4103 <li>showTreeBootstraps (true/false) - show or hide
4104 branch bootstraps (default is to show them if available)</li>
4105 <li>showTreeDistances (true/false) - show or hide
4106 branch lengths (default is to show them if available)</li>
4107 <li>showUnlinkedTreeNodes (true/false) - indicate if
4108 unassociated nodes should be highlighted in the tree
4110 <li>heightScale and widthScale (1.0 or more) -
4111 increase the height or width of a cell in the alignment
4112 grid relative to the current font size.</li>
4115 <li>Non-positional features displayed in sequence ID
4117 </ul> <em>Other</em>
4119 <li>Features format: graduated colour definitions and
4120 specification of feature scores</li>
4121 <li>Alignment Annotations format: new keywords for group
4122 associated annotation (GROUP_REF) and annotation row display
4123 properties (ROW_PROPERTIES)</li>
4124 <li>XML formats extended to support graduated feature
4125 colourschemes, group associated annotation, and profile
4126 visualization settings.</li></td>
4129 <li>Source field in GFF files parsed as feature source
4130 rather than description</li>
4131 <li>Non-positional features are now included in sequence
4132 feature and gff files (controlled via non-positional feature
4133 visibility in tooltip).</li>
4134 <li>URL links generated for all feature links (bugfix)</li>
4135 <li>Added URL embedding instructions to features file
4137 <li>Codons containing ambiguous nucleotides translated as
4138 'X' in peptide product</li>
4139 <li>Match case switch in find dialog box works for both
4140 sequence ID and sequence string and query strings do not
4141 have to be in upper case to match case-insensitively.</li>
4142 <li>AMSA files only contain first column of
4143 multi-character column annotation labels</li>
4144 <li>Jalview Annotation File generation/parsing consistent
4145 with documentation (e.g. Stockholm annotation can be
4146 exported and re-imported)</li>
4147 <li>PDB files without embedded PDB IDs given a friendly
4149 <li>Find incrementally searches ID string matches as well
4150 as subsequence matches, and correctly reports total number
4154 <li>Better handling of exceptions during sequence
4156 <li>Dasobert generated non-positional feature URL
4157 link text excludes the start_end suffix</li>
4158 <li>DAS feature and source retrieval buttons disabled
4159 when fetch or registry operations in progress.</li>
4160 <li>PDB files retrieved from URLs are cached properly</li>
4161 <li>Sequence description lines properly shared via
4163 <li>Sequence fetcher fetches multiple records for all
4165 <li>Ensured that command line das feature retrieval
4166 completes before alignment figures are generated.</li>
4167 <li>Reduced time taken when opening file browser for
4169 <li>isAligned check prior to calculating tree, PCA or
4170 submitting an MSA to JNet now excludes hidden sequences.</li>
4171 <li>User defined group colours properly recovered
4172 from Jalview projects.</li>
4181 <div align="center">
4182 <strong>2.4.0.b2</strong><br> 28/10/2009
4187 <li>Experimental support for google analytics usage
4189 <li>Jalview privacy settings (user preferences and docs).</li>
4194 <li>Race condition in applet preventing startup in
4196 <li>Exception when feature created from selection beyond
4197 length of sequence.</li>
4198 <li>Allow synthetic PDB files to be imported gracefully</li>
4199 <li>Sequence associated annotation rows associate with
4200 all sequences with a given id</li>
4201 <li>Find function matches case-insensitively for sequence
4202 ID string searches</li>
4203 <li>Non-standard characters do not cause pairwise
4204 alignment to fail with exception</li>
4205 </ul> <em>Application Issues</em>
4207 <li>Sequences are now validated against EMBL database</li>
4208 <li>Sequence fetcher fetches multiple records for all
4210 </ul> <em>InstallAnywhere Issues</em>
4212 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4213 issue with installAnywhere mechanism)</li>
