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>02/07/2019</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 -->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)
481 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
482 sequence's End is greater than its length
484 <li><strong>Bugs fixed for Java 11 Support (not
485 yet on general release)</strong>
488 <!-- JAL-3288 -->Menus work properly in split-screen
491 </ul> <em>New Known Defects</em>
493 <li><!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
496 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
497 regions of protein alignment.
500 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
501 is restored from a Jalview 2.11 project
504 <!-- JAL-3213 -->Alignment panel height can be too small after
508 <!-- JAL-3240 -->Display is incorrect after removing gapped
509 columns within hidden columns
512 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
513 window after dragging left to select columns to left of visible
517 <!-- JAL-2876 -->Features coloured according to their description
518 string and thresholded by score in earlier versions of Jalview are
519 not shown as thresholded features in 2.11. To workaround please
520 create a Score filter instead.
522 <li><!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
524 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
527 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
528 alignments with multiple views can close views unexpectedly
530 <li><strong>Java 11 Specific defects</strong>
533 <!-- JAL-3235 -->Jalview Properties file is not sorted alphabetically when saved</li>
541 <td width="60" nowrap>
543 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
546 <td><div align="left">
550 <!-- JAL-3101 -->Default memory for Jalview webstart and
551 InstallAnywhere increased to 1G.
554 <!-- JAL-247 -->Hidden sequence markers and representative
555 sequence bolding included when exporting alignment as EPS,
556 SVG, PNG or HTML. <em>Display is configured via the
557 Format menu, or for command-line use via a jalview
558 properties file.</em>
561 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
562 API and sequence data now imported as JSON.
565 <!-- JAL-3065 -->Change in recommended way of starting
566 Jalview via a Java command line: add jars in lib directory
567 to CLASSPATH, rather than via the deprecated java.ext.dirs
574 <!-- JAL-3047 -->Support added to execute test suite
575 instrumented with <a href="http://openclover.org/">Open
580 <td><div align="left">
584 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
585 row shown in Feredoxin Structure alignment view of example
589 <!-- JAL-2854 -->Annotation obscures sequences if lots of
590 annotation displayed.
593 <!-- JAL-3107 -->Group conservation/consensus not shown
594 for newly created group when 'Apply to all groups'
598 <!-- JAL-3087 -->Corrupted display when switching to
599 wrapped mode when sequence panel's vertical scrollbar is
603 <!-- JAL-3003 -->Alignment is black in exported EPS file
604 when sequences are selected in exported view.</em>
607 <!-- JAL-3059 -->Groups with different coloured borders
608 aren't rendered with correct colour.
611 <!-- JAL-3092 -->Jalview could hang when importing certain
612 types of knotted RNA secondary structure.
615 <!-- JAL-3095 -->Sequence highlight and selection in
616 trimmed VARNA 2D structure is incorrect for sequences that
620 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
621 annotation when columns are inserted into an alignment,
622 and when exporting as Stockholm flatfile.
625 <!-- JAL-3053 -->Jalview annotation rows containing upper
626 and lower-case 'E' and 'H' do not automatically get
627 treated as RNA secondary structure.
630 <!-- JAL-3106 -->.jvp should be used as default extension
631 (not .jar) when saving a jalview project file.
634 <!-- JAL-3105 -->Mac Users: closing a window correctly
635 transfers focus to previous window on OSX
638 <em>Java 10 Issues Resolved</em>
641 <!-- JAL-2988 -->OSX - Can't save new files via the File
642 or export menus by typing in a name into the Save dialog
646 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
647 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
648 'look and feel' which has improved compatibility with the
649 latest version of OSX.
656 <td width="60" nowrap>
658 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
659 <em>7/06/2018</em></strong>
662 <td><div align="left">
666 <!-- JAL-2920 -->Use HGVS nomenclature for variant
667 annotation retrieved from Uniprot
670 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
671 onto the Jalview Desktop
675 <td><div align="left">
679 <!-- JAL-3017 -->Cannot import features with multiple
680 variant elements (blocks import of some Uniprot records)
683 <!-- JAL-2997 -->Clustal files with sequence positions in
684 right-hand column parsed correctly
687 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
688 not alignment area in exported graphic
691 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
692 window has input focus
695 <!-- JAL-2992 -->Annotation panel set too high when
696 annotation added to view (Windows)
699 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
700 network connectivity is poor
703 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
704 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
705 the currently open URL and links from a page viewed in
706 Firefox or Chrome on Windows is now fully supported. If
707 you are using Edge, only links in the page can be
708 dragged, and with Internet Explorer, only the currently
709 open URL in the browser can be dropped onto Jalview.</em>
712 <em>New Known Defects</em>
714 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
719 <td width="60" nowrap>
721 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
724 <td><div align="left">
728 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
729 for disabling automatic superposition of multiple
730 structures and open structures in existing views
733 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
734 ID and annotation area margins can be click-dragged to
738 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
742 <!-- JAL-2759 -->Improved performance for large alignments
743 and lots of hidden columns
746 <!-- JAL-2593 -->Improved performance when rendering lots
747 of features (particularly when transparency is disabled)
750 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
751 exchange of Jalview features and Chimera attributes made
757 <td><div align="left">
760 <!-- JAL-2899 -->Structure and Overview aren't updated
761 when Colour By Annotation threshold slider is adjusted
764 <!-- JAL-2778 -->Slow redraw when Overview panel shown
765 overlapping alignment panel
768 <!-- JAL-2929 -->Overview doesn't show end of unpadded
772 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
773 improved: CDS not handled correctly if transcript has no
777 <!-- JAL-2321 -->Secondary structure and temperature
778 factor annotation not added to sequence when local PDB
779 file associated with it by drag'n'drop or structure
783 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
784 dialog doesn't import PDB files dropped on an alignment
787 <!-- JAL-2666 -->Linked scrolling via protein horizontal
788 scroll bar doesn't work for some CDS/Protein views
791 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
792 Java 1.8u153 onwards and Java 1.9u4+.
795 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
796 columns in annotation row
799 <!-- JAL-2913 -->Preferences panel's ID Width control is not
800 honored in batch mode
803 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
804 for structures added to existing Jmol view
807 <!-- JAL-2223 -->'View Mappings' includes duplicate
808 entries after importing project with multiple views
811 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
812 protein sequences via SIFTS from associated PDB entries
813 with negative residue numbers or missing residues fails
816 <!-- JAL-2952 -->Exception when shading sequence with negative
817 Temperature Factor values from annotated PDB files (e.g.
818 as generated by CONSURF)
821 <!-- JAL-2920 -->Uniprot 'sequence variant' features
822 tooltip doesn't include a text description of mutation
825 <!-- JAL-2922 -->Invert displayed features very slow when
826 structure and/or overview windows are also shown
829 <!-- JAL-2954 -->Selecting columns from highlighted regions
830 very slow for alignments with large numbers of sequences
833 <!-- JAL-2925 -->Copy Consensus fails for group consensus
834 with 'StringIndexOutOfBounds'
837 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
838 platforms running Java 10
841 <!-- JAL-2960 -->Adding a structure to existing structure
842 view appears to do nothing because the view is hidden behind the alignment view
848 <!-- JAL-2926 -->Copy consensus sequence option in applet
849 should copy the group consensus when popup is opened on it
855 <!-- JAL-2913 -->Fixed ID width preference is not respected
858 <em>New Known Defects</em>
861 <!-- JAL-2973 --> Exceptions occasionally raised when
862 editing a large alignment and overview is displayed
865 <!-- JAL-2974 -->'Overview updating' progress bar is shown
866 repeatedly after a series of edits even when the overview
867 is no longer reflecting updates
870 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
871 structures for protein subsequence (if 'Trim Retrieved
872 Sequences' enabled) or Ensembl isoforms (Workaround in
873 2.10.4 is to fail back to N&W mapping)
876 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
877 option gives blank output
884 <td width="60" nowrap>
886 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
889 <td><div align="left">
890 <ul><li>Updated Certum Codesigning Certificate
891 (Valid till 30th November 2018)</li></ul></div></td>
892 <td><div align="left">
895 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
896 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
897 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
898 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
899 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
900 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
901 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
907 <td width="60" nowrap>
909 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
912 <td><div align="left">
916 <!-- JAL-2446 -->Faster and more efficient management and
917 rendering of sequence features
920 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
921 429 rate limit request hander
924 <!-- JAL-2773 -->Structure views don't get updated unless
925 their colours have changed
928 <!-- JAL-2495 -->All linked sequences are highlighted for
929 a structure mousover (Jmol) or selection (Chimera)
932 <!-- JAL-2790 -->'Cancel' button in progress bar for
933 JABAWS AACon, RNAAliFold and Disorder prediction jobs
936 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
937 view from Ensembl locus cross-references
940 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
944 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
945 feature can be disabled
948 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
949 PDB easier retrieval of sequences for lists of IDs
952 <!-- JAL-2758 -->Short names for sequences retrieved from
958 <li>Groovy interpreter updated to 2.4.12</li>
959 <li>Example groovy script for generating a matrix of
960 percent identity scores for current alignment.</li>
962 <em>Testing and Deployment</em>
965 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
969 <td><div align="left">
973 <!-- JAL-2643 -->Pressing tab after updating the colour
974 threshold text field doesn't trigger an update to the
978 <!-- JAL-2682 -->Race condition when parsing sequence ID
982 <!-- JAL-2608 -->Overview windows are also closed when
983 alignment window is closed
986 <!-- JAL-2548 -->Export of features doesn't always respect
990 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
991 takes a long time in Cursor mode
997 <!-- JAL-2777 -->Structures with whitespace chainCode
998 cannot be viewed in Chimera
1001 <!-- JAL-2728 -->Protein annotation panel too high in
1005 <!-- JAL-2757 -->Can't edit the query after the server
1006 error warning icon is shown in Uniprot and PDB Free Text
1010 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1013 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1016 <!-- JAL-2739 -->Hidden column marker in last column not
1017 rendered when switching back from Wrapped to normal view
1020 <!-- JAL-2768 -->Annotation display corrupted when
1021 scrolling right in unwapped alignment view
1024 <!-- JAL-2542 -->Existing features on subsequence
1025 incorrectly relocated when full sequence retrieved from
1029 <!-- JAL-2733 -->Last reported memory still shown when
1030 Desktop->Show Memory is unticked (OSX only)
1033 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1034 features of same type and group to be selected for
1038 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1039 alignments when hidden columns are present
1042 <!-- JAL-2392 -->Jalview freezes when loading and
1043 displaying several structures
1046 <!-- JAL-2732 -->Black outlines left after resizing or
1050 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1051 within the Jalview desktop on OSX
1054 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1055 when in wrapped alignment mode
1058 <!-- JAL-2636 -->Scale mark not shown when close to right
1059 hand end of alignment
1062 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1063 each selected sequence do not have correct start/end
1067 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1068 after canceling the Alignment Window's Font dialog
1071 <!-- JAL-2036 -->Show cross-references not enabled after
1072 restoring project until a new view is created
1075 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1076 URL links appears when only default EMBL-EBI link is
1077 configured (since 2.10.2b2)
1080 <!-- JAL-2775 -->Overview redraws whole window when box
1081 position is adjusted
1084 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1085 in a multi-chain structure when viewing alignment
1086 involving more than one chain (since 2.10)
1089 <!-- JAL-2811 -->Double residue highlights in cursor mode
1090 if new selection moves alignment window
1093 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1094 arrow key in cursor mode to pass hidden column marker
1097 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1098 that produces correctly annotated transcripts and products
1101 <!-- JAL-2776 -->Toggling a feature group after first time
1102 doesn't update associated structure view
1105 <em>Applet</em><br />
1108 <!-- JAL-2687 -->Concurrent modification exception when
1109 closing alignment panel
1112 <em>BioJSON</em><br />
1115 <!-- JAL-2546 -->BioJSON export does not preserve
1116 non-positional features
1119 <em>New Known Issues</em>
1122 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1123 sequence features correctly (for many previous versions of
1127 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1128 using cursor in wrapped panel other than top
1131 <!-- JAL-2791 -->Select columns containing feature ignores
1132 graduated colour threshold
1135 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1136 always preserve numbering and sequence features
1139 <em>Known Java 9 Issues</em>
1142 <!-- JAL-2902 -->Groovy Console very slow to open and is
1143 not responsive when entering characters (Webstart, Java
1150 <td width="60" nowrap>
1151 <div align="center">
1152 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1153 <em>2/10/2017</em></strong>
1156 <td><div align="left">
1157 <em>New features in Jalview Desktop</em>
1160 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1162 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1166 <td><div align="left">
1170 <td width="60" nowrap>
1171 <div align="center">
1172 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1173 <em>7/9/2017</em></strong>
1176 <td><div align="left">
1180 <!-- JAL-2588 -->Show gaps in overview window by colouring
1181 in grey (sequences used to be coloured grey, and gaps were
1185 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1189 <!-- JAL-2587 -->Overview updates immediately on increase
1190 in size and progress bar shown as higher resolution
1191 overview is recalculated
1196 <td><div align="left">
1200 <!-- JAL-2664 -->Overview window redraws every hidden
1201 column region row by row
1204 <!-- JAL-2681 -->duplicate protein sequences shown after
1205 retrieving Ensembl crossrefs for sequences from Uniprot
1208 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1209 format setting is unticked
1212 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1213 if group has show boxes format setting unticked
1216 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1217 autoscrolling whilst dragging current selection group to
1218 include sequences and columns not currently displayed
1221 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1222 assemblies are imported via CIF file
1225 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1226 displayed when threshold or conservation colouring is also
1230 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1234 <!-- JAL-2673 -->Jalview continues to scroll after
1235 dragging a selected region off the visible region of the
1239 <!-- JAL-2724 -->Cannot apply annotation based
1240 colourscheme to all groups in a view
1243 <!-- JAL-2511 -->IDs don't line up with sequences
1244 initially after font size change using the Font chooser or
1251 <td width="60" nowrap>
1252 <div align="center">
1253 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1256 <td><div align="left">
1257 <em>Calculations</em>
1261 <!-- JAL-1933 -->Occupancy annotation row shows number of
1262 ungapped positions in each column of the alignment.
