3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
34 /* separate the items from eachother */
41 /* doesnt get processed in javahelp */
50 <strong>Release History</strong>
54 <th nowrap><em>Release</em></th>
55 <th><em>New Features</em></th>
56 <th><em>Issues Resolved</em></th>
59 <td width="60" align="center" nowrap><strong><a
60 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
61 <em>27/03/2020</em></strong></td>
62 <td align="left" valign="top">
65 <!-- JAL-3187 -->Option to show 'virtual' codon features on protein (or vice versa)
68 <!-- JAL-3304 -->Option to export virtual features if shown
71 <!-- JAL-3302 -->Option to transfer virtual features to Chimera
74 <!-- JAL-3121 -->Feature attributes from VCF files can be exported and re-imported as GFF3 files
77 <!-- JAL-3376 -->Capture VCF "fixed column" values POS,
78 ID, QUAL, FILTER as Feature Attributes
81 <!-- JAL-3375 -->More robust VCF numeric data field validation while parsing
84 <!-- JAL-3533 -->Feature Settings dialog keeps same screen position if reopened
87 <!-- JAL-3538 -->Font anti-aliasing in alignment views enabled by default
90 <!-- JAL-3468 -->Very long feature descriptions truncated in tooltips and menus
92 </ul><em>Jalview Installer</em>
95 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
96 in console (may be null when Jalview launched as executable jar or via conda)
99 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
102 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
105 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
107 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
108 </ul> <em>Release processes</em>
111 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
113 </ul> <em>Build System</em>
116 <!-- JAL-3510 -->Clover updated to 4.4.1
119 <!-- JAL-3513 -->Test code included in Clover coverage
124 <td align="left" valign="top">
127 <!-- JAL-3412 -->ID margins for CDS and Protein views not equal when split frame is first opened
130 <!-- JAL-3296 -->Sequence position numbers in status bar not correct after editing a sequence's start position
133 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
134 with annotation and exceptions thrown when only a few
135 columns shown in wrapped mode
138 <!-- JAL-3386 -->Sequence IDs missing in headless export of
139 wrapped alignment figure with annotations
142 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
143 ID fails with ClassCastException
146 <!-- JAL-3389 -->Chimera session not restored from Jalview
150 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
151 feature settings dialog also selects columns
154 <!-- JAL-3473 -->SpinnerNumberModel causes
155 IllegalArgumentException in some circumstances
158 <!-- JAL-3534 -->Multiple feature settings dialogs can be opened for a view
161 <!-- JAL-2764 -->Feature Settings dialog is orphaned if alignment window is closed
164 <!-- JAL-3406 -->Credits missing some authors in Jalview
165 help documentation for 2.11.0 release
167 </ul> <em>Java 11 Compatibility issues</em>
170 <!-- JAL-2987 -->OSX - Can't view some search results in PDB/Uniprot search panel
172 </ul> <em>Installer</em>
174 <li><!-- JAL-3447 -->Jalview should not create file associations for 3D structure files (.pdb, .mmcif. .cif)
176 </ul> <em>Repository and Source Release</em>
179 <!-- JAL-3474 -->removed obsolete .cvsignore files from repository
182 <!-- JAL-3541 -->Clover report generation running out of memory
185 <em>New Known Issues</em>
188 <!-- JAL-3523 -->OSX - Current working directory not
189 preserved when Jalview.app launched with parameters from
193 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
194 clipped in headless figure export when Right Align option
198 <!-- JAL-3542 -->Jalview Installation type always reports 'Source' in console output
204 <td width="60" align="center" nowrap>
205 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
206 <em>04/07/2019</em></strong>
208 <td align="left" valign="top">
211 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
212 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
213 source project) rather than InstallAnywhere
216 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
217 settings, receive over the air updates and launch specific
218 versions via (<a href="https://github.com/threerings/getdown">Three
222 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
223 formats supported by Jalview (including .jvp project files)
226 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
227 arguments and switch between different getdown channels
230 <!-- JAL-3141 -->Backup files created when saving Jalview project
235 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
236 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
238 <!-- JAL-2620 -->Alternative genetic code tables for
239 'Translate as cDNA'</li>
241 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
242 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
245 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
246 implementation that allows updates) used for Sequence Feature collections</li>
248 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
249 features can be filtered and shaded according to any
250 associated attributes (e.g. variant attributes from VCF
251 file, or key-value pairs imported from column 9 of GFF
255 <!-- JAL-2879 -->Feature Attributes and shading schemes
256 stored and restored from Jalview Projects
259 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
260 recognise variant features
263 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
264 sequences (also coloured red by default)
267 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
271 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
272 algorithm (Z-sort/transparency and filter aware)
275 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
281 <!-- JAL-3205 -->Symmetric score matrices for faster
282 tree and PCA calculations
284 <li><strong>Principal Components Analysis Viewer</strong>
287 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
288 and Viewer state saved in Jalview Project
290 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
293 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
297 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
302 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
304 <li><strong>Speed and Efficiency</strong>
307 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
308 multiple groups when working with large alignments
311 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
315 <li><strong>User Interface</strong>
318 <!-- JAL-2933 -->Finder panel remembers last position in each
322 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
323 what is shown)<br />Only visible regions of alignment are shown by
324 default (can be changed in user preferences)
327 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
328 to the Overwrite Dialog
331 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
335 <!-- JAL-1244 -->Status bar shows bounds when dragging a
336 selection region, and gap count when inserting or deleting gaps
339 <!-- JAL-3132 -->Status bar updates over sequence and annotation
343 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
347 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
351 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
354 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
358 <!-- JAL-3181 -->Consistent ordering of links in sequence id
362 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
364 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
368 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
369 <li><strong>Java 11 Support (not yet on general release)</strong>
372 <!-- -->OSX GUI integrations for App menu's 'About' entry and
377 <em>Deprecations</em>
379 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
380 capabilities removed from the Jalview Desktop
382 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
383 unmarshalling has been replaced by JAXB for Jalview projects
384 and XML based data retrieval clients</li>
385 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
386 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
387 </ul> <em>Documentation</em>
389 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
390 not supported in EPS figure export
392 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
393 </ul> <em>Development and Release Processes</em>
396 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
399 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
401 <!-- JAL-3225 -->Eclipse project configuration managed with
405 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
406 Bamboo continuous integration for unattended Test Suite
410 <!-- JAL-2864 -->Memory test suite to detect leaks in common
414 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
418 <!-- JAL-3248 -->Developer documentation migrated to
419 markdown (with HTML rendering)
422 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
425 <!-- JAL-3289 -->New URLs for publishing development
430 <td align="left" valign="top">
433 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
436 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
437 superposition in Jmol fail on Windows
440 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
441 structures for sequences with lots of PDB structures
444 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
448 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
449 project involving multiple views
452 <!-- JAL-3164 -->Overview for complementary view in a linked
453 CDS/Protein alignment is not updated when Hide Columns by
454 Annotation dialog hides columns
457 <!-- JAL-3158 -->Selection highlighting in the complement of a
458 CDS/Protein alignment stops working after making a selection in
459 one view, then making another selection in the other view
462 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
466 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
467 Settings and Jalview Preferences panels
470 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
471 overview with large alignments
474 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
475 region if columns were selected by dragging right-to-left and the
476 mouse moved to the left of the first column
479 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
480 hidden column marker via scale popup menu
483 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
484 doesn't tell users the invalid URL
487 <!-- JAL-2816 -->Tooltips displayed for features filtered by
491 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
492 show cross references or Fetch Database References are shown in
496 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
497 peptide sequence (computed variant shown as p.Res.null)
500 <!-- JAL-2060 -->'Graduated colour' option not offered for
501 manually created features (where feature score is Float.NaN)
504 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
505 when columns are hidden
508 <!-- JAL-3082 -->Regular expression error for '(' in Select
509 Columns by Annotation description
512 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
513 out of Scale or Annotation Panel
516 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
520 <!-- JAL-3074 -->Left/right drag in annotation can scroll
524 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
528 <!-- JAL-3002 -->Column display is out by one after Page Down,
529 Page Up in wrapped mode
532 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
535 <!-- JAL-2932 -->Finder searches in minimised alignments
538 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
539 on opening an alignment
542 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
546 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
547 different groups in the alignment are selected
550 <!-- JAL-2717 -->Internationalised colour scheme names not shown
554 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
558 <!-- JAL-3125 -->Value input for graduated feature colour
559 threshold gets 'unrounded'
562 <!-- JAL-2982 -->PCA image export doesn't respect background
566 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
569 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
572 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
576 <!-- JAL-2964 -->Associate Tree with All Views not restored from
580 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
581 shown in complementary view
584 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
585 without normalisation
588 <!-- JAL-3021 -->Sequence Details report should open positioned at top
592 <!-- JAL-914 -->Help page can be opened twice
595 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
597 </ul> <em>Editing</em>
600 <!-- JAL-2822 -->Start and End should be updated when sequence
601 data at beginning or end of alignment added/removed via 'Edit'
605 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
606 relocate sequence features correctly when start of sequence is
607 removed (Known defect since 2.10)
610 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
611 dialog corrupts dataset sequence
614 <!-- JAL-868 -->Structure colours not updated when associated tree
615 repartitions the alignment view (Regression in 2.10.5)
617 </ul> <em>Datamodel</em>
620 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
621 sequence's End is greater than its length
623 </ul> <em>Bugs fixed for Java 11 Support (not yet on
624 general release)</em>
627 <!-- JAL-3288 -->Menus work properly in split-screen
629 </ul> <em>New Known Defects</em>
632 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
635 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
636 regions of protein alignment.
639 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
640 is restored from a Jalview 2.11 project
643 <!-- JAL-3213 -->Alignment panel height can be too small after
647 <!-- JAL-3240 -->Display is incorrect after removing gapped
648 columns within hidden columns
651 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
652 window after dragging left to select columns to left of visible
656 <!-- JAL-2876 -->Features coloured according to their description
657 string and thresholded by score in earlier versions of Jalview are
658 not shown as thresholded features in 2.11. To workaround please
659 create a Score filter instead.
662 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
664 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
667 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
668 alignments with multiple views can close views unexpectedly
671 <em>Java 11 Specific defects</em>
674 <!-- JAL-3235 -->Jalview Properties file is not sorted
675 alphabetically when saved
681 <td width="60" nowrap>
683 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
686 <td><div align="left">
690 <!-- JAL-3101 -->Default memory for Jalview webstart and
691 InstallAnywhere increased to 1G.
694 <!-- JAL-247 -->Hidden sequence markers and representative
695 sequence bolding included when exporting alignment as EPS,
696 SVG, PNG or HTML. <em>Display is configured via the
697 Format menu, or for command-line use via a Jalview
698 properties file.</em>
701 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
702 API and sequence data now imported as JSON.
705 <!-- JAL-3065 -->Change in recommended way of starting
706 Jalview via a Java command line: add jars in lib directory
707 to CLASSPATH, rather than via the deprecated java.ext.dirs
714 <!-- JAL-3047 -->Support added to execute test suite
715 instrumented with <a href="http://openclover.org/">Open
720 <td><div align="left">
724 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
725 row shown in Feredoxin Structure alignment view of example
729 <!-- JAL-2854 -->Annotation obscures sequences if lots of
730 annotation displayed.
733 <!-- JAL-3107 -->Group conservation/consensus not shown
734 for newly created group when 'Apply to all groups'
738 <!-- JAL-3087 -->Corrupted display when switching to
739 wrapped mode when sequence panel's vertical scrollbar is
743 <!-- JAL-3003 -->Alignment is black in exported EPS file
744 when sequences are selected in exported view.</em>
747 <!-- JAL-3059 -->Groups with different coloured borders
748 aren't rendered with correct colour.
751 <!-- JAL-3092 -->Jalview could hang when importing certain
752 types of knotted RNA secondary structure.
755 <!-- JAL-3095 -->Sequence highlight and selection in
756 trimmed VARNA 2D structure is incorrect for sequences that
760 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
761 annotation when columns are inserted into an alignment,
762 and when exporting as Stockholm flatfile.
765 <!-- JAL-3053 -->Jalview annotation rows containing upper
766 and lower-case 'E' and 'H' do not automatically get
767 treated as RNA secondary structure.
770 <!-- JAL-3106 -->.jvp should be used as default extension
771 (not .jar) when saving a Jalview project file.
774 <!-- JAL-3105 -->Mac Users: closing a window correctly
775 transfers focus to previous window on OSX
778 <em>Java 10 Issues Resolved</em>
781 <!-- JAL-2988 -->OSX - Can't save new files via the File
782 or export menus by typing in a name into the Save dialog
786 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
787 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
788 'look and feel' which has improved compatibility with the
789 latest version of OSX.
