3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
34 /* separate the items from eachother */
41 /* doesnt get processed in javahelp */
50 <strong>Release History</strong>
54 <th nowrap><em>Release</em></th>
55 <th><em>New Features</em></th>
56 <th><em>Issues Resolved</em></th>
59 <td width="60" align="center" nowrap><strong><a
60 name="Jalview.2.11.1">2.11.1</a><a name="Jalview.2.11.1.0">.0</a><br />
61 <em>25/2/2020</em></strong></td>
62 <td align="left" valign="top">
65 <!-- JAL-3376 -->Record "fixed column" values POS, ID, QUAL, FILTER from VCF as Feature Attributes
68 <!-- JAL-3375 -->More robust VCF numeric data field validation
69 while parsing (e.g. AF* attributes)
75 </ul> <em>Release processes</em>
78 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
80 </ul> <em>Build System</em>
83 <!-- JAL-3510 -->Clover updated to 4.4.1
86 <!-- JAL-3513 -->Test code included in Clover coverage
89 </ul> <em>Deprecations</em>
91 <td align="left" valign="top">
97 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
98 with annotation and exceptions thrown when only a few
99 columns shown in wrapped mode
102 <!-- JAL-3386 -->Sequence IDs missing in headless export of
103 wrapped alignment figure with annotations
106 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
107 ID fails with ClassCastException
110 <!-- JAL-3389 -->Chimera session not restored from Jalview
114 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
115 feature settings dialog also selects columns
118 <!-- JAL-3473 -->SpinnerNumberModel causing
119 IllegalArgumentException in some circumstances
122 <!-- JAL-3406 -->Credits missing some authors in Jalview
123 help documentation for 2.11.0 release
125 </ul> <em>Java 11 Compatibility issues</em>
128 <!-- JAL-2987 -->OSX - Can't view results in PDB/Uniprot FTS
130 </ul> <em>Repository and Source Release</em>
133 <!-- JAL-3474 -->removed redundant .gitignore files from
137 <em>New Known Issues</em>
140 <!-- JAL-3523 -->OSX - Current working directory not
141 preserved when Jalview.app launched with parameters from
145 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
146 clipped in headless figure export when Right Align option
153 <td width="60" align="center" nowrap>
154 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
155 <em>04/07/2019</em></strong>
157 <td align="left" valign="top">
160 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
161 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
162 source project) rather than InstallAnywhere
165 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
166 settings, receive over the air updates and launch specific
167 versions via (<a href="https://github.com/threerings/getdown">Three
171 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
172 formats supported by Jalview (including .jvp project files)
175 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
176 arguments and switch between different getdown channels
179 <!-- JAL-3141 -->Backup files created when saving Jalview project
184 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
185 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
187 <!-- JAL-2620 -->Alternative genetic code tables for
188 'Translate as cDNA'</li>
190 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
191 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
194 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
195 implementation that allows updates) used for Sequence Feature collections</li>
197 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
198 features can be filtered and shaded according to any
199 associated attributes (e.g. variant attributes from VCF
200 file, or key-value pairs imported from column 9 of GFF
204 <!-- JAL-2879 -->Feature Attributes and shading schemes
205 stored and restored from Jalview Projects
208 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
209 recognise variant features
212 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
213 sequences (also coloured red by default)
216 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
220 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
221 algorithm (Z-sort/transparency and filter aware)
224 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
230 <!-- JAL-3205 -->Symmetric score matrices for faster
231 tree and PCA calculations
233 <li><strong>Principal Components Analysis Viewer</strong>
236 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
237 and Viewer state saved in Jalview Project
239 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
242 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
246 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
251 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
253 <li><strong>Speed and Efficiency</strong>
256 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
257 multiple groups when working with large alignments
260 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
264 <li><strong>User Interface</strong>
267 <!-- JAL-2933 -->Finder panel remembers last position in each
271 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
272 what is shown)<br />Only visible regions of alignment are shown by
273 default (can be changed in user preferences)
276 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
277 to the Overwrite Dialog
280 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
284 <!-- JAL-1244 -->Status bar shows bounds when dragging a
285 selection region, and gap count when inserting or deleting gaps
288 <!-- JAL-3132 -->Status bar updates over sequence and annotation
292 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
296 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
300 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
303 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
307 <!-- JAL-3181 -->Consistent ordering of links in sequence id
311 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
313 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
317 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
318 <li><strong>Java 11 Support (not yet on general release)</strong>
321 <!-- -->OSX GUI integrations for App menu's 'About' entry and
326 <em>Deprecations</em>
328 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
329 capabilities removed from the Jalview Desktop
331 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
332 unmarshalling has been replaced by JAXB for Jalview projects
333 and XML based data retrieval clients</li>
334 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
335 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
336 </ul> <em>Documentation</em>
338 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
339 not supported in EPS figure export
341 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
342 </ul> <em>Development and Release Processes</em>
345 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
348 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
350 <!-- JAL-3225 -->Eclipse project configuration managed with
354 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
355 Bamboo continuous integration for unattended Test Suite
359 <!-- JAL-2864 -->Memory test suite to detect leaks in common
363 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
367 <!-- JAL-3248 -->Developer documentation migrated to
368 markdown (with HTML rendering)
371 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
374 <!-- JAL-3289 -->New URLs for publishing development
379 <td align="left" valign="top">
382 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
385 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
386 superposition in Jmol fail on Windows
389 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
390 structures for sequences with lots of PDB structures
393 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
397 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
398 project involving multiple views
401 <!-- JAL-3164 -->Overview for complementary view in a linked
402 CDS/Protein alignment is not updated when Hide Columns by
403 Annotation dialog hides columns
406 <!-- JAL-3158 -->Selection highlighting in the complement of a
407 CDS/Protein alignment stops working after making a selection in
408 one view, then making another selection in the other view
411 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
415 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
416 Settings and Jalview Preferences panels
419 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
420 overview with large alignments
423 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
424 region if columns were selected by dragging right-to-left and the
425 mouse moved to the left of the first column
428 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
429 hidden column marker via scale popup menu
432 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
433 doesn't tell users the invalid URL
436 <!-- JAL-2816 -->Tooltips displayed for features filtered by
440 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
441 show cross references or Fetch Database References are shown in
445 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
446 peptide sequence (computed variant shown as p.Res.null)
449 <!-- JAL-2060 -->'Graduated colour' option not offered for
450 manually created features (where feature score is Float.NaN)
453 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
454 when columns are hidden
457 <!-- JAL-3082 -->Regular expression error for '(' in Select
458 Columns by Annotation description
461 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
462 out of Scale or Annotation Panel
465 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
469 <!-- JAL-3074 -->Left/right drag in annotation can scroll
473 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
477 <!-- JAL-3002 -->Column display is out by one after Page Down,
478 Page Up in wrapped mode
481 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
484 <!-- JAL-2932 -->Finder searches in minimised alignments
487 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
488 on opening an alignment
491 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
495 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
496 different groups in the alignment are selected
499 <!-- JAL-2717 -->Internationalised colour scheme names not shown
503 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
507 <!-- JAL-3125 -->Value input for graduated feature colour
508 threshold gets 'unrounded'
511 <!-- JAL-2982 -->PCA image export doesn't respect background
515 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
518 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
521 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
525 <!-- JAL-2964 -->Associate Tree with All Views not restored from
529 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
530 shown in complementary view
533 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
534 without normalisation
537 <!-- JAL-3021 -->Sequence Details report should open positioned at top
541 <!-- JAL-914 -->Help page can be opened twice
544 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
546 </ul> <em>Editing</em>
549 <!-- JAL-2822 -->Start and End should be updated when sequence
550 data at beginning or end of alignment added/removed via 'Edit'
554 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
555 relocate sequence features correctly when start of sequence is
556 removed (Known defect since 2.10)
559 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
560 dialog corrupts dataset sequence
563 <!-- JAL-868 -->Structure colours not updated when associated tree
564 repartitions the alignment view (Regression in 2.10.5)
566 </ul> <em>Datamodel</em>
569 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
570 sequence's End is greater than its length
572 </ul> <em>Bugs fixed for Java 11 Support (not yet on
573 general release)</em>
576 <!-- JAL-3288 -->Menus work properly in split-screen
578 </ul> <em>New Known Defects</em>
581 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
584 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
585 regions of protein alignment.
588 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
589 is restored from a Jalview 2.11 project
592 <!-- JAL-3213 -->Alignment panel height can be too small after
596 <!-- JAL-3240 -->Display is incorrect after removing gapped
597 columns within hidden columns
600 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
601 window after dragging left to select columns to left of visible
605 <!-- JAL-2876 -->Features coloured according to their description
606 string and thresholded by score in earlier versions of Jalview are
607 not shown as thresholded features in 2.11. To workaround please
608 create a Score filter instead.
611 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
613 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
616 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
617 alignments with multiple views can close views unexpectedly
620 <em>Java 11 Specific defects</em>
623 <!-- JAL-3235 -->Jalview Properties file is not sorted
624 alphabetically when saved
630 <td width="60" nowrap>
632 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
635 <td><div align="left">
639 <!-- JAL-3101 -->Default memory for Jalview webstart and
640 InstallAnywhere increased to 1G.
643 <!-- JAL-247 -->Hidden sequence markers and representative
644 sequence bolding included when exporting alignment as EPS,
645 SVG, PNG or HTML. <em>Display is configured via the
646 Format menu, or for command-line use via a Jalview
647 properties file.</em>
650 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
651 API and sequence data now imported as JSON.
654 <!-- JAL-3065 -->Change in recommended way of starting
655 Jalview via a Java command line: add jars in lib directory
656 to CLASSPATH, rather than via the deprecated java.ext.dirs
663 <!-- JAL-3047 -->Support added to execute test suite
664 instrumented with <a href="http://openclover.org/">Open
669 <td><div align="left">
673 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
674 row shown in Feredoxin Structure alignment view of example
678 <!-- JAL-2854 -->Annotation obscures sequences if lots of
679 annotation displayed.
682 <!-- JAL-3107 -->Group conservation/consensus not shown
683 for newly created group when 'Apply to all groups'
687 <!-- JAL-3087 -->Corrupted display when switching to
688 wrapped mode when sequence panel's vertical scrollbar is
692 <!-- JAL-3003 -->Alignment is black in exported EPS file
693 when sequences are selected in exported view.</em>
696 <!-- JAL-3059 -->Groups with different coloured borders
697 aren't rendered with correct colour.
700 <!-- JAL-3092 -->Jalview could hang when importing certain
701 types of knotted RNA secondary structure.
704 <!-- JAL-3095 -->Sequence highlight and selection in
705 trimmed VARNA 2D structure is incorrect for sequences that
709 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
710 annotation when columns are inserted into an alignment,
711 and when exporting as Stockholm flatfile.
714 <!-- JAL-3053 -->Jalview annotation rows containing upper
715 and lower-case 'E' and 'H' do not automatically get
716 treated as RNA secondary structure.
719 <!-- JAL-3106 -->.jvp should be used as default extension
720 (not .jar) when saving a Jalview project file.
723 <!-- JAL-3105 -->Mac Users: closing a window correctly
724 transfers focus to previous window on OSX
727 <em>Java 10 Issues Resolved</em>
730 <!-- JAL-2988 -->OSX - Can't save new files via the File
731 or export menus by typing in a name into the Save dialog
735 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
736 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
737 'look and feel' which has improved compatibility with the
738 latest version of OSX.
745 <td width="60" nowrap>
747 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
748 <em>7/06/2018</em></strong>
751 <td><div align="left">
755 <!-- JAL-2920 -->Use HGVS nomenclature for variant
756 annotation retrieved from Uniprot
759 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
760 onto the Jalview Desktop
764 <td><div align="left">
768 <!-- JAL-3017 -->Cannot import features with multiple
769 variant elements (blocks import of some Uniprot records)
772 <!-- JAL-2997 -->Clustal files with sequence positions in
773 right-hand column parsed correctly
776 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
777 not alignment area in exported graphic
780 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
781 window has input focus
784 <!-- JAL-2992 -->Annotation panel set too high when
785 annotation added to view (Windows)
788 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
789 network connectivity is poor
792 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
793 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
794 the currently open URL and links from a page viewed in
795 Firefox or Chrome on Windows is now fully supported. If
796 you are using Edge, only links in the page can be
797 dragged, and with Internet Explorer, only the currently
798 open URL in the browser can be dropped onto Jalview.</em>
801 <em>New Known Defects</em>
803 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
808 <td width="60" nowrap>
810 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
813 <td><div align="left">
817 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
818 for disabling automatic superposition of multiple
819 structures and open structures in existing views
822 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
823 ID and annotation area margins can be click-dragged to
827 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
831 <!-- JAL-2759 -->Improved performance for large alignments
832 and lots of hidden columns
835 <!-- JAL-2593 -->Improved performance when rendering lots
836 of features (particularly when transparency is disabled)