1265 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1266 a calculation dialog box
1269 <!-- JAL-2379 -->Revised implementation of PCA for speed
1270 and memory efficiency (~30x faster)
1273 <!-- JAL-2403 -->Revised implementation of sequence
1274 similarity scores as used by Tree, PCA, Shading Consensus
1275 and other calculations
1278 <!-- JAL-2416 -->Score matrices are stored as resource
1279 files within the Jalview codebase
1282 <!-- JAL-2500 -->Trees computed on Sequence Feature
1283 Similarity may have different topology due to increased
1290 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1291 model for alignments and groups
1294 <!-- JAL-384 -->Custom shading schemes created via groovy
1301 <!-- JAL-2526 -->Efficiency improvements for interacting
1302 with alignment and overview windows
1305 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1309 <!-- JAL-2388 -->Hidden columns and sequences can be
1313 <!-- JAL-2611 -->Click-drag in visible area allows fine
1314 adjustment of visible position
1318 <em>Data import/export</em>
1321 <!-- JAL-2535 -->Posterior probability annotation from
1322 Stockholm files imported as sequence associated annotation
1325 <!-- JAL-2507 -->More robust per-sequence positional
1326 annotation input/output via stockholm flatfile
1329 <!-- JAL-2533 -->Sequence names don't include file
1330 extension when importing structure files without embedded
1331 names or PDB accessions
1334 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1335 format sequence substitution matrices
1338 <em>User Interface</em>
1341 <!-- JAL-2447 --> Experimental Features Checkbox in
1342 Desktop's Tools menu to hide or show untested features in
1346 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1347 via Overview or sequence motif search operations
1350 <!-- JAL-2547 -->Amend sequence features dialog box can be
1351 opened by double clicking gaps within sequence feature
1355 <!-- JAL-1476 -->Status bar message shown when not enough
1356 aligned positions were available to create a 3D structure
1360 <em>3D Structure</em>
1363 <!-- JAL-2430 -->Hidden regions in alignment views are not
1364 coloured in linked structure views
1367 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1368 file-based command exchange
1371 <!-- JAL-2375 -->Structure chooser automatically shows
1372 Cached Structures rather than querying the PDBe if
1373 structures are already available for sequences
1376 <!-- JAL-2520 -->Structures imported via URL are cached in
1377 the Jalview project rather than downloaded again when the
1378 project is reopened.
1381 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1382 to transfer Chimera's structure attributes as Jalview
1383 features, and vice-versa (<strong>Experimental
1387 <em>Web Services</em>
1390 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1393 <!-- JAL-2335 -->Filter non-standard amino acids and
1394 nucleotides when submitting to AACon and other MSA
1398 <!-- JAL-2316, -->URLs for viewing database
1399 cross-references provided by identifiers.org and the
1400 EMBL-EBI's MIRIAM DB
1407 <!-- JAL-2344 -->FileFormatI interface for describing and
1408 identifying file formats (instead of String constants)
1411 <!-- JAL-2228 -->FeatureCounter script refactored for
1412 efficiency when counting all displayed features (not
1413 backwards compatible with 2.10.1)
1416 <em>Example files</em>
1419 <!-- JAL-2631 -->Graduated feature colour style example
1420 included in the example feature file
1423 <em>Documentation</em>
1426 <!-- JAL-2339 -->Release notes reformatted for readability
1427 with the built-in Java help viewer
1430 <!-- JAL-1644 -->Find documentation updated with 'search
1431 sequence description' option
1437 <!-- JAL-2485, -->External service integration tests for
1438 Uniprot REST Free Text Search Client
1441 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1444 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1449 <td><div align="left">
1450 <em>Calculations</em>
1453 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1454 matrix - C->R should be '-3'<br />Old matrix restored
1455 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1457 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1458 Jalview's treatment of gaps in PCA and substitution matrix
1459 based Tree calculations.<br /> <br />In earlier versions
1460 of Jalview, gaps matching gaps were penalised, and gaps
1461 matching non-gaps penalised even more. In the PCA
1462 calculation, gaps were actually treated as non-gaps - so
1463 different costs were applied, which meant Jalview's PCAs
1464 were different to those produced by SeqSpace.<br />Jalview
1465 now treats gaps in the same way as SeqSpace (ie it scores
1466 them as 0). <br /> <br />Enter the following in the
1467 Groovy console to restore pre-2.10.2 behaviour:<br />
1468 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1469 // for 2.10.1 mode <br />
1470 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1471 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1472 these settings will affect all subsequent tree and PCA
1473 calculations (not recommended)</em></li>
1475 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1476 scaling of branch lengths for trees computed using
1477 Sequence Feature Similarity.
1480 <!-- JAL-2377 -->PCA calculation could hang when
1481 generating output report when working with highly
1482 redundant alignments
1485 <!-- JAL-2544 --> Sort by features includes features to
1486 right of selected region when gaps present on right-hand
1490 <em>User Interface</em>
1493 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1494 doesn't reselect a specific sequence's associated
1495 annotation after it was used for colouring a view
1498 <!-- JAL-2419 -->Current selection lost if popup menu
1499 opened on a region of alignment without groups
1502 <!-- JAL-2374 -->Popup menu not always shown for regions
1503 of an alignment with overlapping groups
1506 <!-- JAL-2310 -->Finder double counts if both a sequence's
1507 name and description match
1510 <!-- JAL-2370 -->Hiding column selection containing two
1511 hidden regions results in incorrect hidden regions
1514 <!-- JAL-2386 -->'Apply to all groups' setting when
1515 changing colour does not apply Conservation slider value
1519 <!-- JAL-2373 -->Percentage identity and conservation menu
1520 items do not show a tick or allow shading to be disabled
1523 <!-- JAL-2385 -->Conservation shading or PID threshold
1524 lost when base colourscheme changed if slider not visible
1527 <!-- JAL-2547 -->Sequence features shown in tooltip for
1528 gaps before start of features
1531 <!-- JAL-2623 -->Graduated feature colour threshold not
1532 restored to UI when feature colour is edited
1535 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1536 a time when scrolling vertically in wrapped mode.
1539 <!-- JAL-2630 -->Structure and alignment overview update
1540 as graduate feature colour settings are modified via the
1544 <!-- JAL-2034 -->Overview window doesn't always update
1545 when a group defined on the alignment is resized
1548 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1549 wrapped view result in positional status updates
1553 <!-- JAL-2563 -->Status bar doesn't show position for
1554 ambiguous amino acid and nucleotide symbols
1557 <!-- JAL-2602 -->Copy consensus sequence failed if
1558 alignment included gapped columns
1561 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1562 widgets don't permanently disappear
1565 <!-- JAL-2503 -->Cannot select or filter quantitative
1566 annotation that are shown only as column labels (e.g.
1567 T-Coffee column reliability scores)
1570 <!-- JAL-2594 -->Exception thrown if trying to create a
1571 sequence feature on gaps only
1574 <!-- JAL-2504 -->Features created with 'New feature'
1575 button from a Find inherit previously defined feature type
1576 rather than the Find query string
1579 <!-- JAL-2423 -->incorrect title in output window when
1580 exporting tree calculated in Jalview
1583 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1584 and then revealing them reorders sequences on the
1588 <!-- JAL-964 -->Group panel in sequence feature settings
1589 doesn't update to reflect available set of groups after
1590 interactively adding or modifying features
1593 <!-- JAL-2225 -->Sequence Database chooser unusable on
1597 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1598 only excluded gaps in current sequence and ignored
1605 <!-- JAL-2421 -->Overview window visible region moves
1606 erratically when hidden rows or columns are present
1609 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1610 Structure Viewer's colour menu don't correspond to
1614 <!-- JAL-2405 -->Protein specific colours only offered in
1615 colour and group colour menu for protein alignments
1618 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1619 reflect currently selected view or group's shading
1623 <!-- JAL-2624 -->Feature colour thresholds not respected
1624 when rendered on overview and structures when opacity at
1628 <!-- JAL-2589 -->User defined gap colour not shown in
1629 overview when features overlaid on alignment
1632 <!-- JAL-2567 -->Feature settings for different views not
1633 recovered correctly from Jalview project file
1636 <!-- JAL-2256 -->Feature colours in overview when first opened
1637 (automatically via preferences) are different to the main
1641 <em>Data import/export</em>
1644 <!-- JAL-2576 -->Very large alignments take a long time to
1648 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1649 added after a sequence was imported are not written to
1653 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1654 when importing RNA secondary structure via Stockholm
1657 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1658 not shown in correct direction for simple pseudoknots
1661 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1662 with lightGray or darkGray via features file (but can
1666 <!-- JAL-2383 -->Above PID colour threshold not recovered
1667 when alignment view imported from project
1670 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1671 structure and sequences extracted from structure files
1672 imported via URL and viewed in Jmol
1675 <!-- JAL-2520 -->Structures loaded via URL are saved in
1676 Jalview Projects rather than fetched via URL again when
1677 the project is loaded and the structure viewed
1680 <em>Web Services</em>
1683 <!-- JAL-2519 -->EnsemblGenomes example failing after
1684 release of Ensembl v.88
1687 <!-- JAL-2366 -->Proxy server address and port always
1688 appear enabled in Preferences->Connections
1691 <!-- JAL-2461 -->DAS registry not found exceptions
1692 removed from console output
1695 <!-- JAL-2582 -->Cannot retrieve protein products from
1696 Ensembl by Peptide ID
1699 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1700 created from SIFTs, and spurious 'Couldn't open structure
1701 in Chimera' errors raised after April 2017 update (problem
1702 due to 'null' string rather than empty string used for
1703 residues with no corresponding PDB mapping).
1706 <em>Application UI</em>
1709 <!-- JAL-2361 -->User Defined Colours not added to Colour
1713 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1714 case' residues (button in colourscheme editor debugged and
1715 new documentation and tooltips added)
1718 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1719 doesn't restore group-specific text colour thresholds
1722 <!-- JAL-2243 -->Feature settings panel does not update as
1723 new features are added to alignment
1726 <!-- JAL-2532 -->Cancel in feature settings reverts
1727 changes to feature colours via the Amend features dialog
1730 <!-- JAL-2506 -->Null pointer exception when attempting to
1731 edit graduated feature colour via amend features dialog
1735 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1736 selection menu changes colours of alignment views
1739 <!-- JAL-2426 -->Spurious exceptions in console raised
1740 from alignment calculation workers after alignment has
1744 <!-- JAL-1608 -->Typo in selection popup menu - Create
1745 groups now 'Create Group'
1748 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1749 Create/Undefine group doesn't always work
1752 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1753 shown again after pressing 'Cancel'
1756 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1757 adjusts start position in wrap mode
1760 <!-- JAL-2563 -->Status bar doesn't show positions for
1761 ambiguous amino acids
1764 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1765 CDS/Protein view after CDS sequences added for aligned
1769 <!-- JAL-2592 -->User defined colourschemes called 'User
1770 Defined' don't appear in Colours menu
1776 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1777 score models doesn't always result in an updated PCA plot
1780 <!-- JAL-2442 -->Features not rendered as transparent on
1781 overview or linked structure view
1784 <!-- JAL-2372 -->Colour group by conservation doesn't
1788 <!-- JAL-2517 -->Hitting Cancel after applying
1789 user-defined colourscheme doesn't restore original
1796 <!-- JAL-2314 -->Unit test failure:
1797 jalview.ws.jabaws.RNAStructExportImport setup fails
1800 <!-- JAL-2307 -->Unit test failure:
1801 jalview.ws.sifts.SiftsClientTest due to compatibility
1802 problems with deep array comparison equality asserts in
1803 successive versions of TestNG
1806 <!-- JAL-2479 -->Relocated StructureChooserTest and
1807 ParameterUtilsTest Unit tests to Network suite
1810 <em>New Known Issues</em>
1813 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1814 phase after a sequence motif find operation
1817 <!-- JAL-2550 -->Importing annotation file with rows
1818 containing just upper and lower case letters are
1819 interpreted as WUSS RNA secondary structure symbols
1822 <!-- JAL-2590 -->Cannot load and display Newick trees
1823 reliably from eggnog Ortholog database
1826 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1827 containing features of type Highlight' when 'B' is pressed
1828 to mark columns containing highlighted regions.
1831 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1832 doesn't always add secondary structure annotation.
1837 <td width="60" nowrap>
1838 <div align="center">
1839 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1842 <td><div align="left">
1846 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1847 for all consensus calculations
1850 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1853 <li>Updated Jalview's Certum code signing certificate
1856 <em>Application</em>
1859 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1860 set of database cross-references, sorted alphabetically
1863 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1864 from database cross references. Users with custom links
1865 will receive a <a href="webServices/urllinks.html#warning">warning
1866 dialog</a> asking them to update their preferences.
