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>
60 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
61 <em>04/07/2019</em></strong>
63 <td align="left" valign="top">
66 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
67 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
68 source project) rather than InstallAnywhere
71 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
72 settings, receive over the air updates and launch specific
73 versions via (<a href="https://github.com/threerings/getdown">Three
77 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
78 formats supported by jalview (including .jvp project files)
81 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
82 arguments and switch between different getdown channels
85 <!-- JAL-3141 -->Backup files created when saving Jalview project
90 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
91 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
93 <!-- JAL-2620 -->Alternative genetic code tables for
94 'Translate as cDNA'</li>
96 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
97 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
100 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
101 implementation that allows updates) used for Sequence Feature collections</li>
104 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
105 features can be filtered and shaded according to any
106 associated attributes (e.g. variant attributes from VCF
107 file, or key-value pairs imported from column 9 of GFF
111 <!-- JAL-2879 -->Feature Attributes and shading schemes
112 stored and restored from Jalview Projects
115 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
116 recognise variant features
119 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
120 sequences (also coloured red by default)
123 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
127 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
128 algorithm (Z-sort/transparency and filter aware)
131 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
137 <!-- JAL-3205 -->Symmetric score matrices for faster
138 tree and PCA calculations
140 <li><strong>Principal Components Analysis Viewer</strong>
143 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
144 and Viewer state saved in Jalview Project
146 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
149 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
153 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
158 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
160 <li><strong>Speed and Efficiency</strong>
163 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
164 multiple groups when working with large alignments
167 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
171 <li><strong>User Interface</strong>
174 <!-- JAL-2933 -->Finder panel remembers last position in each
178 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
179 what is shown)<br />Only visible region of alignment is shown by
180 default (can be changed in user preferences)
183 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
184 to the Overwrite Dialog
187 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
191 <!-- JAL-1244 -->Status bar shows bounds when dragging a
192 selection region, and gap count when inserting or deleting gaps
195 <!-- JAL-3132 -->Status bar updates over sequence and annotation
199 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
203 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
207 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
210 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
214 <!-- JAL-3181 -->Consistent ordering of links in sequence id
218 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
220 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
224 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
225 <li><strong>Java 11 Support (not yet on general release)</strong>
228 <!-- -->OSX GUI integrations for App menu's 'About' entry and
233 <em>Deprecations</em>
236 <!-- JAL-3035 -->DAS sequence retrieval and annotation
237 capabilities removed from the Jalview Desktop
240 <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
241 unmarshalling has been replaced by JAXB for Jalview projects
242 and XML based data retrieval clients</li>
243 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
244 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
245 </ul> <em>Documentation</em>
248 <!-- JAL-3003 -->Added remarks about transparent rendering effects
249 not supported in EPS figure export
251 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
252 </ul> <em>Development and Release Processes</em>
255 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
257 <li><!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
259 <!-- JAL-3225 -->Eclipse project configuration managed with
263 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 --> Atlassian
264 Bamboo continuous integration for unattended Test Suite
268 <!-- JAL-2864 -->Memory test suite to detect leaks in common
272 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
276 <!-- JAL-3248 -->Developer documentation migrated to
277 markdown (with HTML rendering)
280 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
283 <!-- JAL-3289 -->New URLs for publishing development
290 <td align="left" valign="top">
293 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
296 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
297 superposition in Jmol fail on Windows
300 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
301 structures for sequences with lots of PDB structures
304 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
308 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
309 project involving multiple views
312 <!-- JAL-3164 -->Overview for complementary view in a linked
313 CDS/Protein alignment is not updated when Hide Columns by
314 Annotation dialog hides columns
317 <!-- JAL-3158 -->Selection highlighting in the complement of a
318 CDS/Protein alignment stops working after making a selection in
319 one view, then making another selection in the other view
322 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
326 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
327 Settings and Jalview Preferences panels
330 <!-- JAL-2865 -->Jalview hangs when closing windows or the
331 overview updates with large alignments
334 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
335 region if columns were selected by dragging right-to-left and the
336 mouse moved to the left of the first column
339 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
340 hidden column marker via scale popup menu
343 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
344 doesn't tell users the invalid URL
347 <!-- JAL-2816 -->Tooltips displayed for features filtered by
351 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
352 show cross references or Fetch Database References are shown in
356 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
357 peptide sequence (computed variant shown as p.Res.null)
360 <!-- JAL-2060 -->'Graduated colour' option not offered for
361 manually created features (where if feature score is Float.NaN)
364 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
365 when columns are hidden
368 <!-- JAL-3082 -->Regular expression error for '(' in Select
369 Columns by Annotation description
372 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
373 out of Scale or Annotation Panel
376 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
380 <!-- JAL-3074 -->Left/right drag in annotation can scroll
384 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
388 <!-- JAL-3002 -->Column display is out by one after Page Down,
389 Page Up in wrapped mode
392 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
395 <!-- JAL-2932 -->Finder searches in minimised alignments
398 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
399 on opening an alignment
402 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
406 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
407 different groups in the alignment are selected
410 <!-- JAL-2717 -->Internationalised colour scheme names not shown
414 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
418 <!-- JAL-3125 -->Value input for graduated feature colour
419 threshold gets 'unrounded'
422 <!-- JAL-2982 -->PCA image export doesn't respect background
426 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
429 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
432 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
436 <!-- JAL-2964 -->Associate Tree with All Views not restored from
440 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
441 shown in complementary view
444 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
445 without normalisation
448 <!-- JAL-3021 -->Sequence Details report should open positioned at top
452 <!-- JAL-914 -->Help page can be opened twice
455 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
457 </ul> <em>Editing</em>
460 <!-- JAL-2822 -->Start and End should be updated when sequence
461 data at beginning or end of alignment added/removed via 'Edit'
465 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
466 relocate sequence features correctly when start of sequence is
467 removed (Known defect since 2.10)
470 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
471 dialog corrupts dataset sequence
474 <!-- JAL-868 -->Structure colours not updated when associated tree
475 repartitions the alignment view (Regression in 2.10.5)
477 </ul> <em>Datamodel</em>
480 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
481 sequence's End is greater than its length
483 </ul> <em>Bugs fixed for Java 11 Support (not yet on
484 general release)</em>
487 <!-- JAL-3288 -->Menus work properly in split-screen
489 </ul> <em>New Known Defects</em>
491 <li><!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
494 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
495 regions of protein alignment.
498 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
499 is restored from a Jalview 2.11 project
502 <!-- JAL-3213 -->Alignment panel height can be too small after
506 <!-- JAL-3240 -->Display is incorrect after removing gapped
507 columns within hidden columns
510 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
511 window after dragging left to select columns to left of visible
515 <!-- JAL-2876 -->Features coloured according to their description
516 string and thresholded by score in earlier versions of Jalview are
517 not shown as thresholded features in 2.11. To workaround please
518 create a Score filter instead.
520 <li><!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
522 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
525 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
526 alignments with multiple views can close views unexpectedly
529 <em>Java 11 Specific defects</em>
532 <!-- JAL-3235 -->Jalview Properties file is not sorted
533 alphabetically when saved
539 <td width="60" nowrap>
541 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
544 <td><div align="left">
548 <!-- JAL-3101 -->Default memory for Jalview webstart and
549 InstallAnywhere increased to 1G.
552 <!-- JAL-247 -->Hidden sequence markers and representative
553 sequence bolding included when exporting alignment as EPS,
554 SVG, PNG or HTML. <em>Display is configured via the
555 Format menu, or for command-line use via a jalview
556 properties file.</em>
559 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
560 API and sequence data now imported as JSON.
563 <!-- JAL-3065 -->Change in recommended way of starting
564 Jalview via a Java command line: add jars in lib directory
565 to CLASSPATH, rather than via the deprecated java.ext.dirs
572 <!-- JAL-3047 -->Support added to execute test suite
573 instrumented with <a href="http://openclover.org/">Open
578 <td><div align="left">
582 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
583 row shown in Feredoxin Structure alignment view of example
587 <!-- JAL-2854 -->Annotation obscures sequences if lots of
588 annotation displayed.
591 <!-- JAL-3107 -->Group conservation/consensus not shown
592 for newly created group when 'Apply to all groups'
596 <!-- JAL-3087 -->Corrupted display when switching to
597 wrapped mode when sequence panel's vertical scrollbar is
601 <!-- JAL-3003 -->Alignment is black in exported EPS file
602 when sequences are selected in exported view.</em>
605 <!-- JAL-3059 -->Groups with different coloured borders
606 aren't rendered with correct colour.
609 <!-- JAL-3092 -->Jalview could hang when importing certain
610 types of knotted RNA secondary structure.
613 <!-- JAL-3095 -->Sequence highlight and selection in
614 trimmed VARNA 2D structure is incorrect for sequences that
618 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
619 annotation when columns are inserted into an alignment,
620 and when exporting as Stockholm flatfile.
623 <!-- JAL-3053 -->Jalview annotation rows containing upper
624 and lower-case 'E' and 'H' do not automatically get
625 treated as RNA secondary structure.
628 <!-- JAL-3106 -->.jvp should be used as default extension
629 (not .jar) when saving a jalview project file.
632 <!-- JAL-3105 -->Mac Users: closing a window correctly
633 transfers focus to previous window on OSX
636 <em>Java 10 Issues Resolved</em>
639 <!-- JAL-2988 -->OSX - Can't save new files via the File
640 or export menus by typing in a name into the Save dialog
644 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
645 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
646 'look and feel' which has improved compatibility with the
647 latest version of OSX.
654 <td width="60" nowrap>
656 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
657 <em>7/06/2018</em></strong>
660 <td><div align="left">
664 <!-- JAL-2920 -->Use HGVS nomenclature for variant
665 annotation retrieved from Uniprot
668 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
669 onto the Jalview Desktop
673 <td><div align="left">
677 <!-- JAL-3017 -->Cannot import features with multiple
678 variant elements (blocks import of some Uniprot records)
681 <!-- JAL-2997 -->Clustal files with sequence positions in
682 right-hand column parsed correctly
685 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
686 not alignment area in exported graphic
689 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
690 window has input focus
693 <!-- JAL-2992 -->Annotation panel set too high when
694 annotation added to view (Windows)
697 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
698 network connectivity is poor
701 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
702 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
703 the currently open URL and links from a page viewed in
704 Firefox or Chrome on Windows is now fully supported. If
705 you are using Edge, only links in the page can be
706 dragged, and with Internet Explorer, only the currently
707 open URL in the browser can be dropped onto Jalview.</em>
710 <em>New Known Defects</em>
712 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
717 <td width="60" nowrap>
719 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
722 <td><div align="left">
726 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
727 for disabling automatic superposition of multiple
728 structures and open structures in existing views
731 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
732 ID and annotation area margins can be click-dragged to
736 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
740 <!-- JAL-2759 -->Improved performance for large alignments
741 and lots of hidden columns
744 <!-- JAL-2593 -->Improved performance when rendering lots
745 of features (particularly when transparency is disabled)