796 <td width="60" nowrap>
798 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
799 <em>7/06/2018</em></strong>
802 <td><div align="left">
806 <!-- JAL-2920 -->Use HGVS nomenclature for variant
807 annotation retrieved from Uniprot
810 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
811 onto the Jalview Desktop
815 <td><div align="left">
819 <!-- JAL-3017 -->Cannot import features with multiple
820 variant elements (blocks import of some Uniprot records)
823 <!-- JAL-2997 -->Clustal files with sequence positions in
824 right-hand column parsed correctly
827 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
828 not alignment area in exported graphic
831 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
832 window has input focus
835 <!-- JAL-2992 -->Annotation panel set too high when
836 annotation added to view (Windows)
839 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
840 network connectivity is poor
843 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
844 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
845 the currently open URL and links from a page viewed in
846 Firefox or Chrome on Windows is now fully supported. If
847 you are using Edge, only links in the page can be
848 dragged, and with Internet Explorer, only the currently
849 open URL in the browser can be dropped onto Jalview.</em>
852 <em>New Known Defects</em>
854 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
859 <td width="60" nowrap>
861 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
864 <td><div align="left">
868 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
869 for disabling automatic superposition of multiple
870 structures and open structures in existing views
873 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
874 ID and annotation area margins can be click-dragged to
878 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
882 <!-- JAL-2759 -->Improved performance for large alignments
883 and lots of hidden columns
886 <!-- JAL-2593 -->Improved performance when rendering lots
887 of features (particularly when transparency is disabled)
890 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
891 exchange of Jalview features and Chimera attributes made
897 <td><div align="left">
900 <!-- JAL-2899 -->Structure and Overview aren't updated
901 when Colour By Annotation threshold slider is adjusted
904 <!-- JAL-2778 -->Slow redraw when Overview panel shown
905 overlapping alignment panel
908 <!-- JAL-2929 -->Overview doesn't show end of unpadded
912 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
913 improved: CDS not handled correctly if transcript has no
917 <!-- JAL-2321 -->Secondary structure and temperature
918 factor annotation not added to sequence when local PDB
919 file associated with it by drag'n'drop or structure
923 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
924 dialog doesn't import PDB files dropped on an alignment
927 <!-- JAL-2666 -->Linked scrolling via protein horizontal
928 scroll bar doesn't work for some CDS/Protein views
931 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
932 Java 1.8u153 onwards and Java 1.9u4+.
935 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
936 columns in annotation row
939 <!-- JAL-2913 -->Preferences panel's ID Width control is not
940 honored in batch mode
943 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
944 for structures added to existing Jmol view
947 <!-- JAL-2223 -->'View Mappings' includes duplicate
948 entries after importing project with multiple views
951 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
952 protein sequences via SIFTS from associated PDB entries
953 with negative residue numbers or missing residues fails
956 <!-- JAL-2952 -->Exception when shading sequence with negative
957 Temperature Factor values from annotated PDB files (e.g.
958 as generated by CONSURF)
961 <!-- JAL-2920 -->Uniprot 'sequence variant' features
962 tooltip doesn't include a text description of mutation
965 <!-- JAL-2922 -->Invert displayed features very slow when
966 structure and/or overview windows are also shown
969 <!-- JAL-2954 -->Selecting columns from highlighted regions
970 very slow for alignments with large numbers of sequences
973 <!-- JAL-2925 -->Copy Consensus fails for group consensus
974 with 'StringIndexOutOfBounds'
977 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
978 platforms running Java 10
981 <!-- JAL-2960 -->Adding a structure to existing structure
982 view appears to do nothing because the view is hidden behind the alignment view
988 <!-- JAL-2926 -->Copy consensus sequence option in applet
989 should copy the group consensus when popup is opened on it
995 <!-- JAL-2913 -->Fixed ID width preference is not respected
998 <em>New Known Defects</em>
1001 <!-- JAL-2973 --> Exceptions occasionally raised when
1002 editing a large alignment and overview is displayed
1005 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1006 repeatedly after a series of edits even when the overview
1007 is no longer reflecting updates
1010 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1011 structures for protein subsequence (if 'Trim Retrieved
1012 Sequences' enabled) or Ensembl isoforms (Workaround in
1013 2.10.4 is to fail back to N&W mapping)
1016 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1017 option gives blank output
1024 <td width="60" nowrap>
1025 <div align="center">
1026 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1029 <td><div align="left">
1030 <ul><li>Updated Certum Codesigning Certificate
1031 (Valid till 30th November 2018)</li></ul></div></td>
1032 <td><div align="left">
1033 <em>Desktop</em><ul>
1035 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1036 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1037 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1038 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1039 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1040 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1041 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1047 <td width="60" nowrap>
1048 <div align="center">
1049 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1052 <td><div align="left">
1056 <!-- JAL-2446 -->Faster and more efficient management and
1057 rendering of sequence features
1060 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1061 429 rate limit request hander
1064 <!-- JAL-2773 -->Structure views don't get updated unless
1065 their colours have changed
1068 <!-- JAL-2495 -->All linked sequences are highlighted for
1069 a structure mousover (Jmol) or selection (Chimera)
1072 <!-- JAL-2790 -->'Cancel' button in progress bar for
1073 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1076 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1077 view from Ensembl locus cross-references
1080 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1084 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1085 feature can be disabled
1088 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1089 PDB easier retrieval of sequences for lists of IDs
1092 <!-- JAL-2758 -->Short names for sequences retrieved from
1098 <li>Groovy interpreter updated to 2.4.12</li>
1099 <li>Example groovy script for generating a matrix of
1100 percent identity scores for current alignment.</li>
1102 <em>Testing and Deployment</em>
1105 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1109 <td><div align="left">
1113 <!-- JAL-2643 -->Pressing tab after updating the colour
1114 threshold text field doesn't trigger an update to the
1118 <!-- JAL-2682 -->Race condition when parsing sequence ID
1122 <!-- JAL-2608 -->Overview windows are also closed when
1123 alignment window is closed
1126 <!-- JAL-2548 -->Export of features doesn't always respect
1130 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1131 takes a long time in Cursor mode
1137 <!-- JAL-2777 -->Structures with whitespace chainCode
1138 cannot be viewed in Chimera
1141 <!-- JAL-2728 -->Protein annotation panel too high in
1145 <!-- JAL-2757 -->Can't edit the query after the server
1146 error warning icon is shown in Uniprot and PDB Free Text
1150 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1153 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1156 <!-- JAL-2739 -->Hidden column marker in last column not
1157 rendered when switching back from Wrapped to normal view
1160 <!-- JAL-2768 -->Annotation display corrupted when
1161 scrolling right in unwapped alignment view
1164 <!-- JAL-2542 -->Existing features on subsequence
1165 incorrectly relocated when full sequence retrieved from
1169 <!-- JAL-2733 -->Last reported memory still shown when
1170 Desktop->Show Memory is unticked (OSX only)
1173 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1174 features of same type and group to be selected for
1178 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1179 alignments when hidden columns are present
1182 <!-- JAL-2392 -->Jalview freezes when loading and
1183 displaying several structures
1186 <!-- JAL-2732 -->Black outlines left after resizing or
1190 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1191 within the Jalview desktop on OSX
1194 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1195 when in wrapped alignment mode
1198 <!-- JAL-2636 -->Scale mark not shown when close to right
1199 hand end of alignment
1202 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1203 each selected sequence do not have correct start/end
1207 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1208 after canceling the Alignment Window's Font dialog
1211 <!-- JAL-2036 -->Show cross-references not enabled after
1212 restoring project until a new view is created
1215 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1216 URL links appears when only default EMBL-EBI link is
1217 configured (since 2.10.2b2)
1220 <!-- JAL-2775 -->Overview redraws whole window when box
1221 position is adjusted
1224 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1225 in a multi-chain structure when viewing alignment
1226 involving more than one chain (since 2.10)
1229 <!-- JAL-2811 -->Double residue highlights in cursor mode
1230 if new selection moves alignment window
1233 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1234 arrow key in cursor mode to pass hidden column marker
1237 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1238 that produces correctly annotated transcripts and products
1241 <!-- JAL-2776 -->Toggling a feature group after first time
1242 doesn't update associated structure view
1245 <em>Applet</em><br />
1248 <!-- JAL-2687 -->Concurrent modification exception when
1249 closing alignment panel
1252 <em>BioJSON</em><br />
1255 <!-- JAL-2546 -->BioJSON export does not preserve
1256 non-positional features
1259 <em>New Known Issues</em>
1262 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1263 sequence features correctly (for many previous versions of
1267 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1268 using cursor in wrapped panel other than top
1271 <!-- JAL-2791 -->Select columns containing feature ignores
1272 graduated colour threshold
1275 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1276 always preserve numbering and sequence features
1279 <em>Known Java 9 Issues</em>
1282 <!-- JAL-2902 -->Groovy Console very slow to open and is
1283 not responsive when entering characters (Webstart, Java
1290 <td width="60" nowrap>
1291 <div align="center">
1292 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1293 <em>2/10/2017</em></strong>
1296 <td><div align="left">
1297 <em>New features in Jalview Desktop</em>
1300 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1302 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1306 <td><div align="left">
1310 <td width="60" nowrap>
1311 <div align="center">
1312 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1313 <em>7/9/2017</em></strong>
1316 <td><div align="left">
1320 <!-- JAL-2588 -->Show gaps in overview window by colouring
1321 in grey (sequences used to be coloured grey, and gaps were
1325 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1329 <!-- JAL-2587 -->Overview updates immediately on increase
1330 in size and progress bar shown as higher resolution
1331 overview is recalculated
1336 <td><div align="left">
1340 <!-- JAL-2664 -->Overview window redraws every hidden
1341 column region row by row
1344 <!-- JAL-2681 -->duplicate protein sequences shown after
1345 retrieving Ensembl crossrefs for sequences from Uniprot
1348 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1349 format setting is unticked
1352 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1353 if group has show boxes format setting unticked
1356 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1357 autoscrolling whilst dragging current selection group to
1358 include sequences and columns not currently displayed
1361 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1362 assemblies are imported via CIF file
1365 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1366 displayed when threshold or conservation colouring is also
1370 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1374 <!-- JAL-2673 -->Jalview continues to scroll after
1375 dragging a selected region off the visible region of the
1379 <!-- JAL-2724 -->Cannot apply annotation based
1380 colourscheme to all groups in a view
1383 <!-- JAL-2511 -->IDs don't line up with sequences
1384 initially after font size change using the Font chooser or
1391 <td width="60" nowrap>
1392 <div align="center">
1393 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1396 <td><div align="left">
1397 <em>Calculations</em>
1401 <!-- JAL-1933 -->Occupancy annotation row shows number of
1402 ungapped positions in each column of the alignment.
1405 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1406 a calculation dialog box
1409 <!-- JAL-2379 -->Revised implementation of PCA for speed
1410 and memory efficiency (~30x faster)
1413 <!-- JAL-2403 -->Revised implementation of sequence
1414 similarity scores as used by Tree, PCA, Shading Consensus
1415 and other calculations
1418 <!-- JAL-2416 -->Score matrices are stored as resource
1419 files within the Jalview codebase
1422 <!-- JAL-2500 -->Trees computed on Sequence Feature
1423 Similarity may have different topology due to increased
1430 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1431 model for alignments and groups
1434 <!-- JAL-384 -->Custom shading schemes created via groovy
1441 <!-- JAL-2526 -->Efficiency improvements for interacting
1442 with alignment and overview windows
1445 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1449 <!-- JAL-2388 -->Hidden columns and sequences can be
1453 <!-- JAL-2611 -->Click-drag in visible area allows fine
1454 adjustment of visible position
1458 <em>Data import/export</em>
1461 <!-- JAL-2535 -->Posterior probability annotation from
1462 Stockholm files imported as sequence associated annotation
1465 <!-- JAL-2507 -->More robust per-sequence positional
1466 annotation input/output via stockholm flatfile
1469 <!-- JAL-2533 -->Sequence names don't include file
1470 extension when importing structure files without embedded
1471 names or PDB accessions
1474 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1475 format sequence substitution matrices
1478 <em>User Interface</em>
1481 <!-- JAL-2447 --> Experimental Features Checkbox in
1482 Desktop's Tools menu to hide or show untested features in
1486 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1487 via Overview or sequence motif search operations
1490 <!-- JAL-2547 -->Amend sequence features dialog box can be
1491 opened by double clicking gaps within sequence feature
1495 <!-- JAL-1476 -->Status bar message shown when not enough
1496 aligned positions were available to create a 3D structure
1500 <em>3D Structure</em>
1503 <!-- JAL-2430 -->Hidden regions in alignment views are not
1504 coloured in linked structure views
1507 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1508 file-based command exchange
1511 <!-- JAL-2375 -->Structure chooser automatically shows
1512 Cached Structures rather than querying the PDBe if
1513 structures are already available for sequences
1516 <!-- JAL-2520 -->Structures imported via URL are cached in
1517 the Jalview project rather than downloaded again when the
1518 project is reopened.
1521 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1522 to transfer Chimera's structure attributes as Jalview
1523 features, and vice-versa (<strong>Experimental
1527 <em>Web Services</em>
1530 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1533 <!-- JAL-2335 -->Filter non-standard amino acids and
1534 nucleotides when submitting to AACon and other MSA
1538 <!-- JAL-2316, -->URLs for viewing database
1539 cross-references provided by identifiers.org and the
1540 EMBL-EBI's MIRIAM DB
1547 <!-- JAL-2344 -->FileFormatI interface for describing and
1548 identifying file formats (instead of String constants)
1551 <!-- JAL-2228 -->FeatureCounter script refactored for
1552 efficiency when counting all displayed features (not
1553 backwards compatible with 2.10.1)
1556 <em>Example files</em>
1559 <!-- JAL-2631 -->Graduated feature colour style example
1560 included in the example feature file
1563 <em>Documentation</em>
1566 <!-- JAL-2339 -->Release notes reformatted for readability
1567 with the built-in Java help viewer
1570 <!-- JAL-1644 -->Find documentation updated with 'search
1571 sequence description' option
1577 <!-- JAL-2485, -->External service integration tests for
1578 Uniprot REST Free Text Search Client
1581 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1584 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1589 <td><div align="left">
1590 <em>Calculations</em>
1593 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1594 matrix - C->R should be '-3'<br />Old matrix restored
1595 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1597 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1598 Jalview's treatment of gaps in PCA and substitution matrix
1599 based Tree calculations.<br /> <br />In earlier versions
1600 of Jalview, gaps matching gaps were penalised, and gaps
1601 matching non-gaps penalised even more. In the PCA
1602 calculation, gaps were actually treated as non-gaps - so
1603 different costs were applied, which meant Jalview's PCAs
1604 were different to those produced by SeqSpace.<br />Jalview
1605 now treats gaps in the same way as SeqSpace (ie it scores
1606 them as 0). <br /> <br />Enter the following in the
1607 Groovy console to restore pre-2.10.2 behaviour:<br />
1608 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1609 // for 2.10.1 mode <br />
1610 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1611 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1612 these settings will affect all subsequent tree and PCA
1613 calculations (not recommended)</em></li>
1615 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1616 scaling of branch lengths for trees computed using
1617 Sequence Feature Similarity.
1620 <!-- JAL-2377 -->PCA calculation could hang when
1621 generating output report when working with highly
1622 redundant alignments
1625 <!-- JAL-2544 --> Sort by features includes features to
1626 right of selected region when gaps present on right-hand
1630 <em>User Interface</em>
1633 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1634 doesn't reselect a specific sequence's associated
1635 annotation after it was used for colouring a view
1638 <!-- JAL-2419 -->Current selection lost if popup menu
1639 opened on a region of alignment without groups
1642 <!-- JAL-2374 -->Popup menu not always shown for regions
1643 of an alignment with overlapping groups
1646 <!-- JAL-2310 -->Finder double counts if both a sequence's
1647 name and description match
1650 <!-- JAL-2370 -->Hiding column selection containing two
1651 hidden regions results in incorrect hidden regions
1654 <!-- JAL-2386 -->'Apply to all groups' setting when
1655 changing colour does not apply Conservation slider value
1659 <!-- JAL-2373 -->Percentage identity and conservation menu
1660 items do not show a tick or allow shading to be disabled
1663 <!-- JAL-2385 -->Conservation shading or PID threshold
1664 lost when base colourscheme changed if slider not visible
1667 <!-- JAL-2547 -->Sequence features shown in tooltip for
1668 gaps before start of features
1671 <!-- JAL-2623 -->Graduated feature colour threshold not
1672 restored to UI when feature colour is edited
1675 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1676 a time when scrolling vertically in wrapped mode.