839 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
840 exchange of Jalview features and Chimera attributes made
846 <td><div align="left">
849 <!-- JAL-2899 -->Structure and Overview aren't updated
850 when Colour By Annotation threshold slider is adjusted
853 <!-- JAL-2778 -->Slow redraw when Overview panel shown
854 overlapping alignment panel
857 <!-- JAL-2929 -->Overview doesn't show end of unpadded
861 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
862 improved: CDS not handled correctly if transcript has no
866 <!-- JAL-2321 -->Secondary structure and temperature
867 factor annotation not added to sequence when local PDB
868 file associated with it by drag'n'drop or structure
872 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
873 dialog doesn't import PDB files dropped on an alignment
876 <!-- JAL-2666 -->Linked scrolling via protein horizontal
877 scroll bar doesn't work for some CDS/Protein views
880 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
881 Java 1.8u153 onwards and Java 1.9u4+.
884 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
885 columns in annotation row
888 <!-- JAL-2913 -->Preferences panel's ID Width control is not
889 honored in batch mode
892 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
893 for structures added to existing Jmol view
896 <!-- JAL-2223 -->'View Mappings' includes duplicate
897 entries after importing project with multiple views
900 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
901 protein sequences via SIFTS from associated PDB entries
902 with negative residue numbers or missing residues fails
905 <!-- JAL-2952 -->Exception when shading sequence with negative
906 Temperature Factor values from annotated PDB files (e.g.
907 as generated by CONSURF)
910 <!-- JAL-2920 -->Uniprot 'sequence variant' features
911 tooltip doesn't include a text description of mutation
914 <!-- JAL-2922 -->Invert displayed features very slow when
915 structure and/or overview windows are also shown
918 <!-- JAL-2954 -->Selecting columns from highlighted regions
919 very slow for alignments with large numbers of sequences
922 <!-- JAL-2925 -->Copy Consensus fails for group consensus
923 with 'StringIndexOutOfBounds'
926 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
927 platforms running Java 10
930 <!-- JAL-2960 -->Adding a structure to existing structure
931 view appears to do nothing because the view is hidden behind the alignment view
937 <!-- JAL-2926 -->Copy consensus sequence option in applet
938 should copy the group consensus when popup is opened on it
944 <!-- JAL-2913 -->Fixed ID width preference is not respected
947 <em>New Known Defects</em>
950 <!-- JAL-2973 --> Exceptions occasionally raised when
951 editing a large alignment and overview is displayed
954 <!-- JAL-2974 -->'Overview updating' progress bar is shown
955 repeatedly after a series of edits even when the overview
956 is no longer reflecting updates
959 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
960 structures for protein subsequence (if 'Trim Retrieved
961 Sequences' enabled) or Ensembl isoforms (Workaround in
962 2.10.4 is to fail back to N&W mapping)
965 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
966 option gives blank output
973 <td width="60" nowrap>
975 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
978 <td><div align="left">
979 <ul><li>Updated Certum Codesigning Certificate
980 (Valid till 30th November 2018)</li></ul></div></td>
981 <td><div align="left">
984 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
985 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
986 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
987 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
988 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
989 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
990 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
996 <td width="60" nowrap>
998 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1001 <td><div align="left">
1005 <!-- JAL-2446 -->Faster and more efficient management and
1006 rendering of sequence features
1009 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1010 429 rate limit request hander
1013 <!-- JAL-2773 -->Structure views don't get updated unless
1014 their colours have changed
1017 <!-- JAL-2495 -->All linked sequences are highlighted for
1018 a structure mousover (Jmol) or selection (Chimera)
1021 <!-- JAL-2790 -->'Cancel' button in progress bar for
1022 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1025 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1026 view from Ensembl locus cross-references
1029 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1033 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1034 feature can be disabled
1037 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1038 PDB easier retrieval of sequences for lists of IDs
1041 <!-- JAL-2758 -->Short names for sequences retrieved from
1047 <li>Groovy interpreter updated to 2.4.12</li>
1048 <li>Example groovy script for generating a matrix of
1049 percent identity scores for current alignment.</li>
1051 <em>Testing and Deployment</em>
1054 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1058 <td><div align="left">
1062 <!-- JAL-2643 -->Pressing tab after updating the colour
1063 threshold text field doesn't trigger an update to the
1067 <!-- JAL-2682 -->Race condition when parsing sequence ID
1071 <!-- JAL-2608 -->Overview windows are also closed when
1072 alignment window is closed
1075 <!-- JAL-2548 -->Export of features doesn't always respect
1079 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1080 takes a long time in Cursor mode
1086 <!-- JAL-2777 -->Structures with whitespace chainCode
1087 cannot be viewed in Chimera
1090 <!-- JAL-2728 -->Protein annotation panel too high in
1094 <!-- JAL-2757 -->Can't edit the query after the server
1095 error warning icon is shown in Uniprot and PDB Free Text
1099 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1102 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1105 <!-- JAL-2739 -->Hidden column marker in last column not
1106 rendered when switching back from Wrapped to normal view
1109 <!-- JAL-2768 -->Annotation display corrupted when
1110 scrolling right in unwapped alignment view
1113 <!-- JAL-2542 -->Existing features on subsequence
1114 incorrectly relocated when full sequence retrieved from
1118 <!-- JAL-2733 -->Last reported memory still shown when
1119 Desktop->Show Memory is unticked (OSX only)
1122 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1123 features of same type and group to be selected for
1127 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1128 alignments when hidden columns are present
1131 <!-- JAL-2392 -->Jalview freezes when loading and
1132 displaying several structures
1135 <!-- JAL-2732 -->Black outlines left after resizing or
1139 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1140 within the Jalview desktop on OSX
1143 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1144 when in wrapped alignment mode
1147 <!-- JAL-2636 -->Scale mark not shown when close to right
1148 hand end of alignment
1151 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1152 each selected sequence do not have correct start/end
1156 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1157 after canceling the Alignment Window's Font dialog
1160 <!-- JAL-2036 -->Show cross-references not enabled after
1161 restoring project until a new view is created
1164 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1165 URL links appears when only default EMBL-EBI link is
1166 configured (since 2.10.2b2)
1169 <!-- JAL-2775 -->Overview redraws whole window when box
1170 position is adjusted
1173 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1174 in a multi-chain structure when viewing alignment
1175 involving more than one chain (since 2.10)
1178 <!-- JAL-2811 -->Double residue highlights in cursor mode
1179 if new selection moves alignment window
1182 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1183 arrow key in cursor mode to pass hidden column marker
1186 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1187 that produces correctly annotated transcripts and products
1190 <!-- JAL-2776 -->Toggling a feature group after first time
1191 doesn't update associated structure view
1194 <em>Applet</em><br />
1197 <!-- JAL-2687 -->Concurrent modification exception when
1198 closing alignment panel
1201 <em>BioJSON</em><br />
1204 <!-- JAL-2546 -->BioJSON export does not preserve
1205 non-positional features
1208 <em>New Known Issues</em>
1211 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1212 sequence features correctly (for many previous versions of
1216 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1217 using cursor in wrapped panel other than top
1220 <!-- JAL-2791 -->Select columns containing feature ignores
1221 graduated colour threshold
1224 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1225 always preserve numbering and sequence features
1228 <em>Known Java 9 Issues</em>
1231 <!-- JAL-2902 -->Groovy Console very slow to open and is
1232 not responsive when entering characters (Webstart, Java
1239 <td width="60" nowrap>
1240 <div align="center">
1241 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1242 <em>2/10/2017</em></strong>
1245 <td><div align="left">
1246 <em>New features in Jalview Desktop</em>
1249 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1251 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1255 <td><div align="left">
1259 <td width="60" nowrap>
1260 <div align="center">
1261 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1262 <em>7/9/2017</em></strong>
1265 <td><div align="left">
1269 <!-- JAL-2588 -->Show gaps in overview window by colouring
1270 in grey (sequences used to be coloured grey, and gaps were
1274 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1278 <!-- JAL-2587 -->Overview updates immediately on increase
1279 in size and progress bar shown as higher resolution
1280 overview is recalculated
1285 <td><div align="left">
1289 <!-- JAL-2664 -->Overview window redraws every hidden
1290 column region row by row
1293 <!-- JAL-2681 -->duplicate protein sequences shown after
1294 retrieving Ensembl crossrefs for sequences from Uniprot
1297 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1298 format setting is unticked
1301 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1302 if group has show boxes format setting unticked
1305 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1306 autoscrolling whilst dragging current selection group to
1307 include sequences and columns not currently displayed
1310 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1311 assemblies are imported via CIF file
1314 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1315 displayed when threshold or conservation colouring is also
1319 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1323 <!-- JAL-2673 -->Jalview continues to scroll after
1324 dragging a selected region off the visible region of the
1328 <!-- JAL-2724 -->Cannot apply annotation based
1329 colourscheme to all groups in a view
1332 <!-- JAL-2511 -->IDs don't line up with sequences
1333 initially after font size change using the Font chooser or
1340 <td width="60" nowrap>
1341 <div align="center">
1342 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1345 <td><div align="left">
1346 <em>Calculations</em>
1350 <!-- JAL-1933 -->Occupancy annotation row shows number of
1351 ungapped positions in each column of the alignment.
1354 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1355 a calculation dialog box
1358 <!-- JAL-2379 -->Revised implementation of PCA for speed
1359 and memory efficiency (~30x faster)
1362 <!-- JAL-2403 -->Revised implementation of sequence
1363 similarity scores as used by Tree, PCA, Shading Consensus
1364 and other calculations
1367 <!-- JAL-2416 -->Score matrices are stored as resource
1368 files within the Jalview codebase
1371 <!-- JAL-2500 -->Trees computed on Sequence Feature
1372 Similarity may have different topology due to increased
1379 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1380 model for alignments and groups
1383 <!-- JAL-384 -->Custom shading schemes created via groovy
1390 <!-- JAL-2526 -->Efficiency improvements for interacting
1391 with alignment and overview windows
1394 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1398 <!-- JAL-2388 -->Hidden columns and sequences can be
1402 <!-- JAL-2611 -->Click-drag in visible area allows fine
1403 adjustment of visible position
1407 <em>Data import/export</em>
1410 <!-- JAL-2535 -->Posterior probability annotation from
1411 Stockholm files imported as sequence associated annotation
1414 <!-- JAL-2507 -->More robust per-sequence positional
1415 annotation input/output via stockholm flatfile
1418 <!-- JAL-2533 -->Sequence names don't include file
1419 extension when importing structure files without embedded
1420 names or PDB accessions
1423 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1424 format sequence substitution matrices
1427 <em>User Interface</em>
1430 <!-- JAL-2447 --> Experimental Features Checkbox in
1431 Desktop's Tools menu to hide or show untested features in
1435 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1436 via Overview or sequence motif search operations
1439 <!-- JAL-2547 -->Amend sequence features dialog box can be
1440 opened by double clicking gaps within sequence feature
1444 <!-- JAL-1476 -->Status bar message shown when not enough
1445 aligned positions were available to create a 3D structure
1449 <em>3D Structure</em>
1452 <!-- JAL-2430 -->Hidden regions in alignment views are not
1453 coloured in linked structure views
1456 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1457 file-based command exchange
1460 <!-- JAL-2375 -->Structure chooser automatically shows
1461 Cached Structures rather than querying the PDBe if
1462 structures are already available for sequences
1465 <!-- JAL-2520 -->Structures imported via URL are cached in
1466 the Jalview project rather than downloaded again when the
1467 project is reopened.
1470 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1471 to transfer Chimera's structure attributes as Jalview
1472 features, and vice-versa (<strong>Experimental
1476 <em>Web Services</em>
1479 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1482 <!-- JAL-2335 -->Filter non-standard amino acids and
1483 nucleotides when submitting to AACon and other MSA
1487 <!-- JAL-2316, -->URLs for viewing database
1488 cross-references provided by identifiers.org and the
1489 EMBL-EBI's MIRIAM DB
1496 <!-- JAL-2344 -->FileFormatI interface for describing and
1497 identifying file formats (instead of String constants)
1500 <!-- JAL-2228 -->FeatureCounter script refactored for
1501 efficiency when counting all displayed features (not
1502 backwards compatible with 2.10.1)
1505 <em>Example files</em>
1508 <!-- JAL-2631 -->Graduated feature colour style example
1509 included in the example feature file
1512 <em>Documentation</em>
1515 <!-- JAL-2339 -->Release notes reformatted for readability
1516 with the built-in Java help viewer
1519 <!-- JAL-1644 -->Find documentation updated with 'search
1520 sequence description' option
1526 <!-- JAL-2485, -->External service integration tests for
1527 Uniprot REST Free Text Search Client
1530 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1533 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1538 <td><div align="left">
1539 <em>Calculations</em>
1542 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1543 matrix - C->R should be '-3'<br />Old matrix restored
1544 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1546 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1547 Jalview's treatment of gaps in PCA and substitution matrix
1548 based Tree calculations.<br /> <br />In earlier versions
1549 of Jalview, gaps matching gaps were penalised, and gaps
1550 matching non-gaps penalised even more. In the PCA
1551 calculation, gaps were actually treated as non-gaps - so
1552 different costs were applied, which meant Jalview's PCAs
1553 were different to those produced by SeqSpace.<br />Jalview
1554 now treats gaps in the same way as SeqSpace (ie it scores
1555 them as 0). <br /> <br />Enter the following in the
1556 Groovy console to restore pre-2.10.2 behaviour:<br />
1557 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1558 // for 2.10.1 mode <br />
1559 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1560 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1561 these settings will affect all subsequent tree and PCA
1562 calculations (not recommended)</em></li>
1564 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1565 scaling of branch lengths for trees computed using
1566 Sequence Feature Similarity.
1569 <!-- JAL-2377 -->PCA calculation could hang when
1570 generating output report when working with highly
1571 redundant alignments
1574 <!-- JAL-2544 --> Sort by features includes features to
1575 right of selected region when gaps present on right-hand
1579 <em>User Interface</em>
1582 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1583 doesn't reselect a specific sequence's associated
1584 annotation after it was used for colouring a view
1587 <!-- JAL-2419 -->Current selection lost if popup menu
1588 opened on a region of alignment without groups
1591 <!-- JAL-2374 -->Popup menu not always shown for regions
1592 of an alignment with overlapping groups
1595 <!-- JAL-2310 -->Finder double counts if both a sequence's
1596 name and description match
1599 <!-- JAL-2370 -->Hiding column selection containing two
1600 hidden regions results in incorrect hidden regions
1603 <!-- JAL-2386 -->'Apply to all groups' setting when
1604 changing colour does not apply Conservation slider value
1608 <!-- JAL-2373 -->Percentage identity and conservation menu
1609 items do not show a tick or allow shading to be disabled
1612 <!-- JAL-2385 -->Conservation shading or PID threshold
1613 lost when base colourscheme changed if slider not visible
1616 <!-- JAL-2547 -->Sequence features shown in tooltip for
1617 gaps before start of features
1620 <!-- JAL-2623 -->Graduated feature colour threshold not
1621 restored to UI when feature colour is edited
1624 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1625 a time when scrolling vertically in wrapped mode.
1628 <!-- JAL-2630 -->Structure and alignment overview update
1629 as graduate feature colour settings are modified via the
1633 <!-- JAL-2034 -->Overview window doesn't always update
1634 when a group defined on the alignment is resized
1637 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1638 wrapped view result in positional status updates
1642 <!-- JAL-2563 -->Status bar doesn't show position for
1643 ambiguous amino acid and nucleotide symbols
1646 <!-- JAL-2602 -->Copy consensus sequence failed if
1647 alignment included gapped columns
1650 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1651 widgets don't permanently disappear
1654 <!-- JAL-2503 -->Cannot select or filter quantitative
1655 annotation that are shown only as column labels (e.g.