748 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
749 exchange of Jalview features and Chimera attributes made
755 <td><div align="left">
758 <!-- JAL-2899 -->Structure and Overview aren't updated
759 when Colour By Annotation threshold slider is adjusted
762 <!-- JAL-2778 -->Slow redraw when Overview panel shown
763 overlapping alignment panel
766 <!-- JAL-2929 -->Overview doesn't show end of unpadded
770 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
771 improved: CDS not handled correctly if transcript has no
775 <!-- JAL-2321 -->Secondary structure and temperature
776 factor annotation not added to sequence when local PDB
777 file associated with it by drag'n'drop or structure
781 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
782 dialog doesn't import PDB files dropped on an alignment
785 <!-- JAL-2666 -->Linked scrolling via protein horizontal
786 scroll bar doesn't work for some CDS/Protein views
789 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
790 Java 1.8u153 onwards and Java 1.9u4+.
793 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
794 columns in annotation row
797 <!-- JAL-2913 -->Preferences panel's ID Width control is not
798 honored in batch mode
801 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
802 for structures added to existing Jmol view
805 <!-- JAL-2223 -->'View Mappings' includes duplicate
806 entries after importing project with multiple views
809 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
810 protein sequences via SIFTS from associated PDB entries
811 with negative residue numbers or missing residues fails
814 <!-- JAL-2952 -->Exception when shading sequence with negative
815 Temperature Factor values from annotated PDB files (e.g.
816 as generated by CONSURF)
819 <!-- JAL-2920 -->Uniprot 'sequence variant' features
820 tooltip doesn't include a text description of mutation
823 <!-- JAL-2922 -->Invert displayed features very slow when
824 structure and/or overview windows are also shown
827 <!-- JAL-2954 -->Selecting columns from highlighted regions
828 very slow for alignments with large numbers of sequences
831 <!-- JAL-2925 -->Copy Consensus fails for group consensus
832 with 'StringIndexOutOfBounds'
835 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
836 platforms running Java 10
839 <!-- JAL-2960 -->Adding a structure to existing structure
840 view appears to do nothing because the view is hidden behind the alignment view
846 <!-- JAL-2926 -->Copy consensus sequence option in applet
847 should copy the group consensus when popup is opened on it
853 <!-- JAL-2913 -->Fixed ID width preference is not respected
856 <em>New Known Defects</em>
859 <!-- JAL-2973 --> Exceptions occasionally raised when
860 editing a large alignment and overview is displayed
863 <!-- JAL-2974 -->'Overview updating' progress bar is shown
864 repeatedly after a series of edits even when the overview
865 is no longer reflecting updates
868 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
869 structures for protein subsequence (if 'Trim Retrieved
870 Sequences' enabled) or Ensembl isoforms (Workaround in
871 2.10.4 is to fail back to N&W mapping)
874 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
875 option gives blank output
882 <td width="60" nowrap>
884 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
887 <td><div align="left">
888 <ul><li>Updated Certum Codesigning Certificate
889 (Valid till 30th November 2018)</li></ul></div></td>
890 <td><div align="left">
893 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
894 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
895 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
896 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
897 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
898 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
899 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
905 <td width="60" nowrap>
907 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
910 <td><div align="left">
914 <!-- JAL-2446 -->Faster and more efficient management and
915 rendering of sequence features
918 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
919 429 rate limit request hander
922 <!-- JAL-2773 -->Structure views don't get updated unless
923 their colours have changed
926 <!-- JAL-2495 -->All linked sequences are highlighted for
927 a structure mousover (Jmol) or selection (Chimera)
930 <!-- JAL-2790 -->'Cancel' button in progress bar for
931 JABAWS AACon, RNAAliFold and Disorder prediction jobs
934 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
935 view from Ensembl locus cross-references
938 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
942 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
943 feature can be disabled
946 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
947 PDB easier retrieval of sequences for lists of IDs
950 <!-- JAL-2758 -->Short names for sequences retrieved from
956 <li>Groovy interpreter updated to 2.4.12</li>
957 <li>Example groovy script for generating a matrix of
958 percent identity scores for current alignment.</li>
960 <em>Testing and Deployment</em>
963 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
967 <td><div align="left">
971 <!-- JAL-2643 -->Pressing tab after updating the colour
972 threshold text field doesn't trigger an update to the
976 <!-- JAL-2682 -->Race condition when parsing sequence ID
980 <!-- JAL-2608 -->Overview windows are also closed when
981 alignment window is closed
984 <!-- JAL-2548 -->Export of features doesn't always respect
988 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
989 takes a long time in Cursor mode
995 <!-- JAL-2777 -->Structures with whitespace chainCode
996 cannot be viewed in Chimera
999 <!-- JAL-2728 -->Protein annotation panel too high in
1003 <!-- JAL-2757 -->Can't edit the query after the server
1004 error warning icon is shown in Uniprot and PDB Free Text
1008 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1011 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1014 <!-- JAL-2739 -->Hidden column marker in last column not
1015 rendered when switching back from Wrapped to normal view
1018 <!-- JAL-2768 -->Annotation display corrupted when
1019 scrolling right in unwapped alignment view
1022 <!-- JAL-2542 -->Existing features on subsequence
1023 incorrectly relocated when full sequence retrieved from
1027 <!-- JAL-2733 -->Last reported memory still shown when
1028 Desktop->Show Memory is unticked (OSX only)
1031 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1032 features of same type and group to be selected for
1036 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1037 alignments when hidden columns are present
1040 <!-- JAL-2392 -->Jalview freezes when loading and
1041 displaying several structures
1044 <!-- JAL-2732 -->Black outlines left after resizing or
1048 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1049 within the Jalview desktop on OSX
1052 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1053 when in wrapped alignment mode
1056 <!-- JAL-2636 -->Scale mark not shown when close to right
1057 hand end of alignment
1060 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1061 each selected sequence do not have correct start/end
1065 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1066 after canceling the Alignment Window's Font dialog
1069 <!-- JAL-2036 -->Show cross-references not enabled after
1070 restoring project until a new view is created
1073 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1074 URL links appears when only default EMBL-EBI link is
1075 configured (since 2.10.2b2)
1078 <!-- JAL-2775 -->Overview redraws whole window when box
1079 position is adjusted
1082 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1083 in a multi-chain structure when viewing alignment
1084 involving more than one chain (since 2.10)
1087 <!-- JAL-2811 -->Double residue highlights in cursor mode
1088 if new selection moves alignment window
1091 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1092 arrow key in cursor mode to pass hidden column marker
1095 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1096 that produces correctly annotated transcripts and products
1099 <!-- JAL-2776 -->Toggling a feature group after first time
1100 doesn't update associated structure view
1103 <em>Applet</em><br />
1106 <!-- JAL-2687 -->Concurrent modification exception when
1107 closing alignment panel
1110 <em>BioJSON</em><br />
1113 <!-- JAL-2546 -->BioJSON export does not preserve
1114 non-positional features
1117 <em>New Known Issues</em>
1120 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1121 sequence features correctly (for many previous versions of
1125 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1126 using cursor in wrapped panel other than top
1129 <!-- JAL-2791 -->Select columns containing feature ignores
1130 graduated colour threshold
1133 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1134 always preserve numbering and sequence features
1137 <em>Known Java 9 Issues</em>
1140 <!-- JAL-2902 -->Groovy Console very slow to open and is
1141 not responsive when entering characters (Webstart, Java
1148 <td width="60" nowrap>
1149 <div align="center">
1150 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1151 <em>2/10/2017</em></strong>
1154 <td><div align="left">
1155 <em>New features in Jalview Desktop</em>
1158 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1160 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1164 <td><div align="left">
1168 <td width="60" nowrap>
1169 <div align="center">
1170 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1171 <em>7/9/2017</em></strong>
1174 <td><div align="left">
1178 <!-- JAL-2588 -->Show gaps in overview window by colouring
1179 in grey (sequences used to be coloured grey, and gaps were
1183 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1187 <!-- JAL-2587 -->Overview updates immediately on increase
1188 in size and progress bar shown as higher resolution
1189 overview is recalculated
1194 <td><div align="left">
1198 <!-- JAL-2664 -->Overview window redraws every hidden
1199 column region row by row
1202 <!-- JAL-2681 -->duplicate protein sequences shown after
1203 retrieving Ensembl crossrefs for sequences from Uniprot
1206 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1207 format setting is unticked
1210 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1211 if group has show boxes format setting unticked
1214 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1215 autoscrolling whilst dragging current selection group to
1216 include sequences and columns not currently displayed
1219 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1220 assemblies are imported via CIF file
1223 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1224 displayed when threshold or conservation colouring is also
1228 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1232 <!-- JAL-2673 -->Jalview continues to scroll after
1233 dragging a selected region off the visible region of the
1237 <!-- JAL-2724 -->Cannot apply annotation based
1238 colourscheme to all groups in a view
1241 <!-- JAL-2511 -->IDs don't line up with sequences
1242 initially after font size change using the Font chooser or
1249 <td width="60" nowrap>
1250 <div align="center">
1251 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1254 <td><div align="left">
1255 <em>Calculations</em>
1259 <!-- JAL-1933 -->Occupancy annotation row shows number of
1260 ungapped positions in each column of the alignment.
1263 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1264 a calculation dialog box
1267 <!-- JAL-2379 -->Revised implementation of PCA for speed
1268 and memory efficiency (~30x faster)
1271 <!-- JAL-2403 -->Revised implementation of sequence
1272 similarity scores as used by Tree, PCA, Shading Consensus
1273 and other calculations
1276 <!-- JAL-2416 -->Score matrices are stored as resource
1277 files within the Jalview codebase
1280 <!-- JAL-2500 -->Trees computed on Sequence Feature
1281 Similarity may have different topology due to increased
1288 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1289 model for alignments and groups
1292 <!-- JAL-384 -->Custom shading schemes created via groovy
1299 <!-- JAL-2526 -->Efficiency improvements for interacting
1300 with alignment and overview windows
1303 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1307 <!-- JAL-2388 -->Hidden columns and sequences can be
1311 <!-- JAL-2611 -->Click-drag in visible area allows fine
1312 adjustment of visible position
1316 <em>Data import/export</em>
1319 <!-- JAL-2535 -->Posterior probability annotation from
1320 Stockholm files imported as sequence associated annotation
1323 <!-- JAL-2507 -->More robust per-sequence positional
1324 annotation input/output via stockholm flatfile
1327 <!-- JAL-2533 -->Sequence names don't include file
1328 extension when importing structure files without embedded
1329 names or PDB accessions
1332 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1333 format sequence substitution matrices
1336 <em>User Interface</em>
1339 <!-- JAL-2447 --> Experimental Features Checkbox in
1340 Desktop's Tools menu to hide or show untested features in
1344 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1345 via Overview or sequence motif search operations
1348 <!-- JAL-2547 -->Amend sequence features dialog box can be
1349 opened by double clicking gaps within sequence feature
1353 <!-- JAL-1476 -->Status bar message shown when not enough
1354 aligned positions were available to create a 3D structure
1358 <em>3D Structure</em>
1361 <!-- JAL-2430 -->Hidden regions in alignment views are not
1362 coloured in linked structure views
1365 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1366 file-based command exchange
1369 <!-- JAL-2375 -->Structure chooser automatically shows
1370 Cached Structures rather than querying the PDBe if
1371 structures are already available for sequences
1374 <!-- JAL-2520 -->Structures imported via URL are cached in
1375 the Jalview project rather than downloaded again when the
1376 project is reopened.
1379 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1380 to transfer Chimera's structure attributes as Jalview
1381 features, and vice-versa (<strong>Experimental
1385 <em>Web Services</em>
1388 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1391 <!-- JAL-2335 -->Filter non-standard amino acids and
1392 nucleotides when submitting to AACon and other MSA
1396 <!-- JAL-2316, -->URLs for viewing database
1397 cross-references provided by identifiers.org and the
1398 EMBL-EBI's MIRIAM DB
1405 <!-- JAL-2344 -->FileFormatI interface for describing and
1406 identifying file formats (instead of String constants)
1409 <!-- JAL-2228 -->FeatureCounter script refactored for
1410 efficiency when counting all displayed features (not
1411 backwards compatible with 2.10.1)
1414 <em>Example files</em>
1417 <!-- JAL-2631 -->Graduated feature colour style example
1418 included in the example feature file
1421 <em>Documentation</em>
1424 <!-- JAL-2339 -->Release notes reformatted for readability
1425 with the built-in Java help viewer
1428 <!-- JAL-1644 -->Find documentation updated with 'search
1429 sequence description' option
1435 <!-- JAL-2485, -->External service integration tests for
1436 Uniprot REST Free Text Search Client
1439 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1442 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1447 <td><div align="left">
1448 <em>Calculations</em>
1451 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1452 matrix - C->R should be '-3'<br />Old matrix restored
1453 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1455 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1456 Jalview's treatment of gaps in PCA and substitution matrix
1457 based Tree calculations.<br /> <br />In earlier versions
1458 of Jalview, gaps matching gaps were penalised, and gaps
1459 matching non-gaps penalised even more. In the PCA
1460 calculation, gaps were actually treated as non-gaps - so
1461 different costs were applied, which meant Jalview's PCAs
1462 were different to those produced by SeqSpace.<br />Jalview
1463 now treats gaps in the same way as SeqSpace (ie it scores
1464 them as 0). <br /> <br />Enter the following in the
1465 Groovy console to restore pre-2.10.2 behaviour:<br />
1466 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1467 // for 2.10.1 mode <br />
1468 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1469 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1470 these settings will affect all subsequent tree and PCA
1471 calculations (not recommended)</em></li>
1473 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1474 scaling of branch lengths for trees computed using
1475 Sequence Feature Similarity.
1478 <!-- JAL-2377 -->PCA calculation could hang when
1479 generating output report when working with highly
1480 redundant alignments
1483 <!-- JAL-2544 --> Sort by features includes features to
1484 right of selected region when gaps present on right-hand
1488 <em>User Interface</em>
1491 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1492 doesn't reselect a specific sequence's associated
1493 annotation after it was used for colouring a view
1496 <!-- JAL-2419 -->Current selection lost if popup menu
1497 opened on a region of alignment without groups
1500 <!-- JAL-2374 -->Popup menu not always shown for regions
1501 of an alignment with overlapping groups
1504 <!-- JAL-2310 -->Finder double counts if both a sequence's
1505 name and description match
1508 <!-- JAL-2370 -->Hiding column selection containing two
1509 hidden regions results in incorrect hidden regions
1512 <!-- JAL-2386 -->'Apply to all groups' setting when
1513 changing colour does not apply Conservation slider value
1517 <!-- JAL-2373 -->Percentage identity and conservation menu
1518 items do not show a tick or allow shading to be disabled
1521 <!-- JAL-2385 -->Conservation shading or PID threshold
1522 lost when base colourscheme changed if slider not visible
1525 <!-- JAL-2547 -->Sequence features shown in tooltip for
1526 gaps before start of features
1529 <!-- JAL-2623 -->Graduated feature colour threshold not
1530 restored to UI when feature colour is edited
1533 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1534 a time when scrolling vertically in wrapped mode.
1537 <!-- JAL-2630 -->Structure and alignment overview update
1538 as graduate feature colour settings are modified via the
1542 <!-- JAL-2034 -->Overview window doesn't always update
1543 when a group defined on the alignment is resized
1546 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1547 wrapped view result in positional status updates
1551 <!-- JAL-2563 -->Status bar doesn't show position for
1552 ambiguous amino acid and nucleotide symbols
1555 <!-- JAL-2602 -->Copy consensus sequence failed if
1556 alignment included gapped columns
1559 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1560 widgets don't permanently disappear
1563 <!-- JAL-2503 -->Cannot select or filter quantitative
1564 annotation that are shown only as column labels (e.g.