1679 <!-- JAL-2630 -->Structure and alignment overview update
1680 as graduate feature colour settings are modified via the
1684 <!-- JAL-2034 -->Overview window doesn't always update
1685 when a group defined on the alignment is resized
1688 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1689 wrapped view result in positional status updates
1693 <!-- JAL-2563 -->Status bar doesn't show position for
1694 ambiguous amino acid and nucleotide symbols
1697 <!-- JAL-2602 -->Copy consensus sequence failed if
1698 alignment included gapped columns
1701 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1702 widgets don't permanently disappear
1705 <!-- JAL-2503 -->Cannot select or filter quantitative
1706 annotation that are shown only as column labels (e.g.
1707 T-Coffee column reliability scores)
1710 <!-- JAL-2594 -->Exception thrown if trying to create a
1711 sequence feature on gaps only
1714 <!-- JAL-2504 -->Features created with 'New feature'
1715 button from a Find inherit previously defined feature type
1716 rather than the Find query string
1719 <!-- JAL-2423 -->incorrect title in output window when
1720 exporting tree calculated in Jalview
1723 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1724 and then revealing them reorders sequences on the
1728 <!-- JAL-964 -->Group panel in sequence feature settings
1729 doesn't update to reflect available set of groups after
1730 interactively adding or modifying features
1733 <!-- JAL-2225 -->Sequence Database chooser unusable on
1737 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1738 only excluded gaps in current sequence and ignored
1745 <!-- JAL-2421 -->Overview window visible region moves
1746 erratically when hidden rows or columns are present
1749 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1750 Structure Viewer's colour menu don't correspond to
1754 <!-- JAL-2405 -->Protein specific colours only offered in
1755 colour and group colour menu for protein alignments
1758 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1759 reflect currently selected view or group's shading
1763 <!-- JAL-2624 -->Feature colour thresholds not respected
1764 when rendered on overview and structures when opacity at
1768 <!-- JAL-2589 -->User defined gap colour not shown in
1769 overview when features overlaid on alignment
1772 <!-- JAL-2567 -->Feature settings for different views not
1773 recovered correctly from Jalview project file
1776 <!-- JAL-2256 -->Feature colours in overview when first opened
1777 (automatically via preferences) are different to the main
1781 <em>Data import/export</em>
1784 <!-- JAL-2576 -->Very large alignments take a long time to
1788 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1789 added after a sequence was imported are not written to
1793 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1794 when importing RNA secondary structure via Stockholm
1797 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1798 not shown in correct direction for simple pseudoknots
1801 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1802 with lightGray or darkGray via features file (but can
1806 <!-- JAL-2383 -->Above PID colour threshold not recovered
1807 when alignment view imported from project
1810 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1811 structure and sequences extracted from structure files
1812 imported via URL and viewed in Jmol
1815 <!-- JAL-2520 -->Structures loaded via URL are saved in
1816 Jalview Projects rather than fetched via URL again when
1817 the project is loaded and the structure viewed
1820 <em>Web Services</em>
1823 <!-- JAL-2519 -->EnsemblGenomes example failing after
1824 release of Ensembl v.88
1827 <!-- JAL-2366 -->Proxy server address and port always
1828 appear enabled in Preferences->Connections
1831 <!-- JAL-2461 -->DAS registry not found exceptions
1832 removed from console output
1835 <!-- JAL-2582 -->Cannot retrieve protein products from
1836 Ensembl by Peptide ID
1839 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1840 created from SIFTs, and spurious 'Couldn't open structure
1841 in Chimera' errors raised after April 2017 update (problem
1842 due to 'null' string rather than empty string used for
1843 residues with no corresponding PDB mapping).
1846 <em>Application UI</em>
1849 <!-- JAL-2361 -->User Defined Colours not added to Colour
1853 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1854 case' residues (button in colourscheme editor debugged and
1855 new documentation and tooltips added)
1858 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1859 doesn't restore group-specific text colour thresholds
1862 <!-- JAL-2243 -->Feature settings panel does not update as
1863 new features are added to alignment
1866 <!-- JAL-2532 -->Cancel in feature settings reverts
1867 changes to feature colours via the Amend features dialog
1870 <!-- JAL-2506 -->Null pointer exception when attempting to
1871 edit graduated feature colour via amend features dialog
1875 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1876 selection menu changes colours of alignment views
1879 <!-- JAL-2426 -->Spurious exceptions in console raised
1880 from alignment calculation workers after alignment has
1884 <!-- JAL-1608 -->Typo in selection popup menu - Create
1885 groups now 'Create Group'
1888 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1889 Create/Undefine group doesn't always work
1892 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1893 shown again after pressing 'Cancel'
1896 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1897 adjusts start position in wrap mode
1900 <!-- JAL-2563 -->Status bar doesn't show positions for
1901 ambiguous amino acids
1904 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1905 CDS/Protein view after CDS sequences added for aligned
1909 <!-- JAL-2592 -->User defined colourschemes called 'User
1910 Defined' don't appear in Colours menu
1916 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1917 score models doesn't always result in an updated PCA plot
1920 <!-- JAL-2442 -->Features not rendered as transparent on
1921 overview or linked structure view
1924 <!-- JAL-2372 -->Colour group by conservation doesn't
1928 <!-- JAL-2517 -->Hitting Cancel after applying
1929 user-defined colourscheme doesn't restore original
1936 <!-- JAL-2314 -->Unit test failure:
1937 jalview.ws.jabaws.RNAStructExportImport setup fails
1940 <!-- JAL-2307 -->Unit test failure:
1941 jalview.ws.sifts.SiftsClientTest due to compatibility
1942 problems with deep array comparison equality asserts in
1943 successive versions of TestNG
1946 <!-- JAL-2479 -->Relocated StructureChooserTest and
1947 ParameterUtilsTest Unit tests to Network suite
1950 <em>New Known Issues</em>
1953 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1954 phase after a sequence motif find operation
1957 <!-- JAL-2550 -->Importing annotation file with rows
1958 containing just upper and lower case letters are
1959 interpreted as WUSS RNA secondary structure symbols
1962 <!-- JAL-2590 -->Cannot load and display Newick trees
1963 reliably from eggnog Ortholog database
1966 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1967 containing features of type Highlight' when 'B' is pressed
1968 to mark columns containing highlighted regions.
1971 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1972 doesn't always add secondary structure annotation.
1977 <td width="60" nowrap>
1978 <div align="center">
1979 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1982 <td><div align="left">
1986 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1987 for all consensus calculations
1990 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1993 <li>Updated Jalview's Certum code signing certificate
1996 <em>Application</em>
1999 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2000 set of database cross-references, sorted alphabetically
2003 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2004 from database cross references. Users with custom links
2005 will receive a <a href="webServices/urllinks.html#warning">warning
2006 dialog</a> asking them to update their preferences.
2009 <!-- JAL-2287-->Cancel button and escape listener on
2010 dialog warning user about disconnecting Jalview from a
2014 <!-- JAL-2320-->Jalview's Chimera control window closes if
2015 the Chimera it is connected to is shut down
2018 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2019 columns menu item to mark columns containing highlighted
2020 regions (e.g. from structure selections or results of a
2024 <!-- JAL-2284-->Command line option for batch-generation
2025 of HTML pages rendering alignment data with the BioJS
2035 <!-- JAL-2286 -->Columns with more than one modal residue
2036 are not coloured or thresholded according to percent
2037 identity (first observed in Jalview 2.8.2)
2040 <!-- JAL-2301 -->Threonine incorrectly reported as not
2044 <!-- JAL-2318 -->Updates to documentation pages (above PID
2045 threshold, amino acid properties)
2048 <!-- JAL-2292 -->Lower case residues in sequences are not
2049 reported as mapped to residues in a structure file in the
2053 <!--JAL-2324 -->Identical features with non-numeric scores
2054 could be added multiple times to a sequence
2057 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2058 bond features shown as two highlighted residues rather
2059 than a range in linked structure views, and treated
2060 correctly when selecting and computing trees from features
2063 <!-- JAL-2281-->Custom URL links for database
2064 cross-references are matched to database name regardless
2069 <em>Application</em>
2072 <!-- JAL-2282-->Custom URL links for specific database
2073 names without regular expressions also offer links from
2077 <!-- JAL-2315-->Removing a single configured link in the
2078 URL links pane in Connections preferences doesn't actually
2079 update Jalview configuration
2082 <!-- JAL-2272-->CTRL-Click on a selected region to open
2083 the alignment area popup menu doesn't work on El-Capitan
2086 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2087 files with similarly named sequences if dropped onto the
2091 <!-- JAL-2312 -->Additional mappings are shown for PDB
2092 entries where more chains exist in the PDB accession than
2093 are reported in the SIFTS file
2096 <!-- JAL-2317-->Certain structures do not get mapped to
2097 the structure view when displayed with Chimera
2100 <!-- JAL-2317-->No chains shown in the Chimera view
2101 panel's View->Show Chains submenu
2104 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2105 work for wrapped alignment views
2108 <!--JAL-2197 -->Rename UI components for running JPred
2109 predictions from 'JNet' to 'JPred'
2112 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2113 corrupted when annotation panel vertical scroll is not at
2114 first annotation row
2117 <!--JAL-2332 -->Attempting to view structure for Hen
2118 lysozyme results in a PDB Client error dialog box
2121 <!-- JAL-2319 -->Structure View's mapping report switched
2122 ranges for PDB and sequence for SIFTS
2125 SIFTS 'Not_Observed' residues mapped to non-existant
2129 <!-- <em>New Known Issues</em>
2136 <td width="60" nowrap>
2137 <div align="center">
2138 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2139 <em>25/10/2016</em></strong>
2142 <td><em>Application</em>
2144 <li>3D Structure chooser opens with 'Cached structures'
2145 view if structures already loaded</li>
2146 <li>Progress bar reports models as they are loaded to
2147 structure views</li>
2153 <li>Colour by conservation always enabled and no tick
2154 shown in menu when BLOSUM or PID shading applied</li>
2155 <li>FER1_ARATH and FER2_ARATH labels were switched in
2156 example sequences/projects/trees</li>
2158 <em>Application</em>
2160 <li>Jalview projects with views of local PDB structure
2161 files saved on Windows cannot be opened on OSX</li>
2162 <li>Multiple structure views can be opened and superposed
2163 without timeout for structures with multiple models or
2164 multiple sequences in alignment</li>
2165 <li>Cannot import or associated local PDB files without a
2166 PDB ID HEADER line</li>
2167 <li>RMSD is not output in Jmol console when superposition
2169 <li>Drag and drop of URL from Browser fails for Linux and
2170 OSX versions earlier than El Capitan</li>
2171 <li>ENA client ignores invalid content from ENA server</li>
2172 <li>Exceptions are not raised in console when ENA client
2173 attempts to fetch non-existent IDs via Fetch DB Refs UI
2175 <li>Exceptions are not raised in console when a new view
2176 is created on the alignment</li>
2177 <li>OSX right-click fixed for group selections: CMD-click
2178 to insert/remove gaps in groups and CTRL-click to open group
2181 <em>Build and deployment</em>
2183 <li>URL link checker now copes with multi-line anchor
2186 <em>New Known Issues</em>
2188 <li>Drag and drop from URL links in browsers do not work
2195 <td width="60" nowrap>
2196 <div align="center">
2197 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2200 <td><em>General</em>
2203 <!-- JAL-2124 -->Updated Spanish translations.
2206 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2207 for importing structure data to Jalview. Enables mmCIF and
2211 <!-- JAL-192 --->Alignment ruler shows positions relative to
2215 <!-- JAL-2202 -->Position/residue shown in status bar when
2216 mousing over sequence associated annotation
2219 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2223 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2224 '()', canonical '[]' and invalid '{}' base pair populations
2228 <!-- JAL-2092 -->Feature settings popup menu options for
2229 showing or hiding columns containing a feature
2232 <!-- JAL-1557 -->Edit selected group by double clicking on
2233 group and sequence associated annotation labels
2236 <!-- JAL-2236 -->Sequence name added to annotation label in
2237 select/hide columns by annotation and colour by annotation
2241 </ul> <em>Application</em>
2244 <!-- JAL-2050-->Automatically hide introns when opening a
2245 gene/transcript view
2248 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2252 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2253 structure mappings with the EMBL-EBI PDBe SIFTS database
2256 <!-- JAL-2079 -->Updated download sites used for Rfam and
2257 Pfam sources to xfam.org
2260 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2263 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2264 over sequences in Jalview
2267 <!-- JAL-2027-->Support for reverse-complement coding
2268 regions in ENA and EMBL
2271 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2272 for record retrieval via ENA rest API
2275 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2279 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2280 groovy script execution
2283 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2284 alignment window's Calculate menu
2287 <!-- JAL-1812 -->Allow groovy scripts that call
2288 Jalview.getAlignFrames() to run in headless mode
2291 <!-- JAL-2068 -->Support for creating new alignment
2292 calculation workers from groovy scripts
2295 <!-- JAL-1369 --->Store/restore reference sequence in
2299 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2300 associations are now saved/restored from project
2303 <!-- JAL-1993 -->Database selection dialog always shown
2304 before sequence fetcher is opened
2307 <!-- JAL-2183 -->Double click on an entry in Jalview's
2308 database chooser opens a sequence fetcher
2311 <!-- JAL-1563 -->Free-text search client for UniProt using
2312 the UniProt REST API
2315 <!-- JAL-2168 -->-nonews command line parameter to prevent
2316 the news reader opening
2319 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2320 querying stored in preferences
2323 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2327 <!-- JAL-1977-->Tooltips shown on database chooser
2330 <!-- JAL-391 -->Reverse complement function in calculate
2331 menu for nucleotide sequences
2334 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2335 and feature counts preserves alignment ordering (and
2336 debugged for complex feature sets).
2339 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2340 viewing structures with Jalview 2.10
2343 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2344 genome, transcript CCDS and gene ids via the Ensembl and
2345 Ensembl Genomes REST API
2348 <!-- JAL-2049 -->Protein sequence variant annotation
2349 computed for 'sequence_variant' annotation on CDS regions
2353 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2357 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2358 Ref Fetcher fails to match, or otherwise updates sequence
2359 data from external database records.