1869 <!-- JAL-2287-->Cancel button and escape listener on
1870 dialog warning user about disconnecting Jalview from a
1874 <!-- JAL-2320-->Jalview's Chimera control window closes if
1875 the Chimera it is connected to is shut down
1878 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1879 columns menu item to mark columns containing highlighted
1880 regions (e.g. from structure selections or results of a
1884 <!-- JAL-2284-->Command line option for batch-generation
1885 of HTML pages rendering alignment data with the BioJS
1895 <!-- JAL-2286 -->Columns with more than one modal residue
1896 are not coloured or thresholded according to percent
1897 identity (first observed in Jalview 2.8.2)
1900 <!-- JAL-2301 -->Threonine incorrectly reported as not
1904 <!-- JAL-2318 -->Updates to documentation pages (above PID
1905 threshold, amino acid properties)
1908 <!-- JAL-2292 -->Lower case residues in sequences are not
1909 reported as mapped to residues in a structure file in the
1913 <!--JAL-2324 -->Identical features with non-numeric scores
1914 could be added multiple times to a sequence
1917 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1918 bond features shown as two highlighted residues rather
1919 than a range in linked structure views, and treated
1920 correctly when selecting and computing trees from features
1923 <!-- JAL-2281-->Custom URL links for database
1924 cross-references are matched to database name regardless
1929 <em>Application</em>
1932 <!-- JAL-2282-->Custom URL links for specific database
1933 names without regular expressions also offer links from
1937 <!-- JAL-2315-->Removing a single configured link in the
1938 URL links pane in Connections preferences doesn't actually
1939 update Jalview configuration
1942 <!-- JAL-2272-->CTRL-Click on a selected region to open
1943 the alignment area popup menu doesn't work on El-Capitan
1946 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1947 files with similarly named sequences if dropped onto the
1951 <!-- JAL-2312 -->Additional mappings are shown for PDB
1952 entries where more chains exist in the PDB accession than
1953 are reported in the SIFTS file
1956 <!-- JAL-2317-->Certain structures do not get mapped to
1957 the structure view when displayed with Chimera
1960 <!-- JAL-2317-->No chains shown in the Chimera view
1961 panel's View->Show Chains submenu
1964 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1965 work for wrapped alignment views
1968 <!--JAL-2197 -->Rename UI components for running JPred
1969 predictions from 'JNet' to 'JPred'
1972 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1973 corrupted when annotation panel vertical scroll is not at
1974 first annotation row
1977 <!--JAL-2332 -->Attempting to view structure for Hen
1978 lysozyme results in a PDB Client error dialog box
1981 <!-- JAL-2319 -->Structure View's mapping report switched
1982 ranges for PDB and sequence for SIFTS
1985 SIFTS 'Not_Observed' residues mapped to non-existant
1989 <!-- <em>New Known Issues</em>
1996 <td width="60" nowrap>
1997 <div align="center">
1998 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1999 <em>25/10/2016</em></strong>
2002 <td><em>Application</em>
2004 <li>3D Structure chooser opens with 'Cached structures'
2005 view if structures already loaded</li>
2006 <li>Progress bar reports models as they are loaded to
2007 structure views</li>
2013 <li>Colour by conservation always enabled and no tick
2014 shown in menu when BLOSUM or PID shading applied</li>
2015 <li>FER1_ARATH and FER2_ARATH labels were switched in
2016 example sequences/projects/trees</li>
2018 <em>Application</em>
2020 <li>Jalview projects with views of local PDB structure
2021 files saved on Windows cannot be opened on OSX</li>
2022 <li>Multiple structure views can be opened and superposed
2023 without timeout for structures with multiple models or
2024 multiple sequences in alignment</li>
2025 <li>Cannot import or associated local PDB files without a
2026 PDB ID HEADER line</li>
2027 <li>RMSD is not output in Jmol console when superposition
2029 <li>Drag and drop of URL from Browser fails for Linux and
2030 OSX versions earlier than El Capitan</li>
2031 <li>ENA client ignores invalid content from ENA server</li>
2032 <li>Exceptions are not raised in console when ENA client
2033 attempts to fetch non-existent IDs via Fetch DB Refs UI
2035 <li>Exceptions are not raised in console when a new view
2036 is created on the alignment</li>
2037 <li>OSX right-click fixed for group selections: CMD-click
2038 to insert/remove gaps in groups and CTRL-click to open group
2041 <em>Build and deployment</em>
2043 <li>URL link checker now copes with multi-line anchor
2046 <em>New Known Issues</em>
2048 <li>Drag and drop from URL links in browsers do not work
2055 <td width="60" nowrap>
2056 <div align="center">
2057 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2060 <td><em>General</em>
2063 <!-- JAL-2124 -->Updated Spanish translations.
2066 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2067 for importing structure data to Jalview. Enables mmCIF and
2071 <!-- JAL-192 --->Alignment ruler shows positions relative to
2075 <!-- JAL-2202 -->Position/residue shown in status bar when
2076 mousing over sequence associated annotation
2079 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2083 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2084 '()', canonical '[]' and invalid '{}' base pair populations
2088 <!-- JAL-2092 -->Feature settings popup menu options for
2089 showing or hiding columns containing a feature
2092 <!-- JAL-1557 -->Edit selected group by double clicking on
2093 group and sequence associated annotation labels
2096 <!-- JAL-2236 -->Sequence name added to annotation label in
2097 select/hide columns by annotation and colour by annotation
2101 </ul> <em>Application</em>
2104 <!-- JAL-2050-->Automatically hide introns when opening a
2105 gene/transcript view
2108 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2112 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2113 structure mappings with the EMBL-EBI PDBe SIFTS database
2116 <!-- JAL-2079 -->Updated download sites used for Rfam and
2117 Pfam sources to xfam.org
2120 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2123 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2124 over sequences in Jalview
2127 <!-- JAL-2027-->Support for reverse-complement coding
2128 regions in ENA and EMBL
2131 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2132 for record retrieval via ENA rest API
2135 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2139 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2140 groovy script execution
2143 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2144 alignment window's Calculate menu
2147 <!-- JAL-1812 -->Allow groovy scripts that call
2148 Jalview.getAlignFrames() to run in headless mode
2151 <!-- JAL-2068 -->Support for creating new alignment
2152 calculation workers from groovy scripts
2155 <!-- JAL-1369 --->Store/restore reference sequence in
2159 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2160 associations are now saved/restored from project
2163 <!-- JAL-1993 -->Database selection dialog always shown
2164 before sequence fetcher is opened
2167 <!-- JAL-2183 -->Double click on an entry in Jalview's
2168 database chooser opens a sequence fetcher
2171 <!-- JAL-1563 -->Free-text search client for UniProt using
2172 the UniProt REST API
2175 <!-- JAL-2168 -->-nonews command line parameter to prevent
2176 the news reader opening
2179 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2180 querying stored in preferences
2183 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2187 <!-- JAL-1977-->Tooltips shown on database chooser
2190 <!-- JAL-391 -->Reverse complement function in calculate
2191 menu for nucleotide sequences
2194 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2195 and feature counts preserves alignment ordering (and
2196 debugged for complex feature sets).
2199 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2200 viewing structures with Jalview 2.10
2203 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2204 genome, transcript CCDS and gene ids via the Ensembl and
2205 Ensembl Genomes REST API
2208 <!-- JAL-2049 -->Protein sequence variant annotation
2209 computed for 'sequence_variant' annotation on CDS regions
2213 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2217 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2218 Ref Fetcher fails to match, or otherwise updates sequence
2219 data from external database records.
2222 <!-- JAL-2154 -->Revised Jalview Project format for
2223 efficient recovery of sequence coding and alignment
2224 annotation relationships.
2226 </ul> <!-- <em>Applet</em>
2237 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2241 <!-- JAL-2018-->Export features in Jalview format (again)
2242 includes graduated colourschemes
2245 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2246 working with big alignments and lots of hidden columns
2249 <!-- JAL-2053-->Hidden column markers not always rendered
2250 at right of alignment window
2253 <!-- JAL-2067 -->Tidied up links in help file table of
2257 <!-- JAL-2072 -->Feature based tree calculation not shown
2261 <!-- JAL-2075 -->Hidden columns ignored during feature
2262 based tree calculation
2265 <!-- JAL-2065 -->Alignment view stops updating when show
2266 unconserved enabled for group on alignment
2269 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2273 <!-- JAL-2146 -->Alignment column in status incorrectly
2274 shown as "Sequence position" when mousing over
2278 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2279 hidden columns present
2282 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2283 user created annotation added to alignment
2286 <!-- JAL-1841 -->RNA Structure consensus only computed for
2287 '()' base pair annotation
2290 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2291 in zero scores for all base pairs in RNA Structure
2295 <!-- JAL-2174-->Extend selection with columns containing
2299 <!-- JAL-2275 -->Pfam format writer puts extra space at
2300 beginning of sequence
2303 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2307 <!-- JAL-2238 -->Cannot create groups on an alignment from
2308 from a tree when t-coffee scores are shown
2311 <!-- JAL-1836,1967 -->Cannot import and view PDB
2312 structures with chains containing negative resnums (4q4h)
2315 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2319 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2320 to Clustal, PIR and PileUp output
2323 <!-- JAL-2008 -->Reordering sequence features that are
2324 not visible causes alignment window to repaint
2327 <!-- JAL-2006 -->Threshold sliders don't work in
2328 graduated colour and colour by annotation row for e-value
2329 scores associated with features and annotation rows
2332 <!-- JAL-1797 -->amino acid physicochemical conservation
2333 calculation should be case independent
2336 <!-- JAL-2173 -->Remove annotation also updates hidden
2340 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2341 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2342 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2345 <!-- JAL-2065 -->Null pointer exceptions and redraw
2346 problems when reference sequence defined and 'show
2347 non-conserved' enabled
2350 <!-- JAL-1306 -->Quality and Conservation are now shown on
2351 load even when Consensus calculation is disabled
2354 <!-- JAL-1932 -->Remove right on penultimate column of
2355 alignment does nothing
2358 <em>Application</em>
2361 <!-- JAL-1552-->URLs and links can't be imported by
2362 drag'n'drop on OSX when launched via webstart (note - not
2363 yet fixed for El Capitan)
2366 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2367 output when running on non-gb/us i18n platforms
2370 <!-- JAL-1944 -->Error thrown when exporting a view with
2371 hidden sequences as flat-file alignment
2374 <!-- JAL-2030-->InstallAnywhere distribution fails when
2378 <!-- JAL-2080-->Jalview very slow to launch via webstart
2379 (also hotfix for 2.9.0b2)
2382 <!-- JAL-2085 -->Cannot save project when view has a
2383 reference sequence defined
2386 <!-- JAL-1011 -->Columns are suddenly selected in other
2387 alignments and views when revealing hidden columns
2390 <!-- JAL-1989 -->Hide columns not mirrored in complement
2391 view in a cDNA/Protein splitframe
2394 <!-- JAL-1369 -->Cannot save/restore representative
2395 sequence from project when only one sequence is
2399 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2400 in Structure Chooser
2403 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2404 structure consensus didn't refresh annotation panel
2407 <!-- JAL-1962 -->View mapping in structure view shows
2408 mappings between sequence and all chains in a PDB file
2411 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2412 dialogs format columns correctly, don't display array
2413 data, sort columns according to type
2416 <!-- JAL-1975 -->Export complete shown after destination
2417 file chooser is cancelled during an image export
2420 <!-- JAL-2025 -->Error when querying PDB Service with
2421 sequence name containing special characters
2424 <!-- JAL-2024 -->Manual PDB structure querying should be
2428 <!-- JAL-2104 -->Large tooltips with broken HTML
2429 formatting don't wrap
2432 <!-- JAL-1128 -->Figures exported from wrapped view are
2433 truncated so L looks like I in consensus annotation
2436 <!-- JAL-2003 -->Export features should only export the
2437 currently displayed features for the current selection or
2441 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2442 after fetching cross-references, and restoring from
2446 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2447 followed in the structure viewer
2450 <!-- JAL-2163 -->Titles for individual alignments in
2451 splitframe not restored from project
2454 <!-- JAL-2145 -->missing autocalculated annotation at
2455 trailing end of protein alignment in transcript/product
2456 splitview when pad-gaps not enabled by default
2459 <!-- JAL-1797 -->amino acid physicochemical conservation
2463 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2464 article has been read (reopened issue due to
2465 internationalisation problems)
2468 <!-- JAL-1960 -->Only offer PDB structures in structure
2469 viewer based on sequence name, PDB and UniProt
2474 <!-- JAL-1976 -->No progress bar shown during export of
2478 <!-- JAL-2213 -->Structures not always superimposed after
2479 multiple structures are shown for one or more sequences.
2482 <!-- JAL-1370 -->Reference sequence characters should not
2483 be replaced with '.' when 'Show unconserved' format option
2487 <!-- JAL-1823 -->Cannot specify chain code when entering
2488 specific PDB id for sequence
2491 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2492 'Export hidden sequences' is enabled, but 'export hidden
2493 columns' is disabled.