1565 T-Coffee column reliability scores)
1568 <!-- JAL-2594 -->Exception thrown if trying to create a
1569 sequence feature on gaps only
1572 <!-- JAL-2504 -->Features created with 'New feature'
1573 button from a Find inherit previously defined feature type
1574 rather than the Find query string
1577 <!-- JAL-2423 -->incorrect title in output window when
1578 exporting tree calculated in Jalview
1581 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1582 and then revealing them reorders sequences on the
1586 <!-- JAL-964 -->Group panel in sequence feature settings
1587 doesn't update to reflect available set of groups after
1588 interactively adding or modifying features
1591 <!-- JAL-2225 -->Sequence Database chooser unusable on
1595 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1596 only excluded gaps in current sequence and ignored
1603 <!-- JAL-2421 -->Overview window visible region moves
1604 erratically when hidden rows or columns are present
1607 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1608 Structure Viewer's colour menu don't correspond to
1612 <!-- JAL-2405 -->Protein specific colours only offered in
1613 colour and group colour menu for protein alignments
1616 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1617 reflect currently selected view or group's shading
1621 <!-- JAL-2624 -->Feature colour thresholds not respected
1622 when rendered on overview and structures when opacity at
1626 <!-- JAL-2589 -->User defined gap colour not shown in
1627 overview when features overlaid on alignment
1630 <!-- JAL-2567 -->Feature settings for different views not
1631 recovered correctly from Jalview project file
1634 <!-- JAL-2256 -->Feature colours in overview when first opened
1635 (automatically via preferences) are different to the main
1639 <em>Data import/export</em>
1642 <!-- JAL-2576 -->Very large alignments take a long time to
1646 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1647 added after a sequence was imported are not written to
1651 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1652 when importing RNA secondary structure via Stockholm
1655 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1656 not shown in correct direction for simple pseudoknots
1659 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1660 with lightGray or darkGray via features file (but can
1664 <!-- JAL-2383 -->Above PID colour threshold not recovered
1665 when alignment view imported from project
1668 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1669 structure and sequences extracted from structure files
1670 imported via URL and viewed in Jmol
1673 <!-- JAL-2520 -->Structures loaded via URL are saved in
1674 Jalview Projects rather than fetched via URL again when
1675 the project is loaded and the structure viewed
1678 <em>Web Services</em>
1681 <!-- JAL-2519 -->EnsemblGenomes example failing after
1682 release of Ensembl v.88
1685 <!-- JAL-2366 -->Proxy server address and port always
1686 appear enabled in Preferences->Connections
1689 <!-- JAL-2461 -->DAS registry not found exceptions
1690 removed from console output
1693 <!-- JAL-2582 -->Cannot retrieve protein products from
1694 Ensembl by Peptide ID
1697 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1698 created from SIFTs, and spurious 'Couldn't open structure
1699 in Chimera' errors raised after April 2017 update (problem
1700 due to 'null' string rather than empty string used for
1701 residues with no corresponding PDB mapping).
1704 <em>Application UI</em>
1707 <!-- JAL-2361 -->User Defined Colours not added to Colour
1711 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1712 case' residues (button in colourscheme editor debugged and
1713 new documentation and tooltips added)
1716 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1717 doesn't restore group-specific text colour thresholds
1720 <!-- JAL-2243 -->Feature settings panel does not update as
1721 new features are added to alignment
1724 <!-- JAL-2532 -->Cancel in feature settings reverts
1725 changes to feature colours via the Amend features dialog
1728 <!-- JAL-2506 -->Null pointer exception when attempting to
1729 edit graduated feature colour via amend features dialog
1733 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1734 selection menu changes colours of alignment views
1737 <!-- JAL-2426 -->Spurious exceptions in console raised
1738 from alignment calculation workers after alignment has
1742 <!-- JAL-1608 -->Typo in selection popup menu - Create
1743 groups now 'Create Group'
1746 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1747 Create/Undefine group doesn't always work
1750 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1751 shown again after pressing 'Cancel'
1754 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1755 adjusts start position in wrap mode
1758 <!-- JAL-2563 -->Status bar doesn't show positions for
1759 ambiguous amino acids
1762 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1763 CDS/Protein view after CDS sequences added for aligned
1767 <!-- JAL-2592 -->User defined colourschemes called 'User
1768 Defined' don't appear in Colours menu
1774 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1775 score models doesn't always result in an updated PCA plot
1778 <!-- JAL-2442 -->Features not rendered as transparent on
1779 overview or linked structure view
1782 <!-- JAL-2372 -->Colour group by conservation doesn't
1786 <!-- JAL-2517 -->Hitting Cancel after applying
1787 user-defined colourscheme doesn't restore original
1794 <!-- JAL-2314 -->Unit test failure:
1795 jalview.ws.jabaws.RNAStructExportImport setup fails
1798 <!-- JAL-2307 -->Unit test failure:
1799 jalview.ws.sifts.SiftsClientTest due to compatibility
1800 problems with deep array comparison equality asserts in
1801 successive versions of TestNG
1804 <!-- JAL-2479 -->Relocated StructureChooserTest and
1805 ParameterUtilsTest Unit tests to Network suite
1808 <em>New Known Issues</em>
1811 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1812 phase after a sequence motif find operation
1815 <!-- JAL-2550 -->Importing annotation file with rows
1816 containing just upper and lower case letters are
1817 interpreted as WUSS RNA secondary structure symbols
1820 <!-- JAL-2590 -->Cannot load and display Newick trees
1821 reliably from eggnog Ortholog database
1824 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1825 containing features of type Highlight' when 'B' is pressed
1826 to mark columns containing highlighted regions.
1829 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1830 doesn't always add secondary structure annotation.
1835 <td width="60" nowrap>
1836 <div align="center">
1837 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1840 <td><div align="left">
1844 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1845 for all consensus calculations
1848 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1851 <li>Updated Jalview's Certum code signing certificate
1854 <em>Application</em>
1857 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1858 set of database cross-references, sorted alphabetically
1861 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1862 from database cross references. Users with custom links
1863 will receive a <a href="webServices/urllinks.html#warning">warning
1864 dialog</a> asking them to update their preferences.
1867 <!-- JAL-2287-->Cancel button and escape listener on
1868 dialog warning user about disconnecting Jalview from a
1872 <!-- JAL-2320-->Jalview's Chimera control window closes if
1873 the Chimera it is connected to is shut down
1876 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1877 columns menu item to mark columns containing highlighted
1878 regions (e.g. from structure selections or results of a
1882 <!-- JAL-2284-->Command line option for batch-generation
1883 of HTML pages rendering alignment data with the BioJS
1893 <!-- JAL-2286 -->Columns with more than one modal residue
1894 are not coloured or thresholded according to percent
1895 identity (first observed in Jalview 2.8.2)
1898 <!-- JAL-2301 -->Threonine incorrectly reported as not
1902 <!-- JAL-2318 -->Updates to documentation pages (above PID
1903 threshold, amino acid properties)
1906 <!-- JAL-2292 -->Lower case residues in sequences are not
1907 reported as mapped to residues in a structure file in the
1911 <!--JAL-2324 -->Identical features with non-numeric scores
1912 could be added multiple times to a sequence
1915 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1916 bond features shown as two highlighted residues rather
1917 than a range in linked structure views, and treated
1918 correctly when selecting and computing trees from features
1921 <!-- JAL-2281-->Custom URL links for database
1922 cross-references are matched to database name regardless
1927 <em>Application</em>
1930 <!-- JAL-2282-->Custom URL links for specific database
1931 names without regular expressions also offer links from
1935 <!-- JAL-2315-->Removing a single configured link in the
1936 URL links pane in Connections preferences doesn't actually
1937 update Jalview configuration
1940 <!-- JAL-2272-->CTRL-Click on a selected region to open
1941 the alignment area popup menu doesn't work on El-Capitan
1944 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1945 files with similarly named sequences if dropped onto the
1949 <!-- JAL-2312 -->Additional mappings are shown for PDB
1950 entries where more chains exist in the PDB accession than
1951 are reported in the SIFTS file
1954 <!-- JAL-2317-->Certain structures do not get mapped to
1955 the structure view when displayed with Chimera
1958 <!-- JAL-2317-->No chains shown in the Chimera view
1959 panel's View->Show Chains submenu
1962 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1963 work for wrapped alignment views
1966 <!--JAL-2197 -->Rename UI components for running JPred
1967 predictions from 'JNet' to 'JPred'
1970 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1971 corrupted when annotation panel vertical scroll is not at
1972 first annotation row
1975 <!--JAL-2332 -->Attempting to view structure for Hen
1976 lysozyme results in a PDB Client error dialog box
1979 <!-- JAL-2319 -->Structure View's mapping report switched
1980 ranges for PDB and sequence for SIFTS
1983 SIFTS 'Not_Observed' residues mapped to non-existant
1987 <!-- <em>New Known Issues</em>
1994 <td width="60" nowrap>
1995 <div align="center">
1996 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1997 <em>25/10/2016</em></strong>
2000 <td><em>Application</em>
2002 <li>3D Structure chooser opens with 'Cached structures'
2003 view if structures already loaded</li>
2004 <li>Progress bar reports models as they are loaded to
2005 structure views</li>
2011 <li>Colour by conservation always enabled and no tick
2012 shown in menu when BLOSUM or PID shading applied</li>
2013 <li>FER1_ARATH and FER2_ARATH labels were switched in
2014 example sequences/projects/trees</li>
2016 <em>Application</em>
2018 <li>Jalview projects with views of local PDB structure
2019 files saved on Windows cannot be opened on OSX</li>
2020 <li>Multiple structure views can be opened and superposed
2021 without timeout for structures with multiple models or
2022 multiple sequences in alignment</li>
2023 <li>Cannot import or associated local PDB files without a
2024 PDB ID HEADER line</li>
2025 <li>RMSD is not output in Jmol console when superposition
2027 <li>Drag and drop of URL from Browser fails for Linux and
2028 OSX versions earlier than El Capitan</li>
2029 <li>ENA client ignores invalid content from ENA server</li>
2030 <li>Exceptions are not raised in console when ENA client
2031 attempts to fetch non-existent IDs via Fetch DB Refs UI
2033 <li>Exceptions are not raised in console when a new view
2034 is created on the alignment</li>
2035 <li>OSX right-click fixed for group selections: CMD-click
2036 to insert/remove gaps in groups and CTRL-click to open group
2039 <em>Build and deployment</em>
2041 <li>URL link checker now copes with multi-line anchor
2044 <em>New Known Issues</em>
2046 <li>Drag and drop from URL links in browsers do not work
2053 <td width="60" nowrap>
2054 <div align="center">
2055 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2058 <td><em>General</em>
2061 <!-- JAL-2124 -->Updated Spanish translations.
2064 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2065 for importing structure data to Jalview. Enables mmCIF and
2069 <!-- JAL-192 --->Alignment ruler shows positions relative to
2073 <!-- JAL-2202 -->Position/residue shown in status bar when
2074 mousing over sequence associated annotation
2077 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2081 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2082 '()', canonical '[]' and invalid '{}' base pair populations
2086 <!-- JAL-2092 -->Feature settings popup menu options for
2087 showing or hiding columns containing a feature
2090 <!-- JAL-1557 -->Edit selected group by double clicking on
2091 group and sequence associated annotation labels
2094 <!-- JAL-2236 -->Sequence name added to annotation label in
2095 select/hide columns by annotation and colour by annotation
2099 </ul> <em>Application</em>
2102 <!-- JAL-2050-->Automatically hide introns when opening a
2103 gene/transcript view
2106 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2110 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2111 structure mappings with the EMBL-EBI PDBe SIFTS database
2114 <!-- JAL-2079 -->Updated download sites used for Rfam and
2115 Pfam sources to xfam.org
2118 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2121 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2122 over sequences in Jalview
2125 <!-- JAL-2027-->Support for reverse-complement coding
2126 regions in ENA and EMBL
2129 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2130 for record retrieval via ENA rest API
2133 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2137 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2138 groovy script execution
2141 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2142 alignment window's Calculate menu
2145 <!-- JAL-1812 -->Allow groovy scripts that call
2146 Jalview.getAlignFrames() to run in headless mode
2149 <!-- JAL-2068 -->Support for creating new alignment
2150 calculation workers from groovy scripts
2153 <!-- JAL-1369 --->Store/restore reference sequence in
2157 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2158 associations are now saved/restored from project
2161 <!-- JAL-1993 -->Database selection dialog always shown
2162 before sequence fetcher is opened
2165 <!-- JAL-2183 -->Double click on an entry in Jalview's
2166 database chooser opens a sequence fetcher
2169 <!-- JAL-1563 -->Free-text search client for UniProt using
2170 the UniProt REST API
2173 <!-- JAL-2168 -->-nonews command line parameter to prevent
2174 the news reader opening
2177 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2178 querying stored in preferences
2181 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2185 <!-- JAL-1977-->Tooltips shown on database chooser
2188 <!-- JAL-391 -->Reverse complement function in calculate
2189 menu for nucleotide sequences
2192 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2193 and feature counts preserves alignment ordering (and
2194 debugged for complex feature sets).
2197 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2198 viewing structures with Jalview 2.10
2201 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2202 genome, transcript CCDS and gene ids via the Ensembl and
2203 Ensembl Genomes REST API
2206 <!-- JAL-2049 -->Protein sequence variant annotation
2207 computed for 'sequence_variant' annotation on CDS regions
2211 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2215 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2216 Ref Fetcher fails to match, or otherwise updates sequence
2217 data from external database records.
2220 <!-- JAL-2154 -->Revised Jalview Project format for
2221 efficient recovery of sequence coding and alignment
2222 annotation relationships.