2362 <!-- JAL-2154 -->Revised Jalview Project format for
2363 efficient recovery of sequence coding and alignment
2364 annotation relationships.
2366 </ul> <!-- <em>Applet</em>
2377 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2381 <!-- JAL-2018-->Export features in Jalview format (again)
2382 includes graduated colourschemes
2385 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2386 working with big alignments and lots of hidden columns
2389 <!-- JAL-2053-->Hidden column markers not always rendered
2390 at right of alignment window
2393 <!-- JAL-2067 -->Tidied up links in help file table of
2397 <!-- JAL-2072 -->Feature based tree calculation not shown
2401 <!-- JAL-2075 -->Hidden columns ignored during feature
2402 based tree calculation
2405 <!-- JAL-2065 -->Alignment view stops updating when show
2406 unconserved enabled for group on alignment
2409 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2413 <!-- JAL-2146 -->Alignment column in status incorrectly
2414 shown as "Sequence position" when mousing over
2418 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2419 hidden columns present
2422 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2423 user created annotation added to alignment
2426 <!-- JAL-1841 -->RNA Structure consensus only computed for
2427 '()' base pair annotation
2430 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2431 in zero scores for all base pairs in RNA Structure
2435 <!-- JAL-2174-->Extend selection with columns containing
2439 <!-- JAL-2275 -->Pfam format writer puts extra space at
2440 beginning of sequence
2443 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2447 <!-- JAL-2238 -->Cannot create groups on an alignment from
2448 from a tree when t-coffee scores are shown
2451 <!-- JAL-1836,1967 -->Cannot import and view PDB
2452 structures with chains containing negative resnums (4q4h)
2455 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2459 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2460 to Clustal, PIR and PileUp output
2463 <!-- JAL-2008 -->Reordering sequence features that are
2464 not visible causes alignment window to repaint
2467 <!-- JAL-2006 -->Threshold sliders don't work in
2468 graduated colour and colour by annotation row for e-value
2469 scores associated with features and annotation rows
2472 <!-- JAL-1797 -->amino acid physicochemical conservation
2473 calculation should be case independent
2476 <!-- JAL-2173 -->Remove annotation also updates hidden
2480 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2481 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2482 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2485 <!-- JAL-2065 -->Null pointer exceptions and redraw
2486 problems when reference sequence defined and 'show
2487 non-conserved' enabled
2490 <!-- JAL-1306 -->Quality and Conservation are now shown on
2491 load even when Consensus calculation is disabled
2494 <!-- JAL-1932 -->Remove right on penultimate column of
2495 alignment does nothing
2498 <em>Application</em>
2501 <!-- JAL-1552-->URLs and links can't be imported by
2502 drag'n'drop on OSX when launched via webstart (note - not
2503 yet fixed for El Capitan)
2506 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2507 output when running on non-gb/us i18n platforms
2510 <!-- JAL-1944 -->Error thrown when exporting a view with
2511 hidden sequences as flat-file alignment
2514 <!-- JAL-2030-->InstallAnywhere distribution fails when
2518 <!-- JAL-2080-->Jalview very slow to launch via webstart
2519 (also hotfix for 2.9.0b2)
2522 <!-- JAL-2085 -->Cannot save project when view has a
2523 reference sequence defined
2526 <!-- JAL-1011 -->Columns are suddenly selected in other
2527 alignments and views when revealing hidden columns
2530 <!-- JAL-1989 -->Hide columns not mirrored in complement
2531 view in a cDNA/Protein splitframe
2534 <!-- JAL-1369 -->Cannot save/restore representative
2535 sequence from project when only one sequence is
2539 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2540 in Structure Chooser
2543 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2544 structure consensus didn't refresh annotation panel
2547 <!-- JAL-1962 -->View mapping in structure view shows
2548 mappings between sequence and all chains in a PDB file
2551 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2552 dialogs format columns correctly, don't display array
2553 data, sort columns according to type
2556 <!-- JAL-1975 -->Export complete shown after destination
2557 file chooser is cancelled during an image export
2560 <!-- JAL-2025 -->Error when querying PDB Service with
2561 sequence name containing special characters
2564 <!-- JAL-2024 -->Manual PDB structure querying should be
2568 <!-- JAL-2104 -->Large tooltips with broken HTML
2569 formatting don't wrap
2572 <!-- JAL-1128 -->Figures exported from wrapped view are
2573 truncated so L looks like I in consensus annotation
2576 <!-- JAL-2003 -->Export features should only export the
2577 currently displayed features for the current selection or
2581 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2582 after fetching cross-references, and restoring from
2586 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2587 followed in the structure viewer
2590 <!-- JAL-2163 -->Titles for individual alignments in
2591 splitframe not restored from project
2594 <!-- JAL-2145 -->missing autocalculated annotation at
2595 trailing end of protein alignment in transcript/product
2596 splitview when pad-gaps not enabled by default
2599 <!-- JAL-1797 -->amino acid physicochemical conservation
2603 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2604 article has been read (reopened issue due to
2605 internationalisation problems)
2608 <!-- JAL-1960 -->Only offer PDB structures in structure
2609 viewer based on sequence name, PDB and UniProt
2614 <!-- JAL-1976 -->No progress bar shown during export of
2618 <!-- JAL-2213 -->Structures not always superimposed after
2619 multiple structures are shown for one or more sequences.
2622 <!-- JAL-1370 -->Reference sequence characters should not
2623 be replaced with '.' when 'Show unconserved' format option
2627 <!-- JAL-1823 -->Cannot specify chain code when entering
2628 specific PDB id for sequence
2631 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2632 'Export hidden sequences' is enabled, but 'export hidden
2633 columns' is disabled.
2636 <!--JAL-2026-->Best Quality option in structure chooser
2637 selects lowest rather than highest resolution structures
2641 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2642 to sequence mapping in 'View Mappings' report
2645 <!-- JAL-2284 -->Unable to read old Jalview projects that
2646 contain non-XML data added after Jalvew wrote project.
2649 <!-- JAL-2118 -->Newly created annotation row reorders
2650 after clicking on it to create new annotation for a
2654 <!-- JAL-1980 -->Null Pointer Exception raised when
2655 pressing Add on an orphaned cut'n'paste window.
2657 <!-- may exclude, this is an external service stability issue JAL-1941
2658 -- > RNA 3D structure not added via DSSR service</li> -->
2663 <!-- JAL-2151 -->Incorrect columns are selected when
2664 hidden columns present before start of sequence
2667 <!-- JAL-1986 -->Missing dependencies on applet pages
2671 <!-- JAL-1947 -->Overview pixel size changes when
2672 sequences are hidden in applet
2675 <!-- JAL-1996 -->Updated instructions for applet
2676 deployment on examples pages.
2683 <td width="60" nowrap>
2684 <div align="center">
2685 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2686 <em>16/10/2015</em></strong>
2689 <td><em>General</em>
2691 <li>Time stamps for signed Jalview application and applet
2696 <em>Application</em>
2698 <li>Duplicate group consensus and conservation rows
2699 shown when tree is partitioned</li>
2700 <li>Erratic behaviour when tree partitions made with
2701 multiple cDNA/Protein split views</li>
2707 <td width="60" nowrap>
2708 <div align="center">
2709 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2710 <em>8/10/2015</em></strong>
2713 <td><em>General</em>
2715 <li>Updated Spanish translations of localized text for
2717 </ul> <em>Application</em>
2719 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2720 <li>Signed OSX InstallAnywhere installer<br></li>
2721 <li>Support for per-sequence based annotations in BioJSON</li>
2722 </ul> <em>Applet</em>
2724 <li>Split frame example added to applet examples page</li>
2725 </ul> <em>Build and Deployment</em>
2728 <!-- JAL-1888 -->New ant target for running Jalview's test
2736 <li>Mapping of cDNA to protein in split frames
2737 incorrect when sequence start > 1</li>
2738 <li>Broken images in filter column by annotation dialog
2740 <li>Feature colours not parsed from features file</li>
2741 <li>Exceptions and incomplete link URLs recovered when
2742 loading a features file containing HTML tags in feature
2746 <em>Application</em>
2748 <li>Annotations corrupted after BioJS export and
2750 <li>Incorrect sequence limits after Fetch DB References
2751 with 'trim retrieved sequences'</li>
2752 <li>Incorrect warning about deleting all data when
2753 deleting selected columns</li>
2754 <li>Patch to build system for shipping properly signed
2755 JNLP templates for webstart launch</li>
2756 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2757 unreleased structures for download or viewing</li>
2758 <li>Tab/space/return keystroke operation of EMBL-PDBe
2759 fetcher/viewer dialogs works correctly</li>
2760 <li>Disabled 'minimise' button on Jalview windows
2761 running on OSX to workaround redraw hang bug</li>
2762 <li>Split cDNA/Protein view position and geometry not
2763 recovered from jalview project</li>
2764 <li>Initial enabled/disabled state of annotation menu
2765 sorter 'show autocalculated first/last' corresponds to
2767 <li>Restoring of Clustal, RNA Helices and T-Coffee
2768 color schemes from BioJSON</li>
2772 <li>Reorder sequences mirrored in cDNA/Protein split
2774 <li>Applet with Jmol examples not loading correctly</li>
2780 <td><div align="center">
2781 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2783 <td><em>General</em>
2785 <li>Linked visualisation and analysis of DNA and Protein
2788 <li>Translated cDNA alignments shown as split protein
2789 and DNA alignment views</li>
2790 <li>Codon consensus annotation for linked protein and
2791 cDNA alignment views</li>
2792 <li>Link cDNA or Protein product sequences by loading
2793 them onto Protein or cDNA alignments</li>
2794 <li>Reconstruct linked cDNA alignment from aligned
2795 protein sequences</li>
2798 <li>Jmol integration updated to Jmol v14.2.14</li>
2799 <li>Import and export of Jalview alignment views as <a
2800 href="features/bioJsonFormat.html">BioJSON</a></li>
2801 <li>New alignment annotation file statements for
2802 reference sequences and marking hidden columns</li>
2803 <li>Reference sequence based alignment shading to
2804 highlight variation</li>
2805 <li>Select or hide columns according to alignment
2807 <li>Find option for locating sequences by description</li>
2808 <li>Conserved physicochemical properties shown in amino
2809 acid conservation row</li>
2810 <li>Alignments can be sorted by number of RNA helices</li>
2811 </ul> <em>Application</em>
2813 <li>New cDNA/Protein analysis capabilities
2815 <li>Get Cross-References should open a Split Frame
2816 view with cDNA/Protein</li>
2817 <li>Detect when nucleotide sequences and protein
2818 sequences are placed in the same alignment</li>
2819 <li>Split cDNA/Protein views are saved in Jalview
2824 <li>Use REST API to talk to Chimera</li>
2825 <li>Selected regions in Chimera are highlighted in linked
2826 Jalview windows</li>
2828 <li>VARNA RNA viewer updated to v3.93</li>
2829 <li>VARNA views are saved in Jalview Projects</li>
2830 <li>Pseudoknots displayed as Jalview RNA annotation can
2831 be shown in VARNA</li>
2833 <li>Make groups for selection uses marked columns as well
2834 as the active selected region</li>
2836 <li>Calculate UPGMA and NJ trees using sequence feature
2838 <li>New Export options
2840 <li>New Export Settings dialog to control hidden
2841 region export in flat file generation</li>
2843 <li>Export alignment views for display with the <a
2844 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2846 <li>Export scrollable SVG in HTML page</li>
2847 <li>Optional embedding of BioJSON data when exporting
2848 alignment figures to HTML</li>
2850 <li>3D structure retrieval and display
2852 <li>Free text and structured queries with the PDBe
2854 <li>PDBe Search API based discovery and selection of
2855 PDB structures for a sequence set</li>
2859 <li>JPred4 employed for protein secondary structure
2861 <li>Hide Insertions menu option to hide unaligned columns
2862 for one or a group of sequences</li>
2863 <li>Automatically hide insertions in alignments imported
2864 from the JPred4 web server</li>
2865 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2866 system on OSX<br />LGPL libraries courtesy of <a
2867 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2869 <li>changed 'View nucleotide structure' submenu to 'View
2870 VARNA 2D Structure'</li>
2871 <li>change "View protein structure" menu option to "3D
2874 </ul> <em>Applet</em>
2876 <li>New layout for applet example pages</li>
2877 <li>New parameters to enable SplitFrame view
2878 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2879 <li>New example demonstrating linked viewing of cDNA and
2880 Protein alignments</li>
2881 </ul> <em>Development and deployment</em>
2883 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2884 <li>Include installation type and git revision in build
2885 properties and console log output</li>
2886 <li>Jalview Github organisation, and new github site for
2887 storing BioJsMSA Templates</li>
2888 <li>Jalview's unit tests now managed with TestNG</li>
2891 <!-- <em>General</em>
2893 </ul> --> <!-- issues resolved --> <em>Application</em>
2895 <li>Escape should close any open find dialogs</li>
2896 <li>Typo in select-by-features status report</li>
2897 <li>Consensus RNA secondary secondary structure
2898 predictions are not highlighted in amber</li>
2899 <li>Missing gap character in v2.7 example file means
2900 alignment appears unaligned when pad-gaps is not enabled</li>
2901 <li>First switch to RNA Helices colouring doesn't colour
2902 associated structure views</li>
2903 <li>ID width preference option is greyed out when auto
2904 width checkbox not enabled</li>
2905 <li>Stopped a warning dialog from being shown when
2906 creating user defined colours</li>
2907 <li>'View Mapping' in structure viewer shows sequence
2908 mappings for just that viewer's sequences</li>
2909 <li>Workaround for superposing PDB files containing
2910 multiple models in Chimera</li>
2911 <li>Report sequence position in status bar when hovering