2496 <!--JAL-2026-->Best Quality option in structure chooser
2497 selects lowest rather than highest resolution structures
2501 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2502 to sequence mapping in 'View Mappings' report
2505 <!-- JAL-2284 -->Unable to read old Jalview projects that
2506 contain non-XML data added after Jalvew wrote project.
2509 <!-- JAL-2118 -->Newly created annotation row reorders
2510 after clicking on it to create new annotation for a
2514 <!-- JAL-1980 -->Null Pointer Exception raised when
2515 pressing Add on an orphaned cut'n'paste window.
2517 <!-- may exclude, this is an external service stability issue JAL-1941
2518 -- > RNA 3D structure not added via DSSR service</li> -->
2523 <!-- JAL-2151 -->Incorrect columns are selected when
2524 hidden columns present before start of sequence
2527 <!-- JAL-1986 -->Missing dependencies on applet pages
2531 <!-- JAL-1947 -->Overview pixel size changes when
2532 sequences are hidden in applet
2535 <!-- JAL-1996 -->Updated instructions for applet
2536 deployment on examples pages.
2543 <td width="60" nowrap>
2544 <div align="center">
2545 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2546 <em>16/10/2015</em></strong>
2549 <td><em>General</em>
2551 <li>Time stamps for signed Jalview application and applet
2556 <em>Application</em>
2558 <li>Duplicate group consensus and conservation rows
2559 shown when tree is partitioned</li>
2560 <li>Erratic behaviour when tree partitions made with
2561 multiple cDNA/Protein split views</li>
2567 <td width="60" nowrap>
2568 <div align="center">
2569 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2570 <em>8/10/2015</em></strong>
2573 <td><em>General</em>
2575 <li>Updated Spanish translations of localized text for
2577 </ul> <em>Application</em>
2579 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2580 <li>Signed OSX InstallAnywhere installer<br></li>
2581 <li>Support for per-sequence based annotations in BioJSON</li>
2582 </ul> <em>Applet</em>
2584 <li>Split frame example added to applet examples page</li>
2585 </ul> <em>Build and Deployment</em>
2588 <!-- JAL-1888 -->New ant target for running Jalview's test
2596 <li>Mapping of cDNA to protein in split frames
2597 incorrect when sequence start > 1</li>
2598 <li>Broken images in filter column by annotation dialog
2600 <li>Feature colours not parsed from features file</li>
2601 <li>Exceptions and incomplete link URLs recovered when
2602 loading a features file containing HTML tags in feature
2606 <em>Application</em>
2608 <li>Annotations corrupted after BioJS export and
2610 <li>Incorrect sequence limits after Fetch DB References
2611 with 'trim retrieved sequences'</li>
2612 <li>Incorrect warning about deleting all data when
2613 deleting selected columns</li>
2614 <li>Patch to build system for shipping properly signed
2615 JNLP templates for webstart launch</li>
2616 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2617 unreleased structures for download or viewing</li>
2618 <li>Tab/space/return keystroke operation of EMBL-PDBe
2619 fetcher/viewer dialogs works correctly</li>
2620 <li>Disabled 'minimise' button on Jalview windows
2621 running on OSX to workaround redraw hang bug</li>
2622 <li>Split cDNA/Protein view position and geometry not
2623 recovered from jalview project</li>
2624 <li>Initial enabled/disabled state of annotation menu
2625 sorter 'show autocalculated first/last' corresponds to
2627 <li>Restoring of Clustal, RNA Helices and T-Coffee
2628 color schemes from BioJSON</li>
2632 <li>Reorder sequences mirrored in cDNA/Protein split
2634 <li>Applet with Jmol examples not loading correctly</li>
2640 <td><div align="center">
2641 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2643 <td><em>General</em>
2645 <li>Linked visualisation and analysis of DNA and Protein
2648 <li>Translated cDNA alignments shown as split protein
2649 and DNA alignment views</li>
2650 <li>Codon consensus annotation for linked protein and
2651 cDNA alignment views</li>
2652 <li>Link cDNA or Protein product sequences by loading
2653 them onto Protein or cDNA alignments</li>
2654 <li>Reconstruct linked cDNA alignment from aligned
2655 protein sequences</li>
2658 <li>Jmol integration updated to Jmol v14.2.14</li>
2659 <li>Import and export of Jalview alignment views as <a
2660 href="features/bioJsonFormat.html">BioJSON</a></li>
2661 <li>New alignment annotation file statements for
2662 reference sequences and marking hidden columns</li>
2663 <li>Reference sequence based alignment shading to
2664 highlight variation</li>
2665 <li>Select or hide columns according to alignment
2667 <li>Find option for locating sequences by description</li>
2668 <li>Conserved physicochemical properties shown in amino
2669 acid conservation row</li>
2670 <li>Alignments can be sorted by number of RNA helices</li>
2671 </ul> <em>Application</em>
2673 <li>New cDNA/Protein analysis capabilities
2675 <li>Get Cross-References should open a Split Frame
2676 view with cDNA/Protein</li>
2677 <li>Detect when nucleotide sequences and protein
2678 sequences are placed in the same alignment</li>
2679 <li>Split cDNA/Protein views are saved in Jalview
2684 <li>Use REST API to talk to Chimera</li>
2685 <li>Selected regions in Chimera are highlighted in linked
2686 Jalview windows</li>
2688 <li>VARNA RNA viewer updated to v3.93</li>
2689 <li>VARNA views are saved in Jalview Projects</li>
2690 <li>Pseudoknots displayed as Jalview RNA annotation can
2691 be shown in VARNA</li>
2693 <li>Make groups for selection uses marked columns as well
2694 as the active selected region</li>
2696 <li>Calculate UPGMA and NJ trees using sequence feature
2698 <li>New Export options
2700 <li>New Export Settings dialog to control hidden
2701 region export in flat file generation</li>
2703 <li>Export alignment views for display with the <a
2704 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2706 <li>Export scrollable SVG in HTML page</li>
2707 <li>Optional embedding of BioJSON data when exporting
2708 alignment figures to HTML</li>
2710 <li>3D structure retrieval and display
2712 <li>Free text and structured queries with the PDBe
2714 <li>PDBe Search API based discovery and selection of
2715 PDB structures for a sequence set</li>
2719 <li>JPred4 employed for protein secondary structure
2721 <li>Hide Insertions menu option to hide unaligned columns
2722 for one or a group of sequences</li>
2723 <li>Automatically hide insertions in alignments imported
2724 from the JPred4 web server</li>
2725 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2726 system on OSX<br />LGPL libraries courtesy of <a
2727 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2729 <li>changed 'View nucleotide structure' submenu to 'View
2730 VARNA 2D Structure'</li>
2731 <li>change "View protein structure" menu option to "3D
2734 </ul> <em>Applet</em>
2736 <li>New layout for applet example pages</li>
2737 <li>New parameters to enable SplitFrame view
2738 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2739 <li>New example demonstrating linked viewing of cDNA and
2740 Protein alignments</li>
2741 </ul> <em>Development and deployment</em>
2743 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2744 <li>Include installation type and git revision in build
2745 properties and console log output</li>
2746 <li>Jalview Github organisation, and new github site for
2747 storing BioJsMSA Templates</li>
2748 <li>Jalview's unit tests now managed with TestNG</li>
2751 <!-- <em>General</em>
2753 </ul> --> <!-- issues resolved --> <em>Application</em>
2755 <li>Escape should close any open find dialogs</li>
2756 <li>Typo in select-by-features status report</li>
2757 <li>Consensus RNA secondary secondary structure
2758 predictions are not highlighted in amber</li>
2759 <li>Missing gap character in v2.7 example file means
2760 alignment appears unaligned when pad-gaps is not enabled</li>
2761 <li>First switch to RNA Helices colouring doesn't colour
2762 associated structure views</li>
2763 <li>ID width preference option is greyed out when auto
2764 width checkbox not enabled</li>
2765 <li>Stopped a warning dialog from being shown when
2766 creating user defined colours</li>
2767 <li>'View Mapping' in structure viewer shows sequence
2768 mappings for just that viewer's sequences</li>
2769 <li>Workaround for superposing PDB files containing
2770 multiple models in Chimera</li>
2771 <li>Report sequence position in status bar when hovering
2772 over Jmol structure</li>
2773 <li>Cannot output gaps as '.' symbols with Selection ->
2774 output to text box</li>
2775 <li>Flat file exports of alignments with hidden columns
2776 have incorrect sequence start/end</li>
2777 <li>'Aligning' a second chain to a Chimera structure from
2779 <li>Colour schemes applied to structure viewers don't
2780 work for nucleotide</li>
2781 <li>Loading/cut'n'pasting an empty or invalid file leads
2782 to a grey/invisible alignment window</li>
2783 <li>Exported Jpred annotation from a sequence region
2784 imports to different position</li>
2785 <li>Space at beginning of sequence feature tooltips shown
2786 on some platforms</li>
2787 <li>Chimera viewer 'View | Show Chain' menu is not
2789 <li>'New View' fails with a Null Pointer Exception in
2790 console if Chimera has been opened</li>
2791 <li>Mouseover to Chimera not working</li>
2792 <li>Miscellaneous ENA XML feature qualifiers not
2794 <li>NPE in annotation renderer after 'Extract Scores'</li>
2795 <li>If two structures in one Chimera window, mouseover of
2796 either sequence shows on first structure</li>
2797 <li>'Show annotations' options should not make
2798 non-positional annotations visible</li>
2799 <li>Subsequence secondary structure annotation not shown
2800 in right place after 'view flanking regions'</li>
2801 <li>File Save As type unset when current file format is
2803 <li>Save as '.jar' option removed for saving Jalview
2805 <li>Colour by Sequence colouring in Chimera more
2807 <li>Cannot 'add reference annotation' for a sequence in
2808 several views on same alignment</li>
2809 <li>Cannot show linked products for EMBL / ENA records</li>
2810 <li>Jalview's tooltip wraps long texts containing no
2812 </ul> <em>Applet</em>
2814 <li>Jmol to JalviewLite mouseover/link not working</li>
2815 <li>JalviewLite can't import sequences with ID
2816 descriptions containing angle brackets</li>
2817 </ul> <em>General</em>
2819 <li>Cannot export and reimport RNA secondary structure
2820 via jalview annotation file</li>
2821 <li>Random helix colour palette for colour by annotation
2822 with RNA secondary structure</li>
2823 <li>Mouseover to cDNA from STOP residue in protein
2824 translation doesn't work.</li>
2825 <li>hints when using the select by annotation dialog box</li>
2826 <li>Jmol alignment incorrect if PDB file has alternate CA
2828 <li>FontChooser message dialog appears to hang after
2829 choosing 1pt font</li>
2830 <li>Peptide secondary structure incorrectly imported from
2831 annotation file when annotation display text includes 'e' or
2833 <li>Cannot set colour of new feature type whilst creating
2835 <li>cDNA translation alignment should not be sequence
2836 order dependent</li>
2837 <li>'Show unconserved' doesn't work for lower case
2839 <li>Nucleotide ambiguity codes involving R not recognised</li>
2840 </ul> <em>Deployment and Documentation</em>
2842 <li>Applet example pages appear different to the rest of
2843 www.jalview.org</li>
2844 </ul> <em>Application Known issues</em>
2846 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2847 <li>Misleading message appears after trying to delete
2849 <li>Jalview icon not shown in dock after InstallAnywhere
2850 version launches</li>
2851 <li>Fetching EMBL reference for an RNA sequence results
2852 fails with a sequence mismatch</li>
2853 <li>Corrupted or unreadable alignment display when
2854 scrolling alignment to right</li>
2855 <li>ArrayIndexOutOfBoundsException thrown when remove
2856 empty columns called on alignment with ragged gapped ends</li>
2857 <li>auto calculated alignment annotation rows do not get
2858 placed above or below non-autocalculated rows</li>
2859 <li>Jalview dekstop becomes sluggish at full screen in
2860 ultra-high resolution</li>
2861 <li>Cannot disable consensus calculation independently of
2862 quality and conservation</li>
2863 <li>Mouseover highlighting between cDNA and protein can
2864 become sluggish with more than one splitframe shown</li>
2865 </ul> <em>Applet Known Issues</em>
2867 <li>Core PDB parsing code requires Jmol</li>
2868 <li>Sequence canvas panel goes white when alignment
2869 window is being resized</li>
2875 <td><div align="center">
2876 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2878 <td><em>General</em>
2880 <li>Updated Java code signing certificate donated by
2882 <li>Features and annotation preserved when performing
2883 pairwise alignment</li>
2884 <li>RNA pseudoknot annotation can be
2885 imported/exported/displayed</li>
2886 <li>'colour by annotation' can colour by RNA and
2887 protein secondary structure</li>
2888 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2889 post-hoc with 2.9 release</em>)
2892 </ul> <em>Application</em>
2894 <li>Extract and display secondary structure for sequences
2895 with 3D structures</li>
2896 <li>Support for parsing RNAML</li>
2897 <li>Annotations menu for layout
2899 <li>sort sequence annotation rows by alignment</li>
2900 <li>place sequence annotation above/below alignment
2903 <li>Output in Stockholm format</li>
2904 <li>Internationalisation: improved Spanish (es)
2906 <li>Structure viewer preferences tab</li>
2907 <li>Disorder and Secondary Structure annotation tracks
2908 shared between alignments</li>
2909 <li>UCSF Chimera launch and linked highlighting from
2911 <li>Show/hide all sequence associated annotation rows for
2912 all or current selection</li>
2913 <li>disorder and secondary structure predictions
2914 available as dataset annotation</li>
2915 <li>Per-sequence rna helices colouring</li>