1656 T-Coffee column reliability scores)
1659 <!-- JAL-2594 -->Exception thrown if trying to create a
1660 sequence feature on gaps only
1663 <!-- JAL-2504 -->Features created with 'New feature'
1664 button from a Find inherit previously defined feature type
1665 rather than the Find query string
1668 <!-- JAL-2423 -->incorrect title in output window when
1669 exporting tree calculated in Jalview
1672 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1673 and then revealing them reorders sequences on the
1677 <!-- JAL-964 -->Group panel in sequence feature settings
1678 doesn't update to reflect available set of groups after
1679 interactively adding or modifying features
1682 <!-- JAL-2225 -->Sequence Database chooser unusable on
1686 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1687 only excluded gaps in current sequence and ignored
1694 <!-- JAL-2421 -->Overview window visible region moves
1695 erratically when hidden rows or columns are present
1698 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1699 Structure Viewer's colour menu don't correspond to
1703 <!-- JAL-2405 -->Protein specific colours only offered in
1704 colour and group colour menu for protein alignments
1707 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1708 reflect currently selected view or group's shading
1712 <!-- JAL-2624 -->Feature colour thresholds not respected
1713 when rendered on overview and structures when opacity at
1717 <!-- JAL-2589 -->User defined gap colour not shown in
1718 overview when features overlaid on alignment
1721 <!-- JAL-2567 -->Feature settings for different views not
1722 recovered correctly from Jalview project file
1725 <!-- JAL-2256 -->Feature colours in overview when first opened
1726 (automatically via preferences) are different to the main
1730 <em>Data import/export</em>
1733 <!-- JAL-2576 -->Very large alignments take a long time to
1737 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1738 added after a sequence was imported are not written to
1742 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1743 when importing RNA secondary structure via Stockholm
1746 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1747 not shown in correct direction for simple pseudoknots
1750 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1751 with lightGray or darkGray via features file (but can
1755 <!-- JAL-2383 -->Above PID colour threshold not recovered
1756 when alignment view imported from project
1759 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1760 structure and sequences extracted from structure files
1761 imported via URL and viewed in Jmol
1764 <!-- JAL-2520 -->Structures loaded via URL are saved in
1765 Jalview Projects rather than fetched via URL again when
1766 the project is loaded and the structure viewed
1769 <em>Web Services</em>
1772 <!-- JAL-2519 -->EnsemblGenomes example failing after
1773 release of Ensembl v.88
1776 <!-- JAL-2366 -->Proxy server address and port always
1777 appear enabled in Preferences->Connections
1780 <!-- JAL-2461 -->DAS registry not found exceptions
1781 removed from console output
1784 <!-- JAL-2582 -->Cannot retrieve protein products from
1785 Ensembl by Peptide ID
1788 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1789 created from SIFTs, and spurious 'Couldn't open structure
1790 in Chimera' errors raised after April 2017 update (problem
1791 due to 'null' string rather than empty string used for
1792 residues with no corresponding PDB mapping).
1795 <em>Application UI</em>
1798 <!-- JAL-2361 -->User Defined Colours not added to Colour
1802 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1803 case' residues (button in colourscheme editor debugged and
1804 new documentation and tooltips added)
1807 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1808 doesn't restore group-specific text colour thresholds
1811 <!-- JAL-2243 -->Feature settings panel does not update as
1812 new features are added to alignment
1815 <!-- JAL-2532 -->Cancel in feature settings reverts
1816 changes to feature colours via the Amend features dialog
1819 <!-- JAL-2506 -->Null pointer exception when attempting to
1820 edit graduated feature colour via amend features dialog
1824 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1825 selection menu changes colours of alignment views
1828 <!-- JAL-2426 -->Spurious exceptions in console raised
1829 from alignment calculation workers after alignment has
1833 <!-- JAL-1608 -->Typo in selection popup menu - Create
1834 groups now 'Create Group'
1837 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1838 Create/Undefine group doesn't always work
1841 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1842 shown again after pressing 'Cancel'
1845 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1846 adjusts start position in wrap mode
1849 <!-- JAL-2563 -->Status bar doesn't show positions for
1850 ambiguous amino acids
1853 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1854 CDS/Protein view after CDS sequences added for aligned
1858 <!-- JAL-2592 -->User defined colourschemes called 'User
1859 Defined' don't appear in Colours menu
1865 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1866 score models doesn't always result in an updated PCA plot
1869 <!-- JAL-2442 -->Features not rendered as transparent on
1870 overview or linked structure view
1873 <!-- JAL-2372 -->Colour group by conservation doesn't
1877 <!-- JAL-2517 -->Hitting Cancel after applying
1878 user-defined colourscheme doesn't restore original
1885 <!-- JAL-2314 -->Unit test failure:
1886 jalview.ws.jabaws.RNAStructExportImport setup fails
1889 <!-- JAL-2307 -->Unit test failure:
1890 jalview.ws.sifts.SiftsClientTest due to compatibility
1891 problems with deep array comparison equality asserts in
1892 successive versions of TestNG
1895 <!-- JAL-2479 -->Relocated StructureChooserTest and
1896 ParameterUtilsTest Unit tests to Network suite
1899 <em>New Known Issues</em>
1902 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1903 phase after a sequence motif find operation
1906 <!-- JAL-2550 -->Importing annotation file with rows
1907 containing just upper and lower case letters are
1908 interpreted as WUSS RNA secondary structure symbols
1911 <!-- JAL-2590 -->Cannot load and display Newick trees
1912 reliably from eggnog Ortholog database
1915 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1916 containing features of type Highlight' when 'B' is pressed
1917 to mark columns containing highlighted regions.
1920 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1921 doesn't always add secondary structure annotation.
1926 <td width="60" nowrap>
1927 <div align="center">
1928 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1931 <td><div align="left">
1935 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1936 for all consensus calculations
1939 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1942 <li>Updated Jalview's Certum code signing certificate
1945 <em>Application</em>
1948 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1949 set of database cross-references, sorted alphabetically
1952 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1953 from database cross references. Users with custom links
1954 will receive a <a href="webServices/urllinks.html#warning">warning
1955 dialog</a> asking them to update their preferences.
1958 <!-- JAL-2287-->Cancel button and escape listener on
1959 dialog warning user about disconnecting Jalview from a
1963 <!-- JAL-2320-->Jalview's Chimera control window closes if
1964 the Chimera it is connected to is shut down
1967 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1968 columns menu item to mark columns containing highlighted
1969 regions (e.g. from structure selections or results of a
1973 <!-- JAL-2284-->Command line option for batch-generation
1974 of HTML pages rendering alignment data with the BioJS
1984 <!-- JAL-2286 -->Columns with more than one modal residue
1985 are not coloured or thresholded according to percent
1986 identity (first observed in Jalview 2.8.2)
1989 <!-- JAL-2301 -->Threonine incorrectly reported as not
1993 <!-- JAL-2318 -->Updates to documentation pages (above PID
1994 threshold, amino acid properties)
1997 <!-- JAL-2292 -->Lower case residues in sequences are not
1998 reported as mapped to residues in a structure file in the
2002 <!--JAL-2324 -->Identical features with non-numeric scores
2003 could be added multiple times to a sequence
2006 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2007 bond features shown as two highlighted residues rather
2008 than a range in linked structure views, and treated
2009 correctly when selecting and computing trees from features
2012 <!-- JAL-2281-->Custom URL links for database
2013 cross-references are matched to database name regardless
2018 <em>Application</em>
2021 <!-- JAL-2282-->Custom URL links for specific database
2022 names without regular expressions also offer links from
2026 <!-- JAL-2315-->Removing a single configured link in the
2027 URL links pane in Connections preferences doesn't actually
2028 update Jalview configuration
2031 <!-- JAL-2272-->CTRL-Click on a selected region to open
2032 the alignment area popup menu doesn't work on El-Capitan
2035 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2036 files with similarly named sequences if dropped onto the
2040 <!-- JAL-2312 -->Additional mappings are shown for PDB
2041 entries where more chains exist in the PDB accession than
2042 are reported in the SIFTS file
2045 <!-- JAL-2317-->Certain structures do not get mapped to
2046 the structure view when displayed with Chimera
2049 <!-- JAL-2317-->No chains shown in the Chimera view
2050 panel's View->Show Chains submenu
2053 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2054 work for wrapped alignment views
2057 <!--JAL-2197 -->Rename UI components for running JPred
2058 predictions from 'JNet' to 'JPred'
2061 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2062 corrupted when annotation panel vertical scroll is not at
2063 first annotation row
2066 <!--JAL-2332 -->Attempting to view structure for Hen
2067 lysozyme results in a PDB Client error dialog box
2070 <!-- JAL-2319 -->Structure View's mapping report switched
2071 ranges for PDB and sequence for SIFTS
2074 SIFTS 'Not_Observed' residues mapped to non-existant
2078 <!-- <em>New Known Issues</em>
2085 <td width="60" nowrap>
2086 <div align="center">
2087 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2088 <em>25/10/2016</em></strong>
2091 <td><em>Application</em>
2093 <li>3D Structure chooser opens with 'Cached structures'
2094 view if structures already loaded</li>
2095 <li>Progress bar reports models as they are loaded to
2096 structure views</li>
2102 <li>Colour by conservation always enabled and no tick
2103 shown in menu when BLOSUM or PID shading applied</li>
2104 <li>FER1_ARATH and FER2_ARATH labels were switched in
2105 example sequences/projects/trees</li>
2107 <em>Application</em>
2109 <li>Jalview projects with views of local PDB structure
2110 files saved on Windows cannot be opened on OSX</li>
2111 <li>Multiple structure views can be opened and superposed
2112 without timeout for structures with multiple models or
2113 multiple sequences in alignment</li>
2114 <li>Cannot import or associated local PDB files without a
2115 PDB ID HEADER line</li>
2116 <li>RMSD is not output in Jmol console when superposition
2118 <li>Drag and drop of URL from Browser fails for Linux and
2119 OSX versions earlier than El Capitan</li>
2120 <li>ENA client ignores invalid content from ENA server</li>
2121 <li>Exceptions are not raised in console when ENA client
2122 attempts to fetch non-existent IDs via Fetch DB Refs UI
2124 <li>Exceptions are not raised in console when a new view
2125 is created on the alignment</li>
2126 <li>OSX right-click fixed for group selections: CMD-click
2127 to insert/remove gaps in groups and CTRL-click to open group
2130 <em>Build and deployment</em>
2132 <li>URL link checker now copes with multi-line anchor
2135 <em>New Known Issues</em>
2137 <li>Drag and drop from URL links in browsers do not work
2144 <td width="60" nowrap>
2145 <div align="center">
2146 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2149 <td><em>General</em>
2152 <!-- JAL-2124 -->Updated Spanish translations.
2155 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2156 for importing structure data to Jalview. Enables mmCIF and
2160 <!-- JAL-192 --->Alignment ruler shows positions relative to
2164 <!-- JAL-2202 -->Position/residue shown in status bar when
2165 mousing over sequence associated annotation
2168 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2172 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2173 '()', canonical '[]' and invalid '{}' base pair populations
2177 <!-- JAL-2092 -->Feature settings popup menu options for
2178 showing or hiding columns containing a feature
2181 <!-- JAL-1557 -->Edit selected group by double clicking on
2182 group and sequence associated annotation labels
2185 <!-- JAL-2236 -->Sequence name added to annotation label in
2186 select/hide columns by annotation and colour by annotation
2190 </ul> <em>Application</em>
2193 <!-- JAL-2050-->Automatically hide introns when opening a
2194 gene/transcript view
2197 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2201 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2202 structure mappings with the EMBL-EBI PDBe SIFTS database
2205 <!-- JAL-2079 -->Updated download sites used for Rfam and
2206 Pfam sources to xfam.org
2209 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2212 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2213 over sequences in Jalview
2216 <!-- JAL-2027-->Support for reverse-complement coding
2217 regions in ENA and EMBL
2220 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2221 for record retrieval via ENA rest API
2224 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2228 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2229 groovy script execution
2232 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2233 alignment window's Calculate menu
2236 <!-- JAL-1812 -->Allow groovy scripts that call
2237 Jalview.getAlignFrames() to run in headless mode
2240 <!-- JAL-2068 -->Support for creating new alignment
2241 calculation workers from groovy scripts
2244 <!-- JAL-1369 --->Store/restore reference sequence in
2248 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2249 associations are now saved/restored from project
2252 <!-- JAL-1993 -->Database selection dialog always shown
2253 before sequence fetcher is opened
2256 <!-- JAL-2183 -->Double click on an entry in Jalview's
2257 database chooser opens a sequence fetcher
2260 <!-- JAL-1563 -->Free-text search client for UniProt using
2261 the UniProt REST API
2264 <!-- JAL-2168 -->-nonews command line parameter to prevent
2265 the news reader opening
2268 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2269 querying stored in preferences
2272 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2276 <!-- JAL-1977-->Tooltips shown on database chooser
2279 <!-- JAL-391 -->Reverse complement function in calculate
2280 menu for nucleotide sequences
2283 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2284 and feature counts preserves alignment ordering (and
2285 debugged for complex feature sets).
2288 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2289 viewing structures with Jalview 2.10
2292 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2293 genome, transcript CCDS and gene ids via the Ensembl and
2294 Ensembl Genomes REST API
2297 <!-- JAL-2049 -->Protein sequence variant annotation
2298 computed for 'sequence_variant' annotation on CDS regions
2302 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2306 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2307 Ref Fetcher fails to match, or otherwise updates sequence
2308 data from external database records.
2311 <!-- JAL-2154 -->Revised Jalview Project format for
2312 efficient recovery of sequence coding and alignment
2313 annotation relationships.
