3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
34 /* separate the items from eachother */
41 /* doesnt get processed in javahelp */
50 <strong>Release History</strong>
54 <th nowrap><em>Release</em></th>
55 <th><em>New Features</em></th>
56 <th><em>Issues Resolved</em></th>
59 <td width="60" align="center" nowrap><strong><a
60 name="Jalview.2.11.1">2.11.1</a><a name="Jalview.2.11.1.0">.0</a><br />
61 <em>25/2/2020</em></strong></td>
62 <td align="left" valign="top">
64 <li><!-- JAL-3121 -->Feature attributes from VCF files can be exported and re-imported as GFF3 files
67 <!-- JAL-3376 -->Record "fixed column" values POS,
68 ID, QUAL, FILTER from VCF as Feature Attributes
71 <!-- JAL-3375 -->More robust VCF numeric data field
72 validation while parsing (e.g. AF* attributes)
75 <!-- JAL-3538 -->Font anti-aliasing in alignment views
81 </ul><em>Jalview Installer</em>
84 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
85 in console (may be null when Jalview launched as executable jar or via conda)
88 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
91 <!-- JAL-3393 -->New installer/application launcher generated with install4j 8.0.4
93 <li><!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
94 <li><!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
95 </ul> <em>Release processes</em>
98 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
100 </ul> <em>Build System</em>
103 <!-- JAL-3510 -->Clover updated to 4.4.1
106 <!-- JAL-3513 -->Test code included in Clover coverage
109 </ul> <em>Deprecations</em>
111 <td align="left" valign="top">
117 <!-- JAL-3296 -->Sequence position numbers in status bar not correct after editing a sequence's start position via GUI
120 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
121 with annotation and exceptions thrown when only a few
122 columns shown in wrapped mode
125 <!-- JAL-3386 -->Sequence IDs missing in headless export of
126 wrapped alignment figure with annotations
129 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
130 ID fails with ClassCastException
133 <!-- JAL-3389 -->Chimera session not restored from Jalview
137 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
138 feature settings dialog also selects columns
141 <!-- JAL-3473 -->SpinnerNumberModel causing
142 IllegalArgumentException in some circumstances
145 <!-- JAL-3406 -->Credits missing some authors in Jalview
146 help documentation for 2.11.0 release
148 </ul> <em>Java 11 Compatibility issues</em>
151 <!-- JAL-2987 -->OSX - Can't view results in PDB/Uniprot FTS
153 </ul> <em>Installer</em>
155 <li><!-- JAL-3447 -->Jalview does not automatically create file associations for 3D structure files (.pdb, .mmcif. .cif)</li>
156 </ul> <em>Repository and Source Release</em>
159 <!-- JAL-3474 -->removed redundant .gitignore files from
163 <em>New Known Issues</em>
166 <!-- JAL-3523 -->OSX - Current working directory not
167 preserved when Jalview.app launched with parameters from
171 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
172 clipped in headless figure export when Right Align option
176 <!-- JAL-3542 -->Jalview Installation type always reports 'Source' in console output.
182 <td width="60" align="center" nowrap>
183 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
184 <em>04/07/2019</em></strong>
186 <td align="left" valign="top">
189 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
190 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
191 source project) rather than InstallAnywhere
194 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
195 settings, receive over the air updates and launch specific
196 versions via (<a href="https://github.com/threerings/getdown">Three
200 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
201 formats supported by Jalview (including .jvp project files)
204 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
205 arguments and switch between different getdown channels
208 <!-- JAL-3141 -->Backup files created when saving Jalview project
213 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
214 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
216 <!-- JAL-2620 -->Alternative genetic code tables for
217 'Translate as cDNA'</li>
219 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
220 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
223 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
224 implementation that allows updates) used for Sequence Feature collections</li>
226 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
227 features can be filtered and shaded according to any
228 associated attributes (e.g. variant attributes from VCF
229 file, or key-value pairs imported from column 9 of GFF
233 <!-- JAL-2879 -->Feature Attributes and shading schemes
234 stored and restored from Jalview Projects
237 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
238 recognise variant features
241 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
242 sequences (also coloured red by default)
245 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
249 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
250 algorithm (Z-sort/transparency and filter aware)
253 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
259 <!-- JAL-3205 -->Symmetric score matrices for faster
260 tree and PCA calculations
262 <li><strong>Principal Components Analysis Viewer</strong>
265 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
266 and Viewer state saved in Jalview Project
268 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
271 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
275 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
280 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
282 <li><strong>Speed and Efficiency</strong>
285 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
286 multiple groups when working with large alignments
289 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
293 <li><strong>User Interface</strong>
296 <!-- JAL-2933 -->Finder panel remembers last position in each
300 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
301 what is shown)<br />Only visible regions of alignment are shown by
302 default (can be changed in user preferences)
305 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
306 to the Overwrite Dialog
309 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
313 <!-- JAL-1244 -->Status bar shows bounds when dragging a
314 selection region, and gap count when inserting or deleting gaps
317 <!-- JAL-3132 -->Status bar updates over sequence and annotation
321 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
325 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
329 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
332 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
336 <!-- JAL-3181 -->Consistent ordering of links in sequence id
340 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
342 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
346 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
347 <li><strong>Java 11 Support (not yet on general release)</strong>
350 <!-- -->OSX GUI integrations for App menu's 'About' entry and
355 <em>Deprecations</em>
357 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
358 capabilities removed from the Jalview Desktop
360 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
361 unmarshalling has been replaced by JAXB for Jalview projects
362 and XML based data retrieval clients</li>
363 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
364 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
365 </ul> <em>Documentation</em>
367 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
368 not supported in EPS figure export
370 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
371 </ul> <em>Development and Release Processes</em>
374 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
377 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
379 <!-- JAL-3225 -->Eclipse project configuration managed with
383 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
384 Bamboo continuous integration for unattended Test Suite
388 <!-- JAL-2864 -->Memory test suite to detect leaks in common
392 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
396 <!-- JAL-3248 -->Developer documentation migrated to
397 markdown (with HTML rendering)
400 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
403 <!-- JAL-3289 -->New URLs for publishing development
408 <td align="left" valign="top">
411 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
414 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
415 superposition in Jmol fail on Windows
418 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
419 structures for sequences with lots of PDB structures
422 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
426 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
427 project involving multiple views
430 <!-- JAL-3164 -->Overview for complementary view in a linked
431 CDS/Protein alignment is not updated when Hide Columns by
432 Annotation dialog hides columns
435 <!-- JAL-3158 -->Selection highlighting in the complement of a
436 CDS/Protein alignment stops working after making a selection in
437 one view, then making another selection in the other view
440 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
444 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
445 Settings and Jalview Preferences panels
448 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
449 overview with large alignments
452 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
453 region if columns were selected by dragging right-to-left and the
454 mouse moved to the left of the first column
457 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
458 hidden column marker via scale popup menu
461 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
462 doesn't tell users the invalid URL
465 <!-- JAL-2816 -->Tooltips displayed for features filtered by
469 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
470 show cross references or Fetch Database References are shown in
474 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
475 peptide sequence (computed variant shown as p.Res.null)
478 <!-- JAL-2060 -->'Graduated colour' option not offered for
479 manually created features (where feature score is Float.NaN)
482 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
483 when columns are hidden
486 <!-- JAL-3082 -->Regular expression error for '(' in Select
487 Columns by Annotation description
490 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
491 out of Scale or Annotation Panel
494 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
498 <!-- JAL-3074 -->Left/right drag in annotation can scroll
502 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
506 <!-- JAL-3002 -->Column display is out by one after Page Down,
507 Page Up in wrapped mode
510 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
513 <!-- JAL-2932 -->Finder searches in minimised alignments
516 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
517 on opening an alignment
520 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
524 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
525 different groups in the alignment are selected
528 <!-- JAL-2717 -->Internationalised colour scheme names not shown
532 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
536 <!-- JAL-3125 -->Value input for graduated feature colour
537 threshold gets 'unrounded'
540 <!-- JAL-2982 -->PCA image export doesn't respect background
544 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
547 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
550 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
554 <!-- JAL-2964 -->Associate Tree with All Views not restored from
558 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
559 shown in complementary view
562 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
563 without normalisation
566 <!-- JAL-3021 -->Sequence Details report should open positioned at top
570 <!-- JAL-914 -->Help page can be opened twice
573 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
575 </ul> <em>Editing</em>
578 <!-- JAL-2822 -->Start and End should be updated when sequence
579 data at beginning or end of alignment added/removed via 'Edit'
583 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
584 relocate sequence features correctly when start of sequence is
585 removed (Known defect since 2.10)
588 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
589 dialog corrupts dataset sequence
592 <!-- JAL-868 -->Structure colours not updated when associated tree
593 repartitions the alignment view (Regression in 2.10.5)
595 </ul> <em>Datamodel</em>
598 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
599 sequence's End is greater than its length
601 </ul> <em>Bugs fixed for Java 11 Support (not yet on
602 general release)</em>
605 <!-- JAL-3288 -->Menus work properly in split-screen
607 </ul> <em>New Known Defects</em>
610 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
613 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
614 regions of protein alignment.
617 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
618 is restored from a Jalview 2.11 project
621 <!-- JAL-3213 -->Alignment panel height can be too small after
625 <!-- JAL-3240 -->Display is incorrect after removing gapped
626 columns within hidden columns
629 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
630 window after dragging left to select columns to left of visible
634 <!-- JAL-2876 -->Features coloured according to their description
635 string and thresholded by score in earlier versions of Jalview are
636 not shown as thresholded features in 2.11. To workaround please
637 create a Score filter instead.
640 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
642 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
645 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
646 alignments with multiple views can close views unexpectedly
649 <em>Java 11 Specific defects</em>
652 <!-- JAL-3235 -->Jalview Properties file is not sorted
653 alphabetically when saved
659 <td width="60" nowrap>
661 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
664 <td><div align="left">
668 <!-- JAL-3101 -->Default memory for Jalview webstart and
669 InstallAnywhere increased to 1G.
672 <!-- JAL-247 -->Hidden sequence markers and representative
673 sequence bolding included when exporting alignment as EPS,
674 SVG, PNG or HTML. <em>Display is configured via the
675 Format menu, or for command-line use via a Jalview
676 properties file.</em>
679 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
680 API and sequence data now imported as JSON.
683 <!-- JAL-3065 -->Change in recommended way of starting
684 Jalview via a Java command line: add jars in lib directory
685 to CLASSPATH, rather than via the deprecated java.ext.dirs
692 <!-- JAL-3047 -->Support added to execute test suite
693 instrumented with <a href="http://openclover.org/">Open
698 <td><div align="left">
702 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
703 row shown in Feredoxin Structure alignment view of example
707 <!-- JAL-2854 -->Annotation obscures sequences if lots of
708 annotation displayed.
711 <!-- JAL-3107 -->Group conservation/consensus not shown
712 for newly created group when 'Apply to all groups'
716 <!-- JAL-3087 -->Corrupted display when switching to
717 wrapped mode when sequence panel's vertical scrollbar is
721 <!-- JAL-3003 -->Alignment is black in exported EPS file
722 when sequences are selected in exported view.</em>
725 <!-- JAL-3059 -->Groups with different coloured borders
726 aren't rendered with correct colour.
729 <!-- JAL-3092 -->Jalview could hang when importing certain
730 types of knotted RNA secondary structure.
733 <!-- JAL-3095 -->Sequence highlight and selection in
734 trimmed VARNA 2D structure is incorrect for sequences that
738 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
739 annotation when columns are inserted into an alignment,
740 and when exporting as Stockholm flatfile.
743 <!-- JAL-3053 -->Jalview annotation rows containing upper
744 and lower-case 'E' and 'H' do not automatically get
745 treated as RNA secondary structure.
748 <!-- JAL-3106 -->.jvp should be used as default extension
749 (not .jar) when saving a Jalview project file.
752 <!-- JAL-3105 -->Mac Users: closing a window correctly
753 transfers focus to previous window on OSX
756 <em>Java 10 Issues Resolved</em>
759 <!-- JAL-2988 -->OSX - Can't save new files via the File
760 or export menus by typing in a name into the Save dialog
764 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
765 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
766 'look and feel' which has improved compatibility with the
767 latest version of OSX.
774 <td width="60" nowrap>
776 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
777 <em>7/06/2018</em></strong>
780 <td><div align="left">
784 <!-- JAL-2920 -->Use HGVS nomenclature for variant
785 annotation retrieved from Uniprot
788 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
789 onto the Jalview Desktop
793 <td><div align="left">
797 <!-- JAL-3017 -->Cannot import features with multiple
798 variant elements (blocks import of some Uniprot records)
801 <!-- JAL-2997 -->Clustal files with sequence positions in
802 right-hand column parsed correctly
805 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
806 not alignment area in exported graphic
809 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
810 window has input focus
813 <!-- JAL-2992 -->Annotation panel set too high when
814 annotation added to view (Windows)
817 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
818 network connectivity is poor
821 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
822 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
823 the currently open URL and links from a page viewed in
824 Firefox or Chrome on Windows is now fully supported. If
825 you are using Edge, only links in the page can be
826 dragged, and with Internet Explorer, only the currently
827 open URL in the browser can be dropped onto Jalview.</em>
830 <em>New Known Defects</em>
832 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
837 <td width="60" nowrap>
839 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
842 <td><div align="left">
846 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
847 for disabling automatic superposition of multiple
848 structures and open structures in existing views
851 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
852 ID and annotation area margins can be click-dragged to
856 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
860 <!-- JAL-2759 -->Improved performance for large alignments
861 and lots of hidden columns
864 <!-- JAL-2593 -->Improved performance when rendering lots
865 of features (particularly when transparency is disabled)