2918 <li>Sequence database accessions imported when fetching
2919 alignments from Rfam</li>
2920 <li>update VARNA version to 3.91</li>
2922 <li>New groovy scripts for exporting aligned positions,
2923 conservation values, and calculating sum of pairs scores.</li>
2924 <li>Command line argument to set default JABAWS server</li>
2925 <li>include installation type in build properties and
2926 console log output</li>
2927 <li>Updated Jalview project format to preserve dataset
2931 <!-- issues resolved --> <em>Application</em>
2933 <li>Distinguish alignment and sequence associated RNA
2934 structure in structure->view->VARNA</li>
2935 <li>Raise dialog box if user deletes all sequences in an
2937 <li>Pressing F1 results in documentation opening twice</li>
2938 <li>Sequence feature tooltip is wrapped</li>
2939 <li>Double click on sequence associated annotation
2940 selects only first column</li>
2941 <li>Redundancy removal doesn't result in unlinked
2942 leaves shown in tree</li>
2943 <li>Undos after several redundancy removals don't undo
2945 <li>Hide sequence doesn't hide associated annotation</li>
2946 <li>User defined colours dialog box too big to fit on
2947 screen and buttons not visible</li>
2948 <li>author list isn't updated if already written to
2949 Jalview properties</li>
2950 <li>Popup menu won't open after retrieving sequence
2952 <li>File open window for associate PDB doesn't open</li>
2953 <li>Left-then-right click on a sequence id opens a
2954 browser search window</li>
2955 <li>Cannot open sequence feature shading/sort popup menu
2956 in feature settings dialog</li>
2957 <li>better tooltip placement for some areas of Jalview
2959 <li>Allow addition of JABAWS Server which doesn't
2960 pass validation</li>
2961 <li>Web services parameters dialog box is too large to
2963 <li>Muscle nucleotide alignment preset obscured by
2965 <li>JABAWS preset submenus don't contain newly
2966 defined user preset</li>
2967 <li>MSA web services warns user if they were launched
2968 with invalid input</li>
2969 <li>Jalview cannot contact DAS Registy when running on
2972 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2973 'Superpose with' submenu not shown when new view
2977 </ul> <!-- <em>Applet</em>
2979 </ul> <em>General</em>
2981 </ul>--> <em>Deployment and Documentation</em>
2983 <li>2G and 1G options in launchApp have no effect on
2984 memory allocation</li>
2985 <li>launchApp service doesn't automatically open
2986 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2988 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2989 InstallAnywhere reports cannot find valid JVM when Java
2990 1.7_055 is available
2992 </ul> <em>Application Known issues</em>
2995 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2996 corrupted or unreadable alignment display when scrolling
3000 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3001 retrieval fails but progress bar continues for DAS retrieval
3002 with large number of ID
3005 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3006 flatfile output of visible region has incorrect sequence
3010 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3011 rna structure consensus doesn't update when secondary
3012 structure tracks are rearranged
3015 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3016 invalid rna structure positional highlighting does not
3017 highlight position of invalid base pairs
3020 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3021 out of memory errors are not raised when saving Jalview
3022 project from alignment window file menu
3025 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3026 Switching to RNA Helices colouring doesn't propagate to
3030 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3031 colour by RNA Helices not enabled when user created
3032 annotation added to alignment
3035 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3036 Jalview icon not shown on dock in Mountain Lion/Webstart
3038 </ul> <em>Applet Known Issues</em>
3041 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3042 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3045 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3046 Jalview and Jmol example not compatible with IE9
3049 <li>Sort by annotation score doesn't reverse order
3055 <td><div align="center">
3056 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3059 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3062 <li>Internationalisation of user interface (usually
3063 called i18n support) and translation for Spanish locale</li>
3064 <li>Define/Undefine group on current selection with
3065 Ctrl-G/Shift Ctrl-G</li>
3066 <li>Improved group creation/removal options in
3067 alignment/sequence Popup menu</li>
3068 <li>Sensible precision for symbol distribution
3069 percentages shown in logo tooltip.</li>
3070 <li>Annotation panel height set according to amount of
3071 annotation when alignment first opened</li>
3072 </ul> <em>Application</em>
3074 <li>Interactive consensus RNA secondary structure
3075 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3076 <li>Select columns containing particular features from
3077 Feature Settings dialog</li>
3078 <li>View all 'representative' PDB structures for selected
3080 <li>Update Jalview project format:
3082 <li>New file extension for Jalview projects '.jvp'</li>
3083 <li>Preserve sequence and annotation dataset (to
3084 store secondary structure annotation,etc)</li>
3085 <li>Per group and alignment annotation and RNA helix
3089 <li>New similarity measures for PCA and Tree calculation
3091 <li>Experimental support for retrieval and viewing of
3092 flanking regions for an alignment</li>
3096 <!-- issues resolved --> <em>Application</em>
3098 <li>logo keeps spinning and status remains at queued or
3099 running after job is cancelled</li>
3100 <li>cannot export features from alignments imported from
3101 Jalview/VAMSAS projects</li>
3102 <li>Buggy slider for web service parameters that take
3104 <li>Newly created RNA secondary structure line doesn't
3105 have 'display all symbols' flag set</li>
3106 <li>T-COFFEE alignment score shading scheme and other
3107 annotation shading not saved in Jalview project</li>
3108 <li>Local file cannot be loaded in freshly downloaded
3110 <li>Jalview icon not shown on dock in Mountain
3112 <li>Load file from desktop file browser fails</li>
3113 <li>Occasional NPE thrown when calculating large trees</li>
3114 <li>Cannot reorder or slide sequences after dragging an
3115 alignment onto desktop</li>
3116 <li>Colour by annotation dialog throws NPE after using
3117 'extract scores' function</li>
3118 <li>Loading/cut'n'pasting an empty file leads to a grey
3119 alignment window</li>
3120 <li>Disorder thresholds rendered incorrectly after
3121 performing IUPred disorder prediction</li>
3122 <li>Multiple group annotated consensus rows shown when
3123 changing 'normalise logo' display setting</li>
3124 <li>Find shows blank dialog after 'finished searching' if
3125 nothing matches query</li>
3126 <li>Null Pointer Exceptions raised when sorting by
3127 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3129 <li>Errors in Jmol console when structures in alignment
3130 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3132 <li>Not all working JABAWS services are shown in
3134 <li>JAVAWS version of Jalview fails to launch with
3135 'invalid literal/length code'</li>
3136 <li>Annotation/RNA Helix colourschemes cannot be applied
3137 to alignment with groups (actually fixed in 2.8.0b1)</li>
3138 <li>RNA Helices and T-Coffee Scores available as default
3141 </ul> <em>Applet</em>
3143 <li>Remove group option is shown even when selection is
3145 <li>Apply to all groups ticked but colourscheme changes
3146 don't affect groups</li>
3147 <li>Documented RNA Helices and T-Coffee Scores as valid
3148 colourscheme name</li>
3149 <li>Annotation labels drawn on sequence IDs when
3150 Annotation panel is not displayed</li>
3151 <li>Increased font size for dropdown menus on OSX and
3152 embedded windows</li>
3153 </ul> <em>Other</em>
3155 <li>Consensus sequence for alignments/groups with a
3156 single sequence were not calculated</li>
3157 <li>annotation files that contain only groups imported as
3158 annotation and junk sequences</li>
3159 <li>Fasta files with sequences containing '*' incorrectly
3160 recognised as PFAM or BLC</li>
3161 <li>conservation/PID slider apply all groups option
3162 doesn't affect background (2.8.0b1)
3164 <li>redundancy highlighting is erratic at 0% and 100%</li>
3165 <li>Remove gapped columns fails for sequences with ragged
3167 <li>AMSA annotation row with leading spaces is not
3168 registered correctly on import</li>
3169 <li>Jalview crashes when selecting PCA analysis for
3170 certain alignments</li>
3171 <li>Opening the colour by annotation dialog for an
3172 existing annotation based 'use original colours'
3173 colourscheme loses original colours setting</li>
3178 <td><div align="center">
3179 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3180 <em>30/1/2014</em></strong>
3184 <li>Trusted certificates for JalviewLite applet and
3185 Jalview Desktop application<br />Certificate was donated by
3186 <a href="https://www.certum.eu">Certum</a> to the Jalview
3187 open source project).
3189 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3190 <li>Output in Stockholm format</li>
3191 <li>Allow import of data from gzipped files</li>
3192 <li>Export/import group and sequence associated line
3193 graph thresholds</li>
3194 <li>Nucleotide substitution matrix that supports RNA and
3195 ambiguity codes</li>
3196 <li>Allow disorder predictions to be made on the current
3197 selection (or visible selection) in the same way that JPred
3199 <li>Groovy scripting for headless Jalview operation</li>
3200 </ul> <em>Other improvements</em>
3202 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3203 <li>COMBINE statement uses current SEQUENCE_REF and
3204 GROUP_REF scope to group annotation rows</li>
3205 <li>Support '' style escaping of quotes in Newick
3207 <li>Group options for JABAWS service by command line name</li>
3208 <li>Empty tooltip shown for JABA service options with a
3209 link but no description</li>
3210 <li>Select primary source when selecting authority in
3211 database fetcher GUI</li>
3212 <li>Add .mfa to FASTA file extensions recognised by
3214 <li>Annotation label tooltip text wrap</li>
3219 <li>Slow scrolling when lots of annotation rows are
3221 <li>Lots of NPE (and slowness) after creating RNA
3222 secondary structure annotation line</li>
3223 <li>Sequence database accessions not imported when
3224 fetching alignments from Rfam</li>
3225 <li>Incorrect SHMR submission for sequences with
3227 <li>View all structures does not always superpose
3229 <li>Option widgets in service parameters not updated to
3230 reflect user or preset settings</li>
3231 <li>Null pointer exceptions for some services without
3232 presets or adjustable parameters</li>
3233 <li>Discover PDB IDs entry in structure menu doesn't
3234 discover PDB xRefs</li>
3235 <li>Exception encountered while trying to retrieve
3236 features with DAS</li>
3237 <li>Lowest value in annotation row isn't coloured
3238 when colour by annotation (per sequence) is coloured</li>
3239 <li>Keyboard mode P jumps to start of gapped region when
3240 residue follows a gap</li>
3241 <li>Jalview appears to hang importing an alignment with
3242 Wrap as default or after enabling Wrap</li>
3243 <li>'Right click to add annotations' message
3244 shown in wrap mode when no annotations present</li>
3245 <li>Disorder predictions fail with NPE if no automatic
3246 annotation already exists on alignment</li>
3247 <li>oninit javascript function should be called after
3248 initialisation completes</li>
3249 <li>Remove redundancy after disorder prediction corrupts
3250 alignment window display</li>
3251 <li>Example annotation file in documentation is invalid</li>
3252 <li>Grouped line graph annotation rows are not exported
3253 to annotation file</li>
3254 <li>Multi-harmony analysis cannot be run when only two
3256 <li>Cannot create multiple groups of line graphs with
3257 several 'combine' statements in annotation file</li>
3258 <li>Pressing return several times causes Number Format
3259 exceptions in keyboard mode</li>
3260 <li>Multi-harmony (SHMMR) method doesn't submit
3261 correct partitions for input data</li>
3262 <li>Translation from DNA to Amino Acids fails</li>
3263 <li>Jalview fail to load newick tree with quoted label</li>
3264 <li>--headless flag isn't understood</li>
3265 <li>ClassCastException when generating EPS in headless
3267 <li>Adjusting sequence-associated shading threshold only
3268 changes one row's threshold</li>
3269 <li>Preferences and Feature settings panel panel
3270 doesn't open</li>
3271 <li>hide consensus histogram also hides conservation and
3272 quality histograms</li>
3277 <td><div align="center">
3278 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3280 <td><em>Application</em>
3282 <li>Support for JABAWS 2.0 Services (AACon alignment
3283 conservation, protein disorder and Clustal Omega)</li>
3284 <li>JABAWS server status indicator in Web Services
3286 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3287 in Jalview alignment window</li>
3288 <li>Updated Jalview build and deploy framework for OSX
3289 mountain lion, windows 7, and 8</li>
3290 <li>Nucleotide substitution matrix for PCA that supports
3291 RNA and ambiguity codes</li>
3293 <li>Improved sequence database retrieval GUI</li>
3294 <li>Support fetching and database reference look up
3295 against multiple DAS sources (Fetch all from in 'fetch db
3297 <li>Jalview project improvements
3299 <li>Store and retrieve the 'belowAlignment'
3300 flag for annotation</li>
3301 <li>calcId attribute to group annotation rows on the
3303 <li>Store AACon calculation settings for a view in
3304 Jalview project</li>
3308 <li>horizontal scrolling gesture support</li>