2912 over Jmol structure</li>
2913 <li>Cannot output gaps as '.' symbols with Selection ->
2914 output to text box</li>
2915 <li>Flat file exports of alignments with hidden columns
2916 have incorrect sequence start/end</li>
2917 <li>'Aligning' a second chain to a Chimera structure from
2919 <li>Colour schemes applied to structure viewers don't
2920 work for nucleotide</li>
2921 <li>Loading/cut'n'pasting an empty or invalid file leads
2922 to a grey/invisible alignment window</li>
2923 <li>Exported Jpred annotation from a sequence region
2924 imports to different position</li>
2925 <li>Space at beginning of sequence feature tooltips shown
2926 on some platforms</li>
2927 <li>Chimera viewer 'View | Show Chain' menu is not
2929 <li>'New View' fails with a Null Pointer Exception in
2930 console if Chimera has been opened</li>
2931 <li>Mouseover to Chimera not working</li>
2932 <li>Miscellaneous ENA XML feature qualifiers not
2934 <li>NPE in annotation renderer after 'Extract Scores'</li>
2935 <li>If two structures in one Chimera window, mouseover of
2936 either sequence shows on first structure</li>
2937 <li>'Show annotations' options should not make
2938 non-positional annotations visible</li>
2939 <li>Subsequence secondary structure annotation not shown
2940 in right place after 'view flanking regions'</li>
2941 <li>File Save As type unset when current file format is
2943 <li>Save as '.jar' option removed for saving Jalview
2945 <li>Colour by Sequence colouring in Chimera more
2947 <li>Cannot 'add reference annotation' for a sequence in
2948 several views on same alignment</li>
2949 <li>Cannot show linked products for EMBL / ENA records</li>
2950 <li>Jalview's tooltip wraps long texts containing no
2952 </ul> <em>Applet</em>
2954 <li>Jmol to JalviewLite mouseover/link not working</li>
2955 <li>JalviewLite can't import sequences with ID
2956 descriptions containing angle brackets</li>
2957 </ul> <em>General</em>
2959 <li>Cannot export and reimport RNA secondary structure
2960 via jalview annotation file</li>
2961 <li>Random helix colour palette for colour by annotation
2962 with RNA secondary structure</li>
2963 <li>Mouseover to cDNA from STOP residue in protein
2964 translation doesn't work.</li>
2965 <li>hints when using the select by annotation dialog box</li>
2966 <li>Jmol alignment incorrect if PDB file has alternate CA
2968 <li>FontChooser message dialog appears to hang after
2969 choosing 1pt font</li>
2970 <li>Peptide secondary structure incorrectly imported from
2971 annotation file when annotation display text includes 'e' or
2973 <li>Cannot set colour of new feature type whilst creating
2975 <li>cDNA translation alignment should not be sequence
2976 order dependent</li>
2977 <li>'Show unconserved' doesn't work for lower case
2979 <li>Nucleotide ambiguity codes involving R not recognised</li>
2980 </ul> <em>Deployment and Documentation</em>
2982 <li>Applet example pages appear different to the rest of
2983 www.jalview.org</li>
2984 </ul> <em>Application Known issues</em>
2986 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2987 <li>Misleading message appears after trying to delete
2989 <li>Jalview icon not shown in dock after InstallAnywhere
2990 version launches</li>
2991 <li>Fetching EMBL reference for an RNA sequence results
2992 fails with a sequence mismatch</li>
2993 <li>Corrupted or unreadable alignment display when
2994 scrolling alignment to right</li>
2995 <li>ArrayIndexOutOfBoundsException thrown when remove
2996 empty columns called on alignment with ragged gapped ends</li>
2997 <li>auto calculated alignment annotation rows do not get
2998 placed above or below non-autocalculated rows</li>
2999 <li>Jalview dekstop becomes sluggish at full screen in
3000 ultra-high resolution</li>
3001 <li>Cannot disable consensus calculation independently of
3002 quality and conservation</li>
3003 <li>Mouseover highlighting between cDNA and protein can
3004 become sluggish with more than one splitframe shown</li>
3005 </ul> <em>Applet Known Issues</em>
3007 <li>Core PDB parsing code requires Jmol</li>
3008 <li>Sequence canvas panel goes white when alignment
3009 window is being resized</li>
3015 <td><div align="center">
3016 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3018 <td><em>General</em>
3020 <li>Updated Java code signing certificate donated by
3022 <li>Features and annotation preserved when performing
3023 pairwise alignment</li>
3024 <li>RNA pseudoknot annotation can be
3025 imported/exported/displayed</li>
3026 <li>'colour by annotation' can colour by RNA and
3027 protein secondary structure</li>
3028 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3029 post-hoc with 2.9 release</em>)
3032 </ul> <em>Application</em>
3034 <li>Extract and display secondary structure for sequences
3035 with 3D structures</li>
3036 <li>Support for parsing RNAML</li>
3037 <li>Annotations menu for layout
3039 <li>sort sequence annotation rows by alignment</li>
3040 <li>place sequence annotation above/below alignment
3043 <li>Output in Stockholm format</li>
3044 <li>Internationalisation: improved Spanish (es)
3046 <li>Structure viewer preferences tab</li>
3047 <li>Disorder and Secondary Structure annotation tracks
3048 shared between alignments</li>
3049 <li>UCSF Chimera launch and linked highlighting from
3051 <li>Show/hide all sequence associated annotation rows for
3052 all or current selection</li>
3053 <li>disorder and secondary structure predictions
3054 available as dataset annotation</li>
3055 <li>Per-sequence rna helices colouring</li>
3058 <li>Sequence database accessions imported when fetching
3059 alignments from Rfam</li>
3060 <li>update VARNA version to 3.91</li>
3062 <li>New groovy scripts for exporting aligned positions,
3063 conservation values, and calculating sum of pairs scores.</li>
3064 <li>Command line argument to set default JABAWS server</li>
3065 <li>include installation type in build properties and
3066 console log output</li>
3067 <li>Updated Jalview project format to preserve dataset
3071 <!-- issues resolved --> <em>Application</em>
3073 <li>Distinguish alignment and sequence associated RNA
3074 structure in structure->view->VARNA</li>
3075 <li>Raise dialog box if user deletes all sequences in an
3077 <li>Pressing F1 results in documentation opening twice</li>
3078 <li>Sequence feature tooltip is wrapped</li>
3079 <li>Double click on sequence associated annotation
3080 selects only first column</li>
3081 <li>Redundancy removal doesn't result in unlinked
3082 leaves shown in tree</li>
3083 <li>Undos after several redundancy removals don't undo
3085 <li>Hide sequence doesn't hide associated annotation</li>
3086 <li>User defined colours dialog box too big to fit on
3087 screen and buttons not visible</li>
3088 <li>author list isn't updated if already written to
3089 Jalview properties</li>
3090 <li>Popup menu won't open after retrieving sequence
3092 <li>File open window for associate PDB doesn't open</li>
3093 <li>Left-then-right click on a sequence id opens a
3094 browser search window</li>
3095 <li>Cannot open sequence feature shading/sort popup menu
3096 in feature settings dialog</li>
3097 <li>better tooltip placement for some areas of Jalview
3099 <li>Allow addition of JABAWS Server which doesn't
3100 pass validation</li>
3101 <li>Web services parameters dialog box is too large to
3103 <li>Muscle nucleotide alignment preset obscured by
3105 <li>JABAWS preset submenus don't contain newly
3106 defined user preset</li>
3107 <li>MSA web services warns user if they were launched
3108 with invalid input</li>
3109 <li>Jalview cannot contact DAS Registy when running on
3112 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3113 'Superpose with' submenu not shown when new view
3117 </ul> <!-- <em>Applet</em>
3119 </ul> <em>General</em>
3121 </ul>--> <em>Deployment and Documentation</em>
3123 <li>2G and 1G options in launchApp have no effect on
3124 memory allocation</li>
3125 <li>launchApp service doesn't automatically open
3126 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3128 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3129 InstallAnywhere reports cannot find valid JVM when Java
3130 1.7_055 is available
3132 </ul> <em>Application Known issues</em>
3135 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3136 corrupted or unreadable alignment display when scrolling
3140 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3141 retrieval fails but progress bar continues for DAS retrieval
3142 with large number of ID
3145 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3146 flatfile output of visible region has incorrect sequence
3150 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3151 rna structure consensus doesn't update when secondary
3152 structure tracks are rearranged
3155 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3156 invalid rna structure positional highlighting does not
3157 highlight position of invalid base pairs
3160 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3161 out of memory errors are not raised when saving Jalview
3162 project from alignment window file menu
3165 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3166 Switching to RNA Helices colouring doesn't propagate to
3170 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3171 colour by RNA Helices not enabled when user created
3172 annotation added to alignment
3175 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3176 Jalview icon not shown on dock in Mountain Lion/Webstart
3178 </ul> <em>Applet Known Issues</em>
3181 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3182 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3185 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3186 Jalview and Jmol example not compatible with IE9
3189 <li>Sort by annotation score doesn't reverse order
3195 <td><div align="center">
3196 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3199 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3202 <li>Internationalisation of user interface (usually
3203 called i18n support) and translation for Spanish locale</li>
3204 <li>Define/Undefine group on current selection with
3205 Ctrl-G/Shift Ctrl-G</li>
3206 <li>Improved group creation/removal options in
3207 alignment/sequence Popup menu</li>
3208 <li>Sensible precision for symbol distribution
3209 percentages shown in logo tooltip.</li>
3210 <li>Annotation panel height set according to amount of
3211 annotation when alignment first opened</li>
3212 </ul> <em>Application</em>
3214 <li>Interactive consensus RNA secondary structure
3215 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3216 <li>Select columns containing particular features from
3217 Feature Settings dialog</li>
3218 <li>View all 'representative' PDB structures for selected
3220 <li>Update Jalview project format:
3222 <li>New file extension for Jalview projects '.jvp'</li>
3223 <li>Preserve sequence and annotation dataset (to
3224 store secondary structure annotation,etc)</li>
3225 <li>Per group and alignment annotation and RNA helix
3229 <li>New similarity measures for PCA and Tree calculation
3231 <li>Experimental support for retrieval and viewing of
3232 flanking regions for an alignment</li>
3236 <!-- issues resolved --> <em>Application</em>
3238 <li>logo keeps spinning and status remains at queued or
3239 running after job is cancelled</li>
3240 <li>cannot export features from alignments imported from
3241 Jalview/VAMSAS projects</li>
3242 <li>Buggy slider for web service parameters that take
3244 <li>Newly created RNA secondary structure line doesn't
3245 have 'display all symbols' flag set</li>
3246 <li>T-COFFEE alignment score shading scheme and other
3247 annotation shading not saved in Jalview project</li>
3248 <li>Local file cannot be loaded in freshly downloaded
3250 <li>Jalview icon not shown on dock in Mountain
3252 <li>Load file from desktop file browser fails</li>
3253 <li>Occasional NPE thrown when calculating large trees</li>
3254 <li>Cannot reorder or slide sequences after dragging an
3255 alignment onto desktop</li>
3256 <li>Colour by annotation dialog throws NPE after using
3257 'extract scores' function</li>
3258 <li>Loading/cut'n'pasting an empty file leads to a grey
3259 alignment window</li>
3260 <li>Disorder thresholds rendered incorrectly after
3261 performing IUPred disorder prediction</li>
3262 <li>Multiple group annotated consensus rows shown when
3263 changing 'normalise logo' display setting</li>
3264 <li>Find shows blank dialog after 'finished searching' if
3265 nothing matches query</li>
3266 <li>Null Pointer Exceptions raised when sorting by
3267 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3269 <li>Errors in Jmol console when structures in alignment
3270 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3272 <li>Not all working JABAWS services are shown in
3274 <li>JAVAWS version of Jalview fails to launch with
3275 'invalid literal/length code'</li>
3276 <li>Annotation/RNA Helix colourschemes cannot be applied
3277 to alignment with groups (actually fixed in 2.8.0b1)</li>
3278 <li>RNA Helices and T-Coffee Scores available as default
3281 </ul> <em>Applet</em>
3283 <li>Remove group option is shown even when selection is
3285 <li>Apply to all groups ticked but colourscheme changes
3286 don't affect groups</li>
3287 <li>Documented RNA Helices and T-Coffee Scores as valid
3288 colourscheme name</li>
3289 <li>Annotation labels drawn on sequence IDs when
3290 Annotation panel is not displayed</li>
3291 <li>Increased font size for dropdown menus on OSX and
3292 embedded windows</li>
3293 </ul> <em>Other</em>
3295 <li>Consensus sequence for alignments/groups with a
3296 single sequence were not calculated</li>
3297 <li>annotation files that contain only groups imported as
3298 annotation and junk sequences</li>
3299 <li>Fasta files with sequences containing '*' incorrectly
3300 recognised as PFAM or BLC</li>
3301 <li>conservation/PID slider apply all groups option
3302 doesn't affect background (2.8.0b1)
3304 <li>redundancy highlighting is erratic at 0% and 100%</li>
3305 <li>Remove gapped columns fails for sequences with ragged
3307 <li>AMSA annotation row with leading spaces is not
3308 registered correctly on import</li>
3309 <li>Jalview crashes when selecting PCA analysis for
3310 certain alignments</li>
3311 <li>Opening the colour by annotation dialog for an
3312 existing annotation based 'use original colours'
3313 colourscheme loses original colours setting</li>
3318 <td><div align="center">
3319 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3320 <em>30/1/2014</em></strong>
3324 <li>Trusted certificates for JalviewLite applet and
3325 Jalview Desktop application<br />Certificate was donated by
3326 <a href="https://www.certum.eu">Certum</a> to the Jalview
3327 open source project).