868 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
869 exchange of Jalview features and Chimera attributes made
875 <td><div align="left">
878 <!-- JAL-2899 -->Structure and Overview aren't updated
879 when Colour By Annotation threshold slider is adjusted
882 <!-- JAL-2778 -->Slow redraw when Overview panel shown
883 overlapping alignment panel
886 <!-- JAL-2929 -->Overview doesn't show end of unpadded
890 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
891 improved: CDS not handled correctly if transcript has no
895 <!-- JAL-2321 -->Secondary structure and temperature
896 factor annotation not added to sequence when local PDB
897 file associated with it by drag'n'drop or structure
901 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
902 dialog doesn't import PDB files dropped on an alignment
905 <!-- JAL-2666 -->Linked scrolling via protein horizontal
906 scroll bar doesn't work for some CDS/Protein views
909 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
910 Java 1.8u153 onwards and Java 1.9u4+.
913 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
914 columns in annotation row
917 <!-- JAL-2913 -->Preferences panel's ID Width control is not
918 honored in batch mode
921 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
922 for structures added to existing Jmol view
925 <!-- JAL-2223 -->'View Mappings' includes duplicate
926 entries after importing project with multiple views
929 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
930 protein sequences via SIFTS from associated PDB entries
931 with negative residue numbers or missing residues fails
934 <!-- JAL-2952 -->Exception when shading sequence with negative
935 Temperature Factor values from annotated PDB files (e.g.
936 as generated by CONSURF)
939 <!-- JAL-2920 -->Uniprot 'sequence variant' features
940 tooltip doesn't include a text description of mutation
943 <!-- JAL-2922 -->Invert displayed features very slow when
944 structure and/or overview windows are also shown
947 <!-- JAL-2954 -->Selecting columns from highlighted regions
948 very slow for alignments with large numbers of sequences
951 <!-- JAL-2925 -->Copy Consensus fails for group consensus
952 with 'StringIndexOutOfBounds'
955 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
956 platforms running Java 10
959 <!-- JAL-2960 -->Adding a structure to existing structure
960 view appears to do nothing because the view is hidden behind the alignment view
966 <!-- JAL-2926 -->Copy consensus sequence option in applet
967 should copy the group consensus when popup is opened on it
973 <!-- JAL-2913 -->Fixed ID width preference is not respected
976 <em>New Known Defects</em>
979 <!-- JAL-2973 --> Exceptions occasionally raised when
980 editing a large alignment and overview is displayed
983 <!-- JAL-2974 -->'Overview updating' progress bar is shown
984 repeatedly after a series of edits even when the overview
985 is no longer reflecting updates
988 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
989 structures for protein subsequence (if 'Trim Retrieved
990 Sequences' enabled) or Ensembl isoforms (Workaround in
991 2.10.4 is to fail back to N&W mapping)
994 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
995 option gives blank output
1002 <td width="60" nowrap>
1003 <div align="center">
1004 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1007 <td><div align="left">
1008 <ul><li>Updated Certum Codesigning Certificate
1009 (Valid till 30th November 2018)</li></ul></div></td>
1010 <td><div align="left">
1011 <em>Desktop</em><ul>
1013 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1014 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1015 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1016 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1017 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1018 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1019 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1025 <td width="60" nowrap>
1026 <div align="center">
1027 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1030 <td><div align="left">
1034 <!-- JAL-2446 -->Faster and more efficient management and
1035 rendering of sequence features
1038 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1039 429 rate limit request hander
1042 <!-- JAL-2773 -->Structure views don't get updated unless
1043 their colours have changed
1046 <!-- JAL-2495 -->All linked sequences are highlighted for
1047 a structure mousover (Jmol) or selection (Chimera)
1050 <!-- JAL-2790 -->'Cancel' button in progress bar for
1051 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1054 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1055 view from Ensembl locus cross-references
1058 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1062 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1063 feature can be disabled
1066 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1067 PDB easier retrieval of sequences for lists of IDs
1070 <!-- JAL-2758 -->Short names for sequences retrieved from
1076 <li>Groovy interpreter updated to 2.4.12</li>
1077 <li>Example groovy script for generating a matrix of
1078 percent identity scores for current alignment.</li>
1080 <em>Testing and Deployment</em>
1083 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1087 <td><div align="left">
1091 <!-- JAL-2643 -->Pressing tab after updating the colour
1092 threshold text field doesn't trigger an update to the
1096 <!-- JAL-2682 -->Race condition when parsing sequence ID
1100 <!-- JAL-2608 -->Overview windows are also closed when
1101 alignment window is closed
1104 <!-- JAL-2548 -->Export of features doesn't always respect
1108 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1109 takes a long time in Cursor mode
1115 <!-- JAL-2777 -->Structures with whitespace chainCode
1116 cannot be viewed in Chimera
1119 <!-- JAL-2728 -->Protein annotation panel too high in
1123 <!-- JAL-2757 -->Can't edit the query after the server
1124 error warning icon is shown in Uniprot and PDB Free Text
1128 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1131 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1134 <!-- JAL-2739 -->Hidden column marker in last column not
1135 rendered when switching back from Wrapped to normal view
1138 <!-- JAL-2768 -->Annotation display corrupted when
1139 scrolling right in unwapped alignment view
1142 <!-- JAL-2542 -->Existing features on subsequence
1143 incorrectly relocated when full sequence retrieved from
1147 <!-- JAL-2733 -->Last reported memory still shown when
1148 Desktop->Show Memory is unticked (OSX only)
1151 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1152 features of same type and group to be selected for
1156 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1157 alignments when hidden columns are present
1160 <!-- JAL-2392 -->Jalview freezes when loading and
1161 displaying several structures
1164 <!-- JAL-2732 -->Black outlines left after resizing or
1168 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1169 within the Jalview desktop on OSX
1172 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1173 when in wrapped alignment mode
1176 <!-- JAL-2636 -->Scale mark not shown when close to right
1177 hand end of alignment
1180 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1181 each selected sequence do not have correct start/end
1185 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1186 after canceling the Alignment Window's Font dialog
1189 <!-- JAL-2036 -->Show cross-references not enabled after
1190 restoring project until a new view is created
1193 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1194 URL links appears when only default EMBL-EBI link is
1195 configured (since 2.10.2b2)
1198 <!-- JAL-2775 -->Overview redraws whole window when box
1199 position is adjusted
1202 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1203 in a multi-chain structure when viewing alignment
1204 involving more than one chain (since 2.10)
1207 <!-- JAL-2811 -->Double residue highlights in cursor mode
1208 if new selection moves alignment window
1211 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1212 arrow key in cursor mode to pass hidden column marker
1215 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1216 that produces correctly annotated transcripts and products
1219 <!-- JAL-2776 -->Toggling a feature group after first time
1220 doesn't update associated structure view
1223 <em>Applet</em><br />
1226 <!-- JAL-2687 -->Concurrent modification exception when
1227 closing alignment panel
1230 <em>BioJSON</em><br />
1233 <!-- JAL-2546 -->BioJSON export does not preserve
1234 non-positional features
1237 <em>New Known Issues</em>
1240 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1241 sequence features correctly (for many previous versions of
1245 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1246 using cursor in wrapped panel other than top
1249 <!-- JAL-2791 -->Select columns containing feature ignores
1250 graduated colour threshold
1253 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1254 always preserve numbering and sequence features
1257 <em>Known Java 9 Issues</em>
1260 <!-- JAL-2902 -->Groovy Console very slow to open and is
1261 not responsive when entering characters (Webstart, Java
1268 <td width="60" nowrap>
1269 <div align="center">
1270 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1271 <em>2/10/2017</em></strong>
1274 <td><div align="left">
1275 <em>New features in Jalview Desktop</em>
1278 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1280 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1284 <td><div align="left">
1288 <td width="60" nowrap>
1289 <div align="center">
1290 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1291 <em>7/9/2017</em></strong>
1294 <td><div align="left">
1298 <!-- JAL-2588 -->Show gaps in overview window by colouring
1299 in grey (sequences used to be coloured grey, and gaps were
1303 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1307 <!-- JAL-2587 -->Overview updates immediately on increase
1308 in size and progress bar shown as higher resolution
1309 overview is recalculated
1314 <td><div align="left">
1318 <!-- JAL-2664 -->Overview window redraws every hidden
1319 column region row by row
1322 <!-- JAL-2681 -->duplicate protein sequences shown after
1323 retrieving Ensembl crossrefs for sequences from Uniprot
1326 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1327 format setting is unticked
1330 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1331 if group has show boxes format setting unticked
1334 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1335 autoscrolling whilst dragging current selection group to
1336 include sequences and columns not currently displayed
1339 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1340 assemblies are imported via CIF file
1343 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1344 displayed when threshold or conservation colouring is also
1348 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1352 <!-- JAL-2673 -->Jalview continues to scroll after
1353 dragging a selected region off the visible region of the
1357 <!-- JAL-2724 -->Cannot apply annotation based
1358 colourscheme to all groups in a view
1361 <!-- JAL-2511 -->IDs don't line up with sequences
1362 initially after font size change using the Font chooser or
1369 <td width="60" nowrap>
1370 <div align="center">
1371 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1374 <td><div align="left">
1375 <em>Calculations</em>
1379 <!-- JAL-1933 -->Occupancy annotation row shows number of
1380 ungapped positions in each column of the alignment.
1383 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1384 a calculation dialog box
1387 <!-- JAL-2379 -->Revised implementation of PCA for speed
1388 and memory efficiency (~30x faster)
1391 <!-- JAL-2403 -->Revised implementation of sequence
1392 similarity scores as used by Tree, PCA, Shading Consensus
1393 and other calculations
1396 <!-- JAL-2416 -->Score matrices are stored as resource
1397 files within the Jalview codebase
1400 <!-- JAL-2500 -->Trees computed on Sequence Feature
1401 Similarity may have different topology due to increased
1408 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1409 model for alignments and groups
1412 <!-- JAL-384 -->Custom shading schemes created via groovy
1419 <!-- JAL-2526 -->Efficiency improvements for interacting
1420 with alignment and overview windows
1423 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1427 <!-- JAL-2388 -->Hidden columns and sequences can be
1431 <!-- JAL-2611 -->Click-drag in visible area allows fine
1432 adjustment of visible position
1436 <em>Data import/export</em>
1439 <!-- JAL-2535 -->Posterior probability annotation from
1440 Stockholm files imported as sequence associated annotation
1443 <!-- JAL-2507 -->More robust per-sequence positional
1444 annotation input/output via stockholm flatfile
1447 <!-- JAL-2533 -->Sequence names don't include file
1448 extension when importing structure files without embedded
1449 names or PDB accessions
1452 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1453 format sequence substitution matrices
1456 <em>User Interface</em>
1459 <!-- JAL-2447 --> Experimental Features Checkbox in
1460 Desktop's Tools menu to hide or show untested features in
1464 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1465 via Overview or sequence motif search operations
1468 <!-- JAL-2547 -->Amend sequence features dialog box can be
1469 opened by double clicking gaps within sequence feature
1473 <!-- JAL-1476 -->Status bar message shown when not enough
1474 aligned positions were available to create a 3D structure
1478 <em>3D Structure</em>
1481 <!-- JAL-2430 -->Hidden regions in alignment views are not
1482 coloured in linked structure views
1485 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1486 file-based command exchange
1489 <!-- JAL-2375 -->Structure chooser automatically shows
1490 Cached Structures rather than querying the PDBe if
1491 structures are already available for sequences
1494 <!-- JAL-2520 -->Structures imported via URL are cached in
1495 the Jalview project rather than downloaded again when the
1496 project is reopened.
1499 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1500 to transfer Chimera's structure attributes as Jalview
1501 features, and vice-versa (<strong>Experimental
1505 <em>Web Services</em>
1508 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1511 <!-- JAL-2335 -->Filter non-standard amino acids and
1512 nucleotides when submitting to AACon and other MSA
1516 <!-- JAL-2316, -->URLs for viewing database
1517 cross-references provided by identifiers.org and the
1518 EMBL-EBI's MIRIAM DB
1525 <!-- JAL-2344 -->FileFormatI interface for describing and
1526 identifying file formats (instead of String constants)
1529 <!-- JAL-2228 -->FeatureCounter script refactored for
1530 efficiency when counting all displayed features (not
1531 backwards compatible with 2.10.1)
1534 <em>Example files</em>
1537 <!-- JAL-2631 -->Graduated feature colour style example
1538 included in the example feature file
1541 <em>Documentation</em>
1544 <!-- JAL-2339 -->Release notes reformatted for readability
1545 with the built-in Java help viewer
1548 <!-- JAL-1644 -->Find documentation updated with 'search
1549 sequence description' option
1555 <!-- JAL-2485, -->External service integration tests for
1556 Uniprot REST Free Text Search Client
1559 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1562 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1567 <td><div align="left">
1568 <em>Calculations</em>
1571 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1572 matrix - C->R should be '-3'<br />Old matrix restored
1573 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1575 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1576 Jalview's treatment of gaps in PCA and substitution matrix
1577 based Tree calculations.<br /> <br />In earlier versions
1578 of Jalview, gaps matching gaps were penalised, and gaps
1579 matching non-gaps penalised even more. In the PCA
1580 calculation, gaps were actually treated as non-gaps - so
1581 different costs were applied, which meant Jalview's PCAs
1582 were different to those produced by SeqSpace.<br />Jalview
1583 now treats gaps in the same way as SeqSpace (ie it scores
1584 them as 0). <br /> <br />Enter the following in the
1585 Groovy console to restore pre-2.10.2 behaviour:<br />
1586 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1587 // for 2.10.1 mode <br />
1588 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1589 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1590 these settings will affect all subsequent tree and PCA
1591 calculations (not recommended)</em></li>
1593 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1594 scaling of branch lengths for trees computed using
1595 Sequence Feature Similarity.
1598 <!-- JAL-2377 -->PCA calculation could hang when
1599 generating output report when working with highly
1600 redundant alignments
1603 <!-- JAL-2544 --> Sort by features includes features to
1604 right of selected region when gaps present on right-hand
1608 <em>User Interface</em>
1611 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1612 doesn't reselect a specific sequence's associated
1613 annotation after it was used for colouring a view
1616 <!-- JAL-2419 -->Current selection lost if popup menu
1617 opened on a region of alignment without groups
1620 <!-- JAL-2374 -->Popup menu not always shown for regions
1621 of an alignment with overlapping groups
1624 <!-- JAL-2310 -->Finder double counts if both a sequence's
1625 name and description match
1628 <!-- JAL-2370 -->Hiding column selection containing two
1629 hidden regions results in incorrect hidden regions
1632 <!-- JAL-2386 -->'Apply to all groups' setting when
1633 changing colour does not apply Conservation slider value
1637 <!-- JAL-2373 -->Percentage identity and conservation menu
1638 items do not show a tick or allow shading to be disabled
1641 <!-- JAL-2385 -->Conservation shading or PID threshold
1642 lost when base colourscheme changed if slider not visible
1645 <!-- JAL-2547 -->Sequence features shown in tooltip for
1646 gaps before start of features
1649 <!-- JAL-2623 -->Graduated feature colour threshold not
1650 restored to UI when feature colour is edited
1653 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1654 a time when scrolling vertically in wrapped mode.