2315 </ul> <!-- <em>Applet</em>
2326 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2330 <!-- JAL-2018-->Export features in Jalview format (again)
2331 includes graduated colourschemes
2334 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2335 working with big alignments and lots of hidden columns
2338 <!-- JAL-2053-->Hidden column markers not always rendered
2339 at right of alignment window
2342 <!-- JAL-2067 -->Tidied up links in help file table of
2346 <!-- JAL-2072 -->Feature based tree calculation not shown
2350 <!-- JAL-2075 -->Hidden columns ignored during feature
2351 based tree calculation
2354 <!-- JAL-2065 -->Alignment view stops updating when show
2355 unconserved enabled for group on alignment
2358 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2362 <!-- JAL-2146 -->Alignment column in status incorrectly
2363 shown as "Sequence position" when mousing over
2367 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2368 hidden columns present
2371 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2372 user created annotation added to alignment
2375 <!-- JAL-1841 -->RNA Structure consensus only computed for
2376 '()' base pair annotation
2379 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2380 in zero scores for all base pairs in RNA Structure
2384 <!-- JAL-2174-->Extend selection with columns containing
2388 <!-- JAL-2275 -->Pfam format writer puts extra space at
2389 beginning of sequence
2392 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2396 <!-- JAL-2238 -->Cannot create groups on an alignment from
2397 from a tree when t-coffee scores are shown
2400 <!-- JAL-1836,1967 -->Cannot import and view PDB
2401 structures with chains containing negative resnums (4q4h)
2404 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2408 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2409 to Clustal, PIR and PileUp output
2412 <!-- JAL-2008 -->Reordering sequence features that are
2413 not visible causes alignment window to repaint
2416 <!-- JAL-2006 -->Threshold sliders don't work in
2417 graduated colour and colour by annotation row for e-value
2418 scores associated with features and annotation rows
2421 <!-- JAL-1797 -->amino acid physicochemical conservation
2422 calculation should be case independent
2425 <!-- JAL-2173 -->Remove annotation also updates hidden
2429 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2430 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2431 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2434 <!-- JAL-2065 -->Null pointer exceptions and redraw
2435 problems when reference sequence defined and 'show
2436 non-conserved' enabled
2439 <!-- JAL-1306 -->Quality and Conservation are now shown on
2440 load even when Consensus calculation is disabled
2443 <!-- JAL-1932 -->Remove right on penultimate column of
2444 alignment does nothing
2447 <em>Application</em>
2450 <!-- JAL-1552-->URLs and links can't be imported by
2451 drag'n'drop on OSX when launched via webstart (note - not
2452 yet fixed for El Capitan)
2455 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2456 output when running on non-gb/us i18n platforms
2459 <!-- JAL-1944 -->Error thrown when exporting a view with
2460 hidden sequences as flat-file alignment
2463 <!-- JAL-2030-->InstallAnywhere distribution fails when
2467 <!-- JAL-2080-->Jalview very slow to launch via webstart
2468 (also hotfix for 2.9.0b2)
2471 <!-- JAL-2085 -->Cannot save project when view has a
2472 reference sequence defined
2475 <!-- JAL-1011 -->Columns are suddenly selected in other
2476 alignments and views when revealing hidden columns
2479 <!-- JAL-1989 -->Hide columns not mirrored in complement
2480 view in a cDNA/Protein splitframe
2483 <!-- JAL-1369 -->Cannot save/restore representative
2484 sequence from project when only one sequence is
2488 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2489 in Structure Chooser
2492 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2493 structure consensus didn't refresh annotation panel
2496 <!-- JAL-1962 -->View mapping in structure view shows
2497 mappings between sequence and all chains in a PDB file
2500 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2501 dialogs format columns correctly, don't display array
2502 data, sort columns according to type
2505 <!-- JAL-1975 -->Export complete shown after destination
2506 file chooser is cancelled during an image export
2509 <!-- JAL-2025 -->Error when querying PDB Service with
2510 sequence name containing special characters
2513 <!-- JAL-2024 -->Manual PDB structure querying should be
2517 <!-- JAL-2104 -->Large tooltips with broken HTML
2518 formatting don't wrap
2521 <!-- JAL-1128 -->Figures exported from wrapped view are
2522 truncated so L looks like I in consensus annotation
2525 <!-- JAL-2003 -->Export features should only export the
2526 currently displayed features for the current selection or
2530 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2531 after fetching cross-references, and restoring from
2535 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2536 followed in the structure viewer
2539 <!-- JAL-2163 -->Titles for individual alignments in
2540 splitframe not restored from project
2543 <!-- JAL-2145 -->missing autocalculated annotation at
2544 trailing end of protein alignment in transcript/product
2545 splitview when pad-gaps not enabled by default
2548 <!-- JAL-1797 -->amino acid physicochemical conservation
2552 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2553 article has been read (reopened issue due to
2554 internationalisation problems)
2557 <!-- JAL-1960 -->Only offer PDB structures in structure
2558 viewer based on sequence name, PDB and UniProt
2563 <!-- JAL-1976 -->No progress bar shown during export of
2567 <!-- JAL-2213 -->Structures not always superimposed after
2568 multiple structures are shown for one or more sequences.
2571 <!-- JAL-1370 -->Reference sequence characters should not
2572 be replaced with '.' when 'Show unconserved' format option
2576 <!-- JAL-1823 -->Cannot specify chain code when entering
2577 specific PDB id for sequence
2580 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2581 'Export hidden sequences' is enabled, but 'export hidden
2582 columns' is disabled.
2585 <!--JAL-2026-->Best Quality option in structure chooser
2586 selects lowest rather than highest resolution structures
2590 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2591 to sequence mapping in 'View Mappings' report
2594 <!-- JAL-2284 -->Unable to read old Jalview projects that
2595 contain non-XML data added after Jalvew wrote project.
2598 <!-- JAL-2118 -->Newly created annotation row reorders
2599 after clicking on it to create new annotation for a
2603 <!-- JAL-1980 -->Null Pointer Exception raised when
2604 pressing Add on an orphaned cut'n'paste window.
2606 <!-- may exclude, this is an external service stability issue JAL-1941
2607 -- > RNA 3D structure not added via DSSR service</li> -->
2612 <!-- JAL-2151 -->Incorrect columns are selected when
2613 hidden columns present before start of sequence
2616 <!-- JAL-1986 -->Missing dependencies on applet pages
2620 <!-- JAL-1947 -->Overview pixel size changes when
2621 sequences are hidden in applet
2624 <!-- JAL-1996 -->Updated instructions for applet
2625 deployment on examples pages.
2632 <td width="60" nowrap>
2633 <div align="center">
2634 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2635 <em>16/10/2015</em></strong>
2638 <td><em>General</em>
2640 <li>Time stamps for signed Jalview application and applet
2645 <em>Application</em>
2647 <li>Duplicate group consensus and conservation rows
2648 shown when tree is partitioned</li>
2649 <li>Erratic behaviour when tree partitions made with
2650 multiple cDNA/Protein split views</li>
2656 <td width="60" nowrap>
2657 <div align="center">
2658 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2659 <em>8/10/2015</em></strong>
2662 <td><em>General</em>
2664 <li>Updated Spanish translations of localized text for
2666 </ul> <em>Application</em>
2668 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2669 <li>Signed OSX InstallAnywhere installer<br></li>
2670 <li>Support for per-sequence based annotations in BioJSON</li>
2671 </ul> <em>Applet</em>
2673 <li>Split frame example added to applet examples page</li>
2674 </ul> <em>Build and Deployment</em>
2677 <!-- JAL-1888 -->New ant target for running Jalview's test
2685 <li>Mapping of cDNA to protein in split frames
2686 incorrect when sequence start > 1</li>
2687 <li>Broken images in filter column by annotation dialog
2689 <li>Feature colours not parsed from features file</li>
2690 <li>Exceptions and incomplete link URLs recovered when
2691 loading a features file containing HTML tags in feature
2695 <em>Application</em>
2697 <li>Annotations corrupted after BioJS export and
2699 <li>Incorrect sequence limits after Fetch DB References
2700 with 'trim retrieved sequences'</li>
2701 <li>Incorrect warning about deleting all data when
2702 deleting selected columns</li>
2703 <li>Patch to build system for shipping properly signed
2704 JNLP templates for webstart launch</li>
2705 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2706 unreleased structures for download or viewing</li>
2707 <li>Tab/space/return keystroke operation of EMBL-PDBe
2708 fetcher/viewer dialogs works correctly</li>
2709 <li>Disabled 'minimise' button on Jalview windows
2710 running on OSX to workaround redraw hang bug</li>
2711 <li>Split cDNA/Protein view position and geometry not
2712 recovered from jalview project</li>
2713 <li>Initial enabled/disabled state of annotation menu
2714 sorter 'show autocalculated first/last' corresponds to
2716 <li>Restoring of Clustal, RNA Helices and T-Coffee
2717 color schemes from BioJSON</li>
2721 <li>Reorder sequences mirrored in cDNA/Protein split
2723 <li>Applet with Jmol examples not loading correctly</li>
2729 <td><div align="center">
2730 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2732 <td><em>General</em>
2734 <li>Linked visualisation and analysis of DNA and Protein
2737 <li>Translated cDNA alignments shown as split protein
2738 and DNA alignment views</li>
2739 <li>Codon consensus annotation for linked protein and
2740 cDNA alignment views</li>
2741 <li>Link cDNA or Protein product sequences by loading
2742 them onto Protein or cDNA alignments</li>
2743 <li>Reconstruct linked cDNA alignment from aligned
2744 protein sequences</li>
2747 <li>Jmol integration updated to Jmol v14.2.14</li>
2748 <li>Import and export of Jalview alignment views as <a
2749 href="features/bioJsonFormat.html">BioJSON</a></li>
2750 <li>New alignment annotation file statements for
2751 reference sequences and marking hidden columns</li>
2752 <li>Reference sequence based alignment shading to
2753 highlight variation</li>
2754 <li>Select or hide columns according to alignment
2756 <li>Find option for locating sequences by description</li>
2757 <li>Conserved physicochemical properties shown in amino
2758 acid conservation row</li>
2759 <li>Alignments can be sorted by number of RNA helices</li>
2760 </ul> <em>Application</em>
2762 <li>New cDNA/Protein analysis capabilities
2764 <li>Get Cross-References should open a Split Frame
2765 view with cDNA/Protein</li>
2766 <li>Detect when nucleotide sequences and protein
2767 sequences are placed in the same alignment</li>
2768 <li>Split cDNA/Protein views are saved in Jalview
2773 <li>Use REST API to talk to Chimera</li>
2774 <li>Selected regions in Chimera are highlighted in linked
2775 Jalview windows</li>
2777 <li>VARNA RNA viewer updated to v3.93</li>
2778 <li>VARNA views are saved in Jalview Projects</li>
2779 <li>Pseudoknots displayed as Jalview RNA annotation can
2780 be shown in VARNA</li>
2782 <li>Make groups for selection uses marked columns as well
2783 as the active selected region</li>
2785 <li>Calculate UPGMA and NJ trees using sequence feature
2787 <li>New Export options
2789 <li>New Export Settings dialog to control hidden
2790 region export in flat file generation</li>
2792 <li>Export alignment views for display with the <a
2793 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2795 <li>Export scrollable SVG in HTML page</li>
2796 <li>Optional embedding of BioJSON data when exporting
2797 alignment figures to HTML</li>
2799 <li>3D structure retrieval and display
2801 <li>Free text and structured queries with the PDBe
2803 <li>PDBe Search API based discovery and selection of
2804 PDB structures for a sequence set</li>
2808 <li>JPred4 employed for protein secondary structure
2810 <li>Hide Insertions menu option to hide unaligned columns
2811 for one or a group of sequences</li>
2812 <li>Automatically hide insertions in alignments imported
2813 from the JPred4 web server</li>
2814 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2815 system on OSX<br />LGPL libraries courtesy of <a
2816 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2818 <li>changed 'View nucleotide structure' submenu to 'View
2819 VARNA 2D Structure'</li>
2820 <li>change "View protein structure" menu option to "3D
2823 </ul> <em>Applet</em>
2825 <li>New layout for applet example pages</li>
2826 <li>New parameters to enable SplitFrame view
2827 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2828 <li>New example demonstrating linked viewing of cDNA and
2829 Protein alignments</li>
2830 </ul> <em>Development and deployment</em>
2832 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2833 <li>Include installation type and git revision in build
2834 properties and console log output</li>
2835 <li>Jalview Github organisation, and new github site for
2836 storing BioJsMSA Templates</li>
2837 <li>Jalview's unit tests now managed with TestNG</li>
2840 <!-- <em>General</em>
2842 </ul> --> <!-- issues resolved --> <em>Application</em>
2844 <li>Escape should close any open find dialogs</li>
2845 <li>Typo in select-by-features status report</li>
2846 <li>Consensus RNA secondary secondary structure
2847 predictions are not highlighted in amber</li>
2848 <li>Missing gap character in v2.7 example file means
2849 alignment appears unaligned when pad-gaps is not enabled</li>
2850 <li>First switch to RNA Helices colouring doesn't colour
2851 associated structure views</li>
2852 <li>ID width preference option is greyed out when auto
2853 width checkbox not enabled</li>
2854 <li>Stopped a warning dialog from being shown when
2855 creating user defined colours</li>
2856 <li>'View Mapping' in structure viewer shows sequence
2857 mappings for just that viewer's sequences</li>
2858 <li>Workaround for superposing PDB files containing
2859 multiple models in Chimera</li>
2860 <li>Report sequence position in status bar when hovering
2861 over Jmol structure</li>