3309 <li>Visual progress indicator when PCA calculation is
3311 <li>Simpler JABA web services menus</li>
3312 <li>visual indication that web service results are still
3313 being retrieved from server</li>
3314 <li>Serialise the dialogs that are shown when Jalview
3315 starts up for first time</li>
3316 <li>Jalview user agent string for interacting with HTTP
3318 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3320 <li>Examples directory and Groovy library included in
3321 InstallAnywhere distribution</li>
3322 </ul> <em>Applet</em>
3324 <li>RNA alignment and secondary structure annotation
3325 visualization applet example</li>
3326 </ul> <em>General</em>
3328 <li>Normalise option for consensus sequence logo</li>
3329 <li>Reset button in PCA window to return dimensions to
3331 <li>Allow seqspace or Jalview variant of alignment PCA
3333 <li>PCA with either nucleic acid and protein substitution
3335 <li>Allow windows containing HTML reports to be exported
3337 <li>Interactive display and editing of RNA secondary
3338 structure contacts</li>
3339 <li>RNA Helix Alignment Colouring</li>
3340 <li>RNA base pair logo consensus</li>
3341 <li>Parse sequence associated secondary structure
3342 information in Stockholm files</li>
3343 <li>HTML Export database accessions and annotation
3344 information presented in tooltip for sequences</li>
3345 <li>Import secondary structure from LOCARNA clustalw
3346 style RNA alignment files</li>
3347 <li>import and visualise T-COFFEE quality scores for an
3349 <li>'colour by annotation' per sequence option to
3350 shade each sequence according to its associated alignment
3352 <li>New Jalview Logo</li>
3353 </ul> <em>Documentation and Development</em>
3355 <li>documentation for score matrices used in Jalview</li>
3356 <li>New Website!</li>
3358 <td><em>Application</em>
3360 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3361 wsdbfetch REST service</li>
3362 <li>Stop windows being moved outside desktop on OSX</li>
3363 <li>Filetype associations not installed for webstart
3365 <li>Jalview does not always retrieve progress of a JABAWS
3366 job execution in full once it is complete</li>
3367 <li>revise SHMR RSBS definition to ensure alignment is
3368 uploaded via ali_file parameter</li>
3369 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3370 <li>View all structures superposed fails with exception</li>
3371 <li>Jnet job queues forever if a very short sequence is
3372 submitted for prediction</li>
3373 <li>Cut and paste menu not opened when mouse clicked on
3375 <li>Putting fractional value into integer text box in
3376 alignment parameter dialog causes Jalview to hang</li>
3377 <li>Structure view highlighting doesn't work on
3379 <li>View all structures fails with exception shown in
3381 <li>Characters in filename associated with PDBEntry not
3382 escaped in a platform independent way</li>
3383 <li>Jalview desktop fails to launch with exception when
3385 <li>Tree calculation reports 'you must have 2 or more
3386 sequences selected' when selection is empty</li>
3387 <li>Jalview desktop fails to launch with jar signature
3388 failure when java web start temporary file caching is
3390 <li>DAS Sequence retrieval with range qualification
3391 results in sequence xref which includes range qualification</li>
3392 <li>Errors during processing of command line arguments
3393 cause progress bar (JAL-898) to be removed</li>
3394 <li>Replace comma for semi-colon option not disabled for
3395 DAS sources in sequence fetcher</li>
3396 <li>Cannot close news reader when JABAWS server warning
3397 dialog is shown</li>
3398 <li>Option widgets not updated to reflect user settings</li>
3399 <li>Edited sequence not submitted to web service</li>
3400 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3401 <li>InstallAnywhere installer doesn't unpack and run
3402 on OSX Mountain Lion</li>
3403 <li>Annotation panel not given a scroll bar when
3404 sequences with alignment annotation are pasted into the
3406 <li>Sequence associated annotation rows not associated
3407 when loaded from Jalview project</li>
3408 <li>Browser launch fails with NPE on java 1.7</li>
3409 <li>JABAWS alignment marked as finished when job was
3410 cancelled or job failed due to invalid input</li>
3411 <li>NPE with v2.7 example when clicking on Tree
3412 associated with all views</li>
3413 <li>Exceptions when copy/paste sequences with grouped
3414 annotation rows to new window</li>
3415 </ul> <em>Applet</em>
3417 <li>Sequence features are momentarily displayed before
3418 they are hidden using hidefeaturegroups applet parameter</li>
3419 <li>loading features via javascript API automatically
3420 enables feature display</li>
3421 <li>scrollToColumnIn javascript API method doesn't
3423 </ul> <em>General</em>
3425 <li>Redundancy removal fails for rna alignment</li>
3426 <li>PCA calculation fails when sequence has been selected
3427 and then deselected</li>
3428 <li>PCA window shows grey box when first opened on OSX</li>
3429 <li>Letters coloured pink in sequence logo when alignment
3430 coloured with clustalx</li>
3431 <li>Choosing fonts without letter symbols defined causes
3432 exceptions and redraw errors</li>
3433 <li>Initial PCA plot view is not same as manually
3434 reconfigured view</li>
3435 <li>Grouped annotation graph label has incorrect line
3437 <li>Grouped annotation graph label display is corrupted
3438 for lots of labels</li>
3443 <div align="center">
3444 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3447 <td><em>Application</em>
3449 <li>Jalview Desktop News Reader</li>
3450 <li>Tweaked default layout of web services menu</li>
3451 <li>View/alignment association menu to enable user to
3452 easily specify which alignment a multi-structure view takes
3453 its colours/correspondences from</li>
3454 <li>Allow properties file location to be specified as URL</li>
3455 <li>Extend Jalview project to preserve associations
3456 between many alignment views and a single Jmol display</li>
3457 <li>Store annotation row height in Jalview project file</li>
3458 <li>Annotation row column label formatting attributes
3459 stored in project file</li>
3460 <li>Annotation row order for auto-calculated annotation
3461 rows preserved in Jalview project file</li>
3462 <li>Visual progress indication when Jalview state is
3463 saved using Desktop window menu</li>
3464 <li>Visual indication that command line arguments are
3465 still being processed</li>
3466 <li>Groovy script execution from URL</li>
3467 <li>Colour by annotation default min and max colours in
3469 <li>Automatically associate PDB files dragged onto an
3470 alignment with sequences that have high similarity and
3472 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3473 <li>'view structures' option to open many
3474 structures in same window</li>
3475 <li>Sort associated views menu option for tree panel</li>
3476 <li>Group all JABA and non-JABA services for a particular
3477 analysis function in its own submenu</li>
3478 </ul> <em>Applet</em>
3480 <li>Userdefined and autogenerated annotation rows for
3482 <li>Adjustment of alignment annotation pane height</li>
3483 <li>Annotation scrollbar for annotation panel</li>
3484 <li>Drag to reorder annotation rows in annotation panel</li>
3485 <li>'automaticScrolling' parameter</li>
3486 <li>Allow sequences with partial ID string matches to be
3487 annotated from GFF/Jalview features files</li>
3488 <li>Sequence logo annotation row in applet</li>
3489 <li>Absolute paths relative to host server in applet
3490 parameters are treated as such</li>
3491 <li>New in the JalviewLite javascript API:
3493 <li>JalviewLite.js javascript library</li>
3494 <li>Javascript callbacks for
3496 <li>Applet initialisation</li>
3497 <li>Sequence/alignment mouse-overs and selections</li>
3500 <li>scrollTo row and column alignment scrolling
3502 <li>Select sequence/alignment regions from javascript</li>
3503 <li>javascript structure viewer harness to pass
3504 messages between Jmol and Jalview when running as
3505 distinct applets</li>
3506 <li>sortBy method</li>
3507 <li>Set of applet and application examples shipped
3508 with documentation</li>
3509 <li>New example to demonstrate JalviewLite and Jmol
3510 javascript message exchange</li>
3512 </ul> <em>General</em>
3514 <li>Enable Jmol displays to be associated with multiple
3515 multiple alignments</li>
3516 <li>Option to automatically sort alignment with new tree</li>
3517 <li>User configurable link to enable redirects to a
3518 www.Jalview.org mirror</li>
3519 <li>Jmol colours option for Jmol displays</li>
3520 <li>Configurable newline string when writing alignment
3521 and other flat files</li>
3522 <li>Allow alignment annotation description lines to
3523 contain html tags</li>
3524 </ul> <em>Documentation and Development</em>
3526 <li>Add groovy test harness for bulk load testing to
3528 <li>Groovy script to load and align a set of sequences
3529 using a web service before displaying the result in the
3530 Jalview desktop</li>
3531 <li>Restructured javascript and applet api documentation</li>
3532 <li>Ant target to publish example html files with applet
3534 <li>Netbeans project for building Jalview from source</li>
3535 <li>ant task to create online javadoc for Jalview source</li>
3537 <td><em>Application</em>
3539 <li>User defined colourscheme throws exception when
3540 current built in colourscheme is saved as new scheme</li>
3541 <li>AlignFrame->Save in application pops up save
3542 dialog for valid filename/format</li>
3543 <li>Cannot view associated structure for UniProt sequence</li>
3544 <li>PDB file association breaks for UniProt sequence
3546 <li>Associate PDB from file dialog does not tell you
3547 which sequence is to be associated with the file</li>
3548 <li>Find All raises null pointer exception when query
3549 only matches sequence IDs</li>
3550 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3551 <li>Jalview project with Jmol views created with Jalview
3552 2.4 cannot be loaded</li>
3553 <li>Filetype associations not installed for webstart
3555 <li>Two or more chains in a single PDB file associated
3556 with sequences in different alignments do not get coloured
3557 by their associated sequence</li>
3558 <li>Visibility status of autocalculated annotation row
3559 not preserved when project is loaded</li>
3560 <li>Annotation row height and visibility attributes not
3561 stored in Jalview project</li>
3562 <li>Tree bootstraps are not preserved when saved as a
3563 Jalview project</li>
3564 <li>Envision2 workflow tooltips are corrupted</li>
3565 <li>Enabling show group conservation also enables colour
3566 by conservation</li>
3567 <li>Duplicate group associated conservation or consensus
3568 created on new view</li>
3569 <li>Annotation scrollbar not displayed after 'show
3570 all hidden annotation rows' option selected</li>
3571 <li>Alignment quality not updated after alignment
3572 annotation row is hidden then shown</li>
3573 <li>Preserve colouring of structures coloured by
3574 sequences in pre Jalview 2.7 projects</li>
3575 <li>Web service job parameter dialog is not laid out
3577 <li>Web services menu not refreshed after 'reset
3578 services' button is pressed in preferences</li>
3579 <li>Annotation off by one in Jalview v2_3 example project</li>
3580 <li>Structures imported from file and saved in project
3581 get name like jalview_pdb1234.txt when reloaded</li>
3582 <li>Jalview does not always retrieve progress of a JABAWS
3583 job execution in full once it is complete</li>
3584 </ul> <em>Applet</em>
3586 <li>Alignment height set incorrectly when lots of
3587 annotation rows are displayed</li>
3588 <li>Relative URLs in feature HTML text not resolved to
3590 <li>View follows highlighting does not work for positions
3592 <li><= shown as = in tooltip</li>
3593 <li>Export features raises exception when no features
3595 <li>Separator string used for serialising lists of IDs
3596 for javascript api is modified when separator string
3597 provided as parameter</li>
3598 <li>Null pointer exception when selecting tree leaves for
3599 alignment with no existing selection</li>
3600 <li>Relative URLs for datasources assumed to be relative
3601 to applet's codebase</li>
3602 <li>Status bar not updated after finished searching and
3603 search wraps around to first result</li>
3604 <li>StructureSelectionManager instance shared between
3605 several Jalview applets causes race conditions and memory
3607 <li>Hover tooltip and mouseover of position on structure
3608 not sent from Jmol in applet</li>
3609 <li>Certain sequences of javascript method calls to
3610 applet API fatally hang browser</li>
3611 </ul> <em>General</em>
3613 <li>View follows structure mouseover scrolls beyond
3614 position with wrapped view and hidden regions</li>
3615 <li>Find sequence position moves to wrong residue
3616 with/without hidden columns</li>
3617 <li>Sequence length given in alignment properties window
3619 <li>InvalidNumberFormat exceptions thrown when trying to
3620 import PDB like structure files</li>
3621 <li>Positional search results are only highlighted
3622 between user-supplied sequence start/end bounds</li>
3623 <li>End attribute of sequence is not validated</li>
3624 <li>Find dialog only finds first sequence containing a
3625 given sequence position</li>
3626 <li>Sequence numbering not preserved in MSF alignment
3628 <li>Jalview PDB file reader does not extract sequence
3629 from nucleotide chains correctly</li>
3630 <li>Structure colours not updated when tree partition
3631 changed in alignment</li>
3632 <li>Sequence associated secondary structure not correctly
3633 parsed in interleaved stockholm</li>
3634 <li>Colour by annotation dialog does not restore current
3636 <li>Hiding (nearly) all sequences doesn't work
3638 <li>Sequences containing lowercase letters are not
3639 properly associated with their pdb files</li>
3640 </ul> <em>Documentation and Development</em>
3642 <li>schemas/JalviewWsParamSet.xsd corrupted by
3643 ApplyCopyright tool</li>