1657 <!-- JAL-2630 -->Structure and alignment overview update
1658 as graduate feature colour settings are modified via the
1662 <!-- JAL-2034 -->Overview window doesn't always update
1663 when a group defined on the alignment is resized
1666 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1667 wrapped view result in positional status updates
1671 <!-- JAL-2563 -->Status bar doesn't show position for
1672 ambiguous amino acid and nucleotide symbols
1675 <!-- JAL-2602 -->Copy consensus sequence failed if
1676 alignment included gapped columns
1679 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1680 widgets don't permanently disappear
1683 <!-- JAL-2503 -->Cannot select or filter quantitative
1684 annotation that are shown only as column labels (e.g.
1685 T-Coffee column reliability scores)
1688 <!-- JAL-2594 -->Exception thrown if trying to create a
1689 sequence feature on gaps only
1692 <!-- JAL-2504 -->Features created with 'New feature'
1693 button from a Find inherit previously defined feature type
1694 rather than the Find query string
1697 <!-- JAL-2423 -->incorrect title in output window when
1698 exporting tree calculated in Jalview
1701 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1702 and then revealing them reorders sequences on the
1706 <!-- JAL-964 -->Group panel in sequence feature settings
1707 doesn't update to reflect available set of groups after
1708 interactively adding or modifying features
1711 <!-- JAL-2225 -->Sequence Database chooser unusable on
1715 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1716 only excluded gaps in current sequence and ignored
1723 <!-- JAL-2421 -->Overview window visible region moves
1724 erratically when hidden rows or columns are present
1727 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1728 Structure Viewer's colour menu don't correspond to
1732 <!-- JAL-2405 -->Protein specific colours only offered in
1733 colour and group colour menu for protein alignments
1736 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1737 reflect currently selected view or group's shading
1741 <!-- JAL-2624 -->Feature colour thresholds not respected
1742 when rendered on overview and structures when opacity at
1746 <!-- JAL-2589 -->User defined gap colour not shown in
1747 overview when features overlaid on alignment
1750 <!-- JAL-2567 -->Feature settings for different views not
1751 recovered correctly from Jalview project file
1754 <!-- JAL-2256 -->Feature colours in overview when first opened
1755 (automatically via preferences) are different to the main
1759 <em>Data import/export</em>
1762 <!-- JAL-2576 -->Very large alignments take a long time to
1766 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1767 added after a sequence was imported are not written to
1771 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1772 when importing RNA secondary structure via Stockholm
1775 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1776 not shown in correct direction for simple pseudoknots
1779 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1780 with lightGray or darkGray via features file (but can
1784 <!-- JAL-2383 -->Above PID colour threshold not recovered
1785 when alignment view imported from project
1788 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1789 structure and sequences extracted from structure files
1790 imported via URL and viewed in Jmol
1793 <!-- JAL-2520 -->Structures loaded via URL are saved in
1794 Jalview Projects rather than fetched via URL again when
1795 the project is loaded and the structure viewed
1798 <em>Web Services</em>
1801 <!-- JAL-2519 -->EnsemblGenomes example failing after
1802 release of Ensembl v.88
1805 <!-- JAL-2366 -->Proxy server address and port always
1806 appear enabled in Preferences->Connections
1809 <!-- JAL-2461 -->DAS registry not found exceptions
1810 removed from console output
1813 <!-- JAL-2582 -->Cannot retrieve protein products from
1814 Ensembl by Peptide ID
1817 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1818 created from SIFTs, and spurious 'Couldn't open structure
1819 in Chimera' errors raised after April 2017 update (problem
1820 due to 'null' string rather than empty string used for
1821 residues with no corresponding PDB mapping).
1824 <em>Application UI</em>
1827 <!-- JAL-2361 -->User Defined Colours not added to Colour
1831 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1832 case' residues (button in colourscheme editor debugged and
1833 new documentation and tooltips added)
1836 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1837 doesn't restore group-specific text colour thresholds
1840 <!-- JAL-2243 -->Feature settings panel does not update as
1841 new features are added to alignment
1844 <!-- JAL-2532 -->Cancel in feature settings reverts
1845 changes to feature colours via the Amend features dialog
1848 <!-- JAL-2506 -->Null pointer exception when attempting to
1849 edit graduated feature colour via amend features dialog
1853 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1854 selection menu changes colours of alignment views
1857 <!-- JAL-2426 -->Spurious exceptions in console raised
1858 from alignment calculation workers after alignment has
1862 <!-- JAL-1608 -->Typo in selection popup menu - Create
1863 groups now 'Create Group'
1866 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1867 Create/Undefine group doesn't always work
1870 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1871 shown again after pressing 'Cancel'
1874 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1875 adjusts start position in wrap mode
1878 <!-- JAL-2563 -->Status bar doesn't show positions for
1879 ambiguous amino acids
1882 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1883 CDS/Protein view after CDS sequences added for aligned
1887 <!-- JAL-2592 -->User defined colourschemes called 'User
1888 Defined' don't appear in Colours menu
1894 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1895 score models doesn't always result in an updated PCA plot
1898 <!-- JAL-2442 -->Features not rendered as transparent on
1899 overview or linked structure view
1902 <!-- JAL-2372 -->Colour group by conservation doesn't
1906 <!-- JAL-2517 -->Hitting Cancel after applying
1907 user-defined colourscheme doesn't restore original
1914 <!-- JAL-2314 -->Unit test failure:
1915 jalview.ws.jabaws.RNAStructExportImport setup fails
1918 <!-- JAL-2307 -->Unit test failure:
1919 jalview.ws.sifts.SiftsClientTest due to compatibility
1920 problems with deep array comparison equality asserts in
1921 successive versions of TestNG
1924 <!-- JAL-2479 -->Relocated StructureChooserTest and
1925 ParameterUtilsTest Unit tests to Network suite
1928 <em>New Known Issues</em>
1931 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1932 phase after a sequence motif find operation
1935 <!-- JAL-2550 -->Importing annotation file with rows
1936 containing just upper and lower case letters are
1937 interpreted as WUSS RNA secondary structure symbols
1940 <!-- JAL-2590 -->Cannot load and display Newick trees
1941 reliably from eggnog Ortholog database
1944 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1945 containing features of type Highlight' when 'B' is pressed
1946 to mark columns containing highlighted regions.
1949 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1950 doesn't always add secondary structure annotation.
1955 <td width="60" nowrap>
1956 <div align="center">
1957 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1960 <td><div align="left">
1964 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1965 for all consensus calculations
1968 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1971 <li>Updated Jalview's Certum code signing certificate
1974 <em>Application</em>
1977 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1978 set of database cross-references, sorted alphabetically
1981 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1982 from database cross references. Users with custom links
1983 will receive a <a href="webServices/urllinks.html#warning">warning
1984 dialog</a> asking them to update their preferences.
1987 <!-- JAL-2287-->Cancel button and escape listener on
1988 dialog warning user about disconnecting Jalview from a
1992 <!-- JAL-2320-->Jalview's Chimera control window closes if
1993 the Chimera it is connected to is shut down
1996 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1997 columns menu item to mark columns containing highlighted
1998 regions (e.g. from structure selections or results of a
2002 <!-- JAL-2284-->Command line option for batch-generation
2003 of HTML pages rendering alignment data with the BioJS
2013 <!-- JAL-2286 -->Columns with more than one modal residue
2014 are not coloured or thresholded according to percent
2015 identity (first observed in Jalview 2.8.2)
2018 <!-- JAL-2301 -->Threonine incorrectly reported as not
2022 <!-- JAL-2318 -->Updates to documentation pages (above PID
2023 threshold, amino acid properties)
2026 <!-- JAL-2292 -->Lower case residues in sequences are not
2027 reported as mapped to residues in a structure file in the
2031 <!--JAL-2324 -->Identical features with non-numeric scores
2032 could be added multiple times to a sequence
2035 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2036 bond features shown as two highlighted residues rather
2037 than a range in linked structure views, and treated
2038 correctly when selecting and computing trees from features
2041 <!-- JAL-2281-->Custom URL links for database
2042 cross-references are matched to database name regardless
2047 <em>Application</em>
2050 <!-- JAL-2282-->Custom URL links for specific database
2051 names without regular expressions also offer links from
2055 <!-- JAL-2315-->Removing a single configured link in the
2056 URL links pane in Connections preferences doesn't actually
2057 update Jalview configuration
2060 <!-- JAL-2272-->CTRL-Click on a selected region to open
2061 the alignment area popup menu doesn't work on El-Capitan
2064 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2065 files with similarly named sequences if dropped onto the
2069 <!-- JAL-2312 -->Additional mappings are shown for PDB
2070 entries where more chains exist in the PDB accession than
2071 are reported in the SIFTS file
2074 <!-- JAL-2317-->Certain structures do not get mapped to
2075 the structure view when displayed with Chimera
2078 <!-- JAL-2317-->No chains shown in the Chimera view
2079 panel's View->Show Chains submenu
2082 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2083 work for wrapped alignment views
2086 <!--JAL-2197 -->Rename UI components for running JPred
2087 predictions from 'JNet' to 'JPred'
2090 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2091 corrupted when annotation panel vertical scroll is not at
2092 first annotation row
2095 <!--JAL-2332 -->Attempting to view structure for Hen
2096 lysozyme results in a PDB Client error dialog box
2099 <!-- JAL-2319 -->Structure View's mapping report switched
2100 ranges for PDB and sequence for SIFTS
2103 SIFTS 'Not_Observed' residues mapped to non-existant
2107 <!-- <em>New Known Issues</em>
2114 <td width="60" nowrap>
2115 <div align="center">
2116 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2117 <em>25/10/2016</em></strong>
2120 <td><em>Application</em>
2122 <li>3D Structure chooser opens with 'Cached structures'
2123 view if structures already loaded</li>
2124 <li>Progress bar reports models as they are loaded to
2125 structure views</li>
2131 <li>Colour by conservation always enabled and no tick
2132 shown in menu when BLOSUM or PID shading applied</li>
2133 <li>FER1_ARATH and FER2_ARATH labels were switched in
2134 example sequences/projects/trees</li>
2136 <em>Application</em>
2138 <li>Jalview projects with views of local PDB structure
2139 files saved on Windows cannot be opened on OSX</li>
2140 <li>Multiple structure views can be opened and superposed
2141 without timeout for structures with multiple models or
2142 multiple sequences in alignment</li>
2143 <li>Cannot import or associated local PDB files without a
2144 PDB ID HEADER line</li>
2145 <li>RMSD is not output in Jmol console when superposition
2147 <li>Drag and drop of URL from Browser fails for Linux and
2148 OSX versions earlier than El Capitan</li>
2149 <li>ENA client ignores invalid content from ENA server</li>
2150 <li>Exceptions are not raised in console when ENA client
2151 attempts to fetch non-existent IDs via Fetch DB Refs UI
2153 <li>Exceptions are not raised in console when a new view
2154 is created on the alignment</li>
2155 <li>OSX right-click fixed for group selections: CMD-click
2156 to insert/remove gaps in groups and CTRL-click to open group
2159 <em>Build and deployment</em>
2161 <li>URL link checker now copes with multi-line anchor
2164 <em>New Known Issues</em>
2166 <li>Drag and drop from URL links in browsers do not work
2173 <td width="60" nowrap>
2174 <div align="center">
2175 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2178 <td><em>General</em>
2181 <!-- JAL-2124 -->Updated Spanish translations.
2184 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2185 for importing structure data to Jalview. Enables mmCIF and
2189 <!-- JAL-192 --->Alignment ruler shows positions relative to
2193 <!-- JAL-2202 -->Position/residue shown in status bar when
2194 mousing over sequence associated annotation
2197 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2201 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2202 '()', canonical '[]' and invalid '{}' base pair populations
2206 <!-- JAL-2092 -->Feature settings popup menu options for
2207 showing or hiding columns containing a feature
2210 <!-- JAL-1557 -->Edit selected group by double clicking on
2211 group and sequence associated annotation labels
2214 <!-- JAL-2236 -->Sequence name added to annotation label in
2215 select/hide columns by annotation and colour by annotation
2219 </ul> <em>Application</em>
2222 <!-- JAL-2050-->Automatically hide introns when opening a
2223 gene/transcript view
2226 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2230 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2231 structure mappings with the EMBL-EBI PDBe SIFTS database
2234 <!-- JAL-2079 -->Updated download sites used for Rfam and
2235 Pfam sources to xfam.org
2238 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2241 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2242 over sequences in Jalview
2245 <!-- JAL-2027-->Support for reverse-complement coding
2246 regions in ENA and EMBL
2249 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2250 for record retrieval via ENA rest API
2253 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2257 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2258 groovy script execution
2261 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2262 alignment window's Calculate menu
2265 <!-- JAL-1812 -->Allow groovy scripts that call
2266 Jalview.getAlignFrames() to run in headless mode
2269 <!-- JAL-2068 -->Support for creating new alignment
2270 calculation workers from groovy scripts
2273 <!-- JAL-1369 --->Store/restore reference sequence in
2277 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2278 associations are now saved/restored from project
2281 <!-- JAL-1993 -->Database selection dialog always shown
2282 before sequence fetcher is opened
2285 <!-- JAL-2183 -->Double click on an entry in Jalview's
2286 database chooser opens a sequence fetcher
2289 <!-- JAL-1563 -->Free-text search client for UniProt using
2290 the UniProt REST API
2293 <!-- JAL-2168 -->-nonews command line parameter to prevent
2294 the news reader opening
2297 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2298 querying stored in preferences
2301 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2305 <!-- JAL-1977-->Tooltips shown on database chooser
2308 <!-- JAL-391 -->Reverse complement function in calculate
2309 menu for nucleotide sequences
2312 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2313 and feature counts preserves alignment ordering (and
2314 debugged for complex feature sets).
2317 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2318 viewing structures with Jalview 2.10
2321 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2322 genome, transcript CCDS and gene ids via the Ensembl and
2323 Ensembl Genomes REST API
2326 <!-- JAL-2049 -->Protein sequence variant annotation
2327 computed for 'sequence_variant' annotation on CDS regions
2331 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2335 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2336 Ref Fetcher fails to match, or otherwise updates sequence
2337 data from external database records.
2340 <!-- JAL-2154 -->Revised Jalview Project format for
2341 efficient recovery of sequence coding and alignment
2342 annotation relationships.