4214 <li>Command line launching of JARs from InstallAnywhere
4215 version (java class versioning error fixed)</li>
4222 <div align="center">
4223 <strong>2.4</strong><br> 27/8/2008
4226 <td><em>User Interface</em>
4228 <li>Linked highlighting of codon and amino acid from
4229 translation and protein products</li>
4230 <li>Linked highlighting of structure associated with
4231 residue mapping to codon position</li>
4232 <li>Sequence Fetcher provides example accession numbers
4233 and 'clear' button</li>
4234 <li>MemoryMonitor added as an option under Desktop's
4236 <li>Extract score function to parse whitespace separated
4237 numeric data in description line</li>
4238 <li>Column labels in alignment annotation can be centred.</li>
4239 <li>Tooltip for sequence associated annotation give name
4241 </ul> <em>Web Services and URL fetching</em>
4243 <li>JPred3 web service</li>
4244 <li>Prototype sequence search client (no public services
4246 <li>Fetch either seed alignment or full alignment from
4248 <li>URL Links created for matching database cross
4249 references as well as sequence ID</li>
4250 <li>URL Links can be created using regular-expressions</li>
4251 </ul> <em>Sequence Database Connectivity</em>
4253 <li>Retrieval of cross-referenced sequences from other
4255 <li>Generalised database reference retrieval and
4256 validation to all fetchable databases</li>
4257 <li>Fetch sequences from DAS sources supporting the
4258 sequence command</li>
4259 </ul> <em>Import and Export</em>
4260 <li>export annotation rows as CSV for spreadsheet import</li>
4261 <li>Jalview projects record alignment dataset associations,
4262 EMBL products, and cDNA sequence mappings</li>
4263 <li>Sequence Group colour can be specified in Annotation
4265 <li>Ad-hoc colouring of group in Annotation File using RGB
4266 triplet as name of colourscheme</li>
4267 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4269 <li>treenode binding for VAMSAS tree exchange</li>
4270 <li>local editing and update of sequences in VAMSAS
4271 alignments (experimental)</li>
4272 <li>Create new or select existing session to join</li>
4273 <li>load and save of vamsas documents</li>
4274 </ul> <em>Application command line</em>
4276 <li>-tree parameter to open trees (introduced for passing
4278 <li>-fetchfrom command line argument to specify nicknames
4279 of DAS servers to query for alignment features</li>
4280 <li>-dasserver command line argument to add new servers
4281 that are also automatically queried for features</li>
4282 <li>-groovy command line argument executes a given groovy
4283 script after all input data has been loaded and parsed</li>
4284 </ul> <em>Applet-Application data exchange</em>
4286 <li>Trees passed as applet parameters can be passed to
4287 application (when using "View in full
4288 application")</li>
4289 </ul> <em>Applet Parameters</em>
4291 <li>feature group display control parameter</li>
4292 <li>debug parameter</li>
4293 <li>showbutton parameter</li>
4294 </ul> <em>Applet API methods</em>
4296 <li>newView public method</li>
4297 <li>Window (current view) specific get/set public methods</li>
4298 <li>Feature display control methods</li>
4299 <li>get list of currently selected sequences</li>
4300 </ul> <em>New Jalview distribution features</em>
4302 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4303 <li>RELEASE file gives build properties for the latest
4304 Jalview release.</li>
4305 <li>Java 1.1 Applet build made easier and donotobfuscate
4306 property controls execution of obfuscator</li>
4307 <li>Build target for generating source distribution</li>
4308 <li>Debug flag for javacc</li>
4309 <li>.jalview_properties file is documented (slightly) in
4310 jalview.bin.Cache</li>
4311 <li>Continuous Build Integration for stable and
4312 development version of Application, Applet and source
4317 <li>selected region output includes visible annotations
4318 (for certain formats)</li>
4319 <li>edit label/displaychar contains existing label/char