2224 </ul> <!-- <em>Applet</em>
2235 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2239 <!-- JAL-2018-->Export features in Jalview format (again)
2240 includes graduated colourschemes
2243 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2244 working with big alignments and lots of hidden columns
2247 <!-- JAL-2053-->Hidden column markers not always rendered
2248 at right of alignment window
2251 <!-- JAL-2067 -->Tidied up links in help file table of
2255 <!-- JAL-2072 -->Feature based tree calculation not shown
2259 <!-- JAL-2075 -->Hidden columns ignored during feature
2260 based tree calculation
2263 <!-- JAL-2065 -->Alignment view stops updating when show
2264 unconserved enabled for group on alignment
2267 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2271 <!-- JAL-2146 -->Alignment column in status incorrectly
2272 shown as "Sequence position" when mousing over
2276 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2277 hidden columns present
2280 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2281 user created annotation added to alignment
2284 <!-- JAL-1841 -->RNA Structure consensus only computed for
2285 '()' base pair annotation
2288 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2289 in zero scores for all base pairs in RNA Structure
2293 <!-- JAL-2174-->Extend selection with columns containing
2297 <!-- JAL-2275 -->Pfam format writer puts extra space at
2298 beginning of sequence
2301 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2305 <!-- JAL-2238 -->Cannot create groups on an alignment from
2306 from a tree when t-coffee scores are shown
2309 <!-- JAL-1836,1967 -->Cannot import and view PDB
2310 structures with chains containing negative resnums (4q4h)
2313 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2317 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2318 to Clustal, PIR and PileUp output
2321 <!-- JAL-2008 -->Reordering sequence features that are
2322 not visible causes alignment window to repaint
2325 <!-- JAL-2006 -->Threshold sliders don't work in
2326 graduated colour and colour by annotation row for e-value
2327 scores associated with features and annotation rows
2330 <!-- JAL-1797 -->amino acid physicochemical conservation
2331 calculation should be case independent
2334 <!-- JAL-2173 -->Remove annotation also updates hidden
2338 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2339 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2340 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2343 <!-- JAL-2065 -->Null pointer exceptions and redraw
2344 problems when reference sequence defined and 'show
2345 non-conserved' enabled
2348 <!-- JAL-1306 -->Quality and Conservation are now shown on
2349 load even when Consensus calculation is disabled
2352 <!-- JAL-1932 -->Remove right on penultimate column of
2353 alignment does nothing
2356 <em>Application</em>
2359 <!-- JAL-1552-->URLs and links can't be imported by
2360 drag'n'drop on OSX when launched via webstart (note - not
2361 yet fixed for El Capitan)
2364 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2365 output when running on non-gb/us i18n platforms
2368 <!-- JAL-1944 -->Error thrown when exporting a view with
2369 hidden sequences as flat-file alignment
2372 <!-- JAL-2030-->InstallAnywhere distribution fails when
2376 <!-- JAL-2080-->Jalview very slow to launch via webstart
2377 (also hotfix for 2.9.0b2)
2380 <!-- JAL-2085 -->Cannot save project when view has a
2381 reference sequence defined
2384 <!-- JAL-1011 -->Columns are suddenly selected in other
2385 alignments and views when revealing hidden columns
2388 <!-- JAL-1989 -->Hide columns not mirrored in complement
2389 view in a cDNA/Protein splitframe
2392 <!-- JAL-1369 -->Cannot save/restore representative
2393 sequence from project when only one sequence is
2397 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2398 in Structure Chooser
2401 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2402 structure consensus didn't refresh annotation panel
2405 <!-- JAL-1962 -->View mapping in structure view shows
2406 mappings between sequence and all chains in a PDB file
2409 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2410 dialogs format columns correctly, don't display array
2411 data, sort columns according to type
2414 <!-- JAL-1975 -->Export complete shown after destination
2415 file chooser is cancelled during an image export
2418 <!-- JAL-2025 -->Error when querying PDB Service with
2419 sequence name containing special characters
2422 <!-- JAL-2024 -->Manual PDB structure querying should be
2426 <!-- JAL-2104 -->Large tooltips with broken HTML
2427 formatting don't wrap
2430 <!-- JAL-1128 -->Figures exported from wrapped view are
2431 truncated so L looks like I in consensus annotation
2434 <!-- JAL-2003 -->Export features should only export the
2435 currently displayed features for the current selection or
2439 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2440 after fetching cross-references, and restoring from
2444 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2445 followed in the structure viewer
2448 <!-- JAL-2163 -->Titles for individual alignments in
2449 splitframe not restored from project
2452 <!-- JAL-2145 -->missing autocalculated annotation at
2453 trailing end of protein alignment in transcript/product
2454 splitview when pad-gaps not enabled by default
2457 <!-- JAL-1797 -->amino acid physicochemical conservation
2461 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2462 article has been read (reopened issue due to
2463 internationalisation problems)
2466 <!-- JAL-1960 -->Only offer PDB structures in structure
2467 viewer based on sequence name, PDB and UniProt
2472 <!-- JAL-1976 -->No progress bar shown during export of
2476 <!-- JAL-2213 -->Structures not always superimposed after
2477 multiple structures are shown for one or more sequences.
2480 <!-- JAL-1370 -->Reference sequence characters should not
2481 be replaced with '.' when 'Show unconserved' format option
2485 <!-- JAL-1823 -->Cannot specify chain code when entering
2486 specific PDB id for sequence
2489 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2490 'Export hidden sequences' is enabled, but 'export hidden
2491 columns' is disabled.
2494 <!--JAL-2026-->Best Quality option in structure chooser
2495 selects lowest rather than highest resolution structures
2499 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2500 to sequence mapping in 'View Mappings' report
2503 <!-- JAL-2284 -->Unable to read old Jalview projects that
2504 contain non-XML data added after Jalvew wrote project.
2507 <!-- JAL-2118 -->Newly created annotation row reorders
2508 after clicking on it to create new annotation for a
2512 <!-- JAL-1980 -->Null Pointer Exception raised when
2513 pressing Add on an orphaned cut'n'paste window.
2515 <!-- may exclude, this is an external service stability issue JAL-1941
2516 -- > RNA 3D structure not added via DSSR service</li> -->
2521 <!-- JAL-2151 -->Incorrect columns are selected when
2522 hidden columns present before start of sequence
2525 <!-- JAL-1986 -->Missing dependencies on applet pages
2529 <!-- JAL-1947 -->Overview pixel size changes when
2530 sequences are hidden in applet
2533 <!-- JAL-1996 -->Updated instructions for applet
2534 deployment on examples pages.
2541 <td width="60" nowrap>
2542 <div align="center">
2543 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2544 <em>16/10/2015</em></strong>
2547 <td><em>General</em>
2549 <li>Time stamps for signed Jalview application and applet
2554 <em>Application</em>
2556 <li>Duplicate group consensus and conservation rows
2557 shown when tree is partitioned</li>
2558 <li>Erratic behaviour when tree partitions made with
2559 multiple cDNA/Protein split views</li>
2565 <td width="60" nowrap>
2566 <div align="center">
2567 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2568 <em>8/10/2015</em></strong>
2571 <td><em>General</em>
2573 <li>Updated Spanish translations of localized text for
2575 </ul> <em>Application</em>
2577 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2578 <li>Signed OSX InstallAnywhere installer<br></li>
2579 <li>Support for per-sequence based annotations in BioJSON</li>
2580 </ul> <em>Applet</em>
2582 <li>Split frame example added to applet examples page</li>
2583 </ul> <em>Build and Deployment</em>
2586 <!-- JAL-1888 -->New ant target for running Jalview's test
2594 <li>Mapping of cDNA to protein in split frames
2595 incorrect when sequence start > 1</li>
2596 <li>Broken images in filter column by annotation dialog
2598 <li>Feature colours not parsed from features file</li>
2599 <li>Exceptions and incomplete link URLs recovered when
2600 loading a features file containing HTML tags in feature
2604 <em>Application</em>
2606 <li>Annotations corrupted after BioJS export and
2608 <li>Incorrect sequence limits after Fetch DB References
2609 with 'trim retrieved sequences'</li>
2610 <li>Incorrect warning about deleting all data when
2611 deleting selected columns</li>
2612 <li>Patch to build system for shipping properly signed
2613 JNLP templates for webstart launch</li>
2614 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2615 unreleased structures for download or viewing</li>
2616 <li>Tab/space/return keystroke operation of EMBL-PDBe
2617 fetcher/viewer dialogs works correctly</li>
2618 <li>Disabled 'minimise' button on Jalview windows
2619 running on OSX to workaround redraw hang bug</li>
2620 <li>Split cDNA/Protein view position and geometry not
2621 recovered from jalview project</li>
2622 <li>Initial enabled/disabled state of annotation menu
2623 sorter 'show autocalculated first/last' corresponds to
2625 <li>Restoring of Clustal, RNA Helices and T-Coffee
2626 color schemes from BioJSON</li>
2630 <li>Reorder sequences mirrored in cDNA/Protein split
2632 <li>Applet with Jmol examples not loading correctly</li>
2638 <td><div align="center">
2639 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2641 <td><em>General</em>
2643 <li>Linked visualisation and analysis of DNA and Protein
2646 <li>Translated cDNA alignments shown as split protein
2647 and DNA alignment views</li>
2648 <li>Codon consensus annotation for linked protein and
2649 cDNA alignment views</li>
2650 <li>Link cDNA or Protein product sequences by loading
2651 them onto Protein or cDNA alignments</li>
2652 <li>Reconstruct linked cDNA alignment from aligned
2653 protein sequences</li>
2656 <li>Jmol integration updated to Jmol v14.2.14</li>
2657 <li>Import and export of Jalview alignment views as <a
2658 href="features/bioJsonFormat.html">BioJSON</a></li>
2659 <li>New alignment annotation file statements for
2660 reference sequences and marking hidden columns</li>
2661 <li>Reference sequence based alignment shading to
2662 highlight variation</li>
2663 <li>Select or hide columns according to alignment
2665 <li>Find option for locating sequences by description</li>
2666 <li>Conserved physicochemical properties shown in amino
2667 acid conservation row</li>
2668 <li>Alignments can be sorted by number of RNA helices</li>
2669 </ul> <em>Application</em>
2671 <li>New cDNA/Protein analysis capabilities
2673 <li>Get Cross-References should open a Split Frame
2674 view with cDNA/Protein</li>
2675 <li>Detect when nucleotide sequences and protein
2676 sequences are placed in the same alignment</li>
2677 <li>Split cDNA/Protein views are saved in Jalview
2682 <li>Use REST API to talk to Chimera</li>
2683 <li>Selected regions in Chimera are highlighted in linked
2684 Jalview windows</li>
2686 <li>VARNA RNA viewer updated to v3.93</li>
2687 <li>VARNA views are saved in Jalview Projects</li>
2688 <li>Pseudoknots displayed as Jalview RNA annotation can
2689 be shown in VARNA</li>
2691 <li>Make groups for selection uses marked columns as well
2692 as the active selected region</li>
2694 <li>Calculate UPGMA and NJ trees using sequence feature
2696 <li>New Export options
2698 <li>New Export Settings dialog to control hidden
2699 region export in flat file generation</li>
2701 <li>Export alignment views for display with the <a
2702 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2704 <li>Export scrollable SVG in HTML page</li>
2705 <li>Optional embedding of BioJSON data when exporting
2706 alignment figures to HTML</li>
2708 <li>3D structure retrieval and display
2710 <li>Free text and structured queries with the PDBe
2712 <li>PDBe Search API based discovery and selection of
2713 PDB structures for a sequence set</li>
2717 <li>JPred4 employed for protein secondary structure
2719 <li>Hide Insertions menu option to hide unaligned columns
2720 for one or a group of sequences</li>
2721 <li>Automatically hide insertions in alignments imported
2722 from the JPred4 web server</li>
2723 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2724 system on OSX<br />LGPL libraries courtesy of <a
2725 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2727 <li>changed 'View nucleotide structure' submenu to 'View
2728 VARNA 2D Structure'</li>
2729 <li>change "View protein structure" menu option to "3D
2732 </ul> <em>Applet</em>
2734 <li>New layout for applet example pages</li>
2735 <li>New parameters to enable SplitFrame view
2736 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2737 <li>New example demonstrating linked viewing of cDNA and
2738 Protein alignments</li>
2739 </ul> <em>Development and deployment</em>
2741 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2742 <li>Include installation type and git revision in build
2743 properties and console log output</li>
2744 <li>Jalview Github organisation, and new github site for
2745 storing BioJsMSA Templates</li>
2746 <li>Jalview's unit tests now managed with TestNG</li>
2749 <!-- <em>General</em>
2751 </ul> --> <!-- issues resolved --> <em>Application</em>
2753 <li>Escape should close any open find dialogs</li>
2754 <li>Typo in select-by-features status report</li>
2755 <li>Consensus RNA secondary secondary structure
2756 predictions are not highlighted in amber</li>
2757 <li>Missing gap character in v2.7 example file means
2758 alignment appears unaligned when pad-gaps is not enabled</li>
2759 <li>First switch to RNA Helices colouring doesn't colour
2760 associated structure views</li>
2761 <li>ID width preference option is greyed out when auto
2762 width checkbox not enabled</li>
2763 <li>Stopped a warning dialog from being shown when
2764 creating user defined colours</li>
2765 <li>'View Mapping' in structure viewer shows sequence
2766 mappings for just that viewer's sequences</li>
2767 <li>Workaround for superposing PDB files containing
2768 multiple models in Chimera</li>
2769 <li>Report sequence position in status bar when hovering
2770 over Jmol structure</li>