2344 </ul> <!-- <em>Applet</em>
2355 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2359 <!-- JAL-2018-->Export features in Jalview format (again)
2360 includes graduated colourschemes
2363 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2364 working with big alignments and lots of hidden columns
2367 <!-- JAL-2053-->Hidden column markers not always rendered
2368 at right of alignment window
2371 <!-- JAL-2067 -->Tidied up links in help file table of
2375 <!-- JAL-2072 -->Feature based tree calculation not shown
2379 <!-- JAL-2075 -->Hidden columns ignored during feature
2380 based tree calculation
2383 <!-- JAL-2065 -->Alignment view stops updating when show
2384 unconserved enabled for group on alignment
2387 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2391 <!-- JAL-2146 -->Alignment column in status incorrectly
2392 shown as "Sequence position" when mousing over
2396 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2397 hidden columns present
2400 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2401 user created annotation added to alignment
2404 <!-- JAL-1841 -->RNA Structure consensus only computed for
2405 '()' base pair annotation
2408 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2409 in zero scores for all base pairs in RNA Structure
2413 <!-- JAL-2174-->Extend selection with columns containing
2417 <!-- JAL-2275 -->Pfam format writer puts extra space at
2418 beginning of sequence
2421 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2425 <!-- JAL-2238 -->Cannot create groups on an alignment from
2426 from a tree when t-coffee scores are shown
2429 <!-- JAL-1836,1967 -->Cannot import and view PDB
2430 structures with chains containing negative resnums (4q4h)
2433 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2437 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2438 to Clustal, PIR and PileUp output
2441 <!-- JAL-2008 -->Reordering sequence features that are
2442 not visible causes alignment window to repaint
2445 <!-- JAL-2006 -->Threshold sliders don't work in
2446 graduated colour and colour by annotation row for e-value
2447 scores associated with features and annotation rows
2450 <!-- JAL-1797 -->amino acid physicochemical conservation
2451 calculation should be case independent
2454 <!-- JAL-2173 -->Remove annotation also updates hidden
2458 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2459 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2460 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2463 <!-- JAL-2065 -->Null pointer exceptions and redraw
2464 problems when reference sequence defined and 'show
2465 non-conserved' enabled
2468 <!-- JAL-1306 -->Quality and Conservation are now shown on
2469 load even when Consensus calculation is disabled
2472 <!-- JAL-1932 -->Remove right on penultimate column of
2473 alignment does nothing
2476 <em>Application</em>
2479 <!-- JAL-1552-->URLs and links can't be imported by
2480 drag'n'drop on OSX when launched via webstart (note - not
2481 yet fixed for El Capitan)
2484 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2485 output when running on non-gb/us i18n platforms
2488 <!-- JAL-1944 -->Error thrown when exporting a view with
2489 hidden sequences as flat-file alignment
2492 <!-- JAL-2030-->InstallAnywhere distribution fails when
2496 <!-- JAL-2080-->Jalview very slow to launch via webstart
2497 (also hotfix for 2.9.0b2)
2500 <!-- JAL-2085 -->Cannot save project when view has a
2501 reference sequence defined
2504 <!-- JAL-1011 -->Columns are suddenly selected in other
2505 alignments and views when revealing hidden columns
2508 <!-- JAL-1989 -->Hide columns not mirrored in complement
2509 view in a cDNA/Protein splitframe
2512 <!-- JAL-1369 -->Cannot save/restore representative
2513 sequence from project when only one sequence is
2517 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2518 in Structure Chooser
2521 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2522 structure consensus didn't refresh annotation panel
2525 <!-- JAL-1962 -->View mapping in structure view shows
2526 mappings between sequence and all chains in a PDB file
2529 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2530 dialogs format columns correctly, don't display array
2531 data, sort columns according to type
2534 <!-- JAL-1975 -->Export complete shown after destination
2535 file chooser is cancelled during an image export
2538 <!-- JAL-2025 -->Error when querying PDB Service with
2539 sequence name containing special characters
2542 <!-- JAL-2024 -->Manual PDB structure querying should be
2546 <!-- JAL-2104 -->Large tooltips with broken HTML
2547 formatting don't wrap
2550 <!-- JAL-1128 -->Figures exported from wrapped view are
2551 truncated so L looks like I in consensus annotation
2554 <!-- JAL-2003 -->Export features should only export the
2555 currently displayed features for the current selection or
2559 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2560 after fetching cross-references, and restoring from
2564 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2565 followed in the structure viewer
2568 <!-- JAL-2163 -->Titles for individual alignments in
2569 splitframe not restored from project
2572 <!-- JAL-2145 -->missing autocalculated annotation at
2573 trailing end of protein alignment in transcript/product
2574 splitview when pad-gaps not enabled by default
2577 <!-- JAL-1797 -->amino acid physicochemical conservation
2581 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2582 article has been read (reopened issue due to
2583 internationalisation problems)
2586 <!-- JAL-1960 -->Only offer PDB structures in structure
2587 viewer based on sequence name, PDB and UniProt
2592 <!-- JAL-1976 -->No progress bar shown during export of
2596 <!-- JAL-2213 -->Structures not always superimposed after
2597 multiple structures are shown for one or more sequences.
2600 <!-- JAL-1370 -->Reference sequence characters should not
2601 be replaced with '.' when 'Show unconserved' format option
2605 <!-- JAL-1823 -->Cannot specify chain code when entering
2606 specific PDB id for sequence
2609 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2610 'Export hidden sequences' is enabled, but 'export hidden
2611 columns' is disabled.
2614 <!--JAL-2026-->Best Quality option in structure chooser
2615 selects lowest rather than highest resolution structures
2619 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2620 to sequence mapping in 'View Mappings' report
2623 <!-- JAL-2284 -->Unable to read old Jalview projects that
2624 contain non-XML data added after Jalvew wrote project.
2627 <!-- JAL-2118 -->Newly created annotation row reorders
2628 after clicking on it to create new annotation for a
2632 <!-- JAL-1980 -->Null Pointer Exception raised when
2633 pressing Add on an orphaned cut'n'paste window.
2635 <!-- may exclude, this is an external service stability issue JAL-1941
2636 -- > RNA 3D structure not added via DSSR service</li> -->
2641 <!-- JAL-2151 -->Incorrect columns are selected when
2642 hidden columns present before start of sequence
2645 <!-- JAL-1986 -->Missing dependencies on applet pages
2649 <!-- JAL-1947 -->Overview pixel size changes when
2650 sequences are hidden in applet
2653 <!-- JAL-1996 -->Updated instructions for applet
2654 deployment on examples pages.
2661 <td width="60" nowrap>
2662 <div align="center">
2663 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2664 <em>16/10/2015</em></strong>
2667 <td><em>General</em>
2669 <li>Time stamps for signed Jalview application and applet
2674 <em>Application</em>
2676 <li>Duplicate group consensus and conservation rows
2677 shown when tree is partitioned</li>
2678 <li>Erratic behaviour when tree partitions made with
2679 multiple cDNA/Protein split views</li>
2685 <td width="60" nowrap>
2686 <div align="center">
2687 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2688 <em>8/10/2015</em></strong>
2691 <td><em>General</em>
2693 <li>Updated Spanish translations of localized text for
2695 </ul> <em>Application</em>
2697 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2698 <li>Signed OSX InstallAnywhere installer<br></li>
2699 <li>Support for per-sequence based annotations in BioJSON</li>
2700 </ul> <em>Applet</em>
2702 <li>Split frame example added to applet examples page</li>
2703 </ul> <em>Build and Deployment</em>
2706 <!-- JAL-1888 -->New ant target for running Jalview's test
2714 <li>Mapping of cDNA to protein in split frames
2715 incorrect when sequence start > 1</li>
2716 <li>Broken images in filter column by annotation dialog
2718 <li>Feature colours not parsed from features file</li>
2719 <li>Exceptions and incomplete link URLs recovered when
2720 loading a features file containing HTML tags in feature
2724 <em>Application</em>
2726 <li>Annotations corrupted after BioJS export and
2728 <li>Incorrect sequence limits after Fetch DB References
2729 with 'trim retrieved sequences'</li>
2730 <li>Incorrect warning about deleting all data when
2731 deleting selected columns</li>
2732 <li>Patch to build system for shipping properly signed
2733 JNLP templates for webstart launch</li>
2734 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2735 unreleased structures for download or viewing</li>
2736 <li>Tab/space/return keystroke operation of EMBL-PDBe
2737 fetcher/viewer dialogs works correctly</li>
2738 <li>Disabled 'minimise' button on Jalview windows
2739 running on OSX to workaround redraw hang bug</li>
2740 <li>Split cDNA/Protein view position and geometry not
2741 recovered from jalview project</li>
2742 <li>Initial enabled/disabled state of annotation menu
2743 sorter 'show autocalculated first/last' corresponds to
2745 <li>Restoring of Clustal, RNA Helices and T-Coffee
2746 color schemes from BioJSON</li>
2750 <li>Reorder sequences mirrored in cDNA/Protein split
2752 <li>Applet with Jmol examples not loading correctly</li>
2758 <td><div align="center">
2759 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2761 <td><em>General</em>
2763 <li>Linked visualisation and analysis of DNA and Protein
2766 <li>Translated cDNA alignments shown as split protein
2767 and DNA alignment views</li>
2768 <li>Codon consensus annotation for linked protein and
2769 cDNA alignment views</li>
2770 <li>Link cDNA or Protein product sequences by loading
2771 them onto Protein or cDNA alignments</li>
2772 <li>Reconstruct linked cDNA alignment from aligned
2773 protein sequences</li>
2776 <li>Jmol integration updated to Jmol v14.2.14</li>
2777 <li>Import and export of Jalview alignment views as <a
2778 href="features/bioJsonFormat.html">BioJSON</a></li>
2779 <li>New alignment annotation file statements for
2780 reference sequences and marking hidden columns</li>
2781 <li>Reference sequence based alignment shading to
2782 highlight variation</li>
2783 <li>Select or hide columns according to alignment
2785 <li>Find option for locating sequences by description</li>
2786 <li>Conserved physicochemical properties shown in amino
2787 acid conservation row</li>
2788 <li>Alignments can be sorted by number of RNA helices</li>
2789 </ul> <em>Application</em>
2791 <li>New cDNA/Protein analysis capabilities
2793 <li>Get Cross-References should open a Split Frame
2794 view with cDNA/Protein</li>
2795 <li>Detect when nucleotide sequences and protein
2796 sequences are placed in the same alignment</li>
2797 <li>Split cDNA/Protein views are saved in Jalview
2802 <li>Use REST API to talk to Chimera</li>
2803 <li>Selected regions in Chimera are highlighted in linked
2804 Jalview windows</li>
2806 <li>VARNA RNA viewer updated to v3.93</li>
2807 <li>VARNA views are saved in Jalview Projects</li>
2808 <li>Pseudoknots displayed as Jalview RNA annotation can
2809 be shown in VARNA</li>
2811 <li>Make groups for selection uses marked columns as well
2812 as the active selected region</li>
2814 <li>Calculate UPGMA and NJ trees using sequence feature
2816 <li>New Export options
2818 <li>New Export Settings dialog to control hidden
2819 region export in flat file generation</li>
2821 <li>Export alignment views for display with the <a
2822 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2824 <li>Export scrollable SVG in HTML page</li>
2825 <li>Optional embedding of BioJSON data when exporting
2826 alignment figures to HTML</li>
2828 <li>3D structure retrieval and display
2830 <li>Free text and structured queries with the PDBe
2832 <li>PDBe Search API based discovery and selection of
2833 PDB structures for a sequence set</li>
2837 <li>JPred4 employed for protein secondary structure
2839 <li>Hide Insertions menu option to hide unaligned columns
2840 for one or a group of sequences</li>
2841 <li>Automatically hide insertions in alignments imported
2842 from the JPred4 web server</li>
2843 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2844 system on OSX<br />LGPL libraries courtesy of <a
2845 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2847 <li>changed 'View nucleotide structure' submenu to 'View
2848 VARNA 2D Structure'</li>
2849 <li>change "View protein structure" menu option to "3D
2852 </ul> <em>Applet</em>
2854 <li>New layout for applet example pages</li>
2855 <li>New parameters to enable SplitFrame view
2856 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2857 <li>New example demonstrating linked viewing of cDNA and
2858 Protein alignments</li>
2859 </ul> <em>Development and deployment</em>
2861 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2862 <li>Include installation type and git revision in build
2863 properties and console log output</li>
2864 <li>Jalview Github organisation, and new github site for
2865 storing BioJsMSA Templates</li>
2866 <li>Jalview's unit tests now managed with TestNG</li>
2869 <!-- <em>General</em>
2871 </ul> --> <!-- issues resolved --> <em>Application</em>
2873 <li>Escape should close any open find dialogs</li>
2874 <li>Typo in select-by-features status report</li>
2875 <li>Consensus RNA secondary secondary structure
2876 predictions are not highlighted in amber</li>
2877 <li>Missing gap character in v2.7 example file means
2878 alignment appears unaligned when pad-gaps is not enabled</li>
2879 <li>First switch to RNA Helices colouring doesn't colour
2880 associated structure views</li>
2881 <li>ID width preference option is greyed out when auto
2882 width checkbox not enabled</li>
2883 <li>Stopped a warning dialog from being shown when
2884 creating user defined colours</li>
2885 <li>'View Mapping' in structure viewer shows sequence
2886 mappings for just that viewer's sequences</li>
2887 <li>Workaround for superposing PDB files containing
2888 multiple models in Chimera</li>
2889 <li>Report sequence position in status bar when hovering
2890 over Jmol structure</li>