3648 <div align="center">
3649 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3652 <td><em>Application</em>
3654 <li>New warning dialog when the Jalview Desktop cannot
3655 contact web services</li>
3656 <li>JABA service parameters for a preset are shown in
3657 service job window</li>
3658 <li>JABA Service menu entries reworded</li>
3662 <li>Modeller PIR IO broken - cannot correctly import a
3663 pir file emitted by Jalview</li>
3664 <li>Existing feature settings transferred to new
3665 alignment view created from cut'n'paste</li>
3666 <li>Improved test for mixed amino/nucleotide chains when
3667 parsing PDB files</li>
3668 <li>Consensus and conservation annotation rows
3669 occasionally become blank for all new windows</li>
3670 <li>Exception raised when right clicking above sequences
3671 in wrapped view mode</li>
3672 </ul> <em>Application</em>
3674 <li>multiple multiply aligned structure views cause cpu
3675 usage to hit 100% and computer to hang</li>
3676 <li>Web Service parameter layout breaks for long user
3677 parameter names</li>
3678 <li>Jaba service discovery hangs desktop if Jaba server
3685 <div align="center">
3686 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3689 <td><em>Application</em>
3691 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3692 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3695 <li>Web Services preference tab</li>
3696 <li>Analysis parameters dialog box and user defined
3698 <li>Improved speed and layout of Envision2 service menu</li>
3699 <li>Superpose structures using associated sequence
3701 <li>Export coordinates and projection as CSV from PCA
3703 </ul> <em>Applet</em>
3705 <li>enable javascript: execution by the applet via the
3706 link out mechanism</li>
3707 </ul> <em>Other</em>
3709 <li>Updated the Jmol Jalview interface to work with Jmol
3711 <li>The Jalview Desktop and JalviewLite applet now
3712 require Java 1.5</li>
3713 <li>Allow Jalview feature colour specification for GFF
3714 sequence annotation files</li>
3715 <li>New 'colour by label' keword in Jalview feature file
3716 type colour specification</li>
3717 <li>New Jalview Desktop Groovy API method that allows a
3718 script to check if it being run in an interactive session or
3719 in a batch operation from the Jalview command line</li>
3723 <li>clustalx colourscheme colours Ds preferentially when
3724 both D+E are present in over 50% of the column</li>
3725 </ul> <em>Application</em>
3727 <li>typo in AlignmentFrame->View->Hide->all but
3728 selected Regions menu item</li>
3729 <li>sequence fetcher replaces ',' for ';' when the ',' is
3730 part of a valid accession ID</li>
3731 <li>fatal OOM if object retrieved by sequence fetcher
3732 runs out of memory</li>
3733 <li>unhandled Out of Memory Error when viewing pca
3734 analysis results</li>
3735 <li>InstallAnywhere builds fail to launch on OS X java
3736 10.5 update 4 (due to apple Java 1.6 update)</li>
3737 <li>Installanywhere Jalview silently fails to launch</li>
3738 </ul> <em>Applet</em>
3740 <li>Jalview.getFeatureGroups() raises an
3741 ArrayIndexOutOfBoundsException if no feature groups are
3748 <div align="center">
3749 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3755 <li>Alignment prettyprinter doesn't cope with long
3757 <li>clustalx colourscheme colours Ds preferentially when
3758 both D+E are present in over 50% of the column</li>
3759 <li>nucleic acid structures retrieved from PDB do not
3760 import correctly</li>
3761 <li>More columns get selected than were clicked on when a
3762 number of columns are hidden</li>
3763 <li>annotation label popup menu not providing correct
3764 add/hide/show options when rows are hidden or none are
3766 <li>Stockholm format shown in list of readable formats,
3767 and parser copes better with alignments from RFAM.</li>
3768 <li>CSV output of consensus only includes the percentage
3769 of all symbols if sequence logo display is enabled</li>
3771 </ul> <em>Applet</em>
3773 <li>annotation panel disappears when annotation is
3775 </ul> <em>Application</em>
3777 <li>Alignment view not redrawn properly when new
3778 alignment opened where annotation panel is visible but no
3779 annotations are present on alignment</li>
3780 <li>pasted region containing hidden columns is
3781 incorrectly displayed in new alignment window</li>
3782 <li>Jalview slow to complete operations when stdout is
3783 flooded (fix is to close the Jalview console)</li>
3784 <li>typo in AlignmentFrame->View->Hide->all but
3785 selected Rregions menu item.</li>
3786 <li>inconsistent group submenu and Format submenu entry
3787 'Un' or 'Non'conserved</li>
3788 <li>Sequence feature settings are being shared by
3789 multiple distinct alignments</li>
3790 <li>group annotation not recreated when tree partition is
3792 <li>double click on group annotation to select sequences
3793 does not propagate to associated trees</li>
3794 <li>Mac OSX specific issues:
3796 <li>exception raised when mouse clicked on desktop
3797 window background</li>
3798 <li>Desktop menu placed on menu bar and application
3799 name set correctly</li>
3800 <li>sequence feature settings not wide enough for the
3801 save feature colourscheme button</li>
3810 <div align="center">
3811 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3814 <td><em>New Capabilities</em>
3816 <li>URL links generated from description line for
3817 regular-expression based URL links (applet and application)
3819 <li>Non-positional feature URL links are shown in link
3821 <li>Linked viewing of nucleic acid sequences and
3823 <li>Automatic Scrolling option in View menu to display
3824 the currently highlighted region of an alignment.</li>
3825 <li>Order an alignment by sequence length, or using the
3826 average score or total feature count for each sequence.</li>
3827 <li>Shading features by score or associated description</li>
3828 <li>Subdivide alignment and groups based on identity of
3829 selected subsequence (Make Groups from Selection).</li>
3830 <li>New hide/show options including Shift+Control+H to
3831 hide everything but the currently selected region.</li>
3832 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3833 </ul> <em>Application</em>
3835 <li>Fetch DB References capabilities and UI expanded to
3836 support retrieval from DAS sequence sources</li>
3837 <li>Local DAS Sequence sources can be added via the
3838 command line or via the Add local source dialog box.</li>
3839 <li>DAS Dbref and DbxRef feature types are parsed as
3840 database references and protein_name is parsed as
3841 description line (BioSapiens terms).</li>
3842 <li>Enable or disable non-positional feature and database
3843 references in sequence ID tooltip from View menu in
3845 <!-- <li>New hidden columns and rows and representatives capabilities
3846 in annotations file (in progress - not yet fully implemented)</li> -->
3847 <li>Group-associated consensus, sequence logos and
3848 conservation plots</li>
3849 <li>Symbol distributions for each column can be exported
3850 and visualized as sequence logos</li>
3851 <li>Optionally scale multi-character column labels to fit
3852 within each column of annotation row<!-- todo for applet -->
3854 <li>Optional automatic sort of associated alignment view
3855 when a new tree is opened.</li>
3856 <li>Jalview Java Console</li>
3857 <li>Better placement of desktop window when moving
3858 between different screens.</li>
3859 <li>New preference items for sequence ID tooltip and
3860 consensus annotation</li>
3861 <li>Client to submit sequences and IDs to Envision2
3863 <li><em>Vamsas Capabilities</em>
3865 <li>Improved VAMSAS synchronization (Jalview archive
3866 used to preserve views, structures, and tree display
3868 <li>Import of vamsas documents from disk or URL via
3870 <li>Sharing of selected regions between views and
3871 with other VAMSAS applications (Experimental feature!)</li>
3872 <li>Updated API to VAMSAS version 0.2</li>
3874 </ul> <em>Applet</em>
3876 <li>Middle button resizes annotation row height</li>
3879 <li>sortByTree (true/false) - automatically sort the
3880 associated alignment view by the tree when a new tree is
3882 <li>showTreeBootstraps (true/false) - show or hide
3883 branch bootstraps (default is to show them if available)</li>
3884 <li>showTreeDistances (true/false) - show or hide
3885 branch lengths (default is to show them if available)</li>
3886 <li>showUnlinkedTreeNodes (true/false) - indicate if
3887 unassociated nodes should be highlighted in the tree
3889 <li>heightScale and widthScale (1.0 or more) -
3890 increase the height or width of a cell in the alignment
3891 grid relative to the current font size.</li>
3894 <li>Non-positional features displayed in sequence ID
3896 </ul> <em>Other</em>
3898 <li>Features format: graduated colour definitions and
3899 specification of feature scores</li>
3900 <li>Alignment Annotations format: new keywords for group
3901 associated annotation (GROUP_REF) and annotation row display
3902 properties (ROW_PROPERTIES)</li>
3903 <li>XML formats extended to support graduated feature
3904 colourschemes, group associated annotation, and profile
3905 visualization settings.</li></td>
3908 <li>Source field in GFF files parsed as feature source
3909 rather than description</li>
3910 <li>Non-positional features are now included in sequence
3911 feature and gff files (controlled via non-positional feature
3912 visibility in tooltip).</li>
3913 <li>URL links generated for all feature links (bugfix)</li>
3914 <li>Added URL embedding instructions to features file
3916 <li>Codons containing ambiguous nucleotides translated as
3917 'X' in peptide product</li>
3918 <li>Match case switch in find dialog box works for both
3919 sequence ID and sequence string and query strings do not
3920 have to be in upper case to match case-insensitively.</li>
3921 <li>AMSA files only contain first column of
3922 multi-character column annotation labels</li>
3923 <li>Jalview Annotation File generation/parsing consistent
3924 with documentation (e.g. Stockholm annotation can be
3925 exported and re-imported)</li>
3926 <li>PDB files without embedded PDB IDs given a friendly
3928 <li>Find incrementally searches ID string matches as well
3929 as subsequence matches, and correctly reports total number
3933 <li>Better handling of exceptions during sequence
3935 <li>Dasobert generated non-positional feature URL
3936 link text excludes the start_end suffix</li>
3937 <li>DAS feature and source retrieval buttons disabled
3938 when fetch or registry operations in progress.</li>
3939 <li>PDB files retrieved from URLs are cached properly</li>
3940 <li>Sequence description lines properly shared via
3942 <li>Sequence fetcher fetches multiple records for all
3944 <li>Ensured that command line das feature retrieval
3945 completes before alignment figures are generated.</li>
3946 <li>Reduced time taken when opening file browser for
3948 <li>isAligned check prior to calculating tree, PCA or
3949 submitting an MSA to JNet now excludes hidden sequences.</li>
3950 <li>User defined group colours properly recovered
3951 from Jalview projects.</li>
3960 <div align="center">
3961 <strong>2.4.0.b2</strong><br> 28/10/2009
3966 <li>Experimental support for google analytics usage
3968 <li>Jalview privacy settings (user preferences and docs).</li>
3973 <li>Race condition in applet preventing startup in
3975 <li>Exception when feature created from selection beyond
3976 length of sequence.</li>
3977 <li>Allow synthetic PDB files to be imported gracefully</li>
3978 <li>Sequence associated annotation rows associate with
3979 all sequences with a given id</li>
3980 <li>Find function matches case-insensitively for sequence
3981 ID string searches</li>
3982 <li>Non-standard characters do not cause pairwise
3983 alignment to fail with exception</li>
3984 </ul> <em>Application Issues</em>
3986 <li>Sequences are now validated against EMBL database</li>
3987 <li>Sequence fetcher fetches multiple records for all
3989 </ul> <em>InstallAnywhere Issues</em>
3991 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3992 issue with installAnywhere mechanism)</li>
3993 <li>Command line launching of JARs from InstallAnywhere
3994 version (java class versioning error fixed)</li>
4001 <div align="center">
4002 <strong>2.4</strong><br> 27/8/2008
4005 <td><em>User Interface</em>
4007 <li>Linked highlighting of codon and amino acid from
4008 translation and protein products</li>
4009 <li>Linked highlighting of structure associated with
4010 residue mapping to codon position</li>
4011 <li>Sequence Fetcher provides example accession numbers
4012 and 'clear' button</li>
4013 <li>MemoryMonitor added as an option under Desktop's
4015 <li>Extract score function to parse whitespace separated
4016 numeric data in description line</li>
4017 <li>Column labels in alignment annotation can be centred.</li>
4018 <li>Tooltip for sequence associated annotation give name
4020 </ul> <em>Web Services and URL fetching</em>
4022 <li>JPred3 web service</li>
4023 <li>Prototype sequence search client (no public services
4025 <li>Fetch either seed alignment or full alignment from
4027 <li>URL Links created for matching database cross
4028 references as well as sequence ID</li>
4029 <li>URL Links can be created using regular-expressions</li>
4030 </ul> <em>Sequence Database Connectivity</em>
4032 <li>Retrieval of cross-referenced sequences from other
4034 <li>Generalised database reference retrieval and
4035 validation to all fetchable databases</li>
4036 <li>Fetch sequences from DAS sources supporting the
4037 sequence command</li>
4038 </ul> <em>Import and Export</em>
4039 <li>export annotation rows as CSV for spreadsheet import</li>
4040 <li>Jalview projects record alignment dataset associations,
4041 EMBL products, and cDNA sequence mappings</li>
4042 <li>Sequence Group colour can be specified in Annotation
4044 <li>Ad-hoc colouring of group in Annotation File using RGB
4045 triplet as name of colourscheme</li>