2862 <li>Cannot output gaps as '.' symbols with Selection ->
2863 output to text box</li>
2864 <li>Flat file exports of alignments with hidden columns
2865 have incorrect sequence start/end</li>
2866 <li>'Aligning' a second chain to a Chimera structure from
2868 <li>Colour schemes applied to structure viewers don't
2869 work for nucleotide</li>
2870 <li>Loading/cut'n'pasting an empty or invalid file leads
2871 to a grey/invisible alignment window</li>
2872 <li>Exported Jpred annotation from a sequence region
2873 imports to different position</li>
2874 <li>Space at beginning of sequence feature tooltips shown
2875 on some platforms</li>
2876 <li>Chimera viewer 'View | Show Chain' menu is not
2878 <li>'New View' fails with a Null Pointer Exception in
2879 console if Chimera has been opened</li>
2880 <li>Mouseover to Chimera not working</li>
2881 <li>Miscellaneous ENA XML feature qualifiers not
2883 <li>NPE in annotation renderer after 'Extract Scores'</li>
2884 <li>If two structures in one Chimera window, mouseover of
2885 either sequence shows on first structure</li>
2886 <li>'Show annotations' options should not make
2887 non-positional annotations visible</li>
2888 <li>Subsequence secondary structure annotation not shown
2889 in right place after 'view flanking regions'</li>
2890 <li>File Save As type unset when current file format is
2892 <li>Save as '.jar' option removed for saving Jalview
2894 <li>Colour by Sequence colouring in Chimera more
2896 <li>Cannot 'add reference annotation' for a sequence in
2897 several views on same alignment</li>
2898 <li>Cannot show linked products for EMBL / ENA records</li>
2899 <li>Jalview's tooltip wraps long texts containing no
2901 </ul> <em>Applet</em>
2903 <li>Jmol to JalviewLite mouseover/link not working</li>
2904 <li>JalviewLite can't import sequences with ID
2905 descriptions containing angle brackets</li>
2906 </ul> <em>General</em>
2908 <li>Cannot export and reimport RNA secondary structure
2909 via jalview annotation file</li>
2910 <li>Random helix colour palette for colour by annotation
2911 with RNA secondary structure</li>
2912 <li>Mouseover to cDNA from STOP residue in protein
2913 translation doesn't work.</li>
2914 <li>hints when using the select by annotation dialog box</li>
2915 <li>Jmol alignment incorrect if PDB file has alternate CA
2917 <li>FontChooser message dialog appears to hang after
2918 choosing 1pt font</li>
2919 <li>Peptide secondary structure incorrectly imported from
2920 annotation file when annotation display text includes 'e' or
2922 <li>Cannot set colour of new feature type whilst creating
2924 <li>cDNA translation alignment should not be sequence
2925 order dependent</li>
2926 <li>'Show unconserved' doesn't work for lower case
2928 <li>Nucleotide ambiguity codes involving R not recognised</li>
2929 </ul> <em>Deployment and Documentation</em>
2931 <li>Applet example pages appear different to the rest of
2932 www.jalview.org</li>
2933 </ul> <em>Application Known issues</em>
2935 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2936 <li>Misleading message appears after trying to delete
2938 <li>Jalview icon not shown in dock after InstallAnywhere
2939 version launches</li>
2940 <li>Fetching EMBL reference for an RNA sequence results
2941 fails with a sequence mismatch</li>
2942 <li>Corrupted or unreadable alignment display when
2943 scrolling alignment to right</li>
2944 <li>ArrayIndexOutOfBoundsException thrown when remove
2945 empty columns called on alignment with ragged gapped ends</li>
2946 <li>auto calculated alignment annotation rows do not get
2947 placed above or below non-autocalculated rows</li>
2948 <li>Jalview dekstop becomes sluggish at full screen in
2949 ultra-high resolution</li>
2950 <li>Cannot disable consensus calculation independently of
2951 quality and conservation</li>
2952 <li>Mouseover highlighting between cDNA and protein can
2953 become sluggish with more than one splitframe shown</li>
2954 </ul> <em>Applet Known Issues</em>
2956 <li>Core PDB parsing code requires Jmol</li>
2957 <li>Sequence canvas panel goes white when alignment
2958 window is being resized</li>
2964 <td><div align="center">
2965 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2967 <td><em>General</em>
2969 <li>Updated Java code signing certificate donated by
2971 <li>Features and annotation preserved when performing
2972 pairwise alignment</li>
2973 <li>RNA pseudoknot annotation can be
2974 imported/exported/displayed</li>
2975 <li>'colour by annotation' can colour by RNA and
2976 protein secondary structure</li>
2977 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2978 post-hoc with 2.9 release</em>)
2981 </ul> <em>Application</em>
2983 <li>Extract and display secondary structure for sequences
2984 with 3D structures</li>
2985 <li>Support for parsing RNAML</li>
2986 <li>Annotations menu for layout
2988 <li>sort sequence annotation rows by alignment</li>
2989 <li>place sequence annotation above/below alignment
2992 <li>Output in Stockholm format</li>
2993 <li>Internationalisation: improved Spanish (es)
2995 <li>Structure viewer preferences tab</li>
2996 <li>Disorder and Secondary Structure annotation tracks
2997 shared between alignments</li>
2998 <li>UCSF Chimera launch and linked highlighting from
3000 <li>Show/hide all sequence associated annotation rows for
3001 all or current selection</li>
3002 <li>disorder and secondary structure predictions
3003 available as dataset annotation</li>
3004 <li>Per-sequence rna helices colouring</li>
3007 <li>Sequence database accessions imported when fetching
3008 alignments from Rfam</li>
3009 <li>update VARNA version to 3.91</li>
3011 <li>New groovy scripts for exporting aligned positions,
3012 conservation values, and calculating sum of pairs scores.</li>
3013 <li>Command line argument to set default JABAWS server</li>
3014 <li>include installation type in build properties and
3015 console log output</li>
3016 <li>Updated Jalview project format to preserve dataset
3020 <!-- issues resolved --> <em>Application</em>
3022 <li>Distinguish alignment and sequence associated RNA
3023 structure in structure->view->VARNA</li>
3024 <li>Raise dialog box if user deletes all sequences in an
3026 <li>Pressing F1 results in documentation opening twice</li>
3027 <li>Sequence feature tooltip is wrapped</li>
3028 <li>Double click on sequence associated annotation
3029 selects only first column</li>
3030 <li>Redundancy removal doesn't result in unlinked
3031 leaves shown in tree</li>
3032 <li>Undos after several redundancy removals don't undo
3034 <li>Hide sequence doesn't hide associated annotation</li>
3035 <li>User defined colours dialog box too big to fit on
3036 screen and buttons not visible</li>
3037 <li>author list isn't updated if already written to
3038 Jalview properties</li>
3039 <li>Popup menu won't open after retrieving sequence
3041 <li>File open window for associate PDB doesn't open</li>
3042 <li>Left-then-right click on a sequence id opens a
3043 browser search window</li>
3044 <li>Cannot open sequence feature shading/sort popup menu
3045 in feature settings dialog</li>
3046 <li>better tooltip placement for some areas of Jalview
3048 <li>Allow addition of JABAWS Server which doesn't
3049 pass validation</li>
3050 <li>Web services parameters dialog box is too large to
3052 <li>Muscle nucleotide alignment preset obscured by
3054 <li>JABAWS preset submenus don't contain newly
3055 defined user preset</li>
3056 <li>MSA web services warns user if they were launched
3057 with invalid input</li>
3058 <li>Jalview cannot contact DAS Registy when running on
3061 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3062 'Superpose with' submenu not shown when new view
3066 </ul> <!-- <em>Applet</em>
3068 </ul> <em>General</em>
3070 </ul>--> <em>Deployment and Documentation</em>
3072 <li>2G and 1G options in launchApp have no effect on
3073 memory allocation</li>
3074 <li>launchApp service doesn't automatically open
3075 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3077 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3078 InstallAnywhere reports cannot find valid JVM when Java
3079 1.7_055 is available
3081 </ul> <em>Application Known issues</em>
3084 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3085 corrupted or unreadable alignment display when scrolling
3089 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3090 retrieval fails but progress bar continues for DAS retrieval
3091 with large number of ID
3094 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3095 flatfile output of visible region has incorrect sequence
3099 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3100 rna structure consensus doesn't update when secondary
3101 structure tracks are rearranged
3104 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3105 invalid rna structure positional highlighting does not
3106 highlight position of invalid base pairs
3109 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3110 out of memory errors are not raised when saving Jalview
3111 project from alignment window file menu
3114 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3115 Switching to RNA Helices colouring doesn't propagate to
3119 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3120 colour by RNA Helices not enabled when user created
3121 annotation added to alignment
3124 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3125 Jalview icon not shown on dock in Mountain Lion/Webstart
3127 </ul> <em>Applet Known Issues</em>
3130 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3131 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3134 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3135 Jalview and Jmol example not compatible with IE9
3138 <li>Sort by annotation score doesn't reverse order
3144 <td><div align="center">
3145 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3148 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3151 <li>Internationalisation of user interface (usually
3152 called i18n support) and translation for Spanish locale</li>
3153 <li>Define/Undefine group on current selection with
3154 Ctrl-G/Shift Ctrl-G</li>
3155 <li>Improved group creation/removal options in
3156 alignment/sequence Popup menu</li>
3157 <li>Sensible precision for symbol distribution
3158 percentages shown in logo tooltip.</li>
3159 <li>Annotation panel height set according to amount of
3160 annotation when alignment first opened</li>
3161 </ul> <em>Application</em>
3163 <li>Interactive consensus RNA secondary structure
3164 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3165 <li>Select columns containing particular features from
3166 Feature Settings dialog</li>
3167 <li>View all 'representative' PDB structures for selected
3169 <li>Update Jalview project format:
3171 <li>New file extension for Jalview projects '.jvp'</li>
3172 <li>Preserve sequence and annotation dataset (to
3173 store secondary structure annotation,etc)</li>
3174 <li>Per group and alignment annotation and RNA helix
3178 <li>New similarity measures for PCA and Tree calculation
3180 <li>Experimental support for retrieval and viewing of
3181 flanking regions for an alignment</li>
3185 <!-- issues resolved --> <em>Application</em>
3187 <li>logo keeps spinning and status remains at queued or
3188 running after job is cancelled</li>
3189 <li>cannot export features from alignments imported from
3190 Jalview/VAMSAS projects</li>
3191 <li>Buggy slider for web service parameters that take
3193 <li>Newly created RNA secondary structure line doesn't
3194 have 'display all symbols' flag set</li>
3195 <li>T-COFFEE alignment score shading scheme and other
3196 annotation shading not saved in Jalview project</li>
3197 <li>Local file cannot be loaded in freshly downloaded
3199 <li>Jalview icon not shown on dock in Mountain
3201 <li>Load file from desktop file browser fails</li>
3202 <li>Occasional NPE thrown when calculating large trees</li>
3203 <li>Cannot reorder or slide sequences after dragging an
3204 alignment onto desktop</li>
3205 <li>Colour by annotation dialog throws NPE after using
3206 'extract scores' function</li>
3207 <li>Loading/cut'n'pasting an empty file leads to a grey
3208 alignment window</li>
3209 <li>Disorder thresholds rendered incorrectly after
3210 performing IUPred disorder prediction</li>
3211 <li>Multiple group annotated consensus rows shown when
3212 changing 'normalise logo' display setting</li>
3213 <li>Find shows blank dialog after 'finished searching' if
3214 nothing matches query</li>
3215 <li>Null Pointer Exceptions raised when sorting by
3216 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3218 <li>Errors in Jmol console when structures in alignment
3219 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3221 <li>Not all working JABAWS services are shown in
3223 <li>JAVAWS version of Jalview fails to launch with
3224 'invalid literal/length code'</li>
3225 <li>Annotation/RNA Helix colourschemes cannot be applied
3226 to alignment with groups (actually fixed in 2.8.0b1)</li>
3227 <li>RNA Helices and T-Coffee Scores available as default
3230 </ul> <em>Applet</em>
3232 <li>Remove group option is shown even when selection is
3234 <li>Apply to all groups ticked but colourscheme changes
3235 don't affect groups</li>
3236 <li>Documented RNA Helices and T-Coffee Scores as valid
3237 colourscheme name</li>
3238 <li>Annotation labels drawn on sequence IDs when
3239 Annotation panel is not displayed</li>
3240 <li>Increased font size for dropdown menus on OSX and
3241 embedded windows</li>
3242 </ul> <em>Other</em>
3244 <li>Consensus sequence for alignments/groups with a
3245 single sequence were not calculated</li>
3246 <li>annotation files that contain only groups imported as
3247 annotation and junk sequences</li>
3248 <li>Fasta files with sequences containing '*' incorrectly
3249 recognised as PFAM or BLC</li>
3250 <li>conservation/PID slider apply all groups option
3251 doesn't affect background (2.8.0b1)
3253 <li>redundancy highlighting is erratic at 0% and 100%</li>
3254 <li>Remove gapped columns fails for sequences with ragged
3256 <li>AMSA annotation row with leading spaces is not
3257 registered correctly on import</li>
3258 <li>Jalview crashes when selecting PCA analysis for
3259 certain alignments</li>
3260 <li>Opening the colour by annotation dialog for an
3261 existing annotation based 'use original colours'
3262 colourscheme loses original colours setting</li>
3267 <td><div align="center">
3268 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3269 <em>30/1/2014</em></strong>
3273 <li>Trusted certificates for JalviewLite applet and
3274 Jalview Desktop application<br />Certificate was donated by
3275 <a href="https://www.certum.eu">Certum</a> to the Jalview
3276 open source project).