2891 <li>Cannot output gaps as '.' symbols with Selection ->
2892 output to text box</li>
2893 <li>Flat file exports of alignments with hidden columns
2894 have incorrect sequence start/end</li>
2895 <li>'Aligning' a second chain to a Chimera structure from
2897 <li>Colour schemes applied to structure viewers don't
2898 work for nucleotide</li>
2899 <li>Loading/cut'n'pasting an empty or invalid file leads
2900 to a grey/invisible alignment window</li>
2901 <li>Exported Jpred annotation from a sequence region
2902 imports to different position</li>
2903 <li>Space at beginning of sequence feature tooltips shown
2904 on some platforms</li>
2905 <li>Chimera viewer 'View | Show Chain' menu is not
2907 <li>'New View' fails with a Null Pointer Exception in
2908 console if Chimera has been opened</li>
2909 <li>Mouseover to Chimera not working</li>
2910 <li>Miscellaneous ENA XML feature qualifiers not
2912 <li>NPE in annotation renderer after 'Extract Scores'</li>
2913 <li>If two structures in one Chimera window, mouseover of
2914 either sequence shows on first structure</li>
2915 <li>'Show annotations' options should not make
2916 non-positional annotations visible</li>
2917 <li>Subsequence secondary structure annotation not shown
2918 in right place after 'view flanking regions'</li>
2919 <li>File Save As type unset when current file format is
2921 <li>Save as '.jar' option removed for saving Jalview
2923 <li>Colour by Sequence colouring in Chimera more
2925 <li>Cannot 'add reference annotation' for a sequence in
2926 several views on same alignment</li>
2927 <li>Cannot show linked products for EMBL / ENA records</li>
2928 <li>Jalview's tooltip wraps long texts containing no
2930 </ul> <em>Applet</em>
2932 <li>Jmol to JalviewLite mouseover/link not working</li>
2933 <li>JalviewLite can't import sequences with ID
2934 descriptions containing angle brackets</li>
2935 </ul> <em>General</em>
2937 <li>Cannot export and reimport RNA secondary structure
2938 via jalview annotation file</li>
2939 <li>Random helix colour palette for colour by annotation
2940 with RNA secondary structure</li>
2941 <li>Mouseover to cDNA from STOP residue in protein
2942 translation doesn't work.</li>
2943 <li>hints when using the select by annotation dialog box</li>
2944 <li>Jmol alignment incorrect if PDB file has alternate CA
2946 <li>FontChooser message dialog appears to hang after
2947 choosing 1pt font</li>
2948 <li>Peptide secondary structure incorrectly imported from
2949 annotation file when annotation display text includes 'e' or
2951 <li>Cannot set colour of new feature type whilst creating
2953 <li>cDNA translation alignment should not be sequence
2954 order dependent</li>
2955 <li>'Show unconserved' doesn't work for lower case
2957 <li>Nucleotide ambiguity codes involving R not recognised</li>
2958 </ul> <em>Deployment and Documentation</em>
2960 <li>Applet example pages appear different to the rest of
2961 www.jalview.org</li>
2962 </ul> <em>Application Known issues</em>
2964 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2965 <li>Misleading message appears after trying to delete
2967 <li>Jalview icon not shown in dock after InstallAnywhere
2968 version launches</li>
2969 <li>Fetching EMBL reference for an RNA sequence results
2970 fails with a sequence mismatch</li>
2971 <li>Corrupted or unreadable alignment display when
2972 scrolling alignment to right</li>
2973 <li>ArrayIndexOutOfBoundsException thrown when remove
2974 empty columns called on alignment with ragged gapped ends</li>
2975 <li>auto calculated alignment annotation rows do not get
2976 placed above or below non-autocalculated rows</li>
2977 <li>Jalview dekstop becomes sluggish at full screen in
2978 ultra-high resolution</li>
2979 <li>Cannot disable consensus calculation independently of
2980 quality and conservation</li>
2981 <li>Mouseover highlighting between cDNA and protein can
2982 become sluggish with more than one splitframe shown</li>
2983 </ul> <em>Applet Known Issues</em>
2985 <li>Core PDB parsing code requires Jmol</li>
2986 <li>Sequence canvas panel goes white when alignment
2987 window is being resized</li>
2993 <td><div align="center">
2994 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2996 <td><em>General</em>
2998 <li>Updated Java code signing certificate donated by
3000 <li>Features and annotation preserved when performing
3001 pairwise alignment</li>
3002 <li>RNA pseudoknot annotation can be
3003 imported/exported/displayed</li>
3004 <li>'colour by annotation' can colour by RNA and
3005 protein secondary structure</li>
3006 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3007 post-hoc with 2.9 release</em>)
3010 </ul> <em>Application</em>
3012 <li>Extract and display secondary structure for sequences
3013 with 3D structures</li>
3014 <li>Support for parsing RNAML</li>
3015 <li>Annotations menu for layout
3017 <li>sort sequence annotation rows by alignment</li>
3018 <li>place sequence annotation above/below alignment
3021 <li>Output in Stockholm format</li>
3022 <li>Internationalisation: improved Spanish (es)
3024 <li>Structure viewer preferences tab</li>
3025 <li>Disorder and Secondary Structure annotation tracks
3026 shared between alignments</li>
3027 <li>UCSF Chimera launch and linked highlighting from
3029 <li>Show/hide all sequence associated annotation rows for
3030 all or current selection</li>
3031 <li>disorder and secondary structure predictions
3032 available as dataset annotation</li>
3033 <li>Per-sequence rna helices colouring</li>
3036 <li>Sequence database accessions imported when fetching
3037 alignments from Rfam</li>
3038 <li>update VARNA version to 3.91</li>
3040 <li>New groovy scripts for exporting aligned positions,
3041 conservation values, and calculating sum of pairs scores.</li>
3042 <li>Command line argument to set default JABAWS server</li>
3043 <li>include installation type in build properties and
3044 console log output</li>
3045 <li>Updated Jalview project format to preserve dataset
3049 <!-- issues resolved --> <em>Application</em>
3051 <li>Distinguish alignment and sequence associated RNA
3052 structure in structure->view->VARNA</li>
3053 <li>Raise dialog box if user deletes all sequences in an
3055 <li>Pressing F1 results in documentation opening twice</li>
3056 <li>Sequence feature tooltip is wrapped</li>
3057 <li>Double click on sequence associated annotation
3058 selects only first column</li>
3059 <li>Redundancy removal doesn't result in unlinked
3060 leaves shown in tree</li>
3061 <li>Undos after several redundancy removals don't undo
3063 <li>Hide sequence doesn't hide associated annotation</li>
3064 <li>User defined colours dialog box too big to fit on
3065 screen and buttons not visible</li>
3066 <li>author list isn't updated if already written to
3067 Jalview properties</li>
3068 <li>Popup menu won't open after retrieving sequence
3070 <li>File open window for associate PDB doesn't open</li>
3071 <li>Left-then-right click on a sequence id opens a
3072 browser search window</li>
3073 <li>Cannot open sequence feature shading/sort popup menu
3074 in feature settings dialog</li>
3075 <li>better tooltip placement for some areas of Jalview
3077 <li>Allow addition of JABAWS Server which doesn't
3078 pass validation</li>
3079 <li>Web services parameters dialog box is too large to
3081 <li>Muscle nucleotide alignment preset obscured by
3083 <li>JABAWS preset submenus don't contain newly
3084 defined user preset</li>
3085 <li>MSA web services warns user if they were launched
3086 with invalid input</li>
3087 <li>Jalview cannot contact DAS Registy when running on
3090 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3091 'Superpose with' submenu not shown when new view
3095 </ul> <!-- <em>Applet</em>
3097 </ul> <em>General</em>
3099 </ul>--> <em>Deployment and Documentation</em>
3101 <li>2G and 1G options in launchApp have no effect on
3102 memory allocation</li>
3103 <li>launchApp service doesn't automatically open
3104 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3106 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3107 InstallAnywhere reports cannot find valid JVM when Java
3108 1.7_055 is available
3110 </ul> <em>Application Known issues</em>
3113 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3114 corrupted or unreadable alignment display when scrolling
3118 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3119 retrieval fails but progress bar continues for DAS retrieval
3120 with large number of ID
3123 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3124 flatfile output of visible region has incorrect sequence
3128 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3129 rna structure consensus doesn't update when secondary
3130 structure tracks are rearranged
3133 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3134 invalid rna structure positional highlighting does not
3135 highlight position of invalid base pairs
3138 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3139 out of memory errors are not raised when saving Jalview
3140 project from alignment window file menu
3143 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3144 Switching to RNA Helices colouring doesn't propagate to
3148 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3149 colour by RNA Helices not enabled when user created
3150 annotation added to alignment
3153 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3154 Jalview icon not shown on dock in Mountain Lion/Webstart
3156 </ul> <em>Applet Known Issues</em>
3159 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3160 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3163 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3164 Jalview and Jmol example not compatible with IE9
3167 <li>Sort by annotation score doesn't reverse order
3173 <td><div align="center">
3174 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3177 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3180 <li>Internationalisation of user interface (usually
3181 called i18n support) and translation for Spanish locale</li>
3182 <li>Define/Undefine group on current selection with
3183 Ctrl-G/Shift Ctrl-G</li>
3184 <li>Improved group creation/removal options in
3185 alignment/sequence Popup menu</li>
3186 <li>Sensible precision for symbol distribution
3187 percentages shown in logo tooltip.</li>
3188 <li>Annotation panel height set according to amount of
3189 annotation when alignment first opened</li>
3190 </ul> <em>Application</em>
3192 <li>Interactive consensus RNA secondary structure
3193 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3194 <li>Select columns containing particular features from
3195 Feature Settings dialog</li>
3196 <li>View all 'representative' PDB structures for selected
3198 <li>Update Jalview project format:
3200 <li>New file extension for Jalview projects '.jvp'</li>
3201 <li>Preserve sequence and annotation dataset (to
3202 store secondary structure annotation,etc)</li>
3203 <li>Per group and alignment annotation and RNA helix
3207 <li>New similarity measures for PCA and Tree calculation
3209 <li>Experimental support for retrieval and viewing of
3210 flanking regions for an alignment</li>
3214 <!-- issues resolved --> <em>Application</em>
3216 <li>logo keeps spinning and status remains at queued or
3217 running after job is cancelled</li>
3218 <li>cannot export features from alignments imported from
3219 Jalview/VAMSAS projects</li>
3220 <li>Buggy slider for web service parameters that take
3222 <li>Newly created RNA secondary structure line doesn't
3223 have 'display all symbols' flag set</li>
3224 <li>T-COFFEE alignment score shading scheme and other
3225 annotation shading not saved in Jalview project</li>
3226 <li>Local file cannot be loaded in freshly downloaded
3228 <li>Jalview icon not shown on dock in Mountain
3230 <li>Load file from desktop file browser fails</li>
3231 <li>Occasional NPE thrown when calculating large trees</li>
3232 <li>Cannot reorder or slide sequences after dragging an
3233 alignment onto desktop</li>
3234 <li>Colour by annotation dialog throws NPE after using
3235 'extract scores' function</li>
3236 <li>Loading/cut'n'pasting an empty file leads to a grey
3237 alignment window</li>
3238 <li>Disorder thresholds rendered incorrectly after
3239 performing IUPred disorder prediction</li>
3240 <li>Multiple group annotated consensus rows shown when
3241 changing 'normalise logo' display setting</li>
3242 <li>Find shows blank dialog after 'finished searching' if
3243 nothing matches query</li>
3244 <li>Null Pointer Exceptions raised when sorting by
3245 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3247 <li>Errors in Jmol console when structures in alignment
3248 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3250 <li>Not all working JABAWS services are shown in
3252 <li>JAVAWS version of Jalview fails to launch with
3253 'invalid literal/length code'</li>
3254 <li>Annotation/RNA Helix colourschemes cannot be applied
3255 to alignment with groups (actually fixed in 2.8.0b1)</li>
3256 <li>RNA Helices and T-Coffee Scores available as default
3259 </ul> <em>Applet</em>
3261 <li>Remove group option is shown even when selection is
3263 <li>Apply to all groups ticked but colourscheme changes
3264 don't affect groups</li>
3265 <li>Documented RNA Helices and T-Coffee Scores as valid
3266 colourscheme name</li>
3267 <li>Annotation labels drawn on sequence IDs when
3268 Annotation panel is not displayed</li>
3269 <li>Increased font size for dropdown menus on OSX and
3270 embedded windows</li>
3271 </ul> <em>Other</em>
3273 <li>Consensus sequence for alignments/groups with a
3274 single sequence were not calculated</li>
3275 <li>annotation files that contain only groups imported as
3276 annotation and junk sequences</li>
3277 <li>Fasta files with sequences containing '*' incorrectly
3278 recognised as PFAM or BLC</li>
3279 <li>conservation/PID slider apply all groups option
3280 doesn't affect background (2.8.0b1)
3282 <li>redundancy highlighting is erratic at 0% and 100%</li>
3283 <li>Remove gapped columns fails for sequences with ragged
3285 <li>AMSA annotation row with leading spaces is not
3286 registered correctly on import</li>
3287 <li>Jalview crashes when selecting PCA analysis for
3288 certain alignments</li>
3289 <li>Opening the colour by annotation dialog for an
3290 existing annotation based 'use original colours'
3291 colourscheme loses original colours setting</li>
3296 <td><div align="center">
3297 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3298 <em>30/1/2014</em></strong>
3302 <li>Trusted certificates for JalviewLite applet and
3303 Jalview Desktop application<br />Certificate was donated by
3304 <a href="https://www.certum.eu">Certum</a> to the Jalview
3305 open source project).