2771 <li>Cannot output gaps as '.' symbols with Selection ->
2772 output to text box</li>
2773 <li>Flat file exports of alignments with hidden columns
2774 have incorrect sequence start/end</li>
2775 <li>'Aligning' a second chain to a Chimera structure from
2777 <li>Colour schemes applied to structure viewers don't
2778 work for nucleotide</li>
2779 <li>Loading/cut'n'pasting an empty or invalid file leads
2780 to a grey/invisible alignment window</li>
2781 <li>Exported Jpred annotation from a sequence region
2782 imports to different position</li>
2783 <li>Space at beginning of sequence feature tooltips shown
2784 on some platforms</li>
2785 <li>Chimera viewer 'View | Show Chain' menu is not
2787 <li>'New View' fails with a Null Pointer Exception in
2788 console if Chimera has been opened</li>
2789 <li>Mouseover to Chimera not working</li>
2790 <li>Miscellaneous ENA XML feature qualifiers not
2792 <li>NPE in annotation renderer after 'Extract Scores'</li>
2793 <li>If two structures in one Chimera window, mouseover of
2794 either sequence shows on first structure</li>
2795 <li>'Show annotations' options should not make
2796 non-positional annotations visible</li>
2797 <li>Subsequence secondary structure annotation not shown
2798 in right place after 'view flanking regions'</li>
2799 <li>File Save As type unset when current file format is
2801 <li>Save as '.jar' option removed for saving Jalview
2803 <li>Colour by Sequence colouring in Chimera more
2805 <li>Cannot 'add reference annotation' for a sequence in
2806 several views on same alignment</li>
2807 <li>Cannot show linked products for EMBL / ENA records</li>
2808 <li>Jalview's tooltip wraps long texts containing no
2810 </ul> <em>Applet</em>
2812 <li>Jmol to JalviewLite mouseover/link not working</li>
2813 <li>JalviewLite can't import sequences with ID
2814 descriptions containing angle brackets</li>
2815 </ul> <em>General</em>
2817 <li>Cannot export and reimport RNA secondary structure
2818 via jalview annotation file</li>
2819 <li>Random helix colour palette for colour by annotation
2820 with RNA secondary structure</li>
2821 <li>Mouseover to cDNA from STOP residue in protein
2822 translation doesn't work.</li>
2823 <li>hints when using the select by annotation dialog box</li>
2824 <li>Jmol alignment incorrect if PDB file has alternate CA
2826 <li>FontChooser message dialog appears to hang after
2827 choosing 1pt font</li>
2828 <li>Peptide secondary structure incorrectly imported from
2829 annotation file when annotation display text includes 'e' or
2831 <li>Cannot set colour of new feature type whilst creating
2833 <li>cDNA translation alignment should not be sequence
2834 order dependent</li>
2835 <li>'Show unconserved' doesn't work for lower case
2837 <li>Nucleotide ambiguity codes involving R not recognised</li>
2838 </ul> <em>Deployment and Documentation</em>
2840 <li>Applet example pages appear different to the rest of
2841 www.jalview.org</li>
2842 </ul> <em>Application Known issues</em>
2844 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2845 <li>Misleading message appears after trying to delete
2847 <li>Jalview icon not shown in dock after InstallAnywhere
2848 version launches</li>
2849 <li>Fetching EMBL reference for an RNA sequence results
2850 fails with a sequence mismatch</li>
2851 <li>Corrupted or unreadable alignment display when
2852 scrolling alignment to right</li>
2853 <li>ArrayIndexOutOfBoundsException thrown when remove
2854 empty columns called on alignment with ragged gapped ends</li>
2855 <li>auto calculated alignment annotation rows do not get
2856 placed above or below non-autocalculated rows</li>
2857 <li>Jalview dekstop becomes sluggish at full screen in
2858 ultra-high resolution</li>
2859 <li>Cannot disable consensus calculation independently of
2860 quality and conservation</li>
2861 <li>Mouseover highlighting between cDNA and protein can
2862 become sluggish with more than one splitframe shown</li>
2863 </ul> <em>Applet Known Issues</em>
2865 <li>Core PDB parsing code requires Jmol</li>
2866 <li>Sequence canvas panel goes white when alignment
2867 window is being resized</li>
2873 <td><div align="center">
2874 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2876 <td><em>General</em>
2878 <li>Updated Java code signing certificate donated by
2880 <li>Features and annotation preserved when performing
2881 pairwise alignment</li>
2882 <li>RNA pseudoknot annotation can be
2883 imported/exported/displayed</li>
2884 <li>'colour by annotation' can colour by RNA and
2885 protein secondary structure</li>
2886 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2887 post-hoc with 2.9 release</em>)
2890 </ul> <em>Application</em>
2892 <li>Extract and display secondary structure for sequences
2893 with 3D structures</li>
2894 <li>Support for parsing RNAML</li>
2895 <li>Annotations menu for layout
2897 <li>sort sequence annotation rows by alignment</li>
2898 <li>place sequence annotation above/below alignment
2901 <li>Output in Stockholm format</li>
2902 <li>Internationalisation: improved Spanish (es)
2904 <li>Structure viewer preferences tab</li>
2905 <li>Disorder and Secondary Structure annotation tracks
2906 shared between alignments</li>
2907 <li>UCSF Chimera launch and linked highlighting from
2909 <li>Show/hide all sequence associated annotation rows for
2910 all or current selection</li>
2911 <li>disorder and secondary structure predictions
2912 available as dataset annotation</li>
2913 <li>Per-sequence rna helices colouring</li>
2916 <li>Sequence database accessions imported when fetching
2917 alignments from Rfam</li>
2918 <li>update VARNA version to 3.91</li>
2920 <li>New groovy scripts for exporting aligned positions,
2921 conservation values, and calculating sum of pairs scores.</li>
2922 <li>Command line argument to set default JABAWS server</li>
2923 <li>include installation type in build properties and
2924 console log output</li>
2925 <li>Updated Jalview project format to preserve dataset
2929 <!-- issues resolved --> <em>Application</em>
2931 <li>Distinguish alignment and sequence associated RNA
2932 structure in structure->view->VARNA</li>
2933 <li>Raise dialog box if user deletes all sequences in an
2935 <li>Pressing F1 results in documentation opening twice</li>
2936 <li>Sequence feature tooltip is wrapped</li>
2937 <li>Double click on sequence associated annotation
2938 selects only first column</li>
2939 <li>Redundancy removal doesn't result in unlinked
2940 leaves shown in tree</li>
2941 <li>Undos after several redundancy removals don't undo
2943 <li>Hide sequence doesn't hide associated annotation</li>
2944 <li>User defined colours dialog box too big to fit on
2945 screen and buttons not visible</li>
2946 <li>author list isn't updated if already written to
2947 Jalview properties</li>
2948 <li>Popup menu won't open after retrieving sequence
2950 <li>File open window for associate PDB doesn't open</li>
2951 <li>Left-then-right click on a sequence id opens a
2952 browser search window</li>
2953 <li>Cannot open sequence feature shading/sort popup menu
2954 in feature settings dialog</li>
2955 <li>better tooltip placement for some areas of Jalview
2957 <li>Allow addition of JABAWS Server which doesn't
2958 pass validation</li>
2959 <li>Web services parameters dialog box is too large to
2961 <li>Muscle nucleotide alignment preset obscured by
2963 <li>JABAWS preset submenus don't contain newly
2964 defined user preset</li>
2965 <li>MSA web services warns user if they were launched
2966 with invalid input</li>
2967 <li>Jalview cannot contact DAS Registy when running on
2970 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2971 'Superpose with' submenu not shown when new view
2975 </ul> <!-- <em>Applet</em>
2977 </ul> <em>General</em>
2979 </ul>--> <em>Deployment and Documentation</em>
2981 <li>2G and 1G options in launchApp have no effect on
2982 memory allocation</li>
2983 <li>launchApp service doesn't automatically open
2984 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2986 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2987 InstallAnywhere reports cannot find valid JVM when Java
2988 1.7_055 is available
2990 </ul> <em>Application Known issues</em>
2993 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2994 corrupted or unreadable alignment display when scrolling
2998 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2999 retrieval fails but progress bar continues for DAS retrieval
3000 with large number of ID
3003 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3004 flatfile output of visible region has incorrect sequence
3008 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3009 rna structure consensus doesn't update when secondary
3010 structure tracks are rearranged
3013 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3014 invalid rna structure positional highlighting does not
3015 highlight position of invalid base pairs
3018 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3019 out of memory errors are not raised when saving Jalview
3020 project from alignment window file menu
3023 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3024 Switching to RNA Helices colouring doesn't propagate to
3028 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3029 colour by RNA Helices not enabled when user created
3030 annotation added to alignment
3033 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3034 Jalview icon not shown on dock in Mountain Lion/Webstart
3036 </ul> <em>Applet Known Issues</em>
3039 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3040 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3043 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3044 Jalview and Jmol example not compatible with IE9
3047 <li>Sort by annotation score doesn't reverse order
3053 <td><div align="center">
3054 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3057 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3060 <li>Internationalisation of user interface (usually
3061 called i18n support) and translation for Spanish locale</li>
3062 <li>Define/Undefine group on current selection with
3063 Ctrl-G/Shift Ctrl-G</li>
3064 <li>Improved group creation/removal options in
3065 alignment/sequence Popup menu</li>
3066 <li>Sensible precision for symbol distribution
3067 percentages shown in logo tooltip.</li>
3068 <li>Annotation panel height set according to amount of
3069 annotation when alignment first opened</li>
3070 </ul> <em>Application</em>
3072 <li>Interactive consensus RNA secondary structure
3073 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3074 <li>Select columns containing particular features from
3075 Feature Settings dialog</li>
3076 <li>View all 'representative' PDB structures for selected
3078 <li>Update Jalview project format:
3080 <li>New file extension for Jalview projects '.jvp'</li>
3081 <li>Preserve sequence and annotation dataset (to
3082 store secondary structure annotation,etc)</li>
3083 <li>Per group and alignment annotation and RNA helix
3087 <li>New similarity measures for PCA and Tree calculation
3089 <li>Experimental support for retrieval and viewing of
3090 flanking regions for an alignment</li>
3094 <!-- issues resolved --> <em>Application</em>
3096 <li>logo keeps spinning and status remains at queued or
3097 running after job is cancelled</li>
3098 <li>cannot export features from alignments imported from
3099 Jalview/VAMSAS projects</li>
3100 <li>Buggy slider for web service parameters that take
3102 <li>Newly created RNA secondary structure line doesn't
3103 have 'display all symbols' flag set</li>
3104 <li>T-COFFEE alignment score shading scheme and other
3105 annotation shading not saved in Jalview project</li>
3106 <li>Local file cannot be loaded in freshly downloaded
3108 <li>Jalview icon not shown on dock in Mountain
3110 <li>Load file from desktop file browser fails</li>
3111 <li>Occasional NPE thrown when calculating large trees</li>
3112 <li>Cannot reorder or slide sequences after dragging an
3113 alignment onto desktop</li>
3114 <li>Colour by annotation dialog throws NPE after using
3115 'extract scores' function</li>
3116 <li>Loading/cut'n'pasting an empty file leads to a grey
3117 alignment window</li>
3118 <li>Disorder thresholds rendered incorrectly after
3119 performing IUPred disorder prediction</li>
3120 <li>Multiple group annotated consensus rows shown when
3121 changing 'normalise logo' display setting</li>
3122 <li>Find shows blank dialog after 'finished searching' if
3123 nothing matches query</li>
3124 <li>Null Pointer Exceptions raised when sorting by
3125 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3127 <li>Errors in Jmol console when structures in alignment
3128 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3130 <li>Not all working JABAWS services are shown in
3132 <li>JAVAWS version of Jalview fails to launch with
3133 'invalid literal/length code'</li>
3134 <li>Annotation/RNA Helix colourschemes cannot be applied
3135 to alignment with groups (actually fixed in 2.8.0b1)</li>
3136 <li>RNA Helices and T-Coffee Scores available as default
3139 </ul> <em>Applet</em>
3141 <li>Remove group option is shown even when selection is
3143 <li>Apply to all groups ticked but colourscheme changes
3144 don't affect groups</li>
3145 <li>Documented RNA Helices and T-Coffee Scores as valid
3146 colourscheme name</li>
3147 <li>Annotation labels drawn on sequence IDs when
3148 Annotation panel is not displayed</li>
3149 <li>Increased font size for dropdown menus on OSX and
3150 embedded windows</li>
3151 </ul> <em>Other</em>
3153 <li>Consensus sequence for alignments/groups with a
3154 single sequence were not calculated</li>
3155 <li>annotation files that contain only groups imported as
3156 annotation and junk sequences</li>
3157 <li>Fasta files with sequences containing '*' incorrectly
3158 recognised as PFAM or BLC</li>
3159 <li>conservation/PID slider apply all groups option
3160 doesn't affect background (2.8.0b1)
3162 <li>redundancy highlighting is erratic at 0% and 100%</li>
3163 <li>Remove gapped columns fails for sequences with ragged
3165 <li>AMSA annotation row with leading spaces is not
3166 registered correctly on import</li>
3167 <li>Jalview crashes when selecting PCA analysis for
3168 certain alignments</li>
3169 <li>Opening the colour by annotation dialog for an
3170 existing annotation based 'use original colours'
3171 colourscheme loses original colours setting</li>
3176 <td><div align="center">
3177 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3178 <em>30/1/2014</em></strong>
3182 <li>Trusted certificates for JalviewLite applet and
3183 Jalview Desktop application<br />Certificate was donated by
3184 <a href="https://www.certum.eu">Certum</a> to the Jalview
3185 open source project).