3278 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3279 <li>Output in Stockholm format</li>
3280 <li>Allow import of data from gzipped files</li>
3281 <li>Export/import group and sequence associated line
3282 graph thresholds</li>
3283 <li>Nucleotide substitution matrix that supports RNA and
3284 ambiguity codes</li>
3285 <li>Allow disorder predictions to be made on the current
3286 selection (or visible selection) in the same way that JPred
3288 <li>Groovy scripting for headless Jalview operation</li>
3289 </ul> <em>Other improvements</em>
3291 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3292 <li>COMBINE statement uses current SEQUENCE_REF and
3293 GROUP_REF scope to group annotation rows</li>
3294 <li>Support '' style escaping of quotes in Newick
3296 <li>Group options for JABAWS service by command line name</li>
3297 <li>Empty tooltip shown for JABA service options with a
3298 link but no description</li>
3299 <li>Select primary source when selecting authority in
3300 database fetcher GUI</li>
3301 <li>Add .mfa to FASTA file extensions recognised by
3303 <li>Annotation label tooltip text wrap</li>
3308 <li>Slow scrolling when lots of annotation rows are
3310 <li>Lots of NPE (and slowness) after creating RNA
3311 secondary structure annotation line</li>
3312 <li>Sequence database accessions not imported when
3313 fetching alignments from Rfam</li>
3314 <li>Incorrect SHMR submission for sequences with
3316 <li>View all structures does not always superpose
3318 <li>Option widgets in service parameters not updated to
3319 reflect user or preset settings</li>
3320 <li>Null pointer exceptions for some services without
3321 presets or adjustable parameters</li>
3322 <li>Discover PDB IDs entry in structure menu doesn't
3323 discover PDB xRefs</li>
3324 <li>Exception encountered while trying to retrieve
3325 features with DAS</li>
3326 <li>Lowest value in annotation row isn't coloured
3327 when colour by annotation (per sequence) is coloured</li>
3328 <li>Keyboard mode P jumps to start of gapped region when
3329 residue follows a gap</li>
3330 <li>Jalview appears to hang importing an alignment with
3331 Wrap as default or after enabling Wrap</li>
3332 <li>'Right click to add annotations' message
3333 shown in wrap mode when no annotations present</li>
3334 <li>Disorder predictions fail with NPE if no automatic
3335 annotation already exists on alignment</li>
3336 <li>oninit javascript function should be called after
3337 initialisation completes</li>
3338 <li>Remove redundancy after disorder prediction corrupts
3339 alignment window display</li>
3340 <li>Example annotation file in documentation is invalid</li>
3341 <li>Grouped line graph annotation rows are not exported
3342 to annotation file</li>
3343 <li>Multi-harmony analysis cannot be run when only two
3345 <li>Cannot create multiple groups of line graphs with
3346 several 'combine' statements in annotation file</li>
3347 <li>Pressing return several times causes Number Format
3348 exceptions in keyboard mode</li>
3349 <li>Multi-harmony (SHMMR) method doesn't submit
3350 correct partitions for input data</li>
3351 <li>Translation from DNA to Amino Acids fails</li>
3352 <li>Jalview fail to load newick tree with quoted label</li>
3353 <li>--headless flag isn't understood</li>
3354 <li>ClassCastException when generating EPS in headless
3356 <li>Adjusting sequence-associated shading threshold only
3357 changes one row's threshold</li>
3358 <li>Preferences and Feature settings panel panel
3359 doesn't open</li>
3360 <li>hide consensus histogram also hides conservation and
3361 quality histograms</li>
3366 <td><div align="center">
3367 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3369 <td><em>Application</em>
3371 <li>Support for JABAWS 2.0 Services (AACon alignment
3372 conservation, protein disorder and Clustal Omega)</li>
3373 <li>JABAWS server status indicator in Web Services
3375 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3376 in Jalview alignment window</li>
3377 <li>Updated Jalview build and deploy framework for OSX
3378 mountain lion, windows 7, and 8</li>
3379 <li>Nucleotide substitution matrix for PCA that supports
3380 RNA and ambiguity codes</li>
3382 <li>Improved sequence database retrieval GUI</li>
3383 <li>Support fetching and database reference look up
3384 against multiple DAS sources (Fetch all from in 'fetch db
3386 <li>Jalview project improvements
3388 <li>Store and retrieve the 'belowAlignment'
3389 flag for annotation</li>
3390 <li>calcId attribute to group annotation rows on the
3392 <li>Store AACon calculation settings for a view in
3393 Jalview project</li>
3397 <li>horizontal scrolling gesture support</li>
3398 <li>Visual progress indicator when PCA calculation is
3400 <li>Simpler JABA web services menus</li>
3401 <li>visual indication that web service results are still
3402 being retrieved from server</li>
3403 <li>Serialise the dialogs that are shown when Jalview
3404 starts up for first time</li>
3405 <li>Jalview user agent string for interacting with HTTP
3407 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3409 <li>Examples directory and Groovy library included in
3410 InstallAnywhere distribution</li>
3411 </ul> <em>Applet</em>
3413 <li>RNA alignment and secondary structure annotation
3414 visualization applet example</li>
3415 </ul> <em>General</em>
3417 <li>Normalise option for consensus sequence logo</li>
3418 <li>Reset button in PCA window to return dimensions to
3420 <li>Allow seqspace or Jalview variant of alignment PCA
3422 <li>PCA with either nucleic acid and protein substitution
3424 <li>Allow windows containing HTML reports to be exported
3426 <li>Interactive display and editing of RNA secondary
3427 structure contacts</li>
3428 <li>RNA Helix Alignment Colouring</li>
3429 <li>RNA base pair logo consensus</li>
3430 <li>Parse sequence associated secondary structure
3431 information in Stockholm files</li>
3432 <li>HTML Export database accessions and annotation
3433 information presented in tooltip for sequences</li>
3434 <li>Import secondary structure from LOCARNA clustalw
3435 style RNA alignment files</li>
3436 <li>import and visualise T-COFFEE quality scores for an
3438 <li>'colour by annotation' per sequence option to
3439 shade each sequence according to its associated alignment
3441 <li>New Jalview Logo</li>
3442 </ul> <em>Documentation and Development</em>
3444 <li>documentation for score matrices used in Jalview</li>
3445 <li>New Website!</li>
3447 <td><em>Application</em>
3449 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3450 wsdbfetch REST service</li>
3451 <li>Stop windows being moved outside desktop on OSX</li>
3452 <li>Filetype associations not installed for webstart
3454 <li>Jalview does not always retrieve progress of a JABAWS
3455 job execution in full once it is complete</li>
3456 <li>revise SHMR RSBS definition to ensure alignment is
3457 uploaded via ali_file parameter</li>
3458 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3459 <li>View all structures superposed fails with exception</li>
3460 <li>Jnet job queues forever if a very short sequence is
3461 submitted for prediction</li>
3462 <li>Cut and paste menu not opened when mouse clicked on
3464 <li>Putting fractional value into integer text box in
3465 alignment parameter dialog causes Jalview to hang</li>
3466 <li>Structure view highlighting doesn't work on
3468 <li>View all structures fails with exception shown in
3470 <li>Characters in filename associated with PDBEntry not
3471 escaped in a platform independent way</li>
3472 <li>Jalview desktop fails to launch with exception when
3474 <li>Tree calculation reports 'you must have 2 or more
3475 sequences selected' when selection is empty</li>
3476 <li>Jalview desktop fails to launch with jar signature
3477 failure when java web start temporary file caching is
3479 <li>DAS Sequence retrieval with range qualification
3480 results in sequence xref which includes range qualification</li>
3481 <li>Errors during processing of command line arguments
3482 cause progress bar (JAL-898) to be removed</li>
3483 <li>Replace comma for semi-colon option not disabled for
3484 DAS sources in sequence fetcher</li>
3485 <li>Cannot close news reader when JABAWS server warning
3486 dialog is shown</li>
3487 <li>Option widgets not updated to reflect user settings</li>
3488 <li>Edited sequence not submitted to web service</li>
3489 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3490 <li>InstallAnywhere installer doesn't unpack and run
3491 on OSX Mountain Lion</li>
3492 <li>Annotation panel not given a scroll bar when
3493 sequences with alignment annotation are pasted into the
3495 <li>Sequence associated annotation rows not associated
3496 when loaded from Jalview project</li>
3497 <li>Browser launch fails with NPE on java 1.7</li>
3498 <li>JABAWS alignment marked as finished when job was
3499 cancelled or job failed due to invalid input</li>
3500 <li>NPE with v2.7 example when clicking on Tree
3501 associated with all views</li>
3502 <li>Exceptions when copy/paste sequences with grouped
3503 annotation rows to new window</li>
3504 </ul> <em>Applet</em>
3506 <li>Sequence features are momentarily displayed before
3507 they are hidden using hidefeaturegroups applet parameter</li>
3508 <li>loading features via javascript API automatically
3509 enables feature display</li>
3510 <li>scrollToColumnIn javascript API method doesn't
3512 </ul> <em>General</em>
3514 <li>Redundancy removal fails for rna alignment</li>
3515 <li>PCA calculation fails when sequence has been selected
3516 and then deselected</li>
3517 <li>PCA window shows grey box when first opened on OSX</li>
3518 <li>Letters coloured pink in sequence logo when alignment
3519 coloured with clustalx</li>
3520 <li>Choosing fonts without letter symbols defined causes
3521 exceptions and redraw errors</li>
3522 <li>Initial PCA plot view is not same as manually
3523 reconfigured view</li>
3524 <li>Grouped annotation graph label has incorrect line
3526 <li>Grouped annotation graph label display is corrupted
3527 for lots of labels</li>
3532 <div align="center">
3533 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3536 <td><em>Application</em>
3538 <li>Jalview Desktop News Reader</li>
3539 <li>Tweaked default layout of web services menu</li>
3540 <li>View/alignment association menu to enable user to
3541 easily specify which alignment a multi-structure view takes
3542 its colours/correspondences from</li>
3543 <li>Allow properties file location to be specified as URL</li>
3544 <li>Extend Jalview project to preserve associations
3545 between many alignment views and a single Jmol display</li>
3546 <li>Store annotation row height in Jalview project file</li>
3547 <li>Annotation row column label formatting attributes
3548 stored in project file</li>
3549 <li>Annotation row order for auto-calculated annotation
3550 rows preserved in Jalview project file</li>
3551 <li>Visual progress indication when Jalview state is
3552 saved using Desktop window menu</li>
3553 <li>Visual indication that command line arguments are
3554 still being processed</li>
3555 <li>Groovy script execution from URL</li>
3556 <li>Colour by annotation default min and max colours in
3558 <li>Automatically associate PDB files dragged onto an
3559 alignment with sequences that have high similarity and
3561 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3562 <li>'view structures' option to open many
3563 structures in same window</li>
3564 <li>Sort associated views menu option for tree panel</li>
3565 <li>Group all JABA and non-JABA services for a particular
3566 analysis function in its own submenu</li>
3567 </ul> <em>Applet</em>
3569 <li>Userdefined and autogenerated annotation rows for
3571 <li>Adjustment of alignment annotation pane height</li>
3572 <li>Annotation scrollbar for annotation panel</li>
3573 <li>Drag to reorder annotation rows in annotation panel</li>
3574 <li>'automaticScrolling' parameter</li>
3575 <li>Allow sequences with partial ID string matches to be
3576 annotated from GFF/Jalview features files</li>
3577 <li>Sequence logo annotation row in applet</li>
3578 <li>Absolute paths relative to host server in applet
3579 parameters are treated as such</li>
3580 <li>New in the JalviewLite javascript API:
3582 <li>JalviewLite.js javascript library</li>
3583 <li>Javascript callbacks for
3585 <li>Applet initialisation</li>
3586 <li>Sequence/alignment mouse-overs and selections</li>
3589 <li>scrollTo row and column alignment scrolling
3591 <li>Select sequence/alignment regions from javascript</li>
3592 <li>javascript structure viewer harness to pass
3593 messages between Jmol and Jalview when running as
3594 distinct applets</li>
3595 <li>sortBy method</li>
3596 <li>Set of applet and application examples shipped
3597 with documentation</li>
3598 <li>New example to demonstrate JalviewLite and Jmol
3599 javascript message exchange</li>
3601 </ul> <em>General</em>
3603 <li>Enable Jmol displays to be associated with multiple
3604 multiple alignments</li>
3605 <li>Option to automatically sort alignment with new tree</li>
3606 <li>User configurable link to enable redirects to a
3607 www.Jalview.org mirror</li>
3608 <li>Jmol colours option for Jmol displays</li>
3609 <li>Configurable newline string when writing alignment
3610 and other flat files</li>
3611 <li>Allow alignment annotation description lines to
3612 contain html tags</li>
3613 </ul> <em>Documentation and Development</em>
3615 <li>Add groovy test harness for bulk load testing to
3617 <li>Groovy script to load and align a set of sequences
3618 using a web service before displaying the result in the
3619 Jalview desktop</li>
3620 <li>Restructured javascript and applet api documentation</li>
3621 <li>Ant target to publish example html files with applet
3623 <li>Netbeans project for building Jalview from source</li>
3624 <li>ant task to create online javadoc for Jalview source</li>
3626 <td><em>Application</em>
3628 <li>User defined colourscheme throws exception when
3629 current built in colourscheme is saved as new scheme</li>
3630 <li>AlignFrame->Save in application pops up save
3631 dialog for valid filename/format</li>
3632 <li>Cannot view associated structure for UniProt sequence</li>
3633 <li>PDB file association breaks for UniProt sequence
3635 <li>Associate PDB from file dialog does not tell you
3636 which sequence is to be associated with the file</li>
3637 <li>Find All raises null pointer exception when query
3638 only matches sequence IDs</li>
3639 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3640 <li>Jalview project with Jmol views created with Jalview
3641 2.4 cannot be loaded</li>
3642 <li>Filetype associations not installed for webstart
3644 <li>Two or more chains in a single PDB file associated
3645 with sequences in different alignments do not get coloured
3646 by their associated sequence</li>
3647 <li>Visibility status of autocalculated annotation row
3648 not preserved when project is loaded</li>
3649 <li>Annotation row height and visibility attributes not
3650 stored in Jalview project</li>
3651 <li>Tree bootstraps are not preserved when saved as a
3652 Jalview project</li>
3653 <li>Envision2 workflow tooltips are corrupted</li>
3654 <li>Enabling show group conservation also enables colour
3655 by conservation</li>
3656 <li>Duplicate group associated conservation or consensus
3657 created on new view</li>
3658 <li>Annotation scrollbar not displayed after 'show
3659 all hidden annotation rows' option selected</li>