3307 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3308 <li>Output in Stockholm format</li>
3309 <li>Allow import of data from gzipped files</li>
3310 <li>Export/import group and sequence associated line
3311 graph thresholds</li>
3312 <li>Nucleotide substitution matrix that supports RNA and
3313 ambiguity codes</li>
3314 <li>Allow disorder predictions to be made on the current
3315 selection (or visible selection) in the same way that JPred
3317 <li>Groovy scripting for headless Jalview operation</li>
3318 </ul> <em>Other improvements</em>
3320 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3321 <li>COMBINE statement uses current SEQUENCE_REF and
3322 GROUP_REF scope to group annotation rows</li>
3323 <li>Support '' style escaping of quotes in Newick
3325 <li>Group options for JABAWS service by command line name</li>
3326 <li>Empty tooltip shown for JABA service options with a
3327 link but no description</li>
3328 <li>Select primary source when selecting authority in
3329 database fetcher GUI</li>
3330 <li>Add .mfa to FASTA file extensions recognised by
3332 <li>Annotation label tooltip text wrap</li>
3337 <li>Slow scrolling when lots of annotation rows are
3339 <li>Lots of NPE (and slowness) after creating RNA
3340 secondary structure annotation line</li>
3341 <li>Sequence database accessions not imported when
3342 fetching alignments from Rfam</li>
3343 <li>Incorrect SHMR submission for sequences with
3345 <li>View all structures does not always superpose
3347 <li>Option widgets in service parameters not updated to
3348 reflect user or preset settings</li>
3349 <li>Null pointer exceptions for some services without
3350 presets or adjustable parameters</li>
3351 <li>Discover PDB IDs entry in structure menu doesn't
3352 discover PDB xRefs</li>
3353 <li>Exception encountered while trying to retrieve
3354 features with DAS</li>
3355 <li>Lowest value in annotation row isn't coloured
3356 when colour by annotation (per sequence) is coloured</li>
3357 <li>Keyboard mode P jumps to start of gapped region when
3358 residue follows a gap</li>
3359 <li>Jalview appears to hang importing an alignment with
3360 Wrap as default or after enabling Wrap</li>
3361 <li>'Right click to add annotations' message
3362 shown in wrap mode when no annotations present</li>
3363 <li>Disorder predictions fail with NPE if no automatic
3364 annotation already exists on alignment</li>
3365 <li>oninit javascript function should be called after
3366 initialisation completes</li>
3367 <li>Remove redundancy after disorder prediction corrupts
3368 alignment window display</li>
3369 <li>Example annotation file in documentation is invalid</li>
3370 <li>Grouped line graph annotation rows are not exported
3371 to annotation file</li>
3372 <li>Multi-harmony analysis cannot be run when only two
3374 <li>Cannot create multiple groups of line graphs with
3375 several 'combine' statements in annotation file</li>
3376 <li>Pressing return several times causes Number Format
3377 exceptions in keyboard mode</li>
3378 <li>Multi-harmony (SHMMR) method doesn't submit
3379 correct partitions for input data</li>
3380 <li>Translation from DNA to Amino Acids fails</li>
3381 <li>Jalview fail to load newick tree with quoted label</li>
3382 <li>--headless flag isn't understood</li>
3383 <li>ClassCastException when generating EPS in headless
3385 <li>Adjusting sequence-associated shading threshold only
3386 changes one row's threshold</li>
3387 <li>Preferences and Feature settings panel panel
3388 doesn't open</li>
3389 <li>hide consensus histogram also hides conservation and
3390 quality histograms</li>
3395 <td><div align="center">
3396 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3398 <td><em>Application</em>
3400 <li>Support for JABAWS 2.0 Services (AACon alignment
3401 conservation, protein disorder and Clustal Omega)</li>
3402 <li>JABAWS server status indicator in Web Services
3404 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3405 in Jalview alignment window</li>
3406 <li>Updated Jalview build and deploy framework for OSX
3407 mountain lion, windows 7, and 8</li>
3408 <li>Nucleotide substitution matrix for PCA that supports
3409 RNA and ambiguity codes</li>
3411 <li>Improved sequence database retrieval GUI</li>
3412 <li>Support fetching and database reference look up
3413 against multiple DAS sources (Fetch all from in 'fetch db
3415 <li>Jalview project improvements
3417 <li>Store and retrieve the 'belowAlignment'
3418 flag for annotation</li>
3419 <li>calcId attribute to group annotation rows on the
3421 <li>Store AACon calculation settings for a view in
3422 Jalview project</li>
3426 <li>horizontal scrolling gesture support</li>
3427 <li>Visual progress indicator when PCA calculation is
3429 <li>Simpler JABA web services menus</li>
3430 <li>visual indication that web service results are still
3431 being retrieved from server</li>
3432 <li>Serialise the dialogs that are shown when Jalview
3433 starts up for first time</li>
3434 <li>Jalview user agent string for interacting with HTTP
3436 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3438 <li>Examples directory and Groovy library included in
3439 InstallAnywhere distribution</li>
3440 </ul> <em>Applet</em>
3442 <li>RNA alignment and secondary structure annotation
3443 visualization applet example</li>
3444 </ul> <em>General</em>
3446 <li>Normalise option for consensus sequence logo</li>
3447 <li>Reset button in PCA window to return dimensions to
3449 <li>Allow seqspace or Jalview variant of alignment PCA
3451 <li>PCA with either nucleic acid and protein substitution
3453 <li>Allow windows containing HTML reports to be exported
3455 <li>Interactive display and editing of RNA secondary
3456 structure contacts</li>
3457 <li>RNA Helix Alignment Colouring</li>
3458 <li>RNA base pair logo consensus</li>
3459 <li>Parse sequence associated secondary structure
3460 information in Stockholm files</li>
3461 <li>HTML Export database accessions and annotation
3462 information presented in tooltip for sequences</li>
3463 <li>Import secondary structure from LOCARNA clustalw
3464 style RNA alignment files</li>
3465 <li>import and visualise T-COFFEE quality scores for an
3467 <li>'colour by annotation' per sequence option to
3468 shade each sequence according to its associated alignment
3470 <li>New Jalview Logo</li>
3471 </ul> <em>Documentation and Development</em>
3473 <li>documentation for score matrices used in Jalview</li>
3474 <li>New Website!</li>
3476 <td><em>Application</em>
3478 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3479 wsdbfetch REST service</li>
3480 <li>Stop windows being moved outside desktop on OSX</li>
3481 <li>Filetype associations not installed for webstart
3483 <li>Jalview does not always retrieve progress of a JABAWS
3484 job execution in full once it is complete</li>
3485 <li>revise SHMR RSBS definition to ensure alignment is
3486 uploaded via ali_file parameter</li>
3487 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3488 <li>View all structures superposed fails with exception</li>
3489 <li>Jnet job queues forever if a very short sequence is
3490 submitted for prediction</li>
3491 <li>Cut and paste menu not opened when mouse clicked on
3493 <li>Putting fractional value into integer text box in
3494 alignment parameter dialog causes Jalview to hang</li>
3495 <li>Structure view highlighting doesn't work on
3497 <li>View all structures fails with exception shown in
3499 <li>Characters in filename associated with PDBEntry not
3500 escaped in a platform independent way</li>
3501 <li>Jalview desktop fails to launch with exception when
3503 <li>Tree calculation reports 'you must have 2 or more
3504 sequences selected' when selection is empty</li>
3505 <li>Jalview desktop fails to launch with jar signature
3506 failure when java web start temporary file caching is
3508 <li>DAS Sequence retrieval with range qualification
3509 results in sequence xref which includes range qualification</li>
3510 <li>Errors during processing of command line arguments
3511 cause progress bar (JAL-898) to be removed</li>
3512 <li>Replace comma for semi-colon option not disabled for
3513 DAS sources in sequence fetcher</li>
3514 <li>Cannot close news reader when JABAWS server warning
3515 dialog is shown</li>
3516 <li>Option widgets not updated to reflect user settings</li>
3517 <li>Edited sequence not submitted to web service</li>
3518 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3519 <li>InstallAnywhere installer doesn't unpack and run
3520 on OSX Mountain Lion</li>
3521 <li>Annotation panel not given a scroll bar when
3522 sequences with alignment annotation are pasted into the
3524 <li>Sequence associated annotation rows not associated
3525 when loaded from Jalview project</li>
3526 <li>Browser launch fails with NPE on java 1.7</li>
3527 <li>JABAWS alignment marked as finished when job was
3528 cancelled or job failed due to invalid input</li>
3529 <li>NPE with v2.7 example when clicking on Tree
3530 associated with all views</li>
3531 <li>Exceptions when copy/paste sequences with grouped
3532 annotation rows to new window</li>
3533 </ul> <em>Applet</em>
3535 <li>Sequence features are momentarily displayed before
3536 they are hidden using hidefeaturegroups applet parameter</li>
3537 <li>loading features via javascript API automatically
3538 enables feature display</li>
3539 <li>scrollToColumnIn javascript API method doesn't
3541 </ul> <em>General</em>
3543 <li>Redundancy removal fails for rna alignment</li>
3544 <li>PCA calculation fails when sequence has been selected
3545 and then deselected</li>
3546 <li>PCA window shows grey box when first opened on OSX</li>
3547 <li>Letters coloured pink in sequence logo when alignment
3548 coloured with clustalx</li>
3549 <li>Choosing fonts without letter symbols defined causes
3550 exceptions and redraw errors</li>
3551 <li>Initial PCA plot view is not same as manually
3552 reconfigured view</li>
3553 <li>Grouped annotation graph label has incorrect line
3555 <li>Grouped annotation graph label display is corrupted
3556 for lots of labels</li>
3561 <div align="center">
3562 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3565 <td><em>Application</em>
3567 <li>Jalview Desktop News Reader</li>
3568 <li>Tweaked default layout of web services menu</li>
3569 <li>View/alignment association menu to enable user to
3570 easily specify which alignment a multi-structure view takes
3571 its colours/correspondences from</li>
3572 <li>Allow properties file location to be specified as URL</li>
3573 <li>Extend Jalview project to preserve associations
3574 between many alignment views and a single Jmol display</li>
3575 <li>Store annotation row height in Jalview project file</li>
3576 <li>Annotation row column label formatting attributes
3577 stored in project file</li>
3578 <li>Annotation row order for auto-calculated annotation
3579 rows preserved in Jalview project file</li>
3580 <li>Visual progress indication when Jalview state is
3581 saved using Desktop window menu</li>
3582 <li>Visual indication that command line arguments are
3583 still being processed</li>
3584 <li>Groovy script execution from URL</li>
3585 <li>Colour by annotation default min and max colours in
3587 <li>Automatically associate PDB files dragged onto an
3588 alignment with sequences that have high similarity and
3590 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3591 <li>'view structures' option to open many
3592 structures in same window</li>
3593 <li>Sort associated views menu option for tree panel</li>
3594 <li>Group all JABA and non-JABA services for a particular
3595 analysis function in its own submenu</li>
3596 </ul> <em>Applet</em>
3598 <li>Userdefined and autogenerated annotation rows for
3600 <li>Adjustment of alignment annotation pane height</li>
3601 <li>Annotation scrollbar for annotation panel</li>
3602 <li>Drag to reorder annotation rows in annotation panel</li>
3603 <li>'automaticScrolling' parameter</li>
3604 <li>Allow sequences with partial ID string matches to be
3605 annotated from GFF/Jalview features files</li>
3606 <li>Sequence logo annotation row in applet</li>
3607 <li>Absolute paths relative to host server in applet
3608 parameters are treated as such</li>
3609 <li>New in the JalviewLite javascript API:
3611 <li>JalviewLite.js javascript library</li>
3612 <li>Javascript callbacks for
3614 <li>Applet initialisation</li>
3615 <li>Sequence/alignment mouse-overs and selections</li>
3618 <li>scrollTo row and column alignment scrolling
3620 <li>Select sequence/alignment regions from javascript</li>
3621 <li>javascript structure viewer harness to pass
3622 messages between Jmol and Jalview when running as
3623 distinct applets</li>
3624 <li>sortBy method</li>
3625 <li>Set of applet and application examples shipped
3626 with documentation</li>
3627 <li>New example to demonstrate JalviewLite and Jmol
3628 javascript message exchange</li>
3630 </ul> <em>General</em>
3632 <li>Enable Jmol displays to be associated with multiple
3633 multiple alignments</li>
3634 <li>Option to automatically sort alignment with new tree</li>
3635 <li>User configurable link to enable redirects to a
3636 www.Jalview.org mirror</li>
3637 <li>Jmol colours option for Jmol displays</li>
3638 <li>Configurable newline string when writing alignment
3639 and other flat files</li>
3640 <li>Allow alignment annotation description lines to
3641 contain html tags</li>
3642 </ul> <em>Documentation and Development</em>
3644 <li>Add groovy test harness for bulk load testing to
3646 <li>Groovy script to load and align a set of sequences
3647 using a web service before displaying the result in the
3648 Jalview desktop</li>
3649 <li>Restructured javascript and applet api documentation</li>
3650 <li>Ant target to publish example html files with applet
3652 <li>Netbeans project for building Jalview from source</li>
3653 <li>ant task to create online javadoc for Jalview source</li>
3655 <td><em>Application</em>
3657 <li>User defined colourscheme throws exception when
3658 current built in colourscheme is saved as new scheme</li>
3659 <li>AlignFrame->Save in application pops up save
3660 dialog for valid filename/format</li>
3661 <li>Cannot view associated structure for UniProt sequence</li>
3662 <li>PDB file association breaks for UniProt sequence
3664 <li>Associate PDB from file dialog does not tell you
3665 which sequence is to be associated with the file</li>
3666 <li>Find All raises null pointer exception when query
3667 only matches sequence IDs</li>
3668 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3669 <li>Jalview project with Jmol views created with Jalview
3670 2.4 cannot be loaded</li>
3671 <li>Filetype associations not installed for webstart
3673 <li>Two or more chains in a single PDB file associated
3674 with sequences in different alignments do not get coloured
3675 by their associated sequence</li>
3676 <li>Visibility status of autocalculated annotation row
3677 not preserved when project is loaded</li>
3678 <li>Annotation row height and visibility attributes not
3679 stored in Jalview project</li>
3680 <li>Tree bootstraps are not preserved when saved as a
3681 Jalview project</li>
3682 <li>Envision2 workflow tooltips are corrupted</li>
3683 <li>Enabling show group conservation also enables colour
3684 by conservation</li>
3685 <li>Duplicate group associated conservation or consensus
3686 created on new view</li>
3687 <li>Annotation scrollbar not displayed after 'show
3688 all hidden annotation rows' option selected</li>