3329 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3330 <li>Output in Stockholm format</li>
3331 <li>Allow import of data from gzipped files</li>
3332 <li>Export/import group and sequence associated line
3333 graph thresholds</li>
3334 <li>Nucleotide substitution matrix that supports RNA and
3335 ambiguity codes</li>
3336 <li>Allow disorder predictions to be made on the current
3337 selection (or visible selection) in the same way that JPred
3339 <li>Groovy scripting for headless Jalview operation</li>
3340 </ul> <em>Other improvements</em>
3342 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3343 <li>COMBINE statement uses current SEQUENCE_REF and
3344 GROUP_REF scope to group annotation rows</li>
3345 <li>Support '' style escaping of quotes in Newick
3347 <li>Group options for JABAWS service by command line name</li>
3348 <li>Empty tooltip shown for JABA service options with a
3349 link but no description</li>
3350 <li>Select primary source when selecting authority in
3351 database fetcher GUI</li>
3352 <li>Add .mfa to FASTA file extensions recognised by
3354 <li>Annotation label tooltip text wrap</li>
3359 <li>Slow scrolling when lots of annotation rows are
3361 <li>Lots of NPE (and slowness) after creating RNA
3362 secondary structure annotation line</li>
3363 <li>Sequence database accessions not imported when
3364 fetching alignments from Rfam</li>
3365 <li>Incorrect SHMR submission for sequences with
3367 <li>View all structures does not always superpose
3369 <li>Option widgets in service parameters not updated to
3370 reflect user or preset settings</li>
3371 <li>Null pointer exceptions for some services without
3372 presets or adjustable parameters</li>
3373 <li>Discover PDB IDs entry in structure menu doesn't
3374 discover PDB xRefs</li>
3375 <li>Exception encountered while trying to retrieve
3376 features with DAS</li>
3377 <li>Lowest value in annotation row isn't coloured
3378 when colour by annotation (per sequence) is coloured</li>
3379 <li>Keyboard mode P jumps to start of gapped region when
3380 residue follows a gap</li>
3381 <li>Jalview appears to hang importing an alignment with
3382 Wrap as default or after enabling Wrap</li>
3383 <li>'Right click to add annotations' message
3384 shown in wrap mode when no annotations present</li>
3385 <li>Disorder predictions fail with NPE if no automatic
3386 annotation already exists on alignment</li>
3387 <li>oninit javascript function should be called after
3388 initialisation completes</li>
3389 <li>Remove redundancy after disorder prediction corrupts
3390 alignment window display</li>
3391 <li>Example annotation file in documentation is invalid</li>
3392 <li>Grouped line graph annotation rows are not exported
3393 to annotation file</li>
3394 <li>Multi-harmony analysis cannot be run when only two
3396 <li>Cannot create multiple groups of line graphs with
3397 several 'combine' statements in annotation file</li>
3398 <li>Pressing return several times causes Number Format
3399 exceptions in keyboard mode</li>
3400 <li>Multi-harmony (SHMMR) method doesn't submit
3401 correct partitions for input data</li>
3402 <li>Translation from DNA to Amino Acids fails</li>
3403 <li>Jalview fail to load newick tree with quoted label</li>
3404 <li>--headless flag isn't understood</li>
3405 <li>ClassCastException when generating EPS in headless
3407 <li>Adjusting sequence-associated shading threshold only
3408 changes one row's threshold</li>
3409 <li>Preferences and Feature settings panel panel
3410 doesn't open</li>
3411 <li>hide consensus histogram also hides conservation and
3412 quality histograms</li>
3417 <td><div align="center">
3418 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3420 <td><em>Application</em>
3422 <li>Support for JABAWS 2.0 Services (AACon alignment
3423 conservation, protein disorder and Clustal Omega)</li>
3424 <li>JABAWS server status indicator in Web Services
3426 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3427 in Jalview alignment window</li>
3428 <li>Updated Jalview build and deploy framework for OSX
3429 mountain lion, windows 7, and 8</li>
3430 <li>Nucleotide substitution matrix for PCA that supports
3431 RNA and ambiguity codes</li>
3433 <li>Improved sequence database retrieval GUI</li>
3434 <li>Support fetching and database reference look up
3435 against multiple DAS sources (Fetch all from in 'fetch db
3437 <li>Jalview project improvements
3439 <li>Store and retrieve the 'belowAlignment'
3440 flag for annotation</li>
3441 <li>calcId attribute to group annotation rows on the
3443 <li>Store AACon calculation settings for a view in
3444 Jalview project</li>
3448 <li>horizontal scrolling gesture support</li>
3449 <li>Visual progress indicator when PCA calculation is
3451 <li>Simpler JABA web services menus</li>
3452 <li>visual indication that web service results are still
3453 being retrieved from server</li>
3454 <li>Serialise the dialogs that are shown when Jalview
3455 starts up for first time</li>
3456 <li>Jalview user agent string for interacting with HTTP
3458 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3460 <li>Examples directory and Groovy library included in
3461 InstallAnywhere distribution</li>
3462 </ul> <em>Applet</em>
3464 <li>RNA alignment and secondary structure annotation
3465 visualization applet example</li>
3466 </ul> <em>General</em>
3468 <li>Normalise option for consensus sequence logo</li>
3469 <li>Reset button in PCA window to return dimensions to
3471 <li>Allow seqspace or Jalview variant of alignment PCA
3473 <li>PCA with either nucleic acid and protein substitution
3475 <li>Allow windows containing HTML reports to be exported
3477 <li>Interactive display and editing of RNA secondary
3478 structure contacts</li>
3479 <li>RNA Helix Alignment Colouring</li>
3480 <li>RNA base pair logo consensus</li>
3481 <li>Parse sequence associated secondary structure
3482 information in Stockholm files</li>
3483 <li>HTML Export database accessions and annotation
3484 information presented in tooltip for sequences</li>
3485 <li>Import secondary structure from LOCARNA clustalw
3486 style RNA alignment files</li>
3487 <li>import and visualise T-COFFEE quality scores for an
3489 <li>'colour by annotation' per sequence option to
3490 shade each sequence according to its associated alignment
3492 <li>New Jalview Logo</li>
3493 </ul> <em>Documentation and Development</em>
3495 <li>documentation for score matrices used in Jalview</li>
3496 <li>New Website!</li>
3498 <td><em>Application</em>
3500 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3501 wsdbfetch REST service</li>
3502 <li>Stop windows being moved outside desktop on OSX</li>
3503 <li>Filetype associations not installed for webstart
3505 <li>Jalview does not always retrieve progress of a JABAWS
3506 job execution in full once it is complete</li>
3507 <li>revise SHMR RSBS definition to ensure alignment is
3508 uploaded via ali_file parameter</li>
3509 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3510 <li>View all structures superposed fails with exception</li>
3511 <li>Jnet job queues forever if a very short sequence is
3512 submitted for prediction</li>
3513 <li>Cut and paste menu not opened when mouse clicked on
3515 <li>Putting fractional value into integer text box in
3516 alignment parameter dialog causes Jalview to hang</li>
3517 <li>Structure view highlighting doesn't work on
3519 <li>View all structures fails with exception shown in
3521 <li>Characters in filename associated with PDBEntry not
3522 escaped in a platform independent way</li>
3523 <li>Jalview desktop fails to launch with exception when
3525 <li>Tree calculation reports 'you must have 2 or more
3526 sequences selected' when selection is empty</li>
3527 <li>Jalview desktop fails to launch with jar signature
3528 failure when java web start temporary file caching is
3530 <li>DAS Sequence retrieval with range qualification
3531 results in sequence xref which includes range qualification</li>
3532 <li>Errors during processing of command line arguments
3533 cause progress bar (JAL-898) to be removed</li>
3534 <li>Replace comma for semi-colon option not disabled for
3535 DAS sources in sequence fetcher</li>
3536 <li>Cannot close news reader when JABAWS server warning
3537 dialog is shown</li>
3538 <li>Option widgets not updated to reflect user settings</li>
3539 <li>Edited sequence not submitted to web service</li>
3540 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3541 <li>InstallAnywhere installer doesn't unpack and run
3542 on OSX Mountain Lion</li>
3543 <li>Annotation panel not given a scroll bar when
3544 sequences with alignment annotation are pasted into the
3546 <li>Sequence associated annotation rows not associated
3547 when loaded from Jalview project</li>
3548 <li>Browser launch fails with NPE on java 1.7</li>
3549 <li>JABAWS alignment marked as finished when job was
3550 cancelled or job failed due to invalid input</li>
3551 <li>NPE with v2.7 example when clicking on Tree
3552 associated with all views</li>
3553 <li>Exceptions when copy/paste sequences with grouped
3554 annotation rows to new window</li>
3555 </ul> <em>Applet</em>
3557 <li>Sequence features are momentarily displayed before
3558 they are hidden using hidefeaturegroups applet parameter</li>
3559 <li>loading features via javascript API automatically
3560 enables feature display</li>
3561 <li>scrollToColumnIn javascript API method doesn't
3563 </ul> <em>General</em>
3565 <li>Redundancy removal fails for rna alignment</li>
3566 <li>PCA calculation fails when sequence has been selected
3567 and then deselected</li>
3568 <li>PCA window shows grey box when first opened on OSX</li>
3569 <li>Letters coloured pink in sequence logo when alignment
3570 coloured with clustalx</li>
3571 <li>Choosing fonts without letter symbols defined causes
3572 exceptions and redraw errors</li>
3573 <li>Initial PCA plot view is not same as manually
3574 reconfigured view</li>
3575 <li>Grouped annotation graph label has incorrect line
3577 <li>Grouped annotation graph label display is corrupted
3578 for lots of labels</li>
3583 <div align="center">
3584 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3587 <td><em>Application</em>
3589 <li>Jalview Desktop News Reader</li>
3590 <li>Tweaked default layout of web services menu</li>
3591 <li>View/alignment association menu to enable user to
3592 easily specify which alignment a multi-structure view takes
3593 its colours/correspondences from</li>
3594 <li>Allow properties file location to be specified as URL</li>
3595 <li>Extend Jalview project to preserve associations
3596 between many alignment views and a single Jmol display</li>
3597 <li>Store annotation row height in Jalview project file</li>
3598 <li>Annotation row column label formatting attributes
3599 stored in project file</li>
3600 <li>Annotation row order for auto-calculated annotation
3601 rows preserved in Jalview project file</li>
3602 <li>Visual progress indication when Jalview state is
3603 saved using Desktop window menu</li>
3604 <li>Visual indication that command line arguments are
3605 still being processed</li>
3606 <li>Groovy script execution from URL</li>
3607 <li>Colour by annotation default min and max colours in
3609 <li>Automatically associate PDB files dragged onto an
3610 alignment with sequences that have high similarity and
3612 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3613 <li>'view structures' option to open many
3614 structures in same window</li>
3615 <li>Sort associated views menu option for tree panel</li>
3616 <li>Group all JABA and non-JABA services for a particular
3617 analysis function in its own submenu</li>
3618 </ul> <em>Applet</em>
3620 <li>Userdefined and autogenerated annotation rows for
3622 <li>Adjustment of alignment annotation pane height</li>
3623 <li>Annotation scrollbar for annotation panel</li>
3624 <li>Drag to reorder annotation rows in annotation panel</li>
3625 <li>'automaticScrolling' parameter</li>
3626 <li>Allow sequences with partial ID string matches to be
3627 annotated from GFF/Jalview features files</li>
3628 <li>Sequence logo annotation row in applet</li>
3629 <li>Absolute paths relative to host server in applet
3630 parameters are treated as such</li>
3631 <li>New in the JalviewLite javascript API:
3633 <li>JalviewLite.js javascript library</li>
3634 <li>Javascript callbacks for
3636 <li>Applet initialisation</li>
3637 <li>Sequence/alignment mouse-overs and selections</li>
3640 <li>scrollTo row and column alignment scrolling
3642 <li>Select sequence/alignment regions from javascript</li>
3643 <li>javascript structure viewer harness to pass
3644 messages between Jmol and Jalview when running as
3645 distinct applets</li>
3646 <li>sortBy method</li>
3647 <li>Set of applet and application examples shipped
3648 with documentation</li>
3649 <li>New example to demonstrate JalviewLite and Jmol
3650 javascript message exchange</li>
3652 </ul> <em>General</em>
3654 <li>Enable Jmol displays to be associated with multiple
3655 multiple alignments</li>
3656 <li>Option to automatically sort alignment with new tree</li>
3657 <li>User configurable link to enable redirects to a
3658 www.Jalview.org mirror</li>
3659 <li>Jmol colours option for Jmol displays</li>
3660 <li>Configurable newline string when writing alignment
3661 and other flat files</li>
3662 <li>Allow alignment annotation description lines to
3663 contain html tags</li>
3664 </ul> <em>Documentation and Development</em>
3666 <li>Add groovy test harness for bulk load testing to
3668 <li>Groovy script to load and align a set of sequences
3669 using a web service before displaying the result in the
3670 Jalview desktop</li>
3671 <li>Restructured javascript and applet api documentation</li>
3672 <li>Ant target to publish example html files with applet
3674 <li>Netbeans project for building Jalview from source</li>
3675 <li>ant task to create online javadoc for Jalview source</li>
3677 <td><em>Application</em>
3679 <li>User defined colourscheme throws exception when
3680 current built in colourscheme is saved as new scheme</li>
3681 <li>AlignFrame->Save in application pops up save
3682 dialog for valid filename/format</li>
3683 <li>Cannot view associated structure for UniProt sequence</li>
3684 <li>PDB file association breaks for UniProt sequence
3686 <li>Associate PDB from file dialog does not tell you
3687 which sequence is to be associated with the file</li>
3688 <li>Find All raises null pointer exception when query
3689 only matches sequence IDs</li>
3690 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3691 <li>Jalview project with Jmol views created with Jalview
3692 2.4 cannot be loaded</li>
3693 <li>Filetype associations not installed for webstart
3695 <li>Two or more chains in a single PDB file associated
3696 with sequences in different alignments do not get coloured
3697 by their associated sequence</li>
3698 <li>Visibility status of autocalculated annotation row
3699 not preserved when project is loaded</li>
3700 <li>Annotation row height and visibility attributes not
3701 stored in Jalview project</li>
3702 <li>Tree bootstraps are not preserved when saved as a
3703 Jalview project</li>
3704 <li>Envision2 workflow tooltips are corrupted</li>
3705 <li>Enabling show group conservation also enables colour
3706 by conservation</li>
3707 <li>Duplicate group associated conservation or consensus
3708 created on new view</li>
3709 <li>Annotation scrollbar not displayed after 'show
3710 all hidden annotation rows' option selected</li>