3660 <li>Alignment quality not updated after alignment
3661 annotation row is hidden then shown</li>
3662 <li>Preserve colouring of structures coloured by
3663 sequences in pre Jalview 2.7 projects</li>
3664 <li>Web service job parameter dialog is not laid out
3666 <li>Web services menu not refreshed after 'reset
3667 services' button is pressed in preferences</li>
3668 <li>Annotation off by one in Jalview v2_3 example project</li>
3669 <li>Structures imported from file and saved in project
3670 get name like jalview_pdb1234.txt when reloaded</li>
3671 <li>Jalview does not always retrieve progress of a JABAWS
3672 job execution in full once it is complete</li>
3673 </ul> <em>Applet</em>
3675 <li>Alignment height set incorrectly when lots of
3676 annotation rows are displayed</li>
3677 <li>Relative URLs in feature HTML text not resolved to
3679 <li>View follows highlighting does not work for positions
3681 <li><= shown as = in tooltip</li>
3682 <li>Export features raises exception when no features
3684 <li>Separator string used for serialising lists of IDs
3685 for javascript api is modified when separator string
3686 provided as parameter</li>
3687 <li>Null pointer exception when selecting tree leaves for
3688 alignment with no existing selection</li>
3689 <li>Relative URLs for datasources assumed to be relative
3690 to applet's codebase</li>
3691 <li>Status bar not updated after finished searching and
3692 search wraps around to first result</li>
3693 <li>StructureSelectionManager instance shared between
3694 several Jalview applets causes race conditions and memory
3696 <li>Hover tooltip and mouseover of position on structure
3697 not sent from Jmol in applet</li>
3698 <li>Certain sequences of javascript method calls to
3699 applet API fatally hang browser</li>
3700 </ul> <em>General</em>
3702 <li>View follows structure mouseover scrolls beyond
3703 position with wrapped view and hidden regions</li>
3704 <li>Find sequence position moves to wrong residue
3705 with/without hidden columns</li>
3706 <li>Sequence length given in alignment properties window
3708 <li>InvalidNumberFormat exceptions thrown when trying to
3709 import PDB like structure files</li>
3710 <li>Positional search results are only highlighted
3711 between user-supplied sequence start/end bounds</li>
3712 <li>End attribute of sequence is not validated</li>
3713 <li>Find dialog only finds first sequence containing a
3714 given sequence position</li>
3715 <li>Sequence numbering not preserved in MSF alignment
3717 <li>Jalview PDB file reader does not extract sequence
3718 from nucleotide chains correctly</li>
3719 <li>Structure colours not updated when tree partition
3720 changed in alignment</li>
3721 <li>Sequence associated secondary structure not correctly
3722 parsed in interleaved stockholm</li>
3723 <li>Colour by annotation dialog does not restore current
3725 <li>Hiding (nearly) all sequences doesn't work
3727 <li>Sequences containing lowercase letters are not
3728 properly associated with their pdb files</li>
3729 </ul> <em>Documentation and Development</em>
3731 <li>schemas/JalviewWsParamSet.xsd corrupted by
3732 ApplyCopyright tool</li>
3737 <div align="center">
3738 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3741 <td><em>Application</em>
3743 <li>New warning dialog when the Jalview Desktop cannot
3744 contact web services</li>
3745 <li>JABA service parameters for a preset are shown in
3746 service job window</li>
3747 <li>JABA Service menu entries reworded</li>
3751 <li>Modeller PIR IO broken - cannot correctly import a
3752 pir file emitted by Jalview</li>
3753 <li>Existing feature settings transferred to new
3754 alignment view created from cut'n'paste</li>
3755 <li>Improved test for mixed amino/nucleotide chains when
3756 parsing PDB files</li>
3757 <li>Consensus and conservation annotation rows
3758 occasionally become blank for all new windows</li>
3759 <li>Exception raised when right clicking above sequences
3760 in wrapped view mode</li>
3761 </ul> <em>Application</em>
3763 <li>multiple multiply aligned structure views cause cpu
3764 usage to hit 100% and computer to hang</li>
3765 <li>Web Service parameter layout breaks for long user
3766 parameter names</li>
3767 <li>Jaba service discovery hangs desktop if Jaba server
3774 <div align="center">
3775 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3778 <td><em>Application</em>
3780 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3781 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3784 <li>Web Services preference tab</li>
3785 <li>Analysis parameters dialog box and user defined
3787 <li>Improved speed and layout of Envision2 service menu</li>
3788 <li>Superpose structures using associated sequence
3790 <li>Export coordinates and projection as CSV from PCA
3792 </ul> <em>Applet</em>
3794 <li>enable javascript: execution by the applet via the
3795 link out mechanism</li>
3796 </ul> <em>Other</em>
3798 <li>Updated the Jmol Jalview interface to work with Jmol
3800 <li>The Jalview Desktop and JalviewLite applet now
3801 require Java 1.5</li>
3802 <li>Allow Jalview feature colour specification for GFF
3803 sequence annotation files</li>
3804 <li>New 'colour by label' keword in Jalview feature file
3805 type colour specification</li>
3806 <li>New Jalview Desktop Groovy API method that allows a
3807 script to check if it being run in an interactive session or
3808 in a batch operation from the Jalview command line</li>
3812 <li>clustalx colourscheme colours Ds preferentially when
3813 both D+E are present in over 50% of the column</li>
3814 </ul> <em>Application</em>
3816 <li>typo in AlignmentFrame->View->Hide->all but
3817 selected Regions menu item</li>
3818 <li>sequence fetcher replaces ',' for ';' when the ',' is
3819 part of a valid accession ID</li>
3820 <li>fatal OOM if object retrieved by sequence fetcher
3821 runs out of memory</li>
3822 <li>unhandled Out of Memory Error when viewing pca
3823 analysis results</li>
3824 <li>InstallAnywhere builds fail to launch on OS X java
3825 10.5 update 4 (due to apple Java 1.6 update)</li>
3826 <li>Installanywhere Jalview silently fails to launch</li>
3827 </ul> <em>Applet</em>
3829 <li>Jalview.getFeatureGroups() raises an
3830 ArrayIndexOutOfBoundsException if no feature groups are
3837 <div align="center">
3838 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3844 <li>Alignment prettyprinter doesn't cope with long
3846 <li>clustalx colourscheme colours Ds preferentially when
3847 both D+E are present in over 50% of the column</li>
3848 <li>nucleic acid structures retrieved from PDB do not
3849 import correctly</li>
3850 <li>More columns get selected than were clicked on when a
3851 number of columns are hidden</li>
3852 <li>annotation label popup menu not providing correct
3853 add/hide/show options when rows are hidden or none are
3855 <li>Stockholm format shown in list of readable formats,
3856 and parser copes better with alignments from RFAM.</li>
3857 <li>CSV output of consensus only includes the percentage
3858 of all symbols if sequence logo display is enabled</li>
3860 </ul> <em>Applet</em>
3862 <li>annotation panel disappears when annotation is
3864 </ul> <em>Application</em>
3866 <li>Alignment view not redrawn properly when new
3867 alignment opened where annotation panel is visible but no
3868 annotations are present on alignment</li>
3869 <li>pasted region containing hidden columns is
3870 incorrectly displayed in new alignment window</li>
3871 <li>Jalview slow to complete operations when stdout is
3872 flooded (fix is to close the Jalview console)</li>
3873 <li>typo in AlignmentFrame->View->Hide->all but
3874 selected Rregions menu item.</li>
3875 <li>inconsistent group submenu and Format submenu entry
3876 'Un' or 'Non'conserved</li>
3877 <li>Sequence feature settings are being shared by
3878 multiple distinct alignments</li>
3879 <li>group annotation not recreated when tree partition is
3881 <li>double click on group annotation to select sequences
3882 does not propagate to associated trees</li>
3883 <li>Mac OSX specific issues:
3885 <li>exception raised when mouse clicked on desktop
3886 window background</li>
3887 <li>Desktop menu placed on menu bar and application
3888 name set correctly</li>
3889 <li>sequence feature settings not wide enough for the
3890 save feature colourscheme button</li>
3899 <div align="center">
3900 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3903 <td><em>New Capabilities</em>
3905 <li>URL links generated from description line for
3906 regular-expression based URL links (applet and application)
3908 <li>Non-positional feature URL links are shown in link
3910 <li>Linked viewing of nucleic acid sequences and
3912 <li>Automatic Scrolling option in View menu to display
3913 the currently highlighted region of an alignment.</li>
3914 <li>Order an alignment by sequence length, or using the
3915 average score or total feature count for each sequence.</li>
3916 <li>Shading features by score or associated description</li>
3917 <li>Subdivide alignment and groups based on identity of
3918 selected subsequence (Make Groups from Selection).</li>
3919 <li>New hide/show options including Shift+Control+H to
3920 hide everything but the currently selected region.</li>
3921 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3922 </ul> <em>Application</em>
3924 <li>Fetch DB References capabilities and UI expanded to
3925 support retrieval from DAS sequence sources</li>
3926 <li>Local DAS Sequence sources can be added via the
3927 command line or via the Add local source dialog box.</li>
3928 <li>DAS Dbref and DbxRef feature types are parsed as
3929 database references and protein_name is parsed as
3930 description line (BioSapiens terms).</li>
3931 <li>Enable or disable non-positional feature and database
3932 references in sequence ID tooltip from View menu in
3934 <!-- <li>New hidden columns and rows and representatives capabilities
3935 in annotations file (in progress - not yet fully implemented)</li> -->
3936 <li>Group-associated consensus, sequence logos and
3937 conservation plots</li>
3938 <li>Symbol distributions for each column can be exported
3939 and visualized as sequence logos</li>
3940 <li>Optionally scale multi-character column labels to fit
3941 within each column of annotation row<!-- todo for applet -->
3943 <li>Optional automatic sort of associated alignment view
3944 when a new tree is opened.</li>
3945 <li>Jalview Java Console</li>
3946 <li>Better placement of desktop window when moving
3947 between different screens.</li>
3948 <li>New preference items for sequence ID tooltip and
3949 consensus annotation</li>
3950 <li>Client to submit sequences and IDs to Envision2
3952 <li><em>Vamsas Capabilities</em>
3954 <li>Improved VAMSAS synchronization (Jalview archive
3955 used to preserve views, structures, and tree display
3957 <li>Import of vamsas documents from disk or URL via
3959 <li>Sharing of selected regions between views and
3960 with other VAMSAS applications (Experimental feature!)</li>
3961 <li>Updated API to VAMSAS version 0.2</li>
3963 </ul> <em>Applet</em>
3965 <li>Middle button resizes annotation row height</li>
3968 <li>sortByTree (true/false) - automatically sort the
3969 associated alignment view by the tree when a new tree is
3971 <li>showTreeBootstraps (true/false) - show or hide
3972 branch bootstraps (default is to show them if available)</li>
3973 <li>showTreeDistances (true/false) - show or hide
3974 branch lengths (default is to show them if available)</li>
3975 <li>showUnlinkedTreeNodes (true/false) - indicate if
3976 unassociated nodes should be highlighted in the tree
3978 <li>heightScale and widthScale (1.0 or more) -
3979 increase the height or width of a cell in the alignment
3980 grid relative to the current font size.</li>
3983 <li>Non-positional features displayed in sequence ID
3985 </ul> <em>Other</em>
3987 <li>Features format: graduated colour definitions and
3988 specification of feature scores</li>
3989 <li>Alignment Annotations format: new keywords for group
3990 associated annotation (GROUP_REF) and annotation row display
3991 properties (ROW_PROPERTIES)</li>
3992 <li>XML formats extended to support graduated feature
3993 colourschemes, group associated annotation, and profile
3994 visualization settings.</li></td>
3997 <li>Source field in GFF files parsed as feature source
3998 rather than description</li>
3999 <li>Non-positional features are now included in sequence
4000 feature and gff files (controlled via non-positional feature
4001 visibility in tooltip).</li>
4002 <li>URL links generated for all feature links (bugfix)</li>
4003 <li>Added URL embedding instructions to features file
4005 <li>Codons containing ambiguous nucleotides translated as
4006 'X' in peptide product</li>
4007 <li>Match case switch in find dialog box works for both
4008 sequence ID and sequence string and query strings do not
4009 have to be in upper case to match case-insensitively.</li>
4010 <li>AMSA files only contain first column of
4011 multi-character column annotation labels</li>
4012 <li>Jalview Annotation File generation/parsing consistent
4013 with documentation (e.g. Stockholm annotation can be
4014 exported and re-imported)</li>
4015 <li>PDB files without embedded PDB IDs given a friendly
4017 <li>Find incrementally searches ID string matches as well
4018 as subsequence matches, and correctly reports total number
4022 <li>Better handling of exceptions during sequence
4024 <li>Dasobert generated non-positional feature URL
4025 link text excludes the start_end suffix</li>
4026 <li>DAS feature and source retrieval buttons disabled
4027 when fetch or registry operations in progress.</li>
4028 <li>PDB files retrieved from URLs are cached properly</li>
4029 <li>Sequence description lines properly shared via
4031 <li>Sequence fetcher fetches multiple records for all
4033 <li>Ensured that command line das feature retrieval
4034 completes before alignment figures are generated.</li>
4035 <li>Reduced time taken when opening file browser for
4037 <li>isAligned check prior to calculating tree, PCA or
4038 submitting an MSA to JNet now excludes hidden sequences.</li>
4039 <li>User defined group colours properly recovered
4040 from Jalview projects.</li>
4049 <div align="center">
4050 <strong>2.4.0.b2</strong><br> 28/10/2009
4055 <li>Experimental support for google analytics usage
4057 <li>Jalview privacy settings (user preferences and docs).</li>
4062 <li>Race condition in applet preventing startup in
4064 <li>Exception when feature created from selection beyond
4065 length of sequence.</li>
4066 <li>Allow synthetic PDB files to be imported gracefully</li>
4067 <li>Sequence associated annotation rows associate with
4068 all sequences with a given id</li>
4069 <li>Find function matches case-insensitively for sequence
4070 ID string searches</li>
4071 <li>Non-standard characters do not cause pairwise
4072 alignment to fail with exception</li>
4073 </ul> <em>Application Issues</em>
4075 <li>Sequences are now validated against EMBL database</li>
4076 <li>Sequence fetcher fetches multiple records for all
4078 </ul> <em>InstallAnywhere Issues</em>
4080 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4081 issue with installAnywhere mechanism)</li>
4082 <li>Command line launching of JARs from InstallAnywhere
4083 version (java class versioning error fixed)</li>
4090 <div align="center">
4091 <strong>2.4</strong><br> 27/8/2008
4094 <td><em>User Interface</em>
4096 <li>Linked highlighting of codon and amino acid from
4097 translation and protein products</li>