3689 <li>Alignment quality not updated after alignment
3690 annotation row is hidden then shown</li>
3691 <li>Preserve colouring of structures coloured by
3692 sequences in pre Jalview 2.7 projects</li>
3693 <li>Web service job parameter dialog is not laid out
3695 <li>Web services menu not refreshed after 'reset
3696 services' button is pressed in preferences</li>
3697 <li>Annotation off by one in Jalview v2_3 example project</li>
3698 <li>Structures imported from file and saved in project
3699 get name like jalview_pdb1234.txt when reloaded</li>
3700 <li>Jalview does not always retrieve progress of a JABAWS
3701 job execution in full once it is complete</li>
3702 </ul> <em>Applet</em>
3704 <li>Alignment height set incorrectly when lots of
3705 annotation rows are displayed</li>
3706 <li>Relative URLs in feature HTML text not resolved to
3708 <li>View follows highlighting does not work for positions
3710 <li><= shown as = in tooltip</li>
3711 <li>Export features raises exception when no features
3713 <li>Separator string used for serialising lists of IDs
3714 for javascript api is modified when separator string
3715 provided as parameter</li>
3716 <li>Null pointer exception when selecting tree leaves for
3717 alignment with no existing selection</li>
3718 <li>Relative URLs for datasources assumed to be relative
3719 to applet's codebase</li>
3720 <li>Status bar not updated after finished searching and
3721 search wraps around to first result</li>
3722 <li>StructureSelectionManager instance shared between
3723 several Jalview applets causes race conditions and memory
3725 <li>Hover tooltip and mouseover of position on structure
3726 not sent from Jmol in applet</li>
3727 <li>Certain sequences of javascript method calls to
3728 applet API fatally hang browser</li>
3729 </ul> <em>General</em>
3731 <li>View follows structure mouseover scrolls beyond
3732 position with wrapped view and hidden regions</li>
3733 <li>Find sequence position moves to wrong residue
3734 with/without hidden columns</li>
3735 <li>Sequence length given in alignment properties window
3737 <li>InvalidNumberFormat exceptions thrown when trying to
3738 import PDB like structure files</li>
3739 <li>Positional search results are only highlighted
3740 between user-supplied sequence start/end bounds</li>
3741 <li>End attribute of sequence is not validated</li>
3742 <li>Find dialog only finds first sequence containing a
3743 given sequence position</li>
3744 <li>Sequence numbering not preserved in MSF alignment
3746 <li>Jalview PDB file reader does not extract sequence
3747 from nucleotide chains correctly</li>
3748 <li>Structure colours not updated when tree partition
3749 changed in alignment</li>
3750 <li>Sequence associated secondary structure not correctly
3751 parsed in interleaved stockholm</li>
3752 <li>Colour by annotation dialog does not restore current
3754 <li>Hiding (nearly) all sequences doesn't work
3756 <li>Sequences containing lowercase letters are not
3757 properly associated with their pdb files</li>
3758 </ul> <em>Documentation and Development</em>
3760 <li>schemas/JalviewWsParamSet.xsd corrupted by
3761 ApplyCopyright tool</li>
3766 <div align="center">
3767 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3770 <td><em>Application</em>
3772 <li>New warning dialog when the Jalview Desktop cannot
3773 contact web services</li>
3774 <li>JABA service parameters for a preset are shown in
3775 service job window</li>
3776 <li>JABA Service menu entries reworded</li>
3780 <li>Modeller PIR IO broken - cannot correctly import a
3781 pir file emitted by Jalview</li>
3782 <li>Existing feature settings transferred to new
3783 alignment view created from cut'n'paste</li>
3784 <li>Improved test for mixed amino/nucleotide chains when
3785 parsing PDB files</li>
3786 <li>Consensus and conservation annotation rows
3787 occasionally become blank for all new windows</li>
3788 <li>Exception raised when right clicking above sequences
3789 in wrapped view mode</li>
3790 </ul> <em>Application</em>
3792 <li>multiple multiply aligned structure views cause cpu
3793 usage to hit 100% and computer to hang</li>
3794 <li>Web Service parameter layout breaks for long user
3795 parameter names</li>
3796 <li>Jaba service discovery hangs desktop if Jaba server
3803 <div align="center">
3804 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3807 <td><em>Application</em>
3809 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3810 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3813 <li>Web Services preference tab</li>
3814 <li>Analysis parameters dialog box and user defined
3816 <li>Improved speed and layout of Envision2 service menu</li>
3817 <li>Superpose structures using associated sequence
3819 <li>Export coordinates and projection as CSV from PCA
3821 </ul> <em>Applet</em>
3823 <li>enable javascript: execution by the applet via the
3824 link out mechanism</li>
3825 </ul> <em>Other</em>
3827 <li>Updated the Jmol Jalview interface to work with Jmol
3829 <li>The Jalview Desktop and JalviewLite applet now
3830 require Java 1.5</li>
3831 <li>Allow Jalview feature colour specification for GFF
3832 sequence annotation files</li>
3833 <li>New 'colour by label' keword in Jalview feature file
3834 type colour specification</li>
3835 <li>New Jalview Desktop Groovy API method that allows a
3836 script to check if it being run in an interactive session or
3837 in a batch operation from the Jalview command line</li>
3841 <li>clustalx colourscheme colours Ds preferentially when
3842 both D+E are present in over 50% of the column</li>
3843 </ul> <em>Application</em>
3845 <li>typo in AlignmentFrame->View->Hide->all but
3846 selected Regions menu item</li>
3847 <li>sequence fetcher replaces ',' for ';' when the ',' is
3848 part of a valid accession ID</li>
3849 <li>fatal OOM if object retrieved by sequence fetcher
3850 runs out of memory</li>
3851 <li>unhandled Out of Memory Error when viewing pca
3852 analysis results</li>
3853 <li>InstallAnywhere builds fail to launch on OS X java
3854 10.5 update 4 (due to apple Java 1.6 update)</li>
3855 <li>Installanywhere Jalview silently fails to launch</li>
3856 </ul> <em>Applet</em>
3858 <li>Jalview.getFeatureGroups() raises an
3859 ArrayIndexOutOfBoundsException if no feature groups are
3866 <div align="center">
3867 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3873 <li>Alignment prettyprinter doesn't cope with long
3875 <li>clustalx colourscheme colours Ds preferentially when
3876 both D+E are present in over 50% of the column</li>
3877 <li>nucleic acid structures retrieved from PDB do not
3878 import correctly</li>
3879 <li>More columns get selected than were clicked on when a
3880 number of columns are hidden</li>
3881 <li>annotation label popup menu not providing correct
3882 add/hide/show options when rows are hidden or none are
3884 <li>Stockholm format shown in list of readable formats,
3885 and parser copes better with alignments from RFAM.</li>
3886 <li>CSV output of consensus only includes the percentage
3887 of all symbols if sequence logo display is enabled</li>
3889 </ul> <em>Applet</em>
3891 <li>annotation panel disappears when annotation is
3893 </ul> <em>Application</em>
3895 <li>Alignment view not redrawn properly when new
3896 alignment opened where annotation panel is visible but no
3897 annotations are present on alignment</li>
3898 <li>pasted region containing hidden columns is
3899 incorrectly displayed in new alignment window</li>
3900 <li>Jalview slow to complete operations when stdout is
3901 flooded (fix is to close the Jalview console)</li>
3902 <li>typo in AlignmentFrame->View->Hide->all but
3903 selected Rregions menu item.</li>
3904 <li>inconsistent group submenu and Format submenu entry
3905 'Un' or 'Non'conserved</li>
3906 <li>Sequence feature settings are being shared by
3907 multiple distinct alignments</li>
3908 <li>group annotation not recreated when tree partition is
3910 <li>double click on group annotation to select sequences
3911 does not propagate to associated trees</li>
3912 <li>Mac OSX specific issues:
3914 <li>exception raised when mouse clicked on desktop
3915 window background</li>
3916 <li>Desktop menu placed on menu bar and application
3917 name set correctly</li>
3918 <li>sequence feature settings not wide enough for the
3919 save feature colourscheme button</li>
3928 <div align="center">
3929 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3932 <td><em>New Capabilities</em>
3934 <li>URL links generated from description line for
3935 regular-expression based URL links (applet and application)
3937 <li>Non-positional feature URL links are shown in link
3939 <li>Linked viewing of nucleic acid sequences and
3941 <li>Automatic Scrolling option in View menu to display
3942 the currently highlighted region of an alignment.</li>
3943 <li>Order an alignment by sequence length, or using the
3944 average score or total feature count for each sequence.</li>
3945 <li>Shading features by score or associated description</li>
3946 <li>Subdivide alignment and groups based on identity of
3947 selected subsequence (Make Groups from Selection).</li>
3948 <li>New hide/show options including Shift+Control+H to
3949 hide everything but the currently selected region.</li>
3950 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3951 </ul> <em>Application</em>
3953 <li>Fetch DB References capabilities and UI expanded to
3954 support retrieval from DAS sequence sources</li>
3955 <li>Local DAS Sequence sources can be added via the
3956 command line or via the Add local source dialog box.</li>
3957 <li>DAS Dbref and DbxRef feature types are parsed as
3958 database references and protein_name is parsed as
3959 description line (BioSapiens terms).</li>
3960 <li>Enable or disable non-positional feature and database
3961 references in sequence ID tooltip from View menu in
3963 <!-- <li>New hidden columns and rows and representatives capabilities
3964 in annotations file (in progress - not yet fully implemented)</li> -->
3965 <li>Group-associated consensus, sequence logos and
3966 conservation plots</li>
3967 <li>Symbol distributions for each column can be exported
3968 and visualized as sequence logos</li>
3969 <li>Optionally scale multi-character column labels to fit
3970 within each column of annotation row<!-- todo for applet -->
3972 <li>Optional automatic sort of associated alignment view
3973 when a new tree is opened.</li>
3974 <li>Jalview Java Console</li>
3975 <li>Better placement of desktop window when moving
3976 between different screens.</li>
3977 <li>New preference items for sequence ID tooltip and
3978 consensus annotation</li>
3979 <li>Client to submit sequences and IDs to Envision2
3981 <li><em>Vamsas Capabilities</em>
3983 <li>Improved VAMSAS synchronization (Jalview archive
3984 used to preserve views, structures, and tree display
3986 <li>Import of vamsas documents from disk or URL via
3988 <li>Sharing of selected regions between views and
3989 with other VAMSAS applications (Experimental feature!)</li>
3990 <li>Updated API to VAMSAS version 0.2</li>
3992 </ul> <em>Applet</em>
3994 <li>Middle button resizes annotation row height</li>
3997 <li>sortByTree (true/false) - automatically sort the
3998 associated alignment view by the tree when a new tree is
4000 <li>showTreeBootstraps (true/false) - show or hide
4001 branch bootstraps (default is to show them if available)</li>
4002 <li>showTreeDistances (true/false) - show or hide
4003 branch lengths (default is to show them if available)</li>
4004 <li>showUnlinkedTreeNodes (true/false) - indicate if
4005 unassociated nodes should be highlighted in the tree
4007 <li>heightScale and widthScale (1.0 or more) -
4008 increase the height or width of a cell in the alignment
4009 grid relative to the current font size.</li>
4012 <li>Non-positional features displayed in sequence ID
4014 </ul> <em>Other</em>
4016 <li>Features format: graduated colour definitions and
4017 specification of feature scores</li>
4018 <li>Alignment Annotations format: new keywords for group
4019 associated annotation (GROUP_REF) and annotation row display
4020 properties (ROW_PROPERTIES)</li>
4021 <li>XML formats extended to support graduated feature
4022 colourschemes, group associated annotation, and profile
4023 visualization settings.</li></td>
4026 <li>Source field in GFF files parsed as feature source
4027 rather than description</li>
4028 <li>Non-positional features are now included in sequence
4029 feature and gff files (controlled via non-positional feature
4030 visibility in tooltip).</li>
4031 <li>URL links generated for all feature links (bugfix)</li>
4032 <li>Added URL embedding instructions to features file
4034 <li>Codons containing ambiguous nucleotides translated as
4035 'X' in peptide product</li>
4036 <li>Match case switch in find dialog box works for both
4037 sequence ID and sequence string and query strings do not
4038 have to be in upper case to match case-insensitively.</li>
4039 <li>AMSA files only contain first column of
4040 multi-character column annotation labels</li>
4041 <li>Jalview Annotation File generation/parsing consistent
4042 with documentation (e.g. Stockholm annotation can be
4043 exported and re-imported)</li>
4044 <li>PDB files without embedded PDB IDs given a friendly
4046 <li>Find incrementally searches ID string matches as well
4047 as subsequence matches, and correctly reports total number
4051 <li>Better handling of exceptions during sequence
4053 <li>Dasobert generated non-positional feature URL
4054 link text excludes the start_end suffix</li>
4055 <li>DAS feature and source retrieval buttons disabled
4056 when fetch or registry operations in progress.</li>
4057 <li>PDB files retrieved from URLs are cached properly</li>
4058 <li>Sequence description lines properly shared via
4060 <li>Sequence fetcher fetches multiple records for all
4062 <li>Ensured that command line das feature retrieval
4063 completes before alignment figures are generated.</li>
4064 <li>Reduced time taken when opening file browser for
4066 <li>isAligned check prior to calculating tree, PCA or
4067 submitting an MSA to JNet now excludes hidden sequences.</li>
4068 <li>User defined group colours properly recovered
4069 from Jalview projects.</li>
4078 <div align="center">
4079 <strong>2.4.0.b2</strong><br> 28/10/2009
4084 <li>Experimental support for google analytics usage
4086 <li>Jalview privacy settings (user preferences and docs).</li>
4091 <li>Race condition in applet preventing startup in
4093 <li>Exception when feature created from selection beyond
4094 length of sequence.</li>
4095 <li>Allow synthetic PDB files to be imported gracefully</li>
4096 <li>Sequence associated annotation rows associate with
4097 all sequences with a given id</li>
4098 <li>Find function matches case-insensitively for sequence
4099 ID string searches</li>
4100 <li>Non-standard characters do not cause pairwise
4101 alignment to fail with exception</li>
4102 </ul> <em>Application Issues</em>
4104 <li>Sequences are now validated against EMBL database</li>
4105 <li>Sequence fetcher fetches multiple records for all
4107 </ul> <em>InstallAnywhere Issues</em>
4109 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4110 issue with installAnywhere mechanism)</li>
4111 <li>Command line launching of JARs from InstallAnywhere
4112 version (java class versioning error fixed)</li>
4119 <div align="center">
4120 <strong>2.4</strong><br> 27/8/2008
4123 <td><em>User Interface</em>
4125 <li>Linked highlighting of codon and amino acid from
4126 translation and protein products</li>