3711 <li>Alignment quality not updated after alignment
3712 annotation row is hidden then shown</li>
3713 <li>Preserve colouring of structures coloured by
3714 sequences in pre Jalview 2.7 projects</li>
3715 <li>Web service job parameter dialog is not laid out
3717 <li>Web services menu not refreshed after 'reset
3718 services' button is pressed in preferences</li>
3719 <li>Annotation off by one in Jalview v2_3 example project</li>
3720 <li>Structures imported from file and saved in project
3721 get name like jalview_pdb1234.txt when reloaded</li>
3722 <li>Jalview does not always retrieve progress of a JABAWS
3723 job execution in full once it is complete</li>
3724 </ul> <em>Applet</em>
3726 <li>Alignment height set incorrectly when lots of
3727 annotation rows are displayed</li>
3728 <li>Relative URLs in feature HTML text not resolved to
3730 <li>View follows highlighting does not work for positions
3732 <li><= shown as = in tooltip</li>
3733 <li>Export features raises exception when no features
3735 <li>Separator string used for serialising lists of IDs
3736 for javascript api is modified when separator string
3737 provided as parameter</li>
3738 <li>Null pointer exception when selecting tree leaves for
3739 alignment with no existing selection</li>
3740 <li>Relative URLs for datasources assumed to be relative
3741 to applet's codebase</li>
3742 <li>Status bar not updated after finished searching and
3743 search wraps around to first result</li>
3744 <li>StructureSelectionManager instance shared between
3745 several Jalview applets causes race conditions and memory
3747 <li>Hover tooltip and mouseover of position on structure
3748 not sent from Jmol in applet</li>
3749 <li>Certain sequences of javascript method calls to
3750 applet API fatally hang browser</li>
3751 </ul> <em>General</em>
3753 <li>View follows structure mouseover scrolls beyond
3754 position with wrapped view and hidden regions</li>
3755 <li>Find sequence position moves to wrong residue
3756 with/without hidden columns</li>
3757 <li>Sequence length given in alignment properties window
3759 <li>InvalidNumberFormat exceptions thrown when trying to
3760 import PDB like structure files</li>
3761 <li>Positional search results are only highlighted
3762 between user-supplied sequence start/end bounds</li>
3763 <li>End attribute of sequence is not validated</li>
3764 <li>Find dialog only finds first sequence containing a
3765 given sequence position</li>
3766 <li>Sequence numbering not preserved in MSF alignment
3768 <li>Jalview PDB file reader does not extract sequence
3769 from nucleotide chains correctly</li>
3770 <li>Structure colours not updated when tree partition
3771 changed in alignment</li>
3772 <li>Sequence associated secondary structure not correctly
3773 parsed in interleaved stockholm</li>
3774 <li>Colour by annotation dialog does not restore current
3776 <li>Hiding (nearly) all sequences doesn't work
3778 <li>Sequences containing lowercase letters are not
3779 properly associated with their pdb files</li>
3780 </ul> <em>Documentation and Development</em>
3782 <li>schemas/JalviewWsParamSet.xsd corrupted by
3783 ApplyCopyright tool</li>
3788 <div align="center">
3789 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3792 <td><em>Application</em>
3794 <li>New warning dialog when the Jalview Desktop cannot
3795 contact web services</li>
3796 <li>JABA service parameters for a preset are shown in
3797 service job window</li>
3798 <li>JABA Service menu entries reworded</li>
3802 <li>Modeller PIR IO broken - cannot correctly import a
3803 pir file emitted by Jalview</li>
3804 <li>Existing feature settings transferred to new
3805 alignment view created from cut'n'paste</li>
3806 <li>Improved test for mixed amino/nucleotide chains when
3807 parsing PDB files</li>
3808 <li>Consensus and conservation annotation rows
3809 occasionally become blank for all new windows</li>
3810 <li>Exception raised when right clicking above sequences
3811 in wrapped view mode</li>
3812 </ul> <em>Application</em>
3814 <li>multiple multiply aligned structure views cause cpu
3815 usage to hit 100% and computer to hang</li>
3816 <li>Web Service parameter layout breaks for long user
3817 parameter names</li>
3818 <li>Jaba service discovery hangs desktop if Jaba server
3825 <div align="center">
3826 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3829 <td><em>Application</em>
3831 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3832 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3835 <li>Web Services preference tab</li>
3836 <li>Analysis parameters dialog box and user defined
3838 <li>Improved speed and layout of Envision2 service menu</li>
3839 <li>Superpose structures using associated sequence
3841 <li>Export coordinates and projection as CSV from PCA
3843 </ul> <em>Applet</em>
3845 <li>enable javascript: execution by the applet via the
3846 link out mechanism</li>
3847 </ul> <em>Other</em>
3849 <li>Updated the Jmol Jalview interface to work with Jmol
3851 <li>The Jalview Desktop and JalviewLite applet now
3852 require Java 1.5</li>
3853 <li>Allow Jalview feature colour specification for GFF
3854 sequence annotation files</li>
3855 <li>New 'colour by label' keword in Jalview feature file
3856 type colour specification</li>
3857 <li>New Jalview Desktop Groovy API method that allows a
3858 script to check if it being run in an interactive session or
3859 in a batch operation from the Jalview command line</li>
3863 <li>clustalx colourscheme colours Ds preferentially when
3864 both D+E are present in over 50% of the column</li>
3865 </ul> <em>Application</em>
3867 <li>typo in AlignmentFrame->View->Hide->all but
3868 selected Regions menu item</li>
3869 <li>sequence fetcher replaces ',' for ';' when the ',' is
3870 part of a valid accession ID</li>
3871 <li>fatal OOM if object retrieved by sequence fetcher
3872 runs out of memory</li>
3873 <li>unhandled Out of Memory Error when viewing pca
3874 analysis results</li>
3875 <li>InstallAnywhere builds fail to launch on OS X java
3876 10.5 update 4 (due to apple Java 1.6 update)</li>
3877 <li>Installanywhere Jalview silently fails to launch</li>
3878 </ul> <em>Applet</em>
3880 <li>Jalview.getFeatureGroups() raises an
3881 ArrayIndexOutOfBoundsException if no feature groups are
3888 <div align="center">
3889 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3895 <li>Alignment prettyprinter doesn't cope with long
3897 <li>clustalx colourscheme colours Ds preferentially when
3898 both D+E are present in over 50% of the column</li>
3899 <li>nucleic acid structures retrieved from PDB do not
3900 import correctly</li>
3901 <li>More columns get selected than were clicked on when a
3902 number of columns are hidden</li>
3903 <li>annotation label popup menu not providing correct
3904 add/hide/show options when rows are hidden or none are
3906 <li>Stockholm format shown in list of readable formats,
3907 and parser copes better with alignments from RFAM.</li>
3908 <li>CSV output of consensus only includes the percentage
3909 of all symbols if sequence logo display is enabled</li>
3911 </ul> <em>Applet</em>
3913 <li>annotation panel disappears when annotation is
3915 </ul> <em>Application</em>
3917 <li>Alignment view not redrawn properly when new
3918 alignment opened where annotation panel is visible but no
3919 annotations are present on alignment</li>
3920 <li>pasted region containing hidden columns is
3921 incorrectly displayed in new alignment window</li>
3922 <li>Jalview slow to complete operations when stdout is
3923 flooded (fix is to close the Jalview console)</li>
3924 <li>typo in AlignmentFrame->View->Hide->all but
3925 selected Rregions menu item.</li>
3926 <li>inconsistent group submenu and Format submenu entry
3927 'Un' or 'Non'conserved</li>
3928 <li>Sequence feature settings are being shared by
3929 multiple distinct alignments</li>
3930 <li>group annotation not recreated when tree partition is
3932 <li>double click on group annotation to select sequences
3933 does not propagate to associated trees</li>
3934 <li>Mac OSX specific issues:
3936 <li>exception raised when mouse clicked on desktop
3937 window background</li>
3938 <li>Desktop menu placed on menu bar and application
3939 name set correctly</li>
3940 <li>sequence feature settings not wide enough for the
3941 save feature colourscheme button</li>
3950 <div align="center">
3951 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3954 <td><em>New Capabilities</em>
3956 <li>URL links generated from description line for
3957 regular-expression based URL links (applet and application)
3959 <li>Non-positional feature URL links are shown in link
3961 <li>Linked viewing of nucleic acid sequences and
3963 <li>Automatic Scrolling option in View menu to display
3964 the currently highlighted region of an alignment.</li>
3965 <li>Order an alignment by sequence length, or using the
3966 average score or total feature count for each sequence.</li>
3967 <li>Shading features by score or associated description</li>
3968 <li>Subdivide alignment and groups based on identity of
3969 selected subsequence (Make Groups from Selection).</li>
3970 <li>New hide/show options including Shift+Control+H to
3971 hide everything but the currently selected region.</li>
3972 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3973 </ul> <em>Application</em>
3975 <li>Fetch DB References capabilities and UI expanded to
3976 support retrieval from DAS sequence sources</li>
3977 <li>Local DAS Sequence sources can be added via the
3978 command line or via the Add local source dialog box.</li>
3979 <li>DAS Dbref and DbxRef feature types are parsed as
3980 database references and protein_name is parsed as
3981 description line (BioSapiens terms).</li>
3982 <li>Enable or disable non-positional feature and database
3983 references in sequence ID tooltip from View menu in
3985 <!-- <li>New hidden columns and rows and representatives capabilities
3986 in annotations file (in progress - not yet fully implemented)</li> -->
3987 <li>Group-associated consensus, sequence logos and
3988 conservation plots</li>
3989 <li>Symbol distributions for each column can be exported
3990 and visualized as sequence logos</li>
3991 <li>Optionally scale multi-character column labels to fit
3992 within each column of annotation row<!-- todo for applet -->
3994 <li>Optional automatic sort of associated alignment view
3995 when a new tree is opened.</li>
3996 <li>Jalview Java Console</li>
3997 <li>Better placement of desktop window when moving
3998 between different screens.</li>
3999 <li>New preference items for sequence ID tooltip and
4000 consensus annotation</li>
4001 <li>Client to submit sequences and IDs to Envision2
4003 <li><em>Vamsas Capabilities</em>
4005 <li>Improved VAMSAS synchronization (Jalview archive
4006 used to preserve views, structures, and tree display
4008 <li>Import of vamsas documents from disk or URL via
4010 <li>Sharing of selected regions between views and
4011 with other VAMSAS applications (Experimental feature!)</li>
4012 <li>Updated API to VAMSAS version 0.2</li>
4014 </ul> <em>Applet</em>
4016 <li>Middle button resizes annotation row height</li>
4019 <li>sortByTree (true/false) - automatically sort the
4020 associated alignment view by the tree when a new tree is
4022 <li>showTreeBootstraps (true/false) - show or hide
4023 branch bootstraps (default is to show them if available)</li>
4024 <li>showTreeDistances (true/false) - show or hide
4025 branch lengths (default is to show them if available)</li>
4026 <li>showUnlinkedTreeNodes (true/false) - indicate if
4027 unassociated nodes should be highlighted in the tree
4029 <li>heightScale and widthScale (1.0 or more) -
4030 increase the height or width of a cell in the alignment
4031 grid relative to the current font size.</li>
4034 <li>Non-positional features displayed in sequence ID
4036 </ul> <em>Other</em>
4038 <li>Features format: graduated colour definitions and
4039 specification of feature scores</li>
4040 <li>Alignment Annotations format: new keywords for group
4041 associated annotation (GROUP_REF) and annotation row display
4042 properties (ROW_PROPERTIES)</li>
4043 <li>XML formats extended to support graduated feature
4044 colourschemes, group associated annotation, and profile
4045 visualization settings.</li></td>
4048 <li>Source field in GFF files parsed as feature source
4049 rather than description</li>
4050 <li>Non-positional features are now included in sequence
4051 feature and gff files (controlled via non-positional feature
4052 visibility in tooltip).</li>
4053 <li>URL links generated for all feature links (bugfix)</li>
4054 <li>Added URL embedding instructions to features file
4056 <li>Codons containing ambiguous nucleotides translated as
4057 'X' in peptide product</li>
4058 <li>Match case switch in find dialog box works for both
4059 sequence ID and sequence string and query strings do not
4060 have to be in upper case to match case-insensitively.</li>
4061 <li>AMSA files only contain first column of
4062 multi-character column annotation labels</li>
4063 <li>Jalview Annotation File generation/parsing consistent
4064 with documentation (e.g. Stockholm annotation can be
4065 exported and re-imported)</li>
4066 <li>PDB files without embedded PDB IDs given a friendly
4068 <li>Find incrementally searches ID string matches as well
4069 as subsequence matches, and correctly reports total number
4073 <li>Better handling of exceptions during sequence
4075 <li>Dasobert generated non-positional feature URL
4076 link text excludes the start_end suffix</li>
4077 <li>DAS feature and source retrieval buttons disabled
4078 when fetch or registry operations in progress.</li>
4079 <li>PDB files retrieved from URLs are cached properly</li>
4080 <li>Sequence description lines properly shared via
4082 <li>Sequence fetcher fetches multiple records for all
4084 <li>Ensured that command line das feature retrieval
4085 completes before alignment figures are generated.</li>
4086 <li>Reduced time taken when opening file browser for
4088 <li>isAligned check prior to calculating tree, PCA or
4089 submitting an MSA to JNet now excludes hidden sequences.</li>
4090 <li>User defined group colours properly recovered
4091 from Jalview projects.</li>
4100 <div align="center">
4101 <strong>2.4.0.b2</strong><br> 28/10/2009
4106 <li>Experimental support for google analytics usage
4108 <li>Jalview privacy settings (user preferences and docs).</li>
4113 <li>Race condition in applet preventing startup in
4115 <li>Exception when feature created from selection beyond
4116 length of sequence.</li>
4117 <li>Allow synthetic PDB files to be imported gracefully</li>
4118 <li>Sequence associated annotation rows associate with
4119 all sequences with a given id</li>
4120 <li>Find function matches case-insensitively for sequence
4121 ID string searches</li>
4122 <li>Non-standard characters do not cause pairwise
4123 alignment to fail with exception</li>
4124 </ul> <em>Application Issues</em>
4126 <li>Sequences are now validated against EMBL database</li>
4127 <li>Sequence fetcher fetches multiple records for all
4129 </ul> <em>InstallAnywhere Issues</em>
4131 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4132 issue with installAnywhere mechanism)</li>
4133 <li>Command line launching of JARs from InstallAnywhere
4134 version (java class versioning error fixed)</li>
4141 <div align="center">
4142 <strong>2.4</strong><br> 27/8/2008
4145 <td><em>User Interface</em>
4147 <li>Linked highlighting of codon and amino acid from
4148 translation and protein products</li>