4098 <li>Linked highlighting of structure associated with
4099 residue mapping to codon position</li>
4100 <li>Sequence Fetcher provides example accession numbers
4101 and 'clear' button</li>
4102 <li>MemoryMonitor added as an option under Desktop's
4104 <li>Extract score function to parse whitespace separated
4105 numeric data in description line</li>
4106 <li>Column labels in alignment annotation can be centred.</li>
4107 <li>Tooltip for sequence associated annotation give name
4109 </ul> <em>Web Services and URL fetching</em>
4111 <li>JPred3 web service</li>
4112 <li>Prototype sequence search client (no public services
4114 <li>Fetch either seed alignment or full alignment from
4116 <li>URL Links created for matching database cross
4117 references as well as sequence ID</li>
4118 <li>URL Links can be created using regular-expressions</li>
4119 </ul> <em>Sequence Database Connectivity</em>
4121 <li>Retrieval of cross-referenced sequences from other
4123 <li>Generalised database reference retrieval and
4124 validation to all fetchable databases</li>
4125 <li>Fetch sequences from DAS sources supporting the
4126 sequence command</li>
4127 </ul> <em>Import and Export</em>
4128 <li>export annotation rows as CSV for spreadsheet import</li>
4129 <li>Jalview projects record alignment dataset associations,
4130 EMBL products, and cDNA sequence mappings</li>
4131 <li>Sequence Group colour can be specified in Annotation
4133 <li>Ad-hoc colouring of group in Annotation File using RGB
4134 triplet as name of colourscheme</li>
4135 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4137 <li>treenode binding for VAMSAS tree exchange</li>
4138 <li>local editing and update of sequences in VAMSAS
4139 alignments (experimental)</li>
4140 <li>Create new or select existing session to join</li>
4141 <li>load and save of vamsas documents</li>
4142 </ul> <em>Application command line</em>
4144 <li>-tree parameter to open trees (introduced for passing
4146 <li>-fetchfrom command line argument to specify nicknames
4147 of DAS servers to query for alignment features</li>
4148 <li>-dasserver command line argument to add new servers
4149 that are also automatically queried for features</li>
4150 <li>-groovy command line argument executes a given groovy
4151 script after all input data has been loaded and parsed</li>
4152 </ul> <em>Applet-Application data exchange</em>
4154 <li>Trees passed as applet parameters can be passed to
4155 application (when using "View in full
4156 application")</li>
4157 </ul> <em>Applet Parameters</em>
4159 <li>feature group display control parameter</li>
4160 <li>debug parameter</li>
4161 <li>showbutton parameter</li>
4162 </ul> <em>Applet API methods</em>
4164 <li>newView public method</li>
4165 <li>Window (current view) specific get/set public methods</li>
4166 <li>Feature display control methods</li>
4167 <li>get list of currently selected sequences</li>
4168 </ul> <em>New Jalview distribution features</em>
4170 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4171 <li>RELEASE file gives build properties for the latest
4172 Jalview release.</li>
4173 <li>Java 1.1 Applet build made easier and donotobfuscate
4174 property controls execution of obfuscator</li>
4175 <li>Build target for generating source distribution</li>
4176 <li>Debug flag for javacc</li>
4177 <li>.jalview_properties file is documented (slightly) in
4178 jalview.bin.Cache</li>
4179 <li>Continuous Build Integration for stable and
4180 development version of Application, Applet and source
4185 <li>selected region output includes visible annotations
4186 (for certain formats)</li>
4187 <li>edit label/displaychar contains existing label/char
4189 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4190 <li>shorter peptide product names from EMBL records</li>
4191 <li>Newick string generator makes compact representations</li>
4192 <li>bootstrap values parsed correctly for tree files with
4194 <li>pathological filechooser bug avoided by not allowing
4195 filenames containing a ':'</li>
4196 <li>Fixed exception when parsing GFF files containing
4197 global sequence features</li>
4198 <li>Alignment datasets are finalized only when number of
4199 references from alignment sequences goes to zero</li>
4200 <li>Close of tree branch colour box without colour
4201 selection causes cascading exceptions</li>
4202 <li>occasional negative imgwidth exceptions</li>
4203 <li>better reporting of non-fatal warnings to user when
4204 file parsing fails.</li>
4205 <li>Save works when Jalview project is default format</li>
4206 <li>Save as dialog opened if current alignment format is
4207 not a valid output format</li>
4208 <li>UniProt canonical names introduced for both das and
4210 <li>Histidine should be midblue (not pink!) in Zappo</li>
4211 <li>error messages passed up and output when data read
4213 <li>edit undo recovers previous dataset sequence when
4214 sequence is edited</li>
4215 <li>allow PDB files without pdb ID HEADER lines (like
4216 those generated by MODELLER) to be read in properly</li>
4217 <li>allow reading of JPred concise files as a normal
4219 <li>Stockholm annotation parsing and alignment properties
4220 import fixed for PFAM records</li>
4221 <li>Structure view windows have correct name in Desktop
4223 <li>annotation consisting of sequence associated scores
4224 can be read and written correctly to annotation file</li>
4225 <li>Aligned cDNA translation to aligned peptide works
4227 <li>Fixed display of hidden sequence markers and
4228 non-italic font for representatives in Applet</li>
4229 <li>Applet Menus are always embedded in applet window on
4231 <li>Newly shown features appear at top of stack (in
4233 <li>Annotations added via parameter not drawn properly
4234 due to null pointer exceptions</li>
4235 <li>Secondary structure lines are drawn starting from
4236 first column of alignment</li>
4237 <li>UniProt XML import updated for new schema release in
4239 <li>Sequence feature to sequence ID match for Features
4240 file is case-insensitive</li>
4241 <li>Sequence features read from Features file appended to
4242 all sequences with matching IDs</li>
4243 <li>PDB structure coloured correctly for associated views
4244 containing a sub-sequence</li>
4245 <li>PDB files can be retrieved by applet from Jar files</li>
4246 <li>feature and annotation file applet parameters
4247 referring to different directories are retrieved correctly</li>
4248 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4249 <li>Fixed application hang whilst waiting for
4250 splash-screen version check to complete</li>
4251 <li>Applet properly URLencodes input parameter values
4252 when passing them to the launchApp service</li>
4253 <li>display name and local features preserved in results
4254 retrieved from web service</li>
4255 <li>Visual delay indication for sequence retrieval and
4256 sequence fetcher initialisation</li>
4257 <li>updated Application to use DAS 1.53e version of
4258 dasobert DAS client</li>
4259 <li>Re-instated Full AMSA support and .amsa file
4261 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4269 <div align="center">
4270 <strong>2.3</strong><br> 9/5/07
4275 <li>Jmol 11.0.2 integration</li>
4276 <li>PDB views stored in Jalview XML files</li>
4277 <li>Slide sequences</li>
4278 <li>Edit sequence in place</li>
4279 <li>EMBL CDS features</li>
4280 <li>DAS Feature mapping</li>
4281 <li>Feature ordering</li>
4282 <li>Alignment Properties</li>
4283 <li>Annotation Scores</li>
4284 <li>Sort by scores</li>
4285 <li>Feature/annotation editing in applet</li>
4290 <li>Headless state operation in 2.2.1</li>
4291 <li>Incorrect and unstable DNA pairwise alignment</li>
4292 <li>Cut and paste of sequences with annotation</li>
4293 <li>Feature group display state in XML</li>
4294 <li>Feature ordering in XML</li>
4295 <li>blc file iteration selection using filename # suffix</li>
4296 <li>Stockholm alignment properties</li>
4297 <li>Stockhom alignment secondary structure annotation</li>
4298 <li>2.2.1 applet had no feature transparency</li>
4299 <li>Number pad keys can be used in cursor mode</li>
4300 <li>Structure Viewer mirror image resolved</li>
4307 <div align="center">
4308 <strong>2.2.1</strong><br> 12/2/07
4313 <li>Non standard characters can be read and displayed
4314 <li>Annotations/Features can be imported/exported to the
4316 <li>Applet allows editing of sequence/annotation/group
4317 name & description
4318 <li>Preference setting to display sequence name in
4320 <li>Annotation file format extended to allow
4321 Sequence_groups to be defined
4322 <li>Default opening of alignment overview panel can be
4323 specified in preferences
4324 <li>PDB residue numbering annotation added to associated
4330 <li>Applet crash under certain Linux OS with Java 1.6
4332 <li>Annotation file export / import bugs fixed
4333 <li>PNG / EPS image output bugs fixed
4339 <div align="center">
4340 <strong>2.2</strong><br> 27/11/06
4345 <li>Multiple views on alignment
4346 <li>Sequence feature editing
4347 <li>"Reload" alignment
4348 <li>"Save" to current filename
4349 <li>Background dependent text colour
4350 <li>Right align sequence ids
4351 <li>User-defined lower case residue colours
4354 <li>Menu item accelerator keys
4355 <li>Control-V pastes to current alignment
4356 <li>Cancel button for DAS Feature Fetching
4357 <li>PCA and PDB Viewers zoom via mouse roller
4358 <li>User-defined sub-tree colours and sub-tree selection
4360 <li>'New Window' button on the 'Output to Text box'
4365 <li>New memory efficient Undo/Redo System
4366 <li>Optimised symbol lookups and conservation/consensus
4368 <li>Region Conservation/Consensus recalculated after
4370 <li>Fixed Remove Empty Columns Bug (empty columns at end
4372 <li>Slowed DAS Feature Fetching for increased robustness.
4374 <li>Made angle brackets in ASCII feature descriptions
4376 <li>Re-instated Zoom function for PCA
4377 <li>Sequence descriptions conserved in web service
4379 <li>UniProt ID discoverer uses any word separated by
4381 <li>WsDbFetch query/result association resolved
4382 <li>Tree leaf to sequence mapping improved
4383 <li>Smooth fonts switch moved to FontChooser dialog box.
4390 <div align="center">
4391 <strong>2.1.1</strong><br> 12/9/06
4396 <li>Copy consensus sequence to clipboard</li>
4401 <li>Image output - rightmost residues are rendered if
4402 sequence id panel has been resized</li>
4403 <li>Image output - all offscreen group boundaries are
4405 <li>Annotation files with sequence references - all
4406 elements in file are relative to sequence position</li>
4407 <li>Mac Applet users can use Alt key for group editing</li>
4413 <div align="center">
4414 <strong>2.1</strong><br> 22/8/06
4419 <li>MAFFT Multiple Alignment in default Web Service list</li>
4420 <li>DAS Feature fetching</li>
4421 <li>Hide sequences and columns</li>
4422 <li>Export Annotations and Features</li>
4423 <li>GFF file reading / writing</li>
4424 <li>Associate structures with sequences from local PDB
4426 <li>Add sequences to exisiting alignment</li>
4427 <li>Recently opened files / URL lists</li>
4428 <li>Applet can launch the full application</li>
4429 <li>Applet has transparency for features (Java 1.2
4431 <li>Applet has user defined colours parameter</li>
4432 <li>Applet can load sequences from parameter
4433 "sequence<em>x</em>"
4439 <li>Redundancy Panel reinstalled in the Applet</li>
4440 <li>Monospaced font - EPS / rescaling bug fixed</li>
4441 <li>Annotation files with sequence references bug fixed</li>
4447 <div align="center">
4448 <strong>2.08.1</strong><br> 2/5/06
4453 <li>Change case of selected region from Popup menu</li>
4454 <li>Choose to match case when searching</li>
4455 <li>Middle mouse button and mouse movement can compress /
4456 expand the visible width and height of the alignment</li>
4461 <li>Annotation Panel displays complete JNet results</li>
4467 <div align="center">
4468 <strong>2.08b</strong><br> 18/4/06
4474 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4475 <li>Righthand label on wrapped alignments shows correct
4482 <div align="center">
4483 <strong>2.08</strong><br> 10/4/06
4488 <li>Editing can be locked to the selection area</li>
4489 <li>Keyboard editing</li>
4490 <li>Create sequence features from searches</li>
4491 <li>Precalculated annotations can be loaded onto
4493 <li>Features file allows grouping of features</li>
4494 <li>Annotation Colouring scheme added</li>
4495 <li>Smooth fonts off by default - Faster rendering</li>
4496 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4501 <li>Drag & Drop fixed on Linux</li>
4502 <li>Jalview Archive file faster to load/save, sequence
4503 descriptions saved.</li>
4509 <div align="center">
4510 <strong>2.07</strong><br> 12/12/05
4515 <li>PDB Structure Viewer enhanced</li>
4516 <li>Sequence Feature retrieval and display enhanced</li>
4517 <li>Choose to output sequence start-end after sequence
4518 name for file output</li>
4519 <li>Sequence Fetcher WSDBFetch@EBI</li>
4520 <li>Applet can read feature files, PDB files and can be
4521 used for HTML form input</li>
4526 <li>HTML output writes groups and features</li>
4527 <li>Group editing is Control and mouse click</li>
4528 <li>File IO bugs</li>
4534 <div align="center">
4535 <strong>2.06</strong><br> 28/9/05
4540 <li>View annotations in wrapped mode</li>
4541 <li>More options for PCA viewer</li>
4546 <li>GUI bugs resolved</li>
4547 <li>Runs with -nodisplay from command line</li>
4553 <div align="center">
4554 <strong>2.05b</strong><br> 15/9/05
4559 <li>Choose EPS export as lineart or text</li>
4560 <li>Jar files are executable</li>
4561 <li>Can read in Uracil - maps to unknown residue</li>
4566 <li>Known OutOfMemory errors give warning message</li>
4567 <li>Overview window calculated more efficiently</li>
4568 <li>Several GUI bugs resolved</li>
4574 <div align="center">
4575 <strong>2.05</strong><br> 30/8/05
4580 <li>Edit and annotate in "Wrapped" view</li>
4585 <li>Several GUI bugs resolved</li>
4591 <div align="center">
4592 <strong>2.04</strong><br> 24/8/05
4597 <li>Hold down mouse wheel & scroll to change font
4603 <li>Improved JPred client reliability</li>
4604 <li>Improved loading of Jalview files</li>
4610 <div align="center">
4611 <strong>2.03</strong><br> 18/8/05
4616 <li>Set Proxy server name and port in preferences</li>
4617 <li>Multiple URL links from sequence ids</li>
4618 <li>User Defined Colours can have a scheme name and added
4620 <li>Choose to ignore gaps in consensus calculation</li>
4621 <li>Unix users can set default web browser</li>
4622 <li>Runs without GUI for batch processing</li>
4623 <li>Dynamically generated Web Service Menus</li>
4628 <li>InstallAnywhere download for Sparc Solaris</li>
4634 <div align="center">
4635 <strong>2.02</strong><br> 18/7/05
4641 <li>Copy & Paste order of sequences maintains
4642 alignment order.</li>
4648 <div align="center">
4649 <strong>2.01</strong><br> 12/7/05
4654 <li>Use delete key for deleting selection.</li>
4655 <li>Use Mouse wheel to scroll sequences.</li>
4656 <li>Help file updated to describe how to add alignment
4658 <li>Version and build date written to build properties
4660 <li>InstallAnywhere installation will check for updates
4661 at launch of Jalview.</li>
4666 <li>Delete gaps bug fixed.</li>
4667 <li>FileChooser sorts columns.</li>
4668 <li>Can remove groups one by one.</li>
4669 <li>Filechooser icons installed.</li>
4670 <li>Finder ignores return character when searching.
4671 Return key will initiate a search.<br>
4678 <div align="center">
4679 <strong>2.0</strong><br> 20/6/05
4684 <li>New codebase</li>