4127 <li>Linked highlighting of structure associated with
4128 residue mapping to codon position</li>
4129 <li>Sequence Fetcher provides example accession numbers
4130 and 'clear' button</li>
4131 <li>MemoryMonitor added as an option under Desktop's
4133 <li>Extract score function to parse whitespace separated
4134 numeric data in description line</li>
4135 <li>Column labels in alignment annotation can be centred.</li>
4136 <li>Tooltip for sequence associated annotation give name
4138 </ul> <em>Web Services and URL fetching</em>
4140 <li>JPred3 web service</li>
4141 <li>Prototype sequence search client (no public services
4143 <li>Fetch either seed alignment or full alignment from
4145 <li>URL Links created for matching database cross
4146 references as well as sequence ID</li>
4147 <li>URL Links can be created using regular-expressions</li>
4148 </ul> <em>Sequence Database Connectivity</em>
4150 <li>Retrieval of cross-referenced sequences from other
4152 <li>Generalised database reference retrieval and
4153 validation to all fetchable databases</li>
4154 <li>Fetch sequences from DAS sources supporting the
4155 sequence command</li>
4156 </ul> <em>Import and Export</em>
4157 <li>export annotation rows as CSV for spreadsheet import</li>
4158 <li>Jalview projects record alignment dataset associations,
4159 EMBL products, and cDNA sequence mappings</li>
4160 <li>Sequence Group colour can be specified in Annotation
4162 <li>Ad-hoc colouring of group in Annotation File using RGB
4163 triplet as name of colourscheme</li>
4164 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4166 <li>treenode binding for VAMSAS tree exchange</li>
4167 <li>local editing and update of sequences in VAMSAS
4168 alignments (experimental)</li>
4169 <li>Create new or select existing session to join</li>
4170 <li>load and save of vamsas documents</li>
4171 </ul> <em>Application command line</em>
4173 <li>-tree parameter to open trees (introduced for passing
4175 <li>-fetchfrom command line argument to specify nicknames
4176 of DAS servers to query for alignment features</li>
4177 <li>-dasserver command line argument to add new servers
4178 that are also automatically queried for features</li>
4179 <li>-groovy command line argument executes a given groovy
4180 script after all input data has been loaded and parsed</li>
4181 </ul> <em>Applet-Application data exchange</em>
4183 <li>Trees passed as applet parameters can be passed to
4184 application (when using "View in full
4185 application")</li>
4186 </ul> <em>Applet Parameters</em>
4188 <li>feature group display control parameter</li>
4189 <li>debug parameter</li>
4190 <li>showbutton parameter</li>
4191 </ul> <em>Applet API methods</em>
4193 <li>newView public method</li>
4194 <li>Window (current view) specific get/set public methods</li>
4195 <li>Feature display control methods</li>
4196 <li>get list of currently selected sequences</li>
4197 </ul> <em>New Jalview distribution features</em>
4199 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4200 <li>RELEASE file gives build properties for the latest
4201 Jalview release.</li>
4202 <li>Java 1.1 Applet build made easier and donotobfuscate
4203 property controls execution of obfuscator</li>
4204 <li>Build target for generating source distribution</li>
4205 <li>Debug flag for javacc</li>
4206 <li>.jalview_properties file is documented (slightly) in
4207 jalview.bin.Cache</li>
4208 <li>Continuous Build Integration for stable and
4209 development version of Application, Applet and source
4214 <li>selected region output includes visible annotations
4215 (for certain formats)</li>
4216 <li>edit label/displaychar contains existing label/char
4218 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4219 <li>shorter peptide product names from EMBL records</li>
4220 <li>Newick string generator makes compact representations</li>
4221 <li>bootstrap values parsed correctly for tree files with
4223 <li>pathological filechooser bug avoided by not allowing
4224 filenames containing a ':'</li>
4225 <li>Fixed exception when parsing GFF files containing
4226 global sequence features</li>
4227 <li>Alignment datasets are finalized only when number of
4228 references from alignment sequences goes to zero</li>
4229 <li>Close of tree branch colour box without colour
4230 selection causes cascading exceptions</li>
4231 <li>occasional negative imgwidth exceptions</li>
4232 <li>better reporting of non-fatal warnings to user when
4233 file parsing fails.</li>
4234 <li>Save works when Jalview project is default format</li>
4235 <li>Save as dialog opened if current alignment format is
4236 not a valid output format</li>
4237 <li>UniProt canonical names introduced for both das and
4239 <li>Histidine should be midblue (not pink!) in Zappo</li>
4240 <li>error messages passed up and output when data read
4242 <li>edit undo recovers previous dataset sequence when
4243 sequence is edited</li>
4244 <li>allow PDB files without pdb ID HEADER lines (like
4245 those generated by MODELLER) to be read in properly</li>
4246 <li>allow reading of JPred concise files as a normal
4248 <li>Stockholm annotation parsing and alignment properties
4249 import fixed for PFAM records</li>
4250 <li>Structure view windows have correct name in Desktop
4252 <li>annotation consisting of sequence associated scores
4253 can be read and written correctly to annotation file</li>
4254 <li>Aligned cDNA translation to aligned peptide works
4256 <li>Fixed display of hidden sequence markers and
4257 non-italic font for representatives in Applet</li>
4258 <li>Applet Menus are always embedded in applet window on
4260 <li>Newly shown features appear at top of stack (in
4262 <li>Annotations added via parameter not drawn properly
4263 due to null pointer exceptions</li>
4264 <li>Secondary structure lines are drawn starting from
4265 first column of alignment</li>
4266 <li>UniProt XML import updated for new schema release in
4268 <li>Sequence feature to sequence ID match for Features
4269 file is case-insensitive</li>
4270 <li>Sequence features read from Features file appended to
4271 all sequences with matching IDs</li>
4272 <li>PDB structure coloured correctly for associated views
4273 containing a sub-sequence</li>
4274 <li>PDB files can be retrieved by applet from Jar files</li>
4275 <li>feature and annotation file applet parameters
4276 referring to different directories are retrieved correctly</li>
4277 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4278 <li>Fixed application hang whilst waiting for
4279 splash-screen version check to complete</li>
4280 <li>Applet properly URLencodes input parameter values
4281 when passing them to the launchApp service</li>
4282 <li>display name and local features preserved in results
4283 retrieved from web service</li>
4284 <li>Visual delay indication for sequence retrieval and
4285 sequence fetcher initialisation</li>
4286 <li>updated Application to use DAS 1.53e version of
4287 dasobert DAS client</li>
4288 <li>Re-instated Full AMSA support and .amsa file
4290 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4298 <div align="center">
4299 <strong>2.3</strong><br> 9/5/07
4304 <li>Jmol 11.0.2 integration</li>
4305 <li>PDB views stored in Jalview XML files</li>
4306 <li>Slide sequences</li>
4307 <li>Edit sequence in place</li>
4308 <li>EMBL CDS features</li>
4309 <li>DAS Feature mapping</li>
4310 <li>Feature ordering</li>
4311 <li>Alignment Properties</li>
4312 <li>Annotation Scores</li>
4313 <li>Sort by scores</li>
4314 <li>Feature/annotation editing in applet</li>
4319 <li>Headless state operation in 2.2.1</li>
4320 <li>Incorrect and unstable DNA pairwise alignment</li>
4321 <li>Cut and paste of sequences with annotation</li>
4322 <li>Feature group display state in XML</li>
4323 <li>Feature ordering in XML</li>
4324 <li>blc file iteration selection using filename # suffix</li>
4325 <li>Stockholm alignment properties</li>
4326 <li>Stockhom alignment secondary structure annotation</li>
4327 <li>2.2.1 applet had no feature transparency</li>
4328 <li>Number pad keys can be used in cursor mode</li>
4329 <li>Structure Viewer mirror image resolved</li>
4336 <div align="center">
4337 <strong>2.2.1</strong><br> 12/2/07
4342 <li>Non standard characters can be read and displayed
4343 <li>Annotations/Features can be imported/exported to the
4345 <li>Applet allows editing of sequence/annotation/group
4346 name & description
4347 <li>Preference setting to display sequence name in
4349 <li>Annotation file format extended to allow
4350 Sequence_groups to be defined
4351 <li>Default opening of alignment overview panel can be
4352 specified in preferences
4353 <li>PDB residue numbering annotation added to associated
4359 <li>Applet crash under certain Linux OS with Java 1.6
4361 <li>Annotation file export / import bugs fixed
4362 <li>PNG / EPS image output bugs fixed
4368 <div align="center">
4369 <strong>2.2</strong><br> 27/11/06
4374 <li>Multiple views on alignment
4375 <li>Sequence feature editing
4376 <li>"Reload" alignment
4377 <li>"Save" to current filename
4378 <li>Background dependent text colour
4379 <li>Right align sequence ids
4380 <li>User-defined lower case residue colours
4383 <li>Menu item accelerator keys
4384 <li>Control-V pastes to current alignment
4385 <li>Cancel button for DAS Feature Fetching
4386 <li>PCA and PDB Viewers zoom via mouse roller
4387 <li>User-defined sub-tree colours and sub-tree selection
4389 <li>'New Window' button on the 'Output to Text box'
4394 <li>New memory efficient Undo/Redo System
4395 <li>Optimised symbol lookups and conservation/consensus
4397 <li>Region Conservation/Consensus recalculated after
4399 <li>Fixed Remove Empty Columns Bug (empty columns at end
4401 <li>Slowed DAS Feature Fetching for increased robustness.
4403 <li>Made angle brackets in ASCII feature descriptions
4405 <li>Re-instated Zoom function for PCA
4406 <li>Sequence descriptions conserved in web service
4408 <li>UniProt ID discoverer uses any word separated by
4410 <li>WsDbFetch query/result association resolved
4411 <li>Tree leaf to sequence mapping improved
4412 <li>Smooth fonts switch moved to FontChooser dialog box.
4419 <div align="center">
4420 <strong>2.1.1</strong><br> 12/9/06
4425 <li>Copy consensus sequence to clipboard</li>
4430 <li>Image output - rightmost residues are rendered if
4431 sequence id panel has been resized</li>
4432 <li>Image output - all offscreen group boundaries are
4434 <li>Annotation files with sequence references - all
4435 elements in file are relative to sequence position</li>
4436 <li>Mac Applet users can use Alt key for group editing</li>
4442 <div align="center">
4443 <strong>2.1</strong><br> 22/8/06
4448 <li>MAFFT Multiple Alignment in default Web Service list</li>
4449 <li>DAS Feature fetching</li>
4450 <li>Hide sequences and columns</li>
4451 <li>Export Annotations and Features</li>
4452 <li>GFF file reading / writing</li>
4453 <li>Associate structures with sequences from local PDB
4455 <li>Add sequences to exisiting alignment</li>
4456 <li>Recently opened files / URL lists</li>
4457 <li>Applet can launch the full application</li>
4458 <li>Applet has transparency for features (Java 1.2
4460 <li>Applet has user defined colours parameter</li>
4461 <li>Applet can load sequences from parameter
4462 "sequence<em>x</em>"
4468 <li>Redundancy Panel reinstalled in the Applet</li>
4469 <li>Monospaced font - EPS / rescaling bug fixed</li>
4470 <li>Annotation files with sequence references bug fixed</li>
4476 <div align="center">
4477 <strong>2.08.1</strong><br> 2/5/06
4482 <li>Change case of selected region from Popup menu</li>
4483 <li>Choose to match case when searching</li>
4484 <li>Middle mouse button and mouse movement can compress /
4485 expand the visible width and height of the alignment</li>
4490 <li>Annotation Panel displays complete JNet results</li>
4496 <div align="center">
4497 <strong>2.08b</strong><br> 18/4/06
4503 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4504 <li>Righthand label on wrapped alignments shows correct
4511 <div align="center">
4512 <strong>2.08</strong><br> 10/4/06
4517 <li>Editing can be locked to the selection area</li>
4518 <li>Keyboard editing</li>
4519 <li>Create sequence features from searches</li>
4520 <li>Precalculated annotations can be loaded onto
4522 <li>Features file allows grouping of features</li>
4523 <li>Annotation Colouring scheme added</li>
4524 <li>Smooth fonts off by default - Faster rendering</li>
4525 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4530 <li>Drag & Drop fixed on Linux</li>
4531 <li>Jalview Archive file faster to load/save, sequence
4532 descriptions saved.</li>
4538 <div align="center">
4539 <strong>2.07</strong><br> 12/12/05
4544 <li>PDB Structure Viewer enhanced</li>
4545 <li>Sequence Feature retrieval and display enhanced</li>
4546 <li>Choose to output sequence start-end after sequence
4547 name for file output</li>
4548 <li>Sequence Fetcher WSDBFetch@EBI</li>
4549 <li>Applet can read feature files, PDB files and can be
4550 used for HTML form input</li>
4555 <li>HTML output writes groups and features</li>
4556 <li>Group editing is Control and mouse click</li>
4557 <li>File IO bugs</li>
4563 <div align="center">
4564 <strong>2.06</strong><br> 28/9/05
4569 <li>View annotations in wrapped mode</li>
4570 <li>More options for PCA viewer</li>
4575 <li>GUI bugs resolved</li>
4576 <li>Runs with -nodisplay from command line</li>
4582 <div align="center">
4583 <strong>2.05b</strong><br> 15/9/05
4588 <li>Choose EPS export as lineart or text</li>
4589 <li>Jar files are executable</li>
4590 <li>Can read in Uracil - maps to unknown residue</li>
4595 <li>Known OutOfMemory errors give warning message</li>
4596 <li>Overview window calculated more efficiently</li>
4597 <li>Several GUI bugs resolved</li>
4603 <div align="center">
4604 <strong>2.05</strong><br> 30/8/05
4609 <li>Edit and annotate in "Wrapped" view</li>
4614 <li>Several GUI bugs resolved</li>
4620 <div align="center">
4621 <strong>2.04</strong><br> 24/8/05
4626 <li>Hold down mouse wheel & scroll to change font
4632 <li>Improved JPred client reliability</li>
4633 <li>Improved loading of Jalview files</li>
4639 <div align="center">
4640 <strong>2.03</strong><br> 18/8/05
4645 <li>Set Proxy server name and port in preferences</li>
4646 <li>Multiple URL links from sequence ids</li>
4647 <li>User Defined Colours can have a scheme name and added
4649 <li>Choose to ignore gaps in consensus calculation</li>
4650 <li>Unix users can set default web browser</li>
4651 <li>Runs without GUI for batch processing</li>
4652 <li>Dynamically generated Web Service Menus</li>
4657 <li>InstallAnywhere download for Sparc Solaris</li>
4663 <div align="center">
4664 <strong>2.02</strong><br> 18/7/05
4670 <li>Copy & Paste order of sequences maintains
4671 alignment order.</li>
4677 <div align="center">
4678 <strong>2.01</strong><br> 12/7/05
4683 <li>Use delete key for deleting selection.</li>
4684 <li>Use Mouse wheel to scroll sequences.</li>
4685 <li>Help file updated to describe how to add alignment
4687 <li>Version and build date written to build properties
4689 <li>InstallAnywhere installation will check for updates
4690 at launch of Jalview.</li>
4695 <li>Delete gaps bug fixed.</li>
4696 <li>FileChooser sorts columns.</li>
4697 <li>Can remove groups one by one.</li>
4698 <li>Filechooser icons installed.</li>
4699 <li>Finder ignores return character when searching.
4700 Return key will initiate a search.<br>
4707 <div align="center">
4708 <strong>2.0</strong><br> 20/6/05
4713 <li>New codebase</li>