4321 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4322 <li>shorter peptide product names from EMBL records</li>
4323 <li>Newick string generator makes compact representations</li>
4324 <li>bootstrap values parsed correctly for tree files with
4326 <li>pathological filechooser bug avoided by not allowing
4327 filenames containing a ':'</li>
4328 <li>Fixed exception when parsing GFF files containing
4329 global sequence features</li>
4330 <li>Alignment datasets are finalized only when number of
4331 references from alignment sequences goes to zero</li>
4332 <li>Close of tree branch colour box without colour
4333 selection causes cascading exceptions</li>
4334 <li>occasional negative imgwidth exceptions</li>
4335 <li>better reporting of non-fatal warnings to user when
4336 file parsing fails.</li>
4337 <li>Save works when Jalview project is default format</li>
4338 <li>Save as dialog opened if current alignment format is
4339 not a valid output format</li>
4340 <li>UniProt canonical names introduced for both das and
4342 <li>Histidine should be midblue (not pink!) in Zappo</li>
4343 <li>error messages passed up and output when data read
4345 <li>edit undo recovers previous dataset sequence when
4346 sequence is edited</li>
4347 <li>allow PDB files without pdb ID HEADER lines (like
4348 those generated by MODELLER) to be read in properly</li>
4349 <li>allow reading of JPred concise files as a normal
4351 <li>Stockholm annotation parsing and alignment properties
4352 import fixed for PFAM records</li>
4353 <li>Structure view windows have correct name in Desktop
4355 <li>annotation consisting of sequence associated scores
4356 can be read and written correctly to annotation file</li>
4357 <li>Aligned cDNA translation to aligned peptide works
4359 <li>Fixed display of hidden sequence markers and
4360 non-italic font for representatives in Applet</li>
4361 <li>Applet Menus are always embedded in applet window on
4363 <li>Newly shown features appear at top of stack (in
4365 <li>Annotations added via parameter not drawn properly
4366 due to null pointer exceptions</li>
4367 <li>Secondary structure lines are drawn starting from
4368 first column of alignment</li>
4369 <li>UniProt XML import updated for new schema release in
4371 <li>Sequence feature to sequence ID match for Features
4372 file is case-insensitive</li>
4373 <li>Sequence features read from Features file appended to
4374 all sequences with matching IDs</li>
4375 <li>PDB structure coloured correctly for associated views
4376 containing a sub-sequence</li>
4377 <li>PDB files can be retrieved by applet from Jar files</li>
4378 <li>feature and annotation file applet parameters
4379 referring to different directories are retrieved correctly</li>
4380 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4381 <li>Fixed application hang whilst waiting for
4382 splash-screen version check to complete</li>
4383 <li>Applet properly URLencodes input parameter values
4384 when passing them to the launchApp service</li>
4385 <li>display name and local features preserved in results
4386 retrieved from web service</li>
4387 <li>Visual delay indication for sequence retrieval and
4388 sequence fetcher initialisation</li>
4389 <li>updated Application to use DAS 1.53e version of
4390 dasobert DAS client</li>
4391 <li>Re-instated Full AMSA support and .amsa file
4393 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4401 <div align="center">
4402 <strong>2.3</strong><br> 9/5/07
4407 <li>Jmol 11.0.2 integration</li>
4408 <li>PDB views stored in Jalview XML files</li>
4409 <li>Slide sequences</li>
4410 <li>Edit sequence in place</li>
4411 <li>EMBL CDS features</li>
4412 <li>DAS Feature mapping</li>
4413 <li>Feature ordering</li>
4414 <li>Alignment Properties</li>
4415 <li>Annotation Scores</li>
4416 <li>Sort by scores</li>
4417 <li>Feature/annotation editing in applet</li>
4422 <li>Headless state operation in 2.2.1</li>