3187 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3188 <li>Output in Stockholm format</li>
3189 <li>Allow import of data from gzipped files</li>
3190 <li>Export/import group and sequence associated line
3191 graph thresholds</li>
3192 <li>Nucleotide substitution matrix that supports RNA and
3193 ambiguity codes</li>
3194 <li>Allow disorder predictions to be made on the current
3195 selection (or visible selection) in the same way that JPred
3197 <li>Groovy scripting for headless Jalview operation</li>
3198 </ul> <em>Other improvements</em>
3200 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3201 <li>COMBINE statement uses current SEQUENCE_REF and
3202 GROUP_REF scope to group annotation rows</li>
3203 <li>Support '' style escaping of quotes in Newick
3205 <li>Group options for JABAWS service by command line name</li>
3206 <li>Empty tooltip shown for JABA service options with a
3207 link but no description</li>
3208 <li>Select primary source when selecting authority in
3209 database fetcher GUI</li>
3210 <li>Add .mfa to FASTA file extensions recognised by
3212 <li>Annotation label tooltip text wrap</li>
3217 <li>Slow scrolling when lots of annotation rows are
3219 <li>Lots of NPE (and slowness) after creating RNA
3220 secondary structure annotation line</li>
3221 <li>Sequence database accessions not imported when
3222 fetching alignments from Rfam</li>
3223 <li>Incorrect SHMR submission for sequences with
3225 <li>View all structures does not always superpose
3227 <li>Option widgets in service parameters not updated to
3228 reflect user or preset settings</li>
3229 <li>Null pointer exceptions for some services without
3230 presets or adjustable parameters</li>
3231 <li>Discover PDB IDs entry in structure menu doesn't
3232 discover PDB xRefs</li>
3233 <li>Exception encountered while trying to retrieve
3234 features with DAS</li>
3235 <li>Lowest value in annotation row isn't coloured
3236 when colour by annotation (per sequence) is coloured</li>
3237 <li>Keyboard mode P jumps to start of gapped region when
3238 residue follows a gap</li>
3239 <li>Jalview appears to hang importing an alignment with
3240 Wrap as default or after enabling Wrap</li>
3241 <li>'Right click to add annotations' message
3242 shown in wrap mode when no annotations present</li>
3243 <li>Disorder predictions fail with NPE if no automatic
3244 annotation already exists on alignment</li>
3245 <li>oninit javascript function should be called after
3246 initialisation completes</li>
3247 <li>Remove redundancy after disorder prediction corrupts
3248 alignment window display</li>
3249 <li>Example annotation file in documentation is invalid</li>
3250 <li>Grouped line graph annotation rows are not exported
3251 to annotation file</li>
3252 <li>Multi-harmony analysis cannot be run when only two
3254 <li>Cannot create multiple groups of line graphs with
3255 several 'combine' statements in annotation file</li>
3256 <li>Pressing return several times causes Number Format
3257 exceptions in keyboard mode</li>
3258 <li>Multi-harmony (SHMMR) method doesn't submit
3259 correct partitions for input data</li>
3260 <li>Translation from DNA to Amino Acids fails</li>
3261 <li>Jalview fail to load newick tree with quoted label</li>
3262 <li>--headless flag isn't understood</li>
3263 <li>ClassCastException when generating EPS in headless
3265 <li>Adjusting sequence-associated shading threshold only
3266 changes one row's threshold</li>
3267 <li>Preferences and Feature settings panel panel
3268 doesn't open</li>
3269 <li>hide consensus histogram also hides conservation and
3270 quality histograms</li>
3275 <td><div align="center">
3276 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3278 <td><em>Application</em>
3280 <li>Support for JABAWS 2.0 Services (AACon alignment
3281 conservation, protein disorder and Clustal Omega)</li>
3282 <li>JABAWS server status indicator in Web Services
3284 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3285 in Jalview alignment window</li>
3286 <li>Updated Jalview build and deploy framework for OSX
3287 mountain lion, windows 7, and 8</li>
3288 <li>Nucleotide substitution matrix for PCA that supports
3289 RNA and ambiguity codes</li>
3291 <li>Improved sequence database retrieval GUI</li>
3292 <li>Support fetching and database reference look up
3293 against multiple DAS sources (Fetch all from in 'fetch db
3295 <li>Jalview project improvements
3297 <li>Store and retrieve the 'belowAlignment'
3298 flag for annotation</li>
3299 <li>calcId attribute to group annotation rows on the
3301 <li>Store AACon calculation settings for a view in
3302 Jalview project</li>
3306 <li>horizontal scrolling gesture support</li>
3307 <li>Visual progress indicator when PCA calculation is
3309 <li>Simpler JABA web services menus</li>
3310 <li>visual indication that web service results are still
3311 being retrieved from server</li>
3312 <li>Serialise the dialogs that are shown when Jalview
3313 starts up for first time</li>
3314 <li>Jalview user agent string for interacting with HTTP
3316 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3318 <li>Examples directory and Groovy library included in
3319 InstallAnywhere distribution</li>
3320 </ul> <em>Applet</em>
3322 <li>RNA alignment and secondary structure annotation
3323 visualization applet example</li>
3324 </ul> <em>General</em>
3326 <li>Normalise option for consensus sequence logo</li>
3327 <li>Reset button in PCA window to return dimensions to
3329 <li>Allow seqspace or Jalview variant of alignment PCA
3331 <li>PCA with either nucleic acid and protein substitution
3333 <li>Allow windows containing HTML reports to be exported
3335 <li>Interactive display and editing of RNA secondary
3336 structure contacts</li>
3337 <li>RNA Helix Alignment Colouring</li>
3338 <li>RNA base pair logo consensus</li>
3339 <li>Parse sequence associated secondary structure
3340 information in Stockholm files</li>
3341 <li>HTML Export database accessions and annotation
3342 information presented in tooltip for sequences</li>
3343 <li>Import secondary structure from LOCARNA clustalw
3344 style RNA alignment files</li>
3345 <li>import and visualise T-COFFEE quality scores for an
3347 <li>'colour by annotation' per sequence option to
3348 shade each sequence according to its associated alignment
3350 <li>New Jalview Logo</li>
3351 </ul> <em>Documentation and Development</em>
3353 <li>documentation for score matrices used in Jalview</li>
3354 <li>New Website!</li>
3356 <td><em>Application</em>
3358 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3359 wsdbfetch REST service</li>
3360 <li>Stop windows being moved outside desktop on OSX</li>
3361 <li>Filetype associations not installed for webstart
3363 <li>Jalview does not always retrieve progress of a JABAWS
3364 job execution in full once it is complete</li>
3365 <li>revise SHMR RSBS definition to ensure alignment is
3366 uploaded via ali_file parameter</li>
3367 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3368 <li>View all structures superposed fails with exception</li>
3369 <li>Jnet job queues forever if a very short sequence is
3370 submitted for prediction</li>
3371 <li>Cut and paste menu not opened when mouse clicked on
3373 <li>Putting fractional value into integer text box in
3374 alignment parameter dialog causes Jalview to hang</li>
3375 <li>Structure view highlighting doesn't work on
3377 <li>View all structures fails with exception shown in
3379 <li>Characters in filename associated with PDBEntry not
3380 escaped in a platform independent way</li>
3381 <li>Jalview desktop fails to launch with exception when
3383 <li>Tree calculation reports 'you must have 2 or more
3384 sequences selected' when selection is empty</li>
3385 <li>Jalview desktop fails to launch with jar signature
3386 failure when java web start temporary file caching is
3388 <li>DAS Sequence retrieval with range qualification
3389 results in sequence xref which includes range qualification</li>
3390 <li>Errors during processing of command line arguments
3391 cause progress bar (JAL-898) to be removed</li>
3392 <li>Replace comma for semi-colon option not disabled for
3393 DAS sources in sequence fetcher</li>
3394 <li>Cannot close news reader when JABAWS server warning
3395 dialog is shown</li>
3396 <li>Option widgets not updated to reflect user settings</li>
3397 <li>Edited sequence not submitted to web service</li>
3398 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3399 <li>InstallAnywhere installer doesn't unpack and run
3400 on OSX Mountain Lion</li>
3401 <li>Annotation panel not given a scroll bar when
3402 sequences with alignment annotation are pasted into the
3404 <li>Sequence associated annotation rows not associated
3405 when loaded from Jalview project</li>
3406 <li>Browser launch fails with NPE on java 1.7</li>
3407 <li>JABAWS alignment marked as finished when job was
3408 cancelled or job failed due to invalid input</li>
3409 <li>NPE with v2.7 example when clicking on Tree
3410 associated with all views</li>
3411 <li>Exceptions when copy/paste sequences with grouped
3412 annotation rows to new window</li>
3413 </ul> <em>Applet</em>
3415 <li>Sequence features are momentarily displayed before
3416 they are hidden using hidefeaturegroups applet parameter</li>
3417 <li>loading features via javascript API automatically
3418 enables feature display</li>
3419 <li>scrollToColumnIn javascript API method doesn't
3421 </ul> <em>General</em>
3423 <li>Redundancy removal fails for rna alignment</li>
3424 <li>PCA calculation fails when sequence has been selected
3425 and then deselected</li>
3426 <li>PCA window shows grey box when first opened on OSX</li>
3427 <li>Letters coloured pink in sequence logo when alignment
3428 coloured with clustalx</li>
3429 <li>Choosing fonts without letter symbols defined causes
3430 exceptions and redraw errors</li>
3431 <li>Initial PCA plot view is not same as manually
3432 reconfigured view</li>
3433 <li>Grouped annotation graph label has incorrect line
3435 <li>Grouped annotation graph label display is corrupted
3436 for lots of labels</li>
3441 <div align="center">
3442 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3445 <td><em>Application</em>
3447 <li>Jalview Desktop News Reader</li>
3448 <li>Tweaked default layout of web services menu</li>
3449 <li>View/alignment association menu to enable user to
3450 easily specify which alignment a multi-structure view takes
3451 its colours/correspondences from</li>
3452 <li>Allow properties file location to be specified as URL</li>
3453 <li>Extend Jalview project to preserve associations
3454 between many alignment views and a single Jmol display</li>
3455 <li>Store annotation row height in Jalview project file</li>
3456 <li>Annotation row column label formatting attributes
3457 stored in project file</li>
3458 <li>Annotation row order for auto-calculated annotation
3459 rows preserved in Jalview project file</li>
3460 <li>Visual progress indication when Jalview state is
3461 saved using Desktop window menu</li>
3462 <li>Visual indication that command line arguments are
3463 still being processed</li>
3464 <li>Groovy script execution from URL</li>
3465 <li>Colour by annotation default min and max colours in
3467 <li>Automatically associate PDB files dragged onto an
3468 alignment with sequences that have high similarity and
3470 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3471 <li>'view structures' option to open many
3472 structures in same window</li>
3473 <li>Sort associated views menu option for tree panel</li>
3474 <li>Group all JABA and non-JABA services for a particular
3475 analysis function in its own submenu</li>
3476 </ul> <em>Applet</em>
3478 <li>Userdefined and autogenerated annotation rows for
3480 <li>Adjustment of alignment annotation pane height</li>
3481 <li>Annotation scrollbar for annotation panel</li>
3482 <li>Drag to reorder annotation rows in annotation panel</li>
3483 <li>'automaticScrolling' parameter</li>
3484 <li>Allow sequences with partial ID string matches to be
3485 annotated from GFF/Jalview features files</li>
3486 <li>Sequence logo annotation row in applet</li>
3487 <li>Absolute paths relative to host server in applet
3488 parameters are treated as such</li>
3489 <li>New in the JalviewLite javascript API:
3491 <li>JalviewLite.js javascript library</li>
3492 <li>Javascript callbacks for
3494 <li>Applet initialisation</li>
3495 <li>Sequence/alignment mouse-overs and selections</li>
3498 <li>scrollTo row and column alignment scrolling
3500 <li>Select sequence/alignment regions from javascript</li>
3501 <li>javascript structure viewer harness to pass
3502 messages between Jmol and Jalview when running as
3503 distinct applets</li>
3504 <li>sortBy method</li>
3505 <li>Set of applet and application examples shipped
3506 with documentation</li>
3507 <li>New example to demonstrate JalviewLite and Jmol
3508 javascript message exchange</li>
3510 </ul> <em>General</em>
3512 <li>Enable Jmol displays to be associated with multiple
3513 multiple alignments</li>
3514 <li>Option to automatically sort alignment with new tree</li>
3515 <li>User configurable link to enable redirects to a
3516 www.Jalview.org mirror</li>
3517 <li>Jmol colours option for Jmol displays</li>
3518 <li>Configurable newline string when writing alignment
3519 and other flat files</li>
3520 <li>Allow alignment annotation description lines to
3521 contain html tags</li>
3522 </ul> <em>Documentation and Development</em>
3524 <li>Add groovy test harness for bulk load testing to
3526 <li>Groovy script to load and align a set of sequences
3527 using a web service before displaying the result in the
3528 Jalview desktop</li>
3529 <li>Restructured javascript and applet api documentation</li>
3530 <li>Ant target to publish example html files with applet
3532 <li>Netbeans project for building Jalview from source</li>
3533 <li>ant task to create online javadoc for Jalview source</li>
3535 <td><em>Application</em>
3537 <li>User defined colourscheme throws exception when
3538 current built in colourscheme is saved as new scheme</li>
3539 <li>AlignFrame->Save in application pops up save
3540 dialog for valid filename/format</li>
3541 <li>Cannot view associated structure for UniProt sequence</li>
3542 <li>PDB file association breaks for UniProt sequence
3544 <li>Associate PDB from file dialog does not tell you
3545 which sequence is to be associated with the file</li>
3546 <li>Find All raises null pointer exception when query
3547 only matches sequence IDs</li>
3548 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3549 <li>Jalview project with Jmol views created with Jalview
3550 2.4 cannot be loaded</li>
3551 <li>Filetype associations not installed for webstart
3553 <li>Two or more chains in a single PDB file associated
3554 with sequences in different alignments do not get coloured
3555 by their associated sequence</li>
3556 <li>Visibility status of autocalculated annotation row
3557 not preserved when project is loaded</li>
3558 <li>Annotation row height and visibility attributes not
3559 stored in Jalview project</li>
3560 <li>Tree bootstraps are not preserved when saved as a
3561 Jalview project</li>
3562 <li>Envision2 workflow tooltips are corrupted</li>
3563 <li>Enabling show group conservation also enables colour
3564 by conservation</li>
3565 <li>Duplicate group associated conservation or consensus
3566 created on new view</li>
3567 <li>Annotation scrollbar not displayed after 'show
3568 all hidden annotation rows' option selected</li>