4149 <li>Linked highlighting of structure associated with
4150 residue mapping to codon position</li>
4151 <li>Sequence Fetcher provides example accession numbers
4152 and 'clear' button</li>
4153 <li>MemoryMonitor added as an option under Desktop's
4155 <li>Extract score function to parse whitespace separated
4156 numeric data in description line</li>
4157 <li>Column labels in alignment annotation can be centred.</li>
4158 <li>Tooltip for sequence associated annotation give name
4160 </ul> <em>Web Services and URL fetching</em>
4162 <li>JPred3 web service</li>
4163 <li>Prototype sequence search client (no public services
4165 <li>Fetch either seed alignment or full alignment from
4167 <li>URL Links created for matching database cross
4168 references as well as sequence ID</li>
4169 <li>URL Links can be created using regular-expressions</li>
4170 </ul> <em>Sequence Database Connectivity</em>
4172 <li>Retrieval of cross-referenced sequences from other
4174 <li>Generalised database reference retrieval and
4175 validation to all fetchable databases</li>
4176 <li>Fetch sequences from DAS sources supporting the
4177 sequence command</li>
4178 </ul> <em>Import and Export</em>
4179 <li>export annotation rows as CSV for spreadsheet import</li>
4180 <li>Jalview projects record alignment dataset associations,
4181 EMBL products, and cDNA sequence mappings</li>
4182 <li>Sequence Group colour can be specified in Annotation
4184 <li>Ad-hoc colouring of group in Annotation File using RGB
4185 triplet as name of colourscheme</li>
4186 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4188 <li>treenode binding for VAMSAS tree exchange</li>
4189 <li>local editing and update of sequences in VAMSAS
4190 alignments (experimental)</li>
4191 <li>Create new or select existing session to join</li>
4192 <li>load and save of vamsas documents</li>
4193 </ul> <em>Application command line</em>
4195 <li>-tree parameter to open trees (introduced for passing
4197 <li>-fetchfrom command line argument to specify nicknames
4198 of DAS servers to query for alignment features</li>
4199 <li>-dasserver command line argument to add new servers
4200 that are also automatically queried for features</li>
4201 <li>-groovy command line argument executes a given groovy
4202 script after all input data has been loaded and parsed</li>
4203 </ul> <em>Applet-Application data exchange</em>
4205 <li>Trees passed as applet parameters can be passed to
4206 application (when using "View in full
4207 application")</li>
4208 </ul> <em>Applet Parameters</em>
4210 <li>feature group display control parameter</li>
4211 <li>debug parameter</li>
4212 <li>showbutton parameter</li>
4213 </ul> <em>Applet API methods</em>
4215 <li>newView public method</li>
4216 <li>Window (current view) specific get/set public methods</li>
4217 <li>Feature display control methods</li>
4218 <li>get list of currently selected sequences</li>
4219 </ul> <em>New Jalview distribution features</em>
4221 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4222 <li>RELEASE file gives build properties for the latest
4223 Jalview release.</li>
4224 <li>Java 1.1 Applet build made easier and donotobfuscate
4225 property controls execution of obfuscator</li>
4226 <li>Build target for generating source distribution</li>
4227 <li>Debug flag for javacc</li>
4228 <li>.jalview_properties file is documented (slightly) in
4229 jalview.bin.Cache</li>
4230 <li>Continuous Build Integration for stable and
4231 development version of Application, Applet and source
4236 <li>selected region output includes visible annotations
4237 (for certain formats)</li>
4238 <li>edit label/displaychar contains existing label/char
4240 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4241 <li>shorter peptide product names from EMBL records</li>
4242 <li>Newick string generator makes compact representations</li>
4243 <li>bootstrap values parsed correctly for tree files with
4245 <li>pathological filechooser bug avoided by not allowing
4246 filenames containing a ':'</li>
4247 <li>Fixed exception when parsing GFF files containing
4248 global sequence features</li>
4249 <li>Alignment datasets are finalized only when number of
4250 references from alignment sequences goes to zero</li>
4251 <li>Close of tree branch colour box without colour
4252 selection causes cascading exceptions</li>
4253 <li>occasional negative imgwidth exceptions</li>
4254 <li>better reporting of non-fatal warnings to user when
4255 file parsing fails.</li>
4256 <li>Save works when Jalview project is default format</li>
4257 <li>Save as dialog opened if current alignment format is
4258 not a valid output format</li>
4259 <li>UniProt canonical names introduced for both das and
4261 <li>Histidine should be midblue (not pink!) in Zappo</li>
4262 <li>error messages passed up and output when data read
4264 <li>edit undo recovers previous dataset sequence when
4265 sequence is edited</li>
4266 <li>allow PDB files without pdb ID HEADER lines (like
4267 those generated by MODELLER) to be read in properly</li>
4268 <li>allow reading of JPred concise files as a normal
4270 <li>Stockholm annotation parsing and alignment properties
4271 import fixed for PFAM records</li>
4272 <li>Structure view windows have correct name in Desktop
4274 <li>annotation consisting of sequence associated scores
4275 can be read and written correctly to annotation file</li>
4276 <li>Aligned cDNA translation to aligned peptide works
4278 <li>Fixed display of hidden sequence markers and
4279 non-italic font for representatives in Applet</li>
4280 <li>Applet Menus are always embedded in applet window on
4282 <li>Newly shown features appear at top of stack (in
4284 <li>Annotations added via parameter not drawn properly
4285 due to null pointer exceptions</li>
4286 <li>Secondary structure lines are drawn starting from
4287 first column of alignment</li>
4288 <li>UniProt XML import updated for new schema release in
4290 <li>Sequence feature to sequence ID match for Features
4291 file is case-insensitive</li>
4292 <li>Sequence features read from Features file appended to
4293 all sequences with matching IDs</li>
4294 <li>PDB structure coloured correctly for associated views
4295 containing a sub-sequence</li>
4296 <li>PDB files can be retrieved by applet from Jar files</li>
4297 <li>feature and annotation file applet parameters
4298 referring to different directories are retrieved correctly</li>
4299 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4300 <li>Fixed application hang whilst waiting for
4301 splash-screen version check to complete</li>
4302 <li>Applet properly URLencodes input parameter values
4303 when passing them to the launchApp service</li>
4304 <li>display name and local features preserved in results
4305 retrieved from web service</li>
4306 <li>Visual delay indication for sequence retrieval and
4307 sequence fetcher initialisation</li>
4308 <li>updated Application to use DAS 1.53e version of
4309 dasobert DAS client</li>
4310 <li>Re-instated Full AMSA support and .amsa file
4312 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4320 <div align="center">
4321 <strong>2.3</strong><br> 9/5/07
4326 <li>Jmol 11.0.2 integration</li>
4327 <li>PDB views stored in Jalview XML files</li>
4328 <li>Slide sequences</li>
4329 <li>Edit sequence in place</li>
4330 <li>EMBL CDS features</li>
4331 <li>DAS Feature mapping</li>
4332 <li>Feature ordering</li>
4333 <li>Alignment Properties</li>
4334 <li>Annotation Scores</li>
4335 <li>Sort by scores</li>
4336 <li>Feature/annotation editing in applet</li>
4341 <li>Headless state operation in 2.2.1</li>
4342 <li>Incorrect and unstable DNA pairwise alignment</li>
4343 <li>Cut and paste of sequences with annotation</li>
4344 <li>Feature group display state in XML</li>
4345 <li>Feature ordering in XML</li>
4346 <li>blc file iteration selection using filename # suffix</li>
4347 <li>Stockholm alignment properties</li>
4348 <li>Stockhom alignment secondary structure annotation</li>
4349 <li>2.2.1 applet had no feature transparency</li>
4350 <li>Number pad keys can be used in cursor mode</li>
4351 <li>Structure Viewer mirror image resolved</li>
4358 <div align="center">
4359 <strong>2.2.1</strong><br> 12/2/07
4364 <li>Non standard characters can be read and displayed
4365 <li>Annotations/Features can be imported/exported to the
4367 <li>Applet allows editing of sequence/annotation/group
4368 name & description
4369 <li>Preference setting to display sequence name in
4371 <li>Annotation file format extended to allow
4372 Sequence_groups to be defined
4373 <li>Default opening of alignment overview panel can be
4374 specified in preferences
4375 <li>PDB residue numbering annotation added to associated
4381 <li>Applet crash under certain Linux OS with Java 1.6
4383 <li>Annotation file export / import bugs fixed
4384 <li>PNG / EPS image output bugs fixed
4390 <div align="center">
4391 <strong>2.2</strong><br> 27/11/06
4396 <li>Multiple views on alignment
4397 <li>Sequence feature editing
4398 <li>"Reload" alignment
4399 <li>"Save" to current filename
4400 <li>Background dependent text colour
4401 <li>Right align sequence ids
4402 <li>User-defined lower case residue colours
4405 <li>Menu item accelerator keys
4406 <li>Control-V pastes to current alignment
4407 <li>Cancel button for DAS Feature Fetching
4408 <li>PCA and PDB Viewers zoom via mouse roller
4409 <li>User-defined sub-tree colours and sub-tree selection
4411 <li>'New Window' button on the 'Output to Text box'
4416 <li>New memory efficient Undo/Redo System
4417 <li>Optimised symbol lookups and conservation/consensus
4419 <li>Region Conservation/Consensus recalculated after
4421 <li>Fixed Remove Empty Columns Bug (empty columns at end
4423 <li>Slowed DAS Feature Fetching for increased robustness.
4425 <li>Made angle brackets in ASCII feature descriptions
4427 <li>Re-instated Zoom function for PCA
4428 <li>Sequence descriptions conserved in web service
4430 <li>UniProt ID discoverer uses any word separated by
4432 <li>WsDbFetch query/result association resolved
4433 <li>Tree leaf to sequence mapping improved
4434 <li>Smooth fonts switch moved to FontChooser dialog box.
4441 <div align="center">
4442 <strong>2.1.1</strong><br> 12/9/06
4447 <li>Copy consensus sequence to clipboard</li>
4452 <li>Image output - rightmost residues are rendered if
4453 sequence id panel has been resized</li>
4454 <li>Image output - all offscreen group boundaries are
4456 <li>Annotation files with sequence references - all
4457 elements in file are relative to sequence position</li>
4458 <li>Mac Applet users can use Alt key for group editing</li>
4464 <div align="center">
4465 <strong>2.1</strong><br> 22/8/06
4470 <li>MAFFT Multiple Alignment in default Web Service list</li>
4471 <li>DAS Feature fetching</li>
4472 <li>Hide sequences and columns</li>
4473 <li>Export Annotations and Features</li>
4474 <li>GFF file reading / writing</li>
4475 <li>Associate structures with sequences from local PDB
4477 <li>Add sequences to exisiting alignment</li>
4478 <li>Recently opened files / URL lists</li>
4479 <li>Applet can launch the full application</li>
4480 <li>Applet has transparency for features (Java 1.2
4482 <li>Applet has user defined colours parameter</li>
4483 <li>Applet can load sequences from parameter
4484 "sequence<em>x</em>"
4490 <li>Redundancy Panel reinstalled in the Applet</li>
4491 <li>Monospaced font - EPS / rescaling bug fixed</li>
4492 <li>Annotation files with sequence references bug fixed</li>
4498 <div align="center">
4499 <strong>2.08.1</strong><br> 2/5/06
4504 <li>Change case of selected region from Popup menu</li>
4505 <li>Choose to match case when searching</li>
4506 <li>Middle mouse button and mouse movement can compress /
4507 expand the visible width and height of the alignment</li>
4512 <li>Annotation Panel displays complete JNet results</li>
4518 <div align="center">
4519 <strong>2.08b</strong><br> 18/4/06
4525 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4526 <li>Righthand label on wrapped alignments shows correct
4533 <div align="center">
4534 <strong>2.08</strong><br> 10/4/06
4539 <li>Editing can be locked to the selection area</li>
4540 <li>Keyboard editing</li>
4541 <li>Create sequence features from searches</li>
4542 <li>Precalculated annotations can be loaded onto
4544 <li>Features file allows grouping of features</li>
4545 <li>Annotation Colouring scheme added</li>
4546 <li>Smooth fonts off by default - Faster rendering</li>
4547 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4552 <li>Drag & Drop fixed on Linux</li>
4553 <li>Jalview Archive file faster to load/save, sequence
4554 descriptions saved.</li>
4560 <div align="center">
4561 <strong>2.07</strong><br> 12/12/05
4566 <li>PDB Structure Viewer enhanced</li>
4567 <li>Sequence Feature retrieval and display enhanced</li>
4568 <li>Choose to output sequence start-end after sequence
4569 name for file output</li>
4570 <li>Sequence Fetcher WSDBFetch@EBI</li>
4571 <li>Applet can read feature files, PDB files and can be
4572 used for HTML form input</li>
4577 <li>HTML output writes groups and features</li>
4578 <li>Group editing is Control and mouse click</li>
4579 <li>File IO bugs</li>
4585 <div align="center">
4586 <strong>2.06</strong><br> 28/9/05
4591 <li>View annotations in wrapped mode</li>
4592 <li>More options for PCA viewer</li>
4597 <li>GUI bugs resolved</li>
4598 <li>Runs with -nodisplay from command line</li>
4604 <div align="center">
4605 <strong>2.05b</strong><br> 15/9/05
4610 <li>Choose EPS export as lineart or text</li>
4611 <li>Jar files are executable</li>
4612 <li>Can read in Uracil - maps to unknown residue</li>
4617 <li>Known OutOfMemory errors give warning message</li>
4618 <li>Overview window calculated more efficiently</li>
4619 <li>Several GUI bugs resolved</li>
4625 <div align="center">
4626 <strong>2.05</strong><br> 30/8/05
4631 <li>Edit and annotate in "Wrapped" view</li>
4636 <li>Several GUI bugs resolved</li>
4642 <div align="center">
4643 <strong>2.04</strong><br> 24/8/05
4648 <li>Hold down mouse wheel & scroll to change font
4654 <li>Improved JPred client reliability</li>
4655 <li>Improved loading of Jalview files</li>
4661 <div align="center">
4662 <strong>2.03</strong><br> 18/8/05
4667 <li>Set Proxy server name and port in preferences</li>
4668 <li>Multiple URL links from sequence ids</li>
4669 <li>User Defined Colours can have a scheme name and added
4671 <li>Choose to ignore gaps in consensus calculation</li>
4672 <li>Unix users can set default web browser</li>
4673 <li>Runs without GUI for batch processing</li>
4674 <li>Dynamically generated Web Service Menus</li>
4679 <li>InstallAnywhere download for Sparc Solaris</li>
4685 <div align="center">
4686 <strong>2.02</strong><br> 18/7/05
4692 <li>Copy & Paste order of sequences maintains
4693 alignment order.</li>
4699 <div align="center">
4700 <strong>2.01</strong><br> 12/7/05
4705 <li>Use delete key for deleting selection.</li>
4706 <li>Use Mouse wheel to scroll sequences.</li>
4707 <li>Help file updated to describe how to add alignment
4709 <li>Version and build date written to build properties
4711 <li>InstallAnywhere installation will check for updates
4712 at launch of Jalview.</li>
4717 <li>Delete gaps bug fixed.</li>
4718 <li>FileChooser sorts columns.</li>
4719 <li>Can remove groups one by one.</li>
4720 <li>Filechooser icons installed.</li>
4721 <li>Finder ignores return character when searching.
4722 Return key will initiate a search.<br>
4729 <div align="center">
4730 <strong>2.0</strong><br> 20/6/05
4735 <li>New codebase</li>