4423 <li>Incorrect and unstable DNA pairwise alignment</li>
4424 <li>Cut and paste of sequences with annotation</li>
4425 <li>Feature group display state in XML</li>
4426 <li>Feature ordering in XML</li>
4427 <li>blc file iteration selection using filename # suffix</li>
4428 <li>Stockholm alignment properties</li>
4429 <li>Stockhom alignment secondary structure annotation</li>
4430 <li>2.2.1 applet had no feature transparency</li>
4431 <li>Number pad keys can be used in cursor mode</li>
4432 <li>Structure Viewer mirror image resolved</li>
4439 <div align="center">
4440 <strong>2.2.1</strong><br> 12/2/07
4445 <li>Non standard characters can be read and displayed
4446 <li>Annotations/Features can be imported/exported to the
4448 <li>Applet allows editing of sequence/annotation/group
4449 name & description
4450 <li>Preference setting to display sequence name in
4452 <li>Annotation file format extended to allow
4453 Sequence_groups to be defined
4454 <li>Default opening of alignment overview panel can be
4455 specified in preferences
4456 <li>PDB residue numbering annotation added to associated
4462 <li>Applet crash under certain Linux OS with Java 1.6
4464 <li>Annotation file export / import bugs fixed
4465 <li>PNG / EPS image output bugs fixed
4471 <div align="center">
4472 <strong>2.2</strong><br> 27/11/06
4477 <li>Multiple views on alignment
4478 <li>Sequence feature editing
4479 <li>"Reload" alignment
4480 <li>"Save" to current filename
4481 <li>Background dependent text colour
4482 <li>Right align sequence ids
4483 <li>User-defined lower case residue colours
4486 <li>Menu item accelerator keys
4487 <li>Control-V pastes to current alignment
4488 <li>Cancel button for DAS Feature Fetching
4489 <li>PCA and PDB Viewers zoom via mouse roller
4490 <li>User-defined sub-tree colours and sub-tree selection
4492 <li>'New Window' button on the 'Output to Text box'
4497 <li>New memory efficient Undo/Redo System
4498 <li>Optimised symbol lookups and conservation/consensus
4500 <li>Region Conservation/Consensus recalculated after
4502 <li>Fixed Remove Empty Columns Bug (empty columns at end
4504 <li>Slowed DAS Feature Fetching for increased robustness.
4506 <li>Made angle brackets in ASCII feature descriptions
4508 <li>Re-instated Zoom function for PCA
4509 <li>Sequence descriptions conserved in web service
4511 <li>UniProt ID discoverer uses any word separated by
4513 <li>WsDbFetch query/result association resolved
4514 <li>Tree leaf to sequence mapping improved
4515 <li>Smooth fonts switch moved to FontChooser dialog box.
4522 <div align="center">
4523 <strong>2.1.1</strong><br> 12/9/06
4528 <li>Copy consensus sequence to clipboard</li>
4533 <li>Image output - rightmost residues are rendered if
4534 sequence id panel has been resized</li>
4535 <li>Image output - all offscreen group boundaries are
4537 <li>Annotation files with sequence references - all
4538 elements in file are relative to sequence position</li>
4539 <li>Mac Applet users can use Alt key for group editing</li>
4545 <div align="center">
4546 <strong>2.1</strong><br> 22/8/06
4551 <li>MAFFT Multiple Alignment in default Web Service list</li>
4552 <li>DAS Feature fetching</li>
4553 <li>Hide sequences and columns</li>
4554 <li>Export Annotations and Features</li>
4555 <li>GFF file reading / writing</li>
4556 <li>Associate structures with sequences from local PDB
4558 <li>Add sequences to exisiting alignment</li>
4559 <li>Recently opened files / URL lists</li>
4560 <li>Applet can launch the full application</li>
4561 <li>Applet has transparency for features (Java 1.2
4563 <li>Applet has user defined colours parameter</li>
4564 <li>Applet can load sequences from parameter
4565 "sequence<em>x</em>"
4571 <li>Redundancy Panel reinstalled in the Applet</li>
4572 <li>Monospaced font - EPS / rescaling bug fixed</li>
4573 <li>Annotation files with sequence references bug fixed</li>
4579 <div align="center">
4580 <strong>2.08.1</strong><br> 2/5/06
4585 <li>Change case of selected region from Popup menu</li>