3569 <li>Alignment quality not updated after alignment
3570 annotation row is hidden then shown</li>
3571 <li>Preserve colouring of structures coloured by
3572 sequences in pre Jalview 2.7 projects</li>
3573 <li>Web service job parameter dialog is not laid out
3575 <li>Web services menu not refreshed after 'reset
3576 services' button is pressed in preferences</li>
3577 <li>Annotation off by one in Jalview v2_3 example project</li>
3578 <li>Structures imported from file and saved in project
3579 get name like jalview_pdb1234.txt when reloaded</li>
3580 <li>Jalview does not always retrieve progress of a JABAWS
3581 job execution in full once it is complete</li>
3582 </ul> <em>Applet</em>
3584 <li>Alignment height set incorrectly when lots of
3585 annotation rows are displayed</li>
3586 <li>Relative URLs in feature HTML text not resolved to
3588 <li>View follows highlighting does not work for positions
3590 <li><= shown as = in tooltip</li>
3591 <li>Export features raises exception when no features
3593 <li>Separator string used for serialising lists of IDs
3594 for javascript api is modified when separator string
3595 provided as parameter</li>
3596 <li>Null pointer exception when selecting tree leaves for
3597 alignment with no existing selection</li>
3598 <li>Relative URLs for datasources assumed to be relative
3599 to applet's codebase</li>
3600 <li>Status bar not updated after finished searching and
3601 search wraps around to first result</li>
3602 <li>StructureSelectionManager instance shared between
3603 several Jalview applets causes race conditions and memory
3605 <li>Hover tooltip and mouseover of position on structure
3606 not sent from Jmol in applet</li>
3607 <li>Certain sequences of javascript method calls to
3608 applet API fatally hang browser</li>
3609 </ul> <em>General</em>
3611 <li>View follows structure mouseover scrolls beyond
3612 position with wrapped view and hidden regions</li>
3613 <li>Find sequence position moves to wrong residue
3614 with/without hidden columns</li>
3615 <li>Sequence length given in alignment properties window
3617 <li>InvalidNumberFormat exceptions thrown when trying to
3618 import PDB like structure files</li>
3619 <li>Positional search results are only highlighted
3620 between user-supplied sequence start/end bounds</li>
3621 <li>End attribute of sequence is not validated</li>
3622 <li>Find dialog only finds first sequence containing a
3623 given sequence position</li>
3624 <li>Sequence numbering not preserved in MSF alignment
3626 <li>Jalview PDB file reader does not extract sequence
3627 from nucleotide chains correctly</li>
3628 <li>Structure colours not updated when tree partition
3629 changed in alignment</li>
3630 <li>Sequence associated secondary structure not correctly
3631 parsed in interleaved stockholm</li>
3632 <li>Colour by annotation dialog does not restore current
3634 <li>Hiding (nearly) all sequences doesn't work
3636 <li>Sequences containing lowercase letters are not
3637 properly associated with their pdb files</li>
3638 </ul> <em>Documentation and Development</em>
3640 <li>schemas/JalviewWsParamSet.xsd corrupted by
3641 ApplyCopyright tool</li>
3646 <div align="center">
3647 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3650 <td><em>Application</em>
3652 <li>New warning dialog when the Jalview Desktop cannot
3653 contact web services</li>
3654 <li>JABA service parameters for a preset are shown in
3655 service job window</li>
3656 <li>JABA Service menu entries reworded</li>
3660 <li>Modeller PIR IO broken - cannot correctly import a
3661 pir file emitted by Jalview</li>
3662 <li>Existing feature settings transferred to new
3663 alignment view created from cut'n'paste</li>
3664 <li>Improved test for mixed amino/nucleotide chains when
3665 parsing PDB files</li>
3666 <li>Consensus and conservation annotation rows
3667 occasionally become blank for all new windows</li>
3668 <li>Exception raised when right clicking above sequences
3669 in wrapped view mode</li>
3670 </ul> <em>Application</em>
3672 <li>multiple multiply aligned structure views cause cpu
3673 usage to hit 100% and computer to hang</li>
3674 <li>Web Service parameter layout breaks for long user
3675 parameter names</li>
3676 <li>Jaba service discovery hangs desktop if Jaba server
3683 <div align="center">
3684 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3687 <td><em>Application</em>
3689 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3690 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3693 <li>Web Services preference tab</li>
3694 <li>Analysis parameters dialog box and user defined
3696 <li>Improved speed and layout of Envision2 service menu</li>
3697 <li>Superpose structures using associated sequence
3699 <li>Export coordinates and projection as CSV from PCA
3701 </ul> <em>Applet</em>
3703 <li>enable javascript: execution by the applet via the
3704 link out mechanism</li>
3705 </ul> <em>Other</em>
3707 <li>Updated the Jmol Jalview interface to work with Jmol
3709 <li>The Jalview Desktop and JalviewLite applet now
3710 require Java 1.5</li>
3711 <li>Allow Jalview feature colour specification for GFF
3712 sequence annotation files</li>
3713 <li>New 'colour by label' keword in Jalview feature file
3714 type colour specification</li>
3715 <li>New Jalview Desktop Groovy API method that allows a
3716 script to check if it being run in an interactive session or
3717 in a batch operation from the Jalview command line</li>
3721 <li>clustalx colourscheme colours Ds preferentially when
3722 both D+E are present in over 50% of the column</li>
3723 </ul> <em>Application</em>
3725 <li>typo in AlignmentFrame->View->Hide->all but
3726 selected Regions menu item</li>
3727 <li>sequence fetcher replaces ',' for ';' when the ',' is
3728 part of a valid accession ID</li>
3729 <li>fatal OOM if object retrieved by sequence fetcher
3730 runs out of memory</li>
3731 <li>unhandled Out of Memory Error when viewing pca
3732 analysis results</li>
3733 <li>InstallAnywhere builds fail to launch on OS X java
3734 10.5 update 4 (due to apple Java 1.6 update)</li>
3735 <li>Installanywhere Jalview silently fails to launch</li>
3736 </ul> <em>Applet</em>
3738 <li>Jalview.getFeatureGroups() raises an
3739 ArrayIndexOutOfBoundsException if no feature groups are
3746 <div align="center">
3747 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3753 <li>Alignment prettyprinter doesn't cope with long
3755 <li>clustalx colourscheme colours Ds preferentially when
3756 both D+E are present in over 50% of the column</li>
3757 <li>nucleic acid structures retrieved from PDB do not
3758 import correctly</li>
3759 <li>More columns get selected than were clicked on when a
3760 number of columns are hidden</li>
3761 <li>annotation label popup menu not providing correct
3762 add/hide/show options when rows are hidden or none are
3764 <li>Stockholm format shown in list of readable formats,
3765 and parser copes better with alignments from RFAM.</li>
3766 <li>CSV output of consensus only includes the percentage
3767 of all symbols if sequence logo display is enabled</li>
3769 </ul> <em>Applet</em>
3771 <li>annotation panel disappears when annotation is
3773 </ul> <em>Application</em>
3775 <li>Alignment view not redrawn properly when new
3776 alignment opened where annotation panel is visible but no
3777 annotations are present on alignment</li>
3778 <li>pasted region containing hidden columns is
3779 incorrectly displayed in new alignment window</li>
3780 <li>Jalview slow to complete operations when stdout is
3781 flooded (fix is to close the Jalview console)</li>
3782 <li>typo in AlignmentFrame->View->Hide->all but
3783 selected Rregions menu item.</li>
3784 <li>inconsistent group submenu and Format submenu entry
3785 'Un' or 'Non'conserved</li>
3786 <li>Sequence feature settings are being shared by
3787 multiple distinct alignments</li>
3788 <li>group annotation not recreated when tree partition is
3790 <li>double click on group annotation to select sequences
3791 does not propagate to associated trees</li>
3792 <li>Mac OSX specific issues:
3794 <li>exception raised when mouse clicked on desktop
3795 window background</li>
3796 <li>Desktop menu placed on menu bar and application
3797 name set correctly</li>
3798 <li>sequence feature settings not wide enough for the
3799 save feature colourscheme button</li>
3808 <div align="center">
3809 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3812 <td><em>New Capabilities</em>
3814 <li>URL links generated from description line for
3815 regular-expression based URL links (applet and application)
3817 <li>Non-positional feature URL links are shown in link
3819 <li>Linked viewing of nucleic acid sequences and
3821 <li>Automatic Scrolling option in View menu to display
3822 the currently highlighted region of an alignment.</li>
3823 <li>Order an alignment by sequence length, or using the
3824 average score or total feature count for each sequence.</li>
3825 <li>Shading features by score or associated description</li>
3826 <li>Subdivide alignment and groups based on identity of
3827 selected subsequence (Make Groups from Selection).</li>
3828 <li>New hide/show options including Shift+Control+H to
3829 hide everything but the currently selected region.</li>
3830 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3831 </ul> <em>Application</em>
3833 <li>Fetch DB References capabilities and UI expanded to
3834 support retrieval from DAS sequence sources</li>
3835 <li>Local DAS Sequence sources can be added via the
3836 command line or via the Add local source dialog box.</li>
3837 <li>DAS Dbref and DbxRef feature types are parsed as
3838 database references and protein_name is parsed as
3839 description line (BioSapiens terms).</li>
3840 <li>Enable or disable non-positional feature and database
3841 references in sequence ID tooltip from View menu in
3843 <!-- <li>New hidden columns and rows and representatives capabilities
3844 in annotations file (in progress - not yet fully implemented)</li> -->
3845 <li>Group-associated consensus, sequence logos and
3846 conservation plots</li>
3847 <li>Symbol distributions for each column can be exported
3848 and visualized as sequence logos</li>
3849 <li>Optionally scale multi-character column labels to fit
3850 within each column of annotation row<!-- todo for applet -->
3852 <li>Optional automatic sort of associated alignment view
3853 when a new tree is opened.</li>
3854 <li>Jalview Java Console</li>
3855 <li>Better placement of desktop window when moving
3856 between different screens.</li>
3857 <li>New preference items for sequence ID tooltip and
3858 consensus annotation</li>
3859 <li>Client to submit sequences and IDs to Envision2
3861 <li><em>Vamsas Capabilities</em>
3863 <li>Improved VAMSAS synchronization (Jalview archive
3864 used to preserve views, structures, and tree display
3866 <li>Import of vamsas documents from disk or URL via
3868 <li>Sharing of selected regions between views and
3869 with other VAMSAS applications (Experimental feature!)</li>
3870 <li>Updated API to VAMSAS version 0.2</li>
3872 </ul> <em>Applet</em>
3874 <li>Middle button resizes annotation row height</li>
3877 <li>sortByTree (true/false) - automatically sort the
3878 associated alignment view by the tree when a new tree is
3880 <li>showTreeBootstraps (true/false) - show or hide
3881 branch bootstraps (default is to show them if available)</li>
3882 <li>showTreeDistances (true/false) - show or hide
3883 branch lengths (default is to show them if available)</li>
3884 <li>showUnlinkedTreeNodes (true/false) - indicate if
3885 unassociated nodes should be highlighted in the tree
3887 <li>heightScale and widthScale (1.0 or more) -
3888 increase the height or width of a cell in the alignment
3889 grid relative to the current font size.</li>
3892 <li>Non-positional features displayed in sequence ID
3894 </ul> <em>Other</em>
3896 <li>Features format: graduated colour definitions and
3897 specification of feature scores</li>
3898 <li>Alignment Annotations format: new keywords for group
3899 associated annotation (GROUP_REF) and annotation row display
3900 properties (ROW_PROPERTIES)</li>
3901 <li>XML formats extended to support graduated feature
3902 colourschemes, group associated annotation, and profile
3903 visualization settings.</li></td>
3906 <li>Source field in GFF files parsed as feature source
3907 rather than description</li>
3908 <li>Non-positional features are now included in sequence
3909 feature and gff files (controlled via non-positional feature
3910 visibility in tooltip).</li>
3911 <li>URL links generated for all feature links (bugfix)</li>
3912 <li>Added URL embedding instructions to features file
3914 <li>Codons containing ambiguous nucleotides translated as
3915 'X' in peptide product</li>
3916 <li>Match case switch in find dialog box works for both
3917 sequence ID and sequence string and query strings do not
3918 have to be in upper case to match case-insensitively.</li>
3919 <li>AMSA files only contain first column of
3920 multi-character column annotation labels</li>
3921 <li>Jalview Annotation File generation/parsing consistent
3922 with documentation (e.g. Stockholm annotation can be
3923 exported and re-imported)</li>
3924 <li>PDB files without embedded PDB IDs given a friendly
3926 <li>Find incrementally searches ID string matches as well
3927 as subsequence matches, and correctly reports total number
3931 <li>Better handling of exceptions during sequence
3933 <li>Dasobert generated non-positional feature URL
3934 link text excludes the start_end suffix</li>
3935 <li>DAS feature and source retrieval buttons disabled
3936 when fetch or registry operations in progress.</li>
3937 <li>PDB files retrieved from URLs are cached properly</li>
3938 <li>Sequence description lines properly shared via
3940 <li>Sequence fetcher fetches multiple records for all
3942 <li>Ensured that command line das feature retrieval
3943 completes before alignment figures are generated.</li>
3944 <li>Reduced time taken when opening file browser for
3946 <li>isAligned check prior to calculating tree, PCA or
3947 submitting an MSA to JNet now excludes hidden sequences.</li>
3948 <li>User defined group colours properly recovered
3949 from Jalview projects.</li>
3958 <div align="center">
3959 <strong>2.4.0.b2</strong><br> 28/10/2009
3964 <li>Experimental support for google analytics usage
3966 <li>Jalview privacy settings (user preferences and docs).</li>
3971 <li>Race condition in applet preventing startup in
3973 <li>Exception when feature created from selection beyond
3974 length of sequence.</li>
3975 <li>Allow synthetic PDB files to be imported gracefully</li>
3976 <li>Sequence associated annotation rows associate with
3977 all sequences with a given id</li>
3978 <li>Find function matches case-insensitively for sequence
3979 ID string searches</li>
3980 <li>Non-standard characters do not cause pairwise
3981 alignment to fail with exception</li>
3982 </ul> <em>Application Issues</em>
3984 <li>Sequences are now validated against EMBL database</li>
3985 <li>Sequence fetcher fetches multiple records for all
3987 </ul> <em>InstallAnywhere Issues</em>
3989 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3990 issue with installAnywhere mechanism)</li>
3991 <li>Command line launching of JARs from InstallAnywhere
3992 version (java class versioning error fixed)</li>
3999 <div align="center">
4000 <strong>2.4</strong><br> 27/8/2008
4003 <td><em>User Interface</em>
4005 <li>Linked highlighting of codon and amino acid from
4006 translation and protein products</li>