4046 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4048 <li>treenode binding for VAMSAS tree exchange</li>
4049 <li>local editing and update of sequences in VAMSAS
4050 alignments (experimental)</li>
4051 <li>Create new or select existing session to join</li>
4052 <li>load and save of vamsas documents</li>
4053 </ul> <em>Application command line</em>
4055 <li>-tree parameter to open trees (introduced for passing
4057 <li>-fetchfrom command line argument to specify nicknames
4058 of DAS servers to query for alignment features</li>
4059 <li>-dasserver command line argument to add new servers
4060 that are also automatically queried for features</li>
4061 <li>-groovy command line argument executes a given groovy
4062 script after all input data has been loaded and parsed</li>
4063 </ul> <em>Applet-Application data exchange</em>
4065 <li>Trees passed as applet parameters can be passed to
4066 application (when using "View in full
4067 application")</li>
4068 </ul> <em>Applet Parameters</em>
4070 <li>feature group display control parameter</li>
4071 <li>debug parameter</li>
4072 <li>showbutton parameter</li>
4073 </ul> <em>Applet API methods</em>
4075 <li>newView public method</li>
4076 <li>Window (current view) specific get/set public methods</li>
4077 <li>Feature display control methods</li>
4078 <li>get list of currently selected sequences</li>
4079 </ul> <em>New Jalview distribution features</em>
4081 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4082 <li>RELEASE file gives build properties for the latest
4083 Jalview release.</li>
4084 <li>Java 1.1 Applet build made easier and donotobfuscate
4085 property controls execution of obfuscator</li>
4086 <li>Build target for generating source distribution</li>
4087 <li>Debug flag for javacc</li>
4088 <li>.jalview_properties file is documented (slightly) in
4089 jalview.bin.Cache</li>
4090 <li>Continuous Build Integration for stable and
4091 development version of Application, Applet and source
4096 <li>selected region output includes visible annotations
4097 (for certain formats)</li>
4098 <li>edit label/displaychar contains existing label/char
4100 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4101 <li>shorter peptide product names from EMBL records</li>
4102 <li>Newick string generator makes compact representations</li>
4103 <li>bootstrap values parsed correctly for tree files with
4105 <li>pathological filechooser bug avoided by not allowing
4106 filenames containing a ':'</li>
4107 <li>Fixed exception when parsing GFF files containing
4108 global sequence features</li>
4109 <li>Alignment datasets are finalized only when number of
4110 references from alignment sequences goes to zero</li>
4111 <li>Close of tree branch colour box without colour
4112 selection causes cascading exceptions</li>
4113 <li>occasional negative imgwidth exceptions</li>
4114 <li>better reporting of non-fatal warnings to user when
4115 file parsing fails.</li>
4116 <li>Save works when Jalview project is default format</li>
4117 <li>Save as dialog opened if current alignment format is
4118 not a valid output format</li>
4119 <li>UniProt canonical names introduced for both das and
4121 <li>Histidine should be midblue (not pink!) in Zappo</li>
4122 <li>error messages passed up and output when data read
4124 <li>edit undo recovers previous dataset sequence when
4125 sequence is edited</li>
4126 <li>allow PDB files without pdb ID HEADER lines (like
4127 those generated by MODELLER) to be read in properly</li>
4128 <li>allow reading of JPred concise files as a normal
4130 <li>Stockholm annotation parsing and alignment properties
4131 import fixed for PFAM records</li>
4132 <li>Structure view windows have correct name in Desktop
4134 <li>annotation consisting of sequence associated scores
4135 can be read and written correctly to annotation file</li>
4136 <li>Aligned cDNA translation to aligned peptide works
4138 <li>Fixed display of hidden sequence markers and
4139 non-italic font for representatives in Applet</li>
4140 <li>Applet Menus are always embedded in applet window on
4142 <li>Newly shown features appear at top of stack (in
4144 <li>Annotations added via parameter not drawn properly
4145 due to null pointer exceptions</li>
4146 <li>Secondary structure lines are drawn starting from
4147 first column of alignment</li>
4148 <li>UniProt XML import updated for new schema release in
4150 <li>Sequence feature to sequence ID match for Features
4151 file is case-insensitive</li>
4152 <li>Sequence features read from Features file appended to
4153 all sequences with matching IDs</li>
4154 <li>PDB structure coloured correctly for associated views
4155 containing a sub-sequence</li>
4156 <li>PDB files can be retrieved by applet from Jar files</li>
4157 <li>feature and annotation file applet parameters
4158 referring to different directories are retrieved correctly</li>
4159 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4160 <li>Fixed application hang whilst waiting for
4161 splash-screen version check to complete</li>
4162 <li>Applet properly URLencodes input parameter values
4163 when passing them to the launchApp service</li>
4164 <li>display name and local features preserved in results
4165 retrieved from web service</li>
4166 <li>Visual delay indication for sequence retrieval and
4167 sequence fetcher initialisation</li>
4168 <li>updated Application to use DAS 1.53e version of
4169 dasobert DAS client</li>
4170 <li>Re-instated Full AMSA support and .amsa file
4172 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4180 <div align="center">
4181 <strong>2.3</strong><br> 9/5/07
4186 <li>Jmol 11.0.2 integration</li>
4187 <li>PDB views stored in Jalview XML files</li>
4188 <li>Slide sequences</li>
4189 <li>Edit sequence in place</li>
4190 <li>EMBL CDS features</li>
4191 <li>DAS Feature mapping</li>
4192 <li>Feature ordering</li>
4193 <li>Alignment Properties</li>
4194 <li>Annotation Scores</li>
4195 <li>Sort by scores</li>
4196 <li>Feature/annotation editing in applet</li>
4201 <li>Headless state operation in 2.2.1</li>
4202 <li>Incorrect and unstable DNA pairwise alignment</li>
4203 <li>Cut and paste of sequences with annotation</li>
4204 <li>Feature group display state in XML</li>
4205 <li>Feature ordering in XML</li>
4206 <li>blc file iteration selection using filename # suffix</li>
4207 <li>Stockholm alignment properties</li>
4208 <li>Stockhom alignment secondary structure annotation</li>
4209 <li>2.2.1 applet had no feature transparency</li>
4210 <li>Number pad keys can be used in cursor mode</li>
4211 <li>Structure Viewer mirror image resolved</li>
4218 <div align="center">
4219 <strong>2.2.1</strong><br> 12/2/07
4224 <li>Non standard characters can be read and displayed
4225 <li>Annotations/Features can be imported/exported to the
4227 <li>Applet allows editing of sequence/annotation/group
4228 name & description
4229 <li>Preference setting to display sequence name in
4231 <li>Annotation file format extended to allow
4232 Sequence_groups to be defined
4233 <li>Default opening of alignment overview panel can be
4234 specified in preferences
4235 <li>PDB residue numbering annotation added to associated
4241 <li>Applet crash under certain Linux OS with Java 1.6
4243 <li>Annotation file export / import bugs fixed
4244 <li>PNG / EPS image output bugs fixed
4250 <div align="center">
4251 <strong>2.2</strong><br> 27/11/06
4256 <li>Multiple views on alignment
4257 <li>Sequence feature editing
4258 <li>"Reload" alignment
4259 <li>"Save" to current filename
4260 <li>Background dependent text colour
4261 <li>Right align sequence ids
4262 <li>User-defined lower case residue colours
4265 <li>Menu item accelerator keys
4266 <li>Control-V pastes to current alignment
4267 <li>Cancel button for DAS Feature Fetching
4268 <li>PCA and PDB Viewers zoom via mouse roller
4269 <li>User-defined sub-tree colours and sub-tree selection
4271 <li>'New Window' button on the 'Output to Text box'
4276 <li>New memory efficient Undo/Redo System
4277 <li>Optimised symbol lookups and conservation/consensus
4279 <li>Region Conservation/Consensus recalculated after
4281 <li>Fixed Remove Empty Columns Bug (empty columns at end
4283 <li>Slowed DAS Feature Fetching for increased robustness.
4285 <li>Made angle brackets in ASCII feature descriptions
4287 <li>Re-instated Zoom function for PCA
4288 <li>Sequence descriptions conserved in web service
4290 <li>UniProt ID discoverer uses any word separated by
4292 <li>WsDbFetch query/result association resolved
4293 <li>Tree leaf to sequence mapping improved
4294 <li>Smooth fonts switch moved to FontChooser dialog box.
4301 <div align="center">
4302 <strong>2.1.1</strong><br> 12/9/06
4307 <li>Copy consensus sequence to clipboard</li>
4312 <li>Image output - rightmost residues are rendered if
4313 sequence id panel has been resized</li>
4314 <li>Image output - all offscreen group boundaries are
4316 <li>Annotation files with sequence references - all
4317 elements in file are relative to sequence position</li>
4318 <li>Mac Applet users can use Alt key for group editing</li>
4324 <div align="center">
4325 <strong>2.1</strong><br> 22/8/06
4330 <li>MAFFT Multiple Alignment in default Web Service list</li>
4331 <li>DAS Feature fetching</li>
4332 <li>Hide sequences and columns</li>
4333 <li>Export Annotations and Features</li>
4334 <li>GFF file reading / writing</li>
4335 <li>Associate structures with sequences from local PDB
4337 <li>Add sequences to exisiting alignment</li>
4338 <li>Recently opened files / URL lists</li>
4339 <li>Applet can launch the full application</li>
4340 <li>Applet has transparency for features (Java 1.2
4342 <li>Applet has user defined colours parameter</li>
4343 <li>Applet can load sequences from parameter
4344 "sequence<em>x</em>"
4350 <li>Redundancy Panel reinstalled in the Applet</li>
4351 <li>Monospaced font - EPS / rescaling bug fixed</li>
4352 <li>Annotation files with sequence references bug fixed</li>
4358 <div align="center">
4359 <strong>2.08.1</strong><br> 2/5/06
4364 <li>Change case of selected region from Popup menu</li>
4365 <li>Choose to match case when searching</li>
4366 <li>Middle mouse button and mouse movement can compress /
4367 expand the visible width and height of the alignment</li>
4372 <li>Annotation Panel displays complete JNet results</li>
4378 <div align="center">
4379 <strong>2.08b</strong><br> 18/4/06
4385 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4386 <li>Righthand label on wrapped alignments shows correct
4393 <div align="center">
4394 <strong>2.08</strong><br> 10/4/06
4399 <li>Editing can be locked to the selection area</li>
4400 <li>Keyboard editing</li>
4401 <li>Create sequence features from searches</li>
4402 <li>Precalculated annotations can be loaded onto
4404 <li>Features file allows grouping of features</li>
4405 <li>Annotation Colouring scheme added</li>
4406 <li>Smooth fonts off by default - Faster rendering</li>
4407 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4412 <li>Drag & Drop fixed on Linux</li>
4413 <li>Jalview Archive file faster to load/save, sequence
4414 descriptions saved.</li>
4420 <div align="center">
4421 <strong>2.07</strong><br> 12/12/05
4426 <li>PDB Structure Viewer enhanced</li>
4427 <li>Sequence Feature retrieval and display enhanced</li>
4428 <li>Choose to output sequence start-end after sequence
4429 name for file output</li>
4430 <li>Sequence Fetcher WSDBFetch@EBI</li>
4431 <li>Applet can read feature files, PDB files and can be
4432 used for HTML form input</li>
4437 <li>HTML output writes groups and features</li>
4438 <li>Group editing is Control and mouse click</li>
4439 <li>File IO bugs</li>
4445 <div align="center">
4446 <strong>2.06</strong><br> 28/9/05
4451 <li>View annotations in wrapped mode</li>
4452 <li>More options for PCA viewer</li>
4457 <li>GUI bugs resolved</li>
4458 <li>Runs with -nodisplay from command line</li>
4464 <div align="center">
4465 <strong>2.05b</strong><br> 15/9/05
4470 <li>Choose EPS export as lineart or text</li>
4471 <li>Jar files are executable</li>
4472 <li>Can read in Uracil - maps to unknown residue</li>
4477 <li>Known OutOfMemory errors give warning message</li>
4478 <li>Overview window calculated more efficiently</li>
4479 <li>Several GUI bugs resolved</li>
4485 <div align="center">
4486 <strong>2.05</strong><br> 30/8/05
4491 <li>Edit and annotate in "Wrapped" view</li>
4496 <li>Several GUI bugs resolved</li>
4502 <div align="center">
4503 <strong>2.04</strong><br> 24/8/05
4508 <li>Hold down mouse wheel & scroll to change font
4514 <li>Improved JPred client reliability</li>
4515 <li>Improved loading of Jalview files</li>
4521 <div align="center">
4522 <strong>2.03</strong><br> 18/8/05
4527 <li>Set Proxy server name and port in preferences</li>
4528 <li>Multiple URL links from sequence ids</li>
4529 <li>User Defined Colours can have a scheme name and added
4531 <li>Choose to ignore gaps in consensus calculation</li>
4532 <li>Unix users can set default web browser</li>
4533 <li>Runs without GUI for batch processing</li>
4534 <li>Dynamically generated Web Service Menus</li>
4539 <li>InstallAnywhere download for Sparc Solaris</li>
4545 <div align="center">
4546 <strong>2.02</strong><br> 18/7/05
4552 <li>Copy & Paste order of sequences maintains
4553 alignment order.</li>
4559 <div align="center">
4560 <strong>2.01</strong><br> 12/7/05
4565 <li>Use delete key for deleting selection.</li>
4566 <li>Use Mouse wheel to scroll sequences.</li>
4567 <li>Help file updated to describe how to add alignment
4569 <li>Version and build date written to build properties
4571 <li>InstallAnywhere installation will check for updates
4572 at launch of Jalview.</li>
4577 <li>Delete gaps bug fixed.</li>
4578 <li>FileChooser sorts columns.</li>
4579 <li>Can remove groups one by one.</li>
4580 <li>Filechooser icons installed.</li>
4581 <li>Finder ignores return character when searching.
4582 Return key will initiate a search.<br>
4589 <div align="center">
4590 <strong>2.0</strong><br> 20/6/05
4595 <li>New codebase</li>