4586 <li>Choose to match case when searching</li>
4587 <li>Middle mouse button and mouse movement can compress /
4588 expand the visible width and height of the alignment</li>
4593 <li>Annotation Panel displays complete JNet results</li>
4599 <div align="center">
4600 <strong>2.08b</strong><br> 18/4/06
4606 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4607 <li>Righthand label on wrapped alignments shows correct
4614 <div align="center">
4615 <strong>2.08</strong><br> 10/4/06
4620 <li>Editing can be locked to the selection area</li>
4621 <li>Keyboard editing</li>
4622 <li>Create sequence features from searches</li>
4623 <li>Precalculated annotations can be loaded onto
4625 <li>Features file allows grouping of features</li>
4626 <li>Annotation Colouring scheme added</li>
4627 <li>Smooth fonts off by default - Faster rendering</li>
4628 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4633 <li>Drag & Drop fixed on Linux</li>
4634 <li>Jalview Archive file faster to load/save, sequence
4635 descriptions saved.</li>
4641 <div align="center">
4642 <strong>2.07</strong><br> 12/12/05
4647 <li>PDB Structure Viewer enhanced</li>
4648 <li>Sequence Feature retrieval and display enhanced</li>
4649 <li>Choose to output sequence start-end after sequence
4650 name for file output</li>
4651 <li>Sequence Fetcher WSDBFetch@EBI</li>
4652 <li>Applet can read feature files, PDB files and can be
4653 used for HTML form input</li>
4658 <li>HTML output writes groups and features</li>
4659 <li>Group editing is Control and mouse click</li>
4660 <li>File IO bugs</li>
4666 <div align="center">
4667 <strong>2.06</strong><br> 28/9/05
4672 <li>View annotations in wrapped mode</li>
4673 <li>More options for PCA viewer</li>
4678 <li>GUI bugs resolved</li>
4679 <li>Runs with -nodisplay from command line</li>
4685 <div align="center">
4686 <strong>2.05b</strong><br> 15/9/05
4691 <li>Choose EPS export as lineart or text</li>
4692 <li>Jar files are executable</li>
4693 <li>Can read in Uracil - maps to unknown residue</li>
4698 <li>Known OutOfMemory errors give warning message</li>
4699 <li>Overview window calculated more efficiently</li>
4700 <li>Several GUI bugs resolved</li>
4706 <div align="center">
4707 <strong>2.05</strong><br> 30/8/05
4712 <li>Edit and annotate in "Wrapped" view</li>
4717 <li>Several GUI bugs resolved</li>
4723 <div align="center">
4724 <strong>2.04</strong><br> 24/8/05
4729 <li>Hold down mouse wheel & scroll to change font
4735 <li>Improved JPred client reliability</li>
4736 <li>Improved loading of Jalview files</li>
4742 <div align="center">
4743 <strong>2.03</strong><br> 18/8/05
4748 <li>Set Proxy server name and port in preferences</li>
4749 <li>Multiple URL links from sequence ids</li>
4750 <li>User Defined Colours can have a scheme name and added
4752 <li>Choose to ignore gaps in consensus calculation</li>
4753 <li>Unix users can set default web browser</li>
4754 <li>Runs without GUI for batch processing</li>
4755 <li>Dynamically generated Web Service Menus</li>
4760 <li>InstallAnywhere download for Sparc Solaris</li>
4766 <div align="center">
4767 <strong>2.02</strong><br> 18/7/05
4773 <li>Copy & Paste order of sequences maintains
4774 alignment order.</li>
4780 <div align="center">
4781 <strong>2.01</strong><br> 12/7/05
4786 <li>Use delete key for deleting selection.</li>
4787 <li>Use Mouse wheel to scroll sequences.</li>
4788 <li>Help file updated to describe how to add alignment
4790 <li>Version and build date written to build properties
4792 <li>InstallAnywhere installation will check for updates
4793 at launch of Jalview.</li>
4798 <li>Delete gaps bug fixed.</li>
4799 <li>FileChooser sorts columns.</li>
4800 <li>Can remove groups one by one.</li>
4801 <li>Filechooser icons installed.</li>
4802 <li>Finder ignores return character when searching.
4803 Return key will initiate a search.<br>
4810 <div align="center">
4811 <strong>2.0</strong><br> 20/6/05
4816 <li>New codebase</li>