4007 <li>Linked highlighting of structure associated with
4008 residue mapping to codon position</li>
4009 <li>Sequence Fetcher provides example accession numbers
4010 and 'clear' button</li>
4011 <li>MemoryMonitor added as an option under Desktop's
4013 <li>Extract score function to parse whitespace separated
4014 numeric data in description line</li>
4015 <li>Column labels in alignment annotation can be centred.</li>
4016 <li>Tooltip for sequence associated annotation give name
4018 </ul> <em>Web Services and URL fetching</em>
4020 <li>JPred3 web service</li>
4021 <li>Prototype sequence search client (no public services
4023 <li>Fetch either seed alignment or full alignment from
4025 <li>URL Links created for matching database cross
4026 references as well as sequence ID</li>
4027 <li>URL Links can be created using regular-expressions</li>
4028 </ul> <em>Sequence Database Connectivity</em>
4030 <li>Retrieval of cross-referenced sequences from other
4032 <li>Generalised database reference retrieval and
4033 validation to all fetchable databases</li>
4034 <li>Fetch sequences from DAS sources supporting the
4035 sequence command</li>
4036 </ul> <em>Import and Export</em>
4037 <li>export annotation rows as CSV for spreadsheet import</li>
4038 <li>Jalview projects record alignment dataset associations,
4039 EMBL products, and cDNA sequence mappings</li>
4040 <li>Sequence Group colour can be specified in Annotation
4042 <li>Ad-hoc colouring of group in Annotation File using RGB
4043 triplet as name of colourscheme</li>
4044 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4046 <li>treenode binding for VAMSAS tree exchange</li>
4047 <li>local editing and update of sequences in VAMSAS
4048 alignments (experimental)</li>
4049 <li>Create new or select existing session to join</li>
4050 <li>load and save of vamsas documents</li>
4051 </ul> <em>Application command line</em>
4053 <li>-tree parameter to open trees (introduced for passing
4055 <li>-fetchfrom command line argument to specify nicknames
4056 of DAS servers to query for alignment features</li>
4057 <li>-dasserver command line argument to add new servers
4058 that are also automatically queried for features</li>
4059 <li>-groovy command line argument executes a given groovy
4060 script after all input data has been loaded and parsed</li>
4061 </ul> <em>Applet-Application data exchange</em>
4063 <li>Trees passed as applet parameters can be passed to
4064 application (when using "View in full
4065 application")</li>
4066 </ul> <em>Applet Parameters</em>
4068 <li>feature group display control parameter</li>
4069 <li>debug parameter</li>
4070 <li>showbutton parameter</li>
4071 </ul> <em>Applet API methods</em>
4073 <li>newView public method</li>
4074 <li>Window (current view) specific get/set public methods</li>
4075 <li>Feature display control methods</li>
4076 <li>get list of currently selected sequences</li>
4077 </ul> <em>New Jalview distribution features</em>
4079 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4080 <li>RELEASE file gives build properties for the latest
4081 Jalview release.</li>
4082 <li>Java 1.1 Applet build made easier and donotobfuscate
4083 property controls execution of obfuscator</li>
4084 <li>Build target for generating source distribution</li>
4085 <li>Debug flag for javacc</li>
4086 <li>.jalview_properties file is documented (slightly) in
4087 jalview.bin.Cache</li>
4088 <li>Continuous Build Integration for stable and
4089 development version of Application, Applet and source
4094 <li>selected region output includes visible annotations
4095 (for certain formats)</li>
4096 <li>edit label/displaychar contains existing label/char
4098 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4099 <li>shorter peptide product names from EMBL records</li>
4100 <li>Newick string generator makes compact representations</li>
4101 <li>bootstrap values parsed correctly for tree files with
4103 <li>pathological filechooser bug avoided by not allowing
4104 filenames containing a ':'</li>
4105 <li>Fixed exception when parsing GFF files containing
4106 global sequence features</li>
4107 <li>Alignment datasets are finalized only when number of
4108 references from alignment sequences goes to zero</li>
4109 <li>Close of tree branch colour box without colour
4110 selection causes cascading exceptions</li>
4111 <li>occasional negative imgwidth exceptions</li>
4112 <li>better reporting of non-fatal warnings to user when
4113 file parsing fails.</li>
4114 <li>Save works when Jalview project is default format</li>
4115 <li>Save as dialog opened if current alignment format is
4116 not a valid output format</li>
4117 <li>UniProt canonical names introduced for both das and
4119 <li>Histidine should be midblue (not pink!) in Zappo</li>
4120 <li>error messages passed up and output when data read
4122 <li>edit undo recovers previous dataset sequence when
4123 sequence is edited</li>
4124 <li>allow PDB files without pdb ID HEADER lines (like
4125 those generated by MODELLER) to be read in properly</li>
4126 <li>allow reading of JPred concise files as a normal
4128 <li>Stockholm annotation parsing and alignment properties
4129 import fixed for PFAM records</li>
4130 <li>Structure view windows have correct name in Desktop
4132 <li>annotation consisting of sequence associated scores
4133 can be read and written correctly to annotation file</li>
4134 <li>Aligned cDNA translation to aligned peptide works
4136 <li>Fixed display of hidden sequence markers and
4137 non-italic font for representatives in Applet</li>
4138 <li>Applet Menus are always embedded in applet window on
4140 <li>Newly shown features appear at top of stack (in
4142 <li>Annotations added via parameter not drawn properly
4143 due to null pointer exceptions</li>
4144 <li>Secondary structure lines are drawn starting from
4145 first column of alignment</li>
4146 <li>UniProt XML import updated for new schema release in
4148 <li>Sequence feature to sequence ID match for Features
4149 file is case-insensitive</li>
4150 <li>Sequence features read from Features file appended to
4151 all sequences with matching IDs</li>
4152 <li>PDB structure coloured correctly for associated views
4153 containing a sub-sequence</li>
4154 <li>PDB files can be retrieved by applet from Jar files</li>
4155 <li>feature and annotation file applet parameters
4156 referring to different directories are retrieved correctly</li>
4157 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4158 <li>Fixed application hang whilst waiting for
4159 splash-screen version check to complete</li>
4160 <li>Applet properly URLencodes input parameter values
4161 when passing them to the launchApp service</li>
4162 <li>display name and local features preserved in results
4163 retrieved from web service</li>
4164 <li>Visual delay indication for sequence retrieval and
4165 sequence fetcher initialisation</li>
4166 <li>updated Application to use DAS 1.53e version of
4167 dasobert DAS client</li>
4168 <li>Re-instated Full AMSA support and .amsa file
4170 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4178 <div align="center">
4179 <strong>2.3</strong><br> 9/5/07
4184 <li>Jmol 11.0.2 integration</li>
4185 <li>PDB views stored in Jalview XML files</li>
4186 <li>Slide sequences</li>
4187 <li>Edit sequence in place</li>
4188 <li>EMBL CDS features</li>
4189 <li>DAS Feature mapping</li>
4190 <li>Feature ordering</li>
4191 <li>Alignment Properties</li>
4192 <li>Annotation Scores</li>
4193 <li>Sort by scores</li>
4194 <li>Feature/annotation editing in applet</li>
4199 <li>Headless state operation in 2.2.1</li>
4200 <li>Incorrect and unstable DNA pairwise alignment</li>
4201 <li>Cut and paste of sequences with annotation</li>
4202 <li>Feature group display state in XML</li>
4203 <li>Feature ordering in XML</li>
4204 <li>blc file iteration selection using filename # suffix</li>
4205 <li>Stockholm alignment properties</li>
4206 <li>Stockhom alignment secondary structure annotation</li>
4207 <li>2.2.1 applet had no feature transparency</li>
4208 <li>Number pad keys can be used in cursor mode</li>
4209 <li>Structure Viewer mirror image resolved</li>
4216 <div align="center">
4217 <strong>2.2.1</strong><br> 12/2/07
4222 <li>Non standard characters can be read and displayed
4223 <li>Annotations/Features can be imported/exported to the
4225 <li>Applet allows editing of sequence/annotation/group
4226 name & description
4227 <li>Preference setting to display sequence name in
4229 <li>Annotation file format extended to allow
4230 Sequence_groups to be defined
4231 <li>Default opening of alignment overview panel can be
4232 specified in preferences
4233 <li>PDB residue numbering annotation added to associated
4239 <li>Applet crash under certain Linux OS with Java 1.6
4241 <li>Annotation file export / import bugs fixed
4242 <li>PNG / EPS image output bugs fixed
4248 <div align="center">
4249 <strong>2.2</strong><br> 27/11/06
4254 <li>Multiple views on alignment
4255 <li>Sequence feature editing
4256 <li>"Reload" alignment
4257 <li>"Save" to current filename
4258 <li>Background dependent text colour
4259 <li>Right align sequence ids
4260 <li>User-defined lower case residue colours
4263 <li>Menu item accelerator keys
4264 <li>Control-V pastes to current alignment
4265 <li>Cancel button for DAS Feature Fetching
4266 <li>PCA and PDB Viewers zoom via mouse roller
4267 <li>User-defined sub-tree colours and sub-tree selection
4269 <li>'New Window' button on the 'Output to Text box'
4274 <li>New memory efficient Undo/Redo System
4275 <li>Optimised symbol lookups and conservation/consensus
4277 <li>Region Conservation/Consensus recalculated after
4279 <li>Fixed Remove Empty Columns Bug (empty columns at end
4281 <li>Slowed DAS Feature Fetching for increased robustness.
4283 <li>Made angle brackets in ASCII feature descriptions
4285 <li>Re-instated Zoom function for PCA
4286 <li>Sequence descriptions conserved in web service
4288 <li>UniProt ID discoverer uses any word separated by
4290 <li>WsDbFetch query/result association resolved
4291 <li>Tree leaf to sequence mapping improved
4292 <li>Smooth fonts switch moved to FontChooser dialog box.
4299 <div align="center">
4300 <strong>2.1.1</strong><br> 12/9/06
4305 <li>Copy consensus sequence to clipboard</li>
4310 <li>Image output - rightmost residues are rendered if
4311 sequence id panel has been resized</li>
4312 <li>Image output - all offscreen group boundaries are
4314 <li>Annotation files with sequence references - all
4315 elements in file are relative to sequence position</li>
4316 <li>Mac Applet users can use Alt key for group editing</li>
4322 <div align="center">
4323 <strong>2.1</strong><br> 22/8/06
4328 <li>MAFFT Multiple Alignment in default Web Service list</li>
4329 <li>DAS Feature fetching</li>
4330 <li>Hide sequences and columns</li>
4331 <li>Export Annotations and Features</li>
4332 <li>GFF file reading / writing</li>
4333 <li>Associate structures with sequences from local PDB
4335 <li>Add sequences to exisiting alignment</li>
4336 <li>Recently opened files / URL lists</li>
4337 <li>Applet can launch the full application</li>
4338 <li>Applet has transparency for features (Java 1.2
4340 <li>Applet has user defined colours parameter</li>
4341 <li>Applet can load sequences from parameter
4342 "sequence<em>x</em>"
4348 <li>Redundancy Panel reinstalled in the Applet</li>
4349 <li>Monospaced font - EPS / rescaling bug fixed</li>
4350 <li>Annotation files with sequence references bug fixed</li>
4356 <div align="center">
4357 <strong>2.08.1</strong><br> 2/5/06
4362 <li>Change case of selected region from Popup menu</li>
4363 <li>Choose to match case when searching</li>
4364 <li>Middle mouse button and mouse movement can compress /
4365 expand the visible width and height of the alignment</li>
4370 <li>Annotation Panel displays complete JNet results</li>
4376 <div align="center">
4377 <strong>2.08b</strong><br> 18/4/06
4383 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4384 <li>Righthand label on wrapped alignments shows correct
4391 <div align="center">
4392 <strong>2.08</strong><br> 10/4/06
4397 <li>Editing can be locked to the selection area</li>
4398 <li>Keyboard editing</li>
4399 <li>Create sequence features from searches</li>
4400 <li>Precalculated annotations can be loaded onto
4402 <li>Features file allows grouping of features</li>
4403 <li>Annotation Colouring scheme added</li>
4404 <li>Smooth fonts off by default - Faster rendering</li>
4405 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4410 <li>Drag & Drop fixed on Linux</li>
4411 <li>Jalview Archive file faster to load/save, sequence
4412 descriptions saved.</li>
4418 <div align="center">
4419 <strong>2.07</strong><br> 12/12/05
4424 <li>PDB Structure Viewer enhanced</li>
4425 <li>Sequence Feature retrieval and display enhanced</li>
4426 <li>Choose to output sequence start-end after sequence
4427 name for file output</li>
4428 <li>Sequence Fetcher WSDBFetch@EBI</li>
4429 <li>Applet can read feature files, PDB files and can be
4430 used for HTML form input</li>
4435 <li>HTML output writes groups and features</li>
4436 <li>Group editing is Control and mouse click</li>
4437 <li>File IO bugs</li>
4443 <div align="center">
4444 <strong>2.06</strong><br> 28/9/05
4449 <li>View annotations in wrapped mode</li>
4450 <li>More options for PCA viewer</li>
4455 <li>GUI bugs resolved</li>
4456 <li>Runs with -nodisplay from command line</li>
4462 <div align="center">
4463 <strong>2.05b</strong><br> 15/9/05
4468 <li>Choose EPS export as lineart or text</li>
4469 <li>Jar files are executable</li>
4470 <li>Can read in Uracil - maps to unknown residue</li>
4475 <li>Known OutOfMemory errors give warning message</li>
4476 <li>Overview window calculated more efficiently</li>
4477 <li>Several GUI bugs resolved</li>
4483 <div align="center">
4484 <strong>2.05</strong><br> 30/8/05
4489 <li>Edit and annotate in "Wrapped" view</li>
4494 <li>Several GUI bugs resolved</li>
4500 <div align="center">
4501 <strong>2.04</strong><br> 24/8/05
4506 <li>Hold down mouse wheel & scroll to change font
4512 <li>Improved JPred client reliability</li>
4513 <li>Improved loading of Jalview files</li>
4519 <div align="center">
4520 <strong>2.03</strong><br> 18/8/05
4525 <li>Set Proxy server name and port in preferences</li>
4526 <li>Multiple URL links from sequence ids</li>
4527 <li>User Defined Colours can have a scheme name and added
4529 <li>Choose to ignore gaps in consensus calculation</li>
4530 <li>Unix users can set default web browser</li>
4531 <li>Runs without GUI for batch processing</li>
4532 <li>Dynamically generated Web Service Menus</li>
4537 <li>InstallAnywhere download for Sparc Solaris</li>
4543 <div align="center">
4544 <strong>2.02</strong><br> 18/7/05
4550 <li>Copy & Paste order of sequences maintains
4551 alignment order.</li>
4557 <div align="center">
4558 <strong>2.01</strong><br> 12/7/05
4563 <li>Use delete key for deleting selection.</li>
4564 <li>Use Mouse wheel to scroll sequences.</li>
4565 <li>Help file updated to describe how to add alignment
4567 <li>Version and build date written to build properties
4569 <li>InstallAnywhere installation will check for updates
4570 at launch of Jalview.</li>
4575 <li>Delete gaps bug fixed.</li>
4576 <li>FileChooser sorts columns.</li>
4577 <li>Can remove groups one by one.</li>
4578 <li>Filechooser icons installed.</li>
4579 <li>Finder ignores return character when searching.
4580 Return key will initiate a search.<br>
4587 <div align="center">
4588 <strong>2.0</strong><br> 20/6/05
4593 <li>New codebase</li>